Hugo_Symbol	Entrez_Gene_Id	Center	Tumor_Sample_Barcode	Fusion	DNA_support	RNA_support	Method	Frame	Comments
EP300	0	MSKCC-DMP	P-0010758-T01-IM5	EP300-intragenic	yes	unknown		in frame	EP300 (NM_001429) rearrangement: c.4617+54_c.4780-1066del Note: The EP300 rearrangement is an intragenic deletion of exon 29. The functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0014470-T01-IM6	RPTOR-intragenic	yes	unknown		unknown	RPTOR (NM_020761) Rearrangement :  c.284_c.348+4045dup Note: The RPTOR Rearrangement results in the intragenic duplication of RPTOR exon 3. One of the breakpoints is within exon 3 of RPTOR. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0011577-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-511:TMPRSS2_c.40-47146:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0011577-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-511:TMPRSS2_c.40-47146:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
ARID1B	0	MSKCC-DMP	P-0012253-T01-IM5	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.83_c.1777-2523del Note: The ARID1B rearrangement is an intragenic deletion of exons 1-4. One of the breakpoints is within exon 1.
BAP1	0	MSKCC-DMP	P-0011443-T01-IM5	BAP1-intragenic	yes	unknown		out of frame	BAP1 (NM_004656) rearrangement : c.68-1_256-75del Note: The BAP1 rearrangement event results in the deleion of BAP1 exons 3-4. One of the breakpoints is within the 5 splice site of BAP1 exon3.
BRCA2	0	MSKCC-DMP	P-0013956-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_00005) rearrangement: c.3575_c.6269inv Note: The BRCA2 rearrangement is an inversion of exon 11. Both breakpoints are within exon. The functional significance is undetermined.
DNAH9	0	MSKCC-DMP	P-0014576-T01-IM6	MAP2K4-DNAH9 fusion	yes	unknown		unknown	DNAH9 (NM_001372) - MAP2K4 (NM_003010) rearrangement: c.5552+2579:DNAH9_c.1168:MAP2K4inv Note: The DNAH9 - MAP2K4 rearrangement is an inversions which that results in the antisense fusion of DNAH9 exon 26 to MAP2K4 exon 11. One of the breakpoints is within exon 11 of MAP2K4. The functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0014576-T01-IM6	MAP2K4-DNAH9 fusion	yes	unknown		unknown	DNAH9 (NM_001372) - MAP2K4 (NM_003010) rearrangement: c.5552+2579:DNAH9_c.1168:MAP2K4inv Note: The DNAH9 - MAP2K4 rearrangement is an inversions which that results in the antisense fusion of DNAH9 exon 26 to MAP2K4 exon 11. One of the breakpoints is within exon 11 of MAP2K4. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0012116-T01-IM5	CWH43-NBN fusion	yes	unknown		unknown	NBN (NM_002485) Rearrangement : t(4,8)(p11,q21.3)(chr4:g.131062050::chr8:g.143130066) Note: The NBN Rearrangement results in the possible truncation of exons11-16. One of the breakpoints is within exon 11. Its functional significance is undetermined.
CWH43	0	MSKCC-DMP	P-0012116-T01-IM5	CWH43-NBN fusion	yes	unknown		unknown	NBN (NM_002485) Rearrangement : t(4,8)(p11,q21.3)(chr4:g.131062050::chr8:g.143130066) Note: The NBN Rearrangement results in the possible truncation of exons11-16. One of the breakpoints is within exon 11. Its functional significance is undetermined.
MMP16	0	MSKCC-DMP	P-0011098-T01-IM5	SPEN-MMP16 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: t(1;8)(p36.13;q21.3)(chr1:g.16259712::chr8:g.89816597) Note: The SPEN rearrangement is a translocation with a breakpoint within exon 11 of SPEN. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0011098-T01-IM5	SPEN-MMP16 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: t(1;8)(p36.13;q21.3)(chr1:g.16259712::chr8:g.89816597) Note: The SPEN rearrangement is a translocation with a breakpoint within exon 11 of SPEN. The functional significance is undetermined.
PRKAR1A	0	MSKCC-DMP	P-0013732-T01-IM5	UTRN-PRKAR1A fusion	yes	unknown		unknown	PRKAR1A (NM_212471) rearrangement: t(6;17)(q24.2;q24.2)(chr6:g.144894222::chr17:g.66526189) Note: The PRKAR1A rearrangement is a translocation that may result in the truncation of exons 10-11. The functional significance is undetermined.
UTRN	0	MSKCC-DMP	P-0013732-T01-IM5	UTRN-PRKAR1A fusion	yes	unknown		unknown	PRKAR1A (NM_212471) rearrangement: t(6;17)(q24.2;q24.2)(chr6:g.144894222::chr17:g.66526189) Note: The PRKAR1A rearrangement is a translocation that may result in the truncation of exons 10-11. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0012110-T01-IM5	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) Rearrangement :  c.4576+131_c.3459-453dup Note: The PBRM1 Rearrangement  results in the intragenic duplication of exons 23-29. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015015-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11) : c.127-1516:TMPRSS2_c.40-44007:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015015-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11) : c.127-1516:TMPRSS2_c.40-44007:ERGdel
PDGFRB	0	MSKCC-DMP	P-0013271-T01-IM5	CAMK2A-PDGFRB fusion	yes	unknown		in frame	PDGFRB (NM_002609) - CAMK2A (NM_015981)  rearrangement: c.1579+9:PDGFRB_c.157+1527:CAMK2Adup Note: The PDGFRB - CAMK2A rearrangement is a duplication that results in the fusion of PDGFRB exons 1-10 with CAMK2A exons 3 - 19. The functional significance is undetermined.
CAMK2A	0	MSKCC-DMP	P-0013271-T01-IM5	CAMK2A-PDGFRB fusion	yes	unknown		in frame	PDGFRB (NM_002609) - CAMK2A (NM_015981)  rearrangement: c.1579+9:PDGFRB_c.157+1527:CAMK2Adup Note: The PDGFRB - CAMK2A rearrangement is a duplication that results in the fusion of PDGFRB exons 1-10 with CAMK2A exons 3 - 19. The functional significance is undetermined.
NAP1L2	0	MSKCC-DMP	P-0012153-T01-IM5	ATRX-NAP1L2 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.72499356_c.5226inv Note: The ATRX rearrangement is an inversion of exons 20-35. One of the breakpoints is within exon  20.
ATRX	0	MSKCC-DMP	P-0012153-T01-IM5	ATRX-NAP1L2 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.72499356_c.5226inv Note: The ATRX rearrangement is an inversion of exons 20-35. One of the breakpoints is within exon  20.
CDKN2A	0	MSKCC-DMP	P-0010948-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.194-3397_chr9:g.22028649del CDKN2Ap16INK4A (NM_000077) rearrangement : c.150+73_chr9:g.22028649del Note: The CDKN2Ap14ARF and CDKN2Ap16INK4A rearrangements are a single event affecting two isoforms of CDKN2A gene. The rearrangement results in the deletion of CDKN2Ap14ARF exon1 and CDKN2Ap16INK4A exon1.
CDKN2BAS	0	MSKCC-DMP	P-0010948-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.194-3397_chr9:g.22028649del CDKN2Ap16INK4A (NM_000077) rearrangement : c.150+73_chr9:g.22028649del Note: The CDKN2Ap14ARF and CDKN2Ap16INK4A rearrangements are a single event affecting two isoforms of CDKN2A gene. The rearrangement results in the deletion of CDKN2Ap14ARF exon1 and CDKN2Ap16INK4A exon1.
TMPRSS2	0	MSKCC-DMP	P-0014395-T01-IM6	ARHGAP26-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ARHGAP26 (NM_015071) fusion (TMPRSS2 exons 1-2 fused in-frame to ARHGAP26 exons 12-23): t(5;21)(q31.3;q22.3)(chr5:g.142324441::chr21:g.42868024)
ARHGAP26	0	MSKCC-DMP	P-0014395-T01-IM6	ARHGAP26-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ARHGAP26 (NM_015071) fusion (TMPRSS2 exons 1-2 fused in-frame to ARHGAP26 exons 12-23): t(5;21)(q31.3;q22.3)(chr5:g.142324441::chr21:g.42868024)
SMARCA4	0	MSKCC-DMP	P-0012909-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) Rearrangement : c.4301_4424+659del Note: The SMARCA4 Rearrangement results in the intragenic deletion of exon 30 of SMARCA4. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0012596-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3547-184_c.3804dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 26-27. One of the breakpoints is within exon 27.
MGA	0	MSKCC-DMP	P-0012623-T01-IM5	CACNA1B-MGA fusion	yes	unknown		out of frame	CACNA1B (NM_000718) - MGA (NM_001164273) Rearrangement : t(9;15)(q22.3;p11.1)(chr9:g.140896610::chr15:g.42041234) Note: The CACNA1B - MGA Rearrangement results in the fusion of exons 1-15 of CACNA1B with exons 16-24 of MGA.Its functional significance is undetermined.
CACNA1B	0	MSKCC-DMP	P-0012623-T01-IM5	CACNA1B-MGA fusion	yes	unknown		out of frame	CACNA1B (NM_000718) - MGA (NM_001164273) Rearrangement : t(9;15)(q22.3;p11.1)(chr9:g.140896610::chr15:g.42041234) Note: The CACNA1B - MGA Rearrangement results in the fusion of exons 1-15 of CACNA1B with exons 16-24 of MGA.Its functional significance is undetermined.
GFRA2	0	MSKCC-DMP	P-0011259-T01-IM5	EIF4E-GFRA2 fusion	yes	unknown		unknown	EIF4E (NM_001130678) Rearrangement : t(4;8)(q23;p21.3)(chr4:g.99849955::chr8:g.21254285) Note: The EIF4E Rearrangement is a translocation event which results in the possible truncation of exon1 of EIF4E. Its functional significance is undetermined.
EIF4E	0	MSKCC-DMP	P-0011259-T01-IM5	EIF4E-GFRA2 fusion	yes	unknown		unknown	EIF4E (NM_001130678) Rearrangement : t(4;8)(q23;p21.3)(chr4:g.99849955::chr8:g.21254285) Note: The EIF4E Rearrangement is a translocation event which results in the possible truncation of exon1 of EIF4E. Its functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0014631-T01-IM6	LTBP4-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626)  rearrangement: c.752:AKT2_c.4032+747:LTBP4del Note: The AKT2 rearrangement is a deletion which includes exons 1-9 of AKT2. One of the breakpoints is within exon9. The functional significance is undetermined.
LTBP4	0	MSKCC-DMP	P-0014631-T01-IM6	LTBP4-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626)  rearrangement: c.752:AKT2_c.4032+747:LTBP4del Note: The AKT2 rearrangement is a deletion which includes exons 1-9 of AKT2. One of the breakpoints is within exon9. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0013660-T01-IM5	NCAM1-ATM fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangement : c.8162_chr11:g.112801427del Note: The ATM Rearrangement results in the deletion of exons 56 -63 of ATM. The breakpoint in ATM is within exon 56. Its functional significance is undetermined.
NCAM1	0	MSKCC-DMP	P-0013660-T01-IM5	NCAM1-ATM fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangement : c.8162_chr11:g.112801427del Note: The ATM Rearrangement results in the deletion of exons 56 -63 of ATM. The breakpoint in ATM is within exon 56. Its functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0013443-T01-IM5	SRD5A3-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: c.2510-129:KDR_chr4:g.56104211del Note: The KDR rearrangement is a deletion of 5UTR and exons 1-17.
SRD5A3	0	MSKCC-DMP	P-0013443-T01-IM5	SRD5A3-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: c.2510-129:KDR_chr4:g.56104211del Note: The KDR rearrangement is a deletion of 5UTR and exons 1-17.
PIK3C2G	0	MSKCC-DMP	P-0011135-T01-IM5	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement : c.3889-80_3965-4589inv Note: The PIK3C2G rearrangement event results in the inversion of PIK3C2G exon29.
ERG	0	MSKCC-DMP	P-0014414-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_004449) - TMPRRS2 (NM_001135099) rearrangement: c.39+51460:ERG_c.56-2388:TMPRRS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exon 3 to TMPRSS2 exon 2.  The functional significance is undetermined. Although this rearrangement does not result in a TMPRSS2 - ERG fusion, a more complex rearrangement that results in a TMPRSS2 - ERG fusion is possible.
TMPRSS2	0	MSKCC-DMP	P-0014414-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_004449) - TMPRRS2 (NM_001135099) rearrangement: c.39+51460:ERG_c.56-2388:TMPRRS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exon 3 to TMPRSS2 exon 2.  The functional significance is undetermined. Although this rearrangement does not result in a TMPRSS2 - ERG fusion, a more complex rearrangement that results in a TMPRSS2 - ERG fusion is possible.
CBX6	0	MSKCC-DMP	P-0014077-T01-IM5	EP300-CBX6 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.39268126_c.1380:EP300del Note: The EP300 rearrangement is a deletion of 5UTR and exons 1-6. One of the breakpoints is within exon 6.
EP300	0	MSKCC-DMP	P-0014077-T01-IM5	EP300-CBX6 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.39268126_c.1380:EP300del Note: The EP300 rearrangement is a deletion of 5UTR and exons 1-6. One of the breakpoints is within exon 6.
NEDD8	0	MSKCC-DMP	P-0014732-T01-IM6	BAP1-NEDD8 fusion	yes	unknown		unknown	NEDD8 (NM_001199823) - BAP1 (NM_004656) rearrangement: t(3;14)(p21.1;q12)(chr3:g.52444003::chr14:g.24689227) Note: The NEDD8 - BAP1 rearrangement is a translocation which results in the fusion of NEDD8 exon 1 to the 5UTR of BAP1. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0014732-T01-IM6	BAP1-NEDD8 fusion	yes	unknown		unknown	NEDD8 (NM_001199823) - BAP1 (NM_004656) rearrangement: t(3;14)(p21.1;q12)(chr3:g.52444003::chr14:g.24689227) Note: The NEDD8 - BAP1 rearrangement is a translocation which results in the fusion of NEDD8 exon 1 to the 5UTR of BAP1. The functional significance is undetermined.
DOK6	0	MSKCC-DMP	P-0014732-T01-IM6	PBRM1-DOK6 fusion	yes	unknown		unknown	DOK6 (NM_152721) - PBRM1 (NM_018313) rearrangement: t(3;18)(p21.1;q22.2)(chr3:g.52692284::chr18:g.67099152) Note: The DOK6 - PBRM1 rearrangement is a translocation which results in the fusion of DOK6 exon 1 to PBRM1 exon 6. One of the breakpoints is within exon 6 of PBRM1. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0014732-T01-IM6	PBRM1-DOK6 fusion	yes	unknown		unknown	DOK6 (NM_152721) - PBRM1 (NM_018313) rearrangement: t(3;18)(p21.1;q22.2)(chr3:g.52692284::chr18:g.67099152) Note: The DOK6 - PBRM1 rearrangement is a translocation which results in the fusion of DOK6 exon 1 to PBRM1 exon 6. One of the breakpoints is within exon 6 of PBRM1. The functional significance is undetermined.
CDCP1	0	MSKCC-DMP	P-0014732-T01-IM6	PIK3CB-CDCP1 fusion	yes	unknown		unknown	PIK3CB (NM_006219) rearrangement: chr3:g.45114508_c.1581+9del Note: The PIK3CB rearrangement is a deletion which includes exons 11-22. The functional significance is undetermined.
PIK3CB	0	MSKCC-DMP	P-0014732-T01-IM6	PIK3CB-CDCP1 fusion	yes	unknown		unknown	PIK3CB (NM_006219) rearrangement: chr3:g.45114508_c.1581+9del Note: The PIK3CB rearrangement is a deletion which includes exons 11-22. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0013451-T01-IM5	STX7-ROS1 fusion	yes	unknown		out of frame	STX7 (NM_003569) - ROS1 (NM_002944) rearrangement: c.86-3411:STX7_c.5366+1036:ROS1del Note: The STX7 - ROS1 rearrangement is a deletion that results in the fusion of STX7 exons 1-2 with ROS1 exons 33-43, which include the kinase domain.
STX7	0	MSKCC-DMP	P-0013451-T01-IM5	STX7-ROS1 fusion	yes	unknown		out of frame	STX7 (NM_003569) - ROS1 (NM_002944) rearrangement: c.86-3411:STX7_c.5366+1036:ROS1del Note: The STX7 - ROS1 rearrangement is a deletion that results in the fusion of STX7 exons 1-2 with ROS1 exons 33-43, which include the kinase domain.
STK11	0	MSKCC-DMP	P-0010320-T01-IM5	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) Rearrangement :  c.465-98_1108+1298dup Note: The STK11 Rearrangement results in the intragenic duplication of exons 4-8 of STK11. Its functional significance is undetermined.
CTCF	0	MSKCC-DMP	P-0013182-T01-IM5	CTCF-intragenic	yes	unknown		unknown	CTCF (NM_006565) rearrangement: c.953-1108_c.1157dup Note: The CTCF rearrangement is a duplication of exons 5-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0010994-T01-IM5	MTMR3-EWSR1 fusion	yes	unknown		unknown	MTMR3 (NM_021090) - EWSR1 (NM_013986) rearrangement: c.-85+3820:MTMR3_c.992+1294:EWSR1dup Note: The MTMR3 - EWSR1 rearrangement is a duplication that results in fusion of 5-UTR of MTMR3 with EWSR1 exons 9-18. The functional significance is undetermined.
MTMR3	0	MSKCC-DMP	P-0010994-T01-IM5	MTMR3-EWSR1 fusion	yes	unknown		unknown	MTMR3 (NM_021090) - EWSR1 (NM_013986) rearrangement: c.-85+3820:MTMR3_c.992+1294:EWSR1dup Note: The MTMR3 - EWSR1 rearrangement is a duplication that results in fusion of 5-UTR of MTMR3 with EWSR1 exons 9-18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0014992-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2429:TMPRSS2_c.18+5301:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014992-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2429:TMPRSS2_c.18+5301:ERGdel
CTNNB1	0	MSKCC-DMP	P-0014460-T01-IM6	FAM198A-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement : c.1082-37:CTNNB1_c.4-17540:FAM198inv Note: The CTNNB1 Rearrangement results in the inversion of exons 8-15 of CTNNB1. Its functional significance is undetermined.
FAM198A	0	MSKCC-DMP	P-0014460-T01-IM6	FAM198A-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement : c.1082-37:CTNNB1_c.4-17540:FAM198inv Note: The CTNNB1 Rearrangement results in the inversion of exons 8-15 of CTNNB1. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0011343-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1708_c.1813-1667dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 9-10. One of the breakpoint is within exon 9.
RAD21	0	MSKCC-DMP	P-0011343-T01-IM5	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.374+128_c.812dup Note: The RAD21 rearrangement is an intragenic duplication of exons 5-7. One of the breakpoints is within exon 7.
CNTN1	0	MSKCC-DMP	P-0011542-T01-IM5	MLL2-CNTN1 fusion	yes	unknown		out of frame	MLL2 (NM_003482) - CNTN1 (NM_001843) rearrangement: c.5320-13:MLL2_c.2113+2294:CNTN1inv Note: The MLL2 - CNTN1 rearrangement is an inversion that results int the fusion of MLL2 exons 1-22 with CNTN1 exons 18-24. The functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0011542-T01-IM5	MLL2-CNTN1 fusion	yes	unknown		out of frame	MLL2 (NM_003482) - CNTN1 (NM_001843) rearrangement: c.5320-13:MLL2_c.2113+2294:CNTN1inv Note: The MLL2 - CNTN1 rearrangement is an inversion that results int the fusion of MLL2 exons 1-22 with CNTN1 exons 18-24. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0012731-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.278_c.492+4373del Note: The PTEN rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
AKAP11	0	MSKCC-DMP	P-0013277-T01-IM5	FH-AKAP11 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241665743::chr13:g.42830282) Note: The FH rearrangement is a translocation with a breakpoint within exon 8. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a fusion.
FH	0	MSKCC-DMP	P-0013277-T01-IM5	FH-AKAP11 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241665743::chr13:g.42830282) Note: The FH rearrangement is a translocation with a breakpoint within exon 8. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a fusion.
NUP35	0	MSKCC-DMP	P-0012513-T01-IM5	PMS1-NUP35 fusion	yes	unknown		unknown	PMS1 (NM_000534) rearrangement: chr2:g.183973880_c.668:PMS1del Note: The PMS1 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6 of PMS1. The functional significance is undetermined.
PMS1	0	MSKCC-DMP	P-0012513-T01-IM5	PMS1-NUP35 fusion	yes	unknown		unknown	PMS1 (NM_000534) rearrangement: chr2:g.183973880_c.668:PMS1del Note: The PMS1 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6 of PMS1. The functional significance is undetermined.
PRMT8	0	MSKCC-DMP	P-0010742-T01-IM5	APC-PRMT8 fusion	yes	unknown		unknown	APC (NM_000038) - PRMT8 (NM_019854) rearrangement : t(5;12)(q22.2;p12.32)(chr5:g.112175904::chr12:g.3608058) Note: The APC-PRMT8 rearrangement is a translocation which results in the fusion of APC exons 1-16 with PRMT8 exon1. One of the breakpoints is within APC exon16. This fusion could also be interpreted as a truncation of APC gene at exon16.
APC	0	MSKCC-DMP	P-0010742-T01-IM5	APC-PRMT8 fusion	yes	unknown		unknown	APC (NM_000038) - PRMT8 (NM_019854) rearrangement : t(5;12)(q22.2;p12.32)(chr5:g.112175904::chr12:g.3608058) Note: The APC-PRMT8 rearrangement is a translocation which results in the fusion of APC exons 1-16 with PRMT8 exon1. One of the breakpoints is within APC exon16. This fusion could also be interpreted as a truncation of APC gene at exon16.
TP53	0	MSKCC-DMP	P-0012925-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.-28-1687_c.207del Note: The TP53 rearrangement is a deletion of 5UTR and exons 1-4. One of the breakpoints is within exon 4.
APC	0	MSKCC-DMP	P-0011350-T01-IM5	REEP5-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1743+2749:APC_chr5:g.112213830inv Note: The APC rearrangement is an inversion of exons 15-16.
REEP5	0	MSKCC-DMP	P-0011350-T01-IM5	REEP5-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1743+2749:APC_chr5:g.112213830inv Note: The APC rearrangement is an inversion of exons 15-16.
ERG	0	MSKCC-DMP	P-0014202-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 2-10): c.126+456:TMPRSS2_c.18+59:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014202-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 2-10): c.126+456:TMPRSS2_c.18+59:ERGdel
DNMT1	0	MSKCC-DMP	P-0010789-T01-IM5	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement : c.72_1232+762dup Note: The DNMT1 rearrangement event results in the intragenic duplication of DNMT1 exons 1-16. One of the breakpoints is within DNMT1 exon1.
AR	0	MSKCC-DMP	P-0003101-T03-IM5	AR-intragenic	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2182_c.*970del Note: The AR rearrangement is an intragenic deletion of exons 5-8. One of the breakpoints is within exon 5. This structural alteration may represent a possible splicing variant (AR-V7), with the loss of ligand binding domain of androgen receptor. The AR-V7 isoform is constitutively active in transcription, irrespective of androgen binding. It may represent a way of cancer escaping androgen deprivation therapy and has been reported to be associated with resistence to enzalutamide or abiraterone (see references). References: 1. Antonarakis ES, Lu C, Wang H, Luber B, Nakazawa M, Roeser JC, et al. AR-V7 and resistance to enzalutamide and abiraterone in prostate cancer. N Engl J Med. 2014 Sep 11;371(11):1028-38. PMID: 25184630; PubMed Central PMCID: PMC4201502. 2. Ciccarese C, Santoni M, Brunelli M, Buti S, Modena A, Nabissi M, et al. AR-V7 and prostate cancer: The watershed for treatment selection? Cancer Treat Rev. 2016 Feb;43:27-35. PMID: 26827690.
TPPP	0	MSKCC-DMP	P-0011157-T01-IM5	TERT-TPPP fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.1573+12:TERT_chr5:g.682643del Note: The TERT rearrangement is an intragenic deletion of exons 3-16. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0011157-T01-IM5	TERT-TPPP fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.1573+12:TERT_chr5:g.682643del Note: The TERT rearrangement is an intragenic deletion of exons 3-16. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0012779-T01-IM5	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.67_c.68-1del Note: The B2M rearrangement is an intragenic deletion of a part of exon 1, including the splice site. One of the breakpoints is within exon 1.
ERG	0	MSKCC-DMP	P-0012555-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4576:TMPRSS2_c.-4791:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012555-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4576:TMPRSS2_c.-4791:ERGdel
SPEN	0	MSKCC-DMP	P-0013526-T01-IM5	EPHA2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement : c.6934:SPEN_c.153+110:EPHA2 Note: The SPEN Rearrangement results in the duplication of exons 11-15. One of the breakpoints is within exon 11. Its functional significance is undetermined.
EPHA2	0	MSKCC-DMP	P-0013526-T01-IM5	EPHA2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement : c.6934:SPEN_c.153+110:EPHA2 Note: The SPEN Rearrangement results in the duplication of exons 11-15. One of the breakpoints is within exon 11. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0013962-T01-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140)  Rearrangement : c.654+6760_c.2938+22dup Note: The KDM6A Rearrangement results in the intragenic duplication of exons 9-19 of KDM6A. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0013825-T01-IM5	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1782:KIF5B_c.2137-512:RETinv Note: The KIF5B - RET fusion involves the kinase domain of RET.
RET	0	MSKCC-DMP	P-0013825-T01-IM5	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1782:KIF5B_c.2137-512:RETinv Note: The KIF5B - RET fusion involves the kinase domain of RET.
ERG	0	MSKCC-DMP	P-0012321-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1622:TMPRSS2_c.40-58417:ERGdel Note: The TMPRSS2-ERG fusion is an in-frame fusion.
TMPRSS2	0	MSKCC-DMP	P-0012321-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1622:TMPRSS2_c.40-58417:ERGdel Note: The TMPRSS2-ERG fusion is an in-frame fusion.
ALK	0	MSKCC-DMP	P-0012679-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1489+2812:EML4_c.3172+861:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
EML4	0	MSKCC-DMP	P-0012679-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1489+2812:EML4_c.3172+861:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
ATP1B2	0	MSKCC-DMP	P-0012773-T01-IM5	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangment: chr17:g.7552584_c.455:TP53del Note: The TP53 rearrangement in a deletion of exons 5-11. One of the breakpoints is within exon 5.
TP53	0	MSKCC-DMP	P-0012773-T01-IM5	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangment: chr17:g.7552584_c.455:TP53del Note: The TP53 rearrangement in a deletion of exons 5-11. One of the breakpoints is within exon 5.
RARA	0	MSKCC-DMP	P-0011365-T01-IM5	COPZ2-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - COPZ2 (NM_016429) rearrangement : c.1284:RARA_c.543-37:COPZ2del Note: The RARA rearrangement event  results in the deletion of RARA exon9. One of the breakpoints is within RARA exon9.
COPZ2	0	MSKCC-DMP	P-0011365-T01-IM5	COPZ2-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - COPZ2 (NM_016429) rearrangement : c.1284:RARA_c.543-37:COPZ2del Note: The RARA rearrangement event  results in the deletion of RARA exon9. One of the breakpoints is within RARA exon9.
EP300	0	MSKCC-DMP	P-0014591-T01-IM6	ETV1-EP300 fusion	yes	unknown		in frame	ETV1 (NM_001163147)_EP300 (NM_001429)  rearrangement: t(7;22)(p21.2;q13.2)(chr7:g.14022908::chr22:g.41562739) Note: The EP300 (NM_001429) _ETV1 (NM_001163147)   rearrangement is a translocation that results in the in-frame fusion of exons 1-22 of EP300 with ETV1 exons 2 -12. The functional significance is undetermined.
ETV1	0	MSKCC-DMP	P-0014591-T01-IM6	ETV1-EP300 fusion	yes	unknown		in frame	ETV1 (NM_001163147)_EP300 (NM_001429)  rearrangement: t(7;22)(p21.2;q13.2)(chr7:g.14022908::chr22:g.41562739) Note: The EP300 (NM_001429) _ETV1 (NM_001163147)   rearrangement is a translocation that results in the in-frame fusion of exons 1-22 of EP300 with ETV1 exons 2 -12. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012328-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2792:TMPRSS2_c.19-6300:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012328-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2792:TMPRSS2_c.19-6300:ERGdel
PDGFRA	0	MSKCC-DMP	P-0012919-T01-IM5	PDGFRA-intragenic	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: c.-12-8153_c.2562+25dup Note: The PDGFRA rearrangement is a duplication of exons 2-18. The functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0012919-T01-IM5	RAP1GDS1-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: chr4:g.99136655_c.2510-15del Note: The KDR rearrangement is a deletion which includes exons 1-17 of KDR. The functional significance is undetermined.
RAP1GDS1	0	MSKCC-DMP	P-0012919-T01-IM5	RAP1GDS1-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: chr4:g.99136655_c.2510-15del Note: The KDR rearrangement is a deletion which includes exons 1-17 of KDR. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0010098-T02-IM5	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.1088-275_c.2960dup Note: The PBRM1 rearrangement is a duplication of exons 12-19. One of the breakpoints is within exon 19. The functional significance is undetermined.
LALBA	0	MSKCC-DMP	P-0014158-T01-IM5	MLL2-LALBA fusion	yes	unknown		unknown	MLL2 (NM_003482) rearrangement:chr12:g.48956575_c.15959:MLL2del Note: The MLL2 (NM_003482) rearrangement results in the deletion of MLL2 exons 50-54. One of the breakpoints is within MLL2 exon 50.  The functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0014158-T01-IM5	MLL2-LALBA fusion	yes	unknown		unknown	MLL2 (NM_003482) rearrangement:chr12:g.48956575_c.15959:MLL2del Note: The MLL2 (NM_003482) rearrangement results in the deletion of MLL2 exons 50-54. One of the breakpoints is within MLL2 exon 50.  The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0011534-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11):  c.55+1941:TMPRSS2_c.39+64333:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0011534-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11):  c.55+1941:TMPRSS2_c.39+64333:ERGdel
MGA	0	MSKCC-DMP	P-0011377-T01-IM5	MGA-intragenic	yes	unknown		in frame	MGA (NM_001164273) rearrangement: c.3085-167_c.7009-102del Note: The MGA rearrangement is an intragenic deletion of exons 9-17.
ERG	0	MSKCC-DMP	P-0011377-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-10): c.127-1163:TMPRSS2_c.19-14268:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0011377-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-10): c.127-1163:TMPRSS2_c.19-14268:ERGdel
BRAF	0	MSKCC-DMP	P-0010398-T01-IM5	OSBPL9-BRAF fusion	yes	unknown		in frame	OSBPL9 (NM_148909) - BRAF (NM_004333) Rearrangement : t(1;7)(p32.3;q34)(chr1:g.52228623::chr7:g.140484912) Note: The OSBPL9 - BRAF Rearrangement is a translocation event that results in the fusion of exons 1-11 of  OSBPL9 with exons 10-18 of BRAF. The rearrangement includes the kinase domain of BRAF.
OSBPL9	0	MSKCC-DMP	P-0010398-T01-IM5	OSBPL9-BRAF fusion	yes	unknown		in frame	OSBPL9 (NM_148909) - BRAF (NM_004333) Rearrangement : t(1;7)(p32.3;q34)(chr1:g.52228623::chr7:g.140484912) Note: The OSBPL9 - BRAF Rearrangement is a translocation event that results in the fusion of exons 1-11 of  OSBPL9 with exons 10-18 of BRAF. The rearrangement includes the kinase domain of BRAF.
SMARCA4	0	MSKCC-DMP	P-0014860-T01-IM6	TRAM1L1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(4;19)(q26;p13.2)(chr4:g.118193638::chr19:g.11121062) Note: The SMARCA4 rearrangement is a translocation with a breakpoint within exon 15. The functional significance is undetermined.
TRAM1L1	0	MSKCC-DMP	P-0014860-T01-IM6	TRAM1L1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(4;19)(q26;p13.2)(chr4:g.118193638::chr19:g.11121062) Note: The SMARCA4 rearrangement is a translocation with a breakpoint within exon 15. The functional significance is undetermined.
C9orf106	0	MSKCC-DMP	P-0013344-T01-IM5	SPEN-C9orf106 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: t(1;9)(1p36.13;9q34.13)(chr1:g.16235959::chr9:g.132142700) Note: The SPEN rearrangement is a translocation event which results in the possible truncation of SPEN. One of the breakpoints is within exon 4 of SPEN. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0013344-T01-IM5	SPEN-C9orf106 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: t(1;9)(1p36.13;9q34.13)(chr1:g.16235959::chr9:g.132142700) Note: The SPEN rearrangement is a translocation event which results in the possible truncation of SPEN. One of the breakpoints is within exon 4 of SPEN. Its functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0012416-T01-IM5	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.3037-275_c.3972del Note: The KDM5A rearrangement is an intragenic deletion of exons 21-24. One of breakpoints is within exon 24.
ZNF398	0	MSKCC-DMP	P-0014486-T01-IM6	MLL3-ZNF398 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: chr7:g.148881016_c.6187dup Note: The MLL3 (NM_170606) rearrangement is a duplication of MLL3 exons 36-59. One of the breakpoints is within exon 36. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0014486-T01-IM6	MLL3-ZNF398 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: chr7:g.148881016_c.6187dup Note: The MLL3 (NM_170606) rearrangement is a duplication of MLL3 exons 36-59. One of the breakpoints is within exon 36. The functional significance is undetermined.
SERPINE2	0	MSKCC-DMP	P-0010741-T01-IM5	CUL3-SERPINE2 fusion	yes	unknown		unknown	CUL3 (NM_003590) rearrangement : c.1206+19:CUL3_chr2:g.225008101del Note: CUL3 rearrangement event results in the deletion of CUL3 exons 9-16.
CUL3	0	MSKCC-DMP	P-0010741-T01-IM5	CUL3-SERPINE2 fusion	yes	unknown		unknown	CUL3 (NM_003590) rearrangement : c.1206+19:CUL3_chr2:g.225008101del Note: CUL3 rearrangement event results in the deletion of CUL3 exons 9-16.
MGA	0	MSKCC-DMP	P-0010660-T01-IM5	MAPKBP1-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) - MAPKBP1 (NM_001128608) rearrangement: c.2259:MGA_c.206+4637:MAPKBP1del Note: The MGA - MAPKBP1 rearrangement is a deletion that results in the fusion of MGA exons 1-6 with MAPKBP1 exons 4-32. One of the breakpoints is within MGA exon 6. The functional significance is undetermined.
MAPKBP1	0	MSKCC-DMP	P-0010660-T01-IM5	MAPKBP1-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) - MAPKBP1 (NM_001128608) rearrangement: c.2259:MGA_c.206+4637:MAPKBP1del Note: The MGA - MAPKBP1 rearrangement is a deletion that results in the fusion of MGA exons 1-6 with MAPKBP1 exons 4-32. One of the breakpoints is within MGA exon 6. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0012600-T01-IM5	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.2014+248_c.4271dup Note: The FANCA rearrangement is an intragenic duplication of exons 23-43. One of the breakpoint is within exon 43.
CTNNB1	0	MSKCC-DMP	P-0010044-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement : c.13+78_c.271del Note: The CTNNB1 Rearrangement results in the deletion of exons 2-4 of CTNNB1. The breakpoints are within exon2 and exon4 respectively.  Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012046-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement : c.40-45795:ERG_c.56-2111:TMPRSS2dup Note: The ERG-TMPRSS2 rearrangement event is a duplication which results in the fusion of ERG exons 1-3 with TMPRSS2 exons 2-14. Addition testing could be performed to confirm if this event is the canonical TMPRSS2-ERG fusion.
TMPRSS2	0	MSKCC-DMP	P-0012046-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement : c.40-45795:ERG_c.56-2111:TMPRSS2dup Note: The ERG-TMPRSS2 rearrangement event is a duplication which results in the fusion of ERG exons 1-3 with TMPRSS2 exons 2-14. Addition testing could be performed to confirm if this event is the canonical TMPRSS2-ERG fusion.
RET	0	MSKCC-DMP	P-0013886-T01-IM5	EML4-RET fusion	yes	unknown		unknown	EML4 (NM_019063) - RET (NM_020975) rearrangement: t(2;10)(p21;q11.21)(chr2:g.42550559::chr10:g.43610067) Note: The EML4 - RET rearrangement is a translocation which results in the fusion of EML4 exons 1-19 with RET exons 11-20, including the kinase domain of RET. One of the breakpoints is within exon 11 of RET. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0013886-T01-IM5	EML4-RET fusion	yes	unknown		unknown	EML4 (NM_019063) - RET (NM_020975) rearrangement: t(2;10)(p21;q11.21)(chr2:g.42550559::chr10:g.43610067) Note: The EML4 - RET rearrangement is a translocation which results in the fusion of EML4 exons 1-19 with RET exons 11-20, including the kinase domain of RET. One of the breakpoints is within exon 11 of RET. The functional significance is undetermined.
SDHC	0	MSKCC-DMP	P-0014201-T01-IM6	LAMC1-SDHC fusion	yes	unknown		unknown	SDHC (NM_003001) Rearrangement : c.296:SDHC_chr1:g.182949452inv Note: The SDHC Rearrangement results in the inversion of exons 4-6 of SDHC. One of the breakpoints is within exon4. Its functional significance is undetermined.
LAMC1	0	MSKCC-DMP	P-0014201-T01-IM6	LAMC1-SDHC fusion	yes	unknown		unknown	SDHC (NM_003001) Rearrangement : c.296:SDHC_chr1:g.182949452inv Note: The SDHC Rearrangement results in the inversion of exons 4-6 of SDHC. One of the breakpoints is within exon4. Its functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0014201-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) Rearrangement : c.485-87_c.4558-4836inv Note: The ATRX Rearrangement results in the inversion of exons 7 to 15 of ATRX. Its functional significance is undetermined.
DNAJC11	0	MSKCC-DMP	P-0010429-T01-IM5	ARID1A-DNAJC11 fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement :  chr1:g.6744104_c.3886:ARID1Adel Note: The ARID1A (NM_006015) Rearrangement results in the deletion of exons 1-16 of ARID1A. The breakpoint is within exon16. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0010429-T01-IM5	ARID1A-DNAJC11 fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement :  chr1:g.6744104_c.3886:ARID1Adel Note: The ARID1A (NM_006015) Rearrangement results in the deletion of exons 1-16 of ARID1A. The breakpoint is within exon16. Its functional significance is undetermined.
EIF3H	0	MSKCC-DMP	P-0014120-T01-IM5	XRCC2-EIF3H fusion	yes	unknown		unknown	XRCC2 (NM_005431) rearrangement: t(7;8)(q36.1;q23.3)(chr7:g.152346274::chr8:g.117398324) Note: The XRCC2 rearrangement is a translocation that may result in the truncation of exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.
XRCC2	0	MSKCC-DMP	P-0014120-T01-IM5	XRCC2-EIF3H fusion	yes	unknown		unknown	XRCC2 (NM_005431) rearrangement: t(7;8)(q36.1;q23.3)(chr7:g.152346274::chr8:g.117398324) Note: The XRCC2 rearrangement is a translocation that may result in the truncation of exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0014531-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRRS2 (NM_001135099) -ERG (NM_004449) Fusion: c.56-3954:TMPRSS2_c.18+11943:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014531-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRRS2 (NM_001135099) -ERG (NM_004449) Fusion: c.56-3954:TMPRSS2_c.18+11943:ERGdel
CDK12	0	MSKCC-DMP	P-0010822-T01-IM5	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement :  c.2911_c.2963+1045dup Note: The CDK12 Rearrangement results in the duplication of exon 10. One of the breakpoints is within exon10. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0012777-T01-IM5	SMARCE1-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.741:CDK12_chr17:g.38747170inv Note: The CDK12 rearrangement is an inversion of exons 1-14. One of the breakpoints is within exon 1.
SMARCE1	0	MSKCC-DMP	P-0012777-T01-IM5	SMARCE1-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.741:CDK12_chr17:g.38747170inv Note: The CDK12 rearrangement is an inversion of exons 1-14. One of the breakpoints is within exon 1.
SMAD3	0	MSKCC-DMP	P-0005436-T02-IM5	KLF4-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) Rearrangement :  t(9;15)(q31.3;q23)(chr9:g.110787568::chr15:g.67459189) Note: The SMAD3 Rearrangement results in the possible truncation of exons 4-9 of SMAD3. One of the breakpoints is within exon4. Its functional significance is undetermined.
KLF4	0	MSKCC-DMP	P-0005436-T02-IM5	KLF4-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) Rearrangement :  t(9;15)(q31.3;q23)(chr9:g.110787568::chr15:g.67459189) Note: The SMAD3 Rearrangement results in the possible truncation of exons 4-9 of SMAD3. One of the breakpoints is within exon4. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009786-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.126+493:TMPRSS2_c.40-60552:ERG
TMPRSS2	0	MSKCC-DMP	P-0009786-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.126+493:TMPRSS2_c.40-60552:ERG
TMPRSS2	0	MSKCC-DMP	P-0014701-T01-IM6	ARNT2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: t(15,21)(q25.1,q22.3)(chr15:g.15:80623299::chr21:g.42843748) Note: The TMPRSS2 Rearrangement is a translocation event which results in the possible truncation of exons 10-14 of TMPRSS2. One of the breakpoints is within exon 10.  Its functional significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion , the possibility of similar events not detected by IMPACT cannot be ruled out.
ARNT2	0	MSKCC-DMP	P-0014701-T01-IM6	ARNT2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: t(15,21)(q25.1,q22.3)(chr15:g.15:80623299::chr21:g.42843748) Note: The TMPRSS2 Rearrangement is a translocation event which results in the possible truncation of exons 10-14 of TMPRSS2. One of the breakpoints is within exon 10.  Its functional significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion , the possibility of similar events not detected by IMPACT cannot be ruled out.
CLDN14	0	MSKCC-DMP	P-0014701-T01-IM6	ERG-CLDN14 fusion	yes	unknown		unknown	ERG (NM_182918) Rearrangement : chr21:g.37828386_c.-109:ERGinv Note: The ERG Rearrangement results in the inversion of exons 1-10. While this is not the canonical TMPRSS2-ERG fusion , the possibility of similar events not detected by IMPACT cannot be ruled out.
ERG	0	MSKCC-DMP	P-0014701-T01-IM6	ERG-CLDN14 fusion	yes	unknown		unknown	ERG (NM_182918) Rearrangement : chr21:g.37828386_c.-109:ERGinv Note: The ERG Rearrangement results in the inversion of exons 1-10. While this is not the canonical TMPRSS2-ERG fusion , the possibility of similar events not detected by IMPACT cannot be ruled out.
ERG	0	MSKCC-DMP	P-0004297-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-10): c.126+619:TMPRSS2_c.-867:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004297-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-10): c.126+619:TMPRSS2_c.-867:ERGdel
ALK	0	MSKCC-DMP	P-0011018-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29) Note: The EML4-ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0011018-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29) Note: The EML4-ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
ARID1B	0	MSKCC-DMP	P-0011395-T01-IM5	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.5016_chr6:g.157544399del Note: The ARID1B rearrangement is a deletion of exon 20. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0014076-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3633:TMPRSS2_c.18+24406:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014076-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3633:TMPRSS2_c.18+24406:ERGdel
ALK	0	MSKCC-DMP	P-0010978-T01-IM5	EML4-ALK fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 fused with ALK exons 20-29): c.2154+2237:EML4_c.3173-20:ALKinv None
EML4	0	MSKCC-DMP	P-0010978-T01-IM5	EML4-ALK fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 fused with ALK exons 20-29): c.2154+2237:EML4_c.3173-20:ALKinv None
SOX17	0	MSKCC-DMP	P-0012055-T01-IM5	SOX17-intragenic	yes	unknown		unknown	SOX17 (NM_022454) rearrangement: c.-4513_c.-3197inv Note: The SOX17 rearrangement is an inversion which includes the promoter region of SOX17. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0013790-T01-IM5	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) Rearrangement : c.1333-4282_1404del Note: The RASA1 Rearrangement results in the deletion of exon 10 . One of the breakpoints is within exon 10. Its functional significance is undetermined,
ETV6	0	MSKCC-DMP	P-0011506-T01-IM5	CDKN1B-ETV6 fusion	yes	unknown		out of frame	ETV6 (NM_001987) - CDKN1B (NM_004064) rearrangement: c.34-10600:ETV6_c.476-58:CDKN1Bdel Note: The ETV6 - CDKN1B rearrangement is a deletion which results in the fusion of ETV6 exon 1 with CDKN1B exon 2. The functional significance is undetermined.
CDKN1B	0	MSKCC-DMP	P-0011506-T01-IM5	CDKN1B-ETV6 fusion	yes	unknown		out of frame	ETV6 (NM_001987) - CDKN1B (NM_004064) rearrangement: c.34-10600:ETV6_c.476-58:CDKN1Bdel Note: The ETV6 - CDKN1B rearrangement is a deletion which results in the fusion of ETV6 exon 1 with CDKN1B exon 2. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0011433-T01-IM5	FBXO11-MSH6 fusion	yes	unknown		unknown	MSH6 (NM_000179) - FBXO11 (NM_001190274) rearrangement : c.1738:MSH6_c.232+22604:FBXO11del Note: The MSH6-FBXO11 rearrangement event results in the deletion of MSH6 exons 4-10. One of the breakpoints is within MSH6 exon4.
FBXO11	0	MSKCC-DMP	P-0011433-T01-IM5	FBXO11-MSH6 fusion	yes	unknown		unknown	MSH6 (NM_000179) - FBXO11 (NM_001190274) rearrangement : c.1738:MSH6_c.232+22604:FBXO11del Note: The MSH6-FBXO11 rearrangement event results in the deletion of MSH6 exons 4-10. One of the breakpoints is within MSH6 exon4.
FOXA1	0	MSKCC-DMP	P-0014368-T01-IM6	SSTR1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.932_chr14:g.38567231del Note: The FOXA1 rearrangement is a deletion which includes exons 1-2 of FOXA1. One of the breakpoints is within exon2. The functional significance is undetermined.
SSTR1	0	MSKCC-DMP	P-0014368-T01-IM6	SSTR1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.932_chr14:g.38567231del Note: The FOXA1 rearrangement is a deletion which includes exons 1-2 of FOXA1. One of the breakpoints is within exon2. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0012260-T01-IM5	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.719-308_c.862-188del Note: The RB1 rearrangement is an intragenic deletion of exon 8.
ERBB2	0	MSKCC-DMP	P-0012260-T01-IM5	C17orf37-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.3413-57:ERBB2_chr17:g.37886288del Note: The ERBB2 rearrangement is a deletion of exon 27.
C17orf37	0	MSKCC-DMP	P-0012260-T01-IM5	C17orf37-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.3413-57:ERBB2_chr17:g.37886288del Note: The ERBB2 rearrangement is a deletion of exon 27.
CEBPB	0	MSKCC-DMP	P-0012260-T01-IM5	CEBPB-intragenic	yes	unknown		unknown	CEBPB (NM_005194) rearrangement: c.978:CEBPB_chr20:g.48840052inv Note: The CEBPB rearrangement in an inversion of a part of exon 1. The breakpoint is within exon 1.
ERG	0	MSKCC-DMP	P-0007307-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.126+159:TMPRSS2_c.18+25874:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007307-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.126+159:TMPRSS2_c.18+25874:ERGdel
SMARCA4	0	MSKCC-DMP	P-0014237-T01-IM6	GTSF1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(12;19)(q13.3;p13.2)(chr12:g.:54842304::chr19:g.11172477) Note: The SMARCA4 rearrangement is a translocation with one of the breakpoints within exon35 of SMARCA4. The functional significance is undetermined.
GTSF1	0	MSKCC-DMP	P-0014237-T01-IM6	GTSF1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(12;19)(q13.3;p13.2)(chr12:g.:54842304::chr19:g.11172477) Note: The SMARCA4 rearrangement is a translocation with one of the breakpoints within exon35 of SMARCA4. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0014237-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 10-16): c.2390:FGFR3_c.1836+80:TACC3dup Note: The FGFR3 - TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within exon 18 of FGFR3.
FGFR3	0	MSKCC-DMP	P-0014237-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 10-16): c.2390:FGFR3_c.1836+80:TACC3dup Note: The FGFR3 - TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within exon 18 of FGFR3.
ERG	0	MSKCC-DMP	P-0010659-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 2-10): c.127-1011:TMPRSS2_c.18+2079:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010659-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 2-10): c.127-1011:TMPRSS2_c.18+2079:ERGdel
TACC3	0	MSKCC-DMP	P-0014530-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) Fusion (FGFR3 exons 1-17 fused with TACC3 exons 6-16) : c.2274+54:FGFR3_c.1462-52:TACC3dup Note: The FGFR3-TACC3 fusion is predicted to be in-frame and includes the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0014530-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) Fusion (FGFR3 exons 1-17 fused with TACC3 exons 6-16) : c.2274+54:FGFR3_c.1462-52:TACC3dup Note: The FGFR3-TACC3 fusion is predicted to be in-frame and includes the kinase domain of FGFR3.
PIK3R2	0	MSKCC-DMP	P-0013879-T01-IM5	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement: c.323-139_c.1123del Note: The PIK3R2 rearrangement is an intragenic deletion of exons 3 -10. One of the breakpoints is within 10.  The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0012145-T01-IM5	ALDH4A1-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: t(1;17)(p36.13;q22)(chr1:g.19206599::chr17:g.56434626) Note: The RNF43 rearrangement is a translocation that may result in a truncation of exon 10. The functional significance is undetermined.
ALDH4A1	0	MSKCC-DMP	P-0012145-T01-IM5	ALDH4A1-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: t(1;17)(p36.13;q22)(chr1:g.19206599::chr17:g.56434626) Note: The RNF43 rearrangement is a translocation that may result in a truncation of exon 10. The functional significance is undetermined.
MCL1	0	MSKCC-DMP	P-0011192-T01-IM5	ENSA-MCL1 fusion	yes	unknown		unknown	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement : c.-565:MCL1_c.57+728:ENSAdup Note: The MCL1-ENSA rearrangement event is a duplication which results in the fusion of MCL1 promoter region with ENSA exons 2-4.
ENSA	0	MSKCC-DMP	P-0011192-T01-IM5	ENSA-MCL1 fusion	yes	unknown		unknown	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement : c.-565:MCL1_c.57+728:ENSAdup Note: The MCL1-ENSA rearrangement event is a duplication which results in the fusion of MCL1 promoter region with ENSA exons 2-4.
TERT	0	MSKCC-DMP	P-0011192-T01-IM5	SDHAP3-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-338:TERT_chr5:g.1536135del Note: The TERT rearrangement events results in the deletion of TERT promoter region. One of the breakpoints is within the TERT promoter.
SDHAP3	0	MSKCC-DMP	P-0011192-T01-IM5	SDHAP3-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-338:TERT_chr5:g.1536135del Note: The TERT rearrangement events results in the deletion of TERT promoter region. One of the breakpoints is within the TERT promoter.
CBL	0	MSKCC-DMP	P-0011175-T01-IM5	CBL-intragenic	yes	unknown		in frame	CBL (NM_005188) rearrangement: c.1095+35_c.1432-291del Note: The CBL rearrangement is a intragenic deletion of exons 8-9.
MSH2	0	MSKCC-DMP	P-0011175-T01-IM5	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) rearrangement: c.346_c.1387-6199del Note: The MSH2 rearrangement is a intragenic deletion of exons 2-8. One of the breakpoints is within exon 2.
ELP4	0	MSKCC-DMP	P-0011281-T01-IM5	WT1-ELP4 fusion	yes	unknown		out of frame	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.1432+64:WT1_c.1144-56067:ELP4inv Note: The WT1 - ELP4 rearrangement is an inversion which leads to the fusion of WT1 exons 1-9 with ELP4 exon 10. The functional significance is undetermined.
WT1	0	MSKCC-DMP	P-0011281-T01-IM5	WT1-ELP4 fusion	yes	unknown		out of frame	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.1432+64:WT1_c.1144-56067:ELP4inv Note: The WT1 - ELP4 rearrangement is an inversion which leads to the fusion of WT1 exons 1-9 with ELP4 exon 10. The functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0012562-T01-IM5	SDPR-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) rearrangement: t(2;19)(q32.3;p13.12)(chr2:g.192746391::chr19:g.14627434) Note: The DNAJB1 rearrangement is a reciprocal truncation that may result in the truncation of exons 2-3. One of the breakpoints is within exon 2. The functional significance is undetermined.
SDPR	0	MSKCC-DMP	P-0012562-T01-IM5	SDPR-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) rearrangement: t(2;19)(q32.3;p13.12)(chr2:g.192746391::chr19:g.14627434) Note: The DNAJB1 rearrangement is a reciprocal truncation that may result in the truncation of exons 2-3. One of the breakpoints is within exon 2. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0013985-T01-IM5	PEX5L-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) Rearrangement : t(3,6)(q26.33,p21.33)(chr3:g.179829046::chr6:g.30681978) Note: MDC1 Rearrangement results in the possible truncation of MDC1. One of the breakpoints is 18bp before exon 3. Its functional significance is undetermined.
PEX5L	0	MSKCC-DMP	P-0013985-T01-IM5	PEX5L-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) Rearrangement : t(3,6)(q26.33,p21.33)(chr3:g.179829046::chr6:g.30681978) Note: MDC1 Rearrangement results in the possible truncation of MDC1. One of the breakpoints is 18bp before exon 3. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0013925-T01-IM5	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: c.-94-2961_c.237+67inv Note: The PTPRS rearrangement is an inversion of 5UTR and exons 1-3.
TSC2	0	MSKCC-DMP	P-0014007-T01-IM5	TSC2-intragenic	yes	unknown		out of frame	TSC2 (NM_000548) rearrangement: c.1717-568_c.3884-80del Note: The TSC2 rearrangement is an intragenic deletion of exons 17 -32. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0010782-T01-IM5	TMEM64-NBN fusion	yes	unknown		unknown	NBN (NM_002485) - TMEM64 (NM_001008495) rearrangement: c.572:NBN_c.795+4539:TMEM64dup Note: The NBN - TMEM64 rearrangement is a duplication which results in the fusion of NBN exons 1-5 with TMEM64 exons 2-3. One of the breakpoints is within exon5 of NBN. The functional significance is undetermined.
TMEM64	0	MSKCC-DMP	P-0010782-T01-IM5	TMEM64-NBN fusion	yes	unknown		unknown	NBN (NM_002485) - TMEM64 (NM_001008495) rearrangement: c.572:NBN_c.795+4539:TMEM64dup Note: The NBN - TMEM64 rearrangement is a duplication which results in the fusion of NBN exons 1-5 with TMEM64 exons 2-3. One of the breakpoints is within exon5 of NBN. The functional significance is undetermined.
MEN1	0	MSKCC-DMP	P-0013749-T02-IM6	MEN1-intragenic	yes	unknown		unknown	MEN1 (NM_000244) rearrangement : c.407_722del Note: The MEN1 rearrangement results in the deletion of exons of 2-4 of MEN1. The breakpoints are within exon 2 and 4 respectively. The functional significance is undetermined.
UBAC1	0	MSKCC-DMP	P-0010208-T01-IM5	NOTCH1-UBAC1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - UBAC1 (NM_016172) rearrangement : c.6082+10:NOTCH1_c.333+1482:UBAC1inv Note: The NOTCH1 - UBAC1 rearrangement results in the inversion of NOTCH1 exons 32-34.
NOTCH1	0	MSKCC-DMP	P-0010208-T01-IM5	NOTCH1-UBAC1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - UBAC1 (NM_016172) rearrangement : c.6082+10:NOTCH1_c.333+1482:UBAC1inv Note: The NOTCH1 - UBAC1 rearrangement results in the inversion of NOTCH1 exons 32-34.
EWSR1	0	MSKCC-DMP	P-0010553-T01-IM5	EWSR1-intragenic	yes	unknown		in frame	EWSR1 (NM_013986) rearrangement: c.14-1270_c.1027+240dup Note: The EWSR1 rearrangement is a duplication of exons 2-8. The functional significance is undetermined.
RRAGC	0	MSKCC-DMP	P-0014973-T01-IM6	RRAGC-intragenic	yes	unknown		out of frame	RRAGC (NM_022157) Rearrangement : c.756+92_899+1584del Note: The RRAGC Rearrangement results in the intragenic deletion of exon 5 of RRAGC. Its functional significance is undetermined.
A2BP1	0	MSKCC-DMP	P-0015002-T01-IM6	ZFHX3-A2BP1 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement : c.5225:ZFHX3_g.6119693inv Note: The ZFHX3 (NM_006885) rearrangement results in an inversion of ZFHX3 exons 9-10 . The breakpoint in ZFHX3 is within exon 9. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0015002-T01-IM6	ZFHX3-A2BP1 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement : c.5225:ZFHX3_g.6119693inv Note: The ZFHX3 (NM_006885) rearrangement results in an inversion of ZFHX3 exons 9-10 . The breakpoint in ZFHX3 is within exon 9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005454-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1943:TMPRSS2_c.18+13593:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005454-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1943:TMPRSS2_c.18+13593:ERGdel
ERG	0	MSKCC-DMP	P-0013372-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1734:TMPRSS2_c.237-2384:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013372-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1734:TMPRSS2_c.237-2384:ERGdel
NOTCH4	0	MSKCC-DMP	P-0014807-T01-IM6	C6orf222-NOTCH4 fusion	yes	unknown		unknown	C6orf222 (NM_001010903) - NOTCH4 (NM_004557) rearrangement: c.1924-105:C6orf222_c.2188:NOTCH4del Note: The C6orf222 - NOTCH4 rearrangement is a deletion which results in the fusion of C6orf222 exon 11 to NOTCH4 exon 14. The functional significance is undetermined.
C6orf222	0	MSKCC-DMP	P-0014807-T01-IM6	C6orf222-NOTCH4 fusion	yes	unknown		unknown	C6orf222 (NM_001010903) - NOTCH4 (NM_004557) rearrangement: c.1924-105:C6orf222_c.2188:NOTCH4del Note: The C6orf222 - NOTCH4 rearrangement is a deletion which results in the fusion of C6orf222 exon 11 to NOTCH4 exon 14. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0014697-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement : c.-33+2576_c.275-14del Note: The RAD21 Rearrangement results in the deletion of exons 1-4 of RAD21. One of the breakpoints is within 5'UTR  before coding start site of RAD21. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0013355-T01-IM5	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.464+468_c.782dup Note: The STK11 rearrangement is an intragenic duplication of exons 4-6. One of the breakpoints is within exon 6.
NOTCH1	0	MSKCC-DMP	P-0014892-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: chr9:g.139383644_c.742+20del Note: The NOTCH1 (NM_017617) rearrangement is a deletion of exons 5-34. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012741-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.55+1605:TMPRSS2_c.40-54554:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012741-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.55+1605:TMPRSS2_c.40-54554:ERGdel
CTRC	0	MSKCC-DMP	P-0014859-T01-IM6	NTRK1-CTRC fusion	yes	unknown		unknown	CTRC (NM_007272)  - NTRK1 (NM_002529) rearrangement: c.88:CTRC_c.850+45:NTRK1del Note: The CTRC - NTRK1 rearrangement is a deletion which results in the fusion of CTRC exon2 to NTRK1 exon8 and includes the kinase domain of NTRK1. One of the breakpoints is within exon2 of CTRC.
NTRK1	0	MSKCC-DMP	P-0014859-T01-IM6	NTRK1-CTRC fusion	yes	unknown		unknown	CTRC (NM_007272)  - NTRK1 (NM_002529) rearrangement: c.88:CTRC_c.850+45:NTRK1del Note: The CTRC - NTRK1 rearrangement is a deletion which results in the fusion of CTRC exon2 to NTRK1 exon8 and includes the kinase domain of NTRK1. One of the breakpoints is within exon2 of CTRC.
ARID2	0	MSKCC-DMP	P-0014859-T01-IM6	ARID2-intragenic	yes	unknown		in frame	ARID2 (NM_152641) rearrangement: c.419-2860_c.638-69del Note: The ARID2 rearrangement is an intragenic deletion of exon5. The functional significance is undetermined.
ZFP30	0	MSKCC-DMP	P-0014990-T01-IM6	MLL2-ZFP30 fusion	yes	unknown		unknown	MLL2 (NM_003482) -  ZFP30 (NM_014898) Rearrangement : t(12;19)(q13.12;q13.13)(chr12:g.49432673::chr19:g.38141811) Note: The MLL2 - ZFP30 Rearrangement results in the fusion of exons 1-34 of MLL2 with exon 1-6 of ZFP30. The breakpoint for MLL2 is within exon 34, and the breakpoint for ZFP30 is in the 5'UTR region before the transcription start site of ZFP30. IMPACT detected this rearrangement occurring in the background of other rearrangement events affecting MLL2, and this may reflect a more complex rearrangement event involving MLL2 that is not fully characterized by IMPACT. If clinically indicated, additional testing to characterize gene fusion can be considered.
MLL2	0	MSKCC-DMP	P-0014990-T01-IM6	MLL2-ZFP30 fusion	yes	unknown		unknown	MLL2 (NM_003482) -  ZFP30 (NM_014898) Rearrangement : t(12;19)(q13.12;q13.13)(chr12:g.49432673::chr19:g.38141811) Note: The MLL2 - ZFP30 Rearrangement results in the fusion of exons 1-34 of MLL2 with exon 1-6 of ZFP30. The breakpoint for MLL2 is within exon 34, and the breakpoint for ZFP30 is in the 5'UTR region before the transcription start site of ZFP30. IMPACT detected this rearrangement occurring in the background of other rearrangement events affecting MLL2, and this may reflect a more complex rearrangement event involving MLL2 that is not fully characterized by IMPACT. If clinically indicated, additional testing to characterize gene fusion can be considered.
SOX9	0	MSKCC-DMP	P-0013704-T01-IM5	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.685+256_c.1477dup Note: The SOX9 rearrangement is a duplication of exon3. One of the breakpoints within exon 3. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0011370-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) Rearrangement :  c.240+3096_c.1314+210del Note: The BRAF Rearrangement  results in the deletion of exons3-10 of BRAF. It doesn't include the kinase domain and it's functional significance is unknown.
PTEN	0	MSKCC-DMP	P-0014905-T01-IM6	MYOF-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314)- MYOF (NM_013451) Rearrangement : c.855:PTEN_c.236+8749:MYOFinv Note: The PTEN - MYOF  Rearrangement is an inversion which results in the fusion of exons 1-8 of PTEN with exons 4- 54 of MYOF. The breakpoint in PTEN is within exon8. Its functional significance is undetermined.
MYOF	0	MSKCC-DMP	P-0014905-T01-IM6	MYOF-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314)- MYOF (NM_013451) Rearrangement : c.855:PTEN_c.236+8749:MYOFinv Note: The PTEN - MYOF  Rearrangement is an inversion which results in the fusion of exons 1-8 of PTEN with exons 4- 54 of MYOF. The breakpoint in PTEN is within exon8. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0010953-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2147:TMPRSS2_c.40-37761:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010953-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2147:TMPRSS2_c.40-37761:ERGdel
ERG	0	MSKCC-DMP	P-0010731-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement : c.56-2331:TMPRSS2_c.40-63084:ERGinv Note: The TMPRSS2-ERG rearrangement event is an inversion involving TMPRSS2 exon 2-14 and ERG exons 1-3. Additional testing will be performed to confirm if this event is a TMPRSS2-ERG fusion.
TMPRSS2	0	MSKCC-DMP	P-0010731-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement : c.56-2331:TMPRSS2_c.40-63084:ERGinv Note: The TMPRSS2-ERG rearrangement event is an inversion involving TMPRSS2 exon 2-14 and ERG exons 1-3. Additional testing will be performed to confirm if this event is a TMPRSS2-ERG fusion.
ERG	0	MSKCC-DMP	P-0000373-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3994:TMPRSS2_c.19-24499:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0000373-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3994:TMPRSS2_c.19-24499:ERGdel
AKT1	0	MSKCC-DMP	P-0014824-T01-IM6	PLD4-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) rearrangement: c.971:AKT1_chr14:g.105380925inv Note: The AKT1 rearrangement is an inversion of exons 11-14. One of the breakpoints is within exon 11.
PLD4	0	MSKCC-DMP	P-0014824-T01-IM6	PLD4-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) rearrangement: c.971:AKT1_chr14:g.105380925inv Note: The AKT1 rearrangement is an inversion of exons 11-14. One of the breakpoints is within exon 11.
PCSK1	0	MSKCC-DMP	P-0013828-T01-IM5	APC-PCSK1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.95664163_c.261:APCdup Note: The APC rearrangement is a duplication of 5UTR and exons 1-4. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0013828-T01-IM5	APC-PCSK1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.95664163_c.261:APCdup Note: The APC rearrangement is a duplication of 5UTR and exons 1-4. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0013835-T01-IM5	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.4146_c.7806+339del Note: The ANKRD11 rearrangement is a deletion of exons 9-12. One of the breakpoints is within exon 9.
ETV6	0	MSKCC-DMP	P-0013392-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.163+13216_c.464-2446dup Note: The ETV6 rearrangement is an intragenic duplication of exons 3-4.
WWOX	0	MSKCC-DMP	P-0014511-T01-IM6	FANCA-WWOX fusion	yes	unknown		out of frame	FANCA (NM_000135) - WWOX (NM_016373) rearrangement: c.3348+22:FANCA_c.409+15919:WWOXinv Note: The FANCA - WWOX rearrangement is an inversion that results in the fusion of FANCA exons 1-34 to WWOX exons 5-9. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0014511-T01-IM6	FANCA-WWOX fusion	yes	unknown		out of frame	FANCA (NM_000135) - WWOX (NM_016373) rearrangement: c.3348+22:FANCA_c.409+15919:WWOXinv Note: The FANCA - WWOX rearrangement is an inversion that results in the fusion of FANCA exons 1-34 to WWOX exons 5-9. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0014511-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.207_c.751del Note: The TP53 rearrangement is an intragenic deletion of exons 4-7. The breakpoints are within exons 4 and 7.
PIK3R2	0	MSKCC-DMP	P-0011321-T01-IM5	ZNF714-PIK3R2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - ZNF714 (NM_18251) rearrangement: c.1078:PIK3R2_c.142+1169:ZNF714del Note: The PIK3R2 - ZNF714 rearrangement is a deletion which results in the fusion of PIK3R2 exons 1-9 with ZNF714 exon 5. One of the breakpoints is within exon 9 of PIK3R2. The functional significance is undetermined.
ZNF714	0	MSKCC-DMP	P-0011321-T01-IM5	ZNF714-PIK3R2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - ZNF714 (NM_18251) rearrangement: c.1078:PIK3R2_c.142+1169:ZNF714del Note: The PIK3R2 - ZNF714 rearrangement is a deletion which results in the fusion of PIK3R2 exons 1-9 with ZNF714 exon 5. One of the breakpoints is within exon 9 of PIK3R2. The functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0010214-T01-IM5	HADHB-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) rearrangement : t(2;20)(p23.3;q12)(chr2:g.26507418::chr20:g.39728683) Note: The TOP1 rearrangement event is a translocation which results in the truncation of TOP1 exons 12-21.
HADHB	0	MSKCC-DMP	P-0010214-T01-IM5	HADHB-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) rearrangement : t(2;20)(p23.3;q12)(chr2:g.26507418::chr20:g.39728683) Note: The TOP1 rearrangement event is a translocation which results in the truncation of TOP1 exons 12-21.
KEAP1	0	MSKCC-DMP	P-0012151-T01-IM5	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.640-1439_c.844del Note: The KEAP1 rearrangement is an intragenic deletion of a part of exon 3. One of the breakpoints is within exon 3.
POLD1	0	MSKCC-DMP	P-0014626-T01-IM6	SRRM1-POLD1 fusion	yes	unknown		out of frame	SRRM1 (NM_005839) - POLD1 (NM_002691) rearrangement: t(1;19)(p36.11;q13.33)(chr1:g.24979609::chr19:g.50919623) Note: The SRRM1 - POLD1 rearrangement is a translocation which results in the fusion of SRRM1 exon 8 to POLD1 exon 23. The functional significance is undetermined.
SRRM1	0	MSKCC-DMP	P-0014626-T01-IM6	SRRM1-POLD1 fusion	yes	unknown		out of frame	SRRM1 (NM_005839) - POLD1 (NM_002691) rearrangement: t(1;19)(p36.11;q13.33)(chr1:g.24979609::chr19:g.50919623) Note: The SRRM1 - POLD1 rearrangement is a translocation which results in the fusion of SRRM1 exon 8 to POLD1 exon 23. The functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0014626-T01-IM6	MSH3-intragenic	yes	unknown		unknown	MSH3 (NM_002439) rearrangement: c.3044_c.3130+3040dup Note: The MSH3 rearrangement is a duplication of exon 22. One of the breakpoints is within exon. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0012820-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : chr16:g.72984364_g.72523259del Note: The ZFHX3 (NM_006885) rearrangement results in the intragenic deletion of exons 4 to 10 of ZFHX3. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0014844-T01-IM6	MIR1973-RET fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: t(4;10)(q26;q11.21)(chr4:g.117039927)(chr10:g.43606798) Note: The RET rearrangement is a translocation with a breakpoint within exon7 of RET. The functional significance is undetermined.
MIR1973	0	MSKCC-DMP	P-0014844-T01-IM6	MIR1973-RET fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: t(4;10)(q26;q11.21)(chr4:g.117039927)(chr10:g.43606798) Note: The RET rearrangement is a translocation with a breakpoint within exon7 of RET. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0010177-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4  (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused in frame with ALK exons 20-29): c.1490-2649:EML4_c.3173-964:ALKinv
EML4	0	MSKCC-DMP	P-0010177-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4  (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused in frame with ALK exons 20-29): c.1490-2649:EML4_c.3173-964:ALKinv
NLRC3	0	MSKCC-DMP	P-0014455-T01-IM6	CREBBP-NLRC3 fusion	yes	unknown		out of frame	CREBBP (NM_004380) - NLRC3(NM_178844) Rearrangement : c.2880+66:CREBBP_c.2184-571:NLRC3del Note: The CREBBP - NLRC3 Rearrangement results in the fusion of exons 1-14 of CREBBP with exons 9-21 of NLRC3. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0014455-T01-IM6	CREBBP-NLRC3 fusion	yes	unknown		out of frame	CREBBP (NM_004380) - NLRC3(NM_178844) Rearrangement : c.2880+66:CREBBP_c.2184-571:NLRC3del Note: The CREBBP - NLRC3 Rearrangement results in the fusion of exons 1-14 of CREBBP with exons 9-21 of NLRC3. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0014430-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.-32+4013_c.2368del Note: The SMARCA4 (NM_003072) rearrangement is a deletion of exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0001184-T02-IM5	LOC100101266-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement : c.1093+25:TCF3_chr19:g.24369803del Note1: The TCF3 rearrangement event results in the deletion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.
LOC100101266	0	MSKCC-DMP	P-0001184-T02-IM5	LOC100101266-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement : c.1093+25:TCF3_chr19:g.24369803del Note1: The TCF3 rearrangement event results in the deletion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.
TCF3	0	MSKCC-DMP	P-0001184-T02-IM5	FAM108A1-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - ABHD17A (NM_001130111) rearrangement : c.1093+25:TCF3_chr19:g.24369803del Note2: The TCF3 - ABHD17A rearrangement event results in the inversion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.
FAM108A1	0	MSKCC-DMP	P-0001184-T02-IM5	FAM108A1-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - ABHD17A (NM_001130111) rearrangement : c.1093+25:TCF3_chr19:g.24369803del Note2: The TCF3 - ABHD17A rearrangement event results in the inversion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.
CDKL5	0	MSKCC-DMP	P-0012246-T01-IM5	ATM-CDKL5 fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangement : t(11;X)(q22.3;p22.13)(chr11:g.108168152::chrX:g.18639068) Note: The ATM Rearrangement is a translocation event that results in the possible truncation of exons 34-63. Its functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0012246-T01-IM5	ATM-CDKL5 fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangement : t(11;X)(q22.3;p22.13)(chr11:g.108168152::chrX:g.18639068) Note: The ATM Rearrangement is a translocation event that results in the possible truncation of exons 34-63. Its functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0009297-T02-IM5	MED12-intragenic	yes	unknown		in frame	MED12 (NM_005120) Rearrangement : c.3867+20_c.4864-30dup Note: The MED12  Rearrangement results in the intragenic duplication of exons28-35. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012104-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_001243428) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11): (c.126+879:TMRPSS2_c.40-63033:ERGdel)
TMPRSS2	0	MSKCC-DMP	P-0012104-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_001243428) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11): (c.126+879:TMRPSS2_c.40-63033:ERGdel)
ERG	0	MSKCC-DMP	P-0011156-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4374:TMPRSS2_c.18+15905:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0011156-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4374:TMPRSS2_c.18+15905:ERGdel
ALK	0	MSKCC-DMP	P-0012778-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1320:EML4_c.3172+885:ALKinv
EML4	0	MSKCC-DMP	P-0012778-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1320:EML4_c.3172+885:ALKinv
TERT	0	MSKCC-DMP	P-0012028-T01-IM5	CDH18-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.-198_chr5:g.19154622inv Note: The TERT rearrangement event results in the inversion of the TERT promoter region.
CDH18	0	MSKCC-DMP	P-0012028-T01-IM5	CDH18-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.-198_chr5:g.19154622inv Note: The TERT rearrangement event results in the inversion of the TERT promoter region.
BRCA2	0	MSKCC-DMP	P-0014583-T01-IM6	C2orf86-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: t(2;13)(p15;q13.1)(chr2:g.63335220::chr13:g.:32912064) Note: The BRCA2 rearrangement is a translocation with a breakpoint within exon 11 of BRCA2. The functional significance is undetermined.
C2orf86	0	MSKCC-DMP	P-0014583-T01-IM6	C2orf86-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: t(2;13)(p15;q13.1)(chr2:g.63335220::chr13:g.:32912064) Note: The BRCA2 rearrangement is a translocation with a breakpoint within exon 11 of BRCA2. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0014583-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.96_c.920-17dup. Note: The TP53 rearrangement is a duplication of exons 3-8. One of the breakpoints is within exon 3. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0014583-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.732+628_c.1503dup Note: The NCOR1 rearrangement is a duplication of exons 7-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0014583-T01-IM6	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) rearrangement: c.1746+23_c.1858del Note: The TP63 rearrangement is an intragenic deletion. One of the breakpoints is within exon 14. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0014583-T01-IM6	NBN-intragenic	yes	unknown		out of frame	NBN (NM_002485) rearrangement: c.38-93_c.584+810dup Note: The NBN rearrangement is a duplication of exons 2-5. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0013241-T01-IM5	KLHL29-FGFR2 fusion	yes	unknown		unknown	KLHL29 (NM_052920) - FGFR2 (NM_000141) rearrangement: t(2;10)(p24.1;q26.13)(chr2:g.:23647979::chr10:g.123241923) Note: The KLHL29 - FGFR2 rearrangement is a translocation which results in the fusion of KLHL29 exon 1 with FGFR2 exon 18
KLHL29	0	MSKCC-DMP	P-0013241-T01-IM5	KLHL29-FGFR2 fusion	yes	unknown		unknown	KLHL29 (NM_052920) - FGFR2 (NM_000141) rearrangement: t(2;10)(p24.1;q26.13)(chr2:g.:23647979::chr10:g.123241923) Note: The KLHL29 - FGFR2 rearrangement is a translocation which results in the fusion of KLHL29 exon 1 with FGFR2 exon 18
ATP6V1D	0	MSKCC-DMP	P-0013241-T01-IM5	FGFR2-ATP6V1D fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ATP6V1D (NM_015994) rearrangement: t(10;14)(q26.13;q23.2)(chr10:g.123242048::chr14:g.67818116) Note: The FGFR2 - ATP6V1D rearrangement is a translocation which results in the fusion of FGFR2 exons 1-17 with ATP6V1D exons 3 - 9. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0013241-T01-IM5	FGFR2-ATP6V1D fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ATP6V1D (NM_015994) rearrangement: t(10;14)(q26.13;q23.2)(chr10:g.123242048::chr14:g.67818116) Note: The FGFR2 - ATP6V1D rearrangement is a translocation which results in the fusion of FGFR2 exons 1-17 with ATP6V1D exons 3 - 9. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
EGFR	0	MSKCC-DMP	P-0004961-T02-IM5	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) Rearrangement :  c.2062-143_c.3115-117dup Note: The EGFR Rearrangement results in the tandem internal duplication of EGFR exons 18-25.
ALK	0	MSKCC-DMP	P-0013869-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1 to 13 with exons 20-29 of ALK) : c.1490-187:EML4_c.3173-318:ALKinv Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0013869-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1 to 13 with exons 20-29 of ALK) : c.1490-187:EML4_c.3173-318:ALKinv Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.
ERG	0	MSKCC-DMP	P-0013336-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2 to 10) : c.56-4272:TMPRSS2_c.19-13796:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013336-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2 to 10) : c.56-4272:TMPRSS2_c.19-13796:ERGdel
RUNX1	0	MSKCC-DMP	P-0014502-T01-IM6	RUNX1-intragenic	yes	unknown		in frame	RUNX1 (NM_001754) rearrangement: c.613+3474_c.805+12632del Note: The RUNX1 rearrangement is an intragenic deletion of exon 4.
NBN	0	MSKCC-DMP	P-0010087-T01-IM5	C8orf38-NBN fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: chr8;g.96017141_c.481-43:NBNinv The NBN rearrangement is an inversion of exons 1-4. The functional significance is undetermined.
C8orf38	0	MSKCC-DMP	P-0010087-T01-IM5	C8orf38-NBN fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: chr8;g.96017141_c.481-43:NBNinv The NBN rearrangement is an inversion of exons 1-4. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0014976-T01-IM6	SFRS2IP-ARID2 fusion	yes	unknown		out of frame	SCAF11 (NM_004719) - ARID2 (NM_152641) Rearrangement : c.220-1748:SCAF11_c.5364-623:ARID2inv Note: The SCAF11- ARID2 Rearrangement results in the fusion of exons 1-3 of SCAF11 with exon 21 of ARID2. Its functional significance is undetermined.
SFRS2IP	0	MSKCC-DMP	P-0014976-T01-IM6	SFRS2IP-ARID2 fusion	yes	unknown		out of frame	SCAF11 (NM_004719) - ARID2 (NM_152641) Rearrangement : c.220-1748:SCAF11_c.5364-623:ARID2inv Note: The SCAF11- ARID2 Rearrangement results in the fusion of exons 1-3 of SCAF11 with exon 21 of ARID2. Its functional significance is undetermined.
MIAT	0	MSKCC-DMP	P-0014976-T01-IM6	EWSR1-MIAT fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : c.945+718:EWSR1_chr22:27475510del Note: The EWSR1 Rearrangement results in the deletion of exons 1-12 of EWSR1. This event was detected in the background of other rearrangements involving EWSR1 which may suggest a more complex rearrangement event that may not be fully characterized by IMPACT. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0014976-T01-IM6	EWSR1-MIAT fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : c.945+718:EWSR1_chr22:27475510del Note: The EWSR1 Rearrangement results in the deletion of exons 1-12 of EWSR1. This event was detected in the background of other rearrangements involving EWSR1 which may suggest a more complex rearrangement event that may not be fully characterized by IMPACT. Its functional significance is undetermined.
NUP93	0	MSKCC-DMP	P-0014690-T01-IM6	SLC12A3-NUP93 fusion	yes	unknown		unknown	NUP93 (NM_014669) rearrangement: c.1345+48:NUP93_chr16:g.56898209del Note: The NUP93 rearrangement is a deletion of exons 13-22.
SLC12A3	0	MSKCC-DMP	P-0014690-T01-IM6	SLC12A3-NUP93 fusion	yes	unknown		unknown	NUP93 (NM_014669) rearrangement: c.1345+48:NUP93_chr16:g.56898209del Note: The NUP93 rearrangement is a deletion of exons 13-22.
ERG	0	MSKCC-DMP	P-0012327-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-913:TMPRSS2_c.-150+10700:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012327-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-913:TMPRSS2_c.-150+10700:ERGdel
MLL3	0	MSKCC-DMP	P-0012199-T01-IM5	MLL3-intragenic	yes	unknown		out of frame	MLL3 (NM_170606) rearrangement: c.161+27464_c.9517+76dup Note: The MLL3 rearrangement in an intragenic duplication of exons 2-41.
NRG1	0	MSKCC-DMP	P-0011180-T01-IM5	CD74-NRG1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NRG1 (NM_013956) rearrangement: t(5;8)(q32;p12)(chr5:g.149782758::chr8:g.32513214) Note: The CD74 - NRG1 rearrangement is a translocation that results in the fusion of CD74 exons 1-7 with  NRG1 exons 2-13. One of the breakpoints is within CD74 exon 7. The somatic gene fusion CD74 - NRG1 has been identified in invasive mucinous lung adenocarcinomas.  Additionally, this fusion has been shown to confer oncogenic properties in cell lines. . See references: 1.) Oncogenic Fusion Gene CD74-NRG1 Confers Cancer Stem Cell-like Properties in Lung Cancer through a IGF2 Autocrine/Paracrine Circuit. Cancer Research 2016 Feb 15; 76(4): 974-83. 2.) CD74?NRG1 Fusions in Lung Adenocarcinoma. Cancer Discovery 2014 April 1; 4: 415-22.
CD74	0	MSKCC-DMP	P-0011180-T01-IM5	CD74-NRG1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NRG1 (NM_013956) rearrangement: t(5;8)(q32;p12)(chr5:g.149782758::chr8:g.32513214) Note: The CD74 - NRG1 rearrangement is a translocation that results in the fusion of CD74 exons 1-7 with  NRG1 exons 2-13. One of the breakpoints is within CD74 exon 7. The somatic gene fusion CD74 - NRG1 has been identified in invasive mucinous lung adenocarcinomas.  Additionally, this fusion has been shown to confer oncogenic properties in cell lines. . See references: 1.) Oncogenic Fusion Gene CD74-NRG1 Confers Cancer Stem Cell-like Properties in Lung Cancer through a IGF2 Autocrine/Paracrine Circuit. Cancer Research 2016 Feb 15; 76(4): 974-83. 2.) CD74?NRG1 Fusions in Lung Adenocarcinoma. Cancer Discovery 2014 April 1; 4: 415-22.
CDKN2A	0	MSKCC-DMP	P-0014635-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.150+130:CDKN2Ap16INK4A_chr9:21981216inv Note: The CDKN2Ap16INK4A Rearrangement results in the inversion of exon1 of CDKN2Ap16INK4A. One of the breakpoints is within exon1. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0010934-T01-IM5	EGFR-intragenic	yes	unknown		unknown	EFGR VIII Intragenic deletion:  c.169_889+121del Note: One of the breakpoints of the EFGR VIII Intragenic deletion is within EGFR exon2.
PRKAG1	0	MSKCC-DMP	P-0006311-T02-IM5	MLL2-PRKAG1 fusion	yes	unknown		unknown	PRKAG1 (NM_002733) - MLL2 (NM_003482) Rearrangement : c.9+2460:PRKAG1_c.11934:MLL2dup Note: The PRKAG1 - MLL2  Rearrangement results in the fusion of exon 1 of PRKAG1with exons 39-54 of MLL2. Its functional significance is undetermined. This rearrangement could be part of the other complex events in MLL2.Additional testing is suggested if clinically indicated.
MLL2	0	MSKCC-DMP	P-0006311-T02-IM5	MLL2-PRKAG1 fusion	yes	unknown		unknown	PRKAG1 (NM_002733) - MLL2 (NM_003482) Rearrangement : c.9+2460:PRKAG1_c.11934:MLL2dup Note: The PRKAG1 - MLL2  Rearrangement results in the fusion of exon 1 of PRKAG1with exons 39-54 of MLL2. Its functional significance is undetermined. This rearrangement could be part of the other complex events in MLL2.Additional testing is suggested if clinically indicated.
DNMT1	0	MSKCC-DMP	P-0014421-T01-IM6	FRAT2-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(10;19)(q24.1; p13.2)(chr10:g.99096319::chr19:g.10244272) Note: The DNMT1 rearrangement is a translocation with a breakpoint within the 3UTR of DNMT1. The functional significance is undetermined.
FRAT2	0	MSKCC-DMP	P-0014421-T01-IM6	FRAT2-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(10;19)(q24.1; p13.2)(chr10:g.99096319::chr19:g.10244272) Note: The DNMT1 rearrangement is a translocation with a breakpoint within the 3UTR of DNMT1. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0013417-T01-IM5	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement : c.327_2609+3398dup Note: The CDK12 Rearrangement results in the duplication of exons 1-6 of CDK12. One of the breakpoints is within exon1. Its functional significance is undetermined.
TMEM132C	0	MSKCC-DMP	P-0014597-T01-IM6	POLE-TMEM132C fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.128237816_c.1227-6:POLEinv Note: The POLE (NM_006231) rearrangement is an inversion of exons 13-49. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0014597-T01-IM6	POLE-TMEM132C fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.128237816_c.1227-6:POLEinv Note: The POLE (NM_006231) rearrangement is an inversion of exons 13-49. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0010222-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.319:CDKN2Ap16INK4A_chr9:g.22027267del CDKN2Ap14ARF (NM_058195) rearrangement : c.362:CDKN2Ap14ARF_chr9:g.22027267del Note: The CDKN2Ap16INK4A and CDKN2Ap14ARF structural rearrangements reported constitute a single event affecting both isoforms of the protein, deleting CDKN2A exons 1-2. One of the breakpoints is within exon2.
CDKN2BAS	0	MSKCC-DMP	P-0010222-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.319:CDKN2Ap16INK4A_chr9:g.22027267del CDKN2Ap14ARF (NM_058195) rearrangement : c.362:CDKN2Ap14ARF_chr9:g.22027267del Note: The CDKN2Ap16INK4A and CDKN2Ap14ARF structural rearrangements reported constitute a single event affecting both isoforms of the protein, deleting CDKN2A exons 1-2. One of the breakpoints is within exon2.
C2orf67	0	MSKCC-DMP	P-0010171-T01-IM5	ARID1A-C2orf67 fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;2)(p36.11;q34)(chr1:g.27059158::chr2:g.210926778) Note: The ARID1A rearrangement is a translocation that may result in the truncation of ARID1A exons 4-20. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0010171-T01-IM5	ARID1A-C2orf67 fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;2)(p36.11;q34)(chr1:g.27059158::chr2:g.210926778) Note: The ARID1A rearrangement is a translocation that may result in the truncation of ARID1A exons 4-20. The functional significance is undetermined.
MBD3	0	MSKCC-DMP	P-0012373-T01-IM5	TCF3-MBD3 fusion	yes	unknown		out of frame	TCF3 (NM_001136139) - MBD3 (NM_003926) rearrangement: c.1813+71:TCF3_c.110+3139:MBD3del Note: The TCF3 - MBD3 rearrangement is a deletion which results in the fusion of TCF3 exons 1-17 with MDB3 exons 2-6. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0012373-T01-IM5	TCF3-MBD3 fusion	yes	unknown		out of frame	TCF3 (NM_001136139) - MBD3 (NM_003926) rearrangement: c.1813+71:TCF3_c.110+3139:MBD3del Note: The TCF3 - MBD3 rearrangement is a deletion which results in the fusion of TCF3 exons 1-17 with MDB3 exons 2-6. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0012373-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 with TACC3 exons 10-16 ): c.2274+69:FGFR3_c.1837-70:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0012373-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 with TACC3 exons 10-16 ): c.2274+69:FGFR3_c.1837-70:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
ARID1A	0	MSKCC-DMP	P-0013379-T01-IM5	PIGV-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) - PIGV (NM_017837) rearrangement: c.1137+68:ARID1A_c.-57-235:PIGVdel Note: The ARID1A - PIGV rearrangement is a deletion which results in the fusion of ARID1A exon 1 to PIGV exon 2. The functional significance is undetermined.
PIGV	0	MSKCC-DMP	P-0013379-T01-IM5	PIGV-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) - PIGV (NM_017837) rearrangement: c.1137+68:ARID1A_c.-57-235:PIGVdel Note: The ARID1A - PIGV rearrangement is a deletion which results in the fusion of ARID1A exon 1 to PIGV exon 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0011364-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.55+2676:TMPRSS2_c.40-58736:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0011364-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.55+2676:TMPRSS2_c.40-58736:ERGdel
FAM123B	0	MSKCC-DMP	P-0011066-T01-IM5	FAM123B-intragenic	yes	unknown		unknown	AMER1 (NM_152424) rearrangement: c.-98-2113_c.3043del Note: The AMER1 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon2. The functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0014624-T02-IM6	RAD23A-CALR fusion	yes	unknown		in frame	CALR (NM_004343) - RAD23A (NM_005053) Rearrangement : c.960+111:CALR_c.73-349:RAD23Adel Note: The CALR - RAD23A Rearrangement results in the fusion of exons 1-7 of CALR with exons 2-9 of RAD23A. Its functional significance is undetermined.
RAD23A	0	MSKCC-DMP	P-0014624-T02-IM6	RAD23A-CALR fusion	yes	unknown		in frame	CALR (NM_004343) - RAD23A (NM_005053) Rearrangement : c.960+111:CALR_c.73-349:RAD23Adel Note: The CALR - RAD23A Rearrangement results in the fusion of exons 1-7 of CALR with exons 2-9 of RAD23A. Its functional significance is undetermined.
LCP2	0	MSKCC-DMP	P-0014624-T02-IM6	EPAS1-LCP2 fusion	yes	unknown		unknown	LCP2 (NM_005565)- EPAS1 (NM_001430) Rearrangement : t(2;5)(p21;q35.1)(chr2:g.46588195::chr5:g.169707068) Note: The LCP2 - EPAS1  Rearrangement is a translocation event which results in the fusion of exons1-3 of LCP2 with exons 6-16 of EPAS1. The breakpoint in EPAS1 is within exon 6. Its functional significance is undetermined.
EPAS1	0	MSKCC-DMP	P-0014624-T02-IM6	EPAS1-LCP2 fusion	yes	unknown		unknown	LCP2 (NM_005565)- EPAS1 (NM_001430) Rearrangement : t(2;5)(p21;q35.1)(chr2:g.46588195::chr5:g.169707068) Note: The LCP2 - EPAS1  Rearrangement is a translocation event which results in the fusion of exons1-3 of LCP2 with exons 6-16 of EPAS1. The breakpoint in EPAS1 is within exon 6. Its functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0010712-T01-IM5	AKT1-intragenic	yes	unknown		unknown	AKT1 (NM_001014431) Rearrangement : c.1260+1_c.1261del Note: The AKT1 Rearrangement results in the partial deletion of exon13. One of the breakpoints is within exon13. Its functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0010712-T01-IM5	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) Rearrangement :  c.956+728_c.1323del Note: The AXIN2 Rearrangement results in the intragenic deletion of exons4-6. One of the breakpoints is within exon6. Its functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0013672-T01-IM5	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.194-370_c.398del Note: The CDKN2Ap14ARF rearrangement is a deletion of exon 2.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0013672-T01-IM5	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement:  c.151-370_c.355del Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2.
FERMT1	0	MSKCC-DMP	P-0012782-T01-IM5	PAK7-FERMT1 fusion	yes	unknown		unknown	PAK7 (NM_177990) rearrangement: chr20:g.9524889_c.1869+127:PAK7del Note: The PAK7 rearrangement in a deletion of exons 9-10.
PAK7	0	MSKCC-DMP	P-0012782-T01-IM5	PAK7-FERMT1 fusion	yes	unknown		unknown	PAK7 (NM_177990) rearrangement: chr20:g.9524889_c.1869+127:PAK7del Note: The PAK7 rearrangement in a deletion of exons 9-10.
MLL3	0	MSKCC-DMP	P-0014481-T01-IM6	ACTR3B-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.7593_chr7:g.152705153dup Note: The MLL3 (NM_170606) rearrangement is a duplication of exons 1-38. One of the breakpoints is within exon 38. The functional significance is undetermined.
ACTR3B	0	MSKCC-DMP	P-0014481-T01-IM6	ACTR3B-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.7593_chr7:g.152705153dup Note: The MLL3 (NM_170606) rearrangement is a duplication of exons 1-38. One of the breakpoints is within exon 38. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0010338-T01-IM5	C14orf176-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement : t(X;14)(q21.1;q11.2)(chrX:g.76918982::chr14:g.21586971) Note: ATRX rearrangement event is a translocation which results in the truncation of ATRX exons 12-35.
C14orf176	0	MSKCC-DMP	P-0010338-T01-IM5	C14orf176-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement : t(X;14)(q21.1;q11.2)(chrX:g.76918982::chr14:g.21586971) Note: ATRX rearrangement event is a translocation which results in the truncation of ATRX exons 12-35.
CDC42EP5	0	MSKCC-DMP	P-0014004-T01-IM5	TNFRSF14-CDC42EP5 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: t(1;19)(p36.32; q13.42)(chr1:g.2494783::chr19:g.54979682) Note: The TNFRSF14 rearrangement is a translocation with a breakpoint within the 3UTR of TNFRS14. The functional significance is undetermined.
TNFRSF14	0	MSKCC-DMP	P-0014004-T01-IM5	TNFRSF14-CDC42EP5 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: t(1;19)(p36.32; q13.42)(chr1:g.2494783::chr19:g.54979682) Note: The TNFRSF14 rearrangement is a translocation with a breakpoint within the 3UTR of TNFRS14. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0014004-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3828_c.40-59410del
TMPRSS2	0	MSKCC-DMP	P-0014004-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3828_c.40-59410del
CD74	0	MSKCC-DMP	P-0014797-T01-IM6	B3GNT7-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) rearrangement: t(2;5)(q37.1;q32)(chr2:g.232240463::chr5:g.149784283) Note: The CD74 rearrangement is a translocation with a breakpoint within exon6 of CD74. The functional significance is undetermined.
B3GNT7	0	MSKCC-DMP	P-0014797-T01-IM6	B3GNT7-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) rearrangement: t(2;5)(q37.1;q32)(chr2:g.232240463::chr5:g.149784283) Note: The CD74 rearrangement is a translocation with a breakpoint within exon6 of CD74. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0014935-T01-IM6	TMPRSS2-intragenic	yes	unknown		in frame	TMPRSS2 (NM_001135099) Rearrangement : c.55+3606_556+853dup Note: The TMPRSS2 Rearrangement results in the duplication of exons 2-5. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0013864-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1 to 13 with exons 20-29 of ALK) : c.1489+658:EML4_c.3172+118:ALKinv Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0013864-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1 to 13 with exons 20-29 of ALK) : c.1489+658:EML4_c.3172+118:ALKinv Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.
CD180	0	MSKCC-DMP	P-0014596-T01-IM6	PIK3R1-CD180 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1986-56_chr5:g.66569460inv Note: The PIK3R1 (NM_181523) rearrangement is an inversion of PIK3R1 exons 1-15. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0014596-T01-IM6	PIK3R1-CD180 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1986-56_chr5:g.66569460inv Note: The PIK3R1 (NM_181523) rearrangement is an inversion of PIK3R1 exons 1-15. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0014437-T01-IM6	EZR-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) _EZR (NM_003379) rearrangement: c.1090+229:EZR_c.5366+129:ROS1del Note: The ROS1 (NM_002944) _EZR (NM_003379) rearrangement is a deletion that results in the fusion of EZR exons 1-9 to ROS1 exons 33-43. The functional significance is undetermined.
EZR	0	MSKCC-DMP	P-0014437-T01-IM6	EZR-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) _EZR (NM_003379) rearrangement: c.1090+229:EZR_c.5366+129:ROS1del Note: The ROS1 (NM_002944) _EZR (NM_003379) rearrangement is a deletion that results in the fusion of EZR exons 1-9 to ROS1 exons 33-43. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012197-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11 ): c.56-2534_c.39+38157del
TMPRSS2	0	MSKCC-DMP	P-0012197-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11 ): c.56-2534_c.39+38157del
XPO1	0	MSKCC-DMP	P-0014879-T01-IM6	XPO1-intragenic	yes	unknown		unknown	XPO1 (NM_003400) rearrangement: c.1098_c.759+824dup Note: The XPO1 (NM_003400) rearrangement is a duplication of XPO1 exons 10-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0012105-T01-IM5	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) Rearrangement : c.2546-258_c.3363dup Note: The TSC2  Rearrangement results in the intragenic duplication of exons 23-29. One of the breakpoints is within exon29. Its functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0012105-T01-IM5	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) Rearrangement : c.793_c.1559+68dup Note: The PIK3R2 Rearrangement results in the duplication of exons 6-12 of PIK3R2.One of the breakpoints is within exon6. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0012578-T01-IM5	LRCH3-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) - LRCH3 (NM_032773) rearrangement: t(3;13)(q29;q14.2)(chr3:g.197595964::chr13:g.48916931) Note: The RB1 - LRCH3 rearrangement is a translocation in which LRCH3 exons 1-17 fuse to RB1 exons 1-3 in an antisense manner and may result in a truncated RB1. The functional significance is undetermined.
LRCH3	0	MSKCC-DMP	P-0012578-T01-IM5	LRCH3-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) - LRCH3 (NM_032773) rearrangement: t(3;13)(q29;q14.2)(chr3:g.197595964::chr13:g.48916931) Note: The RB1 - LRCH3 rearrangement is a translocation in which LRCH3 exons 1-17 fuse to RB1 exons 1-3 in an antisense manner and may result in a truncated RB1. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0010271-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*101+1_c.*102del CDKN2Ap16INK4A (NM_00007) rearrangement: c.457+1_c.458del Note: The CDKN2Ap14ARF rearrangement is a deletion of exon3. One of the breakpoints is within exon3. The functional significance is undetermined. Note: The CDKN2Ap16INK4A rearrangement is a deletion of exon3. One of the breakpoints is within exon3. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0014391-T01-IM6	ZGPAT-RTEL1 fusion	yes	unknown		unknown	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-11505:ZGPAT_c.3326:RTEL1dup Note: The ZGPAT - RTEL1 rearrangement is a duplication that results in the fusion of ZGPAT exons 1-2 to RTEL1 exons 32-35. One of the breakpoints is within exon 32 of RTEL1. The functional significance is undetermined.
ZGPAT	0	MSKCC-DMP	P-0014391-T01-IM6	ZGPAT-RTEL1 fusion	yes	unknown		unknown	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-11505:ZGPAT_c.3326:RTEL1dup Note: The ZGPAT - RTEL1 rearrangement is a duplication that results in the fusion of ZGPAT exons 1-2 to RTEL1 exons 32-35. One of the breakpoints is within exon 32 of RTEL1. The functional significance is undetermined.
RBM10	0	MSKCC-DMP	P-0010159-T01-IM5	PHIP-RBM10 fusion	yes	unknown		unknown	RBM10 (NM_001204468) - PHIP (NM_017934) rearrangement: t(6;X)(q14.1;p11.23)(chr6:g.79678650::chrX:g.47004857) Note: The RBM10 - PHIP rearrangement is a translocation that results in the fusion of RBM10 exon 1 with PHIP exons 28-40. One of the breakpoints is within RBM10 exon 1. The functional significance is undetermined.
PHIP	0	MSKCC-DMP	P-0010159-T01-IM5	PHIP-RBM10 fusion	yes	unknown		unknown	RBM10 (NM_001204468) - PHIP (NM_017934) rearrangement: t(6;X)(q14.1;p11.23)(chr6:g.79678650::chrX:g.47004857) Note: The RBM10 - PHIP rearrangement is a translocation that results in the fusion of RBM10 exon 1 with PHIP exons 28-40. One of the breakpoints is within RBM10 exon 1. The functional significance is undetermined.
KCNH3	0	MSKCC-DMP	P-0013948-T01-IM5	TBX3-KCNH3 fusion	yes	unknown		out of frame	TBX3 (NM_016569) - KCNH3 (NM_012284) rearrangement: c.1770+32:TBX3_c.76+84:KCNH3inv Note: The TBX3 - KCNH3 rearrangement is an inversion which results in the fusion of TBX3 exons 1-6 with KCHN3 exons 2-15. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0013948-T01-IM5	TBX3-KCNH3 fusion	yes	unknown		out of frame	TBX3 (NM_016569) - KCNH3 (NM_012284) rearrangement: c.1770+32:TBX3_c.76+84:KCNH3inv Note: The TBX3 - KCNH3 rearrangement is an inversion which results in the fusion of TBX3 exons 1-6 with KCHN3 exons 2-15. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013733-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1667:TMPRSS2_c.18+2781:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013733-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1667:TMPRSS2_c.18+2781:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015026-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42903820_c.56-1077del Note: The TMPRSS2 rearrangement is a deletion which includes exon 1 of TMPRSS2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015026-T01-IM6	U2AF1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - U2AF1 (NM_006758) rearrangement: c.56-1132:TMPRSS2_c.44+1088:U2AF1dup Note: The TMPRSS2 - U2AF1 rearrangement is a duplication which results in the fusion of TMPRSS2 exon1 to U2AF1 exon2.  A more complex rearrangement which results in a TMPRSS2 -ERG fusion cannot be ruled out.
U2AF1	0	MSKCC-DMP	P-0015026-T01-IM6	U2AF1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - U2AF1 (NM_006758) rearrangement: c.56-1132:TMPRSS2_c.44+1088:U2AF1dup Note: The TMPRSS2 - U2AF1 rearrangement is a duplication which results in the fusion of TMPRSS2 exon1 to U2AF1 exon2.  A more complex rearrangement which results in a TMPRSS2 -ERG fusion cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0014412-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-934_c.349+276inv Note: The TMPRSS2 rearrangement in an inversion of exons 2-3.
RET	0	MSKCC-DMP	P-0013394-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+18884:CCDC6_c.2136+48:RETinv
CCDC6	0	MSKCC-DMP	P-0013394-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+18884:CCDC6_c.2136+48:RETinv
CWF19L2	0	MSKCC-DMP	P-0011554-T01-IM5	CHEK1-CWF19L2 fusion	yes	unknown		unknown	CHEK1 (NM_001274) rearrangement: chr11:g.107213566_c.544:CHEK1del Note: The CHEK1 rearrangement results in the deletion of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
CHEK1	0	MSKCC-DMP	P-0011554-T01-IM5	CHEK1-CWF19L2 fusion	yes	unknown		unknown	CHEK1 (NM_001274) rearrangement: chr11:g.107213566_c.544:CHEK1del Note: The CHEK1 rearrangement results in the deletion of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
RHOA	0	MSKCC-DMP	P-0013867-T01-IM5	SUCLG2-RHOA fusion	yes	unknown		unknown	RHOA (NM_001664) Rearrangement : c.522:RHOA_c.758-3500:SUCLG2inv Note: The RHOA Rearrangement results in the inversion of exons 1-5 of RHOA. One of the breakpoints is within exon 5.Its functional significance is undetermined.
SUCLG2	0	MSKCC-DMP	P-0013867-T01-IM5	SUCLG2-RHOA fusion	yes	unknown		unknown	RHOA (NM_001664) Rearrangement : c.522:RHOA_c.758-3500:SUCLG2inv Note: The RHOA Rearrangement results in the inversion of exons 1-5 of RHOA. One of the breakpoints is within exon 5.Its functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0010604-T01-IM5	MLL3-intragenic	yes	unknown		unknown	MLL3 rearrangement: c.9610_c.13025del Note: The MLL3 rearrangement is an intragenic deletion of exons 42-52. The breakpoints are within exon 42 and 52. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0012525-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1(NM_002944) fusion (CD74 exons 1-6 with ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783203::chr6:g.117647385) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1
CD74	0	MSKCC-DMP	P-0012525-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1(NM_002944) fusion (CD74 exons 1-6 with ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783203::chr6:g.117647385) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1
ERG	0	MSKCC-DMP	P-0010794-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-32:TMPRSS2_c.18+3305:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010794-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-32:TMPRSS2_c.18+3305:ERGdel
MLL2	0	MSKCC-DMP	P-0011367-T01-IM5	ZNF804A-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) Rearrangement   : t(2;12)(q32.1;q13.12)(chr2:g.185336965::chr12:g.185336965) Note: The MLL2  Rearrangement results in the possible truncation of exons 39-54 of MLL2. One of the breakpoints is within exon39 .Its functional significance is undetermined.
ZNF804A	0	MSKCC-DMP	P-0011367-T01-IM5	ZNF804A-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) Rearrangement   : t(2;12)(q32.1;q13.12)(chr2:g.185336965::chr12:g.185336965) Note: The MLL2  Rearrangement results in the possible truncation of exons 39-54 of MLL2. One of the breakpoints is within exon39 .Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0011367-T01-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) Rearrangement :  c.619+504_3879-130del Note: The KDM6A  Rearrangement results in the deletion of exons 8-26 of KDM6A. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0011376-T01-IM5	ETV6-intragenic	yes	unknown		out of frame	ETV6 (NM_001987) Rearrangement :  c.463+6963_c.1254-1581dup Note: The ETV6 Rearrangement results in the intragenic duplication of exons5-7 of ETV6. It's functional significance is undetermined.
PLCXD2	0	MSKCC-DMP	P-0011376-T01-IM5	GATA2-PLCXD2 fusion	yes	unknown		out of frame	PLCXD2 (NM_153268) -GATA2(NM_032638) Rearrangement :  c.164-5416:PLCXD2 _c.1144-34:GATA2inv Note: The PLCXD2 -GATA2 Rearrangement results in the fusion of exons1 of PLCXD2 with exon6 of GATA2. Its functional significance is undetermined
GATA2	0	MSKCC-DMP	P-0011376-T01-IM5	GATA2-PLCXD2 fusion	yes	unknown		out of frame	PLCXD2 (NM_153268) -GATA2(NM_032638) Rearrangement :  c.164-5416:PLCXD2 _c.1144-34:GATA2inv Note: The PLCXD2 -GATA2 Rearrangement results in the fusion of exons1 of PLCXD2 with exon6 of GATA2. Its functional significance is undetermined
CREBBP	0	MSKCC-DMP	P-0014257-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement : c.798+9898_4530dup Note: The CREBBP (NM_004380) rearrangement is a duplication of exons 3-27. One of the breakpoints is within exon 27. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0010426-T01-IM5	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) Rearrangement :  c.673_c.865-468inv Note: The TBX3 Rearrangement results in the inversion of exon3 of TBX3. One of the breakpoints is within exon3. Its functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0010066-T01-IM5	PLA2G4F-MGA fusion	yes	unknown		unknown	MGA (NM_001164273): c.1955:MGA_chr15:g.42450405del The MGA rearrangement is a deletion which includes exons 3-24. One of the breakpoints is within exon 3 . The functional significance is undetermined.
PLA2G4F	0	MSKCC-DMP	P-0010066-T01-IM5	PLA2G4F-MGA fusion	yes	unknown		unknown	MGA (NM_001164273): c.1955:MGA_chr15:g.42450405del The MGA rearrangement is a deletion which includes exons 3-24. One of the breakpoints is within exon 3 . The functional significance is undetermined.
BBC3	0	MSKCC-DMP	P-0010066-T01-IM5	BBC3-intragenic	yes	unknown		unknown	BBC3 (NM_001127240) rearrangement: c.434_c.569-1611del Note: The BBC3 rearrangement is a deletion of exon3. On of the breakpoints is within exon3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013911-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) Rearrangement: c.40-58465:ERG_c.56-1062:TMPRSS2inv Note: The ERG (NM_004449) - TMPRSS2 Rearrangement results in an inversion of exons 2-14 of TMPRSS2 and exons 1-3 of the non-canonical ERG transcript. While the event is not the canonical TMRPSS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion. This rearrangement occurs in the background of other events involving TMPRSS2. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0013911-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) Rearrangement: c.40-58465:ERG_c.56-1062:TMPRSS2inv Note: The ERG (NM_004449) - TMPRSS2 Rearrangement results in an inversion of exons 2-14 of TMPRSS2 and exons 1-3 of the non-canonical ERG transcript. While the event is not the canonical TMRPSS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion. This rearrangement occurs in the background of other events involving TMPRSS2. Its functional significance is undetermined.
MX1	0	MSKCC-DMP	P-0014225-T01-IM6	TMPRSS2-MX1 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.1187-41:TMPRSS2_c.1009-200:MX1dup Note: The TMPRSS2 Rearrangement results in the duplication of exons 11-14 of TMPRSS2. One of the breakpoints is within 11. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0014225-T01-IM6	TMPRSS2-MX1 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.1187-41:TMPRSS2_c.1009-200:MX1dup Note: The TMPRSS2 Rearrangement results in the duplication of exons 11-14 of TMPRSS2. One of the breakpoints is within 11. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0001876-T03-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (Exon 1 of TMPRSS2 fused to exons 5-10 of ERG): c.56-497:TMPRSS2_c.236+6602:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0001876-T03-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (Exon 1 of TMPRSS2 fused to exons 5-10 of ERG): c.56-497:TMPRSS2_c.236+6602:ERGdel
CRKL	0	MSKCC-DMP	P-0014222-T01-IM6	RASGEF1C-CRKL fusion	yes	unknown		unknown	CRKL (NM_005207) - RASGEF1C (NM_175062) Rearrangement :  t(5;22)(q35.3;q11.21)(chr5:g.179616450::chr22:g.21288518) Note: The CRKL - RASGEF1C Rearrangement is a translocation event which results in the fusion of exons 1-2 of CRKL with exons 1-14 of RASGEF1C. The breakpoints are within exon 2 of CRKL and in the 5'-UTR region of RASGEF1C. The functional significance is undetermined.
RASGEF1C	0	MSKCC-DMP	P-0014222-T01-IM6	RASGEF1C-CRKL fusion	yes	unknown		unknown	CRKL (NM_005207) - RASGEF1C (NM_175062) Rearrangement :  t(5;22)(q35.3;q11.21)(chr5:g.179616450::chr22:g.21288518) Note: The CRKL - RASGEF1C Rearrangement is a translocation event which results in the fusion of exons 1-2 of CRKL with exons 1-14 of RASGEF1C. The breakpoints are within exon 2 of CRKL and in the 5'-UTR region of RASGEF1C. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0010172-T01-IM5	TSG1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(6;16)(q16.1;p13.3)(chr6:g.94711700::chr16:g.3843541) Note: The CREBBP rearrangement is a translocation that may result in the truncation of CREBBP exons 4-31. The breakpoint is within exon4. The functional significance is undetermined.
TSG1	0	MSKCC-DMP	P-0010172-T01-IM5	TSG1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(6;16)(q16.1;p13.3)(chr6:g.94711700::chr16:g.3843541) Note: The CREBBP rearrangement is a translocation that may result in the truncation of CREBBP exons 4-31. The breakpoint is within exon4. The functional significance is undetermined.
SOX2	0	MSKCC-DMP	P-0010172-T01-IM5	SOX2OT-SOX2 fusion	yes	unknown		unknown	SOX2 (NM_003106) rearrangement: c.840_c.*1122del Note: The SOX2 rearrangement is an intragenic deletion of a part of exon 1. One of the breakpoint is within exon 1. The functional significance is undetermined.
SOX2OT	0	MSKCC-DMP	P-0010172-T01-IM5	SOX2OT-SOX2 fusion	yes	unknown		unknown	SOX2 (NM_003106) rearrangement: c.840_c.*1122del Note: The SOX2 rearrangement is an intragenic deletion of a part of exon 1. One of the breakpoint is within exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013957-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion: c.55+4588:TMPRSS2_c.40-54610:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013957-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion: c.55+4588:TMPRSS2_c.40-54610:ERGdel
ROS1	0	MSKCC-DMP	P-0010760-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(5q32;6q22.1)(chr5:g.149783763::chr6:g.117647234 ) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0010760-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(5q32;6q22.1)(chr5:g.149783763::chr6:g.117647234 ) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
FOXA1	0	MSKCC-DMP	P-0014527-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) Rearrangement: chr14:g.38057086_c.1344:FOXA1del Note: The FOXA1  Rearrangement results in the partial deletion of exon 2 of FOXA1. One of the breakpoints is in exon 2. Its functional significance is undetermined
ACPP	0	MSKCC-DMP	P-0013245-T01-IM5	ATR-ACPP fusion	yes	unknown		unknown	ACPP (NM_001134194) - ATR (NM_001184) rearrangement: c.1138+17:ACPP_c.4853-39:ATRinv Note: The ACPP - ATR rearrangement is an inversion that results in the fusion of ACPP exons 1-10 with ATR exons 28-47, including the kinase domain of ATR. The functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0013245-T01-IM5	ATR-ACPP fusion	yes	unknown		unknown	ACPP (NM_001134194) - ATR (NM_001184) rearrangement: c.1138+17:ACPP_c.4853-39:ATRinv Note: The ACPP - ATR rearrangement is an inversion that results in the fusion of ACPP exons 1-10 with ATR exons 28-47, including the kinase domain of ATR. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0010507-T01-IM5	CNTNAP4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement : t(16;19)(q23.1;p13.12)(chr16:g.76278026::chr19:g.15291977) Note: The NOTCH3 rearrangement event is a translocation which results in the truncation of NOTCH3 exons 18-33. One of the breakpoints is within NOTCH3 exon33.
CNTNAP4	0	MSKCC-DMP	P-0010507-T01-IM5	CNTNAP4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement : t(16;19)(q23.1;p13.12)(chr16:g.76278026::chr19:g.15291977) Note: The NOTCH3 rearrangement event is a translocation which results in the truncation of NOTCH3 exons 18-33. One of the breakpoints is within NOTCH3 exon33.
STK11	0	MSKCC-DMP	P-0010507-T01-IM5	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement : c.374+220_863-2del Note: The STK11 rearrangement event results in the intragenic deletion of STK11 exons 3-7.
MIR384	0	MSKCC-DMP	P-0013724-T01-IM5	ATRX-MIR384 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.76184089_c.4699+50:ATRXinv Note: The ATRX rearrangement is an inversion of exons 17-35.
ATRX	0	MSKCC-DMP	P-0013724-T01-IM5	ATRX-MIR384 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.76184089_c.4699+50:ATRXinv Note: The ATRX rearrangement is an inversion of exons 17-35.
FBXL20	0	MSKCC-DMP	P-0014403-T01-IM6	CDK12-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.43-9338:FBXL20_c.3362:CDK12inv Note: The FBXL20 - CDK12 rearrangement in an inversion that results in the fusion of FBXL20 exon 1 to CDK12 exons 13-14. One of the breakpoints is within CDK12 exon 13. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0014403-T01-IM6	CDK12-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.43-9338:FBXL20_c.3362:CDK12inv Note: The FBXL20 - CDK12 rearrangement in an inversion that results in the fusion of FBXL20 exon 1 to CDK12 exons 13-14. One of the breakpoints is within CDK12 exon 13. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0015085-T01-IM6	MZF1-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - MZF1 (NM_003422) rearrangement: c.197+23:NOTCH3_c.773-2319:MZF1 Note: The NOTCH3 - MZF1 rearrangement is an inversion which results in the antisense fusion of NOTCH3 exon2 to MZF1 exon 5. The functional significance is undetermined.
MZF1	0	MSKCC-DMP	P-0015085-T01-IM6	MZF1-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - MZF1 (NM_003422) rearrangement: c.197+23:NOTCH3_c.773-2319:MZF1 Note: The NOTCH3 - MZF1 rearrangement is an inversion which results in the antisense fusion of NOTCH3 exon2 to MZF1 exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0010015-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused with ERG exons 2-9): c.56-1374:TMPRSS2_c.18+8903:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010015-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused with ERG exons 2-9): c.56-1374:TMPRSS2_c.18+8903:ERGdel
EIF3G	0	MSKCC-DMP	P-0010221-T01-IM5	JAK3-EIF3G fusion	yes	unknown		unknown	JAK3 (NM_000215) rearrangement : c.184+16:JAK3_chr19:g.10234948inv Note: The JAK3 rearrangement results in the inversion of JAK3 exons 3-24.
JAK3	0	MSKCC-DMP	P-0010221-T01-IM5	JAK3-EIF3G fusion	yes	unknown		unknown	JAK3 (NM_000215) rearrangement : c.184+16:JAK3_chr19:g.10234948inv Note: The JAK3 rearrangement results in the inversion of JAK3 exons 3-24.
JHDM1D	0	MSKCC-DMP	P-0011111-T01-IM5	BRAF-JHDM1D fusion	yes	unknown		unknown	BRAF (NM_004333) - JHDM1D (NM_030647) rearrangement: c.1178-1831:BRAF_c.*1672:JHDM1Ddel Note: The BRAF rearrangement is a deletion of exons 11-18, including the kinase domain of BRAF. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0011111-T01-IM5	BRAF-JHDM1D fusion	yes	unknown		unknown	BRAF (NM_004333) - JHDM1D (NM_030647) rearrangement: c.1178-1831:BRAF_c.*1672:JHDM1Ddel Note: The BRAF rearrangement is a deletion of exons 11-18, including the kinase domain of BRAF. The functional significance is undetermined.
BRMS1L	0	MSKCC-DMP	P-0004605-T02-IM5	RB1-BRMS1L fusion	yes	unknown		unknown	RB1(NM_000321) - BRMS1L (NM_032352) rearrangement : t(13;14)(q14.2;q13.2)(chr13:g.48877982::chr14:g.36312640) Note: The RB1 - BRMS1L rearrangement is a translocation that results in a partial deletion of the RB1 5'UTR. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0004605-T02-IM5	RB1-BRMS1L fusion	yes	unknown		unknown	RB1(NM_000321) - BRMS1L (NM_032352) rearrangement : t(13;14)(q14.2;q13.2)(chr13:g.48877982::chr14:g.36312640) Note: The RB1 - BRMS1L rearrangement is a translocation that results in a partial deletion of the RB1 5'UTR. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0014861-T01-IM6	MYO1F-PTPRS fusion	yes	unknown		unknown	MYO1F (NM_012335) - PTPRS (NM_002850) rearrangement: c.772-497:MYO1F_c.1570+25:PTPRS_inv Note: The MYO1F - PTPRS rearrangement is an inversion which results an antisense fusion of MYO1F exon 8 to PTPRS exon 11. The functional significance is undetermined.
MYO1F	0	MSKCC-DMP	P-0014861-T01-IM6	MYO1F-PTPRS fusion	yes	unknown		unknown	MYO1F (NM_012335) - PTPRS (NM_002850) rearrangement: c.772-497:MYO1F_c.1570+25:PTPRS_inv Note: The MYO1F - PTPRS rearrangement is an inversion which results an antisense fusion of MYO1F exon 8 to PTPRS exon 11. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0010093-T01-IM5	PPM1D-intragenic	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: c.1261-735_c.1633inv Note: The PPM1D rearrangement is an inversion of a part of PPM1D exon 6. One of the breakpoint is within exon 6. The functional significance is undetermined.
TRAF2	0	MSKCC-DMP	P-0013359-T01-IM5	FBXW5-TRAF2 fusion	yes	unknown		unknown	TRAF2 (NM_021138) rearrangement: c.960+46:TRAF2_chr9:g.139833316inv Note: The TRAF2 rearrangement is an inversion of exons 9-11.
FBXW5	0	MSKCC-DMP	P-0013359-T01-IM5	FBXW5-TRAF2 fusion	yes	unknown		unknown	TRAF2 (NM_021138) rearrangement: c.960+46:TRAF2_chr9:g.139833316inv Note: The TRAF2 rearrangement is an inversion of exons 9-11.
RPS6KA4	0	MSKCC-DMP	P-0012674-T01-IM5	DOCK2-RPS6KA4 fusion	yes	unknown		in frame	DOCK2 (NM_004946) - RPS6KA4 (NM_003942) rearrangement:t(5;11)(q35.1;q13.1)(chr5:g.169409522::chr11:g.64135589) Note: The DOCK2 - RPS6KA4 rearrangement is a translocation which results in the fusion of DOCK2 exons 1 - 27 with RPS6KA4 exons 10 - 17. The functional significance is undetermined.
DOCK2	0	MSKCC-DMP	P-0012674-T01-IM5	DOCK2-RPS6KA4 fusion	yes	unknown		in frame	DOCK2 (NM_004946) - RPS6KA4 (NM_003942) rearrangement:t(5;11)(q35.1;q13.1)(chr5:g.169409522::chr11:g.64135589) Note: The DOCK2 - RPS6KA4 rearrangement is a translocation which results in the fusion of DOCK2 exons 1 - 27 with RPS6KA4 exons 10 - 17. The functional significance is undetermined.
HNF1B	0	MSKCC-DMP	P-0012674-T01-IM5	HNF1B-intragenic	yes	unknown		unknown	HNF1B (NM_000458) rearrangement: c.1207-2700_c.1524dup Note: The HNF1B rarrangement is a duplication of exons 6-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
ANKFN1	0	MSKCC-DMP	P-0013457-T01-IM5	BRIP1-ANKFN1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: chr17:g.54569323_c.918+65:BRIP1del Note: The BRIP1 rearrangement is a deletion of exons 8-20.
BRIP1	0	MSKCC-DMP	P-0013457-T01-IM5	BRIP1-ANKFN1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: chr17:g.54569323_c.918+65:BRIP1del Note: The BRIP1 rearrangement is a deletion of exons 8-20.
CARM1	0	MSKCC-DMP	P-0014623-T01-IM6	LDLR-CARM1 fusion	yes	unknown		in frame	CARM1 (NM_199141) - LDLR (NM_000527) rearrangement: c.1615+14:CARM1_c.191-355:LDLRdel Note: The CARM1 - LDLR rearrangement is a deletion which results in the fusion of CARM1 exon 14 to LDLR exon 3. The functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0014623-T01-IM6	LDLR-CARM1 fusion	yes	unknown		in frame	CARM1 (NM_199141) - LDLR (NM_000527) rearrangement: c.1615+14:CARM1_c.191-355:LDLRdel Note: The CARM1 - LDLR rearrangement is a deletion which results in the fusion of CARM1 exon 14 to LDLR exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013465-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+842:TMPRSS2_c.40-57378:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0013465-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+842:TMPRSS2_c.40-57378:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TRIO	0	MSKCC-DMP	P-0014684-T01-IM6	RAD50-TRIO fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: chr5:g.14088337_c.2208-31:RAD50del Note: The RAD50 rearrangement is a deletion of exons 14-25.
RAD50	0	MSKCC-DMP	P-0014684-T01-IM6	RAD50-TRIO fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: chr5:g.14088337_c.2208-31:RAD50del Note: The RAD50 rearrangement is a deletion of exons 14-25.
DNMT1	0	MSKCC-DMP	P-0014790-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) Rearrangement : c.117+99_445+969inv Note: The DNMT1 Rearrangement results in the intragenic inversion of exons 3-4 of DNMT1. Its functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0011161-T01-IM5	MGAT4C-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.1092-166:NAB2_chr12:g.87188994del Note: The NAB2 rearrangement is a deletion of exons 4-7. The functional significance is undetermined.
MGAT4C	0	MSKCC-DMP	P-0011161-T01-IM5	MGAT4C-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.1092-166:NAB2_chr12:g.87188994del Note: The NAB2 rearrangement is a deletion of exons 4-7. The functional significance is undetermined.
IKBKE	0	MSKCC-DMP	P-0014509-T01-IM6	IKBKE-intragenic	yes	unknown		unknown	IKBKE (NM_014002) rearrangement: c.978_c.1428-692dup Note: The IKBKE rearrangement is an intragenic duplication of exons 9-14. One of the breakpoints is within exon 9. The functional significance is undetermined.
BARD1	0	MSKCC-DMP	P-0014509-T01-IM6	BARD1-intragenic	yes	unknown		unknown	BARD1 (NM_000465) rearrangement: c.365-1696_c.1277del Note: The BARD1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0014509-T01-IM6	TOP1-intragenic	yes	unknown		unknown	TOP1 (NM_003286) rearrangement: c.1308+4201_c.1741dup Note: The TOP1 rearrangement is an intragenic duplication of exons 14-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
LOC150197	0	MSKCC-DMP	P-0014509-T01-IM6	SMARCB1-LOC150197 fusion	yes	unknown		unknown	SMARCB1 (NM_003073) rearrangement: chr22:g.20196291_c.842:SMARCB1inv Note: The SMARCB1 rearrangement is an inversion of 5UTR and exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
SMARCB1	0	MSKCC-DMP	P-0014509-T01-IM6	SMARCB1-LOC150197 fusion	yes	unknown		unknown	SMARCB1 (NM_003073) rearrangement: chr22:g.20196291_c.842:SMARCB1inv Note: The SMARCB1 rearrangement is an inversion of 5UTR and exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
KIT	0	MSKCC-DMP	P-0012985-T01-IM5	KIT-intragenic	yes	unknown		unknown	KIT (NM_000222) rearrangement: c.2697-144_chr4:g.55618064dup Note: The KIT rearrangement is a duplication which includes exons 20 -21. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0011405-T01-IM5	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.640-2668_c.2026del Note: The DNMT3A rearrangement is an intragenic deletion of exons 7-17. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0011589-T01-IM5	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.3780_c.5912del Note: The SPEN rearrangement is an intragenic deletion within exon 11.
CHEK2	0	MSKCC-DMP	P-0011039-T01-IM5	KIAA1984-CHEK2 fusion	yes	unknown		out of frame	CHEK2 (NM_007194) - KIAA1984 (NM_001039374) rearrangement : t(9;22)(q34.3;q12.1)(chr9:g.139692272::chr22:g.29092840) Note: The CHEK2-KIAA1984 rearrangement event is a translocation which results in the truncation of CHEK2 exons 11-15.
KIAA1984	0	MSKCC-DMP	P-0011039-T01-IM5	KIAA1984-CHEK2 fusion	yes	unknown		out of frame	CHEK2 (NM_007194) - KIAA1984 (NM_001039374) rearrangement : t(9;22)(q34.3;q12.1)(chr9:g.139692272::chr22:g.29092840) Note: The CHEK2-KIAA1984 rearrangement event is a translocation which results in the truncation of CHEK2 exons 11-15.
FANCA	0	MSKCC-DMP	P-0010247-T01-IM5	CDCA8-FANCA fusion	yes	unknown		in frame	FANCA (NM_000135) - CDCA8 (NM_018101) rearrangement: t(1;16)(p34.3;q24.3)(chr1:g.38170600::chr16:g.89828353) Note: The FANCA - CDCA8 is a reciprocal translocation that results in an in frame fusion of FANCA exons 1-29 with CDCA8 exons 9-11. The functional significance is undetermined.
CDCA8	0	MSKCC-DMP	P-0010247-T01-IM5	CDCA8-FANCA fusion	yes	unknown		in frame	FANCA (NM_000135) - CDCA8 (NM_018101) rearrangement: t(1;16)(p34.3;q24.3)(chr1:g.38170600::chr16:g.89828353) Note: The FANCA - CDCA8 is a reciprocal translocation that results in an in frame fusion of FANCA exons 1-29 with CDCA8 exons 9-11. The functional significance is undetermined.
CKM	0	MSKCC-DMP	P-0014757-T01-IM6	ERCC2-CKM fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: chr19:g.45814599_c.5+40inv Note: The ERCC2 rearrangement is an inversion of exons 2-23. The functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0014757-T01-IM6	ERCC2-CKM fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: chr19:g.45814599_c.5+40inv Note: The ERCC2 rearrangement is an inversion of exons 2-23. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0013309-T01-IM5	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.265_c.289-2038dup Note: The NF1 rearrangement is an intragenic duplication of a part of exon 3. One of the breakpoints is within exon 3.
PARK2	0	MSKCC-DMP	P-0011455-T01-IM5	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) Rearrangement : c.618+25127_c.670del Note: The PARK2 Rearrangement results in the partial deletion of exon 6 of PARK2. One of the breakpoints is within exon6. Its functional significance is undetermined,
APOL3	0	MSKCC-DMP	P-0009908-T02-IM6	NTRK2-APOL3 fusion	yes	unknown		unknown	NTRK2 (NM_006180) rearrangement: t(9;22)(q21.33;q12.3)(chr9:g.87479148::chr22:g.36567977) Note: The NTRK2 rearrangement is a translocation that may result in a truncation of exons 16-21. The functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0009908-T02-IM6	NTRK2-APOL3 fusion	yes	unknown		unknown	NTRK2 (NM_006180) rearrangement: t(9;22)(q21.33;q12.3)(chr9:g.87479148::chr22:g.36567977) Note: The NTRK2 rearrangement is a translocation that may result in a truncation of exons 16-21. The functional significance is undetermined.
FBXO31	0	MSKCC-DMP	P-0015075-T01-IM6	FANCA-FBXO31 fusion	yes	unknown		unknown	FANCA (NM_000135) - FBXO31 (NM_024735) rearrangement: c.2060:FANCA_c.412+3880:FBXO31inv Note: The FANCA - FBXO31 rearrangement is an inversion which includes exons 23-43 of FANCA. One of the breakpoints is within exon23. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0015075-T01-IM6	FANCA-FBXO31 fusion	yes	unknown		unknown	FANCA (NM_000135) - FBXO31 (NM_024735) rearrangement: c.2060:FANCA_c.412+3880:FBXO31inv Note: The FANCA - FBXO31 rearrangement is an inversion which includes exons 23-43 of FANCA. One of the breakpoints is within exon23. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012507-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2176:TMPRSS2_c.18+2263:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012507-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2176:TMPRSS2_c.18+2263:ERGdel
ZFHX3	0	MSKCC-DMP	P-0012026-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement : chr16:g.72802720_c.2850inv Note: The ZFHX3 rearrangement results in the inversion of ZFHX3 exons 3-10. One of the breakpoints is on ZFHX3 exon3.
VANGL1	0	MSKCC-DMP	P-0014142-T01-IM5	NOTCH2-VANGL1 fusion	yes	unknown		unknown	VANGL1 (NM_138959) - NOTCH2 (NM_024408) rearrangement: c.947-704:VANGL1_c.3334:NOTCH2inv Note: The VANGL1 - NOTCH2 rearrangement in an inversion that results in the fusion of VANGL1 exons 1-5 to NOTCH2 exons 20-34. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0014142-T01-IM5	NOTCH2-VANGL1 fusion	yes	unknown		unknown	VANGL1 (NM_138959) - NOTCH2 (NM_024408) rearrangement: c.947-704:VANGL1_c.3334:NOTCH2inv Note: The VANGL1 - NOTCH2 rearrangement in an inversion that results in the fusion of VANGL1 exons 1-5 to NOTCH2 exons 20-34. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0011285-T01-IM5	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.539+39_c.607+910del Note: The RB1 rearrangement is a deletion of exon6. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0010041-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fuses with ALK exons 20-29) : c.701-6977:EML4_c.3172+385:ALKinv
EML4	0	MSKCC-DMP	P-0010041-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fuses with ALK exons 20-29) : c.701-6977:EML4_c.3172+385:ALKinv
NCOR1	0	MSKCC-DMP	P-0015059-T01-IM6	RNASE12-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(14;17)(q11.2;p12)(chr14:g.21071817::chr17:g.15976930) Note: The NCOR1 rearrangement is a translocation with a breakpoint within intron 27 of NCOR1. The functional significance is undetermined.
RNASE12	0	MSKCC-DMP	P-0015059-T01-IM6	RNASE12-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(14;17)(q11.2;p12)(chr14:g.21071817::chr17:g.15976930) Note: The NCOR1 rearrangement is a translocation with a breakpoint within intron 27 of NCOR1. The functional significance is undetermined.
STAT5B	0	MSKCC-DMP	P-0015059-T01-IM6	STAT5B-intragenic	yes	unknown		unknown	STAT5B (NM_012448) rearrangement: c.1474-1132_c.1906+38inv Note: The STAT5B rearrangement is an inversion of exons 13-15. The functional significance is undetermined
SDHB	0	MSKCC-DMP	P-0014952-T01-IM6	ARHGEF10L-SDHB fusion	yes	unknown		unknown	SDHB (NM_003000) rearrangement: c.73-72:SDHB_chr1:g.18019595del Note: The SDHB rearrangement is a deletion of 5UTR and exon 1.
ARHGEF10L	0	MSKCC-DMP	P-0014952-T01-IM6	ARHGEF10L-SDHB fusion	yes	unknown		unknown	SDHB (NM_003000) rearrangement: c.73-72:SDHB_chr1:g.18019595del Note: The SDHB rearrangement is a deletion of 5UTR and exon 1.
CNOT6	0	MSKCC-DMP	P-0013891-T01-IM5	FLT4-CNOT6 fusion	yes	unknown		unknown	FLT4 (NM_182925) - CNOT6 (NM_01545) rearrangement: c.1195:FLT4_c.113-5116:CNOT6inv Note: The FLT4 - CNOT6 rearrangement is an inversion which leads to the fusion of FLT4 exons 1-9 with CNOT6 exons 3 - 12. One of the breakpoints is within exon 9 of FLT4. The functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0013891-T01-IM5	FLT4-CNOT6 fusion	yes	unknown		unknown	FLT4 (NM_182925) - CNOT6 (NM_01545) rearrangement: c.1195:FLT4_c.113-5116:CNOT6inv Note: The FLT4 - CNOT6 rearrangement is an inversion which leads to the fusion of FLT4 exons 1-9 with CNOT6 exons 3 - 12. One of the breakpoints is within exon 9 of FLT4. The functional significance is undetermined.
CDH15	0	MSKCC-DMP	P-0011242-T01-IM5	ANKRD11-CDH15 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.6168:ANKRD11_chr16:g.89266867del Note: The ANKRD11 rearrangement is a deletion of exons 9-13. One of the breakpoints is within exon 9.
ANKRD11	0	MSKCC-DMP	P-0011242-T01-IM5	ANKRD11-CDH15 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.6168:ANKRD11_chr16:g.89266867del Note: The ANKRD11 rearrangement is a deletion of exons 9-13. One of the breakpoints is within exon 9.
C17orf51	0	MSKCC-DMP	P-0012976-T01-IM5	ATR-C17orf51 fusion	yes	unknown		unknown	ATR (NM_00118) rearrangement: t(3;17)(q23;p11.2)(chr3:g.142297572::chr17:g.21429234) Note: The ATR rearrangement is a translocation with a breakpoint within the 5'UTR of ATR. The functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0012976-T01-IM5	ATR-C17orf51 fusion	yes	unknown		unknown	ATR (NM_00118) rearrangement: t(3;17)(q23;p11.2)(chr3:g.142297572::chr17:g.21429234) Note: The ATR rearrangement is a translocation with a breakpoint within the 5'UTR of ATR. The functional significance is undetermined.
PDGFRB	0	MSKCC-DMP	P-0012976-T01-IM5	SH3PXD2B-PDGFRB fusion	yes	unknown		unknown	SH3PXD2B (NM_001017995) - PDGFRB (NM_002609) rearrangement: c.76-7984:SH3PXD2B_c.1308:PDGFRBdel Note: The SH3PXD2B - PDGFRB rearrangement is a deletion which results in the fusion of SH3PXD2B exon 1  with PDGFRB exons 9-23. One of the breakpoints is within exon 9 of PDGFRB. The functional significance is undetermined.
SH3PXD2B	0	MSKCC-DMP	P-0012976-T01-IM5	SH3PXD2B-PDGFRB fusion	yes	unknown		unknown	SH3PXD2B (NM_001017995) - PDGFRB (NM_002609) rearrangement: c.76-7984:SH3PXD2B_c.1308:PDGFRBdel Note: The SH3PXD2B - PDGFRB rearrangement is a deletion which results in the fusion of SH3PXD2B exon 1  with PDGFRB exons 9-23. One of the breakpoints is within exon 9 of PDGFRB. The functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0013866-T01-IM5	TGFBR1-intragenic	yes	unknown		unknown	TGFBR1 (NM_004612) Rearrangement : c.49_97+2083del Note: The TGFBR1 Rearrangement results in the  partial intragenic deletion of exon 1 of TGFBR1. One of the breakpoints is within exon1. Its functional significance is undetermined.
SMARCB1	0	MSKCC-DMP	P-0009828-T02-IM5	SMARCB1-intragenic	yes	unknown		unknown	SMARCB1 (NM_003073) rearrangement: c.923_c.986+3541inv Note: The SMARCB1 rearrangement is an inversion of a part of exon 7. One of the breakpoints is within exon 7.
RB1	0	MSKCC-DMP	P-0011456-T01-IM5	PTPRG-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) -PTPRG (NM_002841) Rearrangement : t(3,13)(p14.2,q14.2)(chr3:g.62225879::chr13:g.49038089 ) Note: The RB1 - PTPRG  Rearrangement results in the possible truncation of exons 22-27. Its functional significance is undetermined.
PTPRG	0	MSKCC-DMP	P-0011456-T01-IM5	PTPRG-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) -PTPRG (NM_002841) Rearrangement : t(3,13)(p14.2,q14.2)(chr3:g.62225879::chr13:g.49038089 ) Note: The RB1 - PTPRG  Rearrangement results in the possible truncation of exons 22-27. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0014462-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) Rearrangement : c.2672+141_c.3900+61inv Note:The DNMT1 Rearrangement results in the intragenic inversion of exons 28-33 of DNMT1. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0014462-T01-IM6	TACC1-INSR fusion	yes	unknown		unknown	INSR(NM_000208)Rearrangement : t(8;19)(p11.22.1;p13.2)(chr8:g.38571591::chr19:g38571591) Note: The INSR Rearrangement results in a translocation event in INSR. One of the breakpoints is in exon12 . Its functional significance is undetermined.
TACC1	0	MSKCC-DMP	P-0014462-T01-IM6	TACC1-INSR fusion	yes	unknown		unknown	INSR(NM_000208)Rearrangement : t(8;19)(p11.22.1;p13.2)(chr8:g.38571591::chr19:g38571591) Note: The INSR Rearrangement results in a translocation event in INSR. One of the breakpoints is in exon12 . Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0012107-T01-IM5	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) Rearrangement : c.3371_c.3583del Note: The EP300 Rearrangement results in the intragenic deletion of exons 18-19 of EP300. The breakpoints are within exon 18 and 19 respectively. Its functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0012107-T01-IM5	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) Rearrangement : chr6:g.157090092_c.928:ARID1Bdel Note: The ARID1B Rearrangement results in the deletion of exon1 of ARID1B . One of the breakpoints is within exon1. Its functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0012273-T01-IM5	SLC46A3-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: t(13;16)(q12.3;q24.3)(chr13:g.29376791::chr16:g.89349155 ) Note: The ANKRD11 rearrangement is a translocation with a breakpoint within exon9 of ANKRD11. The functional significance is undetermined.
SLC46A3	0	MSKCC-DMP	P-0012273-T01-IM5	SLC46A3-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: t(13;16)(q12.3;q24.3)(chr13:g.29376791::chr16:g.89349155 ) Note: The ANKRD11 rearrangement is a translocation with a breakpoint within exon9 of ANKRD11. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0010238-T01-IM5	APC-intragenic	yes	unknown		unknown	APC (NM_000038) Rearrangement : c.3156_4880del Note: The APC Rearrangement results in the partial deletion of exon 16 of APC. Both the breakpoints are within exon16. Its functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0012516-T01-IM5	SETD2-intragenic	yes	unknown		unknown	SETD2 (NM_014159) rearrangement: c.907_c.4586+694dup Note: The SETD2 rearrangement is a duplication of exons 3-4. One of the breakpoints is within exon 3. The functional significance is undetermined.
MTMR3	0	MSKCC-DMP	P-0012993-T01-IM5	ERBB3-MTMR3 fusion	yes	unknown		unknown	MTMR3 (NM_021090) - ERBB3 (NM_001982) Rearrangement :  t(12;22)(q13.3;q12.2)(chr12:g.56487886::chr22:g.30290490) Note: The MTMR3 - ERBB3 Rearrangement is a translocation event which results in the fusion of the 5'UTR region of MTMR3 with exons 14-28 of ERBB3. This includes the kinase domain of ERBB3.
ERBB3	0	MSKCC-DMP	P-0012993-T01-IM5	ERBB3-MTMR3 fusion	yes	unknown		unknown	MTMR3 (NM_021090) - ERBB3 (NM_001982) Rearrangement :  t(12;22)(q13.3;q12.2)(chr12:g.56487886::chr22:g.30290490) Note: The MTMR3 - ERBB3 Rearrangement is a translocation event which results in the fusion of the 5'UTR region of MTMR3 with exons 14-28 of ERBB3. This includes the kinase domain of ERBB3.
PHC1	0	MSKCC-DMP	P-0010761-T01-IM5	FGFR2-PHC1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;p13.31)(chr10:g.123243116::chr12:g.9059183 ) Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16 of FGFR2. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0010761-T01-IM5	FGFR2-PHC1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;p13.31)(chr10:g.123243116::chr12:g.9059183 ) Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16 of FGFR2. The functional significance is undetermined.
MAST3	0	MSKCC-DMP	P-0005884-T02-IM5	PIK3R2-MAST3 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement : c.902-70:PIK3R2_chr19:g.18201958del Note: The PIK3R2 rearrangement event results in the inversion of PIK3R2 exons 1-7.
PIK3R2	0	MSKCC-DMP	P-0005884-T02-IM5	PIK3R2-MAST3 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement : c.902-70:PIK3R2_chr19:g.18201958del Note: The PIK3R2 rearrangement event results in the inversion of PIK3R2 exons 1-7.
IDH2	0	MSKCC-DMP	P-0006458-T01-IM5	SEMA4B-IDH2 fusion	yes	unknown		out of frame	IDH2 (NM_002168) - SEMA4B (NM_198925) fusion: c.678+88:IDH2_c.158-3282:SEMA4Binv Note: IDH2 (NM_002168) - SEMA4B (NM_198925) fusion is a reciprocal inversion.
SEMA4B	0	MSKCC-DMP	P-0006458-T01-IM5	SEMA4B-IDH2 fusion	yes	unknown		out of frame	IDH2 (NM_002168) - SEMA4B (NM_198925) fusion: c.678+88:IDH2_c.158-3282:SEMA4Binv Note: IDH2 (NM_002168) - SEMA4B (NM_198925) fusion is a reciprocal inversion.
LATS1	0	MSKCC-DMP	P-0006909-T01-IM5	PCMT1-LATS1 fusion	yes	unknown		unknown	LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement : c.349-11:LATS1_c.229+8402:PCMT1del Note: The LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement results in the deletion of LATS1 exons1-2.
PCMT1	0	MSKCC-DMP	P-0006909-T01-IM5	PCMT1-LATS1 fusion	yes	unknown		unknown	LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement : c.349-11:LATS1_c.229+8402:PCMT1del Note: The LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement results in the deletion of LATS1 exons1-2.
GON4L	0	MSKCC-DMP	P-0009855-T01-IM5	NTRK1-GON4L fusion	yes	unknown		unknown	GON4L (NM_001037533) - NTRK1 (NM_002529) rearrangement : c.4141:GON4L_c.1137:NTRK1inv Note: The GON4L (NM_001037533) - NTRK1 (NM_002529) rearrangement event is an inversion which results in the fusion of GON4L exons 1-21 with NTRK1 exons 8-17. The breakpoints are within GON4L exon21 and NTRK1 exon8. The fusion includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0009855-T01-IM5	NTRK1-GON4L fusion	yes	unknown		unknown	GON4L (NM_001037533) - NTRK1 (NM_002529) rearrangement : c.4141:GON4L_c.1137:NTRK1inv Note: The GON4L (NM_001037533) - NTRK1 (NM_002529) rearrangement event is an inversion which results in the fusion of GON4L exons 1-21 with NTRK1 exons 8-17. The breakpoints are within GON4L exon21 and NTRK1 exon8. The fusion includes the kinase domain of NTRK1.
TIGD7	0	MSKCC-DMP	P-0000842-T02-IM5	CREBBP-TIGD7 fusion	yes	unknown		unknown	TIGD7 (NM_033208) - CREBBP (NM_004380) rearrangement: c.375:TIGD7_c.1155:CREBBPdup The TIGD7 (NM_033208) - CREBBP (NM_004380) rearrangement is a duplication which results in the fusion of TIGD7 exons 1-2 with CREBBP exons 4-31. The TIGD7 exon 1 and CREBBP exon 4 breakpoints are both within exon. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0000842-T02-IM5	CREBBP-TIGD7 fusion	yes	unknown		unknown	TIGD7 (NM_033208) - CREBBP (NM_004380) rearrangement: c.375:TIGD7_c.1155:CREBBPdup The TIGD7 (NM_033208) - CREBBP (NM_004380) rearrangement is a duplication which results in the fusion of TIGD7 exons 1-2 with CREBBP exons 4-31. The TIGD7 exon 1 and CREBBP exon 4 breakpoints are both within exon. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007576-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2 to 10) :  c.126+462:TMPRSS2_c.19-14230:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007576-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2 to 10) :  c.126+462:TMPRSS2_c.19-14230:ERGdel
MIPOL1	0	MSKCC-DMP	P-0001795-T02-IM5	FOXA1-MIPOL1 fusion	yes	unknown		unknown	MIPOL1 (NM_138731) - FOXA1 (NM_004496) rearrangement: c.1031+21430:MIPOL1_c.867:FOXA1del Note: The MIPOL1 (NM_138731) - FOXA1 (NM_004496) rearrangement is a deletion of MIPOL1 exons 13-14 and FOXA1 exons 1-2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0001795-T02-IM5	FOXA1-MIPOL1 fusion	yes	unknown		unknown	MIPOL1 (NM_138731) - FOXA1 (NM_004496) rearrangement: c.1031+21430:MIPOL1_c.867:FOXA1del Note: The MIPOL1 (NM_138731) - FOXA1 (NM_004496) rearrangement is a deletion of MIPOL1 exons 13-14 and FOXA1 exons 1-2. The functional significance is undetermined.
NCRNA00114	0	MSKCC-DMP	P-0006894-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 1-11) : c.56-3760:TMPRSS2_chr21:g.40054809del The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion  is a deletion with a breakpoint 20kb upstream of ERG.
TMPRSS2	0	MSKCC-DMP	P-0006894-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 1-11) : c.56-3760:TMPRSS2_chr21:g.40054809del The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion  is a deletion with a breakpoint 20kb upstream of ERG.
CALR	0	MSKCC-DMP	P-0008750-T01-IM5	C19orf53-CALR fusion	yes	unknown		unknown	CALR (NM_004343) -  C19orf53 (NM_014047) Rearrangement : c.925:CALR_c.154-280:C19orf53del Note: The CALR (NM_004343) -  C19orf53 (NM_014047) Rearrangement results in the fusion of exons 1 to 7 of CALR with exon 3 of C19orf53. The breakpoint in CALR is within exon 7. Its functional significance is undetermined.
C19orf53	0	MSKCC-DMP	P-0008750-T01-IM5	C19orf53-CALR fusion	yes	unknown		unknown	CALR (NM_004343) -  C19orf53 (NM_014047) Rearrangement : c.925:CALR_c.154-280:C19orf53del Note: The CALR (NM_004343) -  C19orf53 (NM_014047) Rearrangement results in the fusion of exons 1 to 7 of CALR with exon 3 of C19orf53. The breakpoint in CALR is within exon 7. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0006268-T01-IM5	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) Rearrangement : c.2061+100_3114+140dup Note: The EGFR (NM_005228) rearrangement results in the duplication of exons 18 to 25 of EGFR.  Its functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0005144-T01-IM5	RPTOR-intragenic	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: c.1213-3708_c.1949dup Note2: The RPTOR (NM_020761) rearrangement event results in the duplication of RPTOR exons 11-17. One of the breakpoints is within RPTOR exon 17. The functional significance of this event is unknown.
STK11	0	MSKCC-DMP	P-0005191-T01-IM5	MIDN-STK11 fusion	yes	unknown		out of frame	STK11 (NM_000455) - MIDN (NM_177401) Rearrangement :  c.1108+6:STK11_c.384+251:MIDNdel Note: The STK11 (NM_000455) - MIDN (NM_177401) Rearrangement  results in the fusion of exons 1 to 8 of STK11 with exons 5 to 8 of MIDN. Its functional significance is undetermined.
MIDN	0	MSKCC-DMP	P-0005191-T01-IM5	MIDN-STK11 fusion	yes	unknown		out of frame	STK11 (NM_000455) - MIDN (NM_177401) Rearrangement :  c.1108+6:STK11_c.384+251:MIDNdel Note: The STK11 (NM_000455) - MIDN (NM_177401) Rearrangement  results in the fusion of exons 1 to 8 of STK11 with exons 5 to 8 of MIDN. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005571-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon4) : c.55+2350:TMPRSS2_c.40-58808:ERG
TMPRSS2	0	MSKCC-DMP	P-0005571-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon4) : c.55+2350:TMPRSS2_c.40-58808:ERG
FGFR2	0	MSKCC-DMP	P-0005291-T01-IM5	TFEC-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_022970) - TFEC (NM_012252) Rearrangement: t(10;7)(q26.13;q31.2)(chr10:g.123241729;chr7:g.115644112) FGFR2-TFEC rearrangement is a translocation event where exons 1-16 of FGFR2 are fused to TFEC gene. FGFR2 portion includes the Tyrosine Kinase domain as described in other FGFR2 fusions. TFEC portion includes the bHLH domain of the protein. Significance of this event is not determined.
TFEC	0	MSKCC-DMP	P-0005291-T01-IM5	TFEC-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_022970) - TFEC (NM_012252) Rearrangement: t(10;7)(q26.13;q31.2)(chr10:g.123241729;chr7:g.115644112) FGFR2-TFEC rearrangement is a translocation event where exons 1-16 of FGFR2 are fused to TFEC gene. FGFR2 portion includes the Tyrosine Kinase domain as described in other FGFR2 fusions. TFEC portion includes the bHLH domain of the protein. Significance of this event is not determined.
TP53	0	MSKCC-DMP	P-0009702-T01-IM5	PSMD14-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement :t(2;17)(q24.2;p13.1)(chr2:g.162135135::chr17:g.7578268) Note: The TP53 (NM_000546) Rearrangement results in the possible truncation of exons 6-11 of TP53. One of the breakpoints is within exon6. Its functional significance is undetermined.
PSMD14	0	MSKCC-DMP	P-0009702-T01-IM5	PSMD14-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement :t(2;17)(q24.2;p13.1)(chr2:g.162135135::chr17:g.7578268) Note: The TP53 (NM_000546) Rearrangement results in the possible truncation of exons 6-11 of TP53. One of the breakpoints is within exon6. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008812-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1-2 with ERG exons 2-10): c.127-23:TMPRSS2_c.19-9142:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion  is an in-frame fusion.
TMPRSS2	0	MSKCC-DMP	P-0008812-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1-2 with ERG exons 2-10): c.127-23:TMPRSS2_c.19-9142:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion  is an in-frame fusion.
TACC3	0	MSKCC-DMP	P-0005966-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1 to 17 with TACC3 exons 11 to 16) : c.2285:FGFR3_c.1941+423:TACC3dup
FGFR3	0	MSKCC-DMP	P-0005966-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1 to 17 with TACC3 exons 11 to 16) : c.2285:FGFR3_c.1941+423:TACC3dup
KIF5B	0	MSKCC-DMP	P-0004995-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B(NM_004521) -RET (NM_020975)  Fusion ( KIF5B exon 15 fused to RET exon 12) : c.1726-2366:KIF5B_c.2136+476:RETinv
RET	0	MSKCC-DMP	P-0004995-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B(NM_004521) -RET (NM_020975)  Fusion ( KIF5B exon 15 fused to RET exon 12) : c.1726-2366:KIF5B_c.2136+476:RETinv
BRAF	0	MSKCC-DMP	P-0004795-T01-IM5	CUL1-BRAF fusion	yes	unknown		in frame	CUL1(NM_003592) - BRAF (NM_004333) Rearrangement :c.790-427:CUL1_c.1140+297:BRAFinv Note: The CUL1(NM_003592) - BRAF (NM_004333) Rearrangement  results in the fusion of exons 1 to 7 of CUL1 and exons 9 to 18 of BRAF.Its functional significance is undetermined.
CUL1	0	MSKCC-DMP	P-0004795-T01-IM5	CUL1-BRAF fusion	yes	unknown		in frame	CUL1(NM_003592) - BRAF (NM_004333) Rearrangement :c.790-427:CUL1_c.1140+297:BRAFinv Note: The CUL1(NM_003592) - BRAF (NM_004333) Rearrangement  results in the fusion of exons 1 to 7 of CUL1 and exons 9 to 18 of BRAF.Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0006639-T01-IM5	PTEN-intragenic	yes	unknown		out of frame	PTEN (NM_000314) rearrangement : c.635-1095_801+52dup Note: The PTEN (NM_000314) rearrangement event results in the duplication of PTEN exon 7.
COX7C	0	MSKCC-DMP	P-0005761-T01-IM5	APC-COX7C fusion	yes	unknown		unknown	APC (NM_000038) rearrangement : chr5:g.85990826_c.94:APCdel Note: The APC (NM_000038) rearrangement event results in the deletion of APC exons 1-2, truncating the gene.
APC	0	MSKCC-DMP	P-0005761-T01-IM5	APC-COX7C fusion	yes	unknown		unknown	APC (NM_000038) rearrangement : chr5:g.85990826_c.94:APCdel Note: The APC (NM_000038) rearrangement event results in the deletion of APC exons 1-2, truncating the gene.
NPM1	0	MSKCC-DMP	P-0005761-T01-IM5	NPM1-intragenic	yes	unknown		out of frame	NPM1 (NM_002520) rearrangement : c.353-26_525-118dup Note: The NPM1 (NM_002520) rearrangement event results in the intragenic duplication of NPM1 exons 5-6.
FUBP1	0	MSKCC-DMP	P-0005761-T01-IM5	FUBP1-intragenic	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement : c.212-844_473+192inv Note: The FUBP1 (NM_003902) rearrangement event results in the intragenic inversion of FUBP1 exons 3-7.
BRCA2	0	MSKCC-DMP	P-0008187-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement :  c.8633-663_9080dup Note: The BRCA2 Rearrangement  results in the intragenic duplication of exon 21 to exon 23. One of the breakpoints is within exon23. Its functional signIficance is undetermined.
KDM6A	0	MSKCC-DMP	P-0007622-T01-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.334+4130_1329+521del Note: The KDM6A (NM_021140) rearrangement event results in the deletion of KDM6A exons 4-13. This event is is predicted to result in an out of frame transcript.
FAT1	0	MSKCC-DMP	P-0009239-T01-IM5	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.88073170_c.13499del Note: The FAT1 (NM_005245) rearrangement is a deletion of exons 1-27. One of the breakpoints is within exon 27. The functional significance is undetermined.
RAB35	0	MSKCC-DMP	P-0009556-T01-IM5	SPPL3-RAB35 fusion	yes	unknown		out of frame	RAB35 (NM_006861) - SPPL3(NM_139015) Rearrangement :  c.477+135:RAB35_c.503-5676:SPPL3dup Note: The RAB35 (NM_006861) - SPPL3(NM_139015) Rearrangement results in the fusion of exons 1-5 of RAB35 with exons 7-11 of SPPL3. Its functional significance is undetermined.
SPPL3	0	MSKCC-DMP	P-0009556-T01-IM5	SPPL3-RAB35 fusion	yes	unknown		out of frame	RAB35 (NM_006861) - SPPL3(NM_139015) Rearrangement :  c.477+135:RAB35_c.503-5676:SPPL3dup Note: The RAB35 (NM_006861) - SPPL3(NM_139015) Rearrangement results in the fusion of exons 1-5 of RAB35 with exons 7-11 of SPPL3. Its functional significance is undetermined.
P2RY8	0	MSKCC-DMP	P-0006172-T01-IM5	NTRK1-P2RY8 fusion	yes	unknown		unknown	P2RY8(NM_178129) - NTRK1 (NM_002529) rearrangement: t(X;1)(chrX:g.1598513::chr1:g.156838012) P2RY8(NM_178129) - NTRK1 (NM_002529) rearrangement is a translocation event which results in the fusion of NTRK1 exon1-5 and P2RY8 exon2. One of the breakpoints is within NTRK1 exon5 and the other breakpoint is in 5-UTR of P2RY8 Its functional significance is not determined.
NTRK1	0	MSKCC-DMP	P-0006172-T01-IM5	NTRK1-P2RY8 fusion	yes	unknown		unknown	P2RY8(NM_178129) - NTRK1 (NM_002529) rearrangement: t(X;1)(chrX:g.1598513::chr1:g.156838012) P2RY8(NM_178129) - NTRK1 (NM_002529) rearrangement is a translocation event which results in the fusion of NTRK1 exon1-5 and P2RY8 exon2. One of the breakpoints is within NTRK1 exon5 and the other breakpoint is in 5-UTR of P2RY8 Its functional significance is not determined.
NOTCH3	0	MSKCC-DMP	P-0006091-T01-IM5	BRD4-NOTCH3 fusion	yes	unknown		unknown	BRD4 (NM_058243) - NOTCH3 (NM_000435 )  Rearrangement :  c.-1598:BRD4_c.4588:NOTCH3del Note: The BRD4 (NM_058243) - NOTCH3 (NM_000435 )  Rearrangement results in the deletion of exons 1 to 20 of BRD4 and exons 1 to 25 of NOTCH3.  The breakpoint is within exon25 of NOTCH3. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0006091-T01-IM5	BRD4-NOTCH3 fusion	yes	unknown		unknown	BRD4 (NM_058243) - NOTCH3 (NM_000435 )  Rearrangement :  c.-1598:BRD4_c.4588:NOTCH3del Note: The BRD4 (NM_058243) - NOTCH3 (NM_000435 )  Rearrangement results in the deletion of exons 1 to 20 of BRD4 and exons 1 to 25 of NOTCH3.  The breakpoint is within exon25 of NOTCH3. Its functional significance is undetermined.
XPO1	0	MSKCC-DMP	P-0006091-T01-IM5	XPO1-intragenic	yes	unknown		in frame	XPO1 (NM_003400) Rearrangement :  c.1888-38_1048-118del Note: The XPO1 (NM_003400) Rearrangement  results in the intragenic deletion of exons 12  to 17 of XPO1. Its functional significance is undetermined.
DNAH1	0	MSKCC-DMP	P-0005352-T01-IM5	PBRM1-DNAH1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) - DNAH1 (NM_015512) rearrangement: c.714:PBRM1_c.11736:DNAH1inv The PBRM1 (NM_018313) - DNAH1 (NM_015512) rearrangement is an inversion which results in the fusion of PBRM1 exons 1-7 with DNAH1 exons 73-78. One of the breakpoints is within exon 73 of DNAH1. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0005352-T01-IM5	PBRM1-DNAH1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) - DNAH1 (NM_015512) rearrangement: c.714:PBRM1_c.11736:DNAH1inv The PBRM1 (NM_018313) - DNAH1 (NM_015512) rearrangement is an inversion which results in the fusion of PBRM1 exons 1-7 with DNAH1 exons 73-78. One of the breakpoints is within exon 73 of DNAH1. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0009339-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.668-6870:EML4_c.3172+438:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0009339-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.668-6870:EML4_c.3172+438:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
ZNF207	0	MSKCC-DMP	P-0008920-T01-IM5	BRAF-ZNF207 fusion	yes	unknown		in frame	ZNF207 (NM_001098507) - BRAF (NM_004333) rearrangement: t(7;17)(q34;q11.2)(chr7:g.140485847::chr17:g.30687533) Note: The ZNF207 (NM_001098507) - BRAF (NM_004333) rearrangement results in an in frame fusion of ZNF407 exons 1-3 and BRAF exons 10-18, which include the BRAF kinase domain. The functional significance of this rearrangement is undetermined.
BRAF	0	MSKCC-DMP	P-0008920-T01-IM5	BRAF-ZNF207 fusion	yes	unknown		in frame	ZNF207 (NM_001098507) - BRAF (NM_004333) rearrangement: t(7;17)(q34;q11.2)(chr7:g.140485847::chr17:g.30687533) Note: The ZNF207 (NM_001098507) - BRAF (NM_004333) rearrangement results in an in frame fusion of ZNF407 exons 1-3 and BRAF exons 10-18, which include the BRAF kinase domain. The functional significance of this rearrangement is undetermined.
MLL	0	MSKCC-DMP	P-0006756-T01-IM5	MLL-intragenic	yes	unknown		unknown	MLL (NM_001197104) rearrangement : c.5366_5665-198del Note: The MLL (NM_001197104) rearrangement event results in the deletion of MLL exons 19-20.
NOTCH3	0	MSKCC-DMP	P-0006756-T01-IM5	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement : c.4527_chr19:g.15414856del Note: The NOTCH3 (NM_000435) rearrangement event results in the deletion of NOTCH3 exons 1-25. One of the breakpoints is within NOTCH3 exon25.
AKAP8	0	MSKCC-DMP	P-0006756-T01-IM5	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement : c.4527_chr19:g.15414856del Note: The NOTCH3 (NM_000435) rearrangement event results in the deletion of NOTCH3 exons 1-25. One of the breakpoints is within NOTCH3 exon25.
GPS2	0	MSKCC-DMP	P-0005011-T01-IM5	TP53-GPS2 fusion	yes	unknown		unknown	TP53 (NM_000546) - GPS2 (NM_004489) rearrangement: c.179:TP53_c.538:GPS2del The TP53 (NM_000546) - GPS2 (NM_004489) rearrangement is a deletion which results in the fusion of exons 1-4 of TP53 (NM_000546) with exons 7-11 of GPS2. The breakpoints fall within exon 4 and exon7 of TP53 and GPS2, respectively. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0005011-T01-IM5	TP53-GPS2 fusion	yes	unknown		unknown	TP53 (NM_000546) - GPS2 (NM_004489) rearrangement: c.179:TP53_c.538:GPS2del The TP53 (NM_000546) - GPS2 (NM_004489) rearrangement is a deletion which results in the fusion of exons 1-4 of TP53 (NM_000546) with exons 7-11 of GPS2. The breakpoints fall within exon 4 and exon7 of TP53 and GPS2, respectively. The functional significance is undetermined.
PRDM1	0	MSKCC-DMP	P-0009546-T01-IM5	PRDM1-intragenic	yes	unknown		unknown	PRDM1 (NM_001198 ) Rearrangement :  c.1998_*1216del Note: The PRDM1  (NM_001198 ) Rearrangement  results in the intragenic deletion of exons 7 of PRDM1.One of the breakpoints is within exon7 . Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0009260-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement:  c.458-27_chr9:g.22078146del Note: The CDKN2Ap16INK4A (NM_000077) Rearrangement results in the deletion of exons1 and 2 of CDKN2Ap16INK4A. Its functional significance is undetermined.
CDKN2BAS	0	MSKCC-DMP	P-0009260-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement:  c.458-27_chr9:g.22078146del Note: The CDKN2Ap16INK4A (NM_000077) Rearrangement results in the deletion of exons1 and 2 of CDKN2Ap16INK4A. Its functional significance is undetermined.
DPP9	0	MSKCC-DMP	P-0009709-T01-IM5	PTPRS-DPP9 fusion	yes	unknown		unknown	DPP9 (NM_139159) PTPRS (NM_002850) rearrangement: c.2179-101:DPP9_c.2567:PTPRSdup Note: DPP9 (NM_139159) PTPRS (NM_002850) rearrangement is a duplication that results in the fusion of exons 1-18 of DPP9 with exons 18-38 of PTPRS. One of the breakpoints is within exon18 of PTPRS. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0009709-T01-IM5	PTPRS-DPP9 fusion	yes	unknown		unknown	DPP9 (NM_139159) PTPRS (NM_002850) rearrangement: c.2179-101:DPP9_c.2567:PTPRSdup Note: DPP9 (NM_139159) PTPRS (NM_002850) rearrangement is a duplication that results in the fusion of exons 1-18 of DPP9 with exons 18-38 of PTPRS. One of the breakpoints is within exon18 of PTPRS. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0007855-T01-IM5	INSR-intragenic	yes	unknown		unknown	INSR (NM_000208) rearrangement : c.2945+229_2979inv Note: The INSR (NM_000208) rearrangement event results in the inversion of INSR exon16, potentially disrupting the splice site of the exon. One of the breakpoints is within INSR exon16.
PIK3C2G	0	MSKCC-DMP	P-0009565-T02-IM5	PDE3A-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) - PDE3A (NM_000921) rearrangement: c.3357+99:PIK3C2G_c.961-27266:PDE3Ainv Note: The PIK3C2G (NM_004570) - PDE3A (NM_000921) rearrangement results in the inversion of PIK3C2G exons 25-32 and PDE3A upstream promoter region, transcription start site, and exon 1. The functional significance of this rearrangement is undetermined.
PDE3A	0	MSKCC-DMP	P-0009565-T02-IM5	PDE3A-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) - PDE3A (NM_000921) rearrangement: c.3357+99:PIK3C2G_c.961-27266:PDE3Ainv Note: The PIK3C2G (NM_004570) - PDE3A (NM_000921) rearrangement results in the inversion of PIK3C2G exons 25-32 and PDE3A upstream promoter region, transcription start site, and exon 1. The functional significance of this rearrangement is undetermined.
ERG	0	MSKCC-DMP	P-0008452-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-2582:TMPRSS2_c.39+45360:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008452-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-2582:TMPRSS2_c.39+45360:ERGdel
CDH3	0	MSKCC-DMP	P-0009703-T01-IM5	CDH1-CDH3 fusion	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement :  chr16:g.68664883_ c.2165-112:CDH1del Note: The CDH1 (NM_004360) Rearrangement  results in the deletion of exons 1-13 of CDH1. Its functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0009703-T01-IM5	CDH1-CDH3 fusion	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement :  chr16:g.68664883_ c.2165-112:CDH1del Note: The CDH1 (NM_004360) Rearrangement  results in the deletion of exons 1-13 of CDH1. Its functional significance is undetermined.
TMCO5A	0	MSKCC-DMP	P-0009249-T01-IM5	MGA-TMCO5A fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.6492_chr15:g.37922302inv Note: The MGA (NM_001164273) rearrangement is an inversion (4119995 bp) which includes exons 1-17 of MGA. One of the breakpoints is within exon 17. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0009249-T01-IM5	MGA-TMCO5A fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.6492_chr15:g.37922302inv Note: The MGA (NM_001164273) rearrangement is an inversion (4119995 bp) which includes exons 1-17 of MGA. One of the breakpoints is within exon 17. The functional significance is undetermined.
SMARCD1	0	MSKCC-DMP	P-0006225-T01-IM5	SMARCD1-intragenic	yes	unknown		in frame	SMARCD1 (NM_003076) rearrangement: c.771+59_c.873+101del The SMARCD1 (NM_003076) rearrangement is an intragenic deletion of exon7. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0007233-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement : c.2123_3876del Note: The BRCA2 (NM_000059) rearrangement event is a deletion within BRCA2 exon11.
EYA2	0	MSKCC-DMP	P-0007071-T01-IM5	NCOA3-EYA2 fusion	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement :  c.-11+4624:EYA2_c.423:NCOA3inv Note: The NCOA3 (NM_181659) rearrangement results in the intragenic inversion of exons 1 to 6 of NCOA3. One of the breakpoints is within exon6.Its functional significance is undetermined
NCOA3	0	MSKCC-DMP	P-0007071-T01-IM5	NCOA3-EYA2 fusion	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement :  c.-11+4624:EYA2_c.423:NCOA3inv Note: The NCOA3 (NM_181659) rearrangement results in the intragenic inversion of exons 1 to 6 of NCOA3. One of the breakpoints is within exon6.Its functional significance is undetermined
FGFR2	0	MSKCC-DMP	P-0008657-T01-IM5	KLRAQ1-FGFR2 fusion	yes	unknown		in frame	FGFR1 (NM_000141) - PPP1R21 (NM_152994)  Rearrangement  : t(2;10)(2p16.3;10q26.13)(chr2:g.48721864::chr10:g.123240684) Note: The FGFR2 (NM_000141) - PPP1R21 (NM_152994)  Rearrangement is a translocation that results in the fusion of exons 1 to 17 of FGFR2 and exons 18 to 21 of PPP1R21.The fusion product includes kinase domain of FGFR1. Its functional significance is undetermined.
KLRAQ1	0	MSKCC-DMP	P-0008657-T01-IM5	KLRAQ1-FGFR2 fusion	yes	unknown		in frame	FGFR1 (NM_000141) - PPP1R21 (NM_152994)  Rearrangement  : t(2;10)(2p16.3;10q26.13)(chr2:g.48721864::chr10:g.123240684) Note: The FGFR2 (NM_000141) - PPP1R21 (NM_152994)  Rearrangement is a translocation that results in the fusion of exons 1 to 17 of FGFR2 and exons 18 to 21 of PPP1R21.The fusion product includes kinase domain of FGFR1. Its functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0009840-T01-IM5	SRC-intragenic	yes	unknown		unknown	SRC (NM_198291) rearrangement: c.703+242_c.1327dup Note: The SRC (NM_198291) rearrangement is a duplication of exons 8-13, including part of the kinase domain. One of the breakpoints is within exon 13. The functional significance is undetermined.
CCL2	0	MSKCC-DMP	P-0008856-T01-IM5	CD79B-CCL2 fusion	yes	unknown		unknown	CD79B (NM_001039933) rearrangement: chr17:g.32525586_c.433+14:CD79Bdel Note: The CD79B (NM_001039933) rearrangement results in the deletion of CD79B exons 4-6. The functional significance of this rearrangement is undetermined.
CD79B	0	MSKCC-DMP	P-0008856-T01-IM5	CD79B-CCL2 fusion	yes	unknown		unknown	CD79B (NM_001039933) rearrangement: chr17:g.32525586_c.433+14:CD79Bdel Note: The CD79B (NM_001039933) rearrangement results in the deletion of CD79B exons 4-6. The functional significance of this rearrangement is undetermined.
NAB2	0	MSKCC-DMP	P-0005578-T01-IM5	STAT6-NAB2 fusion	yes	unknown		in frame	NAB2 (NM_005967) - STAT6 (NM_003153) Fusion (NAB2 exon4 fused with STAT6 exon5) :  c.1144-31:NAB2_c.340-81:STAT6inv Note: The NAB2 (NM_005967) - STAT6 (NM_003153) Fusion is a reciprocal inversion.
STAT6	0	MSKCC-DMP	P-0005578-T01-IM5	STAT6-NAB2 fusion	yes	unknown		in frame	NAB2 (NM_005967) - STAT6 (NM_003153) Fusion (NAB2 exon4 fused with STAT6 exon5) :  c.1144-31:NAB2_c.340-81:STAT6inv Note: The NAB2 (NM_005967) - STAT6 (NM_003153) Fusion is a reciprocal inversion.
ERG	0	MSKCC-DMP	P-0005756-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.127-1214:TMPRSS2_c.18+26157:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005756-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.127-1214:TMPRSS2_c.18+26157:ERGdel
BBC3	0	MSKCC-DMP	P-0004861-T01-IM5	C2orf63-BBC3 fusion	yes	unknown		unknown	BBC3 (NM_001127240) - CLHC1 (NM_001135598) rearrangement: t(19;2)(q13;p16.1)(chr19:g.47729876::chr2:g.55436488) The BBC3 (NM_001127240) rearrangement is a translocation which may result in a truncated BBC3. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion.
C2orf63	0	MSKCC-DMP	P-0004861-T01-IM5	C2orf63-BBC3 fusion	yes	unknown		unknown	BBC3 (NM_001127240) - CLHC1 (NM_001135598) rearrangement: t(19;2)(q13;p16.1)(chr19:g.47729876::chr2:g.55436488) The BBC3 (NM_001127240) rearrangement is a translocation which may result in a truncated BBC3. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion.
ROS1	0	MSKCC-DMP	P-0002707-T03-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944)  fusion (CD274 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.49783748::chr6:g.117646946 ) The CD74 (NM_001025159) - ROS1 (NM_002944)  fusion is a reciprocal translocation
CD74	0	MSKCC-DMP	P-0002707-T03-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944)  fusion (CD274 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.49783748::chr6:g.117646946 ) The CD74 (NM_001025159) - ROS1 (NM_002944)  fusion is a reciprocal translocation
BRD4	0	MSKCC-DMP	P-0009503-T01-IM5	RSL1D1-BRD4 fusion	yes	unknown		unknown	RSL1D1 (NM_015659) - BRD4 (NM_058243) rearrangement: t(16;19)(p13.13;p13.12)(chr16:g.11933572::chr19:g.15376304) Note: The RSL1D1 (NM_015659) - BRD4 (NM_058243) rearrangement is a translocation that results in the fusion of RSL1D1 exons 1-8 with BRD4 exons 5-20. The breakpoints are within RSLD1 exon 8 and BRD4 exon 5. The functional significance of this rearrangement is undetermined.
RSL1D1	0	MSKCC-DMP	P-0009503-T01-IM5	RSL1D1-BRD4 fusion	yes	unknown		unknown	RSL1D1 (NM_015659) - BRD4 (NM_058243) rearrangement: t(16;19)(p13.13;p13.12)(chr16:g.11933572::chr19:g.15376304) Note: The RSL1D1 (NM_015659) - BRD4 (NM_058243) rearrangement is a translocation that results in the fusion of RSL1D1 exons 1-8 with BRD4 exons 5-20. The breakpoints are within RSLD1 exon 8 and BRD4 exon 5. The functional significance of this rearrangement is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0009503-T01-IM5	ZNF236-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: t(18;19)(q23;q13.41)(chr18:g.74482654::chr19:g.52719830) Note: The PPP2R1A (NM_014225) rearrangement is a translocation which may result in the truncation of PPP2R1A exons 9-15. The breakpoint is within exon 9. The functional significance of this rearrangement is undetermined.
ZNF236	0	MSKCC-DMP	P-0009503-T01-IM5	ZNF236-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: t(18;19)(q23;q13.41)(chr18:g.74482654::chr19:g.52719830) Note: The PPP2R1A (NM_014225) rearrangement is a translocation which may result in the truncation of PPP2R1A exons 9-15. The breakpoint is within exon 9. The functional significance of this rearrangement is undetermined.
NFKBIA	0	MSKCC-DMP	P-0006808-T01-IM5	RPS29-NFKBIA fusion	yes	unknown		unknown	NFKBIA(NM_020529) Rearrangement :  c.473_chr14:g.49675988del Note: The NFKBIA(NM_020529) rearrangement results in the deletion of exons 1 to 3 of NFKBIA. One of the breakpoints is within exon 3 .Its functional significance is undetermined.
RPS29	0	MSKCC-DMP	P-0006808-T01-IM5	RPS29-NFKBIA fusion	yes	unknown		unknown	NFKBIA(NM_020529) Rearrangement :  c.473_chr14:g.49675988del Note: The NFKBIA(NM_020529) rearrangement results in the deletion of exons 1 to 3 of NFKBIA. One of the breakpoints is within exon 3 .Its functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0004704-T01-IM5	MUC1-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) - MUC (NM_001204287) rearrangement : t(1;5)(1q22;5q13.1)(chr1:g.155160349::chr5:g.67591974) Note: The PIK3R1 (NM_181523) - MUC (NM_001204287) rearrangement event is a translocation which potentially results in forming a truncated PIK3R1. Its functional significance is undetermined.
MUC1	0	MSKCC-DMP	P-0004704-T01-IM5	MUC1-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) - MUC (NM_001204287) rearrangement : t(1;5)(1q22;5q13.1)(chr1:g.155160349::chr5:g.67591974) Note: The PIK3R1 (NM_181523) - MUC (NM_001204287) rearrangement event is a translocation which potentially results in forming a truncated PIK3R1. Its functional significance is undetermined.
FOXO1	0	MSKCC-DMP	P-0008711-T01-IM5	FOXO1-intragenic	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement: c.631-292_c.*9inv The FOXO1 (NM_002015) rearrangement is an inversion of exon2. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0009303-T01-IM5	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.75-22_c.672+197del. Note: The TP53 (NM_000546) rearrangement is an intragenic deletion of exons 3-6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007366-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 2 to 10) : c.56-2329:TMPRSS2_c.40-19374:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007366-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 2 to 10) : c.56-2329:TMPRSS2_c.40-19374:ERGdel
SND1	0	MSKCC-DMP	P-0009619-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1968+2394:SND1_ c.1314+327:BRAFinv Note: The SND1 (NM_014390) - BRAF (NM_004333) rearrangement is an inversion which results in the fusion of  SND1 exons 1-17 with BRAF exons 11-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0009619-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1968+2394:SND1_ c.1314+327:BRAFinv Note: The SND1 (NM_014390) - BRAF (NM_004333) rearrangement is an inversion which results in the fusion of  SND1 exons 1-17 with BRAF exons 11-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
ROS1	0	MSKCC-DMP	P-0004747-T01-IM5	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 33-43): t(5;6) (q32;q22.1) (chr5:g.149782561::chr6:g.117649107)
CD74	0	MSKCC-DMP	P-0004747-T01-IM5	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 33-43): t(5;6) (q32;q22.1) (chr5:g.149782561::chr6:g.117649107)
NDFIP2	0	MSKCC-DMP	P-0008795-T01-IM5	ERCC5-NDFIP2 fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement : chr13:g.80173550_c.2727:ERCC5inv Note: The ERCC5 (NM_000123) rearrangement event results in the inversion of ERCC5 exons 1-13. One of the breakpoints is within ERCC5 exon13.
ERCC5	0	MSKCC-DMP	P-0008795-T01-IM5	ERCC5-NDFIP2 fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement : chr13:g.80173550_c.2727:ERCC5inv Note: The ERCC5 (NM_000123) rearrangement event results in the inversion of ERCC5 exons 1-13. One of the breakpoints is within ERCC5 exon13.
MYO16	0	MSKCC-DMP	P-0008795-T01-IM5	IRS2-MYO16 fusion	yes	unknown		out of frame	MYO16 (NM_015011) - IRS2 (NM_003749) rearrangement : c.442-17465:MYO16_c.4013-10805:IRS2inv Note: The MYO16 (NM_015011) - IRS2 (NM_003749) rearrangement event is an inversion which results in the fusion of MYO16 exons 1-4 with IRS exon2.
IRS2	0	MSKCC-DMP	P-0008795-T01-IM5	IRS2-MYO16 fusion	yes	unknown		out of frame	MYO16 (NM_015011) - IRS2 (NM_003749) rearrangement : c.442-17465:MYO16_c.4013-10805:IRS2inv Note: The MYO16 (NM_015011) - IRS2 (NM_003749) rearrangement event is an inversion which results in the fusion of MYO16 exons 1-4 with IRS exon2.
FOXA1	0	MSKCC-DMP	P-0008795-T01-IM5	CASZ1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) - CASZ1 (NM_001079843) rearrangement : t(1;14)(p36.22;q21.2)(chr1:g.10708606::chr14:g.38061338) Note: The FOXA1 (NM_004496) - CASZ1 (NM_001079843) rearrangement event is a translocation which results in the truncation of FOXA1 exon2. One of the breakpoints is within FOXA1 exon2.
CASZ1	0	MSKCC-DMP	P-0008795-T01-IM5	CASZ1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) - CASZ1 (NM_001079843) rearrangement : t(1;14)(p36.22;q21.2)(chr1:g.10708606::chr14:g.38061338) Note: The FOXA1 (NM_004496) - CASZ1 (NM_001079843) rearrangement event is a translocation which results in the truncation of FOXA1 exon2. One of the breakpoints is within FOXA1 exon2.
FOXA1	0	MSKCC-DMP	P-0008795-T01-IM5	NRG1-FOXA1 fusion	yes	unknown		unknown	NRG1 (NM_013962) - FOXA1 (NM_004496) rearrangement : t(8;14)(p12;q21.1)(chr8:g.32309025::chr14:g.38061417) Note: The NRG1 (NM_013956) - FOXA1 (NM_004496) rearrangement event is a translocation which results in the fusion of NRG1 exon1 with FOXA1 exon2. One of the breakpoints is within FOXA1 exon2.
NRG1	0	MSKCC-DMP	P-0008795-T01-IM5	NRG1-FOXA1 fusion	yes	unknown		unknown	NRG1 (NM_013962) - FOXA1 (NM_004496) rearrangement : t(8;14)(p12;q21.1)(chr8:g.32309025::chr14:g.38061417) Note: The NRG1 (NM_013956) - FOXA1 (NM_004496) rearrangement event is a translocation which results in the fusion of NRG1 exon1 with FOXA1 exon2. One of the breakpoints is within FOXA1 exon2.
NCOR1	0	MSKCC-DMP	P-0007515-T01-IM5	SLFN12-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311)  -  SLFN12 (NM_018042) rearrangement : c.2583:NCOR1_c.-41+1038:SLFN12inv Note: The NCOR1 (NM_006311)  -  SLFN12 (NM_018042) rearrangement is not a functional fusion and results in the inversion of exons 1 to 20 of NCOR1. The breakpoint in NCOR1 is within exon 20.Its functional significance is undetermined.
SLFN12	0	MSKCC-DMP	P-0007515-T01-IM5	SLFN12-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311)  -  SLFN12 (NM_018042) rearrangement : c.2583:NCOR1_c.-41+1038:SLFN12inv Note: The NCOR1 (NM_006311)  -  SLFN12 (NM_018042) rearrangement is not a functional fusion and results in the inversion of exons 1 to 20 of NCOR1. The breakpoint in NCOR1 is within exon 20.Its functional significance is undetermined.
SND1	0	MSKCC-DMP	P-0002071-T02-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 fused with BRAF exons 9-18) : c.1152+18606:SND1_c.1141-1908:BRAFinv Note: The SND1 (NM_014390) - BRAF (NM_004333) fusion includes the kinase domain of BRAF and the resulting fusion is predicted to be in-frame.
BRAF	0	MSKCC-DMP	P-0002071-T02-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 fused with BRAF exons 9-18) : c.1152+18606:SND1_c.1141-1908:BRAFinv Note: The SND1 (NM_014390) - BRAF (NM_004333) fusion includes the kinase domain of BRAF and the resulting fusion is predicted to be in-frame.
EP300	0	MSKCC-DMP	P-0006830-T01-IM5	LRRC20-EP300 fusion	yes	unknown		unknown	LRRC20 (NM_207119) - EP300 (NM_001429) translocation : t(10;22)(q22.1;q13.2)(chr10:g.72085428::chr22:g.41488964) The LRRC20 (NM_207119) - EP300 (NM_001429) rearrangement is a translocation which results in fusion of LRRC20 exons 1-3 with the 5-UTR of EP300. Its functional significance is undetermined.
LRRC20	0	MSKCC-DMP	P-0006830-T01-IM5	LRRC20-EP300 fusion	yes	unknown		unknown	LRRC20 (NM_207119) - EP300 (NM_001429) translocation : t(10;22)(q22.1;q13.2)(chr10:g.72085428::chr22:g.41488964) The LRRC20 (NM_207119) - EP300 (NM_001429) rearrangement is a translocation which results in fusion of LRRC20 exons 1-3 with the 5-UTR of EP300. Its functional significance is undetermined.
FH	0	MSKCC-DMP	P-0005712-T01-IM5	FH-intragenic	yes	unknown		in frame	FH (NM_000143) rearrangement: c.556-906_c.1236+14dup The FH (NM_000143) rearrangement is an intragenic in frame duplication of FH exons 5-8. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0005712-T01-IM5	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.4714_c.4922+3493dup The ARID2 (NM_152641) rearrangement is a duplication of ARID2 exons 15 and 16. One of the breakpoints is within exon 15. The functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0006948-T01-IM5	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: c.3020-294_c.3350dup The CARD11 (NM_032415) rearrangement is an intragenic duplication of  exons 23-25. One of the breakpoints is within exon 25 of CARD11. The functional significance is undetermined.
TFE3	0	MSKCC-DMP	P-0005177-T01-IM5	NONO-TFE3 fusion	yes	unknown		in frame	NONO (NM_001145409) -TFE3 (NM_006521) fusion (NONO exons 1-8  with  TFE3 exons 6-10):  c.1131+68:NONO_ c.885+401:TFE3inv
NONO	0	MSKCC-DMP	P-0005177-T01-IM5	NONO-TFE3 fusion	yes	unknown		in frame	NONO (NM_001145409) -TFE3 (NM_006521) fusion (NONO exons 1-8  with  TFE3 exons 6-10):  c.1131+68:NONO_ c.885+401:TFE3inv
ZNF778	0	MSKCC-DMP	P-0008023-T01-IM5	ANKRD11-ZNF778 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.5336:ANKRD11_chr16:g.89300582dup The ANKRD11 (NM_013275) rearrangement is duplication (47032 bp) of exons 9-13 of ANKRD11. One of the breakpoints is within exon 9. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0008023-T01-IM5	ANKRD11-ZNF778 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.5336:ANKRD11_chr16:g.89300582dup The ANKRD11 (NM_013275) rearrangement is duplication (47032 bp) of exons 9-13 of ANKRD11. One of the breakpoints is within exon 9. The functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0006074-T01-IM5	SLC13A3-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) - SLC13A3 (NM_022829) rearrangement event : c.1813:TOP1_c.1494+1294: SLC13A3del Note: The TOP1 (NM_003286) - SLC13A3 (NM_022829) rearrangement event results in the deletion of TOP1 exons 17-21. One of the breakpoints is within TOP1 exon17.
SLC13A3	0	MSKCC-DMP	P-0006074-T01-IM5	SLC13A3-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) - SLC13A3 (NM_022829) rearrangement event : c.1813:TOP1_c.1494+1294: SLC13A3del Note: The TOP1 (NM_003286) - SLC13A3 (NM_022829) rearrangement event results in the deletion of TOP1 exons 17-21. One of the breakpoints is within TOP1 exon17.
SBNO2	0	MSKCC-DMP	P-0007518-T01-IM5	STK11-SBNO2 fusion	yes	unknown		unknown	SBNO2 (NM_014963) - STK11 (NM_000455)  Rearrangement  : c.3851:SBNO2_c.375-58:STK11inv Note: The SBNO2 (NM_014963) - STK11 (NM_000455)  Rearrangement results in the fusin of exons 1 to 32 of SBNO2 and exons 3 to 9 of STK11. The breakpoint in SBNO2 is within exon 32. Its functional signficance is undetermined.
STK11	0	MSKCC-DMP	P-0007518-T01-IM5	STK11-SBNO2 fusion	yes	unknown		unknown	SBNO2 (NM_014963) - STK11 (NM_000455)  Rearrangement  : c.3851:SBNO2_c.375-58:STK11inv Note: The SBNO2 (NM_014963) - STK11 (NM_000455)  Rearrangement results in the fusin of exons 1 to 32 of SBNO2 and exons 3 to 9 of STK11. The breakpoint in SBNO2 is within exon 32. Its functional signficance is undetermined.
STK11	0	MSKCC-DMP	P-0007518-T01-IM5	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) Rearrangement : c.*16+129_750inv Note: The STK11 (NM_000455) Rearrangement results in the inversion of first 6 exons of STK11 . One of the breakpoints is within exon 6. This event could be part of the complex events in STK11.Its functional significance is undetermined.
SOCS1	0	MSKCC-DMP	P-0006071-T01-IM5	SOCS1-intragenic	yes	unknown		unknown	SOCS1 (NM_003745) rearrangment : c.-956_-151del Note: The SOCS1 (NM_003745) rearrangment event results in the deletion of SOCS1 exon1 and the promoter region of SOCS1.
NCOA3	0	MSKCC-DMP	P-0006071-T01-IM5	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement : c.2336_3252+1027inv Note: The NCOA3 (NM_181659) rearrangement event results in the inversion of NCOA3 exons 12-17. One of the breakpoints is within NCOA3 exon12.
PARK2	0	MSKCC-DMP	P-0006864-T01-IM5	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.162_c.172-79382del The PARK2 (NM_004562) rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2. (PMID: 19946270)
SMARCA4	0	MSKCC-DMP	P-0008334-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement : c.4425-3445_4606inv Note: The SMARCA4 (NM_003072) rearrangement event results in the inversion of SMARCA4 exons 31-32. One of the breakpoints is within SMARCA4 exon32.
JAK3	0	MSKCC-DMP	P-0005174-T01-IM5	SLC5A2-JAK3 fusion	yes	unknown		out of frame	JAK3 (NM_000215) - SLC5A2 (NM_003041) rearrangement: t(16;19)(p13.11;p11.2)(chr16:g.31501596::chr19:g.17945650) The JAK3 (NM_000215) - SLC5A2 (NM_003041) rearrangement is a translocation which results in the out of frame fusion of  JAK3 exons 1-16 with SLCSA2 exon 14. The functional significance is undetermined.
SLC5A2	0	MSKCC-DMP	P-0005174-T01-IM5	SLC5A2-JAK3 fusion	yes	unknown		out of frame	JAK3 (NM_000215) - SLC5A2 (NM_003041) rearrangement: t(16;19)(p13.11;p11.2)(chr16:g.31501596::chr19:g.17945650) The JAK3 (NM_000215) - SLC5A2 (NM_003041) rearrangement is a translocation which results in the out of frame fusion of  JAK3 exons 1-16 with SLCSA2 exon 14. The functional significance is undetermined.
MIR873	0	MSKCC-DMP	P-0008664-T01-IM5	EGFL7-MIR873 fusion	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: chr9:g.30093113_c.290:EGFL7del Note: The EGFL7 (NM_201446) rearrangement results in the deletion of EGFL7 exons 1-5. One of the breakpoints is within exon 5 of EGFL7. The functional significance of this rearrangement is undetermined.
EGFL7	0	MSKCC-DMP	P-0008664-T01-IM5	EGFL7-MIR873 fusion	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: chr9:g.30093113_c.290:EGFL7del Note: The EGFL7 (NM_201446) rearrangement results in the deletion of EGFL7 exons 1-5. One of the breakpoints is within exon 5 of EGFL7. The functional significance of this rearrangement is undetermined.
NCOR1	0	MSKCC-DMP	P-0008932-T01-IM5	CD82-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) Rearrangement : t(11;17)(11p11.2;17p12)(chr11:g.44516827::chr17:g.15935918 ) Note: The NCOR1 (NM_006311) Rearrangement results in the partial deletion of the exon 46 of NCOR1. Its functional significance is undetermined.
CD82	0	MSKCC-DMP	P-0008932-T01-IM5	CD82-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) Rearrangement : t(11;17)(11p11.2;17p12)(chr11:g.44516827::chr17:g.15935918 ) Note: The NCOR1 (NM_006311) Rearrangement results in the partial deletion of the exon 46 of NCOR1. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0009044-T01-IM5	ANTXR2-TP53 fusion	yes	unknown		unknown	TP53 ( NM_000546) Rearrangement : t(4;17)(4q21.21;17p13.1)(chr4:g.80921091::chr17:g.7580615 ) Note: The TP53 ( NM_000546) Rearrangement is a translocation event which results in the truncation of exons 2 to 11 of TP53.The breakpoint is 703bp before the transcription start site. Its functional significance is undetermined.
ANTXR2	0	MSKCC-DMP	P-0009044-T01-IM5	ANTXR2-TP53 fusion	yes	unknown		unknown	TP53 ( NM_000546) Rearrangement : t(4;17)(4q21.21;17p13.1)(chr4:g.80921091::chr17:g.7580615 ) Note: The TP53 ( NM_000546) Rearrangement is a translocation event which results in the truncation of exons 2 to 11 of TP53.The breakpoint is 703bp before the transcription start site. Its functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0007176-T01-IM5	CLMN-DICER1 fusion	yes	unknown		out of frame	DICER1 (NM_030621) - CLMN (NM_024734) rearrangement : c.573+134_c.609-390dup Note: DICER1 (NM_030621) - CLMN (NM_024734) rearrangement event is a duplication which results in the fusion of DICER1 exons 1-5 and CLMN exons 7-13. The functional significance is undetermined.
CLMN	0	MSKCC-DMP	P-0007176-T01-IM5	CLMN-DICER1 fusion	yes	unknown		out of frame	DICER1 (NM_030621) - CLMN (NM_024734) rearrangement : c.573+134_c.609-390dup Note: DICER1 (NM_030621) - CLMN (NM_024734) rearrangement event is a duplication which results in the fusion of DICER1 exons 1-5 and CLMN exons 7-13. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0007861-T01-IM5	AGAP3-BRAF fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1326+220:AGAP3_c.1141-3313:BRAFinv Note: The AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement is an inversion which results the fusion of AGAP3 exons 1-10 with BRAF exons 9-18, including the kinase domain of BRAF. This fusion has been previously described in colon cancer and melanoma. (PMID: 26314551)
AGAP3	0	MSKCC-DMP	P-0007861-T01-IM5	AGAP3-BRAF fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1326+220:AGAP3_c.1141-3313:BRAFinv Note: The AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement is an inversion which results the fusion of AGAP3 exons 1-10 with BRAF exons 9-18, including the kinase domain of BRAF. This fusion has been previously described in colon cancer and melanoma. (PMID: 26314551)
ASXL1	0	MSKCC-DMP	P-0005933-T01-IM5	ASXL1-intragenic	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.253-14849_c.1253dup. The ASXL1 (NM_015338) rearrangement is an intragenic duplication exons 4-11. One of the breakpoints is with exon 11 of ASXL1. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0005691-T01-IM5	PITPNC1-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043)  -  PITPNC1 (NM_012417)  Rearrangement : c.3745:BRIP1_c.48+1232:PITPNC1inv Note: The BRIP1 (NM_032043)  -  PITPNC1 (NM_012417)  Rearrangement  results in the fusion of exons 1 to 20 of BRIP1 with exons 1 to 9 of PITPNC1 .The breakpoint in BRIP1 is within exon 20. Its functional significance is undetermined.
PITPNC1	0	MSKCC-DMP	P-0005691-T01-IM5	PITPNC1-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043)  -  PITPNC1 (NM_012417)  Rearrangement : c.3745:BRIP1_c.48+1232:PITPNC1inv Note: The BRIP1 (NM_032043)  -  PITPNC1 (NM_012417)  Rearrangement  results in the fusion of exons 1 to 20 of BRIP1 with exons 1 to 9 of PITPNC1 .The breakpoint in BRIP1 is within exon 20. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0005255-T01-IM5	PIP5K1A-NOTCH2 fusion	yes	unknown		unknown	PIP5K1A  (NM_001135638) - NOTCH2 (NM_024408) Rearrangement: c.86-2440:PIP5K1A_c.4982:NOTCH2inv PIP5K1A  (NM_001135638) - NOTCH2 (NM_024408) rearrangement is an inversion that results in the fusion of exon 1 of PIP5K1A with exons 27-34 of NOTCH2. One of the breakpoints is within exon 27 of NOTCH2. Its functional significance is undetermined.
PIP5K1A	0	MSKCC-DMP	P-0005255-T01-IM5	PIP5K1A-NOTCH2 fusion	yes	unknown		unknown	PIP5K1A  (NM_001135638) - NOTCH2 (NM_024408) Rearrangement: c.86-2440:PIP5K1A_c.4982:NOTCH2inv PIP5K1A  (NM_001135638) - NOTCH2 (NM_024408) rearrangement is an inversion that results in the fusion of exon 1 of PIP5K1A with exons 27-34 of NOTCH2. One of the breakpoints is within exon 27 of NOTCH2. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0006217-T01-IM5	TRAF2-NOTCH1 fusion	yes	unknown		unknown	TRAF2 (NM_021138) - NOTCH1 (NM_017617) rearrangement: c.-28-4310:TRAF2_c.3204:NOTCH1inv The TRAF2 (NM_021138) - NOTCH1 (NM_017617) rearrangement is an inversion (386050 bp) which results in the fusion of the 5-UTR region of TRAF2 with NOTCH1 exons 20-34. One of the breakpoints is within exon 20 of NOTCH1. The functional significance is undetermined.
TRAF2	0	MSKCC-DMP	P-0006217-T01-IM5	TRAF2-NOTCH1 fusion	yes	unknown		unknown	TRAF2 (NM_021138) - NOTCH1 (NM_017617) rearrangement: c.-28-4310:TRAF2_c.3204:NOTCH1inv The TRAF2 (NM_021138) - NOTCH1 (NM_017617) rearrangement is an inversion (386050 bp) which results in the fusion of the 5-UTR region of TRAF2 with NOTCH1 exons 20-34. One of the breakpoints is within exon 20 of NOTCH1. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0008406-T01-IM5	TACC1-FGFR1 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: chr8:g.38577463_c.716inv The FGFR1 (NM_001174067) rearrangement is an inversion of exons 1-7 of FGFR1. One of the breakpoints is within exon 7. The functional significance is undetermined.
TACC1	0	MSKCC-DMP	P-0008406-T01-IM5	TACC1-FGFR1 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: chr8:g.38577463_c.716inv The FGFR1 (NM_001174067) rearrangement is an inversion of exons 1-7 of FGFR1. One of the breakpoints is within exon 7. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0005168-T01-IM5	CCDC6-RET fusion	yes	unknown		out of frame	CCDC6  (NM_005436) - RET  (NM_020975)  Fusion ( CCDC6 Exon1 fused to RET Exon10 )  :  c.304-11493:CCDC6_c.1760-207:RETinv
CCDC6	0	MSKCC-DMP	P-0005168-T01-IM5	CCDC6-RET fusion	yes	unknown		out of frame	CCDC6  (NM_005436) - RET  (NM_020975)  Fusion ( CCDC6 Exon1 fused to RET Exon10 )  :  c.304-11493:CCDC6_c.1760-207:RETinv
KIF5B	0	MSKCC-DMP	P-0000208-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused with RET exons 12- 20): c.1726-1971:KIF5B_c.2137-385:RETinv (PMID: 22327624)
RET	0	MSKCC-DMP	P-0000208-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused with RET exons 12- 20): c.1726-1971:KIF5B_c.2137-385:RETinv (PMID: 22327624)
SLIT3	0	MSKCC-DMP	P-0007500-T01-IM5	FGFR4-SLIT3 fusion	yes	unknown		unknown	FGFR4 (NM_213647) rearrangement: chr5:g.168772933 _c.1057+108:FGFR4dup The FGFR4 (NM_213647) rearrangement is a duplication of exons 1-8. The functional significance is undetermined.
FGFR4	0	MSKCC-DMP	P-0007500-T01-IM5	FGFR4-SLIT3 fusion	yes	unknown		unknown	FGFR4 (NM_213647) rearrangement: chr5:g.168772933 _c.1057+108:FGFR4dup The FGFR4 (NM_213647) rearrangement is a duplication of exons 1-8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008869-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exons 2-10) : c.56-2234:TMPRSS2_c.19-7662:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008869-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exons 2-10) : c.56-2234:TMPRSS2_c.19-7662:ERGdel
MRE11A	0	MSKCC-DMP	P-0005065-T03-IM5	FEZ1-MRE11A fusion	yes	unknown		unknown	MRE11A(NM_005591)  Rearrangement :  c.-92:MRE11A_chr11:125397563del Note: The MRE11A(NM_005591)  Rearrangement results in the deletion of exons 1 and 2. The breakpoint is within the 5-UTR region before the coding start site.  Its functional significance is undetermined.
FEZ1	0	MSKCC-DMP	P-0005065-T03-IM5	FEZ1-MRE11A fusion	yes	unknown		unknown	MRE11A(NM_005591)  Rearrangement :  c.-92:MRE11A_chr11:125397563del Note: The MRE11A(NM_005591)  Rearrangement results in the deletion of exons 1 and 2. The breakpoint is within the 5-UTR region before the coding start site.  Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0005065-T03-IM5	TOP2A-EP300 fusion	yes	unknown		unknown	EP300(NM_001429) Rearrangement :  t(22;17)(22q13.2;17q21.2)(chr22:g.41523648::chr17:g.38565813) Note: The EP300(NM_001429) Rearrangement results in the translocation of exons 1 to 4 of EP300.Its functional significance is undetermined.
TOP2A	0	MSKCC-DMP	P-0005065-T03-IM5	TOP2A-EP300 fusion	yes	unknown		unknown	EP300(NM_001429) Rearrangement :  t(22;17)(22q13.2;17q21.2)(chr22:g.41523648::chr17:g.38565813) Note: The EP300(NM_001429) Rearrangement results in the translocation of exons 1 to 4 of EP300.Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0009856-T01-IM5	C19orf26-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) rearrangement : c.402_*3697del Note: The STK11 (NM_000455) rearrangement event results in the deletion of STK11 exons 3-9. One of the breakpoints is within STK11 exon3.
C19orf26	0	MSKCC-DMP	P-0009856-T01-IM5	C19orf26-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) rearrangement : c.402_*3697del Note: The STK11 (NM_000455) rearrangement event results in the deletion of STK11 exons 3-9. One of the breakpoints is within STK11 exon3.
ALK	0	MSKCC-DMP	P-0007705-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1594:EML4_c.3172+910:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0007705-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1594:EML4_c.3172+910:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK.
STK11	0	MSKCC-DMP	P-0004759-T01-IM5	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement : c.862+203_1141del Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of STK11 exons 7-9. One of the breakpoints is within exon9.
TCF3	0	MSKCC-DMP	P-0004759-T01-IM5	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement : c.500-52_1586+316del Note: The TCF3 (NM_001136139) rearrangement event results in the intragenic deletion of TCF3 exons 7-16.
MSL3	0	MSKCC-DMP	P-0004759-T01-IM5	RB1-MSL3 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement : t(13;X)(13q14.2;Xp22.2)(chr13:g.49047485::chrX:g.11732599) Note: The RB1 (NM_000321) rearrangement event is a reciprocal translocation which results in the truncation of RB1 exons 24-27.
RB1	0	MSKCC-DMP	P-0004759-T01-IM5	RB1-MSL3 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement : t(13;X)(13q14.2;Xp22.2)(chr13:g.49047485::chrX:g.11732599) Note: The RB1 (NM_000321) rearrangement event is a reciprocal translocation which results in the truncation of RB1 exons 24-27.
TCF7L2	0	MSKCC-DMP	P-0006136-T01-IM5	TCF7L2-intragenic	yes	unknown		in frame	TCF7L2 (NM_001146274) rearrangement: c.875+93_c.1391+920del The TCF7L2 (NM_001146274) rearrangement is an intragenic deletion of exons  9-14. The functional significance is unknown.
SLC41A3	0	MSKCC-DMP	P-0004952-T01-IM5	MCL1-SLC41A3 fusion	yes	unknown		unknown	SLC41A3 (NM_001008485) - MCL1 (NM_021960) rearrangement : t(1;3)(1q21.3;3q21.2)(chr1:g.150551707::chr3:g.125736765) Note: SLC41A3 (NM_001008485) - MCL1 (NM_021960) rearrangement event is a translocation which leads to the fusion of SLC41A3 exons 1-6 with MCL1 exons 1-3. One of the breakpoints is within MCL1 exon1.
MCL1	0	MSKCC-DMP	P-0004952-T01-IM5	MCL1-SLC41A3 fusion	yes	unknown		unknown	SLC41A3 (NM_001008485) - MCL1 (NM_021960) rearrangement : t(1;3)(1q21.3;3q21.2)(chr1:g.150551707::chr3:g.125736765) Note: SLC41A3 (NM_001008485) - MCL1 (NM_021960) rearrangement event is a translocation which leads to the fusion of SLC41A3 exons 1-6 with MCL1 exons 1-3. One of the breakpoints is within MCL1 exon1.
ZFHX3	0	MSKCC-DMP	P-0009375-T01-IM5	ZFHX3-intragenic	yes	unknown		out of frame	ZFHX3 (NM_006885) rearrangement: c.3216+21118_c.9428-168del Note: The ZFHX3 (NM_006885) rearrangement results in the deletion of exons 4-9. The functional significance of this rearrangement is undetermined.
RPLP0P2	0	MSKCC-DMP	P-0009813-T01-IM5	RPS6KA4-RPLP0P2 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement : c.1325:RPS6KA4_chr11:g.61400293inv Note: The RPS6KA4 (NM_003942) rearrangement event results in the inversion of RPS6KA4 exons 1-11. One of the breakpoints is within RPS6KA4 exon11.
RPS6KA4	0	MSKCC-DMP	P-0009813-T01-IM5	RPS6KA4-RPLP0P2 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement : c.1325:RPS6KA4_chr11:g.61400293inv Note: The RPS6KA4 (NM_003942) rearrangement event results in the inversion of RPS6KA4 exons 1-11. One of the breakpoints is within RPS6KA4 exon11.
MEN1	0	MSKCC-DMP	P-0009813-T01-IM5	MEN1-intragenic	yes	unknown		unknown	MEN1 (NM_000244) rearrangement : c.-1283_220del Note: The MEN1 (NM_000244) rearrangement event results in the deletion of MEN1 exons 1-2. One of the breakpoints is within MEN1 exon2.
AR	0	MSKCC-DMP	P-0008344-T01-IM5	AR-intragenic	yes	unknown		unknown	AR (NM_000044) Rearrangement : chrX:g.66673283_c.2049:ARdup Note: The AR (NM_000044) Rearrangement  results in the intragenic duplication of exons 1 to 4 of AR.One of the breakpoints is within exon4. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0007771-T01-IM5	LOC284100-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(17;19)(q12;p12)(chr17:g.36167655::chr19:g.2228256 ) The DOT1L (NM_032482) rearrangement is a translocation which may result in a truncated  DOT1L. The functional significance is undetermined.
LOC284100	0	MSKCC-DMP	P-0007771-T01-IM5	LOC284100-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(17;19)(q12;p12)(chr17:g.36167655::chr19:g.2228256 ) The DOT1L (NM_032482) rearrangement is a translocation which may result in a truncated  DOT1L. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0004790-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.163+28658_c.464-6383dup The ETV6 (NM_001987) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0004790-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (exons 1-7 of CD74 fused to exons 34-43 of ROS1) : t(5;6)(q32;q22.1)(chr5:g.149782207::chr6:g.117646467) exons 1-7 of CD74 (NM_001025159) fused to exons 34-43 of ROS1 (NM_002944)
CD74	0	MSKCC-DMP	P-0004790-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (exons 1-7 of CD74 fused to exons 34-43 of ROS1) : t(5;6)(q32;q22.1)(chr5:g.149782207::chr6:g.117646467) exons 1-7 of CD74 (NM_001025159) fused to exons 34-43 of ROS1 (NM_002944)
NCRNA00114	0	MSKCC-DMP	P-0007267-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : c.56-1208:TMPRSS2_chr21:g.40058491del Note: The TMPRSS2 (NM_001135099) rearrangement results in the deletion of exons 2 to 14 of TMPRSS2. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0007267-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : c.56-1208:TMPRSS2_chr21:g.40058491del Note: The TMPRSS2 (NM_001135099) rearrangement results in the deletion of exons 2 to 14 of TMPRSS2. Its functional significance is undetermined.
SND1	0	MSKCC-DMP	P-0007533-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 with BRAF exons 11-18)  : c.1152+31738:SND1_c.1314+595:BRAFinv Note: The SND1-BRAF fusion includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0007533-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 with BRAF exons 11-18)  : c.1152+31738:SND1_c.1314+595:BRAFinv Note: The SND1-BRAF fusion includes the kinase domain of BRAF.
AR	0	MSKCC-DMP	P-0007533-T01-IM5	OPHN1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement : c.2004:AR_chrX:g.67175446inv Note: The AR (NM_000044) rearrangement event is a reciprocal inversion.
OPHN1	0	MSKCC-DMP	P-0007533-T01-IM5	OPHN1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement : c.2004:AR_chrX:g.67175446inv Note: The AR (NM_000044) rearrangement event is a reciprocal inversion.
ACAP1	0	MSKCC-DMP	P-0005976-T01-IM5	TP53-ACAP1 fusion	yes	unknown		unknown	ACAP1(NM_014716) and TP53(NM_000546) rearrangement : c.1344-331:ACAP1_c.-28-696:TP53inv ACAP1(NM_014716)-TP53(NM_000546) rearrangement is a reciprocal inversion that results in the fusion of exons 1-11 of ACAP1 with exons 2-11 of TP53. Its functional significance is undetermined
TP53	0	MSKCC-DMP	P-0005976-T01-IM5	TP53-ACAP1 fusion	yes	unknown		unknown	ACAP1(NM_014716) and TP53(NM_000546) rearrangement : c.1344-331:ACAP1_c.-28-696:TP53inv ACAP1(NM_014716)-TP53(NM_000546) rearrangement is a reciprocal inversion that results in the fusion of exons 1-11 of ACAP1 with exons 2-11 of TP53. Its functional significance is undetermined
PDE3A	0	MSKCC-DMP	P-0009501-T01-IM5	PDE3A-intragenic	yes	unknown		unknown	PDE3A (NM_000921) rearrangement: chr12:g.20290558_c.1760+1670inv Note: The PDE3A (NM_000921) rearrangement results in the inversion of PDE3A upstream promoter region and exons 1-6. The functional significance of this rearrangement is undetermined.
TP53	0	MSKCC-DMP	P-0007169-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.824_c.*1124del The TP53 (NM_000546) rearrangement is an intragenic deletion of exons 8-11. One of the breakpoints is within exon 8. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0007169-T01-IM5	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.534+18201_c.686del The PARK2 (NM_004562) rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6. The functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0007871-T01-IM5	TOP1-intragenic	yes	unknown		out of frame	TOP1 (NM_003286) rearrangement: c.58+9432_ c.2196-7del Note: The TOP1 (NM_003286) rearrangement is an intragenic deletion of exons  3-20. The functional significance is undetermined.
ZCCHC6	0	MSKCC-DMP	P-0006873-T01-IM5	EGFR-ZCCHC6 fusion	yes	unknown		unknown	EGFR (NM_005228) - ZCCHC6  (NM_024617) rearrangement :  : t(7;9)(chr7p11.2;chr9q21.33)(chr7:g.55238031::chr9:g.88930920)     Note: The EGFR (NM_005228) - ZCCHC6  (NM_024617) rearrangement results in the fusion of exons 1 to 15 of EGFR and exons 18 to 22. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0006873-T01-IM5	EGFR-ZCCHC6 fusion	yes	unknown		unknown	EGFR (NM_005228) - ZCCHC6  (NM_024617) rearrangement :  : t(7;9)(chr7p11.2;chr9q21.33)(chr7:g.55238031::chr9:g.88930920)     Note: The EGFR (NM_005228) - ZCCHC6  (NM_024617) rearrangement results in the fusion of exons 1 to 15 of EGFR and exons 18 to 22. Its functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0009914-T01-IM5	FGF12-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - FGF12 (NM_021032) rearrangement: t(3;8)(q28;q24.11)(chr3:g.191588402::chr8:g.117866571) Note: The RAD2 - FGF12 rearrangement is a translocation which may result in the truncation of RAD21 exons 9-14. The breakpoint is within exon 9. The functional significance is undetermined.
FGF12	0	MSKCC-DMP	P-0009914-T01-IM5	FGF12-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - FGF12 (NM_021032) rearrangement: t(3;8)(q28;q24.11)(chr3:g.191588402::chr8:g.117866571) Note: The RAD2 - FGF12 rearrangement is a translocation which may result in the truncation of RAD21 exons 9-14. The breakpoint is within exon 9. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0005508-T01-IM5	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) Rearrangement : c.1156_c.3281inv Note: DOT1L rearrangement is an intragenic inversion involving exons 14 to 24. It is potentially a truncating event
EP300	0	MSKCC-DMP	P-0005888-T01-IM5	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429)  Rearrangement :  c.2818-100_ 3931del Note: The EP300 (NM_001429)  rearrangement results in the intragenic deletion of exons 15 to 24 of EP300. The breakpoint is within exon 24. Its functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0008283-T01-IM5	RGS17-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: t(6;18)(q36.2;q21.2)(chr6:g.153659215::chr18:g.48591962) The SMAD4 (NM_005359) rearrangement is a translocation which results in the truncation of SMAD4 exons 9-12. One of the breakpoints is within exon 9 of SMAD4. The functional significance is undetermined.
RGS17	0	MSKCC-DMP	P-0008283-T01-IM5	RGS17-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: t(6;18)(q36.2;q21.2)(chr6:g.153659215::chr18:g.48591962) The SMAD4 (NM_005359) rearrangement is a translocation which results in the truncation of SMAD4 exons 9-12. One of the breakpoints is within exon 9 of SMAD4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0004826-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-10) :  c.56-936:TMPRS2_c.-150+18179:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion loci is also indicative of an inversion at the breakpoints which results in an non-functional transcript between TMPRSS2 and ERG.
TMPRSS2	0	MSKCC-DMP	P-0004826-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-10) :  c.56-936:TMPRS2_c.-150+18179:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion loci is also indicative of an inversion at the breakpoints which results in an non-functional transcript between TMPRSS2 and ERG.
PCBP3	0	MSKCC-DMP	P-0008426-T01-IM5	NCOA3-PCBP3 fusion	yes	unknown		out of frame	NCOA3 (NM_181659) - PCBP3 (NM_020528) Rearrangement : t(20;21)(20q13.12;21q22.3)(chr20:g.46268900::chr21:g.47336467)     Note: The NCOA3 (NM_181659) - PCBP3 (NM_020528) Rearrangement results in the fusion of exons of 1 to 16 of NCOA3 and exons 9 to 14 of PCBP3.Its functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0008426-T01-IM5	NCOA3-PCBP3 fusion	yes	unknown		out of frame	NCOA3 (NM_181659) - PCBP3 (NM_020528) Rearrangement : t(20;21)(20q13.12;21q22.3)(chr20:g.46268900::chr21:g.47336467)     Note: The NCOA3 (NM_181659) - PCBP3 (NM_020528) Rearrangement results in the fusion of exons of 1 to 16 of NCOA3 and exons 9 to 14 of PCBP3.Its functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0008146-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21) : c.2302-619:FGFR2_c.2182-744:BICC1inv Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0008146-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21) : c.2302-619:FGFR2_c.2182-744:BICC1inv Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
MLL3	0	MSKCC-DMP	P-0009833-T01-IM5	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: chr7:g.151824753_c.12981:MLL3del Note: The MLL3 (NM_170606) rearrangement results in the deletion of upstream promoter region, transcription start site, and exons 1-52 of MLL3. One of the breakpoints is within exon 52. The functional significance is undetermined.
SMO	0	MSKCC-DMP	P-0004996-T02-IM5	MKRN1-SMO fusion	yes	unknown		unknown	SMO (NM_005631) - MKRN1 (NM_013446) rearrangement : c.740:SMO_c.315-4269:MKRN1del Note: The SMO (NM_005631) - MKRN1 (NM_013446) rearrangement event results in the deletion of SMO exons 3-12. One of the breakpoints is within SMO exon3.
MKRN1	0	MSKCC-DMP	P-0004996-T02-IM5	MKRN1-SMO fusion	yes	unknown		unknown	SMO (NM_005631) - MKRN1 (NM_013446) rearrangement : c.740:SMO_c.315-4269:MKRN1del Note: The SMO (NM_005631) - MKRN1 (NM_013446) rearrangement event results in the deletion of SMO exons 3-12. One of the breakpoints is within SMO exon3.
MAP3K13	0	MSKCC-DMP	P-0004801-T01-IM5	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13(NM_004721) Rearrangement :  c.1506-338_2020dup Note: The MAP3K13(NM_004721) Rearrangement  results in the intragenic duplication of exons 10 and 11.The breakpoint is within exon11.Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0009102-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused in frame with ALK exons 20-29, which include the ALK kinase domain): c.1490-244:EML4_c.3173-119:ALKinv
EML4	0	MSKCC-DMP	P-0009102-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused in frame with ALK exons 20-29, which include the ALK kinase domain): c.1490-244:EML4_c.3173-119:ALKinv
RET	0	MSKCC-DMP	P-0005863-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon1 with RET exons 12-20): c.304-24354:CCDC6_ c.2136+467:RETinv. THe  CCDC6 (NM_005436) - RET (NM_020975) fusion is a reciiprocal inversion. The fusion is in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0005863-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon1 with RET exons 12-20): c.304-24354:CCDC6_ c.2136+467:RETinv. THe  CCDC6 (NM_005436) - RET (NM_020975) fusion is a reciiprocal inversion. The fusion is in frame and includes the kinase domain of RET.
RB1	0	MSKCC-DMP	P-0009715-T01-IM5	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.-1956_c.128del Note: RB1 (NM_000321) rearrangement results in the deletion of promoter region and exon1 of RB1. One of the breakpoints is within exon1 of RB1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008383-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11) : c.56-4549:TMPRSS2_c.40-54245:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008383-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11) : c.56-4549:TMPRSS2_c.40-54245:ERGdel
RNF43	0	MSKCC-DMP	P-0008868-T01-IM5	MTMR4-RNF43 fusion	yes	unknown		unknown	MTMR4 (NM_004687) - RNF43 (NM_017763) rearrangement: c.1811+1658:MTMR4_c.246:RNF43del Note: The MTMR4 (NM_004687) - RNF43 (NM_017763) rearrangement is a deletion that results in the fusion of MTMR4 exons 2-15 with RNF43 exons 2-10. One of the breakpoints is within RNF43 exon 2. The functional significance of this rearrangement is undetermined.
MTMR4	0	MSKCC-DMP	P-0008868-T01-IM5	MTMR4-RNF43 fusion	yes	unknown		unknown	MTMR4 (NM_004687) - RNF43 (NM_017763) rearrangement: c.1811+1658:MTMR4_c.246:RNF43del Note: The MTMR4 (NM_004687) - RNF43 (NM_017763) rearrangement is a deletion that results in the fusion of MTMR4 exons 2-15 with RNF43 exons 2-10. One of the breakpoints is within RNF43 exon 2. The functional significance of this rearrangement is undetermined.
KDM5C	0	MSKCC-DMP	P-0007240-T01-IM5	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement : c.1541_1746+1791del Note: The KDM5C (NM_004187) rearrangement event results in the intragenic deletion of KDM5C exons 11-12. One of the breakpoints is within KDM5C exon11.
NF1	0	MSKCC-DMP	P-0008003-T01-IM5	TIMP2-NF1 fusion	yes	unknown		in frame	NF1  (NM_001042492) - TIMP2  (NM_003255) rearrangement :  c.3496+59:NF1_c.130+6597:TIMP2inv Note: The TIMP2  (NM_003255) - NF1  (NM_001042492) rearrangement is a reciprocal inversion that results in the fusion of exon 1 of TIMP2 with exons 27-58 of NF1. The functional significance is undetermined.
TIMP2	0	MSKCC-DMP	P-0008003-T01-IM5	TIMP2-NF1 fusion	yes	unknown		in frame	NF1  (NM_001042492) - TIMP2  (NM_003255) rearrangement :  c.3496+59:NF1_c.130+6597:TIMP2inv Note: The TIMP2  (NM_003255) - NF1  (NM_001042492) rearrangement is a reciprocal inversion that results in the fusion of exon 1 of TIMP2 with exons 27-58 of NF1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005953-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exons 3 to 10) : c.55+3161:TMPRSS2_c.237-9105:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005953-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exons 3 to 10) : c.55+3161:TMPRSS2_c.237-9105:ERGdel
ERG	0	MSKCC-DMP	P-0005546-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 and ERG exons 2-10) : c.126+1491:TMPRSS2_c.19-14111:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005546-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 and ERG exons 2-10) : c.126+1491:TMPRSS2_c.19-14111:ERGdel
RBM10	0	MSKCC-DMP	P-0007890-T01-IM5	CLCN5-RBM10 fusion	yes	unknown		unknown	RBM10 (NM_001204468) - CLCN5 (NM_001127898) rearrangement: c.1675:RBM10_c.*5988:CLCN5del Note: The RBM10 (NM_001204468) rearrangement event results in the deletion of RBM10 exons 14-24.
CLCN5	0	MSKCC-DMP	P-0007890-T01-IM5	CLCN5-RBM10 fusion	yes	unknown		unknown	RBM10 (NM_001204468) - CLCN5 (NM_001127898) rearrangement: c.1675:RBM10_c.*5988:CLCN5del Note: The RBM10 (NM_001204468) rearrangement event results in the deletion of RBM10 exons 14-24.
TCF7L2	0	MSKCC-DMP	P-0005910-T01-IM5	LRRC27-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) and LRRC27 (NM_030626) rearrangement : c.553-12:TCF7L2_c.1290-649:LRRC27inv Note: The TCF7L2 (NM_001146274) and LRRC27 (NM_030626) rearrangement  event results in the inversion of TCF7L2 exons 6-14, potentially disabling the function of the gene.
LRRC27	0	MSKCC-DMP	P-0005910-T01-IM5	LRRC27-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) and LRRC27 (NM_030626) rearrangement : c.553-12:TCF7L2_c.1290-649:LRRC27inv Note: The TCF7L2 (NM_001146274) and LRRC27 (NM_030626) rearrangement  event results in the inversion of TCF7L2 exons 6-14, potentially disabling the function of the gene.
SCRIB	0	MSKCC-DMP	P-0007392-T01-IM5	BRAF-SCRIB fusion	yes	unknown		in frame	SCRIB (NM_182706) - BRAF (NM_004333) rearrangement: t(7;8)(q34;q24.3)(chr7:g.140482150::chr8:g.144876675) The SCRIB (NM_182706) - BRAF (NM_004333) rearrangemen is a reciprocal translocation which results in the fusion of SCRIB exons 1-27 with BRAF exons 11-18. The fusion is predicted to be in frame and   includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0007392-T01-IM5	BRAF-SCRIB fusion	yes	unknown		in frame	SCRIB (NM_182706) - BRAF (NM_004333) rearrangement: t(7;8)(q34;q24.3)(chr7:g.140482150::chr8:g.144876675) The SCRIB (NM_182706) - BRAF (NM_004333) rearrangemen is a reciprocal translocation which results in the fusion of SCRIB exons 1-27 with BRAF exons 11-18. The fusion is predicted to be in frame and   includes the kinase domain of BRAF.
NF1	0	MSKCC-DMP	P-0009759-T01-IM5	SHISA9-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - SHISA9 (NM_001145204) rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.13117863::chr17:g.29550486 ) Note: The NF1 (NM_001042492) - SHISA9 (NM_001145204) rearrangement is a translocation which results in the fusion of NF1 exons 1-16 with SHISA9 exons 3-5. One of the breakpoints is within exon 16 of NF1. The functional significance is undetermined.
SHISA9	0	MSKCC-DMP	P-0009759-T01-IM5	SHISA9-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - SHISA9 (NM_001145204) rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.13117863::chr17:g.29550486 ) Note: The NF1 (NM_001042492) - SHISA9 (NM_001145204) rearrangement is a translocation which results in the fusion of NF1 exons 1-16 with SHISA9 exons 3-5. One of the breakpoints is within exon 16 of NF1. The functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0009759-T01-IM5	ZNF91-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) rearrangement: c.770_ chr19:g.23268574del Note: The DNAJB1 (NM_006145) rearrangement is an inversion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ZNF91	0	MSKCC-DMP	P-0009759-T01-IM5	ZNF91-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) rearrangement: c.770_ chr19:g.23268574del Note: The DNAJB1 (NM_006145) rearrangement is an inversion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0004963-T01-IM5	BCOR-intragenic	yes	unknown		out of frame	BCOR (NM_001123385) rearrangement : c.4429-1339_4595+3del Note: The BCOR (NM_001123385) rearrangement event results in the intragenic deletion of BCOR exon 10.
MET	0	MSKCC-DMP	P-0008915-T01-IM5	PTPRZ1-MET fusion	yes	unknown		unknown	PTPRZ1 (NM_002851) - MET (NM_000245) rearrangement: c.58+3144:PTPRZ1_c.177:METdup Note: The PTPRZ1 (NM_002851) - MET (NM_000245) rearrangement is a duplication which results in the fusion of PTPRZ1 exon 1 with MET exons 2-21. One of the breakpoints is within exon 2 of MET.
PTPRZ1	0	MSKCC-DMP	P-0008915-T01-IM5	PTPRZ1-MET fusion	yes	unknown		unknown	PTPRZ1 (NM_002851) - MET (NM_000245) rearrangement: c.58+3144:PTPRZ1_c.177:METdup Note: The PTPRZ1 (NM_002851) - MET (NM_000245) rearrangement is a duplication which results in the fusion of PTPRZ1 exon 1 with MET exons 2-21. One of the breakpoints is within exon 2 of MET.
ALK	0	MSKCC-DMP	P-0004516-T02-IM5	GCC2-ALK fusion	yes	unknown		in frame	GCC2 (NM_181453) - ALK (NM_004304) rearrangement : c.4448-1230:GCC2_c.3173-132:ALKinv Note: The GCC2 (NM_181453) - ALK (NM_004304) rearrangement results in the in frame fusion of exons 1 to 19 of GCC2 with exons 20 to 29 of ALK.  This fusion includes the kinase domain of ALK.
GCC2	0	MSKCC-DMP	P-0004516-T02-IM5	GCC2-ALK fusion	yes	unknown		in frame	GCC2 (NM_181453) - ALK (NM_004304) rearrangement : c.4448-1230:GCC2_c.3173-132:ALKinv Note: The GCC2 (NM_181453) - ALK (NM_004304) rearrangement results in the in frame fusion of exons 1 to 19 of GCC2 with exons 20 to 29 of ALK.  This fusion includes the kinase domain of ALK.
RET	0	MSKCC-DMP	P-0004916-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6(NM_005436)-RET(NM_020975) Fusion(CCDC6 exon 2 fused to RET exon11) : c.304-1153:CCDC6_c.2136+169:RETinv Note:The CCDC6(NM_005436)-RET(NM_020975) Fusion is a reciprocal inversion.
CCDC6	0	MSKCC-DMP	P-0004916-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6(NM_005436)-RET(NM_020975) Fusion(CCDC6 exon 2 fused to RET exon11) : c.304-1153:CCDC6_c.2136+169:RETinv Note:The CCDC6(NM_005436)-RET(NM_020975) Fusion is a reciprocal inversion.
DLG4	0	MSKCC-DMP	P-0005698-T01-IM5	TP53-DLG4 fusion	yes	unknown		unknown	TP53 (NM_000546) - DLG4  (NM_001128827) rearrangement :  c.96+41:TP53_c.778+1336:DLG4inv Note: The TP53 (NM_000546) - DLG4  (NM_001128827) rearrangement event results in the reciprocal inversion of TP53 exons 4-11. This event truncates TP53 gene.
TP53	0	MSKCC-DMP	P-0005698-T01-IM5	TP53-DLG4 fusion	yes	unknown		unknown	TP53 (NM_000546) - DLG4  (NM_001128827) rearrangement :  c.96+41:TP53_c.778+1336:DLG4inv Note: The TP53 (NM_000546) - DLG4  (NM_001128827) rearrangement event results in the reciprocal inversion of TP53 exons 4-11. This event truncates TP53 gene.
ERG	0	MSKCC-DMP	P-0005698-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10) : c.126+396:TMPRSS2_c.39+21608:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005698-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10) : c.126+396:TMPRSS2_c.39+21608:ERGdel
ZFHX3	0	MSKCC-DMP	P-0008591-T01-IM5	BATF-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) - BATF (NM_006399) rearrangement: t(14;16)(q24.3;q22.2)(chr14:g.76000033::chr16:g.72829355 ) The ZFHX3 (NM_006885) - BATF (NM_006399) rearrangement is a translocation which results in the fusion of ZFHX3 exons 1-9 with BATF exon 3. One of the breakpoints is within exon 9 of ZFHX3. The functional significance is undetermined.
BATF	0	MSKCC-DMP	P-0008591-T01-IM5	BATF-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) - BATF (NM_006399) rearrangement: t(14;16)(q24.3;q22.2)(chr14:g.76000033::chr16:g.72829355 ) The ZFHX3 (NM_006885) - BATF (NM_006399) rearrangement is a translocation which results in the fusion of ZFHX3 exons 1-9 with BATF exon 3. One of the breakpoints is within exon 9 of ZFHX3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008591-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 4 to 11) : c.127-1512:TMPRSS2_c.39+64467:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008591-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 4 to 11) : c.127-1512:TMPRSS2_c.39+64467:ERGdel
NOTCH3	0	MSKCC-DMP	P-0004889-T01-IM5	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement:c.3522_chr19:g.15416060del The NOTCH3 (NM_000435) rearrangement is a deletion of exons 1-22 of NOTCH3. One of the breakpoints is within exon 22. The functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0004889-T01-IM5	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement:c.3522_chr19:g.15416060del The NOTCH3 (NM_000435) rearrangement is a deletion of exons 1-22 of NOTCH3. One of the breakpoints is within exon 22. The functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0005779-T01-IM5	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement : c.1564-6299_c.2113del Note: The INPP4B (NM_001101669) rearrangement results in the deletion of INPP4B exons 18-21. One of the breakpoints is within INPP4B exon21.
ARID2	0	MSKCC-DMP	P-0005122-T01-IM5	ARID2-intragenic	yes	unknown		unknown	ARID2(NM_152641) Rearrangement :  c.284+5753_4618del Note: The ARID2(NM_152641) Rearrangement results in the intragenic deletion of exons 4 to 15.The breakpoint is within exon 15.Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0008691-T01-IM5	ITPR2-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - ITPR2 (NM_002223) rearrangement: c.1009+6762:ETV6_c.163+2322:ITPR2dup. Note: The ETV6 (NM_001987) - ITPR2 (NM_002223) rearrangement is a duplication (14911103 bp) which includes ETV6 exons 6-8. The functional significance is undetermined.
ITPR2	0	MSKCC-DMP	P-0008691-T01-IM5	ITPR2-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - ITPR2 (NM_002223) rearrangement: c.1009+6762:ETV6_c.163+2322:ITPR2dup. Note: The ETV6 (NM_001987) - ITPR2 (NM_002223) rearrangement is a duplication (14911103 bp) which includes ETV6 exons 6-8. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0008691-T01-IM5	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.191-7470_c.541+117inv Note: The FGFR1 (NM_001174067) rearrangement is an inversion (9183 bp) of exons 4-5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0003908-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0003908-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
EP300	0	MSKCC-DMP	P-0004880-T02-IM5	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement : c.-269_7215del Note: The EP300 (NM_001429) rearrangement event results in the deletion of EP300 exons 1-31. One of the breakpoints is within EP300 exon31.
MLL2	0	MSKCC-DMP	P-0009943-T01-IM5	MLL2-intragenic	yes	unknown		unknown	MLL2 (NM_003482) rearrangement: c.3431_c.4702dup Note: The MLL2 rearrangement is a intragenic duplication. The breakpoints are within exons 11 and 18. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0009221-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.3865-1437_c.4821dup Note: The ZFHX3 (NM_006885) rearrangement is an intragenic duplication of exons 8-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
LUC7L2	0	MSKCC-DMP	P-0006412-T01-IM5	BRAF-LUC7L2 fusion	yes	unknown		unknown	LUC7L2 (NM_001244584) - BRAF (NM_004333) Rearrangement : c.1008-2090:LUC7L2_c.860+103:BRAFdel Note: The LUC7L2 (NM_001244584) - BRAF (NM_004333) rearrangement results in the intragenic deletion of exons 7 to 18 of BRAF, which includes the kinase domain.
BRAF	0	MSKCC-DMP	P-0006412-T01-IM5	BRAF-LUC7L2 fusion	yes	unknown		unknown	LUC7L2 (NM_001244584) - BRAF (NM_004333) Rearrangement : c.1008-2090:LUC7L2_c.860+103:BRAFdel Note: The LUC7L2 (NM_001244584) - BRAF (NM_004333) rearrangement results in the intragenic deletion of exons 7 to 18 of BRAF, which includes the kinase domain.
FGFR3	0	MSKCC-DMP	P-0008771-T01-IM5	C4orf48-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.1535-35:FGFR3_chr4:g.202468dup Note: The FGFR3 (NM_000142) rearrangement results in a duplication of FGFR3 exons 12-18, which includes the kinase domain. The functional significance of this rearrangement is undetermined.
C4orf48	0	MSKCC-DMP	P-0008771-T01-IM5	C4orf48-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.1535-35:FGFR3_chr4:g.202468dup Note: The FGFR3 (NM_000142) rearrangement results in a duplication of FGFR3 exons 12-18, which includes the kinase domain. The functional significance of this rearrangement is undetermined.
SMARCA4	0	MSKCC-DMP	P-0005142-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - LDLR (NM_000527) rearrangement: c.4533+94:SMARCA4_c.8:LDLRdel The SMARCA4 (NM_003072) - LDLR (NM_000527) rearrangement is a deletion which results in the fusion of SMARCA4 exons 1-31 with  LDLR exons 1-18. One of the breakpoints is within exon 1 of LDLR. The functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0005142-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - LDLR (NM_000527) rearrangement: c.4533+94:SMARCA4_c.8:LDLRdel The SMARCA4 (NM_003072) - LDLR (NM_000527) rearrangement is a deletion which results in the fusion of SMARCA4 exons 1-31 with  LDLR exons 1-18. One of the breakpoints is within exon 1 of LDLR. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0005811-T01-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A  (NM_021140) Rearrangement :  c.3145-812_3209+31del Note: The KDM6A  (NM_021140) rearrangement results in the  intragenic deletion of  exon 21.  Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0007600-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement : c.9_367del Note: The CTNNB1 (NM_001904) rearrangement event results in the deletion of exons 2-4 of CTNBB1. The breakpoints for this event are within CTNNB1 exon2 and exon4.
CTCF	0	MSKCC-DMP	P-0004589-T01-IM5	CTCF-intragenic	yes	unknown		unknown	CTCF (NM_006565) rearrangement : c.-9-2751_782-31del Note: The CTCF (NM_006565) rearrangement event results in the intragenic deletion of CTCF exon3.
POLD1	0	MSKCC-DMP	P-0007749-T01-IM5	POLD1-intragenic	yes	unknown		in frame	POLD1 (NM_002691) rearrangement:  c.202+69_c.463+16dup The POLD1 (NM_002691) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007749-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 fused with ERG exons 4 to 10): c.55+4353:TMPRSS2_c.40-54655:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007749-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 fused with ERG exons 4 to 10): c.55+4353:TMPRSS2_c.40-54655:ERGdel
SOX17	0	MSKCC-DMP	P-0004998-T01-IM5	MOS-SOX17 fusion	yes	unknown		unknown	SOX17(NM_022454) Rearrangement : c.1168:SOX17_chr8:57024193del Note: The SOX17(NM_022454) Rearrangement results in the partial deletion of exon 2 causing loss of stop codon. Its functional significance is undetermined.
MOS	0	MSKCC-DMP	P-0004998-T01-IM5	MOS-SOX17 fusion	yes	unknown		unknown	SOX17(NM_022454) Rearrangement : c.1168:SOX17_chr8:57024193del Note: The SOX17(NM_022454) Rearrangement results in the partial deletion of exon 2 causing loss of stop codon. Its functional significance is undetermined.
DDX4	0	MSKCC-DMP	P-0006990-T01-IM5	MAP3K1-DDX4 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement : chr5:g.55024979_c.2904:MAP3K1inv Note: The MAP3K1 (NM_005921) rearrangement results in the inversion of exon 1 to 14 of MAP3K1. One of the breakpoints is within exon14 . Its functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0006990-T01-IM5	MAP3K1-DDX4 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement : chr5:g.55024979_c.2904:MAP3K1inv Note: The MAP3K1 (NM_005921) rearrangement results in the inversion of exon 1 to 14 of MAP3K1. One of the breakpoints is within exon14 . Its functional significance is undetermined.
SKIV2L2	0	MSKCC-DMP	P-0007398-T02-IM5	APC-SKIV2L2 fusion	yes	unknown		unknown	SKIV2L2 (NM_015360) - APC (NM_000038) Rearrangement : c.1811-660:SKIV2L2_c.4089:APCdel Note: The SKIV2L2 (NM_015360) - APC (NM_000038) Rearrangement results in the fusion of exons 1 to 16 of SKIV2L2 and exon 16 of APC. The breakpoint is within exon 16 of APC.Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0007398-T02-IM5	APC-SKIV2L2 fusion	yes	unknown		unknown	SKIV2L2 (NM_015360) - APC (NM_000038) Rearrangement : c.1811-660:SKIV2L2_c.4089:APCdel Note: The SKIV2L2 (NM_015360) - APC (NM_000038) Rearrangement results in the fusion of exons 1 to 16 of SKIV2L2 and exon 16 of APC. The breakpoint is within exon 16 of APC.Its functional significance is undetermined.
ASAP2	0	MSKCC-DMP	P-0006617-T01-IM5	ALK-ASAP2 fusion	yes	unknown		unknown	ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event : c.127-20148:ASAP2_c.667+106:ALKdel Note: The ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event results in the deletion of ALK exons 2-29.
ALK	0	MSKCC-DMP	P-0006617-T01-IM5	ALK-ASAP2 fusion	yes	unknown		unknown	ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event : c.127-20148:ASAP2_c.667+106:ALKdel Note: The ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event results in the deletion of ALK exons 2-29.
TP53	0	MSKCC-DMP	P-0001347-T02-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1001_c.*608del The TP53 (NM_000546) rearrangement is an intragenic deletion of exons 10-11. The functional significance is undetermined.
ZMAT4	0	MSKCC-DMP	P-0006151-T01-IM5	RECQL4-ZMAT4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - ZMAT4 (NM_024645) rearrangement : c.357:RECQL4_c.578-20947:ZMAT4inv Note: The RECQL4 (NM_004260) - ZMAT4 (NM_024645) rearrangement event results in the inversion of RECQL4 exons 5-22. One of the breakpoints is within RECQL4 exon5.
RECQL4	0	MSKCC-DMP	P-0006151-T01-IM5	RECQL4-ZMAT4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - ZMAT4 (NM_024645) rearrangement : c.357:RECQL4_c.578-20947:ZMAT4inv Note: The RECQL4 (NM_004260) - ZMAT4 (NM_024645) rearrangement event results in the inversion of RECQL4 exons 5-22. One of the breakpoints is within RECQL4 exon5.
JAK3	0	MSKCC-DMP	P-0009598-T01-IM5	JAK3-intragenic	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: c.-13-314_c.1012inv Note: The JAK3 (NM_000215) rearrangement is an inversion of exons 2-8. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0009018-T01-IM5	TP53-intragenic	yes	unknown		in frame	TP53 (NM_000546) rearrangement : c.375+28_993+500del Note: The TP53 (NM_000546) rearrangement event results in the intragenic deletion of TP53 exons 5-9.
EEA1	0	MSKCC-DMP	P-0008064-T01-IM5	CDKN2A-EEA1 fusion	yes	unknown		unknown	EEA1 (NM_003566) - CDKN2A (NM_000077) rearrangement : t(9;12)(p21.3;q22)(chr9:g.21968207::chr12:g.93282009) Note: The EEA1 (NM_003566) - CDKN2A (NM_000077) rearrangement event is a translocation involving the 3 UTR of CDKN2A. The significance of this event is unknown.
CDKN2A	0	MSKCC-DMP	P-0008064-T01-IM5	CDKN2A-EEA1 fusion	yes	unknown		unknown	EEA1 (NM_003566) - CDKN2A (NM_000077) rearrangement : t(9;12)(p21.3;q22)(chr9:g.21968207::chr12:g.93282009) Note: The EEA1 (NM_003566) - CDKN2A (NM_000077) rearrangement event is a translocation involving the 3 UTR of CDKN2A. The significance of this event is unknown.
KDM4C	0	MSKCC-DMP	P-0009490-T01-IM5	PTPRD-KDM4C fusion	yes	unknown		in frame	KDM4C (NM_015061) - PTPRD (NM_002839) rearrangement: c.2782-15487:KDM4C_c.211-65:PTPRDinv Note: The KDM4C (NM_015061) - PTPRD (NM_002839) rearrangement is an inversion that results in an in frame fusion of KDM4C exons 1-19 with PTPRD exons 14-46. The functional significance of this rearrangement is undetermined.
PTPRD	0	MSKCC-DMP	P-0009490-T01-IM5	PTPRD-KDM4C fusion	yes	unknown		in frame	KDM4C (NM_015061) - PTPRD (NM_002839) rearrangement: c.2782-15487:KDM4C_c.211-65:PTPRDinv Note: The KDM4C (NM_015061) - PTPRD (NM_002839) rearrangement is an inversion that results in an in frame fusion of KDM4C exons 1-19 with PTPRD exons 14-46. The functional significance of this rearrangement is undetermined.
RB1	0	MSKCC-DMP	P-0003925-T01-IM3	RB1-intragenic	yes	unknown		unknown	null
RB1	0	MSKCC-DMP	P-0006195-T01-IM5	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) Rearrangement :  c.264+176_264+975del Note: The RB1 (NM_000321) rearrangement results in the intragenic deletion of RB1 .The breakpoints are within the intron after exon 2. Its functional significance is undetermined.
GDPD4	0	MSKCC-DMP	P-0006360-T01-IM5	PAK1-GDPD4 fusion	yes	unknown		out of frame	PAK1 (NM_002576) - GDPD4 (NM_182833) rearrangement: c.1552-1930:PAK1_ c.708-4336:GDPD4del The PAK1 (NM_002576) - GDPD4 (NM_182833) rearrangement is a deletion which results in the fusion of PAK1 exons 1-15 with GDPD4 exons 10-16, including the kinase domain of PAK1. The functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0006360-T01-IM5	PAK1-GDPD4 fusion	yes	unknown		out of frame	PAK1 (NM_002576) - GDPD4 (NM_182833) rearrangement: c.1552-1930:PAK1_ c.708-4336:GDPD4del The PAK1 (NM_002576) - GDPD4 (NM_182833) rearrangement is a deletion which results in the fusion of PAK1 exons 1-15 with GDPD4 exons 10-16, including the kinase domain of PAK1. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0008429-T02-IM5	PIK3R1-intragenic	yes	unknown		out of frame	PIK3R1 (NM_181523) rearrangement : c.917-2817_1745+22dup Note: The PIK3R1 (NM_181523) rearrangement event results in the duplication of PIK3R1 exons 8-13.
MLL2	0	MSKCC-DMP	P-0005889-T01-IM5	MLL2-intragenic	yes	unknown		unknown	MLL2 (NM_003482) Rearrangement :  c.15716_13954inv Note: The MLL2 (NM_003482) rearrangement  results in the intragenic inversion of exons  42 to 48 of MLL2. The breakpoints are within exon 42 and 48 respectively. Its functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0005518-T01-IM5	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) Rearrangement :  c.3651_3583-740del Note: The POLE (NM_006231) rearrangement results in the partial deletion of exon 30  of POLE. The breakpoint is within exon 30. Its functional significance is undetermined.
MET	0	MSKCC-DMP	P-0006787-T01-IM5	ST7-MET fusion	yes	unknown		out of frame	ST7 (NM_021908) - MET (NM_000245)  rearrangement: c.151+32541:ST7_c.2364+47:METdup. The ST7 (NM_021908) - MET (NM_000245)  rearrangement is a duplication which results in the fusion of ST7  exon 1 with MET exons 11-21. The functional significance is undetermined.
ST7	0	MSKCC-DMP	P-0006787-T01-IM5	ST7-MET fusion	yes	unknown		out of frame	ST7 (NM_021908) - MET (NM_000245)  rearrangement: c.151+32541:ST7_c.2364+47:METdup. The ST7 (NM_021908) - MET (NM_000245)  rearrangement is a duplication which results in the fusion of ST7  exon 1 with MET exons 11-21. The functional significance is undetermined.
MIR548H2	0	MSKCC-DMP	P-0009111-T01-IM5	CDKN2Ap14ARF-MIR548H2 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.21124920_c.194-3618:CDKN2Ap14ARFinv Note: The CDKN2Ap14ARF (NM_058195) rearrangement results in the inversion of exons 2-3 of CDKN2Ap14ARF. The functional significance of this rearrangement is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0009111-T01-IM5	CDKN2Ap14ARF-MIR548H2 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.21124920_c.194-3618:CDKN2Ap14ARFinv Note: The CDKN2Ap14ARF (NM_058195) rearrangement results in the inversion of exons 2-3 of CDKN2Ap14ARF. The functional significance of this rearrangement is undetermined.
MIR548H2	0	MSKCC-DMP	P-0009111-T01-IM5	CDKN2Ap16INK4A-MIR548H2 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.21124920_c.2:CDKN2Ap16INK4Ainv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement results in the inversion of the entire coding region of CDKN2Ap16INK4A. The breakpoint is within CDKN2Ap16INK4A exon 1. The functional significance of this rearrangement is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0009111-T01-IM5	CDKN2Ap16INK4A-MIR548H2 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.21124920_c.2:CDKN2Ap16INK4Ainv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement results in the inversion of the entire coding region of CDKN2Ap16INK4A. The breakpoint is within CDKN2Ap16INK4A exon 1. The functional significance of this rearrangement is undetermined.
CTNNB1	0	MSKCC-DMP	P-0005058-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1094_c.386del. The CTNNB1 (NM_001904) rearrangement is an intragenic deletion of exons 2-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
RHPN1	0	MSKCC-DMP	P-0009065-T01-IM5	RECQL4-RHPN1 fusion	yes	unknown		in frame	RECQL4 (NM_004260) - RHPN1 (NM_052924) rearrangement : c.1704+13:RECQL4_c.61-826:RHPN1inv Note: The RECQL4 (NM_004260) - RHPN1 (NM_052924) rearrangement event is an inversion which results in the fusion of RECQL4 exons 1-10 with RHPN1 exons 2-15. The fusion is predicted to be in-frame.
RECQL4	0	MSKCC-DMP	P-0009065-T01-IM5	RECQL4-RHPN1 fusion	yes	unknown		in frame	RECQL4 (NM_004260) - RHPN1 (NM_052924) rearrangement : c.1704+13:RECQL4_c.61-826:RHPN1inv Note: The RECQL4 (NM_004260) - RHPN1 (NM_052924) rearrangement event is an inversion which results in the fusion of RECQL4 exons 1-10 with RHPN1 exons 2-15. The fusion is predicted to be in-frame.
CIC	0	MSKCC-DMP	P-0005930-T01-IM5	CIC-intragenic	yes	unknown		unknown	CIC  (NM_015125) Rearrangement :  c.1912_3796-8del Note: The  CIC  (NM_015125) Rearrangement results in the intragenic deletion of exons 10 to 15 of CIC.The breakpoint is within exon10.  Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0005821-T01-IM5	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement event : c.1921-5117_4862inv Note: The ARID1A (NM_006015) rearrangement event results in the intragenic inversion of exons 5-18 of ARID1A, potentially disabling the function of the gene. One of the breakpoints is within exon18.
MALT1	0	MSKCC-DMP	P-0009147-T01-IM5	PIGN-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.558_chr18:g.59652061inv (Note) Note: The MALT1 (NM_006785) rearrangement is an inversion of exons 4-17. The functional significance is undetermined.
PIGN	0	MSKCC-DMP	P-0009147-T01-IM5	PIGN-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.558_chr18:g.59652061inv (Note) Note: The MALT1 (NM_006785) rearrangement is an inversion of exons 4-17. The functional significance is undetermined.
ANXA6	0	MSKCC-DMP	P-0009147-T01-IM5	NSD1-ANXA6 fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: chr5:g.150541610_c.224:NSD1dup (Note) Note: The NSD1 (NM_022455) rearrangement is a duplication (26020718 bp) that includes exons 1-2 of NSD1. One of the breakpoints is within exon 2 of NSD1. The functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0009147-T01-IM5	NSD1-ANXA6 fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: chr5:g.150541610_c.224:NSD1dup (Note) Note: The NSD1 (NM_022455) rearrangement is a duplication (26020718 bp) that includes exons 1-2 of NSD1. One of the breakpoints is within exon 2 of NSD1. The functional significance is undetermined.
SLC1A2	0	MSKCC-DMP	P-0008291-T01-IM5	MET-SLC1A2 fusion	yes	unknown		unknown	SLC1A2 (NM_004171) - MET (NM_000245) rearrangement: t(7;11)(q34;p13)(chr7:g.116411931::chr111:g.35443621) The SLC1A2 (NM_004171) - MET (NM_000245) rearrangement is a reciprocal translocation which results in the fusion of the promoter region of SLC1A2 with MET exons 14-21, including the kinase domain of MET. One of the breakpoints is within exon 14 of MET. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0008291-T01-IM5	MET-SLC1A2 fusion	yes	unknown		unknown	SLC1A2 (NM_004171) - MET (NM_000245) rearrangement: t(7;11)(q34;p13)(chr7:g.116411931::chr111:g.35443621) The SLC1A2 (NM_004171) - MET (NM_000245) rearrangement is a reciprocal translocation which results in the fusion of the promoter region of SLC1A2 with MET exons 14-21, including the kinase domain of MET. One of the breakpoints is within exon 14 of MET. The functional significance is undetermined.
SLC12A6	0	MSKCC-DMP	P-0004815-T01-IM5	MDM2-SLC12A6 fusion	yes	unknown		unknown	SLC12A6 (NM_133647) - MDM2 (NM_002392) rearrangement: t(15;12)(q14;q15)(chr15:g.34539975::chr12:g.69233428) The SLC12A6 (NM_133647) - MDM2 (NM_002392) rearrangement is a translocation which results in the fusion of exons 1-12 of SLC12A6 with exon 11 of  MDM2. One of the breakpoints is within exon 11 of MDM2. The functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0004815-T01-IM5	MDM2-SLC12A6 fusion	yes	unknown		unknown	SLC12A6 (NM_133647) - MDM2 (NM_002392) rearrangement: t(15;12)(q14;q15)(chr15:g.34539975::chr12:g.69233428) The SLC12A6 (NM_133647) - MDM2 (NM_002392) rearrangement is a translocation which results in the fusion of exons 1-12 of SLC12A6 with exon 11 of  MDM2. One of the breakpoints is within exon 11 of MDM2. The functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0004815-T01-IM5	SPEN-TP63 fusion	yes	unknown		unknown	TP63 (NM_00372 ) - SPEN (NM_015001) rearrangement: t(3;1)(q28;p36.13)(chr3:g.189533530::chr1:g.16247389) The TP63 (NM_00372 ) - SPEN (NM_015001) rearrangement is a translocation which results in the fusion of exons 1-4 of TP63 with exons 9-15 of SPEN. One of the breakpoints is within exon 9 of SPEN. The functional  significance is undetermined.
SPEN	0	MSKCC-DMP	P-0004815-T01-IM5	SPEN-TP63 fusion	yes	unknown		unknown	TP63 (NM_00372 ) - SPEN (NM_015001) rearrangement: t(3;1)(q28;p36.13)(chr3:g.189533530::chr1:g.16247389) The TP63 (NM_00372 ) - SPEN (NM_015001) rearrangement is a translocation which results in the fusion of exons 1-4 of TP63 with exons 9-15 of SPEN. One of the breakpoints is within exon 9 of SPEN. The functional  significance is undetermined.
ERG	0	MSKCC-DMP	P-0009082-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-2840:TMPRSS2_c.40-50568:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009082-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-2840:TMPRSS2_c.40-50568:ERGdel
MUC16	0	MSKCC-DMP	P-0009648-T01-IM5	RARA-MUC16 fusion	yes	unknown		unknown	RARA (NM_000964) - MUC16 (NM_024690) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.38512460::chr19:g.9019793) Note: The RARA (NM_000964) - MUC16 (NM_024690) rearrangement is a translocation that results in the fusion of RARA exons 1-9 with MUC16 exons 22-84. One of the breakpoints is within RARA exon 9. The functional significance of this rearrangement is undetermined.
RARA	0	MSKCC-DMP	P-0009648-T01-IM5	RARA-MUC16 fusion	yes	unknown		unknown	RARA (NM_000964) - MUC16 (NM_024690) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.38512460::chr19:g.9019793) Note: The RARA (NM_000964) - MUC16 (NM_024690) rearrangement is a translocation that results in the fusion of RARA exons 1-9 with MUC16 exons 22-84. One of the breakpoints is within RARA exon 9. The functional significance of this rearrangement is undetermined.
BRAF	0	MSKCC-DMP	P-0008098-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) rearrangement : c.139-17798_1314+634del Note: The BRAF (NM_004333) rearrangement event results in the deletion of BRAF exons 2-9.
ZFHX3	0	MSKCC-DMP	P-0006167-T01-IM5	CNTNAP4-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement :  c.11028:ZFHX3_chr16:g.76628585inv Note: The ZFHX3 (NM_006885) rearrangement results in the inversion of exons 1 to 10 of ZFHX3. The breakpoint is within exon10. Its functional significance is undetermined.
CNTNAP4	0	MSKCC-DMP	P-0006167-T01-IM5	CNTNAP4-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement :  c.11028:ZFHX3_chr16:g.76628585inv Note: The ZFHX3 (NM_006885) rearrangement results in the inversion of exons 1 to 10 of ZFHX3. The breakpoint is within exon10. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008879-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+804:TMPRSS2_c.18+212:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion is an in-frame fusion.
TMPRSS2	0	MSKCC-DMP	P-0008879-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+804:TMPRSS2_c.18+212:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion is an in-frame fusion.
ALK	0	MSKCC-DMP	P-0009343-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.668-1093:EML4_c.3173-127:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0009343-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.668-1093:EML4_c.3173-127:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
MAPK3	0	MSKCC-DMP	P-0009624-T01-IM5	TP53TG3B-MAPK3 fusion	yes	unknown		unknown	MAPK3 (NM_002746) Rearrangement : c.847_chr16:g.32609076inv Note: The MAPK3 (NM_002746) Rearrangement  results in the inversion of exons 1-6 of MAPK3. One of the breakpoints is within exon6 of MAPK3 .Its functional significance is undetermined.
TP53TG3B	0	MSKCC-DMP	P-0009624-T01-IM5	TP53TG3B-MAPK3 fusion	yes	unknown		unknown	MAPK3 (NM_002746) Rearrangement : c.847_chr16:g.32609076inv Note: The MAPK3 (NM_002746) Rearrangement  results in the inversion of exons 1-6 of MAPK3. One of the breakpoints is within exon6 of MAPK3 .Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0003913-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0003913-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0005895-T01-IM5	TMPRSS2-intragenic	yes	unknown		in frame	TMPRSS2 (NM_001135099) rearrangement: c.55+249_c.436+457del The TMPRSS2 (NM_001135099) rearrangement is an intragenic deletion of exons 2-4. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0003762-T02-IM5	ADCY9-CDK12 fusion	yes	unknown		unknown	ADCY9 (NM_001116) - CDK12 (NM_016507) rearrangement: t(16;17)(p13.3;q12)(chr16:g.4033430::chr17:g.37646665) The ADCY9 (NM_001116) - CDK12 (NM_016507) rearrangement is a translocation which results in the fusion of ADCY9 exons 1-7  with CDK12 exons 3-14,  including the kinase domain of CDK12. One of the breakpoints is within exon 7 of ADCY9. The functional significance is undetermined.
ADCY9	0	MSKCC-DMP	P-0003762-T02-IM5	ADCY9-CDK12 fusion	yes	unknown		unknown	ADCY9 (NM_001116) - CDK12 (NM_016507) rearrangement: t(16;17)(p13.3;q12)(chr16:g.4033430::chr17:g.37646665) The ADCY9 (NM_001116) - CDK12 (NM_016507) rearrangement is a translocation which results in the fusion of ADCY9 exons 1-7  with CDK12 exons 3-14,  including the kinase domain of CDK12. One of the breakpoints is within exon 7 of ADCY9. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0003762-T02-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.226-33170_c.335-77del. The KDM6A (NM_021140) rearrangement is an intragenic deletion of exon3. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0006963-T01-IM5	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.-1357_-259del Note: The TERT (NM_198253) rearrangement event results in a deletion in the TERT promoter region. Significance of this event is unknown.
ERG	0	MSKCC-DMP	P-0006815-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exon 2) :  c.55+4833:TMPRSS2_c.-150+8005:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006815-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exon 2) :  c.55+4833:TMPRSS2_c.-150+8005:ERGdel
HS3ST5	0	MSKCC-DMP	P-0008956-T01-IM5	ROS1-HS3ST5 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.2125+20_chr6:g.115008053del Note: The ROS1 (NM_002944) rearrangement is a deletion of exons 15-43, including the kinase domain.  The functional significance is undetermined
ROS1	0	MSKCC-DMP	P-0008956-T01-IM5	ROS1-HS3ST5 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.2125+20_chr6:g.115008053del Note: The ROS1 (NM_002944) rearrangement is a deletion of exons 15-43, including the kinase domain.  The functional significance is undetermined
CDK12	0	MSKCC-DMP	P-0005993-T01-IM5	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement: c.1520_c.2609+3524del CDK12 (NM_016507) rearrangement is an intragenic deletion which results in deletion of exons 2 to 6 and occurs within a background of overall CDK12 amplification. One of the breakpoints is within exon 2 of CDK12.
ERG	0	MSKCC-DMP	P-0008441-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1612:TMPRSS2_c.39+60626:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008441-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1612:TMPRSS2_c.39+60626:ERGdel
PBRM1	0	MSKCC-DMP	P-0009596-T01-IM5	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.620_c.3616+4824dup Note: The PBRM1 (NM_018313) rearrangement is a duplication of exons 6-23. One of the breakpoints is within exon 6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0006057-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.40-57547:ERG_c.56-2503:TMPRSS2inv The TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement is an inversion that leads to fusion of  exon1 of TMPRSS2 to exon3 of ERG in an antisense manner. While the event is not the canonical TMRPSS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion.
TMPRSS2	0	MSKCC-DMP	P-0006057-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.40-57547:ERG_c.56-2503:TMPRSS2inv The TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement is an inversion that leads to fusion of  exon1 of TMPRSS2 to exon3 of ERG in an antisense manner. While the event is not the canonical TMRPSS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion.
IDH2	0	MSKCC-DMP	P-0006138-T01-IM5	CHN1-IDH2 fusion	yes	unknown		unknown	CHN1(NM_001822) - IDH2 (NM_002168) rearrangement: t(2;15)(q31.1;q26)(chr2:g.175847561::chr15:g.90627553) The CHN1(NM_001822) - IDH2 (NM_002168) rearrangement is a translocation which results in the fusion of exon1 of  CHN1 with exon 11 of  IDH2. One of the breakpoints is within exon 11 of IDH2. The functional significance is undetermined.
CHN1	0	MSKCC-DMP	P-0006138-T01-IM5	CHN1-IDH2 fusion	yes	unknown		unknown	CHN1(NM_001822) - IDH2 (NM_002168) rearrangement: t(2;15)(q31.1;q26)(chr2:g.175847561::chr15:g.90627553) The CHN1(NM_001822) - IDH2 (NM_002168) rearrangement is a translocation which results in the fusion of exon1 of  CHN1 with exon 11 of  IDH2. One of the breakpoints is within exon 11 of IDH2. The functional significance is undetermined.
FAM13C	0	MSKCC-DMP	P-0005140-T01-IM5	FGFR2-FAM13C fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-1537:FGFR2_chr10:g.61197618inv The FGFR2 (NM_000141) rearrangement is an inversion of exon 18. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0005140-T01-IM5	FGFR2-FAM13C fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-1537:FGFR2_chr10:g.61197618inv The FGFR2 (NM_000141) rearrangement is an inversion of exon 18. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0005034-T01-IM5	SP2-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.7278:NF1_chr17:g.45958328del Note1: The NF1 (NM_001042492) rearrangement event results in the deletion of NF1 exons 48-58. One of the breakpoints is within NF1 exon 48. The functional significance of this event is unknown.
SP2	0	MSKCC-DMP	P-0005034-T01-IM5	SP2-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.7278:NF1_chr17:g.45958328del Note1: The NF1 (NM_001042492) rearrangement event results in the deletion of NF1 exons 48-58. One of the breakpoints is within NF1 exon 48. The functional significance of this event is unknown.
MYH14	0	MSKCC-DMP	P-0005034-T01-IM5	POLD1-MYH14 fusion	yes	unknown		unknown	MYH14 (NM_001145809) - POLD1 (NM_002691) rearrangement : c.5678+1575:MYH14_c.972:POLD1inv Note3: The MYH14 (NM_001145809) - POLD1 (NM_002691) rearrangement event results in the inversion of POLD1 exons 1-9. One of the breakpoints is within exon9.
POLD1	0	MSKCC-DMP	P-0005034-T01-IM5	POLD1-MYH14 fusion	yes	unknown		unknown	MYH14 (NM_001145809) - POLD1 (NM_002691) rearrangement : c.5678+1575:MYH14_c.972:POLD1inv Note3: The MYH14 (NM_001145809) - POLD1 (NM_002691) rearrangement event results in the inversion of POLD1 exons 1-9. One of the breakpoints is within exon9.
STK11	0	MSKCC-DMP	P-0007338-T01-IM5	REEP6-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - REEP6 (NM_138393) rearrangement : c.460:STK11_c.137:REEP6del Note: The STK11 (NM_000455) - REEP6 (NM_138393) rearrangement event is a deletion which results in the fusion of STK11 exons 1-3 and REEP6 exons 2-5. The breakpoints for this event are within STK11 exon3 and REEP6 exon2.
REEP6	0	MSKCC-DMP	P-0007338-T01-IM5	REEP6-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - REEP6 (NM_138393) rearrangement : c.460:STK11_c.137:REEP6del Note: The STK11 (NM_000455) - REEP6 (NM_138393) rearrangement event is a deletion which results in the fusion of STK11 exons 1-3 and REEP6 exons 2-5. The breakpoints for this event are within STK11 exon3 and REEP6 exon2.
SRC	0	MSKCC-DMP	P-0008104-T01-IM5	LBP-SRC fusion	yes	unknown		unknown	SRC (NM_198291) rearrangement : c.-3642_chr20:g.36971011del Note: The SRC (NM_198291) rearrangement event is a deletion which is predicted to truncate the promoter region of SRC. Significance of this event is unknown.
LBP	0	MSKCC-DMP	P-0008104-T01-IM5	LBP-SRC fusion	yes	unknown		unknown	SRC (NM_198291) rearrangement : c.-3642_chr20:g.36971011del Note: The SRC (NM_198291) rearrangement event is a deletion which is predicted to truncate the promoter region of SRC. Significance of this event is unknown.
DIS3	0	MSKCC-DMP	P-0005711-T01-IM5	DAOA-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) rearrangement (31899083 bp) : c.2838_chr13:g.105233055inv The DIS3 (NM_014953) rearrangement is an inversion of DIS3 exons1-21. The functional significance is undetermined.
DAOA	0	MSKCC-DMP	P-0005711-T01-IM5	DAOA-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) rearrangement (31899083 bp) : c.2838_chr13:g.105233055inv The DIS3 (NM_014953) rearrangement is an inversion of DIS3 exons1-21. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0009872-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement :  c.479_936+93del Note: The CTNNB1 (NM_001904) rearrangement event results in the deletion of CTNNB1 exons 4-6. One of the breakpoints is within CTBBB1 exon4.
TACC3	0	MSKCC-DMP	P-0004902-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 11-16) : c.2338:FGFR3_:c.1941+300TACC3dup Note: One of the breakpoints in the FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is within FGFR3 exon18.
FGFR3	0	MSKCC-DMP	P-0004902-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 11-16) : c.2338:FGFR3_:c.1941+300TACC3dup Note: One of the breakpoints in the FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is within FGFR3 exon18.
NUP93	0	MSKCC-DMP	P-0009100-T01-IM5	NUP93-intragenic	yes	unknown		unknown	NUP93 (NM_014669) rearrangement: c.1251+106_c.1900del Note: The NUP93 (NM_014669) rearrangement results in the deletion of NUP93 exons 12-18. One of the breakpoints is within NUP93 exon 18. The functional significance of this rearrangement is undetermined.
BBS9	0	MSKCC-DMP	P-0009480-T01-IM5	IKZF1-BBS9 fusion	yes	unknown		in frame	BBS9 (NM_198428) - IKZF1 (NM_006060) rearrangement: c.442+24705:BBS9_c.855-35:IKZF1del Note: The BBS9 (NM_198428) - IKZF1 (NM_006060) rearrangement is a deletion that results in the fusion of BBS9 exons 1-5 with IKZF1 exon 8. The functional significance of this rearrangement is undetermined.
IKZF1	0	MSKCC-DMP	P-0009480-T01-IM5	IKZF1-BBS9 fusion	yes	unknown		in frame	BBS9 (NM_198428) - IKZF1 (NM_006060) rearrangement: c.442+24705:BBS9_c.855-35:IKZF1del Note: The BBS9 (NM_198428) - IKZF1 (NM_006060) rearrangement is a deletion that results in the fusion of BBS9 exons 1-5 with IKZF1 exon 8. The functional significance of this rearrangement is undetermined.
MGA	0	MSKCC-DMP	P-0006776-T01-IM5	MESP2-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3925:MGA_chr15:g.90306603dup The MGA (NM_001164273) rearrangement is a duplication (48278216 bp) of MGA exons 13-24. The functional significance is undetermined.
MESP2	0	MSKCC-DMP	P-0006776-T01-IM5	MESP2-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3925:MGA_chr15:g.90306603dup The MGA (NM_001164273) rearrangement is a duplication (48278216 bp) of MGA exons 13-24. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0006776-T01-IM5	DYSF-ALK fusion	yes	unknown		unknown	ALK (NM_004304) - DYSF (NM_001130987) rearrangement: c.3172+909:ALK_c.3402+7348:DYSFdup The ALK (NM_004304) - DYSF (NM_001130987) rearrangement is a duplication (42361431 bp) of ALK exons 1-19. The functional significance is undetermined.
DYSF	0	MSKCC-DMP	P-0006776-T01-IM5	DYSF-ALK fusion	yes	unknown		unknown	ALK (NM_004304) - DYSF (NM_001130987) rearrangement: c.3172+909:ALK_c.3402+7348:DYSFdup The ALK (NM_004304) - DYSF (NM_001130987) rearrangement is a duplication (42361431 bp) of ALK exons 1-19. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0007001-T01-IM5	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) VIII intragenic deletion : c.89-39131_890-78del
ERG	0	MSKCC-DMP	P-0006619-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-11) : c.127-1066:TMPRSS2_c.40-44616:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006619-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-11) : c.127-1066:TMPRSS2_c.40-44616:ERGdel
ERG	0	MSKCC-DMP	P-0008139-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-11) : c.127-615:TMPRSS2_c.40-33298:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008139-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-11) : c.127-615:TMPRSS2_c.40-33298:ERGdel
SMARCA4	0	MSKCC-DMP	P-0008778-T01-IM5	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.3547-951_c.3874-73del Note: The SMARCA4 (NM_003072) rearrangement is an intragenic deletion of exons 26-27. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0007888-T01-IM5	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) rearrangement : c.6906:MLL3_9453+395inv Note: The MLL3 (NM_170606) rearrangement event results in the inversion of MLL3 exons 36-40. One of the breakpoints is within MLL3 exon36.
ROCK1	0	MSKCC-DMP	P-0006235-T01-IM5	FGFR2-ROCK1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ROCK1 (NM_005406) rearrangement: t(10;18)(q26.13;q11.1)(chr10:g.123240133::chr18:g18680051) The FGFR2 (NM_000141) - ROCK1 (NM_005406) rearrangement is a translocation which results in the fusion of exons 1-17 of FGFR2 with exons 2-33 of ROCK1, including the kinase domain of FGFR2. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0006235-T01-IM5	FGFR2-ROCK1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ROCK1 (NM_005406) rearrangement: t(10;18)(q26.13;q11.1)(chr10:g.123240133::chr18:g18680051) The FGFR2 (NM_000141) - ROCK1 (NM_005406) rearrangement is a translocation which results in the fusion of exons 1-17 of FGFR2 with exons 2-33 of ROCK1, including the kinase domain of FGFR2. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0005800-T01-IM5	PPM1D-intragenic	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: c.-98_c.472+283dup The PPM1D (NM_003620) rearrangement is an intragenic duplicaition of exon1. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0005800-T01-IM5	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.3989-529_c.4086+14114dup The  PTPRD (NM_002839) rearrangement is an intragenic duplication of exon 35. One of the breakpoints is within exon 35 PTPRD. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0009463-T01-IM5	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) Rearrangement :  c.1746-31_*2815del Note: The PIK3R1 (NM_181523) Rearrangement results in the deletion of exons 8-16 of PIK3R1. One of the breakpoints is the UTR region 3000bp after the coding stop site. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0009463-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement :  c.-3788_c.33del Note: The CDKN2Ap16INK4A (NM_000077) Rearrangement results in the intragenic deletion of exon1 of CDKN2Ap16INK4A.One of the breakpoints is within exon1. Its functional significance is undetermined.
LMNA	0	MSKCC-DMP	P-0003705-T01-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	c.686:LMNA_c.1476:NTRK1del LMNA (NM_170707) - NTRK (NM_002529) fusion (LMNA exons 1-4 fused to NTRK1 exons 12-17)
NTRK1	0	MSKCC-DMP	P-0003705-T01-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	c.686:LMNA_c.1476:NTRK1del LMNA (NM_170707) - NTRK (NM_002529) fusion (LMNA exons 1-4 fused to NTRK1 exons 12-17)
HIST1H1E	0	MSKCC-DMP	P-0004107-T01-IM5	HIST1H2BD-HIST1H1E fusion	yes	unknown		unknown	HIST1H1E (NM_005321)  - HIST1H2BD (NM_021063) rearrangement: c.-2778:HIST1H1E _c.10:HIST1H2BDdel The HIST1H1E (NM_005321)  - HIST1H2BD (NM_021063) rearrangement is a deletion of HIST1H1E and HIST1H2BD. One of the breakpoints is within exon 1 of HIST1H2BD. The functional significance is undetermined.
HIST1H2BD	0	MSKCC-DMP	P-0004107-T01-IM5	HIST1H2BD-HIST1H1E fusion	yes	unknown		unknown	HIST1H1E (NM_005321)  - HIST1H2BD (NM_021063) rearrangement: c.-2778:HIST1H1E _c.10:HIST1H2BDdel The HIST1H1E (NM_005321)  - HIST1H2BD (NM_021063) rearrangement is a deletion of HIST1H1E and HIST1H2BD. One of the breakpoints is within exon 1 of HIST1H2BD. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0003867-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.-28-1048_c.26_:TP53dup The TP53 (NM_000546) rearrangement is an intragenic duplication of exons 1 and 2. The breakpoint in exon 2 is within exon. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0003207-T01-IM5	TPM3-ROS1 fusion	yes	unknown		in frame	null Note: The TPM3-ROS1 fusion event results in the fusion of exon 35 of TPM3 to exons 10 to 43 of ROS1. For more information please check PMID:22327623
TPM3	0	MSKCC-DMP	P-0003207-T01-IM5	TPM3-ROS1 fusion	yes	unknown		in frame	null Note: The TPM3-ROS1 fusion event results in the fusion of exon 35 of TPM3 to exons 10 to 43 of ROS1. For more information please check PMID:22327623
ROS1	0	MSKCC-DMP	P-0000047-T01-IM3	TMEM181-ROS1 fusion	yes	unknown		unknown	null
TMEM181	0	MSKCC-DMP	P-0000047-T01-IM3	TMEM181-ROS1 fusion	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0003226-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0003226-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
FGFR2	0	MSKCC-DMP	P-0000644-T01-IM3	AHCYL1-FGFR2 fusion	yes	unknown		in frame	null
AHCYL1	0	MSKCC-DMP	P-0000644-T01-IM3	AHCYL1-FGFR2 fusion	yes	unknown		in frame	null
ERG	0	MSKCC-DMP	P-0000479-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0000479-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
ARID2	0	MSKCC-DMP	P-0001635-T01-IM3	ARID2-intragenic	yes	unknown		in frame	None
EWSR1	0	MSKCC-DMP	P-0001021-T01-IM3	GAS2L1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - GAS2L1 (NM_006478) Deletion: c.1179+844_c.634-343del
GAS2L1	0	MSKCC-DMP	P-0001021-T01-IM3	GAS2L1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - GAS2L1 (NM_006478) Deletion: c.1179+844_c.634-343del
HDAC7	0	MSKCC-DMP	P-0002649-T01-IM3	MLL2-HDAC7 fusion	yes	unknown		out of frame	null Note: The MLL2-HDAC7 deletion is a structural rearrangement in which exons 1 to 23 of MLL2 are fused to exons 20 to 26 of HDAC7. Functional significance of this fusion is not determined.
MLL2	0	MSKCC-DMP	P-0002649-T01-IM3	MLL2-HDAC7 fusion	yes	unknown		out of frame	null Note: The MLL2-HDAC7 deletion is a structural rearrangement in which exons 1 to 23 of MLL2 are fused to exons 20 to 26 of HDAC7. Functional significance of this fusion is not determined.
PTCH1	0	MSKCC-DMP	P-0002382-T01-IM3	C9orf130-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) deletion (211947bp) : PTCH1:c.585-89_chr9:g.98456521del Note: PTCH1 deletion is a rearrangement event which removes exons 1 to 3 potentially disabling PTCH1 protein.
C9orf130	0	MSKCC-DMP	P-0002382-T01-IM3	C9orf130-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) deletion (211947bp) : PTCH1:c.585-89_chr9:g.98456521del Note: PTCH1 deletion is a rearrangement event which removes exons 1 to 3 potentially disabling PTCH1 protein.
MAP2K4	0	MSKCC-DMP	P-0003334-T02-IM5	COX19-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) - COX19 (NM_001031617) translocation: t(17;7) (p12;p22.3) chr17:g.11935583::chr7:g.1005376 The MAP2K4 (NM_003010) - COX19 (NM_001031617) rearrangement is a translocation which results in the truncation of MAP2K4 exons 2-11. The functional significance is undetermined.
COX19	0	MSKCC-DMP	P-0003334-T02-IM5	COX19-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) - COX19 (NM_001031617) translocation: t(17;7) (p12;p22.3) chr17:g.11935583::chr7:g.1005376 The MAP2K4 (NM_003010) - COX19 (NM_001031617) rearrangement is a translocation which results in the truncation of MAP2K4 exons 2-11. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0004670-T01-IM5	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1920+6791_c.2668del The ARID1A (NM_006015) rearrangement is an intragenic deletion of exons 5-8 of ARID1A. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0002050-T01-IM3	CREBBP-intragenic	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0002397-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion : c.55+2513:TMPRSS2_c.237-5242:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0002397-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion : c.55+2513:TMPRSS2_c.237-5242:ERGdel
ARID2	0	MSKCC-DMP	P-0002336-T01-IM3	ARID2-intragenic	yes	unknown		in frame	ARID2 (NM_152641) Duplication : c.1120+11_c.1498+402dup Note: ARID2 duplication is a structural rearrangement in which exons 10 and 11 are duplicated
ERG	0	MSKCC-DMP	P-0001128-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032278 bp): c.112_c.19-20238del
TMPRSS2	0	MSKCC-DMP	P-0001128-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032278 bp): c.112_c.19-20238del
CASC3	0	MSKCC-DMP	P-0002887-T01-IM3	BRCA1-CASC3 fusion	yes	unknown		unknown	null Note: The CASC3 (NM_007359)-BRCA1 (NM_007300) inversion is a rearrangement event which results in the fusion of CASC3 exons 1 to 3 and BRCA1 exons 15 to 24. The breakpoint in BRCA1 is within exon15. Its functional significance is not determined.
BRCA1	0	MSKCC-DMP	P-0002887-T01-IM3	BRCA1-CASC3 fusion	yes	unknown		unknown	null Note: The CASC3 (NM_007359)-BRCA1 (NM_007300) inversion is a rearrangement event which results in the fusion of CASC3 exons 1 to 3 and BRCA1 exons 15 to 24. The breakpoint in BRCA1 is within exon15. Its functional significance is not determined.
ERG	0	MSKCC-DMP	P-0004539-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.55+2908:TMPRSS2_c.40-50360:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004539-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.55+2908:TMPRSS2_c.40-50360:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004539-T01-IM5	ZNF295-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099)  - ZNF295 (NM_020727) rearrangement (530676 bp) : c.55+2996_c.*3447:ZNF295inv The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.
ZNF295	0	MSKCC-DMP	P-0004539-T01-IM5	ZNF295-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099)  - ZNF295 (NM_020727) rearrangement (530676 bp) : c.55+2996_c.*3447:ZNF295inv The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.
ROS1	0	MSKCC-DMP	P-0000569-T01-IM3	CD74-ROS1 fusion	yes	unknown		out of frame	null
CD74	0	MSKCC-DMP	P-0000569-T01-IM3	CD74-ROS1 fusion	yes	unknown		out of frame	null
NFE2L2	0	MSKCC-DMP	P-0004410-T01-IM5	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2(NM_006164)  Rearrangement :  c.313-78_c.46-3539del Note: The NFE2L2(NM_006164)  Rearrangement results in the intragenic deletion of exon 2.Its functional significance is undetermined.
ACAA1	0	MSKCC-DMP	P-0003852-T01-IM5	MYD88-ACAA1 fusion	yes	unknown		unknown	ACAA1 (NM_001607) - MYD88 (NM_002468) rearrangement : c.700:ACAA1_c.368-122:MYD88inv Note: The ACAA1 (NM_001607) - MYD88 (NM_002468) rearrangement event is an inversion which results in the fusion of ACAA1 exons 1 to 8 and MYD88 exons 2 to 5. The breakpoint on ACAA1 is within exon 8.
MYD88	0	MSKCC-DMP	P-0003852-T01-IM5	MYD88-ACAA1 fusion	yes	unknown		unknown	ACAA1 (NM_001607) - MYD88 (NM_002468) rearrangement : c.700:ACAA1_c.368-122:MYD88inv Note: The ACAA1 (NM_001607) - MYD88 (NM_002468) rearrangement event is an inversion which results in the fusion of ACAA1 exons 1 to 8 and MYD88 exons 2 to 5. The breakpoint on ACAA1 is within exon 8.
CXorf26	0	MSKCC-DMP	P-0002890-T01-IM3	FGFR3-CXorf26 fusion	yes	unknown		unknown	null Note: EGFR translocation is a structural rearrangement that involves exon5 of EGFR and an intergenic region on Chromosome X. Its functional significance is not determined.
FGFR3	0	MSKCC-DMP	P-0002890-T01-IM3	FGFR3-CXorf26 fusion	yes	unknown		unknown	null Note: EGFR translocation is a structural rearrangement that involves exon5 of EGFR and an intergenic region on Chromosome X. Its functional significance is not determined.
SUFU	0	MSKCC-DMP	P-0003819-T01-IM5	TRIM8-SUFU fusion	yes	unknown		in frame	TRIM8 (NM_030912) - SUFU (NM_016169) rearrangement : c.570+4652:TRIM8_c.1297-69:SUFUdup Note: The TRIM8 (NM_030912) - SUFU (NM_016169) rearrangement event is a duplication which results in the fusion of TRIM8 exon1 and SUFU exons 11-12 .
TRIM8	0	MSKCC-DMP	P-0003819-T01-IM5	TRIM8-SUFU fusion	yes	unknown		in frame	TRIM8 (NM_030912) - SUFU (NM_016169) rearrangement : c.570+4652:TRIM8_c.1297-69:SUFUdup Note: The TRIM8 (NM_030912) - SUFU (NM_016169) rearrangement event is a duplication which results in the fusion of TRIM8 exon1 and SUFU exons 11-12 .
ARID1A	0	MSKCC-DMP	P-0004108-T01-IM5	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1920+5685_c.3866+3dup The ARID1A (NM_006015) rearrangement is an intragenic duplication of exons 5-15. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0001698-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032220 bp):(TMRPSS2:c.56-4673_ERG:c.19-25025del)
TMPRSS2	0	MSKCC-DMP	P-0001698-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032220 bp):(TMRPSS2:c.56-4673_ERG:c.19-25025del)
RAD21	0	MSKCC-DMP	P-0003478-T01-IM5	RAD21-intragenic	yes	unknown		unknown	null The RAD21 (NM_006265) rearrangement reslts in the deletion of exon2. The breakpoint is within exon2.Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0004201-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.463+744_c.1009+7228del The  ETV6 (NM_001987) rearrangement is an intragenic deletion of exon 5. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0002536-T01-IM3	ESYT1-ERBB3 fusion	yes	unknown		unknown	null
ESYT1	0	MSKCC-DMP	P-0002536-T01-IM3	ESYT1-ERBB3 fusion	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0002206-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0002206-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
GSK3B	0	MSKCC-DMP	P-0001297-T01-IM3	FSTL1-GSK3B fusion	yes	unknown		unknown	None
FSTL1	0	MSKCC-DMP	P-0001297-T01-IM3	FSTL1-GSK3B fusion	yes	unknown		unknown	None
SDC4	0	MSKCC-DMP	P-0001840-T02-IM5	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(20;6) (q13.12;q22.1) (chr20:g.43962893::chr6:g.117650732) The SDC4-ROS1 fusion is a reciprocal translocation that results in the fusion of exons 1-2 of SDC4 with exons 32-43 of ROS1. (PMID 25870798)
ROS1	0	MSKCC-DMP	P-0001840-T02-IM5	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(20;6) (q13.12;q22.1) (chr20:g.43962893::chr6:g.117650732) The SDC4-ROS1 fusion is a reciprocal translocation that results in the fusion of exons 1-2 of SDC4 with exons 32-43 of ROS1. (PMID 25870798)
CREBBP	0	MSKCC-DMP	P-0001440-T01-IM3	CREBBP-intragenic	yes	unknown		unknown	None
ERG	0	MSKCC-DMP	P-0003592-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_001243428) fusion: c.127-55:TMPRSS2_c.40-16879:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0003592-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_001243428) fusion: c.127-55:TMPRSS2_c.40-16879:ERGdel
ERG	0	MSKCC-DMP	P-0004283-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.55+4621:TMPRSS2_c.18+7946:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004283-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.55+4621:TMPRSS2_c.18+7946:ERGdel
MX1	0	MSKCC-DMP	P-0004283-T01-IM5	TMPRSS2-MX1 fusion	yes	unknown		out of frame	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement : c.1759-351:MX1_c.56-4378:TMPRSS2inv Note: The MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement is an inversion which results in the fusion of MX1 exons 1-14 with TMPRSS2 exons 2-14.
TMPRSS2	0	MSKCC-DMP	P-0004283-T01-IM5	TMPRSS2-MX1 fusion	yes	unknown		out of frame	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement : c.1759-351:MX1_c.56-4378:TMPRSS2inv Note: The MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement is an inversion which results in the fusion of MX1 exons 1-14 with TMPRSS2 exons 2-14.
MLL2	0	MSKCC-DMP	P-0004215-T01-IM5	FAM19A2-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) rearrangement: c.8672:MLL2_chr12:61283478del Note: The MLL2 (NM_003482) rearrangement event results in the deletion of MLL2 exons 1-34, potentially disabling the function of the gene. One of the breakpoints is within MLL2 exon 34.
FAM19A2	0	MSKCC-DMP	P-0004215-T01-IM5	FAM19A2-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) rearrangement: c.8672:MLL2_chr12:61283478del Note: The MLL2 (NM_003482) rearrangement event results in the deletion of MLL2 exons 1-34, potentially disabling the function of the gene. One of the breakpoints is within MLL2 exon 34.
APC	0	MSKCC-DMP	P-0001867-T01-IM3	APC-intragenic	yes	unknown		unknown	null
TNFAIP3	0	MSKCC-DMP	P-0002178-T01-IM3	TNFAIP3-intragenic	yes	unknown		unknown	null
POLE	0	MSKCC-DMP	P-0004529-T01-IM5	POLE-intragenic	yes	unknown		out of frame	POLE(NM_006231) Rearrangement : c.5552+59_3583-2741del Note: POLE(NM_006231) Rearrangement  results in the intragenic deletion of exons 30 to 40 of POLE.Its functional significance is undetermined.
RAB35	0	MSKCC-DMP	P-0004529-T01-IM5	CDH12-RAB35 fusion	yes	unknown		unknown	CDH12 (NM_004061) Rearrangement :  t(12;5)(12q24.23;5p14.3)(chr12:g.1120554384::chr5:g.21898797)    Note: The CDH12 rearrangement is a translocation which results in the deletion of exons 7 to 15.Its functional significance is undetermined.
CDH12	0	MSKCC-DMP	P-0004529-T01-IM5	CDH12-RAB35 fusion	yes	unknown		unknown	CDH12 (NM_004061) Rearrangement :  t(12;5)(12q24.23;5p14.3)(chr12:g.1120554384::chr5:g.21898797)    Note: The CDH12 rearrangement is a translocation which results in the deletion of exons 7 to 15.Its functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0004600-T01-IM5	ACPP-FGFR1 fusion	yes	unknown		in frame	ACPP (NM_001134194) - FGFR1 (NM_001174067) rearrangement :t(3;8)(3q22.1;8p11.33)(chr3:g.132081259::chr8:g.38286054) Note: The ACPP (NM_001134194) - FGFR1 (NM_001174067) rearrangement event is a translocation which results in the in-frame fusion of ACPP exons 1-10 to FGFR1 exons 5-19. The fusion event includes the kinase domain of FGFR1.
ACPP	0	MSKCC-DMP	P-0004600-T01-IM5	ACPP-FGFR1 fusion	yes	unknown		in frame	ACPP (NM_001134194) - FGFR1 (NM_001174067) rearrangement :t(3;8)(3q22.1;8p11.33)(chr3:g.132081259::chr8:g.38286054) Note: The ACPP (NM_001134194) - FGFR1 (NM_001174067) rearrangement event is a translocation which results in the in-frame fusion of ACPP exons 1-10 to FGFR1 exons 5-19. The fusion event includes the kinase domain of FGFR1.
ALK	0	MSKCC-DMP	P-0003297-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0003297-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null
NF1	0	MSKCC-DMP	P-0001226-T01-IM3	PPM1D-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) Deletion (29052537bp): c.4430+118_g.17:58638802del Note: Deletion variant in NF1 is predicted to remove exons following exon 32, generating a truncating mutation.
PPM1D	0	MSKCC-DMP	P-0001226-T01-IM3	PPM1D-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) Deletion (29052537bp): c.4430+118_g.17:58638802del Note: Deletion variant in NF1 is predicted to remove exons following exon 32, generating a truncating mutation.
NF1	0	MSKCC-DMP	P-0004284-T01-IM5	STAT5B-NF1 fusion	yes	unknown		unknown	STAT5B (NM_012448) rearrangement : c.40_chr17:g.29412409inv Note: The STAT5B (NM_012448) rearrangement event results in the inversion of STAT5B exons 1-2. One of the breakpoints is within STAT5B exon2.
STAT5B	0	MSKCC-DMP	P-0004284-T01-IM5	STAT5B-NF1 fusion	yes	unknown		unknown	STAT5B (NM_012448) rearrangement : c.40_chr17:g.29412409inv Note: The STAT5B (NM_012448) rearrangement event results in the inversion of STAT5B exons 1-2. One of the breakpoints is within STAT5B exon2.
TMPRSS2	0	MSKCC-DMP	P-0002971-T02-IM5	CHD3-TMPRSS2 fusion	yes	unknown		in frame	CHD3 (NM_001005271) - TMPRSS2 (NM_001135099)  Rearrangement : t(17;21)(17p13.1;21q22.3)(chr17:g.7811475::chr21:g.42871618)     Note: The CHD3 (NM_001005271) - TMPRSS2 (NM_001135099)  Rearrangement results in the fusion of exon 1 to 34 of CHD3 with exons 2  to 14 of TMPRSS2.Its functional significance is undetermined.
CHD3	0	MSKCC-DMP	P-0002971-T02-IM5	CHD3-TMPRSS2 fusion	yes	unknown		in frame	CHD3 (NM_001005271) - TMPRSS2 (NM_001135099)  Rearrangement : t(17;21)(17p13.1;21q22.3)(chr17:g.7811475::chr21:g.42871618)     Note: The CHD3 (NM_001005271) - TMPRSS2 (NM_001135099)  Rearrangement results in the fusion of exon 1 to 34 of CHD3 with exons 2  to 14 of TMPRSS2.Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0002971-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) Fusion  (TMPRSS2 exon 2 fused to ERG exon 4):  c.127-1520:TMPRSS2_c.39+27766:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0002971-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) Fusion  (TMPRSS2 exon 2 fused to ERG exon 4):  c.127-1520:TMPRSS2_c.39+27766:ERGdel
NCOR1	0	MSKCC-DMP	P-0003599-T01-IM5	NCOR1-intragenic	yes	unknown		unknown	c.6393-29_6537-785inv Note: The NCOR1 (NM_006311)  rearrangement event results in the inversion of NCOR1 exon41.
TNRC6B	0	MSKCC-DMP	P-0002803-T01-IM3	EPHA5-TNRC6B fusion	yes	unknown		unknown	null The EPHA5-TNR6CB translocation is a structural rearrangement which results in EPHA5 exon 3 fused to exons 5 to 24 of TNRC6B. The breakpoint in EPHA5 exon 3 is in the middle of the exon.Its functional significance is undetermined
EPHA5	0	MSKCC-DMP	P-0002803-T01-IM3	EPHA5-TNRC6B fusion	yes	unknown		unknown	null The EPHA5-TNR6CB translocation is a structural rearrangement which results in EPHA5 exon 3 fused to exons 5 to 24 of TNRC6B. The breakpoint in EPHA5 exon 3 is in the middle of the exon.Its functional significance is undetermined
NAB2	0	MSKCC-DMP	P-0001699-T02-IM5	STAT6-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) - STAT6 (NM_003153) rearrangement: c.1469-97:NAB2_c.*2057:STAT6dup The NAB2 (NM_005967) - STAT6 (NM_003153) rearrangement is a duplication of exon 7 of NAB2 and exons 1-22 of STAT6. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion between NAB2 and STAT6.
STAT6	0	MSKCC-DMP	P-0001699-T02-IM5	STAT6-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) - STAT6 (NM_003153) rearrangement: c.1469-97:NAB2_c.*2057:STAT6dup The NAB2 (NM_005967) - STAT6 (NM_003153) rearrangement is a duplication of exon 7 of NAB2 and exons 1-22 of STAT6. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion between NAB2 and STAT6.
PBRM1	0	MSKCC-DMP	P-0001699-T02-IM5	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) rearrangement: c.3292-1256_c.2966-169dup The PBRM1 (NM_018313) rearrangement is an intragenic duplication of exons 18-21. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0003701-T01-IM5	BRCA1-intragenic	yes	unknown		unknown	c.2553_c.4186-2131dup BRCA1 (NM_007294) rearrangement results in the duplication of exons 10 and 11. The breakpoint is within exon 10. Its functional significance is undetermined
MAP3K1	0	MSKCC-DMP	P-0003701-T01-IM5	MAP3K1-intragenic	yes	unknown		unknown	g.55923853_c.4401:MAP3K1del MAP3K1 (NM_005921)  rearrangement event results in the deletion of exons 1-20. The breakpoint is within exon 20. Its functional significance is undetermined
ESR1	0	MSKCC-DMP	P-0003701-T01-IM5	TACR1-ESR1 fusion	yes	unknown		unknown	t(6;2)(q21;p12)(c.888_c.585-2327) ESR1 (NM_001122740) - TACR1 (NM_001058) rearrangement is a translocation that results in the fusion of exons 1-5 of ESR1 with exons 3-5 of TACR1. The functional significance is undetermined.
TACR1	0	MSKCC-DMP	P-0003701-T01-IM5	TACR1-ESR1 fusion	yes	unknown		unknown	t(6;2)(q21;p12)(c.888_c.585-2327) ESR1 (NM_001122740) - TACR1 (NM_001058) rearrangement is a translocation that results in the fusion of exons 1-5 of ESR1 with exons 3-5 of TACR1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0003419-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	c.40-58284:ERG_c.55+1883:TMPRSS2del TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4 to 11)
TMPRSS2	0	MSKCC-DMP	P-0003419-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	c.40-58284:ERG_c.55+1883:TMPRSS2del TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4 to 11)
RET	0	MSKCC-DMP	P-0001155-T01-IM3	NCOA4-RET fusion	yes	unknown		in frame	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2136+757_c.715-617dup Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH is recommended.
NCOA4	0	MSKCC-DMP	P-0001155-T01-IM3	NCOA4-RET fusion	yes	unknown		in frame	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2136+757_c.715-617dup Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH is recommended.
LRCH1	0	MSKCC-DMP	P-0000673-T01-IM3	RB1-LRCH1 fusion	yes	unknown		unknown	null
RB1	0	MSKCC-DMP	P-0000673-T01-IM3	RB1-LRCH1 fusion	yes	unknown		unknown	null
MTOR	0	MSKCC-DMP	P-0002001-T01-IM3	RGL1-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) - RGL1 (NM_015149) inversion: c.2779+66:MTOR_c.-32-42343:RGL1inv
RGL1	0	MSKCC-DMP	P-0002001-T01-IM3	RGL1-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) - RGL1 (NM_015149) inversion: c.2779+66:MTOR_c.-32-42343:RGL1inv
ARID1A	0	MSKCC-DMP	P-0001717-T01-IM3	EPB41-ARID1A fusion	yes	unknown		unknown	EPB41 (NM_001166005) - ARID1A (NM_006015) duplication:  c.-8+27610_c.4239del The EPB41-ARID1A duplication is a rearrangement event which results in the deletion of ARID1A exons 1 to 18, likely disabling the function of the ARID1A gene.
EPB41	0	MSKCC-DMP	P-0001717-T01-IM3	EPB41-ARID1A fusion	yes	unknown		unknown	EPB41 (NM_001166005) - ARID1A (NM_006015) duplication:  c.-8+27610_c.4239del The EPB41-ARID1A duplication is a rearrangement event which results in the deletion of ARID1A exons 1 to 18, likely disabling the function of the ARID1A gene.
MLL3	0	MSKCC-DMP	P-0001717-T01-IM3	DPP6-MLL3 fusion	yes	unknown		in frame	DPP6 (NM_130797) - MLL3 (NM_170606) inversion: c.458-17058_c.9518-33inv The DPP6-MLL3 inversion is a rearrangement event which results in the fusion of DPP6 exons 1 to 3 and MLL3 exons 43 to 59.
DPP6	0	MSKCC-DMP	P-0001717-T01-IM3	DPP6-MLL3 fusion	yes	unknown		in frame	DPP6 (NM_130797) - MLL3 (NM_170606) inversion: c.458-17058_c.9518-33inv The DPP6-MLL3 inversion is a rearrangement event which results in the fusion of DPP6 exons 1 to 3 and MLL3 exons 43 to 59.
ERCC2	0	MSKCC-DMP	P-0003603-T01-IM5	ERCC2-intragenic	yes	unknown		unknown	c.1237+857_1745inv Note: The ERCC2 (NM_000400) rearrangement event results in the inversion of exons 13-18, likely disabling the function of the gene. One of the breakpoints is within exon18.
SHBG	0	MSKCC-DMP	P-0002304-T01-IM3	TP53-SHBG fusion	yes	unknown		unknown	TP53 (NM_000546) Deletion : g.7541002_c.96+41del
TP53	0	MSKCC-DMP	P-0002304-T01-IM3	TP53-SHBG fusion	yes	unknown		unknown	TP53 (NM_000546) Deletion : g.7541002_c.96+41del
TP53	0	MSKCC-DMP	P-0002304-T01-IM3	SPDYE4-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Deletion : c.96+6_g.8654277del
SPDYE4	0	MSKCC-DMP	P-0002304-T01-IM3	SPDYE4-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Deletion : c.96+6_g.8654277del
ERG	0	MSKCC-DMP	P-0002364-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0002364-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
ZFHX3	0	MSKCC-DMP	P-0004213-T01-IM5	AGBL1-ZFHX3 fusion	yes	unknown		unknown	GBL1 (NM_152336) - ZFHX3 (NM_006885) rearrangement: t(15;16)(15q25.3;16q22.2)(chr15:g.87282028::chr16:72827570) Note: AGBL1 (NM_152336) - ZFHX3 (NM_006885) rearrangement event is a translocation in which AGBL1 exons 1-22 is fused to ZFHX3 exons 9-10. This translocation event occurs amid a more complex rearrangement involving ZFHX3 gene. Its functional significance is undetermined.
AGBL1	0	MSKCC-DMP	P-0004213-T01-IM5	AGBL1-ZFHX3 fusion	yes	unknown		unknown	GBL1 (NM_152336) - ZFHX3 (NM_006885) rearrangement: t(15;16)(15q25.3;16q22.2)(chr15:g.87282028::chr16:72827570) Note: AGBL1 (NM_152336) - ZFHX3 (NM_006885) rearrangement event is a translocation in which AGBL1 exons 1-22 is fused to ZFHX3 exons 9-10. This translocation event occurs amid a more complex rearrangement involving ZFHX3 gene. Its functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0003998-T01-IM5	LOC729234-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) and LOC729234 translocation: t(6;2) (q25.3;q11.1)  (chr6:g.157521845::chr2:g.96603238) The ARID1B (NM_020732) rearrangement event is a translocation which results in the truncation of ARID1B exons 18-20. The functional significance is undetermined.
LOC729234	0	MSKCC-DMP	P-0003998-T01-IM5	LOC729234-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) and LOC729234 translocation: t(6;2) (q25.3;q11.1)  (chr6:g.157521845::chr2:g.96603238) The ARID1B (NM_020732) rearrangement event is a translocation which results in the truncation of ARID1B exons 18-20. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0000224-T01-IM3	WFDC3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Translocation t(21;20)(q13.12;q22.3)(g.42873074_g.44383097)
WFDC3	0	MSKCC-DMP	P-0000224-T01-IM3	WFDC3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Translocation t(21;20)(q13.12;q22.3)(g.42873074_g.44383097)
TMPRSS2	0	MSKCC-DMP	P-0000224-T01-IM3	RIPK4-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - RIPK4 (NM_012309) 297750bp Deletion: c.56-1254G_c.1632-813del
RIPK4	0	MSKCC-DMP	P-0000224-T01-IM3	RIPK4-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - RIPK4 (NM_012309) 297750bp Deletion: c.56-1254G_c.1632-813del
TACC3	0	MSKCC-DMP	P-0002351-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  and TACC3 (NM_006342) duplication (71843bp): FGFR3:c.2303_TACC3:c.1620dup Note: The FGFR3-TACC3 duplication is a rearrangement event which results in the fusion of FGFR3 exons 1 to 18 and TACC3 exons 7 to 16.
FGFR3	0	MSKCC-DMP	P-0002351-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  and TACC3 (NM_006342) duplication (71843bp): FGFR3:c.2303_TACC3:c.1620dup Note: The FGFR3-TACC3 duplication is a rearrangement event which results in the fusion of FGFR3 exons 1 to 18 and TACC3 exons 7 to 16.
ALK	0	MSKCC-DMP	P-0000557-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0000557-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0003450-T01-IM5	TMPRSS2-intragenic	yes	unknown		out of frame	null The TMPRSS2 (NM_001135099) rearrangement results in the intragenic duplication of exons 3 to 5. Its functional significance is undetermined
IRS2	0	MSKCC-DMP	P-0003556-T01-IM5	IRS2-intragenic	yes	unknown		unknown	None
RND1	0	MSKCC-DMP	P-0001323-T01-IM3	MLL2-RND1 fusion	yes	unknown		unknown	None
MLL2	0	MSKCC-DMP	P-0001323-T01-IM3	MLL2-RND1 fusion	yes	unknown		unknown	None
NFASC	0	MSKCC-DMP	P-0001902-T01-IM3	IKBKE-NFASC fusion	yes	unknown		in frame	IKBKE (NM_014002) - NFASC (NM_001005388) Duplication  : c.1183+3_c.2782+2783dup The IKBKE - NFASC duplication is a structural variant in which exons 1-9 of IKBKE is fused to exons 25-30 of NFASC. The functional significance of this structural variant is undetermined at this time
IKBKE	0	MSKCC-DMP	P-0001902-T01-IM3	IKBKE-NFASC fusion	yes	unknown		in frame	IKBKE (NM_014002) - NFASC (NM_001005388) Duplication  : c.1183+3_c.2782+2783dup The IKBKE - NFASC duplication is a structural variant in which exons 1-9 of IKBKE is fused to exons 25-30 of NFASC. The functional significance of this structural variant is undetermined at this time
DIS3	0	MSKCC-DMP	P-0002665-T01-IM3	PIBF1-DIS3 fusion	yes	unknown		unknown	null Note: DIS3-PIBF1 deletion is a rearrangement event in which DIS3 fuses to PIBF1 in an anti-sense manner and does not produce a meaningful fusion transcript, however, it could potentially disable DIS3 function.
PIBF1	0	MSKCC-DMP	P-0002665-T01-IM3	PIBF1-DIS3 fusion	yes	unknown		unknown	null Note: DIS3-PIBF1 deletion is a rearrangement event in which DIS3 fuses to PIBF1 in an anti-sense manner and does not produce a meaningful fusion transcript, however, it could potentially disable DIS3 function.
SKINTL	0	MSKCC-DMP	P-0005535-T01-IM5	CDKN2C-SKINTL fusion	yes	unknown		unknown	CDKN2C (NM_078626) rearrangement: c.-1684:CDKN2C_chr1:g.48479133del The CDKN2C (NM_078626) rearrangement is a deletion of the promoter region of CDKN2C. The functional significance is undetermined
CDKN2C	0	MSKCC-DMP	P-0005535-T01-IM5	CDKN2C-SKINTL fusion	yes	unknown		unknown	CDKN2C (NM_078626) rearrangement: c.-1684:CDKN2C_chr1:g.48479133del The CDKN2C (NM_078626) rearrangement is a deletion of the promoter region of CDKN2C. The functional significance is undetermined
RAD21	0	MSKCC-DMP	P-0005261-T01-IM5	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement: c.-508_c.274+21inv RAD21 (NM_006265) rearrangement results in the inversion of exons 1-3 of RAD21. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0006108-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.126+300:TMPRSS2_c.18+8285:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006108-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.126+300:TMPRSS2_c.18+8285:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006108-T01-IM5	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement : c.127-48_795-950dup Note: The TMPRSS2 (NM_001135099) rearrangement results in the duplication of TMPRSS2 exons 3-7. The event is predicted to result in an out of frame transcript.
GNA11	0	MSKCC-DMP	P-0004850-T01-IM5	TYK2-GNA11 fusion	yes	unknown		unknown	None
TYK2	0	MSKCC-DMP	P-0004850-T01-IM5	TYK2-GNA11 fusion	yes	unknown		unknown	None
DNMT1	0	MSKCC-DMP	P-0004850-T01-IM5	C19orf38-DNMT1 fusion	yes	unknown		unknown	DNMT1(NM_001379) Rearrangement :  c.4475:DNMT1_c.340+2519:C19orf38del Note:The DNMT1(NM_001379)  Rearrangement results in the deletion of exons 1 to 38 of DNMT1, the breakpoint is within exon 38.Its functional significance is undetermined.
C19orf38	0	MSKCC-DMP	P-0004850-T01-IM5	C19orf38-DNMT1 fusion	yes	unknown		unknown	DNMT1(NM_001379) Rearrangement :  c.4475:DNMT1_c.340+2519:C19orf38del Note:The DNMT1(NM_001379)  Rearrangement results in the deletion of exons 1 to 38 of DNMT1, the breakpoint is within exon 38.Its functional significance is undetermined.
ABCF3	0	MSKCC-DMP	P-0004850-T01-IM5	EIF4A2-ABCF3 fusion	yes	unknown		out of frame	EIF4A2(NM_001967) - ABCF3(NM_018358) Rearrangement : c.999+72:EIF4A2_c.1751-99:ABCF3dup Note:The EIF4A2(NM_001967) - ABCF3(NM_018358) Rearrangement results in the fusion of exons 1 to 9 of EIF4A2 and exons 19 to 21 of ABCF3.Its functional significance is undetermined.
EIF4A2	0	MSKCC-DMP	P-0004850-T01-IM5	EIF4A2-ABCF3 fusion	yes	unknown		out of frame	EIF4A2(NM_001967) - ABCF3(NM_018358) Rearrangement : c.999+72:EIF4A2_c.1751-99:ABCF3dup Note:The EIF4A2(NM_001967) - ABCF3(NM_018358) Rearrangement results in the fusion of exons 1 to 9 of EIF4A2 and exons 19 to 21 of ABCF3.Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0006370-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1490-2147:EML4_c.3172+203:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0006370-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1490-2147:EML4_c.3172+203:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.
KEAP1	0	MSKCC-DMP	P-0006730-T01-IM5	ZNF599-KEAP1 fusion	yes	unknown		unknown	KEAP1(NM_203500) Rearrangement: c.513_chr19:35248755del Note: The KEAP1(NM_203500) Rearrangement results in the deletion of exons 1 and 2 of KEAP1.The breakpoint is within exon2 .Its functional significance is undetermined.
ZNF599	0	MSKCC-DMP	P-0006730-T01-IM5	ZNF599-KEAP1 fusion	yes	unknown		unknown	KEAP1(NM_203500) Rearrangement: c.513_chr19:35248755del Note: The KEAP1(NM_203500) Rearrangement results in the deletion of exons 1 and 2 of KEAP1.The breakpoint is within exon2 .Its functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0009639-T01-IM5	CDKN2BAS-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+108_chr9:g.22170544inv Note: The CDKN2B (NM_004936) rearrangement is an inversion of the CDKN2B promoter region, transcription start site, and exon 1. The functional significance is undetermined.
CDKN2BAS	0	MSKCC-DMP	P-0009639-T01-IM5	CDKN2BAS-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+108_chr9:g.22170544inv Note: The CDKN2B (NM_004936) rearrangement is an inversion of the CDKN2B promoter region, transcription start site, and exon 1. The functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0004737-T01-IM5	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) Fusion (ETV6 exons 1 to 4 fused to NTRK3 exons 13 to 20) : t(12;15)(p13.2;q25.3)(chr12:g.12006809::chr15:g.88632786)
ETV6	0	MSKCC-DMP	P-0004737-T01-IM5	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) Fusion (ETV6 exons 1 to 4 fused to NTRK3 exons 13 to 20) : t(12;15)(p13.2;q25.3)(chr12:g.12006809::chr15:g.88632786)
BAGE2	0	MSKCC-DMP	P-0006656-T01-IM5	MGA-BAGE2 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement : t(15;21)(q15.1;p11.1)(chr15:g.41991303::chr21:g.11034318) The MGA (NM_001164273) rearrangement is a translocation which may result in the truncation of MGA. One of the breakpoints is within exon5 of MGA. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0006656-T01-IM5	MGA-BAGE2 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement : t(15;21)(q15.1;p11.1)(chr15:g.41991303::chr21:g.11034318) The MGA (NM_001164273) rearrangement is a translocation which may result in the truncation of MGA. One of the breakpoints is within exon5 of MGA. The functional significance is undetermined.
LOC442459	0	MSKCC-DMP	P-0008427-T01-IM5	BTK-LOC442459 fusion	yes	unknown		unknown	BTK (NM_000061) Rearrangement : chr10:g.97658964_c.1746:BTKinv Note: The BTK (NM_000061) Rearrangement results in the inversion of exons 17 to 19 of BTK .The breakpoint in BTK is within exon 17. Its functional significance is undetermined.
BTK	0	MSKCC-DMP	P-0008427-T01-IM5	BTK-LOC442459 fusion	yes	unknown		unknown	BTK (NM_000061) Rearrangement : chr10:g.97658964_c.1746:BTKinv Note: The BTK (NM_000061) Rearrangement results in the inversion of exons 17 to 19 of BTK .The breakpoint in BTK is within exon 17. Its functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0004893-T01-IM5	RUNX1-intragenic	yes	unknown		unknown	RUNX1(NM_001754) rearrangement: c.362_c.509-5397dup. The RUNX1(NM_001754) rearrangement is an intragenic duplication of exon 5. The breakpoint is within exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007359-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 1 to 10) : c.56-3620:TMPRSS2_c.40-55852:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007359-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 1 to 10) : c.56-3620:TMPRSS2_c.40-55852:ERGdel
MLL	0	MSKCC-DMP	P-0009726-T01-IM5	MLL-intragenic	yes	unknown		unknown	MLL (NM_001197104) rearrangement : c.7225_10350del Note: The MLL (NM_001197104) rearrangement event results in a large deletion within MLL exon27.
KIF5B	0	MSKCC-DMP	P-0008764-T01-IM5	ALK-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - ALK (NM_004304) fusion (KIF5B exons 1-24 fused with ALK exons 19-29) : t(2;10)(p23.2;p11.22)(chr2:g.29448327::chr10:g.32305750) Note: The KIF5B (NM_004521) - ALK (NM_004304) fusion is a reciprocal event and one of the breakpoints is within ALK exon19. The reported fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0008764-T01-IM5	ALK-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - ALK (NM_004304) fusion (KIF5B exons 1-24 fused with ALK exons 19-29) : t(2;10)(p23.2;p11.22)(chr2:g.29448327::chr10:g.32305750) Note: The KIF5B (NM_004521) - ALK (NM_004304) fusion is a reciprocal event and one of the breakpoints is within ALK exon19. The reported fusion includes the kinase domain of ALK.
NF1	0	MSKCC-DMP	P-0008161-T02-IM5	NF1-intragenic	yes	unknown		in frame	NF1(NM_001042492) Rearrangement :  c.655-91_889-8627dup Note: The NF1(NM_001042492) Rearrangement results in the intragenic duplication of exons 7 and 8 of NF1.Its functional signficance is undetermined.
ERG	0	MSKCC-DMP	P-0008206-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-385:TMPRSS2_c.39+41500:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008206-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-385:TMPRSS2_c.39+41500:ERGdel
KIF5B	0	MSKCC-DMP	P-0008101-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-18 fused with RET exons 12-20) : c.2095-38:KIF5B_c.2136+271:RETinv Note: The KIF5B (NM_004521) - RET (NM_020975) fusion is an inversion which is predicted to be in-frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0008101-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-18 fused with RET exons 12-20) : c.2095-38:KIF5B_c.2136+271:RETinv Note: The KIF5B (NM_004521) - RET (NM_020975) fusion is an inversion which is predicted to be in-frame and includes the kinase domain of RET.
CDK12	0	MSKCC-DMP	P-0009835-T01-IM5	RECQL4-CDK12 fusion	yes	unknown		out of frame	CDK12 (NM_016507) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q12)(chr8:g.145739493::chr17:g.37656296) Note: The CDK12 (NM_016507) - RECQL4 (NM_004260) rearrangement is a translocation that results in the fusion of CDK12 exons 1-5 with RECQL4 exons 12-22. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0009835-T01-IM5	RECQL4-CDK12 fusion	yes	unknown		out of frame	CDK12 (NM_016507) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q12)(chr8:g.145739493::chr17:g.37656296) Note: The CDK12 (NM_016507) - RECQL4 (NM_004260) rearrangement is a translocation that results in the fusion of CDK12 exons 1-5 with RECQL4 exons 12-22. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0009835-T01-IM5	RIPK4-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - RIPK4 (NM_020639) rearrangement: c.56-289:TMPRSS2_c.474+2297:RIPK4dup Note: The TMPRSS2 (NM_001135099) - RIPK4 (NM_020639) rearrangement is a duplication that results in the fusion of TMPRSS2 exon 1 with RIPK4 exons 3-8. The functional significance is undetermined.
RIPK4	0	MSKCC-DMP	P-0009835-T01-IM5	RIPK4-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - RIPK4 (NM_020639) rearrangement: c.56-289:TMPRSS2_c.474+2297:RIPK4dup Note: The TMPRSS2 (NM_001135099) - RIPK4 (NM_020639) rearrangement is a duplication that results in the fusion of TMPRSS2 exon 1 with RIPK4 exons 3-8. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0009353-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.667+2407:EML4_c.3173-71:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0009353-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29) : c.667+2407:EML4_c.3173-71:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.
ERG	0	MSKCC-DMP	P-0007416-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and fused with ERG exons 2 to 10) : c.55+4057:TMPRSS2_c.-11:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007416-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exons 1 and fused with ERG exons 2 to 10) : c.55+4057:TMPRSS2_c.-11:ERGdel
IDH1	0	MSKCC-DMP	P-0006310-T01-IM5	IDH1-intragenic	yes	unknown		unknown	IDH1 (NM_005896) Rearrangement :  c.454_521-489dup Note: The IDH1 (NM_005896) Rearrangement results in the intragenic duplication of exon 5. The breakpoint is within exon5. Its functional significance is undetermined.
HCK	0	MSKCC-DMP	P-0007808-T01-IM5	DNMT3B-HCK fusion	yes	unknown		unknown	DNMT3B (NM_006892) Rearrangement : chr20:g.30634953_c.433-68:DNMT3Binv Note: The DNMT3B (NM_006892) Rearrangement results in the inversion of exons 1 to 6 of DNMT3B.Its functional significance is undetremined.
DNMT3B	0	MSKCC-DMP	P-0007808-T01-IM5	DNMT3B-HCK fusion	yes	unknown		unknown	DNMT3B (NM_006892) Rearrangement : chr20:g.30634953_c.433-68:DNMT3Binv Note: The DNMT3B (NM_006892) Rearrangement results in the inversion of exons 1 to 6 of DNMT3B.Its functional significance is undetremined.
DAZAP2	0	MSKCC-DMP	P-0006640-T01-IM5	ERBB3-DAZAP2 fusion	yes	unknown		unknown	DAZAP2 (NM_001136266) - ERBB3 (NM_001982) rearrangement : c.-1685: DAZAP2_c.2899:ERBB3dup Note: The DAZAP2 (NM_001136266) - ERBB3 (NM_001982) rearrangement event is a deletion which results in the fusion of DAZAP2 promoter with ERBB3 exons 24-28. One of the breakpoints is within ERBB3 exon24.
ERBB3	0	MSKCC-DMP	P-0006640-T01-IM5	ERBB3-DAZAP2 fusion	yes	unknown		unknown	DAZAP2 (NM_001136266) - ERBB3 (NM_001982) rearrangement : c.-1685: DAZAP2_c.2899:ERBB3dup Note: The DAZAP2 (NM_001136266) - ERBB3 (NM_001982) rearrangement event is a deletion which results in the fusion of DAZAP2 promoter with ERBB3 exons 24-28. One of the breakpoints is within ERBB3 exon24.
MYOF	0	MSKCC-DMP	P-0006409-T01-IM5	FGFR2-MYOF fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement : chr10:g.95246173_c.2301+983:FGFR2inv Note: The FGFR2 (NM_000141) rearrangement event results in the inversion of FRGR2 exon18. The event involves the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0006409-T01-IM5	FGFR2-MYOF fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement : chr10:g.95246173_c.2301+983:FGFR2inv Note: The FGFR2 (NM_000141) rearrangement event results in the inversion of FRGR2 exon18. The event involves the kinase domain of FGFR2.
BICC1	0	MSKCC-DMP	P-0005538-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) reciprocal fusion (FGFR2 exons 1-17 with BICC1 exons 16-21): c.2301+459:FGFR2_c.2182-276:BICC1inv  The FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement is a reciprocal inversion which results in the in frame fusion of  FGFR2 exons 1-17, including the kinase domain, with BICC1 exons 16-21. (PMID: 24122810)
FGFR2	0	MSKCC-DMP	P-0005538-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) reciprocal fusion (FGFR2 exons 1-17 with BICC1 exons 16-21): c.2301+459:FGFR2_c.2182-276:BICC1inv  The FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement is a reciprocal inversion which results in the in frame fusion of  FGFR2 exons 1-17, including the kinase domain, with BICC1 exons 16-21. (PMID: 24122810)
TTC28	0	MSKCC-DMP	P-0006826-T01-IM5	FBXW7-TTC28 fusion	yes	unknown		out of frame	TTC28 (NM_001145418) - FBXW7 (NM_033632) rearrangement : t(4;22)(q31.3;q12.1)(chr4:g.153244355::chr22:g.29066046) Note: The TTC28 (NM_001145418) - FBXW7 (NM_033632) rearrangement event is a translocation which results in the fusion of TTC28 exon1 with FBXW7 exon12. The resulting transcript is predicated to be out of frame.
FBXW7	0	MSKCC-DMP	P-0006826-T01-IM5	FBXW7-TTC28 fusion	yes	unknown		out of frame	TTC28 (NM_001145418) - FBXW7 (NM_033632) rearrangement : t(4;22)(q31.3;q12.1)(chr4:g.153244355::chr22:g.29066046) Note: The TTC28 (NM_001145418) - FBXW7 (NM_033632) rearrangement event is a translocation which results in the fusion of TTC28 exon1 with FBXW7 exon12. The resulting transcript is predicated to be out of frame.
ERG	0	MSKCC-DMP	P-0006837-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 1-10): c.55+3696:TMPRSS2_c.-3317:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006837-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 1-10): c.55+3696:TMPRSS2_c.-3317:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006837-T02-IM5	NLGN1-TMPRSS2 fusion	yes	unknown		in frame	NLGN1 (NM_014932) - TMPRSS2 (NM_001135099) rearrangement: t(3;21)(q26.31;q22.3)(chr3:g.173935988::chr21:g.42872495) Note: The NLGN1 -TMPRSS2 rearrangement is a translocation that results in an in frame fusion of NLGN1 exons 1-4 with TMPRSS2 exons 2-14. The functional significance is undetermined.
NLGN1	0	MSKCC-DMP	P-0006837-T02-IM5	NLGN1-TMPRSS2 fusion	yes	unknown		in frame	NLGN1 (NM_014932) - TMPRSS2 (NM_001135099) rearrangement: t(3;21)(q26.31;q22.3)(chr3:g.173935988::chr21:g.42872495) Note: The NLGN1 -TMPRSS2 rearrangement is a translocation that results in an in frame fusion of NLGN1 exons 1-4 with TMPRSS2 exons 2-14. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005463-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.127-1566:TMPRSS2 _c.40-59106:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005463-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.127-1566:TMPRSS2 _c.40-59106:ERGdel
ROS1	0	MSKCC-DMP	P-0006047-T02-IM5	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 with ROS1 exons 34-43): c.1091-355:EZR_c.5557+146:ROS1del Note: The EZR (NM_003379) - ROS1 (NM_002944) fusion is predicted to be in frame and includes the kinase domain of ROS1
EZR	0	MSKCC-DMP	P-0006047-T02-IM5	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 with ROS1 exons 34-43): c.1091-355:EZR_c.5557+146:ROS1del Note: The EZR (NM_003379) - ROS1 (NM_002944) fusion is predicted to be in frame and includes the kinase domain of ROS1
NRBF2	0	MSKCC-DMP	P-0006328-T01-IM5	FGFR2-NRBF2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NRBF2 (NM_030759) rearrangement: c.2302-1710:FGFR2_c.157-364:NRBF2inv The FGFR2 (NM_000141) - NRBF2 (NM_030759) rearrangement is an inversion (58328338 bp) which results in the in frame fusion of exons 1-17 of FGFR2 with exon 4 of NRBF2, including the kinase domain of FGFR2. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0006328-T01-IM5	FGFR2-NRBF2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NRBF2 (NM_030759) rearrangement: c.2302-1710:FGFR2_c.157-364:NRBF2inv The FGFR2 (NM_000141) - NRBF2 (NM_030759) rearrangement is an inversion (58328338 bp) which results in the in frame fusion of exons 1-17 of FGFR2 with exon 4 of NRBF2, including the kinase domain of FGFR2. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0001047-T02-IM5	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570)  rearrangement : c.2382-7747_c.3159:PIK3C2Gdel Note: The PIK3C2G (NM_004570)  rearrangement event results in the intragenic deletion of PIK3C2G exons 17-23.. The functional significance is undetermined. One of the breakpoints is within PIK3C2G exon 23
TERT	0	MSKCC-DMP	P-0001047-T02-IM5	CDH6-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.443:TERT_chr5:g.29735590inv Note: TERT (NM_198253) rearrangement event results in the inversion of TERT exon 2.  The breakpoint on TERT is within exon 2. The functional significance of this is undetermined.
CDH6	0	MSKCC-DMP	P-0001047-T02-IM5	CDH6-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.443:TERT_chr5:g.29735590inv Note: TERT (NM_198253) rearrangement event results in the inversion of TERT exon 2.  The breakpoint on TERT is within exon 2. The functional significance of this is undetermined.
FLJ33360	0	MSKCC-DMP	P-0001047-T02-IM5	IL7R-FLJ33360 fusion	yes	unknown		unknown	FLJ33360  (NM_001001702) - IL7R (NM_002185) rearrangement : chr5:g.29735590_c.773:IL7Rinv Note: FLJ33360  (NM_001001702) - IL7R (NM_002185) rearrangement results in the inversion of  IL7R exon 1-6. The breakpoint is within IL7R exon 6. The functional significance is undetermined.
IL7R	0	MSKCC-DMP	P-0001047-T02-IM5	IL7R-FLJ33360 fusion	yes	unknown		unknown	FLJ33360  (NM_001001702) - IL7R (NM_002185) rearrangement : chr5:g.29735590_c.773:IL7Rinv Note: FLJ33360  (NM_001001702) - IL7R (NM_002185) rearrangement results in the inversion of  IL7R exon 1-6. The breakpoint is within IL7R exon 6. The functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0008215-T01-IM5	RPS6KA4-intragenic	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement: c.907-82_c.1072-795inv RPS6KA4 (NM_003942) rearrangement results in an inversion of exon 9 including the protein kinase C-terminal domain. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0007032-T01-IM5	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement : c.2706-5309_3057inv Note: The ARID1B (NM_020732) rearrangement results in the intragenic inversion of exons 1o to 12. One of the breakpoints is within exon12. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0007547-T01-IM5	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement :  c.56-1201_1282+555inv Note: The TMPRSS2 (NM_001135099)  Rearrangement  results in the inversion of exons 2 to 11 of TMPRSS2. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0004808-T01-IM5	BET1-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;7)(q26.13;q21.3)(chr10:g.123242018::chr7:g.93694043)  The FGFR2 (NM_000141) rearrangement is a translocation which results in the truncation of FGFR2  exons 17-18. The functional significance is undetermined.
BET1	0	MSKCC-DMP	P-0004808-T01-IM5	BET1-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;7)(q26.13;q21.3)(chr10:g.123242018::chr7:g.93694043)  The FGFR2 (NM_000141) rearrangement is a translocation which results in the truncation of FGFR2  exons 17-18. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0005758-T01-IM5	MAFG-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) - MAFG (NM_032711) rearrangement : c.896:PPM1D_c.-1017:MAFGinv Note: The PPM1D (NM_003620) - MAFG (NM_032711) rearrangement event results in the fusion of PPM1B exons 1-4 with MAFG exons 1-2. One of the breakpoints is within PPM1D exon4.
MAFG	0	MSKCC-DMP	P-0005758-T01-IM5	MAFG-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) - MAFG (NM_032711) rearrangement : c.896:PPM1D_c.-1017:MAFGinv Note: The PPM1D (NM_003620) - MAFG (NM_032711) rearrangement event results in the fusion of PPM1B exons 1-4 with MAFG exons 1-2. One of the breakpoints is within PPM1D exon4.
CDKN2A	0	MSKCC-DMP	P-0009271-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement :  c.75_chr9:g.22179390inv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement  results in the inversion of exons 1-3  CDKN2Ap16INK4A. The breakpoint is within exon1. Its functional significance  is undetermined.
CDKN2BAS	0	MSKCC-DMP	P-0009271-T01-IM5	CDKN2BAS-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement :  c.75_chr9:g.22179390inv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement  results in the inversion of exons 1-3  CDKN2Ap16INK4A. The breakpoint is within exon1. Its functional significance  is undetermined.
ERG	0	MSKCC-DMP	P-0008542-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1 fused with ERG exons 2 -10 ) : c.55+4310:TMPRSS2_c.19-7094:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008542-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1 fused with ERG exons 2 -10 ) : c.55+4310:TMPRSS2_c.19-7094:ERGdel
RNFT1	0	MSKCC-DMP	P-0006622-T01-IM5	PPM1D-RNFT1 fusion	yes	unknown		unknown	RNFT1 (NM_016125) - PPM1D (NM_003620) rearrangement : c.592-123:RNFT1_c.94:PPM1Dinv Note: The RNFT1 (NM_016125) - PPM1D (NM_003620) rearrangement event is a deletion which results in the fusion of RNFT1 exons 1-4 within PPM1D exons 1-6. One of the breakpoints is within PPM1D exon1.
PPM1D	0	MSKCC-DMP	P-0006622-T01-IM5	PPM1D-RNFT1 fusion	yes	unknown		unknown	RNFT1 (NM_016125) - PPM1D (NM_003620) rearrangement : c.592-123:RNFT1_c.94:PPM1Dinv Note: The RNFT1 (NM_016125) - PPM1D (NM_003620) rearrangement event is a deletion which results in the fusion of RNFT1 exons 1-4 within PPM1D exons 1-6. One of the breakpoints is within PPM1D exon1.
ERG	0	MSKCC-DMP	P-0005422-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2(NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 ERG exon4 ) :  c.55+4168:TMPRSS2_c.40-60922:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005422-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2(NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 ERG exon4 ) :  c.55+4168:TMPRSS2_c.40-60922:ERGdel
RPTOR	0	MSKCC-DMP	P-0009434-T01-IM5	ONECUT1-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) Rearrangement t(15;17)(15q21.3;17q25.3)(15:g.53194795::chr17:g.78831704) RPTOR (NM_020761) rearrangement is results in translocation of genomic region after exon 13 of RPTOR and a genomic region on chromosome 15 that could potentially truncate RPTOR exons 14-34. Its functional significance is undetermined.
ONECUT1	0	MSKCC-DMP	P-0009434-T01-IM5	ONECUT1-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) Rearrangement t(15;17)(15q21.3;17q25.3)(15:g.53194795::chr17:g.78831704) RPTOR (NM_020761) rearrangement is results in translocation of genomic region after exon 13 of RPTOR and a genomic region on chromosome 15 that could potentially truncate RPTOR exons 14-34. Its functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0007793-T01-IM5	IQCH-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - IQCH (NM_001031715) Rearrangement : c.1175:SMAD3_c.1188:IQCHdel Note: The SMAD3 (NM_005902) - IQCH (NM_001031715) Rearrangement results in the fusion of exons 1 to 9 of SMAD3 with exon 9 of ICQH. One of the breakpoints is within exon 9 of SMAD3.Its functional significance is undetermined.
IQCH	0	MSKCC-DMP	P-0007793-T01-IM5	IQCH-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - IQCH (NM_001031715) Rearrangement : c.1175:SMAD3_c.1188:IQCHdel Note: The SMAD3 (NM_005902) - IQCH (NM_001031715) Rearrangement results in the fusion of exons 1 to 9 of SMAD3 with exon 9 of ICQH. One of the breakpoints is within exon 9 of SMAD3.Its functional significance is undetermined.
FCER1G	0	MSKCC-DMP	P-0007661-T01-IM5	SDHC-FCER1G fusion	yes	unknown		unknown	FCER1G (NM_004106) - SDHC (NM_003001) rearrangement  c.49+1219:FCER1G_c.21:SDHCdel Note: The FCER1G (NM_004106) - SDHC (NM_003001) rearrangement event is a deletion which results in the fusion of FCER1G exon1 with SDHC exons 2-6. One of the breakpoints is within SDHC exon2.
SDHC	0	MSKCC-DMP	P-0007661-T01-IM5	SDHC-FCER1G fusion	yes	unknown		unknown	FCER1G (NM_004106) - SDHC (NM_003001) rearrangement  c.49+1219:FCER1G_c.21:SDHCdel Note: The FCER1G (NM_004106) - SDHC (NM_003001) rearrangement event is a deletion which results in the fusion of FCER1G exon1 with SDHC exons 2-6. One of the breakpoints is within SDHC exon2.
ETV6	0	MSKCC-DMP	P-0007661-T01-IM5	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement : chr12:g.11779457_c.1010-497:ETV6del Note: The ETV6 (NM_001987) rearrangement event results in the deletion of ETV6 exons 1-5.
FLRT2	0	MSKCC-DMP	P-0006507-T01-IM5	DICER1-FLRT2 fusion	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: chr14:g.87018577_c.3160:DICER1del.  The DICER1 (NM_030621) rearrangement is a deletion of exons 21-28 of DICER1. The functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0006507-T01-IM5	DICER1-FLRT2 fusion	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: chr14:g.87018577_c.3160:DICER1del.  The DICER1 (NM_030621) rearrangement is a deletion of exons 21-28 of DICER1. The functional significance is undetermined.
MCF2L2	0	MSKCC-DMP	P-0006896-T01-IM5	TP63-MCF2L2 fusion	yes	unknown		in frame	TP63 (NM_003722) - MCF2L2 (NM_015078) rearrangement: c.766+112:TP63_c.77-18778:MCF2L2inv The TP63 (NM_003722) - MCF2L2 (NM_015078) rearrangement is an inversion which leads to the fusion of TP63 exons 1-5 with MCF2L2 exons 2-30 . The functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0006896-T01-IM5	TP63-MCF2L2 fusion	yes	unknown		in frame	TP63 (NM_003722) - MCF2L2 (NM_015078) rearrangement: c.766+112:TP63_c.77-18778:MCF2L2inv The TP63 (NM_003722) - MCF2L2 (NM_015078) rearrangement is an inversion which leads to the fusion of TP63 exons 1-5 with MCF2L2 exons 2-30 . The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0006895-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077)  rearrangement: c.150+436del_c.263del CDKN2Ap14ARF (NM_058195)  rearrangement: c.194-3034_c.306del The CDKN2Ap16INK4A (NM_000077)  rearrangement  is an intragenic deletion of exon 2.  One of the breakpoints is within exon 2.  The CDKN2Ap14ARF (NM_058195)  rearrangement  is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.
FANCA	0	MSKCC-DMP	P-0008534-T01-IM5	CLMN-FANCA fusion	yes	unknown		out of frame	CLMN (NM_024734) - FANCA (NM_000135) rearrangement : t(14;16)(q32.13;q24.3)(chr14:g.95776664::chr16:g.89849554)
CLMN	0	MSKCC-DMP	P-0008534-T01-IM5	CLMN-FANCA fusion	yes	unknown		out of frame	CLMN (NM_024734) - FANCA (NM_000135) rearrangement : t(14;16)(q32.13;q24.3)(chr14:g.95776664::chr16:g.89849554)
NF1	0	MSKCC-DMP	P-0006916-T01-IM5	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement : c.888+6204_c.1260+16NF1dup Note: The NF1 (NM_001042492) rearrangement is a in-frame duplication of exon 9-11 of NF1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005864-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11):  c.56-4819:TMPRSS2_c.19-12436:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005864-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11):  c.56-4819:TMPRSS2_c.19-12436:ERGdel
ATP1B2	0	MSKCC-DMP	P-0008178-T01-IM5	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) - ATP1B2 (NM_001678) rearrangement: c.594:TP53_c.112+727:ATP1B2inv The TP53 (NM_000546) - ATP1B2 (NM_001678) rearrangement is an inversion which leads to the fusion of TP53 exons 1-6 with ATP1B2 exons 2-7.  One of the breakpoints is within exon 6 of TP53. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0008178-T01-IM5	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) - ATP1B2 (NM_001678) rearrangement: c.594:TP53_c.112+727:ATP1B2inv The TP53 (NM_000546) - ATP1B2 (NM_001678) rearrangement is an inversion which leads to the fusion of TP53 exons 1-6 with ATP1B2 exons 2-7.  One of the breakpoints is within exon 6 of TP53. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0009590-T01-IM5	NUP107-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.2181_chr12:g.69098856inv Note: The ARID2 (NM_152641) rearrangement is an inversion which includes exons 15-21 of ARID2. The functional significance  is undetermined.
NUP107	0	MSKCC-DMP	P-0009590-T01-IM5	NUP107-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.2181_chr12:g.69098856inv Note: The ARID2 (NM_152641) rearrangement is an inversion which includes exons 15-21 of ARID2. The functional significance  is undetermined.
ERG	0	MSKCC-DMP	P-0009361-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-11): c.127-1387:TMPRSS2_c.40-63140:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009361-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 4-11): c.127-1387:TMPRSS2_c.40-63140:ERGdel
BAP1	0	MSKCC-DMP	P-0008036-T01-IM5	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.-677_c.37+16del The BAP1 (NM_004656) rearrangement is a deletion of exon 1 of BAP1. The functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0008036-T01-IM5	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.-677_c.37+16del The BAP1 (NM_004656) rearrangement is a deletion of exon 1 of BAP1. The functional significance is undetermined.
MRPS15	0	MSKCC-DMP	P-0008551-T01-IM5	CSF3R-MRPS15 fusion	yes	unknown		unknown	CSF3R (NM_000760) - MRPS15 (NM_031280) rearrangement: c.630:CSF3R_c.175+21:MRPS15del The CSF3R (NM_000760) - MRPS15 (NM_031280) rearrangement is a deletion which results in the fusion of CSF3R exons 1-6 of  with MRPS1 exons 3-8. One of the breakpoints is within exon 6 of CSF3R. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0008551-T01-IM5	CSF3R-MRPS15 fusion	yes	unknown		unknown	CSF3R (NM_000760) - MRPS15 (NM_031280) rearrangement: c.630:CSF3R_c.175+21:MRPS15del The CSF3R (NM_000760) - MRPS15 (NM_031280) rearrangement is a deletion which results in the fusion of CSF3R exons 1-6 of  with MRPS1 exons 3-8. One of the breakpoints is within exon 6 of CSF3R. The functional significance is undetermined.
LATS2	0	MSKCC-DMP	P-0007556-T01-IM5	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) rearrangement : c.1006_1900-1285inv Note: The LATS2 (NM_014572) rearrangement events results in the inversion of LATS2 exon4. One of the breakpoints is within LATS2 exon4.
FGFR2	0	MSKCC-DMP	P-0006043-T01-IM5	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-801_chr10:g.123170710inv The FGFR2 (NM_000141) rearrangement is an intragenic inversion of exon 18. The functional significance is undetermined.
BTC	0	MSKCC-DMP	P-0000690-T03-IM5	FAT1-BTC fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.75641997_c.4883:FAT1inv Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 10-27. One of the breakpoints is within exon10.
FAT1	0	MSKCC-DMP	P-0000690-T03-IM5	FAT1-BTC fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.75641997_c.4883:FAT1inv Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 10-27. One of the breakpoints is within exon10.
KIAA1267	0	MSKCC-DMP	P-0005903-T01-IM5	BRIP1-KIAA1267 fusion	yes	unknown		unknown	BRIP1 (NM_032043)  rearrangement: c.1340+36:BRIP1_chr17:g.44165620inv.  The BRIP1 (NM_032043)  rearrangement is an inversion (15710805 bp) which may result in the truncation of BRIP1 exons 10-20. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0005903-T01-IM5	BRIP1-KIAA1267 fusion	yes	unknown		unknown	BRIP1 (NM_032043)  rearrangement: c.1340+36:BRIP1_chr17:g.44165620inv.  The BRIP1 (NM_032043)  rearrangement is an inversion (15710805 bp) which may result in the truncation of BRIP1 exons 10-20. The functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0008757-T01-IM5	BCAS1-NCOA3 fusion	yes	unknown		unknown	BCAS1 (NM_003657) - NCOA3 (NM_181659) rearrangement : c.142+720:BCAS1_c.1307:NCOA3inv Note: The BCAS1 (NM_003657) - NCOA3 (NM_181659) rearrangement event is a inversion which results in the fusion of BCAS1 exons 1-3 with NCOA3 exons 11-23. One of the breakpoints is within NCOA3 exon11.
BCAS1	0	MSKCC-DMP	P-0008757-T01-IM5	BCAS1-NCOA3 fusion	yes	unknown		unknown	BCAS1 (NM_003657) - NCOA3 (NM_181659) rearrangement : c.142+720:BCAS1_c.1307:NCOA3inv Note: The BCAS1 (NM_003657) - NCOA3 (NM_181659) rearrangement event is a inversion which results in the fusion of BCAS1 exons 1-3 with NCOA3 exons 11-23. One of the breakpoints is within NCOA3 exon11.
TGFBR2	0	MSKCC-DMP	P-0007287-T01-IM5	GADL1-TGFBR2 fusion	yes	unknown		unknown	GALD1 (NM_207359) - TGFBR2 (NM_001024847) rearrangement: c.1392+20317:GALD1_c.7:TGFBR2inv The GALD1 ( NM_207359) - TGFBR2 (NM_001024847) rearrangement is a reciprocal inversion that results in the fusion of exons 1-14 of GADL1 with exons 1-8 of TGFBR2, including kinase domain of TGFBR2. The functional significance is undetermined.
GADL1	0	MSKCC-DMP	P-0007287-T01-IM5	GADL1-TGFBR2 fusion	yes	unknown		unknown	GALD1 (NM_207359) - TGFBR2 (NM_001024847) rearrangement: c.1392+20317:GALD1_c.7:TGFBR2inv The GALD1 ( NM_207359) - TGFBR2 (NM_001024847) rearrangement is a reciprocal inversion that results in the fusion of exons 1-14 of GADL1 with exons 1-8 of TGFBR2, including kinase domain of TGFBR2. The functional significance is undetermined.
C15orf57	0	MSKCC-DMP	P-0001357-T02-IM5	IGF1R-C15orf57 fusion	yes	unknown		unknown	IGF1R (NM_000875) - C15orf57 (NM_001080792) Rearrangement :  c.682:IGF1R_c.245-1296:C15orf57 Note: The IGF1R (NM_000875) - C15orf57 (NM_052849) Rearrangement results in the fusion of exons 1 to 3 of IGF1R with exons 3 to 4 of C15orf57 . The breakpoint in APC is within exon3. Its functional significance is  undetermined.
IGF1R	0	MSKCC-DMP	P-0001357-T02-IM5	IGF1R-C15orf57 fusion	yes	unknown		unknown	IGF1R (NM_000875) - C15orf57 (NM_001080792) Rearrangement :  c.682:IGF1R_c.245-1296:C15orf57 Note: The IGF1R (NM_000875) - C15orf57 (NM_052849) Rearrangement results in the fusion of exons 1 to 3 of IGF1R with exons 3 to 4 of C15orf57 . The breakpoint in APC is within exon3. Its functional significance is  undetermined.
PBRM1	0	MSKCC-DMP	P-0008267-T01-IM5	CACNA1D-PBRM1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.104:PBRM1_chr3.g.53498367del Note: PBRM1 (NM_018313) rearrangement results in the deletion of exons 1 to 2. The breakpoint is within exon2. Its functional significance is undetermined.
CACNA1D	0	MSKCC-DMP	P-0008267-T01-IM5	CACNA1D-PBRM1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.104:PBRM1_chr3.g.53498367del Note: PBRM1 (NM_018313) rearrangement results in the deletion of exons 1 to 2. The breakpoint is within exon2. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0004779-T01-IM5	RB1-intragenic	yes	unknown		unknown	RB1(NM_000321) Rearrangement :  c.1696-3779_1961-25inv Note: The RB1(NM_000321) Rearrangement results in the intragenic inversion of exons 18 and 19 of RB1. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0009958-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.333_*101+1244del CDKN2Ap16INK4A (NM_000077) rearrangement : c.290_457+1244del Note: The CDKN2Ap14ARF rearrangement event results in the deletion of CDKN2Ap14ARF exon2. One of the breakpoints is within CDKN2Ap14ARF exon2. Note: The CDKN2Ap16INK4A rearrangement event results in the deletion of CDKN2Ap16INK4A exon 2. One of the breakpoints is within CDKN2Ap16INK4A exon2.
ERG	0	MSKCC-DMP	P-0009787-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2(NM_001135099)  -ERG ()Fusion (TMPRS22 exon1 fused with ERG exons  4-10) :  c.55+4268:TMPRSS2_c.40-58604:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009787-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2(NM_001135099)  -ERG ()Fusion (TMPRS22 exon1 fused with ERG exons  4-10) :  c.55+4268:TMPRSS2_c.40-58604:ERGdel
ROS1	0	MSKCC-DMP	P-0008134-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD274 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(5q32;6q22.1)(chr5:g.149783121::chr6:g.117646080  ) Note:CD74 (NM_001025159) - ROS1 (NM_002944) fusion includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0008134-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD274 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(5q32;6q22.1)(chr5:g.149783121::chr6:g.117646080  ) Note:CD74 (NM_001025159) - ROS1 (NM_002944) fusion includes the kinase domain of ROS1.
NF1	0	MSKCC-DMP	P-0007832-T01-IM5	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.-1684_c.17del Note: The NF1 (NM_001042492) rearrangement is a deletion of NF1 exon 1. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0008978-T01-IM5	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.-622_c.4411dup Note: The APC (NM_000038) rearrangement results in the duplication of APC exons 2-16. One of the breakpoints is within exon 16. The functional significance of this rearrangement is undetermined.
SH3BGRL	0	MSKCC-DMP	P-0009105-T01-IM5	NF1-SH3BGRL fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(17;X)(q11.2;q22.1)(chr17:g.29562678::chrX:g.81529667) Note: The NF1 (NM_001042492) rearrangement results in the deletion of NF1 exons 28-58. One of the breakpoints is within NF1 exon 28. The functional significance of this rearrangement is undetermined.
NF1	0	MSKCC-DMP	P-0009105-T01-IM5	NF1-SH3BGRL fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(17;X)(q11.2;q22.1)(chr17:g.29562678::chrX:g.81529667) Note: The NF1 (NM_001042492) rearrangement results in the deletion of NF1 exons 28-58. One of the breakpoints is within NF1 exon 28. The functional significance of this rearrangement is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0002123-T02-IM5	ACPP-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ACPP (NM_001134194) rearrangement: t(3;21)(q22.1;q22.3)(chr3:g.132053847::chr21:g.42868047) Note: The TMPRSS2 (NM_001135099) - ACPP (NM_001134194) rearrangement is a translocation that results in the truncation of TMPRSS2 exons 3-14 and ACPP exons 5-11. The functional significance of this rearrangement is undetermined.
ACPP	0	MSKCC-DMP	P-0002123-T02-IM5	ACPP-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ACPP (NM_001134194) rearrangement: t(3;21)(q22.1;q22.3)(chr3:g.132053847::chr21:g.42868047) Note: The TMPRSS2 (NM_001135099) - ACPP (NM_001134194) rearrangement is a translocation that results in the truncation of TMPRSS2 exons 3-14 and ACPP exons 5-11. The functional significance of this rearrangement is undetermined.
SPSB4	0	MSKCC-DMP	P-0008437-T01-IM5	ATR-SPSB4 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement : chr3:g.140760042_c.6800:ATRdel Note: The ATR (NM_001184) rearrangement event results in the deletion of ATR exons 40-47.
ATR	0	MSKCC-DMP	P-0008437-T01-IM5	ATR-SPSB4 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement : chr3:g.140760042_c.6800:ATRdel Note: The ATR (NM_001184) rearrangement event results in the deletion of ATR exons 40-47.
GLI1	0	MSKCC-DMP	P-0009246-T01-IM5	ATXN7L3B-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.1636_chr12:74478822dup Note: The GLI1 (NM_005269) rearrangement is a duplication (16614663 bp) which includes exon 12 of GLI1. The functional significance is undetermined.
ATXN7L3B	0	MSKCC-DMP	P-0009246-T01-IM5	ATXN7L3B-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.1636_chr12:74478822dup Note: The GLI1 (NM_005269) rearrangement is a duplication (16614663 bp) which includes exon 12 of GLI1. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0009246-T01-IM5	RBM33-BRAF fusion	yes	unknown		in frame	RBM33 (NM_053043) - BRAF (NM_004333) rearrangement: c.171+526:RBM33_c.1314+160:BRAFinv Note: The RBM33 (NM_053043) - BRAF (NM_004333) rearrangement is an inversion which results in the fusion of RBM33 exons 1-3 with BRAF exons 11-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
RBM33	0	MSKCC-DMP	P-0009246-T01-IM5	RBM33-BRAF fusion	yes	unknown		in frame	RBM33 (NM_053043) - BRAF (NM_004333) rearrangement: c.171+526:RBM33_c.1314+160:BRAFinv Note: The RBM33 (NM_053043) - BRAF (NM_004333) rearrangement is an inversion which results in the fusion of RBM33 exons 1-3 with BRAF exons 11-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
TMPRSS2	0	MSKCC-DMP	P-0005047-T01-IM5	CYP4Z1-TMPRSS2 fusion	yes	unknown		out of frame	CYP4Z1 (NM_178134) - TMPRSS2 (NM_001135099) rearrangement : t(1;21)(1p33;21q22.3)(chr1:g.47561132::chr21:g.42874735) Note1: The CYP4Z1 (NM_178134) - TMPRSS2 (NM_001135099) rearrangement event is a translocation that results in the fusion of CYP4Z1 exons 1-7 with TMPRSS2 exons 2-14. The resulting fusion is predicted to be out of frame.
CYP4Z1	0	MSKCC-DMP	P-0005047-T01-IM5	CYP4Z1-TMPRSS2 fusion	yes	unknown		out of frame	CYP4Z1 (NM_178134) - TMPRSS2 (NM_001135099) rearrangement : t(1;21)(1p33;21q22.3)(chr1:g.47561132::chr21:g.42874735) Note1: The CYP4Z1 (NM_178134) - TMPRSS2 (NM_001135099) rearrangement event is a translocation that results in the fusion of CYP4Z1 exons 1-7 with TMPRSS2 exons 2-14. The resulting fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0005047-T01-IM5	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : t(17;21)(17q21.31;21q22.3)(chr17:g.41635162::chr21:g.42875052) Note2: The TMPRSS2 (NM_001135099) rearrangement event is a translocation which results in the truncation of TMPRSS2 exons 2-14. The functional significance of this event is unknown.
ETV4	0	MSKCC-DMP	P-0005047-T01-IM5	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : t(17;21)(17q21.31;21q22.3)(chr17:g.41635162::chr21:g.42875052) Note2: The TMPRSS2 (NM_001135099) rearrangement event is a translocation which results in the truncation of TMPRSS2 exons 2-14. The functional significance of this event is unknown.
TCF7L2	0	MSKCC-DMP	P-0005792-T01-IM5	LOC100169752-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.382:TCF7L2_chr10:g.127151116dup The TCF7L2 (NM_001146274) rearrangement is a duplication of TCF7L2 exons 4-14. The functional significance is undetermined.
LOC100169752	0	MSKCC-DMP	P-0005792-T01-IM5	LOC100169752-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.382:TCF7L2_chr10:g.127151116dup The TCF7L2 (NM_001146274) rearrangement is a duplication of TCF7L2 exons 4-14. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0009842-T01-IM5	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.2433_c.6227del Note: The APC (NM_000038) rearrangement is an intragenic deletion. Both breakpoints are within exon16.
NAALADL2	0	MSKCC-DMP	P-0009190-T01-IM5	PIK3CA-NAALADL2 fusion	yes	unknown		unknown	NAALADL2 (NM_207015) - PIK3CA (NM_006218)  rearrangement :  c.44-96015:NAALADL2_c.105:PIK3CAdel Note: The NAALADL2 (NM_207015) - PIK3CA (NM_006218)  rearrangement event is a deletion which results in the fusion of NAALADL2 exon 1 with PIK3CA exons 2-21. One of the breakpoints is within PIK3CA exon2.
PIK3CA	0	MSKCC-DMP	P-0009190-T01-IM5	PIK3CA-NAALADL2 fusion	yes	unknown		unknown	NAALADL2 (NM_207015) - PIK3CA (NM_006218)  rearrangement :  c.44-96015:NAALADL2_c.105:PIK3CAdel Note: The NAALADL2 (NM_207015) - PIK3CA (NM_006218)  rearrangement event is a deletion which results in the fusion of NAALADL2 exon 1 with PIK3CA exons 2-21. One of the breakpoints is within PIK3CA exon2.
KIF5B	0	MSKCC-DMP	P-0009514-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	Note: The KIF5B (NM_004521) - RET (NM_020975) reciprocal rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20. The clinical trial research is currently ongoing with cabozantinib. PMID: 23533264 KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1461:KIF5B_c.2137-221:RETinv
RET	0	MSKCC-DMP	P-0009514-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	Note: The KIF5B (NM_004521) - RET (NM_020975) reciprocal rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20. The clinical trial research is currently ongoing with cabozantinib. PMID: 23533264 KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1461:KIF5B_c.2137-221:RETinv
JAK2	0	MSKCC-DMP	P-0007794-T01-IM5	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) Rearrangement :  c.3035_c.3059+6450del Note: The JAK2 (NM_004972) Rearrangement results in the intragenic deletion of exon 22 of JAK2.One of the breakpoints is within exon22. Its functional significance  is undetermined.
ALK	0	MSKCC-DMP	P-0006950-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1489+2302:EML4_c.3172+943:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0006950-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1489+2302:EML4_c.3172+943:ALKinv The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.
RAF1	0	MSKCC-DMP	P-0004958-T01-IM5	RAF1-intragenic	yes	unknown		unknown	RAF1 (NM_002880) rearrangement : c.1370+1077_1438del Note: The RAF1 (NM_002880) rearrangement event results in the intragenic deletion of RAF1 exons 13-14. One of the breakpoints is within RAF1 exon14.
FAT1	0	MSKCC-DMP	P-0009991-T01-IM5	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement :  c.-19+745_c.235del Note: The FAT1 Rearrangement results in the deletion of the first two exons of FAT1. One of the breakpoints is within exon2 .Its functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0006184-T01-IM5	EXTL3-PGR fusion	yes	unknown		unknown	PGR(NM_000926)-EXTL3(NM_001440) rearrangement: t(8,11)(p21.1;q22.1)(chr8:g.28568217::chr11:g.100996767) The EXTL3-PGR translocation is a rearrangement which involves exon2 of PGR and 5-UTR region of EXTL3. Its functional significance is not determined.
EXTL3	0	MSKCC-DMP	P-0006184-T01-IM5	EXTL3-PGR fusion	yes	unknown		unknown	PGR(NM_000926)-EXTL3(NM_001440) rearrangement: t(8,11)(p21.1;q22.1)(chr8:g.28568217::chr11:g.100996767) The EXTL3-PGR translocation is a rearrangement which involves exon2 of PGR and 5-UTR region of EXTL3. Its functional significance is not determined.
NF1	0	MSKCC-DMP	P-0006184-T01-IM5	MIR365-2-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - MIR365-2 (NR_029856) rearrangement: c.4831:NF1_g.29900286del NF1 (NM_001042492) - MIR365-2 (NR_029856) rearrangement event results in the deletion of NF1 of exon36. One of the breakpoints is within NF1 exon36.
MIR365-2	0	MSKCC-DMP	P-0006184-T01-IM5	MIR365-2-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - MIR365-2 (NR_029856) rearrangement: c.4831:NF1_g.29900286del NF1 (NM_001042492) - MIR365-2 (NR_029856) rearrangement event results in the deletion of NF1 of exon36. One of the breakpoints is within NF1 exon36.
CDKN2A	0	MSKCC-DMP	P-0003096-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	null Note: The CDKN2Ap14ARF (NM_058195) rearrangement event is an intragenic duplication which results in the duplication of exon 2. Its functional significance is undetermined.          Note: The CDKN2Ap16INK4A (NM_000077) rearrangement event is an intragenic duplication which results in the duplication of exon 2. Its functional significance is undetermined.
CDC73	0	MSKCC-DMP	P-0001077-T01-IM3	CDC73-intragenic	yes	unknown		out of frame	CDC73 (NM_024529) intragenic deletion: c.908-21_c.972+806del Note: The MAP2K1 copy number gain falls slightly below the cut off criteria for amplification. Confirmatory testing is suggested, if clinically indicated.
ATRX	0	MSKCC-DMP	P-0002195-T01-IM3	ATRX-intragenic	yes	unknown		unknown	null
ALK	0	MSKCC-DMP	P-0003323-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null Known EML4-ALK. Fits LUAD Dx.
EML4	0	MSKCC-DMP	P-0003323-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null Known EML4-ALK. Fits LUAD Dx.
ROS1	0	MSKCC-DMP	P-0004318-T01-IM5	EZR-ROS1 fusion	yes	unknown		unknown	EZR (NM_003379) - ROS1 (NM_002944) rearrangement: c.1090+13:EZR_c.5401:ROS1del The EZR (NM_003379) - ROS1 (NM_002944) rearrangement is a deletion which leads to the fusion of exons 1-9 of EZR with exons 33-43 of ROS1, including the kinase domain. One of the breakpoints is within exon 33 of ROS1. (PMID:23418494) (PMID: 22327623)
EZR	0	MSKCC-DMP	P-0004318-T01-IM5	EZR-ROS1 fusion	yes	unknown		unknown	EZR (NM_003379) - ROS1 (NM_002944) rearrangement: c.1090+13:EZR_c.5401:ROS1del The EZR (NM_003379) - ROS1 (NM_002944) rearrangement is a deletion which leads to the fusion of exons 1-9 of EZR with exons 33-43 of ROS1, including the kinase domain. One of the breakpoints is within exon 33 of ROS1. (PMID:23418494) (PMID: 22327623)
CDKN2A	0	MSKCC-DMP	P-0002603-T01-IM3	CDKN2A-intragenic	yes	unknown		unknown	null affects splice site
TOP1MT	0	MSKCC-DMP	P-0002855-T01-IM3	RECQL4-TOP1MT fusion	yes	unknown		unknown	null Note: The RECQL4-TOP1MT deletion is a rearrangement event which results in the fusion between RECQL4 (NM_004260) exons 1-4 and TOP1MT (NM_052963) exons 13-14.
RECQL4	0	MSKCC-DMP	P-0002855-T01-IM3	RECQL4-TOP1MT fusion	yes	unknown		unknown	null Note: The RECQL4-TOP1MT deletion is a rearrangement event which results in the fusion between RECQL4 (NM_004260) exons 1-4 and TOP1MT (NM_052963) exons 13-14.
TRAF7	0	MSKCC-DMP	P-0001911-T01-IM3	E4F1-TRAF7 fusion	yes	unknown		unknown	E4F1 (NM_004424) - TRAF7 (NM_032271) Duplication: c.983:E4F1_c.442-63:TRAF7dup (See Note) Note: The E4F1 - TRAF7 duplication is a structural variant in which exons 1 to 7 of E4F1 are fused to exons 7 to 21 of TRAF7. The functional significance of this structural variant is undetermined at this time.
E4F1	0	MSKCC-DMP	P-0001911-T01-IM3	E4F1-TRAF7 fusion	yes	unknown		unknown	E4F1 (NM_004424) - TRAF7 (NM_032271) Duplication: c.983:E4F1_c.442-63:TRAF7dup (See Note) Note: The E4F1 - TRAF7 duplication is a structural variant in which exons 1 to 7 of E4F1 are fused to exons 7 to 21 of TRAF7. The functional significance of this structural variant is undetermined at this time.
POU2F2	0	MSKCC-DMP	P-0001884-T01-IM3	CIC-POU2F2 fusion	yes	unknown		unknown	CIC (NM_015125) inversion: chr19:g.42645881_CIC:c.415inv Note: The CIC inversion is a rearrangement event which results in the deletion of exons 1 to 3, likely disrupting the function of the gene.
CIC	0	MSKCC-DMP	P-0001884-T01-IM3	CIC-POU2F2 fusion	yes	unknown		unknown	CIC (NM_015125) inversion: chr19:g.42645881_CIC:c.415inv Note: The CIC inversion is a rearrangement event which results in the deletion of exons 1 to 3, likely disrupting the function of the gene.
SLC1A6	0	MSKCC-DMP	P-0000485-T01-IM3	NOTCH3-SLC1A6 fusion	yes	unknown		unknown	null
NOTCH3	0	MSKCC-DMP	P-0000485-T01-IM3	NOTCH3-SLC1A6 fusion	yes	unknown		unknown	null
KDM5A	0	MSKCC-DMP	P-0001992-T01-IM3	KDM5A-intragenic	yes	unknown		unknown	null
BRAF	0	MSKCC-DMP	P-0003502-T01-IM5	PJA2-BRAF fusion	yes	unknown		in frame	null Note: The BRAF (NM_004333) PJA2 (NM_014819) rearrangement event is a translocation that results in the fusion of exons 1-10 of BRAF with exons 8-10 of PJA2. The functional significance is undetermined.
PJA2	0	MSKCC-DMP	P-0003502-T01-IM5	PJA2-BRAF fusion	yes	unknown		in frame	null Note: The BRAF (NM_004333) PJA2 (NM_014819) rearrangement event is a translocation that results in the fusion of exons 1-10 of BRAF with exons 8-10 of PJA2. The functional significance is undetermined.
RAB35	0	MSKCC-DMP	P-0004564-T01-IM5	HCN1-RAB35 fusion	yes	unknown		unknown	RAB35 (NM_006861) translocation : t(12;5)(q24.23; p11)(chr12:g.20536539::chr5:g.46027045) The RAB35 (NM_006861) rearrangement is a translocation potentially truncating RAB35 after exon 5. The functional significance is undetermined.
HCN1	0	MSKCC-DMP	P-0004564-T01-IM5	HCN1-RAB35 fusion	yes	unknown		unknown	RAB35 (NM_006861) translocation : t(12;5)(q24.23; p11)(chr12:g.20536539::chr5:g.46027045) The RAB35 (NM_006861) rearrangement is a translocation potentially truncating RAB35 after exon 5. The functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0004564-T01-IM5	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.420_c.59-33199del The RUNX1 (NM_001754) rearrangement is an intragenic deletion of exons 3-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
SPPL2B	0	MSKCC-DMP	P-0003171-T01-IM5	MAP2K2-SPPL2B fusion	yes	unknown		unknown	null Note: The SPPL2B (NM_152988) - MAP2K2 (NM_030662) rearrangement event results in the deletion of MAP2K2 exons 8-11, potentially disabling the function of the gene. The breakpoint in MAP2K2 is within exon8.
MAP2K2	0	MSKCC-DMP	P-0003171-T01-IM5	MAP2K2-SPPL2B fusion	yes	unknown		unknown	null Note: The SPPL2B (NM_152988) - MAP2K2 (NM_030662) rearrangement event results in the deletion of MAP2K2 exons 8-11, potentially disabling the function of the gene. The breakpoint in MAP2K2 is within exon8.
SBNO2	0	MSKCC-DMP	P-0004133-T01-IM5	JAK3-SBNO2 fusion	yes	unknown		unknown	JAK3 (NM_000215) -SBNO2 (NM_014963) Rearrangement :  c.184+8:JAK3_c.3112:SBNO2del Note: JAK3 (NM_000215) -SBNO2 (NM_014963) Rearrangement results in the fusion of of exons 1 to 2 of JAK3 with exons 27 to 32 of SBNO2.The breakpoint in SBNO2 is within exon 27. Its functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0004133-T01-IM5	JAK3-SBNO2 fusion	yes	unknown		unknown	JAK3 (NM_000215) -SBNO2 (NM_014963) Rearrangement :  c.184+8:JAK3_c.3112:SBNO2del Note: JAK3 (NM_000215) -SBNO2 (NM_014963) Rearrangement results in the fusion of of exons 1 to 2 of JAK3 with exons 27 to 32 of SBNO2.The breakpoint in SBNO2 is within exon 27. Its functional significance is undetermined.
LIMD1	0	MSKCC-DMP	P-0002260-T01-IM3	BAP1-LIMD1 fusion	yes	unknown		out of frame	LIMD1 (NM_014240) - BAP1 (NM_004656) Inversion : c.1511-4586:LIMD1_c.2056+6:BAP1inv Note: LIMD1-BAP1 is a reciprocal inversion event in which the exons 1 and 2 of LIMD1 is fused to exons 16 and 17. It is predicted to disable BAP1 protein.
BAP1	0	MSKCC-DMP	P-0002260-T01-IM3	BAP1-LIMD1 fusion	yes	unknown		out of frame	LIMD1 (NM_014240) - BAP1 (NM_004656) Inversion : c.1511-4586:LIMD1_c.2056+6:BAP1inv Note: LIMD1-BAP1 is a reciprocal inversion event in which the exons 1 and 2 of LIMD1 is fused to exons 16 and 17. It is predicted to disable BAP1 protein.
ALK	0	MSKCC-DMP	P-0001811-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Inversion: c.1315+2666:EML4_c.3172+122:ALKinv
EML4	0	MSKCC-DMP	P-0001811-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Inversion: c.1315+2666:EML4_c.3172+122:ALKinv
NOTCH2	0	MSKCC-DMP	P-0001343-T01-IM3	NOTCH2-intragenic	yes	unknown		unknown	None
AXL	0	MSKCC-DMP	P-0003818-T01-IM5	AXL-intragenic	yes	unknown		in frame	AXL (NM_021913) rearrangement : c.1538-760_1634-49del Note: The AXL (NM_021913) rearrangement event results in the deletion of AXL exon12.
ERG	0	MSKCC-DMP	P-0003619-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.126+467:TMPRSS2_c.39+43704:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0003619-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.126+467:TMPRSS2_c.39+43704:ERGdel
STK11	0	MSKCC-DMP	P-0003754-T01-IM5	CACNA1A-STK11 fusion	yes	unknown		unknown	c.4870-2423:CACNA1A_c.87:STK11inv Note: The CACNA1A (NM_001127222) - STK11 (NM_000455) rearrangement event is an inversion which results in the fusion of CACNA1A exons 1 to 30 and STK11 exons 1 to 9. Functional significance of this is undetermined. The breakpoint on STK11 is within exon1.
CACNA1A	0	MSKCC-DMP	P-0003754-T01-IM5	CACNA1A-STK11 fusion	yes	unknown		unknown	c.4870-2423:CACNA1A_c.87:STK11inv Note: The CACNA1A (NM_001127222) - STK11 (NM_000455) rearrangement event is an inversion which results in the fusion of CACNA1A exons 1 to 30 and STK11 exons 1 to 9. Functional significance of this is undetermined. The breakpoint on STK11 is within exon1.
ALK	0	MSKCC-DMP	P-0000058-T01-IM3	DDX11L2-ALK fusion	yes	unknown		unknown	null
DDX11L2	0	MSKCC-DMP	P-0000058-T01-IM3	DDX11L2-ALK fusion	yes	unknown		unknown	null
RET	0	MSKCC-DMP	P-0001898-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) inversion: c.304-12339_c.2137-333inv5
CCDC6	0	MSKCC-DMP	P-0001898-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) inversion: c.304-12339_c.2137-333inv5
RET	0	MSKCC-DMP	P-0001898-T01-IM3	RASSF4-RET fusion	yes	unknown		in frame	RET (NM_020975) - RASSF4 (NM_032023) deletion: c.2137-283_c.138+357del
RASSF4	0	MSKCC-DMP	P-0001898-T01-IM3	RASSF4-RET fusion	yes	unknown		in frame	RET (NM_020975) - RASSF4 (NM_032023) deletion: c.2137-283_c.138+357del
SORBS2	0	MSKCC-DMP	P-0002997-T01-IM3	FAT1-SORBS2 fusion	yes	unknown		unknown	null Note: The FAT1(NM_005245) -SORBS2 (NM_021069) rearrangement is an inversion event which results in the fusion between FAT1 exons 1-21 and SORBS2 gene.
FAT1	0	MSKCC-DMP	P-0002997-T01-IM3	FAT1-SORBS2 fusion	yes	unknown		unknown	null Note: The FAT1(NM_005245) -SORBS2 (NM_021069) rearrangement is an inversion event which results in the fusion between FAT1 exons 1-21 and SORBS2 gene.
SND1	0	MSKCC-DMP	P-0004103-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) -  BRAF (NM_004333) rearrangement: c.1038+5799:SND1_c.1315-192:BRAFinv. The SND1 (NM_014390) -  BRAF (NM_004333) rearrangement is an inversion that results in the fusion of SND1 exons 1-9 with BRAF exons 11-18. (PMID: 25266736) (PMID: 22745804)
BRAF	0	MSKCC-DMP	P-0004103-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) -  BRAF (NM_004333) rearrangement: c.1038+5799:SND1_c.1315-192:BRAFinv. The SND1 (NM_014390) -  BRAF (NM_004333) rearrangement is an inversion that results in the fusion of SND1 exons 1-9 with BRAF exons 11-18. (PMID: 25266736) (PMID: 22745804)
TRAP1	0	MSKCC-DMP	P-0002323-T01-IM3	CREBBP-TRAP1 fusion	yes	unknown		unknown	TRAP1 (NM_016292) and CREBBP (NM_004380) duplication (42233bp):   TRAP1:c.331-780_CREBBP:c.5898dup Note: The TRAP1-CREBBP duplication is a rearrangement event which results in   the fusion of TRAP1 exons 1 to 4 and CREBBP exon 31. Its functional   significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0002323-T01-IM3	CREBBP-TRAP1 fusion	yes	unknown		unknown	TRAP1 (NM_016292) and CREBBP (NM_004380) duplication (42233bp):   TRAP1:c.331-780_CREBBP:c.5898dup Note: The TRAP1-CREBBP duplication is a rearrangement event which results in   the fusion of TRAP1 exons 1 to 4 and CREBBP exon 31. Its functional   significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0002873-T01-IM3	RET-KIF5B fusion	yes	unknown		in frame	null Note:The KIF5B-RET inversion is a structural rearrangement which results in the in frame fusion of exons 1 to 16 of KIF5B and exons 12 to 20 of  RET1.
RET	0	MSKCC-DMP	P-0002873-T01-IM3	RET-KIF5B fusion	yes	unknown		in frame	null Note:The KIF5B-RET inversion is a structural rearrangement which results in the in frame fusion of exons 1 to 16 of KIF5B and exons 12 to 20 of  RET1.
DOT1L	0	MSKCC-DMP	P-0002873-T01-IM3	DOT1L-intragenic	yes	unknown		unknown	null Note:The DOT1L deletion is a structural rearrangement event which results in the deletion of exons 10 to 26 of DOT1L.The breakpoint in exon 26 is within the exon. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0002702-T01-IM3	PARK2-intragenic	yes	unknown		unknown	null Note: The PARK2 intragenic deletion is a rearrangement event which results in the deletion of exons 5 to 6.
NOTCH2	0	MSKCC-DMP	P-0004386-T01-IM5	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement : c.6548_*2211inv Note: The NOTCH2 (NM_024408) rearrangement event results in the inversion of exon34. One of the breakpoints is within exon34.
CUL5	0	MSKCC-DMP	P-0004386-T01-IM5	NOTCH1-CUL5 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - CUL5 (NM_003478) rearrangement : t(9;11)(9q34.3;11q22.3)(chr9:g.139390931::chr11:g.107944759) Note: NOTCH1 (NM_017617) - CUL5 (NM_003478) rearrangement event is a translocation which results in the fusion of NOTCH1 exons 1-34 with CUL5 exons 11-19 . The breakpoint on NOTCH1 is within exon34. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0004386-T01-IM5	NOTCH1-CUL5 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - CUL5 (NM_003478) rearrangement : t(9;11)(9q34.3;11q22.3)(chr9:g.139390931::chr11:g.107944759) Note: NOTCH1 (NM_017617) - CUL5 (NM_003478) rearrangement event is a translocation which results in the fusion of NOTCH1 exons 1-34 with CUL5 exons 11-19 . The breakpoint on NOTCH1 is within exon34. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0003716-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - LDLR (NM_000527)  rearrangement: c.3168+11:SMARCA4_c.2141-262:LDLRdel The SMARCA4 (NM_003072) - LDLR (NM_000527)  rearrangement results in the fusion of exons 1 to 22 of SMARCA4 with exons 15 to 18 of LDLR .The breakpoint in SMARCA4 Is within exon 22.Its functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0003716-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - LDLR (NM_000527)  rearrangement: c.3168+11:SMARCA4_c.2141-262:LDLRdel The SMARCA4 (NM_003072) - LDLR (NM_000527)  rearrangement results in the fusion of exons 1 to 22 of SMARCA4 with exons 15 to 18 of LDLR .The breakpoint in SMARCA4 Is within exon 22.Its functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0004389-T01-IM5	RNF43-intragenic	yes	unknown		in frame	RNF43 (NM_017763) rearrangement: c.952+44_c.2309-120del The RNF43 (NM_017763) rearrangement is an intragenic deletion of exon 9. The functional significance is undetermined
ROS1	0	MSKCC-DMP	P-0004336-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 with ROS1 exons 34-43 ) : t(5;6)(5q32;6q22.1)(chr5:g.149783071::chr6:g.117647249)
CD74	0	MSKCC-DMP	P-0004336-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 with ROS1 exons 34-43 ) : t(5;6)(5q32;6q22.1)(chr5:g.149783071::chr6:g.117647249)
TBL3	0	MSKCC-DMP	P-0004504-T01-IM5	CREBBP-TBL3 fusion	yes	unknown		unknown	CREBBP (NM_004380) - TBL3 (NM_006453) rearrangement : c.157:TBL3_c.3779+40:CREBBPinv Note: The CREBBP (NM_004380) - TBL3 (NM_006453) rearrangement event is an inversion which results in the fusion of CREBBP exons 1 to 20 and TBL3 exons 3 to 22.
CREBBP	0	MSKCC-DMP	P-0004504-T01-IM5	CREBBP-TBL3 fusion	yes	unknown		unknown	CREBBP (NM_004380) - TBL3 (NM_006453) rearrangement : c.157:TBL3_c.3779+40:CREBBPinv Note: The CREBBP (NM_004380) - TBL3 (NM_006453) rearrangement event is an inversion which results in the fusion of CREBBP exons 1 to 20 and TBL3 exons 3 to 22.
RNF43	0	MSKCC-DMP	P-0004140-T01-IM5	RNF43-intragenic	yes	unknown		in frame	RNF43(NM_017763) Rearrangement: c.849+196_253-3498dup The RNF43(NM_017763) Rearrangement results in the duplication of exons 3 to 7 .Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0004140-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF(NM_004333) Rearrangement : c.1141-973_139-1097del The BRAF(NM_004333) Rearrangement results in the deletion of exons 2 to 8. Its functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0002866-T01-IM3	JAK3-intragenic	yes	unknown		out of frame	null Note: The JAK3 deletion is structural rearrangement event which results in the deletion of exon 10, likely disabling its function
EYA2	0	MSKCC-DMP	P-0002866-T01-IM3	JAK3-EYA2 fusion	yes	unknown		out of frame	null Note: The JAK3-EYA2 translocation is a structural rearrangement event which results in the out of frame fusion of exons 1 to 10 of JAK3 with exons 11 to 16 of EYA2.Its functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0002866-T01-IM3	JAK3-EYA2 fusion	yes	unknown		out of frame	null Note: The JAK3-EYA2 translocation is a structural rearrangement event which results in the out of frame fusion of exons 1 to 10 of JAK3 with exons 11 to 16 of EYA2.Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0002894-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0002894-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
BAP1	0	MSKCC-DMP	P-0000260-T01-IM3	PHF7-BAP1 fusion	yes	unknown		unknown	null
PHF7	0	MSKCC-DMP	P-0000260-T01-IM3	PHF7-BAP1 fusion	yes	unknown		unknown	null
KDM6A	0	MSKCC-DMP	P-0001272-T01-IM3	KDM6A-intragenic	yes	unknown		unknown	null
PPFIBP1	0	MSKCC-DMP	P-0003293-T01-IM5	MLL2-PPFIBP1 fusion	yes	unknown		unknown	null The MLL2 (NM_003482) -PPFIBP1 (NM_177444) structural rearrangement results in the fusion of exons 34 to 54 of MLL2 with exons 18 to 29 of PPFIBP1.The breakpoint in MLL2 is within exon 34.Its functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0003293-T01-IM5	MLL2-PPFIBP1 fusion	yes	unknown		unknown	null The MLL2 (NM_003482) -PPFIBP1 (NM_177444) structural rearrangement results in the fusion of exons 34 to 54 of MLL2 with exons 18 to 29 of PPFIBP1.The breakpoint in MLL2 is within exon 34.Its functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0003293-T01-IM5	MED12-intragenic	yes	unknown		in frame	null The MED12 (NM_005120) rearrangement results in the  duplication of exons 29 to 39.Its functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0002841-T01-IM3	BRIP1-BCAS3 fusion	yes	unknown		unknown	null Note: BRIP1 - BCAS3 deletion is a structural rearrangement event in which BCAS3 exon4 and BRIP1 exon15 are fused in an anti-sense manner. The event could lead to reduced expression of BRIP1 via removal of the promoter/enhancer sequences.
BRIP1	0	MSKCC-DMP	P-0002841-T01-IM3	BRIP1-BCAS3 fusion	yes	unknown		unknown	null Note: BRIP1 - BCAS3 deletion is a structural rearrangement event in which BCAS3 exon4 and BRIP1 exon15 are fused in an anti-sense manner. The event could lead to reduced expression of BRIP1 via removal of the promoter/enhancer sequences.
SPEN	0	MSKCC-DMP	P-0001664-T01-IM3	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) intragenic deletion: c.405-536_c.600del The SPEN intragenic deletion is a rearrangement event which results in  deletion of exon 3 and is likely inactivating.
ARID1A	0	MSKCC-DMP	P-0001664-T01-IM3	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) intragenic deletion: c.4103_c.5124+941del The ARID1A intragenic deletion is a rearrangement event which results  in deletion of exons 18 and 19, and is likely inactivating
LATS1	0	MSKCC-DMP	P-0001664-T01-IM3	LATS1-intragenic	yes	unknown		unknown	LATS1 (NM_004690) intragenic deletion: c.3026_c.2883+6854del The LATS1 intragenic deletion is a rearrangement event which results in deletion of exon 9, and is likely inactivating.
MTAP	0	MSKCC-DMP	P-0003402-T01-IM5	CDKN2A-MTAP fusion	yes	unknown		unknown	null The CDKN2Ap14ARF (NM_058195)  rearrangement results in deletion of CDKN2Ap14ARF exons 1 to 3. The break point is within exon1. This event also results in deletion of CDKN2Ap16INK4A.
CDKN2A	0	MSKCC-DMP	P-0003402-T01-IM5	CDKN2A-MTAP fusion	yes	unknown		unknown	null The CDKN2Ap14ARF (NM_058195)  rearrangement results in deletion of CDKN2Ap14ARF exons 1 to 3. The break point is within exon1. This event also results in deletion of CDKN2Ap16INK4A.
ALK	0	MSKCC-DMP	P-0003383-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null EML4 (NM_019063) exons 1-13 fuses with ALK (NM_004304) exons 20-29.
EML4	0	MSKCC-DMP	P-0003383-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null EML4 (NM_019063) exons 1-13 fuses with ALK (NM_004304) exons 20-29.
KDR	0	MSKCC-DMP	P-0002359-T01-IM3	CAMK2D-KDR fusion	yes	unknown		unknown	CAMK2D (NM_001221) and KDR (NM_002253) deletion (58606888bp): CAMK2D:c.220+19784_KDR:c.3118del Note: The CAMK2D-KDR deletion is a rearrangement event which results in the in-frame fusion of CAMK2D exons 1 to 3 and KDR exons 23 to 30.
CAMK2D	0	MSKCC-DMP	P-0002359-T01-IM3	CAMK2D-KDR fusion	yes	unknown		unknown	CAMK2D (NM_001221) and KDR (NM_002253) deletion (58606888bp): CAMK2D:c.220+19784_KDR:c.3118del Note: The CAMK2D-KDR deletion is a rearrangement event which results in the in-frame fusion of CAMK2D exons 1 to 3 and KDR exons 23 to 30.
TERT	0	MSKCC-DMP	P-0003144-T01-IM5	ZNF595-TERT fusion	yes	unknown		unknown	null Note: The ZNF718 - TERT translocation event is a rearrangement event which results in fusion of promoter/enhancer region of  ZNF718 gene to TERT, replacing the promoter of TERT. Its functional significance is undetermined.
ZNF595	0	MSKCC-DMP	P-0003144-T01-IM5	ZNF595-TERT fusion	yes	unknown		unknown	null Note: The ZNF718 - TERT translocation event is a rearrangement event which results in fusion of promoter/enhancer region of  ZNF718 gene to TERT, replacing the promoter of TERT. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0003234-T01-IM5	DOT1L-intragenic	yes	unknown		unknown	null The DOT1L rearrangement results in the intragenic deletion of exons 17 to 19. The breakpoint in exon 17 is within the exon. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0003813-T01-IM5	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.2844_3381+330dup Note: The ROS1 (NM_002944) rearrangement event results in the duplication of ROS1 exons 19-21. One of the breakpoints is within exon19.
FGFR3	0	MSKCC-DMP	P-0002016-T01-IM3	FGFR3-intragenic	yes	unknown		unknown	null  FGFR3 deletion of last 4 exons (14-18)
ERG	0	MSKCC-DMP	P-0004221-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion  (TMPRSS2 exon 2 fused to ERG exon 3):  c.127-1520:TMPRSS2_c.237-8364:ERGdel Known fusion
TMPRSS2	0	MSKCC-DMP	P-0004221-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion  (TMPRSS2 exon 2 fused to ERG exon 3):  c.127-1520:TMPRSS2_c.237-8364:ERGdel Known fusion
RET	0	MSKCC-DMP	P-0001151-T01-IM3	NCOA4-RET fusion	yes	unknown		in frame	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2137-387_c.1840-75dup Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH is recommended.
NCOA4	0	MSKCC-DMP	P-0001151-T01-IM3	NCOA4-RET fusion	yes	unknown		in frame	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2137-387_c.1840-75dup Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH is recommended.
ROS1	0	MSKCC-DMP	P-0001437-T01-IM3	CD74-ROS1 fusion	yes	unknown		out of frame	None
CD74	0	MSKCC-DMP	P-0001437-T01-IM3	CD74-ROS1 fusion	yes	unknown		out of frame	None
ERBB3	0	MSKCC-DMP	P-0004492-T01-IM5	CREG1-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement : t(1;12)(1q24.2;12q13.2)(chr1:g.167500617::chr12:g.56486697) Note: ERBB3 (NM_001982) rearrangement event  is a translocation which results in truncation of ERBB3 exons 10-17. Its functional significance is undetermined.
CREG1	0	MSKCC-DMP	P-0004492-T01-IM5	CREG1-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement : t(1;12)(1q24.2;12q13.2)(chr1:g.167500617::chr12:g.56486697) Note: ERBB3 (NM_001982) rearrangement event  is a translocation which results in truncation of ERBB3 exons 10-17. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0003125-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	null Note: The KIF5B (NM_004521) - RET (NM_020975) rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20.
RET	0	MSKCC-DMP	P-0003125-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	null Note: The KIF5B (NM_004521) - RET (NM_020975) rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20.
BRAF	0	MSKCC-DMP	P-0004477-T01-IM5	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) fusion ( AGK exons 1 to 2 and  BRAF exons 8 to 18): c.101+10076:AGK_c.981-1138:BRAFinv The AGK (NM_018238) - BRAF (NM_004333 fusion is a reciprocal inversion (PMID: 23890088)
AGK	0	MSKCC-DMP	P-0004477-T01-IM5	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) fusion ( AGK exons 1 to 2 and  BRAF exons 8 to 18): c.101+10076:AGK_c.981-1138:BRAFinv The AGK (NM_018238) - BRAF (NM_004333 fusion is a reciprocal inversion (PMID: 23890088)
BMPR1B	0	MSKCC-DMP	P-0002778-T01-IM3	TET2-BMPR1B fusion	yes	unknown		unknown	null Note: The TET2-BMPR1B inversion is a rearrangement event, which inverts part of exon 3 and exons 4-11 of TET2 with exons 4-13 of BMPR1B. Its functional significance is undetermined.
TET2	0	MSKCC-DMP	P-0002778-T01-IM3	TET2-BMPR1B fusion	yes	unknown		unknown	null Note: The TET2-BMPR1B inversion is a rearrangement event, which inverts part of exon 3 and exons 4-11 of TET2 with exons 4-13 of BMPR1B. Its functional significance is undetermined.
TET2	0	MSKCC-DMP	P-0002778-T01-IM3	SEC24B-TET2 fusion	yes	unknown		unknown	null Note: The TET2 deletion is a rearrangement event, which results in partial deletion of exon 3 and exons 4-11 of TET2. Its functional significance is undetermined
SEC24B	0	MSKCC-DMP	P-0002778-T01-IM3	SEC24B-TET2 fusion	yes	unknown		unknown	null Note: The TET2 deletion is a rearrangement event, which results in partial deletion of exon 3 and exons 4-11 of TET2. Its functional significance is undetermined
TET2	0	MSKCC-DMP	P-0002778-T01-IM3	PAPSS1-TET2 fusion	yes	unknown		unknown	null Note: The TET2 duplication is a rearrangement event, which includes duplication of part of exon 3 and exons 4-11 of TET2. Its functional significance is undetermined.
PAPSS1	0	MSKCC-DMP	P-0002778-T01-IM3	PAPSS1-TET2 fusion	yes	unknown		unknown	null Note: The TET2 duplication is a rearrangement event, which includes duplication of part of exon 3 and exons 4-11 of TET2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0003446-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null Known fusion
EML4	0	MSKCC-DMP	P-0003446-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	null Known fusion
RERGL	0	MSKCC-DMP	P-0003160-T01-IM5	PIK3C2G-RERGL fusion	yes	unknown		unknown	null Note: The PIK3C2G rearrangement event is an intragenic inversion which results in the inversion of exons 1-5, likely disabling the function of the gene. One of the breakpoints is within exon5.
PIK3C2G	0	MSKCC-DMP	P-0003160-T01-IM5	PIK3C2G-RERGL fusion	yes	unknown		unknown	null Note: The PIK3C2G rearrangement event is an intragenic inversion which results in the inversion of exons 1-5, likely disabling the function of the gene. One of the breakpoints is within exon5.
BICC1	0	MSKCC-DMP	P-0003177-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	null Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion is a reciprocal inversion which results in the in frame fusion of FGFR2 exons 1 to 17 and BICC1 exons 3 to 21. Refer to PMID: 24122810 for more information on the FGFR2 - BICC1 fusion.
FGFR2	0	MSKCC-DMP	P-0003177-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	null Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion is a reciprocal inversion which results in the in frame fusion of FGFR2 exons 1 to 17 and BICC1 exons 3 to 21. Refer to PMID: 24122810 for more information on the FGFR2 - BICC1 fusion.
NOTCH2	0	MSKCC-DMP	P-0001909-T01-IM3	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) Deletion: c.875-51_c.1410del
ERG	0	MSKCC-DMP	P-0003597-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1878:TMPRSS2_c.18+11694:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2 to 10)
TMPRSS2	0	MSKCC-DMP	P-0003597-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1878:TMPRSS2_c.18+11694:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2 to 10)
STK11	0	MSKCC-DMP	P-0004335-T01-IM5	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement: c.291-521_597+36del Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of STK11 exons 2-4.
PARK2	0	MSKCC-DMP	P-0001086-T01-IM3	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) intragenic deletion: c.1168-3962_1206del Note: The PARK2 intragenic deletion is a rearrangement event which results in the deletion of exon 11, and may represent an inactivating rearrangement.
RNF43	0	MSKCC-DMP	P-0004433-T01-IM5	BCAS3-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) Rearrangement : c.586:RNF43_chr17.g.59452393inv Note: The RNF43 (NM_017763) Rearrangement  results in the inversion of exons 1 to 6 of RNF43.The breakpoint is within exon6.Its functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0004433-T01-IM5	BCAS3-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) Rearrangement : c.586:RNF43_chr17.g.59452393inv Note: The RNF43 (NM_017763) Rearrangement  results in the inversion of exons 1 to 6 of RNF43.The breakpoint is within exon6.Its functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0004681-T01-IM5	SFRS6-SRC fusion	yes	unknown		unknown	SRC (NM_198291) rearrangement : c.350+21:SRC_chr20:g.42113618del Note: The SRC (NM_198291) rearrangement event results in the deletion of SRC exons 6-14.
SFRS6	0	MSKCC-DMP	P-0004681-T01-IM5	SFRS6-SRC fusion	yes	unknown		unknown	SRC (NM_198291) rearrangement : c.350+21:SRC_chr20:g.42113618del Note: The SRC (NM_198291) rearrangement event results in the deletion of SRC exons 6-14.
EWSR1	0	MSKCC-DMP	P-0004681-T01-IM5	RASL10A-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement : c.1179+848:EWSR1_chr22:g.29715368del Note: The EWSR1 (NM_013986) rearrangement event results in the deletion of EWSR1 exons 13-18.
RASL10A	0	MSKCC-DMP	P-0004681-T01-IM5	RASL10A-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement : c.1179+848:EWSR1_chr22:g.29715368del Note: The EWSR1 (NM_013986) rearrangement event results in the deletion of EWSR1 exons 13-18.
MYOD1	0	MSKCC-DMP	P-0003381-T01-IM5	INCENP-MYOD1 fusion	yes	unknown		out of frame	null Note: The INCENP (NM_001040694) - MYOD1 (NM_002478)  rearrangement event is a duplication which results in the fusion of INCENP exons 1 to 11 and MYOD1 exon 3.
INCENP	0	MSKCC-DMP	P-0003381-T01-IM5	INCENP-MYOD1 fusion	yes	unknown		out of frame	null Note: The INCENP (NM_001040694) - MYOD1 (NM_002478)  rearrangement event is a duplication which results in the fusion of INCENP exons 1 to 11 and MYOD1 exon 3.
MLL	0	MSKCC-DMP	P-0003381-T01-IM5	USP2-MLL fusion	yes	unknown		in frame	null Note: The MLL (NM_001197104) - USP2 (NM_004205) rearrangement event is an inversion which results in the fusion of MLL exons 1 to 8 and USP2 exons 3 to 13.
USP2	0	MSKCC-DMP	P-0003381-T01-IM5	USP2-MLL fusion	yes	unknown		in frame	null Note: The MLL (NM_001197104) - USP2 (NM_004205) rearrangement event is an inversion which results in the fusion of MLL exons 1 to 8 and USP2 exons 3 to 13.
MYOD1	0	MSKCC-DMP	P-0003381-T01-IM5	LRRC4C-MYOD1 fusion	yes	unknown		unknown	null Note: The MYOD1 (NM_002478) rearrangement event results in the inversion of the gene. The breakpoint on MYOD1 is within exon1.
LRRC4C	0	MSKCC-DMP	P-0003381-T01-IM5	LRRC4C-MYOD1 fusion	yes	unknown		unknown	null Note: The MYOD1 (NM_002478) rearrangement event results in the inversion of the gene. The breakpoint on MYOD1 is within exon1.
SYK	0	MSKCC-DMP	P-0004130-T01-IM5	SYK-intragenic	yes	unknown		in frame	SYK(NM_003177) Rearrangement : c.846+52_915+2724del Note: SYK(NM_003177) Rearrangement results in the intragenic deletion of  exon 7.Its functional significance is undetermined
FLG2	0	MSKCC-DMP	P-0002075-T01-IM3	RIT1-FLG2 fusion	yes	unknown		unknown	RIT1 (NM_006912) Deletion : c.313_g.152308085del
RIT1	0	MSKCC-DMP	P-0002075-T01-IM3	RIT1-FLG2 fusion	yes	unknown		unknown	RIT1 (NM_006912) Deletion : c.313_g.152308085del
DYRK1A	0	MSKCC-DMP	P-0003519-T01-IM5	TMPRSS2-DYRK1A fusion	yes	unknown		unknown	chr21:g.38896651_c.56-4127:TMPRSS2inv Note: The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.
TMPRSS2	0	MSKCC-DMP	P-0003519-T01-IM5	TMPRSS2-DYRK1A fusion	yes	unknown		unknown	chr21:g.38896651_c.56-4127:TMPRSS2inv Note: The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.
ERG	0	MSKCC-DMP	P-0003519-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	c.-149-17599:ERG_c.56-3874:TMPRSS2del TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10)
TMPRSS2	0	MSKCC-DMP	P-0003519-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	c.-149-17599:ERG_c.56-3874:TMPRSS2del TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10)
ALK	0	MSKCC-DMP	P-0000732-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0000732-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
ERG	0	MSKCC-DMP	P-0001845-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (2939631bp): (TMRPSS2:c.127-626_ERG:c.39+20086del) Note: This interstitial deletion is consistent with TMPRSS2-ERG fusion.
TMPRSS2	0	MSKCC-DMP	P-0001845-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (2939631bp): (TMRPSS2:c.127-626_ERG:c.39+20086del) Note: This interstitial deletion is consistent with TMPRSS2-ERG fusion.
ERG	0	MSKCC-DMP	P-0001141-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3028438bp): (TMRPSS2:c.55+1206_ERG:c.18+20054del) Note: this interstitial deletion is consistent with TMPRSS2ERG fusion.
TMPRSS2	0	MSKCC-DMP	P-0001141-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3028438bp): (TMRPSS2:c.55+1206_ERG:c.18+20054del) Note: this interstitial deletion is consistent with TMPRSS2ERG fusion.
ERG	0	MSKCC-DMP	P-0003511-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.39+52408:ERG_c.55+1182:TMPRSS2del
TMPRSS2	0	MSKCC-DMP	P-0003511-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.39+52408:ERG_c.55+1182:TMPRSS2del
CDK6	0	MSKCC-DMP	P-0003511-T02-IM5	SAMD9-CDK6 fusion	yes	unknown		unknown	CDK6 (NM_001145306) rearrangement: c.90:CDK6_chr7:g.92656964inv Note: The CDK6 (NM_001145306) rearrangement event results in the inversion of exons 1-2, potentially disabling the function of the gene. One of the breakpoints is within CDK6 exon2.
SAMD9	0	MSKCC-DMP	P-0003511-T02-IM5	SAMD9-CDK6 fusion	yes	unknown		unknown	CDK6 (NM_001145306) rearrangement: c.90:CDK6_chr7:g.92656964inv Note: The CDK6 (NM_001145306) rearrangement event results in the inversion of exons 1-2, potentially disabling the function of the gene. One of the breakpoints is within CDK6 exon2.
ERG	0	MSKCC-DMP	P-0003971-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fuses with ERG exons 4-10): c.55+4079:TMPRSS2_c.19-16151:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0003971-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fuses with ERG exons 4-10): c.55+4079:TMPRSS2_c.19-16151:ERGdel
GLRA2	0	MSKCC-DMP	P-0002840-T01-IM3	KDM5C-GLRA2 fusion	yes	unknown		unknown	null Note: The KDM5C-GLRA2 inversion is a structural rearrangement which results in the fusion of exons 1 to 26 of  KDM5C  with exon 10 of GLRA2.The breakpoint in KDM5C is within exon 26.  Its functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0002840-T01-IM3	KDM5C-GLRA2 fusion	yes	unknown		unknown	null Note: The KDM5C-GLRA2 inversion is a structural rearrangement which results in the fusion of exons 1 to 26 of  KDM5C  with exon 10 of GLRA2.The breakpoint in KDM5C is within exon 26.  Its functional significance is undetermined.
HIST1H2BC	0	MSKCC-DMP	P-0003216-T01-IM5	HIST1H2BD-HIST1H2BC fusion	yes	unknown		unknown	null  Note: The HIST1H2BC (NM_003526) - HIST1H2BD (NM_021063) rearrangement event results in the deletion of HIST1H2BC (NM_003526), HIST1H2AC  (NM_003512), HIST1H1E (NM_005321) and HIST1H2BD (NM_021063) exon1. The breakpoint in HIST1H2BD is within exon1. Its functional significance is undetermined.
HIST1H2BD	0	MSKCC-DMP	P-0003216-T01-IM5	HIST1H2BD-HIST1H2BC fusion	yes	unknown		unknown	null  Note: The HIST1H2BC (NM_003526) - HIST1H2BD (NM_021063) rearrangement event results in the deletion of HIST1H2BC (NM_003526), HIST1H2AC  (NM_003512), HIST1H1E (NM_005321) and HIST1H2BD (NM_021063) exon1. The breakpoint in HIST1H2BD is within exon1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0003535-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.56-3669:TMPRSS2_c.39+60775:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0003535-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.56-3669:TMPRSS2_c.39+60775:ERGdel
LEMD3	0	MSKCC-DMP	P-0003390-T01-IM5	POLE-LEMD3 fusion	yes	unknown		out of frame	null The POLE-LEMD3 rearrangement is a fusion which results in the fusion of exons 1 to 31 of POLE to exons 2 to 13 of LEMD3.Its functional significance is unknown.
POLE	0	MSKCC-DMP	P-0003390-T01-IM5	POLE-LEMD3 fusion	yes	unknown		out of frame	null The POLE-LEMD3 rearrangement is a fusion which results in the fusion of exons 1 to 31 of POLE to exons 2 to 13 of LEMD3.Its functional significance is unknown.
RAB11FIP4	0	MSKCC-DMP	P-0003390-T01-IM5	POLE-RAB11FIP4 fusion	yes	unknown		in frame	null The POLE-RAB11FIP4 rearrangement is a fusion which results in the fusion of exons 1 to 31 of POLE to exons 4 to 15 of RAB11F1P4.Its functional significance is unknown.
POLE	0	MSKCC-DMP	P-0003390-T01-IM5	POLE-RAB11FIP4 fusion	yes	unknown		in frame	null The POLE-RAB11FIP4 rearrangement is a fusion which results in the fusion of exons 1 to 31 of POLE to exons 4 to 15 of RAB11F1P4.Its functional significance is unknown.
ARID1A	0	MSKCC-DMP	P-0003722-T01-IM5	ARID1A-intragenic	yes	unknown		in frame	c.1920+1713_c.4102-30:ARID1Adel  The ARID1A  (NM_006015) rearrangement results in intragenic deletion of exons 5 to 18.
TNS3	0	MSKCC-DMP	P-0003722-T01-IM5	EGFR-TNS3 fusion	yes	unknown		unknown	TNS3 (NM_022748) - EGFR (NM_005228) inversion (8585063bp) : g.46674498:TNS3_c.2619:EGFRinv The EGFR (NM_005228) rearrangement is an inversion that results in the truncation of exons 21-28.
EGFR	0	MSKCC-DMP	P-0003722-T01-IM5	EGFR-TNS3 fusion	yes	unknown		unknown	TNS3 (NM_022748) - EGFR (NM_005228) inversion (8585063bp) : g.46674498:TNS3_c.2619:EGFRinv The EGFR (NM_005228) rearrangement is an inversion that results in the truncation of exons 21-28.
BRCA2	0	MSKCC-DMP	P-0005741-T01-IM5	BRCA2-intragenic	yes	unknown		in frame	BRCA2 (NM_000059) Rearrangement :  c.7435+72_9257-4656del Note: The BRCA2 (NM_000059) rearrangement results in the intragenic deletion of exon15 to exon24 . Its functional significance is undetermined.
NCRNA00158	0	MSKCC-DMP	P-0014397-T01-IM6	FAT1-NCRNA00158 fusion	yes	unknown		unknown	FAT1(NM_005245) rearrangement: t(4:21)(q35.2;q21.2)(chr4:g.187518320::chr21:g.25402034) Note: The FAT1 rearrangement is a translocation that may result in a truncation of exons 25-27. One of the breakpoints is within exon 25. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0014397-T01-IM6	FAT1-NCRNA00158 fusion	yes	unknown		unknown	FAT1(NM_005245) rearrangement: t(4:21)(q35.2;q21.2)(chr4:g.187518320::chr21:g.25402034) Note: The FAT1 rearrangement is a translocation that may result in a truncation of exons 25-27. One of the breakpoints is within exon 25. The functional significance is undetermined.
CDK5RAP2	0	MSKCC-DMP	P-0014969-T01-IM6	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	BRAF (NM_004333) - CDK5RAP2 (NM_018249) Rearrangement : t(7;9)(q34;q33.3)(chr7:g.140493700::chr9:g.123269531) Note: The BRAF - CDK5RAP2 Rearrangement is a translocation event which results in the fusion of exons 1-8 of BRAF with exons 13-38 of CDK5RAP2. This fusion does not include the protein kinase domain of BRAF but may be associated with an undetected functional CDK5RAP2-BRAF reciprocal fusion.Additional studies will be performed and reported separately.
BRAF	0	MSKCC-DMP	P-0014969-T01-IM6	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	BRAF (NM_004333) - CDK5RAP2 (NM_018249) Rearrangement : t(7;9)(q34;q33.3)(chr7:g.140493700::chr9:g.123269531) Note: The BRAF - CDK5RAP2 Rearrangement is a translocation event which results in the fusion of exons 1-8 of BRAF with exons 13-38 of CDK5RAP2. This fusion does not include the protein kinase domain of BRAF but may be associated with an undetected functional CDK5RAP2-BRAF reciprocal fusion.Additional studies will be performed and reported separately.
APC	0	MSKCC-DMP	P-0015010-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4970_g.112190339del Note: The APC (NM_000038) rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0015010-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4970_g.112190339del Note: The APC (NM_000038) rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0006793-T02-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement: c.-28-1107_c.249del Note: The TP53 Rearrangement is an intragenic deletion of exons 1-4. One of the breakpoints is within exon 4 of TP53. The functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0014544-T01-IM6	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669) Rearrangement : c.1082_c.1360-2791del Note: The INPP4B Rearrangement results in the deletion of exons 15-16  of INPP4B. One of the breakpoints is within exon15. Its functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0008577-T01-IM5	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.-144-15970_28del Note: The ANKRD11 (NM_013275) rearrangement event results in the intragenic deletion of ANKRD11 exons 1-3. One of the breakpoints is within ANKRD11 exon3.
PRKAR2B	0	MSKCC-DMP	P-0008567-T01-IM5	BRAF-PRKAR2B fusion	yes	unknown		in frame	PRKAR2B (NM_002736) - BRAF (NM_004333) rearrangement: c.307+8063:PRKAR2B_c.1177+932:BRAFinv Note: The PRKAR2B (NM_002736) - BRAF (NM_004333) rearrangement event is an inversion which results in the fusion of PRKAR2B exon1 with BRAF exons 10-18. The resulting fusion is predicted to be in-frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0008567-T01-IM5	BRAF-PRKAR2B fusion	yes	unknown		in frame	PRKAR2B (NM_002736) - BRAF (NM_004333) rearrangement: c.307+8063:PRKAR2B_c.1177+932:BRAFinv Note: The PRKAR2B (NM_002736) - BRAF (NM_004333) rearrangement event is an inversion which results in the fusion of PRKAR2B exon1 with BRAF exons 10-18. The resulting fusion is predicted to be in-frame and includes the kinase domain of BRAF.
RAD52	0	MSKCC-DMP	P-0012119-T01-IM5	ERC1-RAD52 fusion	yes	unknown		unknown	RAD52 (NM_134424) -ERC1 (NM_178040) Rearrangement : c.385:RAD52_c.1318-276:ERC1 Note: The RAD52 -ERC1 Rearrangement results in the deletion of exons1-6 of RAD52. The breakpoint in RAD52 is within exon6. Its functional significance is undetermined.
ERC1	0	MSKCC-DMP	P-0012119-T01-IM5	ERC1-RAD52 fusion	yes	unknown		unknown	RAD52 (NM_134424) -ERC1 (NM_178040) Rearrangement : c.385:RAD52_c.1318-276:ERC1 Note: The RAD52 -ERC1 Rearrangement results in the deletion of exons1-6 of RAD52. The breakpoint in RAD52 is within exon6. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0006779-T01-IM5	AKAP8-INSR fusion	yes	unknown		unknown	INSR (NM_000208) rearrangement: c.2513:INSR_chr19:g.15462870inv The INSR (NM_000208) rearrangement is an inversion (8320014 bp) of exons 1-12. The functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0006779-T01-IM5	AKAP8-INSR fusion	yes	unknown		unknown	INSR (NM_000208) rearrangement: c.2513:INSR_chr19:g.15462870inv The INSR (NM_000208) rearrangement is an inversion (8320014 bp) of exons 1-12. The functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0010202-T01-IM5	PPP3R2-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) rearrangement : c.3933:PTCH1_chr9:g.104623233del Note: The PTCH1 rearrangement event results in the deletion of PTCH1 exons 1-23. One of the breakpoints is within PTCH1 exon23.
PPP3R2	0	MSKCC-DMP	P-0010202-T01-IM5	PPP3R2-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) rearrangement : c.3933:PTCH1_chr9:g.104623233del Note: The PTCH1 rearrangement event results in the deletion of PTCH1 exons 1-23. One of the breakpoints is within PTCH1 exon23.
SMARCA4	0	MSKCC-DMP	P-0003063-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	null The SMARCA4 duplication is a structural rearangement event which results in the duplication of exons 15 to 20 of SMARCA4.The breakpoint in exon 20 is within the exon. Its functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0003055-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	null Note: The BRCA2 (NM_000059) rearrangement event is a duplication which results in the  duplication of exons 10 to 18. Its functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0010099-T01-IM5	CMIP-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1590:CDH1_chr16:g.81431871inv Note: The CDH1 rearrangement is an inversion of exons 11 to 16. The breakpoint is within exon 11. The functional significance is undetermined.
CMIP	0	MSKCC-DMP	P-0010099-T01-IM5	CMIP-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1590:CDH1_chr16:g.81431871inv Note: The CDH1 rearrangement is an inversion of exons 11 to 16. The breakpoint is within exon 11. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0001532-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0001532-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
DOT1L	0	MSKCC-DMP	P-0013971-T01-IM5	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) Rearrangement : c.200+69_c.647dup Note: The DOT1L Rearrangement results in the duplication of exons 4-7 of DOT1L. One of the breakpoints is within exon 7. Its functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0008877-T01-IM5	PTPRT-intragenic	yes	unknown		out of frame	PTPRT (NM_133170) Rearrangement :  c.486+20_c.2400-16496del Note: The PTPRT (NM_133170) Rearrangement  results in the deletion of exons 4 to 15 of PTPRT.Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0009592-T01-IM5	NCOA4-RET fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-9 with RET exons 12=20: c.872:NCOA4_c.2136+621:RETdup Note: The NCOA4 (NM_001145260) - RET (NM_020975) fusion is a duplication which includes the kinase domain of RET. One of the breakpoints is within exon 9 of NCOA4.
NCOA4	0	MSKCC-DMP	P-0009592-T01-IM5	NCOA4-RET fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-9 with RET exons 12=20: c.872:NCOA4_c.2136+621:RETdup Note: The NCOA4 (NM_001145260) - RET (NM_020975) fusion is a duplication which includes the kinase domain of RET. One of the breakpoints is within exon 9 of NCOA4.
ERG	0	MSKCC-DMP	P-0012368-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  fusion (TMPRSS2 exons 1-2  with ERG exons 2-10): c.126+409:TMPRSS2_c.18+18604:ERGdel Note: The TMPRSS2 - ERG fusion (TMPRSS2 exons 1-2  with ERG exons 2-10) is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0012368-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  fusion (TMPRSS2 exons 1-2  with ERG exons 2-10): c.126+409:TMPRSS2_c.18+18604:ERGdel Note: The TMPRSS2 - ERG fusion (TMPRSS2 exons 1-2  with ERG exons 2-10) is predicted to be in frame.
ZNF335	0	MSKCC-DMP	P-0010904-T01-IM5	GNAS-ZNF335 fusion	yes	unknown		in frame	GNAS (NM_000516) -  ZNF335 (NM_022095) Rearrangement :  c.970+1:GNAS_c.1103-72:ZNF335inv Note: The GNAS -  ZNF335 Rearrangement results in the fusion of exons 1-10 of GNAS with exons 8-28 of  ZNF335. Its functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0010904-T01-IM5	GNAS-ZNF335 fusion	yes	unknown		in frame	GNAS (NM_000516) -  ZNF335 (NM_022095) Rearrangement :  c.970+1:GNAS_c.1103-72:ZNF335inv Note: The GNAS -  ZNF335 Rearrangement results in the fusion of exons 1-10 of GNAS with exons 8-28 of  ZNF335. Its functional significance is undetermined.
PRB2	0	MSKCC-DMP	P-0008709-T01-IM5	ETV6-PRB2 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.326_chr12:g.11570805dup Note: The ETV6 (NM_001987) rearrangement is a duplication of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0008709-T01-IM5	ETV6-PRB2 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.326_chr12:g.11570805dup Note: The ETV6 (NM_001987) rearrangement is a duplication of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
PDE1A	0	MSKCC-DMP	P-0008709-T01-IM5	SF3B1-PDE1A fusion	yes	unknown		out of frame	SF3B1 (NM_012433) - PDE1A (NM_005019) rearrangement: c.495+79:SF3B1_c.101+118:PDE1Adel Note: The SF3B1 (NM_012433) - PDE1A (NM_005019) rearrangement is a deletion which results in the fusion of SF3B1 exons 1-5 with PDE1A exons 2-14. The functional significance is undetermined.
SF3B1	0	MSKCC-DMP	P-0008709-T01-IM5	SF3B1-PDE1A fusion	yes	unknown		out of frame	SF3B1 (NM_012433) - PDE1A (NM_005019) rearrangement: c.495+79:SF3B1_c.101+118:PDE1Adel Note: The SF3B1 (NM_012433) - PDE1A (NM_005019) rearrangement is a deletion which results in the fusion of SF3B1 exons 1-5 with PDE1A exons 2-14. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0008709-T01-IM5	DDR1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2758_chr6:g.30822725dup. Note: The MDC1 (NM_014641) rearrangement is a duplication of exons 1-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
DDR1	0	MSKCC-DMP	P-0008709-T01-IM5	DDR1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2758_chr6:g.30822725dup. Note: The MDC1 (NM_014641) rearrangement is a duplication of exons 1-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0006926-T02-IM5	LRRC24-RECQL4 fusion	yes	unknown		out of frame	LRRC24 (NM_001024678) - RECQL4 (NM_004260) rearrangement : 2464+40:RECQL4_c.607+132: LRRC24del Note: The LRRC24 (NM_001024678) - RECQL4 (NM_004260) rearrangement event is a deletion which results in the fusion of LRRC24 exons 1-4 with RECQL4 exons 16-22. The resulting fusion is predicted to be out of frame.
LRRC24	0	MSKCC-DMP	P-0006926-T02-IM5	LRRC24-RECQL4 fusion	yes	unknown		out of frame	LRRC24 (NM_001024678) - RECQL4 (NM_004260) rearrangement : 2464+40:RECQL4_c.607+132: LRRC24del Note: The LRRC24 (NM_001024678) - RECQL4 (NM_004260) rearrangement event is a deletion which results in the fusion of LRRC24 exons 1-4 with RECQL4 exons 16-22. The resulting fusion is predicted to be out of frame.
MSH2	0	MSKCC-DMP	P-0014756-T01-IM6	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) rearrangement: c.211+1295_c.688del Note: The MSH2 rearrangement is an intragenic deletion of exons 2-4. One of the breakpoints is within exon 4.
RASA1	0	MSKCC-DMP	P-0010406-T01-IM5	RASA1-intragenic	yes	unknown		out of frame	RASA1 (NM_002890) Rearrangement : c.2691-74_ 3060+57dup Note: The RASA1 Rearrangement results in the intragenic duplication of exons 21-24 of RASA1. Its functional significance is undetermined.
NOVA1	0	MSKCC-DMP	P-0000624-T02-IM5	NFKBIA-NOVA1 fusion	yes	unknown		unknown	NFKBIA (NM_020529) Rearrangement: chr14:g.26301883_c.*232:NFKBIAinv NFKBIA (NM_020529) rearrangement results in the inversion of genomic region including 3-UTR of NFKBIA. Its functional significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0000624-T02-IM5	NFKBIA-NOVA1 fusion	yes	unknown		unknown	NFKBIA (NM_020529) Rearrangement: chr14:g.26301883_c.*232:NFKBIAinv NFKBIA (NM_020529) rearrangement results in the inversion of genomic region including 3-UTR of NFKBIA. Its functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0002435-T01-IM3	ACBD6-IGF1R fusion	yes	unknown		unknown	null
ACBD6	0	MSKCC-DMP	P-0002435-T01-IM3	ACBD6-IGF1R fusion	yes	unknown		unknown	null
BRIP1	0	MSKCC-DMP	P-0002435-T01-IM3	BRIP1-intragenic	yes	unknown		out of frame	null duplication of exons 12-14
HEATR2	0	MSKCC-DMP	P-0002245-T01-IM3	CARD11-HEATR2 fusion	yes	unknown		unknown	null
CARD11	0	MSKCC-DMP	P-0002245-T01-IM3	CARD11-HEATR2 fusion	yes	unknown		unknown	null
FLT1	0	MSKCC-DMP	P-0002796-T01-IM3	IRS2-FLT1 fusion	yes	unknown		in frame	null Note: IRS2 (NM_003749) - FLT1 (NM_002019) fusion is a deletion rearrangement event which results in the in-frame fusion between IRS2 exon 1 and FLT1 exons 2-30.
IRS2	0	MSKCC-DMP	P-0002796-T01-IM3	IRS2-FLT1 fusion	yes	unknown		in frame	null Note: IRS2 (NM_003749) - FLT1 (NM_002019) fusion is a deletion rearrangement event which results in the in-frame fusion between IRS2 exon 1 and FLT1 exons 2-30.
CIC	0	MSKCC-DMP	P-0006281-T01-IM5	PAFAH1B3-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement : c.4734:CIC_chr19:g.42800643inv Note: The CIC (NM_015125) rearrangement results in the inversion of CIC exon20. One of the breakpoints is within CIC exon20.
PAFAH1B3	0	MSKCC-DMP	P-0006281-T01-IM5	PAFAH1B3-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement : c.4734:CIC_chr19:g.42800643inv Note: The CIC (NM_015125) rearrangement results in the inversion of CIC exon20. One of the breakpoints is within CIC exon20.
RBM10	0	MSKCC-DMP	P-0006281-T01-IM5	ZNF157-RBM10 fusion	yes	unknown		unknown	ZNF157 (NM_003446) - RBM10 (NM_001204468) rearrangement : c.2208:RBM10_c.73-19442:ZNF157dup Note: The ZNF157 (NM_003446) - RBM10 (NM_001204468) rearrangement event is a duplication which results in the fusion of ZNF157 exon1  with  RBM10 exons 18-24. One of the breakpoints is within RBM10 exon18.
ZNF157	0	MSKCC-DMP	P-0006281-T01-IM5	ZNF157-RBM10 fusion	yes	unknown		unknown	ZNF157 (NM_003446) - RBM10 (NM_001204468) rearrangement : c.2208:RBM10_c.73-19442:ZNF157dup Note: The ZNF157 (NM_003446) - RBM10 (NM_001204468) rearrangement event is a duplication which results in the fusion of ZNF157 exon1  with  RBM10 exons 18-24. One of the breakpoints is within RBM10 exon18.
ERBB2	0	MSKCC-DMP	P-0001317-T01-IM3	GRB7-ERBB2 fusion	yes	unknown		unknown	null
GRB7	0	MSKCC-DMP	P-0001317-T01-IM3	GRB7-ERBB2 fusion	yes	unknown		unknown	null
TPM3	0	MSKCC-DMP	P-0014143-T01-IM5	NTRK1-TPM3 fusion	yes	unknown		in frame	TPM3 (NM_152263) - NTRK1 (NM_002529) fusion (TPM3 exons 1-10 fused in-frame to NTRK1 exons 9-17): c.*1568:TPM3_c.1178-173:NTRK1inv Note: The TPM3 - NTRK1 fusion includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0014143-T01-IM5	NTRK1-TPM3 fusion	yes	unknown		in frame	TPM3 (NM_152263) - NTRK1 (NM_002529) fusion (TPM3 exons 1-10 fused in-frame to NTRK1 exons 9-17): c.*1568:TPM3_c.1178-173:NTRK1inv Note: The TPM3 - NTRK1 fusion includes the kinase domain of NTRK1.
ARID1A	0	MSKCC-DMP	P-0003870-T01-IM5	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1138-3396_c.2419+5:ARID1Adup The ARID1A (NM_006015) rearrangement is an intragenic duplication of exons 2-7. Its functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0006965-T01-IM5	NTRK2-intragenic	yes	unknown		unknown	NTRK2 (NM_006180) rearrangement : c.1873_1937+1677del Note: The NTRK2 (NM_006180) rearrangement event is a deletion which disrupts the 3 splice site of NTRK2 exon18. One of the breakpoints is on NTRK2 exon18.
ERG	0	MSKCC-DMP	P-0007538-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exons 2 to 10) : c.55+2904:TMPRSS2_c.19-10639:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007538-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exons 2 to 10) : c.55+2904:TMPRSS2_c.19-10639:ERGdel
PLK2	0	MSKCC-DMP	P-0005216-T01-IM5	PDE4D-PLK2 fusion	yes	unknown		out of frame	PLK2 (NM_006622) - PDE4D (NM_001104631) Rearrangement: c.378+18_c.455+337033dup The PLK2 - PDE4D rearrangement is a duplication event in which exons 1-2 of PLK2 (includes partial kinase domain) are fused to exons 2-15 of PDE4D. Its functional significance is not determined.
PDE4D	0	MSKCC-DMP	P-0005216-T01-IM5	PDE4D-PLK2 fusion	yes	unknown		out of frame	PLK2 (NM_006622) - PDE4D (NM_001104631) Rearrangement: c.378+18_c.455+337033dup The PLK2 - PDE4D rearrangement is a duplication event in which exons 1-2 of PLK2 (includes partial kinase domain) are fused to exons 2-15 of PDE4D. Its functional significance is not determined.
KIF5B	0	MSKCC-DMP	P-0001010-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-780:KIF5B_c.2136+679:RETinv
RET	0	MSKCC-DMP	P-0001010-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-780:KIF5B_c.2136+679:RETinv
AR	0	MSKCC-DMP	P-0005452-T01-IM5	AR-intragenic	yes	unknown		unknown	AR (NM_000044) Rearrangement : chrX:g.66753057_c.1131:ARdel Note: The AR (NM_000044) rearrangement results in the intragenic  partial deletion of exon 1. The breakpoint is within exon 1. Its functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0007903-T01-IM5	EPHA6-PPM1D fusion	yes	unknown		unknown	EPHA6 (NM_001080448) - PPM1D (NM_003620) rearrangement : t(3;17)(q11.2;q23.2)(chr3::g.97452596::chr17:g.58734016) Note: The EPHA6 (NM_001080448) - PPM1D (NM_003620) rearrangement event is a translocation which results in the fusion of EPHA6 exons 1-15 with PPM1D exons 5-6. One of the breakpoints is within EPHA6 exon5.
EPHA6	0	MSKCC-DMP	P-0007903-T01-IM5	EPHA6-PPM1D fusion	yes	unknown		unknown	EPHA6 (NM_001080448) - PPM1D (NM_003620) rearrangement : t(3;17)(q11.2;q23.2)(chr3::g.97452596::chr17:g.58734016) Note: The EPHA6 (NM_001080448) - PPM1D (NM_003620) rearrangement event is a translocation which results in the fusion of EPHA6 exons 1-15 with PPM1D exons 5-6. One of the breakpoints is within EPHA6 exon5.
MYD88	0	MSKCC-DMP	P-0005931-T01-IM5	OXSR1-MYD88 fusion	yes	unknown		in frame	OXSR1 (NM_005109) - MYD88 (NM_002468)   Rearrangement :  c.71-7437:OXSR1_c.502+38:MYD88dup Note: The OXSR1 (NM_005109) - MYD88 (NM_002468) rearrangement results in the fusion of exon 1 of OXSR1 to exons3 to 5 of MYD88.  Its functional significance is undetermined.
OXSR1	0	MSKCC-DMP	P-0005931-T01-IM5	OXSR1-MYD88 fusion	yes	unknown		in frame	OXSR1 (NM_005109) - MYD88 (NM_002468)   Rearrangement :  c.71-7437:OXSR1_c.502+38:MYD88dup Note: The OXSR1 (NM_005109) - MYD88 (NM_002468) rearrangement results in the fusion of exon 1 of OXSR1 to exons3 to 5 of MYD88.  Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009892-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 2-10): c.127-551:TMPRSS2_c.18+3860:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009892-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in frame with ERG exons 2-10): c.127-551:TMPRSS2_c.18+3860:ERGdel
RAD51C	0	MSKCC-DMP	P-0003353-T01-IM5	ABCA8-RAD51C fusion	yes	unknown		unknown	null Note: The RAD51C (NM_058216) rearrangement event results in the inversion of the gene. One of the breakpoints is within the promoter region of RAD51C.
ABCA8	0	MSKCC-DMP	P-0003353-T01-IM5	ABCA8-RAD51C fusion	yes	unknown		unknown	null Note: The RAD51C (NM_058216) rearrangement event results in the inversion of the gene. One of the breakpoints is within the promoter region of RAD51C.
MAP2K2	0	MSKCC-DMP	P-0014785-T01-IM6	CHAF1A-MAP2K2 fusion	yes	unknown		out of frame	MAP2K2 (NM_030662) -  CHAF1A (NM_005483) Rearrangement : c.984+60:MAP2K2_c.52+798:CHAF1Ainv Note: The MAP2K2-CHAF1A Rearrangement is an inversion event which results in the fusion of exons 1-8 of MAP2K2 with exons 2-15 of CHAF1A. The fusion includes the protein kinase domain of MAP2K2. Its functional significance is undetermined.
CHAF1A	0	MSKCC-DMP	P-0014785-T01-IM6	CHAF1A-MAP2K2 fusion	yes	unknown		out of frame	MAP2K2 (NM_030662) -  CHAF1A (NM_005483) Rearrangement : c.984+60:MAP2K2_c.52+798:CHAF1Ainv Note: The MAP2K2-CHAF1A Rearrangement is an inversion event which results in the fusion of exons 1-8 of MAP2K2 with exons 2-15 of CHAF1A. The fusion includes the protein kinase domain of MAP2K2. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0007860-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.13+101_c.208del The CTNNB1 (NM_001904) rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon3 of CTNNB1. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0010824-T01-IM5	CDKN2A-RB1 fusion	yes	unknown		out of frame	CDKN2Ap16INK4A (NM_000077) -RB1 (NM_000321) Rearrangement : t(9;13)(p21.3;q14.2)(chr9:g.21970234::chr13:g.48919023) CDKN2Ap14ARF (NM_058195) -RB1 (NM_000321) Rearrangement : t(9;13)(p21.3;q14.2)(chr9:g.21970234::chr13:g.48919023) Note: The CDKN2Ap16INK4A  -RB1 Rearrangement results in the fusion of exons 1-2 of CDKN2Ap16INK4A with exons4-27 of RB1.Its functional significance is undetermined. Note: The CDKN2Ap14ARF -RB1 Rearrangement results in the fusion of exons 1-2 of CDKN2Ap14ARF with exons4-27 of RB1.Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0010824-T01-IM5	CDKN2A-RB1 fusion	yes	unknown		out of frame	CDKN2Ap16INK4A (NM_000077) -RB1 (NM_000321) Rearrangement : t(9;13)(p21.3;q14.2)(chr9:g.21970234::chr13:g.48919023) CDKN2Ap14ARF (NM_058195) -RB1 (NM_000321) Rearrangement : t(9;13)(p21.3;q14.2)(chr9:g.21970234::chr13:g.48919023) Note: The CDKN2Ap16INK4A  -RB1 Rearrangement results in the fusion of exons 1-2 of CDKN2Ap16INK4A with exons4-27 of RB1.Its functional significance is undetermined. Note: The CDKN2Ap14ARF -RB1 Rearrangement results in the fusion of exons 1-2 of CDKN2Ap14ARF with exons4-27 of RB1.Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0010824-T01-IM5	HHIP-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement :  t(4;X)(q31.21.3;p11.3)(chr4:g.145331332::chrX:g.44969451) Note: The KDM6A Rearrangement results in the possible truncation of exons28-29. Its functional significance is undetermined.
HHIP	0	MSKCC-DMP	P-0010824-T01-IM5	HHIP-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement :  t(4;X)(q31.21.3;p11.3)(chr4:g.145331332::chrX:g.44969451) Note: The KDM6A Rearrangement results in the possible truncation of exons28-29. Its functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0012179-T01-IM5	MAP2K4-intragenic	yes	unknown		out of frame	MAP2K4 (NM_003010) Rearrangement :  c.219-11508_c.513+2709del Note: The MAP2K4 Rearrangement results in the intragenic deletion of exons 3-4 of MAP2K4. This includes the kinase domain of MAP2K4.
DSCAM	0	MSKCC-DMP	P-0000449-T02-IM5	TMPRSS2-DSCAM fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.684-15:TMPRSS2_c.509-91895:DSCAMdel Note: The TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement is a deletion that results in the fusion of TMPRSS2 exons 1-6 with DSCAM exons 4-33. The functional significance of this rearrangement is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0000449-T02-IM5	TMPRSS2-DSCAM fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.684-15:TMPRSS2_c.509-91895:DSCAMdel Note: The TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement is a deletion that results in the fusion of TMPRSS2 exons 1-6 with DSCAM exons 4-33. The functional significance of this rearrangement is undetermined.
ABL1	0	MSKCC-DMP	P-0011363-T01-IM5	ABL1-intragenic	yes	unknown		unknown	ABL1 (NM_005157) rearrangement : c.1279_1424-259del Note: The ABL1 rearrangement event results in the deletion of ABL1 exon8. One of the breakpoints is within ABL1 exon8.
TRPC6	0	MSKCC-DMP	P-0008945-T01-IM5	YAP1-TRPC6 fusion	yes	unknown		unknown	YAP1 (NM_001130145) - TRPC6 (NM_004621) Rearrangement :  c.668:YAP1_c.171-25820:TRPC6inv Note: The YAP1 (NM_001130145) - TRPC6 (NM_004621) Rearrangement results in the fusion of exons 1-3 of YAP1 with exons 2-3 of TRPC6. Its functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0008945-T01-IM5	YAP1-TRPC6 fusion	yes	unknown		unknown	YAP1 (NM_001130145) - TRPC6 (NM_004621) Rearrangement :  c.668:YAP1_c.171-25820:TRPC6inv Note: The YAP1 (NM_001130145) - TRPC6 (NM_004621) Rearrangement results in the fusion of exons 1-3 of YAP1 with exons 2-3 of TRPC6. Its functional significance is undetermined.
TET1	0	MSKCC-DMP	P-0002915-T01-IM3	TET1-intragenic	yes	unknown		unknown	null Note: The TET1 (NM_030625) duplication is a rearrangement event which results in the  duplication of exon 2.The breakpoint is within exon 2.
NF1	0	MSKCC-DMP	P-0002915-T01-IM3	NF1-intragenic	yes	unknown		in frame	null Note: The NF1 (NM_001042492) duplication is a rearrangement event which results in the duplication of exons 30 to 35.
ASXL1	0	MSKCC-DMP	P-0003140-T01-IM5	ASXL1-intragenic	yes	unknown		unknown	null The ASXL1 rearrangement is an inversion event which results in the inversion of exon 3. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0004912-T01-IM5	WDTC1-ARID1A fusion	yes	unknown		unknown	ARID1A(NM_006015) Rearrangement : c.4486:ARID1A_chr1:g.27552578inv Note: The ARID1A(NM_006015) Rearrangement results in the inversion of exons 18 to 20.The breakpoint is within exon 18.Its functional significance is undetermined.
WDTC1	0	MSKCC-DMP	P-0004912-T01-IM5	WDTC1-ARID1A fusion	yes	unknown		unknown	ARID1A(NM_006015) Rearrangement : c.4486:ARID1A_chr1:g.27552578inv Note: The ARID1A(NM_006015) Rearrangement results in the inversion of exons 18 to 20.The breakpoint is within exon 18.Its functional significance is undetermined.
IGSF8	0	MSKCC-DMP	P-0004912-T01-IM5	SDHC-IGSF8 fusion	yes	unknown		out of frame	IGSF8(NM_001206665) - SDHC(NM_003001) Rearrangement :  c.65-1579:IGSF8_c.78-10:SDHCinv Note: The IGSF8(NM_001206665) - SDHC(NM_003001) Rearrangement results in fusion of exons 1 and 2 of IGSF8 with exons 3 to 6 of SDHC.its functional significance is undetermined.
SDHC	0	MSKCC-DMP	P-0004912-T01-IM5	SDHC-IGSF8 fusion	yes	unknown		out of frame	IGSF8(NM_001206665) - SDHC(NM_003001) Rearrangement :  c.65-1579:IGSF8_c.78-10:SDHCinv Note: The IGSF8(NM_001206665) - SDHC(NM_003001) Rearrangement results in fusion of exons 1 and 2 of IGSF8 with exons 3 to 6 of SDHC.its functional significance is undetermined.
SORBS2	0	MSKCC-DMP	P-0003009-T01-IM3	FAT1-SORBS2 fusion	yes	unknown		unknown	null Note: The FAT1(NM_005245) -SORBS2 (NM_021069) rearrangement is a deletion event which results in the  fusion between FAT1 exons 1-10 and SORBS2 exons 2-21. The breakpoint in on exon 10 of FAT1.
FAT1	0	MSKCC-DMP	P-0003009-T01-IM3	FAT1-SORBS2 fusion	yes	unknown		unknown	null Note: The FAT1(NM_005245) -SORBS2 (NM_021069) rearrangement is a deletion event which results in the  fusion between FAT1 exons 1-10 and SORBS2 exons 2-21. The breakpoint in on exon 10 of FAT1.
PIK3R3	0	MSKCC-DMP	P-0006838-T01-IM5	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: PIK3R3:c.215+705_c.901del The PIK3R3 (NM_003629) rearrangement results in an intra-genic deletion of PIK3R3 exons 3-7 and one of the the breakpoints is within exon 7.
STAT5A	0	MSKCC-DMP	P-0006838-T01-IM5	ZNF804A-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) rearrangment : t(2;17)(q32.1;q21.2)(c.2282: STAT5A_g.185422175) The STAT5A (NM_003152) rearrangement is a reciprocal translocation involving a breakpoint with exon 20 of STAT5A and a genomic location on chromosome 2. Its functional significance is undetermined.
ZNF804A	0	MSKCC-DMP	P-0006838-T01-IM5	ZNF804A-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) rearrangment : t(2;17)(q32.1;q21.2)(c.2282: STAT5A_g.185422175) The STAT5A (NM_003152) rearrangement is a reciprocal translocation involving a breakpoint with exon 20 of STAT5A and a genomic location on chromosome 2. Its functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0003725-T01-IM5	CLVS1-FGFR1 fusion	yes	unknown		unknown	c.1359:FGFR1_g.62143239inv The FGFR1 (NM_001174067) rearrangement event results in the inversion of exons 9-19. The functional significance is undetermined.
CLVS1	0	MSKCC-DMP	P-0003725-T01-IM5	CLVS1-FGFR1 fusion	yes	unknown		unknown	c.1359:FGFR1_g.62143239inv The FGFR1 (NM_001174067) rearrangement event results in the inversion of exons 9-19. The functional significance is undetermined.
MIAT	0	MSKCC-DMP	P-0003768-T01-IM5	NF2-MIAT fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: chr22:g.27323591_c.1738-167:NF2inv The NF2 (NM_000268) rearrangement is an inversion in which exons 1-4 of NF2 are inverted. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0003768-T01-IM5	NF2-MIAT fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: chr22:g.27323591_c.1738-167:NF2inv The NF2 (NM_000268) rearrangement is an inversion in which exons 1-4 of NF2 are inverted. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0014954-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.3175_c.3434-1006del Note: The KDM6A rearrangement is an intragenic deletion of exons 21-23. One of the breakpoints is within exon 21.
ASCC3	0	MSKCC-DMP	P-0011369-T01-IM5	PRDM1-ASCC3 fusion	yes	unknown		unknown	PRDM1 (NM_001198) Rearrangement: chr6:g.101334934_c.291+22:PRDM1inv Note: The PRDM1 Rearrangement results in the inversion of exons1-2 of PRDM1. Its functional significance is undetermined.
PRDM1	0	MSKCC-DMP	P-0011369-T01-IM5	PRDM1-ASCC3 fusion	yes	unknown		unknown	PRDM1 (NM_001198) Rearrangement: chr6:g.101334934_c.291+22:PRDM1inv Note: The PRDM1 Rearrangement results in the inversion of exons1-2 of PRDM1. Its functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0012505-T01-IM5	UNC13C-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) - UNC13C (NM_001080534) rearrangement: t(15;18)(q21.3;q21.2)(chr15:g.54879988::chr18:g.48584727) Note: The SMAD4 - UNC13C rearrangement is a translocation that results in a fusion of SMAD4 exons 1-7 with UNC13C exons  29-31. One of the breakpoints is within SMAD4 exon7. The functionals significance is undetermined.
UNC13C	0	MSKCC-DMP	P-0012505-T01-IM5	UNC13C-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) - UNC13C (NM_001080534) rearrangement: t(15;18)(q21.3;q21.2)(chr15:g.54879988::chr18:g.48584727) Note: The SMAD4 - UNC13C rearrangement is a translocation that results in a fusion of SMAD4 exons 1-7 with UNC13C exons  29-31. One of the breakpoints is within SMAD4 exon7. The functionals significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0014332-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.1207_c.1308+3512del Note: The SMAD4 (NM_005359) rearrangement is a deletion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007025-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-3598:TMPRSS2_c.-150+4207:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement is a deletion with a breakpoint 82kb upstream of ERG.
TMPRSS2	0	MSKCC-DMP	P-0007025-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-3598:TMPRSS2_c.-150+4207:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement is a deletion with a breakpoint 82kb upstream of ERG.
SUPT4H1	0	MSKCC-DMP	P-0005824-T01-IM5	RNF43-SUPT4H1 fusion	yes	unknown		out of frame	SUPT4H1 (NM_003168) - RNF43 (NM_017763) rearrangement event : :SUPT4H1_:RNF43dup Note: The SUPT4H1 (NM_003168) - RNF43 (NM_017763) rearrangement event is a duplication which results in the fusion of SUPT4H1 1-2 exons with RNF43 exon10. The fusion is predicted to be out of frame.
RNF43	0	MSKCC-DMP	P-0005824-T01-IM5	RNF43-SUPT4H1 fusion	yes	unknown		out of frame	SUPT4H1 (NM_003168) - RNF43 (NM_017763) rearrangement event : :SUPT4H1_:RNF43dup Note: The SUPT4H1 (NM_003168) - RNF43 (NM_017763) rearrangement event is a duplication which results in the fusion of SUPT4H1 1-2 exons with RNF43 exon10. The fusion is predicted to be out of frame.
MTAP	0	MSKCC-DMP	P-0002886-T01-IM3	CDKN2B-MTAP fusion	yes	unknown		in frame	null Note: The MTAP (NM_002451) - CDKN2B (NM_004936) inversion is a rearrangement event which results in the fusion of MTAP exons 1 to 7 and CDKN2B exon 2. Its functional significance is not known
CDKN2B	0	MSKCC-DMP	P-0002886-T01-IM3	CDKN2B-MTAP fusion	yes	unknown		in frame	null Note: The MTAP (NM_002451) - CDKN2B (NM_004936) inversion is a rearrangement event which results in the fusion of MTAP exons 1 to 7 and CDKN2B exon 2. Its functional significance is not known
MAPK4	0	MSKCC-DMP	P-0005211-T01-IM5	SMAD4-MAPK4 fusion	yes	unknown		unknown	MAPK4 (NM_002747) - SMAD4 (NM_005359) Rearrangement: c.547-13524:MAPK4_c.48:SMAD4del MAPK4 (NM_002747) - SMAD4 (NM_005359) rearrangement is a deletion that results in the fusion of exons 1-2 of MAPK4 (including kinase domain) with exons 2-12 of SMAD4. One of the breakpoints is within the exon of SMAD4. Its functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0005211-T01-IM5	SMAD4-MAPK4 fusion	yes	unknown		unknown	MAPK4 (NM_002747) - SMAD4 (NM_005359) Rearrangement: c.547-13524:MAPK4_c.48:SMAD4del MAPK4 (NM_002747) - SMAD4 (NM_005359) rearrangement is a deletion that results in the fusion of exons 1-2 of MAPK4 (including kinase domain) with exons 2-12 of SMAD4. One of the breakpoints is within the exon of SMAD4. Its functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0013705-T01-IM5	RALGAPB-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) - RALGAPB (NM_020336) rearrangement:  c.3667:ASXL1_c.3268:RALGAPBdel Note: The ASXL1 - RALGAPB rearrangement is a deletion which results in the fusion of ASXL1 exon 12 to RALGAPB. Both breakpoints are within exon. The functional significance is undetermined.
RALGAPB	0	MSKCC-DMP	P-0013705-T01-IM5	RALGAPB-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) - RALGAPB (NM_020336) rearrangement:  c.3667:ASXL1_c.3268:RALGAPBdel Note: The ASXL1 - RALGAPB rearrangement is a deletion which results in the fusion of ASXL1 exon 12 to RALGAPB. Both breakpoints are within exon. The functional significance is undetermined.
KIF1B	0	MSKCC-DMP	P-0013861-T01-IM5	MTOR-KIF1B fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : c.1413-12:MTOR_c.1978-4081:KIF1Bdup Note: The MTOR Rearrangement results in the duplication of exons 10-58 of MTOR. It includes the kinase domain of MTOR. Its functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0013861-T01-IM5	MTOR-KIF1B fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : c.1413-12:MTOR_c.1978-4081:KIF1Bdup Note: The MTOR Rearrangement results in the duplication of exons 10-58 of MTOR. It includes the kinase domain of MTOR. Its functional significance is undetermined.
MRE11A	0	MSKCC-DMP	P-0011029-T02-IM5	ST6GALNAC3-MRE11A fusion	yes	unknown		unknown	ST6GALNAC3 (NM_152996) - MRE11A (NM_005591) rearrangement : t(1;11)(p31.1;q21)(chr1:g.76791695::chr11:g.94192656) Note: The ST6GALNAC3-MRE11A rearrangement event is a translocation which results in the possible truncation of MRE11A exons 13-20. One of the breakpoints is within MRE11A exon13. The functional significance is undetermined.
ST6GALNAC3	0	MSKCC-DMP	P-0011029-T02-IM5	ST6GALNAC3-MRE11A fusion	yes	unknown		unknown	ST6GALNAC3 (NM_152996) - MRE11A (NM_005591) rearrangement : t(1;11)(p31.1;q21)(chr1:g.76791695::chr11:g.94192656) Note: The ST6GALNAC3-MRE11A rearrangement event is a translocation which results in the possible truncation of MRE11A exons 13-20. One of the breakpoints is within MRE11A exon13. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0012307-T01-IM5	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.1299+79_c.7689dup Note: The MLL3 rearrangement is an intragenic duplication of exons 10 - 38. One of the breakpoint is within exon 38.
IGF1R	0	MSKCC-DMP	P-0010464-T01-IM5	PPP1R3A-IGF1R fusion	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: t(7;15)(q31.1;q25.3)(chr7:g.113198852::chr15:g.99434762) Note: The IGF1R rearrangement is a translocation with a breakpoint within exon3 of IGF1R. The functional significance is undetermined.
PPP1R3A	0	MSKCC-DMP	P-0010464-T01-IM5	PPP1R3A-IGF1R fusion	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: t(7;15)(q31.1;q25.3)(chr7:g.113198852::chr15:g.99434762) Note: The IGF1R rearrangement is a translocation with a breakpoint within exon3 of IGF1R. The functional significance is undetermined.
ERMP1	0	MSKCC-DMP	P-0002088-T01-IM3	TGFBR1-ERMP1 fusion	yes	unknown		unknown	TGFBR1 (NM_004612) Deletion : c.575-98_g.5801401del
TGFBR1	0	MSKCC-DMP	P-0002088-T01-IM3	TGFBR1-ERMP1 fusion	yes	unknown		unknown	TGFBR1 (NM_004612) Deletion : c.575-98_g.5801401del
LOC100128554	0	MSKCC-DMP	P-0014235-T01-IM6	POLE-LOC100128554 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.2195_chr12:g.126611209dup Note: The POLE rearrangement is a duplication which includes exons 20-49 of POLE. One of the breakpoints is within exon 20. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0014235-T01-IM6	POLE-LOC100128554 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.2195_chr12:g.126611209dup Note: The POLE rearrangement is a duplication which includes exons 20-49 of POLE. One of the breakpoints is within exon 20. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0003408-T01-IM5	PTPRN2-EP300 fusion	yes	unknown		out of frame	null Note: The TEP300 (NM_001429) - PTPRN2 (NM_002847) rearrangement event is a translocation which results in the fusion of EP300 exons 1-20 and PTPRN2 exons 17-23.
PTPRN2	0	MSKCC-DMP	P-0003408-T01-IM5	PTPRN2-EP300 fusion	yes	unknown		out of frame	null Note: The TEP300 (NM_001429) - PTPRN2 (NM_002847) rearrangement event is a translocation which results in the fusion of EP300 exons 1-20 and PTPRN2 exons 17-23.
MRPS22	0	MSKCC-DMP	P-0013774-T01-IM5	MAP3K13-MRPS22 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: chr3:g.139046929_c.428:MAP3K13inv Note: The MAP3K13 rearrangement is an inversion which includes exons 1-2 of MAP3K13. One of the breakpoints is within exon2. The functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0013774-T01-IM5	MAP3K13-MRPS22 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: chr3:g.139046929_c.428:MAP3K13inv Note: The MAP3K13 rearrangement is an inversion which includes exons 1-2 of MAP3K13. One of the breakpoints is within exon2. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0013089-T01-IM5	FLJ39534-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement : c.2025:SETD2_chr3:g.47250984del Note: The SETD2 Rearrangement results in the deletion of exons 1-3 of SETD2. One of the breakpoints is within exon3 of SETD2. Its functional significance is undetermined.
FLJ39534	0	MSKCC-DMP	P-0013089-T01-IM5	FLJ39534-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement : c.2025:SETD2_chr3:g.47250984del Note: The SETD2 Rearrangement results in the deletion of exons 1-3 of SETD2. One of the breakpoints is within exon3 of SETD2. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0003613-T01-IM5	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141)  Rearrangement:  c.2301+149_g.123741897inv Note: The FGFR2 rearrangement results in the inversion of exons 1 to 16 of FGFR2 .It includes the kinase domain of FGFR2.
TACC2	0	MSKCC-DMP	P-0003613-T01-IM5	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141)  Rearrangement:  c.2301+149_g.123741897inv Note: The FGFR2 rearrangement results in the inversion of exons 1 to 16 of FGFR2 .It includes the kinase domain of FGFR2.
NOTCH3	0	MSKCC-DMP	P-0001278-T01-IM3	EPHX3-NOTCH3 fusion	yes	unknown		unknown	null
EPHX3	0	MSKCC-DMP	P-0001278-T01-IM3	EPHX3-NOTCH3 fusion	yes	unknown		unknown	null
EMID1	0	MSKCC-DMP	P-0005190-T01-IM5	EWSR1-EMID1 fusion	yes	unknown		out of frame	EMID1 (NM_133455) - EWSR1 (NM_013986) Rearrangement :  c.101+811:EMID1_c.794-373:EWSR1del Note: The EMID1 (NM_133455) - EWSR1 (NM_013986) Rearrangement results in fusion of exon 1 of EMID1 with exons 11 to 18 of EWSR1.Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0005190-T01-IM5	EWSR1-EMID1 fusion	yes	unknown		out of frame	EMID1 (NM_133455) - EWSR1 (NM_013986) Rearrangement :  c.101+811:EMID1_c.794-373:EWSR1del Note: The EMID1 (NM_133455) - EWSR1 (NM_013986) Rearrangement results in fusion of exon 1 of EMID1 with exons 11 to 18 of EWSR1.Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0010588-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.-50+15973_c.4758del. Note: The ZFHX3 rearrangement is an intragenic deletion of exons 2-9. One of the breakpoints is within exon9. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0009356-T01-IM5	CA10-STAT5A fusion	yes	unknown		unknown	CA10 (NM_001082533) - STAT5A (NM_003152) rearrangement: c.280-87866:CA10_c.1146:STAT5Ainv Note: The CA10 (NM_001082533) - STAT5A (NM_003152) rearrangement is an inversion that results in the fusion of CA10 exons 1-3 with STAT5A exons 10-20. One of the breakpoints is within STAT4A exon 10. The functional significance of this rearrangement is undetermined.
CA10	0	MSKCC-DMP	P-0009356-T01-IM5	CA10-STAT5A fusion	yes	unknown		unknown	CA10 (NM_001082533) - STAT5A (NM_003152) rearrangement: c.280-87866:CA10_c.1146:STAT5Ainv Note: The CA10 (NM_001082533) - STAT5A (NM_003152) rearrangement is an inversion that results in the fusion of CA10 exons 1-3 with STAT5A exons 10-20. One of the breakpoints is within STAT4A exon 10. The functional significance of this rearrangement is undetermined.
VEGFA	0	MSKCC-DMP	P-0012821-T01-IM5	VEGFA-intragenic	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement : g.43797417_c.393-90:VEGFAdup Note: The VEGFA (NM_001171623) rearrangement is a duplication which includes VEGFA exons 1-4. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0007143-T02-IM5	PCDH7-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(4;21)(p15.1;q22.3)(chr4:g.29662732::chr21:g.42875074) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint after exon1. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion. Additional testing by an alternate platform is suggested, if clinically indicated.
PCDH7	0	MSKCC-DMP	P-0007143-T02-IM5	PCDH7-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(4;21)(p15.1;q22.3)(chr4:g.29662732::chr21:g.42875074) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint after exon1. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion. Additional testing by an alternate platform is suggested, if clinically indicated.
CCND1	0	MSKCC-DMP	P-0014680-T01-IM6	PGR-CCND1 fusion	yes	unknown		unknown	PGR (NM_000926) - CCND1 (NM_053056) rearrangement: c.1906+67:PGR_c.-1379:CCND1inv Note: The PGR - CCND1 rearrangement is an inversion, with breakpoints in the promoter region of CCND1 and intron 3 of PGR. The functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0014680-T01-IM6	PGR-CCND1 fusion	yes	unknown		unknown	PGR (NM_000926) - CCND1 (NM_053056) rearrangement: c.1906+67:PGR_c.-1379:CCND1inv Note: The PGR - CCND1 rearrangement is an inversion, with breakpoints in the promoter region of CCND1 and intron 3 of PGR. The functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0012317-T01-IM5	BSN-RICTOR fusion	yes	unknown		out of frame	BSN (NM_003458) - RICTOR (NM_152756) Rearrangement : t(3;5)(p21.312;p13.1)(chr3:g49594666::chr5:g.38991280) Note: The BSN - RICTOR Rearrangement results in the fusion of exon1 of BSN with exons 7-38 of RICTOR. Its functional significance is undetermined.
BSN	0	MSKCC-DMP	P-0012317-T01-IM5	BSN-RICTOR fusion	yes	unknown		out of frame	BSN (NM_003458) - RICTOR (NM_152756) Rearrangement : t(3;5)(p21.312;p13.1)(chr3:g49594666::chr5:g.38991280) Note: The BSN - RICTOR Rearrangement results in the fusion of exon1 of BSN with exons 7-38 of RICTOR. Its functional significance is undetermined.
CBL	0	MSKCC-DMP	P-0001430-T01-IM3	CBL-intragenic	yes	unknown		in frame	None
DOCK7	0	MSKCC-DMP	P-0006840-T01-IM5	JAK1-DOCK7 fusion	yes	unknown		out of frame	DOCK7 (NM_033407) - JAK1 (NM_002227) rearrangement : c.6120-7503:DOCK7_c.483+17:JAK1del The DOCK7 (NM_033407) - JAK1 (NM_002227) is a rearrangement event which results in the deletion of  DOCK7 exon 1-48 and JAK1 exon 5-25
JAK1	0	MSKCC-DMP	P-0006840-T01-IM5	JAK1-DOCK7 fusion	yes	unknown		out of frame	DOCK7 (NM_033407) - JAK1 (NM_002227) rearrangement : c.6120-7503:DOCK7_c.483+17:JAK1del The DOCK7 (NM_033407) - JAK1 (NM_002227) is a rearrangement event which results in the deletion of  DOCK7 exon 1-48 and JAK1 exon 5-25
ERG	0	MSKCC-DMP	P-0006840-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exons 4 to 10) : c.55+3696:TMPRSS2:c.39+61789:ERG_del
TMPRSS2	0	MSKCC-DMP	P-0006840-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exons 4 to 10) : c.55+3696:TMPRSS2:c.39+61789:ERG_del
OR3A2	0	MSKCC-DMP	P-0008752-T01-IM5	RB1-OR3A2 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement :  t(13;17)(13q14.2;17p13.3)(chr13:g.48916707::chr17:g.3170417) Note: The RB1 (NM_000321) Rearrangement  is a translocation event which results in the  truncation of exons 3-27 of RB1. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0008752-T01-IM5	RB1-OR3A2 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement :  t(13;17)(13q14.2;17p13.3)(chr13:g.48916707::chr17:g.3170417) Note: The RB1 (NM_000321) Rearrangement  is a translocation event which results in the  truncation of exons 3-27 of RB1. Its functional significance is undetermined.
RAD51C	0	MSKCC-DMP	P-0009325-T02-IM5	DHX40-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - DHX40 (NM_024612) rearrangement: c.1003:RAD51C_c.1901+399:DHX40del Note: The RAD51C (NM_058216) - DHX40 (NM_024612) rearrangement is a deletion which results in the fusion of RAD51C exons 1-8 with DHX40 exons 16-18. One of the breakpoints is within exon 8 of RAD51C. The functional significance is undetermined.
DHX40	0	MSKCC-DMP	P-0009325-T02-IM5	DHX40-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - DHX40 (NM_024612) rearrangement: c.1003:RAD51C_c.1901+399:DHX40del Note: The RAD51C (NM_058216) - DHX40 (NM_024612) rearrangement is a deletion which results in the fusion of RAD51C exons 1-8 with DHX40 exons 16-18. One of the breakpoints is within exon 8 of RAD51C. The functional significance is undetermined.
SYK	0	MSKCC-DMP	P-0001903-T01-IM3	SYK-intragenic	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0003023-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 1)
TMPRSS2	0	MSKCC-DMP	P-0003023-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 1)
FLT1	0	MSKCC-DMP	P-0006090-T01-IM5	FLT1-intragenic	yes	unknown		unknown	FLT1 (NM_002019)  Rearrangement :  c.3570_*451del Note: The FLT1 (NM_002019)  rearrangement results in the intragenic deletion of exons 27 to 30 of FLT1. The breakpoint is within exon 27 . Its functional significance is unknown.
TOP1	0	MSKCC-DMP	P-0010382-T01-IM5	TOP1-intragenic	yes	unknown		out of frame	TOP1 (NM_003286) rearrangement: c.1163+18_c.1308+706del Note: The TOP1 rearrangement is an intragenic deletion of exon 13. The functional significance is undetermined.
SLC16A7	0	MSKCC-DMP	P-0005567-T01-IM5	POLE-SLC16A7 fusion	yes	unknown		unknown	POLE (NM_006231) Rearrangement :  c.6843:POLE_chr12:g.61019594inv Note: The POLE (NM_006231) Rearrangement results in the inversion of exon 49 of POLE. The breakpoint is within exon49. Its functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0005567-T01-IM5	POLE-SLC16A7 fusion	yes	unknown		unknown	POLE (NM_006231) Rearrangement :  c.6843:POLE_chr12:g.61019594inv Note: The POLE (NM_006231) Rearrangement results in the inversion of exon 49 of POLE. The breakpoint is within exon49. Its functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0003130-T01-IM5	TSPAN8-GLI1 fusion	yes	unknown		unknown	null c.1941:GLI1_g.71414253dup    Note 2: The GLI1 (NM_005269) rearrangement event is a duplication which results in the duplication of part of exon 11 and all of exon 12 of GLI1. Its functional significance is undetermined    duplication of last exon and UTR, might not do anything!   undetermined function note
TSPAN8	0	MSKCC-DMP	P-0003130-T01-IM5	TSPAN8-GLI1 fusion	yes	unknown		unknown	null c.1941:GLI1_g.71414253dup    Note 2: The GLI1 (NM_005269) rearrangement event is a duplication which results in the duplication of part of exon 11 and all of exon 12 of GLI1. Its functional significance is undetermined    duplication of last exon and UTR, might not do anything!   undetermined function note
VGLL3	0	MSKCC-DMP	P-0011558-T01-IM5	EPHA3-VGLL3 fusion	yes	unknown		unknown	EPHA3 (NM_005233) rearrangement: chr3:g.86628511_c.2467inv Note: The EPHA3 rearrangement results in an inversion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
EPHA3	0	MSKCC-DMP	P-0011558-T01-IM5	EPHA3-VGLL3 fusion	yes	unknown		unknown	EPHA3 (NM_005233) rearrangement: chr3:g.86628511_c.2467inv Note: The EPHA3 rearrangement results in an inversion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0010812-T01-IM5	PKD1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) - PKD1 (NM_001009944) rearrangement : c.4662+1:TSC2_c.3162-137:PKD1del Note: The TSC2 - PKD1 rearrangement event results in the deletion of TSC2 exons 35-40. One of the breakpoints is on exon35 splice site.
PKD1	0	MSKCC-DMP	P-0010812-T01-IM5	PKD1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) - PKD1 (NM_001009944) rearrangement : c.4662+1:TSC2_c.3162-137:PKD1del Note: The TSC2 - PKD1 rearrangement event results in the deletion of TSC2 exons 35-40. One of the breakpoints is on exon35 splice site.
ANXA10	0	MSKCC-DMP	P-0013772-T01-IM5	FAT1-ANXA10 fusion	yes	unknown		unknown	ANXA10 (NM_007193) - FAT1 (NM_005245) rearrangement: c.19-6085:ANXA10_c.5713:FAT1inv Note: The ANXA10 - FAT1 rearrangement is an inversion which results in the fusion of ANXA10 exon 1 with FAT1 exons 10-27. One of the breakpoints is within exon 10 of FAT1. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0013772-T01-IM5	FAT1-ANXA10 fusion	yes	unknown		unknown	ANXA10 (NM_007193) - FAT1 (NM_005245) rearrangement: c.19-6085:ANXA10_c.5713:FAT1inv Note: The ANXA10 - FAT1 rearrangement is an inversion which results in the fusion of ANXA10 exon 1 with FAT1 exons 10-27. One of the breakpoints is within exon 10 of FAT1. The functional significance is undetermined.
PROCA1	0	MSKCC-DMP	P-0005984-T01-IM5	BRCA1-PROCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) -  PROCA1 (NM_152465) rearrangement: c.1574:BRCA1_c.92-1069:PROCA1inv.  The BRCA1 (NM_007294) -  PROCA1 (NM_152465) rearrangement is an inversion (14213044 bp) which may result in the truncation of BRCA1 exons 10-23. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0005984-T01-IM5	BRCA1-PROCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) -  PROCA1 (NM_152465) rearrangement: c.1574:BRCA1_c.92-1069:PROCA1inv.  The BRCA1 (NM_007294) -  PROCA1 (NM_152465) rearrangement is an inversion (14213044 bp) which may result in the truncation of BRCA1 exons 10-23. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0008516-T01-IM5	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement :  c.998_1780dup Note: The KDM6A (NM_021140) Rearrangement  results in the intragenic duplication of exons 12 to 16 of KDM6A. The breakpoints are within exon 12 and exon16 respectively. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0011303-T01-IM5	STK11-intragenic	yes	unknown		in frame	STK11 (NM_000455) rearrangement: c.375-384_c.735-5dup Note: The STK11 rearrangement is an intragenic duplication of exons 3-5.
KDR	0	MSKCC-DMP	P-0006402-T01-IM5	KDR-intragenic	yes	unknown		unknown	KDR (NM_002253) rearrangement : c.1255+49_*5959inv Note: The KDR (NM_002253) rearrangement event results in the inversion of KDR exons 10-30, likely truncating KDR. The event involves the kinase domain of KDR.
EP300	0	MSKCC-DMP	P-0001286-T01-IM3	EP300-intragenic	yes	unknown		out of frame	null
ERG	0	MSKCC-DMP	P-0003052-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0003052-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
BRIP1	0	MSKCC-DMP	P-0011331-T01-IM5	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) Rearrangement :  c.2575+2706_c.3570del Note: The BRIP1 Rearrangement  results in the intragenic deletion of exons 19-20 of BRIP1. One of the breakpoints is within exon20. Its functional significance is undetermined,
PLEKHG4B	0	MSKCC-DMP	P-0011331-T01-IM5	TERT-PLEKHG4B fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :  chr5:g.23741_c.2287-76:TERTinv Note: The TERT Rearrangement  results in the inversion of  exons7-16 of TERT .Its functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0011331-T01-IM5	TERT-PLEKHG4B fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :  chr5:g.23741_c.2287-76:TERTinv Note: The TERT Rearrangement  results in the inversion of  exons7-16 of TERT .Its functional significance is undetermined.
ATAD1	0	MSKCC-DMP	P-0004892-T01-IM5	PTEN-ATAD1 fusion	yes	unknown		unknown	ATAD1 (NM_032810) - PTEN (NM_000314) rearrangement: c.583+1858:ATAD1_NM_000314.4:c.960:PTENdel The ATAD1 (NM_032810) - PTEN (NM_000314) rearrangement is a deletion of exons 1-5 of ATAD1 and exons 1-8 of PTEN. One of the breakpoints is within exon 8 of PTEN. (PMID: 22705054)
PTEN	0	MSKCC-DMP	P-0004892-T01-IM5	PTEN-ATAD1 fusion	yes	unknown		unknown	ATAD1 (NM_032810) - PTEN (NM_000314) rearrangement: c.583+1858:ATAD1_NM_000314.4:c.960:PTENdel The ATAD1 (NM_032810) - PTEN (NM_000314) rearrangement is a deletion of exons 1-5 of ATAD1 and exons 1-8 of PTEN. One of the breakpoints is within exon 8 of PTEN. (PMID: 22705054)
BRCA2	0	MSKCC-DMP	P-0004892-T01-IM5	INSC-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: t(13;11)(q13;p15.2)(chr13:g.32893422::chr11:g.11:15549664) The BRCA2 (NM_000059) rearrangement is a translocation that may result in the truncation of BRCA2 exons 3-27. One of the breakpoints is within exon 3 of BRCA2. The functional significance is undetermined.
INSC	0	MSKCC-DMP	P-0004892-T01-IM5	INSC-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: t(13;11)(q13;p15.2)(chr13:g.32893422::chr11:g.11:15549664) The BRCA2 (NM_000059) rearrangement is a translocation that may result in the truncation of BRCA2 exons 3-27. One of the breakpoints is within exon 3 of BRCA2. The functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0007700-T01-IM5	ZNF525-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: c.256:AXL_chr19:g.53878345inv The AXL (NM_021913) rearrangement is an inversion (12151634 bp) which includes exons 2-20 of AXL. One of the breakpoints is within exon 2 of AXL. The functional significance is undetermined.
ZNF525	0	MSKCC-DMP	P-0007700-T01-IM5	ZNF525-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: c.256:AXL_chr19:g.53878345inv The AXL (NM_021913) rearrangement is an inversion (12151634 bp) which includes exons 2-20 of AXL. One of the breakpoints is within exon 2 of AXL. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0000632-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null
CD74	0	MSKCC-DMP	P-0000632-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null
RAD51C	0	MSKCC-DMP	P-0012122-T01-IM5	BCAS3-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - BCAS3 (NM_001099432) Rearrangement : c.1026+48:RAD51C_c.215-6649:BCAS3inv Note: The RAD51C -BCAS3  Rearrangement results in the inversion of exon9 of RAD51C. Its functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0012122-T01-IM5	BCAS3-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - BCAS3 (NM_001099432) Rearrangement : c.1026+48:RAD51C_c.215-6649:BCAS3inv Note: The RAD51C -BCAS3  Rearrangement results in the inversion of exon9 of RAD51C. Its functional significance is undetermined.
LATS2	0	MSKCC-DMP	P-0004708-T01-IM5	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) rearrangement : c.343-7641_1003del Note: The LATS2 (NM_014572) rearrangement event results in the intragenic deletion of LATS2 exons 3-4. One of the breakpoints is within LATS2 exon4.
TP53	0	MSKCC-DMP	P-0004113-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement event: c.994-497_1101-80inv Note: The TP53 rearrangement event results in the intragenic inversion of TP53 exon10.
CTNNB1	0	MSKCC-DMP	P-0012683-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1917_c.690inv Note: The CTNNB1 rearrangement is an inversion of exons 1-5. One of the breakpoints is within exon5. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0005879-T01-IM5	RGS9-STAT3 fusion	yes	unknown		unknown	RGS9  (NM_003835) - STAT3 (NM_139276) Rearrangement :  c.1203+101:RGS9_c.1520:STAT3inv Note: The RGS9  (NM_003835) - STAT3 (NM_139276) rearrangement results in the fusion of exons 1 to 15 of RGS9  to exons 17 to 24 of STAT3. The breakpoint is within exon17 of STAT3. Its functional significance is undetermined.
RGS9	0	MSKCC-DMP	P-0005879-T01-IM5	RGS9-STAT3 fusion	yes	unknown		unknown	RGS9  (NM_003835) - STAT3 (NM_139276) Rearrangement :  c.1203+101:RGS9_c.1520:STAT3inv Note: The RGS9  (NM_003835) - STAT3 (NM_139276) rearrangement results in the fusion of exons 1 to 15 of RGS9  to exons 17 to 24 of STAT3. The breakpoint is within exon17 of STAT3. Its functional significance is undetermined.
FSCB	0	MSKCC-DMP	P-0007971-T01-IM5	ARID5B-FSCB fusion	yes	unknown		unknown	ARID5B (NM_032199) rearrangement : t(10;14)(q21.2;q21.2)(chr10:.g.63851226::chr14:g.44208017 ) Note: The ARID5B (NM_032199) rearrangement event is a reciprocal translocation which results in the truncation of ARID5B exons10. One of the breakpoints is within ARID5B exon10.
ARID5B	0	MSKCC-DMP	P-0007971-T01-IM5	ARID5B-FSCB fusion	yes	unknown		unknown	ARID5B (NM_032199) rearrangement : t(10;14)(q21.2;q21.2)(chr10:.g.63851226::chr14:g.44208017 ) Note: The ARID5B (NM_032199) rearrangement event is a reciprocal translocation which results in the truncation of ARID5B exons10. One of the breakpoints is within ARID5B exon10.
FANCC	0	MSKCC-DMP	P-0007971-T01-IM5	FANCC-intragenic	yes	unknown		out of frame	FANCC (NM_000136) rearrangement: c.686+3158_843+10del Note: The FANCC (NM_000136) rearrangement event results in the intragenic deletion of FANCC exon8.
CDH1	0	MSKCC-DMP	P-0009469-T01-IM5	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement : c.303_387+2011del Note: The CDH1 (NM_004360) Rearrangement results in the intragenic deletion of exon3 of CDH1. one of the breakpoints is within exon3. Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0007037-T01-IM5	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement :  c.171_237-643dup Note: The PBRM1 (NM_018313) rearrangement results in the partial duplication of exon 3 of PBRM1. One of the breakpoints is within exon3. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0005176-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.209+2245_c.853dup The PTEN (NM_000314) rearrangement is an intragenic duplication of exons 4-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0005176-T01-IM5	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) rearrangement: c.940-8_c.1695+7932dup The RB1 (NM_000321) rearrangement is an intragenic duplication of exons 10-17. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0005176-T01-IM5	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.3551_c.3672-734dup The EP300 (NM_001429) rearrangement is an intragenic duplication of exons 19-20. One of the breakpoints is within exon 19. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0005428-T01-IM5	EIF4A2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(21;3)(q22.3;q27.3)(chr21:g.42874720::chr3:g.186488282) Note: TMPRSS2 rearrangement is a translocation event in which exon 1 of TMPRSS2 is fused to an intergenic region. While we did not detect the canonical TMPRSS2-ERG fusion, we can not rule out the possibility of another event connecting TMRPSS2 and ERG which MSK-IMPACT is not designed to detect.
EIF4A2	0	MSKCC-DMP	P-0005428-T01-IM5	EIF4A2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(21;3)(q22.3;q27.3)(chr21:g.42874720::chr3:g.186488282) Note: TMPRSS2 rearrangement is a translocation event in which exon 1 of TMPRSS2 is fused to an intergenic region. While we did not detect the canonical TMPRSS2-ERG fusion, we can not rule out the possibility of another event connecting TMRPSS2 and ERG which MSK-IMPACT is not designed to detect.
NF1	0	MSKCC-DMP	P-0011284-T01-IM5	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.-1819_c.-84del Note: The NF1 rearrangement is a deletion of the 5UTR and promoter region of NF1. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0008682-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement :  c.493-150_ 878inv Note: The PTEN (NM_000314) rearrangement event results in the inversion of PTEN exons 6-8. One of the breakpoints is within PTEN exon8.
ERG	0	MSKCC-DMP	P-0006905-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) reciprocal fusion (TMPRSS exon1 fused with ERG exons 4-11) : c.56-1143:TMPRSS2_c.40-62829:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006905-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) reciprocal fusion (TMPRSS exon1 fused with ERG exons 4-11) : c.56-1143:TMPRSS2_c.40-62829:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0006905-T01-IM5	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : c.56-1098_349+1397inv Note: The TMPRSS2 (NM_001135099) rearrangement event results in the intragenic inversion of TMPRSS2 exons 2-3.
ERG	0	MSKCC-DMP	P-0004981-T01-IM5	FZD10-ERG fusion	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(12;21)(q24.33;q13.1)(chr12:g.130616610::chr21:g.39755710) The ERG (NM_182918) rearrangement is a translocation which may result in a truncated ERG. One of the breakpoints is within exon 10. The functional significance is undetermined.
FZD10	0	MSKCC-DMP	P-0004981-T01-IM5	FZD10-ERG fusion	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(12;21)(q24.33;q13.1)(chr12:g.130616610::chr21:g.39755710) The ERG (NM_182918) rearrangement is a translocation which may result in a truncated ERG. One of the breakpoints is within exon 10. The functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0006611-T01-IM5	KCNJ15-STAG2 fusion	yes	unknown		unknown	STAG2 (NM_001042749) - KCNJ15 (NM_170737) rearrangement : t(X;21)(q25;q22.13)(chrX:g.123164894::chr21:g.39629841) Note: The STAG2 (NM_001042749) - KCNJ15 (NM_170737) rearrangement event is a translocation which results in the truncation of STAG2 exons 5-35. One of the breakpoints is within STAG2 exon5. The significance of this event is undetermined.
KCNJ15	0	MSKCC-DMP	P-0006611-T01-IM5	KCNJ15-STAG2 fusion	yes	unknown		unknown	STAG2 (NM_001042749) - KCNJ15 (NM_170737) rearrangement : t(X;21)(q25;q22.13)(chrX:g.123164894::chr21:g.39629841) Note: The STAG2 (NM_001042749) - KCNJ15 (NM_170737) rearrangement event is a translocation which results in the truncation of STAG2 exons 5-35. One of the breakpoints is within STAG2 exon5. The significance of this event is undetermined.
TSHZ3	0	MSKCC-DMP	P-0003536-T02-IM5	AKT2-TSHZ3 fusion	yes	unknown		out of frame	TSHZ3 (NM_020856) - AKT2 (NM_001626) rearrangement: c.41-819:TSHZ3_c.574-15:AKT2dup The TSHZ3 (NM_020856) - AKT2 (NM_001626) rearrangement is a duplication which results in the fusion of TSHZ3 exon1 with AKT2 exons 7-14, including kinase domain of AKT2. The functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0003536-T02-IM5	AKT2-TSHZ3 fusion	yes	unknown		out of frame	TSHZ3 (NM_020856) - AKT2 (NM_001626) rearrangement: c.41-819:TSHZ3_c.574-15:AKT2dup The TSHZ3 (NM_020856) - AKT2 (NM_001626) rearrangement is a duplication which results in the fusion of TSHZ3 exon1 with AKT2 exons 7-14, including kinase domain of AKT2. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0010465-T01-IM5	WHSC1-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - WHSC1 (NM_001042424) rearrangement:c.1959+17:FGFR3_c.-29-12740:WHSC1del Note: The FGFR3 - WHSC1 rearrangement is a deletion which results in the fusion of FGFR3 exons 1-14 with WHSC1 exons 1-22.  The fusion includes part of kinase domain of FGFR3.
WHSC1	0	MSKCC-DMP	P-0010465-T01-IM5	WHSC1-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - WHSC1 (NM_001042424) rearrangement:c.1959+17:FGFR3_c.-29-12740:WHSC1del Note: The FGFR3 - WHSC1 rearrangement is a deletion which results in the fusion of FGFR3 exons 1-14 with WHSC1 exons 1-22.  The fusion includes part of kinase domain of FGFR3.
E2F3	0	MSKCC-DMP	P-0010465-T01-IM5	E2F3-intragenic	yes	unknown		unknown	E2F3 (NM_001949) rearrangement: c.87_c.393+25392del Note: The E2F3 rearrangement is an intragenic deletion of exon1. One of the breakpoints is within exon 1. The functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0004346-T01-IM5	C6orf10-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) - C6orf10 (NM_006781) rearrangement: c.4557:NOTCH4_c.638-666:C6orf10dup The NOTCH4 (NM_004557) - C6orf10 (NM_006781) rearrangement is a duplication which results in the fusion of exons 1-25 of NOTCH4 with exon 11 of C6orf10. The breakpoint in NOTCH4 exon25 is within exon. The functional significance is undetermined.
C6orf10	0	MSKCC-DMP	P-0004346-T01-IM5	C6orf10-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) - C6orf10 (NM_006781) rearrangement: c.4557:NOTCH4_c.638-666:C6orf10dup The NOTCH4 (NM_004557) - C6orf10 (NM_006781) rearrangement is a duplication which results in the fusion of exons 1-25 of NOTCH4 with exon 11 of C6orf10. The breakpoint in NOTCH4 exon25 is within exon. The functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0002630-T01-IM3	RUNX1-intragenic	yes	unknown		in frame	null RUNX1 duplication is a structural rearrangement event in which exons 3 and 4 are duplicated. Its functional significance is not determined.
PAK1	0	MSKCC-DMP	P-0013498-T01-IM5	PAK1-intragenic	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.1552-1074_c.*11inv Note: The PAK1 rearrangement is an inversion of exon 15.
B2M	0	MSKCC-DMP	P-0013498-T01-IM5	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.346_c.*15-3del Note: The B2M rearrangement is a deletion of exons 2-3. One of the breakpoints is within exon 2.
BRCA1	0	MSKCC-DMP	P-0002792-T01-IM3	SMAD3-BRCA1 fusion	yes	unknown		unknown	null Note: BRCA1 - SMAD3 translocation is a translocation event in which 3 UTR of BRCA1 is fused to exons 7 to 9 of SMAD3 gene. Its functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0002792-T01-IM3	SMAD3-BRCA1 fusion	yes	unknown		unknown	null Note: BRCA1 - SMAD3 translocation is a translocation event in which 3 UTR of BRCA1 is fused to exons 7 to 9 of SMAD3 gene. Its functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0013050-T01-IM5	WDFY4-CHEK2 fusion	yes	unknown		unknown	CHEK2 (NM_007194) rearrangement: t(10;22)(q11.22;q12.1)(chr10:g.49868405::chr22:g.29093021) Note: The CHEK2 rearrangement is a translocation with a breakpoint within intron 9 of CHEK2. The functional significance is undetermined.
WDFY4	0	MSKCC-DMP	P-0013050-T01-IM5	WDFY4-CHEK2 fusion	yes	unknown		unknown	CHEK2 (NM_007194) rearrangement: t(10;22)(q11.22;q12.1)(chr10:g.49868405::chr22:g.29093021) Note: The CHEK2 rearrangement is a translocation with a breakpoint within intron 9 of CHEK2. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0005070-T01-IM5	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231)  Rearrangement:  c.6658-243_4728+8inv Note: The POLE (NM_006231)  Rearrangement results in the intragenic inversion of exons 37 to 47.Its functional significance is undetermined.
BMPR1A	0	MSKCC-DMP	P-0008852-T01-IM5	BMPR1A-intragenic	yes	unknown		unknown	BMPR1A (NM_004329) rearrangement: c.-267-34168_c.91inv Note: The BMPR1A (NM_004329) rearrangement is an inversion of exons 2-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0005862-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (exons 1-17 of FGFR3 fused to exons 14-16 of TACC3): c.2274+46:FGFR3_c.2223+896:TACC3dup. The  FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is in frame and includes the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0005862-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (exons 1-17 of FGFR3 fused to exons 14-16 of TACC3): c.2274+46:FGFR3_c.2223+896:TACC3dup. The  FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is in frame and includes the kinase domain of FGFR3.
CTNNB1	0	MSKCC-DMP	P-0008929-T01-IM5	CTNNB1-intragenic	yes	unknown		in frame	CTNNB1 (NM_001904) Rearrangement : c.13+97_242-92del Note: The CTNNB1 (NM_001904) Rearrangement  results in the deletion of exon3 of CTNNB1. Its functional significance is undetermined.
MAFB	0	MSKCC-DMP	P-0009346-T01-IM5	ARID2-MAFB fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement : t(12;20)(q12;q12)(chr12:g.46230848::chr20:g.38766766) Note: The ARID2 (NM_152641) rearrangement event is a translocation which results in the truncation of ARID2 exons 9-21.
ARID2	0	MSKCC-DMP	P-0009346-T01-IM5	ARID2-MAFB fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement : t(12;20)(q12;q12)(chr12:g.46230848::chr20:g.38766766) Note: The ARID2 (NM_152641) rearrangement event is a translocation which results in the truncation of ARID2 exons 9-21.
CREBBP	0	MSKCC-DMP	P-0009393-T01-IM5	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.85+13476_c.161del Note: The CREBBP (NM_004380) rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon2. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0003665-T01-IM5	BCL2L14-ETV6 fusion	yes	unknown		unknown	c.464-7460:ETV6_chr12:g.12175381inv Note: The ETV6 (NM_001987) rearrangement event results in the inversion of exons 5 to 8.
BCL2L14	0	MSKCC-DMP	P-0003665-T01-IM5	BCL2L14-ETV6 fusion	yes	unknown		unknown	c.464-7460:ETV6_chr12:g.12175381inv Note: The ETV6 (NM_001987) rearrangement event results in the inversion of exons 5 to 8.
LOC100134259	0	MSKCC-DMP	P-0009985-T01-IM5	MSH6-LOC100134259 fusion	yes	unknown		unknown	MSH6 (NM_000179) Rearrangement :  chr2:g.47072226_ c.2515:MSH6inv Note: The MSH6 Rearrangement  results in the inversion of exons 1-4 of MSH6. The breakpoint in MSH6 is within exon4. Its functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0009985-T01-IM5	MSH6-LOC100134259 fusion	yes	unknown		unknown	MSH6 (NM_000179) Rearrangement :  chr2:g.47072226_ c.2515:MSH6inv Note: The MSH6 Rearrangement  results in the inversion of exons 1-4 of MSH6. The breakpoint in MSH6 is within exon4. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0005109-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) rearrangement: c.504+6767_c.1140+2849del The BRAF (NM_004333) rearrangement is an intragenic deletion of exons 4-8, including the RAS-binding domain.
ERG	0	MSKCC-DMP	P-0003541-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.127-1068:TMPRSS2_c.40-44654:ERGdel Known fusion, TMPRSS2 exon 3 fused to ERG exon 2
TMPRSS2	0	MSKCC-DMP	P-0003541-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.127-1068:TMPRSS2_c.40-44654:ERGdel Known fusion, TMPRSS2 exon 3 fused to ERG exon 2
STAG2	0	MSKCC-DMP	P-0004999-T01-IM5	OR13H1-STAG2 fusion	yes	unknown		unknown	STAG2(NM_001042749)  Rearrangement : c.2026-10:STAG2_chrX:g.130653015 Note: The STAG2(NM_001042749)  Rearrangement results in the inversion of exons 21 to 35 of STAG2. Its functional significance is undetermined.
OR13H1	0	MSKCC-DMP	P-0004999-T01-IM5	OR13H1-STAG2 fusion	yes	unknown		unknown	STAG2(NM_001042749)  Rearrangement : c.2026-10:STAG2_chrX:g.130653015 Note: The STAG2(NM_001042749)  Rearrangement results in the inversion of exons 21 to 35 of STAG2. Its functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0004999-T01-IM5	ALOX5AP-STAT3 fusion	yes	unknown		unknown	STAT3(NM_139276) Rearrangement  : t(17;13)(17q21.2;13p12.3)(chr17:g.40490706::chr13:g.31343786) Note: The STAT3(NM_139276) Rearrangement results in translocation of exons 7-24 of STAT3. Its functional significance is undetermined.
ALOX5AP	0	MSKCC-DMP	P-0004999-T01-IM5	ALOX5AP-STAT3 fusion	yes	unknown		unknown	STAT3(NM_139276) Rearrangement  : t(17;13)(17q21.2;13p12.3)(chr17:g.40490706::chr13:g.31343786) Note: The STAT3(NM_139276) Rearrangement results in translocation of exons 7-24 of STAT3. Its functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0003097-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	null FGFR3 (NM_000142) exons 1-17 fused to TACC3 (NM_006342) exons 6-16
FGFR3	0	MSKCC-DMP	P-0003097-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		in frame	null FGFR3 (NM_000142) exons 1-17 fused to TACC3 (NM_006342) exons 6-16
NCOA3	0	MSKCC-DMP	P-0010809-T01-IM5	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.2512+456_ 2946del Note: The NCOA3 rearrangement event results in the intragenic deletion of NCOA3 exons 14-15.
TNFRSF19	0	MSKCC-DMP	P-0010075-T01-IM5	RB1-TNFRSF19 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : chr13:g.24150799_c.265-55:RB1del Note: The RB1  Rearrangement results in the deletion of   exons1-2 of RB1. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0010075-T01-IM5	RB1-TNFRSF19 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : chr13:g.24150799_c.265-55:RB1del Note: The RB1  Rearrangement results in the deletion of   exons1-2 of RB1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009819-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1480:TMPRSS2_c.40-52376:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0009819-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1480:TMPRSS2_c.40-52376:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion is predicted to be in-frame.
FAR2	0	MSKCC-DMP	P-0007842-T01-IM5	KDR-FAR2 fusion	yes	unknown		unknown	FAR2 (NM_018099) - KDR (NM_002253.2) translocation : t(12,4)(p11.22; q12)(chr12:g.29059026::chr4:g.55970822) Note: The FAR2 (NM_018099) - KDR (NM_002253.2) rearrangement is a translocation event which results in the fusion of KDR exon1-13 and FAR2. Its functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0007842-T01-IM5	KDR-FAR2 fusion	yes	unknown		unknown	FAR2 (NM_018099) - KDR (NM_002253.2) translocation : t(12,4)(p11.22; q12)(chr12:g.29059026::chr4:g.55970822) Note: The FAR2 (NM_018099) - KDR (NM_002253.2) rearrangement is a translocation event which results in the fusion of KDR exon1-13 and FAR2. Its functional significance is undetermined.
ZFP64	0	MSKCC-DMP	P-0007014-T01-IM5	RAD51C-ZFP64 fusion	yes	unknown		unknown	RAD51C (NM_058216) rearrangement: t(17;20)(q22;q13.2)(chr17:g.56809889::chr20:g.50920486) The RAD51C (NM_058216) rearrangement is a translocation which may result in the truncation of RAD51C. The functional significance is undetermined.
RAD51C	0	MSKCC-DMP	P-0007014-T01-IM5	RAD51C-ZFP64 fusion	yes	unknown		unknown	RAD51C (NM_058216) rearrangement: t(17;20)(q22;q13.2)(chr17:g.56809889::chr20:g.50920486) The RAD51C (NM_058216) rearrangement is a translocation which may result in the truncation of RAD51C. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0012986-T01-IM5	RCBTB2-RB1 fusion	yes	unknown		unknown	RB1 (NM_00032) rearrangement: c.2335_ chr13:g.49107711dup Note: The RB1 rearrangement is a duplication which includes exons 23-27 of RB1. One of the breakpoints is within exon 23. The functional significance is undetermined.
RCBTB2	0	MSKCC-DMP	P-0012986-T01-IM5	RCBTB2-RB1 fusion	yes	unknown		unknown	RB1 (NM_00032) rearrangement: c.2335_ chr13:g.49107711dup Note: The RB1 rearrangement is a duplication which includes exons 23-27 of RB1. One of the breakpoints is within exon 23. The functional significance is undetermined.
MARVELD3	0	MSKCC-DMP	P-0000386-T02-IM5	FGFR2-MARVELD3 fusion	yes	unknown		unknown	MARVELD3 (NM_001017967) - FGFR2 (NM_000141) rearrangement: t(16;10)(16q22.2;10q26.13) (chr16:g.71660650::chr10:123243101) The MARVELD3 (NM_001017967) - FGFR2 (NM_000141) rearrangement  is a translocation that results in an antisense fusion potentially disabling the function of the FGFR2 gene. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0000386-T02-IM5	FGFR2-MARVELD3 fusion	yes	unknown		unknown	MARVELD3 (NM_001017967) - FGFR2 (NM_000141) rearrangement: t(16;10)(16q22.2;10q26.13) (chr16:g.71660650::chr10:123243101) The MARVELD3 (NM_001017967) - FGFR2 (NM_000141) rearrangement  is a translocation that results in an antisense fusion potentially disabling the function of the FGFR2 gene. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0010979-T02-IM5	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.-74_chr12:g.115414371del Note: The TBX3 rearrangement is a deletion of the 5'UTR of TBX3. The functional significance undetermined.
IFNGR1	0	MSKCC-DMP	P-0008838-T01-IM5	OLIG3-IFNGR1 fusion	yes	unknown		unknown	IFNGR1 (NM_000416) rearrangement : c.1311:IFNGR1_chr6:g.137953996inv Note: The IFNGR1 (NM_000416) rearrangement event results in the inversion of IFNGR1 exons 1-7. One of the breakpoints is within IFNGR1 exon7.
OLIG3	0	MSKCC-DMP	P-0008838-T01-IM5	OLIG3-IFNGR1 fusion	yes	unknown		unknown	IFNGR1 (NM_000416) rearrangement : c.1311:IFNGR1_chr6:g.137953996inv Note: The IFNGR1 (NM_000416) rearrangement event results in the inversion of IFNGR1 exons 1-7. One of the breakpoints is within IFNGR1 exon7.
TET2	0	MSKCC-DMP	P-0011348-T01-IM5	NR3C2-TET2 fusion	yes	unknown		unknown	NR3C2 (NM_000901) - TET2 (NM_001127208) rearrangement: c.1757+79314:NR3C2_c.359:TET2inv Note: The NR3C2 - TET2 rearrangement is an inversion that results in a fusion of  NR3C2 exons 1-2 with TET2 exons 3-11. One of the breakpoints is within TET2 exon 3. The functional significance is undetermined.
NR3C2	0	MSKCC-DMP	P-0011348-T01-IM5	NR3C2-TET2 fusion	yes	unknown		unknown	NR3C2 (NM_000901) - TET2 (NM_001127208) rearrangement: c.1757+79314:NR3C2_c.359:TET2inv Note: The NR3C2 - TET2 rearrangement is an inversion that results in a fusion of  NR3C2 exons 1-2 with TET2 exons 3-11. One of the breakpoints is within TET2 exon 3. The functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0014755-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.-8-162_c.382dup Note: The ELF3 rearrangement is an intragenic duplication with breakpoints in the 5UTR and exon 3. The functional significance is undetermined.
KIT	0	MSKCC-DMP	P-0009106-T01-IM5	KDR-KIT fusion	yes	unknown		unknown	KIT (NM_000222) - KDR (NM_002253) rearrangement: c.620-145:KIT_c.-115:KDRdup Note: The KIT (NM_000222) - KDR (NM_002253) rearrangement results in the duplication of KIT exons 4-21 and the entire coding region of KDR. The functional significance of this rearrangement is undetermined.
KDR	0	MSKCC-DMP	P-0009106-T01-IM5	KDR-KIT fusion	yes	unknown		unknown	KIT (NM_000222) - KDR (NM_002253) rearrangement: c.620-145:KIT_c.-115:KDRdup Note: The KIT (NM_000222) - KDR (NM_002253) rearrangement results in the duplication of KIT exons 4-21 and the entire coding region of KDR. The functional significance of this rearrangement is undetermined.
ZFAND1	0	MSKCC-DMP	P-0012142-T01-IM5	PIK3R1-ZFAND1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: t(5;8)(q13.1;q21.13)(chr5:g.67589202::chr8:g.82618895) Note: The PIK3R1 rearrangement is a translocation that may result in a truncation of PIK3R1 exons 4-16. One of the breakpoints is within exon 4. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0012142-T01-IM5	PIK3R1-ZFAND1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: t(5;8)(q13.1;q21.13)(chr5:g.67589202::chr8:g.82618895) Note: The PIK3R1 rearrangement is a translocation that may result in a truncation of PIK3R1 exons 4-16. One of the breakpoints is within exon 4. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0012566-T01-IM5	FAT1-intragenic	yes	unknown		in frame	FAT1 (NM_005245) rearrangement: c.3265+14735_c.4184-6del Note: The FAT1 rearrangement is an intragenic deletion of exons 3-6.
PTEN	0	MSKCC-DMP	P-0000447-T01-IM3	PTEN-intragenic	yes	unknown		unknown	null
TP53	0	MSKCC-DMP	P-0004827-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement : c.-28-1339_97-1del Note: The TP53 (NM_000546) rearrangement event results in the intragenic deletion of TP53 exons 2-3.
USP34	0	MSKCC-DMP	P-0004827-T01-IM5	XPO1-USP34 fusion	yes	unknown		in frame	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement : c.590+39:XPO1_c.8840+827:USP34del Note: The XPO1 (NM_003400) - USP34 (NM_014709) rearrangement event is a deletion which results in the fusion of XPO1 exons 1-7 with USP34 exons 70-80.
XPO1	0	MSKCC-DMP	P-0004827-T01-IM5	XPO1-USP34 fusion	yes	unknown		in frame	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement : c.590+39:XPO1_c.8840+827:USP34del Note: The XPO1 (NM_003400) - USP34 (NM_014709) rearrangement event is a deletion which results in the fusion of XPO1 exons 1-7 with USP34 exons 70-80.
HIST1H4B	0	MSKCC-DMP	P-0005855-T01-IM5	HIST1H3B-HIST1H4B fusion	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: c.103:HIST1H3B_chr:6g.26025427dup The HIST1H3B (NM_003537) rearrangement is a duplication of HIST1H3B. One of the breakpoints is within exon1 of HIST1H3B. The functional significance is undetermined.
HIST1H3B	0	MSKCC-DMP	P-0005855-T01-IM5	HIST1H3B-HIST1H4B fusion	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: c.103:HIST1H3B_chr:6g.26025427dup The HIST1H3B (NM_003537) rearrangement is a duplication of HIST1H3B. One of the breakpoints is within exon1 of HIST1H3B. The functional significance is undetermined.
PAX5	0	MSKCC-DMP	P-0005855-T01-IM5	PAX5-intragenic	yes	unknown		unknown	PAX5 (NM_016734) rearrangement: c.781-5874_c.866dup The PAX5 (NM_016734) rearrangement: is an intragenic duplication of exon 7. One of the breakpoints is within exon1 of PAX5.. The functional significance is undetermined.
MLL	0	MSKCC-DMP	P-0010984-T01-IM5	MLL-intragenic	yes	unknown		out of frame	MLL (NM_001197104) rearrangement: c.6080-93_c.10835+329dup Note: The MLL rearrangement is an intragenic duplication of exons 24-28. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0010984-T01-IM5	SLC4A4-ROS1 fusion	yes	unknown		in frame	SLC4A4 (NM_001134742) - ROS1 (NM_002944) rearrangement: t(4;6)(q13.3;q22.1)(chr4:g.72429843::chr6:g.117646719) Note: The SLC4A4 - ROS1 rearrangement is a translocation that results in an in frame fusion of SLC4A4 exons 1-23 with ROS1 exons 34-43, which include the ROS1 kinase domain. The functional significance is undetermined.
SLC4A4	0	MSKCC-DMP	P-0010984-T01-IM5	SLC4A4-ROS1 fusion	yes	unknown		in frame	SLC4A4 (NM_001134742) - ROS1 (NM_002944) rearrangement: t(4;6)(q13.3;q22.1)(chr4:g.72429843::chr6:g.117646719) Note: The SLC4A4 - ROS1 rearrangement is a translocation that results in an in frame fusion of SLC4A4 exons 1-23 with ROS1 exons 34-43, which include the ROS1 kinase domain. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0004967-T01-IM5	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement : c.2639+10_2913del Note: The TSC2 (NM_000548) rearrangement event results in the intragenic deletion of exons TSC2 exons 24-26. One of the breakpoints is within TSC2 exon26.
TERT	0	MSKCC-DMP	P-0007852-T02-IM5	SUB1-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.2970+5:TERT_chr5:g.32544184del Note: The TERT (NM_198253) rearrangement event results in the deletion of TERT exons 1-12.
SUB1	0	MSKCC-DMP	P-0007852-T02-IM5	SUB1-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement : c.2970+5:TERT_chr5:g.32544184del Note: The TERT (NM_198253) rearrangement event results in the deletion of TERT exons 1-12.
CDH12	0	MSKCC-DMP	P-0007852-T02-IM5	RAI14-CDH12 fusion	yes	unknown		unknown	CDH12 (NM_004061) rearrangement : c.815-7428:CDH1_chr5:g.34625690inv Note: The CDH12 (NM_004061) rearrangement event results in the inversion of CDH12 exons 1-8.
RAI14	0	MSKCC-DMP	P-0007852-T02-IM5	RAI14-CDH12 fusion	yes	unknown		unknown	CDH12 (NM_004061) rearrangement : c.815-7428:CDH1_chr5:g.34625690inv Note: The CDH12 (NM_004061) rearrangement event results in the inversion of CDH12 exons 1-8.
ANKRD11	0	MSKCC-DMP	P-0003625-T01-IM5	ANKRD11-intragenic	yes	unknown		unknown	The ANKRD11 (NM_013275) duplication is a rearrangement event which results in the intragenic duplication of exons 3-9.
ERG	0	MSKCC-DMP	P-0009728-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1101:TMPRSS2_c.40-52949:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion is predicted to be in-frame. Given the presence of this fusion, a metastatic lesion from prostate primary should be considered.  Molecular profiling of the prostate primary for comparison would be of value.
TMPRSS2	0	MSKCC-DMP	P-0009728-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1101:TMPRSS2_c.40-52949:ERGdel Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion is predicted to be in-frame. Given the presence of this fusion, a metastatic lesion from prostate primary should be considered.  Molecular profiling of the prostate primary for comparison would be of value.
NF1	0	MSKCC-DMP	P-0001044-T01-IM3	NF1-intragenic	yes	unknown		unknown	None
CUL1	0	MSKCC-DMP	P-0005529-T01-IM5	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) - CUL1 (NM_003592) rearrangement: c.2029+34:EZH2_c.1808:CUL1del The EZH2 (NM_004456) - CUL1 (NM_003592) rearrangement is a deletion of EZH2 exons 17-20 and CUL1 exons 17-22.  The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0005529-T01-IM5	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) - CUL1 (NM_003592) rearrangement: c.2029+34:EZH2_c.1808:CUL1del The EZH2 (NM_004456) - CUL1 (NM_003592) rearrangement is a deletion of EZH2 exons 17-20 and CUL1 exons 17-22.  The functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0010264-T01-IM5	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_0010112338) fusion (ETV6 exons 1-4 fused in frame with NTRK3 exons 13-20): t(12;15)(p13.2;q25.3)(chr12:g.12014962::chr15:g.88588255)
ETV6	0	MSKCC-DMP	P-0010264-T01-IM5	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_0010112338) fusion (ETV6 exons 1-4 fused in frame with NTRK3 exons 13-20): t(12;15)(p13.2;q25.3)(chr12:g.12014962::chr15:g.88588255)
ASXL1	0	MSKCC-DMP	P-0011276-T01-IM5	ASXL1-intragenic	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.253-19600_c.572dup Note: The ASXL1 rearrangement is a duplication of exons 4-7. One of the breakpoints is within exon 7 of ASXL1. The functional significance us unknown.
PAK1	0	MSKCC-DMP	P-0009328-T01-IM5	PAK1-intragenic	yes	unknown		unknown	PAK1 (NM_002576) rearrangement : c.-21-5812_292-11del Note: The PAK1 (NM_002576) rearrangement event results in the deletion of PAK1 exons 2-3.
EPCAM	0	MSKCC-DMP	P-0009328-T01-IM5	NRXN1-EPCAM fusion	yes	unknown		unknown	EPCAM (NM_002354) - NRXN1 (NM_004801) rearrangement : c.540:EPCAM_c.832+71570:NRXN1del Note: The EPCAM (NM_002354) - NRXN1 (NM_004801) rearrangement event results in the deletion of EPCAM exons 1-5. One of the breakpoints is within EPCAM exon5.
NRXN1	0	MSKCC-DMP	P-0009328-T01-IM5	NRXN1-EPCAM fusion	yes	unknown		unknown	EPCAM (NM_002354) - NRXN1 (NM_004801) rearrangement : c.540:EPCAM_c.832+71570:NRXN1del Note: The EPCAM (NM_002354) - NRXN1 (NM_004801) rearrangement event results in the deletion of EPCAM exons 1-5. One of the breakpoints is within EPCAM exon5.
CREBBP	0	MSKCC-DMP	P-0013882-T01-IM5	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.975+679_c.6669del Note: The CREBBP rearrangement is an intragenic deletion of exons 4 - 31. One of the breakpoints is within exon 31. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0006711-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.164-19692_c.464-1622dup The ETV6 (NM_001987) rearrangement is an intragenic in frame duplication of exons 3-4.  The functional significance is undetermined.
RAB9BP1	0	MSKCC-DMP	P-0008061-T01-IM5	APC-RAB9BP1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.104183424_c.797inv The APC (NM_000038) rearrangement is an inversion of APC exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0008061-T01-IM5	APC-RAB9BP1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.104183424_c.797inv The APC (NM_000038) rearrangement is an inversion of APC exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
CDK8	0	MSKCC-DMP	P-0005080-T01-IM5	CDK8-intragenic	yes	unknown		unknown	CDK8(NM_001260)  Rearrangement :  c.-1302_70del Note: The CDK8(NM_001260)  Rearrangement  results in the partial deletion of the first exon of CDK8.The breakpoint is within exon1 . Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008304-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1145:TMPRSS2_c.40-48890:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008304-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1145:TMPRSS2_c.40-48890:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008304-T01-IM5	MYL5-TMPRSS2 fusion	yes	unknown		unknown	MYL5 (NM_002477) - TMPRSS2 (NM_001135099) rearrangement : t(4;21)(p16.3;q22.3)(chr4:g.674327::chr21:g.42871261) Note: The MYL5 (NM_002477) - TMPRSS2 (NM_001135099) rearrangement event is a translocation which results in the fusion of MYL5 exons 1-5 with TMPRSS2 exons 2-14. One of the breakpoints is within MYL5 exon5.
MYL5	0	MSKCC-DMP	P-0008304-T01-IM5	MYL5-TMPRSS2 fusion	yes	unknown		unknown	MYL5 (NM_002477) - TMPRSS2 (NM_001135099) rearrangement : t(4;21)(p16.3;q22.3)(chr4:g.674327::chr21:g.42871261) Note: The MYL5 (NM_002477) - TMPRSS2 (NM_001135099) rearrangement event is a translocation which results in the fusion of MYL5 exons 1-5 with TMPRSS2 exons 2-14. One of the breakpoints is within MYL5 exon5.
GOSR1	0	MSKCC-DMP	P-0012176-T01-IM5	NF1-GOSR1 fusion	yes	unknown		unknown	NF1 (NM_001042492) Rearrangement : chr17:g.28802813_c.480-42:NF1del Note: The NF1 Rearrangement results in the possible deletion of exons 1-4 of NF1. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0012176-T01-IM5	NF1-GOSR1 fusion	yes	unknown		unknown	NF1 (NM_001042492) Rearrangement : chr17:g.28802813_c.480-42:NF1del Note: The NF1 Rearrangement results in the possible deletion of exons 1-4 of NF1. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0000584-T03-IM6	PRKCA-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954): chr17:g.64282318_c.2267:MAP3K14inv Note: The MAP3K14 rearrangement is an inversion of 5UTR and exons 1-12. One of the breakpoints is within exon 12.
PRKCA	0	MSKCC-DMP	P-0000584-T03-IM6	PRKCA-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954): chr17:g.64282318_c.2267:MAP3K14inv Note: The MAP3K14 rearrangement is an inversion of 5UTR and exons 1-12. One of the breakpoints is within exon 12.
FYN	0	MSKCC-DMP	P-0005307-T01-IM5	NT5DC1-FYN fusion	yes	unknown		unknown	FYN (NM_153047) rearrangement:  c.345-80_chr6:g.116410524del The FYN (NM_153047) rearrangement is a deletion of FYN exons 1-2. The functional significance is undetermined.
NT5DC1	0	MSKCC-DMP	P-0005307-T01-IM5	NT5DC1-FYN fusion	yes	unknown		unknown	FYN (NM_153047) rearrangement:  c.345-80_chr6:g.116410524del The FYN (NM_153047) rearrangement is a deletion of FYN exons 1-2. The functional significance is undetermined.
HELZ	0	MSKCC-DMP	P-0006086-T01-IM5	NEGR1-HELZ fusion	yes	unknown		unknown	HELZ (NM_014877) - NEGR1 (NM_173808) Rearrangement :  t(17;1)(chr17q24.2;chr1p31.1)(chr17:g.65231020::chr1:g.72748066) Note: The HELZ (NM_014877) - NEGR1 (NM_173808) Rearrangement results in the fusion of exons 1 to 3 of HELZ1 to exons 1 to 7 of NEGR1. The breakpoint is within exon 1 of NEGR1. Its functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0006086-T01-IM5	NEGR1-HELZ fusion	yes	unknown		unknown	HELZ (NM_014877) - NEGR1 (NM_173808) Rearrangement :  t(17;1)(chr17q24.2;chr1p31.1)(chr17:g.65231020::chr1:g.72748066) Note: The HELZ (NM_014877) - NEGR1 (NM_173808) Rearrangement results in the fusion of exons 1 to 3 of HELZ1 to exons 1 to 7 of NEGR1. The breakpoint is within exon 1 of NEGR1. Its functional significance is undetermined.
BTK	0	MSKCC-DMP	P-0010361-T01-IM5	TSC22D2-BTK fusion	yes	unknown		unknown	BTK (NM_000061) rearrangement: t(3;X)(q25.1;q22.1)(chr3:g.149988968::chrX:g.100605050) Note: The BTK rearrangement is a translocation with a breakpoint within intron 18 of BTK. The functional significance is undetermined.
TSC22D2	0	MSKCC-DMP	P-0010361-T01-IM5	TSC22D2-BTK fusion	yes	unknown		unknown	BTK (NM_000061) rearrangement: t(3;X)(q25.1;q22.1)(chr3:g.149988968::chrX:g.100605050) Note: The BTK rearrangement is a translocation with a breakpoint within intron 18 of BTK. The functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0008373-T01-IM5	MYC-intragenic	yes	unknown		unknown	MYC (NM_002467) rearrangement : chr8:g.128706398_c.*92:MYC:dup Note: The MYC (NM_002467) rearrangement events results in the duplication of the MYC gene. This assay cannot rule out a more complex rearrangement event involving MYC. Additional testing is recommended if clinically indicative.
AATF	0	MSKCC-DMP	P-0010084-T01-IM5	SOX9-AATF fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: chr17:g. 35352875_c.*1850:SOX9del Note: The SOX9 rearrangement is a deletion which includes exons 1-3 of SOX9. The functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0010084-T01-IM5	SOX9-AATF fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: chr17:g. 35352875_c.*1850:SOX9del Note: The SOX9 rearrangement is a deletion which includes exons 1-3 of SOX9. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0008169-T01-IM5	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489)  rearrangement: c.3340_c.*303inv Note: The ATRX (NM_000489)  rearrangement in an inversion (173882 bp) of exons 9-35 of ATRX. The functional significance is undetermined
PTEN	0	MSKCC-DMP	P-0013385-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314)  rearrangement: c.493-2070_c.525inv Note: The PTEN rearrangement is an inversion with a breakpoint within exon 6. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0012205-T01-IM5	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.2250_c.*1492del Note: The FGFR3 rearrangement is a deletion of exons 17-18. One of the breakpoints is within exon 17. The functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0003863-T01-IM5	FLT4-intragenic	yes	unknown		out of frame	FLT4 (NM_182925) rearrangement: c.1421+431_c.1549-83:FLT4del The FLT4 (NM_182925) rearrangement is an intragenic deletion of exon 11. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013858-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons  4-11) c.55+4344:TMPRSS2_c.39+49391:ERGdel Note: The TMPRSS2-ERG fusion was detected in the background of other events involving TMPRSS2.
TMPRSS2	0	MSKCC-DMP	P-0013858-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons  4-11) c.55+4344:TMPRSS2_c.39+49391:ERGdel Note: The TMPRSS2-ERG fusion was detected in the background of other events involving TMPRSS2.
PALB2	0	MSKCC-DMP	P-0010817-T01-IM5	PALB2-intragenic	yes	unknown		unknown	PALB2 (NM_024675) Rearrangement :  c.2922_3202-1323inv Note: The PALB2 Rearrangement results in the inversion of exons9-11 . One of the breakpoints is within exon 9. Its functional significance is undetermined.
CHEK1	0	MSKCC-DMP	P-0011439-T01-IM5	CDON-CHEK1 fusion	yes	unknown		unknown	CHEK1 (NM_001274) rearrangement : c.424+30:CHEK1_chr11:125970119del Note: The CHEK1 rearrangement event results in the deletion of CHEK1 exons 6-13.
CDON	0	MSKCC-DMP	P-0011439-T01-IM5	CDON-CHEK1 fusion	yes	unknown		unknown	CHEK1 (NM_001274) rearrangement : c.424+30:CHEK1_chr11:125970119del Note: The CHEK1 rearrangement event results in the deletion of CHEK1 exons 6-13.
LMNA	0	MSKCC-DMP	P-0013121-T02-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) rearrangement: c.*885:LMNA_c.1355-127:NTRK1del Note: The LMNA - NTRK1 rearrangement is a deletion which includes the 3UTR of LMNA and exons 1-11 of NTRK1. One of the breakpoints is within the 3UTR of LMNA.
NTRK1	0	MSKCC-DMP	P-0013121-T02-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) rearrangement: c.*885:LMNA_c.1355-127:NTRK1del Note: The LMNA - NTRK1 rearrangement is a deletion which includes the 3UTR of LMNA and exons 1-11 of NTRK1. One of the breakpoints is within the 3UTR of LMNA.
ATXN7L3B	0	MSKCC-DMP	P-0020491-T01-IM6	POLE-ATXN7L3B fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.74843421_c.4878Ginv Note: The POLE rearrangement is an inversion which includes exons 37-49 of POLE. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0020491-T01-IM6	POLE-ATXN7L3B fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.74843421_c.4878Ginv Note: The POLE rearrangement is an inversion which includes exons 37-49 of POLE. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0020494-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656):  c.255+82_c.597del Note: The BAP1 rearrangement is an intragenic deletion of exons 5-8. One of the breakpoints is within exon 8.
ABHD3	0	MSKCC-DMP	P-0015826-T03-IM6	FANCA-ABHD3 fusion	yes	unknown		in frame	FANCA (NM_000135) - ABHD3 (NM_138340) rearrangement: t(16;18)(q24.3;q11.2)(chr16:g.89839561::chr18:g.19233543) Note: The FANCA - ABHD3 rearrangement is a translocation that results in the in-frame fusion of FANCA exons 1-22 with ABHD3 exon 9.  The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0015826-T03-IM6	FANCA-ABHD3 fusion	yes	unknown		in frame	FANCA (NM_000135) - ABHD3 (NM_138340) rearrangement: t(16;18)(q24.3;q11.2)(chr16:g.89839561::chr18:g.19233543) Note: The FANCA - ABHD3 rearrangement is a translocation that results in the in-frame fusion of FANCA exons 1-22 with ABHD3 exon 9.  The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0020515-T01-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4  (NM_003072) rearrangement:  c.3952-20_c.4170+628dup Note: The SMARCA4 Rearrangement results in the intragenic duplication of exon 29. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0020458-T01-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 fused with ROS1 exons 34-43): c.1090+207:EZR_c.5558-455:ROS1del Note: EZR - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
EZR	0	MSKCC-DMP	P-0020458-T01-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 fused with ROS1 exons 34-43): c.1090+207:EZR_c.5558-455:ROS1del Note: EZR - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
LMNA	0	MSKCC-DMP	P-0003329-T03-IM6	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) fusion (LMNA exons 1-2 fused to NTRK1 exons 12 - 17): c.495:LMNA_c.1355-112:NTRK1del Note: The LMNA - NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within LMNA exon 2.
NTRK1	0	MSKCC-DMP	P-0003329-T03-IM6	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) fusion (LMNA exons 1-2 fused to NTRK1 exons 12 - 17): c.495:LMNA_c.1355-112:NTRK1del Note: The LMNA - NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within LMNA exon 2.
AXIN1	0	MSKCC-DMP	P-0003329-T03-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: c.2031_chr16:g.344783del Note: The AXIN1 rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. The functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0020579-T01-IM6	GLYATL2-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) rearrangement: t(11;20)(q12.2;q12)(chr11:g.58574196::chr20:g.39706279) Note: The TOP1 rearrangement is a translocation that may result in a truncation of exons 6-21. The functional significance is undetermined.
GLYATL2	0	MSKCC-DMP	P-0020579-T01-IM6	GLYATL2-TOP1 fusion	yes	unknown		unknown	TOP1 (NM_003286) rearrangement: t(11;20)(q12.2;q12)(chr11:g.58574196::chr20:g.39706279) Note: The TOP1 rearrangement is a translocation that may result in a truncation of exons 6-21. The functional significance is undetermined.
SHANK2	0	MSKCC-DMP	P-0020644-T01-IM6	AGO2-SHANK2 fusion	yes	unknown		unknown	AGO2 (NM_012154) - SHANK2 (NM_012309) rearrangement: t(8;11)(q24.3;q13.4)(chr8:g.141542519::chr11:g.70919699) Note: The AGO2 - SHANK2 rearrangement is a translocation with a breakpoint within AGO2 exon 18. The functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0020644-T01-IM6	AGO2-SHANK2 fusion	yes	unknown		unknown	AGO2 (NM_012154) - SHANK2 (NM_012309) rearrangement: t(8;11)(q24.3;q13.4)(chr8:g.141542519::chr11:g.70919699) Note: The AGO2 - SHANK2 rearrangement is a translocation with a breakpoint within AGO2 exon 18. The functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0020644-T01-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: c.432+18_c.495del Note: The GNAS rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0020644-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.4386_c.5101del Note: The NOTCH1 rearrangement is an intragenic deletion which includes exons 25-27 of NOTCH1. Both breakpoints are within exon. The functional significance is undetermined.
ARID5B	0	MSKCC-DMP	P-0020588-T01-IM6	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.-278_c.503-37del Note: The ARID5B rearrangement results in the deletion of the 5UTR and exons 1-3. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0020701-T01-IM6	FOXO3-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(6;X)(q21;q21.1)(chr6:g.108910877::chrX:g.76889220) Note: The ATRX rearrangement is a translocation that may result in a truncation of exons 18-35. The functional significance is undetermined.
FOXO3	0	MSKCC-DMP	P-0020701-T01-IM6	FOXO3-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(6;X)(q21;q21.1)(chr6:g.108910877::chrX:g.76889220) Note: The ATRX rearrangement is a translocation that may result in a truncation of exons 18-35. The functional significance is undetermined.
MAPK8IP3	0	MSKCC-DMP	P-0020730-T01-IM6	NTHL1-MAPK8IP3 fusion	yes	unknown		out of frame	MAPK8IP3 (NM_015133) - NTHL1 (NM_002528) rearrangement: c.319-1439:MAPK8IP3_c.816-1:NTHL1inv Note: The MAPK8IP3 - NTHL1 rearrangement is an inversion that results in the fusion of MAPK8IP3 exon 1 with NTHL1 exon 6. The functional significance is undetermined.
NTHL1	0	MSKCC-DMP	P-0020730-T01-IM6	NTHL1-MAPK8IP3 fusion	yes	unknown		out of frame	MAPK8IP3 (NM_015133) - NTHL1 (NM_002528) rearrangement: c.319-1439:MAPK8IP3_c.816-1:NTHL1inv Note: The MAPK8IP3 - NTHL1 rearrangement is an inversion that results in the fusion of MAPK8IP3 exon 1 with NTHL1 exon 6. The functional significance is undetermined.
OCEL1	0	MSKCC-DMP	P-0020730-T01-IM6	BABAM1-OCEL1 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement: g.17334216_c.416inv Note: The BABAM1 rearrangement results in the inversion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
BABAM1	0	MSKCC-DMP	P-0020730-T01-IM6	BABAM1-OCEL1 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement: g.17334216_c.416inv Note: The BABAM1 rearrangement results in the inversion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0020585-T01-IM6	RBBP8-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: t(18;22)(q11.2;q12.2)(chr18:g.20498773::chr22:g.30070884) Note: The NF2 rearrangement is a translocation that may result in a truncation of exons 13-16. One of the breakpoints is within exon 13. The functional significance is undetermined.
RBBP8	0	MSKCC-DMP	P-0020585-T01-IM6	RBBP8-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: t(18;22)(q11.2;q12.2)(chr18:g.20498773::chr22:g.30070884) Note: The NF2 rearrangement is a translocation that may result in a truncation of exons 13-16. One of the breakpoints is within exon 13. The functional significance is undetermined.
PALLD	0	MSKCC-DMP	P-0020649-T01-IM6	CTNNB1-PALLD fusion	yes	unknown		unknown	CTNNB1 (NM_00190) - PALLD (NM_001166108) rearrangement: t(3;4)(p22.1;q32.3)(chr3:g.41275813::chr4:g.169820018) Note: The CTNNB1 - PALLD rearrangement is a translocation which may result in the truncation of CTNNB1 after exon 10. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0020649-T01-IM6	CTNNB1-PALLD fusion	yes	unknown		unknown	CTNNB1 (NM_00190) - PALLD (NM_001166108) rearrangement: t(3;4)(p22.1;q32.3)(chr3:g.41275813::chr4:g.169820018) Note: The CTNNB1 - PALLD rearrangement is a translocation which may result in the truncation of CTNNB1 after exon 10. The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0020501-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.-8+11574_c.45del Note: The EZH2 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0020764-T01-IM6	KIAA0825-MAP3K1 fusion	yes	unknown		out of frame	KIAA0825 (NM_001145678) - MAP3K1 (NM_005921) rearrangement: c.3710+59208:KIAA0852_c.4258-64:MAP3K1inv Note: The KIAA0825-MAP3K1 rearrangement is an inversion which results in the fusion of KIAA0825 exon 25 to MAP3K1 exons 1-19
KIAA0825	0	MSKCC-DMP	P-0020764-T01-IM6	KIAA0825-MAP3K1 fusion	yes	unknown		out of frame	KIAA0825 (NM_001145678) - MAP3K1 (NM_005921) rearrangement: c.3710+59208:KIAA0852_c.4258-64:MAP3K1inv Note: The KIAA0825-MAP3K1 rearrangement is an inversion which results in the fusion of KIAA0825 exon 25 to MAP3K1 exons 1-19
ETV6	0	MSKCC-DMP	P-0020661-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.164-14151_c.463+4339dup Note: The ETV6 rearrangement results in the duplication of exons 3-4. Its functional significance is undetermined.
TMED1	0	MSKCC-DMP	P-0020586-T01-IM6	CD79A-TMED1 fusion	yes	unknown		unknown	CD79A (NM_001783) rearrangement: g.10947654_c.594del Note: The CD79A rearrangement results in the inversion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
CD79A	0	MSKCC-DMP	P-0020586-T01-IM6	CD79A-TMED1 fusion	yes	unknown		unknown	CD79A (NM_001783) rearrangement: g.10947654_c.594del Note: The CD79A rearrangement results in the inversion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
KRT6A	0	MSKCC-DMP	P-0020678-T01-IM6	NAB2-KRT6A fusion	yes	unknown		in frame	KRT6A (NM_005554) - NAB2 (NM_005967) rearrangement: c.1204-574:KRT6A_c.1144-29:NAB2inv Note: The KRT6A - NAB2 rearrangement is an inversion that results in an in-frame fusion of KRT6A exons 1-6 with NAB2 exons 5-7. The functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0020678-T01-IM6	NAB2-KRT6A fusion	yes	unknown		in frame	KRT6A (NM_005554) - NAB2 (NM_005967) rearrangement: c.1204-574:KRT6A_c.1144-29:NAB2inv Note: The KRT6A - NAB2 rearrangement is an inversion that results in an in-frame fusion of KRT6A exons 1-6 with NAB2 exons 5-7. The functional significance is undetermined.
AEBP2	0	MSKCC-DMP	P-0020763-T01-IM6	RECQL-AEBP2 fusion	yes	unknown		unknown	AEBP2 (NM_001114176) - RECQL (NM_032941) rearrangement: g.19703521_c.1534Gdel Note: The RECQL rearrangement results in the deletion of RECQL exons 14-16. One of the breakpoints is within RECQL exons 14. Its functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0020763-T01-IM6	RECQL-AEBP2 fusion	yes	unknown		unknown	AEBP2 (NM_001114176) - RECQL (NM_032941) rearrangement: g.19703521_c.1534Gdel Note: The RECQL rearrangement results in the deletion of RECQL exons 14-16. One of the breakpoints is within RECQL exons 14. Its functional significance is undetermined.
VHL	0	MSKCC-DMP	P-0020760-T01-IM6	VHL-intragenic	yes	unknown		unknown	VHL (NM_000551) rearrangement: c.-1293_c.83del Note: The VHL rearrangement results in the deletion of the promoter of VHL and exon 1. The breakpoints are within the promoter region and exon 1. Its functional significance is undetermined
PTPRD	0	MSKCC-DMP	P-0020684-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.4087-5781_c.1298del Note: The PTPRD rearrangement is an intragenic deletion of exons 21-35. One of the breakpoints is within exon 21.
PTCD3	0	MSKCC-DMP	P-0019030-T02-IM6	BCL2L11-PTCD3 fusion	yes	unknown		out of frame	BCL2L11 (NM_138621) - PTCD3(NM_017952) rearrangement: c.394+1328_c.805-130dup Note: The BCL2L11 (NM_002529) - PTCD3 (NM_014857) rearrangement is a duplication that results in the fusion of BCL2L11 exons 1-2 with PTCD3 exons 11-24. The functional significance is undetermined.
BCL2L11	0	MSKCC-DMP	P-0019030-T02-IM6	BCL2L11-PTCD3 fusion	yes	unknown		out of frame	BCL2L11 (NM_138621) - PTCD3(NM_017952) rearrangement: c.394+1328_c.805-130dup Note: The BCL2L11 (NM_002529) - PTCD3 (NM_014857) rearrangement is a duplication that results in the fusion of BCL2L11 exons 1-2 with PTCD3 exons 11-24. The functional significance is undetermined.
HIST1H3A	0	MSKCC-DMP	P-0019030-T02-IM6	HIST1H3B-HIST1H3A fusion	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: g.26021830_c.18del Note: The HIST1H3B rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
HIST1H3B	0	MSKCC-DMP	P-0019030-T02-IM6	HIST1H3B-HIST1H3A fusion	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: g.26021830_c.18del Note: The HIST1H3B rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0020806-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3472_c.5124+318del Note: The ARID1A rearrangement is a deletion of exons 13-19. One of the breakpoints is within exon 13.
AXL	0	MSKCC-DMP	P-0020861-T01-IM6	CHEK2P2-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: t(15;19)(q11.1;q13.2)(chr15:g.20101904::chr19:g.41763332) Note: The AXL rearrangement is a translocation that may result in the truncation of exons 1-18. The functional significance is undetermined.
CHEK2P2	0	MSKCC-DMP	P-0020861-T01-IM6	CHEK2P2-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: t(15;19)(q11.1;q13.2)(chr15:g.20101904::chr19:g.41763332) Note: The AXL rearrangement is a translocation that may result in the truncation of exons 1-18. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0020833-T01-IM6	FOXP1-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) - FOXP1 (NM_001244814) rearrangement: t(3,17)(p13,p11.2)(chr3:g.71571851::chr17:g.17129138) Note: The FLCN - FOXP1 rearrangement is a translocation. One of the breakpoints is 351bp after exon 5 of FLCN, and the other breakpoint is 275kb upstream of FOXP1.
FOXP1	0	MSKCC-DMP	P-0020833-T01-IM6	FOXP1-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) - FOXP1 (NM_001244814) rearrangement: t(3,17)(p13,p11.2)(chr3:g.71571851::chr17:g.17129138) Note: The FLCN - FOXP1 rearrangement is a translocation. One of the breakpoints is 351bp after exon 5 of FLCN, and the other breakpoint is 275kb upstream of FOXP1.
ZNF70	0	MSKCC-DMP	P-0020833-T01-IM6	EWSR1-ZNF70 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: g.24063333:ZNF70_c.1393:EWSR1del Note: The EWSR1 rearrangement results in the deletion of exons 1-14.  Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0020833-T01-IM6	EWSR1-ZNF70 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: g.24063333:ZNF70_c.1393:EWSR1del Note: The EWSR1 rearrangement results in the deletion of exons 1-14.  Its functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0020793-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1814+8_g.67812667del Note: The PIK3R1 rearrangement results in the deletion of exons 14-16. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0020884-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.920-8_c.673-87del Note: The TP53 rearrangement results in an intragenic deletion of exons 7-8. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0020620-T01-IM6	LOC101928035-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.10364_g.73987269inv Note: The ZFHX3 rearrangement results in the inversion of exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
PSMD7-DT	0	MSKCC-DMP	P-0020620-T01-IM6	PSMD7-DT-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.10364_g.73987269inv Note: The ZFHX3 rearrangement results in the inversion of exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0020792-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 3-11):c.56-1041:TMPRSS2_c.-149-14766:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0020792-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 3-11):c.56-1041:TMPRSS2_c.-149-14766:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
ALK	0	MSKCC-DMP	P-0020780-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1 - 13 fused to ALK exons 20 - 29 ): c.1489+1278:EML4_c.3173-690:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0020780-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1 - 13 fused to ALK exons 20 - 29 ): c.1489+1278:EML4_c.3173-690:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
APC	0	MSKCC-DMP	P-0020876-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.3901:APC_g.112190069:SRP19del Note: The APC rearrangement results in the deletion of APC exon 16. One of the breakpoints is within APC exon 16. It's functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0020876-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.3901:APC_g.112190069:SRP19del Note: The APC rearrangement results in the deletion of APC exon 16. One of the breakpoints is within APC exon 16. It's functional significance is undetermined.
SMO	0	MSKCC-DMP	P-0020831-T01-IM6	KLHDC10-SMO fusion	yes	unknown		unknown	SMO (NM_005631) rearrangement: c.166+10844:KLHDC10_c.2163:SMOdup Note: The KLDHC10 - SMO rearrangement is a duplication which results in the fusion of KLDHC10 exon 1 to SMO exon 12. One of the breakpoints is within SMO exon 12. Its functional significance is undetermined.
KLHDC10	0	MSKCC-DMP	P-0020831-T01-IM6	KLHDC10-SMO fusion	yes	unknown		unknown	SMO (NM_005631) rearrangement: c.166+10844:KLHDC10_c.2163:SMOdup Note: The KLDHC10 - SMO rearrangement is a duplication which results in the fusion of KLDHC10 exon 1 to SMO exon 12. One of the breakpoints is within SMO exon 12. Its functional significance is undetermined.
RHOQ	0	MSKCC-DMP	P-0020799-T01-IM6	MSH6-RHOQ fusion	yes	unknown		out of frame	MSH6 (NM_000179) - RHOQ (NM_012249) rearrangement: c.3646+4:MSH6_c.202-2802:RHOQdup Note: The MSH6 - RHOQ rearrangement is a duplication that results in the fusion of MSH6 exons 1-7 with RHOQ exons 3-5. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0020799-T01-IM6	MSH6-RHOQ fusion	yes	unknown		out of frame	MSH6 (NM_000179) - RHOQ (NM_012249) rearrangement: c.3646+4:MSH6_c.202-2802:RHOQdup Note: The MSH6 - RHOQ rearrangement is a duplication that results in the fusion of MSH6 exons 1-7 with RHOQ exons 3-5. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0020773-T01-IM6	BRE-FGFR3 fusion	yes	unknown		unknown	BRE (NM_004899) - FGFR3 (NM_000142 ) rearrangement: t(2;4)(p23.2;p16.3)(chr2:g.28322454::chr4:g.1803105) Note: The BRE - FGFR3 rearrangement is a translocation which results in the fusion of BRE exons 1-6 to FGFR3 exons 5 - 18. The fusion includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 5. The functional significance of this translocation is uncertain.
BRE	0	MSKCC-DMP	P-0020773-T01-IM6	BRE-FGFR3 fusion	yes	unknown		unknown	BRE (NM_004899) - FGFR3 (NM_000142 ) rearrangement: t(2;4)(p23.2;p16.3)(chr2:g.28322454::chr4:g.1803105) Note: The BRE - FGFR3 rearrangement is a translocation which results in the fusion of BRE exons 1-6 to FGFR3 exons 5 - 18. The fusion includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 5. The functional significance of this translocation is uncertain.
CCND3	0	MSKCC-DMP	P-0020829-T01-IM6	LPHN2-CCND3 fusion	yes	unknown		unknown	CCND3 (NM_001760) rearrangement: t(1,6)(p31.1,p21.1)(chr1:g.82121584::chr6:g.41903877) Note: The CCND3 rearrangement is a translocation that may result in a truncation of exon 5. The functional significance is undetermined.
LPHN2	0	MSKCC-DMP	P-0020829-T01-IM6	LPHN2-CCND3 fusion	yes	unknown		unknown	CCND3 (NM_001760) rearrangement: t(1,6)(p31.1,p21.1)(chr1:g.82121584::chr6:g.41903877) Note: The CCND3 rearrangement is a translocation that may result in a truncation of exon 5. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0020882-T01-IM6	PTPRD-intragenic	yes	unknown		out of frame	PTPRD (NM_002839) rearrangement: c.5534+5222_c.5253+71del Note: The PTPRD rearrangement is an intragenic deletion of PTPRD exons 43-44. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0020791-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4744_g.112192034del Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0020791-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4744_g.112192034del Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0020837-T01-IM6	RBCK1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(20,22)(p13,q12.2)(chr20:g.404212::chr22:g.29694204) Note: The EWSR1 rearrangement is a translocation that may result in the truncation of exons 15-18. Its functional significance is undetermined.
RBCK1	0	MSKCC-DMP	P-0020837-T01-IM6	RBCK1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(20,22)(p13,q12.2)(chr20:g.404212::chr22:g.29694204) Note: The EWSR1 rearrangement is a translocation that may result in the truncation of exons 15-18. Its functional significance is undetermined.
ARID5B	0	MSKCC-DMP	P-0020777-T01-IM6	ARID5B-intragenic	yes	unknown		out of frame	ARID5B (NM_032199) rearrangement: c.502+21040_c.847-56del Note: The ARID5B rearrangement is an intragenic deletion of exons 4 - 5. The functional significance is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0020909-T01-IM6	FRMD4A-PPP2R1A fusion	yes	unknown		in frame	PPP2R1A (NM_014225) - FRMD4A (NM_018027) rearrangement: t(10;19)(p13;q13.41)(chr10:g.14320979::chr19:g.52719936) Note: The PPP2R1A - FRMD4A rearrangement is a translocation which results in the fusion of PPP2R1A exons 1-9  with FRMD4A exons 3-24. The fusion is predicted to be in frame. The functional significance is undetermined.
FRMD4A	0	MSKCC-DMP	P-0020909-T01-IM6	FRMD4A-PPP2R1A fusion	yes	unknown		in frame	PPP2R1A (NM_014225) - FRMD4A (NM_018027) rearrangement: t(10;19)(p13;q13.41)(chr10:g.14320979::chr19:g.52719936) Note: The PPP2R1A - FRMD4A rearrangement is a translocation which results in the fusion of PPP2R1A exons 1-9  with FRMD4A exons 3-24. The fusion is predicted to be in frame. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0020910-T01-IM6	ATM-intragenic	yes	unknown		in frame	ATM (NM_000051) rearrangement:  c.1607+13_c.6572+82del Note: The ATM rearrangement is an intragenic deletion of exons 11-45. The functional significance is undetermined.
CUL1	0	MSKCC-DMP	P-0020973-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: g.148465400_c.1437del Note: The EZH2 rearrangement results in the deletion of exons 12-20. One of the breakpoints is within exon 12. The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0020973-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: g.148465400_c.1437del Note: The EZH2 rearrangement results in the deletion of exons 12-20. One of the breakpoints is within exon 12. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0020974-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.303+2543:CCDC6_c.2137-848:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0020974-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.303+2543:CCDC6_c.2137-848:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0020612-T01-IM6	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*101+817_c.231del Note: The CDKN2Ap14ARF rearrangement is an intragenic deletion of exon 2. One breakpoint is within CDK2NA exon 2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0020612-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement:  c.457+817_c.188del Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of exon 2. One breakpoint is within CDKN2Ap16INK4A exon 2. The functional significance is undetermined.
SLCO2B1	0	MSKCC-DMP	P-0020964-T01-IM6	MSH3-SLCO2B1 fusion	yes	unknown		unknown	SLCO2B1 (NM_007256) - MSH3 (NM_002439) rearrangement: t(5;11)(q14.1;q13.4)(chr5:g.80149840::chr11:g.74883584) Note: The SLCO2B1 - MSH3 rearrangement is a translocation that results in the fusion of SLCO2B1 exons 1-7 with MSH3 exons 21-24. One of the breakpoints is within SLCO2B1 exon 7. The functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0020964-T01-IM6	MSH3-SLCO2B1 fusion	yes	unknown		unknown	SLCO2B1 (NM_007256) - MSH3 (NM_002439) rearrangement: t(5;11)(q14.1;q13.4)(chr5:g.80149840::chr11:g.74883584) Note: The SLCO2B1 - MSH3 rearrangement is a translocation that results in the fusion of SLCO2B1 exons 1-7 with MSH3 exons 21-24. One of the breakpoints is within SLCO2B1 exon 7. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0020919-T01-IM6	AEBP2-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.1815:PIK3C2G_g.19682908:AEBP2del Note: The PIK3C2G rearrangement results in the deletion of exons 13-32. One of the breakpoints is within exon 13. Its significance is undetermined.
AEBP2	0	MSKCC-DMP	P-0020919-T01-IM6	AEBP2-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.1815:PIK3C2G_g.19682908:AEBP2del Note: The PIK3C2G rearrangement results in the deletion of exons 13-32. One of the breakpoints is within exon 13. Its significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0020926-T01-IM6	LINC00052-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(15,17)(q25.3,q12)(chr15:g.88160146::chr17:g.37882881) Note: The ERBB2 rearrangement is a translocation which may result in the truncation of ERBB2 exons 24-27.  One of the breakpoints is within exon 24. Its functional significance is undetermined.
LINC00052	0	MSKCC-DMP	P-0020926-T01-IM6	LINC00052-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(15,17)(q25.3,q12)(chr15:g.88160146::chr17:g.37882881) Note: The ERBB2 rearrangement is a translocation which may result in the truncation of ERBB2 exons 24-27.  One of the breakpoints is within exon 24. Its functional significance is undetermined.
RAMP3	0	MSKCC-DMP	P-0020926-T01-IM6	CDC73-RAMP3 fusion	yes	unknown		unknown	CDC73 (NM_024529) - RAMP3 (NM_005856) rearrangement: t(1,7)(q31.2,p13)(chr1:g.193218905::chr7:g.45238072) Note: The CDC73 rearrangement is a translocation which may result in the truncation of CDC73 exons 16-17.  One of the breakpoints is within exon 16. Its functional significance is undetermined.
CDC73	0	MSKCC-DMP	P-0020926-T01-IM6	CDC73-RAMP3 fusion	yes	unknown		unknown	CDC73 (NM_024529) - RAMP3 (NM_005856) rearrangement: t(1,7)(q31.2,p13)(chr1:g.193218905::chr7:g.45238072) Note: The CDC73 rearrangement is a translocation which may result in the truncation of CDC73 exons 16-17.  One of the breakpoints is within exon 16. Its functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0017478-T02-IM6	DDR2-intragenic	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: c.672-562_c.2434-112inv Note: The DDR2 rearrangement is an intragenic inversion of exons 8-17. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0021038-T01-IM6	EGFR-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - EGFR (NM_005228) rearrangement: t(7;10)(p11.2;q11.22)(chr7:g.55241486::chr10:g.32312089) Note: The KIF5B - EGFR rearrangement is a translocation that results in the in frame fusion of KIF5B exons 1-15 with EGFR exons 18-28 and includes the kinase domain of EGFR. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0021038-T01-IM6	EGFR-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - EGFR (NM_005228) rearrangement: t(7;10)(p11.2;q11.22)(chr7:g.55241486::chr10:g.32312089) Note: The KIF5B - EGFR rearrangement is a translocation that results in the in frame fusion of KIF5B exons 1-15 with EGFR exons 18-28 and includes the kinase domain of EGFR. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0021054-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783021::chr6:g.117647162) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0021054-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783021::chr6:g.117647162) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
IL7R	0	MSKCC-DMP	P-0020961-T01-IM6	LIFR-IL7R fusion	yes	unknown		unknown	IL7R (NM_002185) - LIFR (NM_002310) rearrangement: c.1338:IL7R_c.-20+19953:LIFRinv Note: The IL7R - LIFR rearrangement is an inversion that results in the fusion of IL7R exons 1-8 with LIFR exons 2-20. One of the breakpoints is within IL7R exon 8. The functional significance is undetermined.
LIFR	0	MSKCC-DMP	P-0020961-T01-IM6	LIFR-IL7R fusion	yes	unknown		unknown	IL7R (NM_002185) - LIFR (NM_002310) rearrangement: c.1338:IL7R_c.-20+19953:LIFRinv Note: The IL7R - LIFR rearrangement is an inversion that results in the fusion of IL7R exons 1-8 with LIFR exons 2-20. One of the breakpoints is within IL7R exon 8. The functional significance is undetermined.
GPX5	0	MSKCC-DMP	P-0021044-T01-IM6	TAP1-GPX5 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: g.28495308_c.566del Note: The TAP1 rearrangement results in the deletion of exons 1-11. One of the breakpoints is within exon 1. The functional significance is undetermined.
TAP1	0	MSKCC-DMP	P-0021044-T01-IM6	TAP1-GPX5 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: g.28495308_c.566del Note: The TAP1 rearrangement results in the deletion of exons 1-11. One of the breakpoints is within exon 1. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0021034-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.3803_c.-104+141113del Note: The PTPRD rearrangement results in the deletion of exons 12-33. One of the breakpoints is within exon 33. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0021116-T01-IM6	KDM6A-intragenic	yes	unknown		in frame	KDM6A (NM_021140) rearrangement: c.384+1046_c.655-111del Note: The KDM6A rearrangement is an intragenic deletion of exons 5 - 8. Its significance is undetermined.
ROS1	0	MSKCC-DMP	P-0021120-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5079+1257_c.4960del Note: The ROS1 rearrangement is an intragenic deletion of exon 30. One of the breakpoints is within exon 30. Its significance is undetermined.
MGA	0	MSKCC-DMP	P-0021078-T01-IM6	TNFAIP8L3-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3834:MGA_chr15:g.51318549inv Note: The MGA rearrangement is an inversion of exons 11-24. One of the breakpoints is within exon 11.
TNFAIP8L3	0	MSKCC-DMP	P-0021078-T01-IM6	TNFAIP8L3-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3834:MGA_chr15:g.51318549inv Note: The MGA rearrangement is an inversion of exons 11-24. One of the breakpoints is within exon 11.
RB1	0	MSKCC-DMP	P-0021155-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.2663+49_c.2713+222del Note: The RB1 rearrangement results in the deletion of exon 26. The functional significance is undetermined.
LINC01568	0	MSKCC-DMP	P-0021061-T01-IM6	ANKRD11-LINC01568 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: chr16:g.73410859_c.2182:ANKRD11inv Note: The ANKRD11 rearrangement is an inversion of exons 9-13. One of the breakpoints is within exon 9. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0021061-T01-IM6	ANKRD11-LINC01568 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: chr16:g.73410859_c.2182:ANKRD11inv Note: The ANKRD11 rearrangement is an inversion of exons 9-13. One of the breakpoints is within exon 9. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0021150-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+312:KIF5B_c.2137-441:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0021150-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+312:KIF5B_c.2137-441:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
ZNF77	0	MSKCC-DMP	P-0021028-T01-IM6	GNA11-ZNF77 fusion	yes	unknown		unknown	GNA11 (NM_002067) rearrangement: chr19:g.2925382_c.137-2del Note: The GNA11 rearrangement is a deletion which includes exon 1 of GNA11. The functional significance is undetermined.
GNA11	0	MSKCC-DMP	P-0021028-T01-IM6	GNA11-ZNF77 fusion	yes	unknown		unknown	GNA11 (NM_002067) rearrangement: chr19:g.2925382_c.137-2del Note: The GNA11 rearrangement is a deletion which includes exon 1 of GNA11. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0021028-T01-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.5914-67_chr19:g.15454199del Note: The NOTCH3 rearrangement is a deletion which includes exons 1-32 of NOTCH3. The functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0021028-T01-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.5914-67_chr19:g.15454199del Note: The NOTCH3 rearrangement is a deletion which includes exons 1-32 of NOTCH3. The functional significance is undetermined.
ST6GAL2	0	MSKCC-DMP	P-0021233-T01-IM6	IRS1-ST6GAL2 fusion	yes	unknown		unknown	IRS1 (NM_005544) rearrangement: g.107724645_c.1872inv Note: The IRS1 rearrangement results in the inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
IRS1	0	MSKCC-DMP	P-0021233-T01-IM6	IRS1-ST6GAL2 fusion	yes	unknown		unknown	IRS1 (NM_005544) rearrangement: g.107724645_c.1872inv Note: The IRS1 rearrangement results in the inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
HMGCS2	0	MSKCC-DMP	P-0021235-T01-IM6	NOTCH2-HMGCS2 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: g.120292852_c.3480inv Note: The NOTCH2 rearrangement results in the inversion of exons 21-34. One of the breakpoints is within exon 21. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0021235-T01-IM6	NOTCH2-HMGCS2 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: g.120292852_c.3480inv Note: The NOTCH2 rearrangement results in the inversion of exons 21-34. One of the breakpoints is within exon 21. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021239-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-3436:TMPRSS2_c.40-63140:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0021239-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-3436:TMPRSS2_c.40-63140:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
KMT2C	0	MSKCC-DMP	P-0021239-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8452_c.7011del Note: The KMT2C rearrangement results in the deletion of exons 36-38. One of the breakpoints is within exon 36 and the other is within exon 38. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0021228-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43):t(5;6)(q32;q22.1)(chr5:g.149783729::chr6:g.117646295) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0021228-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43):t(5;6)(q32;q22.1)(chr5:g.149783729::chr6:g.117646295) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
FLT1	0	MSKCC-DMP	P-0021253-T01-IM6	DIAPH3-FLT1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.1010_chr13:g.59883399del Note: The FLT1 rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon 8. Its significance is undetermined.
DIAPH3	0	MSKCC-DMP	P-0021253-T01-IM6	DIAPH3-FLT1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.1010_chr13:g.59883399del Note: The FLT1 rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon 8. Its significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021254-T01-IM6	PRDM15-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2956_chr21:g.43199377inv Note: The TMPRSS2 rearrangement results in the inversion of exon 1. Its significance is undetermined.
PRDM15	0	MSKCC-DMP	P-0021254-T01-IM6	PRDM15-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2956_chr21:g.43199377inv Note: The TMPRSS2 rearrangement results in the inversion of exon 1. Its significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021254-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion (TMPRSS2 exons 1 fused to ETV1 exons 6-12):  t(7;21)(p21.2;q22.3)(chr7:g.14016215::chr21:g.42874388) Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.
ETV1	0	MSKCC-DMP	P-0021254-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion (TMPRSS2 exons 1 fused to ETV1 exons 6-12):  t(7;21)(p21.2;q22.3)(chr7:g.14016215::chr21:g.42874388) Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.
PELI2	0	MSKCC-DMP	P-0021255-T01-IM6	FLT3-PELI2 fusion	yes	unknown		unknown	PELI2 (NM_021255) FLT3 (NM_004119) rearrangement: t(13,14)(q12.2,q22.3)(chr13:g.28608118::chr14:g.56582755) Note: The PELI2 - FLT3 rearrangement is a translocation which results in the fusion of PELI2 exons 1-6 with FLT3 exons 15-24. Its significance is undetermined.
FLT3	0	MSKCC-DMP	P-0021255-T01-IM6	FLT3-PELI2 fusion	yes	unknown		unknown	PELI2 (NM_021255) FLT3 (NM_004119) rearrangement: t(13,14)(q12.2,q22.3)(chr13:g.28608118::chr14:g.56582755) Note: The PELI2 - FLT3 rearrangement is a translocation which results in the fusion of PELI2 exons 1-6 with FLT3 exons 15-24. Its significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0021001-T01-IM6	CDKN2B-AS1-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.1544-103_g.22097196 Note: The PTPRD rearrangement results in the deletion of exons 1-21.
CDKN2B-AS1	0	MSKCC-DMP	P-0021001-T01-IM6	CDKN2B-AS1-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.1544-103_g.22097196 Note: The PTPRD rearrangement results in the deletion of exons 1-21.
FAM198A	0	MSKCC-DMP	P-0019401-T02-IM6	MTOR-FAM198A fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: t(1;3)(p36.22;p22.1)(chr1:g.11217066::chr3:g.43055777) Note: The MTOR rearrangement is a translocation that may result in a truncation of MTOR exons 31-58. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0019401-T02-IM6	MTOR-FAM198A fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: t(1;3)(p36.22;p22.1)(chr1:g.11217066::chr3:g.43055777) Note: The MTOR rearrangement is a translocation that may result in a truncation of MTOR exons 31-58. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021282-T01-IM6	PLCD3-TMPRSS2 fusion	yes	unknown		unknown	PLCD3 (NM_133373) - TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43207457::chr21:g.42843839) Note: The PLCD3 - TMPRSS2 rearrangement is a translocation that results in the fusion of PLCD3 exon 1 with TMPRSS2 exons 10-14. One of the breakpoints is within TMPRSS2 exon10. The functional significance is undetermined.
PLCD3	0	MSKCC-DMP	P-0021282-T01-IM6	PLCD3-TMPRSS2 fusion	yes	unknown		unknown	PLCD3 (NM_133373) - TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43207457::chr21:g.42843839) Note: The PLCD3 - TMPRSS2 rearrangement is a translocation that results in the fusion of PLCD3 exon 1 with TMPRSS2 exons 10-14. One of the breakpoints is within TMPRSS2 exon10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021183-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+659:TMPRSS2_c.18+25615:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0021183-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+659:TMPRSS2_c.18+25615:ERGdel
HLA-DOB	0	MSKCC-DMP	P-0021290-T01-IM6	TAP2-HLA-DOB fusion	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: g.32764970_c.945+11inv Note: The TAP2 rearrangement results in the inversion of exons 5-12. The functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0021290-T01-IM6	TAP2-HLA-DOB fusion	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: g.32764970_c.945+11inv Note: The TAP2 rearrangement results in the inversion of exons 5-12. The functional significance is undetermined.
CUL1	0	MSKCC-DMP	P-0021328-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangemen: chr7:g.148497861_c.1547-42:EZH2inv Note: The EZH2 rearrangement is an inversion of exons 14-20. The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0021328-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangemen: chr7:g.148497861_c.1547-42:EZH2inv Note: The EZH2 rearrangement is an inversion of exons 14-20. The functional significance is undetermined.
ATP1B2	0	MSKCC-DMP	P-0021104-T01-IM6	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: g.7562760_c.966del Note: The TP53 rearrangement results in the deletion of exons 9-11. One of the breakpoints is within exon 9. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0021104-T01-IM6	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: g.7562760_c.966del Note: The TP53 rearrangement results in the deletion of exons 9-11. One of the breakpoints is within exon 9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021104-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-55:TMPRSS2_c.40-55445:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0021104-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-55:TMPRSS2_c.40-55445:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.
SLC12A7	0	MSKCC-DMP	P-0021288-T01-IM6	TERT-SLC12A7 fusion	yes	unknown		unknown	SLC12A7 (NM_006598) - TERT (NM_198253) rearrangement: c.125-1849:SLC12A7_c.-15:TERTdup Note: The SLC12A7 - TERT rearrangement is a duplication that results in the fusion of SLC12A7 exon 1 with TERT exons 1-16. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0021288-T01-IM6	TERT-SLC12A7 fusion	yes	unknown		unknown	SLC12A7 (NM_006598) - TERT (NM_198253) rearrangement: c.125-1849:SLC12A7_c.-15:TERTdup Note: The SLC12A7 - TERT rearrangement is a duplication that results in the fusion of SLC12A7 exon 1 with TERT exons 1-16. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0021166-T01-IM6	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) rearrangement: c.2107-434_c.2325+22del Note: The RB1 rearrangement is an intragenic deletion of exons 21-22.
ATM	0	MSKCC-DMP	P-0021201-T01-IM6	C11orf87-ATM fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.3919:ATM_chr11:g.109110999inv Note: The ATM rearrangement results in the inversion of ATM exons 26-63. One of the breakpoints is within exon 26. Its significance is undetermined.
C11orf87	0	MSKCC-DMP	P-0021201-T01-IM6	C11orf87-ATM fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.3919:ATM_chr11:g.109110999inv Note: The ATM rearrangement results in the inversion of ATM exons 26-63. One of the breakpoints is within exon 26. Its significance is undetermined.
BRD4	0	MSKCC-DMP	P-0021383-T01-IM6	CRLF1-BRD4 fusion	yes	unknown		out of frame	CRLF1 (NM_004750) - BRD4 (NM_058243) rearrangement: c.1024+39_c.1752-31del Note: The CRLF1 - BRD4 rearrangement is a deletion which results in the fusion of CRLF1 exons 1-6 to BRD4 exons 10-20. The functional significance is undetermined.
CRLF1	0	MSKCC-DMP	P-0021383-T01-IM6	CRLF1-BRD4 fusion	yes	unknown		out of frame	CRLF1 (NM_004750) - BRD4 (NM_058243) rearrangement: c.1024+39_c.1752-31del Note: The CRLF1 - BRD4 rearrangement is a deletion which results in the fusion of CRLF1 exons 1-6 to BRD4 exons 10-20. The functional significance is undetermined.
NKAIN1	0	MSKCC-DMP	P-0021105-T01-IM6	CDKN2C-NKAIN1 fusion	yes	unknown		in frame	NKAIN1 (NM_024522) - CDKN2C (NM_078626) rearrangement: c.55-5172:NKAIN1_c.130-80:CDKN2Cinv Note: The NKAIN1 - CDKN2C rearrangement is an inversion that results in the fusion of NKAIN1 exon 1 with CDKN2C exon 2. The functional significance is undetermined.
CDKN2C	0	MSKCC-DMP	P-0021105-T01-IM6	CDKN2C-NKAIN1 fusion	yes	unknown		in frame	NKAIN1 (NM_024522) - CDKN2C (NM_078626) rearrangement: c.55-5172:NKAIN1_c.130-80:CDKN2Cinv Note: The NKAIN1 - CDKN2C rearrangement is an inversion that results in the fusion of NKAIN1 exon 1 with CDKN2C exon 2. The functional significance is undetermined.
SLC38A7	0	MSKCC-DMP	P-0021105-T01-IM6	CSF3R-SLC38A7 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: t(1;16)(p34.4;q21)(chr1:g.36937176::chr16:g.58687670) Note: The CSF3R rearrangement is a translocation that may result in a truncation of exons 10-17. One of the breakpoints is within exon 10. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0021105-T01-IM6	CSF3R-SLC38A7 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: t(1;16)(p34.4;q21)(chr1:g.36937176::chr16:g.58687670) Note: The CSF3R rearrangement is a translocation that may result in a truncation of exons 10-17. One of the breakpoints is within exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021388-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.127-29:TMPRSS2_c.39+17938:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0021388-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.127-29:TMPRSS2_c.39+17938:ERGdel
LINC01573	0	MSKCC-DMP	P-0021271-T01-IM6	EGFL7-LINC01573 fusion	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: g.139473248_c.81-52del Note: The EGFL7 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.
EGFL7	0	MSKCC-DMP	P-0021271-T01-IM6	EGFL7-LINC01573 fusion	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: g.139473248_c.81-52del Note: The EGFL7 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.
SCARA3	0	MSKCC-DMP	P-0021102-T01-IM6	ARID1B-SCARA3 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;8)(q25.3;p21.1)(chr6:g.157528010::chr8:g.27481234) Note: The ARID1B rearrangement is a translocation that may result in a truncation of exon 20. One of the breakpoints is within exon 20. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0021102-T01-IM6	ARID1B-SCARA3 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;8)(q25.3;p21.1)(chr6:g.157528010::chr8:g.27481234) Note: The ARID1B rearrangement is a translocation that may result in a truncation of exon 20. One of the breakpoints is within exon 20. The functional significance is undetermined.
ARAF	0	MSKCC-DMP	P-0021274-T01-IM6	ZNF81-ARAF fusion	yes	unknown		unknown	ZNF81 (NM_007137) - ARAF (NM_001654) rearrangement: c.55-16531:ZNF81_c.-40:ARAFdup Note: The ZNF81 - ARAF rearrangement is a duplication that results in the fusion of ZNF81 exons 1-2 with ARAF exons 2-16. The functional significance is undetermined.
ZNF81	0	MSKCC-DMP	P-0021274-T01-IM6	ZNF81-ARAF fusion	yes	unknown		unknown	ZNF81 (NM_007137) - ARAF (NM_001654) rearrangement: c.55-16531:ZNF81_c.-40:ARAFdup Note: The ZNF81 - ARAF rearrangement is a duplication that results in the fusion of ZNF81 exons 1-2 with ARAF exons 2-16. The functional significance is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0021173-T01-IM6	PPP2R1A-intragenic	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.-434_c.78+176dup Note: The PPP2R1A rearrangement is a tandem duplication involving exon 1. The functional significance is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0021173-T01-IM6	U2AF2-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.26:PPP2R1A_chr19:g.56185948inv Note: The PPP2R1A rearrangement is an inversion with a breakpoint in exon 1. The presence of multiple structural variants involving PPP2R1A suggests a complex rearrangement. The functional significance is undetermined.
U2AF2	0	MSKCC-DMP	P-0021173-T01-IM6	U2AF2-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.26:PPP2R1A_chr19:g.56185948inv Note: The PPP2R1A rearrangement is an inversion with a breakpoint in exon 1. The presence of multiple structural variants involving PPP2R1A suggests a complex rearrangement. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0021351-T01-IM6	LINC00293-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(8;12)(q11.1;p13.33)(chr8:g.47164681::chr12:g.495087) Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 2. The functional significance is undetermined.
LINC00293	0	MSKCC-DMP	P-0021351-T01-IM6	LINC00293-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(8;12)(q11.1;p13.33)(chr8:g.47164681::chr12:g.495087) Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 2. The functional significance is undetermined.
LINC00581	0	MSKCC-DMP	P-0021168-T01-IM6	TAP2-LINC00581 fusion	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: chr6:g.21376128_c.81:TAP2inv Note: The TAP2 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0021168-T01-IM6	TAP2-LINC00581 fusion	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: chr6:g.21376128_c.81:TAP2inv Note: The TAP2 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0009955-T02-IM6	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.240+276_c.278del Note: The NF2 rearrangement is an intragenic deletion of exon3. One of the breakpoints is within exon 3. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0021262-T01-IM6	F11R-NTRK1 fusion	yes	unknown		in frame	F11R (NM_016946) - NTRK1 (NM_002529) rearrangement: c.389-101:F11R_c.1196-75:NTRK1inv Note: The F11R - NTRK1 rearrangement is an inversion that results in the fusion of F11R exons 1-4 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
F11R	0	MSKCC-DMP	P-0021262-T01-IM6	F11R-NTRK1 fusion	yes	unknown		in frame	F11R (NM_016946) - NTRK1 (NM_002529) rearrangement: c.389-101:F11R_c.1196-75:NTRK1inv Note: The F11R - NTRK1 rearrangement is an inversion that results in the fusion of F11R exons 1-4 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0021355-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.5674+735_c.6545del Note: The ATM rearrangement is an intragenic deletion of exons 38-45. One of the breakpoints is within exon 45.
BRAF	0	MSKCC-DMP	P-0021469-T01-IM6	TRIM33-BRAF fusion	yes	unknown		in frame	TRIM33 (NM_015906) - BRAF(NM_004333) rearrangement: t(1;7)(p13.2;q34)(chr1:g.114963985::chr7:g.140481644) Note: The TRIM33 - BRAF rearrangement is a translocation that results in the in-frame fusion of TRIM33 exons 1-11 with BRAF exons 11-18, and includes the kinase domain of BRAF. The functional significance is undetermined.
TRIM33	0	MSKCC-DMP	P-0021469-T01-IM6	TRIM33-BRAF fusion	yes	unknown		in frame	TRIM33 (NM_015906) - BRAF(NM_004333) rearrangement: t(1;7)(p13.2;q34)(chr1:g.114963985::chr7:g.140481644) Note: The TRIM33 - BRAF rearrangement is a translocation that results in the in-frame fusion of TRIM33 exons 1-11 with BRAF exons 11-18, and includes the kinase domain of BRAF. The functional significance is undetermined.
CDKN1B	0	MSKCC-DMP	P-0021482-T01-IM6	RAPGEF2-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(4;12)(q32.1;p13.1)(chr4:g.161050010::chr12:g.12870987) Note: The CDKN1B rearrangement is a translocation that may result in a truncation of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
RAPGEF2	0	MSKCC-DMP	P-0021482-T01-IM6	RAPGEF2-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(4;12)(q32.1;p13.1)(chr4:g.161050010::chr12:g.12870987) Note: The CDKN1B rearrangement is a translocation that may result in a truncation of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
ATAD1	0	MSKCC-DMP	P-0021391-T01-IM6	PTEN-ATAD1 fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.80-25_chr10:g.89539234del Note: The PTEN rearrangement results in the deletion of PTEN exon 1. Its significance is undetermined.
PTEN	0	MSKCC-DMP	P-0021391-T01-IM6	PTEN-ATAD1 fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.80-25_chr10:g.89539234del Note: The PTEN rearrangement results in the deletion of PTEN exon 1. Its significance is undetermined.
MED1	0	MSKCC-DMP	P-0021363-T01-IM6	WHSC1L1-MED1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) - MED1 (NM_004774) rearrangement: t(8;17)(p11.23;q12)(chr8:g.38148034::chr17:g.37599287) Note: The WHSC1L1 - MED1 rearrangement is a translocation that results in the fusion of WHSC1L1 exons 1-17 with MED1 exons 4-17. One of the breakpoints is within WHSC1L1 exon 17. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0021363-T01-IM6	WHSC1L1-MED1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) - MED1 (NM_004774) rearrangement: t(8;17)(p11.23;q12)(chr8:g.38148034::chr17:g.37599287) Note: The WHSC1L1 - MED1 rearrangement is a translocation that results in the fusion of WHSC1L1 exons 1-17 with MED1 exons 4-17. One of the breakpoints is within WHSC1L1 exon 17. The functional significance is undetermined.
POMC	0	MSKCC-DMP	P-0021458-T01-IM6	DNMT3A-POMC fusion	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: chr2:g.25419699_c.2716del Note: The DNMT3A rearrangement results in the deletion of exon 23. One of the breakpoints is within Exon 23. Its significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0021458-T01-IM6	DNMT3A-POMC fusion	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: chr2:g.25419699_c.2716del Note: The DNMT3A rearrangement results in the deletion of exon 23. One of the breakpoints is within Exon 23. Its significance is undetermined.
COLGALT1	0	MSKCC-DMP	P-0021409-T01-IM6	KDM5A-COLGALT1 fusion	yes	unknown		unknown	COLGALT1 (NM_024656) - KDM5A (NM_001042603) rearrangement: t(19;12)(p13.11;p13.33)(chr19:g.17669210::chr12:g.416253) Note: The COLGALT1 - KDM5A rearrangement is a translocation which results in fusion of COLGALT1 exons1-2 with KDM5A exon 24-28. Its functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0021409-T01-IM6	KDM5A-COLGALT1 fusion	yes	unknown		unknown	COLGALT1 (NM_024656) - KDM5A (NM_001042603) rearrangement: t(19;12)(p13.11;p13.33)(chr19:g.17669210::chr12:g.416253) Note: The COLGALT1 - KDM5A rearrangement is a translocation which results in fusion of COLGALT1 exons1-2 with KDM5A exon 24-28. Its functional significance is undetermined.
AATK-AS1	0	MSKCC-DMP	P-0021471-T01-IM6	CREBBP-AATK-AS1 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.3788736::chr17:g.79143420) Note: The CREBBP rearrangement is a translocation that may result in a truncation of exons 26-31. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0021471-T01-IM6	CREBBP-AATK-AS1 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.3788736::chr17:g.79143420) Note: The CREBBP rearrangement is a translocation that may result in a truncation of exons 26-31. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0021495-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.493+2355:EML4_c.3172+14:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0021495-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.493+2355:EML4_c.3172+14:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
LINC01309	0	MSKCC-DMP	P-0021503-T01-IM6	ATR-LINC01309 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(3;13)(q23;q33.1)(chr3:g.142188327::chr13:g.104696707) Note: The ATR rearrangement is a translocation that may result in a truncation of exons 38-47. One of the breakpoints is within exon 38.
ATR	0	MSKCC-DMP	P-0021503-T01-IM6	ATR-LINC01309 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(3;13)(q23;q33.1)(chr3:g.142188327::chr13:g.104696707) Note: The ATR rearrangement is a translocation that may result in a truncation of exons 38-47. One of the breakpoints is within exon 38.
TMPRSS2	0	MSKCC-DMP	P-0021503-T01-IM6	CAP2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangment: t(6;21)(p22.3;q22.3)(chr6:g.17413047::chr21:g.42878352) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined
CAP2	0	MSKCC-DMP	P-0021503-T01-IM6	CAP2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangment: t(6;21)(p22.3;q22.3)(chr6:g.17413047::chr21:g.42878352) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined
DNAJB1	0	MSKCC-DMP	P-0021601-T01-IM6	TECR-DNAJB1 fusion	yes	unknown		in frame	TECR (NM_138501) - DNAJB1 (NM_006145) rearrangement: c.119-27:TECR_c.212-543:DNAJB1inv Note: The TECR - DNAJB1 rearrangement is an inversion that results in the in-frame fusion of TECR exons 1-3 with DNAJB1 exons 2-3. The functional significance is undetermined.
TECR	0	MSKCC-DMP	P-0021601-T01-IM6	TECR-DNAJB1 fusion	yes	unknown		in frame	TECR (NM_138501) - DNAJB1 (NM_006145) rearrangement: c.119-27:TECR_c.212-543:DNAJB1inv Note: The TECR - DNAJB1 rearrangement is an inversion that results in the in-frame fusion of TECR exons 1-3 with DNAJB1 exons 2-3. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0021573-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: g.27021676_c.928del Note: The ARID1A rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
PLEKHA2	0	MSKCC-DMP	P-0021573-T01-IM6	CDK6-PLEKHA2 fusion	yes	unknown		unknown	CDK6 (NM_001145306) rearrangement: t(7;8)(q21.2;p11.22)(chr7:g.92392894::chr8:g.38736050) Note: The CDK6 rearrangement is a translocation that may result in a truncation of exons 4-8. The functional significance is undetermined.
CDK6	0	MSKCC-DMP	P-0021573-T01-IM6	CDK6-PLEKHA2 fusion	yes	unknown		unknown	CDK6 (NM_001145306) rearrangement: t(7;8)(q21.2;p11.22)(chr7:g.92392894::chr8:g.38736050) Note: The CDK6 rearrangement is a translocation that may result in a truncation of exons 4-8. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0021663-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.-150-29_c.2301+1480del Note: The FGFR2 rearrangement is an intragenic deletion of exons 1-17 which includes the kinase domain. Its functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0021630-T01-IM6	MTHFS-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.1154+36:SMAD3_chr15:g.80014264inv Note: The SMAD3 rearrangement is an inversion of exon 9. The functional significance is undetermined.
MTHFS	0	MSKCC-DMP	P-0021630-T01-IM6	MTHFS-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.1154+36:SMAD3_chr15:g.80014264inv Note: The SMAD3 rearrangement is an inversion of exon 9. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0021528-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.2970+6_c.*1538del Note: The ERBB2 rearrangement is a deletion which includes exons 25-27 of ERBB2. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0021578-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1231:KIF5B_c.2136+624:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0021578-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1231:KIF5B_c.2136+624:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
TBC1D10C	0	MSKCC-DMP	P-0021549-T01-IM6	RPS6KB2-TBC1D10C fusion	yes	unknown		out of frame	RPS6KB2 (NM_003952) rearrangement: c.120-43_chr11:g.67176716dup Note: The RPS6KB2 rearrangement is a duplication which results in the fusion of RPS6KB2 exons 1-2 with TBC1D10C exons 9-10. Its functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0021549-T01-IM6	RPS6KB2-TBC1D10C fusion	yes	unknown		out of frame	RPS6KB2 (NM_003952) rearrangement: c.120-43_chr11:g.67176716dup Note: The RPS6KB2 rearrangement is a duplication which results in the fusion of RPS6KB2 exons 1-2 with TBC1D10C exons 9-10. Its functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0021700-T01-IM6	BPTF-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.3250_g.65862975del Note: The BRIP1 rearrangement results in the deletion of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
BPTF	0	MSKCC-DMP	P-0021700-T01-IM6	BPTF-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.3250_g.65862975del Note: The BRIP1 rearrangement results in the deletion of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0021721-T01-IM6	DHH-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.49421954_c.14383-30del Note: The KMT2D rearrangement results in the deletion of exons 1-46. Its functional significance is undetermined.
DHH	0	MSKCC-DMP	P-0021721-T01-IM6	DHH-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.49421954_c.14383-30del Note: The KMT2D rearrangement results in the deletion of exons 1-46. Its functional significance is undetermined.
ELP4	0	MSKCC-DMP	P-0021728-T01-IM6	WT1-ELP4 fusion	yes	unknown		in frame	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.769+68:WT1_c.223+2679:ELP4del Note: The WT1 - ELP4 rearrangement is an inversion which results in the in frame fusion of WT1 exons 1-2 with ELP4 exons 2-10. Its functional significance is undetermined.
WT1	0	MSKCC-DMP	P-0021728-T01-IM6	WT1-ELP4 fusion	yes	unknown		in frame	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.769+68:WT1_c.223+2679:ELP4del Note: The WT1 - ELP4 rearrangement is an inversion which results in the in frame fusion of WT1 exons 1-2 with ELP4 exons 2-10. Its functional significance is undetermined.
CASZ1	0	MSKCC-DMP	P-0021742-T01-IM6	MTOR-CASZ1 fusion	yes	unknown		unknown	CASZ1 (NM_001079843) - MTOR (NM_004958) Rearrangement : c.-76-722:CASZ1_c.3286-88:MTORdup Note: The CASZ1 - MTOR  Rearrangement results in the fusion of exons 1-3 of CASZ1 with exons 22-58 of MTOR. Its functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0021742-T01-IM6	MTOR-CASZ1 fusion	yes	unknown		unknown	CASZ1 (NM_001079843) - MTOR (NM_004958) Rearrangement : c.-76-722:CASZ1_c.3286-88:MTORdup Note: The CASZ1 - MTOR  Rearrangement results in the fusion of exons 1-3 of CASZ1 with exons 22-58 of MTOR. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0021725-T01-IM6	ARID2-intragenic	yes	unknown		in frame	ARID2 (NM_152641) rearrangement: c.637+919_c.1121-13del Note: The ARID2 rearrangement is an intragenic deletion of exons 6-10. Its functional significance is undetermined.
RIT1	0	MSKCC-DMP	P-0021826-T01-IM6	PMF1-BGLAP-RIT1 fusion	yes	unknown		out of frame	RIT1 (NM_006912) - PMF1-BGLAP (NM_001199662) rearrangement: c.163+175:RIT1_c.162-7502:PMF1-BGLAPinv Note: The RIT1 - PMF1-BGLAP rearrangement is an inversion which results in the fusion of RIT1 exons 1-3 with PMF1-BGLAP exons 2-6.  Its functional significance is undetermined.
PMF1-BGLAP	0	MSKCC-DMP	P-0021826-T01-IM6	PMF1-BGLAP-RIT1 fusion	yes	unknown		out of frame	RIT1 (NM_006912) - PMF1-BGLAP (NM_001199662) rearrangement: c.163+175:RIT1_c.162-7502:PMF1-BGLAPinv Note: The RIT1 - PMF1-BGLAP rearrangement is an inversion which results in the fusion of RIT1 exons 1-3 with PMF1-BGLAP exons 2-6.  Its functional significance is undetermined.
RAD51B	0	MSKCC-DMP	P-0021826-T01-IM6	RAD51B-intragenic	yes	unknown		out of frame	RAD51B (NM_133509) rearrangement: c.757-5121_c.1036+28903del Note: The RAD51B rearrangement is an intragenic deletion of exons 8-10. Its functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0021826-T01-IM6	FGFR2-ANKRD11 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - ANKRD11 (NM_013275) rearrangement: t(10,16)(q26.13,q24.3)(chr10:g.123243799::chr16:g.89538175) Note: The FGFR2 - ANKRD11 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-16 with ANKRD11 exons 1-13. This includes the kinase domain of FGFR2. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0021826-T01-IM6	FGFR2-ANKRD11 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - ANKRD11 (NM_013275) rearrangement: t(10,16)(q26.13,q24.3)(chr10:g.123243799::chr16:g.89538175) Note: The FGFR2 - ANKRD11 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-16 with ANKRD11 exons 1-13. This includes the kinase domain of FGFR2. Its functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0021826-T01-IM6	KLHL18-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) rearrangement: c.4587-57:SETD2_chr3:g.47362971del Note: The SETD2 rearrangement results in the deletion of exons 1-4. Its functional significance is undetermined.
KLHL18	0	MSKCC-DMP	P-0021826-T01-IM6	KLHL18-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) rearrangement: c.4587-57:SETD2_chr3:g.47362971del Note: The SETD2 rearrangement results in the deletion of exons 1-4. Its functional significance is undetermined.
TRAPPC9	0	MSKCC-DMP	P-0021826-T01-IM6	AGO2-TRAPPC9 fusion	yes	unknown		unknown	AGO2 (NM_012154) - TRAPPC9 (NM_031466) rearrangement: c.1448:AGO2_c.3349+13144:TRAPPC9del Note: The AGO2 - TRAPCC9 rearrangement is a deletion which results in the fusion of AGO2 exons 1-12 with TRAPPC9 exons 22-23. One of the breakpoints is within AGO2 exon 12.  It's functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0021826-T01-IM6	AGO2-TRAPPC9 fusion	yes	unknown		unknown	AGO2 (NM_012154) - TRAPPC9 (NM_031466) rearrangement: c.1448:AGO2_c.3349+13144:TRAPPC9del Note: The AGO2 - TRAPCC9 rearrangement is a deletion which results in the fusion of AGO2 exons 1-12 with TRAPPC9 exons 22-23. One of the breakpoints is within AGO2 exon 12.  It's functional significance is undetermined.
ETV1	0	MSKCC-DMP	P-0021829-T01-IM6	WIPF3-ETV1 fusion	yes	unknown		unknown	ETV1 (NM_001163147) rearrangement: chr7:g.29894609_c.986:ETV1del Note: The ETV1 rearrangement results in the deletion of exons 1-10. One of the breakpoints is within exon 10. Its functional significance is undetermined.
WIPF3	0	MSKCC-DMP	P-0021829-T01-IM6	WIPF3-ETV1 fusion	yes	unknown		unknown	ETV1 (NM_001163147) rearrangement: chr7:g.29894609_c.986:ETV1del Note: The ETV1 rearrangement results in the deletion of exons 1-10. One of the breakpoints is within exon 10. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0021831-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4024_c.4606+997inv Note: The DOT1L rearrangement is an inversion of exon 27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0021804-T01-IM6	KMT2E-ERBB3 fusion	yes	unknown		unknown	KMT2E (NM_018682) - ERBB3 (NM_001982) rearrangement: t(7;12)(q22.3;q13.2)(chr7:g.104661375::chr12:g.56493836) Note: The KMT2E - ERBB3 rearrangement is a translocation that results in the fusion of KMT2E exon 1 with ERBB3 exons 26-28. The functional significance is undetermined.
KMT2E	0	MSKCC-DMP	P-0021804-T01-IM6	KMT2E-ERBB3 fusion	yes	unknown		unknown	KMT2E (NM_018682) - ERBB3 (NM_001982) rearrangement: t(7;12)(q22.3;q13.2)(chr7:g.104661375::chr12:g.56493836) Note: The KMT2E - ERBB3 rearrangement is a translocation that results in the fusion of KMT2E exon 1 with ERBB3 exons 26-28. The functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0021822-T01-IM6	RSG1-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: t(1,19)(p36.13,q13.2)(chr1:g.16550370::chr19:g.40762860) Note: The AKT2 rearrangement is a translocation which results in the possible truncation of exons 3-14 including the kinase domain. One of the breakpoints is within exon 3. Its functional significance is undetermined.
RSG1	0	MSKCC-DMP	P-0021822-T01-IM6	RSG1-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: t(1,19)(p36.13,q13.2)(chr1:g.16550370::chr19:g.40762860) Note: The AKT2 rearrangement is a translocation which results in the possible truncation of exons 3-14 including the kinase domain. One of the breakpoints is within exon 3. Its functional significance is undetermined.
KANSL2	0	MSKCC-DMP	P-0021675-T01-IM6	KMT2D-KANSL2 fusion	yes	unknown		unknown	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.973+2973:KANSL2_c.2726:KMT2Ddup Note: The KANSL2 - KMT2D rearrangement is a duplication which results in the fusion of KANSL2 exons 1-7 to KMT2D exons 10-54. One of the breakpoints is within KMT2D exon 10. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0021675-T01-IM6	KMT2D-KANSL2 fusion	yes	unknown		unknown	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.973+2973:KANSL2_c.2726:KMT2Ddup Note: The KANSL2 - KMT2D rearrangement is a duplication which results in the fusion of KANSL2 exons 1-7 to KMT2D exons 10-54. One of the breakpoints is within KMT2D exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021698-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-2467:TMPRSS2_c.19-2116:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0021698-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-2467:TMPRSS2_c.19-2116:ERGdel
LINC00114	0	MSKCC-DMP	P-0021711-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-568_chr21:g.40054074del Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021711-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-568_chr21:g.40054074del Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0021833-T01-IM6	AP3M2-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) Rearrangement : c.2758+22:WHSC1L1_chr8:g.41953873inv Note: The WHSC1L1 Rearrangement results in the inversion of exons 1-15 of WHSC1L1 exons.Its functional significance is undetermined.
AP3M2	0	MSKCC-DMP	P-0021833-T01-IM6	AP3M2-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) Rearrangement : c.2758+22:WHSC1L1_chr8:g.41953873inv Note: The WHSC1L1 Rearrangement results in the inversion of exons 1-15 of WHSC1L1 exons.Its functional significance is undetermined.
SPG11	0	MSKCC-DMP	P-0021863-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	B2M (NM_004048) rearrangement: g.44883857_c.68-82del Note: The B2M rearrangement results in the deletion of exon 1. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0021863-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	B2M (NM_004048) rearrangement: g.44883857_c.68-82del Note: The B2M rearrangement results in the deletion of exon 1. The functional significance is undetermined.
SRRM4	0	MSKCC-DMP	P-0021873-T01-IM6	DROSHA-SRRM4 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;12)(p13.3;q24.23)(chr5:g.31483658::chr12:g.119252705) Note: The DROSHA rearrangement is a translocation that may result in a truncation of exons 16-35. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0021873-T01-IM6	DROSHA-SRRM4 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;12)(p13.3;q24.23)(chr5:g.31483658::chr12:g.119252705) Note: The DROSHA rearrangement is a translocation that may result in a truncation of exons 16-35. The functional significance is undetermined.
NPTX2	0	MSKCC-DMP	P-0021862-T01-IM6	PARK2-NPTX2 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: t(6;7)(p22.3;q22.1)(chr6:g.162206907::chr7:g.98151994) Note: The PARK2 rearrangement is a translocation that may result in a truncation of exons 7-12. One of the breakpoints is within exon 7. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0021862-T01-IM6	PARK2-NPTX2 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: t(6;7)(p22.3;q22.1)(chr6:g.162206907::chr7:g.98151994) Note: The PARK2 rearrangement is a translocation that may result in a truncation of exons 7-12. One of the breakpoints is within exon 7. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0021882-T01-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.847_c.850+524del Note: The NTRK1 rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7. Its functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0021882-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.4195+27_c.4370del Note: The CIC rearrangement is an intragenic deletion of exons 18-19. One of the breakpoints is within exon 19. Its functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0021922-T01-IM6	TMBIM6-KMT2D fusion	yes	unknown		unknown	TMBIM6 (NM_001098576) - KMT2D (NM_003482) rearrangement: c.144+4807:TMBIM6_c.2409:KMT2Dinv Note: The TMBIM6 - KMT2D rearrangement is an inversion which results in the fusion of TMBIM6 exon 1 to KMT2D exons 10-54. One of the breakpoints is within KMT2D exon 10. Multiple KMT2D rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in functional gene fusion.
TMBIM6	0	MSKCC-DMP	P-0021922-T01-IM6	TMBIM6-KMT2D fusion	yes	unknown		unknown	TMBIM6 (NM_001098576) - KMT2D (NM_003482) rearrangement: c.144+4807:TMBIM6_c.2409:KMT2Dinv Note: The TMBIM6 - KMT2D rearrangement is an inversion which results in the fusion of TMBIM6 exon 1 to KMT2D exons 10-54. One of the breakpoints is within KMT2D exon 10. Multiple KMT2D rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in functional gene fusion.
NF1	0	MSKCC-DMP	P-0021064-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.4759_c.4835+22210del Note: The NF1 rearrangement is an intragenic deletion of exon 36. One of the breakpoints is within exon 36.
EWSR1	0	MSKCC-DMP	P-0021947-T01-IM6	SEC14L3-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : c.794-828:EWSR1_c.-716:SEC14LR Note: The EWSR1 Rearrangement results in the deletion of exons 10-18 of EWSR1.Its functional significance is undetermined.
SEC14L3	0	MSKCC-DMP	P-0021947-T01-IM6	SEC14L3-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : c.794-828:EWSR1_c.-716:SEC14LR Note: The EWSR1 Rearrangement results in the deletion of exons 10-18 of EWSR1.Its functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0022003-T01-IM6	ERBB4-intragenic	yes	unknown		in frame	ERBB4 (NM_005235) rearrangement: c.2643+122_c.3135+4521del Note: The ERBB4 rearrangement is an intragenic deletion of exons 22-25. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0022179-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.56-135_c.126+592del Note: The TMPRSS2 rearrangement is an intragenic  deletion of exon 2. The functional significance is undetermined. The possibility of a more complex rearrangement resulting in a TMPRSS2 -ERG fusion cannot be excluded.
RRNAD1	0	MSKCC-DMP	P-0022046-T01-IM6	NTRK1-RRNAD1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: g.156703825_c.1354+180inv Note: The NTRK1 rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0022046-T01-IM6	NTRK1-RRNAD1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: g.156703825_c.1354+180inv Note: The NTRK1 rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.
FBXW7	0	MSKCC-DMP	P-0022046-T01-IM6	FBXW7-intragenic	yes	unknown		unknown	FBXW7 (NM_033632) rearrangement: c.501+1999_c.371del Note: The FBXW7 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0021980-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-8 fused to RET exons 12- 20): c.763-591:NCOA4_c.2136+366:RETdup Note: The NCOA4 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
TIMM23B	0	MSKCC-DMP	P-0021980-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-8 fused to RET exons 12- 20): c.763-591:NCOA4_c.2136+366:RETdup Note: The NCOA4 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
GK	0	MSKCC-DMP	P-0022110-T01-IM6	ERBB2-GK fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(17;X)(q12;p21.2)(chr17:g.37883536::chrX:g.30637819) Note: The ERBB2 rearrangement is a translocation that may result in a truncation of exons 26-27. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0022110-T01-IM6	ERBB2-GK fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(17;X)(q12;p21.2)(chr17:g.37883536::chrX:g.30637819) Note: The ERBB2 rearrangement is a translocation that may result in a truncation of exons 26-27. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0022083-T01-IM6	PTRF-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) Rearrangement : c.274-1:STAT3_chr17:g.40549182del Note: The STAT3 Rearrangement results in the deletion of exons 1-4 of STAT3. The functional significance is undetermined.
PTRF	0	MSKCC-DMP	P-0022083-T01-IM6	PTRF-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) Rearrangement : c.274-1:STAT3_chr17:g.40549182del Note: The STAT3 Rearrangement results in the deletion of exons 1-4 of STAT3. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0022083-T01-IM6	KATNBL1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : t(15;22)(q14;q12.2)(chr15:g.34430755::chr22:g.29686911) Note: The EWSR1 Rearrangement results in the possible truncation of EWSR1. The functional significance is undetermined.
KATNBL1	0	MSKCC-DMP	P-0022083-T01-IM6	KATNBL1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : t(15;22)(q14;q12.2)(chr15:g.34430755::chr22:g.29686911) Note: The EWSR1 Rearrangement results in the possible truncation of EWSR1. The functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0022372-T01-IM6	NBPF20-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NBPF10 (NM_001039703) rearrangement: t(1;5)(q21.1;q32)(chr1:g.145430829::chr5:g.149782962) Note: The CD74 - NBPF10 rearrangement is a translocation with breakpoints within CD74 intron 6 and NBPF10 intron 68. The functional significance is undetermined. We cannot exclude the possibility of a more complex rearrangement resulting in a CD74 fusion.
NBPF20	0	MSKCC-DMP	P-0022372-T01-IM6	NBPF20-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NBPF10 (NM_001039703) rearrangement: t(1;5)(q21.1;q32)(chr1:g.145430829::chr5:g.149782962) Note: The CD74 - NBPF10 rearrangement is a translocation with breakpoints within CD74 intron 6 and NBPF10 intron 68. The functional significance is undetermined. We cannot exclude the possibility of a more complex rearrangement resulting in a CD74 fusion.
ROS1	0	MSKCC-DMP	P-0022372-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.2496+345_c.5367-1454inv Note: The ROS1 rearrangement is an intragenic inversion of exons 17- 32. The functional significance is undetermined. We cannot exclude the possibility of a more complex rearrangement resulting in a ROS1 gene fusion.
FGFR4	0	MSKCC-DMP	P-0022170-T01-IM6	NSD1-FGFR4 fusion	yes	unknown		in frame	FGFR4 (NM_213647) - NSD1 (NM_022455) rearrangement: c.603+17:FGFR4_c.927+12349:NSD1del Note: The FGFR4 - NDS1 rearrangement is a deletion which results in the fusion of FGFR4 exons 1-5 with NSD1 exons 3-23. The fusion is predicted to be in frame. The functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0022170-T01-IM6	NSD1-FGFR4 fusion	yes	unknown		in frame	FGFR4 (NM_213647) - NSD1 (NM_022455) rearrangement: c.603+17:FGFR4_c.927+12349:NSD1del Note: The FGFR4 - NDS1 rearrangement is a deletion which results in the fusion of FGFR4 exons 1-5 with NSD1 exons 3-23. The fusion is predicted to be in frame. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0022088-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) Rearrangement: c.993+232_c.1101-324del Note: The TP53 Rearrangement results in the intragenic deletion of exon 10 of TP53. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0022088-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) Rearrangement : c.3008_c.3819+291del Note: The MAP3K1 Rearrangement results in the intragenic deletion of exons 14-15. One of the breakpoints is within exon14. It includes the protein kinase domain of MAP3K1.
PVT1	0	MSKCC-DMP	P-0022185-T01-IM6	PAX8-PVT1 fusion	yes	unknown		unknown	PAX8 (NM_003466)  rearrangement: t(2;8)(q13;q24.21)(chr2:g.113979260::chr8:g.129096859) Note: The PAX8 rearrangement is a translocation with a breakpoint within intron 10 that may result in the truncation of PAX8 exons 11-12. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0022185-T01-IM6	PAX8-PVT1 fusion	yes	unknown		unknown	PAX8 (NM_003466)  rearrangement: t(2;8)(q13;q24.21)(chr2:g.113979260::chr8:g.129096859) Note: The PAX8 rearrangement is a translocation with a breakpoint within intron 10 that may result in the truncation of PAX8 exons 11-12. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0022118-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement : c.4019_c.4531inv Note: The CIC rearrangement results in an inversion of exons 16-20 . One of the breakpoints is within exon 16 and the other is within exon 20. The functional significance is undetermined.
MAD1L1	0	MSKCC-DMP	P-0022058-T01-IM6	CARD11-MAD1L1 fusion	yes	unknown		out of frame	MAD1L1 (NM_001013837) - CARD11 (NM_032415) rearrangement: c.1505+8166:MAD1L1_c.1654-67:CARD11dup Note: The MAD1L1 - CARD11 rearrangement is a duplication that results in the fusion of MAD1L1 exons 1-15 with CARD11 exons 14-25. The functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0022058-T01-IM6	CARD11-MAD1L1 fusion	yes	unknown		out of frame	MAD1L1 (NM_001013837) - CARD11 (NM_032415) rearrangement: c.1505+8166:MAD1L1_c.1654-67:CARD11dup Note: The MAD1L1 - CARD11 rearrangement is a duplication that results in the fusion of MAD1L1 exons 1-15 with CARD11 exons 14-25. The functional significance is undetermined.
CDKN1B	0	MSKCC-DMP	P-0022092-T01-IM6	ALG10B-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) Rearrangement : c.476-90:CDKN1B_chr12:g.38741621inv Note: The CDKN1B Rearrangement results in the inversion of exon1 of CDKN1B. Its functional significance is undetermined.
ALG10B	0	MSKCC-DMP	P-0022092-T01-IM6	ALG10B-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) Rearrangement : c.476-90:CDKN1B_chr12:g.38741621inv Note: The CDKN1B Rearrangement results in the inversion of exon1 of CDKN1B. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0022197-T01-IM6	LOC100507195-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.4773+92_chr12:g.68840062inv Note: The ARID2 rearrangement results in the inversion of exons 16-21. The functional significance is undetermined.
LOC100507195	0	MSKCC-DMP	P-0022197-T01-IM6	LOC100507195-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.4773+92_chr12:g.68840062inv Note: The ARID2 rearrangement results in the inversion of exons 16-21. The functional significance is undetermined.
CCT2	0	MSKCC-DMP	P-0022197-T01-IM6	POLE-CCT2 fusion	yes	unknown		unknown	CCT2 (NM_006431) - POLE (NM_006231) rearrangement: c.1470:CCT2_c.4885:POLEinv Note: The CCT2 - POLE rearrangement is an inversion that results in the fusion of CCT2 exons 1-15 with POLE exons 37-49. One of the breakpoints is within CCT2 exon 15 and the other is within POLE exon 37. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0022197-T01-IM6	POLE-CCT2 fusion	yes	unknown		unknown	CCT2 (NM_006431) - POLE (NM_006231) rearrangement: c.1470:CCT2_c.4885:POLEinv Note: The CCT2 - POLE rearrangement is an inversion that results in the fusion of CCT2 exons 1-15 with POLE exons 37-49. One of the breakpoints is within CCT2 exon 15 and the other is within POLE exon 37. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0022189-T01-IM6	SKIL-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - SKIL (NM_001248008) rearrangement: t(3;21)(q26.2;q22.3)(chr3:g.170075134::chr21:g.42867710) Note: The TMPRSS2 - SKIL rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-3 with the promoter of SKIL and exons 1- 6. The functional significance is undetermined.
SKIL	0	MSKCC-DMP	P-0022189-T01-IM6	SKIL-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - SKIL (NM_001248008) rearrangement: t(3;21)(q26.2;q22.3)(chr3:g.170075134::chr21:g.42867710) Note: The TMPRSS2 - SKIL rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-3 with the promoter of SKIL and exons 1- 6. The functional significance is undetermined.
UHMK1	0	MSKCC-DMP	P-0022364-T01-IM6	PARP1-UHMK1 fusion	yes	unknown		unknown	PARP1 (NM_001618) rearrangement: chr1:g.162434663_c.2505+39inv Note: The PARP1 rearrangement results in the inversion of exons 1-18. The functional significance is undetermined.
PARP1	0	MSKCC-DMP	P-0022364-T01-IM6	PARP1-UHMK1 fusion	yes	unknown		unknown	PARP1 (NM_001618) rearrangement: chr1:g.162434663_c.2505+39inv Note: The PARP1 rearrangement results in the inversion of exons 1-18. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0022364-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.2380-766_c.1936-105inv Note: The BRIP1 rearrangement results in the inversion of exons 14-16. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0022086-T01-IM6	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) Rearrangement: c.2720_c.2897+2215del Note: The KDM5A Rearrangement results in the intragenic deletion of exon19. One of the breakpoints is within exon19. The functional significance is undetermined.
SYT6	0	MSKCC-DMP	P-0022128-T01-IM6	CSDE1-SYT6 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: chr1:g.114598243_c.2487+20:CSDE1del Note: The CSDE1 rearrangement is a deletion of exon 21. The functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0022128-T01-IM6	CSDE1-SYT6 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: chr1:g.114598243_c.2487+20:CSDE1del Note: The CSDE1 rearrangement is a deletion of exon 21. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0022117-T01-IM6	SNRPE-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.684_chr1:g.203839162inv Note: The NTRK1 rearrangement results in the inversion of exons 6-17 and includes the kinase domain of NTRK1. One of the breakpoints is within exon 6. The functional significance is undetermined.
SNRPE	0	MSKCC-DMP	P-0022117-T01-IM6	SNRPE-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.684_chr1:g.203839162inv Note: The NTRK1 rearrangement results in the inversion of exons 6-17 and includes the kinase domain of NTRK1. One of the breakpoints is within exon 6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022117-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-3 fused to ERG exons 2-10): c.304:TMPRSS2_c.18+8044:ERGdel Note: One of the breakpoints is within TMPRSS2 exon 3.
TMPRSS2	0	MSKCC-DMP	P-0022117-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-3 fused to ERG exons 2-10): c.304:TMPRSS2_c.18+8044:ERGdel Note: One of the breakpoints is within TMPRSS2 exon 3.
SESN3	0	MSKCC-DMP	P-0022084-T01-IM6	SESN3-intragenic	yes	unknown		unknown	SESN3 (NM_144665) Rearrangement: c.526-1622_c.1106del Note: The SESN3 Rearrangement results in the intragenic deletion of exons 5-8 of SESN3. One of the breakpoints is within exon 8. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0022084-T01-IM6	NBPF18P-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement : t(1;19)(q21.3;p13.12)(chr1:g.151973890::chr19:g.15281223) Note: The NOTCH3 Rearrangement results in the possible truncation of NOTCH3. One of the breakpoints is within exon 27.  The functional significance is undetermined.
NBPF18P	0	MSKCC-DMP	P-0022084-T01-IM6	NBPF18P-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement : t(1;19)(q21.3;p13.12)(chr1:g.151973890::chr19:g.15281223) Note: The NOTCH3 Rearrangement results in the possible truncation of NOTCH3. One of the breakpoints is within exon 27.  The functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0022099-T01-IM6	KDM5C-intragenic	yes	unknown		in frame	KDM5C (NM_004187) Rearrangement : c.963+158_c.1746+3254del Note: The KDM5C Rearrangement results in the intragenic deletion of exons 8-12. Its functional significance is undetermined.
XIAP	0	MSKCC-DMP	P-0022358-T01-IM6	XIAP-intragenic	yes	unknown		unknown	XIAP (NM_001167) rearrangement: c.-33+7954_c.1100-72del Note: The XIAP rearrangement results in the deletion of the 5'UTR and exons 1-5. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0022456-T01-IM6	SP3-FGFR1 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: t(2;8)(q31.1;p11.23)(chr2:g.174604210::chr8:g.38276953) Note: The FGFR1 rearrangement is a translocation which may result in the truncation of FGFR1 after exon 10. The functional significance is undetermined.
SP3	0	MSKCC-DMP	P-0022456-T01-IM6	SP3-FGFR1 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: t(2;8)(q31.1;p11.23)(chr2:g.174604210::chr8:g.38276953) Note: The FGFR1 rearrangement is a translocation which may result in the truncation of FGFR1 after exon 10. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0022348-T01-IM6	PABPC1P2-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(2;12)(q22.3;p13.2)(chr2:g.146814969::chr12:g.12022241) Note: The ETV6 rearrangement is a translocation which may result in the truncation of exons 1-4. Its functional significance is undetermined.  Multiple ETV6 rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in a ETV6 gene fusion.
PABPC1P2	0	MSKCC-DMP	P-0022348-T01-IM6	PABPC1P2-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(2;12)(q22.3;p13.2)(chr2:g.146814969::chr12:g.12022241) Note: The ETV6 rearrangement is a translocation which may result in the truncation of exons 1-4. Its functional significance is undetermined.  Multiple ETV6 rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in a ETV6 gene fusion.
USHBP1	0	MSKCC-DMP	P-0022444-T01-IM6	KDM5A-USHBP1 fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(12;19)(p13.33;p13.11)(chr12:g.459868::chr19:g.17358572) Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0022444-T01-IM6	KDM5A-USHBP1 fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(12;19)(p13.33;p13.11)(chr12:g.459868::chr19:g.17358572) Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022446-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+1508:TMPRSS2_c.39+58986:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0022446-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+1508:TMPRSS2_c.39+58986:ERGdel
FAT1	0	MSKCC-DMP	P-0022425-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.2732_c.3265+636inv Note: The FAT1 rearrangement results in an inversion of exon 2. One of the breakpoints is within exon 2. Its functional significance is undetermined. In addition, multiple other FAT1 rearrangements were detected. The possibility of a more complex rearrangement resulting in a FAT1 gene fusion cannot be excluded.
SCNN1B	0	MSKCC-DMP	P-0022284-T01-IM6	PALB2-SCNN1B fusion	yes	unknown		unknown	PALB2 (NM_024675) - SCNN1B (NM_000336) rearrangement: c.3201+79:PALB2_c.777-356:SCNN1Bdel Note: The PALB2 - SCNN1B rearrangement is a deletion which includes exons 12-13 of PALB2. The deletion is observed in the context of a PALB2 copy number gain. The functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0022284-T01-IM6	PALB2-SCNN1B fusion	yes	unknown		unknown	PALB2 (NM_024675) - SCNN1B (NM_000336) rearrangement: c.3201+79:PALB2_c.777-356:SCNN1Bdel Note: The PALB2 - SCNN1B rearrangement is a deletion which includes exons 12-13 of PALB2. The deletion is observed in the context of a PALB2 copy number gain. The functional significance is undetermined.
NRG3	0	MSKCC-DMP	P-0022337-T01-IM6	FGFR2-NRG3 fusion	yes	unknown		out of frame	NRG3 (NM_001010848) - FGFR2 (NM_000141) Rearrangement : c.953+89877:NRG3_c.2301+1489:FGFR2inv Note: The NRG3  - FGFR2 Rearrangement  results in the fusion of NRG3 exons 1-2 with FGFR2 exon 18. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0022337-T01-IM6	FGFR2-NRG3 fusion	yes	unknown		out of frame	NRG3 (NM_001010848) - FGFR2 (NM_000141) Rearrangement : c.953+89877:NRG3_c.2301+1489:FGFR2inv Note: The NRG3  - FGFR2 Rearrangement  results in the fusion of NRG3 exons 1-2 with FGFR2 exon 18. Its functional significance is undetermined.
TBC1D4	0	MSKCC-DMP	P-0022337-T01-IM6	FGFR2-TBC1D4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TBC1D4 (NM_014832) Rearrangement : t(10;13)(q26.13;q22.2)(chr10:g.123241723::chr13:g.75946348) Note: The FGFR2 - TBC1D4 Rearrangement  results in the fusion of FGFR2 exons 1-17 with TBC1D4 exon 2-24. It includes the protein kinase domain of FGFR2. This event occurs in the background of other complex events involving FGFR2.
FGFR2	0	MSKCC-DMP	P-0022337-T01-IM6	FGFR2-TBC1D4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TBC1D4 (NM_014832) Rearrangement : t(10;13)(q26.13;q22.2)(chr10:g.123241723::chr13:g.75946348) Note: The FGFR2 - TBC1D4 Rearrangement  results in the fusion of FGFR2 exons 1-17 with TBC1D4 exon 2-24. It includes the protein kinase domain of FGFR2. This event occurs in the background of other complex events involving FGFR2.
RBM10	0	MSKCC-DMP	P-0022337-T01-IM6	RBM10-intragenic	yes	unknown		in frame	RBM10 (NM_001204468) Rearrangement: c.2146-1291_c.2362-19del Note: The RBM10 Rearrangement results in the intragenic deletion of exons 18-19. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022420-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1656:TMPRSS2_c.-149-19186:ERGdel Note: The TMPRSS2 - ERG rearrangement results in the deletion of TMPRSS2 exons 2-14. The breakpoints lie within intron 1 of TMPRSS2 and the promoter region of ERG 19Kb before coding start of the non-canonical transcript NM_004449. The possibility of a more complex rearrangement resulting in the fusion of TMPRSS2 - ERG can not be excluded. Further testing is recommended if clinically signified.
TMPRSS2	0	MSKCC-DMP	P-0022420-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1656:TMPRSS2_c.-149-19186:ERGdel Note: The TMPRSS2 - ERG rearrangement results in the deletion of TMPRSS2 exons 2-14. The breakpoints lie within intron 1 of TMPRSS2 and the promoter region of ERG 19Kb before coding start of the non-canonical transcript NM_004449. The possibility of a more complex rearrangement resulting in the fusion of TMPRSS2 - ERG can not be excluded. Further testing is recommended if clinically signified.
RERE	0	MSKCC-DMP	P-0022383-T01-IM6	MTOR-RERE fusion	yes	unknown		out of frame	RERE (NM_001042681) - MTOR (NM_004958) rearrangement: c.725+7095:RERE_c.7301-72:MTORdup Note: The RERE - MTOR rearrangement is a duplication that results in the fusion of RERE exons 1-6 with MTOR exons 54-58.
MTOR	0	MSKCC-DMP	P-0022383-T01-IM6	MTOR-RERE fusion	yes	unknown		out of frame	RERE (NM_001042681) - MTOR (NM_004958) rearrangement: c.725+7095:RERE_c.7301-72:MTORdup Note: The RERE - MTOR rearrangement is a duplication that results in the fusion of RERE exons 1-6 with MTOR exons 54-58.
BRCA2	0	MSKCC-DMP	P-0022383-T01-IM6	NUFIP1-BRCA2 fusion	yes	unknown		out of frame	NUFIP1 (NM_012345) - BRCA2 (NM_000059) rearrangement: c.412+1126:NUFIP1_c.516+46:BRCA2inv Note: The NUFIP1 - BRCA2 rearrangement is an inversion that results in the fusion of NUFIP1 exon 1 with BRCA2 exons 7-27.
NUFIP1	0	MSKCC-DMP	P-0022383-T01-IM6	NUFIP1-BRCA2 fusion	yes	unknown		out of frame	NUFIP1 (NM_012345) - BRCA2 (NM_000059) rearrangement: c.412+1126:NUFIP1_c.516+46:BRCA2inv Note: The NUFIP1 - BRCA2 rearrangement is an inversion that results in the fusion of NUFIP1 exon 1 with BRCA2 exons 7-27.
MDC1	0	MSKCC-DMP	P-0022385-T01-IM6	SMYD3-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(1;6)(q44;p21.33)(chr1:g.246673483::chr6:g.30680457) Note: The MDC1 rearrangement is a translocation that may result in a truncation of exons 5-15. One of the breakpoints is within exon 5. The functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0022385-T01-IM6	SMYD3-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(1;6)(q44;p21.33)(chr1:g.246673483::chr6:g.30680457) Note: The MDC1 rearrangement is a translocation that may result in a truncation of exons 5-15. One of the breakpoints is within exon 5. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0022421-T01-IM6	LINC01191-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: chr2:g.114793050_c.1088-161:PAX8inv Note: The PAX8 rearrangement results in the inversion of exons 1-9. Its functional significance is undetermined.
LINC01191	0	MSKCC-DMP	P-0022421-T01-IM6	LINC01191-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: chr2:g.114793050_c.1088-161:PAX8inv Note: The PAX8 rearrangement results in the inversion of exons 1-9. Its functional significance is undetermined.
HIST1H3D	0	MSKCC-DMP	P-0022421-T01-IM6	HIST1H3D-intragenic	yes	unknown		unknown	HIST1H3D (NM_003530) rearrangement: c.-2287_c.72del Note: The HIST1H3D rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0022423-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.-145+32530_c.1482del Note: The ANKRD11 rearrangement is a deletion of exons 1-9. One of the breakpoints is within exon 9. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0022502-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) Rearrangement : c.4068_c.4967del Note: The NOTCH1 Rearrangement results in the deletion of exons 25-26 of NOTCH1. The breakpoints are within exon25 and exon26 respectively.Its functional significance is undetermined.
PRPF8	0	MSKCC-DMP	P-0022533-T02-IM6	ERBB2-PRPF8 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) rearrangement: c.1022-127:ERBB2_chr17:g.1574221inv Note: The ERBB2 rearrangement is an inversion which results in the truncation of exons 9-27 which includes the kinase domain. Its functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0022533-T02-IM6	ERBB2-PRPF8 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) rearrangement: c.1022-127:ERBB2_chr17:g.1574221inv Note: The ERBB2 rearrangement is an inversion which results in the truncation of exons 9-27 which includes the kinase domain. Its functional significance is undetermined.
CCDC130	0	MSKCC-DMP	P-0022533-T02-IM6	BABAM1-CCDC130 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement:  chr19:g.13693284_c.134:BABAM1inv Note: The BABAM1 rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
BABAM1	0	MSKCC-DMP	P-0022533-T02-IM6	BABAM1-CCDC130 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement:  chr19:g.13693284_c.134:BABAM1inv Note: The BABAM1 rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
CYP4F22	0	MSKCC-DMP	P-0022533-T02-IM6	BABAM1-CYP4F22 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement:  chr19:g.15602332_c.-4:BABAM1del Note: The BABAM1 rearrangement results in the deletion of the promoter region and 5-UTR of BABAM1. Its functional significance is undetermined.
BABAM1	0	MSKCC-DMP	P-0022533-T02-IM6	BABAM1-CYP4F22 fusion	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement:  chr19:g.15602332_c.-4:BABAM1del Note: The BABAM1 rearrangement results in the deletion of the promoter region and 5-UTR of BABAM1. Its functional significance is undetermined.
RAD52	0	MSKCC-DMP	P-0022509-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) Rearrangement : c.-18-5943_c.349-18del Note: The RAD52 Rearrangement results in the deletion of exons 1-5. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0022509-T01-IM6	ARL6IP6-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement : c.3173-264:ALK_chr2:g.153686528del Note: The ALK Rearrangement results in the deletion of exons 1-19 of ALK. This doesnt include the protein kinase domain of ALK. Its functional significance is undetermined.
ARL6IP6	0	MSKCC-DMP	P-0022509-T01-IM6	ARL6IP6-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement : c.3173-264:ALK_chr2:g.153686528del Note: The ALK Rearrangement results in the deletion of exons 1-19 of ALK. This doesnt include the protein kinase domain of ALK. Its functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0022577-T01-IM6	DRAM2-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: t(1;12)(p13.3;p13.q)(chr1:g.111592651::chr12:g.57860272) Note: The GLI1 rearrangement is a translocation that may result in a truncation of exons 9-12. The functional significance is undetermined.
DRAM2	0	MSKCC-DMP	P-0022577-T01-IM6	DRAM2-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: t(1;12)(p13.3;p13.q)(chr1:g.111592651::chr12:g.57860272) Note: The GLI1 rearrangement is a translocation that may result in a truncation of exons 9-12. The functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0022489-T01-IM6	PDCD1LG2-JAK2 fusion	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.710_chr9:g.5484812del Note: The JAK2 rearrangement results in the deletion of exons 7-25. One of the breakpoints is within exon 7. The functional significance is undetermined.
PDCD1LG2	0	MSKCC-DMP	P-0022489-T01-IM6	PDCD1LG2-JAK2 fusion	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.710_chr9:g.5484812del Note: The JAK2 rearrangement results in the deletion of exons 7-25. One of the breakpoints is within exon 7. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0022579-T01-IM6	KIAA1467-ETV6 fusion	yes	unknown		in frame	KIAA1467 (NM_020853) - ETV6 (NM_001987) rearrangement: c.1643-1210:KIAA1467_c.1010-2295:ETV6dup Note: The KIAA1467 - ETV6 rearrangement is a duplication that results in an inframe fusion of KIAA1467 exons 1-11 with ETV6 exons 6-8. The functional significance is undetermined.
KIAA1467	0	MSKCC-DMP	P-0022579-T01-IM6	KIAA1467-ETV6 fusion	yes	unknown		in frame	KIAA1467 (NM_020853) - ETV6 (NM_001987) rearrangement: c.1643-1210:KIAA1467_c.1010-2295:ETV6dup Note: The KIAA1467 - ETV6 rearrangement is a duplication that results in an inframe fusion of KIAA1467 exons 1-11 with ETV6 exons 6-8. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0022431-T01-IM6	GUSBP1-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.2693:TERT_chr5:g.21230021del Note: The TERT rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
GUSBP1	0	MSKCC-DMP	P-0022431-T01-IM6	GUSBP1-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.2693:TERT_chr5:g.21230021del Note: The TERT rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0022479-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.5628_c.-144-248del Note: The ANKRD11 rearrangement results in the deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
RALGAPA1	0	MSKCC-DMP	P-0022436-T01-IM6	FOXA1-RALGAPA1 fusion	yes	unknown		unknown	RALGAPA1 (NM_194301) - FOXA1 (NM_004496) rearrangement: c.4159-1266:RALGAPA1_c.1001:FOXA1dup Note: The RALGAPA1 - FOXA1 rearrangement is a duplication that results in the fusion of RALGAPA1 exons 1-30 with FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0022436-T01-IM6	FOXA1-RALGAPA1 fusion	yes	unknown		unknown	RALGAPA1 (NM_194301) - FOXA1 (NM_004496) rearrangement: c.4159-1266:RALGAPA1_c.1001:FOXA1dup Note: The RALGAPA1 - FOXA1 rearrangement is a duplication that results in the fusion of RALGAPA1 exons 1-30 with FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. The functional significance is undetermined.
GSPT1	0	MSKCC-DMP	P-0022436-T01-IM6	TERT-GSPT1 fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;16)(p15.33;p13.13)(chr5:g.1260698::chr16:g.11963343) Note: The TERT rearrangement is a translocation that may result in a truncation of exons 12-16. One of the breakpoints is within exon 12. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0022436-T01-IM6	TERT-GSPT1 fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;16)(p15.33;p13.13)(chr5:g.1260698::chr16:g.11963343) Note: The TERT rearrangement is a translocation that may result in a truncation of exons 12-16. One of the breakpoints is within exon 12. The functional significance is undetermined.
RCAN1	0	MSKCC-DMP	P-0022436-T01-IM6	RUNX1-RCAN1 fusion	yes	unknown		unknown	RCAN1 (NM_004414) - RUNX1 (NM_001754)  rearrangement: c.252+38208:RCAN1_c.862:RUNX1dup Note: The RCAN1 - RUNX1 rearrangement is a duplication that results in the fusion of RCAN1 exon 1 with RUNX1 exons 8-9. One of the breakpoints is within RUNX1 exon 8. The functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0022436-T01-IM6	RUNX1-RCAN1 fusion	yes	unknown		unknown	RCAN1 (NM_004414) - RUNX1 (NM_001754)  rearrangement: c.252+38208:RCAN1_c.862:RUNX1dup Note: The RCAN1 - RUNX1 rearrangement is a duplication that results in the fusion of RCAN1 exon 1 with RUNX1 exons 8-9. One of the breakpoints is within RUNX1 exon 8. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0022529-T01-IM6	YPEL5-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement : c.3173-887:ALK_chr2:g.30245608del Note: The ALK Rearrangement results in the deletion of exons 1-19 of ALK. It doesnt include the protein kinase domain of ALK.
YPEL5	0	MSKCC-DMP	P-0022529-T01-IM6	YPEL5-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement : c.3173-887:ALK_chr2:g.30245608del Note: The ALK Rearrangement results in the deletion of exons 1-19 of ALK. It doesnt include the protein kinase domain of ALK.
SDC4	0	MSKCC-DMP	P-0022578-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117652158::chr20:g.43962266) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0022578-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117652158::chr20:g.43962266) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
CARD11	0	MSKCC-DMP	P-0022482-T01-IM6	SDK1-CARD11 fusion	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: c.908_chr7:g.3588919del Note: The CARD11 rearrangement results in the deletion of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
SDK1	0	MSKCC-DMP	P-0022482-T01-IM6	SDK1-CARD11 fusion	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: c.908_chr7:g.3588919del Note: The CARD11 rearrangement results in the deletion of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0022526-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement : c.-1565_c.756del Note: The ARID1A Rearrangement results in the deletion of exon1 of ARID1A. One of the breakpoints is within exon1.
TMPRSS2	0	MSKCC-DMP	P-0022557-T01-IM6	FOXP1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - FOXP1 (NM_001244814) rearrangement: t(3;21)(p13;q22.3)(chr3:g.71060348::chr21:g.:42869050) Note: The TMPRSS2 - FOXP1 rearrangement is a translocation which results is the fusion of TMPRSS2 exons 1-2 with FOXP1 exons 9-17. We cannot exclude the possibility of a more complex rearrangement that results in a TMPRSS2 - ERG fusion. The functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0022557-T01-IM6	FOXP1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - FOXP1 (NM_001244814) rearrangement: t(3;21)(p13;q22.3)(chr3:g.71060348::chr21:g.:42869050) Note: The TMPRSS2 - FOXP1 rearrangement is a translocation which results is the fusion of TMPRSS2 exons 1-2 with FOXP1 exons 9-17. We cannot exclude the possibility of a more complex rearrangement that results in a TMPRSS2 - ERG fusion. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0022607-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-414:CCDC6_c.2137-820:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET
CCDC6	0	MSKCC-DMP	P-0022607-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-414:CCDC6_c.2137-820:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET
TMPRSS2	0	MSKCC-DMP	P-0022778-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(7;21)(q34;q22.3)(chr7:g.140483147::chr21:g.42878796) Note: TMPRSS2 - BRAF rearrangement is a translocation which results in an in-frame fusion of TMPRSS2 exon1 with BRAF exons 10-18. The fusion includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0022778-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(7;21)(q34;q22.3)(chr7:g.140483147::chr21:g.42878796) Note: TMPRSS2 - BRAF rearrangement is a translocation which results in an in-frame fusion of TMPRSS2 exon1 with BRAF exons 10-18. The fusion includes the kinase domain of BRAF.
ERG	0	MSKCC-DMP	P-0022611-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3513:TMPRSS2_c.18+11133:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0022611-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3513:TMPRSS2_c.18+11133:ERGdel
PDPK1	0	MSKCC-DMP	P-0022566-T01-IM6	CPPED1-PDPK1 fusion	yes	unknown		unknown	PDPK1 (NM_002613) rearrangement: c.24+4:PDPK1_chr16:g.12881579del Note: The PDPK1 rearrangement results in the deletion of exons 2-11. Its functional significance is undetermined.
CPPED1	0	MSKCC-DMP	P-0022566-T01-IM6	CPPED1-PDPK1 fusion	yes	unknown		unknown	PDPK1 (NM_002613) rearrangement: c.24+4:PDPK1_chr16:g.12881579del Note: The PDPK1 rearrangement results in the deletion of exons 2-11. Its functional significance is undetermined.
GRIN2A	0	MSKCC-DMP	P-0022566-T01-IM6	TMC7-GRIN2A fusion	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: chr16:g.18959069_c.450:GRIN2inv Note: The GRIN2A rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
TMC7	0	MSKCC-DMP	P-0022566-T01-IM6	TMC7-GRIN2A fusion	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: chr16:g.18959069_c.450:GRIN2inv Note: The GRIN2A rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
TGFBR2	0	MSKCC-DMP	P-0022660-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: chr3:g.30383935_c.180del Note: The TGFBR2 rearrangement results in the deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0022642-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6(NM_005436) - RET(NM_020975) Fusion (CCDC6 exon1 fused to RET exon12) : c.304-14214:CCDC6_c.2137-273:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0022642-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6(NM_005436) - RET(NM_020975) Fusion (CCDC6 exon1 fused to RET exon12) : c.304-14214:CCDC6_c.2137-273:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
ETV6	0	MSKCC-DMP	P-0022569-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.34-33802_c.463+2619inv Note: The ETV6 rearrangement results in the inversion of exons 2-4. Its functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0022569-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused with TACC3 exons 8-16. This includes the kinase domain of FGFR3.): c.2274+44:FGFR3_c.1645-194:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.
FGFR3	0	MSKCC-DMP	P-0022569-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused with TACC3 exons 8-16. This includes the kinase domain of FGFR3.): c.2274+44:FGFR3_c.1645-194:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.
LATS2	0	MSKCC-DMP	P-0022716-T01-IM6	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) rearrangement: c.1562_c.*900del Note: The LATS2 rearrangement is a deletion of exons 4-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0022798-T01-IM6	OSBPL8-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) - OSBPL8 (NM_020841) Rearrangement : c.567:KDM5A_c.1630+2182:OSBPL8dup Note: The KDM5A - OSBPL8 Rearrangement results in the fusion of exons 1-5 of KDM5A with exons 16-24 of OSBPL8. The breakpoint in KDM5A is within exon5. Its functional significance is undetermined.
OSBPL8	0	MSKCC-DMP	P-0022798-T01-IM6	OSBPL8-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) - OSBPL8 (NM_020841) Rearrangement : c.567:KDM5A_c.1630+2182:OSBPL8dup Note: The KDM5A - OSBPL8 Rearrangement results in the fusion of exons 1-5 of KDM5A with exons 16-24 of OSBPL8. The breakpoint in KDM5A is within exon5. Its functional significance is undetermined.
THUMPD3	0	MSKCC-DMP	P-0022798-T01-IM6	PPARG-THUMPD3 fusion	yes	unknown		unknown	PPARG (NM_015869) Rearrangement : chr3:g.9389622_c.866:PPARGinv Note: The PPARG Rearrangement results in the inversion of exons 1-6 of PPARG. One of the breakpoints is within exon6. Its functional significance is undetermined.
PPARG	0	MSKCC-DMP	P-0022798-T01-IM6	PPARG-THUMPD3 fusion	yes	unknown		unknown	PPARG (NM_015869) Rearrangement : chr3:g.9389622_c.866:PPARGinv Note: The PPARG Rearrangement results in the inversion of exons 1-6 of PPARG. One of the breakpoints is within exon6. Its functional significance is undetermined.
ARSA	0	MSKCC-DMP	P-0022813-T01-IM6	DOT1L-ARSA fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(19;22)(p13.3;q13.33)(chr19:g.2228505::chr22:g.51076614) Note: The DOT1L rearrangement is a translocation that may result in a truncation of exon 28. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0022813-T01-IM6	DOT1L-ARSA fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(19;22)(p13.3;q13.33)(chr19:g.2228505::chr22:g.51076614) Note: The DOT1L rearrangement is a translocation that may result in a truncation of exon 28. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0022818-T01-IM6	NCOA4-RET fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-8 fused with RET exons 12-20): c.618+42:NCOA4_c.2137-860:RETdup Note: The NCOA4 - RET fusion includes the kinase domain of RET. One of the breakpoints is within NCOA4 exon 8.
NCOA4	0	MSKCC-DMP	P-0022818-T01-IM6	NCOA4-RET fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-8 fused with RET exons 12-20): c.618+42:NCOA4_c.2137-860:RETdup Note: The NCOA4 - RET fusion includes the kinase domain of RET. One of the breakpoints is within NCOA4 exon 8.
XPO1	0	MSKCC-DMP	P-0022767-T01-IM6	EXOC6B-XPO1 fusion	yes	unknown		out of frame	XPO1 (NM_003400) rearrangement: chr2:g.72977233_c.2023-4:XPO1del Note: The XPO1 rearrangement results in the deletion of XPO1 exons 1-18. Its functional significance is undetermined.
EXOC6B	0	MSKCC-DMP	P-0022767-T01-IM6	EXOC6B-XPO1 fusion	yes	unknown		out of frame	XPO1 (NM_003400) rearrangement: chr2:g.72977233_c.2023-4:XPO1del Note: The XPO1 rearrangement results in the deletion of XPO1 exons 1-18. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0022866-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) Fusion (KIF5B exons 1-15 fused to RET exons 12-20):  c.1726-767:KIF5B_c.2137-161:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0022866-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) Fusion (KIF5B exons 1-15 fused to RET exons 12-20):  c.1726-767:KIF5B_c.2137-161:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.
PSMG2	0	MSKCC-DMP	P-0022750-T01-IM6	TP53-PSMG2 fusion	yes	unknown		unknown	TP53 (NM_000546) - PSMG2 (NM_020232) rearrangement: t(17;18)(p13.1;p11.21)(chr17:g.7579703::chr18:g.12724031) Note: The TP53 - PSMG2 rearrangement is a translocation which may result in the fusion of TP53 exons 1-3 with PSMG2 exons 6-7. One of the breakpoints is within TP53 exon 3. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0022750-T01-IM6	TP53-PSMG2 fusion	yes	unknown		unknown	TP53 (NM_000546) - PSMG2 (NM_020232) rearrangement: t(17;18)(p13.1;p11.21)(chr17:g.7579703::chr18:g.12724031) Note: The TP53 - PSMG2 rearrangement is a translocation which may result in the fusion of TP53 exons 1-3 with PSMG2 exons 6-7. One of the breakpoints is within TP53 exon 3. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0022863-T01-IM6	PTEN-intragenic	yes	unknown		out of frame	PTEN (NM_000314) Rearrangement: c.209+165_c.492+3477del Note: The PTEN Rearrangement results in the intragenic deletion of exons 4-5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022865-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.56-2979:TMPRSS2_c.90:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0022865-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.56-2979:TMPRSS2_c.90:ERGdel
RIPK2	0	MSKCC-DMP	P-0022691-T01-IM6	NBN-RIPK2 fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: chr8:g.90818092_c.2234+109:NBNdel Note: The NBN rearrangement results in the deletion of exon 16. Its functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0022691-T01-IM6	NBN-RIPK2 fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: chr8:g.90818092_c.2234+109:NBNdel Note: The NBN rearrangement results in the deletion of exon 16. Its functional significance is undetermined.
TOX	0	MSKCC-DMP	P-0022864-T01-IM6	BAP1-TOX fusion	yes	unknown		unknown	BAP1 (NM_004656) Rearrangement :  t(3;8)(p21.31;q12.1)(chr3:g.52441973::chr8:g.60352046) Note: The BAP1 Rearrangement results in the possible truncation of BAP1. The breakpoint is within exon5. Its functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0022864-T01-IM6	BAP1-TOX fusion	yes	unknown		unknown	BAP1 (NM_004656) Rearrangement :  t(3;8)(p21.31;q12.1)(chr3:g.52441973::chr8:g.60352046) Note: The BAP1 Rearrangement results in the possible truncation of BAP1. The breakpoint is within exon5. Its functional significance is undetermined.
DGAT1	0	MSKCC-DMP	P-0022820-T01-IM6	RECQL4-DGAT1 fusion	yes	unknown		unknown	DGAT1 (NM_012079) - RECQL4 (NM_004260) rearrangement: c.-436:DGAT1_c.1464:RECQL4dup Note: The DGAT1 - RECQL4 rearrangement is a duplication which includes the promoter region of DGAT1 and RECQL4 exons 8-22. One of the breakpoints is within RECQL4 exon 8. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0022820-T01-IM6	RECQL4-DGAT1 fusion	yes	unknown		unknown	DGAT1 (NM_012079) - RECQL4 (NM_004260) rearrangement: c.-436:DGAT1_c.1464:RECQL4dup Note: The DGAT1 - RECQL4 rearrangement is a duplication which includes the promoter region of DGAT1 and RECQL4 exons 8-22. One of the breakpoints is within RECQL4 exon 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022700-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.126+631:TMPRSS2_c.40-60817:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0022700-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.126+631:TMPRSS2_c.40-60817:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
FGF16	0	MSKCC-DMP	P-0022706-T01-IM6	ATRX-FGF16 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.76625205_c.7200+64del Note: The ATRX rearrangement results in the deletion of exon 35. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0022706-T01-IM6	ATRX-FGF16 fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.76625205_c.7200+64del Note: The ATRX rearrangement results in the deletion of exon 35. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0022672-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.-3010_c.79+246inv Note: The PTEN rearrangement results in the inversion of exon 1. Its functional significance is undetermined
MGA	0	MSKCC-DMP	P-0022688-T01-IM6	LRRC49-MGA fusion	yes	unknown		unknown	LRRC49 (NM_001199017) - MGA (NM_001164273) rearrangement: c.515+1095:LRRC49_c.8623:MGAdup Note: The LRRC49 - MGA rearrangement is a duplication which results in the fusion of LRRC49 exons 1-6 with MGA exon 24. One of the breakpoints is within MGA exon 24. Its functional significance is undetermined.
LRRC49	0	MSKCC-DMP	P-0022688-T01-IM6	LRRC49-MGA fusion	yes	unknown		unknown	LRRC49 (NM_001199017) - MGA (NM_001164273) rearrangement: c.515+1095:LRRC49_c.8623:MGAdup Note: The LRRC49 - MGA rearrangement is a duplication which results in the fusion of LRRC49 exons 1-6 with MGA exon 24. One of the breakpoints is within MGA exon 24. Its functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0022896-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) Rearrangement :  c.59-4793_c.272del Note : The RUNX1 Rearrangement results in the intragenic deletion of exon4 of RUNX1. One of the breakpoints is within exon4. Its functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0022896-T01-IM6	TGFBR1-intragenic	yes	unknown		unknown	TGFBR1 (NM_004612) Rearrangement : c.974-24_c.1169del Note: The TGFBR1 Rearrangement results in the intragenic deletion of exon7 of TGFBR1. One of the breakpoints is within exon7. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0022926-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.493+983:EML4_c.3173-164:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0022926-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.493+983:EML4_c.3173-164:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
C12orf42	0	MSKCC-DMP	P-0022968-T01-IM6	RPS6KA4-C12orf42 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) Rearrangement : t(11;12)(q34;q12)(chr11:g.64136052::chr12:g.103764727) Note: The RPS6KA4 Rearrangement results in the possible truncation of RPS6KA4. The breakpoint is within exon11. Its functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0022968-T01-IM6	RPS6KA4-C12orf42 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) Rearrangement : t(11;12)(q34;q12)(chr11:g.64136052::chr12:g.103764727) Note: The RPS6KA4 Rearrangement results in the possible truncation of RPS6KA4. The breakpoint is within exon11. Its functional significance is undetermined.
NOL4	0	MSKCC-DMP	P-0023103-T01-IM6	FGFR2-NOL4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion (FGFR2 exons 1-17 fused to NOL4 exons  10-11): t(10;18)(q26.13;q12.1)(chr10:g.123241921::chr18:g.31518701) Note: The FGFR2 - NOL4 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0023103-T01-IM6	FGFR2-NOL4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion (FGFR2 exons 1-17 fused to NOL4 exons  10-11): t(10;18)(q26.13;q12.1)(chr10:g.123241921::chr18:g.31518701) Note: The FGFR2 - NOL4 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
RB1	0	MSKCC-DMP	P-0023031-T01-IM6	LINC01358-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : t(1;13)(p32.2;p21.2)(chr1:g.59514813::chr13:g.48916708) Note: The RB1 Rearrangement results in the possible truncation of RB1. One of the breakpoints is within intron2.Its functional significance is undetermined.
LINC01358	0	MSKCC-DMP	P-0023031-T01-IM6	LINC01358-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : t(1;13)(p32.2;p21.2)(chr1:g.59514813::chr13:g.48916708) Note: The RB1 Rearrangement results in the possible truncation of RB1. One of the breakpoints is within intron2.Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0023023-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.10928_chr4:g.187500064del Note: The FAT1 rearrangement is a deletion of FAT1 exons 19-27. One of the breakpoints is within FAT1 exon 19. The functional significance is undetermined.
LRIG3	0	MSKCC-DMP	P-0023007-T01-IM6	ROS1-LRIG3 fusion	yes	unknown		in frame	LRIG3 (NM_153377) - ROS1 (NM_002944) fusion: (LRIG3 exons 1-15 fused to ROS1 exons 35 - 43): t(6;12)(q22.1;q14.1)(chr6:g.117645256::chr12:g.59270940) Note: The LRIG3 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0023007-T01-IM6	ROS1-LRIG3 fusion	yes	unknown		in frame	LRIG3 (NM_153377) - ROS1 (NM_002944) fusion: (LRIG3 exons 1-15 fused to ROS1 exons 35 - 43): t(6;12)(q22.1;q14.1)(chr6:g.117645256::chr12:g.59270940) Note: The LRIG3 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CDK12	0	MSKCC-DMP	P-0023066-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507)  rearrangement: c.1931+3153_c.1047-87inv Note: The CDK12 rearrangement result in the inversion of exon 2. Its functional significance is undetermined,
CDH1	0	MSKCC-DMP	P-0023159-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement : c.164-4993_c.873del Note: The CDH1 Rearrangement results in the intragenic deletion of exons 3-7. One of the breakpoints is within exon7. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0022953-T01-IM6	CERS6-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - CERS6 (NM_203463) rearrangement: t(2;21)(q24.3;q22.3)(chr2:g.169560626::chr21:g.42873665) Note: The TMPRSS2 - CERS6 rearrangement is a translocation that results in the fusion of TMPRSS2 exon 1 with CERS6 exon 6-10. The functional significance is undetermined.
CERS6	0	MSKCC-DMP	P-0022953-T01-IM6	CERS6-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - CERS6 (NM_203463) rearrangement: t(2;21)(q24.3;q22.3)(chr2:g.169560626::chr21:g.42873665) Note: The TMPRSS2 - CERS6 rearrangement is a translocation that results in the fusion of TMPRSS2 exon 1 with CERS6 exon 6-10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023067-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+2229:TMPRSS2_c.18+4015:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0023067-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+2229:TMPRSS2_c.18+4015:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
B2M	0	MSKCC-DMP	P-0023057-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.67_c.68del Note: The B2M rearrangement is an intragenic deletion with breakpoints at the splice sites of exons 1 and 2. Its functional significance is undetermined. Multiple rearrangements involving B2M were detected in this sample and a more complex rearrangement resulting in a B2M fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SLC16A7	0	MSKCC-DMP	P-0023059-T01-IM6	KMT2C-SLC16A7 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: t(7;12)(q36.1;q14.1)(chr7:g.151846068::chr12:g.60040921) Note: The KMT2C rearrangement is a translocation which may result in the truncation of exons 1-52. One of the breakpoints is within exon 52. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0023059-T01-IM6	KMT2C-SLC16A7 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: t(7;12)(q36.1;q14.1)(chr7:g.151846068::chr12:g.60040921) Note: The KMT2C rearrangement is a translocation which may result in the truncation of exons 1-52. One of the breakpoints is within exon 52. Its functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0023059-T01-IM6	PRR5L-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: t(11;19)(p13;q13.2)(chr11:g.36316873::chr19:g.40761254) Note: The AKT2 rearrangement is a translocation which may result in the truncation of exons 1-3. Its functional significance is undetermined.
PRR5L	0	MSKCC-DMP	P-0023059-T01-IM6	PRR5L-AKT2 fusion	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: t(11;19)(p13;q13.2)(chr11:g.36316873::chr19:g.40761254) Note: The AKT2 rearrangement is a translocation which may result in the truncation of exons 1-3. Its functional significance is undetermined.
SHOC2	0	MSKCC-DMP	P-0023014-T01-IM6	SHOC2-intragenic	yes	unknown		unknown	SHOC2 (NM_007373) rearrangement: c.890_c.972+809inv Note: The SHOC2 rearrangement is an inversion of exon 4. One of the breakpoints is within exon. The functional significance is undetermined.
SYNGR3	0	MSKCC-DMP	P-0023014-T01-IM6	TSC2-SYNGR3 fusion	yes	unknown		unknown	TSC2 (NM_000548) - SYNGR3 (NM_004209) rearrangement: c.1319:TSC2_c.99+446:SYNGR3dup Note: The TSC2 - SYNGR3 rearrangement is a duplication which results in the fusion of TSC2 exons 1-13 with SYNGR3 exons 2-4. One of the breakpoints is within TSC2 exon 13. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0023014-T01-IM6	TSC2-SYNGR3 fusion	yes	unknown		unknown	TSC2 (NM_000548) - SYNGR3 (NM_004209) rearrangement: c.1319:TSC2_c.99+446:SYNGR3dup Note: The TSC2 - SYNGR3 rearrangement is a duplication which results in the fusion of TSC2 exons 1-13 with SYNGR3 exons 2-4. One of the breakpoints is within TSC2 exon 13. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0023049-T01-IM6	FAM134C-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.1140-27:STAT3_chr17:g.40749768inv Note: The STAT3 rearrangement is an inversion of exons 1-12. The functional significance is undetermined.
FAM134C	0	MSKCC-DMP	P-0023049-T01-IM6	FAM134C-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.1140-27:STAT3_chr17:g.40749768inv Note: The STAT3 rearrangement is an inversion of exons 1-12. The functional significance is undetermined.
PKM	0	MSKCC-DMP	P-0023039-T01-IM6	JAK1-PKM fusion	yes	unknown		unknown	JAK1 (NM_002227) - PKM (NM_001206796) rearrangement: t(1;15)(p31.3;q23)(chr1:g.65323406::chr15:g.72499346) Note: The JAK1 - PKM rearrangement is a translocation that results in the fusion of JAK1 exons 1-10 with PKM exons 8-12. One of the breakpoints is within exon 10. The functional significance is undetermined.
JAK1	0	MSKCC-DMP	P-0023039-T01-IM6	JAK1-PKM fusion	yes	unknown		unknown	JAK1 (NM_002227) - PKM (NM_001206796) rearrangement: t(1;15)(p31.3;q23)(chr1:g.65323406::chr15:g.72499346) Note: The JAK1 - PKM rearrangement is a translocation that results in the fusion of JAK1 exons 1-10 with PKM exons 8-12. One of the breakpoints is within exon 10. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0011038-T02-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.826_c.1937inv Note: The KMT2B rearrangement results in the inversion of exon 3. Both breakpoints are within exon 3. its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0022856-T02-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.1678-1280_c.5085del Note: The PTPRD rearrangement results in the intragenic deletion of exons 23-41. One of the breakpoints is within exon 41. Its functional significance is undetermined.
GATA3	0	MSKCC-DMP	P-0023194-T01-IM6	GATA3-intragenic	yes	unknown		unknown	GATA3 (NM_002051) rearrangement: c.242-736_c.772del Note: The GATA3 rearrangement is an intragenic partial deletion of exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023194-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.376-16_c.688del Note: The TP53 rearrangement is an intragenic deletion of exons 5-7. One of the breakpoints is within exon 7.
FAM135A	0	MSKCC-DMP	P-0023297-T01-IM6	PARK2-FAM135A fusion	yes	unknown		unknown	PARK2 (NM_004562) - FAM135A (NM_001162529) rearrangement: c.236:PARK2_c.823+2866:FAM135Ainv Note: The PARK2 - FAM135A rearrangement is an inversion which results in the fusion of PARK2 exons 1-3 with FAM135A exons 9-20.  One of the breakpoints is within PARK2 exon 3. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0023297-T01-IM6	PARK2-FAM135A fusion	yes	unknown		unknown	PARK2 (NM_004562) - FAM135A (NM_001162529) rearrangement: c.236:PARK2_c.823+2866:FAM135Ainv Note: The PARK2 - FAM135A rearrangement is an inversion which results in the fusion of PARK2 exons 1-3 with FAM135A exons 9-20.  One of the breakpoints is within PARK2 exon 3. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0023211-T01-IM6	FBLN1-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.2633_chr22:g.45878564inv Note: The EP300 rearrangement is an inversion which includes exons 14-31. One of the breakpoints is within exon 14. The functional significance is undetermined.
FBLN1	0	MSKCC-DMP	P-0023211-T01-IM6	FBLN1-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.2633_chr22:g.45878564inv Note: The EP300 rearrangement is an inversion which includes exons 14-31. One of the breakpoints is within exon 14. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0023321-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.372+1043_c.103del Note: The STAT3 rearrangement results in the deletion of exons 2-4. One of the breakpoints is within exon 2. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0023321-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: c.684_c.-427del Note: The NFE2L2 rearrangement results in the deletion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
SRGAP2	0	MSKCC-DMP	P-0022004-T02-IM6	IKBKE-SRGAP2 fusion	yes	unknown		unknown	SRGAP2 (NM_015326) - IKBKE (NM_014002) rearrangement: c.2085:SRGAP2_c.1714:IKBKEdel Note: The SRGAP2 - IKBKE rearrangement is a deletion which results in the fusion of SRGAP2 exons 1-17 with IKBKE exons 17-22. Both breakpoints are within exon. The functional significance is undetermined.
IKBKE	0	MSKCC-DMP	P-0022004-T02-IM6	IKBKE-SRGAP2 fusion	yes	unknown		unknown	SRGAP2 (NM_015326) - IKBKE (NM_014002) rearrangement: c.2085:SRGAP2_c.1714:IKBKEdel Note: The SRGAP2 - IKBKE rearrangement is a deletion which results in the fusion of SRGAP2 exons 1-17 with IKBKE exons 17-22. Both breakpoints are within exon. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0023197-T01-IM6	ACTR3B-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.11863:KMT2C_chr7:g.152760077del Note: The KMT2C rearrangement is a deletion of exons 1-46. One of the breakpoints is within exon 46. The functional significance is undetermined.
ACTR3B	0	MSKCC-DMP	P-0023197-T01-IM6	ACTR3B-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.11863:KMT2C_chr7:g.152760077del Note: The KMT2C rearrangement is a deletion of exons 1-46. One of the breakpoints is within exon 46. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0023261-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to exons 11-16 of TACC3): c.2359:FGFR3_c.1941+673:TACC3dup Note: The FGFR3-TACC3 fusion includes the protein kinase domain of FGFR3, the breakpoint in FGFR3 is within exon 18.
FGFR3	0	MSKCC-DMP	P-0023261-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to exons 11-16 of TACC3): c.2359:FGFR3_c.1941+673:TACC3dup Note: The FGFR3-TACC3 fusion includes the protein kinase domain of FGFR3, the breakpoint in FGFR3 is within exon 18.
ERG	0	MSKCC-DMP	P-0023270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with exon4) : c.56-3945:TMPRSS2_c.40-62862:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0023270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with exon4) : c.56-3945:TMPRSS2_c.40-62862:ERGdel
KDM5A	0	MSKCC-DMP	P-0023281-T01-IM6	HLA-E-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(6;12)(p22.1;p13.33)(chr6:g.30437747::chr12:g.438110) Note: The KDM5A rearrangement is a translocation which may result in the truncation of exons 14-28. One of the breakpoints is within exon 14. Its functional significance is undetermined.
HLA-E	0	MSKCC-DMP	P-0023281-T01-IM6	HLA-E-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(6;12)(p22.1;p13.33)(chr6:g.30437747::chr12:g.438110) Note: The KDM5A rearrangement is a translocation which may result in the truncation of exons 14-28. One of the breakpoints is within exon 14. Its functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0023287-T01-IM6	PTP4A2-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: t(1;17)(p35.2;q25.3)(chr1:g.32370243::chr17:g.78854227) Note: The RPTOR rearrangement is a translocation which may result in the truncation of exons 1-14. One of the breakpoints is within exon 14. its functional significance is undetermined.
PTP4A2	0	MSKCC-DMP	P-0023287-T01-IM6	PTP4A2-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: t(1;17)(p35.2;q25.3)(chr1:g.32370243::chr17:g.78854227) Note: The RPTOR rearrangement is a translocation which may result in the truncation of exons 1-14. One of the breakpoints is within exon 14. its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0023368-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29 including the kinase domain) : c.667+7004:EML4_c.3173-319:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame.
EML4	0	MSKCC-DMP	P-0023368-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29 including the kinase domain) : c.667+7004:EML4_c.3173-319:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame.
ITM2B	0	MSKCC-DMP	P-0023371-T01-IM6	RB1-ITM2B fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: chr13:g.48785947_c.607+1:RB1inv Note: The RB1 rearrangement results in the inversion of exons 7-27. its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0023371-T01-IM6	RB1-ITM2B fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: chr13:g.48785947_c.607+1:RB1inv Note: The RB1 rearrangement results in the inversion of exons 7-27. its functional significance is undetermined.
CYLD	0	MSKCC-DMP	P-0023388-T01-IM6	TACC1-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) rearrangement: t(8;16)(p11.22;q12.1)(chr8:g.38590620::chr16:g.50826532) Note: The CYLD rearrangement is a translocation that may result in the truncation of exons 15-18. One of the breakpoints is within exon 15. The functional significance is undetermined.
TACC1	0	MSKCC-DMP	P-0023388-T01-IM6	TACC1-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) rearrangement: t(8;16)(p11.22;q12.1)(chr8:g.38590620::chr16:g.50826532) Note: The CYLD rearrangement is a translocation that may result in the truncation of exons 15-18. One of the breakpoints is within exon 15. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0023471-T01-IM6	POU1F1-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(3;19)(p11.2;p13.12)(chr3:g.87561351::chr19:g.15271620) Note: The NOTCH3 rearrangement is a translocation with a breakpoint within NOTCH3 exon 33. The functional significance is undetermined.
POU1F1	0	MSKCC-DMP	P-0023471-T01-IM6	POU1F1-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(3;19)(p11.2;p13.12)(chr3:g.87561351::chr19:g.15271620) Note: The NOTCH3 rearrangement is a translocation with a breakpoint within NOTCH3 exon 33. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0015921-T03-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29): c.667+516:EML4_c.3173-415:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0015921-T03-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused with ALK exons 20-29): c.667+516:EML4_c.3173-415:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
FOXA1	0	MSKCC-DMP	P-0023401-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.73-52:FOXA1_chr14:g.38074562inv Note: The FOXA1 rearrangement is an inversion of exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023404-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-3420:TMPRSS2_c.40-59054:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0023404-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-3420:TMPRSS2_c.40-59054:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
PANX2	0	MSKCC-DMP	P-0023404-T01-IM6	TP53-PANX2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(17;22)(p13.1;q13.33)(chr17:g.7576891::chr22:g.50604157) Note: The TP53 rearrangement is a translocation that may result in a truncation of exons 9-11. One of the breakpoints is within exon 9. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023404-T01-IM6	TP53-PANX2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(17;22)(p13.1;q13.33)(chr17:g.7576891::chr22:g.50604157) Note: The TP53 rearrangement is a translocation that may result in a truncation of exons 9-11. One of the breakpoints is within exon 9. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023407-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.920-17_c.993+610del Note: The TP53 rearrangement is an intragenic deletion of exon 9.
SMARCA4	0	MSKCC-DMP	P-0023453-T01-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.223-176_c.1812+451dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 4-11. The functional significance is undetermined.
THOC2	0	MSKCC-DMP	P-0023453-T01-IM6	EIF4A2-THOC2 fusion	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: t(X;3)(q25;q27.3)(chrX:g.122823360::chr3:g.186506986) Note: The EIF4A2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.
EIF4A2	0	MSKCC-DMP	P-0023453-T01-IM6	EIF4A2-THOC2 fusion	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: t(X;3)(q25;q27.3)(chrX:g.122823360::chr3:g.186506986) Note: The EIF4A2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0023457-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement :  c.632-1319_c.4115inv Note: The BRCA2 rearrangement results in the intragenic inversion of exons 9-11 of BRCA2. One of the breakpoints is within exon11. This event is expected to lead to a disrupted BRCA2 protein.  Additionally, this occurs in the background of other structural rearrangements involving BRCA2.
CALR	0	MSKCC-DMP	P-0023507-T01-IM6	NFIX-CALR fusion	yes	unknown		unknown	CALR (NM_004343) - NFIX (NM_002501) rearrangement: c.689:CALR_c.559+10828:NFIXdel Note: The CALR - NFIX rearrangement is a deletion which results in the fusion of CALR exons 1-5 with NFIX exons 3-9. One of the breakpoints is within CALR exon 5. Its functional significance is undetermined.
NFIX	0	MSKCC-DMP	P-0023507-T01-IM6	NFIX-CALR fusion	yes	unknown		unknown	CALR (NM_004343) - NFIX (NM_002501) rearrangement: c.689:CALR_c.559+10828:NFIXdel Note: The CALR - NFIX rearrangement is a deletion which results in the fusion of CALR exons 1-5 with NFIX exons 3-9. One of the breakpoints is within CALR exon 5. Its functional significance is undetermined.
TMIE	0	MSKCC-DMP	P-0023526-T01-IM6	SETD2-TMIE fusion	yes	unknown		unknown	SETD2 (NM_014159) - TMIE (NM_147196) rearrangement: c.155:SETD2_c.211+223:TMIEinv Note: The SETD2 rearrangement is an inversion that results in the fusion of SETD2 exons 1-3 with TMIE exons 3-4. One of the breakpoints is within SETD2 exon 3. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0023526-T01-IM6	SETD2-TMIE fusion	yes	unknown		unknown	SETD2 (NM_014159) - TMIE (NM_147196) rearrangement: c.155:SETD2_c.211+223:TMIEinv Note: The SETD2 rearrangement is an inversion that results in the fusion of SETD2 exons 1-3 with TMIE exons 3-4. One of the breakpoints is within SETD2 exon 3. The functional significance is undetermined.
COLEC12	0	MSKCC-DMP	P-0023516-T01-IM6	CDK12-COLEC12 fusion	yes	unknown		out of frame	COLEC12 (NM_130386) - CDK12(NM_016507) rearrangement: t(17;18)(q12;p11.32)(chr17:g.37665943::chr18:g.386902) Note: The COLEC12 - CDK12 rearrangement is a translocation that results in the fusion of COLEC12 exons 1-2 with CDK12 exons 7-14. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0023516-T01-IM6	CDK12-COLEC12 fusion	yes	unknown		out of frame	COLEC12 (NM_130386) - CDK12(NM_016507) rearrangement: t(17;18)(q12;p11.32)(chr17:g.37665943::chr18:g.386902) Note: The COLEC12 - CDK12 rearrangement is a translocation that results in the fusion of COLEC12 exons 1-2 with CDK12 exons 7-14. The functional significance is undetermined.
ZNF174	0	MSKCC-DMP	P-0023547-T01-IM6	CREBBP-ZNF174 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.3461991_c.2463+91del Note: The CREBBP rearrangement results in the deletion of exons 13-31. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0023547-T01-IM6	CREBBP-ZNF174 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.3461991_c.2463+91del Note: The CREBBP rearrangement results in the deletion of exons 13-31. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0023613-T01-IM6	TP53-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - TP53 (NM_000546) rearrangement: t(17;19)(p13.1;q13.2)(chr17:g.7572859::chr19:g.42791952) Note: The CIC -TP53 rearrangement is a translocation with breakpoints within CIC intron 5 and the 3UTR of TP53. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023613-T01-IM6	TP53-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - TP53 (NM_000546) rearrangement: t(17;19)(p13.1;q13.2)(chr17:g.7572859::chr19:g.42791952) Note: The CIC -TP53 rearrangement is a translocation with breakpoints within CIC intron 5 and the 3UTR of TP53. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0023617-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_00102515) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149782946::chr6:g.117646444) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0023617-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_00102515) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149782946::chr6:g.117646444) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
ERG	0	MSKCC-DMP	P-0023621-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-10): c.126+482:TMPRSS2_c.19-21174:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0023621-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-10): c.126+482:TMPRSS2_c.19-21174:ERGdel
MAP3K1	0	MSKCC-DMP	P-0022282-T01-IM6	ARFIP1-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - ARFIP1 (NM_001025595)  rearrangement: t(4;5)(q31.3;q11.2)(chr4:g.153712327::chr5:g.56161250) Note: The MAP3K1 - ARFIP1 rearrangement is a translocation which results in the fusion of MAP3K1 exons 1-5 to ARFIP1 exons 2-9. One of the breakpoints is within MAP3K1 exon 5. The functional significance is undetermined.
ARFIP1	0	MSKCC-DMP	P-0022282-T01-IM6	ARFIP1-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - ARFIP1 (NM_001025595)  rearrangement: t(4;5)(q31.3;q11.2)(chr4:g.153712327::chr5:g.56161250) Note: The MAP3K1 - ARFIP1 rearrangement is a translocation which results in the fusion of MAP3K1 exons 1-5 to ARFIP1 exons 2-9. One of the breakpoints is within MAP3K1 exon 5. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0022282-T01-IM6	GPM6A-BRAF fusion	yes	unknown		unknown	BRAF (NM_004333) - GPM6A (NM_005277) rearrangement: t(4;7)(q34.2;q34)(chr4:g.176630702::chr7:g.140454168) Note: The BRAF rearrangement is a translocation with breakpoints within BRAF intron 13 and GPM6A intron 2. The functional significance is undetermined.
GPM6A	0	MSKCC-DMP	P-0022282-T01-IM6	GPM6A-BRAF fusion	yes	unknown		unknown	BRAF (NM_004333) - GPM6A (NM_005277) rearrangement: t(4;7)(q34.2;q34)(chr4:g.176630702::chr7:g.140454168) Note: The BRAF rearrangement is a translocation with breakpoints within BRAF intron 13 and GPM6A intron 2. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0022335-T01-IM6	SYDE1-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - SYDE1 (NM_033025) Rearrangement : c.2350-60:PTPRS_c.540:SYDE1 Note : The PTPRS -SYDE1 Rearrangement results in the deletion of exons 1-15 of PTPRS. Its functional significance is undetermined.
SYDE1	0	MSKCC-DMP	P-0022335-T01-IM6	SYDE1-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - SYDE1 (NM_033025) Rearrangement : c.2350-60:PTPRS_c.540:SYDE1 Note : The PTPRS -SYDE1 Rearrangement results in the deletion of exons 1-15 of PTPRS. Its functional significance is undetermined.
CTCF	0	MSKCC-DMP	P-0023644-T01-IM6	CTCF-intragenic	yes	unknown		unknown	CTCF (NM_006565) Rearrangement : c.-9-3099_c.-9-3del Note: The CTCF Rearrangement results in the partial deletion of the promoter region of CTCF. Both the breakpoints are within the 5' promoter region before coding start site. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0006602-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-10): c.127-568:TMPRSS2_c.19-17587:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0006602-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-10): c.127-568:TMPRSS2_c.19-17587:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
PALB2	0	MSKCC-DMP	P-0008083-T03-IM6	PALB2-intragenic	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: c.212-247_c.1291del Note: The PALB2 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. its functional significance is undetermined.
MKRN1	0	MSKCC-DMP	P-0008083-T03-IM6	BRAF-MKRN1 fusion	yes	unknown		out of frame	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.315-432:MKRN1_c.1178-1554:BRAFdup Note: The MKRN1 - BRAF rearrangement is a duplication which results in the fusion of MKRN1 exons 1-3 with BRAF exons 10-18 including the kinase domain. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0008083-T03-IM6	BRAF-MKRN1 fusion	yes	unknown		out of frame	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.315-432:MKRN1_c.1178-1554:BRAFdup Note: The MKRN1 - BRAF rearrangement is a duplication which results in the fusion of MKRN1 exons 1-3 with BRAF exons 10-18 including the kinase domain. Its functional significance is undetermined.
PARVA	0	MSKCC-DMP	P-0008346-T03-IM6	EGFR-PARVA fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;11)(p11.2;p15.3)(chr7:g.55269578::chr11:g.12552528) Note: The EGFR rearrangement is a translocation which may result in the truncation of exons 27-28. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0008346-T03-IM6	EGFR-PARVA fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;11)(p11.2;p15.3)(chr7:g.55269578::chr11:g.12552528) Note: The EGFR rearrangement is a translocation which may result in the truncation of exons 27-28. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023605-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-10): c.127-1583:TMPRSS2_c.-3842:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0023605-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-10): c.127-1583:TMPRSS2_c.-3842:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
ERG	0	MSKCC-DMP	P-0023625-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.-56-420:TMPRSS2_chr21:g.39863632del Note: The TMPRSS2 rearrangement is a deletion of exons 2-14. Its functional significance is undetermined. Multiple TMPRSS2 rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in a TMPRSS2 - ERG gene fusion.
TMPRSS2	0	MSKCC-DMP	P-0023625-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.-56-420:TMPRSS2_chr21:g.39863632del Note: The TMPRSS2 rearrangement is a deletion of exons 2-14. Its functional significance is undetermined. Multiple TMPRSS2 rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in a TMPRSS2 - ERG gene fusion.
CSDE1	0	MSKCC-DMP	P-0023629-T01-IM6	HIST2H2BF-CSDE1 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.2119:CSDE1_chr1:g.149712153del Note: The CSDE1 rearrangement results in the deletion of exons 1-18. One of the breakpoints is within exon 18. Its functional significance is undetermined.
HIST2H2BF	0	MSKCC-DMP	P-0023629-T01-IM6	HIST2H2BF-CSDE1 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.2119:CSDE1_chr1:g.149712153del Note: The CSDE1 rearrangement results in the deletion of exons 1-18. One of the breakpoints is within exon 18. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023629-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.-56-1903:TMPRSS2_c.19-17475:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 2-10. Its functional significance is undetermined
TMPRSS2	0	MSKCC-DMP	P-0023629-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.-56-1903:TMPRSS2_c.19-17475:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 2-10. Its functional significance is undetermined
ERG	0	MSKCC-DMP	P-0023663-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-10): c.126+455:TMPRSS2_c.19-16612:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0023663-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 3-10): c.126+455:TMPRSS2_c.19-16612:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
AR	0	MSKCC-DMP	P-0023666-T01-IM6	AR-intragenic	yes	unknown		out of frame	AR (NM_000044) rearrangement: c.2174-1690_c.2608-163del Note: The AR rearrangement is an intragenic deletion of exons  5-7. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0023678-T01-IM6	LRRC24-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - LRRC24 (NM_001024678) Rearrangement : c.2574:RECQL4_c.607+2:LRRC24dup Note: The RECQL4  - LRRC24 Rearrangement results in the fusion of exons 1-16 of RECQL4 with exon 5 of LRRC24. The breakpoint in RECQL4 is within exon 16. Its functional significance is undetermined.
LRRC24	0	MSKCC-DMP	P-0023678-T01-IM6	LRRC24-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - LRRC24 (NM_001024678) Rearrangement : c.2574:RECQL4_c.607+2:LRRC24dup Note: The RECQL4  - LRRC24 Rearrangement results in the fusion of exons 1-16 of RECQL4 with exon 5 of LRRC24. The breakpoint in RECQL4 is within exon 16. Its functional significance is undetermined.
PSMF1	0	MSKCC-DMP	P-0023680-T01-IM6	RNF43-PSMF1 fusion	yes	unknown		unknown	RNF43 (NM_017763) Rearrangement : t(17,20)(q23.1,p13)(chr17:g.56492855::chr20:g.1042563) Note: The RNF43 Rearrangement is a translocation event that may result in the possible truncation of RNF43. One of the breakpoints is within exon2. Its functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0023680-T01-IM6	RNF43-PSMF1 fusion	yes	unknown		unknown	RNF43 (NM_017763) Rearrangement : t(17,20)(q23.1,p13)(chr17:g.56492855::chr20:g.1042563) Note: The RNF43 Rearrangement is a translocation event that may result in the possible truncation of RNF43. One of the breakpoints is within exon2. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0023682-T01-IM6	CDC42-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - CDC42 (NM_001791) Rearrangement : t(1,19)(p13.3; p36.13)(chr1:g.22405880::chr19:g.1221235) Note: The STK11- CDC42  Rearrangement results in the fusion of exons 1-6 of STK11 with exons 3-6 of CDC42. The breakpoint in STK11 is within exon6. This rearrangement was observed in the background of other events involving CDC42. Its functional significance is undetermined.
CDC42	0	MSKCC-DMP	P-0023682-T01-IM6	CDC42-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - CDC42 (NM_001791) Rearrangement : t(1,19)(p13.3; p36.13)(chr1:g.22405880::chr19:g.1221235) Note: The STK11- CDC42  Rearrangement results in the fusion of exons 1-6 of STK11 with exons 3-6 of CDC42. The breakpoint in STK11 is within exon6. This rearrangement was observed in the background of other events involving CDC42. Its functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0023701-T01-IM6	BAIAP2-RPTOR fusion	yes	unknown		unknown	BAIAP2 (NM_017451) - RPTOR (NM_020761) Rearrangement : c.54+5781:BAIAP2_c.3611:RPTORdup Note: The BAIAP2  - RPTOR  Rearrangement results in the fusion of exon1 of BAIAP2 with exons 31-34 of RPTOR. The breakpoint in RPTOR is within exon31. Its functional significance is undetermined.
BAIAP2	0	MSKCC-DMP	P-0023701-T01-IM6	BAIAP2-RPTOR fusion	yes	unknown		unknown	BAIAP2 (NM_017451) - RPTOR (NM_020761) Rearrangement : c.54+5781:BAIAP2_c.3611:RPTORdup Note: The BAIAP2  - RPTOR  Rearrangement results in the fusion of exon1 of BAIAP2 with exons 31-34 of RPTOR. The breakpoint in RPTOR is within exon31. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0023716-T01-IM6	EP300-intragenic	yes	unknown		in frame	EP300 (NM_001429) rearrangement: c.3672-25_c.3729-6del Note: The EP300 rearrangement is an intragenic deletion of exon 21. Its functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0023721-T01-IM6	CARM1-intragenic	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: c.558+1395_c.999del Note: The CARM1 rearrangement is an intragenic deletion of exons 5-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0023732-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: chr9:g.139385688inv_c.4015-1inv Note: The NOTCH1 rearrangement is an inversion that includes NOTCH1 exons 25-34. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023741-T01-IM6	AFAP1L2-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) - AFAP1L2 (NM_001001936) rearrangement: t(10;17)(q25.3;p13.1)(chr10:g.116100904::chr17:g.7580804) Note: The TP53 - AFAP1L2 rearrangement is a translocation with breakpoints within TP53 intron 1 and AFAP1L2 intron 1. The functional significance is undetermined.
AFAP1L2	0	MSKCC-DMP	P-0023741-T01-IM6	AFAP1L2-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) - AFAP1L2 (NM_001001936) rearrangement: t(10;17)(q25.3;p13.1)(chr10:g.116100904::chr17:g.7580804) Note: The TP53 - AFAP1L2 rearrangement is a translocation with breakpoints within TP53 intron 1 and AFAP1L2 intron 1. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0023789-T01-IM6	LOC101927460-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : chr5:g.124747396_c.422+47:APCdel Note: The APC Rearrangement results in the deletion of exons 5-16 of APC. Its functional significance is undetermined.
LOC101927460	0	MSKCC-DMP	P-0023789-T01-IM6	LOC101927460-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : chr5:g.124747396_c.422+47:APCdel Note: The APC Rearrangement results in the deletion of exons 5-16 of APC. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0023746-T01-IM6	DMRTA1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077, NM_058195) rearrangement: c.78:CDKN2Ap16INK4A_chr9:g.22278766del, c.194-3542:CDKN2Ap14ARF_chr9:g.22278766del Note: The CDKN2A rearrangement is a deletion that includes exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms of CDKN2A.
DMRTA1	0	MSKCC-DMP	P-0023746-T01-IM6	DMRTA1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077, NM_058195) rearrangement: c.78:CDKN2Ap16INK4A_chr9:g.22278766del, c.194-3542:CDKN2Ap14ARF_chr9:g.22278766del Note: The CDKN2A rearrangement is a deletion that includes exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms of CDKN2A.
ERG	0	MSKCC-DMP	P-0023753-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2085:TMPRSS2_:c.18+21555:ERGdel TMPRSS2 exon 1 is  fused to ERG exons 2-10. The TMPRSS2-ERG fusion is known to be oncogenic.
TMPRSS2	0	MSKCC-DMP	P-0023753-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2085:TMPRSS2_:c.18+21555:ERGdel TMPRSS2 exon 1 is  fused to ERG exons 2-10. The TMPRSS2-ERG fusion is known to be oncogenic.
FH	0	MSKCC-DMP	P-0023272-T01-IM6	FH-intragenic	yes	unknown		unknown	FH (NM_000143) Rearrangement : c.1390+169_c.*1652_del Note: The FH Rearrangement results in the deletion of exon 10 of FH. Its functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0023756-T01-IM6	HMGXB4-NF2 fusion	yes	unknown		unknown	HMGXB4 (NM_001003681) - NF2 (NM_000268) rearrangement: c.-68-2330:HMGXB4_c.1738-103:NF2dup Note: The HMGXB4 - NF2 rearrangement is a duplication that results in the fusion of HMGXB4 exon 1 with NF2 exon 16. The functional significance is undetermined.
HMGXB4	0	MSKCC-DMP	P-0023756-T01-IM6	HMGXB4-NF2 fusion	yes	unknown		unknown	HMGXB4 (NM_001003681) - NF2 (NM_000268) rearrangement: c.-68-2330:HMGXB4_c.1738-103:NF2dup Note: The HMGXB4 - NF2 rearrangement is a duplication that results in the fusion of HMGXB4 exon 1 with NF2 exon 16. The functional significance is undetermined.
DRD4	0	MSKCC-DMP	P-0023764-T01-IM6	ATM-DRD4 fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: chr11:g.638545_c.8932inv Note: The ATM rearrangement results in the inversion of exons 1-62. One of the breakpoints is within exon 62. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0023764-T01-IM6	ATM-DRD4 fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: chr11:g.638545_c.8932inv Note: The ATM rearrangement results in the inversion of exons 1-62. One of the breakpoints is within exon 62. The functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0023764-T01-IM6	EXPH5-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.647_chr11:g.108447231del Note: The RPS6KB2 rearrangement results in the deletion of exons 8-15. One of the breakpoints is within exon 8. The functional significance is undetermined.
EXPH5	0	MSKCC-DMP	P-0023764-T01-IM6	EXPH5-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.647_chr11:g.108447231del Note: The RPS6KB2 rearrangement results in the deletion of exons 8-15. One of the breakpoints is within exon 8. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0023768-T01-IM6	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.1450+596_c.1167+29inv Note: The TCF3 rearrangement results in the inversion of exons 14-15. The functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0023776-T01-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.553-11414_chr10:g.115137987inv Note: The TCF7L2 rearrangement results in the inversion of exons 6-14. The functional significance is undetermined.
HABP2	0	MSKCC-DMP	P-0023776-T01-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.553-11414_chr10:g.115137987inv Note: The TCF7L2 rearrangement results in the inversion of exons 6-14. The functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0023776-T01-IM6	ERCC1-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.1591_chr19:g.45933447del Note: The ERCC2 rearrangement results in the deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
ERCC1	0	MSKCC-DMP	P-0023776-T01-IM6	ERCC1-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.1591_chr19:g.45933447del Note: The ERCC2 rearrangement results in the deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0002266-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0002266-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
ALK	0	MSKCC-DMP	P-0004218-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 20 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv Note: The EML4 (NM_001145076) - ALK (NM_004304)  Fusion  is a reciprocal inversion.
EML4	0	MSKCC-DMP	P-0004218-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 20 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv Note: The EML4 (NM_001145076) - ALK (NM_004304)  Fusion  is a reciprocal inversion.
E2F3	0	MSKCC-DMP	P-0004634-T01-IM5	E2F3-intragenic	yes	unknown		unknown	E2F3 (NM_001949) rearrangement: c.-653_c.176del The E2F3 (NM_001949) rearrangement is an intragenic deletion of exon 1. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0021909-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.911:PTEN_chr10:g.89755903del Note: The PTEN rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0023866-T01-IM6	ACPP-FGFR1 fusion	yes	unknown		in frame	ACPP (NM_001134194) -FGFR1 (NM_001174067) rearrangement: t(3;8)(q22.1;p11.23)(chr3:g.132078761::chr8:g.38287577) Note: The ACPP - FGFFR1 rearrangement is a translocation that results in the fusion of ACPP exons 1-10 with FGFR1 exons 4-11. The fusion is predicted to be in frame and includes the kinase domain of FGFR1.
ACPP	0	MSKCC-DMP	P-0023866-T01-IM6	ACPP-FGFR1 fusion	yes	unknown		in frame	ACPP (NM_001134194) -FGFR1 (NM_001174067) rearrangement: t(3;8)(q22.1;p11.23)(chr3:g.132078761::chr8:g.38287577) Note: The ACPP - FGFFR1 rearrangement is a translocation that results in the fusion of ACPP exons 1-10 with FGFR1 exons 4-11. The fusion is predicted to be in frame and includes the kinase domain of FGFR1.
APAF1	0	MSKCC-DMP	P-0023827-T01-IM6	FH-APAF1 fusion	yes	unknown		unknown	FH (NM_000143) Rearrangement : t(1;12)(q42.3;q23.1)(chr1:g.241669480::chr12:g.99115177) Note: The FH Rearrangement is a translocation event which results in the possible truncation of FH. One of the breakpoints is within intron5. Its functional significance is undetermined.
FH	0	MSKCC-DMP	P-0023827-T01-IM6	FH-APAF1 fusion	yes	unknown		unknown	FH (NM_000143) Rearrangement : t(1;12)(q42.3;q23.1)(chr1:g.241669480::chr12:g.99115177) Note: The FH Rearrangement is a translocation event which results in the possible truncation of FH. One of the breakpoints is within intron5. Its functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0023827-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) Rearrangement : c.4083_c.6679+831del Note: The NCOR1 Rearrangement results in the intragenic deletion of exons 30-42. One of the exons is within exon 30. Its functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0023838-T01-IM6	NAB2-intragenic	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.1091+159_c.1468+272inv Note: The NAB2 rearrangement results in the inversion of exons 4-6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023838-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-1424:TMPRSS2_c.40-59243:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0023838-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-1424:TMPRSS2_c.40-59243:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.
PIK3R1	0	MSKCC-DMP	P-0023855-T01-IM6	UBR3-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) - UBR3 (NM_172070) Rearrangement : t(2;5)(q24.3;q13.1)(chr2:g.170688316::chr5:g. 67592113) Note: The PIK3R1 - UBR3  Rearrangement results in the fusion of PIK3R1 exons 1-15 with UBR3 exons 2-39. Its functional significance is undetermined.
UBR3	0	MSKCC-DMP	P-0023855-T01-IM6	UBR3-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) - UBR3 (NM_172070) Rearrangement : t(2;5)(q24.3;q13.1)(chr2:g.170688316::chr5:g. 67592113) Note: The PIK3R1 - UBR3  Rearrangement results in the fusion of PIK3R1 exons 1-15 with UBR3 exons 2-39. Its functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0023898-T01-IM6	XRCC6BP1-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: t(12;16)(q14.1;q22.1)(chr12:g.58632676::chr16:g.68845628) Note: The CDH1 rearrangement is a translocation which involves a breakpoint within exon 7. Its functional significance is undetermined.
XRCC6BP1	0	MSKCC-DMP	P-0023898-T01-IM6	XRCC6BP1-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: t(12;16)(q14.1;q22.1)(chr12:g.58632676::chr16:g.68845628) Note: The CDH1 rearrangement is a translocation which involves a breakpoint within exon 7. Its functional significance is undetermined.
CAMTA1	0	MSKCC-DMP	P-0023899-T01-IM6	NOTCH2-CAMTA1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.2599+41:NOTCH2_chr1:g.7232798del Note: The NOTCH2 rearrangement is a deletion of exons 17-34. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0023899-T01-IM6	NOTCH2-CAMTA1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.2599+41:NOTCH2_chr1:g.7232798del Note: The NOTCH2 rearrangement is a deletion of exons 17-34. Its functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0023899-T01-IM6	LOC101928944-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.457+274: RPS6KB2_chr11:g.80143138del Note: The RPS6KB2 rearrangement is a deletion of exons 6-15. Its functional significance is undetermined.
LOC101928944	0	MSKCC-DMP	P-0023899-T01-IM6	LOC101928944-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.457+274: RPS6KB2_chr11:g.80143138del Note: The RPS6KB2 rearrangement is a deletion of exons 6-15. Its functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0023913-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.3434_c.5722inv Note: The MDC1 rearrangement is an intragenic inversion of exon 10-12. The breakpoints are within exons 10 and 12. Its functional significance is undetermined.
BCL2L1	0	MSKCC-DMP	P-0002587-T01-IM3	TSC2-BCL2L1 fusion	yes	unknown		out of frame	null
TSC2	0	MSKCC-DMP	P-0002587-T01-IM3	TSC2-BCL2L1 fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0003001-T01-IM3	SIK1-TMPRSS2 fusion	yes	unknown		out of frame	null Note: TMPRSS2-SIK1 duplication is a rearrangement event that results in the fusion of TMPRSS2 exons 2-14 to SIK1 exons 4-14.
SIK1	0	MSKCC-DMP	P-0003001-T01-IM3	SIK1-TMPRSS2 fusion	yes	unknown		out of frame	null Note: TMPRSS2-SIK1 duplication is a rearrangement event that results in the fusion of TMPRSS2 exons 2-14 to SIK1 exons 4-14.
ERG	0	MSKCC-DMP	P-0003139-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	null
TMPRSS2	0	MSKCC-DMP	P-0003139-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	null
CDK12	0	MSKCC-DMP	P-0008960-T01-IM5	HTR1E-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - HTR1E (NM_000865)  rearrangement: t(6;17)(q14.3;q12)(chr6:g.87697112::chr17:g.37646977) Note: The CDK12 (NM_016507) - HTR1E (NM_000865)  rearrangement: is a translocation which results in the fusion of CDK12 exons 1-3 with HTR1E exon 2. One of the breakpoints is within exon 3 of CDK12. The functional significance is undetermined.
HTR1E	0	MSKCC-DMP	P-0008960-T01-IM5	HTR1E-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - HTR1E (NM_000865)  rearrangement: t(6;17)(q14.3;q12)(chr6:g.87697112::chr17:g.37646977) Note: The CDK12 (NM_016507) - HTR1E (NM_000865)  rearrangement: is a translocation which results in the fusion of CDK12 exons 1-3 with HTR1E exon 2. One of the breakpoints is within exon 3 of CDK12. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008960-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 4 to 11): c.127-1144:TMPRSS2_c.39+62016:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008960-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 and 2 fused with ERG exons 4 to 11): c.127-1144:TMPRSS2_c.39+62016:ERGdel
TERT	0	MSKCC-DMP	P-0008960-T01-IM5	CDH6-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-476_chr5:g.30794048del The TERT (NM_198253) rearrangement is a deletion which includes part of the promoter region of TERT. The functional significance is undetermined.
CDH6	0	MSKCC-DMP	P-0008960-T01-IM5	CDH6-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-476_chr5:g.30794048del The TERT (NM_198253) rearrangement is a deletion which includes part of the promoter region of TERT. The functional significance is undetermined.
ERCC4	0	MSKCC-DMP	P-0013729-T01-IM5	MYC-ERCC4 fusion	yes	unknown		unknown	ERCC4 (NM_005236) - MYC (NM_002467) rearrangement: t(8;16)(q24.21;p13.12)(chr8:g.128753292::chr16:g.14015306) Note: The ERCC4 - MYC rearrangement is a translocation with breakpoints in ERCC4 intron1 and MYC 3UTR that may result in the truncation of ERCC4 exons 2-11. The functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0013729-T01-IM5	MYC-ERCC4 fusion	yes	unknown		unknown	ERCC4 (NM_005236) - MYC (NM_002467) rearrangement: t(8;16)(q24.21;p13.12)(chr8:g.128753292::chr16:g.14015306) Note: The ERCC4 - MYC rearrangement is a translocation with breakpoints in ERCC4 intron1 and MYC 3UTR that may result in the truncation of ERCC4 exons 2-11. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0013729-T01-IM5	CASZ1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - CASZ1 (NM_001079843) rearrangement: t(1;21)(p36.22;q22.3)(chr1:g.10703925::chr21:g.42868002) Note: The TMPRSS2 - CASZ1 rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-2 to CASZ1 exons 19-21. The functional significance is undetermined.
CASZ1	0	MSKCC-DMP	P-0013729-T01-IM5	CASZ1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - CASZ1 (NM_001079843) rearrangement: t(1;21)(p36.22;q22.3)(chr1:g.10703925::chr21:g.42868002) Note: The TMPRSS2 - CASZ1 rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-2 to CASZ1 exons 19-21. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013729-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+2996:TMPRSS2_c.18+1445:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013729-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+2996:TMPRSS2_c.18+1445:ERGdel
MLL3	0	MSKCC-DMP	P-0013729-T01-IM5	XRCC2-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.14470:MLL3_chr7:g.152256329del Note: The MLL3 rearrangement is a deletion of 5UTR and exons 1-57, with one of the breakpoint within exon 57.
XRCC2	0	MSKCC-DMP	P-0013729-T01-IM5	XRCC2-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.14470:MLL3_chr7:g.152256329del Note: The MLL3 rearrangement is a deletion of 5UTR and exons 1-57, with one of the breakpoint within exon 57.
TRAF2	0	MSKCC-DMP	P-0013937-T01-IM5	TRAF2-intragenic	yes	unknown		unknown	TRAF2 (NM_021138) rearrangement:c.-28-2168_c.345dup Note: The TRAF2 (NM_021138) rearrangement is a duplication that results in a fusion of the 5' UTR region of TRAF2 with exons 4-11.
ERG	0	MSKCC-DMP	P-0014819-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (M_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1266:TMRPSS2_c.18+21077del
TMPRSS2	0	MSKCC-DMP	P-0014819-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (M_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1266:TMRPSS2_c.18+21077del
ROS1	0	MSKCC-DMP	P-0021671-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) rearrangement: t(5,6)(q33.1,q22.1)(chr5:g.149783453::chr6:g.117657267) Note: The CD74-ROS1 rearrangement is a translocation which results in the antisense fusion of CD74 exons 1-7 with ROS1 exons 31-43 and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0021671-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) rearrangement: t(5,6)(q33.1,q22.1)(chr5:g.149783453::chr6:g.117657267) Note: The CD74-ROS1 rearrangement is a translocation which results in the antisense fusion of CD74 exons 1-7 with ROS1 exons 31-43 and includes the kinase domain of ROS1.
CDK12	0	MSKCC-DMP	P-0023550-T01-IM6	RPS6KB1-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.4173_chr17:g.58028299dup Note: The CDK12 rearrangement results in the duplication of exon 14. One of the breakpoints is within exon 14. The functional significance is undetermined.
RPS6KB1	0	MSKCC-DMP	P-0023550-T01-IM6	RPS6KB1-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.4173_chr17:g.58028299dup Note: The CDK12 rearrangement results in the duplication of exon 14. One of the breakpoints is within exon 14. The functional significance is undetermined.
MYH9	0	MSKCC-DMP	P-0024094-T01-IM6	FGFR2-MYH9 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYH9 (NM_002473) rearrangement: t(10;22)(q26.13;q12.3)(chr10:g.123240418::chr22:g.36682296) Note: The FGFR2 - MYH9 rearrangement is a reciprocal translocation that results in the in-frame fusion of FGFR2 exons 1-17 with MYH9 exons 36-41 and includes the kinase domain of FGFR2. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0024094-T01-IM6	FGFR2-MYH9 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYH9 (NM_002473) rearrangement: t(10;22)(q26.13;q12.3)(chr10:g.123240418::chr22:g.36682296) Note: The FGFR2 - MYH9 rearrangement is a reciprocal translocation that results in the in-frame fusion of FGFR2 exons 1-17 with MYH9 exons 36-41 and includes the kinase domain of FGFR2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0024097-T01-IM6	ZNF577-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.41;q22.3)(chr19:g.52343327::chr21:g.42872775) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. A complex rearrangement cannot be ruled out and its functional significance is undetermined.
ZNF577	0	MSKCC-DMP	P-0024097-T01-IM6	ZNF577-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.41;q22.3)(chr19:g.52343327::chr21:g.42872775) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. A complex rearrangement cannot be ruled out and its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0001117-T01-IM3	EZR-ROS1 fusion	yes	unknown		unknown	EZR (NM_003379) - ROS1 (NM_002944) Deletion: c.1090+214_c.5263del
EZR	0	MSKCC-DMP	P-0001117-T01-IM3	EZR-ROS1 fusion	yes	unknown		unknown	EZR (NM_003379) - ROS1 (NM_002944) Deletion: c.1090+214_c.5263del
RAD51C	0	MSKCC-DMP	P-0001818-T01-IM3	PPM1D-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - PPM1D (NM_003620) Deletion :   c.463:RAD51C_c.1260+1492:PPM1Ddel (see note) Note: The RAD51C alteration results in a deletion of a portion of the gene,   likely resulting in protein truncation.
PPM1D	0	MSKCC-DMP	P-0001818-T01-IM3	PPM1D-RAD51C fusion	yes	unknown		unknown	RAD51C (NM_058216) - PPM1D (NM_003620) Deletion :   c.463:RAD51C_c.1260+1492:PPM1Ddel (see note) Note: The RAD51C alteration results in a deletion of a portion of the gene,   likely resulting in protein truncation.
TACC3	0	MSKCC-DMP	P-0003677-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	c.2363:FGFR3 _c.1784:TACC3dup FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 9-17 fused to TACC3 exons 9-16)
FGFR3	0	MSKCC-DMP	P-0003677-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	c.2363:FGFR3 _c.1784:TACC3dup FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 9-17 fused to TACC3 exons 9-16)
PIK3R1	0	MSKCC-DMP	P-0012603-T01-IM5	TMEM171-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) Rearrangement :  c.1858:PIK3R1_chr5:g.72437149inv Note: The PIK3R1 rearrangement event results in the inversion of exons 15-16 of PIK3R1. One of the breakpoints is within exon 15. Its functional significance is undetermined.
TMEM171	0	MSKCC-DMP	P-0012603-T01-IM5	TMEM171-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) Rearrangement :  c.1858:PIK3R1_chr5:g.72437149inv Note: The PIK3R1 rearrangement event results in the inversion of exons 15-16 of PIK3R1. One of the breakpoints is within exon 15. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0013453-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 fused in-frame with ALK exons 20-29): c.2056+551:EML4_c.3173-203:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0013453-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 fused in-frame with ALK exons 20-29): c.2056+551:EML4_c.3173-203:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
SMARCB1	0	MSKCC-DMP	P-0023477-T01-IM6	SEZ6L-SMARCB1 fusion	yes	unknown		unknown	SMARCB1 (NM_003073) - SEZ6L (NM_021115) rearrangement: c.840:SMARCB1_c.95-11223:SEZ6Ldel Note: The SMARCB1 - SEZ6L rearrangement is a deletion which results in the fusion of SMARCB1 exons 1-7 with SEZ6L exons 2-17. One of the breakpoints is within SMARCB1 exon 7. The functional significance is undetermined.
SEZ6L	0	MSKCC-DMP	P-0023477-T01-IM6	SEZ6L-SMARCB1 fusion	yes	unknown		unknown	SMARCB1 (NM_003073) - SEZ6L (NM_021115) rearrangement: c.840:SMARCB1_c.95-11223:SEZ6Ldel Note: The SMARCB1 - SEZ6L rearrangement is a deletion which results in the fusion of SMARCB1 exons 1-7 with SEZ6L exons 2-17. One of the breakpoints is within SMARCB1 exon 7. The functional significance is undetermined.
AMPH	0	MSKCC-DMP	P-0023586-T01-IM6	EGFR-AMPH fusion	yes	unknown		unknown	EGFR (NM_005228) Rearrangement : c.69+16262:AMPH_c.3163-234:EGFRdel Note: The EGFR Rearrangement results in the deletion of exons 1-26. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0023586-T01-IM6	EGFR-AMPH fusion	yes	unknown		unknown	EGFR (NM_005228) Rearrangement : c.69+16262:AMPH_c.3163-234:EGFRdel Note: The EGFR Rearrangement results in the deletion of exons 1-26. Its functional significance is undetermined.
SMARCD1	0	MSKCC-DMP	P-0023599-T01-IM6	SMARCD1-intragenic	yes	unknown		unknown	SMARCD1 (NM_003076) Rearrangement : c.772-348_c.970del Note: The SMARCD1 Rearrangement results in the intragenic deletion of exons 7-8. One of the breakpoints is within exon8.Its functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0000521-T01-IM3	PAXIP1-MLL3 fusion	yes	unknown		unknown	null
PAXIP1	0	MSKCC-DMP	P-0000521-T01-IM3	PAXIP1-MLL3 fusion	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0003626-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 3 fuses with ERG exons 4-10): c.127-643:ERG_c.40-61697:TMPRSS2del
TMPRSS2	0	MSKCC-DMP	P-0003626-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 3 fuses with ERG exons 4-10): c.127-643:ERG_c.40-61697:TMPRSS2del
ERG	0	MSKCC-DMP	P-0004816-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.56-3787:TMPRSS2_c.39+54953:ERGdel.
TMPRSS2	0	MSKCC-DMP	P-0004816-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.56-3787:TMPRSS2_c.39+54953:ERGdel.
BAP1	0	MSKCC-DMP	P-0004842-T01-IM5	PBRM1-BAP1 fusion	yes	unknown		out of frame	PBRM1(NM_018313) -BAP1 (NM_004656) Rearrangement : c.2567+1284:PBRM1_ c.932-129:BAP1 Note: The PBRM1(NM_018313) -BAP1 (NM_004656) Rearrangement results in the fusion of exons 1 to 17 of PBRM1 with exons 11 to 17 of BAP1.The breakpoint in  BAP1 is within exon11.   Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0004842-T01-IM5	PBRM1-BAP1 fusion	yes	unknown		out of frame	PBRM1(NM_018313) -BAP1 (NM_004656) Rearrangement : c.2567+1284:PBRM1_ c.932-129:BAP1 Note: The PBRM1(NM_018313) -BAP1 (NM_004656) Rearrangement results in the fusion of exons 1 to 17 of PBRM1 with exons 11 to 17 of BAP1.The breakpoint in  BAP1 is within exon11.   Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0005914-T01-IM5	STK11-intragenic	yes	unknown		in frame	STK11 (NM_000455) rearrangement : c.291-486_375-30del Note: The STK11 (NM_000455) rearrangement results in the intragenic deletion of STK11 exon2.
ALK	0	MSKCC-DMP	P-0006313-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) Fusion ( EML4 exons 1 to 18 fused with exons 20 to 29 of ALK ) Note: The fusion is an in frame fusion which includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0006313-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) Fusion ( EML4 exons 1 to 18 fused with exons 20 to 29 of ALK ) Note: The fusion is an in frame fusion which includes the kinase domain of ALK.
ERG	0	MSKCC-DMP	P-0006389-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_001243432) - TMPRSS2 (NM_001135099) rearrangement : c.40-64167:ERG_c.56-3097:TMPRSS2del Note: The ERG (NM_001243432) - TMPRSS2 (NM_001135099) rearrangement event is a deletion which results in the fusion of EGR exons 4-11 and TMPRSS2 exons 2-14.
TMPRSS2	0	MSKCC-DMP	P-0006389-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_001243432) - TMPRSS2 (NM_001135099) rearrangement : c.40-64167:ERG_c.56-3097:TMPRSS2del Note: The ERG (NM_001243432) - TMPRSS2 (NM_001135099) rearrangement event is a deletion which results in the fusion of EGR exons 4-11 and TMPRSS2 exons 2-14.
NTRK1	0	MSKCC-DMP	P-0007050-T01-IM5	NTRK1-intragenic	yes	unknown		unknown	NTRK1(NM_002529) rearrangement : c.10-7071_c.1355-199inv Note: The NTRK1(NM_002529) rearrangement results in inversion of exons 2-11
NTRK1	0	MSKCC-DMP	P-0007050-T01-IM5	VANGL2-NTRK1 fusion	yes	unknown		unknown	VANGL2 (NM_020335) - NTRK1(NM_002529) rearrangement : c.-191+4456:VANGL2_c.1355-171:NTRK1dup Note: The NTRK1(NM_002529) - VANGL2 (NM_020335) rearrangement event is a duplication which results in the fusion of VANGL2 exon1 to NTRK1 exon 12-17. The functional significance is undetermined.
VANGL2	0	MSKCC-DMP	P-0007050-T01-IM5	VANGL2-NTRK1 fusion	yes	unknown		unknown	VANGL2 (NM_020335) - NTRK1(NM_002529) rearrangement : c.-191+4456:VANGL2_c.1355-171:NTRK1dup Note: The NTRK1(NM_002529) - VANGL2 (NM_020335) rearrangement event is a duplication which results in the fusion of VANGL2 exon1 to NTRK1 exon 12-17. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0007098-T01-IM5	SYF2-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement : c.2998-12:PIK3CD_chr1:g.25533354inv Note: The PIK3CD (NM_005026) rearrangement results in the inversion of exon24 of PIK3CD . Its functional significance is undetermined.
SYF2	0	MSKCC-DMP	P-0007098-T01-IM5	SYF2-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement : c.2998-12:PIK3CD_chr1:g.25533354inv Note: The PIK3CD (NM_005026) rearrangement results in the inversion of exon24 of PIK3CD . Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0007211-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29) : c.667+165:EML4_c.3172+838:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK. The fusion is predicted to be in-frame.
EML4	0	MSKCC-DMP	P-0007211-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29) : c.667+165:EML4_c.3172+838:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK. The fusion is predicted to be in-frame.
SMARCA4	0	MSKCC-DMP	P-0007341-T03-IM6	ZNF791-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1119-51:SMARCA4_chr19:g.12729256inv Note: The SMARCA4 rearrangement is an inversion of exons 7-35.
ZNF791	0	MSKCC-DMP	P-0007341-T03-IM6	ZNF791-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1119-51:SMARCA4_chr19:g.12729256inv Note: The SMARCA4 rearrangement is an inversion of exons 7-35.
CDYL	0	MSKCC-DMP	P-0007341-T03-IM6	DAXX-CDYL fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: chr6:g.4959186_c.1501+44:DAXXdel Note: The DAXX rearrangement is a deletion of exons 6-8.
DAXX	0	MSKCC-DMP	P-0007341-T03-IM6	DAXX-CDYL fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: chr6:g.4959186_c.1501+44:DAXXdel Note: The DAXX rearrangement is a deletion of exons 6-8.
C6orf136	0	MSKCC-DMP	P-0007341-T03-IM6	TAP1-C6orf136 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: chr6:g.30619601_c.762:TAP1del Note: The TAP1 rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 1.
TAP1	0	MSKCC-DMP	P-0007341-T03-IM6	TAP1-C6orf136 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: chr6:g.30619601_c.762:TAP1del Note: The TAP1 rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 1.
TACR3	0	MSKCC-DMP	P-0007647-T01-IM5	TET2-TACR3 fusion	yes	unknown		unknown	TET2 (NM_001127208) rearrangement: chr4:g.104768006 _c.3685dup Note: The TET2 rearrangement is a duplication of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
TET2	0	MSKCC-DMP	P-0007647-T01-IM5	TET2-TACR3 fusion	yes	unknown		unknown	TET2 (NM_001127208) rearrangement: chr4:g.104768006 _c.3685dup Note: The TET2 rearrangement is a duplication of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007770-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exon 1-2 fused with ERG exons 4-11) : c.126+457:TMPRSS2_c.39+35604:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007770-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exon 1-2 fused with ERG exons 4-11) : c.126+457:TMPRSS2_c.39+35604:ERGdel
ERG	0	MSKCC-DMP	P-0008147-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) c.56-4181:TMPRSS2_c.40-58022:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008147-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) c.56-4181:TMPRSS2_c.40-58022:ERGdel
NRAP	0	MSKCC-DMP	P-0008693-T01-IM5	FGFR2-NRAP fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NRAP (NM_198060) rearrangement: c.2301+935:FGFR2_c.2458-427:NRAPdel The FGFR2 (NM_000141) - NRAP (NM_198060) rearrangement is a deletion which results in the fusion of FGFR2 exons 1-17 with NRAP exons 24-42. The fusion is predicted to be in frame and includes the kinase domain of FGFR2
FGFR2	0	MSKCC-DMP	P-0008693-T01-IM5	FGFR2-NRAP fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NRAP (NM_198060) rearrangement: c.2301+935:FGFR2_c.2458-427:NRAPdel The FGFR2 (NM_000141) - NRAP (NM_198060) rearrangement is a deletion which results in the fusion of FGFR2 exons 1-17 with NRAP exons 24-42. The fusion is predicted to be in frame and includes the kinase domain of FGFR2
ERG	0	MSKCC-DMP	P-0009073-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-3497:TMPRSS2_c.40-8505:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009073-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-3497:TMPRSS2_c.40-8505:ERGdel
ERG	0	MSKCC-DMP	P-0009077-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-671:TMPRSS2_c.40-59954:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009077-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-671:TMPRSS2_c.40-59954:ERGdel
SDHAF2	0	MSKCC-DMP	P-0010032-T02-IM5	SDHAF2-intragenic	yes	unknown		unknown	SDHAF2 (NM_017841) rearrangement: c.36+2562_c.330del Note: The SDHAF2  rearrangement is an intragenic deletion of exons 2-3. One of the breakpoints is within exon3. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0011134-T01-IM5	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement : c.5101+341_5473del Note: The NCOR1 rearrangement event results in the intragenic deletion of NCOR1 exons 35-37. One of the breakpoints is within NCOR1 exon37.
ERG	0	MSKCC-DMP	P-0012029-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1653:TMPRSS2_c.19-13747:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0012029-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.127-1653:TMPRSS2_c.19-13747:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0012275-T01-IM5	UTRN-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(6;21)(q24.2;q22.3)(chr6:g.145232571::chr21:g.42869596) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint after exon2. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion. Additional testing by an alternate method is suggested, if clinically indicated.
UTRN	0	MSKCC-DMP	P-0012275-T01-IM5	UTRN-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(6;21)(q24.2;q22.3)(chr6:g.145232571::chr21:g.42869596) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint after exon2. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion. Additional testing by an alternate method is suggested, if clinically indicated.
ERG	0	MSKCC-DMP	P-0012322-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) Rearrangement : c.56-2615:TMPRSS2_c.-150+18956:ERGinv Note: The TMPRSS2  - ERG  Rearrangement is an inversion that leads to fusion of exon1 of TMPRSS2 to exon2 of ERG in an antisense manner. While the event is not the canonical TMRPS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion.
TMPRSS2	0	MSKCC-DMP	P-0012322-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) Rearrangement : c.56-2615:TMPRSS2_c.-150+18956:ERGinv Note: The TMPRSS2  - ERG  Rearrangement is an inversion that leads to fusion of exon1 of TMPRSS2 to exon2 of ERG in an antisense manner. While the event is not the canonical TMRPS2-ERG fusion, there might be additional events, not detected by MSK-IMPACT, which might contribute to a functional fusion.
RET	0	MSKCC-DMP	P-0013023-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-17904:CCDC6_c.2137-222:RETinv
CCDC6	0	MSKCC-DMP	P-0013023-T01-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-17904:CCDC6_c.2137-222:RETinv
ERG	0	MSKCC-DMP	P-0013791-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.126+516:TMPRSS2_c.40-64952:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013791-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11) : c.126+516:TMPRSS2_c.40-64952:ERGdel
ALK	0	MSKCC-DMP	P-0014270-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused in-frame to ALK exons 20-29) : c.667+2294:EML4_c.3173-285:ALKinv Note: The EML4 - ALK fusion includes  the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0014270-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused in-frame to ALK exons 20-29) : c.667+2294:EML4_c.3173-285:ALKinv Note: The EML4 - ALK fusion includes  the kinase domain of ALK.
NTRK1	0	MSKCC-DMP	P-0015004-T01-IM6	RABGAP1L-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - RABGAP1L (NM_014857) rearrangement: c.1354+172:NTRK1_c.2340+50594:RABGAP1Ldel Note: The NTRK1 (NM_002529) - RABGAP1L (NM_014857) rearrangement is a deletion that results in the fusion of NTRK1 exons 1-11 with RABGAP1L exons 20-21. The functional significance is undetermined.
RABGAP1L	0	MSKCC-DMP	P-0015004-T01-IM6	RABGAP1L-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - RABGAP1L (NM_014857) rearrangement: c.1354+172:NTRK1_c.2340+50594:RABGAP1Ldel Note: The NTRK1 (NM_002529) - RABGAP1L (NM_014857) rearrangement is a deletion that results in the fusion of NTRK1 exons 1-11 with RABGAP1L exons 20-21. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0015034-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.2130_c.2165-534del Note: The CDH1 rearrangement is an intragenic deletion of exon 13. One of the breakpoints is within exon 13.
CIC	0	MSKCC-DMP	P-0020959-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.3915_c.4678inv Note: The CIC rearrangement results in the inversion of exons 16-20. One of the breakpoints is within exon 16 and the other is within exon 20. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0021908-T01-IM6	GABRB2-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(5,19)(q34,p13.2)(chr5:g.160948114::chr19:g.15299881) Note: The NOTCH3 rearrangement is a translocation which may result in the truncation of exons 8-33. One of the breakpoints is within exon 8. Its functional significance is undetermined.
GABRB2	0	MSKCC-DMP	P-0021908-T01-IM6	GABRB2-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(5,19)(q34,p13.2)(chr5:g.160948114::chr19:g.15299881) Note: The NOTCH3 rearrangement is a translocation which may result in the truncation of exons 8-33. One of the breakpoints is within exon 8. Its functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0021924-T01-IM6	LRP1B-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) - LRP1B (NM_018557) rearrangement: t(2;16)(q22.1;p12.2)(chr2:g.141570009::chr16:g.23652478) Note: The PALB2 - LRP1B rearrangement is a translocation which results in the antisense fusion of PALB2 exon 1 to LRP1B exons 1-32. The functional significance is undetermined.
LRP1B	0	MSKCC-DMP	P-0021924-T01-IM6	LRP1B-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) - LRP1B (NM_018557) rearrangement: t(2;16)(q22.1;p12.2)(chr2:g.141570009::chr16:g.23652478) Note: The PALB2 - LRP1B rearrangement is a translocation which results in the antisense fusion of PALB2 exon 1 to LRP1B exons 1-32. The functional significance is undetermined.
LINC01554	0	MSKCC-DMP	P-0021924-T01-IM6	FAT1-LINC01554 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: t(4;5)(q35.2;q15)(chr4:g.187525213::chr5:g.95189699) Note: The FAT1 rearrangement is a translocation with a breakpoint within intron 18 of FAT1. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0021924-T01-IM6	FAT1-LINC01554 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: t(4;5)(q35.2;q15)(chr4:g.187525213::chr5:g.95189699) Note: The FAT1 rearrangement is a translocation with a breakpoint within intron 18 of FAT1. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0022406-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.1221_c.*3160del Note: The TMPRSS2 rearrangement is a deletion of exons 11-14. One of the breakpoints is within exon 11. The functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0022486-T01-IM6	MIR5700-CDK4 fusion	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.567_chr12:g.94954944del Note: The CDK4 rearrangement results in the deletion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
MIR5700	0	MSKCC-DMP	P-0022486-T01-IM6	MIR5700-CDK4 fusion	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.567_chr12:g.94954944del Note: The CDK4 rearrangement results in the deletion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0000474-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0000474-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
SPINT2	0	MSKCC-DMP	P-0000913-T04-IM6	AXL-SPINT2 fusion	yes	unknown		unknown	AXL (NM_021913) Rearrangement : chr19:g.38751353_c.155:AXLinv Note: The AXL Rearrangement results in the intragenic inversion of exons 1-2 of AXL. The breakpoint in AXL is within exon2. Its functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0000913-T04-IM6	AXL-SPINT2 fusion	yes	unknown		unknown	AXL (NM_021913) Rearrangement : chr19:g.38751353_c.155:AXLinv Note: The AXL Rearrangement results in the intragenic inversion of exons 1-2 of AXL. The breakpoint in AXL is within exon2. Its functional significance is undetermined.
PDGFRA	0	MSKCC-DMP	P-0000913-T04-IM6	PDGFRA-intragenic	yes	unknown		unknown	PDGFRA (NM_006206) Rearrangement : c.661_c.1558+131del Note: The PDGFRA Rearrangement results in the intragenic inversion of exons 5-10.One of the breakpoints is within exon5. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0001745-T02-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - (RET (NM_020975) rearrangement: c.304-9458:CCDC6_c.2137-787:RETinv Note: The CCDC6 - RET rearrangement is an inversion that results in the in frame fusion of CCDC6 exon 1 with RET exons 12-20.
CCDC6	0	MSKCC-DMP	P-0001745-T02-IM5	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - (RET (NM_020975) rearrangement: c.304-9458:CCDC6_c.2137-787:RETinv Note: The CCDC6 - RET rearrangement is an inversion that results in the in frame fusion of CCDC6 exon 1 with RET exons 12-20.
ALK	0	MSKCC-DMP	P-0002024-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) inversion:   c.2242+31:EML4_c.3173-739:ALKinv Note: The EML4-ALK Fusion is confirmed by FISH
EML4	0	MSKCC-DMP	P-0002024-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) inversion:   c.2242+31:EML4_c.3173-739:ALKinv Note: The EML4-ALK Fusion is confirmed by FISH
TMPRSS2	0	MSKCC-DMP	P-0002583-T01-IM3	TMPRSS2-intragenic	yes	unknown		unknown	null
CDH11	0	MSKCC-DMP	P-0003294-T02-IM5	CBFB-CDH11 fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement : chr16:g.63947171_c.399+72:CBFBinv Note: The CBFB (NM_022845) rearrangement results in the inversion of CBFB exons 1-4.
CBFB	0	MSKCC-DMP	P-0003294-T02-IM5	CBFB-CDH11 fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement : chr16:g.63947171_c.399+72:CBFBinv Note: The CBFB (NM_022845) rearrangement results in the inversion of CBFB exons 1-4.
ERG	0	MSKCC-DMP	P-0003294-T02-IM5	PDE1C-ERG fusion	yes	unknown		unknown	PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement : t(7;21)(p14.3;q22.2)(chr7:g.32062232::chr21:g.39817322) Note: The PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement event is a reciprocal translocation which results in the truncation of ERG exons 5-11.
PDE1C	0	MSKCC-DMP	P-0003294-T02-IM5	PDE1C-ERG fusion	yes	unknown		unknown	PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement : t(7;21)(p14.3;q22.2)(chr7:g.32062232::chr21:g.39817322) Note: The PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement event is a reciprocal translocation which results in the truncation of ERG exons 5-11.
ERG	0	MSKCC-DMP	P-0003689-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	c.55+2193:TMPRSS2_c.18+716:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_182918) reciprocal fusion (TMPRSS2 exon 1  fused with ERG exons 2-10)
TMPRSS2	0	MSKCC-DMP	P-0003689-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	c.55+2193:TMPRSS2_c.18+716:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_182918) reciprocal fusion (TMPRSS2 exon 1  fused with ERG exons 2-10)
SMARCA4	0	MSKCC-DMP	P-0003874-T01-IM5	SLITRK5-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(19,13)(19p13.2:13q31.2) (chr19:g.11137036::chr13g.88339972) The SMARCA4 (NM_003072 ) rearrangement is a translocation that results in the truncation of SMARCA4 exons 23-35. The functional significance is undetermined.
SLITRK5	0	MSKCC-DMP	P-0003874-T01-IM5	SLITRK5-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(19,13)(19p13.2:13q31.2) (chr19:g.11137036::chr13g.88339972) The SMARCA4 (NM_003072 ) rearrangement is a translocation that results in the truncation of SMARCA4 exons 23-35. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0004774-T01-IM5	GALK2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - GALK2 (NM_002044) Rearrrangement : t(17;15)(17p11.2;15q21.1)(chr17:g.16040646:chr15:g.49477846)     Note: The NCOR1 (NM_006311) - GALK2 (NM_002044) Rearrrangement is a translocation event which results in the fusion of  exons 1 to 14 of NCOR1 and exons 2 to 10  of GALK2.Its functional significance is undetermined.
GALK2	0	MSKCC-DMP	P-0004774-T01-IM5	GALK2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - GALK2 (NM_002044) Rearrrangement : t(17;15)(17p11.2;15q21.1)(chr17:g.16040646:chr15:g.49477846)     Note: The NCOR1 (NM_006311) - GALK2 (NM_002044) Rearrrangement is a translocation event which results in the fusion of  exons 1 to 14 of NCOR1 and exons 2 to 10  of GALK2.Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0005557-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-3810:TMPRSS2_c.19-16939:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0005557-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-3810:TMPRSS2_c.19-16939:ERGdel
ERG	0	MSKCC-DMP	P-0009536-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11)   :  c.55+1957:TMPRSS2_c.39+43307:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009536-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11)   :  c.55+1957:TMPRSS2_c.39+43307:ERGdel
KIF5B	0	MSKCC-DMP	P-0011035-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused with RET exons 12-20) : c.1726-2296:KIF5B_c.2137-710:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0011035-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused with RET exons 12-20) : c.1726-2296:KIF5B_c.2137-710:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.
ERG	0	MSKCC-DMP	P-0011472-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (exon 1 of TMPRSS2 with exons 2-10 of ERG): c.56-2395:TMPRSS2_c.18+9580:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0011472-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (exon 1 of TMPRSS2 with exons 2-10 of ERG): c.56-2395:TMPRSS2_c.18+9580:ERGdel
MLL	0	MSKCC-DMP	P-0013221-T01-IM5	PHC2-MLL fusion	yes	unknown		unknown	MLL (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.1;q23.3)(chr1:g.33801002::chr11:g.118342886) Note: The MLL - PHC2 rearrangement is a reciprocal translocation that results in the fusion of MLL exons 1-3 with PHC2 exons 9-14. One of the breakpoints is within MLL exon 3. The functional significance is undetermined.
PHC2	0	MSKCC-DMP	P-0013221-T01-IM5	PHC2-MLL fusion	yes	unknown		unknown	MLL (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.1;q23.3)(chr1:g.33801002::chr11:g.118342886) Note: The MLL - PHC2 rearrangement is a reciprocal translocation that results in the fusion of MLL exons 1-3 with PHC2 exons 9-14. One of the breakpoints is within MLL exon 3. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0013919-T01-IM5	MET-intragenic	yes	unknown		in frame	MET (NM_000245) rearrangement: c.2887+35_c.3029-1182del Note: The MET rearrangement is an intragenic deletion of exon 14.
TSC2	0	MSKCC-DMP	P-0014876-T01-IM6	C12orf64-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(12;16)(q21.31;p13.3)(chr12:g.80592188::chr16:g.2104408) Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 5 of TSC2. The functional significance is undetermined.
C12orf64	0	MSKCC-DMP	P-0014876-T01-IM6	C12orf64-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(12;16)(q21.31;p13.3)(chr12:g.80592188::chr16:g.2104408) Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 5 of TSC2. The functional significance is undetermined.
PHF14	0	MSKCC-DMP	P-0021915-T01-IM6	ARID1A-PHF14 fusion	yes	unknown		unknown	ARID1A (NM_006015) - PHF14 (NM_014660) rearrangement: t(1,7)(p36.11,p21.3)(chr1:g.27101386::chr7:g.11032042) Note: The ARID1A - PHF14 rearrangement is a translocation which may form a fusion of ARID1A exons 1-18 with PHF14 exons 5-17. One of the breakpoints is within ARID1A exon 18. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0021915-T01-IM6	ARID1A-PHF14 fusion	yes	unknown		unknown	ARID1A (NM_006015) - PHF14 (NM_014660) rearrangement: t(1,7)(p36.11,p21.3)(chr1:g.27101386::chr7:g.11032042) Note: The ARID1A - PHF14 rearrangement is a translocation which may form a fusion of ARID1A exons 1-18 with PHF14 exons 5-17. One of the breakpoints is within ARID1A exon 18. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0024225-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-24 fused to RET exons 10-20): c.2762-430:KIF5B_c.1866:RETinv Note: The KIF5B - RET fusion includes the kinase domain of RET. One of the breakpoints is within RET exon 10.
RET	0	MSKCC-DMP	P-0024225-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-24 fused to RET exons 10-20): c.2762-430:KIF5B_c.1866:RETinv Note: The KIF5B - RET fusion includes the kinase domain of RET. One of the breakpoints is within RET exon 10.
PTPRT	0	MSKCC-DMP	P-0024225-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: c.2177-23_c.88+88442inv Note: The PTPRT rearrangement is an intragenic inversion of exons 2-13. The functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0024249-T01-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.1318+23_chr10:g.115014274del Note: The TCF7L2 rearrangement is a deletion that includes TCF7L2 exons 13-14. The functional significance is undetermined.
HABP2	0	MSKCC-DMP	P-0024249-T01-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.1318+23_chr10:g.115014274del Note: The TCF7L2 rearrangement is a deletion that includes TCF7L2 exons 13-14. The functional significance is undetermined.
CHMP1A	0	MSKCC-DMP	P-0024249-T01-IM6	IRS2-CHMP1A fusion	yes	unknown		unknown	IRS2 (NM_003749) - CHMP1A (NM_002768) rearrangement: t(13;16)(q34;q24.3)(chr13:g.110437384::chr16:g.89721445) Note: The IRS2 - CHMP1A rearrangement is an translocation that results in the fusion of IRS2 exon1 to CHMP1A exons 2-7. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0024249-T01-IM6	IRS2-CHMP1A fusion	yes	unknown		unknown	IRS2 (NM_003749) - CHMP1A (NM_002768) rearrangement: t(13;16)(q34;q24.3)(chr13:g.110437384::chr16:g.89721445) Note: The IRS2 - CHMP1A rearrangement is an translocation that results in the fusion of IRS2 exon1 to CHMP1A exons 2-7. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024249-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused to ERG exons 4 -11): c.56-608:TMPRSS2_c.39+56905:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0024249-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused to ERG exons 4 -11): c.56-608:TMPRSS2_c.39+56905:ERGdel
IKBKE	0	MSKCC-DMP	P-0024266-T01-IM6	IKBKE-intragenic	yes	unknown		in frame	IKBKE (NM_014002) Rearrangement : c.1427+76_c.1616+931del Note: The IKBKE Rearrangement results in the intragenic deletion of exons 14-15. Its functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0024266-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) Rearrangement : c.4586-420_c.7204del Note: The MGA Rearrangement results in the intragenic deletion of exons 15-20. One of the breakpoints is within exon20. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0002217-T02-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0002217-T02-IM3	EML4-ALK fusion	yes	unknown		in frame	null
MAST3	0	MSKCC-DMP	P-0003208-T01-IM5	PIK3R2-MAST3 fusion	yes	unknown		unknown	null Note: The PIK3R2 (NM_005027) - MAST3 (NM_015016) rearrangement event results in the intragenic deletion of exons 1-8 PIK3R2 and a portion of the 3prime UTR of MAST3.
PIK3R2	0	MSKCC-DMP	P-0003208-T01-IM5	PIK3R2-MAST3 fusion	yes	unknown		unknown	null Note: The PIK3R2 (NM_005027) - MAST3 (NM_015016) rearrangement event results in the intragenic deletion of exons 1-8 PIK3R2 and a portion of the 3prime UTR of MAST3.
ERG	0	MSKCC-DMP	P-0004345-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.56-651:TMPRSS2_c.18+6726:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004345-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.56-651:TMPRSS2_c.18+6726:ERGdel
ERG	0	MSKCC-DMP	P-0004532-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 4) :  c.126+104:TMPRSS2_c.39+63265:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004532-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 4) :  c.126+104:TMPRSS2_c.39+63265:ERGdel
ALK	0	MSKCC-DMP	P-0005321-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 13 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv
EML4	0	MSKCC-DMP	P-0005321-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 13 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv
PIK3C2G	0	MSKCC-DMP	P-0006689-T01-IM5	KIAA0947-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement : t(5;12)(p15.32;p12.3)(chr5:g.5556235::chr12:g.18552720) Note: The PIK3C2G (NM_004570) rearrangement event results in the truncation of PIK3C2G exons 15-32. One of the breakpoints is within PIK3C2G exon15.
KIAA0947	0	MSKCC-DMP	P-0006689-T01-IM5	KIAA0947-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement : t(5;12)(p15.32;p12.3)(chr5:g.5556235::chr12:g.18552720) Note: The PIK3C2G (NM_004570) rearrangement event results in the truncation of PIK3C2G exons 15-32. One of the breakpoints is within PIK3C2G exon15.
ERG	0	MSKCC-DMP	P-0006689-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement :  c.40-31716:ERG_c.127-715:TMPRSS2inv Note: The ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement event results in the antisense fusion of ERG exon4 and TMPRSS2 exons3. This does NOT result in a functional transcript. Confirmatory testing using alternative platform is suggested to confirm the functional fusion if clinically indicative.
TMPRSS2	0	MSKCC-DMP	P-0006689-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement :  c.40-31716:ERG_c.127-715:TMPRSS2inv Note: The ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement event results in the antisense fusion of ERG exon4 and TMPRSS2 exons3. This does NOT result in a functional transcript. Confirmatory testing using alternative platform is suggested to confirm the functional fusion if clinically indicative.
TMPRSS2	0	MSKCC-DMP	P-0006689-T01-IM5	MLLT4-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - MLLT4 (NM_001207008) rearrangement : t(6;21)(q27;q22.3)(chr6:168293792::chr21:42875775) Note: The TMPRSS2 (NM_001135099) - MLLT4 (NM_001207008) rearrangement event results in the fusion of TMPRRS2 exon1 with MLLT4 exons 9-32. The resulting fusion is predicted to be in-frame.
MLLT4	0	MSKCC-DMP	P-0006689-T01-IM5	MLLT4-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - MLLT4 (NM_001207008) rearrangement : t(6;21)(q27;q22.3)(chr6:168293792::chr21:42875775) Note: The TMPRSS2 (NM_001135099) - MLLT4 (NM_001207008) rearrangement event results in the fusion of TMPRRS2 exon1 with MLLT4 exons 9-32. The resulting fusion is predicted to be in-frame.
EED	0	MSKCC-DMP	P-0008054-T01-IM5	FAT3-EED fusion	yes	unknown		unknown	EED (NM_003797) rearrangement: c.1125+52_chr11:g.91474496del The EED (NM_003797) rearrangement is a deletion of EED exons 11-12. The functional significance is undetermined.
FAT3	0	MSKCC-DMP	P-0008054-T01-IM5	FAT3-EED fusion	yes	unknown		unknown	EED (NM_003797) rearrangement: c.1125+52_chr11:g.91474496del The EED (NM_003797) rearrangement is a deletion of EED exons 11-12. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0011525-T01-IM5	ABCG1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement :  c.557-24:TMPRSS2_chr21:g.43616717del Note: The TMPRSS2 Rearrangement results in the deletion of exons1-5 of TMPRSS2.Its functional significance is undetermined.
ABCG1	0	MSKCC-DMP	P-0011525-T01-IM5	ABCG1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement :  c.557-24:TMPRSS2_chr21:g.43616717del Note: The TMPRSS2 Rearrangement results in the deletion of exons1-5 of TMPRSS2.Its functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0012141-T01-IM5	PIK3R1-intragenic	yes	unknown		out of frame	PIK3R1 (NM_181523) rearrangement: c.917-5504_c.1300-2del Note: The PIK3R1 rearrangement is an intragenic deletion of exons 5-6.
MKRN1	0	MSKCC-DMP	P-0013536-T01-IM5	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.544+172:MKRN1_c.1178-661:BRAFdup Note: The MKRN1 - BRAF rearrangement is a duplication which leads to the fusion of MKRN1 exons 1-3 of MKRN1 with BRAF exons 10-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0013536-T01-IM5	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.544+172:MKRN1_c.1178-661:BRAFdup Note: The MKRN1 - BRAF rearrangement is a duplication which leads to the fusion of MKRN1 exons 1-3 of MKRN1 with BRAF exons 10-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
ERG	0	MSKCC-DMP	P-0014341-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 4-10): c.56-2247:TMPRSS2_c.-4097:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014341-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 4-10): c.56-2247:TMPRSS2_c.-4097:ERGdel
ERG	0	MSKCC-DMP	P-0020847-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.127-601:TMPRSS2_c.19-17357:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0020847-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.127-601:TMPRSS2_c.19-17357:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
NF2	0	MSKCC-DMP	P-0021916-T01-IM6	CABP7-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) -  rearrangement: c.109:NF2_chr22:g.30109685del Note: The NF2 rearrangement is a deletion of exons 1-16. One of the breakpoints is within exon 1. Its functional significance is undetermined.
CABP7	0	MSKCC-DMP	P-0021916-T01-IM6	CABP7-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) -  rearrangement: c.109:NF2_chr22:g.30109685del Note: The NF2 rearrangement is a deletion of exons 1-16. One of the breakpoints is within exon 1. Its functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0024178-T01-IM6	PABPC1P2-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) Rearrangement : t(2,17)(q23.1,p12)(chr2:g.147903758::chr17:g.12028641) Note: The MAP2K4 Rearrangement results in the possible truncation of MAP2K4. One of the breakpoints is within exon8. The rearrangement includes the protein kinase domain of MAP2K4.
PABPC1P2	0	MSKCC-DMP	P-0024178-T01-IM6	PABPC1P2-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) Rearrangement : t(2,17)(q23.1,p12)(chr2:g.147903758::chr17:g.12028641) Note: The MAP2K4 Rearrangement results in the possible truncation of MAP2K4. One of the breakpoints is within exon8. The rearrangement includes the protein kinase domain of MAP2K4.
FGFR2	0	MSKCC-DMP	P-0024183-T01-IM6	PLXNA2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) Rearrangement : t(1;10)(q32.3;q26.11)(chr1:g.208433127::chr10:g.123242818) Note: The FGFR2 Rearrangement results in the possible truncation of FGFR2. One of the breakpoints is within intron 17. The functional significance is undetermined.
PLXNA2	0	MSKCC-DMP	P-0024183-T01-IM6	PLXNA2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) Rearrangement : t(1;10)(q32.3;q26.11)(chr1:g.208433127::chr10:g.123242818) Note: The FGFR2 Rearrangement results in the possible truncation of FGFR2. One of the breakpoints is within intron 17. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0024187-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) Fusion (FGFR2 exon 17 with TACC2 exon12) : c.2302-1038:FGFR2_c.8009:TACC2inv Note: The FGFR2 fusion includes the kinase domain of FGFR2.
TACC2	0	MSKCC-DMP	P-0024187-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) Fusion (FGFR2 exon 17 with TACC2 exon12) : c.2302-1038:FGFR2_c.8009:TACC2inv Note: The FGFR2 fusion includes the kinase domain of FGFR2.
IKZF4	0	MSKCC-DMP	P-0024193-T01-IM6	ERBB3-IKZF4 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: chr12: 56408400 _c.558dup Note: The ERBB3 rearrangement results in the duplication of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0024193-T01-IM6	ERBB3-IKZF4 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: chr12: 56408400 _c.558dup Note: The ERBB3 rearrangement results in the duplication of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
PIM1	0	MSKCC-DMP	P-0024201-T01-IM6	TMEM217-PIM1 fusion	yes	unknown		unknown	PIM1 (NM_002648) rearrangement: c.608-304_chr6:g.37178326dup Note: The PIM1 rearrangement results in the duplication of exons 5-6. The functional significance is undetermined.
TMEM217	0	MSKCC-DMP	P-0024201-T01-IM6	TMEM217-PIM1 fusion	yes	unknown		unknown	PIM1 (NM_002648) rearrangement: c.608-304_chr6:g.37178326dup Note: The PIM1 rearrangement results in the duplication of exons 5-6. The functional significance is undetermined.
USP25	0	MSKCC-DMP	P-0024203-T01-IM6	TERT-USP25 fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;21)(p15.33;q21.1)(chr5:g.1279360::chr21:g.17011913) Note: The TERT rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0024203-T01-IM6	TERT-USP25 fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;21)(p15.33;q21.1)(chr5:g.1279360::chr21:g.17011913) Note: The TERT rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
RNF213	0	MSKCC-DMP	P-0024206-T01-IM6	RPTOR-RNF213 fusion	yes	unknown		in frame	RNF213 (NM_001256071) - RPTOR (NM_020761) rearrangement: c.14539+250:RNF213_c.2102-56:RPTORdel Note: The RNF213 - RPTOR rearrangement is a deletion that results in the in-frame fusion of RNF213 exons 1-61 with RPTOR exon 19-34. The functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0024206-T01-IM6	RPTOR-RNF213 fusion	yes	unknown		in frame	RNF213 (NM_001256071) - RPTOR (NM_020761) rearrangement: c.14539+250:RNF213_c.2102-56:RPTORdel Note: The RNF213 - RPTOR rearrangement is a deletion that results in the in-frame fusion of RNF213 exons 1-61 with RPTOR exon 19-34. The functional significance is undetermined.
EXOC4	0	MSKCC-DMP	P-0024206-T01-IM6	BRAF-EXOC4 fusion	yes	unknown		out of frame	EXOC4 (NM_021807) - BRAF (NM_004333) rearrangement: c.87-8072:EXOC4_c.1141-572:BRAFinv Note: The EXOC4 - BRAF rearrangement is an inversion that results in the fusion of EXOC4 exon 1 with BRAF exon 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0024206-T01-IM6	BRAF-EXOC4 fusion	yes	unknown		out of frame	EXOC4 (NM_021807) - BRAF (NM_004333) rearrangement: c.87-8072:EXOC4_c.1141-572:BRAFinv Note: The EXOC4 - BRAF rearrangement is an inversion that results in the fusion of EXOC4 exon 1 with BRAF exon 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
TTC7A	0	MSKCC-DMP	P-0024219-T01-IM6	MSH6-TTC7A fusion	yes	unknown		unknown	TTC7A (NM_020458) - MSH6 (NM_000179) rearrangement: c.518-7732:TTC7A_c.481:MSH6del Note: The TTC7A - MSH6 rearrangement is a deletion that results in the fusion of TTC7A exons 1-3 with MSH6 exons 3-10. One of the breakpoints is within MSH6 exon 10. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0024219-T01-IM6	MSH6-TTC7A fusion	yes	unknown		unknown	TTC7A (NM_020458) - MSH6 (NM_000179) rearrangement: c.518-7732:TTC7A_c.481:MSH6del Note: The TTC7A - MSH6 rearrangement is a deletion that results in the fusion of TTC7A exons 1-3 with MSH6 exons 3-10. One of the breakpoints is within MSH6 exon 10. The functional significance is undetermined.
ATP1A1	0	MSKCC-DMP	P-0024296-T01-IM6	NOTCH2-ATP1A1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.4393:NOTCH2_chr1:g.116787704del Note: The NOTCH2 rearrangement is a deletion of exons 25-34. One of the breakpoints is within exon 25. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0024296-T01-IM6	NOTCH2-ATP1A1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.4393:NOTCH2_chr1:g.116787704del Note: The NOTCH2 rearrangement is a deletion of exons 25-34. One of the breakpoints is within exon 25. Its functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0024349-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.-3698_c.451del Note: The RAS1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0024099-T01-IM6	CDKN2B-AS1-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*114_chr9:g.22030267inv Note: The CDKN2Ap14ARF rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
CDKN2B-AS1	0	MSKCC-DMP	P-0024099-T01-IM6	CDKN2B-AS1-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*114_chr9:g.22030267inv Note: The CDKN2Ap14ARF rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0024099-T01-IM6	CDKN2B-AS1-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.470_chr9:g.22030267inv Note: The CDKN2Ap16INK4A rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
CDKN2B-AS1	0	MSKCC-DMP	P-0024099-T01-IM6	CDKN2B-AS1-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.470_chr9:g.22030267inv Note: The CDKN2Ap16INK4A rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0024105-T01-IM6	COLQ-EP300 fusion	yes	unknown		out of frame	EP300 (NM_001429) - COLQ (NM_005677) rearrangement: t(3;22)(p25.1;q13.2)(chr3:g.15513123::chr22:g.41562715) Note: The EP300 - COLQ rearrangement is a translocation which may result in an out of frame fusion of EP300 exons 1-23 with COLQ exon 10-17. Its functional significance is undetermined.
COLQ	0	MSKCC-DMP	P-0024105-T01-IM6	COLQ-EP300 fusion	yes	unknown		out of frame	EP300 (NM_001429) - COLQ (NM_005677) rearrangement: t(3;22)(p25.1;q13.2)(chr3:g.15513123::chr22:g.41562715) Note: The EP300 - COLQ rearrangement is a translocation which may result in an out of frame fusion of EP300 exons 1-23 with COLQ exon 10-17. Its functional significance is undetermined.
E2F3	0	MSKCC-DMP	P-0024105-T01-IM6	CDKAL1-E2F3 fusion	yes	unknown		out of frame	CDKAL1 (NM_017774) - E2F3 (NM_001949) rearrangement: c.1055+24367:CDKAL1_c.506-2:E2F3dup Note: The CDKAL1 - E2F3 rearrangement is a duplication which results in the out of frame fusion of CDKAL1 exons 1-2 with E2F3 exons 3-7. Its functional significance is undetermined.
CDKAL1	0	MSKCC-DMP	P-0024105-T01-IM6	CDKAL1-E2F3 fusion	yes	unknown		out of frame	CDKAL1 (NM_017774) - E2F3 (NM_001949) rearrangement: c.1055+24367:CDKAL1_c.506-2:E2F3dup Note: The CDKAL1 - E2F3 rearrangement is a duplication which results in the out of frame fusion of CDKAL1 exons 1-2 with E2F3 exons 3-7. Its functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0024128-T01-IM6	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.1165_c.*3255del Note: The TCF3 rearrangement is an intragenic deletion of exons 13-18. One of the breakpoints is within exon 13. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0024129-T01-IM6	RAB28-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(4;12)(p15.33;q13.12)(chr4:g.12861485::chr12:g.49443742) Note: The KMT2D rearrangement is a translocation with a breakpoint within exon 11. The functional significance is undetermined.
RAB28	0	MSKCC-DMP	P-0024129-T01-IM6	RAB28-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(4;12)(p15.33;q13.12)(chr4:g.12861485::chr12:g.49443742) Note: The KMT2D rearrangement is a translocation with a breakpoint within exon 11. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0024136-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons  1-6 fused to ALK exons 20 -29): c.668-4498:EML4_c.3172+61:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0024136-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons  1-6 fused to ALK exons 20 -29): c.668-4498:EML4_c.3172+61:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
NF1	0	MSKCC-DMP	P-0024215-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.6559_c.7190-2264dup Note: The NF1 rearrangement results in the duplication of exons 43-48. One of the breakpoints is within exon 43. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0022245-T01-IM6	CDC16-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.8754+23:BRCA2_chr13:g.114995748del Note: The BRCA2 rearrangement is a deletion of exons 22-27.
CDC16	0	MSKCC-DMP	P-0022245-T01-IM6	CDC16-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.8754+23:BRCA2_chr13:g.114995748del Note: The BRCA2 rearrangement is a deletion of exons 22-27.
ATM	0	MSKCC-DMP	P-0021321-T01-IM6	DDX10-ATM fusion	yes	unknown		unknown	DDX10 (NM_004398) - ATM (NM_000051) rearrangement: c.1966-28956:DDX10_c.4831:ATMdup Note: The DDX - ATM rearrangement is a duplication that results in the fusion of DDX10 exons 1-13 with ATM exons 32-63. One of the breakpoints is within ATM exon 32. The functional significance is undetermined.
DDX10	0	MSKCC-DMP	P-0021321-T01-IM6	DDX10-ATM fusion	yes	unknown		unknown	DDX10 (NM_004398) - ATM (NM_000051) rearrangement: c.1966-28956:DDX10_c.4831:ATMdup Note: The DDX - ATM rearrangement is a duplication that results in the fusion of DDX10 exons 1-13 with ATM exons 32-63. One of the breakpoints is within ATM exon 32. The functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0021676-T01-IM6	EZH1-intragenic	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: c.1132_c.1402-5del Note: The EZH1 rearrangement is an intragenic deletion of exons 11-12. One of the breakpoints is within EZH1 exon 11. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024169-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.56-785:TMPRSS2_c.40-59113:ERGinv Note: The TMPRSS2  - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 1-3 of ERG. While the event is not the canonical TMPRSS2-ERG fusion, there might be additional events that are not detected by MSK-IMPACT which may contribute to a functional fusion.
TMPRSS2	0	MSKCC-DMP	P-0024169-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.56-785:TMPRSS2_c.40-59113:ERGinv Note: The TMPRSS2  - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 1-3 of ERG. While the event is not the canonical TMPRSS2-ERG fusion, there might be additional events that are not detected by MSK-IMPACT which may contribute to a functional fusion.
TRAPPC9	0	MSKCC-DMP	P-0019967-T02-IM6	AGO2-TRAPPC9 fusion	yes	unknown		unknown	TRAPPC9 (NM_031466) - AGO2 (NM_012154) rearrangement: c.3105-25933:TRAPPC9_c.2273:AGO2dup Note: The TRAPPC9 - AGO2 rearrangement is a duplication which results in the fusion of TRAPPC9 exons 1-19 with AGO2 exons 18-19. One of the breakpoints is within AGO2 exon 18. Its functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0019967-T02-IM6	AGO2-TRAPPC9 fusion	yes	unknown		unknown	TRAPPC9 (NM_031466) - AGO2 (NM_012154) rearrangement: c.3105-25933:TRAPPC9_c.2273:AGO2dup Note: The TRAPPC9 - AGO2 rearrangement is a duplication which results in the fusion of TRAPPC9 exons 1-19 with AGO2 exons 18-19. One of the breakpoints is within AGO2 exon 18. Its functional significance is undetermined.
POGK	0	MSKCC-DMP	P-0024168-T01-IM6	IL10-POGK fusion	yes	unknown		in frame	POGK (NM_017542) - IL10 (NM_000572) Rearrangement :  c.132+1054:POGK_c.226-132:IL10inv Note: The POGK - IL10 Rearrangement results in the fusion of exons 1-2 of POGK with exons 3-5 of IL10. The functional significance is undetermined.
IL10	0	MSKCC-DMP	P-0024168-T01-IM6	IL10-POGK fusion	yes	unknown		in frame	POGK (NM_017542) - IL10 (NM_000572) Rearrangement :  c.132+1054:POGK_c.226-132:IL10inv Note: The POGK - IL10 Rearrangement results in the fusion of exons 1-2 of POGK with exons 3-5 of IL10. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0024448-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.307_c.482+2736del Note: The MAP3K1 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
PPAN-P2RY11	0	MSKCC-DMP	P-0024450-T01-IM6	NTHL1-PPAN-P2RY11 fusion	yes	unknown		unknown	NTHL1 (NM_002528) rearrangement: t(16;19)(p13.3;p13.2)(chr16:g.2090167::chr19:g.10213963) Note: The NTHL1 rearrangement is a translocation with a breakpoint within NTHL1 exon 5. The functional significance is undetermined.
NTHL1	0	MSKCC-DMP	P-0024450-T01-IM6	NTHL1-PPAN-P2RY11 fusion	yes	unknown		unknown	NTHL1 (NM_002528) rearrangement: t(16;19)(p13.3;p13.2)(chr16:g.2090167::chr19:g.10213963) Note: The NTHL1 rearrangement is a translocation with a breakpoint within NTHL1 exon 5. The functional significance is undetermined.
SEC16A	0	MSKCC-DMP	P-0024450-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) fusion (SEC16A exon 1 fused to NOTCH1 exons 27-34): c.-192+5:SEC16A_c.5019-187:NOTCH1dup
NOTCH1	0	MSKCC-DMP	P-0024450-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) fusion (SEC16A exon 1 fused to NOTCH1 exons 27-34): c.-192+5:SEC16A_c.5019-187:NOTCH1dup
CTNNB1	0	MSKCC-DMP	P-0024418-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement :  c.-48-123_c.346del Note: The CTNNB1 Rearrangement results in the deletion of exons 1-4 of CTNNB1.The breakpoints are within the 5'UTR and exon4 respectively. Its functional significance is undetermined.
LINC00935	0	MSKCC-DMP	P-0006009-T02-IM6	KMT2D-LINC00935 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.11662:KMT2D_chr12:g.49153129del Note: The KMT2D rearrangement results in the deletion of exons 39-54. One of the breakpoints is within exon 39. Its functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0006009-T02-IM6	KMT2D-LINC00935 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.11662:KMT2D_chr12:g.49153129del Note: The KMT2D rearrangement results in the deletion of exons 39-54. One of the breakpoints is within exon 39. Its functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0006009-T02-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.565:ASXL2_chr2:g.25927220del Note: The ASXL2 rearrangement results in the deletion of exons 6-12. One of the breakpoints is within exon 6. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023839-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused with ERG exons 2-10): c.56-2993:TMPRSS2_c.19-8540:ERGdel Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0023839-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused with ERG exons 2-10): c.56-2993:TMPRSS2_c.19-8540:ERGdel Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.
ERG	0	MSKCC-DMP	P-0024461-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449): c.56-2094:TMPRSS2_:c.40-59950:ERGdel Note: The TMPRSS2  - ERG rearrangement results in fusion of TMPRSS2 exon 1 with ERG exons 4 - 10.
TMPRSS2	0	MSKCC-DMP	P-0024461-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449): c.56-2094:TMPRSS2_:c.40-59950:ERGdel Note: The TMPRSS2  - ERG rearrangement results in fusion of TMPRSS2 exon 1 with ERG exons 4 - 10.
CASP10	0	MSKCC-DMP	P-0024543-T01-IM6	CASP8-CASP10 fusion	yes	unknown		unknown	CASP8 (NM_001080125) - CASP10 (NM_032977) rearrangement: c.151+17:CASP8_c.-1793dup Note: The CASP8 - CASP10 rearrangement is a duplication which results in the fusion of CASP8 exon 1 with CASP10 exons 1-10. It's functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0024543-T01-IM6	CASP8-CASP10 fusion	yes	unknown		unknown	CASP8 (NM_001080125) - CASP10 (NM_032977) rearrangement: c.151+17:CASP8_c.-1793dup Note: The CASP8 - CASP10 rearrangement is a duplication which results in the fusion of CASP8 exon 1 with CASP10 exons 1-10. It's functional significance is undetermined.
SOCS1	0	MSKCC-DMP	P-0024554-T01-IM6	SOCS1-intragenic	yes	unknown		unknown	SOCS1 (NM_003745) rearrangement: c.-572_c.48inv Note: The SOCS1 rearrangement is an intragenic inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0024518-T01-IM6	HCN1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(5;17)(p11;q11.2)(chr5:g.46356017::chr17:g.29665106) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 45. The functional significance is undetermined.
HCN1	0	MSKCC-DMP	P-0024518-T01-IM6	HCN1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(5;17)(p11;q11.2)(chr5:g.46356017::chr17:g.29665106) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 45. The functional significance is undetermined.
RAD54L	0	MSKCC-DMP	P-0024524-T01-IM6	AGBL4-RAD54L fusion	yes	unknown		unknown	AGBL4 (NM_032785) - RAD54L (NM_001142548) rearrangement: c.1364+2079:AGBL4_c.1245-1:RAD54Linv Note: The AGBL4 - RAD54L rearrangement is an inversion which results in the fusion of AGBL4 exons 1-12 with RAD54L exons 13-29. One of the breakpoints is within RAD54L exon 13. Multiple rearrangements involving RAD54L were detected in this sample and a more complex rearrangement resulting in a complex RAD54L fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
AGBL4	0	MSKCC-DMP	P-0024524-T01-IM6	AGBL4-RAD54L fusion	yes	unknown		unknown	AGBL4 (NM_032785) - RAD54L (NM_001142548) rearrangement: c.1364+2079:AGBL4_c.1245-1:RAD54Linv Note: The AGBL4 - RAD54L rearrangement is an inversion which results in the fusion of AGBL4 exons 1-12 with RAD54L exons 13-29. One of the breakpoints is within RAD54L exon 13. Multiple rearrangements involving RAD54L were detected in this sample and a more complex rearrangement resulting in a complex RAD54L fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
NOL4L	0	MSKCC-DMP	P-0024530-T01-IM6	DNMT3B-NOL4L fusion	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.1906-133:DNMT3B_chr20:g.31140058del Note: The DNMT3B rearrangement is a deletion of exons 1-17. Its functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0024530-T01-IM6	DNMT3B-NOL4L fusion	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.1906-133:DNMT3B_chr20:g.31140058del Note: The DNMT3B rearrangement is a deletion of exons 1-17. Its functional significance is undetermined.
LOC440982	0	MSKCC-DMP	P-0024530-T01-IM6	MAP3K13-LOC440982 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.569:MAP3K13_chr3:g.147659711del Note: The MAP3K13 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0024530-T01-IM6	MAP3K13-LOC440982 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.569:MAP3K13_chr3:g.147659711del Note: The MAP3K13 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
CNTN1	0	MSKCC-DMP	P-0024531-T01-IM6	ARID2-CNTN1 fusion	yes	unknown		unknown	ARID2 (NM_152641): c.3061:ARID2_chr12:g.41070584inv Note: The ARID2 rearrangement is an inversion of exons 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0024531-T01-IM6	ARID2-CNTN1 fusion	yes	unknown		unknown	ARID2 (NM_152641): c.3061:ARID2_chr12:g.41070584inv Note: The ARID2 rearrangement is an inversion of exons 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0024532-T01-IM6	CHAT-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(10;22)(q11.23;q12.2)(chr10:g.50812403::chr22:g.29683485) Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined.
CHAT	0	MSKCC-DMP	P-0024532-T01-IM6	CHAT-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(10;22)(q11.23;q12.2)(chr10:g.50812403::chr22:g.29683485) Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0024534-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-562:TMPRSS2_chr21:g.40083159del Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a ERG - TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0024534-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-562:TMPRSS2_chr21:g.40083159del Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a ERG - TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ATR	0	MSKCC-DMP	P-0024537-T01-IM6	AGTR1-ATR fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.1886-81:ATR_chr3:g.147951936inv Note: The ATR rearrangement results in the inversion of exons 1-8. Its functional significance is undetermined.
AGTR1	0	MSKCC-DMP	P-0024537-T01-IM6	AGTR1-ATR fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.1886-81:ATR_chr3:g.147951936inv Note: The ATR rearrangement results in the inversion of exons 1-8. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0004787-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.8474_c.9037del The ZFHX3 (NM_006885) rearrangement is an intragenic deletion within exon 9. The functional significance is undetermined.
FLT1	0	MSKCC-DMP	P-0024586-T01-IM6	UBL3-FLT1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.1106+66_chr13:g.30250041inv Note: The FLT1 rearrangement is an inversion that includes FLT1 exons 1-8. The inversion does not include the kinase domain of FLT1. The functional significance is undetermined.
UBL3	0	MSKCC-DMP	P-0024586-T01-IM6	UBL3-FLT1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.1106+66_chr13:g.30250041inv Note: The FLT1 rearrangement is an inversion that includes FLT1 exons 1-8. The inversion does not include the kinase domain of FLT1. The functional significance is undetermined.
SMARCD1	0	MSKCC-DMP	P-0024602-T01-IM6	CTDSP2-SMARCD1 fusion	yes	unknown		in frame	SMARCD1 (NM_003076) - CTDSP2 (NM_005730) rearrangement: c.1269+187:SMARCD1_c.213+511:CTDSP2inv Note: The SMARCD1 - CTDSP2 rearrangement is an inversion that results in an in-frame fusion of SMARCD1 exons 1-10 with CTDSP2 exons 3-8. The functional significance is undetermined.
CTDSP2	0	MSKCC-DMP	P-0024602-T01-IM6	CTDSP2-SMARCD1 fusion	yes	unknown		in frame	SMARCD1 (NM_003076) - CTDSP2 (NM_005730) rearrangement: c.1269+187:SMARCD1_c.213+511:CTDSP2inv Note: The SMARCD1 - CTDSP2 rearrangement is an inversion that results in an in-frame fusion of SMARCD1 exons 1-10 with CTDSP2 exons 3-8. The functional significance is undetermined.
ANKRD12	0	MSKCC-DMP	P-0024672-T01-IM6	TP53-ANKRD12 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : t(17;18)(p13.1;p11.22)(chr17:g.7580666;18:9253524) Note: The TP53 Rearrangement results in the possible truncation of TP53. The breakpoint in TP53 is within the 5-UTR region of TP53 before transcription start site. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0024672-T01-IM6	TP53-ANKRD12 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : t(17;18)(p13.1;p11.22)(chr17:g.7580666;18:9253524) Note: The TP53 Rearrangement results in the possible truncation of TP53. The breakpoint in TP53 is within the 5-UTR region of TP53 before transcription start site. Its functional significance is undetermined.
KCNV2	0	MSKCC-DMP	P-0024672-T01-IM6	JAK2-KCNV2 fusion	yes	unknown		unknown	JAK2 (NM_004972) Rearrangement : c.1514-48:JAK2_chr9:g.2692334del Note: The JAK2  Rearrangement results in the deletion of exon 1-11 of JAK2. Its functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0024672-T01-IM6	JAK2-KCNV2 fusion	yes	unknown		unknown	JAK2 (NM_004972) Rearrangement : c.1514-48:JAK2_chr9:g.2692334del Note: The JAK2  Rearrangement results in the deletion of exon 1-11 of JAK2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0024679-T01-IM6	CTSE-ALK fusion	yes	unknown		unknown	ALK (NM_004304) - CTSE(NM_001910) Rearrangement: t(1;2)(q32.1;p23.3)(chr1:g.206318648; chr2:g.29543594) Note: The ALK - CTSE Rearrangement results in possible truncation of ALK, with the breakpoint in intron 7 of ALK.Its functional significance is unknown.
CTSE	0	MSKCC-DMP	P-0024679-T01-IM6	CTSE-ALK fusion	yes	unknown		unknown	ALK (NM_004304) - CTSE(NM_001910) Rearrangement: t(1;2)(q32.1;p23.3)(chr1:g.206318648; chr2:g.29543594) Note: The ALK - CTSE Rearrangement results in possible truncation of ALK, with the breakpoint in intron 7 of ALK.Its functional significance is unknown.
ERG	0	MSKCC-DMP	P-0024679-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11 ) : c.56-4747:TMPRSS2_c.40-54816:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0024679-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11 ) : c.56-4747:TMPRSS2_c.40-54816:ERGdel
DNAJB1	0	MSKCC-DMP	P-0024680-T01-IM6	VSTM1-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) Rearrangement: c.212-537:DNAJB1_c.394+79:VSTM1inv Note:The DNAJB1 Rearrangement results in the inversion of exon1 of DNAJB1. Its functional significance is undetermined.
VSTM1	0	MSKCC-DMP	P-0024680-T01-IM6	VSTM1-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) Rearrangement: c.212-537:DNAJB1_c.394+79:VSTM1inv Note:The DNAJB1 Rearrangement results in the inversion of exon1 of DNAJB1. Its functional significance is undetermined.
CCNE1	0	MSKCC-DMP	P-0024687-T01-IM6	URI1-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) rearrangement: c.1088:CCNE1_chr19:g.30433580inv Note: The CCNE1 rearrangement is an inversion of exons 11-12. One of the breakpoints is within exon 11. Its functional significance is undetermined.
URI1	0	MSKCC-DMP	P-0024687-T01-IM6	URI1-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) rearrangement: c.1088:CCNE1_chr19:g.30433580inv Note: The CCNE1 rearrangement is an inversion of exons 11-12. One of the breakpoints is within exon 11. Its functional significance is undetermined.
LOC102467213	0	MSKCC-DMP	P-0024689-T01-IM6	NSD1-LOC102467213 fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: c.6428:NSD1_chr5:g.106346069inv Note: The NSD1 rearrangement results in the inversion of NSD1 exons 1-22. One of the breakpoints is within exon 22. Its functional significance is unknown.
NSD1	0	MSKCC-DMP	P-0024689-T01-IM6	NSD1-LOC102467213 fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: c.6428:NSD1_chr5:g.106346069inv Note: The NSD1 rearrangement results in the inversion of NSD1 exons 1-22. One of the breakpoints is within exon 22. Its functional significance is unknown.
MAP2K1	0	MSKCC-DMP	P-0024691-T01-IM6	MAP2K1-intragenic	yes	unknown		out of frame	MAP2K1 (NM_002755) rearrangement: c.895+136_c.1068+241del Note: The MAP2K1 rearrangement is an intragenic deletion of exons 8-10. Its functional significance is undetermined.
POU2F2	0	MSKCC-DMP	P-0024691-T01-IM6	ERF-POU2F2 fusion	yes	unknown		out of frame	POU2F2 (NM_001207025) - ERF (NM_006494) rearrangement: c.186+1304:POU2F2_c.22+14:ERFdup Note: The POU2F2 - ERF rearrangement is a duplication which results in the fusion of POU2F2 exons 1-4 with ERF exons 2-4. Its functional significance is undetermined.
ERF	0	MSKCC-DMP	P-0024691-T01-IM6	ERF-POU2F2 fusion	yes	unknown		out of frame	POU2F2 (NM_001207025) - ERF (NM_006494) rearrangement: c.186+1304:POU2F2_c.22+14:ERFdup Note: The POU2F2 - ERF rearrangement is a duplication which results in the fusion of POU2F2 exons 1-4 with ERF exons 2-4. Its functional significance is undetermined.
CWH43	0	MSKCC-DMP	P-0024695-T01-IM6	HIST3H3-CWH43 fusion	yes	unknown		unknown	HIST3H3 (NM_003493) rearrangement: t(1;4)(q42.13;p11)(chr1:g.228612839::chr4:g.49583945) Note: The HIST3H3 rearrangement is a translocation involving HIST3H3 exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
HIST3H3	0	MSKCC-DMP	P-0024695-T01-IM6	HIST3H3-CWH43 fusion	yes	unknown		unknown	HIST3H3 (NM_003493) rearrangement: t(1;4)(q42.13;p11)(chr1:g.228612839::chr4:g.49583945) Note: The HIST3H3 rearrangement is a translocation involving HIST3H3 exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0024741-T01-IM6	LOC102724874-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: t(8;17)(q21.11;q12)(chr8:g.78247787::chr17:g.37627932) Note: The CDK12 rearrangement is a translocation with a breakpoint in exon 2. This event occurs in the background of CDK12 amplification. The functional significance is undetermined.
LOC102724874	0	MSKCC-DMP	P-0024741-T01-IM6	LOC102724874-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: t(8;17)(q21.11;q12)(chr8:g.78247787::chr17:g.37627932) Note: The CDK12 rearrangement is a translocation with a breakpoint in exon 2. This event occurs in the background of CDK12 amplification. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0024844-T01-IM6	ERBB4-intragenic	yes	unknown		out of frame	ERBB4 (NM_005235) rearrangement: c.556+7326_c.2965-8del Note: The ERBB4 rearrangement is an intragenic deletion of exons 5-25. Its functional significance is undetermined.
BCL2L1	0	MSKCC-DMP	P-0024865-T01-IM6	FSIP1-BCL2L1 fusion	yes	unknown		in frame	BCL2L1 (NM_138578) - FSIP1 (NM_152597) rearrangement: t(15;20)(q14;q11.21)(chr15:g.40027488::chr20:g.30263448) Note: The BCL2L1 (NM_138578) - FSIP1 (NM_152597) rearrangement is a translocation that results in the fusion of BCL2L1 exons 1-2 with FSIP1 exons 9-12. The functional significance is undetermined.
FSIP1	0	MSKCC-DMP	P-0024865-T01-IM6	FSIP1-BCL2L1 fusion	yes	unknown		in frame	BCL2L1 (NM_138578) - FSIP1 (NM_152597) rearrangement: t(15;20)(q14;q11.21)(chr15:g.40027488::chr20:g.30263448) Note: The BCL2L1 (NM_138578) - FSIP1 (NM_152597) rearrangement is a translocation that results in the fusion of BCL2L1 exons 1-2 with FSIP1 exons 9-12. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0024873-T01-IM6	CXorf36-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.2994_chrX:g.45005757del Note: The KDM6A rearrangement results in the deletion of exons 20-29. One of the breakpoints is within exon 20. The functional significance is undetermined.
CXorf36	0	MSKCC-DMP	P-0024873-T01-IM6	CXorf36-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.2994_chrX:g.45005757del Note: The KDM6A rearrangement results in the deletion of exons 20-29. One of the breakpoints is within exon 20. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0024166-T02-IM6	WNT4-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.10863+15:SPEN_chr1:g.22588125del Note: The SPEN rearrangement results in the deletion of exons 14-15. Its functional significance is undetermined.
WNT4	0	MSKCC-DMP	P-0024166-T02-IM6	WNT4-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.10863+15:SPEN_chr1:g.22588125del Note: The SPEN rearrangement results in the deletion of exons 14-15. Its functional significance is undetermined.
OS9	0	MSKCC-DMP	P-0024838-T01-IM6	CDK4-OS9 fusion	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.819+33:CDK4_chr12:g.58082608del Note: The CDK4 rearrangement is a deletion of exon 8. Its functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0024838-T01-IM6	CDK4-OS9 fusion	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.819+33:CDK4_chr12:g.58082608del Note: The CDK4 rearrangement is a deletion of exon 8. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0024843-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 with RET exons 12-20): c.1726-1339:KIF5B_c.2137-299:RETinv Note: The KIF5B - RET fusion is predicted to be in-frame and including the RET kinase domain.
RET	0	MSKCC-DMP	P-0024843-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 with RET exons 12-20): c.1726-1339:KIF5B_c.2137-299:RETinv Note: The KIF5B - RET fusion is predicted to be in-frame and including the RET kinase domain.
NLRP6	0	MSKCC-DMP	P-0024858-T01-IM6	INPPL1-NLRP6 fusion	yes	unknown		unknown	INPPL1 (NM_001567) - NLRP6 (NM_138329) rearrangement: c.617:INPPL1_c.2138:NLRP6dup Note: The INPPL1 - NLRP6 rearrangement is a duplication which results in the fusion of INPPL1 exons 1-5 with NLRP6 exons 5-8. The breakpoints are within INPPL1 exon 5 and NLRP6 exon 5. Its functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0024858-T01-IM6	INPPL1-NLRP6 fusion	yes	unknown		unknown	INPPL1 (NM_001567) - NLRP6 (NM_138329) rearrangement: c.617:INPPL1_c.2138:NLRP6dup Note: The INPPL1 - NLRP6 rearrangement is a duplication which results in the fusion of INPPL1 exons 1-5 with NLRP6 exons 5-8. The breakpoints are within INPPL1 exon 5 and NLRP6 exon 5. Its functional significance is undetermined.
TTTY3B	0	MSKCC-DMP	P-0024858-T01-IM6	ARID2-TTTY3B fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: t(12;23)(q13.11;q11.23)(chr12:g.46297969::chrY:g.28562161) Note: The ARID2 rearrangement is a translocation involving exon 21. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0024858-T01-IM6	ARID2-TTTY3B fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: t(12;23)(q13.11;q11.23)(chr12:g.46297969::chrY:g.28562161) Note: The ARID2 rearrangement is a translocation involving exon 21. Its functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0024080-T02-IM6	FLI1-ATM fusion	yes	unknown		out of frame	FLI1 (NM_002017) - ATM (NM_000051) rearrangement: c.781+147:FLI1_c.8269-128:ATMdup Note: The FLI1 - ATM rearrangement is a duplication that results in the fusion of FLI1 exons 1-7 with ATM exons 57- 63. The functional significance is undetermined.
FLI1	0	MSKCC-DMP	P-0024080-T02-IM6	FLI1-ATM fusion	yes	unknown		out of frame	FLI1 (NM_002017) - ATM (NM_000051) rearrangement: c.781+147:FLI1_c.8269-128:ATMdup Note: The FLI1 - ATM rearrangement is a duplication that results in the fusion of FLI1 exons 1-7 with ATM exons 57- 63. The functional significance is undetermined.
FOXG1-AS1	0	MSKCC-DMP	P-0024648-T01-IM6	PRKD1-FOXG1-AS1 fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: c.2015:PRKD1_chr14:g.29161076inv Note: The PRKD1 rearrangement results in the intragenic inversion of exons 14-18. One of the breakpoints is within exon 14. Its functional significance is undetermined.
PRKD1	0	MSKCC-DMP	P-0024648-T01-IM6	PRKD1-FOXG1-AS1 fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: c.2015:PRKD1_chr14:g.29161076inv Note: The PRKD1 rearrangement results in the intragenic inversion of exons 14-18. One of the breakpoints is within exon 14. Its functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0024649-T01-IM6	ALG10-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.3357+121:PIK3C2G_chr12:g.34715595inv Note: The PIK3C2G rearrangement results in the inversion of exons 1-24. Its functional significance is undetermined.
ALG10	0	MSKCC-DMP	P-0024649-T01-IM6	ALG10-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.3357+121:PIK3C2G_chr12:g.34715595inv Note: The PIK3C2G rearrangement results in the inversion of exons 1-24. Its functional significance is undetermined.
VEGFA	0	MSKCC-DMP	P-0024660-T01-IM6	TXNDC12-VEGFA fusion	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement: t(1;6)(p32.3;p21.1)(chr1:g.52516077::chr6:g.43748572) Note: The VEGFA rearrangement is a translocation with a breakpoint in exon 6. The functional significance is undetermined.
TXNDC12	0	MSKCC-DMP	P-0024660-T01-IM6	TXNDC12-VEGFA fusion	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement: t(1;6)(p32.3;p21.1)(chr1:g.52516077::chr6:g.43748572) Note: The VEGFA rearrangement is a translocation with a breakpoint in exon 6. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0024666-T01-IM6	TESK2-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.45867214::chr16:g.68846063) Note: The CDH1 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
TESK2	0	MSKCC-DMP	P-0024666-T01-IM6	TESK2-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.45867214::chr16:g.68846063) Note: The CDH1 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
JAK1	0	MSKCC-DMP	P-0024786-T01-IM6	JAK1-intragenic	yes	unknown		out of frame	JAK1 (NM_002227) Rearrangement : c.1649-50_c.3141-534dup Note: The JAK1 Rearrangement results in the duplication of exons 12-22. It includes the protein kinase domain of JAK1.
SLC16A7	0	MSKCC-DMP	P-0024788-T01-IM6	CDKN2Ap16INK4A-SLC16A7 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801) Note: The CDKN2Ap16INK4A Rearrangement results in the possible truncation of CDKN2Ap16INK4A. One of the breakpoints is within exon2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0024788-T01-IM6	CDKN2Ap16INK4A-SLC16A7 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801) Note: The CDKN2Ap16INK4A Rearrangement results in the possible truncation of CDKN2Ap16INK4A. One of the breakpoints is within exon2. The functional significance is undetermined.
SLC16A7	0	MSKCC-DMP	P-0024788-T01-IM6	CDKN2Ap14ARF-SLC16A7 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement :  t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801) Note: The CDKN2Ap14ARF Rearrangement results in the possible truncation of CDKN2Ap16INK4A. One of the breakpoints is in the 3-UTR after the transcription stop site. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0024788-T01-IM6	CDKN2Ap14ARF-SLC16A7 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement :  t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801) Note: The CDKN2Ap14ARF Rearrangement results in the possible truncation of CDKN2Ap16INK4A. One of the breakpoints is in the 3-UTR after the transcription stop site. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0024859-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.3144_c.3926dup Note: The MAP3K1 rearrangement is an intragenic duplication of 14-16. The breakpoints are within exons 14 and 16. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0024859-T01-IM6	TMPRSS11E-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) - TMPRSS11E (NM_014058) rearrangement: t(4;7)(q13.2;q36.1)(chr4:g.69356592::chr7:g.152009024) Note: The KMT2C rearrangement is a translocation involving KMT2C exon 5 and TMPRSS11E exon 10. One of the breakpoints is within KMT2C exon 5. Its functional significance is undetermined.
TMPRSS11E	0	MSKCC-DMP	P-0024859-T01-IM6	TMPRSS11E-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) - TMPRSS11E (NM_014058) rearrangement: t(4;7)(q13.2;q36.1)(chr4:g.69356592::chr7:g.152009024) Note: The KMT2C rearrangement is a translocation involving KMT2C exon 5 and TMPRSS11E exon 10. One of the breakpoints is within KMT2C exon 5. Its functional significance is undetermined.
PPAP2C	0	MSKCC-DMP	P-0024886-T01-IM6	DOT1L-PPAP2C fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: chr19:g.261784_c.1558-11inv Note: The DOT1L rearrangement is an inversion that includes DOT1L exons 1016. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0024886-T01-IM6	DOT1L-PPAP2C fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: chr19:g.261784_c.1558-11inv Note: The DOT1L rearrangement is an inversion that includes DOT1L exons 1016. The functional significance is undetermined.
TMTC2	0	MSKCC-DMP	P-0024889-T01-IM6	TEK-TMTC2 fusion	yes	unknown		out of frame	TEK (NM_000459) - TMTC2 (NM_152588) rearrangement: t(9;12)(p21.2;q21.31)(chr9:g.27168693::chr12:g.83239788) Note: The TEK - TMTC2 rearrangement is a translocation that results in the fusion of TEK exons 1-3 with TMTC2 exons 2-12. The functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0024889-T01-IM6	TEK-TMTC2 fusion	yes	unknown		out of frame	TEK (NM_000459) - TMTC2 (NM_152588) rearrangement: t(9;12)(p21.2;q21.31)(chr9:g.27168693::chr12:g.83239788) Note: The TEK - TMTC2 rearrangement is a translocation that results in the fusion of TEK exons 1-3 with TMTC2 exons 2-12. The functional significance is undetermined.
FXYD6-FXYD2	0	MSKCC-DMP	P-0024919-T01-IM6	KMT2A-FXYD6-FXYD2 fusion	yes	unknown		unknown	KMT2A (NM_001197104)  - FXYD6-FXYD2 (NM_001204268) rearrangement: c.7363:KMT2A_c.-5-14181:FXYD6-FXYD2del Note: The KMT2A - FXYD6-FXYD2 rearrangement is a deletion that includes exons 1-27 of KMT2A, and the 5UTR of FXYD6-FXYD2. One of the breakpoints is within KMT2A exon 27. The functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0024919-T01-IM6	KMT2A-FXYD6-FXYD2 fusion	yes	unknown		unknown	KMT2A (NM_001197104)  - FXYD6-FXYD2 (NM_001204268) rearrangement: c.7363:KMT2A_c.-5-14181:FXYD6-FXYD2del Note: The KMT2A - FXYD6-FXYD2 rearrangement is a deletion that includes exons 1-27 of KMT2A, and the 5UTR of FXYD6-FXYD2. One of the breakpoints is within KMT2A exon 27. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0024919-T01-IM6	RAB30-CREBBP fusion	yes	unknown		unknown	RAB30 (NM_014488) - CREBBP (NM_004380) rearrangement: t(11;16)(q14.1;p13.3)(chr11:g.:82712245::chr16:g.3900638) Note: The RAB30 - CREBBP rearrangement is a translocation that results in the fusion of RAB30 exons 1-2 with CREBBP exons 2-31. One of the breakpoints is within CREBBP exon 2. The functional significance is undetermined.
RAB30	0	MSKCC-DMP	P-0024919-T01-IM6	RAB30-CREBBP fusion	yes	unknown		unknown	RAB30 (NM_014488) - CREBBP (NM_004380) rearrangement: t(11;16)(q14.1;p13.3)(chr11:g.:82712245::chr16:g.3900638) Note: The RAB30 - CREBBP rearrangement is a translocation that results in the fusion of RAB30 exons 1-2 with CREBBP exons 2-31. One of the breakpoints is within CREBBP exon 2. The functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0025010-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 3-21) : c.2302-67:FGFR2_c.238-6757:BICC1inv Note: The FGFR2 -BICC1 fusion is predicted to be in-frame and includes the FGFR2 kinase domain.
FGFR2	0	MSKCC-DMP	P-0025010-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 3-21) : c.2302-67:FGFR2_c.238-6757:BICC1inv Note: The FGFR2 -BICC1 fusion is predicted to be in-frame and includes the FGFR2 kinase domain.
ERG	0	MSKCC-DMP	P-0025044-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  Fusion (TMPRSS2 exon1 fused with ERG exon 2) :  c.56-2252:TMPRSS2_c.18+17253:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025044-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  Fusion (TMPRSS2 exon1 fused with ERG exon 2) :  c.56-2252:TMPRSS2_c.18+17253:ERGdel
MSH2	0	MSKCC-DMP	P-0025047-T01-IM6	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) Rearrangement : c.1386+5577_c.2030del Note: The MSH2 Rearrangement results in the intragenic deletion of exons 9-13 of MSH2. One of the breakpoints is within exon13. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0025049-T01-IM6	SUZ12-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - SUZ12 (NM_015355) Rearrangement :  c.4297:NF1_c.1874+641:SUZ12del Note: The NF1-SUZ12 Rearrangement results in the fusion of exons 1-32 of NF1 with exon 16 of SUZ12. The breakpoint in NF1 is within exon 32. Its functional significance is undetermined.
SUZ12	0	MSKCC-DMP	P-0025049-T01-IM6	SUZ12-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - SUZ12 (NM_015355) Rearrangement :  c.4297:NF1_c.1874+641:SUZ12del Note: The NF1-SUZ12 Rearrangement results in the fusion of exons 1-32 of NF1 with exon 16 of SUZ12. The breakpoint in NF1 is within exon 32. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007043-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused to ERG exons  2-10  ): c.126+1017:TMPRSS2_c.18+3315:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0007043-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused to ERG exons  2-10  ): c.126+1017:TMPRSS2_c.18+3315:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0024947-T01-IM6	PRC1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q26.1;q22.3)(chr15:g.91513764::chr21:g.42870521) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
PRC1	0	MSKCC-DMP	P-0024947-T01-IM6	PRC1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q26.1;q22.3)(chr15:g.91513764::chr21:g.42870521) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0024987-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1868_c.316del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0025024-T01-IM6	SPG11-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: c.5576:TP53BP1_chr15:g.44950938inv Note: The TP53BP1 rearrangement is an inversion of exons 1-26. One of the breakpoints is within exon 26. Its functional significance is undetermined.
SPG11	0	MSKCC-DMP	P-0025024-T01-IM6	SPG11-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: c.5576:TP53BP1_chr15:g.44950938inv Note: The TP53BP1 rearrangement is an inversion of exons 1-26. One of the breakpoints is within exon 26. Its functional significance is undetermined.
C15orf41	0	MSKCC-DMP	P-0025024-T01-IM6	CARD11-C15orf41 fusion	yes	unknown		unknown	CARD11 (NM_032415) rearrangemnt: t(7;15)(p22.2;q14)(chr7:g.2972275::chr15:g.36753672) Note: The CARD11 rearrangement is a translocation involving exon 11. Its functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0025024-T01-IM6	CARD11-C15orf41 fusion	yes	unknown		unknown	CARD11 (NM_032415) rearrangemnt: t(7;15)(p22.2;q14)(chr7:g.2972275::chr15:g.36753672) Note: The CARD11 rearrangement is a translocation involving exon 11. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0025024-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.889-3831_c.969inv Note: The NF1 rearrangement is an inversion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025030-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 with ERG exons 2-10): c.55+2244:TMPRSS2_c.19-2444:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025030-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 with ERG exons 2-10): c.55+2244:TMPRSS2_c.19-2444:ERGdel
ARID2	0	MSKCC-DMP	P-0024598-T02-IM6	ARID2-intragenic	yes	unknown		out of frame	ARID2 (NM_152641) rearrangement: c.705+38_c.1580+893del Note: The ARID2 rearrangement results in the deletion of exons 7-12. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024598-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4407:ERG_c.56-37:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion with breakpoints in intron 1 of ERG and intron 1 of TMPRSS2. A more complex event not fully characterized by this assay may lead to the canonical TMPRSS2-ERG fusion. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0024598-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4407:ERG_c.56-37:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion with breakpoints in intron 1 of ERG and intron 1 of TMPRSS2. A more complex event not fully characterized by this assay may lead to the canonical TMPRSS2-ERG fusion. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0024598-T02-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.349+291_c.56-17inv Note: The TMPRSS2 rearrangement results in an inversion of exons 2-3. The functional significance is undetermined.
CDK2	0	MSKCC-DMP	P-0024661-T01-IM6	ERBB3-CDK2 fusion	yes	unknown		unknown	ERBB3 (NM_001982) - CDK2 (NM_001798) rearrangement: c.192:ERBB3_c.589-107:CDK2dup Note: The ERBB3 - CDK2 rearrangement is a duplication that results in the fusion of ERBB3 exons 1-2 with CDK2 exons 5-7. One of the breakpoints is within ERBB3 exon 2. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0024661-T01-IM6	ERBB3-CDK2 fusion	yes	unknown		unknown	ERBB3 (NM_001982) - CDK2 (NM_001798) rearrangement: c.192:ERBB3_c.589-107:CDK2dup Note: The ERBB3 - CDK2 rearrangement is a duplication that results in the fusion of ERBB3 exons 1-2 with CDK2 exons 5-7. One of the breakpoints is within ERBB3 exon 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024903-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion : c.56-3842:TMPRSS2_c.40-40790:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0024903-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion : c.56-3842:TMPRSS2_c.40-40790:ERGdel
ALK	0	MSKCC-DMP	P-0024907-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons  1-2 fused to ALK exons 20 -29): c.209-990:EML4_c.3173-483:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0024907-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons  1-2 fused to ALK exons 20 -29): c.209-990:EML4_c.3173-483:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
CMAS	0	MSKCC-DMP	P-0024995-T01-IM6	BRAF-CMAS fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: t(7;12)(q34;p12.1)(chr7:g.140488046::chr12:g.22218755) Note: The BRAF rearrangement is a translocation with a breakpoint in intron 8 and may include the kinase domain. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0024995-T01-IM6	BRAF-CMAS fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: t(7;12)(q34;p12.1)(chr7:g.140488046::chr12:g.22218755) Note: The BRAF rearrangement is a translocation with a breakpoint in intron 8 and may include the kinase domain. The functional significance is undetermined.
FURIN	0	MSKCC-DMP	P-0025000-T01-IM6	IL10-FURIN fusion	yes	unknown		unknown	IL10 (NM_000572) rearrangement: t(1;15)(q32.1;q26.1)(chr1:g.206942213::chr15:g.91379749) Note: The IL10 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.
IL10	0	MSKCC-DMP	P-0025000-T01-IM6	IL10-FURIN fusion	yes	unknown		unknown	IL10 (NM_000572) rearrangement: t(1;15)(q32.1;q26.1)(chr1:g.206942213::chr15:g.91379749) Note: The IL10 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.
LOC101928135	0	MSKCC-DMP	P-0025000-T01-IM6	MITF-LOC101928135 fusion	yes	unknown		unknown	MITF (NM_198159) rearrangement: chr3:g.34891227_c.666+108inv Note: The MITF rearrangement results in the inversion of exons 1-4. The functional significance is undetermined.
MITF	0	MSKCC-DMP	P-0025000-T01-IM6	MITF-LOC101928135 fusion	yes	unknown		unknown	MITF (NM_198159) rearrangement: chr3:g.34891227_c.666+108inv Note: The MITF rearrangement results in the inversion of exons 1-4. The functional significance is undetermined.
MYRIP	0	MSKCC-DMP	P-0025000-T01-IM6	ATR-MYRIP fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: chr3:g.39857396_c.1026inv Note: The ATR rearrangement results in the inversion of exons 4-47. One of the breakpoints is within exon 4. The functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0025000-T01-IM6	ATR-MYRIP fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: chr3:g.39857396_c.1026inv Note: The ATR rearrangement results in the inversion of exons 4-47. One of the breakpoints is within exon 4. The functional significance is undetermined.
BCL6	0	MSKCC-DMP	P-0025000-T01-IM6	BCL6-intragenic	yes	unknown		out of frame	BCL6 (NM_001706) rearrangement: c.1977+473_c.162-80dup Note: The BCL6 rearrangement results in the duplication of exons 4-9. The functional significance is undetermined.
GSX2	0	MSKCC-DMP	P-0025001-T01-IM6	PDGFRA-GSX2 fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: chr4:g.55026895_c.2321inv Note: The PDGFRA rearrangement results in the inversion of exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
PDGFRA	0	MSKCC-DMP	P-0025001-T01-IM6	PDGFRA-GSX2 fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: chr4:g.55026895_c.2321inv Note: The PDGFRA rearrangement results in the inversion of exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0025002-T01-IM6	TLE1-ATM fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: t(9;11)(q21.31;q22.3)(chr9:g.83867679::chr11:g.108190712) Note: The ATM rearrangement is a translocation with a breakpoint in exon 44. The functional significance is undetermined.
TLE1	0	MSKCC-DMP	P-0025002-T01-IM6	TLE1-ATM fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: t(9;11)(q21.31;q22.3)(chr9:g.83867679::chr11:g.108190712) Note: The ATM rearrangement is a translocation with a breakpoint in exon 44. The functional significance is undetermined.
MS4A15	0	MSKCC-DMP	P-0025092-T01-IM6	EGFL7-MS4A15 fusion	yes	unknown		out of frame	EGFL7 (NM_201446) rearrangement: t(9;11)(q34.3;q12.2)(chr9:g.139563132::chr11:g.60541820) Note: The EGFL7 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
EGFL7	0	MSKCC-DMP	P-0025092-T01-IM6	EGFL7-MS4A15 fusion	yes	unknown		out of frame	EGFL7 (NM_201446) rearrangement: t(9;11)(q34.3;q12.2)(chr9:g.139563132::chr11:g.60541820) Note: The EGFL7 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025097-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4281:TMPRSS2_c.40-57110:ERGdel Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0025097-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4281:TMPRSS2_c.40-57110:ERGdel Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).
ROS1	0	MSKCC-DMP	P-0025107-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149782204::chr6:g.117647170) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0025107-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149782204::chr6:g.117647170) Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
KAZN	0	MSKCC-DMP	P-0025071-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement : c.226+83445:KAZN_c.3176:SPENinv Note: The SPEN Rearrangement is an inversion with a breakpoint in exon 11 of SPEN. This event was detected in the background of other events involving SPEN. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0025071-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement : c.226+83445:KAZN_c.3176:SPENinv Note: The SPEN Rearrangement is an inversion with a breakpoint in exon 11 of SPEN. This event was detected in the background of other events involving SPEN. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0025071-T01-IM6	ZNF733P-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) Rearrangement : c.890-22:EGFR_chr7:g.61055640inv Note: The  EGFR  Rearrangement is an inversion with the breakpoint in intron7. Its functional significance is undetermined.
ZNF733P	0	MSKCC-DMP	P-0025071-T01-IM6	ZNF733P-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) Rearrangement : c.890-22:EGFR_chr7:g.61055640inv Note: The  EGFR  Rearrangement is an inversion with the breakpoint in intron7. Its functional significance is undetermined.
NEURL1	0	MSKCC-DMP	P-0025176-T01-IM6	ABL1-NEURL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) - NEURL (NM_004210) rearrangement: t(9;10)(q34.12; q24.33)(chr9:g.133760386::chr10:g.105305536) Note: The ABL1 - NEURL rearrangement is a translocation that results in the fusion of ABL1 exon 11 with NEURL exon 2. One of the breakpoints is within ABL1 exon 11. The functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0025176-T01-IM6	ABL1-NEURL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) - NEURL (NM_004210) rearrangement: t(9;10)(q34.12; q24.33)(chr9:g.133760386::chr10:g.105305536) Note: The ABL1 - NEURL rearrangement is a translocation that results in the fusion of ABL1 exon 11 with NEURL exon 2. One of the breakpoints is within ABL1 exon 11. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0025176-T01-IM6	PCSK1-POLE fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(5;12)(q15;q24.33)(chr5:g.95682436::chr12:g.133210987) Note: The POLE rearrangement is a translocation with a breakpoint within POLE intron 42. The functional significance is undetermined.
PCSK1	0	MSKCC-DMP	P-0025176-T01-IM6	PCSK1-POLE fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(5;12)(q15;q24.33)(chr5:g.95682436::chr12:g.133210987) Note: The POLE rearrangement is a translocation with a breakpoint within POLE intron 42. The functional significance is undetermined.
COMMD1	0	MSKCC-DMP	P-0025176-T01-IM6	MTOR-COMMD1 fusion	yes	unknown		unknown	MTOR (NM_004958) - COMMD1 (NM_152516) rearrangement: t(1;2)(p36.22;p15)(chr1:g.11187048::chr2:g.62259442) Note: The MTOR - COMMD1 rearrangement is a translocation with breakpoints within MTOR intron 45 and COMMD1 intron 2. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0025176-T01-IM6	MTOR-COMMD1 fusion	yes	unknown		unknown	MTOR (NM_004958) - COMMD1 (NM_152516) rearrangement: t(1;2)(p36.22;p15)(chr1:g.11187048::chr2:g.62259442) Note: The MTOR - COMMD1 rearrangement is a translocation with breakpoints within MTOR intron 45 and COMMD1 intron 2. The functional significance is undetermined.
GRM8	0	MSKCC-DMP	P-0025176-T01-IM6	BRAF-GRM8 fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: chr7:g.126063024_c.980+1766:BRAFdel Note: The BRAF rearrangement is a deletion of BRAF exons 8-18, including the kinase domain. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0025176-T01-IM6	BRAF-GRM8 fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: chr7:g.126063024_c.980+1766:BRAFdel Note: The BRAF rearrangement is a deletion of BRAF exons 8-18, including the kinase domain. The functional significance is undetermined.
PARP10	0	MSKCC-DMP	P-0025176-T01-IM6	RECQL4-PARP10 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - PARP10 (NM_032789) rearrangement: c.278:RECQL4_c.798:PARP10del Note: The RECQL4 - PARP10 rearrangement is a deletion that results in the fusion of RECQL4 exon 4 - PARP10 exon 5. Both breakpoints are within exon. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0025176-T01-IM6	RECQL4-PARP10 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - PARP10 (NM_032789) rearrangement: c.278:RECQL4_c.798:PARP10del Note: The RECQL4 - PARP10 rearrangement is a deletion that results in the fusion of RECQL4 exon 4 - PARP10 exon 5. Both breakpoints are within exon. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0024631-T01-IM6	KRT86-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.888_chr12:g.52691392inv Note: The KMT2D rearrangement results in the inversion of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
KRT86	0	MSKCC-DMP	P-0024631-T01-IM6	KRT86-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.888_chr12:g.52691392inv Note: The KMT2D rearrangement results in the inversion of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
ATP1B2	0	MSKCC-DMP	P-0024631-T01-IM6	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: chr17:g.7554166_c.10del Note: The TP53 rearrangement results in the deletion of exons 2-11. One of the breakpoints is within exon 2. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0024631-T01-IM6	TP53-ATP1B2 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: chr17:g.7554166_c.10del Note: The TP53 rearrangement results in the deletion of exons 2-11. One of the breakpoints is within exon 2. The functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0024867-T01-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: c.1255-712_c.1222inv Note: The AXIN1 rearrangement results in the inversion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0024867-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.9483_c.4660+2595dup Note: The KMT2C rearrangement results in the duplication of exons 32-41. One of the breakpoints is within exon 41. The functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0025086-T01-IM6	RNF144A-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: t(2;12)(p25.2;q13.3)(chr2:g.7076725::chr12:g.57864177) Note: The GLI1 rearrangement is a translocation with a breakpoint in exon 12. The functional significance is undetermined.
RNF144A	0	MSKCC-DMP	P-0025086-T01-IM6	RNF144A-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: t(2;12)(p25.2;q13.3)(chr2:g.7076725::chr12:g.57864177) Note: The GLI1 rearrangement is a translocation with a breakpoint in exon 12. The functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0025086-T01-IM6	CD53-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: t(1;16)(p13.3;p13.3)(chr1:g.111333805::chr16:g.347118) Note: The AXIN1 rearrangement is a translocation with a breakpoint is exon 7. The functional significance is undetermined.
CD53	0	MSKCC-DMP	P-0025086-T01-IM6	CD53-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: t(1;16)(p13.3;p13.3)(chr1:g.111333805::chr16:g.347118) Note: The AXIN1 rearrangement is a translocation with a breakpoint is exon 7. The functional significance is undetermined.
GALNTL6	0	MSKCC-DMP	P-0025087-T01-IM6	FAT1-GALNTL6 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.173406850_c.3099:FAT1del Note: The FAT1 rearrangement is a deletion of exons 2-27. One of the breakpoins is within exon 2.
FAT1	0	MSKCC-DMP	P-0025087-T01-IM6	FAT1-GALNTL6 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.173406850_c.3099:FAT1del Note: The FAT1 rearrangement is a deletion of exons 2-27. One of the breakpoins is within exon 2.
INADL	0	MSKCC-DMP	P-0025139-T01-IM6	JAK1-INADL fusion	yes	unknown		unknown	JAK1 (NM_002227) - INADL (NM_176877) rearrangement: c.2535:JAK1_c.4032+5742:INADLinv Note: The JAK1 - INADL rearrangement is an inversion which results in the fusion of JAK1 exons 1-18 with INADL exons 31-41. One of the breakpoints is within JAK1 exon 18. Its functional significance is undetermined.
JAK1	0	MSKCC-DMP	P-0025139-T01-IM6	JAK1-INADL fusion	yes	unknown		unknown	JAK1 (NM_002227) - INADL (NM_176877) rearrangement: c.2535:JAK1_c.4032+5742:INADLinv Note: The JAK1 - INADL rearrangement is an inversion which results in the fusion of JAK1 exons 1-18 with INADL exons 31-41. One of the breakpoints is within JAK1 exon 18. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025139-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.-56-2374:TMPRSS2_c.39+3700:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the non canonical fusion of TMPRSS2 exons 1 with ERG exons 4-10
TMPRSS2	0	MSKCC-DMP	P-0025139-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.-56-2374:TMPRSS2_c.39+3700:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the non canonical fusion of TMPRSS2 exons 1 with ERG exons 4-10
VCX3B	0	MSKCC-DMP	P-0025139-T01-IM6	BCOR-VCX3B fusion	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.1107:BCOR_chrX:g.8440800del Note: The BCOR rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0025139-T01-IM6	BCOR-VCX3B fusion	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.1107:BCOR_chrX:g.8440800del Note: The BCOR rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
TSHR	0	MSKCC-DMP	P-0025144-T01-IM6	TSHR-intragenic	yes	unknown		unknown	TSHR (NM_000369) rearrangement: c.445_c.545+1767del Note: The TSHR rearrangement is an intragenic deletion of exons 5-6. One of the breakpoints is within exon 5. Its functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0025144-T01-IM6	PAX8-intragenic	yes	unknown		in frame	PAX8 (NM_003466) rearrangement: c.25+15154_c.1189+1729dup Note: The PAX8 rearrangement is an intragenic duplication of exons 3-10. Its functional significance is undetermined.
SARS2	0	MSKCC-DMP	P-0025149-T01-IM6	AKT2-SARS2 fusion	yes	unknown		out of frame	SARS2 (NM_017827) - AKT2 (NM_001626) rearrangement: c.363+1679:SARS2_c.47-28:AKT2dup Note: The SARS2 - AKT2 rearrangement is a duplication which results in the fusion of SARS2 exons 1-2 with AKT2 exons 3-14. This includes the kinase domain of AKT2. its functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0025149-T01-IM6	AKT2-SARS2 fusion	yes	unknown		out of frame	SARS2 (NM_017827) - AKT2 (NM_001626) rearrangement: c.363+1679:SARS2_c.47-28:AKT2dup Note: The SARS2 - AKT2 rearrangement is a duplication which results in the fusion of SARS2 exons 1-2 with AKT2 exons 3-14. This includes the kinase domain of AKT2. its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025150-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 3-10): c.127-1226:TMPRSS2_c.18+10530:ERGdel Note: The TMPRSS2 - ERG rearrangement is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0025150-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 3-10): c.127-1226:TMPRSS2_c.18+10530:ERGdel Note: The TMPRSS2 - ERG rearrangement is predicted to be in-frame.
LOC728175	0	MSKCC-DMP	P-0025153-T01-IM6	FAT1-LOC728175 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.185165018_c.13397dup Note: The FAT1 rearrangement results in the duplication of exon 27. One of the breakpoints is within exon 27. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0025153-T01-IM6	FAT1-LOC728175 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: chr4:g.185165018_c.13397dup Note: The FAT1 rearrangement results in the duplication of exon 27. One of the breakpoints is within exon 27. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0025187-T02-IM6	NOX3-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: t(6;16)(q25.3;q22.3)(chr6:g.156231802::chr16:g.72992119) Note: The ZFHX3 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
NOX3	0	MSKCC-DMP	P-0025187-T02-IM6	NOX3-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: t(6;16)(q25.3;q22.3)(chr6:g.156231802::chr16:g.72992119) Note: The ZFHX3 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0025187-T02-IM6	KCNU1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(8;20)(p11.23;q13.33)(chr8:g.36806047::chr20:g.62323185) Note: The RTEL1 rearrangement is a translocation with a breakpoint in exon 28. The functional significance is undetermined.
KCNU1	0	MSKCC-DMP	P-0025187-T02-IM6	KCNU1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(8;20)(p11.23;q13.33)(chr8:g.36806047::chr20:g.62323185) Note: The RTEL1 rearrangement is a translocation with a breakpoint in exon 28. The functional significance is undetermined.
SESN3	0	MSKCC-DMP	P-0025197-T01-IM6	SIK3-SESN3 fusion	yes	unknown		unknown	SIK3 (NM_025164) - SESN3 (NM_144665) rearrangement: c.100-66582:SIK3_c.380:SESN3del Note: The SIK3 - SESN3 rearrangement is a deletion that results in the fusion of SIK3 exon 1 with SESN3 exon 4-10. One of the breakpoints is within SESN3 exon 4. The functional significance is undetermined.
SIK3	0	MSKCC-DMP	P-0025197-T01-IM6	SIK3-SESN3 fusion	yes	unknown		unknown	SIK3 (NM_025164) - SESN3 (NM_144665) rearrangement: c.100-66582:SIK3_c.380:SESN3del Note: The SIK3 - SESN3 rearrangement is a deletion that results in the fusion of SIK3 exon 1 with SESN3 exon 4-10. One of the breakpoints is within SESN3 exon 4. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0025198-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.3077_chrX:g.77133337del Note: The ATRX rearrangement results in the deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
MAGT1	0	MSKCC-DMP	P-0025198-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.3077_chrX:g.77133337del Note: The ATRX rearrangement results in the deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0025250-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused to BICC1 exons 16-21): c.2302-956:FGFR2_c.2182-297:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2. This particular fusion has been reported in intrahepatic cholangiocarcinomas (Arai Y et al. Hepatology. 2014 Apr;59(4):1427-34. PMID: 24122810)
FGFR2	0	MSKCC-DMP	P-0025250-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused to BICC1 exons 16-21): c.2302-956:FGFR2_c.2182-297:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2. This particular fusion has been reported in intrahepatic cholangiocarcinomas (Arai Y et al. Hepatology. 2014 Apr;59(4):1427-34. PMID: 24122810)
PARK2	0	MSKCC-DMP	P-0025273-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) rearrangement: c.7+48_c.535-65122del Note: The PARK2 rearrangement is an intragenic deletion of exons 2-4. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0025200-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (AML4 exons 1-5 fused with ALK exons 20-29, including the kinase domain of ALK): c.667+6687:EML4_c.3172+29:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame.
EML4	0	MSKCC-DMP	P-0025200-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (AML4 exons 1-5 fused with ALK exons 20-29, including the kinase domain of ALK): c.667+6687:EML4_c.3172+29:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame.
RICTOR	0	MSKCC-DMP	P-0025207-T01-IM6	FYB-RICTOR fusion	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.4853:RICTOR_chr5:g.39130440inv Note: The RICTOR rearrangement is an inversion of exons 1-36. One of the breakpoints is within exon 36. Its functional significance is undetermined.
FYB	0	MSKCC-DMP	P-0025207-T01-IM6	FYB-RICTOR fusion	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.4853:RICTOR_chr5:g.39130440inv Note: The RICTOR rearrangement is an inversion of exons 1-36. One of the breakpoints is within exon 36. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0025215-T01-IM6	GEMIN5-RET fusion	yes	unknown		in frame	GEMIN5 (NM_015465) - RET (NM_020975) rearrangement: t(5;10)(q33.2;q11.21)(chr5:g.154274993::chr10:g.43611067) Note: The GEMIN5 - RET rearrangement is a translocation which results in the fusion of GEMIN5 exons 1-24 with RET exons 12-20. This includes the kinase domain of RET. Its functional significance is undetermined.
GEMIN5	0	MSKCC-DMP	P-0025215-T01-IM6	GEMIN5-RET fusion	yes	unknown		in frame	GEMIN5 (NM_015465) - RET (NM_020975) rearrangement: t(5;10)(q33.2;q11.21)(chr5:g.154274993::chr10:g.43611067) Note: The GEMIN5 - RET rearrangement is a translocation which results in the fusion of GEMIN5 exons 1-24 with RET exons 12-20. This includes the kinase domain of RET. Its functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0025216-T01-IM6	RHEBL1-KMT2D fusion	yes	unknown		unknown	RHEBL1 (NM_144593) - KMT2D (NM_003482) rearrangement: c.-1442:RHEBL1_c.4053:KMT2Ddel Note: The RHEBL1 - KMT2D rearrangement is a deletion which may result in the fusion of the Promoter region of RHEBL1 with KMT2D exons 13-54. One of the breakpoints is within KMT2D exon 13. Its functional significance is undetermined.
RHEBL1	0	MSKCC-DMP	P-0025216-T01-IM6	RHEBL1-KMT2D fusion	yes	unknown		unknown	RHEBL1 (NM_144593) - KMT2D (NM_003482) rearrangement: c.-1442:RHEBL1_c.4053:KMT2Ddel Note: The RHEBL1 - KMT2D rearrangement is a deletion which may result in the fusion of the Promoter region of RHEBL1 with KMT2D exons 13-54. One of the breakpoints is within KMT2D exon 13. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0006424-T03-IM6	PUM1-KMT2C fusion	yes	unknown		unknown	PUM1 (NM_001020658) - KMT2C (NM_170606): t(1;7)(p35.2;q36.1)(chr1:g.31532327::chr7:g.151873311) Note: The PUM1 - KMT2C rearrangement is a translocation that results in the fusion of PUM1 exons 1-2 with KMT2C exons 38-59. Both breakpoints are within exon. The functional significance is undetermined.
PUM1	0	MSKCC-DMP	P-0006424-T03-IM6	PUM1-KMT2C fusion	yes	unknown		unknown	PUM1 (NM_001020658) - KMT2C (NM_170606): t(1;7)(p35.2;q36.1)(chr1:g.31532327::chr7:g.151873311) Note: The PUM1 - KMT2C rearrangement is a translocation that results in the fusion of PUM1 exons 1-2 with KMT2C exons 38-59. Both breakpoints are within exon. The functional significance is undetermined.
KCNQ3	0	MSKCC-DMP	P-0025326-T01-IM6	DROSHA-KCNQ3 fusion	yes	unknown		out of frame	DROSHA (NM_013235) - KCNQ3 (NM_004519) rearrangement: t(5;8)(p13.3;q24.22)(chr5:g.31464126::chr8:g.133361970) Note: The DROSHA - KCNQ3 rearrangement is a translocation that results in the fusion of DROSHA exons 1-19 with KCNQ3 exons 2-15. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0025326-T01-IM6	DROSHA-KCNQ3 fusion	yes	unknown		out of frame	DROSHA (NM_013235) - KCNQ3 (NM_004519) rearrangement: t(5;8)(p13.3;q24.22)(chr5:g.31464126::chr8:g.133361970) Note: The DROSHA - KCNQ3 rearrangement is a translocation that results in the fusion of DROSHA exons 1-19 with KCNQ3 exons 2-15. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0025343-T01-IM6	GCNT2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - GCNT2 (NM_145655) rearrangement: t(6;17)(p24.3;q12)(chr6:g.10592776::chr17:g.37687185) Note: The CDK12 - GCNT2 rearrangement is a translocation with breakpoints within CDK12 exon 14 and GCNT2 intron 1. The functional significance is undetermined.
GCNT2	0	MSKCC-DMP	P-0025343-T01-IM6	GCNT2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - GCNT2 (NM_145655) rearrangement: t(6;17)(p24.3;q12)(chr6:g.10592776::chr17:g.37687185) Note: The CDK12 - GCNT2 rearrangement is a translocation with breakpoints within CDK12 exon 14 and GCNT2 intron 1. The functional significance is undetermined.
NRG3	0	MSKCC-DMP	P-0025346-T01-IM6	PTEN-NRG3 fusion	yes	unknown		unknown	NRG3 (NM_001010848) - PTEN (NM_000314) rearrangement: c.954-176223:NRG3_c.1026+82:PTENinv Note: The NRG3 - PTEN rearrangement is an inversion that includes NRG3 exons 3-9 and PTEN exons 1-8. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0025346-T01-IM6	PTEN-NRG3 fusion	yes	unknown		unknown	NRG3 (NM_001010848) - PTEN (NM_000314) rearrangement: c.954-176223:NRG3_c.1026+82:PTENinv Note: The NRG3 - PTEN rearrangement is an inversion that includes NRG3 exons 3-9 and PTEN exons 1-8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0001242-T05-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.127-1488:TMPRSS2_c.18+9956:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0001242-T05-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.127-1488:TMPRSS2_c.18+9956:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
CNTN1	0	MSKCC-DMP	P-0025398-T01-IM6	ARID2-CNTN1 fusion	yes	unknown		unknown	ARID2 (NM_152641) - CNTN1 (NM_001843) rearrangement: c.575:ARID2_c.1380-720:CNTN1dup Note: The ARID2 - CNTN1 rearrangement is a duplication that results in the fusion of ARID2 exons 1-5 to CNTN1 exons 11-24. One of the breakpoints is within ARID2 exon 5. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0025398-T01-IM6	ARID2-CNTN1 fusion	yes	unknown		unknown	ARID2 (NM_152641) - CNTN1 (NM_001843) rearrangement: c.575:ARID2_c.1380-720:CNTN1dup Note: The ARID2 - CNTN1 rearrangement is a duplication that results in the fusion of ARID2 exons 1-5 to CNTN1 exons 11-24. One of the breakpoints is within ARID2 exon 5. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0025401-T01-IM6	NEUROD2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.1615:CDK12_chr17:g.37748036del Note: The CDK12 rearrangement is a deletion of exons 2-14. One of the breakpoints is within exon 2. The functional significance is undetermined.
NEUROD2	0	MSKCC-DMP	P-0025401-T01-IM6	NEUROD2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.1615:CDK12_chr17:g.37748036del Note: The CDK12 rearrangement is a deletion of exons 2-14. One of the breakpoints is within exon 2. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0025401-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.2970+68:ERBB2_chr17:g.37884495del Note: The ERBB2 rearrangement is a deletion of exons 25-27. The functional significance is undetermined.
CUBN	0	MSKCC-DMP	P-0000252-T01-IM3	RET-CUBN fusion	yes	unknown		unknown	null
RET	0	MSKCC-DMP	P-0000252-T01-IM3	RET-CUBN fusion	yes	unknown		unknown	null
KIF5B	0	MSKCC-DMP	P-0000252-T01-IM3	RET-KIF5B fusion	yes	unknown		in frame	RET (NM_020975) Inversion (c.2136+413_KIF5B:c.1726-153inv)
RET	0	MSKCC-DMP	P-0000252-T01-IM3	RET-KIF5B fusion	yes	unknown		in frame	RET (NM_020975) Inversion (c.2136+413_KIF5B:c.1726-153inv)
TACC3	0	MSKCC-DMP	P-0000289-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  TACC3 (NM_006342) Duplication (c.1128_c.1592-1871dup)
FGFR3	0	MSKCC-DMP	P-0000289-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  TACC3 (NM_006342) Duplication (c.1128_c.1592-1871dup)
MALT1	0	MSKCC-DMP	P-0000509-T02-IM5	IQCF5-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) Rearrangement : t(3;18)(3p21.2;18q21.32)(chr3:g.51906799::chr18:g.56376920) Note: The MALT1 (NM_006785) Rearrangement results in the possible truncation of  MALT1. Its functional significance is undetermined.
IQCF5	0	MSKCC-DMP	P-0000509-T02-IM5	IQCF5-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) Rearrangement : t(3;18)(3p21.2;18q21.32)(chr3:g.51906799::chr18:g.56376920) Note: The MALT1 (NM_006785) Rearrangement results in the possible truncation of  MALT1. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0001204-T02-IM5	APC-intragenic	yes	unknown		unknown	c.8155_g.112183450del  The APC (NM_000038) rearrangement results in the partial intragenic deletion of exon 16 extending into the 3-prime UTR.
CDH1	0	MSKCC-DMP	P-0001260-T01-IM3	CDH1-intragenic	yes	unknown		in frame	None
ERG	0	MSKCC-DMP	P-0001319-T03-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11) : c.55+746:TMPRSS2_c.40-60506:ERG_del
TMPRSS2	0	MSKCC-DMP	P-0001319-T03-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11) : c.55+746:TMPRSS2_c.40-60506:ERG_del
NOTCH3	0	MSKCC-DMP	P-0001384-T01-IM3	WDR89-NOTCH3 fusion	yes	unknown		unknown	null
WDR89	0	MSKCC-DMP	P-0001384-T01-IM3	WDR89-NOTCH3 fusion	yes	unknown		unknown	null
EGFR	0	MSKCC-DMP	P-0001445-T01-IM3	EGFR-intragenic	yes	unknown		in frame	None
TMPRSS2	0	MSKCC-DMP	P-0001449-T02-IM5	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Fusion  (TMPRSS2 exon 1 fused with ETV1 exon 6) :  t(21;7)(q22.3;p21.2)(chr21:g.42871485::chr7:g.14003184)
ETV1	0	MSKCC-DMP	P-0001449-T02-IM5	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Fusion  (TMPRSS2 exon 1 fused with ETV1 exon 6) :  t(21;7)(q22.3;p21.2)(chr21:g.42871485::chr7:g.14003184)
STK11	0	MSKCC-DMP	P-0001539-T01-IM3	STK11-intragenic	yes	unknown		out of frame	None
ATRX	0	MSKCC-DMP	P-0001701-T01-IM3	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) duplication: c.4843_c.5134+5045dup The ATRX duplication is a rearrangement event which results in  duplication of exon 19.
DIP2B	0	MSKCC-DMP	P-0001784-T01-IM3	NOTCH4-DIP2B fusion	yes	unknown		unknown	DIP2B (NM_173602) - NOTCH4 (NM_004557) Translocation :  t(12;6)(q13.12;p21.32)(chr12:g.50969571::chr6:32163293)
NOTCH4	0	MSKCC-DMP	P-0001784-T01-IM3	NOTCH4-DIP2B fusion	yes	unknown		unknown	DIP2B (NM_173602) - NOTCH4 (NM_004557) Translocation :  t(12;6)(q13.12;p21.32)(chr12:g.50969571::chr6:32163293)
BRAF	0	MSKCC-DMP	P-0001832-T02-IM6	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) fusion (AGK exon 1 fused in-frame to BRAF exons 8-18): c.102-572:AGK_c.981-222:BRAFinv Note: The AGK - BRAF fusion includes the kinase domain of BRAF.
AGK	0	MSKCC-DMP	P-0001832-T02-IM6	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) fusion (AGK exon 1 fused in-frame to BRAF exons 8-18): c.102-572:AGK_c.981-222:BRAFinv Note: The AGK - BRAF fusion includes the kinase domain of BRAF.
CTNNB1	0	MSKCC-DMP	P-0002395-T01-IM3	CTNNB1-intragenic	yes	unknown		unknown	null
TMPRSS2	0	MSKCC-DMP	P-0002398-T01-IM3	ARF4-TMPRSS2 fusion	yes	unknown		out of frame	ARF4 (NM_001660) - TMPRSS2 (NM_001135099) Translocation :   t(3;21)(p14.3;q22.3)(chr3:g.57572612::chr21:g.42867618) Note: ARF4 - TMPRSS2 translocation is a structural rearrangement in which  the first exon of ARF4 is fused to exons 3 to 14 of TMPRSS2
ARF4	0	MSKCC-DMP	P-0002398-T01-IM3	ARF4-TMPRSS2 fusion	yes	unknown		out of frame	ARF4 (NM_001660) - TMPRSS2 (NM_001135099) Translocation :   t(3;21)(p14.3;q22.3)(chr3:g.57572612::chr21:g.42867618) Note: ARF4 - TMPRSS2 translocation is a structural rearrangement in which  the first exon of ARF4 is fused to exons 3 to 14 of TMPRSS2
TMPRSS2	0	MSKCC-DMP	P-0002398-T01-IM3	ETV1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Translocation :   t(21;7)(q22.3;p21.2)(chr21:g.42867877::chr7:g.13988492) Note: TMPRSS2 - ETV1 is a structural rearrangement in which the first 2  exons of TMPRSS2 is fused to exons 6 to 12 of ETV1
ETV1	0	MSKCC-DMP	P-0002398-T01-IM3	ETV1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Translocation :   t(21;7)(q22.3;p21.2)(chr21:g.42867877::chr7:g.13988492) Note: TMPRSS2 - ETV1 is a structural rearrangement in which the first 2  exons of TMPRSS2 is fused to exons 6 to 12 of ETV1
DNMT1	0	MSKCC-DMP	P-0002436-T01-IM3	DNMT1-intragenic	yes	unknown		unknown	null exons 6-39 deleted
KIF5B	0	MSKCC-DMP	P-0002694-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	null Note: The KIF5B (NM_004521) - RET (NM_020975) rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20.
RET	0	MSKCC-DMP	P-0002694-T02-IM5	RET-KIF5B fusion	yes	unknown		in frame	null Note: The KIF5B (NM_004521) - RET (NM_020975) rearrangement event is an inversion which results in the fusion of KIF5B exons 1 to 15 and RET exons 12 to 20.
ERBB2	0	MSKCC-DMP	P-0002705-T01-IM3	C1orf87-ERBB2 fusion	yes	unknown		unknown	null Note: The ERBB2-C1orf87 reciprocal translocation is a rearrangement event which results in the fusion of ERBB2 exons 1 to   26 with C1orf87 exons 10 to 12.
C1orf87	0	MSKCC-DMP	P-0002705-T01-IM3	C1orf87-ERBB2 fusion	yes	unknown		unknown	null Note: The ERBB2-C1orf87 reciprocal translocation is a rearrangement event which results in the fusion of ERBB2 exons 1 to   26 with C1orf87 exons 10 to 12.
ERG	0	MSKCC-DMP	P-0002895-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null TMPRSS2 (NM_001135099) ERG (NM_182918) fusion: c.18+8871:ERG_c.56-1160:TMPRSS2del
TMPRSS2	0	MSKCC-DMP	P-0002895-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null TMPRSS2 (NM_001135099) ERG (NM_182918) fusion: c.18+8871:ERG_c.56-1160:TMPRSS2del
ERG	0	MSKCC-DMP	P-0002990-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion (TMPRSS2 exons 1 to 2 fused to ERG exons 4 to 10) : c.126+879:TMPRSS2_c.40-63033:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0002990-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion (TMPRSS2 exons 1 to 2 fused to ERG exons 4 to 10) : c.126+879:TMPRSS2_c.40-63033:ERGdel
BRCA2	0	MSKCC-DMP	P-0003108-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	null Note: The BRCA2 (NM_000059) intragenic rearrangement event is a deletion which affects the splice site of exon 11, potentially disabling the function of the gene.
HMHA1	0	MSKCC-DMP	P-0003108-T01-IM5	STK11-HMHA1 fusion	yes	unknown		unknown	null Note: The HMHA1 (NM_012292) - STK11 (NM_000455) rearrangement event is a deletion which results in the fusion of HMHA1 exons 1-2 and STK11 exons 1-9. Breakpoint on STK11 is within exon1. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0003108-T01-IM5	STK11-HMHA1 fusion	yes	unknown		unknown	null Note: The HMHA1 (NM_012292) - STK11 (NM_000455) rearrangement event is a deletion which results in the fusion of HMHA1 exons 1-2 and STK11 exons 1-9. Breakpoint on STK11 is within exon1. Its functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0003108-T01-IM5	AXL-intragenic	yes	unknown		unknown	null Note: The AXL (NM_021913) rearrangement event is an intragenic deletion which results in the deletion of exon 1, potentially disabling the function of the gene.
KLHL13	0	MSKCC-DMP	P-0003108-T01-IM5	RB1-KLHL13 fusion	yes	unknown		unknown	null Note: The RB1 (NM_000321) rearrangement event is a translocation which results in the truncation of RB1 excluding exons 26-27, potentially disabling the function of the gene.
RB1	0	MSKCC-DMP	P-0003108-T01-IM5	RB1-KLHL13 fusion	yes	unknown		unknown	null Note: The RB1 (NM_000321) rearrangement event is a translocation which results in the truncation of RB1 excluding exons 26-27, potentially disabling the function of the gene.
MED23	0	MSKCC-DMP	P-0003271-T01-IM5	TNFAIP3-MED23 fusion	yes	unknown		unknown	null
TNFAIP3	0	MSKCC-DMP	P-0003271-T01-IM5	TNFAIP3-MED23 fusion	yes	unknown		unknown	null
TNFAIP3	0	MSKCC-DMP	P-0003271-T01-IM5	PERP-TNFAIP3 fusion	yes	unknown		unknown	null
PERP	0	MSKCC-DMP	P-0003271-T01-IM5	PERP-TNFAIP3 fusion	yes	unknown		unknown	null
MX1	0	MSKCC-DMP	P-0003395-T01-IM5	TMPRSS2-MX1 fusion	yes	unknown		unknown	null
TMPRSS2	0	MSKCC-DMP	P-0003395-T01-IM5	TMPRSS2-MX1 fusion	yes	unknown		unknown	null
RB1	0	MSKCC-DMP	P-0003466-T01-IM5	RB1-intragenic	yes	unknown		out of frame	null Note: The RB1 (NM_000321) rearrangement event results in the deletion of RB1 exons 25-26, potentially disabling the function of the gene.
FLT3	0	MSKCC-DMP	P-0003540-T01-IM5	FLT3-intragenic	yes	unknown		unknown	c.368+690_c.347del Note: The FLT3 (NM_004119) rearrangement event is a deletion which affects the splice site of exon 3, potentially disabling the function of the gene.
IGF1R	0	MSKCC-DMP	P-0003779-T01-IM5	IGF1R-intragenic	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: c.954-1844_1009del Note: The IGF1R(NM_000875) rearrangement results in the intragenic deletion of exon 4 . The breakpoint is within exon 4.Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0004285-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-2530:TMPRSS2_c.18+10159:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0004285-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-2530:TMPRSS2_c.18+10159:ERGdel
LATS2	0	MSKCC-DMP	P-0004401-T01-IM5	ATP8A2-LATS2 fusion	yes	unknown		out of frame	ATP8A2 (NM_016529) - LATS2( NM_01457) rearrangement: c.76+23397:ATP8A2_c.2773-21:LATS2inv The ATP8A2 (NM_016529) - LATS2( NM_01457) rearrangement (4420299 bp) is an inversion  that results in the fusion of exon1 of ATP8A2 with exon 8 of LATS2. The functional significance is undetermined.
ATP8A2	0	MSKCC-DMP	P-0004401-T01-IM5	ATP8A2-LATS2 fusion	yes	unknown		out of frame	ATP8A2 (NM_016529) - LATS2( NM_01457) rearrangement: c.76+23397:ATP8A2_c.2773-21:LATS2inv The ATP8A2 (NM_016529) - LATS2( NM_01457) rearrangement (4420299 bp) is an inversion  that results in the fusion of exon1 of ATP8A2 with exon 8 of LATS2. The functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0004414-T01-IM5	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-4 fused with ROS1 exons 32-43): t(6;20) (q22.1; q13.12)(chr6:g.117651952::chr20:g.43957039) The SDC4-ROS1 fusion is a translocation that results in the fusion of exons 1-4 of SDC4 with exons 32-43 of ROS1. (PMID 25870798)
ROS1	0	MSKCC-DMP	P-0004414-T01-IM5	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-4 fused with ROS1 exons 32-43): t(6;20) (q22.1; q13.12)(chr6:g.117651952::chr20:g.43957039) The SDC4-ROS1 fusion is a translocation that results in the fusion of exons 1-4 of SDC4 with exons 32-43 of ROS1. (PMID 25870798)
ERBB3	0	MSKCC-DMP	P-0004545-T01-IM5	SEMA3A-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) - SEMA3A (NM_006080) translocation: t(12,7)(q13.2; q21.11) (chr12:g.56481635::chr7:g.83729009) The ERBB3 (NM_001982) - SEMA3A (NM_006080) rearrangement is a translocation, possibly resulting in a truncated ERBB3. The functional significance is undetermined.
SEMA3A	0	MSKCC-DMP	P-0004545-T01-IM5	SEMA3A-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) - SEMA3A (NM_006080) translocation: t(12,7)(q13.2; q21.11) (chr12:g.56481635::chr7:g.83729009) The ERBB3 (NM_001982) - SEMA3A (NM_006080) rearrangement is a translocation, possibly resulting in a truncated ERBB3. The functional significance is undetermined.
DIS3	0	MSKCC-DMP	P-0004545-T01-IM5	PIBF1-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) -PIBF1(NM_006346) rearrangement: c.387-54:DIS3_c.672+1677:PIBF1del The DIS3 (NM_014953) -PIBF1(NM_006346) rearrangement is a deletion of exons 1-2 of DIS3, potentially disabling the function of DIS3. The functional significance is undetermined.
PIBF1	0	MSKCC-DMP	P-0004545-T01-IM5	PIBF1-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) -PIBF1(NM_006346) rearrangement: c.387-54:DIS3_c.672+1677:PIBF1del The DIS3 (NM_014953) -PIBF1(NM_006346) rearrangement is a deletion of exons 1-2 of DIS3, potentially disabling the function of DIS3. The functional significance is undetermined.
ACCN1	0	MSKCC-DMP	P-0004551-T01-IM5	STAT3-ACCN1 fusion	yes	unknown		in frame	STAT3  (NM_139276) -AACN1(NM_001094) Rearangement : c.556-173146:ACCN1_c.1281+104:STAT3del Note: STAT3  (NM_139276) -AACN1(NM_001094) Rearangement  results in the fusion of exons 1 to 14 of STAT3 with 2 to 10 of ACCN1.Its functional significance is undetermined
STAT3	0	MSKCC-DMP	P-0004551-T01-IM5	STAT3-ACCN1 fusion	yes	unknown		in frame	STAT3  (NM_139276) -AACN1(NM_001094) Rearangement : c.556-173146:ACCN1_c.1281+104:STAT3del Note: STAT3  (NM_139276) -AACN1(NM_001094) Rearangement  results in the fusion of exons 1 to 14 of STAT3 with 2 to 10 of ACCN1.Its functional significance is undetermined
FH	0	MSKCC-DMP	P-0004616-T01-IM5	FH-intragenic	yes	unknown		unknown	FH(NM_000143) : Rearrangement : c.740_738+2del Note: The FH(NM_000143) : Rearrangement  results in the intragenic deletion of exon 6 of FH.The breakpoint in FH is within exon 6.Its functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0004616-T01-IM5	MLL2-intragenic	yes	unknown		unknown	MLL2(NM_003482) Rearrangement : c.10217_7184del Note: The MLL2(NM_003482) Rearrangement results in the intragenic deletion of exons 31 to 34.The breakpoints are within exon 31 and 34 respectively.Its functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0004659-T01-IM5	NBN-intragenic	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.1295_c.1914+531dup The NBN (NM_002485) rearrangement is an intragenic duplication of exons 10-12. One of the breakpoints is within exon 10. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0004860-T01-IM5	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.235-44962_c.652del The ERBB4 (NM_005235) rearrangement is an intrangenic deletion of exons 3-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
C19orf12	0	MSKCC-DMP	P-0004867-T01-IM5	AKT2-C19orf12 fusion	yes	unknown		out of frame	C19orf12 (NM_001031726) - AKT2 (NM_001626) rearrangement: c.193+680:C19orf12_c.709-62:AKT2dup Note: The C19orf12 (NM_001031726) - AKT2 (NM_001626) rearrangement event is a duplication which results in an out of frame fusion of C19orf12 exons 1-2 with AKR2 exons 9-14. Its functional significance is unknown.
AKT2	0	MSKCC-DMP	P-0004867-T01-IM5	AKT2-C19orf12 fusion	yes	unknown		out of frame	C19orf12 (NM_001031726) - AKT2 (NM_001626) rearrangement: c.193+680:C19orf12_c.709-62:AKT2dup Note: The C19orf12 (NM_001031726) - AKT2 (NM_001626) rearrangement event is a duplication which results in an out of frame fusion of C19orf12 exons 1-2 with AKR2 exons 9-14. Its functional significance is unknown.
ST6GALNAC5	0	MSKCC-DMP	P-0005085-T01-IM5	FUBP1-ST6GALNAC5 fusion	yes	unknown		unknown	FUBP1(NM_003902) Rearrangement : chr15:g.23699654_c.1822:FUBP1dup Note: The FUBP1(NM_003902) Rearrangement results in the duplication of exons 19 to 20 of FUBP1.The breakpoint is within exon 19. Its functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0005085-T01-IM5	FUBP1-ST6GALNAC5 fusion	yes	unknown		unknown	FUBP1(NM_003902) Rearrangement : chr15:g.23699654_c.1822:FUBP1dup Note: The FUBP1(NM_003902) Rearrangement results in the duplication of exons 19 to 20 of FUBP1.The breakpoint is within exon 19. Its functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0005091-T01-IM5	CARD11-intragenic	yes	unknown		out of frame	CARD11 (NM_032415) rearrangement: c.8-3148_c.684+36dup The CARD11 (NM_032415) rearrangement is an intragenic duplicaion of exons 3-5. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0005106-T01-IM5	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3096-970_c.3610inv The CDK12 (NM_016507) rearrangement is an intragenic inversion of exons 12 and 13. One of the breakpoints is within exon 13. The functional significance is undetermined.
NUB1	0	MSKCC-DMP	P-0005220-T01-IM5	MLL3-NUB1 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement: g.15107551_c.62794inv Note: MLL3 rearrangement is an inversion event where exons 1 to 36 are inverted. Internal breakpoint is within exon 36. Its functional significance is not determined.
MLL3	0	MSKCC-DMP	P-0005220-T01-IM5	MLL3-NUB1 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement: g.15107551_c.62794inv Note: MLL3 rearrangement is an inversion event where exons 1 to 36 are inverted. Internal breakpoint is within exon 36. Its functional significance is not determined.
MLL3	0	MSKCC-DMP	P-0005220-T01-IM5	DPP6-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement: c.6102_g.153526905inv Note: MLL3 rearrangement is an inversion event where exons 36 to 59 are inverted. Internal breakpoint is within exon 36. Its functional significance is not determined.
DPP6	0	MSKCC-DMP	P-0005220-T01-IM5	DPP6-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement: c.6102_g.153526905inv Note: MLL3 rearrangement is an inversion event where exons 36 to 59 are inverted. Internal breakpoint is within exon 36. Its functional significance is not determined.
CIC	0	MSKCC-DMP	P-0005393-T01-IM5	CSMD1-CIC fusion	yes	unknown		unknown	CSMD1 (NM_033225) - CIC (NM_015125) rearrangement: t(8;19)(p23.2;q13.2)(chr8:g.4567111::chr19:g.42792003) The CSMD1 (NM_033225) - CIC (NM_015125) rearrangement is a translocation which results in the fusion of CSMD1 exon 1 to CIC exons 6-20. One of the breakpoints is within exons 6 of CIC. The functional significance is undetermined.
CSMD1	0	MSKCC-DMP	P-0005393-T01-IM5	CSMD1-CIC fusion	yes	unknown		unknown	CSMD1 (NM_033225) - CIC (NM_015125) rearrangement: t(8;19)(p23.2;q13.2)(chr8:g.4567111::chr19:g.42792003) The CSMD1 (NM_033225) - CIC (NM_015125) rearrangement is a translocation which results in the fusion of CSMD1 exon 1 to CIC exons 6-20. One of the breakpoints is within exons 6 of CIC. The functional significance is undetermined.
PLK2	0	MSKCC-DMP	P-0005582-T01-IM5	PDE4D-PLK2 fusion	yes	unknown		in frame	PLK2 (NM_006622) -PDE4D (NM_001104631) rearrangement: c.1625+27: PLK2_c.456-334412:PDE4Ddup The PLK2 (NM_006622) -PDE4D (NM_001104631) rearrangement is a duplication which leads to the in frame fusion of  PLK2 exons 1-11 to PDE4D  exons 2-15
PDE4D	0	MSKCC-DMP	P-0005582-T01-IM5	PDE4D-PLK2 fusion	yes	unknown		in frame	PLK2 (NM_006622) -PDE4D (NM_001104631) rearrangement: c.1625+27: PLK2_c.456-334412:PDE4Ddup The PLK2 (NM_006622) -PDE4D (NM_001104631) rearrangement is a duplication which leads to the in frame fusion of  PLK2 exons 1-11 to PDE4D  exons 2-15
PTPRS	0	MSKCC-DMP	P-0005613-T01-IM5	ACER1-PTPRS fusion	yes	unknown		unknown	PTRPRS (NM_002850) - ACER1 (NM_133492) rearrangement : c.4986:PTPRS_c.93+5133:ACER1inv Note: The PTRPRS (NM_002850) - ACER1 (NM_133492) rearrangement event results in the inversion of PTPRS exons 1-32. One of the breakpoints is within PTPRS exon32.
ACER1	0	MSKCC-DMP	P-0005613-T01-IM5	ACER1-PTPRS fusion	yes	unknown		unknown	PTRPRS (NM_002850) - ACER1 (NM_133492) rearrangement : c.4986:PTPRS_c.93+5133:ACER1inv Note: The PTRPRS (NM_002850) - ACER1 (NM_133492) rearrangement event results in the inversion of PTPRS exons 1-32. One of the breakpoints is within PTPRS exon32.
PTPRS	0	MSKCC-DMP	P-0005613-T01-IM5	UNC5D-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - UNC5D (NM_080872) rearrangement : t(8;19)(8p12;19p13.3)(chr8:g.35547181::chr19:g.5211611) Note: The PTPRS (NM_002850) - UNC5D (NM_080872) rearrangement is a translocation which results in the fusion of PTPRS exons 1-33 with UNC5D exons 8-17. One of the breakpoints is within PTPRS exon33.
UNC5D	0	MSKCC-DMP	P-0005613-T01-IM5	UNC5D-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - UNC5D (NM_080872) rearrangement : t(8;19)(8p12;19p13.3)(chr8:g.35547181::chr19:g.5211611) Note: The PTPRS (NM_002850) - UNC5D (NM_080872) rearrangement is a translocation which results in the fusion of PTPRS exons 1-33 with UNC5D exons 8-17. One of the breakpoints is within PTPRS exon33.
IGF1R	0	MSKCC-DMP	P-0005818-T01-IM5	IGF1R-intragenic	yes	unknown		unknown	IGF1R (NM_000875)  Rearrangement:  c.640+53564_808dup Note: The IGF1R (NM_000875)  rearrangement results in the intragenic duplication of exon3 of IGF1R . Its functional significance is undetermined.
EPHA3	0	MSKCC-DMP	P-0005818-T01-IM5	EPHA3-intragenic	yes	unknown		unknown	EPHA3 (NM_005233) Rearrangement :  c.267_996dup Note: The EPHA3 (NM_005233) rearrangement results in the intragenic duplication of exon3 to exon5 of EPHA3. The breakpoints are within exon3 and exon5 respectively.  Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0005959-T01-IM5	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : chr16:g.72795737_c.5172del Note: The ZFHX3 (NM_006885) rearrangement results in the intragenic deletion of exons 1 to 9 of ZFHX3. The breakpoint is within exon 9. Its functional significance is undetermined.
PIK3CA	0	MSKCC-DMP	P-0005985-T01-IM5	PIK3CA-intragenic	yes	unknown		unknown	PIK3CA (NM_006218) rearrangement: c.1539+3416_c.2324del The PIK3CA (NM_006218) rearrangement is an intragenic deletion of exons 10-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0006072-T01-IM5	RSAD1-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement : c.2741:MAP3K14_chr17:g.48567110inv Note: The MAP3K14 (NM_003954) rearrangement event results in the inversion of MAP3K14 exons 1-16. One of the breakpoints is within MAP3K14 exon16.
RSAD1	0	MSKCC-DMP	P-0006072-T01-IM5	RSAD1-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement : c.2741:MAP3K14_chr17:g.48567110inv Note: The MAP3K14 (NM_003954) rearrangement event results in the inversion of MAP3K14 exons 1-16. One of the breakpoints is within MAP3K14 exon16.
RARA	0	MSKCC-DMP	P-0006137-T01-IM5	APPBP2-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - APPBP2 (NM_0063) rearrangement: c.650:RARA_c.139-2641:APPBP2del The RARA (NM_000964) - APPBP2 (NM_0063) rearrangement is a deletion of RARA exons 6-9. One of the breakpoints is within exon 6 of RARA. The functional significance is unknown.
APPBP2	0	MSKCC-DMP	P-0006137-T01-IM5	APPBP2-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - APPBP2 (NM_0063) rearrangement: c.650:RARA_c.139-2641:APPBP2del The RARA (NM_000964) - APPBP2 (NM_0063) rearrangement is a deletion of RARA exons 6-9. One of the breakpoints is within exon 6 of RARA. The functional significance is unknown.
UNCX	0	MSKCC-DMP	P-0006221-T02-IM5	MITF-UNCX fusion	yes	unknown		unknown	MITF (NM_198159) rearrangement : t(3;7)(p13;p22.3)(chr3:g.70008546::chr7:g.1244112)  Note: MITF (NM_198159) rearrangement event is a translocation which leads to the truncation of MITF exons 9-10. One of the breakpoints is within MITF exon9.
MITF	0	MSKCC-DMP	P-0006221-T02-IM5	MITF-UNCX fusion	yes	unknown		unknown	MITF (NM_198159) rearrangement : t(3;7)(p13;p22.3)(chr3:g.70008546::chr7:g.1244112)  Note: MITF (NM_198159) rearrangement event is a translocation which leads to the truncation of MITF exons 9-10. One of the breakpoints is within MITF exon9.
BRCA2	0	MSKCC-DMP	P-0006245-T02-IM5	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement :  c.793+502_1531dup Note: The BRCA2 (NM_000059) rearrangement results in the partial duplication of exon 10. The breakpoint is within exon 10.  Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0006247-T01-IM5	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-2170_557-2689inv Note: The TMPRSS2 (NM_001135099) rearrangement results in the inversion of exons 2 to 5 of TMPRSS2. While the canonical TMPRSS2-ERG fusion is not detected in this sample, due to the way MSK-IMPACT captures DNA, this event might lead to a TMPRSS2-ERG fusion with further DNA rearrangements.
SMARCA4	0	MSKCC-DMP	P-0006297-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_00307) - LDLR (NM_000527) rearrangement : c.4520:SMARCA4_c.1186+572:LDLRdel SMARCA4 (NM_00307) - LDLR (NM_000527) rearrangement event is a deletion which results in the fusion of SMARCA4 exon 1-29 and LDLR exon 9-18. Breakpoint on SMARCA4 is within exon 29. Its functional significance is not determined
LDLR	0	MSKCC-DMP	P-0006297-T01-IM5	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_00307) - LDLR (NM_000527) rearrangement : c.4520:SMARCA4_c.1186+572:LDLRdel SMARCA4 (NM_00307) - LDLR (NM_000527) rearrangement event is a deletion which results in the fusion of SMARCA4 exon 1-29 and LDLR exon 9-18. Breakpoint on SMARCA4 is within exon 29. Its functional significance is not determined
PTEN	0	MSKCC-DMP	P-0006378-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) Rearrangement :  c.164+31_chr10:g.89738911del Note: The PTEN (NM_000314) rearrangement  results in the intragenic deletion of exons 3 to 9 of PTEN. Its functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0006429-T01-IM5	TNIP2-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) -TNIP2 (NM_024309) rearrangement: c.2275-42:FGFR3_c.147:TNIP2inv The FGFR3 (NM_000142) -TNIP2 (NM_024309) rearrangement is a reciprocal inversion which leads to the fusion of FGFR3 exons 1-17 with TNIP2 exons 1-6, including the kinase domain of FGFR3. The functional significance is undetermined.
TNIP2	0	MSKCC-DMP	P-0006429-T01-IM5	TNIP2-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) -TNIP2 (NM_024309) rearrangement: c.2275-42:FGFR3_c.147:TNIP2inv The FGFR3 (NM_000142) -TNIP2 (NM_024309) rearrangement is a reciprocal inversion which leads to the fusion of FGFR3 exons 1-17 with TNIP2 exons 1-6, including the kinase domain of FGFR3. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0006442-T01-IM5	CAPZA3-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement : c.3779+35:PIK3C2G_chr12:g.18912315del Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of PIK3C2G exons 28-32.
CAPZA3	0	MSKCC-DMP	P-0006442-T01-IM5	CAPZA3-PIK3C2G fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement : c.3779+35:PIK3C2G_chr12:g.18912315del Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of PIK3C2G exons 28-32.
PAX8	0	MSKCC-DMP	P-0006442-T01-IM5	PAX8-intragenic	yes	unknown		out of frame	PAX8 (NM_003466) rearrangement : c.26-11156_1190-2615dup Note: The PAX8 (NM_003466) rearrangement event results in the intragenic duplication of PAX8 exons 3-10. The resulting transcript is predicted to be out of frame.
STAG2	0	MSKCC-DMP	P-0006644-T01-IM5	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement : c.158_3054-988dup Note: The STAG2 (NM_001042749) rearrangement event results in the duplication of STAG2 exons4-29. One of the breakpoints is within STAG2 exon4.
DNMT3A	0	MSKCC-DMP	P-0006670-T01-IM5	ASXL2-DNMT3A fusion	yes	unknown		unknown	ASXL2 (NM_018263) - DNMT3A (NM_022552) Rearrangement: c.2235:ASXL2_c.639+13202:DNMT3Adel Note: The ASXL2 (NM_018263) - DNMT3A (NM_022552) rearrangement results in the fusion of exons 1 to 12 of ASXL2 and exons 7 to 23 of  DNMT3A. One of the breakpoints is within exon 12 . Its functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0006670-T01-IM5	ASXL2-DNMT3A fusion	yes	unknown		unknown	ASXL2 (NM_018263) - DNMT3A (NM_022552) Rearrangement: c.2235:ASXL2_c.639+13202:DNMT3Adel Note: The ASXL2 (NM_018263) - DNMT3A (NM_022552) rearrangement results in the fusion of exons 1 to 12 of ASXL2 and exons 7 to 23 of  DNMT3A. One of the breakpoints is within exon 12 . Its functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0006809-T01-IM5	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) Rearrangement :  c.3431-1105_3812dup Note: The MGA (NM_001164273) rearrangement results in the duplication of exons 10 and 11. One of the breakpoints is within exon 11. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0006809-T01-IM5	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) Rearrangement : c.620-274_875+95dup Note: The KDM6A (NM_021140) Rearrangement results in the duplication of exons 8 to 10. Its functional significance is undetermined.
ERCC5	0	MSKCC-DMP	P-0006812-T01-IM5	ERCC5-intragenic	yes	unknown		unknown	ERCC5 (NM_000123) Rearrangement :  c.88+1135_1209dup Note: The ERCC5 (NM_000123) rearrangement  results in the duplication of exons 2 to 8 .One of the breakpoints is within exon 8. Its functional significance is undetermined.
RPS29	0	MSKCC-DMP	P-0006839-T01-IM5	MLL3-RPS29 fusion	yes	unknown		unknown	MLL3 (NM_170606) - RPS29 (NM_001030001) translocation : t(7;14)(q36.1;q21.3)(chr7:g.151873899::chr14:g.50046598) The MLL3 (NM_170606) and RPS29 (NM_001030001) rearrangement is translocation involving a breakpoint within MLL3 exon 38 and a breakpoint in intron2 of RPS29. Its functional significance is undetermined
MLL3	0	MSKCC-DMP	P-0006839-T01-IM5	MLL3-RPS29 fusion	yes	unknown		unknown	MLL3 (NM_170606) - RPS29 (NM_001030001) translocation : t(7;14)(q36.1;q21.3)(chr7:g.151873899::chr14:g.50046598) The MLL3 (NM_170606) and RPS29 (NM_001030001) rearrangement is translocation involving a breakpoint within MLL3 exon 38 and a breakpoint in intron2 of RPS29. Its functional significance is undetermined
DNMT1	0	MSKCC-DMP	P-0006842-T01-IM5	AP1M2-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - AP1M2 (NM_005498) rearrangement :  c.1036:DNMT1_c.-2215:AP1M2dup The DNMT1 (NM_001379) - AP1M2 (NM_005498) rearrangement is a duplication that results in the fusion of DNMT1 exons 1-15 with AP1M2 exons 1-12. One of the breakpoints is within exon15 of DNMT1 and the other breakpoint is 2kb before transcription start of AP1M2. Its functional significance is undetermined.
AP1M2	0	MSKCC-DMP	P-0006842-T01-IM5	AP1M2-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - AP1M2 (NM_005498) rearrangement :  c.1036:DNMT1_c.-2215:AP1M2dup The DNMT1 (NM_001379) - AP1M2 (NM_005498) rearrangement is a duplication that results in the fusion of DNMT1 exons 1-15 with AP1M2 exons 1-12. One of the breakpoints is within exon15 of DNMT1 and the other breakpoint is 2kb before transcription start of AP1M2. Its functional significance is undetermined.
C10orf76	0	MSKCC-DMP	P-0006869-T01-IM5	MDC1-C10orf76 fusion	yes	unknown		unknown	MDC1 (NM_014641) - C10orf76 (NM_024541) rearrangement: t(6;10)(p21.33;q24.32)(chr6:g.30671699::chr10:g.103741063) The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0006869-T01-IM5	MDC1-C10orf76 fusion	yes	unknown		unknown	MDC1 (NM_014641) - C10orf76 (NM_024541) rearrangement: t(6;10)(p21.33;q24.32)(chr6:g.30671699::chr10:g.103741063) The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0006869-T01-IM5	SPOCK1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(5;6)( q31.1;p21.33)(chr5:g.136020145::chr6:g.30671642) The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.
SPOCK1	0	MSKCC-DMP	P-0006869-T01-IM5	SPOCK1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(5;6)( q31.1;p21.33)(chr5:g.136020145::chr6:g.30671642) The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.
RBM24	0	MSKCC-DMP	P-0006869-T01-IM5	MDC1-RBM24 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5400:MDC1_chr6:g.17200957inv The MDC1 (NM_014641) rearrangement is an inversion (13470603 bp) which may result in a truncated MDC1. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0006869-T01-IM5	MDC1-RBM24 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5400:MDC1_chr6:g.17200957inv The MDC1 (NM_014641) rearrangement is an inversion (13470603 bp) which may result in a truncated MDC1. The functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0006913-T01-IM5	ZBP1-NCOA3 fusion	yes	unknown		unknown	NCOA3 (NM_181659) - ZBP1 (NM_030776) rearrangement : c.1832:NCOA3_c.35-191inv Note: NCOA3 (NM_181659) - ZBP1 (NM_030776) rearrangement is a inversion which results in the fusion of exon 1-12 of NCOA3 and exon 2-8 of ZBP1. One of breakpoints is within exon 12 of NCOA3. The functional significance is undetermined.
ZBP1	0	MSKCC-DMP	P-0006913-T01-IM5	ZBP1-NCOA3 fusion	yes	unknown		unknown	NCOA3 (NM_181659) - ZBP1 (NM_030776) rearrangement : c.1832:NCOA3_c.35-191inv Note: NCOA3 (NM_181659) - ZBP1 (NM_030776) rearrangement is a inversion which results in the fusion of exon 1-12 of NCOA3 and exon 2-8 of ZBP1. One of breakpoints is within exon 12 of NCOA3. The functional significance is undetermined.
GALNT11	0	MSKCC-DMP	P-0006913-T01-IM5	MLL3-GALNT11 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement : chr7:g.151756949_c.11670+985:MLL3del Note: MLL3 (NM_170606) rearrangement is a deletion which results in the deletion of exon 45-59 of MLL3. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0006913-T01-IM5	MLL3-GALNT11 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement : chr7:g.151756949_c.11670+985:MLL3del Note: MLL3 (NM_170606) rearrangement is a deletion which results in the deletion of exon 45-59 of MLL3. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0007000-T01-IM5	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement :  c.2159-464_2290del Note: The CREBBP (NM_004380) rearrangement event results in the intragenic deletion of CREBBP exons 12-13. One of the breakpoints is within CREBBP exon13.
ROS1	0	MSKCC-DMP	P-0007108-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944)  fusion (CD74 exons 1 to 6 fused with ROS1 exons 34 to 43)  :  t(5;6)(chr5q32;chr6q22.1)(chr5:g.149783704::chr6:g.117646132)
CD74	0	MSKCC-DMP	P-0007108-T01-IM5	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944)  fusion (CD74 exons 1 to 6 fused with ROS1 exons 34 to 43)  :  t(5;6)(chr5q32;chr6q22.1)(chr5:g.149783704::chr6:g.117646132)
CREBBP	0	MSKCC-DMP	P-0007114-T01-IM5	CREBBP-intragenic	yes	unknown		in frame	CREBBP (NM_004380) rearrangement :  c.2463+552_5173-158del Note: The CREBBP (NM_004380) rearrangement results in the intragenic deletion of exons 14 to 30. Its functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0007281-T01-IM5	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: c.*72_chr13.g.110398923del The IRS2 (NM_003749) rearrangement is a deletion with a breakpoint within the 3-UTR of IRS2. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0007413-T01-IM5	ROS1-intragenic	yes	unknown		unknown	ROS1(NM_002944.2) rearrangement : c.4602_c.4321+3009inv Note: The ROS1(NM_002944.2) rearrangement is an intragenic inversion involving exon 27-28. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0007587-T01-IM5	RARA-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) RARA (NM_000964) rearrangement: c.2011:CDK12_c.178+4818:RARAinv CDK12 (NM_016507) RARA (NM_000964) rearrangement results in the inversion of the genomic region on chromosome 17 involving exons 3-14 of CDK12 including the kinase domain and exons 1-2 of RARA. One of the breakpoints is within exon3 of CDK12 and its functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0007587-T01-IM5	RARA-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) RARA (NM_000964) rearrangement: c.2011:CDK12_c.178+4818:RARAinv CDK12 (NM_016507) RARA (NM_000964) rearrangement results in the inversion of the genomic region on chromosome 17 involving exons 3-14 of CDK12 including the kinase domain and exons 1-2 of RARA. One of the breakpoints is within exon3 of CDK12 and its functional significance is undetermined.
LOC284661	0	MSKCC-DMP	P-0007638-T01-IM5	MTOR-LOC284661 fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : chr1:g.4431259_c.4747:MTORinv Note: The MTOR (NM_004958) Rearrangement  results in the inversion of exons 33 TO 58 of MTOR.One of the breakpoints is within exon 33.Its functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0007638-T01-IM5	MTOR-LOC284661 fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : chr1:g.4431259_c.4747:MTORinv Note: The MTOR (NM_004958) Rearrangement  results in the inversion of exons 33 TO 58 of MTOR.One of the breakpoints is within exon 33.Its functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0007759-T01-IM5	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.615-1087_c.633del Note: The JAK2 (NM_004972) rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7 of JAK2. The functional significance is undetermined.
ZNF157	0	MSKCC-DMP	P-0007870-T02-IM6	ROS1-ZNF157 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement :  t(X;6)(p11.23;q22.1)(chrX:g.47262831;chr6:g.117659405) Note: The ROS1 Rearrangement is a translocation with a breakpoint in intron 30 of ROS1. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0007870-T02-IM6	ROS1-ZNF157 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement :  t(X;6)(p11.23;q22.1)(chrX:g.47262831;chr6:g.117659405) Note: The ROS1 Rearrangement is a translocation with a breakpoint in intron 30 of ROS1. Its functional significance is undetermined.
GPS2	0	MSKCC-DMP	P-0008168-T01-IM5	TNFSF12-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) rearrangement: c.634+21_chr17:g.439993dup The GPS2 (NM_004489) rearrangement is a duplication exons 1-7 of GPS2. The functional significance is undetermined.
TNFSF12	0	MSKCC-DMP	P-0008168-T01-IM5	TNFSF12-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) rearrangement: c.634+21_chr17:g.439993dup The GPS2 (NM_004489) rearrangement is a duplication exons 1-7 of GPS2. The functional significance is undetermined.
DCUN1D1	0	MSKCC-DMP	P-0008229-T01-IM5	DCUN1D1-intragenic	yes	unknown		unknown	DCUN1D1 (NM_020640) rearrangement : :c.603+49:DCUN1D1_chr3:g.182650622inv Note: The DCUN1D1 (NM_020640) rearrangement event results in the inversion of DCUN1D1 exon 6-7.
KIF5B	0	MSKCC-DMP	P-0008289-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20) : c.1726-824:KIF5B_c.2137-284:RETinv Note: The KIF5B (NM_004521) - RET (NM_020975) fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0008289-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20) : c.1726-824:KIF5B_c.2137-284:RETinv Note: The KIF5B (NM_004521) - RET (NM_020975) fusion is predicted to be in frame and includes the kinase domain of RET.
ETV6	0	MSKCC-DMP	P-0008434-T01-IM5	LMO3-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement : c.464-5719:ETV6_chr12:17005932dup Note: The ETV6 (NM_001987) rearrangement event is a duplication involving ETV6 exons 5-8.
LMO3	0	MSKCC-DMP	P-0008434-T01-IM5	LMO3-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement : c.464-5719:ETV6_chr12:17005932dup Note: The ETV6 (NM_001987) rearrangement event is a duplication involving ETV6 exons 5-8.
ATRX	0	MSKCC-DMP	P-0008434-T01-IM5	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement : c.3809+3373_3972del Note: The ATRX (NM_000489) rearrangement event results in the deletion of ATRX exons 11-12. One of the breakpoints is within ATRX exon12.
KDM5C	0	MSKCC-DMP	P-0008483-T01-IM5	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: c.817_c.1746+1318inv The KDM5C (NM_004187) rearrangement is an inversion of exons 7-12. One of the breakpoints is within exon 7. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0008538-T01-IM5	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement : c.381-56_608-3120dup Note: The RB1 (NM_000321) rearrangement event results in the duplication of exons 4-6 of RB1.
TMPRSS2	0	MSKCC-DMP	P-0008669-T01-IM5	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) in frame fusion (TMPRSS2 exon 1 fused with ETV1 exons 7-12): t(7;21)(p21.2;q22.3)(chr7:g.13999067::chr21:g.42872919)
ETV1	0	MSKCC-DMP	P-0008669-T01-IM5	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) in frame fusion (TMPRSS2 exon 1 fused with ETV1 exons 7-12): t(7;21)(p21.2;q22.3)(chr7:g.13999067::chr21:g.42872919)
SALL1	0	MSKCC-DMP	P-0008840-T01-IM5	ANKRD11-SALL1 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.1914_chr16:g.50994355del Note: The ANKRD11 (NM_013275) rearrangement is a deletion of exons 9-13. One of the breakpoints is within exon 9. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0008840-T01-IM5	ANKRD11-SALL1 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.1914_chr16:g.50994355del Note: The ANKRD11 (NM_013275) rearrangement is a deletion of exons 9-13. One of the breakpoints is within exon 9. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0008908-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904)  rearrangement: c.-48-1284_c.328del Note: The CTNNB1 (NM_001904)  rearrangement is an intragenic deletion of exons 2-4. One of the breakpoints is within exon4. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0008908-T01-IM5	TRPS1-NBN fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.1914+130_chr8:g.116744050inv Note: The NBN (NM_002485) rearrangement is an inversion of exons 1-12. The functional significance is undetermined.
TRPS1	0	MSKCC-DMP	P-0008908-T01-IM5	TRPS1-NBN fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.1914+130_chr8:g.116744050inv Note: The NBN (NM_002485) rearrangement is an inversion of exons 1-12. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0008948-T01-IM5	FAM20A-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement : t(17;19)(17q24.2;19p13.12)(chr17:g.66644028::chr19:g.15298008) Note: The NOTCH3 (NM_000435) Rearrangement is a translocation event that results in the possible truncation of exons 1 to 11 of NOTCH3. The breakpoint is within exon11 of NOTCH3. Its functional significance is undetermined.
FAM20A	0	MSKCC-DMP	P-0008948-T01-IM5	FAM20A-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement : t(17;19)(17q24.2;19p13.12)(chr17:g.66644028::chr19:g.15298008) Note: The NOTCH3 (NM_000435) Rearrangement is a translocation event that results in the possible truncation of exons 1 to 11 of NOTCH3. The breakpoint is within exon11 of NOTCH3. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0008948-T01-IM5	MCC-APC fusion	yes	unknown		unknown	APC (NM_000038) - MCC (NM_001085377) Rearrangement :  c.8117:APC_c.2449-2146:MCC inv Note: The APC (NM_000038) - MCC (NM_001085377) Rearrangement results in the fusion of exons 1-16 with exons 14-19 of MCC. The breakpoint in APC is within exon16. Its functional significance is undetermined.
MCC	0	MSKCC-DMP	P-0008948-T01-IM5	MCC-APC fusion	yes	unknown		unknown	APC (NM_000038) - MCC (NM_001085377) Rearrangement :  c.8117:APC_c.2449-2146:MCC inv Note: The APC (NM_000038) - MCC (NM_001085377) Rearrangement results in the fusion of exons 1-16 with exons 14-19 of MCC. The breakpoint in APC is within exon16. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009002-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons1-11) : c.56-190:TMPRSS2_c.-150+10247:ERGdel Note: In the TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion, one of the breakpoints in the the 5-UTR of ERG. Confirmation of the fusion using an alternate method is suggested if clinically indicative.
TMPRSS2	0	MSKCC-DMP	P-0009002-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons1-11) : c.56-190:TMPRSS2_c.-150+10247:ERGdel Note: In the TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion, one of the breakpoints in the the 5-UTR of ERG. Confirmation of the fusion using an alternate method is suggested if clinically indicative.
IRF1	0	MSKCC-DMP	P-0009109-T01-IM5	RAD50-IRF1 fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: chr5:g.131815508_c.2346:RAD50dup Note: The RAD50 (NM_005732) rearrangement results in the duplication of RAD50 exons 1-14. One of the breakpoints is within RAD50 exon 14. The functional significance of this rearrangement is undetermined.
RAD50	0	MSKCC-DMP	P-0009109-T01-IM5	RAD50-IRF1 fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: chr5:g.131815508_c.2346:RAD50dup Note: The RAD50 (NM_005732) rearrangement results in the duplication of RAD50 exons 1-14. One of the breakpoints is within RAD50 exon 14. The functional significance of this rearrangement is undetermined.
ERBB4	0	MSKCC-DMP	P-0009223-T01-IM5	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.557-7050_c.991del Note: The ERBB4 (NM_005235) rearrangement is an intragenic deletion of exons 5-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0009307-T01-IM5	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.2061+79_c.3115-25dup Note: The EGFR (NM_005228) rearrangement: is a duplication of exons 18-25. The duplication is predicted to be in frame and includes the kinase domain of EGFR.  (PMID: 26286086 )
CDKN2B	0	MSKCC-DMP	P-0009347-T01-IM5	CDKN2BAS-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement : c.341_chr9:g.22015263inv Note: The CDKN2B (NM_004936) rearrangement event results in the inversion of CDKN2B exons 1-2. One of the breakpoints is within CDKN2B exon2.
CDKN2BAS	0	MSKCC-DMP	P-0009347-T01-IM5	CDKN2BAS-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement : c.341_chr9:g.22015263inv Note: The CDKN2B (NM_004936) rearrangement event results in the inversion of CDKN2B exons 1-2. One of the breakpoints is within CDKN2B exon2.
ERG	0	MSKCC-DMP	P-0009374-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.127-1152:TMPRSS2_c.18+82:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009374-T02-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.127-1152:TMPRSS2_c.18+82:ERGdel
GATA3	0	MSKCC-DMP	P-0009431-T01-IM5	LOC100128811-GATA3 fusion	yes	unknown		unknown	GATA3 (NM_002051) rearrangement : c.192:GATA3_chr10:g.25463753inv Note: The GATA3 (NM_002051) rearrangement event results in the inversion of GATA3 exons 2-6.
LOC100128811	0	MSKCC-DMP	P-0009431-T01-IM5	LOC100128811-GATA3 fusion	yes	unknown		unknown	GATA3 (NM_002051) rearrangement : c.192:GATA3_chr10:g.25463753inv Note: The GATA3 (NM_002051) rearrangement event results in the inversion of GATA3 exons 2-6.
ERG	0	MSKCC-DMP	P-0009448-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009448-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel
BICC1	0	MSKCC-DMP	P-0009512-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) reciprocal rearrangement event is an inversion which results in the fusion of FGFR2 exons 1-17  with  BICC1 exons 3-21 . The fusion is predicted to be in frame and includes the kinase domain of FGFR2. FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement :  c.2302-914:FGFR2_c.238-9180:BICC1inv
FGFR2	0	MSKCC-DMP	P-0009512-T01-IM5	FGFR2-BICC1 fusion	yes	unknown		in frame	Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) reciprocal rearrangement event is an inversion which results in the fusion of FGFR2 exons 1-17  with  BICC1 exons 3-21 . The fusion is predicted to be in frame and includes the kinase domain of FGFR2. FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement :  c.2302-914:FGFR2_c.238-9180:BICC1inv
SH2B3	0	MSKCC-DMP	P-0009542-T01-IM5	TMEM116-SH2B3 fusion	yes	unknown		unknown	TMEM116 (NM_001193531) -SH2B3 (NM_005475) Rearrangement : c.315+1899:TMEM116_ c.540:SH2B3_inv Note: The  TMEM116 (NM_001193531) -SH2B3 (NM_005475) Rearrangement results in the fusion of  exons 1 to 7 of TMEM116 with exons 2 to 5 of SH2B3. One of the breakpoints is within exon2 .Its functional significance is undetermined.
TMEM116	0	MSKCC-DMP	P-0009542-T01-IM5	TMEM116-SH2B3 fusion	yes	unknown		unknown	TMEM116 (NM_001193531) -SH2B3 (NM_005475) Rearrangement : c.315+1899:TMEM116_ c.540:SH2B3_inv Note: The  TMEM116 (NM_001193531) -SH2B3 (NM_005475) Rearrangement results in the fusion of  exons 1 to 7 of TMEM116 with exons 2 to 5 of SH2B3. One of the breakpoints is within exon2 .Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0009626-T01-IM5	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : c.1131_1695+23010inv Note: The RB1 (NM_000321) Rearrangement results in the  intragenic inversion of exons 12-17. One of the breakpoints is within exon12. Its functional significance is undetermined,
PLCG2	0	MSKCC-DMP	P-0009699-T01-IM5	NUDT12-PLCG2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) Rearrangement : t(5;16)(q21.1;q23.3)(chr5:g.103163734::chr16:g. 81934177) Note: The PLCG2 (NM_002661) Rearrangement  results in the possible truncation of exons 14-33 of PLCG2. Its functional significance is undetermined.
NUDT12	0	MSKCC-DMP	P-0009699-T01-IM5	NUDT12-PLCG2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) Rearrangement : t(5;16)(q21.1;q23.3)(chr5:g.103163734::chr16:g. 81934177) Note: The PLCG2 (NM_002661) Rearrangement  results in the possible truncation of exons 14-33 of PLCG2. Its functional significance is undetermined.
KEAP1	0	MSKCC-DMP	P-0009714-T01-IM5	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) Rearrangement: c.1325+658_c.1617del Note: KEAP1 (NM_203500) Rearrangement results in the deletion of exons 4 and 5 of KEAP1. One of the breakpoints is within exon5 of KEAP1. Its functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0009740-T01-IM5	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.1926_c.1926+804del Note: The ARID1B (NM_020732) rearrangement is a an intragenic deletion involving exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0009757-T01-IM5	AGAP3-BRAF fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1222-2154:AGAP3_c.1140+237:BRAFinv Note: The AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement is a reciprocal inversion which results the fusion of AGAP3 exons 1-9 with BRAF exons 9-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. (PMID: 26314551)
AGAP3	0	MSKCC-DMP	P-0009757-T01-IM5	AGAP3-BRAF fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1222-2154:AGAP3_c.1140+237:BRAFinv Note: The AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement is a reciprocal inversion which results the fusion of AGAP3 exons 1-9 with BRAF exons 9-18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. (PMID: 26314551)
GPS2	0	MSKCC-DMP	P-0009867-T01-IM5	NEURL4-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) rearrangement : c.-560_119inv Note: The GPS2 (NM_004489) rearrangement event results in the inversion of GPS2 exons 1-3. One of the breakpoints is within GPS2 exon3.
NEURL4	0	MSKCC-DMP	P-0009867-T01-IM5	NEURL4-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) rearrangement : c.-560_119inv Note: The GPS2 (NM_004489) rearrangement event results in the inversion of GPS2 exons 1-3. One of the breakpoints is within GPS2 exon3.
ERG	0	MSKCC-DMP	P-0010071-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 to 2 fused to ERG exons 3 to 10) : c.126+1007:TMPRSS2_c.19-18011:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010071-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 to 2 fused to ERG exons 3 to 10) : c.126+1007:TMPRSS2_c.19-18011:ERGdel
MIR548H3	0	MSKCC-DMP	P-0010071-T01-IM5	TSC1-MIR548H3 fusion	yes	unknown		unknown	TSC1 (NM_000368) Rearrangement :  chr9:g.78358260_c.1964:TSC1inv Note: The TSC1 Rearrangement results in the inversion of exons15-23 of TSC1 .One of the breakpoints is within exon15. Its functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0010071-T01-IM5	TSC1-MIR548H3 fusion	yes	unknown		unknown	TSC1 (NM_000368) Rearrangement :  chr9:g.78358260_c.1964:TSC1inv Note: The TSC1 Rearrangement results in the inversion of exons15-23 of TSC1 .One of the breakpoints is within exon15. Its functional significance is undetermined.
CCRN4L	0	MSKCC-DMP	P-0010126-T01-IM5	FAT1-CCRN4L fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement : c.8570:FAT1_chr4:g.139877853del Note: The FAT1 rearrangement event results in the deletion of FAT1 exons 10-27. One of the breakpoints is within FAT1 exon10.
FAT1	0	MSKCC-DMP	P-0010126-T01-IM5	FAT1-CCRN4L fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement : c.8570:FAT1_chr4:g.139877853del Note: The FAT1 rearrangement event results in the deletion of FAT1 exons 10-27. One of the breakpoints is within FAT1 exon10.
TP53	0	MSKCC-DMP	P-0010243-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement :  c.375+81_c.*417del Note: The TP53  Rearrangement results in the intragenic deletion of exons 4-11 of TP53. Its functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0010334-T01-IM5	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement : c.46-3018_156del Note: The NFE2L2 rearrangement event results in the intragenic deletion of NFE2L2 exon2. One of the breakpoints is within NFE2L2.
JAK1	0	MSKCC-DMP	P-0010512-T01-IM5	ASB17-JAK1 fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement : c.2403+100:JAK1_chr1:g.76414149inv see note1 Note1: The JAK1 rearrangement event results in the inversion of JAK1 exons 1-17.
ASB17	0	MSKCC-DMP	P-0010512-T01-IM5	ASB17-JAK1 fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement : c.2403+100:JAK1_chr1:g.76414149inv see note1 Note1: The JAK1 rearrangement event results in the inversion of JAK1 exons 1-17.
YTHDC1	0	MSKCC-DMP	P-0010512-T01-IM5	JAK1-YTHDC1 fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement : t(1;4)(p31.3;q13.2)(chr1:g.65326020::chr4:g.69246009) see note2 Note2: The JAK1 rearrangement is a translocation which results in the truncation of JAK1 exons 9-25.
JAK1	0	MSKCC-DMP	P-0010512-T01-IM5	JAK1-YTHDC1 fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement : t(1;4)(p31.3;q13.2)(chr1:g.65326020::chr4:g.69246009) see note2 Note2: The JAK1 rearrangement is a translocation which results in the truncation of JAK1 exons 9-25.
RAB35	0	MSKCC-DMP	P-0010600-T01-IM5	RAB35-intragenic	yes	unknown		unknown	RAB35 (NM_006861) rearrangement: c.14_c.52+1593del Note: The RAB35 rearrangement is an intragenic deletion of exon1. One of the breakpoints is within exon 1. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0010704-T01-IM5	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) Rearrangement :  c.3150_c.4646del Note: The ARID2 (NM_152641) Rearrangement results in the partial deletion of exon 15 of ARID2. Both the breakpoints are within exon15. Its functional significance is undetermined.
N4BP1	0	MSKCC-DMP	P-0010711-T01-IM5	MAP3K1-N4BP1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921)Rearrangement : t(5;16)(q11.2;q12.1)(chr5:g.56171040::chr16:g.48661649) Note: The MAP3K1 Rearrangement is a translocation event which results in the possible truncation of exons 10-20 of MAP3K1. One of the breakpoints is within exon 10. The rearrangement includes the kinase domain of MAP3K1.
MAP3K1	0	MSKCC-DMP	P-0010711-T01-IM5	MAP3K1-N4BP1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921)Rearrangement : t(5;16)(q11.2;q12.1)(chr5:g.56171040::chr16:g.48661649) Note: The MAP3K1 Rearrangement is a translocation event which results in the possible truncation of exons 10-20 of MAP3K1. One of the breakpoints is within exon 10. The rearrangement includes the kinase domain of MAP3K1.
MLL2	0	MSKCC-DMP	P-0010740-T01-IM5	KCNC2-MLL2 fusion	yes	unknown		out of frame	KCNC2 (NM_139137) - MLL2 (NM_003482) rearrangement : c.687+77124:KCNC2_c.10355+12:MLL2del Note: The KCNC2-MLL2 rearrangement event is a deletion which results in the fusion of KCNC2 exons 1-2 with MLL2 exons 36-54.
KCNC2	0	MSKCC-DMP	P-0010740-T01-IM5	KCNC2-MLL2 fusion	yes	unknown		out of frame	KCNC2 (NM_139137) - MLL2 (NM_003482) rearrangement : c.687+77124:KCNC2_c.10355+12:MLL2del Note: The KCNC2-MLL2 rearrangement event is a deletion which results in the fusion of KCNC2 exons 1-2 with MLL2 exons 36-54.
CREBBP	0	MSKCC-DMP	P-0010740-T01-IM5	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement : c.527_798+3835del Note: The CREBBP rearrangement results in the intragenic deletion of CREBBP exon2. One of the breakpoints is within CREBBP exon2.
ERBB2	0	MSKCC-DMP	P-0010811-T01-IM5	C17orf37-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement : c.3049:ERBB2_chr17:g.37886757del ERBB2 rearrangement event results in the deletion of ERBB2 exons 25-27. One of the breakpoints is within ERBB2 exon25.
C17orf37	0	MSKCC-DMP	P-0010811-T01-IM5	C17orf37-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement : c.3049:ERBB2_chr17:g.37886757del ERBB2 rearrangement event results in the deletion of ERBB2 exons 25-27. One of the breakpoints is within ERBB2 exon25.
BRAF	0	MSKCC-DMP	P-0010945-T01-IM5	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) rearrangement :  c.101+12646:AGK_c.980+2552:BRAFinv Note: The AGK-BRAF rearrangement is an inversion which results in the fusion of AGK exons 1-2 with BRAF exons 8-18. The resulting fusion is predicted to be in-frame and includes the kinase domain of BRAF.
AGK	0	MSKCC-DMP	P-0010945-T01-IM5	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) rearrangement :  c.101+12646:AGK_c.980+2552:BRAFinv Note: The AGK-BRAF rearrangement is an inversion which results in the fusion of AGK exons 1-2 with BRAF exons 8-18. The resulting fusion is predicted to be in-frame and includes the kinase domain of BRAF.
ROS1	0	MSKCC-DMP	P-0010989-T01-IM5	EZR-ROS1 fusion	yes	unknown		out of frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 fused with ROS1 exons 33-43): c.1090+215:EZR_c.5366+763:ROS1del
EZR	0	MSKCC-DMP	P-0010989-T01-IM5	EZR-ROS1 fusion	yes	unknown		out of frame	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 fused with ROS1 exons 33-43): c.1090+215:EZR_c.5366+763:ROS1del
SETD2	0	MSKCC-DMP	P-0011183-T01-IM5	MAP4-SETD2 fusion	yes	unknown		out of frame	MAP4 (NM_002375) - SETD2 (NM_014159) rearrangement: c.2000-9359:MAP4_c.5278-1:SETD2del Note: The MAP4 - SETD2 rearrangement is a deletion that results in a fusion of MAP4 exons 1-8 with SETD2 exons 11-21. The functional significance is undetermined.
MAP4	0	MSKCC-DMP	P-0011183-T01-IM5	MAP4-SETD2 fusion	yes	unknown		out of frame	MAP4 (NM_002375) - SETD2 (NM_014159) rearrangement: c.2000-9359:MAP4_c.5278-1:SETD2del Note: The MAP4 - SETD2 rearrangement is a deletion that results in a fusion of MAP4 exons 1-8 with SETD2 exons 11-21. The functional significance is undetermined.
RGS2	0	MSKCC-DMP	P-0011201-T01-IM5	CDC73-RGS2 fusion	yes	unknown		unknown	CDC73 (NM_024529) rearrangement : c.926_chr1:192828282del Note: The CDC73 rearrangement event results in the deletion of CDC73 exons 1-10. One of the breakpoints is within CDC73 exon10.
CDC73	0	MSKCC-DMP	P-0011201-T01-IM5	CDC73-RGS2 fusion	yes	unknown		unknown	CDC73 (NM_024529) rearrangement : c.926_chr1:192828282del Note: The CDC73 rearrangement event results in the deletion of CDC73 exons 1-10. One of the breakpoints is within CDC73 exon10.
MLL2	0	MSKCC-DMP	P-0011290-T01-IM5	C7orf60-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) - C7orf60 (NM_152556) rearrangement : t(7;12)(q31.1;q13.12)(chr7:g.112507139::chr12:g.49420106) Note: The MLL2-C7orf60 rearrangement event in a translocation which results in the fusion of MLL2 exons 1-48 with C7orf60 exons 4-5.
C7orf60	0	MSKCC-DMP	P-0011290-T01-IM5	C7orf60-MLL2 fusion	yes	unknown		unknown	MLL2 (NM_003482) - C7orf60 (NM_152556) rearrangement : t(7;12)(q31.1;q13.12)(chr7:g.112507139::chr12:g.49420106) Note: The MLL2-C7orf60 rearrangement event in a translocation which results in the fusion of MLL2 exons 1-48 with C7orf60 exons 4-5.
VPS35	0	MSKCC-DMP	P-0011335-T01-IM5	CDH1-VPS35 fusion	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement :  chr16:g.46718598_c.391:CDH1del Note: The CDH1 (NM_004360) Rearrangement results in the deletion of exons 1-4 of CDH1. One of the breakpoints is within exon4 .Its functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0011335-T01-IM5	CDH1-VPS35 fusion	yes	unknown		unknown	CDH1 (NM_004360) Rearrangement :  chr16:g.46718598_c.391:CDH1del Note: The CDH1 (NM_004360) Rearrangement results in the deletion of exons 1-4 of CDH1. One of the breakpoints is within exon4 .Its functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0012134-T01-IM5	ADCY8-MYC fusion	yes	unknown		unknown	MYC (NM_002467) rearrangement: c.1245_chr8:g.132081862del Note: The MYC rearrangement is a deletion of MYC exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ADCY8	0	MSKCC-DMP	P-0012134-T01-IM5	ADCY8-MYC fusion	yes	unknown		unknown	MYC (NM_002467) rearrangement: c.1245_chr8:g.132081862del Note: The MYC rearrangement is a deletion of MYC exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012271-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-2767:TMPRSS2_c.39+13672:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012271-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-2767:TMPRSS2_c.39+13672:ERGdel
GRK5	0	MSKCC-DMP	P-0012288-T01-IM5	NSD1-GRK5 fusion	yes	unknown		unknown	NSD1 (NM_022455) - GRK5 (NM_005308) rearrangement: t(5;10)(q35.3; q26.1)(chr5:g.176721806::chr10:g.121033310) Note: The NSD1 - GRK5 rearrangement is a translocation which results in the antisense fusion of NDS1 exons 1 - 23 with GRK5 exon1 and may result in a truncated NSD1. The functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0012288-T01-IM5	NSD1-GRK5 fusion	yes	unknown		unknown	NSD1 (NM_022455) - GRK5 (NM_005308) rearrangement: t(5;10)(q35.3; q26.1)(chr5:g.176721806::chr10:g.121033310) Note: The NSD1 - GRK5 rearrangement is a translocation which results in the antisense fusion of NDS1 exons 1 - 23 with GRK5 exon1 and may result in a truncated NSD1. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0012306-T01-IM5	CDKN2BAS-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.22056567_c.377:CDKN2Ap14ARFdel Note: The CDKN2Ap14ARF  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.
CDKN2BAS	0	MSKCC-DMP	P-0012306-T01-IM5	CDKN2BAS-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.22056567_c.377:CDKN2Ap14ARFdel Note: The CDKN2Ap14ARF  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0012306-T01-IM5	CDKN2BAS-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.22056567_c.334:CDKN2Ap16INK4Adel Note: The CDKN2Ap16INK4A  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.
CDKN2BAS	0	MSKCC-DMP	P-0012306-T01-IM5	CDKN2BAS-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.22056567_c.334:CDKN2Ap16INK4Adel Note: The CDKN2Ap16INK4A  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.
ERG	0	MSKCC-DMP	P-0012375-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-59:TMPRSS2_c.40-58424:ERGdel Note: The TMPRSS2 - ERG (NM_004449) fusion is a deletion which results in the fusion of TMPRSS2 exon1 with ERG exons 4-11.
TMPRSS2	0	MSKCC-DMP	P-0012375-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-59:TMPRSS2_c.40-58424:ERGdel Note: The TMPRSS2 - ERG (NM_004449) fusion is a deletion which results in the fusion of TMPRSS2 exon1 with ERG exons 4-11.
SND1	0	MSKCC-DMP	P-0012395-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1152+27174:SND1_c.1140+581:BRAFinv Note: The SND1 - BRAF rearrangement is an inversion that results in an in frame fusion of SND1 exons 1-10 with BRAF exons 8-18, which include the BRAF kinase domain. This fusion may be associated with treatment sensitivities to MEK inhibitors  ( PMID: 25266736).
BRAF	0	MSKCC-DMP	P-0012395-T01-IM5	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1152+27174:SND1_c.1140+581:BRAFinv Note: The SND1 - BRAF rearrangement is an inversion that results in an in frame fusion of SND1 exons 1-10 with BRAF exons 8-18, which include the BRAF kinase domain. This fusion may be associated with treatment sensitivities to MEK inhibitors  ( PMID: 25266736).
NF2	0	MSKCC-DMP	P-0012456-T01-IM5	RASD2-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : c.1123-129_22:35955753inv Note: The NF2 Rearrangement results in the inversion of exons 12-16 of NF2. Its functional significance is undetermined.
RASD2	0	MSKCC-DMP	P-0012456-T01-IM5	RASD2-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : c.1123-129_22:35955753inv Note: The NF2 Rearrangement results in the inversion of exons 12-16 of NF2. Its functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0012557-T01-IM5	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) rearrangement: c.1836_c.*2723del Note: The TP63 rearrangement is a deletion of a part of exon 14. One of the breakpoints is within exon 14.
PIK3CD	0	MSKCC-DMP	P-0012577-T01-IM5	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.1689+30_c.2234+10inv Note: The PIK3CD rearrangement is an inversion of exons 14-17. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0012587-T01-IM5	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: c.46-6982_c.376del Note: The NFE2L2 rearrangement is an intragenic deletion of exons 2-3. One of the breakpoints is within exon 3.
KIF5B	0	MSKCC-DMP	P-0012648-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-335:RETinv
RET	0	MSKCC-DMP	P-0012648-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-335:RETinv
ERG	0	MSKCC-DMP	P-0012914-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+935:TMPRSS2_c.18+7096:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012914-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+935:TMPRSS2_c.18+7096:ERGdel
FLJ42709	0	MSKCC-DMP	P-0012914-T01-IM5	APC-FLJ42709 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.92746031_c.4532del Note: The APC rearrangement is a deletion which includes exons 1-16 of APC. One of the breakpoints is within exon 16 of APC. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0012914-T01-IM5	APC-FLJ42709 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.92746031_c.4532del Note: The APC rearrangement is a deletion which includes exons 1-16 of APC. One of the breakpoints is within exon 16 of APC. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012930-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-102:TMPRSS2_c.18+5504:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012930-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-102:TMPRSS2_c.18+5504:ERGdel
AKT1	0	MSKCC-DMP	P-0013077-T01-IM5	PLD4-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) Rearrangement: c.703-18:AKT1_chr14:g.105380826del Note: The AKT1 Rearrangement results in the deletion of exons 1-8 of AKT1.This includes the kinase domain of AKT1.
PLD4	0	MSKCC-DMP	P-0013077-T01-IM5	PLD4-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) Rearrangement: c.703-18:AKT1_chr14:g.105380826del Note: The AKT1 Rearrangement results in the deletion of exons 1-8 of AKT1.This includes the kinase domain of AKT1.
NCOR1	0	MSKCC-DMP	P-0013105-T01-IM5	USP28-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - USP8 (NM_020886) rearrangement: t(11;17)(q23.2;p12)(chr11:g.113706887::chr17:g.15968849) Note: The NCOR1 - USP28 rearrangement is a translocation that results in a fusion of NCOR1 exons 1-33 with USP28 exons 6-20. One of the breakpoints is within NCOR1 exon 33. The functional significance is undetermined.
USP28	0	MSKCC-DMP	P-0013105-T01-IM5	USP28-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - USP8 (NM_020886) rearrangement: t(11;17)(q23.2;p12)(chr11:g.113706887::chr17:g.15968849) Note: The NCOR1 - USP28 rearrangement is a translocation that results in a fusion of NCOR1 exons 1-33 with USP28 exons 6-20. One of the breakpoints is within NCOR1 exon 33. The functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0013151-T01-IM5	PBX4-CALR fusion	yes	unknown		unknown	CALR (NM_004343) Rearrangement : c.781:CALR_c.442-131:PBX4dup Note: The CALR Rearrangement results in the duplication of exons 6-9 of CALR. One of the breakpoints is within exon 6 of CALR. Its functional significance is undetermined.
PBX4	0	MSKCC-DMP	P-0013151-T01-IM5	PBX4-CALR fusion	yes	unknown		unknown	CALR (NM_004343) Rearrangement : c.781:CALR_c.442-131:PBX4dup Note: The CALR Rearrangement results in the duplication of exons 6-9 of CALR. One of the breakpoints is within exon 6 of CALR. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0013202-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+2565:EML4_c.3173-784:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0013202-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+2565:EML4_c.3173-784:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
ANKRD11	0	MSKCC-DMP	P-0013232-T01-IM5	SPG7-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2449:ANKRD11_c.184-519:SPG7del Note: The ANKRD11 - SPG7 rearrangement is a deletion which includes exons 1-9 of ANKRD11. One of the breakpoints is within exon 9 of ANKRD11. The functional significance is unknown.
SPG7	0	MSKCC-DMP	P-0013232-T01-IM5	SPG7-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2449:ANKRD11_c.184-519:SPG7del Note: The ANKRD11 - SPG7 rearrangement is a deletion which includes exons 1-9 of ANKRD11. One of the breakpoints is within exon 9 of ANKRD11. The functional significance is unknown.
JUN	0	MSKCC-DMP	P-0013401-T01-IM5	JUN-intragenic	yes	unknown		unknown	JUN (NM_002228) rearrangement: c.912:JUN_chr1:g.59238243inv Note: The JUN rearrangement is an inversion of a part of exon 1. One of the breakpoint is within exon 1.
ERG	0	MSKCC-DMP	P-0013401-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4108:TMPRSS2_c.19-22056:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0013401-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4108:TMPRSS2_c.19-22056:ERGdel
CTNNB1	0	MSKCC-DMP	P-0013404-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement : c.13+88_443del Note: The CTNNB1 Rearrangement results in the intragenic deletion of exons 2-4 of CTNNB1.  The breakpoints are within exons 2 and 4 respectively. Its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0013598-T01-IM5	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.3414-1949_c.3988+83del Note: The PTPRD rearrangement is an intragenic inversion of exons 31-34.
MET	0	MSKCC-DMP	P-0013695-T01-IM5	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: c.3028+410_c.3420dup Note: The MET rearrangement is a duplication of exons 15- 17. One of the breakpoints is within exon 17. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0013810-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 4-11): c.127-1377:TMPRSS2_c.40-64863:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0013810-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 4-11): c.127-1377:TMPRSS2_c.40-64863:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
ERG	0	MSKCC-DMP	P-0013837-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.55+4832:TMPRSS2_c.-149-29687:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0013837-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.55+4832:TMPRSS2_c.-149-29687:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
MAP3K7	0	MSKCC-DMP	P-0013928-T01-IM5	EPHA7-MAP3K7 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: c.98-3:EPHA7_chr6:g.92082925inv Note: The EPHA7 rearrangement is an inversion of exons 2-17.
EPHA7	0	MSKCC-DMP	P-0013928-T01-IM5	EPHA7-MAP3K7 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: c.98-3:EPHA7_chr6:g.92082925inv Note: The EPHA7 rearrangement is an inversion of exons 2-17.
PTEN	0	MSKCC-DMP	P-0014162-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.212_c.492+3506PTENdel Note: The PTEN (NM_000314) rearrangement results in the deletion of exons 4-5. One of the breakpoints is within exon 4. The functional significance is undetermined.
LRRK2	0	MSKCC-DMP	P-0014380-T01-IM6	ERBB3-LRRK2 fusion	yes	unknown		unknown	LRRK2 (NM_198578) - ERBB3 (NM_001982) rearrangement: c.1892:LRRK2_c.1786:ERBB2del Note: The LRRK2 - ERBB3 rearrangement is  a deletion which results in the fusion of LRRK2 exon 16 to ERBB3 exon 15. Both breakpoints are within exon and the rearrangement includes the kinase domain of ERBB3. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0014380-T01-IM6	ERBB3-LRRK2 fusion	yes	unknown		unknown	LRRK2 (NM_198578) - ERBB3 (NM_001982) rearrangement: c.1892:LRRK2_c.1786:ERBB2del Note: The LRRK2 - ERBB3 rearrangement is  a deletion which results in the fusion of LRRK2 exon 16 to ERBB3 exon 15. Both breakpoints are within exon and the rearrangement includes the kinase domain of ERBB3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0014425-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2528:TMPRSS2_c.19-4354:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014425-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2528:TMPRSS2_c.19-4354:ERGdel
EIF2C2	0	MSKCC-DMP	P-0014474-T01-IM6	EIF2C2-intragenic	yes	unknown		unknown	AGO2(NM_012154) Rearrangement : c.23-1240_c.1618del Note: The AGO2 Rearrangement results in the intragenic deletion of exons 2-13 of AGO2. One of the breakpoints is within exon13 of AGO2. Its functional significance is undetermined.
C1QL1	0	MSKCC-DMP	P-0014506-T01-IM6	RPTOR-C1QL1 fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: chr17:g.43042059_c.2298:RPTORdel Note: The RPTOR rearrangement is a deletion of exons 20-34. One of the breakpoints is within exon 20.
RPTOR	0	MSKCC-DMP	P-0014506-T01-IM6	RPTOR-C1QL1 fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: chr17:g.43042059_c.2298:RPTORdel Note: The RPTOR rearrangement is a deletion of exons 20-34. One of the breakpoints is within exon 20.
ROS1	0	MSKCC-DMP	P-0014506-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 32-43): t(5;6)(q32;q22.1)(chr5:g.149782871::chr6:g.117650623) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0014506-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 32-43): t(5;6)(q32;q22.1)(chr5:g.149782871::chr6:g.117650623) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.
EIF5A	0	MSKCC-DMP	P-0014682-T01-IM6	TP53-EIF5A fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: chr17:g.7209489_c.672+10:TP53del Note: The TP53 rearrangement is a deletion of exons 7-11.
TP53	0	MSKCC-DMP	P-0014682-T01-IM6	TP53-EIF5A fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: chr17:g.7209489_c.672+10:TP53del Note: The TP53 rearrangement is a deletion of exons 7-11.
ERG	0	MSKCC-DMP	P-0014841-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.56-3050:TMPRSS2_c.39+61126:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0014841-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.56-3050:TMPRSS2_c.39+61126:ERGdel
TCF7L2	0	MSKCC-DMP	P-0014874-T01-IM6	TCF7L2-intragenic	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.-1835_c.257-76del Note: The TCF7L2 (NM_001146274) rearrangement is a deletion of TCF7L2 exons 1 and 2. The functional significance is undetermined.
MCHR1	0	MSKCC-DMP	P-0014894-T01-IM6	EP300-MCHR1 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.41099971_c.1449del Note: The EP300 (NM_001429) rearrangement is a deletion with a breakpoint  in a genomic region on chr22 and the other breakpoint within exon 6 of EP300. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0014894-T01-IM6	EP300-MCHR1 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.41099971_c.1449del Note: The EP300 (NM_001429) rearrangement is a deletion with a breakpoint  in a genomic region on chr22 and the other breakpoint within exon 6 of EP300. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015012-T01-IM6	GDF6-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099)  rearrangement: t(8;21)(q22.1;q22.3)(chr8:g.96904156::chr21:g.42877101) Note: The TMPRSS2 (NM_001135099) rearrangement is a translocation of the intron1 of TMPRSS2 with a genomic region on chr 8. The functional significance is undetermined.
GDF6	0	MSKCC-DMP	P-0015012-T01-IM6	GDF6-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099)  rearrangement: t(8;21)(q22.1;q22.3)(chr8:g.96904156::chr21:g.42877101) Note: The TMPRSS2 (NM_001135099) rearrangement is a translocation of the intron1 of TMPRSS2 with a genomic region on chr 8. The functional significance is undetermined.
EIF1AX	0	MSKCC-DMP	P-0015029-T01-IM6	SPTLC3-EIF1AX fusion	yes	unknown		unknown	EIF1AX (NM_001412) rearrangement: t(X;20)(p22.12;p12.1)(chrX:g.20156591::chr20:g.12665904) Note: The EIF1AX rearrangement is a translocation that may result in the truncation of exons 3-7. The functional significance is undetermined.
SPTLC3	0	MSKCC-DMP	P-0015029-T01-IM6	SPTLC3-EIF1AX fusion	yes	unknown		unknown	EIF1AX (NM_001412) rearrangement: t(X;20)(p22.12;p12.1)(chrX:g.20156591::chr20:g.12665904) Note: The EIF1AX rearrangement is a translocation that may result in the truncation of exons 3-7. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0015039-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.2038-21549_c.2183del Note: The ARID1B rearrangement is an intragenic deletion of exon 6.
KMT2B	0	MSKCC-DMP	P-0020076-T02-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.358_c.1686inv Note: The MKT2B rearrangement results in the inversion of exons 1 - 3. The breakpoints are within MKT2B exons 1 and 3. Its functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0020482-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement : c.1322-1:RAD21_chr8:g.117833120del Note: The RAD21 Rearrangement results in the deletion of exons 11-14. Its functional significance is undetermined.
RHEB	0	MSKCC-DMP	P-0020546-T01-IM6	RHEB-intragenic	yes	unknown		unknown	RHEB (NM_005614) rearrangment: chr7:g.151218860_c.16:RHEBdel Note: The RHEB rearrangement is a partial deletion of exon 1. One of the breakpoints is within exon 1.
JAK1	0	MSKCC-DMP	P-0020670-T01-IM6	BCL10-JAK1 fusion	yes	unknown		unknown	BCL10 (NM_003921) rearrangement: g.65408657_c.605inv Note: The BCL10 rearrangement is an inversion of exon 3. Its functional significance is undetermined.
BCL10	0	MSKCC-DMP	P-0020670-T01-IM6	BCL10-JAK1 fusion	yes	unknown		unknown	BCL10 (NM_003921) rearrangement: g.65408657_c.605inv Note: The BCL10 rearrangement is an inversion of exon 3. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0020812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused with ERG exons 4-11): c.55+3638:TMPRSS2_c.39+63429:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0020812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused with ERG exons 4-11): c.55+3638:TMPRSS2_c.39+63429:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG (NM_004449) transcript.
JAK1	0	MSKCC-DMP	P-0020823-T02-IM6	MSH4-JAK1 fusion	yes	unknown		unknown	JAK1 (NM_002227) - MSH4 (NM_002440) rearrangement: c.1860:JAK1_c.244+1113:MSH4del Note: The JAK1 - MSH4 rearrangement is a deletion which includes JAK1 exons 1-13 and MSH4 exon 1. One of the breakpoints is within JAK1 exon 13. The functional significance is undetermined.
MSH4	0	MSKCC-DMP	P-0020823-T02-IM6	MSH4-JAK1 fusion	yes	unknown		unknown	JAK1 (NM_002227) - MSH4 (NM_002440) rearrangement: c.1860:JAK1_c.244+1113:MSH4del Note: The JAK1 - MSH4 rearrangement is a deletion which includes JAK1 exons 1-13 and MSH4 exon 1. One of the breakpoints is within JAK1 exon 13. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0020865-T01-IM6	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.281_c.762-1516del Note: The PIK3C2G rearrangement results in the deletion of exons 2-3. One of the breakpoints is within exon 2. The functional significance is undetermined.
MPRIP	0	MSKCC-DMP	P-0020962-T01-IM6	FLCN-MPRIP fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: g.16994136_c.1062+33del Note: The FLCN rearrangement results in the deletion of exons 10-14. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0020962-T01-IM6	FLCN-MPRIP fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: g.16994136_c.1062+33del Note: The FLCN rearrangement results in the deletion of exons 10-14. The functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0021063-T01-IM6	CREBBP-SLX4 fusion	yes	unknown		out of frame	CREBBP (NM_004380) -  SLX4 (NM_032444) rearrangement: c.4395-651:CREBBP_c.4637-57:SLX4 Note: The CREBBP - SLX4 rearrangement is a deletion that results in the fusion of CREBBP exons 1-26 with SLX4 exons 13-15. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0021063-T01-IM6	CREBBP-SLX4 fusion	yes	unknown		out of frame	CREBBP (NM_004380) -  SLX4 (NM_032444) rearrangement: c.4395-651:CREBBP_c.4637-57:SLX4 Note: The CREBBP - SLX4 rearrangement is a deletion that results in the fusion of CREBBP exons 1-26 with SLX4 exons 13-15. The functional significance is undetermined.
LYN	0	MSKCC-DMP	P-0021241-T01-IM6	LOC101927915-LYN fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: c.1050+108_g.137719703del Note: The LYN rearrangement results in the deletion of exons 11-13. The functional significance is undetermined.
LOC101927915	0	MSKCC-DMP	P-0021241-T01-IM6	LOC101927915-LYN fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: c.1050+108_g.137719703del Note: The LYN rearrangement results in the deletion of exons 11-13. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0021342-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.1287_c.1656inv Note: The PIK3CD rearrangement is an intragenic inversion of exons 10-13. Both breakpoints are within exon. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021342-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.127-1752:TMPRSS2_c.39+51696:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0021342-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.127-1752:TMPRSS2_c.39+51696:ERGdel
NOTCH3	0	MSKCC-DMP	P-0021476-T01-IM6	BRD4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.3328-160_g.15396709del Note: The NOTCH3 rearrangement results in the deletion of exons 1-20. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0021476-T01-IM6	BRD4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.3328-160_g.15396709del Note: The NOTCH3 rearrangement results in the deletion of exons 1-20. The functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0021501-T01-IM6	PRICKLE4-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.74-115:NOTCH4_chr6:g.41754978del Note: The NOTCH4 rearrangement is a deletion of exon 1. The functional significance is undetermined.
PRICKLE4	0	MSKCC-DMP	P-0021501-T01-IM6	PRICKLE4-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.74-115:NOTCH4_chr6:g.41754978del Note: The NOTCH4 rearrangement is a deletion of exon 1. The functional significance is undetermined.
COL15A1	0	MSKCC-DMP	P-0021527-T01-IM6	TGFBR1-COL15A1 fusion	yes	unknown		in frame	COL15A1 (NM_001855) -TGFBR1 (NM_004612) rearrangement: c.101-17543:COL15A1_c.98-4C:TGFBR1del Note: The COL15A1 - TFGBR1 rearrangement is a deletion which results in the fusion of COL15A1 exons 1-2 with TFGBR1 exons 2-9. The fusion is predicted to be in frame and includes the kinase domain of TGFBR1. The functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0021527-T01-IM6	TGFBR1-COL15A1 fusion	yes	unknown		in frame	COL15A1 (NM_001855) -TGFBR1 (NM_004612) rearrangement: c.101-17543:COL15A1_c.98-4C:TGFBR1del Note: The COL15A1 - TFGBR1 rearrangement is a deletion which results in the fusion of COL15A1 exons 1-2 with TFGBR1 exons 2-9. The fusion is predicted to be in frame and includes the kinase domain of TGFBR1. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0021550-T01-IM6	SIPA1L2-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3866+3_chr1:g.232497627inv Note: The ARID1A rearrangement results in the inversion of exons 16-20. Its functional significance is undetermined.
SIPA1L2	0	MSKCC-DMP	P-0021550-T01-IM6	SIPA1L2-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3866+3_chr1:g.232497627inv Note: The ARID1A rearrangement results in the inversion of exons 16-20. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021577-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.126+569:TMPRSS2_c.19-13687:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0021577-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.126+569:TMPRSS2_c.19-13687:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.
RUNX1	0	MSKCC-DMP	P-0021618-T01-IM6	ALKBH7-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(19;21)(p13.3;q22.12)(chr19:g.6377157::chr21:g.36164635) Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
ALKBH7	0	MSKCC-DMP	P-0021618-T01-IM6	ALKBH7-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(19;21)(p13.3;q22.12)(chr19:g.6377157::chr21:g.36164635) Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
MYO9B	0	MSKCC-DMP	P-0021674-T01-IM6	PIK3R2-MYO9B fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - MYO9B (NM_004145) rearrangement: c.206:PIK3R2_c.2219+1922:MYO9Bdup Note: The PIK3R2 - MYO9B rearrangement is a duplication which results in the fusion of PIK3R2 exons 1-2 with MYO9B exons 15-40. One of the breakpoints is within PIK3R2 exon 2. The functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0021674-T01-IM6	PIK3R2-MYO9B fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - MYO9B (NM_004145) rearrangement: c.206:PIK3R2_c.2219+1922:MYO9Bdup Note: The PIK3R2 - MYO9B rearrangement is a duplication which results in the fusion of PIK3R2 exons 1-2 with MYO9B exons 15-40. One of the breakpoints is within PIK3R2 exon 2. The functional significance is undetermined.
CASC6	0	MSKCC-DMP	P-0021702-T01-IM6	EPHA7-CASC6 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: g.92924560_c.242del Note: The EPHA7 rearrangement results in the deletion of exons 3-17. One of the breakpoints is within exon 3. The functional significance is undetermined.
EPHA7	0	MSKCC-DMP	P-0021702-T01-IM6	EPHA7-CASC6 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: g.92924560_c.242del Note: The EPHA7 rearrangement results in the deletion of exons 3-17. One of the breakpoints is within exon 3. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0021709-T01-IM6	SGK223-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(8,19)(p23.1,p13.3)(chr8:g.8188507::chr19:g.2226441) Note: The DOT1L rearrangement is a translocation which results in the possible truncation of DOT1L exons 1-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
PRAG1	0	MSKCC-DMP	P-0021709-T01-IM6	PRAG1-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(8,19)(p23.1,p13.3)(chr8:g.8188507::chr19:g.2226441) Note: The DOT1L rearrangement is a translocation which results in the possible truncation of DOT1L exons 1-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0021772-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.7+55469_c.271del Note: The PARK2 rearrangement is an intragenic deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021853-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exon4) : c.56-3032:TMPRSS2_c.40-59421:ERGdel Note: TMPRSS2 is fused with non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0021853-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exon4) : c.56-3032:TMPRSS2_c.40-59421:ERGdel Note: TMPRSS2 is fused with non-canonical ERG (NM_004449) transcript.
KIF5B	0	MSKCC-DMP	P-0021879-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B1 exons 1-15 fused with RET exons 12-20 including the kinase domain.): c.1726-882:KIF5B_c.2136+515_RETinv Note: The KIF5B - RET fusion is predicted to be in frame.
RET	0	MSKCC-DMP	P-0021879-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B1 exons 1-15 fused with RET exons 12-20 including the kinase domain.): c.1726-882:KIF5B_c.2136+515_RETinv Note: The KIF5B - RET fusion is predicted to be in frame.
APC	0	MSKCC-DMP	P-0021927-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1312+557_c.1506del Note: The APC rearrangement is an intragenic deletion of exons 11-12. One of the breakpoints is within APC exon 12. The functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0021983-T01-IM6	SIRT5-IGF1R fusion	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: t(6;15)(p23;q26.3)(chr6:g.13582729::chr15:g.99467786) Note: The IGF1R rearrangement is a translocation that may result in a truncation of exons 13-21. One of the breakpoints is within exon 13. The functional significance is undetermined.
SIRT5	0	MSKCC-DMP	P-0021983-T01-IM6	SIRT5-IGF1R fusion	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: t(6;15)(p23;q26.3)(chr6:g.13582729::chr15:g.99467786) Note: The IGF1R rearrangement is a translocation that may result in a truncation of exons 13-21. One of the breakpoints is within exon 13. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0021983-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.225+7397_c.2330del Note: The KDM6A rearrangement results in the deletion of exons 3-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0021993-T01-IM6	AGO2-intragenic	yes	unknown		in frame	AGO2 (NM_012154) rearrangement: c.768+28_c.23-22677dup Note: The AGO2 rearrangement results in the in-frame duplication of exons 2-6. The functional significance is undetermined.
EEF1A2	0	MSKCC-DMP	P-0022034-T01-IM6	PIK3R2-EEF1A2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) Rearrangement: t(19,20)(p13.11,q13.33)(chr19:g.18271854::chr20:g.62118311) Note: The PIK3R2 Rearrangement results in the possible truncation of PIK3R2. Its functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0022034-T01-IM6	PIK3R2-EEF1A2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) Rearrangement: t(19,20)(p13.11,q13.33)(chr19:g.18271854::chr20:g.62118311) Note: The PIK3R2 Rearrangement results in the possible truncation of PIK3R2. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0022044-T01-IM6	FEV-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - FEV (NM_017521) fusion (EWSR1 exons 1-9 fused to FEV exon 3): t(2;22)(q35;q12.2)(chr2:g.219848798::chr22:g.29684126) Note: The EWSR1 - FEV fusion is predicted to be in-frame.
FEV	0	MSKCC-DMP	P-0022044-T01-IM6	FEV-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - FEV (NM_017521) fusion (EWSR1 exons 1-9 fused to FEV exon 3): t(2;22)(q35;q12.2)(chr2:g.219848798::chr22:g.29684126) Note: The EWSR1 - FEV fusion is predicted to be in-frame.
ERG	0	MSKCC-DMP	P-0022060-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.236+78:ERG_c.350-337:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exons 1-2 to TMPRSS2 exons 4-14. The possibility of a more complex event resulting in the fusion of TMPRSS2-ERG cannot be excluded. Additional testing is recommended.
TMPRSS2	0	MSKCC-DMP	P-0022060-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.236+78:ERG_c.350-337:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exons 1-2 to TMPRSS2 exons 4-14. The possibility of a more complex event resulting in the fusion of TMPRSS2-ERG cannot be excluded. Additional testing is recommended.
ERG	0	MSKCC-DMP	P-0022067-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2776:TMPRSS2_c.18+2138:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0022067-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2776:TMPRSS2_c.18+2138:ERGdel
BRIP1	0	MSKCC-DMP	P-0022174-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.1473_c.2098-9262del Note: The BRIP1 rearrangement results in the deletion of exons 10-14. One of the breakpoints is within exon 10. Its functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0022323-T01-IM6	BRCA1-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - BRCA1 (NM_007294) Rearrangement : c.-102-4603:EZH1_c.5194-65:BRCA1dup Note: The EZH1 - BRCA1 Rearrangement results in the fusion of EZH1 5'UTR region and BRCA1 exon 19-23. Its functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0022323-T01-IM6	BRCA1-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - BRCA1 (NM_007294) Rearrangement : c.-102-4603:EZH1_c.5194-65:BRCA1dup Note: The EZH1 - BRCA1 Rearrangement results in the fusion of EZH1 5'UTR region and BRCA1 exon 19-23. Its functional significance is undetermined.
BAGE2	0	MSKCC-DMP	P-0022323-T01-IM6	KMT2C-BAGE2 fusion	yes	unknown		unknown	KMT2C (NM_170606) Rearrangement : t(7;21)(q36.1;p11.1)(chr7:g.151945542::chr21:g.11039050) Note: The KMT2C Rearrangement results in the possible truncation of KMT2C. One of the breakpoints is within exon14. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0022323-T01-IM6	KMT2C-BAGE2 fusion	yes	unknown		unknown	KMT2C (NM_170606) Rearrangement : t(7;21)(q36.1;p11.1)(chr7:g.151945542::chr21:g.11039050) Note: The KMT2C Rearrangement results in the possible truncation of KMT2C. One of the breakpoints is within exon14. Its functional significance is undetermined.
DGAT1	0	MSKCC-DMP	P-0022323-T01-IM6	RECQL4-DGAT1 fusion	yes	unknown		unknown	DGAT1 (NM_012079) - RECQL4 (NM_004260) Rearrangement : c.1069:DGAT1_c.784:RECQL4dup Note: The DGAT1 - RECQL4 Rearrangement results in the fusion of DGAT1 exon 1-13 with RECQL4 exon 5-22. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0022323-T01-IM6	RECQL4-DGAT1 fusion	yes	unknown		unknown	DGAT1 (NM_012079) - RECQL4 (NM_004260) Rearrangement : c.1069:DGAT1_c.784:RECQL4dup Note: The DGAT1 - RECQL4 Rearrangement results in the fusion of DGAT1 exon 1-13 with RECQL4 exon 5-22. Its functional significance is undetermined.
THSD4	0	MSKCC-DMP	P-0022346-T01-IM6	ALK-THSD4 fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(2;15)(q23.1;q23)(chr2:g.29448144::chr15:g.71944254) Note: The ALK rearrangement is a translocation which may result in the truncation of exons 1-19. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0022346-T01-IM6	ALK-THSD4 fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(2;15)(q23.1;q23)(chr2:g.29448144::chr15:g.71944254) Note: The ALK rearrangement is a translocation which may result in the truncation of exons 1-19. Its functional significance is undetermined.
SEPT12	0	MSKCC-DMP	P-0022424-T01-IM6	ARID1A-SEPT12 fusion	yes	unknown		unknown	ARID1A (NM_006015) - SEPT12 (NM_144605) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.27089562::chr16:g.4838352) Note: The ARID1A - SEPT12 rearrangement is a translocation which may result in the fusion of ARID1A exons 1-8 with SEPT12 exons 1-10. One of the breakpoints is within ARID1A exon 8. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0022424-T01-IM6	ARID1A-SEPT12 fusion	yes	unknown		unknown	ARID1A (NM_006015) - SEPT12 (NM_144605) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.27089562::chr16:g.4838352) Note: The ARID1A - SEPT12 rearrangement is a translocation which may result in the fusion of ARID1A exons 1-8 with SEPT12 exons 1-10. One of the breakpoints is within ARID1A exon 8. Its functional significance is undetermined.
AZIN1	0	MSKCC-DMP	P-0022424-T01-IM6	PDGFRA-AZIN1 fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: t(4;8)(q12;q22.3)(chr4:g.55130160::chr8:g.103867353) Note: The PDGFRA rearrangement is a translocation which may result in a truncation of PDGFRA exons 1-3. Its functional significance is undetermined.
PDGFRA	0	MSKCC-DMP	P-0022424-T01-IM6	PDGFRA-AZIN1 fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: t(4;8)(q12;q22.3)(chr4:g.55130160::chr8:g.103867353) Note: The PDGFRA rearrangement is a translocation which may result in a truncation of PDGFRA exons 1-3. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0022427-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.2062-378_c.3070del Note: The EGFR rearrangement is an intragenic deletion of exons 18-25. One of the breakpoints is within exon 25. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022470-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2657:TMPRSS2_c.40-63048:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0022470-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2657:TMPRSS2_c.40-63048:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TGFBR2	0	MSKCC-DMP	P-0022558-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.530-1560_c.959del Note: The TGFBR2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ARID3A	0	MSKCC-DMP	P-0022800-T01-IM6	STK11-ARID3A fusion	yes	unknown		unknown	STK11 (NM_000455) - ARID3A (NM_005224) Rearrangement : c.80:STK11_c.-601:ARID3Adup Note: The STK11 - ARID3A Rearrangement results in the fusion of exon1 of STK11 with exons 1-9 of ARID3A. The breakpoints are within STK11 exon1 and ARID3A promoter region. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0022800-T01-IM6	STK11-ARID3A fusion	yes	unknown		unknown	STK11 (NM_000455) - ARID3A (NM_005224) Rearrangement : c.80:STK11_c.-601:ARID3Adup Note: The STK11 - ARID3A Rearrangement results in the fusion of exon1 of STK11 with exons 1-9 of ARID3A. The breakpoints are within STK11 exon1 and ARID3A promoter region. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0022800-T01-IM6	FCAR-PTPRS fusion	yes	unknown		unknown	FCAR (NM_002000) - PTPRS (NM_002850) Rearrangement :  c.71-2885:FCAR_c.265:PTPRSinv Note: The FCAR  - PTPRS Rearrangement results in the fusion of exons 1-2 of FCAR with exons 4-38 of PTPRS. The breakpoint in PTPRS is within exon4. Its functional significance is undetermined.
FCAR	0	MSKCC-DMP	P-0022800-T01-IM6	FCAR-PTPRS fusion	yes	unknown		unknown	FCAR (NM_002000) - PTPRS (NM_002850) Rearrangement :  c.71-2885:FCAR_c.265:PTPRSinv Note: The FCAR  - PTPRS Rearrangement results in the fusion of exons 1-2 of FCAR with exons 4-38 of PTPRS. The breakpoint in PTPRS is within exon4. Its functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0022911-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.226-238_c.3557del Note: The ERBB2 rearrangement is an intragenic deletion of exons 3-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0022967-T01-IM6	ATR-intragenic	yes	unknown		out of frame	ATR (NM_001184) Rearrangement : c.2633+72_c.3172-268del Note: The ATR Rearrangement results in the intragenic deletion of exons 12-15. Its functional significance is undetermined.
SUZ12P1	0	MSKCC-DMP	P-0023071-T01-IM6	NF1-SUZ12P1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.60+26655:NF1_chr17:g.29095928dup Note: The NF1 rearrangement is a duplication which results in the duplication of exon 1. its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0023071-T01-IM6	NF1-SUZ12P1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.60+26655:NF1_chr17:g.29095928dup Note: The NF1 rearrangement is a duplication which results in the duplication of exon 1. its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0023091-T01-IM6	PRKD2-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5276+39:KMT2B_chr19:g.47210279del Note: The KMT2B rearrangement results in the deletion of exons 26-37. Its functional significance is undetermined. Multiple rearrangements involving KMT2B were detected in this sample and a more complex rearrangement resulting in a KMT2B fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PRKD2	0	MSKCC-DMP	P-0023091-T01-IM6	PRKD2-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5276+39:KMT2B_chr19:g.47210279del Note: The KMT2B rearrangement results in the deletion of exons 26-37. Its functional significance is undetermined. Multiple rearrangements involving KMT2B were detected in this sample and a more complex rearrangement resulting in a KMT2B fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RIPK2-DT	0	MSKCC-DMP	P-0023091-T01-IM6	NBN-RIPK2-DT fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.1063:NBN_chr8:g.90544955del Note: The NBN rearrangement results in the deletion of exons 9-16. One of the breakpoints is within exon 9. Its functional significance is undetermined. Multiple rearrangements involving NBN were detected in this sample and a more complex rearrangement resulting in a NBN fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
NBN	0	MSKCC-DMP	P-0023091-T01-IM6	NBN-LOC101929709 fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.1063:NBN_chr8:g.90544955del Note: The NBN rearrangement results in the deletion of exons 9-16. One of the breakpoints is within exon 9. Its functional significance is undetermined. Multiple rearrangements involving NBN were detected in this sample and a more complex rearrangement resulting in a NBN fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
GAST	0	MSKCC-DMP	P-0023102-T01-IM6	BRCA1-GAST fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: chr17:g.39859920_c.3986inv Note: The BRCA1 rearrangement is an inversion (1383642 bp) that includes exons 10-23 of BRCA1. One of the breakpoints is within BRCA1 exon 10.
BRCA1	0	MSKCC-DMP	P-0023102-T01-IM6	BRCA1-GAST fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: chr17:g.39859920_c.3986inv Note: The BRCA1 rearrangement is an inversion (1383642 bp) that includes exons 10-23 of BRCA1. One of the breakpoints is within BRCA1 exon 10.
CDH1	0	MSKCC-DMP	P-0023119-T01-IM6	RAD21-CDH1 fusion	yes	unknown		out of frame	RAD21 (NM_006265) - CDH1 (NM_004360) rearrangement: t(8;16)(q24.11;q22.1)(chr8:g.117864146::chr16:g.68852231) Note: The RAD21 - CDH1 rearrangement is a translocation that results in the fusion of RAD21 exons 1-11 with CDH1 exons 11-16. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0023119-T01-IM6	RAD21-CDH1 fusion	yes	unknown		out of frame	RAD21 (NM_006265) - CDH1 (NM_004360) rearrangement: t(8;16)(q24.11;q22.1)(chr8:g.117864146::chr16:g.68852231) Note: The RAD21 - CDH1 rearrangement is a translocation that results in the fusion of RAD21 exons 1-11 with CDH1 exons 11-16. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0023192-T01-IM6	HSF5-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.123:RNF43_chr17:g.56511985inv Note: The RNF43 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.
HSF5	0	MSKCC-DMP	P-0023192-T01-IM6	HSF5-RNF43 fusion	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.123:RNF43_chr17:g.56511985inv Note: The RNF43 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0023192-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: c.1851_c.*3936del Note: The KDM5C rearrangement is a deletion of exons 13-26. One of the breakpoints is within exon 13. The functional significance is undetermined.
VPS51	0	MSKCC-DMP	P-0023273-T01-IM6	INPPL1-VPS51 fusion	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: chr11:g.64878485_c.3664:INPPL1inv Note: The INPPL1 rearrangement results in the inversion of exons 1-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0023273-T01-IM6	INPPL1-VPS51 fusion	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: chr11:g.64878485_c.3664:INPPL1inv Note: The INPPL1 rearrangement results in the inversion of exons 1-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
DNM2	0	MSKCC-DMP	P-0023324-T01-IM6	CARM1-DNM2 fusion	yes	unknown		out of frame	CARM1 (NM_199141) - DNM2 (NM_001005361) rearrangement: c.1020+2:CARM1_c.161+4368:DNM2dup Note: The CARM1 - DNM2 rearrangement is a duplication that results in the fusion of CARM1 exons 1-8 with DNM2 exons 2-21. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0023324-T01-IM6	CARM1-DNM2 fusion	yes	unknown		out of frame	CARM1 (NM_199141) - DNM2 (NM_001005361) rearrangement: c.1020+2:CARM1_c.161+4368:DNM2dup Note: The CARM1 - DNM2 rearrangement is a duplication that results in the fusion of CARM1 exons 1-8 with DNM2 exons 2-21. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0023464-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) Rearrangement : chr2:g.212109143_c.997+95del Note: The ERBB4 rearrangement results in the intragenic deletion of exons 9-28. It includes the protein kinase domain of ERBB4. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0023546-T02-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.126+796_c.55+2609del Note: The TMPRSS2 rearrangement results in the deletion of exon 2. The functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0023588-T01-IM6	SIGLECL1-POLD1 fusion	yes	unknown		unknown	POLD1 (NM_002691) - SIGLECL1(NM_173635) Rearrangement : c.2429:POLD1_c.-191+1669:SIGLECL1del Note: The POLD1 (NM_002691) - SIGLECL1(NM_173635) Rearrangement results in the fusion of exons 1-20 with 2-6 of SIGLECL1. Its functional significance is undetermined.
SIGLECL1	0	MSKCC-DMP	P-0023588-T01-IM6	SIGLECL1-POLD1 fusion	yes	unknown		unknown	POLD1 (NM_002691) - SIGLECL1(NM_173635) Rearrangement : c.2429:POLD1_c.-191+1669:SIGLECL1del Note: The POLD1 (NM_002691) - SIGLECL1(NM_173635) Rearrangement results in the fusion of exons 1-20 with 2-6 of SIGLECL1. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0023588-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : c.4714:APC_chr5:g.112187884del Note: The APC Rearrangement results in the intragenic deletion of exon16. Its functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0023588-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : c.4714:APC_chr5:g.112187884del Note: The APC Rearrangement results in the intragenic deletion of exon16. Its functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0023603-T01-IM6	AIDA-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) rearrangement: t(1;9)(q41,q34.13)(chr1:g.222846177::chr9:g.135779003) Note: The TSC1 rearrangement is a translocation which may result in the truncation of exons 18-23. Its functional significance is undetermined.
AIDA	0	MSKCC-DMP	P-0023603-T01-IM6	AIDA-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) rearrangement: t(1;9)(q41,q34.13)(chr1:g.222846177::chr9:g.135779003) Note: The TSC1 rearrangement is a translocation which may result in the truncation of exons 18-23. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0023707-T01-IM6	EFNB3-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) - EFNB3 (NM_001406) Rearrangement : c.-28-596:TP53_c.123-693inv Note: The TP53-EFNB3 Rearrangement results in the fusion of exon1 of TP53 with EFNB3 exons 2-5. Its functional significance is undetermined.
EFNB3	0	MSKCC-DMP	P-0023707-T01-IM6	EFNB3-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) - EFNB3 (NM_001406) Rearrangement : c.-28-596:TP53_c.123-693inv Note: The TP53-EFNB3 Rearrangement results in the fusion of exon1 of TP53 with EFNB3 exons 2-5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023707-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon 4):c.127-1486:TMPRSS2_c.40-60882:ERGdel Note: The TMPRSS2  - ERG fusion is an in-frame fusion .
TMPRSS2	0	MSKCC-DMP	P-0023707-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon 4):c.127-1486:TMPRSS2_c.40-60882:ERGdel Note: The TMPRSS2  - ERG fusion is an in-frame fusion .
PLEKHG4B	0	MSKCC-DMP	P-0023707-T01-IM6	SDHA-PLEKHG4B fusion	yes	unknown		unknown	SDHA (NM_004168) Rearrangement : chr5:g.55450_c.1001del Note: The SDHA Rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon8. Its functional significance is undetermined.
SDHA	0	MSKCC-DMP	P-0023707-T01-IM6	SDHA-PLEKHG4B fusion	yes	unknown		unknown	SDHA (NM_004168) Rearrangement : chr5:g.55450_c.1001del Note: The SDHA Rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon8. Its functional significance is undetermined.
ATF7	0	MSKCC-DMP	P-0023821-T01-IM6	BRAF-ATF7 fusion	yes	unknown		in frame	ATF7 (NM_006856) - BRAF (NM_004333) Rearrangement :  t(7;12)(q34;q13.13)(chr7:g.140483233::chr12:g. 53913299) Note: The ATF7 - BRAF Rearrangement results in an in-frame fusion of exons 1- 11 of BRAF with exons 10-18 of BRAF. The rearrangement includes the protein kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0023821-T01-IM6	BRAF-ATF7 fusion	yes	unknown		in frame	ATF7 (NM_006856) - BRAF (NM_004333) Rearrangement :  t(7;12)(q34;q13.13)(chr7:g.140483233::chr12:g. 53913299) Note: The ATF7 - BRAF Rearrangement results in an in-frame fusion of exons 1- 11 of BRAF with exons 10-18 of BRAF. The rearrangement includes the protein kinase domain of BRAF.
CDKN1B	0	MSKCC-DMP	P-0023848-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) Rearrangement : c.167_c.*269del Note: The CDKN1B rearrangement results in the deletion of exons 1-2 of CDKN1B. The breakpoints are within exon1 and in the 3' UTR region after transcription stop site respectively. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023961-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 3-11):c.127-1531:TMPRSS2_c.-47-3297:ERGdel Note: The TMPRSS2 - ERG re-arrangement is a non-canonical gene fusion.
TMPRSS2	0	MSKCC-DMP	P-0023961-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 3-11):c.127-1531:TMPRSS2_c.-47-3297:ERGdel Note: The TMPRSS2 - ERG re-arrangement is a non-canonical gene fusion.
EGFL7	0	MSKCC-DMP	P-0023961-T01-IM6	TNS1-EGFL7 fusion	yes	unknown		unknown	EGFL7 (NM_201446) - TNS1 (NM_022648) rearrangement: t(2;9)(q35;q34.3)(chr2:g.218708823::chr9:g.139566440) Note: The EGFL7 - TNS1 rearrangement is a translocation that results in the fusion of EGFL7 exons 1-8 with TNS1 exons 18-33. One of the breakpoints is within EGFL7 exon 8. The functional significance is undetermined.
TNS1	0	MSKCC-DMP	P-0023961-T01-IM6	TNS1-EGFL7 fusion	yes	unknown		unknown	EGFL7 (NM_201446) - TNS1 (NM_022648) rearrangement: t(2;9)(q35;q34.3)(chr2:g.218708823::chr9:g.139566440) Note: The EGFL7 - TNS1 rearrangement is a translocation that results in the fusion of EGFL7 exons 1-8 with TNS1 exons 18-33. One of the breakpoints is within EGFL7 exon 8. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0024095-T01-IM6	GOLGA6B-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.72920652::chr21:g.42874147) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. A complex rearrangement cannot be ruled out and its functional significance is undetermined.
GOLGA6B	0	MSKCC-DMP	P-0024095-T01-IM6	GOLGA6B-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.72920652::chr21:g.42874147) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. A complex rearrangement cannot be ruled out and its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0024263-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) Rearrangement : c.-1480_c.107del Note: The RB1 Rearrangement results in the intragenic deletion of exon1 of RB1.The breakpoints are within the promoter of RB1 and exon1 respectively. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0024344-T01-IM6	SORCS1-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) - SORCS1 (NM_001013031) rearrangement: t(10;19)(q25.1;p13.2)(chr10:g.108617375::chr19:g.15355232) Note: The BRD4 - SORCS1 rearrangement is a translocation which may result in the fusion of BRD4 exons 1-13 with SORCS1 exons 3-27. One of the breakpoints is within BRD4 exon 13. Its functional significance is undetermined.
SORCS1	0	MSKCC-DMP	P-0024344-T01-IM6	SORCS1-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) - SORCS1 (NM_001013031) rearrangement: t(10;19)(q25.1;p13.2)(chr10:g.108617375::chr19:g.15355232) Note: The BRD4 - SORCS1 rearrangement is a translocation which may result in the fusion of BRD4 exons 1-13 with SORCS1 exons 3-27. One of the breakpoints is within BRD4 exon 13. Its functional significance is undetermined.
MITF	0	MSKCC-DMP	P-0024406-T01-IM6	FOXP1-MITF fusion	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: chr3:g.69943237_c.1443del Note: The FOXP1 rearrangement results in the deletion of exons 13-17. One of the breakpoints is within exon 13. The functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0024406-T01-IM6	FOXP1-MITF fusion	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: chr3:g.69943237_c.1443del Note: The FOXP1 rearrangement results in the deletion of exons 13-17. One of the breakpoints is within exon 13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024488-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+2968:TMPRSS2_c.39+16108:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0024488-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+2968:TMPRSS2_c.39+16108:ERGdel
ROS1	0	MSKCC-DMP	P-0024516-T01-IM6	ROS1-intragenic	yes	unknown		in frame	ROS1 (NM_002944) rearrangement: c.1165-29_c.2496+901dup Note: The ROS1 rearrangement is an intragenic duplication of exons 11-16, which do not include the ROS1 kinase domain. The functional significance is undetermined.
MTAP	0	MSKCC-DMP	P-0024526-T01-IM6	CDKN2A-MTAP fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.457+112:CDKN2A_chr9:g.21814419del Note: The CDKN2A rearrangement is a deletion which includes exons 2-3 of both the CDKN2Ap16INK4 and CDKN2Ap14ARF isoforms of CDKN2A. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0024526-T01-IM6	CDKN2A-MTAP fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.457+112:CDKN2A_chr9:g.21814419del Note: The CDKN2A rearrangement is a deletion which includes exons 2-3 of both the CDKN2Ap16INK4 and CDKN2Ap14ARF isoforms of CDKN2A. The functional significance is undetermined.
LINC00397	0	MSKCC-DMP	P-0024614-T01-IM6	ERCC5-LINC00397 fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement: c.3314:ERCC5_chr13:g.88748664inv Note: The ERCC5 rearrangement is an inversion of exon 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.
ERCC5	0	MSKCC-DMP	P-0024614-T01-IM6	ERCC5-LINC00397 fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement: c.3314:ERCC5_chr13:g.88748664inv Note: The ERCC5 rearrangement is an inversion of exon 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.
NELL2	0	MSKCC-DMP	P-0024721-T01-IM6	KMT2D-NELL2 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.44815829_c.5868-95:KMT2Ddel Note: The KMT2D rearrangement is a deletion of exons 1-27. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0024721-T01-IM6	KMT2D-NELL2 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.44815829_c.5868-95:KMT2Ddel Note: The KMT2D rearrangement is a deletion of exons 1-27. The functional significance is undetermined.
EPB41L1	0	MSKCC-DMP	P-0024848-T01-IM6	PTPRT-EPB41L1 fusion	yes	unknown		unknown	PTPRT (NM_133170) - EPB41L1 (NM_012156) rearrangement: c.2281:PTPRT_c.2439+506:EPB41L1inv Note: The PTPRT - EPB41L1 rearrangement results in the fusion of PTPRT exons 1-15 with EPB41L1 exons 20-22. One of the breakpoints is within PTPRT exon 15. Its functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0024848-T01-IM6	PTPRT-EPB41L1 fusion	yes	unknown		unknown	PTPRT (NM_133170) - EPB41L1 (NM_012156) rearrangement: c.2281:PTPRT_c.2439+506:EPB41L1inv Note: The PTPRT - EPB41L1 rearrangement results in the fusion of PTPRT exons 1-15 with EPB41L1 exons 20-22. One of the breakpoints is within PTPRT exon 15. Its functional significance is undetermined.
TTLL6	0	MSKCC-DMP	P-0024959-T01-IM6	MSI2-TTLL6 fusion	yes	unknown		unknown	MSI2 (NM_138962) rearrangement: c.*7:MSI2_chr17:g.46887323del Note: The MSI2 rearrangement results in the deletion of exons 1-13. Its functional significance is undetermined.
MSI2	0	MSKCC-DMP	P-0024959-T01-IM6	MSI2-TTLL6 fusion	yes	unknown		unknown	MSI2 (NM_138962) rearrangement: c.*7:MSI2_chr17:g.46887323del Note: The MSI2 rearrangement results in the deletion of exons 1-13. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0025013-T01-IM6	BCL2L14-ETV6 fusion	yes	unknown		out of frame	BCL2L14 (NM_138722) -ETV6 (NM_001987)  Rearrangement :  c.945+502:BCL2L14_c.1009+2450:ETV6dup Note : The BCL2L14 -ETV6 Rearrangement  results in fusion of exons 1-5 of BCL2L14 with exons 6-8 of ETV6. Its functional significance is undetermined.
BCL2L14	0	MSKCC-DMP	P-0025013-T01-IM6	BCL2L14-ETV6 fusion	yes	unknown		out of frame	BCL2L14 (NM_138722) -ETV6 (NM_001987)  Rearrangement :  c.945+502:BCL2L14_c.1009+2450:ETV6dup Note : The BCL2L14 -ETV6 Rearrangement  results in fusion of exons 1-5 of BCL2L14 with exons 6-8 of ETV6. Its functional significance is undetermined.
CUX2	0	MSKCC-DMP	P-0025013-T01-IM6	SH2B3-CUX2 fusion	yes	unknown		unknown	SH2B3 (NM_005475) - CUX2(NM_015267) Rearrangement: c.901:SH2B3_c.175-230:CUX2dup Note: The SH2B3 - CUX2 Rearrangement results in the fusion of exons 1-4 of SH2B3 with exons 3-22 of CUX2.The breakpoint in SH2B3 is within exon 4.Its functional significance is undetermined.
SH2B3	0	MSKCC-DMP	P-0025013-T01-IM6	SH2B3-CUX2 fusion	yes	unknown		unknown	SH2B3 (NM_005475) - CUX2(NM_015267) Rearrangement: c.901:SH2B3_c.175-230:CUX2dup Note: The SH2B3 - CUX2 Rearrangement results in the fusion of exons 1-4 of SH2B3 with exons 3-22 of CUX2.The breakpoint in SH2B3 is within exon 4.Its functional significance is undetermined.
VSIG10	0	MSKCC-DMP	P-0025130-T01-IM6	VTCN1-VSIG10 fusion	yes	unknown		unknown	VSIG10 (NM_019086 ) - VTCN1 (NM_024626) Rearrangement :  t(1;12)(p12;q24.22)(chr1:g.117753552; chr12:g.118524554) Note: The VSIG10 - VTCN1 Rearrangement results in the fusion of exons 1-2 of VSIG10 with the 5-UTR region of VTCN1. The breakpoint in VTCN1 is within 5'UTR region before the transcription start site of VTCN1. This event occurs in the background of other structural events involving VTCN1. Its functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0025130-T01-IM6	VTCN1-VSIG10 fusion	yes	unknown		unknown	VSIG10 (NM_019086 ) - VTCN1 (NM_024626) Rearrangement :  t(1;12)(p12;q24.22)(chr1:g.117753552; chr12:g.118524554) Note: The VSIG10 - VTCN1 Rearrangement results in the fusion of exons 1-2 of VSIG10 with the 5-UTR region of VTCN1. The breakpoint in VTCN1 is within 5'UTR region before the transcription start site of VTCN1. This event occurs in the background of other structural events involving VTCN1. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0025130-T01-IM6	RAB11FIP4-NF1 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) Rearrangement:  c.337-451:RAB11FIP4_c.5813-1:NF1dup Note: The RAB11FIP4  - NF1 Rearrangement results in the fusion of exons 1-3 of RAB11FIP4 with exons 40-58 of NF1 . Its functional significance is undetermined.
RAB11FIP4	0	MSKCC-DMP	P-0025130-T01-IM6	RAB11FIP4-NF1 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) Rearrangement:  c.337-451:RAB11FIP4_c.5813-1:NF1dup Note: The RAB11FIP4  - NF1 Rearrangement results in the fusion of exons 1-3 of RAB11FIP4 with exons 40-58 of NF1 . Its functional significance is undetermined.
ASIC2	0	MSKCC-DMP	P-0025137-T01-IM6	RAD51D-ASIC2 fusion	yes	unknown		unknown	ASIC2 (NM_001094) - RAD51D (NM_133629) Rearrangement : c.556-520534:ASIC2_c.322:RAD51Ddup Note: The ASIC2  - RAD51D Rearrangement results in the fusion of exon 1 of ASIC2 with exons 4-7 of RAD51D. The breakpoint in RAD51D is within exon4. This event was observed in the background of other structural events involving RAD51D. Its functional significance is undetermined.
RAD51D	0	MSKCC-DMP	P-0025137-T01-IM6	RAD51D-ASIC2 fusion	yes	unknown		unknown	ASIC2 (NM_001094) - RAD51D (NM_133629) Rearrangement : c.556-520534:ASIC2_c.322:RAD51Ddup Note: The ASIC2  - RAD51D Rearrangement results in the fusion of exon 1 of ASIC2 with exons 4-7 of RAD51D. The breakpoint in RAD51D is within exon4. This event was observed in the background of other structural events involving RAD51D. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025137-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -  ERG (NM_182918) Fusion (TMPRSS2 exon 2 fused with ERG exon 3): c.126+367:TMPRSS2_c.237-934:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025137-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -  ERG (NM_182918) Fusion (TMPRSS2 exon 2 fused with ERG exon 3): c.126+367:TMPRSS2_c.237-934:ERGdel
NCOR1	0	MSKCC-DMP	P-0025201-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.6536+1_c.6955+550del Note: The NCOR1 rearrangement is an intragenic deletion of exons 41 to 44. One of the breakpoints is within exon 41. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025319-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-607:TMPRSS2_c.40-55236:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0025319-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-607:TMPRSS2_c.40-55236:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0025319-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.938_c.794+1011inv Note: The TMPRSS2 rearrangement results in the inversion of exons 8-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025332-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4096:TMPRSS2_c.40-55162:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025332-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4096:TMPRSS2_c.40-55162:ERGdel
FLT4	0	MSKCC-DMP	P-0025342-T01-IM6	MGAT1-FLT4 fusion	yes	unknown		unknown	MGAT1 (NM_001114617) - FLT4 (NM_182925) rearrangement: c.-127+1128:MGAT1_c.3097-204:FLT4del Note: The MGAT1 - FLT4 rearrangement is a deletion that results in the fusion of the MGAT1 5UTR and FLT4 exons 23-30. The functional significance is undetermined.
MGAT1	0	MSKCC-DMP	P-0025342-T01-IM6	MGAT1-FLT4 fusion	yes	unknown		unknown	MGAT1 (NM_001114617) - FLT4 (NM_182925) rearrangement: c.-127+1128:MGAT1_c.3097-204:FLT4del Note: The MGAT1 - FLT4 rearrangement is a deletion that results in the fusion of the MGAT1 5UTR and FLT4 exons 23-30. The functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0025408-T01-IM6	PPP1R15B-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.706:PIK3R3_chr1:g.204357692inv Note: The PIK3R3 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined. Multiple rearrangements involving PIK3R3 were detected in this sample and a more complex rearrangement resulting in a PIK3R3 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PPP1R15B	0	MSKCC-DMP	P-0025408-T01-IM6	PPP1R15B-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.706:PIK3R3_chr1:g.204357692inv Note: The PIK3R3 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined. Multiple rearrangements involving PIK3R3 were detected in this sample and a more complex rearrangement resulting in a PIK3R3 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FOXO1	0	MSKCC-DMP	P-0025414-T01-IM6	LINC01309-FOXO1 fusion	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement: c.1774:FOXO1_chr13:g.105039234inv Note: The FOXO1 rearrangement is an inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
LINC01309	0	MSKCC-DMP	P-0025414-T01-IM6	LINC01309-FOXO1 fusion	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement: c.1774:FOXO1_chr13:g.105039234inv Note: The FOXO1 rearrangement is an inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
IKZF1	0	MSKCC-DMP	P-0010823-T02-IM6	POM121L12-IKZF1 fusion	yes	unknown		unknown	IKZF1 (NM_006060) Rearrangement : c.1446:IKZF1_chr7:g.52483056inv Note: The IKZF1 Rearrangement results in the  inversion of exon8.One of the breakpoints is within exon8. Its functional significance is undetermined.
POM121L12	0	MSKCC-DMP	P-0010823-T02-IM6	POM121L12-IKZF1 fusion	yes	unknown		unknown	IKZF1 (NM_006060) Rearrangement : c.1446:IKZF1_chr7:g.52483056inv Note: The IKZF1 Rearrangement results in the  inversion of exon8.One of the breakpoints is within exon8. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0025376-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-5628:EML4_c.3173-350:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
EML4	0	MSKCC-DMP	P-0025376-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-5628:EML4_c.3173-350:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
ZFHX3	0	MSKCC-DMP	P-0025379-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.8197:ZFHX3_chr16:g.72806055del Note: The ZFHX3 rearrangement is a deletion of exons 9-10. One of the breakpoints is within exon 9. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0025405-T01-IM6	AGPAT2-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - AGPAT2 (NM_006412) rearrangement: c.4396:NOTCH1_c.183-2771:AGPAT2dup Note: The NOTCH1 rearrangement is a duplication which results in the fusion of NOTCH1 exons 1-25 with AGPAT2 exons 2-6. One of the breakpoints is within NOTCH1 exon 25. Its functional significance is undetermined.
AGPAT2	0	MSKCC-DMP	P-0025405-T01-IM6	AGPAT2-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - AGPAT2 (NM_006412) rearrangement: c.4396:NOTCH1_c.183-2771:AGPAT2dup Note: The NOTCH1 rearrangement is a duplication which results in the fusion of NOTCH1 exons 1-25 with AGPAT2 exons 2-6. One of the breakpoints is within NOTCH1 exon 25. Its functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0025454-T01-IM6	PLXNA2-CSF3R fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1958+31:CSF3R_chr1:g.208621201inv Note: The CSF3R rearrangement is an inversion of exons 1-15. Its functional significance is undetermined.
PLXNA2	0	MSKCC-DMP	P-0025454-T01-IM6	PLXNA2-CSF3R fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1958+31:CSF3R_chr1:g.208621201inv Note: The CSF3R rearrangement is an inversion of exons 1-15. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025455-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.56-2167:TMPRSS2_c.18+1698:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025455-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.56-2167:TMPRSS2_c.18+1698:ERGdel
LOC100507420	0	MSKCC-DMP	P-0025468-T01-IM6	WHSC1L1-LOC100507420 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: chr8:g.37073664_c.748-1:WHSC1L1inv Note: The WHSC1L1 rearrangement is an inversion with a breakpoint is intron 3. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0025468-T01-IM6	WHSC1L1-LOC100507420 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: chr8:g.37073664_c.748-1:WHSC1L1inv Note: The WHSC1L1 rearrangement is an inversion with a breakpoint is intron 3. The functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0025507-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-5 with NTRK3 exons 15-20) :  t(12;15)(p13.2;q25.3)(chr12:g.12024078::chr15:g.88544573) Note: The ETV6-NTRK3 fusion is predicted to be in-frame and includes the kinase domain of NTRK3.
ETV6	0	MSKCC-DMP	P-0025507-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-5 with NTRK3 exons 15-20) :  t(12;15)(p13.2;q25.3)(chr12:g.12024078::chr15:g.88544573) Note: The ETV6-NTRK3 fusion is predicted to be in-frame and includes the kinase domain of NTRK3.
RET	0	MSKCC-DMP	P-0025531-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) RET (NM_020975) fusion: c.619-108NCOA4_c.2137-657RETdup Note: The NCOA4 (NM_001145260) RET (NM_020975) rearrangement is a duplication that results in the fusion of NCOA4 exons 1-7 with RET exons 12-20. This includes RET kinase domain.
TIMM23B	0	MSKCC-DMP	P-0025531-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) RET (NM_020975) fusion: c.619-108NCOA4_c.2137-657RETdup Note: The NCOA4 (NM_001145260) RET (NM_020975) rearrangement is a duplication that results in the fusion of NCOA4 exons 1-7 with RET exons 12-20. This includes RET kinase domain.
KMT2D	0	MSKCC-DMP	P-0025550-T01-IM6	KMT2D-intragenic	yes	unknown		out of frame	KMT2D (NM_003482) rearrangement: c.840-14_c.10232-1071del Note: The KMT2D rearrangement is an intragenic deletion of exons 7-34. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0025558-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1(NM_004360) Rearrangement : c.388-1507_c.434del Note: The CDH1Rearrangement results in the intragenic deletion of exon4 of CDH1. One of the breakpoint is within exon4.Its functional significance is undetermined.
MIPOL1	0	MSKCC-DMP	P-0025571-T01-IM6	FOXA1-MIPOL1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) - MIPOL1 (NM_138731) rearrangement: c.-25:FOXA1_c.1032-12901:MIPOL1dup Note: The FOXA1 - MIPOL1 rearrangement is a duplication with breakpoints within the FOXA1 5 UTR and MIPOL1 intron 13. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0025571-T01-IM6	FOXA1-MIPOL1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) - MIPOL1 (NM_138731) rearrangement: c.-25:FOXA1_c.1032-12901:MIPOL1dup Note: The FOXA1 - MIPOL1 rearrangement is a duplication with breakpoints within the FOXA1 5 UTR and MIPOL1 intron 13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025571-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10 ):  c.56-2748:TMPRSS2_c.18+2970:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025571-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10 ):  c.56-2748:TMPRSS2_c.18+2970:ERGdel
LOC100507420	0	MSKCC-DMP	P-0025591-T01-IM6	WHSC1L1-LOC100507420 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: chr8:g.37147510_c.1986+96inv Note: The WHSC1L1 rearrangement results in the inversion of exons 11-24. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0025591-T01-IM6	WHSC1L1-LOC100507420 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: chr8:g.37147510_c.1986+96inv Note: The WHSC1L1 rearrangement results in the inversion of exons 11-24. The functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0025595-T01-IM6	RXRB-PIK3R2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - RXRB (NM_021976) rearrangement: t(6;19)(p21.32;p13.11)(chr6:g.33164798::chr19:g.18273076) Note: The PIK3R2 - RXRB rearrangement is a translocation that results in the fusion of PIK3R2 exons 1-8 with RXRB exon 5-10. One of the breakpoints is within PIK3R2 exon 8. The functional significance is undetermined.
RXRB	0	MSKCC-DMP	P-0025595-T01-IM6	RXRB-PIK3R2 fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - RXRB (NM_021976) rearrangement: t(6;19)(p21.32;p13.11)(chr6:g.33164798::chr19:g.18273076) Note: The PIK3R2 - RXRB rearrangement is a translocation that results in the fusion of PIK3R2 exons 1-8 with RXRB exon 5-10. One of the breakpoints is within PIK3R2 exon 8. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0025603-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.2965_c.5504del Note: The CREBBP rearrangement is an intragenic deletion of exons 15-31. Both breakpoints are within exon. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0025603-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.1201_c.1632-102inv Note: The EGFR rearrangement is an intragenic inversion of exons 10-13. One of the breakpoints is within exon 10. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0025609-T01-IM6	SHROOM3-RET fusion	yes	unknown		in frame	SHROOM3 (NM_020859) - RET (NM_020975) rearrangement:  t(4;10)(q21.1;q11.21)(chr4:g.77664882::chr10:g.43611545) Note: The SHROOM3 - RET rearrangement is a translocation that results in the fusion of SHROOM3 exons 1-5 with RET exons 12- 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
SHROOM3	0	MSKCC-DMP	P-0025609-T01-IM6	SHROOM3-RET fusion	yes	unknown		in frame	SHROOM3 (NM_020859) - RET (NM_020975) rearrangement:  t(4;10)(q21.1;q11.21)(chr4:g.77664882::chr10:g.43611545) Note: The SHROOM3 - RET rearrangement is a translocation that results in the fusion of SHROOM3 exons 1-5 with RET exons 12- 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
DOT1L	0	MSKCC-DMP	P-0025609-T01-IM6	TMPRSS9-DOT1L fusion	yes	unknown		out of frame	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.2446+369:TMPRSS9_c.708-36:DOT1Ldup Note: The TMPRSS9 - DOT1L rearrangement is a duplication that results in the fusion of TMPRSS9 exons 1-13 with DOT1L exons 9-28. The functional significance is undetermined.
TMPRSS9	0	MSKCC-DMP	P-0025609-T01-IM6	TMPRSS9-DOT1L fusion	yes	unknown		out of frame	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.2446+369:TMPRSS9_c.708-36:DOT1Ldup Note: The TMPRSS9 - DOT1L rearrangement is a duplication that results in the fusion of TMPRSS9 exons 1-13 with DOT1L exons 9-28. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0025609-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.4323+116_chr4:g.187770197inv Note: The FAT1 rearrangement is an inversion that includes FAT1 exons  1-7. The functional significance is undetermined.
FGFR4	0	MSKCC-DMP	P-0025609-T01-IM6	DPP10-FGFR4 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - DPP10 (NM_001178034) rearrangement: t(2;5)(q14.1;q35.2)(chr2:g.115223375::chr5:g.176518727) Note: The FGFR4 - DPP10 rearrangement is a translocation with breakpoints within FGFR4 exon 6 and DPP10 intron 1. The functional significance is undetermined.
DPP10	0	MSKCC-DMP	P-0025609-T01-IM6	DPP10-FGFR4 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - DPP10 (NM_001178034) rearrangement: t(2;5)(q14.1;q35.2)(chr2:g.115223375::chr5:g.176518727) Note: The FGFR4 - DPP10 rearrangement is a translocation with breakpoints within FGFR4 exon 6 and DPP10 intron 1. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0025686-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.994-1104_c.1157del Note: The TP53 rearrangement is an intragenic deletion of exons 10-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0025693-T01-IM6	EMBP1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(p11.2;p13.2)(chr1:g.121485157::chr19:g.10270971) Note: The DNMT1 rearrangement is a translocation with a breakpoint within intron DNMT1 intron 13. The functional significance is undetermined.
EMBP1	0	MSKCC-DMP	P-0025693-T01-IM6	EMBP1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(p11.2;p13.2)(chr1:g.121485157::chr19:g.10270971) Note: The DNMT1 rearrangement is a translocation with a breakpoint within intron DNMT1 intron 13. The functional significance is undetermined.
PLIN4	0	MSKCC-DMP	P-0025693-T01-IM6	SMARCA4-PLIN4 fusion	yes	unknown		in frame	SMARCA4 (NM_003072) - PLIN4 (NM_001080400) rearrangement: c.1419+91:SMARCA4_c.214-57:PLIN4inv Note: The SMARCA4 - PLIN4 rearrangement is an inversion that results in the fusion of SMARCA4 exons 1-8 with PLIN4 exons 3-6. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0025693-T01-IM6	SMARCA4-PLIN4 fusion	yes	unknown		in frame	SMARCA4 (NM_003072) - PLIN4 (NM_001080400) rearrangement: c.1419+91:SMARCA4_c.214-57:PLIN4inv Note: The SMARCA4 - PLIN4 rearrangement is an inversion that results in the fusion of SMARCA4 exons 1-8 with PLIN4 exons 3-6. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0025693-T01-IM6	ZNF536-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.843+61_chr19:g.30723700inv Note: The DNMT1 rearrangement is an inversion that includes DNMT1 exons 1-10. The functional significance is undetermined.
ZNF536	0	MSKCC-DMP	P-0025693-T01-IM6	ZNF536-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.843+61_chr19:g.30723700inv Note: The DNMT1 rearrangement is an inversion that includes DNMT1 exons 1-10. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0025693-T01-IM6	YJEFN3-SMARCA4 fusion	yes	unknown		in frame	SMARCA4 (NM_003072) - YJEFN3 (NM_001190328) rearrangement:  c.2859+122:SMARCA4_c.169-43C:YJEFN3del Note: The SMARCA4 - YJEFN3 rearrangement is a deletion that results in the fusion of SMARCA4 exons 1-19 to YJEFN3 exons 3-6. The functional significance is undetermined.
YJEFN3	0	MSKCC-DMP	P-0025693-T01-IM6	YJEFN3-SMARCA4 fusion	yes	unknown		in frame	SMARCA4 (NM_003072) - YJEFN3 (NM_001190328) rearrangement:  c.2859+122:SMARCA4_c.169-43C:YJEFN3del Note: The SMARCA4 - YJEFN3 rearrangement is a deletion that results in the fusion of SMARCA4 exons 1-19 to YJEFN3 exons 3-6. The functional significance is undetermined.
PODNL1	0	MSKCC-DMP	P-0025693-T01-IM6	DNAJB1-PODNL1 fusion	yes	unknown		unknown	DNAJB13 (NM_153614) - PODNL1 (NM_001146254) rearrangement: c.211+1:DNAJB1_c.18+1046:PODNL1del Note: The DNAJB13 - PODNL1 rearrangement is a deletion that results in the fusion of DNAJB13 exon 1 to PODNL1 exons 2-8. The functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0025693-T01-IM6	DNAJB1-PODNL1 fusion	yes	unknown		unknown	DNAJB13 (NM_153614) - PODNL1 (NM_001146254) rearrangement: c.211+1:DNAJB1_c.18+1046:PODNL1del Note: The DNAJB13 - PODNL1 rearrangement is a deletion that results in the fusion of DNAJB13 exon 1 to PODNL1 exons 2-8. The functional significance is undetermined.
C19orf60	0	MSKCC-DMP	P-0025693-T01-IM6	UPF1-C19orf60 fusion	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: chr19:g.18703364_c.2458-32del Note: The UPF1 rearrangement is a deletion that includes UPF1 exons 1-17. The functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0025693-T01-IM6	UPF1-C19orf60 fusion	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: chr19:g.18703364_c.2458-32del Note: The UPF1 rearrangement is a deletion that includes UPF1 exons 1-17. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0025698-T01-IM6	PUM1-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: chr1:g.31397626_c.1615del Note: The MTOR rearrangement is a deletion that includes MTOR exons 1-11. One of the breakpoints is within MTOR exon 11. The functional significance is undetermined.
PUM1	0	MSKCC-DMP	P-0025698-T01-IM6	PUM1-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: chr1:g.31397626_c.1615del Note: The MTOR rearrangement is a deletion that includes MTOR exons 1-11. One of the breakpoints is within MTOR exon 11. The functional significance is undetermined.
LINC01192	0	MSKCC-DMP	P-0025663-T01-IM6	PRKCI-LINC01192 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: chr3:g.163003734_c.102-9:PRKCIinv Note: The PRKCI rearrangement is an inversion with a breakpoint in intron 1. The functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0025663-T01-IM6	PRKCI-LINC01192 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: chr3:g.163003734_c.102-9:PRKCIinv Note: The PRKCI rearrangement is an inversion with a breakpoint in intron 1. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0025637-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) Rearrangement : c.1593+9:SMARCA4_c.220+16280:NF1dup Note: The SMARCA4 - CARM1 Rearrangement results in the fusion of exons 1-9 of SMARCA4 with exons 2-16 of CARM1. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0025637-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) Rearrangement : c.1593+9:SMARCA4_c.220+16280:NF1dup Note: The SMARCA4 - CARM1 Rearrangement results in the fusion of exons 1-9 of SMARCA4 with exons 2-16 of CARM1. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0025642-T01-IM6	EP300-intragenic	yes	unknown		out of frame	EP300 (NM_001429) Rearrangement : c.94+9078_c.3672-121del Note: The EP300 Rearrangement results in the intragenic deletion of exons 2-20. The functional significance is undetermined.
SHC2	0	MSKCC-DMP	P-0025647-T01-IM6	MAP3K14-SHC2 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) Rearrangement :  t(17;19)(q21.31;p13.3)(chr17:g.43364016::chr19:g.50046598) Note: The MAP3K14 Rearrangement results in the possible truncation of MAP3K14 with a breakpoint of exon5. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0025647-T01-IM6	MAP3K14-SHC2 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) Rearrangement :  t(17;19)(q21.31;p13.3)(chr17:g.43364016::chr19:g.50046598) Note: The MAP3K14 Rearrangement results in the possible truncation of MAP3K14 with a breakpoint of exon5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025650-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 3) : c.56-2498:TMPRSS2_c.39+45031:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025650-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 3) : c.56-2498:TMPRSS2_c.39+45031:ERGdel
ERG	0	MSKCC-DMP	P-0025676-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+2967:TMPRSS2_c.39+20578:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0025676-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+2967:TMPRSS2_c.39+20578:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
DEDD2	0	MSKCC-DMP	P-0025677-T01-IM6	CIC-DEDD2 fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: chr19:g.42722240_c.4517dup Note: The CIC rearrangement results in the duplication of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0025677-T01-IM6	CIC-DEDD2 fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: chr19:g.42722240_c.4517dup Note: The CIC rearrangement results in the duplication of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
CACNB1	0	MSKCC-DMP	P-0025683-T01-IM6	ERBB2-CACNB1 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: chr17:g.37353947_c.2307+2inv Note: The ERBB2 rearrangement results in the inversion of exons 20-27. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0025683-T01-IM6	ERBB2-CACNB1 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: chr17:g.37353947_c.2307+2inv Note: The ERBB2 rearrangement results in the inversion of exons 20-27. The functional significance is undetermined.
HOXB13	0	MSKCC-DMP	P-0025683-T01-IM6	LPO-HOXB13 fusion	yes	unknown		unknown	LPO (NM_006151) - HOXB13 (NM_006361) rearrangement: c.1106-623:LPO_c.371:HOXB13inv Note: The LPO - HOXB13 rearrangement is an inversion that results in the fusion of LPO exons 1-8 with HOXB13 exons 1-2. One of the breakpoints is within HOXB13 exon 1. The functional significance is undetermined.
LPO	0	MSKCC-DMP	P-0025683-T01-IM6	LPO-HOXB13 fusion	yes	unknown		unknown	LPO (NM_006151) - HOXB13 (NM_006361) rearrangement: c.1106-623:LPO_c.371:HOXB13inv Note: The LPO - HOXB13 rearrangement is an inversion that results in the fusion of LPO exons 1-8 with HOXB13 exons 1-2. One of the breakpoints is within HOXB13 exon 1. The functional significance is undetermined.
SRP68	0	MSKCC-DMP	P-0025683-T01-IM6	RPTOR-SRP68 fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: chr17:g.74050297_c.2442dup Note: The RPTOR rearrangement results in the duplication of exons 1-21. One of the breakpoints is within exon 21. The functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0025683-T01-IM6	RPTOR-SRP68 fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: chr17:g.74050297_c.2442dup Note: The RPTOR rearrangement results in the duplication of exons 1-21. One of the breakpoints is within exon 21. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0025684-T01-IM6	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.2140_c.1936+32del Note: The DNMT3A rearrangement results in the deletion of exons 17-18. One of the breakpoints is within exon 18. The functional significance is undetermined.
CDK6	0	MSKCC-DMP	P-0025704-T01-IM6	CDK6-intragenic	yes	unknown		unknown	CDK6 (NM_001145306) rearrangement: c.728_c.699-1995del Note: The CDK6 rearrangement results in the deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.
MAOB	0	MSKCC-DMP	P-0020938-T02-IM6	KDM6A-MAOB fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.43650588_c.3209+24:KDM6Adel Note: The KDM6A rearrangement is a deletion of exons 1-21.
KDM6A	0	MSKCC-DMP	P-0020938-T02-IM6	KDM6A-MAOB fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.43650588_c.3209+24:KDM6Adel Note: The KDM6A rearrangement is a deletion of exons 1-21.
NF2	0	MSKCC-DMP	P-0025753-T01-IM6	CSNK1E-NF2 fusion	yes	unknown		unknown	CSNK1E (NM_001894) - NF2 (NM_000268) Rearrangement : c.886-1655:CSNK1E_c.288:NF2inv Note: The CSNK1E (NM_001894) - NF2 (NM_000268) Rearrangement results in the fusion of exons of 1-8 of CSNK1E with exons 3-16 of NF2. The breakpoint in NF2 is within exon3. Its functional significance is undetermined.
CSNK1E	0	MSKCC-DMP	P-0025753-T01-IM6	CSNK1E-NF2 fusion	yes	unknown		unknown	CSNK1E (NM_001894) - NF2 (NM_000268) Rearrangement : c.886-1655:CSNK1E_c.288:NF2inv Note: The CSNK1E (NM_001894) - NF2 (NM_000268) Rearrangement results in the fusion of exons of 1-8 of CSNK1E with exons 3-16 of NF2. The breakpoint in NF2 is within exon3. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0025761-T01-IM6	PGAP3-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement : c.1769:CDK12_c.433-135:PGAP3dup Note: The CDK12 Rearrangement results in the duplication of exons 2-14.One of the breakpoints is within exon2. Its functional significance is undetermined.
PGAP3	0	MSKCC-DMP	P-0025761-T01-IM6	PGAP3-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement : c.1769:CDK12_c.433-135:PGAP3dup Note: The CDK12 Rearrangement results in the duplication of exons 2-14.One of the breakpoints is within exon2. Its functional significance is undetermined.
PSD4	0	MSKCC-DMP	P-0025761-T01-IM6	PAX8-PSD4 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - PSD4 (NM_012455) Rearrangement : c.1088-192:PAX8_c.1629-1102:PSD4del Note : The PAX8 - PSD4 Rearrangement results in the fusion of exons 1-10 with PSD4 exons 6-17. Its functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0025761-T01-IM6	PAX8-PSD4 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - PSD4 (NM_012455) Rearrangement : c.1088-192:PAX8_c.1629-1102:PSD4del Note : The PAX8 - PSD4 Rearrangement results in the fusion of exons 1-10 with PSD4 exons 6-17. Its functional significance is undetermined.
OR1F1	0	MSKCC-DMP	P-0025711-T01-IM6	CREBBP-OR1F1 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.3238048_c.1470inv Note: The CREBBP rearrangement results in the inversion of exons 6-31. One of the breakpoints is within exon 6. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0025711-T01-IM6	CREBBP-OR1F1 fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.3238048_c.1470inv Note: The CREBBP rearrangement results in the inversion of exons 6-31. One of the breakpoints is within exon 6. The functional significance is undetermined.
IRF4	0	MSKCC-DMP	P-0025757-T01-IM6	DNAH8-IRF4 fusion	yes	unknown		unknown	DNAH8 (NM_001206927) - IRF4 (NM_002460) Rearrangement : c.13053+1789:DNAH8_c.1073:IRF4dup Note: The DNAH8 - IRF4 Rearrangement results in the fusion of exons 1-87 of DNAH8 with exons 7- 9 of IRF4. The breakpoint in IRF4 is within exon 7. Its functional significance is undetermined.
DNAH8	0	MSKCC-DMP	P-0025757-T01-IM6	DNAH8-IRF4 fusion	yes	unknown		unknown	DNAH8 (NM_001206927) - IRF4 (NM_002460) Rearrangement : c.13053+1789:DNAH8_c.1073:IRF4dup Note: The DNAH8 - IRF4 Rearrangement results in the fusion of exons 1-87 of DNAH8 with exons 7- 9 of IRF4. The breakpoint in IRF4 is within exon 7. Its functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0025763-T01-IM6	NBPF22P-STAG2 fusion	yes	unknown		unknown	STAG2 (NM_001042749) Rearrangement : t(X;5)(q25;q14.2)(chrX:g.123178980::chr5:g.85708121) Note: The STAG2 Rearrangement results in the possible translocation of STAG2, the breakpoint in STAG2 is within intron7. Its functional significance is undetermined.
NBPF22P	0	MSKCC-DMP	P-0025763-T01-IM6	NBPF22P-STAG2 fusion	yes	unknown		unknown	STAG2 (NM_001042749) Rearrangement : t(X;5)(q25;q14.2)(chrX:g.123178980::chr5:g.85708121) Note: The STAG2 Rearrangement results in the possible translocation of STAG2, the breakpoint in STAG2 is within intron7. Its functional significance is undetermined.
TRIM49B	0	MSKCC-DMP	P-0025770-T01-IM6	FGFR1-TRIM49B fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: t(8;11)(p11.23;p11.12)(chr8:g.38275713::chr11:g.48968445) Note: The FGFR1 rearrangement is a translocation involving exon 11. Its functional significance is undetermined. Multiple rearrangements involving FGFR1 were detected in this sample and a more complex rearrangement resulting in a FGFR1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FGFR1	0	MSKCC-DMP	P-0025770-T01-IM6	FGFR1-TRIM49B fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: t(8;11)(p11.23;p11.12)(chr8:g.38275713::chr11:g.48968445) Note: The FGFR1 rearrangement is a translocation involving exon 11. Its functional significance is undetermined. Multiple rearrangements involving FGFR1 were detected in this sample and a more complex rearrangement resulting in a FGFR1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
BICC1	0	MSKCC-DMP	P-0025807-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion ( FGFR2 exons 1-17 fused to BICC1 exons 3-21): c.2301+895:FGFR2_c.238-35107:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0025807-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion ( FGFR2 exons 1-17 fused to BICC1 exons 3-21): c.2301+895:FGFR2_c.238-35107:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0025807-T01-IM6	YTHDF3-FGFR2 fusion	yes	unknown		unknown	YTHDF3 (NM_152758) - FGFR2 (NM_000141) rearrangement: t(8;10)(q12.3;q26.13)(chr8:g.64081967::chr10:g.123242317) Note: The YTHDF3 - FGFR2 rearrangement is a translocation that results in the fusion of YTHDF3 exons 1-2 with FGFR2 exon 18. This does not include the kinase domain of FGFR2 and the functional significance is undetermined.
YTHDF3	0	MSKCC-DMP	P-0025807-T01-IM6	YTHDF3-FGFR2 fusion	yes	unknown		unknown	YTHDF3 (NM_152758) - FGFR2 (NM_000141) rearrangement: t(8;10)(q12.3;q26.13)(chr8:g.64081967::chr10:g.123242317) Note: The YTHDF3 - FGFR2 rearrangement is a translocation that results in the fusion of YTHDF3 exons 1-2 with FGFR2 exon 18. This does not include the kinase domain of FGFR2 and the functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025823-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-246:TMPRSS2_c.18+2365:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025823-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-246:TMPRSS2_c.18+2365:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025823-T01-IM6	SIMC1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_023034) - SIMC1 (NM_001308195) rearrangement: t(5;21)(q35.2;q22.3)(chr5:g.175765852::chr21:g.42870360) Note: The TMPRSS2 - SIMC1 rearrangement is a translocation that results in the fusion of TMPRSS2 exon 1 with SIMC1 exons 9-10 and is predicted to be in-frame. The functional significance is undetermined.
SIMC1	0	MSKCC-DMP	P-0025823-T01-IM6	SIMC1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_023034) - SIMC1 (NM_001308195) rearrangement: t(5;21)(q35.2;q22.3)(chr5:g.175765852::chr21:g.42870360) Note: The TMPRSS2 - SIMC1 rearrangement is a translocation that results in the fusion of TMPRSS2 exon 1 with SIMC1 exons 9-10 and is predicted to be in-frame. The functional significance is undetermined.
RHEB	0	MSKCC-DMP	P-0025823-T01-IM6	DNAJB6-RHEB fusion	yes	unknown		out of frame	RHEB (NM_005614) - DNAJB6 (NM_058246) rearrangement: c.380+103:RHEB_c.346+6811:DNAJB6inv Note: The RHEB - DNAJB6 rearrangement is an inversion that results in the fusion of RHEB exons 1-6 with DNAJB6 exons 6-10. The functional significance is undetermined.
DNAJB6	0	MSKCC-DMP	P-0025823-T01-IM6	DNAJB6-RHEB fusion	yes	unknown		out of frame	RHEB (NM_005614) - DNAJB6 (NM_058246) rearrangement: c.380+103:RHEB_c.346+6811:DNAJB6inv Note: The RHEB - DNAJB6 rearrangement is an inversion that results in the fusion of RHEB exons 1-6 with DNAJB6 exons 6-10. The functional significance is undetermined.
MEF2B	0	MSKCC-DMP	P-0025824-T01-IM6	LINC01224-MEF2B fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: c.258+19_chr19:g.23671215inv Note: The MEF2B rearrangement results in the inversion of exons 13. The functional significance is undetermined.
LINC01224	0	MSKCC-DMP	P-0025824-T01-IM6	LINC01224-MEF2B fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: c.258+19_chr19:g.23671215inv Note: The MEF2B rearrangement results in the inversion of exons 13. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0025880-T01-IM6	CASZ1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(p36.22;p13.2)(chr1:g.10857423::chr19:g.10265403) Note: The DNMT1 rearrangement is a translocation with a breakpoint in exon 20. The functional significance is undetermined.
CASZ1	0	MSKCC-DMP	P-0025880-T01-IM6	CASZ1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(p36.22;p13.2)(chr1:g.10857423::chr19:g.10265403) Note: The DNMT1 rearrangement is a translocation with a breakpoint in exon 20. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0025921-T01-IM6	CCDC85A-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangment t(2;12)(p16.1;p13.33)(chr2:g.56637105::chr12:g.419156) Note: The KDM5A rearrangement is a translocation that involves exon 22. Its functional significance is undetermined.
CCDC85A	0	MSKCC-DMP	P-0025921-T01-IM6	CCDC85A-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangment t(2;12)(p16.1;p13.33)(chr2:g.56637105::chr12:g.419156) Note: The KDM5A rearrangement is a translocation that involves exon 22. Its functional significance is undetermined.
CDKN1B	0	MSKCC-DMP	P-0025924-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.-1037_c.401del Note: The CDKN1B rearrangement results in the intragenic deletion of exon 1. One of the breakpoint is within exon 1. Its functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0025924-T01-IM6	MED12-intragenic	yes	unknown		in frame	MED12 (NM_005120) rearrangement: c.5827-10_c.6267+178del Note: The MED12 rearrangement results in the intragenic deletion of exons 41 and 42. Its functional significance is undetermined.
PRH1-PRR4	0	MSKCC-DMP	P-0025601-T02-IM6	ETV6-PRH1-PRR4 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.464-6797:ETV6_chr12:g.11225690inv Note: The ETV6 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0025601-T02-IM6	ETV6-PRH1-PRR4 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.464-6797:ETV6_chr12:g.11225690inv Note: The ETV6 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0025835-T01-IM6	KCNH8-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(3;10)(p24.3;q26.13)(chr3:g.18908797::chr10:g.123240192) Note: The FGFR2 rearrangement is a translocation involving exon 18. Its functional significance is undetermined. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
KCNH8	0	MSKCC-DMP	P-0025835-T01-IM6	KCNH8-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(3;10)(p24.3;q26.13)(chr3:g.18908797::chr10:g.123240192) Note: The FGFR2 rearrangement is a translocation involving exon 18. Its functional significance is undetermined. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FGFR2	0	MSKCC-DMP	P-0025835-T01-IM6	FOXP1-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - FOXP1 (NM_001244814) rearrangement: t(3;10)(p13;q26.13)(chr3:g.71178081::chr10:g.123242260) Note: The FGFR2 - FOXP1 rearrangement is a translocation involving FGFR2 exon 17 and FOXP1 exon 3. Its functional significance is undetermined. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FOXP1	0	MSKCC-DMP	P-0025835-T01-IM6	FOXP1-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - FOXP1 (NM_001244814) rearrangement: t(3;10)(p13;q26.13)(chr3:g.71178081::chr10:g.123242260) Note: The FGFR2 - FOXP1 rearrangement is a translocation involving FGFR2 exon 17 and FOXP1 exon 3. Its functional significance is undetermined. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
KIF5B	0	MSKCC-DMP	P-0025838-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975)  fusion ( KIF5B exons 1-15 fused with RET exons 12-20.): c.1726-601:KIF5B_c.2136+788:RETinv Note: The KIF5B - RET fusion is predicted to be in-frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0025838-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975)  fusion ( KIF5B exons 1-15 fused with RET exons 12-20.): c.1726-601:KIF5B_c.2136+788:RETinv Note: The KIF5B - RET fusion is predicted to be in-frame and includes the kinase domain of RET.
CDHR3	0	MSKCC-DMP	P-0025841-T01-IM6	KMT2C-CDHR3 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8725:KMT2C_chr7:g.105612673del Note: The KMT2C rearrangement results in the deletion of exons 38 - 59. One of the breakpoints is within exon 59. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0025841-T01-IM6	KMT2C-CDHR3 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8725:KMT2C_chr7:g.105612673del Note: The KMT2C rearrangement results in the deletion of exons 38 - 59. One of the breakpoints is within exon 59. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0025928-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+483:KIF5B_c.2137-122C>T:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0025928-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+483:KIF5B_c.2137-122C>T:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
LOC101928448	0	MSKCC-DMP	P-0025935-T01-IM6	MAP3K1-LOC101928448 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.1085:MAP3K1_chr5:g.55920869inv Note: The MAP3K1 rearrangement results in the inversion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0025935-T01-IM6	MAP3K1-LOC101928448 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.1085:MAP3K1_chr5:g.55920869inv Note: The MAP3K1 rearrangement results in the inversion of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0007343-T02-IM6	ANK2-INPPL1 fusion	yes	unknown		unknown	INPPL1 (NM_001567) - ANK2 (NM_001148) rearrangement: t(4;11)(q25-q26;q13.4)(chr4:g.113898703::chr11:g.71943348) Note: The INPPL1 - ANK2 rearrangement is a reciprocal translocation that results in the mid-exon fusion of INPPL1 exons 1-14 with ANK2 exons 3-46. The functional significance is undetermined.
ANK2	0	MSKCC-DMP	P-0007343-T02-IM6	ANK2-INPPL1 fusion	yes	unknown		unknown	INPPL1 (NM_001567) - ANK2 (NM_001148) rearrangement: t(4;11)(q25-q26;q13.4)(chr4:g.113898703::chr11:g.71943348) Note: The INPPL1 - ANK2 rearrangement is a reciprocal translocation that results in the mid-exon fusion of INPPL1 exons 1-14 with ANK2 exons 3-46. The functional significance is undetermined.
IER2	0	MSKCC-DMP	P-0007343-T02-IM6	TBX3-IER2 fusion	yes	unknown		unknown	TBX3 (NM_016569.3) rearrangement: t(12;19)(q24.21;p13.3)(chr12:g.115112036::chr19:g.13270583) Note: The TBX3 rearrangement is a translocation that involved the TBX3  exon 7 and a genomic region on chromosome 19.  One of the breakpoints is in exon 7 of TBX3. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0007343-T02-IM6	TBX3-IER2 fusion	yes	unknown		unknown	TBX3 (NM_016569.3) rearrangement: t(12;19)(q24.21;p13.3)(chr12:g.115112036::chr19:g.13270583) Note: The TBX3 rearrangement is a translocation that involved the TBX3  exon 7 and a genomic region on chromosome 19.  One of the breakpoints is in exon 7 of TBX3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0007343-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+662TMPRSS2_c.39+64787ERGdel. Note: The TMPRSS2 ERG fusion is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0007343-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+662TMPRSS2_c.39+64787ERGdel. Note: The TMPRSS2 ERG fusion is predicted to be in frame.
SMAD3	0	MSKCC-DMP	P-0020845-T02-IM6	SMAD3-intragenic	yes	unknown		out of frame	SMAD3 (NM_005902) rearrangement: c.207-2606_c.400+4dup Note: The SMAD3 rearrangement results in the duplication of exon 2. The functional significance is undetermined.
DLGAP1-AS5	0	MSKCC-DMP	P-0020845-T02-IM6	TCEB1-DLGAP1-AS5 fusion	yes	unknown		unknown	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373) Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
TCEB1	0	MSKCC-DMP	P-0020845-T02-IM6	TCEB1-DLGAP1-AS5 fusion	yes	unknown		unknown	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373) Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
FUNDC1	0	MSKCC-DMP	P-0025895-T01-IM6	KDM6A-FUNDC1 fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.44430418_c.3091inv Note: The KDM6A rearrangement results in the inversion of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0025895-T01-IM6	KDM6A-FUNDC1 fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.44430418_c.3091inv Note: The KDM6A rearrangement results in the inversion of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0018048-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement : c.3441_c.3715+147del Note: The ARID1A Rearrangement results in the intragenic deletion of exon13. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0025851-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0025851-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
TBC1D10C	0	MSKCC-DMP	P-0025988-T01-IM6	CCND1-TBC1D10C fusion	yes	unknown		unknown	TBC1D10C (NM_198517) - CCND1 (NM_053056) fusion (TBC1D10C exons 1-8 with CCND1 exons 1-5): c.839-966TBC1D10C_c.1CCND1del. Note: The TBC1D10C - CCND1 rearrangement is a deletion which results in the fusion of TBC1D10C exons 1-8 with CCND1 exons 1- 5. One of the breakpoints is within CCND1 exon 1.  Its functional significance is undetermined.
CCND1	0	MSKCC-DMP	P-0025988-T01-IM6	CCND1-TBC1D10C fusion	yes	unknown		unknown	TBC1D10C (NM_198517) - CCND1 (NM_053056) fusion (TBC1D10C exons 1-8 with CCND1 exons 1-5): c.839-966TBC1D10C_c.1CCND1del. Note: The TBC1D10C - CCND1 rearrangement is a deletion which results in the fusion of TBC1D10C exons 1-8 with CCND1 exons 1- 5. One of the breakpoints is within CCND1 exon 1.  Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0025988-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - BRAF (NM_004333) rearrangement: t(7;21)(q34;q22.3)(chr7:g.140484791::chr21:g.42870515) Note: The TMPRSS2 - BRAF rearrangement is a translocation with breakpoints within TMPRSS2 intron 1 and BRAF intron 9. The functional significance is undetermined. Multiple TMPRSS2 rearrangements were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is suggested, if clinically indicated.
BRAF	0	MSKCC-DMP	P-0025988-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - BRAF (NM_004333) rearrangement: t(7;21)(q34;q22.3)(chr7:g.140484791::chr21:g.42870515) Note: The TMPRSS2 - BRAF rearrangement is a translocation with breakpoints within TMPRSS2 intron 1 and BRAF intron 9. The functional significance is undetermined. Multiple TMPRSS2 rearrangements were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is suggested, if clinically indicated.
SETD2	0	MSKCC-DMP	P-0025988-T01-IM6	SETD2-intragenic	yes	unknown		unknown	SETD2 (NM_014159): c.5361SETD2_c.5142+3718dup Note: The SETD2 rearrangement is a duplication of exons 9-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0026009-T01-IM6	GAS7-TP53 fusion	yes	unknown		unknown	GAS7 (NM_201433) - TP53 (NM_000546) rearrangement: c.184-54871:GAS7_c.996:TP53del Note: The GAS7 - TP53 rearrangement is a deletion that results in the fusion of GAS7 exon 1 with TP53 exons 10-11. One of the breakpoints is within TP53 exon 10. The functional significance is undetermined.
GAS7	0	MSKCC-DMP	P-0026009-T01-IM6	GAS7-TP53 fusion	yes	unknown		unknown	GAS7 (NM_201433) - TP53 (NM_000546) rearrangement: c.184-54871:GAS7_c.996:TP53del Note: The GAS7 - TP53 rearrangement is a deletion that results in the fusion of GAS7 exon 1 with TP53 exons 10-11. One of the breakpoints is within TP53 exon 10. The functional significance is undetermined.
CBFB	0	MSKCC-DMP	P-0026012-T01-IM6	RUFY4-CBFB fusion	yes	unknown		unknown	CBFB(NM_022845) - RUFY4 (NM_198483) rearrangement: t(2;16)(q35;q22.1)(chr2:g.218917363::chr16:g.67063596) Note: The CBFB - RUFY4 rearrangement is a translocation with breakpoints within CBFB intron 1 and RUFY4 intron 2. The functional significance is undetermined.
RUFY4	0	MSKCC-DMP	P-0026012-T01-IM6	RUFY4-CBFB fusion	yes	unknown		unknown	CBFB(NM_022845) - RUFY4 (NM_198483) rearrangement: t(2;16)(q35;q22.1)(chr2:g.218917363::chr16:g.67063596) Note: The CBFB - RUFY4 rearrangement is a translocation with breakpoints within CBFB intron 1 and RUFY4 intron 2. The functional significance is undetermined.
SPG11	0	MSKCC-DMP	P-0025974-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	B2M (NM_004048) Rearrangement : c.5867-701:SPG1_c.150:B2Mdel Note: The B2M Rearrangement results in the deletion of exons 1-2 of B2M. One of the breakpoints is within exon2. Its functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0025974-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	B2M (NM_004048) Rearrangement : c.5867-701:SPG1_c.150:B2Mdel Note: The B2M Rearrangement results in the deletion of exons 1-2 of B2M. One of the breakpoints is within exon2. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0025980-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : c.2480-581_c.4880inv Note: The NOTCH2 Rearrangement results in the intragenic inversion of exons 16-27. One of the breakpoints is within exon27. Its functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0025980-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) Rearrangement :  c.2173+1_c.5379-1098del Note: The POLE Rearrangement results in the deletion of exons 19-39. One of the breakpoints is within exon 19. Its functional significance is undetermined.
MEN1	0	MSKCC-DMP	P-0000541-T03-IM6	MEN1-intragenic	yes	unknown		unknown	MEN1 (NM_000244) Rearrangement : c.1256_1791del Note: The MEN1 Rearrangement event results in the intragenic deletion of MEN1 exons 9-10. The breakpoints are within MEN1 exon9 and exon10.Its functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0000541-T03-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement : c.5355_c.6841+201del Note: The BRCA2 Rearrangement results in the intragenic deletion of exon 11. One of the breakpoints is within exon 11. Its functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0003150-T03-IM6	MLLT4-MYC fusion	yes	unknown		unknown	MYC (NM_002467) Rearrangement : t(6,8)(q27,q24.21)(chr6:g.168309690::chr8:g.128753250) Note: The MYC Rearrangement results in the possible truncation of MYC. One of the breakpoints is within the 3-UTR region after transcription stop site. Its functional significance is undetermined.
MLLT4	0	MSKCC-DMP	P-0003150-T03-IM6	MLLT4-MYC fusion	yes	unknown		unknown	MYC (NM_002467) Rearrangement : t(6,8)(q27,q24.21)(chr6:g.168309690::chr8:g.128753250) Note: The MYC Rearrangement results in the possible truncation of MYC. One of the breakpoints is within the 3-UTR region after transcription stop site. Its functional significance is undetermined.
TPK1	0	MSKCC-DMP	P-0003195-T02-IM6	KMT2C-TPK1 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement : chr7:g.144838860_c.13395:KMT2Cinv Note: The MLL3 Rearrangement results in the inversion of  exons 52-59 of KMT2C. One of the breakpoints is within exons 52. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0003195-T02-IM6	KMT2C-TPK1 fusion	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement : chr7:g.144838860_c.13395:KMT2Cinv Note: The MLL3 Rearrangement results in the inversion of  exons 52-59 of KMT2C. One of the breakpoints is within exons 52. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0003357-T02-IM6	IPO8-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.463+2187:ETV6_chr12:g.30656812inv Note: The ETV6 rearrangement is an inversion of exons 5-8, potentially disrupting gene function.
IPO8	0	MSKCC-DMP	P-0003357-T02-IM6	IPO8-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.463+2187:ETV6_chr12:g.30656812inv Note: The ETV6 rearrangement is an inversion of exons 5-8, potentially disrupting gene function.
ALOX12B	0	MSKCC-DMP	P-0003684-T02-IM6	BRAF-ALOX12B fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: t(7;17)(q34;p13.1)(chr7:g.140486105::chr17:g.7963177) Note: The BRAF rearrangement is a translocation that may result in the truncation of exons 10-18. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0003684-T02-IM6	BRAF-ALOX12B fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: t(7;17)(q34;p13.1)(chr7:g.140486105::chr17:g.7963177) Note: The BRAF rearrangement is a translocation that may result in the truncation of exons 10-18. The functional significance is undetermined.
PTRH2	0	MSKCC-DMP	P-0004835-T02-IM6	BRIP1-PTRH2 fusion	yes	unknown		unknown	BRIP1 (NM_032043) - PTRH2 (NM_016077) rearrangement: c.2575+19: BRIP1_c.-1+243: PTRH2del Note: The BRIP1 - PTRH2 rearrangement is a deletion that results in the fusion of BRIP1 exons 1-18 with PTRH2 exon 2. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0004835-T02-IM6	BRIP1-PTRH2 fusion	yes	unknown		unknown	BRIP1 (NM_032043) - PTRH2 (NM_016077) rearrangement: c.2575+19: BRIP1_c.-1+243: PTRH2del Note: The BRIP1 - PTRH2 rearrangement is a deletion that results in the fusion of BRIP1 exons 1-18 with PTRH2 exon 2. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0005445-T03-IM6	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) Rearrangement : c.250+10968_c.10446dup Note: The MLL3 Rearrangement results in the intragenic duplication of exons 3-43. One of the breakpoints is within exon 43. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0006008-T02-IM6	NOTCH1-intragenic	yes	unknown		out of frame	NOTCH1 (NM_017617) rearrangement: c.3644-7_c.141-7069del Note: The NOTCH1 rearrangement results in the deletion of exons 3-22. The functional significance is undetermined.
C17orf104	0	MSKCC-DMP	P-0007898-T02-IM6	MAP3K14-C17orf104 fusion	yes	unknown		out of frame	MAP3K14 (NM_003954) - C17orf104 (NM_001145080) Rearrangement : c.1656+179:MAP3K1_c.360-1358:C17orf104inv Note: The MAP3K14 -C17orf104 Rearrangement results in the fusion of exons 1-9 of MAP3K1 with exons 4-8 of C17orf104. This event includes the protein kinase domain of MAP3K14.
MAP3K14	0	MSKCC-DMP	P-0007898-T02-IM6	MAP3K14-C17orf104 fusion	yes	unknown		out of frame	MAP3K14 (NM_003954) - C17orf104 (NM_001145080) Rearrangement : c.1656+179:MAP3K1_c.360-1358:C17orf104inv Note: The MAP3K14 -C17orf104 Rearrangement results in the fusion of exons 1-9 of MAP3K1 with exons 4-8 of C17orf104. This event includes the protein kinase domain of MAP3K14.
KMT2B	0	MSKCC-DMP	P-0008599-T02-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) : c.3656_4487inv Note: KMT2B (NM_014727) rearrangement results in an intragenic inversion of exons 12-18. Both the breakpoints are within exon 12 and 18 respectively. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009056-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-864:TMPRSS2_c.18+12444:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009056-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-864:TMPRSS2_c.18+12444:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009640-T02-IM6	ETV1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Fusion (TMPRSS2 exons 1-2 fused with ETV1 exons 5-12):  t(7;21)(p21.2;q22.3)(chr7:g.14024117::chr21:g.42867556)
ETV1	0	MSKCC-DMP	P-0009640-T02-IM6	ETV1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Fusion (TMPRSS2 exons 1-2 fused with ETV1 exons 5-12):  t(7;21)(p21.2;q22.3)(chr7:g.14024117::chr21:g.42867556)
ABL1	0	MSKCC-DMP	P-0009640-T02-IM6	NUP214-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) Rearrangement : c.2658:ABL1_3:c.-70:NUP214inv Note: The ABL1 Rearrangement results in the inversion of exon 11 of ABL1. One of the breakpoints is within exon 11. Its functional significance is undetermined.
NUP214	0	MSKCC-DMP	P-0009640-T02-IM6	NUP214-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) Rearrangement : c.2658:ABL1_3:c.-70:NUP214inv Note: The ABL1 Rearrangement results in the inversion of exon 11 of ABL1. One of the breakpoints is within exon 11. Its functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0010796-T02-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) Rearrangement : c.7139+105_7887del Note: The MGA rearrangement event results in the intragenic deletion of MGA exons 19-23. One of the breakpoints is within MGA exon23.
ERG	0	MSKCC-DMP	P-0010796-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-1410:TMPRSS2_c.19-20820:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0010796-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-1410:TMPRSS2_c.19-20820:ERGdel
STAT3	0	MSKCC-DMP	P-0010983-T02-IM6	CNOT2-STAT3 fusion	yes	unknown		unknown	CNOT2 (NM_014515) - STAT3 (NM_139276) Rearrangement : t(12,17)(q15,q21.1)(chr12:g.70671823::chr17:g.40475061) Note: The CNOT2 - STAT3 Rearrangement results in the fusion of exon 1 of CNOT2 with exons 20-24 of STAT3. The breakpoint in CNOT2 is before the transcription start site and the breakpoint in STAT3 is within exon20. Its functional significance is undetermined.
CNOT2	0	MSKCC-DMP	P-0010983-T02-IM6	CNOT2-STAT3 fusion	yes	unknown		unknown	CNOT2 (NM_014515) - STAT3 (NM_139276) Rearrangement : t(12,17)(q15,q21.1)(chr12:g.70671823::chr17:g.40475061) Note: The CNOT2 - STAT3 Rearrangement results in the fusion of exon 1 of CNOT2 with exons 20-24 of STAT3. The breakpoint in CNOT2 is before the transcription start site and the breakpoint in STAT3 is within exon20. Its functional significance is undetermined.
E2F3	0	MSKCC-DMP	P-0010983-T02-IM6	E2F3-intragenic	yes	unknown		out of frame	E2F3 (NM_001949) Rearrangement : c.394-36841_c.506-3del Note: The E2F3 Rearrangement results in the deletion of exon2 of E2F3. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0011198-T02-IM6	ETV5-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV5 (NM_004454) rearrangement : t(3;21)(q27.2;q22.3)(chr3:g.185827431::chr21:g.42867759) Note: The TMPRSS2-ETV5 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV6 promoter region. PMID: 18172298
ETV5	0	MSKCC-DMP	P-0011198-T02-IM6	ETV5-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV5 (NM_004454) rearrangement : t(3;21)(q27.2;q22.3)(chr3:g.185827431::chr21:g.42867759) Note: The TMPRSS2-ETV5 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV6 promoter region. PMID: 18172298
ERG	0	MSKCC-DMP	P-0012109-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.55+4448:TMPRSS2_c.40-56700:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012109-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.55+4448:TMPRSS2_c.40-56700:ERGdel
POLE	0	MSKCC-DMP	P-0012572-T02-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.86_c.423+93dup Note: The POLE rearrangement is an intragenic duplication of exons 2-5, which includes a part of the POLE exonuclease domain. One of the breakpoints is within exon 2.
KMT2C	0	MSKCC-DMP	P-0012675-T02-IM6	KMT2C-intragenic	yes	unknown		out of frame	KMT2C (NM_170606) rearrangement: c.9263-84_c.162-23697del Note: The KMT2C rearrangement results in the deletion of exons 2-38. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0013613-T02-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) Rearrangement : c.1966-873_c.2087+125inv Note: The MAP3K1 Rearrangement results in the intragenic inversion of exon 11 of MAP3K1. Its functional significance is unknown.
ERG	0	MSKCC-DMP	P-0013844-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-54335:ERG_c.127-1358:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication that results in an in-frame fusion of exons 1-3 of the non-canonical ERG (NM_004449) to exons 3-14 of TMPRSS2.
TMPRSS2	0	MSKCC-DMP	P-0013844-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-54335:ERG_c.127-1358:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication that results in an in-frame fusion of exons 1-3 of the non-canonical ERG (NM_004449) to exons 3-14 of TMPRSS2.
GNAS	0	MSKCC-DMP	P-0014305-T02-IM6	REST-GNAS fusion	yes	unknown		unknown	GNAS (NM_080425) - REST (NM_001193508) rearrangement: t(4;20)(q12;q13.32)(chr4:g.57789330::chr20:g.57429127) Note: The GNAS - REST rearrangement is a translocation which results in the fusion of GNAS (NM_080425)  exon1 to REST exon 4. One of the breakpoints is within GNAS exon 1. The functional significance is undetermined.
REST	0	MSKCC-DMP	P-0014305-T02-IM6	REST-GNAS fusion	yes	unknown		unknown	GNAS (NM_080425) - REST (NM_001193508) rearrangement: t(4;20)(q12;q13.32)(chr4:g.57789330::chr20:g.57429127) Note: The GNAS - REST rearrangement is a translocation which results in the fusion of GNAS (NM_080425)  exon1 to REST exon 4. One of the breakpoints is within GNAS exon 1. The functional significance is undetermined.
EPAS1	0	MSKCC-DMP	P-0014435-T02-IM6	EPAS1-intragenic	yes	unknown		unknown	EPAS1 (NM_001430) rearrangement: c.2045+133_c.2366del Note: The EPAS1 rearrangement is an intragenic deletion of exons 13-15. One of the breakpoints is within exon 15. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0015061-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.3449-1792_c.4412inv Note: The ZFHX3 rearrangement is an inversion of exons 5-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0015063-T02-IM6	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) rearrangement: c.368_c.579+2150inv Note: The TP63 rearrangement is an intragenic inversion of exon 4. One of the breakpoint is within exon 4.
KRAS	0	MSKCC-DMP	P-0015078-T01-IM6	KRAS-intragenic	yes	unknown		unknown	KRAS (NM_033360) rearrangement: chr12:g.25463932_c.267dup Note: The KRAS rearrangement is a duplication which includes exons 1-3. One of the breakpoints is within exon3. The functional significance is undetermined.
FAIM2	0	MSKCC-DMP	P-0015084-T01-IM6	SMARCD1-FAIM2 fusion	yes	unknown		out of frame	FAIM2 (NM_012306) - SMARCD1 (NM_003076) rearrangement: c.211+1026:FAIM2_c.178-116:SMARCD1inv Note: The FAIM2 - SMARCD1 rearrangement is an inversion which results in the fusion of FAIM2 exon2 to SMARCD1 exon2. The functional significance is undetermined.
SMARCD1	0	MSKCC-DMP	P-0015084-T01-IM6	SMARCD1-FAIM2 fusion	yes	unknown		out of frame	FAIM2 (NM_012306) - SMARCD1 (NM_003076) rearrangement: c.211+1026:FAIM2_c.178-116:SMARCD1inv Note: The FAIM2 - SMARCD1 rearrangement is an inversion which results in the fusion of FAIM2 exon2 to SMARCD1 exon2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0015084-T01-IM6	SSTR1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1081_chr14:g.38565335del Note: The FOXA1 rearrangement is a deletion which includes exons 1-2 of FOXA1. One of the breakpoints is within exon2. The functional significance is undetermined.
SSTR1	0	MSKCC-DMP	P-0015084-T01-IM6	SSTR1-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1081_chr14:g.38565335del Note: The FOXA1 rearrangement is a deletion which includes exons 1-2 of FOXA1. One of the breakpoints is within exon2. The functional significance is undetermined.
UBAC2	0	MSKCC-DMP	P-0015099-T01-IM6	IRS2-UBAC2 fusion	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: g.99829420_c.2610del Note: The IRS2 (NM_003749) rearrangement results in the deletion of exons 1 and 2. One of the breakpoints is within exon 1. The functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0015099-T01-IM6	IRS2-UBAC2 fusion	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: g.99829420_c.2610del Note: The IRS2 (NM_003749) rearrangement results in the deletion of exons 1 and 2. One of the breakpoints is within exon 1. The functional significance is undetermined.
LMO3	0	MSKCC-DMP	P-0015102-T01-IM6	PIK3C2G-LMO3 fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: g.16777242_c.2004-131del Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of exons 1-14. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0015102-T01-IM6	PIK3C2G-LMO3 fusion	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: g.16777242_c.2004-131del Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of exons 1-14. The functional significance is undetermined.
LRBA	0	MSKCC-DMP	P-0015107-T01-IM6	FAT1-LRBA fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.5921+19840:LRBA_c.5848:FAT1inv Note: The FAT1 Rearrangement is an inversion event which results in the inversion of exons 10-27 of FAT1. One of the breakpoints is within exon 10 of FAT1. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0015107-T01-IM6	FAT1-LRBA fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.5921+19840:LRBA_c.5848:FAT1inv Note: The FAT1 Rearrangement is an inversion event which results in the inversion of exons 10-27 of FAT1. One of the breakpoints is within exon 10 of FAT1. Its functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0015108-T01-IM6	TGFBR1-intragenic	yes	unknown		unknown	TGFBR1(NM_004612) Rearrangement : chr9:101858947_c.406:TGFBR1del Note: The TGFBR1 Rearrangement results in the deletion of exons 1-3 of TGFBR1. One of the breakpoints is within exon3. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0015110-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1-5 with ALK exons 20-29) : c.668-1726:EML4_c.3173-124:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame and includes the protein kinase domain of ALK
EML4	0	MSKCC-DMP	P-0015110-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1-5 with ALK exons 20-29) : c.668-1726:EML4_c.3173-124:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame and includes the protein kinase domain of ALK
SDHA	0	MSKCC-DMP	P-0015119-T01-IM6	IRX1-SDHA fusion	yes	unknown		unknown	SDHA (NM_004168) rearrangement: c.1794+179:SDHA_g.3790215del Note: The SDHA (NM_004168) rearrangement results in the deletion of exons 14-15. The functional significance is undetermined.
IRX1	0	MSKCC-DMP	P-0015119-T01-IM6	IRX1-SDHA fusion	yes	unknown		unknown	SDHA (NM_004168) rearrangement: c.1794+179:SDHA_g.3790215del Note: The SDHA (NM_004168) rearrangement results in the deletion of exons 14-15. The functional significance is undetermined.
MIR125B2	0	MSKCC-DMP	P-0015121-T01-IM6	TMPRSS2-MIR125B2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : g.18174576_c.55+1974:TMPRSS2inv Note: The TMPRSS2 (NM_001135099) rearrangement results in an inversion of TMPRSS2 exons 2-14 . The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015121-T01-IM6	TMPRSS2-MIR125B2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement : g.18174576_c.55+1974:TMPRSS2inv Note: The TMPRSS2 (NM_001135099) rearrangement results in an inversion of TMPRSS2 exons 2-14 . The functional significance is undetermined.
CSF1R	0	MSKCC-DMP	P-0015122-T01-IM6	GRIA1-CSF1R fusion	yes	unknown		unknown	CSF1R (NM_005211) - GRIA1 (NM_000827) rearrangement: c.1918:CSF1R_c.460+1372:GRIA1dup Note: The CSF1R (NM_005211) - GRIA1 (NM_000827) rearrangement is a duplication of exons 1-14 of CSF1R and exons 1-3 of GRIA1. One of the breakpoints is within CSF1R exon 14. The functional significance is unknown.
GRIA1	0	MSKCC-DMP	P-0015122-T01-IM6	GRIA1-CSF1R fusion	yes	unknown		unknown	CSF1R (NM_005211) - GRIA1 (NM_000827) rearrangement: c.1918:CSF1R_c.460+1372:GRIA1dup Note: The CSF1R (NM_005211) - GRIA1 (NM_000827) rearrangement is a duplication of exons 1-14 of CSF1R and exons 1-3 of GRIA1. One of the breakpoints is within CSF1R exon 14. The functional significance is unknown.
SMAD4	0	MSKCC-DMP	P-0015123-T01-IM6	SMAD4-intragenic	yes	unknown		out of frame	SMAD4 (NM_005359) rearrangement: c.904+25_c.1308+1698del Note: The SMAD4 (NM_005359) rearrangement results in the deletion of exons 8-10. The functional significance is undetermined.
C9orf53	0	MSKCC-DMP	P-0015123-T01-IM6	CDKN2A-C9orf53 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : g.21929130_c.458-3:CDKN2Ap16iNK4Ainv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement results in an inversion of CDKN2Ap16INK4A exon 3 . One of the breakpoints is within exon 3. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0015123-T01-IM6	CDKN2A-C9orf53 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : g.21929130_c.458-3:CDKN2Ap16iNK4Ainv Note: The CDKN2Ap16INK4A (NM_000077) rearrangement results in an inversion of CDKN2Ap16INK4A exon 3 . One of the breakpoints is within exon 3. The functional significance is undetermined.
RXRA	0	MSKCC-DMP	P-0015129-T01-IM6	RXRA-intragenic	yes	unknown		unknown	RXRA (NM_002957) rearrangement : c.1135+988_c.1241+32inv Note: The RXRA (NM_002957) rearrangement results in an inversion of RXRA exon 9 . The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015132-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11):c.127-625:TMPRSS2_c.40-56456:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015132-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-11):c.127-625:TMPRSS2_c.40-56456:ERGdel
CDKN1B	0	MSKCC-DMP	P-0015136-T01-IM6	DAZAP2-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) Rearrangement : c.158:CDKN1B_chr12:5g.1623301inv Note: The CDKN1B Rearrangement results in the inversion of exons 1-2 of CDKN1B. one of the breakpoints is within exon1 of CDKN1B. Its functional significance is undetermined.
DAZAP2	0	MSKCC-DMP	P-0015136-T01-IM6	DAZAP2-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) Rearrangement : c.158:CDKN1B_chr12:5g.1623301inv Note: The CDKN1B Rearrangement results in the inversion of exons 1-2 of CDKN1B. one of the breakpoints is within exon1 of CDKN1B. Its functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0015148-T01-IM6	PIK3C2G-intragenic	yes	unknown		in frame	PIK3C2G (M_004570) rearrangement: c.3658-68_c.3889-8636dup Note: The PIK3C2G rearrangement is an intragenic duplication of exons 27-28.
ALK	0	MSKCC-DMP	P-0015152-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused in-frame to ALK exons 20-29): c.2242+127:EML4_c.3173-685:ALKinv Note: The EML4-ALK fusion includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0015152-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused in-frame to ALK exons 20-29): c.2242+127:EML4_c.3173-685:ALKinv Note: The EML4-ALK fusion includes the kinase domain of ALK.
RECQL4	0	MSKCC-DMP	P-0015184-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: c.665_c.354+27dup Note: The RECQL4 (NM_004260) rearrangement is a duplication of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0015188-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.163+11741_c.1010-6437dup Note: The ETV6 rearrangement is an intragenic duplication of exons 3-5. The functional significance is undetermined.
C1orf52	0	MSKCC-DMP	P-0015191-T01-IM6	BCL10-C1orf52 fusion	yes	unknown		unknown	BCL10 (NM_003921) - C1orf52 (NM_198077) rearrangement: c.447:BCL10_c.276+231:C1orf52inv Note: The BCL10 - C1orf52 rearrangement is an inversion with a breakpoint within exon3 of BCL10. The functional significance is undetermined.
BCL10	0	MSKCC-DMP	P-0015191-T01-IM6	BCL10-C1orf52 fusion	yes	unknown		unknown	BCL10 (NM_003921) - C1orf52 (NM_198077) rearrangement: c.447:BCL10_c.276+231:C1orf52inv Note: The BCL10 - C1orf52 rearrangement is an inversion with a breakpoint within exon3 of BCL10. The functional significance is undetermined.
MLL	0	MSKCC-DMP	P-0015192-T01-IM6	MLL-intragenic	yes	unknown		unknown	MLL (NM_001197104) rearrangement: c.286_chr11:g.118294747dup Note: The MLL rearrangement is a duplication with a breakpoint within exon1 of MLL. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0015195-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exon17 fused to TACC3 exon8): c.2275-86:FGFR3_c.1645-28:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0015195-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exon17 fused to TACC3 exon8): c.2275-86:FGFR3_c.1645-28:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
ALK	0	MSKCC-DMP	P-0015197-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 6 fused to ALK exon 20) : c.668-2108:EML4_c.3172+318:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0015197-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 6 fused to ALK exon 20) : c.668-2108:EML4_c.3172+318:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
NF2	0	MSKCC-DMP	P-0015199-T01-IM6	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.1341-75_c.1446+958inv Note: The NF2 rearrangement is an intragenic inversion of exon 13. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0015204-T01-IM6	STAT3-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - STAT3 (NM_139276) rearrangement: c.1997:STAT5A_c.*1443:STAT3del Note: The STAT5A rearrangement is a deletion with breakpoints within exon17 of STAT5A and the 3UTR of STAT3. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0015204-T01-IM6	STAT3-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - STAT3 (NM_139276) rearrangement: c.1997:STAT5A_c.*1443:STAT3del Note: The STAT5A rearrangement is a deletion with breakpoints within exon17 of STAT5A and the 3UTR of STAT3. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0015204-T01-IM6	ARID1B-intragenic	yes	unknown		in frame	ARID1B (NM_020732) rearrangement: c.3377-2146_c.4720+22 Note: The ARID1B rearrangement is an intragenic duplication of exons 14-18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015209-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused to ERG exon2): c.55+2192:TMPRSS2_c.18+13090:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015209-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused to ERG exon2): c.55+2192:TMPRSS2_c.18+13090:ERGdel
NPW	0	MSKCC-DMP	P-0015215-T01-IM6	TSC2-NPW fusion	yes	unknown		unknown	TSC2 (NM_000548) - NPW (NM_001099456) rearrangement: c.1101:TSC2_c.-3135:NPWdup Note: The TSC2 (NM_000548) - NPW (NM_001099456) rearrangement is a duplication that may result in the fusion of TSC2 exons 1-11 with NPW exons 1-2. One of the breakpoints is within TSC2 exon 11. The other breakpoint is 3kb before NPW. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0015215-T01-IM6	TSC2-NPW fusion	yes	unknown		unknown	TSC2 (NM_000548) - NPW (NM_001099456) rearrangement: c.1101:TSC2_c.-3135:NPWdup Note: The TSC2 (NM_000548) - NPW (NM_001099456) rearrangement is a duplication that may result in the fusion of TSC2 exons 1-11 with NPW exons 1-2. One of the breakpoints is within TSC2 exon 11. The other breakpoint is 3kb before NPW. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0015215-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 32-43): t(5;6)(q32;q22.1)(chr5:g.149783057::chr6:g.117650370) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1. (PMID: 22327623)
CD74	0	MSKCC-DMP	P-0015215-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 32-43): t(5;6)(q32;q22.1)(chr5:g.149783057::chr6:g.117650370) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1. (PMID: 22327623)
TULP4	0	MSKCC-DMP	P-0015239-T01-IM6	PIK3R1-TULP4 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: (5;6)(q13.1;q25.3)(chr5:g.67591907::chr6:g.158681004) Note: The PIK3R1 rearrangement is a translocation that may result in the truncation of exons 9-16. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0015239-T01-IM6	PIK3R1-TULP4 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: (5;6)(q13.1;q25.3)(chr5:g.67591907::chr6:g.158681004) Note: The PIK3R1 rearrangement is a translocation that may result in the truncation of exons 9-16. The functional significance is undetermined.
PLCG2	0	MSKCC-DMP	P-0015240-T01-IM6	EIF4G1-PLCG2 fusion	yes	unknown		out of frame	PLCG2 (NM_002661) rearrangement: t(3;16)(q27.1;q23.3)(chr3:g.184034134::chr16:g.81968167) Note: The PLCG2 rearrangement is a translocation that may result in the truncation of exons 27-33. The functional significance is undetermined.
EIF4G1	0	MSKCC-DMP	P-0015240-T01-IM6	EIF4G1-PLCG2 fusion	yes	unknown		out of frame	PLCG2 (NM_002661) rearrangement: t(3;16)(q27.1;q23.3)(chr3:g.184034134::chr16:g.81968167) Note: The PLCG2 rearrangement is a translocation that may result in the truncation of exons 27-33. The functional significance is undetermined.
CPT1A	0	MSKCC-DMP	P-0015244-T01-IM6	APC-CPT1A fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;11)(q22.2;q13.3)(chr5:g.112043596::chr11:g.68605475) Note: The rearrangement is a translocation with a breakpoint within the 5UTR  of APC. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0015244-T01-IM6	APC-CPT1A fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;11)(q22.2;q13.3)(chr5:g.112043596::chr11:g.68605475) Note: The rearrangement is a translocation with a breakpoint within the 5UTR  of APC. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0015244-T01-IM6	FBXW7-SMAD3 fusion	yes	unknown		unknown	FBXW7 (NM_033632) - SMAD3 (NM_005902) rearrangement: t(4;15)(q31.3;q22.33)(chr4:g.153290194::chr15:g.67479765) Note: The FBXW7 rearrangement is a translocation which results in the fusion of FBXW7 exon2 to SMAD3 exon 8. The functional significance is undetermined.
FBXW7	0	MSKCC-DMP	P-0015244-T01-IM6	FBXW7-SMAD3 fusion	yes	unknown		unknown	FBXW7 (NM_033632) - SMAD3 (NM_005902) rearrangement: t(4;15)(q31.3;q22.33)(chr4:g.153290194::chr15:g.67479765) Note: The FBXW7 rearrangement is a translocation which results in the fusion of FBXW7 exon2 to SMAD3 exon 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015250-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exon 2): c.56-4310:TMPRSS2_c.19-20348:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015250-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exon 2): c.56-4310:TMPRSS2_c.19-20348:ERGdel
RARA	0	MSKCC-DMP	P-0015291-T01-IM6	SMURF2-RARA fusion	yes	unknown		in frame	RARA (NM_000964) - SMURF2 (NM_022739) rearrangement: c.179-5342:RARA_c.400+2094:SMURF2inv Note: The RARA - SMURF2 rearrangement is an inversion which results in the fusion of RARA exon 2 to SMURF2 exon 6. The functional significance is undetermined.
SMURF2	0	MSKCC-DMP	P-0015291-T01-IM6	SMURF2-RARA fusion	yes	unknown		in frame	RARA (NM_000964) - SMURF2 (NM_022739) rearrangement: c.179-5342:RARA_c.400+2094:SMURF2inv Note: The RARA - SMURF2 rearrangement is an inversion which results in the fusion of RARA exon 2 to SMURF2 exon 6. The functional significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0015294-T01-IM6	NFKBIA-intragenic	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: c.548-39_chr14:g.35888329del Note: The NFKBIA rearrangement is a deletion which includes exons 1-3. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0015300-T01-IM6	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.3712+1801_c.6520del Note: The MLL3 rearrangement is an intragenic deletion of exons 24-36. One of the breakpoints is within exon36. The functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0015301-T01-IM6	STAG2-intragenic	yes	unknown		in frame	STAG2 (NM_001042749) rearrangement: c.1417-896_c.2184+26del Note: The STAG2 rearrangement is an intragenic deletion of exons 16-22. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0015302-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.809_c.1047-94del Note: The CDK12 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0015310-T02-IM6	RUFY3-RET fusion	yes	unknown		out of frame	RUFY3 (NM_001037442) - RET (NM_020975) rearrangement: t(4;10)(q13.3;q11.21)(chr4:g.71655316::chr10:g.43610427) Note: The RUFY3 - RET rearrangement is a translocation that results in the fusion of RUFY3 exons 1-12 with RET exons 12-20. The functional significance is undetermined.
RUFY3	0	MSKCC-DMP	P-0015310-T02-IM6	RUFY3-RET fusion	yes	unknown		out of frame	RUFY3 (NM_001037442) - RET (NM_020975) rearrangement: t(4;10)(q13.3;q11.21)(chr4:g.71655316::chr10:g.43610427) Note: The RUFY3 - RET rearrangement is a translocation that results in the fusion of RUFY3 exons 1-12 with RET exons 12-20. The functional significance is undetermined.
SLC7A1	0	MSKCC-DMP	P-0015321-T01-IM6	IRS2-SLC7A1 fusion	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: chr13:g.30177124_c.4013-5776inv Note: The IRS2 rearrangement is an inversion of a part of exon 2. One of the breakpoints is within exon 2.
IRS2	0	MSKCC-DMP	P-0015321-T01-IM6	IRS2-SLC7A1 fusion	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: chr13:g.30177124_c.4013-5776inv Note: The IRS2 rearrangement is an inversion of a part of exon 2. One of the breakpoints is within exon 2.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0015321-T01-IM6	CDKN2BAS-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.244:CDKN2Ap14ARF_chr9:g.22157561del Note: The CDKN2Ap14ARF rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.
CDKN2BAS	0	MSKCC-DMP	P-0015321-T01-IM6	CDKN2BAS-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.244:CDKN2Ap14ARF_chr9:g.22157561del Note: The CDKN2Ap14ARF rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0015321-T01-IM6	CDKN2BAS-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.201:CDKN2Ap16INK4A_chr9:g.22157561del Note: The CDKN2Ap16INK4A rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.
CDKN2BAS	0	MSKCC-DMP	P-0015321-T01-IM6	CDKN2BAS-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.201:CDKN2Ap16INK4A_chr9:g.22157561del Note: The CDKN2Ap16INK4A rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.
TMPRSS2	0	MSKCC-DMP	P-0015333-T01-IM6	RND3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(2;21)(q23.3;q22.3)(chr2:g.151050245::chr21:g.42870305) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.
RND3	0	MSKCC-DMP	P-0015333-T01-IM6	RND3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(2;21)(q23.3;q22.3)(chr2:g.151050245::chr21:g.42870305) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015333-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-211_c.795-1208del Note: The TMPRSS2 rearrangement is an intragenic deletion of exons 2-7.
POLE	0	MSKCC-DMP	P-0015337-T01-IM6	ZNF268-POLE fusion	yes	unknown		unknown	POLE (NM_006231) Rearrangement : chr12:g.133806491_c.802-25:POLEdel Note: The POLE Rearrangement results in the deletion of exons 1-8  of POLE. Its functional significance is undetermined
ZNF268	0	MSKCC-DMP	P-0015337-T01-IM6	ZNF268-POLE fusion	yes	unknown		unknown	POLE (NM_006231) Rearrangement : chr12:g.133806491_c.802-25:POLEdel Note: The POLE Rearrangement results in the deletion of exons 1-8  of POLE. Its functional significance is undetermined
SMARCA4	0	MSKCC-DMP	P-0015337-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) Rearrangement : c.-32+8277_c.222+92del Note: The SMARCA4 Rearrangement results in the inversion of exon2 of SMARCA4. One of the breakpoints is in the 5'UTR region before the transcription start site of SMARCA4. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0015345-T01-IM6	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) Rearrangement : c.138+19968_c.1141-304del Note: The BRAF Rearrangement results in the intragenic deletion of exons 2-8 of BRAF.
WDR88	0	MSKCC-DMP	P-0015358-T01-IM6	EIF2C2-WDR88 fusion	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: t(8;19)(q24.3;q13.11)(chr8:g.141566378::chr19:g.33663503) Note: The AGO2 rearrangement involves the truncation of exons 9-19. One of the breakpoints is within exon 9.
EIF2C2	0	MSKCC-DMP	P-0015358-T01-IM6	EIF2C2-WDR88 fusion	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: t(8;19)(q24.3;q13.11)(chr8:g.141566378::chr19:g.33663503) Note: The AGO2 rearrangement involves the truncation of exons 9-19. One of the breakpoints is within exon 9.
ETV6	0	MSKCC-DMP	P-0015360-T02-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.329-3183_c.463+3169dup Note: The ETV6 (NM_001987) rearrangement results in the duplication of exon 4. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0015372-T01-IM6	CAPZB-MTOR fusion	yes	unknown		unknown	CAPZB (NM_001206540) -MTOR (NM_004958) rearrangement: c.1492:MTOR_c.4-24545:CAPZBdel Note: The CAPZB - MTOR rearrangement is a deletion that results in the fusion of CAPZB exon 1 with MTOR exons 10-58, including the kinase domain of MTOR. One of the breakpoints is within exon 10 of MTOR. The functional significance is undetermined.
CAPZB	0	MSKCC-DMP	P-0015372-T01-IM6	CAPZB-MTOR fusion	yes	unknown		unknown	CAPZB (NM_001206540) -MTOR (NM_004958) rearrangement: c.1492:MTOR_c.4-24545:CAPZBdel Note: The CAPZB - MTOR rearrangement is a deletion that results in the fusion of CAPZB exon 1 with MTOR exons 10-58, including the kinase domain of MTOR. One of the breakpoints is within exon 10 of MTOR. The functional significance is undetermined.
PAK7	0	MSKCC-DMP	P-0015378-T01-IM6	PAK7-intragenic	yes	unknown		unknown	PAK7 (NM_177990) rearrangement: c.1153_c.-11-6786del Note: The PAK7 (NM_177990) rearrangement results in the deletion of exons 3-5. One of the breakpoints is before the TSS site and the other is within exon 5. The functional significance is undetermined.
MAFB	0	MSKCC-DMP	P-0015411-T01-IM6	PTPRT-MAFB fusion	yes	unknown		unknown	PTPRT (NM_133170) Rearrangement : c.1444:PTPRT_c.-903:MAFBinv Note: The PTPRT Rearrangement results in the inversion of exons 1-8 of PTPRT. One of the breakpoints is within exon 8. Its functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0015411-T01-IM6	PTPRT-MAFB fusion	yes	unknown		unknown	PTPRT (NM_133170) Rearrangement : c.1444:PTPRT_c.-903:MAFBinv Note: The PTPRT Rearrangement results in the inversion of exons 1-8 of PTPRT. One of the breakpoints is within exon 8. Its functional significance is undetermined.
PKD1	0	MSKCC-DMP	P-0015414-T01-IM6	TRAF7-PKD1 fusion	yes	unknown		unknown	TRAF7 (NM_032271) Rearrangement : c.6583:PKD1_c.1387-44:TRAF7dup Note: The TRAF7 Rearrangement results in the duplication of exons 1-15 of TRAF7. its functional significance is undetermined
TRAF7	0	MSKCC-DMP	P-0015414-T01-IM6	TRAF7-PKD1 fusion	yes	unknown		unknown	TRAF7 (NM_032271) Rearrangement : c.6583:PKD1_c.1387-44:TRAF7dup Note: The TRAF7 Rearrangement results in the duplication of exons 1-15 of TRAF7. its functional significance is undetermined
EIF2C3	0	MSKCC-DMP	P-0015430-T01-IM6	STK40-EIF2C3 fusion	yes	unknown		unknown	EIF2C3 (NM_024852) - STK40 (NM_032017) rearrangement:  c.2274+4567:EIF2C3_c.870:STK40dup Note: The EIF2C3 - STK40 rearrangement is a duplication with a breakpoint within exon 9 of STK40. The functional significance is undetermined.
STK40	0	MSKCC-DMP	P-0015430-T01-IM6	STK40-EIF2C3 fusion	yes	unknown		unknown	EIF2C3 (NM_024852) - STK40 (NM_032017) rearrangement:  c.2274+4567:EIF2C3_c.870:STK40dup Note: The EIF2C3 - STK40 rearrangement is a duplication with a breakpoint within exon 9 of STK40. The functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0015430-T01-IM6	MAN1A2-VTCN1 fusion	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: c.540_chr1:g.117841527dup Note: The VTCN1 rearrangement is a duplication with a breakpoint within exon 4. The functional significance is undetermined.
MAN1A2	0	MSKCC-DMP	P-0015430-T01-IM6	MAN1A2-VTCN1 fusion	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: c.540_chr1:g.117841527dup Note: The VTCN1 rearrangement is a duplication with a breakpoint within exon 4. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0015430-T01-IM6	DPP7-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(9;15)(q34.3;q15.1)(chr9:g.140014961::chr15:g.42058234) Note: The MGA rearrangement is a translocation with a breakpoint within exon 24. The functional significance is undetermined.
DPP7	0	MSKCC-DMP	P-0015430-T01-IM6	DPP7-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(9;15)(q34.3;q15.1)(chr9:g.140014961::chr15:g.42058234) Note: The MGA rearrangement is a translocation with a breakpoint within exon 24. The functional significance is undetermined.
KEAP1	0	MSKCC-DMP	P-0015430-T01-IM6	STAT5B-KEAP1 fusion	yes	unknown		unknown	STAT5B (NM_012448) - KEAP1 (NM_203500) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.:40354329::chr19:g.10615471) Note: The STAT5B - KEAP1 rearrangement is a translocation which results in the fusion of STAT5B exon 18 to the Promoter region of KEAP1. The functional significance is undetermined. A more complex genomic rearrangement involving KEAP1 cannot be ruled out.
STAT5B	0	MSKCC-DMP	P-0015430-T01-IM6	STAT5B-KEAP1 fusion	yes	unknown		unknown	STAT5B (NM_012448) - KEAP1 (NM_203500) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.:40354329::chr19:g.10615471) Note: The STAT5B - KEAP1 rearrangement is a translocation which results in the fusion of STAT5B exon 18 to the Promoter region of KEAP1. The functional significance is undetermined. A more complex genomic rearrangement involving KEAP1 cannot be ruled out.
CAT	0	MSKCC-DMP	P-0015432-T01-IM6	FGFR2-CAT fusion	yes	unknown		in frame	FGFR2 (NM_000141) - CAT (NM_001752) rearrangement: t(10;11)(q26.13;p13)(chr10:g.123242534::chr11:g.34467980) Note: The FGFR2 - CAT rearrangement is a translocation which results in the fusion of FGFR2 exon 17 to CAT exon 2. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0015432-T01-IM6	FGFR2-CAT fusion	yes	unknown		in frame	FGFR2 (NM_000141) - CAT (NM_001752) rearrangement: t(10;11)(q26.13;p13)(chr10:g.123242534::chr11:g.34467980) Note: The FGFR2 - CAT rearrangement is a translocation which results in the fusion of FGFR2 exon 17 to CAT exon 2. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
MSI1	0	MSKCC-DMP	P-0015440-T01-IM6	LOC338799-MSI1 fusion	yes	unknown		unknown	MSI1 (NM_002442) rearrangement: chr12:g.122241038_c.535-53del Note: The MSI1 rearrangement is a deletion which includes exons 1-8. The functional significance is undetermined.
LOC338799	0	MSKCC-DMP	P-0015440-T01-IM6	LOC338799-MSI1 fusion	yes	unknown		unknown	MSI1 (NM_002442) rearrangement: chr12:g.122241038_c.535-53del Note: The MSI1 rearrangement is a deletion which includes exons 1-8. The functional significance is undetermined.
MYD88	0	MSKCC-DMP	P-0015445-T01-IM6	ROBO2-MYD88 fusion	yes	unknown		in frame	MYD88 (NM_002468) - ROBO2 (NM_002942) rearrangement: c.503-189:MYD88_c.3935-874:ROBO2del Note: The MYD88 - ROBO2 rearrangement is an deletion that results in a in-frame fusion of MYD88 exons 1-2 to ROBO2 exons 25-26. The functional significance is undetermined.
ROBO2	0	MSKCC-DMP	P-0015445-T01-IM6	ROBO2-MYD88 fusion	yes	unknown		in frame	MYD88 (NM_002468) - ROBO2 (NM_002942) rearrangement: c.503-189:MYD88_c.3935-874:ROBO2del Note: The MYD88 - ROBO2 rearrangement is an deletion that results in a in-frame fusion of MYD88 exons 1-2 to ROBO2 exons 25-26. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0015457-T01-IM6	RIMBP2-CREBBP fusion	yes	unknown		unknown	RIMBP2 (NM_015347) - CREBBP (NM_004380) rearrangement: t(12;16)(q24.33;p13.3)(chr12:g.130928970::chr16:g.3779580) Note: The RIMBP2 - CREBBP rearrangement is a translocation that may result in a fusion of RIMBP2 exons 1-7 to CREBBP exon 31. One of the breakpoints is within CREBBP exon 31. The functional significance is undetermined.
RIMBP2	0	MSKCC-DMP	P-0015457-T01-IM6	RIMBP2-CREBBP fusion	yes	unknown		unknown	RIMBP2 (NM_015347) - CREBBP (NM_004380) rearrangement: t(12;16)(q24.33;p13.3)(chr12:g.130928970::chr16:g.3779580) Note: The RIMBP2 - CREBBP rearrangement is a translocation that may result in a fusion of RIMBP2 exons 1-7 to CREBBP exon 31. One of the breakpoints is within CREBBP exon 31. The functional significance is undetermined.
LZTS1	0	MSKCC-DMP	P-0015471-T01-IM6	RAF1-LZTS1 fusion	yes	unknown		out of frame	LZTS1 (NM_021020) - RAF1 (NM_002880) rearrangement: t(3;8)(p25.2;p21.3)(chr3:g.12641856::chr8:g.20111180) Note: The LZTS1 - RAF1 rearrangement is a translocation which results in the fusion of LZTS1 exon1 to RAF1 exon9 and includes the kinase domain of RAF1
RAF1	0	MSKCC-DMP	P-0015471-T01-IM6	RAF1-LZTS1 fusion	yes	unknown		out of frame	LZTS1 (NM_021020) - RAF1 (NM_002880) rearrangement: t(3;8)(p25.2;p21.3)(chr3:g.12641856::chr8:g.20111180) Note: The LZTS1 - RAF1 rearrangement is a translocation which results in the fusion of LZTS1 exon1 to RAF1 exon9 and includes the kinase domain of RAF1
BTBD12	0	MSKCC-DMP	P-0015476-T01-IM6	EIF2C2-BTBD12 fusion	yes	unknown		out of frame	AGO2 (NM_012154)  - SLX4 (NM_032444) rearrangement: t(8;16)(q24.3;p13.3)(chr8:g.141595171::chr16:g.3654062) Note: The AGO2 - SLX4 rearrangement is a translocation which results in the fusion of AGO2 exon 2 to SLX4 exon 4. The functional significance is undetermined.
EIF2C2	0	MSKCC-DMP	P-0015476-T01-IM6	EIF2C2-BTBD12 fusion	yes	unknown		out of frame	AGO2 (NM_012154)  - SLX4 (NM_032444) rearrangement: t(8;16)(q24.3;p13.3)(chr8:g.141595171::chr16:g.3654062) Note: The AGO2 - SLX4 rearrangement is a translocation which results in the fusion of AGO2 exon 2 to SLX4 exon 4. The functional significance is undetermined.
NCOA1	0	MSKCC-DMP	P-0015476-T01-IM6	DNMT3A-NCOA1 fusion	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.957_chr2:g.24788000dup Note: The DNMT3A rearrangement is a duplication with a breakpoint within exon 8. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0015476-T01-IM6	DNMT3A-NCOA1 fusion	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.957_chr2:g.24788000dup Note: The DNMT3A rearrangement is a duplication with a breakpoint within exon 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015482-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon1 fused to ERG exon 2): c.56-1115:TMPRSS2_c.18+11715:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015482-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon1 fused to ERG exon 2): c.56-1115:TMPRSS2_c.18+11715:ERGdel
IGF1R	0	MSKCC-DMP	P-0015494-T01-IM6	ROS1-IGF1R fusion	yes	unknown		in frame	IGF1R (NM_000875) - ROS1 (NM_002944) Rearrangement : t(6,15)(q22.1,q26.3)(chr6:g.117646453::chr15:g.99477638) Note: The IGF1R  - ROS1  Rearrangement results in the fusion of exons 1-15 of IGF1R and exons 34-43 of ROS1. This event includes the protein kinase domain of ROS1. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0015494-T01-IM6	ROS1-IGF1R fusion	yes	unknown		in frame	IGF1R (NM_000875) - ROS1 (NM_002944) Rearrangement : t(6,15)(q22.1,q26.3)(chr6:g.117646453::chr15:g.99477638) Note: The IGF1R  - ROS1  Rearrangement results in the fusion of exons 1-15 of IGF1R and exons 34-43 of ROS1. This event includes the protein kinase domain of ROS1. Its functional significance is undetermined.
CYLD	0	MSKCC-DMP	P-0015510-T01-IM6	IRX3-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) Rearrangement : c.248:CYLD_chr16:g.54625586del Note: The CYLD (NM_001042355) Rearrangement results in the deletion of exons 3-18 of CYLD. The breakpoint is within CYLD. Its functional significance is undetermined.
IRX3	0	MSKCC-DMP	P-0015510-T01-IM6	IRX3-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) Rearrangement : c.248:CYLD_chr16:g.54625586del Note: The CYLD (NM_001042355) Rearrangement results in the deletion of exons 3-18 of CYLD. The breakpoint is within CYLD. Its functional significance is undetermined.
LOC150568	0	MSKCC-DMP	P-0015518-T01-IM6	NOTCH2-LOC150568 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : t(1,2)(p11.2,q12.1)(chr1:g.120510213::chr2:g.104768940) Note: The NOTCH2  Rearrangement results in the possible truncation of exons 8-34 of NOTCH2. The breakpoint is within exon 8. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0015518-T01-IM6	NOTCH2-LOC150568 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : t(1,2)(p11.2,q12.1)(chr1:g.120510213::chr2:g.104768940) Note: The NOTCH2  Rearrangement results in the possible truncation of exons 8-34 of NOTCH2. The breakpoint is within exon 8. Its functional significance is undetermined.
PLCH2	0	MSKCC-DMP	P-0015531-T01-IM6	TNFRSF14-PLCH2 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) - PLCH2 (NM_014638)  rearrangement: c.2547:PLCH2_c.69+32:TNFRSF14dup Note: The TNFRSF14 - PLCH2 rearrangement is a duplication that results in the fusion of TNFRSF14 exon 1 with PLCH2 exons 19-22. One of the breakpoints is with PLCH2 exon 19. The functional significance is undetermined.
TNFRSF14	0	MSKCC-DMP	P-0015531-T01-IM6	TNFRSF14-PLCH2 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) - PLCH2 (NM_014638)  rearrangement: c.2547:PLCH2_c.69+32:TNFRSF14dup Note: The TNFRSF14 - PLCH2 rearrangement is a duplication that results in the fusion of TNFRSF14 exon 1 with PLCH2 exons 19-22. One of the breakpoints is with PLCH2 exon 19. The functional significance is undetermined.
SPATA8	0	MSKCC-DMP	P-0015558-T01-IM6	ETV6-SPATA8 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.2)(chr12:g.12019771::chr15:g.97567900) Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 5-8. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0015558-T01-IM6	ETV6-SPATA8 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.2)(chr12:g.12019771::chr15:g.97567900) Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 5-8. The functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0015572-T01-IM6	FASN-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) - FASN (NM_004104) rearrangement: c.954:MAP2K4_c.4564+7:FASNinv Note: The MAP2K4 - FASN rearrangement is an inversion that results in the fusion of MAP2K4 exons 1-9, including the kinase domain, to FASN exons 27-43. One of the breakpoints is within exon 9. The functional significance is undetermined.
FASN	0	MSKCC-DMP	P-0015572-T01-IM6	FASN-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) - FASN (NM_004104) rearrangement: c.954:MAP2K4_c.4564+7:FASNinv Note: The MAP2K4 - FASN rearrangement is an inversion that results in the fusion of MAP2K4 exons 1-9, including the kinase domain, to FASN exons 27-43. One of the breakpoints is within exon 9. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0015572-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.1399_c.6921+29dup Note: The NF1 rearrangement is an intragenic duplication of exons 13-45. One of the breakpoints is within exon 13.
BAP1	0	MSKCC-DMP	P-0015589-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) Rearrangement : c.932-100:BAP1_c.187-1874:PHF7del Note: The BAP1 Rearrangement results in the deletion of exons 1-10 of BAP1.Its functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0015589-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) Rearrangement : c.932-100:BAP1_c.187-1874:PHF7del Note: The BAP1 Rearrangement results in the deletion of exons 1-10 of BAP1.Its functional significance is undetermined.
TAP1	0	MSKCC-DMP	P-0015600-T01-IM6	COL11A2-TAP1 fusion	yes	unknown		unknown	TAP1 (NM_000593) Rearrangement : c.*35:TAP1_c.939+214:COL11A2dup Note: The TAP1 Rearrangement results in the duplication of exons 1-11 of TAP1. The breakpoint in TAP1 is within the 3' UTR region after transcription stop site. Its functional significance is undetermined.
COL11A2	0	MSKCC-DMP	P-0015600-T01-IM6	COL11A2-TAP1 fusion	yes	unknown		unknown	TAP1 (NM_000593) Rearrangement : c.*35:TAP1_c.939+214:COL11A2dup Note: The TAP1 Rearrangement results in the duplication of exons 1-11 of TAP1. The breakpoint in TAP1 is within the 3' UTR region after transcription stop site. Its functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0015618-T01-IM6	CDH1-intragenic	yes	unknown		in frame	CDH1 (NM_004360) rearrangement: c.388-223_c.688-75del Note: The CDH1 rearrangement is a deletion of exons 4-5. The functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0015618-T01-IM6	FOXP1-intragenic	yes	unknown		in frame	FOXP1 (NM_001244814) rearrangement: c.1429-3_c.1146+678del Note: The FOXP1 rearrangement is a deletion of exons 11-12. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015628-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-27:TMPSS2_c.18+6821:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015628-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-27:TMPSS2_c.18+6821:ERGdel
PPP2R1A	0	MSKCC-DMP	P-0015640-T01-IM6	ZNF468-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.652-19_chr19:g.53344778del Note: The PPP2R1A rearrangement is a deletion of exons 6-15.
ZNF468	0	MSKCC-DMP	P-0015640-T01-IM6	ZNF468-PPP2R1A fusion	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.652-19_chr19:g.53344778del Note: The PPP2R1A rearrangement is a deletion of exons 6-15.
VEGFA	0	MSKCC-DMP	P-0015668-T01-IM6	CAPN11-VEGFA fusion	yes	unknown		unknown	CAPN11 (NM_007058) - VEGFA (NM_001171625) Rearrangement : c.1521:CAPN11_c.423-18:VEGFAdup Note: The CAPN11 - VEGFA Rearrangement results in the fusion of CAPN11 exons 1-14 with VEGFA exons6-8. The breakpoint in CAPN11 is within exon 14 . Its functional significance is undetermined.
CAPN11	0	MSKCC-DMP	P-0015668-T01-IM6	CAPN11-VEGFA fusion	yes	unknown		unknown	CAPN11 (NM_007058) - VEGFA (NM_001171625) Rearrangement : c.1521:CAPN11_c.423-18:VEGFAdup Note: The CAPN11 - VEGFA Rearrangement results in the fusion of CAPN11 exons 1-14 with VEGFA exons6-8. The breakpoint in CAPN11 is within exon 14 . Its functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0015675-T01-IM6	VIPR2-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.10306:MLL3_g.159036888inv Note: The MLL3 rearrangement results in an inversion of MLL3 exons 1-43 . One of the breakpoints is within MLL3 exon 43. The functional significance is undetermined.
VIPR2	0	MSKCC-DMP	P-0015675-T01-IM6	VIPR2-MLL3 fusion	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: c.10306:MLL3_g.159036888inv Note: The MLL3 rearrangement results in an inversion of MLL3 exons 1-43 . One of the breakpoints is within MLL3 exon 43. The functional significance is undetermined.
MLL	0	MSKCC-DMP	P-0015676-T01-IM6	DDX6-MLL fusion	yes	unknown		unknown	MLL (NM_001197104) rearrangement : c.6576:MLL_g.118626801dup Note: The MLL rearrangement is a duplication of MLL exons 27-36 . One of the breakpoints is within exon 27. The functional significance is undetermined.
DDX6	0	MSKCC-DMP	P-0015676-T01-IM6	DDX6-MLL fusion	yes	unknown		unknown	MLL (NM_001197104) rearrangement : c.6576:MLL_g.118626801dup Note: The MLL rearrangement is a duplication of MLL exons 27-36 . One of the breakpoints is within exon 27. The functional significance is undetermined.
CACNA1B	0	MSKCC-DMP	P-0015676-T01-IM6	BAP1-CACNA1B fusion	yes	unknown		unknown	BAP1 (NM_023034) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52437443::chr9:g.140784264) The BAP1 rearrangement is a translocation that may result in a truncation of exons 1-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0015676-T01-IM6	BAP1-CACNA1B fusion	yes	unknown		unknown	BAP1 (NM_023034) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52437443::chr9:g.140784264) The BAP1 rearrangement is a translocation that may result in a truncation of exons 1-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0015689-T01-IM6	ACBD6-RFWD2 fusion	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement : c.832-26:RFWD2_g.180459257inv Note: The RFWD2 rearrangement results in an inversion of RFWD2 exons 1-6. The functional significance is undetermined.
ACBD6	0	MSKCC-DMP	P-0015689-T01-IM6	ACBD6-RFWD2 fusion	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement : c.832-26:RFWD2_g.180459257inv Note: The RFWD2 rearrangement results in an inversion of RFWD2 exons 1-6. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0015692-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.4970_g.112190339del Note: The ZFHX3 rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0015699-T01-IM6	SPTBN1-ALK fusion	yes	unknown		in frame	SPTBN1 (NM_003128) - ALK (NM_004304) fusion (SPTBN1 exon 7  fused to  ALK exon 20):  c.764-1028:SPTBN1_c.3172+890:ALKinv Note: The SPTBN1 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK. (PMID: 27496196)
SPTBN1	0	MSKCC-DMP	P-0015699-T01-IM6	SPTBN1-ALK fusion	yes	unknown		in frame	SPTBN1 (NM_003128) - ALK (NM_004304) fusion (SPTBN1 exon 7  fused to  ALK exon 20):  c.764-1028:SPTBN1_c.3172+890:ALKinv Note: The SPTBN1 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK. (PMID: 27496196)
CDKN1B	0	MSKCC-DMP	P-0015709-T01-IM6	APOLD1-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.564_chr12:g.12948373del Note: The CDKN1B rearrangement is a deletion with a breakpoint within exon 2. The functional significance is undetermined.
APOLD1	0	MSKCC-DMP	P-0015709-T01-IM6	APOLD1-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.564_chr12:g.12948373del Note: The CDKN1B rearrangement is a deletion with a breakpoint within exon 2. The functional significance is undetermined.
CAPZA2	0	MSKCC-DMP	P-0015711-T01-IM6	BRAF-CAPZA2 fusion	yes	unknown		unknown	BRAF (NM_004333) - CAPZA2 (NM_006136) rearrangement:  c.981-1133:BRAF_c.39+8949:CAPZA2dup Note: The BRAF - CAPZA2 rearrangement is a duplication (23983747 bp) which includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0015711-T01-IM6	BRAF-CAPZA2 fusion	yes	unknown		unknown	BRAF (NM_004333) - CAPZA2 (NM_006136) rearrangement:  c.981-1133:BRAF_c.39+8949:CAPZA2dup Note: The BRAF - CAPZA2 rearrangement is a duplication (23983747 bp) which includes the kinase domain of BRAF.
RB1	0	MSKCC-DMP	P-0015713-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1050-15_c.1216-1620dup Note: The RB1 rearrangement is an intragenic duplication of exons 11-12. The functional significance is undetermined.
C1orf130	0	MSKCC-DMP	P-0015726-T01-IM6	ELF3-C1orf130 fusion	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: chr1:g.24920380_c.599-39:ELF3inv Note: The ELF3 rearrangement is an inversion which includes exons 1-5. The functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0015726-T01-IM6	ELF3-C1orf130 fusion	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: chr1:g.24920380_c.599-39:ELF3inv Note: The ELF3 rearrangement is an inversion which includes exons 1-5. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0015727-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) Rearrangement : c.6198+369_6276del Note: The ATM Rearrangement results in the partial deletion of exon 43. One of the breakpoints is within exon 43. Its functional significance is undetermined.
CCDC45	0	MSKCC-DMP	P-0015735-T01-IM6	RPTOR-CCDC45 fusion	yes	unknown		out of frame	RPTOR (NM_020761) - CEP95 (NM_138363) Rearrangement : c.1212+107:RPTOR_c.256+1803:CEPN5dup Note: The RPTOR  - CEP95  Rearrangement results in the fusion of exons 1-10 of RPTOR with exons 4-20 of CEPN5. Its functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0015735-T01-IM6	RPTOR-CCDC45 fusion	yes	unknown		out of frame	RPTOR (NM_020761) - CEP95 (NM_138363) Rearrangement : c.1212+107:RPTOR_c.256+1803:CEPN5dup Note: The RPTOR  - CEP95  Rearrangement results in the fusion of exons 1-10 of RPTOR with exons 4-20 of CEPN5. Its functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0015742-T01-IM6	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: chr12:g.115489107_c.718-41del Note: The TBX3 rearrangement is a deletion of 5UTR and exons 1-3.
ERG	0	MSKCC-DMP	P-0015744-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2  exon 1 fused to ERG exons 4-11): c.56-917:TMPRSS2_c.39+7155:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0015744-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2  exon 1 fused to ERG exons 4-11): c.56-917:TMPRSS2_c.39+7155:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
EWSR1	0	MSKCC-DMP	P-0015744-T01-IM6	NF2-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - NF2 (NM_000268) rearrangement: c.1180-298:EWSR1_c.1738-1347:NF2inv Note: EWSR1 - NF2 rearrangement results in the inversion of EWSR1 exons 13-18 and NF2 5UTR and exons 1-15. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0015744-T01-IM6	NF2-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - NF2 (NM_000268) rearrangement: c.1180-298:EWSR1_c.1738-1347:NF2inv Note: EWSR1 - NF2 rearrangement results in the inversion of EWSR1 exons 13-18 and NF2 5UTR and exons 1-15. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0015751-T01-IM6	LOC341056-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) rearrangement: t(11;17)(q24.1;q21.2)(chr11:g.122871383::chr17:g.40461499) Note: The STAT5A rearrangement is a translocation that may result in a truncation of  exons 19-20. The functional significance is undetermined.
LOC341056	0	MSKCC-DMP	P-0015751-T01-IM6	LOC341056-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) rearrangement: t(11;17)(q24.1;q21.2)(chr11:g.122871383::chr17:g.40461499) Note: The STAT5A rearrangement is a translocation that may result in a truncation of  exons 19-20. The functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0015759-T01-IM6	MLL2-intragenic	yes	unknown		unknown	MLL2 (NM_003482) Rearrangement : c.14076-10_c.14420del Note: The MLL2 Rearrangement results in the intragenic deletion of exons 44-46 of MLL. One of the breakpoints is within exon 46. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0015764-T01-IM6	PDE4DIP-NOTCH2 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) - PDE4DIP (NM_001198834) Rearrangement : c.3289:NOTCH2_c.-1821:PDE4DIPdup Note: The NOTCH2  - PDE4DIP Rearrangement results in the fusion of exons 1-20 of NOTCH2 with exons 1-44 of PDE4DIP . The breakpoint in NOTCH2 is within exon20. Its functional significance is undetermined.
PDE4DIP	0	MSKCC-DMP	P-0015764-T01-IM6	PDE4DIP-NOTCH2 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) - PDE4DIP (NM_001198834) Rearrangement : c.3289:NOTCH2_c.-1821:PDE4DIPdup Note: The NOTCH2  - PDE4DIP Rearrangement results in the fusion of exons 1-20 of NOTCH2 with exons 1-44 of PDE4DIP . The breakpoint in NOTCH2 is within exon20. Its functional significance is undetermined.
DNER	0	MSKCC-DMP	P-0015829-T01-IM6	PDCD1-DNER fusion	yes	unknown		unknown	PDCD1 (NM_005018)  - DNER (NM_139072) rearrangement: c.436+117:PDCD1_c.1855+3458:DNERinv Note: The PDCD1 - DNER rearrangement is an inversion which includes exons 1-3 of PDCD1 and exons 1-11 of DNER. The functional significance is undetermined.
PDCD1	0	MSKCC-DMP	P-0015829-T01-IM6	PDCD1-DNER fusion	yes	unknown		unknown	PDCD1 (NM_005018)  - DNER (NM_139072) rearrangement: c.436+117:PDCD1_c.1855+3458:DNERinv Note: The PDCD1 - DNER rearrangement is an inversion which includes exons 1-3 of PDCD1 and exons 1-11 of DNER. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0015831-T01-IM6	PIK3CD-intragenic	yes	unknown		out of frame	PIK3CD (NM_005026) rearrangement: c.930+139_c.2865-26inv Note: The PIK3CD rearrangement is an intragenic inversion of exons 8-22. The functional significance is undetermined.
GATA3	0	MSKCC-DMP	P-0015831-T01-IM6	LINK01206-GATA3 fusion	yes	unknown		unknown	null
LINK01206	0	MSKCC-DMP	P-0015831-T01-IM6	LINK01206-GATA3 fusion	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0015837-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1324:TMPSS2_c.18+10744:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0015837-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1324:TMPSS2_c.18+10744:ERGdel
FGGY	0	MSKCC-DMP	P-0015839-T01-IM6	JAK1-FGGY fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: g.59823362_c.83del Note: The JAK1 rearrangement results in the deletion of exons 3-25. One of the breakpoints is within exon 3. The functional significance is undetermined.
JAK1	0	MSKCC-DMP	P-0015839-T01-IM6	JAK1-FGGY fusion	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: g.59823362_c.83del Note: The JAK1 rearrangement results in the deletion of exons 3-25. One of the breakpoints is within exon 3. The functional significance is undetermined.
PRKG1	0	MSKCC-DMP	P-0015839-T01-IM6	FGFR2-PRKG1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: g.53199568_c.2302-1423dup Note: The FGFR2 rearrangement results in the duplication of exon 18. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0015839-T01-IM6	FGFR2-PRKG1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: g.53199568_c.2302-1423dup Note: The FGFR2 rearrangement results in the duplication of exon 18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015850-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 to ERG exon 4): c.55+1034:TMPRSS2_c.39+9192:ERG
TMPRSS2	0	MSKCC-DMP	P-0015850-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 to ERG exon 4): c.55+1034:TMPRSS2_c.39+9192:ERG
TMPRSS2	0	MSKCC-DMP	P-0015850-T01-IM6	SGMS2-TMPRSS2 fusion	yes	unknown		unknown	null
SGMS2	0	MSKCC-DMP	P-0015850-T01-IM6	SGMS2-TMPRSS2 fusion	yes	unknown		unknown	null
TACC3	0	MSKCC-DMP	P-0015863-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 8-16): c.2312:FGFR3_c.1644+147:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a know fusion and includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
FGFR3	0	MSKCC-DMP	P-0015863-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 8-16): c.2312:FGFR3_c.1644+147:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a know fusion and includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
CDKN2A	0	MSKCC-DMP	P-0015874-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.21981196_c.150+170del Note: The CDKN2Ap16INK4A rearrangement is a deletion of exon 1.
FLT4	0	MSKCC-DMP	P-0015885-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: c.449_c.770del Note: FLT4 (NM_182925) rearrangement is a intragenic deletion of exon 4-6. The functional significance is undetermined.
KANSL2	0	MSKCC-DMP	P-0015896-T01-IM6	KMT2D-KANSL2 fusion	yes	unknown		unknown	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.974-729:KANSL2_c.9582dup Note: The KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement is a duplication which results in the fusion of KANSL2 exon 1-7 and KMT2D exon 34-54. One of the breakpoints is within KMT2D exon34. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0015896-T01-IM6	KMT2D-KANSL2 fusion	yes	unknown		unknown	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.974-729:KANSL2_c.9582dup Note: The KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement is a duplication which results in the fusion of KANSL2 exon 1-7 and KMT2D exon 34-54. One of the breakpoints is within KMT2D exon34. The functional significance is undetermined.
ORC2	0	MSKCC-DMP	P-0015896-T01-IM6	CASP8-ORC2 fusion	yes	unknown		unknown	CASP8 (NM_00108012) rearrangement: c.1_c.589dup Note: CASP8 (NM_00108012) rearrangement is an intragenic duplication of exon 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0015896-T01-IM6	CASP8-ORC2 fusion	yes	unknown		unknown	CASP8 (NM_00108012) rearrangement: c.1_c.589dup Note: CASP8 (NM_00108012) rearrangement is an intragenic duplication of exon 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
NOS1AP	0	MSKCC-DMP	P-0015903-T01-IM6	NUF2-NOS1AP fusion	yes	unknown		unknown	NUF2 (NM_031423) - NOS1AP (NM_014697) rearrangement: c.488:NUF2_c.105+21977:NOS1APdup Note: The NUF2 - NOS1AP rearrangement is a duplication that results in the fusion of NUF2 exons 1-7 with NOS1AP exons 2-10. One of the breakpoints is within NUF2 exon 7. The functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0015903-T01-IM6	NUF2-NOS1AP fusion	yes	unknown		unknown	NUF2 (NM_031423) - NOS1AP (NM_014697) rearrangement: c.488:NUF2_c.105+21977:NOS1APdup Note: The NUF2 - NOS1AP rearrangement is a duplication that results in the fusion of NUF2 exons 1-7 with NOS1AP exons 2-10. One of the breakpoints is within NUF2 exon 7. The functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0015903-T01-IM6	CD247-DDR2 fusion	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: c.2018_g.167438149del Note: The DDR2 rearrangement results in the deletion of exons 15-18. One of the breakpoints is within exon 15. The functional significance is undetermined.
CD247	0	MSKCC-DMP	P-0015903-T01-IM6	CD247-DDR2 fusion	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: c.2018_g.167438149del Note: The DDR2 rearrangement results in the deletion of exons 15-18. One of the breakpoints is within exon 15. The functional significance is undetermined.
METTL13	0	MSKCC-DMP	P-0015903-T01-IM6	RFWD2-METTL13 fusion	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: g.171760607_c.1051dup Note: The RFWD2 rearrangement results in the duplication of exons 10-20. One of the breakpoints is within exon 10. The functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0015903-T01-IM6	RFWD2-METTL13 fusion	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: g.171760607_c.1051dup Note: The RFWD2 rearrangement results in the duplication of exons 10-20. One of the breakpoints is within exon 10. The functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0015937-T01-IM6	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) Rearrangement : c.1102_c.1178del Note: The CARD11 Rearrangement results in the intragenic deletion of exons 8-9. The breakpoints are within exon 8 and 9 respectively. Its functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0015942-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exons 1-17 with BICC1 exons 9-21) : c.2302-1485:FGFR2_c.1048-60:BICC1inv Note: The FGFR2-BICC1 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0015942-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exons 1-17 with BICC1 exons 9-21) : c.2302-1485:FGFR2_c.1048-60:BICC1inv Note: The FGFR2-BICC1 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
EWSR1	0	MSKCC-DMP	P-0015959-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1159:EWSR1_c.1438-1716:AP1B1del Note: The EWSR1 - AP1B1 rearrangement is a deletion which results in the antisense fusion of EWSR1 exon 12 to AP1B1 exon 11. One of the breakpoints is within exon 12 of EWSR1. The functional significance is undetermined.
AP1B1	0	MSKCC-DMP	P-0015959-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1159:EWSR1_c.1438-1716:AP1B1del Note: The EWSR1 - AP1B1 rearrangement is a deletion which results in the antisense fusion of EWSR1 exon 12 to AP1B1 exon 11. One of the breakpoints is within exon 12 of EWSR1. The functional significance is undetermined.
SPG11	0	MSKCC-DMP	P-0015962-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	SPG11 (NM_025137) - B2M (NM_004048) rearrangement: c.2835-559:SPG11_c.318:B2Mdel Note: The SPG11 - B2M rearrangement is a deletion which includes exons 1-15 of SPG11 and exons 1-2 of B2M. One of the breakpoints is within exon 2 of B2M. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0015962-T01-IM6	B2M-SPG11 fusion	yes	unknown		unknown	SPG11 (NM_025137) - B2M (NM_004048) rearrangement: c.2835-559:SPG11_c.318:B2Mdel Note: The SPG11 - B2M rearrangement is a deletion which includes exons 1-15 of SPG11 and exons 1-2 of B2M. One of the breakpoints is within exon 2 of B2M. The functional significance is undetermined.
REL	0	MSKCC-DMP	P-0015962-T01-IM6	SH3BP4-REL fusion	yes	unknown		unknown	REL (NM_002908) rearrangement: c.1759_chr2:g.236014429inv Note: The REL rearrangement is an inversion (174864860 bp) with a breakpoint within exon 11. The functional significance is undetermined.
SH3BP4	0	MSKCC-DMP	P-0015962-T01-IM6	SH3BP4-REL fusion	yes	unknown		unknown	REL (NM_002908) rearrangement: c.1759_chr2:g.236014429inv Note: The REL rearrangement is an inversion (174864860 bp) with a breakpoint within exon 11. The functional significance is undetermined.
ARHGAP42	0	MSKCC-DMP	P-0015972-T01-IM6	PGR-ARHGAP42 fusion	yes	unknown		unknown	ARHGAP42 (NM_152432) - PGR (NM_000926)  rearrangement: c.1162+197:ARHGAP42_c.2357+60:PGRdel Note: The ARHGAP42 -  PGR rearrangement is a deletion (101211 bp) which includes ARHGAP42 exons 13-24 and PGR exons 6-8. The functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0015972-T01-IM6	PGR-ARHGAP42 fusion	yes	unknown		unknown	ARHGAP42 (NM_152432) - PGR (NM_000926)  rearrangement: c.1162+197:ARHGAP42_c.2357+60:PGRdel Note: The ARHGAP42 -  PGR rearrangement is a deletion (101211 bp) which includes ARHGAP42 exons 13-24 and PGR exons 6-8. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0015972-T01-IM6	ELDR-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.3163-105_chr7:g.55303080del Note: The EGFR rearrangement is a deletion that includes exons 27-28, occurring within the EGFR carboxyl-terminus domain (CTD).
ELDR	0	MSKCC-DMP	P-0015972-T01-IM6	ELDR-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.3163-105_chr7:g.55303080del Note: The EGFR rearrangement is a deletion that includes exons 27-28, occurring within the EGFR carboxyl-terminus domain (CTD).
INPPL1	0	MSKCC-DMP	P-0015973-T01-IM6	LOC220729-INPPL1 fusion	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: t(3;11)(q29;q13.4)(chr3:g.197336862::chr11:g.71944080) Note: The INPPL1 rearrangement is a translocation with a breakpoint within intron 16. The functional significance is undetermined.
LOC220729	0	MSKCC-DMP	P-0015973-T01-IM6	LOC220729-INPPL1 fusion	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: t(3;11)(q29;q13.4)(chr3:g.197336862::chr11:g.71944080) Note: The INPPL1 rearrangement is a translocation with a breakpoint within intron 16. The functional significance is undetermined.
FAM205BP	0	MSKCC-DMP	P-0015980-T01-IM6	RAD21-FAM205BP fusion	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: t(8;9)(q24.11;p13.3)(chr8:g.117864822::chr9:g.34869851) Note: The RAD21 rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0015980-T01-IM6	RAD21-FAM205BP fusion	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: t(8;9)(q24.11;p13.3)(chr8:g.117864822::chr9:g.34869851) Note: The RAD21 rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.
AMIGO2	0	MSKCC-DMP	P-0016006-T01-IM6	KMT2D-AMIGO2 fusion	yes	unknown		unknown	KMDT2D (NM_170606) : c.1_310:KMDT2Ddup Note: The KMDT2D (NM_170606) rearrangement is a duplication of KMDT2D exons 1-3. The functional significance is unknown.
KMT2D	0	MSKCC-DMP	P-0016006-T01-IM6	KMT2D-AMIGO2 fusion	yes	unknown		unknown	KMDT2D (NM_170606) : c.1_310:KMDT2Ddup Note: The KMDT2D (NM_170606) rearrangement is a duplication of KMDT2D exons 1-3. The functional significance is unknown.
GTF2I	0	MSKCC-DMP	P-0016006-T01-IM6	MET-GTF2I fusion	yes	unknown		in frame	GTF2I:NM_032999 - MET:NM_000245 : c.586+712:GTF2I_c.3029-494:METdel The GTF2I (NM_032999) - MET (NM_000245) fusion forms through a deletion and results in the fusion of GTF2I exons 1-6 to MET exons 15-21. This fusion is in frame and includes the kinase domain of MET.  This fusion occurs in the setting of intragenic gain in MET.
MET	0	MSKCC-DMP	P-0016006-T01-IM6	MET-GTF2I fusion	yes	unknown		in frame	GTF2I:NM_032999 - MET:NM_000245 : c.586+712:GTF2I_c.3029-494:METdel The GTF2I (NM_032999) - MET (NM_000245) fusion forms through a deletion and results in the fusion of GTF2I exons 1-6 to MET exons 15-21. This fusion is in frame and includes the kinase domain of MET.  This fusion occurs in the setting of intragenic gain in MET.
EGFR	0	MSKCC-DMP	P-0016009-T01-IM6	VOPP1-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - VOPP1 (NM_030796): c.747+36:EGFR_c.55-23161VOPP1inv Note: The EGFR (NM_005228) - VOPP1 (NM_030796) rearrangement results in an inversion which results in fusion of EGFR exon 6-28 and VOPP1 exon2-5. The functional significance is undetermined
VOPP1	0	MSKCC-DMP	P-0016009-T01-IM6	VOPP1-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - VOPP1 (NM_030796): c.747+36:EGFR_c.55-23161VOPP1inv Note: The EGFR (NM_005228) - VOPP1 (NM_030796) rearrangement results in an inversion which results in fusion of EGFR exon 6-28 and VOPP1 exon2-5. The functional significance is undetermined
GALNT11	0	MSKCC-DMP	P-0016012-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangment: chr7:g.151822136_c.13623:KMT2Cinv Note : KMT2C (NM_170606) is an inversion which results in the fusion of KMT2C exon 1-52 and GALNT11. Breakpoint on KMT2C is within exon 52.
KMT2C	0	MSKCC-DMP	P-0016012-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangment: chr7:g.151822136_c.13623:KMT2Cinv Note : KMT2C (NM_170606) is an inversion which results in the fusion of KMT2C exon 1-52 and GALNT11. Breakpoint on KMT2C is within exon 52.
SMARCA4	0	MSKCC-DMP	P-0016027-T01-IM6	TPM4-SMARCA4 fusion	yes	unknown		out of frame	TPM4 (NM_001145160) - SMARCA4 (NM_003072) rearrangement: c.114+683:TPM4_c.356-46:SMARCA4dup Note: The TPM4 - SMARCA4 rearrangement is a duplication which results in the fusion of TPM4 exon1 to SMARCA4 exon 4. The functional significance is undetermined.
TPM4	0	MSKCC-DMP	P-0016027-T01-IM6	TPM4-SMARCA4 fusion	yes	unknown		out of frame	TPM4 (NM_001145160) - SMARCA4 (NM_003072) rearrangement: c.114+683:TPM4_c.356-46:SMARCA4dup Note: The TPM4 - SMARCA4 rearrangement is a duplication which results in the fusion of TPM4 exon1 to SMARCA4 exon 4. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0016046-T01-IM6	SLC34A2-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) - SLC34A2(NM_006424) fusion: t(4;6) (p15;q22)(chr4:g.25667671::chr6:g.117662059) ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement is a reciprocal translocation that results in the fusion of SLC34A2 exons 1-4 with ROS1 exons 31-43 including the ROS1 protein kinase domain.
SLC34A2	0	MSKCC-DMP	P-0016046-T01-IM6	SLC34A2-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) - SLC34A2(NM_006424) fusion: t(4;6) (p15;q22)(chr4:g.25667671::chr6:g.117662059) ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement is a reciprocal translocation that results in the fusion of SLC34A2 exons 1-4 with ROS1 exons 31-43 including the ROS1 protein kinase domain.
MAP3K14	0	MSKCC-DMP	P-0016054-T01-IM6	KANSL1-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: c.1151+122:MAP3K14_chr17:g.44162424inv MAP3K14 (NM_003954) rearrangement results in the inversion of genomic region including exons 1-5. Its functional significance is undetermined.
KANSL1	0	MSKCC-DMP	P-0016054-T01-IM6	KANSL1-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: c.1151+122:MAP3K14_chr17:g.44162424inv MAP3K14 (NM_003954) rearrangement results in the inversion of genomic region including exons 1-5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016087-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.56-3952:TMPRSS2_c.39+61847:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016087-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.56-3952:TMPRSS2_c.39+61847:ERGdel
NHSL2	0	MSKCC-DMP	P-0016093-T02-IM6	TEK-NHSL2 fusion	yes	unknown		unknown	TEK (NM_000459) - NHSL2 (NM_001013627) rearrangement: t(9;X)(p21.2;q13.1)(chr9:g.27209165::chrX:g.71149521) Note: The TEK - NHSL2 rearrangement is a translocation with breakpoints within NHSL2 intron1 and TEK exon 16, including part of the TEK kinase domain.  The functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0016093-T02-IM6	TEK-NHSL2 fusion	yes	unknown		unknown	TEK (NM_000459) - NHSL2 (NM_001013627) rearrangement: t(9;X)(p21.2;q13.1)(chr9:g.27209165::chrX:g.71149521) Note: The TEK - NHSL2 rearrangement is a translocation with breakpoints within NHSL2 intron1 and TEK exon 16, including part of the TEK kinase domain.  The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0016117-T01-IM6	LOC102724511-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.683_chr6:g.170354686dup Note: The ARID1B rearrangement is a duplication (13254940 bp) with a breakpoint within exon 1. The functional significance is undetermined.
LOC102724511	0	MSKCC-DMP	P-0016117-T01-IM6	LOC102724511-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.683_chr6:g.170354686dup Note: The ARID1B rearrangement is a duplication (13254940 bp) with a breakpoint within exon 1. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0016129-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.-32-8659_c.2526del Note: The PIK3CD rearrangement results in the deletion of exons 3-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016134-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.56-393:TMPRSS2_c.18+26221:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016134-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.56-393:TMPRSS2_c.18+26221:ERGdel
DNMT3B	0	MSKCC-DMP	P-0016175-T01-IM6	C6orf118-DNMT3B fusion	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement:  t(6;20)(q27;q11.21)(chr6:g.165208692::chr20:g.31375366) Note: The DNMT3B rearrangement is a translocation that involves the truncation of exons 1-6.
C6orf118	0	MSKCC-DMP	P-0016175-T01-IM6	C6orf118-DNMT3B fusion	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement:  t(6;20)(q27;q11.21)(chr6:g.165208692::chr20:g.31375366) Note: The DNMT3B rearrangement is a translocation that involves the truncation of exons 1-6.
EYS	0	MSKCC-DMP	P-0016175-T01-IM6	ROS1-EYS fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: g.66194183_c.5557+62:ROS1inv Note: The ROS1 rearrangement results in an inversion of exons 34-43. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0016175-T01-IM6	ROS1-EYS fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: g.66194183_c.5557+62:ROS1inv Note: The ROS1 rearrangement results in an inversion of exons 34-43. The functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0016187-T01-IM6	SMYD3-intragenic	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement : c.1141_chr1:g.245909232del Note : The SMYD3 (NM_001167740) rearrangement results in the deletion of exons 11-12. The functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0016187-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement : c.2550_c.2811inv Note : The UPF1 (NM_002911) rearrangement is an inversion which involves UPF1 exon 18 - 20. One of the breakpoints is within exon 18 and the other is within exon 20. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0016190-T01-IM6	GPBP1-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement : c.1113:MAP3K1_chr5:g.56348204del Note: The MAP3K1 (NM_005921) rearrangement event is a deletion MAP3K1 exon 5-20 including kinase domain (exon 15-20)
GPBP1	0	MSKCC-DMP	P-0016190-T01-IM6	GPBP1-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement : c.1113:MAP3K1_chr5:g.56348204del Note: The MAP3K1 (NM_005921) rearrangement event is a deletion MAP3K1 exon 5-20 including kinase domain (exon 15-20)
ALK	0	MSKCC-DMP	P-0016193-T05-IM6	STRN-ALK fusion	yes	unknown		unknown	STRN (NM_003162) - ALK (NM_004304) fusion (STRN exons 1-3 fused with ALK exons 20-29): c.412+4919:STRN_c.3172+1:ALKdel Note: STRN-ALK fusion includes the kinase domain of ALK.
STRN	0	MSKCC-DMP	P-0016193-T05-IM6	STRN-ALK fusion	yes	unknown		unknown	STRN (NM_003162) - ALK (NM_004304) fusion (STRN exons 1-3 fused with ALK exons 20-29): c.412+4919:STRN_c.3172+1:ALKdel Note: STRN-ALK fusion includes the kinase domain of ALK.
GAB2	0	MSKCC-DMP	P-0016195-T01-IM6	FGFR2-GAB2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - GAB2 (NM_080491) fusion ( FGFR2 exons 1-17 fused with GAB2 exons 2-10 ) : t(10;11)(q26.11;q14.1)(chr10:g.123242812::chr11:g.78030553) Note : The FGFR2 (NM_000141) - GAB2 (NM_080491) rearrangement is a  translocation which results in fusion of FGFR2 exons 1-17 fused with GAB2 exons 2-10
FGFR2	0	MSKCC-DMP	P-0016195-T01-IM6	FGFR2-GAB2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - GAB2 (NM_080491) fusion ( FGFR2 exons 1-17 fused with GAB2 exons 2-10 ) : t(10;11)(q26.11;q14.1)(chr10:g.123242812::chr11:g.78030553) Note : The FGFR2 (NM_000141) - GAB2 (NM_080491) rearrangement is a  translocation which results in fusion of FGFR2 exons 1-17 fused with GAB2 exons 2-10
ROS1	0	MSKCC-DMP	P-0016213-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 33-43): t(5;6)(q32;q22.1)(chr5:g.149783418::chr6:g.117649786) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1. While the detected genomic structural variant is out of frame, CD74-ROS1 fusions are an identified driver in lung adenocarcinoma. It is likely that a functional CD74-ROS1 transcript exists. Further testing can be performed if requested and tissue is available.
CD74	0	MSKCC-DMP	P-0016213-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-7 fused to ROS1 exons 33-43): t(5;6)(q32;q22.1)(chr5:g.149783418::chr6:g.117649786) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1. While the detected genomic structural variant is out of frame, CD74-ROS1 fusions are an identified driver in lung adenocarcinoma. It is likely that a functional CD74-ROS1 transcript exists. Further testing can be performed if requested and tissue is available.
DNMT1	0	MSKCC-DMP	P-0016215-T01-IM6	RAVER1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - RAVER1 (NM_133452) rearrangement: c.4441+115:DNMT1_c.181:RAVER1dup Note: The DNMT1 - RAVER1 rearrangement is a duplication that results in the fusion of DNMT1 exons 1-36 with RAVER1 exons 1-13. One of the breakpoints is within RAVER1 exon 1. The functional significance is undetermined.
RAVER1	0	MSKCC-DMP	P-0016215-T01-IM6	RAVER1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - RAVER1 (NM_133452) rearrangement: c.4441+115:DNMT1_c.181:RAVER1dup Note: The DNMT1 - RAVER1 rearrangement is a duplication that results in the fusion of DNMT1 exons 1-36 with RAVER1 exons 1-13. One of the breakpoints is within RAVER1 exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016218-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 2 with ERG exons 3-11) : c.126+1542:TMPRSS2_c.-150+37585:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016218-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 2 with ERG exons 3-11) : c.126+1542:TMPRSS2_c.-150+37585:ERGdel
KIF5B	0	MSKCC-DMP	P-0016221-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused in-frame to RET exons 12-20) : c.1725+275:KIF5B_c.2137-764:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0016221-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused in-frame to RET exons 12-20) : c.1725+275:KIF5B_c.2137-764:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RFX2	0	MSKCC-DMP	P-0016223-T01-IM6	EGFR-RFX2 fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;19)(p11.2;p13.3)(chr7:g.55223210::chr19:g.6053108) Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 8-28. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0016223-T01-IM6	EGFR-RFX2 fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;19)(p11.2;p13.3)(chr7:g.55223210::chr19:g.6053108) Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 8-28. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016236-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exon 4): c.56-2874:TMPRSS2_c.39+13664:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016236-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exon 4): c.56-2874:TMPRSS2_c.39+13664:ERGdel
LOC101927869	0	MSKCC-DMP	P-0016244-T01-IM6	BRD4-LOC101927869 fusion	yes	unknown		unknown	BRD4:NM_058243 Rearrangement : t(19;21)(p13.12;q21.3)(chr19:g.15350666::chr21:g.25706468) Note: The BRD4 Rearrangement results in the possible truncation of exons 16-20. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0016244-T01-IM6	BRD4-LOC101927869 fusion	yes	unknown		unknown	BRD4:NM_058243 Rearrangement : t(19;21)(p13.12;q21.3)(chr19:g.15350666::chr21:g.25706468) Note: The BRD4 Rearrangement results in the possible truncation of exons 16-20. Its functional significance is undetermined.
EFCAB13	0	MSKCC-DMP	P-0016254-T01-IM6	SMAD3-EFCAB13 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - EFCAB13 (NM_001195192) rearrangement: t(15;17)(q22.33;q21.32)(chr15:g.67477157::chr17:g.45465290) Note: The SMAD3 - EFCAB13 rearrangement is a translocation with a breakpoint within SMAD3 exon 7. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0016254-T01-IM6	SMAD3-EFCAB13 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - EFCAB13 (NM_001195192) rearrangement: t(15;17)(q22.33;q21.32)(chr15:g.67477157::chr17:g.45465290) Note: The SMAD3 - EFCAB13 rearrangement is a translocation with a breakpoint within SMAD3 exon 7. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0016280-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) rearrangement: c.1316-2732:EML4_c.3172+422:ALKinv Note : The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-13 and ALK exons 20-23. (PMID 17625570)
EML4	0	MSKCC-DMP	P-0016280-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) rearrangement: c.1316-2732:EML4_c.3172+422:ALKinv Note : The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-13 and ALK exons 20-23. (PMID 17625570)
MITF	0	MSKCC-DMP	P-0016293-T01-IM6	MITF-intragenic	yes	unknown		in frame	MITF (NM_198159) rearrangment : c.104+56625_c.1014-63MITFdel Note: The MITF rearrangement results in the deletion of exons 2-8. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0016295-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314)  rearrangment : c.-879_c.54PTENdel Note: The PTEN (NM_000314) rearrangement is a deletion of PTEN exon 1. One of the breakpoints is within exon 1. The functional significance is unknown.
ERG	0	MSKCC-DMP	P-0016296-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.40-46781:TMPRSS2_c.18+5962:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016296-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.40-46781:TMPRSS2_c.18+5962:ERGdel
GLYCTK	0	MSKCC-DMP	P-0016296-T01-IM6	PBRM1-GLYCTK fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement :  chr3:g.52327928_c.237-51:PBRM1dup Note: The PBRM1 rearrangement is a duplication of PBRM1 exons 1-4. The functional significance is unknown.
PBRM1	0	MSKCC-DMP	P-0016296-T01-IM6	PBRM1-GLYCTK fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement :  chr3:g.52327928_c.237-51:PBRM1dup Note: The PBRM1 rearrangement is a duplication of PBRM1 exons 1-4. The functional significance is unknown.
ERG	0	MSKCC-DMP	P-0016307-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-11) : c.56-2505:TMPRSS2_c.-150+535:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016307-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-11) : c.56-2505:TMPRSS2_c.-150+535:ERGdel
EWSR1	0	MSKCC-DMP	P-0016311-T01-IM6	TRIOBP-EWSR1 fusion	yes	unknown		out of frame	TRIOBP (NM_001039141) - EWSR1 (NM_013986) rearrangement: c.255-219:TRIOBP_c.1060+2:EWSR1Ldup Note: The TRIOBP - EWSR1 rearrangement is a duplication that results in the fusion of TRIOBP exons 1-4 with EWSR1 exons 12-18. The functional significance is undetermined.
TRIOBP	0	MSKCC-DMP	P-0016311-T01-IM6	TRIOBP-EWSR1 fusion	yes	unknown		out of frame	TRIOBP (NM_001039141) - EWSR1 (NM_013986) rearrangement: c.255-219:TRIOBP_c.1060+2:EWSR1Ldup Note: The TRIOBP - EWSR1 rearrangement is a duplication that results in the fusion of TRIOBP exons 1-4 with EWSR1 exons 12-18. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0016313-T01-IM6	SLC45A3-BRAF fusion	yes	unknown		unknown	SLC45A3 (NM_033102) - BRAF (NM_004333) fusion (SLC45A3 exons 1 fused to BRAF exons 10-18): t(1;7)(q32.1;q34)(chr1:g.205638452::chr7:g.140486608) this is known
SLC45A3	0	MSKCC-DMP	P-0016313-T01-IM6	SLC45A3-BRAF fusion	yes	unknown		unknown	SLC45A3 (NM_033102) - BRAF (NM_004333) fusion (SLC45A3 exons 1 fused to BRAF exons 10-18): t(1;7)(q32.1;q34)(chr1:g.205638452::chr7:g.140486608) this is known
ERG	0	MSKCC-DMP	P-0016325-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+1067:TMPRSS2_c.40-55287:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016325-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+1067:TMPRSS2_c.40-55287:ERGdel
TTC28	0	MSKCC-DMP	P-0016326-T01-IM6	CHEK2-TTC28 fusion	yes	unknown		unknown	CHEK2 (NM_007194) - TTC28 (NM_001145418) rearrangement: c.594:CHEK2_c.102+8045:TTC28inv Note: The CHEK2 - TTC28 rearrangement is an inversion which includes CHEK2 exons 5-15. One of the breakpoints is within CHEK2 exon 5. The functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0016326-T01-IM6	CHEK2-TTC28 fusion	yes	unknown		unknown	CHEK2 (NM_007194) - TTC28 (NM_001145418) rearrangement: c.594:CHEK2_c.102+8045:TTC28inv Note: The CHEK2 - TTC28 rearrangement is an inversion which includes CHEK2 exons 5-15. One of the breakpoints is within CHEK2 exon 5. The functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0016358-T01-IM6	BCL7C-TRAF7 fusion	yes	unknown		unknown	TRAF7 (NM_032271) Rearrangement : c.1087-41:TRAF7_chr16:g.30884849dup Note: The TRAF7 Rearrangement results in the duplication of exons 12-21 of TRAF7. Its functional significance is undetermined,
BCL7C	0	MSKCC-DMP	P-0016358-T01-IM6	BCL7C-TRAF7 fusion	yes	unknown		unknown	TRAF7 (NM_032271) Rearrangement : c.1087-41:TRAF7_chr16:g.30884849dup Note: The TRAF7 Rearrangement results in the duplication of exons 12-21 of TRAF7. Its functional significance is undetermined,
POLD1	0	MSKCC-DMP	P-0016377-T01-IM6	NDUFA3-POLD1 fusion	yes	unknown		unknown	NDUFA3 (NM_004542) - POLD1 (NM_002691) rearrangement: c.85+584:NDUFA3_c.510:POLD1dup Note: The NDUFA3 - POLD1 rearrangement is a duplication which results in the fusion of NDUFA3 exon 2 to POLD1 exon5. One of the breakpoints is within POLD1 exon 5. The functional significance is undetermined.
NDUFA3	0	MSKCC-DMP	P-0016377-T01-IM6	NDUFA3-POLD1 fusion	yes	unknown		unknown	NDUFA3 (NM_004542) - POLD1 (NM_002691) rearrangement: c.85+584:NDUFA3_c.510:POLD1dup Note: The NDUFA3 - POLD1 rearrangement is a duplication which results in the fusion of NDUFA3 exon 2 to POLD1 exon5. One of the breakpoints is within POLD1 exon 5. The functional significance is undetermined.
BMP7	0	MSKCC-DMP	P-0016378-T01-IM6	PPP4R2-BMP7 fusion	yes	unknown		unknown	PPP4R2 (NM_174907) rearrangement: t(3;20)(p13;q13.31)(chr3:g.73046268::chr20:g.55536538) Note: The PPP4R2 rearrangement is a translocation with a breakpoint after exon1. The functional significance is undetermined.
PPP4R2	0	MSKCC-DMP	P-0016378-T01-IM6	PPP4R2-BMP7 fusion	yes	unknown		unknown	PPP4R2 (NM_174907) rearrangement: t(3;20)(p13;q13.31)(chr3:g.73046268::chr20:g.55536538) Note: The PPP4R2 rearrangement is a translocation with a breakpoint after exon1. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0016386-T01-IM6	CHST12-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2452854::chr21:g.42872453) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14.
CHST12	0	MSKCC-DMP	P-0016386-T01-IM6	CHST12-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2452854::chr21:g.42872453) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14.
SH3GL2	0	MSKCC-DMP	P-0016388-T01-IM6	DROSHA-SH3GL2 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515314::chr9:g.17618123) Note: The DROSHA rearrangement is a translocation that may result in a truncation of exons 7-35. One of the breakpoints is within exon 7. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0016388-T01-IM6	DROSHA-SH3GL2 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515314::chr9:g.17618123) Note: The DROSHA rearrangement is a translocation that may result in a truncation of exons 7-35. One of the breakpoints is within exon 7. The functional significance is undetermined.
NTHL1	0	MSKCC-DMP	P-0016391-T01-IM6	TSC2-NTHL1 fusion	yes	unknown		in frame	TSC2 (NM_000548) - NTHL1 (NM_002528) rearrangement: c.648+2:TSC2_c.379-117:NTHL1inv Note: The TSC2 - NTHL1 rearrangement is an inversion that results in an in-frame fusion of TSC2 exons 1-7 to NTHL1 exons 3-6. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0016391-T01-IM6	TSC2-NTHL1 fusion	yes	unknown		in frame	TSC2 (NM_000548) - NTHL1 (NM_002528) rearrangement: c.648+2:TSC2_c.379-117:NTHL1inv Note: The TSC2 - NTHL1 rearrangement is an inversion that results in an in-frame fusion of TSC2 exons 1-7 to NTHL1 exons 3-6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016396-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+797:TMPRSS2_c.18+1126:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016396-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+797:TMPRSS2_c.18+1126:ERGdel
SPINT4	0	MSKCC-DMP	P-0016398-T01-IM6	PTPRS-SPINT4 fusion	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(19;20)(p13.3;q13.12)(chr19:g.5214669::chr20:g.44361214) Note: The PTPRS rearrangement is a translocation that may result in the truncation of exons 29-38. One of the breakpoints is within exon 29. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0016398-T01-IM6	PTPRS-SPINT4 fusion	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(19;20)(p13.3;q13.12)(chr19:g.5214669::chr20:g.44361214) Note: The PTPRS rearrangement is a translocation that may result in the truncation of exons 29-38. One of the breakpoints is within exon 29. The functional significance is undetermined.
KAZN	0	MSKCC-DMP	P-0016450-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) - KAZN (NM_201628) rearrangement: c.2147:SPEN_c.726+4286:KAZNdup Note: The SPEN - KAZN rearrangement is a duplication which results in the fusion of SPEN exon11 to KAZN exon5. One of the breakpoints is within SPEN exon11. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0016450-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) - KAZN (NM_201628) rearrangement: c.2147:SPEN_c.726+4286:KAZNdup Note: The SPEN - KAZN rearrangement is a duplication which results in the fusion of SPEN exon11 to KAZN exon5. One of the breakpoints is within SPEN exon11. The functional significance is undetermined.
SRCIN1	0	MSKCC-DMP	P-0016468-T01-IM6	MAP3K14-SRCIN1 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) - SRCIN1 (NM_025248) rearrangement: c.1069:MAP3K14_c.3417+1021:SRCIN1del Note: The MAP3K14 - SRCIN1 rearrangement is a deletion which results in the fusion of MAP3K14 exon 5 to SRCIN1 exon 19. One of the breakpoints is within MAP3K14 exon 5. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0016468-T01-IM6	MAP3K14-SRCIN1 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) - SRCIN1 (NM_025248) rearrangement: c.1069:MAP3K14_c.3417+1021:SRCIN1del Note: The MAP3K14 - SRCIN1 rearrangement is a deletion which results in the fusion of MAP3K14 exon 5 to SRCIN1 exon 19. One of the breakpoints is within MAP3K14 exon 5. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0016499-T01-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.638-16_c.705+505inv Note: The ARID2 rearrangement is an intragenic inversion of exon 6.
SDC4	0	MSKCC-DMP	P-0016504-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117650681::chr20:g.43961904) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0016504-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117650681::chr20:g.43961904) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ERG	0	MSKCC-DMP	P-0016538-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-11): c.56-1880:TMPRSS2_c.-149-7340:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016538-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-11): c.56-1880:TMPRSS2_c.-149-7340:ERGdel
MAP3K1	0	MSKCC-DMP	P-0016545-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.3666+42_c.*5156del Note: The MAP3K1 rearrangement is an intragenic deletion of exons 15-20. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0016548-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-1658_c.556+3387inv Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2-5.
TMPRSS2	0	MSKCC-DMP	P-0016548-T01-IM6	RSL24D1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.55490150::chr21:g.42876875) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints in intron 1 that may result in a truncation of exons 2-14. The two structural variants in this sample involving TMPRSS2 suggests a more complex rearrangement. Further testing by other assays is recommended.
RSL24D1	0	MSKCC-DMP	P-0016548-T01-IM6	RSL24D1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.55490150::chr21:g.42876875) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints in intron 1 that may result in a truncation of exons 2-14. The two structural variants in this sample involving TMPRSS2 suggests a more complex rearrangement. Further testing by other assays is recommended.
NF1	0	MSKCC-DMP	P-0016563-T01-IM6	MIR193B-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492)  rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.14398973::chr17:g.29664922) Note: The NF1 rearrangement is a translocation that may result in the truncation of exons 1-44. The functional significance is undetermined.
MIR193B	0	MSKCC-DMP	P-0016563-T01-IM6	MIR193B-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492)  rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.14398973::chr17:g.29664922) Note: The NF1 rearrangement is a translocation that may result in the truncation of exons 1-44. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0016568-T01-IM6	KDM6B-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1059_g.7755275del Note: The TP53 rearrangement results in the deletion of exons 10 and 11. One of the breakpoints is within exon 10. The functional significance is undetermined.
KDM6B	0	MSKCC-DMP	P-0016568-T01-IM6	KDM6B-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1059_g.7755275del Note: The TP53 rearrangement results in the deletion of exons 10 and 11. One of the breakpoints is within exon 10. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0016570-T01-IM6	ZNF569-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5898_g.37913327dup Note: The KMT2B rearrangement results in the duplication of exons 28-37. One of the breakpoints is within exon 28. The functional significance is undetermined.
ZNF569	0	MSKCC-DMP	P-0016570-T01-IM6	ZNF569-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5898_g.37913327dup Note: The KMT2B rearrangement results in the duplication of exons 28-37. One of the breakpoints is within exon 28. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0016575-T01-IM6	TUSC1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.151-52_chr9:g.25375257del Note: The CDKN2A rearrangement is a deletion which includes exon 1 of  both the CDKN2Ap16INK4A (NM_000077) and CDKN2Ap14ARF (NM_058195) isoforms.
TUSC1	0	MSKCC-DMP	P-0016575-T01-IM6	TUSC1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.151-52_chr9:g.25375257del Note: The CDKN2A rearrangement is a deletion which includes exon 1 of  both the CDKN2Ap16INK4A (NM_000077) and CDKN2Ap14ARF (NM_058195) isoforms.
ALK	0	MSKCC-DMP	P-0016580-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1489+2257:EML4_c.3172+748:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0016580-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1489+2257:EML4_c.3172+748:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
TMPRSS2	0	MSKCC-DMP	P-0016594-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.126+1418_c.56-2775del Note: The TMPRSS2 rearrangement results in the deletion of exon 2. The functional significance is undetermined.
TMTC1	0	MSKCC-DMP	P-0016605-T01-IM6	H3F3C-TMTC1 fusion	yes	unknown		unknown	H3F3C (NM_001013699) rearrangement: g.30188428_c.240del Note: The H3F3C rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
H3F3C	0	MSKCC-DMP	P-0016605-T01-IM6	H3F3C-TMTC1 fusion	yes	unknown		unknown	H3F3C (NM_001013699) rearrangement: g.30188428_c.240del Note: The H3F3C rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0016614-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.1744_c.3591-369del Note: The EP300 rearrangement is an intragenic deletion of exons 8-19. One of the breakpoints is within exon 8. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0016625-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.*1284_c.1474del Note: The BAP1 rearrangement results in the deletion of exons 13-17. One of the breakpoints is within exon 13. The functional significance is unknown.
TAP1	0	MSKCC-DMP	P-0016625-T01-IM6	TAP1-intragenic	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: c.1025-41_c.470del Note: The TAP1 rearrangement results in the deletion of exons 1-3. One of the breakpoints is within exon 1. The functional significance is unknown.
TENM4	0	MSKCC-DMP	P-0016642-T01-IM6	ATM-TENM4 fusion	yes	unknown		unknown	ATM (NM_000051) - TENM4 (NM_001098816) rearrangement : c.2069:ATM_c.2877-305:TENM4inv Note : The ATM - TENM4 rearrangement is an inversion which results in the fusion of  ATM exon1-13 and TENM4 exon21-34. One of the breakpoints is within ATM exon13. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0016642-T01-IM6	ATM-TENM4 fusion	yes	unknown		unknown	ATM (NM_000051) - TENM4 (NM_001098816) rearrangement : c.2069:ATM_c.2877-305:TENM4inv Note : The ATM - TENM4 rearrangement is an inversion which results in the fusion of  ATM exon1-13 and TENM4 exon21-34. One of the breakpoints is within ATM exon13. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0016643-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546)  rearrangement : chr17:g.7572418_c.994-68:TP53inv Note: The TP53 rearrangement is an inversion which include TP53 exon10-11. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0016661-T01-IM6	IKZF3-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.3159+7:ERBB2_c.827-3270:IKZF3del Note: The ERBB2 - IKZF3 rearrangement is a deletion which includes exons 26-27 of ERBB2 and exon 8 of IKZF3. The functional significance is undetermined.
IKZF3	0	MSKCC-DMP	P-0016661-T01-IM6	IKZF3-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.3159+7:ERBB2_c.827-3270:IKZF3del Note: The ERBB2 - IKZF3 rearrangement is a deletion which includes exons 26-27 of ERBB2 and exon 8 of IKZF3. The functional significance is undetermined.
CD79A	0	MSKCC-DMP	P-0016692-T01-IM6	CIC-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) rearrangement: c.649:CD79A_chr19:g.42777278del Note: The CD79A rearrangement is a deletion of exon 5. One of breakpoints is within exon 5.
CIC	0	MSKCC-DMP	P-0016692-T01-IM6	CIC-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) rearrangement: c.649:CD79A_chr19:g.42777278del Note: The CD79A rearrangement is a deletion of exon 5. One of breakpoints is within exon 5.
ARID1A	0	MSKCC-DMP	P-0016696-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1137+3955_c.4158del Note: The ARID1A rearrangement is an intragenic deletion of exons 2-18. One of the breakpoints is within exon18. The functional significance is undetermined.
PPFIA2	0	MSKCC-DMP	P-0016697-T01-IM6	RAB35-PPFIA2 fusion	yes	unknown		unknown	RAB35 (NM_006861) - PPFIA2 (NM_003625) rearrangement: c.477+69:RAB35_c.303+64413:PPFIA2del Note: The RAB35 - PPFIA2 rearrangement is a deletion which results in the fusion of RAB35 exons 1-5 to PPFIA2 exons 5-32. The functional significance is undetermined.
RAB35	0	MSKCC-DMP	P-0016697-T01-IM6	RAB35-PPFIA2 fusion	yes	unknown		unknown	RAB35 (NM_006861) - PPFIA2 (NM_003625) rearrangement: c.477+69:RAB35_c.303+64413:PPFIA2del Note: The RAB35 - PPFIA2 rearrangement is a deletion which results in the fusion of RAB35 exons 1-5 to PPFIA2 exons 5-32. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016698-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2599:TMPRSS2_c.18+9969:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016698-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2599:TMPRSS2_c.18+9969:ERGdel
ARID5B	0	MSKCC-DMP	P-0016714-T01-IM6	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) Rearrangement : c.847-1236_c.3325del Note: The ARID5B Rearrangement results in the intragenic deletion of exons 6-10 of ARID5B. One of the breakpoints is within exon10. Its functional significance is unknown.
FAT1	0	MSKCC-DMP	P-0016714-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.8879-31:FAT1_chr4:g.190223782del Note: The FAT1 Rearrangement results in the deletion of exons 1-10 of FAT1. This event occurs in the background of other structural rearrangements affecting FAT1. Its functional significance is unknown.
LINC01262	0	MSKCC-DMP	P-0016714-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.8879-31:FAT1_chr4:g.190223782del Note: The FAT1 Rearrangement results in the deletion of exons 1-10 of FAT1. This event occurs in the background of other structural rearrangements affecting FAT1. Its functional significance is unknown.
ERG	0	MSKCC-DMP	P-0016733-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG fusion (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3794:TMRPSS2_c.19-6151:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016733-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG fusion (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3794:TMRPSS2_c.19-6151:ERGdel
AR	0	MSKCC-DMP	P-0016746-T01-IM6	AR-intragenic	yes	unknown		unknown	AR (NM_000044)  Rearrangement : c.2174-1838_c.2191inv Note: The AR Rearrangement results in the partial inversion of exon5 of AR. One of the breakpoints is within exon5. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0016747-T01-IM6	MIR5695-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.5557+603:ROS1_chr6:g.126400977del Note: The ROS1 Rearrangement results in the deletion of exons 1-33. The functional significance is undetermined.
MIR5695	0	MSKCC-DMP	P-0016747-T01-IM6	MIR5695-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.5557+603:ROS1_chr6:g.126400977del Note: The ROS1 Rearrangement results in the deletion of exons 1-33. The functional significance is undetermined.
TJP1	0	MSKCC-DMP	P-0016763-T01-IM6	MGA-TJP1 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement : g.29907619_c.5357:MGAinv Note: The MGA rearrangement results in the inversion of exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0016763-T01-IM6	MGA-TJP1 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement : g.29907619_c.5357:MGAinv Note: The MGA rearrangement results in the inversion of exons 1-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0016776-T01-IM6	RAB11FIP4-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - RAB11FIP4 (NM_032932) rearrangement: c.810:NF1_c.159+14109:RAB11FIP4del Note: The NF1 - RAB11FIP4 rearrangement is a deletion which results in the fusion of NF1 exon 8 to RAB11FIP4 exon 2. One of the breakpoints is within NF1 exon 8. The functional significance is undetermined.
RAB11FIP4	0	MSKCC-DMP	P-0016776-T01-IM6	RAB11FIP4-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - RAB11FIP4 (NM_032932) rearrangement: c.810:NF1_c.159+14109:RAB11FIP4del Note: The NF1 - RAB11FIP4 rearrangement is a deletion which results in the fusion of NF1 exon 8 to RAB11FIP4 exon 2. One of the breakpoints is within NF1 exon 8. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0016777-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.927+476_c.3226dup Note: The WHSC1 rearrangement is an intrangenic duplicaiton of exons 5-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0016785-T01-IM6	STXBP2-STK11 fusion	yes	unknown		out of frame	STXBP2 (NM_006949) - STK11 (NM_000455)  rearrangement: c.1107+62:STXBP2_c.291-17:STK11dup Note: The STXBP2 - STK11 rearrangement is a duplication (6489794 bp) which results in the fusion of STXBP2 exon 13 to STK11 exon 2. The functional significance is undetermined.
STXBP2	0	MSKCC-DMP	P-0016785-T01-IM6	STXBP2-STK11 fusion	yes	unknown		out of frame	STXBP2 (NM_006949) - STK11 (NM_000455)  rearrangement: c.1107+62:STXBP2_c.291-17:STK11dup Note: The STXBP2 - STK11 rearrangement is a duplication (6489794 bp) which results in the fusion of STXBP2 exon 13 to STK11 exon 2. The functional significance is undetermined.
MST1R	0	MSKCC-DMP	P-0016785-T01-IM6	SCHIP1-MST1R fusion	yes	unknown		unknown	MST1R (NM_002447) - IQCJ-SCHIP1 (NM_001197113) rearrangement: c.2829:MST1R_c.292-12602:IQCJ-SCHIP1del Note: The MST1R - IQC-SCHIP1 rearrangement is a deletion  (109422930 bp) which includes exons 1-12 of MST1R. One of the breakpoints is within MST1R exon 12. The functional significance is undetermined.
SCHIP1	0	MSKCC-DMP	P-0016785-T01-IM6	SCHIP1-MST1R fusion	yes	unknown		unknown	MST1R (NM_002447) - IQCJ-SCHIP1 (NM_001197113) rearrangement: c.2829:MST1R_c.292-12602:IQCJ-SCHIP1del Note: The MST1R - IQC-SCHIP1 rearrangement is a deletion  (109422930 bp) which includes exons 1-12 of MST1R. One of the breakpoints is within MST1R exon 12. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0016792-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) Rearrangement : c.-1700_c.708del Note: The STK11 Rearrangement results in the deletion of exons 1-5 of STK11. The breakpoints are within the promoter region and exon 5 respectively. Its functional significance is undetermined.
KIT	0	MSKCC-DMP	P-0016795-T01-IM6	KIT-intragenic	yes	unknown		in frame	KIT (NM_000222) Rearrangement : c.1231+989_2597-55dup Note: The KIT Rearrangement results in the intragenic duplication of exons 8-18. Its functional significance is undetermined.
DDC	0	MSKCC-DMP	P-0016795-T01-IM6	EGFR-DDC fusion	yes	unknown		out of frame	DDC (NM_000790) - EGFR (NM_005228) Rearrangement : c.435+4059:DDC_c.889+359:EGFRinv Note: The DDC - EGFR  Rearrangement results in the fusion of exons 1-4 of DDC with exons 8-28 of EGFR. This includes the protein kinase domain of EGFR. This rearrangement is observed in the background of copy number gain of EGFR. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0016795-T01-IM6	EGFR-DDC fusion	yes	unknown		out of frame	DDC (NM_000790) - EGFR (NM_005228) Rearrangement : c.435+4059:DDC_c.889+359:EGFRinv Note: The DDC - EGFR  Rearrangement results in the fusion of exons 1-4 of DDC with exons 8-28 of EGFR. This includes the protein kinase domain of EGFR. This rearrangement is observed in the background of copy number gain of EGFR. Its functional significance is undetermined.
C16orf72	0	MSKCC-DMP	P-0016807-T01-IM6	KMT2D-C16orf72 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(12;16)(q13.12;p13.2)(chr12:g.49444705::chr16:g.9209176) Note: The KMT2D rearrangement is a translocation that may result in the truncation of exons 10-54. One of the breakpoints is within exon 10. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0016807-T01-IM6	KMT2D-C16orf72 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(12;16)(q13.12;p13.2)(chr12:g.49444705::chr16:g.9209176) Note: The KMT2D rearrangement is a translocation that may result in the truncation of exons 10-54. One of the breakpoints is within exon 10. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0016812-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement : c.1760-157_c.2136+377inv Note: The RET rearrangement results in an inversion of exons 10-11. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0016812-T01-IM6	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement : t(17;21)(q21.31;q22.3)(chr17:g.41623968::chr21:g.42867167) Note: The TMPRSS2-ETV4 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV4 promoter region. PMID: 16585160
ETV4	0	MSKCC-DMP	P-0016812-T01-IM6	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement : t(17;21)(q21.31;q22.3)(chr17:g.41623968::chr21:g.42867167) Note: The TMPRSS2-ETV4 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV4 promoter region. PMID: 16585160
LOC100287592	0	MSKCC-DMP	P-0016815-T01-IM6	MAP3K1-LOC100287592 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: g.50161653_c.3819+27:MAP3K1inv Note: The MAP3K1 rearrangement results in an inversion of exons 1-15. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0016815-T01-IM6	MAP3K1-LOC100287592 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: g.50161653_c.3819+27:MAP3K1inv Note: The MAP3K1 rearrangement results in an inversion of exons 1-15. The functional significance is undetermined.
SNX9	0	MSKCC-DMP	P-0016815-T01-IM6	PARK2-SNX9 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: g.158228249_c.1083+84:PARK2inv Note: The PARK2 rearrangement results in an inversion of exons 10-12. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0016815-T01-IM6	PARK2-SNX9 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: g.158228249_c.1083+84:PARK2inv Note: The PARK2 rearrangement results in an inversion of exons 10-12. The functional significance is undetermined.
ACVR1	0	MSKCC-DMP	P-0016820-T01-IM6	ACVR1-intragenic	yes	unknown		unknown	ACVR1 (NM_001111067) Rearrangement : c.543+1130_754dup Note: The ACVR1 Rearrangement results in the duplication of exons 6-7 of ACVR1. One of the breakpoints is within exon 7. Its functional significance is undetermined.
CLIC4	0	MSKCC-DMP	P-0016842-T01-IM6	CSF3R-CLIC4 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1724-48_chr1:g.25041917del Note: The CSF3R rearrangement is a deletion which includes exons 14-17 of CSF3R. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0016842-T01-IM6	CSF3R-CLIC4 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1724-48_chr1:g.25041917del Note: The CSF3R rearrangement is a deletion which includes exons 14-17 of CSF3R. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0016877-T01-IM6	NSUN4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(1;21)(p33;q22.3)(chr1:g.46831834::chr21:g.42866769) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 3-14.
NSUN4	0	MSKCC-DMP	P-0016877-T01-IM6	NSUN4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(1;21)(p33;q22.3)(chr1:g.46831834::chr21:g.42866769) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 3-14.
ERG	0	MSKCC-DMP	P-0016883-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG(NM_004449) Rearrangement : c.56-1115:TMPRSS2_c.-149-1187:ERGdel Note: The TMPRSS2 -ERG Rearrangement results in the deletion of exons 2-14 of TMPRSS2 and exon1 of ERG. This is not the canonical TMPRRS2-ERG fusion, however the possibility of such a fusion not detected by IMPACT test panel cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0016883-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) -ERG(NM_004449) Rearrangement : c.56-1115:TMPRSS2_c.-149-1187:ERGdel Note: The TMPRSS2 -ERG Rearrangement results in the deletion of exons 2-14 of TMPRSS2 and exon1 of ERG. This is not the canonical TMPRRS2-ERG fusion, however the possibility of such a fusion not detected by IMPACT test panel cannot be ruled out.
EZH1	0	MSKCC-DMP	P-0016895-T01-IM6	FGF14-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - FGF14 (NM_175929) Rearrangement : t(13;17)(q33.1;q21.2)(chr13:g.102490730::chr17:g.40876400) Note: The EZH1 - FGF14 Rearrangement results in the fusion of exons 1-5 of EZH1 with exons 4-5 of FGF14. The breakpoint in EZH1 is within exon5. Its functional significance is undetermined.
FGF14	0	MSKCC-DMP	P-0016895-T01-IM6	FGF14-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - FGF14 (NM_175929) Rearrangement : t(13;17)(q33.1;q21.2)(chr13:g.102490730::chr17:g.40876400) Note: The EZH1 - FGF14 Rearrangement results in the fusion of exons 1-5 of EZH1 with exons 4-5 of FGF14. The breakpoint in EZH1 is within exon5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016895-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10) : c.56-3557:TMPRSS2_c.19-13783:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016895-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10) : c.56-3557:TMPRSS2_c.19-13783:ERGdel
FBRSL1	0	MSKCC-DMP	P-0016910-T01-IM6	POLE-FBRSL1 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.4132:POLE_chr12:g.132997799inv Note: The POLE rearrangement is an inversion of exons 32-49. One of the breakpoints is within exon 32.
POLE	0	MSKCC-DMP	P-0016910-T01-IM6	POLE-FBRSL1 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.4132:POLE_chr12:g.132997799inv Note: The POLE rearrangement is an inversion of exons 32-49. One of the breakpoints is within exon 32.
BRAF	0	MSKCC-DMP	P-0016911-T01-IM6	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) rearrangement: c.1314+303_c.241-7545del Note: The BRAF rearrangement results in the deletion of exons 3-10.  The functional significance is undetermined.
LLGL1	0	MSKCC-DMP	P-0016912-T01-IM6	NF1-LLGL1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - LLGL1 (NM_004140) rearrangement: c.5268+78:NF1_c.-1064: LLGL1dup Note: The NF1 - LLGL1 rearrangement is a duplication which results in the fusion of NF1 exons 1-37 with LLGL1 promoter region.
NF1	0	MSKCC-DMP	P-0016912-T01-IM6	NF1-LLGL1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - LLGL1 (NM_004140) rearrangement: c.5268+78:NF1_c.-1064: LLGL1dup Note: The NF1 - LLGL1 rearrangement is a duplication which results in the fusion of NF1 exons 1-37 with LLGL1 promoter region.
PHB	0	MSKCC-DMP	P-0016912-T01-IM6	SPOP-PHB fusion	yes	unknown		unknown	SPOP (NM_001007228) rearrangement: g.47502627_c.481-35:SPOPinv Note: The SPOP rearrangement is an inversion of exons 6-10. The functional significance is undetermined.
SPOP	0	MSKCC-DMP	P-0016912-T01-IM6	SPOP-PHB fusion	yes	unknown		unknown	SPOP (NM_001007228) rearrangement: g.47502627_c.481-35:SPOPinv Note: The SPOP rearrangement is an inversion of exons 6-10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0016933-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+4812:TMPRSS2_c.40-58894:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0016933-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+4812:TMPRSS2_c.40-58894:ERGdel
NCOR1	0	MSKCC-DMP	P-0016941-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.6956-60_c.6679+487inv Note: The NCOR1 rearrangement is an inversion of exons 43-44. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0016941-T01-IM6	PTPRN2-KMT2C fusion	yes	unknown		out of frame	PTPRN2 (NM_002847) - KMT2C (NM_170606) rearrangement: c.164-76166: PTPRN2_c.14535-47: KMT2Cdel Note: The PTPRN2 - KMT2C rearrangement is a deletion that results in the fusion of PTPRN2 exons 1-2 with KMT2C exons 58-59. The functional significance is undetermined.
PTPRN2	0	MSKCC-DMP	P-0016941-T01-IM6	PTPRN2-KMT2C fusion	yes	unknown		out of frame	PTPRN2 (NM_002847) - KMT2C (NM_170606) rearrangement: c.164-76166: PTPRN2_c.14535-47: KMT2Cdel Note: The PTPRN2 - KMT2C rearrangement is a deletion that results in the fusion of PTPRN2 exons 1-2 with KMT2C exons 58-59. The functional significance is undetermined.
ZSWIM7	0	MSKCC-DMP	P-0016946-T01-IM6	NCOR1-ZSWIM7 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement : g.15887497_c.5603:NCOR1inv Note: The NCOR1 rearrangement results in an inversion of exons 37-46. One of the breakpoints is within exon 37. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0016946-T01-IM6	NCOR1-ZSWIM7 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement : g.15887497_c.5603:NCOR1inv Note: The NCOR1 rearrangement results in an inversion of exons 37-46. One of the breakpoints is within exon 37. The functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0016946-T01-IM6	ENGASE-AXIN2 fusion	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement : c.1201-45: AXIN2_g.77075798del Note: The AXIN2 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.
ENGASE	0	MSKCC-DMP	P-0016946-T01-IM6	ENGASE-AXIN2 fusion	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement : c.1201-45: AXIN2_g.77075798del Note: The AXIN2 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0016946-T01-IM6	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) rearrangement : c.1376_c.-125-13049del Note: The CARD11 rearrangement results in the deletion of exons 1-10. The functional significance is undetermined.
CBL	0	MSKCC-DMP	P-0016958-T01-IM6	ZNF691-CBL fusion	yes	unknown		unknown	ZNF691 (NM_015911) - CBL (NM_00518) rearrangement: t(1;11)(p34.2;q23.3)(chr1:g.43315081::chr11:g.119077286) Note: The ZNF691 - CBL  rearrangement is a translocation with breakpoints within the 5UTR of ZNF691 and exon 1 of CBL. The functional significance is undetermined.
ZNF691	0	MSKCC-DMP	P-0016958-T01-IM6	ZNF691-CBL fusion	yes	unknown		unknown	ZNF691 (NM_015911) - CBL (NM_00518) rearrangement: t(1;11)(p34.2;q23.3)(chr1:g.43315081::chr11:g.119077286) Note: The ZNF691 - CBL  rearrangement is a translocation with breakpoints within the 5UTR of ZNF691 and exon 1 of CBL. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0016960-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.667+7453:EML4_c.3172+489:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0016960-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.667+7453:EML4_c.3172+489:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
PRDM14	0	MSKCC-DMP	P-0016968-T01-IM6	MIR4436A-PRDM14 fusion	yes	unknown		unknown	PRDM14 (NM_024504) rearrangement: t(2;8)(p11.2;q13.3)(chr2:g.89832919::chr8:g.70981692) Note: The PRDM14 rearrangement is a translocation which may result in the truncation of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
MIR4436A	0	MSKCC-DMP	P-0016968-T01-IM6	MIR4436A-PRDM14 fusion	yes	unknown		unknown	PRDM14 (NM_024504) rearrangement: t(2;8)(p11.2;q13.3)(chr2:g.89832919::chr8:g.70981692) Note: The PRDM14 rearrangement is a translocation which may result in the truncation of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0016973-T01-IM6	GREB1L-INSR fusion	yes	unknown		unknown	INSR (NM_000208)rearrangement: t(18;19)(q11.1;p13.2)(chr18:g.18934293::chr19:g.7117210) Note: The INSR rearrangement is a reciprocal translocation that may result in the truncation of exons 1-22. One of the breakpoints is within exon 22. The functional significance is undetermined.
GREB1L	0	MSKCC-DMP	P-0016973-T01-IM6	GREB1L-INSR fusion	yes	unknown		unknown	INSR (NM_000208)rearrangement: t(18;19)(q11.1;p13.2)(chr18:g.18934293::chr19:g.7117210) Note: The INSR rearrangement is a reciprocal translocation that may result in the truncation of exons 1-22. One of the breakpoints is within exon 22. The functional significance is undetermined.
FOXO1	0	MSKCC-DMP	P-0016985-T01-IM6	LINC00443-FOXO1 fusion	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement : c.1116:FOXO1_g.107386743inv Note: The FOXO1 rearrangement results in an inversion of exons 1-2 . One of the breakpoints is within exon 2. The functional significance is undetermined.
LINC00443	0	MSKCC-DMP	P-0016985-T01-IM6	LINC00443-FOXO1 fusion	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement : c.1116:FOXO1_g.107386743inv Note: The FOXO1 rearrangement results in an inversion of exons 1-2 . One of the breakpoints is within exon 2. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0016985-T01-IM6	TDH-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: t(8;17)(p23.1;p11.2)(chr8:g.11209119::chr17:g.17122551) Note: The FLCN rearrangement is a reciprocal translocation that may result in the truncation of exons 9-14. This rearrangement occurs in the background of other structural events involving FLCN. The functional significance is undetermined.
TDH	0	MSKCC-DMP	P-0016985-T01-IM6	TDH-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: t(8;17)(p23.1;p11.2)(chr8:g.11209119::chr17:g.17122551) Note: The FLCN rearrangement is a reciprocal translocation that may result in the truncation of exons 9-14. This rearrangement occurs in the background of other structural events involving FLCN. The functional significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0016991-T01-IM6	NFKBIA-intragenic	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: c.739_c.-1051del Note: The NFKBIA rearrangement results in the deletion of the promoter region and exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0017011-T01-IM6	CCDC141-PAX8 fusion	yes	unknown		in frame	PAX8 (NM_003466) - CCDC141 (NM_173648) Rearrangement : c.1189+3343:PAX8_c.526+1048:CCDC141dup Note: The PAX8 - CCDC141 Rearrangement  results in the fusion of exons 1-10 of PAX8 with exons 5-24 of CCDC141. Its functional significance is undetermined.
CCDC141	0	MSKCC-DMP	P-0017011-T01-IM6	CCDC141-PAX8 fusion	yes	unknown		in frame	PAX8 (NM_003466) - CCDC141 (NM_173648) Rearrangement : c.1189+3343:PAX8_c.526+1048:CCDC141dup Note: The PAX8 - CCDC141 Rearrangement  results in the fusion of exons 1-10 of PAX8 with exons 5-24 of CCDC141. Its functional significance is undetermined.
SEC16A	0	MSKCC-DMP	P-0017011-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement : c.-533:SEC16A_c.5167+178:NOTCH1dup Note: The SEC16A - NOTCH1 Rearrangement results in the fusion of the 5'-UTR region of SEC16A with exons 28-34 of NOTCH1. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0017011-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement : c.-533:SEC16A_c.5167+178:NOTCH1dup Note: The SEC16A - NOTCH1 Rearrangement results in the fusion of the 5'-UTR region of SEC16A with exons 28-34 of NOTCH1. Its functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0017031-T01-IM6	WDR72-TP53BP1 fusion	yes	unknown		in frame	WDR72 (NM_182758) - TP53BP1 (NM_001141980) rearrangement: c.3149-28073:WDR72_c.956-53:TP53BP1del Note: The WDR72 - TP53BP1 rearrangement is a deletion that results in an in-frame fusion of WDR72 exons 1-18 to TP53BP1 exons 9-28. The functional significance is undetermined
WDR72	0	MSKCC-DMP	P-0017031-T01-IM6	WDR72-TP53BP1 fusion	yes	unknown		in frame	WDR72 (NM_182758) - TP53BP1 (NM_001141980) rearrangement: c.3149-28073:WDR72_c.956-53:TP53BP1del Note: The WDR72 - TP53BP1 rearrangement is a deletion that results in an in-frame fusion of WDR72 exons 1-18 to TP53BP1 exons 9-28. The functional significance is undetermined
MT1H	0	MSKCC-DMP	P-0017031-T01-IM6	NUP93-MT1H fusion	yes	unknown		unknown	NUP93 (NM_014669) - MT1H (NM_005951) rearrangement: c.489+58:NUP93_c.-820:MT1Hdup Note: The NUP93 - MT1H rearrangement is a duplication with a breakpoint in the promoter region of MT1H, 802 bp upstream of the transcription start site.  This rearrangement may result in the fusion of NUP93 exons 1-5 to the promoter and the entire coding region of MT1H. The functional significance is undetermined.
NUP93	0	MSKCC-DMP	P-0017031-T01-IM6	NUP93-MT1H fusion	yes	unknown		unknown	NUP93 (NM_014669) - MT1H (NM_005951) rearrangement: c.489+58:NUP93_c.-820:MT1Hdup Note: The NUP93 - MT1H rearrangement is a duplication with a breakpoint in the promoter region of MT1H, 802 bp upstream of the transcription start site.  This rearrangement may result in the fusion of NUP93 exons 1-5 to the promoter and the entire coding region of MT1H. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0017035-T01-IM6	CENPW-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(6;19)(q22.32;p13.3)(chr6:g.126811782::chr19:g.5208512) Note: The PTPRS rearrangement is a translocation that may result in a truncation of exons 36-39. The functional significance is undetermined.
CENPW	0	MSKCC-DMP	P-0017035-T01-IM6	CENPW-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(6;19)(q22.32;p13.3)(chr6:g.126811782::chr19:g.5208512) Note: The PTPRS rearrangement is a translocation that may result in a truncation of exons 36-39. The functional significance is undetermined.
FAM177A1	0	MSKCC-DMP	P-0017043-T01-IM6	NFKBIA-FAM177A1 fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: chr14:g.35505911_c.690:NFKBIAdel Note: The NFKBIA rearrangement is a deletion of exons 5-6. One of the breakpoints is within exon 6.
NFKBIA	0	MSKCC-DMP	P-0017043-T01-IM6	NFKBIA-FAM177A1 fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: chr14:g.35505911_c.690:NFKBIAdel Note: The NFKBIA rearrangement is a deletion of exons 5-6. One of the breakpoints is within exon 6.
KMT2C	0	MSKCC-DMP	P-0017051-T01-IM6	PAXIP1-AS2-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.13636:KMT2C_chr7:g.154725568inv Note: The KMT2C rearrangement is an inversion of the promoter region and exons 1-52 of KMT2C. One of the breakpoints is within exon 52.
PAXIP1-AS2	0	MSKCC-DMP	P-0017051-T01-IM6	PAXIP1-AS2-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.13636:KMT2C_chr7:g.154725568inv Note: The KMT2C rearrangement is an inversion of the promoter region and exons 1-52 of KMT2C. One of the breakpoints is within exon 52.
ERG	0	MSKCC-DMP	P-0017065-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-967:TMPRSS2_c.40-42355:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017065-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-967:TMPRSS2_c.40-42355:ERGdel
RARA	0	MSKCC-DMP	P-0017067-T01-IM6	LINC00910-RARA fusion	yes	unknown		unknown	RARA (NM_000964) Rearrangement : c.252:RARA_chr17:g.41463829inv Note: The RARA Rearrangement  results in the inversion of exons 3-9. Its functional significance is undetermined.
LINC00910	0	MSKCC-DMP	P-0017067-T01-IM6	LINC00910-RARA fusion	yes	unknown		unknown	RARA (NM_000964) Rearrangement : c.252:RARA_chr17:g.41463829inv Note: The RARA Rearrangement  results in the inversion of exons 3-9. Its functional significance is undetermined.
MCL1	0	MSKCC-DMP	P-0017167-T01-IM6	ENSA-MCL1 fusion	yes	unknown		unknown	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement: c.813: MCL1_c.333: ENSAdup Note: The MCL1 - ENSA rearrangement is a duplication that results in the fusion of MCL1 exons 1-2 with ENSA exon 4. One of the breakpoints is within MCL1 exon 2 and the other is within ENSA exon 4. The functional significance is undetermined.
ENSA	0	MSKCC-DMP	P-0017167-T01-IM6	ENSA-MCL1 fusion	yes	unknown		unknown	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement: c.813: MCL1_c.333: ENSAdup Note: The MCL1 - ENSA rearrangement is a duplication that results in the fusion of MCL1 exons 1-2 with ENSA exon 4. One of the breakpoints is within MCL1 exon 2 and the other is within ENSA exon 4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017168-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+1703:TMPRSS2_c.19-17382:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017168-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+1703:TMPRSS2_c.19-17382:ERGdel
DROSHA	0	MSKCC-DMP	P-0017176-T01-IM6	C5orf22-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement : c.1433-63: DROSHA_g.31625311inv Note: The DROSHA rearrangement results in an inversion of exons 1-9 . The functional significance is undetermined.
C5orf22	0	MSKCC-DMP	P-0017176-T01-IM6	C5orf22-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement : c.1433-63: DROSHA_g.31625311inv Note: The DROSHA rearrangement results in an inversion of exons 1-9 . The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0017224-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3547-818_c.4134del Note: The SMARCA4 rearrangement results in the deletion of exons 26-29. One of the breakpoints is within exon 29. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0017224-T01-IM6	FAM205A-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.*102-335:CDKN2Ap14ARF_g.34756956inv Note: The CDKN2Ap14ARF rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.
FAM205A	0	MSKCC-DMP	P-0017224-T01-IM6	FAM205A-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.*102-335:CDKN2Ap14ARF_g.34756956inv Note: The CDKN2Ap14ARF rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0017224-T01-IM6	FAM205A-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.458-335:CDKN2Ap16INK4A_g.34756956inv Note: The CDKN2Ap16INK4A rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.
FAM205A	0	MSKCC-DMP	P-0017224-T01-IM6	FAM205A-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.458-335:CDKN2Ap16INK4A_g.34756956inv Note: The CDKN2Ap16INK4A rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017235-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1-2 with ERG exon 4-11) : c.56-4295:TMPRSS2_c.39+62371:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017235-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1-2 with ERG exon 4-11) : c.56-4295:TMPRSS2_c.39+62371:ERGdel
ERG	0	MSKCC-DMP	P-0017245-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon3) : c.55+3273:TMPRSS2_c.237-9598:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017245-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon3) : c.55+3273:TMPRSS2_c.237-9598:ERGdel
CHRNA5	0	MSKCC-DMP	P-0017262-T01-IM6	SUFU-CHRNA5 fusion	yes	unknown		out of frame	SUFU (NM_016169) - CHRNA5 (NM_000745) rearrangement: t(10;15)(q24.32;q25.1)(chr10:g.104359393::chr15:g.78876527) Note: The SUFU - CHRNA5 rearrangement is a translocation that may result in a fusion of SUFU exons 1-8 with CHRNA exons 3-6. The functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0017262-T01-IM6	SUFU-CHRNA5 fusion	yes	unknown		out of frame	SUFU (NM_016169) - CHRNA5 (NM_000745) rearrangement: t(10;15)(q24.32;q25.1)(chr10:g.104359393::chr15:g.78876527) Note: The SUFU - CHRNA5 rearrangement is a translocation that may result in a fusion of SUFU exons 1-8 with CHRNA exons 3-6. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0017262-T01-IM6	FAM227B-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_00285) - FAM227B (NM_152647) rearrangement: t(15;19)(q21.2;p13.3)(chr15:g.49718958::chr19:g.5216740) Note: The PTPRS - FAM227B rearrangement is a translocation that may result in a fusion of PTPRS exons 1-26 with FAM227B exons 12-16. One of the breakpoints is within PTPRS exon 26. The functional significance is undetermined.
FAM227B	0	MSKCC-DMP	P-0017262-T01-IM6	FAM227B-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_00285) - FAM227B (NM_152647) rearrangement: t(15;19)(q21.2;p13.3)(chr15:g.49718958::chr19:g.5216740) Note: The PTPRS - FAM227B rearrangement is a translocation that may result in a fusion of PTPRS exons 1-26 with FAM227B exons 12-16. One of the breakpoints is within PTPRS exon 26. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017262-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1749:TMPRSS2_c.18+4187:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017262-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1749:TMPRSS2_c.18+4187:ERGdel
SSTR3	0	MSKCC-DMP	P-0017262-T01-IM6	MGA-SSTR3 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(15;22)(q15.1;q13.1)(chr15:g.42042118::chr22:g.37609650) Note: The MGA rearrangement is a translocation with a breakpoint in exon 17 that may result in a truncation of MGA exons 17-24. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0017262-T01-IM6	MGA-SSTR3 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(15;22)(q15.1;q13.1)(chr15:g.42042118::chr22:g.37609650) Note: The MGA rearrangement is a translocation with a breakpoint in exon 17 that may result in a truncation of MGA exons 17-24. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0017265-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1159_c.*1673del Note: The TP53 rearrangement is a deletion of a part of exon 11. One of the breakpoint is within exon 11.
NTNG1	0	MSKCC-DMP	P-0017284-T02-IM5	NOTCH2-NTNG1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: chr1:g.108019818_c.3183+159:NOTCH2del Note: The NOTCH2 rearrangement is a deletion of exons 20-34.
NOTCH2	0	MSKCC-DMP	P-0017284-T02-IM5	NOTCH2-NTNG1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: chr1:g.108019818_c.3183+159:NOTCH2del Note: The NOTCH2 rearrangement is a deletion of exons 20-34.
TSNARE1	0	MSKCC-DMP	P-0017298-T01-IM6	RECQL4-TSNARE1 fusion	yes	unknown		unknown	TSNARE1 (NM_145003) - RECQL4 (NM_004260) rearrangement: c.1446+7353:TSNARE1_c.1278:RECQL4dup Note: The TSNARE1 - RECQL4 rearrangement is a duplication which results in the fusion of TSNARE1 exon12 to RECQL4 exon7.  One of the breakpoints is within RECQL4 exon7. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0017298-T01-IM6	RECQL4-TSNARE1 fusion	yes	unknown		unknown	TSNARE1 (NM_145003) - RECQL4 (NM_004260) rearrangement: c.1446+7353:TSNARE1_c.1278:RECQL4dup Note: The TSNARE1 - RECQL4 rearrangement is a duplication which results in the fusion of TSNARE1 exon12 to RECQL4 exon7.  One of the breakpoints is within RECQL4 exon7. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017312-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 with ERG exon 2) : c.126+1523:TMPRSS2_c.18+7805:ERGdel Note: The fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0017312-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 with ERG exon 2) : c.126+1523:TMPRSS2_c.18+7805:ERGdel Note: The fusion is predicted to be in-frame.
HIST1H3C	0	MSKCC-DMP	P-0017317-T01-IM6	HIST1H3C-intragenic	yes	unknown		unknown	HIST1H3C (NM_003531) Rearrangement : c.-715_c.2del Note: The HIST1H3C Rearrangement results in the partial deletion of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0017325-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117654375::chr20:g.43963860) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0017325-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused in-frame to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117654375::chr20:g.43963860) Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
OSGIN2	0	MSKCC-DMP	P-0017325-T01-IM6	NBN-OSGIN2 fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: g.90932931_c.994+81:NBNdel Note: The NBN rearrangement results in the deletion of exons 9-16. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0017325-T01-IM6	NBN-OSGIN2 fusion	yes	unknown		unknown	NBN (NM_002485) rearrangement: g.90932931_c.994+81:NBNdel Note: The NBN rearrangement results in the deletion of exons 9-16. The functional significance is undetermined.
HIST1H2BD	0	MSKCC-DMP	P-0017368-T01-IM6	PTPRK-HIST1H2BD fusion	yes	unknown		unknown	HIST1H2BD (NM_021063) - PTPRK  (NM_001135648) rearrangement : c.226: HIST1H2BD_c.2158-357:PTPRKinv Note: The HIST1H2BD - PTPRK rearrangement is an inversion that results in the fusion of HIST1H2BD exon 1 with PTPRK exons 12-31. One of the breakpoints is within HIST1H2BD exon 1 and this fusion includes the phosphatase domains of PTPRK. The functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0017368-T01-IM6	PTPRK-HIST1H2BD fusion	yes	unknown		unknown	HIST1H2BD (NM_021063) - PTPRK  (NM_001135648) rearrangement : c.226: HIST1H2BD_c.2158-357:PTPRKinv Note: The HIST1H2BD - PTPRK rearrangement is an inversion that results in the fusion of HIST1H2BD exon 1 with PTPRK exons 12-31. One of the breakpoints is within HIST1H2BD exon 1 and this fusion includes the phosphatase domains of PTPRK. The functional significance is undetermined.
LATS2	0	MSKCC-DMP	P-0017375-T01-IM6	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) rearrangement: c.1743_c.343-9621del Note: The LATS2 rearrangement results in the deletion of exons 3-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017376-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2204:TMPRSS2_c.40-61559:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017376-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2204:TMPRSS2_c.40-61559:ERGdel
BAP1	0	MSKCC-DMP	P-0017412-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.37+27:BAP1_chr3:g.52450493del Note: The BAP1 rearrangement is deletion of BAP1 promoter region and exon 1.
PHF7	0	MSKCC-DMP	P-0017412-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.37+27:BAP1_chr3:g.52450493del Note: The BAP1 rearrangement is deletion of BAP1 promoter region and exon 1.
SMARCA4	0	MSKCC-DMP	P-0017415-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1489_c.1812+903del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 9-11. One of the breakpoint is within exon 9.
FGFR2	0	MSKCC-DMP	P-0017424-T01-IM6	ATE1-FGFR2 fusion	yes	unknown		out of frame	FGFR2 (NM_000141) - ATE1 (NM_001001976) rearrangement: c.2302-908:FGFR2_c.1379-520:ATE1dup Note: The FGFR2 - ATE1 rearrangement is a duplication that results in a fusion of FGFR2 exons 1-17 with ATE1 exon 12. The functional significance is undetermined.
ATE1	0	MSKCC-DMP	P-0017424-T01-IM6	ATE1-FGFR2 fusion	yes	unknown		out of frame	FGFR2 (NM_000141) - ATE1 (NM_001001976) rearrangement: c.2302-908:FGFR2_c.1379-520:ATE1dup Note: The FGFR2 - ATE1 rearrangement is a duplication that results in a fusion of FGFR2 exons 1-17 with ATE1 exon 12. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0017426-T01-IM6	FANCA-intragenic	yes	unknown		in frame	FANCA (NM_000135) rearrangement: c.2779-717_c.2601+28del Note: The FANCA rearrangement is an intragenic deletion of exon 28. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0017428-T01-IM6	MYL4-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.2632_chr17:g.45272565dup Note: The CDK12 rearrangement is a duplication which includes exons 7-14. The functional significance is undetermined.
MYL4	0	MSKCC-DMP	P-0017428-T01-IM6	MYL4-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.2632_chr17:g.45272565dup Note: The CDK12 rearrangement is a duplication which includes exons 7-14. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0017432-T01-IM6	CSF3R-intragenic	yes	unknown		out of frame	CSF3R (NM_000760) rearrangement: c.1071+36_c.1577-198del Note: The CSF3R rearrangement is an intragenic deletion of exons 10-12. The function significance is undetermined.
TACC3	0	MSKCC-DMP	P-0017444-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 11-16): c.2296:FGFR3_c.1941+70:TACC3dup
FGFR3	0	MSKCC-DMP	P-0017444-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 11-16): c.2296:FGFR3_c.1941+70:TACC3dup
STAU1	0	MSKCC-DMP	P-0017448-T01-IM6	RTEL1-STAU1 fusion	yes	unknown		out of frame	RTEL1 (NM_032957) - STAU1 (NM_017453) rearrangement: c.3181+36:RTEL1_c.511-4612:STAU1inv Note: The RTEL1 - STAU1 rearrangement is an inversion that results in the fusion of RTEL1 exons 1-31 with STAU1 exons 6-14. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0017448-T01-IM6	RTEL1-STAU1 fusion	yes	unknown		out of frame	RTEL1 (NM_032957) - STAU1 (NM_017453) rearrangement: c.3181+36:RTEL1_c.511-4612:STAU1inv Note: The RTEL1 - STAU1 rearrangement is an inversion that results in the fusion of RTEL1 exons 1-31 with STAU1 exons 6-14. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0017459-T01-IM6	DCBLD1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.5080-508:ROS1_chr6:g.117776626del Note: The ROS1 Rearrangement results in the deletion of exons 1-30 of ROS1.  This event does not include the protein kinase domain of ROS1.
DCBLD1	0	MSKCC-DMP	P-0017459-T01-IM6	DCBLD1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.5080-508:ROS1_chr6:g.117776626del Note: The ROS1 Rearrangement results in the deletion of exons 1-30 of ROS1.  This event does not include the protein kinase domain of ROS1.
KMT2B	0	MSKCC-DMP	P-0017470-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B(NM_014727) Rearrangement : c.4259_c.7160-309dup Note: The KMT2B Rearrangement results in the duplication of exons 16-30. One of the breakpoints is within exon16. Its functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0017476-T01-IM6	CERS5-TSC2 fusion	yes	unknown		out of frame	CERS5 (NM_147190) - TSC2 (NM_000548) Rearrangement :  t(12,16)(q13.12,p13.3)(chr12:g.131062050::chr16:g.143130066) Note: The CERS5 - TSC2  Rearrangement results in the fusion of exons 1-8 of CERS5 with exons 37 - 42 of TSC2. Its functional significance is undetermined.
CERS5	0	MSKCC-DMP	P-0017476-T01-IM6	CERS5-TSC2 fusion	yes	unknown		out of frame	CERS5 (NM_147190) - TSC2 (NM_000548) Rearrangement :  t(12,16)(q13.12,p13.3)(chr12:g.131062050::chr16:g.143130066) Note: The CERS5 - TSC2  Rearrangement results in the fusion of exons 1-8 of CERS5 with exons 37 - 42 of TSC2. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017491-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-927:TMPRSS2_c.18+14436:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017491-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.56-927:TMPRSS2_c.18+14436:ERGdel
OLIG2	0	MSKCC-DMP	P-0017493-T01-IM6	TMPRSS2-OLIG2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+512_chr21:g.34285242inv Note: The TMPRSS2 rearrangement is an inversion which includes exons 3-14 of TMPRSS2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0017493-T01-IM6	TMPRSS2-OLIG2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+512_chr21:g.34285242inv Note: The TMPRSS2 rearrangement is an inversion which includes exons 3-14 of TMPRSS2. The functional significance is undetermined.
ADAMTS6	0	MSKCC-DMP	P-0017509-T01-IM6	NPM1-ADAMTS6 fusion	yes	unknown		unknown	NPM1(NM_002520) rearrangement: chr5:g.64521538_c.525-19:NPM1del Note: The NPM1 rearrangement is a deletion of NPM1 promoter region and exons 1-6.
NPM1	0	MSKCC-DMP	P-0017509-T01-IM6	NPM1-ADAMTS6 fusion	yes	unknown		unknown	NPM1(NM_002520) rearrangement: chr5:g.64521538_c.525-19:NPM1del Note: The NPM1 rearrangement is a deletion of NPM1 promoter region and exons 1-6.
PDGFRB	0	MSKCC-DMP	P-0017509-T01-IM6	PDGFRB-intragenic	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: c.1973_c.*4684del Note: The PDGFRB rearrangement is a deletion of exons 14-23. One of the breakpoints is within exon 14
MTOR	0	MSKCC-DMP	P-0017529-T01-IM5	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) Rearrangement :  c.1723_c.2208+375del Note: The MTOR Rearrangement results in the deletion of exons 11-13 of MTOR. One of the breakpoints is within exon11. Its functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0017533-T01-IM5	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) Rearrangement : c.1425+51_c.*547del Note: The PIK3R1 Rearrangement results in the deletion of exons 12-16. One of the breakpoints is within the 3-UTR region after the transcription stop site. Its functional significance is undetermined.
EXOSC10	0	MSKCC-DMP	P-0017542-T01-IM5	MTOR-EXOSC10 fusion	yes	unknown		unknown	EXOSC10 (NM_001001998) - MTOR (NM_004958) rearrangement: c.372+1601: EXOSC10_c.6299:MTORdup Note: The EXOSC10 - MTOR rearrangement is a duplication that results in the fusion of EXOSC10 exons 1-3 with MTOR exons 45-58. One of the breakpoints is within MTOR exon 45. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0017542-T01-IM5	MTOR-EXOSC10 fusion	yes	unknown		unknown	EXOSC10 (NM_001001998) - MTOR (NM_004958) rearrangement: c.372+1601: EXOSC10_c.6299:MTORdup Note: The EXOSC10 - MTOR rearrangement is a duplication that results in the fusion of EXOSC10 exons 1-3 with MTOR exons 45-58. One of the breakpoints is within MTOR exon 45. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017548-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2838:TMPRSS2_c.40-58598:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0017548-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2838:TMPRSS2_c.40-58598:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
STK25	0	MSKCC-DMP	P-0017551-T01-IM5	PDCD1-STK25 fusion	yes	unknown		unknown	PDCD1 (NM_005018) rearrangement: chr2:g.242452335_c.206:PDCD1del Note: The PDCD1 rearrangement is a deletion of exons 2-5. One of the breakpoints is within exon 2.
PDCD1	0	MSKCC-DMP	P-0017551-T01-IM5	PDCD1-STK25 fusion	yes	unknown		unknown	PDCD1 (NM_005018) rearrangement: chr2:g.242452335_c.206:PDCD1del Note: The PDCD1 rearrangement is a deletion of exons 2-5. One of the breakpoints is within exon 2.
TACC3	0	MSKCC-DMP	P-0017551-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 10-16): c.2309:FGFR3_c.1836+8:TACC3dup
FGFR3	0	MSKCC-DMP	P-0017551-T01-IM5	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 10-16): c.2309:FGFR3_c.1836+8:TACC3dup
MGA	0	MSKCC-DMP	P-0017582-T01-IM5	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) Rearrangement : c.4586-416_c.5920del Note: The MGA Rearrangement results in the  deletion of exons 15-17 of MGA. One of the breakpoints is within exon17. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0017592-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exon 1-5 fused with ALK exon 20-29) : c.494-5963:EML4_c.3172+779:ALKinv Note: This fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0017592-T01-IM5	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exon 1-5 fused with ALK exon 20-29) : c.494-5963:EML4_c.3172+779:ALKinv Note: This fusion is predicted to be in-frame and includes the kinase domain of ALK.
ZNF284	0	MSKCC-DMP	P-0017653-T01-IM5	POLD1-ZNF284 fusion	yes	unknown		out of frame	POLD1 (NM_002691) - ZNF284 (NM_001037813) rearrangement: c.1892+43: POLD1_c.15+1157: ZNF284dup Note: The POLD1 - ZNF284 rearrangement is a duplication that results in the fusion of POLD1 exons 1-15 with ZNF284 exons 3-5. The functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0017653-T01-IM5	POLD1-ZNF284 fusion	yes	unknown		out of frame	POLD1 (NM_002691) - ZNF284 (NM_001037813) rearrangement: c.1892+43: POLD1_c.15+1157: ZNF284dup Note: The POLD1 - ZNF284 rearrangement is a duplication that results in the fusion of POLD1 exons 1-15 with ZNF284 exons 3-5. The functional significance is undetermined.
COPRS	0	MSKCC-DMP	P-0017656-T01-IM5	CDK12-COPRS fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement : g.30096337_c.754:CDK12inv Note: The CDK12 rearrangement results in an inversion of exon 1. One of the breakpoint is also within exon 1. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0017656-T01-IM5	CDK12-COPRS fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement : g.30096337_c.754:CDK12inv Note: The CDK12 rearrangement results in an inversion of exon 1. One of the breakpoint is also within exon 1. The functional significance is undetermined.
CSF1R	0	MSKCC-DMP	P-0017692-T01-IM6	CSF1R-intragenic	yes	unknown		unknown	CSF1R (NM_005211) rearrangement: c.2491_c.*2654del Note: The CSF1R rearrangement is a deletion of exons 19-21. One of the breakpoints is within exon 19.
ERG	0	MSKCC-DMP	P-0017708-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4676:TMPRSS2_c.40-56300:ERGdel Note: TMPRSS2 is fused with non-canonical ERG  transcript.
TMPRSS2	0	MSKCC-DMP	P-0017708-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4676:TMPRSS2_c.40-56300:ERGdel Note: TMPRSS2 is fused with non-canonical ERG  transcript.
SPIN4	0	MSKCC-DMP	P-0017711-T01-IM6	NTRK3-SPIN4 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) rearrangement: t(X;15)(q11.1;q25.3)(chrX:g.62147342::chr15:g.88678407) Note: The NTRK3 rearrangement is a translocation that may result in the truncation of exons 10-20, which include the kinase domain. One of the breakpoints is within exon 10. The functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0017711-T01-IM6	NTRK3-SPIN4 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) rearrangement: t(X;15)(q11.1;q25.3)(chrX:g.62147342::chr15:g.88678407) Note: The NTRK3 rearrangement is a translocation that may result in the truncation of exons 10-20, which include the kinase domain. One of the breakpoints is within exon 10. The functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0017715-T01-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.655+304_c.816del Note: The AGO2 rearrangement is an intragenic deletion of exons 6-7. One of the breakpoints is within exon 7.
RET	0	MSKCC-DMP	P-0017716-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-7 fused with RET exons 12-20): c.618+42:NCOA4_c.2137-860:RETdup Note: The NCOA4 - RET fusion includes the kinase domain of RET.
TIMM23B	0	MSKCC-DMP	P-0017716-T01-IM6	TIMM23B-RET fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-7 fused with RET exons 12-20): c.618+42:NCOA4_c.2137-860:RETdup Note: The NCOA4 - RET fusion includes the kinase domain of RET.
CREBBP	0	MSKCC-DMP	P-0017718-T01-IM6	LRRC10-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(12;16)(q15;p13.3)(chr12:g.70017642::chr16:g.3777792) Note: The CREBBP rearrangement is a translocation that may result in the truncation of exon 31. One of the breakpoints is within exon 31. The functional significance is undetermined.
LRRC10	0	MSKCC-DMP	P-0017718-T01-IM6	LRRC10-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(12;16)(q15;p13.3)(chr12:g.70017642::chr16:g.3777792) Note: The CREBBP rearrangement is a translocation that may result in the truncation of exon 31. One of the breakpoints is within exon 31. The functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0017718-T01-IM6	TERT-RARA fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;17)(p15.33;q21.2)(chr5:g.1295225::chr17:g.38475855) Note: The TERT rearrangement is a translocation with a breakpoint in the TERT promoter region. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0017718-T01-IM6	TERT-RARA fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;17)(p15.33;q21.2)(chr5:g.1295225::chr17:g.38475855) Note: The TERT rearrangement is a translocation with a breakpoint in the TERT promoter region. The functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0017723-T01-IM6	CADM2-IRS2 fusion	yes	unknown		unknown	IRS2 (NM_003749) - CADM2  (NM_001167674) rearrangement: t(3;13)(p12.1;q34)(chr3:g.86035837::chr13:g.110436835) Note: The IRS2 - CADM2 rearrangement is a translocation that may result in the fusion of IRS2 exon 1 with CADM2 exons 8-10. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
CADM2	0	MSKCC-DMP	P-0017723-T01-IM6	CADM2-IRS2 fusion	yes	unknown		unknown	IRS2 (NM_003749) - CADM2  (NM_001167674) rearrangement: t(3;13)(p12.1;q34)(chr3:g.86035837::chr13:g.110436835) Note: The IRS2 - CADM2 rearrangement is a translocation that may result in the fusion of IRS2 exon 1 with CADM2 exons 8-10. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
LINC01518	0	MSKCC-DMP	P-0017724-T01-IM6	RET-LINC01518 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement : g.43149839_c.1264-2:RETdel Note: The RET rearrangement results in the deletion of exons 1-7. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0017724-T01-IM6	RET-LINC01518 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement : g.43149839_c.1264-2:RETdel Note: The RET rearrangement results in the deletion of exons 1-7. The functional significance is undetermined.
FYN	0	MSKCC-DMP	P-0017724-T01-IM6	LINC01107-FYN fusion	yes	unknown		unknown	FYN (NM_153047) rearrangement: t(2;6)(q37.3;q21)(chr2:g.239377558::chr6:g.112024156) Note: The FYN rearrangement is a translocation that may result in the truncation of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
LINC01107	0	MSKCC-DMP	P-0017724-T01-IM6	LINC01107-FYN fusion	yes	unknown		unknown	FYN (NM_153047) rearrangement: t(2;6)(q37.3;q21)(chr2:g.239377558::chr6:g.112024156) Note: The FYN rearrangement is a translocation that may result in the truncation of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0017730-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-4466:TMPRSS2_c.19-8247:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0017730-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-4466:TMPRSS2_c.19-8247:ERGdel
BRCA2	0	MSKCC-DMP	P-0017744-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement : c.316+811_c.426-1del Note: The BRCA2 Rearrangement results in the deletion of exons  4-5 of BRCA2. Its functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0017760-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) Rearrangement : c.7744+1111_c.8913del Note: The MGA Rearrangement results in the intragenic deletion of exon 23-24. One of the breakpoint is within exon24. Its functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0017760-T01-IM6	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) Rearrangement : c.1200_chr17:g.70140019del Note: The SOX9 Rearrangement results in the partial intragenic deletion of exon3 of SOX9. One of the breakpoints is within exon3. Its functional significance is undetermined.
DIS3	0	MSKCC-DMP	P-0017769-T01-IM6	LINC00377-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) Rearrangement : c.654:DIS3_chr13:g.81632702inv Note: The DIS3 Rearrangement results in the inversion of exons 1-4 of DIS3. One of the breakpoints is within exon4. Its functional significance is undetermined.
LINC00377	0	MSKCC-DMP	P-0017769-T01-IM6	LINC00377-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) Rearrangement : c.654:DIS3_chr13:g.81632702inv Note: The DIS3 Rearrangement results in the inversion of exons 1-4 of DIS3. One of the breakpoints is within exon4. Its functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0017774-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : chr21:g.40091030_c.55+4035:TMPRSS2del Note: The TMPRSS2 Rearrangement results in the deletion of exons3-14.This is not the canonical TMPRSS2-ERG Fusion, however the possibility of a fusion event not detected by IMPACT cannot be ruled out. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0017774-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : chr21:g.40091030_c.55+4035:TMPRSS2del Note: The TMPRSS2 Rearrangement results in the deletion of exons3-14.This is not the canonical TMPRSS2-ERG Fusion, however the possibility of a fusion event not detected by IMPACT cannot be ruled out. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0017807-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) Rearrangement: c.3925_c.*4057del Note: APC rearrangement is a deletion which leads to the partial deletion of exon 16, potentially leading to a truncated protein.
GRIN2A	0	MSKCC-DMP	P-0017817-T01-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: c.3436_c.4030del Note: The GRIN2A rearrangement is a deletion (594 bp) within exon 13. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0017827-T01-IM6	ELDR-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.3028:EGFR_chr7:g.55336682del Note: The EGFR rearrangement is a deletion of exons 25-28. One of the breakpoints is within exon 25. Similar EGFR C terminus deletions have been described in the literature and possess oncogenic properties that may be sensitive to anti-EGFR therapies (PMID: 22001862)
ELDR	0	MSKCC-DMP	P-0017827-T01-IM6	ELDR-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.3028:EGFR_chr7:g.55336682del Note: The EGFR rearrangement is a deletion of exons 25-28. One of the breakpoints is within exon 25. Similar EGFR C terminus deletions have been described in the literature and possess oncogenic properties that may be sensitive to anti-EGFR therapies (PMID: 22001862)
IRX6	0	MSKCC-DMP	P-0017831-T01-IM6	FGFR2-IRX6 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;16)(q26.13;q12.2)(chr10:g.123241224::chr16:g.55238062) Note: The FGFR2 rearrangement is a translocation that may result in the truncation of FGFR2 exon 18. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0017831-T01-IM6	FGFR2-IRX6 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;16)(q26.13;q12.2)(chr10:g.123241224::chr16:g.55238062) Note: The FGFR2 rearrangement is a translocation that may result in the truncation of FGFR2 exon 18. The functional significance is undetermined.
TNNI1	0	MSKCC-DMP	P-0017846-T01-IM6	IL10-TNNI1 fusion	yes	unknown		unknown	IL10 (NM_000572) Rearrangement : chr1:g.201374280_c.378+39:IL10del Note: The IL10 Rearrangement results in the deletion of exons 4-5 of IL10. Its functional significance is undetermined.
IL10	0	MSKCC-DMP	P-0017846-T01-IM6	IL10-TNNI1 fusion	yes	unknown		unknown	IL10 (NM_000572) Rearrangement : chr1:g.201374280_c.378+39:IL10del Note: The IL10 Rearrangement results in the deletion of exons 4-5 of IL10. Its functional significance is undetermined.
SLC39A10	0	MSKCC-DMP	P-0017846-T01-IM6	SF3B1-SLC39A10 fusion	yes	unknown		unknown	SF3B1 (NM_012433) Rearrangement : chr2:g.196301398_c.442:SF3B1inv Note: The SF3B1 Rearrangement results in the inversion of exons 5-25 of SF3B1. The breakpoint in SF3B1 is within exon5.Its functional significance is undetermined.
SF3B1	0	MSKCC-DMP	P-0017846-T01-IM6	SF3B1-SLC39A10 fusion	yes	unknown		unknown	SF3B1 (NM_012433) Rearrangement : chr2:g.196301398_c.442:SF3B1inv Note: The SF3B1 Rearrangement results in the inversion of exons 5-25 of SF3B1. The breakpoint in SF3B1 is within exon5.Its functional significance is undetermined.
MAX	0	MSKCC-DMP	P-0017859-T01-IM6	MAX-intragenic	yes	unknown		unknown	MAX (NM_002382) rearrangement: c.*3102_c.296-91del Note: The MAX rearrangement results in the deletion of exon 5. The functional significance is undetermined.
MAPK4	0	MSKCC-DMP	P-0017882-T01-IM6	PARK2-MAPK4 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: t(6;18)(q26;q21.2)(chr6:g.162170030::chr18:g.48058391) Note: The PARK2 rearrangement is a translocation that may result in a truncation of exons 8-12. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0017882-T01-IM6	PARK2-MAPK4 fusion	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: t(6;18)(q26;q21.2)(chr6:g.162170030::chr18:g.48058391) Note: The PARK2 rearrangement is a translocation that may result in a truncation of exons 8-12. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0017882-T01-IM6	CHD3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(p13.1;q22.3)(chr17:g.7790479::chr21:g.42870483) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.
CHD3	0	MSKCC-DMP	P-0017882-T01-IM6	CHD3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(p13.1;q22.3)(chr17:g.7790479::chr21:g.42870483) Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.
HDAC9	0	MSKCC-DMP	P-0017882-T01-IM6	XPO1-HDAC9 fusion	yes	unknown		out of frame	HDAC9 (NM_178425) - XPO1 (NM_003400) rearrangement: t(2;7)(p15;p21.2)(chr2:g.61721253::chr7:g.18926552) Note: The HDAC9 - XPO1 rearrangement is a translocation that may result in the fusion of HDAC9 exons 1-21 with XPO1 exons 12-25. The functional significance is undetermined.
XPO1	0	MSKCC-DMP	P-0017882-T01-IM6	XPO1-HDAC9 fusion	yes	unknown		out of frame	HDAC9 (NM_178425) - XPO1 (NM_003400) rearrangement: t(2;7)(p15;p21.2)(chr2:g.61721253::chr7:g.18926552) Note: The HDAC9 - XPO1 rearrangement is a translocation that may result in the fusion of HDAC9 exons 1-21 with XPO1 exons 12-25. The functional significance is undetermined.
PTK2B	0	MSKCC-DMP	P-0017892-T01-IM6	RECQL4-PTK2B fusion	yes	unknown		unknown	RECQL4 (NM_004260) Rearrangement : c.-1259:PTK2B_c.1132-19:RECQL4 Note: The RECQL4 Rearrangement results in the deletion of exons 6-21 of RECQL4. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0017892-T01-IM6	RECQL4-PTK2B fusion	yes	unknown		unknown	RECQL4 (NM_004260) Rearrangement : c.-1259:PTK2B_c.1132-19:RECQL4 Note: The RECQL4 Rearrangement results in the deletion of exons 6-21 of RECQL4. Its functional significance is undetermined.
LINC01500	0	MSKCC-DMP	P-0017899-T01-IM6	APC-LINC01500 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(5;14)(q22.1;q23.1)(chr5:g.112174171::chr14:g.59220719) Note: The APC Rearrangement results in the possible truncation of APC. One of the breakpoints is within exon16 of APC.Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0017899-T01-IM6	APC-LINC01500 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(5;14)(q22.1;q23.1)(chr5:g.112174171::chr14:g.59220719) Note: The APC Rearrangement results in the possible truncation of APC. One of the breakpoints is within exon16 of APC.Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0017913-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.*2094_c.3576+51del Note: The BRD4 rearrangement results in the deletion of exons 18-20. The functional significance is undetermined.
ZRSR2	0	MSKCC-DMP	P-0017917-T01-IM6	RAB3IP-ZRSR2 fusion	yes	unknown		unknown	ZRSR2 (NM_005089) rearrangement: t(12;X)(q15;p22.2)(chr12:g.70367195::chrX:g.15841299) Note: The ZRSR2 rearrangement is a translocation that may result in the truncation of exon 11. One of the breakpoints is within exon 11. The functional significance is undetermined.
RAB3IP	0	MSKCC-DMP	P-0017917-T01-IM6	RAB3IP-ZRSR2 fusion	yes	unknown		unknown	ZRSR2 (NM_005089) rearrangement: t(12;X)(q15;p22.2)(chr12:g.70367195::chrX:g.15841299) Note: The ZRSR2 rearrangement is a translocation that may result in the truncation of exon 11. One of the breakpoints is within exon 11. The functional significance is undetermined.
ZRSR2	0	MSKCC-DMP	P-0017917-T01-IM6	ZRSR2-intragenic	yes	unknown		unknown	ZRSR2 (NM_005089) rearrangement : c.828_c.*1222inv Note: The ZRSR2 rearrangement results in an inversion of exons 4-10 . One of the breakpoints is within exon 10. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0017924-T01-IM6	ALK-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - ALK (NM_004304) fusion: t(2;10)(p23.2;p11.22)(chr2:g.29447945::chr10:g.32305310) Note: The KIF5B - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0017924-T01-IM6	ALK-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - ALK (NM_004304) fusion: t(2;10)(p23.2;p11.22)(chr2:g.29447945::chr10:g.32305310) Note: The KIF5B - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
KMT2D	0	MSKCC-DMP	P-0017932-T01-IM6	TUBA1C-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.16368:KMT2D_chr12:g.49628359del Note: The KMT2D rearrangement is a deletion which includes exons 52-54. One of the breakpoints is within KMT2D exon 54. The functional significance is undetermined.
TUBA1C	0	MSKCC-DMP	P-0017932-T01-IM6	TUBA1C-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.16368:KMT2D_chr12:g.49628359del Note: The KMT2D rearrangement is a deletion which includes exons 52-54. One of the breakpoints is within KMT2D exon 54. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0017932-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.3865-625_c.10608del Note: The ZFHX3 rearrangement is an intragenic deletion of exons 8-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0017978-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.667+7306:EML4_c.3173-215:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0017978-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.667+7306:EML4_c.3173-215:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
TMPRSS2	0	MSKCC-DMP	P-0017987-T01-IM6	C1orf112-TMPRSS2 fusion	yes	unknown		out of frame	C1orf112 (NM_018186) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q24.2;q22.3)(chr1:g.169817552::chr21:g.42871817) Note: The C1orf112 - TMPRSS2 rearrangement is a translocation which results in the fusion of C1orf112 exon 20 to TMPRSS2 exon 2. The functional significance is undetermined.
C1orf112	0	MSKCC-DMP	P-0017987-T01-IM6	C1orf112-TMPRSS2 fusion	yes	unknown		out of frame	C1orf112 (NM_018186) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q24.2;q22.3)(chr1:g.169817552::chr21:g.42871817) Note: The C1orf112 - TMPRSS2 rearrangement is a translocation which results in the fusion of C1orf112 exon 20 to TMPRSS2 exon 2. The functional significance is undetermined.
SLC25A21	0	MSKCC-DMP	P-0017989-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_00449) rearrangement: c.71-139753:SLC25A21_c.320:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication which results in the fusion of SLC25A21 exon 1 to FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0017989-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_00449) rearrangement: c.71-139753:SLC25A21_c.320:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication which results in the fusion of SLC25A21 exon 1 to FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0017990-T01-IM6	FOXO6-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.6377:ARID1A_chr1:g.41724708inv Note: The ARID1A rearrangement is an inversion (14617942 bp) which includes exon 20. One of the breakpoints is within  ARID1A exon 20. The functional significance is undetermined.
FOXO6	0	MSKCC-DMP	P-0017990-T01-IM6	FOXO6-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.6377:ARID1A_chr1:g.41724708inv Note: The ARID1A rearrangement is an inversion (14617942 bp) which includes exon 20. One of the breakpoints is within  ARID1A exon 20. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0018003-T01-IM6	LSS-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - LSS (NM_001001438) rearrangement: c.56-147:TMPRSS2_c.1951:LSSdup Note: The TMPRSS2 - LSS rearrangement is a duplication that may result in TMPRSS2 exon 1 fused with LSS exons 19-22. The functional significance is undetermined.
LSS	0	MSKCC-DMP	P-0018003-T01-IM6	LSS-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - LSS (NM_001001438) rearrangement: c.56-147:TMPRSS2_c.1951:LSSdup Note: The TMPRSS2 - LSS rearrangement is a duplication that may result in TMPRSS2 exon 1 fused with LSS exons 19-22. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0018007-T01-IM6	GRB7-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.3412+62:ERBB2_chr17:g.37891043del Note: The ERBB2 rearrangement is a deletion of exon 27.
GRB7	0	MSKCC-DMP	P-0018007-T01-IM6	GRB7-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.3412+62:ERBB2_chr17:g.37891043del Note: The ERBB2 rearrangement is a deletion of exon 27.
EIF3G	0	MSKCC-DMP	P-0018016-T01-IM6	DNMT1-EIF3G fusion	yes	unknown		unknown	DNMT1 (NM_001379) - EIF3G (NM_003755) rearrangement: c.376:DNMT1_c.596-198del Note: The DNMT1 - EIF3G rearrangement is a deletion which results in the fusion of DNMT1 exon 4 to EIF3G exon 8. One of the breakpoints is within exon 4 of DNMT1. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0018016-T01-IM6	DNMT1-EIF3G fusion	yes	unknown		unknown	DNMT1 (NM_001379) - EIF3G (NM_003755) rearrangement: c.376:DNMT1_c.596-198del Note: The DNMT1 - EIF3G rearrangement is a deletion which results in the fusion of DNMT1 exon 4 to EIF3G exon 8. One of the breakpoints is within exon 4 of DNMT1. The functional significance is undetermined.
GNG7	0	MSKCC-DMP	P-0018030-T01-IM6	SMARCA4-GNG7 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.chr19:g.25566206_c.936inv Note: The SMARCA4 (NM_003072) rearrangement results in an inversion of exons 1-6 of SMARCA4. One of the breakpoints is within exon6 of SMARCA4. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0018030-T01-IM6	SMARCA4-GNG7 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.chr19:g.25566206_c.936inv Note: The SMARCA4 (NM_003072) rearrangement results in an inversion of exons 1-6 of SMARCA4. One of the breakpoints is within exon6 of SMARCA4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018038-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.56-3057:TMPRSS2_c.18+11021:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018038-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.56-3057:TMPRSS2_c.18+11021:ERGdel
KIF5B	0	MSKCC-DMP	P-0018069-T01-IM6	RET-KIF5B fusion	yes	unknown		out of frame	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.1648+160:RET_c.1915-72:KIF5Binv Note: The RET - KIF5B rearrangement is an inversion that results in the fusion of RET exons 1-8 with KIF5B exons 17-25. This rearrangement was detected in the background of other RET structural variants.
RET	0	MSKCC-DMP	P-0018069-T01-IM6	RET-KIF5B fusion	yes	unknown		out of frame	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.1648+160:RET_c.1915-72:KIF5Binv Note: The RET - KIF5B rearrangement is an inversion that results in the fusion of RET exons 1-8 with KIF5B exons 17-25. This rearrangement was detected in the background of other RET structural variants.
TFG	0	MSKCC-DMP	P-0018082-T01-IM6	NTRK1-TFG fusion	yes	unknown		in frame	TFG (NM_001195478) - NTRK1 (NM_002529) fusion (TFG exons 1-4 fused with NTRK1 exons 9-17): t(1;3)(q23.1;q12.2)(chr1:g.156843796::chr3:g.100450466) Note: The TFG - NTRK1 fusion is predicted to be in-frame and includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0018082-T01-IM6	NTRK1-TFG fusion	yes	unknown		in frame	TFG (NM_001195478) - NTRK1 (NM_002529) fusion (TFG exons 1-4 fused with NTRK1 exons 9-17): t(1;3)(q23.1;q12.2)(chr1:g.156843796::chr3:g.100450466) Note: The TFG - NTRK1 fusion is predicted to be in-frame and includes the kinase domain of NTRK1.
ERG	0	MSKCC-DMP	P-0018086-T01-IM6	METTL22-ERG fusion	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(16;21)(p13.2;q22.2)(chr16:g.8690703::chr21:g.39817374) Note: The ERG rearrangement is a translocation that may result in the truncation of exons 2-10. One of the breakpoints is within exon 2. The functional significance is undetermined.
METTL22	0	MSKCC-DMP	P-0018086-T01-IM6	METTL22-ERG fusion	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(16;21)(p13.2;q22.2)(chr16:g.8690703::chr21:g.39817374) Note: The ERG rearrangement is a translocation that may result in the truncation of exons 2-10. One of the breakpoints is within exon 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018090-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10):c.127-620:TMPRSS2_c.19-2241:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018090-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10):c.127-620:TMPRSS2_c.19-2241:ERGdel
DGKH	0	MSKCC-DMP	P-0018108-T02-IM6	FH-DGKH fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241667340::chr13:g.42830153) Note: The FH rearrangement is a translocation that may result in a truncation of exons 8-10. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0018108-T02-IM6	FH-DGKH fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241667340::chr13:g.42830153) Note: The FH rearrangement is a translocation that may result in a truncation of exons 8-10. The functional significance is undetermined.
BLM	0	MSKCC-DMP	P-0018109-T01-IM6	ANKLE2-BLM fusion	yes	unknown		unknown	BLM (NM_000057) - ANKLE2 (NM_015114) rearrangement: t(12;15)(q24.33;q26.1)(chr12:g.133320386::chr15:g.91358467) Note: The BLM - ANKLE2 rearrangement is a translocation that results in the fusion of BLM exons 1-22 with ANKLE2 exons 6-13. One of the breakpoints is within BLM exon 22. The functional significance is undetermined.
ANKLE2	0	MSKCC-DMP	P-0018109-T01-IM6	ANKLE2-BLM fusion	yes	unknown		unknown	BLM (NM_000057) - ANKLE2 (NM_015114) rearrangement: t(12;15)(q24.33;q26.1)(chr12:g.133320386::chr15:g.91358467) Note: The BLM - ANKLE2 rearrangement is a translocation that results in the fusion of BLM exons 1-22 with ANKLE2 exons 6-13. One of the breakpoints is within BLM exon 22. The functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0018112-T01-IM6	RFWD2-intragenic	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: c.408-3437_c.467+23inv Note: The RFWD2 rearrangement is an intragenic inversion of exon 2, potentially disrupting the gene function.
BMP2	0	MSKCC-DMP	P-0018113-T01-IM6	TAP1-BMP2 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: t(6;20)(p21.32;p12.3)(chr6:g.32813483::chr20:g.6891743) Note: The TAP1 rearrangement is a translocation that may result in a truncation of exon 11. One of the breakpoint is within exon 11. The functional significance is undetermined.
TAP1	0	MSKCC-DMP	P-0018113-T01-IM6	TAP1-BMP2 fusion	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: t(6;20)(p21.32;p12.3)(chr6:g.32813483::chr20:g.6891743) Note: The TAP1 rearrangement is a translocation that may result in a truncation of exon 11. One of the breakpoint is within exon 11. The functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0018115-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused in-frame with BICC1 exons 3-21):   c.2301+1242:FGFR2_c.237+34947:BICC1dup Note: The FGFR2 - BICC1 fusion is predicted to in-frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0018115-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused in-frame with BICC1 exons 3-21):   c.2301+1242:FGFR2_c.237+34947:BICC1dup Note: The FGFR2 - BICC1 fusion is predicted to in-frame and includes the kinase domain of FGFR2.
TMPRSS2	0	MSKCC-DMP	P-0018122-T01-IM6	ABCG1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ABCG1 (NM_207627) Rearrangement: c.794+15:TMPRSS2_c.48+6119:ABCG1inv Note: The TMPRSS2 - ABCG1 Rearrangement results in the fusion of exons 1-7 of TMPRSS2 with exons 3-16 of ABCG1. Its functional significance is undetermined.
ABCG1	0	MSKCC-DMP	P-0018122-T01-IM6	ABCG1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ABCG1 (NM_207627) Rearrangement: c.794+15:TMPRSS2_c.48+6119:ABCG1inv Note: The TMPRSS2 - ABCG1 Rearrangement results in the fusion of exons 1-7 of TMPRSS2 with exons 3-16 of ABCG1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018127-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.126+1404:TMPRSS2_.c.19-4088:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 2-10 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion not be detected by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0018127-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.126+1404:TMPRSS2_.c.19-4088:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 2-10 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion not be detected by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0018131-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) Rearrangement : c.67_c.68del Note: The B2M Rearrangement results in the deletion of exon1-2 of B2M. Its functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0018131-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) Rearrangement : chrX:g.39891617_c.2500:BCORdel Note : The BCOR Rearrangement results in the deletion of exons 4-15 of BCOR.One of the breakpoints is within exon4. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018149-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4) : c.55+3556:TMPRSS2_c.40-56840:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018149-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4) : c.55+3556:TMPRSS2_c.40-56840:ERGdel
BRCA1	0	MSKCC-DMP	P-0018176-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.671-148_c.4359del Note: The BRCA1 rearrangement is an intragenic deletion of exons 10-13. One of the breakpoints is within exon 13.
EFCAB11	0	MSKCC-DMP	P-0018195-T01-IM6	NTRK2-EFCAB11 fusion	yes	unknown		unknown	NTRK2 (NM_006180) rearrangement: t(9;14)(q21.33;q32.11)(chr9:g.87317072::chr14:g.90393239) Note: The NTRK2 rearrangement is a translocation that may result in the truncation of exons 5-21. The functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0018195-T01-IM6	NTRK2-EFCAB11 fusion	yes	unknown		unknown	NTRK2 (NM_006180) rearrangement: t(9;14)(q21.33;q32.11)(chr9:g.87317072::chr14:g.90393239) Note: The NTRK2 rearrangement is a translocation that may result in the truncation of exons 5-21. The functional significance is undetermined.
A4GALT	0	MSKCC-DMP	P-0018195-T01-IM6	MAP3K14-A4GALT fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.43364113::chr22:g.43080364) Note: The MAP3K14 rearrangement is a translocation that may result in the truncation of exons 5-16. One of the breakpoints is within exon 5. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0018195-T01-IM6	MAP3K14-A4GALT fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.43364113::chr22:g.43080364) Note: The MAP3K14 rearrangement is a translocation that may result in the truncation of exons 5-16. One of the breakpoints is within exon 5. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0018216-T01-IM6	FAM173B-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-94_chr5:g.10249793del Note: The TERT rearrangement results in the deletion of part of the promoter region of TERT and is replaced by the promoter of FAM173B. The functional significance is undetermined.
FAM173B	0	MSKCC-DMP	P-0018216-T01-IM6	FAM173B-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-94_chr5:g.10249793del Note: The TERT rearrangement results in the deletion of part of the promoter region of TERT and is replaced by the promoter of FAM173B. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0018222-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783915::chr6:g.117646209) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0018222-T01-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused to ROS1 exons 34-43): t(5;6)(q32;q22.1)(chr5:g.149783915::chr6:g.117646209) Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.
RPAP3	0	MSKCC-DMP	P-0018233-T01-IM6	KMT2D-RPAP3 fusion	yes	unknown		unknown	KMT2D (NM_003482)  rearrangement: c.5867+21_chr12:g.48015840del Note: The KMT2D rearrangement is a deletion which includes exons 28-54 of KMT2D. Other structural rearrangements involving KMT2D were also detected in this sample suggesting a more complex rearrangement event that may not be fully characterized by IMPACT.
KMT2D	0	MSKCC-DMP	P-0018233-T01-IM6	KMT2D-RPAP3 fusion	yes	unknown		unknown	KMT2D (NM_003482)  rearrangement: c.5867+21_chr12:g.48015840del Note: The KMT2D rearrangement is a deletion which includes exons 28-54 of KMT2D. Other structural rearrangements involving KMT2D were also detected in this sample suggesting a more complex rearrangement event that may not be fully characterized by IMPACT.
LINC00158	0	MSKCC-DMP	P-0018233-T01-IM6	WT1-LINC00158 fusion	yes	unknown		unknown	WT1 (NM_024426) rearrangement: t(11;21)(p13;q21.2)(chr11:g.32414419::chr21:g.26525604) Note: The WT1 rearrangement is a translocation with a breakpoint within intron 7. The functional significance is undetermined.
WT1	0	MSKCC-DMP	P-0018233-T01-IM6	WT1-LINC00158 fusion	yes	unknown		unknown	WT1 (NM_024426) rearrangement: t(11;21)(p13;q21.2)(chr11:g.32414419::chr21:g.26525604) Note: The WT1 rearrangement is a translocation with a breakpoint within intron 7. The functional significance is undetermined.
R3HDM2	0	MSKCC-DMP	P-0018235-T01-IM6	GLI1-R3HDM2 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.41_chr12:g.57715760inv Note: The GLI1 rearrangement is an inversion (141755 bp) which includes exons 1-2 of GLI1. One of the breakpoints is within exon 2. The functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0018235-T01-IM6	GLI1-R3HDM2 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.41_chr12:g.57715760inv Note: The GLI1 rearrangement is an inversion (141755 bp) which includes exons 1-2 of GLI1. One of the breakpoints is within exon 2. The functional significance is undetermined.
LRRC8B	0	MSKCC-DMP	P-0018242-T01-IM6	CSDE1-LRRC8B fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement:  c.666:CSDE1_chr1:g.90028558del Note: The CSDE1 rearrangement is a deletion of exons 8 - 21. One of the breakpoints is within exon 8. The functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0018242-T01-IM6	CSDE1-LRRC8B fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement:  c.666:CSDE1_chr1:g.90028558del Note: The CSDE1 rearrangement is a deletion of exons 8 - 21. One of the breakpoints is within exon 8. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0018242-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused in-frame with ALK exons 20-29): c.668-7560:EML4_c.3172+320:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0018242-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused in-frame with ALK exons 20-29): c.668-7560:EML4_c.3172+320:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.
GPRC5C	0	MSKCC-DMP	P-0018243-T01-IM6	MET-GPRC5C fusion	yes	unknown		in frame	GPRC5C (NM_018653) - MET (NM_000245) rearrangement: t(7;17)(q31.2;q25.1)(chr7:g.116413793::chr17:g.72439446) Note: The GPRC5C - MET rearrangement is a translocation that results in the in-frame fusion of GPRC5C exons 1-2 with MET exons 15-21. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0018243-T01-IM6	MET-GPRC5C fusion	yes	unknown		in frame	GPRC5C (NM_018653) - MET (NM_000245) rearrangement: t(7;17)(q31.2;q25.1)(chr7:g.116413793::chr17:g.72439446) Note: The GPRC5C - MET rearrangement is a translocation that results in the in-frame fusion of GPRC5C exons 1-2 with MET exons 15-21. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0018271-T01-IM6	HAUS8-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.3390+59_g.17159184del Note: The DOT1L rearrangement results in the deletion of exons 25-28. This rearrangement happens in the background of other events involving DOT1L. The functional significance is undetermined.
HAUS8	0	MSKCC-DMP	P-0018271-T01-IM6	HAUS8-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.3390+59_g.17159184del Note: The DOT1L rearrangement results in the deletion of exons 25-28. This rearrangement happens in the background of other events involving DOT1L. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0018274-T01-IM6	SRL-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.2159-98:CREBBP_g.4179394del Note: The CREBBP rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.
SRL	0	MSKCC-DMP	P-0018274-T01-IM6	SRL-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.2159-98:CREBBP_g.4179394del Note: The CREBBP rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0018280-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exon 6 fused with ALK exon 20): c.494-6792:EML4_c.3173-793:ALKinv Note: The Fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0018280-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exon 6 fused with ALK exon 20): c.494-6792:EML4_c.3173-793:ALKinv Note: The Fusion is predicted to be in-frame and includes the kinase domain of ALK.
KMT2C	0	MSKCC-DMP	P-0018289-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C(NM_170606) Rearrangement : c.8688_c.7149+164del Note: The KMT2C Rearrangement results in the deletion of exons 37-38 of KMT2C. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0018294-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.4970_g.112190339del Note: The PARK2 rearrangement results in the intragenic deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018297-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.55+3942:TMPRSS2_c.-149-36900:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0018297-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.55+3942:TMPRSS2_c.-149-36900:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
SETD2	0	MSKCC-DMP	P-0018302-T01-IM6	ZNF148-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) rearrangement : c.7533+80:SETD2_g.125048522inv Note: The SETD2 (NM_014159) rearrangement results in an inversion of exons 1-20. The functional significance is undetermined.
ZNF148	0	MSKCC-DMP	P-0018302-T01-IM6	ZNF148-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) rearrangement : c.7533+80:SETD2_g.125048522inv Note: The SETD2 (NM_014159) rearrangement results in an inversion of exons 1-20. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0018314-T01-IM6	LINC00854-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.-19-61:BRCA1_chr17:g.41382277del Note: The BRCA1 rearrangement is a deletion with a breakpoint in the 5UTR. The functional significance is undetermined.
LINC00854	0	MSKCC-DMP	P-0018314-T01-IM6	LINC00854-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.-19-61:BRCA1_chr17:g.41382277del Note: The BRCA1 rearrangement is a deletion with a breakpoint in the 5UTR. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018315-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1575:TMPRSS2_c.18+18761:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018315-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame with ERG exons 2-10): c.126+1575:TMPRSS2_c.18+18761:ERGdel
KMT2D	0	MSKCC-DMP	P-0018316-T01-IM6	TUBA1B-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4020+20:KMT2D_chr12:g.49530496del Note: The KMT2D rearrangement is a deletion of exons 1-12, potentially resulting in a truncation of the gene. This structural variant was observed in addition to KMT2D intragenic duplication of exons 13 - 38, suggesting a complex rearrangement involving KMT2D.
TUBA1B	0	MSKCC-DMP	P-0018316-T01-IM6	TUBA1B-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4020+20:KMT2D_chr12:g.49530496del Note: The KMT2D rearrangement is a deletion of exons 1-12, potentially resulting in a truncation of the gene. This structural variant was observed in addition to KMT2D intragenic duplication of exons 13 - 38, suggesting a complex rearrangement involving KMT2D.
APC	0	MSKCC-DMP	P-0018329-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.3581_c.4458inv Note: The APC rearrangement is an inversion (877 bp) with both breakpoints within exon 16. The functional significance is undetermined.
CDK8	0	MSKCC-DMP	P-0018351-T01-IM6	CDK8-intragenic	yes	unknown		unknown	CDK8 NM_001260) rearrangement: c.645_c.647-1del Note: The CDK8 rearrangement is an intragenic deletion with breakpoints in exon 6 and 7. The functional significance is undetermined.
CBFB	0	MSKCC-DMP	P-0018351-T01-IM6	CBFB-intragenic	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.495+30_c.496-1del Note: The CBFB rearrangement is an intragenic deletion with a breakpoint in exon 6. The functional significance is undetermined.
F11-AS1	0	MSKCC-DMP	P-0018374-T01-IM6	FAT1-F11-AS1 fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.5344:FAT1_chr4:g.187311035del Note: The FAT1 Rearrangement results in the deletion of FAT1 exons 10-27.The breakpoint in FAT1 is within exon10. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0018374-T01-IM6	FAT1-F11-AS1 fusion	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement : c.5344:FAT1_chr4:g.187311035del Note: The FAT1 Rearrangement results in the deletion of FAT1 exons 10-27.The breakpoint in FAT1 is within exon10. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0018378-T01-IM6	LOC101929504-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.1377:ROS1_chr6:g.169216197inv Note: The ROS1 Rearrangement results in the inversion of exons 1-12 of ROS1. The breakpoint in ROS1 is within exon 12. This event doesn't include the protein kinase domain of ROS1. Its functional significance is undetermined.
LOC101929504	0	MSKCC-DMP	P-0018378-T01-IM6	LOC101929504-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.1377:ROS1_chr6:g.169216197inv Note: The ROS1 Rearrangement results in the inversion of exons 1-12 of ROS1. The breakpoint in ROS1 is within exon 12. This event doesn't include the protein kinase domain of ROS1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018395-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2464:TMPRSS2_c.40-54367:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018395-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2464:TMPRSS2_c.40-54367:ERGdel
LOC102723505	0	MSKCC-DMP	P-0018416-T01-IM6	SOX9-LOC102723505 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: chr17:g.69803812_c.788del Note: The SOX9 rearrangement is a deletion which includes exons 1-3 of SOX9. One of the breakpoints is within SOX9 exon 3. The functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0018416-T01-IM6	SOX9-LOC102723505 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: chr17:g.69803812_c.788del Note: The SOX9 rearrangement is a deletion which includes exons 1-3 of SOX9. One of the breakpoints is within SOX9 exon 3. The functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0018419-T01-IM6	SUFU-intragenic	yes	unknown		unknown	SUFU (NM_016169) rearrangement: c.757-1023_c.894del Note: The SUFU rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.
GUCA1C	0	MSKCC-DMP	P-0018453-T01-IM6	BCL6-GUCA1C fusion	yes	unknown		unknown	BCL6 (NM_001706) rearrangement : g.108661942_c.1709-28:BCL6inv Note: The BCL6 rearrangement results in an inversion of exons 8-10. The functional significance is undetermined.
BCL6	0	MSKCC-DMP	P-0018453-T01-IM6	BCL6-GUCA1C fusion	yes	unknown		unknown	BCL6 (NM_001706) rearrangement : g.108661942_c.1709-28:BCL6inv Note: The BCL6 rearrangement results in an inversion of exons 8-10. The functional significance is undetermined.
TPT1	0	MSKCC-DMP	P-0018461-T01-IM6	RB1-TPT1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement : g.45902093_c.791:RB1inv Note: The RB1 rearrangement results in an inversion of exons 1-8 . One of the breakpoints is within exon 8. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0018461-T01-IM6	RB1-TPT1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement : g.45902093_c.791:RB1inv Note: The RB1 rearrangement results in an inversion of exons 1-8 . One of the breakpoints is within exon 8. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0018462-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.397_c.894del Note: The TP53 rearrangement is an intragenic deletion of exons 5-8. Both breakpoints are within exon. The functional significance is undetermined.
HIST1H1E	0	MSKCC-DMP	P-0018464-T01-IM6	HIST1H3G-HIST1H1E fusion	yes	unknown		unknown	HIST1H3G (NM_003534) rearrangement: c.85_chr6:g.26153113del Note: The HIST1H3G rearrangement is a deletion of exon 1. One of the breakpoints is within exon.  The functional significance is undetermined.
HIST1H3G	0	MSKCC-DMP	P-0018464-T01-IM6	HIST1H3G-HIST1H1E fusion	yes	unknown		unknown	HIST1H3G (NM_003534) rearrangement: c.85_chr6:g.26153113del Note: The HIST1H3G rearrangement is a deletion of exon 1. One of the breakpoints is within exon.  The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0018470-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.3778_c.3807-168del Note: The EP300 rearrangement is an intragenic deletion of exon 22. One of the breakpoints is within exon 22. The functional significance is undetermined.
CYLD	0	MSKCC-DMP	P-0018487-T01-IM6	SPACA7-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) - SPACA7 (NM_145248) rearrangement: t(13, 16)( q12.1, q34)(chr13:g.113008750::chr16:g.50813791) Note: The CYLD  rearrangement is the translocation of  CYLD exon 8-18 and SPACA7. The functional significance is undetermined.
SPACA7	0	MSKCC-DMP	P-0018487-T01-IM6	SPACA7-CYLD fusion	yes	unknown		unknown	CYLD (NM_001042355) - SPACA7 (NM_145248) rearrangement: t(13, 16)( q12.1, q34)(chr13:g.113008750::chr16:g.50813791) Note: The CYLD  rearrangement is the translocation of  CYLD exon 8-18 and SPACA7. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018489-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11): c.56-3860:TMPRSS2_c.40-6101:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018489-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11): c.56-3860:TMPRSS2_c.40-6101:ERGdel
CDKN2A	0	MSKCC-DMP	P-0018490-T01-IM6	IZUMO3-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A(NM_000077) rearrangement: c.406:CDKN2Ap16INK4A_chr9:g.24391640inv Note: The CDKN2Ap16INK4A rearrangement is an inversion which includes exons 1-2 of CDKN2Ap16INK4A. One of the breakpoints is within exon2. The functional significance is undetermined.
IZUMO3	0	MSKCC-DMP	P-0018490-T01-IM6	IZUMO3-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A(NM_000077) rearrangement: c.406:CDKN2Ap16INK4A_chr9:g.24391640inv Note: The CDKN2Ap16INK4A rearrangement is an inversion which includes exons 1-2 of CDKN2Ap16INK4A. One of the breakpoints is within exon2. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0018498-T01-IM6	NOTCH2-intragenic	yes	unknown		in frame	NOTCH1 (NM_017617) rearrangement: chr1:g.120484441:NOTCH1_chr1:g.120521890del Note: The NOTCH1 rearrangement is a deletion of exons 6-17.
NCOR1	0	MSKCC-DMP	P-0018498-T01-IM6	KIF26A-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - KIF26A (NM_01565) rearrangement: t(14, 17)(q32.33, p12)(chr14:g.104672507::chr17:g.15978935) Note: The NCOR1 rearrangement is a deletion of exons 1-27
KIF26A	0	MSKCC-DMP	P-0018498-T01-IM6	KIF26A-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - KIF26A (NM_01565) rearrangement: t(14, 17)(q32.33, p12)(chr14:g.104672507::chr17:g.15978935) Note: The NCOR1 rearrangement is a deletion of exons 1-27
TMPRSS2	0	MSKCC-DMP	P-0018524-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(21;7)(q22.3;q34)(chr21:g.42873801::chr7:g.140490337) Note: TMPRSS2 - BRAF rearrangement is a translocation which results in fusion of TMPRSS2 exon1 with BRAF exons 9-18. The fusion includes the kinase domain of BRAF. Additional testing will be attempted to confirm the fusion and it will be reported under a separate accession number.
BRAF	0	MSKCC-DMP	P-0018524-T01-IM6	BRAF-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(21;7)(q22.3;q34)(chr21:g.42873801::chr7:g.140490337) Note: TMPRSS2 - BRAF rearrangement is a translocation which results in fusion of TMPRSS2 exon1 with BRAF exons 9-18. The fusion includes the kinase domain of BRAF. Additional testing will be attempted to confirm the fusion and it will be reported under a separate accession number.
KMT2C	0	MSKCC-DMP	P-0018536-T01-IM6	PRDM1-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606)  Rearrangement :  t(6;7)(q21;q36.1)(chr6:g.106189129::chr7:g.151891246) Note: The KMT2C Rearrangement results in the possible truncation of exons 31-59. Its functional significance is undetermined.
PRDM1	0	MSKCC-DMP	P-0018536-T01-IM6	PRDM1-KMT2C fusion	yes	unknown		unknown	KMT2C (NM_170606)  Rearrangement :  t(6;7)(q21;q36.1)(chr6:g.106189129::chr7:g.151891246) Note: The KMT2C Rearrangement results in the possible truncation of exons 31-59. Its functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0018537-T01-IM6	PEX6-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) Rearrangement : c.-578:PEX6_c.4316-77:NOTCH4del Note: The NOTCH4  Rearrangement results in the deletion of exons 1-23 of NOTCH4. Its functional significance is undetermined.
PEX6	0	MSKCC-DMP	P-0018537-T01-IM6	PEX6-NOTCH4 fusion	yes	unknown		unknown	NOTCH4 (NM_004557) Rearrangement : c.-578:PEX6_c.4316-77:NOTCH4del Note: The NOTCH4  Rearrangement results in the deletion of exons 1-23 of NOTCH4. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0018541-T01-IM6	LRP1B-ALK fusion	yes	unknown		in frame	ALK (NM_004304) - LRP1B (NM_018557) Rearrangement : c.2914+151:ALK_c.344-85984:LRP1Bdup Note : The ALK - LRP1B Rearrangement results in the fusion of exons 1-17 of ALK with exons of  4-91 of LRP1B . This fusion does not include the protein kinase domain of ALK. Its functional significance is undetermined.
LRP1B	0	MSKCC-DMP	P-0018541-T01-IM6	LRP1B-ALK fusion	yes	unknown		in frame	ALK (NM_004304) - LRP1B (NM_018557) Rearrangement : c.2914+151:ALK_c.344-85984:LRP1Bdup Note : The ALK - LRP1B Rearrangement results in the fusion of exons 1-17 of ALK with exons of  4-91 of LRP1B . This fusion does not include the protein kinase domain of ALK. Its functional significance is undetermined.
PPP6C	0	MSKCC-DMP	P-0018555-T01-IM6	PPP6C-intragenic	yes	unknown		unknown	PPP6C (NM_002721) rearrangements: c.669_c.670del Note: The PPP6C rearrangement is an intragenic deletion with breakpoints in both exon 6 and 7.
ASXL1	0	MSKCC-DMP	P-0018556-T01-IM6	ASXL1-intragenic	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.252+14450_c.1828dup Note: The ASXL1 rearrangement is an intragenic duplication of exons 4 - 12. One of the breakpoints is within exon 12. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0018568-T01-IM6	EZH1-STAT3 fusion	yes	unknown		unknown	EZH1 (NM_001991) - STAT3 (NM_139276) rearrangement: c.2098+21:EZH1_c.-23-2339:STAT3del Note: The EZH1 - STAT3 rearrangement is a deletion that results in the fusion of EZH1 exons 1-19 with STAT3 exons 1-24. One of the breakpoints is within 5-UTR of STAT3. The functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0018568-T01-IM6	EZH1-STAT3 fusion	yes	unknown		unknown	EZH1 (NM_001991) - STAT3 (NM_139276) rearrangement: c.2098+21:EZH1_c.-23-2339:STAT3del Note: The EZH1 - STAT3 rearrangement is a deletion that results in the fusion of EZH1 exons 1-19 with STAT3 exons 1-24. One of the breakpoints is within 5-UTR of STAT3. The functional significance is undetermined.
SEC16A	0	MSKCC-DMP	P-0018568-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - SEC16A (NM_014866) rearrangement: c.6672:NOTCH1_c.3704+620:SEC16Adel Note: The NOTCH1 - SEC16A rearrangement is a deletion that results in the fusion of NOTCH1 exons 1-34 with SEC16A exons 5-32. One of the breakpoints is within NOTCH1 exon 34. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0018568-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - SEC16A (NM_014866) rearrangement: c.6672:NOTCH1_c.3704+620:SEC16Adel Note: The NOTCH1 - SEC16A rearrangement is a deletion that results in the fusion of NOTCH1 exons 1-34 with SEC16A exons 5-32. One of the breakpoints is within NOTCH1 exon 34. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0018575-T01-IM6	RHOT1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - RHOT1 (NM_001033568) rearrangement: c.4953:NF1_c.1958+4664:RHOT1del Note: The NF1 - RHOT1 rearrangement is a deletion that results in the fusion of NF1 exons 1-37 with RHOT1 exons 20-21. One of the breakpoints is within NF1 exon 37. The functional significance is undetermined.
RHOT1	0	MSKCC-DMP	P-0018575-T01-IM6	RHOT1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - RHOT1 (NM_001033568) rearrangement: c.4953:NF1_c.1958+4664:RHOT1del Note: The NF1 - RHOT1 rearrangement is a deletion that results in the fusion of NF1 exons 1-37 with RHOT1 exons 20-21. One of the breakpoints is within NF1 exon 37. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0018575-T01-IM6	ARAP2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: t(4;17)(p15.1;q12)(chr4:g.35688798::chr17:g.37618733) Note: The CDK12 rearrangement is a translocation that may result in the truncation of exons 1-14. One of the breakpoints is within exon 1. The functional significance is undetermined.
ARAP2	0	MSKCC-DMP	P-0018575-T01-IM6	ARAP2-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: t(4;17)(p15.1;q12)(chr4:g.35688798::chr17:g.37618733) Note: The CDK12 rearrangement is a translocation that may result in the truncation of exons 1-14. One of the breakpoints is within exon 1. The functional significance is undetermined.
ASIC2	0	MSKCC-DMP	P-0018576-T01-IM6	LYN-ASIC2 fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: t(8;17)(q12.1;q12)(chr8:g.56911063::chr17:g.32040644) Note: The LYN rearrangement is a translocation that may result in the truncation of exons 12-13. The functional significance is undetermined.
LYN	0	MSKCC-DMP	P-0018576-T01-IM6	LYN-ASIC2 fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: t(8;17)(q12.1;q12)(chr8:g.56911063::chr17:g.32040644) Note: The LYN rearrangement is a translocation that may result in the truncation of exons 12-13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018581-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.127-1554:TMPRSS2_c.18+8829:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018581-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.127-1554:TMPRSS2_c.18+8829:ERGdel
BRD4	0	MSKCC-DMP	P-0018582-T01-IM6	SMIM7-BRD4 fusion	yes	unknown		unknown	SMIM7 (NM_024104.3) - BRD4 (NM_058243) rearrangement: c.213-1319:SMIM7_c.2235:BRD4del Note: The SMIM7 - BRD4 rearrangement is a deletion that results in the fusion of SMIM7  exons 1-4 with BRD4 exons 13-20. One of the breakpoints is within BRD4 exon 13. The functional significance is undetermined.
SMIM7	0	MSKCC-DMP	P-0018582-T01-IM6	SMIM7-BRD4 fusion	yes	unknown		unknown	SMIM7 (NM_024104.3) - BRD4 (NM_058243) rearrangement: c.213-1319:SMIM7_c.2235:BRD4del Note: The SMIM7 - BRD4 rearrangement is a deletion that results in the fusion of SMIM7  exons 1-4 with BRD4 exons 13-20. One of the breakpoints is within BRD4 exon 13. The functional significance is undetermined.
CEBPA	0	MSKCC-DMP	P-0018598-T02-IM6	PEPD-CEBPA fusion	yes	unknown		unknown	PEPD (NM_000285) - CEBPA (NM_004364) rearrangement: c.504-3890:PEPD_c.856:CEBPAdel Note: The PEPD - CEBPA rearrangement is a deletion which results in the fusion of PEPD exons 1-6 with CEBPA exon 1. One of the breakpoints is within CEBPA exon 1. The functional significance is undetermined.
PEPD	0	MSKCC-DMP	P-0018598-T02-IM6	PEPD-CEBPA fusion	yes	unknown		unknown	PEPD (NM_000285) - CEBPA (NM_004364) rearrangement: c.504-3890:PEPD_c.856:CEBPAdel Note: The PEPD - CEBPA rearrangement is a deletion which results in the fusion of PEPD exons 1-6 with CEBPA exon 1. One of the breakpoints is within CEBPA exon 1. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0018598-T02-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.3130_c.*806inv Note: The CIC rearrangement is an inversion (3576 bp) which includes exons 1-13. One of the breakpoints is within exon 13. Multiple CIC rearrangements were detected in this sample and more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ZNF43	0	MSKCC-DMP	P-0018608-T01-IM6	KMT2B-ZNF43 fusion	yes	unknown		in frame	KMT2B (NM_014727) rearrangement: chr19:g.22025862_c.5076+2:KMT2Binv Note: The KMT2B rearrangement is an inversion of exons 1-23, potentially disrupting gene function.
KMT2B	0	MSKCC-DMP	P-0018608-T01-IM6	KMT2B-ZNF43 fusion	yes	unknown		in frame	KMT2B (NM_014727) rearrangement: chr19:g.22025862_c.5076+2:KMT2Binv Note: The KMT2B rearrangement is an inversion of exons 1-23, potentially disrupting gene function.
SMAD6	0	MSKCC-DMP	P-0018624-T01-IM6	SMAD3-SMAD6 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: g.67152286_c.872-33del Note: The SMAD3 rearrangement results in the deletion of exons 1-6. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0018624-T01-IM6	SMAD3-SMAD6 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: g.67152286_c.872-33del Note: The SMAD3 rearrangement results in the deletion of exons 1-6. The functional significance is undetermined.
SH2B3	0	MSKCC-DMP	P-0018626-T01-IM6	LINC01021-SH2B3 fusion	yes	unknown		unknown	SH2B3 (NM_005475) rearrangement: t(5;12)(p14.1;q24.12)(chr5:g.27195354::chr12:g.111856053) Note: The SH2B3 rearrangement is a translocation that may result in the truncation of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
LINC01021	0	MSKCC-DMP	P-0018626-T01-IM6	LINC01021-SH2B3 fusion	yes	unknown		unknown	SH2B3 (NM_005475) rearrangement: t(5;12)(p14.1;q24.12)(chr5:g.27195354::chr12:g.111856053) Note: The SH2B3 rearrangement is a translocation that may result in the truncation of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
TSPAN18	0	MSKCC-DMP	P-0018630-T01-IM6	JAK2-TSPAN18 fusion	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: t(9;11)(q24.12;p11.2)(chr9:g.5044464::chr11:g.44939223) Note: The JAK2 rearrangement is a translocation that may result in the truncation of exons 5-25. One of the breakpoints is within exon 5. The functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0018630-T01-IM6	JAK2-TSPAN18 fusion	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: t(9;11)(q24.12;p11.2)(chr9:g.5044464::chr11:g.44939223) Note: The JAK2 rearrangement is a translocation that may result in the truncation of exons 5-25. One of the breakpoints is within exon 5. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0018647-T01-IM6	DOCK6-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement : c.1615+88:CARM1_c.721-981:DOCK6del Note: The CARM1 Rearrangement results in the deletion of exons 15-16 of CARM1.Its functional significance is undetermined.
DOCK6	0	MSKCC-DMP	P-0018647-T01-IM6	DOCK6-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement : c.1615+88:CARM1_c.721-981:DOCK6del Note: The CARM1 Rearrangement results in the deletion of exons 15-16 of CARM1.Its functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0018647-T01-IM6	AMER1-intragenic	yes	unknown		unknown	AMER1 (NM_152424) Rearrangement : chrX:g.63373392_c.1644:AMER1del Note: The AMER1 Rearrangement results in the partial deletion of exon2. The breakpoint is within exon2. Its functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0018660-T01-IM6	ARFRP1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) Rearrangement : c.3090:RTEL1_c.392:ARFRP1del Note: The RTEL1 Rearrangement results in the deletion of exons 31-35 of RTEL1. The breakpoint in RTEL1 is within exon 31. Its functional significance is undetermined.
ARFRP1	0	MSKCC-DMP	P-0018660-T01-IM6	ARFRP1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) Rearrangement : c.3090:RTEL1_c.392:ARFRP1del Note: The RTEL1 Rearrangement results in the deletion of exons 31-35 of RTEL1. The breakpoint in RTEL1 is within exon 31. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0018667-T01-IM6	AHDC1-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.2161+38_g.27852005del Note: The ARID1A rearrangement results in the deletion of exons 5-20. The functional significance is undetermined.
AHDC1	0	MSKCC-DMP	P-0018667-T01-IM6	AHDC1-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.2161+38_g.27852005del Note: The ARID1A rearrangement results in the deletion of exons 5-20. The functional significance is undetermined.
DRG1	0	MSKCC-DMP	P-0018668-T01-IM6	POLE-DRG1 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(12;22)(q24.33;q12.2)(chr12:g.133257281::chr22:g.31791989) Note: The POLE rearrangement is a translocation that may result in the truncation of exons 3-49. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0018668-T01-IM6	POLE-DRG1 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(12;22)(q24.33;q12.2)(chr12:g.133257281::chr22:g.31791989) Note: The POLE rearrangement is a translocation that may result in the truncation of exons 3-49. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0018690-T01-IM6	SERINC5-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.2172:MAP3K1_chr5:g.79481066del Note: The MAP3K1 rearrangement is a deletion of exons 12- 20, which include the kinase domain of MAP3K1. One of the breakpoints is within exon 12.
SERINC5	0	MSKCC-DMP	P-0018690-T01-IM6	SERINC5-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.2172:MAP3K1_chr5:g.79481066del Note: The MAP3K1 rearrangement is a deletion of exons 12- 20, which include the kinase domain of MAP3K1. One of the breakpoints is within exon 12.
EWSR1	0	MSKCC-DMP	P-0018693-T01-IM6	EWSR1-intragenic	yes	unknown		out of frame	EWSR1 (NM_013986) rearrangement: c.103-123_c.1028-91del Note: The EWSR1 rearrangement is an intragenic deletion of exons 4-10.
LOC101927058	0	MSKCC-DMP	P-0018700-T01-IM6	KMT2D-LOC101927058 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.43055129_c.7303:KMT2Ddel Note: The KMT2D rearrangement is a deletion of exons 31-54. One of the breakpoints is within exon 31.
KMT2D	0	MSKCC-DMP	P-0018700-T01-IM6	KMT2D-LOC101927058 fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.43055129_c.7303:KMT2Ddel Note: The KMT2D rearrangement is a deletion of exons 31-54. One of the breakpoints is within exon 31.
ERG	0	MSKCC-DMP	P-0018704-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.56-2342:TMPRSS2_c.39+63678:ERGdel Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0018704-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.56-2342:TMPRSS2_c.39+63678:ERGdel Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).
SMAD4	0	MSKCC-DMP	P-0018710-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: chr18:g.48526969_c.1409del Note: The SMAD4 rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11.
ERG	0	MSKCC-DMP	P-0018713-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.127-1426:TMPRSS2_c.40-60631:ERGdel Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0018713-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.127-1426:TMPRSS2_c.40-60631:ERGdel Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).
LINC01440	0	MSKCC-DMP	P-0018761-T01-IM6	GNAS-LINC01440 fusion	yes	unknown		unknown	GNAS (NM_000516) Rearrangement : c.938:GNAS_chr20:g.54110650del Note: The GNAS Rearrangement results in the deletion of exons 1-11 of GNAS. The breakpoint in GNAS is within exon 11. Its functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0018761-T01-IM6	GNAS-LINC01440 fusion	yes	unknown		unknown	GNAS (NM_000516) Rearrangement : c.938:GNAS_chr20:g.54110650del Note: The GNAS Rearrangement results in the deletion of exons 1-11 of GNAS. The breakpoint in GNAS is within exon 11. Its functional significance is undetermined.
CTNNA3	0	MSKCC-DMP	P-0018785-T01-IM6	TET1-CTNNA3 fusion	yes	unknown		unknown	TET1 (NM_030625) - CTNNA3 (NM_013266) rearrangement: c.2089:TET1_c.2159+6353:CTNNA3inv Note: The TET1 - CTNNA3 rearrangement is an inversion that results in the fusion of TET1 exons 1-4 with CTNNA3 exons 16-18. One of the breakpoints is within TET1 exon 4. The functional significance is undetermined.
TET1	0	MSKCC-DMP	P-0018785-T01-IM6	TET1-CTNNA3 fusion	yes	unknown		unknown	TET1 (NM_030625) - CTNNA3 (NM_013266) rearrangement: c.2089:TET1_c.2159+6353:CTNNA3inv Note: The TET1 - CTNNA3 rearrangement is an inversion that results in the fusion of TET1 exons 1-4 with CTNNA3 exons 16-18. One of the breakpoints is within TET1 exon 4. The functional significance is undetermined.
KCNJ18	0	MSKCC-DMP	P-0018785-T01-IM6	FGFR2-KCNJ18 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;17)(q26.13;p11.2)(chr10:g.123240775::chr17:g.21369673) Note: The FGFR2 rearrangement is a translocation that may result in the truncation of exon 18. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0018785-T01-IM6	FGFR2-KCNJ18 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;17)(q26.13;p11.2)(chr10:g.123240775::chr17:g.21369673) Note: The FGFR2 rearrangement is a translocation that may result in the truncation of exon 18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1 fused to ERG exons 2-10): c.56-2909:TMPRSS2_c.18+13740:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1 fused to ERG exons 2-10): c.56-2909:TMPRSS2_c.18+13740:ERGdel
ERG	0	MSKCC-DMP	P-0018798-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2155:TMPRSS2_c.19-19621:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018798-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2155:TMPRSS2_c.19-19621:ERGdel
GALNT11	0	MSKCC-DMP	P-0018798-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement : g.151754651_c.14667:KMT2Cinv Note: The KMT2C rearrangement results in an inversion of exon 59. One of the breakpoints is within exon 59. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0018798-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement : g.151754651_c.14667:KMT2Cinv Note: The KMT2C rearrangement results in an inversion of exon 59. One of the breakpoints is within exon 59. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0018800-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: g.123006554_c.2378:FGFR2del Note: The FGFR2 rearrangement results in the deletion of exon 18. One of the breakpoints is within exon 18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1654:TMPRSS2_c.19-10716:ERGinv Note: Multiple rearrangements involving TMPRSS2 were detected in this sample. While the TMPRSS2 - ERG inversion does not produce a functional gene fusion, a more complex rearrangement resulting in a gene fusion is possible.
TMPRSS2	0	MSKCC-DMP	P-0018812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1654:TMPRSS2_c.19-10716:ERGinv Note: Multiple rearrangements involving TMPRSS2 were detected in this sample. While the TMPRSS2 - ERG inversion does not produce a functional gene fusion, a more complex rearrangement resulting in a gene fusion is possible.
MAP3K1	0	MSKCC-DMP	P-0018812-T01-IM6	PDE4D-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - PDE4D (NM_001104631) rearrangement: c.950:MAP3K1_c.456-148209:PDE4Ddup Note: The MAP3K1 - PDE4D rearrangement is a duplication (2499327) which includes exons 4-20 of MAP3K1. One of the breakpoints is within MAP3K1 exon4. The functional significance is undetermined.
PDE4D	0	MSKCC-DMP	P-0018812-T01-IM6	PDE4D-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - PDE4D (NM_001104631) rearrangement: c.950:MAP3K1_c.456-148209:PDE4Ddup Note: The MAP3K1 - PDE4D rearrangement is a duplication (2499327) which includes exons 4-20 of MAP3K1. One of the breakpoints is within MAP3K1 exon4. The functional significance is undetermined.
SLC28A3	0	MSKCC-DMP	P-0018812-T01-IM6	NTRK2-SLC28A3 fusion	yes	unknown		unknown	NTRK2 (NM_006180)  rearrangement: chr9:g.86817107_c.1444+2176dup Note: The NTRK2 rearrangement is a duplication (661071 bp) which includes exons 1-15 of NTRK2. The functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0018812-T01-IM6	NTRK2-SLC28A3 fusion	yes	unknown		unknown	NTRK2 (NM_006180)  rearrangement: chr9:g.86817107_c.1444+2176dup Note: The NTRK2 rearrangement is a duplication (661071 bp) which includes exons 1-15 of NTRK2. The functional significance is undetermined.
HGF	0	MSKCC-DMP	P-0018848-T01-IM6	HGF-intragenic	yes	unknown		out of frame	HGF (NM_000601) Rearrangement : c.483-10_c.865+3831dup Note: The HGF Rearrangement results in the duplication of exons 5-7 of HGF.Its functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0018868-T01-IM6	GAS6-IRS2 fusion	yes	unknown		unknown	GAS6 (NM_000820) - IRS2 (NM_003749) Rearrangement : c.281-566:GAS6_c.2992:IRS2del Note: The GAS6 - IRS2 Rearrangement results in the fusion of exons 1-3 of GAS6 with exons 1-2. The breakpoint in IRS2 is within exon1. Its functional significance is undetermined.
GAS6	0	MSKCC-DMP	P-0018868-T01-IM6	GAS6-IRS2 fusion	yes	unknown		unknown	GAS6 (NM_000820) - IRS2 (NM_003749) Rearrangement : c.281-566:GAS6_c.2992:IRS2del Note: The GAS6 - IRS2 Rearrangement results in the fusion of exons 1-3 of GAS6 with exons 1-2. The breakpoint in IRS2 is within exon1. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0018870-T01-IM6	EXOSC7-CTNNB1 fusion	yes	unknown		out of frame	EXOSC7 (NM_015004) - CTNNB1 (NM_001904) Rearrangement : c.58-5293:EXOSC7_c.1954+10:CTNNB1dup Note: The EXOSC7 - CTNNB1 Rearrangement results in the fusion of exon 1 of EXOSC7 with exons 13-15 of CTNNB1. This event was observed in the background of other structural rearrangements involving CTNNB1.Its functional significance is undetermined.
EXOSC7	0	MSKCC-DMP	P-0018870-T01-IM6	EXOSC7-CTNNB1 fusion	yes	unknown		out of frame	EXOSC7 (NM_015004) - CTNNB1 (NM_001904) Rearrangement : c.58-5293:EXOSC7_c.1954+10:CTNNB1dup Note: The EXOSC7 - CTNNB1 Rearrangement results in the fusion of exon 1 of EXOSC7 with exons 13-15 of CTNNB1. This event was observed in the background of other structural rearrangements involving CTNNB1.Its functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0018893-T01-IM6	TGFBR1-intragenic	yes	unknown		unknown	TGFBR1 (NM_004612) rearrangement: chr9:g.101859374_c.16del Note: The TGFBR1 rearrangement is a partial deletion of exon 1.
ERBB2	0	MSKCC-DMP	P-0018896-T01-IM6	ARHGAP42-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q22.1;q12)(chr11:g.100478828::chr17:g.37879868) Note: The ERBB2 rearrangement is a translocation that may result in a truncation of exons 18-27. One of the breakpoints is within exon 18. The functional significance is undetermined.
ARHGAP42	0	MSKCC-DMP	P-0018896-T01-IM6	ARHGAP42-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q22.1;q12)(chr11:g.100478828::chr17:g.37879868) Note: The ERBB2 rearrangement is a translocation that may result in a truncation of exons 18-27. One of the breakpoints is within exon 18. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0018921-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.*2336_c.458-429del Note:  The CDKN2A rearrangement is a deletion (2778 bp) which includes exon 3 of CDKN2Ap16INK4A. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0018925-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: c.4663-304C>T_c.4865inv Note: The TSC2 rearrangement is an inversion of exons 37-38. One of the breakpoints is within exon 38. The functional significance is undetermined.
EFCAB5	0	MSKCC-DMP	P-0018926-T01-IM6	RNF43-EFCAB5 fusion	yes	unknown		in frame	EFCAB5 (NM_198529) - RNF43 (NM_017763) rearrangement: c.1201-5046:EFCAB5_c.376-2:RNF43inv Note: The EFCAB5 - RNF43 rearrangement is an inversion which results in the fusion of EFCAB5 exon 8 to RNF43 exon 4. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0018926-T01-IM6	RNF43-EFCAB5 fusion	yes	unknown		in frame	EFCAB5 (NM_198529) - RNF43 (NM_017763) rearrangement: c.1201-5046:EFCAB5_c.376-2:RNF43inv Note: The EFCAB5 - RNF43 rearrangement is an inversion which results in the fusion of EFCAB5 exon 8 to RNF43 exon 4. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0018933-T01-IM6	SYT1-KMT2D fusion	yes	unknown		unknown	SYT1 (NM_001135806) - KMT2D (NM_003482) rearrangement: c.-18+8078:SYT1_c.14648:KMT2Dinv Note: The SYT1 - KMT2D rearrangement is an inversion which results in the fusion of SYT1 exon 1 to KMT2D exon 48. One of the breakpoints is within exon 48 of KMT2D. The functional significance is undetermined.
SYT1	0	MSKCC-DMP	P-0018933-T01-IM6	SYT1-KMT2D fusion	yes	unknown		unknown	SYT1 (NM_001135806) - KMT2D (NM_003482) rearrangement: c.-18+8078:SYT1_c.14648:KMT2Dinv Note: The SYT1 - KMT2D rearrangement is an inversion which results in the fusion of SYT1 exon 1 to KMT2D exon 48. One of the breakpoints is within exon 48 of KMT2D. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0018969-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-760:EML4_c.3083:ALKinv Note: The EML4- ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.
EML4	0	MSKCC-DMP	P-0018969-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-760:EML4_c.3083:ALKinv Note: The EML4- ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.
DAXX	0	MSKCC-DMP	P-0018985-T01-IM6	DAXX-intragenic	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.243+67_c.1396inv Note: The DAXX rearrangement is an intragenic inversion of exons 3-5. One of the breakpoints is within exon 5.
ATRX	0	MSKCC-DMP	P-0018987-T01-IM6	NSD1-ATRX fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: t(X;5)(q21.2;q35.3)(chrX:g.76752806::chr5:g.176638676) Note: The NSD1 rearrangement is  a translocation that may result in a truncation of exons 5-23. One of the breakpoints is within exon 5. The functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0018987-T01-IM6	NSD1-ATRX fusion	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: t(X;5)(q21.2;q35.3)(chrX:g.76752806::chr5:g.176638676) Note: The NSD1 rearrangement is  a translocation that may result in a truncation of exons 5-23. One of the breakpoints is within exon 5. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0019022-T02-IM6	ZCCHC11-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - ZCCHC11 (NM_001009881) rearrangement : c.674:SPEN_c.719-3409:ZCCHC11inv Note: The SPEN - ZCCHC11 rearrangement is an inversion that results in the fusion of SPEN exons 1-3 with ZCCHC11 exons 3-30. One of the breakpoints is within SPEN exon 3. The functional significance is undetermined.
ZCCHC11	0	MSKCC-DMP	P-0019022-T02-IM6	ZCCHC11-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - ZCCHC11 (NM_001009881) rearrangement : c.674:SPEN_c.719-3409:ZCCHC11inv Note: The SPEN - ZCCHC11 rearrangement is an inversion that results in the fusion of SPEN exons 1-3 with ZCCHC11 exons 3-30. One of the breakpoints is within SPEN exon 3. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0019022-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.2439_c.3716-77dup Note: The ARID1A rearrangement results in the duplication of exons 8-14. One of the breakpoints is within exon 8. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0019022-T02-IM6	GRK4-FGFR3 fusion	yes	unknown		unknown	GRK4 (NM_182982) - FGFR3 (NM_000142) rearrangement: c.339+3191:GRK4_c.44:FGFR3dup Note: The GRK4 - FGFR3 rearrangement is a duplication that results in the fusion of GRK4 exons 1-4 with FGFR3 exons 2-18. One of the breakpoints is within FGFR3 exon 2. The functional significance is undetermined.
GRK4	0	MSKCC-DMP	P-0019022-T02-IM6	GRK4-FGFR3 fusion	yes	unknown		unknown	GRK4 (NM_182982) - FGFR3 (NM_000142) rearrangement: c.339+3191:GRK4_c.44:FGFR3dup Note: The GRK4 - FGFR3 rearrangement is a duplication that results in the fusion of GRK4 exons 1-4 with FGFR3 exons 2-18. One of the breakpoints is within FGFR3 exon 2. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0019055-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1056_c.201del Note: The CTNNB1 rearrangement results in the deletion of exons 2-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0019058-T01-IM6	AXIN1-intragenic	yes	unknown		out of frame	AXIN1 (NM_003502) rearrangement: c.1255-25_c.878+14756del Note: The AXIN1 rearrangement results in the deletion of exons 3-5. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0019058-T01-IM6	BRIP1-intragenic	yes	unknown		in frame	BRIP1 (NM_032043) rearrangement: c.2380-9185_c.1140+101del Note: The BRIP1 rearrangement results in the in-frame deletion of exons 9-16. The functional significance is undetermined.
ZBTB32	0	MSKCC-DMP	P-0019058-T01-IM6	KMT2B-ZBTB32 fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: g.36188393_c.5995del Note: The KMT2B rearrangement results in the deletion of exons 1-28. One of the breakpoints is within exon 28. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0019058-T01-IM6	KMT2B-ZBTB32 fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: g.36188393_c.5995del Note: The KMT2B rearrangement results in the deletion of exons 1-28. One of the breakpoints is within exon 28. The functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0019058-T01-IM6	AGO2-intragenic	yes	unknown		out of frame	AGO2 (NM_012154) rearrangement: c.2472-52_c.23-10801del Note: The AGO2 rearrangement results in the deletion of exons 2-18. The functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0019062-T01-IM6	AMER1-intragenic	yes	unknown		unknown	AMER1 (NM_152424) rearrangement: c.1984_c.147del Note: The AMER1 rearrangement results in the deletion of exon 2. Both of the breakpoints are within exon 2. The functional significance is undetermined.
OTOGL	0	MSKCC-DMP	P-0019068-T01-IM6	PRDM1-OTOGL fusion	yes	unknown		unknown	PRDM1 (NM_001198) rearrangement: t(6;12)(q21;q21.31)(chr6:g.106554248::chr12:g.80543892) Note: The PRDM1 rearrangement is a translocation that may result in the truncation of exons 6-7. One of the breakpoints is within exon 6. The functional significance is undetermined.
PRDM1	0	MSKCC-DMP	P-0019068-T01-IM6	PRDM1-OTOGL fusion	yes	unknown		unknown	PRDM1 (NM_001198) rearrangement: t(6;12)(q21;q21.31)(chr6:g.106554248::chr12:g.80543892) Note: The PRDM1 rearrangement is a translocation that may result in the truncation of exons 6-7. One of the breakpoints is within exon 6. The functional significance is undetermined.
FBXW7	0	MSKCC-DMP	P-0019088-T01-IM6	FBXW7-intragenic	yes	unknown		unknown	FBXW7 (NM_033632) Rearrangement : c.1123-413_c.1302inv Note: The FBXW7 Rearrangement results in the inversion of exons 8-9 of FBXW7. One of the breakpoints is within exon9. Its functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0019094-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) Rearrangement : c.1676_c.1892-421del Note: The CSDE1 Rearrangement results in the deletion of exons 15-16 of CDSE1. One of the breakpoints is within exon 15. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0019108-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617)  Rearrangement : c.141-37_c.4421del Note: The NOTCH1 Rearrangement results in the inversion of exons 3-25. Its functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0019111-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.999_c.1083-1302inv Note: The NCOR1 rearrangement is predicted to result in an intragenic inversion of a part of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0019126-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) rearrangement: c.412+119_c.534+7569del Note: The PARK2 rearrangement is an intragenic deletion of exon3. The functional significance is undermined.
NCOA3	0	MSKCC-DMP	P-0019129-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.-98-33680_c.721+35dup Note: The NCOA3 rearrangement is an intragenic duplication (78281 bp) of exons 2-7. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0019130-T01-IM6	LINC01252-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.958_chr12:g.11658386inv Note: The KDM5A rearrangement is an inversion (11195073 bp) which includes exons 1-8 of KDM5A. One of the breakpoints is within KDM5A exon 8. The functional significance is undetermined.
LINC01252	0	MSKCC-DMP	P-0019130-T01-IM6	LINC01252-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.958_chr12:g.11658386inv Note: The KDM5A rearrangement is an inversion (11195073 bp) which includes exons 1-8 of KDM5A. One of the breakpoints is within KDM5A exon 8. The functional significance is undetermined.
MRPS6	0	MSKCC-DMP	P-0019130-T01-IM6	TMPRSS2-MRPS6 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement:  chr21:g.35443032_c.150inv Note: The TMPRSS2 rearrangement is an inversion (7423450 bp) which includes exons 3-14 TMPRSS2. One of the breakpoints is within TMPRSS2 exon 3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0019130-T01-IM6	TMPRSS2-MRPS6 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement:  chr21:g.35443032_c.150inv Note: The TMPRSS2 rearrangement is an inversion (7423450 bp) which includes exons 3-14 TMPRSS2. One of the breakpoints is within TMPRSS2 exon 3. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0019136-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.1879_c.1881+2559del Note: The WHSC1 rearrangement is a deletion of exon 9. One of the breakpoints is within exon. Multiple other deletions that span the intronic regions, including the splice sites,  between exons 5-6, exons 6-7, and exons 7-8 were detected in this sample. The functional significance is undetermined.
NBEAL2	0	MSKCC-DMP	P-0019144-T01-IM6	PBRM1-NBEAL2 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: g.47031659_c.995+68del Note: The PBRM1 rearrangement results in the deletion of exons 11-30. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0019144-T01-IM6	PBRM1-NBEAL2 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: g.47031659_c.995+68del Note: The PBRM1 rearrangement results in the deletion of exons 11-30. The functional significance is undetermined.
USP43	0	MSKCC-DMP	P-0019148-T01-IM6	NCOR1-USP43 fusion	yes	unknown		out of frame	NCOR1 (NM_006311) - USP43 (NM_153210) rearrangement: c.4951+83:NCOR1_c.741-2291:USP43inv Note: The NCOR1 - USP43 rearrangement is an inversion that results in the fusion of NCOR1 exons 34-46 with USP43 exons 4-15. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0019148-T01-IM6	NCOR1-USP43 fusion	yes	unknown		out of frame	NCOR1 (NM_006311) - USP43 (NM_153210) rearrangement: c.4951+83:NCOR1_c.741-2291:USP43inv Note: The NCOR1 - USP43 rearrangement is an inversion that results in the fusion of NCOR1 exons 34-46 with USP43 exons 4-15. The functional significance is undetermined.
LINC01115	0	MSKCC-DMP	P-0019148-T01-IM6	ERBB4-LINC01115 fusion	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: g.843212_c.1515:ERBB4del Note: The ERBB4 rearrangement results in the deletion of exons 13-28. One of the breakpoints is within exon 13. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0019148-T01-IM6	ERBB4-LINC01115 fusion	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: g.843212_c.1515:ERBB4del Note: The ERBB4 rearrangement results in the deletion of exons 13-28. One of the breakpoints is within exon 13. The functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0019150-T01-IM6	FUBP1-intragenic	yes	unknown		in frame	FUBP1 (NM_003902) rearrangement: c.637-22_c.121-95del Note: The FUBP1 rearrangement results in the in-frame deletion of exons 2-8. The functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0019153-T01-IM6	ERN2-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: c.2997-115_g.23726499del Note: The PALB2 rearrangement results in the deletion of exons 10-13. The functional significance is undetermined.
ERN2	0	MSKCC-DMP	P-0019153-T01-IM6	ERN2-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: c.2997-115_g.23726499del Note: The PALB2 rearrangement results in the deletion of exons 10-13. The functional significance is undetermined.
RFPL4B	0	MSKCC-DMP	P-0019153-T01-IM6	DDR2-RFPL4B fusion	yes	unknown		unknown	DDR2 (NM_006182)  rearrangement: t(1;6)(q23.3;q21)(chr1:g.162730897::chr6:g.112896512) Note: The DDR2 rearrangement is a translocation that may result in the truncation of exons 9-18. The functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0019153-T01-IM6	DDR2-RFPL4B fusion	yes	unknown		unknown	DDR2 (NM_006182)  rearrangement: t(1;6)(q23.3;q21)(chr1:g.162730897::chr6:g.112896512) Note: The DDR2 rearrangement is a translocation that may result in the truncation of exons 9-18. The functional significance is undetermined.
BCL6	0	MSKCC-DMP	P-0019222-T01-IM6	BCL6-intragenic	yes	unknown		unknown	BCL6 (NM_001706) rearrangement: c.1540+133_c.*2609inv Note: The BCL6 rearrangement is an inversion (8378 bp) of exons 7-10. The functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0019222-T01-IM6	NSD1-intragenic	yes	unknown		out of frame	NSD1 (NM_022455) rearrangement: c.3922-31_c.5146+1203dup Note: The NSD1 rearrangement is a duplication (23165 bp) of exons 7-14. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0019222-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.9453+698_c.10274dup Note: The KMT2C rearrangement is duplication (7263 bp) of exons 41-43. One of the breakpoints is within exon 43. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0019226-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.328+6821_c.464-6237del Note: The ETV6 rearrangement is an intragenic deletion (17062  bp) of exon 4. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0019243-T01-IM6	PRKG1-NF1 fusion	yes	unknown		out of frame	NF1 (NM_001042492) - PRKG1 (NM_001098512) rearrangement: t(10;17)(q21.1;q11.2)(chr10:g.53522352::chr17:g.29422402) Note: The NF1 - PRKG1 rearrangement is a translocation that results in the fusion of NF1 exon 1 with PRKG1 exons 4-18. The functional significance is undetermined.
PRKG1	0	MSKCC-DMP	P-0019243-T01-IM6	PRKG1-NF1 fusion	yes	unknown		out of frame	NF1 (NM_001042492) - PRKG1 (NM_001098512) rearrangement: t(10;17)(q21.1;q11.2)(chr10:g.53522352::chr17:g.29422402) Note: The NF1 - PRKG1 rearrangement is a translocation that results in the fusion of NF1 exon 1 with PRKG1 exons 4-18. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0019262-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.850_c.874+5330del Note; The NOTCH2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
FUBP3	0	MSKCC-DMP	P-0019262-T01-IM6	ABL1-FUBP3 fusion	yes	unknown		out of frame	ABL1 (NM_005157) - FUBP3 (NM_003934) rearrangement: c.822+6:ABL1_c.191-582:FUBP3dup Note: The ABL1 - FUBP3 rearrangement is a duplication which results in the fusion of ABL1 exon 4 to FUBP3 exon 3. The functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0019262-T01-IM6	ABL1-FUBP3 fusion	yes	unknown		out of frame	ABL1 (NM_005157) - FUBP3 (NM_003934) rearrangement: c.822+6:ABL1_c.191-582:FUBP3dup Note: The ABL1 - FUBP3 rearrangement is a duplication which results in the fusion of ABL1 exon 4 to FUBP3 exon 3. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0019266-T01-IM6	CDKN2B-AS1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_058195, NM_000077) rearrangement: c.-453_c.*102-531del Note: The CDKN2A rearrangement is a deletion of exons 1-2 of the CDKN2Ap14ARF and CDKN2Ap16INK4A isoforms of CDKN2A
CDKN2B-AS1	0	MSKCC-DMP	P-0019266-T01-IM6	CDKN2B-AS1-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_058195, NM_000077) rearrangement: c.-453_c.*102-531del Note: The CDKN2A rearrangement is a deletion of exons 1-2 of the CDKN2Ap14ARF and CDKN2Ap16INK4A isoforms of CDKN2A
SMAD3	0	MSKCC-DMP	P-0019285-T01-IM6	IQCH-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902)- IQCH (NM_001031715 Rearrangement : c.1224:SMAD3_c.754-3646:IQCHdel Note: The SMAD3 - IQCH Rearrangement results in the fusion of exons 1-9 with exons 9-21 of IQCH. The breakpoint in SMAD3 is within exon9. Its functional significance is undetermined.
IQCH	0	MSKCC-DMP	P-0019285-T01-IM6	IQCH-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902)- IQCH (NM_001031715 Rearrangement : c.1224:SMAD3_c.754-3646:IQCHdel Note: The SMAD3 - IQCH Rearrangement results in the fusion of exons 1-9 with exons 9-21 of IQCH. The breakpoint in SMAD3 is within exon9. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0019320-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.-51_c.501-1010inv Note: The RB1 rearrangement is predicted to result in the inversion of exons 1-4. The functional significance is undetermined.
EPHA3	0	MSKCC-DMP	P-0019320-T01-IM6	EPHA3-intragenic	yes	unknown		unknown	EPHA3 (NM_005233) rearrangement: c.1306+1_c.1306+20088del Note: The EPHA3 rearrangement is an intragenic deletion with one of the breakpoints in intron 5, 1bp away from exon. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0019324-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2067_c.127-919inv Note: The TMPRSS2 rearrangement is predicted to result in the inversion of the exons 2-3. This structural variant was observed in addition to another rearrangement involving TMRPSS2, suggesting a complex event that may not be detected by the IMPACT assay. The functional significance of this rearrangement is undetermined.
EED	0	MSKCC-DMP	P-0019337-T01-IM6	EED-intragenic	yes	unknown		unknown	EED (NM_003797) rearrangement: c.228_c.360+1399del Note: The EED rearrangement is an intragenic deletion (3230 bp) of exons 2-3. One of the breakpoints is within exon 2. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0019337-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3761-1245_c.3924inv Note: The CDK12 rearrangement is an inversion of exon 14. One of the breakpoints is within exon. The functional significance is undetermined.
IFT140	0	MSKCC-DMP	P-0019340-T01-IM6	RECQL-IFT140 fusion	yes	unknown		unknown	RECQL (NM_032941)  rearrangement: t(12;16)(p12.1;p13.3)(chr12:g.21644586::chr16:g.1564105) Note: The RECQL rearrangement is a translocation that may result in the truncation of exons 4-16. One of the breakpoints is within exon 4. The functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0019340-T01-IM6	RECQL-IFT140 fusion	yes	unknown		unknown	RECQL (NM_032941)  rearrangement: t(12;16)(p12.1;p13.3)(chr12:g.21644586::chr16:g.1564105) Note: The RECQL rearrangement is a translocation that may result in the truncation of exons 4-16. One of the breakpoints is within exon 4. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0019346-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1138-11170_c.4852del Note: The ARID1A rearrangement results in the deletion of exons 2-18. One of the breakpoints is within exon 18. The functional significance is undetermined.
NRG1	0	MSKCC-DMP	P-0019346-T01-IM6	CD74-NRG1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NRG1 (NM_013956) fusion (CD74 exons 1-7 fused with NRG1 exons 6-13) : t(5;8)(q32;p12)(chr5:g.149782781::chr8:g.32584466) known
CD74	0	MSKCC-DMP	P-0019346-T01-IM6	CD74-NRG1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - NRG1 (NM_013956) fusion (CD74 exons 1-7 fused with NRG1 exons 6-13) : t(5;8)(q32;p12)(chr5:g.149782781::chr8:g.32584466) known
THRA	0	MSKCC-DMP	P-0019350-T01-IM6	RARA-THRA fusion	yes	unknown		unknown	RARA (NM_000964) - THRA (NM_003250) rearrangement: c.1196:RARA_c.223-1330:THRAdup Note: The RARA - THRA rearrangement is a duplication that results in the fusion of RARA exons 1-9 with THRA exons 5-10. One of the breakpoints is within RARA exon 9. The functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0019350-T01-IM6	RARA-THRA fusion	yes	unknown		unknown	RARA (NM_000964) - THRA (NM_003250) rearrangement: c.1196:RARA_c.223-1330:THRAdup Note: The RARA - THRA rearrangement is a duplication that results in the fusion of RARA exons 1-9 with THRA exons 5-10. One of the breakpoints is within RARA exon 9. The functional significance is undetermined.
RASAL2	0	MSKCC-DMP	P-0019364-T01-IM6	IKBKE-RASAL2 fusion	yes	unknown		unknown	RASAL2 (NM_170692) - IKBKE(NM_014002) Rearrangement : c.1628-181:RASAL2_c.1076:IKBKEdel Note: The RASAL2 - IKBKE Rearrangement results in the fusion of exons 1-9 of RASAL2 with exons 10-22 of IKBKE. The breakpoint in IKBKE is within exon10. Its functional significance is undetermined.
IKBKE	0	MSKCC-DMP	P-0019364-T01-IM6	IKBKE-RASAL2 fusion	yes	unknown		unknown	RASAL2 (NM_170692) - IKBKE(NM_014002) Rearrangement : c.1628-181:RASAL2_c.1076:IKBKEdel Note: The RASAL2 - IKBKE Rearrangement results in the fusion of exons 1-9 of RASAL2 with exons 10-22 of IKBKE. The breakpoint in IKBKE is within exon10. Its functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0019370-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433)  Rearrangement : c.1097_c.*1138del Note: The ELF3  Rearrangement results in the partial deletion of exon9. One of the breakpoints is within exon9. Its functional significance is undetermined.
TIAM1	0	MSKCC-DMP	P-0019377-T01-IM6	NOTCH2-TIAM1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;21)(p21;q22.11)(chr1:g.120510065::chr21:g.32851230) Note: The NOTCH2 rearrangement is a translocation that may result in a truncation of exons 8-34. One of the breakpoints is within exon 8. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0019377-T01-IM6	NOTCH2-TIAM1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;21)(p21;q22.11)(chr1:g.120510065::chr21:g.32851230) Note: The NOTCH2 rearrangement is a translocation that may result in a truncation of exons 8-34. One of the breakpoints is within exon 8. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0019391-T01-IM6	EIF4A3-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.78114433::chr19:g.10251361) Note: The DNMT1 rearrangement is a translocation that may result in the truncation of exons 32-40. The functional significance is undetermined.
EIF4A3	0	MSKCC-DMP	P-0019391-T01-IM6	EIF4A3-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.78114433::chr19:g.10251361) Note: The DNMT1 rearrangement is a translocation that may result in the truncation of exons 32-40. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0019407-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.9887_c.13555del Note: The KMT2C rearrangement is an intragenic deletion with breakpoints in exons 43 and 52.
DOT1L	0	MSKCC-DMP	P-0019410-T01-IM6	CEACAM4-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482 rearrangement:  c.1797+140:DOT1L_chr19:g.42147951del Note: The DOT1L rearrangement is a deletion of exons 19-28.
CEACAM4	0	MSKCC-DMP	P-0019410-T01-IM6	CEACAM4-DOT1L fusion	yes	unknown		unknown	DOT1L (NM_032482 rearrangement:  c.1797+140:DOT1L_chr19:g.42147951del Note: The DOT1L rearrangement is a deletion of exons 19-28.
ERG	0	MSKCC-DMP	P-0019420-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.56-2768:TMPRSS2_c.-149-9232:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0019420-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.56-2768:TMPRSS2_c.-149-9232:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
ETV6	0	MSKCC-DMP	P-0019427-T01-IM6	ETV6-intragenic	yes	unknown		out of frame	ETV6 (NM_001987) rearrangement: c.33+23133_c.1009+5549dup Note: The ETV6 rearrangement is an intragenic duplication of exons 2-5. The functional significance is undetermined.
MADCAM1	0	MSKCC-DMP	P-0019433-T01-IM6	TCF3-MADCAM1 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: chr19:g.489738_c.101:TCF3inv Note: The TCF3 rearrangement is an inversion of exons 2-13. One of the breakpoints is within exon 2.The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0019433-T01-IM6	TCF3-MADCAM1 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: chr19:g.489738_c.101:TCF3inv Note: The TCF3 rearrangement is an inversion of exons 2-13. One of the breakpoints is within exon 2.The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0019436-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.-1943_c.122inv Note: The STK11 rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0019445-T01-IM6	GRIN2B-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - GRIN2B (NM_000834) rearrangement: c.463+2758:ETV6_c.-19+13931:GRIN2Bdel Note: The ETV6 - GRIN2B rearrangement is a deletion (2109678  bp) which results in the antisense fusion of ETV6 exon 4  to GRIN2B exon 1. The functional significance is undetermined.
GRIN2B	0	MSKCC-DMP	P-0019445-T01-IM6	GRIN2B-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - GRIN2B (NM_000834) rearrangement: c.463+2758:ETV6_c.-19+13931:GRIN2Bdel Note: The ETV6 - GRIN2B rearrangement is a deletion (2109678  bp) which results in the antisense fusion of ETV6 exon 4  to GRIN2B exon 1. The functional significance is undetermined.
PTPN11	0	MSKCC-DMP	P-0019456-T01-IM6	PTPN11-intragenic	yes	unknown		out of frame	PTPN11 (NM_002834)  rearrangement: c.854-145_c.1224+538dup Note: The PTPN11 rearrangement is an intragenic duplication of exons 8-10. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0019460-T01-IM6	LOC100132174-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: c.345_chr17:g.75766061inv Note: The PPM1D rearrangement is an inversion which includes exons 1-6 of PPM1D. One of the breakpoints is within PPM1D exon 1. The functional significance is undetermined.
LOC100132174	0	MSKCC-DMP	P-0019460-T01-IM6	LOC100132174-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: c.345_chr17:g.75766061inv Note: The PPM1D rearrangement is an inversion which includes exons 1-6 of PPM1D. One of the breakpoints is within PPM1D exon 1. The functional significance is undetermined.
OR7D2	0	MSKCC-DMP	P-0019460-T01-IM6	NF1-OR7D2 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(17;19)(q11.2;p13.2)(chr17:g.29646941::chr19:g.9293069) Note: The NF1 rearrangement is a translocation with a breakpoint within intron 36. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0019460-T01-IM6	NF1-OR7D2 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(17;19)(q11.2;p13.2)(chr17:g.29646941::chr19:g.9293069) Note: The NF1 rearrangement is a translocation with a breakpoint within intron 36. The functional significance is undetermined.
CEP85L	0	MSKCC-DMP	P-0019471-T01-IM6	CSF3R-CEP85L fusion	yes	unknown		unknown	CSF3R (NM_000760) Rearrangement : t(1;6)(p34.3;q22.31)(chr1:g.36939288::chr6:g.118964150) Note: The CSF3R Rearrangement results in the possible truncation of CSF3R. One of the breakpoints is within intron 5. Its functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0019471-T01-IM6	CSF3R-CEP85L fusion	yes	unknown		unknown	CSF3R (NM_000760) Rearrangement : t(1;6)(p34.3;q22.31)(chr1:g.36939288::chr6:g.118964150) Note: The CSF3R Rearrangement results in the possible truncation of CSF3R. One of the breakpoints is within intron 5. Its functional significance is undetermined.
CD79A	0	MSKCC-DMP	P-0019473-T01-IM6	MRPL36-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - MRPL36 (NM_032479) Rearrangement : t(5,19)(p15.33,q13.2)(chr5:g.1795958::chr19:g.42384823) Note: The CD79A - MRPL36  Rearrangement results in the fusion of exons 1-4 of CD79A with the promoter region of MRPL36. Its functional significance is undetermined.
MRPL36	0	MSKCC-DMP	P-0019473-T01-IM6	MRPL36-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - MRPL36 (NM_032479) Rearrangement : t(5,19)(p15.33,q13.2)(chr5:g.1795958::chr19:g.42384823) Note: The CD79A - MRPL36  Rearrangement results in the fusion of exons 1-4 of CD79A with the promoter region of MRPL36. Its functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0019489-T01-IM6	CAPN2-ELF3 fusion	yes	unknown		in frame	ELF3 (NM_004433) - CAPN2 (NM_001748) rearrangement: c.163+125:ELF3_c.1135+1210:CAPN2del Note: The ELF3 - CAPN2 rearrangement is a deletion that results in the fusion of ELF3 exons 1-2 with CAPN2 exons 10-21. The functional significance is undetermined.
CAPN2	0	MSKCC-DMP	P-0019489-T01-IM6	CAPN2-ELF3 fusion	yes	unknown		in frame	ELF3 (NM_004433) - CAPN2 (NM_001748) rearrangement: c.163+125:ELF3_c.1135+1210:CAPN2del Note: The ELF3 - CAPN2 rearrangement is a deletion that results in the fusion of ELF3 exons 1-2 with CAPN2 exons 10-21. The functional significance is undetermined.
CCND1	0	MSKCC-DMP	P-0019489-T01-IM6	NUMA1-CCND1 fusion	yes	unknown		unknown	CCND1 (NM_053056) rearrangement: c.574+39_g.71719423del Note: The CCND1 rearrangement results in the deletion of exons 4-5. The functional significance is undetermined.
NUMA1	0	MSKCC-DMP	P-0019489-T01-IM6	NUMA1-CCND1 fusion	yes	unknown		unknown	CCND1 (NM_053056) rearrangement: c.574+39_g.71719423del Note: The CCND1 rearrangement results in the deletion of exons 4-5. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0019491-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1490-486:EML4_c.3173-202:ALKinv Note: The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0019491-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1490-486:EML4_c.3173-202:ALKinv Note: The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.
ERICH1-AS1	0	MSKCC-DMP	P-0019492-T01-IM6	WHSC1L1-ERICH1-AS1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: g.691711_c.1807del Note: The WHSC1L1 rearrangement results in the deletion of exons 8-24. One of the breakpoints is within exon 8. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0019492-T01-IM6	WHSC1L1-ERICH1-AS1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: g.691711_c.1807del Note: The WHSC1L1 rearrangement results in the deletion of exons 8-24. One of the breakpoints is within exon 8. The functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0019512-T01-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: c.182+1384_c.605del Note: The INPPL1 rearrangement is an intragenic deletion of exons 2-5. One of the breakpoints is within exon 5.
ALK	0	MSKCC-DMP	P-0019513-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 19-29): c.1489+2278:EML4_c.3096:ALKinv Note: The EML4 - ALK fusion includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0019513-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 19-29): c.1489+2278:EML4_c.3096:ALKinv Note: The EML4 - ALK fusion includes the kinase domain of ALK.
CSDE1	0	MSKCC-DMP	P-0019529-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.1779-187_c.1892-394inv Note: The CSDE1 rearrangement is an inversion (1124  bp) of exon 16. The functional significance is undetermined.
EIF3H	0	MSKCC-DMP	P-0019529-T01-IM6	RAD21-EIF3H fusion	yes	unknown		in frame	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.688+24:RAD21_c.289+29346:EIF3Hdel Note: The RAD21 - EIF3H rearrangement is a deletion which results in the fusion of RAD21 exon 6 to EIF3H exon 3. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0019529-T01-IM6	RAD21-EIF3H fusion	yes	unknown		in frame	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.688+24:RAD21_c.289+29346:EIF3Hdel Note: The RAD21 - EIF3H rearrangement is a deletion which results in the fusion of RAD21 exon 6 to EIF3H exon 3. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0019533-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+6837:EML4_c.3173-100:ALKinv The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0019533-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+6837:EML4_c.3173-100:ALKinv The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.
KIF5B	0	MSKCC-DMP	P-0019535-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1726-2113:KIF5B_c.2137-119:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0019535-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1726-2113:KIF5B_c.2137-119:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
C1orf127	0	MSKCC-DMP	P-0019552-T01-IM6	MTOR-C1orf127 fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : chr1:g.10998818_c.6764:MTOR Note: The MTOR Rearrangement results in the duplication of exons 1-48. One of the breakpoints is within exon48. Its functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0019552-T01-IM6	MTOR-C1orf127 fusion	yes	unknown		unknown	MTOR (NM_004958) Rearrangement : chr1:g.10998818_c.6764:MTOR Note: The MTOR Rearrangement results in the duplication of exons 1-48. One of the breakpoints is within exon48. Its functional significance is undetermined.
GNB3	0	MSKCC-DMP	P-0019564-T01-IM6	CDK4-GNB3 fusion	yes	unknown		unknown	CDK4 (NM_000075) - GNB3 (NM_002075) rearrangement : c.71:CDK4_c.-155:GNB3inv Note: The CDK4 - GNB3 rearrangement is an inversion that results in the fusion of CDK4 exons 1-2 with GNB3 exons 2-11. One of the breakpoints is within CDK4 exon 2. The functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0019564-T01-IM6	CDK4-GNB3 fusion	yes	unknown		unknown	CDK4 (NM_000075) - GNB3 (NM_002075) rearrangement : c.71:CDK4_c.-155:GNB3inv Note: The CDK4 - GNB3 rearrangement is an inversion that results in the fusion of CDK4 exons 1-2 with GNB3 exons 2-11. One of the breakpoints is within CDK4 exon 2. The functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0019564-T01-IM6	PTPRR-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) rearrangement: c.1008_g.71085394del Note: The MDM2 rearrangement results in the deletion of exon 11. One of the breakpoints is within exon 11. The functional significance is undetermined.
PTPRR	0	MSKCC-DMP	P-0019564-T01-IM6	PTPRR-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) rearrangement: c.1008_g.71085394del Note: The MDM2 rearrangement results in the deletion of exon 11. One of the breakpoints is within exon 11. The functional significance is undetermined.
FXR2	0	MSKCC-DMP	P-0019580-T01-IM6	TP53-FXR2 fusion	yes	unknown		unknown	TP53 (NM_000546) - FXR2 (NM_004860) rearrangement: c.-28-733:TP53_c.660+186:FXR2del Note: The TP53 - FXR2 rearrangement is a deletion which results in the fusion of TP53 exon 2 to FXR2 exon 8. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0019580-T01-IM6	TP53-FXR2 fusion	yes	unknown		unknown	TP53 (NM_000546) - FXR2 (NM_004860) rearrangement: c.-28-733:TP53_c.660+186:FXR2del Note: The TP53 - FXR2 rearrangement is a deletion which results in the fusion of TP53 exon 2 to FXR2 exon 8. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0019581-T01-IM6	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c2478_c.2479del Note: The DNMT3A rearrangement is an intragenic deletion of exons 21-22. Both breakpoints are within exon. Multiple other DNMT3A deletions were detected in this sample. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0019584-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.1139_c.2467del Note: The KMT2D rearrangement is an intragenic deletion (1467 bp) of exons 9-10. Both breakpoints are within exon. The functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0019584-T01-IM6	INPP4B-intragenic	yes	unknown		out of frame	INPP4B (NM_001101669) rearrangement: c.1721-4219_c.1894-71del Note: The INPP4B rearrangement is an intragenic deletion (5493 bp) of exon 19. The functional significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0019600-T01-IM6	NFKBIA-intragenic	yes	unknown		unknown	NFKBIA (NM_020529) Rearrangement : c.-2947_ c.336+54inv Note : The NFKBIA Rearrangement results in the inversion of exons 1-2. One of the breakpoints is within the promoter region of NFKBIA. Its functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0019614-T01-IM6	TCF7L2-intragenic	yes	unknown		unknown	TCF7L2 (NM_001146274) Rearrangement : c.-2525_c.257-102del Note: The TCF7L2 Rearrangement results in the deletion of exons 1-2 of TCF7L2. One of the breakpoints is within the promoter region before the transcription start site of TCF7L2. Its functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0019637-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.544_c.-116-199del Note: The AXIN2 rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0019654-T01-IM6	ZNRF1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.75025150_c.4717inv Note: The CREBBP rearrangement is an inversion which includes exons 1-28 of CREBBP. One of the breakpoints is within CREBBP exon 28. The functional significance is undetermined.
ZNRF1	0	MSKCC-DMP	P-0019654-T01-IM6	ZNRF1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: chr16:g.75025150_c.4717inv Note: The CREBBP rearrangement is an inversion which includes exons 1-28 of CREBBP. One of the breakpoints is within CREBBP exon 28. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0019654-T01-IM6	SNHG7-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: chr9:g.139622044_c.5250dup Note: The NOTCH1 rearrangement is a duplication which includes NOTCH1 exons 1-28. One of the breakpoints is within NOTCH1 exon 28. The functional significance is undetermined.
SNHG7	0	MSKCC-DMP	P-0019654-T01-IM6	SNHG7-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: chr9:g.139622044_c.5250dup Note: The NOTCH1 rearrangement is a duplication which includes NOTCH1 exons 1-28. One of the breakpoints is within NOTCH1 exon 28. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0019659-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangement : c.1417_c.1756+409del Note: The FGFR1 Rearrangement results in the deletion of exons 11-13 of FGFR1. One of the breakpoints is within exon11. This includes the protein kinase domain of FGFR1.
ATXN2	0	MSKCC-DMP	P-0019663-T01-IM6	RET-ATXN2 fusion	yes	unknown		unknown	RET (NM_020975) - ATXN2 (NM_002973) Rearrangement : t(10;12)(q11.21;q24.13)(chr10:g.43608640:chr12:g.111918446) Note : The RET - ATXN2 Rearrangement results in the deletion of exons 10-20 of RET. This includes the protein kinase domain of RET. This event occurs in the background of other structural events affecting RET. Its functional significance is unknown.
RET	0	MSKCC-DMP	P-0019663-T01-IM6	RET-ATXN2 fusion	yes	unknown		unknown	RET (NM_020975) - ATXN2 (NM_002973) Rearrangement : t(10;12)(q11.21;q24.13)(chr10:g.43608640:chr12:g.111918446) Note : The RET - ATXN2 Rearrangement results in the deletion of exons 10-20 of RET. This includes the protein kinase domain of RET. This event occurs in the background of other structural events affecting RET. Its functional significance is unknown.
LIN52	0	MSKCC-DMP	P-0019663-T01-IM6	RET-LIN52 fusion	yes	unknown		out of frame	RET (NM_020975) - LIN52 (NM_001024674) Rearrangement : t(10;14)(p32.1;q12)(chr10:g.43608613:chr14:g.74562750) Note : The RET - LIN52 Rearrangement results in the fusion of exons 1-9 of RET with exons 4-6 of LIN52.This does not include the protein kinase domain of RET. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0019663-T01-IM6	RET-LIN52 fusion	yes	unknown		out of frame	RET (NM_020975) - LIN52 (NM_001024674) Rearrangement : t(10;14)(p32.1;q12)(chr10:g.43608613:chr14:g.74562750) Note : The RET - LIN52 Rearrangement results in the fusion of exons 1-9 of RET with exons 4-6 of LIN52.This does not include the protein kinase domain of RET. Its functional significance is undetermined.
FSTL4	0	MSKCC-DMP	P-0019676-T01-IM6	FLT4-FSTL4 fusion	yes	unknown		unknown	FSTL4 (NM_015082) - FLT4 (NM_182925) rearrangement: c.410-1835:FSTL4_c.867:FLT4dup Note: The FSTL4 - FLT4 rearrangement is an duplication that results in the fusion of FSTL4 exons 1-4 fused with FLT4 exons  7-30. One of the breakpoints is within FLT4 exon 4. The functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0019676-T01-IM6	FLT4-FSTL4 fusion	yes	unknown		unknown	FSTL4 (NM_015082) - FLT4 (NM_182925) rearrangement: c.410-1835:FSTL4_c.867:FLT4dup Note: The FSTL4 - FLT4 rearrangement is an duplication that results in the fusion of FSTL4 exons 1-4 fused with FLT4 exons  7-30. One of the breakpoints is within FLT4 exon 4. The functional significance is undetermined.
SPANXN4	0	MSKCC-DMP	P-0019680-T01-IM6	SMYD3-SPANXN4 fusion	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement: t(X;1)(q27.2;q44)(chrX:g.141735629::chr1:g.246518356) Note: The SMYD3 rearrangement is a translocation that may result in a truncation of  exons 2-12. The functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0019680-T01-IM6	SMYD3-SPANXN4 fusion	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement: t(X;1)(q27.2;q44)(chrX:g.141735629::chr1:g.246518356) Note: The SMYD3 rearrangement is a translocation that may result in a truncation of  exons 2-12. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0019692-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+1604:TMPRSS2_c.40-60431:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0019692-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+1604:TMPRSS2_c.40-60431:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0019695-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-941:TMPRSS2_c.40-61030:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0019695-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-941:TMPRSS2_c.40-61030:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
ARID1B	0	MSKCC-DMP	P-0019720-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.4013+799_c.4766del Note: The ARID1B rearrangement is an intragenic deletion of exons 17-18. One of the breakpoints is within exon 18.
TCF3	0	MSKCC-DMP	P-0019727-T01-IM6	PNPLA6-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.299-1_g.7615432del Note: The TCF3 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.
PNPLA6	0	MSKCC-DMP	P-0019727-T01-IM6	PNPLA6-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.299-1_g.7615432del Note: The TCF3 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0019731-T01-IM6	PHGDH-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement : c.5337:ARID1A_g.120250048inv Note: The ARID1A rearrangement results in the inversion of exon 20. One of the breakpoints is within exon 20. The functional significance is undetermined.
PHGDH	0	MSKCC-DMP	P-0019731-T01-IM6	PHGDH-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) rearrangement : c.5337:ARID1A_g.120250048inv Note: The ARID1A rearrangement results in the inversion of exon 20. One of the breakpoints is within exon 20. The functional significance is undetermined.
GSK3A	0	MSKCC-DMP	P-0019748-T01-IM6	CIC-GSK3A fusion	yes	unknown		unknown	GSK3A (NM_019884) - CIC (NM_015125) rearrangement: c.284-416:GSK3A_c.1531:CICdup Note: The GSK3A - CIC rearrangement is a duplication (49741 bp) which results in the antisense fusion of GSK3A exon 1 to CIC exon 10. One of the breakpoints is within CIC exon 10. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0019748-T01-IM6	CIC-GSK3A fusion	yes	unknown		unknown	GSK3A (NM_019884) - CIC (NM_015125) rearrangement: c.284-416:GSK3A_c.1531:CICdup Note: The GSK3A - CIC rearrangement is a duplication (49741 bp) which results in the antisense fusion of GSK3A exon 1 to CIC exon 10. One of the breakpoints is within CIC exon 10. The functional significance is undetermined.
ZZZ3	0	MSKCC-DMP	P-0019761-T01-IM6	FUBP1-ZZZ3 fusion	yes	unknown		unknown	FUBP1 (NM_003902) - ZZZ3 (NM_015534) rearrangement: c.250+104:FUBP1_c.-403+14447:ZZZ3del Note: The FUBP1 - ZZZ3 rearrangement is a deletion that results in the fusion of FUBP1 exons 1-3 with ZZZ3 exons 2-15. The functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0019761-T01-IM6	FUBP1-ZZZ3 fusion	yes	unknown		unknown	FUBP1 (NM_003902) - ZZZ3 (NM_015534) rearrangement: c.250+104:FUBP1_c.-403+14447:ZZZ3del Note: The FUBP1 - ZZZ3 rearrangement is a deletion that results in the fusion of FUBP1 exons 1-3 with ZZZ3 exons 2-15. The functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0019772-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.878_c.1126+76del Note: The DNMT3B rearrangement is an intragenic deletion of exons 8-10. One of the breakpoints is within exon 8. The functional significance is undetermined.
USP6	0	MSKCC-DMP	P-0019776-T01-IM6	CDK12-USP6 fusion	yes	unknown		in frame	USP6 (NM_004505) - CDK12 (NM_016507) rearrangement: c.2916-470:USP6_c.2847-101:CDK12del Note: The USP6 - CDK12 rearrangement is a deletion which results in the fusion of USP6 exon 24 to CDK12 exon 10. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0019776-T01-IM6	CDK12-USP6 fusion	yes	unknown		in frame	USP6 (NM_004505) - CDK12 (NM_016507) rearrangement: c.2916-470:USP6_c.2847-101:CDK12del Note: The USP6 - CDK12 rearrangement is a deletion which results in the fusion of USP6 exon 24 to CDK12 exon 10. The functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0019776-T01-IM6	INSR-intragenic	yes	unknown		unknown	INSR (NM_000208) rearrangement: c.1484-19_chr19:g.7100343dup Note: The INSR rearrangement is a duplication (67781  bp) which includes exons 7-22 of INSR. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0019776-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.356-254:SMARCA4_c.1334+15:CARM1dup Note: The SMARCA4 - CARM1 rearrangement is a duplication (65347 bp) which results in the fusion of SMARCA4 exon 3 to CARM1 exon 12. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0019776-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.356-254:SMARCA4_c.1334+15:CARM1dup Note: The SMARCA4 - CARM1 rearrangement is a duplication (65347 bp) which results in the fusion of SMARCA4 exon 3 to CARM1 exon 12. The functional significance is undetermined.
C20orf203	0	MSKCC-DMP	P-0019776-T01-IM6	DNMT3B-C20orf203 fusion	yes	unknown		unknown	C20orf203 (NM_182584) - DNMT3B (NM_006892) rearrangement: c.*1178-3794:C20orf203_c.551:DNMT3Bdup Note: The C20orf203 - DNMT3B rearrangement is a duplication (142871 bp) which includes C20orf203 exons 1-3 and DNMT3B exons1-6. One of the breakpoints is within DNMT3B exon 6. The functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0019776-T01-IM6	DNMT3B-C20orf203 fusion	yes	unknown		unknown	C20orf203 (NM_182584) - DNMT3B (NM_006892) rearrangement: c.*1178-3794:C20orf203_c.551:DNMT3Bdup Note: The C20orf203 - DNMT3B rearrangement is a duplication (142871 bp) which includes C20orf203 exons 1-3 and DNMT3B exons1-6. One of the breakpoints is within DNMT3B exon 6. The functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0019777-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: c.1103+333_c.2648-27inv Note: The FLT4 rearrangement is an inversion of exons 9-18. The functional significance is undetermined.
HNRNPA3	0	MSKCC-DMP	P-0019792-T01-IM6	MDM4-HNRNPA3 fusion	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: t(1;2)(q32.1;q31.2)(chr1:g.204518563::chr2:g.178015265) Note: The MDM4 rearrangement is a translocation with a breakpoint in exon 11 that may result in a truncation of a part of exon 11. The functional significance is undetermined.
MDM4	0	MSKCC-DMP	P-0019792-T01-IM6	MDM4-HNRNPA3 fusion	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: t(1;2)(q32.1;q31.2)(chr1:g.204518563::chr2:g.178015265) Note: The MDM4 rearrangement is a translocation with a breakpoint in exon 11 that may result in a truncation of a part of exon 11. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0019802-T01-IM6	TMEM65-RET fusion	yes	unknown		unknown	RET (NM_020975) Rearrangement : t(8;10)(q24.13;q11.21)(chr8:g.125313999::chr10:g.43610696) Note: The RET Rearrangement is a translocation event which results in the possible truncation of exons 12-20. This includes the protein kinase domain of RET.
TMEM65	0	MSKCC-DMP	P-0019802-T01-IM6	TMEM65-RET fusion	yes	unknown		unknown	RET (NM_020975) Rearrangement : t(8;10)(q24.13;q11.21)(chr8:g.125313999::chr10:g.43610696) Note: The RET Rearrangement is a translocation event which results in the possible truncation of exons 12-20. This includes the protein kinase domain of RET.
ETV6	0	MSKCC-DMP	P-0019836-T01-IM6	ANKS1B-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - ANKS1B (NM_152788) Rearrangement : c.463+383:ETV6_c.1757-48649:ANKS1Binv Note: The ETV6  - ANKS1B  Rearrangement results in the fusion of ETV6 exons 1-4 with ANKS1B exon 13-26. Its functional significance is undetermined.
ANKS1B	0	MSKCC-DMP	P-0019836-T01-IM6	ANKS1B-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - ANKS1B (NM_152788) Rearrangement : c.463+383:ETV6_c.1757-48649:ANKS1Binv Note: The ETV6  - ANKS1B  Rearrangement results in the fusion of ETV6 exons 1-4 with ANKS1B exon 13-26. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0019840-T01-IM6	EPHA3-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: t(3;12)(p11.1;p13.2)(chr3:g.88996930::chr12:g.12008769) Note: The ETV6 Rearrangement is a translocation event which results in the possible truncation of exons 4-8 of ETV6. Its functional significance is undetermined.
EPHA3	0	MSKCC-DMP	P-0019840-T01-IM6	EPHA3-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: t(3;12)(p11.1;p13.2)(chr3:g.88996930::chr12:g.12008769) Note: The ETV6 Rearrangement is a translocation event which results in the possible truncation of exons 4-8 of ETV6. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0019840-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-4117:TMPRSS2_c.18+11302:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0019840-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-4117:TMPRSS2_c.18+11302:ERGdel
DAOA-AS1	0	MSKCC-DMP	P-0019842-T01-IM6	IRS2-DAOA-AS1 fusion	yes	unknown		unknown	IRS2 (NM_003749) Rearrangement : c.3413:IRS2_chr13:g.106047899del Note: The IRS2 Rearrangement results in the deletion of exons1-2 of IRS2. One of the breakpoints is within exon1. Its functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0019842-T01-IM6	IRS2-DAOA-AS1 fusion	yes	unknown		unknown	IRS2 (NM_003749) Rearrangement : c.3413:IRS2_chr13:g.106047899del Note: The IRS2 Rearrangement results in the deletion of exons1-2 of IRS2. One of the breakpoints is within exon1. Its functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0019855-T01-IM6	CORO1B-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952)  - CORO1B (NM_020441) rearrangement: c.550:RPS6KB2_c.210:CORO1Bdup Note: The RPS6KB2 - CORO1B rearrangement is a duplication (9309 bp) which includes RPS6KB2 exons 1-7 and CORO1B exons 3-11. Both breakpoints are within exon. The functional significance is undetermined.
CORO1B	0	MSKCC-DMP	P-0019855-T01-IM6	CORO1B-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952)  - CORO1B (NM_020441) rearrangement: c.550:RPS6KB2_c.210:CORO1Bdup Note: The RPS6KB2 - CORO1B rearrangement is a duplication (9309 bp) which includes RPS6KB2 exons 1-7 and CORO1B exons 3-11. Both breakpoints are within exon. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0019855-T01-IM6	ANKFN1-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - ANKFN1 (NM_153228) rearrangement: c.4986:BRCA2_c.919+13903:ANKFN1dup Note: The BRCA1 - ANKFN1 rearrangement is a duplication (13243033 bp) which results in the antisense fusion of BRCA1 exon 15 to ANKFN1 exon 7. One of the breakpoints is within BRCA1 exon 15. The functional significance is undetermined.
ANKFN1	0	MSKCC-DMP	P-0019855-T01-IM6	ANKFN1-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - ANKFN1 (NM_153228) rearrangement: c.4986:BRCA2_c.919+13903:ANKFN1dup Note: The BRCA1 - ANKFN1 rearrangement is a duplication (13243033 bp) which results in the antisense fusion of BRCA1 exon 15 to ANKFN1 exon 7. One of the breakpoints is within BRCA1 exon 15. The functional significance is undetermined.
HIST1H3C	0	MSKCC-DMP	P-0019855-T01-IM6	HIST1H1C-HIST1H3C fusion	yes	unknown		unknown	HIST1H3C (NM_003531) rearrangement:  c.494_chr6:g.26049856dup Note: The HIST1H3C rearrangement is a duplication (6307 bp) of  HIST1H3C exon 1. One of the breakpoints is within exon. The functional significance is undetermined.
HIST1H1C	0	MSKCC-DMP	P-0019855-T01-IM6	HIST1H1C-HIST1H3C fusion	yes	unknown		unknown	HIST1H3C (NM_003531) rearrangement:  c.494_chr6:g.26049856dup Note: The HIST1H3C rearrangement is a duplication (6307 bp) of  HIST1H3C exon 1. One of the breakpoints is within exon. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0019855-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.1902_c.5083-357del Note: The KMT2C rearrangement is an intragenic deletion of exons 14-34. One of the breakpoints is within exon 14. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0019868-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.526_c.607+921del Note: The RB1 rearrangement is an intragenic deletion (2094 bp) of exons 5-6. One of the breakpoints is within exon 5. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0019880-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: chr18:g.48531265_c.37:SMAD4del Note: The SMAD4 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2.
ETV6	0	MSKCC-DMP	P-0019883-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.464-1161_c.1009+1080dup Note: The ETV6 rearrangement is an intragenic duplication of exon  5. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0019918-T01-IM6	TMPRSS2-intragenic	yes	unknown		in frame	TMPRSS2 (NM_001135099) rearrangement: c.56-3507_c.349+2123del Note: The TMPRSS2 rearrangement is an intragenic deletion of exons 2-3. This structural variant was observed in addition to other intragenic rearrangements involving TMRPSS2, suggesting a complex event that may not be detected by the IMPACT assay.
GLI1	0	MSKCC-DMP	P-0019922-T01-IM6	LGR5-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.2776:GLI1_chr12:g.71730061inv Note: The GLI1 rearrangement is an inversion of a part of exon 12. One of the breakpoints is within exon 12. The functional significance is undetermined.
LGR5	0	MSKCC-DMP	P-0019922-T01-IM6	LGR5-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.2776:GLI1_chr12:g.71730061inv Note: The GLI1 rearrangement is an inversion of a part of exon 12. One of the breakpoints is within exon 12. The functional significance is undetermined.
YIF1B	0	MSKCC-DMP	P-0019922-T01-IM6	EGFR-YIF1B fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;19)(p22.1;q13.2)(chr7:g.5523893::chr19:g.38806683) Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 17-28.
EGFR	0	MSKCC-DMP	P-0019922-T01-IM6	EGFR-YIF1B fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;19)(p22.1;q13.2)(chr7:g.5523893::chr19:g.38806683) Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 17-28.
ERBB2	0	MSKCC-DMP	P-0019924-T01-IM6	PITHD1-ERBB2 fusion	yes	unknown		out of frame	PITHD1 (NM_020362) - ERBB2 (NM_004448) rearrangement: t(1;17)(p36.11;q12)(chr1:g.24108131::chr17:g.37871691) Note: The PITHD1 - ERBB2 rearrangement is a translocation that results in an out-of-frame of PITHD1 exons 1-3 with ERBB2 exons 11-27, which include the kinase domain of ERBB2. This structural variant occurs along with ERRB2 copy number gain and may may be part of more complex rearrangement that may not be captured by the IMPACT assay. The functional significance of this rearrangement is undetermined.
PITHD1	0	MSKCC-DMP	P-0019924-T01-IM6	PITHD1-ERBB2 fusion	yes	unknown		out of frame	PITHD1 (NM_020362) - ERBB2 (NM_004448) rearrangement: t(1;17)(p36.11;q12)(chr1:g.24108131::chr17:g.37871691) Note: The PITHD1 - ERBB2 rearrangement is a translocation that results in an out-of-frame of PITHD1 exons 1-3 with ERBB2 exons 11-27, which include the kinase domain of ERBB2. This structural variant occurs along with ERRB2 copy number gain and may may be part of more complex rearrangement that may not be captured by the IMPACT assay. The functional significance of this rearrangement is undetermined.
CDK12	0	MSKCC-DMP	P-0019930-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.578_c.1046+2617del Note: The CDK12 rearrangement is an intragenic deletion of a part of exon 1.
ERG	0	MSKCC-DMP	P-0019930-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-826:TMPRSS2_c.40-59325:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0019930-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-826:TMPRSS2_c.40-59325:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
RUNX1	0	MSKCC-DMP	P-0019933-T01-IM6	LOC646522-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(11;21)(q25;q22.12)(chr11:g.133681309::chr21:g.36259357) Note: The RUNX1 rearrangement is a translocation that may result in the truncation of exons 4-9. One of the breakpoints is within exon 4. The functional significance is undetermined.
LOC646522	0	MSKCC-DMP	P-0019933-T01-IM6	LOC646522-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(11;21)(q25;q22.12)(chr11:g.133681309::chr21:g.36259357) Note: The RUNX1 rearrangement is a translocation that may result in the truncation of exons 4-9. One of the breakpoints is within exon 4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0019933-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4692:TMPRSS2_c.39+60021:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0019933-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4692:TMPRSS2_c.39+60021:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
BAP1	0	MSKCC-DMP	P-0019936-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.1683:BAP1_chr3:g.52454975del Note: BAP1 rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13.
PHF7	0	MSKCC-DMP	P-0019936-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.1683:BAP1_chr3:g.52454975del Note: BAP1 rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13.
BRCA2	0	MSKCC-DMP	P-0019937-T01-IM6	NBEA-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.2801:BRCA2_chr13:g.35518543inv Note: The BRCA2 rearrangement is an inversion of exons 11-27. One of the breakpoints is within exon 11. The functional significance is undetermined.
NBEA	0	MSKCC-DMP	P-0019937-T01-IM6	NBEA-BRCA2 fusion	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.2801:BRCA2_chr13:g.35518543inv Note: The BRCA2 rearrangement is an inversion of exons 11-27. One of the breakpoints is within exon 11. The functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0019957-T01-IM6	LINC00670-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) rearrangement: c.1086+11_chr17:g.12465067del Note: The MAP2K4 rearrangement is a deletion (421855 bp) which includes MAP2K4 exon 11. The functional significance is undetermined.
LINC00670	0	MSKCC-DMP	P-0019957-T01-IM6	LINC00670-MAP2K4 fusion	yes	unknown		unknown	MAP2K4 (NM_003010) rearrangement: c.1086+11_chr17:g.12465067del Note: The MAP2K4 rearrangement is a deletion (421855 bp) which includes MAP2K4 exon 11. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0019966-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement:  c.45+14986_c.263del Note: The NFE2L2 rearrangement is an intragenic deletion (15492 bp) of exon 2. One of the breakpoints is within exon. The functional significance is undetermined.
LINC01281	0	MSKCC-DMP	P-0019976-T01-IM6	MED12-LINC01281 fusion	yes	unknown		unknown	MED12 (NM_005120) Rearrangement : c.736-45:MED12_chrX:g.39187963dup Note: The MED12 Rearrangement results in the duplication of exons 1-5. Its functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0019976-T01-IM6	MED12-LINC01281 fusion	yes	unknown		unknown	MED12 (NM_005120) Rearrangement : c.736-45:MED12_chrX:g.39187963dup Note: The MED12 Rearrangement results in the duplication of exons 1-5. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0019977-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement : c.799-7084_c.1468del Note: The CREBBP Rearrangement results in the deletion of exons 3-6. One of the breakpoints is within exon6. Its functional significance is undetermined.
HCN1	0	MSKCC-DMP	P-0019991-T01-IM6	PAX8-HCN1 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement :  t(2;5)(q14.1;p11)(chr2:g.113978655::chr5:g.46376227) Note: The PAX8 Rearrangement is a translocation event which results in the possible truncation of exons 11-12 of PAX8. Its functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0019991-T01-IM6	PAX8-HCN1 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement :  t(2;5)(q14.1;p11)(chr2:g.113978655::chr5:g.46376227) Note: The PAX8 Rearrangement is a translocation event which results in the possible truncation of exons 11-12 of PAX8. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0020007-T01-IM6	ATP6V1H-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - ATP6V1H (NM_015941) rearrangement: t(8;17)(q11.23;q11.2)(chr8:g.54716159::chr17:g.29588857) Note: The NF1 - ATP6V1H rearrangement is a translocation with breakpoints within NF1 exon 35 and ATP6V1H intron 7. The functional significance is undetermined.
ATP6V1H	0	MSKCC-DMP	P-0020007-T01-IM6	ATP6V1H-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) - ATP6V1H (NM_015941) rearrangement: t(8;17)(q11.23;q11.2)(chr8:g.54716159::chr17:g.29588857) Note: The NF1 - ATP6V1H rearrangement is a translocation with breakpoints within NF1 exon 35 and ATP6V1H intron 7. The functional significance is undetermined.
RHOA	0	MSKCC-DMP	P-0020007-T01-IM6	DAG1-RHOA fusion	yes	unknown		unknown	RHOA (NM_001664) rearrangement: c.277+76_chr3:g.49493880dup Note: The RHOA rearrangement is a duplication (88095 bp) which includes RHOA exons 1-3. The functional significance is undetermined.
DAG1	0	MSKCC-DMP	P-0020007-T01-IM6	DAG1-RHOA fusion	yes	unknown		unknown	RHOA (NM_001664) rearrangement: c.277+76_chr3:g.49493880dup Note: The RHOA rearrangement is a duplication (88095 bp) which includes RHOA exons 1-3. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0020010-T01-IM6	ELAVL2-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - ELAVL2 (NM_004432)  rearrangement: c.156+68:CDKN2B_c.333+6227:ELAVL2inv Note: The CDKN2B - ELAVL2 rearrangement is an inversion which results in the antisense fusion of CDKN2B exon1 to ELAVL2 exon 3. The functional significance is undetermined.
ELAVL2	0	MSKCC-DMP	P-0020010-T01-IM6	ELAVL2-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - ELAVL2 (NM_004432)  rearrangement: c.156+68:CDKN2B_c.333+6227:ELAVL2inv Note: The CDKN2B - ELAVL2 rearrangement is an inversion which results in the antisense fusion of CDKN2B exon1 to ELAVL2 exon 3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0020013-T01-IM6	SEPT11-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - SEPT11 (NM_018243) rearrangement: t(4;21)(q21.1;q22.3)(chr4:g.77953453::chr21:g.42872227) Note: The TMPRSS2 - SEPT11 rearrangement is a translocation which results in the fusion of TMPRSS2 exon 1 to SEPT11 exon 10. The functional significance is undetermined. The possibility of a more complex rearrangement which results in a TMPRSS2 - ERG fusion cannot be excluded.
SEPT11	0	MSKCC-DMP	P-0020013-T01-IM6	SEPT11-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - SEPT11 (NM_018243) rearrangement: t(4;21)(q21.1;q22.3)(chr4:g.77953453::chr21:g.42872227) Note: The TMPRSS2 - SEPT11 rearrangement is a translocation which results in the fusion of TMPRSS2 exon 1 to SEPT11 exon 10. The functional significance is undetermined. The possibility of a more complex rearrangement which results in a TMPRSS2 - ERG fusion cannot be excluded.
ZFHX3	0	MSKCC-DMP	P-0020047-T01-IM6	RASL12-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) - RASL12 (NM_016563) rearrangement: t(15;16)(q22.31;q22.3)(chr15:g.65351569::chr16:g.72992701) Note: The ZFXH3 - RASL12 rearrangement is a reciprocal translocation which results in the antisense fusion of ZFHX3 exon2 to RASL12 exon 3. One of the breakpoints is within ZFHX3 exon 2. The functional significance is undetermined.
RASL12	0	MSKCC-DMP	P-0020047-T01-IM6	RASL12-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) - RASL12 (NM_016563) rearrangement: t(15;16)(q22.31;q22.3)(chr15:g.65351569::chr16:g.72992701) Note: The ZFXH3 - RASL12 rearrangement is a reciprocal translocation which results in the antisense fusion of ZFHX3 exon2 to RASL12 exon 3. One of the breakpoints is within ZFHX3 exon 2. The functional significance is undetermined.
CBFB	0	MSKCC-DMP	P-0020058-T01-IM6	C16orf70-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.282+70:CBFB_chr16:g.67139204del Note: The CBFB rearrangement is a deletion of exons 4-6.
C16orf70	0	MSKCC-DMP	P-0020058-T01-IM6	C16orf70-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.282+70:CBFB_chr16:g.67139204del Note: The CBFB rearrangement is a deletion of exons 4-6.
RET	0	MSKCC-DMP	P-0020078-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: c.1760-133_c.2136+245inv Note: The RET rearrangement is an intragenic inversion of exons 10-11. The functional significance is undetermined.
LOC338797	0	MSKCC-DMP	P-0020078-T01-IM6	POLE-LOC338797 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.131945557_c.801+43del Note: The POLE rearrangement is a deletion of exons 8-49.
POLE	0	MSKCC-DMP	P-0020078-T01-IM6	POLE-LOC338797 fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: chr12:g.131945557_c.801+43del Note: The POLE rearrangement is a deletion of exons 8-49.
ERG	0	MSKCC-DMP	P-0020078-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2608:TMPRSS2_c.236+3010:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0020078-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2608:TMPRSS2_c.236+3010:ERGdel
GATA3	0	MSKCC-DMP	P-0020080-T01-IM6	GATA3-intragenic	yes	unknown		unknown	GATA3 (NM_002051) rearrangement: c.1047+947_c.1179del Note: The GATA3 rearrangement is an intragenic deletion of a part of exon 6. One of the breakpoints is within exon 6.
ERG	0	MSKCC-DMP	P-0020083-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-3084:TMPRSS2_c.18+8091:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0020083-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-3084:TMPRSS2_c.18+8091:ERGdel
GREM1	0	MSKCC-DMP	P-0020086-T01-IM6	CHRNA6-GREM1 fusion	yes	unknown		unknown	GREM1 (NM_013372) rearrangement: t(8;15)(p11.21;q13.3)(chr8:g.42632131::chr15:g.33023043) Note: The GREM1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
CHRNA6	0	MSKCC-DMP	P-0020086-T01-IM6	CHRNA6-GREM1 fusion	yes	unknown		unknown	GREM1 (NM_013372) rearrangement: t(8;15)(p11.21;q13.3)(chr8:g.42632131::chr15:g.33023043) Note: The GREM1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
LINC01347	0	MSKCC-DMP	P-0020107-T01-IM6	AKT3-LINC01347 fusion	yes	unknown		unknown	AKT3 (NM_005465) Rearrangement : c.121:AKT3_chr1:g.242740337del Note: The AKT3 Rearrangement results in the duplication of exons 2-13 of AKT3. One of the breakpoints is within exon2. It included the protein kinase domain of AKT3.
AKT3	0	MSKCC-DMP	P-0020107-T01-IM6	AKT3-LINC01347 fusion	yes	unknown		unknown	AKT3 (NM_005465) Rearrangement : c.121:AKT3_chr1:g.242740337del Note: The AKT3 Rearrangement results in the duplication of exons 2-13 of AKT3. One of the breakpoints is within exon2. It included the protein kinase domain of AKT3.
LINC00114	0	MSKCC-DMP	P-0020111-T01-IM6	INSR-LINC00114 fusion	yes	unknown		unknown	INSR (NM_000208) Rearrangement : t(19,21)(p13.2,q22.2)(chr19:g.7126683::chr21:g.:40105340) Note: The INSR Rearrangement results in the possible truncation of exons 16-22 of INSR. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0020111-T01-IM6	INSR-LINC00114 fusion	yes	unknown		unknown	INSR (NM_000208) Rearrangement : t(19,21)(p13.2,q22.2)(chr19:g.7126683::chr21:g.:40105340) Note: The INSR Rearrangement results in the possible truncation of exons 16-22 of INSR. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0020111-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.127-247:TMPRSS2_c.39+4072:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 1-3 of ERG.  While this rearrangement does not produce a functional gene fusion, a more complex rearrangement resulting in a gene fusion cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0020111-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.127-247:TMPRSS2_c.39+4072:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 1-3 of ERG.  While this rearrangement does not produce a functional gene fusion, a more complex rearrangement resulting in a gene fusion cannot be ruled out.
PIK3R3	0	MSKCC-DMP	P-0020120-T01-IM6	PPAP2B-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.942-117_g.56333264del Note: The PIK3R3 rearrangement results in the inversion of exons 1-7. The functional significance is undetermined.
PPAP2B	0	MSKCC-DMP	P-0020120-T01-IM6	PPAP2B-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.942-117_g.56333264del Note: The PIK3R3 rearrangement results in the inversion of exons 1-7. The functional significance is undetermined.
CBL	0	MSKCC-DMP	P-0020120-T01-IM6	CBL-intragenic	yes	unknown		in frame	CBL (NM_005188) rearrangement: c.1095+42_c.1431+776del Note: The CBL rearrangement results in the deletion of exons 8-9. The functional significance is undetermined.
PPARG	0	MSKCC-DMP	P-0020122-T01-IM6	IQSEC1-PPARG fusion	yes	unknown		unknown	PPARG (NM_015869) rearrangement: c.1324_g.13048437del Note: The PPARG rearrangement results in the deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.
IQSEC1	0	MSKCC-DMP	P-0020122-T01-IM6	IQSEC1-PPARG fusion	yes	unknown		unknown	PPARG (NM_015869) rearrangement: c.1324_g.13048437del Note: The PPARG rearrangement results in the deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0020124-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused in-frame with ALK exons 20-29): c.1489+879:EML4_c.3172+372:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0020124-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused in-frame with ALK exons 20-29): c.1489+879:EML4_c.3172+372:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
ERG	0	MSKCC-DMP	P-0020132-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):c.127-1118:TMPRSS2_c.39+56940:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0020132-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):c.127-1118:TMPRSS2_c.39+56940:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
FGFR2	0	MSKCC-DMP	P-0020135-T01-IM6	BTBD16-FGFR2 fusion	yes	unknown		out of frame	FGFR2 (NM_000141) - BTBD16 (NM_144587) rearrangement: c.2302-167:FGFR2_c.386-107: BTBD16inv Note: The FGFR2 - BTBD16 rearrangement is an inversion which results in the fusion of FGFR2 exons 1-17 with BTBD16 exons 6 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
BTBD16	0	MSKCC-DMP	P-0020135-T01-IM6	BTBD16-FGFR2 fusion	yes	unknown		out of frame	FGFR2 (NM_000141) - BTBD16 (NM_144587) rearrangement: c.2302-167:FGFR2_c.386-107: BTBD16inv Note: The FGFR2 - BTBD16 rearrangement is an inversion which results in the fusion of FGFR2 exons 1-17 with BTBD16 exons 6 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
DMD	0	MSKCC-DMP	P-0020141-T01-IM6	TMPRSS2-DMD fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - DMD (NM_004006) rearrangement: t(21;X)(q22.3;p21.1)(chr21:g.42839577::chrX:g.32030014) Note: The TMPRSS2 - DMD rearrangement is a translocation which results in the antisense fusion of TMPRSS2 exons 1-13 with DMD exons 1-44. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0020141-T01-IM6	TMPRSS2-DMD fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - DMD (NM_004006) rearrangement: t(21;X)(q22.3;p21.1)(chr21:g.42839577::chrX:g.32030014) Note: The TMPRSS2 - DMD rearrangement is a translocation which results in the antisense fusion of TMPRSS2 exons 1-13 with DMD exons 1-44. The functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0020145-T01-IM6	TSC1-intragenic	yes	unknown		in frame	TSC1 (NM_000368) rearrangement: c.2208+230_c.2392-11del Note: The TSC1 rearrangement is an intragenic deletion of exon 18. The functional significance is undetermined.
STEAP4	0	MSKCC-DMP	P-0020148-T01-IM6	SOX2-STEAP4 fusion	yes	unknown		unknown	SOX2 (NM_003106) - STEAP4 (NM_024636) rearrangement: t(3;7)(q26.33;q21.12)(chr3:g.181430851::chr7:g.87911114) Note: The SOX2 - STEAP4 rearrangement is a reciprocal translocation that results in the fusion of SOX2 exon 1 with STEAP4 exon5. The functional significance is undetermined.
SOX2	0	MSKCC-DMP	P-0020148-T01-IM6	SOX2-STEAP4 fusion	yes	unknown		unknown	SOX2 (NM_003106) - STEAP4 (NM_024636) rearrangement: t(3;7)(q26.33;q21.12)(chr3:g.181430851::chr7:g.87911114) Note: The SOX2 - STEAP4 rearrangement is a reciprocal translocation that results in the fusion of SOX2 exon 1 with STEAP4 exon5. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0020151-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.2144_c.-18-941inv Note: The FAT1 rearrangement results in the inversion of 5UTR and exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0020157-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.191-1250_c.355del Note: The FGFR1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon. The functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0020158-T01-IM6	TG-NBN fusion	yes	unknown		out of frame	TG (NM_003235) - NBN (NM_002485) rearrangement: c.7036+2798:TG_c.481-22:NBNinv Note: The TG - NBN rearrangement is an inversion which results in the fusion of TG exons 1-40 to NBN exons 5-16. The functional significance is undetermined.
TG	0	MSKCC-DMP	P-0020158-T01-IM6	TG-NBN fusion	yes	unknown		out of frame	TG (NM_003235) - NBN (NM_002485) rearrangement: c.7036+2798:TG_c.481-22:NBNinv Note: The TG - NBN rearrangement is an inversion which results in the fusion of TG exons 1-40 to NBN exons 5-16. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0020161-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.2733-42_c.4101+196dup Note: The ARID1A rearrangement is a an intragenic duplication of exons 9-17. The functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0020161-T01-IM6	GNAS-intragenic	yes	unknown		out of frame	GNAS (NM_000516) rearrangement: c.213-600_c.719-33dup Note: The GNAS rearrangement is an intragenic duplication of exons 3-9. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0020161-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.-19_c.144+980inv Note: The RAD21 rearrangement is an inversion of exon 2. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0020167-T01-IM6	C6orf15-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.94_chr6:g.31067025dup Note: The MDC1 rearrangement is a duplication which includes exons 2-15 of MDC1. One of the breakpoints is within exon 2. The functional significance is undetermined.
C6orf15	0	MSKCC-DMP	P-0020167-T01-IM6	C6orf15-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.94_chr6:g.31067025dup Note: The MDC1 rearrangement is a duplication which includes exons 2-15 of MDC1. One of the breakpoints is within exon 2. The functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0020169-T01-IM6	TEK-intragenic	yes	unknown		out of frame	TEK (NM_000459) rearrangement: c.1183-76_c.1624+304dup Note: The TEK rearrangement is a duplication of exons 9-11. The functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0020175-T01-IM6	CALR-intragenic	yes	unknown		out of frame	CALR (NM_004343) Rearrangement : c.398-128_c.961-508dup Note: The CALR Rearrangement results in the duplication of exons4-7 of CALR.Its functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0020180-T02-IM6	MTUS2-FANCA fusion	yes	unknown		unknown	MTUS2 (NM_001033602) - FANCA (NM_000135) Rearrangement: t(13,16)(q12.3,q24.3)(chr13:g.29866903::chr16:g.89851360) Note: The MTUS2 - FANCA Rearrangement is a translocation event which results in the fusion of exons 1-4 of MTSU2 with exons 15-43. The breakpoint in FANCA is within exon15. Its functional significance is undetermined.
MTUS2	0	MSKCC-DMP	P-0020180-T02-IM6	MTUS2-FANCA fusion	yes	unknown		unknown	MTUS2 (NM_001033602) - FANCA (NM_000135) Rearrangement: t(13,16)(q12.3,q24.3)(chr13:g.29866903::chr16:g.89851360) Note: The MTUS2 - FANCA Rearrangement is a translocation event which results in the fusion of exons 1-4 of MTSU2 with exons 15-43. The breakpoint in FANCA is within exon15. Its functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0020186-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exon17 fused with BICC1 exon3 ): c.2302-1613:FGFR2_c.237+32254:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0020186-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exon17 fused with BICC1 exon3 ): c.2302-1613:FGFR2_c.237+32254:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
EZH1	0	MSKCC-DMP	P-0020188-T01-IM6	EZH1-intragenic	yes	unknown		unknown	EZH1(NM_001991) Rearrangement : c.367-292_640del Note: The EZH1 Rearrangement results in the intragenic deletion of exons 6-7. One of the breakpoints is within exon7. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0020189-T01-IM6	WDFY3-AS2-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(4,5)(q21.23,q22.1)(chr4:g.85927495::chr5:g.112175197) Note: The APC Rearrangement is a translocation that results in the possible truncation of APC. One of the breakpoints is within exon16. Its functional significance is undetermined.
WDFY3-AS2	0	MSKCC-DMP	P-0020189-T01-IM6	WDFY3-AS2-APC fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(4,5)(q21.23,q22.1)(chr4:g.85927495::chr5:g.112175197) Note: The APC Rearrangement is a translocation that results in the possible truncation of APC. One of the breakpoints is within exon16. Its functional significance is undetermined.
TECRL	0	MSKCC-DMP	P-0020218-T01-IM6	EPHA5-TECRL fusion	yes	unknown		unknown	TECRL (NM_001010874) - EPHA5 (NM_004439) rearrangement: c.234+7990:TECRL_c.1627:EPHA5dup Note: The TECRL - EPHA5 rearrangement is a duplication which results in the fusion of TECRL exon 1 to EPHA5 exon 7. One of the breakpoints is within EPHA5 exon 7. The functional significance is undetermined.
EPHA5	0	MSKCC-DMP	P-0020218-T01-IM6	EPHA5-TECRL fusion	yes	unknown		unknown	TECRL (NM_001010874) - EPHA5 (NM_004439) rearrangement: c.234+7990:TECRL_c.1627:EPHA5dup Note: The TECRL - EPHA5 rearrangement is a duplication which results in the fusion of TECRL exon 1 to EPHA5 exon 7. One of the breakpoints is within EPHA5 exon 7. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0020223-T01-IM6	BCAS3-NF1 fusion	yes	unknown		out of frame	NF1 (NM_001042492) - BCAS3 (NM_001099432) rearrangement: c.2850+95:NF1_c.2471-41787:BCAS3del Note: The NF1 - BCAS3 rearrangement is a deletion which results in the fusion of NF1 exons 1-21 with BCAS3 exons 24 - 25. The functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0020223-T01-IM6	BCAS3-NF1 fusion	yes	unknown		out of frame	NF1 (NM_001042492) - BCAS3 (NM_001099432) rearrangement: c.2850+95:NF1_c.2471-41787:BCAS3del Note: The NF1 - BCAS3 rearrangement is a deletion which results in the fusion of NF1 exons 1-21 with BCAS3 exons 24 - 25. The functional significance is undetermined.
SESN1	0	MSKCC-DMP	P-0020223-T01-IM6	NDST3-SESN1 fusion	yes	unknown		unknown	NDST3 (NM_004784) - SESN1 (NM_014454) rearrangement: t(10;11)(q26;q21)(chr10:g.126280260::chr11:g.17734059) Note: The NDST3 - SESN1 rearrangement is a translocation which results in the fusion of NDST3 exons 1-5 with SESN1 exons 2-10. One of the breakpoints is within SESN1 exon 2. The functional significance is undetermined.
NDST3	0	MSKCC-DMP	P-0020223-T01-IM6	NDST3-SESN1 fusion	yes	unknown		unknown	NDST3 (NM_004784) - SESN1 (NM_014454) rearrangement: t(10;11)(q26;q21)(chr10:g.126280260::chr11:g.17734059) Note: The NDST3 - SESN1 rearrangement is a translocation which results in the fusion of NDST3 exons 1-5 with SESN1 exons 2-10. One of the breakpoints is within SESN1 exon 2. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0020231-T01-IM6	MSH6-intragenic	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: chr2:g.47947631_c.1332:MSH6del Note: The MSH6 rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0020240-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: chr14:g.38310541_c.979:FOXA1del Note: The FOXA1 rearrangement results in the deletion of exons 1 - 2 (including the region upstream of transcription start site). One of the breakpoints is within FOXA1 exon 2. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0020244-T01-IM6	FKBP8-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - FKBP8 (NM_012181) rearrangement: c.3951+53:SMARCA4_c.293-771:FKBP8del Note: The SMARCA4 - FKBP8 rearrangement  is a deletion which results in the antisense fusion of SMARCA4 exons 1-28 to FKBP8 exons 1-2. Its functional significance is undetermined.
FKBP8	0	MSKCC-DMP	P-0020244-T01-IM6	FKBP8-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - FKBP8 (NM_012181) rearrangement: c.3951+53:SMARCA4_c.293-771:FKBP8del Note: The SMARCA4 - FKBP8 rearrangement  is a deletion which results in the antisense fusion of SMARCA4 exons 1-28 to FKBP8 exons 1-2. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0020245-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4021_c.5586del Note: The APC rearrangement results in the intragenic deletion of exon 16. The breakpoints are within exon 16. Its functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0020249-T01-IM6	GRB7-ERBB2 fusion	yes	unknown		unknown	GRB7 (NM_005310) - ERBB2 (NM_004448) rearrangement: c.-489:GRB7_c.1947-146:ERBB2dup Note: The GRB7-ERBB2 rearrangement is a duplication which results in fusion of GRB7 promoter to ERBB2 exons 17-27. Its functional significance is undetermined.
GRB7	0	MSKCC-DMP	P-0020249-T01-IM6	GRB7-ERBB2 fusion	yes	unknown		unknown	GRB7 (NM_005310) - ERBB2 (NM_004448) rearrangement: c.-489:GRB7_c.1947-146:ERBB2dup Note: The GRB7-ERBB2 rearrangement is a duplication which results in fusion of GRB7 promoter to ERBB2 exons 17-27. Its functional significance is undetermined.
CLYBL	0	MSKCC-DMP	P-0020263-T01-IM6	ERCC5-CLYBL fusion	yes	unknown		unknown	CLYBL (NM_206808) - ERCC5 (NM_000123) rearrangement: c.187+6723:CYLBL_c.1692:ERCC5del Note: The CYLBL - ERCC5 rearrangement is a deletion that results in the fusion of CYLBL exons 1-2 with ERCC5 exons 8-15. One of the breakpoints is within exon 8. The functional significance is undetermined
ERCC5	0	MSKCC-DMP	P-0020263-T01-IM6	ERCC5-CLYBL fusion	yes	unknown		unknown	CLYBL (NM_206808) - ERCC5 (NM_000123) rearrangement: c.187+6723:CYLBL_c.1692:ERCC5del Note: The CYLBL - ERCC5 rearrangement is a deletion that results in the fusion of CYLBL exons 1-2 with ERCC5 exons 8-15. One of the breakpoints is within exon 8. The functional significance is undetermined
CTNNB1	0	MSKCC-DMP	P-0020263-T01-IM6	PIGR-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: t(1;3)(q32.1;p22.1)(chr1:g.207117851::chr3:g.41266567) Note: The CTNNB1 rearrangement is a translocation that may result in a truncation of exons 4-15. One of the breakpoints is within exon 4. The functional significance is undetermined.
PIGR	0	MSKCC-DMP	P-0020263-T01-IM6	PIGR-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: t(1;3)(q32.1;p22.1)(chr1:g.207117851::chr3:g.41266567) Note: The CTNNB1 rearrangement is a translocation that may result in a truncation of exons 4-15. One of the breakpoints is within exon 4. The functional significance is undetermined.
GALNT12	0	MSKCC-DMP	P-0020263-T01-IM6	TGFBR1-GALNT12 fusion	yes	unknown		unknown	GALNT12 (NM_024642) - TGFBR1 (NM_004612) rearrangement: c.1606-679:GALNT12_c.156:TGFBR1del Note: The GALNT12 - TGFBR1 rearrangement is a deletion that results in the fusion of GALNT12 1-9 with TGFBR1 exons 2-9. One of the breakpoints is with TGFBR1 exon 2. The functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0020263-T01-IM6	TGFBR1-GALNT12 fusion	yes	unknown		unknown	GALNT12 (NM_024642) - TGFBR1 (NM_004612) rearrangement: c.1606-679:GALNT12_c.156:TGFBR1del Note: The GALNT12 - TGFBR1 rearrangement is a deletion that results in the fusion of GALNT12 1-9 with TGFBR1 exons 2-9. One of the breakpoints is with TGFBR1 exon 2. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0020273-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1914+131:KIF5B_c.2137-213:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0020273-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1914+131:KIF5B_c.2137-213:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CARM1	0	MSKCC-DMP	P-0020306-T01-IM6	OVGP1-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: t(1;19)(p13.2;p13.2)(chr1:g.111953456::chr19:g.11031667) Note: The CARM1 rearrangement is a translocation that may result in the truncation of exons 14-16. The functional significance is undetermined.
OVGP1	0	MSKCC-DMP	P-0020306-T01-IM6	OVGP1-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: t(1;19)(p13.2;p13.2)(chr1:g.111953456::chr19:g.11031667) Note: The CARM1 rearrangement is a translocation that may result in the truncation of exons 14-16. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0020313-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) Rearrangement : c.1921-3491_c.2251+69dup Note: The ARID1A Rearrangement results in the intragenic duplication of exons 5-6 of ARID1A. Its functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0020323-T01-IM6	NFIX-CALR fusion	yes	unknown		in frame	NFIX (NM_002501) - CALR (NM_004343) Rearrangement : c.27+550:NFIX_c.961-42:CALRdup Note: The NFIX - CALR Rearrangement results in the fusion of exons of NFIX with exons of CALR. Its functional significance is undetermined.
NFIX	0	MSKCC-DMP	P-0020323-T01-IM6	NFIX-CALR fusion	yes	unknown		in frame	NFIX (NM_002501) - CALR (NM_004343) Rearrangement : c.27+550:NFIX_c.961-42:CALRdup Note: The NFIX - CALR Rearrangement results in the fusion of exons of NFIX with exons of CALR. Its functional significance is undetermined.
BAZ1A	0	MSKCC-DMP	P-0020334-T01-IM6	MAX-BAZ1A fusion	yes	unknown		unknown	MAX (NM_002382) rearrangement: g.35276358_c.198inv Note: The MAX rearrangement results in the inversion of exons 4-5. One of the breakpoints is within exon 4. The functional significance is undetermined.
MAX	0	MSKCC-DMP	P-0020334-T01-IM6	MAX-BAZ1A fusion	yes	unknown		unknown	MAX (NM_002382) rearrangement: g.35276358_c.198inv Note: The MAX rearrangement results in the inversion of exons 4-5. One of the breakpoints is within exon 4. The functional significance is undetermined.
TSHR	0	MSKCC-DMP	P-0020334-T01-IM6	TSHR-intragenic	yes	unknown		unknown	TSHR (NM_000369) rearrangement: c.317+1950_c.457inv Note: The TSHR rearrangement results in the inversion of exons 4-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0020339-T01-IM6	DCXR-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - DCXR (NM_016286) Rearrangement : c.2297:BRCA1_c.-1737:DCXR Note: The BRCA1 - DCXR Rearrangement results in the fusion of exons 1-10 of BRCA1 with exons 1-8 of DCXR. The breakpoints are within exon10 of BRCA1 and the promoter region, before transcription start site for DCXR. Its functional significance is undetermined.
DCXR	0	MSKCC-DMP	P-0020339-T01-IM6	DCXR-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - DCXR (NM_016286) Rearrangement : c.2297:BRCA1_c.-1737:DCXR Note: The BRCA1 - DCXR Rearrangement results in the fusion of exons 1-10 of BRCA1 with exons 1-8 of DCXR. The breakpoints are within exon10 of BRCA1 and the promoter region, before transcription start site for DCXR. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0020341-T01-IM6	LOC102724927-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement :  chr16:g.3963526_c.-49:CREBBPdel Note: The CREBBP Rearrangement results in the deletion of the 5-UTR region of CREBBP. One of the breakpoints is within the 5-UTR region of CREEBP before the transcription start site. Its functional significance is undetermined.
LOC102724927	0	MSKCC-DMP	P-0020341-T01-IM6	LOC102724927-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement :  chr16:g.3963526_c.-49:CREBBPdel Note: The CREBBP Rearrangement results in the deletion of the 5-UTR region of CREBBP. One of the breakpoints is within the 5-UTR region of CREEBP before the transcription start site. Its functional significance is undetermined.
COQ4	0	MSKCC-DMP	P-0020353-T01-IM6	ABL1-COQ4 fusion	yes	unknown		unknown	ABL1 (NM_005157) - COQ4 (NM_016035) rearrangement: c.866:ABL1_c.402+2158:COQ4dup Note: The ABL1 - COQ4  rearrangement is a duplication that results in the fusion of ABL1 exons 1-5 with COQ4 exons 5-7 and includes part of the kinase domain of ABL1. One of the breakpoints is within ABL1 exon 5. The functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0020353-T01-IM6	ABL1-COQ4 fusion	yes	unknown		unknown	ABL1 (NM_005157) - COQ4 (NM_016035) rearrangement: c.866:ABL1_c.402+2158:COQ4dup Note: The ABL1 - COQ4  rearrangement is a duplication that results in the fusion of ABL1 exons 1-5 with COQ4 exons 5-7 and includes part of the kinase domain of ABL1. One of the breakpoints is within ABL1 exon 5. The functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0020355-T01-IM6	PLVAP-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) - PLVAP (NM_031310) rearrangement: c.774:DNAJB1_c.369+3270:PLVAPdup Note: The DNAJB1 - PLVAP rearrangement is a duplication that results in the fusion of DNAJB1 exons 1-2 with PLVAP exons 2-6. One of the breakpoints is within DNAJB1  exon 2. This event was observed along with a deletion involving these two genes and could be part of a more complex event not fully characterized by this assay. The functional significance is undetermined.
PLVAP	0	MSKCC-DMP	P-0020355-T01-IM6	PLVAP-DNAJB1 fusion	yes	unknown		unknown	DNAJB1 (NM_006145) - PLVAP (NM_031310) rearrangement: c.774:DNAJB1_c.369+3270:PLVAPdup Note: The DNAJB1 - PLVAP rearrangement is a duplication that results in the fusion of DNAJB1 exons 1-2 with PLVAP exons 2-6. One of the breakpoints is within DNAJB1  exon 2. This event was observed along with a deletion involving these two genes and could be part of a more complex event not fully characterized by this assay. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0020355-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 11-16): c.2275-36:FGFR3_c.1942-312:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0020355-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 11-16): c.2275-36:FGFR3_c.1942-312:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
YWHAE	0	MSKCC-DMP	P-0020358-T01-IM6	NOTCH1-YWHAE fusion	yes	unknown		in frame	YWHAE (NM_006761) - NOTCH1 (NM_017617) rearrangement: t(9;17)(q34.3;p13.3)(chr9:g.139397624::chr17:g.1296199) Note: The YWHAE - NOTCH1 rearrangement is a translocation that results in the fusion of YWHAE exon 1 with NOTCH exons 28-34. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0020358-T01-IM6	NOTCH1-YWHAE fusion	yes	unknown		in frame	YWHAE (NM_006761) - NOTCH1 (NM_017617) rearrangement: t(9;17)(q34.3;p13.3)(chr9:g.139397624::chr17:g.1296199) Note: The YWHAE - NOTCH1 rearrangement is a translocation that results in the fusion of YWHAE exon 1 with NOTCH exons 28-34. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0020365-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.3238_c.2732del Note: The POLE rearrangement results in the deletion of exons 24-26. One of the breakpoints is within exon 24 and the other is within exon 26. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0020377-T01-IM6	MEF2C-AS1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement : t(5;19)(q14.3;q13.2)(chr5:g.88595050::chr19:g.10246818) Note: The DNMT1 rearrangement is a translocation that may result in a truncation of exons 37-40. The functional significance is undetermined.
MEF2C-AS1	0	MSKCC-DMP	P-0020377-T01-IM6	MEF2C-AS1-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement : t(5;19)(q14.3;q13.2)(chr5:g.88595050::chr19:g.10246818) Note: The DNMT1 rearrangement is a translocation that may result in a truncation of exons 37-40. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0020394-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4024_c.4606+997inv Note: The DOT1L rearrangement is an intragenic deletion of a part of exon 27. The functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0020395-T01-IM6	LINC00477-RECQL fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.1175:RECQL_chr12:g.24778811del Note: The RECQL rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
LINC00477	0	MSKCC-DMP	P-0020395-T01-IM6	LINC00477-RECQL fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.1175:RECQL_chr12:g.24778811del Note: The RECQL rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0020396-T01-IM6	LINC00378-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1695+33:RB1_chr13:g.61408465del Note: The RB1 rearrangement is a deletion of exons 18-27. The functional significance is undetermined.
LINC00378	0	MSKCC-DMP	P-0020396-T01-IM6	LINC00378-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1695+33:RB1_chr13:g.61408465del Note: The RB1 rearrangement is a deletion of exons 18-27. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0020402-T01-IM6	C12orf74-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.464-5389:ETV6_chr12:g.93097480del Note: The ETV6 rearrangement is a deletion of exons 5-8. The functional significance is undetermined.
C12orf74	0	MSKCC-DMP	P-0020402-T01-IM6	C12orf74-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.464-5389:ETV6_chr12:g.93097480del Note: The ETV6 rearrangement is a deletion of exons 5-8. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0020406-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement:  c.994-345_c.*3317del Note: The TP53 rearrangement is an intragenic deletion of exons 10 -11. The functional significance is undetermined.
DDX21	0	MSKCC-DMP	P-0020410-T01-IM6	FGFR2-DDX21 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - DDX21 (NM_004728) fusion (FGFR2 exons 1-17 fused to DDX21 exons 2-15 ): c.2301+164:FGFR2_c.88-860:DDX21inv Note: The FGFR2 - DDX21 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0020410-T01-IM6	FGFR2-DDX21 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - DDX21 (NM_004728) fusion (FGFR2 exons 1-17 fused to DDX21 exons 2-15 ): c.2301+164:FGFR2_c.88-860:DDX21inv Note: The FGFR2 - DDX21 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
CTNNB1	0	MSKCC-DMP	P-0020414-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-534_c.389del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 2-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
GPS2	0	MSKCC-DMP	P-0020424-T01-IM6	GPS2-intragenic	yes	unknown		unknown	GPS2 (NM_004489) rearrangement: c.95-61_c.-837del Note: The GPS2 rearrangement results in the deletion of the promoter and exons 1-2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0020424-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+590:TMPRSS2_c.40-60250:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0020424-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+590:TMPRSS2_c.40-60250:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.
TP53	0	MSKCC-DMP	P-0020430-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1100+285_c.837del Note: The TP53 rearrangement results in the deletion of exons 8-10. One of the breakpoints is within exon 8. The functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0018779-T02-IM6	CNNM2-SUFU fusion	yes	unknown		unknown	CNNM2 (NM_017649) - SUFU (NM_016169) rearrangement: c.1621+38766:CNNM2_c.91:SUFUdup Note: The CNNM2 - SUFU rearrangement is a duplication that results in the fusion of CNNM2 exon 1 to SUFU exons 1-12. One of the breakpoints is within SUFU exon 1. The functional significance is undetermined.
CNNM2	0	MSKCC-DMP	P-0018779-T02-IM6	CNNM2-SUFU fusion	yes	unknown		unknown	CNNM2 (NM_017649) - SUFU (NM_016169) rearrangement: c.1621+38766:CNNM2_c.91:SUFUdup Note: The CNNM2 - SUFU rearrangement is a duplication that results in the fusion of CNNM2 exon 1 to SUFU exons 1-12. One of the breakpoints is within SUFU exon 1. The functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0025857-T01-IM6	ASB13-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: t(10;15)(p15.1;p13.3)(chr10:g.5637288::chr16:g.347033) Note: The AXIN1 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
ASB13	0	MSKCC-DMP	P-0025857-T01-IM6	ASB13-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: t(10;15)(p15.1;p13.3)(chr10:g.5637288::chr16:g.347033) Note: The AXIN1 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
BCL2	0	MSKCC-DMP	P-0025947-T01-IM6	NFATC1-BCL2 fusion	yes	unknown		unknown	BCL2 (NM_000633) Rearrangement :  c.585+75026:BCL2_c.2475+15186:NFATC1del Note: The BCL2 Rearrangement results in the deletion of exons 1-2 of BCL2. Its functional significance is undetermined.
NFATC1	0	MSKCC-DMP	P-0025947-T01-IM6	NFATC1-BCL2 fusion	yes	unknown		unknown	BCL2 (NM_000633) Rearrangement :  c.585+75026:BCL2_c.2475+15186:NFATC1del Note: The BCL2 Rearrangement results in the deletion of exons 1-2 of BCL2. Its functional significance is undetermined.
TGFBR2	0	MSKCC-DMP	P-0025947-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) Rearrangement : c.2_c.530-9893inv Note: The TGFBR2 Rearrangement results in the inversion of exons 1-4.One of the breakpoints is within exon1. Its functional significance is undetermined.
MIR4422	0	MSKCC-DMP	P-0025950-T01-IM6	NOTCH2-MIR4422 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : chr1:g.56269765_c.1303inv Note: The NOTCH2 Rearrangement results in the inversion of exons 8-34 of NOTCH2. One of the breakpoints is within exon8. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0025950-T01-IM6	NOTCH2-MIR4422 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : chr1:g.56269765_c.1303inv Note: The NOTCH2 Rearrangement results in the inversion of exons 8-34 of NOTCH2. One of the breakpoints is within exon8. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0025950-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement : chrX:g.44725131_c.2554del Note: The KDM6A Rearrangement results in the deletion of exons 1-17 of KDM6A. One of the breakpoints is within exon17.Its functional significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0026033-T01-IM6	MBIP-NFKBIA fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: c.228-99:NFKBIA_chr14:g.36803740del Note: The NFKBIA rearrangement is a deletion of exon 1. The functional significance is undetermined.
MBIP	0	MSKCC-DMP	P-0026033-T01-IM6	MBIP-NFKBIA fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: c.228-99:NFKBIA_chr14:g.36803740del Note: The NFKBIA rearrangement is a deletion of exon 1. The functional significance is undetermined.
EPB41L1	0	MSKCC-DMP	P-0026038-T01-IM6	SRC-EPB41L1 fusion	yes	unknown		in frame	EPB41L1 (NM_012156) - SRC (NM_198291) rearrangement: c.490+1264:EPB41L1_c.1040-143:SRCdel Note: The EPB41L1 - SRC rearrangement is a deletion that results in an in-frame fusion of  EPB41L1 exons 1-6 to SRC exons 11-14. The functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0026038-T01-IM6	SRC-EPB41L1 fusion	yes	unknown		in frame	EPB41L1 (NM_012156) - SRC (NM_198291) rearrangement: c.490+1264:EPB41L1_c.1040-143:SRCdel Note: The EPB41L1 - SRC rearrangement is a deletion that results in an in-frame fusion of  EPB41L1 exons 1-6 to SRC exons 11-14. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0026038-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.12181_c.*5095del Note: The KMT2C rearrangement is a deletion of exons 48 - 59. One of the breakpoints is within exon 48. The functional significance is undetermined.
TYRO3	0	MSKCC-DMP	P-0026039-T01-IM6	MGA-TYRO3 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.736:MGA_chr15:g.41871206inv Note: The MGA rearrangement is an inversion of exons 1-2. One of the breakpoints is in exon 2. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0026039-T01-IM6	MGA-TYRO3 fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.736:MGA_chr15:g.41871206inv Note: The MGA rearrangement is an inversion of exons 1-2. One of the breakpoints is in exon 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026072-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 fused to ERG exons 2-11): c.56-3750:TMPRSS2_c.-149-29688:ERG Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript. This structural variant was observed in addition to other rearrangements involving TMRPSS2, suggesting a complex event that may not be detected by the IMPACT assay.
TMPRSS2	0	MSKCC-DMP	P-0026072-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 fused to ERG exons 2-11): c.56-3750:TMPRSS2_c.-149-29688:ERG Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript. This structural variant was observed in addition to other rearrangements involving TMRPSS2, suggesting a complex event that may not be detected by the IMPACT assay.
SMAD4	0	MSKCC-DMP	P-0026123-T01-IM6	MIR4522-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: t(17;18)(q11.1;q21.1)(chr17:g.:25550206::chr18:g.48591841) Note: The SMAD4 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
MIR4522	0	MSKCC-DMP	P-0026123-T01-IM6	MIR4522-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: t(17;18)(q11.1;q21.1)(chr17:g.:25550206::chr18:g.48591841) Note: The SMAD4 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
LINC00323	0	MSKCC-DMP	P-0026123-T01-IM6	TMPRSS2-LINC00323 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42266771_c.1021inv Note: The TMPRSS2 rearrangement results in the inversion of exons 10-14. One of the breakpoints is within exon 10. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0026123-T01-IM6	TMPRSS2-LINC00323 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42266771_c.1021inv Note: The TMPRSS2 rearrangement results in the inversion of exons 10-14. One of the breakpoints is within exon 10. The functional significance is undetermined.
SULF2	0	MSKCC-DMP	P-0026200-T01-IM6	SPEN-SULF2 fusion	yes	unknown		unknown	SPEN (NM_015001) - SULF2 (NM_018837) rearrangement: t(1;20)(p36.13;q13.12)(chr1:g16265882::chr20:g.46321003) Note: The SPEN - SULF2 rearrangement is a translocation with breakpoints within SPEN exon 15 and SULF2 intron 4. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0026200-T01-IM6	SPEN-SULF2 fusion	yes	unknown		unknown	SPEN (NM_015001) - SULF2 (NM_018837) rearrangement: t(1;20)(p36.13;q13.12)(chr1:g16265882::chr20:g.46321003) Note: The SPEN - SULF2 rearrangement is a translocation with breakpoints within SPEN exon 15 and SULF2 intron 4. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0026106-T01-IM6	CDKN2B-AS1-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.471_chr9:g.22013106del Note: The CDKN2Ap14ARF rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
CDKN2B-AS1	0	MSKCC-DMP	P-0026106-T01-IM6	CDKN2B-AS1-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.471_chr9:g.22013106del Note: The CDKN2Ap14ARF rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0026106-T01-IM6	CDKN2B-AS1-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.305_chr9:g.22013106del Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
CDKN2B-AS1	0	MSKCC-DMP	P-0026106-T01-IM6	CDKN2B-AS1-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.305_chr9:g.22013106del Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0026108-T01-IM6	LOC388942-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+208_chr2:g.41387535del Note: The ALK rearrangement results in the deletion of exons 1-19.
LOC388942	0	MSKCC-DMP	P-0026108-T01-IM6	LOC388942-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+208_chr2:g.41387535del Note: The ALK rearrangement results in the deletion of exons 1-19.
TMPRSS2	0	MSKCC-DMP	P-0026152-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_005656) and ETV1 (NM_001163147) Fusion (TMPRSS2 exon2 with ETV1 exon5) : t(7;21)(p21.3;q22.2)(chr7:g.14017550::chr21:g.42872732)
ETV1	0	MSKCC-DMP	P-0026152-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_005656) and ETV1 (NM_001163147) Fusion (TMPRSS2 exon2 with ETV1 exon5) : t(7;21)(p21.3;q22.2)(chr7:g.14017550::chr21:g.42872732)
ERG	0	MSKCC-DMP	P-0026196-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026196-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
ERG	0	MSKCC-DMP	P-0026212-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026212-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11):  c.126+749:TMPRSS2_c.40-60753:ERGdel
ERG	0	MSKCC-DMP	P-0026159-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused to ERG exon2) : c.55+2059:TMPRSS2_c.19-16879:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026159-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused to ERG exon2) : c.55+2059:TMPRSS2_c.19-16879:ERGdel
FUT10	0	MSKCC-DMP	P-0026139-T01-IM6	FGFR1-FUT10 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangement : chr8:g.32978873_c.1798del Note: The FGFR1 Rearrangement results in the deletion of exons  14-19 of FGFR1. One of the breakpoints is within exon14. This includes the protein kinase domain of FGFR1. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0026139-T01-IM6	FGFR1-FUT10 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangement : chr8:g.32978873_c.1798del Note: The FGFR1 Rearrangement results in the deletion of exons  14-19 of FGFR1. One of the breakpoints is within exon14. This includes the protein kinase domain of FGFR1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026228-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 2-10): c.126+1056:TMPRSS2_c.18+9:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026228-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused in-frame to ERG exons 2-10): c.126+1056:TMPRSS2_c.18+9:ERGdel
ERG	0	MSKCC-DMP	P-0026377-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2) :c.56-3439:TMPRSS2_c.18+2268:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026377-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2) :c.56-3439:TMPRSS2_c.18+2268:ERGdel
ERG	0	MSKCC-DMP	P-0026153-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon4) : c.126+1611:TMPRSS2_c.39+54119:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026153-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon4) : c.126+1611:TMPRSS2_c.39+54119:ERGdel
RB1	0	MSKCC-DMP	P-0026289-T01-IM6	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) Rearrangement: c.1215+58_c.1332+582 Note: The RB1 rearrangement results in the deletion of exon 13.
FAT1	0	MSKCC-DMP	P-0026272-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.10658:FAT1_chr4:g.187636565inv Note: The FAT1 rearrangement is an inversion with breakpoints in exon19 and the 5UTR region. This structural variant was observed in addition to another rearrangement involving FAT1, suggesting a complex event that may not be detected by the IMPACT assay.
ARID1A	0	MSKCC-DMP	P-0026273-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1138-883_c.5122dup Note: The ARID1A rearrangement is an intragenic duplication of exons 2-19. One of the breakpoints is within exon 19. The functional significance is undetermined.
ERF	0	MSKCC-DMP	P-0026279-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: chr19:g.42764612_c.1756:CICdel Note: The CIC rearrangement is a deletion of exons 1-10. One of the breakpoints is within exon 10. The functionals significance is undetermined,
CIC	0	MSKCC-DMP	P-0026279-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: chr19:g.42764612_c.1756:CICdel Note: The CIC rearrangement is a deletion of exons 1-10. One of the breakpoints is within exon 10. The functionals significance is undetermined,
TFE3	0	MSKCC-DMP	P-0026351-T01-IM6	TFE3-intragenic	yes	unknown		out of frame	TFE3 (NM_006521) rearrangement: c.885+214_c.1136+665dup Note: The TFE3 rearrangement is an intragenic duplication of exons 6-8. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0026407-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-18 fused with ALK exons 20-29): c.1981-2450:EML4_c.3175:ALKinv Note: One of the breakpoints is within ALK exon 20 and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0026407-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-18 fused with ALK exons 20-29): c.1981-2450:EML4_c.3175:ALKinv Note: One of the breakpoints is within ALK exon 20 and includes the kinase domain of ALK.
CIC	0	MSKCC-DMP	P-0026409-T01-IM6	IQSEC1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: t(3;19)(p25.2;q13.2)(chr3:g.13023744::chr19:g.42793933) Note: The CIC rearrangement is a translocation involving exon 9. Multiple rearrangements involving CIC were detected in this sample and a more complex rearrangement resulting in a CIC fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated. Its functional significance is undetermined.
IQSEC1	0	MSKCC-DMP	P-0026409-T01-IM6	IQSEC1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: t(3;19)(p25.2;q13.2)(chr3:g.13023744::chr19:g.42793933) Note: The CIC rearrangement is a translocation involving exon 9. Multiple rearrangements involving CIC were detected in this sample and a more complex rearrangement resulting in a CIC fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026409-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+1383:TMPRSS2_c.18+21976:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026409-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+1383:TMPRSS2_c.18+21976:ERGdel
CDH12	0	MSKCC-DMP	P-0026151-T01-IM6	IL7R-CDH12 fusion	yes	unknown		unknown	IL7R (NM_002185) Rearrangement : chr5:g.22317231_c.318dup Note: The IL7R Rearrangement results in the duplication of exons 1-3 of IL7R. One of the breakpoints is within exon 3. The functional significance is undetermined.
IL7R	0	MSKCC-DMP	P-0026151-T01-IM6	IL7R-CDH12 fusion	yes	unknown		unknown	IL7R (NM_002185) Rearrangement : chr5:g.22317231_c.318dup Note: The IL7R Rearrangement results in the duplication of exons 1-3 of IL7R. One of the breakpoints is within exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026162-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-2434:TMPRSS2_c.40-58863:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0026162-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-2434:TMPRSS2_c.40-58863:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
WWTR1	0	MSKCC-DMP	P-0026175-T01-IM6	WWTR1-intragenic	yes	unknown		unknown	WWTR1 (NM_001168280) rearrangement: c.841_c.1018+1550inv Note: The WWTR1 rearrangement is an intragenic inversion of exons 5-6. One of the breakpoints is within exon 5. Its functional significance is undetermined
MAP3K1	0	MSKCC-DMP	P-0026175-T01-IM6	MAP3K1-intragenic	yes	unknown		out of frame	MAP3K1 (NM_005921) rearrangement: c.1965+7_c.2087+6del Note: The MAP3K1 rearrangement is an intragenic deletion of exon 11. Its functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0026390-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20): t(12;15)(p13.2;q25.3)(chr12:g.12016863::chr15:g.88651131) Note: The ETV6-NTRK3 fusion is an in-frame fusion and includes the protein kinase domain of NTRK3.
ETV6	0	MSKCC-DMP	P-0026390-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20): t(12;15)(p13.2;q25.3)(chr12:g.12016863::chr15:g.88651131) Note: The ETV6-NTRK3 fusion is an in-frame fusion and includes the protein kinase domain of NTRK3.
RNF157	0	MSKCC-DMP	P-0026422-T01-IM6	WHSC1L1-RNF157 fusion	yes	unknown		unknown	WHSC1L1 rearrangement: t(8;17)(p11.23;q25.1)(chr8:g.38172814::chr17:g.74191825) Note: The WHSC1L1 rearrangement is a translocation which involves exon 11. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0026422-T01-IM6	WHSC1L1-RNF157 fusion	yes	unknown		unknown	WHSC1L1 rearrangement: t(8;17)(p11.23;q25.1)(chr8:g.38172814::chr17:g.74191825) Note: The WHSC1L1 rearrangement is a translocation which involves exon 11. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0026430-T01-IM6	GNB1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - GNB1 (NM_002074) rearrangement: t(1;12)(p36/33;p13.2)(chr1:g.1785936::chr12:g.12019513) Note: The ETV6 - GNB1 rearrangement is a translocation which may result in the fusion of ETV6 exons 1-4 with GNB1 exons 2-11. Its functional significance is undetermined.
GNB1	0	MSKCC-DMP	P-0026430-T01-IM6	GNB1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) - GNB1 (NM_002074) rearrangement: t(1;12)(p36/33;p13.2)(chr1:g.1785936::chr12:g.12019513) Note: The ETV6 - GNB1 rearrangement is a translocation which may result in the fusion of ETV6 exons 1-4 with GNB1 exons 2-11. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0026448-T01-IM6	FAT1-intragenic	yes	unknown		in frame	FAT1 (NM_005245) rearrangement: c.13139-23_c.3581-5825del Note: The FAT1 rearrangement is an intragenic deletion of exons 4-26.
EPAS1	0	MSKCC-DMP	P-0026449-T01-IM6	EPAS1-intragenic	yes	unknown		unknown	EPAS1 (NM_001430) rearrangement: c.739_c.*265inv Note: The EPAS1 rearrangement is an intragenic inversion of exons 6 - 16. One of the breakpoints is within 3-UTR. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0026514-T01-IM6	WISP3-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - WISP3 (NM_003880) Rearrangement : t(6,21)(q21,q22.2)(chr6:g.112390072::chr21:g.30301865) Note: The TMPRSS2 - WISP3 Rearrangement results in the fusion of exon 1 of TMPRSS2 with exon 6 of WISP3. Its functional significance is undetermined.
WISP3	0	MSKCC-DMP	P-0026514-T01-IM6	WISP3-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - WISP3 (NM_003880) Rearrangement : t(6,21)(q21,q22.2)(chr6:g.112390072::chr21:g.30301865) Note: The TMPRSS2 - WISP3 Rearrangement results in the fusion of exon 1 of TMPRSS2 with exon 6 of WISP3. Its functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0024217-T02-IM6	RMDN2-FLT3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: t(2;13)(p22.2;q12.2)(chr2:g.38136570::chr13:g.28623971) Note: The FLT3 rearrangement is a translocation involving exon 3. ITs functional significance is undetermined.
RMDN2	0	MSKCC-DMP	P-0024217-T02-IM6	RMDN2-FLT3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: t(2;13)(p22.2;q12.2)(chr2:g.38136570::chr13:g.28623971) Note: The FLT3 rearrangement is a translocation involving exon 3. ITs functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024217-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_00444) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-10): c.56-4473:TMPRSS2_c.39+19351:ERG Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.
TMPRSS2	0	MSKCC-DMP	P-0024217-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_00444) fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-10): c.56-4473:TMPRSS2_c.39+19351:ERG Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.
EP300	0	MSKCC-DMP	P-0026484-T01-IM6	OR10H5-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(19;22)(p13.12;q13.2)(chr19:g.15895130::chr22:g.41573283) Note: The EP300 rearrangement is a translocation involving exon 31. One of the breakpoints is within exon 31. Its functional significance is undetermined.
OR10H5	0	MSKCC-DMP	P-0026484-T01-IM6	OR10H5-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(19;22)(p13.12;q13.2)(chr19:g.15895130::chr22:g.41573283) Note: The EP300 rearrangement is a translocation involving exon 31. One of the breakpoints is within exon 31. Its functional significance is undetermined.
SMURF2	0	MSKCC-DMP	P-0026485-T01-IM6	PDGFRB-SMURF2 fusion	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: t(5;17)(q32;q23.3)(chr5:g.149497245::chr17:g.62611355) Note: The PDGFRB rearrangement is a translocation involving exon 22. One of the breakpoints is within exon 22. Its functional significance is undetermined.
PDGFRB	0	MSKCC-DMP	P-0026485-T01-IM6	PDGFRB-SMURF2 fusion	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: t(5;17)(q32;q23.3)(chr5:g.149497245::chr17:g.62611355) Note: The PDGFRB rearrangement is a translocation involving exon 22. One of the breakpoints is within exon 22. Its functional significance is undetermined.
MIR8074	0	MSKCC-DMP	P-0026485-T01-IM6	PDPK1-MIR8074 fusion	yes	unknown		unknown	PDPK1 (NM_002613)  rearrangement: t(16;19)(p13.3;q13.41)(chr16:g.2645831::chr19:g.51698785) Note: The PDPK1 rearrangement is a translocation which involves exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.
PDPK1	0	MSKCC-DMP	P-0026485-T01-IM6	PDPK1-MIR8074 fusion	yes	unknown		unknown	PDPK1 (NM_002613)  rearrangement: t(16;19)(p13.3;q13.41)(chr16:g.2645831::chr19:g.51698785) Note: The PDPK1 rearrangement is a translocation which involves exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0026526-T01-IM6	GLOD4-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - GLOD4 (NM_016080) rearrangement: t(17;19)(p13.3;p13.3)(chr17:g.666026::chr19:g.5231417) Note: The PTPRS - GLOD 4 rearrangement is a translocation which may result in the fusion of PTPRS exons 1-14 with GLOD4 exon 9. One of the breakpoints is within PTPRS exon 14. Its functional significance is undetermined.
GLOD4	0	MSKCC-DMP	P-0026526-T01-IM6	GLOD4-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) - GLOD4 (NM_016080) rearrangement: t(17;19)(p13.3;p13.3)(chr17:g.666026::chr19:g.5231417) Note: The PTPRS - GLOD 4 rearrangement is a translocation which may result in the fusion of PTPRS exons 1-14 with GLOD4 exon 9. One of the breakpoints is within PTPRS exon 14. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0026526-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.404_c.1065+578del Note: The WHSC1L1 rearrangement is an intragenic deletion of exons 2-5. One of the breakpoints is within exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0026650-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fuses with ALK exons 20-29) : c.667+7374:EML4_c.3172+876:ALKinv Note: The EML4-ALK fusion is an in -frame fusion of EML4 exons 1-5 and  ALK exons 20 to 29. It includes the protein kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0026650-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fuses with ALK exons 20-29) : c.667+7374:EML4_c.3172+876:ALKinv Note: The EML4-ALK fusion is an in -frame fusion of EML4 exons 1-5 and  ALK exons 20 to 29. It includes the protein kinase domain of ALK.
MIR5093	0	MSKCC-DMP	P-0026652-T01-IM6	CD276-MIR5093 fusion	yes	unknown		unknown	CD276 (NM_001024736) Rearrangement : t(15,16)(q24.1,q24.1)(chr15:g.73995403::chr16:g.85397630) Note: The CD276 Rearrangement results in the truncation of exons 1-4 of CD276.One of the breakpoints is within exon4. Its functional significance is undetermined.
CD276	0	MSKCC-DMP	P-0026652-T01-IM6	CD276-MIR5093 fusion	yes	unknown		unknown	CD276 (NM_001024736) Rearrangement : t(15,16)(q24.1,q24.1)(chr15:g.73995403::chr16:g.85397630) Note: The CD276 Rearrangement results in the truncation of exons 1-4 of CD276.One of the breakpoints is within exon4. Its functional significance is undetermined.
FRAT1	0	MSKCC-DMP	P-0026667-T01-IM6	FGFR4-FRAT1 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - FRAT1 (NM_005479) rearrangement: t(5;10)(q35.2;q24.1)(chr5:g.:176518004::chr10:g.:99079984) Note: The FGFR4 - FRAT1 rearrangement is a translocation that results in the fusion of FRAT1 exon 1 with FGFR4 exons 5-18, including the kinase domain of FGFR4. Both breakpoints are within exon. The functional significance is undetermined.
FGFR4	0	MSKCC-DMP	P-0026667-T01-IM6	FGFR4-FRAT1 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - FRAT1 (NM_005479) rearrangement: t(5;10)(q35.2;q24.1)(chr5:g.:176518004::chr10:g.:99079984) Note: The FGFR4 - FRAT1 rearrangement is a translocation that results in the fusion of FRAT1 exon 1 with FGFR4 exons 5-18, including the kinase domain of FGFR4. Both breakpoints are within exon. The functional significance is undetermined.
KCTD1	0	MSKCC-DMP	P-0026544-T01-IM6	NAB2-KCTD1 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(12;18)(q13.3;q11.2)(chr12:g.57488056::chr18:g.24061792) Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0026544-T01-IM6	NAB2-KCTD1 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(12;18)(q13.3;q11.2)(chr12:g.57488056::chr18:g.24061792) Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
PLXDC1	0	MSKCC-DMP	P-0026673-T01-IM6	CDK12-PLXDC1 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: chr17:g.37297706_c.2847-104del Note: The CDK12 rearrangement is a deletion of exons 1-9. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0026673-T01-IM6	CDK12-PLXDC1 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: chr17:g.37297706_c.2847-104del Note: The CDK12 rearrangement is a deletion of exons 1-9. The functional significance is undetermined.
TMEM117	0	MSKCC-DMP	P-0026676-T01-IM6	PIK3R1-TMEM117 fusion	yes	unknown		out of frame	PIK3R1 (NM_181523) - TMEM117 (NM_032256) rearrangement: t(5;12)(5q13.1;12q12)(chr5:g.67522870::chr12:g.44739711) Note: The PIK3R1 - TMEME117 rearrangement is a translocation that results in the fusion of PIK3R1 exons 1-2 to TMEM117 exons 7-8. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0026676-T01-IM6	PIK3R1-TMEM117 fusion	yes	unknown		out of frame	PIK3R1 (NM_181523) - TMEM117 (NM_032256) rearrangement: t(5;12)(5q13.1;12q12)(chr5:g.67522870::chr12:g.44739711) Note: The PIK3R1 - TMEME117 rearrangement is a translocation that results in the fusion of PIK3R1 exons 1-2 to TMEM117 exons 7-8. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0026682-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.8814:ZFHX3_chr16:g.72801772del Note: The ZFHX3 rearrangement is a deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
LINC00578	0	MSKCC-DMP	P-0026689-T01-IM6	TP63-LINC00578 fusion	yes	unknown		unknown	TP63 (NM_003722):c.325-30del_g.177279698 Note: The TP63 rearrangement results in the intergenic deletion of TP63 exons 1-3. Its functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0026689-T01-IM6	TP63-LINC00578 fusion	yes	unknown		unknown	TP63 (NM_003722):c.325-30del_g.177279698 Note: The TP63 rearrangement results in the intergenic deletion of TP63 exons 1-3. Its functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0026691-T01-IM6	CDKN2Ap14ARF-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - CDKN2Ap14ARF (NM_058195) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713) Note: The TCF3 - CDKN2Ap14ARF rearrangement is a translocation that results in the fusion of TCF3 exons 1-5 with CDKN2Ap14ARF exon 2.  Its functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0026691-T01-IM6	CDKN2Ap14ARF-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - CDKN2Ap14ARF (NM_058195) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713) Note: The TCF3 - CDKN2Ap14ARF rearrangement is a translocation that results in the fusion of TCF3 exons 1-5 with CDKN2Ap14ARF exon 2.  Its functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0026691-T01-IM6	CDKN2Ap16INK4A-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - CDKN2Ap16INK4A (NM_000077) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713) Note: The TCF3 - CDKN2Ap16INK4A rearrangement is a translocation that results in the fusion of TCF3 exons 1-5 with CDKN2Ap16INK4A exons 2-3.  Its functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0026691-T01-IM6	CDKN2Ap16INK4A-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - CDKN2Ap16INK4A (NM_000077) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713) Note: The TCF3 - CDKN2Ap16INK4A rearrangement is a translocation that results in the fusion of TCF3 exons 1-5 with CDKN2Ap16INK4A exons 2-3.  Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0026693-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion:c.2544+156:KIF5_c.2136+327:RETinv. Note: The KIF58 - RET fusion is predicted to be in frame and it includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0026693-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion:c.2544+156:KIF5_c.2136+327:RETinv. Note: The KIF58 - RET fusion is predicted to be in frame and it includes the kinase domain of RET.
NTRK3	0	MSKCC-DMP	P-0026696-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20):t(12;15)(p13.2;q25.3)(chr12:g.12007967::chr15:g.88657925) The ETV6 - NTRK3 fusion is predicted to be in frame. It includes kinase domain of NTRK3.
ETV6	0	MSKCC-DMP	P-0026696-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20):t(12;15)(p13.2;q25.3)(chr12:g.12007967::chr15:g.88657925) The ETV6 - NTRK3 fusion is predicted to be in frame. It includes kinase domain of NTRK3.
KMT2D	0	MSKCC-DMP	P-0026699-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482):c.8207_c.7157inv. Note: The KMT2D rearrangement results in the inversion of exons 31-32. The breakpoint is within exon 31 and 32. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0026701-T01-IM6	TP53-intragenic	yes	unknown		in frame	TP53 (NM_000546):c.97-42_c.994-858del Note: The TP53 rearrangement is an intragenic deletion of exons 4 to 9.
PGR	0	MSKCC-DMP	P-0026804-T01-IM6	FBXL7-PGR fusion	yes	unknown		unknown	FBXL7 (NM_012304) - PGR (NM_000926) rearrangement: t(5;11)(p15.1;q22.1)(chr5:g.15611089::chr11:g.100920672) Note: The FBXL7 - PGR rearrangement is a translocation which results in the fusion of FBXL7 exon1 with PGR exons6-8. One of the breakpoints is within PGR exon 6. Its functional significance is undetermined.
FBXL7	0	MSKCC-DMP	P-0026804-T01-IM6	FBXL7-PGR fusion	yes	unknown		unknown	FBXL7 (NM_012304) - PGR (NM_000926) rearrangement: t(5;11)(p15.1;q22.1)(chr5:g.15611089::chr11:g.100920672) Note: The FBXL7 - PGR rearrangement is a translocation which results in the fusion of FBXL7 exon1 with PGR exons6-8. One of the breakpoints is within PGR exon 6. Its functional significance is undetermined.
CD79A	0	MSKCC-DMP	P-0026804-T01-IM6	SHMT1-CD79A fusion	yes	unknown		unknown	SHMT1 (NM_005412) - CD79A (NM_001783) rearrangement: t(17;19)(p11.2;q13.2)(chr17:g.18266040::chr19:g.42383410) Note: The SHMT1 - CD79A rearrangement is a translocation that involves 5-UTR of SHMT1 and intron 2 of CD79A. Its functional significance is undetermined.
SHMT1	0	MSKCC-DMP	P-0026804-T01-IM6	SHMT1-CD79A fusion	yes	unknown		unknown	SHMT1 (NM_005412) - CD79A (NM_001783) rearrangement: t(17;19)(p11.2;q13.2)(chr17:g.18266040::chr19:g.42383410) Note: The SHMT1 - CD79A rearrangement is a translocation that involves 5-UTR of SHMT1 and intron 2 of CD79A. Its functional significance is undetermined.
XRN2	0	MSKCC-DMP	P-0026806-T01-IM6	PTPRS-XRN2 fusion	yes	unknown		unknown	PTPRS (NM_002850) - XRN2 (NM_012255) rearrangement :t(19;20)(p13.3;p11.22)(chr19:g.5256123::chr20:g.21300045) Note: The PTPRS - XRN2 rearrangement is a translocation which results in the fusion of PTPRS exons 1 to 9  with XRN2 exons 2 - 30. One of the breakpoints is within the PTPRS exon9. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0026806-T01-IM6	PTPRS-XRN2 fusion	yes	unknown		unknown	PTPRS (NM_002850) - XRN2 (NM_012255) rearrangement :t(19;20)(p13.3;p11.22)(chr19:g.5256123::chr20:g.21300045) Note: The PTPRS - XRN2 rearrangement is a translocation which results in the fusion of PTPRS exons 1 to 9  with XRN2 exons 2 - 30. One of the breakpoints is within the PTPRS exon9. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026808-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3722:TMPRSS2_c.19-15805:ERGdel Note: The TMPRSS2 - ERG rearrangement is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0026808-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3722:TMPRSS2_c.19-15805:ERGdel Note: The TMPRSS2 - ERG rearrangement is predicted to be out of frame.
ERBB2	0	MSKCC-DMP	P-0026763-T01-IM6	LOC101928944-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q14.1;q12)(chr11:g.81026379::chr17:g.37871727) Note: The ERBB2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.
LOC101928944	0	MSKCC-DMP	P-0026763-T01-IM6	LOC101928944-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q14.1;q12)(chr11:g.81026379::chr17:g.37871727) Note: The ERBB2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0026768-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-1013:TMPRSS2_c.39+54142:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion
TMPRSS2	0	MSKCC-DMP	P-0026768-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-1013:TMPRSS2_c.39+54142:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion
KMT2C	0	MSKCC-DMP	P-0026768-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.11460+700_c.10619del Note: The KMT2C rearrangement results in the deletion of exon 43. One of the breakpoints is within exon 43. The functional significance is undetermined.
SVOPL	0	MSKCC-DMP	P-0026773-T01-IM6	BRAF-SVOPL fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1315-604:BRAF_chr7:g.138277426del Note: The BRAF rearrangement results in the deletion of exons 11-18. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0026773-T01-IM6	BRAF-SVOPL fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1315-604:BRAF_chr7:g.138277426del Note: The BRAF rearrangement results in the deletion of exons 11-18. The functional significance is undetermined.
GATA3	0	MSKCC-DMP	P-0026785-T01-IM6	LOC101929234-GATA3 fusion	yes	unknown		unknown	GATA3 (NM_002051) Rearrangement : c.327:GATA3_chr10:g.77209520dup Note: The GATA3 Rearrangement results in the duplication of exons 3-6. One of the breakpoints is within exon3. Its functional significance is unknown.
LOC101929234	0	MSKCC-DMP	P-0026785-T01-IM6	LOC101929234-GATA3 fusion	yes	unknown		unknown	GATA3 (NM_002051) Rearrangement : c.327:GATA3_chr10:g.77209520dup Note: The GATA3 Rearrangement results in the duplication of exons 3-6. One of the breakpoints is within exon3. Its functional significance is unknown.
TGFBR2	0	MSKCC-DMP	P-0026786-T01-IM6	PDE4B-TGFBR2 fusion	yes	unknown		unknown	TGFBR2 (NM_001024847) Rearrangement : t(1;3)(q11.2;p23)(chr1:g.66741811::chr3:g.30664833) Note: The TGFBR2 Rearrangement results in  the possible truncation of TGFBR2.One of the breakpoints is within intron2.Its functional significance is undetermined.
PDE4B	0	MSKCC-DMP	P-0026786-T01-IM6	PDE4B-TGFBR2 fusion	yes	unknown		unknown	TGFBR2 (NM_001024847) Rearrangement : t(1;3)(q11.2;p23)(chr1:g.66741811::chr3:g.30664833) Note: The TGFBR2 Rearrangement results in  the possible truncation of TGFBR2.One of the breakpoints is within intron2.Its functional significance is undetermined.
LOC101927043	0	MSKCC-DMP	P-0026841-T01-IM6	EPCAM-LOC101927043 fusion	yes	unknown		unknown	EPCAM (NM_002354) rearrangement: chr2:g.:47489472_c.209del Note: The EPCAM rearrangement is a deletion that includes EPCAM exons 1-3. One of the breakpoints is within EPCAM exon 3. The functional significance is undetermined.
EPCAM	0	MSKCC-DMP	P-0026841-T01-IM6	EPCAM-LOC101927043 fusion	yes	unknown		unknown	EPCAM (NM_002354) rearrangement: chr2:g.:47489472_c.209del Note: The EPCAM rearrangement is a deletion that includes EPCAM exons 1-3. One of the breakpoints is within EPCAM exon 3. The functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0026847-T01-IM6	B4GALNT3-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.1317_chr12:g.:648356del Note: The KDM5A rearrangement is a deletion that includes KDM5A exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
B4GALNT3	0	MSKCC-DMP	P-0026847-T01-IM6	B4GALNT3-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.1317_chr12:g.:648356del Note: The KDM5A rearrangement is a deletion that includes KDM5A exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
LUZP1	0	MSKCC-DMP	P-0026854-T01-IM6	MPL-LUZP1 fusion	yes	unknown		unknown	LUZP1 (NM_033631) - MPL (NM_005373) Rearrangement : c.-2991:LUZP1_c.1166-11:MPLinv Note: The LUZP1 - MPL Rearrangement results in the fusion of the promoter region of LUZP1, before the transcription start site, with exons 8-12 of MPL. Its functional significance is undetermined.
MPL	0	MSKCC-DMP	P-0026854-T01-IM6	MPL-LUZP1 fusion	yes	unknown		unknown	LUZP1 (NM_033631) - MPL (NM_005373) Rearrangement : c.-2991:LUZP1_c.1166-11:MPLinv Note: The LUZP1 - MPL Rearrangement results in the fusion of the promoter region of LUZP1, before the transcription start site, with exons 8-12 of MPL. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0022151-T01-IM6	ITK-DOT1L fusion	yes	unknown		in frame	DOT1L (NM_032482) - ITK (NM_005546) rearrangement: t(5;19)(q33.3;p13.3)(chr5:g.156631381::chr19:g.2193796) Note: The DOT1L - ITK rearrangement is a translocation that results in an in-frame fusion of DOT1L exons 1-6 with ITK exons 2-17. The functional significance is undetermined.
ITK	0	MSKCC-DMP	P-0022151-T01-IM6	ITK-DOT1L fusion	yes	unknown		in frame	DOT1L (NM_032482) - ITK (NM_005546) rearrangement: t(5;19)(q33.3;p13.3)(chr5:g.156631381::chr19:g.2193796) Note: The DOT1L - ITK rearrangement is a translocation that results in an in-frame fusion of DOT1L exons 1-6 with ITK exons 2-17. The functional significance is undetermined.
CTD-2151A2.1	0	MSKCC-DMP	P-0022151-T01-IM6	APC-CTD-2151A2.1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.98951265_c.7014:APCinv Note: The APC rearrangement is an inversion with a breakpoint within exon 16. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0022151-T01-IM6	APC-CTD-2151A2.1 fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: chr5:g.98951265_c.7014:APCinv Note: The APC rearrangement is an inversion with a breakpoint within exon 16. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0024549-T03-IM6	TPR-NTRK1 fusion	yes	unknown		in frame	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+651_c.1196-73inv Note: The TPR - NTRK1 fusion is predicted to be in frame. One of the breakpoints is within TPR exon 21. The functional significance is undetermined.
TPR	0	MSKCC-DMP	P-0024549-T03-IM6	TPR-NTRK1 fusion	yes	unknown		in frame	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+651_c.1196-73inv Note: The TPR - NTRK1 fusion is predicted to be in frame. One of the breakpoints is within TPR exon 21. The functional significance is undetermined.
RAD51B	0	MSKCC-DMP	P-0026831-T01-IM6	ZFP36L1-RAD51B fusion	yes	unknown		unknown	RAD51B (NM_133509) rearrangement: c.1037-91C:RAD51B_chr14:g.69090674del Note: The RAD51B rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.
ZFP36L1	0	MSKCC-DMP	P-0026831-T01-IM6	ZFP36L1-RAD51B fusion	yes	unknown		unknown	RAD51B (NM_133509) rearrangement: c.1037-91C:RAD51B_chr14:g.69090674del Note: The RAD51B rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0026930-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1351-32_c.3866+5dup Note: The ARID1A rearrangement is an intragenic duplication of exons 3-15.
ADCY1	0	MSKCC-DMP	P-0026930-T01-IM6	CSF1R-ADCY1 fusion	yes	unknown		unknown	ADCY1 (NM_021116) - CSF1R (NM_005211) rearrangement: t(5;7)(q32;p12.3)(chr5:g.149452928::chr7:g.45629335) Note: The ADCY1 - CSF1R rearrangement is a translocation that results in the fusion of ADCY1 exon 1 to CSF1R exons 7-22. One of the breakpoints is within CSF1R exon 7. The functional significance is undetermined.
CSF1R	0	MSKCC-DMP	P-0026930-T01-IM6	CSF1R-ADCY1 fusion	yes	unknown		unknown	ADCY1 (NM_021116) - CSF1R (NM_005211) rearrangement: t(5;7)(q32;p12.3)(chr5:g.149452928::chr7:g.45629335) Note: The ADCY1 - CSF1R rearrangement is a translocation that results in the fusion of ADCY1 exon 1 to CSF1R exons 7-22. One of the breakpoints is within CSF1R exon 7. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0026937-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2437_c.2611+842deldel Note: The WHSC1L1 rearrangement is an intragenic deletion of exons 13-14. One of the breakpoints is within exon 13. The functional significance is undetermined.
EMID1	0	MSKCC-DMP	P-0026992-T01-IM6	EWSR1-EMID1 fusion	yes	unknown		unknown	EMID1 (NM_133455) - EWSR1 (NM_013986) rearrangement: c.320-2287_c.794-10inv. Note: The EMID1 - EWSR1 rearrangement is an inversion that includes EMID1 exons 1-3 and EWSR1 exons 1-10. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0026992-T01-IM6	EWSR1-EMID1 fusion	yes	unknown		unknown	EMID1 (NM_133455) - EWSR1 (NM_013986) rearrangement: c.320-2287_c.794-10inv. Note: The EMID1 - EWSR1 rearrangement is an inversion that includes EMID1 exons 1-3 and EWSR1 exons 1-10. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0009689-T01-IM5	BCAS3-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.365:PPM1D_c.2470+37341:BCAS3del Note: The PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement is a deletion that results in the fusion of PPM1D exon 1 with BCAS3 exons 23-25. One of the breakpoint is within PPM1D exon 1. The functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0009689-T01-IM5	BCAS3-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.365:PPM1D_c.2470+37341:BCAS3del Note: The PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement is a deletion that results in the fusion of PPM1D exon 1 with BCAS3 exons 23-25. One of the breakpoint is within PPM1D exon 1. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0010689-T01-IM5	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.1836_c.3312+2164dup Note: The PBRM1 rearrangement is an intragenic duplication of exons 16-21. One of the breakpoints is within exon 16. The functional significance is undetermined.
CUL1	0	MSKCC-DMP	P-0011147-T01-IM5	EZH2-CUL1 fusion	yes	unknown		unknown	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement : c.790-3028:CUL1_c.2182:EZH2del Note: The CUL1-EZH2 rearrangement event results in the deletion of EZH2 exons 19-20. One of the breakpoints is within EZH2 exon19.
EZH2	0	MSKCC-DMP	P-0011147-T01-IM5	EZH2-CUL1 fusion	yes	unknown		unknown	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement : c.790-3028:CUL1_c.2182:EZH2del Note: The CUL1-EZH2 rearrangement event results in the deletion of EZH2 exons 19-20. One of the breakpoints is within EZH2 exon19.
DUSP26	0	MSKCC-DMP	P-0018197-T01-IM6	FGFR1-DUSP26 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement : g.33895943_c.1744:FGFR1inv Note: The FGFR1 rearrangement results in an inversion of exons 13-19 . One of the breakpoints is within exon 13. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0018197-T01-IM6	FGFR1-DUSP26 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement : g.33895943_c.1744:FGFR1inv Note: The FGFR1 rearrangement results in an inversion of exons 13-19 . One of the breakpoints is within exon 13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0024119-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-1097:TMPRSS2_chr21:g.39992544del Note: The TMPRSS2 rearrangement is a deletion of exons 2-14. The functional significance is undetermined. The possibility of a more complex rearrangement resulting in a TMPRSS2 -ERG fusion cannot be excluded.
TMPRSS2	0	MSKCC-DMP	P-0024119-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-1097:TMPRSS2_chr21:g.39992544del Note: The TMPRSS2 rearrangement is a deletion of exons 2-14. The functional significance is undetermined. The possibility of a more complex rearrangement resulting in a TMPRSS2 -ERG fusion cannot be excluded.
FUBP1	0	MSKCC-DMP	P-0026974-T01-IM6	DDAH1-FUBP1 fusion	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.1705+69:FUBP1_chr1:g.85991712inv Note: The FUBP1 rearrangement is an inversion of exons 1-17. The functional significance is undetermined.
DDAH1	0	MSKCC-DMP	P-0026974-T01-IM6	DDAH1-FUBP1 fusion	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.1705+69:FUBP1_chr1:g.85991712inv Note: The FUBP1 rearrangement is an inversion of exons 1-17. The functional significance is undetermined.
PSMB8	0	MSKCC-DMP	P-0027021-T01-IM6	TAP1-PSMB8 fusion	yes	unknown		unknown	TAP1 (NM_000593) - PSMB8 (NM_148919) Rearrangement (TAP1 exon10 with PSMB8 exon5 ) : c.2219:TAP1_c.538-80:PSMB8del Note: The TAP1 - PSMB8 Rearrangement results in the fusion of TAP1 exon 10 with PSMB8 exon 5. The breakpoint in TAP1 is within exon 10. The functional significance is undetermined.
TAP1	0	MSKCC-DMP	P-0027021-T01-IM6	TAP1-PSMB8 fusion	yes	unknown		unknown	TAP1 (NM_000593) - PSMB8 (NM_148919) Rearrangement (TAP1 exon10 with PSMB8 exon5 ) : c.2219:TAP1_c.538-80:PSMB8del Note: The TAP1 - PSMB8 Rearrangement results in the fusion of TAP1 exon 10 with PSMB8 exon 5. The breakpoint in TAP1 is within exon 10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027073-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3724:TMPRSS2_c.18+19585:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0027073-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3724:TMPRSS2_c.18+19585:ERGdel
OR10A5	0	MSKCC-DMP	P-0027079-T01-IM6	CUL3-OR10A5 fusion	yes	unknown		unknown	CUL3 (NM_003590) rearrangement: t(2;11)(q36.2;p15.4)(chr2:g.225378244::chr11:g.6857883) Note: The CUL3 rearrangement is a translocation with a breakpoint within CUL3 exon 5. The functional significance is undetermined.
CUL3	0	MSKCC-DMP	P-0027079-T01-IM6	CUL3-OR10A5 fusion	yes	unknown		unknown	CUL3 (NM_003590) rearrangement: t(2;11)(q36.2;p15.4)(chr2:g.225378244::chr11:g.6857883) Note: The CUL3 rearrangement is a translocation with a breakpoint within CUL3 exon 5. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0027081-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.1573+53_c.2463+929inv Note: The CREBBP rearrangement is an inversion of exons 7-13. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0027081-T01-IM6	NBR2-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.3576_chr17:g.41287037del Note: The BRCA1 rearrangement is a deletion that includes BRCA1 exons 1-10. One of the breakpoints is within BRCA1 exon 10.
NBR2	0	MSKCC-DMP	P-0027081-T01-IM6	NBR2-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.3576_chr17:g.41287037del Note: The BRCA1 rearrangement is a deletion that includes BRCA1 exons 1-10. One of the breakpoints is within BRCA1 exon 10.
RNU6-33P	0	MSKCC-DMP	P-0027082-T01-IM6	KMT2C-RNU6-33P fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: chr7:g.150053665_c.13391:KMT2Cdel Note: The KMT2C rearrangement is a deletion that includes KMT2C exons 52-59. One of the breakpoints is within exon 52. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0027082-T01-IM6	KMT2C-RNU6-33P fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: chr7:g.150053665_c.13391:KMT2Cdel Note: The KMT2C rearrangement is a deletion that includes KMT2C exons 52-59. One of the breakpoints is within exon 52. The functional significance is undetermined.
CUL1	0	MSKCC-DMP	P-0027086-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.105:EZH2_chr7:g.148458308del Note: The EZH2 rearrangement results in the deletion of exons 2-20. One of the breakpoints is within exon 2. Its functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0027086-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.105:EZH2_chr7:g.148458308del Note: The EZH2 rearrangement results in the deletion of exons 2-20. One of the breakpoints is within exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0027092-T01-IM6	PLEKHH2-ALK fusion	yes	unknown		in frame	PLEKHH2 (NM_172069) - ALK (NM_004304) rearrangement: c.502+545: PLEKHH2_c.3173-112:ALKinv Note: The PLEKHH2 - ALK rearrangement is an inversion which results in the fusion of PLEKHH2 exons 1-6 with ALK exons 20-29. Its functional significance is undetermined.
PLEKHH2	0	MSKCC-DMP	P-0027092-T01-IM6	PLEKHH2-ALK fusion	yes	unknown		in frame	PLEKHH2 (NM_172069) - ALK (NM_004304) rearrangement: c.502+545: PLEKHH2_c.3173-112:ALKinv Note: The PLEKHH2 - ALK rearrangement is an inversion which results in the fusion of PLEKHH2 exons 1-6 with ALK exons 20-29. Its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0027098-T01-IM6	PRIM2-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: t(6;19)(p11.2;q13.12)(chr6:g.57161995::chr19:g.36214642) Note: The KMT2B rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
PRIM2	0	MSKCC-DMP	P-0027098-T01-IM6	PRIM2-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: t(6;19)(p11.2;q13.12)(chr6:g.57161995::chr19:g.36214642) Note: The KMT2B rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027134-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement:c.56-4414:TMPRSS2_c.39+60150:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 4-11 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion not be detected by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0027134-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement:c.56-4414:TMPRSS2_c.39+60150:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 4-11 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion not be detected by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0027141-T01-IM6	AGPAT9-SOX9 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: t(4;17)(q21.23;q24.3)(chr4:g.84464806::chr17:g.70120234) Note: The SOX9 rearrangement is a translocation with a breakpoint within exon 3. The functional significance is undetermined.
AGPAT9	0	MSKCC-DMP	P-0027141-T01-IM6	AGPAT9-SOX9 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: t(4;17)(q21.23;q24.3)(chr4:g.84464806::chr17:g.70120234) Note: The SOX9 rearrangement is a translocation with a breakpoint within exon 3. The functional significance is undetermined.
EIF3H	0	MSKCC-DMP	P-0027161-T01-IM6	RAD21-EIF3H fusion	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.224_g.117769470del The RAD21 rearrangement results in the deletion of exon 3 - 14. One of the breakpoints is within RAD21 exon 3 and the functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0027161-T01-IM6	RAD21-EIF3H fusion	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.224_g.117769470del The RAD21 rearrangement results in the deletion of exon 3 - 14. One of the breakpoints is within RAD21 exon 3 and the functional significance is undetermined.
GZMB	0	MSKCC-DMP	P-0027028-T01-IM6	MAX-GZMB fusion	yes	unknown		unknown	MAX (NM_002382) rearrangement: chr14:g.:25176242_c.172-6244dup Note: The MAX rearrangement is a duplication that includes exons 4-5. The functional significance is undetermined.
MAX	0	MSKCC-DMP	P-0027028-T01-IM6	MAX-GZMB fusion	yes	unknown		unknown	MAX (NM_002382) rearrangement: chr14:g.:25176242_c.172-6244dup Note: The MAX rearrangement is a duplication that includes exons 4-5. The functional significance is undetermined.
DTNB	0	MSKCC-DMP	P-0026969-T01-IM6	ASXL2-DTNB fusion	yes	unknown		unknown	DTNB (NM_021907) - ASXL2 (NM_018263) rearrangement: c.362+2130:DTNB_c.1705:ASLX2dup Note: The DTNB - ASXL2 rearrangement is a duplication that results in the fusion of DTNB exons 1-4 to ASXL2 exons 11-12. One of the breakpoints is within ASXL2 exon 11. The functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0026969-T01-IM6	ASXL2-DTNB fusion	yes	unknown		unknown	DTNB (NM_021907) - ASXL2 (NM_018263) rearrangement: c.362+2130:DTNB_c.1705:ASLX2dup Note: The DTNB - ASXL2 rearrangement is a duplication that results in the fusion of DTNB exons 1-4 to ASXL2 exons 11-12. One of the breakpoints is within ASXL2 exon 11. The functional significance is undetermined.
PLCD3	0	MSKCC-DMP	P-0027203-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		out of frame	PLCD3 (NM_133373) - MAP3K14 (NM_003954) rearrangement: c.164-4289_c.1290-7dup Note: The PLCD3 - MAP3K14 rearrangement is a duplication which involves PLCD3 exon 2- 15 and MAP3K14 exons 1-6. Its functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0027203-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		out of frame	PLCD3 (NM_133373) - MAP3K14 (NM_003954) rearrangement: c.164-4289_c.1290-7dup Note: The PLCD3 - MAP3K14 rearrangement is a duplication which involves PLCD3 exon 2- 15 and MAP3K14 exons 1-6. Its functional significance is undetermined.
RPS19	0	MSKCC-DMP	P-0027203-T01-IM6	CD79A-RPS19 fusion	yes	unknown		unknown	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.197_c.173-1754dup Note: The CD79A - RPS19 rearrangement is a duplication which involves CD79A exons 2-5 and RPS19 exons 1-3
CD79A	0	MSKCC-DMP	P-0027203-T01-IM6	CD79A-RPS19 fusion	yes	unknown		unknown	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.197_c.173-1754dup Note: The CD79A - RPS19 rearrangement is a duplication which involves CD79A exons 2-5 and RPS19 exons 1-3
ERG	0	MSKCC-DMP	P-0027210-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-687:TMPRSS2_c.39+51208:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0027210-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-687:TMPRSS2_c.39+51208:ERGdel
PTPRD	0	MSKCC-DMP	P-0027269-T01-IM6	PTPRD-intragenic	yes	unknown		in frame	PTPRD (NM_002839) rearrangement: c.692-845_c.680-66dup Note: The PTPRD rearrangement results in the duplication of PTPRD exon 19. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027272-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2470_c.19-26014del Note: The variant results in TMPRSS2 exon1 fusing with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0027272-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2470_c.19-26014del Note: The variant results in TMPRSS2 exon1 fusing with ERG exons 2-10.
MBD3	0	MSKCC-DMP	P-0027288-T01-IM6	TCF3-MBD3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: chr19:g.1593723_c.1024dup Note: The TCF3 rearrangement is an duplication that includes exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0027288-T01-IM6	TCF3-MBD3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: chr19:g.1593723_c.1024dup Note: The TCF3 rearrangement is an duplication that includes exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
ZNF621	0	MSKCC-DMP	P-0026370-T02-IM6	CTNNB1-ZNF621 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.991:CTNNB1_chr3:g.40674718dup Note: The CTNNB1 rearrangement results in the duplication of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0026370-T02-IM6	CTNNB1-ZNF621 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.991:CTNNB1_chr3:g.40674718dup Note: The CTNNB1 rearrangement results in the duplication of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
GNAQ	0	MSKCC-DMP	P-0027185-T01-IM6	GNAQ-intragenic	yes	unknown		unknown	GNAQ (NM_002072) rearrangement: c.1054:GNAQ_chr9:g.80320467del Note: The GNAQ rearrangement is an inversion with a breakpoint in exon 7. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0027300-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	LDLR (NM_000527) - SMARCA4 (NM_003072) rearrangement: c.1845+936:LDLR_c.4602:SMARCA4dup Note: The LDLR - SMARCA4 rearrangement is a duplication that results in the fusion of LDLR exons 1-12 with SMARCA4 exons 32-35. The functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0027300-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	LDLR (NM_000527) - SMARCA4 (NM_003072) rearrangement: c.1845+936:LDLR_c.4602:SMARCA4dup Note: The LDLR - SMARCA4 rearrangement is a duplication that results in the fusion of LDLR exons 1-12 with SMARCA4 exons 32-35. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0027311-T01-IM6	RNU6-19P-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.1010-268:ETV6_chr12:g.12056304del Note: The ETV6 rearrangement is a deletion of exons 6-8. The functional significance is undetermined.
RNU6-19P	0	MSKCC-DMP	P-0027311-T01-IM6	RNU6-19P-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.1010-268:ETV6_chr12:g.12056304del Note: The ETV6 rearrangement is a deletion of exons 6-8. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0027321-T01-IM6	KCTD8-TERT fusion	yes	unknown		unknown	TERT (NM_198253)  rearrangement: t(4;5)(p13;p15.33)(chr4:g.44149829::chr5:g.1295406) Note: The TERT rearrangement involves the truncation of the promoter. The functional significance is undetermined.
KCTD8	0	MSKCC-DMP	P-0027321-T01-IM6	KCTD8-TERT fusion	yes	unknown		unknown	TERT (NM_198253)  rearrangement: t(4;5)(p13;p15.33)(chr4:g.44149829::chr5:g.1295406) Note: The TERT rearrangement involves the truncation of the promoter. The functional significance is undetermined.
NKX2-1	0	MSKCC-DMP	P-0027251-T01-IM6	NKX2-8-NKX2-1 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) rearrangement: c.464-11:NKX2-1_chr14:g.37047558del Note: The NKX2-1 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.
NKX2-8	0	MSKCC-DMP	P-0027251-T01-IM6	NKX2-8-NKX2-1 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) rearrangement: c.464-11:NKX2-1_chr14:g.37047558del Note: The NKX2-1 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0027352-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1846_c.336del Note: The CTNNB1 rearrangement is an intragenic deletion which involves CTNNB1 5-UTR region and exon 4. Its functional significance is undetermined.
MUTYH	0	MSKCC-DMP	P-0027353-T01-IM6	NBPF20-MUTYH fusion	yes	unknown		unknown	MUTYH (NM_001128425) rearrangement: c.342:MUTYH_g.144950020del Note: The MUTYH - NBPF20 rearrangement results in the deletion of MUTYH exon 1-3.
NBPF20	0	MSKCC-DMP	P-0027353-T01-IM6	NBPF20-MUTYH fusion	yes	unknown		unknown	MUTYH (NM_001128425) rearrangement: c.342:MUTYH_g.144950020del Note: The MUTYH - NBPF20 rearrangement results in the deletion of MUTYH exon 1-3.
TMPRSS2	0	MSKCC-DMP	P-0027216-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-1525_c.839-18del Note: The TMPRSS2 rearrangement is a deletion of exons 2-8. The possibility of a more complex rearrangement resulting in a TMPRSS2 fusion cannot be excluded. Additional testing is recommended if clinically indicated.
FLJ37453	0	MSKCC-DMP	P-0027226-T01-IM6	SPEN-FLJ37453 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.5202:SPEN_chr1:g.16148632del Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11.
SPEN	0	MSKCC-DMP	P-0027226-T01-IM6	SPEN-FLJ37453 fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.5202:SPEN_chr1:g.16148632del Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11.
AXL	0	MSKCC-DMP	P-0027391-T01-IM6	GDF10-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: t(10;19)(q11.22;q13.2)(chr10:g.48490590::chr19:g.41762374) Note: The AXL rearrangement is a translocation with a breakpoint within AXL exon 18. The functional significance is undetermined. Multiple rearrangements involving AXL were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
GDF10	0	MSKCC-DMP	P-0027391-T01-IM6	GDF10-AXL fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: t(10;19)(q11.22;q13.2)(chr10:g.48490590::chr19:g.41762374) Note: The AXL rearrangement is a translocation with a breakpoint within AXL exon 18. The functional significance is undetermined. Multiple rearrangements involving AXL were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
C1orf234	0	MSKCC-DMP	P-0027395-T01-IM6	SESN2-C1orf234 fusion	yes	unknown		unknown	SESN2 (NM_031459) rearrangement: chr1:g.23343226_c.651dup Note: The SESN2 rearrangement is a duplication that includes SESN2 exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
SESN2	0	MSKCC-DMP	P-0027395-T01-IM6	SESN2-C1orf234 fusion	yes	unknown		unknown	SESN2 (NM_031459) rearrangement: chr1:g.23343226_c.651dup Note: The SESN2 rearrangement is a duplication that includes SESN2 exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
NKX1-1	0	MSKCC-DMP	P-0027075-T01-IM6	FGFR3-NKX1-1 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement:  chr4:g.1504892_c.1204:FGFR3dup Note: The FGFR3 rearrangement is a duplication that includes FGFR3 exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0027075-T01-IM6	FGFR3-NKX1-1 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement:  chr4:g.1504892_c.1204:FGFR3dup Note: The FGFR3 rearrangement is a duplication that includes FGFR3 exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0027453-T01-IM6	LINC01538-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q22.1;q22.3)(chr18:g.62539742::chr21:g.42860348) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.
LINC01538	0	MSKCC-DMP	P-0027453-T01-IM6	LINC01538-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q22.1;q22.3)(chr18:g.62539742::chr21:g.42860348) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027453-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2167:TMPRSS2_c.39+56989:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0027453-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2167:TMPRSS2_c.39+56989:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0027454-T01-IM6	PABPN1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(14;21)(q11.2;q22.3)(chr14:g.23791333::chr21:g.42869346) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 2. The functional significance is undetermined.
PABPN1	0	MSKCC-DMP	P-0027454-T01-IM6	PABPN1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(14;21)(q11.2;q22.3)(chr14:g.23791333::chr21:g.42869346) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 2. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027454-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.126+708:TMPRSS2_c.18+8974:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0027454-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.126+708:TMPRSS2_c.18+8974:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
LATS2	0	MSKCC-DMP	P-0027489-T01-IM6	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) rearrangement: c.1052_c.342+5100del Note: The LATS2 rearrangement results in the deletion of exons 3-4. One of the breakpoints is within exon 4 and Its functional significance is undetermined.
MYOD1	0	MSKCC-DMP	P-0024546-T01-IM6	MYOD1-intragenic	yes	unknown		unknown	MYOD1 (NM_002478): c.64:MYOD1_chr11:g.17737403del Note: The MYOD1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
SGK1	0	MSKCC-DMP	P-0025688-T01-IM6	ARID1A-SGK1 fusion	yes	unknown		unknown	ARID1A (NM_006015) - SGK1 (NM_001143676) rearrangement: t(1;6)(p36.11;q23.2)(chr1:g.1:27106417::chr6:g.134562414) Note: The ARID1A - SGK1 rearrangement is  a translocation that results in the fusion of ARID1A exons 1-20 with SGK1 exons 3-14. One of the breakpoints is within ARID1A exon 20. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0025688-T01-IM6	ARID1A-SGK1 fusion	yes	unknown		unknown	ARID1A (NM_006015) - SGK1 (NM_001143676) rearrangement: t(1;6)(p36.11;q23.2)(chr1:g.1:27106417::chr6:g.134562414) Note: The ARID1A - SGK1 rearrangement is  a translocation that results in the fusion of ARID1A exons 1-20 with SGK1 exons 3-14. One of the breakpoints is within ARID1A exon 20. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0027386-T01-IM6	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195.3) rearrangement: c.*90_c.194-2311del Note: The CDKN2Ap14ARF rearrangement results in the intragenic deletion of intron 1 to exon 2. One of the breakpoints is within exon 2 and its functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0027386-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.446_c.150+1159del Note: The CDKN2Ap16INK4A rearrangement results in the intragenic deletion of intron 1 to exon 2. One of the breakpoints is within exon 2 and its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0027448-T01-IM6	ARHGAP39-RECQL4 fusion	yes	unknown		unknown	ARHGAP39 (NM_025251) - RECQL4 (NM_004260) rearrangement: c.596+183:ARHGAP39_c.3173:RECQL4del Note: The ARHGAP39 - RECQL4 rearrangement is a deletion that results in the fusion of ARHGAP39 exons 1-5 with RECQL4 exons 19-22. One of the breakpoints is within RECQL4 exon 19. The functional significance is undetermined.
ARHGAP39	0	MSKCC-DMP	P-0027448-T01-IM6	ARHGAP39-RECQL4 fusion	yes	unknown		unknown	ARHGAP39 (NM_025251) - RECQL4 (NM_004260) rearrangement: c.596+183:ARHGAP39_c.3173:RECQL4del Note: The ARHGAP39 - RECQL4 rearrangement is a deletion that results in the fusion of ARHGAP39 exons 1-5 with RECQL4 exons 19-22. One of the breakpoints is within RECQL4 exon 19. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0027417-T01-IM6	KCNMA1-RET fusion	yes	unknown		out of frame	KCNMA1 (NM_001161352) -  RET (NM_020975) rearrangement: c.378+15627:KCNMA1_c.1649-143:RET Note: The KCNMA1 - RET rearrangement is an inversion which results in the fusion of KCNMA1 exon 1 with RET exons 9 - 20 including the kinase domain. Its functional significance is undetermined.
KCNMA1	0	MSKCC-DMP	P-0027417-T01-IM6	KCNMA1-RET fusion	yes	unknown		out of frame	KCNMA1 (NM_001161352) -  RET (NM_020975) rearrangement: c.378+15627:KCNMA1_c.1649-143:RET Note: The KCNMA1 - RET rearrangement is an inversion which results in the fusion of KCNMA1 exon 1 with RET exons 9 - 20 including the kinase domain. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027526-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449.4) fusion (TMPRSS2 exon 1-2 with ERG exons 4-10) : c.126+294:TMPRSS2_c.40-60810:ERGdel Note: The TMPRSS2 - ERG rearrangement is a non-canonical fusion predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0027526-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449.4) fusion (TMPRSS2 exon 1-2 with ERG exons 4-10) : c.126+294:TMPRSS2_c.40-60810:ERGdel Note: The TMPRSS2 - ERG rearrangement is a non-canonical fusion predicted to be in frame.
KDR	0	MSKCC-DMP	P-0027530-T01-IM6	KIAA1211-KDR fusion	yes	unknown		unknown	KDR  (NM_002253) rearrangement: c.1646-34:KDR_chr4:g.57171503del. Note: The KDR rearrangement results in the deletion of KDR eons 13-30. This includes the kinase domain of KDR. Its functional significance is undetermined.
KIAA1211	0	MSKCC-DMP	P-0027530-T01-IM6	KIAA1211-KDR fusion	yes	unknown		unknown	KDR  (NM_002253) rearrangement: c.1646-34:KDR_chr4:g.57171503del. Note: The KDR rearrangement results in the deletion of KDR eons 13-30. This includes the kinase domain of KDR. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0027542-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1137+13751_c.3797dup Note: The ARID1A rearrangement results in the duplication of exons 2-15. One of the breakpoints is within exon 15. The functional significance is undetermined.
SLC17A3	0	MSKCC-DMP	P-0027542-T01-IM6	HIST1H1C-SLC17A3 fusion	yes	unknown		unknown	SLC17A3 (NM_001098486) - HIST1H1C (NM_005319) rearrangement: c.92-15:SLC17A3_c.510:HIST1H1Cdup Note: The SLC17A3 - HIST1H1C rearrangement is a duplication that results in the fusion of SLC17A3 exons 1-2 with HIST1H1C exon 1. One of the breakpoints is within HIST1H1C exon 1. The functional significance is undetermined.
HIST1H1C	0	MSKCC-DMP	P-0027542-T01-IM6	HIST1H1C-SLC17A3 fusion	yes	unknown		unknown	SLC17A3 (NM_001098486) - HIST1H1C (NM_005319) rearrangement: c.92-15:SLC17A3_c.510:HIST1H1Cdup Note: The SLC17A3 - HIST1H1C rearrangement is a duplication that results in the fusion of SLC17A3 exons 1-2 with HIST1H1C exon 1. One of the breakpoints is within HIST1H1C exon 1. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0027548-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.1465-115_c.2152inv Note: The CIC rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
HIST1H2AC	0	MSKCC-DMP	P-0027548-T01-IM6	HIST1H3E-HIST1H2AC fusion	yes	unknown		unknown	HIST1H3E (NM_003532) rearrangement: c.275:HIST1H3E_chr6:g.26132417del Note: The HIST1H3E rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
HIST1H3E	0	MSKCC-DMP	P-0027548-T01-IM6	HIST1H3E-HIST1H2AC fusion	yes	unknown		unknown	HIST1H3E (NM_003532) rearrangement: c.275:HIST1H3E_chr6:g.26132417del Note: The HIST1H3E rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
KCNK3	0	MSKCC-DMP	P-0027553-T01-IM6	CENPA-KCNK3 fusion	yes	unknown		in frame	KCNK3 (NM_002246) - CENPA (NM_001809) rearrangement: c.283+1043:KCNK3_c.101-62:CENPA Note: The KCNK3 - CENPA rearrangement is a deletion that results in the in-frame fusion of KCNK3  exon 1 with CENPA exon 2-4. The functional significance is undetermined.
CENPA	0	MSKCC-DMP	P-0027553-T01-IM6	CENPA-KCNK3 fusion	yes	unknown		in frame	KCNK3 (NM_002246) - CENPA (NM_001809) rearrangement: c.283+1043:KCNK3_c.101-62:CENPA Note: The KCNK3 - CENPA rearrangement is a deletion that results in the in-frame fusion of KCNK3  exon 1 with CENPA exon 2-4. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0027627-T01-IM6	NISCH-BAP1 fusion	yes	unknown		unknown	BAP1(NM_004656) rearrangement: c.604:BAP1_chr3:g.52495299del Note: The BAP1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8.
NISCH	0	MSKCC-DMP	P-0027627-T01-IM6	NISCH-BAP1 fusion	yes	unknown		unknown	BAP1(NM_004656) rearrangement: c.604:BAP1_chr3:g.52495299del Note: The BAP1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8.
SDC4	0	MSKCC-DMP	P-0027630-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117651891::chr20:g.43962429) Note: The SDC4 - ROS1 fusion is predicted to be in-frame and includes ROS1 kinase domain.
ROS1	0	MSKCC-DMP	P-0027630-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion (SDC4 exons 1-2 fused to ROS1 exons 32-43): t(6;20)(q22.1;q13.12)(chr6:g.117651891::chr20:g.43962429) Note: The SDC4 - ROS1 fusion is predicted to be in-frame and includes ROS1 kinase domain.
EXOC3L2	0	MSKCC-DMP	P-0027590-T01-IM6	ERCC2-EXOC3L2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - EXOC3L2 (NM_138568) rearrangement: c.1581:ERCC2_c.540+265: EXOC3L2 del Note: The ERCC2 - EXOC3L2 rearrangement is a deletion that results in the fusion of ERCC2 exons 1-17 with EXOC3L2 exons 7-10. One of the breakpoints is within ERCC2 exon 17. The functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0027590-T01-IM6	ERCC2-EXOC3L2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - EXOC3L2 (NM_138568) rearrangement: c.1581:ERCC2_c.540+265: EXOC3L2 del Note: The ERCC2 - EXOC3L2 rearrangement is a deletion that results in the fusion of ERCC2 exons 1-17 with EXOC3L2 exons 7-10. One of the breakpoints is within ERCC2 exon 17. The functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0027597-T01-IM6	GDAP1L1-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1719+44:ASXL1_chr20:g.42888843inv Note: The ASXL1 rearrangement is an inversion of ASXL1 intron 11. Its functional significance is undetermined.
GDAP1L1	0	MSKCC-DMP	P-0027597-T01-IM6	GDAP1L1-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1719+44:ASXL1_chr20:g.42888843inv Note: The ASXL1 rearrangement is an inversion of ASXL1 intron 11. Its functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0027609-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.2707+33_c.3253-806inv Note: The NCOA3 rearrangement results in the inversion of intron 14 to intron 17. Its functional significance is undetermined,
ERG	0	MSKCC-DMP	P-0027635-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.127-1454:TMPRSS2_c.19-17870:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0027635-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10): c.127-1454:TMPRSS2_c.19-17870:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
RFX6	0	MSKCC-DMP	P-0027411-T01-IM6	ROS1-RFX6 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.6800:ROS1_chr6:g.117287744inv Note: The ROS1 rearrangement is an inversion of exons 43. One of the breakpoints is within 43. Its functional significance is undetermined. Multiple rearrangements involving ROS1 were detected in this sample and a more complex rearrangement resulting in a ROS1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ROS1	0	MSKCC-DMP	P-0027411-T01-IM6	ROS1-RFX6 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.6800:ROS1_chr6:g.117287744inv Note: The ROS1 rearrangement is an inversion of exons 43. One of the breakpoints is within 43. Its functional significance is undetermined. Multiple rearrangements involving ROS1 were detected in this sample and a more complex rearrangement resulting in a ROS1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
GATA1	0	MSKCC-DMP	P-0027414-T01-IM6	GATA1-intragenic	yes	unknown		unknown	GATA1 (NM_002049) rearrangement: c.420_c.818inv Note: The GATA1 rearrangement is an intragenic inversion of exons 3-5. The breakpoints are within exons 3 and 5. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0027593-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.461_c.492+1310del Note: The PTEN rearrangement results in the deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0027606-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.163+4431_c.464-6577dup. Note: The ETV6 rearrangement results in the in frame duplication of intron 2 to intron 4. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027645-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1-2 fused to ERG exons 3-11):c.127-75:TMPRSS2_c.-47-3122:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0027645-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1-2 fused to ERG exons 3-11):c.127-75:TMPRSS2_c.-47-3122:ERGdel Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.
SHQ1	0	MSKCC-DMP	P-0027645-T01-IM6	SHQ1-intragenic	yes	unknown		unknown	SHQ1 (NM_018130) rearrangement: c.1182-10735_c.1573inv Note: The SHQ1 rearrangement results in the inversion of exon 11. One breakpoint is in exon 11. Its functional significance is undetermined.
C14orf37	0	MSKCC-DMP	P-0027657-T01-IM6	DICER1-C14orf37 fusion	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: c.4511_chr14:g.58473233inv Note: The DICER1 rearrangement results in the inversion of exons 25-28. One of the breakpoints is within exon 25. The functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0027657-T01-IM6	DICER1-C14orf37 fusion	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: c.4511_chr14:g.58473233inv Note: The DICER1 rearrangement results in the inversion of exons 25-28. One of the breakpoints is within exon 25. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0027661-T01-IM6	RNF43-intragenic	yes	unknown		out of frame	RNF43 (NM_017763) rearrangement: c.952+96_c.376-534dup Note: The RNF43 rearrangement results in the duplication of exons 4-8. The functional significance is undetermined.
FOXL2	0	MSKCC-DMP	P-0027664-T01-IM6	FOXL2-intragenic	yes	unknown		unknown	FOXL2 (NM_023067) rearrangement: c.1012_c.-84inv Note: The FOXL2 rearrangement results in the inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
RAB5C	0	MSKCC-DMP	P-0027685-T01-IM6	ALK-RAB5C fusion	yes	unknown		unknown	RAB5C (NM_001252039) - ALK (NM_004304) fusion: t(2;17)(p23.2;q21.2)(chr2:g.29447944::chr17:g.40279299) Note: The RAB5C - ALK rearrangement is a translocation that results in the fusion of RAB5C exons 1-4 fused in-frame to ALK exons 20-29, which includes the kinase domain.
ALK	0	MSKCC-DMP	P-0027685-T01-IM6	ALK-RAB5C fusion	yes	unknown		unknown	RAB5C (NM_001252039) - ALK (NM_004304) fusion: t(2;17)(p23.2;q21.2)(chr2:g.29447944::chr17:g.40279299) Note: The RAB5C - ALK rearrangement is a translocation that results in the fusion of RAB5C exons 1-4 fused in-frame to ALK exons 20-29, which includes the kinase domain.
TSTA3	0	MSKCC-DMP	P-0022593-T02-IM6	MSH3-TSTA3 fusion	yes	unknown		unknown	MSH3 (NM_002439) - TSTA3 (NM_003313) rearrangement: t(5;8)(q14.1;q24.3)(chr5:g.79966005::chr8:g.144698059) Note: The MSH3 - TSTA3 rearrangement is a translocation that results in the fusion of MSH3 exon 4 to TSTA3 exon 4. One of the breakpoints is within MSH3 exon 4. Multiple rearrangements involving MSH3 were detected in this sample and a more complex rearrangement is possible. The functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0022593-T02-IM6	MSH3-TSTA3 fusion	yes	unknown		unknown	MSH3 (NM_002439) - TSTA3 (NM_003313) rearrangement: t(5;8)(q14.1;q24.3)(chr5:g.79966005::chr8:g.144698059) Note: The MSH3 - TSTA3 rearrangement is a translocation that results in the fusion of MSH3 exon 4 to TSTA3 exon 4. One of the breakpoints is within MSH3 exon 4. Multiple rearrangements involving MSH3 were detected in this sample and a more complex rearrangement is possible. The functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0027741-T01-IM6	ZNF552-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.1378-33:ERCC2_chr19:g.58327100inv Note: The ERCC2 rearrangement is an inversion of exons 1-14. The functional significance is undetermined.
ZNF552	0	MSKCC-DMP	P-0027741-T01-IM6	ZNF552-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.1378-33:ERCC2_chr19:g.58327100inv Note: The ERCC2 rearrangement is an inversion of exons 1-14. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0026777-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1726-1554:KIF5B_c.2136+533:RETinv Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0026777-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1726-1554:KIF5B_c.2136+533:RETinv Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.
AR	0	MSKCC-DMP	P-0027722-T01-IM6	AR-intragenic	yes	unknown		out of frame	AR (NM_000044) rearrangement: c.2174-1943_c.2608-51del Note: The AR rearrangement results in the deletion of exons 5-7. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0027723-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 11-20):c.1725+966:KIF5B_c.2123:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET. One of the breakpoints is within RET exon 11.
RET	0	MSKCC-DMP	P-0027723-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 11-20):c.1725+966:KIF5B_c.2123:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET. One of the breakpoints is within RET exon 11.
CDH1	0	MSKCC-DMP	P-0027731-T01-IM6	TANGO6-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1433:CDH1_chr16:g.68971469inv Note: The CDH1 rearrangement results in the inversion of exons 10-16. One of the breakpoints is within exon 10. The functional significance is undetermined.
TANGO6	0	MSKCC-DMP	P-0027731-T01-IM6	TANGO6-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1433:CDH1_chr16:g.68971469inv Note: The CDH1 rearrangement results in the inversion of exons 10-16. One of the breakpoints is within exon 10. The functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0027754-T02-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.1188+1_c.1190del Note: The CSDE1 rearrangement is an intragenic deletion with breakpoints within exon 12 and the splice donor site of intron 11. Multiple CSDE1 rearrangements were detected in this sample, and a more complex rearrangement is possible. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0027759-T01-IM6	LINC01164-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-919:FGFR2_chr10:g.133670877inv Note: The FGFR2 rearrangement is an inversion with a breakpoint in intron 17. The functional significance is undetermined.
LINC01164	0	MSKCC-DMP	P-0027759-T01-IM6	LINC01164-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-919:FGFR2_chr10:g.133670877inv Note: The FGFR2 rearrangement is an inversion with a breakpoint in intron 17. The functional significance is undetermined.
SLCO1A2	0	MSKCC-DMP	P-0027764-T01-IM6	RET-SLCO1A2 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: t(10;12)(q11.21;p12.2)(chr10:g.43611187::chr12:g.21413909) Note: The RET rearrangement is a translocation involving exon 12. This involves the kinase domain of RET. Its functional significance is undetermined
RET	0	MSKCC-DMP	P-0027764-T01-IM6	RET-SLCO1A2 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: t(10;12)(q11.21;p12.2)(chr10:g.43611187::chr12:g.21413909) Note: The RET rearrangement is a translocation involving exon 12. This involves the kinase domain of RET. Its functional significance is undetermined
MTOR	0	MSKCC-DMP	P-0027811-T01-IM6	HIVEP3-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.3399-24:MTOR_chr1:g.42333975inv Note: The MTOR rearrangement results in the inversion of exons 1-22. The functional significance is undetermined.
HIVEP3	0	MSKCC-DMP	P-0027811-T01-IM6	HIVEP3-MTOR fusion	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.3399-24:MTOR_chr1:g.42333975inv Note: The MTOR rearrangement results in the inversion of exons 1-22. The functional significance is undetermined.
ARID5B	0	MSKCC-DMP	P-0027811-T01-IM6	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.3560:ARID5B_chr10:g.463862183inv Note: The ARID5B rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0027831-T01-IM6	AGAP2-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: t(12;17)(q14.1;q21.31)(chr12:g.58127459::chr17:g.43362279) Note: The MAP3K14 rearrangement is a translocation with a breakpoint within exon 6. The functional significance is undetermined.
AGAP2	0	MSKCC-DMP	P-0027831-T01-IM6	AGAP2-MAP3K14 fusion	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: t(12;17)(q14.1;q21.31)(chr12:g.58127459::chr17:g.43362279) Note: The MAP3K14 rearrangement is a translocation with a breakpoint within exon 6. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0027853-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused to ALK exons 20-29 ): c.2243-157:EML4_c.3172+593:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0027853-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused to ALK exons 20-29 ): c.2243-157:EML4_c.3172+593:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
KIF5B	0	MSKCC-DMP	P-0027991-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-24 fused to RET exons 9-20): c.2762-248:KIF5B_c.1649-100:RETinv Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0027991-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-24 fused to RET exons 9-20): c.2762-248:KIF5B_c.1649-100:RETinv Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.
RGS7	0	MSKCC-DMP	P-0004918-T02-IM6	FH-RGS7 fusion	yes	unknown		out of frame	RGS7 (NM_002924) - FH (NM_000143) rearrangement: c.79-95591:RGS7_c.1109-139:FHdup Note: The RGS7 - FH rearrangement is a duplication that results in the fusion of RGS7 exons 1-2 to FH exons 8-10. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0004918-T02-IM6	FH-RGS7 fusion	yes	unknown		out of frame	RGS7 (NM_002924) - FH (NM_000143) rearrangement: c.79-95591:RGS7_c.1109-139:FHdup Note: The RGS7 - FH rearrangement is a duplication that results in the fusion of RGS7 exons 1-2 to FH exons 8-10. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0004918-T02-IM6	FSCB-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: t(14;17)(q21.2;q21.2)(chr14:g.44234319::chr17:g.40469176) Note: The STAT3 rearrangement is a translocation with a breakpoint in exon 22. The functional significance is undetermined.
FSCB	0	MSKCC-DMP	P-0004918-T02-IM6	FSCB-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: t(14;17)(q21.2;q21.2)(chr14:g.44234319::chr17:g.40469176) Note: The STAT3 rearrangement is a translocation with a breakpoint in exon 22. The functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0004918-T02-IM6	NPTX1-SOX9 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.1234:SOX9_chr17:g.78453502inv Note: The SOX9 rearrangement is an inversion with a breakpoint in exon 3. The functional significance is undetermined.
NPTX1	0	MSKCC-DMP	P-0004918-T02-IM6	NPTX1-SOX9 fusion	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.1234:SOX9_chr17:g.78453502inv Note: The SOX9 rearrangement is an inversion with a breakpoint in exon 3. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0027540-T01-IM6	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*102-661_c.193+6485del Note: The CDKN2Ap14ARF rearrangement results in the deletion of exon 2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0027540-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-661_chr9:g.21987653del Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exons 1 to 2. The functional significance is undetermined.
SYK	0	MSKCC-DMP	P-0027757-T01-IM6	SYK-intragenic	yes	unknown		unknown	SYK (NM_003177) rearrangement: c.578_c.579del Note: The SYK rearrangement is a deletion with breakpoints in exons 3 and 4. Multiple other deletion events in SYK involving exons 3-14 were also detected in the tumor sample  suggesting the presence of somatically acquired processed pseudogenes. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0027874-T01-IM6	RPS24-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(10;12)(q22.3;q13.2)(chr10:g.79794131::chr12:g.56494017) Note: The ERBB3 rearrangement is a translocation involving a breakpoint in exon 26. Its functional significance is undetermined.
RPS24	0	MSKCC-DMP	P-0027874-T01-IM6	RPS24-ERBB3 fusion	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(10;12)(q22.3;q13.2)(chr10:g.79794131::chr12:g.56494017) Note: The ERBB3 rearrangement is a translocation involving a breakpoint in exon 26. Its functional significance is undetermined.
CD2AP	0	MSKCC-DMP	P-0027879-T01-IM6	ROS1-CD2AP fusion	yes	unknown		unknown	ROS1 (NM_002944) - c.5778-469:ROS1_chr6:g.47344251del Note: The ROS1 rearrangement is a deletion of exons 36-43. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0027879-T01-IM6	ROS1-CD2AP fusion	yes	unknown		unknown	ROS1 (NM_002944) - c.5778-469:ROS1_chr6:g.47344251del Note: The ROS1 rearrangement is a deletion of exons 36-43. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0027889-T01-IM6	APOLD1-ETV6 fusion	yes	unknown		out of frame	ETV6:NM_001987) - APOLD1 (NM_001130415) rearrangement: c.1010-6957:ETV6_c.96+30120:APOLD1del Note: The ETV6 - APOLD1 rearrangement is a deletion that results in the fusion of ETV6 exons 1-5 to APOLD1 exon 2. The functional significance is undetermined.
APOLD1	0	MSKCC-DMP	P-0027889-T01-IM6	APOLD1-ETV6 fusion	yes	unknown		out of frame	ETV6:NM_001987) - APOLD1 (NM_001130415) rearrangement: c.1010-6957:ETV6_c.96+30120:APOLD1del Note: The ETV6 - APOLD1 rearrangement is a deletion that results in the fusion of ETV6 exons 1-5 to APOLD1 exon 2. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0027889-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearragement: c.269:STK11_chr19:g.1205538del Note: The STK11 rearrangement is a deletion with breakpoints in the promoter region and exon 1.
NSD1	0	MSKCC-DMP	P-0027892-T01-IM6	NSD1-intragenic	yes	unknown		unknown	NSD1 (NM_022455) rearrangment: c.1515_c.3796+4024del Note: The NSD1 rearrangement is an intragenic deletion of a part of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0027939-T01-IM6	RNF43-intragenic	yes	unknown		in frame	RNF43 (NM_017763) rearrangement: c.849+65_c.376-68dup Note: The RNF43 rearrangement results in the duplication of exons 4-7. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0027953-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+20901:CCDC6_c.2137-754:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0027953-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+20901:CCDC6_c.2137-754:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
DYM	0	MSKCC-DMP	P-0027989-T01-IM6	ROS1-DYM fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: t(6;18)(q22.1;q21.1)(chr6:g.117643946::chr18:g.18:46871756) Note: The ROS1 rearrangement is a translocation with a breakpoint in intron 34. The functional significance is undetermined. Multiple rearrangements involving ROS1 were detected in this sample and a more complex rearrangement resulting in a ROS1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ROS1	0	MSKCC-DMP	P-0027989-T01-IM6	ROS1-DYM fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: t(6;18)(q22.1;q21.1)(chr6:g.117643946::chr18:g.18:46871756) Note: The ROS1 rearrangement is a translocation with a breakpoint in intron 34. The functional significance is undetermined. Multiple rearrangements involving ROS1 were detected in this sample and a more complex rearrangement resulting in a ROS1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ARID1B	0	MSKCC-DMP	P-0027995-T01-IM6	ZDHHC14-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.2961+826:ARID1B_chr6:g.157787825del Note: The ARID1B rearrangement results in the deletion of ARID1B exons 1-11. One of the breakpoints is within the ARID1B intron 11.
ZDHHC14	0	MSKCC-DMP	P-0027995-T01-IM6	ZDHHC14-ARID1B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.2961+826:ARID1B_chr6:g.157787825del Note: The ARID1B rearrangement results in the deletion of ARID1B exons 1-11. One of the breakpoints is within the ARID1B intron 11.
KDM5C	0	MSKCC-DMP	P-0027995-T01-IM6	AMER1-KDM5C fusion	yes	unknown		unknown	KDM5C (NM_004187) - AMER1 (NM_152424) rearrangement: c.1746+1883:KDM5C_c.1896:AMER1inv. Note: The KDM5C - AMER1 rearrangement results in the inversion of KDM5C exons 1-12 and AMER1 exon 2. Its functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0027995-T01-IM6	AMER1-KDM5C fusion	yes	unknown		unknown	KDM5C (NM_004187) - AMER1 (NM_152424) rearrangement: c.1746+1883:KDM5C_c.1896:AMER1inv. Note: The KDM5C - AMER1 rearrangement results in the inversion of KDM5C exons 1-12 and AMER1 exon 2. Its functional significance is undetermined.
ZNF598	0	MSKCC-DMP	P-0028009-T01-IM6	TSC2-ZNF598 fusion	yes	unknown		unknown	NTHL1 (NM_002528) - ZNF598 (NM_178167) rearrangement: c.275:NTHL1_c.338-17:ZNF598dup Note: The NTHL1 rearrangement is a duplication that includes  NTHL1 exons 2-6. One of the breakpoints is within NTHL1 exon 2. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0028009-T01-IM6	TSC2-ZNF598 fusion	yes	unknown		unknown	NTHL1 (NM_002528) - ZNF598 (NM_178167) rearrangement: c.275:NTHL1_c.338-17:ZNF598dup Note: The NTHL1 rearrangement is a duplication that includes  NTHL1 exons 2-6. One of the breakpoints is within NTHL1 exon 2. The functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0028009-T01-IM6	ASB12-AMER1 fusion	yes	unknown		unknown	AMER1 (NM_152424) - ASB12 (NM_130388) rearrangement: c.31:AMER1_c.-25+170:ASB12dup Note: The AMER1 - ASB12 rearrangement is a duplication that results in the fusion of AMER1 exon2 to ASB12 exon 2. One of the breakpoints is within AMER1 exon 2. The functional significance is undetermined.
ASB12	0	MSKCC-DMP	P-0028009-T01-IM6	ASB12-AMER1 fusion	yes	unknown		unknown	AMER1 (NM_152424) - ASB12 (NM_130388) rearrangement: c.31:AMER1_c.-25+170:ASB12dup Note: The AMER1 - ASB12 rearrangement is a duplication that results in the fusion of AMER1 exon2 to ASB12 exon 2. One of the breakpoints is within AMER1 exon 2. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0009301-T02-IM6	SMIM14-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: t(4;17)(p14;p11.2)(chr4:g.39589422::chr17:g.17120488) Note: The FLCN rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
SMIM14	0	MSKCC-DMP	P-0009301-T02-IM6	SMIM14-FLCN fusion	yes	unknown		unknown	FLCN (NM_144997) rearrangement: t(4;17)(p14;p11.2)(chr4:g.39589422::chr17:g.17120488) Note: The FLCN rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
LOC100506474	0	MSKCC-DMP	P-0009301-T02-IM6	MSH6-LOC100506474 fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: c.1202:MSH6_chr2:g.13175938inv Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0009301-T02-IM6	MSH6-LOC100506474 fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: c.1202:MSH6_chr2:g.13175938inv Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0009301-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused to ALK exons 20-29): c.668-6693:EML4_c.3173-257:ALKinv Note: The EML4- ALK fusion is predicted to be in-frame and includes the kinase domain.
EML4	0	MSKCC-DMP	P-0009301-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 fused to ALK exons 20-29): c.668-6693:EML4_c.3173-257:ALKinv Note: The EML4- ALK fusion is predicted to be in-frame and includes the kinase domain.
KIF5B	0	MSKCC-DMP	P-0017214-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-23 fused to RET exons 12-20): c.2545-27:KIF5B_c.2136+463:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0017214-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-23 fused to RET exons 12-20): c.2545-27:KIF5B_c.2136+463:RETinv Note: The KIF5B-RET fusion is predicted to be in-frame and includes the protein kinase domain of RET.
TSC2	0	MSKCC-DMP	P-0017214-T02-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548): c.4662+217_c.4850-100del Note: The TSC2 rearrangement is an intragenic deletion of exon 37.
PARK2	0	MSKCC-DMP	P-0027307-T02-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.413-22549_c.413del Note: The PARK2 rearrangement is an intragenic deletion breakpoints in exon 4 and intron 3. The functional significance is undetermined.
ZC3HAV1	0	MSKCC-DMP	P-0027762-T01-IM6	BRAF-ZC3HAV1 fusion	yes	unknown		in frame	ZC3HAV1 (NM_020119) - BRAF (NM_004333) rearrangement: c.698-431:ZC3HAV1_c.1177+1402:BRAFdup Note: the ZC3HAV1 - BRAF rearrangement is a duplication which results in the fusion of ZC3HAV1 exons 1-4  with BRAF exons 10-18. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0027762-T01-IM6	BRAF-ZC3HAV1 fusion	yes	unknown		in frame	ZC3HAV1 (NM_020119) - BRAF (NM_004333) rearrangement: c.698-431:ZC3HAV1_c.1177+1402:BRAFdup Note: the ZC3HAV1 - BRAF rearrangement is a duplication which results in the fusion of ZC3HAV1 exons 1-4  with BRAF exons 10-18. Its functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0027823-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+490:TMPRSS2_chr21:g.40053392del Note: The TMPRSS2 rearrangement results in the deletion of exons 3-14. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0027823-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+490:TMPRSS2_chr21:g.40053392del Note: The TMPRSS2 rearrangement results in the deletion of exons 3-14. Its functional significance is undetermined.
AP3D1	0	MSKCC-DMP	P-0028037-T01-IM6	DOT1L-AP3D1 fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.-31:DOT1L_chr19:g.2103210del Note: The DOT1L rearrangement is a deletion with a breakpoint in the 5UTR of DOT1L. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0028037-T01-IM6	DOT1L-AP3D1 fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.-31:DOT1L_chr19:g.2103210del Note: The DOT1L rearrangement is a deletion with a breakpoint in the 5UTR of DOT1L. The functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0028038-T01-IM6	RAB37-EZH1 fusion	yes	unknown		out of frame	RAB37 (NM_175738) - EZH1 (NM_001991) rearrangement: c.73-9053:RAB37_c.488-70:EZH1inv Note: The RAB37 - EZH1 rearrangement is an inversion that results in the fusion of RAB37 exon 1 to EZH1 exons 7-21. The functional significance is undetermined.
RAB37	0	MSKCC-DMP	P-0028038-T01-IM6	RAB37-EZH1 fusion	yes	unknown		out of frame	RAB37 (NM_175738) - EZH1 (NM_001991) rearrangement: c.73-9053:RAB37_c.488-70:EZH1inv Note: The RAB37 - EZH1 rearrangement is an inversion that results in the fusion of RAB37 exon 1 to EZH1 exons 7-21. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0028118-T01-IM6	GUSBP4-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.416:MDC1_chr6:g.58454054inv Note: The MDC1 rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
GUSBP4	0	MSKCC-DMP	P-0028118-T01-IM6	GUSBP4-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.416:MDC1_chr6:g.58454054inv Note: The MDC1 rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0021332-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-1976_c.272del Note: The CTNNB1 rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0022192-T01-IM6	LRP1-NAB2 fusion	yes	unknown		out of frame	LRP1 (NM_002332) - NAB2 (NM_005967) rearrangement: c.842-2141:LRP1_c.1092-146:NAB2dup Note: The LRP1 - NAB2 rearrangement is a duplication that results in the fusion of LRP1 exon 1-6 with NAB2 exons 4-7. The functional significance is undetermined.
LRP1	0	MSKCC-DMP	P-0022192-T01-IM6	LRP1-NAB2 fusion	yes	unknown		out of frame	LRP1 (NM_002332) - NAB2 (NM_005967) rearrangement: c.842-2141:LRP1_c.1092-146:NAB2dup Note: The LRP1 - NAB2 rearrangement is a duplication that results in the fusion of LRP1 exon 1-6 with NAB2 exons 4-7. The functional significance is undetermined.
TET1	0	MSKCC-DMP	P-0027091-T01-IM6	TET1-intragenic	yes	unknown		unknown	TET1 (NM_030625) rearrangement: c.5405-202_c.5874del Note: The TET1 rearrangement is an intragenic deletion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0027275-T03-IM6	MSN-AMER1 fusion	yes	unknown		unknown	AMER1 (NM_152424) rearrangement: c.1674:AMER1_chrX:g.65018297inv Note: The AMER1 rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
MSN	0	MSKCC-DMP	P-0027275-T03-IM6	MSN-AMER1 fusion	yes	unknown		unknown	AMER1 (NM_152424) rearrangement: c.1674:AMER1_chrX:g.65018297inv Note: The AMER1 rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0027643-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.329-4344_c.463+7835del Note: The ETV6 rearrangement results in intragenic deletion of exons 4.
APC	0	MSKCC-DMP	P-0027647-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.135+1377_c.6760del Note: The APC rearrangement results in the deletion of exons 13-16. One of the breakpoints is within exon 16.
TP53	0	MSKCC-DMP	P-0027658-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.143_chr17:g.7581086del Note: The TP53 rearrangement results in the deletion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0027658-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.*1996_c.5584inv Note: The NOTCH3 rearrangement results in the inversion of exons 30-33. One of the breakpoints is within exon 30. The functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0028143-T01-IM6	FAM204A-TCF7L2 fusion	yes	unknown		unknown	FAM204A (NM_001134672) - TCF7L2 (NM_001146274) rearrangement: c.544-4180:FAM204A_c.1230:TCF7L2 Note: The FAM204A - TCF7L2 rearrangement is an inversion that results in the fusion of FAM204A exons 1-6 with TCF7L2 exons 11-14. One of the breakpoints is within TCF7L2  exon 11. The functional significance is undetermined.
FAM204A	0	MSKCC-DMP	P-0028143-T01-IM6	FAM204A-TCF7L2 fusion	yes	unknown		unknown	FAM204A (NM_001134672) - TCF7L2 (NM_001146274) rearrangement: c.544-4180:FAM204A_c.1230:TCF7L2 Note: The FAM204A - TCF7L2 rearrangement is an inversion that results in the fusion of FAM204A exons 1-6 with TCF7L2 exons 11-14. One of the breakpoints is within TCF7L2  exon 11. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0028149-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.163+35894_c.464-6807del Note: The ETV6 rearrangement results in the in-frame deletion of exons 3-4. The functional significance is undetermined.
GRIN2A	0	MSKCC-DMP	P-0028149-T01-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: c.4337_c.1007+20851inv Note: The GRIN2A rearrangement results in the inversion of exons 4-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0028149-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.4087+3328_c.4125inv Note: The PREX2 rearrangement results in the inversion of exon 34. One of the breakpoints is within exon 34. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0028155-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.10_chr4:g.187697960del Note: The FAT1 rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
MIPOL1	0	MSKCC-DMP	P-0028160-T01-IM6	FOXA1-MIPOL1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1121:FOXA1_chr14:g.38004592dup Note: The FOXA1 rearrangement results in the duplication of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0028160-T01-IM6	FOXA1-MIPOL1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1121:FOXA1_chr14:g.38004592dup Note: The FOXA1 rearrangement results in the duplication of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0028164-T01-IM6	AGMO-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) - AGMO (NM_001004320) rearrangement: t(7;18)(p21;q21.2)(chr7:g.15569155::chr18:g.48581266) Note: The SMAD4 - AGMO rearrangement is a reciprocal translocation which may result in the fusion of SMAD4 exons 1-5 with AGMO exons 4-13. One of the breakpoints is within exon 5 of SMAD4. Its functional significance is undetermined.
AGMO	0	MSKCC-DMP	P-0028164-T01-IM6	AGMO-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) - AGMO (NM_001004320) rearrangement: t(7;18)(p21;q21.2)(chr7:g.15569155::chr18:g.48581266) Note: The SMAD4 - AGMO rearrangement is a reciprocal translocation which may result in the fusion of SMAD4 exons 1-5 with AGMO exons 4-13. One of the breakpoints is within exon 5 of SMAD4. Its functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0028195-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.-40-3515_c.424inv Note: The BCOR rearrangement is an intragenic inversion of exons 2-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
LINC00911	0	MSKCC-DMP	P-0028200-T01-IM6	RXRA-LINC00911 fusion	yes	unknown		unknown	RXRA (NM_002957) translocation: t(9;14)(q34.2;q31.3)(chr9:g.137321221::chr14:g.85179414) Note: The RXRA rearrangement is a translocation with a breakpoint within RXRA intron 7. The functional significance is undetermined.
RXRA	0	MSKCC-DMP	P-0028200-T01-IM6	RXRA-LINC00911 fusion	yes	unknown		unknown	RXRA (NM_002957) translocation: t(9;14)(q34.2;q31.3)(chr9:g.137321221::chr14:g.85179414) Note: The RXRA rearrangement is a translocation with a breakpoint within RXRA intron 7. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0028206-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.2521-250_c.2664-33del Note: The RB1 rearrangement is a intragenic deletion of exon 25. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0028250-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.-32+6538_c.1419+169dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 2-8. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0028254-T01-IM6	XRCC2-KMT2C fusion	yes	unknown		unknown	XRCC2 (NM_005431) - KMT2C (NM_170606) rearrangement: c.39+1308:XRCC2_c.289:KMT2Cdel Note: The XRCC2 - KMT2C rearrangement is a deletion that results in the fusion of XRCC2 exon 1 - KMT2C exon 3. One of the breakpoints is within KMT2C exon 3. The functional significance is undetermined.
XRCC2	0	MSKCC-DMP	P-0028254-T01-IM6	XRCC2-KMT2C fusion	yes	unknown		unknown	XRCC2 (NM_005431) - KMT2C (NM_170606) rearrangement: c.39+1308:XRCC2_c.289:KMT2Cdel Note: The XRCC2 - KMT2C rearrangement is a deletion that results in the fusion of XRCC2 exon 1 - KMT2C exon 3. One of the breakpoints is within KMT2C exon 3. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0015434-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 13 fused to ALK exon20): c.1489+63:EML4_c.3172+130:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
EML4	0	MSKCC-DMP	P-0015434-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 13 fused to ALK exon20): c.1489+63:EML4_c.3172+130:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
ERG	0	MSKCC-DMP	P-0028090-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+8087:ERG_c.127-641:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion which involves ERG exons 1 with TMPRSS2 exons 3-14. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0028090-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+8087:ERG_c.127-641:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion which involves ERG exons 1 with TMPRSS2 exons 3-14. Its functional significance is undetermined.
CRYL1	0	MSKCC-DMP	P-0028093-T01-IM6	FLT1-CRYL1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.3814:FLT1_chr13:g.20956827del Note: The FLT1 rearrangement is a deletion of FLT1 exons 29-30. One breakpoint is within exon 29. Its functional significance is undetermined.
FLT1	0	MSKCC-DMP	P-0028093-T01-IM6	FLT1-CRYL1 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.3814:FLT1_chr13:g.20956827del Note: The FLT1 rearrangement is a deletion of FLT1 exons 29-30. One breakpoint is within exon 29. Its functional significance is undetermined.
COL5A3	0	MSKCC-DMP	P-0028094-T01-IM6	NOTCH3-COL5A3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.3604:NOTCH3_chr19:g.10091386del Note: The NOTCH3 rearrangement results in the deletion of NOTCH3 exons 1-22. Its functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0028094-T01-IM6	NOTCH3-COL5A3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.3604:NOTCH3_chr19:g.10091386del Note: The NOTCH3 rearrangement results in the deletion of NOTCH3 exons 1-22. Its functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0028098-T01-IM6	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_058195) rearrangement: c.*92_c.194-995del Note: The CDKN2A rearrangement is a deletion of CDKN2Ap14ARF intron 1 to exon 2. Its functional significance is undetermined,
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0028098-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.448_c.151-995del Note: The CDKN2A rearrangement is a deletion of CDKN2Ap16INK4A intron 1 to exon 2. Its functional significance is undetermined,
RAD54L	0	MSKCC-DMP	P-0028377-T01-IM6	LINC00538-RAD54L fusion	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.1169+292:RAD54L_chr1:g.213770090inv Note: The RAD54L rearrangement is an inversion of exons 12-19. The functional significance is undetermined.
LINC00538	0	MSKCC-DMP	P-0028377-T01-IM6	LINC00538-RAD54L fusion	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.1169+292:RAD54L_chr1:g.213770090inv Note: The RAD54L rearrangement is an inversion of exons 12-19. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0022291-T02-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.1685_c.3809+5643inv Note: The ATRX rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. The functional significance is undetermined.
RNPEP	0	MSKCC-DMP	P-0028321-T01-IM6	ELF3-RNPEP fusion	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.435:ELF3_chr1:g.201971987inv Note: The ELF3 rearrangement is an inversion of ELF3 exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0028321-T01-IM6	ELF3-RNPEP fusion	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.435:ELF3_chr1:g.201971987inv Note: The ELF3 rearrangement is an inversion of ELF3 exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.
LOC101929504	0	MSKCC-DMP	P-0013114-T02-IM6	VTCN1-LOC101929504 fusion	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: t(1;6)(p13.1;q27)(chr1:g.117753496::chr6:g.169564182) Note: The VTCN1 rearrangement is a translocation that may disrupt the 5UTR region. The functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0013114-T02-IM6	VTCN1-LOC101929504 fusion	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: t(1;6)(p13.1;q27)(chr1:g.117753496::chr6:g.169564182) Note: The VTCN1 rearrangement is a translocation that may disrupt the 5UTR region. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0028287-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-2623:EML4_c.3173-267:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0028287-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-2623:EML4_c.3173-267:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
PPM1D	0	MSKCC-DMP	P-0028289-T01-IM6	USH2A-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: 1;17)(q41;q23.2)(chr1:g.216077920chr17:g.58740285) Note: The PPM1D rearrangement is a translocation involving exon 6. Its functional significance is undetermined.
USH2A	0	MSKCC-DMP	P-0028289-T01-IM6	USH2A-PPM1D fusion	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: 1;17)(q41;q23.2)(chr1:g.216077920chr17:g.58740285) Note: The PPM1D rearrangement is a translocation involving exon 6. Its functional significance is undetermined.
MYH9	0	MSKCC-DMP	P-0028295-T01-IM6	ROS1-MYH9 fusion	yes	unknown		in frame	MYH9 (NM_002473) - ROS1 (NM_002944) rearrangement: t(6;22)(q22.1;q12.3)(chr6:g.117641564::chr22:g.36691922) Note: The MYH9 - ROS1 rearrangement is a translocation which may result in a fusion of MYH9 exons 1-25 with ROS1 exons 36-43. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0028295-T01-IM6	ROS1-MYH9 fusion	yes	unknown		in frame	MYH9 (NM_002473) - ROS1 (NM_002944) rearrangement: t(6;22)(q22.1;q12.3)(chr6:g.117641564::chr22:g.36691922) Note: The MYH9 - ROS1 rearrangement is a translocation which may result in a fusion of MYH9 exons 1-25 with ROS1 exons 36-43. Its functional significance is undetermined.
XBP1	0	MSKCC-DMP	P-0028363-T01-IM6	EWSR1-XBP1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: c.992+544:EWSR1_chr22:g.29219730del. Note: The EWSR1 rearrangement results in the deletion of EWSR1 exon 1 to exon 9. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0028363-T01-IM6	EWSR1-XBP1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: c.992+544:EWSR1_chr22:g.29219730del. Note: The EWSR1 rearrangement results in the deletion of EWSR1 exon 1 to exon 9. Its functional significance is undetermined.
TPCN2	0	MSKCC-DMP	P-0014689-T02-IM6	FGF3-TPCN2 fusion	yes	unknown		unknown	TPCN2 (NM_139075) - FGF3 (NM_005247) rearrangement: c.1589+280:TPCN2_c.325-1954:FGF3del Note: The TPCN2 - FGF3 rearrangement is a deletion which involves TPCN2 exons 1-17 and FGF3 exons 1-2.
FGF3	0	MSKCC-DMP	P-0014689-T02-IM6	FGF3-TPCN2 fusion	yes	unknown		unknown	TPCN2 (NM_139075) - FGF3 (NM_005247) rearrangement: c.1589+280:TPCN2_c.325-1954:FGF3del Note: The TPCN2 - FGF3 rearrangement is a deletion which involves TPCN2 exons 1-17 and FGF3 exons 1-2.
ALK	0	MSKCC-DMP	P-0027119-T03-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1316-837:EML4_c.3173-317:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0027119-T03-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1316-837:EML4_c.3173-317:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
NOTCH2	0	MSKCC-DMP	P-0027998-T01-IM6	NOTCH2-intragenic	yes	unknown		in frame	NOTCH2 (NM_024408) fusion: c.3337+43_c.1916-44dup Note: The NOTCH2 fusion is predicted to be in frame. Its functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0028344-T01-IM6	PDE4D-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: t(5;11)(q11.2;q22.1)(chr5:g.58795652::chr11:g.102056674) Note: The YAP1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
PDE4D	0	MSKCC-DMP	P-0028344-T01-IM6	PDE4D-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: t(5;11)(q11.2;q22.1)(chr5:g.58795652::chr11:g.102056674) Note: The YAP1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0028344-T01-IM6	MED13L-TBX3 fusion	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.960:TBX3_chr12:g.116070739del Note: The TBX3 rearrangement results in the deletion of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
MED13L	0	MSKCC-DMP	P-0028344-T01-IM6	MED13L-TBX3 fusion	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.960:TBX3_chr12:g.116070739del Note: The TBX3 rearrangement results in the deletion of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
TNFRSF14	0	MSKCC-DMP	P-0028405-T01-IM6	CNKSR1-TNFRSF14 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: c.694+62_chr1:g.26512742inv Note: The TNFRSF14 rearrangement is an inversion that includes TNFRSF14 exons 7-8. The functional significance is undetermined.
CNKSR1	0	MSKCC-DMP	P-0028405-T01-IM6	CNKSR1-TNFRSF14 fusion	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: c.694+62_chr1:g.26512742inv Note: The TNFRSF14 rearrangement is an inversion that includes TNFRSF14 exons 7-8. The functional significance is undetermined.
RHOV	0	MSKCC-DMP	P-0028414-T01-IM6	RIT1-RHOV fusion	yes	unknown		unknown	RIT1 (NM_006912) rearrangement: t(1;15)(q22;q15.1)(chr1:g.155880302::chr15:g.41171099) Note: The RIT1 rearrangement is a translocation with a breakpoint within RIT1 intron 2. The functional significance is undetermined.
RIT1	0	MSKCC-DMP	P-0028414-T01-IM6	RIT1-RHOV fusion	yes	unknown		unknown	RIT1 (NM_006912) rearrangement: t(1;15)(q22;q15.1)(chr1:g.155880302::chr15:g.41171099) Note: The RIT1 rearrangement is a translocation with a breakpoint within RIT1 intron 2. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0006768-T03-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) Rearrangement : c.89-37152_c.890-499inv The EGFR Rearrangement results in the inversion of exons 2 to 7 of EGFR. Its functional significance is undetermined.  Based on read counts, this rearrangement may be subclonal or present on only a minority of amplified EGFR alleles. Its functional significance is undetermined. This rearrangement is the equivalent of and represents an updated annotation of the EGFR rearrangement that was previously reported in M15-17175 and M16-17834.
SMARCA4	0	MSKCC-DMP	P-0007125-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.-32+11329_c.886del The SMARCA4 (NM_003072) rearrangement is an intragenic deletion of exons 2-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0007125-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-14 with ALK exons 20-29) : c.1328:EML4_c.3173-203:ALKinv The EML4 (NM_019063) - ALK (NM_004304) rearrangement is a reciprocal fusion and includes the kinase domain of ALK. One of the breakpoints is within exon 14 of EML4.
EML4	0	MSKCC-DMP	P-0007125-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-14 with ALK exons 20-29) : c.1328:EML4_c.3173-203:ALKinv The EML4 (NM_019063) - ALK (NM_004304) rearrangement is a reciprocal fusion and includes the kinase domain of ALK. One of the breakpoints is within exon 14 of EML4.
SPATS2	0	MSKCC-DMP	P-0021045-T02-IM6	SMARCD1-SPATS2 fusion	yes	unknown		unknown	SMARCD1 (NM_003076) - SPATS2 (NM_023071) rearrangement:  c.365+3:SMARCD1_c.-243-34386:SPATS2dup. Note: The SMARCD1 - SPATS2 rearrangement is a duplication that may results in the fusion of SMARCD1 exons 1-2 and SPATS2 eons 3-14. Its functional significance is undetermined.
SMARCD1	0	MSKCC-DMP	P-0021045-T02-IM6	SMARCD1-SPATS2 fusion	yes	unknown		unknown	SMARCD1 (NM_003076) - SPATS2 (NM_023071) rearrangement:  c.365+3:SMARCD1_c.-243-34386:SPATS2dup. Note: The SMARCD1 - SPATS2 rearrangement is a duplication that may results in the fusion of SMARCD1 exons 1-2 and SPATS2 eons 3-14. Its functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0021177-T02-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.1318+591:TCF7L2_chr10:g.115131344del Note: The TCF7L2 rearrangement is a deletion of exons 13-14.
HABP2	0	MSKCC-DMP	P-0021177-T02-IM6	HABP2-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.1318+591:TCF7L2_chr10:g.115131344del Note: The TCF7L2 rearrangement is a deletion of exons 13-14.
KMT2D	0	MSKCC-DMP	P-0021177-T02-IM6	DHH-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.6450:KMT2D_chr12:g.49487152del Note: The KMT2D rearrangement is a deletion of exons 1-31. One of the breakpoints is within exon 31.
DHH	0	MSKCC-DMP	P-0021177-T02-IM6	DHH-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.6450:KMT2D_chr12:g.49487152del Note: The KMT2D rearrangement is a deletion of exons 1-31. One of the breakpoints is within exon 31.
BAP1	0	MSKCC-DMP	P-0028302-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.68-6:BAP1_chr3:g.52450481del Note: The BAP1 rearrangement is a deletion of BAP1 exons  1-2. Its functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0028302-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.68-6:BAP1_chr3:g.52450481del Note: The BAP1 rearrangement is a deletion of BAP1 exons  1-2. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0028430-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10). Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0028430-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10). Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG (NM_004449) transcript.
NF1	0	MSKCC-DMP	P-0028432-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) rearrangement: c.4111-120_c.4430+350dup. Note: The NF1 rearrangement is an intragenic duplications of exons 31-33. Its functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0028433-T01-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4193:NOTCH3_chr19:g.15441551del Note: The NOTCH3 rearrangement is a deletion of exons 1-24. One of the breakpoints is within exon 24. Its functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0028433-T01-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4193:NOTCH3_chr19:g.15441551del Note: The NOTCH3 rearrangement is a deletion of exons 1-24. One of the breakpoints is within exon 24. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0028470-T01-IM6	MON2-ARID2 fusion	yes	unknown		out of frame	ARID2 (NM_152641) - MON2 (NM_015026) rearrangement: c.186+70:ARID2_c.176-4180del Note: The ARID2 - MON2 rearrangement is a deletion that results in a fusion of ARID2 exons 1-2 to MON2 exons 3-35. The functional significance is undetermined.
MON2	0	MSKCC-DMP	P-0028470-T01-IM6	MON2-ARID2 fusion	yes	unknown		out of frame	ARID2 (NM_152641) - MON2 (NM_015026) rearrangement: c.186+70:ARID2_c.176-4180del Note: The ARID2 - MON2 rearrangement is a deletion that results in a fusion of ARID2 exons 1-2 to MON2 exons 3-35. The functional significance is undetermined.
MLL2	0	MSKCC-DMP	P-0003132-T01-IM5	MLL2-intragenic	yes	unknown		unknown	null   Note: The MLL2 (NM_003482) rearrangement event is an intragenic deletion which results in the deletion of exons 9-54, potentially disabling the function of the gene.
SLIT3	0	MSKCC-DMP	P-0003233-T05-IM6	FGFR4-SLIT3 fusion	yes	unknown		unknown	FGFR4 (NM_213647) rearrangement: c.919-52:FGFR4_chr5:g.168403446dup Note: The FGFR4 rearrangement results in the duplication of exons 1-7. Its functional significance is undetermined.
FGFR4	0	MSKCC-DMP	P-0003233-T05-IM6	FGFR4-SLIT3 fusion	yes	unknown		unknown	FGFR4 (NM_213647) rearrangement: c.919-52:FGFR4_chr5:g.168403446dup Note: The FGFR4 rearrangement results in the duplication of exons 1-7. Its functional significance is undetermined.
KIAA1468	0	MSKCC-DMP	P-0004094-T02-IM6	RET-KIAA1468 fusion	yes	unknown		in frame	KIAA1468 (NM_020854) - RET (NM_020975) fusion (KIAA1468 exons 1-10 fused with RET exons 12-20): t(10;18)(q11.21;q21.33)(chr10:g.43610279::chr18:g.59909399) Note: The KIAA1468 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0004094-T02-IM6	RET-KIAA1468 fusion	yes	unknown		in frame	KIAA1468 (NM_020854) - RET (NM_020975) fusion (KIAA1468 exons 1-10 fused with RET exons 12-20): t(10;18)(q11.21;q21.33)(chr10:g.43610279::chr18:g.59909399) Note: The KIAA1468 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
KMT2D	0	MSKCC-DMP	P-0004756-T02-IM6	WHSC1L1-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - WHSC1L1 (NM_018013) rearrangement: t(8;12)(p11.22;q13.12)(chr8:g.38151870::chr12:g.32312089) Note: The KMT2D - WHSC1L1 is a translocation that results in the fusion of KMT2D exons 1-39 with WHSC1L1 exons 17-24. One of the breakpoints is within the exon 39 of KMT2D. The functional significance is undetermined. In addition, another KMT2D rearrangement was detected. The possibility of a more complex rearrangement resulting in a KMT2D gene fusion cannot be excluded.
WHSC1L1	0	MSKCC-DMP	P-0004756-T02-IM6	WHSC1L1-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - WHSC1L1 (NM_018013) rearrangement: t(8;12)(p11.22;q13.12)(chr8:g.38151870::chr12:g.32312089) Note: The KMT2D - WHSC1L1 is a translocation that results in the fusion of KMT2D exons 1-39 with WHSC1L1 exons 17-24. One of the breakpoints is within the exon 39 of KMT2D. The functional significance is undetermined. In addition, another KMT2D rearrangement was detected. The possibility of a more complex rearrangement resulting in a KMT2D gene fusion cannot be excluded.
KMT2D	0	MSKCC-DMP	P-0004756-T02-IM6	ARFGEF1-KMT2D fusion	yes	unknown		unknown	ARFGEF1 (NM_006421) - KMT2D (NM_003482) rearrangement: t(8;12)(q13.2;q13.12)(chr8:g.68111283::chr12:g.49425875) Note: The ARFGEF1 - KMT2D is a translocation that results in the fusion of ARFGEF1 exons 1-39 with KMT2D exons 39-54. The breakpoints are within exon 39 of ARFGEF1 and exon 39 of KMT2D. The functional significance is undetermined. In addition, another KMT2D rearrangement was detected. The possibility of a more complex rearrangement resulting in a KMT2D gene fusion cannot be excluded.
ARFGEF1	0	MSKCC-DMP	P-0004756-T02-IM6	ARFGEF1-KMT2D fusion	yes	unknown		unknown	ARFGEF1 (NM_006421) - KMT2D (NM_003482) rearrangement: t(8;12)(q13.2;q13.12)(chr8:g.68111283::chr12:g.49425875) Note: The ARFGEF1 - KMT2D is a translocation that results in the fusion of ARFGEF1 exons 1-39 with KMT2D exons 39-54. The breakpoints are within exon 39 of ARFGEF1 and exon 39 of KMT2D. The functional significance is undetermined. In addition, another KMT2D rearrangement was detected. The possibility of a more complex rearrangement resulting in a KMT2D gene fusion cannot be excluded.
DOCK9	0	MSKCC-DMP	P-0004756-T02-IM6	IRS2-DOCK9 fusion	yes	unknown		unknown	IRS2 (NM_003749) - DOCK9 (NM_015296) rearrangement: c.2538:IRS2_c.130-30138:DOCK9del Note: The IRS2 - DOCK9 rearrangement is a deletion that results in the fusion of IRS2 exon 1 with DOCK9 exons 2-56. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0004756-T02-IM6	IRS2-DOCK9 fusion	yes	unknown		unknown	IRS2 (NM_003749) - DOCK9 (NM_015296) rearrangement: c.2538:IRS2_c.130-30138:DOCK9del Note: The IRS2 - DOCK9 rearrangement is a deletion that results in the fusion of IRS2 exon 1 with DOCK9 exons 2-56. One of the breakpoints is within IRS2 exon 1. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0004937-T02-IM6	C11orf65-ATM fusion	yes	unknown		unknown	ATM (NM_000051) - C11orf65 (NM_152587) rearrangement : c.8987+25:ATM_c.*1558:C11orf65del Note: The ATM (NM_000051) - C11orf65 (NM_152587) rearrangement results in the deletion of ATM exon63.
C11orf65	0	MSKCC-DMP	P-0004937-T02-IM6	C11orf65-ATM fusion	yes	unknown		unknown	ATM (NM_000051) - C11orf65 (NM_152587) rearrangement : c.8987+25:ATM_c.*1558:C11orf65del Note: The ATM (NM_000051) - C11orf65 (NM_152587) rearrangement results in the deletion of ATM exon63.
RTEL1	0	MSKCC-DMP	P-0004937-T02-IM6	HAVCR1P1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(19;20)(p11;q13.33)(chr19:g.24531369::chr20:g.62303901) Note: The RTEL1 rearrangement is a translocation with a breakpoint after exon 5. The functional significance is undetermined.
HAVCR1P1	0	MSKCC-DMP	P-0004937-T02-IM6	HAVCR1P1-RTEL1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(19;20)(p11;q13.33)(chr19:g.24531369::chr20:g.62303901) Note: The RTEL1 rearrangement is a translocation with a breakpoint after exon 5. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0005502-T03-IM6	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) rearrangement: c.861+125_c.1696-1106del Note: The RB1 rearrangement results in the in-frame deletion of exons 9-17. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0008082-T01-IM5	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.4945_c.6841+44del Note: The BRCA2 (NM_000059) rearrangement event is a deletion which results in the deletion of a part of BRCA2 exon 11. And one of breakpoints is within exon 11. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0008525-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+622:TMPRSS2_c.40-44718:ERGdel Note: The TMPRSS2 - ERG fusion event involves the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0008525-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+622:TMPRSS2_c.40-44718:ERGdel Note: The TMPRSS2 - ERG fusion event involves the non-canonical ERG (NM_004449) transcript.
CNTRL	0	MSKCC-DMP	P-0008525-T02-IM6	SETD2-CNTRL fusion	yes	unknown		unknown	CNTRL (NM_007018) - SETD2 (NM_014159) rearrangement: t(3;9)(p21.31;q33.2)(chr3:g.47162787::chr9:g.123913096) Note: The CNTRL - SETD2 rearrangement is a translocation which may result in the fusion of CNTRL exons 1-23 with SETD2 exons 2-21. One of the breakpoints is within SETD2 exon 3.
SETD2	0	MSKCC-DMP	P-0008525-T02-IM6	SETD2-CNTRL fusion	yes	unknown		unknown	CNTRL (NM_007018) - SETD2 (NM_014159) rearrangement: t(3;9)(p21.31;q33.2)(chr3:g.47162787::chr9:g.123913096) Note: The CNTRL - SETD2 rearrangement is a translocation which may result in the fusion of CNTRL exons 1-23 with SETD2 exons 2-21. One of the breakpoints is within SETD2 exon 3.
LINGO2	0	MSKCC-DMP	P-0008712-T02-IM6	PAX5-LINGO2 fusion	yes	unknown		unknown	PAX5 (NM_016734) rearrangement: c.910+60_chr9:g.29168846del Note: The PAX5 (NM_016734) rearrangement is a deletion of exons 8-10. The functional significance is undetermined.
PAX5	0	MSKCC-DMP	P-0008712-T02-IM6	PAX5-LINGO2 fusion	yes	unknown		unknown	PAX5 (NM_016734) rearrangement: c.910+60_chr9:g.29168846del Note: The PAX5 (NM_016734) rearrangement is a deletion of exons 8-10. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0009687-T02-IM6	SPG11-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(15;17)(q21.1;p13.1)(chr15:g.44943476::chr17:g.7579206) Note: The TP53 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.
SPG11	0	MSKCC-DMP	P-0009687-T02-IM6	SPG11-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(15;17)(q21.1;p13.1)(chr15:g.44943476::chr17:g.7579206) Note: The TP53 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0009687-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+3180:TMPRSS2_c.18+6016:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0009687-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+3180:TMPRSS2_c.18+6016:ERGdel
DGCR5	0	MSKCC-DMP	P-0009687-T02-IM6	EP300-DGCR5 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.6795:EP300_chr22:g.18946332dup Note: The EP300 rearrangement results in the duplication of exons 1-31. One of the breakpoints is within exon 31. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0009687-T02-IM6	EP300-DGCR5 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.6795:EP300_chr22:g.18946332dup Note: The EP300 rearrangement results in the duplication of exons 1-31. One of the breakpoints is within exon 31. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0012695-T01-IM5	DENND3-TMPRSS2 fusion	yes	unknown		out of frame	DENND3 - TMPRSS2 rearrangement: t(8;21)(q24.3;q22.3)(chr8:g.142204112::chr21:g.42873872) Note: The DENND3 - TMPRSS2 rearrangement is a translocation which results in the fusion of DENND3 exons 1-22 with TMPRSS2 exons 2-14. The functional significance is undetermined. We cannot exclude the possibility of a more complex genomic rearrangement that leads to a TMPRSS2 - ERG fusion. Additional testing by an alternate method is suggested, if clinically indicated.
DENND3	0	MSKCC-DMP	P-0012695-T01-IM5	DENND3-TMPRSS2 fusion	yes	unknown		out of frame	DENND3 - TMPRSS2 rearrangement: t(8;21)(q24.3;q22.3)(chr8:g.142204112::chr21:g.42873872) Note: The DENND3 - TMPRSS2 rearrangement is a translocation which results in the fusion of DENND3 exons 1-22 with TMPRSS2 exons 2-14. The functional significance is undetermined. We cannot exclude the possibility of a more complex genomic rearrangement that leads to a TMPRSS2 - ERG fusion. Additional testing by an alternate method is suggested, if clinically indicated.
ERBB2	0	MSKCC-DMP	P-0013755-T02-IM6	IKZF3-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) Rearrangement :  c.759+36:ERBB2_c.827-2329:IKZF3 Note: The ERBB2 rearrangement results in the duplication of exons 7-27. It includes the kinase domain of ERBB2. Its functional significance is undetermined.
IKZF3	0	MSKCC-DMP	P-0013755-T02-IM6	IKZF3-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) Rearrangement :  c.759+36:ERBB2_c.827-2329:IKZF3 Note: The ERBB2 rearrangement results in the duplication of exons 7-27. It includes the kinase domain of ERBB2. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0013934-T02-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.*1763_c.3310inv Note: The NOTCH1 (NM_017617) rearrangement is an inversion of exons 20 - 34. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0017365-T03-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+25501:CCDC6_c.2137-568:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0017365-T03-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+25501:CCDC6_c.2137-568:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
PIK3C2G	0	MSKCC-DMP	P-0017365-T03-IM6	PIK3C2G-intragenic	yes	unknown		out of frame	PIK3C2G (NM_004570) rearrangement: c.1873-3988_c.2004-111del Note: The PIK3C2G rearrangement is an intragenic deletion of exon 14. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0017365-T03-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.458-15_chr9:g.22143651del Note: The CDKN2A rearrangement is a deletion which includes exons 1-2 of both the CDKN2Ap16INK4 and CDKN2Ap14ARF isoforms of CDKN2A. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0017365-T03-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.458-15_chr9:g.22143651del Note: The CDKN2A rearrangement is a deletion which includes exons 1-2 of both the CDKN2Ap16INK4 and CDKN2Ap14ARF isoforms of CDKN2A. The functional significance is undetermined.
LATS1	0	MSKCC-DMP	P-0018046-T02-IM6	LATS1-intragenic	yes	unknown		out of frame	LATS1 (NM_004690) Rearrangement: c.2883+965_c.2776+12del Note: The LATS1 rearrangement is a deletion of LATS1 exon 7. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0018583-T02-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.1592:SMAD4_chr18:g.48624100del Note: The SMAD4 rearrangement is a deletion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0019246-T03-IM6	LOC100287015-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(8;19)(p23.2;p13.2)(chr8:g.5383702::chr19:g.11100157) Note: The SMARCA4 rearrangement is a translocation involving exon 7. Its functional significance is undetermined.
MCPH1-DT	0	MSKCC-DMP	P-0019246-T03-IM6	MCPH1-DT-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(8;19)(p23.2;p13.2)(chr8:g.5383702::chr19:g.11100157) Note: The SMARCA4 rearrangement is a translocation involving exon 7. Its functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0019246-T03-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.670_c.246+4853del Note: The EZH2 rearrangement is an intragenic deletion of exons 4-7. One of the breakpoints is within exon 7. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0019543-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) Rearrangement : c.4111-53_c.4430+537dup Note: The NF1 Rearrangement results in the duplication of exons 31-33 of NF1. Its functional significance is undetermined.
NPR2	0	MSKCC-DMP	P-0019543-T01-IM6	NOTCH1-NPR2 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - NPR2 (NM_003995) Rearrangement: c.1520:NOTCH1_c.-1180:NPR2inv Note: The NOTCH1 - NPR2 Rearrangement results in the fusion of exons 1-9 of NOTCH1 with the promoter region of NPR2 The breakpoints are within exon9 of NOTCH1 and the promoter region of NPR2 before transcription start site. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0019543-T01-IM6	NOTCH1-NPR2 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - NPR2 (NM_003995) Rearrangement: c.1520:NOTCH1_c.-1180:NPR2inv Note: The NOTCH1 - NPR2 Rearrangement results in the fusion of exons 1-9 of NOTCH1 with the promoter region of NPR2 The breakpoints are within exon9 of NOTCH1 and the promoter region of NPR2 before transcription start site. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0020138-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20 -29): c.668-3016:EML4_c.3172+420:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0020138-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20 -29): c.668-3016:EML4_c.3172+420:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
RTEL1	0	MSKCC-DMP	P-0020766-T01-IM6	LOC401177-RTEL1 fusion	yes	unknown		unknown	RTEL (NM_032957) - rearrangement: t(5,20)(p14.3,q13.33)(chr5:g.18137294::chr20:g.62322308) Note: The RTEL rearrangement is a translocation that may result in the truncation of RTEL1 exons 28-35. Its functional significance is undetermined.
LOC401177	0	MSKCC-DMP	P-0020766-T01-IM6	LOC401177-RTEL1 fusion	yes	unknown		unknown	RTEL (NM_032957) - rearrangement: t(5,20)(p14.3,q13.33)(chr5:g.18137294::chr20:g.62322308) Note: The RTEL rearrangement is a translocation that may result in the truncation of RTEL1 exons 28-35. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0021693-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exons 1-14 fused with ALK exons 20-29): c.1316-1509:EML4_c.3173-608:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0021693-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exons 1-14 fused with ALK exons 20-29): c.1316-1509:EML4_c.3173-608:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
FOLR3	0	MSKCC-DMP	P-0022100-T03-IM6	INPPL1-FOLR3 fusion	yes	unknown		unknown	INPPL1 (NM_001567) Rearrangement: c.2880-103:INPPL1_g.71834974del Note: The INPPL1 rearrangement results in the deletion of INPPL1 exons 1-25. The functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0022100-T03-IM6	INPPL1-FOLR3 fusion	yes	unknown		unknown	INPPL1 (NM_001567) Rearrangement: c.2880-103:INPPL1_g.71834974del Note: The INPPL1 rearrangement results in the deletion of INPPL1 exons 1-25. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0022101-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon18 fused with ALK exon 20): c.2057-510:EML4_c.2057-510:ALKinv Note: The EML4 -ALK Fusion is an in-frame fusion and includes the protein kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0022101-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon18 fused with ALK exon 20): c.2057-510:EML4_c.2057-510:ALKinv Note: The EML4 -ALK Fusion is an in-frame fusion and includes the protein kinase domain of ALK.
NOTCH3	0	MSKCC-DMP	P-0022530-T02-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4812:NOTCH3_chr19:g.15437650del Note: The NOTCH3 rearrangement results in the deletion of NOTCH3 exons 1 to 26. One of the breakpoints is within NOTCH3 exon 26, Its functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0022530-T02-IM6	AKAP8-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4812:NOTCH3_chr19:g.15437650del Note: The NOTCH3 rearrangement results in the deletion of NOTCH3 exons 1 to 26. One of the breakpoints is within NOTCH3 exon 26, Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0023156-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) Rearrangement : c.-13+371_c.236+173inv Note: The PBRM1 Rearrangement results in the inversion of exons 1-3 of PBRM1. One of the breakpoints is within the 5-UTR region of PBRM1. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0024200-T02-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.375-198:STK11_chr19:g.1202435del Note: The STK11 rearrangement is a deletion of exons 1-2.
NFE2L2	0	MSKCC-DMP	P-0024229-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement:  c.46-3198_c.73del Note: The NFE2L2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0024869-T01-IM6	TEX9-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.8484_chr15:g.56553582del Note: The MGA rearrangement results in the deletion of exon 24. One of the breakpoints is within exon 24. The functional significance is undetermined.
TEX9	0	MSKCC-DMP	P-0024869-T01-IM6	TEX9-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.8484_chr15:g.56553582del Note: The MGA rearrangement results in the deletion of exon 24. One of the breakpoints is within exon 24. The functional significance is undetermined.
FGF8	0	MSKCC-DMP	P-0028166-T01-IM6	SUFU-FGF8 fusion	yes	unknown		unknown	SUFU (NM_016169) rearrangement: c.1297-55_g.103512655del Note: SUFU (NM_016169) rearrangement results in the deletion of exons 1-10. Its functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0028166-T01-IM6	SUFU-FGF8 fusion	yes	unknown		unknown	SUFU (NM_016169) rearrangement: c.1297-55_g.103512655del Note: SUFU (NM_016169) rearrangement results in the deletion of exons 1-10. Its functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0028166-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.4121-11_g.77074225del Note: ATRX (NM_000489) rearrangement results in the deletion of exons 1-12. Its functional significance is undetermined.
MAGT1	0	MSKCC-DMP	P-0028166-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.4121-11_g.77074225del Note: ATRX (NM_000489) rearrangement results in the deletion of exons 1-12. Its functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0028361-T01-IM6	YEATS4-GLI1 fusion	yes	unknown		in frame	GLI1 (NM_005269) - YEATS4 (NM_006530) rearrangement: c.912+76:GLI1_c.52-806:YEATS4del Note: The GLI1 - YEATS4 rearrangement is a deletion that may result in fusion of GLI1 exons 1-8 and YEATS4 exons 2-7. Its functional significance is undetermined.
YEATS4	0	MSKCC-DMP	P-0028361-T01-IM6	YEATS4-GLI1 fusion	yes	unknown		in frame	GLI1 (NM_005269) - YEATS4 (NM_006530) rearrangement: c.912+76:GLI1_c.52-806:YEATS4del Note: The GLI1 - YEATS4 rearrangement is a deletion that may result in fusion of GLI1 exons 1-8 and YEATS4 exons 2-7. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0028420-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A  (NM_006015) rearrangement: c.1920+13682_c.2420-85del Note: The ARID1A rearrangement is a deletion of exons 5-7. Its functional significance is undetermined.
MALT1	0	MSKCC-DMP	P-0028513-T01-IM6	SEC11C-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.403:MALT1_g.56805185dup Note: The MALT1 (NM_006785) rearrangement is a duplication of exons 3-17. One of the breakpoints is within exon 3 of MALT1. The functional significance is undetermined.
SEC11C	0	MSKCC-DMP	P-0028513-T01-IM6	SEC11C-MALT1 fusion	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.403:MALT1_g.56805185dup Note: The MALT1 (NM_006785) rearrangement is a duplication of exons 3-17. One of the breakpoints is within exon 3 of MALT1. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0028541-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-2 fused with ALK exons 20-29): c.208+4631:EML4_c.3173-528:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0028541-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-2 fused with ALK exons 20-29): c.208+4631:EML4_c.3173-528:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
CBFB	0	MSKCC-DMP	P-0028548-T01-IM6	CBFB-intragenic	yes	unknown		in frame	CBFB (NM_022845) rearrangement: c.165+7_c.282+11707del Note: The CBFB rearrangement is an intragenic deletions of exon 3. Its functional significance is undetermined,
NSD1	0	MSKCC-DMP	P-0028548-T01-IM6	NSD1-intragenic	yes	unknown		out of frame	NSD1 (NM_022455) rearrangement: c.3797-8075_c.5893-134del Note: The NSD1 rearrangement results in intragenic deletions of exons 6 to 18. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0028551-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2137:TMPRSS_c.40-54306:ERGdel Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0028551-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2137:TMPRSS_c.40-54306:ERGdel Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).
NRG1	0	MSKCC-DMP	P-0028576-T01-IM6	WHSC1L1-NRG1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2758+79:WHSC1L1_chr8:g.32505812del Note: The WHSC1L1 rearrangement is a deletion of exons 16-24. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0028576-T01-IM6	WHSC1L1-NRG1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2758+79:WHSC1L1_chr8:g.32505812del Note: The WHSC1L1 rearrangement is a deletion of exons 16-24. Its functional significance is undetermined.
TOB2	0	MSKCC-DMP	P-0028582-T01-IM6	SH2B3-TOB2 fusion	yes	unknown		unknown	SH2B3 (NM_005475) rearrangement: t(12;22)(q24.12;q13.2)(chr12:g.111885072::chr22:g.41815856) Note: The SH2B3 rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.
SH2B3	0	MSKCC-DMP	P-0028582-T01-IM6	SH2B3-TOB2 fusion	yes	unknown		unknown	SH2B3 (NM_005475) rearrangement: t(12;22)(q24.12;q13.2)(chr12:g.111885072::chr22:g.41815856) Note: The SH2B3 rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0028587-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.-56-1085:TMPRSS2_c.18+6551:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0028587-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.-56-1085:TMPRSS2_c.18+6551:ERGdel
SHROOM4	0	MSKCC-DMP	P-0028601-T01-IM6	KDM5C-SHROOM4 fusion	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: chrX:g.50303622_c.228+26del Note: The KDM5C rearrangement is a deletion that includes KDM5C exons 3-26. The functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0028601-T01-IM6	KDM5C-SHROOM4 fusion	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: chrX:g.50303622_c.228+26del Note: The KDM5C rearrangement is a deletion that includes KDM5C exons 3-26. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0028626-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077, NM_058195) rearrangement: c.68:CDKN2A_chr9:g.22153033del. Note: The CDKN2A rearrangement is a deletion of CDKN2A  exon 1. One of the breakpoints is within CDKN2A exon 1. This alteration affects all CDKN2A isoforms and its functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0028626-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_000077, NM_058195) rearrangement: c.68:CDKN2A_chr9:g.22153033del. Note: The CDKN2A rearrangement is a deletion of CDKN2A  exon 1. One of the breakpoints is within CDKN2A exon 1. This alteration affects all CDKN2A isoforms and its functional significance is undetermined.
WWC2	0	MSKCC-DMP	P-0028631-T01-IM6	FAT1-WWC2 fusion	yes	unknown		unknown	FAT (NM_005245) rearrangement: c.8879-94:FAT1_chr4:g.184216350dup Note: The FAT rearrangement is a duplications of FAT exons 11-27. Its functional significance is undetermined,
FAT1	0	MSKCC-DMP	P-0028631-T01-IM6	FAT1-WWC2 fusion	yes	unknown		unknown	FAT (NM_005245) rearrangement: c.8879-94:FAT1_chr4:g.184216350dup Note: The FAT rearrangement is a duplications of FAT exons 11-27. Its functional significance is undetermined,
TSC2	0	MSKCC-DMP	P-0028632-T01-IM6	ZNF436-AS1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.23695925::chr16:g.2111887) Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 12 of TSC2. The functional significance is undetermined.
ZNF436-AS1	0	MSKCC-DMP	P-0028632-T01-IM6	ZNF436-AS1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.23695925::chr16:g.2111887) Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 12 of TSC2. The functional significance is undetermined.
PKN1	0	MSKCC-DMP	P-0028632-T01-IM6	JAK3-PKN1 fusion	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: c.1446:JAK3_chr19:g.14556834dup Note: The JAK3 rearrangement is a duplications of JAK3 exons 11-24. One of the breakpoints is within exon 11 of JAK3. The functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0028632-T01-IM6	JAK3-PKN1 fusion	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: c.1446:JAK3_chr19:g.14556834dup Note: The JAK3 rearrangement is a duplications of JAK3 exons 11-24. One of the breakpoints is within exon 11 of JAK3. The functional significance is undetermined.
LPPR1	0	MSKCC-DMP	P-0028636-T01-IM6	NOTCH1-LPPR1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.2563:NOTCH1_chr9:g.103795660del Note: The NOTCH1 rearrangement is a deletion of exons 16-34. One of the breakpoints is within exon 16. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0028636-T01-IM6	NOTCH1-LPPR1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.2563:NOTCH1_chr9:g.103795660del Note: The NOTCH1 rearrangement is a deletion of exons 16-34. One of the breakpoints is within exon 16. The functional significance is undetermined.
CRLF2	0	MSKCC-DMP	P-0029930-T01-IM6	EPB41L3-CRLF2 fusion	yes	unknown		unknown	EPB41L3 (NM_012307) - CRLF2 (NM_022148) rearrangement: t(X;18)(p11.31;p22.33)(chrX:g.1325397::chr18:g.5596405) Note: The CRLF2 rearrangement is a translocation with a breakpoint in exon 3. Its functional significance is undetermined.
EPB41L3	0	MSKCC-DMP	P-0029930-T01-IM6	EPB41L3-CRLF2 fusion	yes	unknown		unknown	EPB41L3 (NM_012307) - CRLF2 (NM_022148) rearrangement: t(X;18)(p11.31;p22.33)(chrX:g.1325397::chr18:g.5596405) Note: The CRLF2 rearrangement is a translocation with a breakpoint in exon 3. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029939-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4852:TMPRSS2_c.40-56952:ERG Note: The TMPRSS2 - ERG rearrangement is a duplication which results in the fusion of TMPRSS2 exon 1 with the non-canonical ERG (NM_004449) exons 4-10.
TMPRSS2	0	MSKCC-DMP	P-0029939-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4852:TMPRSS2_c.40-56952:ERG Note: The TMPRSS2 - ERG rearrangement is a duplication which results in the fusion of TMPRSS2 exon 1 with the non-canonical ERG (NM_004449) exons 4-10.
ATF1	0	MSKCC-DMP	P-0029943-T01-IM6	ERBB3-ATF1 fusion	yes	unknown		unknown	ATF1 (NM_005171) - ERBB3 (NM_001982) rearrangement: c.-6-6493:ATF1_c.1818:ERBB3del Note: The ATF1 - ERBB3 rearrangement is a deletion which results in the fusion of ATF1 exon 1 with ERBB3 exons 15-28. One of the breakpoints is within ERBB3 exon 15 and includes the kinase domain. Its functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0029943-T01-IM6	ERBB3-ATF1 fusion	yes	unknown		unknown	ATF1 (NM_005171) - ERBB3 (NM_001982) rearrangement: c.-6-6493:ATF1_c.1818:ERBB3del Note: The ATF1 - ERBB3 rearrangement is a deletion which results in the fusion of ATF1 exon 1 with ERBB3 exons 15-28. One of the breakpoints is within ERBB3 exon 15 and includes the kinase domain. Its functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0029944-T01-IM6	PTCH1-intragenic	yes	unknown		unknown	PTCH1 (NM_000264) rearrangement: c.3804+55:PTCH1_chr9:g.98108601del Note: The PTCH1 rearrangement is a deletion of exons 22-23.
ALK	0	MSKCC-DMP	P-0029971-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-119:EML4_c.3172+520:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-6 fused to ALK exons 20-29. It is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0029971-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-119:EML4_c.3172+520:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-6 fused to ALK exons 20-29. It is predicted to be in frame and includes the kinase domain of ALK.
STAT5B	0	MSKCC-DMP	P-0029972-T01-IM6	STAT5A-STAT5B fusion	yes	unknown		unknown	STAT5B (NM_012448) - STAT5A (NM_003152) rearrangement: c.1052:STAT5B_c.1005:STAT5Ainv Note: The STAT5B - STAT5A rearrangement is an inversion that results in the fusion of STAT5B exons 1-9 with STAT5A exons 10-20. One of the breakpoints is within STAT5B exon 9 and the other is within STAT5A exon 10. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0029972-T01-IM6	STAT5A-STAT5B fusion	yes	unknown		unknown	STAT5B (NM_012448) - STAT5A (NM_003152) rearrangement: c.1052:STAT5B_c.1005:STAT5Ainv Note: The STAT5B - STAT5A rearrangement is an inversion that results in the fusion of STAT5B exons 1-9 with STAT5A exons 10-20. One of the breakpoints is within STAT5B exon 9 and the other is within STAT5A exon 10. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0030000-T01-IM6	SNHG5-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_058195, NM_000077) rearrangement: t(6;9)(q14.3;p21.3)(chr6:g.86363454::chr9:g.21971298) Note: The CDKN2A rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
SNHG5	0	MSKCC-DMP	P-0030000-T01-IM6	SNHG5-CDKN2A fusion	yes	unknown		unknown	CDKN2A (NM_058195, NM_000077) rearrangement: t(6;9)(q14.3;p21.3)(chr6:g.86363454::chr9:g.21971298) Note: The CDKN2A rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
FAM175A	0	MSKCC-DMP	P-0030008-T01-IM6	FAM175A-intragenic	yes	unknown		out of frame	FAM175A (NM_139076) rearrangement: c.476+48_c.179-263dup Note: The FAM175A rearrangement results in the duplication of exons 3-5. The functional significance is undetermined.
CDC73	0	MSKCC-DMP	P-0028640-T01-IM6	CDC73-intragenic	yes	unknown		unknown	CDC73 (NM_024529) rearrangement: c.546_c.829-104del Note: The CDC73 rearrangement is a deletion of exons 7-8. One of the breakpoints is within CDC73 exon 7.
RAB39A	0	MSKCC-DMP	P-0028640-T01-IM6	ATM-RAB39A fusion	yes	unknown		unknown	ATM (NM_000051) - RAB39A (NM_017516) rearrangement: c.6238:ATM_c.227+7554RAB39Adup Note: The ATM - RAB39A rearrangement is a duplication that results in the fusion of ATM exons 1-43 to RAB39A exon 2. One of the breakpoints is within ATM exon 43. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0028640-T01-IM6	ATM-RAB39A fusion	yes	unknown		unknown	ATM (NM_000051) - RAB39A (NM_017516) rearrangement: c.6238:ATM_c.227+7554RAB39Adup Note: The ATM - RAB39A rearrangement is a duplication that results in the fusion of ATM exons 1-43 to RAB39A exon 2. One of the breakpoints is within ATM exon 43. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0028640-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.86-6157_c.352del Note: The CREBBP rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2.
INPP4B	0	MSKCC-DMP	P-0028642-T01-IM6	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement: c.2249_c.2642+1128del Note: The INPP4B rearrangement is an intragenic deletion of exons 22-25. One of the breakpoints is within exon 22.
RPRD2	0	MSKCC-DMP	P-0028658-T01-IM6	MCL1-RPRD2 fusion	yes	unknown		unknown	MCL1 (NM_021960) Rearrangement: c.49:MCL1_chr1:150348305del Note: The MCL1 rearrangement results in the deletion of exons 1-3. One breakpoint is within exon 1. Its functional significance is undetermined.
MCL1	0	MSKCC-DMP	P-0028658-T01-IM6	MCL1-RPRD2 fusion	yes	unknown		unknown	MCL1 (NM_021960) Rearrangement: c.49:MCL1_chr1:150348305del Note: The MCL1 rearrangement results in the deletion of exons 1-3. One breakpoint is within exon 1. Its functional significance is undetermined.
TCAP	0	MSKCC-DMP	P-0028658-T01-IM6	ERBB2-TCAP fusion	yes	unknown		unknown	ERBB2 (NM_004448) - TCAP (NM_003673) Rearrangement:  c.3159+84:ERBB2_c.312:TCAPdup Note: The ERBB2-TCAP rearrangement is a duplication which may result in an in-frame fusion of ERBB2 exons 1-25 with TCAP exons 2. One breakpoint is within TCAP exon 2. The fusion includes the kinase domain of ERBB2. Its functional significance is undetermined
ERBB2	0	MSKCC-DMP	P-0028658-T01-IM6	ERBB2-TCAP fusion	yes	unknown		unknown	ERBB2 (NM_004448) - TCAP (NM_003673) Rearrangement:  c.3159+84:ERBB2_c.312:TCAPdup Note: The ERBB2-TCAP rearrangement is a duplication which may result in an in-frame fusion of ERBB2 exons 1-25 with TCAP exons 2. One breakpoint is within TCAP exon 2. The fusion includes the kinase domain of ERBB2. Its functional significance is undetermined
KMT2D	0	MSKCC-DMP	P-0028678-T01-IM6	TRHDE-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.14644-185:KMT2D_chr12:g.72767423del Note: The KMT2D rearrangement is a deletion of exons 1-47. The detection of this structural variant in addition to amplification observed in exons 48-54 (not reported) on copy number suggests a complex rearrangement in KMT2D that may not be captured by IMPACT. The functional significance of this rearrangement is undetermined.
TRHDE	0	MSKCC-DMP	P-0028678-T01-IM6	TRHDE-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.14644-185:KMT2D_chr12:g.72767423del Note: The KMT2D rearrangement is a deletion of exons 1-47. The detection of this structural variant in addition to amplification observed in exons 48-54 (not reported) on copy number suggests a complex rearrangement in KMT2D that may not be captured by IMPACT. The functional significance of this rearrangement is undetermined.
ITM2B	0	MSKCC-DMP	P-0028689-T01-IM6	RB1-ITM2B fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1389+42:RB1_chr13:g.48812170inv Note: The RB1 rearrangement is an inversion of exons 1-14.
RB1	0	MSKCC-DMP	P-0028689-T01-IM6	RB1-ITM2B fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1389+42:RB1_chr13:g.48812170inv Note: The RB1 rearrangement is an inversion of exons 1-14.
DNAJC16	0	MSKCC-DMP	P-0028695-T01-IM6	SPEN-DNAJC16 fusion	yes	unknown		unknown	SPEN (NM_015001) - DNAJC16 (NM_015291) rearrangement: c.9879:SPEN_c.234+512:DNAJC16dup Note: The SPEN - DNAJC16 rearrangement is a duplication that results in the fusion of SPEN exons 1-11 with DNAJC16 exons 4-15. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0028695-T01-IM6	SPEN-DNAJC16 fusion	yes	unknown		unknown	SPEN (NM_015001) - DNAJC16 (NM_015291) rearrangement: c.9879:SPEN_c.234+512:DNAJC16dup Note: The SPEN - DNAJC16 rearrangement is a duplication that results in the fusion of SPEN exons 1-11 with DNAJC16 exons 4-15. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0028699-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+143_c.-1067inv Note: The CDKN2B rearrangement results in the inversion of exon 1. The functional significance is undetermined.
KATNA1	0	MSKCC-DMP	P-0028710-T01-IM6	LATS1-KATNA1 fusion	yes	unknown		unknown	KATNA1 (NM_007044) - LATS1 (NM_004690) rearrangement: c.644:KATNA1_c.2656:LATS1dup Note: The KATNA1 - LATS1 rearrangement is a duplication that results in the fusion of KATNA1 exons 1-6 with LATS1 exons 6-8. One of the breakpoints is within KATNA1 exon 6 and the other breakpoint is within LATS1 exon 6. The functional significance is undetermined.
LATS1	0	MSKCC-DMP	P-0028710-T01-IM6	LATS1-KATNA1 fusion	yes	unknown		unknown	KATNA1 (NM_007044) - LATS1 (NM_004690) rearrangement: c.644:KATNA1_c.2656:LATS1dup Note: The KATNA1 - LATS1 rearrangement is a duplication that results in the fusion of KATNA1 exons 1-6 with LATS1 exons 6-8. One of the breakpoints is within KATNA1 exon 6 and the other breakpoint is within LATS1 exon 6. The functional significance is undetermined.
S100B	0	MSKCC-DMP	P-0028712-T01-IM6	ETV6-S100B fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;21)(p13.2;q22.3)(chr12:g.11992159::chr21:g.48029480) Note: The ETV6 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0028712-T01-IM6	ETV6-S100B fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;21)(p13.2;q22.3)(chr12:g.11992159::chr21:g.48029480) Note: The ETV6 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0028715-T01-IM6	DSTYK-ERBB3 fusion	yes	unknown		unknown	DSTYK (NM_015375) - ERBB3 (NM_001982) rearrangement: t(1;12)(q32.1;q13.2)(chr1:g.205142365::chr12:g.56487607) Note: The DSTYK - ERBB3 rearrangement is a translocation that results in the fusion of DSTYK exons 1-3 with ERBB3 exons 13-28. One of the breakpoints is within ERBB3 exon 13. The functional significance is undetermined.
DSTYK	0	MSKCC-DMP	P-0028715-T01-IM6	DSTYK-ERBB3 fusion	yes	unknown		unknown	DSTYK (NM_015375) - ERBB3 (NM_001982) rearrangement: t(1;12)(q32.1;q13.2)(chr1:g.205142365::chr12:g.56487607) Note: The DSTYK - ERBB3 rearrangement is a translocation that results in the fusion of DSTYK exons 1-3 with ERBB3 exons 13-28. One of the breakpoints is within ERBB3 exon 13. The functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0028721-T01-IM6	PTCH1-intragenic	yes	unknown		unknown	PTCH1 (NM_000264) rearrangement: c.3550_c.585-138dup Note: The PTCH1 rearrangement results in the duplication of exons 4-22. One of the breakpoints is within exon 22. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0028743-T01-IM6	NELFA-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.2274+82:FGFR3_chr4:g.2007790dup Note: The FGFR3 rearrangement is a duplication of exons 18. This does not include the kinase domain of FGFR3. Its functional significance is undetermined.
NELFA	0	MSKCC-DMP	P-0028743-T01-IM6	NELFA-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.2274+82:FGFR3_chr4:g.2007790dup Note: The FGFR3 rearrangement is a duplication of exons 18. This does not include the kinase domain of FGFR3. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0028745-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1523-2563:EML4_c.3172:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0028745-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1523-2563:EML4_c.3172:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
U2AF1	0	MSKCC-DMP	P-0028754-T01-IM6	FGF12-U2AF1 fusion	yes	unknown		unknown	U2AF1 (NM_006758) rearrangement: t(3;21)(q28-29;q22.3)(chr3:g.192445271::chr21:g.44513280) Note: The U2AF1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined
FGF12	0	MSKCC-DMP	P-0028754-T01-IM6	FGF12-U2AF1 fusion	yes	unknown		unknown	U2AF1 (NM_006758) rearrangement: t(3;21)(q28-29;q22.3)(chr3:g.192445271::chr21:g.44513280) Note: The U2AF1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined
FAT1	0	MSKCC-DMP	P-0028759-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.343:FAT1_chr4:g.190476182del Note: The FAT1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
LINC01262	0	MSKCC-DMP	P-0028759-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.343:FAT1_chr4:g.190476182del Note: The FAT1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0028761-T01-IM6	PTPRD-intragenic	yes	unknown		in frame	PTPRD (NM_002839) rearrangement: c.4387-460_c.4507-118del Note: The PTPRD rearrangement is an intragenic deletion of exon 38. Its functional significance is undetermined.
ZP1	0	MSKCC-DMP	P-0028773-T02-IM6	KMT2A-ZP1 fusion	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: chr11:g.60627032_c.946del Note: The KMT2A rearrangement is a deletion that includes exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0028773-T02-IM6	KMT2A-ZP1 fusion	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: chr11:g.60627032_c.946del Note: The KMT2A rearrangement is a deletion that includes exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0028775-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.127-1430:TMPRSS2_chr21:g.40053713del Note: The TMPRSS2 rearrangement results in the deletion of TMPRSS2 exons 3 to 14. The function significance is undetermined. In addition, multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0028775-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.127-1430:TMPRSS2_chr21:g.40053713del Note: The TMPRSS2 rearrangement results in the deletion of TMPRSS2 exons 3 to 14. The function significance is undetermined. In addition, multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CLDN19	0	MSKCC-DMP	P-0028779-T01-IM6	SZT2-CLDN19 fusion	yes	unknown		unknown	SZT2 (NM_015284) rearrangement: c.347:SZT2_chr1:g.43175179dup Note: The SZT2 rearrangement is a duplication of SZT2 exons 1 to 4. One of the breakpoints is within SZT2 exon 4. The functional significance is undetermined.
SZT2	0	MSKCC-DMP	P-0028779-T01-IM6	SZT2-CLDN19 fusion	yes	unknown		unknown	SZT2 (NM_015284) rearrangement: c.347:SZT2_chr1:g.43175179dup Note: The SZT2 rearrangement is a duplication of SZT2 exons 1 to 4. One of the breakpoints is within SZT2 exon 4. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0028787-T01-IM6	UNC13A-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(19;22)(p13.11;q12.2)(chr19:g.17759728::chr22:g.29692321) Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 13 of EWSR1. Its functional significance is undetermined.
UNC13A	0	MSKCC-DMP	P-0028787-T01-IM6	UNC13A-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(19;22)(p13.11;q12.2)(chr19:g.17759728::chr22:g.29692321) Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 13 of EWSR1. Its functional significance is undetermined.
VHL	0	MSKCC-DMP	P-0028790-T01-IM6	VHL-intragenic	yes	unknown		unknown	VHL (NM_000551) rearrangement: c.-2662_c.340+1702inv Note: The VHL rearrangement is an intragenic inversion of exon 1. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0028842-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1743+2529_c.4265dup Note: The APC rearrangement results in the duplication of APC exons 15 to 16. One of the breakpoints is with APC exon 16. The functional significance is undetermined. Multiple rearrangements involving APC were detected in this sample and a more complex rearrangement resulting in additional APC fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ROS1	0	MSKCC-DMP	P-0028865-T02-IM6	TPM3-ROS1 fusion	yes	unknown		in frame	TPM3 (NM_001278190) - ROS1 (NM_002944) fusion (TPM3 exons 1-6 with ROS1 exons 35-43): t(1;6)(q21.3;q22.1)(chr1:g.154133648::chr6:g.117643589) Note: The TPM3 - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
TPM3	0	MSKCC-DMP	P-0028865-T02-IM6	TPM3-ROS1 fusion	yes	unknown		in frame	TPM3 (NM_001278190) - ROS1 (NM_002944) fusion (TPM3 exons 1-6 with ROS1 exons 35-43): t(1;6)(q21.3;q22.1)(chr1:g.154133648::chr6:g.117643589) Note: The TPM3 - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
KDR	0	MSKCC-DMP	P-0028892-T01-IM6	MIR1973-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: c.1815:KDR_chr4:g.117110034del Note: The KDR rearrangement is a deletion of exons 13 to 30. One of the breakpoints is within exon 13. Its functional significance is undetermined.
MIR1973	0	MSKCC-DMP	P-0028892-T01-IM6	MIR1973-KDR fusion	yes	unknown		unknown	KDR (NM_002253) rearrangement: c.1815:KDR_chr4:g.117110034del Note: The KDR rearrangement is a deletion of exons 13 to 30. One of the breakpoints is within exon 13. Its functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0028915-T01-IM6	PRKCI-intragenic	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.1068-956_c.1156inv Note: the PRKCI rearrangement is an intragenic inversion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.
HIST1H3I	0	MSKCC-DMP	P-0028918-T01-IM6	OR2B6-HIST1H3I fusion	yes	unknown		unknown	HIST1H3I (NM_003533) rearrangement: c.199_chr6:g.27921069del Note: The HIST1H3I rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
OR2B6	0	MSKCC-DMP	P-0028918-T01-IM6	OR2B6-HIST1H3I fusion	yes	unknown		unknown	HIST1H3I (NM_003533) rearrangement: c.199_chr6:g.27921069del Note: The HIST1H3I rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
HNRNPA3	0	MSKCC-DMP	P-0028933-T01-IM6	NFE2L2-HNRNPA3 fusion	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: c.1464:NFE2L2_chr2:g.178089672del. Note: The NFE2L2 rearrangement results in the deletion of NFE2L2 exon 5. One of the breakpoints is within exon 5 of NFE2L2. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0028933-T01-IM6	NFE2L2-HNRNPA3 fusion	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: c.1464:NFE2L2_chr2:g.178089672del. Note: The NFE2L2 rearrangement results in the deletion of NFE2L2 exon 5. One of the breakpoints is within exon 5 of NFE2L2. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0028933-T01-IM6	GPATCH8-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.42537013::chr22:g.41574494) Note: The EP300 rearrangement results in the translocation of EP300 exons 1 to 31. One of the breakpoints is within EP300 exon 1. The functional significance is undetermined.
GPATCH8	0	MSKCC-DMP	P-0028933-T01-IM6	GPATCH8-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.42537013::chr22:g.41574494) Note: The EP300 rearrangement results in the translocation of EP300 exons 1 to 31. One of the breakpoints is within EP300 exon 1. The functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0028936-T01-IM6	CDK4-intragenic	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.354+56_c.-147inv Note: The CDK4 rearrangement is an inversion of CDK4 exons 1 to 3. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0028937-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.3275+23_c.-2875inv Note: The POLE rearrangement results in the inversion of exons 1-26. The functional significance is undetermined.
PROSC	0	MSKCC-DMP	P-0028937-T01-IM6	FGFR1-PROSC fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.2070+59:FGFR1_chr8:g.37619984del Note: The FGFR1 rearrangement results in the deletion of exons 16-19. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0028937-T01-IM6	FGFR1-PROSC fusion	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.2070+59:FGFR1_chr8:g.37619984del Note: The FGFR1 rearrangement results in the deletion of exons 16-19. The functional significance is undetermined.
GHR	0	MSKCC-DMP	P-0028938-T01-IM6	RASA1-GHR fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.2798:RASA1_chr5:g.42683483inv Note: The RASA1 rearrangement results in the inversion of exons 1-22. One of the breakpoints is within exon 22. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0028938-T01-IM6	RASA1-GHR fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.2798:RASA1_chr5:g.42683483inv Note: The RASA1 rearrangement results in the inversion of exons 1-22. One of the breakpoints is within exon 22. The functional significance is undetermined.
PDGFRA	0	MSKCC-DMP	P-0028940-T01-IM6	LOC101928995-PDGFRA fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: t(1;4)(p13.1;q12)(chr1:g.116439067::chr4:g.55146618) Note: The PDGFRA rearrangement is a translocation with a breakpoint in exon 16. The functional significance is undetermined.
LOC101928995	0	MSKCC-DMP	P-0028940-T01-IM6	LOC101928995-PDGFRA fusion	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: t(1;4)(p13.1;q12)(chr1:g.116439067::chr4:g.55146618) Note: The PDGFRA rearrangement is a translocation with a breakpoint in exon 16. The functional significance is undetermined.
CD58	0	MSKCC-DMP	P-0028941-T01-IM6	VTCN1-CD58 fusion	yes	unknown		unknown	CD58 (NM_001779) - VTCN1 (NM_024626) rearrangement: c.364+1033:CD58_c.390:VTCN1dup Note: The CD58 - VTCN1 rearrangement is a duplication that results in the fusion of CD58 exons 1-2 with VTCN1 exons 3-5. One of the breakpoints is within VTCN1 exon 3. The functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0028941-T01-IM6	VTCN1-CD58 fusion	yes	unknown		unknown	CD58 (NM_001779) - VTCN1 (NM_024626) rearrangement: c.364+1033:CD58_c.390:VTCN1dup Note: The CD58 - VTCN1 rearrangement is a duplication that results in the fusion of CD58 exons 1-2 with VTCN1 exons 3-5. One of the breakpoints is within VTCN1 exon 3. The functional significance is undetermined.
PPP6C	0	MSKCC-DMP	P-0028974-T01-IM6	TBCA-PPP6C fusion	yes	unknown		unknown	PPP6C (NM_002721) rearrangement: t(5;9)(q14.1;q33.3)(chr5:g.77053105::chr9:g.127951896) Note: The PPP6C rearrangement is a translocation with a breakpoint within intron 1. The functional significance is undetermined.
TBCA	0	MSKCC-DMP	P-0028974-T01-IM6	TBCA-PPP6C fusion	yes	unknown		unknown	PPP6C (NM_002721) rearrangement: t(5;9)(q14.1;q33.3)(chr5:g.77053105::chr9:g.127951896) Note: The PPP6C rearrangement is a translocation with a breakpoint within intron 1. The functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0028995-T01-IM6	TRPC6-PGR fusion	yes	unknown		unknown	TRPC6 (NM_004621) - PGR (NM_000926) rearrangement: c.170+4756:TRPC6_c.2133:PGRdel Note: The TRPC6 - PGR rearrangement is a deletion which results in the fusion of TRPC6 exons 1 to PGR exons 4 - 8. One of the breakpoints is within exon 4 of PGR. The functional significance is undetermined.
TRPC6	0	MSKCC-DMP	P-0028995-T01-IM6	TRPC6-PGR fusion	yes	unknown		unknown	TRPC6 (NM_004621) - PGR (NM_000926) rearrangement: c.170+4756:TRPC6_c.2133:PGRdel Note: The TRPC6 - PGR rearrangement is a deletion which results in the fusion of TRPC6 exons 1 to PGR exons 4 - 8. One of the breakpoints is within exon 4 of PGR. The functional significance is undetermined.
FANCC	0	MSKCC-DMP	P-0029016-T01-IM6	MAK-FANCC fusion	yes	unknown		out of frame	FANCC (NM_000136) - MAK (NM_001242957) Rearrangement : t(6,9)(p24.2,q22.32)(chr6:g.10809757::chr9:g.97888733) Note: The FANCC - MAK rearrangement is a translocation results in the fusion of FANCC exons  1-9 to MAK exons 6-15. The functional significance is undetermined.
MAK	0	MSKCC-DMP	P-0029016-T01-IM6	MAK-FANCC fusion	yes	unknown		out of frame	FANCC (NM_000136) - MAK (NM_001242957) Rearrangement : t(6,9)(p24.2,q22.32)(chr6:g.10809757::chr9:g.97888733) Note: The FANCC - MAK rearrangement is a translocation results in the fusion of FANCC exons  1-9 to MAK exons 6-15. The functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0029016-T01-IM6	FOXP2-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) Rearrangement : t(7,9)(q31.1,q34.12)(chr7:g.113847210::chr9:g.133710845) Note: The ABL1 rearrangement results in the translocation of ABL1 exon 1. One of the breakpoints is within ABL1 exon 1. The functional significance is undetermined.
FOXP2	0	MSKCC-DMP	P-0029016-T01-IM6	FOXP2-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) Rearrangement : t(7,9)(q31.1,q34.12)(chr7:g.113847210::chr9:g.133710845) Note: The ABL1 rearrangement results in the translocation of ABL1 exon 1. One of the breakpoints is within ABL1 exon 1. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0029018-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: c.1013_c.2246inv Note: The TSC2 rearrangement results in the inversion of TSC2 exons 11 to 21. The breakpoints are in exon 11 and 21 respectively. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0029022-T01-IM6	CDK17-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) Rearrangement : t(12,18)(q23.1,q21.2)(chr12:g.96912182::chr18:g.48584555) Note: The SMAD4 rearrangement is a translocation of SMAD4 exons 1 to 6. One of the breakpoints is within SMAD4 exon 6. The functional significance is undetermined.
CDK17	0	MSKCC-DMP	P-0029022-T01-IM6	CDK17-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) Rearrangement : t(12,18)(q23.1,q21.2)(chr12:g.96912182::chr18:g.48584555) Note: The SMAD4 rearrangement is a translocation of SMAD4 exons 1 to 6. One of the breakpoints is within SMAD4 exon 6. The functional significance is undetermined.
SLC25A51P1	0	MSKCC-DMP	P-0029023-T01-IM6	ARID1B-SLC25A51P1 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3591_chr6:g.67007800del Note: The ARID1B rearrangement results in the deletion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0029023-T01-IM6	ARID1B-SLC25A51P1 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3591_chr6:g.67007800del Note: The ARID1B rearrangement results in the deletion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0029024-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2606_c.2243-974inv Note: The WHSC1L1 rearrangement results in the inversion of exons 13-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0029028-T01-IM6	EMP1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.33+132_chr12:g.13294731del Note: The ETV6 rearrangement results in the deletion of exons 2-8. The functional significance is undetermined.
EMP1	0	MSKCC-DMP	P-0029028-T01-IM6	EMP1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.33+132_chr12:g.13294731del Note: The ETV6 rearrangement results in the deletion of exons 2-8. The functional significance is undetermined.
LINC-PINT	0	MSKCC-DMP	P-0029059-T01-IM6	BRAF-LINC-PINT fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1178-1159:BRAF_chr7:g.130724897del Note: The BRAF rearrangement is a deletion of BRAF exons 1 to 9. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0029059-T01-IM6	BRAF-LINC-PINT fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1178-1159:BRAF_chr7:g.130724897del Note: The BRAF rearrangement is a deletion of BRAF exons 1 to 9. The functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0029067-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 3-21) : c.2302-67:FGFR2_c.238-6757:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0029067-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 3-21) : c.2302-67:FGFR2_c.238-6757:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
FAT1	0	MSKCC-DMP	P-0029084-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement:c.5168:FAT1_chr4:g.189982700del Note: The FAT1 rearrangement is a deletion of exon 10-27. One of the breakpoints is within exon 10. Its functional significance is undetermined.
LINC01262	0	MSKCC-DMP	P-0029084-T01-IM6	LINC01262-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement:c.5168:FAT1_chr4:g.189982700del Note: The FAT1 rearrangement is a deletion of exon 10-27. One of the breakpoints is within exon 10. Its functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0029091-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.2309-1047_c.1983del Note: The RNF43 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029105-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3000:TMPRSS2_c.18+16661:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0029105-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3000:TMPRSS2_c.18+16661:ERGdel
NLRC3	0	MSKCC-DMP	P-0029141-T01-IM6	SLX4-NLRC3 fusion	yes	unknown		unknown	SLX4 (NM_032444) rearrangement: c.3651:SLX4_chr16:g.3617116del Note: The SLX4 rearrangement results in the deletion of exons 12-15. One of the breakpoints is within exon 12. The functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0029141-T01-IM6	SLX4-NLRC3 fusion	yes	unknown		unknown	SLX4 (NM_032444) rearrangement: c.3651:SLX4_chr16:g.3617116del Note: The SLX4 rearrangement results in the deletion of exons 12-15. One of the breakpoints is within exon 12. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0029152-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.137+44_c.264+1746del Note: The RB1 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined but the deletion likely disrupts the function of this tumor suppressor gene.
ALK	0	MSKCC-DMP	P-0029174-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-19 fused with ALK exons 20-29): c.2242+168:EML4_c.3173-262:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0029174-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-19 fused with ALK exons 20-29): c.2242+168:EML4_c.3173-262:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
LINC00114	0	MSKCC-DMP	P-0029183-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+4036:TMPRSS2_chr21:g.40098936del Note: The TMPRSS2 rearrangement is a deletion of exon 2-14. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0029183-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+4036:TMPRSS2_chr21:g.40098936del Note: The TMPRSS2 rearrangement is a deletion of exon 2-14. Its functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0029184-T01-IM6	SKOR1-SMAD3 fusion	yes	unknown		in frame	SMAD3 (NM_005902) - SKOR1 (NM_001258024) rearrangement: c.400+57:SMAD3_c.1585+101:SKOR1del Note: The SMAD3 - SKOR1 rearrangement is a deletion which results in the fusion of SMAD3 exons 1-2 with SKOR1 exons 7-15
SKOR1	0	MSKCC-DMP	P-0029184-T01-IM6	SKOR1-SMAD3 fusion	yes	unknown		in frame	SMAD3 (NM_005902) - SKOR1 (NM_001258024) rearrangement: c.400+57:SMAD3_c.1585+101:SKOR1del Note: The SMAD3 - SKOR1 rearrangement is a deletion which results in the fusion of SMAD3 exons 1-2 with SKOR1 exons 7-15
NF1	0	MSKCC-DMP	P-0029184-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.5073_c.6006+451del Note: The NF1 rearrangement is an intragenic deletion of exons 37-40. One of the breakpoints is within exon 37. Its functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0029216-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: c.56-1639:TMPRSS2_chr21:g.40100480del Note: The TMPRSS2 rearrangement is a deletion of TMPRSS2 exons 2 to 14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0029216-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: c.56-1639:TMPRSS2_chr21:g.40100480del Note: The TMPRSS2 rearrangement is a deletion of TMPRSS2 exons 2 to 14. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0029227-T01-IM6	MIR4303-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.2787:ARDI2_chr12:g.98537965inv Note: The ARID2 rearrangement is a inversion of ARID2 exons 15 to 21. One of the breakpoints is within ARID2 exon 15. The functional significance is undetermined.
MIR4303	0	MSKCC-DMP	P-0029227-T01-IM6	MIR4303-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.2787:ARDI2_chr12:g.98537965inv Note: The ARID2 rearrangement is a inversion of ARID2 exons 15 to 21. One of the breakpoints is within ARID2 exon 15. The functional significance is undetermined.
CCND2	0	MSKCC-DMP	P-0029254-T01-IM6	CASC15-CCND2 fusion	yes	unknown		unknown	CCND2 (NM_001759) rearrangement: t(6;12)(p22.3;p13.32)(chr6:g.21808818::chr12:g.4383256) Note: The CCND2 rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
CASC15	0	MSKCC-DMP	P-0029254-T01-IM6	CASC15-CCND2 fusion	yes	unknown		unknown	CCND2 (NM_001759) rearrangement: t(6;12)(p22.3;p13.32)(chr6:g.21808818::chr12:g.4383256) Note: The CCND2 rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0029273-T01-IM6	NCOR1-intragenic	yes	unknown		out of frame	NCOR1 (NM_006311) Rearrangement: c.2820+1814_ c.843-78dup Note: The NCOR1 rearrangement is a duplication of NCOR1 exons 9 to 21. The functional significance is undetermined.
WDR11	0	MSKCC-DMP	P-0029289-T01-IM6	FGFR2-WDR11 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-756:FGFR2_chr10:g.122889706del Note: The FGFR2 rearrangement is a deletion of FGFR2 exon 18. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0029289-T01-IM6	FGFR2-WDR11 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-756:FGFR2_chr10:g.122889706del Note: The FGFR2 rearrangement is a deletion of FGFR2 exon 18. The functional significance is undetermined.
CYLD	0	MSKCC-DMP	P-0029294-T01-IM6	CYLD-intragenic	yes	unknown		unknown	CYLD (NM_001042355) Rearrangement: c.375_c.661del Note: The CYLD rearrangement is an intragenic deletion of CYLD exons 3 to 4. The breakpoints are within CYLD exon 3 and exon 4. The functional significance is undetermined.
LYN	0	MSKCC-DMP	P-0029294-T01-IM6	PLAG1-LYN fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: c.1205-100:LYN_chr8:g.57070090inv Note: The LYN rearrangement is an inversion of LYN exons 12 to 13. The functional significance is undetermined.
PLAG1	0	MSKCC-DMP	P-0029294-T01-IM6	PLAG1-LYN fusion	yes	unknown		unknown	LYN (NM_002350) rearrangement: c.1205-100:LYN_chr8:g.57070090inv Note: The LYN rearrangement is an inversion of LYN exons 12 to 13. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0029298-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.3723_c.*2367del Note: The APC rearrangement is an intragenic deletion of APC exon 16. One of the breakpoints is within APC exon 16. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0029299-T01-IM6	NF2-intragenic	yes	unknown		in frame	NF2 (NM_000268) rearrangement: c.115-3779_c.448-142del Note: The NF2 rearrangement is an intragenic deletion of NF2 exons 2 to 4. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0029315-T02-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.304-20462:CCDC6_c.2136+447:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0029315-T02-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.304-20462:CCDC6_c.2136+447:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
ERG	0	MSKCC-DMP	P-0029333-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 - ERG exons 4-11):  c.56-3881:TMPRSS2_c.40-57209:ERG
TMPRSS2	0	MSKCC-DMP	P-0029333-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 - ERG exons 4-11):  c.56-3881:TMPRSS2_c.40-57209:ERG
ATM	0	MSKCC-DMP	P-0029353-T01-IM6	C11orf65-ATM fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangment: c.8268:ATM_chr11:g.108253231del Note: The ATM rearrangement is a deletion of exons 56 - 63. One of the breakpoints is within exon 56.  The functional significance is unknown.
C11orf65	0	MSKCC-DMP	P-0029353-T01-IM6	C11orf65-ATM fusion	yes	unknown		unknown	ATM (NM_000051) Rearrangment: c.8268:ATM_chr11:g.108253231del Note: The ATM rearrangement is a deletion of exons 56 - 63. One of the breakpoints is within exon 56.  The functional significance is unknown.
CARM1	0	MSKCC-DMP	P-0029353-T01-IM6	HAVCR1P1-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement: c.346+43:CARM1_chr19:g.24480361inv Note: The CARM1 (NM_199141) rearrangement results the inversion of exons 2-16. Its functional significance is undetermined.
HAVCR1P1	0	MSKCC-DMP	P-0029353-T01-IM6	HAVCR1P1-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement: c.346+43:CARM1_chr19:g.24480361inv Note: The CARM1 (NM_199141) rearrangement results the inversion of exons 2-16. Its functional significance is undetermined.
ERF	0	MSKCC-DMP	P-0029354-T01-IM6	SCHLAP1-ERF fusion	yes	unknown		unknown	ERF (NM_006494) Rearrangement: t(22;19) (2q31.3;19q13.2) (chr2:g.181327407::chr19:g.42754531) Note: The ERF rearrangement is a translocation involving exon 2. One of the breakpoints is in exon 2. The functional significance is unknown.
SCHLAP1	0	MSKCC-DMP	P-0029354-T01-IM6	SCHLAP1-ERF fusion	yes	unknown		unknown	ERF (NM_006494) Rearrangement: t(22;19) (2q31.3;19q13.2) (chr2:g.181327407::chr19:g.42754531) Note: The ERF rearrangement is a translocation involving exon 2. One of the breakpoints is in exon 2. The functional significance is unknown.
EMR3	0	MSKCC-DMP	P-0029354-T01-IM6	FGFR1-EMR3 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangment: t(8;19) (8p11.23;19p13.12)(chr8:g.38272399::chr19:g.14765577) Note: The FGFR1 rearrangment is a translocation involving exon 15. One of the breakpoints is in exon 15. The functional significance is unknown.
FGFR1	0	MSKCC-DMP	P-0029354-T01-IM6	FGFR1-EMR3 fusion	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangment: t(8;19) (8p11.23;19p13.12)(chr8:g.38272399::chr19:g.14765577) Note: The FGFR1 rearrangment is a translocation involving exon 15. One of the breakpoints is in exon 15. The functional significance is unknown.
FOXP1	0	MSKCC-DMP	P-0029368-T01-IM6	FOXP1-intragenic	yes	unknown		out of frame	FOXP1 (NM_001244814) rearrangement: c.282+5739_c.1890-27del Note: The FOXP1 rearrangement is an intragenic deletion of exons 4-16.
BIRC3	0	MSKCC-DMP	P-0029393-T01-IM6	BIRC3-intragenic	yes	unknown		unknown	BIRC3 (NM_182962) rearrangement: c.-114+1099_c.519dup Note: The BIRC3 rearrangement results in the duplication of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0029393-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.3063_c.*3732del Note: The FANCA rearrangement results in the deletion of exons 31-43. One of the breakpoints is within exon 31. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0029393-T01-IM6	PIBF1-RNF43 fusion	yes	unknown		in frame	RNF43 (NM_017763) - PIBF1 (NM_006346) rearrangement: t(13;17)(q22.1;q22)(chr13:g.73547996::chr17:g.56440469) Note: The RNF43 - PIBF1 rearrangement is a translocation that results in the fusion of RNF43 exons 1-5 with PIBF1 exons 17-18. The functional significance is undetermined.
PIBF1	0	MSKCC-DMP	P-0029393-T01-IM6	PIBF1-RNF43 fusion	yes	unknown		in frame	RNF43 (NM_017763) - PIBF1 (NM_006346) rearrangement: t(13;17)(q22.1;q22)(chr13:g.73547996::chr17:g.56440469) Note: The RNF43 - PIBF1 rearrangement is a translocation that results in the fusion of RNF43 exons 1-5 with PIBF1 exons 17-18. The functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0029393-T01-IM6	FAM205A-NCOA3 fusion	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: t(9;20)(p13.3;q13.12)(chr9:g.34739492::chr20:g.46270904) Note: The NCOA3 rearrangement is a translocation with a breakpoint in intron 16. The functional significance is undetermined.
FAM205A	0	MSKCC-DMP	P-0029393-T01-IM6	FAM205A-NCOA3 fusion	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: t(9;20)(p13.3;q13.12)(chr9:g.34739492::chr20:g.46270904) Note: The NCOA3 rearrangement is a translocation with a breakpoint in intron 16. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0029393-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.-32-1505_c.70del Note: The RAD21 rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0029398-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.139-16_c.-12-459del Note: The PBRM1 rearrangement results in the deletion of exon 2. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0029400-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1315+641:EML4_c.3172+659:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0029400-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1315+641:EML4_c.3172+659:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
TRIM62	0	MSKCC-DMP	P-0029402-T01-IM6	CSF3R-TRIM62 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.346:CSF3R_chr1:g.33652766inv Note: The CSF3R rearrangement results in the inversion of exons 4-17. One of the breakpoints is within exon 4. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0029402-T01-IM6	CSF3R-TRIM62 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.346:CSF3R_chr1:g.33652766inv Note: The CSF3R rearrangement results in the inversion of exons 4-17. One of the breakpoints is within exon 4. The functional significance is undetermined.
ZSCAN20	0	MSKCC-DMP	P-0029402-T01-IM6	CSF3R-ZSCAN20 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1647:CSF3R_chr1:g.33893988inv Note: The CSF3R rearrangement results in the inversion of exons 13-17. One of the breakpoints is within exon 13. The functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0029402-T01-IM6	CSF3R-ZSCAN20 fusion	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1647:CSF3R_chr1:g.33893988inv Note: The CSF3R rearrangement results in the inversion of exons 13-17. One of the breakpoints is within exon 13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029405-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10):c.127-1427:TMPRSS2_c.18+20762:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0029405-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-2 fused to ERG exons 2-10):c.127-1427:TMPRSS2_c.18+20762:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
PIK3CB	0	MSKCC-DMP	P-0029406-T01-IM6	KCNAB1-PIK3CB fusion	yes	unknown		unknown	PIK3CB (NM_006219) - KCNAB1 (NM_172160) rearrangement: c.133:PIK3CB_c.275+78559:KCNAB1inv Note: The PIK3CB - KCNAB1 rearrangement is an inversion that results in the fusion of PIK3CB exon 1 with KCNAB1 exons 2-14. The functional significance is undetermined.
KCNAB1	0	MSKCC-DMP	P-0029406-T01-IM6	KCNAB1-PIK3CB fusion	yes	unknown		unknown	PIK3CB (NM_006219) - KCNAB1 (NM_172160) rearrangement: c.133:PIK3CB_c.275+78559:KCNAB1inv Note: The PIK3CB - KCNAB1 rearrangement is an inversion that results in the fusion of PIK3CB exon 1 with KCNAB1 exons 2-14. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0029453-T01-IM6	ACTA2-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.203_chr10:g.90743125del Note: The PTEN rearrangement results in the deletion of exons 3-9. One of the breakpoints is within exon 3. The functional significance is undetermined.
ACTA2	0	MSKCC-DMP	P-0029453-T01-IM6	ACTA2-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.203_chr10:g.90743125del Note: The PTEN rearrangement results in the deletion of exons 3-9. One of the breakpoints is within exon 3. The functional significance is undetermined.
TFAP2D	0	MSKCC-DMP	P-0029460-T01-IM6	ROS1-TFAP2D fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement:  c.6178:ROS1_chr6:g.50511502inv Note: The ROS1 rearrangement in an inversion of exons 39-43.  One breakpoint is in exon 39.  The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0029460-T01-IM6	ROS1-TFAP2D fusion	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement:  c.6178:ROS1_chr6:g.50511502inv Note: The ROS1 rearrangement in an inversion of exons 39-43.  One breakpoint is in exon 39.  The functional significance is undetermined.
ARAF	0	MSKCC-DMP	P-0029465-T01-IM6	LRP1B-ARAF fusion	yes	unknown		unknown	ARAF (NM_001654) Rearrangment: t(X;2) (Xp11.3;2q22.1-q22.2)(chrX:g.47424257::chr2:g.141622159) Note: The ARAF (NM_001654) rearrangement is a translocation involving exon 4. One of the breakpoints is in exon 4. The significance is undetermined.  Multiple events involving ARAF were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
LRP1B	0	MSKCC-DMP	P-0029465-T01-IM6	LRP1B-ARAF fusion	yes	unknown		unknown	ARAF (NM_001654) Rearrangment: t(X;2) (Xp11.3;2q22.1-q22.2)(chrX:g.47424257::chr2:g.141622159) Note: The ARAF (NM_001654) rearrangement is a translocation involving exon 4. One of the breakpoints is in exon 4. The significance is undetermined.  Multiple events involving ARAF were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ARAF	0	MSKCC-DMP	P-0029465-T01-IM6	ARAF-intragenic	yes	unknown		unknown	ARAF (NM_001654) Rearrangement: c.554_c.558-3del Note: The ARAF rearrangement is an intragenic deletion of exon 6.  One of the breakpoints is in exon 6. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0029542-T01-IM6	LINC01339-RASA1 fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.664:RASA1_chr5:g.89498591del Note: The RASA1 rearrangement is a deletion of exons  2-25. One of the breakpoints is within exon 2. Its functional significance is undetermined.
LINC01339	0	MSKCC-DMP	P-0029542-T01-IM6	LINC01339-RASA1 fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.664:RASA1_chr5:g.89498591del Note: The RASA1 rearrangement is a deletion of exons  2-25. One of the breakpoints is within exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0029550-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-721:EML4_c.3172+464:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0029550-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-5 fused with ALK exons 20-29): c.494-721:EML4_c.3172+464:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
TOP1	0	MSKCC-DMP	P-0029559-T01-IM6	PTPRG-TOP1 fusion	yes	unknown		out of frame	TOP1 (NM_003286) - PTPRG (NM_002841) rearrangement: t(3;20)(p14.2;q12)(chr3:g.61957689::chr20:g.39708821) Note: The TOP1 - PTPRG rearrangement is a translocation resulting in the fusion of TOP1 exons 1-6 with PTPRG exons 3-30. Its functional significance is undetermined.
PTPRG	0	MSKCC-DMP	P-0029559-T01-IM6	PTPRG-TOP1 fusion	yes	unknown		out of frame	TOP1 (NM_003286) - PTPRG (NM_002841) rearrangement: t(3;20)(p14.2;q12)(chr3:g.61957689::chr20:g.39708821) Note: The TOP1 - PTPRG rearrangement is a translocation resulting in the fusion of TOP1 exons 1-6 with PTPRG exons 3-30. Its functional significance is undetermined.
OR56A1	0	MSKCC-DMP	P-0029575-T01-IM6	LMO1-OR56A1 fusion	yes	unknown		unknown	LMO1 (NM_002315) rearrangement: c.-62_chr11:g.6081746inv Note: The LMO1 rearrangement results in the inversion of the 5' UTR and exons 1-4. The functional significance is undetermined.
LMO1	0	MSKCC-DMP	P-0029575-T01-IM6	LMO1-OR56A1 fusion	yes	unknown		unknown	LMO1 (NM_002315) rearrangement: c.-62_chr11:g.6081746inv Note: The LMO1 rearrangement results in the inversion of the 5' UTR and exons 1-4. The functional significance is undetermined.
INHBA	0	MSKCC-DMP	P-0029583-T01-IM6	LANCL2-INHBA fusion	yes	unknown		unknown	INHBA (NM_002192) rearrangement: c.1178:INHBA_chr7:g.55480357dup Note: The INHBA rearrangement results in the duplication of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
LANCL2	0	MSKCC-DMP	P-0029583-T01-IM6	LANCL2-INHBA fusion	yes	unknown		unknown	INHBA (NM_002192) rearrangement: c.1178:INHBA_chr7:g.55480357dup Note: The INHBA rearrangement results in the duplication of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0029590-T01-IM6	SCUBE1-NF2 fusion	yes	unknown		out of frame	NF2 (NM_000268) - SCUBE1 (NM_173050) rearrangement: c.1737+1355:NF2_c.1084+692:SCUBE1inv Note: The NF2 - SCUBE1 rearrangement is an inversion that results in the fusion of NF2 exons 1-15 with SCUBE1 exons 10-22. The functional significance is undetermined.
SCUBE1	0	MSKCC-DMP	P-0029590-T01-IM6	SCUBE1-NF2 fusion	yes	unknown		out of frame	NF2 (NM_000268) - SCUBE1 (NM_173050) rearrangement: c.1737+1355:NF2_c.1084+692:SCUBE1inv Note: The NF2 - SCUBE1 rearrangement is an inversion that results in the fusion of NF2 exons 1-15 with SCUBE1 exons 10-22. The functional significance is undetermined.
TSHR	0	MSKCC-DMP	P-0029594-T01-IM6	EYA1-TSHR fusion	yes	unknown		unknown	TSHR (NM_000369) rearrangement: t(8;14)(q13.3;q31.1)(chr8:g.72056267::chr14:g.81609711) Note: The TSHR rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
EYA1	0	MSKCC-DMP	P-0029594-T01-IM6	EYA1-TSHR fusion	yes	unknown		unknown	TSHR (NM_000369) rearrangement: t(8;14)(q13.3;q31.1)(chr8:g.72056267::chr14:g.81609711) Note: The TSHR rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
DIS3	0	MSKCC-DMP	P-0029597-T01-IM6	KLF5-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) rearrangement: c.2128-109:DIS3_chr13:g.73643525del Note: The DIS3 rearrangement results in the deletion of exons 1-16. The functional significance is undetermined.
KLF5	0	MSKCC-DMP	P-0029597-T01-IM6	KLF5-DIS3 fusion	yes	unknown		unknown	DIS3 (NM_014953) rearrangement: c.2128-109:DIS3_chr13:g.73643525del Note: The DIS3 rearrangement results in the deletion of exons 1-16. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0029602-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-5768:CCDC6_c.2137-872:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12-20. The fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0029602-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-5768:CCDC6_c.2137-872:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12-20. The fusion is predicted to be in frame and includes the kinase domain of RET.
POLD1	0	MSKCC-DMP	P-0029604-T01-IM6	POLD1-intragenic	yes	unknown		unknown	POLD1 (NM_002691) rearrangement: c.1494+9_c.1893-26inv Note: The POLD1 rearrangement results in the inversion of exons 13-15. The functional significance is undetermined.
TRAIP	0	MSKCC-DMP	P-0029617-T02-IM6	MST1R-TRAIP fusion	yes	unknown		unknown	MST1R (NM_002447) rearrangement: chr3:g.49859022_c.3065-32dup Note: The MST1R rearrangement is a duplication that includes MST1R exons 14-20. The functional significance is undetermined.
MST1R	0	MSKCC-DMP	P-0029617-T02-IM6	MST1R-TRAIP fusion	yes	unknown		unknown	MST1R (NM_002447) rearrangement: chr3:g.49859022_c.3065-32dup Note: The MST1R rearrangement is a duplication that includes MST1R exons 14-20. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0029644-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.4557+6511_c.4978del Note: The ATRX rearrangement is an intragenic deletion of exons 16-19. One of the breakpoints is within exon 19.
EGFR	0	MSKCC-DMP	P-0029645-T01-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) vIII intragenic deletion: c.89-16253_c.889+66del
TP53BP1	0	MSKCC-DMP	P-0029723-T01-IM6	ADAMTS17-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: c.4514:TP53BP1_chr15:g.100734817inv Note: The TP53BP1 rearrangement is an inversion of exons 1-21. One of the breakpoints is within exon 21.
ADAMTS17	0	MSKCC-DMP	P-0029723-T01-IM6	ADAMTS17-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: c.4514:TP53BP1_chr15:g.100734817inv Note: The TP53BP1 rearrangement is an inversion of exons 1-21. One of the breakpoints is within exon 21.
SND1	0	MSKCC-DMP	P-0029727-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+12095:SND1_c.1314+564:BRAFinv Note: The SND1 - BRAF fusion involves SND1 exons 1-10 and BRAF exons 11-18. The fusion is predicted to be in-frame and includes the kinase domain of BRAF
BRAF	0	MSKCC-DMP	P-0029727-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+12095:SND1_c.1314+564:BRAFinv Note: The SND1 - BRAF fusion involves SND1 exons 1-10 and BRAF exons 11-18. The fusion is predicted to be in-frame and includes the kinase domain of BRAF
ALK	0	MSKCC-DMP	P-0029750-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-2574:EML4_c.3173-266:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0029750-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-2574:EML4_c.3173-266:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
HIST1H3H	0	MSKCC-DMP	P-0029756-T01-IM6	HIST1H2BM-HIST1H3H fusion	yes	unknown		unknown	HIST1H3H (NM_003536) rearrangement: c.-2156_c.*4452del Note: The HIST1H3H rearrangement is a deletion of exon 1. The functional significance is undetermined.
HIST1H2BM	0	MSKCC-DMP	P-0029756-T01-IM6	HIST1H2BM-HIST1H3H fusion	yes	unknown		unknown	HIST1H3H (NM_003536) rearrangement: c.-2156_c.*4452del Note: The HIST1H3H rearrangement is a deletion of exon 1. The functional significance is undetermined.
IL1RAPL1	0	MSKCC-DMP	P-0029793-T01-IM6	RECQL4-IL1RAPL1 fusion	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: t(8;X)(q24.3;p21.2)(chr8:g.145740560::chrX:g.29843951) Note: The RECQL4 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0029793-T01-IM6	RECQL4-IL1RAPL1 fusion	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: t(8;X)(q24.3;p21.2)(chr8:g.145740560::chrX:g.29843951) Note: The RECQL4 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029796-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3489:TMPRSS2_c.40-58375:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 4-11.
TMPRSS2	0	MSKCC-DMP	P-0029796-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3489:TMPRSS2_c.40-58375:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 4-11.
EGFEM1P	0	MSKCC-DMP	P-0029798-T01-IM6	BCL6-EGFEM1P fusion	yes	unknown		unknown	BCL6 (NM_001706) rearrangement: c.2064_chr3:g.168207075inv Note: The BCL6 rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
BCL6	0	MSKCC-DMP	P-0029798-T01-IM6	BCL6-EGFEM1P fusion	yes	unknown		unknown	BCL6 (NM_001706) rearrangement: c.2064_chr3:g.168207075inv Note: The BCL6 rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0029801-T01-IM6	FAM193A-NOTCH4 fusion	yes	unknown		unknown	FAM193A (NM_003704) - NOTCH4 (NM_004557) rearrangement: t(4;6)(p16.3;p21.32)(chr4:g.2664220::chr6:g.32183122) Note: The FAM193A - NOTCH4 rearrangement is a translocation that results in the fusion of FAM193A exons 1-8 with NOTCH4 exons 12-30. One of the breakpoints is within NOTCH4 exon 12. The functional significance is undetermined.
FAM193A	0	MSKCC-DMP	P-0029801-T01-IM6	FAM193A-NOTCH4 fusion	yes	unknown		unknown	FAM193A (NM_003704) - NOTCH4 (NM_004557) rearrangement: t(4;6)(p16.3;p21.32)(chr4:g.2664220::chr6:g.32183122) Note: The FAM193A - NOTCH4 rearrangement is a translocation that results in the fusion of FAM193A exons 1-8 with NOTCH4 exons 12-30. One of the breakpoints is within NOTCH4 exon 12. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0029803-T01-IM6	CLCN6-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(1;3)(p36.22;p21.1)(chr1:g.11870943::chr3:g.52441869) Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
CLCN6	0	MSKCC-DMP	P-0029803-T01-IM6	CLCN6-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(1;3)(p36.22;p21.1)(chr1:g.11870943::chr3:g.52441869) Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029809-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1-2 with ERG exons 4-10) : c.126+1597:TMPRSS2_c.39+39940:ERGdel Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0029809-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1-2 with ERG exons 4-10) : c.126+1597:TMPRSS2_c.39+39940:ERGdel Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).
NF1	0	MSKCC-DMP	P-0029814-T01-IM6	KCNU1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(8;17)(p12;q11.2)(chr8:g.36189531::chr17:g.29588872) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 35. The functional significance is undetermined.
KCNU1	0	MSKCC-DMP	P-0029814-T01-IM6	KCNU1-NF1 fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(8;17)(p12;q11.2)(chr8:g.36189531::chr17:g.29588872) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 35. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0029819-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.164-9463_c.463+2991del Note: The ETV6 rearrangement results in the in-frame deletion of exons 3-4. The functional significance is undetermined.
EPHX3	0	MSKCC-DMP	P-0029821-T01-IM6	BRD4-EPHX3 fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.3967:BRD4_chr19:g.15337047dup Note: The BRD4 rearrangement results in the duplication of exons 19-20. One of the breakpoints is within exon 19. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0029821-T01-IM6	BRD4-EPHX3 fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.3967:BRD4_chr19:g.15337047dup Note: The BRD4 rearrangement results in the duplication of exons 19-20. One of the breakpoints is within exon 19. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0029823-T01-IM6	CLCF1-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q13.2;q12)(chr11:g.67137375::chr17:g.37875982) Note: The ERBB2 rearrangement is a translocation with a breakpoint in intron 15. The functional significance is undetermined.
CLCF1	0	MSKCC-DMP	P-0029823-T01-IM6	CLCF1-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(11;17)(q13.2;q12)(chr11:g.67137375::chr17:g.37875982) Note: The ERBB2 rearrangement is a translocation with a breakpoint in intron 15. The functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0029835-T01-IM6	YAP1-intragenic	yes	unknown		in frame	YAP1 (NM_001130145) Rearrangement: c.802+5150_c.1276+73dup Note: The YAP1 rearrangement is an intragenic duplication of exons 5 to 8. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0029835-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement: c.841_c.144+1356del Note: The RAD21 rearrangement results in the intragenic deletion of exons 3 to 8. One of the breakpoints is within exon 8. The functional significance is undetermined.
SH3BGR	0	MSKCC-DMP	P-0029843-T01-IM6	TMPRSS2-SH3BGR fusion	yes	unknown		out of frame	SH3BGR (NM_007341) - TMPRSS2 (NM_001135099) rearrangement: c.421-1136:SH3BGR_c.56-2096:TMPRSS2inv Note: The SH3BGR - TMPRSS2 rearrangement is an inversion that results in the fusion of SH3BGR exons 1-2 with TMPRSS2 exons 2-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0029843-T01-IM6	TMPRSS2-SH3BGR fusion	yes	unknown		out of frame	SH3BGR (NM_007341) - TMPRSS2 (NM_001135099) rearrangement: c.421-1136:SH3BGR_c.56-2096:TMPRSS2inv Note: The SH3BGR - TMPRSS2 rearrangement is an inversion that results in the fusion of SH3BGR exons 1-2 with TMPRSS2 exons 2-14. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0029849-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.67_c.68del Note: The B2M rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 1 and the other is within exon 2. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0029870-T01-IM6	TRIM69-B2M fusion	yes	unknown		out of frame	B2M (NM_004048) - TRIM69 (NM_182985) rearrangement: c.67+112:B2M_c.6+8770:TRIM69del Note: The B2M - TRIM69 rearrangement is a deletion which results in the fusion of B2M exon 1 with TRIM69 exons 2-7. The functional significance is undetermined.
TRIM69	0	MSKCC-DMP	P-0029870-T01-IM6	TRIM69-B2M fusion	yes	unknown		out of frame	B2M (NM_004048) - TRIM69 (NM_182985) rearrangement: c.67+112:B2M_c.6+8770:TRIM69del Note: The B2M - TRIM69 rearrangement is a deletion which results in the fusion of B2M exon 1 with TRIM69 exons 2-7. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0029946-T01-IM6	RNU5F-1-B2M fusion	yes	unknown		unknown	B2M (NM_004048) rearrangement.t(1;15)(p34.1;q21.1)(chr1:g.220072784::chr15:g.45005885) Note: The B2M rearrangement is a translocation which involves exon 2. Its functional significance is undetermined.
RNU5F-1	0	MSKCC-DMP	P-0029946-T01-IM6	RNU5F-1-B2M fusion	yes	unknown		unknown	B2M (NM_004048) rearrangement.t(1;15)(p34.1;q21.1)(chr1:g.220072784::chr15:g.45005885) Note: The B2M rearrangement is a translocation which involves exon 2. Its functional significance is undetermined.
PLCG2	0	MSKCC-DMP	P-0029946-T01-IM6	PLCG2-intragenic	yes	unknown		out of frame	PLCG2 (NM_002661) rearrangement: c.766-1547_c.1073-108del Note: The PLCG2 rearrangement is an intragenic deletion of exons 10-12. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0029946-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3402:SMARCA4_chr19:g.11239260inv Note: The SMARCA4 rearrangement is an inversion of exons 25-35. One of the breakpoints is within exon 25. Its functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0029946-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3402:SMARCA4_chr19:g.11239260inv Note: The SMARCA4 rearrangement is an inversion of exons 25-35. One of the breakpoints is within exon 25. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0029946-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.4780-794_c.5476del Note: The EP300 rearrangement is an intragenic deletion of exons 30-31. One of the breakpoints is within exon 31. Its functional significance is undetermined.
TRIM33	0	MSKCC-DMP	P-0029948-T01-IM6	NUF2-TRIM33 fusion	yes	unknown		unknown	TRIM33 (NM_015906) - NUF2 (NM_031423) rearrangement: c.1420+682:TRIM33_c.624:NUF2inv Note: The TRIM33 - NUF2 rearrangement is an inversion which results in the fusion of TRIM33 exons 1-8 with NUF2 exons 9-14. One of the breakpoints is within NUF2 exon 9. Its functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0029948-T01-IM6	NUF2-TRIM33 fusion	yes	unknown		unknown	TRIM33 (NM_015906) - NUF2 (NM_031423) rearrangement: c.1420+682:TRIM33_c.624:NUF2inv Note: The TRIM33 - NUF2 rearrangement is an inversion which results in the fusion of TRIM33 exons 1-8 with NUF2 exons 9-14. One of the breakpoints is within NUF2 exon 9. Its functional significance is undetermined.
CDK6	0	MSKCC-DMP	P-0029948-T01-IM6	PPP1R9A-CDK6 fusion	yes	unknown		in frame	CDK6 (NM_001145306) - PPP1R9A (NM_001166161) rearrangement: c.834+73:CDK6_c.1396-13757:PPP1R9Ainv Note: The CDK6 - PPP1R9A rearrangement is an inversion which results in the fusion of CDK6 exons 1-7 with PPP1R9A exons 2-18. Its functional significance is undetermined.
PPP1R9A	0	MSKCC-DMP	P-0029948-T01-IM6	PPP1R9A-CDK6 fusion	yes	unknown		in frame	CDK6 (NM_001145306) - PPP1R9A (NM_001166161) rearrangement: c.834+73:CDK6_c.1396-13757:PPP1R9Ainv Note: The CDK6 - PPP1R9A rearrangement is an inversion which results in the fusion of CDK6 exons 1-7 with PPP1R9A exons 2-18. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0029956-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) Rearrangement : c.535-124_735-37385dup Note: The PARK2 Rearrangement results in the intragenic duplication of exons 5-6 of PARK2.
GABRB3	0	MSKCC-DMP	P-0029963-T01-IM6	NTRK3-GABRB3 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) Rearrangement : c.836-1619:GABRB3_c.1586-40642:NTRK3inv Note: The NTRK3 Rearrangement results in the inversion of exons 15-20 of NTRK3. Its functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0029963-T01-IM6	NTRK3-GABRB3 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) Rearrangement : c.836-1619:GABRB3_c.1586-40642:NTRK3inv Note: The NTRK3 Rearrangement results in the inversion of exons 15-20 of NTRK3. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030029-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) Rearrangement: c.126+73_c.55+4105del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.
TSEN2	0	MSKCC-DMP	P-0030032-T01-IM6	SETD2-TSEN2 fusion	yes	unknown		unknown	TSEN2 (NM_001145392) - SETD2 (NM_014159) Rearrangement: c.309-1282:TSEN2_c.6196:SETD2inv Note: The TSEN2 - SETD2 rearrangement is an inversion which results in the fusion of TSEN2 (exons 2-4 with SETD2 exons 14 to 21. One of the breakpoints is within exon 14 of SETD2. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0030032-T01-IM6	SETD2-TSEN2 fusion	yes	unknown		unknown	TSEN2 (NM_001145392) - SETD2 (NM_014159) Rearrangement: c.309-1282:TSEN2_c.6196:SETD2inv Note: The TSEN2 - SETD2 rearrangement is an inversion which results in the fusion of TSEN2 (exons 2-4 with SETD2 exons 14 to 21. One of the breakpoints is within exon 14 of SETD2. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0030033-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA (NM_013235) Rearrangement: c.2882+9_c.2821+121inv Note: The DROSHA rearrangement is an intragenic inversion of exon 22. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0014464-T02-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement : c.7180_c.7189+2041del Note: The NF1 rearrangement results in the deletion of exon 48. One of the breakpoints is within exon 48. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030107-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4157:TMPRSS2_c.40-57456:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0030107-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4157:TMPRSS2_c.40-57456:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
SLC25A21	0	MSKCC-DMP	P-0030109-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.120-27147:SLC25A21_c.32:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in the fusion of SLC25A21 exons 1-2 with FOXA1 exons 1-2. One of the breakpoints is within FOXA1 exon 1. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0030109-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.120-27147:SLC25A21_c.32:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in the fusion of SLC25A21 exons 1-2 with FOXA1 exons 1-2. One of the breakpoints is within FOXA1 exon 1. The functional significance is undetermined.
ITGAE	0	MSKCC-DMP	P-0030109-T01-IM6	TP53-ITGAE fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.375+66:TP53_chr17:g.3605902del Note: The TP53 rearrangement results in the deletion of exons 5-11. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0030109-T01-IM6	TP53-ITGAE fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.375+66:TP53_chr17:g.3605902del Note: The TP53 rearrangement results in the deletion of exons 5-11. The functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0030109-T01-IM6	EDEM2-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1627:ASXL1_chr20:g.33684946del Note: The ASXL1 rearrangement results in the deletion of exons 11-12. One of the breakpoints is within exon 11. The functional significance is undetermined.
EDEM2	0	MSKCC-DMP	P-0030109-T01-IM6	EDEM2-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1627:ASXL1_chr20:g.33684946del Note: The ASXL1 rearrangement results in the deletion of exons 11-12. One of the breakpoints is within exon 11. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030109-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2838:TMPRSS2_c.40-58598:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0030109-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2838:TMPRSS2_c.40-58598:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0008431-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1980:TMPRSS2_c.40-52619:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0008431-T01-IM5	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1980:TMPRSS2_c.40-52619:ERGdel
LINC01533	0	MSKCC-DMP	P-0021526-T02-IM6	KMT2B-LINC01533 fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5460:KMT2B_chr19:g.32548661inv Note: The KMT2B rearrangement is an inversion of exons 1-27. One of the breakpoints is within exon 27. The inversion is detected within a background of intragenic gain in KMT2B. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0021526-T02-IM6	KMT2B-LINC01533 fusion	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5460:KMT2B_chr19:g.32548661inv Note: The KMT2B rearrangement is an inversion of exons 1-27. One of the breakpoints is within exon 27. The inversion is detected within a background of intragenic gain in KMT2B. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0029892-T04-IM6	PLEKHA6-NTRK1 fusion	yes	unknown		in frame	PLEKHA6 (NM_014935) - NTRK1 (NM_002529) fusion: c.2032+105:PLEKHA6_c.1195+47:NTRK1inv Note: The PLEKHA6  - NTRK1 fusion is an inversion that results in the in-frame fusion of PLEKHA6 exons 1-14 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
PLEKHA6	0	MSKCC-DMP	P-0029892-T04-IM6	PLEKHA6-NTRK1 fusion	yes	unknown		in frame	PLEKHA6 (NM_014935) - NTRK1 (NM_002529) fusion: c.2032+105:PLEKHA6_c.1195+47:NTRK1inv Note: The PLEKHA6  - NTRK1 fusion is an inversion that results in the in-frame fusion of PLEKHA6 exons 1-14 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0029892-T04-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.528_c.1027-1146dup Note: The PTEN rearrangement results in the duplication of exons 6-8. One of the breakpoints is within exon 6. The functional significance is undetermined.
TANGO2	0	MSKCC-DMP	P-0030133-T01-IM6	NF2-TANGO2 fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.1300:NF2_chr22:g.20027873inv Note: The NF2 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0030133-T01-IM6	NF2-TANGO2 fusion	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.1300:NF2_chr22:g.20027873inv Note: The NF2 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0030134-T01-IM6	AKT2-intragenic	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: c.640-179:AKT2_chr19:g.40736136inv Note: The AKT2 rearrangement is an inversion of exons 1-7. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0030135-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.422-572_c.549dup Note: The ERBB4 rearrangement is an intragenic duplication of a part of exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0030184-T01-IM6	CAPS2-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.8096:KMT2D_chr12:g.75706091inv Note: The KMT2D rearrangement is an inversion of exons 1-32. One of the breakpoints is within exon 32. The functional significance is undetermined.
CAPS2	0	MSKCC-DMP	P-0030184-T01-IM6	CAPS2-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.8096:KMT2D_chr12:g.75706091inv Note: The KMT2D rearrangement is an inversion of exons 1-32. One of the breakpoints is within exon 32. The functional significance is undetermined.
ZNF385D-AS2	0	MSKCC-DMP	P-0030184-T01-IM6	PBRM1-ZNF385D-AS2 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement:     c.4386:PBRM1_chr3:g.22617724del Note: The PBRM1 rearrangement is a deletion of exons 29-30. One of the breakpoints is within exon 29. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0030184-T01-IM6	PBRM1-ZNF385D-AS2 fusion	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement:     c.4386:PBRM1_chr3:g.22617724del Note: The PBRM1 rearrangement is a deletion of exons 29-30. One of the breakpoints is within exon 29. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030187-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4546:TMPRSS2_c.18+5296:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0030187-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4546:TMPRSS2_c.18+5296:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
KMT2B	0	MSKCC-DMP	P-0030213-T01-IM6	LIN37-KMT2B fusion	yes	unknown		unknown	LIN37 (NM_019104) - KMT2B (NM_014727) rearrangement: c.444+169:LIN37_c.7483:KMT2Bdup Note: The LIN37 - KMT2B rearrangement is a duplication which results in the fusion of LIN37 exons 1-6 with KMT2B exons 33-37. One of the breakpoints is within KMT2B exon 33. Its functional significance is undetermined.
LIN37	0	MSKCC-DMP	P-0030213-T01-IM6	LIN37-KMT2B fusion	yes	unknown		unknown	LIN37 (NM_019104) - KMT2B (NM_014727) rearrangement: c.444+169:LIN37_c.7483:KMT2Bdup Note: The LIN37 - KMT2B rearrangement is a duplication which results in the fusion of LIN37 exons 1-6 with KMT2B exons 33-37. One of the breakpoints is within KMT2B exon 33. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030261-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4365:TMPRSS2_c.39+58079:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 4-10. This fusion occurs with the non-canonical ERG(NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0030261-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4365:TMPRSS2_c.39+58079:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 4-10. This fusion occurs with the non-canonical ERG(NM_004449) transcript.
CPM	0	MSKCC-DMP	P-0030267-T01-IM6	FGFR1-CPM fusion	yes	unknown		out of frame	CPM (NM_001005502) - FGFR1 (NM_001174067) rearrangement: t(8;12)(q11.23;q15)(chr8:g.38272053::chr12:g.69274149) Note: The CPM - FGFR1 rearrangement is a translocation which may result in the fusion of FGFR1 exons 1-16 with CPM exon 4-9. Its functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0030267-T01-IM6	FGFR1-CPM fusion	yes	unknown		out of frame	CPM (NM_001005502) - FGFR1 (NM_001174067) rearrangement: t(8;12)(q11.23;q15)(chr8:g.38272053::chr12:g.69274149) Note: The CPM - FGFR1 rearrangement is a translocation which may result in the fusion of FGFR1 exons 1-16 with CPM exon 4-9. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012630-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.56-1480:TMPRSS2_c.-47-4326:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0012630-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.56-1480:TMPRSS2_c.-47-4326:ERGdel
PIK3R1	0	MSKCC-DMP	P-0012630-T02-IM6	KCTD16-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1735_chr5:g.143970832inv Note: The PIK3R1 rearrangement is an inversion that includes PIK3R1 exons 13-16. One of the breakpoints is within exon 13.
KCTD16	0	MSKCC-DMP	P-0012630-T02-IM6	KCTD16-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1735_chr5:g.143970832inv Note: The PIK3R1 rearrangement is an inversion that includes PIK3R1 exons 13-16. One of the breakpoints is within exon 13.
FLT3	0	MSKCC-DMP	P-0030345-T01-IM6	LOC101927314-FLT3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: t(6;13)(q16.1;q12.2)(chr6:g.98003011::chr13:g.:28623849) Note: The FLT3 rearrangement is a translocation with a breakpoint within FLT3 exon 7. The functional significance is undetermined.
LOC101927314	0	MSKCC-DMP	P-0030345-T01-IM6	LOC101927314-FLT3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: t(6;13)(q16.1;q12.2)(chr6:g.98003011::chr13:g.:28623849) Note: The FLT3 rearrangement is a translocation with a breakpoint within FLT3 exon 7. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0030345-T01-IM6	RNF112-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.1353-60_chr17:g.19331269inv Note: The NCOR1 rearrangement is an inversion that includes NCOR1 exons 1-12. The functional significance is undetermined.
RNF112	0	MSKCC-DMP	P-0030345-T01-IM6	RNF112-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.1353-60_chr17:g.19331269inv Note: The NCOR1 rearrangement is an inversion that includes NCOR1 exons 1-12. The functional significance is undetermined.
U2AF2	0	MSKCC-DMP	P-0015960-T02-IM6	HIST1H3B-U2AF2 fusion	yes	unknown		unknown	U2AF2 (NM_007279) - HIST1H3B (NM_003537) rearrangement: t(6;19)(p22.2;q13.42)(chr6:g.26032161::chr19:g.56181895) Note: The U2AF2 - HIST1H3B rearrangement is a translocation which results in the fusion of U2AF2 exon 11 to HIST1H3B exon 1. One of the breakpoints is within HIST1H3B exon 1. The functional significance is undetermined.
HIST1H3B	0	MSKCC-DMP	P-0015960-T02-IM6	HIST1H3B-U2AF2 fusion	yes	unknown		unknown	U2AF2 (NM_007279) - HIST1H3B (NM_003537) rearrangement: t(6;19)(p22.2;q13.42)(chr6:g.26032161::chr19:g.56181895) Note: The U2AF2 - HIST1H3B rearrangement is a translocation which results in the fusion of U2AF2 exon 11 to HIST1H3B exon 1. One of the breakpoints is within HIST1H3B exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0015960-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-116:TMPRSS2_c.40-64777:ERGdel Note: The TMPRSS2 is fused with the non-canonical ERG(NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0015960-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-116:TMPRSS2_c.40-64777:ERGdel Note: The TMPRSS2 is fused with the non-canonical ERG(NM_004449) transcript.
PBRM1	0	MSKCC-DMP	P-0015960-T02-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) Rearrangemnet: c.996-371_c.899+68inv Note: The PBRM1 rearrangement is an intragenic inversion of PBRM1 exon 10. The functional significance is undetermined.
IGF1	0	MSKCC-DMP	P-0030228-T01-IM6	GLT8D2-IGF1 fusion	yes	unknown		unknown	IGF1 (NM_001111285) - GLT8D2 (NM_031302) rearrangement: c.307:IGF1_c.112+4819:GLT8D2dup Note: The IGF1 - GLT8D2 rearrangement is a duplication that may result in the fusion of IGF1 exons 1-3 with GLT8D2 exons 5-11. One of the breakpoints is within IGF1 exon 3. The functional significance is undetermined.
GLT8D2	0	MSKCC-DMP	P-0030228-T01-IM6	GLT8D2-IGF1 fusion	yes	unknown		unknown	IGF1 (NM_001111285) - GLT8D2 (NM_031302) rearrangement: c.307:IGF1_c.112+4819:GLT8D2dup Note: The IGF1 - GLT8D2 rearrangement is a duplication that may result in the fusion of IGF1 exons 1-3 with GLT8D2 exons 5-11. One of the breakpoints is within IGF1 exon 3. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0030232-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1138-12301_c.2252-8del Note: The ARID1A rearrangement is an intragenic deletion of exons 2-6.
INSR	0	MSKCC-DMP	P-0030289-T01-IM6	INSR-intragenic	yes	unknown		unknown	INSR (NM_000208) Rearrangement: c.3478_c.2842+540del Note: The INSR rearrangement is an intragenic deletion of exon 15 to 19. One of the breakpoints is within exon 19. The functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0030322-T01-IM6	FOXP1-intragenic	yes	unknown		out of frame	FOXP1 (NM_001244814) Rearrangement: c.869+11517_c.664+50del Note: The FOXP1 rearrangement is an intragenic deletion of exon 7. The functional significance is undetermined.
CCND1	0	MSKCC-DMP	P-0030333-T01-IM6	PICALM-CCND1 fusion	yes	unknown		unknown	CCND1 (NM_053056) Rearrangement: c.20_chr11:g.85739851del Note: The CCND1 rearrangement results in the deletion CCND1 exons 1-5. One of the breakpoints is within CCND1 exon 1. The functional significance is undetermined.
PICALM	0	MSKCC-DMP	P-0030333-T01-IM6	PICALM-CCND1 fusion	yes	unknown		unknown	CCND1 (NM_053056) Rearrangement: c.20_chr11:g.85739851del Note: The CCND1 rearrangement results in the deletion CCND1 exons 1-5. One of the breakpoints is within CCND1 exon 1. The functional significance is undetermined.
GABRG3	0	MSKCC-DMP	P-0030333-T01-IM6	MDC1-GABRG3 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(6;15)(p21.32;q12)(chr6:g.30675950::chr15:g.27671033) Note: The MDC1 rearrangement is a translocation that may result in a truncation of exons 8-15. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0030333-T01-IM6	MDC1-GABRG3 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(6;15)(p21.32;q12)(chr6:g.30675950::chr15:g.27671033) Note: The MDC1 rearrangement is a translocation that may result in a truncation of exons 8-15. The functional significance is undetermined.
ICOSLG	0	MSKCC-DMP	P-0030333-T01-IM6	FAM155A-ICOSLG fusion	yes	unknown		unknown	ICOSLG (NM_015259) Rearrangement: t(12;21)(q33.3;q22.3)(chr13:g.107684536::chr21:g.45656951) Note: The ICOSLG rearrangement is a translocation that may result in a truncation of exons 3-7. The functional significance is undetermined.
FAM155A	0	MSKCC-DMP	P-0030333-T01-IM6	FAM155A-ICOSLG fusion	yes	unknown		unknown	ICOSLG (NM_015259) Rearrangement: t(12;21)(q33.3;q22.3)(chr13:g.107684536::chr21:g.45656951) Note: The ICOSLG rearrangement is a translocation that may result in a truncation of exons 3-7. The functional significance is undetermined.
TCEB2	0	MSKCC-DMP	P-0030408-T01-IM6	BAP1-TCEB2 fusion	yes	unknown		out of frame	TCEB2 (NM_207013) - BAP1 (NM_004656) rearrangement: t(3;16)(p21.1;p13.3)(chr3:g.52438638::chr16:g.2824342) Note: The TCEB2 - BAP1 rearrangement is a translocation that results in the fusion of TCEB2 exons 1-3 with BAP1 exon 12-17. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0030408-T01-IM6	BAP1-TCEB2 fusion	yes	unknown		out of frame	TCEB2 (NM_207013) - BAP1 (NM_004656) rearrangement: t(3;16)(p21.1;p13.3)(chr3:g.52438638::chr16:g.2824342) Note: The TCEB2 - BAP1 rearrangement is a translocation that results in the fusion of TCEB2 exons 1-3 with BAP1 exon 12-17. The functional significance is undetermined.
LINC01186	0	MSKCC-DMP	P-0030449-T01-IM6	RUNX1-LINC01186 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(21;X)(q22.12;p11.3)(chr21:g.36206846::chrX:g.46136512) Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 7. The functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0030449-T01-IM6	RUNX1-LINC01186 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: t(21;X)(q22.12;p11.3)(chr21:g.36206846::chrX:g.46136512) Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 7. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0019765-T02-IM6	LARP4B-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - LARP4B (NM_015155) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.941664::chr19:g.15275995) Note: The NOTCH3 - LARP4B rearrangement is a translocation with breakpoints within NOTCH3 intron 31 and LARP4B intron 1. The functional significance is undetermined.
LARP4B	0	MSKCC-DMP	P-0019765-T02-IM6	LARP4B-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - LARP4B (NM_015155) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.941664::chr19:g.15275995) Note: The NOTCH3 - LARP4B rearrangement is a translocation with breakpoints within NOTCH3 intron 31 and LARP4B intron 1. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0019765-T02-IM6	IDI2-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) - IDI2 (NM_033261) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.1065652::chr19:g.15376225) Note: The BRD4 - IDI2 rearrangement is a translocation with breakpoints within BRD4 exon 5 and IDI2 exon 5. The functional significance is undetermined.
IDI2	0	MSKCC-DMP	P-0019765-T02-IM6	IDI2-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) - IDI2 (NM_033261) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.1065652::chr19:g.15376225) Note: The BRD4 - IDI2 rearrangement is a translocation with breakpoints within BRD4 exon 5 and IDI2 exon 5. The functional significance is undetermined.
IKBKE	0	MSKCC-DMP	P-0027193-T03-IM6	IL20-IKBKE fusion	yes	unknown		unknown	IL20 (NM_018724) - IKBKE (NM_014002) Rearrangement : c.398:IL20_c.2046-146:IKBKE Note: The IL20 - IKBKE Rearrangement results in the fusion of exons 1-4 of IL20 with exons 21-22 of IKBKE.The breakpoint in IL20 is within exon4. Its functional significance is undetermined.
IL20	0	MSKCC-DMP	P-0027193-T03-IM6	IL20-IKBKE fusion	yes	unknown		unknown	IL20 (NM_018724) - IKBKE (NM_014002) Rearrangement : c.398:IL20_c.2046-146:IKBKE Note: The IL20 - IKBKE Rearrangement results in the fusion of exons 1-4 of IL20 with exons 21-22 of IKBKE.The breakpoint in IL20 is within exon4. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0030303-T01-IM6	MTRNR2L6-BRAF fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1141-61:BRAF_chr9:g.142397017inv Note: The BRAF rearrangement results in the inversion of exons 1-8. The functional significance is undetermined.
MTRNR2L6	0	MSKCC-DMP	P-0030303-T01-IM6	MTRNR2L6-BRAF fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1141-61:BRAF_chr9:g.142397017inv Note: The BRAF rearrangement results in the inversion of exons 1-8. The functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0030374-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) Rearrangement : c.2061+750_c.2226del Note: The KDM5C Rearrangement results in the intragenic deletion of exon15 of KDM5C. The breakpoint in KDM5C is within exon15. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030381-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.55+3863:TMPRSS2_c.18+9727:ERGdel TMPRSS2 exon1 with ERG exon2
TMPRSS2	0	MSKCC-DMP	P-0030381-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.55+3863:TMPRSS2_c.18+9727:ERGdel TMPRSS2 exon1 with ERG exon2
NCOR1	0	MSKCC-DMP	P-0030382-T01-IM6	PIGL-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - PIGL (NM_004278) Rearrangement : c.1866:NCOR1_c.335+13717:PIGLinv Note: The NCOR1 - PIGL Rearrangement results in the fusion of exons 1-17 of NCOR1 with exons 3-7 of PIGL.The breakpoint in NCOR1 is within exon 17. Its functional significance is undetermined.
PIGL	0	MSKCC-DMP	P-0030382-T01-IM6	PIGL-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - PIGL (NM_004278) Rearrangement : c.1866:NCOR1_c.335+13717:PIGLinv Note: The NCOR1 - PIGL Rearrangement results in the fusion of exons 1-17 of NCOR1 with exons 3-7 of PIGL.The breakpoint in NCOR1 is within exon 17. Its functional significance is undetermined.
CCDC90B	0	MSKCC-DMP	P-0030520-T01-IM6	HIST2H3D-CCDC90B fusion	yes	unknown		unknown	HIST2H3D (NM_001123375) rearrangement: t(1;11)(q21.2;q14.1)(chr1:g.149785203::chr11:g.82997912) Note: The HIST2H3D rearrangement is a translocation with a breakpoint within exon 1. The functional significance is undetermined.
HIST2H3D	0	MSKCC-DMP	P-0030520-T01-IM6	HIST2H3D-CCDC90B fusion	yes	unknown		unknown	HIST2H3D (NM_001123375) rearrangement: t(1;11)(q21.2;q14.1)(chr1:g.149785203::chr11:g.82997912) Note: The HIST2H3D rearrangement is a translocation with a breakpoint within exon 1. The functional significance is undetermined.
EDF1	0	MSKCC-DMP	P-0030527-T01-IM6	TRAF2-EDF1 fusion	yes	unknown		unknown	EDF1 (NM_003792) - TRAF2 (NM_021138) rearrangement: c.291+54:EDF1_c.970:TRAF2del Note: The EDF1 - TRAF2 rearrangement is a deletion that includes EDF1 exons 1-3 and TRAF2 exons 1-9. The functional significance is undetermined.
TRAF2	0	MSKCC-DMP	P-0030527-T01-IM6	TRAF2-EDF1 fusion	yes	unknown		unknown	EDF1 (NM_003792) - TRAF2 (NM_021138) rearrangement: c.291+54:EDF1_c.970:TRAF2del Note: The EDF1 - TRAF2 rearrangement is a deletion that includes EDF1 exons 1-3 and TRAF2 exons 1-9. The functional significance is undetermined.
ERF	0	MSKCC-DMP	P-0030528-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - CIC (NM_015125) rearrangemnet: c.22+337:ERF_c.1018:CICdel Note: The ERF - CIC rearrangement is a deletion that includes ERF exon 1 and CIC exons 1-7. One of the breakpoints is within CIC exon 7.
CIC	0	MSKCC-DMP	P-0030528-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - CIC (NM_015125) rearrangemnet: c.22+337:ERF_c.1018:CICdel Note: The ERF - CIC rearrangement is a deletion that includes ERF exon 1 and CIC exons 1-7. One of the breakpoints is within CIC exon 7.
TP53	0	MSKCC-DMP	P-0009743-T01-IM5	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546)  rearrangement: c.993+582_c.826del Note: The TP53 (NM_000546) rearrangement is a intragenic deletion of exons 8-9. One of the breakpoints is within exon 8.
CDKN2A	0	MSKCC-DMP	P-0030308-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement : c.*93:_c.193+8893del Note: The CDKN2Ap14ARF rearrangement results in the deletion of exon 2. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0030308-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.449:CDKN2Ap16INK4A_chr9:g.21985245del Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0030462-T01-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: chr7:g.140429032_c.1177+1038dup Note: The BRAF rearrangement is a duplication that includes BRAF exons 10-18, including the kinase domain.
DAXX	0	MSKCC-DMP	P-0030466-T01-IM6	PTP4A1-DAXX fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.2200-20_chr6:g.64186175del Note: The DAXX rearrangement is a deletion that includes DAXX exons 1-7. The functional significance is undetermined.
PTP4A1	0	MSKCC-DMP	P-0030466-T01-IM6	PTP4A1-DAXX fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.2200-20_chr6:g.64186175del Note: The DAXX rearrangement is a deletion that includes DAXX exons 1-7. The functional significance is undetermined.
RAD51D	0	MSKCC-DMP	P-0030469-T01-IM6	CDK5RAP3-RAD51D fusion	yes	unknown		unknown	RAD51D (NM_133629) rearrangement: c.145-32:RAD51D_chr17:g.33433532del Note: The RAD51D rearrangement is a deletion that includes exons 1-2 of RAD51D. The functional significance is undetermined.
CDK5RAP3	0	MSKCC-DMP	P-0030469-T01-IM6	CDK5RAP3-RAD51D fusion	yes	unknown		unknown	RAD51D (NM_133629) rearrangement: c.145-32:RAD51D_chr17:g.33433532del Note: The RAD51D rearrangement is a deletion that includes exons 1-2 of RAD51D. The functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0030472-T01-IM6	NEGR1-intragenic	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: c.901_c.940+11245del Note: The NEGR1 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030580-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.18+1813:ERGdel Note: The TMPRSS2 - ERG fusion includes the TMRSS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0030580-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.18+1813:ERGdel Note: The TMPRSS2 - ERG fusion includes the TMRSS2 exon 1 and ERG exons 2-10.
RET	0	MSKCC-DMP	P-0030622-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-5054:CCDC6_c.2136+566:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0030622-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-5054:CCDC6_c.2136+566:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
MST1R	0	MSKCC-DMP	P-0030626-T01-IM6	PBRM1-MST1R fusion	yes	unknown		out of frame	MST1R (NM_002447) - PBRM1 (NM_018313) rearrangement: c.2650-33_c.1924+418dup Note: The MST1R - PBRM1 rearrangement is a duplication that results in the fusion of MST1R exons 1-10 with PBRM1 exons 17-30.
PBRM1	0	MSKCC-DMP	P-0030626-T01-IM6	PBRM1-MST1R fusion	yes	unknown		out of frame	MST1R (NM_002447) - PBRM1 (NM_018313) rearrangement: c.2650-33_c.1924+418dup Note: The MST1R - PBRM1 rearrangement is a duplication that results in the fusion of MST1R exons 1-10 with PBRM1 exons 17-30.
MDC1	0	MSKCC-DMP	P-0030626-T01-IM6	PTP4A1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5527_chr6:g.64207942dup Note: The MDC1 rearrangement is a duplication that includes MDC1 exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
PTP4A1	0	MSKCC-DMP	P-0030626-T01-IM6	PTP4A1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5527_chr6:g.64207942dup Note: The MDC1 rearrangement is a duplication that includes MDC1 exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
WNT2	0	MSKCC-DMP	P-0030641-T01-IM6	PRKCI-WNT2 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: t(3;7)(q26.2;q31.2)(chr3:g.169997993::chr7:g.116889371) Note: The PRKCI rearrangement is a translocation with a breakpoint within intron 8. The functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0030641-T01-IM6	PRKCI-WNT2 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: t(3;7)(q26.2;q31.2)(chr3:g.169997993::chr7:g.116889371) Note: The PRKCI rearrangement is a translocation with a breakpoint within intron 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030675-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 5-11): c.55+1904:TMPRSS2_c.40-59905:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0030675-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 5-11): c.55+1904:TMPRSS2_c.40-59905:ERGdel
STAT5A	0	MSKCC-DMP	P-0030717-T01-IM6	EZH1-STAT5A fusion	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: c.2098+98:EZH1_chr17:g.40439374del Note: The EZH1 rearrangement results in the deletion of exons 1-19. Its functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0030717-T01-IM6	EZH1-STAT5A fusion	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: c.2098+98:EZH1_chr17:g.40439374del Note: The EZH1 rearrangement results in the deletion of exons 1-19. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0030721-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.29_c.461del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3-4. The breakpoints are within exons 3 and 4. Its functional significance is undetermined.
WT1	0	MSKCC-DMP	P-0002375-T02-IM6	TAPT1-WT1 fusion	yes	unknown		out of frame	WT1 (NM_024426) - TAPT1 (NM_153365) rearrangement: t(4;11)(p15.32;p13)(chr4:g.16168647::chr11:g.32456161) Note: The WT1 - TAPT1 rearrangement is a translocation which may results in the fusion of WT1 exon 1 with TAPT1 exons 13-14. Its functional significance is undetermined.
TAPT1	0	MSKCC-DMP	P-0002375-T02-IM6	TAPT1-WT1 fusion	yes	unknown		out of frame	WT1 (NM_024426) - TAPT1 (NM_153365) rearrangement: t(4;11)(p15.32;p13)(chr4:g.16168647::chr11:g.32456161) Note: The WT1 - TAPT1 rearrangement is a translocation which may results in the fusion of WT1 exon 1 with TAPT1 exons 13-14. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0002375-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-470:TMPRSS2_c.19-14125:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0002375-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-470:TMPRSS2_c.19-14125:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0002901-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0002901-T01-IM3	TMPRSS2-ERG fusion	yes	unknown		in frame	null
TMPRSS2	0	MSKCC-DMP	P-0002901-T01-IM3	NR3C2-TMPRSS2 fusion	yes	unknown		out of frame	null looks real, but same breakpoint as with erg!
NR3C2	0	MSKCC-DMP	P-0002901-T01-IM3	NR3C2-TMPRSS2 fusion	yes	unknown		out of frame	null looks real, but same breakpoint as with erg!
KDM5A	0	MSKCC-DMP	P-0030719-T01-IM6	ARNTL2-KDM5A fusion	yes	unknown		unknown	ARNTL2 (NM_001248002) - KDM5A (NM_001042603) rearrangement: c.285-4357:ARNTL2_c.1992:KDM5A Note: The ARNTL2 - KMD5A rearrangement is an inversion which results in the fusion of ARNTL2 exons 1-2 with KDM5A exons 15-28. One of the breakpoints is within KDM5A exon 15. Its functional significance is undetermined.
ARNTL2	0	MSKCC-DMP	P-0030719-T01-IM6	ARNTL2-KDM5A fusion	yes	unknown		unknown	ARNTL2 (NM_001248002) - KDM5A (NM_001042603) rearrangement: c.285-4357:ARNTL2_c.1992:KDM5A Note: The ARNTL2 - KMD5A rearrangement is an inversion which results in the fusion of ARNTL2 exons 1-2 with KDM5A exons 15-28. One of the breakpoints is within KDM5A exon 15. Its functional significance is undetermined.
LINC01533	0	MSKCC-DMP	P-0030773-T01-IM6	CIC-LINC01533 fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.2934:CIC_chr19:g.32449624inv Note: The CIC rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12.
CIC	0	MSKCC-DMP	P-0030773-T01-IM6	CIC-LINC01533 fusion	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.2934:CIC_chr19:g.32449624inv Note: The CIC rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12.
POLE	0	MSKCC-DMP	P-0030745-T01-IM6	LOC100507651-POLE fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(8;12)(q12.1;q24.33)(chr8:g.58136160::chr12:g.133256566) Note: The POLE rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.
LOC100507651	0	MSKCC-DMP	P-0030745-T01-IM6	LOC100507651-POLE fusion	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(8;12)(q12.1;q24.33)(chr8:g.58136160::chr12:g.133256566) Note: The POLE rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0030749-T01-IM6	BRCA1-intragenic	yes	unknown		in frame	BRCA1 (NM_007294) rearrangement: c.670+105_c.4675+1206del Note: The BRCA1 rearrangement is an intragenic deletion of exons 10-14.
SMAD4	0	MSKCC-DMP	P-0030749-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement:  c.455-2248_c.1139+85inv Note: The SMAD4 rearrangement is an intragenic inversion of exons 5-9.
FGF19	0	MSKCC-DMP	P-0030750-T01-IM6	FGF19-intragenic	yes	unknown		unknown	FGF19 (NM_005117) rearrangement: c.641:FGF19_chr11:g.69526352del Note: The FGF19 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0030750-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.5028_c.7470+1675del Note: The ANKRD11 rearrangement is an intragenic deletion of a part of exon 9. One of the breakpoints is within exon 9.
DCN	0	MSKCC-DMP	P-0030720-T01-IM6	PREX2-DCN fusion	yes	unknown		unknown	PREX2 (NM_024870) - DCN (NM_133503) rearrangement: t(8;12)(q13.2;q21.33)(chr8:g.68965387::chr12:g.91564661) Note: The PREX2 - DCN rearrangement is a translocation which may result in the fusion of PREX2 exons 1-9 with DCN exons 3-8. One of the breakpoints is within PREX2 exon 9. Its functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0030720-T01-IM6	PREX2-DCN fusion	yes	unknown		unknown	PREX2 (NM_024870) - DCN (NM_133503) rearrangement: t(8;12)(q13.2;q21.33)(chr8:g.68965387::chr12:g.91564661) Note: The PREX2 - DCN rearrangement is a translocation which may result in the fusion of PREX2 exons 1-9 with DCN exons 3-8. One of the breakpoints is within PREX2 exon 9. Its functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0003274-T02-IM6	LOC340107-RARA fusion	yes	unknown		unknown	RARA (NM_000964) Rearrangement : t(5;17)(p14.1;q21.1)(chr5:g.25855191::chr17:g. 38510622) Note: The RARA Rearrangement is a translocation event with the breakpoint in exon7. Its functional significance is undetermined.
LOC340107	0	MSKCC-DMP	P-0003274-T02-IM6	LOC340107-RARA fusion	yes	unknown		unknown	RARA (NM_000964) Rearrangement : t(5;17)(p14.1;q21.1)(chr5:g.25855191::chr17:g. 38510622) Note: The RARA Rearrangement is a translocation event with the breakpoint in exon7. Its functional significance is undetermined.
LINC01194	0	MSKCC-DMP	P-0003274-T02-IM6	DROSHA-LINC01194 fusion	yes	unknown		unknown	DROSHA (NM_013235) Rearrangement : chr5:g.13054033_c.1555:DROSHAdel Note: The DROSHA Rearrangement results in the deletion of exons 9-35 of DROSHA. Its functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0003274-T02-IM6	DROSHA-LINC01194 fusion	yes	unknown		unknown	DROSHA (NM_013235) Rearrangement : chr5:g.13054033_c.1555:DROSHAdel Note: The DROSHA Rearrangement results in the deletion of exons 9-35 of DROSHA. Its functional significance is undetermined.
ZNRF3	0	MSKCC-DMP	P-0019819-T02-IM6	EWSR1-ZNRF3 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - ZNRF3 (NM_001206998) rearrangement: c.793+1474:EWSR1_c.744+199:ZNRF3dup Note: The EWSR1 - ZNRF3 rearrangement is a duplication that results in the fusion of EWSR1 exons 1-9 with ZNRF3 exons 6-9. One of the breakpoints is within EWSR1 exon 9. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0019819-T02-IM6	EWSR1-ZNRF3 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - ZNRF3 (NM_001206998) rearrangement: c.793+1474:EWSR1_c.744+199:ZNRF3dup Note: The EWSR1 - ZNRF3 rearrangement is a duplication that results in the fusion of EWSR1 exons 1-9 with ZNRF3 exons 6-9. One of the breakpoints is within EWSR1 exon 9. The functional significance is undetermined.
TET2	0	MSKCC-DMP	P-0019819-T02-IM6	ARHGEF38-TET2 fusion	yes	unknown		out of frame	ARHGEF38 (NM_001242729) - TET2 (NM_001127208) rearrangement: c.197-16141:ARHGEF38_c.3804-40:TET2dup Note: The ARHGEF38 - TET2 rearrangement is a duplication that results in the fusion of ARHGEF38 exon 1 with TET2 exon 7-11. The functional significance is undetermined.
ARHGEF38	0	MSKCC-DMP	P-0019819-T02-IM6	ARHGEF38-TET2 fusion	yes	unknown		out of frame	ARHGEF38 (NM_001242729) - TET2 (NM_001127208) rearrangement: c.197-16141:ARHGEF38_c.3804-40:TET2dup Note: The ARHGEF38 - TET2 rearrangement is a duplication that results in the fusion of ARHGEF38 exon 1 with TET2 exon 7-11. The functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0030792-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: c.127-1213:TMPRSS2_chr21:g.40102198del Note: The TMPRSS2 rearrangement is an deletion of TMPRSS2 exons 3 to 14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030792-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement: c.127-1213:TMPRSS2_chr21:g.40102198del Note: The TMPRSS2 rearrangement is an deletion of TMPRSS2 exons 3 to 14. The functional significance is undetermined.
HMBOX1	0	MSKCC-DMP	P-0030808-T01-IM6	ALK-HMBOX1 fusion	yes	unknown		unknown	HMBOX1 (NM_001135726) ALK (NM_004304) Rearrangement : t(2,8)(p23.3,p21.1)(chr2:g.29447713::chr8:g.28904937) Note: The HMBOX1-ALK Rearrangement results in the fusion of exons 1-8 of HMBOX1 with exons 20-29 of ALK.  It includes the protein kinase of ALK.
ALK	0	MSKCC-DMP	P-0030808-T01-IM6	ALK-HMBOX1 fusion	yes	unknown		unknown	HMBOX1 (NM_001135726) ALK (NM_004304) Rearrangement : t(2,8)(p23.3,p21.1)(chr2:g.29447713::chr8:g.28904937) Note: The HMBOX1-ALK Rearrangement results in the fusion of exons 1-8 of HMBOX1 with exons 20-29 of ALK.  It includes the protein kinase of ALK.
PTEN	0	MSKCC-DMP	P-0030812-T01-IM6	MRPL9-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: t(1;10)(q21.3;q23.31)(chr1:g.151714790::chr10:g.89725115) Note: The PTEN rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
MRPL9	0	MSKCC-DMP	P-0030812-T01-IM6	MRPL9-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) rearrangement: t(1;10)(q21.3;q23.31)(chr1:g.151714790::chr10:g.89725115) Note: The PTEN rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1054:TMPRSS2_c.40-56880:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0030812-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1054:TMPRSS2_c.40-56880:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0030845-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-579:TMPRSS2_c.40-59079:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0030845-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-579:TMPRSS2_c.40-59079:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
SMAD4	0	MSKCC-DMP	P-0030847-T01-IM6	CSRP1-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) Rearrangement: t(1;18)(q32.1;q21.2)(chr1:g.201465436::chr18:g.48584640) Note: The SMAD4 rearrangement is a translocation that results in the possible truncation of SMAD4. The functionals significance is undetermined.
CSRP1	0	MSKCC-DMP	P-0030847-T01-IM6	CSRP1-SMAD4 fusion	yes	unknown		unknown	SMAD4 (NM_005359) Rearrangement: t(1;18)(q32.1;q21.2)(chr1:g.201465436::chr18:g.48584640) Note: The SMAD4 rearrangement is a translocation that results in the possible truncation of SMAD4. The functionals significance is undetermined.
TET1	0	MSKCC-DMP	P-0030872-T01-IM6	SSR3-TET1 fusion	yes	unknown		unknown	TET1 (NM_030625) rearrangement: t(3;10)(q25.31;q21.3)(chr3:g.156287710::chr10:g.70446541) Note: The TET1 rearrangement is a translocation with a breakpoint in intron 11. The functional significance is undetermined.
SSR3	0	MSKCC-DMP	P-0030872-T01-IM6	SSR3-TET1 fusion	yes	unknown		unknown	TET1 (NM_030625) rearrangement: t(3;10)(q25.31;q21.3)(chr3:g.156287710::chr10:g.70446541) Note: The TET1 rearrangement is a translocation with a breakpoint in intron 11. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030872-T01-IM6	TSPAN4-TMPRSS2 fusion	yes	unknown		unknown	TPAN4 (NM_001025238) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p15.5;q22.3)(chr11:g.:865773::chr21:g.42867997) Note: The TSPAN4 - TMPRSS2 rearrangement is a translocation that results in the fusion of TSPAN4 exons 1-7 with TMPRSS2 exons 3-14. One of the breakpoints is within TSPAN4 exon 7. The functional significance is undetermined.
TSPAN4	0	MSKCC-DMP	P-0030872-T01-IM6	TSPAN4-TMPRSS2 fusion	yes	unknown		unknown	TPAN4 (NM_001025238) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p15.5;q22.3)(chr11:g.:865773::chr21:g.42867997) Note: The TSPAN4 - TMPRSS2 rearrangement is a translocation that results in the fusion of TSPAN4 exons 1-7 with TMPRSS2 exons 3-14. One of the breakpoints is within TSPAN4 exon 7. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2562:TMPRSS2_c.18+12161:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2562:TMPRSS2_c.18+12161:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10.
MX1	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-MX1 fusion	yes	unknown		in frame	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement: c.1432+622:MX1_c.56-2534:TMPRSS2inv Note: The MX1 - TMPRSS2 rearrangement is an inversion that results in the in-frame fusion of MX1 exons 1-9 with TMPRSS2 exons 2-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-MX1 fusion	yes	unknown		in frame	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement: c.1432+622:MX1_c.56-2534:TMPRSS2inv Note: The MX1 - TMPRSS2 rearrangement is an inversion that results in the in-frame fusion of MX1 exons 1-9 with TMPRSS2 exons 2-14. The functional significance is undetermined.
POLDIP3	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-POLDIP3 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - POLDIP3 (NM_032311) rearrangement: t(21;22)(q22.3;q13.2)(chr21:g.:42867864::chr22:g.43009989) Note: The TMPRSS2 - POLDIP3 rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-2 with POLDIP3 exons 2-9. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030872-T01-IM6	TMPRSS2-POLDIP3 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - POLDIP3 (NM_032311) rearrangement: t(21;22)(q22.3;q13.2)(chr21:g.:42867864::chr22:g.43009989) Note: The TMPRSS2 - POLDIP3 rearrangement is a translocation that results in the fusion of TMPRSS2 exons 1-2 with POLDIP3 exons 2-9. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0004887-T01-IM5	ZNF385B-NFE2L2 fusion	yes	unknown		unknown	The NFE2L2 (NM_006164) - ZNF385B (NM_152520) rearrangement: c.123:NFE2L2_c.253+111221:ZNF385Bdup The NFE2L2 (NM_006164) - ZNF385B (NM_152520) rearrangement is a duplication which results in the fusion of exons 1-2 of NFE2L2 with exons 4-10 of ZNF385B. One of the breakpoints is within exon2 of NFE2L2. The functional significance is undetermined.
ZNF385B	0	MSKCC-DMP	P-0004887-T01-IM5	ZNF385B-NFE2L2 fusion	yes	unknown		unknown	The NFE2L2 (NM_006164) - ZNF385B (NM_152520) rearrangement: c.123:NFE2L2_c.253+111221:ZNF385Bdup The NFE2L2 (NM_006164) - ZNF385B (NM_152520) rearrangement is a duplication which results in the fusion of exons 1-2 of NFE2L2 with exons 4-10 of ZNF385B. One of the breakpoints is within exon2 of NFE2L2. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0007699-T02-IM5	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: chr14:g.38304410_c.341:FOXA1del The FOXA1 (NM_004496) rearrangement is a deletion of FOXA1 exons 1-2. One of the breakpoints is within exon 2 of FOXA1. The functional significance is undetermined.
GREM1	0	MSKCC-DMP	P-0012051-T01-IM5	SECISBP2L-GREM1 fusion	yes	unknown		unknown	GREM1 (NM_013372) rearrangement : c.*3295_chr15:g.49277656inv Note: The GREM1 rearrangement event results in the inversion of the 3 UTR of GREM1. The functional significance of this event is uncertain.
SECISBP2L	0	MSKCC-DMP	P-0012051-T01-IM5	SECISBP2L-GREM1 fusion	yes	unknown		unknown	GREM1 (NM_013372) rearrangement : c.*3295_chr15:g.49277656inv Note: The GREM1 rearrangement event results in the inversion of the 3 UTR of GREM1. The functional significance of this event is uncertain.
NF1	0	MSKCC-DMP	P-0030660-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) Rearrangement: c.4835+15100_c.5610-70del Note: The NF1 rearrangement is an intragenic deletion of exons 37 to 38. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0030876-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) Rearrangement: c.1283_c.1947-13inv Note: The ERBB2 rearrangement is an inversion of exons 11 to 16. One of the breakpoints is within exon 11. Its functional significance is undetermined.
HOXB13	0	MSKCC-DMP	P-0030897-T01-IM6	HOXB13-intragenic	yes	unknown		unknown	HOXB13 (NM_006361) Rearrangement : c.114_c.602-398dup Note: The HOXB13 Rearrangement results in the intragenic duplication of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0030935-T01-IM6	COL14A1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(8;19)(q24.12;p13.2)(chr8:g.121126818::chr19:g.11097142) Note: The SMARCA4 rearrangement is a translocation involving a breakpoint within exon 4. Its functional significance is undetermined
COL14A1	0	MSKCC-DMP	P-0030935-T01-IM6	COL14A1-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: t(8;19)(q24.12;p13.2)(chr8:g.121126818::chr19:g.11097142) Note: The SMARCA4 rearrangement is a translocation involving a breakpoint within exon 4. Its functional significance is undetermined
STAT3	0	MSKCC-DMP	P-0000122-T02-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.1056_c.2102-1006dup Note: The STAT3 rearrangement is an intragenic duplication of exons 11-21. One of the breakpoints is within exon 11. Its functional significance is undetermined.
C8orf37-AS1	0	MSKCC-DMP	P-0030787-T01-IM6	RAD21-C8orf37-AS1 fusion	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement: c.1470+83:RAD21_chr8:g.96518250del Note: The RAD21 rearrangement is a deletion of exons 12 to 14. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0030787-T01-IM6	RAD21-C8orf37-AS1 fusion	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement: c.1470+83:RAD21_chr8:g.96518250del Note: The RAD21 rearrangement is a deletion of exons 12 to 14. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0031044-T01-IM6	LOC101929095-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) Rearrangement: c.1266+139:FGFR3_chr4:g.15330489del Note: The FGFR3 rearrangement is a deletion of exons 10-18. Its functional significance is undetermined,
LOC101929095	0	MSKCC-DMP	P-0031044-T01-IM6	LOC101929095-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) Rearrangement: c.1266+139:FGFR3_chr4:g.15330489del Note: The FGFR3 rearrangement is a deletion of exons 10-18. Its functional significance is undetermined,
DLGAP1-AS5	0	MSKCC-DMP	P-0031056-T01-IM6	TCEB1-DLGAP1-AS5 fusion	yes	unknown		unknown	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373) Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
TCEB1	0	MSKCC-DMP	P-0031056-T01-IM6	TCEB1-DLGAP1-AS5 fusion	yes	unknown		unknown	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373) Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0030958-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) Rearrangement: c.4780-76_c.6691del Note: The EP300 rearrangement is an intragenic deletion of EP300 exons 30 to 31. One of the breakpoints is within exon 31. The functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0030962-T01-IM6	FBXL7-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement:  t(5;16)(p15.1;p13.3)(chr5:g.15641044::chr16:g.3929765) Note: The CREBBP rearrangement is a translocation which results in the possible truncation of exons 2-31. Its functional significance is undetermined.
FBXL7	0	MSKCC-DMP	P-0030962-T01-IM6	FBXL7-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement:  t(5;16)(p15.1;p13.3)(chr5:g.15641044::chr16:g.3929765) Note: The CREBBP rearrangement is a translocation which results in the possible truncation of exons 2-31. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0030980-T01-IM6	LOC339975-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3990:FAT1_chr4:g.187948271del Note: The FAT1 rearrangement is a deletion of exons 1-6. One of the breakpoints is within exon 6.
LOC339975	0	MSKCC-DMP	P-0030980-T01-IM6	LOC339975-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3990:FAT1_chr4:g.187948271del Note: The FAT1 rearrangement is a deletion of exons 1-6. One of the breakpoints is within exon 6.
PLK2	0	MSKCC-DMP	P-0031082-T01-IM6	LOC101929154-PLK2 fusion	yes	unknown		unknown	PLK2 (NM_006622) Rearrangement : c.969:PLK2_chr5:g.77184889del Note: The PLK2 Rearrangement results in the deletion of exons 1-7 of PLK2. The breakpoint in PLK2 is within exon7. Its functional significance is undetermined.
LOC101929154	0	MSKCC-DMP	P-0031082-T01-IM6	LOC101929154-PLK2 fusion	yes	unknown		unknown	PLK2 (NM_006622) Rearrangement : c.969:PLK2_chr5:g.77184889del Note: The PLK2 Rearrangement results in the deletion of exons 1-7 of PLK2. The breakpoint in PLK2 is within exon7. Its functional significance is undetermined.
MIR99AHG	0	MSKCC-DMP	P-0031188-T01-IM6	CTCF-MIR99AHG fusion	yes	unknown		unknown	CTCF (NM_006565) rearrangement: t(16;21)(q22.1;q21.1)(chr16:g.:67671612::chr21:g.17465819) Note: The CTCF rearrangement is a translocation with with a breakpoint within exon 12. The functional significance is undetermined.
CTCF	0	MSKCC-DMP	P-0031188-T01-IM6	CTCF-MIR99AHG fusion	yes	unknown		unknown	CTCF (NM_006565) rearrangement: t(16;21)(q22.1;q21.1)(chr16:g.:67671612::chr21:g.17465819) Note: The CTCF rearrangement is a translocation with with a breakpoint within exon 12. The functional significance is undetermined.
NAPA	0	MSKCC-DMP	P-0031189-T01-IM6	TSC2-NAPA fusion	yes	unknown		unknown	TSC2 (NM_00054) rearrangement: t(16;19)(p13.3;q13.32)(chr16:g.2122449::chr19:g.47992744) Note: The TSC2 rearrangement is a translocation with a breakpoint within intron 20.
TSC2	0	MSKCC-DMP	P-0031189-T01-IM6	TSC2-NAPA fusion	yes	unknown		unknown	TSC2 (NM_00054) rearrangement: t(16;19)(p13.3;q13.32)(chr16:g.2122449::chr19:g.47992744) Note: The TSC2 rearrangement is a translocation with a breakpoint within intron 20.
TSHZ3	0	MSKCC-DMP	P-0031189-T01-IM6	AXL-TSHZ3 fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: chr19:g.31603461_c.662inv Note: The AXL rearrangement is an inversion that includes AXL exons 1-5. The functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0031189-T01-IM6	AXL-TSHZ3 fusion	yes	unknown		unknown	AXL (NM_021913) rearrangement: chr19:g.31603461_c.662inv Note: The AXL rearrangement is an inversion that includes AXL exons 1-5. The functional significance is undetermined.
UNC5B	0	MSKCC-DMP	P-0031202-T01-IM6	ARID1B-UNC5B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;q22.1)(chr6:g.157505664::chr10:g.73062411) Note: The ARID1B rearrangement is a translocation with a breakpoint within intron 13.
ARID1B	0	MSKCC-DMP	P-0031202-T01-IM6	ARID1B-UNC5B fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;q22.1)(chr6:g.157505664::chr10:g.73062411) Note: The ARID1B rearrangement is a translocation with a breakpoint within intron 13.
CBFB	0	MSKCC-DMP	P-0031208-T01-IM6	HCCAT5-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.165+56_chr16:g.73099214inv Note: The CBFB rearrangement is an inversion that includes exons 3-6.
HCCAT5	0	MSKCC-DMP	P-0031208-T01-IM6	HCCAT5-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.165+56_chr16:g.73099214inv Note: The CBFB rearrangement is an inversion that includes exons 3-6.
ALK	0	MSKCC-DMP	P-0015961-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.668-6666:EML4_c.3173-132:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0015961-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20-29): c.668-6666:EML4_c.3173-132:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
ZFHX3	0	MSKCC-DMP	P-0030981-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.9641_c.10810del Note: The ZFHX3 rearrangement is an intragenic deletion with both breakpoints in exon 10. The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0030981-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.1088_c.1947+246del Note: The EZH2 rearrangement is an intragenic deletion of exons 10-16. One of the breakpoints is within exon 10. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0031131-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) Rearrangement: c.4239_c.9112dup Note: The KMT2D rearrangement is an intragenic duplication of exons 15 to 34. The breakpoints are within exons 15 and 34. Its functional significance is undetermined.
ERCC4	0	MSKCC-DMP	P-0031135-T01-IM6	C16orf52-ERCC4 fusion	yes	unknown		out of frame	C16orf52 (NM_001164579) - ERCC4 (NM_005236) Rearrangement: c.107-5101:C16orf52_c.793-2:ERCC4dup Note: The C16orf52  - ERCC4 rearrangement is a duplication of C16orf52 exon 1 to ERCC4 eonxs 5 to 11. Its functional significance is undetermined.
C16orf52	0	MSKCC-DMP	P-0031135-T01-IM6	C16orf52-ERCC4 fusion	yes	unknown		out of frame	C16orf52 (NM_001164579) - ERCC4 (NM_005236) Rearrangement: c.107-5101:C16orf52_c.793-2:ERCC4dup Note: The C16orf52  - ERCC4 rearrangement is a duplication of C16orf52 exon 1 to ERCC4 eonxs 5 to 11. Its functional significance is undetermined.
COPS7A	0	MSKCC-DMP	P-0031153-T01-IM6	ETV6-COPS7A fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: c.1208:ETV6_chr12:g.6833024inv Note: The ETV6 rearrangement is an inversion of ETV6 exons 1 to 7.  One of the breakpoints is within ETV6 exon 7. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0031153-T01-IM6	ETV6-COPS7A fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: c.1208:ETV6_chr12:g.6833024inv Note: The ETV6 rearrangement is an inversion of ETV6 exons 1 to 7.  One of the breakpoints is within ETV6 exon 7. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0031155-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused with TACC3 exons 8-16. This includes the kinase domain of FGFR3.): c.2274+54:FGFR3_c.1644+125:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.
FGFR3	0	MSKCC-DMP	P-0031155-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused with TACC3 exons 8-16. This includes the kinase domain of FGFR3.): c.2274+54:FGFR3_c.1644+125:TACC3dup Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.
NF2	0	MSKCC-DMP	P-0018493-T01-IM6	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.1000-75:NF2_chr22:g.29992870del Note: The NF2 rearrangement is a deletion of exons 1-11.
EP300	0	MSKCC-DMP	P-0030545-T02-IM6	MAP2K2-EP300 fusion	yes	unknown		unknown	MAP2K2 (NM_030662) rearrangement: t(19;22)(p13.3;q13.2)(chr19:g.4095405::chr22:g.41578462) Note: The MAP2K2 rearrangement is a translocation with breakpoint is exon 9. The functional significance is undetermined.
MAP2K2	0	MSKCC-DMP	P-0030545-T02-IM6	MAP2K2-EP300 fusion	yes	unknown		unknown	MAP2K2 (NM_030662) rearrangement: t(19;22)(p13.3;q13.2)(chr19:g.4095405::chr22:g.41578462) Note: The MAP2K2 rearrangement is a translocation with breakpoint is exon 9. The functional significance is undetermined.
LETM1	0	MSKCC-DMP	P-0030545-T02-IM6	WHSC1-LETM1 fusion	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.3032:WHSC1_chr4:g.1824058del Note: The WHSC1 rearrangement is a deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0030545-T02-IM6	WHSC1-LETM1 fusion	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.3032:WHSC1_chr4:g.1824058del Note: The WHSC1 rearrangement is a deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
VEGFA	0	MSKCC-DMP	P-0030964-T01-IM6	VEGFA-intragenic	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement: c.-325_c.91del Note: The VEGFA rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0030969-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.2183_c.2282-3671del Note: The ARID1B rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0030976-T01-IM6	BMS1P20-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: t(22;X)(q11.22;p11.3)(chr22:g.22661479::chrX:g.44919395) Note: The KDM6A rearrangement is a translocation with a breakpoint in exon 13. The functional significance is undetermined.
BMS1P20	0	MSKCC-DMP	P-0030976-T01-IM6	BMS1P20-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: t(22;X)(q11.22;p11.3)(chr22:g.22661479::chrX:g.44919395) Note: The KDM6A rearrangement is a translocation with a breakpoint in exon 13. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0031265-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement: c.-48-6776_c.382del Note: The CTNNB1 Rearrangement results in the deletion of exons 1-4 of CTNNB1. One of the breakpoints is within exon 4. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0031241-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.-34_c.290+793del Note: The STK11 rearrangement is a deletion of exon 1.
CSMD3	0	MSKCC-DMP	P-0000120-T02-IM6	MDM4-CSMD3 fusion	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: t(1;8)(q32.1;q23.3)(chr1:g.204507560::chr8:g.114388613) Note: The MDM4 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
MDM4	0	MSKCC-DMP	P-0000120-T02-IM6	MDM4-CSMD3 fusion	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: t(1;8)(q32.1;q23.3)(chr1:g.204507560::chr8:g.114388613) Note: The MDM4 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
FKBP9P1	0	MSKCC-DMP	P-0003061-T02-IM6	SHQ1-FKBP9P1 fusion	yes	unknown		unknown	SHQ1 (NM_018130) rearrangement: t(3;7)(p13;p11.2)(chr3:g.72893631::chr7:g.55694452) Note: The SHQ1 rearrangement is a translocation involving exon 2. Its functional significance is undetermined.
SHQ1	0	MSKCC-DMP	P-0003061-T02-IM6	SHQ1-FKBP9P1 fusion	yes	unknown		unknown	SHQ1 (NM_018130) rearrangement: t(3;7)(p13;p11.2)(chr3:g.72893631::chr7:g.55694452) Note: The SHQ1 rearrangement is a translocation involving exon 2. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0003678-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	(NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.127-714:TMPRSS2_c.40-61240:ERGdel Note: The fusion involves the non-canonical transcript of ERG.
TMPRSS2	0	MSKCC-DMP	P-0003678-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	(NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.127-714:TMPRSS2_c.40-61240:ERGdel Note: The fusion involves the non-canonical transcript of ERG.
RET	0	MSKCC-DMP	P-0007322-T02-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.454-1512:CCDC6_c.2136+84:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and involves CCDC6 exons 1-2 and RET exons 12-20, which include RET kinase domain.
CCDC6	0	MSKCC-DMP	P-0007322-T02-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.454-1512:CCDC6_c.2136+84:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and involves CCDC6 exons 1-2 and RET exons 12-20, which include RET kinase domain.
SLC30A6	0	MSKCC-DMP	P-0027418-T01-IM6	MSH6-SLC30A6 fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: c.2542:MSH6_chr2:g.32398951inv Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0027418-T01-IM6	MSH6-SLC30A6 fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: c.2542:MSH6_chr2:g.32398951inv Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
C12orf56	0	MSKCC-DMP	P-0028007-T01-IM6	KDR-C12orf56 fusion	yes	unknown		unknown	C12orf56 (NM_001170633) - KDR (NM_002253) rearrangement: t(4;12)(q12;q14.2)(chr4:g.55984933::chr12:g.64672804) Note: The C12orf56 - KRD rearrangement is a translocation that results in the fusion of C12orf56 exons 1-8 with KRD exons 3-30. One of the breakpoints is within KDR exon 3. The functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0028007-T01-IM6	KDR-C12orf56 fusion	yes	unknown		unknown	C12orf56 (NM_001170633) - KDR (NM_002253) rearrangement: t(4;12)(q12;q14.2)(chr4:g.55984933::chr12:g.64672804) Note: The C12orf56 - KRD rearrangement is a translocation that results in the fusion of C12orf56 exons 1-8 with KRD exons 3-30. One of the breakpoints is within KDR exon 3. The functional significance is undetermined.
SLC12A4	0	MSKCC-DMP	P-0028017-T01-IM6	RAD54L-SLC12A4 fusion	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.46714267::chr16:g.67982423) Note: The RAD54L rearrangement is a translocation with a breakpoint within RD54L exon 3. The functional significance is undetermined.
RAD54L	0	MSKCC-DMP	P-0028017-T01-IM6	RAD54L-SLC12A4 fusion	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.46714267::chr16:g.67982423) Note: The RAD54L rearrangement is a translocation with a breakpoint within RD54L exon 3. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0031030-T02-IM6	PTEN-intragenic	yes	unknown		in frame	PTEN (NM_000314) Rearrangement: c.493-154_c.1027-1433dup Note: The PTEN rearrangement is an intragenic duplication of exons 6 to 8. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement: c.127-1111:TMPRSS2_c.-149-7749:ERGdel Note: The TMPRSS2 -ERG Rearrangement involves exons 1-2 of TMPRSS2 and exons 1-10 of ERG. While the rearrangement is not the canonical TMPRSS2-ERG fusion, the possibility of the canonical fusion cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0031270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement: c.127-1111:TMPRSS2_c.-149-7749:ERGdel Note: The TMPRSS2 -ERG Rearrangement involves exons 1-2 of TMPRSS2 and exons 1-10 of ERG. While the rearrangement is not the canonical TMPRSS2-ERG fusion, the possibility of the canonical fusion cannot be ruled out.
CDH1	0	MSKCC-DMP	P-0031274-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.48+112_c.164-22319inv Note: The CDH1 rearrangement is an intragenic inversion of exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0031406-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 with ALK exons 20-29): c.668-2889:EML4_c.3173-31:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0031406-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 with ALK exons 20-29): c.668-2889:EML4_c.3173-31:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
TP53	0	MSKCC-DMP	P-0031409-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : c.-28-1861_c.811dup Note: The TP53 Rearrangement results in the duplication of exons 1-8 of TP53. The breakpoints are within the 5'UTR region and exon 8 respectively. Its functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0031410-T01-IM6	PPIP5K1-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) Rearrangement : c.7+117:TP53BP1_c.3770:PPIP5K1dup Note: The TP53BP1 - PPIP5K1  Rearrangement results in the fusion of exon1 of TP53BP1 with exon30 of PPIP5K1. The breakpoint in PPIP5K1 is within exon30. Its functional significance is undetermined.
PPIP5K1	0	MSKCC-DMP	P-0031410-T01-IM6	PPIP5K1-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) Rearrangement : c.7+117:TP53BP1_c.3770:PPIP5K1dup Note: The TP53BP1 - PPIP5K1  Rearrangement results in the fusion of exon1 of TP53BP1 with exon30 of PPIP5K1. The breakpoint in PPIP5K1 is within exon30. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031412-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.55+3832:TMPRSS2_c.19-22354:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0031412-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.55+3832:TMPRSS2_c.19-22354:ERGdel
CEP295	0	MSKCC-DMP	P-0031413-T01-IM6	ATM-CEP295 fusion	yes	unknown		out of frame	KIAA1731(NM_033395) -ATM (NM_000051) Rearrangement : c.5750-2662:KIAA1731_ c.5178-173:ATMdel Note: The KIAA1731 -ATM  Rearrangement results in the fusion of exon18 of  KIAA1731  with ATM exon35. Its functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0031413-T01-IM6	ATM-CEP295 fusion	yes	unknown		out of frame	KIAA1731(NM_033395) -ATM (NM_000051) Rearrangement : c.5750-2662:KIAA1731_ c.5178-173:ATMdel Note: The KIAA1731 -ATM  Rearrangement results in the fusion of exon18 of  KIAA1731  with ATM exon35. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0031419-T01-IM6	ZNF733P-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement : t(7,12)(q11.21;p13.2) (chr7:g.62515009::chr7:g.12028600) Note: The ETV6 rearrangement results is a translocation event that results with a breakpoint in intron 5. Its functional significance is undetermined.
ZNF733P	0	MSKCC-DMP	P-0031419-T01-IM6	ZNF733P-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement : t(7,12)(q11.21;p13.2) (chr7:g.62515009::chr7:g.12028600) Note: The ETV6 rearrangement results is a translocation event that results with a breakpoint in intron 5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031429-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2-10) :c.56-2568:TMPRSS2_c.40-46240:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0031429-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2-10) :c.56-2568:TMPRSS2_c.40-46240:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
NOTCH3	0	MSKCC-DMP	P-0031430-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement: c.*2656_c.3587inv Note: The NOTCH3 rearrangement is an intragenic inversion spanning NOTCH3 promoter region to exon 22. One of the breakpoints is within exon 22. The functional significance is undetermined.
LINC01264	0	MSKCC-DMP	P-0031431-T01-IM6	DROSHA-LINC01264 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;10)(p13.3;q11.21)(chr5:g.31526450::chr10:g.43479900) Note: The DROSHA rearrangement results in the translocation with breakpoint in exon 4 of DROSHA. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0031431-T01-IM6	DROSHA-LINC01264 fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;10)(p13.3;q11.21)(chr5:g.31526450::chr10:g.43479900) Note: The DROSHA rearrangement results in the translocation with breakpoint in exon 4 of DROSHA. The functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0031431-T01-IM6	NTRK2-intragenic	yes	unknown		in frame	NTRK2 (NM_006180) Rearrangement: c.1444+1516_c.1633+3654del Note: The NTRK2 rearrangement is an intragenic  duplication of exon 16. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0031438-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) Rearrangement: c.471_c.534+6308del Note: The PARK2 rearrangement is an intragenic deletion of PARK2 exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.
CDKN2A-AS1	0	MSKCC-DMP	P-0031438-T01-IM6	CDKN2A-CDKN2A-AS1 fusion	yes	unknown		unknown	CDKN2A (NM_000077) Rearrangement: c.458-35:CDKN2A_chr9:g.21964007del Note: The  CDKN2A rearrangement results in the deletion of  CDKN2A exon 3. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0031438-T01-IM6	CDKN2A-CDKN2A-AS1 fusion	yes	unknown		unknown	CDKN2A (NM_000077) Rearrangement: c.458-35:CDKN2A_chr9:g.21964007del Note: The  CDKN2A rearrangement results in the deletion of  CDKN2A exon 3. The functional significance is undetermined.
MAPK1	0	MSKCC-DMP	P-0031472-T01-IM6	ZNF280B-MAPK1 fusion	yes	unknown		unknown	MAPK1 (NM_002745) rearrangement: c.967-77:MAPK1_chr22:g.22766451del Note: The MAPK1 rearrangement s a deletion of exons 1-7. The functional significance is undetermined.
ZNF280B	0	MSKCC-DMP	P-0031472-T01-IM6	ZNF280B-MAPK1 fusion	yes	unknown		unknown	MAPK1 (NM_002745) rearrangement: c.967-77:MAPK1_chr22:g.22766451del Note: The MAPK1 rearrangement s a deletion of exons 1-7. The functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0031478-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.7559_c.8632del Note: The KMT2A rearrangement in an intragenic deletion with both breakpoints in exon 27.
KDM5C	0	MSKCC-DMP	P-0031478-T01-IM6	LOC101928254-KDM5C fusion	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: t(X:7)(p11.22;q31.33)(chrX:g.53223929::chr7:g.125243090) Note: The KDM5C rearrangement is a translocation with breakpoint in intron 22. The functional significance is undetermined.
LOC101928254	0	MSKCC-DMP	P-0031478-T01-IM6	LOC101928254-KDM5C fusion	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: t(X:7)(p11.22;q31.33)(chrX:g.53223929::chr7:g.125243090) Note: The KDM5C rearrangement is a translocation with breakpoint in intron 22. The functional significance is undetermined.
EFHD2	0	MSKCC-DMP	P-0031490-T01-IM6	SPEN-EFHD2 fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement: c.5732:SPEN_chr1:g.15748399inv Note: The SPEN rearrangement results in the inversion of SPEN exons 1-11. One of the breakpoints is within exon 11 of SPEN. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0031490-T01-IM6	SPEN-EFHD2 fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement: c.5732:SPEN_chr1:g.15748399inv Note: The SPEN rearrangement results in the inversion of SPEN exons 1-11. One of the breakpoints is within exon 11 of SPEN. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031536-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1017:TMPRSS2_c.18+13014:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0031536-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1017:TMPRSS2_c.18+13014:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
MARK4	0	MSKCC-DMP	P-0030907-T01-IM6	PIK3CD-MARK4 fusion	yes	unknown		in frame	MARK4 (NM_001199867) - PIK3CD (NM_005026) rearrangement: t(1;19)(p36.22;q13.32)(chr1:g.9781425::chr19:g.45804589) Note: The MARK4 - PIK3CD rearrangement is a translocation which may result in the fusion of MARK4 exons 1-16 with PIK3CD exons 15-24. This includes the kinase domain of PIK3CD. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0030907-T01-IM6	PIK3CD-MARK4 fusion	yes	unknown		in frame	MARK4 (NM_001199867) - PIK3CD (NM_005026) rearrangement: t(1;19)(p36.22;q13.32)(chr1:g.9781425::chr19:g.45804589) Note: The MARK4 - PIK3CD rearrangement is a translocation which may result in the fusion of MARK4 exons 1-16 with PIK3CD exons 15-24. This includes the kinase domain of PIK3CD. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0030907-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.58:BAP1_chr3:g.52445834del Note: The BAP1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0030967-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.142-21913_c.600dup Note: The PREX2 rearrangement results in the duplication of exons 2-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0031038-T01-IM6	BCL2L14-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: c.1010-4569:ETV6_chr12:g.12219924del Note: The ETV6 rearrangement is a deletion of ETV6 exons 6 to 8. The functional significance is undetermined.
BCL2L14	0	MSKCC-DMP	P-0031038-T01-IM6	BCL2L14-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement: c.1010-4569:ETV6_chr12:g.12219924del Note: The ETV6 rearrangement is a deletion of ETV6 exons 6 to 8. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0031461-T01-IM6	DNMT1-intragenic	yes	unknown		in frame	DNMT1 (NM_001379) rearrangement: c.1232+773_c.2673-52del Note: The DNMT1 rearrangement is an intrangenic deletion of exons 17-26. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0031583-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.67_c.68del Note: The B2M rearrangement is an intragenic deletion of exons 1-2. Both breakpoints are within exon.
WT1	0	MSKCC-DMP	P-0026326-T02-IM6	WT1-intragenic	yes	unknown		unknown	WT1 (NM_024426) rearrangement: c.769+6:WT1_chr11:g.32372352del Note: The WT1 rearrangement is a deletion of exons 2-10. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0030990-T03-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12-20): c.303+10940:CCDC6_c.2137-151:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0030990-T03-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12-20): c.303+10940:CCDC6_c.2137-151:RETinv Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.
NUP93	0	MSKCC-DMP	P-0030990-T03-IM6	PRIM2-NUP93 fusion	yes	unknown		unknown	NUP93 (NM_014669) Rearrangement : t(6;16)(p11.1;q13)(chr6:g.57189490::chr16:g.56864649) Note: The NUP93 rearrangement results in the possible truncation of NOTCH2. One of the breakpoints is within intron 10. Its functional significance is undetermined.
PRIM2	0	MSKCC-DMP	P-0030990-T03-IM6	PRIM2-NUP93 fusion	yes	unknown		unknown	NUP93 (NM_014669) Rearrangement : t(6;16)(p11.1;q13)(chr6:g.57189490::chr16:g.56864649) Note: The NUP93 rearrangement results in the possible truncation of NOTCH2. One of the breakpoints is within intron 10. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0031489-T01-IM6	PGPEP1-INSR fusion	yes	unknown		unknown	INSR (NM_000208) Rearrangement: c.2286:INSR_chr19:g.18449247inv Note: The INSR rearrangement results in the inversion of INSR exons 1-12. One of the breakpoints is within INSR exon 12. The functional significance is undetermined.
PGPEP1	0	MSKCC-DMP	P-0031489-T01-IM6	PGPEP1-INSR fusion	yes	unknown		unknown	INSR (NM_000208) Rearrangement: c.2286:INSR_chr19:g.18449247inv Note: The INSR rearrangement results in the inversion of INSR exons 1-12. One of the breakpoints is within INSR exon 12. The functional significance is undetermined.
NBEAL2	0	MSKCC-DMP	P-0031640-T01-IM6	SETD2-NBEAL2 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement: c.1703:SETD2_chr3:g.47048057del Note: The SETD2 rearrangement results in the deletion of SETD2 exons 3-21. One of the breakpoints is within exon 3 of SETD2. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0031640-T01-IM6	SETD2-NBEAL2 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement: c.1703:SETD2_chr3:g.47048057del Note: The SETD2 rearrangement results in the deletion of SETD2 exons 3-21. One of the breakpoints is within exon 3 of SETD2. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0031648-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) Rearrangement: c.3388_c.3974+6479del Note: The NF1 rearrangement is an intragenic deletion of NF1 exons 26-29. One of the breakpoints is within exon 26. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0031657-T01-IM6	HSD17B4-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.5226:APC_chr5:g.118822534del Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoints is within exon 16.
HSD17B4	0	MSKCC-DMP	P-0031657-T01-IM6	HSD17B4-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.5226:APC_chr5:g.118822534del Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoints is within exon 16.
ATM	0	MSKCC-DMP	P-0031512-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.577_c.3077+423del Note: The ATM rearrangement is an intragenic deletion of exons 6-20. Its functional significance is undetermined.
HPYR1	0	MSKCC-DMP	P-0031512-T01-IM6	VEGFA-HPYR1 fusion	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement: t(6;8)(p21.1;q24.22)(chr6:g.43738643;chr8:g.133498635) Note: The VEGFA rearrangement is a translocation which involves exon 1. Its functional significance is undetermined.
VEGFA	0	MSKCC-DMP	P-0031512-T01-IM6	VEGFA-HPYR1 fusion	yes	unknown		unknown	VEGFA (NM_001171623) rearrangement: t(6;8)(p21.1;q24.22)(chr6:g.43738643;chr8:g.133498635) Note: The VEGFA rearrangement is a translocation which involves exon 1. Its functional significance is undetermined.
SPIN1	0	MSKCC-DMP	P-0031512-T01-IM6	ASXL2-SPIN1 fusion	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: t(2;9)(p22.3;q22.1)(chr2:g.25967196::chr9:g.90960962) Note: The ASXL2 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0031512-T01-IM6	ASXL2-SPIN1 fusion	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: t(2;9)(p22.3;q22.1)(chr2:g.25967196::chr9:g.90960962) Note: The ASXL2 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031719-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG(NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon1 )  : c.56-1239.3:TMPRSS2_c.-901:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0031719-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG(NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon1 )  : c.56-1239.3:TMPRSS2_c.-901:ERGdel
TERT	0	MSKCC-DMP	P-0031722-T01-IM6	TGFBR3-TERT fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :t(1;5)(p21.3;p15.32)(chr1:g.92107307::chr5:g.1295310) Note: The TERT Rearrangement is a translocation event with the breakpoint in the promoter region of TERT. Its functional significance is undetermined.
TGFBR3	0	MSKCC-DMP	P-0031722-T01-IM6	TGFBR3-TERT fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :t(1;5)(p21.3;p15.32)(chr1:g.92107307::chr5:g.1295310) Note: The TERT Rearrangement is a translocation event with the breakpoint in the promoter region of TERT. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0031725-T01-IM6	HCN1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement : t(5;12)(p12;p13.2)(chr5:g.46092989::chr12:g.12028148) Note: The ETV6 Rearrangement is a translocation event with the breakpoint in intron 5. Its functional significance is undetermined.
HCN1	0	MSKCC-DMP	P-0031725-T01-IM6	HCN1-ETV6 fusion	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement : t(5;12)(p12;p13.2)(chr5:g.46092989::chr12:g.12028148) Note: The ETV6 Rearrangement is a translocation event with the breakpoint in intron 5. Its functional significance is undetermined.
SEC16A	0	MSKCC-DMP	P-0031726-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement: c.6448-85:SEC16A_c.5269:NOTCH1dup Note: The SEC16A - NOTCH1 Rearrangement results in the fusion of exons 1-26 of SEC16A with exons 28-34 of NOTCH1. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0031726-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement: c.6448-85:SEC16A_c.5269:NOTCH1dup Note: The SEC16A - NOTCH1 Rearrangement results in the fusion of exons 1-26 of SEC16A with exons 28-34 of NOTCH1. Its functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0031514-T01-IM6	BTBD11-ERBB3 fusion	yes	unknown		in frame	BTBD11 (NM_001018072) - ERBB3 (NM_001982) rearrangement: c.1136-66952:BTBD11_c.548-379:ERBB3dup Note: The BTBD11 - ERBB3 rearrangement results in the BTBD11 exons 1 fused with ERBB3 exons 5-28. This includes the kinase domain of ERBB3. Its functional significance is undetermined.
BTBD11	0	MSKCC-DMP	P-0031514-T01-IM6	BTBD11-ERBB3 fusion	yes	unknown		in frame	BTBD11 (NM_001018072) - ERBB3 (NM_001982) rearrangement: c.1136-66952:BTBD11_c.548-379:ERBB3dup Note: The BTBD11 - ERBB3 rearrangement results in the BTBD11 exons 1 fused with ERBB3 exons 5-28. This includes the kinase domain of ERBB3. Its functional significance is undetermined.
MACROD2	0	MSKCC-DMP	P-0031693-T01-IM6	LATS1-MACROD2 fusion	yes	unknown		unknown	LATS1 (NM_004690) rearrangement: t(6;20)(q25.1;p12.1)(chr6:g.150004589::chr20:g.14939921) Note: The LATS1 rearrangement is a translocation with a breakpoint within exon 4.
LATS1	0	MSKCC-DMP	P-0031693-T01-IM6	LATS1-MACROD2 fusion	yes	unknown		unknown	LATS1 (NM_004690) rearrangement: t(6;20)(q25.1;p12.1)(chr6:g.150004589::chr20:g.14939921) Note: The LATS1 rearrangement is a translocation with a breakpoint within exon 4.
TSC2	0	MSKCC-DMP	P-0031712-T01-IM6	RNPS1-TSC2 fusion	yes	unknown		in frame	TSC2 (NM_000548) - RNPS1 (NM_006711) Rearrangement : c.3610+22:TSC2_c.676+889:RNPS1inv Note: The TSC2 - RNPS1 Rearrangement results in the fusion of exons 1-30 of TSC2 with exons 7-8 of RNPS1. Its functional significance is undetermined.
RNPS1	0	MSKCC-DMP	P-0031712-T01-IM6	RNPS1-TSC2 fusion	yes	unknown		in frame	TSC2 (NM_000548) - RNPS1 (NM_006711) Rearrangement : c.3610+22:TSC2_c.676+889:RNPS1inv Note: The TSC2 - RNPS1 Rearrangement results in the fusion of exons 1-30 of TSC2 with exons 7-8 of RNPS1. Its functional significance is undetermined.
SRSF2	0	MSKCC-DMP	P-0031712-T01-IM6	SRSF2-intragenic	yes	unknown		unknown	SRSF2 (NM_003016) Rearrangement : c.-744_c.78:SRSF2del Note: The SRSF2 Rearrangement results in the deletion of ex
EP300	0	MSKCC-DMP	P-0031737-T01-IM6	TEF-EP300 fusion	yes	unknown		unknown	TEF (NM_003216) - EP300 (NM_001429) rearrangement: c.697-275:TEF_c.6650:EP300dup Note: The TEF - EP300 rearrangement is a duplication that results in the fusion of TEF exons 1-3 with EP300 exon 31. One of the breakpoints is within EP300 exon 31.
TEF	0	MSKCC-DMP	P-0031737-T01-IM6	TEF-EP300 fusion	yes	unknown		unknown	TEF (NM_003216) - EP300 (NM_001429) rearrangement: c.697-275:TEF_c.6650:EP300dup Note: The TEF - EP300 rearrangement is a duplication that results in the fusion of TEF exons 1-3 with EP300 exon 31. One of the breakpoints is within EP300 exon 31.
PTPRD	0	MSKCC-DMP	P-0031751-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.5185_c.5380-2407del Note: The PTPRD rearrangement is an intragenic deletion of exons 42-43. One of the breakpoints is within exon 42.
RB1	0	MSKCC-DMP	P-0031759-T01-IM6	CYSLTR2-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.968:RB1_chr13:g.49280131dup Note: The RB1 rearrangement is a duplication that includes RB1 exons 10-27. One of the breakpoints is within RB1 exon 10.
CYSLTR2	0	MSKCC-DMP	P-0031759-T01-IM6	CYSLTR2-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.968:RB1_chr13:g.49280131dup Note: The RB1 rearrangement is a duplication that includes RB1 exons 10-27. One of the breakpoints is within RB1 exon 10.
ZFHX3	0	MSKCC-DMP	P-0031759-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: chr16:g.72795012_c.6128del Note: The ZFHX3 rearrangement is a deletion that includes ZFHX3 exons 9-10. One of the breakpoints is within exon 9. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0031759-T01-IM6	FGFR3-intragenic	yes	unknown		in frame	FGFR3 (NM_000142) rearrangement: c.1413-15_c.2030+86del Note: The FGFR3 rearrangement is an intragenic deletion of exons 11-15.
CCND2	0	MSKCC-DMP	P-0031757-T01-IM6	KCNA5-CCND2 fusion	yes	unknown		unknown	CCND2 (NM_001759) rearrangement: c.411+131_chr12:g.5215914del Note: The CCND2 rearrangement is a deletion that includes CCND2 exons 3-5. The functional significance is undetermined.
KCNA5	0	MSKCC-DMP	P-0031757-T01-IM6	KCNA5-CCND2 fusion	yes	unknown		unknown	CCND2 (NM_001759) rearrangement: c.411+131_chr12:g.5215914del Note: The CCND2 rearrangement is a deletion that includes CCND2 exons 3-5. The functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0031844-T01-IM6	CNOT2-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) - CNOT2 (NM_014515) Rearrangement : c.358+70:MDM2_c.137:CNOT2del Note: The MDM2-CNOT2 Rearrangement results in the fusion of exons 1-5 of MDM2 with exons 4-16 of CNOT2. The breakpoint in CNOT2 is within exon2. Its functional significance is undetermined.
CNOT2	0	MSKCC-DMP	P-0031844-T01-IM6	CNOT2-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) - CNOT2 (NM_014515) Rearrangement : c.358+70:MDM2_c.137:CNOT2del Note: The MDM2-CNOT2 Rearrangement results in the fusion of exons 1-5 of MDM2 with exons 4-16 of CNOT2. The breakpoint in CNOT2 is within exon2. Its functional significance is undetermined.
MAST4	0	MSKCC-DMP	P-0031868-T01-IM6	CSDE1-MAST4 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: t(1;5)(p13.2;q12.3)(chr1:g.115282496::chr5:g.66058605) Note: The CSDE1 rearrangement is a translocation with a breakpoint in exon 4. The functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0031868-T01-IM6	CSDE1-MAST4 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: t(1;5)(p13.2;q12.3)(chr1:g.115282496::chr5:g.66058605) Note: The CSDE1 rearrangement is a translocation with a breakpoint in exon 4. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0031874-T01-IM6	TGIF1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(18;22)(p11.31;q12.2)(chr18:g.3359987::chr22:g.29687574) Note: The EWSR1 rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
TGIF1	0	MSKCC-DMP	P-0031874-T01-IM6	TGIF1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(18;22)(p11.31;q12.2)(chr18:g.3359987::chr22:g.29687574) Note: The EWSR1 rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0031881-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.-31-1224_c.4636-12del Note: The SMARCA4 rearrangement results in the deletion of exons 2-32. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0031891-T01-IM6	KCNB2-PTEN fusion	yes	unknown		out of frame	PTEN (NM_000314) - KCNB2 (NM_004770) rearrangement: t(8;10)(q13.3;q23.31)(chr8:g.73786031::chr10:g.89690932) Note: The PTEN - KCNB2 rearrangement is a translocation that results in the fusion of PTEN exons 1-4 with KCNB2 exon 3. The functional significance is undetermined.
KCNB2	0	MSKCC-DMP	P-0031891-T01-IM6	KCNB2-PTEN fusion	yes	unknown		out of frame	PTEN (NM_000314) - KCNB2 (NM_004770) rearrangement: t(8;10)(q13.3;q23.31)(chr8:g.73786031::chr10:g.89690932) Note: The PTEN - KCNB2 rearrangement is a translocation that results in the fusion of PTEN exons 1-4 with KCNB2 exon 3. The functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0031891-T01-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: c.530_c.531del Note: The GNAS rearrangement results in the deletion of exons 6-7. One of the breakpoints is within exon 6 and the other is within exon 7. The functional significance is undetermined.
RBM10	0	MSKCC-DMP	P-0031891-T01-IM6	RBM10-intragenic	yes	unknown		unknown	RBM10 (NM_001204468) rearrangement: c.171_c.213-9160del Note: The RBM10 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0025017-T01-IM6	LINC00376-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(13;21)(q21.31;q22.3)(chr13:g.63655835::chr21:g.42879521) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. The functional significance is undetermined.
LINC00376	0	MSKCC-DMP	P-0025017-T01-IM6	LINC00376-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(13;21)(q21.31;q22.3)(chr13:g.63655835::chr21:g.42879521) Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0031852-T01-IM6	PTOV1-AS1-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) Rearrangement: c.235:KMT2B_chr19:g.50354530inv Note: The KMT2B rearrangement is an inversion of KMT2B exons 1-37. One of the breakpoints is within exon 1 of KMT2B. The functional significance is undetermined.
PTOV1-AS1	0	MSKCC-DMP	P-0031852-T01-IM6	PTOV1-AS1-KMT2B fusion	yes	unknown		unknown	KMT2B (NM_014727) Rearrangement: c.235:KMT2B_chr19:g.50354530inv Note: The KMT2B rearrangement is an inversion of KMT2B exons 1-37. One of the breakpoints is within exon 1 of KMT2B. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0031860-T01-IM6	TACC1-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) Rearrangement: c.521:WHSC1L1_chr8:g.38708526del Note: The WHSC1L1 rearrangement results in the deletion of WHSC1L1 exons 1-2. One of the breakpoints is within exon 1 of WHSC1L1 while the other breakpoint is in 3-UTR of TACC1. The functional significance is undetermined. The functional significance is undetermined.
TACC1	0	MSKCC-DMP	P-0031860-T01-IM6	TACC1-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) Rearrangement: c.521:WHSC1L1_chr8:g.38708526del Note: The WHSC1L1 rearrangement results in the deletion of WHSC1L1 exons 1-2. One of the breakpoints is within exon 1 of WHSC1L1 while the other breakpoint is in 3-UTR of TACC1. The functional significance is undetermined. The functional significance is undetermined.
PSMA6	0	MSKCC-DMP	P-0031928-T01-IM6	NFKBIA-PSMA6 fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: chr14:g.35810679_c.474dup Note: The NFKBIA rearrangement is a duplication that includes exons 3-6. One of the breakpoints is within NFKBIA exon 3. The functional  significance is undetermined.
NFKBIA	0	MSKCC-DMP	P-0031928-T01-IM6	NFKBIA-PSMA6 fusion	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: chr14:g.35810679_c.474dup Note: The NFKBIA rearrangement is a duplication that includes exons 3-6. One of the breakpoints is within NFKBIA exon 3. The functional  significance is undetermined.
ALK	0	MSKCC-DMP	P-0031827-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-639:EML4_c.3173-252:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0031827-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-639:EML4_c.3173-252:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
TP53	0	MSKCC-DMP	P-0031933-T01-IM6	EPHX4-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(1;17)(p22.1;p13.1)(chr1:g.9252773::chr17:g.7576552) Note: The TP53 rearrangement is a translocation with a breakpoint after exon 9.
EPHX4	0	MSKCC-DMP	P-0031933-T01-IM6	EPHX4-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(1;17)(p22.1;p13.1)(chr1:g.9252773::chr17:g.7576552) Note: The TP53 rearrangement is a translocation with a breakpoint after exon 9.
FOXP1	0	MSKCC-DMP	P-0031939-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement:c.869+531_ c.1934del Note: The FOXP1 rearrangement is an intragenic deletion of exons 8-17. One of the breakpoints is within exon 17.
CDKN2A	0	MSKCC-DMP	P-0031864-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.151-200:CDKN2Ap16INK4A_chr9:g.22002380del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-200:CDKN2Ap14ARF_chr9:g.22002380del Note: The CDKN2A rearrangement results in the deletion of exon 1. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0031864-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.151-200:CDKN2Ap16INK4A_chr9:g.22002380del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-200:CDKN2Ap14ARF_chr9:g.22002380del Note: The CDKN2A rearrangement results in the deletion of exon 1. The functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0031952-T01-IM6	AXL-intragenic	yes	unknown		unknown	AXL (NM_021913) Rearrangemnet: c.*16_c.*3769inv Note: The AXL rearrangement is an intragenic inversion of exon 20. One of the breakpoints is within exon 20 of AXL. The functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0032014-T01-IM6	NTRK3-intragenic	yes	unknown		unknown	NTRK3 (NM_001012338) rearrangement: c.1396+73:NTRK3_chr15:g.88406573del Note: The NTRK3 rearrangement results in the deletion of exons 14-20. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032027-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon3 with ERG exon2) : c.303:TMPRSS2_c.19-1548:ERGdel Note: The TMPRSS2 -ERG fusion results in the fusion of TMPRSS2 exon3 with ERG exon2. The breakpoint in TMPRSS2 is within exon3.
TMPRSS2	0	MSKCC-DMP	P-0032027-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon3 with ERG exon2) : c.303:TMPRSS2_c.19-1548:ERGdel Note: The TMPRSS2 -ERG fusion results in the fusion of TMPRSS2 exon3 with ERG exon2. The breakpoint in TMPRSS2 is within exon3.
GALNTL5	0	MSKCC-DMP	P-0032027-T01-IM6	KMT2C-GALNTL5 fusion	yes	unknown		unknown	KMT2C (MLL3) (NM_170606) Rearrangement : c.12139+20:KMT2C_chr7:g.151681695del Note: The KMT2C (MLL3) Rearrangement results in the deletion of exons 48-59 of KMT2C. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0032027-T01-IM6	KMT2C-GALNTL5 fusion	yes	unknown		unknown	KMT2C (MLL3) (NM_170606) Rearrangement : c.12139+20:KMT2C_chr7:g.151681695del Note: The KMT2C (MLL3) Rearrangement results in the deletion of exons 48-59 of KMT2C. Its functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0032044-T01-IM6	RFWD2-intragenic	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: c.467_c.468del Note: The RFWD2 rearrangement results in the deletion of exons 2-3. One of the breakpoints is within exon 2 and the other is within exon 3. The functional significance is undetermined.
RBM10	0	MSKCC-DMP	P-0032044-T01-IM6	RBM10-intragenic	yes	unknown		unknown	RBM10 (NM_001204468) rearrangement: c.768_c.772-3del Note: The RBM10 rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032046-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4862:TMPRSS2_c.40-58959:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0032046-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4862:TMPRSS2_c.40-58959:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
BICC1	0	MSKCC-DMP	P-0032033-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exon 18 fused with BICC1 exon3) : c.2301+1527:FGFR2_c.237+38877:BICC1inv Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and doesn't include the protein kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0032033-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exon 18 fused with BICC1 exon3) : c.2301+1527:FGFR2_c.237+38877:BICC1inv Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and doesn't include the protein kinase domain of FGFR2.
BRCA2	0	MSKCC-DMP	P-0018565-T02-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.6178_c.6841+879del Note: The BRCA2 rearrangement is an intragenic deletion of a part of exon 11. One of the breakpoints is within exon 11.
TP53BP1	0	MSKCC-DMP	P-0031994-T01-IM6	TTC8-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: t(14;15)(q31.3;q15.3)(chr14:g.89311583::chr15:g.43739706) Note: The TP53BP1 rearrangement is a translocation with a breakpoint in TP53BP1 intron 12. The functional significance is undetermined.
TTC8	0	MSKCC-DMP	P-0031994-T01-IM6	TTC8-TP53BP1 fusion	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: t(14;15)(q31.3;q15.3)(chr14:g.89311583::chr15:g.43739706) Note: The TP53BP1 rearrangement is a translocation with a breakpoint in TP53BP1 intron 12. The functional significance is undetermined.
RAD51B	0	MSKCC-DMP	P-0031996-T01-IM6	RAD51B-intragenic	yes	unknown		unknown	RAD51B (NM_133509) rearrangement: c.199-1_c.315+848del Note: The RAD51B rearrangement is an intragenic inverstion of a part of exon 4. One of the breakpoint is within exon 4. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0031996-T01-IM6	ALG10B-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(12;22)(q11;q12.2)(chr12:g.37879543::chr22:g.29684857) Note: The EWSR1 rearrangement is a translocation with a breakpoint in intron 9. The functional significance is undetermined.
ALG10B	0	MSKCC-DMP	P-0031996-T01-IM6	ALG10B-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: t(12;22)(q11;q12.2)(chr12:g.37879543::chr22:g.29684857) Note: The EWSR1 rearrangement is a translocation with a breakpoint in intron 9. The functional significance is undetermined.
NCRNA00114	0	MSKCC-DMP	P-0008954-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_00113509) rearrangement: c.56-883:TMPRSS2_chr21:g.40099405del The TMPRSS2 (NM_00113509) rearrangement is a deletion in which one of the breakpoints is ~66kb upstream of ERG (NM_004449) exon 1. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a TMPRSS2-ERG fusion.
TMPRSS2	0	MSKCC-DMP	P-0008954-T01-IM5	TMPRSS2-NCRNA00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_00113509) rearrangement: c.56-883:TMPRSS2_chr21:g.40099405del The TMPRSS2 (NM_00113509) rearrangement is a deletion in which one of the breakpoints is ~66kb upstream of ERG (NM_004449) exon 1. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a TMPRSS2-ERG fusion.
KCNJ6	0	MSKCC-DMP	P-0014467-T01-IM6	TMPRSS2-KCNJ6 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.350-82:TMPRSS2_chr21:g.38949621dup Note: The TMPRSS2 Rearrangement results in the duplication of exons 4-14 of TMPRSS2.While this is not the canonical TMPRSS2-ERG fusion event, the possibility of such a fusion cannot be ruled out. Additional testing is recommended if clinically correlated.
TMPRSS2	0	MSKCC-DMP	P-0014467-T01-IM6	TMPRSS2-KCNJ6 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.350-82:TMPRSS2_chr21:g.38949621dup Note: The TMPRSS2 Rearrangement results in the duplication of exons 4-14 of TMPRSS2.While this is not the canonical TMPRSS2-ERG fusion event, the possibility of such a fusion cannot be ruled out. Additional testing is recommended if clinically correlated.
TBK1	0	MSKCC-DMP	P-0024797-T02-IM6	SPEN-TBK1 fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement: t(1;12)(p36.13; q14.3)(chr1:g.16261055::chr12:g.64915315) Note: The SPEN Rearrangement is a translocation event with the breakpoint in exon11. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0024797-T02-IM6	SPEN-TBK1 fusion	yes	unknown		unknown	SPEN (NM_015001) Rearrangement: t(1;12)(p36.13; q14.3)(chr1:g.16261055::chr12:g.64915315) Note: The SPEN Rearrangement is a translocation event with the breakpoint in exon11. Its functional significance is undetermined.
ITFG1	0	MSKCC-DMP	P-0026821-T05-IM6	NOTCH2-ITFG1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : t(1;16)(p13.1;q12.1)(chr1:g.120464783::chr16:g.47284570) Note: The NOTCH2 rearrangement is a translocation of intron 28 of NOTCH2 and intron 12 of ITFG1 that may results in the possible truncation of NOTCH2. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0026821-T05-IM6	NOTCH2-ITFG1 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement : t(1;16)(p13.1;q12.1)(chr1:g.120464783::chr16:g.47284570) Note: The NOTCH2 rearrangement is a translocation of intron 28 of NOTCH2 and intron 12 of ITFG1 that may results in the possible truncation of NOTCH2. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0026821-T05-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement: c.3142+73_c.2679inv Note: The NOTCH3 rearrangement is an intragenic inversion of exons 17 to 19. One of the breakpoints is within exon 17. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0029657-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4813_c.6670del Note: The KMT2D rearrangement is an intragenic deletion with breakpoints in exons 19 and 31.
NF1	0	MSKCC-DMP	P-0029936-T01-IM6	ACSF2-NF1 fusion	yes	unknown		unknown	ACSF2 (NM_025149) - NF1 (NM_001042492) rearrangement: c.1215+229:ACSF2_c.2993:NF1dup Note: The ACSF2 - NF1 rearrangement is a duplication which results in the fusion of ACSF2 exons 1-11 with NF1 exons 23-58. One of the breakpoints is within NF1 exon 23. Its functional significance is undetermined.
ACSF2	0	MSKCC-DMP	P-0029936-T01-IM6	ACSF2-NF1 fusion	yes	unknown		unknown	ACSF2 (NM_025149) - NF1 (NM_001042492) rearrangement: c.1215+229:ACSF2_c.2993:NF1dup Note: The ACSF2 - NF1 rearrangement is a duplication which results in the fusion of ACSF2 exons 1-11 with NF1 exons 23-58. One of the breakpoints is within NF1 exon 23. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0030169-T01-IM6	DAD1-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) Rearrangement : t(14;19)(q11.2; p13.3)(chr14:g.22757521::chr19:g.5219993) Note: The PTPRS Rearrangement results in the possible truncation of PTPRS. The breakpoint in PTPRS is within exon22. Its functional significance is undetermined.
DAD1	0	MSKCC-DMP	P-0030169-T01-IM6	DAD1-PTPRS fusion	yes	unknown		unknown	PTPRS (NM_002850) Rearrangement : t(14;19)(q11.2; p13.3)(chr14:g.22757521::chr19:g.5219993) Note: The PTPRS Rearrangement results in the possible truncation of PTPRS. The breakpoint in PTPRS is within exon22. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0030396-T02-IM6	DOCK1-RET fusion	yes	unknown		unknown	DOCK1 (NM_001380) - RET (NM_020975) Rearrangement: c.2515+295:RET_c.1668:RETdup Note: The DOCK1 -RET Rearrangement results in the fusion of exons  1-25 of  DOCK1 with exons 9-20 of RET. The breakpoint in RET is within exon9 . This includes the protein kinase domain of RET.
DOCK1	0	MSKCC-DMP	P-0030396-T02-IM6	DOCK1-RET fusion	yes	unknown		unknown	DOCK1 (NM_001380) - RET (NM_020975) Rearrangement: c.2515+295:RET_c.1668:RETdup Note: The DOCK1 -RET Rearrangement results in the fusion of exons  1-25 of  DOCK1 with exons 9-20 of RET. The breakpoint in RET is within exon9 . This includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0030396-T02-IM6	RBPMS-RET fusion	yes	unknown		unknown	RBPMS (NM_001008712) - RET (NM_020975) Rearrangement : t(8,10)(p21.1,q11.21)(chr8:g.30412656::chr10:g.43610018) Note: The RBPMS-RET Rearrangement results in the fusion of exons 1-6 of RBPMS with exons 11-20 of RET. It includes the protein kinase domain of RET.
RBPMS	0	MSKCC-DMP	P-0030396-T02-IM6	RBPMS-RET fusion	yes	unknown		unknown	RBPMS (NM_001008712) - RET (NM_020975) Rearrangement : t(8,10)(p21.1,q11.21)(chr8:g.30412656::chr10:g.43610018) Note: The RBPMS-RET Rearrangement results in the fusion of exons 1-6 of RBPMS with exons 11-20 of RET. It includes the protein kinase domain of RET.
TMPRSS2	0	MSKCC-DMP	P-0030552-T01-IM6	ABCG1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2965:TMRPSS2_chr21:g.43719730inv Note: The TMPRSS2 rearrangement is an inversion with breakpoint in intron 1. The possibility of a more complex event resulting in a TMPRSS2 fusion cannot be excluded. Additional testing is advised, if clinically indicated.
ABCG1	0	MSKCC-DMP	P-0030552-T01-IM6	ABCG1-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2965:TMRPSS2_chr21:g.43719730inv Note: The TMPRSS2 rearrangement is an inversion with breakpoint in intron 1. The possibility of a more complex event resulting in a TMPRSS2 fusion cannot be excluded. Additional testing is advised, if clinically indicated.
BRCA1	0	MSKCC-DMP	P-0030893-T01-IM6	CACNA2D4-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) Rearrangement : t(12,17)(p13.32,q21.31)(chr12:g.1952789::chr17:g.41244044) Note: The BRCA1 Rearrangement is a translocation event with the breakpoint in exon10. Its functional significance is undetermined.
CACNA2D4	0	MSKCC-DMP	P-0030893-T01-IM6	CACNA2D4-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) Rearrangement : t(12,17)(p13.32,q21.31)(chr12:g.1952789::chr17:g.41244044) Note: The BRCA1 Rearrangement is a translocation event with the breakpoint in exon10. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0030984-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4741:TMPRSS2_c.40-57465:ERGdel Note: The TMPRSS2 - ERG fusion involves exon 1 of TMPRSS1 and exons 4-11 of the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0030984-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4741:TMPRSS2_c.40-57465:ERGdel Note: The TMPRSS2 - ERG fusion involves exon 1 of TMPRSS1 and exons 4-11 of the non-canonical ERG transcript (NM_004449).
RAD52	0	MSKCC-DMP	P-0031219-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: c.132:RAD52_chr12:g.1055374del Note: The RAD52 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031269-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-737:TMPRSS2_ c.19-13490:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0031269-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-737:TMPRSS2_ c.19-13490:ERGdel
NBPF20	0	MSKCC-DMP	P-0032065-T01-IM6	HIST3H3-NBPF20 fusion	yes	unknown		unknown	HIST3H3 (NM_003493) rearrangement: c.161:HIST3H3_chr1:g.145082149dup Note: The HIST3H3 rearrangement results in the duplication of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
HIST3H3	0	MSKCC-DMP	P-0032065-T01-IM6	HIST3H3-NBPF20 fusion	yes	unknown		unknown	HIST3H3 (NM_003493) rearrangement: c.161:HIST3H3_chr1:g.145082149dup Note: The HIST3H3 rearrangement results in the duplication of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0032066-T01-IM6	RPLP0P2-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: t(11;17)(q12.2;q25.3)(chr11:g.61390991::chr17:g.78765364) Note: The RPTOR rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
RPLP0P2	0	MSKCC-DMP	P-0032066-T01-IM6	RPLP0P2-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: t(11;17)(q12.2;q25.3)(chr11:g.61390991::chr17:g.78765364) Note: The RPTOR rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.
NPM1	0	MSKCC-DMP	P-0032067-T01-IM6	NPM1-intragenic	yes	unknown		in frame	NPM1 (NM_002520) rearrangement: c.139-399_c.582+3del Note: The NPM1 rearrangement results in the in-frame deletion of exons 3-7. The functional significance is undetermined.
RIN1	0	MSKCC-DMP	P-0032111-T01-IM6	RPS6KB2-RIN1 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) Rearrangement: c.1156-7:RPS6KB2_chr11:g.66096453inv Note: The RPS6KB2 rearrangement results in the inversion of RPS6KB2 exons 1-13 and intergenic region in chr11:g.66096453. The functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0032111-T01-IM6	RPS6KB2-RIN1 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) Rearrangement: c.1156-7:RPS6KB2_chr11:g.66096453inv Note: The RPS6KB2 rearrangement results in the inversion of RPS6KB2 exons 1-13 and intergenic region in chr11:g.66096453. The functional significance is undetermined.
REL	0	MSKCC-DMP	P-0032111-T01-IM6	REL-intragenic	yes	unknown		unknown	REL (NM_002908) Rearrangement: c.302+833_c.1246del Note: The REL rearrangement results in intragenic deletion of REL exons 4 to 11. One of the breakpoints is within exon 11. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0032131-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2836_c.3231+51inv Note: The WHSC1L1 rearrangement is an intragenic inversion of exons 16-18. One of the breakpoints is within exon 16. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0032153-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.13609:FAT1_chr4:g.187509113inv Note: The FAT1 rearrangement is an inversions with a breakpoint in exon 27. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0032170-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.139:RB1_chr13:g.48876391del Note: The RB1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0032170-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1822:EML4_c.3172+632:ALKinv Note: The EML4 - ALK rearrangement is an inversion which leads to the in-frame fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0032170-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1822:EML4_c.3172+632:ALKinv Note: The EML4 - ALK rearrangement is an inversion which leads to the in-frame fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
MYO18B	0	MSKCC-DMP	P-0032208-T01-IM6	FGFR2-MYO18B fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYO18B (NM_032608) rearrangement: t(10;22)(q26.13;q12.2)(chr10:g.123241929::chr22:g.26280218) Note: The FGFR2 - MYO18B rearrangement is a translocation that results in the fusion of FGFR2 exons 1-17, which includes FGFR2 kinase domain, to MYO18B exons 26-43.
FGFR2	0	MSKCC-DMP	P-0032208-T01-IM6	FGFR2-MYO18B fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYO18B (NM_032608) rearrangement: t(10;22)(q26.13;q12.2)(chr10:g.123241929::chr22:g.26280218) Note: The FGFR2 - MYO18B rearrangement is a translocation that results in the fusion of FGFR2 exons 1-17, which includes FGFR2 kinase domain, to MYO18B exons 26-43.
BIRC3	0	MSKCC-DMP	P-0032215-T01-IM6	BIRC3-intragenic	yes	unknown		unknown	BIRC3 (NM_182962) rearrangement: c.854-42_c.954-1149inv Note: The BIRC3 rearrangement is an intragenic inversion of exon 4. The functional significance is undetermined.
GJA1	0	MSKCC-DMP	P-0032229-T01-IM6	ARID1B-GJA1 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3135+962:ARID1B_chr6:g.121762939inv Note: The ARID1B rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0032229-T01-IM6	ARID1B-GJA1 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3135+962:ARID1B_chr6:g.121762939inv Note: The ARID1B rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.
STAT5B	0	MSKCC-DMP	P-0032237-T01-IM6	STAT3-STAT5B fusion	yes	unknown		unknown	STAT5B (NM_012448) - STAT3 (NM_139276) rearrangement: c.990-166:STAT5B_c.1982:STAT3inv Note: The STAT5B - STAT3 rearrangement is an inversion of STAT5B exons 1-8 and STAT3 exons 21-24. One of the breakpoints is within STAT3 exon 21. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0032237-T01-IM6	STAT3-STAT5B fusion	yes	unknown		unknown	STAT5B (NM_012448) - STAT3 (NM_139276) rearrangement: c.990-166:STAT5B_c.1982:STAT3inv Note: The STAT5B - STAT3 rearrangement is an inversion of STAT5B exons 1-8 and STAT3 exons 21-24. One of the breakpoints is within STAT3 exon 21. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0032311-T01-IM6	SMAD3-intragenic	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.207-129:SMAD3_chr15:g.67353055del Note: The SMAD3 rearrangement results in the deletion of exon 1.
NF1	0	MSKCC-DMP	P-0032376-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) Rearrangement: c.3796_c.4836-21034dup Note: The NF1 rearrangement is an intragenic duplication of exons 28 to 36. One of the breakpoints is within exon 28. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0032394-T01-IM6	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2 (NM_006164) rearrangement: c.45+14851_c.403-223del Note: The NFE2L2 rearrangement is an intragenic deletion of exons 2-3. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0032407-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+230:KIF5B_c.2137-302:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-16 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0032407-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+230:KIF5B_c.2137-302:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-16 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
TACC3	0	MSKCC-DMP	P-0032432-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+13:FGFR3_c.1837-134:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-17 with TACC3 exons 10-16. The fusion is predicted to be in-frame and involves the kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0032432-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+13:FGFR3_c.1837-134:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-17 with TACC3 exons 10-16. The fusion is predicted to be in-frame and involves the kinase domain of FGFR3.
TERT	0	MSKCC-DMP	P-0032432-T01-IM6	FAM173B-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-62_chr5:g.10249995del Note: The TERT rearrangement is a deletion with a breakpoint within the promoter region of TERT. The functional significance is undetermined.
FAM173B	0	MSKCC-DMP	P-0032432-T01-IM6	FAM173B-TERT fusion	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.-62_chr5:g.10249995del Note: The TERT rearrangement is a deletion with a breakpoint within the promoter region of TERT. The functional significance is undetermined.
CDK8	0	MSKCC-DMP	P-0032442-T01-IM6	EXOSC8-CDK8 fusion	yes	unknown		unknown	CDK8 (NM_001260) - EXOSC8 (NM_181503) rearrangement: c.833:CDK8_c.609-51:EXOSC8del Note: The CDK8 - EXOSC8 rearrangement is a deletion that results in the fusion of CDK8 exons 1-8 with EXOSC8 exons 10-11. One of the breakpoints is within CDK8 exon 8. The functional significance is undetermined.
EXOSC8	0	MSKCC-DMP	P-0032442-T01-IM6	EXOSC8-CDK8 fusion	yes	unknown		unknown	CDK8 (NM_001260) - EXOSC8 (NM_181503) rearrangement: c.833:CDK8_c.609-51:EXOSC8del Note: The CDK8 - EXOSC8 rearrangement is a deletion that results in the fusion of CDK8 exons 1-8 with EXOSC8 exons 10-11. One of the breakpoints is within CDK8 exon 8. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0032445-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.70:CDKN2A_chr9:g.21981860del Note: The CDKN2A rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0032457-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) Rearrangement: c.2071-39_c.*2020inv Note: The FGFR1 rearrangement is an intragenic inversion of exons 16-19. The functional significance is undetermined,
NATD1	0	MSKCC-DMP	P-0032467-T01-IM6	HOXB13-NATD1 fusion	yes	unknown		unknown	HOXB3(NM_006361) Rearrangement: c.698:HOXB13_chr17:g.21146664inv Note: The HOXB13 rearrangement is an inversion of exon 2. One of the breakpoints is within exon 2. Multiple rearrangements involving HOXB13 were detected in this sample and a more complex rearrangement resulting in a HOXB13 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
HOXB13	0	MSKCC-DMP	P-0032467-T01-IM6	HOXB13-NATD1 fusion	yes	unknown		unknown	HOXB3(NM_006361) Rearrangement: c.698:HOXB13_chr17:g.21146664inv Note: The HOXB13 rearrangement is an inversion of exon 2. One of the breakpoints is within exon 2. Multiple rearrangements involving HOXB13 were detected in this sample and a more complex rearrangement resulting in a HOXB13 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0032478-T01-IM6	RSU1P2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(10;21)(q11.21;q22.2)(chr10:g.45577774::chr21:g.42861302) Note: The TMPRSS2 Rearrangement is a translocation event with a breakpoint in intron4.Its functional significance is undetermined.
RSU1P2	0	MSKCC-DMP	P-0032478-T01-IM6	RSU1P2-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(10;21)(q11.21;q22.2)(chr10:g.45577774::chr21:g.42861302) Note: The TMPRSS2 Rearrangement is a translocation event with a breakpoint in intron4.Its functional significance is undetermined.
SORBS1	0	MSKCC-DMP	P-0032507-T01-IM6	FGFR2-SORBS1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) Rearrangement : c.2301+944:FGFR2_chr10:g.97250518del Note: The FGFR2 Rearrangement results in the deletion of exon 18 of FGFR2.This does not include the protein kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0032507-T01-IM6	FGFR2-SORBS1 fusion	yes	unknown		unknown	FGFR2 (NM_000141) Rearrangement : c.2301+944:FGFR2_chr10:g.97250518del Note: The FGFR2 Rearrangement results in the deletion of exon 18 of FGFR2.This does not include the protein kinase domain of FGFR2.
STK11	0	MSKCC-DMP	P-0032513-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) Rearrangement : c.122_c.290+2342del Note: The STK11 Rearrangement results in the partial deletion of exon1 of STK11. One of the breakpoints is within exon1. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0032518-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_001145076) - ALK (NM_004304) fusion: c.1315+2607:EML4_c.3140:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-12 with ALK exons 19-29. One of the breakpoints is within exon 19 of ALK. This includes the kinase domain of ALK
EML4	0	MSKCC-DMP	P-0032518-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_001145076) - ALK (NM_004304) fusion: c.1315+2607:EML4_c.3140:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-12 with ALK exons 19-29. One of the breakpoints is within exon 19 of ALK. This includes the kinase domain of ALK
MPL	0	MSKCC-DMP	P-0032550-T01-IM6	MPL-intragenic	yes	unknown		unknown	MPL (NM_005373) rearrangement: c.853+27:MPL_chr1:g.43822389del Note: The MPL rearrangement is a deletion of exons 6-12. Its functional significance is undetermined.
NKX3-1	0	MSKCC-DMP	P-0032550-T01-IM6	MYC-NKX3-1 fusion	yes	unknown		unknown	NKX3-1 (NM_006167) - MYC (NM_002467) rearrangement: c.383:NKX3-1_c.-55:MYCdel Note: The NKX3-1 - MYC rearrangement is a deletion of NKX3-1 exon 2 and the promotor region of MYC. One of the breakpoints is within NKX3-1 exon 2. Its functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0032550-T01-IM6	MYC-NKX3-1 fusion	yes	unknown		unknown	NKX3-1 (NM_006167) - MYC (NM_002467) rearrangement: c.383:NKX3-1_c.-55:MYCdel Note: The NKX3-1 - MYC rearrangement is a deletion of NKX3-1 exon 2 and the promotor region of MYC. One of the breakpoints is within NKX3-1 exon 2. Its functional significance is undetermined.
CSNK1G2	0	MSKCC-DMP	P-0032620-T01-IM6	DOT1L-CSNK1G2 fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement:c.2909:DOT1L_chr19:g.1981791del Note: The DOT1L rearrangement results in the deletion of exons 1-24. One of the breakpoints is within exon 24. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0032620-T01-IM6	DOT1L-CSNK1G2 fusion	yes	unknown		unknown	DOT1L (NM_032482) rearrangement:c.2909:DOT1L_chr19:g.1981791del Note: The DOT1L rearrangement results in the deletion of exons 1-24. One of the breakpoints is within exon 24. The functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0032682-T01-IM6	DMRT2-PGR fusion	yes	unknown		unknown	PGR (NM_000926) rearrangement: t(9;11)(p24.3;q22.1)(chr9:g.1442340::chr11:g.100999195) Note: The PGR rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
DMRT2	0	MSKCC-DMP	P-0032682-T01-IM6	DMRT2-PGR fusion	yes	unknown		unknown	PGR (NM_000926) rearrangement: t(9;11)(p24.3;q22.1)(chr9:g.1442340::chr11:g.100999195) Note: The PGR rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0032683-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2122:EML4_c.3172+564:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-12 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0032683-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2122:EML4_c.3172+564:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-12 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
KIF5B	0	MSKCC-DMP	P-0032686-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2299:KIF5B_c.2137-50:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0032686-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2299:KIF5B_c.2137-50:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
PTPRD	0	MSKCC-DMP	P-0032686-T01-IM6	PTPRD-intragenic	yes	unknown		in frame	PTPRD (NM_002839) rearrangement: c.64+11242_c.352+116dup Note: The PTPRD rearrangement results in the in-frame duplication of exons 13-14. The functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0032778-T01-IM6	KLK10-POLD1 fusion	yes	unknown		unknown	KLK10 (NM_001077500) - POLD1 (NM_002691) Rearrangement :  c.88+823:KLK10_c.2925:POLD1inv Note: The KLK10 - POLD1 Rearrangement results in the fusion of exons 1-2 of KLK10 with exons 23-27 of POLD1. The breakpoint in POLD1 is within exon23. Its functional significance is undetermined.
KLK10	0	MSKCC-DMP	P-0032778-T01-IM6	KLK10-POLD1 fusion	yes	unknown		unknown	KLK10 (NM_001077500) - POLD1 (NM_002691) Rearrangement :  c.88+823:KLK10_c.2925:POLD1inv Note: The KLK10 - POLD1 Rearrangement results in the fusion of exons 1-2 of KLK10 with exons 23-27 of POLD1. The breakpoint in POLD1 is within exon23. Its functional significance is undetermined.
CPD	0	MSKCC-DMP	P-0032702-T01-IM6	NF1-CPD fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2001+12:NF1_chr17:g.28678685inv Note: The NF1 rearrangement results in the inversion of exons 1-17. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0032702-T01-IM6	NF1-CPD fusion	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2001+12:NF1_chr17:g.28678685inv Note: The NF1 rearrangement results in the inversion of exons 1-17. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0032702-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1959-245_c.3438del Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16.
SPANXA2-OT1	0	MSKCC-DMP	P-0032702-T01-IM6	TEK-SPANXA2-OT1 fusion	yes	unknown		unknown	TEK (NM_000459) rearrangement: t(9;X)(p21.2;q27.2)(chr9:g.27217610::chrX:g.140560188) Note: The TEK rearrangement is a translocation with a breakpoint in intron 18. The functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0032702-T01-IM6	TEK-SPANXA2-OT1 fusion	yes	unknown		unknown	TEK (NM_000459) rearrangement: t(9;X)(p21.2;q27.2)(chr9:g.27217610::chrX:g.140560188) Note: The TEK rearrangement is a translocation with a breakpoint in intron 18. The functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0032801-T01-IM6	STAMBPL1-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) Rearrangement: c.165-132:PTEN_chr10:g.90636313inv Note: The PTEN rearrangement is an inversion of PTEN exons 3 to 9. The functional significance is undetermined.
STAMBPL1	0	MSKCC-DMP	P-0032801-T01-IM6	STAMBPL1-PTEN fusion	yes	unknown		unknown	PTEN (NM_000314) Rearrangement: c.165-132:PTEN_chr10:g.90636313inv Note: The PTEN rearrangement is an inversion of PTEN exons 3 to 9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032801-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-595:TMPRSS2_c.19-12368:ERGdel Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0032801-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-595:TMPRSS2_c.19-12368:ERGdel Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.
ERG	0	MSKCC-DMP	P-0032646-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused to ERG exons 2-10): c.56-2331:TMPRSS2_c.18+11761:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0032646-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused to ERG exons 2-10): c.56-2331:TMPRSS2_c.18+11761:ERGdel
PEX5	0	MSKCC-DMP	P-0032650-T01-IM6	ETV6-PEX5 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: chr12:g.7329461_c.163+94inv Note: The ETV6 rearrangement is an inversion that includes  ETV6 exons 1-2. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0032650-T01-IM6	ETV6-PEX5 fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: chr12:g.7329461_c.163+94inv Note: The ETV6 rearrangement is an inversion that includes  ETV6 exons 1-2. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0032681-T01-IM6	NBPF20-PIK3CD fusion	yes	unknown		out of frame	PIK3CD (NM_005026) - NBPF20 (NM_001278267) rearrangement: c.1689+1:PIK3CD_c.5307-228539:NBPF20del Note: The PIK3CD - NBPF20 rearrangement is a deletion that results in the fusion of PIK3CD exons 1-13 with NBPF20 exons 53-131. Multiple PIK3CD rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
NBPF20	0	MSKCC-DMP	P-0032681-T01-IM6	NBPF20-PIK3CD fusion	yes	unknown		out of frame	PIK3CD (NM_005026) - NBPF20 (NM_001278267) rearrangement: c.1689+1:PIK3CD_c.5307-228539:NBPF20del Note: The PIK3CD - NBPF20 rearrangement is a deletion that results in the fusion of PIK3CD exons 1-13 with NBPF20 exons 53-131. Multiple PIK3CD rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
CDKN1B	0	MSKCC-DMP	P-0032681-T01-IM6	TNFSF8-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(9;12)(q33.1;p13.1)(chr9:g.117720034::chr12:g.12871086) Note: The CDKN1B rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
TNFSF8	0	MSKCC-DMP	P-0032681-T01-IM6	TNFSF8-CDKN1B fusion	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(9;12)(q33.1;p13.1)(chr9:g.117720034::chr12:g.12871086) Note: The CDKN1B rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.
PGLS	0	MSKCC-DMP	P-0032681-T01-IM6	PIK3R2-PGLS fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - PGLS (NM_012088) rearrangement: c.536:PIK3R2_c.640-628:PGLSdup Note: The PIK3R2 - PGLS rearrangement is a duplication that results in the fusion of PIK3R2 exons 1-5 with PGLS exon 5. One of the breakpoints is within PIK3R2  exon 5. The functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0032681-T01-IM6	PIK3R2-PGLS fusion	yes	unknown		unknown	PIK3R2 (NM_005027) - PGLS (NM_012088) rearrangement: c.536:PIK3R2_c.640-628:PGLSdup Note: The PIK3R2 - PGLS rearrangement is a duplication that results in the fusion of PIK3R2 exons 1-5 with PGLS exon 5. One of the breakpoints is within PIK3R2  exon 5. The functional significance is undetermined.
HNRNPM	0	MSKCC-DMP	P-0032687-T01-IM6	BRD4-HNRNPM fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2158+84:BRD4_chr19:g.8553970inv Note: The BRD4 rearrangement results in the inversion of exons 12-20. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0032687-T01-IM6	BRD4-HNRNPM fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2158+84:BRD4_chr19:g.8553970inv Note: The BRD4 rearrangement results in the inversion of exons 12-20. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0032896-T01-IM6	NBPF20-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(1;16)(q21.1;p13.3)(chr1:g.145721517::chr16:g.2136314) Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 37.
NBPF20	0	MSKCC-DMP	P-0032896-T01-IM6	NBPF20-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(1;16)(q21.1;p13.3)(chr1:g.145721517::chr16:g.2136314) Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 37.
CDK8	0	MSKCC-DMP	P-0032965-T01-IM6	ESM1-CDK8 fusion	yes	unknown		unknown	CDK8 (NM_001260) Rearrangement: t(5;13)(q11.2;q12.13)(chr5:g.54146908::chr13:g.26975603) Note: The CDK8 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.
ESM1	0	MSKCC-DMP	P-0032965-T01-IM6	ESM1-CDK8 fusion	yes	unknown		unknown	CDK8 (NM_001260) Rearrangement: t(5;13)(q11.2;q12.13)(chr5:g.54146908::chr13:g.26975603) Note: The CDK8 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0007065-T01-IM5	DCTN5-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement : c.1451:PALB2_c.118-6342:DCTN5del Note: The PALB2 (NM_024675) rearrangement results in the deletion of exons 1 to 4 of PALB2. One of the breakpoints is within exon4. This event is likely pathogenic.
DCTN5	0	MSKCC-DMP	P-0007065-T01-IM5	DCTN5-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement : c.1451:PALB2_c.118-6342:DCTN5del Note: The PALB2 (NM_024675) rearrangement results in the deletion of exons 1 to 4 of PALB2. One of the breakpoints is within exon4. This event is likely pathogenic.
RNF43	0	MSKCC-DMP	P-0007065-T01-IM5	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement :  c.252+7204_c.1148del Note: The RNF43 (NM_017763) rearrangement results in the intragenic deletion of exons 3 to 9 of RNF43. One of the breakpoints is within exon9. Its functional significance is undetermined.
GHR	0	MSKCC-DMP	P-0032993-T01-IM6	ARID1A-GHR fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement: t(1;5)(p35.3.3;p12)(chr1:g.27092885::chr5:g.42600647) Note: The ARID1A Rearrangement is a translocation event with the breakpoint in intron9. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0032993-T01-IM6	ARID1A-GHR fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement: t(1;5)(p35.3.3;p12)(chr1:g.27092885::chr5:g.42600647) Note: The ARID1A Rearrangement is a translocation event with the breakpoint in intron9. Its functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0032993-T01-IM6	DLG2-ATRX fusion	yes	unknown		in frame	DLG2 (NM_001142699) -ATRX (NM_000489)  Rearrangement : t(X;11)(q13.3;p21.2)(chrX:g.76888956::chr11:g.83978235) Note: The DLG2-ATRX Rearrangement results in the fusion of exons 1-7 of DLG2 with exons 19-35 of ATRX. Its functional significance is undetermined.
DLG2	0	MSKCC-DMP	P-0032993-T01-IM6	DLG2-ATRX fusion	yes	unknown		in frame	DLG2 (NM_001142699) -ATRX (NM_000489)  Rearrangement : t(X;11)(q13.3;p21.2)(chrX:g.76888956::chr11:g.83978235) Note: The DLG2-ATRX Rearrangement results in the fusion of exons 1-7 of DLG2 with exons 19-35 of ATRX. Its functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0033072-T01-IM6	HMGA2-KMT2D fusion	yes	unknown		out of frame	HMGA2 (NM_003483)  - KMT2D (NM_003482) rearrangement: c.249+19827:HMGA2_c.5189-60:KMT2Dinv Note The HMGA2 - KMT2D rearrangement is an inversion that may result in the fusion of HMGA2 exons 1-3 with KMT2D exons 22-54. Multiple KMT2D rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
HMGA2	0	MSKCC-DMP	P-0033072-T01-IM6	HMGA2-KMT2D fusion	yes	unknown		out of frame	HMGA2 (NM_003483)  - KMT2D (NM_003482) rearrangement: c.249+19827:HMGA2_c.5189-60:KMT2Dinv Note The HMGA2 - KMT2D rearrangement is an inversion that may result in the fusion of HMGA2 exons 1-3 with KMT2D exons 22-54. Multiple KMT2D rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
NAB2	0	MSKCC-DMP	P-0033072-T01-IM6	SRGAP1-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) - SRGAP1 (NM_020762) rearrangement: c.1468+356_c.68-8733:SRGAP1inv Note: The NAB2 rearrangement is an inversion with a breakpoints within NAB2 intron 6 and SRGAP1 intron 1. The functional significance is undetermined.
SRGAP1	0	MSKCC-DMP	P-0033072-T01-IM6	SRGAP1-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) - SRGAP1 (NM_020762) rearrangement: c.1468+356_c.68-8733:SRGAP1inv Note: The NAB2 rearrangement is an inversion with a breakpoints within NAB2 intron 6 and SRGAP1 intron 1. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0033078-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1696-23270_c.1815-127del Note: The RB1 rearrangement is an intragenic deletion of exon 18.
NKX2-1	0	MSKCC-DMP	P-0033097-T01-IM6	PAX9-NKX2-1 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) rearrangement: c.121:NKX2-1_chr14:g.37145781dup Note: The NKX2-1 rearrangement is a duplication with a breakpoint within NKX2-1 exon 2. The functional significance is undetermined.
PAX9	0	MSKCC-DMP	P-0033097-T01-IM6	PAX9-NKX2-1 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) rearrangement: c.121:NKX2-1_chr14:g.37145781dup Note: The NKX2-1 rearrangement is a duplication with a breakpoint within NKX2-1 exon 2. The functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0033126-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-4414:TMPRSS2_chr21:g.40082965del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is the not the canonical TMPRSS2-ERG fusion, the possibility of a TMPRSS2-ERG fusion not detected by IMPACT panel for this sample cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0033126-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-4414:TMPRSS2_chr21:g.40082965del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is the not the canonical TMPRSS2-ERG fusion, the possibility of a TMPRSS2-ERG fusion not detected by IMPACT panel for this sample cannot be ruled out.
FAT1	0	MSKCC-DMP	P-0018607-T03-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement: c.4324-689_c.8287del. Note: The FAT1 rearrangement is a deletion of FAT1 exons 8 to 10. One of the breakpoints is within exon 10 of FAT1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032951-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4118;TMPRSS2_c.-150+11848:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion of TMPRSS2 exons 2-14 and ERG exon 1. This rearrangement involves the non-canonical ERG (NM_004449) transcript. A TMPRSS2-ERG fusion cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0032951-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4118;TMPRSS2_c.-150+11848:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion of TMPRSS2 exons 2-14 and ERG exon 1. This rearrangement involves the non-canonical ERG (NM_004449) transcript. A TMPRSS2-ERG fusion cannot be ruled out.
SCOC	0	MSKCC-DMP	P-0033136-T01-IM6	ARID1A-SCOC fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement: t(1,4)(p36.11; q31.1)(chr1:g.27058209::chr4:g.141107510) Note: The ARID1A Rearrangement is a translocation event with a breakpoint in intron3.Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0033136-T01-IM6	ARID1A-SCOC fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement: t(1,4)(p36.11; q31.1)(chr1:g.27058209::chr4:g.141107510) Note: The ARID1A Rearrangement is a translocation event with a breakpoint in intron3.Its functional significance is undetermined.
HAPLN1	0	MSKCC-DMP	P-0033136-T01-IM6	RASA1-HAPLN1 fusion	yes	unknown		unknown	HAPLN1 (NM_001884) - RASA1 (NM_002890) Rearrangement : c.2604-38:HAPLN1_c.2604-38:RASA1inv Note: The HAPLN1 -RASA1 Rearrangement results in the fusion of exon1 of HAPLN1 with exons  20-25 of RASA1. Its functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0033136-T01-IM6	RASA1-HAPLN1 fusion	yes	unknown		unknown	HAPLN1 (NM_001884) - RASA1 (NM_002890) Rearrangement : c.2604-38:HAPLN1_c.2604-38:RASA1inv Note: The HAPLN1 -RASA1 Rearrangement results in the fusion of exon1 of HAPLN1 with exons  20-25 of RASA1. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0033226-T01-IM6	SEPT9-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : chr17:g.75261748_c.560-35inv Note: The TP53 Rearrangement results in the inversion of exons 6-11 of TP53. Multiple TP53 rearrangements were detected in this sample and a more complex rearrangement is possible. The functional significance is undetermined.
SEPT9	0	MSKCC-DMP	P-0033226-T01-IM6	SEPT9-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : chr17:g.75261748_c.560-35inv Note: The TP53 Rearrangement results in the inversion of exons 6-11 of TP53. Multiple TP53 rearrangements were detected in this sample and a more complex rearrangement is possible. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0033226-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon2) : c.56-1088:TMPRSS2_c.40-47540:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0033226-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon2) : c.56-1088:TMPRSS2_c.40-47540:ERGdel
MET	0	MSKCC-DMP	P-0033178-T01-IM6	ST7-MET fusion	yes	unknown		unknown	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-46812:ST7_c.303:METdup Note: The ST7 - MET rearrangement is a duplication which results in the fusion of ST7 exon 1 with MET exons 2-21. One of the breakpoints is within MET exon 2. Its functional significance is undetermined.
ST7	0	MSKCC-DMP	P-0033178-T01-IM6	ST7-MET fusion	yes	unknown		unknown	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-46812:ST7_c.303:METdup Note: The ST7 - MET rearrangement is a duplication which results in the fusion of ST7 exon 1 with MET exons 2-21. One of the breakpoints is within MET exon 2. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0033180-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3173-106_c.3516-155inv Note: The ALK rearrangement is an intragenic inversion of exons 20-22. Its functional significance is undetermined.
TRAP1	0	MSKCC-DMP	P-0033181-T01-IM6	CREBBP-TRAP1 fusion	yes	unknown		unknown	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.89-1476:TRAP1_c.5376:CREBBPdup Note: The TRAP1 - CREBBP rearrangement is a duplication which results in the fusion of TRAP1 exon 1 with CREBBP exon 31. One of the breakpoints is within CREBBP exon 1. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0033181-T01-IM6	CREBBP-TRAP1 fusion	yes	unknown		unknown	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.89-1476:TRAP1_c.5376:CREBBPdup Note: The TRAP1 - CREBBP rearrangement is a duplication which results in the fusion of TRAP1 exon 1 with CREBBP exon 31. One of the breakpoints is within CREBBP exon 1. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0033193-T01-IM6	ZNF8-DNMT1 fusion	yes	unknown		unknown	DNMT1(NM_001379) Rearrangement:  c.46:DNMT1_chr19:g.58808368inv Note: The DNMT1 rearrangement results in the fusion of DNMT1 exon 1. One of the breakpoints is within exon 1of DNMT1. Its functional significance is undetermined.
ZNF8	0	MSKCC-DMP	P-0033193-T01-IM6	ZNF8-DNMT1 fusion	yes	unknown		unknown	DNMT1(NM_001379) Rearrangement:  c.46:DNMT1_chr19:g.58808368inv Note: The DNMT1 rearrangement results in the fusion of DNMT1 exon 1. One of the breakpoints is within exon 1of DNMT1. Its functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0033205-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.106+5198_c.297del Note: The PIK3R3 rearrangement is an intragenic deletion of exons 2-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0021905-T02-IM6	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: c.2170:IRS2_chr13:g.110468522del Note: The IRS2 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
NPM1	0	MSKCC-DMP	P-0021905-T02-IM6	FGF18-NPM1 fusion	yes	unknown		in frame	NPM1 (NM_002520) - FGF18 (NM_003862) rearrangement: c.582+63:NPM1_c.69+4735:FGF18del Note: The NPM1 - FGF18 rearrangement is a deletion which results in the fusion of NPM1 exons 1-7 with FGF18 exon 3-5. Its functional significance is undetermined.
FGF18	0	MSKCC-DMP	P-0021905-T02-IM6	FGF18-NPM1 fusion	yes	unknown		in frame	NPM1 (NM_002520) - FGF18 (NM_003862) rearrangement: c.582+63:NPM1_c.69+4735:FGF18del Note: The NPM1 - FGF18 rearrangement is a deletion which results in the fusion of NPM1 exons 1-7 with FGF18 exon 3-5. Its functional significance is undetermined.
PAXBP1	0	MSKCC-DMP	P-0033399-T01-IM6	SPOP-PAXBP1 fusion	yes	unknown		out of frame	PAXBP1 (NM_013329) - SPOP (NM_001007228) rearrangement: t(17;21)(q21.33;q22.11)(chr17:g.47699480::chr21:g.:34122819) Note: The PAXBP1 - SPOP rearrangement is a translocation that results in the fusion of PAXBP1 exons 1-10 with SPOP exons 3-10. The fusion is predicted to be in frame. The functional significance is undetermined.
SPOP	0	MSKCC-DMP	P-0033399-T01-IM6	SPOP-PAXBP1 fusion	yes	unknown		out of frame	PAXBP1 (NM_013329) - SPOP (NM_001007228) rearrangement: t(17;21)(q21.33;q22.11)(chr17:g.47699480::chr21:g.:34122819) Note: The PAXBP1 - SPOP rearrangement is a translocation that results in the fusion of PAXBP1 exons 1-10 with SPOP exons 3-10. The fusion is predicted to be in frame. The functional significance is undetermined.
LINC01500	0	MSKCC-DMP	P-0033429-T01-IM6	APC-LINC01500 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(5;14)(q22.2;q23.1)(chr5:g.112175465::chr14:g.59220602) Note: The APC rearrangement is a translocation which involves exon 16 of APC. One of the breakpoints is within exon 16 of APC. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0033429-T01-IM6	APC-LINC01500 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement: t(5;14)(q22.2;q23.1)(chr5:g.112175465::chr14:g.59220602) Note: The APC rearrangement is a translocation which involves exon 16 of APC. One of the breakpoints is within exon 16 of APC. The functional significance is undetermined.
ALOX12B	0	MSKCC-DMP	P-0033465-T01-IM6	HES7-ALOX12B fusion	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.1337_chr17:g.8029057dup Note: The ALOX12B rearrangement is a duplication that includes ALOX12B exons 1-10. One of the breakpoints is within exon 10.
HES7	0	MSKCC-DMP	P-0033465-T01-IM6	HES7-ALOX12B fusion	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.1337_chr17:g.8029057dup Note: The ALOX12B rearrangement is a duplication that includes ALOX12B exons 1-10. One of the breakpoints is within exon 10.
RYBP	0	MSKCC-DMP	P-0033465-T01-IM6	DPT-RYBP fusion	yes	unknown		unknown	RYBP (NM_012234) rearrangemnet: t(1;3)(q24.2;p13)(chr1:g.168626981::chr3:g.72455938) Note: The RYBP rearrangement is a translocation with a breakpoint within intron 1.
DPT	0	MSKCC-DMP	P-0033465-T01-IM6	DPT-RYBP fusion	yes	unknown		unknown	RYBP (NM_012234) rearrangemnet: t(1;3)(q24.2;p13)(chr1:g.168626981::chr3:g.72455938) Note: The RYBP rearrangement is a translocation with a breakpoint within intron 1.
IGSF3	0	MSKCC-DMP	P-0033508-T01-IM6	NOTCH2-IGSF3 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) - IGSF3 (NM_001542) rearrangement: c.855:NOTCH2_c.43+10742:IGSF3del Note: The NOTCH2 - IGSF3 rearrangement is a deletion that results in the fusion of NOTCH2 exons 1-5 with IGSF3 exons 2-12. One of the breakpoints is within NOTCH2 exon 5. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0033508-T01-IM6	NOTCH2-IGSF3 fusion	yes	unknown		unknown	NOTCH2 (NM_024408) - IGSF3 (NM_001542) rearrangement: c.855:NOTCH2_c.43+10742:IGSF3del Note: The NOTCH2 - IGSF3 rearrangement is a deletion that results in the fusion of NOTCH2 exons 1-5 with IGSF3 exons 2-12. One of the breakpoints is within NOTCH2 exon 5. The functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0033529-T01-IM6	ERBB4-intragenic	yes	unknown		out of frame	ERBB4 (NM_005235) rearrangement: c.557-16484_c.1125-2del Note: The ERBB4 rearrangement results in the intragenic deletion of exons 5 to 9. The functional significance is undetermined.
GPS2	0	MSKCC-DMP	P-0033575-T01-IM6	CNTROB-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) Rearrangement : c.241:GPS2_chr17:g.7856267del Note: The GPS2 Rearrangement results in the deletion of exons 1-4 of GPS2.One of the breakpoints is within exon4. This event occurs in the background of other structural rearrangements involving GPS2. Its functional significance is undetermined.
CNTROB	0	MSKCC-DMP	P-0033575-T01-IM6	CNTROB-GPS2 fusion	yes	unknown		unknown	GPS2 (NM_004489) Rearrangement : c.241:GPS2_chr17:g.7856267del Note: The GPS2 Rearrangement results in the deletion of exons 1-4 of GPS2.One of the breakpoints is within exon4. This event occurs in the background of other structural rearrangements involving GPS2. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0033575-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-238:TMPRSS2_c.18+8414:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0033575-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-238:TMPRSS2_c.18+8414:ERGdel
LOC440390	0	MSKCC-DMP	P-0033749-T01-IM6	FANCA-LOC440390 fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.3408+18:FANCA_chr16:g.87145722del Note: The FANCA rearrangement is a deletion of exons 35-43. Its functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0033749-T01-IM6	FANCA-LOC440390 fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.3408+18:FANCA_chr16:g.87145722del Note: The FANCA rearrangement is a deletion of exons 35-43. Its functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0033615-T01-IM6	CREM-GNAS fusion	yes	unknown		out of frame	GNAS (NM_000516) - CREM (NM_181571) rearrangement: t(10;20)(p11.21;q13.32)(chr10:g.35491448::chr20:g.57479028) Note: The GNAS - CREM rearrangement is a translocation that results in the fusion of GNAS exons 1-5 with CREM exons 3-8. The functional significance is undetermined.
CREM	0	MSKCC-DMP	P-0033615-T01-IM6	CREM-GNAS fusion	yes	unknown		out of frame	GNAS (NM_000516) - CREM (NM_181571) rearrangement: t(10;20)(p11.21;q13.32)(chr10:g.35491448::chr20:g.57479028) Note: The GNAS - CREM rearrangement is a translocation that results in the fusion of GNAS exons 1-5 with CREM exons 3-8. The functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0033766-T01-IM6	IGF1R-intragenic	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: c.640+71778_c.2131del Note: The IGF1R rearrangement is an intragenic deletion of exons 3-10. Its functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0033766-T01-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.2271+298_c.2284del Note: The AGO2 rearrangement is an intragenic deletion of exons 18. One of the breakpoints is within exon 18. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0033789-T01-IM6	LINC01031-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: t(1;8)(q31.3;q24.3)(chr1:g.194264448::chr8:g.145739644) Note: The RECQL4 rearrangement is a translocation which involves a breakpoint in exon 11. Its functional significance is undetermined. Multiple rearrangements involving RECQL4 were detected in this sample and a more complex rearrangement resulting in a RECQL4 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
LINC01031	0	MSKCC-DMP	P-0033789-T01-IM6	LINC01031-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: t(1;8)(q31.3;q24.3)(chr1:g.194264448::chr8:g.145739644) Note: The RECQL4 rearrangement is a translocation which involves a breakpoint in exon 11. Its functional significance is undetermined. Multiple rearrangements involving RECQL4 were detected in this sample and a more complex rearrangement resulting in a RECQL4 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ROS1	0	MSKCC-DMP	P-0014304-T02-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: (EZR exons 1 to 9 fused with ROS1 exons 34 to 43): c.1090+79:EZR_c.5558-371:ROS1del Note: The EZR-ROS1 event results in an in-frame fusion which includes the protein kinase domain of ROS1.
EZR	0	MSKCC-DMP	P-0014304-T02-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: (EZR exons 1 to 9 fused with ROS1 exons 34 to 43): c.1090+79:EZR_c.5558-371:ROS1del Note: The EZR-ROS1 event results in an in-frame fusion which includes the protein kinase domain of ROS1.
C11orf70	0	MSKCC-DMP	P-0033523-T01-IM6	BIRC3-C11orf70 fusion	yes	unknown		out of frame	BIRC3 (NM_182962) - C11orf70 (NM_032930) rearrangement: c.853+38:BIRC3_c.193-1514:C11orf70dup Note: The BIRC3 - C11orf70 rearrangement is a duplication that results in the fusion of BIRC3 exons 1-3 with C11orf70 exons 3-7. The functional significance is undetermined.
BIRC3	0	MSKCC-DMP	P-0033523-T01-IM6	BIRC3-C11orf70 fusion	yes	unknown		out of frame	BIRC3 (NM_182962) - C11orf70 (NM_032930) rearrangement: c.853+38:BIRC3_c.193-1514:C11orf70dup Note: The BIRC3 - C11orf70 rearrangement is a duplication that results in the fusion of BIRC3 exons 1-3 with C11orf70 exons 3-7. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0033523-T01-IM6	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) rearrangement: c.2567+498_c.4132+9dup Note: The PBRM1 rearrangement results in the duplication of exons 18-26. Multiple PBRM1 rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0033810-T01-IM6	PDE3A-ETV6 fusion	yes	unknown		out of frame	ETV6 (NM_001987) -PDE3A (NM_000921) Rearrangement : c.1010-1239:ETV6_c.960+53099:PDE3A Note: The ETV6-PDE3A  rearrangement results in the fusion of exons 1-5 of ETV6 with exon 2 of PDE3A. Its functional significance is undetermined.
PDE3A	0	MSKCC-DMP	P-0033810-T01-IM6	PDE3A-ETV6 fusion	yes	unknown		out of frame	ETV6 (NM_001987) -PDE3A (NM_000921) Rearrangement : c.1010-1239:ETV6_c.960+53099:PDE3A Note: The ETV6-PDE3A  rearrangement results in the fusion of exons 1-5 of ETV6 with exon 2 of PDE3A. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0033832-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1767:TMPRSS2_c.39+62909:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0033832-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1767:TMPRSS2_c.39+62909:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
ARID1B	0	MSKCC-DMP	P-0033925-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.6115_c.*395inv Note: The ARID1B rearrangement is an inversion that includes ARID1B exon 20. One of the breakpoints is within exon.
NFE2L2	0	MSKCC-DMP	P-0033975-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: c.46-4925_c.170del Note: The NFE2L2 rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
FBXO33	0	MSKCC-DMP	P-0016870-T02-IM6	PARP1-FBXO33 fusion	yes	unknown		unknown	PARP1 (NM_001618) rearrangement: t(1;14)(q42.12;q21.1)(chr1:g.226549636::chr14:g.40515347) Note: The PARP1 rearrangement is a translocation involving exon 22. Its functional significance is undetermined.
PARP1	0	MSKCC-DMP	P-0016870-T02-IM6	PARP1-FBXO33 fusion	yes	unknown		unknown	PARP1 (NM_001618) rearrangement: t(1;14)(q42.12;q21.1)(chr1:g.226549636::chr14:g.40515347) Note: The PARP1 rearrangement is a translocation involving exon 22. Its functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0016870-T02-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.2735_c.4137-197dup Note: The RICTOR rearrangement is an intragenic duplication of exons 28-31. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0033823-T01-IM6	CHRNB3-WHSC1L1 fusion	yes	unknown		in frame	WHSC1L1 (NM_023034) - CHRNB3 (NM_000749) Rearrangement : c.1986+29:WHSC1L1_c.1242+453:CHRNB3inv Note: The WHSC1L1 - CHRNB3 Rearrangement results in the fusion of exons 1-10 of WHSC1L1 with exon6 of CHRNB3.Its functional significance is undetermined.
CHRNB3	0	MSKCC-DMP	P-0033823-T01-IM6	CHRNB3-WHSC1L1 fusion	yes	unknown		in frame	WHSC1L1 (NM_023034) - CHRNB3 (NM_000749) Rearrangement : c.1986+29:WHSC1L1_c.1242+453:CHRNB3inv Note: The WHSC1L1 - CHRNB3 Rearrangement results in the fusion of exons 1-10 of WHSC1L1 with exon6 of CHRNB3.Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0028180-T02-IM6	DIRC3-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement: c.3068-391:ALK_chr2:g.218382626del Note: The ALK rearrangement is a deletion of exons 1-19. One of the breakpoints is within intron 18 of ALK. The functional significance is undetermined.
DIRC3	0	MSKCC-DMP	P-0028180-T02-IM6	DIRC3-ALK fusion	yes	unknown		unknown	ALK (NM_004304) Rearrangement: c.3068-391:ALK_chr2:g.218382626del Note: The ALK rearrangement is a deletion of exons 1-19. One of the breakpoints is within intron 18 of ALK. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0033988-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.256_c.264+965del Note: The RB1 rearrangement is an intragenic deletion of exon 2.
TMPRSS2	0	MSKCC-DMP	P-0027600-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2: (NM_001135099) rearrangement: c.556+3086_c.55+2661inv Note: The TMPRSS2 rearrangement results in the inversion of intron 1 to intron 5. Its functional significance is undetermined.
LMNA	0	MSKCC-DMP	P-0023994-T05-IM6	NTRK1-LMNA fusion	yes	unknown		in frame	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exon 10 fused with NTRK1 exon 11) : c.1699-362:LMNA_c.1251+107:NTRK1del Note: The LMNA-NTRK1 fusion is predicted to be in-frame and includes the protein kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0023994-T05-IM6	NTRK1-LMNA fusion	yes	unknown		in frame	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exon 10 fused with NTRK1 exon 11) : c.1699-362:LMNA_c.1251+107:NTRK1del Note: The LMNA-NTRK1 fusion is predicted to be in-frame and includes the protein kinase domain of NTRK1.
ALK	0	MSKCC-DMP	P-0032862-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion(EML4 exon 11 fused to ALK exon20 ): c.1489+671:EML4_c.3172+839:ALK Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0032862-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion(EML4 exon 11 fused to ALK exon20 ): c.1489+671:EML4_c.3172+839:ALK Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.
OPTN	0	MSKCC-DMP	P-0032171-T03-IM6	FGFR2-OPTN fusion	yes	unknown		in frame	FGFR2 (NM_000141) - OPTN (NM_021980) rearrangement: c.2302-254:FGFR2_c.553-1543:OPTNinv Note: The FGFR2 - OPTN rearrangement is an inversion which results in the fusion of FGFR2 exons 1-17 with OPTN exons 5-14. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0032171-T03-IM6	FGFR2-OPTN fusion	yes	unknown		in frame	FGFR2 (NM_000141) - OPTN (NM_021980) rearrangement: c.2302-254:FGFR2_c.553-1543:OPTNinv Note: The FGFR2 - OPTN rearrangement is an inversion which results in the fusion of FGFR2 exons 1-17 with OPTN exons 5-14. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
STK11	0	MSKCC-DMP	P-0033884-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.589_c.920+334del Note: The STK11 rearrangement is an intragenic deletion of exons 4-7. One of the breakpoints is within exon 4. Its functional significance is undetermined.
STARD4	0	MSKCC-DMP	P-0034177-T01-IM6	APC-STARD4 fusion	yes	unknown		out of frame	APC (NM_000038) - STARD4 (NM_139164) rearrangement: c.1408+35:APC_c.156-1888:STARD4inv Note: The APC - STARD4 rearrangement is an inversion that may result in the fusion of APC exons 1-11 with STARD4 exons 4-6.
APC	0	MSKCC-DMP	P-0034177-T01-IM6	APC-STARD4 fusion	yes	unknown		out of frame	APC (NM_000038) - STARD4 (NM_139164) rearrangement: c.1408+35:APC_c.156-1888:STARD4inv Note: The APC - STARD4 rearrangement is an inversion that may result in the fusion of APC exons 1-11 with STARD4 exons 4-6.
APC	0	MSKCC-DMP	P-0034177-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038 rearrangement: c.1744-727_c.4040del Note: The APC rearrangement is an intragenic deletion of exons 15-16. One of the breakpoints is within exon 16.
AXIN2	0	MSKCC-DMP	P-0034192-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.1649_chr17:g.63512989dup Note: The AXIN2 rearrangement is a duplication that includes AXIN2 exons 6-11. One of the breakpoints is within exon 6.
MSH2	0	MSKCC-DMP	P-0033848-T01-IM6	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) rearrangement: c.2456_c.2459-2del Note: The MSH2 rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon 14. Its functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0033848-T01-IM6	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2 (NM_006164) rearrangement: c.45+9425_c.594+2dup Note: The NFE2L2 rearrangement is an intragenic duplication of exons 2-4. Its functional significance is undetermined.
KRTAP11-1	0	MSKCC-DMP	P-0033848-T01-IM6	DNMT1-KRTAP11-1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(19;21)(p13.2;q22.11)(chr19:g.10291039::chr21:g.32247604) Note: The DNMT1 rearrangement is a translocation involving a breakpoint in exon 4. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0033848-T01-IM6	DNMT1-KRTAP11-1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(19;21)(p13.2;q22.11)(chr19:g.10291039::chr21:g.32247604) Note: The DNMT1 rearrangement is a translocation involving a breakpoint in exon 4. Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0033848-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.2780-3432_c.4531del Note: The PBRM1 rearrangement is an intragenic deletion of exons 19-29. One of the breakpoints is within exon 29. Its functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0033899-T01-IM6	PHC2-KMT2A fusion	yes	unknown		unknown	KMT2A (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.3;q23.3)(chr1:g.33810963::chr11:g.118342947) Note: The KMT2A (NM_001197104) - PHC2 (NM_198040) rearrangement is a reciprocal translocation which may result in the fusion of KMT2A exons 1-3 with PHC2 exons 9-14. One of the breakpoints is within KMT2A exon 3. Its functional significance is undetermined.
PHC2	0	MSKCC-DMP	P-0033899-T01-IM6	PHC2-KMT2A fusion	yes	unknown		unknown	KMT2A (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.3;q23.3)(chr1:g.33810963::chr11:g.118342947) Note: The KMT2A (NM_001197104) - PHC2 (NM_198040) rearrangement is a reciprocal translocation which may result in the fusion of KMT2A exons 1-3 with PHC2 exons 9-14. One of the breakpoints is within KMT2A exon 3. Its functional significance is undetermined.
AMER2	0	MSKCC-DMP	P-0034092-T01-IM6	FLT1-AMER2 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.3742:FLT1_chr13:g.25721451dup Note: The FLT1 rearrangement results in the duplication of exons 29-30. One of the breakpoints is within exon 29. The functional significance is undetermined.
FLT1	0	MSKCC-DMP	P-0034092-T01-IM6	FLT1-AMER2 fusion	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: c.3742:FLT1_chr13:g.25721451dup Note: The FLT1 rearrangement results in the duplication of exons 29-30. One of the breakpoints is within exon 29. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0034140-T01-IM6	LSM6-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(4;17)(q31.22;p12)(chr4:g.147071771::chr17:g.15983773) Note: The NCOR1 rearrangement is a translocation with a breakpoint in exon 25. The functional significance is undetermined.
LSM6	0	MSKCC-DMP	P-0034140-T01-IM6	LSM6-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(4;17)(q31.22;p12)(chr4:g.147071771::chr17:g.15983773) Note: The NCOR1 rearrangement is a translocation with a breakpoint in exon 25. The functional significance is undetermined.
CSNK1G2	0	MSKCC-DMP	P-0034215-T01-IM6	DOT1L-CSNK1G2 fusion	yes	unknown		unknown	DOT1L (NM_032482) - CSNK1G2 (NM_001319) rearrangement: c.3752:DOT1L_c.-265-8178:CSNK1G2dup Note: The DOT1L - CSNK1G2 rearrangement is a duplication that may result in the fusion of DOT1L exons 1-27 with CSNK1G2 exons 2-12. One of the breakpoints is within DOT1L exon 27. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0034215-T01-IM6	DOT1L-CSNK1G2 fusion	yes	unknown		unknown	DOT1L (NM_032482) - CSNK1G2 (NM_001319) rearrangement: c.3752:DOT1L_c.-265-8178:CSNK1G2dup Note: The DOT1L - CSNK1G2 rearrangement is a duplication that may result in the fusion of DOT1L exons 1-27 with CSNK1G2 exons 2-12. One of the breakpoints is within DOT1L exon 27. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0034256-T01-IM6	C16orf47-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1866_chr16:g.73261464inv Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 12-16. One of the breakpoints is within exon 12.
C16orf47	0	MSKCC-DMP	P-0034256-T01-IM6	C16orf47-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.1866_chr16:g.73261464inv Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 12-16. One of the breakpoints is within exon 12.
RB1	0	MSKCC-DMP	P-0033701-T02-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1696-6786_c.1726del Note: The RB1 rearrangement results in the deletion of exon 18. One of the breakpoints is within exon 18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0033701-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3851:TMPRSS2_c.19-2454:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0033701-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3851:TMPRSS2_c.19-2454:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0033701-T02-IM6	CYP3A43-TMPRSS2 fusion	yes	unknown		in frame	CYP3A43 (NM_022820) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(q22.1;q22.3)(chr7:g.99448887::chr21:g.42873843) Note: The CYP3A43 - TMPRSS2 rearrangement is a translocation that results in the fusion of CYP3A43 exons 1-7 with TMPRSS2 exons 2-14. The functional significance is undetermined.
CYP3A43	0	MSKCC-DMP	P-0033701-T02-IM6	CYP3A43-TMPRSS2 fusion	yes	unknown		in frame	CYP3A43 (NM_022820) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(q22.1;q22.3)(chr7:g.99448887::chr21:g.42873843) Note: The CYP3A43 - TMPRSS2 rearrangement is a translocation that results in the fusion of CYP3A43 exons 1-7 with TMPRSS2 exons 2-14. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0033701-T02-IM6	BDP1-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1814+70:PIK3R1_chr5:g.70728320del Note: The PIK3R1 rearrangement results in the deletion of exons 14-16. The functional significance is undetermined.
BDP1	0	MSKCC-DMP	P-0033701-T02-IM6	BDP1-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1814+70:PIK3R1_chr5:g.70728320del Note: The PIK3R1 rearrangement results in the deletion of exons 14-16. The functional significance is undetermined.
CSTF2	0	MSKCC-DMP	P-0034291-T01-IM6	NPM1-CSTF2 fusion	yes	unknown		unknown	NPM1 (NM_002520) rearrangement: t(X;5)(q22.1;q35.1)(chrX:g.100027214::chr5:g.170820119) Note: The NPM1 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
NPM1	0	MSKCC-DMP	P-0034291-T01-IM6	NPM1-CSTF2 fusion	yes	unknown		unknown	NPM1 (NM_002520) rearrangement: t(X;5)(q22.1;q35.1)(chrX:g.100027214::chr5:g.170820119) Note: The NPM1 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034296-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1303:TMPRSS2_c.40-58938:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0034296-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1303:TMPRSS2_c.40-58938:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
LOC101928539	0	MSKCC-DMP	P-0034296-T01-IM6	PLK2-LOC101928539 fusion	yes	unknown		unknown	PLK2 (NM_006622) rearrangement: c.704:PLK2_chr5:g.57189065del Note: The PLK2 rearrangement is a deletion of exons 5-14. One of the breakpoints is within exon PLK2 exon 5. The functional significance is undetermined.
PLK2	0	MSKCC-DMP	P-0034296-T01-IM6	PLK2-LOC101928539 fusion	yes	unknown		unknown	PLK2 (NM_006622) rearrangement: c.704:PLK2_chr5:g.57189065del Note: The PLK2 rearrangement is a deletion of exons 5-14. One of the breakpoints is within exon PLK2 exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034384-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2506:TMPRSS2_c.18+6601:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0034384-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2506:TMPRSS2_c.18+6601:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
FGFR2	0	MSKCC-DMP	P-0034399-T01-IM6	CUL3-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(2;10)(q36.1;q26.13)(chr2:g.225329353::chr10:g.123240519) Note: The FGFR2 rearrangement is a translocation involving exon 18. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CUL3	0	MSKCC-DMP	P-0034399-T01-IM6	CUL3-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(2;10)(q36.1;q26.13)(chr2:g.225329353::chr10:g.123240519) Note: The FGFR2 rearrangement is a translocation involving exon 18. Multiple rearrangements involving FGFR2 were detected in this sample and a more complex rearrangement resulting in a FGFR2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SDHC	0	MSKCC-DMP	P-0034375-T01-IM6	DDR2-SDHC fusion	yes	unknown		unknown	SDHC(NM_003001) - DDR2(NM_006182) Rearrangement: c.179+1155:SDHC_c.1729-181:DDR2inv Note: The SDHC - DDR2 rearrangement is an inversion of SDHC exons 4-6 and DDR2 14-18. The functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0034375-T01-IM6	DDR2-SDHC fusion	yes	unknown		unknown	SDHC(NM_003001) - DDR2(NM_006182) Rearrangement: c.179+1155:SDHC_c.1729-181:DDR2inv Note: The SDHC - DDR2 rearrangement is an inversion of SDHC exons 4-6 and DDR2 14-18. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0034418-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) : c.2664-76_c.*4633inv Note: The RB1 rearrangement is an inversion that includes RB1 exons 26-27.
FGFR3	0	MSKCC-DMP	P-0034419-T01-IM6	JAKMIP1-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - JAKMIP1 (NM_001099433) fusion (FGFR3 exons 1-17 fused to JAKM1P1 exons 4-21): c.2274+88:FGFR3_c.624+9161:JAKMIP1inv Note: The FGFR3 - JAKMIP1 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
JAKMIP1	0	MSKCC-DMP	P-0034419-T01-IM6	JAKMIP1-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - JAKMIP1 (NM_001099433) fusion (FGFR3 exons 1-17 fused to JAKM1P1 exons 4-21): c.2274+88:FGFR3_c.624+9161:JAKMIP1inv Note: The FGFR3 - JAKMIP1 fusion is predicted to be in frame and includes the kinase domain of FGFR3.
CHRNA6	0	MSKCC-DMP	P-0030503-T01-IM6	IDH1-CHRNA6 fusion	yes	unknown		unknown	IDH1 (NM_005896)  rearrangement: t(2;8)(q34;p11.21)(chr2:g.209116140::chr8:g.42635681) Note: The IDH1 rearrangement is a translocation with the breakpoint in intron 3. The functional significance is undetermined.
IDH1	0	MSKCC-DMP	P-0030503-T01-IM6	IDH1-CHRNA6 fusion	yes	unknown		unknown	IDH1 (NM_005896)  rearrangement: t(2;8)(q34;p11.21)(chr2:g.209116140::chr8:g.42635681) Note: The IDH1 rearrangement is a translocation with the breakpoint in intron 3. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0031352-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.171+46537_c.47del Note: The PARK2 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0031643-T01-IM6	SLX4-intragenic	yes	unknown		unknown	SLX4 (NM_032444) Rearrangement: c.*2394_c.3564del Note: The SLX4 rearrangement is an intragenic deletion of SLX4 exons 12-15. One of the breakpoints is within exon 12. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0031790-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.523_c.849+161del Note: The BRD4 rearrangement is an intragenic deletion of exons 4-5. One of the breakpoints is within exon 4. The functional significance is undetermined.
GALNT11	0	MSKCC-DMP	P-0031833-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8828:KMT2C_chr7:g.151818189del Note: The KMT2C rearrangement results in the deletion of exons 38-59. One of the breakpoints is within exon 38. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0031833-T01-IM6	KMT2C-GALNT11 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8828:KMT2C_chr7:g.151818189del Note: The KMT2C rearrangement results in the deletion of exons 38-59. One of the breakpoints is within exon 38. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0032048-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.-127-3807_c.961del Note: The SMAD4 rearrangement results in the deletion of exons 1-9. One of the breakpoints is within exon 9. The high read support and copy number of these exons is suggestive of a homozygous event/ deep deletion.
TCF7L2	0	MSKCC-DMP	P-0032124-T01-IM6	PPP2CA-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) - PPP2CA (NM_002715) Rearrangement : t(5;10)(q31.1;q25.2)(chr5:g.133531112::chr10:g.114920515) Note: The TCF7L2 - PPP2CA Rearrangement results in the fusion of exons 1-13 of TCF7L2 with the promoter region of PPP2CA before the transcription start site.Its functional significance is undetermined.
PPP2CA	0	MSKCC-DMP	P-0032124-T01-IM6	PPP2CA-TCF7L2 fusion	yes	unknown		unknown	TCF7L2 (NM_001146274) - PPP2CA (NM_002715) Rearrangement : t(5;10)(q31.1;q25.2)(chr5:g.133531112::chr10:g.114920515) Note: The TCF7L2 - PPP2CA Rearrangement results in the fusion of exons 1-13 of TCF7L2 with the promoter region of PPP2CA before the transcription start site.Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032390-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2232:TMPRSS2_c.19-12935:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0032390-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2232:TMPRSS2_c.19-12935:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.
EP300	0	MSKCC-DMP	P-0032458-T01-IM6	RMI2-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) Rearrangement: t(16;22)(p13.13;q13.2)(chr16:g.11453170::chr22:g.41573186) Note: The EP300 rearrangement is a translocation with breakpoints within exon 31 of EP300. The functional significance is undetermined.
RMI2	0	MSKCC-DMP	P-0032458-T01-IM6	RMI2-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) Rearrangement: t(16;22)(p13.13;q13.2)(chr16:g.11453170::chr22:g.41573186) Note: The EP300 rearrangement is a translocation with breakpoints within exon 31 of EP300. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032480-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG(NM_004449) Rearrangement : c.126+617:TMPRSS2_c.39+41589:ERG Note: The TMPRSS2- ERG Rearrangement involves exons 1-2 of TMPRSS2 and exons 4-10 of ERG. While this is not the canonical TMPRSS2-ERG fusion, the possibility of a TMPRSS2-ERG fusion not detected by IMPACT cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0032480-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG(NM_004449) Rearrangement : c.126+617:TMPRSS2_c.39+41589:ERG Note: The TMPRSS2- ERG Rearrangement involves exons 1-2 of TMPRSS2 and exons 4-10 of ERG. While this is not the canonical TMPRSS2-ERG fusion, the possibility of a TMPRSS2-ERG fusion not detected by IMPACT cannot be ruled out.
PAX8	0	MSKCC-DMP	P-0032663-T01-IM6	CBWD2-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement: c.1087+958:PAX8_chr2:g.114132526del Note: The PAX8 rearrangement results in the deletion of PAX8 exons 1-9. The functional significance is undetermined.
CBWD2	0	MSKCC-DMP	P-0032663-T01-IM6	CBWD2-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement: c.1087+958:PAX8_chr2:g.114132526del Note: The PAX8 rearrangement results in the deletion of PAX8 exons 1-9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032663-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+2322:TMPRSS2_c.18+12726:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0032663-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+2322:TMPRSS2_c.18+12726:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
NF1	0	MSKCC-DMP	P-0032819-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.1845+207_c.3708+50dup Note: The NF1 rearrangement is an intragenic duplication of exons 17-27. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0032823-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.1307_c.2719+1741del Note: The ZFHX3 rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0033150-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.-1375_c.346del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-4994_c.389del Note: The CDKN2A rearrangement results in the deletion of exons 1-2 of CDKN2Ap16INK4A and exon 2 of CDKN2Ap14ARF. The breakpoint is within exon 2 of both isoforms.
CIC	0	MSKCC-DMP	P-0033171-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.931+290_c.2481inv Note: The CIC rearrangement is an intragenic inversion of exons 7-10. One of the breakpoints is within exon 10.
PTPRD	0	MSKCC-DMP	P-0033171-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: chr9:g.8208089_c.3153+55del Note: The PTPRD rearrangement is a deletion that includes PTPRD exons 30-46.
SMARCA4	0	MSKCC-DMP	P-0033183-T01-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.1246-40_c.4636-84del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 8-32.
ZFHX3	0	MSKCC-DMP	P-0033292-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.9485:ZFHX3_chr16:g.72812219del Note: The ZFHX3 rearrangement is a deletion of a part of exon 10. One of the breakpoints is in exon 10.
FANCA	0	MSKCC-DMP	P-0033294-T01-IM6	C1orf186-FANCA fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: t(1;16)(q32.1;q24.3)(chr1:g.206279359::chr16:g.89877021) Note: The FANCA rearrangement is a translocation with a breakpoint in intron 5. The translocation is detected within a background of intragenic gain in FANCA. The functional significance is undetermined.
C1orf186	0	MSKCC-DMP	P-0033294-T01-IM6	C1orf186-FANCA fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: t(1;16)(q32.1;q24.3)(chr1:g.206279359::chr16:g.89877021) Note: The FANCA rearrangement is a translocation with a breakpoint in intron 5. The translocation is detected within a background of intragenic gain in FANCA. The functional significance is undetermined.
MGC15885	0	MSKCC-DMP	P-0033383-T01-IM6	SMAD3-MGC15885 fusion	yes	unknown		unknown	SMAD3 (NM_005902) Rearrangement: c.418:SMAD3_chr15:g.62843216inv Note: The SMAD3 rearrangement is an inversion of SMAD3 exons 1 to 3. One of the breakpoints is with exon 3 of SMAD3. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0033383-T01-IM6	SMAD3-MGC15885 fusion	yes	unknown		unknown	SMAD3 (NM_005902) Rearrangement: c.418:SMAD3_chr15:g.62843216inv Note: The SMAD3 rearrangement is an inversion of SMAD3 exons 1 to 3. One of the breakpoints is with exon 3 of SMAD3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0033398-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.126+805_c.350-33del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3.
MAP3K13	0	MSKCC-DMP	P-0033548-T01-IM6	HES1-MAP3K13 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.1011-161_chr3:g.193808028inv Note: The MAP3K13 rearrangement is an inversion that includes MAP3K13 exons 6-14. The functional significance is undetermined.
HES1	0	MSKCC-DMP	P-0033548-T01-IM6	HES1-MAP3K13 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.1011-161_chr3:g.193808028inv Note: The MAP3K13 rearrangement is an inversion that includes MAP3K13 exons 6-14. The functional significance is undetermined.
MC4R	0	MSKCC-DMP	P-0033634-T01-IM6	FGFR2-MC4R fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;18)(q26.13;q21.32)(chr10:g.123244300::chr18:g.58428114) Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16.  The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0033634-T01-IM6	FGFR2-MC4R fusion	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;18)(q26.13;q21.32)(chr10:g.123244300::chr18:g.58428114) Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16.  The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0033634-T01-IM6	NANOS2-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1388_chr19:g.46414845inv Note: The SMARCA4 rearrangement is an inversion that includes SMARCA4 exons 8-35. One of the breakpoints is within exon 8.
NANOS2	0	MSKCC-DMP	P-0033634-T01-IM6	NANOS2-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1388_chr19:g.46414845inv Note: The SMARCA4 rearrangement is an inversion that includes SMARCA4 exons 8-35. One of the breakpoints is within exon 8.
INPP4A	0	MSKCC-DMP	P-0033634-T01-IM6	NPAS2-INPP4A fusion	yes	unknown		unknown	NPAS2 (NM_002518) - INPP4A (NM_001134224) rearrangement: c.485-1:NPAS2_c.580-3:INPP4Adup Note: The NPAS2  - INPP4A rearrangement is a duplication that results in the fusion of NPAS2 exons 1-7 with INPP4A exons 9-26. One of the breakpoints is within NPAS2 exon 7. The functional significance is undetermined.
NPAS2	0	MSKCC-DMP	P-0033634-T01-IM6	NPAS2-INPP4A fusion	yes	unknown		unknown	NPAS2 (NM_002518) - INPP4A (NM_001134224) rearrangement: c.485-1:NPAS2_c.580-3:INPP4Adup Note: The NPAS2  - INPP4A rearrangement is a duplication that results in the fusion of NPAS2 exons 1-7 with INPP4A exons 9-26. One of the breakpoints is within NPAS2 exon 7. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0033634-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.77051146_c.3089del Note: The ATRX rearrangement is a deletion that includes ATRX exons 1-9. One of the breakpoints is within exon 9.
MAGT1	0	MSKCC-DMP	P-0033634-T01-IM6	MAGT1-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.77051146_c.3089del Note: The ATRX rearrangement is a deletion that includes ATRX exons 1-9. One of the breakpoints is within exon 9.
RBFOX2	0	MSKCC-DMP	P-0033742-T01-IM6	TET1-RBFOX2 fusion	yes	unknown		unknown	TET1 (NM_030625) rearrangement: t(10;22)(q21.3;q12.3)(chr10:g.70427055::chr22:g.36131794) Note: The TET1 rearrangement is a translocation which involves exon 7. Its functional significance is undetermined.
TET1	0	MSKCC-DMP	P-0033742-T01-IM6	TET1-RBFOX2 fusion	yes	unknown		unknown	TET1 (NM_030625) rearrangement: t(10;22)(q21.3;q12.3)(chr10:g.70427055::chr22:g.36131794) Note: The TET1 rearrangement is a translocation which involves exon 7. Its functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0033845-T01-IM6	DYRK1A-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.352-96:RUNX1_chr21:g.38829898del Note: The RUNX1 rearrangement is a deletion of exons 1-4. Its functional significance is undetermined.
DYRK1A	0	MSKCC-DMP	P-0033845-T01-IM6	DYRK1A-RUNX1 fusion	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.352-96:RUNX1_chr21:g.38829898del Note: The RUNX1 rearrangement is a deletion of exons 1-4. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0033855-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.582_c.859+185del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 4-5. One of the breakpoints is within exon 4.
LINC01467	0	MSKCC-DMP	P-0034080-T02-IM6	NAB2-LINC01467 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(12;14)(q13.3;q31.1)(chr12:g.57487449::chr14:g.82091713) Note: The NAB2 rearrangement is a translocation with a breakpoint within intron 6. Multiple NAB2 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
NAB2	0	MSKCC-DMP	P-0034080-T02-IM6	NAB2-LINC01467 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(12;14)(q13.3;q31.1)(chr12:g.57487449::chr14:g.82091713) Note: The NAB2 rearrangement is a translocation with a breakpoint within intron 6. Multiple NAB2 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
AXL	0	MSKCC-DMP	P-0034255-T01-IM6	HNRNPUL1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.85+112:AXL_c.296-1265:HNRNPUL1inv Note: The AXL - HNRNPUL1 rearrangement is an inversion that includes AXL exons 2-20 and HNRNPUL1 exon 1. The functional significance is undetermined.
HNRNPUL1	0	MSKCC-DMP	P-0034255-T01-IM6	HNRNPUL1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.85+112:AXL_c.296-1265:HNRNPUL1inv Note: The AXL - HNRNPUL1 rearrangement is an inversion that includes AXL exons 2-20 and HNRNPUL1 exon 1. The functional significance is undetermined.
APC	0	MSKCC-DMP	P-0034289-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4324:APC_chr5:g.112194400del Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoint is within exon 16.
SRP19	0	MSKCC-DMP	P-0034289-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4324:APC_chr5:g.112194400del Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoint is within exon 16.
NEGR1	0	MSKCC-DMP	P-0034352-T01-IM6	NBPF20-NEGR1 fusion	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: c.835:NEGR1_chr1:g.145082046inv Note: The NEGR1 rearrangement results in the inversion of exons 1-6. One of the breakpoints is within NEGR1 exon 6. The functional significance is undetermined.
NBPF20	0	MSKCC-DMP	P-0034352-T01-IM6	NBPF20-NEGR1 fusion	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: c.835:NEGR1_chr1:g.145082046inv Note: The NEGR1 rearrangement results in the inversion of exons 1-6. One of the breakpoints is within NEGR1 exon 6. The functional significance is undetermined.
MSRB3	0	MSKCC-DMP	P-0034379-T01-IM6	ATR-MSRB3 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(3;12)(q23;q14.3)(chr3:g.142277934::chr12:g.65647870) Note: The ATR rearrangement is a translocation involving exon 7. Its functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0034379-T01-IM6	ATR-MSRB3 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(3;12)(q23;q14.3)(chr3:g.142277934::chr12:g.65647870) Note: The ATR rearrangement is a translocation involving exon 7. Its functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0034483-T01-IM6	KIAA1715-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: t(2;16)(q31.1;p12.2)(chr2:g.176432726::chr16:g.23647039) Note: The PALB2 rearrangement is a translocation with a breakpoint within exon 4. Multiple PALB2 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
KIAA1715	0	MSKCC-DMP	P-0034483-T01-IM6	KIAA1715-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: t(2;16)(q31.1;p12.2)(chr2:g.176432726::chr16:g.23647039) Note: The PALB2 rearrangement is a translocation with a breakpoint within exon 4. Multiple PALB2 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
EMR3	0	MSKCC-DMP	P-0034540-T01-IM6	MEF2B-EMR3 fusion	yes	unknown		unknown	EMR3(NM_032571) - MEF2BNB (NM_001145784) Rearrangement :  c.-2027:EMR3_c.337:MEF2BNBdup Note: The EMR3 - MEF2BNB Rearrangement results in the fusion of the promoter region of EMR3 with exon 4-9 of MEF2BNB. The breakpoint in MEF2BNB is within exon4. Its functional significance is undetermined.
MEF2B	0	MSKCC-DMP	P-0034540-T01-IM6	MEF2B-EMR3 fusion	yes	unknown		unknown	EMR3(NM_032571) - MEF2BNB (NM_001145784) Rearrangement :  c.-2027:EMR3_c.337:MEF2BNBdup Note: The EMR3 - MEF2BNB Rearrangement results in the fusion of the promoter region of EMR3 with exon 4-9 of MEF2BNB. The breakpoint in MEF2BNB is within exon4. Its functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0034540-T01-IM6	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) Rearrangement : c.2529_c.2762-204del Note: The JAK2 Rearrangement results in the intragenic deletion of exon19-20 of JAK2. One of the breakpoints is within exon19.Its functional significance is undetermined.
PRSS57	0	MSKCC-DMP	P-0034643-T01-IM6	TCF3-PRSS57 fusion	yes	unknown		out of frame	TCF3 (NM_001136139) - PRSS57 (NM_214710) rearrangement: c.1450+69:TCF3_c.382-485:PRSSS57del Note: The TCF3 - PRSS57 rearrangement is a deletion that results in a fusion of TCF3 exons 1-15 to PRSS57 exons 4-5. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0034643-T01-IM6	TCF3-PRSS57 fusion	yes	unknown		out of frame	TCF3 (NM_001136139) - PRSS57 (NM_214710) rearrangement: c.1450+69:TCF3_c.382-485:PRSSS57del Note: The TCF3 - PRSS57 rearrangement is a deletion that results in a fusion of TCF3 exons 1-15 to PRSS57 exons 4-5. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0034946-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8323_c.13423del Note: The KMT2C rearrangement results in the deletion of exons 38-52. One of the breakpoints is within exon 38 and the other is within exon 52.
TEK	0	MSKCC-DMP	P-0034946-T01-IM6	TEK-intragenic	yes	unknown		unknown	TEK (NM_000459) rearrangement: c.2575+394_c.3119del Note: The TEK rearrangement results in the deletion of exons 16-21. One of the breakpoints is within exon 21. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0035009-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.222_c.920+359del Note: The STK11 rearrangement is an intragenic deletion of exons 1-7. One of the breakpoints is within STK11 exon 1.
STAT3	0	MSKCC-DMP	P-0035013-T01-IM6	MSI2-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.2102-94:STAT3_chr17:g.55289920del Note: The STAT3 rearrangement is a deletion of exons 1-21. The functional significance is undetermined.
MSI2	0	MSKCC-DMP	P-0035013-T01-IM6	MSI2-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.2102-94:STAT3_chr17:g.55289920del Note: The STAT3 rearrangement is a deletion of exons 1-21. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0035021-T01-IM6	SQSTM1-RASA1 fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.1102+114:RASA1_chr5:g.179255094inv Note: The RASA1 rearrangement is an intragenic inversion of exons 8-25.
SQSTM1	0	MSKCC-DMP	P-0035021-T01-IM6	SQSTM1-RASA1 fusion	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.1102+114:RASA1_chr5:g.179255094inv Note: The RASA1 rearrangement is an intragenic inversion of exons 8-25.
ATM	0	MSKCC-DMP	P-0035076-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.7515+274_c.8986del Note: The ATM rearrangement is an intragenic deletion of exon 51-62. One of the breakpoints is within exon 62.
TUBB8	0	MSKCC-DMP	P-0035082-T01-IM6	ARID1B-TUBB8 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;p15.3)(chr6:g.57099972::chr10:g.124553) Note: The ARID1B rearrangement is a translocation with a breakpoint within exon 1.
ARID1B	0	MSKCC-DMP	P-0035082-T01-IM6	ARID1B-TUBB8 fusion	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;p15.3)(chr6:g.57099972::chr10:g.124553) Note: The ARID1B rearrangement is a translocation with a breakpoint within exon 1.
COL5A3	0	MSKCC-DMP	P-0035082-T01-IM6	DNMT1-COL5A3 fusion	yes	unknown		unknown	COL5A3 (NM_015719) - DNMT1 (NM_001379) rearrangement: c.1587+777:COL5A3_c.4459:DNMT1inv Note: The COL5A3 - DNMT1 rearrangement is an inversion that includes COL5A3 exons 1-16 and DNMT1 exons 37-40. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0035082-T01-IM6	DNMT1-COL5A3 fusion	yes	unknown		unknown	COL5A3 (NM_015719) - DNMT1 (NM_001379) rearrangement: c.1587+777:COL5A3_c.4459:DNMT1inv Note: The COL5A3 - DNMT1 rearrangement is an inversion that includes COL5A3 exons 1-16 and DNMT1 exons 37-40. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0035085-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20 - 29): c.667+7361:EML4_c.3173-685:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
EML4	0	MSKCC-DMP	P-0035085-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 fused to ALK exons 20 - 29): c.667+7361:EML4_c.3173-685:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK
BRD4	0	MSKCC-DMP	P-0034907-T01-IM6	OVAAL-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: t(1;19)(q25.3,p13.12)(chr1:g.180481230::chr19:g.15353735) Note: The BRD4 rearrangement is a translocation with a breakpoint in exon 14. Its functional significance is undetermined. Multiple rearrangements involving BRD4 were detected in this sample and a more complex rearrangement resulting in a BRD4 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
OVAAL	0	MSKCC-DMP	P-0034907-T01-IM6	OVAAL-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: t(1;19)(q25.3,p13.12)(chr1:g.180481230::chr19:g.15353735) Note: The BRD4 rearrangement is a translocation with a breakpoint in exon 14. Its functional significance is undetermined. Multiple rearrangements involving BRD4 were detected in this sample and a more complex rearrangement resulting in a BRD4 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MTOR	0	MSKCC-DMP	P-0034912-T01-IM6	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.6663-269_c.6823del Note: The MTOR rearrangement results in the deletion of exons 48-49. One of the breakpoints is within exon 49. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0034912-T01-IM6	CDKN2B-AS1-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.151-90:CDKN2Ap16INK4A_chr9:g.22060034del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-90:CDKN2Ap14ARF_chr9:g.22060034del Note: The CDKN2A rearrangement results in the deletion of exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms.
CDKN2B-AS1	0	MSKCC-DMP	P-0034912-T01-IM6	CDKN2B-AS1-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.151-90:CDKN2Ap16INK4A_chr9:g.22060034del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-90:CDKN2Ap14ARF_chr9:g.22060034del Note: The CDKN2A rearrangement results in the deletion of exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms.
TGFBR2	0	MSKCC-DMP	P-0034916-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.1330-104_c.1471+2213del Note: The TGFBR2 rearrangement is an intragenic deletion of exon 6. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0035075-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.993+650:TP53_chr17:g.7569521inv Note: The TP53 rearrangement is an inversion of exons 10-11.
SEC23A	0	MSKCC-DMP	P-0035163-T01-IM6	CD274-SEC23A fusion	yes	unknown		unknown	CD274 (NM_014143) rearrangement: t(9;14)(p24.1;q21.2)(chr9:g.5457150::chr14:g.39459204) Note: The CD274 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
CD274	0	MSKCC-DMP	P-0035163-T01-IM6	CD274-SEC23A fusion	yes	unknown		unknown	CD274 (NM_014143) rearrangement: t(9;14)(p24.1;q21.2)(chr9:g.5457150::chr14:g.39459204) Note: The CD274 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
NOVA1	0	MSKCC-DMP	P-0035167-T01-IM6	PRKD1-NOVA1 fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: c.1314+197:PRKD1_chr14:g.26379764inv Note: The PRKD1 rearrangement is an inversion of exons 9-18. The functional significance is undetermined.
PRKD1	0	MSKCC-DMP	P-0035167-T01-IM6	PRKD1-NOVA1 fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: c.1314+197:PRKD1_chr14:g.26379764inv Note: The PRKD1 rearrangement is an inversion of exons 9-18. The functional significance is undetermined.
AR	0	MSKCC-DMP	P-0035167-T01-IM6	CYSLTR1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2173+14:AR_chrX:g.77626841del Note: The AR rearrangement is a deletion of exons 5-8. The functional significance is undetermined.
CYSLTR1	0	MSKCC-DMP	P-0035167-T01-IM6	CYSLTR1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2173+14:AR_chrX:g.77626841del Note: The AR rearrangement is a deletion of exons 5-8. The functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0035211-T01-IM6	POLE-intragenic	yes	unknown		in frame	POLE (NM_006231) rearrangement: c.4290+5_c.6330+2503del Note: The POLE rearrangement is an intragenic deletion of exons  34-45.
FANCA	0	MSKCC-DMP	P-0035211-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.2249_c.2852+338del Note: The FANCA intragenic deletion involves exons 25-29. One of the breakpoints is within exon 25.
CDC73	0	MSKCC-DMP	P-0022166-T02-IM6	CDC73-intragenic	yes	unknown		in frame	CDC73 (NM_024529) rearrangement: c.132-1234_c.512+123dup Note: The CDC73 rearrangement results in the intragenic duplication of exons 2-6. The functional significance is undetermined.
KITLG	0	MSKCC-DMP	P-0022166-T02-IM6	ATM-KITLG fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: t(11;12)(q22.3;q21.32)(chr11:g.108224556::chr12:g.88926122) Note: The ATM rearrangement is a translocation with a breakpoint in exon 60. The functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0022166-T02-IM6	ATM-KITLG fusion	yes	unknown		unknown	ATM (NM_000051) rearrangement: t(11;12)(q22.3;q21.32)(chr11:g.108224556::chr12:g.88926122) Note: The ATM rearrangement is a translocation with a breakpoint in exon 60. The functional significance is undetermined.
GRIP1	0	MSKCC-DMP	P-0022861-T02-IM6	EPHA5-GRIP1 fusion	yes	unknown		unknown	EPHA5 (NM_004439) rearrangement: t(4;12)(q13.1;q14.3)(chr4:g.66201820::chr12:g.67086133) Note: The EPHA5 rearrangement is a translocation with a breakpoint within exon 16. The  functional significance is undetermined.
EPHA5	0	MSKCC-DMP	P-0022861-T02-IM6	EPHA5-GRIP1 fusion	yes	unknown		unknown	EPHA5 (NM_004439) rearrangement: t(4;12)(q13.1;q14.3)(chr4:g.66201820::chr12:g.67086133) Note: The EPHA5 rearrangement is a translocation with a breakpoint within exon 16. The  functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0022861-T02-IM6	PPM1H-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) - PPM1H (NM_020700) rearrangement: t(X;12)(q21.1;q14.2)(chrX:g.76907807::chr12:g.63147303) Note: The ATRX - PPM1H rearrangement is a translocation with breakpoints within ATRX exon 15 and PPM1H intron 4.
PPM1H	0	MSKCC-DMP	P-0022861-T02-IM6	PPM1H-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) - PPM1H (NM_020700) rearrangement: t(X;12)(q21.1;q14.2)(chrX:g.76907807::chr12:g.63147303) Note: The ATRX - PPM1H rearrangement is a translocation with breakpoints within ATRX exon 15 and PPM1H intron 4.
ALK	0	MSKCC-DMP	P-0034569-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused to ALK exons 20-29): c.2243-217:EML4_c.3173-120:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0034569-T02-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused to ALK exons 20-29): c.2243-217:EML4_c.3173-120:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
KIT	0	MSKCC-DMP	P-0035120-T01-IM6	SRP72-KIT fusion	yes	unknown		unknown	KIT (NM_000222) rearrangement: c.1775-34:KIT_chr4:g.57331639del Note: The KIT rearrangement results in the deletion of exons 12-21. One of the breakpoints is within exon 16. The functional significance is undetermined.
SRP72	0	MSKCC-DMP	P-0035120-T01-IM6	SRP72-KIT fusion	yes	unknown		unknown	KIT (NM_000222) rearrangement: c.1775-34:KIT_chr4:g.57331639del Note: The KIT rearrangement results in the deletion of exons 12-21. One of the breakpoints is within exon 16. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0035121-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4857:EML4_c.3172+944:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-6 and ALK exons 20-29. The fusion is predicted to be in-frame and involves the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0035121-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4857:EML4_c.3172+944:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-6 and ALK exons 20-29. The fusion is predicted to be in-frame and involves the kinase domain of ALK.
WHSC1	0	MSKCC-DMP	P-0035122-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.-29-1913_c.629inv Note: The WHSC1 rearrangement results in the inversion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0035219-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-1718_c.*1663del Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0035219-T01-IM6	NPR3-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: c.3994+58:DROSHA_chr5:g.32816052inv Note: The DROSHA rearrangement results in the inversion of exons 1-34. The functional significance is undetermined.
NPR3	0	MSKCC-DMP	P-0035219-T01-IM6	NPR3-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: c.3994+58:DROSHA_chr5:g.32816052inv Note: The DROSHA rearrangement results in the inversion of exons 1-34. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0035226-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.2515_c.*636inv Note: The CDH1 rearrangement results in the inversion of exon 16. One of the breakpoints is within exon 16.
SMAD2	0	MSKCC-DMP	P-0035226-T01-IM6	RERE-SMAD2 fusion	yes	unknown		out of frame	RERE (NM_001042681) - SMAD2 (NM_001003652) rearrangement: t(1;18)(p36.23;q21.1)(chr1:g.8565611::chr18:g.45368323) Note: The RERE - SMAD2 rearrangement is a translocation that results in the fusion of RERE exons 1-8 with SMAD2 exon 11. Multiple rearrangements involving SMAD2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RERE	0	MSKCC-DMP	P-0035226-T01-IM6	RERE-SMAD2 fusion	yes	unknown		out of frame	RERE (NM_001042681) - SMAD2 (NM_001003652) rearrangement: t(1;18)(p36.23;q21.1)(chr1:g.8565611::chr18:g.45368323) Note: The RERE - SMAD2 rearrangement is a translocation that results in the fusion of RERE exons 1-8 with SMAD2 exon 11. Multiple rearrangements involving SMAD2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
GNAS	0	MSKCC-DMP	P-0035226-T01-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: c.586-7_c.*4inv Note: The GNAS rearrangement results in the inversion of exons 8-13. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0035227-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.673-50_c.993+375inv Note: The TP53 rearrangement results in the inversion of exons 7-9.
RARA	0	MSKCC-DMP	P-0035240-T01-IM6	GJD3-RARA fusion	yes	unknown		unknown	RARA (NM_000964) rearrangement: c.469+54_chr17:g.38525291del Note: The RARA rearrangement is a deletion that includes RARA exons 5-9. The functional significance is undetermined.
GJD3	0	MSKCC-DMP	P-0035240-T01-IM6	GJD3-RARA fusion	yes	unknown		unknown	RARA (NM_000964) rearrangement: c.469+54_chr17:g.38525291del Note: The RARA rearrangement is a deletion that includes RARA exons 5-9. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0035270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2:NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-11):
TMPRSS2	0	MSKCC-DMP	P-0035270-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2:NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-11):
ALOX12-AS1	0	MSKCC-DMP	P-0035283-T01-IM6	ALOX12B-ALOX12-AS1 fusion	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.1654+71:ALOX12B_chr17:g.6914967del Note: The ALOX12B rearrangement results in the deletion of exons 13-15. The functional significance is undetermined.
ALOX12B	0	MSKCC-DMP	P-0035283-T01-IM6	ALOX12B-ALOX12-AS1 fusion	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.1654+71:ALOX12B_chr17:g.6914967del Note: The ALOX12B rearrangement results in the deletion of exons 13-15. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0035284-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+991:TMPRSS2_c.40-63565:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0035284-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+991:TMPRSS2_c.40-63565:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
MGA	0	MSKCC-DMP	P-0035373-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: chr15:g.41935537_c.7009-11del Note: The MGA rearrangement is an intragenic deletion of exons 1 to 17. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0035373-T01-IM6	PKD1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) Rearrangement: c.5195:TSC2_chr16:g.2161814del Note: The TSC2 rearrangement is a deletion of TSC2 exons 41 to 42. One of the breakpoints is within exon 41 of TSC2. The functional significance is undetermined.
PKD1	0	MSKCC-DMP	P-0035373-T01-IM6	PKD1-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) Rearrangement: c.5195:TSC2_chr16:g.2161814del Note: The TSC2 rearrangement is a deletion of TSC2 exons 41 to 42. One of the breakpoints is within exon 41 of TSC2. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0035373-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement: c.318_c.994-916del Note: The TP53 rearrangement is an intragenic deletion of exons 4 to 9. One of the breakpoints is within exon4. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0035373-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) Rearrangement: c.5278-2343_c.5588del Note: The BRCA1 rearrangement is an intragenic deletion of exons 20 to 23. One of the breakpoints is within exon 23. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0035373-T01-IM6	SETD2-intragenic	yes	unknown		in frame	SETD2 (NM_014159) Rearrangement: c.71+7073_c.5016-30del Note: The SETD2 rearrangement is an intragenic deletion of exons 2 to 8. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0035374-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) Rearrangement: c.-32-30_c.938-196del Note: The RAD21 rearrangement is an intragenic deletion of exons 1 to 8. The functional significance is undetermined.
PDZD8	0	MSKCC-DMP	P-0035375-T01-IM6	TAP1-PDZD8 fusion	yes	unknown		unknown	TAP1 (NM_000593) Rearrangement: t(6;10)(p21.32;q26.11)(chr6:g.32820038::chr10:g.119130943) Note: The TAP1 rearrangement is a translocation involving a breakpoint within intron 2 of TAP1. The functional significance is undetermined.
TAP1	0	MSKCC-DMP	P-0035375-T01-IM6	TAP1-PDZD8 fusion	yes	unknown		unknown	TAP1 (NM_000593) Rearrangement: t(6;10)(p21.32;q26.11)(chr6:g.32820038::chr10:g.119130943) Note: The TAP1 rearrangement is a translocation involving a breakpoint within intron 2 of TAP1. The functional significance is undetermined.
EIF3G	0	MSKCC-DMP	P-0035448-T01-IM6	DNMT1-EIF3G fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.4441+11:DNMT1_chr19:g.10228347inv Note: The DNMT1 rearrangement is an inversion of exons 37-40. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0035448-T01-IM6	DNMT1-EIF3G fusion	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.4441+11:DNMT1_chr19:g.10228347inv Note: The DNMT1 rearrangement is an inversion of exons 37-40. Its functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0035466-T01-IM6	ATP1A2-NTRK1 fusion	yes	unknown		unknown	ATP1A2 (NM_000702) - NTRK1 (NM_002529) rearrangement: c.2563+2:ATP1A2_c.1268:NTRK1dup Note: The ATP1A2 - NTRK1 rearrangement is a duplication that results in a fusion of ATP1A2 exons 1-18 to NTRK1 exons 11-17, which includes the kinase domain. One of the breakpoints is within NTRK1 exon 11.
ATP1A2	0	MSKCC-DMP	P-0035466-T01-IM6	ATP1A2-NTRK1 fusion	yes	unknown		unknown	ATP1A2 (NM_000702) - NTRK1 (NM_002529) rearrangement: c.2563+2:ATP1A2_c.1268:NTRK1dup Note: The ATP1A2 - NTRK1 rearrangement is a duplication that results in a fusion of ATP1A2 exons 1-18 to NTRK1 exons 11-17, which includes the kinase domain. One of the breakpoints is within NTRK1 exon 11.
SMAD4	0	MSKCC-DMP	P-0035473-T01-IM6	SMAD4-intragenic	yes	unknown		in frame	SMAD4 (NM_005359) rearrangement: c.667+761_c.1448-120del Note: The SMAD4 rearrangement is an intragenic deletion of exons 6-11.
KIF5B	0	MSKCC-DMP	P-0025100-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) and RET (NM_020975) Fusion (KIF5B exon 16 fused to RET exon 12): c.1726-2273:KIF5B_c.2137-788:RETinv Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0025100-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) and RET (NM_020975) Fusion (KIF5B exon 16 fused to RET exon 12): c.1726-2273:KIF5B_c.2137-788:RETinv Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the kinase domain of RET.
RAD21	0	MSKCC-DMP	P-0025100-T02-IM6	PARK2-RAD21 fusion	yes	unknown		in frame	PARK2 (NM_004562) - RAD21 (NM_006265) Rearrangement : t(6;8)(q26;q24.11)(chr6:g.162807539::chr8:g.117875650) Note: The PARK2 -RAD21 Rearrangement results in the fusion of exons 1-2 of PARK2 with exons 3-14 of RAD21. Its functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0025100-T02-IM6	PARK2-RAD21 fusion	yes	unknown		in frame	PARK2 (NM_004562) - RAD21 (NM_006265) Rearrangement : t(6;8)(q26;q24.11)(chr6:g.162807539::chr8:g.117875650) Note: The PARK2 -RAD21 Rearrangement results in the fusion of exons 1-2 of PARK2 with exons 3-14 of RAD21. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0035576-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2B (NM_004936)  - CDKN2A (NM_000077) Rearrangement: c.224:CDKN2B_c.153:CDKN2Adel Note: The CDKN2B - CDKN2A rearrangement results in the deletion of CDKN2B exon 2 and CDKN2A exons 1-2   . One of the breakpoints is within exon2. Its functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0035576-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2B (NM_004936)  - CDKN2A (NM_000077) Rearrangement: c.224:CDKN2B_c.153:CDKN2Adel Note: The CDKN2B - CDKN2A rearrangement results in the deletion of CDKN2B exon 2 and CDKN2A exons 1-2   . One of the breakpoints is within exon2. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0020945-T02-IM6	DOT1L-intragenic	yes	unknown		in frame	DOT1L (NM_032482) Rearrangement : c.1006-268_c.1558-159del Note: The DOT1L Rearrangement results in the intragenic deletion of exons 13-16. Its functional significance is undetermined.
IL1RL1	0	MSKCC-DMP	P-0020945-T02-IM6	MDM4-IL1RL1 fusion	yes	unknown		unknown	MDM4 (NM_002393) Rearrangement : t(1,2)(q12.1,q32.1)(chr1:g.204495627::chr2:g.102872474) Note : The MDM4 Rearrangement results in the possible truncation of MDM4. Its functional significance is undetermined.
MDM4	0	MSKCC-DMP	P-0020945-T02-IM6	MDM4-IL1RL1 fusion	yes	unknown		unknown	MDM4 (NM_002393) Rearrangement : t(1,2)(q12.1,q32.1)(chr1:g.204495627::chr2:g.102872474) Note : The MDM4 Rearrangement results in the possible truncation of MDM4. Its functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0022683-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.1228_c.1309-3020del Note: The SMAD4 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10. Its functional significance is undetermined.
POLRMT	0	MSKCC-DMP	P-0022683-T01-IM6	MAP2K2-POLRMT fusion	yes	unknown		in frame	POLRMT (NM_005035) - MAP2K2 (NM_030662) rearrangement: c.823-1775:POLRMT_c.415-84:MAP2K2dup Note: The POLRMT - MAP2K2 rearrangement is a duplication resulting in the fusion of POLRMT exons 1-4 with MAP2K2 exons 9-11 including the kinase domain. Its functional significance is undetermined.
MAP2K2	0	MSKCC-DMP	P-0022683-T01-IM6	MAP2K2-POLRMT fusion	yes	unknown		in frame	POLRMT (NM_005035) - MAP2K2 (NM_030662) rearrangement: c.823-1775:POLRMT_c.415-84:MAP2K2dup Note: The POLRMT - MAP2K2 rearrangement is a duplication resulting in the fusion of POLRMT exons 1-4 with MAP2K2 exons 9-11 including the kinase domain. Its functional significance is undetermined.
CBFB	0	MSKCC-DMP	P-0022871-T01-IM6	CBFB-intragenic	yes	unknown		unknown	CBFB (NM_022845) Rearrangement : c.-616_c.66del Note: The CBFB Rearrangement results in the intragenic deletion of exon1 of CBFB. Its functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0022936-T01-IM6	PEAR1-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.1847_chr1:g.156855832del Note: The NTRK1 rearrangement is a deletion of NTRK1 exons 15-17, including the kinase domain. The functional significance is undetermined.
PEAR1	0	MSKCC-DMP	P-0022936-T01-IM6	PEAR1-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.1847_chr1:g.156855832del Note: The NTRK1 rearrangement is a deletion of NTRK1 exons 15-17, including the kinase domain. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0022936-T01-IM6	NTRK1-STK11 fusion	yes	unknown		unknown	NTRK1 (NM_002529) - STK11 (NM_000455) rearrangement: t(1;19)(;)(chr1:g.56848955::chr19:g.204186) Note: The NTRK1 - STK11 rearrangement is a translocation with breakpoints within NTRK1 exon 15 and the promoter region of STK11. The rearrangement includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0022936-T01-IM6	NTRK1-STK11 fusion	yes	unknown		unknown	NTRK1 (NM_002529) - STK11 (NM_000455) rearrangement: t(1;19)(;)(chr1:g.56848955::chr19:g.204186) Note: The NTRK1 - STK11 rearrangement is a translocation with breakpoints within NTRK1 exon 15 and the promoter region of STK11. The rearrangement includes the kinase domain of NTRK1.
RHCG	0	MSKCC-DMP	P-0023215-T01-IM6	ETV6-RHCG fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.1)(chr12:g.12035854::chr15:g.90039073) Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 7-8. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0023215-T01-IM6	ETV6-RHCG fusion	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.1)(chr12:g.12035854::chr15:g.90039073) Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 7-8. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0023215-T01-IM6	LINC01239-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.194-36:CDKN2Ap14ARF_chr9:g.22734473inv Note: The CDKN2Ap14ARF rearrangement is an inversion of exon 1. The functional significance is undetermined.
LINC01239	0	MSKCC-DMP	P-0023215-T01-IM6	LINC01239-CDKN2Ap14ARF fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.194-36:CDKN2Ap14ARF_chr9:g.22734473inv Note: The CDKN2Ap14ARF rearrangement is an inversion of exon 1. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0023215-T01-IM6	LINC01239-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.151-36:CDKN2Ap16INK4A_chr9:g.22734473inv Note: The CDKN2Ap16INK4A rearrangement is an inversion of exon 1. The functional significance is undetermined.
LINC01239	0	MSKCC-DMP	P-0023215-T01-IM6	LINC01239-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.151-36:CDKN2Ap16INK4A_chr9:g.22734473inv Note: The CDKN2Ap16INK4A rearrangement is an inversion of exon 1. The functional significance is undetermined.
LOC100129055	0	MSKCC-DMP	P-0033407-T01-IM6	RET-LOC100129055 fusion	yes	unknown		unknown	RET (NM_020975) Rearrangement: c.2739:RET_chr10:g.38458902inv Note: The RET rearrangement is an inversion of exons 1 to 16. One of the breakpoints is within exon 16 of RET. The functional significance is undetermined.
RET	0	MSKCC-DMP	P-0033407-T01-IM6	RET-LOC100129055 fusion	yes	unknown		unknown	RET (NM_020975) Rearrangement: c.2739:RET_chr10:g.38458902inv Note: The RET rearrangement is an inversion of exons 1 to 16. One of the breakpoints is within exon 16 of RET. The functional significance is undetermined.
DAXX	0	MSKCC-DMP	P-0035502-T01-IM6	MLN-DAXX fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.1416:DAXX_chr6:g.33806571inv Note: The DAXX rearrangement is an inversion of exons 1-5. One of the breakpoints is within exon 5. Its functional significance is undetermined.
MLN	0	MSKCC-DMP	P-0035502-T01-IM6	MLN-DAXX fusion	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.1416:DAXX_chr6:g.33806571inv Note: The DAXX rearrangement is an inversion of exons 1-5. One of the breakpoints is within exon 5. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0035506-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-16831:ERG_c.55+1176:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exon 1 with TMPRSS2 exons 2-14. A more complex event resulting in a canonical TMPRSS2 - ERG fusion may be possible.
TMPRSS2	0	MSKCC-DMP	P-0035506-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-16831:ERG_c.55+1176:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exon 1 with TMPRSS2 exons 2-14. A more complex event resulting in a canonical TMPRSS2 - ERG fusion may be possible.
SMAD4	0	MSKCC-DMP	P-0035577-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: g.48535585_c.1023del Note: The SMAD4 rearrangement is an intragenic deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0035584-T01-IM6	MED13-CHEK2 fusion	yes	unknown		unknown	CHEK2 (NM_007194) Rearrangement: t(17;22)(q23.2;q12.1)(chr17:g.60026179::chr22:g.29115449) Note: The CHEK2 rearrangement is a translocation with the breakpoint in exon 5 CHEK2. The functional significance is undetermined.
MED13	0	MSKCC-DMP	P-0035584-T01-IM6	MED13-CHEK2 fusion	yes	unknown		unknown	CHEK2 (NM_007194) Rearrangement: t(17;22)(q23.2;q12.1)(chr17:g.60026179::chr22:g.29115449) Note: The CHEK2 rearrangement is a translocation with the breakpoint in exon 5 CHEK2. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0035586-T01-IM6	AAGAB-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.207-26812:SMAD3_chr15:g.67497181del Note: The SMAD3 rearrangement results in the deletion of SMAD3 exons 1-9.  One of the breakpoints is within exon 1 of SMAD3. The functional significance is undetermined.
AAGAB	0	MSKCC-DMP	P-0035586-T01-IM6	AAGAB-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.207-26812:SMAD3_chr15:g.67497181del Note: The SMAD3 rearrangement results in the deletion of SMAD3 exons 1-9.  One of the breakpoints is within exon 1 of SMAD3. The functional significance is undetermined.
NRG1	0	MSKCC-DMP	P-0004752-T03-IM6	CD74-NRG1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - NRG1 (NM_013956) fusion (CD74 exons 1-6 fused with NRG1 exons 6-13) : t(5;8)(5q32;8p12)(chr5:g.149782964::chr8:g.32549504) Note: The CD74 - NRG1 fusion is predicted to be in-frame.
CD74	0	MSKCC-DMP	P-0004752-T03-IM6	CD74-NRG1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - NRG1 (NM_013956) fusion (CD74 exons 1-6 fused with NRG1 exons 6-13) : t(5;8)(5q32;8p12)(chr5:g.149782964::chr8:g.32549504) Note: The CD74 - NRG1 fusion is predicted to be in-frame.
UBL3	0	MSKCC-DMP	P-0015376-T01-IM6	WHSC1L1-UBL3 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: t(8;13)(p11.23;q12.3)(chr8:g.38175374::chr13:g.30470955) Note: The WHSC1L1 rearrangement is a translocation that may result in a truncation of exons 10-24. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0015376-T01-IM6	WHSC1L1-UBL3 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: t(8;13)(p11.23;q12.3)(chr8:g.38175374::chr13:g.30470955) Note: The WHSC1L1 rearrangement is a translocation that may result in a truncation of exons 10-24. The functional significance is undetermined.
IGF2	0	MSKCC-DMP	P-0021497-T01-IM6	ASCL2-IGF2 fusion	yes	unknown		unknown	IGF2 (NM_001127598) rearrangement: c.61:IGF2_chr11:g.2283381inv Note: The IGF2 rearrangement is an inversion with a breakpoint in exon 2. This structural variant occurs along with another distinct rearrangement in IGF2, suggesting a complex rearrangement. The functional significance is undetermined.
ASCL2	0	MSKCC-DMP	P-0021497-T01-IM6	ASCL2-IGF2 fusion	yes	unknown		unknown	IGF2 (NM_001127598) rearrangement: c.61:IGF2_chr11:g.2283381inv Note: The IGF2 rearrangement is an inversion with a breakpoint in exon 2. This structural variant occurs along with another distinct rearrangement in IGF2, suggesting a complex rearrangement. The functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0025764-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) Rearrangement : c.-162-27000_c.2141del Note: The STAG2 Rearrangement results in the duplication of exons 1 -22 of STAG2. One of the breakpoints is within exon22. Its functional significance is undetermined.
URAD	0	MSKCC-DMP	P-0025791-T03-IM6	FLT3-URAD fusion	yes	unknown		unknown	URAD (NM_001105577) - FLT3 (NM_004119) Rearrangement : c.175+4829:URAD_c.1562:FLT3del Note: The URAD-FLT3 Rearrangement results in the fusion of exon1 of URAD with exon 12 of FLT3. The breakpoint in FLT3 is within exon12. Its functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0025791-T03-IM6	FLT3-URAD fusion	yes	unknown		unknown	URAD (NM_001105577) - FLT3 (NM_004119) Rearrangement : c.175+4829:URAD_c.1562:FLT3del Note: The URAD-FLT3 Rearrangement results in the fusion of exon1 of URAD with exon 12 of FLT3. The breakpoint in FLT3 is within exon12. Its functional significance is undetermined.
PPP1R14B	0	MSKCC-DMP	P-0027309-T03-IM6	RPS6KA4-PPP1R14B fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement: c.1958-26:RPS6KA4_chr11:g.64015463del Note: The RPS6KA4 rearrangement is a deletion of exons 1-16.
RPS6KA4	0	MSKCC-DMP	P-0027309-T03-IM6	RPS6KA4-PPP1R14B fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement: c.1958-26:RPS6KA4_chr11:g.64015463del Note: The RPS6KA4 rearrangement is a deletion of exons 1-16.
PARK2	0	MSKCC-DMP	P-0029928-T01-IM6	PARK2-intragenic	yes	unknown		in frame	PARK2 (NM_004562) rearrangement: c.413-24781_c.871+36638del Note: The PARK2 rearrangement is an intragenic deletion of exons 4-7. Its functional significance is undetermined
KMT2C	0	MSKCC-DMP	P-0030526-T01-IM6	KMT2C-intragenic	yes	unknown		in frame	KMT2C (NM_170606) rearrangement: c.251-9913_c.4541-31del Note: The KMT2C rearrangement is an intragenic deletion of exons 3-30.
KDM6A	0	MSKCC-DMP	P-0030526-T01-IM6	KDM6A-intragenic	yes	unknown		in frame	KDM6A (NM_021140) rearrangement: c.1194+7_c.1425+613del Note: The KDM6A rearrangement is an intragenic deletion of exons 13-14.
RB1	0	MSKCC-DMP	P-0031357-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.2160_c.2713+901del Note: The RB1 rearrangement results in the deletion of exons 21-26. One of the breakpoints is within exon 21.
NOS1AP	0	MSKCC-DMP	P-0034908-T01-IM6	DDR2-NOS1AP fusion	yes	unknown		out of frame	DDR2 (NM_006182) - NOS1AP (NM_014697) rearrangement: c.565+75:DDR2_c.453+397:NOS1APdup Note: The DDR2 - NOS1AP rearrangement is a duplication which results in the fusion of DDR2 exons 1-6 with NOS1AP exons 6-10. Its functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0034908-T01-IM6	DDR2-NOS1AP fusion	yes	unknown		out of frame	DDR2 (NM_006182) - NOS1AP (NM_014697) rearrangement: c.565+75:DDR2_c.453+397:NOS1APdup Note: The DDR2 - NOS1AP rearrangement is a duplication which results in the fusion of DDR2 exons 1-6 with NOS1AP exons 6-10. Its functional significance is undetermined.
CAMK2A	0	MSKCC-DMP	P-0035570-T01-IM6	CD74-CAMK2A fusion	yes	unknown		out of frame	CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup
CD74	0	MSKCC-DMP	P-0035570-T01-IM6	CD74-CAMK2A fusion	yes	unknown		out of frame	CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup
TMPRSS2	0	MSKCC-DMP	P-0001768-T02-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.127-734_c.349+1172del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3. The possibility of a more complex rearrangement resulting in a TMPRSS2 - ERG fusion cannot be excluded.The functional significance is undetermined.
VEGFA	0	MSKCC-DMP	P-0001768-T02-IM6	RPS6KC1-VEGFA fusion	yes	unknown		unknown	VEGFA (NM_001171623) - RPS6KC1 (NM_012424) rearrangement: t(1;6)(q32.3;p21.1)(chr1:g.213285654::chr6:g.43741921) Note: The VEGFA - RPS6KC1 rearrangement is a translocation with breakpoints within VEGFA intron 1 and RPS6KC1 intron 4. The functional significance is undetermined.
RPS6KC1	0	MSKCC-DMP	P-0001768-T02-IM6	RPS6KC1-VEGFA fusion	yes	unknown		unknown	VEGFA (NM_001171623) - RPS6KC1 (NM_012424) rearrangement: t(1;6)(q32.3;p21.1)(chr1:g.213285654::chr6:g.43741921) Note: The VEGFA - RPS6KC1 rearrangement is a translocation with breakpoints within VEGFA intron 1 and RPS6KC1 intron 4. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0002334-T02-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.2675_c.-13+2179del Note: The PBRM1 rearrangement results in the deletion of the 5' UTR and exons 1-18. One of the breakpoints is within exon 18. The functional significance is undetermined.
HGF	0	MSKCC-DMP	P-0002334-T02-IM6	HGF-intragenic	yes	unknown		unknown	HGF (NM_000601) rearrangement: c.1271+90_c.1168+2117inv Note: The HGF rearrangement results in the inversion of exon 10. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0010920-T02-IM6	SMARCC1-SETD2 fusion	yes	unknown		unknown	SMARCC1 (NM_003074) - SETD2 (NM_014159) rearrangement: c.647-1684:SMARCC1_c.1125:SETD1del Note: The SMARCC1 - SETD2 rearrangement results in the fusion of SMARCC1 exons 1-6 with SETD2 exons 3-31. One of the breakpoints is within SETD2 exon 3. Its functional significance is undetermined.
SMARCC1	0	MSKCC-DMP	P-0010920-T02-IM6	SMARCC1-SETD2 fusion	yes	unknown		unknown	SMARCC1 (NM_003074) - SETD2 (NM_014159) rearrangement: c.647-1684:SMARCC1_c.1125:SETD1del Note: The SMARCC1 - SETD2 rearrangement results in the fusion of SMARCC1 exons 1-6 with SETD2 exons 3-31. One of the breakpoints is within SETD2 exon 3. Its functional significance is undetermined.
DUSP21	0	MSKCC-DMP	P-0019077-T02-IM6	KDM6A-DUSP21 fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.44666338_c.577del Note: THe KDM6A rearrangement is a deletion which includes KDM6A exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0019077-T02-IM6	KDM6A-DUSP21 fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: chrX:g.44666338_c.577del Note: THe KDM6A rearrangement is a deletion which includes KDM6A exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0022744-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5437+94_c.6008inv Note: The KMT2B rearrangement results in the inversion of exons 27-28. One of the breakpoints is within exon 28. Its functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0022746-T01-IM6	BRCA1-intragenic	yes	unknown		out of frame	BRCA1 (NM_007294) rearrangement: c.593+41_c.670+125del Note: The BRCA1 rearrangement is an intragenic deletion of exon 9. Its functional significance is undetermined.
PDZRN4	0	MSKCC-DMP	P-0022781-T01-IM6	FGFR2-PDZRN4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - PDZRN4 (NM_001164595) rearrangement: t(6;10)(q23.1;q26.1)(chr6:g.130408449::chr10:g.123239680) Note: The FGFR2 - PDZRN4 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-17 with PDZRN4 exons 4-10. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0022781-T01-IM6	FGFR2-PDZRN4 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - PDZRN4 (NM_001164595) rearrangement: t(6;10)(q23.1;q26.1)(chr6:g.130408449::chr10:g.123239680) Note: The FGFR2 - PDZRN4 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-17 with PDZRN4 exons 4-10. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
CMIP	0	MSKCC-DMP	P-0022781-T01-IM6	PLCG2-CMIP fusion	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: c.1409:PLCG2_chr16:g.81726043inv Note: The PLCG2 rearrangement is an inversion of exons 15-33. One of the breakpoints is within exon 15. The functional significance is undetermined.
PLCG2	0	MSKCC-DMP	P-0022781-T01-IM6	PLCG2-CMIP fusion	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: c.1409:PLCG2_chr16:g.81726043inv Note: The PLCG2 rearrangement is an inversion of exons 15-33. One of the breakpoints is within exon 15. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0022782-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused in-frame with ERG exons 2-10): c.56-4767:TMRPSS2_c.18+9054:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0022782-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused in-frame with ERG exons 2-10): c.56-4767:TMRPSS2_c.18+9054:ERGdel
FANCA	0	MSKCC-DMP	P-0023037-T01-IM6	LOC101927459-FANCA fusion	yes	unknown		unknown	FANCA (NM_000135) Rearrangement : t(8,16)(q23.2,q24.2)(chr8:g.111811259::chr16:g.89882953) Note: The FANCA  Rearrangement results in the possible truncation of FANCA. The breakpoint in FANCA is within exon1. Its functional significance is undetermined.
LOC101927459	0	MSKCC-DMP	P-0023037-T01-IM6	LOC101927459-FANCA fusion	yes	unknown		unknown	FANCA (NM_000135) Rearrangement : t(8,16)(q23.2,q24.2)(chr8:g.111811259::chr16:g.89882953) Note: The FANCA  Rearrangement results in the possible truncation of FANCA. The breakpoint in FANCA is within exon1. Its functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0023385-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.-128+5079_c.1308+55dup Note: The SMAD4 rearrangement is a duplication with breakpoints in the 5UTR region and intron 10. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0024048-T01-IM6	EPC2-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement : c.1190-2641:PAX8_chr2:g.149285052del Note: The PAX8 Rearrangement results in the deletion of exons 1-10 of PAX8. Its functional significance is undetermined.
EPC2	0	MSKCC-DMP	P-0024048-T01-IM6	EPC2-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement : c.1190-2641:PAX8_chr2:g.149285052del Note: The PAX8 Rearrangement results in the deletion of exons 1-10 of PAX8. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0024117-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2758_c.3169+795inv Note: The BRD4 rearrangement is an intragenic inversion of exon 14. One of the breakpoints is within exon 14. Its functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0024569-T01-IM6	TP53BP1-intragenic	yes	unknown		in frame	TP53BP1 (NM_001141980) rearrangement: c.4682-1277_c.5746+55dup Note: The TP53BP1 rearrangement is an intragenic duplication of exons 22-27. The functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0024569-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.2459_c.2492+890del Note: The BRIP1 rearrangement is an intragenic deletion of exon 17. One of the breakpoints is within exon 17. The functional significance is undetermined.
GRID1	0	MSKCC-DMP	P-0024640-T01-IM6	BMPR1A-GRID1 fusion	yes	unknown		unknown	BMPR1A (NM_004329) rearrangement: chr10:g.88017504_c.1525:BMPR1Adel Note: The BMPR1A rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
BMPR1A	0	MSKCC-DMP	P-0024640-T01-IM6	BMPR1A-GRID1 fusion	yes	unknown		unknown	BMPR1A (NM_004329) rearrangement: chr10:g.88017504_c.1525:BMPR1Adel Note: The BMPR1A rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0024898-T01-IM6	SLC45A3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(21;1)(q22.3;q32.1)(chr21:42873896::chr1:205610270) The TMPRSS2 rearrangement is a translocation involving TMPRSS2 exon 1. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SLC45A3	0	MSKCC-DMP	P-0024898-T01-IM6	SLC45A3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : t(21;1)(q22.3;q32.1)(chr21:42873896::chr1:205610270) The TMPRSS2 rearrangement is a translocation involving TMPRSS2 exon 1. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ATRX	0	MSKCC-DMP	P-0025437-T02-IM6	BNC2-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(X;9)(p22.3;q21.1)(chrX:g.76845379::chr9:g.16558821) Note: The ATRX rearrangement is a translocation with a breakpoint within exon 27.
BNC2	0	MSKCC-DMP	P-0025437-T02-IM6	BNC2-ATRX fusion	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(X;9)(p22.3;q21.1)(chrX:g.76845379::chr9:g.16558821) Note: The ATRX rearrangement is a translocation with a breakpoint within exon 27.
PIK3C3	0	MSKCC-DMP	P-0028519-T01-IM6	PIK3C3-intragenic	yes	unknown		unknown	PIK3C3 (NM_002647) rearrangement: c.1484+1813_c.1772dup Note: The PIK3C3 rearrangement is an intragenic duplication of exons 14-16. One of the breakpoints is within exon 16. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0030702-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.-29+2212_c.532dup Note: The TP53 rearrangement is an intragenic duplication of exons 1-5. One of the breakpoints is within exon 5. Its functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0032459-T01-IM6	ATXN7L3B-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) Rearrangement: c.1276+90:NAB2_chr12:g.74965141inv Note: The NAB2 rearrangement results in the inversion of exons 6-7. Multiple rearrangements involving NAB2 were detected in this sample and a more complex rearrangement resulting in a NAB2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ATXN7L3B	0	MSKCC-DMP	P-0032459-T01-IM6	ATXN7L3B-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) Rearrangement: c.1276+90:NAB2_chr12:g.74965141inv Note: The NAB2 rearrangement results in the inversion of exons 6-7. Multiple rearrangements involving NAB2 were detected in this sample and a more complex rearrangement resulting in a NAB2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PPP4R2	0	MSKCC-DMP	P-0034038-T01-IM6	PPP4R2-intragenic	yes	unknown		unknown	PPP4R2 (NM_174907) Rearrangement: c.116+22240_c.208del Note: The PPP4R2 rearrangement is an intragenic deletion of exon3. One of the breakpoint is within exon3 of PPP4R2. Its functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0035551-T01-IM6	LOC101927851-TERT fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :t(1;5)(q34.2;q31.3)(chr1:g.235010251::chr5:g.1295257) Note: The TERT Rearrangement is a translocation event with a breakpoint in the promoter region of TERT. Its functional significance is undetermined.
LOC101927851	0	MSKCC-DMP	P-0035551-T01-IM6	LOC101927851-TERT fusion	yes	unknown		unknown	TERT (NM_198253) Rearrangement :t(1;5)(q34.2;q31.3)(chr1:g.235010251::chr5:g.1295257) Note: The TERT Rearrangement is a translocation event with a breakpoint in the promoter region of TERT. Its functional significance is undetermined.
OSMR	0	MSKCC-DMP	P-0035551-T01-IM6	RICTOR-OSMR fusion	yes	unknown		unknown	RICTOR (NM_152756) Rearrangement : c.1715+55_c.-13-9670:OSMRdel Note: The RICTOR Rearrangement results in the deletion of exons 1-19 of RICTOR. Its functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0035551-T01-IM6	RICTOR-OSMR fusion	yes	unknown		unknown	RICTOR (NM_152756) Rearrangement : c.1715+55_c.-13-9670:OSMRdel Note: The RICTOR Rearrangement results in the deletion of exons 1-19 of RICTOR. Its functional significance is undetermined.
MIR548AI	0	MSKCC-DMP	P-0035710-T01-IM6	PRKD1-MIR548AI fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: chr14:g.29876388_c.354del Note: The PRKD1 rearrangement is a deletion that includes PRKD1 exons 2-18. One of the breakpoints is within exon 2. The functional significance is undetermined.
PRKD1	0	MSKCC-DMP	P-0035710-T01-IM6	PRKD1-MIR548AI fusion	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: chr14:g.29876388_c.354del Note: The PRKD1 rearrangement is a deletion that includes PRKD1 exons 2-18. One of the breakpoints is within exon 2. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0035712-T01-IM6	H6PD-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(1;2)(p36.22;p23.2)(chr1:g.9314150::chr2:g.29462508) Note: The ALK rearrangement is a translocation with a breakpoint within ALK intron 13. The functional significance is undetermined.
H6PD	0	MSKCC-DMP	P-0035712-T01-IM6	H6PD-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(1;2)(p36.22;p23.2)(chr1:g.9314150::chr2:g.29462508) Note: The ALK rearrangement is a translocation with a breakpoint within ALK intron 13. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0035736-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) Rearrangement : c.97-17_c.560-23del Note: The TP53  Rearrangement results in the intragenic deletion of exons 4-5 of TP53. Its functional significance is undetermined.
insuf	0	MSKCC-DMP	P-0003357-T02-IM6	insuf-intragenic - Archer	yes	unknown		unknown	RNA insufficient code 1 Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Not Performed
KIAA1468	0	MSKCC-DMP	P-0004094-T02-IM6	RET-KIAA1468 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIAA1468-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIAA1468 Exon10 (NM_020854) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180059 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0004094-T02-IM6	RET-KIAA1468 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIAA1468-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIAA1468 Exon10 (NM_020854) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180059 Macro-dissection: Unknown
CD74	0	MSKCC-DMP	P-0004752-T03-IM6	NRG1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170099 Macro-dissection: Not Performed
NRG1	0	MSKCC-DMP	P-0004752-T03-IM6	NRG1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170099 Macro-dissection: Not Performed
CCDC6	0	MSKCC-DMP	P-0007322-T02-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon2 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180099 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0007322-T02-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon2 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180099 Macro-dissection: Unknown
MKRN1	0	MSKCC-DMP	P-0008083-T03-IM6	BRAF-MKRN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MKRN1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes MKRN1 Exon3 (NM_013446) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170105 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0008083-T03-IM6	BRAF-MKRN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MKRN1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes MKRN1 Exon3 (NM_013446) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170105 Macro-dissection: Not Performed
CCDC6	0	MSKCC-DMP	P-0008504-T03-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon8 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170138 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0008504-T03-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon8 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170138 Macro-dissection: Performed
CASP8	0	MSKCC-DMP	P-0010465-T01-IM5	ETV6-CASP8 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CASP8-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes CASP8 Exon9 (NM_001080125) and ETV6 Exon6 (NM_001987). Lab Notes Run Number: ArcherV2-CLIN-20170027 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0010465-T01-IM5	ETV6-CASP8 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CASP8-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes CASP8 Exon9 (NM_001080125) and ETV6 Exon6 (NM_001987). Lab Notes Run Number: ArcherV2-CLIN-20170027 Macro-dissection: Performed
MKRN1	0	MSKCC-DMP	P-0013536-T01-IM5	BRAF-MKRN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MKRN1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes MKRN1 Exon3 (NM_013446) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160033 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0013536-T01-IM5	BRAF-MKRN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MKRN1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes MKRN1 Exon3 (NM_013446) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160033 Macro-dissection: Not Performed
RBPMS	0	MSKCC-DMP	P-0013859-T01-IM5	NTRK3-RBPMS fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: RBPMS-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes RBPM3 Exon5 (NM_001008710) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170103 Macro-dissection: Performed
NTRK3	0	MSKCC-DMP	P-0013859-T01-IM5	NTRK3-RBPMS fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: RBPMS-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes RBPM3 Exon5 (NM_001008710) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170103 Macro-dissection: Performed
SLC34A2	0	MSKCC-DMP	P-0014177-T01-IM5	ROS1-SLC34A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC34A2-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC34A2 Exon13 (NM_006424) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170105 Macro-dissection: Not Performed
ROS1	0	MSKCC-DMP	P-0014177-T01-IM5	ROS1-SLC34A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC34A2-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC34A2 Exon13 (NM_006424) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170105 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0014524-T03-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20170082 Macro-dissection: Performed
CTRC	0	MSKCC-DMP	P-0014859-T01-IM6	NTRK1-CTRC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CTRC-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes CTRC Exon1 (NM_007272) and NTRK1 Exon8 (NM_002529). Lab Notes Run Number: ArcherV1-CLIN-20160051 Macro-dissection: Performed
NTRK1	0	MSKCC-DMP	P-0014859-T01-IM6	NTRK1-CTRC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CTRC-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes CTRC Exon1 (NM_007272) and NTRK1 Exon8 (NM_002529). Lab Notes Run Number: ArcherV1-CLIN-20160051 Macro-dissection: Performed
SLC3A2	0	MSKCC-DMP	P-0014968-T05-IM6	NRG1-SLC3A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC3A2-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC3A2 Exon5 (NM_002394) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170112 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0014968-T05-IM6	NRG1-SLC3A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC3A2-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC3A2 Exon5 (NM_002394) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170112 Macro-dissection: Unknown
CDK5RAP2	0	MSKCC-DMP	P-0014969-T01-IM6	BRAF-CDK5RAP2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CDK5RAP2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CDK5RAP2 Exon12 (NM_018249) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160052 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0014969-T01-IM6	BRAF-CDK5RAP2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CDK5RAP2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CDK5RAP2 Exon12 (NM_018249) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160052 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0015016-T01-IM6	LOH12CR1-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-LOH12CR1 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon1 (NM_001987) and LOH12CR1 Exon4 (NM_058169). http://www.nature.com/nbt/journal/v33/n3/pdf/nbt.3080.pdf  Lab Notes Run Number: ArcherV1-CLIN-20160053 Macro-dissection: Performed
LOH12CR1	0	MSKCC-DMP	P-0015016-T01-IM6	LOH12CR1-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-LOH12CR1 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon1 (NM_001987) and LOH12CR1 Exon4 (NM_058169). http://www.nature.com/nbt/journal/v33/n3/pdf/nbt.3080.pdf  Lab Notes Run Number: ArcherV1-CLIN-20160053 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0015432-T01-IM6	CAT-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-CAT fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and CAT Exon2 (NM_001752). Lab Notes Run Number: ArcherV1-CLIN-20160059 Macro-dissection: Unknown
CAT	0	MSKCC-DMP	P-0015432-T01-IM6	CAT-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-CAT fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and CAT Exon2 (NM_001752). Lab Notes Run Number: ArcherV1-CLIN-20160059 Macro-dissection: Unknown
IGF1R	0	MSKCC-DMP	P-0015494-T01-IM6	ROS1-IGF1R fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: IGF1R-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes IGF1R Exon15 (NM_000875) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV1-CLIN-20160059 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0015494-T01-IM6	ROS1-IGF1R fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: IGF1R-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes IGF1R Exon15 (NM_000875) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV1-CLIN-20160059 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0015839-T01-IM6	DZANK1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-DZANK1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and DZANK1 Exon11 (NM_001099407). Lab Notes Run Number: ArcherV1-CLIN-20160064 Macro-dissection: Performed
DZANK1	0	MSKCC-DMP	P-0015839-T01-IM6	DZANK1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-DZANK1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and DZANK1 Exon11 (NM_001099407). Lab Notes Run Number: ArcherV1-CLIN-20160064 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0015921-T03-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon7 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170103 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0015921-T03-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon7 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170103 Macro-dissection: Performed
CCDC6	0	MSKCC-DMP	P-0016038-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV1-CLIN-20160066 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0016038-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV1-CLIN-20160066 Macro-dissection: Not Performed
repeat	0	MSKCC-DMP	P-0016175-T01-IM6	repeat-intragenic - Archer	yes	unknown		unknown	repeated on CLIN2017001 Lab Notes Run Number: ArcherV1-CLIN-20160070 Macro-dissection: Not Performed
SLC45A3	0	MSKCC-DMP	P-0016313-T01-IM6	BRAF-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC45A3-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160071 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0016313-T01-IM6	BRAF-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC45A3-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV1-CLIN-20160071 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0016398-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR AN ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: Transcript with MET Exon 14 skipping Detected   Lab Notes Run Number: ArcherV1-CLIN-20160072 Macro-dissection: Performed
MRPS18B	0	MSKCC-DMP	P-0016729-T01-IM6	PDGFB-MRPS18B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MRPS18B-PDGFB fusion. Note: The rearrangement is an in-frame fusion between genes MRPS18B Exon4 (NM_014046) and PDGFB Exon2 (NM_002608). Lab Notes Run Number: ArcherV1-CLIN-20170004 Macro-dissection: Performed
PDGFB	0	MSKCC-DMP	P-0016729-T01-IM6	PDGFB-MRPS18B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MRPS18B-PDGFB fusion. Note: The rearrangement is an in-frame fusion between genes MRPS18B Exon4 (NM_014046) and PDGFB Exon2 (NM_002608). Lab Notes Run Number: ArcherV1-CLIN-20170004 Macro-dissection: Performed
MIR940	0	MSKCC-DMP	P-0016795-T01-IM6	ETV6-MIR940 fusion - Archer	yes	unknown		unknown	Also picked by IMPACT POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MIR940-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes MIR940 Exon1 (NR_030636) and ETV6 Exon6 (NM_001987). Lab Notes Run Number: ArcherV1-CLIN-20170005 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0016795-T01-IM6	ETV6-MIR940 fusion - Archer	yes	unknown		unknown	Also picked by IMPACT POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MIR940-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes MIR940 Exon1 (NR_030636) and ETV6 Exon6 (NM_001987). Lab Notes Run Number: ArcherV1-CLIN-20170005 Macro-dissection: Performed
insufficient	0	MSKCC-DMP	P-0016903-T01-IM6	insufficient-intragenic - Archer	yes	unknown		unknown	Archer Solid Insuf1    Lab Notes Run Number: ArcherV1-CLIN-20170008 Macro-dissection: Unknown
FGFR3	0	MSKCC-DMP	P-0017444-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon11 (NM_006342). Lab Notes Run Number: ArcherV2-CLIN-20170015 Macro-dissection: Not Performed
TACC3	0	MSKCC-DMP	P-0017444-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon11 (NM_006342). Lab Notes Run Number: ArcherV2-CLIN-20170015 Macro-dissection: Not Performed
DNAJB1	0	MSKCC-DMP	P-0017715-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170069 Macro-dissection: Not Performed
PRKACA	0	MSKCC-DMP	P-0017715-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170069 Macro-dissection: Not Performed
SLC34A2	0	MSKCC-DMP	P-0017752-T01-IM6	ROS1-SLC34A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC34A2-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC34A2 Exon13 (NM_006424) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170019 Macro-dissection: Not Performed
ROS1	0	MSKCC-DMP	P-0017752-T01-IM6	ROS1-SLC34A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC34A2-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC34A2 Exon13 (NM_006424) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170019 Macro-dissection: Not Performed
KIF5B	0	MSKCC-DMP	P-0018069-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon16 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0018069-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon16 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
GPRC5C	0	MSKCC-DMP	P-0018243-T01-IM6	MET-GPRC5C fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GPRC5C-MET fusion. Note: The rearrangement is an in-frame fusion between genes GPRC5C Exon2 (NM_018653) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0018243-T01-IM6	MET-GPRC5C fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GPRC5C-MET fusion. Note: The rearrangement is an in-frame fusion between genes GPRC5C Exon2 (NM_018653) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
ROCK1	0	MSKCC-DMP	P-0018378-T01-IM6	NRG1-ROCK1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ROCK1-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes ROCK1 Exon2 (NM_005406) and NRG1 Exon2 (NM_013956). This fusion was detected with low read support. The functional significance of this fusion unclear.  Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
NRG1	0	MSKCC-DMP	P-0018378-T01-IM6	NRG1-ROCK1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ROCK1-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes ROCK1 Exon2 (NM_005406) and NRG1 Exon2 (NM_013956). This fusion was detected with low read support. The functional significance of this fusion unclear.  Lab Notes Run Number: ArcherV2-CLIN-20170022 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0018524-T01-IM6	BRAF-TMPRSS2 fusion - Archer	yes	unknown		unknown	SAMPLE NEEDS A NOTE about low sample quality and low sequencing coverage. POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170024 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0018524-T01-IM6	BRAF-TMPRSS2 fusion - Archer	yes	unknown		unknown	SAMPLE NEEDS A NOTE about low sample quality and low sequencing coverage. POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170024 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0018573-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170024 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0018573-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170024 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0018812-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170028 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0018812-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170028 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0018902-T01-IM6	ITGA4-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ITGA4 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon2 (NM_001987) and ITGA4 Exon11 (NM_000885). Lab Notes Run Number: ArcherV2-CLIN-20170030 Macro-dissection: Performed
ITGA4	0	MSKCC-DMP	P-0018902-T01-IM6	ITGA4-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ITGA4 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon2 (NM_001987) and ITGA4 Exon11 (NM_000885). Lab Notes Run Number: ArcherV2-CLIN-20170030 Macro-dissection: Performed
DNAJB1	0	MSKCC-DMP	P-0019283-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170036 Macro-dissection: Not Performed
PRKACA	0	MSKCC-DMP	P-0019283-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170036 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0019564-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20170040 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0019588-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20170041 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0019663-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656 and ERG Exon4 (NM_004449). NOte-low read support. Lab Notes Run Number: ArcherV2-CLIN-20170040 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0019663-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656 and ERG Exon4 (NM_004449). NOte-low read support. Lab Notes Run Number: ArcherV2-CLIN-20170040 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0019836-T01-IM6	ANKS1B-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ANKS1B fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and ANKS1B Exon13 (NM_152788). Lab Notes Run Number: ArcherV2-CLIN-20170043 Macro-dissection: Not Performed
ANKS1B	0	MSKCC-DMP	P-0019836-T01-IM6	ANKS1B-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ANKS1B fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and ANKS1B Exon13 (NM_152788). Lab Notes Run Number: ArcherV2-CLIN-20170043 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0019840-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170043 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0019840-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170043 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0020013-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170047 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0020013-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170047 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0020041-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon15 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20170047 Macro-dissection: Not Performed
NFIB	0	MSKCC-DMP	P-0020041-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon15 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20170047 Macro-dissection: Not Performed
DNAJB1	0	MSKCC-DMP	P-0020620-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170051 Macro-dissection: Not Performed
PRKACA	0	MSKCC-DMP	P-0020620-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20170051 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0021025-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0021025-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0021031-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon8 (NM_001130173) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV2-CLIN-20170059 Macro-dissection: Not Performed
NFIB	0	MSKCC-DMP	P-0021031-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon8 (NM_001130173) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV2-CLIN-20170059 Macro-dissection: Not Performed
STRN	0	MSKCC-DMP	P-0021124-T01-IM6	NTRK2-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: STRN-NTRK2 fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and NTRK2 Exon16 (NM_006180). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Unknown
NTRK2	0	MSKCC-DMP	P-0021124-T01-IM6	NTRK2-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: STRN-NTRK2 fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and NTRK2 Exon16 (NM_006180). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Unknown
F11	0	MSKCC-DMP	P-0021262-T01-IM6	NTRK1-F11 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: F11-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes F11 Exon4 (NM_000128) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Not Performed
NTRK1	0	MSKCC-DMP	P-0021262-T01-IM6	NTRK1-F11 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: F11-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes F11 Exon4 (NM_000128) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0021282-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	See Results of M17-20664 Lab Notes Run Number: ArcherV2-CLIN-20170066 Macro-dissection: Unknown
ETV4	0	MSKCC-DMP	P-0021282-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	See Results of M17-20664 Lab Notes Run Number: ArcherV2-CLIN-20170066 Macro-dissection: Unknown
ABCC1	0	MSKCC-DMP	P-0021458-T01-IM6	BRAF-ABCC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ABCC1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes ABCC1 Exon5 (NM_004996) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170066 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0021458-T01-IM6	BRAF-ABCC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ABCC1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes ABCC1 Exon5 (NM_004996) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170066 Macro-dissection: Performed
TRIM33	0	MSKCC-DMP	P-0021469-T01-IM6	BRAF-TRIM33 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TRIM33-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM33 Exon11 (NM_015906) and BRAF Exon11 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0021469-T01-IM6	BRAF-TRIM33 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TRIM33-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM33 Exon11 (NM_015906) and BRAF Exon11 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0021538-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon11 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20170068 Macro-dissection: Not Performed
NFIB	0	MSKCC-DMP	P-0021538-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon11 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20170068 Macro-dissection: Not Performed
CBX5	0	MSKCC-DMP	P-0021663-T01-IM6	FGFR2-CBX5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CBX5-FGFR2 fusion. Note: The rearrangement is an in-frame fusion between genes CBX5 Exon2 (NM_001127321) and FGFR2 Exon17 (NM_000141). Lab Notes Run Number: ArcherV2-CLIN-20170070 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0021663-T01-IM6	FGFR2-CBX5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CBX5-FGFR2 fusion. Note: The rearrangement is an in-frame fusion between genes CBX5 Exon2 (NM_001127321) and FGFR2 Exon17 (NM_000141). Lab Notes Run Number: ArcherV2-CLIN-20170070 Macro-dissection: Unknown
CD74	0	MSKCC-DMP	P-0021671-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170073 Macro-dissection: Not Performed
ROS1	0	MSKCC-DMP	P-0021671-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170073 Macro-dissection: Not Performed
RBPMS	0	MSKCC-DMP	P-0021795-T01-IM6	NTRK3-RBPMS fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RBPMS-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes RBPMS Exon5 (NM_001008712) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170073 Macro-dissection: Performed
NTRK3	0	MSKCC-DMP	P-0021795-T01-IM6	NTRK3-RBPMS fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RBPMS-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes RBPMS Exon5 (NM_001008712) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170073 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0021927-T01-IM6	ATF7IP-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ATF7IP fusion. Note: The rearrangement is a fusion between genes ETV6 Exon3 (NM_001987) and ATF7IP undefined (NM_018179). Lab Notes Run Number: ArcherV2-CLIN-20170075 Macro-dissection: Not Performed
ATF7IP	0	MSKCC-DMP	P-0021927-T01-IM6	ATF7IP-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ETV6-ATF7IP fusion. Note: The rearrangement is a fusion between genes ETV6 Exon3 (NM_001987) and ATF7IP undefined (NM_018179). Lab Notes Run Number: ArcherV2-CLIN-20170075 Macro-dissection: Not Performed
EWSR1	0	MSKCC-DMP	P-0022044-T01-IM6	FEV-EWSR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EWSR1-FEV fusion. Note: The rearrangement is an in-frame fusion between genes EWSR1 Exon6 (NM_005243) and FEV Exon3 (NM_017521). Lab Notes Run Number: ArcherV2-CLIN-20170076 Macro-dissection: Not Performed
FEV	0	MSKCC-DMP	P-0022044-T01-IM6	FEV-EWSR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EWSR1-FEV fusion. Note: The rearrangement is an in-frame fusion between genes EWSR1 Exon6 (NM_005243) and FEV Exon3 (NM_017521). Lab Notes Run Number: ArcherV2-CLIN-20170076 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0022129-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20170079 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0022189-T01-IM6	SKIL-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-SKIL fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_001135099) and SKIL Exon1 (NM_001248008). Lab Notes Run Number: ArcherV2-CLIN-20170081 Macro-dissection: Unknown
SKIL	0	MSKCC-DMP	P-0022189-T01-IM6	SKIL-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-SKIL fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_001135099) and SKIL Exon1 (NM_001248008). Lab Notes Run Number: ArcherV2-CLIN-20170081 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0022337-T01-IM6	TBC1D4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-TBC1D4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TBC1D4 Exon2 (NM_014832). Lab Notes Run Number: ArcherV2-CLIN-20170083 Macro-dissection: Not Performed
TBC1D4	0	MSKCC-DMP	P-0022337-T01-IM6	TBC1D4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-TBC1D4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TBC1D4 Exon2 (NM_014832). Lab Notes Run Number: ArcherV2-CLIN-20170083 Macro-dissection: Not Performed
STRN	0	MSKCC-DMP	P-0022346-T01-IM6	ALK-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STRN-ALK fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0022346-T01-IM6	ALK-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STRN-ALK fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0022509-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170085 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0022509-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170085 Macro-dissection: Performed
KIF5B	0	MSKCC-DMP	P-0022529-T01-IM6	ALK-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-ALK fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon24 (NM_004521) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170084 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0022529-T01-IM6	ALK-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-ALK fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon24 (NM_004521) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170084 Macro-dissection: Performed
FGFR3	0	MSKCC-DMP	P-0022569-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon8 (NM_006342). Note 2: Two additional fusions: MTMR2-MAML2 and USP13-PIK3CA were also detected (PMID: 25485619). The functional significance of both fusions is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
TACC3	0	MSKCC-DMP	P-0022569-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon8 (NM_006342). Note 2: Two additional fusions: MTMR2-MAML2 and USP13-PIK3CA were also detected (PMID: 25485619). The functional significance of both fusions is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
SDC4	0	MSKCC-DMP	P-0022765-T01-IM6	NRG1-SDC4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SDC4-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SDC4 Exon2 (NM_002999) and NRG1 Exon6  (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
NRG1	0	MSKCC-DMP	P-0022765-T01-IM6	NRG1-SDC4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SDC4-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SDC4 Exon2 (NM_002999) and NRG1 Exon6  (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170089 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0023103-T01-IM6	NOL4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-NOL4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and NOL4 Exon10 (NM_003787). Lab Notes Run Number: ArcherV2-CLIN-20170095 Macro-dissection: Not Performed
NOL4	0	MSKCC-DMP	P-0023103-T01-IM6	NOL4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-NOL4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and NOL4 Exon10 (NM_003787). Lab Notes Run Number: ArcherV2-CLIN-20170095 Macro-dissection: Not Performed
ETV6	0	MSKCC-DMP	P-0023215-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170100 Macro-dissection: Not Performed
NTRK3	0	MSKCC-DMP	P-0023215-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170100 Macro-dissection: Not Performed
CD74	0	MSKCC-DMP	P-0023476-T02-IM6	NRG1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon8 (NM_001025159) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170112 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0023476-T02-IM6	NRG1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon8 (NM_001025159) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20170112 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0023626-T01-IM6	JAZF1-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-JAZF1 fusion. Note: The rearrangement is a fusion between genes TMPRSS2 Exon1 (NM_005656) and JAZF1 Exon3 (NM_175061). The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170109 Macro-dissection: Performed
JAZF1	0	MSKCC-DMP	P-0023626-T01-IM6	JAZF1-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-JAZF1 fusion. Note: The rearrangement is a fusion between genes TMPRSS2 Exon1 (NM_005656) and JAZF1 Exon3 (NM_175061). The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170109 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0024125-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon11 (NM_001130173) and NFIB Exon11 (NM_001190737). MET Exon14: DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping  Lab Notes Run Number: ArcherV2-CLIN-20170113 Macro-dissection: Unknown
NFIB	0	MSKCC-DMP	P-0024125-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon11 (NM_001130173) and NFIB Exon11 (NM_001190737). MET Exon14: DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping  Lab Notes Run Number: ArcherV2-CLIN-20170113 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0024183-T01-IM6	PLXNA2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-PLXNA2 fusion. Note: The rearrangement is a fusion between genes FGFR2 Exon17 (NM_000141.4) and PLXNA2 Exon2 (NM_025179). Note 2: The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170113 Macro-dissection: Unknown
PLXNA2	0	MSKCC-DMP	P-0024183-T01-IM6	PLXNA2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-PLXNA2 fusion. Note: The rearrangement is a fusion between genes FGFR2 Exon17 (NM_000141.4) and PLXNA2 Exon2 (NM_025179). Note 2: The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20170113 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0024220-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: CAST-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CAST Exon3 (NM_001042440) and BRAF Exon9 (NM_004333). TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). SLC45A3-ERG fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ERG Exon4 (NM_004449). The clinical significance of this event is unknown.  TMPRSS2-BRAF fusion. Note: The rearrangement is a fusion between genes TMPRSS2 Exon2 (NM_001135099) and BRAF Exon10 (NM_004333). The clinical significance of this event is unknown.   Lab Notes Run Number: ArcherV2-CLIN-20170115 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0024220-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: CAST-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CAST Exon3 (NM_001042440) and BRAF Exon9 (NM_004333). TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). SLC45A3-ERG fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ERG Exon4 (NM_004449). The clinical significance of this event is unknown.  TMPRSS2-BRAF fusion. Note: The rearrangement is a fusion between genes TMPRSS2 Exon2 (NM_001135099) and BRAF Exon10 (NM_004333). The clinical significance of this event is unknown.   Lab Notes Run Number: ArcherV2-CLIN-20170115 Macro-dissection: Performed
HDAC5	0	MSKCC-DMP	P-0024571-T01-IM6	PIK3CA-HDAC5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HDAC5-PIK3CA fusion. Note: The rearrangement is an in-frame fusion between genes HDAC5 Exon1 (NM_001015053) and PIK3CA Exon1 (NM_006218). PMID: 26000489 Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
PIK3CA	0	MSKCC-DMP	P-0024571-T01-IM6	PIK3CA-HDAC5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HDAC5-PIK3CA fusion. Note: The rearrangement is an in-frame fusion between genes HDAC5 Exon1 (NM_001015053) and PIK3CA Exon1 (NM_006218). PMID: 26000489 Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
CLTC	0	MSKCC-DMP	P-0024675-T01-IM6	ALK-CLTC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CLTC-ALK fusion. Note: The rearrangement is an in-frame fusion between genes CLTC Exon31 (NM_004859) and ALK Exon19 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0024675-T01-IM6	ALK-CLTC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CLTC-ALK fusion. Note: The rearrangement is an in-frame fusion between genes CLTC Exon31 (NM_004859) and ALK Exon19 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0024679-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0024679-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
CMAS	0	MSKCC-DMP	P-0024995-T01-IM6	BRAF-CMAS fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CMAS-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CMAS Exon8 (NM_018686) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170125 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0024995-T01-IM6	BRAF-CMAS fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CMAS-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CMAS Exon8 (NM_018686) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170125 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0025010-T01-IM6	BICC1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-BICC1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and BICC1 Exon3 (NM_001080512). Lab Notes Run Number: ArcherV2-CLIN-20170130 Macro-dissection: Unknown
BICC1	0	MSKCC-DMP	P-0025010-T01-IM6	BICC1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-BICC1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and BICC1 Exon3 (NM_001080512). Lab Notes Run Number: ArcherV2-CLIN-20170130 Macro-dissection: Unknown
GEMIN5	0	MSKCC-DMP	P-0025215-T01-IM6	RET-GEMIN5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GEMIN5-RET fusion. Note: The rearrangement is an in-frame fusion between genes GEMIN5 Exon24 (NM_015465) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170131 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0025215-T01-IM6	RET-GEMIN5 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GEMIN5-RET fusion. Note: The rearrangement is an in-frame fusion between genes GEMIN5 Exon24 (NM_015465) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170131 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0025280-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20170130 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0025349-T03-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180063 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0025349-T03-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180063 Macro-dissection: Performed
NOTCH1	0	MSKCC-DMP	P-0025405-T01-IM6	AGPAT2-NOTCH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NOTCH1-AGPAT2 fusion. Note: The rearrangement is an in-frame fusion between genes NOTCH1 Exon2 (NM_017617) and AGPAT2 Exon2 (NM_006412). Lab Notes Run Number: ArcherV2-CLIN-20170132 Macro-dissection: Unknown
AGPAT2	0	MSKCC-DMP	P-0025405-T01-IM6	AGPAT2-NOTCH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NOTCH1-AGPAT2 fusion. Note: The rearrangement is an in-frame fusion between genes NOTCH1 Exon2 (NM_017617) and AGPAT2 Exon2 (NM_006412). Lab Notes Run Number: ArcherV2-CLIN-20170132 Macro-dissection: Unknown
ETV6	0	MSKCC-DMP	P-0025507-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170133 Macro-dissection: Unknown
NTRK3	0	MSKCC-DMP	P-0025507-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20170133 Macro-dissection: Unknown
NCOA4	0	MSKCC-DMP	P-0025531-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon7 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170138 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0025531-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon7 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170138 Macro-dissection: Unknown
SHROOM3	0	MSKCC-DMP	P-0025609-T01-IM6	RET-SHROOM3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SHROOM3-RET fusion. Note: The rearrangement is an in-frame fusion between genes SHROOM3 Exon5 (NM_020859) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170136 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0025609-T01-IM6	RET-SHROOM3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SHROOM3-RET fusion. Note: The rearrangement is an in-frame fusion between genes SHROOM3 Exon5 (NM_020859) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170136 Macro-dissection: Unknown
SLC45A3	0	MSKCC-DMP	P-0025718-T01-IM6	ERG-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SLC45A3-ERG fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ERG Exon2 (NM_182918). Lab Notes Run Number: ArcherV2-CLIN-20170139 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0025718-T01-IM6	ERG-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SLC45A3-ERG fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ERG Exon2 (NM_182918). Lab Notes Run Number: ArcherV2-CLIN-20170139 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0025835-T01-IM6	FOXP1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-FOXP1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and FOXP1 Exon3 (NM_001244814). Lab Notes Run Number: ArcherV2-CLIN-20180002 Macro-dissection: Unknown
FOXP1	0	MSKCC-DMP	P-0025835-T01-IM6	FOXP1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-FOXP1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and FOXP1 Exon3 (NM_001244814). Lab Notes Run Number: ArcherV2-CLIN-20180002 Macro-dissection: Unknown
SLC3A2	0	MSKCC-DMP	P-0025836-T01-IM6	NRG1-SLC3A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC3A2-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC3A2 Exon4 (NM_002394) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180002 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0025836-T01-IM6	NRG1-SLC3A2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC3A2-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC3A2 Exon4 (NM_002394) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180002 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0025988-T01-IM6	BRAF-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180005 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0025988-T01-IM6	BRAF-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180005 Macro-dissection: Unknown
HMGA2	0	MSKCC-DMP	P-0026061-T01-IM6	NUP107-HMGA2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HMGA2-NUP107 fusion. Note: The rearrangement is an in-frame fusion between genes HMGA2 Exon3 (NM_003483) and NUP107 Exon21 (NM_020401). Lab Notes Run Number: ArcherV2-CLIN-20180005 Macro-dissection: Performed
NUP107	0	MSKCC-DMP	P-0026061-T01-IM6	NUP107-HMGA2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HMGA2-NUP107 fusion. Note: The rearrangement is an in-frame fusion between genes HMGA2 Exon3 (NM_003483) and NUP107 Exon21 (NM_020401). Lab Notes Run Number: ArcherV2-CLIN-20180005 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0026108-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Note: EML4-ALK fusion transcript includes 93bp of unknown sequence.  Lab Notes Run Number: ArcherV2-CLIN-20180009 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0026108-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Note: EML4-ALK fusion transcript includes 93bp of unknown sequence.  Lab Notes Run Number: ArcherV2-CLIN-20180009 Macro-dissection: Unknown
KIAA1217	0	MSKCC-DMP	P-0026245-T01-IM6	RET-KIAA1217 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIAA1217-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIAA1217 Exon11 (NM_019590) and RET Exon8 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180009 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0026245-T01-IM6	RET-KIAA1217 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIAA1217-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIAA1217 Exon11 (NM_019590) and RET Exon8 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180009 Macro-dissection: Unknown
EML4	0	MSKCC-DMP	P-0026357-T01-IM6	NTRK3-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon2 (NM_019063) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Not Performed
NTRK3	0	MSKCC-DMP	P-0026357-T01-IM6	NTRK3-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon2 (NM_019063) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Not Performed
SLC4A4	0	MSKCC-DMP	P-0026387-T01-IM6	NRG1-SLC4A4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC4A4-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC4A4 Exon14 (NM_001134742) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Performed
NRG1	0	MSKCC-DMP	P-0026387-T01-IM6	NRG1-SLC4A4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC4A4-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC4A4 Exon14 (NM_001134742) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Performed
ETV6	0	MSKCC-DMP	P-0026390-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Performed
NTRK3	0	MSKCC-DMP	P-0026390-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180013 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0026569-T02-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET exon 14 (NM_000245)  skipping was detected. Lab Notes Run Number: ArcherV2-CLIN-20180024 Macro-dissection: Not Performed
SPECC1L	0	MSKCC-DMP	P-0026614-T01-IM6	RET-SPECC1L fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SPECC1L-RET fusion. Note: The rearrangement is an in-frame fusion between genes SPECC1L Exon9 (NM_001145468) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180014 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0026614-T01-IM6	RET-SPECC1L fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SPECC1L-RET fusion. Note: The rearrangement is an in-frame fusion between genes SPECC1L Exon9 (NM_001145468) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180014 Macro-dissection: Unknown
RAP1A	0	MSKCC-DMP	P-0026623-T01-IM6	NOTCH2-RAP1A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RAP1A-NOTCH2 fusion. Note: The rearrangement is an in-frame fusion between genes RAP1A Exon1 (NM_002884) and NOTCH2 Exon26 (NM_024408). Lab Notes Run Number: ArcherV2-CLIN-20180022 Macro-dissection: Not Performed
NOTCH2	0	MSKCC-DMP	P-0026623-T01-IM6	NOTCH2-RAP1A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RAP1A-NOTCH2 fusion. Note: The rearrangement is an in-frame fusion between genes RAP1A Exon1 (NM_002884) and NOTCH2 Exon26 (NM_024408). Lab Notes Run Number: ArcherV2-CLIN-20180022 Macro-dissection: Not Performed
KIF5B	0	MSKCC-DMP	P-0026777-T02-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180037 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0026777-T02-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180037 Macro-dissection: Unknown
CD74	0	MSKCC-DMP	P-0027196-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180026 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0027196-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180026 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0027305-T01-IM6	CCDC6-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-CCDC6 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and CCDC6 Exon4 (NM_005436). Lab Notes Run Number: ArcherV2-CLIN-20180027 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0027305-T01-IM6	CCDC6-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-CCDC6 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and CCDC6 Exon4 (NM_005436). Lab Notes Run Number: ArcherV2-CLIN-20180027 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0027554-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20180034 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0027623-T01-IM6	MYLK-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-MYLK fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and MYLK Exon4 (NM_053025). Lab Notes Run Number: ArcherV2-CLIN-20180035 Macro-dissection: Performed
MYLK	0	MSKCC-DMP	P-0027623-T01-IM6	MYLK-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-MYLK fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and MYLK Exon4 (NM_053025). Lab Notes Run Number: ArcherV2-CLIN-20180035 Macro-dissection: Performed
KIF5B	0	MSKCC-DMP	P-0027723-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180038 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0027723-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180038 Macro-dissection: Performed
ZC3HAV1	0	MSKCC-DMP	P-0027762-T01-IM6	BRAF-ZC3HAV1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ZC3HAV1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes ZC3HAV1 Exon3 (NM_020119) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180040 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0027762-T01-IM6	BRAF-ZC3HAV1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ZC3HAV1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes ZC3HAV1 Exon3 (NM_020119) and BRAF Exon10 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180040 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0027764-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180039 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0027764-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180039 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0027988-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20180042 Macro-dissection: Unknown
MYH9	0	MSKCC-DMP	P-0027989-T01-IM6	ROS1-MYH9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYH9-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes MYH9 Exon40 (NM_002473) and ROS1 Exon36 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180042 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0027989-T01-IM6	ROS1-MYH9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYH9-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes MYH9 Exon40 (NM_002473) and ROS1 Exon36 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180042 Macro-dissection: Unknown
DNAJB1	0	MSKCC-DMP	P-0028420-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20180050 Macro-dissection: Unknown
PRKACA	0	MSKCC-DMP	P-0028420-T01-IM6	PRKACA-DNAJB1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DNAJB1-PRKACA fusion. Note: The rearrangement is an in-frame fusion between genes DNAJB1 Exon1 (NM_006145) and PRKACA Exon2 (NM_002730). Lab Notes Run Number: ArcherV2-CLIN-20180050 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0028529-T01-IM6	ROS1-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon5 (NM_005436) and ROS1 Exon35 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180053 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0028529-T01-IM6	ROS1-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon5 (NM_005436) and ROS1 Exon35 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20180053 Macro-dissection: Unknown
ERBB2	0	MSKCC-DMP	P-0028658-T01-IM6	TCAP-ERBB2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ERBB2-TCAP fusion. Note: The rearrangement is a fusion between genes ERBB2 Exon25 (NM_004448) and TCAP Exon2 (NM_003673). Clinical and functional significance is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20180056 Macro-dissection: Unknown
TCAP	0	MSKCC-DMP	P-0028658-T01-IM6	TCAP-ERBB2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ERBB2-TCAP fusion. Note: The rearrangement is a fusion between genes ERBB2 Exon25 (NM_004448) and TCAP Exon2 (NM_003673). Clinical and functional significance is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20180056 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0028694-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET Exon 14 Skipping Lab Notes Run Number: ArcherV2-CLIN-20180055 Macro-dissection: Unknown
PPA2PA	0	MSKCC-DMP	P-0029059-T01-IM6	BRAF-PPA2PA fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: PPA2PA-BRAF fusion. Note: The rearrangement is an out of frame fusion between genes PPA2PA Exon1 (NM_003711) and BRAF Exon11 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180061 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0029059-T01-IM6	BRAF-PPA2PA fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: PPA2PA-BRAF fusion. Note: The rearrangement is an out of frame fusion between genes PPA2PA Exon1 (NM_003711) and BRAF Exon11 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180061 Macro-dissection: Unknown
DIAPH1	0	MSKCC-DMP	P-0029326-T01-IM6	NTRK1-DIAPH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DIAPH1-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes DIAPH1 Exon26 (NM_005219) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV2-CLIN-20180064 Macro-dissection: Unknown
NTRK1	0	MSKCC-DMP	P-0029326-T01-IM6	NTRK1-DIAPH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DIAPH1-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes DIAPH1 Exon26 (NM_005219) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV2-CLIN-20180064 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0029472-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL MET  Exon 14 (NM_000245) Skipping   Lab Notes Run Number: ArcherV2-CLIN-20180071 Macro-dissection: Unknown
EGFR	0	MSKCC-DMP	P-0029645-T01-IM6	EGFR-intragenic - Archer	yes	unknown		unknown	EGFR vIII: POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  EGFR Exons 2-7 deletion (NM_005228)  Lab Notes Run Number: ArcherV2-CLIN-20180070 Macro-dissection: Unknown
HSF2BP	0	MSKCC-DMP	P-0029726-T01-IM6	ERG-HSF2BP fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HSF2BP-ERG fusion. Note: The rearrangement is an in-frame fusion between genes HSF2BP Exon8 (NM_007031) and ERG Exon6 (NM_004449). Note: Functional significance is unknown for HSF2BP-ERG fusion. Lab Notes Run Number: ArcherV2-CLIN-20180071 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0029726-T01-IM6	ERG-HSF2BP fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HSF2BP-ERG fusion. Note: The rearrangement is an in-frame fusion between genes HSF2BP Exon8 (NM_007031) and ERG Exon6 (NM_004449). Note: Functional significance is unknown for HSF2BP-ERG fusion. Lab Notes Run Number: ArcherV2-CLIN-20180071 Macro-dissection: Unknown
EGFR	0	MSKCC-DMP	P-0029764-T01-IM6	EGFR-intragenic - Archer	yes	unknown		unknown	EGFR vIII: POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  EGFR Exons 2-7 deletion (NM_005228)  Lab Notes Run Number: ArcherV2-CLIN-20180072 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0029843-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GRHL2-RSPO2 fusion. Note: The rearrangement is a fusion between genes GRHL2 Exon9 (NM_024915) and RSPO2 Exon2 (NM_178565). https://link.springer.com/content/pdf/10.1007%2Fs11033-014-3409-x.pdf  Lab Notes Run Number: ArcherV2-CLIN-20180074 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0029843-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GRHL2-RSPO2 fusion. Note: The rearrangement is a fusion between genes GRHL2 Exon9 (NM_024915) and RSPO2 Exon2 (NM_178565). https://link.springer.com/content/pdf/10.1007%2Fs11033-014-3409-x.pdf  Lab Notes Run Number: ArcherV2-CLIN-20180074 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0029846-T02-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET  Exon 14 (NM_000245) Skipping  Lab Notes Run Number: ArcherV2-CLIN-20180074 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0029997-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180075 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0029997-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180075 Macro-dissection: Unknown
AKAP9	0	MSKCC-DMP	P-0030237-T01-IM6	BRAF-AKAP9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AKAP9-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AKAP9 Exon8 (NM_005751) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180081 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0030237-T01-IM6	BRAF-AKAP9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AKAP9-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AKAP9 Exon8 (NM_005751) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20180081 Macro-dissection: Unknown
CNOT2	0	MSKCC-DMP	P-0030267-T01-IM6	STAT6-CNOT2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CNOT2-STAT6 fusion. Note: The rearrangement is an in-frame fusion between genes CNOT2 Exon2 (NM_014515) and STAT6 Exon2 (NM_001178078). Lab Notes Run Number: ArcherV2-CLIN-20180089 Macro-dissection: Performed
STAT6	0	MSKCC-DMP	P-0030267-T01-IM6	STAT6-CNOT2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CNOT2-STAT6 fusion. Note: The rearrangement is an in-frame fusion between genes CNOT2 Exon2 (NM_014515) and STAT6 Exon2 (NM_001178078). Lab Notes Run Number: ArcherV2-CLIN-20180089 Macro-dissection: Performed
KIF5B	0	MSKCC-DMP	P-0030453-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180083 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0030453-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180083 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0030593-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: ArcherV2-CLIN-20180085 Macro-dissection: Unknown
TACC2	0	MSKCC-DMP	P-0030593-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: ArcherV2-CLIN-20180085 Macro-dissection: Unknown
HMBOX1	0	MSKCC-DMP	P-0030808-T01-IM6	ALK-HMBOX1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: HMBOX1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes HMBOX1 Exon7 (NM_001135726) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180089 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0030808-T01-IM6	ALK-HMBOX1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: HMBOX1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes HMBOX1 Exon7 (NM_001135726) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180089 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0031076-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon14 (NM_000245) Deletion  Lab Notes Run Number: ArcherV2-CLIN-20180096 Macro-dissection: Unknown
SEC16A	0	MSKCC-DMP	P-0031993-T01-IM6	NOTCH1-SEC16A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SEC16A-NOTCH1 fusion. Note: The rearrangement is a fusion between genes SEC16A Exon1 (NM_014866) and NOTCH1 Exon27 (NM_017617). Lab Notes Run Number: ArcherV2-CLIN-20180115 Macro-dissection: Performed
NOTCH1	0	MSKCC-DMP	P-0031993-T01-IM6	NOTCH1-SEC16A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SEC16A-NOTCH1 fusion. Note: The rearrangement is a fusion between genes SEC16A Exon1 (NM_014866) and NOTCH1 Exon27 (NM_017617). Lab Notes Run Number: ArcherV2-CLIN-20180115 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0032208-T01-IM6	MYO18B-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-MYO18B fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and MYO18B Exon26 (NM_032608). Lab Notes Run Number: ArcherV2-CLIN-20180115 Macro-dissection: Unknown
MYO18B	0	MSKCC-DMP	P-0032208-T01-IM6	MYO18B-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-MYO18B fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and MYO18B Exon26 (NM_032608). Lab Notes Run Number: ArcherV2-CLIN-20180115 Macro-dissection: Unknown
KIF5B	0	MSKCC-DMP	P-0032407-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon16 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180119 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0032407-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon16 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180119 Macro-dissection: Unknown
TPM1	0	MSKCC-DMP	P-0032514-T01-IM6	ALK-TPM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TPM1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes TPM1 Exon2 (NM_001018020) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180120 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0032514-T01-IM6	ALK-TPM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TPM1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes TPM1 Exon2 (NM_001018020) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180120 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0033072-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:   MET Exon14 (NM_000245) Deletion  Lab Notes Run Number: ArcherV2-CLIN-20180129 Macro-dissection: Unknown
EML4	0	MSKCC-DMP	P-0033180-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0033180-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
ATP1B1	0	MSKCC-DMP	P-0033208-T01-IM6	NRG1-ATP1B1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ATP1B1-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes ATP1B1 Exon2 (NM_001677) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0033208-T01-IM6	NRG1-ATP1B1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ATP1B1-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes ATP1B1 Exon2 (NM_001677) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
SQSTM1	0	MSKCC-DMP	P-0033493-T01-IM6	NTRK3-SQSTM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SQSTM1-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes SQSTM1 Exon4 (NM_003900) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180134 Macro-dissection: Unknown
NTRK3	0	MSKCC-DMP	P-0033493-T01-IM6	NTRK3-SQSTM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: SQSTM1-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes SQSTM1 Exon4 (NM_003900) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV2-CLIN-20180134 Macro-dissection: Unknown
MYB	0	MSKCC-DMP	P-0033681-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon9 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20180136 Macro-dissection: Unknown
NFIB	0	MSKCC-DMP	P-0033681-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon9 (NM_001130173) and NFIB Exon11 (NM_001190737). Lab Notes Run Number: ArcherV2-CLIN-20180136 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0033896-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:   POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL  MET Exon 14 Skipping Lab Notes Run Number: ArcherV3-CLIN-20180142 Macro-dissection: Unknown
FUS	0	MSKCC-DMP	P-0033932-T01-IM6	MYB-FUS fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FUS-MYB fusion. Note: The rearrangement is an in-frame fusion between genes FUS Exon6 (NM_004960) and MYB Exon2 (NM_001130173). Lab Notes Run Number: ArcherV3-CLIN-20180140 Macro-dissection: Unknown
MYB	0	MSKCC-DMP	P-0033932-T01-IM6	MYB-FUS fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FUS-MYB fusion. Note: The rearrangement is an in-frame fusion between genes FUS Exon6 (NM_004960) and MYB Exon2 (NM_001130173). Lab Notes Run Number: ArcherV3-CLIN-20180140 Macro-dissection: Unknown
MYBL1	0	MSKCC-DMP	P-0033964-T01-IM6	NFIB-MYBL1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYBL1-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYBL1 Exon8 (NM_001080416) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV3-CLIN-20180140 Macro-dissection: Unknown
NFIB	0	MSKCC-DMP	P-0033964-T01-IM6	NFIB-MYBL1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYBL1-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYBL1 Exon8 (NM_001080416) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV3-CLIN-20180140 Macro-dissection: Unknown
GOLGA4	0	MSKCC-DMP	P-0034173-T01-IM6	RAF1-GOLGA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GOLGA4-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes GOLGA4 Exon13 (NM_001172713) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
RAF1	0	MSKCC-DMP	P-0034173-T01-IM6	RAF1-GOLGA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GOLGA4-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes GOLGA4 Exon13 (NM_001172713) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0034399-T01-IM6	FAM124B-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-FAM124B fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and FAM124B Exon2 (NM_001122779). Lab Notes Run Number: ArcherV3-CLIN-20180149 Macro-dissection: Performed
FAM124B	0	MSKCC-DMP	P-0034399-T01-IM6	FAM124B-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-FAM124B fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and FAM124B Exon2 (NM_001122779). Lab Notes Run Number: ArcherV3-CLIN-20180149 Macro-dissection: Performed
FGFR3	0	MSKCC-DMP	P-0034419-T01-IM6	JAKMIP1-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-JAKMIP1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and JAKMIP1 Exon4 (NM_144720). Lab Notes Run Number: ArcherV3-CLIN-20180150 Macro-dissection: Unknown
JAKMIP1	0	MSKCC-DMP	P-0034419-T01-IM6	JAKMIP1-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-JAKMIP1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and JAKMIP1 Exon4 (NM_144720). Lab Notes Run Number: ArcherV3-CLIN-20180150 Macro-dissection: Unknown
STAT6	0	MSKCC-DMP	P-0035139-T01-IM6	AKT1-STAT6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STAT6-AKT1 fusion. Note: The rearrangement is an in-frame fusion between genes STAT6 Exon6 (NM_001178078) and AKT1 Exon4 (NM_005163). Lab Notes Run Number: ArcherV3-CLIN-20180163 Macro-dissection: Unknown
AKT1	0	MSKCC-DMP	P-0035139-T01-IM6	AKT1-STAT6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STAT6-AKT1 fusion. Note: The rearrangement is an in-frame fusion between genes STAT6 Exon6 (NM_001178078) and AKT1 Exon4 (NM_005163). Lab Notes Run Number: ArcherV3-CLIN-20180163 Macro-dissection: Unknown
PTPRK	0	MSKCC-DMP	P-0035372-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180166 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0035372-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180166 Macro-dissection: Unknown
MKRN1	0	MSKCC-DMP	P-0035393-T02-IM6	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.771+833:MKRN1_c.1141-1052:BRAFdup Note: The MKRN1 - BRAF fusion involves MKRN1 exons 1-4 with BRAF exons 9-18. The fusion is predicted to be in-frame and involves the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0035393-T02-IM6	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.771+833:MKRN1_c.1141-1052:BRAFdup Note: The MKRN1 - BRAF fusion involves MKRN1 exons 1-4 with BRAF exons 9-18. The fusion is predicted to be in-frame and involves the kinase domain of BRAF.
APC	0	MSKCC-DMP	P-0035720-T01-IM6	FTMT-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.87:APC_chr5:g.121241258inv Note: The APC rearrangement results in the inversion of exons 2-16. One of the breakpoints is within exon 2.
FTMT	0	MSKCC-DMP	P-0035720-T01-IM6	FTMT-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.87:APC_chr5:g.121241258inv Note: The APC rearrangement results in the inversion of exons 2-16. One of the breakpoints is within exon 2.
RTEL1	0	MSKCC-DMP	P-0035723-T01-IM6	YBX2-RTEL1 fusion	yes	unknown		unknown	YBX2 (NM_015982) - RTEL1 (NM_032957) rearrangement: t(17;20)(p13.1;q13.33)(chr17:g.7193375::chr20:g.62292480) Note: The YBX2 - RTEL1 rearrangement is a translocation that results in the fusion of YBX2 exons 1-6 with RTEL exons 3-35. One of the breakpoints is within YBX2 exon 6. The functional significance is undetermined.
YBX2	0	MSKCC-DMP	P-0035723-T01-IM6	YBX2-RTEL1 fusion	yes	unknown		unknown	YBX2 (NM_015982) - RTEL1 (NM_032957) rearrangement: t(17;20)(p13.1;q13.33)(chr17:g.7193375::chr20:g.62292480) Note: The YBX2 - RTEL1 rearrangement is a translocation that results in the fusion of YBX2 exons 1-6 with RTEL exons 3-35. One of the breakpoints is within YBX2 exon 6. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0035764-T01-IM6	ZGPAT-RTEL1 fusion	yes	unknown		unknown	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-8272:ZGPAT_c.2302:RTEL1dup Note: The ZGPAT - RTEL1 rearrangement is a duplication which results in the fusion of ZGPAT exons 1-2 with RTEL1 exons 25-35. One of the breakpoints is within RTEL1 exon 25. Its functional significance is undetermined.
ZGPAT	0	MSKCC-DMP	P-0035764-T01-IM6	ZGPAT-RTEL1 fusion	yes	unknown		unknown	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-8272:ZGPAT_c.2302:RTEL1dup Note: The ZGPAT - RTEL1 rearrangement is a duplication which results in the fusion of ZGPAT exons 1-2 with RTEL1 exons 25-35. One of the breakpoints is within RTEL1 exon 25. Its functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0035772-T01-IM6	KANSL1-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.372+234:STAT3_chr17:g.44240986inv Note: The STAT3 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.
KANSL1	0	MSKCC-DMP	P-0035772-T01-IM6	KANSL1-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.372+234:STAT3_chr17:g.44240986inv Note: The STAT3 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.
HIST1H3G	0	MSKCC-DMP	P-0035786-T01-IM6	HIST1H4H-HIST1H3G fusion	yes	unknown		unknown	HIST1H3G (NM_003534) rearrangement: c.171:HIST1H3G_chr6:g.26309900del Note: The HIST1H3G rearrangement results in the deletion of HIST1H3G exon 1. One of the breakpoint is within exon1 of HIST1H3G. The functional significance is undetermined.
HIST1H4H	0	MSKCC-DMP	P-0035786-T01-IM6	HIST1H4H-HIST1H3G fusion	yes	unknown		unknown	HIST1H3G (NM_003534) rearrangement: c.171:HIST1H3G_chr6:g.26309900del Note: The HIST1H3G rearrangement results in the deletion of HIST1H3G exon 1. One of the breakpoint is within exon1 of HIST1H3G. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0035788-T01-IM6	SOX5-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement: t(12;19)(p12.1;p13.2)(chr12:g.23564653::chr19:g.11032250) Note:  The CARM1 rearrangement is a translocation with breakpoint in intron 15 of CARM1. The functional significance is undetermined.
SOX5	0	MSKCC-DMP	P-0035788-T01-IM6	SOX5-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) Rearrangement: t(12;19)(p12.1;p13.2)(chr12:g.23564653::chr19:g.11032250) Note:  The CARM1 rearrangement is a translocation with breakpoint in intron 15 of CARM1. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0035793-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) Rearrangement: c.3207_c.*573del Note: The ERBB2 rearrangement is an intragenic deletion of exons 26 to 27. One of the breakpoints is within exon 26. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0035868-T01-IM6	DCBLD1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5641+1040:ROS1_chr6:g.117887080del Note: The ROS1 rearrangement is a deletion of exons 1-34. Its functional significance is undetermined.
DCBLD1	0	MSKCC-DMP	P-0035868-T01-IM6	DCBLD1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5641+1040:ROS1_chr6:g.117887080del Note: The ROS1 rearrangement is a deletion of exons 1-34. Its functional significance is undetermined.
LINC01479	0	MSKCC-DMP	P-0013032-T02-IM6	SETD2-LINC01479 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement : t(3,12)(p21.31,q14.3)(chr3:g.47084233::chr12:g.68312811) Note: The SETD2 Rearrangement is a translocation with a breakpoint in intron16. Its functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0013032-T02-IM6	SETD2-LINC01479 fusion	yes	unknown		unknown	SETD2 (NM_014159) Rearrangement : t(3,12)(p21.31,q14.3)(chr3:g.47084233::chr12:g.68312811) Note: The SETD2 Rearrangement is a translocation with a breakpoint in intron16. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0035854-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+533:TMPRSS2_c.39+11353:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 4-10. This involves the noncanonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0035854-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+533:TMPRSS2_c.39+11353:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 4-10. This involves the noncanonical ERG (NM_004449) transcript.
APC	0	MSKCC-DMP	P-0035867-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4505:APC_chr5:g.112181350del Note: The APC rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0002372-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2699:TMPRSS2_c.40-60926:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 4-10. This involves the non-canonical. ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0002372-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2699:TMPRSS2_c.40-60926:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 4-10. This involves the non-canonical. ERG (NM_004449) transcript.
NTRK3	0	MSKCC-DMP	P-0035767-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12029143::chr15:g.88505787) Note: The ETV6 - NTRK3 rearrangement is a translocation which results in the fusion of ETV6 exons 1-5 with NTRK3 exons 15-20. This includes the kinase domain of NTRK3.
ETV6	0	MSKCC-DMP	P-0035767-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12029143::chr15:g.88505787) Note: The ETV6 - NTRK3 rearrangement is a translocation which results in the fusion of ETV6 exons 1-5 with NTRK3 exons 15-20. This includes the kinase domain of NTRK3.
KMT2D	0	MSKCC-DMP	P-0035768-T01-IM6	DUSP22-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(6;12)(p25.3;q13.12)(chr6:g.238826::chr12:g.49432543) Note: The KMT2D rearrangement is a translocation involving a breakpoint in exon 34. Its functional significance is undetermined.
DUSP22	0	MSKCC-DMP	P-0035768-T01-IM6	DUSP22-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(6;12)(p25.3;q13.12)(chr6:g.238826::chr12:g.49432543) Note: The KMT2D rearrangement is a translocation involving a breakpoint in exon 34. Its functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0035812-T01-IM6	ADAMTS12-DROSHA fusion	yes	unknown		out of frame	DROSHA (NM_013235) - ADAMTS12 (NM_030955) Rearrangement : c.2241+102:DROSHA_c.4607-3459_ADAMTS12dup Note: The DROSHA - ADAMTS12  Rearrangement results in the fusion of exons 1-16 of DROSHA with exons 24 of ADAMTS12. Its functional significance is undetermined.
ADAMTS12	0	MSKCC-DMP	P-0035812-T01-IM6	ADAMTS12-DROSHA fusion	yes	unknown		out of frame	DROSHA (NM_013235) - ADAMTS12 (NM_030955) Rearrangement : c.2241+102:DROSHA_c.4607-3459_ADAMTS12dup Note: The DROSHA - ADAMTS12  Rearrangement results in the fusion of exons 1-16 of DROSHA with exons 24 of ADAMTS12. Its functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0035812-T01-IM6	PRELID1-NSD1 fusion	yes	unknown		unknown	PRELID1 (NM_013237) - NSD1 (NM_022455)  Rearrangement :  c.512:PRELID1_c.2220:NSD1dup Note: The PRELID1 - NSD1 Rearrangement results in the fusion of exons 1-5 of PRELID1 with exons 5-23 of NSD1. The breakpoints are within exon5 of both PRELID1 and NSD1. Its functional significance is undetermined.
PRELID1	0	MSKCC-DMP	P-0035812-T01-IM6	PRELID1-NSD1 fusion	yes	unknown		unknown	PRELID1 (NM_013237) - NSD1 (NM_022455)  Rearrangement :  c.512:PRELID1_c.2220:NSD1dup Note: The PRELID1 - NSD1 Rearrangement results in the fusion of exons 1-5 of PRELID1 with exons 5-23 of NSD1. The breakpoints are within exon5 of both PRELID1 and NSD1. Its functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0035812-T01-IM6	GBGT1-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) - GBGT1 (NM_021996) Rearrangement : c.2502+9:TSC1_c.360-218:GBGT1dup Note: The TSC1- GBGT1 Rearrangement results in the fusion of exons 1-19 of TSC1 with exons 6-7 of GBGT1. Its functional significance is undetermined.
GBGT1	0	MSKCC-DMP	P-0035812-T01-IM6	GBGT1-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) - GBGT1 (NM_021996) Rearrangement : c.2502+9:TSC1_c.360-218:GBGT1dup Note: The TSC1- GBGT1 Rearrangement results in the fusion of exons 1-19 of TSC1 with exons 6-7 of GBGT1. Its functional significance is undetermined.
FLJ45079	0	MSKCC-DMP	P-0035814-T01-IM6	INPPL1-FLJ45079 fusion	yes	unknown		unknown	INPPL1 (NM_001567) Rearrangement : t(11,17)(q13.4,q25.3)(chr11:g.71943225::chr17:g.75802681) Note: The INPPL1 Rearrangement is a translocation event with a breakpoint in intron13. Its functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0035814-T01-IM6	INPPL1-FLJ45079 fusion	yes	unknown		unknown	INPPL1 (NM_001567) Rearrangement : t(11,17)(q13.4,q25.3)(chr11:g.71943225::chr17:g.75802681) Note: The INPPL1 Rearrangement is a translocation event with a breakpoint in intron13. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0035926-T01-IM6	LOC650226-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.2947-91_chr7:g.56436684inv Note: The EGFR rearrangement results in the inversion of exons 25-28. This includes the carboxyl terminal domain of EGFR.
LOC650226	0	MSKCC-DMP	P-0035926-T01-IM6	LOC650226-EGFR fusion	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.2947-91_chr7:g.56436684inv Note: The EGFR rearrangement results in the inversion of exons 25-28. This includes the carboxyl terminal domain of EGFR.
BRCA2	0	MSKCC-DMP	P-0035765-T01-IM6	VCAN-BRCA2 fusion	yes	unknown		in frame	BRCA2 (NM_000059) - VCAN (NM_004385) rearrangement: t(5;13)(q14.3;q13.1)(chr5:g.82844662::chr13:g.32918847) Note: The BRCA2 - VCAN rearrangement is translocation which may result in the fusion of BRCA2 exons 1-12 with VCAN exons 11-15. The functional significance is unknown.
VCAN	0	MSKCC-DMP	P-0035765-T01-IM6	VCAN-BRCA2 fusion	yes	unknown		in frame	BRCA2 (NM_000059) - VCAN (NM_004385) rearrangement: t(5;13)(q14.3;q13.1)(chr5:g.82844662::chr13:g.32918847) Note: The BRCA2 - VCAN rearrangement is translocation which may result in the fusion of BRCA2 exons 1-12 with VCAN exons 11-15. The functional significance is unknown.
TET1	0	MSKCC-DMP	P-0036007-T01-IM6	CAMTA1-TET1 fusion	yes	unknown		unknown	TET1 (NM_030625) - CAMTA1 (NM_015215) Rearrangment: c.871:TET1_c.438+35538:CAMTA1 Note: The TET1 - CAMTA1 rearrangement is a translocation which may result in the fusion of TET1 exons 1-2 with CAMTA1 exons 6-23. Its functional significance is undetermined.
CAMTA1	0	MSKCC-DMP	P-0036007-T01-IM6	CAMTA1-TET1 fusion	yes	unknown		unknown	TET1 (NM_030625) - CAMTA1 (NM_015215) Rearrangment: c.871:TET1_c.438+35538:CAMTA1 Note: The TET1 - CAMTA1 rearrangement is a translocation which may result in the fusion of TET1 exons 1-2 with CAMTA1 exons 6-23. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036007-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exon 2) : c.56-4127:TMPRSS2_c.18+10822:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0036007-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exon 2) : c.56-4127:TMPRSS2_c.18+10822:ERGdel
PTPN11	0	MSKCC-DMP	P-0036009-T01-IM6	GRID2-PTPN11 fusion	yes	unknown		unknown	PTPN11 (NM_002834) Rearrangement: t(4,12)(q21.13,q24.12)(chr4:g.93691193::chr12:g.112926914) Note: The PTPN11 Rearrangement is a translocation event with the breakpoint in exon13 of PTPN11. Its functional significance is undetermined.
GRID2	0	MSKCC-DMP	P-0036009-T01-IM6	GRID2-PTPN11 fusion	yes	unknown		unknown	PTPN11 (NM_002834) Rearrangement: t(4,12)(q21.13,q24.12)(chr4:g.93691193::chr12:g.112926914) Note: The PTPN11 Rearrangement is a translocation event with the breakpoint in exon13 of PTPN11. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0036009-T01-IM6	SNX16-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement :  t(8,17)(p13.3,q24.12)(chr8:g.83375277::chr17:g.37673753) Note: The CDK12 Rearrangement is a translocation event with a breakpoint in exon10 of CDK12. Its functional significance is undetermined.
SNX16	0	MSKCC-DMP	P-0036009-T01-IM6	SNX16-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement :  t(8,17)(p13.3,q24.12)(chr8:g.83375277::chr17:g.37673753) Note: The CDK12 Rearrangement is a translocation event with a breakpoint in exon10 of CDK12. Its functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0036009-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) Rearrangement : c.968-3144_c.976del Note: The RUNX1 Rearrangement results in the intragenic deletion of exon9 of RUNX1. One of the breakpoints is within exon9. Its functional significance is undetermined.
CD79A	0	MSKCC-DMP	P-0036010-T01-IM6	ZNF83-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - ZNF83 (NM_018300) Rearrangement : c.239:CD79A_c.-658+9171:ZNF83inv Note: The CD79A  - ZNF83 Rearrangement results in the fusion of exons 1-2 of CD79A with exons 1-3 of ZNF83. The breakpoint in CD79A is within exon2 and the breakpoint in ZNF83 is in the 5-UTR region of ZNF83. Its functional significance is undetermined.
ZNF83	0	MSKCC-DMP	P-0036010-T01-IM6	ZNF83-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - ZNF83 (NM_018300) Rearrangement : c.239:CD79A_c.-658+9171:ZNF83inv Note: The CD79A  - ZNF83 Rearrangement results in the fusion of exons 1-2 of CD79A with exons 1-3 of ZNF83. The breakpoint in CD79A is within exon2 and the breakpoint in ZNF83 is in the 5-UTR region of ZNF83. Its functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0036010-T01-IM6	VRK3-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - VRK3 (NM_016440) Rearrangement : c.986:CIC_c.-65+2216:VRK3inv Note: The CIC-VRK3 Rearrangement results in the fusion of exons 1-7 of CIC with exons 1-14 of VRK3. The breakpoint in CIC is within exon7 and the breakpoint in VRK3 is in the 5-UTR region of VRK3.Its functional significance is undetermined.
VRK3	0	MSKCC-DMP	P-0036010-T01-IM6	VRK3-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - VRK3 (NM_016440) Rearrangement : c.986:CIC_c.-65+2216:VRK3inv Note: The CIC-VRK3 Rearrangement results in the fusion of exons 1-7 of CIC with exons 1-14 of VRK3. The breakpoint in CIC is within exon7 and the breakpoint in VRK3 is in the 5-UTR region of VRK3.Its functional significance is undetermined.
BLM	0	MSKCC-DMP	P-0036015-T01-IM6	BLM-intragenic	yes	unknown		out of frame	BLM (NM_000057) Rearrangement : c.799+331_c.2824-79del Note: The BLM Rearrangement results in the intragenic deletion of exons 4-14. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0036015-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) Rearrangement : c.7457+67_c.7970+132dup Note: The NF1  Rearrangement results in the duplication of exons 51-54 of NF1. Its functional significance is undetermined.
EPAS1	0	MSKCC-DMP	P-0036015-T01-IM6	MSH2-EPAS1 fusion	yes	unknown		out of frame	EPAS1 (NM_001430) - MSH2 (NM_000251) Rearrangement : c.27-5917:EPAS1_c.1760-90:MSH2 Note: The EPAS1-MSH2 Rearrangement results in the fusion of exon 1of EPAS1 with exons 12-16 of MSH2.Its functional significance is undetermined.
MSH2	0	MSKCC-DMP	P-0036015-T01-IM6	MSH2-EPAS1 fusion	yes	unknown		out of frame	EPAS1 (NM_001430) - MSH2 (NM_000251) Rearrangement : c.27-5917:EPAS1_c.1760-90:MSH2 Note: The EPAS1-MSH2 Rearrangement results in the fusion of exon 1of EPAS1 with exons 12-16 of MSH2.Its functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0036020-T01-IM6	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.1133_c.3060-1962del Note: The JAK2 rearrangement is an intragenic deletion of exons 9-22. One of the breakpoints is within exon 9. The functional significance is undetermined.
NUMA1	0	MSKCC-DMP	P-0036028-T01-IM6	EGFR-NUMA1 fusion	yes	unknown		in frame	NUMA1 (NM_006185) - EGFR (NM_005228) rearrangement: t(7;11)(p11.2;q13.4)(chr7:g.55241128::chr11:g.71728415) Note: The NUMA1 - EGFR rearrangement is a translocation that results in the fusion of NUMA1 exons 1-13 with EGFR exons 18-28. The fusion is predicted to be in frame and includes the kinase domain of EGFR.
EGFR	0	MSKCC-DMP	P-0036028-T01-IM6	EGFR-NUMA1 fusion	yes	unknown		in frame	NUMA1 (NM_006185) - EGFR (NM_005228) rearrangement: t(7;11)(p11.2;q13.4)(chr7:g.55241128::chr11:g.71728415) Note: The NUMA1 - EGFR rearrangement is a translocation that results in the fusion of NUMA1 exons 1-13 with EGFR exons 18-28. The fusion is predicted to be in frame and includes the kinase domain of EGFR.
CIC	0	MSKCC-DMP	P-0036003-T01-IM6	LIPE-AS1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) Rearrangement: c.3011:CIC_chr19:g.43041838inv Note: The CIC rearrangement is an inversion of exons 13 to 20. One of the breakpoints is within the exon 13 of CIC. Its functional significance is undetermined.
LIPE-AS1	0	MSKCC-DMP	P-0036003-T01-IM6	LIPE-AS1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) Rearrangement: c.3011:CIC_chr19:g.43041838inv Note: The CIC rearrangement is an inversion of exons 13 to 20. One of the breakpoints is within the exon 13 of CIC. Its functional significance is undetermined.
TFG	0	MSKCC-DMP	P-0035647-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732 Lab Notes Run Number: ArcherV3-CLIN-20180176 Macro-dissection: Unknown
GPR128	0	MSKCC-DMP	P-0035647-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732 Lab Notes Run Number: ArcherV3-CLIN-20180176 Macro-dissection: Unknown
NOTCH3	0	MSKCC-DMP	P-0036054-T01-IM6	KIRREL2-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4530_chr19:g.36346742inv Note: The NOTCH3 rearrangement is an inversion that includes NOTCH3 exons 1-25. One of the breakpoints is within exon 25. Multiple NOTCH3 rearrangements were detected in this sample a more complex rearrangement is possible.
KIRREL2	0	MSKCC-DMP	P-0036054-T01-IM6	KIRREL2-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.4530_chr19:g.36346742inv Note: The NOTCH3 rearrangement is an inversion that includes NOTCH3 exons 1-25. One of the breakpoints is within exon 25. Multiple NOTCH3 rearrangements were detected in this sample a more complex rearrangement is possible.
DEDD2	0	MSKCC-DMP	P-0036054-T01-IM6	CIC-DEDD2 fusion	yes	unknown		unknown	CIC (NM_015125) - DEDD2 (NM_133328) rearrangement: c.1465-67:CIC_c.-1266:DEDD2inv Note: The CIC - DEDD2 rearrangement is an inversion that include CIC exons 1-10 and the 3UTR of DEDD2. One of the breakpoints is within CIC exon 10.
CIC	0	MSKCC-DMP	P-0036054-T01-IM6	CIC-DEDD2 fusion	yes	unknown		unknown	CIC (NM_015125) - DEDD2 (NM_133328) rearrangement: c.1465-67:CIC_c.-1266:DEDD2inv Note: The CIC - DEDD2 rearrangement is an inversion that include CIC exons 1-10 and the 3UTR of DEDD2. One of the breakpoints is within CIC exon 10.
EZH1	0	MSKCC-DMP	P-0036059-T01-IM6	WNT3-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - WNT3 (NM_030753) rearrangement: c.1802:EZH1_c.80+3466:WNT3dup Note: The EZH1 - WNT3 rearrangement is a duplication that results in the fusion of EZH1 exons  1-16 with WNT3 exons 2-4. One of the breakpoints is within EZH1 exon 16.
WNT3	0	MSKCC-DMP	P-0036059-T01-IM6	WNT3-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - WNT3 (NM_030753) rearrangement: c.1802:EZH1_c.80+3466:WNT3dup Note: The EZH1 - WNT3 rearrangement is a duplication that results in the fusion of EZH1 exons  1-16 with WNT3 exons 2-4. One of the breakpoints is within EZH1 exon 16.
ALK	0	MSKCC-DMP	P-0036106-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-2055:EML4_c.3173-536:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0036106-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) fusion (EML4 exons 1-13 fused to ALK exons 20-29): c.1490-2055:EML4_c.3173-536:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
GOPC	0	MSKCC-DMP	P-0035868-T01-IM6	ROS1-GOPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GOPC-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes GOPC Exon8 (NM_020399) and ROS1 Exon35 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20180177 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0035868-T01-IM6	ROS1-GOPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GOPC-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes GOPC Exon8 (NM_020399) and ROS1 Exon35 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20180177 Macro-dissection: Unknown
CDH1	0	MSKCC-DMP	P-0031178-T02-IM6	MIR5093-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.388-226_chr16:g.85385815del Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 4-16.
MIR5093	0	MSKCC-DMP	P-0031178-T02-IM6	MIR5093-CDH1 fusion	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.388-226_chr16:g.85385815del Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 4-16.
ERG	0	MSKCC-DMP	P-0031178-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-4350:TMPRSS2_c.18+11076:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0031178-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-4350:TMPRSS2_c.18+11076:ERGdel
ERG	0	MSKCC-DMP	P-0036120-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+1353:TMPRSS2_c.19-13252:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0036120-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918)  fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+1353:TMPRSS2_c.19-13252:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
ETV6	0	MSKCC-DMP	P-0035767-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20180179 Macro-dissection: Unknown
NTRK3	0	MSKCC-DMP	P-0035767-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon5 (NM_001987) and NTRK3 Exon15 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20180179 Macro-dissection: Unknown
MSI2	0	MSKCC-DMP	P-0027456-T02-IM6	MSI2-intragenic	yes	unknown		out of frame	MSI2 (NM_138962) rearrangement: c.185+86_c.312+20657del Note: The MSI2 rearrangement is an intragenic deletion of exons 4-5. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0027456-T02-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.1082-1244_c.1719dup Note: The CTNNB1 rearrangement is an intragenic duplication of exons 8-11. One of the breakpoints is within exon 11. Its functional significance is undetermined.
POTEA	0	MSKCC-DMP	P-0027456-T02-IM6	MSH6-POTEA fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: t(2;8)(p16.3;p11.21)(chr2:g.48030834::chr8:g.43096828) Note: The MSH6 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0027456-T02-IM6	MSH6-POTEA fusion	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: t(2;8)(p16.3;p11.21)(chr2:g.48030834::chr8:g.43096828) Note: The MSH6 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0036261-T01-IM6	SLC30A5-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1716_chr5:g.5:68233907del Note: The PIK3R1 rearrangement is a deletion that includes PIK3R1 exons 13-15. One of the breakpoints is within exon 13.
SLC30A5	0	MSKCC-DMP	P-0036261-T01-IM6	SLC30A5-PIK3R1 fusion	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1716_chr5:g.5:68233907del Note: The PIK3R1 rearrangement is a deletion that includes PIK3R1 exons 13-15. One of the breakpoints is within exon 13.
ETV6	0	MSKCC-DMP	P-0036282-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.164-37058_c.1009+1038del Note: The ETV6 rearrangement is an intragenic deletion of exons 3-5. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0036321-T01-IM6	SORCS2-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: t(4;17)(p16.1;q21.31)(chr4:g.7544612::chr17:g.41228481) Note: The BRCA1 rearrangement is a translocation with a breakpoint in intron 13. The functional significance is undetermined.
SORCS2	0	MSKCC-DMP	P-0036321-T01-IM6	SORCS2-BRCA1 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: t(4;17)(p16.1;q21.31)(chr4:g.7544612::chr17:g.41228481) Note: The BRCA1 rearrangement is a translocation with a breakpoint in intron 13. The functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0036321-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.208_c.806-9677dup Note: The RUNX1 rearrangement results in the duplication of exons 4-7. One of the breakpoints is within exon 4. The functional significance is undetermined.
RAF1	0	MSKCC-DMP	P-0036321-T01-IM6	SATB1-RAF1 fusion	yes	unknown		unknown	RAF1 (NM_002880) - SATB1 (NM_001131010) rearrangement: c.742:RAF1_c.1576-11367:SATB1dup Note: The RAF1 - SATB1 rearrangement is a duplication that results in the fusion of RAF1 exons 1-7 with SATB1 exons 10-11. One of the breakpoints is within RAF1 exon 7. The functional significance is undetermined.
SATB1	0	MSKCC-DMP	P-0036321-T01-IM6	SATB1-RAF1 fusion	yes	unknown		unknown	RAF1 (NM_002880) - SATB1 (NM_001131010) rearrangement: c.742:RAF1_c.1576-11367:SATB1dup Note: The RAF1 - SATB1 rearrangement is a duplication that results in the fusion of RAF1 exons 1-7 with SATB1 exons 10-11. One of the breakpoints is within RAF1 exon 7. The functional significance is undetermined.
PPP1R9A	0	MSKCC-DMP	P-0031911-T02-IM6	MET-PPP1R9A fusion	yes	unknown		out of frame	MET (NM_000245) - PPP1R9A (NM_001166161) rearrangement: c.3632+34:MET_c.2046+10406:PPP1R9Adup Note: The MET - PPP1R9A rearrangement is a duplication which results in the fusion of MET exons 1-18 with PPP1R9A exons 7-18. This includes the kinase domain of MET. Its functional significance is undetermined.
MET	0	MSKCC-DMP	P-0031911-T02-IM6	MET-PPP1R9A fusion	yes	unknown		out of frame	MET (NM_000245) - PPP1R9A (NM_001166161) rearrangement: c.3632+34:MET_c.2046+10406:PPP1R9Adup Note: The MET - PPP1R9A rearrangement is a duplication which results in the fusion of MET exons 1-18 with PPP1R9A exons 7-18. This includes the kinase domain of MET. Its functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0036305-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 - (NM_000142) TACC3 (NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon3) : c.2334:FGFR3_c.274:TACC3dup Note: The FGFR3 - TACC3 Fusion includes the protein kinase domain of FGFR3. The breakpoints are within exon18 of FGFR3 and exon3 of TACC3.
FGFR3	0	MSKCC-DMP	P-0036305-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 - (NM_000142) TACC3 (NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon3) : c.2334:FGFR3_c.274:TACC3dup Note: The FGFR3 - TACC3 Fusion includes the protein kinase domain of FGFR3. The breakpoints are within exon18 of FGFR3 and exon3 of TACC3.
NOTCH3	0	MSKCC-DMP	P-0031395-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) Rearrangement : c.1192+11_c.2297-104inv Note: The NOTCH3 Rearrangement results in the intragenic inversion of exons 8-16 of NOTCH3. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036164-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.-48+1323:ERG_c.56-2136:TMPRSS2del Note: The ERG - TMPRSS2 rearrangement is a deletion of ERG exons 1-2 and TMPRSS2 exons 3-14. This involves the non-canonical ERG (NM_004449) transcript. The possibility of an TMPRSS2 - ERG fusion can not be excluded. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0036164-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.-48+1323:ERG_c.56-2136:TMPRSS2del Note: The ERG - TMPRSS2 rearrangement is a deletion of ERG exons 1-2 and TMPRSS2 exons 3-14. This involves the non-canonical ERG (NM_004449) transcript. The possibility of an TMPRSS2 - ERG fusion can not be excluded. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036176-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3823:TMPRSS2_c.18+14211:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0036176-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3823:TMPRSS2_c.18+14211:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
MDC1	0	MSKCC-DMP	P-0036178-T01-IM6	TUBB-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2847:MDC1_chr6:g.30692385del Note: The MDC1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.
TUBB	0	MSKCC-DMP	P-0036178-T01-IM6	TUBB-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2847:MDC1_chr6:g.30692385del Note: The MDC1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0036328-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) Rearrangement : c.59-2991_c.1549-50del Note: The FLT4 Rearrangement results in the intragenic inversion of exons 2-11. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0036331-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - LDLR (NM_000527) Rearrangement :  c.2859+79:SMARCA4_c.-3015:LDLRdel Note: The SMARAC4-LDLR Rearrangement results in the fusion of exons 1-19 SMARCA4 with the promoter region of LDLR. Its functional significance is undetermined.
LDLR	0	MSKCC-DMP	P-0036331-T01-IM6	LDLR-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - LDLR (NM_000527) Rearrangement :  c.2859+79:SMARCA4_c.-3015:LDLRdel Note: The SMARAC4-LDLR Rearrangement results in the fusion of exons 1-19 SMARCA4 with the promoter region of LDLR. Its functional significance is undetermined.
CAMTA1	0	MSKCC-DMP	P-0036332-T01-IM6	ARID1A-CAMTA1 fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement : c.1921-42:ARID1A_c.234+77783:CAMTA1inv Note: The ARID1A Rearrangement results in the inversion of exons 1-5 of ARID1A. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0036332-T01-IM6	ARID1A-CAMTA1 fusion	yes	unknown		unknown	ARID1A (NM_006015) Rearrangement : c.1921-42:ARID1A_c.234+77783:CAMTA1inv Note: The ARID1A Rearrangement results in the inversion of exons 1-5 of ARID1A. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0036332-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) Rearrangement : c.60+12161_c.541 Note: The NF1 Rearrangement results in the intragenic deletion of exons 1-5 of NF1. One of the breakpoints is within exon5. Its functional significance is undetermined.
DMRT2	0	MSKCC-DMP	P-0036332-T01-IM6	PTPRD-DMRT2 fusion	yes	unknown		unknown	PTPRD (NM_002839) Rearrangement : chr9:g.1444584_c.2289inv Note: The PTPRD Rearrangement results in the inversion of exons 25-46 of PTPRD. One of the breakpoints in PTPRD is within exon25. Its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0036332-T01-IM6	PTPRD-DMRT2 fusion	yes	unknown		unknown	PTPRD (NM_002839) Rearrangement : chr9:g.1444584_c.2289inv Note: The PTPRD Rearrangement results in the inversion of exons 25-46 of PTPRD. One of the breakpoints in PTPRD is within exon25. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036346-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon4): c.56-484:TMPRSS2_c.39+15996:ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
TMPRSS2	0	MSKCC-DMP	P-0036346-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon4): c.56-484:TMPRSS2_c.39+15996:ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
ANKRD11	0	MSKCC-DMP	P-0036348-T01-IM6	MIR5195-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) Rearrangement : t(14;16)(p32.31;q24.3)(chr14:g.107133040::chr16:g.89351017) Note: The ANKRD11 Rearrangement is a translocation event with a breakpoint in exon9. Its functional significance is undetermined.
MIR5195	0	MSKCC-DMP	P-0036348-T01-IM6	MIR5195-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) Rearrangement : t(14;16)(p32.31;q24.3)(chr14:g.107133040::chr16:g.89351017) Note: The ANKRD11 Rearrangement is a translocation event with a breakpoint in exon9. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036351-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) : c.56-2148:TMPRSS2_c.39+62508:ERG del Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
TMPRSS2	0	MSKCC-DMP	P-0036351-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) : c.56-2148:TMPRSS2_c.39+62508:ERG del Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
MAX	0	MSKCC-DMP	P-0036382-T01-IM6	MAX-intragenic	yes	unknown		out of frame	MAX (NM_002382) Rearrangement: c.64-887_c.296-28del Note: The MAX rearrangement is an intragenic deletion of exons 3 to 4. Its functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0027019-T01-IM6	MARS-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - MARS (NM_004990) rearrangement: c.1748:GLI1_c.1294-196:MARSdel Note: The GLI1 - MARS rearrangement is a deletion which results in the fusion of GLI1 exons 1-12 with MARS exons 11-21. One of the breakpoints is within GLI1 exon 12. Its functional significance is undetermined.
MARS	0	MSKCC-DMP	P-0027019-T01-IM6	MARS-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - MARS (NM_004990) rearrangement: c.1748:GLI1_c.1294-196:MARSdel Note: The GLI1 - MARS rearrangement is a deletion which results in the fusion of GLI1 exons 1-12 with MARS exons 11-21. One of the breakpoints is within GLI1 exon 12. Its functional significance is undetermined.
PKD1L2	0	MSKCC-DMP	P-0029223-T01-IM6	PLCG2-PKD1L2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: c.2254:PLCG2_chr16:g.81159441del Note: The PLCG2 rearrangement is a deletion of exons 1-21. One of the breakpoints is in exon 21. Its functional significance is undetermined.
PLCG2	0	MSKCC-DMP	P-0029223-T01-IM6	PLCG2-PKD1L2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: c.2254:PLCG2_chr16:g.81159441del Note: The PLCG2 rearrangement is a deletion of exons 1-21. One of the breakpoints is in exon 21. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0033090-T01-IM6	MET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - MET (NM_000245) fusion (KIF5B exons 1-24 fused to MET exons 15-21):t(7;10)(q31.2;p11.22)(chr7:g.116412397::chr10:g.32305234) Note: The KIF5B - MET fusion is predicted to be in frame and includes the kinase domain of MET
MET	0	MSKCC-DMP	P-0033090-T01-IM6	MET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - MET (NM_000245) fusion (KIF5B exons 1-24 fused to MET exons 15-21):t(7;10)(q31.2;p11.22)(chr7:g.116412397::chr10:g.32305234) Note: The KIF5B - MET fusion is predicted to be in frame and includes the kinase domain of MET
SUZ12	0	MSKCC-DMP	P-0035212-T01-IM6	KMT2A-SUZ12 fusion	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: t(11;17)(q23.3;q11.2)(chr11:g.118342702::chr17:g.30264018) Note: The KMT2A rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0035212-T01-IM6	KMT2A-SUZ12 fusion	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: t(11;17)(q23.3;q11.2)(chr11:g.118342702::chr17:g.30264018) Note: The KMT2A rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
DNAJC27-AS1	0	MSKCC-DMP	P-0036200-T01-IM6	ASXL2-DNAJC27-AS1 fusion	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.505-138:ASXL2_chr2:g.25223246inv Note: The ASXL2 rearrangement is an inversion of exons 6-12. Its functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0036200-T01-IM6	ASXL2-DNAJC27-AS1 fusion	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.505-138:ASXL2_chr2:g.25223246inv Note: The ASXL2 rearrangement is an inversion of exons 6-12. Its functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0036212-T01-IM6	TTC23-IGF1R fusion	yes	unknown		out of frame	IGF1R (NM_000875) - TTC23 (NM_001040659) rearrangement: c.2782+28:IGF1R_c.1144-2460:TTC23inv Note: The IGF1R - TTC23 rearrangement is an inversion which results in the fusion of IGF1R exons 1-13 with TTC23 exon 11. Its functional significance is undetermined.
TTC23	0	MSKCC-DMP	P-0036212-T01-IM6	TTC23-IGF1R fusion	yes	unknown		out of frame	IGF1R (NM_000875) - TTC23 (NM_001040659) rearrangement: c.2782+28:IGF1R_c.1144-2460:TTC23inv Note: The IGF1R - TTC23 rearrangement is an inversion which results in the fusion of IGF1R exons 1-13 with TTC23 exon 11. Its functional significance is undetermined.
TMC1	0	MSKCC-DMP	P-0036232-T01-IM6	TSC1-TMC1 fusion	yes	unknown		unknown	TSC1 (NM_000368) Rearrangement: c.1571:TSC1_chr9:g.75142084del Note: The TSC1 rearrangement is a deletion of exons 15-23 of TSC1. One of the breakpoints is within exon 15 of TSC1. The functional significance is undetermined. In addition, the presence of multiple TSC1 structural variants may reflect a more complex rearrangement that is not fully characterized by IMPACT.
TSC1	0	MSKCC-DMP	P-0036232-T01-IM6	TSC1-TMC1 fusion	yes	unknown		unknown	TSC1 (NM_000368) Rearrangement: c.1571:TSC1_chr9:g.75142084del Note: The TSC1 rearrangement is a deletion of exons 15-23 of TSC1. One of the breakpoints is within exon 15 of TSC1. The functional significance is undetermined. In addition, the presence of multiple TSC1 structural variants may reflect a more complex rearrangement that is not fully characterized by IMPACT.
SH2B3	0	MSKCC-DMP	P-0036236-T01-IM6	LINC00967-SH2B3 fusion	yes	unknown		unknown	SH2B3 (NM_005475) Rearrangement: t(8;12)(q13.1;q24.11)(chr8:g.67120297::chr12:g.111885689) Note: The SH2B3 rearrangement is a translocation with a breakpoint in intron 7 of SH2B3. The functional significance is undetermined.
LINC00967	0	MSKCC-DMP	P-0036236-T01-IM6	LINC00967-SH2B3 fusion	yes	unknown		unknown	SH2B3 (NM_005475) Rearrangement: t(8;12)(q13.1;q24.11)(chr8:g.67120297::chr12:g.111885689) Note: The SH2B3 rearrangement is a translocation with a breakpoint in intron 7 of SH2B3. The functional significance is undetermined.
PDE6B	0	MSKCC-DMP	P-0036236-T01-IM6	DNMT3A-PDE6B fusion	yes	unknown		unknown	DNMT3A (NM_022552) Rearrangement: t(2;4)(p23.1;p16.3(chr2:g.25467463::chr4:g.561524) Note: The DNMT3A rearrangement is a translocation with a breakpoint in exon 14 of DNMT3A. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0036236-T01-IM6	DNMT3A-PDE6B fusion	yes	unknown		unknown	DNMT3A (NM_022552) Rearrangement: t(2;4)(p23.1;p16.3(chr2:g.25467463::chr4:g.561524) Note: The DNMT3A rearrangement is a translocation with a breakpoint in exon 14 of DNMT3A. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0036244-T01-IM6	MGA-intragenic	yes	unknown		out of frame	MGA (NM_001164273) rearrangement: c.1064+9674_c.7892-53del Note: The MGA rearrangement is an intragenic deletion of exons 3-22. Its functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0036247-T01-IM6	MAP2K4-intragenic	yes	unknown		unknown	MAP2K4 (NM_003010) rearrangement: c.1041-4430_c.1060del Note: The MAP2K4 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10.
ALK	0	MSKCC-DMP	P-0036247-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+107:EML4_c.3172+470:ALKinv Note: The EML4 - ALK rearrangement is a fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0036247-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+107:EML4_c.3172+470:ALKinv Note: The EML4 - ALK rearrangement is a fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
LINC00114	0	MSKCC-DMP	P-0036349-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-1371:TMPRSS2_chr21:g.40097824del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detect by the IMPACT Panel cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0036349-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-1371:TMPRSS2_chr21:g.40097824del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detect by the IMPACT Panel cannot be ruled out.
FAM222B	0	MSKCC-DMP	P-0036357-T01-IM6	CDK12-FAM222B fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3269:CDK12_chr17:g.27096697inv Note: The CDK12 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0036357-T01-IM6	CDK12-FAM222B fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3269:CDK12_chr17:g.27096697inv Note: The CDK12 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
SNAI1	0	MSKCC-DMP	P-0036368-T01-IM6	RTEL1-SNAI1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: c.1794+42:RTEL1_chr20:g.48618565inv Note: The RTEL1 rearrangement is an inversion of exons 1-20. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0036368-T01-IM6	RTEL1-SNAI1 fusion	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: c.1794+42:RTEL1_chr20:g.48618565inv Note: The RTEL1 rearrangement is an inversion of exons 1-20. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0036409-T01-IM6	COPS3-FLCN fusion	yes	unknown		in frame	FLCN (NM_144997) - COPS3 (NM_003653) rearrangement: c.871+334:FLCN_c.55+2283:COPS3dup Note: The FLCN - COPS3 rearrangement is a duplication which results in the fusion of FLCN exons 1-8 with COPS3 exons 2-12. Its functional significance is undetermined.
COPS3	0	MSKCC-DMP	P-0036409-T01-IM6	COPS3-FLCN fusion	yes	unknown		in frame	FLCN (NM_144997) - COPS3 (NM_003653) rearrangement: c.871+334:FLCN_c.55+2283:COPS3dup Note: The FLCN - COPS3 rearrangement is a duplication which results in the fusion of FLCN exons 1-8 with COPS3 exons 2-12. Its functional significance is undetermined.
PTDSS1	0	MSKCC-DMP	P-0036411-T01-IM6	RAD50-PTDSS1 fusion	yes	unknown		out of frame	RAD50 (NM_005732) - PTDSS1 (NM_014754) rearrangement: t(5;8)(q31.1;q22.1)(chr5:g.131923393::chr8:g.97283528) Note: The RAD50 - PTDSS1 rearrangement is a translocation which may result in the fusion of RAD50 exons 1-6 with PTDSS1 exons 2-13. Its functional significance is undetermined.
RAD50	0	MSKCC-DMP	P-0036411-T01-IM6	RAD50-PTDSS1 fusion	yes	unknown		out of frame	RAD50 (NM_005732) - PTDSS1 (NM_014754) rearrangement: t(5;8)(q31.1;q22.1)(chr5:g.131923393::chr8:g.97283528) Note: The RAD50 - PTDSS1 rearrangement is a translocation which may result in the fusion of RAD50 exons 1-6 with PTDSS1 exons 2-13. Its functional significance is undetermined.
WDR7	0	MSKCC-DMP	P-0036423-T01-IM6	MALT1-WDR7 fusion	yes	unknown		unknown	MALT1 (NM_006785) - WDR7 (NM_015285) rearrangement: c.31:MALT1_c.4165-1604:WDR7dup Note: The MALT1 - WDR7 rearrangement is a duplication that results in a fusion of MALT1 exon 1 to WDR7 exons 26-28. One of the breakpoints is within exon 26. The functional significance is undetermined.
MALT1	0	MSKCC-DMP	P-0036423-T01-IM6	MALT1-WDR7 fusion	yes	unknown		unknown	MALT1 (NM_006785) - WDR7 (NM_015285) rearrangement: c.31:MALT1_c.4165-1604:WDR7dup Note: The MALT1 - WDR7 rearrangement is a duplication that results in a fusion of MALT1 exon 1 to WDR7 exons 26-28. One of the breakpoints is within exon 26. The functional significance is undetermined.
CPM	0	MSKCC-DMP	P-0036438-T01-IM6	IDH1-CPM fusion	yes	unknown		in frame	CPM (NM_001005502) - IDH1 (NM_005896) rearrangement t(2;12)(q34;q15)(chr2:g.209108415::chr12:g.69293886) Note: The CPM - IDH1 rearrangement is a translocation that results in a fusion of CPM exons 1-2 to IDH1 exons 6-10. The functional significance is undetermined.
IDH1	0	MSKCC-DMP	P-0036438-T01-IM6	IDH1-CPM fusion	yes	unknown		in frame	CPM (NM_001005502) - IDH1 (NM_005896) rearrangement t(2;12)(q34;q15)(chr2:g.209108415::chr12:g.69293886) Note: The CPM - IDH1 rearrangement is a translocation that results in a fusion of CPM exons 1-2 to IDH1 exons 6-10. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036438-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-1144:TMPRSS2_c.18+2770:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0036438-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-1144:TMPRSS2_c.18+2770:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
PPP2R1A	0	MSKCC-DMP	P-0036441-T01-IM6	ZFC3H1-PPP2R1A fusion	yes	unknown		out of frame	PPP2R1A (NM_014225) - ZFC3H1 (NM_144982) rearrangement: t(12;19)(q21.2;q13.41)(chr12:g.72019702::chr19:g.52715868) Note: The PPP2R1A - ZFC3H1 rearrangement is a translocation that results in a fusion of PPP2R1A exons 1-4 to ZFC3H1 exons 23-35. The functional significance is undetermined.
ZFC3H1	0	MSKCC-DMP	P-0036441-T01-IM6	ZFC3H1-PPP2R1A fusion	yes	unknown		out of frame	PPP2R1A (NM_014225) - ZFC3H1 (NM_144982) rearrangement: t(12;19)(q21.2;q13.41)(chr12:g.72019702::chr19:g.52715868) Note: The PPP2R1A - ZFC3H1 rearrangement is a translocation that results in a fusion of PPP2R1A exons 1-4 to ZFC3H1 exons 23-35. The functional significance is undetermined.
KAZN	0	MSKCC-DMP	P-0036481-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.2132:SPEN_chr1:g.14808094del Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within SPEN exon 11.
SPEN	0	MSKCC-DMP	P-0036481-T01-IM6	SPEN-KAZN fusion	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.2132:SPEN_chr1:g.14808094del Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within SPEN exon 11.
FBXL20	0	MSKCC-DMP	P-0036553-T01-IM6	CDK12-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.697-2344:FBXL20_c.738:CDK12inv Note: The FBXL20 - CDK12 rearrangement is an inversion that results in the fusion of FBXL20 exons 1-10 with CDK12 exons 1-14. One of the breakpoints is within CDK12 exon 1. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0036553-T01-IM6	CDK12-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.697-2344:FBXL20_c.738:CDK12inv Note: The FBXL20 - CDK12 rearrangement is an inversion that results in the fusion of FBXL20 exons 1-10 with CDK12 exons 1-14. One of the breakpoints is within CDK12 exon 1. The functional significance is undetermined.
NEUROD2	0	MSKCC-DMP	P-0036553-T01-IM6	BRCA1-NEUROD2 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.1530:BRCA1_chr17:g.37741308inv Note: The BRCA1 rearrangement results in the deletion of exons 10-23. One of the breakpoints is within exon 10.
BRCA1	0	MSKCC-DMP	P-0036553-T01-IM6	BRCA1-NEUROD2 fusion	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.1530:BRCA1_chr17:g.37741308inv Note: The BRCA1 rearrangement results in the deletion of exons 10-23. One of the breakpoints is within exon 10.
KIF5B	0	MSKCC-DMP	P-0033090-T01-IM6	MET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIF5B-MET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon24 (NM_004521) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20180129 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0033090-T01-IM6	MET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIF5B-MET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon24 (NM_004521) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20180129 Macro-dissection: Unknown
TSC2	0	MSKCC-DMP	P-0036292-T01-IM6	LHFPL3-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(7;16)(q22.3;p13.3)(chr7:g.104453296::chr16:g.2138054) Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 40.
LHFPL3	0	MSKCC-DMP	P-0036292-T01-IM6	LHFPL3-TSC2 fusion	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(7;16)(q22.3;p13.3)(chr7:g.104453296::chr16:g.2138054) Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 40.
ERG	0	MSKCC-DMP	P-0036294-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -  ERG (NM_182918) fusion: c.127-1016:TMPRSS2_c.18+4202:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 2-10. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement involving TMPRSS2 is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0036294-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -  ERG (NM_182918) fusion: c.127-1016:TMPRSS2_c.18+4202:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 2-10. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement involving TMPRSS2 is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CDK4	0	MSKCC-DMP	P-0036375-T01-IM6	ATP6V1C2-CDK4 fusion	yes	unknown		unknown	ATP6V1C2 (NM_001039362) - CDK4 (NM_000075) rearrangement: t(2;12)(p25.1;q13.3)(chr2:g.10902938::chr12:g.58144811) Note: The ATP6V1C2 - CDK4 rearrangement is a translocation which may result in the fusion of ATP6V1C2 exons 1-4 with CDK4 exons 4-8. Its functional significance is undetermined.
ATP6V1C2	0	MSKCC-DMP	P-0036375-T01-IM6	ATP6V1C2-CDK4 fusion	yes	unknown		unknown	ATP6V1C2 (NM_001039362) - CDK4 (NM_000075) rearrangement: t(2;12)(p25.1;q13.3)(chr2:g.10902938::chr12:g.58144811) Note: The ATP6V1C2 - CDK4 rearrangement is a translocation which may result in the fusion of ATP6V1C2 exons 1-4 with CDK4 exons 4-8. Its functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0036531-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.1704+126:RAD21_chr8:g.117854751del Note: The RAD21 rearrangement is a deletion of exon 14.  The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0036545-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-464:TMPRSS2_c.40-59641:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0036545-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-464:TMPRSS2_c.40-59641:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
LOC101929550	0	MSKCC-DMP	P-0036545-T01-IM6	WHSC1L1-LOC101929550 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.1963_chr8:g.36081862inv Note: The WHSC1L1 rearrangement results in the inversion of exons 10-24. One of the breakpoints is within exon 10. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0036545-T01-IM6	WHSC1L1-LOC101929550 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.1963_chr8:g.36081862inv Note: The WHSC1L1 rearrangement results in the inversion of exons 10-24. One of the breakpoints is within exon 10. The functional significance is undetermined.
LINC00114	0	MSKCC-DMP	P-0036573-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-537_chr21:g.40068238del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by IMPACT panel cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0036573-T01-IM6	TMPRSS2-LINC00114 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.56-537_chr21:g.40068238del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by IMPACT panel cannot be ruled out.
MAN1C1	0	MSKCC-DMP	P-0036594-T01-IM6	ARID1A-MAN1C1 fusion	yes	unknown		unknown	ARID1A (NM_006015) - MAN1C1 (NM_020379) Rearrangement: c.3763:ARID1A_c.638-26041:MAN1C1dup Note: The ARID1A-MAN1C1 Rearrangement results in the fusion of exons 1-15 of ARID1A with exons 3-12 of MAN1C1.The breakpoint in ARID1A is within exon15. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0036594-T01-IM6	ARID1A-MAN1C1 fusion	yes	unknown		unknown	ARID1A (NM_006015) - MAN1C1 (NM_020379) Rearrangement: c.3763:ARID1A_c.638-26041:MAN1C1dup Note: The ARID1A-MAN1C1 Rearrangement results in the fusion of exons 1-15 of ARID1A with exons 3-12 of MAN1C1.The breakpoint in ARID1A is within exon15. Its functional significance is undetermined.
C5orf42	0	MSKCC-DMP	P-0036662-T01-IM6	NTRK1-C5orf42 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: t(1;5)(q23.1;p13.2)(chr1:g.156837969::chr5:g.37075787) Note: The NTRK1 rearrangement is a translocation with a breakpoint within exon 5. Multiple NTKR1 rearrangements were detected in this sample and a more complex rearrangement resulting in a functional NTRK1 gene fusion is possible.
NTRK1	0	MSKCC-DMP	P-0036662-T01-IM6	NTRK1-C5orf42 fusion	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: t(1;5)(q23.1;p13.2)(chr1:g.156837969::chr5:g.37075787) Note: The NTRK1 rearrangement is a translocation with a breakpoint within exon 5. Multiple NTKR1 rearrangements were detected in this sample and a more complex rearrangement resulting in a functional NTRK1 gene fusion is possible.
SHPRH	0	MSKCC-DMP	P-0036662-T01-IM6	NTRK1-SHPRH fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - SHPRH (NM_001042683) rearrangement: t(1;6)(q231;q24.3)(chr1:g.156831180::chr6:g.146225530) Note: The NTRK1 - SHPRH rearrangement is a translocation that results in the fusion of NTRK1 exon 1 with SHPRH exons 26-30.
NTRK1	0	MSKCC-DMP	P-0036662-T01-IM6	NTRK1-SHPRH fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - SHPRH (NM_001042683) rearrangement: t(1;6)(q231;q24.3)(chr1:g.156831180::chr6:g.146225530) Note: The NTRK1 - SHPRH rearrangement is a translocation that results in the fusion of NTRK1 exon 1 with SHPRH exons 26-30.
EWSR1	0	MSKCC-DMP	P-0036669-T01-IM6	CDADC1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - CDADC1 (NM_030911) rearrangement: t(13;22)(q14.2;q12.2)(chr13:g.49835899::chr22:g.29694130) Note: The EWSR1 - CDADC1 rearrangement is a translocation that results in the fusion of EWSR1 exons 1-14 with CDADC1 exons 5-10.
CDADC1	0	MSKCC-DMP	P-0036669-T01-IM6	CDADC1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - CDADC1 (NM_030911) rearrangement: t(13;22)(q14.2;q12.2)(chr13:g.49835899::chr22:g.29694130) Note: The EWSR1 - CDADC1 rearrangement is a translocation that results in the fusion of EWSR1 exons 1-14 with CDADC1 exons 5-10.
FAM122B	0	MSKCC-DMP	P-0036669-T01-IM6	EP300-FAM122B fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(X;22)(q26.3;q13.2)(chrX:g.133828640::chr22:g.41560109) Note: The EP300 rearrangement is a translocation with a breakpoint within exon 22. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0036669-T01-IM6	EP300-FAM122B fusion	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(X;22)(q26.3;q13.2)(chrX:g.133828640::chr22:g.41560109) Note: The EP300 rearrangement is a translocation with a breakpoint within exon 22. The functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0036261-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180188 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0036261-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180188 Macro-dissection: Unknown
RAD21	0	MSKCC-DMP	P-0036478-T01-IM6	RSPO2-RAD21 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RAD21-RSPO2 fusion. Note: The rearrangement is an in-frame fusion between genes RAD21 Exon1 (NM_006265) and RSPO2 Exon2 (NM_178565). Lab Notes Run Number: ArcherV3-CLIN-20180188 Macro-dissection: Unknown
RSPO2	0	MSKCC-DMP	P-0036478-T01-IM6	RSPO2-RAD21 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RAD21-RSPO2 fusion. Note: The rearrangement is an in-frame fusion between genes RAD21 Exon1 (NM_006265) and RSPO2 Exon2 (NM_178565). Lab Notes Run Number: ArcherV3-CLIN-20180188 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0024686-T02-IM6	PLCD3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - PLCD3 (NM_133373) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43208249::chr21:g.42840366) Note: The TMPRSS2 rearrangement is a translocation involving TMPRSS2 exon 2 and PLCD3 exon 2. One of the breakpoints is within TMPRSS2 exon 2. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PLCD3	0	MSKCC-DMP	P-0024686-T02-IM6	PLCD3-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - PLCD3 (NM_133373) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43208249::chr21:g.42840366) Note: The TMPRSS2 rearrangement is a translocation involving TMPRSS2 exon 2 and PLCD3 exon 2. One of the breakpoints is within TMPRSS2 exon 2. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0024686-T02-IM6	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41615041::chr21:g.42840400) Note: The TMPRSS2 rearrangement is a translocation which may result in the fusion of TMPRSS2 exons 1-12 with ETV4 exons 5-13. One of the breakpoints is within TMPRSS2 exon 12.Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ETV4	0	MSKCC-DMP	P-0024686-T02-IM6	ETV4-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41615041::chr21:g.42840400) Note: The TMPRSS2 rearrangement is a translocation which may result in the fusion of TMPRSS2 exons 1-12 with ETV4 exons 5-13. One of the breakpoints is within TMPRSS2 exon 12.Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a complex TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
LUZP2	0	MSKCC-DMP	P-0028690-T01-IM6	CCND1-LUZP2 fusion	yes	unknown		unknown	CCND1 (NM_053056) Rearrangement: chr11:g.24441784_c.*93inv Note: The CCND1 Rearranment results in the inversion of exons 1-5 of CCND1. One of the breakpoints in the 3-UTR after the codong stopsite. Its functional significance is undetermined.
CCND1	0	MSKCC-DMP	P-0028690-T01-IM6	CCND1-LUZP2 fusion	yes	unknown		unknown	CCND1 (NM_053056) Rearrangement: chr11:g.24441784_c.*93inv Note: The CCND1 Rearranment results in the inversion of exons 1-5 of CCND1. One of the breakpoints in the 3-UTR after the codong stopsite. Its functional significance is undetermined.
CHST1	0	MSKCC-DMP	P-0036558-T01-IM6	PRDM14-CHST1 fusion	yes	unknown		unknown	PRDM14 (NM_024504) rearrangement: t(8;11)(q13.3;p11.2)(chr8:g.70980437::chr11:g.45629910) Note: The PRDM14 rearrangement is a translocation with a breakpoint in PRDM14 intron 4. The functional significance is undetermined.
PRDM14	0	MSKCC-DMP	P-0036558-T01-IM6	PRDM14-CHST1 fusion	yes	unknown		unknown	PRDM14 (NM_024504) rearrangement: t(8;11)(q13.3;p11.2)(chr8:g.70980437::chr11:g.45629910) Note: The PRDM14 rearrangement is a translocation with a breakpoint in PRDM14 intron 4. The functional significance is undetermined.
CD276	0	MSKCC-DMP	P-0036574-T01-IM6	ESM1-CD276 fusion	yes	unknown		unknown	CD276 (NM_001024736) Rearrangement:  t(5;15)(q11.2;q24.1)(chr5:g.54239847::chr15:g.73996135) Note: The CD276 Rearrangement is a translocation event with a breakpoint in exon5. Its functional significance is undetermined.
ESM1	0	MSKCC-DMP	P-0036574-T01-IM6	ESM1-CD276 fusion	yes	unknown		unknown	CD276 (NM_001024736) Rearrangement:  t(5;15)(q11.2;q24.1)(chr5:g.54239847::chr15:g.73996135) Note: The CD276 Rearrangement is a translocation event with a breakpoint in exon5. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0036582-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2048-99:BRD4_chr19:g.15405858del Note: The BRD4 rearrangement is a deletion of exons 1-11. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0036631-T01-IM6	CXorf36-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement : c.3921_chrX:g.44979900inv Note: The KDM6A Rearrangement results in the inversion of exons 27-29 of KDM6A. The breakpoint in KDM6A is within exon27.Its functional significance is undetermined.
CXorf36	0	MSKCC-DMP	P-0036631-T01-IM6	CXorf36-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement : c.3921_chrX:g.44979900inv Note: The KDM6A Rearrangement results in the inversion of exons 27-29 of KDM6A. The breakpoint in KDM6A is within exon27.Its functional significance is undetermined.
MET	0	MSKCC-DMP	P-0035162-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:     POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL   MET Exon 14 Skipping (NM_000245). This alteration was detected despite the sample quality falling slightly below our established threshold.  Lab Notes Run Number: ArcherV3-CLIN-20180167 Macro-dissection: Unknown
RPL27	0	MSKCC-DMP	P-0036746-T01-IM6	BRCA1-RPL27 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - RPL27 (NM_000988) Rearrangement : c.3356:BRCA1_c.252-1051:RPL27inv Note: The BRCA1- RPL27 Rearrangement results in the fusion of exons 1-10 of BRCA1 with exons 4-5 of RPL27.The breakpoint in BRCA1 is within exon10. Its functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0036746-T01-IM6	BRCA1-RPL27 fusion	yes	unknown		unknown	BRCA1 (NM_007294) - RPL27 (NM_000988) Rearrangement : c.3356:BRCA1_c.252-1051:RPL27inv Note: The BRCA1- RPL27 Rearrangement results in the fusion of exons 1-10 of BRCA1 with exons 4-5 of RPL27.The breakpoint in BRCA1 is within exon10. Its functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0036522-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180190 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0036522-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180190 Macro-dissection: Unknown
CTNND2	0	MSKCC-DMP	P-0036662-T01-IM6	TERT-CTNND2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CTNND2-TERT fusion. Note: The rearrangement is an out of frame fusion between genes CTNND2 Exon16 (NM_001332) and TERT Exon12 (NM_198253). The functional significance of this event is unknown.  Lab Notes Run Number: ArcherV3-CLIN-20180192 Macro-dissection: Unknown
TERT	0	MSKCC-DMP	P-0036662-T01-IM6	TERT-CTNND2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CTNND2-TERT fusion. Note: The rearrangement is an out of frame fusion between genes CTNND2 Exon16 (NM_001332) and TERT Exon12 (NM_198253). The functional significance of this event is unknown.  Lab Notes Run Number: ArcherV3-CLIN-20180192 Macro-dissection: Unknown
APC	0	MSKCC-DMP	P-0020290-T02-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4458_chr5:g.112194235del Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.
SRP19	0	MSKCC-DMP	P-0020290-T02-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4458_chr5:g.112194235del Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.
FAM126B	0	MSKCC-DMP	P-0035898-T01-IM6	CASP8-FAM126B fusion	yes	unknown		unknown	CASP8 (NM_001080125) rearrangement: chr2:g.201843889_c.1327:CASP8dup Note: The CASP8 rearrangement is a duplication that includes CASP8 exon 1-8. One of the breakpoints is within exon 8.
CASP8	0	MSKCC-DMP	P-0035898-T01-IM6	CASP8-FAM126B fusion	yes	unknown		unknown	CASP8 (NM_001080125) rearrangement: chr2:g.201843889_c.1327:CASP8dup Note: The CASP8 rearrangement is a duplication that includes CASP8 exon 1-8. One of the breakpoints is within exon 8.
MEF2B	0	MSKCC-DMP	P-0036613-T01-IM6	ZNF623-MEF2B fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: t(8;19)(q24.3;p13.11)(chr8:g.144708079::chr19:g.19256750) Note: The MEF2B rearrangement is a translocation involving a breakpoint in exon 9. Its functional significance is undetermined.
ZNF623	0	MSKCC-DMP	P-0036613-T01-IM6	ZNF623-MEF2B fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: t(8;19)(q24.3;p13.11)(chr8:g.144708079::chr19:g.19256750) Note: The MEF2B rearrangement is a translocation involving a breakpoint in exon 9. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0036677-T01-IM6	ZHX1-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: t(X;8)(q24.13;p11.3)(chrX:g.44941938::chr8:g.124293775) Note: The KDM6A rearrangement is a translocation with a breakpoint within intron 21. The functional significance is undetermined.
ZHX1	0	MSKCC-DMP	P-0036677-T01-IM6	ZHX1-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: t(X;8)(q24.13;p11.3)(chrX:g.44941938::chr8:g.124293775) Note: The KDM6A rearrangement is a translocation with a breakpoint within intron 21. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0036717-T01-IM6	TNRC6C-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: (17;19)(q25.3;p13.2)(chr17:g.76087542::chr19:g.11141361) Note: The SMARCA4 intragenic rearrangement is a translocation with a breakpoint in intron 24. The functional significance is undetermined.
TNRC6C	0	MSKCC-DMP	P-0036717-T01-IM6	TNRC6C-SMARCA4 fusion	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: (17;19)(q25.3;p13.2)(chr17:g.76087542::chr19:g.11141361) Note: The SMARCA4 intragenic rearrangement is a translocation with a breakpoint in intron 24. The functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0036759-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.1802_c.2997+287del Note: The BCOR rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Its functional significance is undetermined.
GSK3B	0	MSKCC-DMP	P-0036849-T01-IM6	GSK3B-intragenic	yes	unknown		out of frame	GSK3B (NM_002093) rearrangement: c.813+99_c.1235-7556del Note: The GSK3B rearrangement is an intragenic deletion of exons 8-11. The functional significance is undetermined.
PRR20D	0	MSKCC-DMP	P-0036920-T01-IM6	ERCC5-PRR20D fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement: chr13:g.57179785_c.1851del Note: The ERCC5 rearrangement is a deletion that includes ERCC5 exons 1-8. One of the breakpoints is within ERCC5 exon 8. The functional significance is undetermined.
ERCC5	0	MSKCC-DMP	P-0036920-T01-IM6	ERCC5-PRR20D fusion	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement: chr13:g.57179785_c.1851del Note: The ERCC5 rearrangement is a deletion that includes ERCC5 exons 1-8. One of the breakpoints is within ERCC5 exon 8. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0036698-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.484+2165_c.3170del Note: The ATRX rearrangement is an intragenic deletion of exons 7-9. One of the breakpoints is within exon 9.
MGA	0	MSKCC-DMP	P-0036732-T01-IM6	EHD4-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) Rearrangement: c.2013+14:MGA_chr15:g.42199394del Note: The MGA rearrangement results in the deletion of MGA exons 4 to 24. Its functional significance is undetermined.
EHD4	0	MSKCC-DMP	P-0036732-T01-IM6	EHD4-MGA fusion	yes	unknown		unknown	MGA (NM_001164273) Rearrangement: c.2013+14:MGA_chr15:g.42199394del Note: The MGA rearrangement results in the deletion of MGA exons 4 to 24. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0036810-T01-IM6	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement: c.597+30_c.920+31del Note: The STK11 rearrangement is an intragenic deletion of exons 5-7.
APC	0	MSKCC-DMP	P-0036892-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) Rearrangement : c.4189_c.6465del Note: The APC Rearrangement results in the intragenic deletion of exon16 of APC. Both the breakpoints are within 16. Its functional significance is undetermined.
RAB8A	0	MSKCC-DMP	P-0036893-T01-IM6	PIK3R2-RAB8A fusion	yes	unknown		unknown	PIK3R2 (NM_005027) Rearrangement : c.1290+57:PIK3R2_c.-2922:RAB8Ainv Note : The PIK3R2 Rearrangement results in the inversion of exons 1-10 of PIK3R2. Its functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0036893-T01-IM6	PIK3R2-RAB8A fusion	yes	unknown		unknown	PIK3R2 (NM_005027) Rearrangement : c.1290+57:PIK3R2_c.-2922:RAB8Ainv Note : The PIK3R2 Rearrangement results in the inversion of exons 1-10 of PIK3R2. Its functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0036895-T01-IM6	LOC100420587-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : t(19,22)(q11,q12.2)(chr19:g.28825367::chr22:g.30079061) Note: The NF2 Rearrangement is a translocation event with the breakpoint intron 15. Its functional significance is undetermined.
LOC100420587	0	MSKCC-DMP	P-0036895-T01-IM6	LOC100420587-NF2 fusion	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : t(19,22)(q11,q12.2)(chr19:g.28825367::chr22:g.30079061) Note: The NF2 Rearrangement is a translocation event with the breakpoint intron 15. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0036669-T01-IM6	CDADC1-EWSR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EWSR1-CDADC1 fusion. Note: The rearrangement is an in-frame fusion between genes EWSR1 Exon11 (NM_005243) and CDADC1 Exon5 (NM_030911). Lab Notes Run Number: ArcherV3-CLIN-20180193 Macro-dissection: Unknown
CDADC1	0	MSKCC-DMP	P-0036669-T01-IM6	CDADC1-EWSR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EWSR1-CDADC1 fusion. Note: The rearrangement is an in-frame fusion between genes EWSR1 Exon11 (NM_005243) and CDADC1 Exon5 (NM_030911). Lab Notes Run Number: ArcherV3-CLIN-20180193 Macro-dissection: Unknown
ATR	0	MSKCC-DMP	P-0036766-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.1863_c.1885+832del Note: The ATR rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. Its functional significance is undetermined.
EXOC4	0	MSKCC-DMP	P-0036937-T01-IM6	BRAF-EXOC4 fusion	yes	unknown		out of frame	EXOC4 (NM_021807) - BRAF (NM_004333) fusion: c.1514+93469:EXOC4_c.1141-2857:BRAFinv Note: The EXOC4 - BRAF fusion involves EXOC4 exons 1-10 and BRAF exons 9-18, including the BRAF kinase domain.
BRAF	0	MSKCC-DMP	P-0036937-T01-IM6	BRAF-EXOC4 fusion	yes	unknown		out of frame	EXOC4 (NM_021807) - BRAF (NM_004333) fusion: c.1514+93469:EXOC4_c.1141-2857:BRAFinv Note: The EXOC4 - BRAF fusion involves EXOC4 exons 1-10 and BRAF exons 9-18, including the BRAF kinase domain.
ITSN1	0	MSKCC-DMP	P-0037005-T01-IM6	IGF1R-ITSN1 fusion	yes	unknown		out of frame	IGF1R (NM_000875) - ITSN1 (NM_003024) rearrangement: t(15;21)(q26.3;q22.11)(chr15:g.99456690::chr21:g.35197921) Note: The IGF1R - ITSN1 rearrangement is a translocation that results in a fusion of IGF1R exons 1-8 to ITSN1 exons 27-40. The functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0037005-T01-IM6	IGF1R-ITSN1 fusion	yes	unknown		out of frame	IGF1R (NM_000875) - ITSN1 (NM_003024) rearrangement: t(15;21)(q26.3;q22.11)(chr15:g.99456690::chr21:g.35197921) Note: The IGF1R - ITSN1 rearrangement is a translocation that results in a fusion of IGF1R exons 1-8 to ITSN1 exons 27-40. The functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0037005-T01-IM6	EMBP1-ATR fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(1;3)(p11.2;q23)(chr1:g.121485434::chr3:g.142184004) Note: The ATR rearrangement is a translocation with a breakpoint in exon 41. The functional significance is undetermined.
EMBP1	0	MSKCC-DMP	P-0037005-T01-IM6	EMBP1-ATR fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(1;3)(p11.2;q23)(chr1:g.121485434::chr3:g.142184004) Note: The ATR rearrangement is a translocation with a breakpoint in exon 41. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0037008-T01-IM6	ULK4-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.936+16:CTNNB1_chr3:g.41368388del Note: The CTNNB1 rearrangement is a deletion of exons 7-15. The functional significance is undetermined.
ULK4	0	MSKCC-DMP	P-0037008-T01-IM6	ULK4-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.936+16:CTNNB1_chr3:g.41368388del Note: The CTNNB1 rearrangement is a deletion of exons 7-15. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0012649-T02-IM6	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement: c.465-120_c.863-89del Note: The STK11 rearrangement is an intragenic deletion of exons 4-6. Its functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0014384-T02-IM6	DNMT3B-intragenic	yes	unknown		out of frame	DNMT3B (NM_006892) Rearrangement : c.1997-115_c.2231+41dup Note: The DNMT3B Rearrangement results in the duplication of exons 19-20 of DNMT3B. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0015435-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.304-21366:CCDC6_c.2136+785:RETinv Note; The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET
CCDC6	0	MSKCC-DMP	P-0015435-T01-IM6	CCDC6-RET fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.304-21366:CCDC6_c.2136+785:RETinv Note; The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET
BRD4	0	MSKCC-DMP	P-0015507-T01-IM6	PGLYRP2-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) Rearrangement : c.230:BRD4_c.62-157:PGLYRP2inv Note: The BRD4 Rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
PGLYRP2	0	MSKCC-DMP	P-0015507-T01-IM6	PGLYRP2-BRD4 fusion	yes	unknown		unknown	BRD4 (NM_058243) Rearrangement : c.230:BRD4_c.62-157:PGLYRP2inv Note: The BRD4 Rearrangement results in the inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.
LOC101927915	0	MSKCC-DMP	P-0017563-T01-IM5	EPHA7-LOC101927915 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: t(6;8)(q16.1;q24.23)(chr6:g.93982172::chr8:g.138179021) Note: The EPHA7 rearrangement is a translocation that may result in a truncation of exons 6-17. The functional significance is undetermined.
EPHA7	0	MSKCC-DMP	P-0017563-T01-IM5	EPHA7-LOC101927915 fusion	yes	unknown		unknown	EPHA7 (NM_004440) rearrangement: t(6;8)(q16.1;q24.23)(chr6:g.93982172::chr8:g.138179021) Note: The EPHA7 rearrangement is a translocation that may result in a truncation of exons 6-17. The functional significance is undetermined.
ADAMTSL1	0	MSKCC-DMP	P-0017900-T01-IM6	CDKN2Ap14ARF-ADAMTSL1 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement : chr9:g.18389532_c.317-3482:CDKN2Ap14ARFinv Note: The CDKN2Ap14ARF Rearrangement results in the inversion of exon 2. Its functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0017900-T01-IM6	CDKN2Ap14ARF-ADAMTSL1 fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement : chr9:g.18389532_c.317-3482:CDKN2Ap14ARFinv Note: The CDKN2Ap14ARF Rearrangement results in the inversion of exon 2. Its functional significance is undetermined.
ADAMTSL1	0	MSKCC-DMP	P-0017900-T01-IM6	CDKN2Ap16INK4A-ADAMTSL1 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : chr9:g.18389532_c.138:CDKN2Ap16INK4Ainv Note: The CDKN2Ap16INK4A Rearrangement results in the inversion of exons 1-3.The breakpoint in CDKN2Ap16INK4A is within exon1.  Its functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0017900-T01-IM6	CDKN2Ap16INK4A-ADAMTSL1 fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : chr9:g.18389532_c.138:CDKN2Ap16INK4Ainv Note: The CDKN2Ap16INK4A Rearrangement results in the inversion of exons 1-3.The breakpoint in CDKN2Ap16INK4A is within exon1.  Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0018687-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.329-768_c.464-4544del Note: The ETV6 rearrangement results in the deletion of exon 4. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0018886-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMRPSS2 exon 1 fused  with ERG exons 2-10): c.56-2764:TMPRSS2_c.18+8733:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0018886-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMRPSS2 exon 1 fused  with ERG exons 2-10): c.56-2764:TMPRSS2_c.18+8733:ERGdel
CDC37L1	0	MSKCC-DMP	P-0018886-T01-IM6	JAK2-CDC37L1 fusion	yes	unknown		unknown	CDC37L1 (NM_017913) - JAK2 (NM_004972) rearrangement: c.635:CDC37L1_c.3060-11016:JAK2del Note: The CDC37L1 - JAK2 rearrangement is a deletion that results in the fusion of CDC37L1 exons 1-5 with JAK2 exons 23-25. One of the breakpoints is within CDC37L1 exon 5. The functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0018886-T01-IM6	JAK2-CDC37L1 fusion	yes	unknown		unknown	CDC37L1 (NM_017913) - JAK2 (NM_004972) rearrangement: c.635:CDC37L1_c.3060-11016:JAK2del Note: The CDC37L1 - JAK2 rearrangement is a deletion that results in the fusion of CDC37L1 exons 1-5 with JAK2 exons 23-25. One of the breakpoints is within CDC37L1 exon 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0019347-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2419:TMPRSS2_c.19-7767:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0019347-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2419:TMPRSS2_c.19-7767:ERGdel
LOC101928622	0	MSKCC-DMP	P-0020159-T01-IM6	INPP4B-LOC101928622 fusion	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement: chr4:g.34776389_c.526:INPP4Binv Note: The INPP4B rearrangement is an inversion which includes exons 1-10 of INPP4B. One of the breakpoints is within INPP4B exon 10. The functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0020159-T01-IM6	INPP4B-LOC101928622 fusion	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement: chr4:g.34776389_c.526:INPP4Binv Note: The INPP4B rearrangement is an inversion which includes exons 1-10 of INPP4B. One of the breakpoints is within INPP4B exon 10. The functional significance is undetermined.
RTF1	0	MSKCC-DMP	P-0020224-T01-IM6	MGA-RTF1 fusion	yes	unknown		unknown	MGA (NM_001164273) - RTF1 (NM_015138) rearrangement: c.5400:MGA_c.663-1603:RTF1dup Note: The MGA - RTF1 rearrangement is a duplication which results in the fusion of MGA exons 1-16 with RTF1 exons 5-18. One of the breakpoints is within MGA exon 16.
MGA	0	MSKCC-DMP	P-0020224-T01-IM6	MGA-RTF1 fusion	yes	unknown		unknown	MGA (NM_001164273) - RTF1 (NM_015138) rearrangement: c.5400:MGA_c.663-1603:RTF1dup Note: The MGA - RTF1 rearrangement is a duplication which results in the fusion of MGA exons 1-16 with RTF1 exons 5-18. One of the breakpoints is within MGA exon 16.
APC	0	MSKCC-DMP	P-0020433-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement : c.4823:APC_c.-2279:SRP19del Note: The APC - SRP19 Rearrangement results in the fusion of exons 1-16 of APC with the promoter region of SRP19. The breakpoint in APC is within exon16. Its functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0020433-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement : c.4823:APC_c.-2279:SRP19del Note: The APC - SRP19 Rearrangement results in the fusion of exons 1-16 of APC with the promoter region of SRP19. The breakpoint in APC is within exon16. Its functional significance is undetermined.
PCSK5	0	MSKCC-DMP	P-0020459-T01-IM6	ABL1-PCSK5 fusion	yes	unknown		unknown	ABL1 (NM_005157) rearrangement: chr9:g.78504638_c.79+61:ABL1inv Note: The ABL1 rearrangement is an inversion of exon 1. The functional significance is undetermined
ABL1	0	MSKCC-DMP	P-0020459-T01-IM6	ABL1-PCSK5 fusion	yes	unknown		unknown	ABL1 (NM_005157) rearrangement: chr9:g.78504638_c.79+61:ABL1inv Note: The ABL1 rearrangement is an inversion of exon 1. The functional significance is undetermined
LOC101929694	0	MSKCC-DMP	P-0020574-T01-IM6	GSK3B-LOC101929694 fusion	yes	unknown		unknown	GSK3B (NM_002093) rearrangement: chr3:g.112419488_c.1136-76:GSK3Binv Note: The GSK3B rearrangement is an inversion of exons 11-12. The functional significance is undetermined.
GSK3B	0	MSKCC-DMP	P-0020574-T01-IM6	GSK3B-LOC101929694 fusion	yes	unknown		unknown	GSK3B (NM_002093) rearrangement: chr3:g.112419488_c.1136-76:GSK3Binv Note: The GSK3B rearrangement is an inversion of exons 11-12. The functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0020713-T01-IM6	CRABP2-INSR fusion	yes	unknown		unknown	INSR (NM_000208) - CRABP2 (NM_001878) rearrangement: t(1,19)(q23.1,p13.2)(chr1:g.156675691::chr19:c.2667) Note: The INSR-CRABP2 rearrangement is a translocation which may result in the fusion of INSR exons 1-13 with CRABP2 exons 1-4. One of the breakpoints is within INSR exon 13. The functional significance is undetermined.
CRABP2	0	MSKCC-DMP	P-0020713-T01-IM6	CRABP2-INSR fusion	yes	unknown		unknown	INSR (NM_000208) - CRABP2 (NM_001878) rearrangement: t(1,19)(q23.1,p13.2)(chr1:g.156675691::chr19:c.2667) Note: The INSR-CRABP2 rearrangement is a translocation which may result in the fusion of INSR exons 1-13 with CRABP2 exons 1-4. One of the breakpoints is within INSR exon 13. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0020844-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-1626:TMPRSS2_c.40-61304:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.
TMPRSS2	0	MSKCC-DMP	P-0020844-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exons 1-2 fused to ERG exons 4-11):c.127-1626:TMPRSS2_c.40-61304:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.
ST7-AS1	0	MSKCC-DMP	P-0020844-T01-IM6	BRAF-ST7-AS1 fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: g.116584014_c.1141-745inv Note: The BRAF rearrangement results in the inversion of exons 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0020844-T01-IM6	BRAF-ST7-AS1 fusion	yes	unknown		unknown	BRAF (NM_004333) rearrangement: g.116584014_c.1141-745inv Note: The BRAF rearrangement results in the inversion of exons 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
NUB1	0	MSKCC-DMP	P-0020844-T01-IM6	KMT2C-NUB1 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: g.151053870_c.12456del Note: The KMT2C rearrangement results in the deletion of exons 49-59. One of the breakpoints is within exon 49. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0020844-T01-IM6	KMT2C-NUB1 fusion	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: g.151053870_c.12456del Note: The KMT2C rearrangement results in the deletion of exons 49-59. One of the breakpoints is within exon 49. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0021673-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3939:TMPRSS2_c.18+2925:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0021673-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3939:TMPRSS2_c.18+2925:ERGdel
BRCA2	0	MSKCC-DMP	P-0023930-T01-IM6	KL-BRCA2 fusion	yes	unknown		out of frame	BRCA2 (NM_000059) - KL (NM_004795) rearrangement: c.6841+166:BRCA2_c.819+9933:KLdel Note: The BRCA2 - KL rearrangement is a deletion of a portion of BRCA2, which results in the fusion of BRCA2 exons 1-11 with KL exons 2-5
KL	0	MSKCC-DMP	P-0023930-T01-IM6	KL-BRCA2 fusion	yes	unknown		out of frame	BRCA2 (NM_000059) - KL (NM_004795) rearrangement: c.6841+166:BRCA2_c.819+9933:KLdel Note: The BRCA2 - KL rearrangement is a deletion of a portion of BRCA2, which results in the fusion of BRCA2 exons 1-11 with KL exons 2-5
TMPRSS2	0	MSKCC-DMP	P-0023930-T01-IM6	DYM-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q21.1;q22.3)(chr18:g.46767863::chr21:g.42874721) Note: The TMPRSS2 rearrangement is a translocation involving exon 2. By IMPACT, the possibility cannot be excluded of a more complex rearrangement resulting in the expected TMPRSS2 - ERG fusion. The functional significance of this structural variant is undetermined.
DYM	0	MSKCC-DMP	P-0023930-T01-IM6	DYM-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q21.1;q22.3)(chr18:g.46767863::chr21:g.42874721) Note: The TMPRSS2 rearrangement is a translocation involving exon 2. By IMPACT, the possibility cannot be excluded of a more complex rearrangement resulting in the expected TMPRSS2 - ERG fusion. The functional significance of this structural variant is undetermined.
SMARCA4	0	MSKCC-DMP	P-0026232-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.-31-1296_c.1074dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 2-6. One of the breakpoints is within exon 6.
BCL2L11	0	MSKCC-DMP	P-0026232-T01-IM6	BCL2L11-intragenic	yes	unknown		unknown	BCL2L11 (NM_138621) rearrangement: c.498+695_c.506del Note: The BCL2L11 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.
FAM58A	0	MSKCC-DMP	P-0026232-T01-IM6	FAM58A-intragenic	yes	unknown		unknown	FAM58A (NM_152274) rearrangement: c.111-630_c.177dup Note: The FAM58A rearrangement is an intragenic duplication of exon 2. One of the breakpoints is within exon 2.
TP53	0	MSKCC-DMP	P-0026238-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.673-240_c.965del Note: The TP53 rearrangement is an intragenic deletion of exons 7-9. One of the breakpoints is within exon 9.
ERG	0	MSKCC-DMP	P-0026238-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+4255:TMPRSS2_c.18+13682:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0026238-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+4255:TMPRSS2_c.18+13682:ERGdel
SETD2	0	MSKCC-DMP	P-0026384-T01-IM6	SETD2-intragenic	yes	unknown		in frame	SETD2 (NM_014159) Rearrangement : c.4840-828_5142+70dup Note : The SETD2 Rearrangement results in the intragenic duplication of exons 7-9 of SETD2.Its functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0026615-T02-IM6	NRG1-PAK1 fusion	yes	unknown		unknown	PAK1 (NM_002576) Rearrangement: t(8;11)(p12;q13.5)(chr8:g.32259693::chr11:g.77036046) Note: The PAK1 rearrangement is a translocation with breakpoints within intron 15 of PAK1. The functional significance is undetermined.
NRG1	0	MSKCC-DMP	P-0026615-T02-IM6	NRG1-PAK1 fusion	yes	unknown		unknown	PAK1 (NM_002576) Rearrangement: t(8;11)(p12;q13.5)(chr8:g.32259693::chr11:g.77036046) Note: The PAK1 rearrangement is a translocation with breakpoints within intron 15 of PAK1. The functional significance is undetermined.
C11orf30	0	MSKCC-DMP	P-0028258-T01-IM6	PAK1-C11orf30 fusion	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.1181_chr11:g.76259831dup Note: The PAK1 rearrangement is a duplication that includes PAK1 exons 12-15. One of the breakpoints is within PAK1 exon 12. The functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0028258-T01-IM6	PAK1-C11orf30 fusion	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.1181_chr11:g.76259831dup Note: The PAK1 rearrangement is a duplication that includes PAK1 exons 12-15. One of the breakpoints is within PAK1 exon 12. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0028298-T01-IM6	ADAMTS16-TERT fusion	yes	unknown		unknown	ADAMTS16 (NM_139056) - TERT (NM_198253) rearrangement: c.175+1379C:ADAMTS16_c.-237:TERTinv Note: The ADAMTS16 - TERT rearrangement is an inversion which results in the fusion of ADAMTS16 exons 1-2 with TERT exons 1-16. Its functional significance is undetermined.
ADAMTS16	0	MSKCC-DMP	P-0028298-T01-IM6	ADAMTS16-TERT fusion	yes	unknown		unknown	ADAMTS16 (NM_139056) - TERT (NM_198253) rearrangement: c.175+1379C:ADAMTS16_c.-237:TERTinv Note: The ADAMTS16 - TERT rearrangement is an inversion which results in the fusion of ADAMTS16 exons 1-2 with TERT exons 1-16. Its functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0028347-T01-IM6	MGAT4C-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.1056:NAB2_chr12:g.86871854inv Note: The NAB2 rearrangement results in the inversion of exons 3-7. One of the breakpoints is within exon 3. The functional significance is undetermined.
MGAT4C	0	MSKCC-DMP	P-0028347-T01-IM6	MGAT4C-NAB2 fusion	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.1056:NAB2_chr12:g.86871854inv Note: The NAB2 rearrangement results in the inversion of exons 3-7. One of the breakpoints is within exon 3. The functional significance is undetermined.
IRF4	0	MSKCC-DMP	P-0028347-T01-IM6	LINC01108-IRF4 fusion	yes	unknown		unknown	IRF4 (NM_002460) rearrangement: c.157:IRF4_chr6:g.14202222inv Note: The IRF4 rearrangement results in the inversion of exons 2-9. One of the breakpoints is within exon 2. The functional significance is undetermined.
LINC01108	0	MSKCC-DMP	P-0028347-T01-IM6	LINC01108-IRF4 fusion	yes	unknown		unknown	IRF4 (NM_002460) rearrangement: c.157:IRF4_chr6:g.14202222inv Note: The IRF4 rearrangement results in the inversion of exons 2-9. One of the breakpoints is within exon 2. The functional significance is undetermined.
PAX9	0	MSKCC-DMP	P-0028538-T01-IM6	FOXA1-PAX9 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1113:FOXA1_chr14:g.37105233dup Note: The FOXA1 rearrangement is a duplication of exon 2. One of the breakpoints is within FOXA1 exon 2.
FOXA1	0	MSKCC-DMP	P-0028538-T01-IM6	FOXA1-PAX9 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1113:FOXA1_chr14:g.37105233dup Note: The FOXA1 rearrangement is a duplication of exon 2. One of the breakpoints is within FOXA1 exon 2.
ALK	0	MSKCC-DMP	P-0028901-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1316-844:EML4_c.3173-213:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0028901-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1316-844:EML4_c.3173-213:ALKinv Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.
ERG	0	MSKCC-DMP	P-0029163-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.56-23:TMPRSS2_c.39+33015:ERGdel Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0029163-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.56-23:TMPRSS2_c.39+33015:ERGdel Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).
PIK3R1	0	MSKCC-DMP	P-0029163-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1703:PIK3R1_chr5:g.67596143del Note: The PIK3R1 rearrangement is a deletion of exons 13-16. One of the breakpoints is within exon 13. The functional significance is undetermined.
LOC90768	0	MSKCC-DMP	P-0029377-T01-IM6	FAT1-LOC90768 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.7492:FAT_chr4:g.182710429inv Note: The FAT1 rearrangement is an inversion of exons 10-27. One of the breakpoints is within exon 10. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0029377-T01-IM6	FAT1-LOC90768 fusion	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.7492:FAT_chr4:g.182710429inv Note: The FAT1 rearrangement is an inversion of exons 10-27. One of the breakpoints is within exon 10. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0029811-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) Rearrangement: c.1421-191_c.2254inv Note: The RTEL1 rearrangement is an intragenic inversion of exons 17 to 25. One of the breakpoints is within exon 25. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0029811-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 2 fused to ERG exons 2-10): c.56-1741:TMPRSS2_c.18+17833:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0029811-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 2 fused to ERG exons 2-10): c.56-1741:TMPRSS2_c.18+17833:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
NTRK2	0	MSKCC-DMP	P-0030777-T01-IM6	COL5A1-NTRK2 fusion	yes	unknown		out of frame	NTRK2 (NM_006180) - COL5A1 (NM_000093) rearrangement: c.359+58:NTRK2_c.5067+932:COL5A1del Note: The NTRK2 - COL5A1 rearrangement is a deletion that results in the fusion of NTRK2 exons 1-6 to COL5A1 exons 64-66. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NTRK2 and COL5A1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
COL5A1	0	MSKCC-DMP	P-0030777-T01-IM6	COL5A1-NTRK2 fusion	yes	unknown		out of frame	NTRK2 (NM_006180) - COL5A1 (NM_000093) rearrangement: c.359+58:NTRK2_c.5067+932:COL5A1del Note: The NTRK2 - COL5A1 rearrangement is a deletion that results in the fusion of NTRK2 exons 1-6 to COL5A1 exons 64-66. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NTRK2 and COL5A1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
FGFR1	0	MSKCC-DMP	P-0031505-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.1174+39:FGFR1_chr8:g.38270523del Note: The FGFR1 rearrangement is a deletion of exons 9-19. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0031599-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4162:TMPRSS2_c.19-26160:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0031599-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4162:TMPRSS2_c.19-26160:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.
ALK	0	MSKCC-DMP	P-0031661-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-288:EML4_c.3172+830:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame and involves EML4 exons 1-12 and ALK exons 20-29, which include the kinase domain.
EML4	0	MSKCC-DMP	P-0031661-T01-IM6	EML4-ALK fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-288:EML4_c.3172+830:ALKinv Note: The EML4-ALK fusion is predicted to be in-frame and involves EML4 exons 1-12 and ALK exons 20-29, which include the kinase domain.
MTIF3	0	MSKCC-DMP	P-0031666-T01-IM6	FLT3-MTIF3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: c.1942+133:FLT3_chr13:g.28028510inv Note: The FLT3 rearrangement is an inversion of exons 16-24. The functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0031666-T01-IM6	FLT3-MTIF3 fusion	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: c.1942+133:FLT3_chr13:g.28028510inv Note: The FLT3 rearrangement is an inversion of exons 16-24. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0032161-T02-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.2038-30562:c.3990del Note: The ARID1B rearrangement is an intragenic deletion of exons 6-16. One of the breakpoints is within exon 16.
PIK3C3	0	MSKCC-DMP	P-0032490-T01-IM6	PIK3C3-intragenic	yes	unknown		unknown	PIK3C3 (NM_002647) Rearrangement : c.511_c.1840-1208inv Note: The PIK3C3 Rearrangement results in the intragenic inversion of exons 4-16 of PIK3C3. One of the breakpoints is within exon4. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0032543-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.265-6530_c.1013del Note: The RB1 rearrangement is an intragenic deletion of exons 3-10. One of the breakpoints is within exon 10.
ERG	0	MSKCC-DMP	P-0032573-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4: c.126+133:TMPRSS2_c.40-60824:ERGdel Note: This fusion includes the non-canonical transcript of ERG.
TMPRSS2	0	MSKCC-DMP	P-0032573-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4: c.126+133:TMPRSS2_c.40-60824:ERGdel Note: This fusion includes the non-canonical transcript of ERG.
EGFR	0	MSKCC-DMP	P-0032604-T01-IM6	SEPT14-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - SEPT14 (NM_207366) fusion :  c.2947-110:EGFR_c.1120-1204:SEPT14 Note: The EGFR - SEPT14 rearrangement is an inversion that results in the in-frame fusion of EGFR exons 1-24 with SEPT14 exon 10 and includes the kinase domain of EGFR. Further analysis using the Archer targeted RNAseq assay will be performed to characterize this structural variant, if additional material is available, and results will be reported under a separate accession number.
SEPT14	0	MSKCC-DMP	P-0032604-T01-IM6	SEPT14-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - SEPT14 (NM_207366) fusion :  c.2947-110:EGFR_c.1120-1204:SEPT14 Note: The EGFR - SEPT14 rearrangement is an inversion that results in the in-frame fusion of EGFR exons 1-24 with SEPT14 exon 10 and includes the kinase domain of EGFR. Further analysis using the Archer targeted RNAseq assay will be performed to characterize this structural variant, if additional material is available, and results will be reported under a separate accession number.
SLC9A3R2	0	MSKCC-DMP	P-0032637-T01-IM6	TSC2-SLC9A3R2 fusion	yes	unknown		unknown	TSC2 (NM_000548) - SLC9A3R2 (NM_001130012) Rearrangement : c.282:TSC2_c.415-442:SLC9A3R2dup Note: The TSC2 - SLC9A3R2 Rearrangement results in the fusion of exons 1-4 of TSC2 with exons 3-7 of SLC9A3R2. The breakpoint in TSC2 is within exon4. Its functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0032637-T01-IM6	TSC2-SLC9A3R2 fusion	yes	unknown		unknown	TSC2 (NM_000548) - SLC9A3R2 (NM_001130012) Rearrangement : c.282:TSC2_c.415-442:SLC9A3R2dup Note: The TSC2 - SLC9A3R2 Rearrangement results in the fusion of exons 1-4 of TSC2 with exons 3-7 of SLC9A3R2. The breakpoint in TSC2 is within exon4. Its functional significance is undetermined.
PARD6G	0	MSKCC-DMP	P-0032637-T01-IM6	EZH2-PARD6G fusion	yes	unknown		unknown	EZH2 (NM_004456) Rearrangement : t(7,18)(q36.1,q23)(chr7:g.148506395::chr18:g.78016098) Note: The EZH2 Rearrangement is a translocation event with the breakpoint in intron18 of EZH2. Its functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0032637-T01-IM6	EZH2-PARD6G fusion	yes	unknown		unknown	EZH2 (NM_004456) Rearrangement : t(7,18)(q36.1,q23)(chr7:g.148506395::chr18:g.78016098) Note: The EZH2 Rearrangement is a translocation event with the breakpoint in intron18 of EZH2. Its functional significance is undetermined.
NIPBL	0	MSKCC-DMP	P-0032640-T01-IM6	RICTOR-NIPBL fusion	yes	unknown		unknown	RICTOR (NM_152756) - NIPBL (NM_133433) Rearrangement : c.1542:RICTOR_c.4024:NIPBLinv Note: The RICTOR - NIPBL  Rearrangement results in the fusion of exons 1-17 of RICTOR with exons 17-47 of NIPBL. The breakpoints are with exon17 of RICTOR  and exon17 of NIPBL. Its functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0032640-T01-IM6	RICTOR-NIPBL fusion	yes	unknown		unknown	RICTOR (NM_152756) - NIPBL (NM_133433) Rearrangement : c.1542:RICTOR_c.4024:NIPBLinv Note: The RICTOR - NIPBL  Rearrangement results in the fusion of exons 1-17 of RICTOR with exons 17-47 of NIPBL. The breakpoints are with exon17 of RICTOR  and exon17 of NIPBL. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0032722-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944 ) fusion (CD74 exons 1-7 fused to ROS1 exons 34-43):  t(5;6)(q32;q22.1)(chr5:g.149782874::chr6:g.117645677) Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1. One of the breakpoints is within CD74 exon 7
CD74	0	MSKCC-DMP	P-0032722-T01-IM6	CD74-ROS1 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944 ) fusion (CD74 exons 1-7 fused to ROS1 exons 34-43):  t(5;6)(q32;q22.1)(chr5:g.149782874::chr6:g.117645677) Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1. One of the breakpoints is within CD74 exon 7
EZH1	0	MSKCC-DMP	P-0032728-T01-IM6	BCAS3-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - BCAS3 (NM_001099432) rearrangement:  c.1164:EZH1_c.1486+3919:BCAS3inv Note: The EZH1 - BCAS3 rearrangement is an inversion that results in the fusion of EZH1 exons 1-11 with BCAS3 exons 15-25. One of the breakpoints is within EZH1 exon 11. Multiple EZH1 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
BCAS3	0	MSKCC-DMP	P-0032728-T01-IM6	BCAS3-EZH1 fusion	yes	unknown		unknown	EZH1 (NM_001991) - BCAS3 (NM_001099432) rearrangement:  c.1164:EZH1_c.1486+3919:BCAS3inv Note: The EZH1 - BCAS3 rearrangement is an inversion that results in the fusion of EZH1 exons 1-11 with BCAS3 exons 15-25. One of the breakpoints is within EZH1 exon 11. Multiple EZH1 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated.
RGS7	0	MSKCC-DMP	P-0032745-T01-IM6	FH-RGS7 fusion	yes	unknown		out of frame	FH (NM_000143) - RGS7 (NM_002924) rearrangement:  c.738+181:FH_c.386-8492:RGS7del Note: The FH - RGS7 rearrangement is a deletion that results in the fusion of FH exons 1-5 to RGS7 exons 5-18. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0032745-T01-IM6	FH-RGS7 fusion	yes	unknown		out of frame	FH (NM_000143) - RGS7 (NM_002924) rearrangement:  c.738+181:FH_c.386-8492:RGS7del Note: The FH - RGS7 rearrangement is a deletion that results in the fusion of FH exons 1-5 to RGS7 exons 5-18. The functional significance is undetermined.
PDZRN4	0	MSKCC-DMP	P-0032745-T01-IM6	BAP1-PDZRN4 fusion	yes	unknown		unknown	BAP1 (NM_004656) - PDZRN4 (NM_001164595) rearrangement: t(3;12)(p21.2;q12)(chr3:g.52440343::chr12:g.41663465) Note: The BAP1 - PDZRN4 rearrangement is a translocation that results in a fusion of BAP1 exons 1-9 to PDZRN4 exons 4-10. One of the breakpoints is within BAP1 exon 9. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0032745-T01-IM6	BAP1-PDZRN4 fusion	yes	unknown		unknown	BAP1 (NM_004656) - PDZRN4 (NM_001164595) rearrangement: t(3;12)(p21.2;q12)(chr3:g.52440343::chr12:g.41663465) Note: The BAP1 - PDZRN4 rearrangement is a translocation that results in a fusion of BAP1 exons 1-9 to PDZRN4 exons 4-10. One of the breakpoints is within BAP1 exon 9. The functional significance is undetermined.
PRKD1	0	MSKCC-DMP	P-0032748-T01-IM6	PRKD1-intragenic	yes	unknown		in frame	PRKD1 (NM_002742) rearrangement: c.1392+564_c.1906-18del Note: The PRKD1 rearrangement is an intragenic deletion of exons 10-13. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0032753-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1323:KIF5B_c.2136+741:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0032753-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1323:KIF5B_c.2136+741:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
PISRT1	0	MSKCC-DMP	P-0032753-T01-IM6	ATR-PISRT1 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.7426:ATR_chr3:g.138900546del Note: The ATR rearrangement is a deletion of exons 44-47. One of the breakpoints is within exon 44.
ATR	0	MSKCC-DMP	P-0032753-T01-IM6	ATR-PISRT1 fusion	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.7426:ATR_chr3:g.138900546del Note: The ATR rearrangement is a deletion of exons 44-47. One of the breakpoints is within exon 44.
PRKCI	0	MSKCC-DMP	P-0032753-T01-IM6	ZMAT3-PRKCI fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.980+288:PRKCI_chr3:g.178665442del Note: The PRKCI rearrangement is a deletion of exons 11-18. The functional significance is undetermined.
ZMAT3	0	MSKCC-DMP	P-0032753-T01-IM6	ZMAT3-PRKCI fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.980+288:PRKCI_chr3:g.178665442del Note: The PRKCI rearrangement is a deletion of exons 11-18. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0032799-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11): c.55+815:TMPRSS2_c.39+61431:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
TMPRSS2	0	MSKCC-DMP	P-0032799-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11): c.55+815:TMPRSS2_c.39+61431:ERGdel Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.
RAD50	0	MSKCC-DMP	P-0032828-T01-IM6	KIF3A-RAD50 fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: c.472:RAD50_chr5:g.132029280del Note: The RAD50 rearrangement is a deletion of exons 4-25. Onee of the breakpoints is within exon 25. The functional significance is undetermined,
KIF3A	0	MSKCC-DMP	P-0032828-T01-IM6	KIF3A-RAD50 fusion	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: c.472:RAD50_chr5:g.132029280del Note: The RAD50 rearrangement is a deletion of exons 4-25. Onee of the breakpoints is within exon 25. The functional significance is undetermined,
DOT1L	0	MSKCC-DMP	P-0032851-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) Rearrangement : c.1044_c.3391-140dup Note: The DOT1L Rearrangement results in the intragenic duplication of exons 13-24. One of the breakpoints is within exon13. Its functional significance is undetermined.
DDR2	0	MSKCC-DMP	P-0032895-T01-IM6	LINC01363-DDR2 fusion	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: c.1293+41:DDR2_chr1:g.167123216del Note: The DDR2 rearrangement is a deletion of exons 12-18. Its functional significance is undetermined.
LINC01363	0	MSKCC-DMP	P-0032895-T01-IM6	LINC01363-DDR2 fusion	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: c.1293+41:DDR2_chr1:g.167123216del Note: The DDR2 rearrangement is a deletion of exons 12-18. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0032895-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.645+794_c.1240del Note: The APC rearrangement is an intragenic deletion of exons 7-10. One of the breakpoints is in exon 10. Its functional significance is undetermined.
CAPN12	0	MSKCC-DMP	P-0032962-T01-IM6	AKT2-CAPN12 fusion	yes	unknown		unknown	AKT2 (NM_001626) Rearrangement: c.1366+231:AKT2_chr19:g.39236036inv Note: The AKT2 rearrangement results in the inversion of AKT2 exon 14. The functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0032962-T01-IM6	AKT2-CAPN12 fusion	yes	unknown		unknown	AKT2 (NM_001626) Rearrangement: c.1366+231:AKT2_chr19:g.39236036inv Note: The AKT2 rearrangement results in the inversion of AKT2 exon 14. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0032998-T01-IM6	CUX1-NCOR1 fusion	yes	unknown		out of frame	CUX1 (NM_181552) - NCOR1 (NM_006311) rearrangement: t(7;17)(q21.1;p11.2)(chr7:g.101708544::chr17:g.15983467) Note: The CUX1 - NCOR1 rearrangement is a translocation which may result in the fusion of CUX1 exons 1-3 with NCOR1 exons 26-46.
CUX1	0	MSKCC-DMP	P-0032998-T01-IM6	CUX1-NCOR1 fusion	yes	unknown		out of frame	CUX1 (NM_181552) - NCOR1 (NM_006311) rearrangement: t(7;17)(q21.1;p11.2)(chr7:g.101708544::chr17:g.15983467) Note: The CUX1 - NCOR1 rearrangement is a translocation which may result in the fusion of CUX1 exons 1-3 with NCOR1 exons 26-46.
TSC1	0	MSKCC-DMP	P-0032998-T01-IM6	TSC1-intragenic	yes	unknown		in frame	TSC1 (NM_000368) rearrangement: c.2502+103_c.2626-1469del Note: The TSC1 rearrangement results in the deletion of exon 20. Its functional significance is undetermined.
ENOSF1	0	MSKCC-DMP	P-0033034-T01-IM6	TP53-ENOSF1 fusion	yes	unknown		unknown	ENOSF1 (NM_017512) - TP53 (NM_000546) Rearrangement: t(17;18)(p13.1;p11.32)(chr17:g.7577544::chr18:g.687063) Note: The ENOSF1 - TP53 rearrangement results in the fusion of exons 1-9 of ENOSF1 with exons 7-11 of TP53. One of the breakpoints is with exon 7 of TP53. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0033034-T01-IM6	TP53-ENOSF1 fusion	yes	unknown		unknown	ENOSF1 (NM_017512) - TP53 (NM_000546) Rearrangement: t(17;18)(p13.1;p11.32)(chr17:g.7577544::chr18:g.687063) Note: The ENOSF1 - TP53 rearrangement results in the fusion of exons 1-9 of ENOSF1 with exons 7-11 of TP53. One of the breakpoints is with exon 7 of TP53. Its functional significance is undetermined.
GYPC	0	MSKCC-DMP	P-0033034-T01-IM6	ERBB4-GYPC fusion	yes	unknown		unknown	ERBB4 (NM_005235) Rearrangemnet: chr2:g.126960119_c.1198+52:ERBB4inv Note: The ERBB4 rearrangement is an inversion of ERBB4 exons 11 to 28. Its functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0033034-T01-IM6	ERBB4-GYPC fusion	yes	unknown		unknown	ERBB4 (NM_005235) Rearrangemnet: chr2:g.126960119_c.1198+52:ERBB4inv Note: The ERBB4 rearrangement is an inversion of ERBB4 exons 11 to 28. Its functional significance is undetermined.
UBA52	0	MSKCC-DMP	P-0033083-T01-IM6	MEF2B-UBA52 fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: chr19:g.18686772_c.817dup Note: The MEF2B rearrangement is a duplication that includes MEF2B exons 8-9. One of the breakpoints is within exon 8. The functional significance is undetermined.
MEF2B	0	MSKCC-DMP	P-0033083-T01-IM6	MEF2B-UBA52 fusion	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: chr19:g.18686772_c.817dup Note: The MEF2B rearrangement is a duplication that includes MEF2B exons 8-9. One of the breakpoints is within exon 8. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0033083-T01-IM6	DDR1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5224_chr6:g.30794463dup Note: The MDC1 rearrangement is a duplication that includes MDC1 exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
DDR1	0	MSKCC-DMP	P-0033083-T01-IM6	DDR1-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5224_chr6:g.30794463dup Note: The MDC1 rearrangement is a duplication that includes MDC1 exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
BTK	0	MSKCC-DMP	P-0033083-T01-IM6	RPL36A-HNRNPH2-BTK fusion	yes	unknown		unknown	BTK (NM_000061) - RPL36A-HNRNPH2 (NM_001199974) rearrangement : c.681:BTK_c.285+5720:RPL36A-HNRNPH2 dup Note: The BTK - RPL36A-HNRNPH2  rearrangement is a duplication that includes BTK exons 1-8 and RPL36A-HNRNPH2  exons 1-3. One of the breakpoints is within BTK exon 8. The functional significance is undetermined.
RPL36A-HNRNPH2	0	MSKCC-DMP	P-0033083-T01-IM6	RPL36A-HNRNPH2-BTK fusion	yes	unknown		unknown	BTK (NM_000061) - RPL36A-HNRNPH2 (NM_001199974) rearrangement : c.681:BTK_c.285+5720:RPL36A-HNRNPH2 dup Note: The BTK - RPL36A-HNRNPH2  rearrangement is a duplication that includes BTK exons 1-8 and RPL36A-HNRNPH2  exons 1-3. One of the breakpoints is within BTK exon 8. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0033167-T01-IM6	CACNA1A-DNMT1 fusion	yes	unknown		in frame	DNMT1 (NM_001379) - CACNA1A (NM_001127222) rearrangement: c.635+105:DNMT1_c.293+21068:CACNA1A dup Note: The DNMT1 - CACNA1A rearrangement is a duplication that results in the fusion of DNMT1 exons 1-7 with CACNA1A exons 2-47
CACNA1A	0	MSKCC-DMP	P-0033167-T01-IM6	CACNA1A-DNMT1 fusion	yes	unknown		in frame	DNMT1 (NM_001379) - CACNA1A (NM_001127222) rearrangement: c.635+105:DNMT1_c.293+21068:CACNA1A dup Note: The DNMT1 - CACNA1A rearrangement is a duplication that results in the fusion of DNMT1 exons 1-7 with CACNA1A exons 2-47
FOXA1	0	MSKCC-DMP	P-0033175-T01-IM6	FBXO33-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.73-32_chr14:g.40100185del Note: The FOXA1 rearrangement is a deletion that includes FOXA1 exon 1. The functional significance is undetermined.
FBXO33	0	MSKCC-DMP	P-0033175-T01-IM6	FBXO33-FOXA1 fusion	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.73-32_chr14:g.40100185del Note: The FOXA1 rearrangement is a deletion that includes FOXA1 exon 1. The functional significance is undetermined.
BMS1	0	MSKCC-DMP	P-0033301-T01-IM6	RET-BMS1 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: c.2137-171:RET_chr10:g.43288718inv Note: The RET rearrangement is an inversion of exons 12-20, which include the kinase domain. The functional significance is undetermined. Further analysis using the Archer targeted RNAseq assay will be performed if additional material is available and results will be reported under a separate accession number.
RET	0	MSKCC-DMP	P-0033301-T01-IM6	RET-BMS1 fusion	yes	unknown		unknown	RET (NM_020975) rearrangement: c.2137-171:RET_chr10:g.43288718inv Note: The RET rearrangement is an inversion of exons 12-20, which include the kinase domain. The functional significance is undetermined. Further analysis using the Archer targeted RNAseq assay will be performed if additional material is available and results will be reported under a separate accession number.
STAG2	0	MSKCC-DMP	P-0033302-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement: c.3278-1254_c.3467+25inv Note: The STAG2 rearrangement is an intragenic inversion of exon 31. The functional significance is undetermined
GRIN2A	0	MSKCC-DMP	P-0033464-T01-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: c.1778-112_c.2007+1330inv Note: The GRIN2A rearrangement is an inversion of exon 9. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0033474-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.2411-55_c.2792+25Ginv Note: The NOTCH3 rearrangement is an intragenic inversion of exons 16-17. The functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0033474-T01-IM6	BRD4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - BRD4 (NM_058243) rearrangement: c.2661:NOTCH3_c.1551+151:BRD4inv Note: The NOTCH3  - BRD4 rearrangement is an inversion that includes NOTCH3 exons 1-17 and BRD4 exons 9-20. One of the breakpoints is within NOTCH3 exons 17. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0033474-T01-IM6	BRD4-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - BRD4 (NM_058243) rearrangement: c.2661:NOTCH3_c.1551+151:BRD4inv Note: The NOTCH3  - BRD4 rearrangement is an inversion that includes NOTCH3 exons 1-17 and BRD4 exons 9-20. One of the breakpoints is within NOTCH3 exons 17. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0033474-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.793+1788:EWSR1_c.526-940:AP1B1dup Note: The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 10-18 and AP1B1 exons 6-23. The functional significance is undetermined.
AP1B1	0	MSKCC-DMP	P-0033474-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.793+1788:EWSR1_c.526-940:AP1B1dup Note: The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 10-18 and AP1B1 exons 6-23. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0033554-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion (TMPRSS2 exon 1 fused to ETV1 exon 6-12):t(7;21)(p21.2;q22.3)(chr7:g.13992250::chr21:g.42871598) Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.
ETV1	0	MSKCC-DMP	P-0033554-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion (TMPRSS2 exon 1 fused to ETV1 exon 6-12):t(7;21)(p21.2;q22.3)(chr7:g.13992250::chr21:g.42871598) Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.
EWSR1	0	MSKCC-DMP	P-0033555-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1309+253:EWSR1_c.2163+658:AP1B1dup Note; The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 13-18 and AP1B1 exons 17-23. The functional significance is undetermined.
AP1B1	0	MSKCC-DMP	P-0033555-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1309+253:EWSR1_c.2163+658:AP1B1dup Note; The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 13-18 and AP1B1 exons 17-23. The functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0033555-T01-IM6	PBRM1-PHF7 fusion	yes	unknown		unknown	PHF7 (NM_016483) - PBRM1 (NM_018313) rearrangement: c.413+146:PHF7_c.3459-124:PBRM1dup Note: The PHF7 - PBRM1 rearrangement is a duplication that includes PHF7 exons 7-11 and PBRM1 exons 23-30. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0033555-T01-IM6	PBRM1-PHF7 fusion	yes	unknown		unknown	PHF7 (NM_016483) - PBRM1 (NM_018313) rearrangement: c.413+146:PHF7_c.3459-124:PBRM1dup Note: The PHF7 - PBRM1 rearrangement is a duplication that includes PHF7 exons 7-11 and PBRM1 exons 23-30. The functional significance is undetermined.
SLC2A5	0	MSKCC-DMP	P-0033597-T01-IM6	PIK3CD-SLC2A5 fusion	yes	unknown		unknown	SLC2A5 (NM_003039) - PIK3CD (NM_005026) rearrangement: c.294-3232:SLC2A5_c.2830:PIK3CDdel Note: The SLC2A5 -PIK3CD rearrangement is a deletion that includes SLC2A5 exons 1-3, and PIK3CD exons 1-22. One of the breakpoints is within PIK3CD exon 22. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0033597-T01-IM6	PIK3CD-SLC2A5 fusion	yes	unknown		unknown	SLC2A5 (NM_003039) - PIK3CD (NM_005026) rearrangement: c.294-3232:SLC2A5_c.2830:PIK3CDdel Note: The SLC2A5 -PIK3CD rearrangement is a deletion that includes SLC2A5 exons 1-3, and PIK3CD exons 1-22. One of the breakpoints is within PIK3CD exon 22. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0033597-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.8202_c.8378-604del Note: The NF1 rearrangement is an intragenic deletion of exon 57. One of the breakpoints is within exon.
CDKN2A	0	MSKCC-DMP	P-0033602-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.-3363_c.225del Note: The CDKN2A rearrangement is an intragenic deletion of exons 1-2 of CDKN2A. One of the breakpoints is within exon 2. The deletion includes only exon 2 of the CDKN2Ap14ARF (NM_058195) isoform of CDKN2A.
RECQL	0	MSKCC-DMP	P-0033630-T01-IM6	ALG10-RECQL fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.1715_chr12:g.34134949dup Note: The RECQL rearrangement is a duplication that includes RECQL exons 1-15. One of the breakpoints is within RECQL exon 15. The functional significance is undetermined.
ALG10	0	MSKCC-DMP	P-0033630-T01-IM6	ALG10-RECQL fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.1715_chr12:g.34134949dup Note: The RECQL rearrangement is a duplication that includes RECQL exons 1-15. One of the breakpoints is within RECQL exon 15. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0033630-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.909_c.1083-1312inv Note: The NCOR1 rearrangement is an intragenic inversion of exons 9-10. One of the breakpoints is within exon 9.
ETV6	0	MSKCC-DMP	P-0033635-T01-IM6	LOH12CR1-ETV6 fusion	yes	unknown		in frame	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangemnet: c.203-15769:LOH12CR1_c.464-2376:ETV6dup Note: The LOH12CR1 - ETV6 rearrangement is a duplication that results in the fusion of LOH12CR1 exons 1-2 with ETV6 exons 5 - 8. The fusion is predicted to be in frame. The functional significance is undetermined.
LOH12CR1	0	MSKCC-DMP	P-0033635-T01-IM6	LOH12CR1-ETV6 fusion	yes	unknown		in frame	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangemnet: c.203-15769:LOH12CR1_c.464-2376:ETV6dup Note: The LOH12CR1 - ETV6 rearrangement is a duplication that results in the fusion of LOH12CR1 exons 1-2 with ETV6 exons 5 - 8. The fusion is predicted to be in frame. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0033690-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.9570_c.14343+1412dup Note: The KMT2C rearrangement results in the intragenic duplication of exons 42-55. One of the breakpoints is within exon 42. The functional significance is undetermined.
HPN-AS1	0	MSKCC-DMP	P-0033720-T01-IM6	KMT2B-HPN-AS1 fusion	yes	unknown		unknown	KMT2B (NM_014727) Rearrangement :chr19:g.35558580_c.364-2:KMT2Bdel Note: The KMT2B (NM_014727) Rearrangement results in the deletion of exons 1-2 of KMT2B. Its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0033720-T01-IM6	KMT2B-HPN-AS1 fusion	yes	unknown		unknown	KMT2B (NM_014727) Rearrangement :chr19:g.35558580_c.364-2:KMT2Bdel Note: The KMT2B (NM_014727) Rearrangement results in the deletion of exons 1-2 of KMT2B. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0033726-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) Rearrangement : c.165-610_c.621del Note: The PTEN Rearrangement results in the intragenic duplication of exons 3-6 of PTEN. One of the breakpoints is within exon6. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0033726-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement: c.799-13048_c.1509dup Note: The CREBBP Rearrangement results in the intragenic duplication of exons 3-6 of CREBBP. One of the breakpoints is within exon6. Its functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0033769-T01-IM6	ARID2-intragenic	yes	unknown		out of frame	ARID2 (NM_152641) rearrangement: c.4773+767_c.5364-554dup Note: The ARID2 rearrangement is an intragenic duplication of exons 16-20.
FBXO21	0	MSKCC-DMP	P-0033798-T01-IM6	SETD8-FBXO21 fusion	yes	unknown		unknown	SETD8 (NM_020382) rearrangement: c.133-28:SETD8_chr12:g.117582663del Note: The SETD8 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.
SETD8	0	MSKCC-DMP	P-0033798-T01-IM6	SETD8-FBXO21 fusion	yes	unknown		unknown	SETD8 (NM_020382) rearrangement: c.133-28:SETD8_chr12:g.117582663del Note: The SETD8 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0033798-T01-IM6	KRBOX4-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.3672:KDM6A_chrX:g.46333025inv Note: The KDM6A rearrangement is an inversion of exons 25-29. Its functional significance is undetermined.
KRBOX4	0	MSKCC-DMP	P-0033798-T01-IM6	KRBOX4-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.3672:KDM6A_chrX:g.46333025inv Note: The KDM6A rearrangement is an inversion of exons 25-29. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0033812-T01-IM6	LINC01568-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : c.6957:ZFHX3_chr16:g.73684489del Note: The ZFHX3 Rearrangement results in the deletion of exons 1-9 of ZFHX3. One of the breakpoints is within exon9. Its functional significance is undetermined.
LINC01568	0	MSKCC-DMP	P-0033812-T01-IM6	LINC01568-ZFHX3 fusion	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : c.6957:ZFHX3_chr16:g.73684489del Note: The ZFHX3 Rearrangement results in the deletion of exons 1-9 of ZFHX3. One of the breakpoints is within exon9. Its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0033813-T01-IM6	LOC100506422-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) Rearrangement : c.2322+24:PTPRD_chr9:g.26375496inv Note: The PTPRD Rearrangement results in the inversion of exons 1-25 of PTPRD.Its functional significance is undetermined.
LOC100506422	0	MSKCC-DMP	P-0033813-T01-IM6	LOC100506422-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) Rearrangement : c.2322+24:PTPRD_chr9:g.26375496inv Note: The PTPRD Rearrangement results in the inversion of exons 1-25 of PTPRD.Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0033816-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) Rearrangement : c.4549_c.7693del Note: The APC Rearrangement results in the intragenic  partial deletion of exon16. Both the breakpoints are within exon16. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0033821-T01-IM6	SLC7A8-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : t(14,17)(q11.2; q12)(chr14:g.23619168::chr17:g.7578709) The TP53 (NM_000546) Rearrangement is a translocation event with the breakpoint in intron 4.Its functional significance is undetermined.
SLC7A8	0	MSKCC-DMP	P-0033821-T01-IM6	SLC7A8-TP53 fusion	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : t(14,17)(q11.2; q12)(chr14:g.23619168::chr17:g.7578709) The TP53 (NM_000546) Rearrangement is a translocation event with the breakpoint in intron 4.Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0033890-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-616:CDKN2Ap16INK4A_chr9:g.22217818del Note: The CDKN2A rearrangement is a deletion of exons 1-2. This affects the CDKN2Ap16INK4A (NM_000077) transcript.
CDKN2B	0	MSKCC-DMP	P-0033890-T01-IM6	CDKN2B-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-616:CDKN2Ap16INK4A_chr9:g.22217818del Note: The CDKN2A rearrangement is a deletion of exons 1-2. This affects the CDKN2Ap16INK4A (NM_000077) transcript.
ERG	0	MSKCC-DMP	P-0033934-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+665:TMPRSS2_c.40-58822:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0033934-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+665:TMPRSS2_c.40-58822:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
KMT2C	0	MSKCC-DMP	P-0033934-T01-IM6	RBM33-KMT2C fusion	yes	unknown		unknown	RBM33 (NM_053043) - KMT2C (NM_170606) rearrangement: c.123-2768:RBM33_c.6361:KMT2Cinv Note: The RBM33 - KMT2C rearrangement is an inversion that results in the fusion of RBM33 exons 1-2 with KMT2C exons 36-59. One of the breakpoints is within KMT2C  exon 36. The functional significance is undetermined.
RBM33	0	MSKCC-DMP	P-0033934-T01-IM6	RBM33-KMT2C fusion	yes	unknown		unknown	RBM33 (NM_053043) - KMT2C (NM_170606) rearrangement: c.123-2768:RBM33_c.6361:KMT2Cinv Note: The RBM33 - KMT2C rearrangement is an inversion that results in the fusion of RBM33 exons 1-2 with KMT2C exons 36-59. One of the breakpoints is within KMT2C  exon 36. The functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0033937-T01-IM6	RPTOR-intragenic	yes	unknown		out of frame	RPTOR (NM_020761) rearrangement: c.163-35973_c.3266-132del Note: The RPTOR rearrangement results in the deletion of exons 2-27. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0033953-T01-IM6	DNM3-SPEN fusion	yes	unknown		unknown	DNM3 (NM_015569) - SPEN (NM_015001) rearrangement: c.1770-16871:DNM3_c.8790:SPENdup Note: The DNM3 - SPEN rearrangement is a duplication that results in the fusion of DNM3 exons 1-15 with SPEN exons 11-15. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
DNM3	0	MSKCC-DMP	P-0033953-T01-IM6	DNM3-SPEN fusion	yes	unknown		unknown	DNM3 (NM_015569) - SPEN (NM_015001) rearrangement: c.1770-16871:DNM3_c.8790:SPENdup Note: The DNM3 - SPEN rearrangement is a duplication that results in the fusion of DNM3 exons 1-15 with SPEN exons 11-15. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
PLCD3	0	MSKCC-DMP	P-0033962-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		unknown	PLCD3 (NM_133373) - MAP3K14(NM_003954) Rearrangement: c.163+24:PLCD3_c.2611: MAP3K14dup Note: The PLCD3 - MAP3K14  rearrangement results in the fusion of PLCD3 exon1 with MAP3K14 exons 15 - 16. One of the breakpoints is within exon 15 of MAP3K14. Its functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0033962-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		unknown	PLCD3 (NM_133373) - MAP3K14(NM_003954) Rearrangement: c.163+24:PLCD3_c.2611: MAP3K14dup Note: The PLCD3 - MAP3K14  rearrangement results in the fusion of PLCD3 exon1 with MAP3K14 exons 15 - 16. One of the breakpoints is within exon 15 of MAP3K14. Its functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0034025-T01-IM6	MAPRE1-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) Rearrangement: c.2110:ASXL1_chr20:g.31423707inv Note: The ASXL1 rearrangement is an inversion of ASXL1 exon 12. One of the breakpoints is within exon 12 of ASXL1. The functional significance is undetermined.
MAPRE1	0	MSKCC-DMP	P-0034025-T01-IM6	MAPRE1-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) Rearrangement: c.2110:ASXL1_chr20:g.31423707inv Note: The ASXL1 rearrangement is an inversion of ASXL1 exon 12. One of the breakpoints is within exon 12 of ASXL1. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0034031-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) Rearrangement: c.811+32:EWSR1_c.1437+1202:AP1B1dup Note: The EWSR1 - AP1B1 rearrangement is a duplication of EWSR1 exons 9 to 18 and AP1B1 exons 12-23. The functional significance is undetermined.
AP1B1	0	MSKCC-DMP	P-0034031-T01-IM6	AP1B1-EWSR1 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - AP1B1 (NM_001127) Rearrangement: c.811+32:EWSR1_c.1437+1202:AP1B1dup Note: The EWSR1 - AP1B1 rearrangement is a duplication of EWSR1 exons 9 to 18 and AP1B1 exons 12-23. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0034157-T02-IM6	MAP3K3-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3559:CDK12_chr17:g.61753552inv Note: The CDK12 rearrangement is an inversion of exons 13-14. One of the breakpoints is within exon 13. Its functional significance is undetermined.
MAP3K3	0	MSKCC-DMP	P-0034157-T02-IM6	MAP3K3-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.3559:CDK12_chr17:g.61753552inv Note: The CDK12 rearrangement is an inversion of exons 13-14. One of the breakpoints is within exon 13. Its functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0034183-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 7-16): c.2346:FGFR3_c.1591+1975dup Note: The FGFR3 -TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
FGFR3	0	MSKCC-DMP	P-0034183-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 7-16): c.2346:FGFR3_c.1591+1975dup Note: The FGFR3 -TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
CIC	0	MSKCC-DMP	P-0034278-T01-IM6	PVRL2-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangment: c.1019:CIC_chr19:g.45393207inv Note: The CIC rearrangement is an inversion of exons 7-20. One of the breakpoints is within exon 7.
PVRL2	0	MSKCC-DMP	P-0034278-T01-IM6	PVRL2-CIC fusion	yes	unknown		unknown	CIC (NM_015125) rearrangment: c.1019:CIC_chr19:g.45393207inv Note: The CIC rearrangement is an inversion of exons 7-20. One of the breakpoints is within exon 7.
ERG	0	MSKCC-DMP	P-0034298-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2967:TMPRSS2_c.-149-4226:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-11. The fusion involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0034298-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2967:TMPRSS2_c.-149-4226:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-11. The fusion involves the non-canonical ERG transcript.
CDK12	0	MSKCC-DMP	P-0034356-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.-1342_c.467del Note: The CDK12 rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034431-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2658:TMPRSS2_c.18+15598:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
TMPRSS2	0	MSKCC-DMP	P-0034431-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2658:TMPRSS2_c.18+15598:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.
ALK	0	MSKCC-DMP	P-0034450-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon13 fused with ALK exons 20) : c.1641+555:EML4_c.3213:ALKinv Note: The EML4-ALK fusion includes the protein kinase domain of ALK. The breakpoint in ALK is within exon 20
EML4	0	MSKCC-DMP	P-0034450-T01-IM6	EML4-ALK fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon13 fused with ALK exons 20) : c.1641+555:EML4_c.3213:ALKinv Note: The EML4-ALK fusion includes the protein kinase domain of ALK. The breakpoint in ALK is within exon 20
CDC73	0	MSKCC-DMP	P-0034464-T01-IM6	CDC73-intragenic	yes	unknown		unknown	CDC73 (NM_024529) rearrangement: c.776_c.1031-3046del Note: The CDC73 rearrangement is an intragenic deletion of exons 8-11. One of the breakpoints is within exon 8.
GINS2	0	MSKCC-DMP	P-0034464-T01-IM6	FANCA-GINS2 fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: chr16:g.85711453_c.3066+129del Note: The FANCA rearrangement is a deletion that includes FANCA exons 32 - 43.
FANCA	0	MSKCC-DMP	P-0034464-T01-IM6	FANCA-GINS2 fusion	yes	unknown		unknown	FANCA (NM_000135) rearrangement: chr16:g.85711453_c.3066+129del Note: The FANCA rearrangement is a deletion that includes FANCA exons 32 - 43.
PTCH1	0	MSKCC-DMP	P-0034464-T01-IM6	UPP2-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) - UPP2 (NM_001135098) rearrangement: t(2;9)(q24.1;q22.32)(chr2:g.158929185::chr9:g.98212161) Note: The PTCH1 - UPP2 rearrangement is a translocation with breakpoints within PTCH1 exon 21 and UPP2 intron 2.
UPP2	0	MSKCC-DMP	P-0034464-T01-IM6	UPP2-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) - UPP2 (NM_001135098) rearrangement: t(2;9)(q24.1;q22.32)(chr2:g.158929185::chr9:g.98212161) Note: The PTCH1 - UPP2 rearrangement is a translocation with breakpoints within PTCH1 exon 21 and UPP2 intron 2.
ARID2	0	MSKCC-DMP	P-0034506-T01-IM6	AMIGO2-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.705+25_chr12:g.47316536del Note: The ARID2 rearrangement results in the deletion of exons 7-21. The functional significance is undetermined.
AMIGO2	0	MSKCC-DMP	P-0034506-T01-IM6	AMIGO2-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.705+25_chr12:g.47316536del Note: The ARID2 rearrangement results in the deletion of exons 7-21. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0034515-T01-IM6	WASF2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - WASF2 (NM_006990) rearrangement: t(1;17)(p36.11;p12)(chr1:g.27748183::chr17:g.15983299) Note: The NCOR1 - WASF2 rearrangement is a translocation with breakpoints within NCOR1 exon 26 and WASF2 intron 2. Multiple NCOR1 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
WASF2	0	MSKCC-DMP	P-0034515-T01-IM6	WASF2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - WASF2 (NM_006990) rearrangement: t(1;17)(p36.11;p12)(chr1:g.27748183::chr17:g.15983299) Note: The NCOR1 - WASF2 rearrangement is a translocation with breakpoints within NCOR1 exon 26 and WASF2 intron 2. Multiple NCOR1 rearrangements were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
STK11	0	MSKCC-DMP	P-0034577-T01-IM6	METRN-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) rearrangement: t(16;19)(p13.3;p13.3)(chr16:g.762979::chr19:g.1221857) Note: The STK11 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
METRN	0	MSKCC-DMP	P-0034577-T01-IM6	METRN-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) rearrangement: t(16;19)(p13.3;p13.3)(chr16:g.762979::chr19:g.1221857) Note: The STK11 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0034609-T01-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+175:EZR_c.5557+143:ROS1del Note: The EZR - ROS1 rearrangement is a deletion which forms a fusion of EZR exons 1-9 with ROS1 exons 34-43.
EZR	0	MSKCC-DMP	P-0034609-T01-IM6	EZR-ROS1 fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+175:EZR_c.5557+143:ROS1del Note: The EZR - ROS1 rearrangement is a deletion which forms a fusion of EZR exons 1-9 with ROS1 exons 34-43.
TMPRSS2	0	MSKCC-DMP	P-0034620-T01-IM6	CSK-TMPRSS2 fusion	yes	unknown		unknown	CSK (NM_001127190) - TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.75094115::chr21:g.42875844) Note: The CSK - TMPRSS2 rearrangement is a translocation which may result in the fusion of CSK exons 1-12 with TMPRSS2 exons 2-14. One of the breakpoints is within CSK exon 12. Its functional significance is undetermined.
CSK	0	MSKCC-DMP	P-0034620-T01-IM6	CSK-TMPRSS2 fusion	yes	unknown		unknown	CSK (NM_001127190) - TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.75094115::chr21:g.42875844) Note: The CSK - TMPRSS2 rearrangement is a translocation which may result in the fusion of CSK exons 1-12 with TMPRSS2 exons 2-14. One of the breakpoints is within CSK exon 12. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034620-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3990:TMPRSS2_c.18+9776:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which forms a fusion of TMPRSS2 exons 1 with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0034620-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3990:TMPRSS2_c.18+9776:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which forms a fusion of TMPRSS2 exons 1 with ERG exons 2-10.
ARID2	0	MSKCC-DMP	P-0034651-T01-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.285-34697_c.2302del Note: The ARID2 rearrangement is an intragenic deletion of exons 4-15. One of the breakpoints is withiin exon 15.
CDKN1A	0	MSKCC-DMP	P-0034651-T01-IM6	CDKN1A-intragenic	yes	unknown		unknown	CDKN1A (NM_078467) rearrangement: c.446-99:CDKN1A_chr6:g.36650568del Note: The CDKN1A rearrangement is a deletion of exon 3.
SMAD2	0	MSKCC-DMP	P-0034667-T01-IM6	SMAD2-intragenic	yes	unknown		unknown	SMAD2 (NM_001003652) Rearrangement: c.655+92_chr18:g.45343181del Note: The SMAD2 rearrangement is an intragenic deletion of exons 6-11. The functional significance is undetermined.
KDM2B	0	MSKCC-DMP	P-0034684-T01-IM6	SESN1-KDM2B fusion	yes	unknown		unknown	KDM2B (NM_032590) Rearrangement : t(6;12)(q21;q24.31)(chr6:g.109330448::chr12:g.121909964) Note: The KDM2B Rearrangement is a translocation event with a breakpoint in intron12. Its functional significance is undetermined.
SESN1	0	MSKCC-DMP	P-0034684-T01-IM6	SESN1-KDM2B fusion	yes	unknown		unknown	KDM2B (NM_032590) Rearrangement : t(6;12)(q21;q24.31)(chr6:g.109330448::chr12:g.121909964) Note: The KDM2B Rearrangement is a translocation event with a breakpoint in intron12. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0034704-T01-IM6	TRIM24-RET fusion	yes	unknown		in frame	TRIM24 (NM_015905) - RET (NM_020975) Fusion (TRIM24 exon 9 fused with RET exon12) : t(7;10)(q34;q11.21)(chr7:g.138243011::chr10:g.43611827) Note: The TRIM24-RET fusion is predicted to be in-frame and includes the kinase domain of RET
TRIM24	0	MSKCC-DMP	P-0034704-T01-IM6	TRIM24-RET fusion	yes	unknown		in frame	TRIM24 (NM_015905) - RET (NM_020975) Fusion (TRIM24 exon 9 fused with RET exon12) : t(7;10)(q34;q11.21)(chr7:g.138243011::chr10:g.43611827) Note: The TRIM24-RET fusion is predicted to be in-frame and includes the kinase domain of RET
KIF13B	0	MSKCC-DMP	P-0034708-T01-IM6	DUSP4-KIF13B fusion	yes	unknown		out of frame	KIF13B (NM_015254) - DUSP4 (NM_001394) Rearrangement : c.149+15289:KIF13B_c.433+4346:DUSP4dup Note: The KIF13B - DUSP4 Rearrangement results in the fusion of exons 1-2 of KIF13B with exons 2-4 of DUSP4. Its functional significance is undetermined.
DUSP4	0	MSKCC-DMP	P-0034708-T01-IM6	DUSP4-KIF13B fusion	yes	unknown		out of frame	KIF13B (NM_015254) - DUSP4 (NM_001394) Rearrangement : c.149+15289:KIF13B_c.433+4346:DUSP4dup Note: The KIF13B - DUSP4 Rearrangement results in the fusion of exons 1-2 of KIF13B with exons 2-4 of DUSP4. Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0034727-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) Rearrangement : c.645+2057_c.868del Note: The PBRM1 Rearrangement results in the intragenic deletion of exons 7-9 of PBRM1. One of the breakpoints is within exon20. Its functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0034733-T01-IM6	ALK-intragenic	yes	unknown		out of frame	ALK (NM_004304) Rearrangement : c.3172+337_c.3359+71del Note : The ALK Rearrangement results in the partial intragenic deletion of exon20. One of the breakpoints is within exon20. It includes part of the kinase domain.
CCNE1	0	MSKCC-DMP	P-0034750-T01-IM6	ZNF536-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) rearrangement: c.283:CCNE1_chr19:g.30915262inv Note: The CCNE1 rearrangement is an inversion of exons 5-12. One of the breakpoints is within exon 5. Its functional significance is undetermined.
ZNF536	0	MSKCC-DMP	P-0034750-T01-IM6	ZNF536-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) rearrangement: c.283:CCNE1_chr19:g.30915262inv Note: The CCNE1 rearrangement is an inversion of exons 5-12. One of the breakpoints is within exon 5. Its functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0034763-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT (NM_005245) Rearrangement : c.9853+481_c.10960inv Note: The FAT Rearrangement results in the inversion of exons 15-19. One of the breakpoints is within exon19. Its functional significance is undetermined.
EMID1	0	MSKCC-DMP	P-0034773-T01-IM6	EWSR1-EMID1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.812-463:EWSR1_c.1205-1206:EMID1dup Note: The EWSR1 - EMID1 rearrangement is a duplication that results in the in-frame fusion of EWSR1 exons 1-8 with EMID1 exon 15. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0034773-T01-IM6	EWSR1-EMID1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.812-463:EWSR1_c.1205-1206:EMID1dup Note: The EWSR1 - EMID1 rearrangement is a duplication that results in the in-frame fusion of EWSR1 exons 1-8 with EMID1 exon 15. The functional significance is undetermined.
PMS2	0	MSKCC-DMP	P-0034796-T01-IM6	THSD7A-PMS2 fusion	yes	unknown		unknown	PMS2 (NM_000535) rearrangement: c.667:PMS2_chr7:g.11273145inv Note: The PMS2 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.
THSD7A	0	MSKCC-DMP	P-0034796-T01-IM6	THSD7A-PMS2 fusion	yes	unknown		unknown	PMS2 (NM_000535) rearrangement: c.667:PMS2_chr7:g.11273145inv Note: The PMS2 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034815-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3040:TMPRSS2_c.18+3720:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0034815-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3040:TMPRSS2_c.18+3720:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
SND1	0	MSKCC-DMP	P-0034845-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1527+3658:SND1_c.1141-1857:BRAFinv Note: The SND1 - BRAF rearrangement is an inversion that results in the in-frame fusion of SND1 exons 1-14 with BRAF exons 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0034845-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1527+3658:SND1_c.1141-1857:BRAFinv Note: The SND1 - BRAF rearrangement is an inversion that results in the in-frame fusion of SND1 exons 1-14 with BRAF exons 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034865-T01-IM6	OSBPL1A-TMPRSS2 fusion	yes	unknown		in frame	OSBPL1A (NM_080597) - TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q11.2;q22.3)(chr18:g.21746075::chr21:g.42874744) Note: The OSBPL1A - TMPRSS2 rearrangement is a translocation which may result in the fusion of OSBPL1A exons 1-14 with TMPRSS2 exons 2-14. Its functional significance is undetermined.
OSBPL1A	0	MSKCC-DMP	P-0034865-T01-IM6	OSBPL1A-TMPRSS2 fusion	yes	unknown		in frame	OSBPL1A (NM_080597) - TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q11.2;q22.3)(chr18:g.21746075::chr21:g.42874744) Note: The OSBPL1A - TMPRSS2 rearrangement is a translocation which may result in the fusion of OSBPL1A exons 1-14 with TMPRSS2 exons 2-14. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034865-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4544:TMPRSS2_c.40-63678:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 4-10. This involves the non canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0034865-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4544:TMPRSS2_c.40-63678:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 4-10. This involves the non canonical ERG (NM_004449) transcript.
FAM19A2	0	MSKCC-DMP	P-0034917-T01-IM6	MDC1-FAM19A2 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(6;12)(p21.33;q14.1)(chr6:g.30680394::chr12:g.61245740) Note: The MDC1 rearrangement is a translocation involving a breakpoint in exon 5. Its functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0034917-T01-IM6	MDC1-FAM19A2 fusion	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(6;12)(p21.33;q14.1)(chr6:g.30680394::chr12:g.61245740) Note: The MDC1 rearrangement is a translocation involving a breakpoint in exon 5. Its functional significance is undetermined.
GPR160	0	MSKCC-DMP	P-0034928-T01-IM6	PRKCI-GPR160 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.224-1:PRKCI_chr3:g.169756755del Note: The PRKCI rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0034928-T01-IM6	PRKCI-GPR160 fusion	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.224-1:PRKCI_chr3:g.169756755del Note: The PRKCI rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0034975-T01-IM6	ATF7IP-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.4139:KDM5A_chr12:g.14309266inv Note: The KDM5A rearrangement is an inversion of exons 1-25. One of the breakpoints is within exon 25. The functional significance is undetermined.
ATF7IP	0	MSKCC-DMP	P-0034975-T01-IM6	ATF7IP-KDM5A fusion	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.4139:KDM5A_chr12:g.14309266inv Note: The KDM5A rearrangement is an inversion of exons 1-25. One of the breakpoints is within exon 25. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0035065-T01-IM6	NCOR1-intragenic	yes	unknown		out of frame	NCOR1 (NM_006311) rearrangement: c.1082+54_c.1174-1771del Note: The NCOR1 rearrangement is an intragenic deletion of exon 11.
ERG	0	MSKCC-DMP	P-0035065-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4830:TMPRSS2_c.39+38144:ERGdel Note: The TMPRSS2 - ERG fusion involves TMRPSS2 exon 1 and ERG exons 4-10. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0035065-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4830:TMPRSS2_c.39+38144:ERGdel Note: The TMPRSS2 - ERG fusion involves TMRPSS2 exon 1 and ERG exons 4-10. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
AGO2	0	MSKCC-DMP	P-0035078-T01-IM6	DENND3-AGO2 fusion	yes	unknown		unknown	AGO2 (NM_012154): c.1840-54_chr8: g.142022551del Note: The AGO2 rearrangement is a deletion that includes AGO2 exons 1-15. One of the breakpoints is within exon 15. The functional significance is undetermined.
DENND3	0	MSKCC-DMP	P-0035078-T01-IM6	DENND3-AGO2 fusion	yes	unknown		unknown	AGO2 (NM_012154): c.1840-54_chr8: g.142022551del Note: The AGO2 rearrangement is a deletion that includes AGO2 exons 1-15. One of the breakpoints is within exon 15. The functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0035093-T01-IM6	TBX15-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: t(1;11)(p12;q22.1)(chr1:g.119374897::chr11:g.102076978) Note: The YAP1 rearrangement is a translocation with a breakpoint in YAP1 intron 5. The functional significance is undetermined.
TBX15	0	MSKCC-DMP	P-0035093-T01-IM6	TBX15-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: t(1;11)(p12;q22.1)(chr1:g.119374897::chr11:g.102076978) Note: The YAP1 rearrangement is a translocation with a breakpoint in YAP1 intron 5. The functional significance is undetermined.
BCL2	0	MSKCC-DMP	P-0035107-T01-IM6	SERPINB3-BCL2 fusion	yes	unknown		unknown	BCL2(NM_000633)  Rearrangement : c.420:BCL2_chr18:g.61340025inv Note: The BCL2(NM_000633)  Rearrangement results in the inversion of exon2.The breakpoint is within exon2. Its functional significance is undetermined.
SERPINB3	0	MSKCC-DMP	P-0035107-T01-IM6	SERPINB3-BCL2 fusion	yes	unknown		unknown	BCL2(NM_000633)  Rearrangement : c.420:BCL2_chr18:g.61340025inv Note: The BCL2(NM_000633)  Rearrangement results in the inversion of exon2.The breakpoint is within exon2. Its functional significance is undetermined.
ASCC3	0	MSKCC-DMP	P-0035118-T01-IM6	DCUN1D1-ASCC3 fusion	yes	unknown		unknown	DCUN1D1 (NM_020640) rearrangement: t(3;6)(q26.33;q16.3)(chr3:g.182683416::chr6:g.100978161) Note: The DCUN1D1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
DCUN1D1	0	MSKCC-DMP	P-0035118-T01-IM6	DCUN1D1-ASCC3 fusion	yes	unknown		unknown	DCUN1D1 (NM_020640) rearrangement: t(3;6)(q26.33;q16.3)(chr3:g.182683416::chr6:g.100978161) Note: The DCUN1D1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0035118-T01-IM6	PORCN-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.45:KDM6A_chrX:g.48353211inv Note: The KDM6A rearrangement results in the inversion of exons 1-29. One of the breakpoints is within exon 1. The functional significance is undetermined.
PORCN	0	MSKCC-DMP	P-0035118-T01-IM6	PORCN-KDM6A fusion	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.45:KDM6A_chrX:g.48353211inv Note: The KDM6A rearrangement results in the inversion of exons 1-29. One of the breakpoints is within exon 1. The functional significance is undetermined.
DAOA-AS1	0	MSKCC-DMP	P-0035151-T01-IM6	APC-DAOA-AS1 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : t(5;13)(q22.1;q13.2)(chr5:g.112173891::chr13:g.105759777) Note: The APC Rearrangement is a translocation event with a breakpoint in exon16. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0035151-T01-IM6	APC-DAOA-AS1 fusion	yes	unknown		unknown	APC (NM_000038) Rearrangement : t(5;13)(q22.1;q13.2)(chr5:g.112173891::chr13:g.105759777) Note: The APC Rearrangement is a translocation event with a breakpoint in exon16. Its functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0035160-T01-IM6	POLD1-intragenic	yes	unknown		out of frame	POLD1 (NM_002691) rearrangement: c.2155-1243_c.3068-135del Note: The POLD1 rearrangement is an intragenic deletion of exons 18-24. The functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0035160-T01-IM6	DDX58-TEK fusion	yes	unknown		unknown	TEK (NM_000459) - DDX58 (NM_014314) rearrangement: c.610:TEK_c.1103:DDX58inv Note: The TEK - DDX58 rearrangement is an inversion that results in a fusion of TEK exons 1-4 to DDX58 exons 8-18. The breakpoints are within TEK exon 4 and DDX58 exon 8. The functional significance is undetermined.
DDX58	0	MSKCC-DMP	P-0035160-T01-IM6	DDX58-TEK fusion	yes	unknown		unknown	TEK (NM_000459) - DDX58 (NM_014314) rearrangement: c.610:TEK_c.1103:DDX58inv Note: The TEK - DDX58 rearrangement is an inversion that results in a fusion of TEK exons 1-4 to DDX58 exons 8-18. The breakpoints are within TEK exon 4 and DDX58 exon 8. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0035170-T01-IM6	PIGL-KDM6A fusion	yes	unknown		in frame	KDM6A (NM_021140) - PIGL (NM_004278) Rearrangement : t(X,17)(p11.23; p12) (chrX:g.44949188::chr17:g.16127247) Note: The KDM6A - PIGL Rearrangement results in the fusion of exons 1-25 of KDM6A with exons 2-7 of PIGL. Its functional significance is undetermined.
PIGL	0	MSKCC-DMP	P-0035170-T01-IM6	PIGL-KDM6A fusion	yes	unknown		in frame	KDM6A (NM_021140) - PIGL (NM_004278) Rearrangement : t(X,17)(p11.23; p12) (chrX:g.44949188::chr17:g.16127247) Note: The KDM6A - PIGL Rearrangement results in the fusion of exons 1-25 of KDM6A with exons 2-7 of PIGL. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0035221-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4689:TMPRSS2_c.39+50100:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
TMPRSS2	0	MSKCC-DMP	P-0035221-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4689:TMPRSS2_c.39+50100:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
RICTOR	0	MSKCC-DMP	P-0035288-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.-712_c.4662del Note: The RICTOR rearrangement results in the deletion of exons 1-35. One of the breakpoints is within exon 35. The functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0035378-T01-IM6	CA10-BRCA1 fusion	yes	unknown		out of frame	BRCA1 (NM_007294) - CA10 (NM_001082533) rearrangement: c.547+98:BRCA1_c.280-78647:CA10dup Note: The BRCA1 - CA10 rearrangement is a duplication that may result in the fusion of BRCA1 exons 1-7 with CA10 exons 5-10
CA10	0	MSKCC-DMP	P-0035378-T01-IM6	CA10-BRCA1 fusion	yes	unknown		out of frame	BRCA1 (NM_007294) - CA10 (NM_001082533) rearrangement: c.547+98:BRCA1_c.280-78647:CA10dup Note: The BRCA1 - CA10 rearrangement is a duplication that may result in the fusion of BRCA1 exons 1-7 with CA10 exons 5-10
VHL	0	MSKCC-DMP	P-0035378-T01-IM6	IRAK2-VHL fusion	yes	unknown		unknown	IRAK2 (NM_001570) - VHL (NM_000551) : c.95-834:IRAK2_c.568:VHLdup Note: The IRAK2 - VHL rearrangement  is a duplication that results in the fusion of IRAK2 exon1 with VHL exon 3. One of the breakpoints is within VHL exon 3. The functional significance is undetermined.
IRAK2	0	MSKCC-DMP	P-0035378-T01-IM6	IRAK2-VHL fusion	yes	unknown		unknown	IRAK2 (NM_001570) - VHL (NM_000551) : c.95-834:IRAK2_c.568:VHLdup Note: The IRAK2 - VHL rearrangement  is a duplication that results in the fusion of IRAK2 exon1 with VHL exon 3. One of the breakpoints is within VHL exon 3. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0035383-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: chr3:g.3:52432893_c.803del Note: The BAP1 rearrangement is a deletion that includes BAP1 exons 10-17. One of the breakpoints is within exon 10.
STK11	0	MSKCC-DMP	P-0035516-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.598-4_c.921-51inv Note: The ATK11 rearrangement is an intragenic inversion of exons 5-7. Its functional significance is undetermined.
RFC3	0	MSKCC-DMP	P-0035527-T01-IM6	RB1-RFC3 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.2656:RB1_chr13:g.34574296inv Note: The RB1 rearrangement is an inversion of exons 1-25. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0035527-T01-IM6	RB1-RFC3 fusion	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.2656:RB1_chr13:g.34574296inv Note: The RB1 rearrangement is an inversion of exons 1-25. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0035527-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.920-44:TP53_chr17:g.7581782del Note: The TP53 rearrangement is a deletion of exons 1-8.
RNF43	0	MSKCC-DMP	P-0035528-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763)  rearrangement: c.253-14455_c.1745del Note: The RNF43 rearrangement is an intragenic deletion of exons 3-9. One of the breakpoints is within exon 9. Its functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0035552-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20): t(12;15)(p13.2;q25.3)(chr12:g.12020963::chr15:g.88651251) Note: The ETV6 - NTRK3 Fusion is predicted to be in-frame and includes the protein kinase domain of NTRK3.
ETV6	0	MSKCC-DMP	P-0035552-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion (ETV6 exons 1-4 fused with NTRK3 exons 14-20): t(12;15)(p13.2;q25.3)(chr12:g.12020963::chr15:g.88651251) Note: The ETV6 - NTRK3 Fusion is predicted to be in-frame and includes the protein kinase domain of NTRK3.
PDE4A	0	MSKCC-DMP	P-0035563-T01-IM6	SMARCA4-PDE4A fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - PDE4A (NM_001111307) Rearrangement : c.3959:SMARCA4_c.670+11:PDE4Adup Note: The SMARCA4-PDE4A Rearrangement results in the fusion of exons 1-29 of SMARCA4 with exons  6-15 of PDE4A.The breakpoint in SMARCA4 is within exon29. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0035563-T01-IM6	SMARCA4-PDE4A fusion	yes	unknown		unknown	SMARCA4 (NM_003072) - PDE4A (NM_001111307) Rearrangement : c.3959:SMARCA4_c.670+11:PDE4Adup Note: The SMARCA4-PDE4A Rearrangement results in the fusion of exons 1-29 of SMARCA4 with exons  6-15 of PDE4A.The breakpoint in SMARCA4 is within exon29. Its functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0035563-T01-IM6	CENPP-NTRK2 fusion	yes	unknown		out of frame	CENPP (NM_001012267) - NTRK2 (NM_006180) Rearrangement : c.468-791:CENPP_c.1765-10:NTRK2dup Note: The CENPP -NTRK2 Rearrangement results in the fusion of exons 1-3 of CENPP with exon 18 of NTRK2. It includes the protein kinase domain of NTRK2. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help further characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
CENPP	0	MSKCC-DMP	P-0035563-T01-IM6	CENPP-NTRK2 fusion	yes	unknown		out of frame	CENPP (NM_001012267) - NTRK2 (NM_006180) Rearrangement : c.468-791:CENPP_c.1765-10:NTRK2dup Note: The CENPP -NTRK2 Rearrangement results in the fusion of exons 1-3 of CENPP with exon 18 of NTRK2. It includes the protein kinase domain of NTRK2. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help further characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TTC28	0	MSKCC-DMP	P-0035642-T01-IM6	EWSR1-TTC28 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - TTC28 (NM_001145418) rearrangement: c.1179+1655:EWSR1_c.382-16678:TTC28del Note: The EWSR1- TTC28 rearrangement is a deletion that includes EWSR1 exons 1-12 and TTC28 exons 1-2. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0035642-T01-IM6	EWSR1-TTC28 fusion	yes	unknown		unknown	EWSR1 (NM_013986) - TTC28 (NM_001145418) rearrangement: c.1179+1655:EWSR1_c.382-16678:TTC28del Note: The EWSR1- TTC28 rearrangement is a deletion that includes EWSR1 exons 1-12 and TTC28 exons 1-2. The functional significance is undetermined.
SIRT5	0	MSKCC-DMP	P-0036526-T01-IM6	HIST1H3B-SIRT5 fusion	yes	unknown		unknown	HIST1H3B (NM_003537) - SIRT5 (NM_012241) rearrangement: c.243:HIST1H3B_c.654:SIRT5inv Note: The HIST1H3B - SIRT5 rearrangement is an inversion that results in a fusion of HIST1H3B exon 1 to SIRT5 exons 8-10. The breakpoints are within HIST1H3B exon 1 and SIRT5 exon 8. The functional significance is undetermined.
HIST1H3B	0	MSKCC-DMP	P-0036526-T01-IM6	HIST1H3B-SIRT5 fusion	yes	unknown		unknown	HIST1H3B (NM_003537) - SIRT5 (NM_012241) rearrangement: c.243:HIST1H3B_c.654:SIRT5inv Note: The HIST1H3B - SIRT5 rearrangement is an inversion that results in a fusion of HIST1H3B exon 1 to SIRT5 exons 8-10. The breakpoints are within HIST1H3B exon 1 and SIRT5 exon 8. The functional significance is undetermined.
SND1	0	MSKCC-DMP	P-0036567-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) Fusion (SND1 exon10 fused with BRAF exon9) : c.1153-22013:SND1_ c.1140+556:BRAFinv Note: The SND1-BRAF Fusion is an in-frame fusion and includes the protein kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0036567-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) Fusion (SND1 exon10 fused with BRAF exon9) : c.1153-22013:SND1_ c.1140+556:BRAFinv Note: The SND1-BRAF Fusion is an in-frame fusion and includes the protein kinase domain of BRAF.
ERG	0	MSKCC-DMP	P-0036699-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1733:TMPRSS2_c.40-58568:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11 and is predicted to be in-frame. The fusion involves the non-canonical ERG transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0036699-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1733:TMPRSS2_c.40-58568:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11 and is predicted to be in-frame. The fusion involves the non-canonical ERG transcript (NM_004449).
DNM2	0	MSKCC-DMP	P-0036723-T01-IM6	SMARCA4-DNM2 fusion	yes	unknown		unknown	DNM2 (NM_001005361) - SMARCA4 (NM_003072) fusion: c.2543+154:DNM2_c.2644:SMARCA4del Note: The DNM2 - SMARCA4 fusion is the result of DNM2 exons 1-19 fused with SMARCA4 exons 19 to 35. One of the breakpoints is within exon 19 of SMARCA4. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0036723-T01-IM6	SMARCA4-DNM2 fusion	yes	unknown		unknown	DNM2 (NM_001005361) - SMARCA4 (NM_003072) fusion: c.2543+154:DNM2_c.2644:SMARCA4del Note: The DNM2 - SMARCA4 fusion is the result of DNM2 exons 1-19 fused with SMARCA4 exons 19 to 35. One of the breakpoints is within exon 19 of SMARCA4. The functional significance is undetermined.
PDE3A	0	MSKCC-DMP	P-0036757-T01-IM6	RECQL-PDE3A fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.501+118:RECQL_chr12:g.20757854del Note: The RECQL rearrangement is a deletion of exons 7-16. Its functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0036757-T01-IM6	RECQL-PDE3A fusion	yes	unknown		unknown	RECQL (NM_032941) rearrangement: c.501+118:RECQL_chr12:g.20757854del Note: The RECQL rearrangement is a deletion of exons 7-16. Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0036760-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.517_c.993+73del Note: The TP53 rearrangement is an intragenic deletion of exons 5-9.
ERG	0	MSKCC-DMP	P-0036791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3503:TMPRSS2_c.18+1131:ERGdel Note: The TMPRSS2 - ERG fusion is the result of deletion which fuses TMPRSS2 exon 1 with ERG exons 2-10.
TMPRSS2	0	MSKCC-DMP	P-0036791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3503:TMPRSS2_c.18+1131:ERGdel Note: The TMPRSS2 - ERG fusion is the result of deletion which fuses TMPRSS2 exon 1 with ERG exons 2-10.
KEAP1	0	MSKCC-DMP	P-0036807-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.1455_c.1709-149del Note: The KEAP1 rearrangement is an intragenic deletion of exons 4-5. One of the breakpoints is within exon 4.
SLC1A1	0	MSKCC-DMP	P-0036808-T01-IM6	PTPRD-SLC1A1 fusion	yes	unknown		unknown	PTPRD (NM_002839) - SLC1A1 (NM_004170) rearrangement: c.2409:PTPRD_c.92-21484:SLC1A1dup Note: The PTPRD - SLC1A1 rearrangement is a duplication that includes PTPRD exons 27-46 and SLC1A1 exon 1. One of the breakpoints is within PTPRD exon 27.
PTPRD	0	MSKCC-DMP	P-0036808-T01-IM6	PTPRD-SLC1A1 fusion	yes	unknown		unknown	PTPRD (NM_002839) - SLC1A1 (NM_004170) rearrangement: c.2409:PTPRD_c.92-21484:SLC1A1dup Note: The PTPRD - SLC1A1 rearrangement is a duplication that includes PTPRD exons 27-46 and SLC1A1 exon 1. One of the breakpoints is within PTPRD exon 27.
FUBP1	0	MSKCC-DMP	P-0036814-T01-IM6	FUBP1-intragenic	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.474-209_c.1114dup Note: The FUBP1 rearrangement is an intragenic duplication of exons 8-13. One of the breakpoints is within exon 13. The functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0036827-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.-116-866_c.350del Note: The AXIN2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is mid exon.
APC	0	MSKCC-DMP	P-0036827-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038): c.6528_chr5:g.112190800del Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.
SRP19	0	MSKCC-DMP	P-0036827-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038): c.6528_chr5:g.112190800del Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.
NF1	0	MSKCC-DMP	P-0036828-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.1845+66_c.2326-115dup Note: The NF1 rearrangement is an intragenic duplication of exons 17-19.  The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0036845-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.934_chr3:g.52446650del Note: The BAP1 rearrangement is a deletion that includes BAP1 exons 1-11. One of the breakpoints is within BAP1 exon 11.
PTCSC3	0	MSKCC-DMP	P-0036867-T01-IM6	NKX2-1-PTCSC3 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) Rearrangement : c.774_chr14:g.36676003del Note: The NKX2-1 Rearrangement results in the deletion of exons 2-3 of NKX2-1. One of the breakpoints is within exon2. Its functional significance is undetermined.
NKX2-1	0	MSKCC-DMP	P-0036867-T01-IM6	NKX2-1-PTCSC3 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) Rearrangement : c.774_chr14:g.36676003del Note: The NKX2-1 Rearrangement results in the deletion of exons 2-3 of NKX2-1. One of the breakpoints is within exon2. Its functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0036871-T01-IM6	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : c.57_.114+4073del Note: The NF2 Rearrangement results in the intragenic deletion of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0036871-T01-IM6	DMRTA1-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement : c.194-3351:CDKN2Ap14ARF_chr9:g.22393377del Note: The CDKN2Ap14ARF Rearrangement results in the intragenic deletion of exon1. The breakpoint is within exon1. This rearrangement affects both the CDKN2Ap14ARF and CDKN2Ap16INK4A isoforms. Its functional significance is undetermined.
DMRTA1	0	MSKCC-DMP	P-0036871-T01-IM6	DMRTA1-CDKN2A fusion	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) Rearrangement : c.194-3351:CDKN2Ap14ARF_chr9:g.22393377del Note: The CDKN2Ap14ARF Rearrangement results in the intragenic deletion of exon1. The breakpoint is within exon1. This rearrangement affects both the CDKN2Ap14ARF and CDKN2Ap16INK4A isoforms. Its functional significance is undetermined.
BCR	0	MSKCC-DMP	P-0036887-T01-IM6	EZH1-BCR fusion	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: t(17;22)(q21.2;q11.23)(chr17:g.40859970::chr22:g.23513917) Note: The EZH1 rearrangement is a translocation involving exon 15. Its functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0036887-T01-IM6	EZH1-BCR fusion	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: t(17;22)(q21.2;q11.23)(chr17:g.40859970::chr22:g.23513917) Note: The EZH1 rearrangement is a translocation involving exon 15. Its functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0036911-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) Rearrangement: c.266_c.*406inv Note: The B2M rearrangement results in an intragenic inversion spanning exons 2 and 3. The breakpoint is within exon 2. Its functional significance is undetermined. This structural rearrangement is part of a more complex rearrangement involving B2M.
PAX8	0	MSKCC-DMP	P-0036963-T01-IM6	ACMSD-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: c.1189+92:PAX8_chr2:g.135527206del Note: The PAX8 rearrangement is a deletion of exons 11-12. Its functional significance is undetermined.
ACMSD	0	MSKCC-DMP	P-0036963-T01-IM6	ACMSD-PAX8 fusion	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: c.1189+92:PAX8_chr2:g.135527206del Note: The PAX8 rearrangement is a deletion of exons 11-12. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0036970-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q33.1;q22.1)(chr5:g.149783480::chr6:g.117650273) Note: The CD74 - ROS1 rearrangement is a translocation which results in the fusion of CD74 exons 1-6 with ROS1 exons 33-43.
CD74	0	MSKCC-DMP	P-0036970-T01-IM6	CD74-ROS1 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q33.1;q22.1)(chr5:g.149783480::chr6:g.117650273) Note: The CD74 - ROS1 rearrangement is a translocation which results in the fusion of CD74 exons 1-6 with ROS1 exons 33-43.
SMYD3	0	MSKCC-DMP	P-0036974-T01-IM6	SMYD3-intragenic	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement: c.845_c.814-6743el Note: The SMYD3 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0036992-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12015303::chr15:g.88666269) Note: The ETV6 - NTRK3 fusion is predicted to be in-frame and involves ETV6 exons 1-4 and NTRK3 exons 14-20, including NTRK3 kinase domain.
ETV6	0	MSKCC-DMP	P-0036992-T01-IM6	ETV6-NTRK3 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12015303::chr15:g.88666269) Note: The ETV6 - NTRK3 fusion is predicted to be in-frame and involves ETV6 exons 1-4 and NTRK3 exons 14-20, including NTRK3 kinase domain.
CD44	0	MSKCC-DMP	P-0033257-T01-IM6	NRG1-CD44 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD44-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD44 Exon5 (NM_000610) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180132 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0033257-T01-IM6	NRG1-CD44 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD44-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes CD44 Exon5 (NM_000610) and NRG1 Exon2 (NM_004495). Lab Notes Run Number: ArcherV2-CLIN-20180132 Macro-dissection: Unknown
CCDC6	0	MSKCC-DMP	P-0033301-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180132 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0033301-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20180132 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0034040-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0034040-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
TCF12	0	MSKCC-DMP	P-0034919-T01-IM6	TRAPPC12-TCF12 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TCF12-TRAPPC12 fusion. Note: The rearrangement is an out of frame fusion between genes TCF12 Exon5 (NM_207036) and TRAPPC12 Exon2 (NM_016030). Functional significance is unknown. Lab Notes Run Number: ArcherV3-CLIN-20180165 Macro-dissection: Unknown
TRAPPC12	0	MSKCC-DMP	P-0034919-T01-IM6	TRAPPC12-TCF12 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TCF12-TRAPPC12 fusion. Note: The rearrangement is an out of frame fusion between genes TCF12 Exon5 (NM_207036) and TRAPPC12 Exon2 (NM_016030). Functional significance is unknown. Lab Notes Run Number: ArcherV3-CLIN-20180165 Macro-dissection: Unknown
ETV6	0	MSKCC-DMP	P-0035552-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20180170 Macro-dissection: Unknown
NTRK3	0	MSKCC-DMP	P-0035552-T01-IM6	NTRK3-ETV6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ETV6-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes ETV6 Exon4 (NM_001987) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20180170 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0036639-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:   POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET Exon 14 Skipping (NM_000245) Lab Notes Run Number: ArcherV3-CLIN-20180193 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0036870-T01-IM6	PRIM2-BRAF fusion	yes	unknown		in frame	PRIM2 (NM_000947) - BRAF (NM_004333) Rearrangement : t(6;7)(p11.1;q34)(chr6:g.57410815::chr7:g.140493232) Note: The PRIM2- BRAF Rearrangement results in the fusion of exons 1-10 of PRIM2 with exons 9-18 of BRAF.It includes the protein kinase domain of BRAF.
PRIM2	0	MSKCC-DMP	P-0036870-T01-IM6	PRIM2-BRAF fusion	yes	unknown		in frame	PRIM2 (NM_000947) - BRAF (NM_004333) Rearrangement : t(6;7)(p11.1;q34)(chr6:g.57410815::chr7:g.140493232) Note: The PRIM2- BRAF Rearrangement results in the fusion of exons 1-10 of PRIM2 with exons 9-18 of BRAF.It includes the protein kinase domain of BRAF.
ROS1	0	MSKCC-DMP	P-0026589-T02-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) Fusion (CD74 exon6 fused to ROS1 exon34) : t(5;6)(q32;q22.1)(chr5:g.149782990::chr6:g.117646032) Note: The CD74 -ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.
CD74	0	MSKCC-DMP	P-0026589-T02-IM6	CD74-ROS1 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) Fusion (CD74 exon6 fused to ROS1 exon34) : t(5;6)(q32;q22.1)(chr5:g.149782990::chr6:g.117646032) Note: The CD74 -ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.
ERG	0	MSKCC-DMP	P-0035561-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-1709:TMPRSS2_c.18+5540:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0035561-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-1709:TMPRSS2_c.18+5540:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0036960-T01-IM6	MFSD4-TMPRSS2 fusion	yes	unknown		in frame	MFSD4 (NM_181644) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q32.1;q22.3)(chr1:g.205560208::chr21:g.42867222) Note: The TMFSD4 - TMPRSS2 rearrangement is a translocation which may result in the fusion of MFSD4 exons 1-6 with TMPRSS2 exons 3-14. Its functional significance is undetermined.
MFSD4	0	MSKCC-DMP	P-0036960-T01-IM6	MFSD4-TMPRSS2 fusion	yes	unknown		in frame	MFSD4 (NM_181644) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q32.1;q22.3)(chr1:g.205560208::chr21:g.42867222) Note: The TMFSD4 - TMPRSS2 rearrangement is a translocation which may result in the fusion of MFSD4 exons 1-6 with TMPRSS2 exons 3-14. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0036960-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.109_c.889+89dup Note: The EGFR rearrangement is an intragenic duplication of exons 2-7. One of the breakpoints is within exon 7. This does not include the kinase domain. Its functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0036970-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_004355) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190003 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0036970-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_004355) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190003 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0036960-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20190004 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0036960-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20190004 Macro-dissection: Unknown
AKAP9	0	MSKCC-DMP	P-0036937-T01-IM6	BRAF-AKAP9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AKAP9-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AKAP9 Exon8 (NM_005751) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20190005 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0036937-T01-IM6	BRAF-AKAP9 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AKAP9-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AKAP9 Exon8 (NM_005751) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20190005 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0034480-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11 ): c.56-1833:TMPRSS2_c.39+53541:ERGdel
TMPRSS2	0	MSKCC-DMP	P-0034480-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11 ): c.56-1833:TMPRSS2_c.39+53541:ERGdel
TLN2	0	MSKCC-DMP	P-0037101-T01-IM6	RPS6KB2-TLN2 fusion	yes	unknown		unknown	TLN2 (NM_015059) - RPS6KB2 (NM_003952) rearrangement: t(11;15)(q13.2;q22.2)(chr11:g.67201947::chr15:g.63122011) Note: The TLN2 - RPS6KB2 rearrangement is a translocation that results in the fusion of TLN2 exons 1-52 with RPS6KB2 exons 13-15. One of the breakpoints is within RPS6KB2 exon 13. The functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0037101-T01-IM6	RPS6KB2-TLN2 fusion	yes	unknown		unknown	TLN2 (NM_015059) - RPS6KB2 (NM_003952) rearrangement: t(11;15)(q13.2;q22.2)(chr11:g.67201947::chr15:g.63122011) Note: The TLN2 - RPS6KB2 rearrangement is a translocation that results in the fusion of TLN2 exons 1-52 with RPS6KB2 exons 13-15. One of the breakpoints is within RPS6KB2 exon 13. The functional significance is undetermined.
PLAT	0	MSKCC-DMP	P-0026615-T02-IM6	NRG1-PLAT fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PLAT-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes PLAT Exon6 (NM_000930) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV3-CLIN-20190010 Macro-dissection: Unknown
NRG1	0	MSKCC-DMP	P-0026615-T02-IM6	NRG1-PLAT fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PLAT-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes PLAT Exon6 (NM_000930) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: ArcherV3-CLIN-20190010 Macro-dissection: Unknown
AURKA	0	MSKCC-DMP	P-0036525-T01-IM6	RAB3GAP2-AURKA fusion	yes	unknown		out of frame	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.31)(chr1:g.220440791::chr20:g.54958234) Note: The RAB3GAP2 - AURKA rearrangement is a translocation which may result in the fusion of RAB3GAP2 exon 1 with AURKA exons 5-9. Its functional significance is undetermined. Multiple rearrangements involving AURKA were detected in this sample and more complex rearrangement resulting in additional AURKA fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RAB3GAP2	0	MSKCC-DMP	P-0036525-T01-IM6	RAB3GAP2-AURKA fusion	yes	unknown		out of frame	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.31)(chr1:g.220440791::chr20:g.54958234) Note: The RAB3GAP2 - AURKA rearrangement is a translocation which may result in the fusion of RAB3GAP2 exon 1 with AURKA exons 5-9. Its functional significance is undetermined. Multiple rearrangements involving AURKA were detected in this sample and more complex rearrangement resulting in additional AURKA fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
NRG3	0	MSKCC-DMP	P-0036885-T01-IM6	NOTCH4-NRG3 fusion	yes	unknown		unknown	NRG3 (NM_001010848) - NOTCH4 (NM_004557) rearrangement: t(6;10)(p21.32;q23.1)(chr6:g.32163675::chr10:g.84452811) Note: The NRG3 - NOTCH4 rearrangement is a translocation which may result in the fusion of NRG3 exons 1-3 with NOTCH4 exons 30. Its functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0036885-T01-IM6	NOTCH4-NRG3 fusion	yes	unknown		unknown	NRG3 (NM_001010848) - NOTCH4 (NM_004557) rearrangement: t(6;10)(p21.32;q23.1)(chr6:g.32163675::chr10:g.84452811) Note: The NRG3 - NOTCH4 rearrangement is a translocation which may result in the fusion of NRG3 exons 1-3 with NOTCH4 exons 30. Its functional significance is undetermined.
TRMT1	0	MSKCC-DMP	P-0036885-T01-IM6	BRD4-TRMT1 fusion	yes	unknown		out of frame	TRMT1 (NM_001136035) - BRD4 (NM_058243) rearrangement: c.1583+671_c.4021-35dup Note: The TRMT1 - BRD4 rearrangement is a duplication which results in the fusion of TRMT1 exons 1-12 with BRD4 exon 20. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0036885-T01-IM6	BRD4-TRMT1 fusion	yes	unknown		out of frame	TRMT1 (NM_001136035) - BRD4 (NM_058243) rearrangement: c.1583+671_c.4021-35dup Note: The TRMT1 - BRD4 rearrangement is a duplication which results in the fusion of TRMT1 exons 1-12 with BRD4 exon 20. Its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0036885-T01-IM6	KMT2B-intragenic	yes	unknown		in frame	KMT2B (NM_014727) rearrangement: c.363+60_c.2458-18del Note: The KMT2B rearrangement is an intragenic deletion of exons 2-3. Its functional significance is undetermined.
GRIN2A	0	MSKCC-DMP	P-0036886-T01-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: c.1831_c.2356+6658del Note: The GRIN2A rearrangement is an intragenic deletion of exons 9-11. One of the breakpoints is within exon 9. Its functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0036886-T01-IM6	RPTOR-intragenic	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: c.731_c.830+1624del Note: The RPTOR rearrangement is an intragenic deletion of exon 6. Its functional significance is undetermined.
CUL3	0	MSKCC-DMP	P-0036886-T01-IM6	CUL3-intragenic	yes	unknown		unknown	CUL3 (NM_003590) rearrangement: c.1843-5786_c.2029+8inv Note: The CUL3 rearrangement is an intragenic inversion of exon 14. Its functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0036886-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) rearrangement: c.101+10859:AGK_c.981-42:BRAFinv Note: The AGK - BRAF rearrangement is an inversion which results in the fusion of AGK exons 1-2 with BRAF exons 8-18. This includes the kinase domain of BRAF. Its functional significance is undetermined.
AGK	0	MSKCC-DMP	P-0036886-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	AGK (NM_018238) - BRAF (NM_004333) rearrangement: c.101+10859:AGK_c.981-42:BRAFinv Note: The AGK - BRAF rearrangement is an inversion which results in the fusion of AGK exons 1-2 with BRAF exons 8-18. This includes the kinase domain of BRAF. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0036886-T01-IM6	KMT2C-intragenic	yes	unknown		in frame	KMT2C (NM_170606) rearrangement: c.9454-766_c.9751-50del Note: The KMT2C rearrangement is an intragenic deletion of exons 41-42. Its functional significance is undetermined.
FAM58A	0	MSKCC-DMP	P-0036886-T01-IM6	CLVS1-FAM58A fusion	yes	unknown		unknown	FAM58A (NM_152274) rearrangement: t(X;8)(q28;q12.3)(chrX:g.152859987::chr8:g.62373134) Note: The FAM58A rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.
CLVS1	0	MSKCC-DMP	P-0036886-T01-IM6	CLVS1-FAM58A fusion	yes	unknown		unknown	FAM58A (NM_152274) rearrangement: t(X;8)(q28;q12.3)(chrX:g.152859987::chr8:g.62373134) Note: The FAM58A rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0037370-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4544_c.6166del Note: The APC rearrangement is an intragenic deletion of exon 16. Both breakpoints are within exon 16.
PIK3C2G	0	MSKCC-DMP	P-0037688-T01-IM6	FBXO16-PIK3C2G fusion	yes	unknown		out of frame	PIK3C2G (NM_004570) -FBXO16 (NM_172366) Rearrangement: t(8,12)(p11.22; q12)(chr8:g.28324745::chr12:g.18552829) Note: The PIK3C2G-FBXO16 Rearrangement results in the fusion of exons 1-15 of PIK3C2G with exons 3-9 of FBXO16. Its functional significance is undetermined.
FBXO16	0	MSKCC-DMP	P-0037688-T01-IM6	FBXO16-PIK3C2G fusion	yes	unknown		out of frame	PIK3C2G (NM_004570) -FBXO16 (NM_172366) Rearrangement: t(8,12)(p11.22; q12)(chr8:g.28324745::chr12:g.18552829) Note: The PIK3C2G-FBXO16 Rearrangement results in the fusion of exons 1-15 of PIK3C2G with exons 3-9 of FBXO16. Its functional significance is undetermined.
STK19	0	MSKCC-DMP	P-0037688-T01-IM6	C4A-STK19 fusion	yes	unknown		unknown	STK19 (NM_004197) -C4A( (NM_007293) Rearrangement : c.919:STK19_c.3275:C4Adel Note: The STK19-C4A Rearrangement results in the fusion of exons 1-7 of STK19 with exons 26-41 of C4A. The breakpoints are within exon and exon of STK19 and C4A respectively. Its functional significance is undetermined.
C4A	0	MSKCC-DMP	P-0037688-T01-IM6	C4A-STK19 fusion	yes	unknown		unknown	STK19 (NM_004197) -C4A( (NM_007293) Rearrangement : c.919:STK19_c.3275:C4Adel Note: The STK19-C4A Rearrangement results in the fusion of exons 1-7 of STK19 with exons 26-41 of C4A. The breakpoints are within exon and exon of STK19 and C4A respectively. Its functional significance is undetermined.
CA10	0	MSKCC-DMP	P-0037767-T01-IM6	RECQL4-CA10 fusion	yes	unknown		unknown	CA10 (NM_001082533) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q21.33)(chr8:g.145742559::chr17:g.50212204) Note: The CA10-RECQL4 rearrangement is a translocation which may result in the fusion of CA10 exon 1 with RECQL4 exons 4-22. One of the breakpoints is within RECQL4 exon 4. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0037767-T01-IM6	RECQL4-CA10 fusion	yes	unknown		unknown	CA10 (NM_001082533) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q21.33)(chr8:g.145742559::chr17:g.50212204) Note: The CA10-RECQL4 rearrangement is a translocation which may result in the fusion of CA10 exon 1 with RECQL4 exons 4-22. One of the breakpoints is within RECQL4 exon 4. Its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0037777-T01-IM6	MLL5-KMT2B fusion	yes	unknown		in frame	KMT2B (NM_014727) - MLL5 (NM_018682) rearrangement: t(7;19)(q22.3;q13.12)(chr7:g.104695690;chr19:g.36224589) Note: The KMT2B - MLL5 rearrangement is a translocation which may result in a fusion of KMT2B exons 1-29 with MLL5 exons 3-26. Its functional significance is undetermined.
MLL5	0	MSKCC-DMP	P-0037777-T01-IM6	MLL5-KMT2B fusion	yes	unknown		in frame	KMT2B (NM_014727) - MLL5 (NM_018682) rearrangement: t(7;19)(q22.3;q13.12)(chr7:g.104695690;chr19:g.36224589) Note: The KMT2B - MLL5 rearrangement is a translocation which may result in a fusion of KMT2B exons 1-29 with MLL5 exons 3-26. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0037818-T01-IM6	SLX4-CREBBP fusion	yes	unknown		in frame	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2463+8:CREBBP_c.2014-366:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion which results in the fusion of CREBBP exons 1-13 with SLX4 exons 10-15. Its functional significance is undetermined. Multiple rearrangements involving CREBBP were detected in this sample and a more complex rearrangement resulting in additional CREBBP fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SLX4	0	MSKCC-DMP	P-0037818-T01-IM6	SLX4-CREBBP fusion	yes	unknown		in frame	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2463+8:CREBBP_c.2014-366:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion which results in the fusion of CREBBP exons 1-13 with SLX4 exons 10-15. Its functional significance is undetermined. Multiple rearrangements involving CREBBP were detected in this sample and a more complex rearrangement resulting in additional CREBBP fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TEK	0	MSKCC-DMP	P-0038013-T01-IM6	TEK-intragenic	yes	unknown		unknown	TEK (NM_000459) Rearrangment: c.476-100:TEK_chr9:g.16340059inv Note: The TEK rearrangement results in a inversion with breakpoint within intron 3 of TEK. The functional significance is undetermined.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0037803-T01-IM6	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.317-3302:CDKN2Ap14ARF_chr9:g.22066617del Note: The CDKN2Ap14ARF rearrangement is a deletion of exon 1.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0037803-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.150+168:CDKN2Ap16INK4A_chr9:g.22066617del Note: The CDKN2Ap16INK4A rearrangement is a deletion of exon 1.
RBM10	0	MSKCC-DMP	P-0004224-T02-IM6	RBM10-intragenic	yes	unknown		unknown	RBM10 (NM_001204468) rearrangement : t(X;6)(Xp11.23;6p22.3)(chrX:g.47034490::chr6:g.21827554) Note: The RBM10 rearrangement involves a breakpoint in exon 6. Its functional significance is undetermined.
TNFRSF14	0	MSKCC-DMP	P-0037914-T01-IM6	PLXNA2-TNFRSF14 fusion	yes	unknown		in frame	TNFRSF14 (NM_003820) - PLXNA2 (NM_025179) rearrangement: c.70-109:TNFRSF14_c.1371+18891:PLXNA2inv Note: The TNFRSF14 - PLXNA2 rearrangement is a inversion that results in a fusion of TNFRSF14 exon 1 to PLXNA2 exons 4 - 32. The fusion is predicted to be in frame. The functional significance is undetermined.
PLXNA2	0	MSKCC-DMP	P-0037914-T01-IM6	PLXNA2-TNFRSF14 fusion	yes	unknown		in frame	TNFRSF14 (NM_003820) - PLXNA2 (NM_025179) rearrangement: c.70-109:TNFRSF14_c.1371+18891:PLXNA2inv Note: The TNFRSF14 - PLXNA2 rearrangement is a inversion that results in a fusion of TNFRSF14 exon 1 to PLXNA2 exons 4 - 32. The fusion is predicted to be in frame. The functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0037971-T01-IM6	TTC33-RICTOR fusion	yes	unknown		out of frame	RICTOR (NM_152756) - TTC33 (NM_012382) rearrangement: c.4399+34:RICTOR_c.304-865:TTC33dup Note: The RICTOR - TTC33 rearrangement is a duplication that results in a fusion of RICTOR exons 1 - 33 to TTC33 exons 4 - 5. The functional significance is undetermined.
TTC33	0	MSKCC-DMP	P-0037971-T01-IM6	TTC33-RICTOR fusion	yes	unknown		out of frame	RICTOR (NM_152756) - TTC33 (NM_012382) rearrangement: c.4399+34:RICTOR_c.304-865:TTC33dup Note: The RICTOR - TTC33 rearrangement is a duplication that results in a fusion of RICTOR exons 1 - 33 to TTC33 exons 4 - 5. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038012-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+46:TMPRSS2_c.39+11109:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 4-10. This involves the noncanonical ERG (NM_004449) transcript.
ERG	0	MSKCC-DMP	P-0038012-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+46:TMPRSS2_c.39+11109:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with ERG exons 4-10. This involves the noncanonical ERG (NM_004449) transcript.
EML4	0	MSKCC-DMP	P-0037982-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-138:EML4_c.3173-85:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0037982-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-138:EML4_c.3173-85:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-12 with ALK exons 20-29. This includes the kinase domain of ALK.
AR	0	MSKCC-DMP	P-0037983-T01-IM6	AR-intragenic	yes	unknown		unknown	AR (NM_000044) rearrangement: c.289:AR_chrX:g.66764311del Note: The AR rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0038044-T01-IM6	ERG-intragenic	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(13;21)(q33.1;q22.2)(chr13:g.104080776::chr21:g.39772291) Note: The ERG rearrangement is a translocation involving exon 6. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0038047-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.2510:RB1_chr13:g.49055407del Note: The RB1 rearrangement is an intragenic deletion of exons 24-27. One of the breakpoints is within exon 24.
NCOA3	0	MSKCC-DMP	P-0038047-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.823+2670_c.2602del Note: The NCOA3 rearrangement is an intragenic deletion of exons 9-14. One of the breakpoints is within exon 14. Its functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0038081-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.7308-34:ATM_chr11:g.107979515del Note: The ATM rearrangement is a deletion of exons 1 - 49.
TGFBR2	0	MSKCC-DMP	P-0038083-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.530-3362_c.954del The TGFBR2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5.
TMEM132D	0	MSKCC-DMP	P-0038093-T01-IM6	ARID1A-TMEM132D fusion	yes	unknown		unknown	TMEM132D (NM_133448) - ARID1A (NM_006015)  rearrangement: t(1;12)(p36.11;q24.33)(chr1:g.27023940::chr12:g.130356620) Note: The TMEM132D - ARID1A rearrangement is a translocation which may result in the fusion of TMEM132D exon 1 with ARID1A exon 1-20. One of the breakpoints is within ARID1A exon 1. Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0038093-T01-IM6	ARID1A-TMEM132D fusion	yes	unknown		unknown	TMEM132D (NM_133448) - ARID1A (NM_006015)  rearrangement: t(1;12)(p36.11;q24.33)(chr1:g.27023940::chr12:g.130356620) Note: The TMEM132D - ARID1A rearrangement is a translocation which may result in the fusion of TMEM132D exon 1 with ARID1A exon 1-20. One of the breakpoints is within ARID1A exon 1. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0038096-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(10;17)(q26.13;q24.3)(chr10:g.123274680::chr17:g.67640339) Note: The FGFR2 rearrangement is a translocation involving a breakpoint in exon 9. Its functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0038096-T01-IM6	RTEL1-intragenic	yes	unknown		in frame	RTEL1 (NM_032957) rearrangement: c.1420+809_c.3064+55dup Note: The RTEL1 rearrangement is an intragenic duplication of exons 17-30. Its functional significance is undetermined.
TFG	0	MSKCC-DMP	P-0037972-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Lab Notes Run Number: ArcherV3-CLIN-20190025 Macro-dissection: Unknown
GPR128	0	MSKCC-DMP	P-0037972-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Lab Notes Run Number: ArcherV3-CLIN-20190025 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0025990-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1674:TMPRSS2_c.18+4717:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0025990-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1674:TMPRSS2_c.18+4717:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
NF2	0	MSKCC-DMP	P-0037988-T01-IM6	NF2-intragenic	yes	unknown		in frame	NF2 (NM_000268) rearrangement: c.447+4860_c.811-48del Note: The NF2 rearrangement is an intragenic deletion of exons 5-8.
TMPRSS2	0	MSKCC-DMP	P-0037814-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41635815::chr21:g.42873514) Note: The TMPRSS2 rearrangement is a translocation involving exon 2. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0038155-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2302-385:FGFR2_chr10:g.123979249dup Note: The FGFR2 rearrangement is a duplication of exons 1 - 17. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0011429-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3735:TMPRSS2_c.18+9727:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0011429-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3735:TMPRSS2_c.18+9727:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
FGFR3	0	MSKCC-DMP	P-0025859-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) rearrangement: c.126:FGFR3_c.1941+33:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a duplication which results in the fusion of FGFR3 exons 1-3 with TACC3 exons 11-16. One of the breakpoints is within FGFR3 exon 3. Its functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0025859-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) rearrangement: c.126:FGFR3_c.1941+33:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a duplication which results in the fusion of FGFR3 exons 1-3 with TACC3 exons 11-16. One of the breakpoints is within FGFR3 exon 3. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034813-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3457:TMPRSS2_c.18+4434:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0034813-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3457:TMPRSS2_c.18+4434:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
CDKN1B	0	MSKCC-DMP	P-0034813-T03-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(12;X)(p13.1;p22.31)(chr12:g.12871320::chrX:g.9499399) Note: The CDKN1B rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038179-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3703:TMPRSS2_c.40-56593:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0038179-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3703:TMPRSS2_c.40-56593:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
CDK5RAP2	0	MSKCC-DMP	P-0038194-T01-IM6	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(q34;q33.2)(chr7:g.140484954::chr9:g.123187156) Note: The CDK5RAP2 - BRAF rearrangement is a reciprocal translocation that results in the fusion of CDK5RAP2 exons 1-26 with BRAF exons 10-18. The fusion is predicted to be in-frame includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0038194-T01-IM6	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(q34;q33.2)(chr7:g.140484954::chr9:g.123187156) Note: The CDK5RAP2 - BRAF rearrangement is a reciprocal translocation that results in the fusion of CDK5RAP2 exons 1-26 with BRAF exons 10-18. The fusion is predicted to be in-frame includes the kinase domain of BRAF.
MAP2K1	0	MSKCC-DMP	P-0038195-T01-IM6	MAP2K1-intragenic	yes	unknown		unknown	MAP2K1 (NM_002755) rearrangement: c.656:MAP2K1_chr15:g.50987680inv Note: The MAP2K1 rearrangement results in the inversion of exons 1-6 and includes the kinase domain. One of the breakpoints is within exon 6. This structural variant has low read support though it passes our thresholds. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038198-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(1;21)(p33;q22.3)(chr1:g.47143557::chr21:g.42872071) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0038204-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: t(9,10)(p24.1;q21.3)(chr9:g.8521187::chr10:g.67541496) Note: The PTPRD rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0038204-T01-IM6	RPS6KB2-intragenic	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: t(11,14)(q13.2;q12)(chr11:g.67200806::chr14:g.32983149) Note: The RPS6KB2 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0038238-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4576_c.4606+902inv Note: The DOT1L rearrangement results in the inversion of exon 27. One of the breakpoints is within exon 27. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0038238-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.1622_chr22:g.37681407inv Note: The EP300 rearrangement results in the inversion of exons 1-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0038241-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: t(4;17)(p16.3;q21.32)(chr4:g.1978321::chr17:g.47043304) Note: The WHSC1 rearrangement is a translocation with a breakpoint in exon 21. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0038241-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.11569:FAT1_chr4:g.182881463inv Note: The FAT1 rearrangement results in the inversion of exons 21-27. One of the breakpoints is within exon 21. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0038251-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement : c.3877_c.5313del Note: The BRCA2 Rearrangement results in the intragenic deletion of exon11 of BRCA2. Both the breakpoints are within exon11.
TP53	0	MSKCC-DMP	P-0038184-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) Rearrangement: c.672+64_c.783-88del Note: The TP53 rearrangement results in intragenic deletion of exon 7.
TMPRSS2	0	MSKCC-DMP	P-0038348-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+3992:TMPRSS2_c.40-59510:ERGdel
ERG	0	MSKCC-DMP	P-0038348-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+3992:TMPRSS2_c.40-59510:ERGdel
KMT2D	0	MSKCC-DMP	P-0038349-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4634_chr12:g.49478928inv Note: The KMT2D rearrangement is an inversion that includes KMT2D exons 1-17. One of the breakpoints is within exon 17.
NTRK3	0	MSKCC-DMP	P-0038349-T01-IM6	VPS39-NTRK3 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) - VPS39 (NM_015289) rearrangement: c.1662:NTRK3_c.961-770:VPS39inv Note: The NTRK3 -  VPS39 rearrangement is an inversion with breakpoints within NTRK3 exon 15 and VPS39 intron 10. Multiple NTRK3 -  VPS39 rearrangements were detected in this sample, and a more complex rearrangement is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NTRK3 and VPS39 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
VPS39	0	MSKCC-DMP	P-0038349-T01-IM6	VPS39-NTRK3 fusion	yes	unknown		unknown	NTRK3 (NM_001012338) - VPS39 (NM_015289) rearrangement: c.1662:NTRK3_c.961-770:VPS39inv Note: The NTRK3 -  VPS39 rearrangement is an inversion with breakpoints within NTRK3 exon 15 and VPS39 intron 10. Multiple NTRK3 -  VPS39 rearrangements were detected in this sample, and a more complex rearrangement is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NTRK3 and VPS39 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TMPRSS2	0	MSKCC-DMP	P-0038349-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: chr21:g.33128749_c.56-4656inv Note: The TMPRSS2 rearrangement is an inversion that includes TMRSS2 exons 2-14.
ERRFI1	0	MSKCC-DMP	P-0038351-T01-IM6	ERRFI1-intragenic	yes	unknown		unknown	ERRFI1 (NM_018948) rearrangement: t(1;17)(p36.23;q23.3)(chr1:g.8075627::chr17:g.62495243) Note: The ERRFI1 rearrangement is a translocation with a breakpoint within ERRFI1 exon 2. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0038352-T01-IM6	MET-intragenic	yes	unknown		out of frame	MET (NM_000245) rearrangement: c.2731-77_c.3028+772del Note: The MET rearrangement is an intragenic deletion of MET exons 13-14.
RECQL4	0	MSKCC-DMP	P-0038298-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) Rearrangement: t(8;12)(q11.22;q15)(chr8:g.145738716::chr12:g.69857749) Note: The RECQL4 rearrangement is a translocation with breakpoint in exon 15 of RECQL4. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0038299-T01-IM6	TTC7B-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - TTC7B (NM_001010854) rearrangement: t(14;17)(q32.11;q21.2)(chr14:g.91189253::chr17:g.40458420) Note: The STAT5A - TTC7B rearrangement is a translocation that results in the fusion of STAT5A exons 1-14 with TTC7B exons 6-20. The functional significance is undetermined.
TTC7B	0	MSKCC-DMP	P-0038299-T01-IM6	TTC7B-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - TTC7B (NM_001010854) rearrangement: t(14;17)(q32.11;q21.2)(chr14:g.91189253::chr17:g.40458420) Note: The STAT5A - TTC7B rearrangement is a translocation that results in the fusion of STAT5A exons 1-14 with TTC7B exons 6-20. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038299-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1050:TMPRSS2_c.39+51237:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0038299-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1050:TMPRSS2_c.39+51237:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 4-11. The fusion is predicted to be in-frame and involves the non-canonical ERG transcript.
FGFR3	0	MSKCC-DMP	P-0038318-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-87:FGFR3_c.1462-57:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-17 with TACC3 exons 6-16. The fusion is predicted to be in-frame and involves the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0038318-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-87:FGFR3_c.1462-57:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-17 with TACC3 exons 6-16. The fusion is predicted to be in-frame and involves the kinase domain of FGFR3.
EML4	0	MSKCC-DMP	P-0037982-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV3-CLIN-20190028 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0037982-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV3-CLIN-20190028 Macro-dissection: Unknown
AXIN1	0	MSKCC-DMP	P-0038328-T01-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: c.1498_c.1255-1302inv Note: The AXIN1 rearrangement is an intragenic inversion of exon 6. One of the breakpoints is within exon 6.
EPHB1	0	MSKCC-DMP	P-0038329-T01-IM6	EPHB1-intragenic	yes	unknown		unknown	EPHB1 (NM_004441) translocation: t(3;11)(q22.2;q12.1)(chr3:g.134920357::chr11:g.58655556) Note: The EPHB1 rearrangement is a translocation with a breakpoint within EPHB1 exon 12. The functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0038394-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) rearrangement: t(6;20)(q22.1;q13.12)(chr6:g.117654360::chr20:g.43961742) Note: The SDC4 - ROS1 rearrangement is a translocation which may result in the fusion of SDC4 exons 1-2 with ROS1 exons 32-43.
ROS1	0	MSKCC-DMP	P-0038394-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) rearrangement: t(6;20)(q22.1;q13.12)(chr6:g.117654360::chr20:g.43961742) Note: The SDC4 - ROS1 rearrangement is a translocation which may result in the fusion of SDC4 exons 1-2 with ROS1 exons 32-43.
PTPRK	0	MSKCC-DMP	P-0038239-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_002844) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190030 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0038239-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_002844) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190030 Macro-dissection: Unknown
DNMT3A	0	MSKCC-DMP	P-0024325-T02-IM6	ASXL2-DNMT3A fusion	yes	unknown		unknown	DNMT3A (NM_022552) - ASXL2 (NM_018263) rearrangement: c.1294:DNMT3A_c.2054:ASXL2dup Note: The DNMT3A - ASXL2 rearrangement is a duplication that results in the fusion of DNMT3A exons 1-11 with ASXL2 exon 12. One of the breakpoints is within DNMT3A exon 11 and the other is within ASXL2 exon 12. The functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0024325-T02-IM6	ASXL2-DNMT3A fusion	yes	unknown		unknown	DNMT3A (NM_022552) - ASXL2 (NM_018263) rearrangement: c.1294:DNMT3A_c.2054:ASXL2dup Note: The DNMT3A - ASXL2 rearrangement is a duplication that results in the fusion of DNMT3A exons 1-11 with ASXL2 exon 12. One of the breakpoints is within DNMT3A exon 11 and the other is within ASXL2 exon 12. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0038161-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.99_c.164-14352del Note: The CDH1 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2.
AXL	0	MSKCC-DMP	P-0038162-T01-IM6	AXL-intragenic	yes	unknown		unknown	AXL (NM_021913) rearrangement: c.783+2381_c.1711+231inv Note: The AXL rearrangement results in the inversion of exons 7-14. The functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0038166-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) rearrangement: c.7457+59_c.7615+1767del Note: The NF1 rearrangement results in the deletion of exon 51. The functional significance is undetermined
KREMEN1	0	MSKCC-DMP	P-0038166-T01-IM6	CHEK2-KREMEN1 fusion	yes	unknown		in frame	KREMEN1 (NM_032045) - CHEK2 (NM_007194) rearrangement: c.260+797:KREMEN1_c.684-29:CHEK2inv Note: The KREMEN1 - CHEK2 rearrangement is an inversion that results in the in-frame fusion of KREMEN1 exons 1-2 with CHEK2 exons 6-15. The functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0038166-T01-IM6	CHEK2-KREMEN1 fusion	yes	unknown		in frame	KREMEN1 (NM_032045) - CHEK2 (NM_007194) rearrangement: c.260+797:KREMEN1_c.684-29:CHEK2inv Note: The KREMEN1 - CHEK2 rearrangement is an inversion that results in the in-frame fusion of KREMEN1 exons 1-2 with CHEK2 exons 6-15. The functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0038166-T01-IM6	MSH3-intragenic	yes	unknown		unknown	MSH3 (NM_002439) rearrangement: c.1049_c.1569-17inv Note: The MSH3 rearrangement results in the inversion of exons 7-10. One of the breakpoints is within exon 7. The functional significance is undetermined
TAP1	0	MSKCC-DMP	P-0038369-T01-IM6	TAP1-intragenic	yes	unknown		unknown	TAP1 (NM_000593) rearrangement: c.432:TAP1_chr6:g.27816456inv Note: The TAP1 rearrangement is an inversion of exons 1-11. One of the breakpoints is within exon 1. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0038374-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.683+82:DNMT1_chr19:g.10325900inv Note: The DNMT1 rearrangement is an inversion of exons 1-7. Its functional significance is undetermined.
BCL2L11	0	MSKCC-DMP	P-0038374-T01-IM6	BCL2L11-intragenic	yes	unknown		unknown	BCL2L11 (NM_138621) rearrangement: c.394+3437:BCL2L11_chr2:g.112807418del Note: The BCL2L11 rearrangement is a deletion of exons 3-4. Its functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0038381-T01-IM6	NME6-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) - NME6 (NM_005793) rearrangement: t(3;16)(p21.31;p12.2)(chr3:g.48342586::chr16:g.23632769) Note: The PALB2 - NME6 rearrangement is a translocation which may result in the fusion of PALB2 exons 1-10 with NME6 exons 2-6. One of the breakpoints is within exon 10. Its functional significance is undetermined.
NME6	0	MSKCC-DMP	P-0038381-T01-IM6	NME6-PALB2 fusion	yes	unknown		unknown	PALB2 (NM_024675) - NME6 (NM_005793) rearrangement: t(3;16)(p21.31;p12.2)(chr3:g.48342586::chr16:g.23632769) Note: The PALB2 - NME6 rearrangement is a translocation which may result in the fusion of PALB2 exons 1-10 with NME6 exons 2-6. One of the breakpoints is within exon 10. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0021574-T03-IM6	SPEN-intragenic	yes	unknown		in frame	SPEN (NM_015001) Rearrangement :c.10509+10_c.10705-20del Note: The SPEN Rearrangement results in the intragenic deletion of exon13 of SPEN. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0036560-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) : c.126+892:TMPRSS2_c.39+3031:ERGinv Note: The TMPRSS2-ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 1-3 of ERG. While this is not the canonical TMPRSS2-ERG Fusion, the possibility of the fusion not picked by the IMPACT Panel cannot be ruled out.
ERG	0	MSKCC-DMP	P-0036560-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) : c.126+892:TMPRSS2_c.39+3031:ERGinv Note: The TMPRSS2-ERG Rearrangement results in the inversion of exons 3-14 of TMPRSS2 and exons 1-3 of ERG. While this is not the canonical TMPRSS2-ERG Fusion, the possibility of the fusion not picked by the IMPACT Panel cannot be ruled out.
ELF3	0	MSKCC-DMP	P-0038406-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) Rearrangement : c.492_c.1002-71inv Note: The ELF3 Rearrangement results in the intragenic inversion of exons 5-8 of ELF3. Its functional significance is undetermined.
CSF3	0	MSKCC-DMP	P-0038406-T01-IM6	CDK12-CSF3 fusion	yes	unknown		out of frame	CSF3 (NM_000759) - CDK12 (NM_016507) Rearrangement : c.313-58:CSF3_c.2964-126:CDK12dup Note: The CSF3-CDK12 Rearrangement results in the fusion of exons 1-2 of CSF3 with exons11-14 of CDK12. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0038406-T01-IM6	CDK12-CSF3 fusion	yes	unknown		out of frame	CSF3 (NM_000759) - CDK12 (NM_016507) Rearrangement : c.313-58:CSF3_c.2964-126:CDK12dup Note: The CSF3-CDK12 Rearrangement results in the fusion of exons 1-2 of CSF3 with exons11-14 of CDK12. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0038406-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) Rearrangement : c.1300-3465_c.7647del Note: The KMT2C Rearrangement results in the intragenic deletion of exons 10-38 of KMT2C. One of the breakpoints is within exon38. Its functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0038414-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.423:ELF3_chr1:g.16840713inv Note: The ELF3 rearrangement is an inversion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0038414-T01-IM6	KIAA0319L-CSF3R fusion	yes	unknown		in frame	CSF3R (NM_000760) - KIAA0319L (NM_024874) rearrangement: c.673+224:CSF3R_c.1201+1129:KIAA0319Ldel Note: 'The CSF3R - KIAA0319L rearrangement is a deletion that results in a fusion of CSF3R exons 1 - 6 to KIAA0319L exons 8 - 21. The fusion is predicted to be in frame. Functional significance is undetermined.
KIAA0319L	0	MSKCC-DMP	P-0038414-T01-IM6	KIAA0319L-CSF3R fusion	yes	unknown		in frame	CSF3R (NM_000760) - KIAA0319L (NM_024874) rearrangement: c.673+224:CSF3R_c.1201+1129:KIAA0319Ldel Note: 'The CSF3R - KIAA0319L rearrangement is a deletion that results in a fusion of CSF3R exons 1 - 6 to KIAA0319L exons 8 - 21. The fusion is predicted to be in frame. Functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0038414-T01-IM6	RPS6KA4-intragenic	yes	unknown		unknown	RPS6KA4 (NM_003942) rearrangement: c.1219:RPS6KA4_chr11:g.66694825inv Note: The RPS6KA4 rearrangement is an inversion of exons 11 - 17. One of the breakpoints is within exon 11. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0038414-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2301:FGFR3_c.1941+974:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0038414-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2301:FGFR3_c.1941+974:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TMPRSS2	0	MSKCC-DMP	P-0038415-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+2095:TMPRSS2_c.19-14849:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0038415-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+2095:TMPRSS2_c.19-14849:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
MAP3K1	0	MSKCC-DMP	P-0038415-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: t(5,7)(q11.2;q21.11)(chr5:g.56184195::chr7:g.79055104)' Note: The MAP3K1 rearrangement is a translocation with a breakpoint in intron 19. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0038417-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-64882:ERG_c.56-3214:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1 - 3 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0038417-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-64882:ERG_c.56-3214:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1 - 3 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ZNF598	0	MSKCC-DMP	P-0038419-T01-IM6	TSC2-ZNF598 fusion	yes	unknown		unknown	ZNF598 (NM_178167) - TSC2 (NM_000548) rearrangement: c.2446:ZNF598_c.4850-65:TSC2inv Note: The ZNF598 - TSC2 rearrangement is an inversion that results in a fusion of ZNF598 exons 1 - 14 to TSC2 exons 38 - 42. One of the breakpoints is within ZNF598 exon 14. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0038419-T01-IM6	TSC2-ZNF598 fusion	yes	unknown		unknown	ZNF598 (NM_178167) - TSC2 (NM_000548) rearrangement: c.2446:ZNF598_c.4850-65:TSC2inv Note: The ZNF598 - TSC2 rearrangement is an inversion that results in a fusion of ZNF598 exons 1 - 14 to TSC2 exons 38 - 42. One of the breakpoints is within ZNF598 exon 14. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0038419-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.3617-1469_c.4555del Note: The PBRM1 rearrangement is an intragenic deletion of exons 24 - 29. One of the breakpoints is within exon 29.
TMPRSS2	0	MSKCC-DMP	P-0038349-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190032 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0038349-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190032 Macro-dissection: Unknown
ELF3	0	MSKCC-DMP	P-0033527-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.261_chr1:g.202003116dup Note: The ELF3 rearrangement results in the duplication of exons 3-9. One of the breakpoints is within exon 3. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0033527-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2195+509_c.*2131del Note: The FGFR2 rearrangement results in the deletion of exons 17-18 and includes the kinase domain of FGFR2. The functional significance is undetermined.
MON1A	0	MSKCC-DMP	P-0038514-T01-IM6	MST1-MON1A fusion	yes	unknown		unknown	MON1A (NM_032355) - MST1 (NM_020998) rearrangement: c.279-3634:MON1A_c.1420:MST1del Note: The MON1A - MST1 rearrangement is a deletion that results in a fusion of MON1A exon 1 to MST1 exons 12 - 18. One of the breakpoints is within MST1 exon 12. The functional significance is undetermined.
MST1	0	MSKCC-DMP	P-0038514-T01-IM6	MST1-MON1A fusion	yes	unknown		unknown	MON1A (NM_032355) - MST1 (NM_020998) rearrangement: c.279-3634:MON1A_c.1420:MST1del Note: The MON1A - MST1 rearrangement is a deletion that results in a fusion of MON1A exon 1 to MST1 exons 12 - 18. One of the breakpoints is within MST1 exon 12. The functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0038514-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2906:WHSC1L1_chr8:g.34562568del Note: The WHSC1L1 rearrangement is a deletion of exons 16 - 24. One of the breakpoints is within exon 16. Functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0033527-T01-IM6	ATE1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-ATE1 fusion. Note: The rearrangement is a  fusion between genes FGFR2 Exon16 (NM_022970) and ATE1 undefined (NM_001001976). The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20180135 Macro-dissection: Performed
ATE1	0	MSKCC-DMP	P-0033527-T01-IM6	ATE1-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-ATE1 fusion. Note: The rearrangement is a  fusion between genes FGFR2 Exon16 (NM_022970) and ATE1 undefined (NM_001001976). The functional significance of this fusion is unknown.  Lab Notes Run Number: ArcherV2-CLIN-20180135 Macro-dissection: Performed
SDHC	0	MSKCC-DMP	P-0012706-T02-IM6	SDHC-intragenic	yes	unknown		unknown	SDHC (NM_003001) Rearrangement : c.*1834:ITLN1_c.21-152:SDHCdel Note: The SDHC Rearrangement results in the deletion of exon1 of SDHC. Its functional significance is undetermined.
HGF	0	MSKCC-DMP	P-0038426-T01-IM6	HGF-intragenic	yes	unknown		unknown	HGF (NM_000601) rearrangement: c.1752:HGF_chr7:g.85393601inv Note: The HGF rearrangement is an inversion of exons 1 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0038427-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.672:CDK12_chr17:g.55810160inv Note: The CDK12 rearrangement is an inversion of exons 1 - 14. One of the breakpoints is within exon 1. Functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0038428-T02-IM6	MAP3K14-intragenic	yes	unknown		unknown	MAP3K14 (NM_003954) rearrangement: c.1288-505_c.1550-67inv Note: The MAP3K14 rearrangement is an intragenic inversion of exons 7 - 8. Functional significance is undetermined.
MSH2	0	MSKCC-DMP	P-0038483-T01-IM6	MSH6-MSH2 fusion	yes	unknown		unknown	MSH2 (NM_000251) - MSH6 (NM_000179) rearrangement: c.646-879:MSH2_c.3710:MSH6del Note: The MSH2 - MSH6 rearrangement is a deletion which results in the fusion of MSH2 exons 1-3 with MSH6 exons 8-10. One of the breakpoints is within MSH6 exon 8. Its functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0038483-T01-IM6	MSH6-MSH2 fusion	yes	unknown		unknown	MSH2 (NM_000251) - MSH6 (NM_000179) rearrangement: c.646-879:MSH2_c.3710:MSH6del Note: The MSH2 - MSH6 rearrangement is a deletion which results in the fusion of MSH2 exons 1-3 with MSH6 exons 8-10. One of the breakpoints is within MSH6 exon 8. Its functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0038483-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.82+21192_.2774del Note: The ERBB4 rearrangement is an intragenic deletion of exons 2-23. One of the breakpoints is within exon 23. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038584-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon2 ):c.127-1350:TMPRSS2_c.40-14330:ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
ERG	0	MSKCC-DMP	P-0038584-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon2 ):c.127-1350:TMPRSS2_c.40-14330:ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
TAP2	0	MSKCC-DMP	P-0038589-T01-IM6	TAP2-intragenic	yes	unknown		unknown	TAP2 (NM_018833) Rearrangement : c.762_c.946-1126dup Note: The TAP2 Rearrangement results in the intragenic duplication of exon5 of TAP2. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0038658-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : chr16:g.72810206_c.9037del Note: The ZFHX3 Rearrangement results in the intragenic deletion of exons 1-9 of ZFHX3. One of the breakpoints is within exon9. Its functional significance is undetermined.
SMAD2	0	MSKCC-DMP	P-0038658-T01-IM6	SMAD2-intragenic	yes	unknown		unknown	SMAD2 (NM_001003652) Rearrangement : t(18,20)(q21.1; p11.1) (chr12:g.56481635::chr7:g.83729009) Note: The SMAD2 Rearrangement is a translocation event with a breakpoint  in intron7. Its functional signficance is undetermined.
CSF2RA	0	MSKCC-DMP	P-0038683-T01-IM6	EGFR-CSF2RA fusion	yes	unknown		unknown	CSF2RA (NM_001161530) - EGFR (NM_005228) rearrangement: t(7;X)(p11.2;p22.33)(chr7:g.55224220::chrX:g.1401662) Note: The CSF2RA - EGFR rearrangement is a translocation that results in a fusion of CSF2RA exon 1 to EGFR exons 9 - 28. One of the breakpoints is within CSF2RA exon 1. The fusion includes the kinase domain of EGFR. This structural variant was observed in addition to other rearrangements involving EGFR, suggesting a complex event that may not be detected by the IMPACT assay.
EGFR	0	MSKCC-DMP	P-0038683-T01-IM6	EGFR-CSF2RA fusion	yes	unknown		unknown	CSF2RA (NM_001161530) - EGFR (NM_005228) rearrangement: t(7;X)(p11.2;p22.33)(chr7:g.55224220::chrX:g.1401662) Note: The CSF2RA - EGFR rearrangement is a translocation that results in a fusion of CSF2RA exon 1 to EGFR exons 9 - 28. One of the breakpoints is within CSF2RA exon 1. The fusion includes the kinase domain of EGFR. This structural variant was observed in addition to other rearrangements involving EGFR, suggesting a complex event that may not be detected by the IMPACT assay.
FOXA1	0	MSKCC-DMP	P-0004593-T03-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.*686_c.1040del Note: The FOXA1 rearrangement is an intragenic deletion of exon 2. Its significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0006490-T01-IM5	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement : chr1:g.26939894_c.2277:ARID1Adel Note: The ARID1A (NM_006015) rearrangement event results in the deletion of ARID1A exons 1-7. One of the breakpoints is within ARID1A exon7.
VTCN1	0	MSKCC-DMP	P-0006960-T01-IM5	VTCN1-intragenic	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement : c.517_724+1186del Note: The VTCN1 (NM_024626) rearrangement event is a deletion which disrupts the 3 splice site of VTCN1 exon4. One of the breakpoints is on VTCN1 exon4.
ZFHX3	0	MSKCC-DMP	P-0024793-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement : c.798_c.3217-29283dup Note: The ZFHX3 Rearrangement results in the duplication of exons 2-3 of ZFHX3. One of the breakpoints is within exon2. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0024793-T01-IM6	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2 (NM_006164) Rearrangement : c.46-3658_c.403-50del Note: The NFE2L2 Rearrangement results in the intragenic deletion of exons 2-3. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0024793-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) Rearrangement : c.171+87_c.412+22095del Note: The PARK2 Rearrangement results in the intragenic deletion of exon3 of PARK2. The functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0031374-T02-IM6	ACVR2A-DNMT3A fusion	yes	unknown		in frame	DNMT3A (NM_022552) - ACVR2A (NM_001616) rearrangement: c.1014+79:DNMT3A_c.816+170:ACVR2Ainv Note: The DNMT3A - ACVR2A rearrangement is an inversion that results in the in-frame fusion of DNMT3A exons 1-8 with ACVR2A exons 7-11. The functional significance is undetermined.
ACVR2A	0	MSKCC-DMP	P-0031374-T02-IM6	ACVR2A-DNMT3A fusion	yes	unknown		in frame	DNMT3A (NM_022552) - ACVR2A (NM_001616) rearrangement: c.1014+79:DNMT3A_c.816+170:ACVR2Ainv Note: The DNMT3A - ACVR2A rearrangement is an inversion that results in the in-frame fusion of DNMT3A exons 1-8 with ACVR2A exons 7-11. The functional significance is undetermined.
PAPSS2	0	MSKCC-DMP	P-0036253-T01-IM6	PTEN-PAPSS2 fusion	yes	unknown		in frame	PAPSS2 (NM_001015880) - PTEN (NM_000314) rearrangement: c.880+2183:PAPSS2 _c.254-66:PTENdel Note: The PAPSS2 - PTEN rearrangement is a deletion which results in the fusion of PAPSS2 exons 1-7 with PTEN exons 5-9.
PTEN	0	MSKCC-DMP	P-0036253-T01-IM6	PTEN-PAPSS2 fusion	yes	unknown		in frame	PAPSS2 (NM_001015880) - PTEN (NM_000314) rearrangement: c.880+2183:PAPSS2 _c.254-66:PTENdel Note: The PAPSS2 - PTEN rearrangement is a deletion which results in the fusion of PAPSS2 exons 1-7 with PTEN exons 5-9.
CUL1	0	MSKCC-DMP	P-0036253-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement: c.1298+434:CUL1_c.1725:EZH2inv Note: The CUL1 - EZH2 rearrangement is an inversion which results in the fusion of CUL1 exons 1-11 with EZH2 exons 15-20. Its functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0036253-T01-IM6	EZH2-CUL1 fusion	yes	unknown		unknown	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement: c.1298+434:CUL1_c.1725:EZH2inv Note: The CUL1 - EZH2 rearrangement is an inversion which results in the fusion of CUL1 exons 1-11 with EZH2 exons 15-20. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0038443-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.3453:NOTCH2_chr1:g.121485135inv Note: The NOTCH2 rearrangement is an inversion of exons 1-21. One of the breakpoints is within exon 21. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0038444-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: t(3;10)(p13.13;q23.31)(chr3:g.109517319::chr10:g.89720655) Note: The PTEN rearrangement is a translocation with a breakpoint in exon 8.
SMARCA4	0	MSKCC-DMP	P-0038500-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1052:SMARCA4_chr19:g.11084276del Note: The SMARCA4 rearrangement is a deletion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0038534-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: t(7;11)(q21.1;q22.3)(chr7:g.78322725::chr11:g.108196903) Note: The ATM rearrangement is a translocation with a breakpoint in exon 47. Its functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0038540-T01-IM6	KDM4B-PTPRS fusion	yes	unknown		in frame	PTPRS (NM_002850) - KDM4B (NM_015015) rearrangement: c.4195-19:PTPRS_c.919-2474:KDM4Binv Note: The PTPRS - KDM4B rearrangement is an inversion which results in the fusion of PTPRS exons 1-27 with KDM4B exons 10-23. Its functional significance is undetermined.
KDM4B	0	MSKCC-DMP	P-0038540-T01-IM6	KDM4B-PTPRS fusion	yes	unknown		in frame	PTPRS (NM_002850) - KDM4B (NM_015015) rearrangement: c.4195-19:PTPRS_c.919-2474:KDM4Binv Note: The PTPRS - KDM4B rearrangement is an inversion which results in the fusion of PTPRS exons 1-27 with KDM4B exons 10-23. Its functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0038541-T01-IM6	CEP128-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) - CEP128 (NM_152446) rearrangement: c.313:AKT1_c.2856+6472:CEP128del Note: The AKT1 - CEP128 rearrangement is a deletion which results in the fusion of AKT1 exons 1-5 with CEP128 exons 20-24. One of the breakpoints is within AKT1 exon 5. Its functional significance is undetermined.
CEP128	0	MSKCC-DMP	P-0038541-T01-IM6	CEP128-AKT1 fusion	yes	unknown		unknown	AKT1 (NM_001014431) - CEP128 (NM_152446) rearrangement: c.313:AKT1_c.2856+6472:CEP128del Note: The AKT1 - CEP128 rearrangement is a deletion which results in the fusion of AKT1 exons 1-5 with CEP128 exons 20-24. One of the breakpoints is within AKT1 exon 5. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0038543-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.655-45_c.1063-152dup Note: The NF1 rearrangement is an intragenic duplication of exons 7-9. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0038718-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: chr12:g.3165810_c.463+6994del Note: The ETV6 rearrangement is a deletion that includes ETV6 exons 1-4. The functional significance is undetermined.
IL7R	0	MSKCC-DMP	P-0038718-T01-IM6	IL7R-intragenic	yes	unknown		unknown	IL7R (NM_002185) rearrangement: c.1291_chr5:g.38200461del Note: The IL7R rearrangement is a deletion that includes IL7R exon 8. One of the breakpoints is within IL7R exon 8. The functional significance is undetermined.
FLT1	0	MSKCC-DMP	P-0038722-T01-IM6	FLT1-intragenic	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: t(11;13)(p11.12;q12.2)(chr11:g.49412395::chr13:g.28896791) Note: The FLT1 rearrangement is a translocation with a breakpoint within intron 21. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0038745-T01-IM6	STAT3-intragenic	yes	unknown		out of frame	STAT3 (NM_139276) Rearrangement: c.2102-1867_c.2144+45dup Note: The STAT3 rearrangement is an intragenic duplication of exon 22. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0038772-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2341+147:EML4_c.3173-293:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-21 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0038772-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2341+147:EML4_c.3173-293:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-21 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
FNDC3B	0	MSKCC-DMP	P-0038772-T01-IM6	CDKN2A-FNDC3B fusion	yes	unknown		unknown	FNDC3B (NM_022763) - CDKN2A (NM_058195, NM_000077) rearrangement: t(3;9)(q26.31;p21.3)(chr3:g.171854277::chr9:g.21971075) Note: The FNDC3B - CDKN2A rearrangement is a translocation that results in the fusion of FNDC3B exons 1-3 with CDKN2Ap14ARF exon 2 and CDKN2Ap16INK4A exons 2-3.
CDKN2A	0	MSKCC-DMP	P-0038772-T01-IM6	CDKN2A-FNDC3B fusion	yes	unknown		unknown	FNDC3B (NM_022763) - CDKN2A (NM_058195, NM_000077) rearrangement: t(3;9)(q26.31;p21.3)(chr3:g.171854277::chr9:g.21971075) Note: The FNDC3B - CDKN2A rearrangement is a translocation that results in the fusion of FNDC3B exons 1-3 with CDKN2Ap14ARF exon 2 and CDKN2Ap16INK4A exons 2-3.
NF1	0	MSKCC-DMP	P-0038773-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(1;22)(q32.1;q12.2)(chr1:g.201159807::chr22:g.30078654) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 15. The functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0038774-T01-IM6	FLCN-intragenic	yes	unknown		unknown	FLCN (NM_144997) rearrangement: c.397-9:FLCN_chr17:g.17661541del Note: The FLCN rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0038779-T01-IM6	CARM1-intragenic	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: c.221-5521_c.1615+110inv Note: The CARM1 rearrangement results in the inversion of exons 2-14. Multiple rearrangements involving CARM1 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated. The functional significance is undetermined.
CERKL	0	MSKCC-DMP	P-0038779-T01-IM6	CUL3-CERKL fusion	yes	unknown		out of frame	CERKL (NM_201548) - CUL3 (NM_003590) rearrangement: c.482-6652:CERKL_c.1843-74:CUL3dup Note: The CERKL - CUL3 rearrangement is a duplication that results in the fusion of CERKL exons 1-2 with CUL3 exons 14-16. The functional significance is undetermined.
CUL3	0	MSKCC-DMP	P-0038779-T01-IM6	CUL3-CERKL fusion	yes	unknown		out of frame	CERKL (NM_201548) - CUL3 (NM_003590) rearrangement: c.482-6652:CERKL_c.1843-74:CUL3dup Note: The CERKL - CUL3 rearrangement is a duplication that results in the fusion of CERKL exons 1-2 with CUL3 exons 14-16. The functional significance is undetermined.
PEMT	0	MSKCC-DMP	P-0037990-T01-IM6	RNF43-PEMT fusion	yes	unknown		unknown	PEMT (NM_148172) - RNF43 (NM_017763) rearrangement: c.204+11349:PEMT_c.1909:RNF43dup Note: The PEMT - RNF43 rearrangement is a duplication that results in a fusion of PEMT exons 1 - 2 to RNF43 exons 9 - 10. One of the breakpoints is within RNF43 exon 9. Functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0037990-T01-IM6	RNF43-PEMT fusion	yes	unknown		unknown	PEMT (NM_148172) - RNF43 (NM_017763) rearrangement: c.204+11349:PEMT_c.1909:RNF43dup Note: The PEMT - RNF43 rearrangement is a duplication that results in a fusion of PEMT exons 1 - 2 to RNF43 exons 9 - 10. One of the breakpoints is within RNF43 exon 9. Functional significance is undetermined.
DNM2	0	MSKCC-DMP	P-0037990-T01-IM6	SMARCA4-DNM2 fusion	yes	unknown		in frame	DNM2 (NM_001005361) - SMARCA4 (NM_003072) rearrangement: c.1671+1967:DNM2_c.3952-14:SMARCA4del Note: The DNM2 - SMARCA4 rearrangement is a deletion that results in a fusion of DNM2 exons 1 - 14 to SMARCA4 exons 29 - 35. The fusion is predicted to be in frame.
SMARCA4	0	MSKCC-DMP	P-0037990-T01-IM6	SMARCA4-DNM2 fusion	yes	unknown		in frame	DNM2 (NM_001005361) - SMARCA4 (NM_003072) rearrangement: c.1671+1967:DNM2_c.3952-14:SMARCA4del Note: The DNM2 - SMARCA4 rearrangement is a deletion that results in a fusion of DNM2 exons 1 - 14 to SMARCA4 exons 29 - 35. The fusion is predicted to be in frame.
NFKBIA	0	MSKCC-DMP	P-0038133-T02-IM6	NFKBIA-intragenic	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: t(12,14)(q14.3;q13.2)(chr12:g.66469859::chr14:g.35873769) Note: The NFKBIA rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0038557-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) Rearrangement : chr18:g.48486870_c.455-39del Note: The SMAD4 Rearrangement results in the deletion of exons 1-5 of SMAD4. Its functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0038568-T01-IM6	SEMA4A-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - SEMA4A (NM_001193300) rearrangement: c.850+416:NTRK1_c.301-270:SEMA4Adup Note: The NTRK1 - SEMA4A rearrangement is a duplication that results in a fusion of NTRK1 exons 1 - 7 to SEMA4A exons 4 - 15. The fusion includes a part of the kinase domain of NTRK1. Functional significance is undetermined.
SEMA4A	0	MSKCC-DMP	P-0038568-T01-IM6	SEMA4A-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - SEMA4A (NM_001193300) rearrangement: c.850+416:NTRK1_c.301-270:SEMA4Adup Note: The NTRK1 - SEMA4A rearrangement is a duplication that results in a fusion of NTRK1 exons 1 - 7 to SEMA4A exons 4 - 15. The fusion includes a part of the kinase domain of NTRK1. Functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0038625-T01-IM6	TEK-intragenic	yes	unknown		unknown	TEK (NM_000459) rearrangement: c.1183-843_c.1278inv Note: The TEK rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0038631-T01-IM6	PPP1R13L-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - PPP1R13L (NM_006663) rearrangement: c.2157:ERCC2_c.700:PPP1R13Ldup Note: The ERCC2 - PPP1R13L rearrangement is a duplication that results in a fusion of ERCC2 exons 1 - 22 to PPP1R13L exons 4 - 13. The breakpoints are within ERCC2 exon 22 and PPP1R13L exon 4. Functional significance is undetermined.
PPP1R13L	0	MSKCC-DMP	P-0038631-T01-IM6	PPP1R13L-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - PPP1R13L (NM_006663) rearrangement: c.2157:ERCC2_c.700:PPP1R13Ldup Note: The ERCC2 - PPP1R13L rearrangement is a duplication that results in a fusion of ERCC2 exons 1 - 22 to PPP1R13L exons 4 - 13. The breakpoints are within ERCC2 exon 22 and PPP1R13L exon 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0038643-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4433:TMPRSS2_c.40-56242:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0038643-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4433:TMPRSS2_c.40-56242:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
PAX8	0	MSKCC-DMP	P-0038687-T01-IM6	PPARG-PAX8 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PAX8-PPARG fusion. Note: The rearrangement is an in-frame fusion between genes PAX8 Exon2 (NM_013992) and PPARG Exon2 (NM_015869). Lab Notes Run Number: ArcherV3-CLIN-20190038 Macro-dissection: Unknown
PPARG	0	MSKCC-DMP	P-0038687-T01-IM6	PPARG-PAX8 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PAX8-PPARG fusion. Note: The rearrangement is an in-frame fusion between genes PAX8 Exon2 (NM_013992) and PPARG Exon2 (NM_015869). Lab Notes Run Number: ArcherV3-CLIN-20190038 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0023614-T02-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) Rearrangement : chr7:g.97412920_c.1177+1522:BRAFinv Note: The BRAF Rearrangement results in the inversion of exons 10-18 of BRAF. This includes the protein kinase domain of BRAF. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0037865-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) Rearrangement : c.117+48:DNMT1_chr19:g.43650244inv Note: The DNMT1 Rearrangement results in the inversion of exons1-2 of DNMT1. Its functional significance is undetermined.
TFG	0	MSKCC-DMP	P-0038801-T01-IM6	MET-TFG fusion	yes	unknown		in frame	TFG (NM_001195478) - MET (NM_000245) fusion (TFG exons 1-5 fused to MET exons 15-21): t(3;7)(q12.2;q31.2)(chr3:g.100452598::chr7:g.:116413541) Note: The TFG - MET fusion is predicted to be in frame and includes the kinase domain of MET
MET	0	MSKCC-DMP	P-0038801-T01-IM6	MET-TFG fusion	yes	unknown		in frame	TFG (NM_001195478) - MET (NM_000245) fusion (TFG exons 1-5 fused to MET exons 15-21): t(3;7)(q12.2;q31.2)(chr3:g.100452598::chr7:g.:116413541) Note: The TFG - MET fusion is predicted to be in frame and includes the kinase domain of MET
TMPRSS2	0	MSKCC-DMP	P-0038808-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon2) :c.55+3082:TMPRSS2_c.18+25160:ERGdel
ERG	0	MSKCC-DMP	P-0038808-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon2) :c.55+3082:TMPRSS2_c.18+25160:ERGdel
PTPRK	0	MSKCC-DMP	P-0037865-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MTMR2-MAML2 fusion. Note: The rearrangement is an in-frame fusion between genes MTMR2 Exon12 (NM_016156) and MAML2 Exon3 (NM_032427).  Lab Notes Run Number: ArcherV3-CLIN-20190033 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0037865-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon7 (NM_001135648) and RSPO3 Exon2 (NM_032784). POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MTMR2-MAML2 fusion. Note: The rearrangement is an in-frame fusion between genes MTMR2 Exon12 (NM_016156) and MAML2 Exon3 (NM_032427).  Lab Notes Run Number: ArcherV3-CLIN-20190033 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0037866-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2124:TMPRSS2_c.39+60551:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0037866-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2124:TMPRSS2_c.39+60551:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ETV6	0	MSKCC-DMP	P-0038901-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.1010-2332:ETV6_chr12:g.8297469del Note: The ETV6 rearrangement is a deletion of exons 1 - 5. Functional significance is undetermined. Multiple rearrangements involving ETV6 were detected in this sample and a more complex rearrangement resulting in a ETV6 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PAX8	0	MSKCC-DMP	P-0038901-T01-IM6	PAX8-intragenic	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: c.1088-2327:PAX8_chr2:g.184698547del Note: The PAX8 rearrangement is a deletion of exons 1 - 9. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0038970-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.798+162:CREBBP_chr16:g.48497783inv Note: The CREBBP rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0038970-T01-IM6	CDK12-intragenic	yes	unknown		out of frame	CDK12 (NM_016507) rearrangement: c.2249-190_c.2667-159dup Note: The CDK12 rearrangement is an intragenic duplication of exons 5 - 7. The rearrangement includes a part of the kinase domain of CDK12. Functional significance is undetermined.
CDH3	0	MSKCC-DMP	P-0038990-T01-IM6	CDH1-CDH3 fusion	yes	unknown		in frame	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-6760:CDH3_c.164-49:CDH1del Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exons 3 - 16.
CDH1	0	MSKCC-DMP	P-0038990-T01-IM6	CDH1-CDH3 fusion	yes	unknown		in frame	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-6760:CDH3_c.164-49:CDH1del Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exons 3 - 16.
CDK12	0	MSKCC-DMP	P-0038990-T01-IM6	FBXL20-CDK12 fusion	yes	unknown		in frame	CDK12 (NM_016507) - FBXL20 (NM_032875) rearrangement: c.3095+27:CDK12_c.104+18457:FBXL20inv Note: The CDK12 - FBXL20 rearrangement is an inversion that results in a fusion of CDK12 exons 1 - 11 to FBXL20 exons 3 - 15. The fusion is predicted to be in frame and includes the kinase domain of CDK12. Functional significance is undetermined.
FBXL20	0	MSKCC-DMP	P-0038990-T01-IM6	FBXL20-CDK12 fusion	yes	unknown		in frame	CDK12 (NM_016507) - FBXL20 (NM_032875) rearrangement: c.3095+27:CDK12_c.104+18457:FBXL20inv Note: The CDK12 - FBXL20 rearrangement is an inversion that results in a fusion of CDK12 exons 1 - 11 to FBXL20 exons 3 - 15. The fusion is predicted to be in frame and includes the kinase domain of CDK12. Functional significance is undetermined.
JAK2	0	MSKCC-DMP	P-0038995-T01-IM6	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.2791_c.3059+880del Note: The JAK2 rearrangement is an intragenic deletion of exons 21 - 22. One of the breakpoints is within exon 21. Functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0039070-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) Rearrangement: c.8308_c.8332-974del Note: The BRAC2 rearrangement is an intragenic deletion of exon 18. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0038819-T01-IM6	RAB25-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - RAB25 (NM_020387) Rearrangement : Note: The NTRK1-RAB25 Rearrangement results in the fusion of exons 1-10 of NTRK1 with exon 2-5 of RAB25. This does not include the protein kinase domain of NTRK1.Its functional significance is undetermined.
RAB25	0	MSKCC-DMP	P-0038819-T01-IM6	RAB25-NTRK1 fusion	yes	unknown		out of frame	NTRK1 (NM_002529) - RAB25 (NM_020387) Rearrangement : Note: The NTRK1-RAB25 Rearrangement results in the fusion of exons 1-10 of NTRK1 with exon 2-5 of RAB25. This does not include the protein kinase domain of NTRK1.Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0038819-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : c.-28-2585_c.672+67dup Note: The TP53 Rearrangement results in the intragenic duplication of exons 1-6 of TP53. One of the breakpoints is the 5-UTR region of TP53. Its functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0038848-T01-IM6	SMYD3-intragenic	yes	unknown		in frame	SMYD3 (NM_001167740) Rearrangement : c.532-12038_c.703-62del Note: The SMYD3 Rearrangement results in the intragenic deletion of exons 6-7 of SMYD3. Its functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0038907-T01-IM6	PRKCZ-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - PRKCZ (NM_002744) rearrangement: t(1;19)(p36.33;p13.12)(chr1:g.2026923::chr19:g.15290892) Note: The NOTCH3 - PRKCZ rearrangement is a translocation that results in a fusion of NOTCH3 exons 1 - 20 to PRKCZ exons 5 - 18. One of the breakpoints is within NOTCH3 exon 20. Functional significance is undetermined.
PRKCZ	0	MSKCC-DMP	P-0038907-T01-IM6	PRKCZ-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - PRKCZ (NM_002744) rearrangement: t(1;19)(p36.33;p13.12)(chr1:g.2026923::chr19:g.15290892) Note: The NOTCH3 - PRKCZ rearrangement is a translocation that results in a fusion of NOTCH3 exons 1 - 20 to PRKCZ exons 5 - 18. One of the breakpoints is within NOTCH3 exon 20. Functional significance is undetermined.
MPL	0	MSKCC-DMP	P-0038907-T01-IM6	MPL-intragenic	yes	unknown		unknown	MPL (NM_005373) rearrangement: t(1;9)(p34.2;q33.3)(chr1:g.43814976::chr9:g.128023496) Note: The MPL rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.
FBXL20	0	MSKCC-DMP	P-0038937-T01-IM6	ERBB2-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - ERBB2 (NM_004448) fusion: c.105-18648:FBXL20_c.1223-24:ERBB2inv Note: The FBXL20 - ERBB2 fusion involves FBXL20 exons 1 - 2 and ERBB2 exons 11 - 27. The fusion includes the kinase domain of ERBB2.This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ERBB2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.
ERBB2	0	MSKCC-DMP	P-0038937-T01-IM6	ERBB2-FBXL20 fusion	yes	unknown		unknown	FBXL20 (NM_032875) - ERBB2 (NM_004448) fusion: c.105-18648:FBXL20_c.1223-24:ERBB2inv Note: The FBXL20 - ERBB2 fusion involves FBXL20 exons 1 - 2 and ERBB2 exons 11 - 27. The fusion includes the kinase domain of ERBB2.This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ERBB2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.
CTNNB1	0	MSKCC-DMP	P-0038937-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.936+16:CTNNB1_chr3:g.40352713inv Note: The CTNNB1 rearrangement is an inversion of exons 1 - 6. Functional significance is undetermined.
DAXX	0	MSKCC-DMP	P-0038937-T01-IM6	DAXX-intragenic	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.243+38:DAXX_chr6:g.41395990inv Note: The DAXX rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.
DLG1	0	MSKCC-DMP	P-0039001-T01-IM6	PIK3CA-DLG1 fusion	yes	unknown		unknown	DLG1 (NM_004087) - PIK3CA (NM_006218) rearrangement: c.1646-1039:DLG1_c.233:PIK3CAinv Note : The DLG1 - PIK3CA rearrangement is an inversion that results in a fusion of DLG1 exons 1 - 10 to PIK3CA exons 2 - 21. One of the breakpoints is within PIK3CA exon 2. Its functional significance is undetermined.
PIK3CA	0	MSKCC-DMP	P-0039001-T01-IM6	PIK3CA-DLG1 fusion	yes	unknown		unknown	DLG1 (NM_004087) - PIK3CA (NM_006218) rearrangement: c.1646-1039:DLG1_c.233:PIK3CAinv Note : The DLG1 - PIK3CA rearrangement is an inversion that results in a fusion of DLG1 exons 1 - 10 to PIK3CA exons 2 - 21. One of the breakpoints is within PIK3CA exon 2. Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0039003-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.497:PTEN_chr10:g.115299593inv Note : The PTEN rearrangement is an inversion of exons 6 - 9. One of the breakpoints is within exon 6. Functional significance is undetermined.
PRKCE	0	MSKCC-DMP	P-0039021-T01-IM6	ALK-PRKCE fusion	yes	unknown		out of frame	PRKCE (NM_005400) - ALK (NM_004304) fusion: c.348+43259:PRKCE_c.3173-812:ALKinv Note : The PRKCE - ALK fusion involves PRKCE exon 1 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0039021-T01-IM6	ALK-PRKCE fusion	yes	unknown		out of frame	PRKCE (NM_005400) - ALK (NM_004304) fusion: c.348+43259:PRKCE_c.3173-812:ALKinv Note : The PRKCE - ALK fusion involves PRKCE exon 1 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.
SKIL	0	MSKCC-DMP	P-0039058-T01-IM6	PRKCI-SKIL fusion	yes	unknown		out of frame	SKIL (NM_001248008) - PRKCI (NM_002740) rearrangement: c.1099-4405:SKIL_c.1418-3:PRKCIdup Note : The SKIL - PRKCI rearrangement is a duplication that results in a fusion of SKIL exons 1 - 3 to PRKCI exons 15 - 18. The fusion includes a part of the kinase domain of PRKCI.Its functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0039058-T01-IM6	PRKCI-SKIL fusion	yes	unknown		out of frame	SKIL (NM_001248008) - PRKCI (NM_002740) rearrangement: c.1099-4405:SKIL_c.1418-3:PRKCIdup Note : The SKIL - PRKCI rearrangement is a duplication that results in a fusion of SKIL exons 1 - 3 to PRKCI exons 15 - 18. The fusion includes a part of the kinase domain of PRKCI.Its functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0039063-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.189_c.809del Note : The TP53 rearrangement is an intragenic deletion of exons 4 - 8. The breakpoints are within exon 4 and exon 8.
KEAP1	0	MSKCC-DMP	P-0039063-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.1246:KEAP1_chr19:g.10595435del Note : The KEAP1 rearrangement is a deletion of exons 3 - 6. One of the breakpoints is within exon 3.
MFSD11	0	MSKCC-DMP	P-0039064-T01-IM6	NOTCH2-MFSD11 fusion	yes	unknown		unknown	MFSD11 (NM_001242532) - NOTCH2 (NM_024408) rearrangement: t(1;17)(p12;q25.1)(chr1:g.120497842::chr17:g.74746935) Note : The MFSD11 - NOTCH2 rearrangement is a translocation that results in a fusion of MFSD11 exons 1 - 8 to NOTCH2 exons 13 - 34. One of the breakpoints is within NOTCH2 exon 13. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0039064-T01-IM6	NOTCH2-MFSD11 fusion	yes	unknown		unknown	MFSD11 (NM_001242532) - NOTCH2 (NM_024408) rearrangement: t(1;17)(p12;q25.1)(chr1:g.120497842::chr17:g.74746935) Note : The MFSD11 - NOTCH2 rearrangement is a translocation that results in a fusion of MFSD11 exons 1 - 8 to NOTCH2 exons 13 - 34. One of the breakpoints is within NOTCH2 exon 13. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0039064-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;21)(q22.2;p11.2)(chr5:g.112151212::chr21:g.10829409) Note : The APC rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0038162-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190042 Macro-dissection: Not Performed
RSPO3	0	MSKCC-DMP	P-0038162-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190042 Macro-dissection: Not Performed
GLI1	0	MSKCC-DMP	P-0016627-T02-IM6	GLI1-intragenic	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: t(1;12)(q31.1;q13.3)(chr1:g.188655289::chr12:g.57857810) Note: The GLI1 rearrangement is a translocation with breakpoint in exon 3 of GLI1. The functional significance is undetermined.
PIK3C3	0	MSKCC-DMP	P-0038857-T01-IM6	PIK3C3-intragenic	yes	unknown		unknown	PIK3C3 (NM_002647) Rearrangement : chr18:g.6630097_c.2432+13:PIK3C3inv Note: The PIK3C3 Rearrangement results in the inversion of exons 1-22 of PIK3C3. Its functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0039045-T01-IM6	STAT5A-KDM5A fusion	yes	unknown		out of frame	KDM5A (NM_001042603) - STAT5A (NM_003152) rearrangement: t(12;17)(p13.33;q21.2)(chr12:g.470840::chr17:g.40459887) Note: The KDM5A - STAT5A rearrangement is a translocation that results in a fusion of KDM5A exons 1 - 5 to STAT5A exons 17 - 20. Functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0039045-T01-IM6	STAT5A-KDM5A fusion	yes	unknown		out of frame	KDM5A (NM_001042603) - STAT5A (NM_003152) rearrangement: t(12;17)(p13.33;q21.2)(chr12:g.470840::chr17:g.40459887) Note: The KDM5A - STAT5A rearrangement is a translocation that results in a fusion of KDM5A exons 1 - 5 to STAT5A exons 17 - 20. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039047-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4233:TMPRSS2_c.18+8075:ERGdel Note : The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0039047-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4233:TMPRSS2_c.18+8075:ERGdel Note : The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
OSBP2	0	MSKCC-DMP	P-0039180-T01-IM6	EWSR1-OSBP2 fusion	yes	unknown		out of frame	OSBP2 (NM_030758) - EWSR1 (NM_013986) rearrangement: c.853+38356:OSBP2_c.993-1321:EWSR1dup Note: The OSBP2 - EWSR1 rearrangement is a duplication that results in a fusion of OSBP2 exons 1 - 2 to EWSR1 exons 10 - 18. Functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0039180-T01-IM6	EWSR1-OSBP2 fusion	yes	unknown		out of frame	OSBP2 (NM_030758) - EWSR1 (NM_013986) rearrangement: c.853+38356:OSBP2_c.993-1321:EWSR1dup Note: The OSBP2 - EWSR1 rearrangement is a duplication that results in a fusion of OSBP2 exons 1 - 2 to EWSR1 exons 10 - 18. Functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0039087-T01-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21) : c.2301+1153:FGFR2_c.2181+133:BICC1inv Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and include the protein kinase domain of FGFR2.
BICC1	0	MSKCC-DMP	P-0039087-T01-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21) : c.2301+1153:FGFR2_c.2181+133:BICC1inv Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and include the protein kinase domain of FGFR2.
CREBBP	0	MSKCC-DMP	P-0039094-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) Rearrangement: c.435_c.798+6330del Note: The CREBBP rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0039223-T01-IM6	TRAF7-intragenic	yes	unknown		unknown	TRAF7 (NM_032271) rearrangement: t(16;20)(p13.3;q12)(chr16:g.2221580::chr20:g.40221310) Note: The TRAF7 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.
C16orf45	0	MSKCC-DMP	P-0039241-T01-IM6	TSC2-C16orf45 fusion	yes	unknown		out of frame	C16orf45 (NM_033201) - TSC2 (NM_000548) rearrangement: c.106+2910:C16orf45_c.1840-5:TSC2dup Note: The C16orf45 - TSC2 rearrangement is a duplication that results in a fusion of C16orf45 exon 1 to TSC2 exons 18 - 42. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0039241-T01-IM6	TSC2-C16orf45 fusion	yes	unknown		out of frame	C16orf45 (NM_033201) - TSC2 (NM_000548) rearrangement: c.106+2910:C16orf45_c.1840-5:TSC2dup Note: The C16orf45 - TSC2 rearrangement is a duplication that results in a fusion of C16orf45 exon 1 to TSC2 exons 18 - 42. Functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0039245-T01-IM6	EWSR1-intragenic	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: c.1309+219:EWSR1_chr22:g.29890022dup Note: The EWSR1 rearrangement is a duplication of exons 14 - 18. Functional significance is undetermined.
PDGFRB	0	MSKCC-DMP	P-0039245-T01-IM6	PDGFRB-intragenic	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: c.1367+75:PDGFRB_chr5:g.152640215inv Note: The PDGFRB rearrangement is an inversion of exons 1 - 9. The rearrangement does not include the kinase domain of PDGFRB. Functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0039297-T01-IM6	PPM1D-intragenic	yes	unknown		out of frame	PPM1D (NM_003620) rearrangement: c.827-117_c.1017+3546dup Note: The PPM1D rearrangement is an intragenic duplication of exon 4. Functional significance is undetermined.
BTK	0	MSKCC-DMP	P-0039300-T01-IM6	BTK-intragenic	yes	unknown		unknown	BTK (NM_000061) rearrangement: c.1908+94:BTK_chrX:g.99466815del Note: The BTK rearrangement is a deletion of exon 19. The rearrangement includes a part of the kinase domain of BTK. Functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0039306-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.2865-21:POLE_chr12:g.76693286inv Note: The POLE rearrangement is an inversion of exons 25 - 49. Functional significance is undetermined.
FOXK1	0	MSKCC-DMP	P-0039307-T01-IM6	CARD11-FOXK1 fusion	yes	unknown		out of frame	FOXK1 (NM_001037165) - CARD11 (NM_032415) rearrangement: c.1244+854:FOXK1_c.1342-84:CARD11inv Note: The FOXK1 - CARD11 rearrangement is an inversion that results in a fusion of FOXK1 exons 1 - 5 to CARD11 exons 10 - 25. Functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0039307-T01-IM6	CARD11-FOXK1 fusion	yes	unknown		out of frame	FOXK1 (NM_001037165) - CARD11 (NM_032415) rearrangement: c.1244+854:FOXK1_c.1342-84:CARD11inv Note: The FOXK1 - CARD11 rearrangement is an inversion that results in a fusion of FOXK1 exons 1 - 5 to CARD11 exons 10 - 25. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021561-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) :  c.127-1071:TMPRSS2_c.40-56818:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
ERG	0	MSKCC-DMP	P-0021561-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) :  c.127-1071:TMPRSS2_c.40-56818:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in-frame.
NAB2	0	MSKCC-DMP	P-0039139-T01-IM6	KIF5A-NAB2 fusion	yes	unknown		in frame	NAB2 (NM_005967) - KIF5A (NM_004984) rearrangement: c.958-157:NAB2_c.129+5819:KIF5Adel Note: The NAB2 - KIF5A rearrangement is a deletion that results in a fusion of NAB2 exons 1 - 2 to KIF5A exons 2 - 28. The fusion is predicted to be in frame. Functional significance is undetermined.
KIF5A	0	MSKCC-DMP	P-0039139-T01-IM6	KIF5A-NAB2 fusion	yes	unknown		in frame	NAB2 (NM_005967) - KIF5A (NM_004984) rearrangement: c.958-157:NAB2_c.129+5819:KIF5Adel Note: The NAB2 - KIF5A rearrangement is a deletion that results in a fusion of NAB2 exons 1 - 2 to KIF5A exons 2 - 28. The fusion is predicted to be in frame. Functional significance is undetermined.
ESR1	0	MSKCC-DMP	P-0016627-T02-IM6	PLEKHG1-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-PLEKHG1 fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon6 (NM_001122742) and PLEKHG1 Exon13 (NM_001029884). Note: ESR1-CCDC170 fusion: ESR1 Exon3 (NM_001122742) and CCDC170 Exon4 (NM_025059), was also detected with very low frequency. Lab Notes Run Number: ArcherV3-CLIN-20190044 Macro-dissection: Unknown
PLEKHG1	0	MSKCC-DMP	P-0016627-T02-IM6	PLEKHG1-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-PLEKHG1 fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon6 (NM_001122742) and PLEKHG1 Exon13 (NM_001029884). Note: ESR1-CCDC170 fusion: ESR1 Exon3 (NM_001122742) and CCDC170 Exon4 (NM_025059), was also detected with very low frequency. Lab Notes Run Number: ArcherV3-CLIN-20190044 Macro-dissection: Unknown
UPF1	0	MSKCC-DMP	P-0039229-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: c.3019+11:UPF1_chr19:g.16454164inv Note: The UPF1 rearrangement is an inversion of exons 1 - 21. Functional significance is undetermined.
HIGD1A	0	MSKCC-DMP	P-0039229-T01-IM6	CTNNB1-HIGD1A fusion	yes	unknown		in frame	HIGD1A (NM_001099668) - CTNNB1 (NM_001904) rearrangement: c.139+3968:HIGD1A_c.242-64:CTNNB1inv Note: The HIGD1A - CTNNB1 rearrangement is an inversion that results in a fusion of HIGD1A exons 1 - 2 to CTNNB1 exons 4 - 15. The fusion is predicted to be in frame. Functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0039229-T01-IM6	CTNNB1-HIGD1A fusion	yes	unknown		in frame	HIGD1A (NM_001099668) - CTNNB1 (NM_001904) rearrangement: c.139+3968:HIGD1A_c.242-64:CTNNB1inv Note: The HIGD1A - CTNNB1 rearrangement is an inversion that results in a fusion of HIGD1A exons 1 - 2 to CTNNB1 exons 4 - 15. The fusion is predicted to be in frame. Functional significance is undetermined.
ADCY10	0	MSKCC-DMP	P-0039234-T01-IM6	NUF2-ADCY10 fusion	yes	unknown		unknown	ADCY10 (NM_018417) - NUF2 (NM_031423) rearrangement: c.828+205:ADCY10_c.26:NUF2inv Note: The ADCY10 - NUF2 rearrangement is an inversion that results in a fusion of ADCY10 exons 1 - 5 to NUF2 exons 2 - 14. One of the breakpoints is within NUF2 exon 2. Functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0039234-T01-IM6	NUF2-ADCY10 fusion	yes	unknown		unknown	ADCY10 (NM_018417) - NUF2 (NM_031423) rearrangement: c.828+205:ADCY10_c.26:NUF2inv Note: The ADCY10 - NUF2 rearrangement is an inversion that results in a fusion of ADCY10 exons 1 - 5 to NUF2 exons 2 - 14. One of the breakpoints is within NUF2 exon 2. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039234-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.56-2672_c.126+638del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 2. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0039238-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.4198:NF1_chr17:g.34951290inv Note: The NF1 rearrangement is an inversion of exons 32 - 58. One of the breakpoints is within exon 32. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039238-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-480:TMPRSS2_c.18+5750:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0039238-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-480:TMPRSS2_c.18+5750:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
WHSC1	0	MSKCC-DMP	P-0039291-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.2518+51:WHSC1_chr4:g.28355378del Note: The WHSC1 rearrangement is a deletion of exons 14 - 22. Functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0039295-T01-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: t(3;11)(p11.1;q13.4)(chr3:g.90035582::chr11:g.71936263) Note: The INPPL1 rearrangement is a translocation with a breakpoint in intron 1.
ALK	0	MSKCC-DMP	P-0039320-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.2651:ALK_chr2:g.22452824dup Note: The ALK rearrangement is a duplication of exons 16 - 29. One of the breakpoints is within exon 16. The rearrangement includes the kinase domain of ALK. Multiple ALK rearrangements were detected in this sample and a more complex rearrangement resulting in an oncogenic ALK fusion is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
UPF1	0	MSKCC-DMP	P-0039326-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: t(8;19)(p21.2;p13.11)(chr8:g.24400830::chr19:g.18974316) Note: The UPF1 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0038638-T01-IM6	NTRK3-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon2 (NM_019063) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20190045 Macro-dissection: Unknown
NTRK3	0	MSKCC-DMP	P-0038638-T01-IM6	NTRK3-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: EML4-NTRK3 fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon2 (NM_019063) and NTRK3 Exon14 (NM_002530). Lab Notes Run Number: ArcherV3-CLIN-20190045 Macro-dissection: Unknown
None	0	MSKCC-DMP	P-0001507-T01-IM3	None-intragenic	yes	unknown		unknown	None
MEN1	0	MSKCC-DMP	P-0033283-T03-IM6	MEN1-intragenic	yes	unknown		unknown	MEN1 (NM_000244) rearrangement: t(11,18)(q13.1;p11.31)(chr11:g.64574579::chr18:g.4043058) Note: The MEN1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0039109-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-83:FGFR3_c.162+65:TACC3dup Note : The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 3 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0039109-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-83:FGFR3_c.162+65:TACC3dup Note : The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 3 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
PIK3C2G	0	MSKCC-DMP	P-0039365-T01-IM6	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.2491:PIK3C2G_chr12:g.18195353del Note: The PIK3C2G rearrangement is a deletion of exons 1 - 18. One of the breakpoints is within exon 18. Functional significance is undetermined.
RPAP3	0	MSKCC-DMP	P-0039370-T01-IM6	FGFR2-RPAP3 fusion	yes	unknown		in frame	RPAP3 (NM_024604) - FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;q13.11)(chr10:g.123242832::chr12:g.48092574) Note: The RPAP3 - FGFR2 rearrangement is a translocation that results in a fusion of RPAP3 exons 1 - 3 to FGFR2 exon 18. The fusion is predicted to be in frame and does not include the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FGFR2	0	MSKCC-DMP	P-0039370-T01-IM6	FGFR2-RPAP3 fusion	yes	unknown		in frame	RPAP3 (NM_024604) - FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;q13.11)(chr10:g.123242832::chr12:g.48092574) Note: The RPAP3 - FGFR2 rearrangement is a translocation that results in a fusion of RPAP3 exons 1 - 3 to FGFR2 exon 18. The fusion is predicted to be in frame and does not include the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
EIF4A2	0	MSKCC-DMP	P-0039377-T01-IM6	EIF4A2-intragenic	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: t(2;3)(q31.2;q27.3)(chr2:g.180104857::chr3:g.186505193) Note: The EIF4A2 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
NUP210L	0	MSKCC-DMP	P-0039413-T01-IM6	PTCH1-NUP210L fusion	yes	unknown		out of frame	NUP210L (NM_207308) - PTCH1 (NM_000264) rearrangement: t(1;9)(q21.3;q22.32)(chr1:g.153966858::chr9:g.98209832) Note: The NUP210L - PTCH1 rearrangement is a translocation that results in a fusion of NUP210L exons 1 - 36 to PTCH1 exon 23. The functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0039413-T01-IM6	PTCH1-NUP210L fusion	yes	unknown		out of frame	NUP210L (NM_207308) - PTCH1 (NM_000264) rearrangement: t(1;9)(q21.3;q22.32)(chr1:g.153966858::chr9:g.98209832) Note: The NUP210L - PTCH1 rearrangement is a translocation that results in a fusion of NUP210L exons 1 - 36 to PTCH1 exon 23. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0039421-T01-IM6	ZNF77-DOT1L fusion	yes	unknown		in frame	DOT1L (NM_032482) - ZNF77 (NM_021217) rearrangement: c.4606+1182:DOT1L_c.130+1031:ZNF77inv Note: The DOT1L - ZNF77 rearrangement is an inversion that results in a fusion of DOT1L exons 1 - 27 to ZNF77 exons 3 - 4. The fusion is predicted to be in frame. The functional significance is undetermined.
ZNF77	0	MSKCC-DMP	P-0039421-T01-IM6	ZNF77-DOT1L fusion	yes	unknown		in frame	DOT1L (NM_032482) - ZNF77 (NM_021217) rearrangement: c.4606+1182:DOT1L_c.130+1031:ZNF77inv Note: The DOT1L - ZNF77 rearrangement is an inversion that results in a fusion of DOT1L exons 1 - 27 to ZNF77 exons 3 - 4. The fusion is predicted to be in frame. The functional significance is undetermined.
RAD52	0	MSKCC-DMP	P-0039422-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: t(1;12)(q32.1;p13.33)(chr1:g.201991943::chr12:g.1025575) Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039508-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.1010+22:TMPRSS2_c.19-22866:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 9 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0039508-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.1010+22:TMPRSS2_c.19-22866:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 9 and ERG exons 2 - 10.
STK11	0	MSKCC-DMP	P-0003167-T01-IM5	STK11-intragenic	yes	unknown		in frame	null Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of exons 2-5, potentially disabling the function of the gene.
ALK	0	MSKCC-DMP	P-0003206-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	null EML4-ALK Known fusion annotation
EML4	0	MSKCC-DMP	P-0003206-T01-IM5	EML4-ALK fusion	yes	unknown		unknown	null EML4-ALK Known fusion annotation
SLC16A10	0	MSKCC-DMP	P-0003507-T01-IM5	ROS1-SLC16A10 fusion	yes	unknown		in frame	null exon 1 and 2 of ROS1 fuse to exon 4-6 of SLC16A10.  functional significance is undetermined
ROS1	0	MSKCC-DMP	P-0003507-T01-IM5	ROS1-SLC16A10 fusion	yes	unknown		in frame	null exon 1 and 2 of ROS1 fuse to exon 4-6 of SLC16A10.  functional significance is undetermined
c.1726_*7586inv	0	MSKCC-DMP	P-0003560-T01-IM5	c.1726_*7586inv-intragenic	yes	unknown		unknown	c.1726_*7586inv Note: The PIK3R1 (NM_181523) rearrangement event results in the inversion of exons 13-16, likely disrupting the function of the gene. One of the breakpoints is within exon13.
NOTCH2	0	MSKCC-DMP	P-0003700-T01-IM5	NOTCH2-intragenic	yes	unknown		in frame	NOTCH2 (NM_024408) rearrangement: c.1682-62_c.1916-920dup NOTCH2 (NM_024408) rearrangement event is a duplication which results in the duplication of exons 11. Its functional significance is undetermined.
CDK5RAP2	0	MSKCC-DMP	P-0004203-T01-IM5	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(7q34;9q33.2)(chr7:140491585::chr9:123251876) Note: CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement event is a reciprocal translocation in which results in the fusion of CDK5RAP2 exons 1-13 with BRAF exons 9-18. This fusion includes the kinase domain of BRAF gene.
BRAF	0	MSKCC-DMP	P-0004203-T01-IM5	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(7q34;9q33.2)(chr7:140491585::chr9:123251876) Note: CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement event is a reciprocal translocation in which results in the fusion of CDK5RAP2 exons 1-13 with BRAF exons 9-18. This fusion includes the kinase domain of BRAF gene.
KDM5C	0	MSKCC-DMP	P-0004650-T01-IM5	KDM5C-intragenic	yes	unknown		unknown	KDM5C(NM_004187) Rearrangement : chrX:g.42358230_c.1314:KDM5Cinv Note: The KDM5C(NM_004187) Rearrangement results in the inversion of exons 10 to 26 of KDM5C.The breakpoint is within exon 26.Its functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0039159-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: c.1717-2316_c.2082del Note : The TSC2 rearrangement is an intragenic deletion of exons 17 - 19. One of the breakpoints is within exon 19.
AGO2	0	MSKCC-DMP	P-0039159-T01-IM6	PTK2-AGO2 fusion	yes	unknown		in frame	AGO2 (NM_012154) - PTK2 (NM_005607) rearrangement: c.2169+76:AGO2_c.2208+5073:PTK2dup Note : The AGO2 - PTK2 rearrangement is a duplication that results in a fusion of AGO2 exons 1 - 16 to PTK2 exons 24 - 32. The fusion is predicted to be in frame. Functional significance is undetermined.
PTK2	0	MSKCC-DMP	P-0039159-T01-IM6	PTK2-AGO2 fusion	yes	unknown		in frame	AGO2 (NM_012154) - PTK2 (NM_005607) rearrangement: c.2169+76:AGO2_c.2208+5073:PTK2dup Note : The AGO2 - PTK2 rearrangement is a duplication that results in a fusion of AGO2 exons 1 - 16 to PTK2 exons 24 - 32. The fusion is predicted to be in frame. Functional significance is undetermined.
AKAP12	0	MSKCC-DMP	P-0039439-T01-IM6	E2F3-AKAP12 fusion	yes	unknown		out of frame	AKAP12 (NM_005100) - E2F3 (NM_001949) rearrangement: c.163-16213:AKAP12_c.1136-225:E2F3dup Note: The AKAP12 - E2F3 rearrangement is a duplication that results in a fusion of AKAP12 exons 1 - 2 to E2F3 exon 7. Functional significance is undetermined.
E2F3	0	MSKCC-DMP	P-0039439-T01-IM6	E2F3-AKAP12 fusion	yes	unknown		out of frame	AKAP12 (NM_005100) - E2F3 (NM_001949) rearrangement: c.163-16213:AKAP12_c.1136-225:E2F3dup Note: The AKAP12 - E2F3 rearrangement is a duplication that results in a fusion of AKAP12 exons 1 - 2 to E2F3 exon 7. Functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0039473-T01-IM6	MSH3-intragenic	yes	unknown		unknown	MSH3 (NM_002439) rearrangement: c.1341-16442_c.2436-132inv Note: The MSH3 rearrangement is an intragenic inversion of exons 9 - 17. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0036560-T02-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449).  Lab Notes Run Number: ArcherV3-CLIN-20190046 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0036560-T02-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449).  Lab Notes Run Number: ArcherV3-CLIN-20190046 Macro-dissection: Unknown
FAT1	0	MSKCC-DMP	P-0006796-T01-IM5	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement : c.10118_11640+406inv Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 16-21. One of the breakpoints is within FAT1 exon16.
TMPRSS2	0	MSKCC-DMP	P-0006856-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2091:TMPRSS2_c.40-13213:ERGdel
ERG	0	MSKCC-DMP	P-0006856-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2091:TMPRSS2_c.40-13213:ERGdel
MAP3K1	0	MSKCC-DMP	P-0006856-T02-IM5	C5orf64-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - C5orf64 (NM_173667) rearrangement: c.3454:MAP3K1_c.226-4097:C5orf64del Note: The MAP3K1 (NM_005921) - C5orf64 (NM_173667) rearrangement is a deletion which results in the fusion of MAP3K1 exons 1-14 with C5orf64 exon 4. The functional significance is undetermined.
C5orf64	0	MSKCC-DMP	P-0006856-T02-IM5	C5orf64-MAP3K1 fusion	yes	unknown		unknown	MAP3K1 (NM_005921) - C5orf64 (NM_173667) rearrangement: c.3454:MAP3K1_c.226-4097:C5orf64del Note: The MAP3K1 (NM_005921) - C5orf64 (NM_173667) rearrangement is a deletion which results in the fusion of MAP3K1 exons 1-14 with C5orf64 exon 4. The functional significance is undetermined.
PIM1	0	MSKCC-DMP	P-0007980-T01-IM5	PIM1-intragenic	yes	unknown		unknown	PIM1 (NM_002648) rearrangement: t(6;7)(p21.2;p14.3)(chr6:g.37138620::chr7:g.30811615 ) The PIM1 (NM_002648) rearrangement: is a translocation which may result in a truncated PIM1. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0010537-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) Rearrangement : c.163+31820_463+1139dup Note: The ETV6 Rearrangement  results in the duplication of exons 3-4 of ETV6. Its functional significance is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0010537-T01-IM5	PPP2R1A-intragenic	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: t(10;19)(q23.33;q13.41)(chr10:g.95055215::chr19:g.52724231) Note: The PPP2R1A rearrangement is a translocation which may result in the truncation of PPP2R1A exons 12-15. The breakpoint is within exon 12. The functional significance of this rearrangement is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0011515-T01-IM5	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099)  Rearrangement : c.56-954_c.556+505inv Note: The  TMPRSS2 Rearrangement results in the intragenic inversion of exon2-5 of TMPRSS2. Its functional significance is undetermined.
EGFL7	0	MSKCC-DMP	P-0011537-T01-IM5	EGFL7-intragenic	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: t(3;9)(p14.2;q34.3)(chr3:g.59696693::chr9:g.139564655) Note: The EGFL7 rearrangement is a translocation that may result in the truncation of exons 7-9. One of the breakpoints is within exon 7. The functional significance is undetermined.
SDHAF2	0	MSKCC-DMP	P-0011555-T01-IM5	SDHAF2-intragenic	yes	unknown		unknown	SDHAF2 (NM_017841) rearrangement: c.367_c.371-4del Note: The SDHAF2 rearrangement is an intragenic deletion of a part of exon 3. One of the breakpoint is within exon 3.
FAM65B	0	MSKCC-DMP	P-0011555-T01-IM5	SDHAF2-FAM65B fusion	yes	unknown		unknown	FAM65B (NM_014722) - SDHAF2 (NM_017841) rearrangement: t(6;11)(p22.3;q12.2)(chr6:g.24806597::chr11:g.61205093) Note: The FAM65B - SDHAF2 rearrangement is a translocation that may result in the fusion of the FAM65B transcript (exons 1 - 23) with SDHAF2 exons 2-4. The SDHAF2 intragenic deletion and the translocation suggest a complex structural rearrangement involving SDHAF2. The functional significance is undetermined.
SDHAF2	0	MSKCC-DMP	P-0011555-T01-IM5	SDHAF2-FAM65B fusion	yes	unknown		unknown	FAM65B (NM_014722) - SDHAF2 (NM_017841) rearrangement: t(6;11)(p22.3;q12.2)(chr6:g.24806597::chr11:g.61205093) Note: The FAM65B - SDHAF2 rearrangement is a translocation that may result in the fusion of the FAM65B transcript (exons 1 - 23) with SDHAF2 exons 2-4. The SDHAF2 intragenic deletion and the translocation suggest a complex structural rearrangement involving SDHAF2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0012048-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+186:TMPRSS2_c.39+62923:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
ERG	0	MSKCC-DMP	P-0012048-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+186:TMPRSS2_c.39+62923:ERGdel Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
CDKN2A	0	MSKCC-DMP	P-0012736-T01-IM5	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077, NM_058195) rearrangement: c.150+462_c.244del:CDKN2Ap16INK4A ,  c.194-3008_c.287del:CDKN2Ap14ARF Note: The CDKN2Ap14ARF and CDKN2Ap16INK4A rearrangements are a single event affecting two isoforms of the CDKN2A gene. One of the breakpoints is within exon2 of CDKN2A. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0013000-T01-IM5	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) Rearrangement :  c.2015-88:FANCA_c.614+201:TCF25del Note: The FANCA Rearrangement results in the deletion of exons 1-23 of FANCA. One of the breakpoints is within exon23. Its functional significance is undetermined.
AKAP8	0	MSKCC-DMP	P-0013000-T01-IM5	NOTCH3-AKAP8 fusion	yes	unknown		unknown	AKAP8 (NM_005858) -NOTCH3  (NM_000435) Rearrangement : c.1623+359:AKAP8_c.4705:NOTCH3del Note: The AKAP8 -NOTCH3  Rearrangement results in the fusion of exons 1-13 of AKAP8 with exons 25-33 of NOTCH3. The breakpoint in NOTCH3 is within exon 25. Its functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0013000-T01-IM5	NOTCH3-AKAP8 fusion	yes	unknown		unknown	AKAP8 (NM_005858) -NOTCH3  (NM_000435) Rearrangement : c.1623+359:AKAP8_c.4705:NOTCH3del Note: The AKAP8 -NOTCH3  Rearrangement results in the fusion of exons 1-13 of AKAP8 with exons 25-33 of NOTCH3. The breakpoint in NOTCH3 is within exon 25. Its functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0013106-T01-IM5	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: chr16:g.331906_c.1116+53:AXIN1del Note: The AXIN1 rearrangement is a deletion of exons 5-11.
POLD1	0	MSKCC-DMP	P-0013106-T01-IM5	POLD1-intragenic	yes	unknown		unknown	POLD1 (NM_002691) rearrangement: c.1757:POLD1_chr19:g.56784053del Note: The POLD1 rearrangement is a deletion of exons 14-27. One of the breakpoints is within exon 14.
TMPRSS2	0	MSKCC-DMP	P-0013503-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4160:TMPRSS2_c.18+11744:ERGdel
ERG	0	MSKCC-DMP	P-0013503-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4160:TMPRSS2_c.18+11744:ERGdel
ARID5B	0	MSKCC-DMP	P-0013625-T01-IM5	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.734-289_c.991del Note: The ARID5B rearrangement is an intragenic deletion of exons 5-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0013625-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.-48-2076_c.844del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0013831-T01-IM5	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: chr17:g.37597504_c.1301:CDK12del Note: The CDK12 rearrangement is a deletion of 5UTR and exons 1-2.
NF1	0	MSKCC-DMP	P-0014261-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.5268+131_c.6155inv Note: The NF1 rearrangement is an intragenic inversion of exons 36-41. One of the breakpoints is within exon 41.
SYK	0	MSKCC-DMP	P-0014261-T01-IM6	SYK-intragenic	yes	unknown		unknown	SYK (NM_003177) rearrangement: c.1408:SYK_chr9:g.134211866inv Note: The SYK rearrangement is an inversion of exons 11-14. One of the breakpoints is within exon 11.
TMPRSS2	0	MSKCC-DMP	P-0014629-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exon3): c.56-4111:TMPRSS2_c.39+32697:ERGdel
ERG	0	MSKCC-DMP	P-0014629-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exon3): c.56-4111:TMPRSS2_c.39+32697:ERGdel
CIC	0	MSKCC-DMP	P-0014634-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) Rearrangement : c.3008+26:CIC_chr19:42803409del Note: The CIC Rearrangement results in the deletion of exon 12 -20 of CIC. Its functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0016983-T02-IM6	DNAJB1-intragenic	yes	unknown		unknown	DNAJB1 (NM_006145) Rearrangement : 19:47623580_c.211+21:DNAJB1inv Note: The DNAJB1 Rearrangement results in the inversion of exon 1 of DNAJB1. Its functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0016983-T02-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) Rearrangement : c.3045:UPF1_chr19:g.58978895inv Note: The UPF1 Rearrangement results in the inversion of exons 22-23 of UPF1. One of the breakpoints is within exon22. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0016983-T02-IM6	ERG fusion-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG fusion (NM_182918) fusion (TMPRSS2 exon 1-2 fused to ERG exons 2-10): c.127-1367:TMRPSS2_c.19-15431:ERGdel Note: The TMPRSS2  - ERG fusion is predicted to be in-frame.
ERG fusion	0	MSKCC-DMP	P-0016983-T02-IM6	ERG fusion-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG fusion (NM_182918) fusion (TMPRSS2 exon 1-2 fused to ERG exons 2-10): c.127-1367:TMRPSS2_c.19-15431:ERGdel Note: The TMPRSS2  - ERG fusion is predicted to be in-frame.
ROS1	0	MSKCC-DMP	P-0020592-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: g.21888762_c.5367-710del Note: The ROS1 rearrangement results in the deletion of exons 33-43. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0020608-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(12:17)(q23.1;p13.1)(chr12:g.98491631::chr17:g.7579685) Note: The TP53 rearrangement is a translocation that may result in the truncation of TP53 exons 4-11.
TMPRSS2	0	MSKCC-DMP	P-0020843-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.126+1610:TMPRSS2_c.40-60543:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.
ERG	0	MSKCC-DMP	P-0020843-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.126+1610:TMPRSS2_c.40-60543:ERGdel Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.
EP300	0	MSKCC-DMP	P-0020950-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.3806+75_c.4553inv Note: The EP300 rearrangement results in the inversion of exons 23-28. One of the breakpoints is within exon 28. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0020984-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-1454:TMPRSS2_c.18+8460:ERGdel
ERG	0	MSKCC-DMP	P-0020984-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-1454:TMPRSS2_c.18+8460:ERGdel
PTPN11	0	MSKCC-DMP	P-0021179-T01-IM6	PTPN11-intragenic	yes	unknown		unknown	PTPN11 (NM_002834) rearrangement: t(12;22)(q24.13;q11.23)(chr12:g.112927045::chr22:g.25404722) Note: The PTPN11 rearrangement is a translocation that may result in a truncation of PTPN11 exons 14-15. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0021297-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exons 1-2 fused with ERG exons 3-10):c.126+871:TMPRSS2_c.237-7837:ERGdel
ERG	0	MSKCC-DMP	P-0021297-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exons 1-2 fused with ERG exons 3-10):c.126+871:TMPRSS2_c.237-7837:ERGdel
ERG	0	MSKCC-DMP	P-0021310-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.39+53911:ERG_c.126+1319:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exons 1-3 to TMPRSS2 exons 3-14. The possibility of a more complex event resulting in the fusion of TMPRSS2-ERG cannot be excluded.
TMPRSS2	0	MSKCC-DMP	P-0021310-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.39+53911:ERG_c.126+1319:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exons 1-3 to TMPRSS2 exons 3-14. The possibility of a more complex event resulting in the fusion of TMPRSS2-ERG cannot be excluded.
ATM	0	MSKCC-DMP	P-0039132-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.186-51:ATM_chr11:g.88962170inv Note: The ATM rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0039480-T01-IM6	NAB2-intragenic	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: c.850:NAB2_chr12:g.54655657inv Note: The NAB2 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0037712-T01-IM6	GPATCH3-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) - GPATCH3 (NM_022078) rearrangement: c.5053:ARID1A_c.877-1228:GPATCH3inv Note: The ARID1A - GPATCH3 rearrangement is an inversion that results in the fusion of ARID1A exons 1-19 with GPATCH3 exons 3-7. One of the breakpoints is within ARID1A exon 19. The functional significance is undetermined.
GPATCH3	0	MSKCC-DMP	P-0037712-T01-IM6	GPATCH3-ARID1A fusion	yes	unknown		unknown	ARID1A (NM_006015) - GPATCH3 (NM_022078) rearrangement: c.5053:ARID1A_c.877-1228:GPATCH3inv Note: The ARID1A - GPATCH3 rearrangement is an inversion that results in the fusion of ARID1A exons 1-19 with GPATCH3 exons 3-7. One of the breakpoints is within ARID1A exon 19. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0037712-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.539+9413_c.1598dup Note: The RASA1 rearrangement results in the duplication of exons 2-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0037718-T01-IM6	FAM149B1-KMT2D fusion	yes	unknown		out of frame	KMT2D (NM_003482) - FAM149B1 (NM_173348) rearrangement: t(10;12)(q22.2;q13.12)(chr10:g.74969560::chr12:g.49446311) Note: The KMT2D - FAM149B1 rearrangement is a translocation that results in the fusion of KMT2D exons 1-9 with FAM149B1 exons 7-14. The functional significance is undetermined.
FAM149B1	0	MSKCC-DMP	P-0037718-T01-IM6	FAM149B1-KMT2D fusion	yes	unknown		out of frame	KMT2D (NM_003482) - FAM149B1 (NM_173348) rearrangement: t(10;12)(q22.2;q13.12)(chr10:g.74969560::chr12:g.49446311) Note: The KMT2D - FAM149B1 rearrangement is a translocation that results in the fusion of KMT2D exons 1-9 with FAM149B1 exons 7-14. The functional significance is undetermined.
GATA1	0	MSKCC-DMP	P-0037718-T01-IM6	GATA1-intragenic	yes	unknown		unknown	GATA1 (NM_002049) rearrangement: c.298:GATA1_chrX:g.54291385dup Note: The GATA1 rearrangement results in the duplication of exons 3-6. One of the breakpoints is within exon 3. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0039370-T01-IM6	RPAP3-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-RPAP3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and RPAP3 Exon4 (NM_024604). Lab Notes Run Number: ArcherV3-CLIN-20190049 Macro-dissection: Unknown
RPAP3	0	MSKCC-DMP	P-0039370-T01-IM6	RPAP3-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-RPAP3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and RPAP3 Exon4 (NM_024604). Lab Notes Run Number: ArcherV3-CLIN-20190049 Macro-dissection: Unknown
NTRK1	0	MSKCC-DMP	P-0039401-T01-IM6	NTRK1-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: NTRK1 (NM_002529)  exons 3-9 deletion. PMID: 26581861, 29914559 Note1: the functional significance of this event is unknown. Trk inhibitors have not been investigated in this setting. Note2: This event was detected with low read support.  Lab Notes Run Number: ArcherV3-CLIN-20190049 Macro-dissection: Unknown
SMO	0	MSKCC-DMP	P-0026492-T02-IM6	SMO-intragenic	yes	unknown		unknown	SMO (NM_005631) rearrangement: c.1265-185:SMO_chr7:g.117726946inv Note: The SMO rearrangement is an inversion of exons 1 - 6. Functional significance is undetermined.
FER1L6	0	MSKCC-DMP	P-0039584-T01-IM6	AGO2-FER1L6 fusion	yes	unknown		in frame	FER1L6 (NM_001039112) - AGO2 (NM_012154) rearrangement: c.2589+1237:FER1L6_c.1027-3:AGO2inv Note: The FER1L6 - AGO2 rearrangement is an inversion that results in a fusion of FER1L6 exons 1 - 20 to AGO2 exons 9 - 19. The fusion is predicted to be in frame. Functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0039584-T01-IM6	AGO2-FER1L6 fusion	yes	unknown		in frame	FER1L6 (NM_001039112) - AGO2 (NM_012154) rearrangement: c.2589+1237:FER1L6_c.1027-3:AGO2inv Note: The FER1L6 - AGO2 rearrangement is an inversion that results in a fusion of FER1L6 exons 1 - 20 to AGO2 exons 9 - 19. The fusion is predicted to be in frame. Functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0039590-T01-IM6	TRAF7-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) - TRAF7 (NM_032271) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.2226123::chr17:g.78576760) Note: The RPTOR - TRAF7 rearrangement is a translocation with breakpoints in RPTOR intron 1 and TRAF7 exon 19. Functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0039590-T01-IM6	TRAF7-RPTOR fusion	yes	unknown		unknown	RPTOR (NM_020761) - TRAF7 (NM_032271) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.2226123::chr17:g.78576760) Note: The RPTOR - TRAF7 rearrangement is a translocation with breakpoints in RPTOR intron 1 and TRAF7 exon 19. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0039594-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: t(10;19)(q11.21;p13.2)(chr10:g.43611995::chr19:g.11067799) Note: The RET rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. An outside laboratory test identifying a KIF5B-RET fusion is noted.  This sample has been nominated for further analysis using the Archer targeted RNAseq assay to better characterize this event. Archer will be performed and reported under a separate accession number if additional material is available.
SMARCA4	0	MSKCC-DMP	P-0039627-T01-IM6	CARM1-SMARCA4 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.3774+61:SMARCA4_c.221-7710:CARM1dup Note: The SMARCA4 - CARM1 rearrangement is a duplication that results in a fusion of SMARCA4 exons 1 - 26 to CARM1 exons 2 - 16. Functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0039627-T01-IM6	CARM1-SMARCA4 fusion	yes	unknown		out of frame	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.3774+61:SMARCA4_c.221-7710:CARM1dup Note: The SMARCA4 - CARM1 rearrangement is a duplication that results in a fusion of SMARCA4 exons 1 - 26 to CARM1 exons 2 - 16. Functional significance is undetermined.
CDK8	0	MSKCC-DMP	P-0019783-T02-IM6	CDK8-intragenic	yes	unknown		unknown	CDK8 (NM_001260) rearrangement: c.1031+79:CDK8_chr13:g.30676512del Note: The CDK8 rearrangement is a deletion of exons 11 - 13. The rearrangement does not include the kinase domain of CDK8. Functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0039554-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: c.1071_c.1153+5107del Note: The PTPRT rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7.
DNMT1	0	MSKCC-DMP	P-0039569-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.1445-224_c.1721inv Note: The DNMT1 rearrangement is an intragenic inversion of exons 19 - 20. One of the breakpoints is within exon 20. In addition, multiple other structural variants involving DNMT1 were detected, which may reflect a complex rearrangement involving DNMT1 that is not fully characterized by IMPACT. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0039649-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.2017_c.2211+292del Note: The RB1 rearrangement is an intragenic deletion of exons 20 - 21. One of the breakpoints is within exon 20.
BLM	0	MSKCC-DMP	P-0039652-T01-IM6	BLM-intragenic	yes	unknown		unknown	BLM (NM_000057) rearrangement: c.2091:BLM_chr15:g.90779259del Note: The BLM rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.
EIF4A2	0	MSKCC-DMP	P-0039680-T01-IM6	EIF4A2-intragenic	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: t(3;10)(q27.3;q25.2)(chr3:g.186506982::chr10:g.113877258) Note: The EIF4A2 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0023958-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-2153:ERG_c.126+1716:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication that results in a fusion of ERG exon 1 to TMPRSS2 exons 3 - 14. The fusion is predicted to be in-frame. While this is not the canonical TMPRSS2-ERG fusion, the possibility cannot be excluded. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0023958-T02-IM6	TMPRSS2-ERG fusion	yes	unknown		in frame	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-2153:ERG_c.126+1716:TMPRSS2dup Note: The ERG - TMPRSS2 rearrangement is a duplication that results in a fusion of ERG exon 1 to TMPRSS2 exons 3 - 14. The fusion is predicted to be in-frame. While this is not the canonical TMPRSS2-ERG fusion, the possibility cannot be excluded. Its functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0039640-T01-IM6	INSR-intragenic	yes	unknown		unknown	INSR (NM_000208) rearrangement: t(5;19)(q11.2;p13.2)(chr5:g.53033886::chr19:g.7152854) Note: The INSR rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039698-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4258:TMPRSS2_c.18+3607:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0039698-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4258:TMPRSS2_c.18+3607:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
JUN	0	MSKCC-DMP	P-0035722-T02-IM6	JUN-intragenic	yes	unknown		unknown	JUN (NM_002228) rearrangement: c.826:JUN_chr1:g.61042535inv Note: The JUN rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039657-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41632313::chr21:g.42871753) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039689-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-203:TMPRSS2_c.19-1128:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0039689-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-203:TMPRSS2_c.19-1128:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
SMARCA4	0	MSKCC-DMP	P-0039805-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3215+77:SMARCA4_chr19:g.55276048inv Note: The SMARCA4 rearrangement is an inversion of exons 24 - 35. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039805-T01-IM6	TMPRSS2-intragenic	yes	unknown		in frame	TMPRSS2 (NM_001135099) rearrangement: c.56-2856_c.838+696del Note: The TMPRSS2 rearrangement is an intragenic deletion of exons 2 - 8. Multiple TMPRSS2 rearrangements were detected in this sample and a more complex rearrangement resulting in a TMPRSS2-ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PIK3R1	0	MSKCC-DMP	P-0039805-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1985+87:PIK3R1_chr5:g.67667228inv Note: The PIK3R1 rearrangement is an inversion of exon 16. Functional significance is undetermined.
ZNF532	0	MSKCC-DMP	P-0039808-T01-IM6	MALT1-ZNF532 fusion	yes	unknown		in frame	ZNF532 (NM_018181) - MALT1 (NM_006785) rearrangement: c.2868+2087:ZNF532_c.1912-112:MALT1dup Note: The ZNF532 - MALT1 rearrangement is a duplication that results in a fusion of ZNF532 exons 1 - 7 to MALT1 exons 16 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
MALT1	0	MSKCC-DMP	P-0039808-T01-IM6	MALT1-ZNF532 fusion	yes	unknown		in frame	ZNF532 (NM_018181) - MALT1 (NM_006785) rearrangement: c.2868+2087:ZNF532_c.1912-112:MALT1dup Note: The ZNF532 - MALT1 rearrangement is a duplication that results in a fusion of ZNF532 exons 1 - 7 to MALT1 exons 16 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0039808-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2282:MDC1_chr6:g.30741532inv Note: The MDC1 rearrangement is an inversion of exons 1 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.
SMIM19	0	MSKCC-DMP	P-0039478-T01-IM6	FGFR1-SMIM19 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SMIM19-FGFR1 fusion. Note: The rearrangement is a fusion between genes SMIM19 Exon1 (NM_138436) and FGFR1 Exon7 (NM_015850). Lab Notes Run Number: ArcherV3-CLIN-20190053 Macro-dissection: Unknown
FGFR1	0	MSKCC-DMP	P-0039478-T01-IM6	FGFR1-SMIM19 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SMIM19-FGFR1 fusion. Note: The rearrangement is a fusion between genes SMIM19 Exon1 (NM_138436) and FGFR1 Exon7 (NM_015850). Lab Notes Run Number: ArcherV3-CLIN-20190053 Macro-dissection: Unknown
KIF5B	0	MSKCC-DMP	P-0039594-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190053 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0039594-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190053 Macro-dissection: Unknown
DNMT1	0	MSKCC-DMP	P-0000631-T03-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.4736:DNMT1_chr19:g.14487154del Note: The DNMT1 rearrangement is a deletion of exons 1 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.
CLASP1	0	MSKCC-DMP	P-0000631-T03-IM6	INSR-CLASP1 fusion	yes	unknown		in frame	CLASP1 (NM_015282) - INSR (NM_000208) rearrangement: t(2;19)(q14.2;p13.2)(chr2:g.122236197::chr19:g.7152997) Note: The CLASP1 - INSR rearrangement is a translocation that results in a fusion of CLASP1 exons 1 - 8 to INSR exons 10 - 22. The fusion is predicted to be in frame and includes the kinase domain of INSR. Functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0000631-T03-IM6	INSR-CLASP1 fusion	yes	unknown		in frame	CLASP1 (NM_015282) - INSR (NM_000208) rearrangement: t(2;19)(q14.2;p13.2)(chr2:g.122236197::chr19:g.7152997) Note: The CLASP1 - INSR rearrangement is a translocation that results in a fusion of CLASP1 exons 1 - 8 to INSR exons 10 - 22. The fusion is predicted to be in frame and includes the kinase domain of INSR. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0000631-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2516:TMPRSS2_c.39+58475:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0000631-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2516:TMPRSS2_c.39+58475:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ELF3	0	MSKCC-DMP	P-0000631-T03-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: t(1;3)(q32.1;q24)(chr1:g.201984440::chr3:g.146132148) Note: The ELF3 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0010096-T03-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.1207_c.1282+881del Note: The ALK rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FGFR3	0	MSKCC-DMP	P-0010096-T03-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2357:FGFR3_c.1941+378:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0010096-T03-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2357:FGFR3_c.1941+378:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
DOT1L	0	MSKCC-DMP	P-0022760-T02-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4534_c.4606+847inv Note: The DOT1L rearrangement is an intragenic inversion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0039255-T02-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.116_c.1100+344del Note: The TP53 rearrangement is an intragenic deletion of exons 4 - 10. One of the breakpoints is within exon 4.
EGFR	0	MSKCC-DMP	P-0039255-T02-IM6	SEPT14-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - SEPT14 (NM_207366) fusion: c.3271+489:EGFR_c.818-3507:SEPT14inv Note: The EGFR - SEPT14 fusion involves EGFR exons 1 - 27 and SEPT14 exons 8 - 10. The fusion is predicted to be in frame and includes the kinase domain of EGFR.
SEPT14	0	MSKCC-DMP	P-0039255-T02-IM6	SEPT14-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - SEPT14 (NM_207366) fusion: c.3271+489:EGFR_c.818-3507:SEPT14inv Note: The EGFR - SEPT14 fusion involves EGFR exons 1 - 27 and SEPT14 exons 8 - 10. The fusion is predicted to be in frame and includes the kinase domain of EGFR.
CSF3R	0	MSKCC-DMP	P-0039767-T01-IM6	CSF3R-intragenic	yes	unknown		unknown	CSF3R (NM_000760) rearrangement: c.1286-39:CSF3R_chr1:g.39179138del Note: The CSF3R rearrangement is a deletion of exons 1 - 10, observed in the background of a whole gene amplification of CSF3R. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039771-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2539:TMPRSS2_c.39+64394:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0039771-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2539:TMPRSS2_c.39+64394:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
AGAP3	0	MSKCC-DMP	P-0039799-T01-IM6	BRAF-AGAP3 fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) fusion: c.1221+416:AGAP3_c.1314+504:BRAFinv Note: The AGAP3 - BRAF fusion involves AGAP3 exons 1 - 9 and BRAF exons 11 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0039799-T01-IM6	BRAF-AGAP3 fusion	yes	unknown		in frame	AGAP3 (NM_031946) - BRAF (NM_004333) fusion: c.1221+416:AGAP3_c.1314+504:BRAFinv Note: The AGAP3 - BRAF fusion involves AGAP3 exons 1 - 9 and BRAF exons 11 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BCL2L11	0	MSKCC-DMP	P-0039811-T01-IM6	BCL2L11-intragenic	yes	unknown		out of frame	BCL2L11 (NM_138621) rearrangement: c.394+1356_c.498+5499del Note: The BCL2L11 rearrangement is an intragenic deletion of exon 3.
SRC	0	MSKCC-DMP	P-0039926-T01-IM6	LMX1A-SRC fusion	yes	unknown		unknown	SRC (NM_198291) - LMX1A (NM_001174069) rearrangement: t(1;20)(q23.3;q11.23)(chr1:g.165259752::chr20:g.36014560) Note: The SRC - LMX1A rearrangement is a translocation that results in a fusion of SRC exons 1 - 5 to LMX1A exons 4 - 9. One of the breakpoints is within SRC exon 5. The fusion does not include the kinase domain of SRC. Functional significance is undetermined.
LMX1A	0	MSKCC-DMP	P-0039926-T01-IM6	LMX1A-SRC fusion	yes	unknown		unknown	SRC (NM_198291) - LMX1A (NM_001174069) rearrangement: t(1;20)(q23.3;q11.23)(chr1:g.165259752::chr20:g.36014560) Note: The SRC - LMX1A rearrangement is a translocation that results in a fusion of SRC exons 1 - 5 to LMX1A exons 4 - 9. One of the breakpoints is within SRC exon 5. The fusion does not include the kinase domain of SRC. Functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0039927-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3690-20:ARID1B_chr6:g.157631138inv Note: The ARID1B rearrangement is an inversion of exons 15 - 20. Functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0039927-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.3144+558_c.3213dup Note: The KDM6A rearrangement is an intragenic duplication of exons 21 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.
KEAP1	0	MSKCC-DMP	P-0039978-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.775_c.1325+545del Note: The KEAP1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.
NF1	0	MSKCC-DMP	P-0039980-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(8;17)(q11.21;q11.2)(chr8:g.50391945::chr17:g.29528649) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
DHX35	0	MSKCC-DMP	P-0001338-T01-IM3	TOP1-DHX35 fusion	yes	unknown		unknown	null
TOP1	0	MSKCC-DMP	P-0001338-T01-IM3	TOP1-DHX35 fusion	yes	unknown		unknown	null
ERG	0	MSKCC-DMP	P-0001697-T02-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
TMPRSS2	0	MSKCC-DMP	P-0001697-T02-IM3	TMPRSS2-ERG fusion	yes	unknown		out of frame	null
RECQL4	0	MSKCC-DMP	P-0001724-T01-IM3	MYT1-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - MYT1 (NM_004535) Translocation :   t(8;20)(q24.3;q13.33)(chr20:c.3055+13::chr8:c.1-2888) Note: RECQL4 - MYT1 translocation is a translocation event in which exons   1-17 of RECQL4 is fused to all exons of MYT1 gene. Its functional   significance is undetermined.
MYT1	0	MSKCC-DMP	P-0001724-T01-IM3	MYT1-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - MYT1 (NM_004535) Translocation :   t(8;20)(q24.3;q13.33)(chr20:c.3055+13::chr8:c.1-2888) Note: RECQL4 - MYT1 translocation is a translocation event in which exons   1-17 of RECQL4 is fused to all exons of MYT1 gene. Its functional   significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0002039-T01-IM3	RASAL2-FGFR2 fusion	yes	unknown		in frame	null
RASAL2	0	MSKCC-DMP	P-0002039-T01-IM3	RASAL2-FGFR2 fusion	yes	unknown		in frame	null
FGFR2	0	MSKCC-DMP	P-0002039-T01-IM3	TACC2-FGFR2 fusion	yes	unknown		out of frame	null
TACC2	0	MSKCC-DMP	P-0002039-T01-IM3	TACC2-FGFR2 fusion	yes	unknown		out of frame	null
NCOR1	0	MSKCC-DMP	P-0002402-T01-IM3	MPRIP-NCOR1 fusion	yes	unknown		unknown	null
MPRIP	0	MSKCC-DMP	P-0002402-T01-IM3	MPRIP-NCOR1 fusion	yes	unknown		unknown	null
ATR	0	MSKCC-DMP	P-0002407-T01-IM3	ATR-intragenic	yes	unknown		unknown	null deletion of first 3 exons
EML4	0	MSKCC-DMP	P-0002408-T01-IM3	EML4-intragenic	yes	unknown		in frame	EML4 (NM_019063) and ALK (NM_004304) inversion (13096399bp) :  EML4:c.2057-115_ALK:c.3172+274inv
ATR	0	MSKCC-DMP	P-0002469-T01-IM3	ATR-intragenic	yes	unknown		unknown	null slightly amplified but good read support
SMAD4	0	MSKCC-DMP	P-0002488-T01-IM3	SMAD4-intragenic	yes	unknown		unknown	null
RNF43	0	MSKCC-DMP	P-0002495-T01-IM3	RNF43-intragenic	yes	unknown		unknown	null
C6orf97	0	MSKCC-DMP	P-0002497-T01-IM3	ESR1-C6orf97 fusion	yes	unknown		unknown	null
ESR1	0	MSKCC-DMP	P-0002497-T01-IM3	ESR1-C6orf97 fusion	yes	unknown		unknown	null
KDM6A	0	MSKCC-DMP	P-0002499-T02-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.385-14612_c.1547dup Note: The KDM6A rearrangement is an intragenic duplication of exons 5 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.
GNA11	0	MSKCC-DMP	P-0002526-T01-IM3	GNA11-intragenic	yes	unknown		unknown	null deletion of exons 4 to 7
ROS1	0	MSKCC-DMP	P-0002877-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null Note: The CD74-ROS1 translocation is a structural rearrangement event which results in the in-frame fusion of CD74 exons 1 to 7 with ROS1 exons 34 to 43.
CD74	0	MSKCC-DMP	P-0002877-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null Note: The CD74-ROS1 translocation is a structural rearrangement event which results in the in-frame fusion of CD74 exons 1 to 7 with ROS1 exons 34 to 43.
ROS1	0	MSKCC-DMP	P-0002912-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null
CD74	0	MSKCC-DMP	P-0002912-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	null
AXL	0	MSKCC-DMP	P-0003102-T01-IM5	PSG5-AXL fusion	yes	unknown		unknown	null Note: The AXL (NM_021913) rearrangement event is an intragenic deletion which results in the deletion of exons 9-20, potentially disabling the function of the gene.
PSG5	0	MSKCC-DMP	P-0003102-T01-IM5	PSG5-AXL fusion	yes	unknown		unknown	null Note: The AXL (NM_021913) rearrangement event is an intragenic deletion which results in the deletion of exons 9-20, potentially disabling the function of the gene.
C19orf26	0	MSKCC-DMP	P-0003455-T02-IM5	STK11-C19orf26 fusion	yes	unknown		unknown	C19orf26 (NM_152769) - STK11 (NM_000455) rearrangement: c.5:C19orf26_c.1013:STK11inv The C19orf26 (NM_152769) -  STK11 (NM_000455)  rearrangement is an inversion (13019bp) that results in the fusion of C19orf26 exons 2-9 with STK11 exons 8 -9.
STK11	0	MSKCC-DMP	P-0003455-T02-IM5	STK11-C19orf26 fusion	yes	unknown		unknown	C19orf26 (NM_152769) - STK11 (NM_000455) rearrangement: c.5:C19orf26_c.1013:STK11inv The C19orf26 (NM_152769) -  STK11 (NM_000455)  rearrangement is an inversion (13019bp) that results in the fusion of C19orf26 exons 2-9 with STK11 exons 8 -9.
TP53	0	MSKCC-DMP	P-0003948-T01-IM3	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Inversion: c.993+243_g.48892577inv
TSC2	0	MSKCC-DMP	P-0004454-T01-IM5	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement : chr16:g.2088970_c.2838-64:TSC2del Note: The TSC2 (NM_000548) rearrangement event results in the deletion of TSC2 exons 1-25.
SOX17	0	MSKCC-DMP	P-0005152-T01-IM5	XKR4-SOX17 fusion	yes	unknown		out of frame	SOX17 (NM_022454) - XKR4 (NM_052898) Rearrangement: c.307+18:SOX17_c.807-118046:XKR4del SOX17 (NM_022454) - XKR4 (NM_052898) Rearrangement is a deletion that results in the fusion of exon 1 of SOX17 with exons 2-3 of XKR4. Its functional significance is undetermined.
XKR4	0	MSKCC-DMP	P-0005152-T01-IM5	XKR4-SOX17 fusion	yes	unknown		out of frame	SOX17 (NM_022454) - XKR4 (NM_052898) Rearrangement: c.307+18:SOX17_c.807-118046:XKR4del SOX17 (NM_022454) - XKR4 (NM_052898) Rearrangement is a deletion that results in the fusion of exon 1 of SOX17 with exons 2-3 of XKR4. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0005240-T01-IM5	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) Rearrangement :  c.560-2097_889+126del Note: The EGFR (NM_005228) Rearrangement results in the intragenic deletion of exon5 to exon7 . Its functional significance is undetermined.
CDK5RAP2	0	MSKCC-DMP	P-0005461-T02-IM5	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement : t(7;9)(7q34;9q33.2)(chr7:140481684::chr9:123255452) Note: The CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement event is a translocation which results in the fusion of CDK5RAP2 exon 1 to 13 to BRAF exon 11 to 18. The resulting fusion is predicted to be in-frame and includes the protein kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0005461-T02-IM5	BRAF-CDK5RAP2 fusion	yes	unknown		in frame	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement : t(7;9)(7q34;9q33.2)(chr7:140481684::chr9:123255452) Note: The CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement event is a translocation which results in the fusion of CDK5RAP2 exon 1 to 13 to BRAF exon 11 to 18. The resulting fusion is predicted to be in-frame and includes the protein kinase domain of BRAF.
KIF5B	0	MSKCC-DMP	P-0005573-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975)  Fusion (KIF5B exon15 fused with RET exon12): c.1726-860:KIF5B_c.2136+234:RETinv
RET	0	MSKCC-DMP	P-0005573-T01-IM5	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975)  Fusion (KIF5B exon15 fused with RET exon12): c.1726-860:KIF5B_c.2136+234:RETinv
BIRC3	0	MSKCC-DMP	P-0005583-T01-IM5	SIK3-BIRC3 fusion	yes	unknown		unknown	BIRC3 (NM_182962) - SIK3 (NM_025164) rearrangement: c.1159:BIRC3_ c.442+13590:SIK3del The BIRC3 (NM_182962)  rearrangement is a deletion which may result in the truncation of BIRCA3 exons 7-10. One of the breakpoints is within exon 7 of BIRCA3. The functional significance is undetermined
SIK3	0	MSKCC-DMP	P-0005583-T01-IM5	SIK3-BIRC3 fusion	yes	unknown		unknown	BIRC3 (NM_182962) - SIK3 (NM_025164) rearrangement: c.1159:BIRC3_ c.442+13590:SIK3del The BIRC3 (NM_182962)  rearrangement is a deletion which may result in the truncation of BIRCA3 exons 7-10. One of the breakpoints is within exon 7 of BIRCA3. The functional significance is undetermined
EML4	0	MSKCC-DMP	P-0005743-T02-IM5	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 with ALK exons 20-29) : c.2243-181:EML4_c.3172+658:ALKinv
ALK	0	MSKCC-DMP	P-0005743-T02-IM5	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 with ALK exons 20-29) : c.2243-181:EML4_c.3172+658:ALKinv
TMPRSS2	0	MSKCC-DMP	P-0005768-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exons 3-11) : c.56-1181:TMPRSS2_c.-150+10082:ERGdel
ERG	0	MSKCC-DMP	P-0005768-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exons 3-11) : c.56-1181:TMPRSS2_c.-150+10082:ERGdel
IRS1	0	MSKCC-DMP	P-0005868-T02-IM5	IRS1-intragenic	yes	unknown		unknown	IRS1 (NM_005544) rearrangement : t(2;9)(2q36.3;9p21.3)(chr2:g.227663341::chr9:24948307) Note: The IRS1 (NM_005544) rearrangement event is a translocation which leads to the truncation of IRS1 exon1. One of the breakpoints is within IRS1 exon1
SOX9	0	MSKCC-DMP	P-0006023-T02-IM5	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.582_c.*1399del The SOX9 (NM_000346)  rearrangement is an intragenic deletion exon 2 - 3. The breakpoints are within exon2 and the 3-UTR of SOX9. The functional significance is undetermined.
GNA11	0	MSKCC-DMP	P-0006112-T02-IM5	GNA11-intragenic	yes	unknown		unknown	GNA11 (NM_002067) rearrangement: c.506:GNA11_chr19:g.4560347del The GNA11 (NM_002067) rearrangement is a deletion that results in the truncation of GNA11 exons 4-8. One of the breakpoints is within exon 4 of GNA11. The functional significance is undetermined.
RAB11FIP1	0	MSKCC-DMP	P-0006646-T01-IM5	FGFR1-RAB11FIP1 fusion	yes	unknown		unknown	RAB11FIP1 (NM_001002814) - FGFR1 (NM_001174067) rearrangement : c.2027:RAB11FIP1_c.1378-65:FGFR1dup Note: The RAB11FIP1 (NM_001002814) - FGFR1 (NM_001174067) rearrangement event is a duplication which results in the fusion of RAB11FIP1 exons 1-4 with FGFR1 exons 11-19. One of the breakpoints is within RAB11FIP1 exon4.
FGFR1	0	MSKCC-DMP	P-0006646-T01-IM5	FGFR1-RAB11FIP1 fusion	yes	unknown		unknown	RAB11FIP1 (NM_001002814) - FGFR1 (NM_001174067) rearrangement : c.2027:RAB11FIP1_c.1378-65:FGFR1dup Note: The RAB11FIP1 (NM_001002814) - FGFR1 (NM_001174067) rearrangement event is a duplication which results in the fusion of RAB11FIP1 exons 1-4 with FGFR1 exons 11-19. One of the breakpoints is within RAB11FIP1 exon4.
APC	0	MSKCC-DMP	P-0006681-T01-IM5	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement : c.1958+1186_977del Note: The APC (NM_000038) rearrangement event affects of APC exon16 splice site.
TMPRSS2	0	MSKCC-DMP	P-0007078-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2 to 10): c.55+4786G_c.19-20913del
ERG	0	MSKCC-DMP	P-0007078-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2 to 10): c.55+4786G_c.19-20913del
SMAD2	0	MSKCC-DMP	P-0007664-T01-IM5	SMAD2-intragenic	yes	unknown		in frame	SMAD2 (NM_001003652) rearrangement: c.520+88_c.731-2898del The SMAD2 (NM_001003652) rearrangement is an intragenic deletion of exons 5-6. The functional significance is undetermined
AKAP11	0	MSKCC-DMP	P-0007669-T01-IM5	FH-AKAP11 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241661295::chr13:g.42830622 ) The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0007669-T01-IM5	FH-AKAP11 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241661295::chr13:g.42830622 ) The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.
COL1A2	0	MSKCC-DMP	P-0007669-T01-IM5	FH-COL1A2 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;7(q43;q22.31)(chr1:g.241661124::chr7:g.94032373  ) The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0007669-T01-IM5	FH-COL1A2 fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: t(1;7(q43;q22.31)(chr1:g.241661124::chr7:g.94032373  ) The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.
LMNA	0	MSKCC-DMP	P-0007739-T01-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exons 1-8 fused to NTRK1 exons 12-17):  c.1443:LMNA_c.1354+235:NTRK1 Note: The LMNA (NM_170707) - NTRK1 (NM_002529) Fusion includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0007739-T01-IM5	NTRK1-LMNA fusion	yes	unknown		unknown	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exons 1-8 fused to NTRK1 exons 12-17):  c.1443:LMNA_c.1354+235:NTRK1 Note: The LMNA (NM_170707) - NTRK1 (NM_002529) Fusion includes the kinase domain of NTRK1.
FOXP1	0	MSKCC-DMP	P-0007883-T01-IM5	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement : chr3:g.71594017_c.1652+403:FOXP1del Note: The FOXP1 (NM_001244814) rearrangement event results in the deletion of FOXP1 exons 1-14.
BARD1	0	MSKCC-DMP	P-0008308-T01-IM5	BARD1-intragenic	yes	unknown		unknown	BARD1 (NM_000465) rearrangement: chr2:g.215687909_c.255del The BARD1 (NM_000465) rearrangement is a deletion of BARD1 exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.
IP6K1	0	MSKCC-DMP	P-0008488-T02-IM5	MST1R-IP6K1 fusion	yes	unknown		unknown	IP6K1 (NM_153273) - MST1R (NM_002447) rearrangement: c.-128-18075:IP6K1_c.2003:MST1Rdup The IP6K1 (NM_153273) - MST1R (NM_002447) rearrangement is a duplication which leads to the fusion of IP6K1 exon1  with MST1R exons 6-20. One of the breakpoints is within exon 6 of MST1R. The functional significance is undetermined.
MST1R	0	MSKCC-DMP	P-0008488-T02-IM5	MST1R-IP6K1 fusion	yes	unknown		unknown	IP6K1 (NM_153273) - MST1R (NM_002447) rearrangement: c.-128-18075:IP6K1_c.2003:MST1Rdup The IP6K1 (NM_153273) - MST1R (NM_002447) rearrangement is a duplication which leads to the fusion of IP6K1 exon1  with MST1R exons 6-20. One of the breakpoints is within exon 6 of MST1R. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0008536-T02-IM5	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.582+234_c.896del Note: The RNF43 (NM_017763) rearrangement is an intrangenic deletion of exons 6-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0008769-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.56-2251:TMPRSS2_c.40-34826:ERGdel
ERG	0	MSKCC-DMP	P-0008769-T02-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.56-2251:TMPRSS2_c.40-34826:ERGdel
ETV6	0	MSKCC-DMP	P-0009324-T02-IM5	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) Rearrangement :  c.464-1400_chr12:g.12149453del Note: The ETV6 (NM_001987) Rearrangement  results in the intragenic deletion of exons 5-8 of ETV6.Its functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0009402-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1137+5027_c.5984dup Note: The ARID1A rearrangement is an intragenic duplication of exons 2-20. One of the breakpoints is within exon 20.
APC	0	MSKCC-DMP	P-0009741-T01-IM5	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4583_c.6030del Note: The APC (NM_000038) rearrangement is a deletion within APC exon 16.
EPHA5	0	MSKCC-DMP	P-0014014-T01-IM5	EPHA5-intragenic	yes	unknown		unknown	EPHA5 (NM_004439) rearrangement: c.181+9039_c.172inv Note: The EPHA5 (NM_004439) rearrangement is an inversion of EPHA5 exon 1. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0028935-T02-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.454+142_chr18:g.48625572del Note: The SMAD4 rearrangement is a deletion that includes SMAD4 exons 5-12.
KMT2A	0	MSKCC-DMP	P-0030874-T01-IM6	TMPRSS4-KMT2A fusion	yes	unknown		unknown	KMT2A (NM_001197104) - TMPRSS4 (NM_019894) rearrangement: c.2177:KMT2A_c.441-574:TMPRSS4dup Note: The KMT2A - TMPRSS4 rearrangement is a duplication that results in the fusion of KMT2A exons 1-3 with TMPRSS4 exons 6-13. One of the breakpoints is within KMT2A exon 3. The functional significance is undetermined.
TMPRSS4	0	MSKCC-DMP	P-0030874-T01-IM6	TMPRSS4-KMT2A fusion	yes	unknown		unknown	KMT2A (NM_001197104) - TMPRSS4 (NM_019894) rearrangement: c.2177:KMT2A_c.441-574:TMPRSS4dup Note: The KMT2A - TMPRSS4 rearrangement is a duplication that results in the fusion of KMT2A exons 1-3 with TMPRSS4 exons 6-13. One of the breakpoints is within KMT2A exon 3. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0033700-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1454:KIF5B_c.2137-362:RET Note: The KIF5B - RET rearrangement is an inversion which results in the fusion of KIF5B exons 1-15 with RET exons 12-20. This includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0033700-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1454:KIF5B_c.2137-362:RET Note: The KIF5B - RET rearrangement is an inversion which results in the fusion of KIF5B exons 1-15 with RET exons 12-20. This includes the kinase domain of RET.
JAK3	0	MSKCC-DMP	P-0033700-T02-IM6	JAK3-intragenic	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: c.1702-146:JAK3_chr19:g.10451444inv Note: The JAK3 rearrangement is an inversion of exons 14-24. Its functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0033700-T02-IM6	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.1130_c.1644-728del Note: The MAP3K12 rearrangement is an intragenic deletion of exons 6-10. One of the breakpoints is within exon 6. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034079-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2177:TMPRSS2_c.39+60313:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and includes the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0034079-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2177:TMPRSS2_c.39+60313:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and includes the non-canonical ERG transcript.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0034112-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.180_c.*1508del Note: The CDKN2Ap16INK4A  Rearrangement results in the deletion of exons 2-3 of CDKN2Ap16INK4A . One of the breakpoints is within exon2. This rearrangement affects both the isoforms of CDKN2A.
FLCN	0	MSKCC-DMP	P-0034144-T01-IM6	FLCN-intragenic	yes	unknown		unknown	FLCN (NM_144997) rearrangement: c.230:FLCN_chr17:g.14246021del Note: The FLCN rearrangement is a deletion of exons 4-14. One of the breakpoints is within exon 4. The functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0034357-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-845:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0034357-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-845:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0034357-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: t(10;20)(q11.21;p13)(chr10:g.43611134::chr20:g.456852) Note: The RET rearrangement is a translocation with a breakpoint in intron 11. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0034357-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: c.355-36:RECQL4_chr8:g.121672884inv Note: The RECQL4 rearrangement results in the inversion of exons 5-22. The functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0034373-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) Rearrangement: c.143:CDKN2A_chr9:g.25710229del Note: The CDKN2A rearrangement is an inversion of exon 1 of CDKN2A. One of the breakpoints is within exon1 of CDKN2A. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0034383-T01-IM6	BCAS3-PPM1D fusion	yes	unknown		out of frame	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.1017+49:PPM1D_c.2470+111086:BCAS3del Note: The PPM1D - BCAS3 rearrangement is a deletion which results in the fusion of PPM1D exons 1-4 with BCAS3 exons 24-25. Its functional significance is undetermined.
BCAS3	0	MSKCC-DMP	P-0034383-T01-IM6	BCAS3-PPM1D fusion	yes	unknown		out of frame	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.1017+49:PPM1D_c.2470+111086:BCAS3del Note: The PPM1D - BCAS3 rearrangement is a deletion which results in the fusion of PPM1D exons 1-4 with BCAS3 exons 24-25. Its functional significance is undetermined.
NUP93	0	MSKCC-DMP	P-0034425-T01-IM6	NUP93-intragenic	yes	unknown		unknown	NUP93 (NM_014669 ) Rearrangement: c.1910:NUP93_chr16:g.54859823del Note: The NUP93 rearrangement results in the deletion of exons 1-18. One of the breakpoints is within exon 18 . The functional significance is undetermined.
ERRFI1	0	MSKCC-DMP	P-0034441-T01-IM6	ERRFI1-intragenic	yes	unknown		unknown	ERRFI1 (NM_018948) Rearrangement : c.276:ERRFI1_chr1:g.8348413inv Note: The ERRFI1 Rearrangement results in the inversion of exons 1-4 of ERRFI1. One of the breakpoints is within ERRFI1. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0034441-T01-IM6	EWSR1-intragenic	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : t(20;22)(q13.1;q13.1)(chr20:g.51121822::chr22:g.29685243) Note: The EWSR1 Rearrangement is a translocation event with a breakpoint in intron9. Its functional significance is undetermined.
RHOA	0	MSKCC-DMP	P-0034441-T01-IM6	RHOA-intragenic	yes	unknown		unknown	RHOA (NM_001664) Rearrangement : c.-2-16935_c.305del Note: The RHOA Rearrangement results in the intragenic deletion of exons 1-4. The breakpoints are in the 5-UTR region before the transcription start site (TSS)  and exon4 respectively. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034518-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41636514::chr21:g.:42872555) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint within intron 1. The functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0034538-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) Rearrangement : c.253-6871_c.2309-7inv Note: The RNF43 Rearrangement results in the inversion of exons 3-9 of RNF43. Its functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0034538-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) Rearrangement :c.3610:KDM6A_c.188-759:EGFL6inv Note: The KDM6A Rearrangement results in the inversion of exons 1-25 of KDM6A. The breakpoint in KDM6A is within exon 25. Its functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0034557-T01-IM6	IGF1R-intragenic	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: c.3331:IGF1R_chr15:g.99580663dup Note: The IGF1R rearrangement results in the duplication of exons 18-21. One of the breakpoints is within exon 18. The functional significance is undetermined.
MPL	0	MSKCC-DMP	P-0034557-T01-IM6	MPL-intragenic	yes	unknown		unknown	MPL (NM_005373) rearrangement: t(1;8)(p34.2;q24.13)(chr1:g.43803867::chr8:g.124117761) Note: The MPL rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0034557-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.4169:PREX2_chr8:g.141637481dup Note: The PREX2 rearrangement results in the duplication of exons 34-40. One of the breakpoints is within exon 34. The functional significance is undetermined.
ABCC2	0	MSKCC-DMP	P-0034621-T01-IM6	BRAF-ABCC2 fusion	yes	unknown		unknown	ABCC2 (NM_000392) - BRAF (NM_004333) rearrangement: t(7;10)(q34;24.2)(chr7:g.140495500::chr10:g.101559038) Note: The ABCC2 - BRAF rearrangement is a translocation which may form a fusion of ABCC2 exons 1-8 with BRAF exons 8-18. One of the breakpoints is within ABCC2 exon 8. This includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0034621-T01-IM6	BRAF-ABCC2 fusion	yes	unknown		unknown	ABCC2 (NM_000392) - BRAF (NM_004333) rearrangement: t(7;10)(q34;24.2)(chr7:g.140495500::chr10:g.101559038) Note: The ABCC2 - BRAF rearrangement is a translocation which may form a fusion of ABCC2 exons 1-8 with BRAF exons 8-18. One of the breakpoints is within ABCC2 exon 8. This includes the kinase domain of BRAF.
ARID2	0	MSKCC-DMP	P-0034631-T01-IM6	SLC2A13-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) - SLC2A13 (NM_052885) rearrangement: c.1029:ARID2_c.925+4537:SLC2A13inv Note: The ARID2 - SLC2A13 rearrangement is an inversion which results in the fusion of ARID2 exons 1-9 with SLC2A13 exons 4-10. Its functional significance is undetermined.
SLC2A13	0	MSKCC-DMP	P-0034631-T01-IM6	SLC2A13-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) - SLC2A13 (NM_052885) rearrangement: c.1029:ARID2_c.925+4537:SLC2A13inv Note: The ARID2 - SLC2A13 rearrangement is an inversion which results in the fusion of ARID2 exons 1-9 with SLC2A13 exons 4-10. Its functional significance is undetermined.
EGFL7	0	MSKCC-DMP	P-0034631-T01-IM6	EGFL7-intragenic	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: t(9;12)(q34.3;q14.1)(chr9:g.139565498::chr12:g.58414208) Note: The EGFL7 rearrangement is a translocation involving exon 7. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0034642-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(q21.3;p13.2)(chr1:g.152184933::chr19:g.10271012) Note: The DNMT1 rearrangement is a translocation with a breakpoint in intron 13. The functional significance is undetermined.
SLC25A21	0	MSKCC-DMP	P-0034676-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21(NM_030631) -  FOXA1 (NM_004496) rearrangement: c.70+58700:SLC25A21_c.176:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication which results in the fusion of SLC25A21 exon 1 with FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. Its functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0034676-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21(NM_030631) -  FOXA1 (NM_004496) rearrangement: c.70+58700:SLC25A21_c.176:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication which results in the fusion of SLC25A21 exon 1 with FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034686-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon1) : c.55+4815:TMPRSS2_c.40-59886:ERGdel Note: The fusion includes the non-canonical transcript of ERG.
ERG	0	MSKCC-DMP	P-0034686-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon1) : c.55+4815:TMPRSS2_c.40-59886:ERGdel Note: The fusion includes the non-canonical transcript of ERG.
APC	0	MSKCC-DMP	P-0034694-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.8002:APC_chr5:g.20611790inv Note: The APC rearrangement is an inversion of exons 1-16. One of the breakpoints is within exon 16.
GRIPAP1	0	MSKCC-DMP	P-0034781-T01-IM6	RET-GRIPAP1 fusion	yes	unknown		in frame	GRIPAP1 (NM_020137) - RET (NM_020975) rearrangement: t(X;10)(p11.23q11.21)(chrX:g.48831008::chr10:g.43611853) Note: The GRIPAP1 - RET rearrangement is a translocation which may result in the fusion of GRIPAP1 exons 1-25 with RET exons 12-20. This includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0034781-T01-IM6	RET-GRIPAP1 fusion	yes	unknown		in frame	GRIPAP1 (NM_020137) - RET (NM_020975) rearrangement: t(X;10)(p11.23q11.21)(chrX:g.48831008::chr10:g.43611853) Note: The GRIPAP1 - RET rearrangement is a translocation which may result in the fusion of GRIPAP1 exons 1-25 with RET exons 12-20. This includes the kinase domain of RET.
FUBP1	0	MSKCC-DMP	P-0034816-T01-IM6	FUBP1-intragenic	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.1926+106:FUBP1_chr1:g.78156523del Note: The FUBP1 rearrangement results in the deletion of exon 20. The functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0034816-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(16;17)(p13.3;p13.1)(chr16:g.2133763::chr17:g.7043177) Note: The TSC2 rearrangement is a translocation with a breakpoint in exon 33. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0034816-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3844:ALK_chr2:g.28665721dup Note: The ALK rearrangement results in the duplication of exons 26-29. One of the breakpoints is within exon 26. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0034816-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: t(1;3)(q42.11;p21.1)(chr1:g.224289787::chr3:g.52668594) Note: The PBRM1 rearrangement is a translocation with a breakpoint in intron 12. Multiple PBRM1 rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative platform is recommended, if clinically indicated. The functional significance is undetermined.
STK38	0	MSKCC-DMP	P-0034816-T01-IM6	MDC1-STK38 fusion	yes	unknown		unknown	STK38 (NM_007271) - MDC1 (NM_014641) rearrangement: c.835-1890:STK38_c.6230:MDC1del Note: The STK38 - MDC1 rearrangement is a deletion that results in the fusion of STK38 exons 1-10 with MDC1 exon 15. One of the breakpoints is within MDC1 exon 15. The functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0034816-T01-IM6	MDC1-STK38 fusion	yes	unknown		unknown	STK38 (NM_007271) - MDC1 (NM_014641) rearrangement: c.835-1890:STK38_c.6230:MDC1del Note: The STK38 - MDC1 rearrangement is a deletion that results in the fusion of STK38 exons 1-10 with MDC1 exon 15. One of the breakpoints is within MDC1 exon 15. The functional significance is undetermined.
GNA11	0	MSKCC-DMP	P-0034818-T01-IM6	GNA11-intragenic	yes	unknown		unknown	GNA11 (NM_002067) rearrangement: t(6;19)(q22.31;p13.3)(chr6:g.122459052::chr19:g.3119247) Note: The GNA11 rearrangement is a translocation with a breakpoint in exon 6. The functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0034818-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.3221:NOTCH1_chr9:g.140014051dup Note: The NOTCH1 rearrangement results in the duplication of exons 1-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
SHOC2	0	MSKCC-DMP	P-0034877-T01-IM6	TSC22D1-SHOC2 fusion	yes	unknown		unknown	SHOC2 (NM_007373) - TSC22D1 (NM_183422) rearrangement: t(10;13)(q25.2;q14.11)(chr10:g.112769116::chr13:g.45064416) Note: The SHOC2 - TSC22D1 rearrangement is a translocation that results in the fusion of SHOC2 exons 1-7 with TSC22D1 exons 2-3. One of the breakpoints is within SHOC2 exon 7. The functional significance is undetermined.
TSC22D1	0	MSKCC-DMP	P-0034877-T01-IM6	TSC22D1-SHOC2 fusion	yes	unknown		unknown	SHOC2 (NM_007373) - TSC22D1 (NM_183422) rearrangement: t(10;13)(q25.2;q14.11)(chr10:g.112769116::chr13:g.45064416) Note: The SHOC2 - TSC22D1 rearrangement is a translocation that results in the fusion of SHOC2 exons 1-7 with TSC22D1 exons 2-3. One of the breakpoints is within SHOC2 exon 7. The functional significance is undetermined.
HOOK3	0	MSKCC-DMP	P-0034900-T01-IM6	RPS6KB2-HOOK3 fusion	yes	unknown		out of frame	HOOK3 (NM_032410) - RPS6KB2 (NM_003952) rearrangement: t(8;11)(p11.21;q13.2)(chr8:g.42762715::chr11:g.67198652) Note: The HOOK3 - RPS6KB2 rearrangement is a translocation that results in the fusion of HOOK3  exons 1-2 with RPS6KB2 exons 5-15. The functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0034900-T01-IM6	RPS6KB2-HOOK3 fusion	yes	unknown		out of frame	HOOK3 (NM_032410) - RPS6KB2 (NM_003952) rearrangement: t(8;11)(p11.21;q13.2)(chr8:g.42762715::chr11:g.67198652) Note: The HOOK3 - RPS6KB2 rearrangement is a translocation that results in the fusion of HOOK3  exons 1-2 with RPS6KB2 exons 5-15. The functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0034901-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.1983+3:BAP1_chr3:g.52406605del Note: The BAP1 rearrangement results in the deletion of exons 16-17. The functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0034944-T01-IM6	STAT5A-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) - STAT5A (NM_003152) rearrangement: c.1050-680:STAT3_c.2191:STAT5Ainv Note: The STAT3 - STAT5A rearrangement is an inversion that results in the fusion of STAT3 exons 1-10 with STAT5A exons 19-20. One of the breakpoints is within STAT5A  exon 19. The functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0034944-T01-IM6	STAT5A-STAT3 fusion	yes	unknown		unknown	STAT3 (NM_139276) - STAT5A (NM_003152) rearrangement: c.1050-680:STAT3_c.2191:STAT5Ainv Note: The STAT3 - STAT5A rearrangement is an inversion that results in the fusion of STAT3 exons 1-10 with STAT5A exons 19-20. One of the breakpoints is within STAT5A  exon 19. The functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0039719-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: c.2740-3697_c.4037del Note: The PTPRT rearrangement is an intragenic deletion of exons 19 - 30. One of the breakpoints is within exon 30.
GRIPAP1	0	MSKCC-DMP	P-0034781-T01-IM6	RET-GRIPAP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GRIPAP1-RET fusion. Note: The rearrangement is an in-frame fusion between genes GRIPAP1 Exon25 (NM_020137) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20180156 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0034781-T01-IM6	RET-GRIPAP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: GRIPAP1-RET fusion. Note: The rearrangement is an in-frame fusion between genes GRIPAP1 Exon25 (NM_020137) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20180156 Macro-dissection: Unknown
AR	0	MSKCC-DMP	P-0034944-T01-IM6	AR-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20180161 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0039657-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ETV4 fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ETV4 Exon3 (NM_001986). Lab Notes Run Number: Archerv3-CLIN-20190056 Macro-dissection: Unknown
ETV4	0	MSKCC-DMP	P-0039657-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ETV4 fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ETV4 Exon3 (NM_001986). Lab Notes Run Number: Archerv3-CLIN-20190056 Macro-dissection: Unknown
AGAP3	0	MSKCC-DMP	P-0039799-T01-IM6	BRAF-AGAP3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AGAP3-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AGAP3 Exon9 (NM_031946) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190057 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0039799-T01-IM6	BRAF-AGAP3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: AGAP3-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AGAP3 Exon9 (NM_031946) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190057 Macro-dissection: Unknown
KMT2A	0	MSKCC-DMP	P-0022198-T03-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.552:KMT2A_chr11:g.114253339inv Note: The KMT2A rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
CCDC6	0	MSKCC-DMP	P-0036379-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+26500:CCDC6_c.2137-614:RETinv Note: The CCDC6 - RET fusion is a reciprocal inversion and is predicted to be in frame. The fusion involves CCDC6 exon 1 and RET exons 12-20, which include RET kinase domain.
RET	0	MSKCC-DMP	P-0036379-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+26500:CCDC6_c.2137-614:RETinv Note: The CCDC6 - RET fusion is a reciprocal inversion and is predicted to be in frame. The fusion involves CCDC6 exon 1 and RET exons 12-20, which include RET kinase domain.
KIF5B	0	MSKCC-DMP	P-0036637-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1726-1731:KIF5B_c.2137-67:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0036637-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1726-1731:KIF5B_c.2137-67:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
KIF5B	0	MSKCC-DMP	P-0036737-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1487:KIF5B_c.2137-7:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0036737-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1487:KIF5B_c.2137-7:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
DNMT3B	0	MSKCC-DMP	P-0036737-T02-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892): Rearrangement: c.2102:DNMT3B_chr20:g.30803463inv Note: The DNMT3B rearrangement results in the inversion of exons 1-19. One of the breakpoints is within exon 19 of DNMT3B. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0037367-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1038:KIF5B_c.2137-158:RETinv Note: The KIF5B - RET rearrangement is an inversion which results in a fusion of KIF5B exons 1-15 with RET exons 12-20. This includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0037367-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1038:KIF5B_c.2137-158:RETinv Note: The KIF5B - RET rearrangement is an inversion which results in a fusion of KIF5B exons 1-15 with RET exons 12-20. This includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0037412-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-11974:CCDC6_c.2136+655:RETinv Note: the CCDC6 - RET rearrangement is an inversion which results in the fusion of CCDC6 exon 1 with RET exons 12-20. This includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0037412-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-11974:CCDC6_c.2136+655:RETinv Note: the CCDC6 - RET rearrangement is an inversion which results in the fusion of CCDC6 exon 1 with RET exons 12-20. This includes the kinase domain of RET.
KIF5B	0	MSKCC-DMP	P-0037494-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) Fusion (KIF5B exon15 fused with RET exon12 ): c.1725+985:KIF5B_c.2137-277:RETinv Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET
RET	0	MSKCC-DMP	P-0037494-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) Fusion (KIF5B exon15 fused with RET exon12 ): c.1725+985:KIF5B_c.2137-277:RETinv Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET
APC	0	MSKCC-DMP	P-0037494-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement: c.2042:APC_c.-1221:SRP19del Note: The APC-SRP19 Rearrangement results in the fusion of exons 1-16 of APC with the promoter region of SRP19. The breakpoint in APC is within exon16. Its functional significance is undetermined.
SRP19	0	MSKCC-DMP	P-0037494-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement: c.2042:APC_c.-1221:SRP19del Note: The APC-SRP19 Rearrangement results in the fusion of exons 1-16 of APC with the promoter region of SRP19. The breakpoint in APC is within exon16. Its functional significance is undetermined.
NCOA4	0	MSKCC-DMP	P-0037961-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) rearrangement: c.763-360:NCOA4_c.2137-584:RETdup The NCOA4 - RET rearrangement is a duplication that results in a fusion of NCOA4 exons 1 - 6 to RET exons 12 - 20. The fusion includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0037961-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) rearrangement: c.763-360:NCOA4_c.2137-584:RETdup The NCOA4 - RET rearrangement is a duplication that results in a fusion of NCOA4 exons 1 - 6 to RET exons 12 - 20. The fusion includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0038257-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6(NM_005436 ) - RET (NM_020975.4) Fusion (CCDC6 exon1 fused with RET exon12):c.304-2131:CCDC6_c.2136+410:RETinv Note: The CCDC6-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0038257-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6(NM_005436 ) - RET (NM_020975.4) Fusion (CCDC6 exon1 fused with RET exon12):c.304-2131:CCDC6_c.2136+410:RETinv Note: The CCDC6-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET.
NCOA4	0	MSKCC-DMP	P-0038315-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.763-415:NCOA4_c.2137-51:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0038315-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.763-415:NCOA4_c.2137-51:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
CCDC6	0	MSKCC-DMP	P-0039548-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-9501:CCDC6_c.2136+659:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0039548-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-9501:CCDC6_c.2136+659:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
MRE11A	0	MSKCC-DMP	P-0039881-T01-IM6	MRE11A-intragenic	yes	unknown		unknown	MRE11A (NM_005591) rearrangement: c.660-14_c.870inv Note: The MRE11A rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 9. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039881-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-4590:TMPRSS2_chr21:g.43413131del Note: The TMPRSS2 rearrangement is a deletion of exon 1. Functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0039883-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.5215_c.5320-357dup Note: The ATM rearrangement is an intragenic duplication of exon 35. One of the breakpoints is within exon 35. Functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0040077-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.3656-80:NOTCH2_chr1:g.222057559del Note: The NOTCH2 rearrangement is a deletion of exons 1 - 22.
NCOA3	0	MSKCC-DMP	P-0040081-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.2512+178:NCOA3_chr20:g.41905066inv Note: The NCOA3 rearrangement is an inversion of exons 1 - 13. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0040082-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.4092+972_c.5654inv Note: The KMT2C rearrangement is an intragenic inversion of exons 27 - 36. One of the breakpoints is within exon 36. Functional significance is undetermined.
NCOA4	0	MSKCC-DMP	P-0037961-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon7 (NM_001145262) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190024 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0037961-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon7 (NM_001145262) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190024 Macro-dissection: Unknown
CDKN2A	0	MSKCC-DMP	P-0040019-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.348:CDKN2A_chr9:g.21951523del Note: The CDKN2A rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
CASP8	0	MSKCC-DMP	P-0040184-T01-IM6	CASP8-intragenic	yes	unknown		unknown	CASP8 (NM_001080125) rearrangement: c.313:CASP8_chr2:g.202186808del Note: The CASP8 rearrangement is a deletion of exons 2 - 9. One of the breakpoints is within exon 2.
SPEN	0	MSKCC-DMP	P-0040055-T01-IM6	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.10057:SPEN_chr1:g.16281610del Note: The SPEN rearrangement is a deletion of exons 12 - 15. One of the breakpoints is within exon 12.
ANKRD11	0	MSKCC-DMP	P-0040116-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.227-170:ANKRD11_chr16:g.89434071del Note: The ANKRD11 rearrangement is a deletion of exons 1 - 4.
EGFR	0	MSKCC-DMP	P-0040116-T01-IM6	EGFR-intragenic	yes	unknown		out of frame	EGFR (NM_005228) rearrangement: c.1007-89_c.1723-158dup Note: The EGFR rearrangement is an intragenic duplication of exons 9 - 14. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving EGFR is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
AKT2	0	MSKCC-DMP	P-0040118-T01-IM6	AKT2-intragenic	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: c.200_c.287+4668inv Note: The AKT2 rearrangement is an intragenic inversion of exon 4. One of the breakpoints is within exon 4. The rearrangement does not include the kinase domain of AKT2. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0040193-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+281:ALK_chr2:g.31931590del Note: The ALK rearrangement is a deletion of exons 1 - 19. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
EGFR	0	MSKCC-DMP	P-0040338-T01-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.1298+174_c.1919+406del Note: The EGFR rearrangement is an intragenic deletion of exons 12 - 16. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined.
F11R	0	MSKCC-DMP	P-0014896-T02-IM6	NRG1-F11R fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: F11R-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes F11R Exon1 (NM_016946) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: Archerv3-CLIN-20190060 Macro-dissection: Not Performed
NRG1	0	MSKCC-DMP	P-0014896-T02-IM6	NRG1-F11R fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: F11R-NRG1 fusion. Note: The rearrangement is an in-frame fusion between genes F11R Exon1 (NM_016946) and NRG1 Exon6 (NM_004495). Lab Notes Run Number: Archerv3-CLIN-20190060 Macro-dissection: Not Performed
SETD4	0	MSKCC-DMP	P-0006603-T01-IM5	TMPRSS2-SETD4 fusion	yes	unknown		out of frame	SETD4 (NM_017438) - TMPRSS2 (NM_001135099) rearrangement: c.169+807:SETD4_c.126+629:TMPRSS2del The SETD4 (NM_017438) - TMPRSS2 (NM_001135099) rearrangement is a deletion that results in the out of frame fusion of SETD4 exons 1-3 with TMPRSS2 exons 3-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0006603-T01-IM5	TMPRSS2-SETD4 fusion	yes	unknown		out of frame	SETD4 (NM_017438) - TMPRSS2 (NM_001135099) rearrangement: c.169+807:SETD4_c.126+629:TMPRSS2del The SETD4 (NM_017438) - TMPRSS2 (NM_001135099) rearrangement is a deletion that results in the out of frame fusion of SETD4 exons 1-3 with TMPRSS2 exons 3-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0006603-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+554:TMPRSS2_c.40-2798:ERGdel
ERG	0	MSKCC-DMP	P-0006603-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+554:TMPRSS2_c.40-2798:ERGdel
NOTCH4	0	MSKCC-DMP	P-0032012-T01-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.1625-5:NOTCH4_chr6:g.58776688del Note: The NOTCH4 rearrangement results in the deletion of exons 1-9. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0032050-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.1977:PIK3CD_chr1:g.10019018inv Note: The PIK3CD rearrangement results in the inversion of exons 16-24. One of the breakpoints is within exon 16. The functional significance is undetermined. This structural variant was observed in addition to other rearrangements involving PIK3CD, suggesting a complex event that may not be fully characterized by the IMPACT assay.
KMT2D	0	MSKCC-DMP	P-0032068-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) Rearrangement: c.8644:KMT2D_chr12:g.72507173inv Note: The KMT2D rearrangement results in the inversion of exons 1-34. One of the breakpoints is within exon 34 of KMT2D. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0032152-T01-IM6	KIAA1598-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1598 (NM_001127211) fusion: c.2301+1699:FGFR2_c.534+751:KIAA1598 Note: The FGFR2 - KIAA1598 fusion is predicted to be in-frame fusion and involves FGFR2 exons 1-17, which includes the protein kinase domain, and KIAA1598 exons 7-17.
KIAA1598	0	MSKCC-DMP	P-0032152-T01-IM6	KIAA1598-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1598 (NM_001127211) fusion: c.2301+1699:FGFR2_c.534+751:KIAA1598 Note: The FGFR2 - KIAA1598 fusion is predicted to be in-frame fusion and involves FGFR2 exons 1-17, which includes the protein kinase domain, and KIAA1598 exons 7-17.
MGA	0	MSKCC-DMP	P-0032152-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_00116427) rearrangement: c.7191+105:MGA_chr15:g.42229443del Note: The MGA rearrangement is a deletion of exons 20-24.
DROSHA	0	MSKCC-DMP	P-0032152-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;16)(p13.3;p11.2)(chr5:g.31424707::chr16:g.34383454) Note: The DROSHA rearrangement is a translocation with a breakpoint in intron 26. The functional significance is undetermined.
NRAS	0	MSKCC-DMP	P-0032155-T01-IM6	NRAS-intragenic	yes	unknown		unknown	NRAS (NM_002524) rearrangement: c.290+1223_c.397inv Note: The NRAS rearrangement is an intragenic inversion of a part of exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0032187-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) Rearrangement:  c.106_c.46-2233del Note: The NFE2L2 rearrangement results in the intragenic deletion of NFE2L2 exon 2. One of the breakpoints is within exon 2 of NFE2L2. The functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0032187-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) Rearrangement: t(3;5)(p21.3;p14.3)(chr3:g.41277838::chr5:g.20450107) Note: The ctnnb1 rearrangement is a translocation with breakpoints in intron 11 of CTNNB1 and an intergenic region on chr5
KIF5B	0	MSKCC-DMP	P-0032227-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2000:KIF5B_c.2137-907:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
RET	0	MSKCC-DMP	P-0032227-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2000:KIF5B_c.2137-907:RETinv Note: The KIF5B-RET fusion involves KIF5B exons 1-15 and RET exons 12-20. The fusion is predicted to be in-frame and includes the protein kinase domain of RET.
CRTC3	0	MSKCC-DMP	P-0040143-T01-IM6	BLM-CRTC3 fusion	yes	unknown		unknown	CRTC3 (NM_022769) - BLM (NM_000057) rearrangement: c.578-1669:CRTC3_c.3433:BLMdel Note: The CRTC3 - BLM rearrangement is a deletion that results in a fusion of CRTC3 exons 1 - 6 to BLM exons 18 - 22. One of the breakpoints is within BLM exon 18.
BLM	0	MSKCC-DMP	P-0040143-T01-IM6	BLM-CRTC3 fusion	yes	unknown		unknown	CRTC3 (NM_022769) - BLM (NM_000057) rearrangement: c.578-1669:CRTC3_c.3433:BLMdel Note: The CRTC3 - BLM rearrangement is a deletion that results in a fusion of CRTC3 exons 1 - 6 to BLM exons 18 - 22. One of the breakpoints is within BLM exon 18.
ROS1	0	MSKCC-DMP	P-0040134-T01-IM6	ROS1-intragenic	yes	unknown		out of frame	ROS1 (NM_002944) rearrangement: t(1;6)(q21.3;q22.1)(chr1:g.154135115::chr6:g.117647954) Note: The ROS1 rearrangement is a translocation with a breakpoint in intron 32. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ROS1 is recommended.
CSDE1	0	MSKCC-DMP	P-0040292-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.2279:CSDE1_chr1:g.103296617inv Note: The CSDE1 rearrangement is an inversion of exons 19 - 21. One of the breakpoints is within exon 19. Functional significance is undetermined.
DNAJC8	0	MSKCC-DMP	P-0040300-T01-IM6	MTOR-DNAJC8 fusion	yes	unknown		unknown	DNAJC8 (NM_014280) - MTOR (NM_004958) rearrangement: c.181-280:DNAJC8_c.7327:MTORdel Note: The DNAJC8 - MTOR rearrangement is a deletion that results in a fusion of DNAJC8 exons 1 - 2 to MTOR exons 54 - 58. One of the breakpoints is within MTOR exon 54. Functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0040300-T01-IM6	MTOR-DNAJC8 fusion	yes	unknown		unknown	DNAJC8 (NM_014280) - MTOR (NM_004958) rearrangement: c.181-280:DNAJC8_c.7327:MTORdel Note: The DNAJC8 - MTOR rearrangement is a deletion that results in a fusion of DNAJC8 exons 1 - 2 to MTOR exons 54 - 58. One of the breakpoints is within MTOR exon 54. Functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0040300-T01-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.1789:NTRK1_chr1:g.201437190inv Note: The NTRK1 rearrangement is an inversion of exons 14 - 17. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of NTRK1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MGA	0	MSKCC-DMP	P-0040300-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.464:MGA_chr15:g.41846191del Note: The MGA rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.
ERF	0	MSKCC-DMP	P-0040300-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - CIC (NM_015125) rearrangement: c.913:ERF_c.3009-45:CICdel Note: The ERF - CIC rearrangement is a deletion of ERF exons 1 - 4 and CIC exons 1 - 12. One of the breakpoints is within exon 4.
CIC	0	MSKCC-DMP	P-0040300-T01-IM6	CIC-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - CIC (NM_015125) rearrangement: c.913:ERF_c.3009-45:CICdel Note: The ERF - CIC rearrangement is a deletion of ERF exons 1 - 4 and CIC exons 1 - 12. One of the breakpoints is within exon 4.
MET	0	MSKCC-DMP	P-0040127-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION POSITIVE FOR AN ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:   MET Exon 14 skipping (NM_000245) Lab Notes Run Number: Archerv3-CLIN-20190062 Macro-dissection: Not Performed
EML4	0	MSKCC-DMP	P-0040193-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon17 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190063 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0040193-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon17 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190063 Macro-dissection: Performed
RAD54L	0	MSKCC-DMP	P-0040307-T01-IM6	RAD54L-intragenic	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.1610+97:RAD54L_chr1:g.118268672inv Note: The RAD54L rearrangement is an inversion of exons 16 - 19. Functional significance is undetermined.
CCNT1	0	MSKCC-DMP	P-0040307-T01-IM6	KMT2D-CCNT1 fusion	yes	unknown		unknown	CCNT1 (NM_001240) - KMT2D (NM_003482) rearrangement: c.373-613:CCNT1_c.7391:KMT2Ddup Note: The CCNT1 - KMT2D rearrangement is a duplication that results in a fusion of CCNT1 exons 1 - 3 to KMT2D exons 31 - 54. One of the breakpoints is within KMT2D exon 31. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0040307-T01-IM6	KMT2D-CCNT1 fusion	yes	unknown		unknown	CCNT1 (NM_001240) - KMT2D (NM_003482) rearrangement: c.373-613:CCNT1_c.7391:KMT2Ddup Note: The CCNT1 - KMT2D rearrangement is a duplication that results in a fusion of CCNT1 exons 1 - 3 to KMT2D exons 31 - 54. One of the breakpoints is within KMT2D exon 31. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0040307-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(3;22)(q26.2;q13.2)(chr3:g.169670000::chr22:g.41545936) Note: The EP300 rearrangement is a translocation with a breakpoint in exon 14. Functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0040327-T01-IM6	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2 (NM_006164) rearrangement: c.46-1976_c.313-64del Note: The NFE2L2 rearrangement is an intragenic deletion of exon 2. Functional significance is undetermined.
IL10	0	MSKCC-DMP	P-0040343-T01-IM6	IL10-intragenic	yes	unknown		unknown	IL10 (NM_000572) rearrangement: t(1;X)(q32.1;q22.3)(chr1:g.206944654::chrX:g.104497492) Note: The IL10 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0040458-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.7618-1:BRCA2_chr13:g.33938000dup Note: The BRCA2 rearrangement is a duplication of exons 16 - 27. One of the breakpoints is within exon 16. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0008232-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1086:TMPRSS2_c.40-59158:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0008232-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1086:TMPRSS2_c.40-59158:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
PTPRS	0	MSKCC-DMP	P-0021838-T02-IM6	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(12;19)(q22;p13.3)(chr12:g.93413328::chr19:g.5240169) Note: The PTPRS rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0040511-T01-IM6	GDPD5-GNAS fusion	yes	unknown		in frame	GNAS (NM_000516) - GDPD5 (NM_030792) rearrangement: t(11;20)(q13.4;q13.32)(chr11:g.75150246::chr20:g.57474193) Note: The GNAS - GDPD5 rearrangement is a translocation that results in a fusion of GNAS exons 1 - 3 to GDPD5 exons 16 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
GDPD5	0	MSKCC-DMP	P-0040511-T01-IM6	GDPD5-GNAS fusion	yes	unknown		in frame	GNAS (NM_000516) - GDPD5 (NM_030792) rearrangement: t(11;20)(q13.4;q13.32)(chr11:g.75150246::chr20:g.57474193) Note: The GNAS - GDPD5 rearrangement is a translocation that results in a fusion of GNAS exons 1 - 3 to GDPD5 exons 16 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0040519-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.16549:KMT2D_chr12:g.49412345del Note: The KMT2D rearrangement is a deletion of exon 54. One of the breakpoints is within exon 54.
FANCA	0	MSKCC-DMP	P-0040519-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.893+227:FANCA_chr16:g.88532673del Note: The FANCA rearrangement is a deletion of exons 11 - 43.
TMPRSS2	0	MSKCC-DMP	P-0040519-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1047:TMPRSS2_c.40-54812:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040519-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1047:TMPRSS2_c.40-54812:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
PBRM1	0	MSKCC-DMP	P-0040520-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: t(3;16)(p21.1;q24.1)(chr3:g.52643949::chr16:g.85652741) Note: The PBRM1 rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0040443-T02-IM6	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.2222_c.2431-1575del Note: The MAP3K13 rearrangement is an intragenic deletion of exon 11. One of the breakpoints is within exon 11. The rearrangement does not include the kinase domain of MAP3K13. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0040443-T02-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.773:FGFR3_chr4:g.1888480del Note: The FGFR3 rearrangement is a deletion of exons 7 - 18. One of the breakpoints is within exon 7. The rearrangement includes the kinase domain of FGFR3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FGFR3	0	MSKCC-DMP	P-0010096-T03-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon11 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190067 Macro-dissection: Unknown
TACC3	0	MSKCC-DMP	P-0010096-T03-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon11 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190067 Macro-dissection: Unknown
BAZ1A	0	MSKCC-DMP	P-0017005-T01-IM6	DICER1-BAZ1A fusion	yes	unknown		unknown	BAZ1A (NM_013448) - DICER1(NM_030621) Rearrangement : c.-1088:BAZ1A_c.5528-8:DICER1dup Note: The BAZ1A - DICER1 Rearrangement results in the fusion of the promoter region of BAZ1A with exons 27-28 of DICER1. Its functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0017005-T01-IM6	DICER1-BAZ1A fusion	yes	unknown		unknown	BAZ1A (NM_013448) - DICER1(NM_030621) Rearrangement : c.-1088:BAZ1A_c.5528-8:DICER1dup Note: The BAZ1A - DICER1 Rearrangement results in the fusion of the promoter region of BAZ1A with exons 27-28 of DICER1. Its functional significance is undetermined.
PDPK1	0	MSKCC-DMP	P-0017629-T01-IM5	PDPK1-intragenic	yes	unknown		unknown	PDPK1 (NM_002613) rearrangement: c.1402-8:PDPK1_chr16:g.2150327del Note: The PDPK1 rearrangement is a deletion of exons 1-12.
RAD21	0	MSKCC-DMP	P-0017664-T01-IM5	ADH7-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - ADH7 (NM_001166504) rearrangement: t(4;8)(q23;q24.11)(chr4:g.100338146::chr8:g.117869648) Note: The RAD21 - ADH7  rearrangement is a translocation that results in the fusion of RAD21 exons 1-6 with ADH7 exons 8-9. One of the breakpoints is within RAD21 exon 6. The functional significance is undetermined.
ADH7	0	MSKCC-DMP	P-0017664-T01-IM5	ADH7-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - ADH7 (NM_001166504) rearrangement: t(4;8)(q23;q24.11)(chr4:g.100338146::chr8:g.117869648) Note: The RAD21 - ADH7  rearrangement is a translocation that results in the fusion of RAD21 exons 1-6 with ADH7 exons 8-9. One of the breakpoints is within RAD21 exon 6. The functional significance is undetermined.
FH	0	MSKCC-DMP	P-0018345-T01-IM6	FH-intragenic	yes	unknown		unknown	FH (NM_000143) rearrangement: c.267_c.268del Note: The FH rearrangement is an intragenic deletion with breakpoints in both exons 2 and 3. This rearrangement is observed in the background of other FH structural variants, suggesting a complex rearrangement involving FH.
FLT4	0	MSKCC-DMP	P-0021991-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: g.52740102_c.2167+12inv Note: The FLT4 rearrangement results in the inversion of exons 15-30. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0023380-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-4212:TMPRSS2_c.39+64807:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
ERG	0	MSKCC-DMP	P-0023380-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-4212:TMPRSS2_c.39+64807:ERGdel Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.
PIK3C3	0	MSKCC-DMP	P-0024146-T01-IM6	PIK3C3-intragenic	yes	unknown		unknown	PIK3C3 (NM_002647) rearrangement: chr18:g.37483346_c.984+12inv Note: The PIK3C3 rearrangement results in the inversion of exons 1-9. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0024146-T01-IM6	FGFR3-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - FGFR3 (NM_000142) rearrangement: c.761-178:WHSC1_c.380-60:FGFR3dup Note: The WHSC1 - FGFR3 rearrangement is a duplication that results in the fusion of WHSC1 exons 1-3 with FGFR3 exons 4-18 and includes the kinase domain of FGFR3. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0024146-T01-IM6	FGFR3-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - FGFR3 (NM_000142) rearrangement: c.761-178:WHSC1_c.380-60:FGFR3dup Note: The WHSC1 - FGFR3 rearrangement is a duplication that results in the fusion of WHSC1 exons 1-3 with FGFR3 exons 4-18 and includes the kinase domain of FGFR3. The functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0024146-T01-IM6	AMER1-intragenic	yes	unknown		unknown	AMER1 (NM_152424) rearrangement: t(X;11)(q11.2;q13.4)(chrX:g.63412860::chr11:g.74289154) Note: The AMER1 rearrangement is a translocation which involves a breakpoint in exon 2. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0024149-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.1244_c.4725-907inv Note: The NF1 rearrangement results in the inversion of exons 11-35. One of the breakpoints is within exon 11. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0025463-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: t(7;21)(q36.1;p11.1)(chr7:g.151945554::chr21:g.11039052) Note: The KMT2C rearrangement is a translocation involving a breakpoint in exon 14. Its functional significance is undetermined.
APC	0	MSKCC-DMP	P-0025463-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;9)(q22.2;q31.3)(chr5:g.112177163::chr9:g.111567118) Note: The APC rearrangement is a translocation involving a breakpoint in exon 16. Its functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0025737-T01-IM6	MS4A13-PGR fusion	yes	unknown		out of frame	PGR (NM_000926) - MS4A13 (NM_001012417) rearrangement: c.1637+92:PGR_c.129+2012:MS4A13inv Note: The PGR - MS4A13 rearrangement is an inversion which results in the fusion of PGR exon 1 with MS4A13 exons 4-7. Its functional significance is undetermined.
MS4A13	0	MSKCC-DMP	P-0025737-T01-IM6	MS4A13-PGR fusion	yes	unknown		out of frame	PGR (NM_000926) - MS4A13 (NM_001012417) rearrangement: c.1637+92:PGR_c.129+2012:MS4A13inv Note: The PGR - MS4A13 rearrangement is an inversion which results in the fusion of PGR exon 1 with MS4A13 exons 4-7. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0026636-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.*4:FGFR2_c.7896+636:TACC2inv Note: The FGFR2 - TACC2 rearrangement is an inversion with breakpoints in FGFR2 3UTR and TACC2 intron 13. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 and TACC2 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TACC2	0	MSKCC-DMP	P-0026636-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.*4:FGFR2_c.7896+636:TACC2inv Note: The FGFR2 - TACC2 rearrangement is an inversion with breakpoints in FGFR2 3UTR and TACC2 intron 13. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 and TACC2 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
CDKN2B	0	MSKCC-DMP	P-0026636-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.247:CDKN2B_chr9:g.21910667del Note: The CDKN2B rearrangement is a deletion with a breakpoint is exon 2. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0030304-T01-IM6	DOT1L-DNMT1 fusion	yes	unknown		out of frame	DNMT1 (NM_001379) - DOT1L (NM_032482) rearrangement: c.4816+127:DNMT1_c.201-47:DOT1Linv Note: The DNMT1 - DOT1L rearrangement is an inversion that results in the fusion of DNMT1 exons 1-39 with DOT1L exons 4-28. This may represent a more complex event involving DNMT1 that is not fully characterized by this assay. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0030304-T01-IM6	DOT1L-DNMT1 fusion	yes	unknown		out of frame	DNMT1 (NM_001379) - DOT1L (NM_032482) rearrangement: c.4816+127:DNMT1_c.201-47:DOT1Linv Note: The DNMT1 - DOT1L rearrangement is an inversion that results in the fusion of DNMT1 exons 1-39 with DOT1L exons 4-28. This may represent a more complex event involving DNMT1 that is not fully characterized by this assay. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0030304-T01-IM6	TYK2-DNMT1 fusion	yes	unknown		out of frame	DNMT1 (NM_001379) - TYK2 (NM_003331) rearrangement: c.878+94:DNMT1_c.465+110:TYK2dup Note: The DNMT1 - TYK2 rearrangement is a duplication that results in the fusion of DNMT1 exons 1-11 with TYK2 exon 6-25. The functional significance is undetermined.
TYK2	0	MSKCC-DMP	P-0030304-T01-IM6	TYK2-DNMT1 fusion	yes	unknown		out of frame	DNMT1 (NM_001379) - TYK2 (NM_003331) rearrangement: c.878+94:DNMT1_c.465+110:TYK2dup Note: The DNMT1 - TYK2 rearrangement is a duplication that results in the fusion of DNMT1 exons 1-11 with TYK2 exon 6-25. The functional significance is undetermined.
MEGF8	0	MSKCC-DMP	P-0030304-T01-IM6	CIC-MEGF8 fusion	yes	unknown		unknown	MEGF8 (NM_001410) - CIC (NM_015125) rearrangement: c.6703:MEGF8_c.2887-24:CICdup Note: The MEGF8 - CIC rearrangement is a duplication that results in the fusion of MEGF8 exons 1-38 with CIC exons 12-20. One of the breakpoints is within MEGF8 exon 38. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0030304-T01-IM6	CIC-MEGF8 fusion	yes	unknown		unknown	MEGF8 (NM_001410) - CIC (NM_015125) rearrangement: c.6703:MEGF8_c.2887-24:CICdup Note: The MEGF8 - CIC rearrangement is a duplication that results in the fusion of MEGF8 exons 1-38 with CIC exons 12-20. One of the breakpoints is within MEGF8 exon 38. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030304-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(12;21)(q13.13;q22.3)(chr12:g.53196493::chr21:g.42842718) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 10. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0030556-T01-IM6	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) rearrangement: c.3616+5492_c.3800+52dup Note: The PBRM1 rearrangement is an intragenic duplication of exon 24. The functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0031041-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: t(10;12)(q22.3;p12.1)(chr10:g.78493482::chr12:g.21628298) Note: The RECQL4 rearrangement is a translocation with the breakpoint in intron 11. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0033042-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) Rearrangement: chr1:g.101514328_c.1427:NOTCH2del Note: The NOTCH2 rearrangement results in the deletion of NOTCH2 exons 8 to 34. One of the breakpoints is within exon 8 of NOTCH2. The functional significance is undetermined. In addition, multiple rearrangements involving NOTCH2 were detected in this sample and a more complex rearrangement resulting in a NOTCH2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FGFR2	0	MSKCC-DMP	P-0033652-T01-IM6	CCDC186-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - CCDC186(NM_018017) Rearrangement :  c.2302-1295:FGFR2_c.1222-3356:CCDC186del Note: The FGFR2 - CCDC186 Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 7-16 of CCDC186.This includes the protein kinase domain of FGFR2.
CCDC186	0	MSKCC-DMP	P-0033652-T01-IM6	CCDC186-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - CCDC186(NM_018017) Rearrangement :  c.2302-1295:FGFR2_c.1222-3356:CCDC186del Note: The FGFR2 - CCDC186 Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 7-16 of CCDC186.This includes the protein kinase domain of FGFR2.
NCOR1	0	MSKCC-DMP	P-0034258-T01-IM6	DLG2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - DLG2 (NM_001142699) rearrangement: t(11;17)(q14.1;p11.2)(chr11:g.84221683::chr17:g.15952268) Note: The NOTCH1 - DLG2 rearrangement is a translocation which may result in the fusion of NOTCH1 exons 1-41 with DLG2 exons 8-28. One of the breakpoints is within NOTCH1 exon 41. Its functional significance is undetermined.
DLG2	0	MSKCC-DMP	P-0034258-T01-IM6	DLG2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - DLG2 (NM_001142699) rearrangement: t(11;17)(q14.1;p11.2)(chr11:g.84221683::chr17:g.15952268) Note: The NOTCH1 - DLG2 rearrangement is a translocation which may result in the fusion of NOTCH1 exons 1-41 with DLG2 exons 8-28. One of the breakpoints is within NOTCH1 exon 41. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0034784-T01-IM6	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) fusion: c.2301+958:FGFR2_c.355-49659:KIAA1217inv Note: The FGFR2 - KIAA1217 fusion involves FGFR2 exons 1-17 and KIAA1217 exons 3-21. The fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
KIAA1217	0	MSKCC-DMP	P-0034784-T01-IM6	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) fusion: c.2301+958:FGFR2_c.355-49659:KIAA1217inv Note: The FGFR2 - KIAA1217 fusion involves FGFR2 exons 1-17 and KIAA1217 exons 3-21. The fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0034784-T01-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement : c.251:CDKN2Ap16INK4A_chr9:g.21981088del CDKN2Ap14ARF (NM_058195) rearrangement:c.194-9881_c.294del Note: The CDKN2A rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2.
BCAS3	0	MSKCC-DMP	P-0034885-T01-IM6	PPM1D-BCAS3 fusion	yes	unknown		out of frame	BCAS3 (NM_001099432) - PPM1D (NM_003620) rearrangement: c.585-525:BCAS3_c.1261-173:PPM1Ddup Note: The BCAS3 - PPM1D rearrangement is a duplication that results in the fusion of BCAS3 exons 1-8 with PPM1D exon 6. The functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0034885-T01-IM6	PPM1D-BCAS3 fusion	yes	unknown		out of frame	BCAS3 (NM_001099432) - PPM1D (NM_003620) rearrangement: c.585-525:BCAS3_c.1261-173:PPM1Ddup Note: The BCAS3 - PPM1D rearrangement is a duplication that results in the fusion of BCAS3 exons 1-8 with PPM1D exon 6. The functional significance is undetermined.
HIST1H3B	0	MSKCC-DMP	P-0034885-T01-IM6	HIST1H3B-intragenic	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: t(6;20)(p22.2;p12.3)(chr6:g.26031916::chr20:g.5641761) Note: The HIST1H3B rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined
YAP1	0	MSKCC-DMP	P-0036098-T01-IM6	YAP1-intragenic	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: c.-3159_c.283dup Note: The YAP1 rearrangement is a duplication that includes YAP1 exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0036673-T01-IM6	SIK3-PGR fusion	yes	unknown		out of frame	PGR (NM_000926) - SIK3 (NM_025164) rearrangement: c.2488+212:PGR_c.100-14184:SIK3dup Note: The PGR - SIK3 rearrangement is a duplication that results in the fusion of PGR exons 1-6 with SIK3 exons 2-23. The functional significance is undetermined.
SIK3	0	MSKCC-DMP	P-0036673-T01-IM6	SIK3-PGR fusion	yes	unknown		out of frame	PGR (NM_000926) - SIK3 (NM_025164) rearrangement: c.2488+212:PGR_c.100-14184:SIK3dup Note: The PGR - SIK3 rearrangement is a duplication that results in the fusion of PGR exons 1-6 with SIK3 exons 2-23. The functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0039908-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.462:ANKRD11_chr16:g.83930601del Note: The ANKRD11 rearrangement is a deletion of exons 6 - 13. One of the breakpoints is within exon 6.
FGFR2	0	MSKCC-DMP	P-0026636-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: ArcherV2-CLIN-20180016 Macro-dissection: Not Performed
TACC2	0	MSKCC-DMP	P-0026636-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: ArcherV2-CLIN-20180016 Macro-dissection: Not Performed
AR	0	MSKCC-DMP	P-0011475-T02-IM6	AR-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:    AR (NM_000044) Variant 7 (AR V-7)  PMID: 26554309, 19117982 Lab Notes Run Number: Archerv3-CLIN-20190069 Macro-dissection: Unknown
TRIM24	0	MSKCC-DMP	P-0026773-T01-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon2 (NM_015905) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190070 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0026773-T01-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon2 (NM_015905) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190070 Macro-dissection: Performed
INPPL1	0	MSKCC-DMP	P-0020150-T02-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: c.659+75:INPPL1_chr11:g.71982730del Note: The INPPL1 rearrangement is a deletion of exons 6 - 28.
TMPRSS2	0	MSKCC-DMP	P-0020150-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1331:TMPRSS2_c.40-57667:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0020150-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1331:TMPRSS2_c.40-57667:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
TRIM24	0	MSKCC-DMP	P-0025699-T02-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2014+674:TRIM24_c.1177+494:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 12 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
BRAF	0	MSKCC-DMP	P-0025699-T02-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2014+674:TRIM24_c.1177+494:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 12 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
ATR	0	MSKCC-DMP	P-0026050-T04-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.4292_c.4382+1317del Note: The ATR rearrangement is an intragenic deletion of exon 24. One of the breakpoints is within exon 24.
BRAF	0	MSKCC-DMP	P-0026050-T04-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1084:BRAF_chr7:g.145389205del Note: The BRAF rearrangement is a deletion of exons 1 - 8. One of the breakpoints is within exon 8. The rearrangement does not include the kinase domain of BRAF. Functional significance is undetermined.
BTK	0	MSKCC-DMP	P-0026050-T04-IM6	BTK-intragenic	yes	unknown		unknown	BTK (NM_000061) rearrangement: c.392-16:BTK_chrX:g.82536485inv Note: The BTK rearrangement is an inversion of exons 6 - 19. The rearrangement includes the kinase domain of BTK. Functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0038074-T02-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.2017_c.2740del Note: The BRCA2 rearrangement is an intragenic deletion of exon 11. The breakpoints are within exon 11.
NF1	0	MSKCC-DMP	P-0039994-T03-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(5;17)(p13.2;q11.2)(chr5:g.37923642::chr17:g.29527467) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0040536-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.917_c.1819-402dup Note: The PBRM1 rearrangement is an intragenic duplication of exons 10 - 15. One of the breakpoints is within exon 10. Functional significance is undetermined.
TBC1D24	0	MSKCC-DMP	P-0040579-T01-IM6	TSC2-TBC1D24 fusion	yes	unknown		unknown	TBC1D24 (NM_001199107) - TSC2 (NM_000548) rearrangement: c.1143-71:TBC1D24_c.3648:TSC2dup Note: The TBC1D24 - TSC2 rearrangement is a duplication that results in a fusion of TBC1D24 exons 1 - 4 to TSC2 exons 31 - 42. One of the breakpoints is within TSC2 exon 31. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0040579-T01-IM6	TSC2-TBC1D24 fusion	yes	unknown		unknown	TBC1D24 (NM_001199107) - TSC2 (NM_000548) rearrangement: c.1143-71:TBC1D24_c.3648:TSC2dup Note: The TBC1D24 - TSC2 rearrangement is a duplication that results in a fusion of TBC1D24 exons 1 - 4 to TSC2 exons 31 - 42. One of the breakpoints is within TSC2 exon 31. Functional significance is undetermined.
PTPN11	0	MSKCC-DMP	P-0040588-T01-IM6	PTPN11-intragenic	yes	unknown		unknown	PTPN11 (NM_002834) rearrangement: c.1225-5:PTPN11_chr12:g.115772818del Note: The PTPN11 rearrangement is a deletion of exons 11 - 15. Functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0040588-T01-IM6	ATR-intragenic	yes	unknown		out of frame	ATR (NM_001184) rearrangement: c.7042-36:ATR_chr3:g.141768495dup Note: The ATR rearrangement is a duplication of exons 42 - 47. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0040595-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-244:TMPRSS2_c.18+1439:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0040595-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-244:TMPRSS2_c.18+1439:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
STK11	0	MSKCC-DMP	P-0040602-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.375-6_c.536inv Note: The STK11 rearrangement is an intragenic inversion of exons 3 - 4. One of the breakpoints is within exon 4. The rearrangement includes a part of the kinase domain of STK11. Functional significance is undetermined.
AKT3	0	MSKCC-DMP	P-0040684-T01-IM6	AKT3-intragenic	yes	unknown		unknown	AKT3 (NM_005465) rearrangement: c.1040:AKT3_chr1:g.239082557inv Note: The AKT3 rearrangement is an inversion of exons 10 - 13. One of the breakpoints is within exon 10. The rearrangement includes a part of the kinase domain of AKT3. Functional significance is undetermined.
UNK	0	MSKCC-DMP	P-0040684-T01-IM6	H3F3B-UNK fusion	yes	unknown		unknown	UNK (NM_001080419) - H3F3B (NM_005324) rearrangement: c.104+1748:UNK_c.325:H3F3Binv Note: The UNK - H3F3B rearrangement is an inversion that results in a fusion of UNK exon 1 to H3F3B exon 4. One of the breakpoints is within H3F3B exon 4. Functional significance is undetermined.
H3F3B	0	MSKCC-DMP	P-0040684-T01-IM6	H3F3B-UNK fusion	yes	unknown		unknown	UNK (NM_001080419) - H3F3B (NM_005324) rearrangement: c.104+1748:UNK_c.325:H3F3Binv Note: The UNK - H3F3B rearrangement is an inversion that results in a fusion of UNK exon 1 to H3F3B exon 4. One of the breakpoints is within H3F3B exon 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0040739-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+849:TMPRSS2_ c.40-54985:ERGdel
ERG	0	MSKCC-DMP	P-0040739-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 4-11): c.126+849:TMPRSS2_ c.40-54985:ERGdel
NF1	0	MSKCC-DMP	P-0040748-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.7587:NF1_chr17:g.29662315del Note: The NF1 rearrangement is a deletion of exons 41 - 51. One of the breakpoints is within exon 51.
NTRK1	0	MSKCC-DMP	P-0040580-T01-IM6	NTRK1-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:   NTRK1 (NM_002529)  exons 3-9 deletion. PMID: 26581861, 29914559  Note: the functional significance of this event is unknown. Trk inhibitors have not been investigated in this setting. Note: the NTRK1 deletion was detected with low read support.   Lab Notes Run Number: Archerv3-CLIN-20190071 Macro-dissection: Not Performed
CNTLN	0	MSKCC-DMP	P-0030521-T02-IM6	FANCC-CNTLN fusion	yes	unknown		out of frame	CNTLN (NM_017738) - FANCC (NM_000136) rearrangement: c.3855+6228:CNTLN_c.687-96:FANCCinv Note: The CNTLN - FANCC rearrangement is an inversion that results in a fusion of CNTLN exons 1 - 23 to FANCC exons 8 - 15. Functional significance is undetermined.
FANCC	0	MSKCC-DMP	P-0030521-T02-IM6	FANCC-CNTLN fusion	yes	unknown		out of frame	CNTLN (NM_017738) - FANCC (NM_000136) rearrangement: c.3855+6228:CNTLN_c.687-96:FANCCinv Note: The CNTLN - FANCC rearrangement is an inversion that results in a fusion of CNTLN exons 1 - 23 to FANCC exons 8 - 15. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0039523-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;18)(p36.11;q12.3)(chr1:g.27101004::chr18:g.40077260) Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
TRIM24	0	MSKCC-DMP	P-0025699-T02-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon12 (NM_015905) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190072 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0025699-T02-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon12 (NM_015905) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190072 Macro-dissection: Not Performed
JAK1	0	MSKCC-DMP	P-0021969-T02-IM6	JAK1-intragenic	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: c.651:JAK1_chr1:g.65452897del Note: The JAK1 rearrangement is a deletion of exons 1 - 7. One of the breakpoints is within exon 7.
MAP3K13	0	MSKCC-DMP	P-0021969-T02-IM6	TNIK-MAP3K13 fusion	yes	unknown		out of frame	MAP3K13 (NM_004721) - TNIK (NM_015028) rearrangement: c.1010+192:MAP3K13_c.4000-268:TNIKinv Note: The MAP3K13 - TNIK rearrangement is an inversion that results in a fusion of MAP3K13 exons 1 - 5 to TNIK exons 30 - 33. The fusion includes a part of the kinase domain of MAP3K13. Functional significance is undetermined.
TNIK	0	MSKCC-DMP	P-0021969-T02-IM6	TNIK-MAP3K13 fusion	yes	unknown		out of frame	MAP3K13 (NM_004721) - TNIK (NM_015028) rearrangement: c.1010+192:MAP3K13_c.4000-268:TNIKinv Note: The MAP3K13 - TNIK rearrangement is an inversion that results in a fusion of MAP3K13 exons 1 - 5 to TNIK exons 30 - 33. The fusion includes a part of the kinase domain of MAP3K13. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0040754-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-201:TMPRSS2_c.40-54954:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040754-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-201:TMPRSS2_c.40-54954:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
PIK3CD	0	MSKCC-DMP	P-0040947-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.3062:PIK3CD_chr1:g.9911454del Note: The PIK3CD rearrangement is a deletion of exon 24. One of the breakpoints is within exon 24. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0038086-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.422-39327_c.1321del Note: The ERBB4 rearrangement is an intragenic deletion of exons 4 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
GNAQ	0	MSKCC-DMP	P-0038086-T01-IM6	GNAQ-intragenic	yes	unknown		unknown	GNAQ (NM_002072) rearrangement: c.606-60:GNAQ_chr9:g.80877309del Note: The GNAQ rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0040643-T01-IM6	FER1L5-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - FER1L5 (NM_001113382) rearrangement: t(2;17)(q11.2;q21.2)(chr2:g.97351976::chr17:g.38504786) Note: The RARA - FER1L5 rearrangement is a translocation that results in a fusion of RARA exons 1-3 to FER1L5 exons 23 - 52. One of the breakpoints is within FER1L5 exon 23. The functional significance is undetermined.
FER1L5	0	MSKCC-DMP	P-0040643-T01-IM6	FER1L5-RARA fusion	yes	unknown		unknown	RARA (NM_000964) - FER1L5 (NM_001113382) rearrangement: t(2;17)(q11.2;q21.2)(chr2:g.97351976::chr17:g.38504786) Note: The RARA - FER1L5 rearrangement is a translocation that results in a fusion of RARA exons 1-3 to FER1L5 exons 23 - 52. One of the breakpoints is within FER1L5 exon 23. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0041007-T01-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.2002-1888_c.3774+83dup Note: The SMARCA4 rearrangement is an intragenic duplication of exons 14 - 26. Functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0041032-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.1955+71:PIK3CD_chr1:g.20738691del Note: The PIK3CD rearrangement is a deletion of exons 16 - 24. Functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0040422-T02-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5642-856_c.5777+139inv Note: The ROS1 rearrangement is an intragenic inversion of exon 35. The rearrangement does not include the kinase domain of ROS1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ROS1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KMT2C	0	MSKCC-DMP	P-0040995-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.5021:KMT2C_chr7:g.150477103del Note: The KMT2C rearrangement is a deletion of exons 34 - 59. One of the breakpoints is within exon 34.
TMPRSS2	0	MSKCC-DMP	P-0041103-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.13;q22.3)(chr19:g.38571571::chr21:g.42871994) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement involving TMPRSS2 is possible. Functional significance is undetermined.
MAPK3	0	MSKCC-DMP	P-0041108-T01-IM6	MAPK3-intragenic	yes	unknown		unknown	MAPK3 (NM_002746) rearrangement: c.306:MAPK3_chr16:g.30140007del Note: The MAPK3 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. The rearrangement includes a part of the kinase domain of MAPK3. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0041108-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: t(2;4)(p24.3;p16.3)(chr2:g.16434694::chr4:g.1808368) Note: The FGFR3 rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FLT4	0	MSKCC-DMP	P-0023910-T09-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: t(5;12)(q35.3;q23.1)(chr5:g.180046682::chr12:g.97517987) Note: The FLT4 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0023910-T09-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.11482+108:FAT1_chr4:g.29213342inv Note: The FAT1 rearrangement is an inversion of exons 21 - 27. Functional significance is undetermined.
SLIT2	0	MSKCC-DMP	P-0040504-T01-IM6	ETV6-SLIT2 fusion	yes	unknown		out of frame	SLIT2 (NM_004787) - ETV6 (NM_001987) rearrangement: t(4;12)(p15.31;p13.2)(chr4:g.20374490::chr12:g.12034059) Note: The SLIT2 - ETV6 rearrangement is a translocation that results in a fusion of SLIT2 exons 1 - 4 to ETV6 exons 6 - 8. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0040504-T01-IM6	ETV6-SLIT2 fusion	yes	unknown		out of frame	SLIT2 (NM_004787) - ETV6 (NM_001987) rearrangement: t(4;12)(p15.31;p13.2)(chr4:g.20374490::chr12:g.12034059) Note: The SLIT2 - ETV6 rearrangement is a translocation that results in a fusion of SLIT2 exons 1 - 4 to ETV6 exons 6 - 8. Functional significance is undetermined.
BAIAP2	0	MSKCC-DMP	P-0040504-T01-IM6	RPTOR-BAIAP2 fusion	yes	unknown		in frame	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.55-5627:BAIAP2_c.3478-165:RPTORdup Note: The BAIAP2 - RPTOR rearrangement is a duplication that results in a fusion of BAIAP2 exon 1 to RPTOR exons 30 - 34. The fusion is predicted to be in frame. Functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0040504-T01-IM6	RPTOR-BAIAP2 fusion	yes	unknown		in frame	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.55-5627:BAIAP2_c.3478-165:RPTORdup Note: The BAIAP2 - RPTOR rearrangement is a duplication that results in a fusion of BAIAP2 exon 1 to RPTOR exons 30 - 34. The fusion is predicted to be in frame. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0040925-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.4087:KMT2B_chr19:g.31655075del Note: The KMT2B rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15.
SUGP1	0	MSKCC-DMP	P-0040955-T01-IM6	MEF2B-SUGP1 fusion	yes	unknown		unknown	SUGP1 (NM_172231) - MEF2B (NM_001145785) rearrangement: c.585:SUGP1_c.394-2:MEF2Bdel Note: The SUGP1 - MEF2B rearrangement is a deletion that results in a fusion of SUGP1 exons 1 - 5 to MEF2B exons 5 - 9. One of the breakpoints is within SUGP1 exon 5. Functional significance is undetermined. Multiple rearrangements involving MEF2B were detected in this sample and a more complex rearrangement involving MEF2B is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MEF2B	0	MSKCC-DMP	P-0040955-T01-IM6	MEF2B-SUGP1 fusion	yes	unknown		unknown	SUGP1 (NM_172231) - MEF2B (NM_001145785) rearrangement: c.585:SUGP1_c.394-2:MEF2Bdel Note: The SUGP1 - MEF2B rearrangement is a deletion that results in a fusion of SUGP1 exons 1 - 5 to MEF2B exons 5 - 9. One of the breakpoints is within SUGP1 exon 5. Functional significance is undetermined. Multiple rearrangements involving MEF2B were detected in this sample and a more complex rearrangement involving MEF2B is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0040965-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-4759:TMPRSS2_chr21:g.39968609del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help better characterize the rearrangement. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TMPRSS2	0	MSKCC-DMP	P-0040965-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190077 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0040965-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190077 Macro-dissection: Performed
CREBBP	0	MSKCC-DMP	P-0037465-T02-IM6	SLX4-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2159-476:CREBBP_c.1280:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 11 to SLX4 exons 6 - 15. One of the breakpoints is within SLX4 exon 6.
SLX4	0	MSKCC-DMP	P-0037465-T02-IM6	SLX4-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2159-476:CREBBP_c.1280:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 11 to SLX4 exons 6 - 15. One of the breakpoints is within SLX4 exon 6.
NOTCH1	0	MSKCC-DMP	P-0037465-T02-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.1442-30:NOTCH1_chr9:g.139450872del Note: The NOTCH1 rearrangement is a deletion of exons 1 - 8.
SMO	0	MSKCC-DMP	P-0008440-T02-IM6	SMO-intragenic	yes	unknown		unknown	SMO (NM_005631) rearrangement: c.2252:SMO_chr7:g.134549261del Note: The SMO rearrangement is a deletion of exon 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
CCDC6	0	MSKCC-DMP	P-0041192-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+8632:CCDC6_c.2136+387:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0041192-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+8632:CCDC6_c.2136+387:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
FOXP1	0	MSKCC-DMP	P-0041274-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: c.1299_c.1722+7del Note: The FOXP1 rearrangement is an intragenic deletion of exons 11 - 15. One of the breakpoints is within exon 11.
BRAF	0	MSKCC-DMP	P-0000828-T03-IM6	GTF2IRD1-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - GTF2IRD1 (NM_005685) rearrangement: c.1178-597:BRAF_c.2320+14181:GTF2IRD1inv Note: The BRAF - GTF2IRD1 rearrangement is an inversion that results in a fusion of BRAF exons 1 - 9 to GTF2IRD1 exons 23 - 27. The fusion is predicted to be in frame and does not include the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
GTF2IRD1	0	MSKCC-DMP	P-0000828-T03-IM6	GTF2IRD1-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - GTF2IRD1 (NM_005685) rearrangement: c.1178-597:BRAF_c.2320+14181:GTF2IRD1inv Note: The BRAF - GTF2IRD1 rearrangement is an inversion that results in a fusion of BRAF exons 1 - 9 to GTF2IRD1 exons 23 - 27. The fusion is predicted to be in frame and does not include the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
BARD1	0	MSKCC-DMP	P-0041363-T01-IM6	BARD1-intragenic	yes	unknown		unknown	BARD1 (NM_000465) rearrangement: t(2;13)(q35;q21.33)(chr2:g.215610383::chr13:g.69145496) Note: The BARD1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
EIF4A2	0	MSKCC-DMP	P-0005264-T03-IM6	EIF4A2-intragenic	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: c.409:EIF4A2_chr3:g.186523625inv Note: The EIF4A2 rearrangement is an inversion of exons 5 - 11. One of the breakpoints is within exon 5. Functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0041289-T01-IM6	SLC38A10-FLCN fusion	yes	unknown		in frame	FLCN (NM_144997) - SLC38A10 (NM_001037984) rearrangement: c.618+49:FLCN_c.912+1222:SLC38A10dup Note: The FLCN - SLC38A10 rearrangement is a duplication that results in a fusion of FLCN exons 1 - 6 to SLC38A10 exons 9 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
SLC38A10	0	MSKCC-DMP	P-0041289-T01-IM6	SLC38A10-FLCN fusion	yes	unknown		in frame	FLCN (NM_144997) - SLC38A10 (NM_001037984) rearrangement: c.618+49:FLCN_c.912+1222:SLC38A10dup Note: The FLCN - SLC38A10 rearrangement is a duplication that results in a fusion of FLCN exons 1 - 6 to SLC38A10 exons 9 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0041289-T01-IM6	PTCH1-intragenic	yes	unknown		unknown	PTCH1 (NM_000264) rearrangement: c.394+89_c.2212del Note: The PTCH1 rearrangement is an intragenic deletion of exons 3 - 14. One of the breakpoints is within exon 14.
KCNMB3	0	MSKCC-DMP	P-0033315-T03-IM6	PIK3CB-KCNMB3 fusion	yes	unknown		unknown	KCNMB3 (NM_171828) - PIK3CB (NM_006219) rearrangement: c.62+1284:KCNMB3_c.1421:PIK3CBdel Note: The KCNMB3 - PIK3CB rearrangement is a deletion that results in a fusion of KCNMB3 exon 1 to PIK3CB exons 9 - 22. One of the breakpoints is within PIK3CB exon 9. Functional significance is undetermined.
PIK3CB	0	MSKCC-DMP	P-0033315-T03-IM6	PIK3CB-KCNMB3 fusion	yes	unknown		unknown	KCNMB3 (NM_171828) - PIK3CB (NM_006219) rearrangement: c.62+1284:KCNMB3_c.1421:PIK3CBdel Note: The KCNMB3 - PIK3CB rearrangement is a deletion that results in a fusion of KCNMB3 exon 1 to PIK3CB exons 9 - 22. One of the breakpoints is within PIK3CB exon 9. Functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0033315-T03-IM6	KDR-intragenic	yes	unknown		out of frame	KDR (NM_002253) rearrangement: c.1536+23_c.2267-1471del Note: The KDR rearrangement is an intragenic deletion of exons 12 - 15. The rearrangement does not include the kinase domain of KDR. Multiple rearrangements involving KDR were detected in this sample and a more complex rearrangement involving KDR is possible. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0041429-T01-IM6	PTEN-intragenic	yes	unknown		out of frame	PTEN (NM_000314) rearrangement: c.209+2425_c.254-108del Note: The PTEN rearrangement is an intragenic deletion of exon 4.
ALK	0	MSKCC-DMP	P-0041438-T01-IM6	TTC27-ALK fusion	yes	unknown		out of frame	ALK (NM_004304) - TTC27 (NM_017735) rearrangement: c.3172+510:ALK_c.538-4165:TTC27inv Note: The ALK - TTC27 rearrangement is an inversion that results in a fusion of ALK exons 1 - 19 to TTC27 exons 5 - 20. The fusion does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TTC27	0	MSKCC-DMP	P-0041438-T01-IM6	TTC27-ALK fusion	yes	unknown		out of frame	ALK (NM_004304) - TTC27 (NM_017735) rearrangement: c.3172+510:ALK_c.538-4165:TTC27inv Note: The ALK - TTC27 rearrangement is an inversion that results in a fusion of ALK exons 1 - 19 to TTC27 exons 5 - 20. The fusion does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KMT2D	0	MSKCC-DMP	P-0041579-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(8;12)(q22.2;q13.12)(chr8:g.100297214::chr12:g.49431612) Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 34. Functional significance is undetermined.
GLCCI1	0	MSKCC-DMP	P-0041185-T01-IM6	ETV1-GLCCI1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GLCCI1-ETV1 fusion. Note: The rearrangement is an in-frame fusion between genes GLCCI1 Exon1 (NM_138426) and ETV1 Exon10 (NM_004956). Lab Notes Run Number: Archerv3-CLIN-20190084 Macro-dissection: Not Performed
ETV1	0	MSKCC-DMP	P-0041185-T01-IM6	ETV1-GLCCI1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GLCCI1-ETV1 fusion. Note: The rearrangement is an in-frame fusion between genes GLCCI1 Exon1 (NM_138426) and ETV1 Exon10 (NM_004956). Lab Notes Run Number: Archerv3-CLIN-20190084 Macro-dissection: Not Performed
GTF2IRD1	0	MSKCC-DMP	P-0000828-T03-IM6	BRAF-GTF2IRD1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GTF2IRD1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes GTF2IRD1 Exon22 (NM_005685) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190085 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0000828-T03-IM6	BRAF-GTF2IRD1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GTF2IRD1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes GTF2IRD1 Exon22 (NM_005685) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190085 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0040610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2641:TMPRSS2_c.40-59446:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2641:TMPRSS2_c.40-59446:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
INPPL1	0	MSKCC-DMP	P-0041482-T01-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: c.183-51:INPPL1_chr11:g.69426341inv Note: The INPPL1 rearrangement is an inversion of exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+928:TMPRSS2_c.19-15841:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0041610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+928:TMPRSS2_c.19-15841:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
WT1	0	MSKCC-DMP	P-0041658-T01-IM6	WT1-intragenic	yes	unknown		out of frame	WT1 (NM_024426) rearrangement: c.769+60_c.873-2954del Note: The WT1 rearrangement is an intragenic deletion of exon 3.
PPP2R1A	0	MSKCC-DMP	P-0041658-T01-IM6	PPP2R1A-intragenic	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: c.169+39:PPP2R1A_chr19:g.54078970inv Note: The PPP2R1A rearrangement is an inversion of exons 3 - 15. Functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0041658-T01-IM6	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) rearrangement: c.886-938_c.1122+20inv Note: The NF2 rearrangement is an intragenic inversion of exons 10 - 11. Functional significance is undetermined.
ZNF770	0	MSKCC-DMP	P-0017761-T01-IM6	NUTM1-ZNF770 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ZNF770-NUTM1 fusion. Note: The rearrangement is a fusion between genes ZNF770 Exon2 (NM_014106) and NUTM1 Exon2 (NM_175741). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
NUTM1	0	MSKCC-DMP	P-0017761-T01-IM6	NUTM1-ZNF770 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ZNF770-NUTM1 fusion. Note: The rearrangement is a fusion between genes ZNF770 Exon2 (NM_014106) and NUTM1 Exon2 (NM_175741). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
EML4	0	MSKCC-DMP	P-0041438-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0041438-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon13 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
TP53	0	MSKCC-DMP	P-0025678-T02-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.782+149_c.994-1193del Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 9.
ERBB2	0	MSKCC-DMP	P-0000068-T01-IM3	GRB7-ERBB2 fusion	yes	unknown		unknown	null
GRB7	0	MSKCC-DMP	P-0000068-T01-IM3	GRB7-ERBB2 fusion	yes	unknown		unknown	null
KDM5A	0	MSKCC-DMP	P-0000377-T03-IM3	KDM5A-intragenic	yes	unknown		out of frame	KDM5A (NM_001042603) duplication (64425bp): c.672+1652_4234+155dup Note: The KDM5A duplication is a rearrangement event which results in the  within-transcript duplication of exons 6 to 25, impairing the function of  the gene.
KDM5D	0	MSKCC-DMP	P-0000377-T03-IM3	KDM5D-intragenic	yes	unknown		unknown	KDM5D (NM_001146705) inversion (1896bp): c.c.1810-954_2307-34inv Note: The KDM5D intragenic inversion is a rearrangement event which results  in the deletion of exons 15 to 17, likely disabling the function of the  gene.
RET	0	MSKCC-DMP	P-0000425-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	RET (NM_020630) - CCDC6 (NM_005436) Inversion (c.2136+266_c.303+19630inv)
CCDC6	0	MSKCC-DMP	P-0000425-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	RET (NM_020630) - CCDC6 (NM_005436) Inversion (c.2136+266_c.303+19630inv)
RET	0	MSKCC-DMP	P-0000889-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	RET (NM_020630) - CCDC6 (NM_005436) Reciprocal Inversion:  c.2137-38_c.2137-38inv Note: RET-CCDC6 fusion has bee reported in papillary thyroid carcinoma  (PMID: 23145146)
CCDC6	0	MSKCC-DMP	P-0000889-T01-IM3	CCDC6-RET fusion	yes	unknown		in frame	RET (NM_020630) - CCDC6 (NM_005436) Reciprocal Inversion:  c.2137-38_c.2137-38inv Note: RET-CCDC6 fusion has bee reported in papillary thyroid carcinoma  (PMID: 23145146)
ATR	0	MSKCC-DMP	P-0001100-T01-IM3	ATR-intragenic	yes	unknown		unknown	ATR     (NM_001184) Duplication (9066bp): c.1659_c.2850dup Note: ATR intragenic duplication is predicted to be inactivating.
TACC3	0	MSKCC-DMP	P-0001453-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	null
FGFR3	0	MSKCC-DMP	P-0001453-T01-IM3	FGFR3-TACC3 fusion	yes	unknown		unknown	null
None	0	MSKCC-DMP	P-0001638-T01-IM3	None-intragenic	yes	unknown		in frame	None
APC	0	MSKCC-DMP	P-0001710-T01-IM3	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) deletion: c.5840_c.-3529del  The APC-SRP19 deletion is a rearrangement event which results in partial  deletion of exon 16 of APC, likely disabling the function of the gene.
SRP19	0	MSKCC-DMP	P-0001710-T01-IM3	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) deletion: c.5840_c.-3529del  The APC-SRP19 deletion is a rearrangement event which results in partial  deletion of exon 16 of APC, likely disabling the function of the gene.
FAT1	0	MSKCC-DMP	P-0002073-T01-IM3	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) Deletion : c.5963_c.9464-114del
RET	0	MSKCC-DMP	P-0002145-T01-IM3	PDCD10-RET fusion	yes	unknown		out of frame	RET (NM_020975) - PDCD10 (NM_145860) translocation:  t(10,3)(q11.21;q26.1)(chr10:g.43609394::chr3:g.167419184)
PDCD10	0	MSKCC-DMP	P-0002145-T01-IM3	PDCD10-RET fusion	yes	unknown		out of frame	RET (NM_020975) - PDCD10 (NM_145860) translocation:  t(10,3)(q11.21;q26.1)(chr10:g.43609394::chr3:g.167419184)
RET	0	MSKCC-DMP	P-0002145-T01-IM3	TFG-RET fusion	yes	unknown		in frame	RET (NM_020975) - TFG (NM_001195478) translocation:  t(10,3)(q11.21;q12.2)(chr10:g.43609437::chr3:g.100450751)
TFG	0	MSKCC-DMP	P-0002145-T01-IM3	TFG-RET fusion	yes	unknown		in frame	RET (NM_020975) - TFG (NM_001195478) translocation:  t(10,3)(q11.21;q12.2)(chr10:g.43609437::chr3:g.100450751)
NBN	0	MSKCC-DMP	P-0002584-T01-IM3	NBN-intragenic	yes	unknown		in frame	null
FGFR3	0	MSKCC-DMP	P-0002610-T01-IM3	JAKMIP1-FGFR3 fusion	yes	unknown		in frame	null reciprocal event, keeping the FGFR3-JAKMIP1 as it has been reported in literature
JAKMIP1	0	MSKCC-DMP	P-0002610-T01-IM3	JAKMIP1-FGFR3 fusion	yes	unknown		in frame	null reciprocal event, keeping the FGFR3-JAKMIP1 as it has been reported in literature
ALK	0	MSKCC-DMP	P-0002613-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
EML4	0	MSKCC-DMP	P-0002613-T01-IM3	EML4-ALK fusion	yes	unknown		in frame	null
NTRK3	0	MSKCC-DMP	P-0002671-T01-IM3	ETV6-NTRK3 fusion	yes	unknown		in frame	null Note: ETV6 - NTRK3 translocation is a structural rearrangement in which exons 1-6 of ETV6 are fused to exons 15-20 of NTRK3. ETV6-NTRK3 fusions have been described in multiple malignancies including congenital fibrosarcoma, carcinomas of the thyroid and breast, and leukemias (PMID: 9462753, 12450792, 24327398, 9949179). The fusion product is believed to constitutively activate the NTRK3 tyrosine kinase (PMID: 15826836)
ETV6	0	MSKCC-DMP	P-0002671-T01-IM3	ETV6-NTRK3 fusion	yes	unknown		in frame	null Note: ETV6 - NTRK3 translocation is a structural rearrangement in which exons 1-6 of ETV6 are fused to exons 15-20 of NTRK3. ETV6-NTRK3 fusions have been described in multiple malignancies including congenital fibrosarcoma, carcinomas of the thyroid and breast, and leukemias (PMID: 9462753, 12450792, 24327398, 9949179). The fusion product is believed to constitutively activate the NTRK3 tyrosine kinase (PMID: 15826836)
STK11	0	MSKCC-DMP	P-0002758-T01-IM3	MIDN-STK11 fusion	yes	unknown		unknown	null
MIDN	0	MSKCC-DMP	P-0002758-T01-IM3	MIDN-STK11 fusion	yes	unknown		unknown	null
SEC61G	0	MSKCC-DMP	P-0002998-T01-IM3	EGFR-SEC61G fusion	yes	unknown		unknown	null Note: EGFR deletion is a rearrangement event which results in deletion of part of exon 1 potentially disabling EGFR protein.
EGFR	0	MSKCC-DMP	P-0002998-T01-IM3	EGFR-SEC61G fusion	yes	unknown		unknown	null Note: EGFR deletion is a rearrangement event which results in deletion of part of exon 1 potentially disabling EGFR protein.
SMAD4	0	MSKCC-DMP	P-0003008-T01-IM3	SMAD4-intragenic	yes	unknown		out of frame	null Note: The SMAD4 (NM_005359) duplication is a rearrangement event which results in the duplication of exons 3 to 7. Its functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0003078-T01-IM5	RNF43-intragenic	yes	unknown		unknown	null The RNF43 deletion is a structural rearrangement which results in the partiall deletion of exon 9.The breakpoint in exon 9 is within the exon.Its functional significance is undetermined.
CNTROB	0	MSKCC-DMP	P-0003871-T01-IM5	STAT5B-CNTROB fusion	yes	unknown		in frame	CNTROB (NM_001037144) - STAT5B (NM_012448) rearrangement (32504650 bp): c.1994-486:CNTROB_c.2078-227:STAT5Binv The CNTROB (NM_001037144) - STAT5B (NM_012448) rearrangement is an inversion that results in the fusion of exons 1-13 of CNTROB with exons 17 -19 of STAT5B. The functional significance is undetermined
STAT5B	0	MSKCC-DMP	P-0003871-T01-IM5	STAT5B-CNTROB fusion	yes	unknown		in frame	CNTROB (NM_001037144) - STAT5B (NM_012448) rearrangement (32504650 bp): c.1994-486:CNTROB_c.2078-227:STAT5Binv The CNTROB (NM_001037144) - STAT5B (NM_012448) rearrangement is an inversion that results in the fusion of exons 1-13 of CNTROB with exons 17 -19 of STAT5B. The functional significance is undetermined
NCOR1	0	MSKCC-DMP	P-0003871-T01-IM5	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.177:NCOR1_chr17g.77834316inv The NCOR1 (NM_006311) rearrangement is an inversion (61744383 bp) that leads to the truncation of NCOR1 exons 3-46. One of the breakpoints is within exon 3 of NCOR1. The functional significance is undetermined.
MLL3	0	MSKCC-DMP	P-0003871-T01-IM5	MLL3-intragenic	yes	unknown		unknown	MLL3 (NM_170606) rearrangement: chr7g.19462033_c.11670+154:MLL3inv The MLL3 (NM_170606) rearrangement is an inversion (32393761 bp) that leads to the truncation of MLL3 exons 45-59. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0003872-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) rearrangement: c.711+1013_c.1314+129 :BRAFdel The BRAF (NM_004333) rearrangement is an intragenic deletion of exons 5-10. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0003970-T01-IM5	EZR-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) - EZR ( NM_003379 ) rearrangement:  c.1090+142C:EZR_c.5366+794T:ROS1del The ROS1 (NM_002944) - EZR ( NM_003379 ) rearrangement is a deletion that results in the fusion of exons 1-9 of EZR with exons 33-43 of ROS1. (PMID: 22327623)
EZR	0	MSKCC-DMP	P-0003970-T01-IM5	EZR-ROS1 fusion	yes	unknown		out of frame	ROS1 (NM_002944) - EZR ( NM_003379 ) rearrangement:  c.1090+142C:EZR_c.5366+794T:ROS1del The ROS1 (NM_002944) - EZR ( NM_003379 ) rearrangement is a deletion that results in the fusion of exons 1-9 of EZR with exons 33-43 of ROS1. (PMID: 22327623)
RAD52	0	MSKCC-DMP	P-0004174-T01-IM5	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: c.543+3970_1049inv Note: The RAD52 (NM_134424) rearrangement event results in the intragenic inversion of exons 8-11. One of the breakpoints is within RAD52 exon11.
FGFR2	0	MSKCC-DMP	P-0004286-T01-IM5	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement : c.1288-636_2302-755inv Note: The FGFR2 (NM_000141) rearrangement event results in the intragenic inversion of FGFR2 exons 10-17. This rearrangement event includes the FGFR2 kinase domain.
RAD51	0	MSKCC-DMP	P-0004518-T01-IM5	RAD51-intragenic	yes	unknown		unknown	RAD51 (NM_002875) Rearrangement :  c.531-1626_628dup Note: The RAD51 (NM_002875) Rearrangement results in the intragenic duplication of exon 7.The breakpoint is within exon7.Its functional significance is undetermined.
NFE2L2	0	MSKCC-DMP	P-0004617-T01-IM5	NFE2L2-intragenic	yes	unknown		in frame	NFE2L2(NM_006164) Rearrangement : c.313-22_46-4138del Note: The NFE2L2(NM_006164) Rearrangement  results in the intragenic deletion of exon 2 of NFE2L2.Its functional significance is undetermined.
GPATCH8	0	MSKCC-DMP	P-0004700-T02-IM5	ERBB2-GPATCH8 fusion	yes	unknown		unknown	GPATCH8 (NM_001002909) - ERBB2 (NM_004448) Rearrangement :c.492+2954:GPATCH8_c.1565:ERBB2inv Note: The GPATCH8 - ERBB2 Rearrangement results in the fusion of exons 1-6 of GPATCH8 with exons13-27 of ERBB2 .One of the breakpoints is within exon13. The rearrangement includes the kinase domain of ERBB2. This rearrangement could be part of the other complex events in ERBB2. Additional testing is suggested if clinically indicated.
ERBB2	0	MSKCC-DMP	P-0004700-T02-IM5	ERBB2-GPATCH8 fusion	yes	unknown		unknown	GPATCH8 (NM_001002909) - ERBB2 (NM_004448) Rearrangement :c.492+2954:GPATCH8_c.1565:ERBB2inv Note: The GPATCH8 - ERBB2 Rearrangement results in the fusion of exons 1-6 of GPATCH8 with exons13-27 of ERBB2 .One of the breakpoints is within exon13. The rearrangement includes the kinase domain of ERBB2. This rearrangement could be part of the other complex events in ERBB2. Additional testing is suggested if clinically indicated.
PNPLA6	0	MSKCC-DMP	P-0005493-T01-IM5	POLD1-PNPLA6 fusion	yes	unknown		unknown	PNPLA6 (NM_001166111) - POLD1 (NM_002691) rearrangement: c.1323:PNPLA6_c.2155-56:POLD1del The PNPLA6 (NM_001166111) - POLD1 (NM_002691) rearrangement is a deletion which results in the fusion of PNPLA6 exons 1-11 with POLD1 exons 18-27. The breakpoints in PNPLA6 exon 11 and POLD1 exon 18 are within exon.  The functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0005493-T01-IM5	POLD1-PNPLA6 fusion	yes	unknown		unknown	PNPLA6 (NM_001166111) - POLD1 (NM_002691) rearrangement: c.1323:PNPLA6_c.2155-56:POLD1del The PNPLA6 (NM_001166111) - POLD1 (NM_002691) rearrangement is a deletion which results in the fusion of PNPLA6 exons 1-11 with POLD1 exons 18-27. The breakpoints in PNPLA6 exon 11 and POLD1 exon 18 are within exon.  The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0005493-T01-IM5	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement (1871506 bp): c.2758:SMARCA4_c.335-249:GCDHinv The SMARCA4 (NM_003072) rearrangement is an inversion of exons 19-35 of SMARCA4 that potentially inactivates SMARCA4. One of the breakpoints is within exon 19 of SMARCA4. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0005493-T01-IM5	POLD1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - POLD1 (NM_002691)  rearrangement (8120964 bp): c.2155-838:POLD1_c.1961:CICinv The CIC (NM_015125) - POLD1 (NM_002691) rearrangement is an inversion spanning CIC exons 10-20 through POLD1 exons 1-17. One of the breakpoints is within exon 10 of CIC. The functional significance is undetermined.
POLD1	0	MSKCC-DMP	P-0005493-T01-IM5	POLD1-CIC fusion	yes	unknown		unknown	CIC (NM_015125) - POLD1 (NM_002691)  rearrangement (8120964 bp): c.2155-838:POLD1_c.1961:CICinv The CIC (NM_015125) - POLD1 (NM_002691) rearrangement is an inversion spanning CIC exons 10-20 through POLD1 exons 1-17. One of the breakpoints is within exon 10 of CIC. The functional significance is undetermined.
MITF	0	MSKCC-DMP	P-0005725-T01-IM5	MITF-intragenic	yes	unknown		in frame	MITF (NM_198159)  Rearrangement: c.666+21_762+497del Note: The MITF (NM_198159)  rearrangement results in the intragenic deletion of exon5. Its functional significance is undetermined.
NCOA4	0	MSKCC-DMP	P-0005748-T01-IM5	RET-NCOA4 fusion	yes	unknown		in frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion : c.763-260:NCOA4_c.2137-707:RETdup The NCOA4 (NM_001145260) - RET (NM_020975) rearrangement is a duplication which results in the fusion of NCOA4 exons 1-8 to RET exons 12-20, including the kinase domain of RET.
RET	0	MSKCC-DMP	P-0005748-T01-IM5	RET-NCOA4 fusion	yes	unknown		in frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion : c.763-260:NCOA4_c.2137-707:RETdup The NCOA4 (NM_001145260) - RET (NM_020975) rearrangement is a duplication which results in the fusion of NCOA4 exons 1-8 to RET exons 12-20, including the kinase domain of RET.
DICER1	0	MSKCC-DMP	P-0005970-T03-IM5	DICER1-intragenic	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: c.5364+1G_c.5365del Note: The DICER1 rearrangement is a intragenic deletion of intron 25 and the first nucleotide of exon 26. The functional significance is undetermined.
GRIP1	0	MSKCC-DMP	P-0006621-T01-IM5	TCF7L2-GRIP1 fusion	yes	unknown		unknown	GRIP1 (NM_021150) - TCF7L2 (NM_001146274) rearrangement : t(10;12)(q25.3;q14.3)(chr10:g.114900968::chr12:g.66756235) Note: The GRIP1 (NM_021150) - TCF7L2 (NM_001146274) rearrangement event is a translocation which results in the fusion of GRIP1 exons 1-22 and TCF7L2 exons 6-14. One of the breakpoints is within TCF7L2 exon6.
TCF7L2	0	MSKCC-DMP	P-0006621-T01-IM5	TCF7L2-GRIP1 fusion	yes	unknown		unknown	GRIP1 (NM_021150) - TCF7L2 (NM_001146274) rearrangement : t(10;12)(q25.3;q14.3)(chr10:g.114900968::chr12:g.66756235) Note: The GRIP1 (NM_021150) - TCF7L2 (NM_001146274) rearrangement event is a translocation which results in the fusion of GRIP1 exons 1-22 and TCF7L2 exons 6-14. One of the breakpoints is within TCF7L2 exon6.
BRAF	0	MSKCC-DMP	P-0006714-T01-IM5	BRAF-intragenic	yes	unknown		in frame	BRAF (NM_004333) rearrangement: c.139-32224_c.1141-1764del The BRAF (NM_004333) rearrangement is an intragenic deletion of exons 2-8. The deletion is predicted to be in frame. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0006953-T01-IM5	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.164-2418_c.464-7073dup The ETV6 (NM_001987) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.
TRPM8	0	MSKCC-DMP	P-0007755-T02-IM5	NTRK1-TRPM8 fusion	yes	unknown		out of frame	TRPM8 (NM_024080) - NTRK1 (NM_002529) rearrangement: t(1;2)(q23.1; q27.1)(chr1:g.156845664::chr2:g.234866124) Note: The TRPM8 - NTRK1 rearrangement is a translocation which results in the fusion of TRPM8 exons 1-11 with NTRK1 exons 13 - 17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0007755-T02-IM5	NTRK1-TRPM8 fusion	yes	unknown		out of frame	TRPM8 (NM_024080) - NTRK1 (NM_002529) rearrangement: t(1;2)(q23.1; q27.1)(chr1:g.156845664::chr2:g.234866124) Note: The TRPM8 - NTRK1 rearrangement is a translocation which results in the fusion of TRPM8 exons 1-11 with NTRK1 exons 13 - 17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
IP6K1	0	MSKCC-DMP	P-0008080-T01-IM5	SETD2-IP6K1 fusion	yes	unknown		unknown	IP6K1 (NM_153273) - SETD2 (NM_014159) rearrangement: c.-129+8864:IP6K1_c:6110-1:SETD2del Note: The IP6K1 (NM_153273) - SETD2 (NM_014159) rearrangement event is a deletion which results in the fusion between 5-UTR of IP6K1 and SETD2 exons 14-24. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0008080-T01-IM5	SETD2-IP6K1 fusion	yes	unknown		unknown	IP6K1 (NM_153273) - SETD2 (NM_014159) rearrangement: c.-129+8864:IP6K1_c:6110-1:SETD2del Note: The IP6K1 (NM_153273) - SETD2 (NM_014159) rearrangement event is a deletion which results in the fusion between 5-UTR of IP6K1 and SETD2 exons 14-24. The functional significance is undetermined.
GATA3	0	MSKCC-DMP	P-0008103-T01-IM5	GATA3-intragenic	yes	unknown		unknown	GATA3 (NM_002051) rearrangement : c.1047+34:GATA3_chr10:g.9186062del Note: The GATA3 (NM_002051) rearrangement event results in the deletion of GATA3 exon6.
NTRK1	0	MSKCC-DMP	P-0008246-T02-IM5	DDR2-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement : c.1178-14:NTRK1_c.-192+7124:DDR2inv Note: The NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement event is an inversion involving NTRK1 exons 1-9.
DDR2	0	MSKCC-DMP	P-0008246-T02-IM5	DDR2-NTRK1 fusion	yes	unknown		unknown	NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement : c.1178-14:NTRK1_c.-192+7124:DDR2inv Note: The NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement event is an inversion involving NTRK1 exons 1-9.
BTK	0	MSKCC-DMP	P-0008290-T01-IM5	BTK-intragenic	yes	unknown		unknown	BTK (NM_000061) rearrangement: c.392-764_c.1682dup The BTK (NM_000061) rearrangement is an intragenic duplication of exons 6-17 of BTK. One of the breakpoints is within exon 17. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0008715-T01-IM5	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3198+1406_c.5892del Note: The ARID1A (NM_006015) rearrangement is an intragenic deletion of exons 12-20. One of the breakpoints is within exon 20. The functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0008715-T01-IM5	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.636_c.921-244del Note: The STK11 (NM_000455) rearrangement is a intragenic deletion of exons 5-7. One of the breakpoints is within exon 5.  The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0008928-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion ()TMPRSS2 exons 1-2 fused with ERG exons 4-11) :  c.127-1337:TMPRSS2_c.39+60944:ERGdel
ERG	0	MSKCC-DMP	P-0008928-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion ()TMPRSS2 exons 1-2 fused with ERG exons 4-11) :  c.127-1337:TMPRSS2_c.39+60944:ERGdel
PTCH1	0	MSKCC-DMP	P-0008942-T01-IM5	STRN-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) - STRN (NM_003162) Rearrangement : t(2;9)(2p25.1;9q22.32)(chr2:g.7116407::chr9:g.98215861) Note: The PTCH1 (NM_000264) - STRN (NM_003162) Rearrangement  results in the fusion of PTCH1 exons 1 to 20 of PTCH1 with exons 8 to 18 of STRN. Its functional significance is undetermined.
STRN	0	MSKCC-DMP	P-0008942-T01-IM5	STRN-PTCH1 fusion	yes	unknown		unknown	PTCH1 (NM_000264) - STRN (NM_003162) Rearrangement : t(2;9)(2p25.1;9q22.32)(chr2:g.7116407::chr9:g.98215861) Note: The PTCH1 (NM_000264) - STRN (NM_003162) Rearrangement  results in the fusion of PTCH1 exons 1 to 20 of PTCH1 with exons 8 to 18 of STRN. Its functional significance is undetermined.
C19orf47	0	MSKCC-DMP	P-0009563-T01-IM5	AKT2-C19orf47 fusion	yes	unknown		unknown	C19orf47 (NM_001256441) - AKT2 (NM_001626) Rearrangement : c.19+973:NM_001256441_c.832-15AKT2del Note: The C19orf47 (NM_001256441) - AKT2 (NM_001626) Rearrangement results in the fusion of exons 1-2 of C19orf47 with exons 10-14 of AKT2. Its functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0009563-T01-IM5	AKT2-C19orf47 fusion	yes	unknown		unknown	C19orf47 (NM_001256441) - AKT2 (NM_001626) Rearrangement : c.19+973:NM_001256441_c.832-15AKT2del Note: The C19orf47 (NM_001256441) - AKT2 (NM_001626) Rearrangement results in the fusion of exons 1-2 of C19orf47 with exons 10-14 of AKT2. Its functional significance is undetermined.
TUBGCP3	0	MSKCC-DMP	P-0009647-T01-IM5	BRCA2-TUBGCP3 fusion	yes	unknown		out of frame	TUBGCP3 (NM_006322) - BRCA2 (NM_000059) rearrangement: c.1745+7:TUBGCP3_c.794-177:BRCA2inv Note: TUBGCP3 (NM_006322) - BRCA2 (NM_000059) rearrangement is an inversion that results in the fusion of TUBGCP3 exons 1-14 with BRCA2 exons 10-27. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0009647-T01-IM5	BRCA2-TUBGCP3 fusion	yes	unknown		out of frame	TUBGCP3 (NM_006322) - BRCA2 (NM_000059) rearrangement: c.1745+7:TUBGCP3_c.794-177:BRCA2inv Note: TUBGCP3 (NM_006322) - BRCA2 (NM_000059) rearrangement is an inversion that results in the fusion of TUBGCP3 exons 1-14 with BRCA2 exons 10-27. The functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0009647-T01-IM5	LEPREL1-TP63 fusion	yes	unknown		in frame	TP63 (NM_003722) - LEPREL1 (NM_018192) rearrangement: c.324+76:TP63_c.480+38077:LEPREL1inv Note: The TP63 (NM_003722) - LEPREL1 (NM_018192) rearrangement is an inversion that results in an in frame fusion of TP63 exons 1-3 with LEPREL1 exons 2-15. The functional significance is undetermined.
LEPREL1	0	MSKCC-DMP	P-0009647-T01-IM5	LEPREL1-TP63 fusion	yes	unknown		in frame	TP63 (NM_003722) - LEPREL1 (NM_018192) rearrangement: c.324+76:TP63_c.480+38077:LEPREL1inv Note: The TP63 (NM_003722) - LEPREL1 (NM_018192) rearrangement is an inversion that results in an in frame fusion of TP63 exons 1-3 with LEPREL1 exons 2-15. The functional significance is undetermined.
TGFBR2	0	MSKCC-DMP	P-0009876-T01-IM5	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement : c.1611:TGFBR2_chr3:g.24649275del Note: The TGFBR2 (NM_001024847) rearrangement event results in the deletion of TGFBR2 exons 1-8. One of the breakpoints is within TGFBR2 exon8.
MTOR	0	MSKCC-DMP	P-0009940-T01-IM5	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.1588_c.7016+305del Note: The MTOR rearrangement is an intragenic deletion of exons 11-50. One of the breakpoints is within exon11. The functional significance is undetermined.
PAX5	0	MSKCC-DMP	P-0012241-T01-IM5	PAX5-intragenic	yes	unknown		unknown	PAX5 (NM_016734) Rearrangement: c.365_c.605-3847inv Note: The PAX5 Rearrangement results in the intragenic inversion of exon 3-5 of PAX5. One of breakpoints is within exon3. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0012400-T01-IM5	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.3951+88_c.4170+2065del Note: The SMARCA4 rearrangement is an intragenic deletion of exon 29.
LATS1	0	MSKCC-DMP	P-0012400-T01-IM5	GLIS3-LATS1 fusion	yes	unknown		unknown	LATS1 (NM_004690) - GLIS3 (NM_001042413) rearrangement: t(6;9)(q25.1;p24.2)(chr6:g.150001247::chr9:g.3858763) Note: The LATS1- GLIS3 rearrangement is a translocation that results in a fusion of LATS1 exons 1-5 with GLIS3 exons 9-11. One of the breakpoints is within LATS1 exon 5. The functional significance is undetermined.
GLIS3	0	MSKCC-DMP	P-0012400-T01-IM5	GLIS3-LATS1 fusion	yes	unknown		unknown	LATS1 (NM_004690) - GLIS3 (NM_001042413) rearrangement: t(6;9)(q25.1;p24.2)(chr6:g.150001247::chr9:g.3858763) Note: The LATS1- GLIS3 rearrangement is a translocation that results in a fusion of LATS1 exons 1-5 with GLIS3 exons 9-11. One of the breakpoints is within LATS1 exon 5. The functional significance is undetermined.
ARID5B	0	MSKCC-DMP	P-0012696-T01-IM5	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.-1841_c.-182del Note: The ARID5B rearrangement is a deletion of the promoter and 5UTR. The functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0012696-T01-IM5	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.550-172_c.1586+396dup Note: The TCF3 rearrangement is a duplication of exons 8-18. One of the breakpoints is within exon 18. The functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0012696-T01-IM5	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(8;19)(q12.1;p13.3)(chr8:g.61237662::chr19:g.5210677) Note: The PTPRS rearrangement is a translocation with a breakpoint after exon 25 and may result in a truncated PTPRS. The functional significance is undetermined.
PWWP2A	0	MSKCC-DMP	P-0012884-T01-IM5	BRAF-PWWP2A fusion	yes	unknown		in frame	PWWP2A (NM_001130864) - BRAF(NM_004333) Rearrangement : t(5;7)(q33.3;q34)(chr5:g.159539324::chr7:g.140495243) Note: The PWWP2A - BRAF Rearrangement is a translocation event which results in the fusion of exon 1 of PWWP2A with exons 8-18 of BRAF. This includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0012884-T01-IM5	BRAF-PWWP2A fusion	yes	unknown		in frame	PWWP2A (NM_001130864) - BRAF(NM_004333) Rearrangement : t(5;7)(q33.3;q34)(chr5:g.159539324::chr7:g.140495243) Note: The PWWP2A - BRAF Rearrangement is a translocation event which results in the fusion of exon 1 of PWWP2A with exons 8-18 of BRAF. This includes the kinase domain of BRAF.
CDKN2Ap14ARF	0	MSKCC-DMP	P-0012947-T01-IM5	CDKN2Ap14ARF-intragenic	yes	unknown		unknown	CDKN2Ap14ARF (NM_058195) rearrangement: c.*102-382_c.*3284del Note: The CDKN2Ap14ARF rearrangement results in the deletion of 3UTR. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0012947-T01-IM5	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-382_c.*3169del Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exon 3 and 3UTR.
TBX3	0	MSKCC-DMP	P-0013025-T01-IM5	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: chr12:g.124583968_c.211:TBX3inv Note: The TBX3 rearrangement is an inversion of 5UTR and exon 1. One of the breakpoints is within exon 1.
SMARCD1	0	MSKCC-DMP	P-0013782-T01-IM5	SMARCD1-intragenic	yes	unknown		unknown	SMARCD1 (NM_003076) rearrangement:c.1130_c.1134-4del Note: The SMARCD1 (NM_003076) rearrangement results in a deletion of part of exon 9. One of the breakpoints is within exon 9.  The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0013808-T02-IM6	SMG1-PBRM1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) - SMG1 (NM_015092) rearrangement: t(3;16)(p21.1;p12.3)(chr3:g.52695981::chr16:g.18853678) Note: The PBRM1 - SMG1 rearrangement is a translocation that results in the fusion of PBRM1 exons 1-5 with SMG1 exons 40 - 63. One of the breakpoints is within SMG1 exon 40. The functional significance is undetermined.
SMG1	0	MSKCC-DMP	P-0013808-T02-IM6	SMG1-PBRM1 fusion	yes	unknown		unknown	PBRM1 (NM_018313) - SMG1 (NM_015092) rearrangement: t(3;16)(p21.1;p12.3)(chr3:g.52695981::chr16:g.18853678) Note: The PBRM1 - SMG1 rearrangement is a translocation that results in the fusion of PBRM1 exons 1-5 with SMG1 exons 40 - 63. One of the breakpoints is within SMG1 exon 40. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0013808-T02-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.41448977_c.6920dup Note: The EP300 rearrangement is a duplication that includes EP300 exons 1-13. One of the breakpoints is within exon 31.
NF2	0	MSKCC-DMP	P-0014137-T01-IM5	NF2-intragenic	yes	unknown		unknown	NF2 (NM_000268) Rearrangement : c.363+6:NF2_chr22:45151093inv Note: The NF2 Rearrangement results in the inversion of exons 4-16 of NF2. Its functional significance is undetermined.
MLL	0	MSKCC-DMP	P-0015415-T01-IM6	MLL-intragenic	yes	unknown		unknown	MLL (NM_001197104) Rearrangement: c.433-2334_c.1347del Note: The MLL Rearrangement results in the intragenic deletion of exons 2-3 of MLL. One of the breakpoints is within exon3. Its functional significance is undetermined.
LOH12CR1	0	MSKCC-DMP	P-0015724-T01-IM6	ETV6-LOH12CR1 fusion	yes	unknown		in frame	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangement: c.202+1037:LOH12CR1_c.1010-2951:ETV6dup Note: The LOH12CR1 - ETV6 rearrangement is a duplication which results in the fusion of LOH12CR1 exon 2 to ETV6 exon 6. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0015724-T01-IM6	ETV6-LOH12CR1 fusion	yes	unknown		in frame	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangement: c.202+1037:LOH12CR1_c.1010-2951:ETV6dup Note: The LOH12CR1 - ETV6 rearrangement is a duplication which results in the fusion of LOH12CR1 exon 2 to ETV6 exon 6. The functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0015920-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.2733-1053_c.2958del Note: The ARID1A rearrangement results in the deletion of exons 9 and 10. One of the breakpoints is within exon 10. The functional significance is undetermined.
RAD54L	0	MSKCC-DMP	P-0015920-T01-IM6	RAD54L-intragenic	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.1342_c.1869+927del Note: The RAD54L rearrangement results in the deletion of exons 13-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0015920-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.2120_c.2055+4196del Note: The NCOR1 rearrangement results in the deletion of exon 19. One of the breakpoints is within exon 19. The functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0015984-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	TACC3 (NM_006342) - FGFR3 (NM_000142) Rearrangement : c.1645-67:TACC3_c.*18:FGFR3dup Note: The TACC3 - FGFR3 Rearrangement results in the duplication of exons 8-16 of TACC3 and exons 1-18 of FGFR3. The breakpoint in FGFR3 is within exon18. This is not the canonical FGFR3-TACC3 fusion but may be associated with an undetected functional fusion. This event includes the protein kinase domain of FGFR3.
FGFR3	0	MSKCC-DMP	P-0015984-T01-IM6	FGFR3-TACC3 fusion	yes	unknown		unknown	TACC3 (NM_006342) - FGFR3 (NM_000142) Rearrangement : c.1645-67:TACC3_c.*18:FGFR3dup Note: The TACC3 - FGFR3 Rearrangement results in the duplication of exons 8-16 of TACC3 and exons 1-18 of FGFR3. The breakpoint in FGFR3 is within exon18. This is not the canonical FGFR3-TACC3 fusion but may be associated with an undetected functional fusion. This event includes the protein kinase domain of FGFR3.
TRIM63	0	MSKCC-DMP	P-0016347-T01-IM6	NTRK1-TRIM63 fusion	yes	unknown		in frame	TRIM63 (NM_032588) - NTRK1 (NM_002529) Rearrangement : c.1051+386:TRIM63_c.1178-127:NTRK1inv Note: The TRIM63 - NTRK1 Rearrangement results in the fusion of exons 1-8 of TRIM63 with exons 9-17 of NTRK1.This event is predicted to be in-frame and includes the protein kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0016347-T01-IM6	NTRK1-TRIM63 fusion	yes	unknown		in frame	TRIM63 (NM_032588) - NTRK1 (NM_002529) Rearrangement : c.1051+386:TRIM63_c.1178-127:NTRK1inv Note: The TRIM63 - NTRK1 Rearrangement results in the fusion of exons 1-8 of TRIM63 with exons 9-17 of NTRK1.This event is predicted to be in-frame and includes the protein kinase domain of NTRK1.
TP63	0	MSKCC-DMP	P-0016351-T01-IM6	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) Rearrangement : c.580-11:TP63_c.823+1433:LEPREL1dup Note: The TP63 Rearrangement results in the duplication of exons 5-14 of TP63. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0016546-T01-IM6	TMEM51-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - TMEM51 (NM_018022) rearrangement: c.2173:SPEN_c.-193-17536:TMEM51dup Note: The SPEN - TMEM51 rearrangement is a duplication which results in the fusion of SPEN exon11 to TMEM51 exon2. One of the breakpoints is within SPEN exon11. The functional significance is undetermined.
TMEM51	0	MSKCC-DMP	P-0016546-T01-IM6	TMEM51-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - TMEM51 (NM_018022) rearrangement: c.2173:SPEN_c.-193-17536:TMEM51dup Note: The SPEN - TMEM51 rearrangement is a duplication which results in the fusion of SPEN exon11 to TMEM51 exon2. One of the breakpoints is within SPEN exon11. The functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0017217-T01-IM6	AKT1-intragenic	yes	unknown		unknown	AKT1 (NM_001014431) rearrangement: c.1260_c.1261del Note: The AKT1 rearrangement is an intragenic deletion with breakpoints on both the exons 12 and 13.
NCOR1	0	MSKCC-DMP	P-0017217-T01-IM6	NCOR1-intragenic	yes	unknown		out of frame	NCOR1 (NM_006311) rearrangement: c.3178-1644_c.3401-128del Note: The NCOR1 rearrangement is an intragenic deletion of NCOR1 exons 24-25.
CDKN1A	0	MSKCC-DMP	P-0019915-T01-IM6	CDKN1A-intragenic	yes	unknown		unknown	CDKN1A (NM_078467) rearrangement: t(3;6)(q28;p21.2)(chr3:g.191928578::chr6:g.36651921) Note: The CDKN1A rearrangement is a translocation that may result in a truncation of exons 3-4. One of the breakpoints is within exon 3. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0020065-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement : c.8166_c.7194inv Note: The KMT2D rearrangement results in the inversion of exons 31-32. One of the breakpoints is within exon 31 and the other is within exon 32. The functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0020065-T01-IM6	SRC-intragenic	yes	unknown		unknown	SRC (NM_198291) rearrangement : c.704-116:SRC_g.36481250inv Note: The SRC rearrangement results in the inversion of exons 9-14. The functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0020156-T01-IM6	EMID1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.945+800:EWSR1_c.466-2061:EMID1dup Note: The EWSR1 - EMID1 rearrangement is a duplication that results in the fusion of EWSR1 exons 1-12 with EMID1 exons 6-15. The functional significance is undetermined.
EMID1	0	MSKCC-DMP	P-0020156-T01-IM6	EMID1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.945+800:EWSR1_c.466-2061:EMID1dup Note: The EWSR1 - EMID1 rearrangement is a duplication that results in the fusion of EWSR1 exons 1-12 with EMID1 exons 6-15. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0020694-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: chr15:g.44989687_c.143:B2Mdel Note: The B2M rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0020720-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.376-159_c.-28-566del Note: The TP53 rearrangement is an intragenic deletion of exons 1-4.
ARID1A	0	MSKCC-DMP	P-0021390-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1921-1093_c.1949del Note: The ARID1A rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. Its significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0021390-T02-IM6	CDKN2Ap16INK4A-intragenic	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) rearrangement: c.14_c.-969del Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.
SHOC2	0	MSKCC-DMP	P-0021605-T01-IM6	SHOC2-intragenic	yes	unknown		unknown	SHOC2 (NM_007373) Rearrangement : chr10:g.91947785_c.1487:SHOC2del Note: The SHOC2 Rearrangement results in the deletion of exons 1-8 of SHOC2. Its functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0022795-T01-IM6	EWSR1-intragenic	yes	unknown		unknown	EWSR1 (NM_013986) Rearrangement : c.260+2008:KREMEN1_c.993-1354:EWSR1inv Note: The EWSR1 Rearrangement results in the inversion of exons 1-10 of EWSR1. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0023249-T02-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2320_c.839-334inv Note: The TMPRSS2 rearrangement is an inversion of exons 2-8. Multiple TMPRSS2 rearrangements were detected in this sample.A more complex rearrangement resulting in a TMPRSS2 -ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
LANCL2	0	MSKCC-DMP	P-0025018-T01-IM6	EGFR-LANCL2 fusion	yes	unknown		out of frame	LANCL2 (NM_018697) - EGFR (NM_005228) rearrangement: c.1259-255:LANCL2_c.2947-344:EGFRdup Note: The LANCL2 - EGFR rearrangement is a duplication which results in the fusion of LANCL2 exons 1-8 with EGFR exons 25-28. This does not not include the kinase domain. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0025018-T01-IM6	EGFR-LANCL2 fusion	yes	unknown		out of frame	LANCL2 (NM_018697) - EGFR (NM_005228) rearrangement: c.1259-255:LANCL2_c.2947-344:EGFRdup Note: The LANCL2 - EGFR rearrangement is a duplication which results in the fusion of LANCL2 exons 1-8 with EGFR exons 25-28. This does not not include the kinase domain. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0025871-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.738:WHSC1L1 _chr8:g.36973437inv Note: The WHSC1L1 rearrangement is an inversion of exons 3 - 24. One of the breakpoints is within exon 3. Its functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0025973-T01-IM6	SETD2-intragenic	yes	unknown		out of frame	SETD2 (NM_014159) Rearrangement : c.5015+844_c.5142+160dup Note: The SETD2 (NM_014159) Rearrangement results in the intragenic duplication of exon 9. Its functional significance is undetermined.
PRKAR1A	0	MSKCC-DMP	P-0026488-T01-IM6	MYO1D-PRKAR1A fusion	yes	unknown		in frame	PRKAR1A (NM_212471) - MYO1D (NM_015194) rearrangement: c.708+36:PRKAR1A_c.1468-2012:MYO1Dinv Note: The PRKAR1A rearrangement is an inversion resulting in the fusion of PRKAR1A exons 1-7 with MYO1D exons 12-22. Its functional significance is undetermined. Multiple rearrangements involving PRKAR1A were detected in this sample and a more complex rearrangement resulting in additional PRKAR1A fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MYO1D	0	MSKCC-DMP	P-0026488-T01-IM6	MYO1D-PRKAR1A fusion	yes	unknown		in frame	PRKAR1A (NM_212471) - MYO1D (NM_015194) rearrangement: c.708+36:PRKAR1A_c.1468-2012:MYO1Dinv Note: The PRKAR1A rearrangement is an inversion resulting in the fusion of PRKAR1A exons 1-7 with MYO1D exons 12-22. Its functional significance is undetermined. Multiple rearrangements involving PRKAR1A were detected in this sample and a more complex rearrangement resulting in additional PRKAR1A fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
WT1	0	MSKCC-DMP	P-0026506-T01-IM6	WT1-intragenic	yes	unknown		unknown	WT1 (NM_024426) Rearrangement :  t(8;13)(q21.11,p13)(chr8:g.74791141::chr11:g.32414224) Note: The WT1 rearrangement is a translocation that results in the possible truncation of WT1. One of the breakpoints is within exon 8 of WT1. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0026683-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2659:BRD4_chr19:g.15431410del Note: The BRD4 rearrangement is a deletion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0027084-T01-IM6	SLX4-intragenic	yes	unknown		unknown	SLX4 (NM_032444) rearrangement: c.4840:SLX4_chr16:g.34647886inv Note: the SLX4 rearrangement is an inversion of exons 1-14. One of the breakpoints is within exon 14. Its functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0028804-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.1579:NOTCH1_chr9:g.139536999inv Note: The NOTCH1 rearrangement is an inversion of NOTCH1 exons 1-10. One of the breakpoints is within exon 10. The functional significance is undetermined.
CCNE1	0	MSKCC-DMP	P-0029539-T01-IM6	ACTN4-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) - ACTN4 (NM_004924) rearrangement: c.463-68:CCNE1_c.2410:ACTN4del Note: The CCNE1 - ACTN4 rearrangement is a deletion which results in the fusion of CCNE1 exons 1-6 with ACTN4 exons 19-21. One of the breakpoints is within ACTN4 exon 19. Its functional significance is undetermined.
ACTN4	0	MSKCC-DMP	P-0029539-T01-IM6	ACTN4-CCNE1 fusion	yes	unknown		unknown	CCNE1 (NM_001238) - ACTN4 (NM_004924) rearrangement: c.463-68:CCNE1_c.2410:ACTN4del Note: The CCNE1 - ACTN4 rearrangement is a deletion which results in the fusion of CCNE1 exons 1-6 with ACTN4 exons 19-21. One of the breakpoints is within ACTN4 exon 19. Its functional significance is undetermined.
RRAS	0	MSKCC-DMP	P-0029539-T01-IM6	RRAS-intragenic	yes	unknown		unknown	RRAS (NM_006270) rearrangement: t(5;19)(p15.2;q13.33)(chr5:g.12569365::chr19:g.50139900) Note: The RRAS rearrangement is a translocation involving a breakpoint in exon 4. Its functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0030023-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) Rearrangement: c.1123-944_c.1035del Note: The KDM5C rearrangement is an intragenic deletion of exons 8. One of the breakpoints is within exon 8 of KDM5C. The functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0030156-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) Rearrangement : c.2715+497_c.3655del Note: The PREX2 Rearrangement results in the intragenic deletion of exons 23-30 of PREX2. One of the breakpoints is within exon30. Its functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0030309-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: chr7:g.52700313_c.3162+189:EGFR_inv Note: The EGFR rearrangement results in the inversion of exons 1-26. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0030384-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1256:TMPRSS2_c.39+13477:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 4-10. TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
ERG	0	MSKCC-DMP	P-0030384-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1256:TMPRSS2_c.39+13477:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 4-10. TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.
TMPRSS2	0	MSKCC-DMP	P-0030645-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-658:TMPRSS2_c.39+17522:ERGdel
ERG	0	MSKCC-DMP	P-0030645-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-658:TMPRSS2_c.39+17522:ERGdel
SUZ12	0	MSKCC-DMP	P-0030694-T01-IM6	SUZ12-intragenic	yes	unknown		unknown	SUZ12 (NM_015355) rearrangement: t(16;17)(q21;q11.2)(chr16:g.58252801::chr17:g.30320331) Note: The SUZ12 rearrangement is a translocation involving a breakpoint in exon 11. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0030738-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.200_c.2975del Note: The ZFHX3 rearrangement is an intragenic deletion with breakpoints on exons 2 and 3. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0030844-T01-IM6	MTOR-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) - MTOR (NM_004958) Rearrangement: c.2426+2:PIK3CD_c.4254-479:MTORdel Note: The PIK3CD - MTRO rearrangement is an deletion of PIK3CD exons 20-24 to MTOR exons 29-58
MTOR	0	MSKCC-DMP	P-0030844-T01-IM6	MTOR-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) - MTOR (NM_004958) Rearrangement: c.2426+2:PIK3CD_c.4254-479:MTORdel Note: The PIK3CD - MTRO rearrangement is an deletion of PIK3CD exons 20-24 to MTOR exons 29-58
FGFR2	0	MSKCC-DMP	P-0030844-T01-IM6	MYH15-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYH15 (NM_014981) rearrangement: t(3;10)(q13.13;q26.13)(chr3:g.108134575::chr10:g.123240665) Note: The FGFR2 - MYH15 rearrangement is a translocation that results in the in-frame fusion of FGFR2 exons 1-17 with MYH15 exons 31-42 and includes the kinase domain of FGFR2.
MYH15	0	MSKCC-DMP	P-0030844-T01-IM6	MYH15-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - MYH15 (NM_014981) rearrangement: t(3;10)(q13.13;q26.13)(chr3:g.108134575::chr10:g.123240665) Note: The FGFR2 - MYH15 rearrangement is a translocation that results in the in-frame fusion of FGFR2 exons 1-17 with MYH15 exons 31-42 and includes the kinase domain of FGFR2.
BRCA1	0	MSKCC-DMP	P-0030943-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.-1772_c.726del Note: The BRCA1 rearrangement is a deletion of exons 1-10. One of the breakpoints is within exon 10.
ROS1	0	MSKCC-DMP	P-0030943-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5080-1093:ROS1_chr6:g.121016948del Note: The ROS1 rearrangement is a deletion of exons 1-30. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0031008-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3443:TMPRSS2_c.18+19812:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0031008-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3443:TMPRSS2_c.18+19812:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
RTEL1	0	MSKCC-DMP	P-0031031-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) Rearrangement: c.3182-48:RTEL1_chr20:g.57400991del Note: The RTEL1 rearrangement is a deletion of RTEL1 exons 2 to 31. The functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0031152-T01-IM6	NUF2-intragenic	yes	unknown		unknown	NUF2 (NM_031423) Rearrangement: c.1261-1557_c.*112inv Note: The NUF2 rearrangement is an intragenic inversion of exon 14. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0031232-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+303:CDKN1B_chr9:g.21962196del Note: The CDKN2B rearrangement is a deletion of exon 2.
PAX8	0	MSKCC-DMP	P-0031234-T01-IM6	USP37-PAX8 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - USP37 (NM_020935) rearrangement: c.1189+676:PAX8_c.1026-4311:USP37dup Note: The PAX8 - USP37 rearrangement is a duplication that results in the fusion of PAX8 exons 1-10 to USP37 exons 12-26. The functional significance is undetermined.
USP37	0	MSKCC-DMP	P-0031234-T01-IM6	USP37-PAX8 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - USP37 (NM_020935) rearrangement: c.1189+676:PAX8_c.1026-4311:USP37dup Note: The PAX8 - USP37 rearrangement is a duplication that results in the fusion of PAX8 exons 1-10 to USP37 exons 12-26. The functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0031824-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.2171:FANCA_chr16:g.89592277dup Note: The FANCA rearrangement results in the duplication of exons 24-43. One of the breakpoints is within exon 24. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0031824-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.208+2971:EML4_c.2816-19:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-2 and ALK exons 17-29. The fusion is predicted to be in-frame and involves the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0031824-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.208+2971:EML4_c.2816-19:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-2 and ALK exons 17-29. The fusion is predicted to be in-frame and involves the kinase domain of ALK.
TP53	0	MSKCC-DMP	P-0031946-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement: c.993+155_c.*4475inv Note: The TP53 rearrangement is an intragenic inversion of exons 10-11. The functional significance is undetermined.
MSH2	0	MSKCC-DMP	P-0033077-T01-IM6	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) rearrangement: chr2:g.34164010_c.2635-1del Note: The MSH2 rearrangement is a deletion that includes MSH2 exons 1-16. One of the breakpoints is within exon 16.
ROS1	0	MSKCC-DMP	P-0033077-T01-IM6	SLC35F1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) - SLC35F1 (NM_00102985) rearrangement: c.5249-591:ROS1_c.174-110100:SLC35F1del Note: The ROS1 - SLC35F1 rearrangement is a deletion that includes ROS1 exons 1-31 and SLC35F1. The functional significance is undetermined.
SLC35F1	0	MSKCC-DMP	P-0033077-T01-IM6	SLC35F1-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) - SLC35F1 (NM_00102985) rearrangement: c.5249-591:ROS1_c.174-110100:SLC35F1del Note: The ROS1 - SLC35F1 rearrangement is a deletion that includes ROS1 exons 1-31 and SLC35F1. The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0033633-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: c.1040_c.1317dup Note: The DROSHA rearrangement is an intragenic duplication of exons 6-8. Both breakpoints are within exon. The functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0034632-T03-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: t(15;16)(q25.1;q22.1)(chr15:g.79195333::chr16:g.68847420) Note: The CDH1 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
TLK2	0	MSKCC-DMP	P-0034868-T01-IM6	BRIP1-TLK2 fusion	yes	unknown		unknown	TLK2 (NM_006852) - BRIP1 (NM_032043) rearrangement: c.1461-1686:TLK2_c.3392:BRIP1inv Note: The TLK2 - BRIP1 rearrangement is an inversion which results in the fusion of TLK2 exons 1-17 with BRIP1 exon 20. One of the breakpoints is within BRIP1 exon 20. Its functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0034868-T01-IM6	BRIP1-TLK2 fusion	yes	unknown		unknown	TLK2 (NM_006852) - BRIP1 (NM_032043) rearrangement: c.1461-1686:TLK2_c.3392:BRIP1inv Note: The TLK2 - BRIP1 rearrangement is an inversion which results in the fusion of TLK2 exons 1-17 with BRIP1 exon 20. One of the breakpoints is within BRIP1 exon 20. Its functional significance is undetermined.
ERRFI1	0	MSKCC-DMP	P-0035316-T01-IM6	ERRFI1-intragenic	yes	unknown		unknown	ERRFI1 (NM_018948) rearrangement: c.679_chr1:g.12117784del Note: The ERRFI1 rearrangement is a deletion that includes ERRFI1 exon 4.
KLHL12	0	MSKCC-DMP	P-0036680-T01-IM6	BRAF-KLHL12 fusion	yes	unknown		in frame	KLHL12 (NM_021633) - BRAF (NM_004333) fusion (KLHL12 exons 1-4 fused to BRAF exons 9-18): t(1;7)(q32.1;q34)(chr1:g.202880970::chr7:g.140493984) Note: The KLHL12 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0036680-T01-IM6	BRAF-KLHL12 fusion	yes	unknown		in frame	KLHL12 (NM_021633) - BRAF (NM_004333) fusion (KLHL12 exons 1-4 fused to BRAF exons 9-18): t(1;7)(q32.1;q34)(chr1:g.202880970::chr7:g.140493984) Note: The KLHL12 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF.
MAP1A	0	MSKCC-DMP	P-0038250-T01-IM6	TP53BP1-MAP1A fusion	yes	unknown		unknown	MAP1A (NM_002373) - TP53BP1 (NM_001141980) Rearrangement : c.2178:MAP1A_c.4169:TP53BP1inv Note: The MAP1A -TP53BP1  Rearrangement results in the fusion of exons 1-4 of MAP1A with exons20-28 of TP53BP1. The breakpoints are within exon4 of MAP1A and exon20 of TP53BP1. Its functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0038250-T01-IM6	TP53BP1-MAP1A fusion	yes	unknown		unknown	MAP1A (NM_002373) - TP53BP1 (NM_001141980) Rearrangement : c.2178:MAP1A_c.4169:TP53BP1inv Note: The MAP1A -TP53BP1  Rearrangement results in the fusion of exons 1-4 of MAP1A with exons20-28 of TP53BP1. The breakpoints are within exon4 of MAP1A and exon20 of TP53BP1. Its functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0038250-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) Rearrangement : c.5765_c.7570-37dup Note: The ANKRD11 Rearrangement results in the intragenic duplication of exons of ANKRD11. One of the breakpoints is within exon9. Its functional significance is undetermined.
GATA1	0	MSKCC-DMP	P-0038316-T01-IM6	GATA1-intragenic	yes	unknown		unknown	GATA1 (NM_002049) rearrangement: c.838:GATA1_chrX:g.48599163dup Note: The GATA1 rearrangement results in the duplication of exons 1-5. One of the breakpoints is within exon 5. The functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0040452-T01-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.215+103:AGO2_chr8:g.130712714del Note: The AGO2 rearrangement is a deletion of exons 3 - 19. Functional significance is undetermined.
AK9	0	MSKCC-DMP	P-0041672-T01-IM6	IGF1R-AK9 fusion	yes	unknown		unknown	AK9 (NM_001145128) - IGF1R (NM_000875) rearrangement: t(6;15)(q21;q26.3)(chr6:g.109947133::chr15:g.99486197) Note: The AK9 - IGF1R rearrangement is a translocation  that results in a fusion of AK9 exons 1-13 to IGF1R exons 19 - 21. One of the breakpoints is in IGF1R exon 19. Functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0041672-T01-IM6	IGF1R-AK9 fusion	yes	unknown		unknown	AK9 (NM_001145128) - IGF1R (NM_000875) rearrangement: t(6;15)(q21;q26.3)(chr6:g.109947133::chr15:g.99486197) Note: The AK9 - IGF1R rearrangement is a translocation  that results in a fusion of AK9 exons 1-13 to IGF1R exons 19 - 21. One of the breakpoints is in IGF1R exon 19. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0041855-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3266-6560_c.11102del Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 19. One of the breakpoints is within exon 19.
BCAN	0	MSKCC-DMP	P-0041874-T01-IM6	NTRK1-BCAN fusion	yes	unknown		in frame	BCAN (NM_021948) - NTRK1 (NM_002529) fusion: c.92-224:BCAN_c.851-167:NTRK1del Note: The BCAN - NTRK1 fusion involves BCAN exons 1 - 2 and NTRK1 exons 8 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0041874-T01-IM6	NTRK1-BCAN fusion	yes	unknown		in frame	BCAN (NM_021948) - NTRK1 (NM_002529) fusion: c.92-224:BCAN_c.851-167:NTRK1del Note: The BCAN - NTRK1 fusion involves BCAN exons 1 - 2 and NTRK1 exons 8 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
STK11	0	MSKCC-DMP	P-0041900-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.93_c.290+4807del Note: The STK11 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1. The rearrangement includes a part of the kinase domain of STK11.
KMT2B	0	MSKCC-DMP	P-0041985-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.291:KMT2B_chr19:g.36208418del Note: The KMT2B rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
KIF5B	0	MSKCC-DMP	P-0042104-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1056:KIF5B_c.2136+321:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0042104-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1056:KIF5B_c.2136+321:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
SS18	0	MSKCC-DMP	P-0015724-T01-IM6	AP3B1-SS18 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SS18-AP3B1 fusion. Note: The rearrangement is an in-frame fusion between genes SS18 Exon10 (NM_001007559) and AP3B1 Exon8 (NM_003664). Lab Notes Run Number: ArcherV1-CLIN-20160063 Macro-dissection: Performed
AP3B1	0	MSKCC-DMP	P-0015724-T01-IM6	AP3B1-SS18 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SS18-AP3B1 fusion. Note: The rearrangement is an in-frame fusion between genes SS18 Exon10 (NM_001007559) and AP3B1 Exon8 (NM_003664). Lab Notes Run Number: ArcherV1-CLIN-20160063 Macro-dissection: Performed
FGFR3	0	MSKCC-DMP	P-0015984-T01-IM6	TAAC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TAAC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_001163213) and TAAC3 Exon8 (undefined). Lab Notes Run Number: ArcherV1-CLIN-20160066 Macro-dissection: Not Performed
TAAC3	0	MSKCC-DMP	P-0015984-T01-IM6	TAAC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-TAAC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_001163213) and TAAC3 Exon8 (undefined). Lab Notes Run Number: ArcherV1-CLIN-20160066 Macro-dissection: Not Performed
FGFR3	0	MSKCC-DMP	P-0006660-T02-IM6	TACC3-FGFR3 fusion	yes	unknown		out of frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+17:FGFR3_c.1591+1556:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 7 - 16. The fusion includes the kinase domain of FGFR3. This sample has also been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TACC3	0	MSKCC-DMP	P-0006660-T02-IM6	TACC3-FGFR3 fusion	yes	unknown		out of frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+17:FGFR3_c.1591+1556:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 7 - 16. The fusion includes the kinase domain of FGFR3. This sample has also been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
EML4	0	MSKCC-DMP	P-0014385-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1890:EML4_c.3172+651:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple rearrangements involving ALK were detected in this sample and a more complex rearrangement involving ALK is possible.
ALK	0	MSKCC-DMP	P-0014385-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1890:EML4_c.3172+651:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple rearrangements involving ALK were detected in this sample and a more complex rearrangement involving ALK is possible.
RAB3GAP2	0	MSKCC-DMP	P-0042098-T01-IM6	AURKA-RAB3GAP2 fusion	yes	unknown		unknown	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.2)(chr1:g.220440226::chr20:g.54945391) Note: The RAB3GAP2 - AURKA rearrangement is a translocation that results in a fusion of RAB3GAP2 exon 1 to AURKA exon 9. One of the breakpoints is within AURKA exon 9. The fusion includes a part of the kinase domain of AURKA. Functional significance is undetermined.
AURKA	0	MSKCC-DMP	P-0042098-T01-IM6	AURKA-RAB3GAP2 fusion	yes	unknown		unknown	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.2)(chr1:g.220440226::chr20:g.54945391) Note: The RAB3GAP2 - AURKA rearrangement is a translocation that results in a fusion of RAB3GAP2 exon 1 to AURKA exon 9. One of the breakpoints is within AURKA exon 9. The fusion includes a part of the kinase domain of AURKA. Functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0042173-T01-IM6	CADM3-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) - CADM3 (NM_021189) rearrangement: t(1;12)(q23.2;q15)(chr1:g.159155314::chr12:g.69233222) Note: The MDM2 - CADM3 rearrangement is a translocation that results in a fusion of MDM2 exons 1 - 11 to CADM3 exons 2 - 10. One of the breakpoints is within MDM2 exon 11. Functional significance is undetermined.
CADM3	0	MSKCC-DMP	P-0042173-T01-IM6	CADM3-MDM2 fusion	yes	unknown		unknown	MDM2 (NM_002392) - CADM3 (NM_021189) rearrangement: t(1;12)(q23.2;q15)(chr1:g.159155314::chr12:g.69233222) Note: The MDM2 - CADM3 rearrangement is a translocation that results in a fusion of MDM2 exons 1 - 11 to CADM3 exons 2 - 10. One of the breakpoints is within MDM2 exon 11. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0034921-T02-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.492+129:PTEN_chr10:g.90317365del Note: The PTEN rearrangement is a deletion of exons 6 - 9.
FAM46C	0	MSKCC-DMP	P-0035890-T02-IM6	FAM46C-intragenic	yes	unknown		unknown	FAM46C (NM_017709) rearrangement: c.370:FAM46C_chr1:g.118247292del Note: The FAM46C rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0036756-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2587:TMPRSS2_c.19-4454:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0036756-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2587:TMPRSS2_c.19-4454:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
CCDC30	0	MSKCC-DMP	P-0041695-T01-IM6	ROS1-CCDC30 fusion	yes	unknown		out of frame	CCDC30 (NM_001080850) - ROS1 (NM_002944) fusion: t(1;6)(p34.2;q22.1)(chr1:g.43087864::chr6:g.117643359) Note: The CCDC30 - ROS1 fusion involves CCDC30 exons 1 - 10 and ROS1 exons 35 - 43. The fusion includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0041695-T01-IM6	ROS1-CCDC30 fusion	yes	unknown		out of frame	CCDC30 (NM_001080850) - ROS1 (NM_002944) fusion: t(1;6)(p34.2;q22.1)(chr1:g.43087864::chr6:g.117643359) Note: The CCDC30 - ROS1 fusion involves CCDC30 exons 1 - 10 and ROS1 exons 35 - 43. The fusion includes the kinase domain of ROS1.
RSPRY1	0	MSKCC-DMP	P-0010250-T02-IM6	NUP93-RSPRY1 fusion	yes	unknown		out of frame	RSPRY1 (NM_133368) - NUP93 (NM_014669) rearrangement: c.1273+508:RSPRY1_c.565-4:NUP93dup Note: The RSPRY1 - NUP93 rearrangement is a duplication that results in a fusion of RSPRY1 exons 1 - 11 to NUP93 exons 7 - 22. Functional significance is undetermined.
NUP93	0	MSKCC-DMP	P-0010250-T02-IM6	NUP93-RSPRY1 fusion	yes	unknown		out of frame	RSPRY1 (NM_133368) - NUP93 (NM_014669) rearrangement: c.1273+508:RSPRY1_c.565-4:NUP93dup Note: The RSPRY1 - NUP93 rearrangement is a duplication that results in a fusion of RSPRY1 exons 1 - 11 to NUP93 exons 7 - 22. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0042167-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.162-29358_c.8476del Note: The KMT2C rearrangement is an intragenic deletion of exons 2 - 38. One of the breakpoints is within exon 38.
PLEKHM3	0	MSKCC-DMP	P-0042346-T01-IM6	SF3B1-PLEKHM3 fusion	yes	unknown		out of frame	PLEKHM3 (NM_001080475) - SF3B1 (NM_012433) rearrangement: c.2109-15321:PLEKHM3_c.416-181:SF3B1del Note: The PLEKHM3 - SF3B1 rearrangement is a deletion that results in a fusion of PLEKHM3 exons 1 - 7 to SF3B1 exons 5 - 25. Functional significance is undetermined.
SF3B1	0	MSKCC-DMP	P-0042346-T01-IM6	SF3B1-PLEKHM3 fusion	yes	unknown		out of frame	PLEKHM3 (NM_001080475) - SF3B1 (NM_012433) rearrangement: c.2109-15321:PLEKHM3_c.416-181:SF3B1del Note: The PLEKHM3 - SF3B1 rearrangement is a deletion that results in a fusion of PLEKHM3 exons 1 - 7 to SF3B1 exons 5 - 25. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042346-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q21.1;q22.3)(chr15:g.45823222::chr21:g.42873873) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0006660-T02-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon7 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190098 Macro-dissection: Not Performed
TACC3	0	MSKCC-DMP	P-0006660-T02-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon7 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190098 Macro-dissection: Not Performed
MAP3K13	0	MSKCC-DMP	P-0032175-T02-IM6	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.1897_c.2430+522del Note: The MAP3K13 rearrangement is an intragenic deletion of exon 11. One of the breakpoints is within exon 11. The rearrangement does not include the kinase domain of MAP3K13. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0033300-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1125:TMPRSS2_c.19-12860:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0033300-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1125:TMPRSS2_c.19-12860:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
PIK3R1	0	MSKCC-DMP	P-0033300-T02-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1735:PIK3R1_chr5:g.72070476del Note: The PIK3R1 rearrangement is a deletion of exons 13 - 16. One of the breakpoints is within exon 13.
KMT2A	0	MSKCC-DMP	P-0033799-T02-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: t(4;11)(q31.23;q23.3)(chr4:g.150937415::chr11:g.118355175) Note: The KMT2A rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
TRAP1	0	MSKCC-DMP	P-0033799-T02-IM6	SLX4-TRAP1 fusion	yes	unknown		in frame	TRAP1 (NM_016292) - SLX4 (NM_032444) rearrangement: c.88+228:TRAP1_c.4637-72:SLX4del Note: The TRAP1 - SLX4 rearrangement is a deletion that results in a fusion of TRAP1 exon 1 to SLX4 exons 13 - 15. The fusion is predicted to be in frame.
SLX4	0	MSKCC-DMP	P-0033799-T02-IM6	SLX4-TRAP1 fusion	yes	unknown		in frame	TRAP1 (NM_016292) - SLX4 (NM_032444) rearrangement: c.88+228:TRAP1_c.4637-72:SLX4del Note: The TRAP1 - SLX4 rearrangement is a deletion that results in a fusion of TRAP1 exon 1 to SLX4 exons 13 - 15. The fusion is predicted to be in frame.
MALT1	0	MSKCC-DMP	P-0033799-T02-IM6	MALT1-intragenic	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.1594:MALT1_chr18:g.56433959del Note: The MALT1 rearrangement is a deletion of exons 13 - 17. One of the breakpoints is within exon 13. Functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0039522-T03-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.141_c.465del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3 - 4. The breakpoints are within exon 3 and exon 4.
FLT1	0	MSKCC-DMP	P-0042558-T01-IM6	FLT1-intragenic	yes	unknown		unknown	FLT1 (NM_002019) rearrangement: t(13;16)(q12.3;p13.3)(chr13:g.29041141::chr16:g.443668) Note: The FLT1 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
PALB2	0	MSKCC-DMP	P-0019351-T03-IM6	PALB2-intragenic	yes	unknown		unknown	PALB2 (NM_024675) rearrangement: c.3201+1_c.3203del Note: The PALB2 rearrangement is an intragenic deletion of exons 11 - 12. The breakpoints are within exon 11 and exon 12.
STAT5B	0	MSKCC-DMP	P-0019351-T03-IM6	STAT5B-intragenic	yes	unknown		unknown	STAT5B (NM_012448) rearrangement: c.1776-43_c.1906+1041inv Note: The STAT5B rearrangement is an intragenic inversion of exon 15. Functional significance is undetermined.
HIST1H3A	0	MSKCC-DMP	P-0034774-T03-IM6	HIST1H3A-intragenic	yes	unknown		unknown	HIST1H3A (NM_003529) rearrangement: c.115:HIST1H3A_chr6:g.26042531inv Note: The HIST1H3A rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0042332-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.8487+123:BRCA2_chr13:g.61534109del Note: The BRCA2 rearrangement is a deletion of exons 20 - 27.
PTEN	0	MSKCC-DMP	P-0042549-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.80-1356_c.105del Note: The PTEN rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.
ABCC4	0	MSKCC-DMP	P-0014522-T01-IM6	TMPRSS2-ABCC4 fusion	yes	unknown		out of frame	ABCC4 (NM_005845) -  TMPRSS2 (NM_001135099) Rearrangement : t(13;21)(q32.1;q22.3)(chr13:g.:95689572::chr21:g.42873289) Note: The ABCC4  - TMPRSS2  Rearrangement is a translocation event which results in the fusion of exons 1-29 of ABCC4 with exons 2 -14 of TMPRSS2. . Its functional  significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0014522-T01-IM6	TMPRSS2-ABCC4 fusion	yes	unknown		out of frame	ABCC4 (NM_005845) -  TMPRSS2 (NM_001135099) Rearrangement : t(13;21)(q32.1;q22.3)(chr13:g.:95689572::chr21:g.42873289) Note: The ABCC4  - TMPRSS2  Rearrangement is a translocation event which results in the fusion of exons 1-29 of ABCC4 with exons 2 -14 of TMPRSS2. . Its functional  significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion cannot be ruled out.
KIF5B	0	MSKCC-DMP	P-0042580-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1619:KIF5B_c.2136+760:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0042580-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1619:KIF5B_c.2136+760:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RAD52	0	MSKCC-DMP	P-0004234-T02-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: t(4;12)(p16.1;p13.33)(chr4:g.8469708::chr12:g.1039265) Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0012132-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1525:TMPRSS2_c.18+2872:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0012132-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1525:TMPRSS2_c.18+2872:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0012132-T03-IM6	C4orf45-FUBP1 fusion	yes	unknown		in frame	FUBP1 (NM_003902) - C4orf45 (NM_152543) rearrangement: t(1;4)(p31.1;q32.1)(chr1:g.78420821::chr4:g.159924443) Note: The FUBP1 - C4orf45 rearrangement is a translocation that results in a fusion of FUBP1 exons 1 - 18 to C4orf45 exons 2 - 5. The fusion is predicted to be in frame. Functional significance is undetermined.
C4orf45	0	MSKCC-DMP	P-0012132-T03-IM6	C4orf45-FUBP1 fusion	yes	unknown		in frame	FUBP1 (NM_003902) - C4orf45 (NM_152543) rearrangement: t(1;4)(p31.1;q32.1)(chr1:g.78420821::chr4:g.159924443) Note: The FUBP1 - C4orf45 rearrangement is a translocation that results in a fusion of FUBP1 exons 1 - 18 to C4orf45 exons 2 - 5. The fusion is predicted to be in frame. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0042502-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.993+292:TP53_chr17:g.7473200del Note: The TP53 rearrangement is a deletion of exons 10 - 11.
CDKN2B	0	MSKCC-DMP	P-0042672-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+544:CDKN2B_chr9:g.3627278del Note: The CDKN2B rearrangement is a deletion of exon 2.
CCDC6	0	MSKCC-DMP	P-0022380-T03-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+21810:CCDC6_c.2136+475:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0022380-T03-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+21810:CCDC6_c.2136+475:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
TMEM25	0	MSKCC-DMP	P-0022380-T03-IM6	KMT2A-TMEM25 fusion	yes	unknown		unknown	TMEM25 (NM_032780) - KMT2A (NM_001197104) rearrangement: c.674-97:TMEM25_c.6838:KMT2Adup Note: The TMEM25 - KMT2A rearrangement is a duplication that results in a fusion of TMEM25 exons 1 - 4 to KMT2A exons 27 - 36. One of the breakpoints is within KMT2A exon 27. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0022380-T03-IM6	KMT2A-TMEM25 fusion	yes	unknown		unknown	TMEM25 (NM_032780) - KMT2A (NM_001197104) rearrangement: c.674-97:TMEM25_c.6838:KMT2Adup Note: The TMEM25 - KMT2A rearrangement is a duplication that results in a fusion of TMEM25 exons 1 - 4 to KMT2A exons 27 - 36. One of the breakpoints is within KMT2A exon 27. Functional significance is undetermined.
MKRN1	0	MSKCC-DMP	P-0009024-T02-IM6	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.772-185:MKRN1_c.1140+623:BRAFdup Note: The MKRN1 - BRAF fusion involves MKRN1 exons 1 - 4 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0009024-T02-IM6	BRAF-MKRN1 fusion	yes	unknown		in frame	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.772-185:MKRN1_c.1140+623:BRAFdup Note: The MKRN1 - BRAF fusion involves MKRN1 exons 1 - 4 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
CTNNB1	0	MSKCC-DMP	P-0037052-T02-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.212:CTNNB1_chr3:g.41254099inv Note: The CTNNB1 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0038235-T01-IM6	NOL4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion: t(10;18)(q26.13;q12.1)(chr10:g.123240418::chr18:g.31580817) Note: The FGFR2 - NOL4 fusion involves FGFR2 exons 1 - 17 and NOL4 exons 7 - 11. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
NOL4	0	MSKCC-DMP	P-0038235-T01-IM6	NOL4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion: t(10;18)(q26.13;q12.1)(chr10:g.123240418::chr18:g.31580817) Note: The FGFR2 - NOL4 fusion involves FGFR2 exons 1 - 17 and NOL4 exons 7 - 11. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
MGA	0	MSKCC-DMP	P-0038345-T02-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.2014-56:MGA_chr15:g.41942833del Note: The MGA rearrangement is a deletion of exons 1 - 3.
KMT2C	0	MSKCC-DMP	P-0042791-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8135:KMT2C_chr7:g.151824873del Note: The KMT2C rearrangement is a deletion of exons 38 - 59. One of the breakpoints is within exon 38.
BAP1	0	MSKCC-DMP	P-0042865-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(3;12)(p21.1;q24.23)(chr3:g.52440433::chr12:g.119130791) Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0042865-T01-IM6	JAK3-intragenic	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: t(7;19)(p21.3;p13.11)(chr7:g.12881070::chr19:g.17953169) Note: The JAK3 rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0042956-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3580+1189_c.9614del Note: The FAT1 rearrangement is an intragenic deletion of exons 4 - 14. One of the breakpoints is within exon 14.
MET	0	MSKCC-DMP	P-0038228-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET Exon 14 skipping. Lab Notes Run Number: ArcherV3-CLIN-20190033 Macro-dissection: Unknown
FGFR2	0	MSKCC-DMP	P-0038235-T01-IM6	NOL4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-NOL4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and NOL4 Exon7 (NM_003787). Lab Notes Run Number: Archerv3-CLIN-20190108 Macro-dissection: Not Performed
NOL4	0	MSKCC-DMP	P-0038235-T01-IM6	NOL4-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FGFR2-NOL4 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_022970) and NOL4 Exon7 (NM_003787). Lab Notes Run Number: Archerv3-CLIN-20190108 Macro-dissection: Not Performed
RICTOR	0	MSKCC-DMP	P-0031005-T02-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.3480:RICTOR_chr5:g.44977508del Note: The RICTOR rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042826-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-740:TMPRSS2_c.18+14519:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0042826-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-740:TMPRSS2_c.18+14519:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042990-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1517:TMPRSS2_c.39+57418:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in-frame.  The structural variant involves the ERG non-canonical transcript (NM_004449) and the functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0042990-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1517:TMPRSS2_c.39+57418:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in-frame.  The structural variant involves the ERG non-canonical transcript (NM_004449) and the functional significance is undetermined.
LPA	0	MSKCC-DMP	P-0042990-T01-IM6	HIST1H3H-LPA fusion	yes	unknown		unknown	LPA (NM_005577) - HIST1H3H (NM_003536) rearrangement: c.209+271:LPA_c.28:HIST1H3Hinv Note: The LPA - HIST1H3H rearrangement is an inversion that results in a fusion of LPA exons 1 - 3 to HIST1H3H exon 1. One of the breakpoints is within HIST1H3H exon 1. Functional significance is undetermined.
HIST1H3H	0	MSKCC-DMP	P-0042990-T01-IM6	HIST1H3H-LPA fusion	yes	unknown		unknown	LPA (NM_005577) - HIST1H3H (NM_003536) rearrangement: c.209+271:LPA_c.28:HIST1H3Hinv Note: The LPA - HIST1H3H rearrangement is an inversion that results in a fusion of LPA exons 1 - 3 to HIST1H3H exon 1. One of the breakpoints is within HIST1H3H exon 1. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0043076-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2358:FGFR3_c.2019-34:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 12 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0043076-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2358:FGFR3_c.2019-34:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 12 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
MET	0	MSKCC-DMP	P-0036746-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:    MET Exon 14 skipping (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190112 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0038201-T03-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+989:EML4_c.3172+579:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0038201-T03-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+989:EML4_c.3172+579:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
TMPRSS2	0	MSKCC-DMP	P-0043029-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+1728:TMPRSS2_c.18+13223:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0043029-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+1728:TMPRSS2_c.18+13223:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
CSDE1	0	MSKCC-DMP	P-0043120-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.337+773_c.720+37inv Note: The CSDE1 rearrangement is an intragenic inversion of exons 5 - 8. Functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0043120-T01-IM6	DROSHA-intragenic	yes	unknown		in frame	DROSHA (NM_013235) rearrangement: c.3261+11_c.3526-1355del Note: The DROSHA rearrangement is an intragenic deletion of exons 28 - 29. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0043145-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.396:CDKN2A_chr9:g.30796986del Note: The CDKN2A rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. This variant affects CDKN2Ap16INK4A (NM_000077) isoform and may also affect CDKN2Ap14ARF (NM_058195) isoform.
GNAS	0	MSKCC-DMP	P-0043292-T01-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: c.839+18:GNAS_chr20:g.57486231inv Note: The GNAS rearrangement is an inversion of exons 11 - 13. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0031368-T04-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1154:EML4_c.3173-797:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0031368-T04-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1154:EML4_c.3173-797:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
BICC1	0	MSKCC-DMP	P-0002675-T01-IM3	FGFR2-BICC1 fusion	yes	unknown		in frame	null Note: FGFR2-BICC1 reciprocal inversion is a structural rearrangement event in which exons 1-17 of FGFR2 are fused to exons 3-21 of BICC1. In vitro studies have shown that a similar FGFR2-BICC1 inversion, involving fusion of exon 19 of FGFR2 to exon 3 of BICC1, plays a role in transformation and may be sensitive to certain FGFR inhibitors (PMID: 24122810).
FGFR2	0	MSKCC-DMP	P-0002675-T01-IM3	FGFR2-BICC1 fusion	yes	unknown		in frame	null Note: FGFR2-BICC1 reciprocal inversion is a structural rearrangement event in which exons 1-17 of FGFR2 are fused to exons 3-21 of BICC1. In vitro studies have shown that a similar FGFR2-BICC1 inversion, involving fusion of exon 19 of FGFR2 to exon 3 of BICC1, plays a role in transformation and may be sensitive to certain FGFR inhibitors (PMID: 24122810).
FGFR2	0	MSKCC-DMP	P-0006885-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement: c.2302-1052:FGFR2_c.238-5239:BICC1inv The FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement is a reciprocal inversion that results in the fusion of FGFR2 exons 1-17  with  BICC1 exons 3-21 . The fusion is predicted to be in frame and includes the kinase domain of FGFR2 .
BICC1	0	MSKCC-DMP	P-0006885-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement: c.2302-1052:FGFR2_c.238-5239:BICC1inv The FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement is a reciprocal inversion that results in the fusion of FGFR2 exons 1-17  with  BICC1 exons 3-21 . The fusion is predicted to be in frame and includes the kinase domain of FGFR2 .
MAP2K1	0	MSKCC-DMP	P-0007041-T01-IM5	MAP2K1-intragenic	yes	unknown		unknown	MAP2K1 (NM_002755) rearrangement :  c.528_568+1908inv Note: The MAP2K1 (NM_002755) rearrangement results in the partial inversion of exon5 of MAP2K1. One of the breakpoints is within exon 5  and is within the kinase domain of MAP2K1. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0007041-T01-IM5	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement :  c.708-727_2158dup Note: The DOT1L (NM_032482) rearrangement results in the intragenic duplication of exons 9 to 20 of DOT1L. One of the breakpoints is within exon20. Its functional significance is undetermined.
SHBG	0	MSKCC-DMP	P-0007205-T01-IM5	TP53-SHBG fusion	yes	unknown		unknown	SHBG (NM_001040) - TP53 (NM_000546) rearrangement : chr17:g.7522278_c.-28-709:TP53inv Note: The SHBG (NM_001040) - TP53 (NM_000546) rearrangement event is a inversion which results in the fusion of 5 UTR of SHBG with 5 UTR of TP53. The functional significance  of this event is unknown.
TP53	0	MSKCC-DMP	P-0007205-T01-IM5	TP53-SHBG fusion	yes	unknown		unknown	SHBG (NM_001040) - TP53 (NM_000546) rearrangement : chr17:g.7522278_c.-28-709:TP53inv Note: The SHBG (NM_001040) - TP53 (NM_000546) rearrangement event is a inversion which results in the fusion of 5 UTR of SHBG with 5 UTR of TP53. The functional significance  of this event is unknown.
RPS6KB2	0	MSKCC-DMP	P-0007520-T01-IM5	CNIH2-RPS6KB2 fusion	yes	unknown		in frame	RPS6KB2 (NM_003952) - CNIH2 (NM_182553) -  Rearrangement : c.81+215:CNIH2_c.969+56:RPS6KB2dup Note: The CNIH2 (NM_182553) - RPS6KB2 (NM_003952) Rearrangement results in the fusion of exons 1 to 11 of RPS6KB2 with exons 2 to 6 of CNIH2 . The fusion is predicted to be an in-frame fusion and includes the kinase domain of the RPS6KB2.
CNIH2	0	MSKCC-DMP	P-0007520-T01-IM5	CNIH2-RPS6KB2 fusion	yes	unknown		in frame	RPS6KB2 (NM_003952) - CNIH2 (NM_182553) -  Rearrangement : c.81+215:CNIH2_c.969+56:RPS6KB2dup Note: The CNIH2 (NM_182553) - RPS6KB2 (NM_003952) Rearrangement results in the fusion of exons 1 to 11 of RPS6KB2 with exons 2 to 6 of CNIH2 . The fusion is predicted to be an in-frame fusion and includes the kinase domain of the RPS6KB2.
SMARCD1	0	MSKCC-DMP	P-0008286-T01-IM5	PTPRR-SMARCD1 fusion	yes	unknown		out of frame	SMARCD1 (NM_003076) - PTPRR (NM_002849) rearrangement: c.531+104:SMARCD1_c.1008-6669:PTPRRinv The SMARCD1 (NM_003076) - PTPRR (NM_002849) rearrangement is an inversion which results in the fusion of SMARCD1 exons 1-4 with PTPRR exons 7-14. The functional significance is undetermined.
PTPRR	0	MSKCC-DMP	P-0008286-T01-IM5	PTPRR-SMARCD1 fusion	yes	unknown		out of frame	SMARCD1 (NM_003076) - PTPRR (NM_002849) rearrangement: c.531+104:SMARCD1_c.1008-6669:PTPRRinv The SMARCD1 (NM_003076) - PTPRR (NM_002849) rearrangement is an inversion which results in the fusion of SMARCD1 exons 1-4 with PTPRR exons 7-14. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0008658-T01-IM5	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2302-1658:FGFR2_c.355-22274:KIAA1217inv FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement is an inversion that results in an in-frame fusion of FGFR2 exons 1-17 with KIAA1217 exons 4-21. The fusion product includes kinase domain of FGFR2. Its functional significance is undetermined.
KIAA1217	0	MSKCC-DMP	P-0008658-T01-IM5	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2302-1658:FGFR2_c.355-22274:KIAA1217inv FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement is an inversion that results in an in-frame fusion of FGFR2 exons 1-17 with KIAA1217 exons 4-21. The fusion product includes kinase domain of FGFR2. Its functional significance is undetermined.
PRKAR1B	0	MSKCC-DMP	P-0009694-T01-IM5	BRAF-PRKAR1B fusion	yes	unknown		in frame	PRKAR1B (NM_001164758) -BRAF (NM_004333) Rearrangement :  c.892-2551:PRKAR1B_c.1140+2253:BRAFdup Note: The PRKAR1B (NM_001164758) -BRAF (NM_004333)  Rearrangement results in the fusion of exons1-9 of PRKAR1B and exons 9-18 of  BRAF.It includes the BRAF kinase domain.
BRAF	0	MSKCC-DMP	P-0009694-T01-IM5	BRAF-PRKAR1B fusion	yes	unknown		in frame	PRKAR1B (NM_001164758) -BRAF (NM_004333) Rearrangement :  c.892-2551:PRKAR1B_c.1140+2253:BRAFdup Note: The PRKAR1B (NM_001164758) -BRAF (NM_004333)  Rearrangement results in the fusion of exons1-9 of PRKAR1B and exons 9-18 of  BRAF.It includes the BRAF kinase domain.
BCL2L11	0	MSKCC-DMP	P-0010701-T01-IM5	BCL2L11-intragenic	yes	unknown		unknown	BCL2L11 (NM_138621) Rearrangement : c.-13-1249_c.394+2099del BCL2L11 Rearrangement results in the deletion of exons1-2 of BCL2L11. One of the breakpoints lies in the upstream region (5'-UTR)  1kb before the transcription start site. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0011329-T01-IM5	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) Rearrangement :  chr10:g.65610482_ c.2302-649inv Note: The FGFR2 Rearrangement results in the inversion of exon 18 of FGFR2.  This involves the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0011394-T01-IM5	LAMC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - LAMC1 (NM_002293) rearrangment: t(1;10)(q25.3;q26.13)(chr1:g.183109471::chr10:g.123240042 ) Note: The FGFR2 - LAMC1 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-18 with LAMC1 exons 27 - 28. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
LAMC1	0	MSKCC-DMP	P-0011394-T01-IM5	LAMC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - LAMC1 (NM_002293) rearrangment: t(1;10)(q25.3;q26.13)(chr1:g.183109471::chr10:g.123240042 ) Note: The FGFR2 - LAMC1 rearrangement is a translocation which results in the fusion of FGFR2 exons 1-18 with LAMC1 exons 27 - 28. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0011394-T01-IM5	RABGAP1L-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - RABGAP1L (NM_014857) rearrangement: t(1;10)(q25.1;q26.13)(chr1:g.174863117::chr10:g.123240065 ) Note: The FGFR2 - RABGAP1L rearrangement is a translocation which results in the fusion of FGFR2 exons 1-18 with RABGAP1L exons 20 - 21. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
RABGAP1L	0	MSKCC-DMP	P-0011394-T01-IM5	RABGAP1L-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - RABGAP1L (NM_014857) rearrangement: t(1;10)(q25.1;q26.13)(chr1:g.174863117::chr10:g.123240065 ) Note: The FGFR2 - RABGAP1L rearrangement is a translocation which results in the fusion of FGFR2 exons 1-18 with RABGAP1L exons 20 - 21. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
CTNNA3	0	MSKCC-DMP	P-0011516-T01-IM5	FGFR2-CTNNA3 fusion	yes	unknown		in frame	CTNNA3 (NM_013266) -FGFR2 (NM_000141) Rearrangement : c.1048-8479:CTNNA3_c.2301+1272:FGFR2dup Note: The CTNNA3  -FGFR2 Rearrangement results in the fusion of exons 1-7 of CTNNA3 with exons 18 of FGFR2 , this includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0011516-T01-IM5	FGFR2-CTNNA3 fusion	yes	unknown		in frame	CTNNA3 (NM_013266) -FGFR2 (NM_000141) Rearrangement : c.1048-8479:CTNNA3_c.2301+1272:FGFR2dup Note: The CTNNA3  -FGFR2 Rearrangement results in the fusion of exons 1-7 of CTNNA3 with exons 18 of FGFR2 , this includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0011516-T01-IM5	SH2C-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - SH2C (NM_012435) Rearrangement : t(10;19)(q26.13;p13.3)(chr10:g.123243182::chr19:g.447779) Note: The FGFR2  - SH2C Rearrangement results in the fusion of exons1-16 of FGFR2 and exon2-13 of SH2C. Its functional significance is undetermined.
SH2C	0	MSKCC-DMP	P-0011516-T01-IM5	SH2C-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - SH2C (NM_012435) Rearrangement : t(10;19)(q26.13;p13.3)(chr10:g.123243182::chr19:g.447779) Note: The FGFR2  - SH2C Rearrangement results in the fusion of exons1-16 of FGFR2 and exon2-13 of SH2C. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0012376-T01-IM5	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(1;10)(q32.1;q26.13)(chr1:g.205735259::chr10:g.123241306 ) Note: The FGFR2 rearrangement is a translocation which includes the kinase domain of FGFR2. While this event does not appear to produce a functional gene fusion, we cannot exclude the possibility of a more complex genomic rearrangement that leads to a gene fusion. Additional testing by an alternate method is suggested, if clinically indicated.
FGFR2	0	MSKCC-DMP	P-0012423-T02-IM6	NOL4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion (FGFR2 exons 1-17 fused in-frame with NOL4 exons 7-11): t(10;18)(q26.13;q12.1)(chr10:g.123242055::chr18:g.31563418) Note: The FGFR2 - NOL4 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
NOL4	0	MSKCC-DMP	P-0012423-T02-IM6	NOL4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion (FGFR2 exons 1-17 fused in-frame with NOL4 exons 7-11): t(10;18)(q26.13;q12.1)(chr10:g.123242055::chr18:g.31563418) Note: The FGFR2 - NOL4 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0012639-T01-IM5	SEPT10-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - SEPT10 (NM_144710) rearrangement: t(2;10)(q13;q26.13)(chr2:g.110325395::chr10:g.123240798) Note: The FGFR2 - SEPT10 rearrangement is a translocation that results in a fusion of FGFR2 exons 1-17 with SEPT10 exons 6-11.  One of the breakpoints is within SEPT10 exon 6. The functional significance is undetermined.
SEPT10	0	MSKCC-DMP	P-0012639-T01-IM5	SEPT10-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - SEPT10 (NM_144710) rearrangement: t(2;10)(q13;q26.13)(chr2:g.110325395::chr10:g.123240798) Note: The FGFR2 - SEPT10 rearrangement is a translocation that results in a fusion of FGFR2 exons 1-17 with SEPT10 exons 6-11.  One of the breakpoints is within SEPT10 exon 6. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0012666-T01-IM5	AMOT-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - AMOT (NM_001113490) Rearrangement : t(10;X)(q26.13.1;q23)(chr10:g.123241762::chrX:g.112058354) Note: The FGFR2 - AMOT Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 3-10 of AMOT. This includes the kinase domain of FGFR2.
AMOT	0	MSKCC-DMP	P-0012666-T01-IM5	AMOT-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - AMOT (NM_001113490) Rearrangement : t(10;X)(q26.13.1;q23)(chr10:g.123241762::chrX:g.112058354) Note: The FGFR2 - AMOT Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 3-10 of AMOT. This includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0013174-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 with BICC1 exons 16-21): c.2302-588:FGFR2_c.2182-284:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
BICC1	0	MSKCC-DMP	P-0013174-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 with BICC1 exons 16-21): c.2302-588:FGFR2_c.2182-284:BICC1inv Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0013405-T01-IM5	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2301+1446:FGFR2_c.354+73179:KIAA1217inv Note: The FGFR2 - KIAA1217 Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 4-19 of KIAA1217. It includes the kinase domain of FGFR2.
KIAA1217	0	MSKCC-DMP	P-0013405-T01-IM5	KIAA1217-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2301+1446:FGFR2_c.354+73179:KIAA1217inv Note: The FGFR2 - KIAA1217 Rearrangement results in the fusion of exons 1-17 of FGFR2 with exons 4-19 of KIAA1217. It includes the kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0020164-T01-IM6	ADAM9-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ADAM9 (NM_003816) fusion: t(8;10(p11.22;q26.13)(chr8:g.38901161::chr10:g.123242738) Note: The FGFR2 - ADAM9 fusion is predicted to be in frame and includes the kinase domain of FGFR2
ADAM9	0	MSKCC-DMP	P-0020164-T01-IM6	ADAM9-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ADAM9 (NM_003816) fusion: t(8;10(p11.22;q26.13)(chr8:g.38901161::chr10:g.123242738) Note: The FGFR2 - ADAM9 fusion is predicted to be in frame and includes the kinase domain of FGFR2
UPF1	0	MSKCC-DMP	P-0026846-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: t(9;19)(p21.1;p13.11)(chr9:g.31342057::chr19:g.18974414) Note: The UPF1 rearrangement is translocation with a breakpoint within UPF1 exon 19. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0029335-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: chr19:g.42738483_c.3754:CICdel Note: The CIC rearrangement is a deletion that includes CIC exons 1-15. One of the breakpoints is within CIC exon 15. The functional significance is undetermined.
PTCH1	0	MSKCC-DMP	P-0030378-T01-IM6	PTCH1-intragenic	yes	unknown		unknown	PTCH1 (NM_000264) Rearrangement : chr9:g.27937753_c.1425:PTCH1inv Note: The PTCH1 Rearrangement results in the inversion of exons 10-23 of PTCH1. The breakpoint in PTCH1 is within exon10. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0020976-T01-IM6	KIAA1598-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-KIAA1598 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and KIAA1598 Exon7 (NM_001127211). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Not Performed
KIAA1598	0	MSKCC-DMP	P-0020976-T01-IM6	KIAA1598-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-KIAA1598 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and KIAA1598 Exon7 (NM_001127211). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Not Performed
RARA	0	MSKCC-DMP	P-0043132-T01-IM6	RARA-intragenic	yes	unknown		unknown	RARA (NM_000964) rearrangement: c.179-5462:RARA_chr17:g.60911308del Note: The RARA rearrangement is a deletion of exons 3 - 9. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0009948-T03-IM6	VOPP1-EGFR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EGFR-VOPP1 fusion. Note: The rearrangement is a fusion between genes EGFR Exon1 (NM_005228) and VOPP1 Exon3 (NM_030796). Note2: The functional significance of this event is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190119 Macro-dissection: Not Performed
VOPP1	0	MSKCC-DMP	P-0009948-T03-IM6	VOPP1-EGFR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EGFR-VOPP1 fusion. Note: The rearrangement is a fusion between genes EGFR Exon1 (NM_005228) and VOPP1 Exon3 (NM_030796). Note2: The functional significance of this event is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190119 Macro-dissection: Not Performed
TP53	0	MSKCC-DMP	P-0015479-T02-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.993+243:TP53_chr17:g.62224960inv Note: The TP53 rearrangement is an inversion of exons 1 - 9. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015479-T02-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.1425+183:TMPRSS2_chr21:g.42836610del Note: The TMPRSS2 rearrangement is a deletion of exons 13 - 14. Functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0027460-T01-IM6	MACROD1-RPS6KA4 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) - MACROD1 (NM_014067) rearrangement: c.1994:RPS6KA4_c.518-47220:MACROD1inv Note: The RPS6KA4 - MACROD1 rearrangement is an inversion that results in a fusion of RPS6KA4 exons 1 - 16 to MACROD1 exons 4 - 10. One of the breakpoints is within RPS6KA4 exon 16. Functional significance is undetermined.
MACROD1	0	MSKCC-DMP	P-0027460-T01-IM6	MACROD1-RPS6KA4 fusion	yes	unknown		unknown	RPS6KA4 (NM_003942) - MACROD1 (NM_014067) rearrangement: c.1994:RPS6KA4_c.518-47220:MACROD1inv Note: The RPS6KA4 - MACROD1 rearrangement is an inversion that results in a fusion of RPS6KA4 exons 1 - 16 to MACROD1 exons 4 - 10. One of the breakpoints is within RPS6KA4 exon 16. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0037164-T02-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.1696:BAP1_chr3:g.52403726del Note: The BAP1 rearrangement is a deletion of exons 13 - 17. One of the breakpoints is within exon 13.
ERBB3	0	MSKCC-DMP	P-0042780-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(12;16)(q13.2;p13.13)(chr12:g.56493955::chr16:g.11917462) Note: The ERBB3 rearrangement is a translocation with a breakpoint in intron 25. Functional significance is undetermined.
EPC1	0	MSKCC-DMP	P-0043181-T01-IM6	INHBA-EPC1 fusion	yes	unknown		out of frame	EPC1 (NM_025209) - INHBA (NM_002192) rearrangement: t(7;10)(p14.1;p11.22)(chr7:g.41735073::chr10:g.32575797) Note: The EPC1 - INHBA rearrangement is a translocation that results in a fusion of EPC1 exons 1 - 8 to INHBA exon 3. Functional significance is undetermined.
INHBA	0	MSKCC-DMP	P-0043181-T01-IM6	INHBA-EPC1 fusion	yes	unknown		out of frame	EPC1 (NM_025209) - INHBA (NM_002192) rearrangement: t(7;10)(p14.1;p11.22)(chr7:g.41735073::chr10:g.32575797) Note: The EPC1 - INHBA rearrangement is a translocation that results in a fusion of EPC1 exons 1 - 8 to INHBA exon 3. Functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0043319-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: c.3420-168:DROSHA_chr5:g.31395819dup Note: The DROSHA rearrangement is a duplication of exons 29 - 35. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043416-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3800:TMPRSS2_c.19-13761:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0043416-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3800:TMPRSS2_c.19-13761:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
TMPRSS2	0	MSKCC-DMP	P-0043422-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.127-1681_c.350-1608del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0043556-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.464:FGFR1_chr8:g.30003025inv Note: The FGFR1 rearrangement is an inversion of exons 5 - 19. One of the breakpoints is within exon 5. The rearrangement includes the kinase domain of FGFR1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RET	0	MSKCC-DMP	P-0043704-T01-IM6	KIF5B-RET fusion	yes	unknown		in frame	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.2136+147:RET_c.2545-77:KIF5Binv Note: The RET - KIF5B rearrangement is an inversion that results in a fusion of RET exons 1 - 11 to KIF5B exons 24 - 25. The fusion is predicted to be in frame and does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KIF5B	0	MSKCC-DMP	P-0043704-T01-IM6	KIF5B-RET fusion	yes	unknown		in frame	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.2136+147:RET_c.2545-77:KIF5Binv Note: The RET - KIF5B rearrangement is an inversion that results in a fusion of RET exons 1 - 11 to KIF5B exons 24 - 25. The fusion is predicted to be in frame and does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0043817-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.1010+73:TMPRSS2_chr21:g.42836304del Note: The TMPRSS2 rearrangement is a deletion of exons 10 - 14. Functional significance is undetermined.
SFTA3	0	MSKCC-DMP	P-0043823-T01-IM6	NUF2-SFTA3 fusion	yes	unknown		unknown	SFTA3 (NM_001101341) - NUF2 (NM_031423) rearrangement: t(1;14)(q23.3;q13.3)(chr1:g.163309186::chr14:g.36956644) Note: The SFTA3 - NUF2 rearrangement is a translocation that results in a fusion of SFTA3 exons 1 - 2 to NUF2 exons 8 - 14. One of the breakpoints is within NUF2 exon 8. Functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0043823-T01-IM6	NUF2-SFTA3 fusion	yes	unknown		unknown	SFTA3 (NM_001101341) - NUF2 (NM_031423) rearrangement: t(1;14)(q23.3;q13.3)(chr1:g.163309186::chr14:g.36956644) Note: The SFTA3 - NUF2 rearrangement is a translocation that results in a fusion of SFTA3 exons 1 - 2 to NUF2 exons 8 - 14. One of the breakpoints is within NUF2 exon 8. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0043823-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(12;19)(q14.3;p13.12)(chr12:g.66426103::chr19:g.15288174) Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 24. Functional significance is undetermined.
AR	0	MSKCC-DMP	P-0015479-T02-IM6	AR-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:      AR (NM_000044) Variant 7 (AR V-7)    PMID: 26554309, 19117982  Lab Notes Run Number: Archerv3-CLIN-20190120 Macro-dissection: Not Performed
TFG	0	MSKCC-DMP	P-0043422-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note1: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732   Lab Notes Run Number: Archerv3-CLIN-20190120 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0043422-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note1: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732   Lab Notes Run Number: Archerv3-CLIN-20190120 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0014310-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+6128:EML4_c.3172+783:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0014310-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+6128:EML4_c.3172+783:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
KIF5B	0	MSKCC-DMP	P-0043704-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon23 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190124 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0043704-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon23 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190124 Macro-dissection: Not Performed
ARID1A	0	MSKCC-DMP	P-0036062-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1631_c.2251+13del Note: The ARID1A rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 3.
EML4	0	MSKCC-DMP	P-0044042-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-1681:EML4_c.3172+600:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0044042-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-1681:EML4_c.3172+600:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ZFHX3	0	MSKCC-DMP	P-0044176-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.696:ZFHX3_chr16:g.72999556inv Note: The ZFHX3 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined. This event occurs in the background of other events involving ZFHX3 which could lead t a complex event.
ESR1	0	MSKCC-DMP	P-0004654-T02-IM6	CREBBP-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-CREBBP fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon6 (NM_001122742) and CREBBP Exon2 (NM_004380). Lab Notes Run Number: Archerv3-CLIN-20190128 Macro-dissection: Not Performed
CREBBP	0	MSKCC-DMP	P-0004654-T02-IM6	CREBBP-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-CREBBP fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon6 (NM_001122742) and CREBBP Exon2 (NM_004380). Lab Notes Run Number: Archerv3-CLIN-20190128 Macro-dissection: Not Performed
MYB	0	MSKCC-DMP	P-0043948-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon13 (NM_001130173) and NFIB Exon9 (NM_001190738). Lab Notes Run Number: Archerv3-CLIN-20190128 Macro-dissection: Not Performed
NFIB	0	MSKCC-DMP	P-0043948-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon13 (NM_001130173) and NFIB Exon9 (NM_001190738). Lab Notes Run Number: Archerv3-CLIN-20190128 Macro-dissection: Not Performed
YES1	0	MSKCC-DMP	P-0013345-T02-IM6	PTPRM-YES1 fusion	yes	unknown		in frame	YES1 (NM_005433) - PTPRM (NM_001105244) rearrangement: c.271+14:YES1_c.197-45137:PTPRMinv Note: The YES1 - PTPRM rearrangement is an inversion that results in a fusion of YES1 exons 1 - 2 to PTPRM exons 3 - 33. The fusion is predicted to be in frame and does not include the kinase domain of YES1. Functional significance is undetermined.
PTPRM	0	MSKCC-DMP	P-0013345-T02-IM6	PTPRM-YES1 fusion	yes	unknown		in frame	YES1 (NM_005433) - PTPRM (NM_001105244) rearrangement: c.271+14:YES1_c.197-45137:PTPRMinv Note: The YES1 - PTPRM rearrangement is an inversion that results in a fusion of YES1 exons 1 - 2 to PTPRM exons 3 - 33. The fusion is predicted to be in frame and does not include the kinase domain of YES1. Functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0025146-T02-IM6	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.1620:TCF3_chr19:g.1878693inv Note: The TCF3 rearrangement is an inversion of exons 1 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044256-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+939:TMPRSS2_c.18+22179:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0044256-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+939:TMPRSS2_c.18+22179:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10.
TP53	0	MSKCC-DMP	P-0044377-T01-IM6	TLK2-TP53 fusion	yes	unknown		in frame	TP53 (NM_000546) - TLK2 (NM_006852) rearrangement: c.672+231:TP53_c.81+1850:TLK2inv Note: The TP53 - TLK2 rearrangement is an inversion that results in a fusion of TP53 exons 1 - 6 to TLK2 exons 3 - 22. The fusion is predicted to be in frame. Functional significance is undetermined.
TLK2	0	MSKCC-DMP	P-0044377-T01-IM6	TLK2-TP53 fusion	yes	unknown		in frame	TP53 (NM_000546) - TLK2 (NM_006852) rearrangement: c.672+231:TP53_c.81+1850:TLK2inv Note: The TP53 - TLK2 rearrangement is an inversion that results in a fusion of TP53 exons 1 - 6 to TLK2 exons 3 - 22. The fusion is predicted to be in frame. Functional significance is undetermined.
PDCD1LG2	0	MSKCC-DMP	P-0044377-T01-IM6	PDCD1LG2-intragenic	yes	unknown		unknown	PDCD1LG2 (NM_025239) rearrangement: c.816+148:PDCD1LG2_chr9:g.24818667inv Note: The PDCD1LG2 rearrangement is an inversion of exon 7. Functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0005636-T03-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.1470+79:PIK3CD_chr1:g.12569292del Note: The PIK3CD rearrangement is a deletion of exons 12 - 24. Functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0005636-T03-IM6	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) rearrangement: t(1;15)(p36.22;q14)(chr1:g.11184865:chr15:g.37509514) Note: The MTOR rearrangement is a translocation with a breakpoint in intron 46. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0005636-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4760:TMPRSS2_c.19-17111:ERGdel The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0005636-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4760:TMPRSS2_c.19-17111:ERGdel The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
NTRK1	0	MSKCC-DMP	P-0036499-T03-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.1174:NTRK1_chr1:g.201743980inv Note: The NTRK1 rearrangement is an inversion of exons 8 - 17. One of the breakpoints is within exon 8. The rearrangement includes the kinase domain of NTRK1. Functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0036499-T03-IM6	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: t(13;15)(q34;q21.3)(chr13:g.110436723::chr15:g.57613785) Note: The IRS2 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044414-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+4617:TMPRSS2_chr21:g.39982152del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. This rearrangement is suggestive of a TMRPSS2-ERG fusion. Additional testing is recommended if clinically indicated.
EML4	0	MSKCC-DMP	P-0044432-T01-IM6	ALK-EML4 fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2057-576:EML4_c.3155:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 17 and ALK exons 19 - 29. One of the breakpoints is within ALK exon 19. The fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0044432-T01-IM6	ALK-EML4 fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2057-576:EML4_c.3155:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 17 and ALK exons 19 - 29. One of the breakpoints is within ALK exon 19. The fusion includes the kinase domain of ALK.
MAPKAP1	0	MSKCC-DMP	P-0044470-T01-IM6	MAPKAP1-intragenic	yes	unknown		unknown	MAPKAP1 (NM_001006617) rearrangement: t(4;9)(p15.2;q33.3)(chr4:g.23486215::chr9:g.128230200) Note: The MAPKAP1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044536-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2850+12:NF1_chr17:g.33639065inv Note: The NF1 rearrangement is an inversion of exons 22 - 58. Functional significance is undetermined.
INHA	0	MSKCC-DMP	P-0024083-T02-IM6	INHA-intragenic	yes	unknown		unknown	INHA (NM_002191) rearrangement: c.1085:INHA_chr2:g.37386053inv Note: The INHA rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
LAMA4	0	MSKCC-DMP	P-0024083-T02-IM6	ESR1-LAMA4 fusion	yes	unknown		out of frame	LAMA4 (NM_001105206) - ESR1 (NM_001122740) rearrangement: c.4982-618:LAMA4_c.453-83:ESR1inv Note: The LAMA4 - ESR1 rearrangement is an inversion that results in a fusion of LAMA4 exons 1 - 35 to ESR1 exons 3 - 9. Functional significance is undetermined.
ESR1	0	MSKCC-DMP	P-0024083-T02-IM6	ESR1-LAMA4 fusion	yes	unknown		out of frame	LAMA4 (NM_001105206) - ESR1 (NM_001122740) rearrangement: c.4982-618:LAMA4_c.453-83:ESR1inv Note: The LAMA4 - ESR1 rearrangement is an inversion that results in a fusion of LAMA4 exons 1 - 35 to ESR1 exons 3 - 9. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0044178-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.1265_c.1793inv Note: The FGFR3 rearrangement is an intragenic inversion of exons 9 - 13. The breakpoints are within exon 9 and exon 13. The rearrangement includes a part of the kinase domain of FGFR3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PDGFRA	0	MSKCC-DMP	P-0020986-T01-IM6	PDGFRA-intragenic	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: chr4:g.53132170_c.1238-110:PDGFRAdel Note: The PDGFRA rearrangement is a deletion of exons 1-8, which do no include the kinase domain. This deletion is observed along with the PDGFRA amplification. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0021014-T01-IM6	KMT2C-intragenic	yes	unknown		out of frame	KMT2C (NM_170606) rearrangement: c.9517+80_c.849+2148dup Note: The KMT2C rearrangement is an intragenic duplication of exons 7-41. The functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0044916-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.118-94:EZH2_chr7:g.148612082inv Note: The EZH2 rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027245-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+1582:ERG_c.56-2109:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14.
TMPRSS2	0	MSKCC-DMP	P-0027245-T03-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+1582:ERG_c.56-2109:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14.
BRIP1	0	MSKCC-DMP	P-0039885-T02-IM6	DNMT1-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) - DNMT1 (NM_001379) rearrangement: t(17;19)(q23.2;p13.2)(chr17:g.59886338::chr19:g.10288034) Note: The BRIP1 - DNMT1 rearrangement is a translocation that results in a fusion of BRIP1 exons 1 - 6 to DNMT1 exons 5 - 40. One of the breakpoints is within DNMT1 exon 5. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0039885-T02-IM6	DNMT1-BRIP1 fusion	yes	unknown		unknown	BRIP1 (NM_032043) - DNMT1 (NM_001379) rearrangement: t(17;19)(q23.2;p13.2)(chr17:g.59886338::chr19:g.10288034) Note: The BRIP1 - DNMT1 rearrangement is a translocation that results in a fusion of BRIP1 exons 1 - 6 to DNMT1 exons 5 - 40. One of the breakpoints is within DNMT1 exon 5. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0004339-T04-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: t(3;7)(q29;q36.1)(chr3:g.197675580::chr7:g.151860908) Note: The KMT2C rearrangement is a translocation with a breakpoint in exon 43. Functional significance is undetermined.
MET	0	MSKCC-DMP	P-0005114-T03-IM6	MET-intragenic	yes	unknown		in frame	MET (NM_000245) rearrangement: c.2888-8_c.3029-890del Note: :  The MET rearrangement is an intragenic deletion of exon 14. Functional significance is undetermined.  Sequencing RNA is necessary to confirm whether this DNA event leads to the canonical MET Exon 14 deletion variant in expressed transcripts. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ATM	0	MSKCC-DMP	P-0006365-T01-IM5	ATM-intragenic	yes	unknown		out of frame	ATM (NM_000051) rearrangement: c.5178-47_c.5674+821dup The ATM (NM_000051) rearrangement is an out of frame intragenic duplication of exons 35-37. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0010011-T01-IM5	PAX8-intragenic	yes	unknown		out of frame	PAX8 (NM_003466) rearrangement: c.1088-2028_c.25+11587del Note: The PAX8 rearrangement is a deletion of PAX8 exons 3-9. The functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0012008-T02-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) reciprocal fusion (SDC4 exons 1-2 with ROS1 exons 32-43): t(6;20) (q22.1; q13.12) (chr6:g.117652119::chr20:g.43964016) Note: The SDC4 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0012008-T02-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) reciprocal fusion (SDC4 exons 1-2 with ROS1 exons 32-43): t(6;20) (q22.1; q13.12) (chr6:g.117652119::chr20:g.43964016) Note: The SDC4 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
IKZF3	0	MSKCC-DMP	P-0032357-T01-IM6	ERBB2-IKZF3 fusion	yes	unknown		out of frame	IKZF3 (NM_01248) - ERBB2 (NM_004448) rearrangement: c.592+775:IKZF3_c.759+48inv Note: The IKZF3 - ERBB2 rearrangement is an inversion that results in the fusion of IKZF3 exons 1-5 with ERBB2 exons 7-27. The fusion is predicted to be out of frame and includes the kinase domain of ERBB2.
ERBB2	0	MSKCC-DMP	P-0032357-T01-IM6	ERBB2-IKZF3 fusion	yes	unknown		out of frame	IKZF3 (NM_01248) - ERBB2 (NM_004448) rearrangement: c.592+775:IKZF3_c.759+48inv Note: The IKZF3 - ERBB2 rearrangement is an inversion that results in the fusion of IKZF3 exons 1-5 with ERBB2 exons 7-27. The fusion is predicted to be out of frame and includes the kinase domain of ERBB2.
TP53	0	MSKCC-DMP	P-0032703-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(17;20)(p13.1;q13.13)(chr17:g.7579551::chr20:g.48334484) Note: The TP53 rearrangement is a translocation with a breakpoint in exon 4.
SMAD3	0	MSKCC-DMP	P-0033545-T04-IM6	SMAD3-intragenic	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.207-25590_c.719del Note: The SMAD3 rearrangement is an intragenic deletion of exons 2-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0034876-T01-IM6	DICER1-intragenic	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: c.4207-1271_c.4231del Note: The DICER1 rearrangement results in the deletion of exon 25. One of the breakpoints is within exon 25. The functional significance is undetermined.
PAXBP1	0	MSKCC-DMP	P-0034876-T01-IM6	TMPRSS2-PAXBP1 fusion	yes	unknown		out of frame	PAXBP1 (NM_016631) - TMPRSS2 (NM_001135099) rearrangement: c.649+322:PAXBP1_c.127-629:TMPRSS2dup Note: The PAXBP1 - TMPRSS2 rearrangement is a duplication that results in the fusion of PAXBP1 exons 1-3 with TMPRSS2 exons 3-14. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034876-T01-IM6	TMPRSS2-PAXBP1 fusion	yes	unknown		out of frame	PAXBP1 (NM_016631) - TMPRSS2 (NM_001135099) rearrangement: c.649+322:PAXBP1_c.127-629:TMPRSS2dup Note: The PAXBP1 - TMPRSS2 rearrangement is a duplication that results in the fusion of PAXBP1 exons 1-3 with TMPRSS2 exons 3-14. The functional significance is undetermined.
RIT1	0	MSKCC-DMP	P-0036013-T01-IM6	RIT1-intragenic	yes	unknown		unknown	RIT1 (NM_006912) Rearrangement : c.474:RIT1_c.1632-961:ARHGEF2inv Note: The RIT1 Rearrangement results in the inversion of exons 1-6 of RIT1. The breakpoint in RIT1 is within exon6. Its functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0036013-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) Rearrangement :  c.-141:NT5DC2_c.1924+202:PBRMinv Note: The PBRM1 Rearrangement results in the inversion of exons 17-30 of PBRM1. Its functional significance is undetermined.
AMER1	0	MSKCC-DMP	P-0036013-T01-IM6	AMER1-intragenic	yes	unknown		unknown	AMER1 (NM_152424)  Rearrangement : chrX:g.63280801_c.950del Note: The AMER1 Rearrangment results in the intrangenic deletion of exons 1-2. One of the breakpoints is within exon2. Its functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0036233-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) Rearrangement: c.1093+73:PREX2_chr8:g.69483080inv Note: The PREX2 rearrangement is an inversion with the breakpoint in intron 9 of PREX2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0036302-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.40-59382:TMPRSS2_c.127-1153:ERGdel Note: The TMPRSS2 -ERG Fusion includes the non-canonical transcript of ERG.
ERG	0	MSKCC-DMP	P-0036302-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.40-59382:TMPRSS2_c.127-1153:ERGdel Note: The TMPRSS2 -ERG Fusion includes the non-canonical transcript of ERG.
IGF2	0	MSKCC-DMP	P-0037070-T01-IM6	IGF2-intragenic	yes	unknown		unknown	IGF2 (NM_001127598) rearrangement: c.69:IGF2_chr11:g.121451136del Note: The IGF2 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
DNAJB1	0	MSKCC-DMP	P-0037291-T01-IM6	PRKACA-DNAJB1 fusion	yes	unknown		in frame	DNAJB1 (NM_006145) - PRKACA (NM_002730) fusion (DNAJB1 exon 1 fused to PRKACA exons 2-10): c.212-523:DNAJB1_ c.46+3770:PRKACAdel Note: The DNAJB1 - PRKACA fusion is predicted to be in frame and includes the kinase domain of PRKACA
PRKACA	0	MSKCC-DMP	P-0037291-T01-IM6	PRKACA-DNAJB1 fusion	yes	unknown		in frame	DNAJB1 (NM_006145) - PRKACA (NM_002730) fusion (DNAJB1 exon 1 fused to PRKACA exons 2-10): c.212-523:DNAJB1_ c.46+3770:PRKACAdel Note: The DNAJB1 - PRKACA fusion is predicted to be in frame and includes the kinase domain of PRKACA
TMPRSS2	0	MSKCC-DMP	P-0037293-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1238:TMPRSS2_c.40-57682:ERGinv Note: The TMPRSS2 - ERG rearrangement is an inversion with breakpoints within TMPRSS2 intron 1 and ERG intron 3. Multiple TMPRSS2 rearrangements were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 - ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERG	0	MSKCC-DMP	P-0037293-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1238:TMPRSS2_c.40-57682:ERGinv Note: The TMPRSS2 - ERG rearrangement is an inversion with breakpoints within TMPRSS2 intron 1 and ERG intron 3. Multiple TMPRSS2 rearrangements were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 - ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
NAV1	0	MSKCC-DMP	P-0037369-T01-IM6	ELF3-NAV1 fusion	yes	unknown		in frame	NAV1 (NM_020443) - ELF3 (NM_004433) rearrangement: c.758-744:NAV1_c.806-120:ELF3del Note: The NAV1 - ELF3 rearrangement is a deletion which results in the fusion of NAV1 exon 1 with ELF3 exons 8-9. Its functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0037369-T01-IM6	ELF3-NAV1 fusion	yes	unknown		in frame	NAV1 (NM_020443) - ELF3 (NM_004433) rearrangement: c.758-744:NAV1_c.806-120:ELF3del Note: The NAV1 - ELF3 rearrangement is a deletion which results in the fusion of NAV1 exon 1 with ELF3 exons 8-9. Its functional significance is undetermined.
WNT1	0	MSKCC-DMP	P-0037462-T01-IM6	KMT2D-WNT1 fusion	yes	unknown		unknown	WNT1 (NM_005430) - KMT2D (NM_003482) rearrangement: c.625-20:WNT1_c.5989:KMT2Dinv Note: The WNT1 - KMT2D rearrangement is an inversion that results in a fusion of WNT1 exons 1-4 to KMT2D exons 28-54. One of the breakpoints is within KMT2D exon 28. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0037462-T01-IM6	KMT2D-WNT1 fusion	yes	unknown		unknown	WNT1 (NM_005430) - KMT2D (NM_003482) rearrangement: c.625-20:WNT1_c.5989:KMT2Dinv Note: The WNT1 - KMT2D rearrangement is an inversion that results in a fusion of WNT1 exons 1-4 to KMT2D exons 28-54. One of the breakpoints is within KMT2D exon 28. The functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0037462-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.1613_1925-1558dup Note: The PBRM1 rearrangement is an intragenic duplication of exons 15-16. One of the breakpoints is within exon 15. The functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0037478-T01-IM6	PIP5K1B-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) -PIP5K1B(NM_003558) Rearrangement : c.2716:ABL1_c.454:PIP5K1Bdup Note: The ABL1-PIP5K1B Rearrangement results in the fusion of exons 1-11 of ABL1 with exons7-16 of PIP5K1B. The breakpoints are within exon11 of ABL1 and exon7 of PIP5K1B. It includes the protein kinase domain of ABL1.
PIP5K1B	0	MSKCC-DMP	P-0037478-T01-IM6	PIP5K1B-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) -PIP5K1B(NM_003558) Rearrangement : c.2716:ABL1_c.454:PIP5K1Bdup Note: The ABL1-PIP5K1B Rearrangement results in the fusion of exons 1-11 of ABL1 with exons7-16 of PIP5K1B. The breakpoints are within exon11 of ABL1 and exon7 of PIP5K1B. It includes the protein kinase domain of ABL1.
LMLN	0	MSKCC-DMP	P-0037484-T01-IM6	TSC2-LMLN fusion	yes	unknown		unknown	LMLN (NM_001136049) - TSC2 (NM_000548) Rearrangement : t(3,16)(q29; p13.3) (chr3:g.197695630::chr16:g.2121541) Note: The LMLN-TSC2 Rearrangement results in the fusion of exon1 of LMLN with exons18-42 of TSC2. The breakpoint in TSC2 is within exon18. Its functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0037484-T01-IM6	TSC2-LMLN fusion	yes	unknown		unknown	LMLN (NM_001136049) - TSC2 (NM_000548) Rearrangement : t(3,16)(q29; p13.3) (chr3:g.197695630::chr16:g.2121541) Note: The LMLN-TSC2 Rearrangement results in the fusion of exon1 of LMLN with exons18-42 of TSC2. The breakpoint in TSC2 is within exon18. Its functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0037484-T01-IM6	UPF1-intragenic	yes	unknown		out of frame	UPF1 (NM_002911) Rearrangement : c.372-593_c.810+133dup Note: The UPF1 Rearrangement results in the intragenic duplication of exons3-5. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037620-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+982:TMPRSS2_c.236+9086:ERGdel Note: The TMPRSS2 - ERG fusion involves exons TMPRSS2 exons 1-2 and ERG exons 3-10.
ERG	0	MSKCC-DMP	P-0037620-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+982:TMPRSS2_c.236+9086:ERGdel Note: The TMPRSS2 - ERG fusion involves exons TMPRSS2 exons 1-2 and ERG exons 3-10.
PIK3R3	0	MSKCC-DMP	P-0037810-T01-IM6	PIK3R3-intragenic	yes	unknown		out of frame	PIK3R3 (NM_003629) rearrangement: c.107-17501_c.621+33dup Note: The PIK3R3 rearrangement is a duplication of exons 2-5. Its functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0037891-T01-IM6	IGF1R-MAP3K13 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) - IGF1R (NM_000875) rearrangement: t(3,15)(q27.2;q26.3)(chr3:g.185040460::chr15:g.99500351) Note: The MAP3K13 - IFG1R rearrangement is a translocation that results in a fusion of MAP3K13 exon 1 to IGF1R exon 21. One of the breakpoints is within IGF1R exon 21. The functional significance is undetermined.
IGF1R	0	MSKCC-DMP	P-0037891-T01-IM6	IGF1R-MAP3K13 fusion	yes	unknown		unknown	MAP3K13 (NM_004721) - IGF1R (NM_000875) rearrangement: t(3,15)(q27.2;q26.3)(chr3:g.185040460::chr15:g.99500351) Note: The MAP3K13 - IFG1R rearrangement is a translocation that results in a fusion of MAP3K13 exon 1 to IGF1R exon 21. One of the breakpoints is within IGF1R exon 21. The functional significance is undetermined.
IRS1	0	MSKCC-DMP	P-0037904-T01-IM6	IRS1-intragenic	yes	unknown		unknown	IRS1 (NM_005544) rearrangement: c.648:IRS1_chr2:g.227329627dup Note: The IRS1 rearrangement results in the duplication of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0037909-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: c.3724+83:RTEL1_chr20:g.62425706del Note: The RTEL1 rearrangement results in the deletion of exon 35. The functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0037909-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement: c.-163+13306_c.44+20inv Note: The STAG2 rearrangement results in the inversion of exons 1-3. The functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0037919-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: c.4329+44:PTPRT_chr20:g.34150608del Note: The PTPRT rearrangement is a deletion of of exon 32.
HLA	0	MSKCC-DMP	P-0037920-T01-IM6	DMB-HLA fusion	yes	unknown		unknown	HLA-DMB (NM_002118) - TAP1 (NM_000593) rearrangement: c.622+404:HLA-DMB_c.1884:TAP1del Note: The HLA-DMB - TAP1 rearrangement is a deletion that results in a fusion of HLA-DMB exons 1 - 3 to TAP1 exons 8 - 11. One of the breakpoints is within TAP1 exon 8. The functional significance is undetermined.
DMB	0	MSKCC-DMP	P-0037920-T01-IM6	DMB-HLA fusion	yes	unknown		unknown	HLA-DMB (NM_002118) - TAP1 (NM_000593) rearrangement: c.622+404:HLA-DMB_c.1884:TAP1del Note: The HLA-DMB - TAP1 rearrangement is a deletion that results in a fusion of HLA-DMB exons 1 - 3 to TAP1 exons 8 - 11. One of the breakpoints is within TAP1 exon 8. The functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0037962-T01-IM6	NEGR1-intragenic	yes	unknown		out of frame	NEGR1 (NM_173808) rearrangement: c.177-153640_c.410-89del Note: The NEGR1 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0038253-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  -TACC3( NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon8) : c.2284:FGFR3_c.1644+106:TACC3dup Note: The FGFR3-TACC3 Fusion includes the protein kinase domain of FGFR3 and the breakpoint in FGFR3 is within exon18.
TACC3	0	MSKCC-DMP	P-0038253-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142)  -TACC3( NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon8) : c.2284:FGFR3_c.1644+106:TACC3dup Note: The FGFR3-TACC3 Fusion includes the protein kinase domain of FGFR3 and the breakpoint in FGFR3 is within exon18.
NOTCH2	0	MSKCC-DMP	P-0039172-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.5762:NOTCH2_chr1:g.120336534del Note : The NOTCH2 rearrangement is a deletion of exons 31 - 34. One of the breakpoints is within exon 31.
RB1	0	MSKCC-DMP	P-0039227-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1388_c.1695+10356del Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 17. One of the breakpoints is within exon 14.
NDE1	0	MSKCC-DMP	P-0039289-T01-IM6	BLM-NDE1 fusion	yes	unknown		out of frame	NDE1 (NM_017668) - BLM (NM_000057) rearrangement: t(15;16)(q26.1;p13.11)(chr15:g.91310060::chr16:g.15795773) Note: The NDE1 - BLM rearrangement is a translocation that results in a fusion of NDE1 exons 1 - 9 to BLM exons 10 - 22. The functional significance is undetermined.
BLM	0	MSKCC-DMP	P-0039289-T01-IM6	BLM-NDE1 fusion	yes	unknown		out of frame	NDE1 (NM_017668) - BLM (NM_000057) rearrangement: t(15;16)(q26.1;p13.11)(chr15:g.91310060::chr16:g.15795773) Note: The NDE1 - BLM rearrangement is a translocation that results in a fusion of NDE1 exons 1 - 9 to BLM exons 10 - 22. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0039752-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3265+12120_c.7874del Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 10. One of the breakpoints is within exon 10.
MEF2B	0	MSKCC-DMP	P-0039935-T01-IM6	MEF2B-intragenic	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: c.1079:MEF2B_chr19:g.19253625dup Note: The MEF2B rearrangement is a duplication of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.
MGAT4A	0	MSKCC-DMP	P-0039965-T01-IM6	INPP4A-MGAT4A fusion	yes	unknown		unknown	MGAT4A (NM_012214) - INPP4A (NM_001134224) rearrangement: c.1469-2119:MGAT4A_c.2622:INPP4Ainv Note: The MGAT4A - INPP4A rearrangement is an inversion that results in a fusion of MGAT4A exons 1 - 11 to INPP4A exons 24 - 26. One of the breakpoints is within INPP4A exon 24. Functional significance is undetermined.
INPP4A	0	MSKCC-DMP	P-0039965-T01-IM6	INPP4A-MGAT4A fusion	yes	unknown		unknown	MGAT4A (NM_012214) - INPP4A (NM_001134224) rearrangement: c.1469-2119:MGAT4A_c.2622:INPP4Ainv Note: The MGAT4A - INPP4A rearrangement is an inversion that results in a fusion of MGAT4A exons 1 - 11 to INPP4A exons 24 - 26. One of the breakpoints is within INPP4A exon 24. Functional significance is undetermined.
UBE2W	0	MSKCC-DMP	P-0040084-T01-IM6	TEK-UBE2W fusion	yes	unknown		unknown	UBE2W (NM_001001481) - TEK (NM_000459) rearrangement: t(8;9)(q21.11;p21.2)(chr8:g.74735893::chr9:g.27180309) Note: The UBE2W - TEK rearrangement is a translocation that results in a fusion of UBE2W exons 1 - 3 to TEK exons 7 - 23. One of the breakpoints is within TEK exon 7. The fusion includes the kinase domain of TEK. Functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0040084-T01-IM6	TEK-UBE2W fusion	yes	unknown		unknown	UBE2W (NM_001001481) - TEK (NM_000459) rearrangement: t(8;9)(q21.11;p21.2)(chr8:g.74735893::chr9:g.27180309) Note: The UBE2W - TEK rearrangement is a translocation that results in a fusion of UBE2W exons 1 - 3 to TEK exons 7 - 23. One of the breakpoints is within TEK exon 7. The fusion includes the kinase domain of TEK. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0040154-T01-IM6	TSC2-intragenic	yes	unknown		out of frame	TSC2 (NM_000548) rearrangement: c.225+60_c.4849+25dup Note: The TSC2 rearrangement is an intragenic duplication of exons 4 - 37. Functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0040281-T01-IM6	MAP3K1-intragenic	yes	unknown		out of frame	MAP3K1 (NM_005921) rearrangement: c.483-5377_c.1153-69del Note: The MAP3K1 rearrangement is an intragenic deletion of exons 2 - 5. The rearrangement does not include the kinase domain of MAP3K1.
TMPRSS2	0	MSKCC-DMP	P-0040335-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.557-1097:TMPRSS2_c.40-52915:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 5 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040335-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.557-1097:TMPRSS2_c.40-52915:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 5 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
CLIP1	0	MSKCC-DMP	P-0040461-T01-IM6	BRAF-CLIP1 fusion	yes	unknown		in frame	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140488218::chr12:g.122833264) Note: The CLIP1 - BRAF fusion involves CLIP1 exons 1 - 8 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0040461-T01-IM6	BRAF-CLIP1 fusion	yes	unknown		in frame	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140488218::chr12:g.122833264) Note: The CLIP1 - BRAF fusion involves CLIP1 exons 1 - 8 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
MALT1	0	MSKCC-DMP	P-0040618-T01-IM6	MALT1-intragenic	yes	unknown		unknown	MALT1 (NM_006785) rearrangement: c.1604-3055_c.2343del Note: The MALT1 rearrangement is an intragenic deletion of exons 14 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.
THSD4	0	MSKCC-DMP	P-0040618-T01-IM6	EWSR1-THSD4 fusion	yes	unknown		in frame	THSD4 (NM_024817) - EWSR1 (NM_013986) rearrangement: t(15;22)(q23;q12.2)(chr15:g.71660057::chr22:g.29684202) Note: The THSD4 - EWSR1 rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 5 to EWSR1 exons 9 - 18. The fusion is predicted to be in-frame. Functional significance is undetermined. Further analysis using the Archer targeted RNAseq assay will be performed if additional material is available and results will be reported under a separate accession number.
EWSR1	0	MSKCC-DMP	P-0040618-T01-IM6	EWSR1-THSD4 fusion	yes	unknown		in frame	THSD4 (NM_024817) - EWSR1 (NM_013986) rearrangement: t(15;22)(q23;q12.2)(chr15:g.71660057::chr22:g.29684202) Note: The THSD4 - EWSR1 rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 5 to EWSR1 exons 9 - 18. The fusion is predicted to be in-frame. Functional significance is undetermined. Further analysis using the Archer targeted RNAseq assay will be performed if additional material is available and results will be reported under a separate accession number.
BCL2L14	0	MSKCC-DMP	P-0040855-T01-IM6	ETV6-BCL2L14 fusion	yes	unknown		in frame	BCL2L14 (NM_138723) - ETV6 (NM_001987) rearrangement: c.434-2555:BCL2L14_c.1009+5088:ETV6dup Note: The BCL2L14 - ETV6 rearrangement is a duplication that results in a fusion of BCL2L14 exons 1 - 2 to ETV6 exons 6 - 8. The fusion is predicted to be in frame. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0040855-T01-IM6	ETV6-BCL2L14 fusion	yes	unknown		in frame	BCL2L14 (NM_138723) - ETV6 (NM_001987) rearrangement: c.434-2555:BCL2L14_c.1009+5088:ETV6dup Note: The BCL2L14 - ETV6 rearrangement is a duplication that results in a fusion of BCL2L14 exons 1 - 2 to ETV6 exons 6 - 8. The fusion is predicted to be in frame. Functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0041285-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.441+1741_c.3289del Note: The BRCA1 rearrangement is an intragenic deletion of exons 7 - 10. One of the breakpoints is within exon 10.
EP300	0	MSKCC-DMP	P-0041345-T01-IM6	GUCD1-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) - GUCD1 (NM_031444) rearrangement: c.6779:EP300_c.128+261:GUCD1inv Note: The EP300 - GUCD1 rearrangement is an inversion that results in a fusion of EP300 exons 1 - 31 to GUCD1 exons 3 - 6. One of the breakpoints is within EP300 exon 31. Functional significance is undetermined.
GUCD1	0	MSKCC-DMP	P-0041345-T01-IM6	GUCD1-EP300 fusion	yes	unknown		unknown	EP300 (NM_001429) - GUCD1 (NM_031444) rearrangement: c.6779:EP300_c.128+261:GUCD1inv Note: The EP300 - GUCD1 rearrangement is an inversion that results in a fusion of EP300 exons 1 - 31 to GUCD1 exons 3 - 6. One of the breakpoints is within EP300 exon 31. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041659-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1474:TMPRSS2_c.40-62694:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0041659-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1474:TMPRSS2_c.40-62694:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
KIF13A	0	MSKCC-DMP	P-0042153-T01-IM6	RET-KIF13A fusion	yes	unknown		in frame	KIF13A (NM_022113) - RET (NM_020975) fusion: t(6;10)(p22.3;q11.21)(chr6:g.17806558::chr10:g.43610510) Note: The KIF13A - RET fusion involves KIF13A exons 1 - 18 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0042153-T01-IM6	RET-KIF13A fusion	yes	unknown		in frame	KIF13A (NM_022113) - RET (NM_020975) fusion: t(6;10)(p22.3;q11.21)(chr6:g.17806558::chr10:g.43610510) Note: The KIF13A - RET fusion involves KIF13A exons 1 - 18 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
BRCA1	0	MSKCC-DMP	P-0042153-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: t(9;17)(q34.3;q21.31)(chr9:g.140583654::chr17:g.41244909) Note: The BRCA1 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0043229-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3266-11620_c.3704del Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 5. One of the breakpoints is within exon 5.
PTPRD	0	MSKCC-DMP	P-0043229-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.352+36549_c.2926del Note: The PTPRD rearrangement is an intragenic deletion of exons 15 - 28. One of the breakpoints is within exon 28.
RASA1	0	MSKCC-DMP	P-0043240-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.137:RASA1_chr5:g.86555625del Note: The RASA1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
ID3	0	MSKCC-DMP	P-0043241-T01-IM6	ID3-intragenic	yes	unknown		unknown	ID3 (NM_002167) rearrangement: c.300+17:ID3_chr1:g.38197642inv Note: The ID3 rearrangement is an inversion of exon 1. Functional significance is undetermined.
GNL2	0	MSKCC-DMP	P-0043241-T01-IM6	MAPK1-GNL2 fusion	yes	unknown		in frame	GNL2 (NM_013285) - MAPK1 (NM_002745) rearrangement: t(1;22)(p34.3;q11.21)(chr1:g.38056295::chr22:g.22143180) Note: The GNL2 - MAPK1 rearrangement is a translocation that results in a fusion of GNL2 exons 1 - 4 to MAPK1 exons 5 - 8. The fusion is predicted to be in frame and includes a part of the kinase domain of MAPK1. Functional significance is undetermined.
MAPK1	0	MSKCC-DMP	P-0043241-T01-IM6	MAPK1-GNL2 fusion	yes	unknown		in frame	GNL2 (NM_013285) - MAPK1 (NM_002745) rearrangement: t(1;22)(p34.3;q11.21)(chr1:g.38056295::chr22:g.22143180) Note: The GNL2 - MAPK1 rearrangement is a translocation that results in a fusion of GNL2 exons 1 - 4 to MAPK1 exons 5 - 8. The fusion is predicted to be in frame and includes a part of the kinase domain of MAPK1. Functional significance is undetermined.
CCDC171	0	MSKCC-DMP	P-0043241-T01-IM6	PTPRD-CCDC171 fusion	yes	unknown		out of frame	CCDC171 (NM_173550) - PTPRD (NM_002839) rearrangement: c.352+5531:CCDC171_c.3876-4804:PTPRDinv Note: The CCDC171 - PTPRD rearrangement is an inversion  that results in the fusion of exons 1 - 4 of CCDC171 with exons 34-46 of PTPRD . Functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0043241-T01-IM6	PTPRD-CCDC171 fusion	yes	unknown		out of frame	CCDC171 (NM_173550) - PTPRD (NM_002839) rearrangement: c.352+5531:CCDC171_c.3876-4804:PTPRDinv Note: The CCDC171 - PTPRD rearrangement is an inversion  that results in the fusion of exons 1 - 4 of CCDC171 with exons 34-46 of PTPRD . Functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0043567-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(16;17)(q21;p11.2)(chr16:g.59600624::chr17:g.16041505) Note: The NCOR1 rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043581-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-686:TMPRSS2_c.39+8942:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0043581-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-686:TMPRSS2_c.39+8942:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
KMT2B	0	MSKCC-DMP	P-0045030-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.4810_c.5252del Note: The KMT2B rearrangement is an intragenic deletion of exons 22 - 25. The breakpoints are within exon 22 and exon 25.
PTPRT	0	MSKCC-DMP	P-0045030-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: c.2176+75:PTPRT_chr20:g.53084718inv Note: The PTPRT rearrangement is an inversion of exons 1 - 13. Functional significance is undetermined. Multiple rearrangements involving PTPRT were detected in this sample and a more complex rearrangement resulting in a PTPRT fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CARD11	0	MSKCC-DMP	P-0045030-T01-IM6	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: t(3;7)(q13.12;p22.2)(chr3:g.106730609::chr7:g.2959073) Note: The CARD11 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined. Multiple rearrangements involving CARD11 were detected in this sample and a more complex rearrangement resulting in a CARD11 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
IKBKE	0	MSKCC-DMP	P-0045031-T01-IM6	IKBKE-intragenic	yes	unknown		unknown	IKBKE (NM_014002) rearrangement: c.88-463_c.1155del Note: The IKBKE rearrangement is an intragenic deletion of exons 4 - 10. One of the breakpoints is within exon 10. The rearrangement includes a part of the kinase domain of IKBKE. Functional significance is undetermined.
AMPH	0	MSKCC-DMP	P-0045032-T01-IM6	KMT2C-AMPH fusion	yes	unknown		unknown	AMPH (NM_001635) - KMT2C (NM_170606) rearrangement: c.1398+5667:AMPH_c.9907:KMT2Cdup Note: The AMPH - KMT2C rearrangement is a duplication that results in a fusion of AMPH exons 1 - 16 to KMT2C exons 43 - 59. One of the breakpoints is within KMT2C exon 43. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0045032-T01-IM6	KMT2C-AMPH fusion	yes	unknown		unknown	AMPH (NM_001635) - KMT2C (NM_170606) rearrangement: c.1398+5667:AMPH_c.9907:KMT2Cdup Note: The AMPH - KMT2C rearrangement is a duplication that results in a fusion of AMPH exons 1 - 16 to KMT2C exons 43 - 59. One of the breakpoints is within KMT2C exon 43. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0045039-T01-IM6	SH3GL3-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - SH3GL3 (NM_003027) rearrangement: t(15;21)(q25.2;q22.3)(chr15:g.84263952::chr21:g.42872075) Note: The TMPRSS2 - SH3GL3 rearrangement is a translocation that results in a fusion of TMPRSS2 exon 1 to SH3GL3 exons 12 - 9. The fusion is predicted to be in frame. Functional significance is undetermined.
SH3GL3	0	MSKCC-DMP	P-0045039-T01-IM6	SH3GL3-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - SH3GL3 (NM_003027) rearrangement: t(15;21)(q25.2;q22.3)(chr15:g.84263952::chr21:g.42872075) Note: The TMPRSS2 - SH3GL3 rearrangement is a translocation that results in a fusion of TMPRSS2 exon 1 to SH3GL3 exons 12 - 9. The fusion is predicted to be in frame. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0045042-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: c.1840-60:TSC2_chr16:g.2052248del Note: The TSC2 rearrangement is a deletion of exons 1 - 17. Multiple rearrangements involving TSC2 were detected in this sample and a more complex rearrangement resulting in a TSC2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SHOC2	0	MSKCC-DMP	P-0045047-T01-IM6	SHOC2-intragenic	yes	unknown		unknown	SHOC2 (NM_007373) rearrangement: c.779:SHOC2_chr10:g.104144408del Note: The SHOC2 rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
ALOX12B	0	MSKCC-DMP	P-0045047-T01-IM6	ALOX12B-intragenic	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.1384_c.1654+804dup Note: The ALOX12B rearrangement is an intragenic duplication of exons 11 - 12. One of the breakpoints is within exon 11. Functional significance is undetermined.
GATA1	0	MSKCC-DMP	P-0045096-T01-IM6	HDAC6-GATA1 fusion	yes	unknown		unknown	GATA1 (NM_002049) - HDAC6 (NM_006044) rearrangement: c.61:GATA1_c.807-307:HDAC6del Note: The GATA1 - HDAC6 rearrangement is a deletion that results in a fusion of GATA1 exons 1 - 2 to HDAC6 exons 11 - 29. One of the breakpoints is within GATA1 exon 2. Functional significance is undetermined.
HDAC6	0	MSKCC-DMP	P-0045096-T01-IM6	HDAC6-GATA1 fusion	yes	unknown		unknown	GATA1 (NM_002049) - HDAC6 (NM_006044) rearrangement: c.61:GATA1_c.807-307:HDAC6del Note: The GATA1 - HDAC6 rearrangement is a deletion that results in a fusion of GATA1 exons 1 - 2 to HDAC6 exons 11 - 29. One of the breakpoints is within GATA1 exon 2. Functional significance is undetermined.
SF3B1	0	MSKCC-DMP	P-0045101-T01-IM6	SF3B1-intragenic	yes	unknown		unknown	SF3B1 (NM_012433) rearrangement: c.904+126:SF3B1_chr2:g.196075812inv Note: The SF3B1 rearrangement is an inversion of exons 8 - 25. Functional significance is undetermined.
FANCC	0	MSKCC-DMP	P-0045101-T01-IM6	FANCC-intragenic	yes	unknown		unknown	FANCC (NM_000136) rearrangement: c.30:FANCC_chr9:g.98021717inv Note: The FANCC rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0045124-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: c.1252:MAP3K1_chr5:g.53706086del Note: The MAP3K1 rearrangement is a deletion of exons 1 - 6. One of the breakpoints is within exon 6. The rearrangement does not include the kinase domain of MAP3K1.
MET	0	MSKCC-DMP	P-0005114-T03-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET Exon 14 skipping (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20190050 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0034876-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20180160 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0034876-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20180160 Macro-dissection: Unknown
NTRK1	0	MSKCC-DMP	P-0037881-T01-IM6	NTRK1-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: NTRK1 (NM_002529) deletion of exons 3-9. PMID: 26581861, 29914559 The functional significance of this event is unknown. Trk inhibitors have not been investigated in this setting.  Lab Notes Run Number: ArcherV3-CLIN-20190022 Macro-dissection: Unknown
TFG	0	MSKCC-DMP	P-0039739-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion.  Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190055 Macro-dissection: Unknown
GPR128	0	MSKCC-DMP	P-0039739-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion.  Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190055 Macro-dissection: Unknown
BCL2L14	0	MSKCC-DMP	P-0040855-T01-IM6	ETV6-BCL2L14 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: BCL2L14-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes BCL2L14 Exon2 (NM_030766) and ETV6 Exon6 (NM_001987). The functional significance of this event is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190075 Macro-dissection: Not Performed
ETV6	0	MSKCC-DMP	P-0040855-T01-IM6	ETV6-BCL2L14 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: BCL2L14-ETV6 fusion. Note: The rearrangement is an in-frame fusion between genes BCL2L14 Exon2 (NM_030766) and ETV6 Exon6 (NM_001987). The functional significance of this event is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190075 Macro-dissection: Not Performed
ARID1A	0	MSKCC-DMP	P-0044943-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1471:ARID1A_chr1:g.27198047del Note: The ARID1A rearrangement is a deletion of exons 3 - 20. One of the breakpoints is within exon 3.
CDKN2B	0	MSKCC-DMP	P-0045019-T02-IM6	CDKN2A-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - CDKN2A (NM_058195) rearrangement: c.338:CDKN2B_c.303:CDKN2Adel Note: The CDKN2B - CDKN2A rearrangement is a deletion that results in a fusion of CDKN2B exons 1 - 2 to CDKN2A exon 2. The breakpoints are within CDKN2B exon 2 and CDKN2A exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CDKN2A	0	MSKCC-DMP	P-0045019-T02-IM6	CDKN2A-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - CDKN2A (NM_058195) rearrangement: c.338:CDKN2B_c.303:CDKN2Adel Note: The CDKN2B - CDKN2A rearrangement is a deletion that results in a fusion of CDKN2B exons 1 - 2 to CDKN2A exon 2. The breakpoints are within CDKN2B exon 2 and CDKN2A exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
SETD2	0	MSKCC-DMP	P-0045104-T01-IM6	SETD2-intragenic	yes	unknown		unknown	SETD2 (NM_014159) rearrangement: t(3;12)(p21.31;p13.33)(chr3:g.47098917::chr12:g.1531949) Note: The SETD2 rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0045139-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.264:KMT2B_chr19:g.36206971del Note: The KMT2B rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
BRAF	0	MSKCC-DMP	P-0045141-T01-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1177+527:BRAF_chr7:g.140421701dup Note: The BRAF rearrangement is a duplication of exons 10 - 18. The rearrangement includes the kinase domain of BRAF. Functional significance is undetermined .
TMPRSS2	0	MSKCC-DMP	P-0045146-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon2 fused with ERG exon2): c.126+343:TMPRSS2_c.18+8891:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0045146-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon2 fused with ERG exon2): c.126+343:TMPRSS2_c.18+8891:ERGdel Note: The TMPRSS2-ERG fusion is predicted to be in frame.
BABAM1	0	MSKCC-DMP	P-0045153-T01-IM6	BABAM1-intragenic	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement: c.341:BABAM1_chr19:g.8834399inv Note: The BABAM1 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0045153-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.8-27690_c.65del Note: The PARK2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.
ARID1A	0	MSKCC-DMP	P-0045156-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.742:ARID1A_chr1:g.27021996del Note: The ARID1A rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
TMPRSS2	0	MSKCC-DMP	P-0045158-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4406:TMPRSS2_c.39+51706:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0045158-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4406:TMPRSS2_c.39+51706:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
SYN3	0	MSKCC-DMP	P-0045158-T01-IM6	RAC2-SYN3 fusion	yes	unknown		out of frame	SYN3 (NM_003490) - RAC2 (NM_002872) rearrangement: c.712-9002:SYN3_c.108-27:RAC2dup Note: The SYN3 - RAC2 rearrangement is a duplication that results in a fusion of SYN3 exons 1 - 5 to RAC2 exons 3 - 6. Functional significance is undetermined.
RAC2	0	MSKCC-DMP	P-0045158-T01-IM6	RAC2-SYN3 fusion	yes	unknown		out of frame	SYN3 (NM_003490) - RAC2 (NM_002872) rearrangement: c.712-9002:SYN3_c.108-27:RAC2dup Note: The SYN3 - RAC2 rearrangement is a duplication that results in a fusion of SYN3 exons 1 - 5 to RAC2 exons 3 - 6. Functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0045158-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: t(3;5)(q26.33;p13.1)(chr3:g.182061807::chr5:g.39074350) Note: The RICTOR rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
SHQ1	0	MSKCC-DMP	P-0045181-T01-IM6	SHQ1-intragenic	yes	unknown		unknown	SHQ1 (NM_018130) rearrangement: c.1182-15003:SHQ1_chr3:g.89156692inv Note: The SHQ1 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0045185-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-479:FGFR2_c.8128-2249:TACC2inv Note: The FGFR2 - TACC2 fusion involves FGFR2 exons 1 - 17 and TACC2 exons 14 - 23. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
TACC2	0	MSKCC-DMP	P-0045185-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-479:FGFR2_c.8128-2249:TACC2inv Note: The FGFR2 - TACC2 fusion involves FGFR2 exons 1 - 17 and TACC2 exons 14 - 23. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
PIK3C2G	0	MSKCC-DMP	P-0045188-T01-IM6	PIK3C2G-intragenic	yes	unknown		in frame	PIK3C2G (NM_004570) rearrangement: c.1208+177_c.2003+2920del Note: The PIK3C2G rearrangement is an intragenic deletion of exons 8 - 14. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0045188-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(16;X)(p13.3;p22.12)(chr16:g.3843591::chrX:g.19329205) Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0045189-T01-IM6	AXL-intragenic	yes	unknown		unknown	AXL (NM_021913) rearrangement: c.125:AXL_chr19:g.42248893del Note: The AXL rearrangement is a deletion of exons 2 - 20. One of the breakpoints is within exon 2. The rearrangement includes the kinase domain of AXL. Functional significance is undetermined.
MSH6	0	MSKCC-DMP	P-0045189-T01-IM6	MSH6-intragenic	yes	unknown		unknown	MSH6 (NM_000179) rearrangement: c.261-1982_c.587dup Note: The MSH6 rearrangement is an intragenic duplication of exons 2 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
FLCN	0	MSKCC-DMP	P-0045190-T01-IM6	FLCN-intragenic	yes	unknown		unknown	FLCN (NM_144997) rearrangement: c.1147:FLCN_chr17:g.17116943del Note: The FLCN rearrangement is a deletion of exons 10 - 14. One of the breakpoints is within exon 10.
BRAF	0	MSKCC-DMP	P-0045245-T01-IM6	BRAF-intragenic	yes	unknown		out of frame	BRAF (NM_004333) rearrangement: c.1177+1757_c.1694+3327del The BRAF rearrangement is an intragenic deletion of exons 10 - 13. The rearrangement includes a part of the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay tin an effort to further characterize this variant. Archer will be performed and reported under a separate accession number if additional material is available.
SOS1	0	MSKCC-DMP	P-0045250-T01-IM6	SOS1-intragenic	yes	unknown		unknown	SOS1 (NM_005633) rearrangement: c.721-40:SOS1_chr2:g.131846662inv Note: The SOS1 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0045252-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: c.1421+1_c.1658-373del Note: The FLT4 rearrangement is an intragenic deletion of exons 10 - 12. One of the breakpoints is within exon 10. The rearrangement does not include the kinase domain of FLT4. Functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0045275-T01-IM6	MAP2K4-intragenic	yes	unknown		unknown	MAP2K4 (NM_003010) rearrangement: c.685+1323_c.1134del Note: The MAP2K4 rearrangement is an intragenic deletion of exons 7 - 11. One of the breakpoints is within exon 11. The rearrangement includes a part of the kinase domain of MAP2K4.
TCF7L2	0	MSKCC-DMP	P-0045280-T01-IM6	TCF7L2-intragenic	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.1319-504:TCF7L2_chr10:g.116507504del Note: The TCF7L2 rearrangement is a deletion of exons 13 - 14.
MUM1	0	MSKCC-DMP	P-0045225-T01-IM6	STK11-MUM1 fusion	yes	unknown		unknown	MUM1 (NM_032853) - STK11 (NM_000455) rearrangement: c.2078+1394:MUM1_c.304:STK11dup Note: The MUM1 - STK11 rearrangement is a duplication that results in a fusion of MUM1 exons 1 - 13 to STK11 exons 2 - 9. One of the breakpoints is within STK11 exon 2. The fusion includes a part of the kinase domain of STK11. Functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0045225-T01-IM6	STK11-MUM1 fusion	yes	unknown		unknown	MUM1 (NM_032853) - STK11 (NM_000455) rearrangement: c.2078+1394:MUM1_c.304:STK11dup Note: The MUM1 - STK11 rearrangement is a duplication that results in a fusion of MUM1 exons 1 - 13 to STK11 exons 2 - 9. One of the breakpoints is within STK11 exon 2. The fusion includes a part of the kinase domain of STK11. Functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0045225-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: c.2815:RECQL4_chr8:g.145061684inv Note: The RECQL4 rearrangement is an inversion of exons 17 - 22. One of the breakpoints is within exon 17. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0045243-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-3064:EML4_c.3172+29:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0045243-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-3064:EML4_c.3172+29:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
RAD52	0	MSKCC-DMP	P-0044066-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: t(3;12)(p14.2;p13.33)(chr3:g.63578870::chr12:g.1022740) Note: The RAD52 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0044365-T01-IM6	CDK4-intragenic	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: c.727:CDK4_chr12:g.25188035inv Note: The CDK4 rearrangement is an inversion of exons 7 - 8. One of the breakpoints is within exon 7. The rearrangement includes a part of the kinase domain of CDK4. Functional significance is undetermined. Multiple rearrangements involving CDK4 were detected in this sample and a more complex rearrangement resulting in a CDK4 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
KMT2B	0	MSKCC-DMP	P-0044365-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.3424:KMT2B_chr19:g.41160688del Note: The KMT2B rearrangement is a deletion of exons 9 - 37. One of the breakpoints is within exon 9.
TRIM24	0	MSKCC-DMP	P-0045111-T01-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2257-760:TRIM24_c.1141-665:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 14 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0045111-T01-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2257-760:TRIM24_c.1141-665:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 14 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
RAD52	0	MSKCC-DMP	P-0045313-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: t(12;18)(p13.33;q22.1)(chr12:g.1025842::chr18:g.62012153) Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0045318-T01-IM6	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: c.8-106_c.803del Note: The CARD11 rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0045341-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4434:EML4_c.3172+407:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0045341-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4434:EML4_c.3172+407:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
PARK2	0	MSKCC-DMP	P-0045344-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) rearrangement: c.412+92_c.534+40671del Note: The PARK2 rearrangement is an intragenic deletion of exon 4.
TP53	0	MSKCC-DMP	P-0045213-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(6;17)(q22.1;p13.1)(chr6:g.116160774::chr17:g.7579873) Note: The TP53 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0045221-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.172-73931_c.172del Note: The PARK2 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.
ARID2	0	MSKCC-DMP	P-0045256-T02-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.5364-509:ARID2_chr12:g.46304714del Note: The ARID2 rearrangement is a deletion of exon 21.
ERBB3	0	MSKCC-DMP	P-0045286-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(1;12)(p32.3;q13.2)(chr1:g.51595284::chr12:g.56486803) Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0045286-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1624:TMPRSS2_c.19-13251:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0045286-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1624:TMPRSS2_c.19-13251:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
HIST1H1C	0	MSKCC-DMP	P-0045288-T01-IM6	HIST1H1C-intragenic	yes	unknown		unknown	HIST1H1C (NM_005319) rearrangement: c.122:HIST1H1C_chr6:g.26121429del Note: The HIST1H1C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0045291-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4177:TMPRSS2_c.18+8298:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0045291-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4177:TMPRSS2_c.18+8298:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
NTHL1	0	MSKCC-DMP	P-0045434-T01-IM6	TSC2-NTHL1 fusion	yes	unknown		unknown	NTHL1 (NM_002528) - TSC2 (NM_000548) rearrangement: c.815+35:NTHL1_c.3815-318:TSC2del Note: The NTHL1 - TSC2 rearrangement is a deletion of NTHL1 exons 1 - 5 and TSC2 exons 1 - 31.
TSC2	0	MSKCC-DMP	P-0045434-T01-IM6	TSC2-NTHL1 fusion	yes	unknown		unknown	NTHL1 (NM_002528) - TSC2 (NM_000548) rearrangement: c.815+35:NTHL1_c.3815-318:TSC2del Note: The NTHL1 - TSC2 rearrangement is a deletion of NTHL1 exons 1 - 5 and TSC2 exons 1 - 31.
TMPRSS2	0	MSKCC-DMP	P-0044245-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4498:TMPRSS2_c.40-53757:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0044245-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4498:TMPRSS2_c.40-53757:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
SLC25A21	0	MSKCC-DMP	P-0045300-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+63480:SLC25A21_c.872:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in a fusion of SLC25A21 exon 1 to FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. Functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0045300-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		unknown	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+63480:SLC25A21_c.872:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in a fusion of SLC25A21 exon 1 to FOXA1 exon 2. One of the breakpoints is within FOXA1 exon 2. Functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0045300-T01-IM6	RAD21-intragenic	yes	unknown		out of frame	RAD21 (NM_006265) rearrangement: c.275-483_c.1161+134dup Poor read support Note: The RAD21 rearrangement is an intragenic duplication of exons 4 - 9. Functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0045300-T01-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.23-23327_c.1788del Note: The AGO2 rearrangement is an intragenic deletion of exons 2 - 14. One of the breakpoints is within exon 14. Functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0045304-T01-IM6	MIDN-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - MIDN (NM_177401) rearrangement: c.960:STK11_c.1130-7:MIDNdel Note: The STK11 - MIDN rearrangement is a deletion that results in a fusion of STK11 exons 1 - 8 to MIDN exon 8. One of the breakpoints is within STK11 exon 8. The fusion includes the kinase domain of STK11.
MIDN	0	MSKCC-DMP	P-0045304-T01-IM6	MIDN-STK11 fusion	yes	unknown		unknown	STK11 (NM_000455) - MIDN (NM_177401) rearrangement: c.960:STK11_c.1130-7:MIDNdel Note: The STK11 - MIDN rearrangement is a deletion that results in a fusion of STK11 exons 1 - 8 to MIDN exon 8. One of the breakpoints is within STK11 exon 8. The fusion includes the kinase domain of STK11.
FGFR2	0	MSKCC-DMP	P-0045408-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: t(7;10)(q21.13;q26.13)(chr7:g.88585840::chr10:g.123240135) Note: The FGFR2 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FGFR2	0	MSKCC-DMP	P-0045185-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICAL PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: Archerv3-CLIN-20190149 Macro-dissection: Performed
TACC2	0	MSKCC-DMP	P-0045185-T01-IM6	TACC2-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICAL PANEL: FGFR2-TACC2 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon17 (NM_000141.4) and TACC2 Exon17 (NM_206862). Lab Notes Run Number: Archerv3-CLIN-20190149 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0042711-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-543:TMPRSS2_c.40-59085:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0042711-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-543:TMPRSS2_c.40-59085:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
FGFR3	0	MSKCC-DMP	P-0045382-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2335:FGFR3_c.1942-101:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0045382-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2335:FGFR3_c.1942-101:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
PTPRD	0	MSKCC-DMP	P-0045399-T01-IM6	PTPRD-intragenic	yes	unknown		unknown	PTPRD (NM_002839) rearrangement: c.64+52:PTPRD_chr9:g.10203900inv Note: The PTPRD rearrangement is an inversion of exons 1 - 12. Functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0045400-T01-IM6	TAP2-intragenic	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: c.1273-1_c.1795+168inv Note: The TAP2 rearrangement is an intragenic inversion of exons 8 - 10. Functional significance is undetermined.
KIT	0	MSKCC-DMP	P-0045411-T01-IM6	KIT-intragenic	yes	unknown		unknown	KIT (NM_000222) rearrangement: c.564_c.756+33del Note: The KIT rearrangement is an intragenic deletion of exons 3 - 4. One of the breakpoints is within exon 3. The rearrangement does not include the kinase domain of KIT. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving KIT is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0045412-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+3275:TMPRSS2_chr21:g.39987066del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0045414-T01-IM6	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) rearrangement: c.2780-4270_c.3312+97dup Note: The PBRM1 rearrangement is an intragenic duplication of exons 19 - 21. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0045416-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.4149:EP300_chr22:g.42369335inv Note: The EP300 rearrangement is an inversion of exons 25 - 31. One of the breakpoints is within exon 25. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0045466-T01-IM6	RET-intragenic	yes	unknown		out of frame	RET (NM_020975) rearrangement: c.2136+60:RET_chr10:g.51588788dup Note: The RET rearrangement is a duplication of exons 12 - 20. The rearrangement includes the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
IRS2	0	MSKCC-DMP	P-0045466-T01-IM6	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: c.4017:IRS2_chr13:g.113369567del Note: The IRS2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0045468-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: c.772-58:RTEL1_chr20:g.22755561inv Note: The RTEL1 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
MET	0	MSKCC-DMP	P-0045469-T01-IM6	MET-intragenic	yes	unknown		out of frame	MET (NM_000245) rearrangement: c.2583+1379_c.3028+1168del Note: The MET rearrangement is an intragenic deletion of exons 12 - 14. The rearrangement does not include the kinase domain of MET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FOXP1	0	MSKCC-DMP	P-0045462-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: t(3;7)(p13;q11.22)(chr3:g.71027118::chr7:g.68292852) Note: The FOXP1 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
PDGFRB	0	MSKCC-DMP	P-0045496-T01-IM6	PDGFRB-intragenic	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: c.2024-491_c.2900inv Note: The PDGFRB rearrangement is an intragenic inversion of exons 15 - 21. One of the breakpoints is within exon 21. The rearrangement includes a part of the kinase domain of PDGFRB. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0045507-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+72:FGFR3_c.1942-413:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 11 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0045507-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+72:FGFR3_c.1942-413:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 11 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
STAT3	0	MSKCC-DMP	P-0045517-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.2258-32:STAT3_chr17:g.42887976inv Note: The STAT3 rearrangement is an inversion of exons 1 - 23. Functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0045517-T01-IM6	INPP4B-intragenic	yes	unknown		out of frame	INPP4B (NM_001101669) rearrangement: c.837-5974_c.2488-24del Note: The INPP4B rearrangement is an intragenic deletion of exons 13 - 24.
LGR5	0	MSKCC-DMP	P-0045531-T01-IM6	NAB2-LGR5 fusion	yes	unknown		unknown	LGR5 (NM_003667) - NAB2 (NM_005967) rearrangement: c.285-7692:LGR5_c.1532:NAB2dup Note: The LGR5 - NAB2 rearrangement is a duplication that results in a fusion of LGR5 exons 1 - 2 to NAB2 exon 7. One of the breakpoints is within NAB2 exon 7. Functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0045531-T01-IM6	NAB2-LGR5 fusion	yes	unknown		unknown	LGR5 (NM_003667) - NAB2 (NM_005967) rearrangement: c.285-7692:LGR5_c.1532:NAB2dup Note: The LGR5 - NAB2 rearrangement is a duplication that results in a fusion of LGR5 exons 1 - 2 to NAB2 exon 7. One of the breakpoints is within NAB2 exon 7. Functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0045535-T01-IM6	PPARG-PAX8 fusion	yes	unknown		in frame	PAX8 (NM_003466) - PPARG (NM_015869) rearrangement: t(2;3)(q13;p25.2)(chr2:g.113992616::chr3:g.12399709) Note: The PAX8 - PPARG rearrangement is a translocation that results in a fusion of PAX8 exons 1 - 9 to PPARG exons 2 - 7. The fusion is predicted to be in frame. Functional significance is undetermined.
PPARG	0	MSKCC-DMP	P-0045535-T01-IM6	PPARG-PAX8 fusion	yes	unknown		in frame	PAX8 (NM_003466) - PPARG (NM_015869) rearrangement: t(2;3)(q13;p25.2)(chr2:g.113992616::chr3:g.12399709) Note: The PAX8 - PPARG rearrangement is a translocation that results in a fusion of PAX8 exons 1 - 9 to PPARG exons 2 - 7. The fusion is predicted to be in frame. Functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0045139-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_002844) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190150 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0045139-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_002844) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190150 Macro-dissection: Performed
CIC	0	MSKCC-DMP	P-0045191-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.3008+35_c.4297del Note: The CIC rearrangement is an intragenic deletion of exons 13 - 18. One of the breakpoints is within exon 18.
CDKN2A	0	MSKCC-DMP	P-0045224-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-3570:CDKN2A_chr9:g.36781788inv Note: The CDKN2A rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
ALK	0	MSKCC-DMP	P-0045557-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(2;4)(p23.2;q22.1)(chr2:g.29447286::chr4:g.90210936) Note: The ALK rearrangement is a translocation with a breakpoint in intron 19. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
INPPL1	0	MSKCC-DMP	P-0045578-T01-IM6	FOLR2-INPPL1 fusion	yes	unknown		out of frame	INPPL1 (NM_001567) - FOLR2 (NM_001113536) rearrangement: c.397+99:INPPL1_c.151-191:FOLR2dup Note: The INPPL1 - FOLR2 rearrangement is a duplication that results in a fusion of INPPL1 exons 1 - 3 to FOLR2 exons 3 - 5. Functional significance is undetermined.
FOLR2	0	MSKCC-DMP	P-0045578-T01-IM6	FOLR2-INPPL1 fusion	yes	unknown		out of frame	INPPL1 (NM_001567) - FOLR2 (NM_001113536) rearrangement: c.397+99:INPPL1_c.151-191:FOLR2dup Note: The INPPL1 - FOLR2 rearrangement is a duplication that results in a fusion of INPPL1 exons 1 - 3 to FOLR2 exons 3 - 5. Functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0045578-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.932:CDK12_chr17:g.71208276del Note: The CDK12 rearrangement is a deletion of exons 1 - 14. One of the breakpoints is within exon 1. The rearrangement includes the kinase domain of CDK12.
PMAIP1	0	MSKCC-DMP	P-0045583-T01-IM6	PMAIP1-intragenic	yes	unknown		unknown	PMAIP1 (NM_021127) rearrangement: c.57:PMAIP1_chr18:g.60612888inv Note: The PMAIP1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0045583-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.89-8942_c.889+168inv Note: The EGFR rearrangement is a vIII alteration.
ZFPM2	0	MSKCC-DMP	P-0045566-T01-IM6	ALK-ZFPM2 fusion	yes	unknown		in frame	ZFPM2 (NM_012082) - ALK (NM_004304) fusion: t(2;8)(p23.2;q23.1)(chr2:g.29447902::chr8:g.106384092) Note: The ZFPM2 - ALK fusion involves ZFPM2 exon 1 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple rearrangements involving ALK were detected in this sample and a more complex rearrangement resulting in a ALK fusion is possible.
ALK	0	MSKCC-DMP	P-0045566-T01-IM6	ALK-ZFPM2 fusion	yes	unknown		in frame	ZFPM2 (NM_012082) - ALK (NM_004304) fusion: t(2;8)(p23.2;q23.1)(chr2:g.29447902::chr8:g.106384092) Note: The ZFPM2 - ALK fusion involves ZFPM2 exon 1 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple rearrangements involving ALK were detected in this sample and a more complex rearrangement resulting in a ALK fusion is possible.
BRAF	0	MSKCC-DMP	P-0045613-T01-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1315-14:BRAF_chr7:g.140429365dup Note: The BRAF rearrangement is a duplication of exons 11 - 18. The rearrangement includes the kinase domain of BRAF. This sample has been nominated for further analysis using the Archer targeted RNAseq assay  to determine the presence or absence of a  BRAF kinase domain duplication. Archer will be performed and reported under a separate accession number if additional material is available.
CDKN2B	0	MSKCC-DMP	P-0045616-T01-IM6	SLC24A2-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - SLC24A2 (NM_020344) rearrangement: c.113:CDKN2B_c.931-51322:SLC24A2del Note: The CDKN2B - SLC24A2 rearrangement is a deletion that results in a fusion of CDKN2B exon 1 to SLC24A2 exons 2 - 10. One of the breakpoints is within CDKN2B exon 1.
SLC24A2	0	MSKCC-DMP	P-0045616-T01-IM6	SLC24A2-CDKN2B fusion	yes	unknown		unknown	CDKN2B (NM_004936) - SLC24A2 (NM_020344) rearrangement: c.113:CDKN2B_c.931-51322:SLC24A2del Note: The CDKN2B - SLC24A2 rearrangement is a deletion that results in a fusion of CDKN2B exon 1 to SLC24A2 exons 2 - 10. One of the breakpoints is within CDKN2B exon 1.
NEGR1	0	MSKCC-DMP	P-0045617-T01-IM6	NEGR1-intragenic	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: c.536-132:NEGR1_chr1:g.63091106inv Note: The NEGR1 rearrangement is an inversion of exons 4 - 7. Functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0045617-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.6530:NOTCH2_chr1:g.96486979inv Note: The NOTCH2 rearrangement is an inversion of exon 34. One of the breakpoints is within exon 34. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0045617-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.3953:KMT2A_chr11:g.133388889inv Note: The KMT2A rearrangement is an inversion of exons 7 - 36. One of the breakpoints is within exon 7. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0045619-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(2;17)(p11.2;p13.1)(chr2:g.86353784::chr17:g.7576703) Note: The TP53 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0045623-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.2029+32:EZH2_chr7:g.148423587del Note: The EZH2 rearrangement is a deletion of exons 18 - 20.
NF1	0	MSKCC-DMP	P-0045728-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.5610-73:NF1_chr17:g.25695654inv Note: The NF1 rearrangement is an inversion of exons 1 - 38. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0045740-T01-IM6	UNC13D-TP53 fusion	yes	unknown		out of frame	TP53 (NM_000546) - UNC13D (NM_199242) rearrangement: c.993+53:TP53_c.1056-60:UNC13Ddup Note: The TP53 - UNC13D rearrangement is a duplication that results in a fusion of TP53 exons 1 - 9 to UNC13D exons 13 - 32. Functional significance is undetermined.
UNC13D	0	MSKCC-DMP	P-0045740-T01-IM6	UNC13D-TP53 fusion	yes	unknown		out of frame	TP53 (NM_000546) - UNC13D (NM_199242) rearrangement: c.993+53:TP53_c.1056-60:UNC13Ddup Note: The TP53 - UNC13D rearrangement is a duplication that results in a fusion of TP53 exons 1 - 9 to UNC13D exons 13 - 32. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0045633-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.993+1071_c.1059del Note: The TP53 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10.
IGF1R	0	MSKCC-DMP	P-0045643-T01-IM6	IGF1R-intragenic	yes	unknown		unknown	IGF1R (NM_000875) rearrangement: c.641-37313_c.807dup Note: The IGF1R rearrangement is an intragenic duplication of exon 3. One of the breakpoints is within exon 3. The rearrangement does not include the kinase domain of IGF1R. Functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0045669-T01-IM6	EWSR1-intragenic	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: c.600-78_c.811+623inv Note: The EWSR1 rearrangement is an intragenic inversion of exon 8. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0045670-T01-IM6	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) rearrangement: c.2211+135_c.2325+17del Note: The RB1 rearrangement is an intragenic deletion of exon 22.
KIF5B	0	MSKCC-DMP	P-0045773-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2247:KIF5B_c.2137-99:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0045773-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2247:KIF5B_c.2137-99:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
ELF3	0	MSKCC-DMP	P-0045821-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.386-26:ELF3_chr1:g.201992796del Note: The ELF3 rearrangement is a deletion of exons 4 - 9.
ETV6	0	MSKCC-DMP	P-0045832-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.464-5415:ETV6_chr12:g.97487697inv Note: The ETV6 rearrangement is an inversion of exons 5 - 8. Functional significance is undetermined. Multiple rearrangements involving ETV6 were detected in this sample and a more complex rearrangement resulting in a ETV6 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MDM2	0	MSKCC-DMP	P-0045832-T01-IM6	GNPTAB-MDM2 fusion	yes	unknown		out of frame	MDM2 (NM_002392) - GNPTAB (NM_024312) rearrangement: c.523+59:MDM2_c.118-14879:GNPTABinv Note: The MDM2 - GNPTAB rearrangement is an inversion that results in a fusion of MDM2 exons 1 - 7 to GNPTAB exons 2 - 21. Functional significance is undetermined.
GNPTAB	0	MSKCC-DMP	P-0045832-T01-IM6	GNPTAB-MDM2 fusion	yes	unknown		out of frame	MDM2 (NM_002392) - GNPTAB (NM_024312) rearrangement: c.523+59:MDM2_c.118-14879:GNPTABinv Note: The MDM2 - GNPTAB rearrangement is an inversion that results in a fusion of MDM2 exons 1 - 7 to GNPTAB exons 2 - 21. Functional significance is undetermined.
CSF1R	0	MSKCC-DMP	P-0045832-T01-IM6	CPM-CSF1R fusion	yes	unknown		unknown	CSF1R (NM_005211) - CPM (NM_001005502) rearrangement: t(5;12)(q32;q15)(chr5:g.149449803::chr12:g.69319777) Note: The CSF1R - CPM rearrangement is a translocation that results in a fusion of CSF1R exons 1 - 9 to CPM exons 3 - 9. One of the breakpoints is within CSF1R exon 9. The fusion does not include the kinase domain of CSF1R. Functional significance is undetermined.
CPM	0	MSKCC-DMP	P-0045832-T01-IM6	CPM-CSF1R fusion	yes	unknown		unknown	CSF1R (NM_005211) - CPM (NM_001005502) rearrangement: t(5;12)(q32;q15)(chr5:g.149449803::chr12:g.69319777) Note: The CSF1R - CPM rearrangement is a translocation that results in a fusion of CSF1R exons 1 - 9 to CPM exons 3 - 9. One of the breakpoints is within CSF1R exon 9. The fusion does not include the kinase domain of CSF1R. Functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0045836-T01-IM6	RFWD2-intragenic	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: c.79_c.642+114del Note: The RFWD2 rearrangement is an intragenic deletion of exons 1 - 4. One of the breakpoints is within exon 1. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0045875-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.3161_c.3313-593del Note: The PBRM1 rearrangement is an intragenic deletion of exon 21. One of the breakpoints is within exon 21.
TCF3	0	MSKCC-DMP	P-0045878-T01-IM6	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.1893:TCF3_chr19:g.1412534del Note: The TCF3 rearrangement is a deletion of exon 18. One of the breakpoints is within exon 18.Multiple rearrangements involving TCF3 were detected in this sample and a more complex rearrangement resulting in a TCF3 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
EGFL7	0	MSKCC-DMP	P-0045881-T01-IM6	EGFL7-intragenic	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: c.80+43:EGFL7_chr9:g.139685238dup Note: The EGFL7 rearrangement is a duplication of exons 3 - 9. Functional significance is undetermined.
NCOA4	0	MSKCC-DMP	P-0045466-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon9 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190155 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0045466-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon9 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190155 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0045508-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2301+1436:FGFR2_chr10:g.130925993inv Note: The FGFR2 rearrangement is an inversion of exons 1 - 17. The rearrangement includes the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KMT2D	0	MSKCC-DMP	P-0045626-T01-IM6	RILPL1-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - RILPL1 (NM_178314) rearrangement: c.14051:KMT2D_c.461-4396:RILPL1dup Note: The KMT2D - RILPL1 rearrangement is a duplication that results in a fusion of KMT2D exons 1 - 43 to RILPL1 exons 3 - 7. One of the breakpoints is within KMT2D exon 43. Functional significance is undetermined.
RILPL1	0	MSKCC-DMP	P-0045626-T01-IM6	RILPL1-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - RILPL1 (NM_178314) rearrangement: c.14051:KMT2D_c.461-4396:RILPL1dup Note: The KMT2D - RILPL1 rearrangement is a duplication that results in a fusion of KMT2D exons 1 - 43 to RILPL1 exons 3 - 7. One of the breakpoints is within KMT2D exon 43. Functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0026774-T02-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.8262:ZFHX3_chr16:g.73087045del Note: The ZFHX3 rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.
BABAM1	0	MSKCC-DMP	P-0029401-T02-IM6	DNAH14-BABAM1 fusion	yes	unknown		out of frame	BABAM1 (NM_001033549) - DNAH14 (NM_001373) rearrangement: t(1;19)(q42.12;p13.11)(chr1:g.225434872::chr19:g.17386670) Note: The BABAM1 - DNAH14 rearrangement is a translocation that results in a fusion of BABAM1 exons 1 - 6 to DNAH14 exons 43 - 84. Functional significance is undetermined.
DNAH14	0	MSKCC-DMP	P-0029401-T02-IM6	DNAH14-BABAM1 fusion	yes	unknown		out of frame	BABAM1 (NM_001033549) - DNAH14 (NM_001373) rearrangement: t(1;19)(q42.12;p13.11)(chr1:g.225434872::chr19:g.17386670) Note: The BABAM1 - DNAH14 rearrangement is a translocation that results in a fusion of BABAM1 exons 1 - 6 to DNAH14 exons 43 - 84. Functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0045460-T01-IM6	SMYD3-intragenic	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement: c.968:SMYD3_chr1:g.245806197del Note: The SMYD3 rearrangement is a deletion of exons 10 - 12. One of the breakpoints is within exon 10. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0045460-T01-IM6	RET-intragenic	yes	unknown		out of frame	RET (NM_020975) rearrangement: c.2136+101:RET_chr10:g.51588385dup Note: The RET rearrangement is a duplication of exons 12 - 20. The rearrangement includes the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TCF7L2	0	MSKCC-DMP	P-0045713-T01-IM6	TCF7L2-intragenic	yes	unknown		out of frame	TCF7L2 (NM_001146274) rearrangement: c.552+13197_c.1318+655dup Note: The TCF7L2 rearrangement is an intragenic duplication of exons 6 - 12. Functional significance is undetermined.
SPTBN1	0	MSKCC-DMP	P-0045724-T01-IM6	ALK-SPTBN1 fusion	yes	unknown		in frame	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.764-456:SPTBN1_c.3173-402:ALKinv Note: The SPTBN1 - ALK fusion involves SPTBN1 exons 1 - 7 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0045724-T01-IM6	ALK-SPTBN1 fusion	yes	unknown		in frame	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.764-456:SPTBN1_c.3173-402:ALKinv Note: The SPTBN1 - ALK fusion involves SPTBN1 exons 1 - 7 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
BCL2L14	0	MSKCC-DMP	P-0045847-T01-IM6	CDKN1B-BCL2L14 fusion	yes	unknown		unknown	BCL2L14 (NM_138723) - CDKN1B (NM_004064) rearrangement: c.608-223:BCL2L14_c.572:CDKN1Bdel Note: The BCL2L14 - CDKN1B rearrangement is a deletion that results in a fusion of BCL2L14 exons 1 - 3 to CDKN1B exon 2. One of the breakpoints is within CDKN1B exon 2.
CDKN1B	0	MSKCC-DMP	P-0045847-T01-IM6	CDKN1B-BCL2L14 fusion	yes	unknown		unknown	BCL2L14 (NM_138723) - CDKN1B (NM_004064) rearrangement: c.608-223:BCL2L14_c.572:CDKN1Bdel Note: The BCL2L14 - CDKN1B rearrangement is a deletion that results in a fusion of BCL2L14 exons 1 - 3 to CDKN1B exon 2. One of the breakpoints is within CDKN1B exon 2.
WHSC1L1	0	MSKCC-DMP	P-0045858-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2011:WHSC1L1_chr8:g.9352182inv Note: The WHSC1L1 rearrangement is an inversion of exons 11 - 24. One of the breakpoints is within exon 11. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0045861-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: t(10;16)(q25.3;q24.3)(chr10:g.116181365::chr16:g.89350468) Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0045862-T01-IM6	ERBB4-intragenic	yes	unknown		out of frame	ERBB4 (NM_005235) rearrangement: c.1125-403_c.1199-19del Note: The ERBB4 rearrangement is an intragenic deletion of exon 10. The rearrangement does not include the kinase domain of ERBB4. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0045890-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.5947_c.7190-2234dup Note: The NF1 rearrangement is an intragenic duplication of exons 40 - 48. One of the breakpoints is within exon 40. Functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0045898-T01-IM6	STAT5A-intragenic	yes	unknown		unknown	STAT5A (NM_003152) rearrangement: c.1361:STAT5A_chr17:g.61466676inv Note: The STAT5A rearrangement is an inversion of exons 12 - 20. One of the breakpoints is within exon 12. Functional significance is undetermined.
EGFLAM	0	MSKCC-DMP	P-0045902-T01-IM6	RICTOR-EGFLAM fusion	yes	unknown		in frame	EGFLAM (NM_001205301) - RICTOR (NM_152756) rearrangement: c.1350-1227:EGFLAM_c.4914-37:RICTORinv Note: The EGFLAM - RICTOR rearrangement is an inversion that results in a fusion of EGFLAM exons 1 - 10 to RICTOR exons 37 - 38. The fusion is predicted to be in frame. Functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0045902-T01-IM6	RICTOR-EGFLAM fusion	yes	unknown		in frame	EGFLAM (NM_001205301) - RICTOR (NM_152756) rearrangement: c.1350-1227:EGFLAM_c.4914-37:RICTORinv Note: The EGFLAM - RICTOR rearrangement is an inversion that results in a fusion of EGFLAM exons 1 - 10 to RICTOR exons 37 - 38. The fusion is predicted to be in frame. Functional significance is undetermined.
NCOA4	0	MSKCC-DMP	P-0045460-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon10 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190154 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0045460-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon10 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190154 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0045531-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190156 Macro-dissection: Not Performed
RSPO3	0	MSKCC-DMP	P-0045531-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190156 Macro-dissection: Not Performed
EML4	0	MSKCC-DMP	P-0045557-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190156 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0045557-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190156 Macro-dissection: Not Performed
MAD1L1	0	MSKCC-DMP	P-0026158-T04-IM6	BRAF-MAD1L1 fusion	yes	unknown		in frame	MAD1L1 (NM_001013837) - BRAF (NM_004333) fusion: c.1417-9863:MAD1L1_c.1140+2359:BRAFdup Note: The MAD1L1 - BRAF fusion involves MAD1L1 exons 1 - 14 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0026158-T04-IM6	BRAF-MAD1L1 fusion	yes	unknown		in frame	MAD1L1 (NM_001013837) - BRAF (NM_004333) fusion: c.1417-9863:MAD1L1_c.1140+2359:BRAFdup Note: The MAD1L1 - BRAF fusion involves MAD1L1 exons 1 - 14 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
ATRX	0	MSKCC-DMP	P-0026158-T04-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.5448+29:ATRX_chrX:g.76117797del Note: The ATRX rearrangement is a deletion of exons 22 - 35.
ARID2	0	MSKCC-DMP	P-0045651-T01-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: t(12;13)(q12;q22.2)(chr12:g.46245145::chr13:g.77149393) Note: The ARID2 rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0045651-T01-IM6	TACC3-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - TACC3 (NM_006342) rearrangement: c.597+105:WHSC1_c.2224-399:TACC3dup Note: The WHSC1 - TACC3 rearrangement is a duplication that results in a fusion of WHSC1 exons 1 - 2 to TACC3 exons 14 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
TACC3	0	MSKCC-DMP	P-0045651-T01-IM6	TACC3-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - TACC3 (NM_006342) rearrangement: c.597+105:WHSC1_c.2224-399:TACC3dup Note: The WHSC1 - TACC3 rearrangement is a duplication that results in a fusion of WHSC1 exons 1 - 2 to TACC3 exons 14 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
APC	0	MSKCC-DMP	P-0045660-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4203_c.7685del Note: The APC rearrangement is an intragenic deletion of exon 16. The breakpoints are within exon 16.
APC	0	MSKCC-DMP	P-0045661-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1268:APC_chr5:g.77595801inv Note: The APC rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0045709-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(3;13)(p21.1;q33.3)(chr3:g.52442050::chr13:g.108262196) Note: The BAP1 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
INPP4A	0	MSKCC-DMP	P-0045918-T01-IM6	INPP4A-intragenic	yes	unknown		unknown	INPP4A (NM_001134224) rearrangement: c.671-15:INPP4A_chr2:g.98539823del Note: The INPP4A rearrangement is a deletion of exons 1 - 9. Functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0045919-T01-IM6	FUBP1-intragenic	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.1889:FUBP1_chr1:g.78408581del Note: The FUBP1 rearrangement is a deletion of exons 19 - 20. One of the breakpoints is within exon 19.
NSRP1	0	MSKCC-DMP	P-0045926-T01-IM6	BRCA1-NSRP1 fusion	yes	unknown		out of frame	NSRP1 (NM_032141) - BRCA1 (NM_007294) rearrangement: c.114+6366:NSRP1_c.4097-188:BRCA1inv Note: The NSRP1 - BRCA1 rearrangement is an inversion that results in a fusion of NSRP1 exons 1 - 2 to BRCA1 exons 11 - 23. Functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0045926-T01-IM6	BRCA1-NSRP1 fusion	yes	unknown		out of frame	NSRP1 (NM_032141) - BRCA1 (NM_007294) rearrangement: c.114+6366:NSRP1_c.4097-188:BRCA1inv Note: The NSRP1 - BRCA1 rearrangement is an inversion that results in a fusion of NSRP1 exons 1 - 2 to BRCA1 exons 11 - 23. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0046005-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.2148:DNMT1_chr19:g.10214783inv Note: The DNMT1 rearrangement is an inversion of exons 23 - 40. One of the breakpoints is within exon 23. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0046008-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.5631_c.6235-13del Note: The KMT2D rearrangement is an intragenic deletion of exons 25 - 30. One of the breakpoints is within exon 25.
SLC45A3	0	MSKCC-DMP	P-0045690-T01-IM6	ETV1-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC45A3-ETV1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ETV1 Exon6 (NM_004956). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Not Performed
ETV1	0	MSKCC-DMP	P-0045690-T01-IM6	ETV1-SLC45A3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SLC45A3-ETV1 fusion. Note: The rearrangement is an in-frame fusion between genes SLC45A3 Exon1 (NM_033102) and ETV1 Exon6 (NM_004956). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Not Performed
SPTBN1	0	MSKCC-DMP	P-0045724-T01-IM6	ALK-SPTBN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: SPTBN1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes SPTBN1 Exon7 (NM_003128) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0045724-T01-IM6	ALK-SPTBN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: SPTBN1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes SPTBN1 Exon7 (NM_003128) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Performed
DOT1L	0	MSKCC-DMP	P-0009432-T02-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(11;19)(q14.1;p13.3)(chr11:g.79148763::chr19:g.2208868) Note: The DOT1L rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0009432-T02-IM6	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: c.4097-179:PTPRS_chr19:g.3987676inv Note: The PTPRS rearrangement is an inversion of exons 27 - 38. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0014808-T03-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1764:KIF5B_c.2136+872:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0014808-T03-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1764:KIF5B_c.2136+872:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0014808-T03-IM6	ERCC6-RET fusion	yes	unknown		out of frame	RET (NM_020975) - ERCC6 (NM_000124) rearrangement: c.2137-816:RET_c.1397+6822:ERCC6inv Note: The RET - ERCC6 rearrangement is an inversion that results in a fusion of RET exons 1 - 11 to ERCC6 exons 6 - 21. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ERCC6	0	MSKCC-DMP	P-0014808-T03-IM6	ERCC6-RET fusion	yes	unknown		out of frame	RET (NM_020975) - ERCC6 (NM_000124) rearrangement: c.2137-816:RET_c.1397+6822:ERCC6inv Note: The RET - ERCC6 rearrangement is an inversion that results in a fusion of RET exons 1 - 11 to ERCC6 exons 6 - 21. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PIK3R3	0	MSKCC-DMP	P-0019263-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.106+25450_c.198del Note: The PIK3R3 rearrangement is an intragenic deletion (25738 bp) of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0022907-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.5147_c.*1269del Note: The ARID1B rearrangement is an intragenic deletion of exon 20. One of the breakpoints is within exon 20. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0024221-T01-IM6	SMARCA4-intragenic	yes	unknown		out of frame	SMARCA4 (NM_003072) rearrangement: c.2438+1723_c.2860-101del Note: The SMARCA4 rearrangement results in the deletion of exons 17-19. The functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0027735-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.75-2_c.994-1dup Note: The TP53 rearrangement is an intragenic duplication of exons 3-9.
NF1	0	MSKCC-DMP	P-0027735-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(2;17)(p12;q11.2)(chr2:g.80131260::chr17:g.29664530) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 43.
BCL2L11	0	MSKCC-DMP	P-0036844-T02-IM6	BCL2L11-intragenic	yes	unknown		out of frame	BCL2L11 (NM_138621) rearrangement: c.394+3733_c.498+3185del Note: The BCL2L11 rearrangement is an intragenic deletion of exon 3.
TERT	0	MSKCC-DMP	P-0045171-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) Rearrangement : chr5:g.1295249_c.41-346:PCDH1inv Note: The TERT rearrangement results in the inversion of  the promoter region of TERT. One of the breakpoints is within the promoter region before the transcription start site. Its functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0045691-T01-IM6	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.202:SOX9_chr17:g.72219596inv Note: The SOX9 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 1. Functional significance is undetermined.
JUN	0	MSKCC-DMP	P-0045947-T01-IM6	JUN-intragenic	yes	unknown		unknown	JUN (NM_002228) rearrangement: c.753:JUN_chr1:g.59240840del Note: The JUN rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
MSH3	0	MSKCC-DMP	P-0045959-T01-IM6	MSH3-intragenic	yes	unknown		in frame	MSH3 (NM_002439) rearrangement: c.792+611_c.910-63del Note: The MSH3 rearrangement is an intragenic deletion of exon 5.
TP53	0	MSKCC-DMP	P-0045964-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.75-3_c.375+218del Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 4.
SUZ12	0	MSKCC-DMP	P-0045987-T01-IM6	SUZ12-intragenic	yes	unknown		in frame	SUZ12 (NM_015355) rearrangement: c.387-2091_c.1595+6dup Note: The SUZ12 rearrangement is an intragenic duplication of exons 4 - 13. Functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0045994-T01-IM6	TRAF7-intragenic	yes	unknown		in frame	TRAF7 (NM_032271) rearrangement: c.81+182_c.348+4dup Note: The TRAF7 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0045996-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3844-499_c.4568del Note: The MGA rearrangement is an intragenic deletion of exons 12 - 14. One of the breakpoints is within exon 14.
UNC13A	0	MSKCC-DMP	P-0046020-T01-IM6	RAD50-UNC13A fusion	yes	unknown		unknown	UNC13A (NM_001080421) - RAD50 (NM_005732) rearrangement: t(5;19)(q31.1;p13.11)(chr5:g.131915030::chr19:g.17752171) Note: The UNC13A - RAD50 rearrangement is a translocation that results in a fusion of UNC13A exons 1 - 20 to RAD50 exons 4 - 25. One of the breakpoints is within RAD50 exon 4. Functional significance is undetermined.
RAD50	0	MSKCC-DMP	P-0046020-T01-IM6	RAD50-UNC13A fusion	yes	unknown		unknown	UNC13A (NM_001080421) - RAD50 (NM_005732) rearrangement: t(5;19)(q31.1;p13.11)(chr5:g.131915030::chr19:g.17752171) Note: The UNC13A - RAD50 rearrangement is a translocation that results in a fusion of UNC13A exons 1 - 20 to RAD50 exons 4 - 25. One of the breakpoints is within RAD50 exon 4. Functional significance is undetermined.
PNRC1	0	MSKCC-DMP	P-0046026-T01-IM6	PNRC1-intragenic	yes	unknown		unknown	PNRC1 (NM_006813) rearrangement: c.540+1121:PNRC1_chr6:g.89780366del Note: The PNRC1 rearrangement is a deletion of exon 1. Functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0046069-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.821:FOXA1_chr14:g.38055116del Note: The FOXA1 rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2.
ERCC6L2	0	MSKCC-DMP	P-0046069-T01-IM6	TSC1-ERCC6L2 fusion	yes	unknown		unknown	ERCC6L2 (NM_001010895) - TSC1 (NM_000368) rearrangement: c.1880+1309:ERCC6L2_c.474:TSC1inv Note: The ERCC6L2  - TSC1 rearrangement is an inversion that results in a fusion of ERCC6L2 exons 1 - 12 to TSC1 exons 6 - 23. One of the breakpoints is within TSC1 exon 6. Functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0046069-T01-IM6	TSC1-ERCC6L2 fusion	yes	unknown		unknown	ERCC6L2 (NM_001010895) - TSC1 (NM_000368) rearrangement: c.1880+1309:ERCC6L2_c.474:TSC1inv Note: The ERCC6L2  - TSC1 rearrangement is an inversion that results in a fusion of ERCC6L2 exons 1 - 12 to TSC1 exons 6 - 23. One of the breakpoints is within TSC1 exon 6. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0046083-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+986:EML4_c.3173-271:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0046083-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+986:EML4_c.3173-271:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
FLT4	0	MSKCC-DMP	P-0046083-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: c.58+2307_c.1039inv Note: The FLT4 rearrangement is an intragenic inversion of exons 2 - 8. One of the breakpoints is within exon 8. The rearrangement does not include the kinase domain of FLT4. Functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0046092-T01-IM6	ADAM32-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) - ADAM32 (NM_145004) rearrangement: c.611:WHSC1L1_c.1902+1372:ADAM32inv Note: The WHSC1L1 - ADAM32 rearrangement is an inversion that results in a fusion of WHSC1L1 exons 1 - 2 to ADAM32 exons 18 - 25. One of the breakpoints is within WHSC1L1 exon 2. Functional significance is undetermined.
ADAM32	0	MSKCC-DMP	P-0046092-T01-IM6	ADAM32-WHSC1L1 fusion	yes	unknown		unknown	WHSC1L1 (NM_023034) - ADAM32 (NM_145004) rearrangement: c.611:WHSC1L1_c.1902+1372:ADAM32inv Note: The WHSC1L1 - ADAM32 rearrangement is an inversion that results in a fusion of WHSC1L1 exons 1 - 2 to ADAM32 exons 18 - 25. One of the breakpoints is within WHSC1L1 exon 2. Functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0046098-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.106+2442:PIK3R3_chr1:g.46597663inv Note: The PIK3R3 rearrangement is an inversion of exon 1. Functional significance is undetermined.
BBC3	0	MSKCC-DMP	P-0046106-T01-IM6	BBC3-intragenic	yes	unknown		unknown	BBC3 (NM_001127240) rearrangement: t(2;19)(q33.2;q13.32)(chr2:g.204419521::chr19:g.47729968) Note: The BBC3 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0046108-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.815+3064_c.1067del Note: The AXIN2 rearrangement is an intragenic deletion of exons 3 - 5. One of the breakpoints is within exon 5.
RB1	0	MSKCC-DMP	P-0046110-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.607+9_c.940-284del Note: The RB1 rearrangement is an intragenic deletion of exons 7 - 9.
CDKN2A	0	MSKCC-DMP	P-0046151-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-124:CDKN2A_chr9:g.22691184inv Note: The CDKN2A rearrangement is an inversion of exon 1. Functional significance is undetermined. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
CDKN1B	0	MSKCC-DMP	P-0046153-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: t(8;12)(q21.3;p13.1)(chr8:g.87279220::chr12:g.12870997) Note: The CDKN1B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
TP63	0	MSKCC-DMP	P-0046160-T01-IM6	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) rearrangement: c.2026:TP63_chr3:g.189715390del Note: The TP63 rearrangement is a deletion of exon 14. One of the breakpoints is within exon 14.
BRAF	0	MSKCC-DMP	P-0004871-T01-IM5	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement : c.1140+1724:BRAF_chr7:g.156140327inv Note: The BRAF (NM_004333) rearrangement event results in the inversion of BRAF exons 1-8. Functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0005201-T02-IM6	RPTOR-intragenic	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: chr17:g.50212445_c.3226:RPTORdel Note: The RPTOR rearrangement results in the deletion of exons 1-27. One of the breakpoints is within exon 27. Its functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0007293-T01-IM5	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement : t(3;4)(p22.1;q34.3)(chr3:g.41267307::chr4:g.177727721) Note: The CTNNB1 (NM_001904) rearrangement event is a translocation which results in a truncated CTNNB1. One of the breakpoints is within CTBBN1 exon6.
SMARCA4	0	MSKCC-DMP	P-0007690-T02-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.4912-106:SMARCA4_chr19:g.10684923del Note: The SMARCA4 rearrangement is a deletion of exon 35. Its functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0015717-T02-IM6	ATP10A-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) - ATP10A (NM_024490) rearrangement: t(9;15)(p24.1;q12)(chr9:g.8331699::chr15:g.26029000) Note: The PTPRD - ATP10A rearrangement is a translocation with breakpoints within PTPRD exon 44 and ATP10A intron 1. The functional significance is undetermined.
ATP10A	0	MSKCC-DMP	P-0015717-T02-IM6	ATP10A-PTPRD fusion	yes	unknown		unknown	PTPRD (NM_002839) - ATP10A (NM_024490) rearrangement: t(9;15)(p24.1;q12)(chr9:g.8331699::chr15:g.26029000) Note: The PTPRD - ATP10A rearrangement is a translocation with breakpoints within PTPRD exon 44 and ATP10A intron 1. The functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0015717-T02-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.746_chr5:g.17010344inv Note: The RICTOR rearrangement is an inversion which includes exons 8 - 38 of RICTOR. One of the breakpoints is within exon 8. Multiple other structural rearrangements involving RICTOR were detected in this sample and a more complex rearrangement is possible.  The functional significance is undetermined.
DROSHA	0	MSKCC-DMP	P-0015717-T02-IM6	SH3GL2-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_01323) - SH3GL2 (NM_003026) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515270::chr9:g.17618065) Note:  The DROSHA - SH3GL2 rearrangement is a translocation with breakpoints within DROSHA exon 7 and SH3GL2 intron 1. The functional significance is undetermined.
SH3GL2	0	MSKCC-DMP	P-0015717-T02-IM6	SH3GL2-DROSHA fusion	yes	unknown		unknown	DROSHA (NM_01323) - SH3GL2 (NM_003026) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515270::chr9:g.17618065) Note:  The DROSHA - SH3GL2 rearrangement is a translocation with breakpoints within DROSHA exon 7 and SH3GL2 intron 1. The functional significance is undetermined.
GSK3B	0	MSKCC-DMP	P-0021198-T01-IM6	GSK3B-intragenic	yes	unknown		unknown	GSK3B (NM_002093) rearrangement: c.948+12_c.910-742inv Note: The GSK3B rearrangement is an inversion of exon 9. Its significance is undetermined.
YES1	0	MSKCC-DMP	P-0023323-T01-IM6	YES1-intragenic	yes	unknown		unknown	YES1 (NM_005433) rearrangement: c.1343_chr18:g.803969inv Note: The YES1 rearrangement results in the inversion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0045456-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3431-11:MGA_chr15:g.36457287del Note: The MGA rearrangement is a deletion of exons 1 - 9.
TRAF2	0	MSKCC-DMP	P-0019247-T01-IM6	NTRK2-TRAF2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRAF2-NTRK2 fusion. Note: The rearrangement is an in-frame fusion between genes TRAF2 Exon9 (NM_021138) and NTRK2 Exon15 (NM_006180). Lab Notes Run Number: ArcherV2-CLIN-20170033 Macro-dissection: Not Performed
NTRK2	0	MSKCC-DMP	P-0019247-T01-IM6	NTRK2-TRAF2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TRAF2-NTRK2 fusion. Note: The rearrangement is an in-frame fusion between genes TRAF2 Exon9 (NM_021138) and NTRK2 Exon15 (NM_006180). Lab Notes Run Number: ArcherV2-CLIN-20170033 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0023378-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - AGK (NM_018238) rearrangement: c.980+1800:BRAF_c.101+14574:AGKinv Note: The BRAF - AGK rearrangement is an inversion that results in an in-frame fusion of BRAF exons 1-7 with AGK exons 3-16. The functional significance is undetermined.
AGK	0	MSKCC-DMP	P-0023378-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - AGK (NM_018238) rearrangement: c.980+1800:BRAF_c.101+14574:AGKinv Note: The BRAF - AGK rearrangement is an inversion that results in an in-frame fusion of BRAF exons 1-7 with AGK exons 3-16. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0025561-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - AGK (NM_018238) Rearrangement: c.980+1288:BRAF_c.101+772:AGKinv Note: The BRAF-AGK Rearrangement results in the fusion of BRAF exons 1-7 to AGK exons 2 to 16. This rearrangement does not include the protein kinase domain of BRAF. While this rearrangement is not the canonical AGK-BRAF fusion, the possibility of the fusion not picked by IMPACT cannot be ruled out.
AGK	0	MSKCC-DMP	P-0025561-T01-IM6	AGK-BRAF fusion	yes	unknown		in frame	BRAF (NM_004333) - AGK (NM_018238) Rearrangement: c.980+1288:BRAF_c.101+772:AGKinv Note: The BRAF-AGK Rearrangement results in the fusion of BRAF exons 1-7 to AGK exons 2 to 16. This rearrangement does not include the protein kinase domain of BRAF. While this rearrangement is not the canonical AGK-BRAF fusion, the possibility of the fusion not picked by IMPACT cannot be ruled out.
MDM4	0	MSKCC-DMP	P-0028078-T01-IM6	MDM4-intragenic	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: c.288-137:MDM4_chr1:g.248451616inv Note: The MDM4 rearrangement is an inversion of exons 5-11. Its functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0028707-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.597+28:STK11_chr19:g.1279387del Note: The STK11 rearrangement results in the deletion of exons 5-9. The functional significance is undetermined.
FYN	0	MSKCC-DMP	P-0032812-T01-IM6	FYN-intragenic	yes	unknown		unknown	FYN (NM_153047) rearrangement: t(q21;p12.3)(chr6:g.112020748::chr12:g.16974089 Note: The FYN rearrangement is a translocation involving a breakpoint in exon 6. Its functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0032812-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.1929:PREX2_chr8:g.57326304inv Note: The PREX2 rearrangement is an inversion of exons 1-18. One of the breakpoints is within exon 18. Multiple rearrangements involving PREX2 were detected in this sample and a more complex rearrangement resulting in a PREX2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SND1	0	MSKCC-DMP	P-0034168-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 fused to BRAF exons 9-18): c.1152+6972:SND1_c.1141-2037:BRAFinv Note: The SND1 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF
BRAF	0	MSKCC-DMP	P-0034168-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 fused to BRAF exons 9-18): c.1152+6972:SND1_c.1141-2037:BRAFinv Note: The SND1 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF
LATS2	0	MSKCC-DMP	P-0034370-T01-IM6	LATS2-intragenic	yes	unknown		unknown	LATS2 (NM_014572) Rearrangement: t(9;13)(q34.3;q12.11)(chr9:g.139825979::chr13:g.21555688) Note: The LATS2 rearrangement is a translocation with breakpoint in exon 6 of LATS2. The functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0034710-T01-IM6	TP53BP1-intragenic	yes	unknown		unknown	TP53BP1 (NM_001141980) Rearrangement :  t(15;20)(q11.21;p11.21)(chr15:g.43713243::chr20:g.22803318) Note: The TP53BP1 Rearrangement is a translocation event with the breakpoint in exon20. Its functional significance is undetermined.
TFAP2B	0	MSKCC-DMP	P-0034710-T01-IM6	DAXX-TFAP2B fusion	yes	unknown		unknown	TFAP2B (NM_003221) - DAXX (NM_001141970)  Rearrangement : c.82-509:TFAP2B_c.193:DAXXinv Note: The TFAP2B - DAXX  Rearrangement results in the fusion of exons 1-2 of TFAP2B with exons2-8 of DAXX.The breakpoint in DAXX is within exon2 . Its functional significance is undetermined.
DAXX	0	MSKCC-DMP	P-0034710-T01-IM6	DAXX-TFAP2B fusion	yes	unknown		unknown	TFAP2B (NM_003221) - DAXX (NM_001141970)  Rearrangement : c.82-509:TFAP2B_c.193:DAXXinv Note: The TFAP2B - DAXX  Rearrangement results in the fusion of exons 1-2 of TFAP2B with exons2-8 of DAXX.The breakpoint in DAXX is within exon2 . Its functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0036240-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.209+85:PTEN_chr10:g.96615851inv Note: The PTEN rearrangement is an inversion of exons 4-9. Its functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0036862-T01-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) Rearrangement : c.41_c.1020-2030del Note: The AXIN1 Rearrangement results in the intragenic deletion of exons 2-3 of AXIN1. One of the breakpoints is within exon. Its functional significance is undetermined.
SAE1	0	MSKCC-DMP	P-0036862-T01-IM6	NOTCH2-SAE1 fusion	yes	unknown		unknown	SAE1 (NM_005500) - NOTCH2 (NM_024408) Rearrangement : t(1;19)(p11.2;q13.1)(chr1:g.120458500::chr19:g.47633732) Note: The SAE1 -NOTCH2 Rearrangement results in the fusion of  promoter region of SAE1 with exon 34 of NOTCH2. The breakpoint in NOTCH2 is within exon34. Multiple structural variants involving NOTCH2 are detected by the IMPACT assay, and may be representative of a more complex gene rearrangement event that cannot be fully characterized by the assay. Its functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0036862-T01-IM6	NOTCH2-SAE1 fusion	yes	unknown		unknown	SAE1 (NM_005500) - NOTCH2 (NM_024408) Rearrangement : t(1;19)(p11.2;q13.1)(chr1:g.120458500::chr19:g.47633732) Note: The SAE1 -NOTCH2 Rearrangement results in the fusion of  promoter region of SAE1 with exon 34 of NOTCH2. The breakpoint in NOTCH2 is within exon34. Multiple structural variants involving NOTCH2 are detected by the IMPACT assay, and may be representative of a more complex gene rearrangement event that cannot be fully characterized by the assay. Its functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0038799-T01-IM6	RFWD2-intragenic	yes	unknown		out of frame	RFWD2 (NM_022457) rearrangement: c.1530+9_c.1612+6576del Note: The RFWD2 rearrangement is an intragenic deletion of exon 14. The functional significance is undetermined.
MPL	0	MSKCC-DMP	P-0039162-T01-IM6	PDZRN3-MPL fusion	yes	unknown		out of frame	MPL (NM_005373) - PDZRN3 (NM_015009) rearrangement: t(1;3)(p34.2;p13)(chr1:g.43806209::chr3:g.73597756) Note : The MPL - PDZRN3 rearrangement is a translocation that results in a fusion of MPL exons 1 - 6 to PDZRN3 exons 4 - 10. Functional significance is undetermined.
PDZRN3	0	MSKCC-DMP	P-0039162-T01-IM6	PDZRN3-MPL fusion	yes	unknown		out of frame	MPL (NM_005373) - PDZRN3 (NM_015009) rearrangement: t(1;3)(p34.2;p13)(chr1:g.43806209::chr3:g.73597756) Note : The MPL - PDZRN3 rearrangement is a translocation that results in a fusion of MPL exons 1 - 6 to PDZRN3 exons 4 - 10. Functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0039162-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: t(5;6)(p15.1;q25.3)(chr5:g.15008789::chr6:g.157099879) Note : The ARID1B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0039162-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: t(7;16)(p14.3;q22.2)(chr7:g.30224334::chr16:g.72821085) Note : The ZFHX3 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.
MITF	0	MSKCC-DMP	P-0039629-T01-IM6	MITF-intragenic	yes	unknown		unknown	MITF (NM_198159) rearrangement: t(3;16)(p13;q12.2)(chr3:g.69928477::chr16:g.56183319) Note: The MITF rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
ALDOA	0	MSKCC-DMP	P-0040246-T01-IM6	IRS1-ALDOA fusion	yes	unknown		unknown	ALDOA (NM_001243177) - IRS1 (NM_005544) rearrangement: t(2;16)(q36.3;p11.2)(chr2:g.227660770::chr16:g.30081156) Note: The ALDOA - IRS1 rearrangement is a translocation that results in a fusion of ALDOA exons 1 - 8 to IRS1 exon 1. The breakpoints are within ALDOA exon 8 and IRS1 exon 1. Functional significance is undetermined.
IRS1	0	MSKCC-DMP	P-0040246-T01-IM6	IRS1-ALDOA fusion	yes	unknown		unknown	ALDOA (NM_001243177) - IRS1 (NM_005544) rearrangement: t(2;16)(q36.3;p11.2)(chr2:g.227660770::chr16:g.30081156) Note: The ALDOA - IRS1 rearrangement is a translocation that results in a fusion of ALDOA exons 1 - 8 to IRS1 exon 1. The breakpoints are within ALDOA exon 8 and IRS1 exon 1. Functional significance is undetermined.
IRS1	0	MSKCC-DMP	P-0040246-T01-IM6	IRS1-intragenic	yes	unknown		unknown	IRS1 (NM_005544) rearrangement: t(2;22)(q36.3;q13.31)(chr2:g.227660594::chr22:g.47611716) Note: The IRS1 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0043860-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-980:EML4_c.3173-537:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0043860-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-980:EML4_c.3173-537:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
PDGFRA	0	MSKCC-DMP	P-0046112-T01-IM6	PDGFRA-intragenic	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: c.266:PDGFRA_chr4:g.43764201del Note: The PDGFRA rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3. The rearrangement does not include the kinase domain of PDGFRA. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving PDGFRA is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
UBA2	0	MSKCC-DMP	P-0046202-T01-IM6	CEBPA-UBA2 fusion	yes	unknown		unknown	UBA2 (NM_005499) - CEBPA (NM_004364) rearrangement: c.293+574:UBA2_c.1007:CEBPAinv Note: The UBA2 - CEBPA rearrangement is an inversion that results in a fusion of UBA2 exons 1 - 3 to CEBPA exon 1. One of the breakpoints is within CEBPA exon 1. Functional significance is undetermined.
CEBPA	0	MSKCC-DMP	P-0046202-T01-IM6	CEBPA-UBA2 fusion	yes	unknown		unknown	UBA2 (NM_005499) - CEBPA (NM_004364) rearrangement: c.293+574:UBA2_c.1007:CEBPAinv Note: The UBA2 - CEBPA rearrangement is an inversion that results in a fusion of UBA2 exons 1 - 3 to CEBPA exon 1. One of the breakpoints is within CEBPA exon 1. Functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0046202-T01-IM6	TTC28-SMAD4 fusion	yes	unknown		out of frame	SMAD4 (NM_005359) - TTC28 (NM_001145418) rearrangement: t(18;22)(q21.2;q12.1)(chr18:g.48592015::chr22:g.29065731) Note: The SMAD4 - TTC28 rearrangement is a translocation that results in a fusion of SMAD4 exons 1 - 9 to TTC28 exons 2 - 23. Functional significance is undetermined.
TTC28	0	MSKCC-DMP	P-0046202-T01-IM6	TTC28-SMAD4 fusion	yes	unknown		out of frame	SMAD4 (NM_005359) - TTC28 (NM_001145418) rearrangement: t(18;22)(q21.2;q12.1)(chr18:g.48592015::chr22:g.29065731) Note: The SMAD4 - TTC28 rearrangement is a translocation that results in a fusion of SMAD4 exons 1 - 9 to TTC28 exons 2 - 23. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0046212-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.4836-6260:NF1_chr17:g.30703505inv Note: The NF1 rearrangement is an inversion of exons 37 - 58. Functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0046219-T01-IM6	AXL-intragenic	yes	unknown		out of frame	AXL (NM_021913) rearrangement: c.2196+24:AXL_chr19:g.48678698del Note: The AXL rearrangement is a deletion of exons 19 - 20. The rearrangement includes a part of the kinase domain of AXL. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0046235-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.2098:BAP1_chr3:g.51914799inv Note: The BAP1 rearrangement is an inversion of exon 17. One of the breakpoints is within exon 17. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0046236-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.458-18:CDKN2A_chr9:g.21966591del Note: The CDKN2A rearrangement is a deletion of exon 3. This affects the CDKN2Ap16INK4A (NM_000077) isoform and may also affect the CDKN2Ap14ARF (NM_058195) isoform.
RB1	0	MSKCC-DMP	P-0046243-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1:RB1_chr13:g.52414371inv Note: The RB1 rearrangement is an inversion of exons 1 - 27. One of the breakpoints is within exon 1. Functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0046246-T01-IM6	ACPP-AXL fusion	yes	unknown		in frame	AXL (NM_021913) - ACPP (NM_001134194) rearrangement: t(3;19)(q22.1;q13.2)(chr3:g.132075952::chr19:g.41745897) Note: The AXL - ACPP rearrangement is a translocation that results in a fusion of AXL exons 1 - 10 to ACPP exon 11. The fusion is predicted to be in frame and does not include the kinase domain of AXL. Functional significance is undetermined.
ACPP	0	MSKCC-DMP	P-0046246-T01-IM6	ACPP-AXL fusion	yes	unknown		in frame	AXL (NM_021913) - ACPP (NM_001134194) rearrangement: t(3;19)(q22.1;q13.2)(chr3:g.132075952::chr19:g.41745897) Note: The AXL - ACPP rearrangement is a translocation that results in a fusion of AXL exons 1 - 10 to ACPP exon 11. The fusion is predicted to be in frame and does not include the kinase domain of AXL. Functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0046250-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.59-16671_c.805+11inv Note: The RUNX1 rearrangement is an intragenic inversion of exons 3 - 7. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0046253-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: t(3;22)(p21.1;q13.2)(chr3:g.52668553::chr22:g.41866350) Note: The PBRM1 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0046254-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(12;X)(q13.12;q26.2)(chr12:g.49435733::chrX:g.133357229) Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 29. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0046259-T01-IM6	PIEZO1-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - PIEZO1 (NM_001142864) rearrangement: c.7923:ANKRD11_c.65-13589:PIEZO1del Note: The ANKRD11 - PIEZO1 rearrangement is a deletion that results in a fusion of ANKRD11 exons 1 - 13 to PIEZO1 exons 2 - 51. One of the breakpoints is within ANKRD11 exon 13.
PIEZO1	0	MSKCC-DMP	P-0046259-T01-IM6	PIEZO1-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - PIEZO1 (NM_001142864) rearrangement: c.7923:ANKRD11_c.65-13589:PIEZO1del Note: The ANKRD11 - PIEZO1 rearrangement is a deletion that results in a fusion of ANKRD11 exons 1 - 13 to PIEZO1 exons 2 - 51. One of the breakpoints is within ANKRD11 exon 13.
NCOA3	0	MSKCC-DMP	P-0046259-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: t(9;20)(q21.12;q13.12)(chr9:g.72660473::chr20:g.46279928) Note: The NCOA3 rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.
ALG9	0	MSKCC-DMP	P-0046260-T01-IM6	KMT2A-ALG9 fusion	yes	unknown		out of frame	ALG9 (NM_001077690) - KMT2A (NM_001197104) rearrangement: c.1714-9207:ALG9_c.11072-27:KMT2Ainv Note: The ALG9 - KMT2A rearrangement is an inversion that results in a fusion of ALG9 exons 1 - 15 to KMT2A exons 31 - 36. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0046260-T01-IM6	KMT2A-ALG9 fusion	yes	unknown		out of frame	ALG9 (NM_001077690) - KMT2A (NM_001197104) rearrangement: c.1714-9207:ALG9_c.11072-27:KMT2Ainv Note: The ALG9 - KMT2A rearrangement is an inversion that results in a fusion of ALG9 exons 1 - 15 to KMT2A exons 31 - 36. Functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0046261-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: t(5;12)(q11.2;p13.32)(chr5:g.56179537::chr12:g.4987480) Note: The MAP3K1 rearrangement is a translocation with a breakpoint in intron 15.Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0046296-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: t(10;13)(q11.21;q12.11)(chr10:g.43611791::chr13:g.22535936) Note: The RET rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ARID1A	0	MSKCC-DMP	P-0046298-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1137+7077_c.4276del Note: The ARID1A rearrangement is an intragenic deletion of exons 2 - 18. One of the breakpoints is within exon 18.
ATP6V0A1	0	MSKCC-DMP	P-0046298-T01-IM6	STAT5A-ATP6V0A1 fusion	yes	unknown		unknown	ATP6V0A1 (NM_001130020) - STAT5A (NM_003152) rearrangement: c.424-2307:ATP6V0A1_c.1713:STAT5Adup Note: The ATP6V0A1 - STAT5A rearrangement is a duplication that results in a fusion of ATP6V0A1 exons 1 - 5 to STAT5A exons 15 - 20. One of the breakpoints is within STAT5A exon 15. Functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0046298-T01-IM6	STAT5A-ATP6V0A1 fusion	yes	unknown		unknown	ATP6V0A1 (NM_001130020) - STAT5A (NM_003152) rearrangement: c.424-2307:ATP6V0A1_c.1713:STAT5Adup Note: The ATP6V0A1 - STAT5A rearrangement is a duplication that results in a fusion of ATP6V0A1 exons 1 - 5 to STAT5A exons 15 - 20. One of the breakpoints is within STAT5A exon 15. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046315-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+1172:TMPRSS2_c.40-61021:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046315-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+1172:TMPRSS2_c.40-61021:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
STK11	0	MSKCC-DMP	P-0046321-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: t(18;19)(q12.2;p13.3)(chr18:g.32923566::chr19:g.1220489) Note: The STK11 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
AGK	0	MSKCC-DMP	P-0025561-T01-IM6	BRAF-AGK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: AGK-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AGK Exon2 (NM_018238) and BRAF Exon8 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170135 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0025561-T01-IM6	BRAF-AGK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: AGK-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes AGK Exon2 (NM_018238) and BRAF Exon8 (NM_004333). Lab Notes Run Number: ArcherV2-CLIN-20170135 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0046018-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190163 Macro-dissection: Not Performed
RSPO3	0	MSKCC-DMP	P-0046018-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190163 Macro-dissection: Not Performed
INPPL1	0	MSKCC-DMP	P-0004226-T03-IM6	FCHSD2-INPPL1 fusion	yes	unknown		in frame	INPPL1 (NM_001567) - FCHSD2 (NM_014824) rearrangement: c.2415+83:INPPL1_c.705+16440:FCHSD2inv Note: The INPPL1 - FCHSD2 rearrangement is an inversion that results in a fusion of INPPL1 exons 1 - 21 to FCHSD2 exons 9 - 20. The fusion is predicted to be in frame. Functional significance is undetermined.
FCHSD2	0	MSKCC-DMP	P-0004226-T03-IM6	FCHSD2-INPPL1 fusion	yes	unknown		in frame	INPPL1 (NM_001567) - FCHSD2 (NM_014824) rearrangement: c.2415+83:INPPL1_c.705+16440:FCHSD2inv Note: The INPPL1 - FCHSD2 rearrangement is an inversion that results in a fusion of INPPL1 exons 1 - 21 to FCHSD2 exons 9 - 20. The fusion is predicted to be in frame. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0046401-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.4836-1907_c.5762dup Note: The NF1 rearrangement is an intragenic duplication of exons 37 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0020078-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_0056569) and ERG Exon5 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190165 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0020078-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_0056569) and ERG Exon5 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190165 Macro-dissection: Not Performed
AGO2	0	MSKCC-DMP	P-0043747-T02-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.2402:AGO2_chr8:g.141541880inv Note: The AGO2 rearrangement is an inversion of exons 18 - 19. One of the breakpoints is within exon 18. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046463-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4822:TMPRSS2_c.40-53654:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046463-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4822:TMPRSS2_c.40-53654:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
KDM5A	0	MSKCC-DMP	P-0046467-T01-IM6	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: c.4359_c.4455+1117del Note: The KDM5A rearrangement is an intragenic deletion of exon 26. One of the breakpoints is within exon 26. Functional significance is undetermined.
PPM1D	0	MSKCC-DMP	P-0046480-T01-IM6	PPM1D-intragenic	yes	unknown		unknown	PPM1D (NM_003620) rearrangement: c.473-16:PPM1D_chr17:g.58662102del Note: The PPM1D rearrangement is a deletion of exon 1. Functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0046552-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: t(5;20)(p13.1;q13.2)(chr5:g.39074150::chr20:g.50693085) Note: The RICTOR rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0046306-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.210-71_c.405dup Note: The PTEN rearrangement is an intragenic duplication of exons 4 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0046342-T01-IM6	NSD1-intragenic	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: c.928-87:NSD1_chr5:g.175874680del Note: The NSD1 rearrangement is a deletion of exons 1 - 2.
ZFHX3	0	MSKCC-DMP	P-0046360-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.2716:ZFHX3_chr16:g.65619132del Note: The ZFHX3 rearrangement is a deletion of exons 2 - 10. One of the breakpoints is within exon 2. Multiple rearrangements involving ZFHX3 were detected in this sample and a more complex rearrangement resulting in a ZFHX3 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0046362-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2088:TMPRSS2_c.40-58426:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046362-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2088:TMPRSS2_c.40-58426:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ZFHX3	0	MSKCC-DMP	P-0046495-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.6069:ZFHX3_chr16:g.72804103del Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.
PREX2	0	MSKCC-DMP	P-0046527-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: t(8;16)(q13.2;q12.1)(chr8:g.69021796::chr16:g.50865290) Note: The PREX2 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0046527-T01-IM6	NBN-intragenic	yes	unknown		unknown	NBN (NM_002485) rearrangement: c.111_c.333inv Note: The NBN rearrangement is an intragenic inversion of exons 2 - 4. The breakpoints are within exon 2 and exon 4. Functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0046527-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(8;X)(q21.3;q21.1)(chr8:g.89361199::chrX:g.76776451) Note: The ATRX rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0028499-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.1652_c.1952-139del Note: The NOTCH3 rearrangement is an intragenic deletion of exons 11 - 12. One of the breakpoints is within exon 11.
RAC2	0	MSKCC-DMP	P-0046404-T01-IM6	ATP6V0A4-RAC2 fusion	yes	unknown		in frame	RAC2 (NM_002872) - ATP6V0A4 (NM_130841) rearrangement: t(7;22)(q34;q13.1)(chr7:g.138393574::chr22:g.37637553) Note: The RAC2 - ATP6V0A4 rearrangement is a translocation that results in a fusion of RAC2 exons 1 - 2 to ATP6V0A4 exon 21. The fusion is predicted to be in frame. Functional significance is undetermined.
ATP6V0A4	0	MSKCC-DMP	P-0046404-T01-IM6	ATP6V0A4-RAC2 fusion	yes	unknown		in frame	RAC2 (NM_002872) - ATP6V0A4 (NM_130841) rearrangement: t(7;22)(q34;q13.1)(chr7:g.138393574::chr22:g.37637553) Note: The RAC2 - ATP6V0A4 rearrangement is a translocation that results in a fusion of RAC2 exons 1 - 2 to ATP6V0A4 exon 21. The fusion is predicted to be in frame. Functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0046576-T01-IM6	CASP8-intragenic	yes	unknown		unknown	CASP8 (NM_001080125) rearrangement: c.588+53_c.772+743inv Note: The CASP8 rearrangement is an intragenic inversion of exons 4 - 5. Functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0046579-T01-IM6	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: t(12;19)(p12.3;q13.2)(chr12:g.18524131::chr19:g.41278692) Note: The PIK3C2G rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.
ATF6	0	MSKCC-DMP	P-0046580-T01-IM6	NUF2-ATF6 fusion	yes	unknown		in frame	ATF6 (NM_007348) - NUF2 (NM_031423) rearrangement: c.1719+11445:ATF6_c.1261-58:NUF2del Note: The ATF6 - NUF2 rearrangement is a deletion that results in a fusion of ATF6 exons 1 - 14 to NUF2 exon 14. The fusion is predicted to be in frame. Functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0046580-T01-IM6	NUF2-ATF6 fusion	yes	unknown		in frame	ATF6 (NM_007348) - NUF2 (NM_031423) rearrangement: c.1719+11445:ATF6_c.1261-58:NUF2del Note: The ATF6 - NUF2 rearrangement is a deletion that results in a fusion of ATF6 exons 1 - 14 to NUF2 exon 14. The fusion is predicted to be in frame. Functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0046582-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement: c.1240:STAG2_chrX:g.122976403inv Note: The STAG2 rearrangement is an inversion of exons 1 - 14. One of the breakpoints is within exon 14. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0046594-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+2217:EML4_c.3173-51:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0046594-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+2217:EML4_c.3173-51:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
SMARCA4	0	MSKCC-DMP	P-0046612-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.4425-6750_c.4534del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 31 - 32. One of the breakpoints is within exon 32.
WHSC1	0	MSKCC-DMP	P-0046612-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.2206:WHSC1_chr4:g.1817511dup Note: The WHSC1 rearrangement is a duplication of exons 1 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
RAC2	0	MSKCC-DMP	P-0046623-T01-IM6	RAC2-intragenic	yes	unknown		unknown	RAC2 (NM_002872) rearrangement: c.108-318:RAC2_chr22:g.36088023inv Note: The RAC2 rearrangement is an inversion of exons 3 - 6. Functional significance is undetermined.
SPATA2L	0	MSKCC-DMP	P-0046624-T01-IM6	FANCA-SPATA2L fusion	yes	unknown		unknown	SPATA2L (NM_152339) - FANCA (NM_000135) rearrangement: c.304-596:SPATA2L_c.736:FANCAdup Note:The SPATA2L - FANCA rearrangement is a duplication that results in a fusion of SPATA2L exons 1 - 2 to FANCA exons 8 - 43. One of the breakpoints is within FANCA exon 8. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0046624-T01-IM6	FANCA-SPATA2L fusion	yes	unknown		unknown	SPATA2L (NM_152339) - FANCA (NM_000135) rearrangement: c.304-596:SPATA2L_c.736:FANCAdup Note:The SPATA2L - FANCA rearrangement is a duplication that results in a fusion of SPATA2L exons 1 - 2 to FANCA exons 8 - 43. One of the breakpoints is within FANCA exon 8. Functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0046624-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.1853-34:NCOR1_chr17:g.16345142del Note:The NCOR1 rearrangement is a deletion of exons 1 - 16.
APC	0	MSKCC-DMP	P-0046628-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1626+197_c.6225del Note:The APC rearrangement is an intragenic deletion of exons 14 - 16. One of the breakpoints is within exon 16.
CDKN2A	0	MSKCC-DMP	P-0046629-T01-IM6	CDKN2A-intragenic	yes	unknown		in frame	CDKN2A (NM_058195, NM_000077) rearrangement: c.458-28:NM_000077_c.193+1786:NM_058195del Note:The CDKN2A rearrangement is a deletion of CDKN2A exons 1 - 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
KDM6A	0	MSKCC-DMP	P-0046629-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.1269:KDM6A_chrX:g.44623978del Note: The KDM6A rearrangement is a deletion of exons 1 - 13. One of the breakpoints is within exon 13.
KIF5B	0	MSKCC-DMP	P-0021937-T03-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+886:KIF5B_c.2137-477:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0021937-T03-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+886:KIF5B_c.2137-477:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
ATRX	0	MSKCC-DMP	P-0034062-T02-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(11;X)(q24.3;q21.1)(chr11:g.129873889::chrX:g.76907888) Note: The ATRX rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0046564-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: c.98:KDM5C_chrX:g.53255881del Note: The KDM5C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
TMPRSS2	0	MSKCC-DMP	P-0046569-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+526:TMPRSS2_c.19-19800:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0046569-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+526:TMPRSS2_c.19-19800:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0046601-T01-IM6	PAX8-intragenic	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: c.1190-2363:PAX8_chr2:g.160291186inv Note: The PAX8 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0046601-T01-IM6	CD74-intragenic	yes	unknown		unknown	CD74 (NM_001025159) rearrangement: c.442-58:CD74_chr5:g.149771672del Note: The CD74 rearrangement is a deletion of exons 5 - 9. Functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0045809-T02-IM6	SUFU-intragenic	yes	unknown		unknown	SUFU (NM_016169) rearrangement: t(3;10)(p12.1;q24.32)(chr3:g.85786435::chr10:g.104389884) Note: The SUFU rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0045809-T02-IM6	FBXL7-RET fusion	yes	unknown		in frame	RET (NM_020975) - FBXL7 (NM_012304) fusion: t(5;10)(p15.1;q11.21)(chr5:g.15556734::chr10:g.43622269) Note: The RET - FBXL7 fusion involves RET exons 1 - 19 and FBXL7 exons 2 - 4. The fusion is predicted to be in frame and includes the kinase domain of RET.   The functional significance of this DNA event is unknown.
FBXL7	0	MSKCC-DMP	P-0045809-T02-IM6	FBXL7-RET fusion	yes	unknown		in frame	RET (NM_020975) - FBXL7 (NM_012304) fusion: t(5;10)(p15.1;q11.21)(chr5:g.15556734::chr10:g.43622269) Note: The RET - FBXL7 fusion involves RET exons 1 - 19 and FBXL7 exons 2 - 4. The fusion is predicted to be in frame and includes the kinase domain of RET.   The functional significance of this DNA event is unknown.
NTRK3	0	MSKCC-DMP	P-0046563-T01-IM6	NTRK3-intragenic	yes	unknown		out of frame	NTRK3 (NM_001012338) rearrangement: c.395+7789_c.623-25del Note: The NTRK3 rearrangement is an intragenic deletion of exons 6 - 7. The rearrangement does not include the kinase domain of NTRK3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
NF1	0	MSKCC-DMP	P-0046563-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(4;17)(p12;q11.2)(chr4:g.45420174::chr17:g.29661961) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 40. Functional significance is undetermined.
CAPZA2	0	MSKCC-DMP	P-0045809-T02-IM6	MET-CAPZA2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CAPZA2-MET fusion. Note: The rearrangement is an in-frame fusion between genes CAPZA2 Exon1 (NM_006136) and MET Exon6 (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190168 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0045809-T02-IM6	MET-CAPZA2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CAPZA2-MET fusion. Note: The rearrangement is an in-frame fusion between genes CAPZA2 Exon1 (NM_006136) and MET Exon6 (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190168 Macro-dissection: Performed
SMAD4	0	MSKCC-DMP	P-0046474-T02-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.357:SMAD4_chr18:g.61422486inv Note: The SMAD4 rearrangement is an inversion of exons 3 - 12. One of the breakpoints is within exon 3. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0046689-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(3;17)(p21.1;q21.31)(chr3:g.52439384::chr17:g.42111278) Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0046693-T01-IM6	FLI1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - FLI1 (NM_002017) fusion: t(11;22)(q24.3;q12.2)(chr11:g.128656732::chr22:g.29683940) Note: The EWSR1 - FLI1 fusion involves EWSR1 exons 1 - 8 and FLI1 exons 6 - 9. The fusion is predicted to be in frame.
FLI1	0	MSKCC-DMP	P-0046693-T01-IM6	FLI1-EWSR1 fusion	yes	unknown		in frame	EWSR1 (NM_013986) - FLI1 (NM_002017) fusion: t(11;22)(q24.3;q12.2)(chr11:g.128656732::chr22:g.29683940) Note: The EWSR1 - FLI1 fusion involves EWSR1 exons 1 - 8 and FLI1 exons 6 - 9. The fusion is predicted to be in frame.
NOTCH2	0	MSKCC-DMP	P-0046711-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.1369_c.1567+22inv Note: The NOTCH2 rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 8. Functional significance is undetermined. This structural variant was observed in addition to other rearrangements involving NOTCH2, suggesting a complex event that may not be detected by the IMPACT assay.
ALOX12B	0	MSKCC-DMP	P-0046713-T01-IM6	ALOX12B-intragenic	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: t(11;17)(q13.1;p13.1)(chr11:g.65317075::chr17:g.7976987) Note: The ALOX12B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046713-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-342:TMPRSS2_c.40-57445:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046713-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-342:TMPRSS2_c.40-57445:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046736-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-576:ERG_c.56-554:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. Multiple rearrangements involving TMRPSS2 in this sample suggests that a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0046736-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-576:ERG_c.56-554:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. Multiple rearrangements involving TMRPSS2 in this sample suggests that a more complex rearrangement resulting in a TMPRSS2 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0046736-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-4000_c.350-2072inv Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 3. Functional significance is undetermined.
HOXB13	0	MSKCC-DMP	P-0026710-T02-IM6	HOXB13-intragenic	yes	unknown		unknown	HOXB13 (NM_006361) rearrangement: c.602-198:HOXB13_chr17:g.48898867del Note: The HOXB13 rearrangement is a deletion of exon 1.
ASXL1	0	MSKCC-DMP	P-0026710-T02-IM6	TBCD-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) - TBCD (NM_005993) rearrangement: t(17;20)(q25.3;q11.21)(chr17:g.80876983::chr20:g.31023295) Note: The ASXL1 - TBCD rearrangement is a translocation that results in a fusion of ASXL1 exons 1 - 12 to TBCD exons 24 - 39. One of the breakpoints is within ASXL1 exon 12. Functional significance is undetermined.
TBCD	0	MSKCC-DMP	P-0026710-T02-IM6	TBCD-ASXL1 fusion	yes	unknown		unknown	ASXL1 (NM_015338) - TBCD (NM_005993) rearrangement: t(17;20)(q25.3;q11.21)(chr17:g.80876983::chr20:g.31023295) Note: The ASXL1 - TBCD rearrangement is a translocation that results in a fusion of ASXL1 exons 1 - 12 to TBCD exons 24 - 39. One of the breakpoints is within ASXL1 exon 12. Functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0033566-T02-IM6	PDE6A-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - PDE6A (NM_000440) rearrangement: c.442-141:CD74_c.2135+2556:PDE6Adel Note: The CD74 - PDE6A rearrangement is a deletion that results in a fusion of CD74 exons 1 - 4 to PDE6A exons 18 - 22. Functional significance is undetermined.
PDE6A	0	MSKCC-DMP	P-0033566-T02-IM6	PDE6A-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - PDE6A (NM_000440) rearrangement: c.442-141:CD74_c.2135+2556:PDE6Adel Note: The CD74 - PDE6A rearrangement is a deletion that results in a fusion of CD74 exons 1 - 4 to PDE6A exons 18 - 22. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0044109-T02-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.80-4310_c.164+116inv Note: The PTEN rearrangement is an intragenic inversion of exon 2. Functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0046366-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(13;17)(q34;p12)(chr13:g.110777086::chr17:g.15968666) Note: The NCOR1 rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.
GATA1	0	MSKCC-DMP	P-0046660-T01-IM6	GATA1-intragenic	yes	unknown		unknown	GATA1 (NM_002049) rearrangement: c.929:GATA1_chrX:g.48664112inv Note: The GATA1 rearrangement is an inversion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0046676-T01-IM6	CARM1-intragenic	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: c.558+32:CARM1_chr19:g.11085632del Note: The CARM1 rearrangement is a deletion of exons 5 - 16. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0046720-T01-IM6	ALK-EML4 fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1641+1:EML4_c.3173-275:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 13 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0046720-T01-IM6	ALK-EML4 fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1641+1:EML4_c.3173-275:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 13 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.
KDM6A	0	MSKCC-DMP	P-0046725-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.748+97:KDM6A_chrX:g.40408262inv Note: The KDM6A rearrangement is an inversion of exons 1 - 9. Functional significance is undetermined.
RAD52	0	MSKCC-DMP	P-0046755-T01-IM6	RAD52-intragenic	yes	unknown		unknown	RAD52 (NM_134424) rearrangement: c.187-67:RAD52_chr12:g.20234604inv Note: The RAD52 rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0046757-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.4817-119:DNMT1_chr19:g.18537515del Note: The DNMT1 rearrangement is a deletion of exons 1 - 39. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0046758-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: t(4;15)(p16.3;q15.1)(chr4:g.1807488::chr15:g.40834741) Note: The FGFR3 rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
WHSC1	0	MSKCC-DMP	P-0046758-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.1410+4547_c.1751del Note: The WHSC1 rearrangement is an intragenic deletion of exons 6 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046775-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.127-620_c.349+2051del Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0046777-T01-IM6	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: c.4012+90:IRS2_chr13:g.110441644dup Note: The IRS2 rearrangement is a duplication of exon 1. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0046790-T01-IM6	UXS1-RET fusion	yes	unknown		unknown	RET (NM_020975) - UXS1 (NM_001253875) rearrangement: t(2;10)(q12.2;q11.21)(chr2:g.106728260::chr10:g.43600430) Note: The RET - UXS1 rearrangement is a translocation that results in a fusion of RET exons 1 - 4 to UXS1 exons 11 - 15. One of the breakpoints is within RET exon 4. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
UXS1	0	MSKCC-DMP	P-0046790-T01-IM6	UXS1-RET fusion	yes	unknown		unknown	RET (NM_020975) - UXS1 (NM_001253875) rearrangement: t(2;10)(q12.2;q11.21)(chr2:g.106728260::chr10:g.43600430) Note: The RET - UXS1 rearrangement is a translocation that results in a fusion of RET exons 1 - 4 to UXS1 exons 11 - 15. One of the breakpoints is within RET exon 4. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ERBB2	0	MSKCC-DMP	P-0046790-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.225+207:ERBB2_c.1932-6773:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1 - 2 to CDK12 exons 3 - 14. The fusion does not include the kinase domain of ERBB2 and includes the kinase domain of CDK12. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ERBB2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CDK12	0	MSKCC-DMP	P-0046790-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.225+207:ERBB2_c.1932-6773:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1 - 2 to CDK12 exons 3 - 14. The fusion does not include the kinase domain of ERBB2 and includes the kinase domain of CDK12. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ERBB2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
AXIN2	0	MSKCC-DMP	P-0046793-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.703:AXIN2_chr17:g.63555989del Note: The AXIN2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.
TMPRSS2	0	MSKCC-DMP	P-0046798-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2826:TMPRSS2_c.40-53504:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the non-canonical ERG transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0046798-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2826:TMPRSS2_c.40-53504:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the non-canonical ERG transcript (NM_004449).
FGFR3	0	MSKCC-DMP	P-0046837-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: t(4;11)(p16.3;p15.5)(chr4:g.1807338::chr11:g.2505245) Note: The FGFR3 rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CREBBP	0	MSKCC-DMP	P-0046837-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(3;16)(p21.31;p13.3)(chr3:g.50188271::chr16:g.3900582) Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046838-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-319:TMPRSS2_c.19-18320:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0046838-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-319:TMPRSS2_c.19-18320:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
BBC3	0	MSKCC-DMP	P-0046665-T01-IM6	BBC3-intragenic	yes	unknown		unknown	BBC3 (NM_001127240) rearrangement: c.229_c.568+589del Note: The BBC3 rearrangement is an intragenic deletion of exons 2 - 3. One of the breakpoints is within exon 2.
ERBB2	0	MSKCC-DMP	P-0046796-T01-IM6	IKZF3-ERBB2 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.1314-49:ERBB2_c.164-10105:IKZF3inv Note: The ERBB2 - IKZF3 rearrangement is an inversion that results in a fusion of ERBB2 exons 1 - 11 to IKZF3 exons 4 - 8. The fusion does not include the kinase domain of ERBB2. Functional significance is undetermined.
IKZF3	0	MSKCC-DMP	P-0046796-T01-IM6	IKZF3-ERBB2 fusion	yes	unknown		out of frame	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.1314-49:ERBB2_c.164-10105:IKZF3inv Note: The ERBB2 - IKZF3 rearrangement is an inversion that results in a fusion of ERBB2 exons 1 - 11 to IKZF3 exons 4 - 8. The fusion does not include the kinase domain of ERBB2. Functional significance is undetermined.
TCF7L2	0	MSKCC-DMP	P-0046856-T01-IM6	TCF7L2-intragenic	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.190-120:TCF7L2_chr10:g.114979136del Note: The TCF7L2 rearrangement is a deletion of exons 2 - 14.
ACOXL	0	MSKCC-DMP	P-0046857-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		out of frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1169+665:ACOXL_c.394+4550:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 13 to BCL2L11 exons 3 - 4.
BCL2L11	0	MSKCC-DMP	P-0046857-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		out of frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1169+665:ACOXL_c.394+4550:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 13 to BCL2L11 exons 3 - 4.
KIF5B	0	MSKCC-DMP	P-0021937-T03-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190173 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0021937-T03-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190173 Macro-dissection: Not Performed
TFG	0	MSKCC-DMP	P-0046544-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787).PMID: 19797732   Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: ArcherV3-CLIN-20190174 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0046544-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787).PMID: 19797732   Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: ArcherV3-CLIN-20190174 Macro-dissection: Performed
RTEL1	0	MSKCC-DMP	P-0044707-T03-IM6	CDH4-RTEL1 fusion	yes	unknown		in frame	RTEL1 (NM_032957) - CDH4 (NM_001794) rearrangement: c.991+225:RTEL1_c.170-168444:CDH4dup Note: The RTEL1 - CDH4 rearrangement is a duplication that results in a fusion of RTEL1 exons 1 - 10 to CDH4 exons 2 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
CDH4	0	MSKCC-DMP	P-0044707-T03-IM6	CDH4-RTEL1 fusion	yes	unknown		in frame	RTEL1 (NM_032957) - CDH4 (NM_001794) rearrangement: c.991+225:RTEL1_c.170-168444:CDH4dup Note: The RTEL1 - CDH4 rearrangement is a duplication that results in a fusion of RTEL1 exons 1 - 10 to CDH4 exons 2 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0046864-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.2944_c.4185+13inv Note: The BRCA1 rearrangement is an intragenic inversion of exons 10 - 11. One of the breakpoints is within exon 10. Functional significance is undetermined.
RAC1	0	MSKCC-DMP	P-0046870-T01-IM6	RAC1-intragenic	yes	unknown		unknown	RAC1 (NM_018890) rearrangement: c.108-1748_c.174del Note: The RAC1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0046875-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.3860_c.4606+432inv Note: The DOT1L rearrangement is an intragenic inversion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0046881-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: t(7;17)(q36.1;q21.2)(chr7:g.151490268::chr17:g.40477132) Note: The STAT3 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046881-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2519:TMPRSS2_c.18+14885:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0046881-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2519:TMPRSS2_c.18+14885:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0046884-T01-IM6	TCF3-intragenic	yes	unknown		out of frame	TCF3 (NM_001136139) rearrangement: c.73-30_c.145+6490dup Note: The TCF3 rearrangement is an intragenic duplication of exon 2. Functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0046887-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.4150-2330_c.4517inv Note: The POLE rearrangement is an intragenic inversion of exons 33 - 35. One of the breakpoints is within exon 35. Functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0014496-T03-IM6	AKT1-intragenic	yes	unknown		unknown	AKT1 (NM_001014431) rearrangement: c.1212:AKT1_chr14:g.99512393del Note: The AKT1 rearrangement is a deletion of exons 12 - 14. One of the breakpoints is within exon 12. The rearrangement includes a part of the kinase domain of AKT1. Functional significance is undetermined.
HGF	0	MSKCC-DMP	P-0046489-T01-IM6	HGF-intragenic	yes	unknown		unknown	HGF (NM_000601) rearrangement: t(7;22)(q21.11;q12.3)(chr7:g.81355058::chr22:g.34966766) Note: The HGF rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
CEBPA	0	MSKCC-DMP	P-0046868-T01-IM6	CEBPA-intragenic	yes	unknown		unknown	CEBPA (NM_004364) rearrangement: c.29:CEBPA_chr19:g.41809503del Note: The CEBPA rearrangement is a deletion within exon 1.
SOCS1	0	MSKCC-DMP	P-0046906-T01-IM6	SOCS1-intragenic	yes	unknown		unknown	SOCS1 (NM_003745) rearrangement: c.129:SOCS1_chr16:g.762649inv Note: The SOCS1 rearrangement is an inversion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0046910-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.23_c.410del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3 - 4. The breakpoints are within exon 3 and exon 4. Functional significance is undetermined.
AURKA	0	MSKCC-DMP	P-0046931-T02-IM6	AURKA-intragenic	yes	unknown		unknown	AURKA (NM_003600) rearrangement: c.42+114:AURKA_chr20:g.54729689del Note: The AURKA rearrangement is a deletion of exons 3 - 9. The rearrangement includes the kinase domain of AURKA. Functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0046951-T01-IM6	IL1RAPL2-BCOR fusion	yes	unknown		out of frame	BCOR (NM_001123385) - IL1RAPL2 (NM_017416) rearrangement: c.2997+49:BCOR_c.83-155811:IL1RAPL2inv Note: The BCOR - IL1RAPL2 rearrangement is an inversion that results in a fusion of BCOR exons 1 - 4 to IL1RAPL2 exons 3 - 11. Functional significance is undetermined.
IL1RAPL2	0	MSKCC-DMP	P-0046951-T01-IM6	IL1RAPL2-BCOR fusion	yes	unknown		out of frame	BCOR (NM_001123385) - IL1RAPL2 (NM_017416) rearrangement: c.2997+49:BCOR_c.83-155811:IL1RAPL2inv Note: The BCOR - IL1RAPL2 rearrangement is an inversion that results in a fusion of BCOR exons 1 - 4 to IL1RAPL2 exons 3 - 11. Functional significance is undetermined.
AKT3	0	MSKCC-DMP	P-0046952-T01-IM6	AKT3-intragenic	yes	unknown		unknown	AKT3 (NM_005465) rearrangement: c.900_c.948+1841del Note: The AKT3 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. The rearrangement includes a part of the kinase domain of AKT3. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0046957-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: t(12;19)(q14.2;q13.12)(chr12:g.64138499::chr19:g.36229383) Note: The KMT2B rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.
STK40	0	MSKCC-DMP	P-0017386-T04-IM6	STK40-intragenic	yes	unknown		unknown	STK40 (NM_032017) rearrangement: c.1008:STK40_chr1:g.121485036del Note: The STK40 rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11. The rearrangement includes the kinase domain of STK40. Functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0017386-T04-IM6	MGA-intragenic	yes	unknown		in frame	MGA (NM_001164273) rearrangement: c.2189-23_c.3431-2986dup Note: The MGA rearrangement is an intragenic duplication of exons 6 - 9. Functional significance is undetermined.
DUSP4	0	MSKCC-DMP	P-0039285-T02-IM6	DUSP4-intragenic	yes	unknown		unknown	DUSP4 (NM_001394) rearrangement: c.580-163:DUSP4_chr8:g.29044779inv Note: The DUSP4 rearrangement is an inversion of exons 3 - 4. Functional significance is undetermined.
FOXO1	0	MSKCC-DMP	P-0043094-T02-IM6	FOXO1-intragenic	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement: c.630+78:FOXO1_chr13:g.49932326inv Note: The FOXO1 rearrangement is an inversion of exon 1. Functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0046940-T01-IM6	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.404+294_c.10866del Note: The SPEN rearrangement is an intragenic deletion of exons 3 - 15. One of the breakpoints is within exon 15.
ARID2	0	MSKCC-DMP	P-0046940-T01-IM6	SIPA1L3-ARID2 fusion	yes	unknown		out of frame	ARID2 (NM_152641) - SIPA1L3 (NM_015073) rearrangement: t(12;19)(q12;q13.13)(chr12:g.46123998::chr19:g.38692821) Note: The ARID2 - SIPA1L3 rearrangement is a translocation that results in a fusion of ARID2 exons 1 - 2 to SIPA1L3 exons 21 - 22. Functional significance is undetermined.
SIPA1L3	0	MSKCC-DMP	P-0046940-T01-IM6	SIPA1L3-ARID2 fusion	yes	unknown		out of frame	ARID2 (NM_152641) - SIPA1L3 (NM_015073) rearrangement: t(12;19)(q12;q13.13)(chr12:g.46123998::chr19:g.38692821) Note: The ARID2 - SIPA1L3 rearrangement is a translocation that results in a fusion of ARID2 exons 1 - 2 to SIPA1L3 exons 21 - 22. Functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0046943-T01-IM6	GLI1-intragenic	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.389+14:GLI1_chr12:g.116180623inv Note: The GLI1 rearrangement is an inversion of exons 5 - 12. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0046943-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(9;19)(q22.31;p13.12)(chr9:g.95511808::chr19:g.15299695) Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0046943-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+477:TMPRSS2_chr21:g.40030286del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined. "While this is not the canonical TMPRSS2-ERG fusion ,the possibility of the fusion not detected by the IMPACT panel cannot be ruled out. The breakpoint in ERG is in the promoter region before the TSS (transcription start site)."
FAT1	0	MSKCC-DMP	P-0046945-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3265+2110_c.3643-66inv Note: The FAT1 rearrangement is an intragenic inversion of exons 3 - 4. Functional significance is undetermined.
PAWR	0	MSKCC-DMP	P-0046985-T01-IM6	ERBB3-PAWR fusion	yes	unknown		unknown	PAWR (NM_002583) - ERBB3 (NM_001982) rearrangement: c.516+27255:PAWR_c.3251:ERBB3inv Note: The PAWR - ERBB3 rearrangement is an inversion that results in a fusion of PAWR exons 1 - 2 to ERBB3 exons 27 - 28. One of the breakpoints is within ERBB3 exon 27. The fusion does not include the kinase domain of ERBB3. Functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0046985-T01-IM6	ERBB3-PAWR fusion	yes	unknown		unknown	PAWR (NM_002583) - ERBB3 (NM_001982) rearrangement: c.516+27255:PAWR_c.3251:ERBB3inv Note: The PAWR - ERBB3 rearrangement is an inversion that results in a fusion of PAWR exons 1 - 2 to ERBB3 exons 27 - 28. One of the breakpoints is within ERBB3 exon 27. The fusion does not include the kinase domain of ERBB3. Functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0046988-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.2419_c.2970+250inv Note: The TERT rearrangement is an intragenic inversion of exons 8 - 12. One of the breakpoints is within exon 8. Functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0047009-T01-IM6	PIK3CD-intragenic	yes	unknown		in frame	PIK3CD (NM_005026) rearrangement: c.780+70_c.1243-55del Note: The PIK3CD rearrangement is an intragenic deletion of exons 7 - 9. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0047009-T01-IM6	SLC17A8-ARID1A fusion	yes	unknown		out of frame	ARID1A (NM_006015) - SLC17A8 (NM_139319) rearrangement: t(1;12)(p36.11;q23.1)(chr1:g.27100005::chr12:g.100779582) Note: The ARID1A - SLC17A8 rearrangement is a translocation that results in a fusion of ARID1A exons 1 - 15 to SLC17A8 exons 3 - 12. Functional significance is undetermined.
SLC17A8	0	MSKCC-DMP	P-0047009-T01-IM6	SLC17A8-ARID1A fusion	yes	unknown		out of frame	ARID1A (NM_006015) - SLC17A8 (NM_139319) rearrangement: t(1;12)(p36.11;q23.1)(chr1:g.27100005::chr12:g.100779582) Note: The ARID1A - SLC17A8 rearrangement is a translocation that results in a fusion of ARID1A exons 1 - 15 to SLC17A8 exons 3 - 12. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0047080-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.3886-92:KMT2B_chr19:g.57191978inv Note: The KMT2B rearrangement is an inversion of exons 14 - 37. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0047124-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.5458:EP300_chr22:g.45672535del Note: The EP300 rearrangement is a deletion of exon 31. One of the breakpoints is within exon 31.
PTPRK	0	MSKCC-DMP	P-0046861-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190177 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0046861-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190177 Macro-dissection: Performed
FGFR2	0	MSKCC-DMP	P-0018869-T03-IM6	ABLIM1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ABLIM1 (NM_002313) fusion: c.2301+611:FGFR2_c.895-12244:ABLIM1del Note: The FGFR2 - ABLIM1 fusion involves FGFR2 exons 1 - 17 and ABLIM1 exons 7 - 22. The fusion is predicted to be in frame and includes the kinase domain of FGFR2. The functional significance is unknown. If additional material is available, RNAseq by the Archer assay is recommended to further clarify the functional significance of the event.
ABLIM1	0	MSKCC-DMP	P-0018869-T03-IM6	ABLIM1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ABLIM1 (NM_002313) fusion: c.2301+611:FGFR2_c.895-12244:ABLIM1del Note: The FGFR2 - ABLIM1 fusion involves FGFR2 exons 1 - 17 and ABLIM1 exons 7 - 22. The fusion is predicted to be in frame and includes the kinase domain of FGFR2. The functional significance is unknown. If additional material is available, RNAseq by the Archer assay is recommended to further clarify the functional significance of the event.
NFKBIA	0	MSKCC-DMP	P-0046950-T01-IM6	NFKBIA-intragenic	yes	unknown		unknown	NFKBIA (NM_020529) rearrangement: t(1;14)(p36.12;q13.2)(chr1:g.22271508::chr14:g.35871855) Note: The NFKBIA rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
NRAS	0	MSKCC-DMP	P-0046969-T01-IM6	NRAS-intragenic	yes	unknown		unknown	NRAS (NM_002524) rearrangement: t(1;19)(p13.2;q13.33)(chr1:g.115256393::chr19:g.49258664) Note: The NRAS rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0047149-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) rearrangement: c.4836-22676_c.5812+36dup Note: The NF1 rearrangement is an intragenic duplication of exons 37 - 39. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0047149-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.1466-107:DOT1L_chr19:g.2163961del Note: The DOT1L rearrangement is a deletion of exons 1 - 15. Functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0047152-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.1156:AXIN2_chr17:g.63760602inv Note: The AXIN2 rearrangement is an inversion of exons 1 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0047156-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1920+4680_c.3867-20dup Note: The ARID1A rearrangement is an intragenic duplication of exons 5 - 15. Functional significance is undetermined.
KEAP1	0	MSKCC-DMP	P-0047202-T01-IM6	KEAP1-intragenic	yes	unknown		in frame	KEAP1 (NM_203500) rearrangement: c.1532-89_c.1708+772del Note: The KEAP1 rearrangement is an intragenic deletion of exon 5.
KMT2D	0	MSKCC-DMP	P-0047203-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.5982:KMT2D_chr12:g.45466650inv Note: The KMT2D rearrangement is an inversion of exons 28 - 54. One of the breakpoints is within exon 28. Functional significance is undetermined.
ARAF	0	MSKCC-DMP	P-0047206-T01-IM6	SCML2-ARAF fusion	yes	unknown		in frame	ARAF (NM_001654) - SCML2 (NM_006089) rearrangement: c.96+47:ARAF_c.487-4683:SCML2inv Note: The ARAF - SCML2 rearrangement is an inversion that results in a fusion of ARAF exons 1 - 2 to SCML2 exons 7 - 15. The fusion is predicted to be in frame and does not include the kinase domain of ARAF. Functional significance is undetermined.
SCML2	0	MSKCC-DMP	P-0047206-T01-IM6	SCML2-ARAF fusion	yes	unknown		in frame	ARAF (NM_001654) - SCML2 (NM_006089) rearrangement: c.96+47:ARAF_c.487-4683:SCML2inv Note: The ARAF - SCML2 rearrangement is an inversion that results in a fusion of ARAF exons 1 - 2 to SCML2 exons 7 - 15. The fusion is predicted to be in frame and does not include the kinase domain of ARAF. Functional significance is undetermined.
AR	0	MSKCC-DMP	P-0046476-T02-IM6	AR-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:  AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20190179 Macro-dissection: Not Performed
MGA	0	MSKCC-DMP	P-0034561-T01-IM6	MGA-intragenic	yes	unknown		in frame	MGA (NM_001164273) rearrangement: t(14;15)(q24.3;q15.1)(chr14:g.74523162::chr15:g.42049853) Note: The MGA rearrangement is a translocation with a breakpoint in intron 18. Functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0046331-T01-IM6	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(9;12)(p13.2;p13.33)(chr9:g.37548328::chr12:g.465623) Note: The KDM5A rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.
PLCG2	0	MSKCC-DMP	P-0046331-T01-IM6	PLCG2-intragenic	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: t(14;16)(q32.12;q23.3)(chr14:g.92264481::chr16:g.81904561) Note: The PLCG2 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.
TRAP1	0	MSKCC-DMP	P-0046331-T01-IM6	CREBBP-TRAP1 fusion	yes	unknown		out of frame	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.2014-255:TRAP1_c.4281-135:CREBBPdup Note: The TRAP1 - CREBBP rearrangement is a duplication that results in a fusion of TRAP1 exons 1 - 16 to CREBBP exons 26 - 31. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0046331-T01-IM6	CREBBP-TRAP1 fusion	yes	unknown		out of frame	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.2014-255:TRAP1_c.4281-135:CREBBPdup Note: The TRAP1 - CREBBP rearrangement is a duplication that results in a fusion of TRAP1 exons 1 - 16 to CREBBP exons 26 - 31. Functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0046331-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.481:ATR_chr3:g.125082265del Note: The ATR rearrangement is a deletion of exons 4 - 47. One of the breakpoints is within exon 4.
CSDE1	0	MSKCC-DMP	P-0047139-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: c.1778_c.1779del Note: The CSDE1 rearrangement is an intragenic deletion of exons 15 - 16. The breakpoints are within exon 15 and exon 16. Multiple other deletion events in CSDE1 involving exons 13-19 were also detected in the tumor sample  suggesting the presence of somatically acquired processed pseudogenes. The functional significance is undetermined.
CDC73	0	MSKCC-DMP	P-0047139-T01-IM6	CDC73-intragenic	yes	unknown		unknown	CDC73 (NM_024529) rearrangement: c.829-60:CDC73_chr1:g.193002339del Note: The CDC73 rearrangement is a deletion of exons 1 - 8.
TMPRSS2	0	MSKCC-DMP	P-0047211-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+3935:TMPRSS2_c.18+1778:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0047211-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+3935:TMPRSS2_c.18+1778:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0047213-T01-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.1581-39_c.2420del Note: The ARID2 rearrangement is an intragenic deletion of exons 13 - 15. One of the breakpoints is within exon 15.
JAK3	0	MSKCC-DMP	P-0047313-T01-IM6	JAK3-intragenic	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: t(8;19)(q23.1;p13.11)(chr8:g.110031275::chr19:g.17945774) Note: The JAK3 rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0047338-T01-IM6	NUF2-intragenic	yes	unknown		unknown	NUF2 (NM_031423) rearrangement: c.338-270:NUF2_chr1:g.163266615inv Note: The NUF2 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0047343-T01-IM6	ARID1A-intragenic	yes	unknown		out of frame	ARID1A (NM_006015) rearrangement: c.1137+13428_c.2732+57dup Note: The ARID1A rearrangement is an intragenic duplication of exons 2 - 8. Functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0047102-T01-IM6	EZH1-intragenic	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: t(6;17)(q24.1;q21.2)(chr6:g.140038690::chr17:g.40870395) Note: The EZH1 rearrangement is a translocation with a breakpoint in intron 9. Multiple rearrangements involving EZH2 were detected in this sample and a more complex rearrangement involving EZH2 is possible. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0047287-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-710:TMPRSS2_c.18+11070:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0047287-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-710:TMPRSS2_c.18+11070:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0047304-T01-IM6	CYSLTR2-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) - CYSLTR2 (NM_020377) rearrangement: c.2490-1057:RB1_c.884:CYSLTR2del Note: The RB1 - CYSLTR2 rearrangement is a deletion that results in a fusion of RB1 exons 1 - 23 to CYSLTR2 exon 1. One of the breakpoints is within CYSLTR2 exon 1.
CYSLTR2	0	MSKCC-DMP	P-0047304-T01-IM6	CYSLTR2-RB1 fusion	yes	unknown		unknown	RB1 (NM_000321) - CYSLTR2 (NM_020377) rearrangement: c.2490-1057:RB1_c.884:CYSLTR2del Note: The RB1 - CYSLTR2 rearrangement is a deletion that results in a fusion of RB1 exons 1 - 23 to CYSLTR2 exon 1. One of the breakpoints is within CYSLTR2 exon 1.
TMPRSS2	0	MSKCC-DMP	P-0047304-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.127-380:TMPRSS2_chr21:g.27694846inv Note: The TMPRSS2 rearrangement is an inversion of exons 3 - 14. Functional significance is undetermined.
MET	0	MSKCC-DMP	P-0047306-T01-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: c.3799-1570_c.3840inv Note: The MET rearrangement is an intragenic inversion of exon 20. One of the breakpoints is within exon 20. The rearrangement includes a part of the kinase domain of MET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required.
ANKRD11	0	MSKCC-DMP	P-0047332-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: t(2;16)(p11.2;q24.3)(chr2:g.83471575::chr16:g.89357093) Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0047355-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+925:EML4_c.3173-215:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0047355-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+925:EML4_c.3173-215:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
MDC1	0	MSKCC-DMP	P-0047358-T01-IM6	DNAH8-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) - DNAH8 (NM_001206927) rearrangement: c.484:MDC1_c.3523+2614:DNAH8inv Note: The MDC1 - DNAH8 rearrangement is an inversion that results in a fusion of MDC1 exons 1 - 3 to DNAH8 exons 27 - 93. One of the breakpoints is within MDC1 exon 3. Functional significance is undetermined.
DNAH8	0	MSKCC-DMP	P-0047358-T01-IM6	DNAH8-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) - DNAH8 (NM_001206927) rearrangement: c.484:MDC1_c.3523+2614:DNAH8inv Note: The MDC1 - DNAH8 rearrangement is an inversion that results in a fusion of MDC1 exons 1 - 3 to DNAH8 exons 27 - 93. One of the breakpoints is within MDC1 exon 3. Functional significance is undetermined.
MBIP	0	MSKCC-DMP	P-0047359-T01-IM6	RET-MBIP fusion	yes	unknown		unknown	MBIP (NM_016586) - RET (NM_020975) fusion: t(10;14)(q11.21;q13.3)(chr10:g.43610084::chr14:g.36773155) Note: The MBIP - RET fusion involves MBIP exons 1 - 7 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0047359-T01-IM6	RET-MBIP fusion	yes	unknown		unknown	MBIP (NM_016586) - RET (NM_020975) fusion: t(10;14)(q11.21;q13.3)(chr10:g.43610084::chr14:g.36773155) Note: The MBIP - RET fusion involves MBIP exons 1 - 7 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
FGFR3	0	MSKCC-DMP	P-0047290-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.2274+67:FGFR3_chr4:g.1809658inv Note: The FGFR3 rearrangement is an inversion of exon 18. The rearrangement does not include the kinase domain of FGFR3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ETV6	0	MSKCC-DMP	P-0047395-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.463+178:ETV6_chr12:g.12275489del Note: The ETV6 rearrangement is a deletion of exons 5 - 8. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0047438-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3809_c.4269del Note: The ARID1A rearrangement is an intragenic deletion of exons 15 - 18. The breakpoints are within exon 15 and exon 18.
RPTOR	0	MSKCC-DMP	P-0047450-T01-IM6	RPTOR-intragenic	yes	unknown		out of frame	RPTOR (NM_020761) rearrangement: c.3692+40_c.3939+180del Note: The RPTOR rearrangement is an intragenic deletion of exons 32 - 33. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0047465-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.6940:NOTCH3_chr19:g.15393284del Note: The NOTCH3 rearrangement is a deletion of exons 1 - 33. One of the breakpoints is within exon 33.
HIST1H3D	0	MSKCC-DMP	P-0047565-T01-IM6	HIST1H3D-intragenic	yes	unknown		unknown	HIST1H3D (NM_003530) rearrangement: c.84:HIST1H3D_chr6:g.26116722del Note: The HIST1H3D rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
PIK3CG	0	MSKCC-DMP	P-0040655-T02-IM6	PIK3CG-intragenic	yes	unknown		unknown	PIK3CG (NM_002649) rearrangement: c.3256:PIK3CG_chr7:g.147785722inv Note: The PIK3CG rearrangement is an inversion of exon 11. One of the breakpoints is within exon 11. Functional significance is undetermined.
CTTNBP2	0	MSKCC-DMP	P-0040655-T02-IM6	KMT2C-CTTNBP2 fusion	yes	unknown		unknown	CTTNBP2 (NM_033427) - KMT2C (NM_170606) rearrangement: c.82-950:CTTNBP2_c.1690:KMT2Cdup Note: The CTTNBP2 - KMT2C rearrangement is a duplication that results in a fusion of CTTNBP2 exon 1 to KMT2C exons 12 - 59. One of the breakpoints is within KMT2C exon 12. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0040655-T02-IM6	KMT2C-CTTNBP2 fusion	yes	unknown		unknown	CTTNBP2 (NM_033427) - KMT2C (NM_170606) rearrangement: c.82-950:CTTNBP2_c.1690:KMT2Cdup Note: The CTTNBP2 - KMT2C rearrangement is a duplication that results in a fusion of CTTNBP2 exon 1 to KMT2C exons 12 - 59. One of the breakpoints is within KMT2C exon 12. Functional significance is undetermined.
MBIP	0	MSKCC-DMP	P-0047359-T01-IM6	RET-MBIP fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: MBIP-RET fusion. Note: The rearrangement is an in-frame fusion between genes MBIP Exon7 (NM_016586) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190186 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0047359-T01-IM6	RET-MBIP fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: MBIP-RET fusion. Note: The rearrangement is an in-frame fusion between genes MBIP Exon7 (NM_016586) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190186 Macro-dissection: Not Performed
NCOA3	0	MSKCC-DMP	P-0032400-T02-IM6	MDM2-NCOA3 fusion	yes	unknown		in frame	NCOA3 (NM_181659) - MDM2 (NM_002392) rearrangement: t(12;20)(q15;q13.12)(chr12:g.69227313::chr20:g.46265559) Note: The NCOA3 - MDM2 rearrangement is a translocation that results in a fusion of NCOA3 exons 1 - 12 to MDM2 exons 9 - 11. The fusion is predicted to be in frame. Functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0032400-T02-IM6	MDM2-NCOA3 fusion	yes	unknown		in frame	NCOA3 (NM_181659) - MDM2 (NM_002392) rearrangement: t(12;20)(q15;q13.12)(chr12:g.69227313::chr20:g.46265559) Note: The NCOA3 - MDM2 rearrangement is a translocation that results in a fusion of NCOA3 exons 1 - 12 to MDM2 exons 9 - 11. The fusion is predicted to be in frame. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0046827-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1305:KIF5B_c.2136+705:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0046827-T02-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1305:KIF5B_c.2136+705:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
SMARCD1	0	MSKCC-DMP	P-0046827-T02-IM6	SMARCD1-intragenic	yes	unknown		unknown	SMARCD1 (NM_003076) rearrangement: c.177+27:SMARCD1_chr12:g.46300876inv Note: The SMARCD1 rearrangement is an inversion of exon 1. Functional significance is undetermined.
PPARG	0	MSKCC-DMP	P-0047317-T01-IM6	PPARG-intragenic	yes	unknown		unknown	PPARG (NM_015869) rearrangement: t(3;4)(p25.2;p15.1)(chr3:g.12475518::chr4:g.34763475) Note: The PPARG rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined. Multiple rearrangements involving PPARG were detected in this sample and a more complex rearrangement involving PPARG is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MDC1	0	MSKCC-DMP	P-0047317-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.99:MDC1_chr6:g.30684389del Note: The MDC1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
MALT1	0	MSKCC-DMP	P-0047610-T01-IM6	MALT1-intragenic	yes	unknown		out of frame	MALT1 (NM_006785) rearrangement: c.1222+2438_c.1476-21del Note: The MALT1 rearrangement is an intragenic deletion of exons 11 - 12. Functional significance is undetermined.
FUT10	0	MSKCC-DMP	P-0047614-T01-IM6	WHSC1L1-FUT10 fusion	yes	unknown		in frame	FUT10 (NM_032664) - WHSC1L1 (NM_023034) rearrangement: c.81+3371:FUT10_c.2116-177:WHSC1L1dup Note: The FUT10 - WHSC1L1 rearrangement is a duplication that results in a fusion of FUT10 exons 1 - 2 to WHSC1L1 exons 12 - 24. The fusion is predicted to be in frame. Functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0047614-T01-IM6	WHSC1L1-FUT10 fusion	yes	unknown		in frame	FUT10 (NM_032664) - WHSC1L1 (NM_023034) rearrangement: c.81+3371:FUT10_c.2116-177:WHSC1L1dup Note: The FUT10 - WHSC1L1 rearrangement is a duplication that results in a fusion of FUT10 exons 1 - 2 to WHSC1L1 exons 12 - 24. The fusion is predicted to be in frame. Functional significance is undetermined.
ERCC3	0	MSKCC-DMP	P-0047603-T01-IM6	ERCC3-intragenic	yes	unknown		unknown	ERCC3 (NM_000122) rearrangement: c.1635:ERCC3_chr2:g.128053922inv Note: The ERCC3 rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0047604-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+31:FGFR3_c.1941+484:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 11 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0047604-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+31:FGFR3_c.1941+484:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 11 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
RUNX1	0	MSKCC-DMP	P-0047618-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.967+81_c.1255del Note: The RUNX1 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9.
HGF	0	MSKCC-DMP	P-0047183-T02-IM6	HGF-intragenic	yes	unknown		unknown	HGF (NM_000601) rearrangement: c.2104:HGF_chr7:g.81330692inv Note: The HGF rearrangement is an inversion of exon 18. One of the breakpoints is within exon 18. Functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0047544-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.137:ELF3_chr1:g.202099757del Note: The ELF3 rearrangement is a deletion of exons 2 - 9. One of the breakpoints is within exon 2.
ANKRD11	0	MSKCC-DMP	P-0047546-T01-IM6	SPG7-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2114:ANKRD11_c.1553-19:SPG7inv Note: The ANKRD11 - SPG7 rearrangement is an inversion that results in a fusion of ANKRD11 exons 1 - 9 to SPG7 exons 12 - 17. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined. Multiple rearrangements involving ANKRD11 were detected in this sample and a more complex rearrangement resulting in a ANKRD11 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SPG7	0	MSKCC-DMP	P-0047546-T01-IM6	SPG7-ANKRD11 fusion	yes	unknown		unknown	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2114:ANKRD11_c.1553-19:SPG7inv Note: The ANKRD11 - SPG7 rearrangement is an inversion that results in a fusion of ANKRD11 exons 1 - 9 to SPG7 exons 12 - 17. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined. Multiple rearrangements involving ANKRD11 were detected in this sample and a more complex rearrangement resulting in a ANKRD11 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FGFR3	0	MSKCC-DMP	P-0047573-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2276:FGFR3_c.1942-892:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0047573-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2276:FGFR3_c.1942-892:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 18 and TACC3 exons 11 - 16. One of the breakpoints is within FGFR3 exon 18. The fusion includes the kinase domain of FGFR3.
RAD21	0	MSKCC-DMP	P-0047575-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.1322-126:RAD21_chr8:g.117879554del Note: The RAD21 rearrangement is a deletion of exons 1 - 10.
CDK12	0	MSKCC-DMP	P-0026989-T03-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.2964-115:CDK12_chr17:g.36372477del Note: The CDK12 rearrangement is a deletion of exons 1 - 10. The rearrangement includes a part of the kinase domain of CDK12.
KDM6A	0	MSKCC-DMP	P-0026989-T03-IM6	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.225+20377_c.3548+113dup Note: The KDM6A rearrangement is an intragenic duplication of exons 3 - 24. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0046745-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: t(4;10)(p16.3;q26.11)(chr4:g.1808988::chr10:g.119935563) Note: The FGFR3 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KCND2	0	MSKCC-DMP	P-0046745-T01-IM6	BRAF-KCND2 fusion	yes	unknown		out of frame	KCND2 (NM_012281) - BRAF (NM_004333) fusion: c.1115+91797:KCND2_c.1177+1481:BRAFinv Note: The KCND2 - BRAF fusion involves KCND2 exon 1 and BRAF exons 10 - 18. The fusion includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0046745-T01-IM6	BRAF-KCND2 fusion	yes	unknown		out of frame	KCND2 (NM_012281) - BRAF (NM_004333) fusion: c.1115+91797:KCND2_c.1177+1481:BRAFinv Note: The KCND2 - BRAF fusion involves KCND2 exon 1 and BRAF exons 10 - 18. The fusion includes the kinase domain of BRAF.
PIK3R2	0	MSKCC-DMP	P-0047471-T02-IM6	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement: t(1;19)(q23.3;p13.11)(chr1:g.161137226::chr19:g.18271152) Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0047634-T01-IM6	ETV6-intragenic	yes	unknown		out of frame	ETV6 (NM_001987) rearrangement: c.34-29588_c.464-5154del Note: The ETV6 rearrangement is an intragenic deletion of exons 2 - 4. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0047636-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.813:TP53_chr17:g.7569417del Note: The TP53 rearrangement is a deletion of exons 8 - 11. One of the breakpoints is within exon 8.
BRAF	0	MSKCC-DMP	P-0047637-T01-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.853:BRAF_chr7:g.142196577inv Note: The BRAF rearrangement is an inversion of exons 1 - 6. One of the breakpoints is within exon 6. The rearrangement does not include the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KMT2D	0	MSKCC-DMP	P-0047648-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.1576:KMT2D_chr12:g.69859324del Note: The KMT2D rearrangement is a deletion of exons 1 - 10. One of the breakpoints is within exon 10.
RTEL1	0	MSKCC-DMP	P-0047648-T01-IM6	VRK3-RTEL1 fusion	yes	unknown		in frame	RTEL1 (NM_032957) - VRK3 (NM_016440) rearrangement: t(19;20)(q13.33;q13.33)(chr19:g.50499591::chr20:g.62325880) Note: The RTEL1 - VRK3 rearrangement is a translocation that results in a fusion of RTEL1 exons 1 - 31 to VRK3 exons 8 - 14. The fusion is predicted to be in frame. Functional significance is undetermined.
VRK3	0	MSKCC-DMP	P-0047648-T01-IM6	VRK3-RTEL1 fusion	yes	unknown		in frame	RTEL1 (NM_032957) - VRK3 (NM_016440) rearrangement: t(19;20)(q13.33;q13.33)(chr19:g.50499591::chr20:g.62325880) Note: The RTEL1 - VRK3 rearrangement is a translocation that results in a fusion of RTEL1 exons 1 - 31 to VRK3 exons 8 - 14. The fusion is predicted to be in frame. Functional significance is undetermined.
CSF1R	0	MSKCC-DMP	P-0047648-T01-IM6	CSF1R-intragenic	yes	unknown		unknown	CSF1R (NM_005211) rearrangement: c.1875_c.2132+478del Note: The CSF1R rearrangement is an intragenic deletion of exons 14 - 15. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of CSF1R. Functional significance is undetermined.
CLSPN	0	MSKCC-DMP	P-0047650-T01-IM6	CSF3R-CLSPN fusion	yes	unknown		in frame	CLSPN (NM_022111) - CSF3R (NM_000760) rearrangement: c.134-84:CLSPN_c.362-86:CSF3Rdup Note: The CLSPN - CSF3R rearrangement is a duplication that results in a fusion of CLSPN exons 1 - 2 to CSF3R exons 5 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0047650-T01-IM6	CSF3R-CLSPN fusion	yes	unknown		in frame	CLSPN (NM_022111) - CSF3R (NM_000760) rearrangement: c.134-84:CLSPN_c.362-86:CSF3Rdup Note: The CLSPN - CSF3R rearrangement is a duplication that results in a fusion of CLSPN exons 1 - 2 to CSF3R exons 5 - 17. The fusion is predicted to be in frame. Functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0047673-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.3791:ZFHX3_chr16:g.72505498inv Note: The ZFHX3 rearrangement is an inversion of exons 7 - 10. One of the breakpoints is within exon 7. Functional significance is undetermined.
ETV1	0	MSKCC-DMP	P-0021823-T02-IM6	ETV1-intragenic	yes	unknown		unknown	ETV1 (NM_001163147) rearrangement: t(7;14)(p21.2;q11.2)(chr7:g.14026320::chr14:g.21735813) Note: The ETV1 rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0043100-T02-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.902_c.993+1134inv Note: The TP53 rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 8. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0047760-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.761:CREBBP_chr16:g.3573904del Note: The CREBBP rearrangement is a deletion of exons 2 - 31. One of the breakpoints is within exon 2.
RBM10	0	MSKCC-DMP	P-0047760-T01-IM6	RBM10-intragenic	yes	unknown		unknown	RBM10 (NM_001204468) rearrangement: c.1436_c.2145+1288inv Note: The RBM10 rearrangement is an intragenic inversion of exons 12 - 17. One of the breakpoints is within exon 12. Functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0047697-T01-IM6	YAP1-intragenic	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: c.321+26:YAP1_chr11:g.42257177inv Note: The YAP1 rearrangement is an inversion of exon 1. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0047709-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.3393_c.7714-147del Note: The ANKRD11 rearrangement is an intragenic deletion of exons 9 - 11. One of the breakpoints is within exon 9.
WHSC1	0	MSKCC-DMP	P-0047710-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.3942:WHSC1_chr4:g.1981450del Note: The WHSC1 rearrangement is a deletion of exon 22. One of the breakpoints is within exon 22. Functional significance is undetermined.
TGFBR1	0	MSKCC-DMP	P-0047710-T01-IM6	TGFBR1-intragenic	yes	unknown		unknown	TGFBR1 (NM_004612) rearrangement: c.1131-339_c.1314del Note: The TGFBR1 rearrangement is an intragenic deletion of exons 7 - 8. One of the breakpoints is within exon 8. The rearrangement includes a part of the kinase domain of TGFBR1.
POLE	0	MSKCC-DMP	P-0047716-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.5861_c.6159del Note: The POLE rearrangement is an intragenic deletion of exons 43 - 45. The breakpoints are within exon 43 and exon 45.
AKAP8L	0	MSKCC-DMP	P-0047719-T01-IM6	BRD4-AKAP8L fusion	yes	unknown		unknown	AKAP8L (NM_014371) - BRD4 (NM_058243) rearrangement: c.1536+6695:AKAP8L_c.964:BRD4del Note: The AKAP8L - BRD4 rearrangement is a deletion that results in a fusion of AKAP8L exons 1 - 12 to BRD4 exons 6 - 20. One of the breakpoints is within BRD4 exon 6. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0047719-T01-IM6	BRD4-AKAP8L fusion	yes	unknown		unknown	AKAP8L (NM_014371) - BRD4 (NM_058243) rearrangement: c.1536+6695:AKAP8L_c.964:BRD4del Note: The AKAP8L - BRD4 rearrangement is a deletion that results in a fusion of AKAP8L exons 1 - 12 to BRD4 exons 6 - 20. One of the breakpoints is within BRD4 exon 6. Functional significance is undetermined.
KRAS	0	MSKCC-DMP	P-0047737-T01-IM6	PIKFYVE-KRAS fusion	yes	unknown		in frame	KRAS (NM_033360) - PIKFYVE (NM_015040) rearrangement: t(2;12)(q34;p12.1)(chr2:g.209141988::chr12:g.25398161) Note: The KRAS - PIKFYVE rearrangement is a translocation that results in a fusion of KRAS exons 1 - 2 to PIKFYVE exons 5 - 42. The fusion is predicted to be in frame. Functional significance is undetermined.
PIKFYVE	0	MSKCC-DMP	P-0047737-T01-IM6	PIKFYVE-KRAS fusion	yes	unknown		in frame	KRAS (NM_033360) - PIKFYVE (NM_015040) rearrangement: t(2;12)(q34;p12.1)(chr2:g.209141988::chr12:g.25398161) Note: The KRAS - PIKFYVE rearrangement is a translocation that results in a fusion of KRAS exons 1 - 2 to PIKFYVE exons 5 - 42. The fusion is predicted to be in frame. Functional significance is undetermined.
MAOA	0	MSKCC-DMP	P-0047741-T01-IM6	KDM6A-MAOA fusion	yes	unknown		unknown	MAOA (NM_000240) - KDM6A (NM_021140) rearrangement: c.307-1775:MAOA_c.2942:KDM6Adel Note: The MAOA - KDM6A rearrangement is a deletion that results in a fusion of MAOA exons 1 - 3 to KDM6A exons 20 - 29. One of the breakpoints is within KDM6A exon 20.
KDM6A	0	MSKCC-DMP	P-0047741-T01-IM6	KDM6A-MAOA fusion	yes	unknown		unknown	MAOA (NM_000240) - KDM6A (NM_021140) rearrangement: c.307-1775:MAOA_c.2942:KDM6Adel Note: The MAOA - KDM6A rearrangement is a deletion that results in a fusion of MAOA exons 1 - 3 to KDM6A exons 20 - 29. One of the breakpoints is within KDM6A exon 20.
HIST1H3B	0	MSKCC-DMP	P-0047743-T01-IM6	HIST1H3B-intragenic	yes	unknown		unknown	HIST1H3B (NM_003537) rearrangement: t(2;6)(q22.1;p22.2)(chr2:g.137043939::chr6:g.26032075) Note: The HIST1H3B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0047748-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.3430+3672_c.3843+55inv Note: The MGA rearrangement is an intragenic inversion of exons 10 - 11. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0047290-T01-IM6	LETM1-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-LETM1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and LETM1 Exon12 (NM_012318). Lab Notes Run Number: ArcherV3-CLIN-20190191 Macro-dissection: Not Performed
LETM1	0	MSKCC-DMP	P-0047290-T01-IM6	LETM1-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR3-LETM1 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and LETM1 Exon12 (NM_012318). Lab Notes Run Number: ArcherV3-CLIN-20190191 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0016624-T02-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.1282+92:ALK_chr2:g.13865654del Note: The ALK rearrangement is a deletion of exons 6 - 29. The rearrangement includes the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
SEC16A	0	MSKCC-DMP	P-0047576-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.3568-31:SEC16A_c.1455:NOTCH1dup Note: The SEC16A - NOTCH1 rearrangement is a duplication that results in a fusion of SEC16A exons 1 - 3 to NOTCH1 exons 9 - 34. One of the breakpoints is within NOTCH1 exon 9. SEC16A-NOTCH1 fusions have been reported in the literature (PMID: 22101766). Archer RNAseq was performed to clarify if event is expressed; however, the Archer panel does not cover exon 9 of NOTCH1 and a fusion was not identified. Functional significance in undetermined.
NOTCH1	0	MSKCC-DMP	P-0047576-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.3568-31:SEC16A_c.1455:NOTCH1dup Note: The SEC16A - NOTCH1 rearrangement is a duplication that results in a fusion of SEC16A exons 1 - 3 to NOTCH1 exons 9 - 34. One of the breakpoints is within NOTCH1 exon 9. SEC16A-NOTCH1 fusions have been reported in the literature (PMID: 22101766). Archer RNAseq was performed to clarify if event is expressed; however, the Archer panel does not cover exon 9 of NOTCH1 and a fusion was not identified. Functional significance in undetermined.
NTRK1	0	MSKCC-DMP	P-0047878-T01-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.851-206:NTRK1_chr1:g.156997988del Note: The NTRK1 rearrangement is a deletion of exons 8 - 17. The rearrangement includes the kinase domain of NTRK1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PIK3R1	0	MSKCC-DMP	P-0047878-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.1985+199:PIK3R1_chr5:g.136534380del Note: The PIK3R1 rearrangement is a deletion of exon 16.
RECQL4	0	MSKCC-DMP	P-0047880-T01-IM6	ARHGAP39-RECQL4 fusion	yes	unknown		out of frame	RECQL4 (NM_004260) - ARHGAP39 (NM_025251) rearrangement: c.3393+28:RECQL4_c.2615-555:ARHGAP39dup Note: The RECQL4 - ARHGAP39 rearrangement is a duplication that results in a fusion of RECQL4 exons 1 - 20 to ARHGAP39 exons 9 - 13. Functional significance is undetermined.
ARHGAP39	0	MSKCC-DMP	P-0047880-T01-IM6	ARHGAP39-RECQL4 fusion	yes	unknown		out of frame	RECQL4 (NM_004260) - ARHGAP39 (NM_025251) rearrangement: c.3393+28:RECQL4_c.2615-555:ARHGAP39dup Note: The RECQL4 - ARHGAP39 rearrangement is a duplication that results in a fusion of RECQL4 exons 1 - 20 to ARHGAP39 exons 9 - 13. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0047882-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.126+1349_c.556+2440dup Note: The TMPRSS2 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0047889-T01-IM6	RPS6KB2-intragenic	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.2_c.309+873inv Note: The RPS6KB2 rearrangement is an intragenic inversion of exons 1 - 4. One of the breakpoints is within exon 1. The rearrangement includes a part of the kinase domain of RPS6KB2. Functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0047890-T01-IM6	KDM6A-intragenic	yes	unknown		in frame	KDM6A (NM_021140) rearrangement: c.385-9047_c.1528-173del Note: The KDM6A rearrangement is an intragenic deletion of exons 5 - 15.
MET	0	MSKCC-DMP	P-0047892-T01-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: t(7;8)(q31.2;p23.1)(chr7:g.116435712::chr8:g.11529165) Note: The MET rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
JAK1	0	MSKCC-DMP	P-0047902-T01-IM6	JAK1-intragenic	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: t(1;3)(p31.3;q21.3)(chr1:g.65309773::chr3:g.129135343) Note: The JAK1 rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0047905-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.463+4669:ETV6_chr12:g.15129970del Note: The ETV6 rearrangement is a deletion of exons 5 - 8. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0047905-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-41:FGFR3_c.1837-96:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 10 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0047905-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-41:FGFR3_c.1837-96:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 10 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TBL1XR1	0	MSKCC-DMP	P-0047490-T01-IM6	PIK3CA-TBL1XR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TBL1XR1-PIK3CA fusion. Note: The rearrangement is an in-frame fusion between genes TBL1XR1 Exon2 (NM_024665) and PIK3CA Exon2 (NM_006218). Lab Notes Run Number: ArcherV3-CLIN-20190193 Macro-dissection: Performed
PIK3CA	0	MSKCC-DMP	P-0047490-T01-IM6	PIK3CA-TBL1XR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TBL1XR1-PIK3CA fusion. Note: The rearrangement is an in-frame fusion between genes TBL1XR1 Exon2 (NM_024665) and PIK3CA Exon2 (NM_006218). Lab Notes Run Number: ArcherV3-CLIN-20190193 Macro-dissection: Performed
SPEN	0	MSKCC-DMP	P-0047715-T01-IM6	PLEKHM2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement: c.8233:SPEN_c.60+9907:PLEKHM2dup Note: The SPEN - PLEKHM2 rearrangement is a duplication that results in a fusion of SPEN exons 1 - 11 to PLEKHM2 exons 2 - 20. One of the breakpoints is within SPEN exon 11. Functional significance is undetermined.
PLEKHM2	0	MSKCC-DMP	P-0047715-T01-IM6	PLEKHM2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement: c.8233:SPEN_c.60+9907:PLEKHM2dup Note: The SPEN - PLEKHM2 rearrangement is a duplication that results in a fusion of SPEN exons 1 - 11 to PLEKHM2 exons 2 - 20. One of the breakpoints is within SPEN exon 11. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0047715-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4741+60:KMT2D_chr12:g.99540965inv Note: The KMT2D rearrangement is an inversion of exons 1 - 18. Functional significance is undetermined.
PLCD3	0	MSKCC-DMP	P-0047883-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		unknown	PLCD3(NM_133373) - MAP3K14 (NM_003954) rearrangement : c.1126:PLCD3_.3:c.2325+63dup Note: The PLCD3 - MAP3K14 rearrangement is a duplication that results in a fusion of PLCD3 exons 1 - 7 to MAP3K14 exons 13 -16. One of the breakpoints is within PLCD3 exon 7. The functional significance is undetermined.
MAP3K14	0	MSKCC-DMP	P-0047883-T01-IM6	MAP3K14-PLCD3 fusion	yes	unknown		unknown	PLCD3(NM_133373) - MAP3K14 (NM_003954) rearrangement : c.1126:PLCD3_.3:c.2325+63dup Note: The PLCD3 - MAP3K14 rearrangement is a duplication that results in a fusion of PLCD3 exons 1 - 7 to MAP3K14 exons 13 -16. One of the breakpoints is within PLCD3 exon 7. The functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0047883-T01-IM6	CHEK2-intragenic	yes	unknown		unknown	CHEK2 (NM_007194) rearrangement: c.592+2639_c.1461+23inv Note: The CHEK2 rearrangement is an intragenic inversion of exons 5 - 13. The rearrangement includes the kinase domain of CHEK2. Functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0032986-T02-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: t(7;8)(q34;p23.1)(chr7:g.140500362::chr8:g.11716338) Note: The BRAF rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0047795-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+4806_c.557-3057inv Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 5. Functional significance is undetermined.
CCND1	0	MSKCC-DMP	P-0047797-T01-IM6	CCND1-intragenic	yes	unknown		unknown	CCND1 (NM_053056) rearrangement: c.807:CCND1_chr11:g.69469425del Note: The CCND1 rearrangement is a deletion of exon 5. One of the breakpoints is within exon 5. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0047797-T01-IM6	ERBB4-intragenic	yes	unknown		out of frame	ERBB4 (NM_005235) rearrangement: c.1871+28_c.2301+5882del Note: The ERBB4 rearrangement is an intragenic deletion of exons 16 - 19. The rearrangement includes a part of the kinase domain of ERBB4. Functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0047806-T01-IM6	ATM-intragenic	yes	unknown		unknown	ATM (NM_000051) rearrangement: c.335:ATM_chr11:g.108096596del Note: The ATM rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.
TMPRSS2	0	MSKCC-DMP	P-0047937-T01-IM6	TMPRSS2-intragenic	yes	unknown		out of frame	TMPRSS2 (NM_001135099) rearrangement: c.127-1482_c.557-1600dup Note: The TMPRSS2 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0047937-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: t(5;6)(q13.1;q14.1)(chr5:g.67591383::chr6:g.76642727) Note: The PIK3R1 rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.
FANCC	0	MSKCC-DMP	P-0048007-T01-IM6	FANCC-intragenic	yes	unknown		unknown	FANCC (NM_000136) rearrangement: t(9;22)(q22.32;q13.31)(chr9:g.97864041::chr22:g.44300238) Note: The FANCC rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0047982-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: t(5;10)(q11.2;q23.31)(chr5:g.55280572::chr10:g.89624398) Note: The PTEN rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
HNRNPC	0	MSKCC-DMP	P-0021823-T02-IM6	ETV1-HNRNPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HNRNPC-ETV1 fusion. Note: The rearrangement is a fusion between genes HNRNPC Exon1 (5'UTR, NM_001077442) and ETV1 Exon5 (NM_004956). ACIN1-ETV1 fusion. Note: The rearrangement is an out of frame fusion between genes ACIN1 Exon9 (NM_014977) and ETV1 Exon7 (NM_004956). The functional significance of both ETV1 fusion events is unknown. Lab Notes Run Number: ArcherV3-CLIN-20190196 Macro-dissection: Not Performed
ETV1	0	MSKCC-DMP	P-0021823-T02-IM6	ETV1-HNRNPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: HNRNPC-ETV1 fusion. Note: The rearrangement is a fusion between genes HNRNPC Exon1 (5'UTR, NM_001077442) and ETV1 Exon5 (NM_004956). ACIN1-ETV1 fusion. Note: The rearrangement is an out of frame fusion between genes ACIN1 Exon9 (NM_014977) and ETV1 Exon7 (NM_004956). The functional significance of both ETV1 fusion events is unknown. Lab Notes Run Number: ArcherV3-CLIN-20190196 Macro-dissection: Not Performed
WIZ	0	MSKCC-DMP	P-0047827-T02-IM6	BRD4-WIZ fusion	yes	unknown		out of frame	WIZ (NM_021241) - BRD4 (NM_058243) rearrangement: c.529+3652:WIZ_c.2212-31:BRD4del Note: The WIZ - BRD4 rearrangement is a deletion that results in a fusion of WIZ exons 1 - 3 to BRD4 exons 13 - 20. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0047827-T02-IM6	BRD4-WIZ fusion	yes	unknown		out of frame	WIZ (NM_021241) - BRD4 (NM_058243) rearrangement: c.529+3652:WIZ_c.2212-31:BRD4del Note: The WIZ - BRD4 rearrangement is a deletion that results in a fusion of WIZ exons 1 - 3 to BRD4 exons 13 - 20. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0047827-T02-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.2061+304_c.3163-183dup Note: The EGFR rearrangement is a kinase domain duplication (KDD) alteration.
TMPRSS2	0	MSKCC-DMP	P-0047959-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1555:TMPRSS2_c.18+174:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0047959-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1555:TMPRSS2_c.18+174:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0048004-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: c.283-20627_c.298del Note: The FOXP1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.
BAIAP2	0	MSKCC-DMP	P-0048033-T01-IM6	RPTOR-BAIAP2 fusion	yes	unknown		out of frame	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.489+2583:BAIAP2_c.2243-52:RPTORdup Note: The BAIAP2 - RPTOR rearrangement is a duplication that results in a fusion of BAIAP2 exons 1 - 6 to RPTOR exons 20 - 34. Functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0048033-T01-IM6	RPTOR-BAIAP2 fusion	yes	unknown		out of frame	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.489+2583:BAIAP2_c.2243-52:RPTORdup Note: The BAIAP2 - RPTOR rearrangement is a duplication that results in a fusion of BAIAP2 exons 1 - 6 to RPTOR exons 20 - 34. Functional significance is undetermined.
CD274	0	MSKCC-DMP	P-0048038-T01-IM6	CD274-intragenic	yes	unknown		unknown	CD274 (NM_014143) rearrangement: t(9;20)(p24.1;p11.21)(chr9:g.5463221::chr20:g.22314553) Note: The CD274 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0048041-T01-IM6	AK8-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) - AK8 (NM_152572) rearrangement: c.2813+18:TSC1_c.979+5282:AK8del Note: The TSC1 - AK8 rearrangement is a deletion that results in a fusion of TSC1 exons 1 - 21 to AK8 exons 11 - 13.
AK8	0	MSKCC-DMP	P-0048041-T01-IM6	AK8-TSC1 fusion	yes	unknown		out of frame	TSC1 (NM_000368) - AK8 (NM_152572) rearrangement: c.2813+18:TSC1_c.979+5282:AK8del Note: The TSC1 - AK8 rearrangement is a deletion that results in a fusion of TSC1 exons 1 - 21 to AK8 exons 11 - 13.
TMPRSS2	0	MSKCC-DMP	P-0048072-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2:TMPRSS2_c.39+59528:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0048072-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2:TMPRSS2_c.39+59528:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
DIS3	0	MSKCC-DMP	P-0048115-T01-IM6	DIS3-intragenic	yes	unknown		unknown	DIS3 (NM_014953) rearrangement: c.1755+84:DIS3_chr13:g.32297113del Note: The DIS3 rearrangement is a deletion of exons 14 - 21. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0048115-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.4462:FAT1_chr4:g.187335856del Note: The FAT1 rearrangement is a deletion of exons 8 - 27. One of the breakpoints is within exon 8.
BRAF	0	MSKCC-DMP	P-0048159-T01-IM6	BRAF-intragenic	yes	unknown		out of frame	BRAF (NM_004333) rearrangement: c.609-233_c.1177+2191dup Note: The BRAF rearrangement is an intragenic duplication of exons 5 - 9. The rearrangement does not include the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
SMAD4	0	MSKCC-DMP	P-0048161-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.1231:SMAD4_chr18:g.48835676inv Note: The SMAD4 rearrangement is an inversion of exons 10 - 12. One of the breakpoints is within exon 10. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0048169-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1332+101_c.1960+133del Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 19.
ESR1	0	MSKCC-DMP	P-0048141-T01-IM6	ESR1-intragenic	yes	unknown		unknown	ESR1 (NM_001122740) rearrangement: c.1433:ESR1_chr6:g.126953648inv Note: The ESR1 rearrangement is an inversion of exons 1 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0048144-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: t(1;11)(p36.12;q23.3)(chr1:g.23703057::chr11:g.118367285) Note: The KMT2A rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0048174-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.648_c.2756del Note: The FAT1 rearrangement is an intragenic deletion of exon 2. The breakpoints are within exon 2.
TMPRSS2	0	MSKCC-DMP	P-0046943-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190199 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0046943-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190199 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0047795-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190199 Macro-dissection: Performed
ERG	0	MSKCC-DMP	P-0047795-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190199 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0047878-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190198 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0047878-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190198 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0047937-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190200 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0047937-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190200 Macro-dissection: Not Performed
MAP3K1	0	MSKCC-DMP	P-0039030-T03-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: t(5;9)(q11.2;p21.3)(chr5:g.56111607::chr9:g.24253800) Note: The MAP3K1 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0042796-T02-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: t(6;19)(p21.32;p13.3)(chr6:g.32166201::chr19:g.3281852) Note: The NOTCH4 rearrangement is a translocation with a breakpoint in exon 26. Multiple rearrangements involving NOTCH4 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated. Functional significance is undetermined.
APC	0	MSKCC-DMP	P-0047579-T02-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.5580:APC_chr5:g.112190648del Note: The APC rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16.
SF3B1	0	MSKCC-DMP	P-0047762-T01-IM6	SF3B1-intragenic	yes	unknown		unknown	SF3B1 (NM_012433) rearrangement: c.3622:SF3B1_chr2:g.198794918dup Note: The SF3B1 rearrangement is a duplication of exons 1 - 24. One of the breakpoints is within exon 24. Functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0047789-T01-IM6	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.2322+1_c.2324del Note: The DNMT3A rearrangement is an intragenic deletion of exons 19 - 20. The breakpoints are within exon 19 and exon 20.
DUSP4	0	MSKCC-DMP	P-0047823-T01-IM6	DUSP4-intragenic	yes	unknown		unknown	DUSP4 (NM_001394) rearrangement: c.579+18:DUSP4_chr8:g.28791503inv Note: The DUSP4 rearrangement is an inversion of exons 3 - 4. Functional significance is undetermined.
PARP1	0	MSKCC-DMP	P-0047856-T01-IM6	PARP1-intragenic	yes	unknown		unknown	PARP1 (NM_001618) rearrangement: c.2688:PARP1_chr1:g.226446443inv Note: The PARP1 rearrangement is an inversion of exons 20 - 23. One of the breakpoints is within exon 20. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0047859-T01-IM6	CAMTA1-DNMT1 fusion	yes	unknown		in frame	DNMT1 (NM_001379) - CAMTA1 (NM_015215) rearrangement: t(1;19)(p36.31;p13.2)(chr1:g.6958300::chr19:g.10291323) Note: The DNMT1 - CAMTA1 rearrangement is a translocation that results in a fusion of DNMT1 exons 1 - 3 to CAMTA1 exons 4 - 23. The fusion is predicted to be in frame. Functional significance is undetermined.
CAMTA1	0	MSKCC-DMP	P-0047859-T01-IM6	CAMTA1-DNMT1 fusion	yes	unknown		in frame	DNMT1 (NM_001379) - CAMTA1 (NM_015215) rearrangement: t(1;19)(p36.31;p13.2)(chr1:g.6958300::chr19:g.10291323) Note: The DNMT1 - CAMTA1 rearrangement is a translocation that results in a fusion of DNMT1 exons 1 - 3 to CAMTA1 exons 4 - 23. The fusion is predicted to be in frame. Functional significance is undetermined.
FLT4	0	MSKCC-DMP	P-0023366-T03-IM6	REL-FLT4 fusion	yes	unknown		unknown	FLT4 (NM_182925) - REL (NM_002908) rearrangement: t(2;5)(p16.1;q35.3)(chr2:g.61127034::chr5:g.180056861) Note: The FLT4 - REL rearrangement is a translocation with breakpoints in FLT4 intron 5 and REL intron 3. Functional significance is undetermined.
REL	0	MSKCC-DMP	P-0023366-T03-IM6	REL-FLT4 fusion	yes	unknown		unknown	FLT4 (NM_182925) - REL (NM_002908) rearrangement: t(2;5)(p16.1;q35.3)(chr2:g.61127034::chr5:g.180056861) Note: The FLT4 - REL rearrangement is a translocation with breakpoints in FLT4 intron 5 and REL intron 3. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0047763-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-671:TMPRSS2_c.18+16055:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0047763-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-671:TMPRSS2_c.18+16055:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0047811-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: t(6;13)(p21.33;q14.2)(chr6:g.30671876::chr13:g.49335769) Note: The MDC1 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.
SOX17	0	MSKCC-DMP	P-0047811-T01-IM6	SOX17-intragenic	yes	unknown		unknown	SOX17 (NM_022454) rearrangement: c.300:SOX17_chr8:g.72866321del Note: The SOX17 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1.
SESN3	0	MSKCC-DMP	P-0047818-T01-IM6	SESN3-intragenic	yes	unknown		unknown	SESN3 (NM_144665) rearrangement: c.1247+33:SESN3_chr11:g.45757807del Note: The SESN3 rearrangement is a deletion of exons 9 - 10.
YAP1	0	MSKCC-DMP	P-0047961-T01-IM6	YAP1-intragenic	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: c.1241:YAP1_chr11:g.108597375inv Note: The YAP1 rearrangement is an inversion of exons 8 - 9. One of the breakpoints is within exon 8. Functional significance is undetermined.
CLIP1	0	MSKCC-DMP	P-0007266-T02-IM6	BRAF-CLIP1 fusion	yes	unknown		in frame	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140495673::chr12:g.122767026) Note: The CLIP1 - BRAF fusion involves CLIP1 exons 1 - 20 and BRAF exons 8 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0007266-T02-IM6	BRAF-CLIP1 fusion	yes	unknown		in frame	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140495673::chr12:g.122767026) Note: The CLIP1 - BRAF fusion involves CLIP1 exons 1 - 20 and BRAF exons 8 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BMP1	0	MSKCC-DMP	P-0048241-T01-IM6	MTOR-BMP1 fusion	yes	unknown		unknown	BMP1 (NM_006129) - MTOR (NM_004958) rearrangement: t(1;8)(p36.22;p21.3)(chr1:g.11259667::chr8:g.22041165) Note: The BMP1 - MTOR rearrangement is a translocation that results in a fusion of BMP1 exons 1 - 8 to MTOR exons 27 - 58. One of the breakpoints is within MTOR exon 27. Functional significance is undetermined. Multiple rearrangements involving MTOR were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MTOR	0	MSKCC-DMP	P-0048241-T01-IM6	MTOR-BMP1 fusion	yes	unknown		unknown	BMP1 (NM_006129) - MTOR (NM_004958) rearrangement: t(1;8)(p36.22;p21.3)(chr1:g.11259667::chr8:g.22041165) Note: The BMP1 - MTOR rearrangement is a translocation that results in a fusion of BMP1 exons 1 - 8 to MTOR exons 27 - 58. One of the breakpoints is within MTOR exon 27. Functional significance is undetermined. Multiple rearrangements involving MTOR were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
EPHB1	0	MSKCC-DMP	P-0048268-T01-IM6	EPHB1-intragenic	yes	unknown		unknown	EPHB1 (NM_004441) rearrangement: c.962-3651_c.1601del Note: The EPHB1 rearrangement is an intragenic deletion of exons 5 - 8. One of the breakpoints is within exon 8. The rearrangement does not include the kinase domain of EPHB1. Functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0048269-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.9353:ZFHX3_chr16:g.72597392del Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.
CDKN2A	0	MSKCC-DMP	P-0048272-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-5636_c.194-3554del Note: The CDKN2A rearrangement is an intragenic deletion of exons 2 - 1. One of the breakpoints is within exon 1. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
CTSB	0	MSKCC-DMP	P-0032986-T02-IM6	BRAF-CTSB fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CTSB-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CTSB Exon3 (NM_147780) and BRAF Exon7 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20190203 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0032986-T02-IM6	BRAF-CTSB fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CTSB-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes CTSB Exon3 (NM_147780) and BRAF Exon7 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20190203 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0048159-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon 14 skipping (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20190203 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0047008-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1704:TMPRSS2_c.39+10262:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in-frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0047008-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1704:TMPRSS2_c.39+10262:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in-frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
TRMT1L	0	MSKCC-DMP	P-0048251-T01-IM6	FH-TRMT1L fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: c.1390+166:FH_chr1:g.185113306inv Note: The FH rearrangement is an inversion of exon 10. Functional significance is undetermined.
FH	0	MSKCC-DMP	P-0048251-T01-IM6	FH-TRMT1L fusion	yes	unknown		unknown	FH (NM_000143) rearrangement: c.1390+166:FH_chr1:g.185113306inv Note: The FH rearrangement is an inversion of exon 10. Functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0048251-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.1473+29:BRIP1_chr17:g.69421263inv Note: The BRIP1 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.
MDM4	0	MSKCC-DMP	P-0048320-T01-IM6	EFCAB6-MDM4 fusion	yes	unknown		in frame	MDM4 (NM_002393) - EFCAB6 (NM_022785) rearrangement: t(1;22)(q32.1;q13.2)(chr1:g.204516048::chr22:g.44039483) Note: The MDM4 - EFCAB6 rearrangement is a translocation that results in a fusion of MDM4 exons 1 - 10 to EFCAB6 exons 18 - 32. The fusion is predicted to be in frame. Functional significance is undetermined. Multiple rearrangements involving MDM4 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
EFCAB6	0	MSKCC-DMP	P-0048320-T01-IM6	EFCAB6-MDM4 fusion	yes	unknown		in frame	MDM4 (NM_002393) - EFCAB6 (NM_022785) rearrangement: t(1;22)(q32.1;q13.2)(chr1:g.204516048::chr22:g.44039483) Note: The MDM4 - EFCAB6 rearrangement is a translocation that results in a fusion of MDM4 exons 1 - 10 to EFCAB6 exons 18 - 32. The fusion is predicted to be in frame. Functional significance is undetermined. Multiple rearrangements involving MDM4 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SMARCA4	0	MSKCC-DMP	P-0028732-T02-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.1419+1659_c.4171-101del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 9 - 29.
NCOA4	0	MSKCC-DMP	P-0047991-T02-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET  (NM_020975) fusion: c.762+537:NCOA4_c.2137-494:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0047991-T02-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET  (NM_020975) fusion: c.762+537:NCOA4_c.2137-494:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
KMT2D	0	MSKCC-DMP	P-0048293-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4390_c.4741+351del Note: The KMT2D rearrangement is an intragenic deletion of exons 15 - 18. One of the breakpoints is within exon 15.
CDKN2A	0	MSKCC-DMP	P-0048296-T01-IM6	CDKN2A-intragenic	yes	unknown		in frame	CDKN2A (NM_000077) rearrangement: c.458-568_c.193+7281del Note: The CDKN2A rearrangement is a deletion of CDKN2A exons 1 - 2 and CDKN2A exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
RER1	0	MSKCC-DMP	P-0048306-T02-IM6	ARID1A-RER1 fusion	yes	unknown		unknown	RER1 (NM_007033) - ARID1A (NM_006015) rearrangement: c.187-285:RER1_c.1471:ARID1Adel Note: The RER1 - ARID1A rearrangement is a deletion that results in a fusion of RER1 exons 1 - 3 to ARID1A exons 3 - 20. One of the breakpoints is within ARID1A exon 3.
ARID1A	0	MSKCC-DMP	P-0048306-T02-IM6	ARID1A-RER1 fusion	yes	unknown		unknown	RER1 (NM_007033) - ARID1A (NM_006015) rearrangement: c.187-285:RER1_c.1471:ARID1Adel Note: The RER1 - ARID1A rearrangement is a deletion that results in a fusion of RER1 exons 1 - 3 to ARID1A exons 3 - 20. One of the breakpoints is within ARID1A exon 3.
BRCA1	0	MSKCC-DMP	P-0048353-T01-IM6	BRCA1-intragenic	yes	unknown		out of frame	BRCA1 (NM_007294) rearrangement: c.5332+82:BRCA1_chr17:g.41122482del Note: The BRCA1 rearrangement is a deletion of exons 21 - 23.
NOTCH1	0	MSKCC-DMP	P-0048354-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: t(8;9)(p23.2;q34.3)(chr8:g.6125999::chr9:g.139403489) Note: The NOTCH1 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0048355-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.2274+60:FGFR3_chr4:g.6711492inv Note: The FGFR3 rearrangement is an inversion of exon 18. The rearrangement does not include the kinase domain of FGFR3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0048357-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41638942::chr21:g.42867694) Note: The TMPRSS2 structural variant translocates the first 2 exons of TMPRSS2 to the intergenic region before ETV4.
TOP1	0	MSKCC-DMP	P-0048373-T01-IM6	TOP1-intragenic	yes	unknown		unknown	TOP1 (NM_003286) rearrangement: c.976-24_c.2090del Note: The TOP1 rearrangement is an intragenic deletion of exons 12 - 20. One of the breakpoints is within exon 20.
MGA	0	MSKCC-DMP	P-0048408-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(5;15)(p13.3;q15.1)(chr5:g.30242172::chr15:g.41989094) Note: The MGA rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
PTPN11	0	MSKCC-DMP	P-0048434-T01-IM6	PTPN11-intragenic	yes	unknown		unknown	PTPN11 (NM_002834) rearrangement: c.1245:PTPN11_chr12:g.92988526del Note: The PTPN11 rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11. Functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0048473-T01-IM6	NSD1-intragenic	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: t(5;15)(q35.3;q26.3)(chr5:g.176637022::chr15:g.102521137) Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0048473-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: t(3;17)(p22.1;q21.2)(chr3:g.39726709::chr17:g.40474483) Note: The STAT3 rearrangement is a translocation with a breakpoint in exon 21. Functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0048473-T01-IM6	TAP2-intragenic	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: c.1796-139:TAP2_chr6:g.32938006inv Note: The TAP2 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0048484-T01-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: t(6;13)(p21.32;q12.13)(chr6:g.32171958::chr13:g.27435738) Note: The NOTCH4 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.
STK19	0	MSKCC-DMP	P-0048484-T01-IM6	MRPS31-STK19 fusion	yes	unknown		unknown	STK19 (NM_004197) - MRPS31 (NM_005830) rearrangement: t(6;13)(p21.33;q14.11)(chr6:g.31948577::chr13:g.41339661) Note: The STK19 - MRPS31 rearrangement is a translocation that results in a fusion of STK19 exons 1 - 7 to MRPS31 exons 3 - 7. One of the breakpoints is within STK19 exon 7. Functional significance is undetermined.
MRPS31	0	MSKCC-DMP	P-0048484-T01-IM6	MRPS31-STK19 fusion	yes	unknown		unknown	STK19 (NM_004197) - MRPS31 (NM_005830) rearrangement: t(6;13)(p21.33;q14.11)(chr6:g.31948577::chr13:g.41339661) Note: The STK19 - MRPS31 rearrangement is a translocation that results in a fusion of STK19 exons 1 - 7 to MRPS31 exons 3 - 7. One of the breakpoints is within STK19 exon 7. Functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0048484-T01-IM6	NSD1-intragenic	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: t(5;6)(q35.2;p21.33)(chr5:g.176562282::chr6:g.31617932) Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
IL6R	0	MSKCC-DMP	P-0048144-T01-IM6	RAF1-IL6R fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: IL6R-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes IL6R Exon9 (NM_000565) and RAF1 Exon7 (NM_002880). PMID: 30835257 Lab Notes Run Number: ArcherV3-CLIN-20190208 Macro-dissection: Not Performed
RAF1	0	MSKCC-DMP	P-0048144-T01-IM6	RAF1-IL6R fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: IL6R-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes IL6R Exon9 (NM_000565) and RAF1 Exon7 (NM_002880). PMID: 30835257 Lab Notes Run Number: ArcherV3-CLIN-20190208 Macro-dissection: Not Performed
ERBB4	0	MSKCC-DMP	P-0028057-T02-IM6	ERBB4-intragenic	yes	unknown		in frame	ERBB4 (NM_005235) rearrangement: c.422-20667_c.883+57dup Note: The ERBB4 rearrangement is an intragenic duplication of exons 4 - 7. The rearrangement does not include the kinase domain of ERBB4. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0047470-T02-IM6	PRKAG2-KMT2C fusion	yes	unknown		out of frame	KMT2C (NM_170606) - PRKAG2 (NM_016203) rearrangement: c.12774+74:KMT2C_c.466+46558:PRKAG2del Note: The KMT2C - PRKAG2 rearrangement is a deletion that results in a fusion of KMT2C exons 1 - 51 to PRKAG2 exons 4 - 16.
PRKAG2	0	MSKCC-DMP	P-0047470-T02-IM6	PRKAG2-KMT2C fusion	yes	unknown		out of frame	KMT2C (NM_170606) - PRKAG2 (NM_016203) rearrangement: c.12774+74:KMT2C_c.466+46558:PRKAG2del Note: The KMT2C - PRKAG2 rearrangement is a deletion that results in a fusion of KMT2C exons 1 - 51 to PRKAG2 exons 4 - 16.
AURKA	0	MSKCC-DMP	P-0048452-T01-IM6	AURKA-intragenic	yes	unknown		unknown	AURKA (NM_003600) rearrangement: t(20;21)(q13.2;q22.3)(chr20:g.54958225::chr21:g.46653413) Note: The AURKA rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0048454-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.16_c.1342-263del Note: The BRD4 rearrangement is an intragenic deletion of exons 2 - 7. One of the breakpoints is within exon 2. Functional significance is undetermined.
EPHB1	0	MSKCC-DMP	P-0048454-T01-IM6	EPHB1-intragenic	yes	unknown		unknown	EPHB1 (NM_004441) rearrangement: c.2496+386_c.2522del Note: The EPHB1 rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of EPHB1. Functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0048525-T01-IM6	YAP1-intragenic	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: c.803-105:YAP1_chr11:g.91175282del Note: The YAP1 rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.
DERA	0	MSKCC-DMP	P-0048530-T01-IM6	GLI1-DERA fusion	yes	unknown		unknown	DERA (NM_015954) - GLI1 (NM_005269) rearrangement: c.508+217:DERA_c.3081:GLI1del Note: The DERA - GLI1 rearrangement is a deletion that results in a fusion of DERA exons 1 - 5 to GLI1 exon 12. One of the breakpoints is within GLI1 exon 12. Functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0048530-T01-IM6	GLI1-DERA fusion	yes	unknown		unknown	DERA (NM_015954) - GLI1 (NM_005269) rearrangement: c.508+217:DERA_c.3081:GLI1del Note: The DERA - GLI1 rearrangement is a deletion that results in a fusion of DERA exons 1 - 5 to GLI1 exon 12. One of the breakpoints is within GLI1 exon 12. Functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0048531-T01-IM6	MAML2-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) - MAML2 (NM_032427) rearrangement: c.54:YAP1_c.513+33265:MAML2inv Note: The YAP1 - MAML2 rearrangement is an inversion that results in a fusion of YAP1 exon 1 to MAML2 exons 2 - 5. One of the breakpoints is within YAP1 exon 1. Functional significance is undetermined.
MAML2	0	MSKCC-DMP	P-0048531-T01-IM6	MAML2-YAP1 fusion	yes	unknown		unknown	YAP1 (NM_001130145) - MAML2 (NM_032427) rearrangement: c.54:YAP1_c.513+33265:MAML2inv Note: The YAP1 - MAML2 rearrangement is an inversion that results in a fusion of YAP1 exon 1 to MAML2 exons 2 - 5. One of the breakpoints is within YAP1 exon 1. Functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0048586-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: t(1;14)(p13.2;q21.2)(chr1:g.115280412::chr14:g.45909793) Note: The CSDE1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.
PHOX2B	0	MSKCC-DMP	P-0048586-T01-IM6	PHOX2B-intragenic	yes	unknown		unknown	PHOX2B (NM_003924) rearrangement: c.558:PHOX2B_chr4:g.41740029del Note: The PHOX2B rearrangement is a deletion of exon 3. One of the breakpoints is within exon 3.. Functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0048593-T01-IM6	SLX4-intragenic	yes	unknown		unknown	SLX4 (NM_032444) rearrangement: t(16;17)(p13.3;p13.3)(chr16:g.3652199::chr17:g.1815214) Note: The SLX4 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0048593-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.2316:BRD4_chr19:g.15425839del Note: The BRD4 rearrangement is a deletion of exons 1 - 13. One of the breakpoints is within exon 13. Functional significance is undetermined.
ACOXL	0	MSKCC-DMP	P-0048593-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		in frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1370-816:ACOXL_c.394+3154:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 15 to BCL2L11 exons 3 - 4. The fusion is predicted to be in frame.
BCL2L11	0	MSKCC-DMP	P-0048593-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		in frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1370-816:ACOXL_c.394+3154:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 15 to BCL2L11 exons 3 - 4. The fusion is predicted to be in frame.
ELF3	0	MSKCC-DMP	P-0043891-T05-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.806-155:ELF3_chr1:g.201980127del Note: The ELF3 rearrangement is a deletion of exons 1 - 7.
FAT1	0	MSKCC-DMP	P-0048500-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.9967:FAT1_chr4:g.187868727del Note: The FAT1 rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15.
TMPRSS2	0	MSKCC-DMP	P-0048507-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-999:TMPRSS2_c.39+51321:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0048507-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-999:TMPRSS2_c.39+51321:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
MGA	0	MSKCC-DMP	P-0048510-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: c.7191+34:MGA_chr15:g.41775137inv Note: The MGA rearrangement is an inversion of exons 1 - 19. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0048510-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-148:TMPRSS2_c.-149-32518:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion of TMPRSS2 exons 2 - 14 and ERG exon 1-2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by the IMPACT panel cannot be ruled out
ERG	0	MSKCC-DMP	P-0048510-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-148:TMPRSS2_c.-149-32518:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion of TMPRSS2 exons 2 - 14 and ERG exon 1-2. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by the IMPACT panel cannot be ruled out
APC	0	MSKCC-DMP	P-0048551-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) rearrangement: c.7278:APC_c.301+454:SRP19del Note: The APC - SRP19 rearrangement is a deletion that results in a fusion of APC exons 1 - 16 to SRP19 exon 5. One of the breakpoints is within APC exon 16.
SRP19	0	MSKCC-DMP	P-0048551-T01-IM6	SRP19-APC fusion	yes	unknown		unknown	APC (NM_000038) - SRP19 (NM_001204199) rearrangement: c.7278:APC_c.301+454:SRP19del Note: The APC - SRP19 rearrangement is a deletion that results in a fusion of APC exons 1 - 16 to SRP19 exon 5. One of the breakpoints is within APC exon 16.
TBX3	0	MSKCC-DMP	P-0048554-T01-IM6	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.1868:TBX3_chr12:g.117884190del Note: The TBX3 rearrangement is a deletion of exons 1 - 8. One of the breakpoints is within exon 8.
CD79A	0	MSKCC-DMP	P-0048558-T01-IM6	RPS19-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.309:CD79A_c.172+326:RPS19dup Note: The CD79A - RPS19 rearrangement is a duplication that results in a fusion of CD79A exons 1 - 2 to RPS19 exons 4 - 6. One of the breakpoints is within CD79A exon 2. Functional significance is undetermined.
RPS19	0	MSKCC-DMP	P-0048558-T01-IM6	RPS19-CD79A fusion	yes	unknown		unknown	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.309:CD79A_c.172+326:RPS19dup Note: The CD79A - RPS19 rearrangement is a duplication that results in a fusion of CD79A exons 1 - 2 to RPS19 exons 4 - 6. One of the breakpoints is within CD79A exon 2. Functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0048608-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.6193:BRCA2_chr13:g.38945399del Note: The BRCA2 rearrangement is a deletion of exons 11 - 27. One of the breakpoints is within exon 11.
TMPRSS2	0	MSKCC-DMP	P-0048610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.349+100:TMPRSS2_c.40-56888:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 3 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0048610-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.349+100:TMPRSS2_c.40-56888:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 3 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
CCDC6	0	MSKCC-DMP	P-0048611-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+12938:CCDC6_c.2137-795:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET. Multiple rearrangements involving RET were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RET	0	MSKCC-DMP	P-0048611-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+12938:CCDC6_c.2137-795:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET. Multiple rearrangements involving RET were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERBB3	0	MSKCC-DMP	P-0048613-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(12;20)(q13.2;p11.23)(chr12:g.56490271::chr20:g.19043904) The ERBB3 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.
NKX2	0	MSKCC-DMP	P-0048437-T01-IM6	NKX2-1-NKX2 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) - KIAA0391 (NM_014672) rearrangement: c.260:NKX2-1_c.1276-10713:KIAA0391inv Note: The NKX2-1 - KIAA0391 rearrangement is an inversion that results in a fusion of NKX2-1 exons 1 - 2 to KIAA0391 exons 4 - 8. One of the breakpoints is within NKX2-1 exon 2. Functional significance is undetermined.
NKX2-1	0	MSKCC-DMP	P-0048437-T01-IM6	NKX2-1-NKX2 fusion	yes	unknown		unknown	NKX2-1 (NM_001079668) - KIAA0391 (NM_014672) rearrangement: c.260:NKX2-1_c.1276-10713:KIAA0391inv Note: The NKX2-1 - KIAA0391 rearrangement is an inversion that results in a fusion of NKX2-1 exons 1 - 2 to KIAA0391 exons 4 - 8. One of the breakpoints is within NKX2-1 exon 2. Functional significance is undetermined.
IKZF1	0	MSKCC-DMP	P-0048437-T01-IM6	IKZF1-intragenic	yes	unknown		unknown	IKZF1 (NM_006060) Rearrangement: c.1312:IKZF1_chr7:g.25970278inv Note: The IKZF1 Rearrangement results in the inversion of exons 1-8 of IKZF1. One of the breakpoints is within exon8. Its functional significance is undetermined.
TMPRSS2 exon 2 with ERG exon 4	0	MSKCC-DMP	P-0048597-T01-IM6	TMPRSS2 exon 2 with ERG exon 4-intragenic	yes	unknown		in frame	TMPRSS2 exon 2 with ERG exon 4 Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
TMPRSS2	0	MSKCC-DMP	P-0048504-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) fusion: t(17;21)(q21.31;q22.3)(chr17:g.41633928::chr21:g.42866665) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint within intron 2. A more complex rearrangement resulting in a TMPRSS2 fusion cannot be ruled out.
ALK	0	MSKCC-DMP	P-0048621-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.2915-159:ALK_chr2:g.16609882del Note: The ALK rearrangement is a deletion of exons 18 - 29. The rearrangement includes the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CEBPA	0	MSKCC-DMP	P-0048622-T01-IM6	CEBPA-intragenic	yes	unknown		unknown	CEBPA (NM_004364) rearrangement: c.156:CEBPA_chr19:g.33735782inv Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0048624-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;19)(p13.2;p13.12)(chr12:g.12020310::chr19:g.14528519) Note: The ETV6 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0048671-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783869::chr6:g.117647250) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0048671-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783869::chr6:g.117647250) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ST7	0	MSKCC-DMP	P-0048436-T01-IM6	MET-ST7 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ST7-MET fusion. Note: The rearrangement is an in-frame fusion between genes ST7 Exon1 (NM_021908) and MET Exon2 (NM_000245). Note2: This fusion was detected with low read support. See IMPACT M19-39363 - MET amplification was detected.  Lab Notes Run Number: ArcherV3-CLIN-20190211 Macro-dissection: Performed
MET	0	MSKCC-DMP	P-0048436-T01-IM6	MET-ST7 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ST7-MET fusion. Note: The rearrangement is an in-frame fusion between genes ST7 Exon1 (NM_021908) and MET Exon2 (NM_000245). Note2: This fusion was detected with low read support. See IMPACT M19-39363 - MET amplification was detected.  Lab Notes Run Number: ArcherV3-CLIN-20190211 Macro-dissection: Performed
ARID1A	0	MSKCC-DMP	P-0048098-T02-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;5)(p36.11;q35.2)(chr1:g.27101346::chr5:g.175351720) Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0048650-T01-IM6	NKPD1-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - NKPD1 (NM_198478) rearrangement: c.1119-74:ERCC2_c.409:NKPD1del Note: The ERCC2 - NKPD1 rearrangement is a deletion that results in a fusion of ERCC2 exons 1 - 11 to NKPD1 exons 2 - 4. One of the breakpoints is within NKPD1 exon 2.
NKPD1	0	MSKCC-DMP	P-0048650-T01-IM6	NKPD1-ERCC2 fusion	yes	unknown		unknown	ERCC2 (NM_000400) - NKPD1 (NM_198478) rearrangement: c.1119-74:ERCC2_c.409:NKPD1del Note: The ERCC2 - NKPD1 rearrangement is a deletion that results in a fusion of ERCC2 exons 1 - 11 to NKPD1 exons 2 - 4. One of the breakpoints is within NKPD1 exon 2.
AGXT2	0	MSKCC-DMP	P-0048655-T01-IM6	TERT-AGXT2 fusion	yes	unknown		unknown	AGXT2 (NM_031900) - TERT (NM_198253) rearrangement: c.487-607:AGXT2_c.3037:TERTdel Note: The AGXT2 - TERT rearrangement is a deletion that results in a fusion of AGXT2 exons 1 - 4 to TERT exons 14 - 16. One of the breakpoints is within TERT exon 14. Functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0048655-T01-IM6	TERT-AGXT2 fusion	yes	unknown		unknown	AGXT2 (NM_031900) - TERT (NM_198253) rearrangement: c.487-607:AGXT2_c.3037:TERTdel Note: The AGXT2 - TERT rearrangement is a deletion that results in a fusion of AGXT2 exons 1 - 4 to TERT exons 14 - 16. One of the breakpoints is within TERT exon 14. Functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0048657-T01-IM6	SMAD3-intragenic	yes	unknown		out of frame	SMAD3 (NM_005902) rearrangement: c.872-6_c.1154+588dup Note: The SMAD3 rearrangement is an intragenic duplication of exons 7 - 8. Functional significance is undetermined.
PLK2	0	MSKCC-DMP	P-0048660-T01-IM6	PLK2-intragenic	yes	unknown		unknown	PLK2 (NM_006622) rearrangement: c.914:PLK2_chr5:g.57749444del Note: The PLK2 rearrangement is a deletion of exons 7 - 14. One of the breakpoints is within exon 7. The rearrangement includes a part of the kinase domain of PLK2. Functional significance is undetermined.
PMS1	0	MSKCC-DMP	P-0048696-T01-IM6	PMS1-intragenic	yes	unknown		out of frame	PMS1 (NM_000534) rearrangement: c.1856+3301_c.2473+34dup Note: The PMS1 rearrangement is an intragenic duplication of exons 10 - 11. Functional significance is undetermined.
MGA	0	MSKCC-DMP	P-0048750-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: t(3;15)(p24.1;q15.1)(chr3:g.29948992::chr15:g.42042391) The MGA rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0012045-T03-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1141-152:BRAF_chr7:g.141759418del Note: The BRAF rearrangement is a deletion of exons 1 - 8. The rearrangement does not include the kinase domain of BRAF. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TP53	0	MSKCC-DMP	P-0045906-T02-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(5;17)(p14.1;p13.1)(chr5:g.25413095::chr17:g.7578033) Note: The TP53 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0048596-T01-IM6	RARA-intragenic	yes	unknown		unknown	RARA (NM_000964) rearrangement: t(17;20)(q21.2;q12)(chr17:g.38512345::chr20:g.39591760) Note: The RARA rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
TGFBR2	0	MSKCC-DMP	P-0048596-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.1303_c.1330-684del Note: The TGFBR2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The rearrangement includes a part of the kinase domain of TGFBR2.
STIP1	0	MSKCC-DMP	P-0048702-T01-IM6	RPS6KA4-STIP1 fusion	yes	unknown		unknown	STIP1 (NM_006819) - RPS6KA4 (NM_003942) rearrangement: c.1024-379:STIP1_c.1765:RPS6KA4del Note: The STIP1 - RPS6KA4 rearrangement is a deletion that results in a fusion of STIP1 exons 1 - 8 to RPS6KA4 exons 14 - 17. One of the breakpoints is within RPS6KA4 exon 14. Functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0048702-T01-IM6	RPS6KA4-STIP1 fusion	yes	unknown		unknown	STIP1 (NM_006819) - RPS6KA4 (NM_003942) rearrangement: c.1024-379:STIP1_c.1765:RPS6KA4del Note: The STIP1 - RPS6KA4 rearrangement is a deletion that results in a fusion of STIP1 exons 1 - 8 to RPS6KA4 exons 14 - 17. One of the breakpoints is within RPS6KA4 exon 14. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0048708-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1452:TMPRSS2_c.39+39917:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0048708-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1452:TMPRSS2_c.39+39917:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
MTOR	0	MSKCC-DMP	P-0048709-T01-IM6	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.1116+6:MTOR_chr1:g.11492685inv Note: The MTOR rearrangement is an inversion of exons 1 - 7. Functional significance is undetermined.
INSR	0	MSKCC-DMP	P-0048755-T01-IM6	INSR-intragenic	yes	unknown		unknown	INSR (NM_000208) rearrangement: c.2267+139:INSR_chr19:g.5461998inv Note: The INSR rearrangement is an inversion of exons 12 - 22. The rearrangement includes the kinase domain of INSR. Functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0048755-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.85_c.171+6891del Note: The PARK2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2
KDM5A	0	MSKCC-DMP	P-0048756-T01-IM6	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(12;14)(p13.33;q32.32)(chr12:g.461291::chr14:g.103256288) Note: The KDM5A rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0048763-T01-IM6	VTCN1-intragenic	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: c.446-3:VTCN1_chr1:g.81533670inv Note: The VTCN1 rearrangement is an inversion of exons 4 - 5. Functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0048772-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3 (NM_139276) rearrangement: c.1465-8:STAT3_chr17:g.40636770dup Note: The STAT3 rearrangement is a duplication of exons 1 - 16. Functional significance is undetermined.
STAT5B	0	MSKCC-DMP	P-0048772-T01-IM6	STAT5B-intragenic	yes	unknown		unknown	STAT5B (NM_012448) rearrangement: t(6;17)(q25.3;q21.2)(chr6:g.159208883::chr17:g.40364046) Note: The STAT5B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0048773-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.799-11521_c.3610-95inv Note: The CREBBP rearrangement is an intragenic inversion of exons 3 - 18. Functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0048776-T01-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: c.2502+66:TSC1_chr9:g.73622510inv Note: The TSC1 rearrangement is an inversion of exons 20 - 23. Functional significance is undetermined.
HIST1H3E	0	MSKCC-DMP	P-0048786-T01-IM6	HIST1H3E-intragenic	yes	unknown		unknown	HIST1H3E (NM_003532) rearrangement: c.39:HIST1H3E_chr6:g.26032289inv Note: The HIST1H3E rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0048828-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.376-62:TP53_chr17:g.7581327del Note: The TP53 rearrangement is a deletion of exons 1 - 4.
KIF5B	0	MSKCC-DMP	P-0048829-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+948:KIF5B_c.2136+432:RETinv The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET
RET	0	MSKCC-DMP	P-0048829-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+948:KIF5B_c.2136+432:RETinv The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET
NOTCH1	0	MSKCC-DMP	P-0048846-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: t(9;20)(q34.3;q13.12)(chr9:g.139405807::chr20:g.42802904) Note: The NOTCH1 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0048498-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon3 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190213 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0048498-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon3 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190213 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0048504-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ETV4 fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ETV4 Exon2 (NM_001986). Lab Notes Run Number: ArcherV3-CLIN-20190213 Macro-dissection: Performed
ETV4	0	MSKCC-DMP	P-0048504-T01-IM6	ETV4-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ETV4 fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ETV4 Exon2 (NM_001986). Lab Notes Run Number: ArcherV3-CLIN-20190213 Macro-dissection: Performed
TERT	0	MSKCC-DMP	P-0048802-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(5;18)(p15.33;q22.3)(chr5:g.1295313::chr18:g.71923116) Note: The TERT rearrangement is a translocation with a breakpoint in the promoter region. The functional significance is undetermined.
MDM4	0	MSKCC-DMP	P-0048806-T01-IM6	MDM4-intragenic	yes	unknown		unknown	MDM4 (NM_002393) rearrangement: c.512-105:MDM4_chr1:g.151223675inv Note: The MDM4 rearrangement is an inversion of exons 1 - 7. Functional significance is undetermined.
TNFRSF14	0	MSKCC-DMP	P-0048815-T01-IM6	TNFRSF14-intragenic	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: c.694+36:TNFRSF14_chr1:g.78601774del Note: The TNFRSF14 rearrangement is a deletion of exons 7 - 8.
ASB17	0	MSKCC-DMP	P-0048815-T01-IM6	FUBP1-ASB17 fusion	yes	unknown		unknown	ASB17 (NM_080868) - FUBP1 (NM_003902) rearrangement: c.682-1387:ASB17_c.100:FUBP1dup Note: The ASB17 - FUBP1 rearrangement is a duplication that results in a fusion of ASB17 exons 1 - 2 to FUBP1 exons 1 - 20. One of the breakpoints is within FUBP1 exon 1. Functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0048815-T01-IM6	FUBP1-ASB17 fusion	yes	unknown		unknown	ASB17 (NM_080868) - FUBP1 (NM_003902) rearrangement: c.682-1387:ASB17_c.100:FUBP1dup Note: The ASB17 - FUBP1 rearrangement is a duplication that results in a fusion of ASB17 exons 1 - 2 to FUBP1 exons 1 - 20. One of the breakpoints is within FUBP1 exon 1. Functional significance is undetermined.
THSD4	0	MSKCC-DMP	P-0048887-T01-IM6	VTCN1-THSD4 fusion	yes	unknown		unknown	THSD4 (NM_024817) - VTCN1 (NM_024626) rearrangement: t(1;15)(p13.1;q23)(chr1:g.117695948::chr15:g.72060483) Note: The THSD4 - VTCN1 rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 15 to VTCN1 exons 4 - 5. One of the breakpoints is within VTCN1 exon 4. Functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0048887-T01-IM6	VTCN1-THSD4 fusion	yes	unknown		unknown	THSD4 (NM_024817) - VTCN1 (NM_024626) rearrangement: t(1;15)(p13.1;q23)(chr1:g.117695948::chr15:g.72060483) Note: The THSD4 - VTCN1 rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 15 to VTCN1 exons 4 - 5. One of the breakpoints is within VTCN1 exon 4. Functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0048887-T01-IM6	CYP21A2-TAP2 fusion	yes	unknown		unknown	TAP2 (NM_018833) - CYP21A2 (NM_000500) rearrangement: c.283:TAP2_c.871:CYP21A2inv Note: The TAP2 - CYP21A2 rearrangement is an inversion that results in a fusion of TAP2 exons 1 - 2 to CYP21A2 exons 7 - 11. The breakpoints are within TAP2 exon 2 and CYP21A2 exon 7. Functional significance is undetermined.
CYP21A2	0	MSKCC-DMP	P-0048887-T01-IM6	CYP21A2-TAP2 fusion	yes	unknown		unknown	TAP2 (NM_018833) - CYP21A2 (NM_000500) rearrangement: c.283:TAP2_c.871:CYP21A2inv Note: The TAP2 - CYP21A2 rearrangement is an inversion that results in a fusion of TAP2 exons 1 - 2 to CYP21A2 exons 7 - 11. The breakpoints are within TAP2 exon 2 and CYP21A2 exon 7. Functional significance is undetermined.
SPTBN1	0	MSKCC-DMP	P-0048893-T01-IM6	ALK-SPTBN1 fusion	yes	unknown		unknown	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.763+1517:SPTBN1_c.3153:ALKinv Note: The SPTBN1 - ALK fusion involves SPTBN1 exons 1 - 7 and ALK exons 19 - 29. One of the breakpoints is within ALK exon 19. The fusion includes the kinase domain of ALK. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ALK	0	MSKCC-DMP	P-0048893-T01-IM6	ALK-SPTBN1 fusion	yes	unknown		unknown	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.763+1517:SPTBN1_c.3153:ALKinv Note: The SPTBN1 - ALK fusion involves SPTBN1 exons 1 - 7 and ALK exons 19 - 29. One of the breakpoints is within ALK exon 19. The fusion includes the kinase domain of ALK. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PAK7	0	MSKCC-DMP	P-0048898-T01-IM6	RB1-PAK7 fusion	yes	unknown		unknown	PAK7 (NM_177990) - RB1 (NM_000321) rearrangement: t(13;20)(q14.2;p12.2)(chr13:g.48909327::chr20:g.9525034) Note: The PAK7 - RB1 rearrangement is a translocation with breakpoints in PAK7 exon 8 and RB1 intron 2. Functional significance is undetermined. In addition, there is an RB1 intragenic loss. A more complex event involving RB1 is possible.
RB1	0	MSKCC-DMP	P-0048898-T01-IM6	RB1-PAK7 fusion	yes	unknown		unknown	PAK7 (NM_177990) - RB1 (NM_000321) rearrangement: t(13;20)(q14.2;p12.2)(chr13:g.48909327::chr20:g.9525034) Note: The PAK7 - RB1 rearrangement is a translocation with breakpoints in PAK7 exon 8 and RB1 intron 2. Functional significance is undetermined. In addition, there is an RB1 intragenic loss. A more complex event involving RB1 is possible.
CD74	0	MSKCC-DMP	P-0041118-T03-IM6	ROS1-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782265::chr6:g.117647424) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 7 and ROS1 exons 33 - 43. One of the breakpoints is within ROS1 exon 33. The fusion includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0041118-T03-IM6	ROS1-CD74 fusion	yes	unknown		unknown	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782265::chr6:g.117647424) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 7 and ROS1 exons 33 - 43. One of the breakpoints is within ROS1 exon 33. The fusion includes the kinase domain of ROS1.
ERBB3	0	MSKCC-DMP	P-0048904-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(12;18)(q13.2;q21.32)(chr12:g.56493685::chr18:g.57428632) Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.
CCNE1	0	MSKCC-DMP	P-0048904-T01-IM6	CCNE1-intragenic	yes	unknown		unknown	CCNE1 (NM_001238) rearrangement: c.638:CCNE1_chr19:g.42157013del Note: The CCNE1 rearrangement is a deletion of exons 8 - 12. One of the breakpoints is within exon 8. Functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0048904-T01-IM6	EPN1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - EPN1 (NM_001130071) rearrangement: c.704:AXL_c.1300:EPN1del Note: The AXL - EPN1 rearrangement is a deletion that results in a fusion of AXL exons 1 - 6 to EPN1 exons 7 - 11. The breakpoints are within AXL exon 6 and EPN1 exon 7. The fusion does not include the kinase domain of AXL. Functional significance is undetermined. Multiple rearrangements involving AXL were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
EPN1	0	MSKCC-DMP	P-0048904-T01-IM6	EPN1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - EPN1 (NM_001130071) rearrangement: c.704:AXL_c.1300:EPN1del Note: The AXL - EPN1 rearrangement is a deletion that results in a fusion of AXL exons 1 - 6 to EPN1 exons 7 - 11. The breakpoints are within AXL exon 6 and EPN1 exon 7. The fusion does not include the kinase domain of AXL. Functional significance is undetermined. Multiple rearrangements involving AXL were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PDGFRA	0	MSKCC-DMP	P-0048904-T01-IM6	PDGFRA-intragenic	yes	unknown		unknown	PDGFRA (NM_006206) rearrangement: c.1365:PDGFRA_chr4:g.33633229del Note: The PDGFRA rearrangement is a deletion of exons 1 - 10. One of the breakpoints is within exon 10. The rearrangement does not include the kinase domain of PDGFRA. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving PDGFRA is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PTPRS	0	MSKCC-DMP	P-0048909-T01-IM6	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: c.4620:PTPRS_chr19:g.5295751del Note: The PTPRS rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31.
PIK3R1	0	MSKCC-DMP	P-0048923-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.2118:PIK3R1_chr5:g.83476610del Note: The PIK3R1 rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16.
KIF5B	0	MSKCC-DMP	P-0048968-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+211:KIF5B_c.2137-223:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 16 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0048968-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+211:KIF5B_c.2137-223:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 16 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
TET1	0	MSKCC-DMP	P-0048977-T01-IM6	SUPV3L1-TET1 fusion	yes	unknown		in frame	TET1 (NM_030625) - SUPV3L1 (NM_003171) rearrangement: c.4914+152:TET1_c.1518+735:SUPV3L1del Note: The TET1 - SUPV3L1 rearrangement is a deletion that results in a fusion of TET1 exons 1 - 9 to SUPV3L1 exons 13 - 15. The fusion is predicted to be in frame.
SUPV3L1	0	MSKCC-DMP	P-0048977-T01-IM6	SUPV3L1-TET1 fusion	yes	unknown		in frame	TET1 (NM_030625) - SUPV3L1 (NM_003171) rearrangement: c.4914+152:TET1_c.1518+735:SUPV3L1del Note: The TET1 - SUPV3L1 rearrangement is a deletion that results in a fusion of TET1 exons 1 - 9 to SUPV3L1 exons 13 - 15. The fusion is predicted to be in frame.
AR	0	MSKCC-DMP	P-0010077-T02-IM6	AR-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:  AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20190215 Macro-dissection: Not Performed
PREX2	0	MSKCC-DMP	P-0030266-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.706-33:PREX2_chr8:g.68615664del Note: The PREX2 rearrangement is a deletion of exons 1 - 6. Functional significance is undetermined.
CUL5	0	MSKCC-DMP	P-0048920-T01-IM6	ATM-CUL5 fusion	yes	unknown		out of frame	CUL5 (NM_003478) - ATM (NM_000051) rearrangement: c.780+381:CUL5_c.6096-43:ATMdel Note: The CUL5 - ATM rearrangement is a deletion that results in a fusion of CUL5 exons 1 - 7 to ATM exons 42 - 63.
ATM	0	MSKCC-DMP	P-0048920-T01-IM6	ATM-CUL5 fusion	yes	unknown		out of frame	CUL5 (NM_003478) - ATM (NM_000051) rearrangement: c.780+381:CUL5_c.6096-43:ATMdel Note: The CUL5 - ATM rearrangement is a deletion that results in a fusion of CUL5 exons 1 - 7 to ATM exons 42 - 63.
RASA1	0	MSKCC-DMP	P-0048925-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.2345-27:RASA1_chr5:g.86547885del Note: The RASA1 rearrangement is a deletion of exons 1 - 17.
SMARCD1	0	MSKCC-DMP	P-0048936-T01-IM6	SMARCD1-intragenic	yes	unknown		unknown	SMARCD1 (NM_003076) rearrangement: t(6;12)(q21;q13.12)(chr6:g.106876550::chr12:g.50484218) Note: The SMARCD1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
ALG14	0	MSKCC-DMP	P-0048936-T01-IM6	RB1-ALG14 fusion	yes	unknown		out of frame	ALG14 (NM_144988) - RB1 (NM_000321) rearrangement: t(1;13)(p21.3;q14.2)(chr1:g.95496402::chr13:g.49051408) Note: The ALG14 - RB1 rearrangement is a translocation that results in a fusion of ALG14 exons 1 - 2 to RB1 exons 26 - 27. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0048936-T01-IM6	RB1-ALG14 fusion	yes	unknown		out of frame	ALG14 (NM_144988) - RB1 (NM_000321) rearrangement: t(1;13)(p21.3;q14.2)(chr1:g.95496402::chr13:g.49051408) Note: The ALG14 - RB1 rearrangement is a translocation that results in a fusion of ALG14 exons 1 - 2 to RB1 exons 26 - 27. Functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0048936-T01-IM6	KPNA3-ERBB3 fusion	yes	unknown		out of frame	ERBB3 (NM_001982) - KPNA3 (NM_002267) rearrangement: t(12;13)(q13.2;q14.2)(chr12:g.56489142::chr13:g.50346188) Note: The ERBB3 - KPNA3 rearrangement is a translocation that results in a fusion of ERBB3 exons 1 - 16 to KPNA3 exons 2 - 17. The fusion does not include the kinase domain of ERBB3. Functional significance is undetermined.
KPNA3	0	MSKCC-DMP	P-0048936-T01-IM6	KPNA3-ERBB3 fusion	yes	unknown		out of frame	ERBB3 (NM_001982) - KPNA3 (NM_002267) rearrangement: t(12;13)(q13.2;q14.2)(chr12:g.56489142::chr13:g.50346188) Note: The ERBB3 - KPNA3 rearrangement is a translocation that results in a fusion of ERBB3 exons 1 - 16 to KPNA3 exons 2 - 17. The fusion does not include the kinase domain of ERBB3. Functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0048936-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: t(1;6)(p22.1;q22.1)(chr1:g.93761577::chr6:g.117646467) Note: The ROS1 rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.
LMOD1	0	MSKCC-DMP	P-0048936-T01-IM6	IFNGR1-LMOD1 fusion	yes	unknown		unknown	LMOD1 (NM_012134) - IFNGR1 (NM_000416) rearrangement: t(1;6)(q32.1;q23.3)(chr1:g.201913481::chr6:g.137519310) Note: The LMOD1 - IFNGR1 rearrangement is a translocation that results in a fusion of LMOD1 exon 1 to IFNGR1 exon 7. One of the breakpoints is within IFNGR1 exon 7. Functional significance is undetermined.
IFNGR1	0	MSKCC-DMP	P-0048936-T01-IM6	IFNGR1-LMOD1 fusion	yes	unknown		unknown	LMOD1 (NM_012134) - IFNGR1 (NM_000416) rearrangement: t(1;6)(q32.1;q23.3)(chr1:g.201913481::chr6:g.137519310) Note: The LMOD1 - IFNGR1 rearrangement is a translocation that results in a fusion of LMOD1 exon 1 to IFNGR1 exon 7. One of the breakpoints is within IFNGR1 exon 7. Functional significance is undetermined.
SND1	0	MSKCC-DMP	P-0048950-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+30037:SND1_c.1140+2075:BRAFinv Note: The SND1 - BRAF fusion involves SND1 exons 1 - 10 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. This sample has been nominated for further analysis using the Archer targeted RNAseq assay, which will be performed if additional material is available. Results will be reported under a separate accession number.
BRAF	0	MSKCC-DMP	P-0048950-T01-IM6	BRAF-SND1 fusion	yes	unknown		in frame	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+30037:SND1_c.1140+2075:BRAFinv Note: The SND1 - BRAF fusion involves SND1 exons 1 - 10 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. This sample has been nominated for further analysis using the Archer targeted RNAseq assay, which will be performed if additional material is available. Results will be reported under a separate accession number.
TOP1	0	MSKCC-DMP	P-0048954-T01-IM6	TOP1-intragenic	yes	unknown		out of frame	TOP1 (NM_003286) rearrangement: c.335+156_c.1951-1168del Note: The TOP1 rearrangement is an intragenic deletion of exons 6 - 18.
TMPRSS2	0	MSKCC-DMP	P-0048955-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1067:TMPRSS2_c.237-4991:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 3 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0048955-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1067:TMPRSS2_c.237-4991:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 3 - 10. Functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0048958-T01-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) rearrangement: c.172-16_c.412+24205dup Note: The PARK2 rearrangement is an intragenic duplication of exon 3. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0048980-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41631175::chr21:g.42868674) Note: The TMPRSS2 rearrangement involves intron 2.
NF1	0	MSKCC-DMP	P-0048996-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2409+635_c.2664inv Note: The NF1 rearrangement is an intragenic inversion of exon 21. One of the breakpoints is within exon 21. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0048998-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2754:TMPRSS2_c.19-3127:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0048998-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2754:TMPRSS2_c.19-3127:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.
EP300	0	MSKCC-DMP	P-0049127-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.6587:EP300_chr22:g.41577834dup Note: The EP300 rearrangement is a duplication of exon 31. One of the breakpoints is within exon 31. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0049006-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.3837+208_c.5400del Note: The NOTCH3 rearrangement is an intragenic deletion of exons 24 - 30. One of the breakpoints is within exon 30.
SOS1	0	MSKCC-DMP	P-0049006-T01-IM6	FBXO11-SOS1 fusion	yes	unknown		out of frame	SOS1 (NM_005633) - FBXO11 (NM_001190274) rearrangement: c.1074+104:SOS1_c.2006+820:FBXO11dup Note: The SOS1 - FBXO11 rearrangement is a duplication that results in a fusion of SOS1 exons 1 - 8 to FBXO11 exons 17 - 23. Functional significance is undetermined.
FBXO11	0	MSKCC-DMP	P-0049006-T01-IM6	FBXO11-SOS1 fusion	yes	unknown		out of frame	SOS1 (NM_005633) - FBXO11 (NM_001190274) rearrangement: c.1074+104:SOS1_c.2006+820:FBXO11dup Note: The SOS1 - FBXO11 rearrangement is a duplication that results in a fusion of SOS1 exons 1 - 8 to FBXO11 exons 17 - 23. Functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0049006-T01-IM6	RASA1-intragenic	yes	unknown		out of frame	RASA1 (NM_002890) rearrangement: c.2604-73_c.3061-69del Note: The RASA1 rearrangement is an intragenic deletion of exons 20 - 24.
EFTUD1	0	MSKCC-DMP	P-0048936-T01-IM6	ERBB4-EFTUD1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EFTUD1-ERBB4 fusion. Note: The rearrangement is an in-frame fusion between genes EFTUD1 Exon2 (NM_024580) and ERBB4 Exon2 (NM_005235). Note: Clinical significance is undetermined.  Lab Notes Run Number: ArcherV3-CLIN-20190220 Macro-dissection: Unknown
ERBB4	0	MSKCC-DMP	P-0048936-T01-IM6	ERBB4-EFTUD1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EFTUD1-ERBB4 fusion. Note: The rearrangement is an in-frame fusion between genes EFTUD1 Exon2 (NM_024580) and ERBB4 Exon2 (NM_005235). Note: Clinical significance is undetermined.  Lab Notes Run Number: ArcherV3-CLIN-20190220 Macro-dissection: Unknown
FOXP1	0	MSKCC-DMP	P-0048994-T01-IM6	RAF1-FOXP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FOXP1-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes FOXP1 Exon11 (NM_001244813) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20190221 Macro-dissection: Unknown
RAF1	0	MSKCC-DMP	P-0048994-T01-IM6	RAF1-FOXP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FOXP1-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes FOXP1 Exon11 (NM_001244813) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20190221 Macro-dissection: Unknown
TCF3	0	MSKCC-DMP	P-0024088-T02-IM6	TCF3-intragenic	yes	unknown		unknown	TCF3 (NM_001136139) rearrangement: c.1586+307:TCF3_chr19:g.1918294dup Note: The TCF3 rearrangement is a duplication of exons 1 - 16. Functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0024088-T02-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.4585_c.5134+1603inv Note: The ATRX rearrangement is an intragenic inversion of exons 16 - 19. One of the breakpoints is within exon 16. Functional significance is undetermined.
RCN1	0	MSKCC-DMP	P-0046175-T02-IM6	TMPRSS2-RCN1 fusion	yes	unknown		out of frame	RCN1 (NM_002901) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p13;q22.3)(chr11:g.32114150::chr21:g.42875275) Note: The RCN1 - TMPRSS2 rearrangement is a translocation that results in a fusion of RCN1 exon 1 to TMPRSS2 exons 2 - 14. Functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0046175-T02-IM6	TMPRSS2-RCN1 fusion	yes	unknown		out of frame	RCN1 (NM_002901) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p13;q22.3)(chr11:g.32114150::chr21:g.42875275) Note: The RCN1 - TMPRSS2 rearrangement is a translocation that results in a fusion of RCN1 exon 1 to TMPRSS2 exons 2 - 14. Functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
FAT1	0	MSKCC-DMP	P-0046175-T02-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.112:FAT1_chr4:g.188179915inv Note: The FAT1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
AR	0	MSKCC-DMP	P-0046175-T02-IM6	CAGE1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: t(6;X)(p24.3;q12)(chr6:g.7324070::chrX:g.66931498) Note: The AR rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
CAGE1	0	MSKCC-DMP	P-0046175-T02-IM6	CAGE1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: t(6;X)(p24.3;q12)(chr6:g.7324070::chrX:g.66931498) Note: The AR rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0047840-T02-IM6	ROS1-SDC4 fusion	yes	unknown		unknown	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117645871::chr20:g.43955947) Note: The SDC4 - ROS1 fusion involves SDC4 exons 1 - 5 and ROS1 exons 34 - 43. One of the breakpoints is within SDC4 exon 5. The fusion includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0047840-T02-IM6	ROS1-SDC4 fusion	yes	unknown		unknown	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117645871::chr20:g.43955947) Note: The SDC4 - ROS1 fusion involves SDC4 exons 1 - 5 and ROS1 exons 34 - 43. One of the breakpoints is within SDC4 exon 5. The fusion includes the kinase domain of ROS1.
EP300	0	MSKCC-DMP	P-0048861-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.938_c.1529-1999del Note: The EP300 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 4.
RELA	0	MSKCC-DMP	P-0049029-T01-IM6	RELA-intragenic	yes	unknown		unknown	RELA (NM_021975) rearrangement: t(7;11)(q21.11;q13.1)(chr7:g.79622169::chr11:g.65429657) Note: The RELA rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0049048-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.122+101_c.627del Note: The BAP1 rearrangement is an intragenic deletion of exons 4 - 8. One of the breakpoints is within exon 8.
TBX3	0	MSKCC-DMP	P-0049057-T01-IM6	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.1771-85:TBX3_chr12:g.55866104inv Note: The TBX3 rearrangement is an inversion of exon 8. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0049061-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.6771:KMT2D_chr12:g.49468612del Note: The KMT2D rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31.
TMPRSS2	0	MSKCC-DMP	P-0049068-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-736:TMPRSS2_c.18+1656:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0049068-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-736:TMPRSS2_c.18+1656:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0049068-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.850-15790_c.7779dup Note: The KMT2C rearrangement is an intragenic duplication of exons 7 - 38. One of the breakpoints is within exon 38. Functional significance is undetermined.
SPOP	0	MSKCC-DMP	P-0049087-T01-IM6	SPOP-intragenic	yes	unknown		unknown	SPOP (NM_001007228) rearrangement: c.837+52:SPOP_chr17:g.49150995inv Note: The SPOP rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0049091-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.457_c.458del Note: The CDKN2A rearrangement is an intragenic deletion of exons 2-3. This variant affects CDKN2Ap16INK4A (NM_000077) isoform and may also affect CDKN2Ap14ARF (NM_058195) isoform.
PTP4A1	0	MSKCC-DMP	P-0049200-T01-IM6	PTP4A1-intragenic	yes	unknown		unknown	PTP4A1 (NM_003463) rearrangement: t(1;6)(q25.2;q12)(chr1:g.176585817::chr6:g.64286894) Note: The PTP4A1 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined. Multiple rearrangements involving PTP4A1 were detected in this sample and a more complex rearrangement resulting in a PTP4A1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PLCG2	0	MSKCC-DMP	P-0049247-T01-IM6	AP1G1-PLCG2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) - AP1G1 (NM_001128) rearrangement: c.1257:PLCG2_c.202-1294:AP1G1inv Note: The PLCG2 - AP1G1 rearrangement is an inversion that results in a fusion of PLCG2 exons 1 - 14 to AP1G1 exons 3 - 23. One of the breakpoints is within PLCG2 exon 14. Functional significance is undetermined.
AP1G1	0	MSKCC-DMP	P-0049247-T01-IM6	AP1G1-PLCG2 fusion	yes	unknown		unknown	PLCG2 (NM_002661) - AP1G1 (NM_001128) rearrangement: c.1257:PLCG2_c.202-1294:AP1G1inv Note: The PLCG2 - AP1G1 rearrangement is an inversion that results in a fusion of PLCG2 exons 1 - 14 to AP1G1 exons 3 - 23. One of the breakpoints is within PLCG2 exon 14. Functional significance is undetermined.
MLH1	0	MSKCC-DMP	P-0049247-T01-IM6	MLH1-intragenic	yes	unknown		unknown	MLH1 (NM_000249) rearrangement: c.206_c.208-1del Note: The MLH1 rearrangement is an intragenic deletion of exons 2 - 3. The breakpoints are within exon 2 and exon 3.
ZCCHC14	0	MSKCC-DMP	P-0049248-T01-IM6	FANCA-ZCCHC14 fusion	yes	unknown		out of frame	ZCCHC14 (NM_015144) - FANCA (NM_000135) rearrangement: c.429+45:ZCCHC14_c.3935-98:FANCAdup Note: The ZCCHC14 - FANCA rearrangement is a duplication that results in a fusion of ZCCHC14 exons 1 - 4 to FANCA exons 40 - 43. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0049248-T01-IM6	FANCA-ZCCHC14 fusion	yes	unknown		out of frame	ZCCHC14 (NM_015144) - FANCA (NM_000135) rearrangement: c.429+45:ZCCHC14_c.3935-98:FANCAdup Note: The ZCCHC14 - FANCA rearrangement is a duplication that results in a fusion of ZCCHC14 exons 1 - 4 to FANCA exons 40 - 43. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0049248-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.2176:BAP1_chr3:g.52719537dup Note: The BAP1 rearrangement is a duplication of exons 1 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0049262-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.4203:NCOA3_chr20:g.46285828del Note: The NCOA3 rearrangement is a deletion of exons 22 - 23. One of the breakpoints is within exon 22. Functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0049263-T01-IM6	ARID2-intragenic	yes	unknown		unknown	ARID2 (NM_152641) rearrangement: c.5147+98:ARID2_chr12:g.64444814inv Note: The ARID2 rearrangement is an inversion of exons 19 - 21. Functional significance is undetermined.
TAF4	0	MSKCC-DMP	P-0049269-T01-IM6	RTEL1-TAF4 fusion	yes	unknown		unknown	TAF4 (NM_003185) - RTEL1 (NM_032957) rearrangement: c.1360+15853:TAF4_c.1980:RTEL1inv Note: The TAF4 - RTEL1 rearrangement is an inversion that results in a fusion of TAF4 exon 1 to RTEL1 exons 23 - 35. One of the breakpoints is within RTEL1 exon 23. Functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0049269-T01-IM6	RTEL1-TAF4 fusion	yes	unknown		unknown	TAF4 (NM_003185) - RTEL1 (NM_032957) rearrangement: c.1360+15853:TAF4_c.1980:RTEL1inv Note: The TAF4 - RTEL1 rearrangement is an inversion that results in a fusion of TAF4 exon 1 to RTEL1 exons 23 - 35. One of the breakpoints is within RTEL1 exon 23. Functional significance is undetermined.
IRF4	0	MSKCC-DMP	P-0049270-T01-IM6	IFNGR1-IRF4 fusion	yes	unknown		unknown	IRF4 (NM_002460) - IFNGR1 (NM_000416) rearrangement: c.144:IRF4_c.862-1030:IFNGR1del Note: The IRF4 - IFNGR1 rearrangement is a deletion of IRF4 exons 2 - 9 and IFNGR1 exon 7. One of the breakpoints is within IRF4 exon 2. Functional significance is undetermined.
IFNGR1	0	MSKCC-DMP	P-0049270-T01-IM6	IFNGR1-IRF4 fusion	yes	unknown		unknown	IRF4 (NM_002460) - IFNGR1 (NM_000416) rearrangement: c.144:IRF4_c.862-1030:IFNGR1del Note: The IRF4 - IFNGR1 rearrangement is a deletion of IRF4 exons 2 - 9 and IFNGR1 exon 7. One of the breakpoints is within IRF4 exon 2. Functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0049337-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: c.614-7:ERBB3_chr12:g.69067301del Note: The ERBB3 rearrangement is a deletion of exons 6 - 28. The rearrangement includes the kinase domain of ERBB3. Functional significance is undetermined.
PIP5K1A	0	MSKCC-DMP	P-0049346-T01-IM6	PIK3CD-PIP5K1A fusion	yes	unknown		out of frame	PIP5K1A (NM_001135638) - PIK3CD (NM_005026) rearrangement: c.157-70:PIP5K1A_c.2865-64:PIK3CDdup Note: The PIP5K1A - PIK3CD rearrangement is a duplication that results in a fusion of PIP5K1A exons 1 - 2 to PIK3CD exons 23 - 24. Functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0049346-T01-IM6	PIK3CD-PIP5K1A fusion	yes	unknown		out of frame	PIP5K1A (NM_001135638) - PIK3CD (NM_005026) rearrangement: c.157-70:PIP5K1A_c.2865-64:PIK3CDdup Note: The PIP5K1A - PIK3CD rearrangement is a duplication that results in a fusion of PIP5K1A exons 1 - 2 to PIK3CD exons 23 - 24. Functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0049346-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: t(14;20)(q11.2;q11.21)(chr14:g.23983015::chr20:g.31384948) Note: The DNMT3B rearrangement is a translocation with a breakpoint in intron 13. Functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0049346-T01-IM6	ASXL1-intragenic	yes	unknown		out of frame	ASXL1 (NM_015338) rearrangement: c.253-11072_c.719-260del Note: The ASXL1 rearrangement is an intragenic deletion of exons 4 - 7.
ATR	0	MSKCC-DMP	P-0049348-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.3435:ATR_chr3:g.71998222del Note: The ATR rearrangement is a deletion of exons 17 - 47. One of the breakpoints is within exon 17.
TGFBR2	0	MSKCC-DMP	P-0049436-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.95-3598_c.1591del Note: The TGFBR2 rearrangement is an intragenic deletion of exons 2 - 7. One of the breakpoints is within exon 7. The rearrangement includes a part of the kinase domain of TGFBR2.
KLK3	0	MSKCC-DMP	P-0049439-T01-IM6	TMPRSS2-KLK3 fusion	yes	unknown		unknown	KLK3 (NM_001648) - TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.33;q22.3)(chr19:g.51359165::chr21:g.42843855) Note: The KLK3 - TMPRSS2 rearrangement is a translocation that results in a fusion of KLK3 exon 1 to TMPRSS2 exons 10 - 14. One of the breakpoints is within TMPRSS2 exon 10. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049439-T01-IM6	TMPRSS2-KLK3 fusion	yes	unknown		unknown	KLK3 (NM_001648) - TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.33;q22.3)(chr19:g.51359165::chr21:g.42843855) Note: The KLK3 - TMPRSS2 rearrangement is a translocation that results in a fusion of KLK3 exon 1 to TMPRSS2 exons 10 - 14. One of the breakpoints is within TMPRSS2 exon 10. Functional significance is undetermined.
RAD51B	0	MSKCC-DMP	P-0049457-T01-IM6	RAD51B-intragenic	yes	unknown		unknown	RAD51B (NM_133509) rearrangement: c.497_c.756+4846del Note: The RAD51B rearrangement is an intragenic deletion of exons 6 - 7. One of the breakpoints is within exon 6.
TP53	0	MSKCC-DMP	P-0049457-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.75-16:TP53_chr17:g.7549007del Note: The TP53 rearrangement is a deletion of exons 3 - 11.
ZFHX3	0	MSKCC-DMP	P-0047538-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.2465_c.3216+13961del Note: The ZFHX3 rearrangement is an intragenic deletion of exons 2 - 3. One of the breakpoints is within exon 2.
FGFR2	0	MSKCC-DMP	P-0049292-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.110-136:FGFR2_chr10:g.122834769inv The FGFR2 rearrangement is an inversion of exons 3 - 18. The rearrangement includes the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CARM1	0	MSKCC-DMP	P-0049292-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) - SMARCA4 (NM_003072) rearrangement: c.346+1276:CARM1_c.4171-2015:SMARCA4inv The CARM1 - SMARCA4 rearrangement is an inversion of CARM1 exons 3 - 16 and SMARCA4 exons 1 - 29. Functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0049292-T01-IM6	SMARCA4-CARM1 fusion	yes	unknown		unknown	CARM1 (NM_199141) - SMARCA4 (NM_003072) rearrangement: c.346+1276:CARM1_c.4171-2015:SMARCA4inv The CARM1 - SMARCA4 rearrangement is an inversion of CARM1 exons 3 - 16 and SMARCA4 exons 1 - 29. Functional significance is undetermined.
INPPL1	0	MSKCC-DMP	P-0049438-T01-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: c.3553-113:INPPL1_chr11:g.71956569del Note: The INPPL1 rearrangement is a deletion of exons 27 - 28.
TMPRSS2	0	MSKCC-DMP	P-0049438-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(3;21)(q27.2;q22.3)(chr3:g.185825058::chr21:g.42861570) Note: The TMPRSS2 rearrangement is a translocation which involves intron 3.Functional significance is undetermined.
SDC4	0	MSKCC-DMP	P-0048167-T02-IM6	ROS1-SDC4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SDC4-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SDC4 Exon2 (NM_002999) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0048167-T02-IM6	ROS1-SDC4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SDC4-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes SDC4 Exon2 (NM_002999) and ROS1 Exon32 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
PRKAR2A	0	MSKCC-DMP	P-0048864-T01-IM6	RAF1-PRKAR2A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PRKAR2A-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes PRKAR2A Exon4 (NM_004157) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
RAF1	0	MSKCC-DMP	P-0048864-T01-IM6	RAF1-PRKAR2A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PRKAR2A-RAF1 fusion. Note: The rearrangement is an in-frame fusion between genes PRKAR2A Exon4 (NM_004157) and RAF1 Exon8 (NM_002880). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
NOTCH2	0	MSKCC-DMP	P-0049355-T01-IM6	NOTCH2-intragenic	yes	unknown		in frame	NOTCH2 (NM_024408) rearrangement: c.1453+42:NOTCH2_chr1:g.144545453inv Note: The NOTCH2 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
H3F3B	0	MSKCC-DMP	P-0049355-T01-IM6	UNK-H3F3B fusion	yes	unknown		unknown	H3F3B (NM_005324) - UNK (NM_001080419) rearrangement: c.326:H3F3B_c.105-8656:UNKinv Note: The H3F3B - UNK rearrangement is an inversion that results in a fusion of H3F3B exons 1 - 4 to UNK exons 2 - 16. One of the breakpoints is within H3F3B exon 4. Functional significance is undetermined.
UNK	0	MSKCC-DMP	P-0049355-T01-IM6	UNK-H3F3B fusion	yes	unknown		unknown	H3F3B (NM_005324) - UNK (NM_001080419) rearrangement: c.326:H3F3B_c.105-8656:UNKinv Note: The H3F3B - UNK rearrangement is an inversion that results in a fusion of H3F3B exons 1 - 4 to UNK exons 2 - 16. One of the breakpoints is within H3F3B exon 4. Functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0049366-T01-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.4041:NOTCH4_chr6:g.23089705inv Note: The NOTCH4 rearrangement is an inversion of exons 22 - 30. One of the breakpoints is within exon 22. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0049375-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1166:EML4_c.3173-338:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0049375-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1166:EML4_c.3173-338:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
KDM6A	0	MSKCC-DMP	P-0049381-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: t(2;X)(q24.2;p11.3)(chr2:g.163611887::chrX:g.44918272) Note: The KDM6A rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0049383-T01-IM6	DIAPH3-RB1 fusion	yes	unknown		out of frame	RB1 (NM_000321) - DIAPH3 (NM_001042517) rearrangement: c.2489+7:RB1_c.2608-5833:DIAPH3inv Note: The RB1 - DIAPH3 rearrangement is an inversion that results in a fusion of RB1 exons 1 - 23 to DIAPH3 exons 21 - 28. Functional significance is undetermined.
DIAPH3	0	MSKCC-DMP	P-0049383-T01-IM6	DIAPH3-RB1 fusion	yes	unknown		out of frame	RB1 (NM_000321) - DIAPH3 (NM_001042517) rearrangement: c.2489+7:RB1_c.2608-5833:DIAPH3inv Note: The RB1 - DIAPH3 rearrangement is an inversion that results in a fusion of RB1 exons 1 - 23 to DIAPH3 exons 21 - 28. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0049385-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.3951_c.4261-20del Note: The FANCA rearrangement is an intragenic deletion of exons 40 - 42. One of the breakpoints is within exon 40.
RAD50	0	MSKCC-DMP	P-0049385-T01-IM6	RAD50-intragenic	yes	unknown		unknown	RAD50 (NM_005732) rearrangement: c.3478_c.3924inv Note: The RAD50 rearrangement is an intragenic inversion of exons 23 - 25. The breakpoints are within exon 23 and exon 25. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0049407-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: t(10;17)(q23.31;q21.33)(chr10:g.89711879::chr17:g.49865374) Note: The PTEN rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined. Multiple other structural variants involving PTEN were detected, which may reflect a complex rearrangement involving PTEN that is not fully characterized by IMPACT.
TMPRSS2	0	MSKCC-DMP	P-0049411-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1217:TMPRSS2_c.18+11245:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0049411-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1217:TMPRSS2_c.18+11245:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
TFG	0	MSKCC-DMP	P-0049192-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). This has been described as a polymorphic fusion seen in up to 2% of healthy population. However, functional studies on this fusion are limited. PMID: 19797732   Lab Notes Run Number: ArcherV3-CLIN-20190224 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0049192-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). This has been described as a polymorphic fusion seen in up to 2% of healthy population. However, functional studies on this fusion are limited. PMID: 19797732   Lab Notes Run Number: ArcherV3-CLIN-20190224 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0049196-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon8 (NM_001130173) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV3-CLIN-20190225 Macro-dissection: Performed
NFIB	0	MSKCC-DMP	P-0049196-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is an in-frame fusion between genes MYB Exon8 (NM_001130173) and NFIB Exon10 (NM_001282787). Lab Notes Run Number: ArcherV3-CLIN-20190225 Macro-dissection: Performed
WNT2	0	MSKCC-DMP	P-0012098-T06-IM6	CARD11-WNT2 fusion	yes	unknown		out of frame	WNT2 (NM_003391) - CARD11 (NM_032415) rearrangement: c.84-902:WNT2_c.2608-24:CARD11del Note: The WNT2 - CARD11 rearrangement is a deletion that results in a fusion of WNT2 exon 1 to CARD11 exons 20 - 25. Functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0012098-T06-IM6	CARD11-WNT2 fusion	yes	unknown		out of frame	WNT2 (NM_003391) - CARD11 (NM_032415) rearrangement: c.84-902:WNT2_c.2608-24:CARD11del Note: The WNT2 - CARD11 rearrangement is a deletion that results in a fusion of WNT2 exon 1 to CARD11 exons 20 - 25. Functional significance is undetermined.
FUBP1	0	MSKCC-DMP	P-0049417-T01-IM6	FUBP1-intragenic	yes	unknown		unknown	FUBP1 (NM_003902) rearrangement: c.459_c.1576+1058del Note: The FUBP1 rearrangement is an intragenic deletion of exons 7 - 16. One of the breakpoints is within exon 7.
ALS2CR12	0	MSKCC-DMP	P-0049427-T01-IM6	CASP8-ALS2CR12 fusion	yes	unknown		in frame	ALS2CR12 (NM_001127391) - CASP8 (NM_001080125) rearrangement: c.676-5456:ALS2CR12_c.589-79:CASP8inv Note: The ALS2CR12 - CASP8 rearrangement is an inversion that results in a fusion of ALS2CR12 exons 1 - 9 to CASP8 exons 4 - 9. The fusion is predicted to be in frame. Functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0049427-T01-IM6	CASP8-ALS2CR12 fusion	yes	unknown		in frame	ALS2CR12 (NM_001127391) - CASP8 (NM_001080125) rearrangement: c.676-5456:ALS2CR12_c.589-79:CASP8inv Note: The ALS2CR12 - CASP8 rearrangement is an inversion that results in a fusion of ALS2CR12 exons 1 - 9 to CASP8 exons 4 - 9. The fusion is predicted to be in frame. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049427-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3573:TMPRSS2_c.39+64657:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0049427-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3573:TMPRSS2_c.39+64657:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
JAK3	0	MSKCC-DMP	P-0049505-T01-IM6	JAK3-intragenic	yes	unknown		out of frame	JAK3 (NM_000215) rearrangement: c.1914+21_c.2351-26del Note: The JAK3 rearrangement is an intragenic deletion of exons 15 - 17. Functional significance is undetermined.
RUNX1	0	MSKCC-DMP	P-0049542-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.168_c.351+2077del Note: The RUNX1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.
ATRX	0	MSKCC-DMP	P-0049542-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.1733:ATRX_chrX:g.74625189inv Note: The ATRX rearrangement is an inversion of exons 9 - 35. One of the breakpoints is within exon 9. Functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0049543-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(14;20)(q22.1;q13.33)(chr14:g.51787212::chr20:g.62305625) Note: The RTEL1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
EPHA5	0	MSKCC-DMP	P-0049543-T01-IM6	EPHA5-intragenic	yes	unknown		unknown	EPHA5 (NM_004439) rearrangement: t(4;7)(q13.1;q34)(chr4:g.66217161::chr7:g.140209842) Note: The EPHA5 rearrangement is a translocation with a breakpoint in exon 14. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0048875-T03-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: c.2136:RET_chr10:g.56155858del Note: The RET rearrangement is a deletion of exons 11 - 20. One of the breakpoints is within exon 11. The rearrangement includes the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RICTOR	0	MSKCC-DMP	P-0048875-T03-IM6	FYB-RICTOR fusion	yes	unknown		in frame	RICTOR (NM_152756) - FYB (NM_001243093) rearrangement: c.97+4:RICTOR_c.1166-21065:FYBdup Note: The RICTOR - FYB rearrangement is a duplication that results in a fusion of RICTOR exons 1 - 2 to FYB exons 3 - 19. The fusion is predicted to be in frame. Functional significance is undetermined.
FYB	0	MSKCC-DMP	P-0048875-T03-IM6	FYB-RICTOR fusion	yes	unknown		in frame	RICTOR (NM_152756) - FYB (NM_001243093) rearrangement: c.97+4:RICTOR_c.1166-21065:FYBdup Note: The RICTOR - FYB rearrangement is a duplication that results in a fusion of RICTOR exons 1 - 2 to FYB exons 3 - 19. The fusion is predicted to be in frame. Functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0049483-T01-IM6	YAP1-intragenic	yes	unknown		unknown	YAP1 (NM_001130145) rearrangement: t(11;13)(q22.1;q21.33)(chr11:g.102098052::chr13:g.72715658) Note: The YAP1 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0049483-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.640:BRD4_chr19:g.15246720del Note: The BRD4 rearrangement is a deletion of exons 5 - 20. One of the breakpoints is within exon 5. Functional significance is undetermined.
TMPRSS9	0	MSKCC-DMP	P-0049516-T01-IM6	DOT1L-TMPRSS9 fusion	yes	unknown		in frame	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.412+824:TMPRSS9_c.4606+1197:DOT1Ldup Note: The TMPRSS9 - DOT1L rearrangement is a duplication that results in a fusion of TMPRSS9 exons 1 - 3 to DOT1L exon 28. The fusion is predicted to be in frame. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0049516-T01-IM6	DOT1L-TMPRSS9 fusion	yes	unknown		in frame	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.412+824:TMPRSS9_c.4606+1197:DOT1Ldup Note: The TMPRSS9 - DOT1L rearrangement is a duplication that results in a fusion of TMPRSS9 exons 1 - 3 to DOT1L exon 28. The fusion is predicted to be in frame. Functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0049516-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: t(18;X)(p11.31;q21.1)(chr18:g.5234240::chrX:g.76876077) Note: The ATRX rearrangement is a translocation with a breakpoint in intron 19. Functional significance is undetermined.
PPP2R1A	0	MSKCC-DMP	P-0049519-T01-IM6	PPP2R1A-intragenic	yes	unknown		unknown	PPP2R1A (NM_014225) rearrangement: t(8;19)(q23.2;q13.41)(chr8:g.110514912::chr19:g.52714414) Note: The PPP2R1A rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049520-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-4799:TMPRSS2_chr21:g.40822873inv Note: The TMPRSS2 rearrangement is an inversion of exons 2 - 14. Functional significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the canonical fusion not detected by the MSK-IMPACT panel cannot be ruled out
TP63	0	MSKCC-DMP	P-0049520-T01-IM6	TP63-intragenic	yes	unknown		unknown	TP63 (NM_003722) rearrangement: c.88:TP63_chr3:g.190865940del Note: The TP63 rearrangement is a deletion of exons 2 - 14. One of the breakpoints is within exon 2.
DNMT3A	0	MSKCC-DMP	P-0049560-T01-IM6	DTNB-DNMT3A fusion	yes	unknown		unknown	DNMT3A (NM_022552) - DTNB (NM_021907) rearrangement: c.1880:DNMT3A_c.1554+3558:DTNBdup Note: The DNMT3A - DTNB rearrangement is a duplication that results in a fusion of DNMT3A exons 1 - 16 to DTNB exons 15 - 20. One of the breakpoints is within DNMT3A exon 16. Functional significance is undetermined.
DTNB	0	MSKCC-DMP	P-0049560-T01-IM6	DTNB-DNMT3A fusion	yes	unknown		unknown	DNMT3A (NM_022552) - DTNB (NM_021907) rearrangement: c.1880:DNMT3A_c.1554+3558:DTNBdup Note: The DNMT3A - DTNB rearrangement is a duplication that results in a fusion of DNMT3A exons 1 - 16 to DTNB exons 15 - 20. One of the breakpoints is within DNMT3A exon 16. Functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0049560-T01-IM6	PTPRD-intragenic	yes	unknown		out of frame	PTPRD (NM_002839) rearrangement: c.961+360_c.5126+181dup Note: The PTPRD rearrangement is an intragenic duplication of exons 21 - 41. Functional significance is undetermined.
ARHGAP40	0	MSKCC-DMP	P-0018669-T02-IM6	TOP1-ARHGAP40 fusion	yes	unknown		out of frame	ARHGAP40 (NM_001164431) - TOP1 (NM_003286) rearrangement: c.338-1687:ARHGAP40_c.432-137:TOP1del Note: The ARHGAP40 - TOP1 rearrangement is a deletion that results in a fusion of ARHGAP40 exons 1 - 2 to TOP1 exons 7 - 21.
TOP1	0	MSKCC-DMP	P-0018669-T02-IM6	TOP1-ARHGAP40 fusion	yes	unknown		out of frame	ARHGAP40 (NM_001164431) - TOP1 (NM_003286) rearrangement: c.338-1687:ARHGAP40_c.432-137:TOP1del Note: The ARHGAP40 - TOP1 rearrangement is a deletion that results in a fusion of ARHGAP40 exons 1 - 2 to TOP1 exons 7 - 21.
CDKN2A	0	MSKCC-DMP	P-0044017-T02-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-3159:CDKN2A_chr9:g.21958116del Note: The CDKN2A rearrangement is a deletion of exon 2. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
STRN	0	MSKCC-DMP	P-0048102-T02-IM6	ALK-STRN fusion	yes	unknown		in frame	STRN (NM_003162) - ALK (NM_004304) fusion: c.412+2761:STRN_c.3173-662:ALKdel Note: The STRN - ALK fusion involves STRN exons 1 - 3 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0048102-T02-IM6	ALK-STRN fusion	yes	unknown		in frame	STRN (NM_003162) - ALK (NM_004304) fusion: c.412+2761:STRN_c.3173-662:ALKdel Note: The STRN - ALK fusion involves STRN exons 1 - 3 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
SESN2	0	MSKCC-DMP	P-0049522-T01-IM6	SESN2-intragenic	yes	unknown		unknown	SESN2 (NM_031459) rearrangement: c.90+1115_c.1020+90inv Note: The SESN2 rearrangement is an intragenic inversion of exons 2 - 7. Functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0049522-T01-IM6	KALRN-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - KALRN (NM_001024660) rearrangement: t(3;4)(q21.2;p16.3)(chr3:g.124313742::chr4:g.1954066) Note: The WHSC1 - KALRN rearrangement is a translocation that results in a fusion of WHSC1 exons 1 - 11 to KALRN exons 2 - 60. The fusion is predicted to be in frame. Functional significance is undetermined.
KALRN	0	MSKCC-DMP	P-0049522-T01-IM6	KALRN-WHSC1 fusion	yes	unknown		in frame	WHSC1 (NM_001042424) - KALRN (NM_001024660) rearrangement: t(3;4)(q21.2;p16.3)(chr3:g.124313742::chr4:g.1954066) Note: The WHSC1 - KALRN rearrangement is a translocation that results in a fusion of WHSC1 exons 1 - 11 to KALRN exons 2 - 60. The fusion is predicted to be in frame. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0049524-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.950_c.5468-78del Note: The KMT2D rearrangement is an intragenic deletion of exons 7 - 23. One of the breakpoints is within exon 7.
SOX9	0	MSKCC-DMP	P-0049524-T01-IM6	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.560_c.1369del Note: The SOX9 rearrangement is an intragenic deletion of exons 2 - 3. The breakpoints are within exon 2 and exon 3.
KEAP1	0	MSKCC-DMP	P-0049524-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.1591:KEAP1_chr19:g.10612345del Note: The KEAP1 rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.
ASXL2	0	MSKCC-DMP	P-0049524-T01-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.975_c.1037-368del Note: The ASXL2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9.
MED12	0	MSKCC-DMP	P-0049532-T01-IM6	MED12-intragenic	yes	unknown		unknown	MED12 (NM_005120) rearrangement: c.1348+59:MED12_chrX:g.64807314del Note: The MED12 rearrangement is a deletion of exons 1 - 9.
KEAP1	0	MSKCC-DMP	P-0049541-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: t(16;19)(p11.2;p13.2)(chr16:g.33840009::chr19:g.10597674) Note: The KEAP1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049590-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+11:TMPRSS2_chr21:g.42433155dup Note: The TMPRSS2 rearrangement is a duplication of exons 2 - 14. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0049597-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: t(19;X)(p13.12;q26.3)(chr19:g.15350005::chrX:g.137085626) Note: The BRD4 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0049598-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(4;17)(q35.1;q11.2)(chr4:g.185552772::chr17:g.29422420) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0049598-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.5276+36_c.6259inv Note: The KMT2B rearrangement is an intragenic inversion of exons 26 - 28. One of the breakpoints is within exon 28. Functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0049618-T01-IM6	RARA-intragenic	yes	unknown		unknown	RARA (NM_000964) rearrangement: c.1012+25:RARA_chr17:g.58915279inv Note: The RARA rearrangement is an inversion of exons 8 - 9. Functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0049618-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.129:NCOA3_chr20:g.52041710del Note: The NCOA3 rearrangement is a deletion of exons 4 - 23. One of the breakpoints is within exon 4. Functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0049633-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.246_c.252+2378del Note: The RNF43 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.
KANK1	0	MSKCC-DMP	P-0049637-T01-IM6	MET-KANK1 fusion	yes	unknown		in frame	KANK1 (NM_015158) - MET (NM_000245) fusion: t(7;9)(q31.2;p24.3)(chr7:g.116413312::chr9:g.725428) Note: The KANK1 - MET fusion involves KANK1 exons 1 - 7 and MET exons 15 - 21. The fusion is predicted to be in frame and includes the kinase domain of MET. Multiple rearrangements involving MET were detected in this sample and a more complex rearrangement resulting in a MET fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
MET	0	MSKCC-DMP	P-0049637-T01-IM6	MET-KANK1 fusion	yes	unknown		in frame	KANK1 (NM_015158) - MET (NM_000245) fusion: t(7;9)(q31.2;p24.3)(chr7:g.116413312::chr9:g.725428) Note: The KANK1 - MET fusion involves KANK1 exons 1 - 7 and MET exons 15 - 21. The fusion is predicted to be in frame and includes the kinase domain of MET. Multiple rearrangements involving MET were detected in this sample and a more complex rearrangement resulting in a MET fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CTNNB1	0	MSKCC-DMP	P-0049638-T01-IM6	ANKRD28-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) - ANKRD28 (NM_015199) rearrangement: c.1559:CTNNB1_c.112-7220:ANKRD28inv Note: The CTNNB1 - ANKRD28 rearrangement is an inversion that results in a fusion of CTNNB1 exons 1 - 10 to ANKRD28 exons 3 - 28. One of the breakpoints is within CTNNB1 exon 10. Functional significance is undetermined.
ANKRD28	0	MSKCC-DMP	P-0049638-T01-IM6	ANKRD28-CTNNB1 fusion	yes	unknown		unknown	CTNNB1 (NM_001904) - ANKRD28 (NM_015199) rearrangement: c.1559:CTNNB1_c.112-7220:ANKRD28inv Note: The CTNNB1 - ANKRD28 rearrangement is an inversion that results in a fusion of CTNNB1 exons 1 - 10 to ANKRD28 exons 3 - 28. One of the breakpoints is within CTNNB1 exon 10. Functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0049640-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782214::chr6:g.117650417) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 7 and ROS1 exons 33 - 43. The fusion includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0049640-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782214::chr6:g.117650417) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 7 and ROS1 exons 33 - 43. The fusion includes the kinase domain of ROS1.
CDKN2B	0	MSKCC-DMP	P-0049640-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.96:CDKN2B_chr9:g.21895095del Note: The CDKN2B rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1.
KMT2C	0	MSKCC-DMP	P-0049684-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.7103:KMT2C_chr7:g.116254326del Note: The KMT2C rearrangement is a deletion of exons 36 - 59. One of the breakpoints is within exon 36.
TMPRSS2	0	MSKCC-DMP	P-0049439-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190227 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0049439-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190227 Macro-dissection: Not Performed
CCDC6	0	MSKCC-DMP	P-0049461-T02-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-3450:CCDC6_c.2137-327:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0049461-T02-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-3450:CCDC6_c.2137-327:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0049588-T01-IM6	CCDC6-RET fusion	yes	unknown		out of frame	RET (NM_020975) - CCDC6 (NM_005436) rearrangement: c.1879+314:RET_c.304-15222:CCDC6inv Note: The RET - CCDC6 rearrangement is an inversion that results in a fusion of RET exons 1 - 10 to CCDC6 exons 2 - 9. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CCDC6	0	MSKCC-DMP	P-0049588-T01-IM6	CCDC6-RET fusion	yes	unknown		out of frame	RET (NM_020975) - CCDC6 (NM_005436) rearrangement: c.1879+314:RET_c.304-15222:CCDC6inv Note: The RET - CCDC6 rearrangement is an inversion that results in a fusion of RET exons 1 - 10 to CCDC6 exons 2 - 9. The fusion does not include the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RET	0	MSKCC-DMP	P-0049588-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: t(9;10)(p21.3;q11.21)(chr9:g.20531517::chr10:g.43610683) Note: The RET rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0049734-T01-IM6	VAV3-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) - VAV3 (NM_006113) rearrangement: t(1;9)(p13.3;q24.12)(chr1:g.108439901::chr9:g.133589782) Note: the ABL1 - VAV3 rearrangement is a translocation that results in a fusion of ABL1 exon 1 to VAV3 exons 2 - 27. One of the breakpoints is within ABL1 exon 1. The functional significance is undetermined.
VAV3	0	MSKCC-DMP	P-0049734-T01-IM6	VAV3-ABL1 fusion	yes	unknown		unknown	ABL1 (NM_005157) - VAV3 (NM_006113) rearrangement: t(1;9)(p13.3;q24.12)(chr1:g.108439901::chr9:g.133589782) Note: the ABL1 - VAV3 rearrangement is a translocation that results in a fusion of ABL1 exon 1 to VAV3 exons 2 - 27. One of the breakpoints is within ABL1 exon 1. The functional significance is undetermined.
EZH1	0	MSKCC-DMP	P-0049763-T01-IM6	EZH1-intragenic	yes	unknown		unknown	EZH1 (NM_001991) rearrangement: t(12;17)(q23.3;q21.2)(chr12:g.108659733::chr17:g.40865300) Note: The EZH1 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0049763-T01-IM6	CDKN2B-intragenic	yes	unknown		unknown	CDKN2B (NM_004936) rearrangement: c.156+526:CDKN2B_chr9:g.22033412inv Note: The CDKN2B rearrangement is an inversion of exon 1. Functional significance is undetermined.
IRS2	0	MSKCC-DMP	P-0049767-T01-IM6	IRS2-intragenic	yes	unknown		unknown	IRS2 (NM_003749) rearrangement: c.1678:IRS2_chr13:g.110406534del Note: The IRS2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0049776-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.421+70885_c.1883del Note: The ERBB4 rearrangement is an intragenic deletion of exons 4 - 16. One of the breakpoints is within exon 16. The rearrangement does not include the kinase domain of ERBB4. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0049782-T01-IM6	TMC8-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - TMC8 (NM_152468) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.76130996::chr19:g.10260454) Note: The DNMT1 - TMC8 rearrangement is a translocation that results in a fusion of DNMT1 exons 1 - 24 to TMC8 exons 9 - 16. One of the breakpoints is within TMC8 exon 9. Functional significance is undetermined.
TMC8	0	MSKCC-DMP	P-0049782-T01-IM6	TMC8-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - TMC8 (NM_152468) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.76130996::chr19:g.10260454) Note: The DNMT1 - TMC8 rearrangement is a translocation that results in a fusion of DNMT1 exons 1 - 24 to TMC8 exons 9 - 16. One of the breakpoints is within TMC8 exon 9. Functional significance is undetermined.
RAD54L	0	MSKCC-DMP	P-0049795-T01-IM6	RAD54L-intragenic	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: t(1;17)(p34.1;q21.31)(chr1:g.46738180::chr17:g.42742114) Note: The RAD54L rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0049795-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(17;22)(p13.1;q13.31)(chr17:g.7579139::chr22:g.45835284) Note: The TP53 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.
EED	0	MSKCC-DMP	P-0049799-T01-IM6	EED-intragenic	yes	unknown		unknown	EED (NM_003797) rearrangement: c.114+98:EED_chr11:g.86488383del Note: The EED rearrangement is a deletion of exons 2 - 12.
TERT	0	MSKCC-DMP	P-0049807-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.2383-182:TERT_chr5:g.7735518del Note: The TERT rearrangement is a deletion of exons 1 - 7. Functional significance is undetermined.
PREX2	0	MSKCC-DMP	P-0049789-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: t(8;11)(q13.2;q11)(chr8:g.69009227::chr11:g.55663374) Note: The PREX2 rearrangement is a translocation with a breakpoint in intron 21. Functional significance is undetermined.
IGHMBP2	0	MSKCC-DMP	P-0049789-T01-IM6	FGFR1-IGHMBP2 fusion	yes	unknown		unknown	IGHMBP2 (NM_002180) - FGFR1 (NM_001174067) fusion: t(8;11)(p11.23;q13.3)(chr8:g.38275857::chr11:g.68697608) Note: The IGHMBP2 - FGFR1 fusion involves IGHMBP2 exons 1 - 8 and FGFR1 exons 11 - 19. One of the breakpoints is within FGFR1 exon 11. The fusion includes the kinase domain of FGFR1.
FGFR1	0	MSKCC-DMP	P-0049789-T01-IM6	FGFR1-IGHMBP2 fusion	yes	unknown		unknown	IGHMBP2 (NM_002180) - FGFR1 (NM_001174067) fusion: t(8;11)(p11.23;q13.3)(chr8:g.38275857::chr11:g.68697608) Note: The IGHMBP2 - FGFR1 fusion involves IGHMBP2 exons 1 - 8 and FGFR1 exons 11 - 19. One of the breakpoints is within FGFR1 exon 11. The fusion includes the kinase domain of FGFR1.
ESR1	0	MSKCC-DMP	P-0025113-T02-IM6	AKAP12-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-AKAP12 fusion. Note: The rearrangement is a fusion between genes ESR1 Exon6 (NM_000125) and AKAP12 Exon3 (NM_005100). Lab Notes Run Number: ArcherV3-CLIN-20190230 Macro-dissection: Not Performed
AKAP12	0	MSKCC-DMP	P-0025113-T02-IM6	AKAP12-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-AKAP12 fusion. Note: The rearrangement is a fusion between genes ESR1 Exon6 (NM_000125) and AKAP12 Exon3 (NM_005100). Lab Notes Run Number: ArcherV3-CLIN-20190230 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0049427-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: AR-v7 (PMID:    ) Lab Notes Run Number: ArcherV3-CLIN-20190229 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0049427-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: AR-v7 (PMID:    ) Lab Notes Run Number: ArcherV3-CLIN-20190229 Macro-dissection: Not Performed
NRF1	0	MSKCC-DMP	P-0049515-T01-IM6	BRAF-NRF1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NRF1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes NRF1 Exon10 (NM_005011) and BRAF Exon10 (NM_004333). PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190230 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0049515-T01-IM6	BRAF-NRF1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NRF1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes NRF1 Exon10 (NM_005011) and BRAF Exon10 (NM_004333). PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190230 Macro-dissection: Not Performed
TSC1	0	MSKCC-DMP	P-0046749-T02-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: c.211-103:TSC1_chr9:g.135810074del Note: The TSC1 rearrangement is a deletion of exons 1 - 4.
NTHL1	0	MSKCC-DMP	P-0048569-T02-IM6	NTHL1-intragenic	yes	unknown		unknown	NTHL1 (NM_002528) rearrangement: t(12;16)(q13.13;p13.3)(chr12:g.53347002::chr16:g.2093677) Note: The NTHL1 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined. Multiple rearrangements involving NTHL1 were detected in this sample and a more complex rearrangement resulting in a NTHL1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
THOP1	0	MSKCC-DMP	P-0049565-T01-IM6	CALR-THOP1 fusion	yes	unknown		unknown	THOP1 (NM_003249) - CALR (NM_004343) rearrangement: c.750+630:THOP1_c.845:CALRdel Note: The THOP1 - CALR rearrangement is a deletion that results in a fusion of THOP1 exons 1 - 6 to CALR exons 7 - 9. One of the breakpoints is within CALR exon 7. Functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0049565-T01-IM6	CALR-THOP1 fusion	yes	unknown		unknown	THOP1 (NM_003249) - CALR (NM_004343) rearrangement: c.750+630:THOP1_c.845:CALRdel Note: The THOP1 - CALR rearrangement is a deletion that results in a fusion of THOP1 exons 1 - 6 to CALR exons 7 - 9. One of the breakpoints is within CALR exon 7. Functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0049566-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.166-131_c.1719del Note: The BCOR rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.
NCOA4	0	MSKCC-DMP	P-0049600-T01-IM6	RET-NCOA4 fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.1889:NCOA4_c.2137-419:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1 - 11 and RET exons 12 - 20. One of the breakpoints is within NCOA4 exon 11. The fusion includes the kinase domain of RET. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RET	0	MSKCC-DMP	P-0049600-T01-IM6	RET-NCOA4 fusion	yes	unknown		unknown	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.1889:NCOA4_c.2137-419:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1 - 11 and RET exons 12 - 20. One of the breakpoints is within NCOA4 exon 11. The fusion includes the kinase domain of RET. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0049601-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.557-301_c.1101inv Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 6 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a TMPRSS2  - ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
KMT2D	0	MSKCC-DMP	P-0049677-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.3907-52:KMT2D_chr12:g.51463325inv Note: The KMT2D rearrangement is an inversion of exons 1 - 11. Functional significance is undetermined. Multiple rearrangements involving KMT2D were detected in this sample and a more complex rearrangement resulting in a KMT2D fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RNF43	0	MSKCC-DMP	P-0049679-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.2199:RNF43_chr17:g.56419522del Note: The RNF43 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.
KMT2A	0	MSKCC-DMP	P-0030151-T02-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.3570-306_c.10613dup Note: The KMT2A rearrangement is an intragenic duplication of exons 6 - 27. One of the breakpoints is within exon 27. Functional significance is undetermined.
THSD4	0	MSKCC-DMP	P-0045231-T02-IM6	CTCF-THSD4 fusion	yes	unknown		unknown	THSD4 (NM_024817) - CTCF (NM_006565) rearrangement: t(15;16)(q23;q22.1)(chr15:g.71907219::chr16:g.67654689) Note: The THSD4 - CTCF rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 6 to CTCF exons 6 - 12. One of the breakpoints is within CTCF exon 6. Functional significance is undetermined.
CTCF	0	MSKCC-DMP	P-0045231-T02-IM6	CTCF-THSD4 fusion	yes	unknown		unknown	THSD4 (NM_024817) - CTCF (NM_006565) rearrangement: t(15;16)(q23;q22.1)(chr15:g.71907219::chr16:g.67654689) Note: The THSD4 - CTCF rearrangement is a translocation that results in a fusion of THSD4 exons 1 - 6 to CTCF exons 6 - 12. One of the breakpoints is within CTCF exon 6. Functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0045231-T02-IM6	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.226-31834_c.975-49del Note: The KDM6A rearrangement is an intragenic deletion of exons 3 - 11.
CD276	0	MSKCC-DMP	P-0047193-T02-IM6	CD276-intragenic	yes	unknown		unknown	CD276 (NM_001024736) rearrangement: c.1582+191:CD276_chr15:g.89160814inv Note: The CD276 rearrangement is an inversion of exon 10. Functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0048433-T01-IM6	NEGR1-intragenic	yes	unknown		in frame	NEGR1 (NM_173808) rearrangement: c.410-5_c.536-13165dup Note: The NEGR1 rearrangement is an intragenic duplication of exon 3. Functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0049545-T02-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.374:CTNNB1_chr3:g.41264962del Note: The CTNNB1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0049846-T01-IM6	RAD21-intragenic	yes	unknown		unknown	RAD21 (NM_006265) rearrangement: c.145-10:RAD21_chr8:g.118200891del Note: The RAD21 rearrangement is a deletion of exons 1 - 2.
CDKN1B	0	MSKCC-DMP	P-0049869-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.379:CDKN1B_chr12:g.12875422inv Note: The CDKN1B rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049886-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3880:TMPRSS2_c.18+26025:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERG	0	MSKCC-DMP	P-0049886-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3880:TMPRSS2_c.18+26025:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in additional fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
RECQL	0	MSKCC-DMP	P-0049938-T01-IM6	RECQL-intragenic	yes	unknown		unknown	RECQL (NM_032941) rearrangement: t(1;12)(p31.1;p12.1)(chr1:g.84517611::chr12:g.21627727) Note: The RECQL rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.
KIT	0	MSKCC-DMP	P-0049939-T01-IM6	KIT-intragenic	yes	unknown		unknown	KIT (NM_000222) rearrangement: t(1;4)(q42.2;q12)(chr1:g.234269491::chr4:g.55604661) Note: The KIT rearrangement is a translocation with a breakpoint in exon 21. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving KIT is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
EFNA2	0	MSKCC-DMP	P-0049943-T01-IM6	STK11-EFNA2 fusion	yes	unknown		out of frame	EFNA2 (NM_001405) - STK11 (NM_000455) rearrangement: c.455-1105:EFNA2_c.465-73:STK11dup Note: The EFNA2 - STK11 rearrangement is a duplication that results in a fusion of EFNA2 exons 1 - 2 to STK11 exons 4 - 9. The fusion includes a part of the kinase domain of STK11. Functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0049943-T01-IM6	STK11-EFNA2 fusion	yes	unknown		out of frame	EFNA2 (NM_001405) - STK11 (NM_000455) rearrangement: c.455-1105:EFNA2_c.465-73:STK11dup Note: The EFNA2 - STK11 rearrangement is a duplication that results in a fusion of EFNA2 exons 1 - 2 to STK11 exons 4 - 9. The fusion includes a part of the kinase domain of STK11. Functional significance is undetermined.
TPR	0	MSKCC-DMP	P-0049951-T01-IM6	NTRK1-TPR fusion	yes	unknown		in frame	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2610+187:TPR_c.1252-38:NTRK1inv Note: The TPR - NTRK1 fusion involves TPR exons 1 - 20 and NTRK1 exons 11 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0049951-T01-IM6	NTRK1-TPR fusion	yes	unknown		in frame	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2610+187:TPR_c.1252-38:NTRK1inv Note: The TPR - NTRK1 fusion involves TPR exons 1 - 20 and NTRK1 exons 11 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
BRCA2	0	MSKCC-DMP	P-0049954-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.7806-79_c.8283del Note: The BRCA2 rearrangement is an intragenic deletion of exons 17 - 18. One of the breakpoints is within exon 18.
ATRX	0	MSKCC-DMP	P-0049957-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.371-527_c.409del Note: The ATRX rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6.
MEF2B	0	MSKCC-DMP	P-0049959-T01-IM6	MEF2B-intragenic	yes	unknown		unknown	MEF2B (NM_001145785) rearrangement: t(12;19)(q13.11;p13.11)(chr12:g.46501152::chr19:g.19257680) Note: The MEF2B rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049966-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion: t(7;21)(p21.2;q22.3)(chr7:g.14007075::chr21:g.42872833) Note: The TMPRSS2 - ETV1 fusion involves TMPRSS2 exon 1 and ETV1 exons 6 - 12. The fusion is predicted to be in frame.
ETV1	0	MSKCC-DMP	P-0049966-T01-IM6	ETV1-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion: t(7;21)(p21.2;q22.3)(chr7:g.14007075::chr21:g.42872833) Note: The TMPRSS2 - ETV1 fusion involves TMPRSS2 exon 1 and ETV1 exons 6 - 12. The fusion is predicted to be in frame.
CSF1R	0	MSKCC-DMP	P-0049968-T01-IM6	CSF1R-intragenic	yes	unknown		unknown	CSF1R (NM_005211) rearrangement: c.308-24:CSF1R_chr5:g.149479340del Note: The CSF1R rearrangement is a deletion of exons 1 - 3. The rearrangement does not include the kinase domain of CSF1R. Functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0049970-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: c.1201_c.1265del Note: The NOTCH2 rearrangement is an intragenic deletion of exons 7 - 8. The breakpoints are within exon 7 and exon 8.
RRAS	0	MSKCC-DMP	P-0033244-T03-IM6	RRAS-intragenic	yes	unknown		unknown	RRAS (NM_006270) rearrangement: c.199:RRAS_chr19:g.50130834inv Note: The RRAS rearrangement is an inversion of exons 2 - 6. One of the breakpoints is within exon 2. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0049777-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.2356-27:ALK_chr2:g.55625130inv Note: The ALK rearrangement is an inversion of exons 1 - 13. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
HIST1H3E	0	MSKCC-DMP	P-0049777-T01-IM6	HIST1H3E-intragenic	yes	unknown		unknown	HIST1H3E (NM_003532) rearrangement: c.259:HIST1H3E_chr6:g.10278247del Note: The HIST1H3E rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0049870-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement: c.1305-474_c.1916del Note: The STAG2 rearrangement is an intragenic deletion of exons 15 - 20. One of the breakpoints is within exon 20.
NCOA4	0	MSKCC-DMP	P-0049600-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon9 (NM_005437) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190232 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0049600-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon9 (NM_005437) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190232 Macro-dissection: Not Performed
KANK1	0	MSKCC-DMP	P-0049637-T01-IM6	MET-KANK1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KANK1-MET fusion. Note: The rearrangement is an in-frame fusion between genes KANK1 Exon3 (NM_015158) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20190233 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0049637-T01-IM6	MET-KANK1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: KANK1-MET fusion. Note: The rearrangement is an in-frame fusion between genes KANK1 Exon3 (NM_015158) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20190233 Macro-dissection: Not Performed
ROS1	0	MSKCC-DMP	P-0005873-T02-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5641+318:ROS1_chr6:g.117541165del Note: The ROS1 rearrangement is a deletion of exons 35 - 43. The rearrangement includes the kinase domain of ROS1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ROS1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CALR	0	MSKCC-DMP	P-0019607-T06-IM6	CALR-intragenic	yes	unknown		unknown	CALR (NM_004343) rearrangement: t(2;19)(q12.1;p13.2)(chr2:g.105170597::chr19:g.13054653) Note: The CALR rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0019607-T06-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.2680+88:NOTCH4_chr6:g.31401460inv Note: The NOTCH4 rearrangement is an inversion of exons 18 - 30. Functional significance is undetermined.
HGF	0	MSKCC-DMP	P-0019607-T06-IM6	HGF-intragenic	yes	unknown		unknown	HGF (NM_000601) rearrangement: c.997_c.1040+591del Note: The HGF rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0030465-T02-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.1872-136:ERBB4_chr2:g.188632702inv Note: The ERBB4 rearrangement is an inversion of exons 16 - 28. The rearrangement includes the kinase domain of ERBB4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0031015-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2384:TMPRSS2_c.40-63530:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0031015-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2384:TMPRSS2_c.40-63530:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
TERT	0	MSKCC-DMP	P-0049308-T02-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: c.2655-14:TERT_chr5:g.20081454inv Note: The TERT rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.
NOTCH4	0	MSKCC-DMP	P-0049919-T01-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.3643:NOTCH4_chr6:g.32929127del Note: The NOTCH4 rearrangement is a deletion of exons 1 - 21. One of the breakpoints is within exon 21.
CARM1	0	MSKCC-DMP	P-0049921-T01-IM6	CARM1-intragenic	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: c.1787:CARM1_chr19:g.10959120del Note: The CARM1 rearrangement is a deletion of exons 1 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.
CARD11	0	MSKCC-DMP	P-0049921-T01-IM6	CARD11-intragenic	yes	unknown		out of frame	CARD11 (NM_032415) rearrangement: c.2510+153_c.2703+260del Note: The CARD11 rearrangement is an intragenic deletion of exons 19 - 20. Functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0049933-T01-IM6	B2M-intragenic	yes	unknown		in frame	B2M (NM_004048) rearrangement: c.68-1537_c.346+83del Note: The B2M rearrangement is an intragenic deletion of exon 2.
DUSP4	0	MSKCC-DMP	P-0049933-T01-IM6	DUSP4-intragenic	yes	unknown		unknown	DUSP4 (NM_001394) rearrangement: t(6;8)(q23.2;p12)(chr6:g.132934535::chr8:g.29207538) Note: The DUSP4 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049963-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2618_c.557-1792inv Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 5. Functional significance is undetermined.
DAXX	0	MSKCC-DMP	P-0049979-T01-IM6	DAXX-intragenic	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: t(1;6)(q23.1;p21.32)(chr1:g.156682800::chr6:g.33286569) Note: The DAXX rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049985-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4790:TMPRSS2_c.19-24695:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0049985-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4790:TMPRSS2_c.19-24695:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
STAT5B	0	MSKCC-DMP	P-0049986-T01-IM6	STAT5B-intragenic	yes	unknown		unknown	STAT5B (NM_012448) rearrangement: t(3;17)(p21.31;q21.2)(chr3:g.45058637::chr17:g.40384144) Note: The STAT5B rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0049988-T01-IM6	NEGR1-intragenic	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: t(1;16)(p31.1;p13.13)(chr1:g.71924675::chr16:g.11348618) Note: The NEGR1 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0050058-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: t(3;5)(p13;q15)(chr3:g.71026977::chr5:g.96973852) Note: The FOXP1 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0050065-T01-IM6	SETD2-intragenic	yes	unknown		unknown	SETD2 (NM_014159) rearrangement: c.7662:SETD2_chr3:g.47058024inv Note: The SETD2 rearrangement is an inversion of exon 21. One of the breakpoints is within exon 21. Functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0050067-T01-IM6	SLC22A9-RPS6KA4 fusion	yes	unknown		out of frame	RPS6KA4 (NM_003942) - SLC22A9 (NM_080866) rearrangement: c.1957+74:RPS6KA4_c.1073+9725:SLC22A9dup Note: The RPS6KA4 - SLC22A9 rearrangement is a duplication that results in a fusion of RPS6KA4 exons 1 - 15 to SLC22A9 exons 7 - 10. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RPS6KA4 would be required if clinically indicated.
SLC22A9	0	MSKCC-DMP	P-0050067-T01-IM6	SLC22A9-RPS6KA4 fusion	yes	unknown		out of frame	RPS6KA4 (NM_003942) - SLC22A9 (NM_080866) rearrangement: c.1957+74:RPS6KA4_c.1073+9725:SLC22A9dup Note: The RPS6KA4 - SLC22A9 rearrangement is a duplication that results in a fusion of RPS6KA4 exons 1 - 15 to SLC22A9 exons 7 - 10. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RPS6KA4 would be required if clinically indicated.
ERG	0	MSKCC-DMP	P-0050086-T01-IM6	ERG-intragenic	yes	unknown		unknown	ERG (NM_182918) rearrangement: c.18+43:ERG_chr21:g.28329679inv Note: The ERG rearrangement is an inversion of exons 2 - 10. Functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0050112-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3266-1343_c.3378inv Note: The FAT1 rearrangement is an intragenic inversion of exon 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0050114-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3928:ARID1A_chr1:g.235098599del Note: The ARID1A rearrangement is a deletion of exons 16 - 20. One of the breakpoints is within exon 16.
YWHAZ	0	MSKCC-DMP	P-0050121-T01-IM6	CTNNB1-YWHAZ fusion	yes	unknown		in frame	YWHAZ (NM_001135699) - CTNNB1 (NM_001904) rearrangement: t(3;8)(p22.1;q22.3)(chr3:g.41266706::chr8:g.101953077) Note: The YWHAZ - CTNNB1 rearrangement is a translocation that results in a fusion of YWHAZ exons 1 - 2 to CTNNB1 exons 5 - 15. The fusion is predicted to be in frame. Functional significance is undetermined.
CTNNB1	0	MSKCC-DMP	P-0050121-T01-IM6	CTNNB1-YWHAZ fusion	yes	unknown		in frame	YWHAZ (NM_001135699) - CTNNB1 (NM_001904) rearrangement: t(3;8)(p22.1;q22.3)(chr3:g.41266706::chr8:g.101953077) Note: The YWHAZ - CTNNB1 rearrangement is a translocation that results in a fusion of YWHAZ exons 1 - 2 to CTNNB1 exons 5 - 15. The fusion is predicted to be in frame. Functional significance is undetermined.
MAP2K4	0	MSKCC-DMP	P-0050123-T01-IM6	MAP2K4-intragenic	yes	unknown		in frame	MAP2K4 (NM_003010) rearrangement: c.393+199_c.813+183dup Note: The MAP2K4 rearrangement is an intragenic duplication of exons 4 - 7. The rearrangement includes a part of the kinase domain of MAP2K4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0050123-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.127-704:TMPRSS2_chr21:g.40094251del Note: The TMPRSS2 rearrangement is a deletion of exons 3 - 14. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0050148-T01-IM6	FANCA-intragenic	yes	unknown		out of frame	FANCA (NM_000135) rearrangement: c.2778+178_c.2981+713del Note: The FANCA rearrangement is an intragenic deletion of exons 29 - 30.
ERBB4	0	MSKCC-DMP	P-0050148-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.1666_c.2487+14740del Note: The ERBB4 rearrangement is an intragenic deletion of exons 14 - 20. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of ERBB4. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0050153-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.919+18:TP53_chr17:g.7581384inv Note: The TP53 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
SOX17	0	MSKCC-DMP	P-0050187-T01-IM6	SOX17-intragenic	yes	unknown		unknown	SOX17 (NM_022454) rearrangement: c.307+1:SOX17_chr8:g.55373335del Note: The SOX17 rearrangement is a deletion of exon 2.
DBI	0	MSKCC-DMP	P-0050196-T01-IM6	BRAF-DBI fusion	yes	unknown		in frame	DBI (NM_001178017) - BRAF (NM_004333) fusion: t(2;7)(q14.2;q34)(chr2:g.120128894::chr7:g.140486284) Note: The DBI - BRAF fusion involves DBI exons 1 - 3 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0050196-T01-IM6	BRAF-DBI fusion	yes	unknown		in frame	DBI (NM_001178017) - BRAF (NM_004333) fusion: t(2;7)(q14.2;q34)(chr2:g.120128894::chr7:g.140486284) Note: The DBI - BRAF fusion involves DBI exons 1 - 3 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.
RAD51	0	MSKCC-DMP	P-0050209-T01-IM6	RAD51-intragenic	yes	unknown		unknown	RAD51 (NM_002875) rearrangement: c.700:RAD51_chr15:g.40606005del Note: The RAD51 rearrangement is a deletion of exons 1 - 8. One of the breakpoints is within exon 8.
RB1	0	MSKCC-DMP	P-0050234-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.500+75_c.607+1688del Note: The RB1 rearrangement is an intragenic deletion of exons 5 - 6.
PTEN	0	MSKCC-DMP	P-0050249-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.210-94:PTEN_chr10:g.88753165inv Note: The PTEN rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0050249-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+989:TMPRSS2_c.19-20075:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0050249-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+989:TMPRSS2_c.19-20075:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0050250-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-4532_c.294del Note: The CDKN2A rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
ETV6	0	MSKCC-DMP	P-0050253-T01-IM6	ETV6-intragenic	yes	unknown		in frame	ETV6 (NM_001987) rearrangement: c.329-315_c.464-3483dup Note: The ETV6 rearrangement is an intragenic duplication of exon 4. Functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0050257-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.4936:ZFHX3_chr16:g.72795899del Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.
STAG2	0	MSKCC-DMP	P-0050260-T01-IM6	STAG2-intragenic	yes	unknown		unknown	STAG2 (NM_001042749) rearrangement: c.408_c.2775+203dup Note: The STAG2 rearrangement is an intragenic duplication of exons 7 - 27. One of the breakpoints is within exon 7. Functional significance is undetermined.
JAK3	0	MSKCC-DMP	P-0050264-T01-IM6	JAK3-intragenic	yes	unknown		unknown	JAK3 (NM_000215) rearrangement: t(1;19)(p36.22;p13.11)(chr1:g.9448228::chr19:g.17952430) Note: The JAK3 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0050285-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-146:TMPRSS2_c.39+53629:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0050285-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-146:TMPRSS2_c.39+53629:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
FLT4	0	MSKCC-DMP	P-0050286-T01-IM6	FLT4-intragenic	yes	unknown		unknown	FLT4 (NM_182925) rearrangement: c.3611:FLT4_chr5:g.144857146inv Note: The FLT4 rearrangement is an inversion of exons 27 - 30. One of the breakpoints is within exon 27. The rearrangement does not include the kinase domain of FLT4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0050289-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2621:TMPRSS2_c.40-59203:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0050289-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2621:TMPRSS2_c.40-59203:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
NAB2	0	MSKCC-DMP	P-0050309-T01-IM6	NAB2-intragenic	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(2;12)(p24.2;q13.3)(chr2:g.17948133::chr12:g.57487915) Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
NKX3	0	MSKCC-DMP	P-0050350-T01-IM6	NKX3-1-NKX3 fusion	yes	unknown		unknown	NKX3-1 (NM_006167) rearrangement: t(8;17)(p21.2;q21.31)(chr8:g.23539161::chr17:g.41654143) Note: The NKX3-1 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
NKX3-1	0	MSKCC-DMP	P-0050350-T01-IM6	NKX3-1-NKX3 fusion	yes	unknown		unknown	NKX3-1 (NM_006167) rearrangement: t(8;17)(p21.2;q21.31)(chr8:g.23539161::chr17:g.41654143) Note: The NKX3-1 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0050351-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.1009+1555:ETV6_chr12:g.22933086inv Note: The ETV6 rearrangement is an inversion of exons 6 - 8. Functional significance is undetermined.
CLEC1A	0	MSKCC-DMP	P-0050351-T01-IM6	CCNE1-CLEC1A fusion	yes	unknown		out of frame	CLEC1A (NM_016511) - CCNE1 (NM_001238) rearrangement: t(12;19)(p13.2;q12)(chr12:g.10234241::chr19:g.30314505) Note: The CLEC1A - CCNE1 rearrangement is a translocation that results in a fusion of CLEC1A exons 1 - 2 to CCNE1 exon 12. Functional significance is undetermined.
CCNE1	0	MSKCC-DMP	P-0050351-T01-IM6	CCNE1-CLEC1A fusion	yes	unknown		out of frame	CLEC1A (NM_016511) - CCNE1 (NM_001238) rearrangement: t(12;19)(p13.2;q12)(chr12:g.10234241::chr19:g.30314505) Note: The CLEC1A - CCNE1 rearrangement is a translocation that results in a fusion of CLEC1A exons 1 - 2 to CCNE1 exon 12. Functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0050351-T01-IM6	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: c.4770-34:PTPRS_chr19:g.5198769inv Note: The PTPRS rearrangement is an inversion of exons 32 - 38. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0050351-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.2562:NOTCH3_chr19:g.43041943inv Note: The NOTCH3 rearrangement is an inversion of exons 1 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.
MYC	0	MSKCC-DMP	P-0050351-T01-IM6	MYC-intragenic	yes	unknown		unknown	MYC (NM_002467) rearrangement: c.444:MYC_chr8:g.129109519del Note: The MYC rearrangement is a deletion of exons 2 - 3. One of the breakpoints is within exon 2. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0050352-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4572:TMPRSS2_c.39+11100:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0050352-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4572:TMPRSS2_c.39+11100:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
GSK3B	0	MSKCC-DMP	P-0050392-T01-IM6	GSK3B-intragenic	yes	unknown		unknown	GSK3B (NM_002093) rearrangement: c.910-751_c.927inv Note: The GSK3B rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. The rearrangement includes a part of the kinase domain of GSK3B. Functional significance is undetermined.
NBN	0	MSKCC-DMP	P-0050395-T01-IM6	NBN-intragenic	yes	unknown		in frame	NBN (NM_002485) rearrangement: c.585-2804_c.1124+91dup Note: The NBN rearrangement is an intragenic duplication of exons 6 - 9. Functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0050415-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.745:FOXA1_chr14:g.38101340del Note: The FOXA1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.
FGFR4	0	MSKCC-DMP	P-0050433-T01-IM6	EYS-FGFR4 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - EYS (NM_001142800) rearrangement: t(5;6)(q35.2;q12)(chr5:g.176523102::chr6:g.65813208) Note: The FGFR4 - EYS rearrangement is a translocation that results in a fusion of FGFR4 exons 1 - 14 to EYS exons 13 - 43. One of the breakpoints is within FGFR4 exon 14. The fusion includes a part of the kinase domain of FGFR4. Functional significance is undetermined.
EYS	0	MSKCC-DMP	P-0050433-T01-IM6	EYS-FGFR4 fusion	yes	unknown		unknown	FGFR4 (NM_213647) - EYS (NM_001142800) rearrangement: t(5;6)(q35.2;q12)(chr5:g.176523102::chr6:g.65813208) Note: The FGFR4 - EYS rearrangement is a translocation that results in a fusion of FGFR4 exons 1 - 14 to EYS exons 13 - 43. One of the breakpoints is within FGFR4 exon 14. The fusion includes a part of the kinase domain of FGFR4. Functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0050433-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.276:BCOR_chrX:g.39909892inv Note: The BCOR rearrangement is an inversion of exons 4 - 15. One of the breakpoints is within exon 4. Functional significance is undetermined.
RARA	0	MSKCC-DMP	P-0050435-T01-IM6	RARA-intragenic	yes	unknown		unknown	RARA (NM_000964) rearrangement: c.328-35:RARA_chr17:g.48311315inv Note: The RARA rearrangement is an inversion of exons 4 - 9. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0050445-T01-IM6	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.284-420:FANCA_chr16:g.50248117del Note: The FANCA rearrangement is a deletion of exons 4 - 43.
TMPRSS2	0	MSKCC-DMP	P-0050445-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-4720:TMPRSS2_c.18+6052:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0050445-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-4720:TMPRSS2_c.18+6052:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
CCDC6	0	MSKCC-DMP	P-0049588-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190235 Macro-dissection: Not Performed
RET	0	MSKCC-DMP	P-0049588-T01-IM6	RET-CCDC6 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CCDC6-RET fusion. Note: The rearrangement is an in-frame fusion between genes CCDC6 Exon1 (NM_005436) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190235 Macro-dissection: Not Performed
CD74	0	MSKCC-DMP	P-0049640-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_004355) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190234 Macro-dissection: Not Performed
ROS1	0	MSKCC-DMP	P-0049640-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_004355) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV3-CLIN-20190234 Macro-dissection: Not Performed
DBI	0	MSKCC-DMP	P-0050196-T01-IM6	BRAF-DBI fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DBI-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes DBI Exon4 (NM_001282634) and BRAF Exon10 (NM_004333). DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:  AR (NM_000044) Variant 7 (AR V-7) PMID: 26554309, 19117982  Note: The isoform was detected with low frequency.  Lab Notes Run Number: ArcherV3-CLIN-20200001 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0050196-T01-IM6	BRAF-DBI fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: DBI-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes DBI Exon4 (NM_001282634) and BRAF Exon10 (NM_004333). DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:  AR (NM_000044) Variant 7 (AR V-7) PMID: 26554309, 19117982  Note: The isoform was detected with low frequency.  Lab Notes Run Number: ArcherV3-CLIN-20200001 Macro-dissection: Not Performed
NCOR1	0	MSKCC-DMP	P-0036748-T02-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: t(17;20)(p12;p13)(chr17:g.15983421::chr20:g.2327385) Note: The NCOR1 rearrangement is a translocation with a breakpoint in intron 25. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0049848-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.265-51_c.501-802dup Note: The RB1 rearrangement is an intragenic duplication of exons 3 - 4. Functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0049848-T01-IM6	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement: c.373-28621_c.403del Note: The INPP4B rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8.
DNMT3B	0	MSKCC-DMP	P-0050452-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.1126+793_c.1529dup Note: The DNMT3B rearrangement is an intragenic duplication of exons 11 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.
CD79B	0	MSKCC-DMP	P-0050454-T01-IM6	CD79B-intragenic	yes	unknown		unknown	CD79B (NM_001039933) rearrangement: c.678:CD79B_chr17:g.62005175del Note: The CD79B rearrangement is a deletion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0050488-T01-IM6	NSD1-intragenic	yes	unknown		unknown	NSD1 (NM_022455) rearrangement: t(1;5)(p11.2;q35.3)(chr1:g.121484679::chr5:g.176678821) Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.
SHQ1	0	MSKCC-DMP	P-0050495-T01-IM6	SHQ1-intragenic	yes	unknown		unknown	SHQ1 (NM_018130) rearrangement: t(3;8)(p13;p11.21)(chr3:g.72861734::chr8:g.42218035) Note: The SHQ1 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.
GOLPH3L	0	MSKCC-DMP	P-0050499-T01-IM6	PBRM1-GOLPH3L fusion	yes	unknown		unknown	GOLPH3L (NM_018178) - PBRM1 (NM_018313) rearrangement: t(1;3)(q21.3;p21.1)(chr1:g.150659882::chr3:g.52582106) Note: The GOLPH3L - PBRM1 rearrangement is a translocation that results in a fusion of GOLPH3L exons 1 - 2 to PBRM1 exon 30. One of the breakpoints is within PBRM1 exon 30. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0050499-T01-IM6	PBRM1-GOLPH3L fusion	yes	unknown		unknown	GOLPH3L (NM_018178) - PBRM1 (NM_018313) rearrangement: t(1;3)(q21.3;p21.1)(chr1:g.150659882::chr3:g.52582106) Note: The GOLPH3L - PBRM1 rearrangement is a translocation that results in a fusion of GOLPH3L exons 1 - 2 to PBRM1 exon 30. One of the breakpoints is within PBRM1 exon 30. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0050515-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: t(3;12)(p21.1;q24.23)(chr3:g.52439888::chr12:g.120555325) Note: The BAP1 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined. Multiple rearrangements involving BAP1 were detected in this sample and a more complex rearrangement resulting in a BAP1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CDH1	0	MSKCC-DMP	P-0050529-T01-IM6	CDH1-intragenic	yes	unknown		unknown	CDH1 (NM_004360) rearrangement: c.49-148:CDH1_chr16:g.68767896del Note: The CDH1 rearrangement is a deletion of exon 1.
DDX6	0	MSKCC-DMP	P-0050534-T01-IM6	TCF3-DDX6 fusion	yes	unknown		out of frame	DDX6 (NM_004397) - TCF3 (NM_001136139) rearrangement: t(11;19)(q23.3;p13.3)(chr11:g.118643584::chr19:g.1615424) Note: The DDX6 - TCF3 rearrangement is a translocation that results in a fusion of DDX6 exons 1 - 4 to TCF3 exons 17 - 18. Functional significance is undetermined.
TCF3	0	MSKCC-DMP	P-0050534-T01-IM6	TCF3-DDX6 fusion	yes	unknown		out of frame	DDX6 (NM_004397) - TCF3 (NM_001136139) rearrangement: t(11;19)(q23.3;p13.3)(chr11:g.118643584::chr19:g.1615424) Note: The DDX6 - TCF3 rearrangement is a translocation that results in a fusion of DDX6 exons 1 - 4 to TCF3 exons 17 - 18. Functional significance is undetermined.
GRIN2A	0	MSKCC-DMP	P-0050541-T01-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) rearrangement: c.646:GRIN2A_chr16:g.27280740inv Note: The GRIN2A rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0050541-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-55175:ERG_c.838+32:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1 - 4 and TMPRSS2 exons 9 - 14. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449). Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0050541-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-55175:ERG_c.838+32:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1 - 4 and TMPRSS2 exons 9 - 14. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449). Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ETV1	0	MSKCC-DMP	P-0050548-T01-IM6	PTK2-ETV1 fusion	yes	unknown		unknown	ETV1 (NM_001163147) - PTK2 (NM_005607) rearrangement: t(7;8)(p21.2;q24.3)(chr7:g.13975429::chr8:g.141762207) Note: The ETV1 - PTK2 rearrangement is a translocation that results in a fusion of ETV1 exons 1 - 7 to PTK2 exons 18 - 32. One of the breakpoints is within ETV1 exon 7. Multiple rearrangements involving ETV1 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated. Functional significance is undetermined.
PTK2	0	MSKCC-DMP	P-0050548-T01-IM6	PTK2-ETV1 fusion	yes	unknown		unknown	ETV1 (NM_001163147) - PTK2 (NM_005607) rearrangement: t(7;8)(p21.2;q24.3)(chr7:g.13975429::chr8:g.141762207) Note: The ETV1 - PTK2 rearrangement is a translocation that results in a fusion of ETV1 exons 1 - 7 to PTK2 exons 18 - 32. One of the breakpoints is within ETV1 exon 7. Multiple rearrangements involving ETV1 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated. Functional significance is undetermined.
PLIN5	0	MSKCC-DMP	P-0050566-T01-IM6	PTPRS-PLIN5 fusion	yes	unknown		out of frame	PLIN5 (NM_001013706) - PTPRS (NM_002850) rearrangement: c.61-544:PLIN5_c.719-11:PTPRSdup Note: The PLIN5 - PTPRS rearrangement is a duplication that results in a fusion of PLIN5 exons 1 - 2 to PTPRS exons 10 - 38. Functional significance is undetermined.
PTPRS	0	MSKCC-DMP	P-0050566-T01-IM6	PTPRS-PLIN5 fusion	yes	unknown		out of frame	PLIN5 (NM_001013706) - PTPRS (NM_002850) rearrangement: c.61-544:PLIN5_c.719-11:PTPRSdup Note: The PLIN5 - PTPRS rearrangement is a duplication that results in a fusion of PLIN5 exons 1 - 2 to PTPRS exons 10 - 38. Functional significance is undetermined.
MET	0	MSKCC-DMP	P-0050566-T01-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: t(1;7)(p33;q31.2)(chr1:g.47763737::chr7:g.116411552) Note: The MET rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MET	0	MSKCC-DMP	P-0046209-T02-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon 14 skipping (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20200002 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0050024-T02-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon 14 skipping (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20200003 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0050251-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon 14 skipping (NM_000245). Lab Notes Run Number: ArcherV3-CLIN-20200002 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0050442-T01-IM6	BRAF-intragenic	yes	unknown		out of frame	BRAF (NM_004333) rearrangement: c.981-233_c.1141-1349del Note: The BRAF rearrangement is an intragenic deletion of exon 8. The rearrangement does not include the kinase domain of BRAF. Functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0050536-T01-IM6	WDR37-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) - WDR37 (NM_014023) rearrangement: t(10;11)(p15.3;q13.2)(chr10:g.1153634::chr11:g.67198895) Note: The RPS6KB2 - WDR37 rearrangement is a translocation that results in a fusion of RPS6KB2 exons 1 - 5 to WDR37 exons 12 - 14. One of the breakpoints is within RPS6KB2 exon 5. The fusion includes a part of the kinase domain of RPS6KB2. Functional significance is undetermined. Multiple rearrangements involving RPS6KB2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
WDR37	0	MSKCC-DMP	P-0050536-T01-IM6	WDR37-RPS6KB2 fusion	yes	unknown		unknown	RPS6KB2 (NM_003952) - WDR37 (NM_014023) rearrangement: t(10;11)(p15.3;q13.2)(chr10:g.1153634::chr11:g.67198895) Note: The RPS6KB2 - WDR37 rearrangement is a translocation that results in a fusion of RPS6KB2 exons 1 - 5 to WDR37 exons 12 - 14. One of the breakpoints is within RPS6KB2 exon 5. The fusion includes a part of the kinase domain of RPS6KB2. Functional significance is undetermined. Multiple rearrangements involving RPS6KB2 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0050552-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2863:TMPRSS2_c.18+17272:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0050552-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2863:TMPRSS2_c.18+17272:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
WIBG	0	MSKCC-DMP	P-0050553-T01-IM6	ERBB3-WIBG fusion	yes	unknown		out of frame	WIBG (NM_032345) - ERBB3 (NM_001982) rearrangement: c.37+7302:WIBG_c.2617-73:ERBB3inv Note: The WIBG - ERBB3 rearrangement is an inversion that results in a fusion of WIBG exon 1 to ERBB3 exons 22 - 28. The fusion includes a part of the kinase domain of ERBB3. Functional significance is undetermined. Multiple rearrangements involving ERBB3 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERBB3	0	MSKCC-DMP	P-0050553-T01-IM6	ERBB3-WIBG fusion	yes	unknown		out of frame	WIBG (NM_032345) - ERBB3 (NM_001982) rearrangement: c.37+7302:WIBG_c.2617-73:ERBB3inv Note: The WIBG - ERBB3 rearrangement is an inversion that results in a fusion of WIBG exon 1 to ERBB3 exons 22 - 28. The fusion includes a part of the kinase domain of ERBB3. Functional significance is undetermined. Multiple rearrangements involving ERBB3 were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERBB4	0	MSKCC-DMP	P-0050553-T01-IM6	PLCL1-ERBB4 fusion	yes	unknown		in frame	ERBB4 (NM_005235) - PLCL1 (NM_006226) rearrangement: c.2079+117:ERBB4_c.241-50815:PLCL1inv Note: The ERBB4 - PLCL1 rearrangement is an inversion that results in a fusion of ERBB4 exons 1 - 17 to PLCL1 exons 2 - 6. The fusion is predicted to be in frame and does not include the kinase domain of ERBB4. Functional significance is undetermined.
PLCL1	0	MSKCC-DMP	P-0050553-T01-IM6	PLCL1-ERBB4 fusion	yes	unknown		in frame	ERBB4 (NM_005235) - PLCL1 (NM_006226) rearrangement: c.2079+117:ERBB4_c.241-50815:PLCL1inv Note: The ERBB4 - PLCL1 rearrangement is an inversion that results in a fusion of ERBB4 exons 1 - 17 to PLCL1 exons 2 - 6. The fusion is predicted to be in frame and does not include the kinase domain of ERBB4. Functional significance is undetermined.
IL7R	0	MSKCC-DMP	P-0050527-T01-IM6	IL7R-intragenic	yes	unknown		unknown	IL7R (NM_002185) rearrangement: t(5;19)(p13.2;q13.11)(chr5:g.35873544::chr19:g.35201559) Note: The IL7R rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.
PTPRK	0	MSKCC-DMP	P-0050356-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20200005 Macro-dissection: Not Performed
RSPO3	0	MSKCC-DMP	P-0050356-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20200005 Macro-dissection: Not Performed
FOXO4	0	MSKCC-DMP	P-0003018-T01-IM3	MED12-FOXO4 fusion	yes	unknown		unknown	null The FOXO4-MED12 deletion is a structural rearrangement which results in the fusion of the promoter region of FOXO4 to exons 12 to 45 of MED12.
MED12	0	MSKCC-DMP	P-0003018-T01-IM3	MED12-FOXO4 fusion	yes	unknown		unknown	null The FOXO4-MED12 deletion is a structural rearrangement which results in the fusion of the promoter region of FOXO4 to exons 12 to 45 of MED12.
None	0	MSKCC-DMP	P-0003576-T01-IM5	None-intragenic	yes	unknown		unknown	None The FLCN (NM_144997) rearrangement results in the intragenic deletion of exons 4 to 9.The breakpoint is within exon 9. Its functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0050471-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2936_c.3198-479del Note: The NF1 rearrangement is an intragenic deletion of exons 22 - 24. One of the breakpoints is within exon 22.
PLCG2	0	MSKCC-DMP	P-0050471-T01-IM6	PLCG2-intragenic	yes	unknown		unknown	PLCG2 (NM_002661) rearrangement: t(16;21)(q23.3;q21.2)(chr16:g.81927563::chr21:g.26566180) Note: The PLCG2 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.
NRG3	0	MSKCC-DMP	P-0049071-T01-IM6	FGFR2-NRG3 fusion	yes	unknown		out of frame	NRG3 (NM_001010848) - FGFR2 (NM_000141) rearrangement: c.823+108972:NRG3_c.2195+27:FGFR2inv Note: The NRG3 - FGFR2 rearrangement is an inversion that results in a fusion of NRG3 exon 1 to FGFR2 exons 17 - 18. The fusion includes a part of the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FGFR2	0	MSKCC-DMP	P-0049071-T01-IM6	FGFR2-NRG3 fusion	yes	unknown		out of frame	NRG3 (NM_001010848) - FGFR2 (NM_000141) rearrangement: c.823+108972:NRG3_c.2195+27:FGFR2inv Note: The NRG3 - FGFR2 rearrangement is an inversion that results in a fusion of NRG3 exon 1 to FGFR2 exons 17 - 18. The fusion includes a part of the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
KLF4	0	MSKCC-DMP	P-0049071-T01-IM6	KLF4-intragenic	yes	unknown		unknown	KLF4 (NM_004235) rearrangement: c.631:KLF4_chr9:g.110231435del Note: The KLF4 rearrangement is a deletion of exons 3 - 5. One of the breakpoints is within exon 3.
PARP12	0	MSKCC-DMP	P-0010083-T01-IM5	BRAF-PARP12 fusion	yes	unknown		unknown	PARP12 (NM_022750) - BRAF (NM_004333) rearrangement: c.327-1194:PARP12_c.1140+2871;BRAFinv. Note: The PARP12 - BRAF rearrangement is a reciprocal inversion, with breakpoints within intron 1 of PARP12 and intron 8 of BRAF. The functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0010083-T01-IM5	BRAF-PARP12 fusion	yes	unknown		unknown	PARP12 (NM_022750) - BRAF (NM_004333) rearrangement: c.327-1194:PARP12_c.1140+2871;BRAFinv. Note: The PARP12 - BRAF rearrangement is a reciprocal inversion, with breakpoints within intron 1 of PARP12 and intron 8 of BRAF. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0020844-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0020844-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon2 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV2-CLIN-20170067 Macro-dissection: Not Performed
ARID5B	0	MSKCC-DMP	P-0025739-T01-IM6	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.277-3447_c.430del Note: The ARID5B rearrangement is an intragenic deletion of exon 3. Its functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0038853-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C(NM_170606) Rearrangement: c.7568_c.13372dup Note: The KMT2C Rearrangement results in the intragenic duplication of exons 38-52. The breakpoints are within exon38 and exon52 respectively. Its functional significance is undetermined.
MSI2	0	MSKCC-DMP	P-0015914-T01-IM6	MSI2-intragenic	yes	unknown		unknown	MSI2 (NM_138962) rearrangement: t(17;17)(p13.1;q22)(chr17:g.117316023::chr17:g.55334155) Note: The MSI2 rearrangement is a translocation that may result in the truncation of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0019560-T01-IM6	ALK-EML4 fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-16 with ALK exons 20-29): c.1968-2879:EML4_c.3172+375:ALKinv Note: The EML4 - ALK fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0019560-T01-IM6	ALK-EML4 fusion	yes	unknown		out of frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-16 with ALK exons 20-29): c.1968-2879:EML4_c.3172+375:ALKinv Note: The EML4 - ALK fusion includes the kinase domain of ALK.
RB1	0	MSKCC-DMP	P-0022650-T01-IM6	RB1-intragenic	yes	unknown		in frame	RB1 (NM_000321) rearrangement: c.2106+1354_c.2212-148del Note: The RB1 rearrangement is an intragenic deletion of exon 21. The functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0044573-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: c.1122+188:KDM5C_chrX:g.56088205inv Note: The KDM5C rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0049511-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2242+9:EML4_c.3173-597:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 19 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0049511-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2242+9:EML4_c.3173-597:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 19 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ZFHX3	0	MSKCC-DMP	P-0050353-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: t(12;16)(q14.3;q22.2)(chr12:g.66396352::chr16:g.72994092) Note: The ZFHX3 rearrangement is a translocation with a breakpoint in 5-UTR region of ZFHX3. The functional significance is undetermined.
IGSF21	0	MSKCC-DMP	P-0017046-T01-IM6	PIK3R3-IGSF21 fusion	yes	unknown		unknown	IGSF21 (NM_032880) - PIK3R3 (NM_003629) rearrangement: c.306-17554:IGSF21_c.216-2:PIK3R3inv Note: The IGSF21 - PIK3R3 rearrangement is an inversion that results in an in-frame fusion of  IGSF21 exons 1-3 with PIK3R3 exons 4-10. The functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0017046-T01-IM6	PIK3R3-IGSF21 fusion	yes	unknown		unknown	IGSF21 (NM_032880) - PIK3R3 (NM_003629) rearrangement: c.306-17554:IGSF21_c.216-2:PIK3R3inv Note: The IGSF21 - PIK3R3 rearrangement is an inversion that results in an in-frame fusion of  IGSF21 exons 1-3 with PIK3R3 exons 4-10. The functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0017046-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused in-frame with TACC3 exons 11-16): c.2274+10:FGFR3_c.1941+881:TACC3dup None
TACC3	0	MSKCC-DMP	P-0017046-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 fused in-frame with TACC3 exons 11-16): c.2274+10:FGFR3_c.1941+881:TACC3dup None
FGFR1	0	MSKCC-DMP	P-0017046-T01-IM6	FGFR1-intragenic	yes	unknown		unknown	FGFR1 (NM_001174067) rearrangement: c.348:FGFR1_chr8:g.36454836inv Note: The FGFR1 rearrangement is an inversion of exons 4 - 19, potentially disrupting gene function.
NF1	0	MSKCC-DMP	P-0021421-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.2990+21_c.3198-2del Note: The NF1 rearrangement is an intragenic deletion of exons 23-24.
ASXL2	0	MSKCC-DMP	P-0021421-T01-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.144-18272_c.2044del Note: The ASXL2 rearrangement is an intragenic deletion of exons 3-12. One of the breakpoints is within exon 12. One of the breakpoints is within exon 12.
APC	0	MSKCC-DMP	P-0032269-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.4489_chr5:g.112196053del Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0032569-T02-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: c.312+3:GNAS_chr20:g.55438526inv Note: The GNAS rearrangement is an inversion of exons 1 - 4. Functional significance is undetermined.
TRIM24	0	MSKCC-DMP	P-0032569-T02-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.1878+791:TRIM24_c.1141-552:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 11 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.  Multiple rearrangements involving BRAF were detected in this sample and a more complex rearrangement resulting in additional BRAF fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
BRAF	0	MSKCC-DMP	P-0032569-T02-IM6	BRAF-TRIM24 fusion	yes	unknown		in frame	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.1878+791:TRIM24_c.1141-552:BRAFinv Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1 - 11 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.  Multiple rearrangements involving BRAF were detected in this sample and a more complex rearrangement resulting in additional BRAF fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PARK2	0	MSKCC-DMP	P-0034036-T03-IM6	PARK2-intragenic	yes	unknown		out of frame	PARK2 (NM_004562) rearrangement: c.412+91_c.618+29764del Note: The PARK2 rearrangement is an intragenic deletion of exons 4 - 5.
KMT2D	0	MSKCC-DMP	P-0037571-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.4237-484_c.6720del Note: The KMT2D intragenic deletion involves exons 15-31
APC	0	MSKCC-DMP	P-0037673-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;22)(q22.2;q12.1)(chr5:g.112175871::chr22:g.29065471) Note: The APC rearrangement is a translocation with a breakpoint in exon 16.
SPRYD3	0	MSKCC-DMP	P-0040601-T01-IM6	KMT2D-SPRYD3 fusion	yes	unknown		unknown	SPRYD3 (NM_032840) - KMT2D (NM_003482) rearrangement: c.901+391:SPRYD3_c.14350:KMT2Ddel Note: The SPRYD3 - KMT2D rearrangement is a deletion that results in a fusion of SPRYD3 exons 1 - 8 to KMT2D exons 45 - 54. One of the breakpoints is within KMT2D exon 45.
KMT2D	0	MSKCC-DMP	P-0040601-T01-IM6	KMT2D-SPRYD3 fusion	yes	unknown		unknown	SPRYD3 (NM_032840) - KMT2D (NM_003482) rearrangement: c.901+391:SPRYD3_c.14350:KMT2Ddel Note: The SPRYD3 - KMT2D rearrangement is a deletion that results in a fusion of SPRYD3 exons 1 - 8 to KMT2D exons 45 - 54. One of the breakpoints is within KMT2D exon 45.
APC	0	MSKCC-DMP	P-0044143-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: t(5;22)(q22.2;q12.1)(chr5:g.112173427::chr22:g.29065511) Note: The APC rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0045253-T01-IM6	TRAP1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - TRAP1 (NM_016292) rearrangement: c.6286:CREBBP_c.88+22:TRAP1del Note: The CREBBP - TRAP1 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 31 to TRAP1 exons 2 - 18. One of the breakpoints is within CREBBP exon 31.
TRAP1	0	MSKCC-DMP	P-0045253-T01-IM6	TRAP1-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - TRAP1 (NM_016292) rearrangement: c.6286:CREBBP_c.88+22:TRAP1del Note: The CREBBP - TRAP1 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 31 to TRAP1 exons 2 - 18. One of the breakpoints is within CREBBP exon 31.
RAD54L	0	MSKCC-DMP	P-0045717-T01-IM6	RAD54L-intragenic	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.1033:RAD54L_chr1:g.60351411inv Note: The RAD54L rearrangement is an inversion of exons 10 - 19. One of the breakpoints is within exon 10. Functional significance is undetermined.
ALOX12B	0	MSKCC-DMP	P-0046055-T01-IM6	ALOX12B-intragenic	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: t(8;17)(q24.3;p13.1)(chr8:g.144092736::chr17:g.7977072) Note: The ALOX12B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.
ACTN4	0	MSKCC-DMP	P-0046055-T01-IM6	CIC-ACTN4 fusion	yes	unknown		unknown	ACTN4 (NM_004924) - CIC (NM_015125) rearrangement: c.912+17:ACTN4_c.3957:CICdel Note: The ACTN4 - CIC rearrangement is a deletion that results in a fusion of ACTN4 exons 1 - 9 to CIC exons 16 - 20. One of the breakpoints is within CIC exon 16. Multiple rearrangements involving CIC were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
CIC	0	MSKCC-DMP	P-0046055-T01-IM6	CIC-ACTN4 fusion	yes	unknown		unknown	ACTN4 (NM_004924) - CIC (NM_015125) rearrangement: c.912+17:ACTN4_c.3957:CICdel Note: The ACTN4 - CIC rearrangement is a deletion that results in a fusion of ACTN4 exons 1 - 9 to CIC exons 16 - 20. One of the breakpoints is within CIC exon 16. Multiple rearrangements involving CIC were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
LATS1	0	MSKCC-DMP	P-0047197-T01-IM6	LATS1-intragenic	yes	unknown		unknown	LATS1 (NM_004690) rearrangement: t(6;10)(q25.1;q24.31)(chr6:g.149983086::chr10:g.102418032) Note: The LATS1 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.
LRBA	0	MSKCC-DMP	P-0047833-T02-IM6	BRAF-LRBA fusion	yes	unknown		in frame	LRBA (NM_001199282) - BRAF (NM_004333) fusion: t(4;7)(q31.3;q34)(chr4:g.151502269::chr7:g.140493444) Note: The LRBA - BRAF fusion involves LRBA exons 1 - 40 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. Multiple rearrangements involving BRAF were detected in this sample and a more complex rearrangement is possible.
BRAF	0	MSKCC-DMP	P-0047833-T02-IM6	BRAF-LRBA fusion	yes	unknown		in frame	LRBA (NM_001199282) - BRAF (NM_004333) fusion: t(4;7)(q31.3;q34)(chr4:g.151502269::chr7:g.140493444) Note: The LRBA - BRAF fusion involves LRBA exons 1 - 40 and BRAF exons 9 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF. Multiple rearrangements involving BRAF were detected in this sample and a more complex rearrangement is possible.
AR	0	MSKCC-DMP	P-0047833-T02-IM6	AR-intragenic	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2174-2789_c.2567del Note: The AR rearrangement is an intragenic deletion of exons 5 - 7. One of the breakpoints is within exon 7. This represents an ARv567es.
TCF3	0	MSKCC-DMP	P-0048063-T01-IM6	SBNO2-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - SBNO2 (NM_014963) rearrangement: c.24:TCF3_c.93+1074:SBNO2del Note: The TCF3 - SBNO2 rearrangement is a deletion that results in a fusion of TCF3 exon 1 to SBNO2 exons 3 - 32. One of the breakpoints is within TCF3 exon 1.
SBNO2	0	MSKCC-DMP	P-0048063-T01-IM6	SBNO2-TCF3 fusion	yes	unknown		unknown	TCF3 (NM_001136139) - SBNO2 (NM_014963) rearrangement: c.24:TCF3_c.93+1074:SBNO2del Note: The TCF3 - SBNO2 rearrangement is a deletion that results in a fusion of TCF3 exon 1 to SBNO2 exons 3 - 32. One of the breakpoints is within TCF3 exon 1.
RUNX1	0	MSKCC-DMP	P-0048170-T01-IM6	RUNX1-intragenic	yes	unknown		unknown	RUNX1 (NM_001754) rearrangement: c.806-152:RUNX1_chr21:g.20859351inv Note: The RUNX1 rearrangement is an inversion of exons 8 - 9. Functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0048658-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.160:CDK12_chr17:g.37615359del Note: The CDK12 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The rearrangement does not include the kinase domain of CDK12.
RAD21	0	MSKCC-DMP	P-0049065-T01-IM6	EIF3H-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.446:RAD21_c.133-12565:EIF3Hdel Note: The RAD21 - EIF3H rearrangement is a deletion that results in a fusion of RAD21 exons 1 - 5 to EIF3H exons 2 - 8. One of the breakpoints is within RAD21 exon 5.
EIF3H	0	MSKCC-DMP	P-0049065-T01-IM6	EIF3H-RAD21 fusion	yes	unknown		unknown	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.446:RAD21_c.133-12565:EIF3Hdel Note: The RAD21 - EIF3H rearrangement is a deletion that results in a fusion of RAD21 exons 1 - 5 to EIF3H exons 2 - 8. One of the breakpoints is within RAD21 exon 5.
TPM3	0	MSKCC-DMP	P-0049078-T01-IM6	NTRK1-TPM3 fusion	yes	unknown		unknown	TPM3 (NM_001278190) - NTRK1 (NM_002529)  fusion: c.395-6179:TPM3_ c.963:NTRK1inv Note: The TPM3 -NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within NTRK1 exon 8.
NTRK1	0	MSKCC-DMP	P-0049078-T01-IM6	NTRK1-TPM3 fusion	yes	unknown		unknown	TPM3 (NM_001278190) - NTRK1 (NM_002529)  fusion: c.395-6179:TPM3_ c.963:NTRK1inv Note: The TPM3 -NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within NTRK1 exon 8.
KMT2C	0	MSKCC-DMP	P-0049956-T01-IM6	KMT2C-intragenic	yes	unknown		out of frame	KMT2C (NM_170606) rearrangement: c.4794-35_c.14344-1615del Note: The KMT2C rearrangement is an intragenic deletion of exons 33 - 55.
TP53	0	MSKCC-DMP	P-0050143-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.994-4:TP53_chr17:g.8374380del Note: The TP53 rearrangement is a deletion of exons 1 - 9.
TP53	0	MSKCC-DMP	P-0050152-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.673-86:TP53_chr17:g.7582323del Note: The TP53 rearrangement is a deletion of exons 1 - 6.
NCOR1	0	MSKCC-DMP	P-0050437-T01-IM6	NCOR1-intragenic	yes	unknown		unknown	NCOR1 (NM_006311) rearrangement: c.1634+2329_c.1769inv Note: The NCOR1 rearrangement is an intragenic inversion of exon 16. One of the breakpoints is within exon 16. Functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0050437-T01-IM6	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement: t(8;19)(p12;p13.11)(chr8:g.35063141::chr19:g.18273183) Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
EPHA7	0	MSKCC-DMP	P-0050437-T01-IM6	EPHA7-intragenic	yes	unknown		out of frame	EPHA7 (NM_004440) rearrangement: c.1634-602_c.1743-219del Note: The EPHA7 rearrangement is an intragenic deletion of exon 8. The rearrangement does not include the kinase domain of EPHA7.
TP53	0	MSKCC-DMP	P-0050516-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.75-6_c.920-2del Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 8.
TRIM24	0	MSKCC-DMP	P-0032569-T02-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon11 (NM_015905) and BRAF Exon9 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190168 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0032569-T02-IM6	BRAF-TRIM24 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TRIM24-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes TRIM24 Exon11 (NM_015905) and BRAF Exon9 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190168 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0037571-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190019 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0037571-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190019 Macro-dissection: Unknown
MECOM	0	MSKCC-DMP	P-0045582-T01-IM6	RSPO2-MECOM fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MECOM-RSPO2 fusion. Note: The rearrangement is a fusion between genes MECOM Exon2 (NM_004991) and RSPO2 Exon2 (NM_178565).   Note2: The fusion involves the untranslated region of RSPO2 exon2.  Lab Notes Run Number: Archerv3-CLIN-20190157 Macro-dissection: Performed
RSPO2	0	MSKCC-DMP	P-0045582-T01-IM6	RSPO2-MECOM fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MECOM-RSPO2 fusion. Note: The rearrangement is a fusion between genes MECOM Exon2 (NM_004991) and RSPO2 Exon2 (NM_178565).   Note2: The fusion involves the untranslated region of RSPO2 exon2.  Lab Notes Run Number: Archerv3-CLIN-20190157 Macro-dissection: Performed
LRBA	0	MSKCC-DMP	P-0047833-T02-IM6	BRAF-LRBA fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: LRBA-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes LRBA Exon41 (NM_006726) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20200001 Macro-dissection: Not Performed
BRAF	0	MSKCC-DMP	P-0047833-T02-IM6	BRAF-LRBA fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: LRBA-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes LRBA Exon41 (NM_006726) and BRAF Exon9 (NM_004333). Lab Notes Run Number: ArcherV3-CLIN-20200001 Macro-dissection: Not Performed
TFG	0	MSKCC-DMP	P-0048063-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: ArcherV3-CLIN-20190204 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0048063-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: ArcherV3-CLIN-20190204 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0048933-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190221 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0048933-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190221 Macro-dissection: Unknown
TPM3	0	MSKCC-DMP	P-0049078-T01-IM6	NTRK1-TPM3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TPM3-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes TPM3 Exon8 (NM_152263) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
NTRK1	0	MSKCC-DMP	P-0049078-T01-IM6	NTRK1-TPM3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TPM3-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes TPM3 Exon8 (NM_152263) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV3-CLIN-20190223 Macro-dissection: Unknown
TFG	0	MSKCC-DMP	P-0049749-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732   Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: ArcherV3-CLIN-20190239 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0049749-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732   Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: ArcherV3-CLIN-20190239 Macro-dissection: Performed
MKRN1	0	MSKCC-DMP	P-0001036-T01-IM3	BRAF-MKRN1 fusion	yes	unknown		in frame	null
BRAF	0	MSKCC-DMP	P-0001036-T01-IM3	BRAF-MKRN1 fusion	yes	unknown		in frame	null
SPOCK3	0	MSKCC-DMP	P-0013641-T01-IM5	MLL-SPOCK3 fusion	yes	unknown		unknown	SPOCK3 (NM_016950) - MLL (NM_001197104) rearrangement: t(4;11)(11q23.3;4q32.3)(chr11:g.118373285::chr4:g.168136694) Note: The SPOCK3 - MLL rearrangement is a translocation that results in the fusion of SPOCK3 exons 1-2 with MLL exons 27-36. One of the breakpoints is within exon 27 of MLL. The functional significance is undetermined.
MLL	0	MSKCC-DMP	P-0013641-T01-IM5	MLL-SPOCK3 fusion	yes	unknown		unknown	SPOCK3 (NM_016950) - MLL (NM_001197104) rearrangement: t(4;11)(11q23.3;4q32.3)(chr11:g.118373285::chr4:g.168136694) Note: The SPOCK3 - MLL rearrangement is a translocation that results in the fusion of SPOCK3 exons 1-2 with MLL exons 27-36. One of the breakpoints is within exon 27 of MLL. The functional significance is undetermined.
EIF3H	0	MSKCC-DMP	P-0013641-T01-IM5	RAD21-EIF3H fusion	yes	unknown		in frame	EIF3H (NM_003756) - RAD21 (NM_006265)  rearrangement: c.132+13079:EIF3H_c.1471-37:RAD21dup Note: The EIF3H - RAD21 rearrangement is a duplication that results in the in-frame fusion of EIF3H exon 1 with RAD21 exons 12-14. The functional significance is undetermined.
RAD21	0	MSKCC-DMP	P-0013641-T01-IM5	RAD21-EIF3H fusion	yes	unknown		in frame	EIF3H (NM_003756) - RAD21 (NM_006265)  rearrangement: c.132+13079:EIF3H_c.1471-37:RAD21dup Note: The EIF3H - RAD21 rearrangement is a duplication that results in the in-frame fusion of EIF3H exon 1 with RAD21 exons 12-14. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0020006-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.1660_chr19:g.15241142inv Note: The DOT1L rearrangement is an inversion which includes exons 18-28 of DOT1L. One of the breakpoints is within DOT1L exon 18. The functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0020118-T01-IM6	RANBP3-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - RANBP3 (NM_007322) rearrangement: c.1705:DNMT1_c.22+8490:RANBP3del Note: The DNMT1- RANBP3 rearrangement is a deletion that results in the fusion of DNMT1 exons 1-20 with RANBP3 exons 2-17. One of the breakpoints is within DNMT1 exon 20. The functional significance is undetermined.
RANBP3	0	MSKCC-DMP	P-0020118-T01-IM6	RANBP3-DNMT1 fusion	yes	unknown		unknown	DNMT1 (NM_001379) - RANBP3 (NM_007322) rearrangement: c.1705:DNMT1_c.22+8490:RANBP3del Note: The DNMT1- RANBP3 rearrangement is a deletion that results in the fusion of DNMT1 exons 1-20 with RANBP3 exons 2-17. One of the breakpoints is within DNMT1 exon 20. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0022397-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606): t(4;7)(q35.2;q36.1)(chr4:g.188268934::chr7:g.151878590) Note: The KMT2C rearrangement is a translocation that may result in a truncation of exons 36-59. One of the breakpoints is within exon 36. The functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0022507-T01-IM6	FLT3-intragenic	yes	unknown		unknown	FLT3 (NM_004119) Rearrangement : chr13:g.29588123_c.742+49:FLT3inv Note: The FLT3 Rearrangement results in the inversion of exons 1-6 of FLT3. Its functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0023560-T01-IM6	AXL-intragenic	yes	unknown		unknown	AXL (NM_021913) Rearrangement : chr19:g.35782298_c.586+33:AXLdel Note: The AXL Rearrangement results in the inversion of exons 1-4. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0023767-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: chr12:g.49348815_c.12025inv Note: The KMT2D rearrangement results in the inversion of exons 39-54. One of the breakpoints is within exon 39. The functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0023767-T01-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: t(1;16)(p36.22;p13.3)(chr1:g.10744557::chr16:g.360175) Note: The AXIN1 rearrangement is a translocation which involves exons 4-11. Its functional significance is undetermined.
PAK7	0	MSKCC-DMP	P-0024365-T01-IM6	PAK7-intragenic	yes	unknown		unknown	PAK7 (NM_177990) Rearrangement : c.434:PAK7_chr20:g.11058657inv Note: The PAK7 Rearrangement results in the inversion of PAK7 exons 1-4. One of the breakpoints is within exon4. Its functional significance is undetermined.
RIN2	0	MSKCC-DMP	P-0024365-T01-IM6	RTEL1-RIN2 fusion	yes	unknown		out of frame	RIN2 (NM_001242581) -RTEL1 (NM_032957) Rearrangement : c.2348-1384:RIN2_c.2338-6:RTEL1 Note: The RIN2 -RTEL1 Rearrangement results in the fusion of RIN2 exons 1-10 with RTEL1 exons 26-35. Its functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0024365-T01-IM6	RTEL1-RIN2 fusion	yes	unknown		out of frame	RIN2 (NM_001242581) -RTEL1 (NM_032957) Rearrangement : c.2348-1384:RIN2_c.2338-6:RTEL1 Note: The RIN2 -RTEL1 Rearrangement results in the fusion of RIN2 exons 1-10 with RTEL1 exons 26-35. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0024726-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: chr22:g.41442701_c.6996:EP300del Note: The EP300 rearrangement is a deletion of exons 1-30. The functional significance is undetermined.
XRCC2	0	MSKCC-DMP	P-0024726-T01-IM6	XRCC2-intragenic	yes	unknown		unknown	XRCC2 (NM_005431) rearrangement: chr7:g.151369240_c.416:XRCC2inv Note: The XRCC2 rearrangement is an inversion with a breakpoint in exon 3. The functional significance is undetermined.
ACOXL	0	MSKCC-DMP	P-0024740-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		out of frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.753+11588:ACOXL_c.394+1521:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in the fusion of ACOXL exons 1-9 with BCL2L11 exons 3-18. The functional significance is undetermined.
BCL2L11	0	MSKCC-DMP	P-0024740-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		out of frame	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.753+11588:ACOXL_c.394+1521:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in the fusion of ACOXL exons 1-9 with BCL2L11 exons 3-18. The functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0025026-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.4240_c.4779+1208dup Note: The EP300 rearrangement is an intragenic duplication of exons 26-29. One of the breakpoints is within exon 26. Its functional significance is undetermined.
NTRK3	0	MSKCC-DMP	P-0029267-T03-IM6	NTRK3-intragenic	yes	unknown		unknown	NTRK3 (NM_001012338) rearrangement: c.1432:NTRK3_chr15:g.85411017del Note: The NTRK3 rearrangement is a deletion of exons 14 - 20. One of the breakpoints is within exon 14. The rearrangement includes the kinase domain of NTRK3. The functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ERBB2	0	MSKCC-DMP	P-0029267-T03-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.2208+78:ERBB2_chr17:g.43293842del Note: The ERBB2 rearrangement is a deletion of exons 19 - 27. The rearrangement includes a part of the kinase domain of ERBB2. The functional significance is undetermined.
SETD8	0	MSKCC-DMP	P-0037553-T01-IM6	SETD8-intragenic	yes	unknown		unknown	SETD8 (NM_020382) rearrangement: t(10;12)(q21.3;q24.31)(chr10:g.69599715::chr12:g.123891871) Note: The SETD8 rearrangement is a translocation involving exon 8. Its functional significance is undetermined.
PDPK1	0	MSKCC-DMP	P-0038649-T01-IM6	PDPK1-intragenic	yes	unknown		unknown	PDPK1 (NM_002613) rearrangement: t(4,16)(q32.2;p13.3)(chr4:g.163884492::chr16:g.2647209) Note: The PDPK1 rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0038960-T01-IM6	PIK3C2G-intragenic	yes	unknown		in frame	PIK3C2G (NM_004570) rearrangement: c.3965-98:PIK3C2G_chr12:g.11089445inv Note: The PIK3C2G rearrangement is an inversion of exons 1 - 29. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0038960-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: t(14;19)(q24.3;p13.12)(chr14:g.75937499::chr19:g.15364419) Note: The BRD4 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.
EPCAM	0	MSKCC-DMP	P-0039012-T01-IM6	EPCAM-intragenic	yes	unknown		unknown	EPCAM (NM_002354) rearrangement: c.78_c.468dup Note : The EPCAM rearrangement is an intragenic duplication of exons 2 - 4. The breakpoints are within exon 2 and exon 4 respectively. Its functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0039685-T01-IM6	PAX8-intragenic	yes	unknown		unknown	PAX8 (NM_003466) rearrangement: c.1088-1971:PAX8_chr2:g.116993803del Note: The PAX8 rearrangement is a deletion of exons 1 - 9. Functional significance is undetermined.
NPM1	0	MSKCC-DMP	P-0039798-T01-IM6	NPM1-intragenic	yes	unknown		unknown	NPM1 (NM_002520) rearrangement: c.165_c.524+2207del Note: The NPM1 rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 3.
PPP6C	0	MSKCC-DMP	P-0039798-T01-IM6	PPP6C-intragenic	yes	unknown		unknown	PPP6C (NM_002721) rearrangement: c.75+714:PPP6C_chr9:g.127962827del Note: The PPP6C rearrangement is a deletion of exon 1.
DNMT1	0	MSKCC-DMP	P-0044349-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: t(1;19)(q42.2;p13.2)(chr1:g.231871724::chr19:g.10273346) Note: The DNMT1 rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.
ERBB4	0	MSKCC-DMP	P-0044349-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.2487+102:ERBB4_chr2:g.211981994del Note: The ERBB4 rearrangement is a deletion of exons 21 - 28. The rearrangement includes a part of the kinase domain of ERBB4. Functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0044349-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.3239-2441_c.3568del Note: The BCOR rearrangement is an intragenic deletion of exons 7 - 8. One of the breakpoints is within exon 8.
BTK	0	MSKCC-DMP	P-0044349-T01-IM6	BTK-intragenic	yes	unknown		unknown	BTK (NM_000061) rearrangement: c.392-121:BTK_chrX:g.121586039del Note: The BTK rearrangement is a deletion of exons 1 - 5. The rearrangement does not include the kinase domain of BTK. Functional significance is undetermined.
GPS2	0	MSKCC-DMP	P-0044451-T01-IM6	GPS2-intragenic	yes	unknown		unknown	GPS2 (NM_004489) rearrangement: c.850:GPS2_chr17:g.7214985del Note: The GPS2 rearrangement is a deletion of exons 10 - 11. One of the breakpoints is within exon 10.
RFWD2	0	MSKCC-DMP	P-0045544-T01-IM6	RFWD2-intragenic	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: c.566-2043_c.617del Note: The RFWD2 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0045544-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.292+96:ATR_chr3:g.132133790del Note: The ATR rearrangement is a deletion of exons 4 - 47.
PTPRK	0	MSKCC-DMP	P-0034853-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20200103 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0034853-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20200103 Macro-dissection: Performed
FANCA	0	MSKCC-DMP	P-0006124-T01-IM5	FANCA-intragenic	yes	unknown		unknown	FANCA (NM_000135) rearrangement: c.1627-1039_1603del Note: The FANCA (NM_000135)  rearrangement event  results in the intragenic deletion of FANCA exon 17. One of the breakpoints is within FANCA exon 17.
None	0	MSKCC-DMP	P-0006124-T01-IM5	None-intragenic	yes	unknown		unknown	None
TSC1	0	MSKCC-DMP	P-0040386-T01-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: t(9;10)(q34.13;q26.11)(chr9:g.135797351::chr10:g.120090828) Note: The TSC1 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.
ABL1	0	MSKCC-DMP	P-0040386-T01-IM6	ABL1-intragenic	yes	unknown		unknown	ABL1 (NM_005157) rearrangement: c.823-69_c.2132del Note: The ABL1 rearrangement is an intragenic deletion of exons 5 - 11. One of the breakpoints is within exon 11. The rearrangement includes a part of the kinase domain of ABL1. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0037474-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) Rearrangement : c.1885_c.3814+31dup Note: The TSC2 Rearrangement results in the intragenic duplication of exons 18-31 of TSC2. One of the breakpoints is within exon18. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0010497-T01-IM5	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement : c.1996:EP300_chr22:g.41694128del Note: The EP300 rearrangement event results in the deletion of EP300 exons 10-31. One of the breakpoints is within EP300 exon10.
RPS6KA4	0	MSKCC-DMP	P-0014908-T01-IM6	RPS6KA4-intragenic	yes	unknown		unknown	RPS6KA4 (NM_003942) Rearrangement : c.188-3737:BAD_ c.1593:RPS6KA4dup Note: The RPS6KA4 Rearrangement results in the duplication of exons1-13. One of the breakpoints is within exon 13. Its functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0033800-T01-IM6	DDI2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - DDI2 (NM_032341) rearrangement: c.2992:SPEN_c.760+1876:DDI2dup Note: The SPEN - DDI2 rearrangement is a duplication which results in the fusion of SPEN exons 1-11 with DDI2 exons 6-9. One of the breakpoints is within SPEN exon 11. Its functional significance is undetermined.
DDI2	0	MSKCC-DMP	P-0033800-T01-IM6	DDI2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - DDI2 (NM_032341) rearrangement: c.2992:SPEN_c.760+1876:DDI2dup Note: The SPEN - DDI2 rearrangement is a duplication which results in the fusion of SPEN exons 1-11 with DDI2 exons 6-9. One of the breakpoints is within SPEN exon 11. Its functional significance is undetermined.
CCDC6	0	MSKCC-DMP	P-0004901-T01-IM5	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion (CCDC6 exon1 with RET exons 12-20) : :CCDC6_:RETinv Note: The CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion includes the kinase domain of RET gene.
RET	0	MSKCC-DMP	P-0004901-T01-IM5	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion (CCDC6 exon1 with RET exons 12-20) : :CCDC6_:RETinv Note: The CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion includes the kinase domain of RET gene.
RB1	0	MSKCC-DMP	P-0014595-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: t(13;17)(q14.2;q13.1)(chr13:g.48916736::chr17:g.7541457) Note: The RB1 (NM_000321) rearrangement is a translocation with a breakpoint within exon 3 of RB1 and the other breakpoint in a genomic region on chr17 that may result in a truncation of RB1 gene.
MITF	0	MSKCC-DMP	P-0014595-T01-IM6	MITF-intragenic	yes	unknown		unknown	MITF (NM_198159) rearrangement: c.587_c.762+1035inv Note: The MITF (NM_198159) rearrangement is an inversion of exons 4-5. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0015058-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-451:TMPRSS2_c.18+8534:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0015058-T03-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-451:TMPRSS2_c.18+8534:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
CENPE	0	MSKCC-DMP	P-0015058-T03-IM6	FAM175A-CENPE fusion	yes	unknown		out of frame	CENPE (NM_001813) - FAM175A (NM_139076) rearrangement: c.7541-96:CENPE_c.477-36:FAM175Adel The CENPE - FAM175A rearrangement is a deletion that results in a fusion of CENPE exons 1 - 44 to FAM175A exons 6 - 9. The functional significance is undetermined.
FAM175A	0	MSKCC-DMP	P-0015058-T03-IM6	FAM175A-CENPE fusion	yes	unknown		out of frame	CENPE (NM_001813) - FAM175A (NM_139076) rearrangement: c.7541-96:CENPE_c.477-36:FAM175Adel The CENPE - FAM175A rearrangement is a deletion that results in a fusion of CENPE exons 1 - 44 to FAM175A exons 6 - 9. The functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0016886-T01-IM6	GNB4-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) - GNB4 (NM_021629) Rearrangement : c.5128:SETD2_c.-43+6699:GNB4dup Note: The SETD2 - GNB4 Rearrangement results in the fusion of exons 1-9 of  SETD2 with exon 2 of GBN4. Its functional significance is undetermined.
GNB4	0	MSKCC-DMP	P-0016886-T01-IM6	GNB4-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) - GNB4 (NM_021629) Rearrangement : c.5128:SETD2_c.-43+6699:GNB4dup Note: The SETD2 - GNB4 Rearrangement results in the fusion of exons 1-9 of  SETD2 with exon 2 of GBN4. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0027293-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-426:TMPRSS2_c.39+52928:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 1-3 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion is not entirely characterized by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0027293-T02-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-426:TMPRSS2_c.39+52928:ERGinv Note: The TMPRSS2 - ERG Rearrangement results in the inversion of exons 2-14 of TMPRSS2 and exons 1-3 of ERG. This is not the canonical TMPRSS2 - ERG fusion, however the possibility that this fusion is not entirely characterized by IMPACT panel cannot be ruled out. Its functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0031217-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.597_c.3382+1300del Note: The SMARCA4 rearrangement is a deletion of exons 4-24. One of the breakpoints is within exon 4.
NOTCH3	0	MSKCC-DMP	P-0031217-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.2002:NOTCH3_chr19:g.12995615del Note: The NOTCH3 rearrangement is a deletion of exons 13-33. One of the breakpoints is within exon 13. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0031217-T01-IM6	BRD4-intragenic	yes	unknown		unknown	BRD4 (NM_058243) rearrangement: c.850-131:BRD4_chr19:g.15386105del Note: The BRD4 rearrangement is a deletion of exons 1-5. The functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0032339-T01-IM6	STAT6-NAB2 fusion	yes	unknown		unknown	NAB2(NM_005967) - STAT6(NM_003153) Rearrangement: c.*434:NAB2_c.1512+724:STAT6inv Note: The NAB2 - STAT6 rearrangement is an inversion with breakpoints in 3' UTR region of NAB2 and intron 13 of STAT6. A more complex rearrangement resulting in a NAB2 - STAT6 fusion is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NAB2 and STAT6 genes.
STAT6	0	MSKCC-DMP	P-0032339-T01-IM6	STAT6-NAB2 fusion	yes	unknown		unknown	NAB2(NM_005967) - STAT6(NM_003153) Rearrangement: c.*434:NAB2_c.1512+724:STAT6inv Note: The NAB2 - STAT6 rearrangement is an inversion with breakpoints in 3' UTR region of NAB2 and intron 13 of STAT6. A more complex rearrangement resulting in a NAB2 - STAT6 fusion is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NAB2 and STAT6 genes.
SMARCA4	0	MSKCC-DMP	P-0032339-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4(NM_003072) Rearrangement: c.-89_c.2002-30del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 1-13. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0032352-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+414:TMPRSS2_c.18+20493:ERG Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0032352-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.126+414:TMPRSS2_c.18+20493:ERG Note: The TMPRSS2 - ERG fusion is predicted to be in frame.
SOX9	0	MSKCC-DMP	P-0033856-T01-IM6	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.1496:SOX9_chr17:g.70485069del Note: The SOX9 rearrangement is a deletion of exon 3. One of the breakpoints is within exon 3. Its functional significance is undetermined.
RPS6KB2	0	MSKCC-DMP	P-0033879-T01-IM6	RPS6KB2-intragenic	yes	unknown		unknown	RPS6KB2 (NM_003952) rearrangement: c.857_c.*516del Note: The RPS6KB2 rearrangement is a deletion that includes exons 10-15 of RPS6KB2. One of the breakpoints is within exon 10. The functional significance is  undetermined.
HRAS	0	MSKCC-DMP	P-0037022-T01-IM6	HRAS-intragenic	yes	unknown		unknown	HRAS (NM_001130442) rearrangement: t(9;11)(q33.2;p15.5)(chr9:g.124685061::chr11:g.533931) Note: The HRAS rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037022-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2103:TMPRSS2_c.39+59657:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
ERG	0	MSKCC-DMP	P-0037022-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2103:TMPRSS2_c.39+59657:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.
LACE1	0	MSKCC-DMP	P-0037022-T01-IM6	ROS1-LACE1 fusion	yes	unknown		in frame	LACE1 (NM_145315) - ROS1 (NM_002944) rearrangement: c.808-19179:LACE1_c.5079+1435:ROS1inv Note: The LACE1 - ROS1 rearrangement is an inversion that results in the in-frame fusion of LACE1 exons 1-7 with ROS1 exons 31-43 and includes the kinase domain of ROS1. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0037022-T01-IM6	ROS1-LACE1 fusion	yes	unknown		in frame	LACE1 (NM_145315) - ROS1 (NM_002944) rearrangement: c.808-19179:LACE1_c.5079+1435:ROS1inv Note: The LACE1 - ROS1 rearrangement is an inversion that results in the in-frame fusion of LACE1 exons 1-7 with ROS1 exons 31-43 and includes the kinase domain of ROS1. The functional significance is undetermined.
SMAD3	0	MSKCC-DMP	P-0037028-T01-IM6	SMAD3-intragenic	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.401-37:SMAD3_chr15:g.67333415del Note: The SMAD3 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0037105-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.618+20977_c.670del Note: The PARK2 rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6.
DROSHA	0	MSKCC-DMP	P-0037120-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA (NM_013235) rearrangement: t(5;8)(p13.3;q22.1)(chr5:g.31485128::chr8:g.97865366) Note:  The DROSHA rearrangement is a translocation with a breakpoint in intron 13. Multiple rearrangements involving DROSHA were detected in this sample and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ERBB2	0	MSKCC-DMP	P-0037167-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2553:ERBB2_c.2864:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1-21, which do not include the entire kinase domain, to CDK12 exons 10-14. The breakpoints are within ERBB2 exon 21 and CDK12 exon 10. The functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0037167-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2553:ERBB2_c.2864:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1-21, which do not include the entire kinase domain, to CDK12 exons 10-14. The breakpoints are within ERBB2 exon 21 and CDK12 exon 10. The functional significance is undetermined.
ARID2	0	MSKCC-DMP	P-0037307-T01-IM6	TWF1-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) - TWF1 (NM_001242397) rearrangement: c.5096:ARID2_c.283-514:TWF1inv Note: The ARID2 - TWF1 rearrangement is an inversion that results in the fusion of ARID2 exons 1-18 with TWF1 exons 4-10. One of the breakpoints is within ARID2 exon 18.
TWF1	0	MSKCC-DMP	P-0037307-T01-IM6	TWF1-ARID2 fusion	yes	unknown		unknown	ARID2 (NM_152641) - TWF1 (NM_001242397) rearrangement: c.5096:ARID2_c.283-514:TWF1inv Note: The ARID2 - TWF1 rearrangement is an inversion that results in the fusion of ARID2 exons 1-18 with TWF1 exons 4-10. One of the breakpoints is within ARID2 exon 18.
TSC2	0	MSKCC-DMP	P-0037392-T01-IM6	TSC2-intragenic	yes	unknown		in frame	TSC2 (NM_000548) rearrangement: c.2356-81_c.2742+74del Note: The TSC2 rearrangement results in the in-frame intragenic deletion of exons 22 to 24.
ARID5B	0	MSKCC-DMP	P-0037409-T01-IM6	KDM2B-ARID5B fusion	yes	unknown		out of frame	ARID5B (NM_032199) - KDM2B (NM_032590) rearrangement: t(10;12)(q21.2;q24.31)(chr10:g.63760134::chr12:g.121894267) Note: The ARID5B - KDM2B rearrangement is a translocation which may result in the fusion of ARID5B exons 1-4 with KDM2B exons 13-23. Its functional significance is undetermined.
KDM2B	0	MSKCC-DMP	P-0037409-T01-IM6	KDM2B-ARID5B fusion	yes	unknown		out of frame	ARID5B (NM_032199) - KDM2B (NM_032590) rearrangement: t(10;12)(q21.2;q24.31)(chr10:g.63760134::chr12:g.121894267) Note: The ARID5B - KDM2B rearrangement is a translocation which may result in the fusion of ARID5B exons 1-4 with KDM2B exons 13-23. Its functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0037409-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(19;22)(p13.3;q13.1)(chr19:g.2217933::chr22:g.37994256) Note: The DOT1L rearrangement is a translocation involving exon 22. Its functional significance is undetermined.
ST7	0	MSKCC-DMP	P-0037409-T01-IM6	MET-ST7 fusion	yes	unknown		in frame	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-654:ST7_c.3029-571:METdup Note: The ST7 - MET rearrangement is a duplication which results in the fusion of ST7 exon 1 with MET exon 15-21. This includes the kinase domain of MET. Its functional significance is undetermined.
MET	0	MSKCC-DMP	P-0037409-T01-IM6	MET-ST7 fusion	yes	unknown		in frame	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-654:ST7_c.3029-571:METdup Note: The ST7 - MET rearrangement is a duplication which results in the fusion of ST7 exon 1 with MET exon 15-21. This includes the kinase domain of MET. Its functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0037461-T01-IM6	ASXL1-intragenic	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1335:ASXL1_chr20:g.31472710del
EZH2	0	MSKCC-DMP	P-0037461-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.456:EZH2_chr7:g.148410813del
APOOL	0	MSKCC-DMP	P-0037461-T01-IM6	ATRX-APOOL fusion	yes	unknown		in frame	APOOL (NM_198450) - ATRX (NM_000489) rearrangement: c.16-7781:APOOL_c.190-138:ATRXinv Note: The APOOL - ATRX rearrangement is an inversion the results in a fusion of APOOL exon 1 to ATRX exons 4-35. The fusion is predicted to be in-frame. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0037461-T01-IM6	ATRX-APOOL fusion	yes	unknown		in frame	APOOL (NM_198450) - ATRX (NM_000489) rearrangement: c.16-7781:APOOL_c.190-138:ATRXinv Note: The APOOL - ATRX rearrangement is an inversion the results in a fusion of APOOL exon 1 to ATRX exons 4-35. The fusion is predicted to be in-frame. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037664-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-300_c.556+2378inv Note: The TMPRSS2 rearrangement results in the inversion of exons 2-5. The functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0039149-T01-IM6	PAK1-intragenic	yes	unknown		out of frame	PAK1 (NM_002576) rearrangement: c.191-2797_c.598-16del Note: The PAK1 rearrangement is an intragenic deletion of exons 3 - 6. The rearrangement does not include the kinase domain of PAK1. Functional significance is undetermined.
POLE	0	MSKCC-DMP	P-0039149-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: t(1;12)(q21.1;q24.33)(chr1:g.145089130::chr12:g.133248890) Note: The POLE rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0039149-T01-IM6	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) rearrangement: t(1;17)(p36.13;q25.1)(chr1:g.16202815::chr17:g.74507875) Note: The SPEN rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0039725-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.1164:WHSC1L1_chr8:g.37538799inv Note: The WHSC1L1 rearrangement is an inversion of exons 6 - 24. One of the breakpoints is within exon 6. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0039734-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.60+6317_c.1063-65del Note: The NF1 rearrangement is an intragenic deletion of exons 2 - 9.
TMPRSS2	0	MSKCC-DMP	P-0040180-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3769:TMPRSS2_c.19-1393:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0040180-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3769:TMPRSS2_c.19-1393:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
DIS3	0	MSKCC-DMP	P-0040259-T01-IM6	DIS3-intragenic	yes	unknown		unknown	DIS3 (NM_014953) rearrangement: c.1239+8:DIS3_chr13:g.75899289inv Note: The DIS3 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
SETD2	0	MSKCC-DMP	P-0040561-T02-IM6	PHF7-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) - PHF7 (NM_016483) rearrangement: c.310:SETD2_c.681-15:PHF7inv Note: The SETD2 - PHF7 rearrangement is an inversion that results in a fusion of SETD2 exons 1 - 3 to PHF7 exons 9 - 11. One of the breakpoints is within SETD2 exon 3. Functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0040561-T02-IM6	PHF7-SETD2 fusion	yes	unknown		unknown	SETD2 (NM_014159) - PHF7 (NM_016483) rearrangement: c.310:SETD2_c.681-15:PHF7inv Note: The SETD2 - PHF7 rearrangement is an inversion that results in a fusion of SETD2 exons 1 - 3 to PHF7 exons 9 - 11. One of the breakpoints is within SETD2 exon 3. Functional significance is undetermined.
CDK4	0	MSKCC-DMP	P-0040815-T01-IM6	DCC-CDK4 fusion	yes	unknown		unknown	CDK4 (NM_000075) - DCC (NM_005215) rearrangement: t(12;18)(q14.1;q21.2)(chr12:g.58145295::chr18:g.50434781) Note: The CDK4 - DCC rearrangement is a translocation that results in a fusion of CDK4 exons 1 - 2 to DCC exons 4 - 29. One of the breakpoints is within CDK4 exon 2. The fusion includes a part of the kinase domain of CDK4. This fusion occurs in the setting of CDK4 amplification. Functional significance is undetermined.
DCC	0	MSKCC-DMP	P-0040815-T01-IM6	DCC-CDK4 fusion	yes	unknown		unknown	CDK4 (NM_000075) - DCC (NM_005215) rearrangement: t(12;18)(q14.1;q21.2)(chr12:g.58145295::chr18:g.50434781) Note: The CDK4 - DCC rearrangement is a translocation that results in a fusion of CDK4 exons 1 - 2 to DCC exons 4 - 29. One of the breakpoints is within CDK4 exon 2. The fusion includes a part of the kinase domain of CDK4. This fusion occurs in the setting of CDK4 amplification. Functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0040985-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;6)(p12;q12)(chr1:g.120497534::chr6:g.64352374) Note: The NOTCH2 rearrangement is a translocation with a breakpoint in intron 13. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0041149-T01-IM6	RAD51-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - RAD51 (NM_002875) fusion: t(7;15)(p11.2;q15.1)(chr7:g.55268799::chr15:g.40996189) Note: The EGFR - RAD51 fusion involves EGFR exons 1 - 24 and RAD51 exons 4 - 10. The fusion is predicted to be in frame and includes the kinase domain of EGFR. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RAD51	0	MSKCC-DMP	P-0041149-T01-IM6	RAD51-EGFR fusion	yes	unknown		in frame	EGFR (NM_005228) - RAD51 (NM_002875) fusion: t(7;15)(p11.2;q15.1)(chr7:g.55268799::chr15:g.40996189) Note: The EGFR - RAD51 fusion involves EGFR exons 1 - 24 and RAD51 exons 4 - 10. The fusion is predicted to be in frame and includes the kinase domain of EGFR. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TSC1	0	MSKCC-DMP	P-0041211-T01-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: t(9;14)(q34.13;q23.1)(chr9:g.135787874::chr14:g.59220977) Note: The TSC1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
RRBP1	0	MSKCC-DMP	P-0041308-T02-IM6	BRAF-RRBP1 fusion	yes	unknown		in frame	RRBP1 (NM_004587) - BRAF (NM_004333) fusion: t(7;20)(q34;p12.1)(chr7:g.140485917::chr20:g.17634546) Note: The RRBP1 - BRAF fusion involves RRBP1 exons 1 - 3 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.  This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help better characterize this BRAF structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
BRAF	0	MSKCC-DMP	P-0041308-T02-IM6	BRAF-RRBP1 fusion	yes	unknown		in frame	RRBP1 (NM_004587) - BRAF (NM_004333) fusion: t(7;20)(q34;p12.1)(chr7:g.140485917::chr20:g.17634546) Note: The RRBP1 - BRAF fusion involves RRBP1 exons 1 - 3 and BRAF exons 10 - 18. The fusion is predicted to be in frame and includes the kinase domain of BRAF.  This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help better characterize this BRAF structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
HIVEP3	0	MSKCC-DMP	P-0041372-T01-IM6	BRD4-HIVEP3 fusion	yes	unknown		out of frame	HIVEP3 (NM_001127714) - BRD4 (NM_058243) rearrangement: t(1;19)(p34.2;p13.12)(chr1:g.41995508::chr19:g.15378399) Note: The HIVEP3 - BRD4 rearrangement is a translocation that results in a fusion of HIVEP3 exons 1 - 5 to BRD4 exons 4 - 20. Functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0041372-T01-IM6	BRD4-HIVEP3 fusion	yes	unknown		out of frame	HIVEP3 (NM_001127714) - BRD4 (NM_058243) rearrangement: t(1;19)(p34.2;p13.12)(chr1:g.41995508::chr19:g.15378399) Note: The HIVEP3 - BRD4 rearrangement is a translocation that results in a fusion of HIVEP3 exons 1 - 5 to BRD4 exons 4 - 20. Functional significance is undetermined.
TAP2	0	MSKCC-DMP	P-0041386-T01-IM6	TAP2-intragenic	yes	unknown		unknown	TAP2 (NM_018833) rearrangement: c.1932+570:TAP2_chr6:g.27423075inv Note: The TAP2 rearrangement is an inversion of exon 12. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041461-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1651:TMPRSS2_c.18+15743:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0041461-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1651:TMPRSS2_c.18+15743:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0041464-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.9453+372_c.10376del Note: The KMT2C rearrangement is an intragenic deletion of exons 41 - 43. One of the breakpoints is within exon 43.
URI1	0	MSKCC-DMP	P-0041472-T01-IM6	KMT2B-URI1 fusion	yes	unknown		in frame	URI1 (NM_003796) - KMT2B (NM_014727) rearrangement: c.118-14115:URI1_c.2457+43:KMT2Bdel Note: The URI1 - KMT2B rearrangement is a deletion that results in a fusion of URI1 exon 1 to KMT2B exons 4 - 37. The fusion is predicted to be in frame.
KMT2B	0	MSKCC-DMP	P-0041472-T01-IM6	KMT2B-URI1 fusion	yes	unknown		in frame	URI1 (NM_003796) - KMT2B (NM_014727) rearrangement: c.118-14115:URI1_c.2457+43:KMT2Bdel Note: The URI1 - KMT2B rearrangement is a deletion that results in a fusion of URI1 exon 1 to KMT2B exons 4 - 37. The fusion is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0041602-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4147:TMPRSS2_c.39+6989:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 4 - 11 and involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0041602-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4147:TMPRSS2_c.39+6989:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 4 - 11 and involves the ERG non-canonical transcript (NM_004449).
ERI3	0	MSKCC-DMP	P-0041616-T01-IM6	PARP1-ERI3 fusion	yes	unknown		unknown	ERI3 (NM_024066) - PARP1 (NM_001618) rearrangement: c.931+10191:ERI3_c.3021:PARP1dup Note: The ERI3 - PARP1 rearrangement is a duplication that results in a fusion of ERI3 exons 1 - 7 to PARP1 exon 23. One of the breakpoints is within PARP1 exon 23. Functional significance is undetermined.
PARP1	0	MSKCC-DMP	P-0041616-T01-IM6	PARP1-ERI3 fusion	yes	unknown		unknown	ERI3 (NM_024066) - PARP1 (NM_001618) rearrangement: c.931+10191:ERI3_c.3021:PARP1dup Note: The ERI3 - PARP1 rearrangement is a duplication that results in a fusion of ERI3 exons 1 - 7 to PARP1 exon 23. One of the breakpoints is within PARP1 exon 23. Functional significance is undetermined.
RAB11FIP4	0	MSKCC-DMP	P-0041698-T01-IM6	NF1-RAB11FIP4 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.337-2647:RAB11FIP4_c.7402:NF1dup Note: The RAB11FIP4 - NF1 rearrangement is a duplication that results in a fusion of RAB11FIP4 exons 1 - 3 to NF1 exons 50 - 58. One of the breakpoints is within NF1 exon 50. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0041698-T01-IM6	NF1-RAB11FIP4 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.337-2647:RAB11FIP4_c.7402:NF1dup Note: The RAB11FIP4 - NF1 rearrangement is a duplication that results in a fusion of RAB11FIP4 exons 1 - 3 to NF1 exons 50 - 58. One of the breakpoints is within NF1 exon 50. Functional significance is undetermined.
RGS11	0	MSKCC-DMP	P-0041702-T01-IM6	AXIN1-RGS11 fusion	yes	unknown		unknown	RGS11 (NM_183337) - AXIN1 (NM_003502) rearrangement: c.506+22:RGS11_c.2192:AXIN1dup Note: The RGS11 - AXIN1 rearrangement is a duplication that results in a fusion of RGS11 exons 1 - 7 to AXIN1 exons 9 - 11. One of the breakpoints is within AXIN1 exon 9. Functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0041702-T01-IM6	AXIN1-RGS11 fusion	yes	unknown		unknown	RGS11 (NM_183337) - AXIN1 (NM_003502) rearrangement: c.506+22:RGS11_c.2192:AXIN1dup Note: The RGS11 - AXIN1 rearrangement is a duplication that results in a fusion of RGS11 exons 1 - 7 to AXIN1 exons 9 - 11. One of the breakpoints is within AXIN1 exon 9. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041957-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+1817:TMPRSS2_chr21:g.39964163del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help better characterize this structural variant.  If additional material is available and results will be reported under a separate accession number.
SMAD4	0	MSKCC-DMP	P-0042018-T01-IM6	SMAD4-intragenic	yes	unknown		in frame	SMAD4 (NM_005359) rearrangement: c.454+193_c.956-2252del Note: The SMAD4 rearrangement is an intragenic deletion of exons 5 - 8.
PREX2	0	MSKCC-DMP	P-0042082-T01-IM6	PREX2-intragenic	yes	unknown		unknown	PREX2 (NM_024870) rearrangement: c.3421+2_c.3440del Note: The PREX2 rearrangement is an intragenic deletion of exon 28. One of the breakpoints is within exon 28. Functional significance is undetermined.
ANKRD36	0	MSKCC-DMP	P-0042270-T01-IM6	NTRK1-ANKRD36 fusion	yes	unknown		out of frame	ANKRD36 (NM_001164315) - NTRK1 (NM_002529) fusion: t(1;2)(q23.1;q11.2)(chr1:g.156844593::chr2:g.97835462) Note: The ANKRD36 - NTRK1 fusion involves ANKRD36 exons 1 - 22 and NTRK1 exons 11 - 17. The fusion includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0042270-T01-IM6	NTRK1-ANKRD36 fusion	yes	unknown		out of frame	ANKRD36 (NM_001164315) - NTRK1 (NM_002529) fusion: t(1;2)(q23.1;q11.2)(chr1:g.156844593::chr2:g.97835462) Note: The ANKRD36 - NTRK1 fusion involves ANKRD36 exons 1 - 22 and NTRK1 exons 11 - 17. The fusion includes the kinase domain of NTRK1.
XPO1	0	MSKCC-DMP	P-0042342-T01-IM6	USP34-XPO1 fusion	yes	unknown		out of frame	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement: c.3069+76:XPO1_c.3013+938:USP34del Note: The XPO1 - USP34 rearrangement is a deletion that results in a fusion of XPO1 exons 1 - 24 to USP34 exons 22 - 80. Functional significance is undetermined.
USP34	0	MSKCC-DMP	P-0042342-T01-IM6	USP34-XPO1 fusion	yes	unknown		out of frame	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement: c.3069+76:XPO1_c.3013+938:USP34del Note: The XPO1 - USP34 rearrangement is a deletion that results in a fusion of XPO1 exons 1 - 24 to USP34 exons 22 - 80. Functional significance is undetermined.
CBFB	0	MSKCC-DMP	P-0042610-T01-IM6	CDH3-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) - CDH3 (NM_001793) rearrangement: c.4:CBFB_c.45+57:CDH3inv Note: The CBFB rearrangement is an inversion that includes CBFB exon 1 and CDH3 exon 1. One of the breakpoints is within CBFB exon 1. Functional significance is undetermined.
CDH3	0	MSKCC-DMP	P-0042610-T01-IM6	CDH3-CBFB fusion	yes	unknown		unknown	CBFB (NM_022845) - CDH3 (NM_001793) rearrangement: c.4:CBFB_c.45+57:CDH3inv Note: The CBFB rearrangement is an inversion that includes CBFB exon 1 and CDH3 exon 1. One of the breakpoints is within CBFB exon 1. Functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0042696-T01-IM6	CDH1-intragenic	yes	unknown		out of frame	CDH1 (NM_004360) rearrangement: c.1138-504_c.2164+44dup Note: The CDH1 rearrangement is an intragenic duplication of exons 9 - 13. Functional significance is undetermined.
NF2	0	MSKCC-DMP	P-0042814-T01-IM6	NF2-intragenic	yes	unknown		in frame	NF2 (NM_000268) rearrangement: c.114+3348_c.675+206dup Note: The NF2 rearrangement is an intragenic duplication of exons 2 - 7. Functional significance is undetermined.
PTEN	0	MSKCC-DMP	P-0042971-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.14:PTEN_chr10:g.9509369inv Note: The PTEN rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042971-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-4095:TMPRSS2_chr21:g.40014900del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined. The possibility of a TMPRSS2-ERG fusion cannot be excluded.
NOTCH3	0	MSKCC-DMP	P-0042974-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: t(1;19)(p31.1;p13.12)(chr1:g.81334562::chr19:g.15296585) Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0042986-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: t(8;19)(p23.2;p13.3)(chr8:g.3679668::chr19:g.2229723) Note: The DOT1L rearrangement is a translocation with a breakpoint in intron 27. Functional significance is undetermined.
BAP1	0	MSKCC-DMP	P-0042986-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.1117-130:BAP1_chr3:g.52253450dup Note: The BAP1 rearrangement is a duplication of exons 12 - 17. Functional significance is undetermined. Multiple rearrangements involving BAP1 were detected in this sample and a more complex rearrangement involving BAP1 is possible.
INPP4B	0	MSKCC-DMP	P-0042986-T01-IM6	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669) rearrangement: c.2176_c.2277-1036del Note: The INPP4B rearrangement is an intragenic deletion of exon 22. One of the breakpoints is within exon 22.
TP53	0	MSKCC-DMP	P-0043158-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.993+21:TP53_chr17:g.1926474inv Note: The TP53 rearrangement is an inversion of exons 10 - 11. Functional significance is undetermined.
VTCN1	0	MSKCC-DMP	P-0043159-T01-IM6	VTCN1-intragenic	yes	unknown		unknown	VTCN1 (NM_024626) rearrangement: c.510_c.724+2536del Note: The VTCN1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
BRIP1	0	MSKCC-DMP	P-0043489-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: t(17;20)(q23.2;q13.31)(chr17:g.59886002::chr20:g.55040117) Note: The BRIP1 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043489-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1361:TMPRSS2_c.18+110:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0043489-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1361:TMPRSS2_c.18+110:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame. Functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0043532-T01-IM6	WHSC1L1-intragenic	yes	unknown		in frame	WHSC1L1 (NM_023034) rearrangement: c.1855+93_c.2242+1298del Note: The WHSC1L1 rearrangement is an intragenic deletion of exons 10 - 12. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0043587-T01-IM6	CREBBP-intragenic	yes	unknown		out of frame	CREBBP (NM_004380) rearrangement: c.4395-17_c.4728+335dup Note: The CREBBP rearrangement is an intragenic duplication of exons 27 - 28. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0043587-T01-IM6	NF1-intragenic	yes	unknown		in frame	NF1 (NM_001042492) rearrangement: c.61-29266_c.288+96dup Note: The NF1 rearrangement is an intragenic duplication of exons 2 - 3. Functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0043591-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3112:ARID1B_chr6:g.119442122del Note: The ARID1B rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11.
NF1	0	MSKCC-DMP	P-0043789-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) rearrangement: c.61-8307_c.2251+56dup Note: The NF1 rearrangement is an intragenic duplication of exons 2 - 18. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0043789-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.730-1474_c.5798dup Note: The EP300 rearrangement is an intragenic duplication of exons 3 - 31. One of the breakpoints is within exon 31. Functional significance is undetermined.
ERF	0	MSKCC-DMP	P-0043929-T01-IM6	DNAJC4-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - DNAJC4 (NM_005528) rearrangement: t(11;19)(q13.1;q13.2)(chr11:g.64001339::chr19:g.42752786) Note: The ERF - DNAJC4 rearrangement is a translocation that results in a fusion of ERF exons 1 - 4 to DNAJC4 exons 6 - 7. One of the breakpoints is within ERF exon 4. Functional significance is undetermined.
DNAJC4	0	MSKCC-DMP	P-0043929-T01-IM6	DNAJC4-ERF fusion	yes	unknown		unknown	ERF (NM_006494) - DNAJC4 (NM_005528) rearrangement: t(11;19)(q13.1;q13.2)(chr11:g.64001339::chr19:g.42752786) Note: The ERF - DNAJC4 rearrangement is a translocation that results in a fusion of ERF exons 1 - 4 to DNAJC4 exons 6 - 7. One of the breakpoints is within ERF exon 4. Functional significance is undetermined.
PIK3R1	0	MSKCC-DMP	P-0043935-T01-IM6	PIK3R1-intragenic	yes	unknown		unknown	PIK3R1 (NM_181523) rearrangement: c.916+5568_c.1379del Note: The PIK3R1 rearrangement is an intragenic deletion of exons 8 - 11. One of the breakpoints is within exon 11.
CACNA1A	0	MSKCC-DMP	P-0044150-T01-IM6	CARM1-CACNA1A fusion	yes	unknown		unknown	CACNA1A (NM_001127222) - CARM1 (NM_199141) rearrangement: c.5732-2757:CACNA1A_c.49:CARM1inv Note: The CACNA1A - CARM1 rearrangement is an inversion that results in a fusion of CACNA1A exons 1 - 38 to CARM1 exons 1 - 16. One of the breakpoints is within CARM1 exon 1. Functional significance is undetermined.
CARM1	0	MSKCC-DMP	P-0044150-T01-IM6	CARM1-CACNA1A fusion	yes	unknown		unknown	CACNA1A (NM_001127222) - CARM1 (NM_199141) rearrangement: c.5732-2757:CACNA1A_c.49:CARM1inv Note: The CACNA1A - CARM1 rearrangement is an inversion that results in a fusion of CACNA1A exons 1 - 38 to CARM1 exons 1 - 16. One of the breakpoints is within CARM1 exon 1. Functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0044204-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: t(1;4)(q21.3;p16.3)(chr1:g.153840676::chr4:g.1978453) Note: The WHSC1 rearrangement is a translocation with a breakpoint in intron 21. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044288-T01-IM6	MPP5-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - MPP5 (NM_022474) rearrangement: t(14;21)(q23.3;q22.3)(chr14:g.67791033::chr21:g.42869498) Note: The TMPRSS2 - MPP5 rearrangement is a translocation that results in a fusion of TMPRSS2 exons 1 - 2 to MPP5 exon 15. The fusion is predicted to be in frame. Functional significance is undetermined.
MPP5	0	MSKCC-DMP	P-0044288-T01-IM6	MPP5-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - MPP5 (NM_022474) rearrangement: t(14;21)(q23.3;q22.3)(chr14:g.67791033::chr21:g.42869498) Note: The TMPRSS2 - MPP5 rearrangement is a translocation that results in a fusion of TMPRSS2 exons 1 - 2 to MPP5 exon 15. The fusion is predicted to be in frame. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044288-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4464:TMPRSS2_c.18+3461:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0044288-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4464:TMPRSS2_c.18+3461:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
DOT1L	0	MSKCC-DMP	P-0044305-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4068_c.4606+865del Note: The DOT1L rearrangement is an intragenic deletion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0044465-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783638::chr6:g.117646909) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0044465-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783638::chr6:g.117646909) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
FAM172A	0	MSKCC-DMP	P-0044659-T01-IM6	NPM1-FAM172A fusion	yes	unknown		unknown	FAM172A (NM_032042) - NPM1 (NM_002520) rearrangement: c.1109-62102:FAM172A_c.525:NPM1inv Note: The FAM172A - NPM1 rearrangement is an inversion that results in a fusion of FAM172A exons 1 - 8 to NPM1 exons 7 - 11. One of the breakpoints is within NPM1 exon 7. Functional significance is undetermined.
NPM1	0	MSKCC-DMP	P-0044659-T01-IM6	NPM1-FAM172A fusion	yes	unknown		unknown	FAM172A (NM_032042) - NPM1 (NM_002520) rearrangement: c.1109-62102:FAM172A_c.525:NPM1inv Note: The FAM172A - NPM1 rearrangement is an inversion that results in a fusion of FAM172A exons 1 - 8 to NPM1 exons 7 - 11. One of the breakpoints is within NPM1 exon 7. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0044905-T01-IM6	HAGH-TSC2 fusion	yes	unknown		out of frame	TSC2 (NM_000548) - HAGH (NM_005326) rearrangement: c.2742+122:TSC2_c.76+165:HAGHinv Note: The TSC2 - HAGH rearrangement is an inversion that results in a fusion of TSC2 exons 1 - 24 to HAGH exons 2 - 9. Functional significance is undetermined.
HAGH	0	MSKCC-DMP	P-0044905-T01-IM6	HAGH-TSC2 fusion	yes	unknown		out of frame	TSC2 (NM_000548) - HAGH (NM_005326) rearrangement: c.2742+122:TSC2_c.76+165:HAGHinv Note: The TSC2 - HAGH rearrangement is an inversion that results in a fusion of TSC2 exons 1 - 24 to HAGH exons 2 - 9. Functional significance is undetermined.
RAB11FIP4	0	MSKCC-DMP	P-0044905-T01-IM6	NF1-RAB11FIP4 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.159+10486:RAB11FIP4_c.4286:NF1dup Note: The RAB11FIP4 - NF1 rearrangement is a duplication that results in a fusion of RAB11FIP4 exon 1 to NF1 exons 32 - 58. One of the breakpoints is within NF1 exon 32. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044905-T01-IM6	NF1-RAB11FIP4 fusion	yes	unknown		unknown	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.159+10486:RAB11FIP4_c.4286:NF1dup Note: The RAB11FIP4 - NF1 rearrangement is a duplication that results in a fusion of RAB11FIP4 exon 1 to NF1 exons 32 - 58. One of the breakpoints is within NF1 exon 32. Functional significance is undetermined.
IDUA	0	MSKCC-DMP	P-0044999-T01-IM6	LATS1-IDUA fusion	yes	unknown		unknown	IDUA (NM_000203) - LATS1 (NM_004690) rearrangement: t(4;6)(p16.3;q25.1)(chr4:g.981090::chr6:g.149983308) Note: The IDUA - LATS1 rearrangement is a translocation that results in a fusion of IDUA exon 1 to LATS1 exon 8. One of the breakpoints is within LATS1 exon 8. Functional significance is undetermined.
LATS1	0	MSKCC-DMP	P-0044999-T01-IM6	LATS1-IDUA fusion	yes	unknown		unknown	IDUA (NM_000203) - LATS1 (NM_004690) rearrangement: t(4;6)(p16.3;q25.1)(chr4:g.981090::chr6:g.149983308) Note: The IDUA - LATS1 rearrangement is a translocation that results in a fusion of IDUA exon 1 to LATS1 exon 8. One of the breakpoints is within LATS1 exon 8. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0045222-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2243-30:EML4_c.3172+839:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 19 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0045222-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2243-30:EML4_c.3172+839:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 19 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
CDK12	0	MSKCC-DMP	P-0047119-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.682:CDK12_chr17:g.37554870del Note: The CDK12 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The rearrangement does not include the kinase domain of CDK12.
ERG	0	MSKCC-DMP	P-0048791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-23334:ERG_c.56-1202:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by the MSK-IMPACT assay  cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0048791-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-23334:ERG_c.56-1202:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14. Functional significance is undetermined. While this is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not detected by the MSK-IMPACT assay  cannot be ruled out.
TMPRSS2	0	MSKCC-DMP	P-0037022-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190005 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0037022-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20190005 Macro-dissection: Unknown
TFG	0	MSKCC-DMP	P-0037167-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID:19797732  Lab Notes Run Number: ArcherV3-CLIN-20190008 Macro-dissection: Unknown
GPR128	0	MSKCC-DMP	P-0037167-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID:19797732  Lab Notes Run Number: ArcherV3-CLIN-20190008 Macro-dissection: Unknown
TFG	0	MSKCC-DMP	P-0039725-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190059 Macro-dissection: Not Performed
GPR128	0	MSKCC-DMP	P-0039725-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190059 Macro-dissection: Not Performed
EGFR	0	MSKCC-DMP	P-0041149-T01-IM6	RAD51-EGFR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EGFR-RAD51 fusion. Note: The rearrangement is an in-frame fusion between genes EGFR Exon24 (NM_005228) and RAD51 Exon4 (NM_002875). Lab Notes Run Number: Archerv3-CLIN-20190081 Macro-dissection: Not Performed
RAD51	0	MSKCC-DMP	P-0041149-T01-IM6	RAD51-EGFR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EGFR-RAD51 fusion. Note: The rearrangement is an in-frame fusion between genes EGFR Exon24 (NM_005228) and RAD51 Exon4 (NM_002875). Lab Notes Run Number: Archerv3-CLIN-20190081 Macro-dissection: Not Performed
RRBP1	0	MSKCC-DMP	P-0041308-T02-IM6	BRAF-RRBP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RRBP1 -BRAF fusion. Note: The rearrangement is an in-frame fusion between genes RRBP1  Exon2 (XM_005260787) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190140 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0041308-T02-IM6	BRAF-RRBP1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: RRBP1 -BRAF fusion. Note: The rearrangement is an in-frame fusion between genes RRBP1  Exon2 (XM_005260787) and BRAF Exon10 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190140 Macro-dissection: Performed
PROSC	0	MSKCC-DMP	P-0041973-T01-IM6	FGFR1-PROSC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PROSC-FGFR1 fusion. Note: The rearrangement is an in-frame fusion between genes PROSC Exon5 (NM_007198) and FGFR1 Exon3 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190095 Macro-dissection: Performed
FGFR1	0	MSKCC-DMP	P-0041973-T01-IM6	FGFR1-PROSC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PROSC-FGFR1 fusion. Note: The rearrangement is an in-frame fusion between genes PROSC Exon5 (NM_007198) and FGFR1 Exon3 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190095 Macro-dissection: Performed
ANKRD36	0	MSKCC-DMP	P-0042270-T01-IM6	NTRK1-ANKRD36 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ANKRD36-NTRK1 fusion. Note: The rearrangement is an out of frame fusion between genes ANKRD36 Exon22 (NM_001164315) and NTRK1 Exon11 (NM_002529). Note2: This event was detected with a relatively low read support.  Lab Notes Run Number: Archerv3-CLIN-20190099 Macro-dissection: Performed
NTRK1	0	MSKCC-DMP	P-0042270-T01-IM6	NTRK1-ANKRD36 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ANKRD36-NTRK1 fusion. Note: The rearrangement is an out of frame fusion between genes ANKRD36 Exon22 (NM_001164315) and NTRK1 Exon11 (NM_002529). Note2: This event was detected with a relatively low read support.  Lab Notes Run Number: Archerv3-CLIN-20190099 Macro-dissection: Performed
FOXA1	0	MSKCC-DMP	P-0000505-T02-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) Rearrangement : c.700:FOXA1_chr14:g.40011548dup Note: The FOXA1 Rearrangement results in the duplication of exon2 of FOXA1. One of the breakpoints is within exon2. Its functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0008099-T01-IM5	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement : c.4455+404_4798inv Note: The KDM5A (NM_001042603) rearrangement event results in the inversion of KDM5A exon27. One of the breakpoints is within KDM5A and is predicted to disrupt the splice site of KDM5A exon27.
MSH2	0	MSKCC-DMP	P-0008404-T02-IM5	MSH2-intragenic	yes	unknown		out of frame	MSH2 (NM_00025) rearrangement: c.1387-6599_c.1511-124del Note: The MSH2 (NM_00025) rearrangement is an intragenic deletion of exon9. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0021532-T01-IM6	1311del-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement c.2432_c.2356-1311del Note: The ALK rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon. The functional significance is undetermined.
1311del	0	MSKCC-DMP	P-0021532-T01-IM6	1311del-ALK fusion	yes	unknown		unknown	ALK (NM_004304) rearrangement c.2432_c.2356-1311del Note: The ALK rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0022097-T02-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) Rearrangement: c.1606:CIC_chr19:g.42738021del Note: The CIC rearrangement results in the deletion of CIC exons 1 to 10. One of the breakpoints is within exon 10 of CIC. The functional significance is undetermined. Further analysis to characterize this rearrangement will be performed using the Archer targeted RNAseq assay if additional material is available and results will be reported under a separate accession number.
RASA1	0	MSKCC-DMP	P-0030121-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.426_c.540-27225del Note: The RASA1 rearrangement is an intragenic deletion of a part of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
OXCT1	0	MSKCC-DMP	P-0032256-T01-IM6	MAP3K1-OXCT1 fusion	yes	unknown		unknown	OXCT1 (NM_00043) - MAP3K1 (NM_005921) Rearrangement : c.415-379:OXCT1_c.3998:MAP3K1inv Note: The OXCT1 - MAP3K1 Rearrangement results in the fusion of exons 1-4  of OXCT1 with exons 17-20 of MAP3K1. It includes the protein kinase domain of MAP3K1.
MAP3K1	0	MSKCC-DMP	P-0032256-T01-IM6	MAP3K1-OXCT1 fusion	yes	unknown		unknown	OXCT1 (NM_00043) - MAP3K1 (NM_005921) Rearrangement : c.415-379:OXCT1_c.3998:MAP3K1inv Note: The OXCT1 - MAP3K1 Rearrangement results in the fusion of exons 1-4  of OXCT1 with exons 17-20 of MAP3K1. It includes the protein kinase domain of MAP3K1.
TP53	0	MSKCC-DMP	P-0035825-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) Rearrangement : t(11,17)(p11.2,p13.1)(chr11:g.48110744::chr17:g.7578421) Note: The TP53 Rearrangement is a translocation event with a breakpoint in exon5. Its functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0036092-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1138:KIF5B_c.2136+229:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0036092-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 12-20): c.1725+1138:KIF5B_c.2136+229:RETinv Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.
AURKA	0	MSKCC-DMP	P-0036826-T01-IM6	FAM114A2-AURKA fusion	yes	unknown		unknown	AURKA (NM_003600) - FAM114A2 (NM_018691) rearrangement: t(5;20)(q33.2;q13.2)(chr5:g.153381607::chr20:g.54945351) Note: The AUKRA - FAM114A2 rearrangement is a translocation that results in the fusion of AURKA exons 1-9 with FAM114A2 exons 12-14 and includes the kinase domain of AURKA. One of the breakpoints is within AURKA exon 9.
FAM114A2	0	MSKCC-DMP	P-0036826-T01-IM6	FAM114A2-AURKA fusion	yes	unknown		unknown	AURKA (NM_003600) - FAM114A2 (NM_018691) rearrangement: t(5;20)(q33.2;q13.2)(chr5:g.153381607::chr20:g.54945351) Note: The AUKRA - FAM114A2 rearrangement is a translocation that results in the fusion of AURKA exons 1-9 with FAM114A2 exons 12-14 and includes the kinase domain of AURKA. One of the breakpoints is within AURKA exon 9.
TMPRSS2	0	MSKCC-DMP	P-0036826-T01-IM6	ZCCHC6-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ZCCHC6 (NM_024617) rearrangement: t(9;21)(q21.33;q22.3)(chr9:g.88940236::chr21:g.42869032) Note: The TMPRSS2 - ZCCHC6 rearrangement is a translocation with breakpoints with in TMPRSS2 intron 2 and ZCCHC6 intron 12.  Multiple TMPRSS2 rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ZCCHC6	0	MSKCC-DMP	P-0036826-T01-IM6	ZCCHC6-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ZCCHC6 (NM_024617) rearrangement: t(9;21)(q21.33;q22.3)(chr9:g.88940236::chr21:g.42869032) Note: The TMPRSS2 - ZCCHC6 rearrangement is a translocation with breakpoints with in TMPRSS2 intron 2 and ZCCHC6 intron 12.  Multiple TMPRSS2 rearrangements were detected in this sample, and a more complex rearrangement is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0037021-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+1323:TMPRSS2_chr21:g.43538595del Note: The TMPRSS2 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.
MAPK3	0	MSKCC-DMP	P-0037151-T01-IM6	MAPK3-intragenic	yes	unknown		out of frame	MAPK3 (NM_002746) Rearrangement : c.354-685_c.907+9dup Note: The MAPK3 Rearrangement results in the duplication of exons3-6 of MAPK3.This doesn't include the protein kinase domain of MAPK3. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037151-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon2): c.55+3777:TMPRSS2_c.40-18163::ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canaonical transcript of ERG.
ERG	0	MSKCC-DMP	P-0037151-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon2): c.55+3777:TMPRSS2_c.40-18163::ERGdel Note: The TMPRSS2-ERG Fusion includes the non-canaonical transcript of ERG.
ABL1	0	MSKCC-DMP	P-0037171-T01-IM6	ABL1-intragenic	yes	unknown		unknown	ABL1 (NM_005157) rearrangement: c.914:ABL1_chr9:g.133517056inv Note: The ABL1 rearrangement is an inversion of exons 1-6. One of the breakpoints is within ABL1 exon 6. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037177-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1678:TMPRSS2_c.19-9161:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and involves TMPRSS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0037177-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1678:TMPRSS2_c.19-9161:ERGdel Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and involves TMPRSS2 exon 1 and ERG exons 2-10.
PARP1	0	MSKCC-DMP	P-0037198-T01-IM6	NVL-PARP1 fusion	yes	unknown		out of frame	PARP1 (NM_001618) - NVL (NM_002533) rearrangement: c.1941+185:PARP1_c.1180+599:NVLdel Note: The PARP1 - NVL rearrangement is a deletion which results in the fusion of PARP1 exons 1-13 with NVL exons 10-23. Its functional significance is undetermined.
NVL	0	MSKCC-DMP	P-0037198-T01-IM6	NVL-PARP1 fusion	yes	unknown		out of frame	PARP1 (NM_001618) - NVL (NM_002533) rearrangement: c.1941+185:PARP1_c.1180+599:NVLdel Note: The PARP1 - NVL rearrangement is a deletion which results in the fusion of PARP1 exons 1-13 with NVL exons 10-23. Its functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0037198-T01-IM6	ATAT1-UPF1 fusion	yes	unknown		in frame	UPF1 (NM_002911) - ATAT1 (NM_001031722) rearrangement: t(6;19)(p21.33;p13.11)(chr6:g.30606726::chr19:g.18971862) Note: The UPF1 - ATAT1 rearrangement is a translocation which may result in the fusion of UPF1 exons 1-17 with ATAT1 exons 7-13. Its functional significance is undetermined.
ATAT1	0	MSKCC-DMP	P-0037198-T01-IM6	ATAT1-UPF1 fusion	yes	unknown		in frame	UPF1 (NM_002911) - ATAT1 (NM_001031722) rearrangement: t(6;19)(p21.33;p13.11)(chr6:g.30606726::chr19:g.18971862) Note: The UPF1 - ATAT1 rearrangement is a translocation which may result in the fusion of UPF1 exons 1-17 with ATAT1 exons 7-13. Its functional significance is undetermined.
RET	0	MSKCC-DMP	P-0037268-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: c.338-29_chr10:g.43148631del Note: The RET rearrangement is a deletion that includes RET exons 1-2. The functional significance is undetermined.
RASA1	0	MSKCC-DMP	P-0037268-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: chr5:g.86060945_c.1809del Note: The RASA1 rearrangement is a deletion that includes RASA 1 exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.
MTOR	0	MSKCC-DMP	P-0037373-T01-IM6	KAZN-MTOR fusion	yes	unknown		out of frame	MTOR (NM_004958) - KAZN (NM_201628) rearrangement: c.4253+84:MTOR_c.419-17412:KAZNinv Note: The MTOR - KAZN rearrangement is an inversion which results in the fusion of MTOR exons 1-28 with KAZN exons 3-15. Its functional significance is undetermined.
KAZN	0	MSKCC-DMP	P-0037373-T01-IM6	KAZN-MTOR fusion	yes	unknown		out of frame	MTOR (NM_004958) - KAZN (NM_201628) rearrangement: c.4253+84:MTOR_c.419-17412:KAZNinv Note: The MTOR - KAZN rearrangement is an inversion which results in the fusion of MTOR exons 1-28 with KAZN exons 3-15. Its functional significance is undetermined.
PPP1R18	0	MSKCC-DMP	P-0037373-T01-IM6	MDC1-PPP1R18 fusion	yes	unknown		unknown	PPP1R18 (NM_001134870) - MDC1 (NM_014641) rearrangement: c.1611+927:PPP1R18_c.3830:MDC1dup Note: The PPP1R18 - MDC1 rearrangement is a duplication which results in the fusion of PPP1R18 exons 1-2 with MDC1 exons 10-15. One of the breakpoints is within MDC1 exon 10. Its functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0037373-T01-IM6	MDC1-PPP1R18 fusion	yes	unknown		unknown	PPP1R18 (NM_001134870) - MDC1 (NM_014641) rearrangement: c.1611+927:PPP1R18_c.3830:MDC1dup Note: The PPP1R18 - MDC1 rearrangement is a duplication which results in the fusion of PPP1R18 exons 1-2 with MDC1 exons 10-15. One of the breakpoints is within MDC1 exon 10. Its functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0037375-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.67+800_c.2040del Note: The BRCA2 rearrangement is an intragenic deletion of exons 3-11. One of the breakpoints is within exon 11.
BCL2L1	0	MSKCC-DMP	P-0037529-T01-IM6	BCL2L1-intragenic	yes	unknown		unknown	BCL2L1 (NM_138578) rearrangement: c.374_c.565-15091:inv Note: The BCL2L1 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.
TMPRSS2	0	MSKCC-DMP	P-0037751-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4 - 10) : c.56-2526:TMPRSS2_c.39+6198:ERG del Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
ERG	0	MSKCC-DMP	P-0037751-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4 - 10) : c.56-2526:TMPRSS2_c.39+6198:ERG del Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.
ST7	0	MSKCC-DMP	P-0037751-T01-IM6	MET-ST7 fusion	yes	unknown		unknown	ST7 (NM_021908) - MET (NM_000245) Rearrangement: c.235-3291:ST7_c.2347:METdel Note: The ST7 - MET rearrangement is a duplication of ST7 exons 3-16 and MET exons 10-21. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0037751-T01-IM6	MET-ST7 fusion	yes	unknown		unknown	ST7 (NM_021908) - MET (NM_000245) Rearrangement: c.235-3291:ST7_c.2347:METdel Note: The ST7 - MET rearrangement is a duplication of ST7 exons 3-16 and MET exons 10-21. The functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0039513-T01-IM6	WASF3-WHSC1 fusion	yes	unknown		unknown	WHSC1 (NM_001042424) - WASF3 (NM_006646) rearrangement: t(4;13)(p16.3;q12.13)(chr4:g.1941497::chr13:g.27230973) Note: The WHSC1 - WASF3 rearrangement is a translocation that results in a fusion of WHSC1 exons 1 - 9 to WASF3 exons 4 - 10. One of the breakpoints is within WHSC1 exon 9. The functional significance is undetermined.
WASF3	0	MSKCC-DMP	P-0039513-T01-IM6	WASF3-WHSC1 fusion	yes	unknown		unknown	WHSC1 (NM_001042424) - WASF3 (NM_006646) rearrangement: t(4;13)(p16.3;q12.13)(chr4:g.1941497::chr13:g.27230973) Note: The WHSC1 - WASF3 rearrangement is a translocation that results in a fusion of WHSC1 exons 1 - 9 to WASF3 exons 4 - 10. One of the breakpoints is within WHSC1 exon 9. The functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0039794-T01-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.88+21179_c.890-376del Note: The EGFR rearrangement is a vIII alteration.
KDM6A	0	MSKCC-DMP	P-0039794-T01-IM6	KDM6A-intragenic	yes	unknown		unknown	KDM6A (NM_021140) rearrangement: c.384+16262_c.1476dup Note: The KDM6A rearrangement is an intragenic duplication of exons 5 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0039932-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: t(16;19)(p13.3;p13.12)(chr16:g.3781315::chr19:g.15859804) Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 30. Functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0040698-T01-IM6	MEGF6-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) - MEGF6 (NM_001409) rearrangement: c.949:PIK3R3_c.3223+61:MEGF6del Note: The PIK3R3 - MEGF6 rearrangement is a deletion that results in a fusion of PIK3R3 exons 1 - 8 to MEGF6 exons 26 - 37. One of the breakpoints is within PIK3R3 exon 8.
MEGF6	0	MSKCC-DMP	P-0040698-T01-IM6	MEGF6-PIK3R3 fusion	yes	unknown		unknown	PIK3R3 (NM_003629) - MEGF6 (NM_001409) rearrangement: c.949:PIK3R3_c.3223+61:MEGF6del Note: The PIK3R3 - MEGF6 rearrangement is a deletion that results in a fusion of PIK3R3 exons 1 - 8 to MEGF6 exons 26 - 37. One of the breakpoints is within PIK3R3 exon 8.
MTOR	0	MSKCC-DMP	P-0040698-T01-IM6	MTOR-intragenic	yes	unknown		unknown	MTOR (NM_004958) rearrangement: c.6381:MTOR_chr1:g.47367819inv Note: The MTOR rearrangement is an inversion of exons 1 - 46. One of the breakpoints is within exon 46. Functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0040700-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.427_c.1002-401inv Note: The ELF3 rearrangement is an intragenic inversion of exons 4 - 8. One of the breakpoints is within exon 4. Functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0040755-T01-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.360-562:NTRK1_chr1:g.157625604del Note: The NTRK1 rearrangement is a deletion of exons 4 - 17. The rearrangement includes the kinase domain of NTRK1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
NF1	0	MSKCC-DMP	P-0040755-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(3;17)(q21.3;q11.2)(chr3:g.125890858::chr17:g.29664297) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 42 resulting in truncation of gene and corresponding intragenic deletion.
BRIP1	0	MSKCC-DMP	P-0040783-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.1629-16:BRIP1_chr17:g.59757201inv Note: The BRIP1 rearrangement is an inversion of exons 12 - 20. Functional significance is undetermined.
SLC25A21	0	MSKCC-DMP	P-0040854-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		out of frame	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+91433:SLC25A21_c.73-76:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in a fusion of SLC25A21 exon 1 to FOXA1 exon 2. Functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0040854-T01-IM6	FOXA1-SLC25A21 fusion	yes	unknown		out of frame	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+91433:SLC25A21_c.73-76:FOXA1dup Note: The SLC25A21 - FOXA1 rearrangement is a duplication that results in a fusion of SLC25A21 exon 1 to FOXA1 exon 2. Functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0041412-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) rearrangement: c.2768+110_c.4004del Note: The CDK12 rearrangement is an intragenic deletion of exons 9 - 14. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of CDK12.
MTUS2	0	MSKCC-DMP	P-0041420-T01-IM6	BRCA2-MTUS2 fusion	yes	unknown		unknown	MTUS2 (NM_001033602) - BRCA2 (NM_000059) rearrangement: c.2936-3366:MTUS2_c.8205:BRCA2del Note: The MTUS2 - BRCA2 rearrangement is a deletion that results in a fusion of MTUS2 exons 1 - 5 to BRCA2 exons 18 - 27. One of the breakpoints is within BRCA2 exon 18.
BRCA2	0	MSKCC-DMP	P-0041420-T01-IM6	BRCA2-MTUS2 fusion	yes	unknown		unknown	MTUS2 (NM_001033602) - BRCA2 (NM_000059) rearrangement: c.2936-3366:MTUS2_c.8205:BRCA2del Note: The MTUS2 - BRCA2 rearrangement is a deletion that results in a fusion of MTUS2 exons 1 - 5 to BRCA2 exons 18 - 27. One of the breakpoints is within BRCA2 exon 18.
ATR	0	MSKCC-DMP	P-0041420-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: c.4152+7_c.4154del Note: The ATR rearrangement is an intragenic deletion of exon 23. One of the breakpoints is within exon 23.
NF1	0	MSKCC-DMP	P-0041549-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.587-126:NF1_chr17:g.7263421del Note: The NF1 rearrangement is a deletion of exons 1 - 5.
TMPRSS2	0	MSKCC-DMP	P-0041549-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-606:TMPRSS2_c.18+16516:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0041549-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-606:TMPRSS2_c.18+16516:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
TMPRSS2	0	MSKCC-DMP	P-0041945-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-660:TMPRSS2_c.18+1836:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0041945-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-660:TMPRSS2_c.18+1836:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exons 1 - 2 to ERG exons 2 - 10. The fusion is predicted to be in frame.
FOXA1	0	MSKCC-DMP	P-0042084-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.812:FOXA1_chr14:g.38056065del Note: The FOXA1 rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2.
SMAD3	0	MSKCC-DMP	P-0042310-T01-IM6	SMAD3-intragenic	yes	unknown		unknown	SMAD3 (NM_005902) rearrangement: c.1242:SMAD3_chr15:g.67506410del Note: The SMAD3 rearrangement is a deletion of exon 9. One of the breakpoints is within exon 9.
ARID1A	0	MSKCC-DMP	P-0042588-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;15)(p36.11;q24.3)(chr1:g.27107174::chr15:g.78248444) Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0042656-T01-IM6	ERCC2-intragenic	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.1238-75:ERCC2_chr19:g.45903488del Note: The ERCC2 rearrangement is a deletion of exons 1 - 12.
EZH2	0	MSKCC-DMP	P-0042656-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.857:EZH2_chr7:g.148415342del Note: The EZH2 rearrangement is a deletion of exons 8 - 20. One of the breakpoints is within exon 8.
MSI2	0	MSKCC-DMP	P-0042823-T01-IM6	MSI2-intragenic	yes	unknown		unknown	MSI2 (NM_138962) rearrangement: t(2;17)(p11.2;q22)(chr2:g.83485930::chr17:g.55339568) Note: The MSI2 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.
TPR	0	MSKCC-DMP	P-0042965-T01-IM6	NTRK1-TPR fusion	yes	unknown		unknown	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+531:TPR_c.1129:NTRK1inv The TPR - NTRK1 fusion involves TPR exons 1 - 21 and NTRK1 exons 8 - 17. One of the breakpoints is within NTRK1 exon 8. The fusion includes the kinase domain of NTRK1. This sample has been nominated for analysis using the Archer targeted RNAseq assay to help further characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
NTRK1	0	MSKCC-DMP	P-0042965-T01-IM6	NTRK1-TPR fusion	yes	unknown		unknown	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+531:TPR_c.1129:NTRK1inv The TPR - NTRK1 fusion involves TPR exons 1 - 21 and NTRK1 exons 8 - 17. One of the breakpoints is within NTRK1 exon 8. The fusion includes the kinase domain of NTRK1. This sample has been nominated for analysis using the Archer targeted RNAseq assay to help further characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
RNF43	0	MSKCC-DMP	P-0043039-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.655_c.688-139del Note: The RNF43 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6.
RCBTB2	0	MSKCC-DMP	P-0043160-T01-IM6	RB1-RCBTB2 fusion	yes	unknown		unknown	RCBTB2 (NM_001268) - RB1 (NM_000321) rearrangement: c.350-1065:RCBTB2_c.2137:RB1inv Note: The RCBTB2 - RB1 rearrangement is an inversion that results in a fusion of RCBTB2 exons 1 - 6 to RB1 exons 21 - 27. One of the breakpoints is within RB1 exon 21. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0043160-T01-IM6	RB1-RCBTB2 fusion	yes	unknown		unknown	RCBTB2 (NM_001268) - RB1 (NM_000321) rearrangement: c.350-1065:RCBTB2_c.2137:RB1inv Note: The RCBTB2 - RB1 rearrangement is an inversion that results in a fusion of RCBTB2 exons 1 - 6 to RB1 exons 21 - 27. One of the breakpoints is within RB1 exon 21. Functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0043201-T01-IM6	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.451_c.475+3909inv Note: The MAP3K13 rearrangement is an intragenic inversion of exon 2. One of the breakpoints is within exon 2. The rearrangement does not include the kinase domain of MAP3K13. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0043233-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.3798:MDC1_chr6:g.30704580inv Note: The MDC1 rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.
PGR	0	MSKCC-DMP	P-0043237-T01-IM6	PGR-intragenic	yes	unknown		unknown	PGR (NM_000926) rearrangement: c.2730:PGR_chr11:g.100908756inv Note: The PGR rearrangement is an inversion of exon 8. One of the breakpoints is within exon 8. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0043415-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.11441:KMT2A_chr11:g.116498477del Note: The KMT2A rearrangement is a deletion of exons 1 - 34. One of the breakpoints is within exon 34.
CSDE1	0	MSKCC-DMP	P-0043727-T01-IM6	FAM46C-CSDE1 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) - FAM46C (NM_017709) rearrangement: c.976-217:CSDE1_c.710:FAM46Cdel Note: The CSDE1 - FAM46C rearrangement is a deletion of CSDE1 exons 1 - 10 and FAM46C exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
FAM46C	0	MSKCC-DMP	P-0043727-T01-IM6	FAM46C-CSDE1 fusion	yes	unknown		unknown	CSDE1 (NM_001242891) - FAM46C (NM_017709) rearrangement: c.976-217:CSDE1_c.710:FAM46Cdel Note: The CSDE1 - FAM46C rearrangement is a deletion of CSDE1 exons 1 - 10 and FAM46C exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043904-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-113:TMPRSS2_c.236+10174:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.
ERG	0	MSKCC-DMP	P-0043904-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-113:TMPRSS2_c.236+10174:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.
UPF1	0	MSKCC-DMP	P-0043950-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: c.2182+204_c.2857+108inv Note: The UPF1 rearrangement is an intragenic inversion of exons 16 - 20. Functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0044025-T01-IM6	NCOR1-intragenic	yes	unknown		out of frame	NCOR1 (NM_006311) rearrangement: c.2690+1303_c.3671-1del Note: The NCOR1 rearrangement is an intragenic deletion of exons 21 - 27.
PAK1	0	MSKCC-DMP	P-0044084-T01-IM6	PAK1-intragenic	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.1116+20:PAK1_chr11:g.77030392del Note: The PAK1 rearrangement is a deletion of exons 12 - 15. The rearrangement includes a part of the kinase domain of PAK1. Functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0044166-T01-IM6	PIK3CD-intragenic	yes	unknown		unknown	PIK3CD (NM_005026) rearrangement: c.2718+22:PIK3CD_chr1:g.9744256dup Note: The PIK3CD rearrangement is a duplication of exons 1 - 21. Functional significance is undetermined.
EIF4E	0	MSKCC-DMP	P-0044166-T01-IM6	SHROOM3-EIF4E fusion	yes	unknown		in frame	EIF4E (NM_001130678) - SHROOM3 (NM_020859) rearrangement: c.459+782:EIF4E_c.5623-561:SHROOM3inv Note: The EIF4E - SHROOM3 rearrangement is an inversion that results in a fusion of EIF4E exons 1 - 5 to SHROOM3 exon 11. The fusion is predicted to be in frame. Functional significance is undetermined.
SHROOM3	0	MSKCC-DMP	P-0044166-T01-IM6	SHROOM3-EIF4E fusion	yes	unknown		in frame	EIF4E (NM_001130678) - SHROOM3 (NM_020859) rearrangement: c.459+782:EIF4E_c.5623-561:SHROOM3inv Note: The EIF4E - SHROOM3 rearrangement is an inversion that results in a fusion of EIF4E exons 1 - 5 to SHROOM3 exon 11. The fusion is predicted to be in frame. Functional significance is undetermined.
EPCAM	0	MSKCC-DMP	P-0044224-T01-IM6	EPCAM-intragenic	yes	unknown		unknown	EPCAM (NM_002354) rearrangement: c.76+47:EPCAM_chr2:g.47615051del Note: The EPCAM rearrangement is a deletion of exons 2 - 9.
MSH2	0	MSKCC-DMP	P-0044224-T01-IM6	MSH2-intragenic	yes	unknown		in frame	MSH2 (NM_000251) rearrangement: c.367-385_c.793-51del Note: The MSH2 rearrangement is an intragenic deletion of exons 3 - 4.
NF1	0	MSKCC-DMP	P-0044255-T01-IM6	NF1-intragenic	yes	unknown		out of frame	NF1 (NM_001042492) rearrangement: c.1393-80_c.4577+42dup Note: The NF1 rearrangement is an intragenic duplication of exons 13 - 34. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0044255-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.105:DNMT1_chr19:g.8770811inv Note: The DNMT1 rearrangement is an inversion of exons 2 - 40. One of the breakpoints is within exon 2. Functional significance is undetermined.
KDR	0	MSKCC-DMP	P-0044255-T01-IM6	KDR-intragenic	yes	unknown		unknown	KDR (NM_002253) rearrangement: c.926_c.976+798inv Note: The KDR rearrangement is an intragenic inversion of exon 7. One of the breakpoints is within exon 7. The rearrangement does not include the kinase domain of KDR. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0044325-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.3359:KMT2A_chr11:g.117628118del Note: The KMT2A rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.
FGFR2	0	MSKCC-DMP	P-0044366-T01-IM6	FGFR2-intragenic	yes	unknown		unknown	FGFR2 (NM_000141) rearrangement: c.2301+1825:FGFR2_chr10:g.125122504del Note: The FGFR2 rearrangement is a deletion of exons 1 - 17. The rearrangement includes the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RECQL4	0	MSKCC-DMP	P-0044366-T01-IM6	CYHR1-RECQL4 fusion	yes	unknown		out of frame	RECQL4 (NM_004260) - CYHR1 (NM_138496) rearrangement: c.2885+16:RECQL4_c.247-3269:CYHR1del Note: The RECQL4 - CYHR1 rearrangement is a deletion that results in a fusion of RECQL4 exons 1 - 17 to CYHR1 exons 3 - 5.
CYHR1	0	MSKCC-DMP	P-0044366-T01-IM6	CYHR1-RECQL4 fusion	yes	unknown		out of frame	RECQL4 (NM_004260) - CYHR1 (NM_138496) rearrangement: c.2885+16:RECQL4_c.247-3269:CYHR1del Note: The RECQL4 - CYHR1 rearrangement is a deletion that results in a fusion of RECQL4 exons 1 - 17 to CYHR1 exons 3 - 5.
TET1	0	MSKCC-DMP	P-0044600-T01-IM6	TET1-intragenic	yes	unknown		unknown	TET1 (NM_030625) rearrangement: c.1969-3454_c.5533dup Note: The TET1 rearrangement is an intragenic duplication of exons 4 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044647-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.480-1412_c.680inv Note: The NF1 rearrangement is an intragenic inversion of exons 5 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.
STAG2	0	MSKCC-DMP	P-0044784-T01-IM6	STAG2-intragenic	yes	unknown		in frame	STAG2 (NM_001042749) rearrangement: c.1017+48_c.2265+79del Note: The STAG2 rearrangement is an intragenic deletion of exons 12 - 23.
TGFBR2	0	MSKCC-DMP	P-0044856-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.783:TGFBR2_chr3:g.30808859del Note: The TGFBR2 rearrangement is a deletion of exons 5 - 8. One of the breakpoints is within exon 5. The rearrangement includes the kinase domain of TGFBR2.
POLE	0	MSKCC-DMP	P-0044955-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.487:POLE_chr12:g.128462756inv Note: The POLE rearrangement is an inversion of exons 6 - 49. One of the breakpoints is within exon 6. Functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0045046-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: t(19;X)(p13.3;q28)(chr19:g.1207210::chrX:g.155259729) Note: The STK11 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.
PAX5	0	MSKCC-DMP	P-0045257-T02-IM6	PAX5-intragenic	yes	unknown		in frame	PAX5 (NM_016734) rearrangement: c.475+126_c.604+11920del Note: The PAX5 rearrangement is an intragenic deletion of exon 5.
KMT2D	0	MSKCC-DMP	P-0047286-T01-IM6	ACSS3-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - ACSS3 (NM_024560) rearrangement: c.14539:KMT2D_c.780+1040:ACSS3inv Note: The KMT2D - ACSS3 rearrangement is an inversion that results in a fusion of KMT2D exons 1 - 47 to ACSS3 exons 5 - 16. One of the breakpoints is within KMT2D exon 47. Functional significance is undetermined.
ACSS3	0	MSKCC-DMP	P-0047286-T01-IM6	ACSS3-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - ACSS3 (NM_024560) rearrangement: c.14539:KMT2D_c.780+1040:ACSS3inv Note: The KMT2D - ACSS3 rearrangement is an inversion that results in a fusion of KMT2D exons 1 - 47 to ACSS3 exons 5 - 16. One of the breakpoints is within KMT2D exon 47. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0036092-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20180182 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0036092-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20180182 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0037751-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:   AR (NM_000044) Variant 7 (AR V-7) PMID: 26554309, 19117982 POSITIVE FOR THE FOLLOWING GENE FUSION IN THE THE INVESTIGATIONAL PANEL: PER3-CAMTA1 fusion. Note: The rearrangement is an out of frame fusion between genes PER3 Exon7 (NM_016831) and CAMTA1 Exon10 (NM_0152150). The functional significance  of this event is unknown.   Lab Notes Run Number: ArcherV3-CLIN-20190026 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0037751-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon2 (NM_182918). POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:   AR (NM_000044) Variant 7 (AR V-7) PMID: 26554309, 19117982 POSITIVE FOR THE FOLLOWING GENE FUSION IN THE THE INVESTIGATIONAL PANEL: PER3-CAMTA1 fusion. Note: The rearrangement is an out of frame fusion between genes PER3 Exon7 (NM_016831) and CAMTA1 Exon10 (NM_0152150). The functional significance  of this event is unknown.   Lab Notes Run Number: ArcherV3-CLIN-20190026 Macro-dissection: Unknown
EGFR	0	MSKCC-DMP	P-0039794-T01-IM6	EGFR-intragenic - Archer	yes	unknown		unknown	EGFR vIII:  POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:   EGFR (NM_005228) Exons 2-7 Deletion (EGFRvIII).   Note: this alteration was detected at low frequency.  Lab Notes Run Number: Archerv3-CLIN-20190063 Macro-dissection: Performed
TPR	0	MSKCC-DMP	P-0042965-T01-IM6	NTRK1-TPR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TPR-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes TPR Exon21 (NM_003292) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: Archerv3-CLIN-20190111 Macro-dissection: Not Performed
NTRK1	0	MSKCC-DMP	P-0042965-T01-IM6	NTRK1-TPR fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TPR-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes TPR Exon21 (NM_003292) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: Archerv3-CLIN-20190111 Macro-dissection: Not Performed
MAPK14	0	MSKCC-DMP	P-0045167-T01-IM6	TFEB-MAPK14 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MAPK14-TFEB fusion. Note: The rearrangement is an in-frame fusion between genes MAPK14 Exon1 (NM_139012) and TFEB Exon3 (NM_001762). Note2: The functional significance of this event is unknown. Lab Notes Run Number: Archerv3-CLIN-20190149 Macro-dissection: Not Performed
TFEB	0	MSKCC-DMP	P-0045167-T01-IM6	TFEB-MAPK14 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MAPK14-TFEB fusion. Note: The rearrangement is an in-frame fusion between genes MAPK14 Exon1 (NM_139012) and TFEB Exon3 (NM_001762). Note2: The functional significance of this event is unknown. Lab Notes Run Number: Archerv3-CLIN-20190149 Macro-dissection: Not Performed
APC	0	MSKCC-DMP	P-0014026-T01-IM5	REEP5-APC fusion	yes	unknown		unknown	APC(NM_000038) - REEP5(NM_005669)  rearrangement: c.4364:APC_c.352-7191:REEP5del Note: The APC (NM_000038)_REEP5 (NM_005669) rearrangement results in the deletion of APC exon 16. One of the breakpoints is within APC exon 16.  The functional significance is undetermined.
REEP5	0	MSKCC-DMP	P-0014026-T01-IM5	REEP5-APC fusion	yes	unknown		unknown	APC(NM_000038) - REEP5(NM_005669)  rearrangement: c.4364:APC_c.352-7191:REEP5del Note: The APC (NM_000038)_REEP5 (NM_005669) rearrangement results in the deletion of APC exon 16. One of the breakpoints is within APC exon 16.  The functional significance is undetermined.
GRIN2A	0	MSKCC-DMP	P-0017479-T02-IM6	GRIN2A-intragenic	yes	unknown		unknown	GRIN2A (NM_001134407) Rearrangement: c.2270_c.2357-2819dup Note: The GRIN2A rearrangement is an intragenic duplication of exon 11. One breakpoint is in exon 11. The significance is undetermined.
APC	0	MSKCC-DMP	P-0024513-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.313:APC_chr5:g.113610357del Note: The APC rearrangement is a deletion of exons 4-16. One of the breakpoints is within exon 4.
BRCA2	0	MSKCC-DMP	P-0029336-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.1670_chr13:g.51658908 Note: The BRCA2 rearrangement is an inversion that includes BRCA2 exons 10-27. One of the breakpoints is within exon 10.
CREBBP	0	MSKCC-DMP	P-0029585-T01-IM6	CREBBP-intragenic	yes	unknown		unknown	CREBBP (NM_004380) rearrangement: c.1309:CREBBP_chr16:g.3619041del Note: The CREBBP rearrangement results in the deletion of exons 5-31. One of the breakpoints is within exon 5. The functional significance is undetermined.
TRAIP	0	MSKCC-DMP	P-0032092-T01-IM6	MST1R-TRAIP fusion	yes	unknown		in frame	TRAIP (NM_005879) - MST1R (NM_002447) rearrangement: c.240+1000:TRAIP_c.1548+73:MST1Rdup Note: The TRAIP - MST1R rearrangement is a duplication which results in a fusion of TRAIP exons 1-3 with MST1R exons 4-20. Its functional significance is undetermined.
MST1R	0	MSKCC-DMP	P-0032092-T01-IM6	MST1R-TRAIP fusion	yes	unknown		in frame	TRAIP (NM_005879) - MST1R (NM_002447) rearrangement: c.240+1000:TRAIP_c.1548+73:MST1Rdup Note: The TRAIP - MST1R rearrangement is a duplication which results in a fusion of TRAIP exons 1-3 with MST1R exons 4-20. Its functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0032336-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) Rearrangement: t(16;22)(p11.2;q13.2)(chr16:g.30001065::chr22:g.41574417) Note: The EP300 rearrangement results in the translocation with breakpoint in exon 31 of EP300. The functional significance is undetermined.
HIST1H3D	0	MSKCC-DMP	P-0032336-T01-IM6	HIST1H3E-HIST1H3D fusion	yes	unknown		unknown	HIST1H3D(NM_003530) - HIST1H3E(NM_003532) Rearrangement: c.407:HIST1H3D_c.*1927:HIST1H3Edel Note: The HIST1H3D-HIST1H3E rearrangement results in the deletion of HIST1H3D and HIST1H3E. One of the breakpoints is in HIST1H3D exon2.
HIST1H3E	0	MSKCC-DMP	P-0032336-T01-IM6	HIST1H3E-HIST1H3D fusion	yes	unknown		unknown	HIST1H3D(NM_003530) - HIST1H3E(NM_003532) Rearrangement: c.407:HIST1H3D_c.*1927:HIST1H3Edel Note: The HIST1H3D-HIST1H3E rearrangement results in the deletion of HIST1H3D and HIST1H3E. One of the breakpoints is in HIST1H3D exon2.
DROSHA	0	MSKCC-DMP	P-0032342-T01-IM6	DROSHA-intragenic	yes	unknown		unknown	DROSHA(NM_013235) Rearrangement: c.3415:DROSHA_chr5:g.30226624inv Note: The DROSHA rearrangement is an inversion of exons 28 to 35. One of the breakpoints is within exon 28. In addition, the presence of multiple structural variants involving DROSHA suggests a complex rearrangement. The functional significance is undetermined.
PDCD1LG2	0	MSKCC-DMP	P-0032342-T01-IM6	PTPRD-PDCD1LG2 fusion	yes	unknown		unknown	PDCD1LG2(NM_025239) - PTPRD(NM_002839) Rearrangement: c.766+12:PDCD1LG2_c.-545+115685:PTPRDdel Note The PDCD1LG2 - PTPRD rearrangement results in the deletion of PDCD1LG2 exon 5-6 and the entire PTPRD gene. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0032342-T01-IM6	PTPRD-PDCD1LG2 fusion	yes	unknown		unknown	PDCD1LG2(NM_025239) - PTPRD(NM_002839) Rearrangement: c.766+12:PDCD1LG2_c.-545+115685:PTPRDdel Note The PDCD1LG2 - PTPRD rearrangement results in the deletion of PDCD1LG2 exon 5-6 and the entire PTPRD gene. The functional significance is undetermined.
JAK1	0	MSKCC-DMP	P-0033710-T01-IM6	JAK1-intragenic	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: c.3369+182:JAK1_chr1:g.69521361inv Note: The JAK1 rearrangement is an inversion of exons 1-24. This includes the kinase domain of JAK1. Its functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0036358-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-208:FGFR2_c.7344+468:TACC2inv Note: The FGFR2 - TACC2 fusion involves FGFR2 exons 1-18, which includes FGFR2 kinase domain, and TACC2 exons 10-23. The fusion is predicted to be in-frame.
TACC2	0	MSKCC-DMP	P-0036358-T01-IM6	TACC2-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-208:FGFR2_c.7344+468:TACC2inv Note: The FGFR2 - TACC2 fusion involves FGFR2 exons 1-18, which includes FGFR2 kinase domain, and TACC2 exons 10-23. The fusion is predicted to be in-frame.
RPS6KB2	0	MSKCC-DMP	P-0037087-T01-IM6	RPS6KB2-intragenic	yes	unknown		unknown	RPS6KB2 (NM_003952) Rearrangement : c.457+289_c.1083del Note: The RPS6KB2 Rearrangement results in the deletion of exons 6-13 of RPS6KB2.One of the breakpoints is within exon13. Its functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0037087-T01-IM6	ASXL1-intragenic	yes	unknown		in frame	ASXL1 (NM_015338) Rearrangement: c.57+1790_c.252+50dup Note: The ASXL1 Rearrangement results in the intragenic duplication of exons 2-3 of ASXL1.Its functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0037126-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2310:FGFR3_c.1837-16:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-18 with TACC3 exons 10-16 and includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
TACC3	0	MSKCC-DMP	P-0037126-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		unknown	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2310:FGFR3_c.1837-16:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1-18 with TACC3 exons 10-16 and includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.
KRAS	0	MSKCC-DMP	P-0037160-T01-IM6	KRAS-intragenic	yes	unknown		unknown	KRAS (NM_033360) Rearrangement: c.450+3814_c.*58dup Note: The KRAS Rearrangement results in the duplication of exon 5. One of the breakpoints is within the 3-UTR region. Its functional significance is undetermined.
PLEKHA7	0	MSKCC-DMP	P-0037180-T01-IM6	RPS6KA4-PLEKHA7 fusion	yes	unknown		unknown	PLEKHA7 (NM_175058) - RPS6KA4 (NM_003942) rearrangement: c.222-55887:PLEKHA7_c.625:RPS6KA4inv Note: The PLEKHA7 - RPS6KA4 rearrangement is a an inversion that results in a fusion of PLEKHA7 exons 1-3 to RPS6KA4 exons 6-16. One of the breakpoints is within RPS6KA4 exon 6. The functional significance is undetermined.
RPS6KA4	0	MSKCC-DMP	P-0037180-T01-IM6	RPS6KA4-PLEKHA7 fusion	yes	unknown		unknown	PLEKHA7 (NM_175058) - RPS6KA4 (NM_003942) rearrangement: c.222-55887:PLEKHA7_c.625:RPS6KA4inv Note: The PLEKHA7 - RPS6KA4 rearrangement is a an inversion that results in a fusion of PLEKHA7 exons 1-3 to RPS6KA4 exons 6-16. One of the breakpoints is within RPS6KA4 exon 6. The functional significance is undetermined.
PARK2	0	MSKCC-DMP	P-0037180-T01-IM6	PARK2-intragenic	yes	unknown		unknown	PARK2 (NM_004562) rearrangement: c.171+7616_c.256del Note: The PARK2 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.
RECQL4	0	MSKCC-DMP	P-0037180-T01-IM6	CPSF1-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - CPSF1 (NM_013291) rearrangement: c.2487:RECQL4_c.219:CPSF1del Note: The RECQL4 - CPSF1 rearrangement is a deletion that results in a fusion of RECQL4 exons 1-16 to CPSF1 exons 4-38. The breakpoints are within RECQL4 exon 16 and CPSF1 exon 4. The functional significance is undetermined.
CPSF1	0	MSKCC-DMP	P-0037180-T01-IM6	CPSF1-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - CPSF1 (NM_013291) rearrangement: c.2487:RECQL4_c.219:CPSF1del Note: The RECQL4 - CPSF1 rearrangement is a deletion that results in a fusion of RECQL4 exons 1-16 to CPSF1 exons 4-38. The breakpoints are within RECQL4 exon 16 and CPSF1 exon 4. The functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0037253-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.889+6:RICTOR_chr5:g.49952642del Note: The RICTOR rearrangement is a deletion of exons 1-10. The functional significance is undetermined.
RRAS	0	MSKCC-DMP	P-0037257-T01-IM6	RRAS-intragenic	yes	unknown		unknown	RRAS (NM_006270) rearrangement: c.58:RRAS_chr19:g.50572777del Note: The RRAS rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.
DICER1	0	MSKCC-DMP	P-0037263-T01-IM6	DICER1-intragenic	yes	unknown		unknown	DICER1 (NM_030621) rearrangement: t(14;15)(q32.13;q14)(chr14:g.95572446::chr15:g.35039509) Note: The DICER1 rearrangement is a translocation with a breakpoint in exon 20. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037283-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2450:TMPRSS2_c.19-5937:ERGdel
ERG	0	MSKCC-DMP	P-0037283-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2450:TMPRSS2_c.19-5937:ERGdel
PPP6C	0	MSKCC-DMP	P-0037545-T01-IM6	PPP6C-intragenic	yes	unknown		unknown	PPP6C (NM_002721) rearrangement: t(9;10)(q33.3;q25.3)(chr9:g.127951728::chr10:g.111892246) Note: The PPP6C rearrangement is a translocation involving exon 1. Its functional significance is undetermined.
EYA1	0	MSKCC-DMP	P-0037545-T01-IM6	WHSC1L1-EYA1 fusion	yes	unknown		unknown	EYA1 (NM_172058) - WHSC1L1 (NM_023034) rearrangement: c.826+5510:EYA1_c.622:WHSC1L1del Note: The EYA1 - WHSC1L1 rearrangement is a deletion which results in the fusion of EYA1 exons 1-9 with WHSC1L1 exons 2-24. One of the breakpoints is within WHSC1L1 exon 2. Its functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0037545-T01-IM6	WHSC1L1-EYA1 fusion	yes	unknown		unknown	EYA1 (NM_172058) - WHSC1L1 (NM_023034) rearrangement: c.826+5510:EYA1_c.622:WHSC1L1del Note: The EYA1 - WHSC1L1 rearrangement is a deletion which results in the fusion of EYA1 exons 1-9 with WHSC1L1 exons 2-24. One of the breakpoints is within WHSC1L1 exon 2. Its functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0037548-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: t(X;8)(p11.4;q13.1)(chrX:g.39930104::chr8:g.66508332) Note: The BCOR rearrangement is a translocation involving exon 6. Its functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0037834-T01-IM6	DNMT1-intragenic	yes	unknown		unknown	DNMT1 (NM_001379) rearrangement: c.1325:DNMT1_chr19:g.53065226del Note: The DNMT1 rearrangement results in the deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.
NPAS1	0	MSKCC-DMP	P-0037834-T01-IM6	BBC3-NPAS1 fusion	yes	unknown		in frame	NPAS1 (NM_002517) - BBC3 (NM_001127240) rearrangement: c.359-497:NPAS1_c.569-2141:BBC3inv Note: The NPAS1 - BBC3 rearrangement is an inversion that results in the in-frame fusion of NPAS1 exons 1-2 with BBC3 exon 4. The functional significance is undetermined.
BBC3	0	MSKCC-DMP	P-0037834-T01-IM6	BBC3-NPAS1 fusion	yes	unknown		in frame	NPAS1 (NM_002517) - BBC3 (NM_001127240) rearrangement: c.359-497:NPAS1_c.569-2141:BBC3inv Note: The NPAS1 - BBC3 rearrangement is an inversion that results in the in-frame fusion of NPAS1 exons 1-2 with BBC3 exon 4. The functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0037834-T01-IM6	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.225+28705_c.3878+32dup Note: The KDM6A rearrangement results in the intragenic duplication of exons 3-26. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037960-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1742:TMPRSS2_c.39+36464:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0037960-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1742:TMPRSS2_c.39+36464:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
EXOC4	0	MSKCC-DMP	P-0039051-T01-IM6	SMO-EXOC4 fusion	yes	unknown		unknown	EXOC4 (NM_021807) - SMO (NM_005631) rearrangement: c.1514+40892:EXOC4_c.587:SMOdup Note : The EXOC4 - SMO rearrangement is a duplication that results in a fusion of EXOC4 exons 1 - 10 to SMO exons 3 - 12. One of the breakpoints is within SMO exon 3. Functional significance is undetermined.
SMO	0	MSKCC-DMP	P-0039051-T01-IM6	SMO-EXOC4 fusion	yes	unknown		unknown	EXOC4 (NM_021807) - SMO (NM_005631) rearrangement: c.1514+40892:EXOC4_c.587:SMOdup Note : The EXOC4 - SMO rearrangement is a duplication that results in a fusion of EXOC4 exons 1 - 10 to SMO exons 3 - 12. One of the breakpoints is within SMO exon 3. Functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0039753-T01-IM6	GLI1-intragenic	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.2126:GLI1_chr12:g.59094643inv Note: The GLI1 rearrangement is an inversion of exon 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0039753-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1241:TMPRSS2_c.39+60112:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0039753-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1241:TMPRSS2_c.39+60112:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
EPHA3	0	MSKCC-DMP	P-0039804-T01-IM6	EPHA3-intragenic	yes	unknown		unknown	EPHA3 (NM_005233) rearrangement: c.2691-22:EPHA3_chr3:g.88907146inv Note: The EPHA3 rearrangement is an inversion of exons 1 - 15. The rearrangement includes the kinase domain of EPHA3. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0040119-T01-IM6	TUBA1B-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - TUBA1B (NM_006082) rearrangement: c.3297:KMT2D_c.434:TUBA1Bdup Note: The KMT2D - TUBA1B rearrangement is a duplication that results in a fusion of KMT2D exons 1 - 11 to TUBA1B exon 4. The breakpoints are within KMT2D exon 11 and TUBA1B exon 4. Functional significance is undetermined.
TUBA1B	0	MSKCC-DMP	P-0040119-T01-IM6	TUBA1B-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - TUBA1B (NM_006082) rearrangement: c.3297:KMT2D_c.434:TUBA1Bdup Note: The KMT2D - TUBA1B rearrangement is a duplication that results in a fusion of KMT2D exons 1 - 11 to TUBA1B exon 4. The breakpoints are within KMT2D exon 11 and TUBA1B exon 4. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0040355-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12036111::chr15:g.88497191) Note: The ETV6 - NTRK3 fusion involves ETV6 exons 1 - 5 and NTRK3 exons 15 - 20. The fusion is predicted to be in frame and includes the kinase domain of NTRK3.
NTRK3	0	MSKCC-DMP	P-0040355-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12036111::chr15:g.88497191) Note: The ETV6 - NTRK3 fusion involves ETV6 exons 1 - 5 and NTRK3 exons 15 - 20. The fusion is predicted to be in frame and includes the kinase domain of NTRK3.
TMPRSS2	0	MSKCC-DMP	P-0040611-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1208:TMPRSS2_c.39+5853:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040611-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1208:TMPRSS2_c.39+5853:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
KMT2C	0	MSKCC-DMP	P-0040803-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.681_c.11461-1464del Note: The KMT2C rearrangement is an intragenic deletion of exons 5 - 43. One of the breakpoints is within exon 5.
NOTCH1	0	MSKCC-DMP	P-0040817-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.1491:NOTCH1_chr9:g.139456931del Note: The NOTCH1 rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.
ARID1B	0	MSKCC-DMP	P-0041541-T01-IM6	ARID1B-intragenic	yes	unknown		in frame	ARID1B (NM_020732) rearrangement: c.1926+6815_c.4111-128del Note: The ARID1B rearrangement is an intragenic deletion of exons 5 - 17.
APC	0	MSKCC-DMP	P-0041618-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.834+4289_c.1136del Note: The APC rearrangement is an intragenic deletion of exons 9 - 10. One of the breakpoints is within exon 10.
CSF1R	0	MSKCC-DMP	P-0042120-T01-IM6	CSF1R-intragenic	yes	unknown		unknown	CSF1R (NM_005211) rearrangement: c.592+51:CSF1R_chr5:g.55036856del Note: The CSF1R rearrangement is a deletion of exons 5 - 22. The rearrangement includes the kinase domain of CSF1R. Functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0042120-T01-IM6	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.655-6333_c.2939-29del Note: The KDM6A rearrangement is an intragenic deletion of exons 9 - 19.
TSHR	0	MSKCC-DMP	P-0042152-T01-IM6	TSHR-intragenic	yes	unknown		unknown	TSHR (NM_000369) rearrangement: t(3;14)(p11.1;q31.1)(chr3:g.88275067::chr14:g.81574993) Note: The TSHR rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
AXIN2	0	MSKCC-DMP	P-0042152-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.956+117_c.1087del Note: The AXIN2 rearrangement is an intragenic deletion of exons 4 - 5. One of the breakpoints is within exon 5.
PRDM14	0	MSKCC-DMP	P-0042152-T01-IM6	PRDM14-intragenic	yes	unknown		unknown	PRDM14 (NM_024504) rearrangement: c.701-4_c.912+614inv Note: The PRDM14 rearrangement is an intragenic inversion of exons 3 - 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042341-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4078:TMPRSS2_c.40-62578:ERGdel Note: The TMPRSS2 - ERG fusion invovles TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0042341-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4078:TMPRSS2_c.40-62578:ERGdel Note: The TMPRSS2 - ERG fusion invovles TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ARID1A	0	MSKCC-DMP	P-0042358-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.2315:ARID1A_chr1:g.26904763del Note: The ARID1A rearrangement is a deletion of exons 1 - 7. One of the breakpoints is within exon 7.
TMPRSS2	0	MSKCC-DMP	P-0042583-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.126+124:TMPRSS2_chr21:g.39962828del Note: The TMPRSS2 rearrangement is a deletion of exons 3 - 14. Functional significance is undetermined. The possibility of a TMPRSS2 - ERG fusion cannot be ruled out.
CDKN2A	0	MSKCC-DMP	P-0042595-T03-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.406_c.194-1084del Note: The CDKN2A rearrangement is a deletion of CDKN2A exon  2. One of the breakpoints is within exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
NOTCH3	0	MSKCC-DMP	P-0042647-T01-IM6	ZNF30-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - ZNF30 (NM_001099437) rearrangement: c.4379:NOTCH3_c.160+258:ZNF30inv Note: The NOTCH3 - ZNF30 rearrangement is an inversion that results in a fusion of NOTCH3 exons 1 - 24 to ZNF30 exons 4 - 5. One of the breakpoints is within NOTCH3 exon 24. Functional significance is undetermined.
ZNF30	0	MSKCC-DMP	P-0042647-T01-IM6	ZNF30-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - ZNF30 (NM_001099437) rearrangement: c.4379:NOTCH3_c.160+258:ZNF30inv Note: The NOTCH3 - ZNF30 rearrangement is an inversion that results in a fusion of NOTCH3 exons 1 - 24 to ZNF30 exons 4 - 5. One of the breakpoints is within NOTCH3 exon 24. Functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0042662-T01-IM6	AXIN1-intragenic	yes	unknown		unknown	AXIN1 (NM_003502) rearrangement: c.1117-2251_c.1269del Note: The AXIN1 rearrangement is an intragenic deletion of exons 5 - 6. One of the breakpoints is within exon 6.
TMPRSS2	0	MSKCC-DMP	P-0042680-T01-IM6	GCOM1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - GCOM1 (NM_001018090) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.57940741::chr21:g.42877616) Note: The TMPRSS2 - GCOM1 rearrangement is a translocation that results in a fusion of TMPRSS2 exon 1 to GCOM1 exons 11 - 14. Functional significance is undetermined.
GCOM1	0	MSKCC-DMP	P-0042680-T01-IM6	GCOM1-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - GCOM1 (NM_001018090) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.57940741::chr21:g.42877616) Note: The TMPRSS2 - GCOM1 rearrangement is a translocation that results in a fusion of TMPRSS2 exon 1 to GCOM1 exons 11 - 14. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0042880-T01-IM6	RET-intragenic	yes	unknown		out of frame	RET (NM_020975) rearrangement: c.2136+836:RET_chr10:g.51588973del Note: The RET rearrangement is a deletion of exons 12 - 20. The rearrangement includes the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MALT1	0	MSKCC-DMP	P-0042960-T01-IM6	ETV4-MALT1 fusion	yes	unknown		in frame	MALT1 (NM_006785) - ETV4 (NM_001986) rearrangement: t(17;18)(q21.31;q21.32)(chr17:g.41612825::chr18:g.56367894) Note: The MALT1 - ETV4 rearrangement is a translocation that results in the in-frame fusion of MALT1 exons 1 - 4 to ETV4 exons 6 - 13. The fusion is predicted to be in frame. Functional significance is undetermined.
ETV4	0	MSKCC-DMP	P-0042960-T01-IM6	ETV4-MALT1 fusion	yes	unknown		in frame	MALT1 (NM_006785) - ETV4 (NM_001986) rearrangement: t(17;18)(q21.31;q21.32)(chr17:g.41612825::chr18:g.56367894) Note: The MALT1 - ETV4 rearrangement is a translocation that results in the in-frame fusion of MALT1 exons 1 - 4 to ETV4 exons 6 - 13. The fusion is predicted to be in frame. Functional significance is undetermined.
CNTRL	0	MSKCC-DMP	P-0042985-T01-IM6	CDKN2B-CNTRL fusion	yes	unknown		in frame	CNTRL (NM_007018) - CDKN2B (NM_004936) rearrangement: c.1455+1114:CNTRL_c.156+547:CDKN2Binv Note: The CNTRL - CDKN2B rearrangement is an inversion that results in a fusion of CNTRL exons 1 - 9 to CDKN2B exon 2. The fusion is predicted to be in frame. Functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0042985-T01-IM6	CDKN2B-CNTRL fusion	yes	unknown		in frame	CNTRL (NM_007018) - CDKN2B (NM_004936) rearrangement: c.1455+1114:CNTRL_c.156+547:CDKN2Binv Note: The CNTRL - CDKN2B rearrangement is an inversion that results in a fusion of CNTRL exons 1 - 9 to CDKN2B exon 2. The fusion is predicted to be in frame. Functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0043128-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: c.4429-79:BCOR_chrX:g.39699662dup Note: The BCOR rearrangement is a duplication of exons 11 - 15. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0043135-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.2990_c.3836+951del Note: The ALK rearrangement is an intragenic deletion of exons 18 - 25. One of the breakpoints is within exon 18. The rearrangement includes a part of the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TET1	0	MSKCC-DMP	P-0043336-T01-IM6	TET1-intragenic	yes	unknown		unknown	TET1 (NM_030625) rearrangement: t(1;10)(p36.22;q21.3)(chr1:g.9933952::chr10:g.70360699) Note: The TET1 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0043336-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: t(1;2)(q32.1;p23.2)(chr1:g.205559556::chr2:g.29450227) Note: The ALK rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0043336-T01-IM6	SRC-intragenic	yes	unknown		unknown	SRC (NM_198291) rearrangement: c.703+225:SRC_chr20:g.36135046del Note: The SRC rearrangement is a deletion of exons 9 - 14. The rearrangement includes the kinase domain of SRC. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043336-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4684:TMPRSS2_c.19-14284:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0043336-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4684:TMPRSS2_c.19-14284:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
TGFBR2	0	MSKCC-DMP	P-0043661-T01-IM6	TGFBR2-intragenic	yes	unknown		unknown	TGFBR2 (NM_001024847) rearrangement: c.1271_c.1471+1007del Note: The TGFBR2 rearrangement is an intragenic deletion of exons 5 - 6. One of the breakpoints is within exon 5. The rearrangement includes a part of the kinase domain of TGFBR2.
JAK1	0	MSKCC-DMP	P-0043914-T01-IM6	JAK1-intragenic	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: c.163_c.991-585inv Note: The JAK1 rearrangement is an intragenic inversion of exons 3 - 7. One of the breakpoints is within exon 3. Functional significance is undetermined.
EIF4A2	0	MSKCC-DMP	P-0043914-T01-IM6	EIF4A2-intragenic	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: c.808:EIF4A2_chr3:g.195046321dup Note: The EIF4A2 rearrangement is a duplication of exons 8 - 11. One of the breakpoints is within exon 8. Functional significance is undetermined.
ESR1	0	MSKCC-DMP	P-0043914-T01-IM6	ESR1-intragenic	yes	unknown		unknown	ESR1 (NM_001122740) rearrangement: c.453-90_c.643+11644inv Note: The ESR1 rearrangement is an intragenic inversion of exon 3. Functional significance is undetermined.
IDH1	0	MSKCC-DMP	P-0044185-T01-IM6	IDH1-intragenic	yes	unknown		unknown	IDH1 (NM_005896) rearrangement: c.612:IDH1_chr2:g.209116629dup Note: The IDH1 rearrangement is a duplication of exons 1 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
EWSR1	0	MSKCC-DMP	P-0044185-T01-IM6	EWSR1-intragenic	yes	unknown		unknown	EWSR1 (NM_013986) rearrangement: c.811+579_c.998del Note: The EWSR1 rearrangement is an intragenic deletion of exons 9 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044212-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.6148-20:NF1_chr17:g.29355827del Note: The NF1 rearrangement is a deletion of exons 1 - 41.
WHSC1L1	0	MSKCC-DMP	P-0044219-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.431:WHSC1L1_chr8:g.27323508inv Note: The WHSC1L1 rearrangement is an inversion of exons 2 - 24. One of the breakpoints is within exon 2. Functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0044333-T01-IM6	GNL3-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - GNL3 (NM_014366) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52723317::chr9:g.139397753) Note: The NOTCH1 - GNL3 rearrangement is a translocation that results in a fusion of NOTCH1 exons 1 - 27 to GNL3 exons 7 - 15. One of the breakpoints is within NOTCH1 exon 27. Functional significance is undetermined.
GNL3	0	MSKCC-DMP	P-0044333-T01-IM6	GNL3-NOTCH1 fusion	yes	unknown		unknown	NOTCH1 (NM_017617) - GNL3 (NM_014366) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52723317::chr9:g.139397753) Note: The NOTCH1 - GNL3 rearrangement is a translocation that results in a fusion of NOTCH1 exons 1 - 27 to GNL3 exons 7 - 15. One of the breakpoints is within NOTCH1 exon 27. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044376-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4624:TMPRSS2_c.39+51402:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0044376-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4624:TMPRSS2_c.39+51402:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
KIAA1324L	0	MSKCC-DMP	P-0044397-T01-IM6	NOTCH2-KIAA1324L fusion	yes	unknown		unknown	KIAA1324L (NM_001142749) - NOTCH2 (NM_024408) rearrangement: t(1;7)(p12;q21.12)(chr1:g.120465401::chr7:g.86589695) Note: The KIAA1324L - NOTCH2 rearrangement is a translocation that results in a fusion of KIAA1324L exons 1 - 2 to NOTCH2 exons 27 - 34. One of the breakpoints is within NOTCH2 exon 27. Functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0044397-T01-IM6	NOTCH2-KIAA1324L fusion	yes	unknown		unknown	KIAA1324L (NM_001142749) - NOTCH2 (NM_024408) rearrangement: t(1;7)(p12;q21.12)(chr1:g.120465401::chr7:g.86589695) Note: The KIAA1324L - NOTCH2 rearrangement is a translocation that results in a fusion of KIAA1324L exons 1 - 2 to NOTCH2 exons 27 - 34. One of the breakpoints is within NOTCH2 exon 27. Functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0044793-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: c.2970+32:ERBB2_chr17:g.27068786inv Note: The ERBB2 rearrangement is an inversion of exons 1 - 24. The rearrangement includes the kinase domain of ERBB2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ERBB2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MET	0	MSKCC-DMP	P-0044907-T01-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: c.263_c.1702-6554dup Note: The MET rearrangement is an intragenic duplication of exons 2 - 5. One of the breakpoints is within exon 2. The rearrangement does not include the kinase domain of MET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MED12	0	MSKCC-DMP	P-0044907-T01-IM6	NLGN3-MED12 fusion	yes	unknown		out of frame	MED12 (NM_005120) - NLGN3 (NM_181303) rearrangement: c.2226+15:MED12_c.728-587:NLGN3del Note: The MED12 - NLGN3 rearrangement is a deletion that results in a fusion of MED12 exons 1 - 15 to NLGN3 exons 4 - 8.
NLGN3	0	MSKCC-DMP	P-0044907-T01-IM6	NLGN3-MED12 fusion	yes	unknown		out of frame	MED12 (NM_005120) - NLGN3 (NM_181303) rearrangement: c.2226+15:MED12_c.728-587:NLGN3del Note: The MED12 - NLGN3 rearrangement is a deletion that results in a fusion of MED12 exons 1 - 15 to NLGN3 exons 4 - 8.
JAK1	0	MSKCC-DMP	P-0044915-T01-IM6	JAK1-intragenic	yes	unknown		unknown	JAK1 (NM_002227) rearrangement: c.3370-4:JAK1_chr1:g.67621368del Note: The JAK1 rearrangement is a deletion of exons 1 - 24.
TMPRSS2	0	MSKCC-DMP	P-0045358-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3497:TMPRSS2_c.237-3947:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.
ERG	0	MSKCC-DMP	P-0045358-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3497:TMPRSS2_c.237-3947:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.
TMPRSS2	0	MSKCC-DMP	P-0045546-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-401:TMPRSS2_c.40-57469:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0045546-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-401:TMPRSS2_c.40-57469:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
SUFU	0	MSKCC-DMP	P-0047087-T01-IM6	PPAPDC1A-SUFU fusion	yes	unknown		unknown	SUFU (NM_016169) - PPAPDC1A (NM_001030059) rearrangement: c.1136:SUFU_c.445+5423:PPAPDC1Adel Note: The SUFU - PPAPDC1A rearrangement is a deletion that results in a fusion of SUFU exons 1 - 9 to PPAPDC1A exons 6 - 7. One of the breakpoints is within SUFU exon 9.
PPAPDC1A	0	MSKCC-DMP	P-0047087-T01-IM6	PPAPDC1A-SUFU fusion	yes	unknown		unknown	SUFU (NM_016169) - PPAPDC1A (NM_001030059) rearrangement: c.1136:SUFU_c.445+5423:PPAPDC1Adel Note: The SUFU - PPAPDC1A rearrangement is a deletion that results in a fusion of SUFU exons 1 - 9 to PPAPDC1A exons 6 - 7. One of the breakpoints is within SUFU exon 9.
FGFR2	0	MSKCC-DMP	P-0049133-T02-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion: c.2301+1114:FGFR2_c.237+29879:BICC1inv Note: The FGFR2 - BICC1 fusion involves FGFR2 exons 1 - 17 and BICC1 exons 3 - 21. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
BICC1	0	MSKCC-DMP	P-0049133-T02-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion: c.2301+1114:FGFR2_c.237+29879:BICC1inv Note: The FGFR2 - BICC1 fusion involves FGFR2 exons 1 - 17 and BICC1 exons 3 - 21. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
PTPRK	0	MSKCC-DMP	P-0037180-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190008 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0037180-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190008 Macro-dissection: Unknown
TMPRSS2	0	MSKCC-DMP	P-0042680-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190107 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0042680-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190107 Macro-dissection: Not Performed
NCOA4	0	MSKCC-DMP	P-0042880-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon10 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190109 Macro-dissection: Performed
RET	0	MSKCC-DMP	P-0042880-T01-IM6	RET-NCOA4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: NCOA4-RET fusion. Note: The rearrangement is an in-frame fusion between genes NCOA4 Exon10 (NM_001145260) and RET Exon12 (NM_020975). Lab Notes Run Number: Archerv3-CLIN-20190109 Macro-dissection: Performed
ESR1	0	MSKCC-DMP	P-0043135-T01-IM6	KTN1-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-KTN1 fusion. Note: The rearrangement is a fusion between genes ESR1 Exon5 (NM_001122742) and KTN1 Exon29 (NM_001079521). Lab Notes Run Number: Archerv3-CLIN-20190115 Macro-dissection: Not Performed
KTN1	0	MSKCC-DMP	P-0043135-T01-IM6	KTN1-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-KTN1 fusion. Note: The rearrangement is a fusion between genes ESR1 Exon5 (NM_001122742) and KTN1 Exon29 (NM_001079521). Lab Notes Run Number: Archerv3-CLIN-20190115 Macro-dissection: Not Performed
TMPRSS2	0	MSKCC-DMP	P-0005596-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10): c.56-2228:TMPRSS2_c.19-8779:ERGdel
ERG	0	MSKCC-DMP	P-0005596-T01-IM5	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10): c.56-2228:TMPRSS2_c.19-8779:ERGdel
PTEN	0	MSKCC-DMP	P-0011252-T01-IM5	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.1026+87:PTEN_chr10:g.90177234del Note: The PTEN rearrangement is a deletion of exon 9.
MGA	0	MSKCC-DMP	P-0017272-T01-IM6	MGA-intragenic	yes	unknown		unknown	MGA (NM_001164273) rearrangement: chr15:g.28511764_c.8260:MGAdel Note: The MGA rearrangement is a deletion of MGA promoter region and exons 1-24. One of the breakpoint is within exon 24. The functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0020088-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.3255:CIC_chr19:g.48885780inv Note: The CIC rearrangement is an inversion of exons 14-20.  One of the breakpoints is in exon 14. The functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0020450-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+142:ALK_chr2:g.123228344del Note: The ALK rearrangement is a deletion of exons 1-19. The functional significance is undetermined. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ALK gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.
TP53	0	MSKCC-DMP	P-0021318-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.*520_c.1030del Note: The TP53 rearrangement is an intragenic deletion of exons 10-11. One of the breakpoints is within exon 10. Its significance is undetermined.
PTPN11	0	MSKCC-DMP	P-0024150-T01-IM6	PTPN11-intragenic	yes	unknown		unknown	PTPN11 (NM_002834) rearrangement: c.1767_chr12:g.113053952inv Note: The PTPN11 rearrangement results in the inversion of exon 15. One of the breakpoints is within exon 15. The functional significance is undetermined.
TFE3	0	MSKCC-DMP	P-0024831-T01-IM6	TFE3-intragenic	yes	unknown		unknown	TFE3 (NM_006521) rearrangement: c.886-702:TFE3_chrX:g.45846839inv Note: The TFE3 rearrangement results in the inversion of exons 6-10. Its functional significance is undetermined.
BRCA1	0	MSKCC-DMP	P-0025479-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: t(15;17)(q22.2;q21.31)(chr15:g.62705905::chr17:g.41223156) Note: The BRCA1 rearrangement is a translocation with a breakpoint in exon 15. The functional significance is undetermined.
SMAD4	0	MSKCC-DMP	P-0027130-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.1447+25:SMAD4_chr18:g.48624512del Note: The SMAD4 rearrangement results in the deletion of exons 11-12. The functional significance is undetermined.
PLK2	0	MSKCC-DMP	P-0027130-T01-IM6	PDE4D-PLK2 fusion	yes	unknown		out of frame	PLK2 (NM_006622) - PDE4D (NM_001104631) rearrangement: c.1156+14:PLK2_c.922-15282:PDE4Ddup Note: The PLK2 - PDE4D rearrangement is a duplication that results in the fusion of PLK2 exons 1-8 with PDE4D exon 9-15. The functional significance is undetermined.
PDE4D	0	MSKCC-DMP	P-0027130-T01-IM6	PDE4D-PLK2 fusion	yes	unknown		out of frame	PLK2 (NM_006622) - PDE4D (NM_001104631) rearrangement: c.1156+14:PLK2_c.922-15282:PDE4Ddup Note: The PLK2 - PDE4D rearrangement is a duplication that results in the fusion of PLK2 exons 1-8 with PDE4D exon 9-15. The functional significance is undetermined.
BCL6	0	MSKCC-DMP	P-0028066-T01-IM6	BCL6-intragenic	yes	unknown		unknown	BCL6 (NM_001706) rearrangement: c.1540+111:BCL6_chr3:g.187103059del Note: The BCL6 rearrangement is a rearrangement is a deletion of exons 7-10. its functional significance is undetermined.
CDKN1B	0	MSKCC-DMP	P-0028080-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.-9_c.476-73del Note: The CDKN1B rearrangement is a deletion of exon 1. Its functional significance is undetermined.
PRKAR1A	0	MSKCC-DMP	P-0028080-T01-IM6	PRKAR1A-intragenic	yes	unknown		unknown	PRKAR1A (NM_212471) rearrangement: c.503-76:PRKAR1A_chr17:g.65890416inv Note: The PRKAR1A rearrangement is an inversion of exons 1-5. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0028080-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4857:TMPRSS2_c.18+9341:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0028080-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4857:TMPRSS2_c.18+9341:ERGdel Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.
NF1	0	MSKCC-DMP	P-0028328-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(1;17)(q24.3;q11.2)(chr1:g.171191499::chr17:g.29486091) Note: The NF1 rearrangement is a translocation with a breakpoint in exon 3, and may result in truncation of the gene.
BMPR1A	0	MSKCC-DMP	P-0030380-T01-IM6	BMPR1A-intragenic	yes	unknown		out of frame	BMPR1A (NM_004329) Rearrangement : c.530+286_c.1342+81dup Note: The BMPR1A Rearrangement results in the intragenic duplication of exons 8-11. Its functional significance is undetermined.
GREB1L	0	MSKCC-DMP	P-0031582-T01-IM6	LMO1-GREB1L fusion	yes	unknown		unknown	GREB1L (NM_001142966) - LMO1 (NM_002315) rearrangement: t(11;18)(p15.4;q11.1)(chr11:g.8246318::chr18:g.18956391) Note: The GREB1L - LMO1 rearrangement is a translocation that results in the fusion of  the GREB1L promoter region  and 5UTR with LMO1 exon 4. The functional significance is undetermined.
LMO1	0	MSKCC-DMP	P-0031582-T01-IM6	LMO1-GREB1L fusion	yes	unknown		unknown	GREB1L (NM_001142966) - LMO1 (NM_002315) rearrangement: t(11;18)(p15.4;q11.1)(chr11:g.8246318::chr18:g.18956391) Note: The GREB1L - LMO1 rearrangement is a translocation that results in the fusion of  the GREB1L promoter region  and 5UTR with LMO1 exon 4. The functional significance is undetermined.
LIN37	0	MSKCC-DMP	P-0032335-T01-IM6	KMT2B-LIN37 fusion	yes	unknown		unknown	LIN37(NM_019104) - KMT2B(NM_014727) fusion: c.445-100:LIN37_c.5463:KMT2Bdup Note: The LIN37 - KMT2B rearrangement is a duplication which results in the fusion of LIN37 exons 1-6 with KMT2B exons 27-37. One of the breakpoints is within exon 27 of KMT2B. Its functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0032335-T01-IM6	KMT2B-LIN37 fusion	yes	unknown		unknown	LIN37(NM_019104) - KMT2B(NM_014727) fusion: c.445-100:LIN37_c.5463:KMT2Bdup Note: The LIN37 - KMT2B rearrangement is a duplication which results in the fusion of LIN37 exons 1-6 with KMT2B exons 27-37. One of the breakpoints is within exon 27 of KMT2B. Its functional significance is undetermined.
SUZ12	0	MSKCC-DMP	P-0033924-T01-IM6	SUZ12-intragenic	yes	unknown		unknown	SUZ12 (NM_015355) rearrangement: c.274+107_chr17:g.34136244inv Note: The SUZ12 rearrangement is an inversion that includes exons 1-16. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0035993-T01-IM6	POLR1B-PAX8 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - POLR1B (NM_019014) rearrangement: c.1189+1007:PAX8_c.177+886:POLR1Binv Note: The PAX8 - POLR1B rearrangement is an inversion that results in a fusion of PAX8 exons 1 - 10 to POLR1B exons 2 - 15. Functional significance is undetermined.
POLR1B	0	MSKCC-DMP	P-0035993-T01-IM6	POLR1B-PAX8 fusion	yes	unknown		out of frame	PAX8 (NM_003466) - POLR1B (NM_019014) rearrangement: c.1189+1007:PAX8_c.177+886:POLR1Binv Note: The PAX8 - POLR1B rearrangement is an inversion that results in a fusion of PAX8 exons 1 - 10 to POLR1B exons 2 - 15. Functional significance is undetermined.
CPNE4	0	MSKCC-DMP	P-0037023-T01-IM6	CASP8-CPNE4 fusion	yes	unknown		unknown	CPNE4 (NM_130808) - CASP8 (NM_001080125) rearrangement: t(2;3)(q33.1;q22.1)(chr2:g.202131409::chr3:g.131752452) Note: The CPNE4 - CASP8 fusion involves CPNE4 exons 1-2 with CASP8 exons 2-9. One of the breakpoints is within CASP8 exon 2. The functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0037023-T01-IM6	CASP8-CPNE4 fusion	yes	unknown		unknown	CPNE4 (NM_130808) - CASP8 (NM_001080125) rearrangement: t(2;3)(q33.1;q22.1)(chr2:g.202131409::chr3:g.131752452) Note: The CPNE4 - CASP8 fusion involves CPNE4 exons 1-2 with CASP8 exons 2-9. One of the breakpoints is within CASP8 exon 2. The functional significance is undetermined.
PGM5	0	MSKCC-DMP	P-0037608-T01-IM6	TMPRSS2-PGM5 fusion	yes	unknown		in frame	PGM5 (NM_021965) - TMPRSS2 (NM_001135099) rearrangement: t(9;21)(q21.11;q22.3)(chr9:g.71138173::chr21:g.42869299) Note: The PGM5 - TMPRSS2 rearrangement is a translocation which may result in the fusion of PGM5 exons 1-10 with TMPRSS2 exons 3-14. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 - ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0037608-T01-IM6	TMPRSS2-PGM5 fusion	yes	unknown		in frame	PGM5 (NM_021965) - TMPRSS2 (NM_001135099) rearrangement: t(9;21)(q21.11;q22.3)(chr9:g.71138173::chr21:g.42869299) Note: The PGM5 - TMPRSS2 rearrangement is a translocation which may result in the fusion of PGM5 exons 1-10 with TMPRSS2 exons 3-14. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in a TMPRSS2 - ERG fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2	0	MSKCC-DMP	P-0037612-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: (17;21)(q21.31;q22.3)(chr17:g.41635523::chr21:g.42868077) Note: The TMPRSS2 rearrangement is a translocation involving exon 3. Its functional significance is undetermined.
CASP8	0	MSKCC-DMP	P-0037867-T01-IM6	CASP8-intragenic	yes	unknown		unknown	CASP8 (NM_001080125) rearrangement: c.925:CASP8_chr2:g.202108480del Note: The CASP8 rearrangement results in the deletion of exons 1-7. One of the breakpoints is within exon 7.
TMPRSS2	0	MSKCC-DMP	P-0037969-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+662:TMPRSS2_c.18+6989:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
ERG	0	MSKCC-DMP	P-0037969-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+662:TMPRSS2_c.18+6989:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.
MAOB	0	MSKCC-DMP	P-0039939-T01-IM6	KDM6A-MAOB fusion	yes	unknown		in frame	MAOB (NM_000898) - KDM6A (NM_021140) rearrangement: c.280-6009:MAOB_c.1330-47:KDM6Ainv Note: The MAOB - KDM6A rearrangement is an inversion that results in a fusion of MAOB exons 1 - 3 to KDM6A exons 14 - 29. The fusion is predicted to be in frame. Functional significance is undetermined.
KDM6A	0	MSKCC-DMP	P-0039939-T01-IM6	KDM6A-MAOB fusion	yes	unknown		in frame	MAOB (NM_000898) - KDM6A (NM_021140) rearrangement: c.280-6009:MAOB_c.1330-47:KDM6Ainv Note: The MAOB - KDM6A rearrangement is an inversion that results in a fusion of MAOB exons 1 - 3 to KDM6A exons 14 - 29. The fusion is predicted to be in frame. Functional significance is undetermined.
CCDC6	0	MSKCC-DMP	P-0040111-T01-IM6	RET-CCDC6 fusion	yes	unknown		unknown	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-13873:CCDC6_c.1919:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0040111-T01-IM6	RET-CCDC6 fusion	yes	unknown		unknown	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-13873:CCDC6_c.1919:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
KMT2D	0	MSKCC-DMP	P-0040340-T01-IM6	ADCY6-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - ADCY6 (NM_015270) rearrangement: c.13095:KMT2D_c.865-567:ADCY6del Note: The KMT2D - ADCY6 rearrangement is a deletion that results in a fusion of KMT2D exons 1 - 39 to ADCY6 exons 2 - 21. One of the breakpoints is within KMT2D exon 39.
ADCY6	0	MSKCC-DMP	P-0040340-T01-IM6	ADCY6-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - ADCY6 (NM_015270) rearrangement: c.13095:KMT2D_c.865-567:ADCY6del Note: The KMT2D - ADCY6 rearrangement is a deletion that results in a fusion of KMT2D exons 1 - 39 to ADCY6 exons 2 - 21. One of the breakpoints is within KMT2D exon 39.
PRKCI	0	MSKCC-DMP	P-0040593-T01-IM6	PRKCI-intragenic	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.882+63_c.1204-3176inv Note: The PRKCI rearrangement is an intragenic inversion of exons 10 - 12. The rearrangement includes a part of the kinase domain of PRKCI. Functional significance is undetermined.
KCNMA1	0	MSKCC-DMP	P-0040673-T01-IM6	ATM-KCNMA1 fusion	yes	unknown		unknown	KCNMA1 (NM_001161352) - ATM (NM_000051) rearrangement: t(10;11)(q22.3;q22.3)(chr10:g.79012810::chr11:g.108100016) Note: The KCNMA1 - ATM rearrangement is a translocation that results in a fusion of KCNMA1 exons 1 - 2 to ATM exons 4 - 63. One of the breakpoints is within ATM exon 4. Functional significance is undetermined.
ATM	0	MSKCC-DMP	P-0040673-T01-IM6	ATM-KCNMA1 fusion	yes	unknown		unknown	KCNMA1 (NM_001161352) - ATM (NM_000051) rearrangement: t(10;11)(q22.3;q22.3)(chr10:g.79012810::chr11:g.108100016) Note: The KCNMA1 - ATM rearrangement is a translocation that results in a fusion of KCNMA1 exons 1 - 2 to ATM exons 4 - 63. One of the breakpoints is within ATM exon 4. Functional significance is undetermined.
CDKN1A	0	MSKCC-DMP	P-0040742-T01-IM6	CDKN1A-intragenic	yes	unknown		unknown	CDKN1A (NM_078467) rearrangement: t(6;10)(p21.2;q24.1)(chr6:g.36652108::chr10:g.97688301) Note: The CDKN1A rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
PIEZO1	0	MSKCC-DMP	P-0040742-T01-IM6	ANKRD11-PIEZO1 fusion	yes	unknown		unknown	PIEZO1 (NM_001142864) - ANKRD11 (NM_013275) rearrangement: c.64+10713:PIEZO1_c.4215:ANKRD11dup Note: The PIEZO1 - ANKRD11 rearrangement is a duplication that results in a fusion of PIEZO1 exon 1 to ANKRD11 exons 9 - 13. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0040742-T01-IM6	ANKRD11-PIEZO1 fusion	yes	unknown		unknown	PIEZO1 (NM_001142864) - ANKRD11 (NM_013275) rearrangement: c.64+10713:PIEZO1_c.4215:ANKRD11dup Note: The PIEZO1 - ANKRD11 rearrangement is a duplication that results in a fusion of PIEZO1 exon 1 to ANKRD11 exons 9 - 13. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0040742-T01-IM6	FANCA-intragenic	yes	unknown		out of frame	FANCA (NM_000135) rearrangement: c.523-242:FANCA_chr16:g.89845570del Note: The FANCA rearrangement is a deletion of exons 6 - 43.
NOTCH1	0	MSKCC-DMP	P-0040858-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.5638+146_c.7460del Note: The NOTCH1 rearrangement is an intragenic deletion of exons 31 - 34. One of the breakpoints is within exon 34.
NF1	0	MSKCC-DMP	P-0041191-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(6;17)(p21.31;q11.2)(chr6:g.34639847::chr17:g.29486248) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 3. This could potentially lead to loss of function of NF1.
KMT2A	0	MSKCC-DMP	P-0041236-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.5665-631_c.7580inv Note: The KMT2A rearrangement is an intragenic inversion of exons 21 - 27. One of the breakpoints is within exon 27. Functional significance is undetermined.
NCOA3	0	MSKCC-DMP	P-0041479-T01-IM6	NCOA3-intragenic	yes	unknown		unknown	NCOA3 (NM_181659) rearrangement: c.2752:NCOA3_chr20:g.30868436del Note: The NCOA3 rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.
MYCN	0	MSKCC-DMP	P-0041514-T01-IM6	NBAS-MYCN fusion	yes	unknown		unknown	MYCN (NM_005378) - NBAS (NM_015909) rearrangement: c.1140:MYCN_c.3704-2157:NBASinv Note: The MYCN - NBAS rearrangement is an inversion that results in a fusion of MYCN exons 1 - 3 to NBAS exons 32 - 52. One of the breakpoints is within MYCN exon 3. Functional significance is undetermined.
NBAS	0	MSKCC-DMP	P-0041514-T01-IM6	NBAS-MYCN fusion	yes	unknown		unknown	MYCN (NM_005378) - NBAS (NM_015909) rearrangement: c.1140:MYCN_c.3704-2157:NBASinv Note: The MYCN - NBAS rearrangement is an inversion that results in a fusion of MYCN exons 1 - 3 to NBAS exons 32 - 52. One of the breakpoints is within MYCN exon 3. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0041556-T02-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.5604:NF1_chr17:g.29865551del Note: The NF1 rearrangement is a deletion of exons 38 - 58. One of the breakpoints is within exon 38.
BRCA1	0	MSKCC-DMP	P-0041663-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: t(12;17)(q21.31;q21.31)(chr12:g.85813278::chr17:g.41256332) Note: The BRCA1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0041865-T01-IM6	CLUAP1-CREBBP fusion	yes	unknown		in frame	CREBBP (NM_004380) - CLUAP1 (NM_015041) rearrangement: c.4560+81:CREBBP_c.856-1144:CLUAP1inv Note: The CREBBP - CLUAP1 rearrangement is an inversion that results in a fusion of CREBBP exons 1 - 27 to CLUAP1 exons 9 - 12. The fusion is predicted to be in frame. This event occurs in the background of other structural events involving CLUAP1.Functional significance is undetermined.
CLUAP1	0	MSKCC-DMP	P-0041865-T01-IM6	CLUAP1-CREBBP fusion	yes	unknown		in frame	CREBBP (NM_004380) - CLUAP1 (NM_015041) rearrangement: c.4560+81:CREBBP_c.856-1144:CLUAP1inv Note: The CREBBP - CLUAP1 rearrangement is an inversion that results in a fusion of CREBBP exons 1 - 27 to CLUAP1 exons 9 - 12. The fusion is predicted to be in frame. This event occurs in the background of other structural events involving CLUAP1.Functional significance is undetermined.
CLUAP1	0	MSKCC-DMP	P-0041865-T01-IM6	SLX4-CLUAP1 fusion	yes	unknown		unknown	CLUAP1 (NM_015041) - SLX4 (NM_032444) rearrangement: c.856-1082:CLUAP1_c.1795:SLX4inv Note: The CLUAP1 - SLX4 rearrangement is an inversion that results in a fusion of CLUAP1 exons 1 - 8 to SLX4 exons 8 - 15. One of the breakpoints is within SLX4 exon 8. This event occurs in the background of other structural events involving SLX4. Functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0041865-T01-IM6	SLX4-CLUAP1 fusion	yes	unknown		unknown	CLUAP1 (NM_015041) - SLX4 (NM_032444) rearrangement: c.856-1082:CLUAP1_c.1795:SLX4inv Note: The CLUAP1 - SLX4 rearrangement is an inversion that results in a fusion of CLUAP1 exons 1 - 8 to SLX4 exons 8 - 15. One of the breakpoints is within SLX4 exon 8. This event occurs in the background of other structural events involving SLX4. Functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0041865-T01-IM6	SLX4-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.4560+81:CREBBP_c.1793:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 27 to SLX4 exons 8 - 15. One of the breakpoints is within SLX4 exon 8.This event occurs in the background of other structural events involving SLX4..Functional significance is undetermined.
SLX4	0	MSKCC-DMP	P-0041865-T01-IM6	SLX4-CREBBP fusion	yes	unknown		unknown	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.4560+81:CREBBP_c.1793:SLX4del Note: The CREBBP - SLX4 rearrangement is a deletion that results in a fusion of CREBBP exons 1 - 27 to SLX4 exons 8 - 15. One of the breakpoints is within SLX4 exon 8.This event occurs in the background of other structural events involving SLX4..Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0041944-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1216-894_c.1242del Note: The RB1 rearrangement is an intragenic deletion of exon 13. One of the breakpoints is within exon 13.
TMPRSS2	0	MSKCC-DMP	P-0041944-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1755:TMPRSS2_c.40-52948:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0041944-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1755:TMPRSS2_c.40-52948:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
AR	0	MSKCC-DMP	P-0041955-T01-IM6	OPHN1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2063:AR_chrX:g.67117287del Note: The AR rearrangement is a deletion of exons 4 - 8. One of the breakpoints is within exon 4. Functional significance is undetermined.
OPHN1	0	MSKCC-DMP	P-0041955-T01-IM6	OPHN1-AR fusion	yes	unknown		unknown	AR (NM_000044) rearrangement: c.2063:AR_chrX:g.67117287del Note: The AR rearrangement is a deletion of exons 4 - 8. One of the breakpoints is within exon 4. Functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0042144-T01-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.404-492_c.567del Note: The ASXL2 rearrangement is an intragenic deletion of exons 5 - 6. One of the breakpoints is within exon 6.
TMPRSS2	0	MSKCC-DMP	P-0042144-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+3863_c.56-4726del Note: The TMPRSS2 rearrangement is an intragenic deletion with breakpoints in intron 1. Functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0042157-T02-IM6	TRAF7-intragenic	yes	unknown		unknown	TRAF7 (NM_032271) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.2223408::chr17:g.75302737) Note: The TRAF7 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0042157-T02-IM6	TANC2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - TANC2 (NM_025185) rearrangement: c.788:NCOR1_c.2829+1417:TANC2inv Note: The NCOR1 - TANC2 rearrangement is an inversion that results in a fusion of NCOR1 exons 1 - 7 to TANC2 exons 16 - 25. One of the breakpoints is within NCOR1 exon 7. Functional significance is undetermined.
TANC2	0	MSKCC-DMP	P-0042157-T02-IM6	TANC2-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - TANC2 (NM_025185) rearrangement: c.788:NCOR1_c.2829+1417:TANC2inv Note: The NCOR1 - TANC2 rearrangement is an inversion that results in a fusion of NCOR1 exons 1 - 7 to TANC2 exons 16 - 25. One of the breakpoints is within NCOR1 exon 7. Functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0042157-T02-IM6	SMARCA4-intragenic	yes	unknown		in frame	SMARCA4 (NM_003072) rearrangement: c.1593+167_c.4170+2954del Note: The SMARCA4 rearrangement is an intragenic deletion of exons 10 - 29.
DNMT3B	0	MSKCC-DMP	P-0042157-T02-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.45:DNMT3B_chr20:g.31576096del Note: The DNMT3B rearrangement is a deletion of exons 2 - 23. One of the breakpoints is within exon 2.
FAT1	0	MSKCC-DMP	P-0042157-T02-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.3580+5962_c.4049del Note: The FAT1 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 6.
RB1	0	MSKCC-DMP	P-0042162-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: t(13;19)(q14.2;p13.3)(chr13:g.49050895::chr19:g.4443302) Note: The RB1 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042252-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3404:TMPRSS2_c.19-24065:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0042252-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3404:TMPRSS2_c.19-24065:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ALK	0	MSKCC-DMP	P-0042281-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+234:ALK_chr2:g.240030513inv Note: The ALK rearrangement is an inversion of exons 1 - 19. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PTEN	0	MSKCC-DMP	P-0042489-T01-IM6	PTEN-intragenic	yes	unknown		unknown	PTEN (NM_000314) rearrangement: c.573:PTEN_chr10:g.89858758del Note: The PTEN rearrangement is a deletion of exons 6 - 9. One of the breakpoints is within exon 6.
ETV6	0	MSKCC-DMP	P-0042503-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12032802::chr15:g.88556067) Note: The ETV6 - NTRK3 fusion involves ETV6 exons 1 - 5 and NTRK3 exons 15 - 20. The fusion is predicted to be in frame and includes the kinase domain of NTRK3.
NTRK3	0	MSKCC-DMP	P-0042503-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12032802::chr15:g.88556067) Note: The ETV6 - NTRK3 fusion involves ETV6 exons 1 - 5 and NTRK3 exons 15 - 20. The fusion is predicted to be in frame and includes the kinase domain of NTRK3.
ARID1A	0	MSKCC-DMP	P-0042548-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.5676:ARID1A_chr1:g.29532886del Note: The ARID1A rearrangement is a deletion of exon 20. One of the breakpoints is within exon 20.
CARD11	0	MSKCC-DMP	P-0042591-T01-IM6	CARD11-intragenic	yes	unknown		unknown	CARD11 (NM_032415) rearrangement: c.685-259_c.2876inv Note: The CARD11 rearrangement is an intragenic inversion of exons 6 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.
SEC16A	0	MSKCC-DMP	P-0042654-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.6478:SEC16A_c.749:NOTCH1dup Note: The SEC16A - NOTCH1 rearrangement is a duplication that results in a fusion of SEC16A exons 1 - 26 to NOTCH1 exons 5 - 34. The breakpoints are within SEC16A exon 26 and NOTCH1 exon 5. Functional significance is undetermined.
NOTCH1	0	MSKCC-DMP	P-0042654-T01-IM6	NOTCH1-SEC16A fusion	yes	unknown		unknown	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.6478:SEC16A_c.749:NOTCH1dup Note: The SEC16A - NOTCH1 rearrangement is a duplication that results in a fusion of SEC16A exons 1 - 26 to NOTCH1 exons 5 - 34. The breakpoints are within SEC16A exon 26 and NOTCH1 exon 5. Functional significance is undetermined.
MSH2	0	MSKCC-DMP	P-0042741-T01-IM6	MSH2-intragenic	yes	unknown		unknown	MSH2 (NM_000251) rearrangement: c.367-659_c.646-71inv Note: The MSH2 rearrangement is an intragenic inversion of exon 3. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0042741-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.3126_c.3617-3352dup Note: The PBRM1 rearrangement is an intragenic duplication of exons 21 - 23. One of the breakpoints is within exon 21. Functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0042818-T01-IM6	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.1474+76_c.1554+22inv Note: The DNMT3A rearrangement is an intragenic inversion of exon 13. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0043381-T02-IM6	YAP1-KMT2A fusion	yes	unknown		in frame	KMT2A (NM_001197104) - YAP1 (NM_001130145) rearrangement: c.3634+100:KMT2A_c.1277-339:YAP1dup Note: The KMT2A - YAP1 rearrangement is a duplication that results in a fusion of KMT2A exons 1 - 6 to YAP1 exon 9. The fusion is predicted to be in frame. Functional significance is undetermined.
YAP1	0	MSKCC-DMP	P-0043381-T02-IM6	YAP1-KMT2A fusion	yes	unknown		in frame	KMT2A (NM_001197104) - YAP1 (NM_001130145) rearrangement: c.3634+100:KMT2A_c.1277-339:YAP1dup Note: The KMT2A - YAP1 rearrangement is a duplication that results in a fusion of KMT2A exons 1 - 6 to YAP1 exon 9. The fusion is predicted to be in frame. Functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0043706-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2293:ERBB2_c.2768+237:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1 - 19 to CDK12 exons 9 - 14. One of the breakpoints is within ERBB2 exon 19. The fusion includes parts of the kinase domains of ERBB2 and CDK12. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ERBB2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CDK12	0	MSKCC-DMP	P-0043706-T01-IM6	CDK12-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2293:ERBB2_c.2768+237:CDK12dup Note: The ERBB2 - CDK12 rearrangement is a duplication that results in a fusion of ERBB2 exons 1 - 19 to CDK12 exons 9 - 14. One of the breakpoints is within ERBB2 exon 19. The fusion includes parts of the kinase domains of ERBB2 and CDK12. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ERBB2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ERBB4	0	MSKCC-DMP	P-0044075-T01-IM6	ERBB4-intragenic	yes	unknown		unknown	ERBB4 (NM_005235) rearrangement: c.2529:ERBB4_chr2:g.144181408del Note: The ERBB4 rearrangement is a deletion of exons 21 - 28. One of the breakpoints is within exon 21. The rearrangement includes a part of the kinase domain of ERBB4. Functional significance is undetermined.
RAD51	0	MSKCC-DMP	P-0044122-T01-IM6	RAD51-intragenic	yes	unknown		unknown	RAD51 (NM_002875) rearrangement: c.226:RAD51_chr15:g.40878263del Note: The RAD51 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4.
CALR	0	MSKCC-DMP	P-0044136-T01-IM6	CALR-intragenic	yes	unknown		unknown	CALR (NM_004343) rearrangement: t(19;22)(p13.2;q11.21)(chr19:g.13054505::chr22:g.20098581) Note: The CALR rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0044137-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.2222-907_c.4545inv Note: The MDC1 rearrangement is an intragenic inversion of exons 8 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0044146-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.995+93:PBRM1_chr3:g.51878023del Note: The PBRM1 rearrangement is a deletion of exons 11 - 30.
CTNNB1	0	MSKCC-DMP	P-0044188-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.126_c.495+11del Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3 - 4. One of the breakpoints is within exon 3. Functional significance is undetermined.
UBE2W	0	MSKCC-DMP	P-0044216-T01-IM6	TCEB1-UBE2W fusion	yes	unknown		out of frame	UBE2W (NM_001001481) - TCEB1 (NM_005648) rearrangement: c.331-2118:UBE2W_c.5-72:TCEB1dup Note: The UBE2W - TCEB1 rearrangement is a duplication that results in a fusion of UBE2W exons 1 - 3 to TCEB1 exons 3 - 4. Functional significance is undetermined.
TCEB1	0	MSKCC-DMP	P-0044216-T01-IM6	TCEB1-UBE2W fusion	yes	unknown		out of frame	UBE2W (NM_001001481) - TCEB1 (NM_005648) rearrangement: c.331-2118:UBE2W_c.5-72:TCEB1dup Note: The UBE2W - TCEB1 rearrangement is a duplication that results in a fusion of UBE2W exons 1 - 3 to TCEB1 exons 3 - 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044258-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3295:TMPRSS2_c.39+20043:ERGdel Note: The TMPRSS2 - ERG  fusion involves TMPRSS2 exon 1 to ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0044258-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3295:TMPRSS2_c.39+20043:ERGdel Note: The TMPRSS2 - ERG  fusion involves TMPRSS2 exon 1 to ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ETV6	0	MSKCC-DMP	P-0044291-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.34-69:ETV6_chr12:g.3781481del Note: The ETV6 rearrangement is a deletion of exon 1. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0044415-T01-IM6	FGFR3-intragenic	yes	unknown		unknown	FGFR3 (NM_000142) rearrangement: c.1745:FGFR3_chr4:g.1774446del Note: The FGFR3 rearrangement is a deletion of exons 1 - 13. One of the breakpoints is within exon 13. The rearrangement includes a part of the kinase domain of FGFR3. Functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0044482-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.2352:ATRX_chrX:g.72451668inv Note: The ATRX rearrangement is an inversion of exons 9 - 35. One of the breakpoints is within exon 9. Functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0044568-T01-IM6	PRKCI-intragenic	yes	unknown		unknown	PRKCI (NM_002740) rearrangement: c.1324:PRKCI_chr3:g.169921961inv Note: The PRKCI rearrangement is an inversion of exons 1 - 14. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of PRKCI. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0044782-T01-IM6	TP53-intragenic	yes	unknown		out of frame	TP53 (NM_000546) rearrangement: c.782+109_c.994-1104del Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 9.
TSPAN9	0	MSKCC-DMP	P-0044801-T01-IM6	TEK-TSPAN9 fusion	yes	unknown		out of frame	TSPAN9 (NM_001168320) - TEK (NM_000459) rearrangement: t(9;12)(p21.2;p13.32)(chr9:g.27192473::chr12:g.3328633) Note: The TSPAN9 - TEK rearrangement is a translocation that results in a fusion of TSPAN9 exons 1 - 2 to TEK exons 11 - 23. The fusion includes the kinase domain of TEK. Functional significance is undetermined.
TEK	0	MSKCC-DMP	P-0044801-T01-IM6	TEK-TSPAN9 fusion	yes	unknown		out of frame	TSPAN9 (NM_001168320) - TEK (NM_000459) rearrangement: t(9;12)(p21.2;p13.32)(chr9:g.27192473::chr12:g.3328633) Note: The TSPAN9 - TEK rearrangement is a translocation that results in a fusion of TSPAN9 exons 1 - 2 to TEK exons 11 - 23. The fusion includes the kinase domain of TEK. Functional significance is undetermined.
KMT2A	0	MSKCC-DMP	P-0045298-T01-IM6	KMT2A-intragenic	yes	unknown		unknown	KMT2A (NM_001197104) rearrangement: c.9366:KMT2A_chr11:g.80166458del Note: The KMT2A rearrangement is a deletion of exons 1 - 27. One of the breakpoints is within exon 27.
ARID1A	0	MSKCC-DMP	P-0048585-T03-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: t(1;10)(p36.11;q21.3)(chr1:g.27088668::chr10:g.70533678) Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.
CIC	0	MSKCC-DMP	P-0048585-T03-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: t(9;19)(q34.11;q13.2)(chr9:g.130456657::chr19:g.42793014) Note: The CIC rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined. Multiple rearrangements involving CIC were detected in this sample and a more complex rearrangement involving CIC fusion may not be fully characterized by impact. Additional testing by an alternative method is recommended, if clinically indicated.
TMPRSS2 exon 1 to ETV5 exon 6	0	MSKCC-DMP	P-0048761-T01-IM6	TMPRSS2 exon 1 to ETV5 exon 6-intragenic	yes	unknown		in frame	TMPRSS2 exon 1 to ETV5 exon 6 Note: The TMPRSS2 - ETV5 fusion involves TMPRSS2 exon 1 and ETV5 exons 6 - 13. The fusion is predicted to be in frame.
TP53	0	MSKCC-DMP	P-0049188-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1065:TP53_chr17:g.8205033del Note: The TP53 rearrangement is a deletion of exons 1 - 10. One of the breakpoints is within exon 10.
MAD1L1	0	MSKCC-DMP	P-0049188-T01-IM6	TMPRSS2-MAD1L1 fusion	yes	unknown		out of frame	MAD1L1 (NM_001013837) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2217379::chr21:g.42874884) Note: The MAD1L1 - TMPRSS2 rearrangement is a translocation that results in a fusion of MAD1L1 exons 1 - 10 to TMPRSS2 exons 2 - 14. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0049188-T01-IM6	TMPRSS2-MAD1L1 fusion	yes	unknown		out of frame	MAD1L1 (NM_001013837) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2217379::chr21:g.42874884) Note: The MAD1L1 - TMPRSS2 rearrangement is a translocation that results in a fusion of MAD1L1 exons 1 - 10 to TMPRSS2 exons 2 - 14. Functional significance is undetermined.
FUS	0	MSKCC-DMP	P-0015814-T01-IM6	ATRNL1-FUS fusion - Archer	yes	unknown		unknown	AMENDED!!! POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FUS-ATRNL1 fusion. Note: The rearrangement is an in-frame fusion between genes FUS Exon11 (NM_004960) and ATRNL1 Exon1 (NM_207303). Lab Notes Run Number: ArcherV1-CLIN-20160064 Macro-dissection: Performed
ATRNL1	0	MSKCC-DMP	P-0015814-T01-IM6	ATRNL1-FUS fusion - Archer	yes	unknown		unknown	AMENDED!!! POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: FUS-ATRNL1 fusion. Note: The rearrangement is an in-frame fusion between genes FUS Exon11 (NM_004960) and ATRNL1 Exon1 (NM_207303). Lab Notes Run Number: ArcherV1-CLIN-20160064 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0032966-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon3 (NM_032784). Lab Notes Run Number: ArcherV2-CLIN-20180127 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0032966-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon3 (NM_032784). Lab Notes Run Number: ArcherV2-CLIN-20180127 Macro-dissection: Unknown
TACC1	0	MSKCC-DMP	P-0040889-T01-IM6	FGFR1-TACC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TACC1-FGFR1 fusion. Note: The rearrangement is predicted to be an in-frame fusion between genes TACC1 Exon1 (NM_001146216) and FGFR1 Exon2 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190077 Macro-dissection: Not Performed
FGFR1	0	MSKCC-DMP	P-0040889-T01-IM6	FGFR1-TACC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TACC1-FGFR1 fusion. Note: The rearrangement is predicted to be an in-frame fusion between genes TACC1 Exon1 (NM_001146216) and FGFR1 Exon2 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190077 Macro-dissection: Not Performed
AR	0	MSKCC-DMP	P-0041955-T01-IM6	AR-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:      AR (NM_000044) Variant 7 (AR V-7)    PMID: 26554309, 19117982  Lab Notes Run Number: Archerv3-CLIN-20190095 Macro-dissection: Not Performed
EML4	0	MSKCC-DMP	P-0042281-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190099 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0042281-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon6 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190099 Macro-dissection: Performed
ESR1	0	MSKCC-DMP	P-0043706-T01-IM6	CCDC170-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-CCDC170 fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon3 (NM_000125) and CCDC170 Exon10 (NM_025059). The functional significance is unknown. Lab Notes Run Number: Archerv3-CLIN-20190124 Macro-dissection: Performed
CCDC170	0	MSKCC-DMP	P-0043706-T01-IM6	CCDC170-ESR1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ESR1-CCDC170 fusion. Note: The rearrangement is an in-frame fusion between genes ESR1 Exon3 (NM_000125) and CCDC170 Exon10 (NM_025059). The functional significance is unknown. Lab Notes Run Number: Archerv3-CLIN-20190124 Macro-dissection: Performed
LDLR	0	MSKCC-DMP	P-0004863-T01-IM5	SMARCA4-LDLR fusion	yes	unknown		out of frame	LDLR (NM_000527)  - SMARCA4 (NM_003072) rearrangement : c.940+53:LDLR_c.4171-1958:SMARCA4dup The LDLR (NM_000527)  - SMARCA4 (NM_003072) rearrangement is a duplication which results in the fusion of LDLR  exons 1-6 and SMARCA4 exons 30-35. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0004863-T01-IM5	SMARCA4-LDLR fusion	yes	unknown		out of frame	LDLR (NM_000527)  - SMARCA4 (NM_003072) rearrangement : c.940+53:LDLR_c.4171-1958:SMARCA4dup The LDLR (NM_000527)  - SMARCA4 (NM_003072) rearrangement is a duplication which results in the fusion of LDLR  exons 1-6 and SMARCA4 exons 30-35. The functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0009748-T01-IM5	SHC1-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - SHC1 (NM_001130041) rearrangement: t(1;17)(q21.3;q12)(chr1:g.154946879::chr17:g.37883375) Note: The ERBB2 (NM_004448) - SHC1 (NM_001130041) rearrangement is a translocation which may result in a fusion of ERBB2 exons 1-25 with SHC1 exons 1-12. The functional significance is undetermined.
SHC1	0	MSKCC-DMP	P-0009748-T01-IM5	SHC1-ERBB2 fusion	yes	unknown		unknown	ERBB2 (NM_004448) - SHC1 (NM_001130041) rearrangement: t(1;17)(q21.3;q12)(chr1:g.154946879::chr17:g.37883375) Note: The ERBB2 (NM_004448) - SHC1 (NM_001130041) rearrangement is a translocation which may result in a fusion of ERBB2 exons 1-25 with SHC1 exons 1-12. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0014640-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) Rearrangement :  t(4;16)(q35.2;q24.1)(chr4:g.187630430::chr16:g.:84263298) Note: The FAT1 Rearrangement is a translocation event which results in the possible truncation of exons 2-27 of FAT1. One of the breakpoints is within exon2. Its functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0016989-T02-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+57:FGFR3_c.1645-139:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a duplication which results in the fusion of FGFR3 exons 1-17 with TACC3 exons 8-16. This includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0016989-T02-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+57:FGFR3_c.1645-139:TACC3dup Note: The FGFR3 - TACC3 rearrangement is a duplication which results in the fusion of FGFR3 exons 1-17 with TACC3 exons 8-16. This includes the kinase domain of FGFR3.
KMT2C	0	MSKCC-DMP	P-0031769-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.13948_c.14032-558del Note: The KMT2C rearrangement is an intragenic deletion of a part of exon 53. One of the breakpoints is within exon 53.
STRN	0	MSKCC-DMP	P-0033066-T01-IM6	ALK-STRN fusion	yes	unknown		unknown	STRN (NM_003162) - ALK (NM_004304) fusion( STRN exons 1-3 fused to ALK exons 19-29): c.413-1084:STRN_c.3134:ALKdel Note: The STRN - ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.
ALK	0	MSKCC-DMP	P-0033066-T01-IM6	ALK-STRN fusion	yes	unknown		unknown	STRN (NM_003162) - ALK (NM_004304) fusion( STRN exons 1-3 fused to ALK exons 19-29): c.413-1084:STRN_c.3134:ALKdel Note: The STRN - ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.
STAT3	0	MSKCC-DMP	P-0034063-T01-IM6	STAT3-intragenic	yes	unknown		unknown	STAT3(NM_139276) Rearrangement: c.372+1_c.1282-1423 Note: The STAT3 rearrangement is an intragenic deletion of exons 4 to 14. One of the breakpoints is within exon 4 of STAT3. Its functional significance is undetermined
ETV6	0	MSKCC-DMP	P-0034131-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(6;12)(p21.32;p13.2)(chr6:g.32990236::chr12:g.12030529) Note: The ETV6 rearrangement is translocation with a breakpoint in intron 5. The functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0034897-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-56487:ERG_c.56-1366:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1-3 and TMPRSS2 exons 2-14. The non-canonical ERG transcript is involved and a more complex rearrangement resulting in the TMPRSS2-ERG fusion is possible. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0034897-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-56487:ERG_c.56-1366:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exons 1-3 and TMPRSS2 exons 2-14. The non-canonical ERG transcript is involved and a more complex rearrangement resulting in the TMPRSS2-ERG fusion is possible. The functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0036175-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1726:RB1_chr13:g.48827936inv Note: The RB1 rearrangement is an inversion of exons 1-18. One of the breakpoints is within exon 18. Its functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0037381-T01-IM6	FLT3-intragenic	yes	unknown		unknown	FLT3 (NM_004119) rearrangement: c.1309+105:FLT3_chr13:g.28496734del Note: The FLT3 rearrangement results in the deletion of exons 11-24. The functional significance is undetermined.
SRC	0	MSKCC-DMP	P-0037535-T01-IM6	RPN2-SRC fusion	yes	unknown		unknown	SRC (NM_198291) - RPN2 (NM_002951) rearrangement: c.989:SRC_c.986+998:RPN2dup Note: The SRC - RPN2 rearrangement is a duplication that results in a fusion of SRC exons 1-10 to RPN2 exons 8-17. One of the breakpoints is within SRC exon 10. The functional significance is undetermined.
RPN2	0	MSKCC-DMP	P-0037535-T01-IM6	RPN2-SRC fusion	yes	unknown		unknown	SRC (NM_198291) - RPN2 (NM_002951) rearrangement: c.989:SRC_c.986+998:RPN2dup Note: The SRC - RPN2 rearrangement is a duplication that results in a fusion of SRC exons 1-10 to RPN2 exons 8-17. One of the breakpoints is within SRC exon 10. The functional significance is undetermined.
MST1R	0	MSKCC-DMP	P-0037535-T01-IM6	MST1R-intragenic	yes	unknown		unknown	MST1R (NM_002447) rearrangement: c.1231-1449_c.2474:del Note: MST1R rearrangement is an intragenic deletion of exons 2-10. One of the breakpoints is within exon 10. The functionals significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0037541-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.814-51:DNMT3B_chr20:g.36490825inv Note: The DNMT3B rearrangement is an inversion of exons 8-23. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0037610-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) rearrangement: t(12;15)(p13.2;q25.3)(chr12:g.12014663::chr15:g.88594532) Note: The ETV6 - NTRK3 rearrangement is a translocation which results in the fusion of ETV6 exons 1-4 with NTRK3 exons 14-20. This includes the kinase domain of NTRK3.
NTRK3	0	MSKCC-DMP	P-0037610-T01-IM6	NTRK3-ETV6 fusion	yes	unknown		in frame	ETV6 (NM_001987) - NTRK3 (NM_001012338) rearrangement: t(12;15)(p13.2;q25.3)(chr12:g.12014663::chr15:g.88594532) Note: The ETV6 - NTRK3 rearrangement is a translocation which results in the fusion of ETV6 exons 1-4 with NTRK3 exons 14-20. This includes the kinase domain of NTRK3.
TMPRSS2	0	MSKCC-DMP	P-0037750-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3617:TMPRSS2_c.18+9142:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
ERG	0	MSKCC-DMP	P-0037750-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3617:TMPRSS2_c.18+9142:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.
RPTOR	0	MSKCC-DMP	P-0037968-T01-IM6	RPTOR-intragenic	yes	unknown		unknown	RPTOR (NM_020761) rearrangement: c.3074_c.3370+2706del Note: The RPTOR rearrangement is an intragenic deletion of exons 26 - 28. One of the breakpoints is within exon 26. The functional significance is undetermined.
NCOR1	0	MSKCC-DMP	P-0038498-T01-IM6	CENPV-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - CENPV (NM_181716) rearrangement: c.1534:NCOR1_c.579+1344:CENPVdup Note: The NCOR1 - CENPV rearrangement is a duplication which results in the fusion of NCOR1 exons 1-15 with CENPB1 exons 4-5. One of the breakpoints is within NCOR1 exon 15. Its functional significance is undetermined.
CENPV	0	MSKCC-DMP	P-0038498-T01-IM6	CENPV-NCOR1 fusion	yes	unknown		unknown	NCOR1 (NM_006311) - CENPV (NM_181716) rearrangement: c.1534:NCOR1_c.579+1344:CENPVdup Note: The NCOR1 - CENPV rearrangement is a duplication which results in the fusion of NCOR1 exons 1-15 with CENPB1 exons 4-5. One of the breakpoints is within NCOR1 exon 15. Its functional significance is undetermined.
RAD51C	0	MSKCC-DMP	P-0039666-T02-IM6	RAD51C-intragenic	yes	unknown		unknown	RAD51C (NM_058216) rearrangement: t(5;17)(q31.3;q22)(chr5:g.142325223::chr17:g.56772289) Note: The RAD51C rearrangement is a translocation with a breakpoint in intron 1. Multiple other RAD51C rearrangements were also detected in this sample, suggesting that a more complex rearrangement involving RAD51C is possible. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0040447-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1696-28342_c.1960+118dup Note: The RB1 rearrangement is an intragenic duplication of exons 18 - 19. Functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0040447-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.4606+1220:DOT1L_chr19:g.2067589del Note: The DOT1L rearrangement is a deletion of exons 1 - 27. Functional significance is undetermined.
SLC24A3	0	MSKCC-DMP	P-0040532-T01-IM6	BCL2L11-SLC24A3 fusion	yes	unknown		out of frame	SLC24A3 (NM_020689) - BCL2L11 (NM_138621) rearrangement: t(2;20)(q13;p11.23)(chr2:g.111887601::chr20:g.19507624) Note: The SLC24A3 - BCL2L11 rearrangement is a translocation that results in a fusion of SLC24A3 exons 1 - 3 to BCL2L11 exons 3 - 4. Functional significance is undetermined.
BCL2L11	0	MSKCC-DMP	P-0040532-T01-IM6	BCL2L11-SLC24A3 fusion	yes	unknown		out of frame	SLC24A3 (NM_020689) - BCL2L11 (NM_138621) rearrangement: t(2;20)(q13;p11.23)(chr2:g.111887601::chr20:g.19507624) Note: The SLC24A3 - BCL2L11 rearrangement is a translocation that results in a fusion of SLC24A3 exons 1 - 3 to BCL2L11 exons 3 - 4. Functional significance is undetermined.
NUF2	0	MSKCC-DMP	P-0040532-T01-IM6	NUF2-intragenic	yes	unknown		unknown	NUF2 (NM_031423) rearrangement: t(1;8)(q23.3;q21.11)(chr1:g.163307802::chr8:g.78255575) Note: The NUF2 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0040533-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.1187+33:PIK3R3_chr1:g.46508673del Note: The PIK3R3 rearrangement is a deletion of exon 10.
ELF3	0	MSKCC-DMP	P-0040533-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: t(1;6)(q32.1;p22.3)(chr1:g.201982527::chr6:g.21341871) Note: The ELF3 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0040846-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: t(8;12)(q24.22;q13.12)(chr8:g.131599592::chr12:g.49443721) Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
APC	0	MSKCC-DMP	P-0040853-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1351:APC_chr5:g.150062097del Note: The APC rearrangement is a deletion of exons 11 - 16. One of the breakpoints is within exon 11.
ATRX	0	MSKCC-DMP	P-0040973-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.1339_c.5135-6053del Note: The ATRX rearrangement is an intragenic deletion of exons 9 - 19. One of the breakpoints is within exon 9.
TMPRSS2	0	MSKCC-DMP	P-0041027-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4212:TMPRSS2_c.18+1068:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0041027-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4212:TMPRSS2_c.18+1068:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
NRXN2	0	MSKCC-DMP	P-0041234-T01-IM6	MEN1-NRXN2 fusion	yes	unknown		out of frame	NRXN2 (NM_015080) - MEN1 (NM_000244) rearrangement: c.3848-706:NRXN2_c.1365+92:MEN1dup Note: The NRXN2 - MEN1 rearrangement is a duplication that results in a fusion of NRXN2 exons 1 - 20 to MEN1 exon 10. Functional significance is undetermined.
MEN1	0	MSKCC-DMP	P-0041234-T01-IM6	MEN1-NRXN2 fusion	yes	unknown		out of frame	NRXN2 (NM_015080) - MEN1 (NM_000244) rearrangement: c.3848-706:NRXN2_c.1365+92:MEN1dup Note: The NRXN2 - MEN1 rearrangement is a duplication that results in a fusion of NRXN2 exons 1 - 20 to MEN1 exon 10. Functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0041234-T01-IM6	RECQL-intragenic	yes	unknown		out of frame	RECQL (NM_032941) rearrangement: c.1216+238_c.1668-86del Note: The RECQL rearrangement is an intragenic deletion of exons 12 - 14.
EP300	0	MSKCC-DMP	P-0041234-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: t(14;22)(q32.33;q13.2)(chr14:g.107283261::chr22:g.41548197) Note: The EP300 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.
NHSL2	0	MSKCC-DMP	P-0041235-T01-IM6	MED12-NHSL2 fusion	yes	unknown		unknown	NHSL2 (NM_001013627) - MED12 (NM_005120) rearrangement: c.281-101040:NHSL2_c.6021:MED12dup Note: The NHSL2 - MED12 rearrangement is a duplication that results in a fusion of NHSL2 exon 1 to MED12 exons 41 - 45. One of the breakpoints is within MED12 exon 41. Functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0041235-T01-IM6	MED12-NHSL2 fusion	yes	unknown		unknown	NHSL2 (NM_001013627) - MED12 (NM_005120) rearrangement: c.281-101040:NHSL2_c.6021:MED12dup Note: The NHSL2 - MED12 rearrangement is a duplication that results in a fusion of NHSL2 exon 1 to MED12 exons 41 - 45. One of the breakpoints is within MED12 exon 41. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041326-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2260:TMPRSS2_chr21:g.37538498del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0041432-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.1173:TP53_chr17:g.687501del Note: The TP53 rearrangement is a deletion of exon 11. One of the breakpoints is within exon 11.
NOTCH2	0	MSKCC-DMP	P-0041547-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;18)(p12;q12.1)(chr1:g.120462071::chr18:g.27255333) Note: The NOTCH2 rearrangement is a translocation with a breakpoint in exon 31. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041584-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused to ERG exon 2-11): c.56-236:TMPRSS2_c.-150+5808:ERGdel
ERG	0	MSKCC-DMP	P-0041584-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused to ERG exon 2-11): c.56-236:TMPRSS2_c.-150+5808:ERGdel
RB1	0	MSKCC-DMP	P-0041639-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: c.1050-139:RB1_chr13:g.51785980inv Note: The RB1 rearrangement is an inversion of exons 11 - 27. Functional significance is undetermined.
FGFR3	0	MSKCC-DMP	P-0041836-T01-IM6	FGFR3-intragenic	yes	unknown		in frame	FGFR3 (NM_000142) rearrangement: c.930+627_c.1267-143del Note: The FGFR3 rearrangement is an intragenic deletion of exons 8 - 9. The rearrangement does not include the kinase domain of FGFR3. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR3 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PIK3R2	0	MSKCC-DMP	P-0042035-T01-IM6	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement: c.1979+40:PIK3R2_chr19:g.18529061inv Note: The PIK3R2 rearrangement is an inversion of exon 16. Functional significance is undetermined.
BRAF	0	MSKCC-DMP	P-0042036-T01-IM6	BRAF-intragenic	yes	unknown		unknown	BRAF (NM_004333) rearrangement: c.1314+573:BRAF_chr7:g.114530920del Note: The BRAF rearrangement is a deletion of exons 11 - 18. The rearrangement includes the kinase domain of BRAF. Multiple rearrangements involving BRAF were detected in this sample and a more complex rearrangement involving BRAF is possible. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving BRAF is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CTNNB1	0	MSKCC-DMP	P-0042064-T01-IM6	CTNNB1-intragenic	yes	unknown		in frame	CTNNB1 (NM_001904) rearrangement: c.13+185_c.242-54del Note: The CTNNB1 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0042065-T01-IM6	UPF1-intragenic	yes	unknown		unknown	UPF1 (NM_002911) rearrangement: c.133:UPF1_chr19:g.19928130inv Note: The UPF1 rearrangement is an inversion of exons 1 - 23. One of the breakpoints is within exon 1. Functional significance is undetermined.
APC	0	MSKCC-DMP	P-0042166-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.1006_c.1313dup Note: The APC rearrangement is an intragenic duplication of exons 10 - 11. The breakpoints are within exon 10 and exon 11. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042174-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449)rearrangement: c.55+3407:TMPRSS2_ c.-48+2714:ERGdel Note: The TMPRSS2 -ERG rearrangement is a deletion of exons 2 - 14 of TMPRSS2 and exons 1-2 of ERG. The breakpoint in ERG is within the non-canonical transcript and before the transcription start site. While this rearrangement is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not picked up by the IMPACT Panel cannot be ruled out.
ERG	0	MSKCC-DMP	P-0042174-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449)rearrangement: c.55+3407:TMPRSS2_ c.-48+2714:ERGdel Note: The TMPRSS2 -ERG rearrangement is a deletion of exons 2 - 14 of TMPRSS2 and exons 1-2 of ERG. The breakpoint in ERG is within the non-canonical transcript and before the transcription start site. While this rearrangement is not the canonical TMPRSS2-ERG fusion, the possibility of the fusion not picked up by the IMPACT Panel cannot be ruled out.
FUBP1	0	MSKCC-DMP	P-0042223-T01-IM6	GIPC2-FUBP1 fusion	yes	unknown		unknown	FUBP1 (NM_003902) - GIPC2 (NM_017655) rearrangement: c.1024:FUBP1_c.241-9922:GIPC2inv Note: The FUBP1 - GIPC2 rearrangement is an inversion that results in a fusion of FUBP1 exons 1 - 12 to GIPC2 exons 2 - 6. One of the breakpoints is within FUBP1 exon 12. Functional significance is undetermined.
GIPC2	0	MSKCC-DMP	P-0042223-T01-IM6	GIPC2-FUBP1 fusion	yes	unknown		unknown	FUBP1 (NM_003902) - GIPC2 (NM_017655) rearrangement: c.1024:FUBP1_c.241-9922:GIPC2inv Note: The FUBP1 - GIPC2 rearrangement is an inversion that results in a fusion of FUBP1 exons 1 - 12 to GIPC2 exons 2 - 6. One of the breakpoints is within FUBP1 exon 12. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0042223-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.75-44_c.799del Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 8. One of the breakpoints is within exon 8.
TMPRSS2	0	MSKCC-DMP	P-0042378-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1935:TMPRSS2_c.18+16715:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0042378-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1935:TMPRSS2_c.18+16715:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
WWTR1	0	MSKCC-DMP	P-0042507-T01-IM6	WWTR1-intragenic	yes	unknown		unknown	WWTR1 (NM_001168280) rearrangement: c.905+478_c.961del Note: The WWTR1 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
EZH2	0	MSKCC-DMP	P-0042907-T01-IM6	EZH2-intragenic	yes	unknown		unknown	EZH2 (NM_004456) rearrangement: c.2029+29:EZH2_chr7:g.148447872del Note: The EZH2 rearrangement is a deletion of exons 18 - 20.
EML4	0	MSKCC-DMP	P-0043041-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1782:EML4_c.3173-203:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0043041-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1782:EML4_c.3173-203:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
NCOA4	0	MSKCC-DMP	P-0043077-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.762+608:NCOA4_c.2137-452:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0043077-T01-IM6	RET-NCOA4 fusion	yes	unknown		out of frame	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.762+608:NCOA4_c.2137-452:RETdup Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.
FAT1	0	MSKCC-DMP	P-0043253-T01-IM6	FAT1-intragenic	yes	unknown		unknown	FAT1 (NM_005245) rearrangement: c.472:FAT1_chr4:g.186320655del Note: The FAT1 rearrangement is a deletion of exons 2 - 27. One of the breakpoints is within exon 2.
BAI3	0	MSKCC-DMP	P-0043290-T01-IM6	CDKN2A-BAI3 fusion	yes	unknown		in frame	BAI3 (NM_001704) - CDKN2A (NM_000077) rearrangement: t(6;9)(q12;p21.3)(chr6:g.69608821::chr9:g.21968952) Note: The BAI3 - CDKN2A rearrangement is a translocation that results in a fusion of BAI3 exons 1 - 3 to CDKN2A exon 3. The fusion is predicted to be in frame. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CDKN2A	0	MSKCC-DMP	P-0043290-T01-IM6	CDKN2A-BAI3 fusion	yes	unknown		in frame	BAI3 (NM_001704) - CDKN2A (NM_000077) rearrangement: t(6;9)(q12;p21.3)(chr6:g.69608821::chr9:g.21968952) Note: The BAI3 - CDKN2A rearrangement is a translocation that results in a fusion of BAI3 exons 1 - 3 to CDKN2A exon 3. The fusion is predicted to be in frame. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
PIK3R3	0	MSKCC-DMP	P-0043334-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.1016+102:PIK3R3_chr1:g.98035591inv Note: The PIK3R3 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.
CEBPA	0	MSKCC-DMP	P-0043334-T01-IM6	CEBPA-intragenic	yes	unknown		unknown	CEBPA (NM_004364) rearrangement: c.241:CEBPA_chr19:g.39308775inv Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
TP53	0	MSKCC-DMP	P-0043417-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.85_c.672+43inv Note: The TP53 rearrangement is an intragenic inversion of exons 3 - 6. One of the breakpoints is within exon 3. Functional significance is undetermined.
CTC1	0	MSKCC-DMP	P-0043417-T01-IM6	AURKB-CTC1 fusion	yes	unknown		unknown	CTC1 (NM_025099) - AURKB (NM_004217) rearrangement: c.34-1646:CTC1_c.1035:AURKBdel Note: The CTC1 - AURKB rearrangement is a deletion that results in a fusion of CTC1 exon 1 to AURKB exon 9. One of the breakpoints is within AURKB exon 9. The fusion does not include the kinase domain of AURKB. Functional significance is undetermined.
AURKB	0	MSKCC-DMP	P-0043417-T01-IM6	AURKB-CTC1 fusion	yes	unknown		unknown	CTC1 (NM_025099) - AURKB (NM_004217) rearrangement: c.34-1646:CTC1_c.1035:AURKBdel Note: The CTC1 - AURKB rearrangement is a deletion that results in a fusion of CTC1 exon 1 to AURKB exon 9. One of the breakpoints is within AURKB exon 9. The fusion does not include the kinase domain of AURKB. Functional significance is undetermined.
BCL2	0	MSKCC-DMP	P-0043491-T01-IM6	BCL2-intragenic	yes	unknown		unknown	BCL2 (NM_000633) rearrangement: c.586-54070:BCL2_chr18:g.28860403inv Note: The BCL2 rearrangement is an inversion of exon 3. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043565-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q14;q22.3)(chr15:g.37245374::chr21:g.42874936) Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined. Multiple structural variants in TMPRSS2 are present, potentially signifying a more complex event.
KDM6A	0	MSKCC-DMP	P-0043568-T01-IM6	KDM6A-intragenic	yes	unknown		out of frame	KDM6A (NM_021140) rearrangement: c.620-810_c.654+57dup Note: The KDM6A rearrangement is an intragenic duplication of exon 8. Functional significance is undetermined.
EIF4A2	0	MSKCC-DMP	P-0043571-T01-IM6	EIF4A2-intragenic	yes	unknown		unknown	EIF4A2 (NM_001967) rearrangement: c.1025:EIF4A2_chr3:g.186552349del Note: The EIF4A2 rearrangement is a deletion of exons 10 - 11. One of the breakpoints is within exon 10. Functional significance is undetermined.
ERCC2	0	MSKCC-DMP	P-0043634-T01-IM6	ERCC2-intragenic	yes	unknown		unknown	ERCC2 (NM_000400) rearrangement: c.184-11:ERCC2_chr19:g.45882309inv Note: The ERCC2 rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.
WHSC1L1	0	MSKCC-DMP	P-0043634-T01-IM6	WHSC1L1-intragenic	yes	unknown		unknown	WHSC1L1 (NM_023034) rearrangement: c.2361_c.2443del Note: The WHSC1L1 rearrangement is an intragenic deletion of exons 13 - 14. The breakpoints are within exon 13 and exon 14. Functional significance is undetermined.
SLC5A5	0	MSKCC-DMP	P-0043838-T01-IM6	PIK3R2-SLC5A5 fusion	yes	unknown		out of frame	SLC5A5 (NM_000453) - PIK3R2 (NM_005027) rearrangement: c.970-823:SLC5A5_c.1560-134:PIK3R2del Note: The SLC5A5 - PIK3R2 rearrangement is a deletion that results in a fusion of SLC5A5 exons 1 - 7 to PIK3R2 exons 13 - 16.
PIK3R2	0	MSKCC-DMP	P-0043838-T01-IM6	PIK3R2-SLC5A5 fusion	yes	unknown		out of frame	SLC5A5 (NM_000453) - PIK3R2 (NM_005027) rearrangement: c.970-823:SLC5A5_c.1560-134:PIK3R2del Note: The SLC5A5 - PIK3R2 rearrangement is a deletion that results in a fusion of SLC5A5 exons 1 - 7 to PIK3R2 exons 13 - 16.
BRIP1	0	MSKCC-DMP	P-0043870-T01-IM6	BRIP1-intragenic	yes	unknown		unknown	BRIP1 (NM_032043) rearrangement: c.839:BRIP1_chr17:g.59109530del Note: The BRIP1 rearrangement is a deletion of exons 7 - 20. One of the breakpoints is within exon 7.
TFAP2E	0	MSKCC-DMP	P-0043953-T01-IM6	CSF3R-TFAP2E fusion	yes	unknown		unknown	TFAP2E (NM_178548) - CSF3R (NM_000760) rearrangement: c.1047-1011:TFAP2E_c.1291:CSF3Rinv Note: The TFAP2E - CSF3R rearrangement is an inversion that results in a fusion of TFAP2E exons 1 - 6 to CSF3R exons 11 - 17. One of the breakpoints is within CSF3R exon 11. Functional significance is undetermined.
CSF3R	0	MSKCC-DMP	P-0043953-T01-IM6	CSF3R-TFAP2E fusion	yes	unknown		unknown	TFAP2E (NM_178548) - CSF3R (NM_000760) rearrangement: c.1047-1011:TFAP2E_c.1291:CSF3Rinv Note: The TFAP2E - CSF3R rearrangement is an inversion that results in a fusion of TFAP2E exons 1 - 6 to CSF3R exons 11 - 17. One of the breakpoints is within CSF3R exon 11. Functional significance is undetermined.
RAD54L	0	MSKCC-DMP	P-0043953-T01-IM6	RAD54L-intragenic	yes	unknown		unknown	RAD54L (NM_001142548) rearrangement: c.766+40_c.891+2361inv Note: The RAD54L rearrangement is an intragenic inversion of exon 9. Functional significance is undetermined.
WHSC1	0	MSKCC-DMP	P-0043953-T01-IM6	WHSC1-intragenic	yes	unknown		unknown	WHSC1 (NM_001042424) rearrangement: c.4058:WHSC1_chr4:g.4885490inv Note: The WHSC1 rearrangement is an inversion of exon 22. One of the breakpoints is within exon 22. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044041-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(3;17)(p21.1;q11.2)(chr3:g.54146314::chr17:g.29548812) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0044041-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.2381_c.3646-1833del Note: The ALK rearrangement is an intragenic deletion of exons 14 - 23. One of the breakpoints is within exon 14. The rearrangement includes a part of the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
XPO1	0	MSKCC-DMP	P-0044041-T01-IM6	XPO1-intragenic	yes	unknown		unknown	XPO1 (NM_003400) rearrangement: c.270:XPO1_chr2:g.61780951del Note: The XPO1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0044210-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.164:B2M_chr15:g.45009747del Note: The B2M rearrangement is a deletion of exons 2 - 3. One of the breakpoints is within exon 2.
TP53	0	MSKCC-DMP	P-0044296-T01-IM6	TP53-intragenic	yes	unknown		in frame	TP53 (NM_000546) rearrangement: c.782+137_c.1101-252del Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 10.
SMARCB1	0	MSKCC-DMP	P-0044301-T01-IM6	SMARCB1-intragenic	yes	unknown		unknown	SMARCB1 (NM_003073) rearrangement: c.359_c.362+3471del Note: The SMARCB1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.
INPP4A	0	MSKCC-DMP	P-0044346-T01-IM6	INPP4A-intragenic	yes	unknown		unknown	INPP4A (NM_001134224) rearrangement: t(2;3)(q11.2;q26.31)(chr2:g.99182038::chr3:g.174056638) Note: The INPP4A rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.
ARID1A	0	MSKCC-DMP	P-0044391-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.6522:ARID1A_chr1:g.27109427del Note: The ARID1A rearrangement is a deletion of exon 20. One of the breakpoints is within exon 20.
ZFHX3	0	MSKCC-DMP	P-0044391-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.3217-489_c.3409del Note: The ZFHX3 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.
NOTCH1	0	MSKCC-DMP	P-0044393-T01-IM6	PNPLA7-NOTCH1 fusion	yes	unknown		out of frame	NOTCH1 (NM_017617) - PNPLA7 (NM_001098537) rearrangement: c.5018+48:NOTCH1_c.748-7350:PNPLA7dup Note: The NOTCH1 - PNPLA7 rearrangement is a duplication that results in a fusion of NOTCH1 exons 1 - 26 to PNPLA7 exons 9 - 35. Functional significance is undetermined.
PNPLA7	0	MSKCC-DMP	P-0044393-T01-IM6	PNPLA7-NOTCH1 fusion	yes	unknown		out of frame	NOTCH1 (NM_017617) - PNPLA7 (NM_001098537) rearrangement: c.5018+48:NOTCH1_c.748-7350:PNPLA7dup Note: The NOTCH1 - PNPLA7 rearrangement is a duplication that results in a fusion of NOTCH1 exons 1 - 26 to PNPLA7 exons 9 - 35. Functional significance is undetermined.
CBL	0	MSKCC-DMP	P-0044499-T01-IM6	CBL-intragenic	yes	unknown		in frame	CBL (NM_005188) rearrangement: c.1096-156_c.1431+1123del Note: The CBL rearrangement is an intragenic deletion of exons 8 - 9.
POLE	0	MSKCC-DMP	P-0044499-T01-IM6	POLE-intragenic	yes	unknown		unknown	POLE (NM_006231) rearrangement: c.2314:POLE_chr12:g.131958142del Note: The POLE rearrangement is a deletion of exons 20 - 49. One of the breakpoints is within exon 20.
TP53BP1	0	MSKCC-DMP	P-0044499-T01-IM6	TP53BP1-intragenic	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: t(14;15)(q21.1;q15.3)(chr14:g.38880416::chr15:g.43720289) Note: The TP53BP1 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
RNF43	0	MSKCC-DMP	P-0044499-T01-IM6	RNF43-intragenic	yes	unknown		unknown	RNF43 (NM_017763) rearrangement: c.376-862_c.673del Note: The RNF43 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 6.
DNMT3B	0	MSKCC-DMP	P-0044499-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: t(12;20)(q24.33;q11.21)(chr12:g.130228060::chr20:g.31383141) Note: The DNMT3B rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0044607-T01-IM6	NAV3-ATR fusion	yes	unknown		unknown	ATR (NM_001184) - NAV3 (NM_014903) rearrangement: t(3;12)(q23;q21.2)(chr3:g.142281699::chr12:g.78469330) Note: The ATR - NAV3 rearrangement is a translocation that results in a fusion of ATR exons 1 - 4 to NAV3 exons 13 - 39. One of the breakpoints is within ATR exon 4. Functional significance is undetermined.
NAV3	0	MSKCC-DMP	P-0044607-T01-IM6	NAV3-ATR fusion	yes	unknown		unknown	ATR (NM_001184) - NAV3 (NM_014903) rearrangement: t(3;12)(q23;q21.2)(chr3:g.142281699::chr12:g.78469330) Note: The ATR - NAV3 rearrangement is a translocation that results in a fusion of ATR exons 1 - 4 to NAV3 exons 13 - 39. One of the breakpoints is within ATR exon 4. Functional significance is undetermined.
NTRK2	0	MSKCC-DMP	P-0044607-T01-IM6	PRUNE2-NTRK2 fusion	yes	unknown		out of frame	NTRK2 (NM_006180) - PRUNE2 (NM_015225) rearrangement: c.1445-2036:NTRK2_c.756+13664:PRUNE2inv Note: The NTRK2 - PRUNE2 rearrangement is an inversion that results in a fusion of NTRK2 exons 1 - 15 to PRUNE2 exons 7 - 19. The fusion does not include the kinase domain of NTRK2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PRUNE2	0	MSKCC-DMP	P-0044607-T01-IM6	PRUNE2-NTRK2 fusion	yes	unknown		out of frame	NTRK2 (NM_006180) - PRUNE2 (NM_015225) rearrangement: c.1445-2036:NTRK2_c.756+13664:PRUNE2inv Note: The NTRK2 - PRUNE2 rearrangement is an inversion that results in a fusion of NTRK2 exons 1 - 15 to PRUNE2 exons 7 - 19. The fusion does not include the kinase domain of NTRK2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TMPRSS2	0	MSKCC-DMP	P-0044811-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4610:TMPRSS2_c.236+920:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 3 - 10.
ERG	0	MSKCC-DMP	P-0044811-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4610:TMPRSS2_c.236+920:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 3 - 10.
PPAP2A	0	MSKCC-DMP	P-0044819-T01-IM6	BRAF-PPAP2A fusion	yes	unknown		out of frame	PPAP2A (NM_176895) - BRAF (NM_004333) fusion: t(5;7)(q11.2;q34)(chr5:g.54789192::chr7:g.140482123) Note: The PPAP2A - BRAF fusion involves PPAP2A exon 1 and BRAF exons 11 - 18. The fusion includes the kinase domain of BRAF.
BRAF	0	MSKCC-DMP	P-0044819-T01-IM6	BRAF-PPAP2A fusion	yes	unknown		out of frame	PPAP2A (NM_176895) - BRAF (NM_004333) fusion: t(5;7)(q11.2;q34)(chr5:g.54789192::chr7:g.140482123) Note: The PPAP2A - BRAF fusion involves PPAP2A exon 1 and BRAF exons 11 - 18. The fusion includes the kinase domain of BRAF.
AIG1	0	MSKCC-DMP	P-0044968-T01-IM6	TNFAIP3-AIG1 fusion	yes	unknown		unknown	AIG1 (NM_016108) - TNFAIP3 (NM_006290) rearrangement: c.516-18946:AIG1_c.994:TNFAIP3dup Note: The AIG1 - TNFAIP3 rearrangement is a duplication that results in a fusion of AIG1 exons 1 - 4 to TNFAIP3 exons 7 - 9. One of the breakpoints is within TNFAIP3 exon 7. Functional significance is undetermined.
TNFAIP3	0	MSKCC-DMP	P-0044968-T01-IM6	TNFAIP3-AIG1 fusion	yes	unknown		unknown	AIG1 (NM_016108) - TNFAIP3 (NM_006290) rearrangement: c.516-18946:AIG1_c.994:TNFAIP3dup Note: The AIG1 - TNFAIP3 rearrangement is a duplication that results in a fusion of AIG1 exons 1 - 4 to TNFAIP3 exons 7 - 9. One of the breakpoints is within TNFAIP3 exon 7. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0047316-T01-IM6	ERG-intragenic	yes	unknown		unknown	ERG (NM_182918) rearrangement: t(17;21)(p13.1;q22.2)(chr17:g.7965049::chr21:g.39870294) Note: The ERG rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.
STRN	0	MSKCC-DMP	P-0033066-T01-IM6	ALK-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STRN-ALK fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180129 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0033066-T01-IM6	ALK-STRN fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: STRN-ALK fusion. Note: The rearrangement is an in-frame fusion between genes STRN Exon3 (NM_003162) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV2-CLIN-20180129 Macro-dissection: Performed
PTPRK	0	MSKCC-DMP	P-0034063-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0034063-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20180146 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0034897-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20180160 Macro-dissection: Unknown
ERG	0	MSKCC-DMP	P-0034897-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_005656) and ERG Exon4 (NM_004449). Lab Notes Run Number: ArcherV3-CLIN-20180160 Macro-dissection: Unknown
PTPRK	0	MSKCC-DMP	P-0037968-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon13 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190025 Macro-dissection: Unknown
RSPO3	0	MSKCC-DMP	P-0037968-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon13 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: ArcherV3-CLIN-20190025 Macro-dissection: Unknown
SND1	0	MSKCC-DMP	P-0042036-T01-IM6	BRAF-SND1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SND1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes SND1 Exon10 (NM_014390) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190096 Macro-dissection: Performed
BRAF	0	MSKCC-DMP	P-0042036-T01-IM6	BRAF-SND1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SND1-BRAF fusion. Note: The rearrangement is an in-frame fusion between genes SND1 Exon10 (NM_014390) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190096 Macro-dissection: Performed
GSK3B	0	MSKCC-DMP	P-0042785-T01-IM6	FGFR1-GSK3B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GSK3B-FGFR1 fusion. Note: The rearrangement is a fusion between genes GSK3B Exon1 (NM_002093) and FGFR1 Exon2 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190109 Macro-dissection: Perfmed or
FGFR1	0	MSKCC-DMP	P-0042785-T01-IM6	FGFR1-GSK3B fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GSK3B-FGFR1 fusion. Note: The rearrangement is a fusion between genes GSK3B Exon1 (NM_002093) and FGFR1 Exon2 (NM_015850). Lab Notes Run Number: Archerv3-CLIN-20190109 Macro-dissection: Perfmed or
PPAP2A	0	MSKCC-DMP	P-0044819-T01-IM6	BRAF-PPAP2A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: PPAP2A-BRAF fusion. Note: The rearrangement is an out of frame fusion between genes PPAP2A Exon1 (NM_176895) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190146 Macro-dissection: Unknown
BRAF	0	MSKCC-DMP	P-0044819-T01-IM6	BRAF-PPAP2A fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: PPAP2A-BRAF fusion. Note: The rearrangement is an out of frame fusion between genes PPAP2A Exon1 (NM_176895) and BRAF Exon11 (NM_004333). Lab Notes Run Number: Archerv3-CLIN-20190146 Macro-dissection: Unknown
ATR	0	MSKCC-DMP	P-0005459-T02-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) rearrangement: t(3;13)(q23;q12.11)(chr3:g.142279020::chr13:g.20695257) Note: The ATR rearrangement is a translocation involving exon 6. Its functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0005459-T02-IM6	DSCAM-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.127-1405:TMPRSS2_c.3562+3890:DSCAMdel Note: The TMPRSS2 - DSCAM rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with DSCAM exons 20-33. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in additional TMPRSS2 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
DSCAM	0	MSKCC-DMP	P-0005459-T02-IM6	DSCAM-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.127-1405:TMPRSS2_c.3562+3890:DSCAMdel Note: The TMPRSS2 - DSCAM rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1-2 with DSCAM exons 20-33. Its functional significance is undetermined. Multiple rearrangements involving TMPRSS2 were detected in this sample and a more complex rearrangement resulting in additional TMPRSS2 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
PGR	0	MSKCC-DMP	P-0006847-T01-IM5	PGR-intragenic	yes	unknown		unknown	PGR (NM_000926) Rearrangement :  c.469_chr11:g.58736058inv Note: The PGR (NM_000926) rearrangement results in the inversion of exons 1 to 8 of PGR. One of the breakpoints is within exon1.Its functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0009524-T01-IM5	HNRNPUL1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.1369:AXL_c.1000-5031:HNRNPUL1del Note: The AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement is a deletion which results in the fusion of AXL exons 1-11 with HNRNPUL1 exons 8-15. One of the breakpoints is within exon 11 of AXL. The functional significance is undetermined.
HNRNPUL1	0	MSKCC-DMP	P-0009524-T01-IM5	HNRNPUL1-AXL fusion	yes	unknown		unknown	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.1369:AXL_c.1000-5031:HNRNPUL1del Note: The AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement is a deletion which results in the fusion of AXL exons 1-11 with HNRNPUL1 exons 8-15. One of the breakpoints is within exon 11 of AXL. The functional significance is undetermined.
PTPRD	0	MSKCC-DMP	P-0009524-T01-IM5	PTPRD-intragenic	yes	unknown		out of frame	PTPRD (NM_002839) rearrangement: c.65-36596_c.210+2del Note: The PTPRD (NM_002839) rearrangement is an intragenic deletion of exon 13. The functional significance is undetermined.
INPP4B	0	MSKCC-DMP	P-0009791-T01-IM5	INPP4B-intragenic	yes	unknown		unknown	INPP4B (NM_001101669)  Rearrangement: chr4:g.133235766_ c.881:INPP4Binv Note: The INPP4B (NM_001101669)  Rearrangement results in the inversion of exons 14-26 of INPP4B. One of the breakpoints is within exon14 .Its functional significance is undetermined.
PPP6C	0	MSKCC-DMP	P-0009791-T01-IM5	PPP6C-intragenic	yes	unknown		unknown	PPP6C (NM_002721) Rearrangement :  c.460-26:PPP6C_chr9:g.133439773inv Note: The PPP6C (NM_002721) Rearrangement results in the inversion of exons1-5 of PPP6C.Its functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0011025-T01-IM5	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused with ROS1 exons 34-43) : t(5;6)(q32;q22.1)(chr5:g.149783755::chr6:g.117645889) Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0011025-T01-IM5	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused with ROS1 exons 34-43) : t(5;6)(q32;q22.1)(chr5:g.149783755::chr6:g.117645889) Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
DOT1L	0	MSKCC-DMP	P-0012114-T03-IM6	DOT1L-intragenic	yes	unknown		in frame	DOT1L (NM_032482) Rearrangement: c.1006-245_c.3390+36dup Note: The DOT1L rearrangement is an intragenic duplication of exons 13-24. The functional significance us undetermined.
MET	0	MSKCC-DMP	P-0012114-T03-IM6	MYH15-MET fusion	yes	unknown		unknown	MET (NM_000245) - MYH15 (NM_014981) rearrangement: t(3;7)(q13.3;q31.2)(chr3:g.108193597::chr7:g.116412012) Note: The MET - MYH15 rearrangement is a translocation that results in a fusion of MET exons 1-14 to MYH15 exons 14-42.
MYH15	0	MSKCC-DMP	P-0012114-T03-IM6	MYH15-MET fusion	yes	unknown		unknown	MET (NM_000245) - MYH15 (NM_014981) rearrangement: t(3;7)(q13.3;q31.2)(chr3:g.108193597::chr7:g.116412012) Note: The MET - MYH15 rearrangement is a translocation that results in a fusion of MET exons 1-14 to MYH15 exons 14-42.
CD47	0	MSKCC-DMP	P-0012114-T03-IM6	MET-CD47 fusion	yes	unknown		in frame	CD47 (NM_001777) - MET (NM_000245) rearrangement: t(3;7)(q13.12;q31.2)(chr3:g.107772171::chr7:g.116412066) Note: The CD47 - MET rearrangement is a translocation that results in an in-frame fusion of CD47 exons 1-7 to MET exons 15-21. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0012114-T03-IM6	MET-CD47 fusion	yes	unknown		in frame	CD47 (NM_001777) - MET (NM_000245) rearrangement: t(3;7)(q13.12;q31.2)(chr3:g.107772171::chr7:g.116412066) Note: The CD47 - MET rearrangement is a translocation that results in an in-frame fusion of CD47 exons 1-7 to MET exons 15-21. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0015437-T01-IM6	HSPA12A-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - HSPA12A (NM_025015) rearrangement: c.2301+621:FGFR2_c.663+3346:HSPA12Adel Note: The FGFR2 - HSPA12A rearrangement is a deletion which results in the fusion of FGFR2 exon 17 - HSPA12A exon 7. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
HSPA12A	0	MSKCC-DMP	P-0015437-T01-IM6	HSPA12A-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - HSPA12A (NM_025015) rearrangement: c.2301+621:FGFR2_c.663+3346:HSPA12Adel Note: The FGFR2 - HSPA12A rearrangement is a deletion which results in the fusion of FGFR2 exon 17 - HSPA12A exon 7. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
PBRM1	0	MSKCC-DMP	P-0019995-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) Rearrangement :  c.385-2621_c.2522del Note: The PBRM1 Rearrangement results in the deletion of exon 5-17. One of the breakpoints is within exon17. Its functional significance is undetermined.
RFWD2	0	MSKCC-DMP	P-0020970-T01-IM6	RFWD2-intragenic	yes	unknown		unknown	RFWD2 (NM_022457) rearrangement: c.920_c.642+31del Note: The RFWD2 rearrangement results in the deletion of exons 5-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
GOPC	0	MSKCC-DMP	P-0021147-T01-IM6	ROS1-GOPC fusion	yes	unknown		in frame	GOPC (NM_020399) - ROS1 (NM_002944) fusion (GOPC exons 1-4 fused with ROS1 exons 36-43) :c.651-735:GOPC_c.5778-508:ROS1del Note: The GOPC - ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0021147-T01-IM6	ROS1-GOPC fusion	yes	unknown		in frame	GOPC (NM_020399) - ROS1 (NM_002944) fusion (GOPC exons 1-4 fused with ROS1 exons 36-43) :c.651-735:GOPC_c.5778-508:ROS1del Note: The GOPC - ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.
TMPRSS2	0	MSKCC-DMP	P-0021782-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon4) : c.56-2752:TMPRSS2_c.39+30375:ERGdel
ERG	0	MSKCC-DMP	P-0021782-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon4) : c.56-2752:TMPRSS2_c.39+30375:ERGdel
FGFR2	0	MSKCC-DMP	P-0023364-T03-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.2301+1625:FGFR2_c.34-5469:TACC2dup Note: The FGFR2 - TACC2 rearrangement is a duplication of FGFR2 exons 1 - 17 and TACC2 exons 1 - 2. The rearrangement includes the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
TACC2	0	MSKCC-DMP	P-0023364-T03-IM6	TACC2-FGFR2 fusion	yes	unknown		unknown	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.2301+1625:FGFR2_c.34-5469:TACC2dup Note: The FGFR2 - TACC2 rearrangement is a duplication of FGFR2 exons 1 - 17 and TACC2 exons 1 - 2. The rearrangement includes the kinase domain of FGFR2. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving FGFR2 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
FOXA1	0	MSKCC-DMP	P-0027049-T04-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.1148_c.-2851del Note: The FOXA1 rearrangement results in the deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.
NOTCH2	0	MSKCC-DMP	P-0027662-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;6)(p12;q21)(chr1:g.120462040::chr6:g.109700010) Note: The NOTCH2 rearrangement is a translocation with a breakpoint in exon 31. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0028283-T03-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: c.1701+657_c.2937del Note: The MET rearrangement is an intragenic deletion of exons 6 - 14. One of the breakpoints is within exon 14. The rearrangement does not include the kinase domain of MET. Multiple MET rearrangements were detected in this sample and a more complex rearrangement is possible. A novel isoform of MET lacking exons 6-14 was previously confirmed to be present in the patient's RNA (M18-7670), and c-MET IHC was strongly positive in approximately 75% of tumor cells (see addendum, C18-6329).
ARID1A	0	MSKCC-DMP	P-0031772-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.3887:ARID1A_chr1:g.2350666inv Note: The ARID1A rearrangement is an inversion of exons 16. One of the breakpoints is within exon 16.
MPL	0	MSKCC-DMP	P-0032093-T01-IM6	MPL-intragenic	yes	unknown		unknown	MPL (NM_005373) rearrangement: c.80-39:MPL_chr1:g.44094042inv Note: The MPL rearrangement is an inversion of exons 2-12. Its functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0032093-T01-IM6	CREBBP-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) - CREBBP (NM_004380) rearrangement: c.879-4862:AXIN1_c.2161:CREBBPdup Note: The AXIN1- CREBBP rearrangement is a duplication which results in the fusion of AXIN1 exons 1-2 with CREBBP exons 12-31. One of the breakpoints is within CREBBP exon 12. Its functional significance is undetermined.
CREBBP	0	MSKCC-DMP	P-0032093-T01-IM6	CREBBP-AXIN1 fusion	yes	unknown		unknown	AXIN1 (NM_003502) - CREBBP (NM_004380) rearrangement: c.879-4862:AXIN1_c.2161:CREBBPdup Note: The AXIN1- CREBBP rearrangement is a duplication which results in the fusion of AXIN1 exons 1-2 with CREBBP exons 12-31. One of the breakpoints is within CREBBP exon 12. Its functional significance is undetermined.
SF3B1	0	MSKCC-DMP	P-0032956-T01-IM6	SF3B1-intragenic	yes	unknown		unknown	SF3B1 (NM_012433) Rearrangement: c.495+9:SF3B1_chr2:g.42597820inv Note: The SF3B1 rearrangement results in the inversion of SF3B1 exons 6 - 25. The functional significance is undetermined.
B2M	0	MSKCC-DMP	P-0035891-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: t(5;15)(q12.1;q21.1)(chr5:g.61772023::chr15:g.45007799) Note: The B2M rearrangement is a translocation with a breakpoint in exon 2.
MST1	0	MSKCC-DMP	P-0035891-T01-IM6	MST1-intragenic	yes	unknown		unknown	MST1 (NM_020998) rearrangement: c.1236:MST1_chr3:g.49629637dup Note: The MST1 rearrangement results in the duplication of exons 10-18. One of the breakpoints is within MST1 exon 10. The functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0035891-T01-IM6	MAP3K1-intragenic	yes	unknown		out of frame	MAP3K1 (NM_005921) rearrangement: c.482+17975_c.1966-44del Note: The MAP3K1 rearrangement results in the deletion of exons 2-10. The functional significance is undetermined.
FOXA1	0	MSKCC-DMP	P-0036235-T01-IM6	FOXA1-intragenic	yes	unknown		unknown	FOXA1 (NM_004496) rearrangement: c.-34:FOXA1_chr14:g.37143996inv Note: The FOXA1 rearrangement is an inversion with breakpoint in region upstream of FOXA1. The functional significance is undetermined.
KLK2	0	MSKCC-DMP	P-0036235-T01-IM6	ETV1-KLK2 fusion	yes	unknown		unknown	KLK2 (NM_005551) - ETV1(NM_001163147) rearrangement: t(7;19)(p21.2;q13.33)(chr7:g.13975427::chr19:g.51377605) Note: The KLK2 - ETV1 fusion is a translocation results in the fusion of KLK2 exon 1 with ETV1 exons 7-12. Its functional significance is undetermined.
ETV1	0	MSKCC-DMP	P-0036235-T01-IM6	ETV1-KLK2 fusion	yes	unknown		unknown	KLK2 (NM_005551) - ETV1(NM_001163147) rearrangement: t(7;19)(p21.2;q13.33)(chr7:g.13975427::chr19:g.51377605) Note: The KLK2 - ETV1 fusion is a translocation results in the fusion of KLK2 exon 1 with ETV1 exons 7-12. Its functional significance is undetermined.
SYT16	0	MSKCC-DMP	P-0037029-T01-IM6	AKT1-SYT16 fusion	yes	unknown		unknown	SYT16 (NM_031914) - AKT1 (NM_001014431) rearrangement: c.1625-4528:SYT16_c.169:AKT1inv Note: The SYT16 - AKT1 rearrangement is an inversion that results in the fusion of SYT16 exons 1-5 with AKT1 exons 3-14 and includes the kinase domain of AKT1. One of the breakpoints is within AKT1 exon 3. The functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0037029-T01-IM6	AKT1-SYT16 fusion	yes	unknown		unknown	SYT16 (NM_031914) - AKT1 (NM_001014431) rearrangement: c.1625-4528:SYT16_c.169:AKT1inv Note: The SYT16 - AKT1 rearrangement is an inversion that results in the fusion of SYT16 exons 1-5 with AKT1 exons 3-14 and includes the kinase domain of AKT1. One of the breakpoints is within AKT1 exon 3. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037029-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1715:TMPRSS2_c.19-11583:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
ERG	0	MSKCC-DMP	P-0037029-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1715:TMPRSS2_c.19-11583:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.
MDC1	0	MSKCC-DMP	P-0037098-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.5738:MDC1_chr6:g.54282565dup Note: The MDC1 rearrangement results in the duplication of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.
IDH1	0	MSKCC-DMP	P-0037132-T01-IM6	IDH1-intragenic	yes	unknown		unknown	IDH1 (NM_005896) rearrangement: c.414+737_c.768del Note: The IDH1 rearrangement results in the deletion of exons 5-7. One of the breakpoints is within exon 7. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037132-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.56-2141_c.127-1737inv Note: The TMPRSS2 rearrangement results in the inversion of exon 2. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037423-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.237-9913:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 3-10.
ERG	0	MSKCC-DMP	P-0037423-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.237-9913:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 3-10.
BICC1	0	MSKCC-DMP	P-0037617-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	BICC1 (NM_001080512) - FGFR2 (NM_000141) rearrangement: c.238-34060:BICC1_c.2302-1767:FGFR2inv Note: The BICC1 - FGFR2 rearrangement is translocation that results in a fusion of BICC1 exons 1-2 to FGFR2 exon 18.
FGFR2	0	MSKCC-DMP	P-0037617-T01-IM6	FGFR2-BICC1 fusion	yes	unknown		in frame	BICC1 (NM_001080512) - FGFR2 (NM_000141) rearrangement: c.238-34060:BICC1_c.2302-1767:FGFR2inv Note: The BICC1 - FGFR2 rearrangement is translocation that results in a fusion of BICC1 exons 1-2 to FGFR2 exon 18.
SOX2	0	MSKCC-DMP	P-0037666-T01-IM6	PIK3C2G-SOX2 fusion	yes	unknown		unknown	SOX2 (NM_003106) -PIK3C2G (NM_004570) rearrangement: t(3;12)(q26.33;p12.3)(chr3:g.181430991::chr12:g.18665844) Note: The SOX2 - PIK3C2G rearrangement is a translocation that results in the fusion of SOX2 exon 1 with PIK3C2G exons 24-32. One of the breakpoints is within exon 1 of SOX2. The functional significance is undetermined.
PIK3C2G	0	MSKCC-DMP	P-0037666-T01-IM6	PIK3C2G-SOX2 fusion	yes	unknown		unknown	SOX2 (NM_003106) -PIK3C2G (NM_004570) rearrangement: t(3;12)(q26.33;p12.3)(chr3:g.181430991::chr12:g.18665844) Note: The SOX2 - PIK3C2G rearrangement is a translocation that results in the fusion of SOX2 exon 1 with PIK3C2G exons 24-32. One of the breakpoints is within exon 1 of SOX2. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0037668-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2742:EML4_c.3172+696:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-12 with ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0037668-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2742:EML4_c.3172+696:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1-12 with ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
EGFR	0	MSKCC-DMP	P-0037668-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.2469+67:EGFR_chr7:g.84278082del Note: The EGFR rearrangement results in the deletion of exons 21-28. The functional significance is undetermined.
FAT1	0	MSKCC-DMP	P-0037682-T01-IM6	PCGF3-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) - PCGF3 (NM_006315) Rearrangement : c.12441:FAT1_c.600+1304:PCGF3inv Note: The FAT1-PCGF3 Rearrangement results in the fusion of exons 1-25 of FAT1 with exons10-11 of PCGF3. The breakpoint in FAT1 is within exon25. Its functional significance is undetermined.
PCGF3	0	MSKCC-DMP	P-0037682-T01-IM6	PCGF3-FAT1 fusion	yes	unknown		unknown	FAT1 (NM_005245) - PCGF3 (NM_006315) Rearrangement : c.12441:FAT1_c.600+1304:PCGF3inv Note: The FAT1-PCGF3 Rearrangement results in the fusion of exons 1-25 of FAT1 with exons10-11 of PCGF3. The breakpoint in FAT1 is within exon25. Its functional significance is undetermined.
IDH2	0	MSKCC-DMP	P-0037698-T01-IM6	IDH2-intragenic	yes	unknown		unknown	IDH2 (NM_002168) rearrangement: c.1012:IDH2_chr15:g.90523585del Note: The IDH2 rearrangement is a deletion of exons 8-11. One of the breakpoints is within exon 8. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037701-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+524:TMPRSS2_c.237-2747:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 3-10.
ERG	0	MSKCC-DMP	P-0037701-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+524:TMPRSS2_c.237-2747:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 3-10.
ERC1	0	MSKCC-DMP	P-0038256-T01-IM6	RET-ERC1 fusion	yes	unknown		unknown	ERC1 (NM_178040) - RET (NM_020975) Rearrangement : t(10;12)(q11.1; p13.32)(chr10:g.43609964::chr12:g.1264106) Note: The ERC1-RET Rearrangement results in the fusion of exons 1-7 of ERC1 with exons11-20 of RET.The breakpoint in RET is within exon11. It includes the protein kinase domain of RET. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
RET	0	MSKCC-DMP	P-0038256-T01-IM6	RET-ERC1 fusion	yes	unknown		unknown	ERC1 (NM_178040) - RET (NM_020975) Rearrangement : t(10;12)(q11.1; p13.32)(chr10:g.43609964::chr12:g.1264106) Note: The ERC1-RET Rearrangement results in the fusion of exons 1-7 of ERC1 with exons11-20 of RET.The breakpoint in RET is within exon11. It includes the protein kinase domain of RET. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Assay will be performed if additional material is available and results will be reported under a separate accession number.
SPRED1	0	MSKCC-DMP	P-0038720-T01-IM6	SPRED1-intragenic	yes	unknown		unknown	SPRED1 (NM_152594) rearrangement: c.1328_c.*805 Note: The SPRED1 rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7.
BAP1	0	MSKCC-DMP	P-0038720-T01-IM6	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.931+135_c.*24del Note: The BAP1 rearrangement is an intragenic deletion of BAP1 exons 11-17.
BAP1	0	MSKCC-DMP	P-0038793-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) -  PHF7 (NM_016483) rearrangement: c.-22:BAP1_c.186+1887:PHF7del Note: The BAP1 - PHF7 rearrangement is a deletion with a breakpoint within the 5'UTR of BAP1. The functional significance is undetermined.
PHF7	0	MSKCC-DMP	P-0038793-T01-IM6	PHF7-BAP1 fusion	yes	unknown		unknown	BAP1 (NM_004656) -  PHF7 (NM_016483) rearrangement: c.-22:BAP1_c.186+1887:PHF7del Note: The BAP1 - PHF7 rearrangement is a deletion with a breakpoint within the 5'UTR of BAP1. The functional significance is undetermined.
BCOR	0	MSKCC-DMP	P-0038803-T01-IM6	BCOR-intragenic	yes	unknown		unknown	BCOR (NM_001123385) rearrangement: chrX:g.14000773_c.3484dup Note: The BCOR rearrangement is a duplication that includes BCOR exons 7-15. One of the breakpoints is within exon 7.
NOTCH4	0	MSKCC-DMP	P-0039448-T01-IM6	NOTCH4-intragenic	yes	unknown		unknown	NOTCH4 (NM_004557) rearrangement: c.1802:NOTCH4_chr6:g.32202804inv Note: The NOTCH4 rearrangement is an inversion of exons 1 - 11. One of the breakpoints is within exon 11. Functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0039829-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.478+59:ELF3_chr1:g.201984748del Note: The ELF3 rearrangement is a deletion of exons 5 - 9.
ELF3	0	MSKCC-DMP	P-0039901-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) rearrangement: c.681:ELF3_chr1:g.201990452del Note: The ELF3 rearrangement is a deletion of exons 6 - 9. One of the breakpoints is within exon 6.
GATA3	0	MSKCC-DMP	P-0040007-T01-IM6	GATA3-intragenic	yes	unknown		unknown	GATA3 (NM_002051) rearrangement: t(6;10)(q22.31;p14)(chr6:g.121274074::chr10:g.8106070) Note: The GATA3 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
ALK	0	MSKCC-DMP	P-0040032-T01-IM6	ALK-intragenic	yes	unknown		in frame	ALK (NM_004304) rearrangement: c.3067+637_c.3173-299del Note: The ALK rearrangement is an intragenic deletion of exon 19. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0040032-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.388:CDKN2A_chr9:g.21981057 Note: The CDKN2A rearrangement is a deletion of CDKN2A exons 1 - 2. One of the breakpoints is within exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CALR	0	MSKCC-DMP	P-0040094-T01-IM6	CALR-intragenic	yes	unknown		unknown	CALR (NM_004343) rearrangement: t(1;19)(p34.3;p13.2)(chr1:g.36624367::chr19:g.13050882) Note: The CALR rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0040121-T01-IM6	AGO2-intragenic	yes	unknown		unknown	AGO2 (NM_012154) rearrangement: c.501_c.1269+1124del Note: The AGO2 rearrangement is an intragenic deletion of exons 4 - 10. One of the breakpoints is within exon 4. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0040248-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.1879_c.1881-1del Note: The EGFR rearrangement is an intragenic deletion of exons 15 - 16. The breakpoints are within exon 15 and exon 16. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined.
PMAIP1	0	MSKCC-DMP	P-0040444-T01-IM6	PMAIP1-intragenic	yes	unknown		unknown	PMAIP1 (NM_021127) rearrangement: c.55_c.59-3del Note: The PMAIP1 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1.
TMPRSS2	0	MSKCC-DMP	P-0040509-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4323:TMPRSS2_c.39+6430:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040509-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4323:TMPRSS2_c.39+6430:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
PTPRS	0	MSKCC-DMP	P-0040518-T01-IM6	PTPRS-intragenic	yes	unknown		unknown	PTPRS (NM_002850) rearrangement: t(12;19)(q24.21;p13.3)(chr12:g.114898875::chr19:g.5222209) Note: The PTPRS rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.
FLT3	0	MSKCC-DMP	P-0040545-T01-IM6	PDX1-FLT3 fusion	yes	unknown		out of frame	FLT3 (NM_004119) - PDX1 (NM_000209) rearrangement: c.2418+171:FLT3_c.407-1761:PDX1inv Note: The FLT3 - PDX1 rearrangement is an inversion that results in a fusion of FLT3 exons 1 - 19 to PDX1 exon 2. The fusion includes a part of the kinase domain of FLT3. Functional significance is undetermined.
PDX1	0	MSKCC-DMP	P-0040545-T01-IM6	PDX1-FLT3 fusion	yes	unknown		out of frame	FLT3 (NM_004119) - PDX1 (NM_000209) rearrangement: c.2418+171:FLT3_c.407-1761:PDX1inv Note: The FLT3 - PDX1 rearrangement is an inversion that results in a fusion of FLT3 exons 1 - 19 to PDX1 exon 2. The fusion includes a part of the kinase domain of FLT3. Functional significance is undetermined.
ERCC5	0	MSKCC-DMP	P-0040587-T01-IM6	ERCC5-intragenic	yes	unknown		unknown	ERCC5 (NM_000123) rearrangement: c.1234:ERCC5_chr13:g.103600469inv Note: The ERCC5 rearrangement is an inversion of exons 8 - 15. One of the breakpoints is within exon 8. Functional significance is undetermined.
E4F1	0	MSKCC-DMP	P-0040587-T01-IM6	TRAF7-E4F1 fusion	yes	unknown		unknown	E4F1 (NM_004424) - TRAF7 (NM_032271) rearrangement: c.310-104:E4F1_c.1292:TRAF7dup Note: The E4F1 - TRAF7 rearrangement is a duplication that results in a fusion of E4F1 exons 1 - 2 to TRAF7 exons 14 - 21. One of the breakpoints is within TRAF7 exon 14. Functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0040587-T01-IM6	TRAF7-E4F1 fusion	yes	unknown		unknown	E4F1 (NM_004424) - TRAF7 (NM_032271) rearrangement: c.310-104:E4F1_c.1292:TRAF7dup Note: The E4F1 - TRAF7 rearrangement is a duplication that results in a fusion of E4F1 exons 1 - 2 to TRAF7 exons 14 - 21. One of the breakpoints is within TRAF7 exon 14. Functional significance is undetermined.
TP53BP1	0	MSKCC-DMP	P-0040669-T01-IM6	TP53BP1-intragenic	yes	unknown		unknown	TP53BP1 (NM_001141980) rearrangement: c.3829-1967_c.4229inv Note: The TP53BP1 rearrangement is an intragenic inversion of exons 19 - 20. One of the breakpoints is within exon 20. Functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0040672-T01-IM6	ARID1B-intragenic	yes	unknown		unknown	ARID1B (NM_020732) rearrangement: c.3135+743:ARID1B_chr6:g.158764567inv Note: The ARID1B rearrangement is an inversion of exons 12 - 20. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0040749-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1065:TMPRSS2_c.39+63388:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0040749-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		in frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1065:TMPRSS2_c.39+63388:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 4 - 11. The fusion is predicted to be in frame. The structural variant involves the ERG non-canonical transcript (NM_004449).
CDK12	0	MSKCC-DMP	P-0040752-T01-IM6	C6orf203-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - C6orf203 (NM_016487) rearrangement: t(6;17)(q21;q12)(chr6:g.107368450::chr17:g.37687160) Note: The CDK12 - C6orf203 rearrangement is a translocation that results in a fusion of CDK12 exons 1 - 14 to C6orf203 exon 4. One of the breakpoints is within CDK12 exon 14. The fusion includes the kinase domain of CDK12. Functional significance is undetermined.
C6orf203	0	MSKCC-DMP	P-0040752-T01-IM6	C6orf203-CDK12 fusion	yes	unknown		unknown	CDK12 (NM_016507) - C6orf203 (NM_016487) rearrangement: t(6;17)(q21;q12)(chr6:g.107368450::chr17:g.37687160) Note: The CDK12 - C6orf203 rearrangement is a translocation that results in a fusion of CDK12 exons 1 - 14 to C6orf203 exon 4. One of the breakpoints is within CDK12 exon 14. The fusion includes the kinase domain of CDK12. Functional significance is undetermined.
PIK3R3	0	MSKCC-DMP	P-0040752-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: t(1;2)(p34.1;q35)(chr1:g.46532639::chr2:g.218631120) Note: The PIK3R3 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0040956-T01-IM6	KMT2D-intragenic	yes	unknown		out of frame	KMT2D (NM_003482) rearrangement: c.10232-879_c.13531-32del Note: The KMT2D rearrangement is an intragenic deletion of exons 35 - 39.
NOTCH1	0	MSKCC-DMP	P-0040956-T01-IM6	FH-NOTCH1 fusion	yes	unknown		out of frame	NOTCH1 (NM_017617) - FH (NM_000143) rearrangement: t(1;9)(q43;q34.3)(chr1:g.241672198::chr9:g.139417940) Note: The NOTCH1 - FH rearrangement is a translocation that results in a fusion of NOTCH1 exons 1 - 3 to FH exons 5 - 10. Functional significance is undetermined.
FH	0	MSKCC-DMP	P-0040956-T01-IM6	FH-NOTCH1 fusion	yes	unknown		out of frame	NOTCH1 (NM_017617) - FH (NM_000143) rearrangement: t(1;9)(q43;q34.3)(chr1:g.241672198::chr9:g.139417940) Note: The NOTCH1 - FH rearrangement is a translocation that results in a fusion of NOTCH1 exons 1 - 3 to FH exons 5 - 10. Functional significance is undetermined.
SYNRG	0	MSKCC-DMP	P-0040975-T01-IM6	ERBB2-SYNRG fusion	yes	unknown		out of frame	SYNRG (NM_007247) - ERBB2 (NM_004448) fusion: c.2608+2066:SYNRG_c.1899-372:ERBB2inv Note: The SYNRG - ERBB2 fusion involves SYNRG exons 1 - 13 and ERBB2 exons 16 - 27. The fusion includes the kinase domain of ERBB2. This event occurs in the background of other structural events involving ERBB2. Its functional significance is undetermined.
ERBB2	0	MSKCC-DMP	P-0040975-T01-IM6	ERBB2-SYNRG fusion	yes	unknown		out of frame	SYNRG (NM_007247) - ERBB2 (NM_004448) fusion: c.2608+2066:SYNRG_c.1899-372:ERBB2inv Note: The SYNRG - ERBB2 fusion involves SYNRG exons 1 - 13 and ERBB2 exons 16 - 27. The fusion includes the kinase domain of ERBB2. This event occurs in the background of other structural events involving ERBB2. Its functional significance is undetermined.
TRAF7	0	MSKCC-DMP	P-0041034-T01-IM6	TRAF7-intragenic	yes	unknown		unknown	TRAF7 (NM_032271) rearrangement: c.231+167:TRAF7_chr16:g.145124del Note: The TRAF7 rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041034-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1526:TMPRSS2_c.18+3778:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0041034-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1526:TMPRSS2_c.18+3778:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
CDKN2A	0	MSKCC-DMP	P-0041122-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.275:CDKN2A_chr9:g.22045861del Note: The CDKN2A rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
KRAS	0	MSKCC-DMP	P-0041144-T01-IM6	KRAS-intragenic	yes	unknown		unknown	KRAS (NM_033360) rearrangement: t(10;12)(p11.21;p12.1)(chr10:g.36334124::chr12:g.25378602) Note: The KRAS rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
PDGFRA	0	MSKCC-DMP	P-0041176-T01-IM6	ZNF536-PDGFRA fusion	yes	unknown		in frame	PDGFRA (NM_006206) - ZNF536 (NM_014717) rearrangement: t(4;19)(q12;q12)(chr4:g.55130148::chr19:g.30956498) Note: The PDGFRA - ZNF536 rearrangement is a translocation that results in a fusion of PDGFRA exons 1 - 4 to ZNF536 exons 3 - 5. The fusion is predicted to be in frame and does not include the kinase domain of PDGFRA. Functional significance is undetermined.
ZNF536	0	MSKCC-DMP	P-0041176-T01-IM6	ZNF536-PDGFRA fusion	yes	unknown		in frame	PDGFRA (NM_006206) - ZNF536 (NM_014717) rearrangement: t(4;19)(q12;q12)(chr4:g.55130148::chr19:g.30956498) Note: The PDGFRA - ZNF536 rearrangement is a translocation that results in a fusion of PDGFRA exons 1 - 4 to ZNF536 exons 3 - 5. The fusion is predicted to be in frame and does not include the kinase domain of PDGFRA. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0041196-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4101:TMPRSS2_c.40-60529:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0041196-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4101:TMPRSS2_c.40-60529:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
GATA2	0	MSKCC-DMP	P-0041196-T01-IM6	GATA2-intragenic	yes	unknown		unknown	GATA2 (NM_032638) rearrangement: c.6:GATA2_chr3:g.177218975del Note: The GATA2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
STK11	0	MSKCC-DMP	P-0041295-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.324:STK11_chr19:g.1111056del Note: The STK11 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. The rearrangement includes a part of the kinase domain of STK11.
SMARCA4	0	MSKCC-DMP	P-0041298-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.2766:SMARCA4_chr19:g.11086045del Note: The SMARCA4 rearrangement is a deletion of exons 1 - 19. One of the breakpoints is within exon 19.
MAP2K4	0	MSKCC-DMP	P-0041309-T01-IM6	MAP2K4-intragenic	yes	unknown		unknown	MAP2K4 (NM_003010) rearrangement: c.219-6453_c.220del Note: The MAP2K4 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3. The rearrangement does not include the kinase domain of MAP2K4.
TERT	0	MSKCC-DMP	P-0041327-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(1;5)(p21.2;p15.3)(chr1:g.99836853::chr5:g.1295277) Note: The TERT rearrangement is a translocation with a breakpoint in the TERT promoter region. The functional significance of this variant is undetermined.
NOTCH1	0	MSKCC-DMP	P-0041343-T01-IM6	NOTCH1-intragenic	yes	unknown		unknown	NOTCH1 (NM_017617) rearrangement: c.5257:NOTCH1_chr9:g.139239051del Note: The NOTCH1 rearrangement is a deletion of exons 28 - 34. One of the breakpoints is within exon 28.
TSC2	0	MSKCC-DMP	P-0041646-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: c.3611-8:TSC2_chr16:g.63844236inv Note: The TSC2 rearrangement is an inversion of exons 31 - 42. Functional significance is undetermined.
TMEM117	0	MSKCC-DMP	P-0041837-T01-IM6	RECQL-TMEM117 fusion	yes	unknown		out of frame	TMEM117 (NM_032256) - RECQL (NM_032941) rearrangement: c.411-22932:TMEM117_c.950-6:RECQLinv Note: The TMEM117 - RECQL rearrangement is an inversion that results in a fusion of TMEM117 exons 1 - 3 to RECQL exons 10 - 16. Functional significance is undetermined.
RECQL	0	MSKCC-DMP	P-0041837-T01-IM6	RECQL-TMEM117 fusion	yes	unknown		out of frame	TMEM117 (NM_032256) - RECQL (NM_032941) rearrangement: c.411-22932:TMEM117_c.950-6:RECQLinv Note: The TMEM117 - RECQL rearrangement is an inversion that results in a fusion of TMEM117 exons 1 - 3 to RECQL exons 10 - 16. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0042108-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: t(16;17)(q24.3;q25.1)(chr16:g.89350931::chr17:g.73285392) Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.
DNMT1	0	MSKCC-DMP	P-0042108-T01-IM6	DNMT1-intragenic	yes	unknown		out of frame	DNMT1 (NM_001379) rearrangement: c.2539-14_c.2847-607dup Note: The DNMT1 rearrangement is an intragenic duplication of exons 26 - 27. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0042156-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.4453-821_c.4642del Note: The EP300 rearrangement is an intragenic deletion of exons 28 - 29. One of the breakpoints is within exon 29.
CARM1	0	MSKCC-DMP	P-0042200-T01-IM6	CARM1-intragenic	yes	unknown		unknown	CARM1 (NM_199141) rearrangement: t(4;19)(q13.1;p13.2)(chr4:g.65841314::chr19:g.11018608) Note: The CARM1 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.
ACOXL	0	MSKCC-DMP	P-0042215-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		unknown	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1441-12512:ACOXL_c.233:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 16 to BCL2L11 exons 2 - 4. One of the breakpoints is within BCL2L11 exon 2.
BCL2L11	0	MSKCC-DMP	P-0042215-T01-IM6	BCL2L11-ACOXL fusion	yes	unknown		unknown	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1441-12512:ACOXL_c.233:BCL2L11del Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 16 to BCL2L11 exons 2 - 4. One of the breakpoints is within BCL2L11 exon 2.
BRCA2	0	MSKCC-DMP	P-0042238-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: c.9257-5239_c.9844dup Note: The BRCA2 rearrangement is an intragenic duplication of exons 25 - 27. One of the breakpoints is within exon 27.
CBFB	0	MSKCC-DMP	P-0042238-T01-IM6	CBFB-intragenic	yes	unknown		unknown	CBFB (NM_022845) rearrangement: c.399+89:CBFB_chr16:g.1667825inv Note: The CBFB rearrangement is an inversion of exons 1 - 4. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042276-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-2913:TMPRSS2_c.18+14783:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0042276-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-2913:TMPRSS2_c.18+14783:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0042373-T01-IM6	PBRM1-intragenic	yes	unknown		out of frame	PBRM1 (NM_018313) rearrangement: c.714+37_c.1087+3010del Note: The PBRM1 rearrangement is an intragenic deletion of exons 8 - 11.
ZFHX3	0	MSKCC-DMP	P-0042476-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.6087:ZFHX3_chr16:g.72733095inv Note: The ZFHX3 rearrangement is an inversion of exons 9 - 10. One of the breakpoints is within exon 9. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042663-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3014:TMPRSS2_c.18+20952:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0042663-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3014:TMPRSS2_c.18+20952:ERGdel Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
TMPRSS2	0	MSKCC-DMP	P-0042830-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3008:TMPRSS2_c.40-53644:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0042830-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		unknown	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3008:TMPRSS2_c.40-53644:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 4 - 11. The structural variant involves the ERG non-canonical transcript (NM_004449).
PSMA5	0	MSKCC-DMP	P-0042958-T01-IM6	SMYD3-PSMA5 fusion	yes	unknown		unknown	PSMA5 (NM_002790) - SMYD3 (NM_001167740) rearrangement: c.648+1286:PSMA5_c.904:SMYD3dup Note: The PSMA5 - SMYD3 rearrangement is a duplication that results in a fusion of PSMA5 exons 1 - 8 to SMYD3 exons 10 - 12. One of the breakpoints is within SMYD3 exon 10. Functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0042958-T01-IM6	SMYD3-PSMA5 fusion	yes	unknown		unknown	PSMA5 (NM_002790) - SMYD3 (NM_001167740) rearrangement: c.648+1286:PSMA5_c.904:SMYD3dup Note: The PSMA5 - SMYD3 rearrangement is a duplication that results in a fusion of PSMA5 exons 1 - 8 to SMYD3 exons 10 - 12. One of the breakpoints is within SMYD3 exon 10. Functional significance is undetermined.
TOP1	0	MSKCC-DMP	P-0042958-T01-IM6	TOP1-intragenic	yes	unknown		unknown	TOP1 (NM_003286) rearrangement: t(13;20)(q12.2;q12)(chr13:g.28121662::chr20:g.39658076) Note: The TOP1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
AXIN1	0	MSKCC-DMP	P-0043108-T01-IM6	AXIN1-intragenic	yes	unknown		out of frame	AXIN1 (NM_003502) rearrangement: c.879-6318_c.1255-4del Note: The AXIN1 rearrangement is an intragenic deletion of exons 3 - 5.
BRCA2	0	MSKCC-DMP	P-0043113-T01-IM6	BRCA2-intragenic	yes	unknown		unknown	BRCA2 (NM_000059) rearrangement: t(2;13)(q37.3;q13.1)(chr2:g.241343675::chr13:g.32914249) Note: The BRCA2 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.
PAN3	0	MSKCC-DMP	P-0043246-T01-IM6	FLT1-PAN3 fusion	yes	unknown		out of frame	PAN3 (NM_175854) - FLT1 (NM_002019) rearrangement: c.691-7254:PAN3_c.2954-141:FLT1inv Note: The PAN3 - FLT1 rearrangement is an inversion that results in a fusion of PAN3 exons 1 - 4 to FLT1 exons 22 - 30. The fusion includes a part of the kinase domain of FLT1. Functional significance is undetermined.
FLT1	0	MSKCC-DMP	P-0043246-T01-IM6	FLT1-PAN3 fusion	yes	unknown		out of frame	PAN3 (NM_175854) - FLT1 (NM_002019) rearrangement: c.691-7254:PAN3_c.2954-141:FLT1inv Note: The PAN3 - FLT1 rearrangement is an inversion that results in a fusion of PAN3 exons 1 - 4 to FLT1 exons 22 - 30. The fusion includes a part of the kinase domain of FLT1. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0043404-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-164:CDKN2A_chr9:g.11836214inv Note: The CDKN2A rearrangement is an inversion of exon 2. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
ERG	0	MSKCC-DMP	P-0043413-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4013:ERG_c.127-228:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 3 - 14. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043413-T01-IM6	TMPRSS2-ERG fusion	yes	unknown		unknown	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4013:ERG_c.127-228:TMPRSS2inv Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 3 - 14. Functional significance is undetermined.
RBM10	0	MSKCC-DMP	P-0043472-T01-IM6	PLXNA3-RBM10 fusion	yes	unknown		out of frame	RBM10 (NM_001204468) - PLXNA3 (NM_017514) rearrangement: c.2361+33:RBM10_c.5156+49:PLXNA3del Note: The RBM10 - PLXNA3 rearrangement is a deletion that results in a fusion of RBM10 exons 1 - 19 to PLXNA3 exons 31 - 33.
PLXNA3	0	MSKCC-DMP	P-0043472-T01-IM6	PLXNA3-RBM10 fusion	yes	unknown		out of frame	RBM10 (NM_001204468) - PLXNA3 (NM_017514) rearrangement: c.2361+33:RBM10_c.5156+49:PLXNA3del Note: The RBM10 - PLXNA3 rearrangement is a deletion that results in a fusion of RBM10 exons 1 - 19 to PLXNA3 exons 31 - 33.
BRCA1	0	MSKCC-DMP	P-0043583-T01-IM6	BRCA1-intragenic	yes	unknown		unknown	BRCA1 (NM_007294) rearrangement: c.671-35:BRCA1_chr17:g.42410005del Note: The BRCA1 rearrangement is a deletion of exons 1 - 9.
ADHFE1	0	MSKCC-DMP	P-0043583-T01-IM6	TMPRSS2-ADHFE1 fusion	yes	unknown		in frame	ADHFE1 (NM_144650) - TMPRSS2 (NM_001135099) rearrangement: t(8;21)(q13.1;q22.3)(chr8:g.67354656::chr21:g.42875000) Note: The ADHFE1 - TMPRSS2 rearrangement is a translocation that results in a fusion of ADHFE1 exons 1 - 2 to TMPRSS2 exons 2 - 14. The fusion is predicted to be in frame. Multiple other TMPRSS2 rearrangements were also detected in this sample, suggesting that a more complex rearrangement involving TMPRSS2 is possible. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043583-T01-IM6	TMPRSS2-ADHFE1 fusion	yes	unknown		in frame	ADHFE1 (NM_144650) - TMPRSS2 (NM_001135099) rearrangement: t(8;21)(q13.1;q22.3)(chr8:g.67354656::chr21:g.42875000) Note: The ADHFE1 - TMPRSS2 rearrangement is a translocation that results in a fusion of ADHFE1 exons 1 - 2 to TMPRSS2 exons 2 - 14. The fusion is predicted to be in frame. Multiple other TMPRSS2 rearrangements were also detected in this sample, suggesting that a more complex rearrangement involving TMPRSS2 is possible. Functional significance is undetermined.
SMARCB1	0	MSKCC-DMP	P-0043615-T01-IM6	SMARCB1-intragenic	yes	unknown		unknown	SMARCB1 (NM_003073) rearrangement: t(8;22)(q22.2;q11.23)(chr8:g.101422122::chr22:g.24175790) Note: The SMARCB1 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0043633-T01-IM6	MDC1-intragenic	yes	unknown		unknown	MDC1 (NM_014641) rearrangement: c.84:MDC1_chr6:g.30666783del Note: The MDC1 rearrangement is a deletion of exons 2 - 15. One of the breakpoints is within exon 2. Functional significance is undetermined.
ARID1B	0	MSKCC-DMP	P-0043660-T01-IM6	CDKN2A-ARID1B fusion	yes	unknown		out of frame	ARID1B (NM_020732) - CDKN2A (NM_000077) rearrangement: t(6;9)(q25.3;p21.3)(chr6:g.157398404::chr9:g.21968863) Note: The ARID1B - CDKN2A rearrangement is a translocation that results in a fusion of ARID1B exons 1 - 5 to CDKN2A exon 3. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CDKN2A	0	MSKCC-DMP	P-0043660-T01-IM6	CDKN2A-ARID1B fusion	yes	unknown		out of frame	ARID1B (NM_020732) - CDKN2A (NM_000077) rearrangement: t(6;9)(q25.3;p21.3)(chr6:g.157398404::chr9:g.21968863) Note: The ARID1B - CDKN2A rearrangement is a translocation that results in a fusion of ARID1B exons 1 - 5 to CDKN2A exon 3. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
TMPRSS2	0	MSKCC-DMP	P-0043671-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) rearrangement: c.55+1504:TMPRSS2_chr21:g.40039999del Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. While this is not the canonical TMPRSS2-ERG fusion, the possibility of a TMPRSS2-ERG fusion not detected by the IMPACT Panel cannot be ruled out.The functional significance of this fusion is undetermined.
TP53	0	MSKCC-DMP	P-0043698-T01-IM6	SUPT3H-TP53 fusion	yes	unknown		out of frame	TP53 (NM_000546) - SUPT3H (NM_003599) rearrangement: t(6;17)(p21.1;p13.1)(chr6:g.45270502::chr17:g.7579660) Note: The TP53 - SUPT3H rearrangement is a translocation that results in a fusion of TP53 exons 1 - 3 to SUPT3H exons 5 - 11. Functional significance is undetermined.
SUPT3H	0	MSKCC-DMP	P-0043698-T01-IM6	SUPT3H-TP53 fusion	yes	unknown		out of frame	TP53 (NM_000546) - SUPT3H (NM_003599) rearrangement: t(6;17)(p21.1;p13.1)(chr6:g.45270502::chr17:g.7579660) Note: The TP53 - SUPT3H rearrangement is a translocation that results in a fusion of TP53 exons 1 - 3 to SUPT3H exons 5 - 11. Functional significance is undetermined.
TET2	0	MSKCC-DMP	P-0043868-T01-IM6	TET2-intragenic	yes	unknown		unknown	TET2 (NM_001127208) rearrangement: c.5582:TET2_chr4:g.105889922del Note: The TET2 rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11.Functional significance is undetermined.
RRAS2	0	MSKCC-DMP	P-0044010-T01-IM6	RRAS2-intragenic	yes	unknown		unknown	RRAS2 (NM_012250) rearrangement: c.528-8:RRAS2_chr11:g.45787087inv Note: The RRAS2 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.
ABCC1	0	MSKCC-DMP	P-0044010-T01-IM6	HNF1A-ABCC1 fusion	yes	unknown		unknown	ABCC1 (NM_004996) - HNF1A (NM_000545) rearrangement: t(12;16)(q24.31;p13.11)(chr12:g.121416656::chr16:g.16232122) Note: The ABCC1 - HNF1A rearrangement is a translocation that results in a fusion of ABCC1 exons 1 - 29 to HNF1A exons 1 - 10. One of the breakpoints is within HNF1A exon 1. Functional significance is undetermined.
HNF1A	0	MSKCC-DMP	P-0044010-T01-IM6	HNF1A-ABCC1 fusion	yes	unknown		unknown	ABCC1 (NM_004996) - HNF1A (NM_000545) rearrangement: t(12;16)(q24.31;p13.11)(chr12:g.121416656::chr16:g.16232122) Note: The ABCC1 - HNF1A rearrangement is a translocation that results in a fusion of ABCC1 exons 1 - 29 to HNF1A exons 1 - 10. One of the breakpoints is within HNF1A exon 1. Functional significance is undetermined.
CSDE1	0	MSKCC-DMP	P-0044065-T01-IM6	CSDE1-intragenic	yes	unknown		unknown	CSDE1 (NM_001242891) rearrangement: t(1;4)(p13.2;q31.21)(chr1:g.115263350::chr4:g.146051831) Note: The CSDE1 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.
EIF4E	0	MSKCC-DMP	P-0044065-T01-IM6	METAP1-EIF4E fusion	yes	unknown		unknown	
METAP1	0	MSKCC-DMP	P-0044065-T01-IM6	METAP1-EIF4E fusion	yes	unknown		unknown	
OSBPL2	0	MSKCC-DMP	P-0044218-T01-IM6	TMPRSS2-OSBPL2 fusion	yes	unknown		in frame	OSBPL2 (NM_144498) - TMPRSS2 (NM_001135099) rearrangement: t(20;21)(q13.33;q22.3)(chr20:g.60866051::chr21:g.42872237) Note: The OSBPL2 - TMPRSS2 rearrangement is a translocation that results in a fusion of OSBPL2 exons 1 - 12 to TMPRSS2 exons 2 - 14. The fusion is predicted to be in frame. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044218-T01-IM6	TMPRSS2-OSBPL2 fusion	yes	unknown		in frame	OSBPL2 (NM_144498) - TMPRSS2 (NM_001135099) rearrangement: t(20;21)(q13.33;q22.3)(chr20:g.60866051::chr21:g.42872237) Note: The OSBPL2 - TMPRSS2 rearrangement is a translocation that results in a fusion of OSBPL2 exons 1 - 12 to TMPRSS2 exons 2 - 14. The fusion is predicted to be in frame. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044218-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1670:TMPRSS2_c.18+6374:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
ERG	0	MSKCC-DMP	P-0044218-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1670:TMPRSS2_c.18+6374:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10. Functional significance is undetermined.
KDM5A	0	MSKCC-DMP	P-0044503-T01-IM6	KDM5A-intragenic	yes	unknown		unknown	KDM5A (NM_001042603) rearrangement: t(7;12)(q31.33;p13.33)(chr7:g.125904725::chr12:g.465570) Note: The KDM5A rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
KMT2B	0	MSKCC-DMP	P-0044548-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.6537_c.7160-962inv Note: The KMT2B rearrangement is an intragenic inversion of exons 28 - 30. One of the breakpoints is within exon 28. Functional significance is undetermined.
MAP3K1	0	MSKCC-DMP	P-0044579-T01-IM6	MAP3K1-intragenic	yes	unknown		unknown	MAP3K1 (NM_005921) rearrangement: t(1;5)(p12;q11.2)(chr1:g.120024255::chr5:g.56152501) Note: The MAP3K1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0044579-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.-36G>A:CDKN2Ap14ARF_chr9.g:22070476del Note: The CDKN2Ap14ARF rearrangement is a deletion with breakpoint in the 5UTR. The functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0044808-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.14030_c.16336dup Note: The KMT2D rearrangement is an intragenic duplication of exons 43 - 51. The breakpoints are within exon 43 and exon 51. Functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0044862-T01-IM6	KIF5A-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - KIF5A (NM_004984) rearrangement: c.861:GLI1_c.1293+360:KIF5Adel Note: The GLI1 - KIF5A rearrangement is a deletion that results in a fusion of GLI1 exons 1 - 8 to KIF5A exons 13 - 28. One of the breakpoints is within GLI1 exon 8. Functional significance is undetermined.
KIF5A	0	MSKCC-DMP	P-0044862-T01-IM6	KIF5A-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - KIF5A (NM_004984) rearrangement: c.861:GLI1_c.1293+360:KIF5Adel Note: The GLI1 - KIF5A rearrangement is a deletion that results in a fusion of GLI1 exons 1 - 8 to KIF5A exons 13 - 28. One of the breakpoints is within GLI1 exon 8. Functional significance is undetermined.
TSC1	0	MSKCC-DMP	P-0044919-T01-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: t(9;11)(q34.13;p14.1)(chr9:g.135778054::chr11:g.30603418) Note: The TSC1 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0045237-T01-IM6	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: c.1265:TBX3_chr12:g.116583171inv Note: The TBX3 rearrangement is an inversion of exons 1 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0045237-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3428:TMPRSS2_c.18+5115:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0045237-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3428:TMPRSS2_c.18+5115:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.
ARID1A	0	MSKCC-DMP	P-0046024-T01-IM6	ARID1A-intragenic	yes	unknown		unknown	ARID1A (NM_006015) rearrangement: c.1137+5964_c.5571del Note: The ARID1A rearrangement is an intragenic deletion of exons 2 - 20. One of the breakpoints is within exon 20.
CTNNB1	0	MSKCC-DMP	P-0047736-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.284:CTNNB1_chr3:g.41264128del Note: The CTNNB1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.
CD47	0	MSKCC-DMP	P-0012114-T03-IM6	MET-CD47 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD47-MET fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon7 (NM_001777) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0012114-T03-IM6	MET-CD47 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD47-MET fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon7 (NM_001777) and MET Exon15 (NM_000245). Lab Notes Run Number: ArcherV2-CLIN-20180131 Macro-dissection: Unknown
GOPC	0	MSKCC-DMP	P-0021147-T01-IM6	ROS1-GOPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GOPC-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes GOPC Exon4 (NM_020399) and ROS1 Exon36 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Performed
ROS1	0	MSKCC-DMP	P-0021147-T01-IM6	ROS1-GOPC fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: GOPC-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes GOPC Exon4 (NM_020399) and ROS1 Exon36 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170060 Macro-dissection: Performed
CDH1	0	MSKCC-DMP	P-0028283-T03-IM6	MET-CDH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CDH1-MET fusion. Note: The rearrangement is an out of frame fusion between genes CDH1 Exon13 (NM_004360) and MET Exon4 (NM_000245).  This fusion event includes the kinase domain of MET. A deletion involving MET exons 6-14 was also detected. The functional significance of these events is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190140 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0028283-T03-IM6	MET-CDH1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CDH1-MET fusion. Note: The rearrangement is an out of frame fusion between genes CDH1 Exon13 (NM_004360) and MET Exon4 (NM_000245).  This fusion event includes the kinase domain of MET. A deletion involving MET exons 6-14 was also detected. The functional significance of these events is unknown.  Lab Notes Run Number: Archerv3-CLIN-20190140 Macro-dissection: Not Performed
ERC1	0	MSKCC-DMP	P-0038256-T01-IM6	RET-ERC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ERC1-RET fusion. Note: The rearrangement is an in-frame fusion between genes ERC1 Exon7 (NM_178040) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190029 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0038256-T01-IM6	RET-ERC1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: ERC1-RET fusion. Note: The rearrangement is an in-frame fusion between genes ERC1 Exon7 (NM_178040) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV3-CLIN-20190029 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0039269-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL: MET Exon 14 skipping (NM_000245). POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: ST7-MET fusion. Note: The rearrangement is an in-frame fusion between genes ST7 Exon1 (NM_021908) and MET Exon2 (NM_000245). CAPZA2-MET fusion. Note: The rearrangement is an in-frame fusion between genes CAPZA2 Exon1 (NM_006136) and MET Exon2 (NM_000245). Note1: all MET events (Ex14 skipping and fusions) were detected with low frequency due to the high level of MET expression in this sample.  Lab Notes Run Number: ArcherV3-CLIN-20190048 Macro-dissection: Unknown
TFG	0	MSKCC-DMP	P-0041327-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING FUSION IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: Archerv3-CLIN-20190090 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0041327-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING FUSION IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: Archerv3-CLIN-20190090 Macro-dissection: Performed
TFG	0	MSKCC-DMP	P-0042625-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: Archerv3-CLIN-20190107 Macro-dissection: Performed
GPR128	0	MSKCC-DMP	P-0042625-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). Note2: This is a known structural germline polymorphism seen in healthy individuals. PMID: 19797732  Lab Notes Run Number: Archerv3-CLIN-20190107 Macro-dissection: Performed
TMPRSS2	0	MSKCC-DMP	P-0043583-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and ERG Exon4 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190122 Macro-dissection: Not Performed
ERG	0	MSKCC-DMP	P-0043583-T01-IM6	ERG-TMPRSS2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TMPRSS2-ERG fusion. Note: The rearrangement is an in-frame fusion between genes TMPRSS2 Exon1 (NM_001135099) and ERG Exon4 (NM_004449). Lab Notes Run Number: Archerv3-CLIN-20190122 Macro-dissection: Not Performed
PTPRK	0	MSKCC-DMP	P-0044388-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190136 Macro-dissection: Performed
RSPO3	0	MSKCC-DMP	P-0044388-T01-IM6	RSPO3-PTPRK fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: PTPRK-RSPO3 fusion. Note: The rearrangement is an in-frame fusion between genes PTPRK Exon1 (NM_001135648) and RSPO3 Exon2 (NM_032784). Lab Notes Run Number: Archerv3-CLIN-20190136 Macro-dissection: Performed
NTRK1	0	MSKCC-DMP	P-0007687-T02-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.145:NTRK1_chr1:g.218470640inv Note: The NTRK1 rearrangement is an inversion with a breakpoint in exon 1. The functional significance is undetermined.
SMYD3	0	MSKCC-DMP	P-0007687-T02-IM6	SMYD3-intragenic	yes	unknown		unknown	SMYD3 (NM_001167740) rearrangement: c.532-49350_c.771del Note: The SMYD3 rearrangement is an intragenic deletion of exons 6-8. One of the breakpoints is within exon 8. The functional significance is undetermined.
NEGR1	0	MSKCC-DMP	P-0012084-T01-IM5	NEGR1-intragenic	yes	unknown		unknown	NEGR1 (NM_173808) rearrangement: c.139_c.176+96526dup Note: The NEGR1 rearrangement is an intragenic duplication of a part of exon 1.
BAP1	0	MSKCC-DMP	P-0012521-T01-IM5	BAP1-intragenic	yes	unknown		unknown	BAP1 (NM_004656) rearrangement: c.2097_chr3:g.52436397inv Note: The BAP1 rearrangement is an inversion which includes exon 17 and the 3UTR of BAP1. One of the breakpoints is within exon 17. The functional significance is undetermined.
FGFR2	0	MSKCC-DMP	P-0021327-T01-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21): c.2302-1613:FGFR2_c.237+32254:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
BICC1	0	MSKCC-DMP	P-0021327-T01-IM6	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 fused with BICC1 exons 16-21): c.2302-1613:FGFR2_c.237+32254:BICC1inv Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.
ERBB2	0	MSKCC-DMP	P-0021776-T01-IM6	ERBB2-intragenic	yes	unknown		unknown	ERBB2 (NM_004448) rearrangement: t(17;21)(q12;q21.2)(chr17:g.37881392::chr21:g.21176072) Note: The ERBB2 rearrangement is  a translocation that may result in the truncation of exons 21-27. The functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0021776-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: chrX:g.37033335_c.4809+130:ATRXinv Note: The ATRX rearrangement is an inversion of exons 18-35 that may potentially disrupt the gene function.
NOTCH3	0	MSKCC-DMP	P-0025675-T01-IM6	NOTCH3-intragenic	yes	unknown		unknown	NOTCH3 (NM_000435) rearrangement: c.6189_chr19:g.38926895dup Note: The NOTCH3 rearrangement results in the duplication of exons 1-33. One of the breakpoints is within exon 33. The functional significance is undetermined.
PIK3CD	0	MSKCC-DMP	P-0029548-T01-IM6	CLSTN1-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) - CLSTN1 (NM_001009566) rearrangement: c.957:PIK3CD_c.1356+861:CLSTN1inv Note: The PIK3CD - CLSTN1 rearrangement is an inversion which results in the fusion of PIK3CD exons 1-8 with CLSTN1 exons 10-19. One of the breakpoints is within PIK3CD exon 8. Its functional significance is undetermined.
CLSTN1	0	MSKCC-DMP	P-0029548-T01-IM6	CLSTN1-PIK3CD fusion	yes	unknown		unknown	PIK3CD (NM_005026) - CLSTN1 (NM_001009566) rearrangement: c.957:PIK3CD_c.1356+861:CLSTN1inv Note: The PIK3CD - CLSTN1 rearrangement is an inversion which results in the fusion of PIK3CD exons 1-8 with CLSTN1 exons 10-19. One of the breakpoints is within PIK3CD exon 8. Its functional significance is undetermined.
BIRC3	0	MSKCC-DMP	P-0029548-T01-IM6	BIRC3-intragenic	yes	unknown		unknown	BIRC3 (NM_182962) rearrangement: c.-49-281_c.1033-6del Note: The BIRC3 rearrangement is an intragenic deletion of exons 1-5. Its functional significance is undetermined.
SESN3	0	MSKCC-DMP	P-0035498-T01-IM6	SESN3-intragenic	yes	unknown		unknown	SESN3 (NM_144665) Rearrangement: c.1392+102_c.*7865del Note: The SESN3 rearrangement is an intragenic deletion of exons 1-9. The functional significance is undetermined.
PAX 8	0	MSKCC-DMP	P-0035498-T01-IM6	PAX 8-intragenic	yes	unknown		unknown	PAX 8 (NM_003466) Rearrangement: t(2;17)(q13;p13.2)(chr2:g.113987958::chr17:g.4414421) Note: The PAX8 rearrangement is a translocation with breakpoints within intron 9 of PAX8 that may result in the truncation of PAX8 exons 10-12. The functional significance is undetermined. In addition, the presence of multiple PAX8 structural variants may reflect a more complex rearrangement that is not fully characterized by IMPACT.
KMT2B	0	MSKCC-DMP	P-0036117-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: c.4625_chr19:g.36379015inv Note: The KMT2B rearrangement is an inversion that includes KMT2B exons 20-37. One of the breakpoints is within exon 20.
PIK3C2G	0	MSKCC-DMP	P-0043514-T01-IM6	PIK3C2G-intragenic	yes	unknown		unknown	PIK3C2G (NM_004570) rearrangement: c.3888:PIK3C2G_chr12:g.22631196del Note: The PIK3C2G rearrangement is a deletion of exons 28 - 32. One of the breakpoints is within exon 28. Functional significance is undetermined.
NOS1AP	0	MSKCC-DMP	P-0045731-T01-IM6	NTRK1-NOS1AP fusion	yes	unknown		unknown	NOS1AP (NM_014697) - NTRK1 (NM_002529) fusion: c.1106-363:NOS1AP_c.881:NTRK1dup Note: The NOS1AP - NTRK1 fusion involves NOS1AP exons 1 - 9 and NTRK1 exons 8 - 17. One of the breakpoints is within NTRK1 exon 8. The fusion includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0045731-T01-IM6	NTRK1-NOS1AP fusion	yes	unknown		unknown	NOS1AP (NM_014697) - NTRK1 (NM_002529) fusion: c.1106-363:NOS1AP_c.881:NTRK1dup Note: The NOS1AP - NTRK1 fusion involves NOS1AP exons 1 - 9 and NTRK1 exons 8 - 17. One of the breakpoints is within NTRK1 exon 8. The fusion includes the kinase domain of NTRK1.
TPM3	0	MSKCC-DMP	P-0046877-T02-IM6	NTRK1-TPM3 fusion	yes	unknown		in frame	TPM3 (NM_152263) - NTRK1 (NM_002529) fusion: c.776-357:TPM3_c.1177+60:NTRK1inv Note: The TPM3 - NTRK1 fusion involves TPM3 exons 1 - 8 and NTRK1 exons 9 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
NTRK1	0	MSKCC-DMP	P-0046877-T02-IM6	NTRK1-TPM3 fusion	yes	unknown		in frame	TPM3 (NM_152263) - NTRK1 (NM_002529) fusion: c.776-357:TPM3_c.1177+60:NTRK1inv Note: The TPM3 - NTRK1 fusion involves TPM3 exons 1 - 8 and NTRK1 exons 9 - 17. The fusion is predicted to be in frame and includes the kinase domain of NTRK1.
ALOX12B	0	MSKCC-DMP	P-0048150-T01-IM6	ALOX12B-intragenic	yes	unknown		unknown	ALOX12B (NM_001139) rearrangement: c.754+71:ALOX12B_chr17:g.6943000del Note: The ALOX12B rearrangement is a deletion of exons 7 - 15. Functional significance is undetermined.
HIST1H3F	0	MSKCC-DMP	P-0049942-T01-IM6	HIST1H3F-intragenic	yes	unknown		unknown	HIST1H3F (NM_021018) rearrangement: c.339:HIST1H3F_chr6:g.26131239del Note: The HIST1H3F rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
NOS1AP	0	MSKCC-DMP	P-0045731-T01-IM6	NTRK1-NOS1AP fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: NOS1AP-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes NOS1AP Exon9 (NM_014697) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Not Performed
NTRK1	0	MSKCC-DMP	P-0045731-T01-IM6	NTRK1-NOS1AP fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL: NOS1AP-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes NOS1AP Exon9 (NM_014697) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: Archerv3-CLIN-20190159 Macro-dissection: Not Performed
EML4	0	MSKCC-DMP	P-0005786-T01-IM5	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 with ALK exons 20-29) : c.2057-186:EML4_c.3172+88:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame.
ALK	0	MSKCC-DMP	P-0005786-T01-IM5	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 with ALK exons 20-29) : c.2057-186:EML4_c.3172+88:ALKinv Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame.
KMT2C	0	MSKCC-DMP	P-0014129-T03-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: c.8306_chr7:g.152299391dup Note: The KMT2C rearrangement is a duplication that includes KMT2C exons 1-38. One of the breakpoints is within exon 38.
TNFRSF14	0	MSKCC-DMP	P-0015825-T01-IM6	TNFRSF14-intragenic	yes	unknown		unknown	TNFRSF14 (NM_003820) rearrangement: c.764_chr1:g.173990228inv Note: The TNFRSF14 rearrangement is an inversion which includes exon 8 of TNFRSF14. One of the breakpoints is within exon. The functional significance is undetermined.
ZCCHC7	0	MSKCC-DMP	P-0017158-T05-IM6	TEK-ZCCHC7 fusion	yes	unknown		unknown	ZCCHC7 (NM_032226) - TEK (NM_000459) Fusion(ZCCHC7 exon1-2 fused with TEK exons 11-23) : c.611-20860:ZCCHC7_c.1540:TEK Note: The ZCCHC7-TEK Fusion results in the fusion of exons 1-2 of ZCCHC7 with exons 11-23 of TEK. The breakpoint in TEK is within exon11. This includes the protein kinase domain of TEK.
TEK	0	MSKCC-DMP	P-0017158-T05-IM6	TEK-ZCCHC7 fusion	yes	unknown		unknown	ZCCHC7 (NM_032226) - TEK (NM_000459) Fusion(ZCCHC7 exon1-2 fused with TEK exons 11-23) : c.611-20860:ZCCHC7_c.1540:TEK Note: The ZCCHC7-TEK Fusion results in the fusion of exons 1-2 of ZCCHC7 with exons 11-23 of TEK. The breakpoint in TEK is within exon11. This includes the protein kinase domain of TEK.
ASXL2	0	MSKCC-DMP	P-0021722-T01-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.140+46_c.1795del Note: The ASXL2 rearrangement is an intragenic deletion of exons 3-11. One of the breakpoints is within exon 11. Its functional significance is undetermined
KMT2C	0	MSKCC-DMP	P-0022811-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) rearrangement: t(1;7)(p36.33;q36.1)(chr1:g.1500228:chr7:g.151902162) Note: The KMT2C rearrangement is a translocation that may result in a truncation of exons 26-59. The functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0023439-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: chr12:g.10974606_c.1009+48inv Note: The ETV6 rearrangement is an inversion (1048345 bp) that includes ETV6 exons 1-5. The functional significance is undetermined.
CAMK4	0	MSKCC-DMP	P-0023788-T01-IM6	APC-CAMK4 fusion	yes	unknown		unknown	CAMK4 (NM_001744) - APC (NM_000038) Rearrangement : c.241-906:CAMK4_c.6561:APCdel Note: The CAMK4 - APC  rearrangement results in the fusion of exons 1-2 of CAMK4 with exon 16 of APC. The breakpoint in APC is within exon 16. Its functional significance is undetermined, however it may disrupt APC function.
APC	0	MSKCC-DMP	P-0023788-T01-IM6	APC-CAMK4 fusion	yes	unknown		unknown	CAMK4 (NM_001744) - APC (NM_000038) Rearrangement : c.241-906:CAMK4_c.6561:APCdel Note: The CAMK4 - APC  rearrangement results in the fusion of exons 1-2 of CAMK4 with exon 16 of APC. The breakpoint in APC is within exon 16. Its functional significance is undetermined, however it may disrupt APC function.
RET	0	MSKCC-DMP	P-0024559-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: chr10:g.32186894_c.2136+598del Note: The RET rearrangement results in the deletion of exons 1-11. The functional significance is undetermined. This sample has been nominated for Archer targeted RNAseq assay to further characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.
NOTCH2	0	MSKCC-DMP	P-0032284-T01-IM6	NOTCH2-intragenic	yes	unknown		unknown	NOTCH2 (NM_024408) rearrangement: t(1;17)(p12;q24.3)(chr1:g.120510237::chr17:g.68563463) Note: The NOTCH2 rearrangement is a translocation which involves a breakpoint in exon 8. Its functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0032351-T01-IM6	EPHX3-BRD4 fusion	yes	unknown		unknown	BRD4(NM_058243) - EPHX3(NM_024794) Fusion:  c.2673:BRD4_c.616+1381:EPHX3del Note: The BRD4 - EPHX3 rearrangement is a deletion which results in the fusion of BRD4 exons 1-14 with EPHX3 exons 5-7. One of the breakpoints is with exon 14 of BRD4. The functional significance is undetermined.
EPHX3	0	MSKCC-DMP	P-0032351-T01-IM6	EPHX3-BRD4 fusion	yes	unknown		unknown	BRD4(NM_058243) - EPHX3(NM_024794) Fusion:  c.2673:BRD4_c.616+1381:EPHX3del Note: The BRD4 - EPHX3 rearrangement is a deletion which results in the fusion of BRD4 exons 1-14 with EPHX3 exons 5-7. One of the breakpoints is with exon 14 of BRD4. The functional significance is undetermined.
BRD4	0	MSKCC-DMP	P-0032351-T01-IM6	PLEKHA2-BRD4 fusion	yes	unknown		unknown	BRD4(NM_058243) - PLEKHA2(NM_021623) Fusion: t(8;19)(p11.23;p13.13)(chr8:g.38789930::chr19:g.15354210) Note: The BRD4 - PLEKHA2 rearrangement is a translocation which results in the fusion of exons 1-14 of BRD4 and exons 3- 13 of PLEKHA2. The functional significance is undetermined. In addition, the presence of multiple BRD4 structural variants may reflect a more complex rearrangement involving BRD4 that is not fully characterized by IMPACT.
PLEKHA2	0	MSKCC-DMP	P-0032351-T01-IM6	PLEKHA2-BRD4 fusion	yes	unknown		unknown	BRD4(NM_058243) - PLEKHA2(NM_021623) Fusion: t(8;19)(p11.23;p13.13)(chr8:g.38789930::chr19:g.15354210) Note: The BRD4 - PLEKHA2 rearrangement is a translocation which results in the fusion of exons 1-14 of BRD4 and exons 3- 13 of PLEKHA2. The functional significance is undetermined. In addition, the presence of multiple BRD4 structural variants may reflect a more complex rearrangement involving BRD4 that is not fully characterized by IMPACT.
SMAD4	0	MSKCC-DMP	P-0034132-T01-IM6	SMAD4-intragenic	yes	unknown		unknown	SMAD4 (NM_005359) rearrangement: c.-127-6115_c.*50inv Note: The SMAD4 rearrangement is an inversion with breakpoints in SMAD4 5UTR and 3UTR. The functional significance is undetermined.
PAX8	0	MSKCC-DMP	P-0037143-T01-IM6	PAX8-intragenic	yes	unknown		unknown	PAX8 (NM_003466) Rearrangement : c.1189+1224:PAX8_chr2:g.118870847inv Note: The PAX8 Rearrangement results in the inversion of exons1-10 of PAX8. Its functional significance is undetermined.
RTEL1	0	MSKCC-DMP	P-0037172-T01-IM6	RTEL1-intragenic	yes	unknown		unknown	RTEL1 (NM_032957) rearrangement: t(10;20)(q24.3;q13.33)(chr10:g.114961946::chr20:g.62321521) Note: The RTEL1 rearrangement is a translocation with a breakpoint in RTEL1 exon 25. The functional significance is undetermined.
DCTN1	0	MSKCC-DMP	P-0037284-T01-IM6	ALK-DCTN1 fusion	yes	unknown		in frame	DCTN1 (NM_004082) - ALK (NM_004304) fusion (DCTN1 exons 1-26 fused to ALK exons 20-29: c.3197-174:DCTN1_c.3172+436:ALKdel Note: The DCTN1 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple ALK rearrangements were detected in this samples and a more complex rearrangement is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ALK and DCTN1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
ALK	0	MSKCC-DMP	P-0037284-T01-IM6	ALK-DCTN1 fusion	yes	unknown		in frame	DCTN1 (NM_004082) - ALK (NM_004304) fusion (DCTN1 exons 1-26 fused to ALK exons 20-29: c.3197-174:DCTN1_c.3172+436:ALKdel Note: The DCTN1 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK. Multiple ALK rearrangements were detected in this samples and a more complex rearrangement is possible. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ALK and DCTN1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.
ATP5G2	0	MSKCC-DMP	P-0037448-T01-IM6	BRCA2-ATP5G2 fusion	yes	unknown		out of frame	ATP5G2 (NM_005176) - BRCA2 (NM_000059) rearrangement: t(12;13)(q13.13;q13.1)(chr12:g.54062814::chr13:g.32918654) Note: The ATP5G2 - BRCA2 rearrangement is a translocation that results in a fusion of ATP5G2 exons 1-4 to BRCA2 exons 12-27. The functional significance is undetermined.
BRCA2	0	MSKCC-DMP	P-0037448-T01-IM6	BRCA2-ATP5G2 fusion	yes	unknown		out of frame	ATP5G2 (NM_005176) - BRCA2 (NM_000059) rearrangement: t(12;13)(q13.13;q13.1)(chr12:g.54062814::chr13:g.32918654) Note: The ATP5G2 - BRCA2 rearrangement is a translocation that results in a fusion of ATP5G2 exons 1-4 to BRCA2 exons 12-27. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0037491-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon12 fused with ALK exon20): c.1490-1120:EML4_c.3173-392:ALKinv Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0037491-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon12 fused with ALK exon20): c.1490-1120:EML4_c.3173-392:ALKinv Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.
PIK3CB	0	MSKCC-DMP	P-0037601-T01-IM6	PIK3CB-intragenic	yes	unknown		unknown	PIK3CB (NM_006219) rearrangement: c.179:PIK3CB_chr3:g.137751528inv Note: The PIK3CB rearrangement  is an inversion of exons 2-22. One of the breakpoints is within exon 2. Its functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0037642-T01-IM6	RECQL4-intragenic	yes	unknown		unknown	RECQL4 (NM_004260) rearrangement: c.783:RECQL4_chr8:g.143647141del Note: The RECQL4 rearrangement results in the deletion of exons 5-22. One of the breakpoints is within exon 5. The functional significance is undetermined.
MET	0	MSKCC-DMP	P-0037643-T01-IM6	MET-intragenic	yes	unknown		in frame	MET (NM_000245) rearrangement: c.2887+42_c.3029-506del Note: The MET rearrangement results in the in-frame deletion of exon 14. The functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0037692-T01-IM6	ELF3-intragenic	yes	unknown		unknown	ELF3 (NM_004433) Rearrangement : c.-9+151_c.688+24inv Note: The ELF3 Rearrangement results in the inversion of exons 1-6 of ELF3. One of the breakpoints is within the 5-UTR of ELF3. Its functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0037693-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) Rearrangement : c.229-417_c.374inv Note: The ROS1 Rearrangement results in the inversion of exon5 of ROS1. One of the breakpoints is within exon5. Its functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0037925-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4634:EML4_c.3173-128:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0037925-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4634:EML4_c.3173-128:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
OXSR1	0	MSKCC-DMP	P-0037925-T01-IM6	MYD88-OXSR1 fusion	yes	unknown		out of frame	OXSR1 (NM_005109) - MYD88 (NM_002468) rearrangement: c.70+6690:OXSR1_c.684-85:MYD88dup The OXSR1 - MYD88 rearrangement is a duplication that results in a fusion of OXSR1 exons 1 to MYD88 exons 4 - 5. The functional significance is undetermined.
MYD88	0	MSKCC-DMP	P-0037925-T01-IM6	MYD88-OXSR1 fusion	yes	unknown		out of frame	OXSR1 (NM_005109) - MYD88 (NM_002468) rearrangement: c.70+6690:OXSR1_c.684-85:MYD88dup The OXSR1 - MYD88 rearrangement is a duplication that results in a fusion of OXSR1 exons 1 to MYD88 exons 4 - 5. The functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0039219-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1813-3045_c.1920del Note: The SMARCA4 rearrangement is an intragenic deletion of exon 12. One of the breakpoints is within exon 12.
CD74	0	MSKCC-DMP	P-0039219-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783535::chr6:g.117646339) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0039219-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783535::chr6:g.117646339) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
KIF5B	0	MSKCC-DMP	P-0039257-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1132:KIF5B_c.2012:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0039257-T01-IM6	RET-KIF5B fusion	yes	unknown		unknown	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1132:KIF5B_c.2012:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 11 - 20. One of the breakpoints is within RET exon 11. The fusion includes the kinase domain of RET.
B2M	0	MSKCC-DMP	P-0039257-T01-IM6	B2M-intragenic	yes	unknown		unknown	B2M (NM_004048) rearrangement: c.21:B2M_chr15:g.45002849del Note: The B2M rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.
LZTR1	0	MSKCC-DMP	P-0039853-T01-IM6	CRKL-LZTR1 fusion	yes	unknown		unknown	LZTR1 (NM_006767) - CRKL (NM_005207) rearrangement: c.321-170:LZTR1_c.375:CRKLdup Note: The LZTR1 - CRKL rearrangement is a duplication that results in a fusion of LZTR1 exons 1 - 3 to CRKL exons 2 - 3. One of the breakpoints is within CRKL exon 2. Functional significance is undetermined.
CRKL	0	MSKCC-DMP	P-0039853-T01-IM6	CRKL-LZTR1 fusion	yes	unknown		unknown	LZTR1 (NM_006767) - CRKL (NM_005207) rearrangement: c.321-170:LZTR1_c.375:CRKLdup Note: The LZTR1 - CRKL rearrangement is a duplication that results in a fusion of LZTR1 exons 1 - 3 to CRKL exons 2 - 3. One of the breakpoints is within CRKL exon 2. Functional significance is undetermined.
STK19	0	MSKCC-DMP	P-0039853-T01-IM6	STK19-intragenic	yes	unknown		unknown	STK19 (NM_004197) rearrangement: c.901+34:STK19_chr6:g.31981147del Note: The STK19 rearrangement is a deletion of exons 7 - 8. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0039998-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.423_c.194-2195del Note: The CDKN2A rearrangement is a deletion of CDKN2A exons 1 - 2 and CDKN2A exon 2. One of the breakpoints is within exon 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
C20orf194	0	MSKCC-DMP	P-0040095-T01-IM6	CDKN2A-C20orf194 fusion	yes	unknown		out of frame	C20orf194 (NM_001009984) - CDKN2A (NM_000077) rearrangement: t(9;20)(p21.3;p13)(chr9:g.21968295::chr20:g.3271180) Note: The C20orf194 - CDKN2A rearrangement is a translocation that results in a fusion of C20orf194 exons 1 - 25 to CDKN2A exon 3. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CDKN2A	0	MSKCC-DMP	P-0040095-T01-IM6	CDKN2A-C20orf194 fusion	yes	unknown		out of frame	C20orf194 (NM_001009984) - CDKN2A (NM_000077) rearrangement: t(9;20)(p21.3;p13)(chr9:g.21968295::chr20:g.3271180) Note: The C20orf194 - CDKN2A rearrangement is a translocation that results in a fusion of C20orf194 exons 1 - 25 to CDKN2A exon 3. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
NFE2L2	0	MSKCC-DMP	P-0040544-T01-IM6	NFE2L2-intragenic	yes	unknown		unknown	NFE2L2 (NM_006164) rearrangement: t(2;13)(q31.2;q21.31)(chr2:g.178096192::chr13:g.63941965) Note: The NFE2L2 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0040553-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+30:EML4_c.3173-661:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040553-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+30:EML4_c.3173-661:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
CD74	0	MSKCC-DMP	P-0040577-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused with ROS1 exons 32-43) : t(5;6)(q32;q22.1)(chr5:g.149783441::chr6:g.117650159) Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0040577-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion (CD74 exons 1-6 fused with ROS1 exons 32-43) : t(5;6)(q32;q22.1)(chr5:g.149783441::chr6:g.117650159) Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.
RB1	0	MSKCC-DMP	P-0040811-T01-IM6	RB1-intragenic	yes	unknown		unknown	RB1 (NM_000321) rearrangement: t(13;18)(q14.2;q12.1)(chr13:g.49027014::chr18:g.29737371) Note: The RB1 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.
ASXL1	0	MSKCC-DMP	P-0040821-T01-IM6	ASXL1-intragenic	yes	unknown		unknown	ASXL1 (NM_015338) rearrangement: c.1638_c.1730del Note: The ASXL1 rearrangement is an intragenic deletion of exons 11 - 12. The breakpoints are within exon 11 and exon 12.
CD74	0	MSKCC-DMP	P-0040869-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783792::chr6:g.117647263) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0040869-T01-IM6	ROS1-CD74 fusion	yes	unknown		in frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783792::chr6:g.117647263) Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 6 and ROS1 exons 34 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
TP53BP1	0	MSKCC-DMP	P-0040894-T01-IM6	PPIP5K1-TP53BP1 fusion	yes	unknown		in frame	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) rearrangement: c.286+88:TP53BP1_c.3311-2129:PPIP5K1dup Note: The TP53BP1 - PPIP5K1 rearrangement is a duplication that results in a fusion of TP53BP1 exons 1 - 3 to PPIP5K1 exons 28 - 29. The fusion is predicted to be in frame. Functional significance is undetermined.
PPIP5K1	0	MSKCC-DMP	P-0040894-T01-IM6	PPIP5K1-TP53BP1 fusion	yes	unknown		in frame	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) rearrangement: c.286+88:TP53BP1_c.3311-2129:PPIP5K1dup Note: The TP53BP1 - PPIP5K1 rearrangement is a duplication that results in a fusion of TP53BP1 exons 1 - 3 to PPIP5K1 exons 28 - 29. The fusion is predicted to be in frame. Functional significance is undetermined.
PBRM1	0	MSKCC-DMP	P-0041310-T01-IM6	PBRM1-intragenic	yes	unknown		unknown	PBRM1 (NM_018313) rearrangement: c.1087+28:PBRM1_chr3:g.39820565del Note: The PBRM1 rearrangement is a deletion of exons 12 - 30.
KMT2D	0	MSKCC-DMP	P-0041418-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.12670:KMT2D_chr12:g.49607473dup Note: The KMT2D rearrangement is a duplication of exons 1 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.
DNMT3B	0	MSKCC-DMP	P-0041471-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: c.592:DNMT3B_chr20:g.31363836inv Note: The DNMT3B rearrangement is an inversion of exons 1 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0041611-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.3152_c.6606del Note: The ANKRD11 rearrangement is an intragenic deletion of exon 9. The breakpoints are within exon 9.
PDGFRB	0	MSKCC-DMP	P-0041637-T01-IM6	PDGFRB-intragenic	yes	unknown		unknown	PDGFRB (NM_002609) rearrangement: c.403:PDGFRB_chr5:g.67335726inv Note: The PDGFRB rearrangement is an inversion of exons 4 - 23. One of the breakpoints is within exon 4. The rearrangement includes the kinase domain of PDGFRB. Functional significance is undetermined.
ELF3	0	MSKCC-DMP	P-0041866-T01-IM6	CSAD-ELF3 fusion	yes	unknown		out of frame	ELF3 (NM_004433) - CSAD (NM_001244705) rearrangement: t(1;12)(q32.1;q13.13)(chr1:g.201981995::chr12:g.53556508) Note: The ELF3 - CSAD rearrangement is a translocation that results in a fusion of ELF3 exons 1 - 5 to CSAD exons 2 - 17. Functional significance is undetermined.
CSAD	0	MSKCC-DMP	P-0041866-T01-IM6	CSAD-ELF3 fusion	yes	unknown		out of frame	ELF3 (NM_004433) - CSAD (NM_001244705) rearrangement: t(1;12)(q32.1;q13.13)(chr1:g.201981995::chr12:g.53556508) Note: The ELF3 - CSAD rearrangement is a translocation that results in a fusion of ELF3 exons 1 - 5 to CSAD exons 2 - 17. Functional significance is undetermined.
RASAL3	0	MSKCC-DMP	P-0041866-T01-IM6	AXL-RASAL3 fusion	yes	unknown		unknown	RASAL3 (NM_022904) - AXL (NM_021913) rearrangement: c.2683:RASAL3_c.1538-93:AXLinv Note: The RASAL3 - AXL rearrangement is an inversion that results in a fusion of RASAL3 exons 1 - 16 to AXL exons 13 - 20. One of the breakpoints is within RASAL3 exon 16. The fusion includes the kinase domain of AXL. Functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0041866-T01-IM6	AXL-RASAL3 fusion	yes	unknown		unknown	RASAL3 (NM_022904) - AXL (NM_021913) rearrangement: c.2683:RASAL3_c.1538-93:AXLinv Note: The RASAL3 - AXL rearrangement is an inversion that results in a fusion of RASAL3 exons 1 - 16 to AXL exons 13 - 20. One of the breakpoints is within RASAL3 exon 16. The fusion includes the kinase domain of AXL. Functional significance is undetermined.
SLC34A1	0	MSKCC-DMP	P-0041866-T01-IM6	NSD1-SLC34A1 fusion	yes	unknown		unknown	SLC34A1 (NM_003052) - NSD1 (NM_022455) rearrangement: c.936+1867:SLC34A1_c.7929:NSD1dup Note: The SLC34A1 - NSD1 rearrangement is a duplication that results in a fusion of SLC34A1 exons 1 - 8 to NSD1 exon 23. One of the breakpoints is within NSD1 exon 23. Functional significance is undetermined.
NSD1	0	MSKCC-DMP	P-0041866-T01-IM6	NSD1-SLC34A1 fusion	yes	unknown		unknown	SLC34A1 (NM_003052) - NSD1 (NM_022455) rearrangement: c.936+1867:SLC34A1_c.7929:NSD1dup Note: The SLC34A1 - NSD1 rearrangement is a duplication that results in a fusion of SLC34A1 exons 1 - 8 to NSD1 exon 23. One of the breakpoints is within NSD1 exon 23. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0041967-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+447:EML4_c.3172+180:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0041967-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+447:EML4_c.3172+180:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
FOXO1	0	MSKCC-DMP	P-0042214-T01-IM6	FOXO1-intragenic	yes	unknown		unknown	FOXO1 (NM_002015) rearrangement: c.631-8518_c.1277inv Note: The FOXO1 rearrangement is an intragenic inversion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
STAT5A	0	MSKCC-DMP	P-0042214-T01-IM6	GAST-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - GAST (NM_000805) rearrangement: c.669:STAT5A_c.212-26:GASTdup Note: The STAT5A - GAST rearrangement is a duplication that results in a fusion of STAT5A exons 1 - 7 to GAST exon 3. One of the breakpoints is within STAT5A exon 7. Functional significance is undetermined.
GAST	0	MSKCC-DMP	P-0042214-T01-IM6	GAST-STAT5A fusion	yes	unknown		unknown	STAT5A (NM_003152) - GAST (NM_000805) rearrangement: c.669:STAT5A_c.212-26:GASTdup Note: The STAT5A - GAST rearrangement is a duplication that results in a fusion of STAT5A exons 1 - 7 to GAST exon 3. One of the breakpoints is within STAT5A exon 7. Functional significance is undetermined.
DNMT3A	0	MSKCC-DMP	P-0042596-T02-IM6	DNMT3A-intragenic	yes	unknown		unknown	DNMT3A (NM_022552) rearrangement: c.1279+153:DNMT3A_chr2:g.10625811inv Note: The DNMT3A rearrangement is an inversion of exons 11 - 23. Functional significance is undetermined.
SQSTM1	0	MSKCC-DMP	P-0042596-T02-IM6	ALK-SQSTM1 fusion	yes	unknown		in frame	SQSTM1 (NM_003900) - ALK (NM_004304) fusion: t(2;5)(p23.2;q35.3)(chr2:g.29446511::chr5:g.179254603) Note: The SQSTM1 - ALK fusion involves SQSTM1 exons 1 - 6 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0042596-T02-IM6	ALK-SQSTM1 fusion	yes	unknown		in frame	SQSTM1 (NM_003900) - ALK (NM_004304) fusion: t(2;5)(p23.2;q35.3)(chr2:g.29446511::chr5:g.179254603) Note: The SQSTM1 - ALK fusion involves SQSTM1 exons 1 - 6 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
TNFAIP3	0	MSKCC-DMP	P-0042713-T01-IM6	TNFAIP3-intragenic	yes	unknown		unknown	TNFAIP3 (NM_006290) rearrangement: c.805+2:TNFAIP3_chr6:g.138203304del Note: The TNFAIP3 rearrangement is a deletion of exons 6 - 9.
RPGRIP1L	0	MSKCC-DMP	P-0042736-T01-IM6	FANCA-RPGRIP1L fusion	yes	unknown		out of frame	RPGRIP1L (NM_015272) - FANCA (NM_000135) rearrangement: c.231-767:RPGRIP1L_c.1901-65:FANCAdup Note: The RPGRIP1L - FANCA rearrangement is a duplication that results in a fusion of RPGRIP1L exons 1 - 3 to FANCA exons 22 - 43. Functional significance is undetermined.
FANCA	0	MSKCC-DMP	P-0042736-T01-IM6	FANCA-RPGRIP1L fusion	yes	unknown		out of frame	RPGRIP1L (NM_015272) - FANCA (NM_000135) rearrangement: c.231-767:RPGRIP1L_c.1901-65:FANCAdup Note: The RPGRIP1L - FANCA rearrangement is a duplication that results in a fusion of RPGRIP1L exons 1 - 3 to FANCA exons 22 - 43. Functional significance is undetermined.
RPTOR	0	MSKCC-DMP	P-0042800-T01-IM6	MAP3K3-RPTOR fusion	yes	unknown		in frame	RPTOR (NM_020761) - MAP3K3 (NM_002401) rearrangement: c.2101+230:RPTOR_c.5-4456:MAP3K3dup Note: The RPTOR - MAP3K3 rearrangement is a duplication that results in a fusion of RPTOR exons 1 - 18 to MAP3K3 exons 2 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
MAP3K3	0	MSKCC-DMP	P-0042800-T01-IM6	MAP3K3-RPTOR fusion	yes	unknown		in frame	RPTOR (NM_020761) - MAP3K3 (NM_002401) rearrangement: c.2101+230:RPTOR_c.5-4456:MAP3K3dup Note: The RPTOR - MAP3K3 rearrangement is a duplication that results in a fusion of RPTOR exons 1 - 18 to MAP3K3 exons 2 - 16. The fusion is predicted to be in frame. Functional significance is undetermined.
KCNK13	0	MSKCC-DMP	P-0042801-T01-IM6	AKT1-KCNK13 fusion	yes	unknown		unknown	KCNK13 (NM_022054) - AKT1 (NM_001014431) rearrangement: c.334+4464:KCNK13_c.924:AKT1inv Note: The KCNK13 - AKT1 rearrangement is an inversion that results in a fusion of KCNK13 exon 1 to AKT1 exons 10 - 14. One of the breakpoints is within AKT1 exon 10. The fusion includes a part of the kinase domain of AKT1. Functional significance is undetermined.
AKT1	0	MSKCC-DMP	P-0042801-T01-IM6	AKT1-KCNK13 fusion	yes	unknown		unknown	KCNK13 (NM_022054) - AKT1 (NM_001014431) rearrangement: c.334+4464:KCNK13_c.924:AKT1inv Note: The KCNK13 - AKT1 rearrangement is an inversion that results in a fusion of KCNK13 exon 1 to AKT1 exons 10 - 14. One of the breakpoints is within AKT1 exon 10. The fusion includes a part of the kinase domain of AKT1. Functional significance is undetermined.
RHEB	0	MSKCC-DMP	P-0042863-T01-IM6	RHEB-intragenic	yes	unknown		unknown	RHEB (NM_005614) rearrangement: c.50_c.462+196inv Note: The RHEB rearrangement is an intragenic inversion of exons 1 - 7. One of the breakpoints is within exon 1. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0042874-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: t(7;17)(p11.2;p11.2)(chr7:g.55241239::chr17:g.19540903) Note: The EGFR rearrangement is a translocation with a breakpoint in intron 17. The functional significance is undetermined.
PAK7	0	MSKCC-DMP	P-0042874-T01-IM6	PAK7-intragenic	yes	unknown		unknown	PAK7 (NM_177990) rearrangement: t(18;20)(q23;p12.2)(chr18:g.75150951::chr20:g.9546741) Note: The PAK7 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0042912-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-3467:CDKN2A_chr9:g.22055601del Note: The CDKN2A rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. This variant affects CDKN2Ap14ARF (NM_058195) isoform and may also affect CDKN2Ap16INK4A (NM_000077) isoform.
MET	0	MSKCC-DMP	P-0042935-T01-IM6	MET-intragenic	yes	unknown		unknown	MET (NM_000245) rearrangement: t(1;7)(p36.33;q31.2)(chr1:g.1138847::chr7:g.116412969) Note: The MET rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
H3F3C	0	MSKCC-DMP	P-0043242-T01-IM6	H3F3C-intragenic	yes	unknown		unknown	H3F3C (NM_001013699) rearrangement: c.310:H3F3C_chr12:g.25464235del Note: The H3F3C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0043350-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4017:EML4_c.3172+814:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0043350-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4017:EML4_c.3172+814:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
CTNNB1	0	MSKCC-DMP	P-0043612-T01-IM6	CTNNB1-intragenic	yes	unknown		unknown	CTNNB1 (NM_001904) rearrangement: c.242-61:CTNNB1_chr3:g.41259809del Note: The CTNNB1 rearrangement is a deletion of exons 1 - 3. Functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0043628-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) rearrangement: c.457+413_c.194-3286inv Note: The CDKN2A rearrangement is an inversion of CDKN2A exons 1 - 2 and CDKN2A exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
SDC4	0	MSKCC-DMP	P-0043938-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117651208::chr20:g.43962372) Note: The SDC4 - ROS1 fusion involves SDC4 exons 1 - 2 and ROS1 exons 32 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0043938-T01-IM6	ROS1-SDC4 fusion	yes	unknown		in frame	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117651208::chr20:g.43962372) Note: The SDC4 - ROS1 fusion involves SDC4 exons 1 - 2 and ROS1 exons 32 - 43. The fusion is predicted to be in frame and includes the kinase domain of ROS1.
RASA1	0	MSKCC-DMP	P-0044335-T01-IM6	RASA1-intragenic	yes	unknown		unknown	RASA1 (NM_002890) rearrangement: c.2012-145:RASA1_chr5:g.82942092del Note: The RASA1 rearrangement is a deletion of exons 1 - 15.
PTPRD	0	MSKCC-DMP	P-0044335-T01-IM6	PTPRD-intragenic	yes	unknown		out of frame	PTPRD (NM_002839) rearrangement: c.2467+792_c.3153+150dup Note: The PTPRD rearrangement is an intragenic duplication of exons 28 - 29. Functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0044441-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1333-906_c.1421+25del Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 15.
TP53	0	MSKCC-DMP	P-0044475-T01-IM6	TP53-intragenic	yes	unknown		in frame	TP53 (NM_000546) rearrangement: c.672+142_c.993+1324del Note: The TP53 rearrangement is an intragenic deletion of exons 7 - 9.
BCL6	0	MSKCC-DMP	P-0044475-T01-IM6	BCL6-intragenic	yes	unknown		unknown	BCL6 (NM_001706) rearrangement: t(3;22)(q27.3;q12.3)(chr3:g.187444650::chr22:g.34770793) Note: The BCL6 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.
EPHA3	0	MSKCC-DMP	P-0044475-T01-IM6	EPHA3-intragenic	yes	unknown		unknown	EPHA3 (NM_005233) rearrangement: c.1502:EPHA3_chr3:g.106473529inv Note: The EPHA3 rearrangement is an inversion of exons 7 - 17. One of the breakpoints is within exon 7. The rearrangement includes the kinase domain of EPHA3. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0044771-T01-IM6	KMT2D-intragenic	yes	unknown		unknown	KMT2D (NM_003482) rearrangement: c.16228:KMT2D_chr12:g.49330097del Note: The KMT2D rearrangement is a deletion of exons 51 - 54. One of the breakpoints is within exon 51.
SMAD3	0	MSKCC-DMP	P-0044827-T01-IM6	ASPSCR1-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - ASPSCR1 (NM_001251888) rearrangement: t(15;17)(q22.33;q25.3)(chr15:g.67482866::chr17:g.79944678) Note: The SMAD3 - ASPSCR1 rearrangement is a translocation that results in a fusion of SMAD3 exons 1 - 9 to ASPSCR1 exons 5 - 17. One of the breakpoints is within SMAD3 exon 9. Functional significance is undetermined.
ASPSCR1	0	MSKCC-DMP	P-0044827-T01-IM6	ASPSCR1-SMAD3 fusion	yes	unknown		unknown	SMAD3 (NM_005902) - ASPSCR1 (NM_001251888) rearrangement: t(15;17)(q22.33;q25.3)(chr15:g.67482866::chr17:g.79944678) Note: The SMAD3 - ASPSCR1 rearrangement is a translocation that results in a fusion of SMAD3 exons 1 - 9 to ASPSCR1 exons 5 - 17. One of the breakpoints is within SMAD3 exon 9. Functional significance is undetermined.
AR	0	MSKCC-DMP	P-0014129-T03-IM6	AR-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION: POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL: AR (NM_000044) Variant 7 (AR V-7) PMID: 19117982 Lab Notes Run Number: ArcherV3-CLIN-20190010 Macro-dissection: Unknown
KIF5B	0	MSKCC-DMP	P-0024559-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170116 Macro-dissection: Unknown
RET	0	MSKCC-DMP	P-0024559-T01-IM6	RET-KIF5B fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: KIF5B-RET fusion. Note: The rearrangement is an in-frame fusion between genes KIF5B Exon15 (NM_004521) and RET Exon12 (NM_020975). Lab Notes Run Number: ArcherV2-CLIN-20170116 Macro-dissection: Unknown
DCTN1	0	MSKCC-DMP	P-0037284-T01-IM6	ALK-DCTN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: DCTN1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes DCTN1 Exon26 (NM_004082) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV3-CLIN-20190010 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0037284-T01-IM6	ALK-DCTN1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: DCTN1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes DCTN1 Exon26 (NM_004082) and ALK Exon20 (NM_004304). Lab Notes Run Number: ArcherV3-CLIN-20190010 Macro-dissection: Unknown
CD74	0	MSKCC-DMP	P-0040577-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: Archerv3-CLIN-20190071 Macro-dissection: Performed
ROS1	0	MSKCC-DMP	P-0040577-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: Archerv3-CLIN-20190071 Macro-dissection: Performed
EML4	0	MSKCC-DMP	P-0041908-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon5 (NM_001145076) and ALK Exon18 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190095 Macro-dissection: Unknown
ALK	0	MSKCC-DMP	P-0041908-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon5 (NM_001145076) and ALK Exon18 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190095 Macro-dissection: Unknown
SQSTM1	0	MSKCC-DMP	P-0042596-T02-IM6	ALK-SQSTM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SQSTM1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes SQSTM1 Exon5 (NM_003900) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190110 Macro-dissection: Not Performed
ALK	0	MSKCC-DMP	P-0042596-T02-IM6	ALK-SQSTM1 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: SQSTM1-ALK fusion. Note: The rearrangement is an in-frame fusion between genes SQSTM1 Exon5 (NM_003900) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190110 Macro-dissection: Not Performed
TNFRSF18	0	MSKCC-DMP	P-0042935-T01-IM6	MET-TNFRSF18 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TNFRSF18-MET fusion. Note: The rearrangement is an in-frame fusion between genes TNFRSF18 Exon2 (NM_004195) and MET Exon15 (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190111 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0042935-T01-IM6	MET-TNFRSF18 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TNFRSF18-MET fusion. Note: The rearrangement is an in-frame fusion between genes TNFRSF18 Exon2 (NM_004195) and MET Exon15 (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190111 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0000840-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	ROS1 (NM_002944) - CD74 (NM_001025158) Translocation:  t(6;5)(q22.1;q32)(chr6:g.117646938::chr5:g.149783508)
CD74	0	MSKCC-DMP	P-0000840-T01-IM3	CD74-ROS1 fusion	yes	unknown		in frame	ROS1 (NM_002944) - CD74 (NM_001025158) Translocation:  t(6;5)(q22.1;q32)(chr6:g.117646938::chr5:g.149783508)
TAOK1	0	MSKCC-DMP	P-0004934-T01-IM5	NF1-TAOK1 fusion	yes	unknown		in frame	TAOK1 (NM_020791) - NF1 (NM_001042492) rearrangement : c.133-769:TAOK1_c.889-21:NF1del Note: The TAOK1 (NM_020791) - NF1 (NM_001042492) rearrangement event is a deletion which results in the fusion of TAOK1 exons 1-2 and NF1 exons 9-58. The resulting fusion is predicted to be in-frame.
NF1	0	MSKCC-DMP	P-0004934-T01-IM5	NF1-TAOK1 fusion	yes	unknown		in frame	TAOK1 (NM_020791) - NF1 (NM_001042492) rearrangement : c.133-769:TAOK1_c.889-21:NF1del Note: The TAOK1 (NM_020791) - NF1 (NM_001042492) rearrangement event is a deletion which results in the fusion of TAOK1 exons 1-2 and NF1 exons 9-58. The resulting fusion is predicted to be in-frame.
ROS1	0	MSKCC-DMP	P-0006921-T01-IM5	SLC34A2-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement : t(4;6) (p15;q22)(chr4:g.25679037::chr6:g.117648517) Note: ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement is a translocation between exon 33 of ROS1 and 666bp after coding stop of SLC34A2. The functional significance is undetermined.
SLC34A2	0	MSKCC-DMP	P-0006921-T01-IM5	SLC34A2-ROS1 fusion	yes	unknown		unknown	ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement : t(4;6) (p15;q22)(chr4:g.25679037::chr6:g.117648517) Note: ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement is a translocation between exon 33 of ROS1 and 666bp after coding stop of SLC34A2. The functional significance is undetermined.
FAM135B	0	MSKCC-DMP	P-0006921-T01-IM5	ROS1-FAM135B fusion	yes	unknown		unknown	FAM135B (NM_015912) - ROS1 (NM_002944) rearrangement : t(6;8)(q22;q24)(chr6:g.117648534::chr8:g.138220899) Note: FAM135B (NM_015912) - ROS1 (NM_002944) rearrangement is a translocation between the promoter of FAM135B and exon 33 of ROS1. The functional significance is undetermined.
ROS1	0	MSKCC-DMP	P-0006921-T01-IM5	ROS1-FAM135B fusion	yes	unknown		unknown	FAM135B (NM_015912) - ROS1 (NM_002944) rearrangement : t(6;8)(q22;q24)(chr6:g.117648534::chr8:g.138220899) Note: FAM135B (NM_015912) - ROS1 (NM_002944) rearrangement is a translocation between the promoter of FAM135B and exon 33 of ROS1. The functional significance is undetermined.
FGFR1	0	MSKCC-DMP	P-0014932-T01-IM6	FGFR1-intragenic	yes	unknown		out of frame	FGFR1 (NM_001174067) Rearrangement : c.1756+611_c.2142-18del Note: The FGFR1 Rearrangement results in the deletion of exons 14-16.This includes the protein kinase domain of FGFR1.
RAD51B	0	MSKCC-DMP	P-0018245-T01-IM6	RAD51B-intragenic	yes	unknown		unknown	RAD51B (NM_133509) rearrangement: c.780_c.853+1794inv Note: The RAD51B is an intragenic inversion of a part of exon 8, potentially disrupting gene function.
KMT2B	0	MSKCC-DMP	P-0018245-T01-IM6	KMT2B-intragenic	yes	unknown		unknown	KMT2B (NM_014727) rearrangement: t(19;20)(q13.12;p11.23)(chr19:g.36216347::chr20:g.19374059) Note: The KMT2B rearrangement is a translocation that may result in a truncation of KMT2B exons 12-37. The functional significance is undetermined.
CDKN2Ap16INK4A	0	MSKCC-DMP	P-0018916-T01-IM6	CDKN2B-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) - CDKN2B (NM_004936) rearrangement: c.457+275:CDKN2Ap16INK4A_c.156+2:CDKN2Binv Note: The CDKN2Ap16INK4A - CDKN2B rearrangement is predicted to result in the inversion of CDKN2Ap16INK4A exons 1-2 and CDKN2B exon 1. The rearrangement is not predicted to affect CDKN2Ap14ARF. The functional significance is undetermined.
CDKN2B	0	MSKCC-DMP	P-0018916-T01-IM6	CDKN2B-CDKN2Ap16INK4A fusion	yes	unknown		unknown	CDKN2Ap16INK4A (NM_000077) - CDKN2B (NM_004936) rearrangement: c.457+275:CDKN2Ap16INK4A_c.156+2:CDKN2Binv Note: The CDKN2Ap16INK4A - CDKN2B rearrangement is predicted to result in the inversion of CDKN2Ap16INK4A exons 1-2 and CDKN2B exon 1. The rearrangement is not predicted to affect CDKN2Ap14ARF. The functional significance is undetermined.
STAT5B	0	MSKCC-DMP	P-0019303-T02-IM6	STAT5B-intragenic	yes	unknown		unknown	STAT5B (NM_012448) rearrangement: c.2077+32:STAT5B_chr17:g.37367870inv Note: The STAT5B rearrangement is an inversion of exons 17-19. Its functional significance is undetermined.
CDK12	0	MSKCC-DMP	P-0021839-T01-IM6	CDK12-intragenic	yes	unknown		unknown	CDK12 (NM_016507) Rearrangement : t(7,17)(p22.1,q12)(chr7:g.4787537::chr17:g.37681073) Note : The CDK12 Rearrangement possible results in the possible truncation of CDK12.One of the breakpoints is within exon12. Its functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0024556-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) Rearrangement: chr16:g.72718236_c.416:ZFHX3del Note: The ZFHX3 Rearrangement results in the deletion of exons 2-10. One of the breakpoints is within exon2. The functional significance is undetermined.
KMT2C	0	MSKCC-DMP	P-0024556-T01-IM6	KMT2C-intragenic	yes	unknown		unknown	KMT2C (NM_170606) Rearrangement : c.403-41051:CNTNAP2_c.9820:KMT2Cdel Note: The KMT2C Rearrangement results in the deletion of exons 43-59 of KMT2C. One of the breakpoints is within exon43. The functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0025040-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exon 12 fused to ALK exon 20) :  c.1316-1940:EML4_c.3173-758:ALKinv Note: The EML4 -ALK fusion is an in-frame fusion and includes the protein kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0025040-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exon 12 fused to ALK exon 20) :  c.1316-1940:EML4_c.3173-758:ALKinv Note: The EML4 -ALK fusion is an in-frame fusion and includes the protein kinase domain of ALK.
NOS1AP	0	MSKCC-DMP	P-0025714-T03-IM6	MCL1-NOS1AP fusion	yes	unknown		unknown	NOS1AP (NM_014697) - MCL1 (NM_021960) rearrangement: c.345-15882:NOS1AP_c.470:MCL1inv Note: The NOS1AP - MCL1 rearrangement is an inversion that results in a fusion of NOS1AP exons 1-4 to MCL1 exons 1-3. One of the breakpoints is within MCL1 exon 1. The functional significance is undetermined.
MCL1	0	MSKCC-DMP	P-0025714-T03-IM6	MCL1-NOS1AP fusion	yes	unknown		unknown	NOS1AP (NM_014697) - MCL1 (NM_021960) rearrangement: c.345-15882:NOS1AP_c.470:MCL1inv Note: The NOS1AP - MCL1 rearrangement is an inversion that results in a fusion of NOS1AP exons 1-4 to MCL1 exons 1-3. One of the breakpoints is within MCL1 exon 1. The functional significance is undetermined.
DOT1L	0	MSKCC-DMP	P-0026022-T01-IM6	DOT1L-intragenic	yes	unknown		unknown	DOT1L (NM_032482) rearrangement: c.2874_chr19:g.2362078dup Note: The DOT1L rearrangement is a duplication that includes DOT1L exons 24-28. One of the breakpoints is within exon 24. The functional significance is undetermined.
EZR	0	MSKCC-DMP	P-0028081-T01-IM6	ROS1-EZR fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+285:EZR_c.5557+112:ROS1del Note: The EZR - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
ROS1	0	MSKCC-DMP	P-0028081-T01-IM6	ROS1-EZR fusion	yes	unknown		in frame	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+285:EZR_c.5557+112:ROS1del Note: The EZR - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.
SPEN	0	MSKCC-DMP	P-0028917-T01-IM6	PLEKHM2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement:  c.6123:SPEN_c.61-10330:PLEKHM2dup Note: The SPEN - PLEKHM2 rearrangement is a duplication that results in the fusion of SPEN exons 1-11 with PLEKHM2 exons 2-20. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
PLEKHM2	0	MSKCC-DMP	P-0028917-T01-IM6	PLEKHM2-SPEN fusion	yes	unknown		unknown	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement:  c.6123:SPEN_c.61-10330:PLEKHM2dup Note: The SPEN - PLEKHM2 rearrangement is a duplication that results in the fusion of SPEN exons 1-11 with PLEKHM2 exons 2-20. One of the breakpoints is within SPEN exon 11. The functional significance is undetermined.
AXL	0	MSKCC-DMP	P-0029225-T01-IM6	AXL-intragenic	yes	unknown		unknown	AXL (NM_021913) Rearrangement: c.252:AXL_chr19:g.18915509del Note: The AXL rearrangement is a deletion of AXL exons 1 to 2. One of the breakpoints is within AXL exon 2.
TCF7L2	0	MSKCC-DMP	P-0030471-T01-IM6	TCF7L2-intragenic	yes	unknown		unknown	TCF7L2 (NM_001146274) rearrangement: c.876-947_c.937del Note: The TCF7L2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon.
KDM5C	0	MSKCC-DMP	P-0030471-T01-IM6	KDM5C-intragenic	yes	unknown		unknown	KDM5C (NM_004187) rearrangement: chrX:g.:11024795_c.1867-2inv Note: The KDM5C rearrangement is an inversion that includes KDM5C exons 14-26.
TPH2	0	MSKCC-DMP	P-0032211-T02-IM6	MDM2-TPH2 fusion	yes	unknown		unknown	TPH2 (NM_173353) -  MDM2 (NM_002392) Rearrangement : c.256-415:TPH2_c.248:MDM2dup Note : The TPH2-MDM2 Rearrangement results in the fusion of exons 1-2 of TPH2 with exons 4-11 of MDM2. The breakpoint in MDM2 is within exon4. Its functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0032211-T02-IM6	MDM2-TPH2 fusion	yes	unknown		unknown	TPH2 (NM_173353) -  MDM2 (NM_002392) Rearrangement : c.256-415:TPH2_c.248:MDM2dup Note : The TPH2-MDM2 Rearrangement results in the fusion of exons 1-2 of TPH2 with exons 4-11 of MDM2. The breakpoint in MDM2 is within exon4. Its functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0034334-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4909:EML4_c.3173-176:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-6 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0034334-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4909:EML4_c.3173-176:ALKinv Note: The EML4-ALK fusion involves EML4 exons 1-6 and ALK exons 20-29. The fusion is predicted to be in-frame and includes the kinase domain of ALK.
EPYC	0	MSKCC-DMP	P-0035694-T01-IM6	KEAP1-EPYC fusion	yes	unknown		out of frame	EPYC (NM_004950) - KEAP1 (NM_203500) rearrangement: t(12;19)(q21.33;p13.2)(chr12:g.91372652::chr19:g.10600151) Note: The EPYC - KEAP1 rearrangement is a translocation that results in the fusion of EPYC exons 1-2 with KEAP1 exons 5-6.
KEAP1	0	MSKCC-DMP	P-0035694-T01-IM6	KEAP1-EPYC fusion	yes	unknown		out of frame	EPYC (NM_004950) - KEAP1 (NM_203500) rearrangement: t(12;19)(q21.33;p13.2)(chr12:g.91372652::chr19:g.10600151) Note: The EPYC - KEAP1 rearrangement is a translocation that results in the fusion of EPYC exons 1-2 with KEAP1 exons 5-6.
INSR	0	MSKCC-DMP	P-0035694-T01-IM6	TYK2-INSR fusion	yes	unknown		unknown	INSR (NM_000208) - TYK2 (NM_003331) rearrangement: c.3112:INSR_c.2617+238:TYK2dup Note: The INSR - TYK2 rearrangement is a duplication that results in the fusion of INSR exons 1-17 with TYK2 exons 19-25. One of the breakpoints is within INSR exon 17. The functional significance is undetermined.
TYK2	0	MSKCC-DMP	P-0035694-T01-IM6	TYK2-INSR fusion	yes	unknown		unknown	INSR (NM_000208) - TYK2 (NM_003331) rearrangement: c.3112:INSR_c.2617+238:TYK2dup Note: The INSR - TYK2 rearrangement is a duplication that results in the fusion of INSR exons 1-17 with TYK2 exons 19-25. One of the breakpoints is within INSR exon 17. The functional significance is undetermined.
BRD9	0	MSKCC-DMP	P-0035694-T01-IM6	TERT-BRD9 fusion	yes	unknown		unknown	BRD9 (NM_023924) - TERT (NM_198253) rearrangement: c.47:BRD9_c.-56:TERTdup Note: The BRD9 - TERT rearrangement is a duplication that results in the fusion of BRD9 exon 1 with TERT exons 1-16. One of the breakpoints is within BRD9 exon 1. The functional significance is undetermined.
TERT	0	MSKCC-DMP	P-0035694-T01-IM6	TERT-BRD9 fusion	yes	unknown		unknown	BRD9 (NM_023924) - TERT (NM_198253) rearrangement: c.47:BRD9_c.-56:TERTdup Note: The BRD9 - TERT rearrangement is a duplication that results in the fusion of BRD9 exon 1 with TERT exons 1-16. One of the breakpoints is within BRD9 exon 1. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0037082-T01-IM6	TMPRSS2-intragenic	yes	unknown		unknown	TMPRSS2 (NM_001135099) Rearrangement : c.55+4876:TMPRSS2_chr21:g.40091831del Note: The TMPRSS2 Rearrangement results in the deletion of exons 2-14 of TMPRSS2. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the TMPRSS2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.
PIK3R3	0	MSKCC-DMP	P-0037226-T01-IM6	PIK3R3-intragenic	yes	unknown		unknown	PIK3R3 (NM_003629) rearrangement: c.622-1177:PIK3R3_chr1:g.46598399del Note: The PIK3R3 rearrangement is a deletion of exons 1-5. Its functional significance is undetermined.
PAX5	0	MSKCC-DMP	P-0037236-T01-IM6	PAX5-intragenic	yes	unknown		unknown	PAX5 (NM_016734) rearrangement: t(9;17)(p13.2;p13.1)(chr9:g.36923458::chr17:g.8339095) Note: The PAX5 rearrangement is a translocation involving a breakpoint in exon 7. Its functional significance is undetermined.
PRKCI	0	MSKCC-DMP	P-0037238-T01-IM6	MECOM-PRKCI fusion	yes	unknown		unknown	PRKCI (NM_002740) - MECOM (NM_004991) rearrangement: c.581:PRKCI_c.376-48366:MEMCOMinv Note: The PRKCI - MECOM rearrangement is an inversion which results in the fusion of PRKCI exons 1-6 with MECOM exons 3-17. Its functional significance is undetermined.
MECOM	0	MSKCC-DMP	P-0037238-T01-IM6	MECOM-PRKCI fusion	yes	unknown		unknown	PRKCI (NM_002740) - MECOM (NM_004991) rearrangement: c.581:PRKCI_c.376-48366:MEMCOMinv Note: The PRKCI - MECOM rearrangement is an inversion which results in the fusion of PRKCI exons 1-6 with MECOM exons 3-17. Its functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0037404-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4963:EML4_c.3172+455:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-5 with ALK exons 20-29. This contains the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0037404-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4963:EML4_c.3172+455:ALKinv Note: The EML4 - ALK rearrangement is an inversion which results in the fusion of EML4 exons 1-5 with ALK exons 20-29. This contains the kinase domain of ALK.
GNAI2	0	MSKCC-DMP	P-0037477-T01-IM6	MYD88-GNAI2 fusion	yes	unknown		unknown	GNAI2 (NM_002070) - MYD88 (NM_002468) Rearrangement : c.465-109:GNAI2_c.540:MYD88dup Note: The GNAI2-MYD88 Rearrangement results in the duplication of exons1-4 of GNAI2 with exons3-5 of MYD88. The breakpoint in MYD88 is within exon3. Its functional significance is undetermined.
MYD88	0	MSKCC-DMP	P-0037477-T01-IM6	MYD88-GNAI2 fusion	yes	unknown		unknown	GNAI2 (NM_002070) - MYD88 (NM_002468) Rearrangement : c.465-109:GNAI2_c.540:MYD88dup Note: The GNAI2-MYD88 Rearrangement results in the duplication of exons1-4 of GNAI2 with exons3-5 of MYD88. The breakpoint in MYD88 is within exon3. Its functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0037577-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: c.1010-5036:ETV6_chr12:g.18819650del Note: The ETV6 rearrangement is a deletion of exons 6-8. The functional significance is undetermined.
ZFHX3	0	MSKCC-DMP	P-0037729-T01-IM6	ZFHX3-intragenic	yes	unknown		unknown	ZFHX3 (NM_006885) rearrangement: c.7061:ZFHX3_chr16:g.72798880del Note: The ZFHX3 rearrangement results in the deletion of exons 9-10. One of the breakpoints is within exon 9.
ETV1	0	MSKCC-DMP	P-0037729-T01-IM6	ETV1-intragenic	yes	unknown		unknown	ETV1 (NM_001163147) rearrangement: c.181+548:ETV1_chr7:g.6669540del Note: The ETV1 rearrangement results in the deletion of exons 5-12. The functional significance is unknown.
WHSC1	0	MSKCC-DMP	P-0038972-T01-IM6	WHSC1-intragenic	yes	unknown		in frame	WHSC1 (NM_001042424) rearrangement: c.1556-183:WHSC1_chr4:g.119207del Note: The WHSC1 rearrangement is a deletion of exons 1 - 6. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0039604-T01-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: c.2137-515:RET_chr10:g.54088195inv Note: The RET rearrangement is an inversion of exons 12 - 20. The rearrangement includes the kinase domain of RET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required.
DNMT3B	0	MSKCC-DMP	P-0039604-T01-IM6	DNMT3B-intragenic	yes	unknown		unknown	DNMT3B (NM_006892) rearrangement: t(16;20)(p13.13;q11.21)(chr16:g.11628924::chr20:g.31390225) Note: The DNMT3B rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0039604-T01-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.2062-394_c.3115-18dup Note: The EGFR rearrangement is a kinase domain duplication (KDD) alteration, involving exons 18-25.
KIF5B	0	MSKCC-DMP	P-0039941-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2040:KIF5B_c.2137-693:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0039941-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2040:KIF5B_c.2137-693:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
ERRFI1	0	MSKCC-DMP	P-0040258-T01-IM6	ERRFI1-intragenic	yes	unknown		unknown	ERRFI1 (NM_018948) rearrangement: c.1205:ERRFI1_chr1:g.8060312del Note: The ERRFI1 rearrangement is a deletion of exon 4. One of the breakpoints is within exon 4.
INPPL1	0	MSKCC-DMP	P-0040313-T01-IM6	INPPL1-intragenic	yes	unknown		unknown	INPPL1 (NM_001567) rearrangement: c.269:INPPL1_chr11:g.81893992inv Note: The INPPL1 rearrangement is an inversion of exons 3 - 28. One of the breakpoints is within exon 3. Functional significance is undetermined. Multiple rearrangements involving INPPL1 were detected in this sample and a more complex rearrangement resulting in a INPPL1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated.
Note	0	MSKCC-DMP	P-0040571-T01-IM6	Note-intragenic	yes	unknown		unknown	Note: The FAT1 rearrangement is a deletion of exons 13 - 27. FAT1 (NM_005245) rearrangement: c.9229+44:FAT1_chr4:g.186619246del
Note	0	MSKCC-DMP	P-0040576-T01-IM6	Note-intragenic	yes	unknown		unknown	Note: The NF1 rearrangement is an inversion of exons 47 - 58. Functional significance is undetermined. NF1 (NM_001042492) rearrangement: c.6921+26:NF1_chr17:g.29751233inv
EML4	0	MSKCC-DMP	P-0040576-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon5 fused with ALK exon20) : c.668-821:EML4_c.3173-927:ALKinv Note: The EML4-ALK fusion results in an in-frame fusion and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040576-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon5 fused with ALK exon20) : c.668-821:EML4_c.3173-927:ALKinv Note: The EML4-ALK fusion results in an in-frame fusion and includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0040732-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1832:EML4_c.3173-242:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040732-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1832:EML4_c.3173-242:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
CALR	0	MSKCC-DMP	P-0040990-T01-IM6	CALR-intragenic	yes	unknown		unknown	CALR (NM_004343) rearrangement: c.397+48:CALR_chr19:g.10884675inv Note: The CALR rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.
GLI1	0	MSKCC-DMP	P-0041052-T01-IM6	GLI1-intragenic	yes	unknown		unknown	GLI1 (NM_005269) rearrangement: c.442:GLI1_chr12:g.45085414dup Note: The GLI1 rearrangement is a duplication of exons 1 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.
MET	0	MSKCC-DMP	P-0041210-T01-IM6	MET-intragenic	yes	unknown		in frame	MET (NM_000245) rearrangement: c.1201-6894_c.1966-9del Note: The MET rearrangement is an intragenic deletion of exons 3 - 7. The rearrangement does not include the kinase domain of MET. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving MET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
CDK4	0	MSKCC-DMP	P-0041256-T02-IM6	CDK4-intragenic	yes	unknown		unknown	CDK4 (NM_000075) rearrangement: t(5;12)(p14.2;q14.1)(chr5:g.23876068::chr12:g.58143197) Note: The CDK4 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0041269-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.2159_c.3828dup Note: The NF1 rearrangement is an intragenic duplication of exons 18 - 28. The breakpoints are within exon 18 and exon 28. Functional significance is undetermined.
RECQL4	0	MSKCC-DMP	P-0041269-T01-IM6	LRRC24-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - LRRC24 (NM_001024678) rearrangement: c.1620+1:RECQL4_c.608-173:LRRC24dup Note: The RECQL4 - LRRC24 rearrangement is a duplication that results in a fusion of RECQL4 exons 1 - 9 to LRRC24 exon 5. One of the breakpoints is within RECQL4 exon 9. Functional significance is undetermined.
LRRC24	0	MSKCC-DMP	P-0041269-T01-IM6	LRRC24-RECQL4 fusion	yes	unknown		unknown	RECQL4 (NM_004260) - LRRC24 (NM_001024678) rearrangement: c.1620+1:RECQL4_c.608-173:LRRC24dup Note: The RECQL4 - LRRC24 rearrangement is a duplication that results in a fusion of RECQL4 exons 1 - 9 to LRRC24 exon 5. One of the breakpoints is within RECQL4 exon 9. Functional significance is undetermined.
MYEF2	0	MSKCC-DMP	P-0041387-T01-IM6	CALR-MYEF2 fusion	yes	unknown		unknown	MYEF2 (NM_016132) - CALR (NM_004343) rearrangement: t(15;19)(q21.1;p13.2)(chr15:g.48457161::chr19:g.13054420) Note: The MYEF2 - CALR rearrangement is a translocation that results in a fusion of MYEF2 exons 1 - 5 to CALR exons 8 - 9. One of the breakpoints is within CALR exon 8. Functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0041387-T01-IM6	CALR-MYEF2 fusion	yes	unknown		unknown	MYEF2 (NM_016132) - CALR (NM_004343) rearrangement: t(15;19)(q21.1;p13.2)(chr15:g.48457161::chr19:g.13054420) Note: The MYEF2 - CALR rearrangement is a translocation that results in a fusion of MYEF2 exons 1 - 5 to CALR exons 8 - 9. One of the breakpoints is within CALR exon 8. Functional significance is undetermined.
BLM	0	MSKCC-DMP	P-0041459-T01-IM6	BLM-intragenic	yes	unknown		unknown	BLM (NM_000057) rearrangement: c.231:BLM_chr15:g.83638536del Note: The BLM rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3.
NTRK1	0	MSKCC-DMP	P-0041484-T01-IM6	NTRK1-intragenic	yes	unknown		unknown	NTRK1 (NM_002529) rearrangement: c.1109:NTRK1_chr1:g.156627355inv Note: The NTRK1 rearrangement is an inversion of exons 1 - 8. One of the breakpoints is within exon 8. The rearrangement does not include the kinase domain of NTRK1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving NTRK1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
PAK1	0	MSKCC-DMP	P-0041535-T01-IM6	PAK1-intragenic	yes	unknown		in frame	PAK1 (NM_002576) rearrangement: c.191-650_c.439+11dup Note: The PAK1 rearrangement is an intragenic duplication of exons 3 - 4. The rearrangement does not include the kinase domain of PAK1. Functional significance is undetermined.
GLG1	0	MSKCC-DMP	P-0041624-T01-IM6	CDH1-GLG1 fusion	yes	unknown		unknown	GLG1 (NM_012201) - CDH1 (NM_004360) rearrangement: c.438+30436:GLG1_c.2026:CDH1inv Note: The GLG1 - CDH1 rearrangement is an inversion that results in a fusion of GLG1 exon 1 to CDH1 exons 13 - 16. One of the breakpoints is within CDH1 exon 13. Functional significance is undetermined.
CDH1	0	MSKCC-DMP	P-0041624-T01-IM6	CDH1-GLG1 fusion	yes	unknown		unknown	GLG1 (NM_012201) - CDH1 (NM_004360) rearrangement: c.438+30436:GLG1_c.2026:CDH1inv Note: The GLG1 - CDH1 rearrangement is an inversion that results in a fusion of GLG1 exon 1 to CDH1 exons 13 - 16. One of the breakpoints is within CDH1 exon 13. Functional significance is undetermined.
MDC1	0	MSKCC-DMP	P-0041624-T01-IM6	PPP1R10-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) - PPP1R10 (NM_002714) rearrangement: c.4358:MDC1_c.854-290:PPP1R10del Note: The MDC1 - PPP1R10 rearrangement is a deletion that results in a fusion of MDC1 exons 1 - 10 to PPP1R10 exons 11 - 20. One of the breakpoints is within MDC1 exon 10. Functional significance is undetermined.
PPP1R10	0	MSKCC-DMP	P-0041624-T01-IM6	PPP1R10-MDC1 fusion	yes	unknown		unknown	MDC1 (NM_014641) - PPP1R10 (NM_002714) rearrangement: c.4358:MDC1_c.854-290:PPP1R10del Note: The MDC1 - PPP1R10 rearrangement is a deletion that results in a fusion of MDC1 exons 1 - 10 to PPP1R10 exons 11 - 20. One of the breakpoints is within MDC1 exon 10. Functional significance is undetermined.
RAD51D	0	MSKCC-DMP	P-0041852-T02-IM6	SPAG9-RAD51D fusion	yes	unknown		in frame	RAD51D (NM_133629) - SPAG9 (NM_001130528) rearrangement: c.82+31:RAD51D_c.3700+200:SPAG9dup Note: The RAD51D - SPAG9 rearrangement is a duplication that results in a fusion of RAD51D exon 1 to SPAG9 exons 28 - 30. The fusion is predicted to be in frame. Functional significance is undetermined.
SPAG9	0	MSKCC-DMP	P-0041852-T02-IM6	SPAG9-RAD51D fusion	yes	unknown		in frame	RAD51D (NM_133629) - SPAG9 (NM_001130528) rearrangement: c.82+31:RAD51D_c.3700+200:SPAG9dup Note: The RAD51D - SPAG9 rearrangement is a duplication that results in a fusion of RAD51D exon 1 to SPAG9 exons 28 - 30. The fusion is predicted to be in frame. Functional significance is undetermined.
CEBPA	0	MSKCC-DMP	P-0041875-T01-IM6	CEBPA-intragenic	yes	unknown		unknown	CEBPA (NM_004364) rearrangement: c.274:CEBPA_chr19:g.33469519inv Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.
ASXL2	0	MSKCC-DMP	P-0042048-T01-IM6	ASXL2-intragenic	yes	unknown		unknown	ASXL2 (NM_018263) rearrangement: c.404-6653_c.3872inv Note: The ASXL2 rearrangement is an intragenic inversion of exons 5 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0042048-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3652:TMPRSS2_c.39+59577:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
ERG	0	MSKCC-DMP	P-0042048-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3652:TMPRSS2_c.39+59577:ERGdel Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 4 - 11. Functional significance is undetermined. The structural variant involves the ERG non-canonical transcript (NM_004449).
FGFR2	0	MSKCC-DMP	P-0042241-T01-IM6	ZMYM4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ZMYM4 (NM_005095) fusion: t(1;10)(p34.3;q26.13)(chr1:g.35833702::chr10:g.123242889) Note: The FGFR2 - ZMYM4 fusion involves FGFR2 exons 1 - 17 and ZMYM4 exons 6 - 30. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
ZMYM4	0	MSKCC-DMP	P-0042241-T01-IM6	ZMYM4-FGFR2 fusion	yes	unknown		in frame	FGFR2 (NM_000141) - ZMYM4 (NM_005095) fusion: t(1;10)(p34.3;q26.13)(chr1:g.35833702::chr10:g.123242889) Note: The FGFR2 - ZMYM4 fusion involves FGFR2 exons 1 - 17 and ZMYM4 exons 6 - 30. The fusion is predicted to be in frame and includes the kinase domain of FGFR2.
ARID5B	0	MSKCC-DMP	P-0042407-T01-IM6	ARID5B-intragenic	yes	unknown		unknown	ARID5B (NM_032199) rearrangement: c.276+19:ARID5B_chr10:g.63644443dup Note: The ARID5B rearrangement is a duplication of exons 1 - 2. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0042407-T01-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.5442_c.7714-136dup Note: The ANKRD11 rearrangement is an intragenic duplication of exons 9 - 11. One of the breakpoints is within exon 9. Functional significance is undetermined.
RICTOR	0	MSKCC-DMP	P-0042407-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: t(5;X)(p13.1;q26.1)(chr5:g.38943061::chrX:g.129248290) Note: The RICTOR rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.
WIPI2	0	MSKCC-DMP	P-0042620-T01-IM6	CALR-WIPI2 fusion	yes	unknown		unknown	WIPI2 (NM_016003) - CALR (NM_004343) rearrangement: t(7;19)(p22.1;p13.2)(chr7:g.5268169::chr19:g.13049530) Note: The WIPI2 - CALR rearrangement is a translocation that results in a fusion of WIPI2 exons 1 - 11 to CALR exons 1 - 9. One of the breakpoints is within CALR exon 1. Functional significance is undetermined.
CALR	0	MSKCC-DMP	P-0042620-T01-IM6	CALR-WIPI2 fusion	yes	unknown		unknown	WIPI2 (NM_016003) - CALR (NM_004343) rearrangement: t(7;19)(p22.1;p13.2)(chr7:g.5268169::chr19:g.13049530) Note: The WIPI2 - CALR rearrangement is a translocation that results in a fusion of WIPI2 exons 1 - 11 to CALR exons 1 - 9. One of the breakpoints is within CALR exon 1. Functional significance is undetermined.
MAP3K13	0	MSKCC-DMP	P-0042664-T01-IM6	MAP3K13-intragenic	yes	unknown		unknown	MAP3K13 (NM_004721) rearrangement: c.1291_c.1643+1219del Note: The MAP3K13 rearrangement is an intragenic deletion of exons 8 - 10. One of the breakpoints is within exon 8. The rearrangement does not include the kinase domain of MAP3K13. Functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0042755-T01-IM6	ERBB3-intragenic	yes	unknown		unknown	ERBB3 (NM_001982) rearrangement: t(8;12)(q12.1;q13.2)(chr8:g.56386721::chr12:g.56494888) Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 27. Functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0043000-T02-IM6	MED12-intragenic	yes	unknown		unknown	MED12 (NM_005120) rearrangement: t(13;X)(q14.3;q13.1)(chr13:g.53230412::chrX:g.70356437) Note: The MED12 rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0043007-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.2544+168:KIF5B_c.2136+629:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 23 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0043007-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.2544+168:KIF5B_c.2136+629:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 23 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
STK11	0	MSKCC-DMP	P-0043153-T01-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.291-18:STK11_chr19:g.1202211del Note: The STK11 rearrangement is a deletion of exon 1. The rearrangement includes a part of the kinase domain of STK11.
STK19	0	MSKCC-DMP	P-0043250-T01-IM6	STK19-intragenic	yes	unknown		unknown	STK19 (NM_004197) rearrangement: c.901+5:STK19_chr6:g.31981147del Note: The STK19 rearrangement is a deletion of exons 7 - 8. Functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0043277-T01-IM6	PAK1-intragenic	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.885+1210_c.1018del Note: The PAK1 rearrangement is an intragenic deletion of exons 10 - 11. One of the breakpoints is within exon 11. The rearrangement includes a part of the kinase domain of PAK1. Functional significance is undetermined.
KEAP1	0	MSKCC-DMP	P-0043277-T01-IM6	KEAP1-intragenic	yes	unknown		unknown	KEAP1 (NM_203500) rearrangement: c.1:KEAP1_chr19:g.10618964del Note: The KEAP1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.
POLD1	0	MSKCC-DMP	P-0043277-T01-IM6	POLD1-intragenic	yes	unknown		unknown	POLD1 (NM_002691) rearrangement: c.84:POLD1_chr19:g.50186003inv Note: The POLD1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.
SUFU	0	MSKCC-DMP	P-0043314-T02-IM6	SUFU-intragenic	yes	unknown		out of frame	SUFU (NM_016169) rearrangement: c.455-917_c.684-60del Note: The SUFU rearrangement is an intragenic deletion of exons 4 - 5.
EGFR	0	MSKCC-DMP	P-0043314-T02-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.88+53282_c.890-398del Note: The EGFR rearrangement is a vIII alteration.
ESR1	0	MSKCC-DMP	P-0043374-T01-IM6	ESR1-intragenic	yes	unknown		unknown	ESR1 (NM_001122740) rearrangement: c.1236-8227_c.1298inv Note: The ESR1 rearrangement is an intragenic inversion of exon 7. One of the breakpoints is within exon 7. Functional significance is undetermined.
MED12	0	MSKCC-DMP	P-0043502-T02-IM6	MED12-intragenic	yes	unknown		unknown	MED12 (NM_005120) rearrangement: c.3524:MED12_chrX:g.68183411inv Note: The MED12 rearrangement is an inversion of exons 1 - 25. One of the breakpoints is within exon 25. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0043699-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1064:TMPRSS2_c.18+19751:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0043699-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1064:TMPRSS2_c.18+19751:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.
MITF	0	MSKCC-DMP	P-0043699-T01-IM6	MITF-intragenic	yes	unknown		unknown	MITF (NM_198159) rearrangement: c.1161+99:MITF_chr3:g.188085953inv Note: The MITF rearrangement is an inversion of exon 10. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0043854-T01-IM6	MET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - MET (NM_000245) fusion: t(7;10)(q31.2;p11.22)(chr7:g.116412098::chr10:g.32304904) Note: The KIF5B - MET fusion involves KIF5B exons 1 - 24 and MET exons 15 - 21. The fusion is predicted to be in frame and includes the kinase domain of MET.
MET	0	MSKCC-DMP	P-0043854-T01-IM6	MET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - MET (NM_000245) fusion: t(7;10)(q31.2;p11.22)(chr7:g.116412098::chr10:g.32304904) Note: The KIF5B - MET fusion involves KIF5B exons 1 - 24 and MET exons 15 - 21. The fusion is predicted to be in frame and includes the kinase domain of MET.
EP300	0	MSKCC-DMP	P-0043869-T02-IM6	EP300-intragenic	yes	unknown		in frame	EP300 (NM_001429) rearrangement: c.3728+63_c.3806+571del Note: The EP300 rearrangement is an intragenic deletion of exon 22.
STK11	0	MSKCC-DMP	P-0044108-T02-IM6	STK11-intragenic	yes	unknown		unknown	STK11 (NM_000455) rearrangement: c.451:STK11_chr19:g.1142410del Note: The STK11 rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3. The rearrangement includes a part of the kinase domain of STK11.
TERT	0	MSKCC-DMP	P-0044140-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT (NM_198253) rearrangement: t(3;5)(q22.2;p15.33)(chr3:g.3:134091986::chr5:g.1295406) Note: The TERT rearrangement is a translocation with a breakpoint in the promoter region. The functional significance is undetermined.
FGFR4	0	MSKCC-DMP	P-0044207-T01-IM6	FGFR4-intragenic	yes	unknown		unknown	FGFR4 (NM_213647) rearrangement: c.2399:FGFR4_chr5:g.51357750inv Note: The FGFR4 rearrangement is an inversion of exons 1 - 18. One of the breakpoints is within exon 18. The rearrangement includes the kinase domain of FGFR4. Functional significance is undetermined.
KLF4	0	MSKCC-DMP	P-0044328-T01-IM6	KLF4-intragenic	yes	unknown		unknown	KLF4 (NM_004235) rearrangement: c.1199:KLF4_chr9:g.108890966inv Note: The KLF4 rearrangement is an inversion of exons 4 - 5. One of the breakpoints is within exon 4. Functional significance is undetermined.
COL15A1	0	MSKCC-DMP	P-0044518-T01-IM6	TGFBR1-COL15A1 fusion	yes	unknown		unknown	COL15A1 (NM_001855) - TGFBR1 (NM_004612) rearrangement: c.804+1113:COL15A1_c.596:TGFBR1del Note: The COL15A1 - TGFBR1 rearrangement is a deletion that results in a fusion of COL15A1 exons 1 - 5 to TGFBR1 exons 4 - 9. One of the breakpoints is within TGFBR1 exon 4. The fusion includes the kinase domain of TGFBR1.
TGFBR1	0	MSKCC-DMP	P-0044518-T01-IM6	TGFBR1-COL15A1 fusion	yes	unknown		unknown	COL15A1 (NM_001855) - TGFBR1 (NM_004612) rearrangement: c.804+1113:COL15A1_c.596:TGFBR1del Note: The COL15A1 - TGFBR1 rearrangement is a deletion that results in a fusion of COL15A1 exons 1 - 5 to TGFBR1 exons 4 - 9. One of the breakpoints is within TGFBR1 exon 4. The fusion includes the kinase domain of TGFBR1.
TERT	0	MSKCC-DMP	P-0044885-T01-IM6	TERT-intragenic	yes	unknown		unknown	TERT(NM_198253) rearrangement: t(5;12)(p15.33;q14.1)(chr5:g.1295424::chr12:g.58874633) Note: The TERT rearrangement is a translocation with breakpoint within promoter region of TERT. The functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0045005-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: t(6;20)(p23;q12)(chr6:g.14960811::chr20:g.40727119) Note: The PTPRT rearrangement is a translocation with a breakpoint in exon 28. Functional significance is undetermined.
BABAM1	0	MSKCC-DMP	P-0046454-T01-IM6	BABAM1-intragenic	yes	unknown		unknown	BABAM1 (NM_001033549) rearrangement: c.545-696_c.698inv Note: The BABAM1 rearrangement is an intragenic inversion of exons 6 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.
TFG	0	MSKCC-DMP	P-0019303-T02-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID:19797732  Lab Notes Run Number: ArcherV3-CLIN-20190021 Macro-dissection: Unknown
GPR128	0	MSKCC-DMP	P-0019303-T02-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_006070) and GPR128 Exon2 (NM_032787). PMID:19797732  Lab Notes Run Number: ArcherV3-CLIN-20190021 Macro-dissection: Unknown
EGFR	0	MSKCC-DMP	P-0039604-T01-IM6	EGFR-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:  POSITIVE FOR AN ONCOGENIC ISOFORM THE INVESTIGATIONAL PANEL:  EGFR Kinase domain duplication involving Exons 18-25 (NM_005228). PMID: 26286086 Lab Notes Run Number: ArcherV3-CLIN-20190053 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0040649-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:  MET Exon 14 skipping (NM_000245). Lab Notes Run Number: Archerv3-CLIN-20190076 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0041210-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORMS IN THE INVESTIGATIONAL PANEL: A deletion of MET Exons 3-8 (NM_000245) was detected. Lab Notes Run Number: Archerv3-CLIN-20190083 Macro-dissection: Performed
MYB	0	MSKCC-DMP	P-0041411-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon15 (NM_001130173) and NFIB Exon9 (NM_001190738). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
NFIB	0	MSKCC-DMP	P-0041411-T01-IM6	NFIB-MYB fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: MYB-NFIB fusion. Note: The rearrangement is a fusion between genes MYB Exon15 (NM_001130173) and NFIB Exon9 (NM_001190738). Lab Notes Run Number: Archerv3-CLIN-20190087 Macro-dissection: Not Performed
MET	0	MSKCC-DMP	P-0043956-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL:    MET Exon14 (NM_000245) Deletion  Lab Notes Run Number: Archerv3-CLIN-20190128 Macro-dissection: Not Performed
ERRFI1	0	MSKCC-DMP	P-0006713-T01-IM5	ERRFI1-intragenic	yes	unknown		unknown	ERRFI1 (NM_018948) rearrangement: t(1;17)(p36.23;p13.1)(chr1:g.8085068::chr17:g.7619057) The ERRFI1 (NM_018948) rearrangement is a translocation which results in a truncated ERRFI1. The functional significance is undetermined.
MAP2K1	0	MSKCC-DMP	P-0007966-T02-IM6	MAP2K1-intragenic	yes	unknown		unknown	MAP2K1 (NM_002755) rearrangement : c.80+29:MAP2K1_chr15:g.67250578del Note: The MAP2K1 rearrangement is a deletion of exons 2-11. Its functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0013299-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) Fusion(EML4 exon5 fused with ALK exon20) : c.667+1302:EML4_c.3173-644:ALKinv Note: The EML4-ALK Fusion is predicted to be in -frame and includes the protein kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0013299-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) -ALK (NM_004304) Fusion(EML4 exon5 fused with ALK exon20) : c.667+1302:EML4_c.3173-644:ALKinv Note: The EML4-ALK Fusion is predicted to be in -frame and includes the protein kinase domain of ALK.
TSC1	0	MSKCC-DMP	P-0013299-T02-IM6	COL5A1-TSC1 fusion	yes	unknown		unknown	TSC1 (NM_000368) - COL5A1 (NM_000093) rearrangement: c.17:TSC1_c.2899-203:COL5A1del The TSC1 - COL5A1 rearrangement is a deletion of TSC1 exons 1-3 and COL5A1 exons 1-36. One of the breakpoints is within exon 3 of TSC1. The functional significance is undetermined.
COL5A1	0	MSKCC-DMP	P-0013299-T02-IM6	COL5A1-TSC1 fusion	yes	unknown		unknown	TSC1 (NM_000368) - COL5A1 (NM_000093) rearrangement: c.17:TSC1_c.2899-203:COL5A1del The TSC1 - COL5A1 rearrangement is a deletion of TSC1 exons 1-3 and COL5A1 exons 1-36. One of the breakpoints is within exon 3 of TSC1. The functional significance is undetermined.
ERBB3	0	MSKCC-DMP	P-0021785-T01-IM6	ZCRB1-ERBB3 fusion	yes	unknown		in frame	ERBB3 (NM_001982) - ZCRB1 (NM_033114) Rearrangement : c.3201+46:ERBB3_c.333+785:ZCRB1inv Note: The ERBB3 - ZCRB1 Rearrangement results in the fusion of ERBB3 exons 1-26 with ZCRB1 exons 6-8. The rearrangement includes the protein kinase domain of ERBB3.
ZCRB1	0	MSKCC-DMP	P-0021785-T01-IM6	ZCRB1-ERBB3 fusion	yes	unknown		in frame	ERBB3 (NM_001982) - ZCRB1 (NM_033114) Rearrangement : c.3201+46:ERBB3_c.333+785:ZCRB1inv Note: The ERBB3 - ZCRB1 Rearrangement results in the fusion of ERBB3 exons 1-26 with ZCRB1 exons 6-8. The rearrangement includes the protein kinase domain of ERBB3.
VPS26A	0	MSKCC-DMP	P-0021788-T01-IM6	FGFR2-VPS26A fusion	yes	unknown		in frame	VPS26A (NM_004896) - FGFR2 (NM_000141) Rearrangement : c.4-1035:VPS26A_c.2301+986:FGFR2inv Note: The VPS26A - FGFR2 Rearrangement results in the fusion of exon1 of VPS26A with FGFR2 exon 18. The rearrangement includes the protein kinase domain of FGFR2.
FGFR2	0	MSKCC-DMP	P-0021788-T01-IM6	FGFR2-VPS26A fusion	yes	unknown		in frame	VPS26A (NM_004896) - FGFR2 (NM_000141) Rearrangement : c.4-1035:VPS26A_c.2301+986:FGFR2inv Note: The VPS26A - FGFR2 Rearrangement results in the fusion of exon1 of VPS26A with FGFR2 exon 18. The rearrangement includes the protein kinase domain of FGFR2.
EML4	0	MSKCC-DMP	P-0022184-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1315+1386:EML4_c.3173-641:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0022184-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1315+1386:EML4_c.3173-641:ALKinv Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.
APC	0	MSKCC-DMP	P-0022184-T01-IM6	APC-intragenic	yes	unknown		unknown	APC (NM_000038) rearrangement: c.2529_c.6192del Note: The APC rearrangement is an intragenic deletion of exon 16. Both breakpoints are within exon. The functional significance is undetermined.
CD74	0	MSKCC-DMP	P-0024572-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion( CD74 exons 1-6 fused to ROS1 exons 33-43): t(5;6)(q32;q22.1)(chr5:g.149783583::chr6:g.117649758) Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1
ROS1	0	MSKCC-DMP	P-0024572-T01-IM6	ROS1-CD74 fusion	yes	unknown		out of frame	CD74 (NM_001025159) - ROS1 (NM_002944) fusion( CD74 exons 1-6 fused to ROS1 exons 33-43): t(5;6)(q32;q22.1)(chr5:g.149783583::chr6:g.117649758) Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1
STK11	0	MSKCC-DMP	P-0025917-T02-IM6	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement: c.862+268_c.921-34del Note: The STK11 rearrangement is an intragenic deletion of exon 7. Its functional significance is undetermined.
EGFL7	0	MSKCC-DMP	P-0026906-T02-IM6	EGFL7-intragenic	yes	unknown		unknown	EGFL7 (NM_201446) rearrangement: c.636+258_c.*49inv Note: The EGFL7 rearrangement results in the inversion of exons 7-9. The functional significance is undetermined.
RIT1	0	MSKCC-DMP	P-0029514-T01-IM6	GON4L-RIT1 fusion	yes	unknown		unknown	RIT1 (NM_006912) - GON4L (NM_001037533) rearrangement: c.376:RIT1_c.4726+352:GON4Ldel Note: The RIT1 - GON4L rearrangement is a deletion that results in the fusion of RIT1 exons 1-5 to GON4L exons 23-32. One of the breakpoints is within RIT1 exon 5. The functional significance is undetermined.
GON4L	0	MSKCC-DMP	P-0029514-T01-IM6	GON4L-RIT1 fusion	yes	unknown		unknown	RIT1 (NM_006912) - GON4L (NM_001037533) rearrangement: c.376:RIT1_c.4726+352:GON4Ldel Note: The RIT1 - GON4L rearrangement is a deletion that results in the fusion of RIT1 exons 1-5 to GON4L exons 23-32. One of the breakpoints is within RIT1 exon 5. The functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0031449-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.55+3413:TMPRSS2_c.c.40-62452:ERGdel Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.
ERG	0	MSKCC-DMP	P-0031449-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.55+3413:TMPRSS2_c.c.40-62452:ERGdel Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.
CDKN1B	0	MSKCC-DMP	P-0036932-T01-IM6	CDKN1B-intragenic	yes	unknown		unknown	CDKN1B (NM_004064) rearrangement: c.475+58:CDKN1B_chr12:g.14676500del Note: The CDKN1B rearrangement is a deletion of exon 2. The functional significance is undetermined.
FOXP1	0	MSKCC-DMP	P-0037229-T01-IM6	FOXP1-intragenic	yes	unknown		unknown	FOXP1 (NM_001244814) rearrangement: c.1652+397:FOXP1_chr3:g.71306509del Note: The FOXP1 rearrangement is a deletion of exons 1-14. Its functional significance is undetermined.
RB1	0	MSKCC-DMP	P-0037230-T01-IM6	RB1-intragenic	yes	unknown		out of frame	RB1 (NM_000321) rearrangement: c.1498+78_c.1695+10859del Note: The RB1 rearrangement is an intragenic deletion of exon 17. Its functional significance is undetermined.
CHEK2	0	MSKCC-DMP	P-0037297-T01-IM6	CHEK2-intragenic	yes	unknown		unknown	CHEK2 (NM_007194) rearrangement: c.1264_chr22:g.29592609del Note: The CHEK2 rearrangement is a deletion that includes CHEK2 exons 1-12. One of the breakpoints is within exon 12.
DDR2	0	MSKCC-DMP	P-0037322-T01-IM6	DDR2-intragenic	yes	unknown		unknown	DDR2 (NM_006182) rearrangement: t(1;2)(q23.3;q37.3)(chr1:g.162740087::chr2:g.240384262) Note: The DDR2 rearrangement is a translocation with a breakpoint within DDR2 intron 11. The functional significance is undetermined.
DEPDC7	0	MSKCC-DMP	P-0037338-T01-IM6	SMARCB1-DEPDC7 fusion	yes	unknown		unknown	DEPDC7 (NM_001077242) - SMARCB1 (NM_003073) rearrangement: t(11;22)(p13;q11.23)(chr11:g.33040227::chr22:g.24133958) Note: The BEPDC7 - SMARCB1 rearrangement is a translocation which may result in the fusion of DEPDC7 exon 1 with SMARCB1 exons 2-9. One of the breakpoints is within SMARCB1 exon 2. Its functional significance is undetermined. Multiple rearrangements involving SMARCB1 were detected in this sample and a more complex rearrangement resulting in additional SMARCB1 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
SMARCB1	0	MSKCC-DMP	P-0037338-T01-IM6	SMARCB1-DEPDC7 fusion	yes	unknown		unknown	DEPDC7 (NM_001077242) - SMARCB1 (NM_003073) rearrangement: t(11;22)(p13;q11.23)(chr11:g.33040227::chr22:g.24133958) Note: The BEPDC7 - SMARCB1 rearrangement is a translocation which may result in the fusion of DEPDC7 exon 1 with SMARCB1 exons 2-9. One of the breakpoints is within SMARCB1 exon 2. Its functional significance is undetermined. Multiple rearrangements involving SMARCB1 were detected in this sample and a more complex rearrangement resulting in additional SMARCB1 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
YES1	0	MSKCC-DMP	P-0037338-T01-IM6	ADRBK2-YES1 fusion	yes	unknown		unknown	YES1 (NM_005433) - ADRBK2 (NM_005160) rearrangement: t(18;22)(p11.32;q12.1)(chr18:g.742917::chr22:g.26044366) Note: The YES1 - ADRBK2 rearrangement is a translocation which may result in the fusion of YES1 exons 1-8 with ADRBK2 exons 4-21. One of the breakpoints is within YES1 exon 8. Its functional significance is undetermined. Multiple rearrangements involving YES1 were detected in this sample and a more complex rearrangement resulting in additional YES1 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ADRBK2	0	MSKCC-DMP	P-0037338-T01-IM6	ADRBK2-YES1 fusion	yes	unknown		unknown	YES1 (NM_005433) - ADRBK2 (NM_005160) rearrangement: t(18;22)(p11.32;q12.1)(chr18:g.742917::chr22:g.26044366) Note: The YES1 - ADRBK2 rearrangement is a translocation which may result in the fusion of YES1 exons 1-8 with ADRBK2 exons 4-21. One of the breakpoints is within YES1 exon 8. Its functional significance is undetermined. Multiple rearrangements involving YES1 were detected in this sample and a more complex rearrangement resulting in additional YES1 fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ANKRD11	0	MSKCC-DMP	P-0037556-T02-IM6	ANKRD11-intragenic	yes	unknown		unknown	ANKRD11 (NM_013275) rearrangement: c.226+62:ANKRD11_chr16:g.64001177inv Note: The ANKRD11 rearrangement is an inversion of exons 5-13. Its functional significance is undetermined.
UPF1	0	MSKCC-DMP	P-0037639-T01-IM6	ZC3H7B-UPF1 fusion	yes	unknown		unknown	UPF1 (NM_002911) - ZC3H7B (NM_017590) rearrangement: t(19,22)(p13.11;q13.2)(chr19:g.18976550::chr22:g.41744573) Note: The UPF1 rearrangement is a translocation that results in a fusion of UPF1 exons 1-22 to ZC3H7B exons 16-23. One of the breakpoints is within UPF1 exon 22. The functional significance is undetermined.
ZC3H7B	0	MSKCC-DMP	P-0037639-T01-IM6	ZC3H7B-UPF1 fusion	yes	unknown		unknown	UPF1 (NM_002911) - ZC3H7B (NM_017590) rearrangement: t(19,22)(p13.11;q13.2)(chr19:g.18976550::chr22:g.41744573) Note: The UPF1 rearrangement is a translocation that results in a fusion of UPF1 exons 1-22 to ZC3H7B exons 16-23. One of the breakpoints is within UPF1 exon 22. The functional significance is undetermined.
SPEN	0	MSKCC-DMP	P-0037674-T01-IM6	SPEN-intragenic	yes	unknown		unknown	SPEN (NM_015001) rearrangement: c.6550:SPEN_chr1:g.5804200inv Note: The SPEN rearrangement results in the inversion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.
PAK1	0	MSKCC-DMP	P-0037728-T01-IM6	PAK1-intragenic	yes	unknown		unknown	PAK1 (NM_002576) rearrangement: c.1413+172:PAK1_chr11:g.97205904del Note: The PAK1  rearrangement results in the deletion of exons 1-13. The functional significance is undetermined.
BIRC3	0	MSKCC-DMP	P-0037728-T01-IM6	BIRC3-intragenic	yes	unknown		unknown	BIRC3 (NM_182962) rearrangement: t(11;12)(q22.2;q21.1)(chr11:g.102195780::chr12:g.74859022) Note: The BIRC3 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.
NAB2	0	MSKCC-DMP	P-0037728-T01-IM6	NAB2-intragenic	yes	unknown		unknown	NAB2 (NM_005967) rearrangement: t(12;X)(q13.3;p22.11)(chr12:g.57486173::chrX:g.23509870) Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 2. The functional significance is undetermined.
TBX3	0	MSKCC-DMP	P-0037728-T01-IM6	TBX3-intragenic	yes	unknown		unknown	TBX3 (NM_016569) rearrangement: t(12;Y)(q24.21;q11.223)(chr12:g.115109879::chrY:g.22716517) Note: The TBX3 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.
EPS15	0	MSKCC-DMP	P-0037901-T01-IM6	NTRK1-EPS15 fusion	yes	unknown		in frame	EPS15 (NM_001981) - NTRK1 (NM_002529) rearrangement: c.2119+1240:EPS15_c.1195+20:NTRK1inv Note: The EPS15 - NTRK1 rearrangement is an inversion that results in the in-frame fusion of EPS15 exons 1-21 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
NTRK1	0	MSKCC-DMP	P-0037901-T01-IM6	NTRK1-EPS15 fusion	yes	unknown		in frame	EPS15 (NM_001981) - NTRK1 (NM_002529) rearrangement: c.2119+1240:EPS15_c.1195+20:NTRK1inv Note: The EPS15 - NTRK1 rearrangement is an inversion that results in the in-frame fusion of EPS15 exons 1-21 with NTRK1 exons 10-17 and includes the kinase domain of NTRK1. The functional significance is undetermined.
PIK3CA	0	MSKCC-DMP	P-0038398-T03-IM6	NAALADL2-PIK3CA fusion	yes	unknown		unknown	PIK3CA (NM_006218) - NAALADL2 (NM_207015) rearrangement: c.3190:PIK3CA_c.43+3905:NAALADL2dup Note: The PIK3CA - NAALADL2 rearrangement is a duplication that results in a fusion of PIK3CA exons 1 - 21 to NAALADL2 exons 2 - 14. One of the breakpoints is within PIK3CA exon 21. Functional significance is undetermined.
NAALADL2	0	MSKCC-DMP	P-0038398-T03-IM6	NAALADL2-PIK3CA fusion	yes	unknown		unknown	PIK3CA (NM_006218) - NAALADL2 (NM_207015) rearrangement: c.3190:PIK3CA_c.43+3905:NAALADL2dup Note: The PIK3CA - NAALADL2 rearrangement is a duplication that results in a fusion of PIK3CA exons 1 - 21 to NAALADL2 exons 2 - 14. One of the breakpoints is within PIK3CA exon 21. Functional significance is undetermined.
KIF5B	0	MSKCC-DMP	P-0038961-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-293:KIF5B_c.2136+591:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0038961-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-293:KIF5B_c.2136+591:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
STK11	0	MSKCC-DMP	P-0039650-T01-IM6	STK11-intragenic	yes	unknown		out of frame	STK11 (NM_000455) rearrangement: c.920+90_c.1108+1006del Note: The STK11 rearrangement is an intragenic deletion of exon 8. The rearrangement includes a part of the kinase domain of STK11.
TSC1	0	MSKCC-DMP	P-0039992-T01-IM6	TSC1-intragenic	yes	unknown		unknown	TSC1 (NM_000368) rearrangement: c.2892:TSC1_chr9:g.135804870dup Note: The TSC1 rearrangement is a duplication of exons 1 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0040261-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1340:EML4_c.3173-709:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040261-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1340:EML4_c.3173-709:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040309-T01-IM6	ALK-intragenic	yes	unknown		unknown	ALK (NM_004304) rearrangement: c.3172+946:ALK_chr2:g.34064604inv Note: The ALK rearrangement is an inversion of exons 1 - 19. The rearrangement does not include the kinase domain of ALK. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ALK is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
RICTOR	0	MSKCC-DMP	P-0040382-T01-IM6	RICTOR-intragenic	yes	unknown		unknown	RICTOR (NM_152756) rearrangement: c.1400+110:RICTOR_chr5:g.45655385inv Note: The RICTOR rearrangement is an inversion of exons 1 - 16. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0040570-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-2504:EML4_c.3172+167:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040570-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-2504:EML4_c.3172+167:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
AXIN2	0	MSKCC-DMP	P-0040596-T01-IM6	AXIN2-intragenic	yes	unknown		unknown	AXIN2 (NM_004655) rearrangement: c.1495:AXIN2_chr17:g.63504771del Note: The AXIN2 rearrangement is a deletion of exons 6 - 11. One of the breakpoints is within exon 6.
EML4	0	MSKCC-DMP	P-0040600-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1795:EML4_c.3172+639:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0040600-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1795:EML4_c.3172+639:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 5 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
CDH3	0	MSKCC-DMP	P-0041037-T01-IM6	CDH1-CDH3 fusion	yes	unknown		out of frame	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-14482:CDH3_c.2440-54:CDH1del Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exon 16.
CDH1	0	MSKCC-DMP	P-0041037-T01-IM6	CDH1-CDH3 fusion	yes	unknown		out of frame	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-14482:CDH3_c.2440-54:CDH1del Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exon 16.
ROS1	0	MSKCC-DMP	P-0041037-T01-IM6	ROS1-intragenic	yes	unknown		unknown	ROS1 (NM_002944) rearrangement: c.5080-420:ROS1_chr6:g.119045740del Note: The ROS1 rearrangement is a deletion of exons 1 - 30. The rearrangement does not include the kinase domain of ROS1. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving ROS1 is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
MYOM1	0	MSKCC-DMP	P-0041247-T01-IM6	CRLF2-MYOM1 fusion	yes	unknown		out of frame	MYOM1 (NM_003803) - CRLF2 (NM_022148) rearrangement: t(18;X)(p11.31;p22.33)(chr18:g.3191087::chrX:g.1315073) Note: The MYOM1 - CRLF2 rearrangement is a translocation that results in a fusion of MYOM1 exons 1 - 3 to CRLF2 exon 6. Functional significance is undetermined.
CRLF2	0	MSKCC-DMP	P-0041247-T01-IM6	CRLF2-MYOM1 fusion	yes	unknown		out of frame	MYOM1 (NM_003803) - CRLF2 (NM_022148) rearrangement: t(18;X)(p11.31;p22.33)(chr18:g.3191087::chrX:g.1315073) Note: The MYOM1 - CRLF2 rearrangement is a translocation that results in a fusion of MYOM1 exons 1 - 3 to CRLF2 exon 6. Functional significance is undetermined.
ATRX	0	MSKCC-DMP	P-0041247-T01-IM6	ATRX-intragenic	yes	unknown		unknown	ATRX (NM_000489) rearrangement: c.2160_c.3736+115inv Note: The ATRX rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.
ETV6	0	MSKCC-DMP	P-0041422-T01-IM6	ETV6-intragenic	yes	unknown		unknown	ETV6 (NM_001987) rearrangement: t(12;14)(p13.2;q32.33)(chr12:g.12030747::chr14:g.106257006) Note: The ETV6 rearrangement is a translocation with a breakpoint in intron 5. Multiple rearrangements involving ETV6 were detected in this sample and a more complex rearrangement involving ETV6 is possible. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0041513-T01-IM6	IRAK3-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - IRAK3 (NM_007199) rearrangement: c.6888:KMT2D_c.316+2751:IRAK3inv Note: The KMT2D - IRAK3 rearrangement is an inversion that results in a fusion of KMT2D exons 1 - 31 to IRAK3 exons 3 - 12. One of the breakpoints is within KMT2D exon 31. Functional significance is undetermined. Multiple rearrangements involving KMT2D were detected in this sample and a more complex rearrangement resulting in additional KMT2D fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
IRAK3	0	MSKCC-DMP	P-0041513-T01-IM6	IRAK3-KMT2D fusion	yes	unknown		unknown	KMT2D (NM_003482) - IRAK3 (NM_007199) rearrangement: c.6888:KMT2D_c.316+2751:IRAK3inv Note: The KMT2D - IRAK3 rearrangement is an inversion that results in a fusion of KMT2D exons 1 - 31 to IRAK3 exons 3 - 12. One of the breakpoints is within KMT2D exon 31. Functional significance is undetermined. Multiple rearrangements involving KMT2D were detected in this sample and a more complex rearrangement resulting in additional KMT2D fusions is possible. Additional testing by an alternative method is recommended, if clinically indicated.
ABCC4	0	MSKCC-DMP	P-0041513-T01-IM6	MDM2-ABCC4 fusion	yes	unknown		unknown	ABCC4 (NM_005845) - MDM2 (NM_002392) rearrangement: t(12;13)(q15;q32.1)(chr12:g.69229720::chr13:g.95779735) Note: The ABCC4 - MDM2 rearrangement is a translocation that results in a fusion of ABCC4 exons 1 - 18 to MDM2 exons 9 - 11. One of the breakpoints is within MDM2 exon 9. Functional significance is undetermined.
MDM2	0	MSKCC-DMP	P-0041513-T01-IM6	MDM2-ABCC4 fusion	yes	unknown		unknown	ABCC4 (NM_005845) - MDM2 (NM_002392) rearrangement: t(12;13)(q15;q32.1)(chr12:g.69229720::chr13:g.95779735) Note: The ABCC4 - MDM2 rearrangement is a translocation that results in a fusion of ABCC4 exons 1 - 18 to MDM2 exons 9 - 11. One of the breakpoints is within MDM2 exon 9. Functional significance is undetermined.
TSC2	0	MSKCC-DMP	P-0041623-T01-IM6	TSC2-intragenic	yes	unknown		unknown	TSC2 (NM_000548) rearrangement: t(4;16)(q23;p13.3)(chr4:g.99223910::chr16:g.2126001) Note: The TSC2 rearrangement is a translocation with a breakpoint in intron 23. Functional significance is undetermined.
PIK3CG	0	MSKCC-DMP	P-0041623-T01-IM6	PIK3CG-intragenic	yes	unknown		unknown	PIK3CG (NM_002649) rearrangement: t(7;20)(q22.3;p11.23)(chr7:g.106508538::chr20:g.19014680) Note: The PIK3CG rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0041640-T01-IM6	EGFR-intragenic	yes	unknown		in frame	EGFR (NM_005228) rearrangement: c.89-41093_c.889+652del Note: The EGFR rearrangement is a vIII alteration.
SMYD3	0	MSKCC-DMP	P-0042121-T01-IM6	SMYD3-intragenic	yes	unknown		in frame	SMYD3 (NM_001167740) rearrangement: c.164+19:SMYD3_chr1:g.247310040dup Note: The SMYD3 rearrangement is a duplication of exon 1. Functional significance is undetermined.
NOTCH3	0	MSKCC-DMP	P-0042121-T01-IM6	EPHX3-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - EPHX3 (NM_024794) rearrangement: c.736:NOTCH3_c.616+979:EPHX3dup Note: The NOTCH3 - EPHX3 rearrangement is a duplication that results in a fusion of NOTCH3 exons 1 - 5 to EPHX3 exons 5 - 7. One of the breakpoints is within NOTCH3 exon 5. Functional significance is undetermined.
EPHX3	0	MSKCC-DMP	P-0042121-T01-IM6	EPHX3-NOTCH3 fusion	yes	unknown		unknown	NOTCH3 (NM_000435) - EPHX3 (NM_024794) rearrangement: c.736:NOTCH3_c.616+979:EPHX3dup Note: The NOTCH3 - EPHX3 rearrangement is a duplication that results in a fusion of NOTCH3 exons 1 - 5 to EPHX3 exons 5 - 7. One of the breakpoints is within NOTCH3 exon 5. Functional significance is undetermined.
BCL2	0	MSKCC-DMP	P-0042222-T01-IM6	BCL2-intragenic	yes	unknown		unknown	BCL2 (NM_000633) rearrangement: c.585+35197:BCL2_chr18:g.59604842inv Note: The BCL2 rearrangement is an inversion of exon 3. Functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0042222-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.3215+5:SMARCA4_chr19:g.11066021del Note: The SMARCA4 rearrangement is a deletion of exons 1 - 23.
TP53	0	MSKCC-DMP	P-0042222-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: t(17;20)(p13.1;q13.13)(chr17:g.7579702::chr20:g.48337428) Note: The TP53 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.
GNAS	0	MSKCC-DMP	P-0042334-T01-IM6	GNAS-intragenic	yes	unknown		unknown	GNAS (NM_000516) rearrangement: t(1;20)(q32.2;q13.32)(chr1:g.209041232::chr20:g.57484747) Note: The GNAS rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined. Multiple rearrangements involving GNAS were detected in this sample and a more complex rearrangement involving GNAS is possible.
CDKN2A	0	MSKCC-DMP	P-0042334-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_058195) rearrangement: c.194-3668:CDKN2A_chr9:g.22187864del Note: The CDKN2A rearrangement is a deletion of exon 1. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.
CIC	0	MSKCC-DMP	P-0042355-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: t(10;19)(q11.21;q13.2)(chr10:g.42389428::chr19:g.42797695) Note: The CIC rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.
AKT2	0	MSKCC-DMP	P-0042355-T01-IM6	AKT2-intragenic	yes	unknown		unknown	AKT2 (NM_001626) rearrangement: c.441+77:AKT2_chr19:g.13268475inv Note: The AKT2 rearrangement is an inversion of exons 6 - 14. The rearrangement includes the kinase domain of AKT2. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0042402-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: c.4836-18716_c.5021del Note: The NF1 rearrangement is an intragenic deletion of exon 37. One of the breakpoints is within exon 37.
CCDC6	0	MSKCC-DMP	P-0042417-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+16388:CCDC6_c.2136+213:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0042417-T01-IM6	RET-CCDC6 fusion	yes	unknown		in frame	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+16388:CCDC6_c.2136+213:RETinv Note: The CCDC6 - RET fusion involves CCDC6 exon 1 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
KIF5B	0	MSKCC-DMP	P-0042608-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1670:KIF5B_c.2137-230:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
RET	0	MSKCC-DMP	P-0042608-T01-IM6	RET-KIF5B fusion	yes	unknown		in frame	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1670:KIF5B_c.2137-230:RETinv Note: The KIF5B - RET fusion involves KIF5B exons 1 - 15 and RET exons 12 - 20. The fusion is predicted to be in frame and includes the kinase domain of RET.
WNT10B	0	MSKCC-DMP	P-0042608-T01-IM6	KMT2D-WNT10B fusion	yes	unknown		unknown	WNT10B (NM_003394) - KMT2D (NM_003482) rearrangement: c.338-881:WNT10B_c.11911:KMT2Ddup Note: The WNT10B - KMT2D rearrangement is a duplication that results in a fusion of WNT10B exons 1 - 3 to KMT2D exons 39 - 54. One of the breakpoints is within KMT2D exon 39. Functional significance is undetermined.
KMT2D	0	MSKCC-DMP	P-0042608-T01-IM6	KMT2D-WNT10B fusion	yes	unknown		unknown	WNT10B (NM_003394) - KMT2D (NM_003482) rearrangement: c.338-881:WNT10B_c.11911:KMT2Ddup Note: The WNT10B - KMT2D rearrangement is a duplication that results in a fusion of WNT10B exons 1 - 3 to KMT2D exons 39 - 54. One of the breakpoints is within KMT2D exon 39. Functional significance is undetermined.
PIK3R2	0	MSKCC-DMP	P-0042612-T01-IM6	PIK3R2-intragenic	yes	unknown		unknown	PIK3R2 (NM_005027) rearrangement: t(19;20)(p13.11;p11.1)(chr19:g.18272932::chr20:g.25673697) Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined. low read support, no split on PIK3R2
CIC	0	MSKCC-DMP	P-0043170-T01-IM6	CIC-intragenic	yes	unknown		unknown	CIC (NM_015125) rearrangement: c.1464+93:CIC_chr19:g.42785275del Note: The CIC rearrangement is a deletion of exons 1 - 9.
CCND2	0	MSKCC-DMP	P-0043234-T01-IM6	RAD51B-CCND2 fusion	yes	unknown		out of frame	CCND2 (NM_001759) - RAD51B (NM_133509) rearrangement: t(12;14)(p13.32;q24.1)(chr12:g.4388092::chr14:g.68610135) Note: The CCND2 - RAD51B rearrangement is a translocation that results in a fusion of CCND2 exons 1 - 3 to RAD51B exons 8 - 11. Functional significance is undetermined.
RAD51B	0	MSKCC-DMP	P-0043234-T01-IM6	RAD51B-CCND2 fusion	yes	unknown		out of frame	CCND2 (NM_001759) - RAD51B (NM_133509) rearrangement: t(12;14)(p13.32;q24.1)(chr12:g.4388092::chr14:g.68610135) Note: The CCND2 - RAD51B rearrangement is a translocation that results in a fusion of CCND2 exons 1 - 3 to RAD51B exons 8 - 11. Functional significance is undetermined.
STAT3	0	MSKCC-DMP	P-0043243-T01-IM6	STAT3-intragenic	yes	unknown		in frame	STAT3 (NM_139276) rearrangement: c.273+433_c.373-14del Note: The STAT3 rearrangement is an intragenic deletion of exon 4. Functional significance is undetermined.
SIRT2	0	MSKCC-DMP	P-0043243-T01-IM6	ANKRD11-SIRT2 fusion	yes	unknown		unknown	SIRT2 (NM_012237) - ANKRD11 (NM_013275) rearrangement: t(16;19)(q24.3;q13.2)(chr16:g.89351636::chr19:g.39372774) Note: The SIRT2 - ANKRD11 rearrangement is a translocation that results in a fusion of SIRT2 exons 1 - 9 to ANKRD11 exons 9 - 13. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined.
ANKRD11	0	MSKCC-DMP	P-0043243-T01-IM6	ANKRD11-SIRT2 fusion	yes	unknown		unknown	SIRT2 (NM_012237) - ANKRD11 (NM_013275) rearrangement: t(16;19)(q24.3;q13.2)(chr16:g.89351636::chr19:g.39372774) Note: The SIRT2 - ANKRD11 rearrangement is a translocation that results in a fusion of SIRT2 exons 1 - 9 to ANKRD11 exons 9 - 13. One of the breakpoints is within ANKRD11 exon 9. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0043363-T01-IM6	ALK-EML4 fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2254:EML4_c.3172+226:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 20 and ALK exons 20 - 29. One of the breakpoints is within EML4 exon 20. The fusion includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0043363-T01-IM6	ALK-EML4 fusion	yes	unknown		unknown	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2254:EML4_c.3172+226:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 20 and ALK exons 20 - 29. One of the breakpoints is within EML4 exon 20. The fusion includes the kinase domain of ALK.
EML4	0	MSKCC-DMP	P-0043498-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2142:EML4_c.3173-569:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0043498-T02-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2142:EML4_c.3173-569:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
GLI1	0	MSKCC-DMP	P-0043632-T01-IM6	ZFAND3-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - ZFAND3 (NM_021943) rearrangement: t(6;12)(p21.2;q13.3)(chr6:g.38088525::chr12:g.57859454) Note: The GLI1 - ZFAND3 rearrangement is a translocation that results in a fusion of GLI1 exons 1 - 6 to ZFAND3 exon 6. One of the breakpoints is within GLI1 exon 6. Functional significance is undetermined and may be related to the GLI1 amplification.
ZFAND3	0	MSKCC-DMP	P-0043632-T01-IM6	ZFAND3-GLI1 fusion	yes	unknown		unknown	GLI1 (NM_005269) - ZFAND3 (NM_021943) rearrangement: t(6;12)(p21.2;q13.3)(chr6:g.38088525::chr12:g.57859454) Note: The GLI1 - ZFAND3 rearrangement is a translocation that results in a fusion of GLI1 exons 1 - 6 to ZFAND3 exon 6. One of the breakpoints is within GLI1 exon 6. Functional significance is undetermined and may be related to the GLI1 amplification.
JAK2	0	MSKCC-DMP	P-0043696-T01-IM6	JAK2-intragenic	yes	unknown		unknown	JAK2 (NM_004972) rearrangement: c.1057-1491_c.1165del Note: The JAK2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.
EP300	0	MSKCC-DMP	P-0043711-T01-IM6	EP300-intragenic	yes	unknown		unknown	EP300 (NM_001429) rearrangement: c.3261+838_c.3405del Note: The EP300 rearrangement is an intragenic deletion of exon 18. One of the breakpoints is within exon 18.
CBL	0	MSKCC-DMP	P-0043829-T01-IM6	CBL-intragenic	yes	unknown		unknown	CBL (NM_005188) rearrangement: c.1214_c.1431+2134del Note: The CBL rearrangement is an intragenic deletion of exons 8 - 9. One of the breakpoints is within exon 8.
TP53	0	MSKCC-DMP	P-0043867-T01-IM6	TP53-intragenic	yes	unknown		unknown	TP53 (NM_000546) rearrangement: c.227:TP53_chr17:g.7582510del Note: The TP53 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4.
FGFR3	0	MSKCC-DMP	P-0044057-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+53:FGFR3_c.1645-189:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 8 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
TACC3	0	MSKCC-DMP	P-0044057-T01-IM6	TACC3-FGFR3 fusion	yes	unknown		in frame	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+53:FGFR3_c.1645-189:TACC3dup Note: The FGFR3 - TACC3 fusion involves FGFR3 exons 1 - 17 and TACC3 exons 8 - 16. The fusion is predicted to be in frame and includes the kinase domain of FGFR3.
PXN	0	MSKCC-DMP	P-0044077-T01-IM6	MSI1-PXN fusion	yes	unknown		unknown	PXN (NM_001080855) - MSI1 (NM_002442) rearrangement: c.14-9946:PXN_c.709:MSI1dup Note: The PXN - MSI1 rearrangement is a duplication that results in a fusion of PXN exon 1 to MSI1 exons 10 - 14. One of the breakpoints is within MSI1 exon 10. Functional significance is undetermined.
MSI1	0	MSKCC-DMP	P-0044077-T01-IM6	MSI1-PXN fusion	yes	unknown		unknown	PXN (NM_001080855) - MSI1 (NM_002442) rearrangement: c.14-9946:PXN_c.709:MSI1dup Note: The PXN - MSI1 rearrangement is a duplication that results in a fusion of PXN exon 1 to MSI1 exons 10 - 14. One of the breakpoints is within MSI1 exon 10. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0044100-T02-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.89-28860_c.1705inv Note: The EGFR rearrangement is an intragenic inversion of exons 2 - 14. One of the breakpoints is within exon 14. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined.
SMARCA4	0	MSKCC-DMP	P-0044246-T01-IM6	SMARCA4-intragenic	yes	unknown		unknown	SMARCA4 (NM_003072) rearrangement: c.1593+12:SMARCA4_chr19:g.32708379del Note: The SMARCA4 rearrangement is a deletion of exons 10 - 35.
SIPA1L3	0	MSKCC-DMP	P-0044246-T01-IM6	KDM5C-SIPA1L3 fusion	yes	unknown		unknown	SIPA1L3 (NM_015073) - KDM5C (NM_004187) rearrangement: t(19;X)(q13.13;p11.22)(chr19:g.38649964::chrX:g.53231096) Note: The SIPA1L3 - KDM5C rearrangement is a translocation that results in a fusion of SIPA1L3 exons 1 - 13 to KDM5C exons 13 - 26. One of the breakpoints is within KDM5C exon 13. Functional significance is undetermined.
KDM5C	0	MSKCC-DMP	P-0044246-T01-IM6	KDM5C-SIPA1L3 fusion	yes	unknown		unknown	SIPA1L3 (NM_015073) - KDM5C (NM_004187) rearrangement: t(19;X)(q13.13;p11.22)(chr19:g.38649964::chrX:g.53231096) Note: The SIPA1L3 - KDM5C rearrangement is a translocation that results in a fusion of SIPA1L3 exons 1 - 13 to KDM5C exons 13 - 26. One of the breakpoints is within KDM5C exon 13. Functional significance is undetermined.
RET	0	MSKCC-DMP	P-0044380-T02-IM6	RET-intragenic	yes	unknown		unknown	RET (NM_020975) rearrangement: t(7;10)(q21.13;q11.21)(chr7:g.89052378::chr10:g.43607734) Note: The RET rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined and further testing to determine the presence or absence of a targetable oncogenic fusion involving RET is required. This sample has been nominated for further analysis using the Archer targeted RNAseq assay. Archer will be performed and reported under a separate accession number if additional material is available.
ERF	0	MSKCC-DMP	P-0044402-T01-IM6	ERF-intragenic	yes	unknown		unknown	ERF (NM_006494) rearrangement: t(2;19)(p12;q13.2)(chr2:g.76279515::chr19:g.42752863) Note: The ERF rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.
PDCD1LG2	0	MSKCC-DMP	P-0044575-T01-IM6	PDCD1LG2-intragenic	yes	unknown		unknown	PDCD1LG2 (NM_025239) rearrangement: c.134:PDCD1LG2_chr9:g.19387023del Note: The PDCD1LG2 rearrangement is a deletion of exons 3 - 7. One of the breakpoints is within exon 3. Functional significance is undetermined.
SOX9	0	MSKCC-DMP	P-0044656-T01-IM6	SOX9-intragenic	yes	unknown		unknown	SOX9 (NM_000346) rearrangement: c.366:SOX9_chr17:g.70359850inv Note: The SOX9 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 1. Functional significance is undetermined.
TMPRSS2	0	MSKCC-DMP	P-0044656-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3702:TMPRSS2_c.18+1310:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.
ERG	0	MSKCC-DMP	P-0044656-T01-IM6	ERG-TMPRSS2 fusion	yes	unknown		out of frame	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3702:TMPRSS2_c.18+1310:ERGdel Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.
SBF2	0	MSKCC-DMP	P-0044661-T01-IM6	EPAS1-SBF2 fusion	yes	unknown		unknown	SBF2 (NM_030962) - EPAS1 (NM_001430) rearrangement: t(2;11)(p21;p15.4)(chr2:g.46605894::chr11:g.9929559) Note: The SBF2 - EPAS1 rearrangement is a translocation that results in a fusion of SBF2 exons 1 - 16 to EPAS1 exons 11 - 16. One of the breakpoints is within EPAS1 exon 11. Functional significance is undetermined.
EPAS1	0	MSKCC-DMP	P-0044661-T01-IM6	EPAS1-SBF2 fusion	yes	unknown		unknown	SBF2 (NM_030962) - EPAS1 (NM_001430) rearrangement: t(2;11)(p21;p15.4)(chr2:g.46605894::chr11:g.9929559) Note: The SBF2 - EPAS1 rearrangement is a translocation that results in a fusion of SBF2 exons 1 - 16 to EPAS1 exons 11 - 16. One of the breakpoints is within EPAS1 exon 11. Functional significance is undetermined.
DAXX	0	MSKCC-DMP	P-0044902-T01-IM6	DAXX-intragenic	yes	unknown		unknown	DAXX (NM_001141970) rearrangement: c.288:DAXX_chr6:g.37277191del Note: The DAXX rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3.
PRKD1	0	MSKCC-DMP	P-0044969-T01-IM6	PRKD1-intragenic	yes	unknown		unknown	PRKD1 (NM_002742) rearrangement: c.535+269_c.697-39inv Note: The PRKD1 rearrangement is an intragenic inversion of exon 4. The rearrangement does not include the kinase domain of PRKD1. Functional significance is undetermined.
NF1	0	MSKCC-DMP	P-0044969-T01-IM6	NF1-intragenic	yes	unknown		unknown	NF1 (NM_001042492) rearrangement: t(7;17)(q11.22;q11.2)(chr7:g.68108423::chr17:g.29528219) Note: The NF1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.
EML4	0	MSKCC-DMP	P-0044988-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+2670:EML4_c.3172+533:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
ALK	0	MSKCC-DMP	P-0044988-T01-IM6	ALK-EML4 fusion	yes	unknown		in frame	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+2670:EML4_c.3172+533:ALKinv Note: The EML4 - ALK fusion involves EML4 exons 1 - 12 and ALK exons 20 - 29. The fusion is predicted to be in frame and includes the kinase domain of ALK.
PTEN	0	MSKCC-DMP	P-0049880-T01-IM6	PTEN-intragenic	yes	unknown		out of frame	PTEN (NM_000314) rearrangement: c.635-1359_c.802-28del Note: The PTEN rearrangement is an intragenic deletion of exon 7.
FGFR2	0	MSKCC-DMP	P-0021788-T01-IM6	VPS26A-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-VPS26A fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon 17 (NM_000141.4) and VPS26A Exon 2 (NM_004896). Lab Notes Run Number: ArcherV2-CLIN-20170071 Macro-dissection: Unknown
VPS26A	0	MSKCC-DMP	P-0021788-T01-IM6	VPS26A-FGFR2 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: FGFR2-VPS26A fusion. Note: The rearrangement is an in-frame fusion between genes FGFR2 Exon 17 (NM_000141.4) and VPS26A Exon 2 (NM_004896). Lab Notes Run Number: ArcherV2-CLIN-20170071 Macro-dissection: Unknown
CD74	0	MSKCC-DMP	P-0024572-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
ROS1	0	MSKCC-DMP	P-0024572-T01-IM6	ROS1-CD74 fusion - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE FUSION IN THE CLINICALLY VALIDATED PANEL: CD74-ROS1 fusion. Note: The rearrangement is an in-frame fusion between genes CD74 Exon6 (NM_001025159) and ROS1 Exon34 (NM_002944). Lab Notes Run Number: ArcherV2-CLIN-20170119 Macro-dissection: Unknown
MET	0	MSKCC-DMP	P-0035774-T01-IM6	MET-intragenic - Archer	yes	unknown		unknown	DIAGNOSTIC INTERPRETATION:   POSITIVE FOR AN ONCOGENIC ISOFORM IN THE INVESTIGATIONAL PANEL   MET Exon 14 skipping (NM_000245) Lab Notes Run Number: ArcherV3-CLIN-20180172 Macro-dissection: Unknown
EPS15	0	MSKCC-DMP	P-0037901-T01-IM6	NTRK1-EPS15 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EPS15-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes EPS15 Exon21 (NM_001981) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV3-CLIN-20190023 Macro-dissection: Unknown
NTRK1	0	MSKCC-DMP	P-0037901-T01-IM6	NTRK1-EPS15 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EPS15-NTRK1 fusion. Note: The rearrangement is an in-frame fusion between genes EPS15 Exon21 (NM_001981) and NTRK1 Exon10 (NM_002529). Lab Notes Run Number: ArcherV3-CLIN-20190023 Macro-dissection: Unknown
EML4	0	MSKCC-DMP	P-0040309-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon7 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190073 Macro-dissection: Performed
ALK	0	MSKCC-DMP	P-0040309-T01-IM6	ALK-EML4 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: EML4-ALK fusion. Note: The rearrangement is an in-frame fusion between genes EML4 Exon7 (NM_019063) and ALK Exon20 (NM_004304). Lab Notes Run Number: Archerv3-CLIN-20190073 Macro-dissection: Performed
NTRK1	0	MSKCC-DMP	P-0043170-T01-IM6	NTRK1-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING ISOFORM IN THE INVESTIGATIONAL PANEL:   NTRK1 (NM_002529)  exons 3-9 deletion. PMID: 26581861, 29914559  Note1: the functional significance of this event is unknown. Trk inhibitors have not been investigated in this setting.  Note2: This event was detected with low read support.  Lab Notes Run Number: Archerv3-CLIN-20190116 Macro-dissection: Not Performed
FGFR3	0	MSKCC-DMP	P-0044057-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon8 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190164 Macro-dissection: Not Performed
TACC3	0	MSKCC-DMP	P-0044057-T01-IM6	TACC3-FGFR3 fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE CLINICAL PANEL: FGFR3-TACC3 fusion. Note: The rearrangement is an in-frame fusion between genes FGFR3 Exon17 (NM_000142) and TACC3 Exon8 (NM_006342). Lab Notes Run Number: Archerv3-CLIN-20190164 Macro-dissection: Not Performed
TFG	0	MSKCC-DMP	P-0044077-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_001195478) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190130 Macro-dissection: Not Performed
GPR128	0	MSKCC-DMP	P-0044077-T01-IM6	GPR128-TFG fusion - Archer	yes	unknown		unknown	POSITIVE FOR GENE FUSIONS IN THE INVESTIGATIONAL PANEL: TFG-GPR128 fusion. Note: The rearrangement is an in-frame fusion between genes TFG Exon3 (NM_001195478) and GPR128 Exon2 (NM_032787). PMID: 19797732  Note1: This is a known structural germline polymorphism seen in healthy individuals. Lab Notes Run Number: Archerv3-CLIN-20190130 Macro-dissection: Not Performed
RPS6KB2	0	MSKCC-DMP	P-0001716-T01-IM3	ANO5-RPS6KB2 fusion	yes	unknown		in frame	RPS6KB2 (NM_003952) - ANO5 (NM_213599) duplication:  c.970-59_c.1333-371dup The RPS6KB2-ANO5 duplication is a rearrangement event which results in  the in-frame fusion between RPS6KB2 exons 1-11 and ANO5 exons 14-22
ANO5	0	MSKCC-DMP	P-0001716-T01-IM3	ANO5-RPS6KB2 fusion	yes	unknown		in frame	RPS6KB2 (NM_003952) - ANO5 (NM_213599) duplication:  c.970-59_c.1333-371dup The RPS6KB2-ANO5 duplication is a rearrangement event which results in  the in-frame fusion between RPS6KB2 exons 1-11 and ANO5 exons 14-22
NFE2L2	0	MSKCC-DMP	P-0043747-T02-IM6	NFE2L2-intragenic - Archer	yes	unknown		unknown	POSITIVE FOR THE FOLLOWING GENE VARIANT TRANSCRIPT IN THE INVESTIGATIONAL PANEL: NFE2L2 (NM_006164) Exons 2 and 3 deletion. PMID: 27568559. NEGATIVE FOR GENE FUSIONS IN THE CLINICALLY VALIDATED PANEL Lab Notes Run Number: ArcherV4-CLIN-20210048 Macro-dissection: Not Performed
FGFR2	0	MSKCC-DMP	P-0004520-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2(NM_000141) - BICC1( NM_001080512) Fusion (FGFR2 exon 17 fused with exon 10 of BICC1) :  c.2302-734:FGFR2_c.1180-924:BICC1inv Note: The FGFR2(NM_000141) -BICC1( NM_001080512) Fusion results in the fusion of exons 1 to 17 of FGFR2 with exons 10 to 21of BICC1.Its functional significance is undetermined.
BICC1	0	MSKCC-DMP	P-0004520-T01-IM5	BICC1-FGFR2 fusion	yes	unknown		in frame	FGFR2(NM_000141) - BICC1( NM_001080512) Fusion (FGFR2 exon 17 fused with exon 10 of BICC1) :  c.2302-734:FGFR2_c.1180-924:BICC1inv Note: The FGFR2(NM_000141) -BICC1( NM_001080512) Fusion results in the fusion of exons 1 to 17 of FGFR2 with exons 10 to 21of BICC1.Its functional significance is undetermined.
ATR	0	MSKCC-DMP	P-0025754-T01-IM6	ATR-intragenic	yes	unknown		unknown	ATR (NM_001184) Rearrangement : chr3:g.119493103_c.5381-35:ATRdup Note: The ATR Rearrangement results in the intragenic duplication of exons 32-47 of ATR. This event occurs in the background of other structural events involving ATR. Its functional significance is undetermined.
CDKN2A	0	MSKCC-DMP	P-0032991-T01-IM6	CDKN2A-intragenic	yes	unknown		unknown	CDKN2A (NM_000077) Rearrangement:  chr9:g.21675509_c.-44inv Note: The CDKN2A Rearrangement results in the inversion of exons 1-3 of CDKN2A. The rearrangement affects both the p14 and p16 isoforms. Its functional significance is undetermined.
AGO2	0	MSKCC-DMP	P-0047553-T01-IM6	AGO2-intragenic	yes	unknown		in frame	AGO2 (NM_012154) rearrangement: c.1147-2_c.1269+1696dup Note: The AGO2 rearrangement is an intragenic duplication of exon 10. Functional significance is undetermined.
EGFR	0	MSKCC-DMP	P-0048544-T01-IM6	EGFR-intragenic	yes	unknown		unknown	EGFR (NM_005228) rearrangement: c.560-95:EGFR_chr7:g.55081300del Note: The EGFR rearrangement is a deletion of exons 1 - 4. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined.
XPO1	0	MSKCC-DMP	P-0028912-T01-IM6	XPO1-intragenic	yes	unknown		unknown	XPO1 (NM_003400) rearrangement: c.1135:XPO1_chr2:g.57754879inv Note: The XPO1 rearrangement is an inversion of exons 12-25. One of the break points is within exon 12. Multiple rearrangements involving XPO1 were detected in this sample and a more complex rearrangement resulting in a XPO1 fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated. Its functional significance is undetermined.
PTPRT	0	MSKCC-DMP	P-0028912-T01-IM6	PTPRT-intragenic	yes	unknown		unknown	PTPRT (NM_133170) rearrangement: t(10;20)(p15.1;q12)(chr10:g.3968862::chr20:g.40733369) Note: The PTPRT rearrangement is a translocation involving exon 26. Multiple rearrangements involving PTPRT were detected in this sample and a more complex rearrangement resulting in a PTPRT fusion is possible. Additional testing by an alternative method is recommended, if clinically indicated. Its functional significance is undetermined.
