Sample_ID	Annotation	Breakpoint_Type	Comments	Confidence_Class	Conn_Type	Connection_Type	Event_Info	Mapq	Normal_Read_Count	Normal_Variant_Count	Paired_End_Read_Support	Site1_Chrom	Site1_Desc	Site1_Hugo_Symbol	Site1_Pos	Site1_Exon	Site1_Ensembl_Transcript_Id	Site2_Chrom	Site2_Desc	Site2_Hugo_Symbol	Site2_Pos	Site2_Exon	Site2_Ensembl_Transcript_Id	Split_Read_Support	Sv_Class_Name	Sv_Desc	Sv_Length	Sv_VariantId	Tumor_Read_Count	Tumor_Variant_Count	Variant_Status_Name
P-0010758-T01-IM5	EP300 (NM_001429) rearrangement: c.4617+54_c.4780-1066del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exon 29. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2459	0	33	22	Intron of EP300(+): 54bp after exon 28	EP300	41568721			22	Intron of EP300(+): 1Kb before exon 30	EP300	41571185			32	DELETION		2464	149095	1647	32	NEW_VARIANT
P-0014470-T01-IM6	RPTOR (NM_020761) Rearrangement :  c.284_c.348+4045dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		394	0	16	17	Exon 3 of RPTOR(+)	RPTOR	78617546			17	Intron of RPTOR(+): 4Kb after exon 3	RPTOR	78621655			33	DUPLICATION		4109	164594	500	16	NEW_VARIANT
P-0011577-T01-IM5	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	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		31912	0	17	21	Intron of ERG(-): 6Kb after exon 1	ERG	39864690			21	Intron of TMPRSS2(-): 511bp before exon 3	TMPRSS2	42867016			23	DELETION		3002326	155704	26921	17	NEW_VARIANT
P-0012253-T01-IM5	ARID1B (NM_020732) rearrangement: c.83_c.1777-2523del	PRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exons 1-4. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		7520	0	10	6	Exon 1 of ARID1B(+)	ARID1B	157099320			6	Intron of ARID1B(+): 3Kb before exon 4	ARID1B	157219987			23	DELETION		120667	156847	7921	7	NEW_VARIANT
P-0011443-T01-IM5	BAP1 (NM_004656) rearrangement : c.68-1_256-75del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: out of frame		2436	0	8	3	Intron of BAP1(-): 75bp before exon 5	BAP1	52442168			3	Intron of BAP1(-): 1bp before exon 3	BAP1	52443625			17	DELETION		1457	153895	1870	8	NEW_VARIANT
P-0013956-T01-IM5	BRCA2 (NM_00005) rearrangement: c.3575_c.6269inv	PRECISE	Note: The BRCA2 rearrangement is an inversion of exon 11. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		32642	1	74	13	Exon 11 of BRCA2(+)	BRCA2	32912067			13	Exon 11 of BRCA2(+)	BRCA2	32914761			86	INVERSION		2694	162854	22149	72	NEW_VARIANT
P-0014576-T01-IM6	DNAH9 (NM_001372) - MAP2K4 (NM_003010) rearrangement: c.5552+2579:DNAH9_c.1168:MAP2K4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		12610	0	58	17	Intron of DNAH9(+): 3Kb after exon 26	DNAH9	11611081			17	Exon 11 of MAP2K4(+)	MAP2K4	12044545			75	INVERSION		433464	165099	2598	58	NEW_VARIANT
P-0012116-T01-IM5	NBN (NM_002485) Rearrangement : t(4,8)(p11,q21.3)(chr4:g.131062050::chr8:g.143130066)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	30	8	Exon 11 of NBN(-)	NBN	90965856			4	IGR: 6Kb after CWH43(+)	CWH43	49069963			0	TRANSLOCATION		0	156303	0	24	NEW_VARIANT
P-0011098-T01-IM5	SPEN (NM_015001) rearrangement: t(1;8)(p36.13;q21.3)(chr1:g.16259712::chr8:g.89816597)	PRECISE	Note: The SPEN rearrangement is a translocation with a breakpoint within exon 11 of SPEN. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	101	8	IGR: 477Kb after MMP16(-)	MMP16	89816597			1	Exon 11 of SPEN(+)	SPEN	16259712			20	TRANSLOCATION		0	150793	0	99	NEW_VARIANT
P-0013732-T01-IM5	PRKAR1A (NM_212471) rearrangement: t(6;17)(q24.2;q24.2)(chr6:g.144894222::chr17:g.66526189)	PRECISE	Note: The PRKAR1A rearrangement is a translocation that may result in the truncation of exons 10-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	47	17	Intron of PRKAR1A(+): 47bp after exon 10	PRKAR1A	66526189			6	Intron of UTRN(+): 4Kb before exon 50	UTRN	144894222			20	TRANSLOCATION		0	162113	0	39	NEW_VARIANT
P-0012110-T01-IM5	PBRM1 (NM_018313) Rearrangement :  c.4576+131_c.3459-453dup	PRECISE	Note: The PBRM1 Rearrangement  results in the intragenic duplication of exons 23-29. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 7 exons: out of frame		22212	0	5	3	Intron of PBRM1(-): 131bp after exon 29	PBRM1	52584306			3	Intron of PBRM1(-): 453bp before exon 23	PBRM1	52611167			6	DUPLICATION		26861	156265	23494	4	NEW_VARIANT
P-0015015-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		31078	0	5	21	Intron of ERG(-): 9Kb after exon 1	ERG	39861551			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868021			11	DELETION		3006470	166538	39638	5	NEW_VARIANT
P-0013271-T01-IM5	PDGFRB (NM_002609) - CAMK2A (NM_015981)  rearrangement: c.1579+9:PDGFRB_c.157+1527:CAMK2Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (PDGFRB-CAMK2A)		14810	0	22	5	Intron of PDGFRB(-): 9bp after exon 10	PDGFRB	149509311			5	Intron of CAMK2A(-): 2Kb after exon 2	CAMK2A	149651101			31	DUPLICATION		141790	160727	23023	22	NEW_VARIANT
P-0012153-T01-IM5	ATRX (NM_000489) rearrangement: chrX:g.72499356_c.5226inv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 20-35. One of the breakpoints is within exon  20.	MANUAL_OK	5to5	5to5	-		65878	0	17	X	IGR: 67Kb before NAP1L2(-)	NAP1L2	72499356			X	Exon 20 of ATRX(-)	ATRX	76875909			42	INVERSION		4376553	156444	36153	17	NEW_VARIANT
P-0012377-T01-IM5	EWSR1(NM_013986) - AP1B1 (NM_001127) rearrangement: c.1167:EWSR1_c.-1535:AP1B1dup	PRECISE	Note: Targeted RNAseq (Archer FusionPlexTM Custom Solid Panel) will be performed to further characterize the structural variant and reported under a separate accession number. This case was discussed at the Clinical NGS Group Meeting on 6/24/2016.	MANUAL_OK	5to3	5to3	-		4271	0	4	22	Exon 12 of EWSR1(+)	EWSR1	29693908			22	Promoter of AP1B1(-): 1Kb from tx start	AP1B1	29785920			9	DUPLICATION		92012	157234	5078	3	NEW_VARIANT
P-0010948-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement : c.194-3397_chr9:g.22028649del CDKN2Ap16INK4A (NM_000077) rearrangement : c.150+73_chr9:g.22028649del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		16731	0	102	9	Exon 1 of CDKN2A(-)	CDKN2A	21974604			9	5-UTR of CDKN2BAS(+): 92Kb before coding start	CDKN2BAS	22028649			104	DELETION		54045	149842	7856	114	NEW_VARIANT
P-0014395-T01-IM6	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)	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (TMPRSS2-ARHGAP26)		0	0	24	21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868024			5	Intron of ARHGAP26(+): 13Kb after exon 11	ARHGAP26	142324441			31	TRANSLOCATION		0	164386	0	24	NEW_VARIANT
P-0012909-T01-IM5	SMARCA4 (NM_003072) Rearrangement : c.4301_4424+659del	IMPRECISE	Note: The SMARCA4 Rearrangement results in the intragenic deletion of exon 30 of SMARCA4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		981	0	8	19	Exon 28 of SMARCA4(+)	SMARCA4	11152113			19	Intron of SMARCA4(+): 659bp after exon 28	SMARCA4	11152895			0	DELETION		782	159378	675	8	NEW_VARIANT
P-0012596-T01-IM5	SMARCA4 (NM_003072) rearrangement: c.3547-184_c.3804dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 26-27. One of the breakpoints is within exon 27.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		3935	0	16	19	Intron of SMARCA4(+): 184bp before exon 25	SMARCA4	11143782			19	Exon 27 of SMARCA4(+)	SMARCA4	11144472			25	DUPLICATION		690	157965	4029	14	NEW_VARIANT
P-0012623-T01-IM5	CACNA1B (NM_000718) - MGA (NM_001164273) Rearrangement : t(9;15)(q22.3;p11.1)(chr9:g.140896610::chr15:g.42041234)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (CACNA1B-MGA)		0	0	34	15	Intron of MGA(+): 75bp before exon 16	MGA	42041234			9	Intron of CACNA1B(+): 5Kb before exon 16	CACNA1B	140896610			0	TRANSLOCATION		0	158263	0	33	NEW_VARIANT
P-0011259-T01-IM5	EIF4E (NM_001130678) Rearrangement : t(4;8)(q23;p21.3)(chr4:g.99849955::chr8:g.21254285)	PRECISE	Note: The EIF4E Rearrangement is a translocation event which results in the possible truncation of exon1 of EIF4E. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	13	8	IGR: 295Kb before GFRA2(-)	GFRA2	21254285			4	Intron of EIF4E(-): 91bp after exon 1	EIF4E	99849955			6	TRANSLOCATION		0	157136	0	13	NEW_VARIANT
P-0014631-T01-IM6	AKT2 (NM_001626)  rearrangement: c.752:AKT2_c.4032+747:LTBP4del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		12680	0	39	19	Exon 9 of AKT2(-)	AKT2	40743955			19	Intron of LTBP4(+): 747bp after exon 29	LTBP4	41130734			85	DELETION		386779	165268	7233	39	NEW_VARIANT
P-0013660-T01-IM5	ATM (NM_000051) Rearrangement : c.8162_chr11:g.112801427del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		27138	0	8	11	Exon 56 of ATM(+)	ATM	108206582			11	IGR: 31Kb before NCAM1(+)	NCAM1	112801427			18	DELETION		4594845	161939	28701	8	NEW_VARIANT
P-0013443-T01-IM5	KDR (NM_002253) rearrangement: c.2510-129:KDR_chr4:g.56104211del	PRECISE	Note: The KDR rearrangement is a deletion of 5UTR and exons 1-17.	MANUAL_OK	3to5	3to5	-		35474	0	16	4	Intron of KDR(-): 129bp before exon 18	KDR	55964062			4	IGR: 108Kb before SRD5A3(+)	SRD5A3	56104211			15	DELETION		140149	161283	35709	9	NEW_VARIANT
P-0011135-T01-IM5	PIK3C2G (NM_004570) rearrangement : c.3889-80_3965-4589inv	PRECISE	Note: The PIK3C2G rearrangement event results in the inversion of PIK3C2G exon29.	MANUAL_OK	5to5	5to5	-		1057	0	31	12	Intron of PIK3C2G(+): 80bp before exon 29	PIK3C2G	18747348			12	Intron of PIK3C2G(+): 5Kb before exon 30	PIK3C2G	18757880			23	INVERSION		10532	151326	1710	30	NEW_VARIANT
P-0014414-T01-IM6	ERG (NM_004449) - TMPRRS2 (NM_001135099) rearrangement: c.39+51460:ERG_c.56-2388:TMPRRS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (ERG-TMPRSS2)		85235	0	84	21	Intron of ERG(-): 51Kb after exon 3	ERG	39896126			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872504			87	DUPLICATION		2976378	164491	60256	77	NEW_VARIANT
P-0014077-T01-IM5	EP300 (NM_001429) rearrangement: chr22:g.39268126_c.1380:EP300del	PRECISE	Note: The EP300 rearrangement is a deletion of 5UTR and exons 1-6. One of the breakpoints is within exon 6.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (EP300-CBX6)		20294	0	10	22	Intron of CBX6(-): 1bp after exon 1	CBX6	39268126			22	Exon 6 of EP300(+)	EP300	41527489			46	INVERSION		2259363	163232	21328	10	NEW_VARIANT
P-0014732-T01-IM6	NEDD8 (NM_001199823) - BAP1 (NM_004656) rearrangement: t(3;14)(p21.1;q12)(chr3:g.52444003::chr14:g.24689227)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Transcript fusion (NEDD8-BAP1)		0	0	5	14	Intron of NEDD8(-): 2Kb before exon 2	NEDD8	24689227			3	5-UTR of BAP1(-): 109bp before coding start	BAP1	52444003			0	TRANSLOCATION		0	165636	0	3	NEW_VARIANT
P-0014732-T01-IM6	DOK6 (NM_152721) - PBRM1 (NM_018313) rearrangement: t(3;18)(p21.1;q22.2)(chr3:g.52692284::chr18:g.67099152)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (DOK6-PBRM1)		0	0	17	18	Intron of DOK6(+): 31Kb after exon 1	DOK6	67099152			3	Exon 6 of PBRM1(-)	PBRM1	52692284			8	TRANSLOCATION		0	165637	0	17	NEW_VARIANT
P-0014732-T01-IM6	PIK3CB (NM_006219) rearrangement: chr3:g.45114508_c.1581+9del	PRECISE	Note: The PIK3CB rearrangement is a deletion which includes exons 11-22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		376636	0	22	3	IGR: 9Kb before CDCP1(-)	CDCP1	45114508			3	Intron of PIK3CB(-): 9bp after exon 10	PIK3CB	138423276			30	DELETION		93308768	165633	398763	22	NEW_VARIANT
P-0013451-T01-IM5	STX7 (NM_003569) - ROS1 (NM_002944) rearrangement: c.86-3411:STX7_c.5366+1036:ROS1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (STX7-ROS1)		116572	0	102	6	Intron of ROS1(-): 1Kb after exon 32	ROS1	117649456			6	Intron of STX7(-): 3Kb before exon 3	STX7	132800212			211	DELETION		15150756	161304	62818	437	NEW_VARIANT
P-0010320-T01-IM5	STK11 (NM_000455) Rearrangement :  c.465-98_1108+1298dup	PRECISE	Note: The STK11 Rearrangement results in the intragenic duplication of exons 4-8 of STK11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: out of frame		10241	0	25	19	Intron of STK11(+): 98bp before exon 4	STK11	1220274			19	Intron of STK11(+): 1Kb after exon 8	STK11	1224469			22	DUPLICATION		4195	145480	9226	24	NEW_VARIANT
P-0013182-T01-IM5	CTCF (NM_006565) rearrangement: c.953-1108_c.1157dup	PRECISE	Note: The CTCF rearrangement is a duplication of exons 5-6. One of the breakpoints is within exon 6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		4820	0	23	16	Intron of CTCF(+): 1Kb before exon 5	CTCF	67649540			16	Exon 6 of CTCF(+)	CTCF	67654670			29	DUPLICATION		5130	160433	6063	23	NEW_VARIANT
P-0010994-T01-IM5	MTMR3 (NM_021090) - EWSR1 (NM_013986) rearrangement: c.-85+3820:MTMR3_c.992+1294:EWSR1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript fusion (MTMR3-EWSR1)		81722	0	20	22	Intron of EWSR1(+): 333bp before exon 9	EWSR1	29686069			22	5-UTR of MTMR3(+): 10Kb before coding start	MTMR3	30356897			23	DUPLICATION		670828	150289	113478	20	NEW_VARIANT
P-0014992-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2429:TMPRSS2_c.18+5301:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		94178	0	8	21	Intron of ERG(-): 5Kb after exon 1	ERG	39864986			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877448			15	DELETION		3012462	166455	99040	8	NEW_VARIANT
P-0014460-T01-IM6	CTNNB1 (NM_001904) Rearrangement : c.1082-37:CTNNB1_c.4-17540:FAM198inv	PRECISE	Note: The CTNNB1 Rearrangement results in the inversion of exons 8-15 of CTNNB1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		14809	0	21	3	Intron of CTNNB1(+): 37bp before exon 8	CTNNB1	41274795			3	Intron of FAM198A(+): 18Kb before exon 2	FAM198A	43056219			28	INVERSION		1781424	164662	21231	21	NEW_VARIANT
P-0011343-T01-IM5	SMARCA4 (NM_003072) rearrangement: c.1708_c.1813-1667dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 9-10. One of the breakpoint is within exon 9.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1392	0	8	19	Exon 9 of SMARCA4(+)	SMARCA4	11107003			19	Intron of SMARCA4(+): 2Kb before exon 11	SMARCA4	11112038			6	DUPLICATION		5035	153263	1715	7	NEW_VARIANT
P-0011343-T01-IM5	RAD21 (NM_006265) rearrangement: c.374+128_c.812dup	PRECISE	Note: The RAD21 rearrangement is an intragenic duplication of exons 5-7. One of the breakpoints is within exon 7.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		6668	0	5	8	Exon 7 of RAD21(-)	RAD21	117868887			8	Intron of RAD21(-): 128bp after exon 4	RAD21	117873952			6	DUPLICATION		5065	153264	5785	5	NEW_VARIANT
P-0011542-T01-IM5	MLL2 (NM_003482) - CNTN1 (NM_001843) rearrangement: c.5320-13:MLL2_c.2113+2294:CNTN1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (MLL2-CNTN1)		196820	0	47	12	Intron of CNTN1(+): 2Kb after exon 17	CNTN1	41389365			12	Intron of MLL2(-): 13bp before exon 23	MLL2	49437578			44	INVERSION		8048213	155593	286586	43	NEW_VARIANT
P-0012731-T01-IM5	PTEN (NM_000314) rearrangement: c.278_c.492+4373del	PRECISE	Note: The PTEN rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1071	0	17	10	Exon 5 of PTEN(+)	PTEN	89692794			10	Intron of PTEN(+): 4Kb after exon 5	PTEN	89697381			45	DELETION		4587	158742	676	17	NEW_VARIANT
P-0013277-T01-IM5	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241665743::chr13:g.42830282)	IMPRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	38	13	IGR: 16Kb before AKAP11(+)	AKAP11	42830282			1	Exon 8 of FH(-)	FH	241665743			0	TRANSLOCATION		0	160709	0	28	NEW_VARIANT
P-0012513-T01-IM5	PMS1 (NM_000534) rearrangement: chr2:g.183973880_c.668:PMS1del	PRECISE	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.	MANUAL_OK	3to3	3to3	-		9423	0	10	2	IGR: 15Kb before NUP35(+)	NUP35	183973880			2	Exon 6 of PMS1(+)	PMS1	190708775			20	INVERSION		6734895	157636	13176	6	NEW_VARIANT
P-0010742-T01-IM5	APC (NM_000038) - PRMT8 (NM_019854) rearrangement : t(5;12)(q22.2;p12.32)(chr5:g.112175904::chr12:g.3608058)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (APC-PRMT8)		0	0	16	12	Intron of PRMT8(+): 7Kb after exon 1	PRMT8	3608058			5	Exon 16 of APC(+)	APC	112175904			0	TRANSLOCATION		0	148917	0	15	NEW_VARIANT
P-0012925-T01-IM5	TP53 (NM_000546) rearrangement: c.-28-1687_c.207del	PRECISE	Note: The TP53 rearrangement is a deletion of 5UTR and exons 1-4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4231	0	14	17	Exon 4 of TP53(-)	TP53	7579480			17	5-UTR of TP53(-): 2Kb before coding start	TP53	7581627			16	DELETION		2147	159478	869	14	NEW_VARIANT
P-0011350-T01-IM5	APC (NM_000038) rearrangement: c.1743+2749:APC_chr5:g.112213830inv	PRECISE	Note: The APC rearrangement is an inversion of exons 15-16.	MANUAL_OK	3to3	3to3	-		42278	0	12	5	Intron of APC(+): 3Kb after exon 14	APC	112167418			5	3-UTR of REEP5(-): 653bp after coding stop	REEP5	112213830			13	INVERSION		46412	153274	26040	9	NEW_VARIANT
P-0014202-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		47993	0	19	21	Intron of ERG(-): 59bp after exon 1	ERG	39870228			21	Intron of TMPRSS2(-): 456bp after exon 2	TMPRSS2	42869590			22	DELETION		2999362	163757	42808	19	NEW_VARIANT
P-0010789-T01-IM5	DNMT1 (NM_001379) rearrangement : c.72_1232+762dup	PRECISE	Note: The DNMT1 rearrangement event results in the intragenic duplication of DNMT1 exons 1-16. One of the breakpoints is within DNMT1 exon1.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		22265	0	10	19	Intron of DNMT1(-): 762bp after exon 17	DNMT1	10269572			19	Exon 1 of DNMT1(-)	DNMT1	10305504			16	DUPLICATION		35932	149223	24191	10	NEW_VARIANT
P-0003101-T03-IM5	AR (NM_000044) rearrangement: c.2182_c.*970del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		6846	0	22	X	Exon 5 of AR(+)	AR	66937328			X	IGR: 534bp after AR(+)	AR	66944653			49	DELETION		7325	137600	223	22	NEW_VARIANT
P-0011157-T01-IM5	TERT (NM_198253) rearrangement: c.1573+12:TERT_chr5:g.682643del	PRECISE	Note: The TERT rearrangement is an intragenic deletion of exons 3-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript fusion (TERT-TPPP)		33883	0	8	5	5-UTR of TPPP(-): 4Kb before coding start	TPPP	682643			5	Intron of TERT(-): 12bp after exon 2	TERT	1293416			10	DELETION		610773	151497	33398	8	NEW_VARIANT
P-0012779-T01-IM5	B2M (NM_004048) rearrangement: c.67_c.68-1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1820	0	24	15	Exon 1 of B2M(+)	B2M	45003811			15	Intron of B2M(+): 1bp before exon 2	B2M	45007620			43	DELETION		3809	158876	2267	24	NEW_VARIANT
P-0012779-T01-IM5	B2M (NM_004048) rearrangement: c.346_c.*15-3del	PRECISE	Note: The B2M rearrangement is a deletion of exons 2-3. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		949	0	19	15	Exon 2 of B2M(+)	B2M	45007899			15	3-UTR of B2M(+): 1Kb after coding stop	B2M	45009802			21	DELETION		1903	158877	1202	19	NEW_VARIANT
P-0012555-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4576:TMPRSS2_c.-4791:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		127617	0	39	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875095			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875301			36	DELETION		3000206	157755	108508	37	NEW_VARIANT
P-0013526-T01-IM5	SPEN (NM_015001) Rearrangement : c.6934:SPEN_c.153+110:EPHA2	PRECISE	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.	MANUAL_OK	5to3	5to3	-		29954	0	12	1	Exon 11 of SPEN(+)	SPEN	16259669			1	Intron of EPHA2(-): 110bp after exon 2	EPHA2	16477281			11	DUPLICATION		217612	161612	32294	12	NEW_VARIANT
P-0013962-T01-IM5	KDM6A (NM_021140)  Rearrangement : c.654+6760_c.2938+22dup	PRECISE	Note: The KDM6A Rearrangement results in the intragenic duplication of exons 9-19 of KDM6A. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons: out of frame		34366	0	16	X	Intron of KDM6A(+): 7Kb after exon 8	KDM6A	44903694			X	Intron of KDM6A(+): 22bp after exon 19	KDM6A	44937772			21	DUPLICATION		34078	162936	64967	14	NEW_VARIANT
P-0013825-T01-IM5	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-16 fused to RET exons 12-20): c.1782:KIF5B_c.2137-512:RETinv	PRECISE	Note: The KIF5B - RET fusion involves the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (KIF5B-RET)		79648	0	44	10	Exon 16 of KIF5B(-)	KIF5B	32311908			10	Intron of RET(+): 512bp before exon 12	RET	43611520			59	INVERSION		11299612	162448	68737	41	NEW_VARIANT
P-0012321-T01-IM5	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	PRECISE	Note: The TMPRSS2-ERG fusion is an in-frame fusion.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		43160	0	26	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875961			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868127			29	DELETION		2992166	157020	37212	23	NEW_VARIANT
P-0012679-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1489+2812:EML4_c.3172+861:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		82797	0	102	2	Intron of ALK(-): 861bp after exon 19	ALK	29447466			2	Intron of EML4(+): 3Kb after exon 12	EML4	42525468			141	INVERSION		13078002	158511	72304	166	NEW_VARIANT
P-0012773-T01-IM5	TP53 (NM_000546) rearrangment: chr17:g.7552584_c.455:TP53del	PRECISE	Note: The TP53 rearrangement in a deletion of exons 5-11. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Antisense fusion		15344	0	26	17	Promoter of ATP1B2(+): 2Kb from tx start	ATP1B2	7552584			17	Exon 5 of TP53(-)	TP53	7578475			51	DELETION		25891	158884	8759	26	NEW_VARIANT
P-0011365-T01-IM5	RARA (NM_000964) - COPZ2 (NM_016429) rearrangement : c.1284:RARA_c.543-37:COPZ2del	PRECISE	Note: The RARA rearrangement event  results in the deletion of RARA exon9. One of the breakpoints is within RARA exon9.	MANUAL_OK	3to5	3to5	Antisense fusion		318834	0	82	17	Exon 9 of RARA(+)	RARA	38512373			17	Intron of COPZ2(-): 37bp before exon 8	COPZ2	46105913			102	DELETION		7593540	153301	291998	78	NEW_VARIANT
P-0014591-T01-IM6	ETV1 (NM_001163147)_EP300 (NM_001429)  rearrangement: t(7;22)(p21.2;q13.2)(chr7:g.14022908::chr22:g.41562739)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EP300-ETV1)		0	0	6	22	Intron of EP300(+): 69bp after exon 23	EP300	41562739			7	Intron of ETV1(-): 3Kb after exon 1	ETV1	14022908			2	TRANSLOCATION		0	165049	0	6	NEW_VARIANT
P-0012328-T01-IM5	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.55+2792:TMPRSS2_c.19-6300:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		115387	0	14	21	Intron of ERG(-): 6Kb before exon 4	ERG	39823844			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42877085			20	DELETION		3053241	157048	114940	14	NEW_VARIANT
P-0012919-T01-IM5	PDGFRA (NM_006206) rearrangement: c.-12-8153_c.2562+25dup	PRECISE	Note: The PDGFRA rearrangement is a duplication of exons 2-18. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		42698	0	5	4	5-UTR of PDGFRA(+): 8Kb before coding start	PDGFRA	55116771			4	Intron of PDGFRA(+): 25bp after exon 18	PDGFRA	55152155			10	DUPLICATION		35384	159402	39811	5	NEW_VARIANT
P-0012919-T01-IM5	KDR (NM_002253) rearrangement: chr4:g.99136655_c.2510-15del	PRECISE	Note: The KDR rearrangement is a deletion which includes exons 1-17 of KDR. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		138367	0	23	4	Intron of KDR(-): 15bp before exon 18	KDR	55963948			4	IGR: 46Kb before RAP1GDS1(+)	RAP1GDS1	99136655			27	DELETION		43172707	159400	129973	22	NEW_VARIANT
P-0010098-T02-IM5	PBRM1 (NM_018313) rearrangement: c.1088-275_c.2960dup	PRECISE	Note: The PBRM1 rearrangement is a duplication of exons 12-19. One of the breakpoints is within exon 19. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		24388	0	76	3	Exon 19 of PBRM1(-)	PBRM1	52623091			3	Intron of PBRM1(-): 275bp before exon 12	PBRM1	52669106			60	DUPLICATION		46015	160809	25218	72	NEW_VARIANT
P-0014158-T01-IM5	MLL2 (NM_003482) rearrangement:chr12:g.48956575_c.15959:MLL2del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10190	0	30	12	IGR: 5Kb before LALBA(-)	LALBA	48956575			12	Exon 50 of MLL2(-)	MLL2	49418454			35	DELETION		461879	163579	12029	28	NEW_VARIANT
P-0011534-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11):  c.55+1941:TMPRSS2_c.39+64333:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		120015	0	27	21	Intron of ERG(-): 64Kb after exon 3	ERG	39883253			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877936			43	DELETION		2994683	154118	113286	26	NEW_VARIANT
P-0011377-T01-IM5	MGA (NM_001164273) rearrangement: c.3085-167_c.7009-102del	PRECISE	Note: The MGA rearrangement is an intragenic deletion of exons 9-17.	MANUAL_OK	3to5	3to5	Deletion of 8 exons: in frame		79281	0	29	15	Intron of MGA(+): 167bp before exon 9	MGA	42005182			15	Intron of MGA(+): 102bp before exon 17	MGA	42046533			23	DELETION		41351	153534	48513	29	NEW_VARIANT
P-0011377-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		41245	0	71	21	Intron of ERG(-): 14Kb before exon 4	ERG	39831812			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867668			78	DELETION		3035856	153535	41788	68	NEW_VARIANT
P-0010398-T01-IM5	OSBPL9 (NM_148909) - BRAF (NM_004333) Rearrangement : t(1;7)(p32.3;q34)(chr1:g.52228623::chr7:g.140484912)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (OSBPL9-BRAF)		0	0	100	7	Intron of BRAF(-): 2Kb before exon 10	BRAF	140484912			1	Intron of OSBPL9(+): 980bp after exon 11	OSBPL9	52228623			44	TRANSLOCATION		0	145894	0	99	NEW_VARIANT
P-0014860-T01-IM6	SMARCA4 (NM_003072) rearrangement: t(4;19)(q26;p13.2)(chr4:g.118193638::chr19:g.11121062)	PRECISE	Note: The SMARCA4 rearrangement is a translocation with a breakpoint within exon 15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	32	19	Exon 14 of SMARCA4(+)	SMARCA4	11121062			4	IGR: 189Kb before TRAM1L1(-)	TRAM1L1	118193638			26	TRANSLOCATION		0	166019	0	30	NEW_VARIANT
P-0013344-T01-IM5	SPEN (NM_015001) rearrangement: t(1;9)(1p36.13;9q34.13)(chr1:g.16235959::chr9:g.132142700)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	1	27	9	IGR: 59Kb before C9orf106(+)	C9orf106	132142700			1	Exon 4 of SPEN(+)	SPEN	16235959			24	TRANSLOCATION		0	160916	0	26	NEW_VARIANT
P-0012416-T01-IM5	KDM5A (NM_001042603) rearrangement: c.3037-275_c.3972del	PRECISE	Note: The KDM5A rearrangement is an intragenic deletion of exons 21-24. One of breakpoints is within exon 24.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		13965	0	11	12	Exon 24 of KDM5A(-)	KDM5A	416214			12	Intron of KDM5A(-): 275bp before exon 21	KDM5A	420505			29	DELETION		4291	157301	14422	10	NEW_VARIANT
P-0014486-T01-IM6	MLL3 (NM_170606) rearrangement: chr7:g.148881016_c.6187dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		78163	0	26	7	IGR: 900bp after ZNF398(+)	ZNF398	148881016			7	Exon 36 of MLL3(-)	MLL3	151878758			35	DUPLICATION		2997742	164698	95575	25	NEW_VARIANT
P-0010741-T01-IM5	CUL3 (NM_003590) rearrangement : c.1206+19:CUL3_chr2:g.225008101del	PRECISE	Note: CUL3 rearrangement event results in the deletion of CUL3 exons 9-16.	MANUAL_OK	3to5	3to5	-		15830	0	5	2	IGR: 168Kb before SERPINE2(-)	SERPINE2	225008101			2	Intron of CUL3(-): 19bp after exon 8	CUL3	225370654			9	DELETION		362553	148945	15370	4	NEW_VARIANT
P-0010660-T01-IM5	MGA (NM_001164273) - MAPKBP1 (NM_001128608) rearrangement: c.2259:MGA_c.206+4637:MAPKBP1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MGA-MAPKBP1)		133351	0	63	15	Exon 6 of MGA(+)	MGA	41999996			15	Intron of MAPKBP1(+): 5Kb after exon 3	MAPKBP1	42096749			85	DELETION		96753	148099	92090	61	NEW_VARIANT
P-0012600-T01-IM5	FANCA (NM_000135) rearrangement: c.2014+248_c.4271dup	PRECISE	Note: The FANCA rearrangement is an intragenic duplication of exons 23-43. One of the breakpoint is within exon 43.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		35111	0	15	16	Exon 43 of FANCA(-)	FANCA	89805106			16	Intron of FANCA(-): 248bp after exon 22	FANCA	89839431			33	DUPLICATION		34325	157936	43748	15	NEW_VARIANT
P-0010044-T01-IM5	CTNNB1 (NM_001904) Rearrangement : c.13+78_c.271del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3221	0	102	3	Intron of CTNNB1(+): 78bp after exon 2	CTNNB1	41265650			3	Exon 4 of CTNNB1(+)	CTNNB1	41266474			0	DELETION		824	138104	2070	106	NEW_VARIANT
P-0012046-T01-IM5	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement : c.40-45795:ERG_c.56-2111:TMPRSS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (ERG-TMPRSS2)		78904	0	51	21	Intron of ERG(-): 7Kb after exon 1	ERG	39863339			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872227			44	DUPLICATION		3008888	155995	79125	51	NEW_VARIANT
P-0013886-T01-IM5	EML4 (NM_019063) - RET (NM_020975) rearrangement: t(2;10)(p21;q11.21)(chr2:g.42550559::chr10:g.43610067)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (EML4-RET)		0	0	21	10	Exon 11 of RET(+)	RET	43610067			2	Intron of EML4(+): 2Kb before exon 19	EML4	42550559			0	TRANSLOCATION		0	162599	0	20	NEW_VARIANT
P-0014201-T01-IM6	SDHC (NM_003001) Rearrangement : c.296:SDHC_chr1:g.182949452inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		110750	0	102	1	Exon 4 of SDHC(+)	SDHC	161326521			1	IGR: 43Kb before LAMC1(+)	LAMC1	182949452			96	INVERSION		21622931	163676	106704	204	NEW_VARIANT
P-0014201-T01-IM6	ATRX (NM_000489) Rearrangement : c.485-87_c.4558-4836inv	PRECISE	Note: The ATRX Rearrangement results in the inversion of exons 7 to 15 of ATRX. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		17959	0	16	X	Intron of ATRX(-): 5Kb before exon 16	ATRX	76896383			X	Intron of ATRX(-): 87bp before exon 7	ATRX	76944507			14	INVERSION		48124	163678	18576	15	NEW_VARIANT
P-0010429-T01-IM5	ARID1A (NM_006015) Rearrangement :  chr1:g.6744104_c.3886:ARID1Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		444768	0	6	1	Intron of DNAJC11(-): 3Kb before exon 2	DNAJC11	6744104			1	Exon 16 of ARID1A(+)	ARID1A	27100090			12	DELETION		20355986	145930	438021	6	NEW_VARIANT
P-0014120-T01-IM5	XRCC2 (NM_005431) rearrangement: t(7;8)(q36.1;q23.3)(chr7:g.152346274::chr8:g.117398324)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	102	8	IGR: 259Kb before EIF3H(-)	EIF3H	117398324			7	Exon 3 of XRCC2(-)	XRCC2	152346274			0	TRANSLOCATION		0	163478	0	169	NEW_VARIANT
P-0014531-T01-IM6	TMPRRS2 (NM_001135099) -ERG (NM_004449) Fusion: c.56-3954:TMPRSS2_c.18+11943:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		100462	0	19	21	Intron of ERG(-): 12Kb after exon 1	ERG	39858344			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874070			30	DELETION		3015726	164857	69387	19	NEW_VARIANT
P-0010822-T01-IM5	CDK12 (NM_016507) Rearrangement :  c.2911_c.2963+1045dup	PRECISE	Note: The CDK12 Rearrangement results in the duplication of exon 10. One of the breakpoints is within exon10. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		529	0	43	17	Exon 10 of CDK12(+)	CDK12	37673757			17	Intron of CDK12(+): 1Kb after exon 10	CDK12	37674854			55	DUPLICATION		1097	149381	683	43	NEW_VARIANT
P-0012777-T01-IM5	CDK12 (NM_016507) rearrangement: c.741:CDK12_chr17:g.38747170inv	PRECISE	Note: The CDK12 rearrangement is an inversion of exons 1-14. One of the breakpoints is within exon 1.	MANUAL_OK	3to3	3to3	-		158815	0	20	17	Exon 1 of CDK12(+)	CDK12	37619065			17	IGR: 37Kb before SMARCE1(-)	SMARCE1	38747170			12	INVERSION		1128105	158894	835855	19	NEW_VARIANT
P-0005436-T02-IM5	SMAD3 (NM_005902) Rearrangement :  t(9;15)(q31.3;q23)(chr9:g.110787568::chr15:g.67459189)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	36	15	Exon 4 of SMAD3(+)	SMAD3	67459189			9	IGR: 540Kb before KLF4(-)	KLF4	110787568			0	TRANSLOCATION		0	153392	0	35	NEW_VARIANT
P-0009786-T02-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		50340	0	7	21	Intron of ERG(-): 61Kb before exon 4	ERG	39878096			21	Intron of TMPRSS2(-): 493bp after exon 2	TMPRSS2	42869553			15	DELETION		2991457	151420	45509	7	NEW_VARIANT
P-0014701-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement: t(15,21)(q25.1,q22.3)(chr15:g.15:80623299::chr21:g.42843748)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	90	21	Exon 10 of TMPRSS2(-)	TMPRSS2	42843748			15	IGR: 73Kb before ARNT2(+)	ARNT2	80623299			0	TRANSLOCATION		0	165516	0	88	NEW_VARIANT
P-0014701-T01-IM6	ERG (NM_182918) Rearrangement : chr21:g.37828386_c.-109:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		37677	0	24	21	IGR: 5Kb before CLDN14(-)	CLDN14	37828386			21	Intron of ERG(-): 53Kb before exon 4	ERG	39870413			17	INVERSION		2042027	165515	38377	23	NEW_VARIANT
P-0004297-T02-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		30796	0	4	21	Intron of ERG(-): 54Kb before exon 4	ERG	39871171			21	Intron of TMPRSS2(-): 619bp after exon 2	TMPRSS2	42869427			17	DELETION		2998256	148107	46801	4	NEW_VARIANT
P-0011018-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29)	PRECISE	Note: The EML4-ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		56577	0	32	2	Intron of ALK(-): 13bp after exon 19	ALK	29448314			2	Intron of EML4(+): 2Kb before exon 6	EML4	42506102			76	INVERSION		13057788	150409	56306	32	NEW_VARIANT
P-0011395-T01-IM5	ARID1B (NM_020732) rearrangement: c.5016_chr6:g.157544399del	PRECISE	Note: The ARID1B rearrangement is a deletion of exon 20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11795	0	15	6	Exon 20 of ARID1B(+)	ARID1B	157527465			6	IGR: 12Kb after ARID1B(+)	ARID1B	157544399			16	DELETION		16934	153443	11900	15	NEW_VARIANT
P-0014076-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3633:TMPRSS2_c.18+24406:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		122818	0	65	21	Intron of ERG(-): 24Kb after exon 1	ERG	39845881			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873749			52	DELETION		3027868	163225	107617	63	NEW_VARIANT
P-0010978-T01-IM5	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	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (EML4-ALK)		0		76	2	Intron of ALK(-): 20bp before exon 20	ALK	29446414			2	Intron of EML4(+): 2Kb after exon 18	EML4	42546901			114	INVERSION		13100487	150417	48193		NEW_VARIANT
P-0012055-T01-IM5	SOX17 (NM_022454) rearrangement: c.-4513_c.-3197inv	PRECISE	Note: The SOX17 rearrangement is an inversion which includes the promoter region of SOX17. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1443	0	28	8	IGR: 4Kb before SOX17(+)	SOX17	55366186			8	Promoter of SOX17(+): 3Kb from tx start	SOX17	55367502			45	INVERSION		1316	156024	2705	28	NEW_VARIANT
P-0013790-T01-IM5	RASA1 (NM_002890) Rearrangement : c.1333-4282_1404del	PRECISE	Note: The RASA1 Rearrangement results in the deletion of exon 10 . One of the breakpoints is within exon 10. Its functional significance is undetermined,	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1200	0	41	5	Intron of RASA1(+): 4Kb before exon 10	RASA1	86654086			5	Exon 10 of RASA1(+)	RASA1	86658439			54	DELETION		4353	162263	1222	38	NEW_VARIANT
P-0011506-T01-IM5	ETV6 (NM_001987) - CDKN1B (NM_004064) rearrangement: c.34-10600:ETV6_c.476-58:CDKN1Bdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (ETV6-CDKN1B)		308502	0	11	12	Intron of ETV6(+): 11Kb before exon 2	ETV6	11894784			12	Intron of CDKN1B(+): 58bp before exon 2	CDKN1B	12871701			13	DELETION		976917	153924	277961	11	NEW_VARIANT
P-0011433-T01-IM5	MSH6 (NM_000179) - FBXO11 (NM_001190274) rearrangement : c.1738:MSH6_c.232+22604:FBXO11del	PRECISE	Note: The MSH6-FBXO11 rearrangement event results in the deletion of MSH6 exons 4-10. One of the breakpoints is within MSH6 exon4.	MANUAL_OK	3to5	3to5	Antisense fusion		24978	0	22	2	Exon 4 of MSH6(+)	MSH6	48026860			2	Intron of FBXO11(-): 23Kb after exon 1	FBXO11	48110024			31	DELETION		83164	153630	25314	20	NEW_VARIANT
P-0014368-T01-IM6	FOXA1 (NM_004496) rearrangement: c.932_chr14:g.38567231del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10841	0	21	14	Exon 2 of FOXA1(-)	FOXA1	38061057			14	IGR: 110Kb before SSTR1(+)	SSTR1	38567231			24	DELETION		506174	164247	8278	21	NEW_VARIANT
P-0012260-T01-IM5	RB1 (NM_000321) rearrangement: c.719-308_c.862-188del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 8.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1521	0	6	13	Intron of RB1(+): 308bp before exon 8	RB1	48936643			13	Intron of RB1(+): 188bp before exon 9	RB1	48938842			8	DELETION		2199	156863	936	5	NEW_VARIANT
P-0012260-T01-IM5	ERBB2 (NM_004448) rearrangement: c.3413-57:ERBB2_chr17:g.37886288del	PRECISE	Note: The ERBB2 rearrangement is a deletion of exon 27.	MANUAL_OK	3to5	3to5	Antisense fusion		4174	0	50	17	Intron of ERBB2(+): 57bp before exon 27	ERBB2	37883885			17	Intron of C17orf37(-): 159bp after exon 2	C17orf37	37886288			48	DELETION		2403	156864	2768	43	NEW_VARIANT
P-0012260-T01-IM5	CEBPB (NM_005194) rearrangement: c.978:CEBPB_chr20:g.48840052inv	IMPRECISE	Note: The CEBPB rearrangement in an inversion of a part of exon 1. The breakpoint is within exon 1.	MANUAL_OK	3to3	3to3	-		30	0	14	20	Exon 1 of CEBPB(+)	CEBPB	48808548			20	IGR: 33Kb before CEBPB(+)	CEBPB	48840052			0	INVERSION		31504	156865	79	14	NEW_VARIANT
P-0007307-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.126+159:TMPRSS2_c.18+25874:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		58385	0	55	21	Intron of ERG(-): 26Kb after exon 1	ERG	39844413			21	Intron of TMPRSS2(-): 159bp after exon 2	TMPRSS2	42869887			41	DELETION		3025474	153381	44342	52	NEW_VARIANT
P-0014237-T01-IM6	SMARCA4 (NM_003072) rearrangement: t(12;19)(q13.3;p13.2)(chr12:g.:54842304::chr19:g.11172477)	PRECISE	Note: The SMARCA4 rearrangement is a translocation with one of the breakpoints within exon35 of SMARCA4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	47	19	Exon 33 of SMARCA4(+)	SMARCA4	11172477			12	IGR: 7Kb before GTSF1(-)	GTSF1	54842304			48	TRANSLOCATION		0	163821	0	46	NEW_VARIANT
P-0014237-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 10-16): c.2390:FGFR3_c.1836+80:TACC3dup	PRECISE	Note: The FGFR3 - TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within exon 18 of FGFR3.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		35179	0	74	4	Intron of TACC3(+): 80bp after exon 9	TACC3	1739135			4	Exon 18 of FGFR3(+)	FGFR3	1808958			92	DUPLICATION		69823	163818	59949	72	NEW_VARIANT
P-0010659-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		33914	0	7	21	Intron of ERG(-): 2Kb after exon 1	ERG	39868208			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867516			11	DELETION		2999308	148120	29456	7	NEW_VARIANT
P-0014530-T01-IM6	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	PRECISE	Note: The FGFR3-TACC3 fusion is predicted to be in-frame and includes the kinase domain of FGFR3.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-TACC3)		54881	0	18	4	Intron of TACC3(+): 52bp before exon 6	TACC3	1732847			4	Intron of FGFR3(+): 54bp after exon 17	FGFR3	1808715			23	DUPLICATION		75868	164847	48243	17	NEW_VARIANT
P-0013879-T01-IM5	PIK3R2 (NM_005027) rearrangement: c.323-139_c.1123del	PRECISE	Note: The PIK3R2 rearrangement is an intragenic deletion of exons 3 -10. One of the breakpoints is within 10.  The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		14275	0	29	19	Intron of PIK3R2(+): 139bp before exon 3	PIK3R2	18271142			19	Exon 10 of PIK3R2(+)	PIK3R2	18273790			40	DELETION		2648	162612	15754	29	NEW_VARIANT
P-0012145-T01-IM5	RNF43 (NM_017763) rearrangement: t(1;17)(p36.13;q22)(chr1:g.19206599::chr17:g.56434626)	PRECISE	Note: The RNF43 rearrangement is a translocation that may result in a truncation of exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	12	17	Intron of RNF43(-): 203bp after exon 9	RNF43	56434626			1	Intron of ALDH4A1(-): 732bp before exon 9	ALDH4A1	19206599			23	TRANSLOCATION		0	156497	0	12	NEW_VARIANT
P-0011192-T01-IM5	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement : c.-565:MCL1_c.57+728:ENSAdup	PRECISE	Note: The MCL1-ENSA rearrangement event is a duplication which results in the fusion of MCL1 promoter region with ENSA exons 2-4.	MANUAL_OK	5to3	5to3	Transcript fusion (MCL1-ENSA)		378	0	21	1	Promoter of MCL1(-): 435bp from tx start	MCL1	150552571			1	Intron of ENSA(-): 375bp after exon 1	ENSA	150601162			35	DUPLICATION		48591	151659	684	20	NEW_VARIANT
P-0011192-T01-IM5	TERT (NM_198253) rearrangement: c.-338:TERT_chr5:g.1536135del	PRECISE	Note: The TERT rearrangement events results in the deletion of TERT promoter region. One of the breakpoints is within the TERT promoter.	MANUAL_OK	3to5	3to5	-		247	0	47	5	Promoter of TERT(-): 280bp from tx start	TERT	1295442			5	IGR: 36Kb before SDHAP3(-)	SDHAP3	1536135			38	DELETION		240693	151658	497	47	NEW_VARIANT
P-0011175-T01-IM5	CBL (NM_005188) rearrangement: c.1095+35_c.1432-291del	PRECISE	Note: The CBL rearrangement is a intragenic deletion of exons 8-9.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: in frame		4934	0	31	11	Intron of CBL(+): 35bp after exon 7	CBL	119148589			11	Intron of CBL(+): 291bp before exon 10	CBL	119155388			31	DELETION		6799	151544	4950	30	NEW_VARIANT
P-0011175-T01-IM5	MSH2 (NM_000251) rearrangement: c.346_c.1387-6199del	PRECISE	Note: The MSH2 rearrangement is a intragenic deletion of exons 2-8. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		17245	0	16	2	Exon 2 of MSH2(+)	MSH2	47635674			2	Intron of MSH2(+): 6Kb before exon 9	MSH2	47683971			25	DELETION		48297	151545	17271	16	NEW_VARIANT
P-0011281-T01-IM5	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.1432+64:WT1_c.1144-56067:ELP4inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (WT1-ELP4)		3139	0	30	11	Intron of ELP4(+): 56Kb before exon 10	ELP4	31748874			11	Intron of WT1(-): 64bp after exon 9	WT1	32413454			27	INVERSION		664580	152434	3600	29	NEW_VARIANT
P-0012562-T01-IM5	DNAJB1 (NM_006145) rearrangement: t(2;19)(q32.3;p13.12)(chr2:g.192746391::chr19:g.14627434)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	32	19	Exon 2 of DNAJB1(-)	DNAJB1	14627434			2	IGR: 47Kb before SDPR(-)	SDPR	192746391			0	TRANSLOCATION		0	157840	0	13	NEW_VARIANT
P-0013985-T01-IM5	MDC1 (NM_014641) Rearrangement : t(3,6)(q26.33,p21.33)(chr3:g.179829046::chr6:g.30681978)	PRECISE	Note: MDC1 Rearrangement results in the possible truncation of MDC1. One of the breakpoints is 18bp before exon 3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	11	6	Intron of MDC1(-): 18bp before exon 3	MDC1	30681978			3	IGR: 311Kb before PEX5L(-)	PEX5L	179829046			11	TRANSLOCATION		0	162881	0	11	NEW_VARIANT
P-0013925-T01-IM5	PTPRS (NM_002850) rearrangement: c.-94-2961_c.237+67inv	PRECISE	Note: The PTPRS rearrangement is an inversion of 5UTR and exons 1-3.	MANUAL_OK	5to5	5to5	Antisense fusion		3176	0	7	19	Intron of PTPRS(-): 67bp after exon 3	PTPRS	5274143			19	5-UTR of PTPRS(-): 3Kb before coding start	PTPRS	5289206			9	INVERSION		15063	162743	2242	7	NEW_VARIANT
P-0014007-T01-IM5	TSC2 (NM_000548) rearrangement: c.1717-568_c.3884-80del	PRECISE	Note: The TSC2 rearrangement is an intragenic deletion of exons 17 -32. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 15 exons: out of frame		39993	0	12	16	Intron of TSC2(+): 568bp before exon 17	TSC2	2119889			16	Intron of TSC2(+): 80bp before exon 32	TSC2	2133616			13	DELETION		13727	163034	25426	11	NEW_VARIANT
P-0010782-T01-IM5	NBN (NM_002485) - TMEM64 (NM_001008495) rearrangement: c.572:NBN_c.795+4539:TMEM64dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NBN-TMEM64)		7017	0	32	8	Exon 5 of NBN(-)	NBN	90990460			8	Intron of TMEM64(-): 5Kb after exon 1	TMEM64	91652800			39	DUPLICATION		662340	149160	10335	31	NEW_VARIANT
P-0013749-T02-IM6	MEN1 (NM_000244) rearrangement : c.407_722del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5297	0	47	11	Exon 5 of MEN1(-)	MEN1	64575100			11	Exon 3 of MEN1(-)	MEN1	64577175			49	DELETION		2075	166551	4377	46	NEW_VARIANT
P-0010208-T01-IM5	NOTCH1 (NM_017617) - UBAC1 (NM_016172) rearrangement : c.6082+10:NOTCH1_c.333+1482:UBAC1inv	PRECISE	Note: The NOTCH1 - UBAC1 rearrangement results in the inversion of NOTCH1 exons 32-34.	MANUAL_OK	5to5	5to5	Antisense fusion		15773	0	11	9	Intron of UBAC1(-): 1Kb after exon 3	UBAC1	138844044			9	Intron of NOTCH1(-): 10bp after exon 32	NOTCH1	139393554			23	INVERSION		549510	144815	14174	10	NEW_VARIANT
P-0010553-T01-IM5	EWSR1 (NM_013986) rearrangement: c.14-1270_c.1027+240dup	PRECISE	Note: The EWSR1 rearrangement is a duplication of exons 2-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 7 exons: in frame		33314	0	38	22	Intron of EWSR1(+): 1Kb before exon 2	EWSR1	29666935			22	Intron of EWSR1(+): 240bp after exon 8	EWSR1	29687828			31	DUPLICATION		20893	147607	38200	38	NEW_VARIANT
P-0014973-T01-IM6	RRAGC (NM_022157) Rearrangement : c.756+92_899+1584del	PRECISE	Note: The RRAGC Rearrangement results in the intragenic deletion of exon 5 of RRAGC. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		2568	0	12	1	Intron of RRAGC(-): 2Kb after exon 5	RRAGC	39315703			1	Intron of RRAGC(-): 92bp after exon 4	RRAGC	39317954			15	DELETION		2251	166402	1808	9	NEW_VARIANT
P-0015002-T01-IM6	ZFHX3 (NM_006885) rearrangement : c.5225:ZFHX3_g.6119693inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (ZFHX3-A2BP1)		322021	0	23	16	5-UTR of A2BP1(+): 982Kb before coding start	A2BP1	6119693			16	Exon 9 of ZFHX3(-)	ZFHX3	72831356			21	INVERSION		66711663	166534	328704	22	NEW_VARIANT
P-0005454-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1943:TMPRSS2_c.18+13593:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		89728	0	60	21	Intron of ERG(-): 14Kb after exon 1	ERG	39856694			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872059			60	DELETION		3015365	160009	51761	59	NEW_VARIANT
P-0013372-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1734:TMPRSS2_c.237-2384:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		62133	0	102	21	Intron of ERG(-): 2Kb before exon 5	ERG	39797867			21	Intron of TMPRSS2(-): 2Kb after exon 2	TMPRSS2	42868312			73	DELETION		3070445	161012	109995	186	NEW_VARIANT
P-0014807-T01-IM6	C6orf222 (NM_001010903) - NOTCH4 (NM_004557) rearrangement: c.1924-105:C6orf222_c.2188:NOTCH4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (C6orf222-NOTCH4)		111003	0	20	6	Exon 14 of NOTCH4(-)	NOTCH4	32181597			6	Intron of C6orf222(-): 105bp before exon 12	C6orf222	36285273			34	DELETION		4103676	165868	118874	20	NEW_VARIANT
P-0014697-T01-IM6	RAD21 (NM_006265) Rearrangement : c.-33+2576_c.275-14del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		3391	0	29	8	Intron of RAD21(-): 14bp before exon 4	RAD21	117874193			8	5-UTR of RAD21(-): 5Kb before coding start	RAD21	117884274			45	DELETION		10081	165532	3367	29	NEW_VARIANT
P-0013355-T01-IM5	STK11 (NM_000455) rearrangement: c.464+468_c.782dup	PRECISE	Note: The STK11 rearrangement is an intragenic duplication of exons 4-6. One of the breakpoints is within exon 6.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		5705	0	7	19	Intron of STK11(+): 468bp after exon 3	STK11	1219880			19	Exon 6 of STK11(+)	STK11	1221259			14	DUPLICATION		1379	160971	5165	7	NEW_VARIANT
P-0014892-T01-IM6	NOTCH1 (NM_017617) rearrangement: chr9:g.139383644_c.742+20del	PRECISE	Note: The NOTCH1 (NM_017617) rearrangement is a deletion of exons 5-34. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		112351	0	13	9	IGR: 5Kb before NOTCH1(-)	NOTCH1	139383644			9	Intron of NOTCH1(-): 20bp after exon 4	NOTCH1	139417282			26	DELETION		33638	166179	101294	13	NEW_VARIANT
P-0012741-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.55+1605:TMPRSS2_c.40-54554:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		124304	0	13	21	Intron of ERG(-): 55Kb before exon 4	ERG	39872098			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42878272			28	DELETION		3006174	158763	112363	13	NEW_VARIANT
P-0014859-T01-IM6	CTRC (NM_007272)  - NTRK1 (NM_002529) rearrangement: c.88:CTRC_c.850+45:NTRK1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CTRC-NTRK1)		1017341	0	101	1	Exon 2 of CTRC(+)	CTRC	15766843			1	Intron of NTRK1(+): 45bp after exon 8	NTRK1	156841592			85	DELETION		141074749	166013	997809	158	NEW_VARIANT
P-0014859-T01-IM6	ARID2 (NM_152641) rearrangement: c.419-2860_c.638-69del	PRECISE	Note: The ARID2 rearrangement is an intragenic deletion of exon5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2086	0	17	12	Intron of ARID2(+): 3Kb before exon 5	ARID2	46208593			12	Intron of ARID2(+): 69bp before exon 6	ARID2	46215134			20	DELETION		6541	166011	2113	17	NEW_VARIANT
P-0014990-T01-IM6	MLL2 (NM_003482) -  ZFP30 (NM_014898) Rearrangement : t(12;19)(q13.12;q13.13)(chr12:g.49432673::chr19:g.38141811)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MLL2-ZFP30)		0	0	29	19	5-UTR of ZFP30(-): 3Kb before coding start	ZFP30	38141811			12	Exon 34 of MLL2(-)	MLL2	49432673			11	TRANSLOCATION		0	166476	0	27	NEW_VARIANT
P-0013704-T01-IM5	SOX9 (NM_000346) rearrangement: c.685+256_c.1477dup	PRECISE	Note: The SOX9 rearrangement is a duplication of exon3. One of the breakpoints within exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		6716	0	70	17	Intron of SOX9(+): 256bp after exon 2	SOX9	70119369			17	Exon 3 of SOX9(+)	SOX9	70120475			63	DUPLICATION		1106	162064	7051	69	NEW_VARIANT
P-0011370-T01-IM5	BRAF (NM_004333) Rearrangement :  c.240+3096_c.1314+210del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 8 exons: in frame		179793	0	77	7	Intron of BRAF(-): 210bp after exon 10	BRAF	140482611			7	Intron of BRAF(-): 3Kb after exon 2	BRAF	140546815			58	DELETION		64204	153399	109143	74	NEW_VARIANT
P-0014905-T01-IM6	PTEN (NM_000314)- MYOF (NM_013451) Rearrangement : c.855:PTEN_c.236+8749:MYOFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (PTEN-MYOF)		5821	0	38	10	Exon 8 of PTEN(+)	PTEN	89720704			10	Intron of MYOF(-): 9Kb after exon 3	MYOF	95203058			92	INVERSION		5482354	166120	6578	31	NEW_VARIANT
P-0010953-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2147:TMPRSS2_c.40-37761:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		103320	0	25	21	Intron of ERG(-): 15Kb after exon 1	ERG	39855305			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872263			34	DELETION		3016958	149929	94517	24	NEW_VARIANT
P-0010731-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement : c.56-2331:TMPRSS2_c.40-63084:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		52966	0	26	21	Intron of ERG(-): 63Kb before exon 4	ERG	39880628			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872447			39	INVERSION		2991819	148565	53653	26	NEW_VARIANT
P-0000373-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3994:TMPRSS2_c.19-24499:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		93891	0	41	21	Intron of ERG(-): 24Kb before exon 4	ERG	39842043			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874110			63	DELETION		3032067	156611	45556	39	NEW_VARIANT
P-0014824-T01-IM6	AKT1 (NM_001014431) rearrangement: c.971:AKT1_chr14:g.105380925inv	PRECISE	Note: The AKT1 rearrangement is an inversion of exons 11-14. One of the breakpoints is within exon 11.	MANUAL_OK	3to3	3to3	-		22748	0	5	14	Exon 11 of AKT1(-)	AKT1	105239416			14	IGR: 10Kb before PLD4(+)	PLD4	105380925			6	INVERSION		141509	165944	21757	5	NEW_VARIANT
P-0013828-T01-IM5	APC (NM_000038) rearrangement: chr5:g.95664163_c.261:APCdup	PRECISE	Note: The APC rearrangement is a duplication of 5UTR and exons 1-4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		11763	0	31	5	IGR: 62Kb before PCSK1(-)	PCSK1	95664163			5	Exon 4 of APC(+)	APC	112102926			38	DUPLICATION		16438763	162456	11366	31	NEW_VARIANT
P-0013835-T01-IM5	ANKRD11 (NM_013275) rearrangement: c.4146_c.7806+339del	PRECISE	Note: The ANKRD11 rearrangement is a deletion of exons 9-12. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		31287	0	6	16	Intron of ANKRD11(-): 339bp after exon 12	ANKRD11	89336886			16	Exon 9 of ANKRD11(-)	ANKRD11	89348804			11	DELETION		11918	162378	36763	6	NEW_VARIANT
P-0013392-T01-IM5	ETV6 (NM_001987) rearrangement: c.163+13216_c.464-2446dup	PRECISE	Note: The ETV6 rearrangement is an intragenic duplication of exons 3-4.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		157469	0	15	12	Intron of ETV6(+): 13Kb after exon 2	ETV6	11918729			12	Intron of ETV6(+): 2Kb before exon 5	ETV6	12019912			32	DUPLICATION		101183	161113	166156	15	NEW_VARIANT
P-0014511-T01-IM6	FANCA (NM_000135) - WWOX (NM_016373) rearrangement: c.3348+22:FANCA_c.409+15919:WWOXinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (FANCA-WWOX)		276218	0	7	16	Intron of WWOX(+): 16Kb after exon 4	WWOX	78164970			16	Intron of FANCA(-): 22bp after exon 33	FANCA	89815045			13	INVERSION		11650075	164751	252246	7	NEW_VARIANT
P-0014511-T01-IM6	TP53 (NM_000546) rearrangement: c.207_c.751del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 4-7. The breakpoints are within exons 4 and 7.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		13381	0	79	17	Exon 7 of TP53(-)	TP53	7577530			17	Exon 4 of TP53(-)	TP53	7579480			80	DELETION		1950	164748	8817	77	NEW_VARIANT
P-0011321-T01-IM5	PIK3R2 (NM_005027) - ZNF714 (NM_18251) rearrangement: c.1078:PIK3R2_c.142+1169:ZNF714del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (PIK3R2-ZNF714)		39676	0	45	19	Exon 9 of PIK3R2(+)	PIK3R2	18273285			19	Intron of ZNF714(+): 1Kb after exon 4	ZNF714	21282885			39	DELETION		3009600	152612	40593	33	NEW_VARIANT
P-0010214-T01-IM5	TOP1 (NM_003286) rearrangement : t(2;20)(p23.3;q12)(chr2:g.26507418::chr20:g.39728683)	PRECISE	Note: The TOP1 rearrangement event is a translocation which results in the truncation of TOP1 exons 12-21.	MANUAL_OK	5to5	5to5	-		0	0	38	20	Intron of TOP1(+): 13bp before exon 12	TOP1	39728683			2	Intron of HADHB(+): 333bp before exon 14	HADHB	26507418			29	TRANSLOCATION		0	144761	0	38	NEW_VARIANT
P-0012151-T01-IM5	KEAP1 (NM_203500) rearrangement: c.640-1439_c.844del	PRECISE	Note: The KEAP1 rearrangement is an intragenic deletion of a part of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1555	0	10	19	Exon 3 of KEAP1(-)	KEAP1	10602734			19	Intron of KEAP1(-): 1Kb before exon 3	KEAP1	10604377			12	DELETION		1643	156418	1705	9	NEW_VARIANT
P-0014626-T01-IM6	SRRM1 (NM_005839) - POLD1 (NM_002691) rearrangement: t(1;19)(p36.11;q13.33)(chr1:g.24979609::chr19:g.50919623)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (SRRM1-POLD1)		0	0	56	19	Intron of POLD1(+): 30bp before exon 23	POLD1	50919623			1	Intron of SRRM1(+): 86bp after exon 8	SRRM1	24979609			0	TRANSLOCATION		0	165311	0	51	NEW_VARIANT
P-0014626-T01-IM6	MSH3 (NM_002439) rearrangement: c.3044_c.3130+3040dup	PRECISE	Note: The MSH3 rearrangement is a duplication of exon 22. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1217	0	65	5	Exon 22 of MSH3(+)	MSH3	80160675			5	Intron of MSH3(+): 3Kb after exon 22	MSH3	80163801			50	DUPLICATION		3126	165306	1320	62	NEW_VARIANT
P-0012820-T01-IM5	ZFHX3 (NM_006885) Rearrangement : chr16:g.72984364_g.72523259del	PRECISE	Note: The ZFHX3 (NM_006885) rearrangement results in the intragenic deletion of exons 4 to 10 of ZFHX3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		103811	0	80	16	IGR: 294Kb before ZFHX3(-)	ZFHX3	72523259			16	Intron of ZFHX3(-): 4bp after exon 3	ZFHX3	72984364			51	DELETION		461105	159015	67001	78	NEW_VARIANT
P-0014844-T01-IM6	RET (NM_020975) rearrangement: t(4;10)(q26;q11.21)(chr4:g.117039927)(chr10:g.43606798)	PRECISE	Note: The RET rearrangement is a translocation with a breakpoint within exon7 of RET. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	29	10	Exon 7 of RET(+)	RET	43606798			4	IGR: 181Kb before MIR1973(+)	MIR1973	117039927			15	TRANSLOCATION		0	166059	0	26	NEW_VARIANT
P-0010177-T01-IM5	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	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		77753	0	41	2	Intron of ALK(-): 964bp before exon 20	ALK	29447358			2	Intron of EML4(+): 3Kb before exon 13	EML4	42525732			54	INVERSION		13078374	144665	71389	40	NEW_VARIANT
P-0014455-T01-IM6	CREBBP (NM_004380) - NLRC3(NM_178844) Rearrangement : c.2880+66:CREBBP_c.2184-571:NLRC3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (CREBBP-NLRC3)		160138	0	33	16	Intron of NLRC3(-): 571bp before exon 9	NLRC3	3604897			16	Intron of CREBBP(-): 66bp after exon 14	CREBBP	3820505			29	DELETION		215608	164633	76819	32	NEW_VARIANT
P-0014430-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.-32+4013_c.2368del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		41618	0	22	19	5-UTR of SMARCA4(+): 19Kb before coding start	SMARCA4	11075863			19	Exon 15 of SMARCA4(+)	SMARCA4	11123718			28	DELETION		47855	164529	28318	22	NEW_VARIANT
P-0001184-T02-IM5	TCF3 (NM_001136139) rearrangement : c.1093+25:TCF3_chr19:g.24369803del	PRECISE	Note1: The TCF3 rearrangement event results in the deletion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.	MANUAL_OK	3to5	3to5	-		1110631	0	102	19	Intron of TCF3(-): 25bp after exon 12	TCF3	1620942			19	IGR: 25Kb before LOC100101266(-)	LOC100101266	24369803			131	DELETION		22748861	149238	1334403	170	NEW_VARIANT
P-0001184-T02-IM5	TCF3 (NM_001136139) - ABHD17A (NM_001130111) rearrangement : c.1093+25:TCF3_chr19:g.24369803del	PRECISE	Note2: The TCF3 - ABHD17A rearrangement event results in the inversion of TCF3 exons 12-18. One of the breakpoints is within TCF3 exon12.	MANUAL_OK	5to5	5to5	Antisense fusion		43004	0	102	19	Exon 12 of TCF3(-)	TCF3	1620997			19	Intron of FAM108A1(-): 339bp before exon 5	FAM108A1	1878025			263	INVERSION		257028	149240	61742	156	NEW_VARIANT
P-0012246-T01-IM5	ATM (NM_000051) Rearrangement : t(11;X)(q22.3;p22.13)(chr11:g.108168152::chrX:g.18639068)	PRECISE	Note: The ATM Rearrangement is a translocation event that results in the possible truncation of exons 34-63. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	33	X	Intron of CDKL5(+): 982bp after exon 16	CDKL5	18639068			11	Intron of ATM(+): 43bp after exon 33	ATM	108168152			17	TRANSLOCATION		0	156816	0	32	NEW_VARIANT
P-0009297-T02-IM5	MED12 (NM_005120) Rearrangement : c.3867+20_c.4864-30dup	PRECISE	Note: The MED12  Rearrangement results in the intragenic duplication of exons28-35. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 8 exons: in frame		29454	0	8	X	Intron of MED12(+): 20bp after exon 27	MED12	70349725			X	Intron of MED12(+): 30bp before exon 36	MED12	70354912			7	DUPLICATION		5187	156557	30912	6	NEW_VARIANT
P-0012104-T01-IM5	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)	PRECISE		MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		30812	0	8	21	5-UTR of ERG(-): 3Kb before coding start	ERG	39951033			21	Intron of TMPRSS2(-): 424bp after exon 2	TMPRSS2	42869622			20	DELETION		2918589	156272	29387	8	NEW_VARIANT
P-0011156-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4374:TMPRSS2_c.18+15905:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		139356	0	22	21	Intron of ERG(-): 16Kb after exon 1	ERG	39854382			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875503			21	DELETION		3021121	151494	132949	20	NEW_VARIANT
P-0012778-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1320:EML4_c.3172+885:ALKinv	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		68961	0	63	2	Intron of ALK(-): 885bp after exon 19	ALK	29447442			2	Intron of EML4(+): 1Kb after exon 5	EML4	42493191			55	INVERSION		13045749	158849	64403	61	NEW_VARIANT
P-0012028-T01-IM5	TERT (NM_198253) rearrangement : c.-198_chr5:g.19154622inv	PRECISE	Note: The TERT rearrangement event results in the inversion of the TERT promoter region.	MANUAL_OK	3to3	3to3	-		10228	0	102	5	Promoter of TERT(-): 140bp from tx start	TERT	1295302			5	IGR: 319Kb before CDH18(-)	CDH18	19154622			211	INVERSION		17859320	155942	11536	191	NEW_VARIANT
P-0014583-T01-IM6	BRCA2 (NM_000059) rearrangement: t(2;13)(p15;q13.1)(chr2:g.63335220::chr13:g.:32912064)	PRECISE	Note: The BRCA2 rearrangement is a translocation with a breakpoint within exon 11 of BRCA2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	36	13	Exon 11 of BRCA2(+)	BRCA2	32912064			2	IGR: 13Kb before C2orf86(-)	C2orf86	63335220			34	TRANSLOCATION		0	165124	0	35	NEW_VARIANT
P-0014583-T01-IM6	TP53 (NM_000546) rearrangement: c.96_c.920-17dup.	IMPRECISE	Note: The TP53 rearrangement is a duplication of exons 3-8. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		13998	0	18	17	Intron of TP53(-): 17bp before exon 9	TP53	7576943			17	Exon 3 of TP53(-)	TP53	7579700			0	DUPLICATION		2757	165122	9792	18	NEW_VARIANT
P-0014583-T01-IM6	NCOR1 (NM_006311) rearrangement: c.732+628_c.1503dup	PRECISE	Note: The NCOR1 rearrangement is a duplication of exons 7-14. One of the breakpoints is within exon 14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		7896	0	34	17	Exon 14 of NCOR1(-)	NCOR1	16040631			17	Intron of NCOR1(-): 628bp after exon 6	NCOR1	16061446			43	DUPLICATION		20815	165121	11721	30	NEW_VARIANT
P-0014583-T01-IM6	TP63 (NM_003722) rearrangement: c.1746+23_c.1858del	PRECISE	Note: The TP63 rearrangement is an intragenic deletion. One of the breakpoints is within exon 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1447	0	57	3	Intron of TP63(+): 23bp after exon 13	TP63	189608694			3	Exon 14 of TP63(+)	TP63	189612106			71	DELETION		3412	165120	1080	56	NEW_VARIANT
P-0014583-T01-IM6	NBN (NM_002485) rearrangement: c.38-93_c.584+810dup	PRECISE	Note: The NBN rearrangement is a duplication of exons 2-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons: out of frame		4080	0	12	8	Intron of NBN(-): 810bp after exon 5	NBN	90989638			8	Intron of NBN(-): 93bp before exon 2	NBN	90995176			14	DUPLICATION		5538	165123	9482	12	NEW_VARIANT
P-0013241-T01-IM5	KLHL29 (NM_052920) - FGFR2 (NM_000141) rearrangement: t(2;10)(p24.1;q26.13)(chr2:g.:23647979::chr10:g.123241923)	PRECISE	Note: The KLHL29 - FGFR2 rearrangement is a translocation which results in the fusion of KLHL29 exon 1 with FGFR2 exon 18	MANUAL_OK	3to3	3to3	Transcript fusion (KLHL29-FGFR2)		0	0	71	10	Intron of FGFR2(-): 232bp before exon 17	FGFR2	123241923			2	5-UTR of KLHL29(+): 137Kb before coding start	KLHL29	23647979			41	TRANSLOCATION		0	160599	0	70	NEW_VARIANT
P-0013241-T01-IM5	FGFR2 (NM_000141) - ATP6V1D (NM_015994) rearrangement: t(10;14)(q26.13;q23.2)(chr10:g.123242048::chr14:g.67818116)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-ATP6V1D)		0	0	46	14	Intron of ATP6V1D(-): 709bp before exon 3	ATP6V1D	67818116			10	Intron of FGFR2(-): 357bp before exon 17	FGFR2	123242048			21	TRANSLOCATION		0	160601	0	46	NEW_VARIANT
P-0004961-T02-IM5	EGFR (NM_005228) Rearrangement :  c.2062-143_c.3115-117dup	PRECISE	Note: The EGFR Rearrangement results in the tandem internal duplication of EGFR exons 18-25.	MANUAL_OK	5to3	5to3	Duplication of 8 exons: in frame		20809	0	7	7	Intron of EGFR(+): 143bp before exon 18	EGFR	55241471			7	Intron of EGFR(+): 117bp before exon 26	EGFR	55269311			11	DUPLICATION		27840	159856	25591	6	NEW_VARIANT
P-0013869-T01-IM5	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	PRECISE	Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		78356	0	36	2	Intron of ALK(-): 318bp before exon 20	ALK	29446712			2	Intron of EML4(+): 187bp before exon 13	EML4	42528194			39	INVERSION		13081482	162539	62581	36	NEW_VARIANT
P-0013336-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		72198	0	102	21	Intron of ERG(-): 14Kb before exon 4	ERG	39831340			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874388			98	DELETION		3043048	160920	72347	119	NEW_VARIANT
P-0014502-T01-IM6	RUNX1 (NM_001754) rearrangement: c.613+3474_c.805+12632del	PRECISE	Note: The RUNX1 rearrangement is an intragenic deletion of exon 4.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		4349	0	11	21	Intron of RUNX1(-): 82bp before exon 5	RUNX1	36194075			21	Intron of RUNX1(-): 3Kb after exon 3	RUNX1	36228297			13	DELETION		34222	164896	4435	11	NEW_VARIANT
P-0010087-T01-IM5	NBN (NM_002485) rearrangement: chr8;g.96017141_c.481-43:NBNinv	PRECISE	The NBN rearrangement is an inversion of exons 1-4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		10338	0	102	8	Intron of NBN(-): 43bp before exon 5	NBN	90990594			8	IGR: 20Kb before C8orf38(+)	C8orf38	96017141			68	INVERSION		5026547	137906	10778	124	NEW_VARIANT
P-0014976-T01-IM6	SCAF11 (NM_004719) - ARID2 (NM_152641) Rearrangement : c.220-1748:SCAF11_c.5364-623:ARID2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (SFRS2IP-ARID2)		1405	0	22	12	Intron of ARID2(+): 623bp before exon 21	ARID2	46298094			12	Intron of SFRS2IP(-): 2Kb before exon 4	SFRS2IP	46347258			25	INVERSION		49164	166429	2164	18	NEW_VARIANT
P-0014976-T01-IM6	EWSR1 (NM_013986) Rearrangement : c.945+718:EWSR1_chr22:27475510del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		65840	0	26	22	IGR: 422Kb before MIAT(+)	MIAT	27475510			22	Intron of EWSR1(+): 718bp after exon 10	EWSR1	29689313			31	DELETION		2213803	166427	71322	26	NEW_VARIANT
P-0014690-T01-IM6	NUP93 (NM_014669) rearrangement: c.1345+48:NUP93_chr16:g.56898209del	PRECISE	Note: The NUP93 rearrangement is a deletion of exons 13-22.	MANUAL_OK	3to5	3to5	Transcript fusion (NUP93-SLC12A3)		14256	0	12	16	Intron of NUP93(+): 48bp after exon 12	NUP93	56866348			16	Promoter of SLC12A3(+): 910bp from tx start	SLC12A3	56898209			10	DELETION		31861	165480	14726	12	NEW_VARIANT
P-0012327-T01-IM5	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-913:TMPRSS2_c.-150+10700:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		57455	0	29	21	5-UTR of ERG(-): 75Kb before coding start	ERG	40022882			21	Intron of TMPRSS2(-): 913bp before exon 2	TMPRSS2	42871029			35	DELETION		2848147	157043	51410	28	NEW_VARIANT
P-0012199-T01-IM5	MLL3 (NM_170606) rearrangement: c.161+27464_c.9517+76dup	PRECISE	Note: The MLL3 rearrangement in an intragenic duplication of exons 2-41.	MANUAL_OK	5to3	5to3	Duplication of 40 exons: out of frame		96976	0	7	7	Intron of MLL3(-): 76bp after exon 41	MLL3	151866195			7	Intron of MLL3(-): 27Kb after exon 1	MLL3	152105247			12	DUPLICATION		239052	156660	105625	7	NEW_VARIANT
P-0011180-T01-IM5	CD74 (NM_001025159) - NRG1 (NM_013956) rearrangement: t(5;8)(q32;p12)(chr5:g.149782758::chr8:g.32513214)	IMPRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CD74-NRG1)		0	0	8	8	Intron of NRG1(+): 7Kb after exon 1	NRG1	32513214			5	Exon 7 of CD74(-)	CD74	149782758			0	TRANSLOCATION		0	151568	0	7	NEW_VARIANT
P-0014635-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.150+130:CDKN2Ap16INK4A_chr9:21981216inv	PRECISE	Note: The CDKN2Ap16INK4A Rearrangement results in the inversion of exon1 of CDKN2Ap16INK4A. One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		1111	0	11	9	Exon 1 of CDKN2A(-)	CDKN2A	21974547			9	Intron of CDKN2A(-): 10Kb before exon 2	CDKN2A	21981216			16	INVERSION		6669	165349	1087	11	NEW_VARIANT
P-0010934-T01-IM5	EFGR VIII Intragenic deletion:  c.169_889+121del	PRECISE	Note: One of the breakpoints of the EFGR VIII Intragenic deletion is within EGFR exon2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		11915	0	12	7	Exon 2 of EGFR(+)	EGFR	55210059			7	Intron of EGFR(+): 121bp after exon 7	EGFR	55221966			12	DELETION		11907	149765	13337	12	NEW_VARIANT
P-0006311-T02-IM5	PRKAG1 (NM_002733) - MLL2 (NM_003482) Rearrangement : c.9+2460:PRKAG1_c.11934:MLL2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (PRKAG1-MLL2)		56023	0	23	12	Intron of PRKAG1(-): 2Kb after exon 1	PRKAG1	49410055			12	Exon 39 of MLL2(-)	MLL2	49426554			38	DUPLICATION		16499	157038	45216	23	NEW_VARIANT
P-0014421-T01-IM6	DNMT1 (NM_001379) rearrangement: t(10;19)(q24.1; p13.2)(chr10:g.99096319::chr19:g.10244272)	PRECISE	Note: The DNMT1 rearrangement is a translocation with a breakpoint within the 3UTR of DNMT1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	18	19	3-UTR of DNMT1(-): 71bp after coding stop	DNMT1	10244272			10	Promoter of FRAT2(-): 2Kb from tx start	FRAT2	99096319			20	TRANSLOCATION		0	164502	0	18	NEW_VARIANT
P-0013417-T01-IM5	CDK12 (NM_016507) Rearrangement : c.327_2609+3398dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		23161	0	59	17	Exon 1 of CDK12(+)	CDK12	37618651			17	Intron of CDK12(+): 3Kb after exon 6	CDK12	37661090			64	DUPLICATION		42439	161198	30753	57	NEW_VARIANT
P-0014597-T01-IM6	POLE (NM_006231) rearrangement: chr12:g.128237816_c.1227-6:POLEinv	PRECISE	Note: The POLE (NM_006231) rearrangement is an inversion of exons 13-49. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		84719	0	12	12	IGR: 514Kb before TMEM132C(+)	TMEM132C	128237816			12	Intron of POLE(-): 6bp before exon 13	POLE	133250299			21	INVERSION		5012483	165044	74859	12	NEW_VARIANT
P-0010222-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement : c.319:CDKN2Ap16INK4A_chr9:g.22027267del CDKN2Ap14ARF (NM_058195) rearrangement : c.362:CDKN2Ap14ARF_chr9:g.22027267del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24581	0	13	9	Exon 2 of CDKN2A(-)	CDKN2A	21971039			9	5-UTR of CDKN2BAS(+): 94Kb before coding start	CDKN2BAS	22027267			17	DELETION		56228	144916	20575	13	NEW_VARIANT
P-0010171-T01-IM5	ARID1A (NM_006015) rearrangement: t(1;2)(p36.11;q34)(chr1:g.27059158::chr2:g.210926778)	PRECISE	Note: The ARID1A rearrangement is a translocation that may result in the truncation of ARID1A exons 4-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	25	2	Intron of C2orf67(-): 13Kb after exon 6	C2orf67	210926778			1	Intron of ARID1A(+): 9bp before exon 4	ARID1A	27059158			12	TRANSLOCATION		0	144463	0	24	NEW_VARIANT
P-0012373-T01-IM5	TCF3 (NM_001136139) - MBD3 (NM_003926) rearrangement: c.1813+71:TCF3_c.110+3139:MBD3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TCF3-MBD3)		2371	0	10	19	Intron of MBD3(-): 3Kb after exon 1	MBD3	1589382			19	Intron of TCF3(-): 71bp after exon 17	TCF3	1612135			7	DELETION		22753	157224	1584	9	NEW_VARIANT
P-0012373-T01-IM5	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-17 with TACC3 exons 10-16 ): c.2274+69:FGFR3_c.1837-70:TACC3dup	PRECISE	Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-TACC3)		28715	0	33	4	Intron of TACC3(+): 70bp before exon 10	TACC3	1739255			4	Intron of FGFR3(+): 69bp after exon 17	FGFR3	1808730			25	DUPLICATION		69475	157225	28324	32	NEW_VARIANT
P-0013379-T01-IM5	ARID1A (NM_006015) - PIGV (NM_017837) rearrangement: c.1137+68:ARID1A_c.-57-235:PIGVdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (ARID1A-PIGV)		81582	0	8	1	Intron of ARID1A(+): 68bp after exon 1	ARID1A	27024099			1	5-UTR of PIGV(+): 292bp before coding start	PIGV	27117015			13	DELETION		92916	161078	64556	8	NEW_VARIANT
P-0011364-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.55+2676:TMPRSS2_c.40-58736:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		88661	0	17	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876280			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42877201			31	DELETION		3000921	153341	94678	18	NEW_VARIANT
P-0011066-T01-IM5	AMER1 (NM_152424) rearrangement: c.-98-2113_c.3043del	PRECISE	Note: The AMER1 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		41064	0	35	X	Exon 2 of FAM123B(-)	FAM123B	63410124			X	5-UTR of FAM123B(-): 2Kb before coding start	FAM123B	63415377			35	DELETION		5253	150624	29460	34	NEW_VARIANT
P-0014624-T02-IM6	CALR (NM_004343) - RAD23A (NM_005053) Rearrangement : c.960+111:CALR_c.73-349:RAD23Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CALR-RAD23A)		3882	0	17	19	Intron of CALR(+): 111bp after exon 7	CALR	13051812			19	Intron of RAD23A(+): 349bp before exon 2	RAD23A	13058313			15	DELETION		6501	166460	3838	17	NEW_VARIANT
P-0014624-T02-IM6	LCP2 (NM_005565)- EPAS1 (NM_001430) Rearrangement : t(2;5)(p21;q35.1)(chr2:g.46588195::chr5:g.169707068)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (LCP2-EPAS1)		0	0	14	5	Intron of LCP2(-): 4Kb before exon 4	LCP2	169707068			2	Exon 6 of EPAS1(+)	EPAS1	46588195			12	TRANSLOCATION		0	166465	0	14	NEW_VARIANT
P-0010712-T01-IM5	AKT1 (NM_001014431) Rearrangement : c.1260+1_c.1261del	PRECISE	Note: The AKT1 Rearrangement results in the partial deletion of exon13. One of the breakpoints is within exon13. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1367	0	35	14	Exon 13 of AKT1(-)	AKT1	105237184			14	Intron of AKT1(-): 1bp after exon 12	AKT1	105238701			65	DELETION		1517	148473	1449	35	NEW_VARIANT
P-0010712-T01-IM5	AXIN2 (NM_004655) Rearrangement :  c.956+728_c.1323del	PRECISE	Note: The AXIN2 Rearrangement results in the intragenic deletion of exons4-6. One of the breakpoints is within exon6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5219	0	19	17	Exon 6 of AXIN2(-)	AXIN2	63533831			17	Intron of AXIN2(-): 728bp after exon 3	AXIN2	63544910			34	DELETION		11079	148474	5994	18	NEW_VARIANT
P-0013672-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: c.194-370_c.398del	IMPRECISE	Note: The CDKN2Ap14ARF rearrangement is a deletion of exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		0		15	9	3-UTR of CDKN2Ap14ARF(-): 66bp after exon 2 stop codon	CDKN2Ap14ARF	21971003			9	Intron of CDKN2Ap14ARF(-): 370bp before exon 2	CDKN2Ap14ARF	21971577			0	DELETION		574	162116	816		NEW_VARIANT
P-0013672-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement:  c.151-370_c.355del	IMPRECISE	Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		0		15	9	Exon 2 of CDKN2Ap16INK4(-)	CDKN2Ap16INK4A	21971003			9	Intron of CDKN2Ap16INK4(-): 370bp before exon 2	CDKN2Ap16INK4A	21971577			0	DELETION		574	162117	816		NEW_VARIANT
P-0012782-T01-IM5	PAK7 (NM_177990) rearrangement: chr20:g.9524889_c.1869+127:PAK7del	PRECISE	Note: The PAK7 rearrangement in a deletion of exons 9-10.	MANUAL_OK	3to5	3to5	-		9473	0	19	20	IGR: 264Kb before FERMT1(-)	FERMT1	6319114			20	Intron of PAK7(-): 127bp after exon 9	PAK7	9524889			19	DELETION		3205775	158855	8291	19	NEW_VARIANT
P-0014481-T01-IM6	MLL3 (NM_170606) rearrangement: c.7593_chr7:g.152705153dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		70512	0	16	7	Exon 38 of MLL3(-)	MLL3	151874945			7	IGR: 248Kb before ACTR3B(+)	ACTR3B	152705153			26	DUPLICATION		830208	164719	69845	15	NEW_VARIANT
P-0010338-T01-IM5	ATRX (NM_000489) rearrangement : t(X;14)(q21.1;q11.2)(chrX:g.76918982::chr14:g.21586971)	PRECISE	Note: ATRX rearrangement event is a translocation which results in the truncation of ATRX exons 12-35.	MANUAL_OK	3to5	3to5	-		0	0	43	X	Exon 12 of ATRX(-)	ATRX	76918982			14	IGR: 20Kb before C14orf176(+)	C14orf176	21586971			23	TRANSLOCATION		0	145551	0	40	NEW_VARIANT
P-0014004-T01-IM5	TNFRSF14 (NM_003820) rearrangement: t(1;19)(p36.32; q13.42)(chr1:g.2494783::chr19:g.54979682)	IMPRECISE	Note: The TNFRSF14 rearrangement is a translocation with a breakpoint within the 3UTR of TNFRS14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	102	19	5-UTR of CDC42EP5(-): 3Kb before coding start	CDC42EP5	54979682			1	3-UTR of TNFRSF14(+): 71bp after coding stop	TNFRSF14	2494783			0	TRANSLOCATION		0	163040	0	99	NEW_VARIANT
P-0014004-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3828_c.40-59410del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		115686	0	102	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876954			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42876049			127	DELETION		2999095	163037	81909	244	NEW_VARIANT
P-0014797-T01-IM6	CD74 (NM_001025159) rearrangement: t(2;5)(q37.1;q32)(chr2:g.232240463::chr5:g.149784283)	PRECISE	Note: The CD74 rearrangement is a translocation with a breakpoint within exon6 of CD74. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	7	5	Exon 6 of CD74(-)	CD74	149784283			2	IGR: 20Kb before B3GNT7(+)	B3GNT7	232240463			8	TRANSLOCATION		0	165867	0	7	NEW_VARIANT
P-0014935-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.55+3606_556+853dup	PRECISE	Note: The TMPRSS2 Rearrangement results in the duplication of exons 2-5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons: in frame		120566	0	66	21	Intron of TMPRSS2(-): 853bp after exon 5	TMPRSS2	42859468			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42876271			56	DUPLICATION		16803	166241	126084	63	NEW_VARIANT
P-0013864-T01-IM5	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	PRECISE	Note: The EML4  - ALK fusion is an in-frame fusion which includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		67582	0	102	2	Intron of ALK(-): 118bp after exon 19	ALK	29448209			2	Intron of EML4(+): 658bp after exon 12	EML4	42523314			76	INVERSION		13075105	162567	66535	107	NEW_VARIANT
P-0014596-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1986-56_chr5:g.66569460inv	PRECISE	Note: The PIK3R1 (NM_181523) rearrangement is an inversion of PIK3R1 exons 1-15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		22146	0	18	5	IGR: 91Kb before CD180(-)	CD180	66569460			5	Intron of PIK3R1(+): 56bp before exon 10	PIK3R1	67593184			17	INVERSION		1023724	165038	26447	17	NEW_VARIANT
P-0014437-T01-IM6	ROS1 (NM_002944) _EZR (NM_003379) rearrangement: c.1090+229:EZR_c.5366+129:ROS1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (EZR-ROS1)		290568	0	33	6	Intron of ROS1(-): 129bp after exon 32	ROS1	117650363			6	Intron of EZR(-): 229bp after exon 9	EZR	159191567			44	DELETION		41541204	164524	269931	31	NEW_VARIANT
P-0012197-T02-IM5	TMPRSS2 (NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11 ): c.56-2534_c.39+38157del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		80605	0	56	21	Intron of ERG(-): 38Kb after exon 3	ERG	39909429			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872650			57	DELETION		2963221	158923	78616	53	NEW_VARIANT
P-0014879-T01-IM6	XPO1 (NM_003400) rearrangement: c.1098_c.759+824dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		3349	0	9	2	Exon 12 of XPO1(-)	XPO1	61721176			2	Intron of XPO1(-): 824bp after exon 9	XPO1	61724984			11	DUPLICATION		3808	166138	5296	9	NEW_VARIANT
P-0012105-T01-IM5	TSC2 (NM_000548) Rearrangement : c.2546-258_c.3363dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		13419	0	23	16	Intron of TSC2(+): 258bp before exon 23	TSC2	2125542			16	Exon 29 of TSC2(+)	TSC2	2129636			57	DUPLICATION		4094	156258	12202	23	NEW_VARIANT
P-0012105-T01-IM5	PIK3R2 (NM_005027) Rearrangement : c.793_c.1559+68dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		11246	0	8	19	Exon 6 of PIK3R2(+)	PIK3R2	18272283			19	Intron of PIK3R2(+): 68bp after exon 12	PIK3R2	18277180			8	DUPLICATION		4897	156259	14291	8	NEW_VARIANT
P-0012578-T01-IM5	RB1 (NM_000321) - LRCH3 (NM_032773) rearrangement: t(3;13)(q29;q14.2)(chr3:g.197595964::chr13:g.48916931)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	49	13	Intron of RB1(+): 81bp after exon 3	RB1	48916931			3	Intron of LRCH3(+): 1Kb before exon 18	LRCH3	197595964			22	TRANSLOCATION		0	157900	0	44	NEW_VARIANT
P-0010271-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: c.*101+1_c.*102del CDKN2Ap16INK4A (NM_00007) rearrangement: c.457+1_c.458del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2746	0	44	9	Exon 3 of CDKN2A(-)	CDKN2A	21968241			9	Intron of CDKN2A(-): 1bp after exon 2	CDKN2A	21970900			72	DELETION		2659	145268	2599	44	NEW_VARIANT
P-0010271-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: c.193+3_c.196del CDKN2Ap16INK4A (NM_00007) rearrangement: chr9:g.21994135_c.153del	PRECISE	Note: The CDKN2Ap14ARF rearrangement is a deletion of exon2. One of the breakpoints is within exon2. The functional significance is undetermined. Note: The CDKN2Ap16INK4A rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5739	0	21	9	Exon 2 of CDKN2A(-)	CDKN2A	21971205			9	Intron of CDKN2A(-): 3bp after exon 1	CDKN2A	21994135			37	DELETION		22930	145269	5356	13	NEW_VARIANT
P-0014391-T01-IM6	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-11505:ZGPAT_c.3326:RTEL1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (ZGPAT-RTEL1)		19203	0	84	20	Exon 32 of RTEL1(+)	RTEL1	62326238			20	Intron of ZGPAT(+): 12Kb before exon 3	ZGPAT	62353066			89	DUPLICATION		26828	164403	22210	84	NEW_VARIANT
P-0010159-T01-IM5	RBM10 (NM_001204468) - PHIP (NM_017934) rearrangement: t(6;X)(q14.1;p11.23)(chr6:g.79678650::chrX:g.47004857)	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript fusion (RBM10-PHIP)		0	0	9	X	5-UTR of RBM10(+): 2Kb before coding start	RBM10	47004857			6	Intron of PHIP(-): 902bp after exon 27	PHIP	79678650			5	TRANSLOCATION		0	144458	0	9	NEW_VARIANT
P-0013948-T01-IM5	TBX3 (NM_016569) - KCNH3 (NM_012284) rearrangement: c.1770+32:TBX3_c.76+84:KCNH3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (TBX3-KCNH3)		480701	0	12	12	Intron of KCNH3(+): 84bp after exon 1	KCNH3	49933359			12	Intron of TBX3(-): 32bp after exon 6	TBX3	115111938			12	INVERSION		65178579	162834	1300231	12	NEW_VARIANT
P-0013733-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		36956	0	35	21	Intron of ERG(-): 3Kb after exon 1	ERG	39867506			21	Intron of TMPRSS2(-): 2Kb after exon 2	TMPRSS2	42868379			53	DELETION		3000873	162079	33420	35	NEW_VARIANT
P-0015026-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42903820_c.56-1077del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion which includes exon 1 of TMPRSS2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		89824	0	47	21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871193			21	IGR: 24Kb after TMPRSS2(-)	TMPRSS2	42903820			52	DELETION		32627	166546	93789	42	NEW_VARIANT
P-0015026-T01-IM6	TMPRSS2 (NM_001135099) - U2AF1 (NM_006758) rearrangement: c.56-1132:TMPRSS2_c.44+1088:U2AF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-U2AF1)		104825	0	31	21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871248			21	Intron of U2AF1(-): 1Kb after exon 1	U2AF1	44526473			50	DUPLICATION		1655225	166547	110579	29	NEW_VARIANT
P-0014412-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-58976:ERG_c.56-931:TMPRSS2inv	PRECISE	Note: The ERG - TMPRSS2 rearrangement results in an inversion of ERG 5UTR, exons 1-3  and TMPRSS2 exons 2-14. The complex rearrangement involving TMPRSS2 and ERG in this tumor suggests a TMPRSS2 - ERG fusion. Confirmatory testing by archer assay is suggested if clinically indicated.	MANUAL_OK	3to3	3to3	-		66965	0	10	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876520			21	Intron of TMPRSS2(-): 931bp before exon 2	TMPRSS2	42871047			16	INVERSION		2994527	164426	67766	8	NEW_VARIANT
P-0014412-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-934_c.349+276inv	PRECISE	Note: The TMPRSS2 rearrangement in an inversion of exons 2-3.	MANUAL_OK	5to5	5to5	Antisense fusion		39578	0	17	21	Intron of TMPRSS2(-): 276bp after exon 3	TMPRSS2	42866007			21	Intron of TMPRSS2(-): 934bp before exon 2	TMPRSS2	42871050			27	INVERSION		5043	164427	41903	17	NEW_VARIANT
P-0013394-T01-IM5	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+18884:CCDC6_c.2136+48:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		50564	0	32	10	Intron of RET(+): 48bp after exon 11	RET	43610232			10	Intron of CCDC6(-): 19Kb after exon 1	CCDC6	61646996			41	INVERSION		18036764	161127	46690	29	NEW_VARIANT
P-0011554-T01-IM5	CHEK1 (NM_001274) rearrangement: chr11:g.107213566_c.544:CHEK1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		322386	0	15	11	Intron of CWF19L2(-): 6Kb after exon 14	CWF19L2	107213566			11	Exon 6 of CHEK1(+)	CHEK1	125503177			22	DELETION		18289611	155622	327877	15	NEW_VARIANT
P-0013867-T01-IM5	RHOA (NM_001664) Rearrangement : c.522:RHOA_c.758-3500:SUCLG2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		257825	0	26	3	Exon 5 of RHOA(-)	RHOA	49397702			3	Intron of SUCLG2(-): 4Kb before exon 8	SUCLG2	67552219			54	INVERSION		18154517	162572	253600	26	NEW_VARIANT
P-0010604-T01-IM5	MLL3 rearrangement: c.9610_c.13025del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		39979	0	85	7	Exon 52 of MLL3(-)	MLL3	151845987			7	Exon 42 of MLL3(-)	MLL3	151864371			65	DELETION		18384	147909	27534	80	NEW_VARIANT
P-0012525-T01-IM5	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)	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	11	6	Intron of ROS1(-): 2bp after exon 33	ROS1	117647385			5	Intron of CD74(-): 328bp before exon 7	CD74	149783203			21	TRANSLOCATION		0	157645	0	3	NEW_VARIANT
P-0010794-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-32:TMPRSS2_c.18+3305:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		35718	0	8	21	Intron of ERG(-): 3Kb after exon 1	ERG	39866982			21	Intron of TMPRSS2(-): 32bp before exon 2	TMPRSS2	42870148			16	DELETION		3003166	149247	28487	8	NEW_VARIANT
P-0011367-T01-IM5	MLL2 (NM_003482) Rearrangement   : t(2;12)(q32.1;q13.12)(chr2:g.185336965::chr12:g.185336965)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	26	12	Exon 39 of MLL2(-)	MLL2	49425579			2	IGR: 126Kb before ZNF804A(+)	ZNF804A	185336965			25	TRANSLOCATION		0	153362	0	24	NEW_VARIANT
P-0011367-T01-IM5	KDM6A (NM_021140) Rearrangement :  c.619+504_3879-130del	PRECISE	Note: The KDM6A  Rearrangement results in the deletion of exons 8-26 of KDM6A. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 19 exons: out of frame		35983	0	24	X	Intron of KDM6A(+): 504bp after exon 7	KDM6A	44894734			X	Intron of KDM6A(+): 130bp before exon 27	KDM6A	44966525			22	DELETION		71791	153360	13638	21	NEW_VARIANT
P-0011376-T01-IM5	ETV6 (NM_001987) Rearrangement :  c.463+6963_c.1254-1581dup	PRECISE	Note: The ETV6 Rearrangement results in the intragenic duplication of exons5-7 of ETV6. It's functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		201433	0	13	12	Intron of ETV6(+): 7Kb after exon 4	ETV6	12013458			12	Intron of ETV6(+): 2Kb before exon 8	ETV6	12042294			22	DUPLICATION		28836	153410	242020	13	NEW_VARIANT
P-0011376-T01-IM5	PLCXD2 (NM_153268) -GATA2(NM_032638) Rearrangement :  c.164-5416:PLCXD2 _c.1144-34:GATA2inv	PRECISE	Note: The PLCXD2 -GATA2 Rearrangement results in the fusion of exons1 of PLCXD2 with exon6 of GATA2. Its functional significance is undetermined	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (PLCXD2-GATA2)		37971	0	10	3	Intron of PLCXD2(+): 5Kb before exon 2	PLCXD2	111421357			3	Intron of GATA2(-): 34bp before exon 6	GATA2	128200195			17	INVERSION		16778838	153411	60432	9	NEW_VARIANT
P-0014257-T01-IM6	CREBBP (NM_004380) rearrangement : c.798+9898_4530dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		39939	0	28	16	Exon 27 of CREBBP(-)	CREBBP	3786681			16	Intron of CREBBP(-): 10Kb after exon 2	CREBBP	3890400			32	DUPLICATION		103719	163893	48925	28	NEW_VARIANT
P-0010426-T01-IM5	TBX3 (NM_016569) Rearrangement :  c.673_c.865-468inv	PRECISE	Note: The TBX3 Rearrangement results in the inversion of exon3 of TBX3. One of the breakpoints is within exon3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4775	0	22	12	Intron of TBX3(-): 468bp before exon 4	TBX3	115115929			12	Exon 3 of TBX3(-)	TBX3	115117762			48	INVERSION		1833	145992	3587	21	NEW_VARIANT
P-0010066-T01-IM5	MGA (NM_001164273): c.1955:MGA_chr15:g.42450405del	PRECISE	The MGA rearrangement is a deletion which includes exons 3-24. One of the breakpoints is within exon 3 . The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense fusion		158623	0	96	15	Exon 3 of MGA(+)	MGA	41989163			15	Promoter of PLA2G4F(-): 2Kb from tx start	PLA2G4F	42450405			97	DELETION		461242	137809	89643	96	NEW_VARIANT
P-0010066-T01-IM5	BBC3 (NM_001127240) rearrangement: c.434_c.569-1611del	PRECISE	Note: The BBC3 rearrangement is a deletion of exon3. On of the breakpoints is within exon3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5676	0	16	19	Intron of BBC3(-): 2Kb before exon 2	BBC3	47726786			19	Exon 2 of BBC3(-)	BBC3	47729955			39	DELETION		3169	137810	3207	14	NEW_VARIANT
P-0013911-T01-IM5	ERG (NM_004449) - TMPRSS2 (NM_001135099) Rearrangement: c.40-58465:ERG_c.56-1062:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		43572	0	28	21	Intron of ERG(-): 58Kb before exon 4	ERG	39876009			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871178			66	INVERSION		2995169	162690	42935	28	NEW_VARIANT
P-0014225-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.1187-41:TMPRSS2_c.1009-200:MX1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		5577	0	15	21	Intron of MX1(+): 200bp before exon 12	MX1	42817175			21	Intron of TMPRSS2(-): 41bp before exon 11	TMPRSS2	42842711			20	DUPLICATION		25536	163836	5842	15	NEW_VARIANT
P-0001876-T03-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		64854	0	86	21	Intron of ERG(-): 7Kb after exon 4	ERG	39810725			21	Intron of TMPRSS2(-): 497bp before exon 2	TMPRSS2	42870613			76	DELETION		3059888	152617	51253	83	NEW_VARIANT
P-0014222-T01-IM6	CRKL (NM_005207) - RASGEF1C (NM_175062) Rearrangement :  t(5;22)(q35.3;q11.21)(chr5:g.179616450::chr22:g.21288518)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (CRKL-RASGEF1C)		0	0	11	22	Exon 2 of CRKL(+)	CRKL	21288518			5	5-UTR of RASGEF1C(-): 51Kb before coding start	RASGEF1C	179616450			5	TRANSLOCATION		0	163857	0	11	NEW_VARIANT
P-0010172-T01-IM5	CREBBP (NM_004380) rearrangement: t(6;16)(q16.1;p13.3)(chr6:g.94711700::chr16:g.3843541)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	9	16	Exon 4 of CREBBP(-)	CREBBP	3843541			6	IGR: 295Kb before TSG1(+)	TSG1	94711700			13	TRANSLOCATION		0	144469	0	9	NEW_VARIANT
P-0010172-T01-IM5	SOX2 (NM_003106) rearrangement: c.840_c.*1122del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SOX2-SOX2OT)		451	0	12	3	Exon 1 of SOX2(+)	SOX2	181430988			3	5-UTR of SOX2OT(+): 27Kb before coding start	SOX2OT	181432224			0	DELETION		1236	144467	785	12	NEW_VARIANT
P-0013957-T01-IM5	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion: c.55+4588:TMPRSS2_c.40-54610:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		48991	0	8	21	Intron of ERG(-): 55Kb before exon 4	ERG	39872154			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875289			13	DELETION		3003135	162858	91961	8	NEW_VARIANT
P-0010760-T01-IM5	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 )	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	27	6	Intron of ROS1(-): 153bp after exon 33	ROS1	117647234			5	Intron of CD74(-): 480bp after exon 6	CD74	149783763			16	TRANSLOCATION		0	149107	0	26	NEW_VARIANT
P-0014527-T01-IM6	FOXA1 (NM_004496) Rearrangement: chr14:g.38057086_c.1344:FOXA1del	PRECISE	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	MANUAL_OK	3to5	3to5	-		3401	0	6	14	IGR: 2Kb before FOXA1(-)	FOXA1	38057086			14	Exon 2 of FOXA1(-)	FOXA1	38060645			6	DELETION		3559	164835	3422	6	NEW_VARIANT
P-0013245-T01-IM5	ACPP (NM_001134194) - ATR (NM_001184) rearrangement: c.1138+17:ACPP_c.4853-39:ATRinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (ACPP-ATR)		107274	0	8	3	Exon 10 of ACPP(+)	ACPP	132075716			3	Intron of ATR(-): 39bp before exon 28	ATR	142226990			9	INVERSION		10151274	160597	98036	8	NEW_VARIANT
P-0010507-T01-IM5	NOTCH3 (NM_000435) rearrangement : t(16;19)(q23.1;p13.12)(chr16:g.76278026::chr19:g.15291977)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	20	19	Intron of NOTCH3(-): 4bp before exon 18	NOTCH3	15291977			16	IGR: 33Kb before CNTNAP4(+)	CNTNAP4	76278026			11	TRANSLOCATION		0	146732	0	19	NEW_VARIANT
P-0010507-T01-IM5	STK11 (NM_000455) rearrangement : c.374+220_863-2del	PRECISE	Note: The STK11 rearrangement event results in the intragenic deletion of STK11 exons 3-7.	MANUAL_OK	3to5	3to5	Deletion of 4 exons: out of frame		7741	0	19	19	Intron of STK11(+): 220bp after exon 2	STK11	1218719			19	Intron of STK11(+): 2bp before exon 7	STK11	1221946			20	DELETION		3227	146728	6045	17	NEW_VARIANT
P-0013724-T01-IM5	ATRX (NM_000489) rearrangement: chrX:g.76184089_c.4699+50:ATRXinv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 17-35.	MANUAL_OK	5to5	5to5	-		52328	0	17	X	IGR: 44Kb before MIR384(-)	MIR384	76184089			X	Intron of ATRX(-): 50bp after exon 16	ATRX	76891356			26	INVERSION		707267	162098	63331	15	NEW_VARIANT
P-0014403-T01-IM6	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.43-9338:FBXL20_c.3362:CDK12inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (FBXL20-CDK12)		23214	0	6	17	Intron of FBXL20(-): 9Kb before exon 2	FBXL20	37508832			17	Exon 13 of CDK12(+)	CDK12	37682171			9	INVERSION		173339	164406	17990	6	NEW_VARIANT
P-0015085-T01-IM6	NOTCH3 (NM_000435) - MZF1 (NM_003422) rearrangement: c.197+23:NOTCH3_c.773-2319:MZF1	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		754971	0	10	19	Intron of NOTCH3(-): 23bp after exon 2	NOTCH3	15308288			19	Intron of MZF1(-): 2Kb before exon 6	MZF1	59077190			32	INVERSION		43768902	166732	814581	9	NEW_VARIANT
P-0010015-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused with ERG exons 2-9): c.56-1374:TMPRSS2_c.18+8903:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		102581	0	102	21	Intron of ERG(-): 9Kb after exon 1	ERG	39861384			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871490			80	DELETION		3010106	137669	68420	112	NEW_VARIANT
P-0010221-T01-IM5	JAK3 (NM_000215) rearrangement : c.184+16:JAK3_chr19:g.10234948inv	PRECISE	Note: The JAK3 rearrangement results in the inversion of JAK3 exons 3-24.	MANUAL_OK	5to5	5to5	-		270121	0	11	19	IGR: 4Kb after EIF3G(-)	EIF3G	10234948			19	Intron of JAK3(-): 16bp after exon 2	JAK3	17955027			29	INVERSION		7720079	144903	333365	11	NEW_VARIANT
P-0011111-T01-IM5	BRAF (NM_004333) - JHDM1D (NM_030647) rearrangement: c.1178-1831:BRAF_c.*1672:JHDM1Ddel	PRECISE	Note: The BRAF rearrangement is a deletion of exons 11-18, including the kinase domain of BRAF. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17272	0	7	7	3-UTR of JHDM1D(-): 2Kb after coding stop	JHDM1D	139789222			7	Intron of BRAF(-): 2Kb before exon 10	BRAF	140484788			13	DELETION		695566	151216	18154	7	NEW_VARIANT
P-0004605-T02-IM5	RB1(NM_000321) - BRMS1L (NM_032352) rearrangement : t(13;14)(q14.2;q13.2)(chr13:g.48877982::chr14:g.36312640)	PRECISE	Note: The RB1 - BRMS1L rearrangement is a translocation that results in a partial deletion of the RB1 5'UTR. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	86	14	Intron of BRMS1L(+): 9Kb after exon 4	BRMS1L	36312640			13	5-UTR of RB1(+): 67bp before coding start	RB1	48877982			31	TRANSLOCATION		0	137717	0	71	NEW_VARIANT
P-0014861-T01-IM6	MYO1F (NM_012335) - PTPRS (NM_002850) rearrangement: c.772-497:MYO1F_c.1570+25:PTPRS_inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		74332	0	18	19	Intron of PTPRS(-): 25bp after exon 8	PTPRS	5243887			19	Intron of MYO1F(-): 497bp before exon 9	MYO1F	8616075			53	INVERSION		3372188	166023	86440	16	NEW_VARIANT
P-0010093-T01-IM5	PPM1D (NM_003620) rearrangement: c.1261-735_c.1633inv	IMPRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		7623	0	102	17	Intron of PPM1D(+): 735bp before exon 6	PPM1D	58739621			17	Exon 6 of PPM1D(+)	PPM1D	58740728			0	INVERSION		1107	137930	8383	88	NEW_VARIANT
P-0013359-T01-IM5	TRAF2 (NM_021138) rearrangement: c.960+46:TRAF2_chr9:g.139833316inv	PRECISE	Note: The TRAF2 rearrangement is an inversion of exons 9-11.	MANUAL_OK	3to3	3to3	-		10632	0	51	9	Intron of TRAF2(+): 46bp after exon 8	TRAF2	139815013			9	IGR: 2Kb before FBXW5(-)	FBXW5	139833316			44	INVERSION		18303	160973	13343	35	NEW_VARIANT
P-0012674-T01-IM5	DOCK2 (NM_004946) - RPS6KA4 (NM_003942) rearrangement:t(5;11)(q35.1;q13.1)(chr5:g.169409522::chr11:g.64135589)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (DOCK2-RPS6KA4)		0	0	61	11	Intron of RPS6KA4(+): 15bp before exon 10	RPS6KA4	64135589			5	Intron of DOCK2(+): 550bp before exon 28	DOCK2	169409522			0	TRANSLOCATION		0	158479	0	61	NEW_VARIANT
P-0012674-T01-IM5	HNF1B (NM_000458) rearrangement: c.1207-2700_c.1524dup	PRECISE	Note: The HNF1B rarrangement is a duplication of exons 6-7. One of the breakpoints is within exon 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		259	0	12	17	Exon 7 of HNF1B(-)	HNF1B	36060998			17	Intron of HNF1B(-): 3Kb before exon 6	HNF1B	36067756			11	DUPLICATION		6758	158477	477	12	NEW_VARIANT
P-0013457-T01-IM5	BRIP1 (NM_032043) rearrangement: chr17:g.54569323_c.918+65:BRIP1del	PRECISE	Note: The BRIP1 rearrangement is a deletion of exons 8-20.	MANUAL_OK	3to5	3to5	-		118450	0	21	17	IGR: 9Kb after ANKFN1(+)	ANKFN1	54569323			17	Intron of BRIP1(-): 65bp after exon 7	BRIP1	59885763			25	DELETION		5316440	161324	87071	21	NEW_VARIANT
P-0013457-T01-IM5	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.5:ERG_c.349+1625:TMPRSS2dup	PRECISE	Note: The ERG - TMPRSS2 rearrangement is a duplication that results in a fusion of ERG exon 1 with TMPRSS2 exons 4-14. One of the breakpoints is within ERG exon 1. This may represent a more complex gene rearrangement not fully characterized by IMPACT. If necessary, testing with Archer FusionPlex can be considered, which may better characterize the fusion.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (ERG-TMPRSS2)		27511	0	6	21	Exon 1 of ERG(-)	ERG	39870300			21	Intron of TMPRSS2(-): 2Kb after exon 3	TMPRSS2	42864658			10	DUPLICATION		2994358	161325	29382	6	NEW_VARIANT
P-0014623-T01-IM6	CARM1 (NM_199141) - LDLR (NM_000527) rearrangement: c.1615+14:CARM1_c.191-355:LDLRdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CARM1-LDLR)		101250	0	22	19	Intron of CARM1(+): 14bp after exon 14	CARM1	11031817			19	Intron of LDLR(+): 355bp before exon 3	LDLR	11212985			39	DELETION		181168	165315	92283	20	NEW_VARIANT
P-0013465-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+842:TMPRSS2_c.40-57378:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		51249	0	21	21	Intron of ERG(-): 57Kb before exon 4	ERG	39874922			21	Intron of TMPRSS2(-): 842bp after exon 2	TMPRSS2	42869204			35	DELETION		2994282	161343	65385	11	NEW_VARIANT
P-0014684-T01-IM6	RAD50 (NM_005732) rearrangement: chr5:g.14088337_c.2208-31:RAD50del	PRECISE	Note: The RAD50 rearrangement is a deletion of exons 14-25.	MANUAL_OK	3to5	3to5	-		428604	0	8	5	IGR: 55Kb before TRIO(+)	TRIO	14088337			5	Intron of RAD50(+): 31bp before exon 14	RAD50	131938961			4	DELETION		117850624	165488	398639	7	NEW_VARIANT
P-0014790-T01-IM6	DNMT1 (NM_001379) Rearrangement : c.117+99_445+969inv	PRECISE	Note: The DNMT1 Rearrangement results in the intragenic inversion of exons 3-4 of DNMT1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		6037	0	15	19	Intron of DNMT1(-): 806bp after exon 5	DNMT1	10290057			19	Intron of DNMT1(-): 99bp after exon 2	DNMT1	10292618			19	INVERSION		2561	165820	6186	14	NEW_VARIANT
P-0011161-T01-IM5	NAB2 (NM_005967) rearrangement: c.1092-166:NAB2_chr12:g.87188994del	PRECISE	Note: The NAB2 rearrangement is a deletion of exons 4-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense fusion		196426	0	46	12	Intron of NAB2(+): 166bp before exon 4	NAB2	57486534			12	5-UTR of MGAT4C(-): 806Kb before coding start	MGAT4C	87188994			53	DELETION		29702460	151463	287340	44	NEW_VARIANT
P-0014509-T01-IM6	IKBKE (NM_014002) rearrangement: c.978_c.1428-692dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		6970	0	10	1	Exon 9 of IKBKE(+)	IKBKE	206651668			1	Intron of IKBKE(+): 692bp before exon 14	IKBKE	206657642			25	DUPLICATION		5974	164762	8309	10	NEW_VARIANT
P-0014509-T01-IM6	BARD1 (NM_000465) rearrangement: c.365-1696_c.1277del	PRECISE	Note: The BARD1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6111	0	16	2	Exon 4 of BARD1(-)	BARD1	215645321			2	Intron of BARD1(-): 2Kb before exon 4	BARD1	215647929			25	DELETION		2608	164759	5088	16	NEW_VARIANT
P-0014509-T01-IM6	TOP1 (NM_003286) rearrangement: c.1308+4201_c.1741dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		4776	0	14	20	Intron of TOP1(+): 4Kb after exon 13	TOP1	39734194			20	Exon 17 of TOP1(+)	TOP1	39744951			24	DUPLICATION		10757	164763	6546	14	NEW_VARIANT
P-0014509-T01-IM6	SMARCB1 (NM_003073) rearrangement: chr22:g.20196291_c.842:SMARCB1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		41309	0	16	22	IGR: 231bp after LOC150197(+)	LOC150197	20196291			22	Exon 7 of SMARCB1(+)	SMARCB1	24167458			28	INVERSION		3971167	164764	43606	16	NEW_VARIANT
P-0012985-T01-IM5	KIT (NM_000222) rearrangement: c.2697-144_chr4:g.55618064dup	PRECISE	Note: The KIT rearrangement is a duplication which includes exons 20 -21. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		3858	0	10	4	Intron of KIT(+): 144bp before exon 20	KIT	55603197			4	IGR: 11Kb after KIT(+)	KIT	55618064			15	DUPLICATION		14867	159797	4924	10	NEW_VARIANT
P-0011405-T01-IM5	DNMT3A (NM_022552) rearrangement: c.640-2668_c.2026del	PRECISE	Note: The DNMT3A rearrangement is an intragenic deletion of exons 7-17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		27299	0	79	2	Exon 17 of DNMT3A(-)	DNMT3A	25464487			2	Intron of DNMT3A(-): 1Kb before exon 2	DNMT3A	25473789			98	DELETION		9302	153477	18509	79	NEW_VARIANT
P-0011589-T01-IM5	SPEN (NM_015001) rearrangement: c.3780_c.5912del	PRECISE	Note: The SPEN rearrangement is an intragenic deletion within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		11456	0	101	1	Exon 11 of SPEN(+)	SPEN	16256515			1	Exon 11 of SPEN(+)	SPEN	16258647			77	DELETION		2132	155762	7059	96	NEW_VARIANT
P-0011039-T01-IM5	CHEK2 (NM_007194) - KIAA1984 (NM_001039374) rearrangement : t(9;22)(q34.3;q12.1)(chr9:g.139692272::chr22:g.29092840)	PRECISE	Note: The CHEK2-KIAA1984 rearrangement event is a translocation which results in the truncation of CHEK2 exons 11-15.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (CHEK2-KIAA1984)		0	0	80	22	Intron of CHEK2(-): 49bp after exon 10	CHEK2	29092840			9	Intron of KIAA1984(+): 1Kb before exon 2	KIAA1984	139692272			45	TRANSLOCATION		0	150440	0	78	NEW_VARIANT
P-0010247-T01-IM5	FANCA (NM_000135) - CDCA8 (NM_018101) rearrangement: t(1;16)(p34.3;q24.3)(chr1:g.38170600::chr16:g.89828353)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FANCA-CDCA8)		0	0	9	16	Intron of FANCA(-): 4bp after exon 29	FANCA	89828353			1	Intron of CDCA8(+): 513bp before exon 9	CDCA8	38170600			12	TRANSLOCATION		0	145094	0	9	NEW_VARIANT
P-0014757-T01-IM6	ERCC2 (NM_000400) rearrangement: chr19:g.45814599_c.5+40inv	PRECISE	Note: The ERCC2 rearrangement is an inversion of exons 2-23. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		50729	0	9	19	Intron of CKM(-): 408bp after exon 5	CKM	45814599			19	Intron of ERCC2(-): 40bp after exon 1	ERCC2	45873754			15	INVERSION		59155	165723	60546	8	NEW_VARIANT
P-0013309-T01-IM5	NF1 (NM_001042492) rearrangement: c.265_c.289-2038dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of a part of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		261	0	19	17	Exon 3 of NF1(+)	NF1	29486088			17	Intron of NF1(+): 2Kb before exon 4	NF1	29488166			28	DUPLICATION		2078	160873	238	19	NEW_VARIANT
P-0011455-T01-IM5	PARK2 (NM_004562) Rearrangement : c.618+25127_c.670del	PRECISE	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,	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		331	0	28	6	Exon 6 of PARK2(-)	PARK2	162394398			6	Intron of PARK2(-): 25Kb after exon 5	PARK2	162449996			38	DELETION		55598	153674	268	28	NEW_VARIANT
P-0009908-T02-IM6	NTRK2 (NM_006180) rearrangement: t(9;22)(q21.33;q12.3)(chr9:g.87479148::chr22:g.36567977)	PRECISE	Note: The NTRK2 rearrangement is a translocation that may result in a truncation of exons 16-21. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	47	22	IGR: 6Kb after APOL3(-)	APOL3	36567977			9	Intron of NTRK2(+): 3Kb before exon 16	NTRK2	87479148			31	TRANSLOCATION		0	165955	0	47	NEW_VARIANT
P-0015075-T01-IM6	FANCA (NM_000135) - FBXO31 (NM_024735) rearrangement: c.2060:FANCA_c.412+3880:FBXO31inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		141356	0	12	16	Intron of FBXO31(-): 4Kb after exon 2	FBXO31	87390021			16	Exon 23 of FANCA(-)	FANCA	89838177			18	INVERSION		2448156	166759	140563	12	NEW_VARIANT
P-0012507-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2176:TMPRSS2_c.18+2263:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		73880	0	42	21	Intron of ERG(-): 2Kb after exon 1	ERG	39868024			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872292			48	DELETION		3004268	157589	70026	41	NEW_VARIANT
P-0012026-T01-IM5	ZFHX3 (NM_006885) rearrangement : chr16:g.72802720_c.2850inv	PRECISE	Note: The ZFHX3 rearrangement results in the inversion of ZFHX3 exons 3-10. One of the breakpoints is on ZFHX3 exon3.	MANUAL_OK	5to5	5to5	-		132738	0	50	16	IGR: 14Kb before ZFHX3(-)	ZFHX3	72802720			16	Exon 3 of ZFHX3(-)	ZFHX3	72984734			109	INVERSION		182014	155919	83391	49	NEW_VARIANT
P-0014142-T01-IM5	VANGL1 (NM_138959) - NOTCH2 (NM_024408) rearrangement: c.947-704:VANGL1_c.3334:NOTCH2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (VANGL1-NOTCH2)		92351	0	8	1	Intron of VANGL1(+): 704bp before exon 6	VANGL1	116225861			1	Exon 20 of NOTCH2(-)	NOTCH2	120480483			22	INVERSION		4254622	163382	87016	8	NEW_VARIANT
P-0011285-T01-IM5	RB1 (NM_000321) rearrangement: c.539+39_c.607+910del	PRECISE	Note: The RB1 rearrangement is a deletion of exon6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1037	0	12	13	Intron of RB1(+): 39bp after exon 5	RB1	48922038			13	Intron of RB1(+): 910bp after exon 6	RB1	48924069			13	DELETION		2031	152444	792	11	NEW_VARIANT
P-0010041-T01-IM5	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	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		55743	0	69	2	Intron of ALK(-): 385bp after exon 19	ALK	29447942			2	Intron of EML4(+): 7Kb before exon 6	EML4	42501013			83	INVERSION		13053071	138076	58405	68	NEW_VARIANT
P-0015059-T01-IM6	NCOR1 (NM_006311) rearrangement: t(14;17)(q11.2;p12)(chr14:g.21071817::chr17:g.15976930)	PRECISE	Note: The NCOR1 rearrangement is a translocation with a breakpoint within intron 27 of NCOR1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	14	17	Intron of NCOR1(-): 47bp before exon 28	NCOR1	15976930			14	IGR: 14Kb before RNASE12(-)	RNASE12	21071817			15	TRANSLOCATION		0	166685	0	14	NEW_VARIANT
P-0015059-T01-IM6	STAT5B (NM_012448) rearrangement: c.1474-1132_c.1906+38inv	PRECISE	Note: The STAT5B rearrangement is an inversion of exons 13-15. The functional significance is undetermined	MANUAL_OK	5to5	5to5	Antisense fusion		6800	0	6	17	Intron of STAT5B(-): 38bp after exon 15	STAT5B	40362151			17	Intron of STAT5B(-): 1Kb before exon 13	STAT5B	40365340			7	INVERSION		3189	166683	5329	6	NEW_VARIANT
P-0014952-T01-IM6	SDHB (NM_003000) rearrangement: c.73-72:SDHB_chr1:g.18019595del	PRECISE	Note: The SDHB rearrangement is a deletion of 5UTR and exon 1.	MANUAL_OK	3to5	3to5	-		2339	0	10	1	Intron of SDHB(-): 72bp before exon 2	SDHB	17371455			1	Intron of ARHGEF10L(+): 2Kb before exon 28	ARHGEF10L	18019595			14	DELETION		648140	166300	1814	10	NEW_VARIANT
P-0013891-T01-IM5	FLT4 (NM_182925) - CNOT6 (NM_01545) rearrangement: c.1195:FLT4_c.113-5116:CNOT6inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (FLT4-CNOT6)		58822	0	11	5	Intron of CNOT6(+): 5Kb before exon 3	CNOT6	179971815			5	Exon 9 of FLT4(-)	FLT4	180053174			15	INVERSION		81359	162662	78989	11	NEW_VARIANT
P-0011242-T01-IM5	ANKRD11 (NM_013275) rearrangement: c.6168:ANKRD11_chr16:g.89266867del	PRECISE	Note: The ANKRD11 rearrangement is a deletion of exons 9-13. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		19697	0	11	16	IGR: 5Kb after CDH15(+)	CDH15	89266867			16	Exon 9 of ANKRD11(-)	ANKRD11	89346782			12	DELETION		79915	151825	15287	11	NEW_VARIANT
P-0012976-T01-IM5	ATR (NM_00118) rearrangement: t(3;17)(q23;p11.2)(chr3:g.142297572::chr17:g.21429234)	PRECISE	Note: The ATR rearrangement is a translocation with a breakpoint within the 5'UTR of ATR. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	31	17	IGR: 2Kb before C17orf51(-)	C17orf51	21429234			3	5-UTR of ATR(-): 26bp before coding start	ATR	142297572			18	TRANSLOCATION		0	159774	0	30	NEW_VARIANT
P-0012976-T01-IM5	SH3PXD2B (NM_001017995) - PDGFRB (NM_002609) rearrangement: c.76-7984:SH3PXD2B_c.1308:PDGFRBdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SH3PXD2B-PDGFRB)		57882	0	7	5	Exon 9 of PDGFRB(-)	PDGFRB	149510161			5	Intron of SH3PXD2B(-): 8Kb before exon 2	SH3PXD2B	171857484			13	DELETION		22347323	159772	73109	7	NEW_VARIANT
P-0013866-T01-IM5	TGFBR1 (NM_004612) Rearrangement : c.49_97+2083del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		0	0	9	9	Exon 1 of TGFBR1(+)	TGFBR1	101867536			9	Intron of TGFBR1(+): 2Kb after exon 1	TGFBR1	101869667			29	DELETION		2131	162557	2	9	NEW_VARIANT
P-0009828-T02-IM5	SMARCB1 (NM_003073) rearrangement: c.923_c.986+3541inv	PRECISE	Note: The SMARCB1 rearrangement is an inversion of a part of exon 7. One of the breakpoints is within exon 7.	MANUAL_OK	3to3	3to3	Antisense fusion		205	0	28	22	Exon 7 of SMARCB1(+)	SMARCB1	24167539			22	Intron of SMARCB1(+): 4Kb after exon 7	SMARCB1	24171143			37	INVERSION		3604	156649	234	27	NEW_VARIANT
P-0011456-T01-IM5	RB1 (NM_000321) -PTPRG (NM_002841) Rearrangement : t(3,13)(p14.2,q14.2)(chr3:g.62225879::chr13:g.49038089 )	PRECISE	Note: The RB1 - PTPRG  Rearrangement results in the possible truncation of exons 22-27. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	27	13	Intron of RB1(+): 118bp after exon 21	RB1	49038089			3	Intron of PTPRG(+): 4Kb before exon 15	PTPRG	62225879			18	TRANSLOCATION		0	153660	0	23	NEW_VARIANT
P-0014462-T01-IM6	DNMT1 (NM_001379) Rearrangement : c.2672+141_c.3900+61inv	PRECISE	Note:The DNMT1 Rearrangement results in the intragenic inversion of exons 28-33 of DNMT1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		20934	0	34	19	Intron of DNMT1(-): 61bp after exon 34	DNMT1	10250291			19	Intron of DNMT1(-): 141bp after exon 27	DNMT1	10259419			39	INVERSION		9128	164629	27525	29	NEW_VARIANT
P-0014462-T01-IM6	INSR(NM_000208)Rearrangement : t(8;19)(p11.22.1;p13.2)(chr8:g.38571591::chr19:g38571591)	PRECISE	Note: The INSR Rearrangement results in a translocation event in INSR. One of the breakpoints is in exon12 . Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	34	19	Exon 12 of INSR(-)	INSR	7143094			8	IGR: 14Kb before TACC1(+)	TACC1	38571591			25	TRANSLOCATION		0	164631	0	22	NEW_VARIANT
P-0012107-T01-IM5	EP300 (NM_001429) Rearrangement : c.3371_c.3583del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2801	0	20	22	Exon 18 of EP300(+)	EP300	41553282			22	Exon 19 of EP300(+)	EP300	41554497			0	DELETION		1215	156247	2170	19	NEW_VARIANT
P-0012107-T01-IM5	ARID1B (NM_020732) Rearrangement : chr6:g.157090092_c.928:ARID1Bdel	PRECISE	Note: The ARID1B Rearrangement results in the deletion of exon1 of ARID1B . One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5937	0	22	6	IGR: 9Kb before ARID1B(+)	ARID1B	157090092			6	Exon 1 of ARID1B(+)	ARID1B	157100165			44	DELETION		10073	156248	3331	22	NEW_VARIANT
P-0012273-T01-IM5	ANKRD11 (NM_013275) rearrangement: t(13;16)(q12.3;q24.3)(chr13:g.29376791::chr16:g.89349155 )	PRECISE	Note: The ANKRD11 rearrangement is a translocation with a breakpoint within exon9 of ANKRD11. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	102	16	Exon 9 of ANKRD11(-)	ANKRD11	89349155			13	IGR: 103Kb before SLC46A3(-)	SLC46A3	29376791			152	TRANSLOCATION		0	157092	0	141	NEW_VARIANT
P-0012273-T01-IM5	ROS1 (NM_002944) rearrangement: t(1;6)(p13.3;q22.1)(chr1:g.110685599::chr6:g.117650041)	PRECISE	Note: The ROS1 rearrangement is a translocation with a breakpoint after exon 32. 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. If clinically indicated, please request ARCHER FUSIONPLEX test for further characterization.	MANUAL_OK	5to5	5to5	-		0	0	11	6	Intron of ROS1(-): 451bp after exon 32	ROS1	117650041			1	IGR: 8Kb before SLC6A17(+)	SLC6A17	110685599			10	TRANSLOCATION		0	157094	0	11	NEW_VARIANT
P-0010238-T01-IM5	APC (NM_000038) Rearrangement : c.3156_4880del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		12737	0	99	5	Exon 16 of APC(+)	APC	112174447			5	Exon 16 of APC(+)	APC	112176171			125	DELETION		1724	144986	1999	99	NEW_VARIANT
P-0012516-T01-IM5	SETD2 (NM_014159) rearrangement: c.907_c.4586+694dup	PRECISE	Note: The SETD2 rearrangement is a duplication of exons 3-4. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		25328	0	14	3	Intron of SETD2(-): 694bp after exon 4	SETD2	47157419			3	Exon 3 of SETD2(-)	SETD2	47165219			16	DUPLICATION		7800	157653	21396	14	NEW_VARIANT
P-0012993-T01-IM5	MTMR3 (NM_021090) - ERBB3 (NM_001982) Rearrangement :  t(12;22)(q13.3;q12.2)(chr12:g.56487886::chr22:g.30290490)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MTMR3-ERBB3)		0	0	23	22	5-UTR of MTMR3(+): 77Kb before coding start	MTMR3	30290490			12	Exon 14 of ERBB3(+)	ERBB3	56487886			11	TRANSLOCATION		0	159853	0	22	NEW_VARIANT
P-0010761-T01-IM5	FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;p13.31)(chr10:g.123243116::chr12:g.9059183 )	PRECISE	Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16 of FGFR2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	30	12	IGR: 8Kb before PHC1(+)	PHC1	9059183			10	Intron of FGFR2(-): 96bp after exon 16	FGFR2	123243116			25	TRANSLOCATION		0	149093	0	30	NEW_VARIANT
P-0005884-T02-IM5	PIK3R2 (NM_005027) rearrangement : c.902-70:PIK3R2_chr19:g.18201958del	PRECISE	Note: The PIK3R2 rearrangement event results in the inversion of PIK3R2 exons 1-7.	MANUAL_OK	3to5	3to5	-		10973	0	69	19	IGR: 7Kb before MAST3(+)	MAST3	18201958			19	Intron of PIK3R2(+): 70bp before exon 8	PIK3R2	18272942			67	DELETION		70984	144716	7947	68	NEW_VARIANT
P-0006458-T01-IM5	IDH2 (NM_002168) - SEMA4B (NM_198925) fusion: c.678+88:IDH2_c.158-3282:SEMA4Binv	PRECISE	Note: IDH2 (NM_002168) - SEMA4B (NM_198925) fusion is a reciprocal inversion.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (IDH2-SEMA4B)		8022	0	14	15	Intron of IDH2(-): 88bp after exon 5	IDH2	90631503			15	Intron of SEMA4B(+): 3Kb before exon 3	SEMA4B	90757389			22	INVERSION		125886	93044	14516	14	NEW_VARIANT
P-0006909-T01-IM5	LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement : c.349-11:LATS1_c.229+8402:PCMT1del	PRECISE	Note: The LATS1 (NM_004690) - PCMT1 (NM_001252049) rearrangement results in the deletion of LATS1 exons1-2.	MANUAL_OK	3to5	3to5	-		3458	0	9	6	Intron of LATS1(-): 11bp before exon 3	LATS1	150016368			6	Intron of PCMT1(+): 8Kb after exon 1	PCMT1	150079494			31	DELETION		63126	109834	2374	5	NEW_VARIANT
P-0009855-T01-IM5	GON4L (NM_001037533) - NTRK1 (NM_002529) rearrangement : c.4141:GON4L_c.1137:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (GON4L-NTRK1)		37920	0	102	1	Exon 21 of GON4L(-)	GON4L	155735123			1	Exon 9 of NTRK1(+)	NTRK1	156843711			228	INVERSION		1108588	136800	106545	245	NEW_VARIANT
P-0000842-T02-IM5	TIGD7 (NM_033208) - CREBBP (NM_004380) rearrangement: c.375:TIGD7_c.1155:CREBBPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (TIGD7-CREBBP)		42177	0	32	16	Exon 1 of TIGD7(-)	TIGD7	3350240			16	Exon 4 of CREBBP(-)	CREBBP	3843448			27	DUPLICATION		493208	45220	50519	32	NEW_VARIANT
P-0007576-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		39198	0	18	21	Intron of ERG(-): 14Kb before exon 4	ERG	39831774			21	Intron of TMPRSS2(-): 462bp after exon 2	TMPRSS2	42869584			31	DELETION		3037810	117512	31705	18	NEW_VARIANT
P-0001795-T02-IM5	MIPOL1 (NM_138731) - FOXA1 (NM_004496) rearrangement: c.1031+21430:MIPOL1_c.867:FOXA1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		8987	0	16	14	Intron of MIPOL1(+): 21Kb after exon 12	MIPOL1	37913584			14	Exon 2 of FOXA1(-)	FOXA1	38061122			14	DELETION		147538	130476	7614	15	NEW_VARIANT
P-0006894-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 1-11) : c.56-3760:TMPRSS2_chr21:g.40054809del	PRECISE	The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion  is a deletion with a breakpoint 20kb upstream of ERG.	MANUAL_OK	3to5	3to5	-		46276	0	38	21	IGR: 56Kb before NCRNA00114(-)	NCRNA00114	40054809			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873876			36	DELETION		2819067	109793	35233	36	NEW_VARIANT
P-0008750-T01-IM5	CALR (NM_004343) -  C19orf53 (NM_014047) Rearrangement : c.925:CALR_c.154-280:C19orf53del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CALR-C19orf53)		11488	0	45	19	Exon 7 of CALR(+)	CALR	13051666			19	Intron of C19orf53(+): 280bp before exon 3	C19orf53	13888586			61	DELETION		836920	123773	15989	45	NEW_VARIANT
P-0006268-T01-IM5	EGFR (NM_005228) Rearrangement : c.2061+100_3114+140dup	PRECISE	Note: The EGFR (NM_005228) rearrangement results in the duplication of exons 18 to 25 of EGFR.  Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 8 exons: in frame		12482	0	5	7	Intron of EGFR(+): 100bp after exon 17	EGFR	55240917			7	Intron of EGFR(+): 140bp after exon 25	EGFR	55269188			12	DUPLICATION		28271	71018	23514	5	NEW_VARIANT
P-0005144-T01-IM5	RPTOR (NM_020761) rearrangement: c.1213-3708_c.1949dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		10344	0	24	17	Intron of RPTOR(+): 4Kb before exon 11	RPTOR	78816565			17	Exon 17 of RPTOR(+)	RPTOR	78858914			42	DUPLICATION		42349	44209	11591	24	NEW_VARIANT
P-0005191-T01-IM5	STK11 (NM_000455) - MIDN (NM_177401) Rearrangement :  c.1108+6:STK11_c.384+251:MIDNdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (STK11-MIDN)		2020	0	6	19	Intron of STK11(+): 6bp after exon 8	STK11	1223177			19	Intron of MIDN(+): 251bp after exon 4	MIDN	1252151			22	DELETION		28974	45428	1276	6	NEW_VARIANT
P-0005571-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon4) : c.55+2350:TMPRSS2_c.40-58808:ERG	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		65692	0	30	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876352			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877527			33	DELETION		3001175	50787	29931	28	NEW_VARIANT
P-0005291-T01-IM5	FGFR2 (NM_022970) - TFEC (NM_012252) Rearrangement: t(10;7)(q26.13;q31.2)(chr10:g.123241729;chr7:g.115644112)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript fusion (FGFR2-TFEC)		0	0	94	10	Intron of FGFR2(-): 38bp before exon 17	FGFR2	123241729			7	5-UTR of TFEC(-): 20Kb before coding start	TFEC	115644112			49	TRANSLOCATION		0	46728	0	25	NEW_VARIANT
P-0009702-T01-IM5	TP53 (NM_000546) Rearrangement :t(2;17)(q24.2;p13.1)(chr2:g.162135135::chr17:g.7578268)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	17	17	Exon 6 of TP53(-)	TP53	7578268			2	IGR: 30Kb before PSMD14(+)	PSMD14	162135135			24	TRANSLOCATION		0	136044	0	15	NEW_VARIANT
P-0008812-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1-2 with ERG exons 2-10): c.127-23:TMPRSS2_c.19-9142:ERGdel	PRECISE	Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion  is an in-frame fusion.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		33070	0	52	21	Intron of ERG(-): 9Kb before exon 4	ERG	39826686			21	Intron of TMPRSS2(-): 23bp before exon 3	TMPRSS2	42866528			80	DELETION		3039842	124412	26731	50	NEW_VARIANT
P-0005966-T01-IM5	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	PRECISE		MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		33385	0	57	4	Intron of TACC3(+): 423bp after exon 10	TACC3	1739852			4	Exon 18 of FGFR3(+)	FGFR3	1808853			108	DUPLICATION		69001	66731	36564	56	NEW_VARIANT
P-0004995-T01-IM5	KIF5B(NM_004521) -RET (NM_020975)  Fusion ( KIF5B exon 15 fused to RET exon 12) : c.1726-2366:KIF5B_c.2136+476:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		29308	0	36	10	Intron of KIF5B(-): 2Kb before exon 16	KIF5B	32314330			10	Intron of RET(+): 476bp after exon 11	RET	43610660			38	INVERSION		11296330	41740	19872	32	NEW_VARIANT
P-0004795-T01-IM5	CUL1(NM_003592) - BRAF (NM_004333) Rearrangement :c.790-427:CUL1_c.1140+297:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (CUL1-BRAF)		51573	0	15	7	Intron of BRAF(-): 297bp after exon 8	BRAF	140493811			7	Intron of CUL1(+): 427bp before exon 8	CUL1	148463226			20	INVERSION		7969415	40126	47940	15	NEW_VARIANT
P-0006639-T01-IM5	PTEN (NM_000314) rearrangement : c.635-1095_801+52dup	PRECISE	Note: The PTEN (NM_000314) rearrangement event results in the duplication of PTEN exon 7.	MANUAL_OK	5to3	5to3	Duplication of 1 exon: out of frame		975	0	5	10	Intron of PTEN(+): 1Kb before exon 7	PTEN	89716515			10	Intron of PTEN(+): 52bp after exon 7	PTEN	89717828			10	DUPLICATION		1313	107824	863	4	NEW_VARIANT
P-0005761-T01-IM5	APC (NM_000038) rearrangement : chr5:g.85990826_c.94:APCdel	PRECISE	Note: The APC (NM_000038) rearrangement event results in the deletion of APC exons 1-2, truncating the gene.	MANUAL_OK	3to5	3to5	-		65261	0	13	5	IGR: 77Kb before COX7C(+)	COX7C	85990826			5	Exon 2 of APC(+)	APC	112090681			17	DELETION		26099855	58878	58054	12	NEW_VARIANT
P-0005761-T01-IM5	NPM1 (NM_002520) rearrangement : c.353-26_525-118dup	PRECISE	Note: The NPM1 (NM_002520) rearrangement event results in the intragenic duplication of NPM1 exons 5-6.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: out of frame		3013	0	21	5	Intron of NPM1(+): 26bp before exon 5	NPM1	170819688			5	Intron of NPM1(+): 118bp before exon 7	NPM1	170827039			29	DUPLICATION		7351	58879	3236	17	NEW_VARIANT
P-0005761-T01-IM5	FUBP1 (NM_003902) rearrangement : c.212-844_473+192inv	PRECISE	Note: The FUBP1 (NM_003902) rearrangement event results in the intragenic inversion of FUBP1 exons 3-7.	MANUAL_OK	5to5	5to5	Antisense fusion		7265	0	9	1	Intron of FUBP1(-): 192bp after exon 7	FUBP1	78432186			1	Intron of FUBP1(-): 844bp before exon 3	FUBP1	78434731			17	INVERSION		2545	58882	7865	8	NEW_VARIANT
P-0008187-T01-IM5	BRCA2 (NM_000059) Rearrangement :  c.8633-663_9080dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		9623	0	45	13	Intron of BRCA2(+): 663bp before exon 21	BRCA2	32950144			13	Exon 23 of BRCA2(+)	BRCA2	32954013			46	DUPLICATION		3869	120676	17650	45	NEW_VARIANT
P-0007622-T01-IM5	KDM6A (NM_021140) rearrangement: c.334+4130_1329+521del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 10 exons: out of frame		11552	0	36	X	Intron of KDM6A(+): 4Kb after exon 3	KDM6A	44824767			X	Intron of KDM6A(+): 521bp after exon 13	KDM6A	44919922			41	DELETION		95155	117674	9513	36	NEW_VARIANT
P-0009239-T01-IM5	FAT1 (NM_005245) rearrangement: chr4:g.88073170_c.13499del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		155412	0	27	4	Exon 27 of FAT1(-)	FAT1	187510014			4	IGR: 428Kb after FAT1(-)	FAT1	188073170			21	DELETION		563156	129546	128104	27	NEW_VARIANT
P-0009556-T01-IM5	RAB35 (NM_006861) - SPPL3(NM_139015) Rearrangement :  c.477+135:RAB35_c.503-5676:SPPL3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (RAB35-SPPL3)		13333	0	5	12	Intron of RAB35(-): 135bp after exon 5	RAB35	120536480			12	Intron of SPPL3(-): 6Kb before exon 7	SPPL3	121212538			10	DUPLICATION		676058	131267	13776	4	NEW_VARIANT
P-0006172-T01-IM5	P2RY8(NM_178129) - NTRK1 (NM_002529) rearrangement: t(X;1)(chrX:g.1598513::chr1:g.156838012)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (NTRK1-P2RY8)		0	0	14	X	5-UTR of P2RY8(-): 13Kb before coding start	P2RY8	1598513			1	Exon 6 of NTRK1(+)	NTRK1	156838012			9	TRANSLOCATION		0	70181	0	13	NEW_VARIANT
P-0006091-T01-IM5	BRD4 (NM_058243) - NOTCH3 (NM_000435 )  Rearrangement :  c.-1598:BRD4_c.4588:NOTCH3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (BRD4-NOTCH3)		161138	0	102	19	Exon 25 of NOTCH3(-)	NOTCH3	15285027			19	Promoter of BRD4(-): 1Kb from tx start	BRD4	15392638			202	DELETION		107611	67654	127990	336	NEW_VARIANT
P-0006091-T01-IM5	XPO1 (NM_003400) Rearrangement :  c.1888-38_1048-118del	PRECISE	Note: The XPO1 (NM_003400) Rearrangement  results in the intragenic deletion of exons 12  to 17 of XPO1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 5 exons: in frame		13763	0	66	2	Intron of XPO1(-): 38bp before exon 17	XPO1	61717949			2	Intron of XPO1(-): 118bp before exon 12	XPO1	61721344			55	DELETION		3395	67655	12583	64	NEW_VARIANT
P-0005352-T01-IM5	PBRM1 (NM_018313) - DNAH1 (NM_015512) rearrangement: c.714:PBRM1_c.11736:DNAH1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (PBRM1-DNAH1)		118651	0	84	3	Exon 73 of DNAH1(+)	DNAH1	52431009			3	Intron of PBRM1(-): 6bp after exon 7	PBRM1	52685752			74	INVERSION		254743	48355	57083	79	NEW_VARIANT
P-0009339-T01-IM5	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	PRECISE	Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		64410	0	102	2	Intron of ALK(-): 438bp after exon 19	ALK	29447889			2	Intron of EML4(+): 7Kb before exon 6	EML4	42501120			142	INVERSION		13053231	130201	61224	242	NEW_VARIANT
P-0008920-T01-IM5	ZNF207 (NM_001098507) - BRAF (NM_004333) rearrangement: t(7;17)(q34;q11.2)(chr7:g.140485847::chr17:g.30687533)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (ZNF207-BRAF)		0	0	97	17	Intron of ZNF207(+): 84bp before exon 4	ZNF207	30687533			7	Intron of BRAF(-): 2Kb after exon 9	BRAF	140485847			23	TRANSLOCATION		0	124982	0	96	NEW_VARIANT
P-0006756-T01-IM5	MLL (NM_001197104) rearrangement : c.5366_5665-198del	PRECISE	Note: The MLL (NM_001197104) rearrangement event results in the deletion of MLL exons 19-20.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4412	0	7	11	Exon 19 of MLL(+)	MLL	118366417			11	Intron of MLL(+): 198bp before exon 21	MLL	118368453			25	DELETION		2036	108764	4433	7	NEW_VARIANT
P-0006756-T01-IM5	NOTCH3 (NM_000435) rearrangement : c.4527_chr19:g.15414856del	PRECISE	Note: The NOTCH3 (NM_000435) rearrangement event results in the deletion of NOTCH3 exons 1-25. One of the breakpoints is within NOTCH3 exon25.	MANUAL_OK	3to5	3to5	-		140722	0	94	19	Exon 25 of NOTCH3(-)	NOTCH3	15285088			19	IGR: 49Kb before AKAP8(-)	AKAP8	15414856			107	DELETION		129768	108765	101417	90	NEW_VARIANT
P-0005011-T01-IM5	TP53 (NM_000546) - GPS2 (NM_004489) rearrangement: c.179:TP53_c.538:GPS2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (TP53-GPS2)		21892	0	31	17	Exon 7 of GPS2(-)	GPS2	7216983			17	Exon 4 of TP53(-)	TP53	7579508			35	DELETION		362525	42648	20431	29	NEW_VARIANT
P-0009546-T01-IM5	PRDM1 (NM_001198 ) Rearrangement :  c.1998_*1216del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2018	0	17	6	Exon 7 of PRDM1(+)	PRDM1	106554881			6	3-UTR of PRDM1(+): 1Kb after coding stop	PRDM1	106556577			32	DELETION		1696	131203	1582	17	NEW_VARIANT
P-0009260-T01-IM5	CDKN2Ap16INK4A (NM_000077) Rearrangement:  c.458-27_chr9:g.22078146del	PRECISE	Note: The CDKN2Ap16INK4A (NM_000077) Rearrangement results in the deletion of exons1 and 2 of CDKN2Ap16INK4A. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		22142	0	8	9	Intron of CDKN2A(-): 27bp before exon 3	CDKN2A	21968268			9	5-UTR of CDKN2BAS(+): 43Kb before coding start	CDKN2BAS	22078146			12	DELETION		109878	129593	16126	8	NEW_VARIANT
P-0009709-T01-IM5	DPP9 (NM_139159) PTPRS (NM_002850) rearrangement: c.2179-101:DPP9_c.2567:PTPRSdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (DPP9-PTPRS)		49026	0	12	19	Intron of DPP9(-): 101bp before exon 19	DPP9	4683742			19	Exon 18 of PTPRS(-)	PTPRS	5223236			18	DUPLICATION		539494	136120	46245	12	NEW_VARIANT
P-0007855-T01-IM5	INSR (NM_000208) rearrangement : c.2945+229_2979inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		244	0	11	19	Exon 16 of INSR(-)	INSR	7126629			19	Intron of INSR(-): 229bp after exon 15	INSR	7128634			14	INVERSION		2005	118790	665	10	NEW_VARIANT
P-0009565-T02-IM5	PIK3C2G (NM_004570) - PDE3A (NM_000921) rearrangement: c.3357+99:PIK3C2G_c.961-27266:PDE3Ainv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		20740	0	7	12	Intron of PIK3C2G(+): 99bp after exon 24	PIK3C2G	18691345			12	Intron of PDE3A(+): 27Kb before exon 2	PDE3A	20682328			7	INVERSION		1990983	131603	19503	5	NEW_VARIANT
P-0008452-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-2582:TMPRSS2_c.39+45360:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		63239	0	44	21	Intron of ERG(-): 45Kb after exon 3	ERG	39902226			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872698			57	DELETION		2970472	122234	46361	42	NEW_VARIANT
P-0009703-T01-IM5	CDH1 (NM_004360) Rearrangement :   chr16:g.68664883_ c.2165-112:CDH1del	PRECISE	Note: The CDH1 (NM_004360) Rearrangement  results in the deletion of exons 1-13 of CDH1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		44369	0	10	16	IGR: 13Kb before CDH3(+)	CDH3	68664883			16	Intron of CDH1(+): 112bp before exon 14	CDH1	68861965			14	DELETION		197082	136070	35786	10	NEW_VARIANT
P-0009249-T01-IM5	MGA (NM_001164273) rearrangement: c.6492_chr15:g.37922302inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		130571	0	24	15	IGR: 305Kb before TMCO5A(+)	TMCO5A	37922302			15	Exon 16 of MGA(+)	MGA	42042297			39	INVERSION		4119995	129540	135862	24	NEW_VARIANT
P-0006225-T01-IM5	SMARCD1 (NM_003076) rearrangement: c.771+59_c.873+101del	PRECISE	The SMARCD1 (NM_003076) rearrangement is an intragenic deletion of exon7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2045	0	38	12	Intron of SMARCD1(+): 59bp after exon 6	SMARCD1	50482479			12	Intron of SMARCD1(+): 101bp after exon 7	SMARCD1	50483869			39	DELETION		1390	70446	2265	37	NEW_VARIANT
P-0007233-T01-IM5	BRCA2 (NM_000059) rearrangement : c.2123_3876del	PRECISE	Note: The BRCA2 (NM_000059) rearrangement event is a deletion within BRCA2 exon11.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		13897	0	12	13	Exon 11 of BRCA2(+)	BRCA2	32910615			13	Exon 11 of BRCA2(+)	BRCA2	32912368			30	DELETION		1753	114713	6991	12	NEW_VARIANT
P-0007071-T01-IM5	NCOA3 (NM_181659) rearrangement :  c.-11+4624:EYA2_c.423:NCOA3inv	PRECISE	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	MANUAL_OK	5to5	5to5	-		9406	0	12	20	5-UTR of EYA2(+): 90Kb before coding start	EYA2	45528250			20	Exon 6 of NCOA3(+)	NCOA3	46255811			37	INVERSION		727561	112917	8034	11	NEW_VARIANT
P-0008657-T01-IM5	FGFR1 (NM_000141) - PPP1R21 (NM_152994)  Rearrangement  : t(2;10)(2p16.3;10q26.13)(chr2:g.48721864::chr10:g.123240684)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-KLRAQ1)		0	0	16	10	Intron of FGFR2(-): 1Kb before exon 18	FGFR2	123240684			2	Intron of KLRAQ1(+): 954bp before exon 16	KLRAQ1	48721864			25	TRANSLOCATION		0	123330	0	11	NEW_VARIANT
P-0009840-T01-IM5	SRC (NM_198291) rearrangement: c.703+242_c.1327dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		7171	0	13	20	Intron of SRC(+): 242bp after exon 8	SRC	36024956			20	Exon 13 of SRC(+)	SRC	36031208			29	DUPLICATION		6252	136687	7919	13	NEW_VARIANT
P-0008856-T01-IM5	CD79B (NM_001039933) rearrangement: chr17:g.32525586_c.433+14:CD79Bdel	PRECISE	Note: The CD79B (NM_001039933) rearrangement results in the deletion of CD79B exons 4-6. The functional significance of this rearrangement is undetermined.	MANUAL_OK	3to5	3to5	-		827216	0	64	17	IGR: 57Kb before CCL2(+)	CCL2	32525586			17	Intron of CD79B(-): 14bp after exon 3	CD79B	62007420			61	DELETION		29481834	124718	1027149	62	NEW_VARIANT
P-0005578-T01-IM5	NAB2 (NM_005967) - STAT6 (NM_003153) Fusion (NAB2 exon4 fused with STAT6 exon5) :  c.1144-31:NAB2_c.340-81:STAT6inv	PRECISE	Note: The NAB2 (NM_005967) - STAT6 (NM_003153) Fusion is a reciprocal inversion.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (NAB2-STAT6)		30033	0	101	12	Intron of NAB2(+): 31bp before exon 5	NAB2	57486815			12	Intron of STAT6(-): 81bp before exon 5	STAT6	57500695			83	INVERSION		13880	50829	28294	95	NEW_VARIANT
P-0005756-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.127-1214:TMPRSS2_c.18+26157:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		55761	0	102	21	Intron of ERG(-): 26Kb after exon 1	ERG	39844130			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867719			124	DELETION		3023589	58785	53005	143	NEW_VARIANT
P-0004861-T01-IM5	BBC3 (NM_001127240) - CLHC1 (NM_001135598) rearrangement: t(19;2)(q13;p16.1)(chr19:g.47729876::chr2:g.55436488)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	39	19	Exon 2 of BBC3(-)	BBC3	47729876			2	Intron of C2orf63(-): 52bp after exon 5	C2orf63	55436488			32	TRANSLOCATION		0	39759	0	38	NEW_VARIANT
P-0002707-T03-IM5	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 )	PRECISE	The CD74 (NM_001025159) - ROS1 (NM_002944)  fusion is a reciprocal translocation	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	96	6	Intron of ROS1(-): 441bp after exon 33	ROS1	117646946			5	Intron of CD74(-): 495bp after exon 6	CD74	149783748			40	TRANSLOCATION		0	116599	0	91	NEW_VARIANT
P-0009503-T01-IM5	RSL1D1 (NM_015659) - BRD4 (NM_058243) rearrangement: t(16;19)(p13.13;p13.12)(chr16:g.11933572::chr19:g.15376304)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (RSL1D1-BRD4)		0	0	11	19	Exon 5 of BRD4(-)	BRD4	15376304			16	Exon 8 of RSL1D1(-)	RSL1D1	11933572			10	TRANSLOCATION		0	130999	0	11	NEW_VARIANT
P-0009503-T01-IM5	PPP2R1A (NM_014225) rearrangement: t(18;19)(q23;q13.41)(chr18:g.74482654::chr19:g.52719830)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	21	19	Exon 9 of PPP2R1A(+)	PPP2R1A	52719830			18	IGR: 53Kb before ZNF236(+)	ZNF236	74482654			26	TRANSLOCATION		0	131001	0	21	NEW_VARIANT
P-0006808-T01-IM5	NFKBIA(NM_020529) Rearrangement :  c.473_chr14:g.49675988del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		55889	0	102	14	Exon 3 of NFKBIA(-)	NFKBIA	35872430			14	IGR: 368Kb before RPS29(-)	RPS29	49675988			80	DELETION		13803558	109146	63797	94	NEW_VARIANT
P-0004704-T01-IM5	PIK3R1 (NM_181523) - MUC (NM_001204287) rearrangement : t(1;5)(1q22;5q13.1)(chr1:g.155160349::chr5:g.67591974)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	30	5	Intron of PIK3R1(+): 25bp before exon 9	PIK3R1	67591974			1	Intron of MUC1(-): 15bp before exon 5	MUC1	155160349			0	TRANSLOCATION		0	29495	0	28	NEW_VARIANT
P-0008711-T01-IM5	FOXO1 (NM_002015) rearrangement: c.631-292_c.*9inv	PRECISE	The FOXO1 (NM_002015) rearrangement is an inversion of exon2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		21142	0	26	13	3-UTR of FOXO1(-): 9bp after coding stop	FOXO1	41133651			13	Intron of FOXO1(-): 292bp before exon 2	FOXO1	41135289			52	INVERSION		1638	123546	18757	24	NEW_VARIANT
P-0009303-T01-IM5	TP53 (NM_000546) rearrangement: c.75-22_c.672+197del.	PRECISE	Note: The TP53 (NM_000546) rearrangement is an intragenic deletion of exons 3-6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons: out of frame		6377	0	21	17	Intron of TP53(-): 197bp after exon 6	TP53	7577980			17	Intron of TP53(-): 22bp before exon 3	TP53	7579743			42	DELETION		1763	130040	5092	11	NEW_VARIANT
P-0008332-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) rearrangement :  c.1489+828:EML4_c.3173-518:ALKdup	PRECISE	confirm with archer	MANUAL_OK	5to3	5to3	Antisense fusion		44905	0	85	2	Intron of ALK(-): 518bp before exon 20	ALK	29446912			2	Intron of EML4(+): 828bp after exon 12	EML4	42523484			91	DUPLICATION		13076572	121350	54428	82	NEW_VARIANT
P-0007366-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		54809	0	7	21	Intron of ERG(-): 19Kb before exon 4	ERG	39836918			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872445			16	DELETION		3035527	115550	41904	7	NEW_VARIANT
P-0009619-T01-IM5	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1968+2394:SND1_ c.1314+327:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SND1-BRAF)		85031	0	37	7	Intron of SND1(+): 2Kb after exon 17	SND1	127717136			7	Intron of BRAF(-): 327bp after exon 10	BRAF	140482494			52	INVERSION		12765358	131471	84979	35	NEW_VARIANT
P-0004747-T01-IM5	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)	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (CD74-ROS1)		0	0	13	6	Intron of ROS1(-): 1Kb after exon 32	ROS1	117649107			5	Intron of CD74(-): 123bp after exon 7	CD74	149782561			14	TRANSLOCATION		0	34890	0	13	NEW_VARIANT
P-0008795-T01-IM5	ERCC5 (NM_000123) rearrangement : chr13:g.80173550_c.2727:ERCC5inv	PRECISE	Note: The ERCC5 (NM_000123) rearrangement event results in the inversion of ERCC5 exons 1-13. One of the breakpoints is within ERCC5 exon13.	MANUAL_OK	3to3	3to3	-		62644	0	24	13	IGR: 43Kb after NDFIP2(+)	NDFIP2	80173550			13	Exon 13 of ERCC5(+)	ERCC5	103524596			37	INVERSION		23351046	124305	131661	22	NEW_VARIANT
P-0008795-T01-IM5	MYO16 (NM_015011) - IRS2 (NM_003749) rearrangement : c.442-17465:MYO16_c.4013-10805:IRS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (MYO16-IRS2)		4975	0	27	13	Intron of MYO16(+): 17Kb before exon 5	MYO16	109420518			13	Intron of IRS2(-): 11Kb before exon 2	IRS2	110419460			25	INVERSION		998942	124304	124692	26	NEW_VARIANT
P-0008795-T01-IM5	FOXA1 (NM_004496) - CASZ1 (NM_001079843) rearrangement : t(1;14)(p36.22;q21.2)(chr1:g.10708606::chr14:g.38061338)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	42	14	Exon 2 of FOXA1(-)	FOXA1	38061338			1	Intron of CASZ1(-): 410bp before exon 16	CASZ1	10708606			68	TRANSLOCATION		0	124312	0	37	NEW_VARIANT
P-0008795-T01-IM5	NRG1 (NM_013962) - FOXA1 (NM_004496) rearrangement : t(8;14)(p12;q21.1)(chr8:g.32309025::chr14:g.38061417)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (NRG1-FOXA1)		0	0	67	14	Exon 2 of FOXA1(-)	FOXA1	38061417			8	Intron of NRG1(+): 144Kb before exon 2	NRG1	32309025			47	TRANSLOCATION		0	124313	0	55	NEW_VARIANT
P-0007515-T01-IM5	NCOR1 (NM_006311)  -  SLFN12 (NM_018042) rearrangement : c.2583:NCOR1_c.-41+1038:SLFN12inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		284158	0	102	17	Exon 20 of NCOR1(-)	NCOR1	16004671			17	5-UTR of SLFN12(-): 8Kb before coding start	SLFN12	33758169			74	INVERSION		17753498	117087	229095	86	NEW_VARIANT
P-0002071-T02-IM5	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	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SND1-BRAF)		104198	0	31	7	Intron of SND1(+): 19Kb after exon 10	SND1	127380060			7	Intron of BRAF(-): 2Kb before exon 9	BRAF	140489292			42	INVERSION		13109232	70844	120394	30	NEW_VARIANT
P-0006830-T01-IM5	LRRC20 (NM_207119) - EP300 (NM_001429) translocation : t(10;22)(q22.1;q13.2)(chr10:g.72085428::chr22:g.41488964)	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript fusion (LRRC20-EP300)		0	0	35	22	5-UTR of EP300(+): 45bp before coding start	EP300	41488964			10	Intron of LRRC20(-): 2Kb before exon 4	LRRC20	72085428			20	TRANSLOCATION		0	109325	0	32	NEW_VARIANT
P-0005712-T01-IM5	FH (NM_000143) rearrangement: c.556-906_c.1236+14dup	PRECISE	The FH (NM_000143) rearrangement is an intragenic in frame duplication of FH exons 5-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons: in frame		7315	0	72	1	Intron of FH(-): 14bp after exon 8	FH	241665729			1	Intron of FH(-): 906bp before exon 5	FH	241672991			67	DUPLICATION		7262	54192	12373	70	NEW_VARIANT
P-0005712-T01-IM5	ARID2 (NM_152641) rearrangement: c.4714_c.4922+3493dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		2006	0	15	12	Exon 15 of ARID2(+)	ARID2	46246620			12	Intron of ARID2(+): 3Kb after exon 16	ARID2	46258225			25	DUPLICATION		11605	54191	2484	15	NEW_VARIANT
P-0006948-T01-IM5	CARD11 (NM_032415) rearrangement: c.3020-294_c.3350dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		5423	0	47	7	Exon 25 of CARD11(-)	CARD11	2946387			7	Intron of CARD11(-): 294bp before exon 23	CARD11	2952224			53	DUPLICATION		5837	112090	6947	46	NEW_VARIANT
P-0005177-T01-IM5	NONO (NM_001145409) -TFE3 (NM_006521) fusion (NONO exons 1-8  with  TFE3 exons 6-10):  c.1131+68:NONO_ c.885+401:TFE3inv	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (NONO-TFE3)		109392	0	11	X	Intron of TFE3(-): 401bp after exon 5	TFE3	48895134			X	Intron of NONO(+): 68bp after exon 8	NONO	70517856			11	INVERSION		21622722	45156	162354	6	NEW_VARIANT
P-0008023-T01-IM5	ANKRD11 (NM_013275) rearrangement: c.5336:ANKRD11_chr16:g.89300582dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		16412	0	7	16	IGR: 5Kb after ZNF778(+)	ZNF778	89300582			16	Exon 9 of ANKRD11(-)	ANKRD11	89347614			22	DUPLICATION		47032	120072	17763	7	NEW_VARIANT
P-0006074-T01-IM5	TOP1 (NM_003286) - SLC13A3 (NM_022829) rearrangement event : c.1813:TOP1_c.1494+1294: SLC13A3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		69661	0	40	20	Exon 17 of TOP1(+)	TOP1	39745023			20	Intron of SLC13A3(-): 1Kb after exon 11	SLC13A3	45193574			81	DELETION		5448551	67562	53438	37	NEW_VARIANT
P-0007518-T01-IM5	SBNO2 (NM_014963) - STK11 (NM_000455)  Rearrangement  : c.3851:SBNO2_c.375-58:STK11inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (SBNO2-STK11)		4294	0	18	19	Exon 32 of SBNO2(-)	SBNO2	1108469			19	Intron of STK11(+): 58bp before exon 3	STK11	1219265			49	INVERSION		110796	117143	4835	18	NEW_VARIANT
P-0007518-T01-IM5	STK11 (NM_000455) Rearrangement : c.*16+129_750inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		6147	0	58	19	Exon 6 of STK11(+)	STK11	1221227			19	3-UTR of STK11(+): 145bp after coding stop	STK11	1226791			113	INVERSION		5564	117144	7200	58	NEW_VARIANT
P-0006071-T01-IM5	SOCS1 (NM_003745) rearrangment : c.-956_-151del	IMPRECISE	Note: The SOCS1 (NM_003745) rearrangment event results in the deletion of SOCS1 exon1 and the promoter region of SOCS1.	MANUAL_OK	3to5	3to5	Deletion within transcript		1039	0	49	16	5-UTR of SOCS1(-): 701bp before coding start	SOCS1	11350036			16	Promoter of SOCS1(-): 802bp from tx start	SOCS1	11350841			0	DELETION		805	67570	559	48	NEW_VARIANT
P-0006071-T01-IM5	NCOA3 (NM_181659) rearrangement : c.2336_3252+1027inv	PRECISE	Note: The NCOA3 (NM_181659) rearrangement event results in the inversion of NCOA3 exons 12-17. One of the breakpoints is within NCOA3 exon12.	MANUAL_OK	3to3	3to3	Antisense fusion		15949	0	102	20	Exon 12 of NCOA3(+)	NCOA3	46265466			20	Intron of NCOA3(+): 1Kb after exon 17	NCOA3	46272155			125	INVERSION		6689	67573	25441	198	NEW_VARIANT
P-0006864-T01-IM5	PARK2 (NM_004562) rearrangement: c.162_c.172-79382del	PRECISE	The PARK2 (NM_004562) rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2. (PMID: 19946270)	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		936	0	6	6	Intron of PARK2(-): 79Kb before exon 3	PARK2	162763179			6	Exon 2 of PARK2(-)	PARK2	162864351			9	DELETION		101172	109479	683	6	NEW_VARIANT
P-0008334-T01-IM5	SMARCA4 (NM_003072) rearrangement : c.4425-3445_4606inv	PRECISE	Note: The SMARCA4 (NM_003072) rearrangement event results in the inversion of SMARCA4 exons 31-32. One of the breakpoints is within SMARCA4 exon32.	MANUAL_OK	5to5	5to5	-		4407	0	11	19	Intron of SMARCA4(+): 3Kb before exon 29	SMARCA4	11165486			19	Exon 30 of SMARCA4(+)	SMARCA4	11169536			22	INVERSION		4050	121439	4316	11	NEW_VARIANT
P-0005174-T01-IM5	JAK3 (NM_000215) - SLC5A2 (NM_003041) rearrangement: t(16;19)(p13.11;p11.2)(chr16:g.31501596::chr19:g.17945650)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (JAK3-SLC5A2)		0	0	11	19	Intron of JAK3(-): 11bp after exon 16	JAK3	17945650			16	Intron of SLC5A2(+): 34bp before exon 14	SLC5A2	31501596			23	TRANSLOCATION		0	45205	0	11	NEW_VARIANT
P-0008664-T01-IM5	EGFL7 (NM_201446) rearrangement: chr9:g.30093113_c.290:EGFL7del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		483796	0	10	9	IGR: 1Mb before MIR873(-)	MIR873	30093113			9	Exon 5 of EGFL7(+)	EGFL7	139564150			19	DELETION		109471037	123401	455799	10	NEW_VARIANT
P-0008932-T01-IM5	NCOR1 (NM_006311) Rearrangement : t(11;17)(11p11.2;17p12)(chr11:g.44516827::chr17:g.15935918 )	PRECISE	Note: The NCOR1 (NM_006311) Rearrangement results in the partial deletion of the exon 46 of NCOR1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	27	17	Intron of NCOR1(-): 121bp before exon 46	NCOR1	15935918			11	IGR: 70Kb before CD82(+)	CD82	44516827			18	TRANSLOCATION		0	125031	0	23	NEW_VARIANT
P-0009044-T01-IM5	TP53 ( NM_000546) Rearrangement : t(4;17)(4q21.21;17p13.1)(chr4:g.80921091::chr17:g.7580615 )	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	15	17	5-UTR of TP53(-): 703bp before coding start	TP53	7580615			4	Intron of ANTXR2(-): 9Kb after exon 12	ANTXR2	80921091			26	TRANSLOCATION		0	126284	0	14	NEW_VARIANT
P-0007176-T01-IM5	DICER1 (NM_030621) - CLMN (NM_024734) rearrangement : c.573+134_c.609-390dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (DICER1-CLMN)		10652	0	11	14	Intron of DICER1(-): 134bp after exon 6	DICER1	95596261			14	Intron of CLMN(-): 390bp before exon 7	CLMN	95677606			8	DUPLICATION		81345	113860	13933	9	NEW_VARIANT
P-0007861-T01-IM5	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1326+220:AGAP3_c.1141-3313:BRAFinv	PRECISE	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)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (AGAP3-BRAF)		117013	0	3	7	Intron of BRAF(-): 3Kb before exon 9	BRAF	140490697			7	Intron of AGAP3(+): 220bp after exon 10	AGAP3	150825991			8	INVERSION		10335294	119308	133074	3	NEW_VARIANT
P-0005933-T01-IM5	ASXL1 (NM_015338) rearrangement: c.253-14849_c.1253dup.	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		16150	0	11	20	Intron of ASXL1(+): 15Kb before exon 4	ASXL1	31001082			20	Exon 11 of ASXL1(+)	ASXL1	31021254			13	DUPLICATION		20172	64810	13863	11	NEW_VARIANT
P-0005691-T01-IM5	BRIP1 (NM_032043)  -  PITPNC1 (NM_012417)  Rearrangement : c.3745:BRIP1_c.48+1232:PITPNC1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (BRIP1-PITPNC1)		66420	0	15	17	Exon 20 of BRIP1(-)	BRIP1	59760662			17	Intron of PITPNC1(+): 1Kb after exon 1	PITPNC1	65375550			29	INVERSION		5614888	53020	99807	15	NEW_VARIANT
P-0005255-T01-IM5	PIP5K1A  (NM_001135638) - NOTCH2 (NM_024408) Rearrangement: c.86-2440:PIP5K1A_c.4982:NOTCH2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (PIP5K1A-NOTCH2)		66169	0	102	1	Exon 27 of NOTCH2(-)	NOTCH2	120465279			1	Intron of PIP5K1A(+): 2Kb before exon 2	PIP5K1A	151194281			107	INVERSION		30729002	46183	221293	161	NEW_VARIANT
P-0006217-T01-IM5	TRAF2 (NM_021138) - NOTCH1 (NM_017617) rearrangement: c.-28-4310:TRAF2_c.3204:NOTCH1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (TRAF2-NOTCH1)		36547	0	9	9	Exon 20 of NOTCH1(-)	NOTCH1	139402805			9	5-UTR of TRAF2(+): 4Kb before coding start	TRAF2	139788855			16	INVERSION		386050	70393	23247	9	NEW_VARIANT
P-0008406-T01-IM5	FGFR1 (NM_001174067) rearrangement: chr8:g.38577463_c.716inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		15160	0	71	8	Exon 5 of FGFR1(-)	FGFR1	38283762			8	IGR: 8Kb before TACC1(+)	TACC1	38577463			64	INVERSION		293701	121754	15865	52	NEW_VARIANT
P-0005168-T01-IM5	CCDC6  (NM_005436) - RET  (NM_020975)  Fusion ( CCDC6 Exon1 fused to RET Exon10 )  :  c.304-11493:CCDC6_c.1760-207:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: out of frame (CCDC6-RET)		83755	0	7	10	Intron of RET(+): 207bp before exon 10	RET	43608797			10	Intron of CCDC6(-): 11Kb before exon 2	CCDC6	61623953			13	INVERSION		18015156	44324	80266	7	NEW_VARIANT
P-0000208-T02-IM5	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	PRECISE	(PMID: 22327624)	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		43550	0	82	10	Intron of KIF5B(-): 2Kb before exon 16	KIF5B	32313935			10	Intron of RET(+): 385bp before exon 12	RET	43611647			89	INVERSION		11297712	45905	31532	79	NEW_VARIANT
P-0007500-T01-IM5	FGFR4 (NM_213647) rearrangement: chr5:g.168772933 _c.1057+108:FGFR4dup	PRECISE	The FGFR4 (NM_213647) rearrangement is a duplication of exons 1-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		42716	0	12	5	IGR: 45Kb after SLIT3(-)	SLIT3	168772933			5	Intron of FGFR4(+): 108bp after exon 8	FGFR4	176519893			16	DUPLICATION		7746960	116640	42158	12	NEW_VARIANT
P-0008869-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exons 2-10) : c.56-2234:TMPRSS2_c.19-7662:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		53835	0	42	21	Intron of ERG(-): 8Kb before exon 4	ERG	39825206			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872350			46	DELETION		3047144	124811	54454	42	NEW_VARIANT
P-0005065-T03-IM5	MRE11A(NM_005591)  Rearrangement :  c.-92:MRE11A_chr11:125397563del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		319119	0	25	11	5-UTR of MRE11A(-): 92bp before coding start	MRE11A	94226059			11	IGR: 39Kb before FEZ1(-)	FEZ1	125397563			28	DELETION		31171504	42692	328988	22	NEW_VARIANT
P-0005065-T03-IM5	EP300(NM_001429) Rearrangement :  t(22;17)(22q13.2;17q21.2)(chr22:g.41523648::chr17:g.38565813)	IMPRECISE	Note: The EP300(NM_001429) Rearrangement results in the translocation of exons 1 to 4 of EP300.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	59	22	Exon 4 of EP300(+)	EP300	41523648			17	Intron of TOP2A(-): 931bp before exon 11	TOP2A	38565813			0	TRANSLOCATION		0	42705	0	54	NEW_VARIANT
P-0009856-T01-IM5	STK11 (NM_000455) rearrangement : c.402_*3697del	PRECISE	Note: The STK11 (NM_000455) rearrangement event results in the deletion of STK11 exons 3-9. One of the breakpoints is within STK11 exon3.	MANUAL_OK	3to5	3to5	Antisense fusion		13670	0	68	19	Exon 3 of STK11(+)	STK11	1219350			19	Exon 9 of C19orf26(-)	C19orf26	1231272			73	DELETION		11922	136830	8768	68	NEW_VARIANT
P-0007705-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1594:EML4_c.3172+910:ALKinv	PRECISE	The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (EML4-ALK)		67739	0	102	2	Intron of ALK(-): 910bp after exon 19	ALK	29447417			2	Exon 13 of EML4(+)	EML4	42528485			119	INVERSION		13081068	118142	65878	144	NEW_VARIANT
P-0004759-T01-IM5	STK11 (NM_000455) rearrangement : c.862+203_1141del	PRECISE	Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of STK11 exons 7-9. One of the breakpoints is within exon9.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5009	0	18	19	Intron of STK11(+): 203bp after exon 6	STK11	1221542			19	Exon 9 of STK11(+)	STK11	1226485			45	DELETION		4943	34939	2600	18	NEW_VARIANT
P-0004759-T01-IM5	TCF3 (NM_001136139) rearrangement : c.500-52_1586+316del	PRECISE	Note: The TCF3 (NM_001136139) rearrangement event results in the intragenic deletion of TCF3 exons 7-16.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		21586	0	15	19	Exon 18 of TCF3(-)	TCF3	1615369			19	Intron of TCF3(-): 52bp before exon 7	TCF3	1624051			15	DELETION		8682	34940	9639	14	NEW_VARIANT
P-0004759-T01-IM5	RB1 (NM_000321) rearrangement : t(13;X)(13q14.2;Xp22.2)(chr13:g.49047485::chrX:g.11732599)	PRECISE	Note: The RB1 (NM_000321) rearrangement event is a reciprocal translocation which results in the truncation of RB1 exons 24-27.	MANUAL_OK	5to5	5to5	-		0	0	35	X	IGR: 44Kb before MSL3(+)	MSL3	11732599			13	Intron of RB1(+): 11bp before exon 24	RB1	49047485			23	TRANSLOCATION		0	34957	0	34	NEW_VARIANT
P-0006136-T01-IM5	TCF7L2 (NM_001146274) rearrangement: c.875+93_c.1391+920del	PRECISE	The TCF7L2 (NM_001146274) rearrangement is an intragenic deletion of exons  9-14. The functional significance is unknown.	MANUAL_OK	3to5	3to5	Deletion of 6 exons: in frame		20856	0	17	10	Intron of TCF7L2(+): 93bp after exon 7	TCF7L2	114905949			10	Intron of TCF7L2(+): 920bp after exon 13	TCF7L2	114921370			19	DELETION		15421	69057	18862	17	NEW_VARIANT
P-0004952-T01-IM5	SLC41A3 (NM_001008485) - MCL1 (NM_021960) rearrangement : t(1;3)(1q21.3;3q21.2)(chr1:g.150551707::chr3:g.125736765)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (SLC41A3-MCL1)		0	0	27	3	Intron of SLC41A3(-): 1Kb before exon 6	SLC41A3	125736765			1	Exon 1 of MCL1(-)	MCL1	150551707			0	TRANSLOCATION		0	41460	0	26	NEW_VARIANT
P-0009375-T01-IM5	ZFHX3 (NM_006885) rearrangement: c.3216+21118_c.9428-168del	PRECISE	Note: The ZFHX3 (NM_006885) rearrangement results in the deletion of exons 4-9. The functional significance of this rearrangement is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 6 exons: out of frame		94040	0	18	16	Intron of ZFHX3(-): 168bp before exon 10	ZFHX3	72822915			16	Intron of ZFHX3(-): 21Kb after exon 3	ZFHX3	72963250			17	DELETION		140335	130350	75652	17	NEW_VARIANT
P-0009813-T01-IM5	RPS6KA4 (NM_003942) rearrangement : c.1325:RPS6KA4_chr11:g.61400293inv	PRECISE	Note: The RPS6KA4 (NM_003942) rearrangement event results in the inversion of RPS6KA4 exons 1-11. One of the breakpoints is within RPS6KA4 exon11.	MANUAL_OK	3to3	3to3	Antisense fusion		27428	0	32	11	5-UTR of RPLP0P2(+): 7Kb before coding start	RPLP0P2	61400293			11	Exon 11 of RPS6KA4(+)	RPS6KA4	64136064			42	INVERSION		2735771	136546	27206	31	NEW_VARIANT
P-0009813-T01-IM5	MEN1 (NM_000244) rearrangement : c.-1283_220del	PRECISE	Note: The MEN1 (NM_000244) rearrangement event results in the deletion of MEN1 exons 1-2. One of the breakpoints is within MEN1 exon2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1476	0	46	11	Exon 3 of MEN1(-)	MEN1	64577362			11	Promoter of MEN1(-): 595bp from tx start	MEN1	64579361			73	DELETION		1999	136545	261	45	NEW_VARIANT
P-0008344-T01-IM5	AR (NM_000044) Rearrangement : chrX:g.66673283_c.2049:ARdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		21875	0	52	X	IGR: 91Kb before AR(+)	AR	66673283			X	Exon 4 of AR(+)	AR	66931407			63	DUPLICATION		258124	121460	108790	51	NEW_VARIANT
P-0007771-T01-IM5	DOT1L (NM_032482) rearrangement: t(17;19)(q12;p12)(chr17:g.36167655::chr19:g.2228256 )	PRECISE	The DOT1L (NM_032482) rearrangement is a translocation which may result in a truncated  DOT1L. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	13	19	Intron of DOT1L(+): 1Kb after exon 27	DOT1L	2228256			17	IGR: 35Kb before LOC284100(-)	LOC284100	36167655			33	TRANSLOCATION		0	118388	0	13	NEW_VARIANT
P-0004790-T01-IM5	ETV6 (NM_001987) rearrangement: c.163+28658_c.464-6383dup	PRECISE	The ETV6 (NM_001987) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		118858	0	23	12	Intron of ETV6(+): 29Kb after exon 2	ETV6	11934171			12	Intron of ETV6(+): 6Kb before exon 5	ETV6	12015975			19	DUPLICATION		81804	35408	123006	22	NEW_VARIANT
P-0004790-T01-IM5	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)	PRECISE	exons 1-7 of CD74 (NM_001025159) fused to exons 34-43 of ROS1 (NM_002944)	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	42	6	Intron of ROS1(-): 889bp before exon 34	ROS1	117646467			5	Intron of CD74(-): 19bp before exon 7	CD74	149782207			21	TRANSLOCATION		0	35415	0	41	NEW_VARIANT
P-0007267-T01-IM5	TMPRSS2 (NM_001135099) rearrangement : c.56-1208:TMPRSS2_chr21:g.40058491del	PRECISE	Note: The TMPRSS2 (NM_001135099) rearrangement results in the deletion of exons 2 to 14 of TMPRSS2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		64506	0	36	21	IGR: 52Kb before NCRNA00114(-)	NCRNA00114	40058491			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871324			61	DELETION		2812833	114747	48862	36	NEW_VARIANT
P-0007533-T01-IM5	SND1 (NM_014390) - BRAF (NM_004333) fusion (SND1 exons 1-10 with BRAF exons 11-18)  : c.1152+31738:SND1_c.1314+595:BRAFinv	PRECISE	Note: The SND1-BRAF fusion includes the kinase domain of BRAF.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SND1-BRAF)		67415	0	102	7	Intron of SND1(+): 32Kb after exon 10	SND1	127393192			7	Intron of BRAF(-): 595bp after exon 10	BRAF	140482226			102	INVERSION		13089034	117222	105853	199	NEW_VARIANT
P-0007533-T01-IM5	AR (NM_000044) rearrangement : c.2004:AR_chrX:g.67175446inv	PRECISE	Note: The AR (NM_000044) rearrangement event is a reciprocal inversion.	MANUAL_OK	3to3	3to3	-		6861	0	102	X	Exon 4 of AR(+)	AR	66931362			X	IGR: 87Kb before OPHN1(-)	OPHN1	67175446			84	INVERSION		244084	117223	7616	113	NEW_VARIANT
P-0005976-T01-IM5	ACAP1(NM_014716) and TP53(NM_000546) rearrangement : c.1344-331:ACAP1_c.-28-696:TP53inv	PRECISE	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	MANUAL_OK	3to3	3to3	Transcript fusion (ACAP1-TP53)		41486	0	52	17	Intron of ACAP1(+): 331bp before exon 15	ACAP1	7250910			17	5-UTR of TP53(-): 724bp before coding start	TP53	7580636			54	INVERSION		329726	66849	16036	50	NEW_VARIANT
P-0009501-T01-IM5	PDE3A (NM_000921) rearrangement: chr12:g.20290558_c.1760+1670inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		623	0	14	12	IGR: 232Kb before PDE3A(+)	PDE3A	20290558			12	Intron of PDE3A(+): 2Kb after exon 6	PDE3A	20784731			15	INVERSION		494173	130978	617	14	NEW_VARIANT
P-0007169-T01-IM5	TP53 (NM_000546) rearrangement: c.824_c.*1124del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10677	0	64	17	3-UTR of TP53(-): 1Kb after coding stop	TP53	7571803			17	Exon 8 of TP53(-)	TP53	7577114			126	DELETION		5311	113785	5710	64	NEW_VARIANT
P-0007169-T01-IM5	PARK2 (NM_004562) rearrangement: c.534+18201_c.686del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2922	0	11	6	Exon 6 of PARK2(-)	PARK2	162394382			6	Intron of PARK2(-): 18Kb after exon 4	PARK2	162603962			18	DELETION		209580	113786	2209	10	NEW_VARIANT
P-0007871-T01-IM5	TOP1 (NM_003286) rearrangement: c.58+9432_ c.2196-7del	PRECISE	Note: The TOP1 (NM_003286) rearrangement is an intragenic deletion of exons  3-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 18 exons: out of frame		16734	0	23	20	Intron of TOP1(+): 9Kb after exon 2	TOP1	39667527			20	Intron of TOP1(+): 7bp before exon 21	TOP1	39751828			61	DELETION		84301	119322	16758	13	NEW_VARIANT
P-0006873-T01-IM5	EGFR (NM_005228) - ZCCHC6  (NM_024617) rearrangement :  : t(7;9)(chr7p11.2;chr9q21.33)(chr7:g.55238031::chr9:g.88930920)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (EGFR-ZCCHC6)		0	0	27	9	Intron of ZCCHC6(-): 1Kb after exon 17	ZCCHC6	88930920			7	Exon 16 of EGFR(+)	EGFR	55238031			11	TRANSLOCATION		0	109575	0	27	NEW_VARIANT
P-0009914-T01-IM5	RAD21 (NM_006265) - FGF12 (NM_021032) rearrangement: t(3;8)(q28;q24.11)(chr3:g.191588402::chr8:g.117866571)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	33	8	Exon 9 of RAD21(-)	RAD21	117866571			3	IGR: 271Kb before FGF12(-)	FGF12	191588402			44	TRANSLOCATION		0	137047	0	33	NEW_VARIANT
P-0005508-T01-IM5	DOT1L (NM_032482) Rearrangement : c.1156_c.3281inv	PRECISE	Note: DOT1L rearrangement is an intragenic inversion involving exons 14 to 24. It is potentially a truncating event	MANUAL_OK	3to3	3to3	Antisense fusion		24923	0	36	19	Exon 14 of DOT1L(+)	DOT1L	2210659			19	Exon 24 of DOT1L(+)	DOT1L	2222449			48	INVERSION		11790	49700	27088	35	NEW_VARIANT
P-0005888-T01-IM5	EP300 (NM_001429)  Rearrangement :  c.2818-100_ 3931del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		15966	0	84	22	Intron of EP300(+): 100bp before exon 15	EP300	41547737			22	Exon 24 of EP300(+)	EP300	41564509			79	DELETION		16772	64229	11350	80	NEW_VARIANT
P-0008283-T01-IM5	SMAD4 (NM_005359) rearrangement: t(6;18)(q36.2;q21.2)(chr6:g.153659215::chr18:g.48591962)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	20	18	Exon 9 of SMAD4(+)	SMAD4	48591962			6	IGR: 327Kb before RGS17(-)	RGS17	153659215			16	TRANSLOCATION		0	121175	0	18	NEW_VARIANT
P-0004826-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-10) :  c.56-936:TMPRS2_c.-150+18179:ERGdel	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		49853	0	3	21	5-UTR of ERG(-): 68Kb before coding start	ERG	40015403			21	Intron of TMPRSS2(-): 936bp before exon 2	TMPRSS2	42871052			0	DELETION		2855649	35878	39800	3	NEW_VARIANT
P-0008426-T01-IM5	NCOA3 (NM_181659) - PCBP3 (NM_020528) Rearrangement : t(20;21)(20q13.12;21q22.3)(chr20:g.46268900::chr21:g.47336467)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (NCOA3-PCBP3)		0	0	26	21	Intron of PCBP3(+): 1Kb before exon 9	PCBP3	47336467			20	Intron of NCOA3(+): 105bp after exon 16	NCOA3	46268900			0	TRANSLOCATION		0	121935	0	25	NEW_VARIANT
P-0008146-T01-IM5	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	PRECISE	Note: The FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion is predicted to be in-frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		217554	0	47	10	Intron of BICC1(+): 744bp before exon 16	BICC1	60565600			10	Intron of FGFR2(-): 619bp before exon 18	FGFR2	123240154			56	INVERSION		62674554	120475	171382	44	NEW_VARIANT
P-0009833-T01-IM5	MLL3 (NM_170606) rearrangement: chr7:g.151824753_c.12981:MLL3del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24019	0	65	7	IGR: 7Kb before MLL3(-)	MLL3	151824753			7	Exon 52 of MLL3(-)	MLL3	151846031			61	DELETION		21278	136704	20474	62	NEW_VARIANT
P-0004996-T02-IM5	SMO (NM_005631) - MKRN1 (NM_013446) rearrangement : c.740:SMO_c.315-4269:MKRN1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		45508	0	12	7	Exon 3 of SMO(+)	SMO	128845246			7	Intron of MKRN1(-): 4Kb before exon 3	MKRN1	140164005			17	DELETION		11318759	130577	44672	11	NEW_VARIANT
P-0004801-T01-IM5	MAP3K13(NM_004721) Rearrangement :  c.1506-338_2020dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		8621	0	17	3	Intron of MAP3K13(+): 338bp before exon 10	MAP3K13	185184276			3	Exon 11 of MAP3K13(+)	MAP3K13	185191139			33	DUPLICATION		6863	40154	12039	9	NEW_VARIANT
P-0009102-T01-IM5	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	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		55878	0	44	2	Intron of ALK(-): 119bp before exon 20	ALK	29446513			2	Intron of EML4(+): 244bp before exon 13	EML4	42528137			69	INVERSION		13081624	126654	46817	43	NEW_VARIANT
P-0005863-T01-IM5	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon1 with RET exons 12-20): c.304-24354:CCDC6_ c.2136+467:RETinv.	PRECISE	THe  CCDC6 (NM_005436) - RET (NM_020975) fusion is a reciiprocal inversion. The fusion is in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		69737	0	42	10	Intron of RET(+): 467bp after exon 11	RET	43610651			10	Intron of CCDC6(-): 24Kb before exon 2	CCDC6	61636814			61	INVERSION		18026163	62677	79464	41	NEW_VARIANT
P-0009715-T01-IM5	RB1 (NM_000321) rearrangement: c.-1956_c.128del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		781	0	11	13	Promoter of RB1(+): 2Kb from tx start	RB1	48876093			13	Exon 1 of RB1(+)	RB1	48878176			50	DELETION		2083	136148	192	11	NEW_VARIANT
P-0008383-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11) : c.56-4549:TMPRSS2_c.40-54245:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		113311	0	20	21	Intron of ERG(-): 54Kb before exon 4	ERG	39871789			21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874665			29	DELETION		3002876	121603	110453	18	NEW_VARIANT
P-0008868-T01-IM5	MTMR4 (NM_004687) - RNF43 (NM_017763) rearrangement: c.1811+1658:MTMR4_c.246:RNF43del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MTMR4-RNF43)		1237	0	13	17	Exon 2 of RNF43(-)	RNF43	56492693			17	Intron of MTMR4(-): 2Kb after exon 15	MTMR4	56579447			24	DELETION		86754	124709	759	12	NEW_VARIANT
P-0007240-T01-IM5	KDM5C (NM_004187) rearrangement : c.1541_1746+1791del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2186	0	15	X	Intron of KDM5C(-): 2Kb after exon 12	KDM5C	53237805			X	Exon 11 of KDM5C(-)	KDM5C	53239900			12	DELETION		2095	114710	1526	11	NEW_VARIANT
P-0008003-T01-IM5	NF1  (NM_001042492) - TIMP2  (NM_003255) rearrangement :  c.3496+59:NF1_c.130+6597:TIMP2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (TIMP2-NF1)		830525	1	19	17	Intron of NF1(+): 59bp after exon 26	NF1	29559958			17	Intron of TIMP2(-): 7Kb after exon 1	TIMP2	76914444			21	INVERSION		47354486	119919	910627	18	NEW_VARIANT
P-0005953-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		138828	0	86	21	Intron of ERG(-): 9Kb before exon 5	ERG	39804588			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42876716			72	DELETION		3072128	66653	143885	84	NEW_VARIANT
P-0005546-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 and ERG exons 2-10) : c.126+1491:TMPRSS2_c.19-14111:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		45771	0	23	21	Intron of ERG(-): 14Kb before exon 4	ERG	39831655			21	Intron of TMPRSS2(-): 1Kb after exon 2	TMPRSS2	42868555			34	DELETION		3036900	50204	41869	23	NEW_VARIANT
P-0007890-T01-IM5	RBM10 (NM_001204468) - CLCN5 (NM_001127898) rearrangement: c.1675:RBM10_c.*5988:CLCN5del	PRECISE	Note: The RBM10 (NM_001204468) rearrangement event results in the deletion of RBM10 exons 14-24.	MANUAL_OK	3to5	3to5	-		53554	0	92	X	Exon 14 of RBM10(+)	RBM10	47040950			X	3-UTR of CLCN5(+): 6Kb after coding stop	CLCN5	49862864			89	DELETION		2821914	119519	60991	91	NEW_VARIANT
P-0005910-T01-IM5	TCF7L2 (NM_001146274) and LRRC27 (NM_030626) rearrangement : c.553-12:TCF7L2_c.1290-649:LRRC27inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		126962	0	21	10	Intron of TCF7L2(+): 12bp before exon 5	TCF7L2	114900931			10	Intron of LRRC27(+): 649bp before exon 10	LRRC27	134178279			54	INVERSION		19277348	64475	106655	14	NEW_VARIANT
P-0007392-T01-IM5	SCRIB (NM_182706) - BRAF (NM_004333) rearrangement: t(7;8)(q34;q24.3)(chr7:g.140482150::chr8:g.144876675)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (SCRIB-BRAF)		0	0	55	8	Intron of SCRIB(-): 533bp after exon 27	SCRIB	144876675			7	Intron of BRAF(-): 657bp before exon 11	BRAF	140482150			12	TRANSLOCATION		0	115813	0	54	NEW_VARIANT
P-0009759-T01-IM5	NF1 (NM_001042492) - SHISA9 (NM_001145204) rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.13117863::chr17:g.29550486 )	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (NF1-SHISA9)		0	0	15	17	Exon 16 of NF1(+)	NF1	29550486			16	Intron of SHISA9(+): 107Kb after exon 2	SHISA9	13117863			9	TRANSLOCATION		0	136439	0	14	NEW_VARIANT
P-0009759-T01-IM5	DNAJB1 (NM_006145) rearrangement: c.770_ chr19:g.23268574del	PRECISE	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.	MANUAL_OK	5to5	5to5	-		321473	0	29	19	Exon 2 of DNAJB1(-)	DNAJB1	14627300			19	IGR: 272Kb before ZNF91(-)	ZNF91	23268574			61	INVERSION		8641274	136438	333841	27	NEW_VARIANT
P-0004963-T01-IM5	BCOR (NM_001123385) rearrangement : c.4429-1339_4595+3del	PRECISE	Note: The BCOR (NM_001123385) rearrangement event results in the intragenic deletion of BCOR exon 10.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		2065	0	15	X	Intron of BCOR(-): 3bp after exon 10	BCOR	39916405			X	Intron of BCOR(-): 1Kb before exon 10	BCOR	39917913			30	DELETION		1508	41653	946	14	NEW_VARIANT
P-0008915-T01-IM5	PTPRZ1 (NM_002851) - MET (NM_000245) rearrangement: c.58+3144:PTPRZ1_c.177:METdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (PTPRZ1-MET)		58071	0	6	7	Exon 2 of MET(+)	MET	116339315			7	Intron of PTPRZ1(+): 3Kb after exon 1	PTPRZ1	121516755			6	DUPLICATION		5177440	124847	47682	5	NEW_VARIANT
P-0004516-T02-IM5	GCC2 (NM_181453) - ALK (NM_004304) rearrangement : c.4448-1230:GCC2_c.3173-132:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (GCC2-ALK)		581216	0	31	2	Intron of ALK(-): 132bp before exon 20	ALK	29446526			2	Intron of GCC2(+): 1Kb before exon 20	GCC2	109110517			57	INVERSION		79663991	114764	497075	17	NEW_VARIANT
P-0004916-T01-IM5	CCDC6(NM_005436)-RET(NM_020975) Fusion(CCDC6 exon 2 fused to RET exon11) : c.304-1153:CCDC6_c.2136+169:RETinv	PRECISE	Note:The CCDC6(NM_005436)-RET(NM_020975) Fusion is a reciprocal inversion.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		51431	0	90	10	Intron of RET(+): 169bp after exon 11	RET	43610353			10	Intron of CCDC6(-): 1Kb before exon 2	CCDC6	61613613			70	INVERSION		18003260	40779	49199	87	NEW_VARIANT
P-0005698-T01-IM5	TP53 (NM_000546) - DLG4  (NM_001128827) rearrangement :  c.96+41:TP53_c.778+1336:DLG4inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		36450	0	18	17	Intron of DLG4(-): 1Kb after exon 8	DLG4	7104886			17	Intron of TP53(-): 41bp after exon 3	TP53	7579659			41	INVERSION		474773	53120	31625	18	NEW_VARIANT
P-0005698-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10) : c.126+396:TMPRSS2_c.39+21608:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		40105	0	7	21	Intron of ERG(-): 22Kb after exon 3	ERG	39925978			21	Intron of TMPRSS2(-): 396bp after exon 2	TMPRSS2	42869650			9	DELETION		2943672	53114	35015	7	NEW_VARIANT
P-0008591-T01-IM5	ZFHX3 (NM_006885) - BATF (NM_006399) rearrangement: t(14;16)(q24.3;q22.2)(chr14:g.76000033::chr16:g.72829355 )	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (ZFHX3-BATF)		0	0	54	16	Exon 9 of ZFHX3(-)	ZFHX3	72829355			14	Intron of BATF(+): 9Kb after exon 2	BATF	76000033			75	TRANSLOCATION		0	123019	0	51	NEW_VARIANT
P-0008591-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		38946	0	14	21	Intron of ERG(-): 64Kb after exon 3	ERG	39883119			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868017			24	DELETION		2984898	123016	18121	14	NEW_VARIANT
P-0004889-T01-IM5	NOTCH3 (NM_000435) rearrangement:c.3522_chr19:g.15416060del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		91315	0	24	19	Exon 22 of NOTCH3(-)	NOTCH3	15290032			19	IGR: 48Kb before AKAP8(-)	AKAP8	15416060			32	DELETION		126028	40255	67906	23	NEW_VARIANT
P-0005779-T01-IM5	INPP4B (NM_001101669) rearrangement : c.1564-6299_c.2113del	PRECISE	Note: The INPP4B (NM_001101669) rearrangement results in the deletion of INPP4B exons 18-21. One of the breakpoints is within INPP4B exon21.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3710	0	12	4	Exon 22 of INPP4B(-)	INPP4B	143043303			4	Intron of INPP4B(-): 6Kb before exon 19	INPP4B	143073448			21	DELETION		30145	61936	1962	7	NEW_VARIANT
P-0005122-T01-IM5	ARID2(NM_152641) Rearrangement :  c.284+5753_4618del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		54185	0	60	12	Intron of ARID2(+): 6Kb after exon 3	ARID2	46130850			12	Exon 15 of ARID2(+)	ARID2	46246524			51	DELETION		115674	43981	55641	59	NEW_VARIANT
P-0008691-T01-IM5	ETV6 (NM_001987) - ITPR2 (NM_002223) rearrangement: c.1009+6762:ETV6_c.163+2322:ITPR2dup.	PRECISE	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.	MANUAL_OK	5to3	5to3	-		162497	0	30	12	Intron of ETV6(+): 7Kb after exon 5	ETV6	12029665			12	Intron of ITPR2(-): 2Kb after exon 2	ITPR2	26940768			27	DUPLICATION		14911103	123495	190114	24	NEW_VARIANT
P-0008691-T01-IM5	FGFR1 (NM_001174067) rearrangement: c.191-7470_c.541+117inv	PRECISE	Note: The FGFR1 (NM_001174067) rearrangement is an inversion (9183 bp) of exons 4-5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		6794	0	102	8	Intron of FGFR1(-): 111bp after exon 3	FGFR1	38285753			8	Intron of FGFR1(-): 3Kb after exon 3	FGFR1	38294936			90	INVERSION		9183	123505	7597	246	NEW_VARIANT
P-0003908-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		33033	0	10	21	Intron of ERG(-): 13Kb after exon 3	ERG	39934598			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867649			14	DELETION		2933051	71560	24421	12	NEW_VARIANT
P-0004880-T02-IM5	EP300 (NM_001429) rearrangement : c.-269_7215del	PRECISE	Note: The EP300 (NM_001429) rearrangement event results in the deletion of EP300 exons 1-31. One of the breakpoints is within EP300 exon31.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		82249	0	15	22	5-UTR of EP300(+): 269bp before coding start	EP300	41488740			22	Exon 31 of EP300(+)	EP300	41574930			14	DELETION		86190	115435	67236	15	NEW_VARIANT
P-0009943-T01-IM5	MLL2 (NM_003482) rearrangement: c.3431_c.4702dup	PRECISE	Note: The MLL2 rearrangement is a intragenic duplication. The breakpoints are within exons 11 and 18. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		12946	0	49	12	Exon 18 of MLL2(-)	MLL2	49439742			12	Exon 11 of MLL2(-)	MLL2	49443940			46	DUPLICATION		4198	137182	18506	48	NEW_VARIANT
P-0009221-T01-IM5	ZFHX3 (NM_006885) rearrangement: c.3865-1437_c.4821dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		13558	0	44	16	Exon 9 of ZFHX3(-)	ZFHX3	72831760			16	Intron of ZFHX3(-): 1Kb before exon 8	ZFHX3	72835465			58	DUPLICATION		3705	129331	14752	43	NEW_VARIANT
P-0006412-T01-IM5	LUC7L2 (NM_001244584) - BRAF (NM_004333) Rearrangement : c.1008-2090:LUC7L2_c.860+103:BRAFdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		164717	0	20	7	Intron of LUC7L2(+): 2Kb before exon 9	LUC7L2	139100194			7	Intron of BRAF(-): 103bp after exon 6	BRAF	140501109			29	DELETION		1400915	92531	161211	15	NEW_VARIANT
P-0008771-T01-IM5	FGFR3 (NM_000142) rearrangement: c.1535-35:FGFR3_chr4:g.202468dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		13323	0	6	4	Intron of FGFR3(+): 35bp before exon 12	FGFR3	1807251			4	IGR: 19Kb before C4orf48(+)	C4orf48	2024681			2	DUPLICATION		217430	123902	12893	6	NEW_VARIANT
P-0005142-T01-IM5	SMARCA4 (NM_003072) - LDLR (NM_000527) rearrangement: c.4533+94:SMARCA4_c.8:LDLRdel	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SMARCA4-LDLR)		5134	0	7	19	Intron of SMARCA4(+): 94bp after exon 29	SMARCA4	11169133			19	Exon 1 of LDLR(+)	LDLR	11200232			0	DELETION		31099	44024	4807	7	NEW_VARIANT
P-0005811-T01-IM5	KDM6A  (NM_021140) Rearrangement :  c.3145-812_3209+31del	IMPRECISE	Note: The KDM6A  (NM_021140) rearrangement results in the  intragenic deletion of  exon 21.  Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1636	1	102	X	Intron of KDM6A(+): 812bp before exon 21	KDM6A	44941009			X	Intron of KDM6A(+): 31bp after exon 21	KDM6A	44941916			0	DELETION		907	62323	890	116	NEW_VARIANT
P-0007600-T01-IM5	CTNNB1 (NM_001904) rearrangement : c.9_367del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5397	0	54	3	Intron of CTNNB1(+): 94bp after exon 2	CTNNB1	41265666			3	Exon 4 of CTNNB1(+)	CTNNB1	41266570			0	DELETION		904	117595	4895	51	NEW_VARIANT
P-0004589-T01-IM5	CTCF (NM_006565) rearrangement : c.-9-2751_782-31del	PRECISE	Note: The CTCF (NM_006565) rearrangement event results in the intragenic deletion of CTCF exon3.	MANUAL_OK	3to5	3to5	Deletion within transcript		6053	0	18	16	5-UTR of CTCF(+): 3Kb before coding start	CTCF	67641976			16	Intron of CTCF(+): 31bp before exon 4	CTCF	67645823			22	DELETION		3847	29590	4785	15	NEW_VARIANT
P-0007749-T01-IM5	POLD1 (NM_002691) rearrangement:  c.202+69_c.463+16dup	PRECISE	The POLD1 (NM_002691) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		6408	0	56	19	Intron of POLD1(+): 69bp after exon 2	POLD1	50902379			19	Intron of POLD1(+): 16bp after exon 4	POLD1	50905197			68	DUPLICATION		2818	118335	6735	56	NEW_VARIANT
P-0007749-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		103952	0	64	21	Intron of ERG(-): 55Kb before exon 4	ERG	39872199			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875524			67	DELETION		3003325	118334	75118	64	NEW_VARIANT
P-0004998-T01-IM5	SOX17(NM_022454) Rearrangement : c.1168:SOX17_chr8:57024193del	PRECISE	Note: The SOX17(NM_022454) Rearrangement results in the partial deletion of exon 2 causing loss of stop codon. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2843	0	29	8	Exon 2 of SOX17(+)	SOX17	55372478			8	IGR: 1Kb before MOS(-)	MOS	57024193			40	DELETION		1651715	41731	2150	28	NEW_VARIANT
P-0006990-T01-IM5	MAP3K1 (NM_005921) rearrangement : chr5:g.55024979_c.2904:MAP3K1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		22256	0	9	5	IGR: 9Kb before DDX4(+)	DDX4	55024979			5	Exon 14 of MAP3K1(+)	MAP3K1	56177931			17	INVERSION		1152952	112530	22796	8	NEW_VARIANT
P-0007398-T02-IM5	SKIV2L2 (NM_015360) - APC (NM_000038) Rearrangement : c.1811-660:SKIV2L2_c.4089:APCdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SKIV2L2-APC)		294406	0	38	5	Intron of SKIV2L2(+): 660bp before exon 17	SKIV2L2	54673482			5	Exon 16 of APC(+)	APC	112175380			43	DELETION		57501898	118579	211268	37	NEW_VARIANT
P-0006617-T01-IM5	ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event : c.127-20148:ASAP2_c.667+106:ALKdel	PRECISE	Note: The ASAP2 (NM_003887) - ALK (NM_004304) rearrangement event results in the deletion of ALK exons 2-29.	MANUAL_OK	3to5	3to5	Antisense fusion		234507	0	11	2	Intron of ASAP2(+): 20Kb before exon 2	ASAP2	9399298			2	Intron of ALK(-): 106bp after exon 1	ALK	30142753			10	DELETION		20743455	107409	231634	11	NEW_VARIANT
P-0001347-T02-IM5	TP53 (NM_000546) rearrangement: c.1001_c.*608del	PRECISE	The TP53 (NM_000546) rearrangement is an intragenic deletion of exons 10-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4745	0	18	17	3-UTR of TP53(-): 608bp after coding stop	TP53	7572319			17	Exon 10 of TP53(-)	TP53	7574026			40	DELETION		1707	69051	3643	18	NEW_VARIANT
P-0006151-T01-IM5	RECQL4 (NM_004260) - ZMAT4 (NM_024645) rearrangement : c.357:RECQL4_c.578-20947:ZMAT4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		215174	0	22	8	Intron of ZMAT4(-): 21Kb before exon 5	ZMAT4	40459727			8	Exon 5 of RECQL4(-)	RECQL4	145742146			27	INVERSION		105282419	69912	249175	21	NEW_VARIANT
P-0009598-T01-IM5	JAK3 (NM_000215) rearrangement: c.-13-314_c.1012inv	PRECISE	Note: The JAK3 (NM_000215) rearrangement is an inversion of exons 2-8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		9060	0	9	19	Exon 8 of JAK3(-)	JAK3	17952328			19	5-UTR of JAK3(-): 327bp before coding start	JAK3	17955553			23	INVERSION		3225	131422	11070	7	NEW_VARIANT
P-0009018-T01-IM5	TP53 (NM_000546) rearrangement : c.375+28_993+500del	PRECISE	Note: The TP53 (NM_000546) rearrangement event results in the intragenic deletion of TP53 exons 5-9.	MANUAL_OK	3to5	3to5	Deletion of 5 exons: in frame		13918	0	37	17	Intron of TP53(-): 500bp after exon 9	TP53	7576353			17	Intron of TP53(-): 28bp after exon 4	TP53	7579284			55	DELETION		2931	126108	13958	36	NEW_VARIANT
P-0008064-T01-IM5	EEA1 (NM_003566) - CDKN2A (NM_000077) rearrangement : t(9;12)(p21.3;q22)(chr9:g.21968207::chr12:g.93282009)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	13	12	Intron of EEA1(-): 3Kb after exon 2	EEA1	93282009			9	3-UTR of CDKN2A(-): 21bp after coding stop	CDKN2A	21968207			7	TRANSLOCATION		0	120249	0	13	NEW_VARIANT
P-0009490-T01-IM5	KDM4C (NM_015061) - PTPRD (NM_002839) rearrangement: c.2782-15487:KDM4C_c.211-65:PTPRDinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (KDM4C-PTPRD)		80440	0	5	9	Intron of KDM4C(+): 15Kb before exon 20	KDM4C	7149751			9	Intron of PTPRD(-): 65bp before exon 14	PTPRD	8633523			4	INVERSION		1483772	130877	121595	5	NEW_VARIANT
P-0003925-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		232	0	99	13	Exon 1 of RB1(+)	RB1	48878071			13	Intron of RB1(+): 969bp after exon 1	RB1	48879154			91	DELETION		1083	71570	89	118	NEW_VARIANT
P-0006195-T01-IM5	RB1 (NM_000321) Rearrangement :  c.264+176_264+975del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within intron		3	0	16	13	Intron of RB1(+): 176bp after exon 2	RB1	48881718			13	Intron of RB1(+): 975bp after exon 2	RB1	48882517			6	DELETION		799	70186	1	6	NEW_VARIANT
P-0006360-T01-IM5	PAK1 (NM_002576) - GDPD4 (NM_182833) rearrangement: c.1552-1930:PAK1_ c.708-4336:GDPD4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (PAK1-GDPD4)		4181	0	22	11	Intron of GDPD4(-): 4Kb before exon 10	GDPD4	76973923			11	Intron of PAK1(-): 38bp after exon 15	PAK1	77036335			16	DELETION		62412	91915	3946	21	NEW_VARIANT
P-0008429-T02-IM5	PIK3R1 (NM_181523) rearrangement : c.917-2817_1745+22dup	PRECISE	Note: The PIK3R1 (NM_181523) rearrangement event results in the duplication of PIK3R1 exons 8-13.	MANUAL_OK	5to3	5to3	Duplication of 6 exons: out of frame		13294	0	34	5	Intron of PIK3R1(+): 691bp after exon 1	PIK3R1	67585270			5	Intron of PIK3R1(+): 22bp after exon 7	PIK3R1	67591174			44	DUPLICATION		5904	122590	12397	34	NEW_VARIANT
P-0005889-T01-IM5	MLL2 (NM_003482) Rearrangement :  c.15716_13954inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		15529	0	70	12	Exon 48 of MLL2(-)	MLL2	49420033			12	Exon 42 of MLL2(-)	MLL2	49424108			65	INVERSION		4075	64279	24511	70	NEW_VARIANT
P-0005518-T01-IM5	POLE (NM_006231) Rearrangement :  c.3651_3583-740del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		620	0	17	12	Exon 30 of POLE(-)	POLE	133226407			12	Intron of POLE(-): 740bp before exon 30	POLE	133227215			12	DELETION		808	49961	708	15	NEW_VARIANT
P-0006787-T01-IM5	ST7 (NM_021908) - MET (NM_000245)  rearrangement: c.151+32541:ST7_c.2364+47:METdup.	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (ST7-MET)		13343	0	9	7	Intron of MET(+): 47bp after exon 10	MET	116399591			7	Intron of ST7(+): 33Kb after exon 1	ST7	116626286			26	DUPLICATION		226695	108938	9075	9	NEW_VARIANT
P-0009111-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.21124920_c.194-3618:CDKN2Ap14ARFinv	PRECISE	Note: The CDKN2Ap14ARF (NM_058195) rearrangement results in the inversion of exons 2-3 of CDKN2Ap14ARF. The functional significance of this rearrangement is undetermined.	MANUAL_OK	3to3	3to3	-		4866	0	8	9	5-UTR of MIR548H2(+): 8Kb before coding start	MIR548H2	21124920			9	Intron of CDKN2Ap14ARF(-): 3Kb before exon 2	CDKN2Ap14ARF	21974825			10	INVERSION		849905	126668	4501	8	NEW_VARIANT
P-0009111-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.21124920_c.2:CDKN2Ap16INK4Ainv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (MIR548H2-CDKN2Ap16INK4A)		4866	0	8	9	5-UTR of MIR548H2(+): 8Kb before coding start	MIR548H2	21124920			9	Exon 1 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21974825			10	INVERSION		849905	128763	4501	8	NEW_VARIANT
P-0005058-T01-IM5	CTNNB1 (NM_001904) rearrangement: c.-48-1094_c.386del.	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5890	0	6	3	5-UTR of CTNNB1(+): 1Kb before coding start	CTNNB1	41264418			3	Exon 4 of CTNNB1(+)	CTNNB1	41266589			7	DELETION		2171	42353	7033	6	NEW_VARIANT
P-0009065-T01-IM5	RECQL4 (NM_004260) - RHPN1 (NM_052924) rearrangement : c.1704+13:RECQL4_c.61-826:RHPN1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (RECQL4-RHPN1)		23850	0	9	8	Intron of RHPN1(+): 826bp before exon 2	RHPN1	144456897			8	Intron of RECQL4(-): 13bp after exon 10	RECQL4	145739813			16	INVERSION		1282916	126330	26723	9	NEW_VARIANT
P-0005930-T01-IM5	CIC  (NM_015125) Rearrangement :  c.1912_3796-8del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		17381	0	44	19	Exon 10 of CIC(+)	CIC	42794832			19	Intron of CIC(+): 8bp before exon 16	CIC	42797736			94	DELETION		2904	64565	13492	41	NEW_VARIANT
P-0005821-T01-IM5	ARID1A (NM_006015) rearrangement event : c.1921-5117_4862inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		27612	0	54	1	Intron of ARID1A(+): 5Kb before exon 5	ARID1A	27082230			1	Exon 18 of ARID1A(+)	ARID1A	27101580			59	INVERSION		19350	63388	29380	52	NEW_VARIANT
P-0009147-T01-IM5	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.	PRECISE		MANUAL_OK	5to5	5to5	-		32993	0	26	18	Exon 4 of MALT1(+)	MALT1	56367732			18	IGR: 59Kb before PIGN(-)	PIGN	59652061			29	INVERSION		3284329	128822	27236	25	NEW_VARIANT
P-0009147-T01-IM5	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.	PRECISE		MANUAL_OK	5to3	5to3	-		52949	0	18	5	IGR: 4Kb after ANXA6(-)	ANXA6	150541610			5	Exon 2 of NSD1(+)	NSD1	176562328			22	DUPLICATION		26020718	128821	45652	16	NEW_VARIANT
P-0008291-T01-IM5	SLC1A2 (NM_004171) - MET (NM_000245) rearrangement: t(7;11)(q34;p13)(chr7:g.116411931::chr111:g.35443621)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (SLC1A2-MET)		0	0	12	11	Promoter of SLC1A2(-): 3Kb from tx start	SLC1A2	35443621			7	Exon 14 of MET(+)	MET	116411931			12	TRANSLOCATION		0	121140	0	12	NEW_VARIANT
P-0004815-T01-IM5	SLC12A6 (NM_133647) - MDM2 (NM_002392) rearrangement: t(15;12)(q14;q15)(chr15:g.34539975::chr12:g.69233428)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (SLC12A6-MDM2)		0	0	102	15	Intron of SLC12A6(-): 2Kb before exon 13	SLC12A6	34539975			12	Exon 11 of MDM2(+)	MDM2	69233428			38	TRANSLOCATION		0	35533	0	156	NEW_VARIANT
P-0004815-T01-IM5	TP63 (NM_00372 ) - SPEN (NM_015001) rearrangement: t(3;1)(q28;p36.13)(chr3:g.189533530::chr1:g.16247389)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (TP63-SPEN)		0	0	93	3	Intron of TP63(+): 7Kb after exon 4	TP63	189533530			1	Exon 9 of SPEN(+)	SPEN	16247389			24	TRANSLOCATION		0	35538	0	89	NEW_VARIANT
P-0009082-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-2840:TMPRSS2_c.40-50568:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		88496	0	102	21	Intron of ERG(-): 2Kb after exon 1	ERG	39868112			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872956			93	DELETION		3004844	126376	62892	115	NEW_VARIANT
P-0009648-T01-IM5	RARA (NM_000964) - MUC16 (NM_024690) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.38512460::chr19:g.9019793)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (RARA-MUC16)		0	0	35	19	Intron of MUC16(-): 158bp before exon 22	MUC16	9019793			17	Exon 9 of RARA(+)	RARA	38512460			18	TRANSLOCATION		0	131589	0	35	NEW_VARIANT
P-0008098-T01-IM5	BRAF (NM_004333) rearrangement : c.139-17798_1314+634del	PRECISE	Note: The BRAF (NM_004333) rearrangement event results in the deletion of BRAF exons 2-9.	MANUAL_OK	3to5	3to5	Deletion of 9 exons: in frame		198635	0	102	7	Intron of BRAF(-): 634bp after exon 10	BRAF	140482187			7	Intron of BRAF(-): 18Kb before exon 2	BRAF	140567810			106	DELETION		85623	120339	107954	205	NEW_VARIANT
P-0006167-T01-IM5	ZFHX3 (NM_006885) Rearrangement :  c.11028:ZFHX3_chr16:g.76628585inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		119385	0	21	16	Exon 10 of ZFHX3(-)	ZFHX3	72821147			16	IGR: 35Kb after CNTNAP4(+)	CNTNAP4	76628585			29	INVERSION		3807438	70034	113242	20	NEW_VARIANT
P-0008879-T01-IM5	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	PRECISE	Note: The TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion is an in-frame fusion.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		37734	0	11	21	Intron of ERG(-): 212bp after exon 1	ERG	39870075			21	Intron of TMPRSS2(-): 804bp after exon 2	TMPRSS2	42869242			18	DELETION		2999167	124797	34858	11	NEW_VARIANT
P-0009343-T01-IM5	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	PRECISE	Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		100683	0	51	2	Intron of ALK(-): 127bp before exon 20	ALK	29446521			2	Intron of EML4(+): 1Kb before exon 6	EML4	42506897			64	INVERSION		13060376	130213	81631	31	NEW_VARIANT
P-0009624-T01-IM5	MAPK3 (NM_002746) Rearrangement : c.847_chr16:g.32609076inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		24320	0	96	16	Exon 6 of MAPK3(-)	MAPK3	30128535			16	IGR: 76Kb before TP53TG3B(-)	TP53TG3B	32609076			79	INVERSION		2480541	131519	24071	95	NEW_VARIANT
P-0003913-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		78053	0	102	2	Intron of ALK(-): 817bp before exon 20	ALK	29447211			2	Intron of EML4(+): 678bp after exon 12	EML4	42523334			91	INVERSION		13076123	82951	51159	133	NEW_VARIANT
P-0005895-T01-IM5	TMPRSS2 (NM_001135099) rearrangement: c.55+249_c.436+457del	PRECISE	The TMPRSS2 (NM_001135099) rearrangement is an intragenic deletion of exons 2-4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons: in frame		98443	0	23	21	Intron of TMPRSS2(-): 457bp after exon 4	TMPRSS2	42860977			21	Intron of TMPRSS2(-): 249bp after exon 1	TMPRSS2	42879628			38	DELETION		18651	64418	143663	22	NEW_VARIANT
P-0003762-T02-IM5	ADCY9 (NM_001116) - CDK12 (NM_016507) rearrangement: t(16;17)(p13.3;q12)(chr16:g.4033430::chr17:g.37646665)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (ADCY9-CDK12)		0	0	21	17	Intron of CDK12(+): 145bp before exon 3	CDK12	37646665			16	Exon 7 of ADCY9(-)	ADCY9	4033430			10	TRANSLOCATION		0	119603	0	20	NEW_VARIANT
P-0003762-T02-IM5	KDM6A (NM_021140) rearrangement: c.226-33170_c.335-77del.	PRECISE	The KDM6A (NM_021140) rearrangement is an intragenic deletion of exon3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		3214	0	51	X	Intron of KDM6A(+): 33Kb before exon 3	KDM6A	44787359			X	Intron of KDM6A(+): 77bp before exon 4	KDM6A	44833834			47	DELETION		46475	119600	1395	48	NEW_VARIANT
P-0006963-T01-IM5	TERT (NM_198253) rearrangement : c.-1357_-259del	PRECISE	Note: The TERT (NM_198253) rearrangement event results in a deletion in the TERT promoter region. Significance of this event is unknown.	MANUAL_OK	3to5	3to5	Deletion within transcript		4	0	19	5	Promoter of TERT(-): 201bp from tx start	TERT	1295363			5	Promoter of TERT(-): 1Kb from tx start	TERT	1296461			23	DELETION		1098	112449	9	19	NEW_VARIANT
P-0006815-T01-IM5	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exon 2) :  c.55+4833:TMPRSS2_c.-150+8005:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		46193	0	34	21	5-UTR of ERG(-): 78Kb before coding start	ERG	40025577			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875044			35	DELETION		2849467	109213	49556	33	NEW_VARIANT
P-0008956-T01-IM5	ROS1 (NM_002944) rearrangement: c.2125+20_chr6:g.115008053del	PRECISE	Note: The ROS1 (NM_002944) rearrangement is a deletion of exons 15-43, including the kinase domain.  The functional significance is undetermined	MANUAL_OK	3to5	3to5	-		171659	0	37	6	IGR: 631Kb before HS3ST5(-)	HS3ST5	115008053			6	Intron of ROS1(-): 20bp after exon 14	ROS1	117708032			41	DELETION		2699979	125166	171672	37	NEW_VARIANT
P-0005993-T01-IM5	CDK12 (NM_016507) Rearrangement: c.1520_c.2609+3524del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		17232	0	102	17	Exon 2 of CDK12(+)	CDK12	37627605			17	Intron of CDK12(+): 4Kb after exon 6	CDK12	37661216			120	DELETION		33611	66976	307872	318	NEW_VARIANT
P-0008441-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		49145	0	100	21	Intron of ERG(-): 61Kb after exon 3	ERG	39886960			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868117			63	DELETION		2981157	121995	52600	96	NEW_VARIANT
P-0009596-T01-IM5	PBRM1 (NM_018313) rearrangement: c.620_c.3616+4824dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		39741	0	22	3	Intron of PBRM1(-): 5Kb after exon 23	PBRM1	52605733			3	Exon 6 of PBRM1(-)	PBRM1	52692240			35	DUPLICATION		86507	131424	36980	22	NEW_VARIANT
P-0006057-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.40-57547:ERG_c.56-2503:TMPRSS2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		75817	0	10	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875091			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872619			28	INVERSION		2997528	67498	70525	10	NEW_VARIANT
P-0006138-T01-IM5	CHN1(NM_001822) - IDH2 (NM_002168) rearrangement: t(2;15)(q31.1;q26)(chr2:g.175847561::chr15:g.90627553)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CHN1-IDH2)		0	0	5	15	Exon 11 of IDH2(-)	IDH2	90627553			2	Intron of CHN1(-): 22Kb after exon 2	CHN1	175847561			14	TRANSLOCATION		0	69044	0	5	NEW_VARIANT
P-0005140-T01-IM5	FGFR2 (NM_000141) rearrangement: c.2302-1537:FGFR2_chr10:g.61197618inv	PRECISE	The FGFR2 (NM_000141) rearrangement is an inversion of exon 18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		195470	0	37	10	IGR: 192Kb before FAM13C(-)	FAM13C	61197618			10	Intron of FGFR2(-): 2Kb before exon 18	FGFR2	123241072			10	INVERSION		62043454	44148	214713	34	NEW_VARIANT
P-0005034-T01-IM5	NF1 (NM_001042492) rearrangement: c.7278:NF1_chr17:g.45958328del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		606004	0	49	17	Exon 48 of NF1(+)	NF1	29676226			17	IGR: 15Kb before SP2(+)	SP2	45958328			48	DELETION		16282102	42108	692869	46	NEW_VARIANT
P-0005034-T01-IM5	NF1 (NM_001042492) rearrangement : c.7282::NF1_chr17:g.45958318dup	PRECISE	Note2: The NF1 (NM_001042492) rearrangement event results in the duplication of NF1 exons 48-58. One of the breakpoints is within NF1 exon 48. The functional significance of this event is unknown.	MANUAL_OK	5to3	5to3	-		605985	0	27	17	Exon 48 of NF1(+)	NF1	29676230			17	IGR: 15Kb before SP2(+)	SP2	45958318			52	DUPLICATION		16282088	42109	692845	27	NEW_VARIANT
P-0005034-T01-IM5	MYH14 (NM_001145809) - POLD1 (NM_002691) rearrangement : c.5678+1575:MYH14_c.972:POLD1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		22000	0	10	19	Intron of MYH14(+): 2Kb after exon 39	MYH14	50806701			19	Exon 9 of POLD1(+)	POLD1	50906311			18	INVERSION		99610	42122	19406	10	NEW_VARIANT
P-0007338-T01-IM5	STK11 (NM_000455) - REEP6 (NM_138393) rearrangement : c.460:STK11_c.137:REEP6del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (STK11-REEP6)		9392	0	25	19	Exon 3 of STK11(+)	STK11	1219408			19	Exon 2 of REEP6(+)	REEP6	1495314			36	DELETION		275906	115431	8980	25	NEW_VARIANT
P-0008104-T01-IM5	SRC (NM_198291) rearrangement : c.-3642_chr20:g.36971011del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		20493	0	48	20	Promoter of SRC(+): 2Kb from tx start	SRC	35971263			20	IGR: 4Kb before LBP(+)	LBP	36971011			45	DELETION		999748	120349	29813	48	NEW_VARIANT
P-0005711-T01-IM5	DIS3 (NM_014953) rearrangement (31899083 bp) : c.2838_chr13:g.105233055inv	PRECISE	The DIS3 (NM_014953) rearrangement is an inversion of DIS3 exons1-21. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		91158	0	17	13	Exon 21 of DIS3(-)	DIS3	73333972			13	IGR: 885Kb before DAOA(+)	DAOA	105233055			20	INVERSION		31899083	54215	91720	17	NEW_VARIANT
P-0009872-T01-IM5	CTNNB1 (NM_001904) rearrangement :  c.479_936+93del	IMPRECISE	Note: The CTNNB1 (NM_001904) rearrangement event results in the deletion of CTNNB1 exons 4-6. One of the breakpoints is within CTBBB1 exon4.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5863	2	22	3	Exon 4 of CTNNB1(+)	CTNNB1	41266682			3	Intron of CTNNB1(+): 93bp after exon 6	CTNNB1	41267445			0	DELETION		763	136908	4018	21	NEW_VARIANT
P-0004902-T01-IM5	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 with TACC3 exons 11-16) : c.2338:FGFR3_:c.1941+300TACC3dup	PRECISE	Note: One of the breakpoints in the FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is within FGFR3 exon18.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		40530	0	38	4	Intron of TACC3(+): 300bp after exon 10	TACC3	1739729			4	Exon 18 of FGFR3(+)	FGFR3	1808906			53	DUPLICATION		69177	40346	48292	38	NEW_VARIANT
P-0009100-T01-IM5	NUP93 (NM_014669) rearrangement: c.1251+106_c.1900del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		20769	0	76	16	Intron of NUP93(+): 106bp after exon 11	NUP93	56866025			16	Exon 18 of NUP93(+)	NUP93	56871520			75	DELETION		5495	126486	19262	74	NEW_VARIANT
P-0009480-T01-IM5	BBS9 (NM_198428) - IKZF1 (NM_006060) rearrangement: c.442+24705:BBS9_c.855-35:IKZF1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (BBS9-IKZF1)		54652	0	19	7	Intron of BBS9(+): 25Kb after exon 5	BBS9	33241908			7	Intron of IKZF1(+): 35bp before exon 8	IKZF1	50467581			22	DELETION		17225673	130902	55467	18	NEW_VARIANT
P-0006776-T01-IM5	MGA (NM_001164273) rearrangement: c.3925:MGA_chr15:g.90306603dup	PRECISE	The MGA (NM_001164273) rearrangement is a duplication (48278216 bp) of MGA exons 13-24. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		257340	0	54	15	Exon 13 of MGA(+)	MGA	42028387			15	IGR: 13Kb before MESP2(+)	MESP2	90306603			55	DUPLICATION		48278216	108919	274992	44	NEW_VARIANT
P-0006776-T01-IM5	ALK (NM_004304) - DYSF (NM_001130987) rearrangement: c.3172+909:ALK_c.3402+7348:DYSFdup	PRECISE	The ALK (NM_004304) - DYSF (NM_001130987) rearrangement is a duplication (42361431 bp) of ALK exons 1-19. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense fusion		256121	0	18	2	Intron of ALK(-): 909bp after exon 19	ALK	29447418			2	Intron of DYSF(+): 7Kb after exon 30	DYSF	71808849			31	DUPLICATION		42361431	108920	289125	17	NEW_VARIANT
P-0007001-T01-IM5	EGFR (NM_005228) VIII intragenic deletion : c.89-39131_890-78del	IMPRECISE		MANUAL_OK	3to5	3to5	Deletion of 6 exons: in frame		26785	0	48	7	Intron of EGFR(+): 39Kb before exon 2	EGFR	55170848			7	Intron of EGFR(+): 78bp before exon 8	EGFR	55223445			0	DELETION		52597	112588	38556	45	NEW_VARIANT
P-0006619-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-11) : c.127-1066:TMPRSS2_c.40-44616:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		47602	0	10	21	Intron of ERG(-): 8Kb after exon 1	ERG	39862160			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867571			13	DELETION		3005411	107421	46724	10	NEW_VARIANT
P-0008139-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		22811	0	22	21	Intron of ERG(-): 19Kb after exon 1	ERG	39850842			21	Intron of TMPRSS2(-): 615bp before exon 3	TMPRSS2	42867120			27	DELETION		3016278	120481	13781	20	NEW_VARIANT
P-0008778-T01-IM5	SMARCA4 (NM_003072) rearrangement: c.3547-951_c.3874-73del	PRECISE	Note: The SMARCA4 (NM_003072) rearrangement is an intragenic deletion of exons 26-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		4352	0	20	19	Intron of SMARCA4(+): 951bp before exon 25	SMARCA4	11143015			19	Intron of SMARCA4(+): 73bp before exon 26	SMARCA4	11144726			28	DELETION		1711	124246	3848	20	NEW_VARIANT
P-0007888-T01-IM5	MLL3 (NM_170606) rearrangement : c.6906:MLL3_9453+395inv	PRECISE	Note: The MLL3 (NM_170606) rearrangement event results in the inversion of MLL3 exons 36-40. One of the breakpoints is within MLL3 exon36.	MANUAL_OK	3to3	3to3	-		19066	0	20	7	Intron of MLL3(-): 395bp after exon 40	MLL3	151867954			7	Exon 36 of MLL3(-)	MLL3	151878039			21	INVERSION		10085	119510	16704	18	NEW_VARIANT
P-0006235-T01-IM5	FGFR2 (NM_000141) - ROCK1 (NM_005406) rearrangement: t(10;18)(q26.13;q11.1)(chr10:g.123240133::chr18:g18680051)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-ROCK1)		0	1	102	18	Intron of ROCK1(-): 11Kb after exon 1	ROCK1	18680051			10	Intron of FGFR2(-): 598bp before exon 18	FGFR2	123240133			39	TRANSLOCATION		0	70460	0	106	NEW_VARIANT
P-0005800-T01-IM5	PPM1D (NM_003620) rearrangement: c.-98_c.472+283dup	PRECISE	The PPM1D (NM_003620) rearrangement is an intragenic duplicaition of exon1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		6990	0	25	17	5-UTR of PPM1D(+): 98bp before coding start	PPM1D	58677678			17	Intron of PPM1D(+): 283bp after exon 1	PPM1D	58678530			31	DUPLICATION		852	62139	8067	25	NEW_VARIANT
P-0005800-T01-IM5	PPM1D (NM_003620) rearrangement: c.135_c.472+821del	PRECISE	The PPM1D (NM_003620) rearrangement is an intragenic deletion of exon1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4224	0	77	17	Exon 1 of PPM1D(+)	PPM1D	58677910			17	Intron of PPM1D(+): 821bp after exon 1	PPM1D	58679068			96	DELETION		1158	62137	4495	77	NEW_VARIANT
P-0005800-T01-IM5	PTPRD (NM_002839) rearrangement: c.3989-529_c.4086+14114dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		3609	0	19	9	Intron of PTPRD(-): 14Kb after exon 35	PTPRD	8422478			9	Exon 17 of PTPRD(-)	PTPRD	8437218			34	DUPLICATION		14740	62140	3086	19	NEW_VARIANT
P-0009463-T01-IM5	PIK3R1 (NM_181523) Rearrangement :  c.1746-31_*2815del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		5039	0	6	5	Intron of PIK3R1(+): 31bp before exon 8	PIK3R1	67591217			5	3-UTR of PIK3R1(+): 3Kb after coding stop	PIK3R1	67596244			9	DELETION		5027	130832	4287	6	NEW_VARIANT
P-0009463-T01-IM5	CDKN2Ap16INK4A (NM_000077) Rearrangement :  c.-3788_c.33del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		140	0	34	9	Exon 1 of CDKN2A(-)	CDKN2A	21974794			9	Intron of CDKN2A(-): 7Kb before exon 2	CDKN2A	21978614			36	DELETION		3820	130833	88	32	NEW_VARIANT
P-0003705-T01-IM5	c.686:LMNA_c.1476:NTRK1del	PRECISE	LMNA (NM_170707) - NTRK (NM_002529) fusion (LMNA exons 1-4 fused to NTRK1 exons 12-17)	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (LMNA-NTRK1)		31112	0	8	1	Exon 4 of LMNA(+)	LMNA	156104642			1	Exon 12 of NTRK1(+)	NTRK1	156845433			12	DELETION		740791	12640	20997	11	NEW_VARIANT
P-0004107-T01-IM5	HIST1H1E (NM_005321)  - HIST1H2BD (NM_021063) rearrangement: c.-2778:HIST1H1E _c.10:HIST1H2BDdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (HIST1H1E-HIST1H2BD)		863	0	37	6	Promoter of HIST1H1E(+): 939bp from tx start	HIST1H1E	26155620			6	Exon 1 of HIST1H2BD(+)	HIST1H2BD	26158407			61	DELETION		2787	15151	847	51	NEW_VARIANT
P-0003867-T01-IM5	TP53 (NM_000546) rearrangement: c.-28-1048_c.26_:TP53dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		2379	0	69	17	Exon 2 of TP53(-)	TP53	7579887			17	5-UTR of TP53(-): 1Kb before coding start	TP53	7580988			99	DUPLICATION		1101	13855	4429	81	NEW_VARIANT
P-0003207-T01-IM5		PRECISE	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	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TPM3-ROS1)		0	0	9	6	Intron of ROS1(-): 436bp before exon 35	ROS1	117642993			1	Intron of TPM3(-): 3Kb before exon 8	TPM3	154135010			24	TRANSLOCATION		0	9615	0	0	NEW_VARIANT
P-0000047-T01-IM3		35332045-N_bc40		AUTO_OK	3to5	3to5	-		185633	0	19	6	Exon 26 of ROS1(-)	ROS1	117674261			6	3-UTR of TMEM181(+): 3Kb after coding stop	TMEM181	159055858			68	DELETION		41381597	94059	154883	52	NEW_VARIANT
P-0003226-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		72959	0	17	21	Intron of ERG(-): 63Kb before exon 4	ERG	39880933			21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874729			62	DELETION		2993796	9856	35714	60	NEW_VARIANT
P-0000644-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (AHCYL1-FGFR2)		0	0	23	10	Intron of FGFR2(-): 210bp before exon 18	FGFR2	123239745			1	Intron of AHCYL1(+): 2Kb after exon 1	AHCYL1	110529335			39	TRANSLOCATION		0	71720	0	32	NEW_VARIANT
P-0000479-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		29844	0	5	21	Intron of ERG(-): 2Kb before exon 4	ERG	39820000			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872680			12	DELETION		3052680	71538	24085	5	NEW_VARIANT
P-0001635-T01-IM3	None	PRECISE		MANUAL_OK	3to5	3to5	Deletion of 2 exons: in frame		3678	0	44	12	Intron of ARID2(+): 32bp after exon 1	ARID2	46123743			12	Intron of ARID2(+): 17Kb after exon 3	ARID2	46142178			73	DELETION		18435	1420	4338	49	NEW_VARIANT
P-0001021-T01-IM3	EWSR1 (NM_013986) - GAS2L1 (NM_006478) Deletion:  c.1179+844_c.634-343del	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: in frame (EWSR1-GAS2L1)		13280	0	14	22	Intron of EWSR1(+): 844bp after exon 10	EWSR1	29689439			22	Intron of GAS2L1(+): 343bp before exon 3	GAS2L1	29706086			25	DELETION		16647	72282	9998	7	NEW_VARIANT
P-0002649-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (MLL2-HDAC7)		36285	0	7	12	Intron of HDAC7(-): 97bp before exon 20	HDAC7	48182044			12	Intron of MLL2(-): 22bp after exon 23	MLL2	49437396			18	DELETION		1255352	4801	47719	7	NEW_VARIANT
P-0002382-T01-IM3	PTCH1 (NM_000264) deletion (211947bp) :  PTCH1:c.585-89_chr9:g.98456521del	PRECISE	Note: PTCH1 deletion is a rearrangement event which removes exons 1 to 3  potentially disabling PTCH1 protein.	AUTO_OK	3to5	3to5	-		11158	0	8	9	Intron of PTCH1(-): 89bp before exon 4	PTCH1	98244574			9	IGR: 112Kb before C9orf130(-)	C9orf130	98456521			14	DELETION		211947	3217	7560	8	NEW_VARIANT
P-0003334-T02-IM5	MAP2K4 (NM_003010) - COX19 (NM_001031617) translocation: t(17;7) (p12;p22.3) chr17:g.11935583::chr7:g.1005376	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	45	17	Intron of MAP2K4(+): 11Kb after exon 1	MAP2K4	11935583			7	3-UTR of COX19(-): 4Kb after coding stop	COX19	1005376			47	TRANSLOCATION		0	15199	0	43	NEW_VARIANT
P-0004670-T01-IM5	ARID1A (NM_006015) rearrangement: c.1920+6791_c.2668del	PRECISE	The ARID1A (NM_006015) rearrangement is an intragenic deletion of exons 5-8 of ARID1A. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		7471	0	5	1	Intron of ARID1A(+): 7Kb after exon 4	ARID1A	27066074			1	Exon 8 of ARID1A(+)	ARID1A	27089712			6	DELETION		23638	29157	4172	5	NEW_VARIANT
P-0002050-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		26489	0	57	16	Exon 14 of CREBBP(-)	CREBBP	3820620			16	Intron of CREBBP(-): 16Kb before exon 3	CREBBP	3877273			92	DUPLICATION		56653	2226	26381	69	NEW_VARIANT
P-0002397-T01-IM3	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion :  c.55+2513:TMPRSS2_c.237-5242:ERGdel	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		62703	0	17	21	Intron of ERG(-): 5Kb before exon 5	ERG	39800725			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42877364			36	DELETION		3076639	3250	52743	19	NEW_VARIANT
P-0002336-T01-IM3	ARID2 (NM_152641) Duplication : c.1120+11_c.1498+402dup	PRECISE	Note: ARID2 duplication is a structural rearrangement in which exons 10 and  11 are duplicated	AUTO_OK	5to3	5to3	Duplication of 2 exons: in frame		3609	0	16	12	Intron of ARID2(+): 11bp after exon 9	ARID2	46231211			12	Intron of ARID2(+): 402bp after exon 11	ARID2	46233681			37	DUPLICATION		2470	3109	4518	20	NEW_VARIANT
P-0001128-T01-IM3	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032278 bp):  c.112_c.19-20238del	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (TMPRSS2-ERG)		29817	0	6	21	Intron of ERG(-): 20Kb before exon 4	ERG	39837782			21	Exon 2 of TMPRSS2(-)	TMPRSS2	42870060			20	DELETION		3032278	72500	26936	8	NEW_VARIANT
P-0002887-T01-IM3		PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (CASC3-BRCA1)		52181	0	11	17	Intron of CASC3(+): 6Kb after exon 3	CASC3	38304199			17	Exon 13 of BRCA1(-)	BRCA1	41226404			22	INVERSION		2922205	6099	47784	11	NEW_VARIANT
P-0004539-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.55+2908:TMPRSS2_c.40-50360:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		97772	0	45	21	Intron of ERG(-): 2Kb after exon 1	ERG	39867904			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42876969			50	DELETION		3009065	22247	100578	45	NEW_VARIANT
P-0004539-T01-IM5	TMPRSS2 (NM_001135099)  - ZNF295 (NM_020727) rearrangement (530676 bp) : c.55+2996_c.*3447:ZNF295inv	PRECISE	The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.	MANUAL_OK	3to3	3to3	-		19155	0	13	21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42876881			21	3-UTR of ZNF295(-): 3Kb after coding stop	ZNF295	43407557			32	INVERSION		530676	22248	20809	13	NEW_VARIANT
P-0000569-T01-IM3		IMPRECISE		AUTO_OK	5to3	5to3	Protein fusion: out of frame (ROS1-CD74)		0	0	4	6	Intron of ROS1(-): 45bp before exon 33	ROS1	117647622			5	Intron of CD74(-): 37bp after exon 6	CD74	149784206			0	TRANSLOCATION		0	71656	0	35	NEW_VARIANT
P-0004410-T01-IM5	NFE2L2(NM_006164)  Rearrangement :  c.313-78_c.46-3539del	PRECISE	Note: The NFE2L2(NM_006164)  Rearrangement results in the intragenic deletion of exon 2.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		1809	0	26	2	Intron of NFE2L2(-): 78bp before exon 3	NFE2L2	178098145			2	Intron of NFE2L2(-): 4Kb before exon 2	NFE2L2	178102538			21	DELETION		4393	20085	897	22	NEW_VARIANT
P-0003852-T01-IM5	ACAA1 (NM_001607) - MYD88 (NM_002468) rearrangement : c.700:ACAA1_c.368-122:MYD88inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (ACAA1-MYD88)		2304	0	9	3	Exon 7 of ACAA1(-)	ACAA1	38168118			3	Intron of MYD88(+): 122bp before exon 2	MYD88	38181233			9	INVERSION		13115	13787	1423	9	NEW_VARIANT
P-0002890-T01-IM3		PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	40	X	IGR: 76Kb before CXorf26(+)	CXorf26	75468339			4	Exon 5 of FGFR3(+)	FGFR3	1803169			53	TRANSLOCATION		0	6090	0	40	NEW_VARIANT
P-0003819-T01-IM5	TRIM8 (NM_030912) - SUFU (NM_016169) rearrangement : c.570+4652:TRIM8_c.1297-69:SUFUdup	PRECISE	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 .	MANUAL_OK	5to3	5to3	Protein fusion: in frame (TRIM8-SUFU)		3490	0	35	10	Intron of SUFU(+): 69bp before exon 11	SUFU	104386863			10	Intron of TRIM8(+): 5Kb after exon 1	TRIM8	104409596			42	DUPLICATION		22733	13624	6731	47	NEW_VARIANT
P-0004108-T01-IM5	ARID1A (NM_006015) rearrangement: c.1920+5685_c.3866+3dup	PRECISE	The ARID1A (NM_006015) rearrangement is an intragenic duplication of exons 5-15. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons: out of frame		16517	0	8	1	Intron of ARID1A(+): 6Kb after exon 4	ARID1A	27064968			1	Intron of ARID1A(+): 3bp after exon 15	ARID1A	27099990			19	DUPLICATION		35022	15203	15865	9	NEW_VARIANT
P-0001698-T01-IM3	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3032220  bp):(TMRPSS2:c.56-4673_ERG:c.19-25025del)	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		56586	0	9	21	Intron of ERG(-): 25Kb before exon 4	ERG	39842569			21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874789			23	DELETION		3032220	1241	55983	10	NEW_VARIANT
P-0003478-T01-IM5		PRECISE	The RAD21 (NM_006265) rearrangement reslts in the deletion of exon2. The breakpoint is within exon2.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		443	0	5	8	Exon 2 of RAD21(-)	RAD21	117878917			8	5-UTR of RAD21(-): 629bp before coding start	RAD21	117879597			21	DELETION		680	11678	442	6	NEW_VARIANT
P-0004201-T01-IM5	ETV6 (NM_001987) rearrangement: c.463+744_c.1009+7228del	PRECISE	The  ETV6 (NM_001987) rearrangement is an intragenic deletion of exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		188877	0	51	12	Intron of ETV6(+): 744bp after exon 4	ETV6	12007239			12	Intron of ETV6(+): 7Kb after exon 5	ETV6	12030131			35	DELETION		22892	16842	148335	50	NEW_VARIANT
P-0002536-T01-IM3		PRECISE		MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (ESYT1-ERBB3)		603	0	48	12	Exon 28 of ERBB3(+)	ERBB3	56495721			12	Intron of ESYT1(+): 141bp before exon 17	ESYT1	56530861			75	DUPLICATION		35140	3803	1084	57	NEW_VARIANT
P-0002206-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		46802	0	8	21	Intron of ERG(-): 4Kb after exon 1	ERG	39865870			21	Intron of TMPRSS2(-): 695bp after exon 2	TMPRSS2	42869351			14	DELETION		3003481	2627	35875	9	NEW_VARIANT
P-0001297-T01-IM3	None	PRECISE		AUTO_OK	5to3	5to3	Protein fusion: mid-exon (GSK3B-FSTL1)		1674	0	5	3	Exon 2 of GSK3B(-)	GSK3B	119721066			3	Intron of FSTL1(-): 12Kb before exon 3	FSTL1	120146959			17	DUPLICATION		425893	72835	3529	6	NEW_VARIANT
P-0001840-T02-IM5	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(20;6) (q13.12;q22.1) (chr20:g.43962893::chr6:g.117650732)	IMPRECISE	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)	MANUAL_OK	5to3	5to3	Protein fusion: in frame (SDC4-ROS1)		0	0	49	20	Intron of SDC4(-): 1Kb before exon 3	SDC4	43962893			6	Intron of ROS1(-): 123bp before exon 32	ROS1	117650732			0	TRANSLOCATION		0	22398	0	46	NEW_VARIANT
P-0001440-T01-IM3	None	PRECISE		AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		17002	0	30	16	Exon 16 of CREBBP(-)	CREBBP	3817857			16	Intron of CREBBP(-): 4Kb before exon 6	CREBBP	3836919			50	DUPLICATION		19062	2059	19180	25	NEW_VARIANT
P-0003592-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_001243428) fusion: c.127-55:TMPRSS2_c.40-16879:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		20049	0	23	21	Intron of ERG(-): 17Kb before exon 4	ERG	39834423			21	Intron of TMPRSS2(-): 55bp before exon 3	TMPRSS2	42866560			33	DELETION		3032137	12174	20349	26	NEW_VARIANT
P-0004283-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.55+4621:TMPRSS2_c.18+7946:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		124157	0	18	21	Intron of ERG(-): 8Kb after exon 1	ERG	39862341			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875256			28	DELETION		3012915	18638	122619	18	NEW_VARIANT
P-0004283-T01-IM5	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement : c.1759-351:MX1_c.56-4378:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (MX1-TMPRSS2)		100177	0	9	21	Intron of MX1(+): 351bp before exon 17	MX1	42830104			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874494			15	INVERSION		44390	18639	97008	9	NEW_VARIANT
P-0004215-T01-IM5	MLL2 (NM_003482) rearrangement: c.8672:MLL2_chr12:61283478del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		196353	0	20	12	Exon 34 of MLL2(-)	MLL2	49432467			12	IGR: 819Kb before FAM19A2(-)	FAM19A2	61283478			42	DELETION		11851011	16704	151330	20	NEW_VARIANT
P-0001867-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	-		36212	0	22	5	Exon 16 of APC(+)	APC	112173414			5	IGR: 7Kb after APC(+)	APC	112189021			84	DELETION		15607	661	16865	63	NEW_VARIANT
P-0002178-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		978	0	39	6	Intron of TNFAIP3(+): 515bp before exon 3	TNFAIP3	138195467			6	Exon 3 of TNFAIP3(+)	TNFAIP3	138196055			59	DELETION		588	2534	1059	43	NEW_VARIANT
P-0004529-T01-IM5	POLE(NM_006231) Rearrangement : c.5552+59_3583-2741del	PRECISE	Note: POLE(NM_006231) Rearrangement  results in the intragenic deletion of exons 30 to 40 of POLE.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 11 exons: out of frame		19994	0	5	12	Intron of POLE(-): 59bp after exon 40	POLE	133215652			12	Intron of POLE(-): 3Kb before exon 30	POLE	133229216			8	DELETION		13564	22077	13808	5	NEW_VARIANT
P-0004529-T01-IM5	CDH12 (NM_004061) Rearrangement :  t(12;5)(12q24.23;5p14.3)(chr12:g.1120554384::chr5:g.21898797)	PRECISE	Note: The CDH12 rearrangement is a translocation which results in the deletion of exons 7 to 15.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	43	12	Intron of RAB35(-): 19bp after exon 1	RAB35	120554384			5	Intron of CDH12(-): 44Kb before exon 7	CDH12	21898797			60	TRANSLOCATION		0	22082	0	42	NEW_VARIANT
P-0004600-T01-IM5	ACPP (NM_001134194) - FGFR1 (NM_001174067) rearrangement :t(3;8)(3q22.1;8p11.33)(chr3:g.132081259::chr8:g.38286054)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (ACPP-FGFR1)		0	0	30	8	Intron of FGFR1(-): 101bp before exon 3	FGFR1	38286054			3	Intron of ACPP(+): 5Kb before exon 11	ACPP	132081259			22	TRANSLOCATION		0	22958	0	28	NEW_VARIANT
P-0003297-T01-IM5		PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		67717	0	27	2	Intron of ALK(-): 68bp after exon 19	ALK	29448259			2	Intron of EML4(+): 4Kb before exon 6	EML4	42504374			41	INVERSION		13056115	10448	63099	27	NEW_VARIANT
P-0001226-T01-IM3	NF1 (NM_001042492) Deletion (29052537bp): c.4430+118_g.17:58638802del	PRECISE	Note: Deletion variant in NF1 is predicted to remove exons following exon  32, generating a truncating mutation.	AUTO_OK	3to5	3to5	-		475554	0	10	17	Intron of NF1(+): 118bp after exon 32	NF1	29586265			17	IGR: 39Kb before PPM1D(+)	PPM1D	58638802			17	DELETION		29052537	72643	655641	9	NEW_VARIANT
P-0004284-T01-IM5	STAT5B (NM_012448) rearrangement : c.40_chr17:g.29412409inv	PRECISE	Note: The STAT5B (NM_012448) rearrangement event results in the inversion of STAT5B exons 1-2. One of the breakpoints is within STAT5B exon2.	MANUAL_OK	5to5	5to5	-		331777	0	23	17	IGR: 10Kb before NF1(+)	NF1	29412409			17	Exon 2 of STAT5B(-)	STAT5B	40384106			37	INVERSION		10971697	18620	305843	23	NEW_VARIANT
P-0002971-T02-IM5	CHD3 (NM_001005271) - TMPRSS2 (NM_001135099)  Rearrangement : t(17;21)(17p13.1;21q22.3)(chr17:g.7811475::chr21:g.42871618)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (CHD3-TMPRSS2)		0	0	53	21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42871618			17	Intron of CHD3(+): 138bp after exon 33	CHD3	7811475			37	TRANSLOCATION		0	16891	0	54	NEW_VARIANT
P-0002971-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_001136154) Fusion  (TMPRSS2 exon 2 fused to ERG exon 4):  c.127-1520:TMPRSS2_c.39+27766:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		57157	0	19	21	Intron of ERG(-): 28Kb after exon 3	ERG	39919820			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871462			22	DELETION		2951642	16885	58448	19	NEW_VARIANT
P-0003599-T01-IM5	c.6393-29_6537-785inv	PRECISE	Note: The NCOR1 (NM_006311)  rearrangement event results in the inversion of NCOR1 exon41.	MANUAL_OK	3to3	3to3	-		1541	0	43	17	Intron of NCOR1(-): 785bp before exon 42	NCOR1	15951192			17	Intron of NCOR1(-): 29bp before exon 41	NCOR1	15952331			30	INVERSION		1139	12198	1387	42	NEW_VARIANT
P-0002803-T01-IM3		PRECISE	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	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (EPHA5-TNRC6B)		0	0	11	22	Intron of TNRC6B(+): 21Kb after exon 4	TNRC6B	40572956			4	Exon 3 of EPHA5(-)	EPHA5	66467833			24	TRANSLOCATION		0	5647	0	11	NEW_VARIANT
P-0001699-T02-IM5	NAB2 (NM_005967) - STAT6 (NM_003153) rearrangement: c.1469-97:NAB2_c.*2057:STAT6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		14463	0	102	12	Intron of NAB2(+): 97bp before exon 7	NAB2	57488298			12	3-UTR of STAT6(-): 267bp after coding stop	STAT6	57504930			59	DUPLICATION		16632	28775	17169	102	NEW_VARIANT
P-0001699-T02-IM5	PBRM1 (NM_018313) rearrangement: c.3292-1256_c.2966-169dup	PRECISE	The PBRM1 (NM_018313) rearrangement is an intragenic duplication of exons 18-21. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons: out of frame		8037	0	34	3	Intron of PBRM1(-): 1Kb before exon 22	PBRM1	52614471			3	Intron of PBRM1(-): 94bp before exon 18	PBRM1	52621620			12	DUPLICATION		7149	28776	8612	17	NEW_VARIANT
P-0003701-T01-IM5	c.2553_c.4186-2131dup	PRECISE	BRCA1 (NM_007294) rearrangement results in the duplication of exons 10 and 11. The breakpoint is within exon 10. Its functional significance is undetermined	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		14425	0	33	17	Intron of BRCA1(-): 2Kb before exon 11	BRCA1	41236723			17	Exon 10 of BRCA1(-)	BRCA1	41244995			45	DUPLICATION		8272	12608	14897	37	NEW_VARIANT
P-0003701-T01-IM5	g.55923853_c.4401:MAP3K1del	PRECISE	MAP3K1 (NM_005921)  rearrangement event results in the deletion of exons 1-20. The breakpoint is within exon 20. Its functional significance is undetermined	MANUAL_OK	3to5	3to5	-		32658	0	92	5	IGR: 187Kb before MAP3K1(+)	MAP3K1	55923853			5	Exon 20 of MAP3K1(+)	MAP3K1	56189369			86	DELETION		265516	12607	26870	120	NEW_VARIANT
P-0003701-T01-IM5	t(6;2)(q21;p12)(c.888_c.585-2327)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (ESR1-TACR1)		0	0	14	6	Exon 6 of ESR1(+)	ESR1	152265435			2	Intron of TACR1(-): 2Kb before exon 3	TACR1	75283209			17	TRANSLOCATION		0	12609	0	14	NEW_VARIANT
P-0003419-T02-IM5	c.40-58284:ERG_c.55+1883:TMPRSS2del	PRECISE	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4 to 11)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		137285	0	28	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875828			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877994			53	DELETION		3002166	12575	145426	33	NEW_VARIANT
P-0001155-T01-IM3	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2136+757_c.715-617dup	PRECISE	Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH  is recommended.	AUTO_OK	5to3	5to3	Protein fusion: in frame (NCOA4-RET)		37247	0	34	10	Intron of RET(+): 757bp after exon 11	RET	43610941			10	Intron of NCOA4(+): 617bp before exon 9	NCOA4	51583999			47	DUPLICATION		7973058	72542	36688	35	NEW_VARIANT
P-0000673-T01-IM3		PRECISE		AUTO_OK	5to5	5to5	-		6701	0	32	13	Intron of LRCH1(+): 2Kb before exon 16	LRCH1	47294994			13	Intron of RB1(+): 30bp before exon 4	RB1	48919186			64	INVERSION		1624192	71768	3549	32	NEW_VARIANT
P-0002001-T01-IM3	MTOR (NM_004958) - RGL1 (NM_015149) inversion:  c.2779+66:MTOR_c.-32-42343:RGL1inv	PRECISE		AUTO_OK	5to5	5to5	Transcript fusion (MTOR-RGL1)		580977	0	8	1	Intron of MTOR(-): 66bp after exon 18	MTOR	11290916			1	5-UTR of RGL1(+): 42Kb before coding start	RGL1	183668918			17	INVERSION		172378002	1135	632716	8	NEW_VARIANT
P-0001717-T01-IM3	EPB41 (NM_001166005) - ARID1A (NM_006015) duplication:   c.-8+27610_c.4239del	PRECISE	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.	AUTO_OK	5to3	5to3	Protein fusion: mid-exon (EPB41-ARID1A)		28743	0	14	1	Exon 18 of ARID1A(+)	ARID1A	27100957			1	5-UTR of EPB41(+): 73Kb before coding start	EPB41	29241332			36	DUPLICATION		2140375	1204	47567	14	NEW_VARIANT
P-0001717-T01-IM3	DPP6 (NM_130797) - MLL3 (NM_170606) inversion: c.458-17058_c.9518-33inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (DPP6-MLL3)		95722	0	44	7	Intron of MLL3(-): 33bp before exon 42	MLL3	151864496			7	Intron of DPP6(+): 17Kb before exon 4	DPP6	154220559			30	INVERSION		2356063	1206	71982	44	NEW_VARIANT
P-0003603-T01-IM5	c.1237+857_1745inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		8482	0	6	19	Exon 18 of ERCC2(-)	ERCC2	45856513			19	Intron of ERCC2(-): 857bp after exon 11	ERCC2	45863925			14	INVERSION		7412	12215	6743	6	NEW_VARIANT
P-0002304-T01-IM3	TP53 (NM_000546) Deletion : g.7541002_c.96+41del	PRECISE		MANUAL_OK	3to5	3to5	-		22073	0	49	17	IGR: 8Kb before SHBG(+)	SHBG	7541002			17	Intron of TP53(-): 41bp after exon 3	TP53	7579659			69	DELETION		38657	2960	12098	35	NEW_VARIANT
P-0002304-T01-IM3	TP53 (NM_000546) Deletion : c.96+6_g.8654277del	IMPRECISE		AUTO_OK	3to5	3to5	-		56292	0	29	17	Intron of TP53(-): 6bp after exon 3	TP53	7579694			17	IGR: 2Kb before SPDYE4(-)	SPDYE4	8654277			0	DELETION		1074583	2961	39121	34	NEW_VARIANT
P-0002364-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		28621	0	6	21	Intron of ERG(-): 21Kb after exon 3	ERG	39926743			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872677			21	DELETION		2945934	3198	31950	6	NEW_VARIANT
P-0004213-T01-IM5	GBL1 (NM_152336) - ZFHX3 (NM_006885) rearrangement: t(15;16)(15q25.3;16q22.2)(chr15:g.87282028::chr16:72827570)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (AGBL1-ZFHX3)		0	0	54	16	Exon 9 of ZFHX3(-)	ZFHX3	72827570			15	Intron of AGBL1(+): 64Kb after exon 22	AGBL1	87282028			29	TRANSLOCATION		0	16634	0	54	NEW_VARIANT
P-0003998-T01-IM5	ARID1B (NM_020732) and LOC729234 translocation: t(6;2) (q25.3;q11.1)  (chr6:g.157521845::chr2:g.96603238)	PRECISE	The ARID1B (NM_020732) rearrangement event is a translocation which results in the truncation of ARID1B exons 18-20. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	1	33	6	Exon 18 of ARID1B(+)	ARID1B	157521845			2	IGR: 73Kb before LOC729234(+)	LOC729234	96603238			39	TRANSLOCATION		0	14545	0	18	NEW_VARIANT
P-0000224-T01-IM3	TMPRSS2 (NM_001135099) Translocation  t(21;20)(q13.12;q22.3)(g.42873074_g.44383097)	PRECISE		AUTO_OK	5to3	5to3	-		0	0	30	21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42873074			20	IGR: 20Kb before WFDC3(-)	WFDC3	44383097			50	TRANSLOCATION		0	94404	0	0	NEW_VARIANT
P-0000224-T01-IM3	TMPRSS2 (NM_001135099) - RIPK4 (NM_012309) 297750bp Deletion:  c.56-1254G_c.1632-813del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (RIPK4-TMPRSS2)		18360	0	11	21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871370			21	Intron of RIPK4(-): 194bp after exon 4	RIPK4	43169120			26	DELETION		297750	94402	27110	11	NEW_VARIANT
P-0002351-T01-IM3	FGFR3 (NM_000142)  and TACC3 (NM_006342) duplication (71843bp):  FGFR3:c.2303_TACC3:c.1620dup	PRECISE	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.	AUTO_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		34321	0	21	4	Exon 7 of TACC3(+)	TACC3	1737028			4	Exon 18 of FGFR3(+)	FGFR3	1808871			47	DUPLICATION		71843	3128	42233	22	NEW_VARIANT
P-0000557-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		47557	0	10	2	Intron of ALK(-): 149bp before exon 20	ALK	29446543			2	Intron of EML4(+): 3Kb after exon 5	EML4	42494981			19	INVERSION		13048438	71650	38985	10	NEW_VARIANT
P-0003450-T01-IM5		PRECISE	The TMPRSS2 (NM_001135099) rearrangement results in the intragenic duplication of exons 3 to 5. Its functional significance is undetermined	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		16242	0	34	21	Intron of TMPRSS2(-): 929bp before exon 6	TMPRSS2	42853458			21	Intron of TMPRSS2(-): 2Kb after exon 2	TMPRSS2	42868348			41	DUPLICATION		14890	11504	16352	37	NEW_VARIANT
P-0003556-T01-IM5	None	PRECISE		MANUAL_OK	5to3	5to3	-		7142	0	11	13	Exon 1 of IRS2(-)	IRS2	110435056			13	IGR: 129Kb before IRS2(-)	IRS2	110534798			24	DUPLICATION		99742	12012	8398	12	NEW_VARIANT
P-0001323-T01-IM3	None	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MLL2-RND1)		112173	0	39	12	Intron of RND1(-): 407bp before exon 3	RND1	49256308			12	Exon 31 of MLL2(-)	MLL2	49433591			47	DELETION		177283	72992	89138	40	NEW_VARIANT
P-0001902-T01-IM3	IKBKE (NM_014002) - NFASC (NM_001005388) Duplication   : c.1183+3_c.2782+2783dup	PRECISE	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	AUTO_OK	5to3	5to3	Protein fusion: in frame (IKBKE-NFASC)		12465	0	8	1	Intron of NFASC(+): 3Kb after exon 25	NFASC	204963217			1	Intron of IKBKE(+): 3bp after exon 10	IKBKE	206652479			25	DUPLICATION		1689262	359	11381	9	NEW_VARIANT
P-0002665-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	-		1718	0	17	13	Intron of DIS3(-): 15bp before exon 2	DIS3	73355156			13	Intron of PIBF1(+): 214bp after exon 2	PIBF1	73358073			27	DELETION		2917	4507	1415	21	NEW_VARIANT
P-0005535-T01-IM5	CDKN2C (NM_078626) rearrangement: c.-1684:CDKN2C_chr1:g.48479133del	PRECISE	The CDKN2C (NM_078626) rearrangement is a deletion of the promoter region of CDKN2C. The functional significance is undetermined	MANUAL_OK	3to5	3to5	-		1560	0	16	1	IGR: 88Kb before SKINTL(-)	SKINTL	48479133			1	Promoter of CDKN2C(+): 10bp from tx start	CDKN2C	51434357			20	DELETION		2955224	50127	1811	16	NEW_VARIANT
P-0005261-T01-IM5	RAD21 (NM_006265) Rearrangement: c.-508_c.274+21inv	PRECISE	RAD21 (NM_006265) rearrangement results in the inversion of exons 1-3 of RAD21. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		3843	0	24	8	Intron of RAD21(-): 21bp after exon 3	RAD21	117875348			8	Promoter of RAD21(-): 220bp from tx start	RAD21	117887325			30	INVERSION		11977	46117	3816	24	NEW_VARIANT
P-0006108-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10) : c.126+300:TMPRSS2_c.18+8285:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		61540	0	24	21	Intron of ERG(-): 8Kb after exon 1	ERG	39862002			21	Intron of TMPRSS2(-): 300bp after exon 2	TMPRSS2	42869746			24	DELETION		3007744	67804	52673	21	NEW_VARIANT
P-0006108-T01-IM5	TMPRSS2 (NM_001135099) rearrangement : c.127-48_795-950dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: out of frame		14819	0	76	21	Intron of TMPRSS2(-): 950bp before exon 8	TMPRSS2	42849497			21	Intron of TMPRSS2(-): 48bp before exon 3	TMPRSS2	42866553			43	DUPLICATION		17056	67807	14235	72	NEW_VARIANT
P-0004850-T01-IM5	None	PRECISE		MANUAL_OK	5to3	5to3	-		360636	0	16	19	Intron of GNA11(+): 117bp before exon 3	GNA11	3113211			19	3-UTR of TYK2(-): 132bp after coding stop	TYK2	10461378			20	DUPLICATION		7348167	39707	313410	16	NEW_VARIANT
P-0004850-T01-IM5	DNMT1(NM_001379) Rearrangement :  c.4475:DNMT1_c.340+2519:C19orf38del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		129279	0	62	19	Exon 38 of DNMT1(-)	DNMT1	10246930			19	Intron of C19orf38(+): 3Kb after exon 2	C19orf38	10963762			69	DELETION		716832	39706	162685	57	NEW_VARIANT
P-0004850-T01-IM5	EIF4A2(NM_001967) - ABCF3(NM_018358) Rearrangement : c.999+72:EIF4A2_c.1751-99:ABCF3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (EIF4A2-ABCF3)		90656	0	35	3	Intron of ABCF3(+): 99bp before exon 19	ABCF3	183910791			3	Intron of EIF4A2(+): 72bp after exon 9	EIF4A2	186505445			45	DUPLICATION		2594654	39708	123278	35	NEW_VARIANT
P-0006370-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1490-2147:EML4_c.3172+203:ALKinv	PRECISE	The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		49279	0	64	2	Intron of ALK(-): 203bp after exon 19	ALK	29448124			2	Intron of EML4(+): 2Kb before exon 13	EML4	42526234			106	INVERSION		13078110	91912	60768	64	NEW_VARIANT
P-0006730-T01-IM5	KEAP1(NM_203500) Rearrangement: c.513_chr19:35248755del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		382278	0	12	19	Exon 2 of KEAP1(-)	KEAP1	10610197			19	IGR: 224bp before ZNF599(-)	ZNF599	35248755			26	DELETION		24638558	108614	469499	12	NEW_VARIANT
P-0009639-T01-IM5	CDKN2B (NM_004936) rearrangement: c.156+108_chr9:g.22170544inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		3938	0	8	9	Intron of CDKN2B(-): 108bp after exon 1	CDKN2B	22008689			9	IGR: 49Kb after CDKN2BAS(+)	CDKN2BAS	22170544			38	INVERSION		161855	131592	3931	8	NEW_VARIANT
P-0004737-T01-IM5	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)	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (ETV6-NTRK3)		0	0	72	15	Intron of NTRK3(-): 37Kb after exon 12	NTRK3	88632786			12	Intron of ETV6(+): 314bp after exon 4	ETV6	12006809			28	TRANSLOCATION		0	34862	0	71	NEW_VARIANT
P-0006656-T01-IM5	MGA (NM_001164273) rearrangement : t(15;21)(q15.1;p11.1)(chr15:g.41991303::chr21:g.11034318)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	65	21	3-UTR of BAGE2(-): 15Kb after coding stop	BAGE2	11034318			15	Exon 5 of MGA(+)	MGA	41991303			26	TRANSLOCATION		0	107864	0	52	NEW_VARIANT
P-0008427-T01-IM5	BTK (NM_000061) Rearrangement : chr10:g.97658964_c.1746:BTKinv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		36373	0	99	X	IGR: 1Mb before LOC442459(-)	LOC442459	97658964			X	Exon 17 of BTK(-)	BTK	100608862			91	INVERSION		2949898	121905	26474	97	NEW_VARIANT
P-0004893-T01-IM5	RUNX1(NM_001754) rearrangement: c.362_c.509-5397dup.	PRECISE	The RUNX1(NM_001754) rearrangement is an intragenic duplication of exon 5. The breakpoint is within exon 5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		2155	0	57	21	Intron of RUNX1(-): 5Kb before exon 3	RUNX1	36237272			21	Exon 2 of RUNX1(-)	RUNX1	36253000			58	DUPLICATION		15728	40236	2832	57	NEW_VARIANT
P-0007359-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		57789	0	3	21	Intron of ERG(-): 56Kb before exon 4	ERG	39873396			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873736			5	DELETION		3000340	115525	55757	3	NEW_VARIANT
P-0009726-T01-IM5	MLL (NM_001197104) rearrangement : c.7225_10350del	PRECISE	Note: The MLL (NM_001197104) rearrangement event results in a large deletion within MLL exon27.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		32098	0	79	11	Exon 27 of MLL(+)	MLL	118373832			11	Exon 27 of MLL(+)	MLL	118376957			59	DELETION		3125	136213	13090	73	NEW_VARIANT
P-0008764-T01-IM5	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)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (KIF5B-ALK)		0	0	81	10	Intron of KIF5B(-): 321bp after exon 24	KIF5B	32305750			2	Exon 19 of ALK(-)	ALK	29448327			30	TRANSLOCATION		0	123850	0	78	NEW_VARIANT
P-0008161-T02-IM5	NF1(NM_001042492) Rearrangement :  c.655-91_889-8627dup	PRECISE	Note: The NF1(NM_001042492) Rearrangement results in the intragenic duplication of exons 7 and 8 of NF1.Its functional signficance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		3312	0	35	17	Intron of NF1(+): 91bp before exon 7	NF1	29508637			17	Intron of NF1(+): 9Kb before exon 9	NF1	29518813			23	DUPLICATION		10176	121949	2524	35	NEW_VARIANT
P-0008206-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4 to 11): c.56-385:TMPRSS2_c.39+41500:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		78060	0	102	21	Intron of ERG(-): 42Kb after exon 3	ERG	39906086			21	Intron of TMPRSS2(-): 385bp before exon 2	TMPRSS2	42870501			94	DELETION		2964415	120849	71925	113	NEW_VARIANT
P-0008101-T01-IM5	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	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		47810	0	70	10	Intron of KIF5B(-): 38bp before exon 19	KIF5B	32310097			10	Intron of RET(+): 271bp after exon 11	RET	43610455			85	INVERSION		11300358	120361	43201	67	NEW_VARIANT
P-0009835-T01-IM5	CDK12 (NM_016507) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q12)(chr8:g.145739493::chr17:g.37656296)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (CDK12-RECQL4)		0	0	30	17	Intron of CDK12(+): 1Kb before exon 6	CDK12	37656296			8	Intron of RECQL4(-): 2bp before exon 12	RECQL4	145739493			15	TRANSLOCATION		0	136776	0	30	NEW_VARIANT
P-0009835-T01-IM5	TMPRSS2 (NM_001135099) - RIPK4 (NM_020639) rearrangement: c.56-289:TMPRSS2_c.474+2297:RIPK4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-RIPK4)		82514	0	13	21	Intron of TMPRSS2(-): 289bp before exon 2	TMPRSS2	42870405			21	Intron of RIPK4(-): 2Kb after exon 2	RIPK4	43174388			37	DUPLICATION		303983	136774	87628	13	NEW_VARIANT
P-0009353-T01-IM5	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	PRECISE	Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		18565	0	14	2	Intron of ALK(-): 71bp before exon 20	ALK	29446465			2	Intron of EML4(+): 2Kb after exon 5	EML4	42494278			24	INVERSION		13047813	130167	9743	14	NEW_VARIANT
P-0007416-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		52976	0	57	21	Intron of ERG(-): 53Kb before exon 4	ERG	39870315			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875820			51	DELETION		3005505	115887	26380	54	NEW_VARIANT
P-0006310-T01-IM5	IDH1 (NM_005896) Rearrangement :  c.454_521-489dup	PRECISE	Note: The IDH1 (NM_005896) Rearrangement results in the intragenic duplication of exon 5. The breakpoint is within exon5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1161	0	5	2	Intron of IDH1(-): 489bp before exon 6	IDH1	209108817			2	Exon 5 of IDH1(-)	IDH1	209110109			28	DUPLICATION		1292	78440	1141	5	NEW_VARIANT
P-0007808-T01-IM5	DNMT3B (NM_006892) Rearrangement : chr20:g.30634953_c.433-68:DNMT3Binv	IMPRECISE	Note: The DNMT3B (NM_006892) Rearrangement results in the inversion of exons 1 to 6 of DNMT3B.Its functional significance is undetremined.	MANUAL_OK	5to5	5to5	-		67656	0	41	20	IGR: 5Kb before HCK(+)	HCK	30634953			20	Intron of DNMT3B(+): 68bp before exon 6	DNMT3B	31374968			0	INVERSION		740015	118734	59496	36	NEW_VARIANT
P-0006640-T01-IM5	DAZAP2 (NM_001136266) - ERBB3 (NM_001982) rearrangement : c.-1685: DAZAP2_c.2899:ERBB3dup	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (DAZAP2-ERBB3)		71606	0	36	12	Promoter of DAZAP2(+): 2Kb from tx start	DAZAP2	51631007			12	Exon 24 of ERBB3(+)	ERBB3	56493491			49	DELETION		4862484	107750	68734	34	NEW_VARIANT
P-0006409-T01-IM5	FGFR2 (NM_000141) rearrangement : chr10:g.95246173_c.2301+983:FGFR2inv	PRECISE	Note: The FGFR2 (NM_000141) rearrangement event results in the inversion of FRGR2 exon18. The event involves the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	-		155299	0	34	10	IGR: 4Kb after MYOF(-)	MYOF	95246173			10	Intron of FGFR2(-): 538bp before exon 17	FGFR2	123242229			47	INVERSION		27996056	92270	123557	34	NEW_VARIANT
P-0005538-T01-IM5	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	PRECISE	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)	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		338225	0	100	10	Intron of BICC1(+): 276bp before exon 16	BICC1	60566068			10	Intron of FGFR2(-): 459bp after exon 16	FGFR2	123242753			86	INVERSION		62676685	50075	396596	97	NEW_VARIANT
P-0006826-T01-IM5	TTC28 (NM_001145418) - FBXW7 (NM_033632) rearrangement : t(4;22)(q31.3;q12.1)(chr4:g.153244355::chr22:g.29066046)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TTC28-FBXW7)		0	0	18	22	Intron of TTC28(-): 10Kb after exon 1	TTC28	29066046			4	Intron of FBXW7(-): 54bp before exon 12	FBXW7	153244355			0	TRANSLOCATION		0	109268	0	15	NEW_VARIANT
P-0006837-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 1-10): c.55+3696:TMPRSS2_c.-3317:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		142398	0	52	21	Intron of ERG(-): 56Kb before exon 4	ERG	39873621			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42876181			49	DELETION		3002560	136977	135501	48	NEW_VARIANT
P-0006837-T02-IM5	NLGN1 (NM_014932) - TMPRSS2 (NM_001135099) rearrangement: t(3;21)(q26.31;q22.3)(chr3:g.173935988::chr21:g.42872495)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (NLGN1-TMPRSS2)		0	0	94	21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872495			3	Intron of NLGN1(+): 57Kb before exon 5	NLGN1	173935988			48	TRANSLOCATION		0	136980	0	94	NEW_VARIANT
P-0005463-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.127-1566:TMPRSS2 _c.40-59106:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		31559	0	3	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876650			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868071			6	DELETION		2991421	49153	29673	3	NEW_VARIANT
P-0006047-T02-IM5	EZR (NM_003379) - ROS1 (NM_002944) fusion (EZR exons 1-9 with ROS1 exons 34-43): c.1091-355:EZR_c.5557+146:ROS1del	PRECISE	Note: The EZR (NM_003379) - ROS1 (NM_002944) fusion is predicted to be in frame and includes the kinase domain of ROS1	MANUAL_OK	3to5	3to5	Protein fusion: in frame (EZR-ROS1)		427144	0	24	6	Intron of ROS1(-): 146bp after exon 33	ROS1	117647241			6	Intron of EZR(-): 355bp before exon 10	EZR	159191331			28	DELETION		41544090	131324	378221	22	NEW_VARIANT
P-0006328-T01-IM5	FGFR2 (NM_000141) - NRBF2 (NM_030759) rearrangement: c.2302-1710:FGFR2_c.157-364:NRBF2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-NRBF2)		274163	0	102	10	Intron of NRBF2(+): 364bp before exon 4	NRBF2	64912907			10	Intron of FGFR2(-): 2Kb before exon 18	FGFR2	123241245			65	INVERSION		58328338	91230	232921	94	NEW_VARIANT
P-0001047-T02-IM5	PIK3C2G (NM_004570)  rearrangement : c.2382-7747_c.3159:PIK3C2Gdel	PRECISE	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	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		9358	0	48	12	Intron of PIK3C2G(+): 8Kb before exon 18	PIK3C2G	18633636			12	Exon 23 of PIK3C2G(+)	PIK3C2G	18658354			60	DELETION		24718	100761	5788	48	NEW_VARIANT
P-0001047-T02-IM5	TERT (NM_198253) rearrangement : c.443:TERT_chr5:g.29735590inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		42551	0	24	5	Exon 2 of TERT(-)	TERT	1294558			5	IGR: 1Mb before CDH6(+)	CDH6	29735590			33	INVERSION		28441032	100765	32638	23	NEW_VARIANT
P-0001047-T02-IM5	FLJ33360  (NM_001001702) - IL7R (NM_002185) rearrangement : chr5:g.29735590_c.773:IL7Rinv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		46335	0	9	5	IGR: 1Kb before FLJ33360(-)	FLJ33360	6309223			5	Exon 6 of IL7R(+)	IL7R	35874617			16	INVERSION		29565394	100766	40899	7	NEW_VARIANT
P-0008215-T01-IM5	RPS6KA4 (NM_003942) rearrangement: c.907-82_c.1072-795inv	PRECISE	RPS6KA4 (NM_003942) rearrangement results in an inversion of exon 9 including the protein kinase C-terminal domain. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2178	0	17	11	Intron of RPS6KA4(+): 82bp before exon 9	RPS6KA4	64132691			11	Intron of RPS6KA4(+): 795bp before exon 10	RPS6KA4	64134809			20	INVERSION		2118	120828	1969	11	NEW_VARIANT
P-0007032-T01-IM5	ARID1B (NM_020732) rearrangement : c.2706-5309_3057inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		9528	0	24	6	Intron of ARID1B(+): 5Kb before exon 10	ARID1B	157482865			6	Exon 12 of ARID1B(+)	ARID1B	157502198			30	INVERSION		19333	112758	10850	23	NEW_VARIANT
P-0007547-T01-IM5	TMPRSS2 (NM_001135099) Rearrangement :  c.56-1201_1282+555inv	PRECISE	Note: The TMPRSS2 (NM_001135099)  Rearrangement  results in the inversion of exons 2 to 11 of TMPRSS2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		45703	0	57	21	Intron of TMPRSS2(-): 555bp after exon 11	TMPRSS2	42842020			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871317			64	INVERSION		29297	117327	25362	53	NEW_VARIANT
P-0004808-T01-IM5	FGFR2 (NM_000141) rearrangement: t(10;7)(q26.13;q21.3)(chr10:g.123242018::chr7:g.93694043)	PRECISE	The FGFR2 (NM_000141) rearrangement is a translocation which results in the truncation of FGFR2  exons 17-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	24	10	Intron of FGFR2(-): 327bp before exon 17	FGFR2	123242018			7	IGR: 60Kb after BET1(-)	BET1	93694043			36	TRANSLOCATION		0	35679	0	23	NEW_VARIANT
P-0005758-T01-IM5	PPM1D (NM_003620) - MAFG (NM_032711) rearrangement : c.896:PPM1D_c.-1017:MAFGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (PPM1D-MAFG)		263133	0	12	17	Exon 4 of PPM1D(+)	PPM1D	58725322			17	5-UTR of MAFG(-): 1Kb before coding start	MAFG	79882216			20	INVERSION		21156894	58800	273641	12	NEW_VARIANT
P-0009271-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement :  c.75_chr9:g.22179390inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		13885	0	62	9	Exon 1 of CDKN2A(-)	CDKN2A	21974752			9	IGR: 58Kb after CDKN2BAS(+)	CDKN2BAS	22179390			63	INVERSION		204638	129853	3089	43	NEW_VARIANT
P-0008542-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1 fused with ERG exons 2 -10 ) : c.55+4310:TMPRSS2_c.19-7094:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		140381	0	65	21	Intron of ERG(-): 7Kb before exon 4	ERG	39824638			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875567			57	DELETION		3050929	122673	117897	64	NEW_VARIANT
P-0006622-T01-IM5	RNFT1 (NM_016125) - PPM1D (NM_003620) rearrangement : c.592-123:RNFT1_c.94:PPM1Dinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (RNFT1-PPM1D)		3339	0	20	17	Intron of RNFT1(-): 123bp before exon 4	RNFT1	58037652			17	Exon 1 of PPM1D(+)	PPM1D	58677869			58	INVERSION		640217	107353	3265	19	NEW_VARIANT
P-0005422-T01-IM5	TMPRSS2(NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 ERG exon4 ) :  c.55+4168:TMPRSS2_c.40-60922:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		79896	0	9	21	Intron of ERG(-): 61Kb before exon 4	ERG	39878466			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875709			12	DELETION		2997243	48834	71966	9	NEW_VARIANT
P-0009434-T01-IM5	RPTOR (NM_020761) Rearrangement t(15;17)(15q21.3;17q25.3)(15:g.53194795::chr17:g.78831704)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	14	17	Intron of RPTOR(+): 4bp after exon 13	RPTOR	78831704			15	IGR: 145Kb before ONECUT1(-)	ONECUT1	53194795			21	TRANSLOCATION		0	130688	0	11	NEW_VARIANT
P-0007793-T01-IM5	SMAD3 (NM_005902) - IQCH (NM_001031715) Rearrangement : c.1175:SMAD3_c.1188:IQCHdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SMAD3-IQCH)		591	0	16	15	Exon 9 of SMAD3(+)	SMAD3	67482771			15	Exon 9 of IQCH(+)	IQCH	67664883			30	DELETION		182112	118697	551	16	NEW_VARIANT
P-0007661-T01-IM5	FCER1G (NM_004106) - SDHC (NM_003001) rearrangement  c.49+1219:FCER1G_c.21:SDHCdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (FCER1G-SDHC)		4231	0	46	1	Intron of FCER1G(+): 1Kb after exon 1	FCER1G	161186379			1	Exon 2 of SDHC(+)	SDHC	161293404			64	DELETION		107025	117824	15602	38	NEW_VARIANT
P-0007661-T01-IM5	ETV6 (NM_001987) rearrangement : chr12:g.11779457_c.1010-497:ETV6del	PRECISE	Note: The ETV6 (NM_001987) rearrangement event results in the deletion of ETV6 exons 1-5.	MANUAL_OK	3to5	3to5	-		378075	0	53	12	IGR: 23Kb before ETV6(+)	ETV6	11779457			12	Intron of ETV6(+): 497bp before exon 6	ETV6	12036882			56	DELETION		257425	117823	344607	52	NEW_VARIANT
P-0006507-T01-IM5	DICER1 (NM_030621) rearrangement: chr14:g.87018577_c.3160:DICER1del.	PRECISE	The DICER1 (NM_030621) rearrangement is a deletion of exons 21-28 of DICER1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		28551	0	49	14	IGR: 1Mb before FLRT2(+)	FLRT2	87018577			14	Exon 21 of DICER1(-)	DICER1	95571517			59	DELETION		8552940	93760	34653	48	NEW_VARIANT
P-0006896-T01-IM5	TP63 (NM_003722) - MCF2L2 (NM_015078) rearrangement: c.766+112:TP63_c.77-18778:MCF2L2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (TP63-MCF2L2)		78354	0	10	3	Intron of MCF2L2(-): 19Kb before exon 2	MCF2L2	183126345			3	Intron of TP63(+): 112bp after exon 5	TP63	189582319			11	INVERSION		6455974	109678	69082	10	NEW_VARIANT
P-0006895-T01-IM5	CDKN2Ap16INK4A (NM_000077)  rearrangement: c.150+436del_c.263del  CDKN2Ap14ARF (NM_058195)  rearrangement: c.194-3034_c.306del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		458	0	23	9	Exon 2 of CDKN2A(-)	CDKN2A	21971095			9	Intron of CDKN2A(-): 436bp after exon 1	CDKN2A	21974241			23	DELETION		3146	109612	357	15	NEW_VARIANT
P-0008534-T01-IM5	CLMN (NM_024734) - FANCA (NM_000135) rearrangement : t(14;16)(q32.13;q24.3)(chr14:g.95776664::chr16:g.89849554)	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (CLMN-FANCA)		0	0	20	16	Intron of FANCA(-): 44bp before exon 16	FANCA	89849554			14	Intron of CLMN(-): 9Kb after exon 1	CLMN	95776664			39	TRANSLOCATION		0	122599	0	20	NEW_VARIANT
P-0006916-T01-IM5	NF1 (NM_001042492) rearrangement : c.888+6204_c.1260+16NF1dup	PRECISE	Note: The NF1 (NM_001042492) rearrangement is a in-frame duplication of exon 9-11 of NF1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: in frame		5019	0	17	17	Intron of NF1(+): 6Kb after exon 8	NF1	29515887			17	Intron of NF1(+): 16bp after exon 11	NF1	29528519			14	DUPLICATION		12632	109907	5103	16	NEW_VARIANT
P-0005864-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11):  c.56-4819:TMPRSS2_c.19-12436:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		103496	0	39	21	Intron of ERG(-): 12Kb before exon 4	ERG	39829980			21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874935			41	DELETION		3044955	64143	88925	38	NEW_VARIANT
P-0008178-T01-IM5	TP53 (NM_000546) - ATP1B2 (NM_001678) rearrangement: c.594:TP53_c.112+727:ATP1B2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (TP53-ATP1B2)		7314	0	13	17	Intron of ATP1B2(+): 727bp after exon 1	ATP1B2	7555675			17	Exon 6 of TP53(-)	TP53	7578255			24	INVERSION		22580	120630	4757	13	NEW_VARIANT
P-0009590-T01-IM5	ARID2 (NM_152641) rearrangement: c.2181_chr12:g.69098856inv	PRECISE	Note: The ARID2 (NM_152641) rearrangement is an inversion which includes exons 15-21 of ARID2. The functional significance  is undetermined.	MANUAL_OK	5to5	5to5	-		390723	0	23	12	Exon 15 of ARID2(+)	ARID2	46244087			12	Intron of NUP107(+): 2Kb after exon 8	NUP107	69098856			36	INVERSION		22854769	131308	414132	23	NEW_VARIANT
P-0009361-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		35335	0	7	21	Intron of ERG(-): 63Kb before exon 4	ERG	39880684			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867892			20	DELETION		2987208	130285	34851	7	NEW_VARIANT
P-0008036-T01-IM5	BAP1 (NM_004656) rearrangement: c.-677_c.37+16del	IMPRECISE	The BAP1 (NM_004656) rearrangement is a deletion of exon 1 of BAP1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		181	0	17	3	Exon 1 of BAP1(-)	BAP1	52443894			3	5-UTR of PHF7(+): 2Kb before coding start	PHF7	52444579			0	DELETION		685	120115	75	16	NEW_VARIANT
P-0008551-T01-IM5	CSF3R (NM_000760) - MRPS15 (NM_031280) rearrangement: c.630:CSF3R_c.175+21:MRPS15del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CSF3R-MRPS15)		41030	0	8	1	Intron of MRPS15(-): 21bp after exon 2	MRPS15	36929386			1	Exon 6 of CSF3R(-)	CSF3R	36939079			26	DELETION		9693	122725	36126	8	NEW_VARIANT
P-0007556-T01-IM5	LATS2 (NM_014572) rearrangement : c.1006_1900-1285inv	PRECISE	Note: The LATS2 (NM_014572) rearrangement events results in the inversion of LATS2 exon4. One of the breakpoints is within LATS2 exon4.	MANUAL_OK	5to5	5to5	Antisense fusion		6022	0	8	13	Intron of LATS2(-): 1Kb before exon 5	LATS2	21559230			13	Exon 4 of LATS2(-)	LATS2	21562913			13	INVERSION		3683	117389	7092	8	NEW_VARIANT
P-0006043-T01-IM5	FGFR2 (NM_000141) rearrangement: c.2302-801_chr10:g.123170710inv	PRECISE	The FGFR2 (NM_000141) rearrangement is an intragenic inversion of exon 18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		10316	0	89	10	IGR: 67Kb before FGFR2(-)	FGFR2	123170710			10	Intron of FGFR2(-): 801bp before exon 18	FGFR2	123240336			61	INVERSION		69626	67408	8319	83	NEW_VARIANT
P-0000690-T03-IM5	FAT1 (NM_005245) rearrangement: chr4:g.75641997_c.4883:FAT1inv	PRECISE	Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 10-27. One of the breakpoints is within exon10.	MANUAL_OK	5to5	5to5	-		308375	0	25	4	IGR: 29Kb before BTC(-)	BTC	75641997			4	Exon 10 of FAT1(-)	FAT1	187542857			29	INVERSION		111900860	40509	261620	22	NEW_VARIANT
P-0005903-T01-IM5	BRIP1 (NM_032043)  rearrangement: c.1340+36:BRIP1_chr17:g.44165620inv.	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		181678	0	19	17	Intron of KIAA1267(-): 6Kb before exon 3	KIAA1267	44165620			17	Intron of BRIP1(-): 36bp after exon 9	BRIP1	59876425			19	INVERSION		15710805	64382	199057	17	NEW_VARIANT
P-0008757-T01-IM5	BCAS1 (NM_003657) - NCOA3 (NM_181659) rearrangement : c.142+720:BCAS1_c.1307:NCOA3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (BCAS1-NCOA3)		72552	0	102	20	Exon 11 of NCOA3(+)	NCOA3	46264260			20	Intron of BCAS1(-): 720bp after exon 3	BCAS1	52673904			297	INVERSION		6409644	123829	331445	247	NEW_VARIANT
P-0007287-T01-IM5	GALD1 (NM_207359) - TGFBR2 (NM_001024847) rearrangement: c.1392+20317:GALD1_c.7:TGFBR2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (GADL1-TGFBR2)		7626	0	10	3	Exon 1 of TGFBR2(+)	TGFBR2	30648382			3	Intron of GADL1(-): 20Kb after exon 14	GADL1	30799354			43	INVERSION		150972	114799	9128	10	NEW_VARIANT
P-0001357-T02-IM5	IGF1R (NM_000875) - C15orf57 (NM_001080792) Rearrangement :  c.682:IGF1R_c.245-1296:C15orf57	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (IGF1R-C15orf57)		431377	0	12	15	Intron of C15orf57(-): 1Kb before exon 3	C15orf57	40850867			15	Exon 3 of IGF1R(+)	IGF1R	99434595			17	INVERSION		58583728	120737	363715	11	NEW_VARIANT
P-0008267-T01-IM5	PBRM1 (NM_018313) rearrangement: c.104:PBRM1_chr3.g.53498367del	PRECISE	Note: PBRM1 (NM_018313) rearrangement results in the deletion of exons 1 to 2. The breakpoint is within exon2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		765	0	5	3	Exon 2 of PBRM1(-)	PBRM1	52713624			3	IGR: 31Kb before CACNA1D(+)	CACNA1D	53498367			12	DELETION		784743	121073	900	5	NEW_VARIANT
P-0004779-T01-IM5	RB1(NM_000321) Rearrangement :  c.1696-3779_1961-25inv	PRECISE	Note: The RB1(NM_000321) Rearrangement results in the intragenic inversion of exons 18 and 19 of RB1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3526	0	12	13	Intron of RB1(+): 4Kb before exon 18	RB1	49023350			13	Intron of RB1(+): 25bp before exon 20	RB1	49033799			20	INVERSION		10449	35146	3513	12	NEW_VARIANT
P-0009958-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement : c.333_*101+1244del CDKN2Ap16INK4A (NM_000077) rearrangement : c.290_457+1244del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1791	0	16	9	Intron of CDKN2A(-): 1Kb after exon 2	CDKN2A	21969657			9	Exon 2 of CDKN2A(-)	CDKN2A	21971068			32	DELETION		1411	137399	1403	14	NEW_VARIANT
P-0009787-T01-IM5	TMPRSS2(NM_001135099)  -ERG ()Fusion (TMPRS22 exon1 fused with ERG exons  4-10) :  c.55+4268:TMPRSS2_c.40-58604:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		83377	0	76	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876148			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875609			86	DELETION		2999461	136493	60019	75	NEW_VARIANT
P-0008134-T01-IM5	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  )	PRECISE	Note:CD74 (NM_001025159) - ROS1 (NM_002944) fusion includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	34	6	Intron of ROS1(-): 502bp before exon 34	ROS1	117646080			5	Intron of CD74(-): 246bp before exon 7	CD74	149783121			27	TRANSLOCATION		0	120409	0	27	NEW_VARIANT
P-0007832-T01-IM5	NF1 (NM_001042492) rearrangement: c.-1684_c.17del	PRECISE	Note: The NF1 (NM_001042492) rearrangement is a deletion of NF1 exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		762	0	33	17	Promoter of NF1(+): 1Kb from tx start	NF1	29420644			17	Exon 1 of NF1(+)	NF1	29422344			46	DELETION		1700	119383	632	21	NEW_VARIANT
P-0008978-T01-IM5	APC (NM_000038) rearrangement: c.-622_c.4411dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		49950	0	102	5	5-UTR of APC(+): 18Kb before coding start	APC	112073019			5	Exon 16 of APC(+)	APC	112175702			79	DUPLICATION		102683	126007	63500	128	NEW_VARIANT
P-0009105-T01-IM5	NF1 (NM_001042492) rearrangement: t(17;X)(q11.2;q22.1)(chr17:g.29562678::chrX:g.81529667)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	40	X	IGR: 1Mb before SH3BGRL(+)	SH3BGRL	81529667			17	Exon 28 of NF1(+)	NF1	29562678			16	TRANSLOCATION		0	126621	0	38	NEW_VARIANT
P-0002123-T02-IM5	TMPRSS2 (NM_001135099) - ACPP (NM_001134194) rearrangement: t(3;21)(q22.1;q22.3)(chr3:g.132053847::chr21:g.42868047)	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense fusion		0	0	15	21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868047			3	Intron of ACPP(+): 2Kb before exon 5	ACPP	132053847			35	TRANSLOCATION		0	123354	0	15	NEW_VARIANT
P-0008437-T01-IM5	ATR (NM_001184) rearrangement : chr3:g.140760042_c.6800:ATRdel	PRECISE	Note: The ATR (NM_001184) rearrangement event results in the deletion of ATR exons 40-47.	MANUAL_OK	3to5	3to5	-		14174	0	26	3	IGR: 11Kb before SPSB4(+)	SPSB4	140760042			3	Exon 40 of ATR(-)	ATR	142185263			40	DELETION		1425221	122115	9994	26	NEW_VARIANT
P-0009246-T01-IM5	GLI1 (NM_005269) rearrangement: c.1636_chr12:74478822dup	PRECISE	Note: The GLI1 (NM_005269) rearrangement is a duplication (16614663 bp) which includes exon 12 of GLI1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		63741	0	102	12	Exon 11 of GLI1(+)	GLI1	57864159			12	IGR: 453Kb before ATXN7L3B(+)	ATXN7L3B	74478822			434	DUPLICATION		16614663	129552	427141	561	NEW_VARIANT
P-0009246-T01-IM5	RBM33 (NM_053043) - BRAF (NM_004333) rearrangement: c.171+526:RBM33_c.1314+160:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (RBM33-BRAF)		347459	0	42	7	Intron of BRAF(-): 160bp after exon 10	BRAF	140482661			7	Intron of RBM33(+): 526bp after exon 3	RBM33	155466135			25	INVERSION		14983474	129556	317053	42	NEW_VARIANT
P-0005047-T01-IM5	CYP4Z1 (NM_178134) - TMPRSS2 (NM_001135099) rearrangement : t(1;21)(1p33;21q22.3)(chr1:g.47561132::chr21:g.42874735)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (CYP4Z1-TMPRSS2)		0	0	52	21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874735			1	Intron of CYP4Z1(+): 791bp after exon 7	CYP4Z1	47561132			34	TRANSLOCATION		0	42220	0	33	NEW_VARIANT
P-0005047-T01-IM5	TMPRSS2 (NM_001135099) rearrangement : t(17;21)(17q21.31;21q22.3)(chr17:g.41635162::chr21:g.42875052)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	68	21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875052			17	IGR: 30Kb before ETV4(-)	ETV4	41635162			0	TRANSLOCATION		0	42221	0	47	NEW_VARIANT
P-0005792-T01-IM5	TCF7L2 (NM_001146274) rearrangement: c.382:TCF7L2_chr10:g.127151116dup	PRECISE	The TCF7L2 (NM_001146274) rearrangement is a duplication of TCF7L2 exons 4-14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		214725	0	102	10	Exon 4 of TCF7L2(+)	TCF7L2	114724315			10	IGR: 112Kb before LOC100169752(+)	LOC100169752	127151116			112	DUPLICATION		12426801	62253	172301	156	NEW_VARIANT
P-0009842-T01-IM5	APC (NM_000038) rearrangement: c.2433_c.6227del	PRECISE	Note: The APC (NM_000038) rearrangement is an intragenic deletion. Both breakpoints are within exon16.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		20951	0	14	5	Exon 16 of APC(+)	APC	112173724			5	Exon 16 of APC(+)	APC	112177518			22	DELETION		3794	136677	20168	14	NEW_VARIANT
P-0009190-T01-IM5	NAALADL2 (NM_207015) - PIK3CA (NM_006218)  rearrangement :  c.44-96015:NAALADL2_c.105:PIK3CAdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (NAALADL2-PIK3CA)		7600	0	51	3	Intron of NAALADL2(+): 96Kb before exon 2	NAALADL2	174718565			3	Exon 2 of PIK3CA(+)	PIK3CA	178916718			68	DELETION		4198153	129190	7488	48	NEW_VARIANT
P-0009514-T01-IM5	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	PRECISE	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1461:KIF5B_c.2137-221:RETinv	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		104547	0	79	10	Intron of KIF5B(-): 1Kb before exon 16	KIF5B	32313425			10	Intron of RET(+): 221bp before exon 12	RET	43611811			112	INVERSION		11298386	131053	108685	69	NEW_VARIANT
P-0007794-T01-IM5	JAK2 (NM_004972) Rearrangement :  c.3035_c.3059+6450del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		139	0	27	9	Exon 22 of JAK2(+)	JAK2	5090887			9	Intron of JAK2(+): 6Kb after exon 22	JAK2	5097361			38	DELETION		6474	118686	284	27	NEW_VARIANT
P-0006950-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-13 with ALK exons 20-29) : c.1489+2302:EML4_c.3172+943:ALKinv	PRECISE	The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		73718	0	102	2	Intron of ALK(-): 943bp after exon 19	ALK	29447384			2	Intron of EML4(+): 2Kb after exon 12	EML4	42524958			90	INVERSION		13077574	112102	45412	121	NEW_VARIANT
P-0004958-T01-IM5	RAF1 (NM_002880) rearrangement : c.1370+1077_1438del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1641	0	40	3	Exon 14 of RAF1(-)	RAF1	12627278			3	Intron of RAF1(-): 1Kb after exon 12	RAF1	12631220			48	DELETION		3942	41444	1249	38	NEW_VARIANT
P-0009991-T01-IM5	FAT1 (NM_005245) Rearrangement :  c.-19+745_c.235del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1195	0	50	4	Exon 2 of FAT1(-)	FAT1	187630747			4	5-UTR of FAT1(-): 13Kb before coding start	FAT1	187644073			72	DELETION		13326	137442	157	49	NEW_VARIANT
P-0006184-T01-IM5	PGR(NM_000926)-EXTL3(NM_001440) rearrangement: t(8,11)(p21.1;q22.1)(chr8:g.28568217::chr11:g.100996767)	PRECISE	The EXTL3-PGR translocation is a rearrangement which involves exon2 of PGR and 5-UTR region of EXTL3. Its functional significance is not determined.	MANUAL_OK	3to5	3to5	-		0	0	39	11	Exon 2 of PGR(-)	PGR	100996767			8	5-UTR of EXTL3(+): 5Kb before coding start	EXTL3	28568217			46	TRANSLOCATION		0	70121	0	38	NEW_VARIANT
P-0006184-T01-IM5	NF1 (NM_001042492) - MIR365-2 (NR_029856) rearrangement: c.4831:NF1_g.29900286del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (NF1-MIR365-2)		49545	0	50	17	Exon 35 of NF1(+)	NF1	29592353			17	Promoter of MIR365-2(+): 2Kb from tx start	MIR365-2	29900286			40	DELETION		307933	70120	32295	49	NEW_VARIANT
P-0003096-T01-IM5		PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		7376	0	5	9	Intron of CDKN2A(-): 762bp before exon 3	CDKN2A	21969003			9	Exon 1 of CDKN2A(-)	CDKN2A	21974791			6	DUPLICATION		5788	8396	6178	5	NEW_VARIANT
P-0001077-T01-IM3	CDC73 (NM_024529) intragenic deletion: c.908-21_c.972+806del	PRECISE	Note: The MAP2K1 copy number gain falls slightly below the cut off criteria  for amplification. Confirmatory testing is suggested, if clinically  indicated.	AUTO_OK	3to5	3to5	Deletion of 1 exon: out of frame		1131	0	11	1	Intron of CDC73(+): 21bp before exon 10	CDC73	193121489			1	Intron of CDC73(+): 806bp after exon 10	CDC73	193122380			26	DELETION		891	72358	826	12	NEW_VARIANT
P-0002195-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		75402	1	56	X	Exon 30 of ATRX(-)	ATRX	76813029			X	Intron of ATRX(-): 21bp after exon 7	ATRX	76944290			152	DELETION		131261	2640	4757	151	NEW_VARIANT
P-0003323-T01-IM5		PRECISE	Known EML4-ALK. Fits LUAD Dx.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		27639	0	8	2	Intron of ALK(-): 797bp after exon 19	ALK	29447530			2	Intron of EML4(+): 564bp after exon 5	EML4	42492435			15	INVERSION		13044905	10694	26604	7	NEW_VARIANT
P-0004318-T01-IM5	EZR (NM_003379) - ROS1 (NM_002944) rearrangement: c.1090+13:EZR_c.5401:ROS1del	PRECISE	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)	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (EZR-ROS1)		277853	0	16	6	Exon 33 of ROS1(-)	ROS1	117647543			6	Intron of EZR(-): 13bp after exon 9	EZR	159191783			15	DELETION		41544240	18896	306226	16	NEW_VARIANT
P-0002603-T01-IM3		IMPRECISE	affects splice site	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		321	0	15	9	Exon 2 of CDKN2A(-)	CDKN2A	21971106			9	Intron of CDKN2A(-): 468bp before exon 2	CDKN2A	21971675			0	DELETION		569	4085	265	17	NEW_VARIANT
P-0002855-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (RECQL4-TOP1MT)		33564	0	17	8	Intron of TOP1MT(-): 2Kb before exon 13	TOP1MT	144394753			8	Exon 5 of RECQL4(-)	RECQL4	145742055			22	DELETION		1347302	5972	30408	19	NEW_VARIANT
P-0001911-T01-IM3	E4F1 (NM_004424) - TRAF7 (NM_032271) Duplication:  c.983:E4F1_c.442-63:TRAF7dup (See Note)	PRECISE	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.	AUTO_OK	5to3	5to3	Protein fusion: mid-exon (E4F1-TRAF7)		21122	0	39	16	Intron of TRAF7(+): 63bp before exon 7	TRAF7	2221510			16	Exon 7 of E4F1(+)	E4F1	2283111			87	DUPLICATION		61601	367	18696	49	NEW_VARIANT
P-0001884-T01-IM3	CIC (NM_015125) inversion:  chr19:g.42645881_CIC:c.415inv	PRECISE	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.	AUTO_OK	5to5	5to5	-		6447	0	21	19	IGR: 53Kb before POU2F2(-)	POU2F2	42645881			19	Exon 3 of CIC(+)	CIC	42791355			42	INVERSION		145474	676	4158	18	NEW_VARIANT
P-0000485-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Protein fusion: mid-exon (SLC1A6-NOTCH3)		32963	0	9	19	Promoter of SLC1A6(-): 2Kb from tx start	SLC1A6	15085678			19	Exon 19 of NOTCH3(-)	NOTCH3	15291568			18	DUPLICATION		205890	71537	25281	10	NEW_VARIANT
P-0001992-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		9299	0	36	12	Intron of KDM5A(-): 308bp after exon 10	KDM5A	459479			12	Exon 6 of KDM5A(-)	KDM5A	465605			70	DUPLICATION		6126	1080	11809	37	NEW_VARIANT
P-0003502-T01-IM5		PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (BRAF-PJA2)		0	0	6	7	Intron of BRAF(-): 442bp after exon 10	BRAF	140482379			5	Intron of PJA2(-): 3Kb after exon 7	PJA2	108688305			6	TRANSLOCATION		0	11764	0	9	NEW_VARIANT
P-0004564-T01-IM5	RAB35 (NM_006861) translocation : t(12;5)(q24.23; p11)(chr12:g.20536539::chr5:g.46027045)	PRECISE	The RAB35 (NM_006861) rearrangement is a translocation potentially truncating RAB35 after exon 5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	36	12	Intron of RAB35(-): 76bp after exon 5	RAB35	120536539			5	IGR: 331Kb after HCN1(-)	HCN1	46027045			24	TRANSLOCATION		0	28520	0	35	NEW_VARIANT
P-0004564-T01-IM5	RUNX1 (NM_001754) rearrangement: c.420_c.59-33199del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4352	0	33	21	Exon 2 of RUNX1(-)	RUNX1	36252942			21	Intron of RUNX1(-): 33Kb before exon 3	RUNX1	36298459			46	DELETION		45517	28518	3382	33	NEW_VARIANT
P-0003171-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		16098	0	20	19	Intron of SPPL2B(+): 965bp after exon 13	SPPL2B	2346293			19	Exon 8 of MAP2K2(-)	MAP2K2	4097282			39	DELETION		1750989	9315	12542	23	NEW_VARIANT
P-0004133-T01-IM5	JAK3 (NM_000215) -SBNO2 (NM_014963) Rearrangement :  c.184+8:JAK3_c.3112:SBNO2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (JAK3-SBNO2)		746214	0	24	19	Exon 27 of SBNO2(-)	SBNO2	1109693			19	Intron of JAK3(-): 8bp after exon 2	JAK3	17955035			36	DELETION		16845342	15493	660414	25	NEW_VARIANT
P-0002260-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (LIMD1-BAP1)		146563	0	19	3	Intron of LIMD1(+): 5Kb before exon 3	LIMD1	45702556			3	Intron of BAP1(-): 6bp after exon 16	BAP1	52436612			46	INVERSION		6734056	2891	108973	85	NEW_VARIANT
P-0002260-T01-IM3	LIMD1 (NM_014240) - BAP1 (NM_004656) Inversion :  c.1511-4586:LIMD1_c.2056+6:BAP1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (BAP1-LIMD1)		147947	0	68	3	Intron of LIMD1(+): 5Kb before exon 3	LIMD1	45702632			3	Intron of BAP1(-): 50bp after exon 15	BAP1	52436745			96	INVERSION		6734113	2892	109551	86	NEW_VARIANT
P-0001811-T01-IM3	EML4 (NM_001145076) - ALK (NM_004304) Inversion:  c.1315+2666:EML4_c.3172+122:ALKinv	PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		45511	0	6	2	Intron of ALK(-): 122bp after exon 19	ALK	29448205			2	Intron of EML4(+): 3Kb after exon 12	EML4	42525322			19	INVERSION		13077117	583	48979	6	NEW_VARIANT
P-0001343-T01-IM3	None	PRECISE		AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		6388	0	63	1	Intron of NOTCH2(-): 758bp before exon 15	NOTCH2	120494218			1	Exon 11 of NOTCH2(-)	NOTCH2	120506358			70	DELETION		12140	2178	3338	70	NEW_VARIANT
P-0003818-T01-IM5	AXL (NM_021913) rearrangement : c.1538-760_1634-49del	IMPRECISE	Note: The AXL (NM_021913) rearrangement event results in the deletion of AXL exon12.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		1897	0	50	19	Intron of AXL(+): 760bp before exon 12	AXL	41753659			19	Intron of AXL(+): 49bp before exon 13	AXL	41754599			0	DELETION		940	13631	1492	56	NEW_VARIANT
P-0003619-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.126+467:TMPRSS2_c.39+43704:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		33412	0	9	21	Intron of ERG(-): 44Kb after exon 3	ERG	39903882			21	Intron of TMPRSS2(-): 467bp after exon 2	TMPRSS2	42869579			21	DELETION		2965697	12304	31045	12	NEW_VARIANT
P-0003754-T01-IM5	c.4870-2423:CACNA1A_c.87:STK11inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CACNA1A-STK11)		324935	0	11	19	Exon 1 of STK11(+)	STK11	1206999			19	Intron of CACNA1A(-): 2Kb before exon 31	CACNA1A	13358502			34	INVERSION		12151503	13325	240208	7	NEW_VARIANT
P-0000058-T01-IM3		35399162-N_bc20		AUTO_OK	5to5	5to5	-		461680	0	6	2	Intron of ALK(-): 452bp before exon 20	ALK	29446846			2	3-UTR of DDX11L2(-): 307bp after coding stop	DDX11L2	114360988			47	INVERSION		84914142	94065	505392	3	NEW_VARIANT
P-0001898-T01-IM3	CCDC6 (NM_005436) - RET (NM_020975) inversion: c.304-12339_c.2137-333inv5	PRECISE		AUTO_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		38834	0	18	10	Intron of RET(+): 333bp before exon 12	RET	43611699			10	Intron of CCDC6(-): 12Kb before exon 2	CCDC6	61624799			43	INVERSION		18013100	177	41004	18	NEW_VARIANT
P-0001898-T01-IM3	RET (NM_020975) - RASSF4 (NM_032023) deletion: c.2137-283_c.138+357del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (RET-RASSF4)		14419	0	15	10	Intron of RET(+): 283bp before exon 12	RET	43611749			10	Intron of RASSF4(+): 357bp after exon 3	RASSF4	45467653			21	DELETION		1855904	176	13672	17	NEW_VARIANT
P-0002997-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		14449	0	25	4	5-UTR of SORBS2(-): 39Kb before coding start	SORBS2	186650802			4	Intron of FAT1(-): 15bp after exon 21	FAT1	187522408			37	INVERSION		871606	7016	19315	25	NEW_VARIANT
P-0004103-T01-IM5	SND1 (NM_014390) -  BRAF (NM_004333) rearrangement: c.1038+5799:SND1_c.1315-192:BRAFinv.	PRECISE	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)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SND1-BRAF)		65280	0	25	7	Intron of SND1(+): 6Kb after exon 9	SND1	127353500			7	Intron of BRAF(-): 192bp before exon 11	BRAF	140481685			27	INVERSION		13128185	15223	56508	25	NEW_VARIANT
P-0002323-T01-IM3	TRAP1 (NM_016292) and CREBBP (NM_004380) duplication (42233bp):    TRAP1:c.331-780_CREBBP:c.5898dup	PRECISE	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.	AUTO_OK	5to3	5to3	Protein fusion: mid-exon (TRAP1-CREBBP)		11964	0	16	16	Intron of TRAP1(-): 780bp before exon 4	TRAP1	3736917			16	Exon 31 of CREBBP(-)	CREBBP	3779150			39	DUPLICATION		42233	3089	11036	17	NEW_VARIANT
P-0002873-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		47289	0	33	10	Intron of KIF5B(-): 538bp before exon 16	KIF5B	32312502			10	Intron of RET(+): 788bp before exon 12	RET	43611244			45	INVERSION		11298742	6003	46844	33	NEW_VARIANT
P-0002873-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		34119	0	6	19	Intron of DOT1L(+): 1Kb before exon 10	DOT1L	2205552			19	Exon 26 of DOT1L(+)	DOT1L	2225422			13	DELETION		19870	6002	27368	6	NEW_VARIANT
P-0002702-T01-IM3		PRECISE	Note: The PARK2 intragenic deletion is a rearrangement event which results in the deletion of exons 5 to 6.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4228	0	68	6	Intron of PARK2(-): 73Kb after exon 6	PARK2	162321422			6	Exon 5 of PARK2(-)	PARK2	162475147			71	DELETION		153725	4865	1506	74	NEW_VARIANT
P-0004386-T01-IM5	NOTCH2 (NM_024408) rearrangement : c.6548_*2211inv	PRECISE	Note: The NOTCH2 (NM_024408) rearrangement event results in the inversion of exon34. One of the breakpoints is within exon34.	MANUAL_OK	5to5	5to5	-		6155	0	102	1	3-UTR of NOTCH2(-): 2Kb after coding stop	NOTCH2	120455718			1	Exon 34 of NOTCH2(-)	NOTCH2	120458797			82	INVERSION		3079	19934	6016	110	NEW_VARIANT
P-0004386-T01-IM5	NOTCH1 (NM_017617) - CUL5 (NM_003478) rearrangement : t(9;11)(9q34.3;11q22.3)(chr9:g.139390931::chr11:g.107944759)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (NOTCH1-CUL5)		0	0	17	11	Intron of CUL5(+): 535bp after exon 10	CUL5	107944759			9	Exon 34 of NOTCH1(-)	NOTCH1	139390931			8	TRANSLOCATION		0	19935	0	17	NEW_VARIANT
P-0003716-T01-IM5	SMARCA4 (NM_003072) - LDLR (NM_000527)  rearrangement: c.3168+11:SMARCA4_c.2141-262:LDLRdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (SMARCA4-LDLR)		15845	0	41	19	Intron of SMARCA4(+): 11bp after exon 21	SMARCA4	11136195			19	Intron of LDLR(+): 262bp before exon 15	LDLR	11233588			51	DELETION		97393	13120	7371	31	NEW_VARIANT
P-0004389-T01-IM5	RNF43 (NM_017763) rearrangement: c.952+44_c.2309-120del	PRECISE	The RNF43 (NM_017763) rearrangement is an intragenic deletion of exon 9. The functional significance is undetermined	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		8400	0	7	17	Intron of RNF43(-): 1Kb before exon 10	RNF43	56433547			17	Intron of RNF43(-): 44bp after exon 8	RNF43	56437466			4	DELETION		3919	19847	6412	7	NEW_VARIANT
P-0004336-T01-IM5	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)	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	38	6	Intron of ROS1(-): 138bp after exon 33	ROS1	117647249			5	Intron of CD74(-): 196bp before exon 7	CD74	149783071			17	TRANSLOCATION		0	18818	0	34	NEW_VARIANT
P-0004504-T01-IM5	CREBBP (NM_004380) - TBL3 (NM_006453) rearrangement : c.157:TBL3_c.3779+40:CREBBPinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CREBBP-TBL3)		90583	0	6	16	Exon 3 of TBL3(+)	TBL3	2024261			16	Intron of CREBBP(-): 40bp after exon 20	CREBBP	3801687			25	INVERSION		1777426	21969	62007	6	NEW_VARIANT
P-0004140-T01-IM5	RNF43(NM_017763) Rearrangement: c.849+196_253-3498dup	PRECISE	The RNF43(NM_017763) Rearrangement results in the duplication of exons 3 to 7 .Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: in frame		8391	0	5	17	Intron of RNF43(-): 196bp after exon 7	RNF43	56437948			17	Intron of RNF43(-): 3Kb before exon 3	RNF43	56451892			9	DUPLICATION		13944	15295	8966	5	NEW_VARIANT
P-0004140-T01-IM5	BRAF(NM_004333) Rearrangement : c.1141-973_139-1097del	PRECISE	The BRAF(NM_004333) Rearrangement results in the deletion of exons 2 to 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons: in frame		93829	0	38	7	Intron of BRAF(-): 973bp before exon 9	BRAF	140488357			7	Intron of BRAF(-): 1Kb before exon 2	BRAF	140551109			39	DELETION		62752	15294	96140	39	NEW_VARIANT
P-0002866-T01-IM3		IMPRECISE	Note: The JAK3 deletion is structural rearrangement event which results in the deletion of exon 10, likely disabling its function	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1850	0	14	19	Intron of JAK3(-): 103bp after exon 10	JAK3	17950183			19	Intron of JAK3(-): 89bp after exon 9	JAK3	17950950			0	DELETION		767	6017	2060	20	NEW_VARIANT
P-0002866-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (JAK3-EYA2)		0	0	9	20	Intron of EYA2(+): 22Kb before exon 10	EYA2	45749808			19	Intron of JAK3(-): 379bp after exon 10	JAK3	17949907			15	TRANSLOCATION		0	6019	0	8	NEW_VARIANT
P-0002894-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		41086	1	22	21	Intron of ERG(-): 62Kb before exon 4	ERG	39879331			21	Intron of TMPRSS2(-): 2Kb after exon 2	TMPRSS2	42868377			29	DELETION		2989046	6118	31046	24	NEW_VARIANT
P-0000260-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	-		19856	0	11	3	Exon 17 of BAP1(-)	BAP1	52436429			3	5-UTR of PHF7(+): 806bp before coding start	PHF7	52446090			22	DELETION		9661	94436	13983	9	NEW_VARIANT
P-0001272-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		4164	0	11	X	Intron of KDM6A(+): 2Kb after exon 17	KDM6A	44931307			X	Exon 19 of KDM6A(+)	KDM6A	44937708			27	DUPLICATION		6401	72781	4746	9	NEW_VARIANT
P-0003293-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (MLL2-PPFIBP1)		161399	0	34	12	Intron of PPFIBP1(+): 174bp after exon 17	PPFIBP1	27827328			12	Exon 34 of MLL2(-)	MLL2	49432493			67	INVERSION		21605165	10373	164872	34	NEW_VARIANT
P-0003293-T01-IM5		PRECISE	The MED12 (NM_005120) rearrangement results in the  duplication of exons 29 to 39.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons: in frame		29311	0	20	X	Intron of MED12(+): 107bp after exon 28	MED12	70350171			X	Intron of MED12(+): 51bp after exon 39	MED12	70357284			16	DUPLICATION		7113	10372	25816	20	NEW_VARIANT
P-0002841-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		27195	0	30	17	Intron of BCAS3(+): 30Kb before exon 7	BCAS3	58855288			17	Intron of BRIP1(-): 69bp after exon 14	BRIP1	59853693			41	DELETION		998405	5790	35883	34	NEW_VARIANT
P-0001664-T01-IM3	SPEN (NM_015001) intragenic deletion: c.405-536_c.600del	PRECISE	The SPEN intragenic deletion is a rearrangement event which results in   deletion of exon 3 and is likely inactivating.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2696	0	18	1	Intron of SPEN(+): 536bp before exon 3	SPEN	16202161			1	Exon 3 of SPEN(+)	SPEN	16202892			60	DELETION		731	1307	1841	62	NEW_VARIANT
P-0001664-T01-IM3	ARID1A (NM_006015) intragenic deletion: c.4103_c.5124+941del	PRECISE	The ARID1A intragenic deletion is a rearrangement event which results   in deletion of exons 18 and 19, and is likely inactivating	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		11326	0	43	1	Exon 18 of ARID1A(+)	ARID1A	27100821			1	Intron of ARID1A(+): 941bp after exon 19	ARID1A	27103139			61	DELETION		2318	1308	6640	51	NEW_VARIANT
P-0001664-T01-IM3	LATS1 (NM_004690) intragenic deletion: c.3026_c.2883+6854del	PRECISE	The LATS1 intragenic deletion is a rearrangement event which results  in deletion of exon 9, and is likely inactivating.	AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		851	0	36	6	Exon 8 of LATS1(-)	LATS1	149983232			6	Intron of LATS1(-): 7Kb after exon 7	LATS1	149990542			57	DELETION		7310	1309	569	46	NEW_VARIANT
P-0003402-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	-		5141	0	28	9	IGR: 17Kb after MTAP(+)	MTAP	21883147			9	Exon 1 of CDKN2A(-)	CDKN2A	21994235			60	DELETION		111088	11168	2453	30	NEW_VARIANT
P-0003383-T01-IM5		PRECISE	EML4 (NM_019063) exons 1-13 fuses with ALK (NM_004304) exons 20-29.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		79994	0	45	2	Intron of ALK(-): 755bp after exon 19	ALK	29447572			2	Intron of EML4(+): 2Kb after exon 12	EML4	42525071			55	INVERSION		13077499	11079	76803	42	NEW_VARIANT
P-0002359-T01-IM3	CAMK2D (NM_001221) and KDR (NM_002253) deletion (58606888bp):  CAMK2D:c.220+19784_KDR:c.3118del	PRECISE	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.	AUTO_OK	3to5	3to5	Protein fusion: mid-exon (CAMK2D-KDR)		260383	0	9	4	Exon 23 of KDR(-)	KDR	55956197			4	Intron of CAMK2D(-): 20Kb after exon 3	CAMK2D	114563085			18	DELETION		58606888	3149	276733	6	NEW_VARIANT
P-0003144-T01-IM5		PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript fusion (ZNF595-TERT)		0	0	25	5	5-UTR of TERT(-): 19bp before coding start	TERT	1295123			4	5-UTR of ZNF595(+): 139bp before coding start	ZNF595	53244			51	TRANSLOCATION		0	8951	0	25	NEW_VARIANT
P-0003234-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3202	0	8	19	Exon 17 of DOT1L(+)	DOT1L	2213611			19	Intron of DOT1L(+): 452bp before exon 20	DOT1L	2215828			32	DELETION		2217	9938	3589	10	NEW_VARIANT
P-0003813-T01-IM5	ROS1 (NM_002944) rearrangement: c.2844_3381+330dup	PRECISE	Note: The ROS1 (NM_002944) rearrangement event results in the duplication of ROS1 exons 19-21. One of the breakpoints is within exon19.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		5179	0	54	6	Intron of ROS1(-): 330bp after exon 21	ROS1	117683436			6	Exon 19 of ROS1(-)	ROS1	117686873			94	DUPLICATION		3437	13617	9120	69	NEW_VARIANT
P-0002016-T01-IM3		PRECISE	FGFR3 deletion of last 4 exons (14-18)	AUTO_OK	3to5	3to5	-		5083	0	8	4	Intron of FGFR3(+): 34bp before exon 14	FGFR3	1807744			4	3-UTR of FGFR3(+): 109bp after coding stop	FGFR3	1809098			18	DELETION		1354	3262	2369	8	NEW_VARIANT
P-0004221-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion  (TMPRSS2 exon 2 fused to ERG exon 3):  c.127-1520:TMPRSS2_c.237-8364:ERGdel	PRECISE	Known fusion	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		28242	0	13	21	Intron of ERG(-): 8Kb before exon 5	ERG	39803847			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868025			15	DELETION		3064178	16894	21353	14	NEW_VARIANT
P-0001151-T01-IM3	RET (NM_020630) - NCOA4 (NM_005437) Duplication : c.2137-387_c.1840-75dup	PRECISE	Note: rearrangement consistent with NCOA4-RET fusion. Confirmatory RET FISH  is recommended.	AUTO_OK	5to3	5to3	Protein fusion: in frame (NCOA4-RET)		33721	0	14	10	Intron of RET(+): 387bp before exon 12	RET	43611645			10	Intron of NCOA4(+): 75bp before exon 11	NCOA4	51589150			27	DUPLICATION		7977505	72547	35267	16	NEW_VARIANT
P-0001437-T01-IM3	None	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: out of frame (CD74-ROS1)		0	0	10	6	Intron of ROS1(-): 1Kb after exon 32	ROS1	117649412			5	Intron of CD74(-): 629bp before exon 7	CD74	149783504			12	TRANSLOCATION		0	2077	0	0	NEW_VARIANT
P-0004492-T01-IM5	ERBB3 (NM_001982) rearrangement : t(1;12)(1q24.2;12q13.2)(chr1:g.167500617::chr12:g.56486697)	PRECISE	Note: ERBB3 (NM_001982) rearrangement event  is a translocation which results in truncation of ERBB3 exons 10-17. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	16	12	Intron of ERBB3(+): 73bp before exon 11	ERBB3	56486697			1	IGR: 10Kb before CREG1(-)	CREG1	167500617			13	TRANSLOCATION		0	21836	0	13	NEW_VARIANT
P-0003125-T01-IM5		PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (RET-KIF5B)		46081	0	30	10	Intron of KIF5B(-): 2Kb after exon 15	KIF5B	32315549			10	Intron of RET(+): 451bp before exon 12	RET	43611581			48	INVERSION		11296032	8732	41394	64	NEW_VARIANT
P-0003125-T01-IM5		PRECISE	KIF5B (NM_004521) - RET (NM_020975) rearrangement: c.1725+1795:KIF5B_c.2137-448:RETinv   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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		46093	0	35	10	Intron of KIF5B(-): 2Kb after exon 15	KIF5B	32315561			10	Intron of RET(+): 448bp before exon 12	RET	43611584			59	INVERSION		11296023	8733	41382	64	NEW_VARIANT
P-0004477-T01-IM5	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	PRECISE	The AGK (NM_018238) - BRAF (NM_004333 fusion is a reciprocal inversion (PMID: 23890088)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (AGK-BRAF)		34782	0	11	7	Intron of BRAF(-): 1Kb before exon 8	BRAF	140495405			7	Intron of AGK(+): 10Kb after exon 2	AGK	141265443			12	INVERSION		770038	21692	46087	11	NEW_VARIANT
P-0002778-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	-		23692	0	19	4	Exon 4 of BMPR1B(+)	BMPR1B	96025687			4	Exon 3 of TET2(+)	TET2	106156370			40	INVERSION		10130683	5535	28487	9	NEW_VARIANT
P-0002778-T01-IM3		PRECISE	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	MANUAL_OK	3to5	3to5	-		48312	0	28	4	Exon 3 of TET2(+)	TET2	106156519			4	IGR: 3Kb before SEC24B(+)	SEC24B	110351841			61	DELETION		4195322	5533	50902	32	NEW_VARIANT
P-0002778-T01-IM3		PRECISE	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.	MANUAL_OK	5to3	5to3	-		45890	0	13	4	Exon 3 of TET2(+)	TET2	106156573			4	IGR: 35Kb before PAPSS1(-)	PAPSS1	108499812			30	DUPLICATION		2343239	5534	46395	15	NEW_VARIANT
P-0003446-T01-IM5		PRECISE	Known fusion	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		75918	0	49	2	Intron of ALK(-): 140bp before exon 20	ALK	29446534			2	Intron of EML4(+): 597bp after exon 12	EML4	42523253			56	INVERSION		13076719	11520	63443	77	NEW_VARIANT
P-0003160-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	-		11369	0	13	12	IGR: 691Kb before RERGL(-)	RERGL	17542340			12	Intron of PIK3C2G(+): 45bp before exon 5	PIK3C2G	18446790			30	INVERSION		904450	9176	10630	13	NEW_VARIANT
P-0003177-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		222916	0	21	10	Intron of BICC1(+): 7Kb before exon 3	BICC1	60454839			10	Intron of FGFR2(-): 497bp before exon 17	FGFR2	123242188			42	INVERSION		62787349	9340	220142	21	NEW_VARIANT
P-0001909-T01-IM3	NOTCH2 (NM_024408) Deletion: c.875-51_c.1410del	PRECISE		AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		5114	0	11	1	Exon 8 of NOTCH2(-)	NOTCH2	120510099			1	Intron of NOTCH2(-): 51bp before exon 6	NOTCH2	120512418			43	DELETION		2319	371	3737	14	NEW_VARIANT
P-0003597-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1878:TMPRSS2_c.18+11694:ERGdel	PRECISE	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2 to 10)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		60881	0	59	21	Intron of ERG(-): 12Kb after exon 1	ERG	39858593			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42871994			56	DELETION		3013401	22761	36241	66	NEW_VARIANT
P-0004335-T01-IM5	STK11 (NM_000455) rearrangement: c.291-521_597+36del	PRECISE	Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of STK11 exons 2-4.	MANUAL_OK	3to5	3to5	Deletion of 3 exons: out of frame		4064	0	7	19	Intron of STK11(+): 521bp before exon 2	STK11	1217895			19	Intron of STK11(+): 36bp after exon 4	STK11	1220540			5	DELETION		2645	18804	2921	7	NEW_VARIANT
P-0001086-T01-IM3	PARK2 (NM_004562) intragenic deletion: c.1168-3962_1206del	PRECISE	Note: The PARK2 intragenic deletion is a rearrangement event which results  in the deletion of exon 11, and may represent an inactivating rearrangement.	AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		405	0	15	6	Exon 11 of PARK2(-)	PARK2	161781199			6	Intron of PARK2(-): 4Kb before exon 11	PARK2	161785199			14	DELETION		4000	72404	284	14	NEW_VARIANT
P-0004433-T01-IM5	RNF43 (NM_017763) Rearrangement : c.586:RNF43_chr17.g.59452393inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (BCAS3-RNF43)		71240	0	33	17	Exon 6 of RNF43(-)	RNF43	56440006			17	Intron of BCAS3(+): 7Kb after exon 23	BCAS3	59452393			41	INVERSION		3012387	20211	89736	33	NEW_VARIANT
P-0004681-T01-IM5	SRC (NM_198291) rearrangement : c.350+21:SRC_chr20:g.42113618del	PRECISE	Note: The SRC (NM_198291) rearrangement event results in the deletion of SRC exons 6-14.	MANUAL_OK	3to5	3to5	-		69750	0	15	20	Intron of SRC(+): 21bp after exon 5	SRC	36014598			20	IGR: 27Kb before SFRS6(+)	SFRS6	42113618			21	DELETION		6099020	29301	76903	15	NEW_VARIANT
P-0004681-T01-IM5	EWSR1 (NM_013986) rearrangement : c.1179+848:EWSR1_chr22:g.29715368del	PRECISE	Note: The EWSR1 (NM_013986) rearrangement event results in the deletion of EWSR1 exons 13-18.	MANUAL_OK	3to5	3to5	-		12365	0	9	22	Intron of EWSR1(+): 848bp after exon 10	EWSR1	29689443			22	IGR: 6Kb before RASL10A(-)	RASL10A	29715368			17	DELETION		25925	29302	13331	9	NEW_VARIANT
P-0003381-T01-IM5		PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (INCENP-MYOD1)		58860	0	36	11	Intron of MYOD1(+): 57bp before exon 3	MYOD1	17742745			11	Intron of INCENP(+): 1Kb before exon 11	INCENP	61911103			34	DUPLICATION		44168358	10980	59022	36	NEW_VARIANT
P-0003381-T01-IM5		PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (MLL-USP2)		73757	0	9	11	Intron of MLL(+): 153bp after exon 8	MLL	118353363			11	Intron of USP2(-): 3Kb after exon 2	USP2	119240539			12	INVERSION		887176	10984	50996	8	NEW_VARIANT
P-0003381-T01-IM5		PRECISE	Note: The MYOD1 (NM_002478) rearrangement event results in the inversion of the gene. The breakpoint on MYOD1 is within exon1.	MANUAL_OK	3to3	3to3	-		37870	0	88	11	Exon 1 of MYOD1(+)	MYOD1	17741521			11	IGR: 1Mb before LRRC4C(-)	LRRC4C	38708506			44	INVERSION		20966985	10985	36618	87	NEW_VARIANT
P-0004130-T01-IM5	SYK(NM_003177) Rearrangement : c.846+52_915+2724del	PRECISE	Note: SYK(NM_003177) Rearrangement results in the intragenic deletion of  exon 7.Its functional significance is undetermined	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2149	0	9	9	Intron of SYK(+): 52bp after exon 6	SYK	93627431			9	Intron of SYK(+): 3Kb after exon 7	SYK	93632205			21	DELETION		4774	15431	1765	10	NEW_VARIANT
P-0002075-T01-IM3	RIT1 (NM_006912) Deletion : c.313_g.152308085del	PRECISE		MANUAL_OK	3to5	3to5	-		13485	0	21	1	IGR: 13Kb before FLG2(-)	FLG2	152308085			1	Exon 5 of RIT1(-)	RIT1	155874218			39	DELETION		3566133	2306	23153	23	NEW_VARIANT
P-0003519-T01-IM5	chr21:g.38896651_c.56-4127:TMPRSS2inv	PRECISE	Note: The TMPRSS2 (NM_001135099) rearrangement results in  the inversion of TMPRSS2 exons 2-14.	MANUAL_OK	3to3	3to3	-		80002	0	18	21	IGR: 9Kb after DYRK1A(+)	DYRK1A	38896651			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874243			28	INVERSION		3977592	11855	68025	17	NEW_VARIANT
P-0003519-T01-IM5	c.-149-17599:ERG_c.56-3874:TMPRSS2del	PRECISE	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10)	MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		60627	0	27	21	5-UTR of ERG(-): 27Kb before coding start	ERG	39974468			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873990			40	DELETION		2899522	11853	50100	28	NEW_VARIANT
P-0000732-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		39252	0	17	2	Intron of ALK(-): 790bp after exon 19	ALK	29447537			2	Intron of EML4(+): 7Kb after exon 5	EML4	42498669			34	INVERSION		13051132	71932	30226	15	NEW_VARIANT
P-0001845-T01-IM3	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (2939631bp):  (TMRPSS2:c.127-626_ERG:c.39+20086del)	PRECISE	Note: This interstitial deletion is consistent with TMPRSS2-ERG fusion.	AUTO_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		22163	0	16	21	Intron of ERG(-): 20Kb after exon 3	ERG	39927500			21	Intron of TMPRSS2(-): 626bp before exon 3	TMPRSS2	42867131			23	DELETION		2939631	621	17721	19	NEW_VARIANT
P-0001141-T01-IM3	TMPRSS2 (NM_001135099) - ERG (NM_182918) Deletion (3028438bp):  (TMRPSS2:c.55+1206_ERG:c.18+20054del)	PRECISE	Note: this interstitial deletion is consistent with TMPRSS2ERG fusion.	AUTO_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		54019	0	29	21	Intron of ERG(-): 20Kb after exon 1	ERG	39850233			21	Intron of TMPRSS2(-): 1Kb after exon 1	TMPRSS2	42878671			39	DELETION		3028438	72524	60724	31	NEW_VARIANT
P-0003511-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.39+52408:ERG_c.55+1182:TMPRSS2del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		99710	0	26	21	Intron of ERG(-): 52Kb after exon 3	ERG	39895178			21	Intron of TMPRSS2(-): 1Kb after exon 1	TMPRSS2	42878695			24	DELETION		2983517	15994	75821	23	NEW_VARIANT
P-0003511-T02-IM5	CDK6 (NM_001145306) rearrangement: c.90:CDK6_chr7:g.92656964inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		494	0	26	7	Exon 2 of CDK6(-)	CDK6	92462548			7	IGR: 72Kb before SAMD9(-)	SAMD9	92656964			30	INVERSION		194416	15995	708	26	NEW_VARIANT
P-0003971-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fuses with ERG exons 4-10): c.55+4079:TMPRSS2_c.19-16151:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		39360	0	6	21	Intron of ERG(-): 16Kb before exon 4	ERG	39833695			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875798			21	DELETION		3042103	21720	45507	6	NEW_VARIANT
P-0002840-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (KDM5C-GLRA2)		238470	0	5	X	Intron of GLRA2(+): 16Kb after exon 8	GLRA2	14725392			X	Exon 26 of KDM5C(-)	KDM5C	53222372			4	INVERSION		38496980	5716	259353	5	NEW_VARIANT
P-0003216-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	-		5309	0	10	6	IGR: 8Kb before HIST1H2BC(-)	HIST1H2BC	26116007			6	Exon 1 of HIST1H2BD(+)	HIST1H2BD	26158644			18	DELETION		42637	9811	4630	11	NEW_VARIANT
P-0003535-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.56-3669:TMPRSS2_c.39+60775:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		109880	1	67	21	Intron of ERG(-): 61Kb after exon 3	ERG	39886811			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873785			93	DELETION		2986974	11906	59048	160	NEW_VARIANT
P-0003390-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (POLE-LEMD3)		153006	0	5	12	Intron of LEMD3(+): 10Kb after exon 1	LEMD3	65574555			12	Intron of POLE(-): 106bp after exon 31	POLE	133225786			3	INVERSION		67651231	11194	169339	5	NEW_VARIANT
P-0003390-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (POLE-RAB11FIP4)		0	0	11	17	Intron of RAB11FIP4(+): 23Kb before exon 4	RAB11FIP4	29822054			12	Intron of POLE(-): 39bp after exon 31	POLE	133225853			24	TRANSLOCATION		0	11197	0	11	NEW_VARIANT
P-0003722-T01-IM5	c.1920+1713_c.4102-30:ARID1Adel	PRECISE	The ARID1A  (NM_006015) rearrangement results in intragenic deletion of exons 5 to 18.	MANUAL_OK	3to5	3to5	Deletion of 13 exons: in frame		25936	0	64	1	Intron of ARID1A(+): 2Kb after exon 4	ARID1A	27060996			1	Intron of ARID1A(+): 30bp before exon 18	ARID1A	27100790			49	DELETION		39794	13161	21761	72	NEW_VARIANT
P-0003722-T01-IM5	TNS3 (NM_022748) - EGFR (NM_005228) inversion (8585063bp) : g.46674498:TNS3_c.2619:EGFRinv	PRECISE	The EGFR (NM_005228) rearrangement is an inversion that results in the truncation of exons 21-28.	MANUAL_OK	3to3	3to3	-		74660	0	43	7	IGR: 640Kb before TNS3(-)	TNS3	46674498			7	Exon 21 of EGFR(+)	EGFR	55259561			45	INVERSION		8585063	13163	122282	43	NEW_VARIANT
P-0005741-T01-IM5	BRCA2 (NM_000059) Rearrangement :  c.7435+72_9257-4656del	PRECISE	Note: The BRCA2 (NM_000059) rearrangement results in the intragenic deletion of exon15 to exon24 . Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 10 exons: in frame		24705	0	81	13	Intron of BRCA2(+): 72bp after exon 14	BRCA2	32929497			13	Intron of BRCA2(+): 5Kb before exon 25	BRCA2	32964170			75	DELETION		34673	56387	12014	80	NEW_VARIANT
P-0014397-T01-IM6	FAT1(NM_005245) rearrangement: t(4:21)(q35.2;q21.2)(chr4:g.187518320::chr21:g.25402034)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	23	21	IGR: 1Mb before NCRNA00158(-)	NCRNA00158	25402034			4	Exon 25 of FAT1(-)	FAT1	187518320			15	TRANSLOCATION		0	164402	0	23	NEW_VARIANT
P-0014969-T01-IM6	BRAF (NM_004333) - CDK5RAP2 (NM_018249) Rearrangement : t(7;9)(q34;q33.3)(chr7:g.140493700::chr9:g.123269531)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (BRAF-CDK5RAP2)		0	0	26	9	Intron of CDK5RAP2(-): 11Kb after exon 12	CDK5RAP2	123269531			7	Intron of BRAF(-): 408bp after exon 8	BRAF	140493700			8	TRANSLOCATION		0	166431	0	26	NEW_VARIANT
P-0015010-T01-IM6	APC (NM_000038) rearrangement: c.4970_g.112190339del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		18113	0	17	5	Exon 16 of APC(+)	APC	112176261			5	IGR: 7Kb before SRP19(+)	SRP19	112190339			29	DELETION		14078	166505	14013	16	NEW_VARIANT
P-0006793-T02-IM6	TP53 (NM_000546) Rearrangement: c.-28-1107_c.249del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		7944	0	56	17	Exon 4 of TP53(-)	TP53	7579438			17	5-UTR of TP53(-): 1Kb before coding start	TP53	7581047			55	DELETION		1609	165001	6587	56	NEW_VARIANT
P-0014544-T01-IM6	INPP4B (NM_001101669) Rearrangement : c.1082_c.1360-2791del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3652	0	18	4	Intron of INPP4B(-): 3Kb before exon 18	INPP4B	143084505			4	Exon 16 of INPP4B(-)	INPP4B	143114339			23	DELETION		29834	164929	2065	18	NEW_VARIANT
P-0008577-T01-IM5	ANKRD11 (NM_013275) rearrangement: c.-144-15970_28del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1157	0	24	16	Exon 3 of ANKRD11(-)	ANKRD11	89383400			16	5-UTR of ANKRD11(-): 117Kb before coding start	ANKRD11	89500746			40	DELETION		117346	122913	979	21	NEW_VARIANT
P-0008567-T01-IM5	PRKAR2B (NM_002736) - BRAF (NM_004333) rearrangement: c.307+8063:PRKAR2B_c.1177+932:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (PRKAR2B-BRAF)		164995	0	23	7	Intron of PRKAR2B(+): 8Kb after exon 1	PRKAR2B	106693722			7	Intron of BRAF(-): 932bp after exon 9	BRAF	140486416			33	INVERSION		33792694	122862	140889	23	NEW_VARIANT
P-0012119-T01-IM5	RAD52 (NM_134424) -ERC1 (NM_178040) Rearrangement : c.385:RAD52_c.1318-276:ERC1	PRECISE	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.	MANUAL_OK	3to5	3to5	-		6212	0	16	12	Exon 6 of RAD52(-)	RAD52	1036393			12	Intron of ERC1(+): 276bp before exon 6	ERC1	1221105			24	DELETION		184712	156309	5265	16	NEW_VARIANT
P-0006779-T01-IM5	INSR (NM_000208) rearrangement: c.2513:INSR_chr19:g.15462870inv	PRECISE	The INSR (NM_000208) rearrangement is an inversion (8320014 bp) of exons 1-12. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		404057	0	41	19	Exon 12 of INSR(-)	INSR	7142856			19	IGR: 1Kb before AKAP8(-)	AKAP8	15462870			48	INVERSION		8320014	108857	360006	39	NEW_VARIANT
P-0010202-T01-IM5	PTCH1 (NM_000264) rearrangement : c.3933:PTCH1_chr9:g.104623233del	PRECISE	Note: The PTCH1 rearrangement event results in the deletion of PTCH1 exons 1-23. One of the breakpoints is within PTCH1 exon23.	MANUAL_OK	3to5	3to5	-		71048	0	12	9	Exon 23 of PTCH1(-)	PTCH1	98209605			9	IGR: 269Kb before PPP3R2(-)	PPP3R2	104623233			14	DELETION		6413628	144784	68945	12	NEW_VARIANT
P-0003063-T01-IM5		PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		12866	0	36	19	Intron of SMARCA4(+): 389bp before exon 15	SMARCA4	11123236			19	Exon 19 of SMARCA4(+)	SMARCA4	11134227			34	DUPLICATION		10991	7375	11082	36	NEW_VARIANT
P-0003055-T01-IM5		PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		114951	0	9	13	Exon 10 of BRCA2(+)	BRCA2	32906713			13	Intron of BRCA2(+): 3Kb before exon 19	BRCA2	32941266			18	DUPLICATION		34553	7336	122983	9	NEW_VARIANT
P-0010099-T01-IM5	CDH1 (NM_004360) rearrangement: c.1590:CDH1_chr16:g.81431871inv	PRECISE	Note: The CDH1 rearrangement is an inversion of exons 11 to 16. The breakpoint is within exon 11. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		231134	0	12	16	Exon 11 of CDH1(+)	CDH1	68853207			16	IGR: 47Kb before CMIP(+)	CMIP	81431871			20	INVERSION		12578664	137936	205143	12	NEW_VARIANT
P-0001532-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		95917	0	102	2	Intron of ALK(-): 774bp after exon 19	ALK	29447553			2	Intron of EML4(+): 3Kb before exon 13	EML4	42525673			70	INVERSION		13078120	1876	94542	115	NEW_VARIANT
P-0013971-T01-IM5	DOT1L (NM_032482) Rearrangement : c.200+69_c.647dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		8204	0	44	19	Intron of DOT1L(+): 69bp after exon 3	DOT1L	2185997			19	Exon 7 of DOT1L(+)	DOT1L	2194572			53	DUPLICATION		8575	162941	7694	44	NEW_VARIANT
P-0008877-T01-IM5	PTPRT (NM_133170) Rearrangement :  c.486+20_c.2400-16496del	PRECISE	Note: The PTPRT (NM_133170) Rearrangement  results in the deletion of exons 4 to 15 of PTPRT.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 12 exons: out of frame		24486	0	6	20	Intron of PTPRT(-): 16Kb before exon 16	PTPRT	40844524			20	Intron of PTPRT(-): 20bp after exon 3	PTPRT	41419815			10	DELETION		575291	124801	21245	6	NEW_VARIANT
P-0009592-T01-IM5	NCOA4 (NM_001145260) - RET (NM_020975) fusion (NCOA4 exons 1-9 with RET exons 12=20: c.872:NCOA4_c.2136+621:RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NCOA4-RET)		34898	0	71	10	Intron of RET(+): 889bp before exon 12	RET	43611143			10	Exon 9 of NCOA4(+)	NCOA4	51584711			73	DUPLICATION		7973568	131314	33354	71	NEW_VARIANT
P-0012368-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918)  fusion (TMPRSS2 exons 1-2  with ERG exons 2-10): c.126+409:TMPRSS2_c.18+18604:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion (TMPRSS2 exons 1-2  with ERG exons 2-10) is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		43759	0	53	21	Intron of ERG(-): 19Kb after exon 1	ERG	39851683			21	Intron of TMPRSS2(-): 409bp after exon 2	TMPRSS2	42869637			38	DELETION		3017954	157163	21166	50	NEW_VARIANT
P-0010904-T01-IM5	GNAS (NM_000516) -  ZNF335 (NM_022095) Rearrangement :  c.970+1:GNAS_c.1103-72:ZNF335inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (GNAS-ZNF335)		206494	0	66	20	Intron of ZNF335(-): 72bp before exon 8	ZNF335	44592701			20	Intron of GNAS(+): 1bp after exon 11	GNAS	57485137			55	INVERSION		12892436	149630	254964	64	NEW_VARIANT
P-0008709-T01-IM5	ETV6 (NM_001987) rearrangement: c.326_chr12:g.11570805dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		4673	0	24	12	IGR: 26Kb before PRB2(-)	PRB2	11570805			12	Exon 3 of ETV6(+)	ETV6	11992236			17	DUPLICATION		421431	123530	10392	23	NEW_VARIANT
P-0008709-T01-IM5	SF3B1 (NM_012433) - PDE1A (NM_005019) rearrangement: c.495+79:SF3B1_c.101+118:PDE1Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (SF3B1-PDE1A)		102318	0	43	2	Intron of PDE1A(-): 118bp after exon 1	PDE1A	183386885			2	Intron of SF3B1(-): 79bp after exon 5	SF3B1	198283154			36	DELETION		14896269	123529	106667	43	NEW_VARIANT
P-0008709-T01-IM5	MDC1 (NM_014641) rearrangement: c.2758_chr6:g.30822725dup.	PRECISE	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.	MANUAL_OK	5to3	5to3	-		31993	0	28	6	Exon 8 of MDC1(-)	MDC1	30675598			6	IGR: 29Kb before DDR1(+)	DDR1	30822725			38	DUPLICATION		147127	123531	34073	25	NEW_VARIANT
P-0006926-T02-IM5	LRRC24 (NM_001024678) - RECQL4 (NM_004260) rearrangement : 2464+40:RECQL4_c.607+132: LRRC24del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (LRRC24-RECQL4)		27646	0	11	8	Intron of RECQL4(-): 40bp after exon 14	RECQL4	145738561			8	Intron of LRRC24(-): 132bp after exon 4	LRRC24	145749362			9	DELETION		10801	109955	28574	11	NEW_VARIANT
P-0014756-T01-IM6	MSH2 (NM_000251) rearrangement: c.211+1295_c.688del	PRECISE	Note: The MSH2 rearrangement is an intragenic deletion of exons 2-4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5338	1	80	2	Intron of MSH2(+): 1Kb after exon 1	MSH2	47631836			2	Exon 4 of MSH2(+)	MSH2	47639595			57	DELETION		7759	165718	1110	76	NEW_VARIANT
P-0010406-T01-IM5	RASA1 (NM_002890) Rearrangement : c.2691-74_ 3060+57dup	PRECISE	Note: The RASA1 Rearrangement results in the intragenic duplication of exons 21-24 of RASA1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons: out of frame		4834	0	8	5	Intron of RASA1(+): 74bp before exon 21	RASA1	86679456			5	Intron of RASA1(+): 57bp after exon 24	RASA1	86685401			13	DUPLICATION		5945	145886	4064	8	NEW_VARIANT
P-0000624-T02-IM5	NFKBIA (NM_020529) Rearrangement: chr14:g.26301883_c.*232:NFKBIAinv	PRECISE	NFKBIA (NM_020529) rearrangement results in the inversion of genomic region including 3-UTR of NFKBIA. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		7495	0	32	14	IGR: 613Kb before NOVA1(-)	NOVA1	26301883			14	3-UTR of NFKBIA(-): 232bp after coding stop	NFKBIA	35870987			33	INVERSION		9569104	48649	16639	15	NEW_VARIANT
P-0002435-T01-IM3		PRECISE		AUTO_OK	5to5	5to5	Protein fusion: mid-exon (ACBD6-IGF1R)		0	0	7	15	Exon 6 of IGF1R(+)	IGF1R	99452116			1	Intron of ACBD6(-): 142bp after exon 4	ACBD6	180399173			22	TRANSLOCATION		0	3467	0	7	NEW_VARIANT
P-0002435-T01-IM3		PRECISE	duplication of exons 12-14	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		6971	0	41	17	Intron of BRIP1(-): 35bp after exon 14	BRIP1	59853727			17	Intron of BRIP1(-): 173bp after exon 11	BRIP1	59861458			62	DUPLICATION		7731	3466	7745	49	NEW_VARIANT
P-0002245-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Antisense fusion		41023	0	7	7	Intron of HEATR2(+): 2Kb after exon 6	HEATR2	798921			7	Exon 3 of CARD11(-)	CARD11	2987321			58	DELETION		2188400	2865	38158	28	NEW_VARIANT
P-0002796-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (IRS2-FLT1)		229601	0	19	13	Intron of FLT1(-): 7Kb after exon 1	FLT1	29061657			13	Intron of IRS2(-): 11Kb before exon 2	IRS2	110419477			36	DELETION		81357820	5558	147196	21	NEW_VARIANT
P-0006281-T01-IM5	CIC (NM_015125) rearrangement : c.4734:CIC_chr19:g.42800643inv	PRECISE	Note: The CIC (NM_015125) rearrangement results in the inversion of CIC exon20. One of the breakpoints is within CIC exon20.	MANUAL_OK	3to3	3to3	-		61	0	13	19	Exon 20 of CIC(+)	CIC	42799250			19	IGR: 542bp before PAFAH1B3(-)	PAFAH1B3	42800643			7	INVERSION		1393	71084	92	12	NEW_VARIANT
P-0006281-T01-IM5	ZNF157 (NM_003446) - RBM10 (NM_001204468) rearrangement : c.2208:RBM10_c.73-19442:ZNF157dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (ZNF157-RBM10)		2324	0	18	X	Exon 18 of RBM10(+)	RBM10	47044516			X	Intron of ZNF157(+): 19Kb before exon 2	ZNF157	47250233			18	DUPLICATION		205717	71083	3245	17	NEW_VARIANT
P-0001317-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (ERBB2-GRB7)		9711	0	63	17	Exon 25 of ERBB2(+)	ERBB2	37883150			17	Intron of GRB7(+): 68bp before exon 10	GRB7	37901428			92	DELETION		18278	73009	7913	79	NEW_VARIANT
P-0014143-T01-IM5	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	PRECISE	Note: The TPM3 - NTRK1 fusion includes the kinase domain of NTRK1.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (TPM3-NTRK1)		28084	0	4	1	Intron of TPM3(-): 4Kb after exon 7	TPM3	154138845			1	Intron of NTRK1(+): 173bp before exon 9	NTRK1	156844002			75	INVERSION		2705157	163396	30732	5	NEW_VARIANT
P-0003870-T01-IM5	ARID1A (NM_006015) rearrangement: c.1138-3396_c.2419+5:ARID1Adup	PRECISE	The ARID1A (NM_006015) rearrangement is an intragenic duplication of exons 2-7. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 6 exons: out of frame		16510	0	74	1	Intron of ARID1A(+): 3Kb before exon 2	ARID1A	27052746			1	Intron of ARID1A(+): 5bp after exon 7	ARID1A	27088815			65	DUPLICATION		36069	13902	21777	69	NEW_VARIANT
P-0006965-T01-IM5	NTRK2 (NM_006180) rearrangement : c.1873_1937+1677del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		350	0	23	9	Exon 18 of NTRK2(+)	NTRK2	87563485			9	Intron of NTRK2(+): 2Kb after exon 18	NTRK2	87565226			35	DELETION		1741	112418	237	23	NEW_VARIANT
P-0007538-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exons 2 to 10) : c.55+2904:TMPRSS2_c.19-10639:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		73731	0	3	21	Intron of ERG(-): 11Kb before exon 4	ERG	39828183			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42876973			2	DELETION		3048790	117310	55749	3	NEW_VARIANT
P-0005216-T01-IM5	PLK2 (NM_006622) - PDE4D (NM_001104631) Rearrangement: c.378+18_c.455+337033dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (PLK2-PDE4D)		5522	0	87	5	Intron of PLK2(-): 18bp after exon 2	PLK2	57754794			5	Intron of PDE4D(-): 30Kb after exon 1	PDE4D	58851962			63	DUPLICATION		1097168	45790	9135	86	NEW_VARIANT
P-0001010-T02-IM5	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-780:KIF5B_c.2136+679:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		35585	0	8	10	Intron of KIF5B(-): 780bp before exon 16	KIF5B	32312744			10	Intron of RET(+): 679bp after exon 11	RET	43610863			16	INVERSION		11298119	124159	24513	8	NEW_VARIANT
P-0005452-T01-IM5	AR (NM_000044) Rearrangement : chrX:g.66753057_c.1131:ARdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		14324	0	20	X	IGR: 11Kb before AR(+)	AR	66753057			X	Exon 1 of AR(+)	AR	66766119			19	DELETION		13062	49075	13454	19	NEW_VARIANT
P-0007903-T01-IM5	EPHA6 (NM_001080448) - PPM1D (NM_003620) rearrangement : t(3;17)(q11.2;q23.2)(chr3::g.97452596::chr17:g.58734016)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (EPHA6-PPM1D)		0	0	16	17	Exon 5 of PPM1D(+)	PPM1D	58734016			3	Intron of EPHA6(+): 2Kb before exon 16	EPHA6	97452596			0	TRANSLOCATION		0	119471	0	16	NEW_VARIANT
P-0005931-T01-IM5	OXSR1 (NM_005109) - MYD88 (NM_002468)   Rearrangement :  c.71-7437:OXSR1_c.502+38:MYD88dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (OXSR1-MYD88)		5643	0	6	3	Intron of MYD88(+): 38bp after exon 2	MYD88	38181527			3	Intron of OXSR1(+): 7Kb before exon 2	OXSR1	38217057			13	DUPLICATION		35530	64552	5848	6	NEW_VARIANT
P-0009892-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		43178	0	54	21	Intron of ERG(-): 4Kb after exon 1	ERG	39866427			21	Intron of TMPRSS2(-): 551bp before exon 3	TMPRSS2	42867056			28	DELETION		3000629	137009	32883	53	NEW_VARIANT
P-0003353-T01-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	-		80058	0	14	17	Promoter of RAD51C(+): 53bp from tx start	RAD51C	56769910			17	IGR: 46Kb before ABCA8(-)	ABCA8	66817527			16	INVERSION		10047617	10880	106455	14	NEW_VARIANT
P-0014785-T01-IM6	MAP2K2 (NM_030662) -  CHAF1A (NM_005483) Rearrangement : c.984+60:MAP2K2_c.52+798:CHAF1Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (MAP2K2-CHAF1A)		20357	0	60	19	Intron of MAP2K2(-): 60bp after exon 8	MAP2K2	4097217			19	Intron of CHAF1A(+): 798bp after exon 1	CHAF1A	4403609			42	INVERSION		306392	165829	17381	57	NEW_VARIANT
P-0007860-T01-IM5	CTNNB1 (NM_001904) rearrangement: c.13+101_c.208del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2505	0	12	3	Intron of CTNNB1(+): 101bp after exon 2	CTNNB1	41265673			3	Exon 3 of CTNNB1(+)	CTNNB1	41266211			0	DELETION		538	119317	2883	11	NEW_VARIANT
P-0010824-T01-IM5	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)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (CDKN2A-RB1)		0	0	5	13	Intron of RB1(+): 193bp before exon 4	RB1	48919023			9	Intron of CDKN2A(-): 667bp after exon 2	CDKN2A	21970234			3	TRANSLOCATION		0	149396	0	3	NEW_VARIANT
P-0010824-T01-IM5	KDM6A (NM_021140) Rearrangement :  t(4;X)(q31.21.3;p11.3)(chr4:g.145331332::chrX:g.44969451)	PRECISE	Note: The KDM6A Rearrangement results in the possible truncation of exons28-29. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	23	X	Exon 28 of KDM6A(+)	KDM6A	44969451			4	IGR: 236Kb before HHIP(+)	HHIP	145331332			28	TRANSLOCATION		0	149397	0	23	NEW_VARIANT
P-0012179-T01-IM5	MAP2K4 (NM_003010) Rearrangement :  c.219-11508_c.513+2709del	PRECISE	Note: The MAP2K4 Rearrangement results in the intragenic deletion of exons 3-4 of MAP2K4. This includes the kinase domain of MAP2K4.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: out of frame		2426	0	29	17	Intron of MAP2K4(+): 12Kb before exon 3	MAP2K4	11973165			17	Intron of MAP2K4(+): 3Kb after exon 4	MAP2K4	12001720			33	DELETION		28555	156539	1511	20	NEW_VARIANT
P-0000449-T02-IM5	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.684-15:TMPRSS2_c.509-91895:DSCAMdel	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-DSCAM)		18066	0	23	21	Intron of DSCAM(-): 92Kb before exon 4	DSCAM	41833067			21	Intron of TMPRSS2(-): 15bp before exon 7	TMPRSS2	42851224			0	DELETION		1018157	128883	18509	23	NEW_VARIANT
P-0011363-T01-IM5	ABL1 (NM_005157) rearrangement : c.1279_1424-259del	PRECISE	Note: The ABL1 rearrangement event results in the deletion of ABL1 exon8. One of the breakpoints is within ABL1 exon8.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1092	0	9	9	Exon 8 of ABL1(+)	ABL1	133753810			9	Intron of ABL1(+): 259bp before exon 9	ABL1	133755196			16	DELETION		1386	153333	1358	9	NEW_VARIANT
P-0008945-T01-IM5	YAP1 (NM_001130145) - TRPC6 (NM_004621) Rearrangement :  c.668:YAP1_c.171-25820:TRPC6inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (YAP1-TRPC6)		5140	0	53	11	Intron of TRPC6(-): 26Kb before exon 2	TRPC6	101401349			11	Exon 3 of YAP1(+)	YAP1	102033282			61	INVERSION		631933	125136	3758	52	NEW_VARIANT
P-0002915-T01-IM3		PRECISE	Note: The TET1 (NM_030625) duplication is a rearrangement event which results in the  duplication of exon 2.The breakpoint is within exon 2.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		14392	0	14	10	Exon 2 of TET1(+)	TET1	70332166			10	Intron of TET1(+): 6Kb after exon 2	TET1	70339609			13	DUPLICATION		7443	6179	11191	15	NEW_VARIANT
P-0002915-T01-IM3		PRECISE	Note: The NF1 (NM_001042492) duplication is a rearrangement event which results in the duplication of exons 30 to 35.	MANUAL_OK	5to3	5to3	Duplication of 6 exons: in frame		10798	0	21	17	Intron of NF1(+): 2Kb before exon 30	NF1	29574493			17	Intron of NF1(+): 40bp after exon 35	NF1	29592397			34	DUPLICATION		17904	6180	13219	29	NEW_VARIANT
P-0003140-T01-IM5		PRECISE	The ASXL1 rearrangement is an inversion event which results in the inversion of exon 3. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3416	0	15	20	Intron of ASXL1(+): 107bp before exon 3	ASXL1	30956708			20	Intron of ASXL1(+): 3Kb after exon 3	ASXL1	30960274			13	INVERSION		3566	8992	44947	15	NEW_VARIANT
P-0004912-T01-IM5	ARID1A(NM_006015) Rearrangement : c.4486:ARID1A_chr1:g.27552578inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		17285	0	29	1	Exon 18 of ARID1A(+)	ARID1A	27101204			1	IGR: 8Kb before WDTC1(+)	WDTC1	27552578			38	INVERSION		451374	40715	13587	27	NEW_VARIANT
P-0004912-T01-IM5	IGSF8(NM_001206665) - SDHC(NM_003001) Rearrangement :  c.65-1579:IGSF8_c.78-10:SDHCinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (IGSF8-SDHC)		3686	0	21	1	Intron of IGSF8(-): 2Kb before exon 2	IGSF8	160066615			1	Intron of SDHC(+): 10bp before exon 3	SDHC	161298176			25	INVERSION		1231561	40714	5807	20	NEW_VARIANT
P-0003009-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (FAT1-SORBS2)		72118	0	20	4	5-UTR of SORBS2(-): 233Kb before coding start	SORBS2	186816559			4	Exon 10 of FAT1(-)	FAT1	187542224			42	DELETION		725665	7095	55275	25	NEW_VARIANT
P-0006838-T01-IM5	PIK3R3 (NM_003629) rearrangement: PIK3R3:c.215+705_c.901del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		11659	0	40	1	Exon 7 of PIK3R3(-)	PIK3R3	46521507			1	Intron of PIK3R3(-): 705bp after exon 2	PIK3R3	46545609			37	DELETION		24102	109329	9532	39	NEW_VARIANT
P-0006838-T01-IM5	STAT5A (NM_003152) rearrangment : t(2;17)(q32.1;q21.2)(c.2282: STAT5A_g.185422175)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	28	17	Exon 20 of STAT5A(+)	STAT5A	40462584			2	IGR: 41Kb before ZNF804A(+)	ZNF804A	185422175			21	TRANSLOCATION		0	109348	0	27	NEW_VARIANT
P-0003725-T01-IM5	c.1359:FGFR1_g.62143239inv	PRECISE	The FGFR1 (NM_001174067) rearrangement event results in the inversion of exons 9-19. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		59503	0	49	8	Exon 9 of FGFR1(-)	FGFR1	38275811			8	IGR: 57Kb before CLVS1(+)	CLVS1	62143239			65	INVERSION		23867428	13144	76398	46	NEW_VARIANT
P-0003768-T01-IM5	NF2 (NM_000268) rearrangement: chr22:g.27323591_c.1738-167:NF2inv	PRECISE	The NF2 (NM_000268) rearrangement is an inversion in which exons 1-4 of NF2 are inverted. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		69956	0	7	22	IGR: 270Kb before MIAT(+)	MIAT	27323591			22	Intron of NF2(+): 167bp before exon 5	NF2	30090574			12	INVERSION		2766983	13374	54516	7	NEW_VARIANT
P-0014954-T01-IM6	KDM6A (NM_021140) rearrangement: c.3175_c.3434-1006del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 21-23. One of the breakpoints is within exon 21.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4931	0	23	X	Exon 21 of KDM6A(+)	KDM6A	44941851			X	Intron of KDM6A(+): 1Kb before exon 24	KDM6A	44944104			32	DELETION		2253	166308	4290	22	NEW_VARIANT
P-0011369-T01-IM5	PRDM1 (NM_001198) Rearrangement: chr6:g.101334934_c.291+22:PRDM1inv	PRECISE	Note: The PRDM1 Rearrangement results in the inversion of exons1-2 of PRDM1. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		6824	0	27	6	IGR: 6Kb after ASCC3(-)	ASCC3	101334934			6	Intron of PRDM1(+): 22bp after exon 2	PRDM1	106536346			47	INVERSION		5201412	153395	7639	27	NEW_VARIANT
P-0012505-T01-IM5	SMAD4 (NM_005359) - UNC13C (NM_001080534) rearrangement: t(15;18)(q21.3;q21.2)(chr15:g.54879988::chr18:g.48584727)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SMAD4-UNC13C)		0	0	58	18	Exon 7 of SMAD4(+)	SMAD4	48584727			15	Intron of UNC13C(+): 20Kb after exon 28	UNC13C	54879988			34	TRANSLOCATION		0	157604	0	57	NEW_VARIANT
P-0014332-T01-IM6	SMAD4 (NM_005359) rearrangement: c.1207_c.1308+3512del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		378	0	11	18	Exon 10 of SMAD4(+)	SMAD4	48593456			18	Intron of SMAD4(+): 4Kb after exon 10	SMAD4	48597069			16	DELETION		3613	164154	214	11	NEW_VARIANT
P-0007025-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11) : c.56-3598:TMPRSS2_c.-150+4207:ERGdel	PRECISE	Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement is a deletion with a breakpoint 82kb upstream of ERG.	MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		97059	0	49	21	5-UTR of ERG(-): 82Kb before coding start	ERG	40029375			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873714			45	DELETION		2844339	112697	83142	46	NEW_VARIANT
P-0005824-T01-IM5	SUPT4H1 (NM_003168) - RNF43 (NM_017763) rearrangement event : :SUPT4H1_:RNF43dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (SUPT4H1-RNF43)		4933	0	40	17	Intron of SUPT4H1(-): 1Kb after exon 2	SUPT4H1	56427277			17	Intron of RNF43(-): 58bp after exon 9	RNF43	56434771			68	DUPLICATION		7494	63351	6049	40	NEW_VARIANT
P-0002886-T01-IM3		PRECISE	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	MANUAL_OK	3to3	3to3	Protein fusion: in frame (MTAP-CDKN2B)		19377	0	16	9	Intron of MTAP(+): 997bp after exon 7	MTAP	21860421			9	Intron of CDKN2B(-): 505bp after exon 1	CDKN2B	22008292			32	INVERSION		147871	6122	12533	16	NEW_VARIANT
P-0005211-T01-IM5	MAPK4 (NM_002747) - SMAD4 (NM_005359) Rearrangement: c.547-13524:MAPK4_c.48:SMAD4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MAPK4-SMAD4)		854	0	8	18	Intron of MAPK4(+): 14Kb before exon 3	MAPK4	48227925			18	Exon 2 of SMAD4(+)	SMAD4	48573464			10	DELETION		345539	45549	639	7	NEW_VARIANT
P-0013705-T01-IM5	ASXL1 (NM_015338) - RALGAPB (NM_020336) rearrangement:  c.3667:ASXL1_c.3268:RALGAPBdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (ASXL1-RALGAPB)		94368	0	37	20	Exon 12 of ASXL1(+)	ASXL1	31024182			20	Exon 22 of RALGAPB(+)	RALGAPB	37182615			39	DELETION		6158433	162035	70011	37	NEW_VARIANT
P-0013861-T01-IM5	MTOR (NM_004958) Rearrangement : c.1413-12:MTOR_c.1978-4081:KIF1Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		101797	0	7	1	Intron of KIF1B(+): 4Kb before exon 21	KIF1B	10376020			1	Intron of MTOR(-): 12bp before exon 10	MTOR	11301750			7	DUPLICATION		925730	162529	108893	3	NEW_VARIANT
P-0011029-T02-IM5	ST6GALNAC3 (NM_152996) - MRE11A (NM_005591) rearrangement : t(1;11)(p31.1;q21)(chr1:g.76791695::chr11:g.94192656)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	40	11	Exon 13 of MRE11A(-)	MRE11A	94192656			1	Intron of ST6GALNAC3(+): 12Kb after exon 2	ST6GALNAC3	76791695			30	TRANSLOCATION		0	151550	0	39	NEW_VARIANT
P-0012307-T01-IM5	MLL3 (NM_170606) rearrangement: c.1299+79_c.7689dup	PRECISE	Note: The MLL3 rearrangement is an intragenic duplication of exons 10 - 38. One of the breakpoint is within exon 38.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		53097	0	26	7	Exon 38 of MLL3(-)	MLL3	151874849			7	Intron of MLL3(-): 79bp after exon 9	MLL3	151960022			25	DUPLICATION		85173	156956	61363	26	NEW_VARIANT
P-0010464-T01-IM5	IGF1R (NM_000875) rearrangement: t(7;15)(q31.1;q25.3)(chr7:g.113198852::chr15:g.99434762)	PRECISE	Note: The IGF1R rearrangement is a translocation with a breakpoint within exon3 of IGF1R. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	31	15	Exon 3 of IGF1R(+)	IGF1R	99434762			7	IGR: 318Kb before PPP1R3A(-)	PPP1R3A	113198852			16	TRANSLOCATION		0	146229	0	29	NEW_VARIANT
P-0002088-T01-IM3	TGFBR1 (NM_004612) Deletion : c.575-98_g.5801401del	PRECISE		MANUAL_OK	3to5	3to5	-		418162	0	16	9	Intron of ERMP1(-): 73bp before exon 11	ERMP1	5801401			9	Intron of TGFBR1(+): 98bp before exon 4	TGFBR1	101900043			30	DELETION		96098642	2351	354396	18	NEW_VARIANT
P-0014235-T01-IM6	POLE (NM_006231) rearrangement: c.2195_chr12:g.126611209dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		82336	0	20	12	IGR: 316Kb before LOC100128554(+)	LOC100128554	126611209			12	Exon 20 of POLE(-)	POLE	133244213			23	DUPLICATION		6633004	163801	73888	20	NEW_VARIANT
P-0003408-T01-IM5		PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (EP300-PTPRN2)		0	0	13	22	Intron of EP300(+): 14bp before exon 21	EP300	41558713			7	Intron of PTPRN2(-): 2Kb before exon 16	PTPRN2	157390026			29	TRANSLOCATION		0	11242	0	13	NEW_VARIANT
P-0013774-T01-IM5	MAP3K13 (NM_004721) rearrangement: chr3:g.139046929_c.428:MAP3K13inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		213538	0	11	3	IGR: 16Kb before MRPS22(+)	MRPS22	139046929			3	Exon 2 of MAP3K13(+)	MAP3K13	185146797			16	INVERSION		46099868	162186	268579	11	NEW_VARIANT
P-0013089-T01-IM5	SETD2 (NM_014159) Rearrangement : c.2025:SETD2_chr3:g.47250984del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		13897	0	23	3	Exon 3 of SETD2(-)	SETD2	47164101			3	5-UTR of FLJ39534(+): 35Kb before coding start	FLJ39534	47250984			34	DELETION		86883	160200	7448	15	NEW_VARIANT
P-0003613-T01-IM5	FGFR2 (NM_000141)  Rearrangement:  c.2301+149_g.123741897inv	PRECISE	Note: The FGFR2 rearrangement results in the inversion of exons 1 to 16 of FGFR2 .It includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	-		16428	0	4	10	Intron of FGFR2(-): 149bp after exon 16	FGFR2	123243063			10	IGR: 7Kb before TACC2(+)	TACC2	123741897			5	INVERSION		498834	12266	10817	4	NEW_VARIANT
P-0001278-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (EPHX3-NOTCH3)		26058	0	16	19	Exon 13 of NOTCH3(-)	NOTCH3	15296415			19	Intron of EPHX3(-): 1Kb before exon 6	EPHX3	15340016			39	DELETION		43601	72783	23676	16	NEW_VARIANT
P-0005190-T01-IM5	EMID1 (NM_133455) - EWSR1 (NM_013986) Rearrangement :  c.101+811:EMID1_c.794-373:EWSR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (EMID1-EWSR1)		17609	0	13	22	Intron of EMID1(+): 811bp after exon 1	EMID1	29602939			22	Intron of EWSR1(+): 165bp after exon 8	EWSR1	29687753			32	DELETION		84814	45466	22100	13	NEW_VARIANT
P-0010588-T01-IM5	ZFHX3 (NM_006885) rearrangement: c.-50+15973_c.4758del.	PRECISE	Note: The ZFHX3 rearrangement is an intragenic deletion of exons 2-9. One of the breakpoints is within exon9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		75283	0	34	16	Exon 9 of ZFHX3(-)	ZFHX3	72831823			16	5-UTR of ZFHX3(-): 72Kb before coding start	ZFHX3	73065678			51	DELETION		233855	147837	52755	34	NEW_VARIANT
P-0009356-T01-IM5	CA10 (NM_001082533) - STAT5A (NM_003152) rearrangement: c.280-87866:CA10_c.1146:STAT5Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CA10-STAT5A)		175636	0	40	17	Exon 10 of STAT5A(+)	STAT5A	40453449			17	Intron of CA10(-): 88Kb before exon 4	CA10	49913044			92	INVERSION		9459595	130250	157922	40	NEW_VARIANT
P-0012821-T01-IM5	VEGFA (NM_001171623) rearrangement : g.43797417_c.393-90:VEGFAdup	PRECISE	Note: The VEGFA (NM_001171623) rearrangement is a duplication which includes VEGFA exons 1-4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		16109	0	26	6	Intron of VEGFA(+): 90bp before exon 5	VEGFA	43746536			6	IGR: 59Kb before VEGFA(+)	VEGFA	43797417			21	DUPLICATION		50881	159020	20203	26	NEW_VARIANT
P-0007143-T02-IM5	TMPRSS2 (NM_001135099) rearrangement: t(4;21)(p15.1;q22.3)(chr4:g.29662732::chr21:g.42875074)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	55	21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875074			4	IGR: 1Mb before PCDH7(+)	PCDH7	29662732			0	TRANSLOCATION		0	158503	0	50	NEW_VARIANT
P-0014680-T01-IM6	PGR (NM_000926) - CCND1 (NM_053056) rearrangement: c.1906+67:PGR_c.-1379:CCND1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript fusion (PGR-CCND1)		220323	0	11	11	Promoter of CCND1(+): 1Kb from tx start	CCND1	69454703			11	Intron of PGR(-): 67bp after exon 3	PGR	100962424			12	INVERSION		31507721	165494	213195	11	NEW_VARIANT
P-0012317-T01-IM5	BSN (NM_003458) - RICTOR (NM_152756) Rearrangement : t(3;5)(p21.312;p13.1)(chr3:g49594666::chr5:g.38991280)	PRECISE	Note: The BSN - RICTOR Rearrangement results in the fusion of exon1 of BSN with exons 7-38 of RICTOR. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (BSN-RICTOR)		0	0	8	5	Intron of RICTOR(-): 103bp before exon 7	RICTOR	38991280			3	Intron of BSN(+): 2Kb after exon 1	BSN	49594666			2	TRANSLOCATION		0	157005	0	8	NEW_VARIANT
P-0001430-T01-IM3	None	PRECISE		AUTO_OK	3to5	3to5	Deletion of 1 exon: in frame		1665	0	10	11	Intron of CBL(+): 51bp after exon 8	CBL	119149058			11	Intron of CBL(+): 840bp after exon 9	CBL	119150263			20	DELETION		1205	2055	824	13	NEW_VARIANT
P-0006840-T01-IM5	DOCK7 (NM_033407) - JAK1 (NM_002227) rearrangement : c.6120-7503:DOCK7_c.483+17:JAK1del	PRECISE	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	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (JAK1-DOCK7)		50317	0	102	1	Intron of DOCK7(-): 8Kb before exon 48	DOCK7	62930879			1	Intron of JAK1(-): 17bp after exon 5	JAK1	65339036			79	DELETION		2408157	109385	30007	109	NEW_VARIANT
P-0006840-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		88678	0	102	21	Intron of ERG(-): 62Kb after exon 3	ERG	39885797			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872258			92	DELETION		2986461	109386	72989	143	NEW_VARIANT
P-0008752-T01-IM5	RB1 (NM_000321) Rearrangement :  t(13;17)(13q14.2;17p13.3)(chr13:g.48916707::chr17:g.3170417)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	40	17	IGR: 11Kb before OR3A2(-)	OR3A2	3170417			13	Intron of RB1(+): 28bp before exon 3	RB1	48916707			19	TRANSLOCATION		0	123762	0	33	NEW_VARIANT
P-0009325-T02-IM5	RAD51C (NM_058216) - DHX40 (NM_024612) rearrangement: c.1003:RAD51C_c.1901+399:DHX40del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (RAD51C-DHX40)		3021	0	35	17	Exon 8 of RAD51C(+)	RAD51C	56809882			17	Intron of DHX40(+): 399bp after exon 15	DHX40	57680376			47	DELETION		870494	136647	3146	33	NEW_VARIANT
P-0001903-T01-IM3		PRECISE		AUTO_OK	5to5	5to5	-		1028	0	6	9	5-UTR of SYK(+): 15Kb before coding start	SYK	93591197			9	Exon 2 of SYK(+)	SYK	93606313			36	INVERSION		15116	369	342	7	NEW_VARIANT
P-0003023-T01-IM3		PRECISE	TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 1)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		48198	0	6	21	Intron of ERG(-): 11Kb after exon 1	ERG	39859274			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874410			10	DELETION		3015136	7235	46920	7	NEW_VARIANT
P-0006090-T01-IM5	FLT1 (NM_002019)  Rearrangement :  c.3570_*451del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		7313	0	52	13	3-UTR of FLT1(-): 451bp after coding stop	FLT1	28876853			13	Exon 27 of FLT1(-)	FLT1	28885792			71	DELETION		8939	67589	3524	49	NEW_VARIANT
P-0010382-T01-IM5	TOP1 (NM_003286) rearrangement: c.1163+18_c.1308+706del	PRECISE	Note: The TOP1 rearrangement is an intragenic deletion of exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1565	0	22	20	Intron of TOP1(+): 18bp after exon 12	TOP1	39728901			20	Intron of TOP1(+): 706bp after exon 13	TOP1	39730699			32	DELETION		1798	145767	827	21	NEW_VARIANT
P-0005567-T01-IM5	POLE (NM_006231) Rearrangement :  c.6843:POLE_chr12:g.61019594inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		202479	0	32	12	IGR: 936Kb before SLC16A7(+)	SLC16A7	61019594			12	Exon 49 of POLE(-)	POLE	133201301			62	INVERSION		72181707	50881	203028	32	NEW_VARIANT
P-0003130-T01-IM5		PRECISE	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	MANUAL_OK	5to3	5to3	-		71737	1	17	12	Exon 11 of GLI1(+)	GLI1	57864464			12	IGR: 105Kb before TSPAN8(-)	TSPAN8	71414253			29	DUPLICATION		13549789	8723	70316	19	NEW_VARIANT
P-0011558-T01-IM5	EPHA3 (NM_005233) rearrangement: chr3:g.86628511_c.2467inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		21928	0	5	3	IGR: 359Kb before VGLL3(-)	VGLL3	86628511			3	Exon 14 of EPHA3(+)	EPHA3	89498495			8	INVERSION		2869984	155677	19685	5	NEW_VARIANT
P-0010812-T01-IM5	TSC2 (NM_000548) - PKD1 (NM_001009944) rearrangement : c.4662+1:TSC2_c.3162-137:PKD1del	PRECISE	Note: The TSC2 - PKD1 rearrangement event results in the deletion of TSC2 exons 35-40. One of the breakpoints is on exon35 splice site.	MANUAL_OK	3to5	3to5	Antisense fusion		11851	0	6	16	Intron of TSC2(+): 1bp after exon 35	TSC2	2135324			16	Intron of PKD1(-): 137bp before exon 14	PKD1	2162611			6	DELETION		27287	149293	7915	3	NEW_VARIANT
P-0013772-T01-IM5	ANXA10 (NM_007193) - FAT1 (NM_005245) rearrangement: c.19-6085:ANXA10_c.5713:FAT1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (ANXA10-FAT1)		98043	0	21	4	Intron of ANXA10(+): 6Kb before exon 2	ANXA10	169043150			4	Exon 10 of FAT1(-)	FAT1	187542027			32	INVERSION		18498877	162207	92033	15	NEW_VARIANT
P-0005984-T01-IM5	BRCA1 (NM_007294) -  PROCA1 (NM_152465) rearrangement: c.1574:BRCA1_c.92-1069:PROCA1inv.	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		464462	0	31	17	Intron of PROCA1(-): 1Kb before exon 2	PROCA1	27032930			17	Exon 10 of BRCA1(-)	BRCA1	41245974			79	INVERSION		14213044	66884	440103	31	NEW_VARIANT
P-0008516-T01-IM5	KDM6A (NM_021140) Rearrangement :  c.998_1780dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		9135	0	11	X	Exon 12 of KDM6A(+)	KDM6A	44918515			X	Exon 16 of KDM6A(+)	KDM6A	44922919			31	DUPLICATION		4404	122532	6307	11	NEW_VARIANT
P-0011303-T01-IM5	STK11 (NM_000455) rearrangement: c.375-384_c.735-5dup	PRECISE	Note: The STK11 rearrangement is an intragenic duplication of exons 3-5.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: in frame		12348	0	65	19	Intron of STK11(+): 384bp before exon 3	STK11	1218939			19	Intron of STK11(+): 5bp before exon 6	STK11	1221207			75	DUPLICATION		2268	152549	11202	59	NEW_VARIANT
P-0006402-T01-IM5	KDR (NM_002253) rearrangement : c.1255+49_*5959inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		61773	0	33	4	IGR: 4Kb before KDR(-)	KDR	55940149			4	Intron of KDR(-): 49bp after exon 9	KDR	55976521			46	INVERSION		36372	92289	49507	32	NEW_VARIANT
P-0001286-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Deletion of 8 exons: out of frame		13144	0	5	22	Intron of EP300(+): 1Kb before exon 3	EP300	41520433			22	Intron of EP300(+): 157bp before exon 11	EP300	41542586			8	DELETION		22153	72820	9044	6	NEW_VARIANT
P-0003052-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		42536	0	11	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875748			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872061			29	DELETION		2996313	7305	33047	12	NEW_VARIANT
P-0011331-T01-IM5	BRIP1 (NM_032043) Rearrangement :  c.2575+2706_c.3570del	PRECISE	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,	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		8930	0	6	17	Exon 20 of BRIP1(-)	BRIP1	59760837			17	Intron of BRIP1(-): 3Kb after exon 18	BRIP1	59768085			3	DELETION		7248	153184	9565	6	NEW_VARIANT
P-0011331-T01-IM5	TERT (NM_198253) Rearrangement :  chr5:g.23741_c.2287-76:TERTinv	PRECISE	Note: The TERT Rearrangement  results in the inversion of  exons7-16 of TERT .Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		35790	0	12	5	IGR: 117Kb before PLEKHG4B(+)	PLEKHG4B	23741			5	Intron of TERT(-): 76bp before exon 7	TERT	1272471			29	INVERSION		1248730	153186	42340	5	NEW_VARIANT
P-0004892-T01-IM5	ATAD1 (NM_032810) - PTEN (NM_000314) rearrangement: c.583+1858:ATAD1_NM_000314.4:c.960:PTENdel	PRECISE	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)	MANUAL_OK	3to5	3to5	-		10156	0	29	10	Intron of ATAD1(-): 2Kb after exon 5	ATAD1	89542369			10	Exon 8 of PTEN(+)	PTEN	89720809			32	DELETION		178440	40324	6209	15	NEW_VARIANT
P-0004892-T01-IM5	BRCA2 (NM_000059) rearrangement: t(13;11)(q13;p15.2)(chr13:g.32893422::chr11:g.11:15549664)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	16	13	Exon 3 of BRCA2(+)	BRCA2	32893422			11	IGR: 413Kb before INSC(+)	INSC	15549664			26	TRANSLOCATION		0	40329	0	16	NEW_VARIANT
P-0007700-T01-IM5	AXL (NM_021913) rearrangement: c.256:AXL_chr19:g.53878345inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		293564	0	31	19	Exon 2 of AXL(+)	AXL	41726711			19	5-UTR of ZNF525(+): 11Kb before coding start	ZNF525	53878345			38	INVERSION		12151634	118122	267209	29	NEW_VARIANT
P-0000632-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	20	6	Intron of ROS1(-): 735bp before exon 34	ROS1	117646313			5	Intron of CD74(-): 408bp before exon 7	CD74	149783283			32	TRANSLOCATION		0	71730	0	0	NEW_VARIANT
P-0012122-T01-IM5	RAD51C (NM_058216) - BCAS3 (NM_001099432) Rearrangement : c.1026+48:RAD51C_c.215-6649:BCAS3inv	PRECISE	Note: The RAD51C -BCAS3  Rearrangement results in the inversion of exon9 of RAD51C. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		37233	0	23	17	Intron of RAD51C(+): 48bp after exon 8	RAD51C	56809953			17	Intron of BCAS3(+): 7Kb before exon 5	BCAS3	58779931			31	INVERSION		1969978	156322	58614	23	NEW_VARIANT
P-0004708-T01-IM5	LATS2 (NM_014572) rearrangement : c.343-7641_1003del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6032	0	14	13	Exon 4 of LATS2(-)	LATS2	21562916			13	Intron of LATS2(-): 8Kb before exon 3	LATS2	21573184			24	DELETION		10268	34621	4719	14	NEW_VARIANT
P-0004113-T01-IM5	TP53 (NM_000546) rearrangement event: c.994-497_1101-80inv	PRECISE	Note: The TP53 rearrangement event results in the intragenic inversion of TP53 exon10.	MANUAL_OK	3to3	3to3	-		2297	0	7	17	Intron of TP53(-): 80bp before exon 11	TP53	7573088			17	Intron of TP53(-): 497bp before exon 10	TP53	7574530			8	INVERSION		1442	14626	1695	6	NEW_VARIANT
P-0012683-T01-IM5	CTNNB1 (NM_001904) rearrangement: c.-48-1917_c.690inv	PRECISE	Note: The CTNNB1 rearrangement is an inversion of exons 1-5. One of the breakpoints is within exon5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		11367	0	15	3	5-UTR of CTNNB1(+): 2Kb before coding start	CTNNB1	41263595			3	Exon 5 of CTNNB1(+)	CTNNB1	41267019			19	INVERSION		3424	158551	9135	13	NEW_VARIANT
P-0005879-T01-IM5	RGS9  (NM_003835) - STAT3 (NM_139276) Rearrangement :  c.1203+101:RGS9_c.1520:STAT3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (RGS9-STAT3)		285002	0	90	17	Exon 17 of STAT3(-)	STAT3	40476809			17	Intron of RGS9(+): 101bp after exon 15	RGS9	63200520			70	INVERSION		22723711	64292	318633	86	NEW_VARIANT
P-0007971-T01-IM5	ARID5B (NM_032199) rearrangement : t(10;14)(q21.2;q21.2)(chr10:.g.63851226::chr14:g.44208017 )	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	86	14	IGR: 765Kb before FSCB(-)	FSCB	44208017			10	Exon 10 of ARID5B(+)	ARID5B	63851226			24	TRANSLOCATION		0	119804	0	84	NEW_VARIANT
P-0007971-T01-IM5	FANCC (NM_000136) rearrangement: c.686+3158_843+10del	PRECISE	Note: The FANCC (NM_000136) rearrangement event results in the intragenic deletion of FANCC exon8.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1452	0	6	9	Intron of FANCC(-): 10bp after exon 8	FANCC	97897618			9	Intron of FANCC(-): 3Kb after exon 7	FANCC	97909047			9	DELETION		11429	119799	1096	6	NEW_VARIANT
P-0009469-T01-IM5	CDH1 (NM_004360) Rearrangement : c.303_387+2011del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		628	0	7	16	Exon 3 of CDH1(+)	CDH1	68835712			16	Intron of CDH1(+): 2Kb after exon 3	CDH1	68837807			26	DELETION		2095	130829	610	7	NEW_VARIANT
P-0007037-T01-IM5	PBRM1 (NM_018313) rearrangement :  c.171_237-643dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		964	0	15	3	Intron of PBRM1(-): 643bp before exon 4	PBRM1	52703304			3	Exon 3 of PBRM1(-)	PBRM1	52712581			35	DUPLICATION		9277	112817	1114	15	NEW_VARIANT
P-0005176-T01-IM5	PTEN (NM_000314) rearrangement: c.209+2245_c.853dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		3435	0	14	10	Intron of PTEN(+): 2Kb after exon 3	PTEN	89687559			10	Exon 8 of PTEN(+)	PTEN	89720702			13	DUPLICATION		33143	45262	3857	12	NEW_VARIANT
P-0005176-T01-IM5	RB1 (NM_000321) rearrangement: c.940-8_c.1695+7932dup	PRECISE	The RB1 (NM_000321) rearrangement is an intragenic duplication of exons 10-17. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 8 exons: in frame		6011	0	60	13	Intron of RB1(+): 8bp before exon 10	RB1	48941622			13	Intron of RB1(+): 8Kb after exon 17	RB1	48963511			44	DUPLICATION		21889	45263	7560	56	NEW_VARIANT
P-0005176-T01-IM5	EP300 (NM_001429) rearrangement: c.3551_c.3672-734dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		775	0	31	22	Exon 19 of EP300(+)	EP300	41554465			22	Intron of EP300(+): 734bp before exon 21	EP300	41557993			31	DUPLICATION		3528	45264	1259	31	NEW_VARIANT
P-0005428-T01-IM5	TMPRSS2 (NM_001135099) Rearrangement : t(21;3)(q22.3;q27.3)(chr21:g.42874720::chr3:g.186488282)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	29	21	Intron of TMPRSS2(-): 5Kb before exon 2	TMPRSS2	42874720			3	IGR: 13Kb before EIF4A2(+)	EIF4A2	186488282			24	TRANSLOCATION		0	48888	0	29	NEW_VARIANT
P-0011284-T01-IM5	NF1 (NM_001042492) rearrangement: c.-1819_c.-84del	PRECISE	Note: The NF1 rearrangement is a deletion of the 5UTR and promoter region of NF1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		71	0	5	17	Promoter of NF1(+): 1Kb from tx start	NF1	29420509			17	5-UTR of NF1(+): 84bp before coding start	NF1	29422244			6	DELETION		1735	152419	101	5	NEW_VARIANT
P-0008682-T01-IM5	PTEN (NM_000314) rearrangement :  c.493-150_ 878inv	PRECISE	Note: The PTEN (NM_000314) rearrangement event results in the inversion of PTEN exons 6-8. One of the breakpoints is within PTEN exon8.	MANUAL_OK	3to3	3to3	Antisense fusion		2343	0	13	10	Intron of PTEN(+): 150bp before exon 6	PTEN	89711725			10	Exon 8 of PTEN(+)	PTEN	89720727			25	INVERSION		9002	123417	2990	10	NEW_VARIANT
P-0006905-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) reciprocal fusion (TMPRSS exon1 fused with ERG exons 4-11) : c.56-1143:TMPRSS2_c.40-62829:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		77606	0	102	21	Intron of ERG(-): 63Kb before exon 4	ERG	39880373			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871259			79	DELETION		2990886	109817	68157	96	NEW_VARIANT
P-0006905-T01-IM5	TMPRSS2 (NM_001135099) rearrangement : c.56-1098_349+1397inv	PRECISE	Note: The TMPRSS2 (NM_001135099) rearrangement event results in the intragenic inversion of TMPRSS2 exons 2-3.	MANUAL_OK	3to3	3to3	-		41434	0	102	21	Intron of TMPRSS2(-): 1Kb after exon 3	TMPRSS2	42864886			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871214			87	INVERSION		6328	109821	26554	133	NEW_VARIANT
P-0004981-T01-IM5	ERG (NM_182918) rearrangement: t(12;21)(q24.33;q13.1)(chr12:g.130616610::chr21:g.39755710)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	66	21	Exon 11 of ERG(-)	ERG	39755710			12	IGR: 30Kb before FZD10(+)	FZD10	130616610			37	TRANSLOCATION		0	41853	0	65	NEW_VARIANT
P-0006611-T01-IM5	STAG2 (NM_001042749) - KCNJ15 (NM_170737) rearrangement : t(X;21)(q25;q22.13)(chrX:g.123164894::chr21:g.39629841)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	42	X	Exon 4 of STAG2(+)	STAG2	123164894			21	5-UTR of KCNJ15(+): 41Kb before coding start	KCNJ15	39629841			23	TRANSLOCATION		0	107407	0	41	NEW_VARIANT
P-0003536-T02-IM5	TSHZ3 (NM_020856) - AKT2 (NM_001626) rearrangement: c.41-819:TSHZ3_c.574-15:AKT2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TSHZ3-AKT2)		40880	0	8	19	Intron of TSHZ3(-): 819bp before exon 2	TSHZ3	31771477			19	Intron of AKT2(-): 15bp before exon 7	AKT2	40746032			10	DUPLICATION		8974555	112466	36150	8	NEW_VARIANT
P-0010465-T01-IM5	FGFR3 (NM_000142) - WHSC1 (NM_001042424) rearrangement:c.1959+17:FGFR3_c.-29-12740:WHSC1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (FGFR3-WHSC1)		8075	0	22	4	Intron of FGFR3(+): 17bp after exon 14	FGFR3	1807917			4	5-UTR of WHSC1(+): 13Kb before coding start	WHSC1	1889613			36	DELETION		81696	146084	8034	22	NEW_VARIANT
P-0010465-T01-IM5	E2F3 (NM_001949) rearrangement: c.87_c.393+25392del	PRECISE	Note: The E2F3 rearrangement is an intragenic deletion of exon1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1082	0	12	6	Exon 1 of E2F3(+)	E2F3	20402550			6	Intron of E2F3(+): 25Kb after exon 1	E2F3	20428248			13	DELETION		25698	146085	1043	11	NEW_VARIANT
P-0004346-T01-IM5	NOTCH4 (NM_004557) - C6orf10 (NM_006781) rearrangement: c.4557:NOTCH4_c.638-666:C6orf10dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NOTCH4-C6orf10)		36870	0	7	6	Exon 25 of NOTCH4(-)	NOTCH4	32166486			6	Intron of C6orf10(-): 665bp before exon 11	C6orf10	32262478			13	DUPLICATION		95992	19286	24028	6	NEW_VARIANT
P-0002630-T01-IM3		PRECISE	RUNX1 duplication is a structural rearrangement event in which exons 3 and 4 are duplicated. Its functional significance is not determined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		3336	0	29	21	Intron of RUNX1(-): 15bp after exon 4	RUNX1	36206692			21	Intron of RUNX1(-): 10Kb after exon 2	RUNX1	36242387			51	DUPLICATION		35695	4301	5304	35	NEW_VARIANT
P-0013498-T01-IM5	PAK1 (NM_002576) rearrangement: c.1552-1074_c.*11inv	IMPRECISE	Note: The PAK1 rearrangement is an inversion of exon 15.	MANUAL_OK	3to3	3to3	-		713	0	59	11	3-UTR of PAK1(-): 11bp after coding stop	PAK1	77034308			11	Intron of PAK1(-): 894bp after exon 15	PAK1	77035479			0	INVERSION		1171	161428	1173	49	NEW_VARIANT
P-0013498-T01-IM5	B2M (NM_004048) rearrangement: c.346_c.*15-3del	PRECISE	Note: The B2M rearrangement is a deletion of exons 2-3. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		1878	0	30	15	Exon 2 of B2M(+)	B2M	45007899			15	3-UTR of B2M(+): 1Kb after coding stop	B2M	45009802			22	DELETION		1903	161427	1916	29	NEW_VARIANT
P-0002792-T01-IM3		PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	33	17	3-UTR of BRCA1(-): 304bp after coding stop	BRCA1	41197391			15	Exon 7 of SMAD3(+)	SMAD3	67477119			72	TRANSLOCATION		0	5574	0	33	NEW_VARIANT
P-0013050-T01-IM5	CHEK2 (NM_007194) rearrangement: t(10;22)(q11.22;q12.1)(chr10:g.49868405::chr22:g.29093021)	PRECISE	Note: The CHEK2 rearrangement is a translocation with a breakpoint within intron 9 of CHEK2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	24	22	Intron of CHEK2(-): 46bp before exon 10	CHEK2	29093021			10	IGR: 25Kb before WDFY4(+)	WDFY4	49868405			11	TRANSLOCATION		0	160053	0	23	NEW_VARIANT
P-0005070-T01-IM5	POLE (NM_006231)  Rearrangement:  c.6658-243_4728+8inv	PRECISE	Note: The POLE (NM_006231)  Rearrangement results in the intragenic inversion of exons 37 to 47.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		22740	0	25	12	Intron of POLE(-): 243bp before exon 48	POLE	133201823			12	Intron of POLE(-): 8bp after exon 36	POLE	133219398			56	INVERSION		17575	42742	18040	26	NEW_VARIANT
P-0008852-T01-IM5	BMPR1A (NM_004329) rearrangement: c.-267-34168_c.91inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		1355	0	17	10	5-UTR of BMPR1A(+): 71Kb before coding start	BMPR1A	88564454			10	Exon 4 of BMPR1A(+)	BMPR1A	88649842			61	INVERSION		85388	124536	967	9	NEW_VARIANT
P-0005862-T01-IM5	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.	PRECISE	The  FGFR3 (NM_000142) - TACC3 (NM_006342) fusion is in frame and includes the kinase domain of FGFR3.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-TACC3)		20148	0	27	4	Intron of TACC3(+): 896bp after exon 13	TACC3	1743609			4	Intron of FGFR3(+): 46bp after exon 17	FGFR3	1808707			38	DUPLICATION		65098	62721	25195	27	NEW_VARIANT
P-0008929-T01-IM5	CTNNB1 (NM_001904) Rearrangement : c.13+97_242-92del	PRECISE	Note: The CTNNB1 (NM_001904) Rearrangement  results in the deletion of exon3 of CTNNB1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		4221	0	22	3	Intron of CTNNB1(+): 97bp after exon 2	CTNNB1	41265669			3	Intron of CTNNB1(+): 92bp before exon 4	CTNNB1	41266353			25	DELETION		684	125075	2297	20	NEW_VARIANT
P-0009346-T01-IM5	ARID2 (NM_152641) rearrangement : t(12;20)(q12;q12)(chr12:g.46230848::chr20:g.38766766)	IMPRECISE	Note: The ARID2 (NM_152641) rearrangement event is a translocation which results in the truncation of ARID2 exons 9-21.	MANUAL_OK	5to3	5to3	-		0	0	13	20	IGR: 548Kb before MAFB(-)	MAFB	38766766			12	Intron of ARID2(+): 74bp after exon 8	ARID2	46230848			0	TRANSLOCATION		0	130234	0	13	NEW_VARIANT
P-0009393-T01-IM5	CREBBP (NM_004380) rearrangement: c.85+13476_c.161del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		358	0	18	16	Exon 2 of CREBBP(-)	CREBBP	3900935			16	Intron of CREBBP(-): 13Kb after exon 1	CREBBP	3916357			44	DELETION		15422	130433	213	18	NEW_VARIANT
P-0003665-T01-IM5	c.464-7460:ETV6_chr12:g.12175381inv	PRECISE	Note: The ETV6 (NM_001987) rearrangement event results in the inversion of exons 5 to 8.	MANUAL_OK	5to5	5to5	-		130597	0	47	12	Intron of ETV6(+): 7Kb before exon 5	ETV6	12014898			12	IGR: 48Kb before BCL2L14(+)	BCL2L14	12175381			56	INVERSION		160483	12412	120760	47	NEW_VARIANT
P-0009985-T01-IM5	MSH6 (NM_000179) Rearrangement :  chr2:g.47072226_ c.2515:MSH6inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		76192	0	14	2	5-UTR of LOC100134259(+): 14Kb before coding start	LOC100134259	47072226			2	Exon 4 of MSH6(+)	MSH6	48027637			18	INVERSION		955411	137425	89092	14	NEW_VARIANT
P-0005109-T01-IM5	BRAF (NM_004333) rearrangement: c.504+6767_c.1140+2849del	PRECISE	The BRAF (NM_004333) rearrangement is an intragenic deletion of exons 4-8, including the RAS-binding domain.	MANUAL_OK	3to5	3to5	Deletion of 5 exons: in frame		50127	0	45	7	Intron of BRAF(-): 3Kb after exon 8	BRAF	140491259			7	Intron of BRAF(-): 7Kb after exon 3	BRAF	140527642			47	DELETION		36383	43327	57206	42	NEW_VARIANT
P-0003541-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_001136154) fusion : c.127-1068:TMPRSS2_c.40-44654:ERGdel	PRECISE	Known fusion, TMPRSS2 exon 3 fused to ERG exon 2	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		29594	0	63	21	Intron of ERG(-): 8Kb after exon 1	ERG	39862198			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867573			83	DELETION		3005375	11900	26125	68	NEW_VARIANT
P-0004999-T01-IM5	STAG2(NM_001042749)  Rearrangement : c.2026-10:STAG2_chrX:g.130653015	PRECISE	Note: The STAG2(NM_001042749)  Rearrangement results in the inversion of exons 21 to 35 of STAG2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		28456	0	17	X	Intron of STAG2(+): 10bp before exon 20	STAG2	123199716			X	IGR: 25Kb before OR13H1(+)	OR13H1	130653015			12	INVERSION		7453299	41686	26673	17	NEW_VARIANT
P-0004999-T01-IM5	STAT3(NM_139276) Rearrangement  : t(17;13)(17q21.2;13p12.3)(chr17:g.40490706::chr13:g.31343786)	PRECISE	Note: The STAT3(NM_139276) Rearrangement results in translocation of exons 7-24 of STAT3. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	12	17	Intron of STAT3(-): 43bp after exon 6	STAT3	40490706			13	IGR: 5Kb after ALOX5AP(+)	ALOX5AP	31343786			8	TRANSLOCATION		0	41689	0	12	NEW_VARIANT
P-0003097-T01-IM5		PRECISE	FGFR3 (NM_000142) exons 1-17 fused to TACC3 (NM_006342) exons 6-16	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-TACC3)		25075	0	73	4	Intron of TACC3(+): 45bp before exon 6	TACC3	1732854			4	Intron of FGFR3(+): 2bp before exon 18	FGFR3	1808841			94	DUPLICATION		75987	8278	26784	78	NEW_VARIANT
P-0010809-T01-IM5	NCOA3 (NM_181659) rearrangement: c.2512+456_ 2946del	PRECISE	Note: The NCOA3 rearrangement event results in the intragenic deletion of NCOA3 exons 14-15.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		9249	0	32	20	Intron of NCOA3(+): 456bp after exon 13	NCOA3	46266983			20	Exon 15 of NCOA3(+)	NCOA3	46268559			40	DELETION		1576	149275	7447	32	NEW_VARIANT
P-0010075-T01-IM5	RB1 (NM_000321) Rearrangement : chr13:g.24150799_c.265-55:RB1del	PRECISE	Note: The RB1  Rearrangement results in the deletion of   exons1-2 of RB1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript fusion (TNFRSF19-RB1)		232838	0	8	13	5-UTR of TNFRSF19(+): 14Kb before coding start	TNFRSF19	24150799			13	Intron of RB1(+): 55bp before exon 3	RB1	48916680			10	DELETION		24765881	137840	226270	8	NEW_VARIANT
P-0009819-T01-IM5	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	PRECISE	Note: The TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		30257	0	3	21	Intron of ERG(-): 367bp after exon 1	ERG	39869920			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867985			15	DELETION		2998065	136636	23294	3	NEW_VARIANT
P-0007842-T01-IM5	FAR2 (NM_018099) - KDR (NM_002253.2) translocation : t(12,4)(p11.22; q12)(chr12:g.29059026::chr4:g.55970822)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	14	12	IGR: 318Kb before FAR2(+)	FAR2	29059026			4	Exon 13 of KDR(-)	KDR	55970822			10	TRANSLOCATION		0	119334	0	13	NEW_VARIANT
P-0007014-T01-IM5	RAD51C (NM_058216) rearrangement: t(17;20)(q22;q13.2)(chr17:g.56809889::chr20:g.50920486)	PRECISE	The RAD51C (NM_058216) rearrangement is a translocation which may result in the truncation of RAD51C. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	102	20	IGR: 153Kb before ZFP64(-)	ZFP64	50920486			17	Exon 8 of RAD51C(+)	RAD51C	56809889			29	TRANSLOCATION		0	112653	0	102	NEW_VARIANT
P-0012986-T01-IM5	RB1 (NM_00032) rearrangement: c.2335_ chr13:g.49107711dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		5499	0	54	13	Exon 23 of RB1(+)	RB1	49039350			13	Promoter of RCBTB2(-): 395bp from tx start	RCBTB2	49107711			80	DUPLICATION		68361	159807	4554	54	NEW_VARIANT
P-0000386-T02-IM5	MARVELD3 (NM_001017967) - FGFR2 (NM_000141) rearrangement: t(16;10)(16q22.2;10q26.13) (chr16:g.71660650::chr10:123243101)	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		0	0	23	16	Intron of MARVELD3(+): 51bp after exon 1	MARVELD3	71660650			10	Intron of FGFR2(-): 111bp after exon 16	FGFR2	123243101			25	TRANSLOCATION		0	13891	0	0	NEW_VARIANT
P-0010979-T02-IM5	TBX3 (NM_016569) rearrangement: c.-74_chr12:g.115414371del	PRECISE	Note: The TBX3 rearrangement is a deletion of the 5'UTR of TBX3. The functional significance undetermined.	MANUAL_OK	3to5	3to5	-		136	0	26	12	5-UTR of TBX3(-): 74bp before coding start	TBX3	115121079			12	IGR: 306Kb before TBX3(-)	TBX3	115414371			20	DELETION		293292	156353	162	25	NEW_VARIANT
P-0008838-T01-IM5	IFNGR1 (NM_000416) rearrangement : c.1311:IFNGR1_chr6:g.137953996inv	PRECISE	Note: The IFNGR1 (NM_000416) rearrangement event results in the inversion of IFNGR1 exons 1-7. One of the breakpoints is within IFNGR1 exon7.	MANUAL_OK	3to3	3to3	-		13305	0	5	6	Exon 7 of IFNGR1(-)	IFNGR1	137519327			6	IGR: 141Kb before OLIG3(-)	OLIG3	137953996			20	INVERSION		434669	124502	14599	5	NEW_VARIANT
P-0011348-T01-IM5	NR3C2 (NM_000901) - TET2 (NM_001127208) rearrangement: c.1757+79314:NR3C2_c.359:TET2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (NR3C2-TET2)		83074	0	9	4	Exon 3 of TET2(+)	TET2	106155458			4	Intron of NR3C2(-): 79Kb after exon 2	NR3C2	149276942			15	INVERSION		43121484	153248	98713	9	NEW_VARIANT
P-0014755-T01-IM6	ELF3 (NM_004433) rearrangement: c.-8-162_c.382dup	PRECISE	Note: The ELF3 rearrangement is an intragenic duplication with breakpoints in the 5UTR and exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		4973	0	9	1	5-UTR of ELF3(+): 170bp before coding start	ELF3	201980095			1	Exon 3 of ELF3(+)	ELF3	201981303			13	DUPLICATION		1208	165713	5993	9	NEW_VARIANT
P-0009106-T01-IM5	KIT (NM_000222) - KDR (NM_002253) rearrangement: c.620-145:KIT_c.-115:KDRdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		105844	0	5	4	Intron of KIT(+): 145bp before exon 4	KIT	55565651			4	5-UTR of KDR(-): 115bp before coding start	KDR	55991575			14	DUPLICATION		425924	126633	171570	5	NEW_VARIANT
P-0012142-T01-IM5	PIK3R1 (NM_181523) rearrangement: t(5;8)(q13.1;q21.13)(chr5:g.67589202::chr8:g.82618895)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	32	8	Intron of ZFAND1(-): 4Kb before exon 7	ZFAND1	82618895			5	Exon 4 of PIK3R1(+)	PIK3R1	67589202			9	TRANSLOCATION		0	156484	0	32	NEW_VARIANT
P-0012566-T01-IM5	FAT1 (NM_005245) rearrangement: c.3265+14735_c.4184-6del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 3-6.	MANUAL_OK	3to5	3to5	Deletion of 4 exons: in frame		9014	0	9	4	Intron of FAT1(-): 6bp before exon 7	FAT1	187554983			4	Intron of FAT1(-): 15Kb after exon 2	FAT1	187612982			13	DELETION		57999	157825	8053	9	NEW_VARIANT
P-0000447-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		457	0	21	10	Intron of PTEN(+): 938bp after exon 7	PTEN	89718714			10	Exon 8 of PTEN(+)	PTEN	89720711			38	DUPLICATION		1997	71452	291	14	NEW_VARIANT
P-0004827-T01-IM5	TP53 (NM_000546) rearrangement : c.-28-1339_97-1del	PRECISE	Note: The TP53 (NM_000546) rearrangement event results in the intragenic deletion of TP53 exons 2-3.	MANUAL_OK	3to5	3to5	Deletion within transcript		3850	0	20	17	Intron of TP53(-): 1bp before exon 4	TP53	7579591			17	5-UTR of TP53(-): 1Kb before coding start	TP53	7581279			25	DELETION		1688	35712	3681	19	NEW_VARIANT
P-0004827-T01-IM5	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement : c.590+39:XPO1_c.8840+827:USP34del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (XPO1-USP34)		31492	0	15	2	Intron of USP34(-): 827bp after exon 69	USP34	61438080			2	Intron of XPO1(-): 39bp after exon 7	XPO1	61726809			19	DELETION		288729	35713	26278	15	NEW_VARIANT
P-0005855-T01-IM5	HIST1H3B (NM_003537) rearrangement: c.103:HIST1H3B_chr:6g.26025427dup	PRECISE	The HIST1H3B (NM_003537) rearrangement is a duplication of HIST1H3B. One of the breakpoints is within exon1 of HIST1H3B. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		6212	0	43	6	IGR: 2Kb before HIST1H4B(-)	HIST1H4B	26025427			6	Exon 1 of HIST1H3B(-)	HIST1H3B	26032186			80	DUPLICATION		6759	62817	8545	37	NEW_VARIANT
P-0005855-T01-IM5	PAX5 (NM_016734) rearrangement: c.781-5874_c.866dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		593	0	23	9	Exon 7 of PAX5(-)	PAX5	36923396			9	Intron of PAX5(-): 6Kb before exon 7	PAX5	36929355			34	DUPLICATION		5959	62821	580	20	NEW_VARIANT
P-0010984-T01-IM5	MLL (NM_001197104) rearrangement: c.6080-93_c.10835+329dup	IMPRECISE	Note: The MLL rearrangement is an intragenic duplication of exons 24-28. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: out of frame		55289	0	11	11	Intron of MLL(+): 93bp before exon 24	MLL	118370457			11	Intron of MLL(+): 329bp after exon 28	MLL	118378653			0	DUPLICATION		8196	150034	68474	9	NEW_VARIANT
P-0010984-T01-IM5	SLC4A4 (NM_001134742) - ROS1 (NM_002944) rearrangement: t(4;6)(q13.3;q22.1)(chr4:g.72429843::chr6:g.117646719)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SLC4A4-ROS1)		0	0	54	6	Intron of ROS1(-): 668bp after exon 33	ROS1	117646719			4	Intron of SLC4A4(+): 237bp after exon 24	SLC4A4	72429843			34	TRANSLOCATION		0	150038	0	52	NEW_VARIANT
P-0004967-T01-IM5	TSC2 (NM_000548) rearrangement : c.2639+10_2913del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6443	0	102	16	Intron of TSC2(+): 10bp after exon 23	TSC2	2125903			16	Exon 26 of TSC2(+)	TSC2	2127674			143	DELETION		1771	41539	4119	154	NEW_VARIANT
P-0007852-T02-IM5	TERT (NM_198253) rearrangement : c.2970+5:TERT_chr5:g.32544184del	PRECISE	Note: The TERT (NM_198253) rearrangement event results in the deletion of TERT exons 1-12.	MANUAL_OK	3to5	3to5	-		83356	0	15	5	Intron of TERT(-): 5bp after exon 12	TERT	1260584			5	IGR: 41Kb before SUB1(+)	SUB1	32544184			31	DELETION		31283600	118797	121682	15	NEW_VARIANT
P-0007852-T02-IM5	CDH12 (NM_004061) rearrangement : c.815-7428:CDH1_chr5:g.34625690inv	PRECISE	Note: The CDH12 (NM_004061) rearrangement event results in the inversion of CDH12 exons 1-8.	MANUAL_OK	5to5	5to5	-		28558	0	19	5	Intron of CDH12(-): 7Kb before exon 9	CDH12	21824669			5	IGR: 31Kb before RAI14(+)	RAI14	34625690			31	INVERSION		12801021	118798	35870	20	NEW_VARIANT
P-0003625-T01-IM5		PRECISE	The ANKRD11 (NM_013275) duplication is a rearrangement event which results in the intragenic duplication of exons 3-9.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		80348	0	23	16	Exon 9 of ANKRD11(-)	ANKRD11	89346182			16	5-UTR of ANKRD11(-): 129Kb before coding start	ANKRD11	89512768			25	DUPLICATION		166586	12320	56971	23	NEW_VARIANT
P-0009728-T01-IM5	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	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		39743	0	57	21	Intron of ERG(-): 53Kb before exon 4	ERG	39870493			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867606			57	DELETION		2997113	136177	35747	53	NEW_VARIANT
P-0001044-T01-IM3	None	PRECISE		MANUAL_OK	3to3	3to3	Antisense fusion		17148	0	14	17	Intron of NF1(+): 27Kb before exon 36	NF1	29626304			17	Exon 41 of NF1(+)	NF1	29663799			28	INVERSION		37495	72293	11827	8	NEW_VARIANT
P-0005529-T01-IM5	EZH2 (NM_004456) - CUL1 (NM_003592) rearrangement: c.2029+34:EZH2_c.1808:CUL1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		5231	0	23	7	Exon 17 of CUL1(+)	CUL1	148489819			7	Intron of EZH2(-): 34bp after exon 17	EZH2	148507391			41	DELETION		17572	50136	4360	23	NEW_VARIANT
P-0010264-T01-IM5	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)	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (ETV6-NTRK3)		0	0	40	15	Intron of NTRK3(-): 12Kb before exon 13	NTRK3	88588255			12	Intron of ETV6(+): 7Kb before exon 5	ETV6	12014962			13	TRANSLOCATION		0	145116	0	34	NEW_VARIANT
P-0011276-T01-IM5	ASXL1 (NM_015338) rearrangement: c.253-19600_c.572dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		9928	0	32	20	Intron of ASXL1(+): 20Kb before exon 4	ASXL1	30996331			20	Exon 7 of ASXL1(+)	ASXL1	31017710			60	DUPLICATION		21379	152457	11489	32	NEW_VARIANT
P-0009328-T01-IM5	PAK1 (NM_002576) rearrangement : c.-21-5812_292-11del	PRECISE	Note: The PAK1 (NM_002576) rearrangement event results in the deletion of PAK1 exons 2-3.	MANUAL_OK	3to5	3to5	Deletion within transcript		6538	0	14	11	Intron of PAK1(-): 11bp before exon 4	PAK1	77090444			11	5-UTR of PAK1(-): 6Kb before coding start	PAK1	77109398			19	DELETION		18954	130103	8412	14	NEW_VARIANT
P-0009328-T01-IM5	EPCAM (NM_002354) - NRXN1 (NM_004801) rearrangement : c.540:EPCAM_c.832+71570:NRXN1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		122322	0	24	2	Exon 5 of EPCAM(+)	EPCAM	47604201			2	Intron of NRXN1(-): 72Kb after exon 5	NRXN1	51077437			23	DELETION		3473236	130105	176225	24	NEW_VARIANT
P-0013882-T01-IM5	CREBBP (NM_004380) rearrangement: c.975+679_c.6669del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		57095	0	5	16	Exon 31 of CREBBP(-)	CREBBP	3778379			16	Intron of CREBBP(-): 679bp after exon 3	CREBBP	3859925			2	DELETION		81546	162604	39334	5	NEW_VARIANT
P-0006711-T01-IM5	ETV6 (NM_001987) rearrangement: c.164-19692_c.464-1622dup	PRECISE	The ETV6 (NM_001987) rearrangement is an intragenic in frame duplication of exons 3-4.  The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		118810	0	12	12	Intron of ETV6(+): 20Kb before exon 3	ETV6	11972382			12	Intron of ETV6(+): 2Kb before exon 5	ETV6	12020736			24	DUPLICATION		48354	108485	92923	12	NEW_VARIANT
P-0008061-T01-IM5	APC (NM_000038) rearrangement: chr5:g.104183424_c.797inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		70414	0	5	5	IGR: 252Kb before RAB9BP1(+)	RAB9BP1	104183424			5	Exon 16 of APC(+)	APC	112179262			21	INVERSION		7995838	120180	48436	5	NEW_VARIANT
P-0005080-T01-IM5	CDK8(NM_001260)  Rearrangement :  c.-1302_70del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1262	0	70	13	Promoter of CDK8(+): 1Kb from tx start	CDK8	26827477			13	Exon 1 of CDK8(+)	CDK8	26828848			62	DELETION		1371	42803	1151	68	NEW_VARIANT
P-0008304-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1145:TMPRSS2_c.40-48890:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		49284	0	26	21	Intron of ERG(-): 4Kb after exon 1	ERG	39866434			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871261			30	DELETION		3004827	121192	51251	26	NEW_VARIANT
P-0008304-T01-IM5	MYL5 (NM_002477) - TMPRSS2 (NM_001135099) rearrangement : t(4;21)(p16.3;q22.3)(chr4:g.674327::chr21:g.42871261)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (MYL5-TMPRSS2)		0	0	24	21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871261			4	Exon 5 of MYL5(+)	MYL5	674327			17	TRANSLOCATION		0	121194	0	24	NEW_VARIANT
P-0012176-T01-IM5	NF1 (NM_001042492) Rearrangement : chr17:g.28802813_c.480-42:NF1del	PRECISE	Note: The NF1 Rearrangement results in the possible deletion of exons 1-4 of NF1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript fusion (GOSR1-NF1)		9042	0	8	17	Promoter of GOSR1(+): 2Kb from tx start	GOSR1	28802813			17	Intron of NF1(+): 42bp before exon 5	NF1	29496867			16	DELETION		694054	156543	6193	8	NEW_VARIANT
P-0000584-T03-IM6	MAP3K14 (NM_003954): chr17:g.64282318_c.2267:MAP3K14inv	PRECISE	Note: The MAP3K14 rearrangement is an inversion of 5UTR and exons 1-12. One of the breakpoints is within exon 12.	MANUAL_OK	5to5	5to5	-		237238	0	31	17	Exon 12 of MAP3K14(-)	MAP3K14	43344831			17	IGR: 17Kb before PRKCA(+)	PRKCA	64282318			26	INVERSION		20937487	163773	440215	18	NEW_VARIANT
P-0005307-T01-IM5	FYN (NM_153047) rearrangement:  c.345-80_chr6:g.116410524del	PRECISE	The FYN (NM_153047) rearrangement is a deletion of FYN exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9596	0	6	6	Intron of FYN(-): 80bp before exon 6	FYN	112029303			6	IGR: 11Kb before NT5DC1(+)	NT5DC1	116410524			13	DELETION		4381221	46869	8088	6	NEW_VARIANT
P-0006086-T01-IM5	HELZ (NM_014877) - NEGR1 (NM_173808) Rearrangement :  t(17;1)(chr17q24.2;chr1p31.1)(chr17:g.65231020::chr1:g.72748066)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (HELZ-NEGR1)		0	0	18	17	5-UTR of HELZ(-): 16Kb before coding start	HELZ	65231020			1	Exon 1 of NEGR1(-)	NEGR1	72748066			0	TRANSLOCATION		0	67611	0	16	NEW_VARIANT
P-0010361-T01-IM5	BTK (NM_000061) rearrangement: t(3;X)(q25.1;q22.1)(chr3:g.149988968::chrX:g.100605050)	PRECISE	Note: The BTK rearrangement is a translocation with a breakpoint within intron 18 of BTK. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	36	X	Intron of BTK(-): 106bp before exon 19	BTK	100605050			3	IGR: 138Kb before TSC22D2(+)	TSC22D2	149988968			25	TRANSLOCATION		0	145722	0	34	NEW_VARIANT
P-0008373-T01-IM5	MYC (NM_002467) rearrangement : chr8:g.128706398_c.*92:MYC:dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		14260	0	9	8	IGR: 42Kb before MYC(+)	MYC	128706398			8	3-UTR of MYC(+): 92bp after coding stop	MYC	128753296			9	DUPLICATION		46898	121632	27232	8	NEW_VARIANT
P-0010084-T01-IM5	SOX9 (NM_000346) rearrangement: chr17:g. 35352875_c.*1850:SOX9del	PRECISE	Note: The SOX9 rearrangement is a deletion which includes exons 1-3 of SOX9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		427378	0	17	17	Intron of AATF(+): 5Kb after exon 8	AATF	35352875			17	3-UTR of SOX9(+): 2Kb after coding stop	SOX9	70122378			53	DELETION		34769503	137903	591540	17	NEW_VARIANT
P-0008169-T01-IM5	ATRX (NM_000489)  rearrangement: c.3340_c.*303inv	PRECISE	Note: The ATRX (NM_000489)  rearrangement in an inversion (173882 bp) of exons 9-35 of ATRX. The functional significance is undetermined	MANUAL_OK	3to3	3to3	-		51475	0	29	X	3-UTR of ATRX(-): 303bp after coding stop	ATRX	76763526			X	Exon 9 of ATRX(-)	ATRX	76937408			24	INVERSION		173882	120597	41920	25	NEW_VARIANT
P-0013385-T01-IM5	PTEN (NM_000314)  rearrangement: c.493-2070_c.525inv	PRECISE	Note: The PTEN rearrangement is an inversion with a breakpoint within exon 6. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		607	0	14	10	Intron of PTEN(+): 2Kb before exon 6	PTEN	89709805			10	Exon 6 of PTEN(+)	PTEN	89711907			31	INVERSION		2102	161204	319	11	NEW_VARIANT
P-0012205-T01-IM5	FGFR3 (NM_000142) rearrangement: c.2250_c.*1492del	PRECISE	Note: The FGFR3 rearrangement is a deletion of exons 17-18. One of the breakpoints is within exon 17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4048	0	101	4	Exon 17 of FGFR3(+)	FGFR3	1808637			4	3-UTR of FGFR3(+): 1Kb after coding stop	FGFR3	1810481			105	DELETION		1844	156716	2707	101	NEW_VARIANT
P-0003863-T01-IM5	FLT4 (NM_182925) rearrangement: c.1421+431_c.1549-83:FLT4del	PRECISE	The FLT4 (NM_182925) rearrangement is an intragenic deletion of exon 11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1634	0	15	5	Intron of FLT4(-): 83bp before exon 12	FLT4	180049922			5	Intron of FLT4(-): 431bp after exon 10	FLT4	180052438			27	DELETION		2516	13870	1925	20	NEW_VARIANT
P-0013858-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons  4-11) c.55+4344:TMPRSS2_c.39+49391:ERGdel	IMPRECISE	Note: The TMPRSS2-ERG fusion was detected in the background of other events involving TMPRSS2.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		117988	0	15	21	Intron of ERG(-): 49Kb after exon 3	ERG	39898195			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875533			0	DELETION		2977338	162511	75293	14	NEW_VARIANT
P-0010817-T01-IM5	PALB2 (NM_024675) Rearrangement :  c.2922_3202-1323inv	PRECISE	Note: The PALB2 Rearrangement results in the inversion of exons9-11 . One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		5438	0	52	16	Intron of PALB2(-): 1Kb before exon 12	PALB2	23620656			16	Exon 9 of PALB2(-)	PALB2	23634364			51	INVERSION		13708	149358	4360	51	NEW_VARIANT
P-0011439-T01-IM5	CHEK1 (NM_001274) rearrangement : c.424+30:CHEK1_chr11:125970119del	PRECISE	Note: The CHEK1 rearrangement event results in the deletion of CHEK1 exons 6-13.	MANUAL_OK	3to5	3to5	-		23077	0	99	11	Intron of CHEK1(+): 30bp after exon 5	CHEK1	125499385			11	IGR: 37Kb after CDON(-)	CDON	125970119			56	DELETION		470734	153904	15332	93	NEW_VARIANT
P-0012257-T01-IM5	FGFR3 (NM_000142) - LPCAT2 (NM_017839) rearrangement: t(4;16)(p16.3;q12.2)(chr4:g.1808759::chr16:g.55556795)	IMPRECISE	Note: The FGFR3 - LPCAT2 rearrangement is a translocation that results in an in frame fusion of FGFR3 exons 1-17 with LPCAT2 exons 2-14. Archer results confirming FGFR3-TACC3 fusion was reported under M16-13801.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-LPCAT2)		0	0	100	16	Intron of LPCAT2(+): 3Kb before exon 2	LPCAT2	55556795			4	Intron of FGFR3(+): 84bp before exon 18	FGFR3	1808759			0	TRANSLOCATION		0	156875	0	99	NEW_VARIANT
P-0013121-T02-IM5	LMNA (NM_170707) - NTRK1 (NM_002529) rearrangement: c.*885:LMNA_c.1355-127:NTRK1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		66596	0	101	1	3-UTR of LMNA(+): 885bp after coding stop	LMNA	156109782			1	Intron of NTRK1(+): 127bp before exon 12	NTRK1	156845185			141	DELETION		735403	160458	43434	157	NEW_VARIANT
P-0020491-T01-IM6	POLE (NM_006231) rearrangement: chr12:g.74843421_c.4878Ginv	PRECISE	Note: The POLE rearrangement is an inversion which includes exons 37-49 of POLE. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		277391	0	29	12	IGR: 88Kb before ATXN7L3B(+)	ATXN7L3B	74843421			12	Exon 37 of POLE(-)	POLE	133219166			10	INVERSION		58375745	184566	283357	29	NEW_VARIANT
P-0020494-T01-IM6	BAP1 (NM_004656):  c.255+82_c.597del	PRECISE	Note: The BAP1 rearrangement is an intragenic deletion of exons 5-8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6146	0	41	3	Exon 8 of BAP1(-)	BAP1	52440907			3	Intron of BAP1(-):81bp after exon 4	BAP1	52442408			10	DELETION		1501	184578	3545	65	NEW_VARIANT
P-0015826-T03-IM6	FANCA (NM_000135) - ABHD3 (NM_138340) rearrangement: t(16;18)(q24.3;q11.2)(chr16:g.89839561::chr18:g.19233543)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FANCA:ABHD3}		0	0	16	18	Intron of ABHD3(-):2Kb before exon 9	ABHD3	19233543			16	Intron of FANCA(-):117bp after exon 22	FANCA	89839561			10	TRANSLOCATION		0	184372	0	16	NEW_VARIANT
P-0020515-T01-IM6	SMARCA4  (NM_003072) rearrangement:  c.3952-20_c.4170+628dup	PRECISE	Note: The SMARCA4 Rearrangement results in the intragenic duplication of exon 29. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		3499	0	22	19	Intron of SMARCA4(+):19bp before exon 29	SMARCA4	11145570			19	Intron of SMARCA4(+):628bp after exon 29	SMARCA4	11146436			10	DUPLICATION		866	184673	2833	22	NEW_VARIANT
P-0020458-T01-IM6	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	IMPPRECISE	Note: EZR - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EZR:ROS1}		322248	0	24	6	Intron of ROS1(-):455bp before exon 34	ROS1	117646033			6	Intron of EZR(-):206bp after exon 9	EZR	159191589			0	DELETION		41545556	184468	208870	23	NEW_VARIANT
P-0003329-T03-IM6	LMNA (NM_170707) - NTRK1 (NM_002529) fusion (LMNA exons 1-2 fused to NTRK1 exons 12 - 17): c.495:LMNA_c.1355-112:NTRK1del	PRECISE	Note: The LMNA - NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within LMNA exon 2.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {LMNA:NTRK1}		82540	0	32	1	Exon 3 of LMNA(+)	LMNA	156100546			1	Intron of NTRK1(+):111bp before exon 12	NTRK1	156845200			10	DELETION		744654	184569	63865	32	NEW_VARIANT
P-0003329-T03-IM6	AXIN1 (NM_003502) rearrangement: c.2031_chr16:g.344783del	PRECISE	Note: The AXIN1 rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1985	0	27	16	Exon 8 of AXIN1(-)	AXIN1	343643			16	Intron of AXIN1(-):1Kb before exon 8	AXIN1	344783			10	DELETION		1140	184570	1332	35	NEW_VARIANT
P-0020579-T01-IM6	TOP1 (NM_003286) rearrangement: t(11;20)(q12.2;q12)(chr11:g.58574196::chr20:g.39706279)	PRECISE	Note: The TOP1 rearrangement is a translocation that may result in a truncation of exons 6-21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	20	Intron of TOP1(+):2bp after exon 5	TOP1	39706279			11	IGR: 27Kb before GLYATL2(-)	GLYATL2	58574196			10	TRANSLOCATION		0	184764	0	6	NEW_VARIANT
P-0020644-T01-IM6	AGO2 (NM_012154) - SHANK2 (NM_012309) rearrangement: t(8;11)(q24.3;q13.4)(chr8:g.141542519::chr11:g.70919699)	PRECISE	Note: The AGO2 - SHANK2 rearrangement is a translocation with a breakpoint within AGO2 exon 18. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	11	5-UTR of SHANK2(-):601Kb before coding start	SHANK2	70919699			8	Exon 18 of AGO2(-)	AGO2	141542519			10	TRANSLOCATION		0	184907	0	7	NEW_VARIANT
P-0020644-T01-IM6	GNAS (NM_000516) rearrangement: c.432+18_c.495del	PRECISE	Note: The GNAS rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		703	0	46	20	Intron of GNAS(+):18bp after exon 5	GNAS	57478864			20	Exon 6 of GNAS(+)	GNAS	57480500			10	DELETION		1636	184906	700	46	NEW_VARIANT
P-0020644-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.4386_c.5101del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14305	0	65	9	Exon 27 of NOTCH1(-)	NOTCH1	139397700			9	Exon 25 of NOTCH1(-)	NOTCH1	139399962			10	DELETION		2262	184905	7096	71	NEW_VARIANT
P-0020588-T01-IM6	ARID5B (NM_032199) rearrangement: c.-278_c.503-37del	PRECISE	Note: The ARID5B rearrangement results in the deletion of the 5UTR and exons 1-3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		4480	0	14	10	5-UTR of ARID5B(+):277bp before coding start	ARID5B	63661191			10	Intron of ARID5B(+):36bp before exon 4	ARID5B	63759813			10	DELETION		98622	184793	3374	15	NEW_VARIANT
P-0020701-T01-IM6	ATRX (NM_000489) rearrangement: t(6;X)(q21;q21.1)(chr6:g.108910877::chrX:g.76889220)	PRECISE	Note: The ATRX rearrangement is a translocation that may result in a truncation of exons 18-35. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	X	Intron of ATRX(-):20bp before exon 18	ATRX	76889220			6	Intron of FOXO3(+):28Kb after exon 1	FOXO3	108910877			10	TRANSLOCATION		0	185095	0	12	NEW_VARIANT
P-0020730-T01-IM6	MAPK8IP3 (NM_015133) - NTHL1 (NM_002528) rearrangement: c.319-1439:MAPK8IP3_c.816-1:NTHL1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {MAPK8IP3:NTHL1}		3153	0	47	16	Intron of MAPK8IP3(+):1Kb before exon 2	MAPK8IP3	1773119			16	Intron of NTHL1(-):1bp before exon 6	NTHL1	2090049			10	INVERSION		316930	185144	3107	45	NEW_VARIANT
P-0020730-T01-IM6	BABAM1 (NM_001033549) rearrangement: g.17334216_c.416inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		7360	0	5	19	Promoter of OCEL1(+):3Kb from tx start	OCEL1	17334216			19	Exon 4 of BABAM1(+)	BABAM1	17384784			10	INVERSION		50568	185145	7168	7	NEW_VARIANT
P-0020585-T01-IM6	NF2 (NM_000268) rearrangement: t(18;22)(q11.2;q12.2)(chr18:g.20498773::chr22:g.30070884)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	14	22	Exon 13 of NF2(+)	NF2	30070884			18	IGR: 15Kb before RBBP8(+)	RBBP8	20498773			10	TRANSLOCATION		0	184790	0	14	NEW_VARIANT
P-0020649-T01-IM6	CTNNB1 (NM_00190) - PALLD (NM_001166108) rearrangement: t(3;4)(p22.1;q32.3)(chr3:g.41275813::chr4:g.169820018)	PRECISE	Note: The CTNNB1 - PALLD rearrangement is a translocation which may result in the truncation of CTNNB1 after exon 10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	73	4	Intron of PALLD(+):153bp after exon 12	PALLD	169820018			3	Intron of CTNNB1(+):25bp after exon 10	CTNNB1	41275813			10	TRANSLOCATION		0	184913	0	71	NEW_VARIANT
P-0020683-T01-IM6	FGFR3 (NM_000142) rearrangement: c.2360:FGFR3_chr4:g.20464483inv	PRECISE	Note: The FGFR3 rearrangement is an inversion of a part of exon 18. One of the breakpoints is within exon 18. 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 FGFR3 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	Antisense Fusion		77548	0	5	4	Exon 18 of FGFR3(+)	FGFR3	1808928			4	Intron of SLIT2(+):5Kb before exon 5	SLIT2	20464483			7	INVERSION		18655555	185038	82075	5	NEW_VARIANT
P-0020501-T01-IM6	EZH2 (NM_004456) rearrangement: c.-8+11574_c.45del	PRECISE	Note: The EZH2 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1187	0	19	7	Exon 2 of EZH2(-)	EZH2	148544346			7	5-UTR of EZH2(-):65Kb before coding start	EZH2	148569682			10	DELETION		25336	184590	1164	19	NEW_VARIANT
P-0020764-T01-IM6	KIAA0825 (NM_001145678) - MAP3K1 (NM_005921) rearrangement: c.3710+59208:KIAA0852_c.4258-64:MAP3K1inv	PRECISE	Note: The KIAA0825-MAP3K1 rearrangement is an inversion which results in the fusion of KIAA0825 exon 25 to MAP3K1 exons 1-19	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {KIAA0825:MAP3K1}		149580	0	4	5	Intron of MAP3K1(+):63bp before exon 19	MAP3K1	56183989			5	Intron of KIAA0825(-):59Kb after exon 20	KIAA0825	93660865			7	INVERSION		37476876	185266	175995	4	NEW_VARIANT
P-0020661-T01-IM6	ETV6 (NM_001987) rearrangement: c.164-14151_c.463+4339dup	PRECISE	Note: The ETV6 rearrangement results in the duplication of exons 3-4. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		30249	1	24	12	Intron of ETV6(+):14Kb before exon 3	ETV6	11977923			12	Intron of ETV6(+):4Kb after exon 4	ETV6	12010834			10	DUPLICATION		32911	185007	40094	23	NEW_VARIANT
P-0020586-T01-IM6	CD79A (NM_001783) rearrangement: g.10947654_c.594del	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CD79A:TMED1}		780561	0	5	19	Promoter of TMED1(-):5Kb from tx start	TMED1	10947654			19	Exon 5 of CD79A(+)	CD79A	42384960			10	INVERSION		31437306	184796	820699	5	NEW_VARIANT
P-0020678-T01-IM6	KRT6A (NM_005554) - NAB2 (NM_005967) rearrangement: c.1204-574:KRT6A_c.1144-29:NAB2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KRT6A:NAB2}		70316	0	57	12	Intron of KRT6A(-):574bp before exon 7	KRT6A	52882906			12	Intron of NAB2(+):28bp before exon 5	NAB2	57486817			10	INVERSION		4603911	185044	108699	82	NEW_VARIANT
P-0020763-T01-IM6	AEBP2 (NM_001114176) - RECQL (NM_032941) rearrangement: g.19703521_c.1534Gdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		6871	0	33	12	IGR: 110Kb before AEBP2(+)	AEBP2	19703521			12	Exon 14 of RECQL(-)	RECQL	21624495			10	DELETION		1920974	185306	14267	33	NEW_VARIANT
P-0020760-T01-IM6	VHL (NM_000551) rearrangement: c.-1293_c.83del	PRECISE	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	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1392	0	42	3	Promoter of VHL(+):1Kb from tx start	VHL	10182239			3	Exon 1 of VHL(+)	VHL	10183614			10	DELETION		1375	185319	1087	48	NEW_VARIANT
P-0020684-T01-IM6	PTPRD (NM_002839) rearrangement: c.4087-5781_c.1298del	PRECISE	Note: The PTPRD rearrangement is an intragenic deletion of exons 21-35. One of the breakpoints is within exon 21.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		33745	0	7	9	Intron of PTPRD(-):6Kb before exon 36	PTPRD	8410441			9	Exon 21 of PTPRD(-)	PTPRD	8518093			6	DELETION		107652	185078	44728	7	NEW_VARIANT
P-0019030-T02-IM6	BCL2L11 (NM_138621) - PTCD3(NM_017952) rearrangement: c.394+1328_c.805-130dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BCL2L11:PTCD3}		77553	0	29	2	Intron of PTCD3(+):129bp before exon 11	PTCD3	86352448			2	Intron of BCL2L11(+):1Kb after exon 2	BCL2L11	111883044			10	DUPLICATION		25530596	184888	72170	30	NEW_VARIANT
P-0019030-T02-IM6	HIST1H3B (NM_003537) rearrangement: g.26021830_c.18del	PRECISE	Note: The HIST1H3B rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		3245	0	3	6	Promoter of HIST1H3A(+):1Kb from tx start	HIST1H3A	26021830			6	Exon 1 of HIST1H3B(-)	HIST1H3B	26032271			10	DELETION		10441	184887	2234	3	NEW_VARIANT
P-0020806-T01-IM6	ARID1A (NM_006015) rearrangement: c.3472_c.5124+318del	IMPPRECISE	Note: The ARID1A rearrangement is a deletion of exons 13-19. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		22137	0	40	1	Exon 13 of ARID1A(+)	ARID1A	27099056			1	Intron of ARID1A(+):318bp after exon 19	ARID1A	27102516			0	DELETION		3460	185482	16930	43	NEW_VARIANT
P-0020861-T01-IM6	AXL (NM_021913) rearrangement: t(15;19)(q11.1;q13.2)(chr15:g.20101904::chr19:g.41763332)	IMPPRECISE	Note: The AXL rearrangement is a translocation that may result in the truncation of exons 1-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	5	19	Intron of AXL(+):65bp before exon 19	AXL	41763332			15	IGR: 386Kb before CHEK2P2(+)	CHEK2P2	20101904			0	TRANSLOCATION		0	185647	0	6	NEW_VARIANT
P-0020833-T01-IM6	FLCN (NM_144997) - FOXP1 (NM_001244814) rearrangement: t(3,17)(p13,p11.2)(chr3:g.71571851::chr17:g.17129138)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {FLCN:FOXP1}		0	0	13	17	Intron of FLCN(-):351bp after exon 5	FLCN	17129138			3	5-UTR of FOXP1(-):563Kb before coding start	FOXP1	71571851			10	TRANSLOCATION		0	185525	0	13	NEW_VARIANT
P-0020833-T01-IM6	EWSR1 (NM_013986) rearrangement: g.24063333:ZNF70_c.1393:EWSR1del	PRECISE	Note: The EWSR1 rearrangement results in the deletion of exons 1-14.  Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		159410	0	11	22	IGR: 20Kb before ZNF70(-)	ZNF70	24063333			22	Exon 14 of EWSR1(+)	EWSR1	29693900			10	DELETION		5630567	185524	208219	16	NEW_VARIANT
P-0020793-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1814+8_g.67812667del	PRECISE	Note: The PIK3R1 rearrangement results in the deletion of exons 14-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2787	0	6	5	Intron of PIK3R1(+):8bp after exon 14	PIK3R1	67591324			5	IGR: 224Kb before PIK3R1(+)	PIK3R1	67812667			10	DELETION		221343	185467	2257	6	NEW_VARIANT
P-0020884-T01-IM6	TP53 (NM_000546) rearrangement: c.920-8_c.673-87del	PRECISE	Note: The TP53 rearrangement results in an intragenic deletion of exons 7-8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		4419	0	24	17	Intron of TP53(-):8bp before exon 9	TP53	7576934			17	Intron of TP53(-):87bp before exon 7	TP53	7577695			10	DELETION		761	185720	2641	33	NEW_VARIANT
P-0020620-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.10364_g.73987269inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		90443	0	3	16	Exon 10 of ZFHX3(-)	ZFHX3	72821811			16	IGR: 239Kb before LOC101928035(-)	LOC101928035	73987269			10	INVERSION		1165458	184864	73651	3	NEW_VARIANT
P-0020620-T01-IM6	DNAJB1 (NM_006145) rearrangement: g.14229613_c.311del	PRECISE	Note: The DNAJB1 rearrangement results in the deletion of exons 2-3. One of the breakpoints is within exon 2 while the other breakpoint is 27Kb from transcription start of PRKACA. The presence of a DNAJB1-PRKACA fusion is confirmed with the Archer assay (see M17-15081), suggesting this is a complex re-arrangement at the DNA level.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNAJB1:PRKACA}		10335	0	5	19	Promoter of PRKACA(-):27Kb from tx start	PRKACA	14229613			19	Exon 2 of DNAJB1(-)	DNAJB1	14627759			10	DELETION		398146	184862	8399	5	NEW_VARIANT
P-0020792-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 3-11):c.56-1041:TMPRSS2_c.-149-14766:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	-		72755	0	34	21	3-UTR of ERG(-):62Kb after coding stop	ERG	39971635			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871157			10	DELETION		2899522	185460	14705	36	NEW_VARIANT
P-0020780-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		124187	0	100	2	Intron of ALK(-):690bp before exon 20	ALK	29447084			2	Intron of EML4(+):1Kb after exon 12	EML4	42523934			10	INVERSION		13076850	185331	147040	98	NEW_VARIANT
P-0020876-T01-IM6	APC (NM_000038) rearrangement: c.3901:APC_g.112190069:SRP19del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		23887	0	7	5	Exon 16 of APC(+)	APC	112175192			5	IGR: 7Kb before SRP19(+)	SRP19	112190069			10	DELETION		14877	185713	33956	7	NEW_VARIANT
P-0020831-T01-IM6	SMO (NM_005631) rearrangement: c.166+10844:KLHDC10_c.2163:SMOdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KLHDC10:SMO}		3374	0	26	7	Exon 12 of SMO(+)	SMO	128852091			7	Intron of KLHDC10(+):11Kb after exon 1	KLHDC10	129721493			10	DUPLICATION		869402	185518	5008	27	NEW_VARIANT
P-0020799-T01-IM6	MSH6 (NM_000179) - RHOQ (NM_012249) rearrangement: c.3646+4:MSH6_c.202-2802:RHOQdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {MSH6:RHOQ}		73259	0	3	2	Intron of RHOQ(+):3Kb before exon 3	RHOQ	46800424			2	Intron of MSH6(+):4bp after exon 7	MSH6	48032850			6	DUPLICATION		1232426	185449	65361	3	NEW_VARIANT
P-0020773-T01-IM6	BRE (NM_004899) - FGFR3 (NM_000142 ) rearrangement: t(2;4)(p23.2;p16.3)(chr2:g.28322454::chr4:g.1803105)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BRE:FGFR3}		0	0	9	4	Exon 5 of FGFR3(+)	FGFR3	1803105			2	Intron of BRE(+):30Kb before exon 8	BRE	28322454			10	TRANSLOCATION		0	185330	0	9	NEW_VARIANT
P-0020829-T01-IM6	CCND3 (NM_001760) rearrangement: t(1,6)(p31.1,p21.1)(chr1:g.82121584::chr6:g.41903877)	PRECISE	Note: The CCND3 rearrangement is a translocation that may result in a truncation of exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	33	6	Intron of CCND3(-):32bp before exon 5	CCND3	41903877			1	IGR: 44Kb before LPHN2(+)	LPHN2	82121584			10	TRANSLOCATION		0	185519	0	34	NEW_VARIANT
P-0020882-T01-IM6	PTPRD (NM_002839) rearrangement: c.5534+5222_c.5253+71del	PRECISE	Note: The PTPRD rearrangement is an intragenic deletion of PTPRD exons 43-44. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3465	0	2	9	Intron of PTPRD(-):5Kb after exon 44	PTPRD	8326360			9	Intron of PTPRD(-):70bp after exon 42	PTPRD	8340272			10	DELETION		13912	185718	4752	4	NEW_VARIANT
P-0020791-T01-IM6	APC (NM_000038) rearrangement: c.4744_g.112192034del	PRECISE	Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		23542	0	10	5	Exon 16 of APC(+)	APC	112176035			5	IGR: 5Kb before SRP19(+)	SRP19	112192034			10	DELETION		15999	185459	17449	10	NEW_VARIANT
P-0020750-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.39+2008:ERG_c.127-585:TMPRSS2dup	PRECISE	Note: The ERG - TMPRSS2 rearrangement is a duplication which results in the fusion of ERG exon 3 to TMPRSS2 exon 3. While this rearrangement does not appear to result in the classical TMPRSS2 - ERG fusion, it may be part of a more complex event which may not be fully characterized by this assay.  Further testing by Archer may be performed upon request.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ERG:TMPRSS2}		27468	0	4	21	Intron of ERG(-):2Kb after exon 3	ERG	39945578			21	Intron of TMPRSS2(-):585bp before exon 3	TMPRSS2	42867090			10	DUPLICATION		2921512	185186	35212	16	NEW_VARIANT
P-0020837-T01-IM6	EWSR1 (NM_013986) rearrangement: t(20,22)(p13,q12.2)(chr20:g.404212::chr22:g.29694204)	PRECISE	Note: The EWSR1 rearrangement is a translocation that may result in the truncation of exons 15-18. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	6	22	Intron of EWSR1(+):265bp after exon 14	EWSR1	29694204			20	Intron of RBCK1(+):1Kb after exon 7	RBCK1	404212			10	TRANSLOCATION		0	185534	0	6	NEW_VARIANT
P-0020777-T01-IM6	ARID5B (NM_032199) rearrangement: c.502+21040_c.847-56del	PRECISE	Note: The ARID5B rearrangement is an intragenic deletion of exons 4 - 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3377	0	17	10	Intron of ARID5B(+):21Kb after exon 3	ARID5B	63721207			10	Intron of ARID5B(+):55bp before exon 6	ARID5B	63816820			10	DELETION		95613	185321	5048	17	NEW_VARIANT
P-0020777-T01-IM6	ARID5B (NM_032199) rearrangement: c.1200-2888_c.1325del	PRECISE	Note: The ARID5B rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		721	0	14	10	Intron of ARID5B(+):3Kb before exon 9	ARID5B	63842573			10	Exon 9 of ARID5B(+)	ARID5B	63845586			10	DELETION		3013	185322	891	14	NEW_VARIANT
P-0020909-T01-IM6	PPP2R1A (NM_014225) - FRMD4A (NM_018027) rearrangement: t(10;19)(p13;q13.41)(chr10:g.14320979::chr19:g.52719936)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {PPP2R1A:FRMD4A}		0	0	107	19	Intron of PPP2R1A(+):20bp after exon 9	PPP2R1A	52719936			10	Intron of FRMD4A(-):51Kb after exon 2	FRMD4A	14320979			10	TRANSLOCATION		0	185757	0	104	NEW_VARIANT
P-0020910-T01-IM6	ATM (NM_000051) rearrangement:  c.1607+13_c.6572+82del	PRECISE	Note: The ATM rearrangement is an intragenic deletion of exons 11-45. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 35 exons : in frame		54510	0	16	11	Intron of ATM(+):13bp after exon 10	ATM	108121812			11	Intron of ATM(+):82bp after exon 45	ATM	108192229			10	DELETION		70417	185740	40112	20	NEW_VARIANT
P-0020973-T01-IM6	EZH2 (NM_004456) rearrangement: g.148465400_c.1437del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		14334	0	6	7	Intron of CUL1(+):559bp after exon 9	CUL1	148465400			7	Exon 12 of EZH2(-)	EZH2	148513844			10	DELETION		48444	185872	13018	6	NEW_VARIANT
P-0020974-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.303+2543:CCDC6_c.2137-848:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		52016	0	20	10	Intron of RET(+):847bp before exon 12	RET	43611184			10	Intron of CCDC6(-):3Kb after exon 1	CCDC6	61663337			10	INVERSION		18052153	185876	34110	32	NEW_VARIANT
P-0020612-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.*101+817_c.231del	PRECISE	Note: The CDKN2Ap14ARF rearrangement is an intragenic deletion of exon 2. One breakpoint is within CDK2NA exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2880		11	9	Intron of CDKN2Ap14ARF(-):816bp after exon 2	CDKN2Ap14ARF	21970084			9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21971170			10	DELETION		1086	185160	3775		NEW_VARIANT
P-0020612-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement:  c.457+817_c.188del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of exon 2. One breakpoint is within CDKN2Ap16INK4A exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2880		11	9	Intron of CDKN2Ap16INK4A(-):816bp after exon 2	CDKN2Ap16INK4A	21970084			9	Exon 2 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21971170			10	DELETION		1086	185162	3775		NEW_VARIANT
P-0020964-T01-IM6	SLCO2B1 (NM_007256) - MSH3 (NM_002439) rearrangement: t(5;11)(q14.1;q13.4)(chr5:g.80149840::chr11:g.74883584)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SLCO2B1:MSH3}		0	0	8	11	Exon 7 of SLCO2B1(+)	SLCO2B1	74883584			5	Intron of MSH3(+):108bp before exon 21	MSH3	80149840			10	TRANSLOCATION		0	185873	0	8	NEW_VARIANT
P-0020919-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.1815:PIK3C2G_g.19682908:AEBP2del	PRECISE	Note: The PIK3C2G rearrangement results in the deletion of exons 13-32. One of the breakpoints is within exon 13. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		35730	0	2	12	Exon 13 of PIK3C2G(+)	PIK3C2G	18534757			12	IGR: 89Kb before AEBP2(+)	AEBP2	19682908			10	DELETION		1148151	185778	18617	2	NEW_VARIANT
P-0020926-T01-IM6	ERBB2 (NM_004448) rearrangement: t(15,17)(q25.3,q12)(chr15:g.88160146::chr17:g.37882881)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	32	17	Exon 24 of ERBB2(+)	ERBB2	37882881			15	IGR: 40Kb before LINC00052(+)	LINC00052	88160146			10	TRANSLOCATION		0	185790	0	37	NEW_VARIANT
P-0020926-T01-IM6	CDC73 (NM_024529) - RAMP3 (NM_005856) rearrangement: t(1,7)(q31.2,p13)(chr1:g.193218905::chr7:g.45238072)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	10	7	IGR: 41Kb before RAMP3(+)	RAMP3	45238072			1	Exon 16 of CDC73(+)	CDC73	193218905			10	TRANSLOCATION		0	185789	0	11	NEW_VARIANT
P-0017478-T02-IM6	DDR2 (NM_006182) rearrangement: c.672-562_c.2434-112inv	PRECISE	Note: The DDR2 rearrangement is an intragenic inversion of exons 8-17. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		19068	0	3	1	Intron of DDR2(+):561bp before exon 8	DDR2	162729024			1	Intron of DDR2(+):111bp before exon 18	DDR2	162749790			5	INVERSION		20766	186164	14937	3	NEW_VARIANT
P-0021038-T01-IM6	KIF5B (NM_004521) - EGFR (NM_005228) rearrangement: t(7;10)(p11.2;q11.22)(chr7:g.55241486::chr10:g.32312089)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:EGFR}		0	0	9	10	Intron of KIF5B(-):125bp before exon 16	KIF5B	32312089			7	Intron of EGFR(+):127bp before exon 18	EGFR	55241486			10	TRANSLOCATION		0	186140	0	12	NEW_VARIANT
P-0021054-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	94	6	Intron of ROS1(-):224bp after exon 33	ROS1	117647162			5	Intron of CD74(-):146bp before exon 7	CD74	149783021			10	TRANSLOCATION		0	186153	0	102	NEW_VARIANT
P-0020961-T01-IM6	IL7R (NM_002185) - LIFR (NM_002310) rearrangement: c.1338:IL7R_c.-20+19953:LIFRinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {IL7R:LIFR}		2348	0	29	5	Exon 8 of IL7R(+)	IL7R	35876546			5	5-UTR of LIFR(-):94Kb before coding start	LIFR	38575410			10	INVERSION		2698864	185856	2336	27	NEW_VARIANT
P-0021044-T01-IM6	TAP1 (NM_000593) rearrangement: g.28495308_c.566del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		348482	0	39	6	Intron of GPX5(+):1Kb after exon 1	GPX5	28495308			6	Exon 1 of TAP1(-)	TAP1	32821028			10	DELETION		4325720	186130	479195	40	NEW_VARIANT
P-0021034-T01-IM6	PTPRD (NM_002839) rearrangement: c.3803_c.-104+141113del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		48775	0	9	9	Exon 33 of PTPRD(-)	PTPRD	8460483			9	5-UTR of PTPRD(-):560Kb before coding start	PTPRD	8877584			10	DELETION		417101	186141	41993	9	NEW_VARIANT
P-0021116-T01-IM6	KDM6A (NM_021140) rearrangement: c.384+1046_c.655-111del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 5 - 8. Its significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		7507	0	6	X	Intron of KDM6A(+):1Kb after exon 4	KDM6A	44835006			X	Intron of KDM6A(+):110bp before exon 9	KDM6A	44910843			7	DELETION		75837	186236	8854	6	NEW_VARIANT
P-0021120-T01-IM6	ROS1 (NM_002944) rearrangement: c.5079+1257_c.4960del	PRECISE	Note: The ROS1 rearrangement is an intragenic deletion of exon 30. One of the breakpoints is within exon 30. Its significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16856	0	42	6	Intron of ROS1(-):1Kb after exon 30	ROS1	117661041			6	Exon 30 of ROS1(-)	ROS1	117662417			10	DELETION		1376	186234	6717	45	NEW_VARIANT
P-0021078-T01-IM6	MGA (NM_001164273) rearrangement: c.3834:MGA_chr15:g.51318549inv	PRECISE	Note: The MGA rearrangement is an inversion of exons 11-24. One of the breakpoints is within exon 11.	MANUAL_OK	5to5	5to5	-		178745	0	9	15	Exon 11 of MGA(+)	MGA	42021538			15	IGR: 30Kb before TNFAIP8L3(-)	TNFAIP8L3	51318549			10	INVERSION		9297011	186200	129494	9	NEW_VARIANT
P-0021155-T01-IM6	RB1 (NM_000321) rearrangement: c.2663+49_c.2713+222del	IMPPRECISE	Note: The RB1 rearrangement results in the deletion of exon 26. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1095	0	28	13	Intron of RB1(+):49bp after exon 25	RB1	49051028			13	Intron of RB1(+):222bp after exon 26	RB1	49051762			0	DELETION		734	186302	79	32	NEW_VARIANT
P-0021061-T01-IM6	ANKRD11 (NM_013275) rearrangement: chr16:g.73410859_c.2182:ANKRD11inv	IMPPRECISE	Note: The ANKRD11 rearrangement is an inversion of exons 9-13. One of the breakpoints is within exon 9. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		151865	0	71	16	IGR: 10Kb before LINC01568(+)	LINC01568	73410859			16	Exon 9 of ANKRD11(-)	ANKRD11	89350768			0	INVERSION		15939909	186175	124728	104	NEW_VARIANT
P-0021150-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		73334	0	23	10	Intron of KIF5B(-):311bp after exon 15	KIF5B	32317044			10	Intron of RET(+):440bp before exon 12	RET	43611591			10	INVERSION		11294547	186299	81114	25	NEW_VARIANT
P-0021028-T01-IM6	GNA11 (NM_002067) rearrangement: chr19:g.2925382_c.137-2del	PRECISE	Note: The GNA11 rearrangement is a deletion which includes exon 1 of GNA11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1357	0	28	19	IGR: 8Kb before ZNF77(-)	ZNF77	2925382			19	Intron of GNA11(+):1bp before exon 2	GNA11	3110145			10	DELETION		184763	186051	1433	30	NEW_VARIANT
P-0021028-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.5914-67_chr19:g.15454199del	PRECISE	Note: The NOTCH3 rearrangement is a deletion which includes exons 1-32 of NOTCH3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		131184	0	9	19	Intron of NOTCH3(-):67bp before exon 33	NOTCH3	15272592			19	IGR: 10Kb before AKAP8(-)	AKAP8	15454199			10	DELETION		181607	186052	105581	9	NEW_VARIANT
P-0021233-T01-IM6	IRS1 (NM_005544) rearrangement: g.107724645_c.1872inv	PRECISE	Note: The IRS1 rearrangement results in the inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		764532	0	17	2	IGR: 295Kb before ST6GAL2(-)	ST6GAL2	107724645			2	Exon 1 of IRS1(-)	IRS1	227661583			10	INVERSION		119936938	186598	566416	20	NEW_VARIANT
P-0021235-T01-IM6	NOTCH2 (NM_024408) rearrangement: g.120292852_c.3480inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		40997	0	6	1	3-UTR of HMGCS2(-):572bp after coding stop	HMGCS2	120292852			1	Exon 21 of NOTCH2(-)	NOTCH2	120479947			10	INVERSION		187095	186601	70998	10	NEW_VARIANT
P-0021239-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-3436:TMPRSS2_c.40-63140:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		76456	0	29	21	Intron of ERG(-):63Kb before exon 4	ERG	39880684			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873552			10	DELETION		2992868	186605	63145	29	NEW_VARIANT
P-0021239-T01-IM6	KMT2C (NM_170606) rearrangement: c.8452_c.7011del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9176	0	9	7	Exon 38 of KMT2C(-)	KMT2C	151874086			7	Exon 36 of KMT2C(-)	KMT2C	151877934			10	DELETION		3848	186604	10526	10	NEW_VARIANT
P-0021228-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	21	6	Intron of ROS1(-):717bp before exon 34	ROS1	117646295			5	Intron of CD74(-):513bp after exon 6	CD74	149783729			10	TRANSLOCATION		0	186435	0	21	NEW_VARIANT
P-0021253-T01-IM6	FLT1 (NM_002019) rearrangement: c.1010_chr13:g.59883399del	PRECISE	Note: The FLT1 rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon 8. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		204184	0	8	13	Exon 8 of FLT1(-)	FLT1	29004283			13	IGR: 356Kb before DIAPH3(-)	DIAPH3	59883399			10	DELETION		30879116	186677	87483	8	NEW_VARIANT
P-0021254-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2956_chr21:g.43199377inv	PRECISE	Note: The TMPRSS2 rearrangement results in the inversion of exon 1. Its significance is undetermined.	MANUAL_OK	3to3	3to3	-		53319	0	10	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873072			21	IGR: 19Kb before PRDM15(-)	PRDM15	43199377			10	INVERSION		326305	186675	41637	9	NEW_VARIANT
P-0021254-T01-IM6	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)	PRECISE	Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:ETV1}		0	0	24	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874388			7	Intron of ETV1(-):836bp after exon 5	ETV1	14016215			10	TRANSLOCATION		0	186676	0	27	NEW_VARIANT
P-0021255-T01-IM6	PELI2 (NM_021255) FLT3 (NM_004119) rearrangement: t(13,14)(q12.2,q22.3)(chr13:g.28608118::chr14:g.56582755)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PELI2:FLT3}		0	0	24	14	Promoter of PELI2(+):2Kb from tx start	PELI2	56582755			13	Exon 15 of FLT3(-)	FLT3	28608118			10	TRANSLOCATION		0	186683	0	23	NEW_VARIANT
P-0021001-T01-IM6	PTPRD (NM_002839) rearrangement: c.1544-103_g.22097196	PRECISE	Note: The PTPRD rearrangement results in the deletion of exons 1-21.	MANUAL_OK	3to5	3to5	-		43070	0	9	9	Intron of PTPRD(-):103bp before exon 22	PTPRD	8507537			9	5-UTR of CDKN2B-AS1(+):24Kb before coding start	CDKN2B-AS1	22097196			10	DELETION		13589659	186621	21574	9	NEW_VARIANT
P-0019401-T02-IM6	MTOR (NM_004958) rearrangement: t(1;3)(p36.22;p22.1)(chr1:g.11217066::chr3:g.43055777)	PRECISE	Note: The MTOR rearrangement is a translocation that may result in a truncation of MTOR exons 31-58. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	19	3	Intron of FAM198A(+):18Kb before exon 2	FAM198A	43055777			1	Intron of MTOR(-):142bp after exon 30	MTOR	11217066			10	TRANSLOCATION		0	186894	0	19	NEW_VARIANT
P-0021282-T01-IM6	PLCD3 (NM_133373) - TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43207457::chr21:g.42843839)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PLCD3:TMPRSS2}		0	0	10	21	Exon 10 of TMPRSS2(-)	TMPRSS2	42843839			17	Intron of PLCD3(-):2Kb after exon 1	PLCD3	43207457			10	TRANSLOCATION		0	186808	0	10	NEW_VARIANT
P-0021183-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		60564	0	3	21	Intron of ERG(-):26Kb after exon 1	ERG	39844672			21	Intron of TMPRSS2(-):658bp after exon 2	TMPRSS2	42869387			8	DELETION		3024715	186327	33562	3	NEW_VARIANT
P-0021290-T01-IM6	TAP2 (NM_018833) rearrangement: g.32764970_c.945+11inv	IMPPRECISE	Note: The TAP2 rearrangement results in the inversion of exons 5-12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		17370	0	22	6	IGR: 16Kb before HLA-DOB(-)	HLA-DOB	32764970			6	Intron of TAP2(-):10bp after exon 5	TAP2	32802920			0	INVERSION		37950	186803	11123	29	NEW_VARIANT
P-0021328-T01-IM6	EZH2 (NM_004456) rearrangemen: chr7:g.148497861_c.1547-42:EZH2inv	IMPPRECISE	Note: The EZH2 rearrangement is an inversion of exons 14-20. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		10134	0	42	7	3-UTR of CUL1(+):71Kb after coding stop	CUL1	148497861			7	Intron of EZH2(-):42bp before exon 14	EZH2	148512173			0	INVERSION		14312	186898	18100	39	NEW_VARIANT
P-0021104-T01-IM6	TP53 (NM_000546) rearrangement: g.7562760_c.966del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		7629	0	21	17	Promoter of ATP1B2(+):9Kb from tx start	ATP1B2	7562760			17	Exon 9 of TP53(-)	TP53	7576880			10	DELETION		14120	186721	3337	23	NEW_VARIANT
P-0021104-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		31636	0	30	21	Promoter of ERG(-):121Kb from tx start	ERG	39872989			21	Intron of TMPRSS2(-):55bp before exon 3	TMPRSS2	42866560			10	DELETION		2993571	186722	17911	30	NEW_VARIANT
P-0021288-T01-IM6	SLC12A7 (NM_006598) - TERT (NM_198253) rearrangement: c.125-1849:SLC12A7_c.-15:TERTdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {SLC12A7:TERT}		44423	0	27	5	Intron of SLC12A7(-):2Kb before exon 2	SLC12A7	1096212			5	5-UTR of TERT(-):41Kb before coding start	TERT	1295119			10	DUPLICATION		198907	186813	54222	30	NEW_VARIANT
P-0021166-T01-IM6	RB1 (NM_000321) rearrangement: c.2107-434_c.2325+22del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 21-22.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		2176	0	94	13	Intron of RB1(+):433bp before exon 21	RB1	49037433			13	Intron of RB1(+):22bp after exon 22	RB1	49039269			10	DELETION		1836	186313	843	96	NEW_VARIANT
P-0021201-T01-IM6	ATM (NM_000051) rearrangement: c.3919:ATM_chr11:g.109110999inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		49931	0	4	11	Exon 26 of ATM(+)	ATM	108155126			11	IGR: 182Kb before C11orf87(+)	C11orf87	109110999			10	INVERSION		955873	186404	85282	3	NEW_VARIANT
P-0021383-T01-IM6	CRLF1 (NM_004750) - BRD4 (NM_058243) rearrangement: c.1024+39_c.1752-31del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CRLF1:BRD4}		115034	0	19	19	Intron of BRD4(-):31bp before exon 10	BRD4	15366434			19	Intron of CRLF1(-):38bp after exon 6	CRLF1	18707393			10	DELETION		3340959	186998	477800	19	NEW_VARIANT
P-0021105-T01-IM6	NKAIN1 (NM_024522) - CDKN2C (NM_078626) rearrangement: c.55-5172:NKAIN1_c.130-80:CDKN2Cinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {NKAIN1:CDKN2C}		263628	0	2	1	Intron of NKAIN1(-):5Kb before exon 2	NKAIN1	31666206			1	Intron of CDKN2C(+):79bp before exon 2	CDKN2C	51439485			10	INVERSION		19773279	186740	221977	2	NEW_VARIANT
P-0021105-T01-IM6	CSF3R (NM_000760) rearrangement: t(1;16)(p34.4;q21)(chr1:g.36937176::chr16:g.58687670)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	6	16	IGR: 13Kb before SLC38A7(-)	SLC38A7	58687670			1	Exon 10 of CSF3R(-)	CSF3R	36937176			10	TRANSLOCATION		0	186741	0	8	NEW_VARIANT
P-0021388-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		30218	0	10	21	Intron of ERG(-):18Kb after exon 3	ERG	39929648			21	Intron of TMPRSS2(-):29bp before exon 3	TMPRSS2	42866534			10	DELETION		2936886	186999	23159	10	NEW_VARIANT
P-0021271-T01-IM6	EGFL7 (NM_201446) rearrangement: g.139473248_c.81-52del	PRECISE	Note: The EGFL7 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2838	0	35	9	IGR: 31Kb before LINC01573(+)	LINC01573	139473248			9	Intron of EGFL7(+):51bp before exon 3	EGFL7	139562957			10	DELETION		89709	186752	1400	36	NEW_VARIANT
P-0021102-T01-IM6	ARID1B (NM_020732) rearrangement: t(6;8)(q25.3;p21.1)(chr6:g.157528010::chr8:g.27481234)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	11	8	IGR: 10Kb before SCARA3(+)	SCARA3	27481234			6	Exon 20 of ARID1B(+)	ARID1B	157528010			10	TRANSLOCATION		0	186736	0	11	NEW_VARIANT
P-0021274-T01-IM6	ZNF81 (NM_007137) - ARAF (NM_001654) rearrangement: c.55-16531:ZNF81_c.-40:ARAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {ZNF81:ARAF}		15344	0	8	X	5-UTR of ARAF(+):39bp before coding start	ARAF	47422327			X	Intron of ZNF81(+):17Kb before exon 3	ZNF81	47730867			10	DUPLICATION		308540	186766	18758	8	NEW_VARIANT
P-0021173-T01-IM6	PPP2R1A (NM_014225) rearrangement: c.-434_c.78+176dup	PRECISE	Note: The PPP2R1A rearrangement is a tandem duplication involving exon 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		3296	0	6	19	Promoter of PPP2R1A(+):138bp from tx start	PPP2R1A	52692916			19	Intron of PPP2R1A(+):176bp after exon 1	PPP2R1A	52693603			10	DUPLICATION		687	186325	3061	6	NEW_VARIANT
P-0021173-T01-IM6	PPP2R1A (NM_014225) rearrangement: c.26:PPP2R1A_chr19:g.56185948inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		41331	0	24	19	Exon 1 of PPP2R1A(+)	PPP2R1A	52693375			19	3-UTR of U2AF2(+):19Kb after coding stop	U2AF2	56185948			10	INVERSION		3492573	186326	36510	25	NEW_VARIANT
P-0021351-T01-IM6	KDM5A (NM_001042603) rearrangement: t(8;12)(q11.1;p13.33)(chr8:g.47164681::chr12:g.495087)	PRECISE	Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	25	12	Exon 2 of KDM5A(-)	KDM5A	495087			8	IGR: 588Kb before LINC00293(+)	LINC00293	47164681			10	TRANSLOCATION		0	186928	0	25	NEW_VARIANT
P-0021168-T01-IM6	TAP2 (NM_018833) rearrangement: chr6:g.21376128_c.81:TAP2inv	PRECISE	Note: The TAP2 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		353828	0	50	6	IGR: 110Kb before LINC00581(-)	LINC00581	21376128			6	Exon 2 of TAP2(-)	TAP2	32805930			10	INVERSION		11429802	186312	547471	68	NEW_VARIANT
P-0009955-T02-IM6	NF2 (NM_000268) rearrangement: c.240+276_c.278del	PRECISE	Note: The NF2 rearrangement is an intragenic deletion of exon3. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		521	0	103	22	Intron of NF2(+):276bp after exon 2	NF2	30033141			22	Exon 3 of NF2(+)	NF2	30035116			10	DELETION		1975	187006	104	111	NEW_VARIANT
P-0021262-T01-IM6	F11R (NM_016946) - NTRK1 (NM_002529) rearrangement: c.389-101:F11R_c.1196-75:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {F11R:NTRK1}		42669	0	50	1	Intron of NTRK1(+):74bp before exon 10	NTRK1	156844288			1	Intron of F11R(-):101bp before exon 5	F11R	160970239			10	INVERSION		4125951	186762	38082	62	NEW_VARIANT
P-0021355-T01-IM6	ATM (NM_000051) rearrangement: c.5674+735_c.6545del	PRECISE	Note: The ATM rearrangement is an intragenic deletion of exons 38-45. One of the breakpoints is within exon 45.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10240	0	12	11	Intron of ATM(+):735bp after exon 37	ATM	108176314			11	Exon 45 of ATM(+)	ATM	108192120			10	DELETION		15806	186938	2821	12	NEW_VARIANT
P-0021469-T01-IM6	TRIM33 (NM_015906) - BRAF(NM_004333) rearrangement: t(1;7)(p13.2;q34)(chr1:g.114963985::chr7:g.140481644)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TRIM33:BRAF}		0	0	60	7	Intron of BRAF(-):151bp before exon 11	BRAF	140481644			1	Intron of TRIM33(-):72bp after exon 11	TRIM33	114963985			10	TRANSLOCATION		0	187436	0	69	NEW_VARIANT
P-0021482-T01-IM6	CDKN1B (NM_004064) rearrangement: t(4;12)(q32.1;p13.1)(chr4:g.161050010::chr12:g.12870987)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	31	12	Exon 1 of CDKN1B(+)	CDKN1B	12870987			4	IGR: 861Kb before RAPGEF2(+)	RAPGEF2	161050010			10	TRANSLOCATION		0	187507	0	36	NEW_VARIANT
P-0021391-T01-IM6	PTEN (NM_000314) rearrangement: c.80-25_chr10:g.89539234del	PRECISE	Note: The PTEN rearrangement results in the deletion of PTEN exon 1. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		1619	0	29	10	Intron of ATAD1(-):3Kb before exon 6	ATAD1	89539234			10	Intron of PTEN(+):24bp before exon 2	PTEN	89653757			10	DELETION		114523	187051	2021	29	NEW_VARIANT
P-0021363-T01-IM6	WHSC1L1 (NM_023034) - MED1 (NM_004774) rearrangement: t(8;17)(p11.23;q12)(chr8:g.38148034::chr17:g.37599287)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {WHSC1L1:MED1}		0	0	193	17	Intron of MED1(-):515bp after exon 3	MED1	37599287			8	Exon 17 of WHSC1L1(-)	WHSC1L1	38148034			0	TRANSLOCATION		0	186941	0	251	NEW_VARIANT
P-0021458-T01-IM6	ABCC1 (NM_004996) - BRAF (NM_004333) rearrangement: t(7,16)(q34,p13.11)(chr7:g.140493152::chr16:g.16116105)	PRECISE	The ABCC1 - BRAF rearrangement is a translocation which results in the fusion of ABCC1 exons 1-5 with BRAF exons 9-18, including the kinase domain. It is predicted to be in-frame. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant. Assay will be performed and reported under a separate accession number.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ABCC1:BRAF}		0	0	36	16	Intron of ABCC1(+):6Kb after exon 5	ABCC1	16116105			7	Intron of BRAF(-):955bp after exon 8	BRAF	140493152			10	TRANSLOCATION		0	187362	0	36	NEW_VARIANT
P-0021458-T01-IM6	DNMT3A (NM_022552) rearrangement: chr2:g.25419699_c.2716del	PRECISE	Note: The DNMT3A rearrangement results in the deletion of exon 23. One of the breakpoints is within Exon 23. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		849	0	33	2	IGR: 36Kb before POMC(-)	POMC	25419699			2	Exon 23 of DNMT3A(-)	DNMT3A	25457171			10	DELETION		37472	187361	440	34	NEW_VARIANT
P-0021409-T01-IM6	COLGALT1 (NM_024656) - KDM5A (NM_001042603) rearrangement: t(19;12)(p13.11;p13.33)(chr19:g.17669210::chr12:g.416253)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {COLGALT1:KDM5A}		0	0	33	19	Intron of COLGALT1(+):909bp before exon 2	COLGALT1	17669210			12	Exon 24 of KDM5A(-)	KDM5A	416253			10	TRANSLOCATION		0	187120	0	38	NEW_VARIANT
P-0021471-T01-IM6	CREBBP (NM_004380) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.3788736::chr17:g.79143420)	PRECISE	Note: The CREBBP rearrangement is a translocation that may result in a truncation of exons 26-31. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {AATK-AS1:CREBBP}		0	0	12	17	5-UTR of AATK-AS1(+):14Kb before coding start	AATK-AS1	79143420			16	Intron of CREBBP(-):63bp before exon 26	CREBBP	3788736			10	TRANSLOCATION		0	187431	0	12	NEW_VARIANT
P-0021495-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		114740	0	26	2	Intron of ALK(-):13bp after exon 19	ALK	29448313			2	Intron of EML4(+):2Kb after exon 5	EML4	42494226			10	INVERSION		13045913	187556	103359	24	NEW_VARIANT
P-0021503-T01-IM6	ATR (NM_001184) rearrangement: t(3;13)(q23;q33.1)(chr3:g.142188327::chr13:g.104696707)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	29	13	IGR: 619Kb before LINC01309(+)	LINC01309	104696707			3	Exon 38 of ATR(-)	ATR	142188327			10	TRANSLOCATION		0	187560	0	41	NEW_VARIANT
P-0021503-T01-IM6	TMPRSS2 (NM_001135099) rearrangment: t(6;21)(p22.3;q22.3)(chr6:g.17413047::chr21:g.42878352)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined	MANUAL_OK	3to5	3to5	-		0	0	65	21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42878352			6	5-UTR of CAP2(+):9Kb before coding start	CAP2	17413047			10	TRANSLOCATION		0	187561	0	69	NEW_VARIANT
P-0021601-T01-IM6	TECR (NM_138501) - DNAJB1 (NM_006145) rearrangement: c.119-27:TECR_c.212-543:DNAJB1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TECR:DNAJB1}		3273	0	12	19	Intron of DNAJB1(-):543bp before exon 2	DNAJB1	14628401			19	Intron of TECR(+):26bp before exon 4	TECR	14674443			10	INVERSION		46042	187762	3722	12	NEW_VARIANT
P-0021573-T01-IM6	ARID1A (NM_006015) rearrangement: g.27021676_c.928del	PRECISE	Note: The ARID1A rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4382	0	5	1	Promoter of ARID1A(+):845bp from tx start	ARID1A	27021676			1	Exon 1 of ARID1A(+)	ARID1A	27023822			10	DELETION		2146	187714	4920	5	NEW_VARIANT
P-0021573-T01-IM6	CDK6 (NM_001145306) rearrangement: t(7;8)(q21.2;p11.22)(chr7:g.92392894::chr8:g.38736050)	PRECISE	Note: The CDK6 rearrangement is a translocation that may result in a truncation of exons 4-8. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	7	8	IGR: 23Kb before PLEKHA2(+)	PLEKHA2	38736050			7	Intron of CDK6(-):11Kb after exon 3	CDK6	92392894			10	TRANSLOCATION		0	187715	0	7	NEW_VARIANT
P-0021663-T01-IM6	FGFR2 (NM_000141) rearrangement: c.-150-29_c.2301+1480del	PRECISE	Note: The FGFR2 rearrangement is an intragenic deletion of exons 1-17 which includes the kinase domain. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		57823	0	42	10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241732			10	5-UTR of FGFR2(-):114Kb before coding start	FGFR2	123353510			10	DELETION		111778	188012	62494	45	NEW_VARIANT
P-0021630-T01-IM6	SMAD3 (NM_005902) rearrangement: c.1154+36:SMAD3_chr15:g.80014264inv	PRECISE	Note: The SMAD3 rearrangement is an inversion of exon 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		35503	0	13	15	Intron of SMAD3(+):36bp after exon 8	SMAD3	67479883			15	IGR: 122Kb before MTHFS(-)	MTHFS	80014264			10	INVERSION		12534381	187907	27563	12	NEW_VARIANT
P-0021528-T01-IM6	ERBB2 (NM_004448) rearrangement: c.2970+6_c.*1538del	PRECISE	Note: The ERBB2 rearrangement is a deletion which includes exons 25-27 of ERBB2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		11127	0	32	17	Intron of ERBB2(+):6bp after exon 24	ERBB2	37882918			17	Promoter of ERBB2(+):30Kb from tx start	ERBB2	37885835			10	DELETION		2917	187639	8555	32	NEW_VARIANT
P-0021578-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		65277	0	107	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32316137			10	Intron of RET(+):625bp after exon 11	RET	43610809			10	INVERSION		11294672	187719	78931	153	NEW_VARIANT
P-0021549-T01-IM6	RPS6KB2 (NM_003952) rearrangement: c.120-43_chr11:g.67176716dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RPS6KB2:TBC1D10C}		3548	0	15	11	Intron of TBC1D10C(+):112bp after exon 9	TBC1D10C	67176716			11	Intron of RPS6KB2(+):42bp before exon 3	RPS6KB2	67196548			10	DUPLICATION		19832	187658	2584	15	NEW_VARIANT
P-0021700-T01-IM6	BRIP1 (NM_032043) rearrangement: c.3250_g.65862975del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		77919	0	5	17	Exon 20 of BRIP1(-)	BRIP1	59761157			17	Intron of BPTF(+):172bp after exon 3	BPTF	65862975			10	DELETION		6101818	188095	89668	5	NEW_VARIANT
P-0021721-T01-IM6	KMT2D (NM_003482) rearrangement: chr12:g.49421954_c.14383-30del	PRECISE	Note: The KMT2D rearrangement results in the deletion of exons 1-46. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		148453	0	8	12	Intron of KMT2D(-):30bp before exon 46	KMT2D	49421954			12	IGR: 6Kb before DHH(-)	DHH	49476991			10	DELETION		55037	188166	110820	8	NEW_VARIANT
P-0021728-T01-IM6	WT1 (NM_024426) - ELP4 (NM_019040) rearrangement: c.769+68:WT1_c.223+2679:ELP4del	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {WT1:ELP4}		12150	0	26	11	Intron of ELP4(+):3Kb after exon 1	ELP4	31534233			11	Intron of WT1(-):67bp after exon 2	WT1	32449975			10	INVERSION		915742	188146	15655	27	NEW_VARIANT
P-0021742-T01-IM6	CASZ1 (NM_001079843) - MTOR (NM_004958) Rearrangement : c.-76-722:CASZ1_c.3286-88:MTORdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {CASZ1:MTOR}		64402	0	17	1	5-UTR of CASZ1(-):74Kb before coding start	CASZ1	10772821			1	Intron of MTOR(-):88bp before exon 22	MTOR	11273053			10	DUPLICATION		500232	188174	121191	18	NEW_VARIANT
P-0021725-T01-IM6	ARID2 (NM_152641) rearrangement: c.637+919_c.1121-13del	PRECISE	Note: The ARID2 rearrangement is an intragenic deletion of exons 6-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		7378	0	42	12	Intron of ARID2(+):919bp after exon 5	ARID2	46212590			12	Intron of ARID2(+):12bp before exon 10	ARID2	46231268			10	DELETION		18678	188156	4448	45	NEW_VARIANT
P-0021826-T01-IM6	RIT1 (NM_006912) - PMF1-BGLAP (NM_001199662) rearrangement: c.163+175:RIT1_c.162-7502:PMF1-BGLAPinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {RIT1:PMF1-BGLAP}		3982	0	10	1	Intron of RIT1(-):174bp after exon 3	RIT1	155880066			1	Intron of PMF1-BGLAP(+):11Kb before exon 2	PMF1-BGLAP	156194609			10	INVERSION		314543	188288	14496	10	NEW_VARIANT
P-0021826-T01-IM6	RAD51B (NM_133509) rearrangement: c.757-5121_c.1036+28903del	PRECISE	Note: The RAD51B rearrangement is an intragenic deletion of exons 8-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		4882	0	9	14	Intron of RAD51B(+):5Kb before exon 8	RAD51B	68753480			14	Intron of RAD51B(+):29Kb after exon 10	RAD51B	68963870			10	DELETION		210390	188285	4332	9	NEW_VARIANT
P-0021826-T01-IM6	FGFR2 (NM_000141) - ANKRD11 (NM_013275) rearrangement: t(10,16)(q26.13,q24.3)(chr10:g.123243799::chr16:g.89538175)	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {FGFR2:ANKRD11}		0	0	51	16	5-UTR of ANKRD11(-):203Kb before coding start	ANKRD11	89538175			10	Intron of FGFR2(-):482bp before exon 17	FGFR2	123243799			10	TRANSLOCATION		0	188291	0	58	NEW_VARIANT
P-0021826-T01-IM6	SETD2 (NM_014159) rearrangement: c.4587-57:SETD2_chr3:g.47362971del	PRECISE	Note: The SETD2 rearrangement results in the deletion of exons 1-4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		28010	0	14	3	Intron of SETD2(-):57bp before exon 5	SETD2	47155551			3	Intron of KLHL18(+):1Kb before exon 3	KLHL18	47362971			10	DELETION		207420	188282	30117	17	NEW_VARIANT
P-0021826-T01-IM6	AGO2 (NM_012154) - TRAPPC9 (NM_031466) rearrangement: c.1448:AGO2_c.3349+13144:TRAPPC9del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {AGO2:TRAPPC9}		15054	0	23	8	Intron of TRAPPC9(-):13Kb after exon 21	TRAPPC9	140884979			8	Exon 12 of AGO2(-)	AGO2	141559353			0	DELETION		674374	188283	31634	26	NEW_VARIANT
P-0021829-T01-IM6	ETV1 (NM_001163147) rearrangement: chr7:g.29894609_c.986:ETV1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24680	0	3	7	Exon 10 of ETV1(-)	ETV1	13946110			7	Intron of WIPF3(+):20Kb after exon 2	WIPF3	29894609			10	DELETION		15948499	188262	36465	3	NEW_VARIANT
P-0021831-T01-IM6	DOT1L (NM_032482) rearrangement: c.4024_c.4606+997inv	IMPPRECISE	Note: The DOT1L rearrangement is an inversion of exon 27. One of the breakpoints is within exon 27. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		7329	0	6	19	Exon 27 of DOT1L(+)	DOT1L	2226544			19	Intron of DOT1L(+):997bp after exon 27	DOT1L	2228123			0	INVERSION		1579	188265	8526	6	NEW_VARIANT
P-0021804-T01-IM6	KMT2E (NM_018682) - ERBB3 (NM_001982) rearrangement: t(7;12)(q22.3;q13.2)(chr7:g.104661375::chr12:g.56493836)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {KMT2E:ERBB3}		0	0	6	12	Intron of ERBB3(+):23bp after exon 25	ERBB3	56493836			7	5-UTR of KMT2E(+):20Kb before coding start	KMT2E	104661375			10	TRANSLOCATION		0	188256	0	6	NEW_VARIANT
P-0021822-T01-IM6	AKT2 (NM_001626) rearrangement: t(1,19)(p36.13,q13.2)(chr1:g.16550370::chr19:g.40762860)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	37	19	Exon 3 of AKT2(-)	AKT2	40762860			1	IGR: 8Kb before RSG1(-)	RSG1	16550370			10	TRANSLOCATION		0	188272	0	40	NEW_VARIANT
P-0021675-T01-IM6	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.973+2973:KANSL2_c.2726:KMT2Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KANSL2:KMT2D}		110720	0	27	12	Intron of KANSL2(-):3Kb after exon 7	KANSL2	49058503			12	Exon 10 of KMT2D(-)	KMT2D	49444740			10	DUPLICATION		386237	188076	134930	35	NEW_VARIANT
P-0021698-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		84910	0	73	21	Intron of ERG(-):2Kb before exon 2	ERG	39819660			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872583			10	DELETION		3052923	188093	53991	79	NEW_VARIANT
P-0021711-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-568_chr21:g.40054074del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		54178	0	9	21	IGR: 57Kb before LINC00114(-)	LINC00114	40054074			21	Intron of TMPRSS2(-):568bp before exon 2	TMPRSS2	42870684			10	DELETION		2816610	188129	41083	9	NEW_VARIANT
P-0021833-T01-IM6	WHSC1L1 (NM_023034) Rearrangement : c.2758+22:WHSC1L1_chr8:g.41953873inv	PRECISE	Note: The WHSC1L1 Rearrangement results in the inversion of exons 1-15 of WHSC1L1 exons.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		74687	0	27	8	Intron of WHSC1L1(-):21bp after exon 15	WHSC1L1	38156940			8	IGR: 57Kb before AP3M2(+)	AP3M2	41953873			10	INVERSION		3796933	188296	130120	29	NEW_VARIANT
P-0021863-T01-IM6	B2M (NM_004048) rearrangement: g.44883857_c.68-82del	PRECISE	Note: The B2M rearrangement results in the deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3188	0	5	15	Intron of SPG11(-):671bp after exon 27	SPG11	44883857			15	Intron of B2M(+):81bp before exon 2	B2M	45007539			10	DELETION		123682	188409	3631	5	NEW_VARIANT
P-0021873-T01-IM6	DROSHA (NM_013235) rearrangement: t(5;12)(p13.3;q24.23)(chr5:g.31483658::chr12:g.119252705)	PRECISE	Note: The DROSHA rearrangement is a translocation that may result in a truncation of exons 16-35. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	84	12	IGR: 167Kb before SRRM4(+)	SRRM4	119252705			5	Intron of DROSHA(-):2bp after exon 15	DROSHA	31483658			10	TRANSLOCATION		0	188414	0	96	NEW_VARIANT
P-0021862-T01-IM6	PARK2 (NM_004562) rearrangement: t(6;7)(p22.3;q22.1)(chr6:g.162206907::chr7:g.98151994)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	76	7	IGR: 95Kb before NPTX2(+)	NPTX2	98151994			6	Exon 7 of PARK2(-)	PARK2	162206907			10	TRANSLOCATION		0	188408	0	74	NEW_VARIANT
P-0021882-T01-IM6	NTRK1 (NM_002529) rearrangement: c.847_c.850+524del	PRECISE	Note: The NTRK1 rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4419	4	3	1	Exon 7 of NTRK1(+)	NTRK1	156841544			1	Intron of NTRK1(+):524bp after exon 7	NTRK1	156842071			9	DELETION		527	188437	6380	0	NEW_VARIANT
P-0021882-T01-IM6	CIC (NM_015125) rearrangement: c.4195+27_c.4370del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2563	3	2	19	Intron of CIC(+):27bp after exon 17	CIC	42798268			19	Exon 19 of CIC(+)	CIC	42798798			8	DELETION		530	188439	3558	0	NEW_VARIANT
P-0021922-T01-IM6	TMBIM6 (NM_001098576) - KMT2D (NM_003482) rearrangement: c.144+4807:TMBIM6_c.2409:KMT2Dinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TMBIM6:KMT2D}		31840	0	34	12	Exon 10 of KMT2D(-)	KMT2D	49445057			12	Intron of TMBIM6(+):5Kb after exon 1	TMBIM6	50140870			10	INVERSION		695813	188510	25191	42	NEW_VARIANT
P-0021064-T01-IM6	NF1 (NM_001042492) rearrangement: c.4759_c.4835+22210del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exon 36. One of the breakpoints is within exon 36.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		735	0	2	17	Exon 36 of NF1(+)	NF1	29592281			17	Intron of NF1(+):22Kb after exon 36	NF1	29614567			8	DELETION		22286	186171	201	2	NEW_VARIANT
P-0021947-T01-IM6	EWSR1 (NM_013986) Rearrangement : c.794-828:EWSR1_c.-716:SEC14LR	PRECISE	Note: The EWSR1 Rearrangement results in the deletion of exons 10-18 of EWSR1.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		67500	0	44	22	Intron of EWSR1(+):255bp before exon 10	EWSR1	29687298			22	Promoter of SEC14L3(-):13Kb from tx start	SEC14L3	30868661			10	DELETION		1181363	188555	44811	52	NEW_VARIANT
P-0022003-T01-IM6	ERBB4 (NM_005235) rearrangement: c.2643+122_c.3135+4521del	PRECISE	Note: The ERBB4 rearrangement is an intragenic deletion of exons 22-25. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		4832	0	3	2	Intron of ERBB4(-):5Kb after exon 25	ERBB4	212280645			2	Intron of ERBB4(-):121bp after exon 21	ERBB4	212295548			7	DELETION		14903	188707	3996	3	NEW_VARIANT
P-0022179-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-135_c.126+592del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		6851	0	58	21	Intron of TMPRSS2(-):591bp after exon 2	TMPRSS2	42869454			21	Intron of TMPRSS2(-):135bp before exon 2	TMPRSS2	42870251			10	DELETION		797	189908	4484	68	NEW_VARIANT
P-0022046-T01-IM6	NTRK1 (NM_002529) rearrangement: g.156703825_c.1354+180inv	PRECISE	Note: The NTRK1 rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		54056	0	117	1	Exon 6 of RRNAD1(+)	RRNAD1	156703825			1	Intron of NTRK1(+):180bp after exon 11	NTRK1	156844980			10	INVERSION		141155	189141	88471	116	NEW_VARIANT
P-0022046-T01-IM6	FBXW7 (NM_033632) rearrangement: c.501+1999_c.371del	PRECISE	Note: The FBXW7 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		886	0	22	4	Intron of FBXW7(-):2Kb after exon 2	FBXW7	153330456			4	Exon 2 of FBXW7(-)	FBXW7	153332585			10	DELETION		2129	189137	560	23	NEW_VARIANT
P-0021980-T01-IM6	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	PRECISE	Note: The NCOA4 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		33042	0	13	10	Intron of RET(+):366bp after exon 11	RET	43610550			10	Intron of TIMM23B(+):149Kb before exon 7	TIMM23B	51584025			10	DUPLICATION		7973475	188640	25330	38	NEW_VARIANT
P-0022110-T01-IM6	ERBB2 (NM_004448) rearrangement: t(17;X)(q12;p21.2)(chr17:g.37883536::chrX:g.30637819)	PRECISE	Note: The ERBB2 rearrangement is a translocation that may result in a truncation of exons 26-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	X	IGR: 34Kb before GK(+)	GK	30637819			17	Intron of ERBB2(+):11bp before exon 26	ERBB2	37883536			10	TRANSLOCATION		0	189649	0	8	NEW_VARIANT
P-0022083-T01-IM6	STAT3 (NM_139276) Rearrangement : c.274-1:STAT3_chr17:g.40549182del	PRECISE	Note: The STAT3 Rearrangement results in the deletion of exons 1-4 of STAT3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3491	0	5	17	Intron of STAT3(-):1bp before exon 4	STAT3	40497676			17	IGR: 5Kb before PTRF(-)	PTRF	40549182			10	DELETION		51506	189340	3648	6	NEW_VARIANT
P-0022083-T01-IM6	EWSR1 (NM_013986) Rearrangement : t(15;22)(q14;q12.2)(chr15:g.34430755::chr22:g.29686911)	PRECISE	Note: The EWSR1 Rearrangement results in the possible truncation of EWSR1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	20	22	Intron of EWSR1(+):642bp before exon 10	EWSR1	29686911			15	Promoter of KATNBL1(-):2Kb from tx start	KATNBL1	34430755			10	TRANSLOCATION		0	189341	0	23	NEW_VARIANT
P-0022372-T01-IM6	CD74 (NM_001025159) - NBPF10 (NM_001039703) rearrangement: t(1;5)(q21.1;q32)(chr1:g.145430829::chr5:g.149782962)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	8	5	Intron of CD74(-):87bp before exon 7	CD74	149782962			1	Intron of NBPF20(+):66Kb after exon 99	NBPF20	145430829			10	TRANSLOCATION		0	190451	0	10	NEW_VARIANT
P-0022372-T01-IM6	ROS1 (NM_002944) rearrangement: c.2496+345_c.5367-1454inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		95691	0	32	6	Intron of ROS1(-):1Kb before exon 33	ROS1	117649031			6	Intron of ROS1(-):344bp after exon 16	ROS1	117704135			10	INVERSION		55104	190450	54886	34	NEW_VARIANT
P-0022170-T01-IM6	FGFR4 (NM_213647) - NSD1 (NM_022455) rearrangement: c.603+17:FGFR4_c.927+12349:NSD1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR4:NSD1}		32530	0	5	5	Intron of FGFR4(+):17bp after exon 5	FGFR4	176518122			5	Intron of NSD1(+):12Kb after exon 2	NSD1	176575380			10	DELETION		57258	189832	30842	5	NEW_VARIANT
P-0022088-T01-IM6	TP53 (NM_000546) Rearrangement: c.993+232_c.1101-324del	PRECISE	Note: The TP53 Rearrangement results in the intragenic deletion of exon 10 of TP53. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2060	0	12	17	Intron of TP53(-):324bp before exon 11	TP53	7573332			17	Intron of TP53(-):231bp after exon 9	TP53	7576621			10	DELETION		3289	189351	472	25	NEW_VARIANT
P-0022088-T01-IM6	MAP3K1 (NM_005921) Rearrangement : c.3008_c.3819+291del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2634	0	71	5	Exon 14 of MAP3K1(+)	MAP3K1	56178035			5	Intron of MAP3K1(+):291bp after exon 15	MAP3K1	56179797			10	DELETION		1762	189350	2319	144	NEW_VARIANT
P-0022185-T01-IM6	PAX8 (NM_003466)  rearrangement: t(2;8)(q13;q24.21)(chr2:g.113979260::chr8:g.129096859)	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript Fusion {PAX8:PVT1}		0	0	26	8	5-UTR of PVT1(+):17Kb before coding start	PVT1	129096859			2	Intron of PAX8(-):2Kb before exon 11	PAX8	113979260			10	TRANSLOCATION		0	189902	0	28	NEW_VARIANT
P-0022118-T01-IM6	CIC (NM_015125) rearrangement : c.4019_c.4531inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		7024	0	3	19	Exon 16 of CIC(+)	CIC	42797967			19	Exon 20 of CIC(+)	CIC	42799047			8	INVERSION		1080	189668	15785	3	NEW_VARIANT
P-0022058-T01-IM6	MAD1L1 (NM_001013837) - CARD11 (NM_032415) rearrangement: c.1505+8166:MAD1L1_c.1654-67:CARD11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {MAD1L1:CARD11}		23505	0	21	7	Intron of MAD1L1(-):8Kb after exon 15	MAD1L1	2011922			7	Intron of CARD11(-):67bp before exon 13	CARD11	2968399			10	DUPLICATION		956477	189219	21728	24	NEW_VARIANT
P-0022092-T01-IM6	CDKN1B (NM_004064) Rearrangement : c.476-90:CDKN1B_chr12:g.38741621inv	PRECISE	Note: The CDKN1B Rearrangement results in the inversion of exon1 of CDKN1B. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		85717	0	3	12	Intron of CDKN1B(+):89bp before exon 2	CDKN1B	12871669			12	IGR: 31Kb before ALG10B(+)	ALG10B	38741621			7	INVERSION		25869952	189534	67516	4	NEW_VARIANT
P-0022197-T01-IM6	ARID2 (NM_152641) rearrangement: c.4773+92_chr12:g.68840062inv	PRECISE	Note: The ARID2 rearrangement results in the inversion of exons 16-21. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		325443	0	17	12	Intron of ARID2(+):92bp after exon 15	ARID2	46246771			12	3-UTR of LOC100507195(-):5Kb after coding stop	LOC100507195	68840062			10	INVERSION		22593291	189935	307708	17	NEW_VARIANT
P-0022197-T01-IM6	CCT2 (NM_006431) - POLE (NM_006231) rearrangement: c.1470:CCT2_c.4885:POLEinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CCT2:POLE}		183167	0	77	12	Exon 15 of CCT2(+)	CCT2	69993677			12	Exon 37 of POLE(-)	POLE	133219159			0	INVERSION		63225482	189936	202858	76	NEW_VARIANT
P-0022189-T01-IM6	TMPRSS2 (NM_001135099) - SKIL (NM_001248008) rearrangement: t(3;21)(q26.2;q22.3)(chr3:g.170075134::chr21:g.42867710)	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript Fusion {TMPRSS2:SKIL}		0	0	19	21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867710			3	Promoter of SKIL(+):338bp from tx start	SKIL	170075134			10	TRANSLOCATION		0	189950	0	31	NEW_VARIANT
P-0022364-T01-IM6	PARP1 (NM_001618) rearrangement: chr1:g.162434663_c.2505+39inv	PRECISE	Note: The PARP1 rearrangement results in the inversion of exons 1-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		210123	0	3	1	IGR: 32Kb before UHMK1(+)	UHMK1	162434663			1	Intron of PARP1(-):38bp after exon 18	PARP1	226553616			10	INVERSION		64118953	190394	328677	3	NEW_VARIANT
P-0022364-T01-IM6	BRIP1 (NM_032043) rearrangement: c.2380-766_c.1936-105inv	PRECISE	Note: The BRIP1 rearrangement results in the inversion of exons 14-16. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4442	0	27	17	Intron of BRIP1(-):766bp before exon 17	BRIP1	59794190			17	Intron of BRIP1(-):105bp before exon 14	BRIP1	59854028			10	INVERSION		59838	190395	13939	25	NEW_VARIANT
P-0022086-T01-IM6	KDM5A (NM_001042603) Rearrangement: c.2720_c.2897+2215del	IMPPRECISE	Note: The KDM5A Rearrangement results in the intragenic deletion of exon19. One of the breakpoints is within exon19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1839	0	6	12	Intron of KDM5A(-):2Kb after exon 19	KDM5A	425057			12	Exon 19 of KDM5A(-)	KDM5A	427449			0	DELETION		2392	189348	1637	6	NEW_VARIANT
P-0022128-T01-IM6	CSDE1 (NM_001242891) rearrangement: chr1:g.114598243_c.2487+20:CSDE1del	PRECISE	Note: The CSDE1 rearrangement is a deletion of exon 21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		10579	0	12	1	IGR: 34Kb before SYT6(-)	SYT6	114598243			1	Intron of CSDE1(-):19bp after exon 20	CSDE1	115261214			10	DELETION		662971	189681	6887	12	NEW_VARIANT
P-0022117-T01-IM6	NTRK1 (NM_002529) rearrangement: c.684_chr1:g.203839162inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		199054	0	17	1	Exon 6 of NTRK1(+)	NTRK1	156838406			1	3-UTR of SNRPE(+):8Kb after coding stop	SNRPE	203839162			10	INVERSION		47000756	189665	130033	22	NEW_VARIANT
P-0022117-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1-3 fused to ERG exons 2-10): c.304:TMPRSS2_c.18+8044:ERGdel	PRECISE	Note: One of the breakpoints is within TMPRSS2 exon 3.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TMPRSS2:ERG}		24314	0	48	21	Intron of ERG(-):8Kb after exon 1	ERG	39862243			21	Exon 3 of TMPRSS2(-)	TMPRSS2	42866328			10	DELETION		3004085	189664	5357	50	NEW_VARIANT
P-0021975-T01-IM6	NID2 (NM_007361) - FGFR2 (NM_000141) rearrangement: t(10;14)(q26.13;q22.1)(chr10:g.123240637::chr14:g.52482743)	PRECISE	Note: The NID2 - FGFR2 rearrangement is a translocation which results in the fusion of NID2 exon 14 to FGFR2 exon 18. Multiple FGFR2 rearrangements were detected and this sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NID2:FGFR2}		0	0	103	14	Intron of NID2(-):750bp before exon 15	NID2	52482743			10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240637			10	TRANSLOCATION		0	188657	0	123	NEW_VARIANT
P-0022084-T01-IM6	SESN3 (NM_144665) Rearrangement: c.526-1622_c.1106del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7427	0	61	11	Exon 8 of SESN3(-)	SESN3	94911024			11	Intron of SESN3(-):2Kb before exon 5	SESN3	94920278			10	DELETION		9254	189342	4658	135	NEW_VARIANT
P-0022084-T01-IM6	NOTCH3 (NM_000435) Rearrangement : t(1;19)(q21.3;p13.12)(chr1:g.151973890::chr19:g.15281223)	PRECISE	Note: The NOTCH3 Rearrangement results in the possible truncation of NOTCH3. One of the breakpoints is within exon 27.  The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	32	19	Exon 27 of NOTCH3(-)	NOTCH3	15281223			1	IGR: 17Kb before NBPF18P(+)	NBPF18P	151973890			10	TRANSLOCATION		0	189346	0	50	NEW_VARIANT
P-0022099-T01-IM6	KDM5C (NM_004187) Rearrangement : c.963+158_c.1746+3254del	PRECISE	Note: The KDM5C Rearrangement results in the intragenic deletion of exons 8-12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		4894	0	2	X	Intron of KDM5C(-):3Kb after exon 12	KDM5C	53236342			X	Intron of KDM5C(-):157bp after exon 7	KDM5C	53244819			6	DELETION		8477	189554	5388	3	NEW_VARIANT
P-0022358-T01-IM6	XIAP (NM_001167) rearrangement: c.-33+7954_c.1100-72del	PRECISE	Note: The XIAP rearrangement results in the deletion of the 5'UTR and exons 1-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		12147	0	16	X	5-UTR of XIAP(+):17Kb before coding start	XIAP	123002097			X	Intron of XIAP(+):71bp before exon 6	XIAP	123034271			10	DELETION		32174	190391	6484	17	NEW_VARIANT
P-0022456-T01-IM6	FGFR1 (NM_001174067) rearrangement: t(2;8)(q31.1;p11.23)(chr2:g.174604210::chr8:g.38276953)	PRECISE	Note: The FGFR1 rearrangement is a translocation which may result in the truncation of FGFR1 after exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	34	8	Intron of FGFR1(-):97bp after exon 10	FGFR1	38276953			2	IGR: 167Kb before SP3(-)	SP3	174604210			10	TRANSLOCATION		0	190858	0	39	NEW_VARIANT
P-0022348-T01-IM6	ETV6 (NM_001987) rearrangement: t(2;12)(q22.3;p13.2)(chr2:g.146814969::chr12:g.12022241)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	44	12	Intron of ETV6(+):116bp before exon 5	ETV6	12022241			2	IGR: 530Kb before PABPC1P2(+)	PABPC1P2	146814969			10	TRANSLOCATION		0	190330	0	47	NEW_VARIANT
P-0022444-T01-IM6	KDM5A (NM_001042603) rearrangement: t(12;19)(p13.33;p13.11)(chr12:g.459868::chr19:g.17358572)	PRECISE	Note: The KDM5A rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	47	19	Promoter of USHBP1(-):2Kb from tx start	USHBP1	17358572			12	Exon 10 of KDM5A(-)	KDM5A	459868			10	TRANSLOCATION		0	190856	0	67	NEW_VARIANT
P-0022446-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		47793	0	61	21	Intron of ERG(-):59Kb after exon 3	ERG	39888600			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868538			10	DELETION		2979938	190870	37382	75	NEW_VARIANT
P-0022425-T01-IM6	FAT1 (NM_005245) rearrangement: c.2732_c.3265+636inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		4446	0	82	4	Intron of FAT1(-):635bp after exon 2	FAT1	187627081			4	Exon 2 of FAT1(-)	FAT1	187628250			10	INVERSION		1169	190809	6104	78	NEW_VARIANT
P-0022284-T01-IM6	PALB2 (NM_024675) - SCNN1B (NM_000336) rearrangement: c.3201+79:PALB2_c.777-356:SCNN1Bdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		3861	0	82	16	Intron of SCNN1B(+):355bp before exon 5	SCNN1B	23378821			16	Intron of PALB2(-):78bp after exon 11	PALB2	23625246			10	DELETION		246425	190092	6604	83	NEW_VARIANT
P-0022337-T01-IM6	NRG3 (NM_001010848) - FGFR2 (NM_000141) Rearrangement : c.953+89877:NRG3_c.2301+1489:FGFR2inv	PRECISE	Note: The NRG3  - FGFR2 Rearrangement  results in the fusion of NRG3 exons 1-2 with FGFR2 exon 18. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NRG3:FGFR2}		170853	0	38	10	Intron of NRG3(+):90Kb after exon 3	NRG3	84208501			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241723			10	INVERSION		39033222	190654	125154	39	NEW_VARIANT
P-0022337-T01-IM6	FGFR2 (NM_000141) - TBC1D4 (NM_014832) Rearrangement : t(10;13)(q26.13;q22.2)(chr10:g.123241723::chr13:g.75946348)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:TBC1D4}		0	0	70	13	Intron of TBC1D4(-):10Kb before exon 2	TBC1D4	75946348			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241723			10	TRANSLOCATION		0	190655	0	79	NEW_VARIANT
P-0022337-T01-IM6	RBM10 (NM_001204468) Rearrangement: c.2146-1291_c.2362-19del	PRECISE	Note: The RBM10 Rearrangement results in the intragenic deletion of exons 18-19. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		3993	0	10	X	Intron of RBM10(+):1Kb before exon 18	RBM10	47043163			X	Intron of RBM10(+):18bp before exon 20	RBM10	47044822			10	DELETION		1659	190653	2840	16	NEW_VARIANT
P-0022420-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1656:TMPRSS2_c.-149-19186:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		78190	0	70	21	3-UTR of ERG(-):58Kb after coding stop	ERG	39976055			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871772			10	DELETION		2895717	190819	29132	87	NEW_VARIANT
P-0022383-T01-IM6	RERE (NM_001042681) - MTOR (NM_004958) rearrangement: c.725+7095:RERE_c.7301-72:MTORdup	PRECISE	Note: The RERE - MTOR rearrangement is a duplication that results in the fusion of RERE exons 1-6 with MTOR exons 54-58.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RERE:MTOR}		59041	0	21	1	Intron of RERE(-):7Kb after exon 6	RERE	8609439			1	Intron of MTOR(-):72bp before exon 54	MTOR	11173046			10	DUPLICATION		2563607	190502	52645	21	NEW_VARIANT
P-0022383-T01-IM6	NUFIP1 (NM_012345) - BRCA2 (NM_000059) rearrangement: c.412+1126:NUFIP1_c.516+46:BRCA2inv	PRECISE	Note: The NUFIP1 - BRCA2 rearrangement is an inversion that results in the fusion of NUFIP1 exon 1 with BRCA2 exons 7-27.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {NUFIP1:BRCA2}		119085	0	6	13	Intron of BRCA2(+):46bp after exon 6	BRCA2	32900465			13	Intron of NUFIP1(-):1Kb after exon 1	NUFIP1	45562034			10	INVERSION		12661569	190503	84491	6	NEW_VARIANT
P-0022385-T01-IM6	MDC1 (NM_014641) rearrangement: t(1;6)(q44;p21.33)(chr1:g.246673483::chr6:g.30680457)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMYD3:MDC1}		0	0	26	6	Exon 5 of MDC1(-)	MDC1	30680457			1	Promoter of SMYD3(-):761Kb from tx start	SMYD3	246673483			10	TRANSLOCATION		0	190491	0	27	NEW_VARIANT
P-0022421-T01-IM6	PAX8 (NM_003466) rearrangement: chr2:g.114793050_c.1088-161:PAX8inv	PRECISE	Note: The PAX8 rearrangement results in the inversion of exons 1-9. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		77035	0	43	2	Intron of PAX8(-):161bp before exon 10	PAX8	113984994			2	IGR: 56Kb before LINC01191(+)	LINC01191	114793050			10	INVERSION		808056	190841	122467	53	NEW_VARIANT
P-0022421-T01-IM6	HIST1H3D (NM_003530) rearrangement: c.-2287_c.72del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1342	0	23	6	Exon 2 of HIST1H3D(-)	HIST1H3D	26197407			6	Promoter of HIST1H3D(-):4Kb from tx start	HIST1H3D	26201354			10	DELETION		3947	190839	1675	22	NEW_VARIANT
P-0022423-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.-145+32530_c.1482del	PRECISE	Note: The ANKRD11 rearrangement is a deletion of exons 1-9. One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		25800	0	38	16	Exon 9 of ANKRD11(-)	ANKRD11	89351468			16	5-UTR of ANKRD11(-):189Kb before coding start	ANKRD11	89524123			10	DELETION		172655	190837	22959	38	NEW_VARIANT
P-0022502-T01-IM6	NOTCH1 (NM_017617) Rearrangement : c.4068_c.4967del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9447	0	86	9	Exon 26 of NOTCH1(-)	NOTCH1	139399176			9	Exon 25 of NOTCH1(-)	NOTCH1	139400280			0	DELETION		1104	191031	15164	89	NEW_VARIANT
P-0022533-T02-IM6	ERBB2 (NM_004448) rearrangement: c.1022-127:ERBB2_chr17:g.1574221inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ERBB2:PRPF8}		404129	0	10	17	Intron of PRPF8(-):2Kb after exon 24	PRPF8	1574221			17	Intron of ERBB2(+):126bp before exon 9	ERBB2	37868448			10	INVERSION		36294227	191153	402683	10	NEW_VARIANT
P-0022533-T02-IM6	BABAM1 (NM_001033549) rearrangement:  chr19:g.13693284_c.134:BABAM1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		187245	0	39	19	IGR: 165Kb before CCDC130(+)	CCDC130	13693284			19	Exon 2 of BABAM1(+)	BABAM1	17379749			10	INVERSION		3686465	191155	359401	107	NEW_VARIANT
P-0022533-T02-IM6	BABAM1 (NM_001033549) rearrangement:  chr19:g.15602332_c.-4:BABAM1del	PRECISE	Note: The BABAM1 rearrangement results in the deletion of the promoter region and 5-UTR of BABAM1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3408	0	12	19	IGR: 17Kb before CYP4F22(+)	CYP4F22	15602332			19	5-UTR of BABAM1(+):3bp before coding start	BABAM1	17379612			10	DELETION		1777280	191152	5080	26	NEW_VARIANT
P-0022509-T01-IM6	RAD52 (NM_134424) Rearrangement : c.-18-5943_c.349-18del	PRECISE	Note: The RAD52 Rearrangement results in the deletion of exons 1-5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		7272	0	33	12	Intron of RAD52(-):18bp before exon 6	RAD52	1036447			12	5-UTR of RAD52(-):26Kb before coding start	RAD52	1048185			10	DELETION		11738	191052	5259	40	NEW_VARIANT
P-0022509-T01-IM6	ALK (NM_004304) Rearrangement : c.3173-264:ALK_chr2:g.153686528del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		732678	0	57	2	Intron of ALK(-):264bp before exon 20	ALK	29446658			2	IGR: 112Kb before ARL6IP6(+)	ARL6IP6	153686528			10	DELETION		124239870	191050	559639	61	NEW_VARIANT
P-0022577-T01-IM6	GLI1 (NM_005269) rearrangement: t(1;12)(p13.3;p13.q)(chr1:g.111592651::chr12:g.57860272)	IMPPRECISE	Note: The GLI1 rearrangement is a translocation that may result in a truncation of exons 9-12. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	11	12	Intron of GLI1(+):100bp after exon 8	GLI1	57860272			1	IGR: 67Kb before DRAM2(-)	DRAM2	111592651			0	TRANSLOCATION		0	191288	0	10	NEW_VARIANT
P-0022489-T01-IM6	JAK2 (NM_004972) rearrangement: c.710_chr9:g.5484812del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		30011	0	8	9	Exon 7 of JAK2(+)	JAK2	5054658			9	IGR: 26Kb before PDCD1LG2(+)	PDCD1LG2	5484812			10	DELETION		430154	190946	13673	9	NEW_VARIANT
P-0022579-T01-IM6	KIAA1467 (NM_020853) - ETV6 (NM_001987) rearrangement: c.1643-1210:KIAA1467_c.1010-2295:ETV6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {KIAA1467:ETV6}		15758	0	3	12	Intron of ETV6(+):2Kb before exon 6	ETV6	12035084			12	Intron of KIAA1467(+):1Kb before exon 12	KIAA1467	13231513			10	DUPLICATION		1196429	191296	30777	7	NEW_VARIANT
P-0022431-T01-IM6	TERT (NM_198253) rearrangement: c.2693:TERT_chr5:g.21230021del	PRECISE	Note: The TERT rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		51567	0	2	5	Exon 11 of TERT(-)	TERT	1264669			5	IGR: 230Kb before GUSBP1(+)	GUSBP1	21230021			10	DELETION		19965352	190733	58148	4	NEW_VARIANT
P-0022479-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.5628_c.-144-248del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		60721	0	10	16	Exon 9 of ANKRD11(-)	ANKRD11	89347322			16	5-UTR of ANKRD11(-):150Kb before coding start	ANKRD11	89485024			10	DELETION		137702	190962	53778	13	NEW_VARIANT
P-0022436-T01-IM6	RALGAPA1 (NM_194301) - FOXA1 (NM_004496) rearrangement: c.4159-1266:RALGAPA1_c.1001:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RALGAPA1:FOXA1}		27811	0	16	14	Intron of RALGAPA1(-):1Kb before exon 31	RALGAPA1	36106070			14	Exon 2 of FOXA1(-)	FOXA1	38060988			10	DUPLICATION		1954918	190736	21770	16	NEW_VARIANT
P-0022436-T01-IM6	TERT (NM_198253) rearrangement: t(5;16)(p15.33;p13.13)(chr5:g.1260698::chr16:g.11963343)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	6	16	3-UTR of GSPT1(-):4Kb after coding stop	GSPT1	11963343			5	Exon 12 of TERT(-)	TERT	1260698			10	TRANSLOCATION		0	190738	0	6	NEW_VARIANT
P-0022436-T01-IM6	RCAN1 (NM_004414) - RUNX1 (NM_001754)  rearrangement: c.252+38208:RCAN1_c.862:RUNX1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RCAN1:RUNX1}		6283	0	12	21	Intron of RCAN1(-):38Kb after exon 1	RCAN1	35948851			21	Exon 8 of RUNX1(-)	RUNX1	36171703			0	DUPLICATION		222852	190737	8479	12	NEW_VARIANT
P-0022529-T01-IM6	ALK (NM_004304) Rearrangement : c.3173-887:ALK_chr2:g.30245608del	PRECISE	Note: The ALK Rearrangement results in the deletion of exons 1-19 of ALK. It doesnt include the protein kinase domain of ALK.	MANUAL_OK	3to5	3to5	-		78105	0	36	2	Intron of ALK(-):887bp before exon 20	ALK	29447281			2	IGR: 124Kb before YPEL5(+)	YPEL5	30245608			10	DELETION		798327	191084	85736	36	NEW_VARIANT
P-0022578-T01-IM6	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)	PRECISE	Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	7	20	Intron of SDC4(-):557bp before exon 3	SDC4	43962266			6	Intron of ROS1(-):2Kb before exon 32	ROS1	117652158			10	TRANSLOCATION		0	191293	0	9	NEW_VARIANT
P-0022482-T01-IM6	CARD11 (NM_032415) rearrangement: c.908_chr7:g.3588919del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		13002	0	41	7	Exon 7 of CARD11(-)	CARD11	2978422			7	Intron of SDK1(+):70Kb before exon 2	SDK1	3588919			10	DELETION		610497	190937	17096	42	NEW_VARIANT
P-0022526-T01-IM6	ARID1A (NM_006015) Rearrangement : c.-1565_c.756del	PRECISE	Note: The ARID1A Rearrangement results in the deletion of exon1 of ARID1A. One of the breakpoints is within exon1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3479	0	72	1	Promoter of ARID1A(+):1Kb from tx start	ARID1A	27021330			1	Exon 1 of ARID1A(+)	ARID1A	27023650			10	DELETION		2320	191071	3210	81	NEW_VARIANT
P-0022557-T01-IM6	TMPRSS2 (NM_001135099) - FOXP1 (NM_001244814) rearrangement: t(3;21)(p13;q22.3)(chr3:g.71060348::chr21:g.:42869050)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TMPRSS2:FOXP1}		0	0	61	21	Intron of TMPRSS2(-):995bp after exon 2	TMPRSS2	42869050			3	Intron of FOXP1(-):4Kb after exon 8	FOXP1	71060348			10	TRANSLOCATION		0	191245	0	61	NEW_VARIANT
P-0022437-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q23;q22.3)(chr15:g.70805740::chr21:g.42874076)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined. The possibility of a more complex rearrangement resulting in a fusion of TMPRSS2 with another gene cannot be excluded. If clinically indicated, further analysis using the Archer targeted RNAseq assay can be performed.	MANUAL_OK	3to5	3to5	-		0	0	95	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874076			15	IGR: 102Kb before SALRNA3(+)	SALRNA3	70805740			10	TRANSLOCATION		0	190711	0	94	NEW_VARIANT
P-0022607-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-414:CCDC6_c.2137-820:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		41230	0	22	10	Intron of RET(+):819bp before exon 12	RET	43611212			10	Intron of CCDC6(-):414bp before exon 2	CCDC6	61612874			10	INVERSION		18001662	191414	11091	24	NEW_VARIANT
P-0022778-T01-IM6	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(7;21)(q34;q22.3)(chr7:g.140483147::chr21:g.42878796)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:BRAF}		0	0	51	21	Intron of TMPRSS2(-):1Kb after exon 1	TMPRSS2	42878796			7	Intron of BRAF(-):190bp before exon 10	BRAF	140483147			10	TRANSLOCATION		0	192173	0	56	NEW_VARIANT
P-0022611-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3513:TMPRSS2_c.18+11133:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		81670	0	67	21	Intron of ERG(-):11Kb after exon 1	ERG	39859154			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873629			10	DELETION		3014475	191432	62360	69	NEW_VARIANT
P-0022566-T01-IM6	PDPK1 (NM_002613) rearrangement: c.24+4:PDPK1_chr16:g.12881579del	PRECISE	Note: The PDPK1 rearrangement results in the deletion of exons 2-11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		194790	0	11	16	Intron of PDPK1(+):4bp after exon 1	PDPK1	2588141			16	Intron of CPPED1(-):6Kb before exon 2	CPPED1	12881579			10	DELETION		10293438	191367	124345	12	NEW_VARIANT
P-0022566-T01-IM6	GRIN2A (NM_001134407) rearrangement: chr16:g.18959069_c.450:GRIN2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		34157	0	6	16	Exon 3 of GRIN2A(-)	GRIN2A	10032373			16	IGR: 36Kb before TMC7(+)	TMC7	18959069			10	INVERSION		8926696	191368	24263	7	NEW_VARIANT
P-0022660-T01-IM6	TGFBR2 (NM_001024847) rearrangement: chr3:g.30383935_c.180del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2413	0	31	3	IGR: 264Kb before TGFBR2(+)	TGFBR2	30383935			3	Exon 3 of TGFBR2(+)	TGFBR2	30686249			10	DELETION		302314	191647	1324	72	NEW_VARIANT
P-0022642-T01-IM6	CCDC6(NM_005436) - RET(NM_020975) Fusion (CCDC6 exon1 fused to RET exon12) : c.304-14214:CCDC6_c.2137-273:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		37542	0	18	10	Intron of RET(+):263bp before exon 12	RET	43611768			10	Intron of CCDC6(-):14Kb before exon 2	CCDC6	61626673			10	INVERSION		18014905	191579	17640	27	NEW_VARIANT
P-0022569-T01-IM6	ETV6 (NM_001987) rearrangement: c.34-33802_c.463+2619inv	IMPPRECISE	Note: The ETV6 rearrangement results in the inversion of exons 2-4. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		22157	0	30	12	Intron of ETV6(+):34Kb before exon 2	ETV6	11871582			12	Intron of ETV6(+):3Kb after exon 4	ETV6	12009114			0	INVERSION		137532	191361	44314	44	NEW_VARIANT
P-0022569-T01-IM6	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	PRECISE	Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		40582	0	4	4	Intron of TACC3(+):193bp before exon 8	TACC3	1737264			4	Intron of FGFR3(+):44bp after exon 17	FGFR3	1808705			10	DUPLICATION		71441	191358	35987	4	NEW_VARIANT
P-0022716-T01-IM6	LATS2 (NM_014572) rearrangement: c.1562_c.*900del	PRECISE	Note: The LATS2 rearrangement is a deletion of exons 4-8. One of the breakpoints is within exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17269	0	12	13	3-UTR of LATS2(-):899bp after coding stop	LATS2	21548109			13	Exon 4 of LATS2(-)	LATS2	21562357			10	DELETION		14248	191966	22168	14	NEW_VARIANT
P-0022798-T01-IM6	KDM5A (NM_001042603) - OSBPL8 (NM_020841) Rearrangement : c.567:KDM5A_c.1630+2182:OSBPL8dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KDM5A:OSBPL8}		986778	0	18	12	Exon 5 of KDM5A(-)	KDM5A	472234			12	Intron of OSBPL8(-):2Kb after exon 15	OSBPL8	76775852			10	DUPLICATION		76303618	192284	1305737	19	NEW_VARIANT
P-0022798-T01-IM6	PPARG (NM_015869) Rearrangement : chr3:g.9389622_c.866:PPARGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		27122	0	14	3	IGR: 15Kb before THUMPD3(+)	THUMPD3	9389622			3	Exon 6 of PPARG(+)	PPARG	12458249			10	INVERSION		3068627	192285	35779	13	NEW_VARIANT
P-0022813-T01-IM6	DOT1L (NM_032482) rearrangement: t(19;22)(p13.3;q13.33)(chr19:g.2228505::chr22:g.51076614)	PRECISE	Note: The DOT1L rearrangement is a translocation that may result in a truncation of exon 28. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	22	IGR: 15Kb before ARSA(-)	ARSA	51076614			19	Intron of DOT1L(+):1Kb before exon 28	DOT1L	2228505			10	TRANSLOCATION		0	192359	0	6	NEW_VARIANT
P-0022818-T01-IM6	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	PRECISE	Note: The NCOA4 - RET fusion includes the kinase domain of RET. One of the breakpoints is within NCOA4 exon 8.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NCOA4:RET}		27535	0	81	10	Intron of RET(+):285bp before exon 12	RET	43611746			10	Exon 8 of NCOA4(+)	NCOA4	51585221			10	DUPLICATION		7973475	192353	27426	121	NEW_VARIANT
P-0022767-T01-IM6	XPO1 (NM_003400) rearrangement: chr2:g.72977233_c.2023-4:XPO1del	PRECISE	Note: The XPO1 rearrangement results in the deletion of XPO1 exons 1-18. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {EXOC6B:XPO1}		31418	0	4	2	Intron of XPO1(-):4bp before exon 18	XPO1	61715910			2	Intron of EXOC6B(-):9Kb before exon 2	EXOC6B	72977233			7	DELETION		11261323	192084	42856	4	NEW_VARIANT
P-0022866-T01-IM6	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	PRECISE	Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		53098	0	52	10	Intron of KIF5B(-):767bp before exon 16	KIF5B	32312731			10	Intron of RET(+):160bp before exon 12	RET	43611871			10	INVERSION		11299140	192868	57874	72	NEW_VARIANT
P-0022750-T01-IM6	TP53 (NM_000546) - PSMG2 (NM_020232) rearrangement: t(17;18)(p13.1;p11.21)(chr17:g.7579703::chr18:g.12724031)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TP53:PSMG2}		0	0	7	18	Intron of PSMG2(+):466bp before exon 6	PSMG2	12724031			17	Exon 3 of TP53(-)	TP53	7579703			10	TRANSLOCATION		0	192160	0	10	NEW_VARIANT
P-0022863-T01-IM6	PTEN (NM_000314) Rearrangement: c.209+165_c.492+3477del	PRECISE	Note: The PTEN Rearrangement results in the intragenic deletion of exons 4-5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3307	0	12	10	Intron of PTEN(+):165bp after exon 3	PTEN	89685479			10	Intron of PTEN(+):3Kb after exon 5	PTEN	89696485			9	DELETION		11006	192860	2018	9	NEW_VARIANT
P-0022865-T01-IM6	TMPRSS2 (NM_001135099) ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 2-10): c.56-2979:TMPRSS2_c.90:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TMPRSS2:ERG}		81559	0	38	21	Exon 2 of ERG(-)	ERG	39817473			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873095			10	DELETION		3055622	192866	35161	42	NEW_VARIANT
P-0022691-T01-IM6	NBN (NM_002485) rearrangement: chr8:g.90818092_c.2234+109:NBNdel	PRECISE	Note: The NBN rearrangement results in the deletion of exon 16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1238	0	4	8	IGR: 48Kb before RIPK2(+)	RIPK2	90818092			8	Intron of NBN(-):108bp after exon 15	NBN	90949145			10	DELETION		131053	191848	1481	4	NEW_VARIANT
P-0022864-T01-IM6	BAP1 (NM_004656) Rearrangement :  t(3;8)(p21.31;q12.1)(chr3:g.52441973::chr8:g.60352046)	PRECISE	Note: The BAP1 Rearrangement results in the possible truncation of BAP1. The breakpoint is within exon5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	27	8	IGR: 634Kb before TOX(-)	TOX	60352046			3	Exon 5 of BAP1(-)	BAP1	52441973			10	TRANSLOCATION		0	192864	0	27	NEW_VARIANT
P-0022820-T01-IM6	DGAT1 (NM_012079) - RECQL4 (NM_004260) rearrangement: c.-436:DGAT1_c.1464:RECQL4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DGAT1:RECQL4}		29236	0	14	8	Promoter of DGAT1(-):12Kb from tx start	DGAT1	145550735			8	Exon 8 of RECQL4(-)	RECQL4	145740553			10	DUPLICATION		189818	192362	41047	14	NEW_VARIANT
P-0022700-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		46891	0	57	21	Intron of ERG(-):61Kb before exon 4	ERG	39878361			21	Intron of TMPRSS2(-):630bp after exon 2	TMPRSS2	42869415			10	DELETION		2991054	191805	39320	60	NEW_VARIANT
P-0022706-T01-IM6	ATRX (NM_000489) rearrangement: chrX:g.76625205_c.7200+64del	PRECISE	Note: The ATRX rearrangement results in the deletion of exon 35. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1547	0	86	X	IGR: 84Kb before FGF16(+)	FGF16	76625205			X	Intron of ATRX(-):63bp after exon 34	ATRX	76776202			10	DELETION		150997	191773	201	92	NEW_VARIANT
P-0022672-T01-IM6	PTEN (NM_000314) rearrangement: c.-3010_c.79+246inv	PRECISE	Note: The PTEN rearrangement results in the inversion of exon 1. Its functional significance is undetermined	MANUAL_OK	3to3	3to3	Antisense Fusion		1403	0	3	10	Promoter of PTEN(+):2Kb from tx start	PTEN	89621217			10	Intron of PTEN(+):246bp after exon 1	PTEN	89624551			7	INVERSION		3334	191712	1474	4	NEW_VARIANT
P-0022688-T01-IM6	LRRC49 (NM_001199017) - MGA (NM_001164273) rearrangement: c.515+1095:LRRC49_c.8623:MGAdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LRRC49:MGA}		144598	0	4	15	Exon 24 of MGA(+)	MGA	42058903			15	Intron of LRRC49(+):1Kb after exon 6	LRRC49	71198189			10	DUPLICATION		29139286	191836	188403	4	NEW_VARIANT
P-0022896-T01-IM6	RUNX1 (NM_001754) Rearrangement :  c.59-4793_c.272del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3682	0	79	21	Exon 4 of RUNX1(-)	RUNX1	36259219			21	Intron of RUNX1(-):48Kb before exon 3	RUNX1	36313194			10	DELETION		53975	192676	2640	87	NEW_VARIANT
P-0022896-T01-IM6	TGFBR1 (NM_004612) Rearrangement : c.974-24_c.1169del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2074	0	35	9	Intron of TGFBR1(+):23bp before exon 6	TGFBR1	101906990			9	Exon 7 of TGFBR1(+)	TGFBR1	101908805			10	DELETION		1815	192675	1499	37	NEW_VARIANT
P-0022926-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		128137	0	15	2	Intron of ALK(-):164bp before exon 20	ALK	29446558			2	Intron of EML4(+):983bp after exon 5	EML4	42492854			10	INVERSION		13046296	192941	157756	15	NEW_VARIANT
P-0022968-T01-IM6	RPS6KA4 (NM_003942) Rearrangement : t(11;12)(q34;q12)(chr11:g.64136052::chr12:g.103764727)	PRECISE	Note: The RPS6KA4 Rearrangement results in the possible truncation of RPS6KA4. The breakpoint is within exon11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	287	12	Intron of C12orf42(-):2Kb before exon 4	C12orf42	103764727			11	Exon 11 of RPS6KA4(+)	RPS6KA4	64136052			10	TRANSLOCATION		0	193189	0	374	NEW_VARIANT
P-0023103-T01-IM6	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)	PRECISE	Note: The FGFR2 - NOL4 fusion is predicted to be in frame and includes the kinase domain of FGFR2.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:NOL4}		0	0	9	18	Intron of NOL4(-):4Kb after exon 9	NOL4	31518701			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241921			10	TRANSLOCATION		0	193958	0	27	NEW_VARIANT
P-0023031-T01-IM6	RB1 (NM_000321) Rearrangement : t(1;13)(p32.2;p21.2)(chr1:g.59514813::chr13:g.48916708)	PRECISE	Note: The RB1 Rearrangement results in the possible truncation of RB1. One of the breakpoints is within intron2.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	53	13	Intron of RB1(+):26bp before exon 3	RB1	48916708			1	5-UTR of LINC01358(+):39Kb before coding start	LINC01358	59514813			10	TRANSLOCATION		0	193569	0	61	NEW_VARIANT
P-0023023-T01-IM6	FAT1 (NM_005245) rearrangement: c.10928_chr4:g.187500064del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24276	0	8	4	IGR: 9Kb before FAT1(-)	FAT1	187500064			4	Exon 19 of FAT1(-)	FAT1	187524752			10	DELETION		24688	193448	20764	14	NEW_VARIANT
P-0023007-T01-IM6	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)	IMPPRECISE	Note: The LRIG3 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {LRIG3:ROS1}		0	0	16	12	Intron of LRIG3(-):241bp after exon 15	LRIG3	59270940			6	Intron of ROS1(-):238bp after exon 34	ROS1	117645256			0	TRANSLOCATION		0	193363	0	14	NEW_VARIANT
P-0023066-T01-IM6	CDK12 (NM_016507)  rearrangement: c.1931+3153_c.1047-87inv	PRECISE	Note: The CDK12 rearrangement result in the inversion of exon 2. Its functional significance is undetermined,	MANUAL_OK	5to5	5to5	-		6903	0	3	17	Intron of CDK12(+):86bp before exon 2	CDK12	37627045			17	Intron of CDK12(+):3Kb after exon 2	CDK12	37631169			8	INVERSION		4124	193837	7344	5	NEW_VARIANT
P-0023159-T01-IM6	CDH1 (NM_004360) Rearrangement : c.164-4993_c.873del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9547	0	21	16	Intron of CDH1(+):5Kb before exon 3	CDH1	68830580			16	Exon 7 of CDH1(+)	CDH1	68845627			10	DELETION		15047	194252	7684	21	NEW_VARIANT
P-0022953-T01-IM6	TMPRSS2 (NM_001135099) - CERS6 (NM_203463) rearrangement: t(2;21)(q24.3;q22.3)(chr2:g.169560626::chr21:g.42873665)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {TMPRSS2:CERS6}		0	0	14	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873665			2	Intron of CERS6(+):9Kb after exon 6	CERS6	169560626			10	TRANSLOCATION		0	193089	0	33	NEW_VARIANT
P-0023000-T01-IM6	ALK (NM_004304) rearrangement: chr2:g.19979335_c.3172+199:ALKdup	PRECISE	Note: The ALK rearrangement is a duplication of exons 20-29. 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.	MANUAL_OK	5to3	5to3	-		148540	0	32	2	IGR: 89Kb before LINC00954(+)	LINC00954	19979335			2	Intron of ALK(-):198bp after exon 19	ALK	29448128			10	DUPLICATION		9468793	193345	175505	33	NEW_VARIANT
P-0023067-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+2229:TMPRSS2_c.18+4015:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		86458	0	5	21	Intron of ERG(-):4Kb after exon 1	ERG	39866272			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877648			0	DELETION		3011376	193829	27294	7	NEW_VARIANT
P-0023057-T01-IM6	B2M (NM_004048) rearrangement: c.67_c.68del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2223	0	19	15	Exon 1 of B2M(+)	B2M	45003811			15	Exon 2 of B2M(+)	B2M	45007621			10	DELETION		3810	193746	2334	23	NEW_VARIANT
P-0023059-T01-IM6	KMT2C (NM_170606) rearrangement: t(7;12)(q36.1;q14.1)(chr7:g.151846068::chr12:g.60040921)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SLC16A7:KMT2C}		0	0	18	12	5-UTR of SLC16A7(+):58Kb before coding start	SLC16A7	60040921			7	Exon 52 of KMT2C(-)	KMT2C	151846068			10	TRANSLOCATION		0	193753	0	17	NEW_VARIANT
P-0023059-T01-IM6	AKT2 (NM_001626) rearrangement: t(11;19)(p13;q13.2)(chr11:g.36316873::chr19:g.40761254)	PRECISE	Note: The AKT2 rearrangement is a translocation which may result in the truncation of exons 1-3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {PRR5L:AKT2}		0	0	22	19	Intron of AKT2(-):78bp before exon 4	AKT2	40761254			11	Promoter of PRR5L(+):851bp from tx start	PRR5L	36316873			10	TRANSLOCATION		0	193755	0	22	NEW_VARIANT
P-0023014-T01-IM6	SHOC2 (NM_007373) rearrangement: c.890_c.972+809inv	PRECISE	Note: The SHOC2 rearrangement is an inversion of exon 4. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		740	0	66	10	Exon 4 of SHOC2(+)	SHOC2	112760221			10	Intron of SHOC2(+):809bp after exon 4	SHOC2	112761112			10	INVERSION		891	193359	587	66	NEW_VARIANT
P-0023014-T01-IM6	TSC2 (NM_000548) - SYNGR3 (NM_004209) rearrangement: c.1319:TSC2_c.99+446:SYNGR3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TSC2:SYNGR3}		38530	0	3	16	Intron of SYNGR3(+):446bp after exon 1	SYNGR3	2040648			16	Exon 13 of TSC2(+)	TSC2	2112559			8	DUPLICATION		71911	193358	44166	3	NEW_VARIANT
P-0023049-T01-IM6	STAT3 (NM_139276) rearrangement: c.1140-27:STAT3_chr17:g.40749768inv	PRECISE	Note: The STAT3 rearrangement is an inversion of exons 1-12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		17326	0	26	17	Intron of STAT3(-):27bp before exon 13	STAT3	40481692			17	Intron of FAM134C(-):6Kb before exon 2	FAM134C	40749768			10	INVERSION		268076	193739	29548	39	NEW_VARIANT
P-0023039-T01-IM6	JAK1 (NM_002227) - PKM (NM_001206796) rearrangement: t(1;15)(p31.3;q23)(chr1:g.65323406::chr15:g.72499346)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {JAK1:PKM}		0	0	32	15	Intron of PKM(-):121bp after exon 7	PKM	72499346			1	Exon 10 of JAK1(-)	JAK1	65323406			10	TRANSLOCATION		0	193690	0	32	NEW_VARIANT
P-0011038-T02-IM6	KMT2B (NM_014727) rearrangement: c.826_c.1937inv	PRECISE	Note: The KMT2B rearrangement results in the inversion of exon 3. Both breakpoints are within exon 3. its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		8276	0	3	19	Exon 3 of KMT2B(+)	KMT2B	36211075			19	Exon 3 of KMT2B(+)	KMT2B	36212186			10	INVERSION		1111	194015	40730	3	NEW_VARIANT
P-0022856-T02-IM6	PTPRD (NM_002839) rearrangement: c.1678-1280_c.5085del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		30870	0	7	9	Exon 41 of PTPRD(-)	PTPRD	8341131			9	Intron of PTPRD(-):1Kb before exon 23	PTPRD	8505685			8	DELETION		164554	194011	29977	7	NEW_VARIANT
P-0023194-T01-IM6	GATA3 (NM_002051) rearrangement: c.242-736_c.772del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5924	0	11	10	Intron of GATA3(+):735bp before exon 3	GATA3	8099532			10	Exon 3 of GATA3(+)	GATA3	8100798			10	DELETION		1266	194319	6076	11	NEW_VARIANT
P-0023194-T01-IM6	TP53 (NM_000546) rearrangement: c.376-16_c.688del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 5-7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5137	0	60	17	Exon 7 of TP53(-)	TP53	7577593			17	Intron of TP53(-):16bp before exon 5	TP53	7578570			10	DELETION		977	194320	4782	67	NEW_VARIANT
P-0023297-T01-IM6	PARK2 (NM_004562) - FAM135A (NM_001162529) rearrangement: c.236:PARK2_c.823+2866:FAM135Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PARK2:FAM135A}		566671	0	32	6	Intron of FAM135A(+):3Kb after exon 8	FAM135A	71194723			6	Exon 3 of PARK2(-)	PARK2	162683733			10	INVERSION		91489010	194616	457371	46	NEW_VARIANT
P-0023211-T01-IM6	EP300 (NM_001429) rearrangement: c.2633_chr22:g.45878564inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		47751	0	4	22	Exon 14 of EP300(+)	EP300	41546018			22	IGR: 20Kb before FBLN1(+)	FBLN1	45878564			6	INVERSION		4332546	194404	23331	3	NEW_VARIANT
P-0023321-T01-IM6	STAT3 (NM_139276) rearrangement: c.372+1043_c.103del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5095	0	40	17	Intron of STAT3(-):1Kb after exon 4	STAT3	40496534			17	Exon 2 of STAT3(-)	STAT3	40500432			10	DELETION		3898	194734	4370	42	NEW_VARIANT
P-0023321-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.684_c.-427del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9365	0	14	2	Exon 5 of NFE2L2(-)	NFE2L2	178096647			2	5-UTR of NFE2L2(-):34Kb before coding start	NFE2L2	178129731			10	DELETION		33084	194733	13014	15	NEW_VARIANT
P-0022004-T02-IM6	SRGAP2 (NM_015326) - IKBKE (NM_014002) rearrangement: c.2085:SRGAP2_c.1714:IKBKEdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SRGAP2:IKBKE}		21699	0	8	1	Exon 17 of SRGAP2(+)	SRGAP2	206626708			1	Exon 17 of IKBKE(+)	IKBKE	206664172			10	DELETION		37464	194415	26922	10	NEW_VARIANT
P-0023197-T01-IM6	KMT2C (NM_170606) rearrangement: c.11863:KMT2C_chr7:g.152760077del	PRECISE	Note: The KMT2C rearrangement is a deletion of exons 1-46. One of the breakpoints is within exon 46. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		99340	0	5	7	Exon 46 of KMT2C(-)	KMT2C	151853092			7	IGR: 303Kb before ACTR3B(+)	ACTR3B	152760077			7	DELETION		906985	194337	100218	5	NEW_VARIANT
P-0023261-T01-IM6	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	PRECISE	Note: The FGFR3-TACC3 fusion includes the protein kinase domain of FGFR3, the breakpoint in FGFR3 is within exon 18.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		39692	0	14	4	Intron of TACC3(+):673bp after exon 10	TACC3	1740102			4	Exon 18 of FGFR3(+)	FGFR3	1808927			10	DUPLICATION		68825	194520	36342	14	NEW_VARIANT
P-0023270-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with exon4) : c.56-3945:TMPRSS2_c.40-62862:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75136	0	6	21	Intron of ERG(-):63Kb before exon 4	ERG	39880406			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874061			10	DELETION		2993655	194453	48502	6	NEW_VARIANT
P-0023281-T01-IM6	KDM5A (NM_001042603) rearrangement: t(6;12)(p22.1;p13.33)(chr6:g.30437747::chr12:g.438110)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	42	12	Exon 14 of KDM5A(-)	KDM5A	438110			6	IGR: 19Kb before HLA-E(+)	HLA-E	30437747			10	TRANSLOCATION		0	194523	0	48	NEW_VARIANT
P-0023287-T01-IM6	RPTOR (NM_020761) rearrangement: t(1;17)(p35.2;q25.3)(chr1:g.32370243::chr17:g.78854227)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	12	17	Exon 14 of RPTOR(+)	RPTOR	78854227			1	Promoter of PTP4A2(-):2Kb from tx start	PTP4A2	32370243			10	TRANSLOCATION		0	194551	0	13	NEW_VARIANT
P-0023368-T01-IM6	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	PRECISE	Note: The EML4-ALK fusion is predicted to be in-frame.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		116001	0	23	2	Intron of ALK(-):319bp before exon 20	ALK	29446713			2	Intron of EML4(+):7Kb after exon 5	EML4	42498875			10	INVERSION		13052162	195392	125363	32	NEW_VARIANT
P-0023371-T01-IM6	RB1 (NM_000321) rearrangement: chr13:g.48785947_c.607+1:RB1inv	PRECISE	Note: The RB1 rearrangement results in the inversion of exons 7-27. its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4671	0	32	13	IGR: 21Kb before ITM2B(+)	ITM2B	48785947			13	Intron of RB1(+):1bp after exon 6	RB1	48923160			10	INVERSION		137213	195380	3367	32	NEW_VARIANT
P-0023388-T01-IM6	CYLD (NM_001042355) rearrangement: t(8;16)(p11.22;q12.1)(chr8:g.38590620::chr16:g.50826532)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CYLD:TACC1}		0	0	101	16	Exon 15 of CYLD(+)	CYLD	50826532			8	5-UTR of TACC1(+):87Kb before coding start	TACC1	38590620			10	TRANSLOCATION		0	194917	0	106	NEW_VARIANT
P-0023471-T01-IM6	NOTCH3 (NM_000435) rearrangement: t(3;19)(p11.2;p13.12)(chr3:g.87561351::chr19:g.15271620)	PRECISE	Note: The NOTCH3 rearrangement is a translocation with a breakpoint within NOTCH3 exon 33. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	21	19	Exon 33 of NOTCH3(-)	NOTCH3	15271620			3	IGR: 253Kb before POU1F1(-)	POU1F1	87561351			10	TRANSLOCATION		0	195617	0	27	NEW_VARIANT
P-0015921-T03-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		90414	0	41	2	Intron of ALK(-):415bp before exon 20	ALK	29446809			2	Intron of EML4(+):516bp after exon 5	EML4	42492387			10	INVERSION		13045578	195089	199054	41	NEW_VARIANT
P-0023401-T01-IM6	FOXA1 (NM_004496) rearrangement: c.73-52:FOXA1_chr14:g.38074562inv	IMPPRECISE	Note: The FOXA1 rearrangement is an inversion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2684	0	110	14	Intron of FOXA1(-):52bp before exon 2	FOXA1	38061968			14	IGR: 16Kb before FOXA1(-)	FOXA1	38074562			0	INVERSION		12594	195020	5032	108	NEW_VARIANT
P-0023404-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-3420:TMPRSS2_c.40-59054:ERGdel	PRECISE	Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75311	0	23	21	Intron of ERG(-):59Kb before exon 4	ERG	39876598			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873536			10	DELETION		2996938	195021	40678	23	NEW_VARIANT
P-0023404-T01-IM6	TP53 (NM_000546) rearrangement: t(17;22)(p13.1;q13.33)(chr17:g.7576891::chr22:g.50604157)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	12	22	IGR: 5Kb before PANX2(+)	PANX2	50604157			17	Exon 9 of TP53(-)	TP53	7576891			10	TRANSLOCATION		0	195024	0	15	NEW_VARIANT
P-0023407-T01-IM6	TP53 (NM_000546) rearrangement: c.920-17_c.993+610del	IMPPRECISE	Note: The TP53 rearrangement is an intragenic deletion of exon 9.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2874	0	130	17	Intron of TP53(-):609bp after exon 9	TP53	7576243			17	Intron of TP53(-):17bp before exon 9	TP53	7576943			0	DELETION		700	195004	179	190	NEW_VARIANT
P-0023453-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.223-176_c.1812+451dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 4-11. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 9 exons : in frame		24543	0	8	19	Intron of SMARCA4(+):175bp before exon 3	SMARCA4	11095773			19	Intron of SMARCA4(+):451bp after exon 11	SMARCA4	11107671			8	DUPLICATION		11898	195501	34902	8	NEW_VARIANT
P-0023453-T01-IM6	EIF4A2 (NM_001967) rearrangement: t(X;3)(q25;q27.3)(chrX:g.122823360::chr3:g.186506986)	PRECISE	Note: The EIF4A2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	19	X	Intron of THOC2(-):3Kb before exon 8	THOC2	122823360			3	Exon 11 of EIF4A2(+)	EIF4A2	186506986			10	TRANSLOCATION		0	195506	0	23	NEW_VARIANT
P-0023457-T01-IM6	BRCA2 (NM_000059) Rearrangement :  c.632-1319_c.4115inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		29529	0	123	13	Intron of BRCA2(+):1Kb before exon 8	BRCA2	32902261			13	Exon 11 of BRCA2(+)	BRCA2	32912607			10	INVERSION		10346	195523	41486	138	NEW_VARIANT
P-0023507-T01-IM6	CALR (NM_004343) - NFIX (NM_002501) rearrangement: c.689:CALR_c.559+10828:NFIXdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CALR:NFIX}		3809	0	55	19	Exon 5 of CALR(+)	CALR	13051253			19	Intron of NFIX(+):11Kb after exon 2	NFIX	13147194			10	DELETION		95941	195680	6258	56	NEW_VARIANT
P-0023526-T01-IM6	SETD2 (NM_014159) - TMIE (NM_147196) rearrangement: c.155:SETD2_c.211+223:TMIEinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {SETD2:TMIE}		62532	0	36	3	Intron of TMIE(+):223bp after exon 2	TMIE	46747620			3	Exon 3 of SETD2(-)	SETD2	47165971			10	INVERSION		418351	195854	43552	38	NEW_VARIANT
P-0023516-T01-IM6	COLEC12 (NM_130386) - CDK12(NM_016507) rearrangement: t(17;18)(q12;p11.32)(chr17:g.37665943::chr18:g.386902)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {COLEC12:CDK12}		0	0	44	18	Intron of COLEC12(-):29Kb before exon 3	COLEC12	386902			17	Intron of CDK12(+):14bp before exon 7	CDK12	37665943			10	TRANSLOCATION		0	195755	0	64	NEW_VARIANT
P-0023547-T01-IM6	CREBBP (NM_004380) rearrangement: chr16:g.3461991_c.2463+91del	PRECISE	Note: The CREBBP rearrangement results in the deletion of exons 13-31. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		106440	0	21	16	Promoter of ZNF174(+):11Kb from tx start	ZNF174	3461991			16	Intron of CREBBP(-):90bp after exon 13	CREBBP	3823661			10	DELETION		361670	195824	46349	25	NEW_VARIANT
P-0023613-T01-IM6	CIC (NM_015125) - TP53 (NM_000546) rearrangement: t(17;19)(p13.1;q13.2)(chr17:g.7572859::chr19:g.42791952)	PRECISE	Note: The CIC -TP53 rearrangement is a translocation with breakpoints within CIC intron 5 and the 3UTR of TP53. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	65	19	Intron of CIC(+):9bp before exon 6	CIC	42791952			17	3-UTR of TP53(-):67bp after coding stop	TP53	7572859			10	TRANSLOCATION		0	196173	0	74	NEW_VARIANT
P-0023617-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	37	6	Intron of ROS1(-):866bp before exon 34	ROS1	117646444			5	Intron of CD74(-):71bp before exon 7	CD74	149782946			10	TRANSLOCATION		0	196208	0	36	NEW_VARIANT
P-0023621-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		41914	0	43	21	Intron of ERG(-):21Kb before exon 2	ERG	39838718			21	Intron of TMPRSS2(-):481bp after exon 2	TMPRSS2	42869564			10	DELETION		3030846	196164	51099	44	NEW_VARIANT
P-0022282-T01-IM6	MAP3K1 (NM_005921) - ARFIP1 (NM_001025595)  rearrangement: t(4;5)(q31.3;q11.2)(chr4:g.153712327::chr5:g.56161250)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MAP3K1:ARFIP1}		0	0	5	5	Exon 5 of MAP3K1(+)	MAP3K1	56161250			4	5-UTR of ARFIP1(+):38Kb before coding start	ARFIP1	153712327			10	TRANSLOCATION		0	190079	0	5	NEW_VARIANT
P-0022282-T01-IM6	BRAF (NM_004333) - GPM6A (NM_005277) rearrangement: t(4;7)(q34.2;q34)(chr4:g.176630702::chr7:g.140454168)	PRECISE	Note: The BRAF rearrangement is a translocation with breakpoints within BRAF intron 13 and GPM6A intron 2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	10	7	Intron of BRAF(-):135bp before exon 14	BRAF	140454168			4	Intron of GPM6A(-):8Kb before exon 3	GPM6A	176630702			10	TRANSLOCATION		0	190080	0	10	NEW_VARIANT
P-0022335-T01-IM6	PTPRS (NM_002850) - SYDE1 (NM_033025) Rearrangement : c.2350-60:PTPRS_c.540:SYDE1	PRECISE	Note : The PTPRS -SYDE1 Rearrangement results in the deletion of exons 1-15 of PTPRS. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		340195	0	27	19	Intron of PTPRS(-):60bp before exon 16	PTPRS	5229413			19	Exon 3 of SYDE1(+)	SYDE1	15220624			10	DELETION		9991211	190667	407111	29	NEW_VARIANT
P-0023644-T01-IM6	CTCF (NM_006565) Rearrangement : c.-9-3099_c.-9-3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		302	1	26	16	5-UTR of CTCF(+):3Kb before coding start	CTCF	67641628			16	5-UTR of CTCF(+):11bp before coding start	CTCF	67644724			10	DELETION		3096	196262	136	26	NEW_VARIANT
P-0006602-T03-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29085	0	106	21	Intron of ERG(-):18Kb before exon 2	ERG	39835131			21	Intron of TMPRSS2(-):568bp before exon 3	TMPRSS2	42867073			10	DELETION		3031942	196828	9884	113	NEW_VARIANT
P-0008083-T03-IM6	PALB2 (NM_024675) rearrangement: c.212-247_c.1291del	PRECISE	Note: The PALB2 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7922	0	31	16	Exon 4 of PALB2(-)	PALB2	23646576			16	Intron of PALB2(-):247bp before exon 4	PALB2	23647902			10	DELETION		1326	196338	5327	31	NEW_VARIANT
P-0008083-T03-IM6	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.315-432:MKRN1_c.1178-1554:BRAFdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {MKRN1:BRAF}		28423	0	9	7	Intron of MKRN1(-):432bp before exon 3	MKRN1	140160168			7	Intron of BRAF(-):2Kb before exon 10	BRAF	140484511			0	DUPLICATION		324343	196340	42252	12	NEW_VARIANT
P-0008346-T03-IM6	EGFR (NM_005228) rearrangement: t(7;11)(p11.2;p15.3)(chr7:g.55269578::chr11:g.12552528)	PRECISE	Note: The EGFR rearrangement is a translocation which may result in the truncation of exons 27-28. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	27	11	3-UTR of PARVA(+):153Kb after coding stop	PARVA	12552528			7	Intron of EGFR(+):103bp after exon 26	EGFR	55269578			10	TRANSLOCATION		0	196353	0	28	NEW_VARIANT
P-0023605-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exons 1-2 fused with ERG exons 4-10): c.127-1583:TMPRSS2_c.-3842:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25249	0	17	21	Intron of ERG(-):57Kb before exon 4	ERG	39874146			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868088			0	DELETION		2993942	196101	29846	18	NEW_VARIANT
P-0023625-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.-56-420:TMPRSS2_chr21:g.39863632del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49436	0	10	21	Intron of ERG(-):7Kb after exon 1	ERG	39863632			21	Intron of TMPRSS2(-):420bp before exon 2	TMPRSS2	42870536			10	DELETION		3006904	196333	40384	10	NEW_VARIANT
P-0023629-T01-IM6	CSDE1 (NM_001242891) rearrangement: c.2119:CSDE1_chr1:g.149712153del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		122424	0	3	1	Exon 18 of CSDE1(-)	CSDE1	115263231			1	IGR: 42Kb before HIST2H2BF(-)	HIST2H2BF	149712153			10	DELETION		34448922	196316	90692	4	NEW_VARIANT
P-0023629-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.-56-1903:TMPRSS2_c.19-17475:ERGdel	PRECISE	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	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		57973	0	7	21	Intron of ERG(-):17Kb before exon 2	ERG	39835019			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872019			9	DELETION		3037000	196317	41411	7	NEW_VARIANT
P-0023663-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		41410	0	69	21	Intron of ERG(-):17Kb before exon 2	ERG	39834156			21	Intron of TMPRSS2(-):454bp after exon 2	TMPRSS2	42869591			10	DELETION		3035435	196830	38115	87	NEW_VARIANT
P-0023666-T01-IM6	AR (NM_000044) rearrangement: c.2174-1690_c.2608-163del	PRECISE	Note: The AR rearrangement is an intragenic deletion of exons  5-7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		2328	0	6	X	Intron of AR(+):2Kb before exon 5	AR	66935630			X	Intron of AR(+):162bp before exon 8	AR	66943365			9	DELETION		7735	196809	1461	6	NEW_VARIANT
P-0023678-T01-IM6	RECQL4 (NM_004260) - LRRC24 (NM_001024678) Rearrangement : c.2574:RECQL4_c.607+2:LRRC24dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RECQL4:LRRC24}		33657	0	20	8	Exon 16 of RECQL4(-)	RECQL4	145738412			8	Intron of LRRC24(-):26bp after exon 4	LRRC24	145749467			10	DUPLICATION		11055	196445	56702	20	NEW_VARIANT
P-0023680-T01-IM6	RNF43 (NM_017763) Rearrangement : t(17,20)(q23.1,p13)(chr17:g.56492855::chr20:g.1042563)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	41	20	IGR: 51Kb before PSMF1(+)	PSMF1	1042563			17	Exon 2 of RNF43(-)	RNF43	56492855			10	TRANSLOCATION		0	196440	0	41	NEW_VARIANT
P-0023682-T01-IM6	STK11 (NM_000455) - CDC42 (NM_001791) Rearrangement : t(1,19)(p13.3; p36.13)(chr1:g.22405880::chr19:g.1221235)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STK11:CDC42}		0	0	33	19	Exon 6 of STK11(+)	STK11	1221235			1	Intron of CDC42(+):804bp after exon 2	CDC42	22405880			10	TRANSLOCATION		0	196431	0	44	NEW_VARIANT
P-0023701-T01-IM6	BAIAP2 (NM_017451) - RPTOR (NM_020761) Rearrangement : c.54+5781:BAIAP2_c.3611:RPTORdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BAIAP2:RPTOR}		6934	0	28	17	Exon 31 of RPTOR(+)	RPTOR	78935199			17	Intron of BAIAP2(+):6Kb after exon 1	BAIAP2	79014889			10	DUPLICATION		79690	196701	3479	29	NEW_VARIANT
P-0023716-T01-IM6	EP300 (NM_001429) rearrangement: c.3672-25_c.3729-6del	IMPPRECISE	Note: The EP300 rearrangement is an intragenic deletion of exon 21. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1727	0	83	22	Intron of EP300(+):24bp before exon 21	EP300	41558702			22	Intron of EP300(+):5bp before exon 22	EP300	41560051			0	DELETION		1349	196520	612	84	NEW_VARIANT
P-0023721-T01-IM6	CARM1 (NM_199141) rearrangement: c.558+1395_c.999del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8109	0	4	19	Intron of CARM1(+):1Kb after exon 4	CARM1	11021278			19	Exon 8 of CARM1(+)	CARM1	11027432			10	DELETION		6154	196515	8312	5	NEW_VARIANT
P-0023732-T01-IM6	NOTCH1 (NM_017617) rearrangement: chr9:g.139385688inv_c.4015-1inv	PRECISE	Note: The NOTCH1 rearrangement is an inversion that includes NOTCH1 exons 25-34. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		39105	0	41	9	IGR: 3Kb before NOTCH1(-)	NOTCH1	139385688			9	Intron of NOTCH1(-):1bp before exon 25	NOTCH1	139400334			10	INVERSION		14646	196851	45710	40	NEW_VARIANT
P-0023741-T01-IM6	TP53 (NM_000546) - AFAP1L2 (NM_001001936) rearrangement: t(10;17)(q25.3;p13.1)(chr10:g.116100904::chr17:g.7580804)	PRECISE	Note: The TP53 - AFAP1L2 rearrangement is a translocation with breakpoints within TP53 intron 1 and AFAP1L2 intron 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	14	17	5-UTR of TP53(-):8Kb before coding start	TP53	7580804			10	Intron of AFAP1L2(-):414bp before exon 2	AFAP1L2	116100904			10	TRANSLOCATION		0	196842	0	14	NEW_VARIANT
P-0023789-T01-IM6	APC (NM_000038) Rearrangement : chr5:g.124747396_c.422+47:APCdel	PRECISE	Note: The APC Rearrangement results in the deletion of exons 5-16 of APC. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		68167	0	10	5	Intron of APC(+):47bp after exon 4	APC	112103134			5	IGR: 82Kb before LOC101927460(+)	LOC101927460	124747396			9	DELETION		12644262	196949	46148	13	NEW_VARIANT
P-0023746-T01-IM6	CDKN2A (NM_000077, NM_058195) rearrangement: c.78:CDKN2Ap16INK4A_chr9:g.22278766del, c.194-3542:CDKN2Ap14ARF_chr9:g.22278766del	PRECISE	Note: The CDKN2A rearrangement is a deletion that includes exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms of CDKN2A.	MANUAL_OK	3to5	3to5	-		10179	0	9	9	Exon 1 of CDKN2A(-)	CDKN2A	21974749			9	IGR: 168Kb before DMRTA1(+)	DMRTA1	22278766			10	DELETION		304017	196885	7809	9	NEW_VARIANT
P-0023753-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2085:TMPRSS2_:c.18+21555:ERGdel	PRECISE	TMPRSS2 exon 1 is  fused to ERG exons 2-10. The TMPRSS2-ERG fusion is known to be oncogenic.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		71813	0	18	21	Intron of ERG(-):22Kb after exon 1	ERG	39848732			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872201			10	DELETION		3023469	196893	48756	20	NEW_VARIANT
P-0023272-T01-IM6	FH (NM_000143) Rearrangement : c.1390+169_c.*1652_del	PRECISE	Note: The FH Rearrangement results in the deletion of exon 10 of FH. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1769	0	5	1	Promoter of FH(-):1Kb from tx start	FH	241659476			1	Intron of FH(-):168bp after exon 9	FH	241663568			9	DELETION		4092	194461	1078	5	NEW_VARIANT
P-0023756-T01-IM6	HMGXB4 (NM_001003681) - NF2 (NM_000268) rearrangement: c.-68-2330:HMGXB4_c.1738-103:NF2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {HMGXB4:NF2}		19546	0	13	22	Intron of NF2(+):102bp before exon 16	NF2	30090638			22	5-UTR of HMGXB4(+):36Kb before coding start	HMGXB4	35655986			10	DUPLICATION		5565348	196901	14494	15	NEW_VARIANT
P-0023764-T01-IM6	ATM (NM_000051) rearrangement: chr11:g.638545_c.8932inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		532371	0	2	11	Intron of DRD4(+):887bp before exon 2	DRD4	638545			11	Exon 62 of ATM(+)	ATM	108235890			5	INVERSION		107597345	196906	494109	2	NEW_VARIANT
P-0023764-T01-IM6	RPS6KB2 (NM_003952) rearrangement: c.647_chr11:g.108447231del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		284661	0	2	11	Exon 8 of RPS6KB2(+)	RPS6KB2	67200453			11	Intron of EXPH5(-):17Kb after exon 1	EXPH5	108447231			8	DELETION		41246778	196905	220720	2	NEW_VARIANT
P-0023768-T01-IM6	TCF3 (NM_001136139) rearrangement: c.1450+596_c.1167+29inv	PRECISE	Note: The TCF3 rearrangement results in the inversion of exons 14-15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		2235	0	2	19	Intron of TCF3(-):595bp after exon 15	TCF3	1618514			19	Intron of TCF3(-):28bp after exon 13	TCF3	1619750			4	INVERSION		1236	196910	2985	2	NEW_VARIANT
P-0023776-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.553-11414_chr10:g.115137987inv	PRECISE	Note: The TCF7L2 rearrangement results in the inversion of exons 6-14. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		13284	0	4	10	Intron of TCF7L2(+):11Kb before exon 6	TCF7L2	114889529			10	IGR: 173Kb before HABP2(+)	HABP2	115137987			10	INVERSION		248458	196936	10215	4	NEW_VARIANT
P-0023776-T01-IM6	ERCC2 (NM_000400) rearrangement: c.1591_chr19:g.45933447del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		18079	0	27	19	Exon 17 of ERCC2(-)	ERCC2	45858062			19	IGR: 17Kb before ERCC1(-)	ERCC1	45933447			10	DELETION		75385	196935	9275	28	NEW_VARIANT
P-0002266-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		58272	0	5	2	Intron of ALK(-): 889bp before exon 20	ALK	29447283			2	Intron of EML4(+): 1Kb after exon 2	EML4	42473849			5	INVERSION		13026566	2931	57102	8	NEW_VARIANT
P-0002266-T01-IM3	ALK (NM_004304) and EML4 (NM_019063) reciprocal inversion (13026566bp):  c.3173-889:ALK_c.208+1022:EML4inv	PRECISE	Note: The EML4-ALK inversion is a rearrangement event.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (ALK-EML4)		58234	0	4	2	Intron of ALK(-): 894bp before exon 20	ALK	29447288			2	Intron of EML4(+): 1Kb after exon 2	EML4	42473852			14	INVERSION		13026564	2932	57072	8	NEW_VARIANT
P-0004218-T01-IM5	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 20 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv	PRECISE	Note: The EML4 (NM_001145076) - ALK (NM_004304)  Fusion  is a reciprocal inversion.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		57824	0	49	2	Intron of ALK(-): 693bp before exon 20	ALK	29447087			2	Intron of EML4(+): 156bp after exon 19	EML4	42552850			61	INVERSION		13105763	16907	59445	48	NEW_VARIANT
P-0004634-T01-IM5	E2F3 (NM_001949) rearrangement: c.-653_c.176del	IMPRECISE	The E2F3 (NM_001949) rearrangement is an intragenic deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1455	0	9	6	Promoter of E2F3(+): 326bp from tx start	E2F3	20401811			6	Exon 1 of E2F3(+)	E2F3	20402639			0	DELETION		828	28741	1501	9	NEW_VARIANT
P-0021909-T01-IM6	PTEN (NM_000314) rearrangement: c.911:PTEN_chr10:g.89755903del	PRECISE	Note: The PTEN rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1794	0	4	10	Exon 8 of PTEN(+)	PTEN	89720760			10	IGR: 133Kb before PTEN(+)	PTEN	89755903			10	DELETION		35143	188492	2489	16	NEW_VARIANT
P-0023866-T01-IM6	ACPP (NM_001134194) -FGFR1 (NM_001174067) rearrangement: t(3;8)(q22.1;p11.23)(chr3:g.132078761::chr8:g.38287577)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ACPP:FGFR1}		0	0	16	8	Intron of FGFR1(-):111bp before exon 4	FGFR1	38287577			3	Intron of ACPP(+):3Kb after exon 10	ACPP	132078761			10	TRANSLOCATION		0	197174	0	15	NEW_VARIANT
P-0023827-T01-IM6	FH (NM_000143) Rearrangement : t(1;12)(q42.3;q23.1)(chr1:g.241669480::chr12:g.99115177)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	12	12	Intron of APAF1(+):2Kb before exon 22	APAF1	99115177			1	Intron of FH(-):12bp before exon 6	FH	241669480			10	TRANSLOCATION		0	196978	0	12	NEW_VARIANT
P-0023827-T01-IM6	NCOR1 (NM_006311) Rearrangement : c.4083_c.6679+831del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11886	0	12	17	Intron of NCOR1(-):830bp after exon 42	NCOR1	15949434			17	Exon 30 of NCOR1(-)	NCOR1	15974792			10	DELETION		25358	196977	10457	12	NEW_VARIANT
P-0023838-T01-IM6	NAB2 (NM_005967) rearrangement: c.1091+159_c.1468+272inv	PRECISE	Note: The NAB2 rearrangement results in the inversion of exons 4-6. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4170	0	2	12	Intron of NAB2(+):159bp after exon 3	NAB2	57486523			12	Intron of NAB2(+):272bp after exon 6	NAB2	57487653			6	INVERSION		1130	197055	4327	2	NEW_VARIANT
P-0023838-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion and it is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28648	0	36	21	Intron of ERG(-):59Kb before exon 4	ERG	39876787			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867929			10	DELETION		2991142	197049	29819	41	NEW_VARIANT
P-0023855-T01-IM6	PIK3R1 (NM_181523) - UBR3 (NM_172070) Rearrangement : t(2;5)(q24.3;q13.1)(chr2:g.170688316::chr5:g. 67592113)	PRECISE	Note: The PIK3R1 - UBR3  Rearrangement results in the fusion of PIK3R1 exons 1-15 with UBR3 exons 2-39. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PIK3R1:UBR3}		0	0	5	5	Exon 15 of PIK3R1(+)	PIK3R1	67592113			2	Intron of UBR3(+):4Kb after exon 1	UBR3	170688316			10	TRANSLOCATION		0	197069	0	4	NEW_VARIANT
P-0023898-T01-IM6	CDH1 (NM_004360) rearrangement: t(12;16)(q14.1;q22.1)(chr12:g.58632676::chr16:g.68845628)	PRECISE	Note: The CDH1 rearrangement is a translocation which involves a breakpoint within exon 7. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	10	16	Exon 7 of CDH1(+)	CDH1	68845628			12	IGR: 297Kb before XRCC6BP1(+)	XRCC6BP1	58632676			10	TRANSLOCATION		0	197199	0	10	NEW_VARIANT
P-0023899-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.2599+41:NOTCH2_chr1:g.7232798del	PRECISE	Note: The NOTCH2 rearrangement is a deletion of exons 17-34. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		898634	0	8	1	Intron of CAMTA1(+):77Kb before exon 5	CAMTA1	7232798			1	Intron of NOTCH2(-):40bp after exon 16	NOTCH2	120491589			10	DELETION		113258791	197202	719898	8	NEW_VARIANT
P-0023899-T01-IM6	RPS6KB2 (NM_003952) rearrangement: c.457+274: RPS6KB2_chr11:g.80143138del	PRECISE	Note: The RPS6KB2 rearrangement is a deletion of exons 6-15. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		134992	0	7	11	Intron of RPS6KB2(+):274bp after exon 5	RPS6KB2	67199260			11	IGR: 319Kb before LOC101928944(-)	LOC101928944	80143138			10	DELETION		12943878	197203	146109	6	NEW_VARIANT
P-0023913-T01-IM6	MDC1 (NM_014641) rearrangement: c.3434_c.5722inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		11448	0	2	6	Exon 12 of MDC1(-)	MDC1	30671024			6	Exon 10 of MDC1(-)	MDC1	30673526			5	INVERSION		2502	197217	12676	1	NEW_VARIANT
P-0002587-T01-IM3		PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: out of frame (TSC2-BCL2L1)		0	0	102	20	Intron of BCL2L1(-): 8Kb after exon 2	BCL2L1	30301865			16	Intron of TSC2(+): 35bp after exon 23	TSC2	2125928			101	TRANSLOCATION		0	4047	0	113	NEW_VARIANT
P-0003001-T01-IM3		PRECISE	Note: TMPRSS2-SIK1 duplication is a rearrangement event that results in the fusion of TMPRSS2 exons 2-14 to SIK1 exons 4-14.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-SIK1)		29300	0	5	21	Intron of TMPRSS2(-): 519bp before exon 2	TMPRSS2	42870635			21	Intron of SIK1(-): 2Kb before exon 4	SIK1	44843452			8	DUPLICATION		1972817	7000	32724	5	NEW_VARIANT
P-0003139-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (TMPRSS2-ERG)		30000	0	19	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876764			21	Exon 3 of TMPRSS2(-)	TMPRSS2	42866368			50	DELETION		2989604	9008	22193	25	NEW_VARIANT
P-0008960-T01-IM5	CDK12 (NM_016507) - HTR1E (NM_000865)  rearrangement: t(6;17)(q14.3;q12)(chr6:g.87697112::chr17:g.37646977)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CDK12-HTR1E)		0	0	61	17	Exon 3 of CDK12(+)	CDK12	37646977			6	5-UTR of HTR1E(+): 28Kb before coding start	HTR1E	87697112			51	TRANSLOCATION		0	125341	0	58	NEW_VARIANT
P-0008960-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		41750	0	53	21	Intron of ERG(-): 62Kb after exon 3	ERG	39885570			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867649			53	DELETION		2982079	125335	26859	48	NEW_VARIANT
P-0008960-T01-IM5	TERT (NM_198253) rearrangement: c.-476_chr5:g.30794048del	PRECISE	The TERT (NM_198253) rearrangement is a deletion which includes part of the promoter region of TERT. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		43911	0	24	5	Promoter of TERT(-): 418bp from tx start	TERT	1295580			5	IGR: 400Kb before CDH6(+)	CDH6	30794048			19	DELETION		29498468	125336	44393	4	NEW_VARIANT
P-0013729-T01-IM5	ERCC4 (NM_005236) - MYC (NM_002467) rearrangement: t(8;16)(q24.21;p13.12)(chr8:g.128753292::chr16:g.14015306)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	21	16	Intron of ERCC4(+): 582bp before exon 2	ERCC4	14015306			8	3-UTR of MYC(+): 88bp after coding stop	MYC	128753292			7	TRANSLOCATION		0	162095	0	19	NEW_VARIANT
P-0013729-T01-IM5	TMPRSS2 (NM_001135099) - CASZ1 (NM_001079843) rearrangement: t(1;21)(p36.22;q22.3)(chr1:g.10703925::chr21:g.42868002)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-CASZ1)		0	0	19	21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42868002			1	Intron of CASZ1(-): 557bp before exon 19	CASZ1	10703925			0	TRANSLOCATION		0	162096	0	18	NEW_VARIANT
P-0013729-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+2996:TMPRSS2_c.18+1445:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		118017	0	72	21	Intron of ERG(-): 1Kb after exon 1	ERG	39868842			21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42876881			72	DELETION		3008039	162090	84075	71	NEW_VARIANT
P-0013729-T01-IM5	MLL3 (NM_170606) rearrangement: c.14470:MLL3_chr7:g.152256329del	PRECISE	Note: The MLL3 rearrangement is a deletion of 5UTR and exons 1-57, with one of the breakpoint within exon 57.	MANUAL_OK	3to5	3to5	-		134340	0	21	7	Exon 57 of MLL3(-)	MLL3	151836335			7	IGR: 87Kb before XRCC2(-)	XRCC2	152256329			40	DELETION		419994	162093	89412	20	NEW_VARIANT
P-0013937-T01-IM5	TRAF2 (NM_021138) rearrangement:c.-28-2168_c.345dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		9409	0	60	9	5-UTR of TRAF2(+): 2Kb before coding start	TRAF2	139790997			9	Exon 4 of TRAF2(+)	TRAF2	139794951			55	DUPLICATION		3954	162787	52806	59	NEW_VARIANT
P-0014819-T01-IM6	TMPRSS2 (NM_001135099) - ERG (M_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1266:TMRPSS2_c.18+21077del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		74992	0	16	21	Intron of ERG(-): 21Kb after exon 1	ERG	39849210			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871382			18	DELETION		3022172	165933	58612	15	NEW_VARIANT
P-0021671-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) rearrangement: t(5,6)(q33.1,q22.1)(chr5:g.149783453::chr6:g.117657267)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	18	6	Intron of ROS1(-):1Kb after exon 31	ROS1	117657267			5	Intron of CD74(-):578bp before exon 7	CD74	149783453			10	TRANSLOCATION		0	188045	0	24	NEW_VARIANT
P-0021918-T01-IM6	ETV6 (NM_001987) - SUFU (NM_016169) rearrangement: t(10,12)(q24.32,p13.2)(chr10:g.104320248::chr12:g.12033406)	PRECISE	Note: The ETV6 - SUFU rearrangement is a translocation which results in the possible fusion of ETV6 exons 1-5 with SUFU exons 4-12. Its functional significance is undetermined. This case is being considered for Archer FusionPlex targeted RNAseq assay to help characterize any fusion transcript involving the ETV6 gene. If performed, the results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {ETV6:SUFU}		0	0	10	12	Intron of ETV6(+):4Kb before exon 6	ETV6	12033406			10	Intron of SUFU(+):10Kb after exon 3	SUFU	104320248			10	TRANSLOCATION		0	188503	0	11	NEW_VARIANT
P-0023550-T01-IM6	CDK12 (NM_016507) rearrangement: c.4173_chr17:g.58028299dup	PRECISE	Note: The CDK12 rearrangement results in the duplication of exon 14. One of the breakpoints is within exon 14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RPS6KB1:CDK12}		416751	0	22	17	Exon 14 of CDK12(+)	CDK12	37687269			17	Promoter of RPS6KB1(+):58Kb from tx start	RPS6KB1	58028299			10	DUPLICATION		20341030	195828	401370	26	NEW_VARIANT
P-0024094-T01-IM6	FGFR2 (NM_000141) - MYH9 (NM_002473) rearrangement: t(10;22)(q26.13;q12.3)(chr10:g.123240418::chr22:g.36682296)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:MYH9}		0	0	41	22	Intron of MYH9(-):297bp before exon 36	MYH9	36682296			10	Intron of FGFR2(-):883bp before exon 18	FGFR2	123240418			10	TRANSLOCATION		0	198130	0	41	NEW_VARIANT
P-0024097-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.41;q22.3)(chr19:g.52343327::chr21:g.42872775)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	10	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872775			19	IGR: 16Kb before ZNF577(-)	ZNF577	52343327			10	TRANSLOCATION		0	198116	0	10	NEW_VARIANT
P-0001117-T01-IM3	EZR (NM_003379) - ROS1 (NM_002944) Deletion: c.1090+214_c.5263del	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (EZR-ROS1)		252713	0	78	6	Exon 32 of ROS1(-)	ROS1	117650595			6	Intron of EZR(-): 214bp after exon 9	EZR	159191582			77	DELETION		41540987	72465	194332	95	NEW_VARIANT
P-0001818-T01-IM3	RAD51C (NM_058216) - PPM1D (NM_003620) Deletion :   c.463:RAD51C_c.1260+1492:PPM1Ddel (see note)	PRECISE	Note: The RAD51C alteration results in a deletion of a portion of the gene,   likely resulting in protein truncation.	AUTO_OK	3to5	3to5	Protein fusion: mid-exon (RAD51C-PPM1D)		9071	0	6	17	Exon 3 of RAD51C(+)	RAD51C	56774112			17	Intron of PPM1D(+): 1Kb after exon 5	PPM1D	58735694			14	DELETION		1961582	616	14521	6	NEW_VARIANT
P-0003677-T01-IM5	c.2363:FGFR3 _c.1784:TACC3dup	PRECISE	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 9-17 fused to TACC3 exons 9-16)	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		28230	0	35	4	Exon 9 of TACC3(+)	TACC3	1739003			4	Exon 18 of FGFR3(+)	FGFR3	1808931			63	DUPLICATION		69928	12472	34539	72	NEW_VARIANT
P-0012603-T01-IM5	PIK3R1 (NM_181523) Rearrangement :  c.1858:PIK3R1_chr5:g.72437149inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		3976	0	11	5	Exon 9 of PIK3R1(+)	PIK3R1	67592042			5	IGR: 21Kb before TMEM171(+)	TMEM171	72437149			23	INVERSION		4845107	158167	5013	11	NEW_VARIANT
P-0013453-T01-IM5	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		52027	0	64	2	Intron of ALK(-): 203bp before exon 20	ALK	29446597			2	Intron of EML4(+): 551bp after exon 17	EML4	42543741			81	INVERSION		13097144	161327	40816	62	NEW_VARIANT
P-0023477-T01-IM6	SMARCB1 (NM_003073) - SEZ6L (NM_021115) rearrangement: c.840:SMARCB1_c.95-11223:SEZ6Ldel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMARCB1:SEZ6L}		23413	0	30	22	Exon 7 of SMARCB1(+)	SMARCB1	24167456			22	Intron of SEZ6L(+):11Kb before exon 2	SEZ6L	26677149			10	DELETION		2509693	195615	39987	34	NEW_VARIANT
P-0023586-T01-IM6	EGFR (NM_005228) Rearrangement : c.69+16262:AMPH_c.3163-234:EGFRdel	PRECISE	Note: The EGFR Rearrangement results in the deletion of exons 1-26. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		116751	0	8	7	Intron of AMPH(-):16Kb after exon 1	AMPH	38654621			7	Intron of EGFR(+):233bp before exon 27	EGFR	55269976			10	DELETION		16615355	195993	153736	8	NEW_VARIANT
P-0023599-T01-IM6	SMARCD1 (NM_003076) Rearrangement : c.772-348_c.970del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2878	0	13	12	Intron of SMARCD1(+):347bp before exon 7	SMARCD1	50483319			12	Exon 8 of SMARCD1(+)	SMARCD1	50484120			0	DELETION		801	196062	1954	18	NEW_VARIANT
P-0000521-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (PAXIP1-MLL3)		65405	0	63	7	Exon 36 of MLL3(-)	MLL3	151879362			7	Intron of PAXIP1(-): 152bp after exon 6	PAXIP1	154767254			69	DELETION		2887892	71583	34050	78	NEW_VARIANT
P-0003626-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 3 fuses with ERG exons 4-10): c.127-643:ERG_c.40-61697:TMPRSS2del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		29768	0	89	21	Intron of ERG(-): 62Kb before exon 4	ERG	39879241			21	Intron of TMPRSS2(-): 643bp before exon 3	TMPRSS2	42867148			57	DELETION		2987907	12338	25221	95	NEW_VARIANT
P-0004816-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fuses with ERG exons 2-10): c.56-3787:TMPRSS2_c.39+54953:ERGdel.	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		63440	0	14	21	Intron of ERG(-): 5Kb after exon 1	ERG	39865199			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873903			30	DELETION		3008704	35488	83554	14	NEW_VARIANT
P-0004842-T01-IM5	PBRM1(NM_018313) -BAP1 (NM_004656) Rearrangement : c.2567+1284:PBRM1_ c.932-129:BAP1	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (PBRM1-BAP1)		49497	0	6	3	Intron of BAP1(-): 129bp before exon 11	BAP1	52439439			3	Intron of PBRM1(-): 1Kb after exon 17	PBRM1	52642045			11	DELETION		202606	39697	41588	5	NEW_VARIANT
P-0005914-T01-IM5	STK11 (NM_000455) rearrangement : c.291-486_375-30del	PRECISE	Note: The STK11 (NM_000455) rearrangement results in the intragenic deletion of STK11 exon2.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2161	0	5	19	Intron of STK11(+): 486bp before exon 2	STK11	1217930			19	Intron of STK11(+): 30bp before exon 3	STK11	1219293			5	DELETION		1363	64432	1718	5	NEW_VARIANT
P-0006313-T01-IM5	EML4 (NM_019063) -ALK (NM_004304) Fusion ( EML4 exons 1 to 18 fused with exons 20 to 29 of ALK )	PRECISE	Note: The fusion is an in frame fusion which includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		59368	0	55	2	Intron of ALK(-): 361bp after exon 19	ALK	29447966			2	Intron of EML4(+): 210bp before exon 18	EML4	42544357			73	INVERSION		13096391	78470	55062	55	NEW_VARIANT
P-0006389-T01-IM5	ERG (NM_001243432) - TMPRSS2 (NM_001135099) rearrangement : c.40-64167:ERG_c.56-3097:TMPRSS2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		52795	0	4	21	Intron of ERG(-): 64Kb before exon 4	ERG	39881711			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42873213			5	DELETION		2991502	92038	56516	4	NEW_VARIANT
P-0007050-T01-IM5	NTRK1(NM_002529) rearrangement : c.10-7071_c.1355-199inv	PRECISE	Note: The NTRK1(NM_002529) rearrangement results in inversion of exons 2-11	MANUAL_OK	3to3	3to3	Antisense fusion		36334	0	77	1	Intron of NTRK1(+): 7Kb before exon 2	NTRK1	156804802			1	Intron of NTRK1(+): 199bp before exon 12	NTRK1	156845113			64	INVERSION		40311	112851	29765	75	NEW_VARIANT
P-0007050-T01-IM5	VANGL2 (NM_020335) - NTRK1(NM_002529) rearrangement : c.-191+4456:VANGL2_c.1355-171:NTRK1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript fusion (VANGL2-NTRK1)		23485	0	59	1	Intron of NTRK1(+): 171bp before exon 12	NTRK1	156845141			1	5-UTR of VANGL2(+): 11Kb before coding start	VANGL2	160375115			51	DUPLICATION		3529974	112850	20463	59	NEW_VARIANT
P-0007098-T01-IM5	PIK3CD (NM_005026) rearrangement : c.2998-12:PIK3CD_chr1:g.25533354inv	PRECISE	Note: The PIK3CD (NM_005026) rearrangement results in the inversion of exon24 of PIK3CD . Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		175978	0	8	1	Intron of PIK3CD(+): 12bp before exon 24	PIK3CD	9786955			1	IGR: 15Kb before SYF2(-)	SYF2	25533354			34	INVERSION		15746399	113400	204815	7	NEW_VARIANT
P-0007211-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29) : c.667+165:EML4_c.3172+838:ALKinv	PRECISE	Note: The EML4 (NM_019063) - ALK (NM_004304) fusion includes the kinase domain of ALK. The fusion is predicted to be in-frame.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		50944	0	61	2	Intron of ALK(-): 838bp after exon 19	ALK	29447489			2	Intron of EML4(+): 165bp after exon 5	EML4	42492036			84	INVERSION		13044547	114593	34801	61	NEW_VARIANT
P-0007341-T03-IM6	SMARCA4 (NM_003072) rearrangement: c.1119-51:SMARCA4_chr19:g.12729256inv	PRECISE	Note: The SMARCA4 rearrangement is an inversion of exons 7-35.	MANUAL_OK	5to5	5to5	-		89514	0	6	19	Intron of SMARCA4(+): 51bp before exon 6	SMARCA4	11099942			19	Intron of ZNF791(+): 5Kb before exon 2	ZNF791	12729256			10	INVERSION		1629314	165991	80002	6	NEW_VARIANT
P-0007341-T03-IM6	DAXX (NM_001141970) rearrangement: chr6:g.4959186_c.1501+44:DAXXdel	PRECISE	Note: The DAXX rearrangement is a deletion of exons 6-8.	MANUAL_OK	3to5	3to5	-		525523	0	11	6	IGR: 3Kb after CDYL(+)	CDYL	4959186			6	Intron of DAXX(-): 44bp after exon 5	DAXX	33287744			17	DELETION		28328558	165987	497866	11	NEW_VARIANT
P-0007341-T03-IM6	TAP1 (NM_000593) rearrangement: chr6:g.30619601_c.762:TAP1del	PRECISE	Note: The TAP1 rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Antisense fusion		313972	0	9	6	Intron of C6orf136(+): 358bp after exon 4	C6orf136	30619601			6	Exon 1 of TAP1(-)	TAP1	32820832			21	DELETION		2201231	165986	285475	9	NEW_VARIANT
P-0007647-T01-IM5	TET2 (NM_001127208) rearrangement: chr4:g.104768006 _c.3685dup	PRECISE	Note: The TET2 rearrangement is a duplication of exons 1-6. One of the breakpoints is within exon 6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		38581	0	26	4	IGR: 257Kb before TACR3(-)	TACR3	104768006			4	Exon 6 of TET2(+)	TET2	106164817			31	DUPLICATION		1396811	117776	48942	25	NEW_VARIANT
P-0007770-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		69314	0	59	21	Intron of ERG(-): 36Kb after exon 3	ERG	39911982			21	Intron of TMPRSS2(-): 457bp after exon 2	TMPRSS2	42869589			43	DELETION		2957607	118370	53494	49	NEW_VARIANT
P-0008147-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) c.56-4181:TMPRSS2_c.40-58022:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		76796	0	3	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875566			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874297			6	DELETION		2998731	120489	80380	3	NEW_VARIANT
P-0008693-T01-IM5	FGFR2 (NM_000141) - NRAP (NM_198060) rearrangement: c.2301+935:FGFR2_c.2458-427:NRAPdel	PRECISE	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	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-NRAP)		58411	0	12	10	Intron of NRAP(-): 427bp before exon 23	NRAP	115382366			10	Intron of FGFR2(-): 586bp before exon 17	FGFR2	123242277			36	DELETION		7859911	123469	54573	12	NEW_VARIANT
P-0009073-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-3497:TMPRSS2_c.40-8505:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		54559	0	5	21	Intron of ERG(-): 9Kb before exon 4	ERG	39826049			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42873613			19	DELETION		3047564	126402	60277	5	NEW_VARIANT
P-0009077-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-671:TMPRSS2_c.40-59954:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		40572	0	5	21	Intron of ERG(-): 60Kb before exon 4	ERG	39877498			21	Intron of TMPRSS2(-): 671bp before exon 2	TMPRSS2	42870787			12	DELETION		2993289	126388	40408	5	NEW_VARIANT
P-0010032-T02-IM5	SDHAF2 (NM_017841) rearrangement: c.36+2562_c.330del	PRECISE	Note: The SDHAF2  rearrangement is an intragenic deletion of exons 2-3. One of the breakpoints is within exon3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		7461	0	10	11	Intron of SDHAF2(+): 3Kb after exon 1	SDHAF2	61200216			11	Exon 3 of SDHAF2(+)	SDHAF2	61205545			9	DELETION		5329	147670	7480	10	NEW_VARIANT
P-0011134-T01-IM5	NCOR1 (NM_006311) rearrangement : c.5101+341_5473del	PRECISE	Note: The NCOR1 rearrangement event results in the intragenic deletion of NCOR1 exons 35-37. One of the breakpoints is within NCOR1 exon37.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4292	0	33	17	Exon 37 of NCOR1(-)	NCOR1	15965123			17	Intron of NCOR1(-): 341bp after exon 34	NCOR1	15967843			26	DELETION		2720	151348	3068	27	NEW_VARIANT
P-0012029-T01-IM5	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	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		37727	0	48	21	Intron of ERG(-): 14Kb before exon 4	ERG	39831291			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868158			73	DELETION		3036867	155945	28747	48	NEW_VARIANT
P-0012275-T01-IM5	TMPRSS2 (NM_001135099) rearrangement: t(6;21)(q24.2;q22.3)(chr6:g.145232571::chr21:g.42869596)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	33	21	Intron of TMPRSS2(-): 450bp after exon 2	TMPRSS2	42869596			6	IGR: 58Kb after UTRN(+)	UTRN	145232571			0	TRANSLOCATION		0	157085	0	33	NEW_VARIANT
P-0012322-T01-IM5	TMPRSS2 (NM_001135099) -ERG (NM_004449) Rearrangement : c.56-2615:TMPRSS2_c.-150+18956:ERGinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		65251	0	6	21	5-UTR of ERG(-): 67Kb before coding start	ERG	40014626			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872731			13	INVERSION		2858105	157024	64840	5	NEW_VARIANT
P-0013023-T01-IM5	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-17904:CCDC6_c.2137-222:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		38571	0	8	10	Intron of RET(+): 222bp before exon 12	RET	43611810			10	Intron of CCDC6(-): 18Kb before exon 2	CCDC6	61630364			44	INVERSION		18018554	159948	38042	8	NEW_VARIANT
P-0013791-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		34532	0	4	21	Intron of ERG(-): 65Kb before exon 4	ERG	39882496			21	Intron of TMPRSS2(-): 516bp after exon 2	TMPRSS2	42869530			8	DELETION		2987034	162253	30074	4	NEW_VARIANT
P-0014270-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion includes  the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		127026	0	24	2	Intron of ALK(-): 285bp before exon 20	ALK	29446679			2	Intron of EML4(+): 2Kb after exon 5	EML4	42494165			38	INVERSION		13047486	163954	126808	23	NEW_VARIANT
P-0015004-T01-IM6	NTRK1 (NM_002529) - RABGAP1L (NM_014857) rearrangement: c.1354+172:NTRK1_c.2340+50594:RABGAP1Ldel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (NTRK1-RABGAP1L)		117163	0	26	1	Intron of NTRK1(+): 172bp after exon 11	NTRK1	156844972			1	Intron of RABGAP1L(+): 51Kb after exon 19	RABGAP1L	174831692			29	DELETION		17986720	166508	120363	26	NEW_VARIANT
P-0015034-T01-IM6	CDH1 (NM_004360) rearrangement: c.2130_c.2165-534del	PRECISE	Note: The CDH1 rearrangement is an intragenic deletion of exon 13. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		192	0	102	16	Exon 13 of CDH1(+)	CDH1	68857495			16	Intron of CDH1(+): 534bp before exon 14	CDH1	68861543			79	DELETION		4048	166625	189	115	NEW_VARIANT
P-0020959-T01-IM6	CIC (NM_015125) rearrangement: c.3915_c.4678inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		12830	0	2	19	Exon 16 of CIC(+)	CIC	42797863			19	Exon 20 of CIC(+)	CIC	42799194			9	INVERSION		1331	185850	11407	2	NEW_VARIANT
P-0021908-T01-IM6	NOTCH3 (NM_000435) rearrangement: t(5,19)(q34,p13.2)(chr5:g.160948114::chr19:g.15299881)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	27	19	Exon 8 of NOTCH3(-)	NOTCH3	15299881			5	Intron of GABRB2(-):24Kb after exon 4	GABRB2	160948114			10	TRANSLOCATION		0	188490	0	29	NEW_VARIANT
P-0021924-T01-IM6	PALB2 (NM_024675) - LRP1B (NM_018557) rearrangement: t(2;16)(q22.1;p12.2)(chr2:g.141570009::chr16:g.23652478)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	30	16	Exon 1 of PALB2(-)	PALB2	23652478			2	Intron of LRP1B(-):1Kb after exon 32	LRP1B	141570009			10	TRANSLOCATION		0	188518	0	51	NEW_VARIANT
P-0021924-T01-IM6	FAT1 (NM_005245) rearrangement: t(4;5)(q35.2;q15)(chr4:g.187525213::chr5:g.95189699)	PRECISE	Note: The FAT1 rearrangement is a translocation with a breakpoint within intron 18 of FAT1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	5	5-UTR of LINC01554(+):6Kb before coding start	LINC01554	95189699			4	Intron of FAT1(-):82bp before exon 19	FAT1	187525213			10	TRANSLOCATION		0	188517	0	5	NEW_VARIANT
P-0022406-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.1221_c.*3160del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 11-14. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7960	0	23	21	Promoter of TMPRSS2(-):2Kb from tx start	TMPRSS2	42834909			21	Exon 11 of TMPRSS2(-)	TMPRSS2	42842636			10	DELETION		7727	190537	7067	38	NEW_VARIANT
P-0022486-T01-IM6	CDK4 (NM_000075) rearrangement: c.567_chr12:g.94954944del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		40446	0	26	12	Exon 5 of CDK4(-)	CDK4	58144504			12	Promoter of MIR5700(+):620bp from tx start	MIR5700	94954944			10	DELETION		36810440	190936	190833	27	NEW_VARIANT
P-0000474-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		65955	0	16	2	Intron of ALK(-): 608bp before exon 20	ALK	29447002			2	Intron of EML4(+): 5Kb after exon 5	EML4	42497097			26	INVERSION		13050095	71542	52938	14	NEW_VARIANT
P-0000913-T04-IM6	AXL (NM_021913) Rearrangement : chr19:g.38751353_c.155:AXLinv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		27138	0	8	19	IGR: 4Kb before SPINT2(+)	SPINT2	38751353			19	Exon 2 of AXL(+)	AXL	41726610			8	INVERSION		2975257	197934	31188	8	NEW_VARIANT
P-0000913-T04-IM6	PDGFRA (NM_006206) Rearrangement : c.661_c.1558+131del	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		6793	0	13	4	Exon 5 of PDGFRA(+)	PDGFRA	55131118			4	Intron of PDGFRA(+):131bp after exon 10	PDGFRA	55140028			10	INVERSION		8910	197933	8348	12	NEW_VARIANT
P-0001745-T02-IM5	CCDC6 (NM_005436) - (RET (NM_020975) rearrangement: c.304-9458:CCDC6_c.2137-787:RETinv	PRECISE	Note: The CCDC6 - RET rearrangement is an inversion that results in the in frame fusion of CCDC6 exon 1 with RET exons 12-20.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		112682	0	3	10	Intron of RET(+): 787bp before exon 12	RET	43611245			10	Intron of CCDC6(-): 9Kb before exon 2	CCDC6	61621918			10	INVERSION		18010673	145068	117943	3	NEW_VARIANT
P-0002024-T01-IM3	EML4 (NM_019063) - ALK (NM_004304) inversion:   c.2242+31:EML4_c.3173-739:ALKinv	PRECISE	Note: The EML4-ALK Fusion is confirmed by FISH	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		50594	0	6	2	Intron of ALK(-): 739bp before exon 20	ALK	29447133			2	Intron of EML4(+): 31bp after exon 19	EML4	42552725			19	INVERSION		13105592	1153	46776	5	NEW_VARIANT
P-0002583-T01-IM3		PRECISE		MANUAL_OK	3to3	3to3	-		33453	0	14	21	3-UTR of TMPRSS2(-): 36bp after coding stop	TMPRSS2	42838033			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875108			23	INVERSION		37075	4069	34252	13	NEW_VARIANT
P-0003294-T02-IM5	CBFB (NM_022845) rearrangement : chr16:g.63947171_c.399+72:CBFBinv	PRECISE	Note: The CBFB (NM_022845) rearrangement results in the inversion of CBFB exons 1-4.	MANUAL_OK	3to3	3to3	-		5973	0	13	16	IGR: 1Mb before CDH11(-)	CDH11	63947171			16	Intron of CBFB(+): 72bp after exon 4	CBFB	67100773			15	INVERSION		3153602	130560	5352	13	NEW_VARIANT
P-0003294-T02-IM5	PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement : t(7;21)(p14.3;q22.2)(chr7:g.32062232::chr21:g.39817322)	PRECISE	Note: The PEDE1C (NM_001191058) - ERG (NM_004449) rearrangement event is a reciprocal translocation which results in the truncation of ERG exons 5-11.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	24	21	Intron of ERG(-): 5bp after exon 4	ERG	39817322			7	Intron of PDE1C(-): 29Kb after exon 3	PDE1C	32062232			30	TRANSLOCATION		0	130562	0	23	NEW_VARIANT
P-0003689-T01-IM5	c.55+2193:TMPRSS2_c.18+716:ERGdel	PRECISE	TMPRSS2 (NM_001135099) - ERG (NM_182918) reciprocal fusion (TMPRSS2 exon 1  fused with ERG exons 2-10)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		36698	0	6	21	Intron of ERG(-): 716bp after exon 1	ERG	39869571			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877684			7	DELETION		3008113	12521	20230	6	NEW_VARIANT
P-0003874-T01-IM5	SMARCA4 (NM_003072) rearrangement: t(19,13)(19p13.2:13q31.2) (chr19:g.11137036::chr13g.88339972)	PRECISE	The SMARCA4 (NM_003072 ) rearrangement is a translocation that results in the truncation of SMARCA4 exons 23-35. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	48	19	Intron of SMARCA4(+): 14bp after exon 22	SMARCA4	11137036			13	IGR: 15Kb before SLITRK5(+)	SLITRK5	88339972			76	TRANSLOCATION		0	13887	0	95	NEW_VARIANT
P-0004774-T01-IM5	NCOR1 (NM_006311) - GALK2 (NM_002044) Rearrrangement : t(17;15)(17p11.2;15q21.1)(chr17:g.16040646:chr15:g.49477846)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (NCOR1-GALK2)		0	0	40	17	Exon 14 of NCOR1(-)	NCOR1	16040646			15	Intron of GALK2(+): 15Kb after exon 1	GALK2	49477846			22	TRANSLOCATION		0	35191	0	39	NEW_VARIANT
P-0005557-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-3810:TMPRSS2_c.19-16939:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		70312	0	4	21	Intron of ERG(-): 17Kb before exon 4	ERG	39834483			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873926			12	DELETION		3039443	50729	65703	4	NEW_VARIANT
P-0009536-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused with ERG exons 4-11)   :  c.55+1957:TMPRSS2_c.39+43307:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		108409	0	8	21	Intron of ERG(-): 43Kb after exon 3	ERG	39904279			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877920			7	DELETION		2973641	131226	91795	8	NEW_VARIANT
P-0011035-T01-IM5	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	PRECISE	Note: The KIF5B-RET fusion is predicted to be in-frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		64054	0	25	10	Intron of KIF5B(-): 2Kb before exon 16	KIF5B	32314260			10	Intron of RET(+): 710bp before exon 12	RET	43611322			37	INVERSION		11297062	150476	59287	24	NEW_VARIANT
P-0011472-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		45382	0	42	21	Intron of ERG(-): 10Kb after exon 1	ERG	39860707			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872511			62	DELETION		3011804	153781	51971	42	NEW_VARIANT
P-0013221-T01-IM5	MLL (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.1;q23.3)(chr1:g.33801002::chr11:g.118342886)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (MLL-PHC2)		0	0	60	11	Exon 3 of MLL(+)	MLL	118342886			1	Intron of PHC2(-): 1Kb before exon 9	PHC2	33801002			44	TRANSLOCATION		0	160550	0	59	NEW_VARIANT
P-0013919-T01-IM5	MET (NM_000245) rearrangement: c.2887+35_c.3029-1182del	PRECISE	Note: The MET rearrangement is an intragenic deletion of exon 14.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		2079	0	40	7	Intron of MET(+): 35bp after exon 13	MET	116411743			7	Intron of MET(+): 1Kb before exon 15	MET	116413753			39	DELETION		2010	162749	1630	38	NEW_VARIANT
P-0014876-T01-IM6	TSC2 (NM_000548) rearrangement: t(12;16)(q21.31;p13.3)(chr12:g.80592188::chr16:g.2104408)	PRECISE	Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 5 of TSC2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	32	16	Exon 5 of TSC2(+)	TSC2	2104408			12	IGR: 11Kb before C12orf64(+)	C12orf64	80592188			30	TRANSLOCATION		0	166151	0	25	NEW_VARIANT
P-0021915-T01-IM6	ARID1A (NM_006015) - PHF14 (NM_014660) rearrangement: t(1,7)(p36.11,p21.3)(chr1:g.27101386::chr7:g.11032042)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ARID1A:PHF14}		0	0	6	7	Intron of PHF14(+):2Kb after exon 4	PHF14	11032042			1	Exon 18 of ARID1A(+)	ARID1A	27101386			10	TRANSLOCATION		0	188505	0	8	NEW_VARIANT
P-0024225-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-24 fused to RET exons 10-20): c.2762-430:KIF5B_c.1866:RETinv	PRECISE	Note: The KIF5B - RET fusion includes the kinase domain of RET. One of the breakpoints is within RET exon 10.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KIF5B:RET}		47729	0	46	10	Intron of KIF5B(-):430bp before exon 25	KIF5B	32305017			10	Exon 10 of RET(+)	RET	43609110			10	INVERSION		11304093	198990	37514	57	NEW_VARIANT
P-0024225-T01-IM6	PTPRT (NM_133170) rearrangement: c.2177-23_c.88+88442inv	PRECISE	Note: The PTPRT rearrangement is an intragenic inversion of exons 2-13. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		21654	0	15	20	Intron of PTPRT(-):23bp before exon 14	PTPRT	40899116			20	Intron of PTPRT(-):88Kb after exon 1	PTPRT	41729844			10	INVERSION		830728	198991	20655	18	NEW_VARIANT
P-0024249-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.1318+23_chr10:g.115014274del	PRECISE	Note: The TCF7L2 rearrangement is a deletion that includes TCF7L2 exons 13-14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		10866	0	23	10	Intron of TCF7L2(+):23bp after exon 12	TCF7L2	114917851			10	IGR: 296Kb before HABP2(+)	HABP2	115014274			10	DELETION		96423	199047	4714	23	NEW_VARIANT
P-0024249-T01-IM6	IRS2 (NM_003749) - CHMP1A (NM_002768) rearrangement: t(13;16)(q34;q24.3)(chr13:g.110437384::chr16:g.89721445)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {IRS2:CHMP1A}		0	0	9	16	Intron of CHMP1A(-):1Kb before exon 2	CHMP1A	89721445			13	Exon 1 of IRS2(-)	IRS2	110437384			0	TRANSLOCATION		0	199051	0	10	NEW_VARIANT
P-0024249-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused to ERG exons 4 -11): c.56-608:TMPRSS2_c.39+56905:ERGdel	IMPPRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		60804	0	100	21	Intron of ERG(-):57Kb after exon 3	ERG	39890681			21	Intron of TMPRSS2(-):608bp before exon 2	TMPRSS2	42870724			0	DELETION		2980043	199048	41084	105	NEW_VARIANT
P-0024266-T01-IM6	IKBKE (NM_014002) Rearrangement : c.1427+76_c.1616+931del	PRECISE	Note: The IKBKE Rearrangement results in the intragenic deletion of exons 14-15. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		2891	0	24	1	Intron of IKBKE(+):76bp after exon 13	IKBKE	206653952			1	Intron of IKBKE(+):931bp after exon 15	IKBKE	206659574			10	DELETION		5622	199107	2106	27	NEW_VARIANT
P-0024266-T01-IM6	MGA (NM_001164273) Rearrangement : c.4586-420_c.7204del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23824	0	48	15	Intron of MGA(+):419bp before exon 15	MGA	42034324			15	Exon 20 of MGA(+)	MGA	42052533			10	DELETION		18209	199108	16056	49	NEW_VARIANT
P-0002217-T02-IM3		PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		57365	0	16	2	Intron of ALK(-): 200bp before exon 20	ALK	29446594			2	Intron of EML4(+): 588bp after exon 12	EML4	42523244			26	INVERSION		13076650	3381	53910	16	NEW_VARIANT
P-0003208-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	-		6698	0	17	19	3-UTR of MAST3(+): 1Kb after coding stop	MAST3	18261614			19	Exon 8 of PIK3R2(+)	PIK3R2	18273074			34	DELETION		11460	9793	6968	17	NEW_VARIANT
P-0004345-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10) : c.56-651:TMPRSS2_c.18+6726:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		37101	0	9	21	Intron of ERG(-): 7Kb after exon 1	ERG	39863561			21	Intron of TMPRSS2(-): 651bp before exon 2	TMPRSS2	42870767			12	DELETION		3007206	18764	34929	9	NEW_VARIANT
P-0004532-T01-IM5	TMPRSS2-ERG Fusion (TMPRSS2 exon 2 fused to ERG exon 4) :  c.126+104:TMPRSS2_c.39+63265:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		24853	0	11	21	Intron of ERG(-): 63Kb after exon 3	ERG	39884321			21	Intron of TMPRSS2(-): 104bp after exon 2	TMPRSS2	42869942			28	DELETION		2985621	22099	29182	11	NEW_VARIANT
P-0005321-T01-IM5	EML4 (NM_001145076) - ALK (NM_004304)  Fusion (EML4 exon 13 fused with ALK exon 20) :  c.2068+156:EML4_c.3173-693:ALKinv	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		54026	0	75	2	Intron of ALK(-): 77bp after exon 19	ALK	29448250			2	Intron of EML4(+): 138bp before exon 13	EML4	42528243			62	INVERSION		13079993	47346	59175	72	NEW_VARIANT
P-0006689-T01-IM5	PIK3C2G (NM_004570) rearrangement : t(5;12)(p15.32;p12.3)(chr5:g.5556235::chr12:g.18552720)	PRECISE	Note: The PIK3C2G (NM_004570) rearrangement event results in the truncation of PIK3C2G exons 15-32. One of the breakpoints is within PIK3C2G exon15.	MANUAL_OK	3to5	3to5	-		0	0	33	12	Exon 15 of PIK3C2G(+)	PIK3C2G	18552720			5	IGR: 133Kb before KIAA0947(+)	KIAA0947	5556235			29	TRANSLOCATION		0	108250	0	33	NEW_VARIANT
P-0006689-T01-IM5	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement :  c.40-31716:ERG_c.127-715:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		26481	0	21	21	Intron of ERG(-): 21Kb after exon 1	ERG	39849260			21	Intron of TMPRSS2(-): 715bp before exon 3	TMPRSS2	42867220			24	INVERSION		3017960	108249	27321	21	NEW_VARIANT
P-0006689-T01-IM5	TMPRSS2 (NM_001135099) - MLLT4 (NM_001207008) rearrangement : t(6;21)(q27;q22.3)(chr6:168293792::chr21:42875775)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (TMPRSS2-MLLT4)		0	0	15	21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875775			6	Intron of MLLT4(+): 750bp before exon 9	MLLT4	168293792			27	TRANSLOCATION		0	108253	0	14	NEW_VARIANT
P-0008054-T01-IM5	EED (NM_003797) rearrangement: c.1125+52_chr11:g.91474496del	PRECISE	The EED (NM_003797) rearrangement is a deletion of EED exons 11-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6519	0	66	11	Intron of EED(+): 52bp after exon 10	EED	85988232			11	IGR: 611Kb before FAT3(+)	FAT3	91474496			98	DELETION		5486264	120177	6288	66	NEW_VARIANT
P-0011525-T01-IM5	TMPRSS2 (NM_001135099) Rearrangement :  c.557-24:TMPRSS2_chr21:g.43616717del	PRECISE	Note: The TMPRSS2 Rearrangement results in the deletion of exons1-5 of TMPRSS2.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		121710	0	5	21	Intron of TMPRSS2(-): 24bp before exon 6	TMPRSS2	42852553			21	IGR: 3Kb before ABCG1(+)	ABCG1	43616717			15	DELETION		764164	154124	121007	5	NEW_VARIANT
P-0012141-T01-IM5	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-58782:ERG_c.126+259:TMPRSS2inv	PRECISE	Note: The ERG (NM_004449) - TMPRSS2 rearrangement results in an inversion of TMPRSS2 exons 3-14 and exons 1-3 of the non-canonical ERG transcript. This complex rearrangement is suggestive of a TMPRSS2-ERG fusion. Confirmatory testing  of the fusion by the Archer assay is suggested, if clinically indicated.	MANUAL_OK	3to3	3to3	-		39065	0	64	21	Intron of ERG(-): 59Kb before exon 4	ERG	39876326			21	Intron of TMPRSS2(-): 259bp after exon 2	TMPRSS2	42869787			67	INVERSION		2993461	156474	38915	63	NEW_VARIANT
P-0012141-T01-IM5	PIK3R1 (NM_181523) rearrangement: c.917-5504_c.1300-2del	PRECISE	Note: The PIK3R1 rearrangement is an intragenic deletion of exons 5-6.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: out of frame		5108	0	16	5	Intron of PIK3R1(+): 6Kb before exon 7	PIK3R1	67582583			5	Intron of PIK3R1(+): 2bp before exon 5	PIK3R1	67589535			23	DELETION		6952	156473	7337	16	NEW_VARIANT
P-0013536-T01-IM5	MKRN1 (NM_013446) - BRAF (NM_004333) rearrangement: c.544+172:MKRN1_c.1178-661:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (MKRN1-BRAF)		19716	0	8	7	Intron of MKRN1(-): 172bp after exon 3	MKRN1	140159335			7	Intron of BRAF(-): 661bp before exon 10	BRAF	140483618			12	DUPLICATION		324283	161626	18997	8	NEW_VARIANT
P-0014341-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 4-10): c.56-2247:TMPRSS2_c.-4097:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		67752	0	35	21	Intron of ERG(-): 57Kb before exon 4	ERG	39874401			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872363			53	DELETION		2997962	164179	66298	35	NEW_VARIANT
P-0020847-T02-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		34617	0	26	21	Intron of ERG(-):17Kb before exon 2	ERG	39834901			21	Intron of TMPRSS2(-):601bp before exon 3	TMPRSS2	42867106			10	DELETION		3032205	187659	20988	27	NEW_VARIANT
P-0021914-T01-IM6	ROS1 (NM_002944) - LARS (NM_020117) rearrangement: t(5,6)(q32,q22.1)(chr5:g.145500267::chr6:g.117646519)	PRECISE	Note: The ROS1 - LARS rearrangement is a translocation which may form a fusion between ROS1 exons 1-33 with LARS exons 31-32. This does not include the kinase domain of ROS1. Its functional significance is undetermined. This case is being considered for Archer FusionPlex targeted RNA sequencing for characterization of any fusion transcript involving ROS1. If performed, the results will be reported separately in a different case number.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ROS1:LARS}		0	0	22	6	Intron of ROS1(-):867bp after exon 33	ROS1	117646519			5	Intron of LARS(-):201bp before exon 31	LARS	145500267			10	TRANSLOCATION		0	188498	0	24	NEW_VARIANT
P-0021916-T01-IM6	NF2 (NM_000268) -  rearrangement: c.109:NF2_chr22:g.30109685del	PRECISE	Note: The NF2 rearrangement is a deletion of exons 1-16. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		22272	0	27	22	Exon 1 of NF2(+)	NF2	30000096			22	IGR: 7Kb before CABP7(+)	CABP7	30109685			10	DELETION		109589	188491	14050	28	NEW_VARIANT
P-0024178-T01-IM6	MAP2K4 (NM_003010) Rearrangement : t(2,17)(q23.1,p12)(chr2:g.147903758::chr17:g.12028641)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	10	17	Exon 8 of MAP2K4(+)	MAP2K4	12028641			2	IGR: 559Kb before PABPC1P2(+)	PABPC1P2	147903758			8	TRANSLOCATION		0	198658	0	10	NEW_VARIANT
P-0024183-T01-IM6	FGFR2 (NM_000141) Rearrangement : t(1;10)(q32.3;q26.11)(chr1:g.208433127::chr10:g.123242818)	IMPPRECISE	Note: The FGFR2 Rearrangement results in the possible truncation of FGFR2. One of the breakpoints is within intron 17. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	8	10	Intron of FGFR2(-):393bp after exon 17	FGFR2	123242818			1	IGR: 238Kb before PLXNA2(-)	PLXNA2	208433127			0	TRANSLOCATION		0	198667	0	8	NEW_VARIANT
P-0024187-T01-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) Fusion (FGFR2 exon 17 with TACC2 exon12) : c.2302-1038:FGFR2_c.8009:TACC2inv	PRECISE	Note: The FGFR2 fusion includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FGFR2:TACC2}		63921	0	7	10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240573			10	Exon 12 of TACC2(+)	TACC2	123988973			10	INVERSION		748400	198672	57485	7	NEW_VARIANT
P-0024193-T01-IM6	ERBB3 (NM_001982) rearrangement: chr12: 56408400 _c.558dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		10210	0	16	12	IGR: 6Kb before IKZF4(+)	IKZF4	56408400			12	Exon 5 of ERBB3(+)	ERBB3	56481371			10	DUPLICATION		72971	198765	11444	16	NEW_VARIANT
P-0024201-T01-IM6	PIM1 (NM_002648) rearrangement: c.608-304_chr6:g.37178326dup	PRECISE	Note: The PIM1 rearrangement results in the duplication of exons 5-6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		4769	0	30	6	Intron of PIM1(+):303bp before exon 5	PIM1	37140468			6	Promoter of TMEM217(-):2Kb from tx start	TMEM217	37178326			10	DUPLICATION		37858	198757	6628	31	NEW_VARIANT
P-0024203-T01-IM6	TERT (NM_198253) rearrangement: t(5;21)(p15.33;q21.1)(chr5:g.1279360::chr21:g.17011913)	PRECISE	Note: The TERT rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	134	21	IGR: 90Kb before USP25(+)	USP25	17011913			5	Intron of TERT(-):45bp after exon 5	TERT	1279360			10	TRANSLOCATION		0	198771	0	140	NEW_VARIANT
P-0024206-T01-IM6	RNF213 (NM_001256071) - RPTOR (NM_020761) rearrangement: c.14539+250:RNF213_c.2102-56:RPTORdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {RNF213:RPTOR}		33344	0	47	17	Intron of RNF213(+):250bp after exon 61	RNF213	78359671			17	Intron of RPTOR(+):55bp before exon 19	RPTOR	78866473			10	DELETION		506802	198781	70022	48	NEW_VARIANT
P-0024206-T01-IM6	EXOC4 (NM_021807) - BRAF (NM_004333) rearrangement: c.87-8072:EXOC4_c.1141-572:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {EXOC4:BRAF}		70391	0	9	7	Intron of EXOC4(+):8Kb before exon 2	EXOC4	132951665			7	Intron of BRAF(-):572bp before exon 9	BRAF	140487956			10	INVERSION		7536291	198782	79924	9	NEW_VARIANT
P-0024219-T01-IM6	TTC7A (NM_020458) - MSH6 (NM_000179) rearrangement: c.518-7732:TTC7A_c.481:MSH6del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TTC7A:MSH6}		48122	0	3	2	Intron of TTC7A(+):8Kb before exon 4	TTC7A	47194380			2	Exon 3 of MSH6(+)	MSH6	48023056			10	DELETION		828676	198862	22685	4	NEW_VARIANT
P-0024296-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.4393:NOTCH2_chr1:g.116787704del	PRECISE	Note: The NOTCH2 rearrangement is a deletion of exons 25-34. One of the breakpoints is within exon 25. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		42611	0	127	1	IGR: 128Kb before ATP1A1(+)	ATP1A1	116787704			1	Exon 25 of NOTCH2(-)	NOTCH2	120468046			10	DELETION		3680342	199284	34767	136	NEW_VARIANT
P-0024349-T01-IM6	RASA1 (NM_002890) rearrangement: c.-3698_c.451del	PRECISE	Note: The RAS1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3156	0	50	5	IGR: 3Kb before RASA1(+)	RASA1	86560571			5	Exon 1 of RASA1(+)	RASA1	86564719			10	DELETION		4148	199852	1541	59	NEW_VARIANT
P-0024099-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.*114_chr9:g.22030267inv	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		6	9	Exon 3 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21968229			9	5-UTR of CDKN2B-AS1(+):91Kb before coding start	CDKN2B-AS1	22030267			0	INVERSION		62038	198678	7059		NEW_VARIANT
P-0024099-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.470_chr9:g.22030267inv	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		6	9	Exon 3 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21968229			9	5-UTR of CDKN2B-AS1(+):91Kb before coding start	CDKN2B-AS1	22030267			0	INVERSION		62038	198677	7059		NEW_VARIANT
P-0024105-T01-IM6	EP300 (NM_001429) - COLQ (NM_005677) rearrangement: t(3;22)(p25.1;q13.2)(chr3:g.15513123::chr22:g.41562715)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {EP300:COLQ}		0	0	21	22	Intron of EP300(+):45bp after exon 23	EP300	41562715			3	Intron of COLQ(-):1Kb before exon 10	COLQ	15513123			0	TRANSLOCATION		0	198367	0	21	NEW_VARIANT
P-0024105-T01-IM6	CDKAL1 (NM_017774) - E2F3 (NM_001949) rearrangement: c.1055+24367:CDKAL1_c.506-2:E2F3dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CDKAL1:E2F3}		8908	0	14	6	Intron of E2F3(+):1bp before exon 3	E2F3	20481435			6	Intron of CDKAL1(+):24Kb after exon 11	CDKAL1	21024970			0	DUPLICATION		543535	198366	10624	14	NEW_VARIANT
P-0024128-T01-IM6	TCF3 (NM_001136139) rearrangement: c.1165_c.*3255del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16200	0	34	19	Promoter of TCF3(-):1Kb from tx start	TCF3	1608117			19	Exon 13 of TCF3(-)	TCF3	1619781			10	DELETION		11664	198572	10137	42	NEW_VARIANT
P-0024129-T01-IM6	KMT2D (NM_003482) rearrangement: t(4;12)(p15.33;q13.12)(chr4:g.12861485::chr12:g.49443742)	PRECISE	Note: The KMT2D rearrangement is a translocation with a breakpoint within exon 11. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	62	12	Exon 11 of KMT2D(-)	KMT2D	49443742			4	IGR: 508Kb before RAB28(-)	RAB28	12861485			10	TRANSLOCATION		0	198574	0	87	NEW_VARIANT
P-0024136-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		114705	0	61	2	Intron of ALK(-):60bp after exon 19	ALK	29448266			2	Intron of EML4(+):4Kb before exon 6	EML4	42503492			10	INVERSION		13055226	198586	94009	61	NEW_VARIANT
P-0024215-T01-IM6	NF1 (NM_001042492) rearrangement: c.6559_c.7190-2264dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		6594	0	2	17	Exon 43 of NF1(+)	NF1	29664517			17	Intron of NF1(+):2Kb before exon 49	NF1	29673874			10	DUPLICATION		9357	198841	14733	17	NEW_VARIANT
P-0022245-T01-IM6	BRCA2 (NM_000059) rearrangement: c.8754+23:BRCA2_chr13:g.114995748del	PRECISE	Note: The BRCA2 rearrangement is a deletion of exons 22-27.	MANUAL_OK	3to5	3to5	-		203102	0	26	13	Intron of BRCA2(+):23bp after exon 21	BRCA2	32950951			13	IGR: 5Kb before CDC16(+)	CDC16	114995748			10	DELETION		82044797	190016	190202	28	NEW_VARIANT
P-0021321-T01-IM6	DDX10 (NM_004398) - ATM (NM_000051) rearrangement: c.1966-28956:DDX10_c.4831:ATMdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DDX10:ATM}		39656	0	17	11	Exon 32 of ATM(+)	ATM	108165708			11	Intron of DDX10(+):29Kb before exon 14	DDX10	108680217			10	DUPLICATION		514509	186866	48675	18	NEW_VARIANT
P-0021676-T01-IM6	EZH1 (NM_001991) rearrangement: c.1132_c.1402-5del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4415	0	40	17	Intron of EZH1(-):5bp before exon 13	EZH1	40861960			17	Exon 11 of EZH1(-)	EZH1	40865299			10	DELETION		3339	188075	4079	41	NEW_VARIANT
P-0024169-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.56-785:TMPRSS2_c.40-59113:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		40571	0	15	21	Intron of ERG(-):59Kb before exon 4	ERG	39876657			21	Intron of TMPRSS2(-):785bp before exon 2	TMPRSS2	42870901			10	INVERSION		2994244	198711	32779	14	NEW_VARIANT
P-0019967-T02-IM6	TRAPPC9 (NM_031466) - AGO2 (NM_012154) rearrangement: c.3105-25933:TRAPPC9_c.2273:AGO2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TRAPPC9:AGO2}		4979	0	10	8	Intron of TRAPPC9(-):26Kb before exon 20	TRAPPC9	140948477			8	Exon 18 of AGO2(-)	AGO2	141542713			10	DUPLICATION		594236	197200	4983	10	NEW_VARIANT
P-0024168-T01-IM6	POGK (NM_017542) - IL10 (NM_000572) Rearrangement :  c.132+1054:POGK_c.226-132:IL10inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {POGK:IL10}		123058	0	4	1	Intron of POGK(+):1Kb after exon 2	POGK	166811379			1	Intron of IL10(-):132bp before exon 3	IL10	206944536			8	INVERSION		40133157	198735	232610	4	NEW_VARIANT
P-0024448-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.307_c.482+2736del	PRECISE	Note: The MAP3K1 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		175	0	62	5	Exon 1 of MAP3K1(+)	MAP3K1	56111707			5	Intron of MAP3K1(+):3Kb after exon 1	MAP3K1	56114618			10	DELETION		2911	200454	83	72	NEW_VARIANT
P-0024450-T01-IM6	NTHL1 (NM_002528) rearrangement: t(16;19)(p13.3;p13.2)(chr16:g.2090167::chr19:g.10213963)	PRECISE	Note: The NTHL1 rearrangement is a translocation with a breakpoint within NTHL1 exon 5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	19	Promoter of PPAN-P2RY11(+):3Kb from tx start	PPAN-P2RY11	10213963			16	Exon 5 of NTHL1(-)	NTHL1	2090167			10	TRANSLOCATION		0	200462	0	22	NEW_VARIANT
P-0024450-T01-IM6	SEC16A (NM_014866) - NOTCH1 (NM_017617) fusion (SEC16A exon 1 fused to NOTCH1 exons 27-34): c.-192+5:SEC16A_c.5019-187:NOTCH1dup	PRECISE		MANUAL_OK	5to3	5to3	Transcript Fusion {SEC16A:NOTCH1}		29672	0	20	9	5-UTR of SEC16A(-):41Kb before coding start	SEC16A	139377385			9	Intron of NOTCH1(-):187bp before exon 27	NOTCH1	139397969			10	DUPLICATION		20584	200460	57623	19	NEW_VARIANT
P-0024418-T01-IM6	CTNNB1 (NM_001904) Rearrangement :  c.-48-123_c.346del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2500	0	39	3	5-UTR of CTNNB1(+):170bp before coding start	CTNNB1	41265389			3	Exon 4 of CTNNB1(+)	CTNNB1	41266549			0	DELETION		1160	200056	3008	43	NEW_VARIANT
P-0006009-T02-IM6	KMT2D (NM_003482) rearrangement: c.11662:KMT2D_chr12:g.49153129del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		59129	0	4	12	5-UTR of LINC00935(+):6Kb before coding start	LINC00935	49153129			12	Exon 39 of KMT2D(-)	KMT2D	49426826			10	DELETION		273697	199719	33103	4	NEW_VARIANT
P-0006009-T02-IM6	ASXL2 (NM_018263) rearrangement: c.565:ASXL2_chr2:g.25927220del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		36258	0	10	2	IGR: 35Kb before ASXL2(-)	ASXL2	25927220			2	Exon 6 of ASXL2(-)	ASXL2	25991677			10	DELETION		64457	199715	17888	13	NEW_VARIANT
P-0023839-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused with ERG exons 2-10): c.56-2993:TMPRSS2_c.19-8540:ERGdel	PRECISE	Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		79340	0	16	21	Intron of ERG(-):9Kb before exon 2	ERG	39826084			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873109			10	DELETION		3047025	199711	72849	16	NEW_VARIANT
P-0024461-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449): c.56-2094:TMPRSS2_:c.40-59950:ERGdel	PRECISE	Note: The TMPRSS2  - ERG rearrangement results in fusion of TMPRSS2 exon 1 with ERG exons 4 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		73142	0	63	21	Intron of ERG(-):60Kb before exon 4	ERG	39877494			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872210			10	DELETION		2994716	200169	76545	69	NEW_VARIANT
P-0024543-T01-IM6	CASP8 (NM_001080125) - CASP10 (NM_032977) rearrangement: c.151+17:CASP8_c.-1793dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {CASP8:CASP10}		1730	0	40	2	Promoter of CASP10(+):1Kb from tx start	CASP10	202046246			2	Intron of CASP8(+):17bp after exon 1	CASP8	202123122			10	DUPLICATION		76876	200689	2541	46	NEW_VARIANT
P-0024554-T01-IM6	SOCS1 (NM_003745) rearrangement: c.-572_c.48inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		877	0	3	16	Exon 2 of SOCS1(-)	SOCS1	11349288			16	Promoter of SOCS1(-):2Kb from tx start	SOCS1	11350457			7	INVERSION		1169	200676	1022	3	NEW_VARIANT
P-0024518-T01-IM6	NF1 (NM_001042492) rearrangement: t(5;17)(p11;q11.2)(chr5:g.46356017::chr17:g.29665106)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 45. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	17	Exon 45 of NF1(+)	NF1	29665106			5	IGR: 1Mb before HCN1(-)	HCN1	46356017			10	TRANSLOCATION		0	200539	0	6	NEW_VARIANT
P-0024524-T01-IM6	AGBL4 (NM_032785) - RAD54L (NM_001142548) rearrangement: c.1364+2079:AGBL4_c.1245-1:RAD54Linv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {AGBL4:RAD54L}		11169	0	83	1	Exon 13 of RAD54L(+)	RAD54L	46738343			1	Intron of AGBL4(-):2Kb after exon 12	AGBL4	49003235			10	INVERSION		2264892	200626	18297	94	NEW_VARIANT
P-0024530-T01-IM6	DNMT3B (NM_006892) rearrangement: c.1906-133:DNMT3B_chr20:g.31140058del	PRECISE	Note: The DNMT3B rearrangement is a deletion of exons 1-17. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		26048	0	7	20	Intron of NOL4L(-):24Kb before exon 2	NOL4L	31140058			20	Intron of DNMT3B(+):132bp before exon 18	DNMT3B	31388508			6	DELETION		248450	200631	34627	7	NEW_VARIANT
P-0024530-T01-IM6	MAP3K13 (NM_004721) rearrangement: c.569:MAP3K13_chr3:g.147659711del	PRECISE	Note: The MAP3K13 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		118902	0	18	3	IGR: 521Kb before LOC440982(+)	LOC440982	147659711			3	Exon 3 of MAP3K13(+)	MAP3K13	185155328			10	DELETION		37495617	200630	189583	22	NEW_VARIANT
P-0024531-T01-IM6	ARID2 (NM_152641): c.3061:ARID2_chr12:g.41070584inv	PRECISE	Note: The ARID2 rearrangement is an inversion of exons 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		25280	0	13	12	IGR: 16Kb before CNTN1(+)	CNTN1	41070584			12	Exon 15 of ARID2(+)	ARID2	46244967			10	INVERSION		5174383	200637	30857	13	NEW_VARIANT
P-0024532-T01-IM6	EWSR1 (NM_013986) rearrangement: t(10;22)(q11.23;q12.2)(chr10:g.50812403::chr22:g.29683485)	PRECISE	Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	49	22	Intron of EWSR1(+):362bp after exon 8	EWSR1	29683485			10	IGR: 5Kb before CHAT(+)	CHAT	50812403			10	TRANSLOCATION		0	200629	0	61	NEW_VARIANT
P-0024534-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-562:TMPRSS2_chr21:g.40083159del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		46351	0	155	21	IGR: 28Kb before LINC00114(-)	LINC00114	40083159			21	Intron of TMPRSS2(-):562bp before exon 2	TMPRSS2	42870678			10	DELETION		2787519	200606	65099	170	NEW_VARIANT
P-0024537-T01-IM6	ATR (NM_001184) rearrangement: c.1886-81:ATR_chr3:g.147951936inv	PRECISE	Note: The ATR rearrangement results in the inversion of exons 1-8. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		15368	0	3	3	Intron of ATR(-):81bp before exon 9	ATR	142275498			3	IGR: 464Kb before AGTR1(+)	AGTR1	147951936			7	INVERSION		5676438	200591	9936	3	NEW_VARIANT
P-0004787-T01-IM5	ZFHX3 (NM_006885) rearrangement: c.8474_c.9037del	PRECISE	The ZFHX3 (NM_006885) rearrangement is an intragenic deletion within exon 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		8819	2	100	16	Exon 9 of ZFHX3(-)	ZFHX3	72827544			16	Exon 9 of ZFHX3(-)	ZFHX3	72828107			125	DELETION		563	35397	1184	348	NEW_VARIANT
P-0024586-T01-IM6	FLT1 (NM_002019) rearrangement: c.1106+66_chr13:g.30250041inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		11732	0	15	13	Intron of FLT1(-):65bp after exon 8	FLT1	29004121			13	IGR: 89Kb before UBL3(-)	UBL3	30250041			10	INVERSION		1245920	200973	8862	15	NEW_VARIANT
P-0024600-T01-IM6	NTRK1 (NM_002529) rearrangement: c.360-386:NTRK1_chr1:g.160259587del	PRECISE	Note: The NTRK1 rearrangement is deletion with a breakpoint in intron 3. 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 NTRK1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	-		50417	0	18	1	Intron of NTRK1(+):385bp before exon 4	NTRK1	156836316			1	3-UTR of COPA(-):359bp after coding stop	COPA	160259587			10	DELETION		3423271	200962	24325	19	NEW_VARIANT
P-0024602-T01-IM6	SMARCD1 (NM_003076) - CTDSP2 (NM_005730) rearrangement: c.1269+187:SMARCD1_c.213+511:CTDSP2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SMARCD1:CTDSP2}		136707	0	19	12	Intron of SMARCD1(+):187bp after exon 10	SMARCD1	50488542			12	Intron of CTDSP2(-):510bp after exon 2	CTDSP2	58222720			10	INVERSION		7734178	200967	130889	19	NEW_VARIANT
P-0024672-T01-IM6	TP53 (NM_000546) Rearrangement : t(17;18)(p13.1;p11.22)(chr17:g.7580666;18:9253524)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	41	18	Intron of ANKRD12(+):684bp before exon 8	ANKRD12	9253524			17	5-UTR of TP53(-):8Kb before coding start	TP53	7580666			10	TRANSLOCATION		0	201208	0	40	NEW_VARIANT
P-0024672-T01-IM6	JAK2 (NM_004972) Rearrangement : c.1514-48:JAK2_chr9:g.2692334del	PRECISE	Note: The JAK2  Rearrangement results in the deletion of exon 1-11 of JAK2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17291	0	6	9	IGR: 25Kb before KCNV2(+)	KCNV2	2692334			9	Intron of JAK2(+):47bp before exon 12	JAK2	5069877			10	DELETION		2377543	201206	13112	6	NEW_VARIANT
P-0024679-T01-IM6	ALK (NM_004304) - CTSE(NM_001910) Rearrangement: t(1;2)(q32.1;p23.3)(chr1:g.206318648; chr2:g.29543594)	PRECISE	Note: The ALK - CTSE Rearrangement results in possible truncation of ALK, with the breakpoint in intron 7 of ALK.Its functional significance is unknown.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	44	2	Intron of ALK(-):22bp after exon 7	ALK	29543594			1	Intron of CTSE(+):181bp after exon 2	CTSE	206318648			10	TRANSLOCATION		0	201251	0	45	NEW_VARIANT
P-0024679-T01-IM6	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exon 4-11 ) : c.56-4747:TMPRSS2_c.40-54816:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		72131	0	34	21	Promoter of ERG(-):120Kb from tx start	ERG	39872360			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874863			10	DELETION		3002503	201250	66064	35	NEW_VARIANT
P-0024680-T01-IM6	DNAJB1 (NM_006145) Rearrangement: c.212-537:DNAJB1_c.394+79:VSTM1inv	PRECISE	Note:The DNAJB1 Rearrangement results in the inversion of exon1 of DNAJB1. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		564936	0	2	19	Intron of DNAJB1(-):537bp before exon 2	DNAJB1	14628395			19	Intron of VSTM1(-):9Kb before exon 2	VSTM1	54554585			9	INVERSION		39926190	201244	475412	3	NEW_VARIANT
P-0024687-T01-IM6	CCNE1 (NM_001238) rearrangement: c.1088:CCNE1_chr19:g.30433580inv	PRECISE	Note: The CCNE1 rearrangement is an inversion of exons 11-12. One of the breakpoints is within exon 11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2779	0	11	19	Exon 11 of CCNE1(+)	CCNE1	30313488			19	Intron of URI1(+):9bp after exon 1	URI1	30433580			10	INVERSION		120092	201368	1495	10	NEW_VARIANT
P-0024689-T01-IM6	NSD1 (NM_022455) rearrangement: c.6428:NSD1_chr5:g.106346069inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		367385	0	90	5	3-UTR of LOC102467213(-):646bp after coding stop	LOC102467213	106346069			5	Exon 22 of NSD1(+)	NSD1	176719124			10	INVERSION		70373055	201381	534864	90	NEW_VARIANT
P-0024691-T01-IM6	MAP2K1 (NM_002755) rearrangement: c.895+136_c.1068+241del	PRECISE	Note: The MAP2K1 rearrangement is an intragenic deletion of exons 8-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		2819	0	15	15	Intron of MAP2K1(+):136bp after exon 7	MAP2K1	66777665			15	Intron of MAP2K1(+):241bp after exon 10	MAP2K1	66782342			10	DELETION		4677	201364	3422	21	NEW_VARIANT
P-0024691-T01-IM6	POU2F2 (NM_001207025) - ERF (NM_006494) rearrangement: c.186+1304:POU2F2_c.22+14:ERFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {POU2F2:ERF}		12767	0	90	19	Intron of POU2F2(-):1Kb after exon 4	POU2F2	42624974			19	Intron of ERF(-):13bp after exon 1	ERF	42759116			10	DUPLICATION		134142	201365	45547	104	NEW_VARIANT
P-0024695-T01-IM6	HIST3H3 (NM_003493) rearrangement: t(1;4)(q42.13;p11)(chr1:g.228612839::chr4:g.49583945)	IMPPRECISE	Note: The HIST3H3 rearrangement is a translocation involving HIST3H3 exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	4	IGR: 595Kb before CWH43(+)	CWH43	49583945			1	Exon 1 of HIST3H3(-)	HIST3H3	228612839			0	TRANSLOCATION		0	201405	0	18	NEW_VARIANT
P-0024741-T01-IM6	CDK12 (NM_016507) rearrangement: t(8;17)(q21.11;q12)(chr8:g.78247787::chr17:g.37627932)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	79	17	Exon 2 of CDK12(+)	CDK12	37627932			8	IGR: 115Kb before LOC102724874(+)	LOC102724874	78247787			10	TRANSLOCATION		0	201312	0	84	NEW_VARIANT
P-0024844-T01-IM6	ERBB4 (NM_005235) rearrangement: c.556+7326_c.2965-8del	IMPPRECISE	Note: The ERBB4 rearrangement is an intragenic deletion of exons 5-25. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 20 exons : out of frame		21570	0	59	2	Intron of ERBB4(-):8bp before exon 25	ERBB4	212285344			2	Intron of ERBB4(-):7Kb after exon 4	ERBB4	212645424			0	DELETION		360080	202048	35765	62	NEW_VARIANT
P-0024865-T01-IM6	BCL2L1 (NM_138578) - FSIP1 (NM_152597) rearrangement: t(15;20)(q14;q11.21)(chr15:g.40027488::chr20:g.30263448)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {BCL2L1:FSIP1}		0	0	8	20	Intron of BCL2L1(-):10Kb before exon 3	BCL2L1	30263448			15	Intron of FSIP1(-):3Kb after exon 8	FSIP1	40027488			10	TRANSLOCATION		0	202455	0	8	NEW_VARIANT
P-0024873-T01-IM6	KDM6A (NM_021140) rearrangement: c.2994_chrX:g.45005757del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		5584	0	36	X	Exon 20 of KDM6A(+)	KDM6A	44938446			X	Promoter of CXorf36(-):2Kb from tx start	CXorf36	45005757			10	DELETION		67311	202448	2907	40	NEW_VARIANT
P-0024166-T02-IM6	SPEN (NM_015001) rearrangement: c.10863+15:SPEN_chr1:g.22588125del	PRECISE	Note: The SPEN rearrangement results in the deletion of exons 14-15. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		73384	0	4	1	Intron of SPEN(+):15bp after exon 14	SPEN	16265386			1	IGR: 144Kb before WNT4(-)	WNT4	22588125			8	DELETION		6322739	202044	112088	4	NEW_VARIANT
P-0024838-T01-IM6	CDK4 (NM_000075) rearrangement: c.819+33:CDK4_chr12:g.58082608del	PRECISE	Note: The CDK4 rearrangement is a deletion of exon 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		913	0	26	12	IGR: 5Kb before OS9(+)	OS9	58082608			12	Intron of CDK4(-):32bp after exon 7	CDK4	58142932			10	DELETION		60324	202046	935	29	NEW_VARIANT
P-0024843-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 with RET exons 12-20): c.1726-1339:KIF5B_c.2137-299:RETinv	IMPPRECISE	Note: The KIF5B - RET fusion is predicted to be in-frame and including the RET kinase domain.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		52354	0	5	10	Intron of KIF5B(-):1Kb before exon 16	KIF5B	32313303			10	Intron of RET(+):298bp before exon 12	RET	43611733			0	INVERSION		11298430	201956	60063	6	NEW_VARIANT
P-0024858-T01-IM6	INPPL1 (NM_001567) - NLRP6 (NM_138329) rearrangement: c.617:INPPL1_c.2138:NLRP6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {INPPL1:NLRP6}		202253	0	20	11	Exon 5 of NLRP6(+)	NLRP6	282734			11	Exon 5 of INPPL1(+)	INPPL1	71940232			10	DUPLICATION		71657498	202153	322217	20	NEW_VARIANT
P-0024858-T01-IM6	ARID2 (NM_152641) rearrangement: t(12;23)(q13.11;q11.23)(chr12:g.46297969::chrY:g.28562161)	PRECISE	Note: The ARID2 rearrangement is a translocation involving exon 21. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	Y	IGR: 688Kb before TTTY3B(+)	TTTY3B	28562161			12	Intron of ARID2(+):747bp before exon 21	ARID2	46297969			10	TRANSLOCATION		0	202154	0	11	NEW_VARIANT
P-0024080-T02-IM6	FLI1 (NM_002017) - ATM (NM_000051) rearrangement: c.781+147:FLI1_c.8269-128:ATMdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {FLI1:ATM}		141899	0	16	11	Intron of ATM(+):127bp before exon 57	ATM	108213821			11	Intron of FLI1(+):147bp after exon 7	FLI1	128677281			9	DUPLICATION		20463460	202544	205935	17	NEW_VARIANT
P-0024660-T01-IM6	VEGFA (NM_001171623) rearrangement: t(1;6)(p32.3;p21.1)(chr1:g.52516077::chr6:g.43748572)	PRECISE	Note: The VEGFA rearrangement is a translocation with a breakpoint in exon 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	55	6	Exon 6 of VEGFA(+)	VEGFA	43748572			1	Intron of TXNDC12(-):5Kb after exon 1	TXNDC12	52516077			10	TRANSLOCATION		0	201163	0	59	NEW_VARIANT
P-0024666-T01-IM6	CDH1 (NM_004360) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.45867214::chr16:g.68846063)	PRECISE	Note: The CDH1 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	38	16	Exon 8 of CDH1(+)	CDH1	68846063			1	Intron of TESK2(-):16Kb before exon 4	TESK2	45867214			10	TRANSLOCATION		0	201156	0	41	NEW_VARIANT
P-0024786-T01-IM6	JAK1 (NM_002227) Rearrangement : c.1649-50_c.3141-534dup	PRECISE	Note: The JAK1 Rearrangement results in the duplication of exons 12-22. It includes the protein kinase domain of JAK1.	MANUAL_OK	5to3	5to3	Duplication of 11 exons : out of frame		16004	0	25	1	Intron of JAK1(-):534bp before exon 23	JAK1	65302432			1	Intron of JAK1(-):50bp before exon 12	JAK1	65316643			10	DUPLICATION		14211	201491	22997	25	NEW_VARIANT
P-0024788-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801)	PRECISE	Note: The CDKN2Ap16INK4A Rearrangement results in the possible truncation of CDKN2Ap16INK4A. One of the breakpoints is within exon2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0		35	12	IGR: 68Kb before SLC16A7(+)	SLC16A7	59921801			9	Exon 2 of CDKN2A(-)	CDKN2Ap16INK4A	21970920			10	TRANSLOCATION		0	202822	0		NEW_VARIANT
P-0024788-T01-IM6	CDKN2Ap14ARF (NM_058195) Rearrangement :  t(9;12)(p21.3;q14.1)(chr9:g.21970920;chr12:g.59921801)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0		35	12	IGR: 68Kb before SLC16A7(+)	SLC16A7	59921801			9	Exon 2 of CDKN2A(-)	CDKN2Ap14ARF	21970920			10	TRANSLOCATION		0	202823	0		NEW_VARIANT
P-0024859-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.3144_c.3926dup	PRECISE	Note: The MAP3K1 rearrangement is an intragenic duplication of 14-16. The breakpoints are within exons 14 and 16. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3022	0	3	5	Exon 14 of MAP3K1(+)	MAP3K1	56178171			5	Exon 16 of MAP3K1(+)	MAP3K1	56180597			10	DUPLICATION		2426	202169	2395	3	NEW_VARIANT
P-0024859-T01-IM6	KMT2C (NM_170606) - TMPRSS11E (NM_014058) rearrangement: t(4;7)(q13.2;q36.1)(chr4:g.69356592::chr7:g.152009024)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	7	7	Exon 5 of KMT2C(-)	KMT2C	152009024			4	Intron of TMPRSS11E(+):6Kb before exon 10	TMPRSS11E	69356592			10	TRANSLOCATION		0	202171	0	8	NEW_VARIANT
P-0024886-T01-IM6	DOT1L (NM_032482) rearrangement: chr19:g.261784_c.1558-11inv	PRECISE	Note: The DOT1L rearrangement is an inversion that includes DOT1L exons 1016. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		54736	0	11	19	IGR: 19Kb before PPAP2C(-)	PPAP2C	261784			19	Intron of DOT1L(+):10bp before exon 17	DOT1L	2213527			10	INVERSION		1951743	202609	59125	13	NEW_VARIANT
P-0024889-T01-IM6	TEK (NM_000459) - TMTC2 (NM_152588) rearrangement: t(9;12)(p21.2;q21.31)(chr9:g.27168693::chr12:g.83239788)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TEK:TMTC2}		0	0	6	12	Intron of TMTC2(+):11Kb before exon 2	TMTC2	83239788			9	Intron of TEK(+):90bp after exon 3	TEK	27168693			10	TRANSLOCATION		0	202585	0	7	NEW_VARIANT
P-0024919-T01-IM6	KMT2A (NM_001197104)  - FXYD6-FXYD2 (NM_001204268) rearrangement: c.7363:KMT2A_c.-5-14181:FXYD6-FXYD2del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		58024	0	55	11	5-UTR of FXYD6-FXYD2(-):36Kb before coding start	FXYD6-FXYD2	117727677			11	Exon 27 of KMT2A(+)	KMT2A	118373970			10	DELETION		646293	202704	33007	56	NEW_VARIANT
P-0024919-T01-IM6	RAB30 (NM_014488) - CREBBP (NM_004380) rearrangement: t(11;16)(q14.1;p13.3)(chr11:g.:82712245::chr16:g.3900638)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RAB30:CREBBP}		0	0	62	16	Exon 2 of CREBBP(-)	CREBBP	3900638			11	5-UTR of RAB30(-):19Kb before coding start	RAB30	82712245			10	TRANSLOCATION		0	202710	0	65	NEW_VARIANT
P-0025010-T01-IM6	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	PRECISE	Note: The FGFR2 -BICC1 fusion is predicted to be in-frame and includes the FGFR2 kinase domain.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		184778	0	3	10	Intron of BICC1(+):7Kb before exon 3	BICC1	60455077			10	Intron of FGFR2(-):67bp before exon 18	FGFR2	123239602			8	INVERSION		62784525	203120	180929	4	NEW_VARIANT
P-0025044-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918)  Fusion (TMPRSS2 exon1 fused with ERG exon 2) :  c.56-2252:TMPRSS2_c.18+17253:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		61115	0	119	21	Intron of ERG(-):17Kb after exon 1	ERG	39853034			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872368			10	DELETION		3019334	203294	54512	133	NEW_VARIANT
P-0025047-T01-IM6	MSH2 (NM_000251) Rearrangement : c.1386+5577_c.2030del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4001	0	71	2	Intron of MSH2(+):6Kb after exon 8	MSH2	47678373			2	Exon 13 of MSH2(+)	MSH2	47703530			10	DELETION		25157	203296	4466	77	NEW_VARIANT
P-0025049-T01-IM6	NF1 (NM_001042492) - SUZ12 (NM_015355) Rearrangement :  c.4297:NF1_c.1874+641:SUZ12del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NF1:SUZ12}		55011	0	29	17	Exon 32 of NF1(+)	NF1	29585485			17	Intron of SUZ12(+):641bp after exon 15	SUZ12	30324537			10	DELETION		739052	203293	31521	31	NEW_VARIANT
P-0007043-T02-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		31381	0	50	21	Intron of ERG(-):3Kb after exon 1	ERG	39866972			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42869029			10	DELETION		3002057	202594	41576	50	NEW_VARIANT
P-0024947-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q26.1;q22.3)(chr15:g.91513764::chr21:g.42870521)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	20	21	Intron of TMPRSS2(-):405bp before exon 2	TMPRSS2	42870521			15	Intron of PRC1(-):20bp before exon 12	PRC1	91513764			10	TRANSLOCATION		0	202788	0	18	NEW_VARIANT
P-0024987-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.-48-1868_c.316del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2345	0	30	3	5-UTR of CTNNB1(+):2Kb before coding start	CTNNB1	41263644			3	Exon 4 of CTNNB1(+)	CTNNB1	41266519			10	DELETION		2875	203090	2180	30	NEW_VARIANT
P-0025024-T01-IM6	TP53BP1 (NM_001141980) rearrangement: c.5576:TP53BP1_chr15:g.44950938inv	PRECISE	Note: The TP53BP1 rearrangement is an inversion of exons 1-26. One of the breakpoints is within exon 26. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		33951	0	13	15	Exon 26 of TP53BP1(-)	TP53BP1	43701119			15	Intron of SPG11(-):338bp after exon 3	SPG11	44950938			10	INVERSION		1249819	203265	66505	16	NEW_VARIANT
P-0025024-T01-IM6	CARD11 (NM_032415) rearrangemnt: t(7;15)(p22.2;q14)(chr7:g.2972275::chr15:g.36753672)	IMPPRECISE	Note: The CARD11 rearrangement is a translocation involving exon 11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	28	15	IGR: 118Kb before C15orf41(+)	C15orf41	36753672			7	Intron of CARD11(-):55bp before exon 11	CARD11	2972275			0	TRANSLOCATION		0	203269	0	29	NEW_VARIANT
P-0025024-T01-IM6	NF1 (NM_001042492) rearrangement: c.889-3831_c.969inv	PRECISE	Note: The NF1 rearrangement is an inversion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		488	0	9	17	Intron of NF1(+):4Kb before exon 9	NF1	29523609			17	Exon 9 of NF1(+)	NF1	29527520			10	INVERSION		3911	203266	1037	13	NEW_VARIANT
P-0025030-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 with ERG exons 2-10): c.55+2244:TMPRSS2_c.19-2444:ERGdel	IMPPRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		94807	0	5	21	Intron of ERG(-):2Kb before exon 2	ERG	39819988			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877633			0	DELETION		3057645	203246	107421	5	NEW_VARIANT
P-0024598-T02-IM6	ARID2 (NM_152641) rearrangement: c.705+38_c.1580+893del	PRECISE	Note: The ARID2 rearrangement results in the deletion of exons 7-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : out of frame		5849	0	44	12	Intron of ARID2(+):38bp after exon 6	ARID2	46215308			12	Intron of ARID2(+):893bp after exon 12	ARID2	46241613			10	DELETION		26305	203211	7741	46	NEW_VARIANT
P-0024598-T02-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4407:ERG_c.56-37:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		29795	0	78	21	Intron of ERG(-):4Kb before exon 2	ERG	39821951			21	Intron of TMPRSS2(-):37bp before exon 2	TMPRSS2	42870153			10	INVERSION		3048202	203212	52350	78	NEW_VARIANT
P-0024598-T02-IM6	TMPRSS2 (NM_001135099) rearrangement: c.349+291_c.56-17inv	PRECISE	Note: The TMPRSS2 rearrangement results in an inversion of exons 2-3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		14532	0	71	21	Intron of TMPRSS2(-):290bp after exon 3	TMPRSS2	42865992			21	Intron of TMPRSS2(-):17bp before exon 2	TMPRSS2	42870133			10	INVERSION		4141	203213	32410	93	NEW_VARIANT
P-0024661-T01-IM6	ERBB3 (NM_001982) - CDK2 (NM_001798) rearrangement: c.192:ERBB3_c.589-107:CDK2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERBB3:CDK2}		2348	0	9	12	Intron of CDK2(+):106bp before exon 5	CDK2	56364721			12	Exon 2 of ERBB3(+)	ERBB3	56477644			9	DUPLICATION		112923	201164	3462	9	NEW_VARIANT
P-0024903-T01-IM6	TMPRSS2 (NM_001135099) -  ERG (NM_004449) Fusion : c.56-3842:TMPRSS2_c.40-40790:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		57011	0	26	21	Intron of ERG(-):12Kb after exon 1	ERG	39858334			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873958			10	DELETION		3015624	202655	87777	28	NEW_VARIANT
P-0024907-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		131646	0	109	2	Intron of ALK(-):483bp before exon 20	ALK	29446877			2	Intron of EML4(+):989bp before exon 3	EML4	42482651			10	INVERSION		13035774	202621	160110	106	NEW_VARIANT
P-0024995-T01-IM6	BRAF (NM_004333) rearrangement: t(7;12)(q34;p12.1)(chr7:g.140488046::chr12:g.22218755)	PRECISE	Note: The BRAF rearrangement is a translocation with a breakpoint in intron 8 and may include the kinase domain. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {CMAS:BRAF}		0	0	27	12	Promoter of CMAS(+):20Kb from tx start	CMAS	22218755			7	Intron of BRAF(-):662bp before exon 9	BRAF	140488046			10	TRANSLOCATION		0	203184	0	24	NEW_VARIANT
P-0025000-T01-IM6	IL10 (NM_000572) rearrangement: t(1;15)(q32.1;q26.1)(chr1:g.206942213::chr15:g.91379749)	PRECISE	Note: The IL10 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	20	15	IGR: 32Kb before FURIN(+)	FURIN	91379749			1	Intron of IL10(-):140bp before exon 5	IL10	206942213			10	TRANSLOCATION		0	203179	0	19	NEW_VARIANT
P-0025000-T01-IM6	MITF (NM_198159) rearrangement: chr3:g.34891227_c.666+108inv	IMPPRECISE	Note: The MITF rearrangement results in the inversion of exons 1-4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		261073	0	27	3	IGR: 26Kb before LOC101928135(-)	LOC101928135	34891227			3	Intron of MITF(+):108bp after exon 4	MITF	69988440			0	INVERSION		35097213	203176	407167	26	NEW_VARIANT
P-0025000-T01-IM6	ATR (NM_001184) rearrangement: chr3:g.39857396_c.1026inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MYRIP:ATR}		486756	0	223	3	5-UTR of MYRIP(+):85Kb before coding start	MYRIP	39857396			3	Exon 4 of ATR(-)	ATR	142281218			0	INVERSION		102423822	203177	913036	221	NEW_VARIANT
P-0025000-T01-IM6	BCL6 (NM_001706) rearrangement: c.1977+473_c.162-80dup	PRECISE	Note: The BCL6 rearrangement results in the duplication of exons 4-9. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : out of frame		13049	0	39	3	Intron of BCL6(-):472bp after exon 9	BCL6	187442256			3	Intron of BCL6(-):80bp before exon 4	BCL6	187449798			10	DUPLICATION		7542	203174	31507	39	NEW_VARIANT
P-0025001-T01-IM6	PDGFRA (NM_006206) rearrangement: chr4:g.55026895_c.2321inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		23057	0	38	4	IGR: 61Kb before GSX2(+)	GSX2	55026895			4	Exon 16 of PDGFRA(+)	PDGFRA	55146647			10	INVERSION		119752	203163	26712	47	NEW_VARIANT
P-0025002-T01-IM6	ATM (NM_000051) rearrangement: t(9;11)(q21.31;q22.3)(chr9:g.83867679::chr11:g.108190712)	PRECISE	Note: The ATM rearrangement is a translocation with a breakpoint in exon 44. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	17	11	Exon 44 of ATM(+)	ATM	108190712			9	IGR: 331Kb before TLE1(-)	TLE1	83867679			10	TRANSLOCATION		0	203202	0	20	NEW_VARIANT
P-0025092-T01-IM6	EGFL7 (NM_201446) rearrangement: t(9;11)(q34.3;q12.2)(chr9:g.139563132::chr11:g.60541820)	IMPPRECISE	Note: The EGFL7 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {EGFL7:MS4A15}		0	0	6	11	Intron of MS4A15(+):397bp after exon 6	MS4A15	60541820			9	Intron of EGFL7(+):7bp after exon 3	EGFL7	139563132			0	TRANSLOCATION		0	203473	0	6	NEW_VARIANT
P-0025097-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4281:TMPRSS2_c.40-57110:ERGdel	PRECISE	Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		71362	0	110	21	Intron of ERG(-):57Kb before exon 4	ERG	39874654			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875596			10	DELETION		3000942	203440	62265	116	NEW_VARIANT
P-0025103-T01-IM6	ROS1 (NM_002944) rearrangement: c.5641+56:ROS1_chr6:g.117884687del	PRECISE	Note: The ROS1 rearrangement is a deletion of exons 1-34, which do not include the kinase domain. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ROS1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	-		104834	0	7	6	Intron of ROS1(-):55bp after exon 34	ROS1	117645439			6	Intron of DCBLD1(+):6Kb before exon 15	DCBLD1	117884687			10	DELETION		239248	203479	103022	8	NEW_VARIANT
P-0025107-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	70	6	Intron of ROS1(-):216bp after exon 33	ROS1	117647170			5	Intron of CD74(-):16bp before exon 8	CD74	149782204			10	TRANSLOCATION		0	204775	0	70	NEW_VARIANT
P-0025071-T01-IM6	SPEN (NM_015001) Rearrangement : c.226+83445:KAZN_c.3176:SPENinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		23555	0	9	1	Intron of KAZN(+):83Kb after exon 1	KAZN	15009164			1	Exon 11 of SPEN(+)	SPEN	16255911			0	INVERSION		1246747	203561	38438	9	NEW_VARIANT
P-0025071-T01-IM6	EGFR (NM_005228) Rearrangement : c.890-22:EGFR_chr7:g.61055640inv	IMPPRECISE	Note: The  EGFR  Rearrangement is an inversion with the breakpoint in intron7. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		54929	0	10	7	Intron of EGFR(+):21bp before exon 8	EGFR	55223501			7	IGR: 2Mb before ZNF733P(-)	ZNF733P	61055640			0	INVERSION		5832139	203564	80148	13	NEW_VARIANT
P-0025176-T01-IM6	ABL1 (NM_005157) - NEURL (NM_004210) rearrangement: t(9;10)(q34.12; q24.33)(chr9:g.133760386::chr10:g.105305536)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ABL1:NEURL1}		0	0	5	10	Intron of NEURL1(+):25Kb before exon 2	NEURL1	105305536			9	Exon 11 of ABL1(+)	ABL1	133760386			10	TRANSLOCATION		0	204917	0	5	NEW_VARIANT
P-0025176-T01-IM6	POLE (NM_006231) rearrangement: t(5;12)(q15;q24.33)(chr5:g.95682436::chr12:g.133210987)	PRECISE	Note: The POLE rearrangement is a translocation with a breakpoint within POLE intron 42. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	29	12	Intron of POLE(-):23bp before exon 43	POLE	133210987			5	IGR: 44Kb before PCSK1(-)	PCSK1	95682436			10	TRANSLOCATION		0	204918	0	29	NEW_VARIANT
P-0025176-T01-IM6	MTOR (NM_004958) - COMMD1 (NM_152516) rearrangement: t(1;2)(p36.22;p15)(chr1:g.11187048::chr2:g.62259442)	IMPPRECISE	Note: The MTOR - COMMD1 rearrangement is a translocation with breakpoints within MTOR intron 45 and COMMD1 intron 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	6	2	Intron of COMMD1(+):31Kb after exon 2	COMMD1	62259442			1	Intron of MTOR(-):18bp after exon 45	MTOR	11187048			0	TRANSLOCATION		0	204916	0	6	NEW_VARIANT
P-0025176-T01-IM6	BRAF (NM_004333) rearrangement: chr7:g.126063024_c.980+1766:BRAFdel	IMPPRECISE	Note: The BRAF rearrangement is a deletion of BRAF exons 8-18, including the kinase domain. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		152020	0	7	7	IGR: 16Kb before GRM8(-)	GRM8	126063024			7	Intron of BRAF(-):2Kb after exon 7	BRAF	140498396			0	DELETION		14435372	204913	271606	8	NEW_VARIANT
P-0025176-T01-IM6	RECQL4 (NM_004260) - PARP10 (NM_032789) rearrangement: c.278:RECQL4_c.798:PARP10del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RECQL4:PARP10}		29089	0	37	8	Exon 5 of PARP10(-)	PARP10	145059372			8	Exon 4 of RECQL4(-)	RECQL4	145742510			10	DELETION		683138	204914	62024	37	NEW_VARIANT
P-0024631-T01-IM6	KMT2D (NM_003482) rearrangement: c.888_chr12:g.52691392inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		28550	0	13	12	Exon 7 of KMT2D(-)	KMT2D	49447056			12	IGR: 4Kb before KRT86(+)	KRT86	52691392			10	INVERSION		3244336	204750	43775	13	NEW_VARIANT
P-0024631-T01-IM6	TP53 (NM_000546) rearrangement: chr17:g.7554166_c.10del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		17747	0	12	17	Promoter of ATP1B2(+):87bp from tx start	ATP1B2	7554166			17	Exon 2 of TP53(-)	TP53	7579903			10	DELETION		25737	204748	11897	13	NEW_VARIANT
P-0024867-T01-IM6	AXIN1 (NM_003502) rearrangement: c.1255-712_c.1222inv	PRECISE	Note: The AXIN1 rearrangement results in the inversion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		346	0	35	16	Intron of AXIN1(-):712bp before exon 6	AXIN1	348963			16	Exon 5 of AXIN1(-)	AXIN1	354336			10	INVERSION		5373	202441	571	36	NEW_VARIANT
P-0024867-T01-IM6	KMT2C (NM_170606) rearrangement: c.9483_c.4660+2595dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		21356	0	38	7	Exon 41 of KMT2C(-)	KMT2C	151866305			7	Intron of KMT2C(-):3Kb after exon 31	KMT2C	151888499			10	DUPLICATION		22194	202440	59835	45	NEW_VARIANT
P-0025086-T01-IM6	GLI1 (NM_005269) rearrangement: t(2;12)(p25.2;q13.3)(chr2:g.7076725::chr12:g.57864177)	PRECISE	Note: The GLI1 rearrangement is a translocation with a breakpoint in exon 12. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RNF144A:GLI1}		0	0	5	12	Exon 12 of GLI1(+)	GLI1	57864177			2	5-UTR of RNF144A(+):60Kb before coding start	RNF144A	7076725			10	TRANSLOCATION		0	203419	0	5	NEW_VARIANT
P-0025086-T01-IM6	AXIN1 (NM_003502) rearrangement: t(1;16)(p13.3;p13.3)(chr1:g.111333805::chr16:g.347118)	PRECISE	Note: The AXIN1 rearrangement is a translocation with a breakpoint is exon 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	16	16	Exon 7 of AXIN1(-)	AXIN1	347118			1	IGR: 80Kb before CD53(+)	CD53	111333805			10	TRANSLOCATION		0	203420	0	16	NEW_VARIANT
P-0025087-T01-IM6	FAT1 (NM_005245) rearrangement: chr4:g.173406850_c.3099:FAT1del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 2-27. One of the breakpoins is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		66806	0	75	4	Intron of GALNTL6(+):137Kb after exon 5	GALNTL6	173406850			4	Exon 2 of FAT1(-)	FAT1	187627883			10	DELETION		14221033	203425	108379	80	NEW_VARIANT
P-0025139-T01-IM6	JAK1 (NM_002227) - INADL (NM_176877) rearrangement: c.2535:JAK1_c.4032+5742:INADLinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {JAK1:INADL}		8566	0	59	1	Intron of INADL(+):6Kb after exon 30	INADL	62509463			1	Exon 18 of JAK1(-)	JAK1	65307153			10	INVERSION		2797690	203881	7920	69	NEW_VARIANT
P-0025139-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.-56-2374:TMPRSS2_c.39+3700:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the non canonical fusion of TMPRSS2 exons 1 with ERG exons 4-10	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52733	0	115	21	Intron of ERG(-):37Kb after exon 3	ERG	39910579			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872490			10	DELETION		2961911	203879	48078	122	NEW_VARIANT
P-0025139-T01-IM6	BCOR (NM_001123385) rearrangement: c.1107:BCOR_chrX:g.8440800del	PRECISE	Note: The BCOR rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		36359	0	3	X	IGR: 8Kb before VCX3B(+)	VCX3B	8440800			X	Exon 4 of BCOR(-)	BCOR	39933492			7	DELETION		31492692	203880	83152	3	NEW_VARIANT
P-0025144-T01-IM6	TSHR (NM_000369) rearrangement: c.445_c.545+1767del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1765	0	22	14	Exon 5 of TSHR(+)	TSHR	81557465			14	Intron of TSHR(+):2Kb after exon 6	TSHR	81560719			10	DELETION		3254	203889	2355	22	NEW_VARIANT
P-0025144-T01-IM6	PAX8 (NM_003466) rearrangement: c.25+15154_c.1189+1729dup	PRECISE	Note: The PAX8 rearrangement is an intragenic duplication of exons 3-10. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 8 exons : in frame		76600	0	26	2	Intron of PAX8(-):2Kb after exon 10	PAX8	113983003			2	Intron of PAX8(-):15Kb after exon 2	PAX8	114020793			10	DUPLICATION		37790	203890	106669	28	NEW_VARIANT
P-0025149-T01-IM6	SARS2 (NM_017827) - AKT2 (NM_001626) rearrangement: c.363+1679:SARS2_c.47-28:AKT2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SARS2:AKT2}		17952	0	6	19	Intron of SARS2(-):2Kb after exon 2	SARS2	39415166			19	Intron of AKT2(-):28bp before exon 3	AKT2	40762989			10	DUPLICATION		1347823	203900	21134	7	NEW_VARIANT
P-0025150-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 3-10): c.127-1226:TMPRSS2_c.18+10530:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28719	0	42	21	Intron of ERG(-):11Kb after exon 1	ERG	39859757			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867731			10	DELETION		3007974	203902	18230	44	NEW_VARIANT
P-0025153-T01-IM6	FAT1 (NM_005245) rearrangement: chr4:g.185165018_c.13397dup	PRECISE	Note: The FAT1 rearrangement results in the duplication of exon 27. One of the breakpoints is within exon 27. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		2631	0	28	4	IGR: 97Kb before LOC728175(-)	LOC728175	185165018			4	Exon 27 of FAT1(-)	FAT1	187510116			10	DUPLICATION		2345098	204739	5452	29	NEW_VARIANT
P-0025187-T02-IM6	ZFHX3 (NM_006885) rearrangement: t(6;16)(q25.3;q22.3)(chr6:g.156231802::chr16:g.72992119)	PRECISE	Note: The ZFHX3 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	110	16	Exon 2 of ZFHX3(-)	ZFHX3	72992119			6	IGR: 515Kb before NOX3(-)	NOX3	156231802			10	TRANSLOCATION		0	204818	0	115	NEW_VARIANT
P-0025187-T02-IM6	RTEL1 (NM_032957) rearrangement: t(8;20)(p11.23;q13.33)(chr8:g.36806047::chr20:g.62323185)	PRECISE	Note: The RTEL1 rearrangement is a translocation with a breakpoint in exon 28. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	735	20	Exon 28 of RTEL1(+)	RTEL1	62323185			8	IGR: 164Kb before KCNU1(+)	KCNU1	36806047			10	TRANSLOCATION		0	204820	0	738	NEW_VARIANT
P-0025197-T01-IM6	SIK3 (NM_025164) - SESN3 (NM_144665) rearrangement: c.100-66582:SIK3_c.380:SESN3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SIK3:SESN3}		113022	0	4	11	Exon 4 of SESN3(-)	SESN3	94923088			11	Intron of SIK3(-):67Kb before exon 2	SIK3	116894362			10	DELETION		21971274	204811	111376	5	NEW_VARIANT
P-0025198-T01-IM6	ATRX (NM_000489) rearrangement: c.3077_chrX:g.77133337del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MAGT1:ATRX}		20895	0	4	X	Exon 9 of ATRX(-)	ATRX	76937671			X	Intron of MAGT1(-):2Kb before exon 2	MAGT1	77133337			8	DELETION		195666	204802	25974	4	NEW_VARIANT
P-0025250-T01-IM6	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	PRECISE	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)	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {BICC1:FGFR2}		208324	0	34	10	Intron of BICC1(+):296bp before exon 16	BICC1	60566047			10	Intron of FGFR2(-):956bp before exon 18	FGFR2	123240491			10	INVERSION		62674444	204992	194262	33	NEW_VARIANT
P-0025273-T01-IM6	PARK2 (NM_004562) rearrangement: c.7+48_c.535-65122del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exons 2-4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		4404	0	2	6	Intron of PARK2(-):65Kb before exon 5	PARK2	162540328			6	Intron of PARK2(-):47bp after exon 1	PARK2	163148646			5	DELETION		608318	205081	6695	2	NEW_VARIANT
P-0025200-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		104729	0	6	2	Intron of ALK(-):28bp after exon 19	ALK	29448298			2	Intron of EML4(+):7Kb after exon 5	EML4	42498558			10	INVERSION		13050260	204856	143044	6	NEW_VARIANT
P-0025207-T01-IM6	RICTOR (NM_152756) rearrangement: c.4853:RICTOR_chr5:g.39130440inv	PRECISE	Note: The RICTOR rearrangement is an inversion of exons 1-36. One of the breakpoints is within exon 36. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		43210	0	2	5	Exon 36 of RICTOR(-)	RICTOR	38944608			5	Intron of FYB(-):251bp after exon 10	FYB	39130440			4	INVERSION		185832	204852	24223	2	NEW_VARIANT
P-0025215-T01-IM6	GEMIN5 (NM_015465) - RET (NM_020975) rearrangement: t(5;10)(q33.2;q11.21)(chr5:g.154274993::chr10:g.43611067)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {GEMIN5:RET}		0	0	19	10	Intron of RET(+):883bp after exon 11	RET	43611067			5	Intron of GEMIN5(-):658bp after exon 24	GEMIN5	154274993			0	TRANSLOCATION		0	204945	0	23	NEW_VARIANT
P-0025216-T01-IM6	RHEBL1 (NM_144593) - KMT2D (NM_003482) rearrangement: c.-1442:RHEBL1_c.4053:KMT2Ddel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RHEBL1:KMT2D}		25515	0	11	12	Exon 13 of KMT2D(-)	KMT2D	49442520			12	Promoter of RHEBL1(-):7Kb from tx start	RHEBL1	49465010			10	DELETION		22490	204932	32799	11	NEW_VARIANT
P-0006424-T03-IM6	PUM1 (NM_001020658) - KMT2C (NM_170606): t(1;7)(p35.2;q36.1)(chr1:g.31532327::chr7:g.151873311)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PUM1:KMT2C}		0	0	11	7	Exon 38 of KMT2C(-)	KMT2C	151873311			1	Exon 2 of PUM1(-)	PUM1	31532327			10	TRANSLOCATION		0	205371	0	11	NEW_VARIANT
P-0025326-T01-IM6	DROSHA (NM_013235) - KCNQ3 (NM_004519) rearrangement: t(5;8)(p13.3;q24.22)(chr5:g.31464126::chr8:g.133361970)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {DROSHA:KCNQ3}		0	0	13	8	Intron of KCNQ3(-):130Kb after exon 1	KCNQ3	133361970			5	Intron of DROSHA(-):216bp after exon 19	DROSHA	31464126			10	TRANSLOCATION		0	205355	0	13	NEW_VARIANT
P-0025343-T01-IM6	CDK12 (NM_016507) - GCNT2 (NM_145655) rearrangement: t(6;17)(p24.3;q12)(chr6:g.10592776::chr17:g.37687185)	PRECISE	Note: The CDK12 - GCNT2 rearrangement is a translocation with breakpoints within CDK12 exon 14 and GCNT2 intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	29	17	Exon 14 of CDK12(+)	CDK12	37687185			6	Intron of GCNT2(+):29Kb before exon 4	GCNT2	10592776			10	TRANSLOCATION		0	205430	0	31	NEW_VARIANT
P-0025346-T01-IM6	NRG3 (NM_001010848) - PTEN (NM_000314) rearrangement: c.954-176223:NRG3_c.1026+82:PTENinv	PRECISE	Note: The NRG3 - PTEN rearrangement is an inversion that includes NRG3 exons 3-9 and PTEN exons 1-8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		32496	0	5	10	Intron of NRG3(+):176Kb before exon 4	NRG3	84322110			10	Intron of PTEN(+):82bp after exon 8	PTEN	89720957			10	INVERSION		5398847	205431	45285	7	NEW_VARIANT
P-0001242-T05-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.127-1488:TMPRSS2_c.18+9956:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		19800	0	39	21	Intron of ERG(-):10Kb after exon 1	ERG	39860331			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867993			10	DELETION		3007662	205305	27788	40	NEW_VARIANT
P-0025398-T01-IM6	ARID2 (NM_152641) - CNTN1 (NM_001843) rearrangement: c.575:ARID2_c.1380-720:CNTN1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ARID2:CNTN1}		5612	0	10	12	Intron of CNTN1(+):719bp before exon 11	CNTN1	41336679			12	Exon 5 of ARID2(+)	ARID2	46211609			10	DUPLICATION		4874930	205601	7853	11	NEW_VARIANT
P-0025401-T01-IM6	CDK12 (NM_016507) rearrangement: c.1615:CDK12_chr17:g.37748036del	PRECISE	Note: The CDK12 rearrangement is a deletion of exons 2-14. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		30077	0	24	17	Exon 2 of CDK12(+)	CDK12	37627700			17	IGR: 12Kb before NEUROD2(-)	NEUROD2	37748036			10	DELETION		120336	205602	30603	24	NEW_VARIANT
P-0025401-T01-IM6	ERBB2 (NM_004448) rearrangement: c.2970+68:ERBB2_chr17:g.37884495del	PRECISE	Note: The ERBB2 rearrangement is a deletion of exons 25-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9793	0	10	17	Intron of ERBB2(+):68bp after exon 24	ERBB2	37882980			17	3-UTR of ERBB2(+):28Kb after coding stop	ERBB2	37884495			10	DELETION		1515	205603	9088	10	NEW_VARIANT
P-0000252-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Antisense fusion		60571	0	17	10	Intron of CUBN(-): 356bp after exon 50	CUBN	16947846			10	Intron of RET(+): 310bp after exon 11	RET	43610494			30	DUPLICATION		26662648	94440	55502	19	NEW_VARIANT
P-0000252-T01-IM3	RET (NM_020975) Inversion (c.2136+413_KIF5B:c.1726-153inv)	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		44662	0	9	10	Intron of KIF5B(-): 2Kb before exon 16	KIF5B	32313497			10	Intron of RET(+): 413bp after exon 11	RET	43610597			22	INVERSION		11297100	94441	33323	8	NEW_VARIANT
P-0000289-T01-IM3	FGFR3 (NM_000142)  TACC3 (NM_006342) Duplication (c.1128_c.1592-1871dup)	PRECISE		AUTO_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		10007	0	12	4	Intron of TACC3(+): 2Kb before exon 7	TACC3	1735129			4	Exon 9 of FGFR3(+)	FGFR3	1806109			21	DUPLICATION		70980	94520	9020	13	NEW_VARIANT
P-0000509-T02-IM5	MALT1 (NM_006785) Rearrangement : t(3;18)(3p21.2;18q21.32)(chr3:g.51906799::chr18:g.56376920)	PRECISE	Note: The MALT1 (NM_006785) Rearrangement results in the possible truncation of  MALT1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	15	18	Intron of MALT1(+): 132bp after exon 5	MALT1	56376920			3	IGR: 939bp before IQCF5(-)	IQCF5	51906799			11	TRANSLOCATION		0	122660	0	13	NEW_VARIANT
P-0001204-T02-IM5	c.8155_g.112183450del	PRECISE	The APC (NM_000038) rearrangement results in the partial intragenic deletion of exon 16 extending into the 3-prime UTR.	MANUAL_OK	3to5	3to5	-		2475	0	28	5	Exon 16 of APC(+)	APC	112179446			5	IGR: 2Kb after APC(+)	APC	112183450			37	DELETION		4004	12255	914	30	NEW_VARIANT
P-0001260-T01-IM3	None	PRECISE		MANUAL_OK	3to5	3to5	Deletion of 3 exons: in frame		8402	0	9	16	Intron of CDH1(+): 82bp after exon 5	CDH1	68842833			16	Intron of CDH1(+): 173bp before exon 9	CDH1	68847043			21	DELETION		4210	72719	6143	9	NEW_VARIANT
P-0001319-T03-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		101108	0	8	21	Intron of ERG(-): 61Kb before exon 4	ERG	39878050			21	Intron of TMPRSS2(-): 746bp after exon 1	TMPRSS2	42879131			8	DELETION		3001081	14599	86494	11	NEW_VARIANT
P-0001384-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	-		0	0	12	19	Intron of NOTCH3(-): 19bp before exon 2	NOTCH3	15308408			14	IGR: 7Kb after WDR89(-)	WDR89	64115182			19	TRANSLOCATION		0	2140	0	12	NEW_VARIANT
P-0001445-T01-IM3	None	PRECISE		AUTO_OK	3to5	3to5	Deletion of 6 exons: in frame		11171	0	4	7	Intron of EGFR(+): 30Kb before exon 2	EGFR	55179677			7	Intron of EGFR(+): 402bp before exon 8	EGFR	55223121			8	DELETION		43444	2027	17655	4	NEW_VARIANT
P-0001449-T02-IM5	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)	IMPRECISE		MANUAL_OK	5to3	5to3	Protein fusion: in frame (TMPRSS2-ETV1)		0	0	102	21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871485			7	Intron of ETV1(-): 14Kb after exon 6	ETV1	14003184			0	TRANSLOCATION		0	16950	0	124	NEW_VARIANT
P-0001539-T01-IM3	None	PRECISE		AUTO_OK	3to5	3to5	Deletion of 3 exons: out of frame		4491	0	5	19	Intron of STK11(+): 4Kb after exon 1	STK11	1211254			19	Intron of STK11(+): 30bp after exon 4	STK11	1220534			5	DELETION		9280	1841	4511	5	NEW_VARIANT
P-0001701-T01-IM3	ATRX (NM_000489) duplication: c.4843_c.5134+5045dup	PRECISE	The ATRX duplication is a rearrangement event which results in  duplication of exon 19.	AUTO_OK	5to3	5to3	Duplication within transcript: mid-exon		3015	0	11	X	Intron of ATRX(-): 5Kb after exon 19	ATRX	76883650			X	Exon 18 of ATRX(-)	ATRX	76889167			36	DUPLICATION		5517	1231	2410	13	NEW_VARIANT
P-0001784-T01-IM3	DIP2B (NM_173602) - NOTCH4 (NM_004557) Translocation :  t(12;6)(q13.12;p21.32)(chr12:g.50969571::chr6:32163293)	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (DIP2B-NOTCH4)		0	0	69	12	Intron of DIP2B(+): 50Kb before exon 2	DIP2B	50969571			6	Exon 30 of NOTCH4(-)	NOTCH4	32163293			95	TRANSLOCATION		0	445	0	67	NEW_VARIANT
P-0001832-T02-IM6	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	IMPRECISE	Note: The AGK - BRAF fusion includes the kinase domain of BRAF.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (AGK-BRAF)		55494	0	5	7	Intron of BRAF(-): 222bp before exon 8	BRAF	140494489			7	Intron of AGK(+): 572bp before exon 3	AGK	141292374			0	INVERSION		797885	166311	54911	4	NEW_VARIANT
P-0002395-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		5157	0	32	3	5-UTR of CTNNB1(+): 2Kb before coding start	CTNNB1	41263417			3	Exon 5 of CTNNB1(+)	CTNNB1	41266858			51	DELETION		3441	3237	13566	35	NEW_VARIANT
P-0002398-T01-IM3	ARF4 (NM_001660) - TMPRSS2 (NM_001135099) Translocation :   t(3;21)(p14.3;q22.3)(chr3:g.57572612::chr21:g.42867618)	PRECISE	Note: ARF4 - TMPRSS2 translocation is a structural rearrangement in which  the first exon of ARF4 is fused to exons 3 to 14 of TMPRSS2	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (ARF4-TMPRSS2)		0	0	5	21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867618			3	Intron of ARF4(-): 2Kb before exon 2	ARF4	57572612			13	TRANSLOCATION		0	3246	0	0	NEW_VARIANT
P-0002398-T01-IM3	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) Translocation :   t(21;7)(q22.3;p21.2)(chr21:g.42867877::chr7:g.13988492)	PRECISE	Note: TMPRSS2 - ETV1 is a structural rearrangement in which the first 2  exons of TMPRSS2 is fused to exons 6 to 12 of ETV1	AUTO_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-ETV1)		0	0	25	21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867877			7	Intron of ETV1(-): 10Kb before exon 7	ETV1	13988492			35	TRANSLOCATION		0	3247	0	0	NEW_VARIANT
P-0002436-T01-IM3		PRECISE	exons 6-39 deleted	AUTO_OK	3to5	3to5	Deletion within transcript: mid-exon		64917	0	5	19	Exon 39 of DNMT1(-)	DNMT1	10246516			19	Intron of DNMT1(-): 637bp after exon 5	DNMT1	10290226			59	DELETION		43710	3484	38054	33	NEW_VARIANT
P-0002694-T02-IM5		PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		68269	0	28	10	Intron of KIF5B(-): 2Kb before exon 16	KIF5B	32314319			10	Intron of RET(+): 350bp before exon 12	RET	43611682			56	INVERSION		11297363	7325	64074	27	NEW_VARIANT
P-0002705-T01-IM3		PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (ERBB2-C1orf87)		0	0	55	17	Exon 26 of ERBB2(+)	ERBB2	37883789			1	Intron of C1orf87(-): 4Kb after exon 9	C1orf87	60472564			29	TRANSLOCATION		0	4879	0	65	NEW_VARIANT
P-0002895-T01-IM3		PRECISE	TMPRSS2 (NM_001135099) ERG (NM_182918) fusion: c.18+8871:ERG_c.56-1160:TMPRSS2del	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		19327	0	8	21	Intron of ERG(-): 9Kb after exon 1	ERG	39861416			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871276			24	DELETION		3009860	6164	17649	12	NEW_VARIANT
P-0002990-T03-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		64846	0	102	21	Intron of ERG(-): 63Kb before exon 4	ERG	39880577			21	Intron of TMPRSS2(-): 879bp after exon 2	TMPRSS2	42869167			91	DELETION		2988590	165591	39598	152	NEW_VARIANT
P-0003108-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		25954	1	77	13	Exon 11 of BRCA2(+)	BRCA2	32913614			13	Intron of BRCA2(+): 199bp after exon 11	BRCA2	32915532			82	DELETION		1918	8306	10515	87	NEW_VARIANT
P-0003108-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (HMHA1-STK11)		1634	0	25	19	Intron of HMHA1(+): 2Kb before exon 3	HMHA1	1071286			19	Exon 1 of STK11(+)	STK11	1207046			47	DELETION		135760	8307	856	28	NEW_VARIANT
P-0003108-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		1492	0	22	19	5-UTR of AXL(+): 63bp before coding start	AXL	41725235			19	Intron of AXL(+): 44bp before exon 2	AXL	41726497			41	DELETION		1262	8308	1203	30	NEW_VARIANT
P-0003108-T01-IM5		IMPRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	21	X	IGR: 54Kb after KLHL13(-)	KLHL13	117305158			13	Intron of RB1(+): 74bp after exon 25	RB1	49051053			0	TRANSLOCATION		0	8313	0	19	NEW_VARIANT
P-0003271-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	-		18354	0	23	6	Intron of MED23(-): 265bp before exon 5	MED23	131944867			6	Exon 7 of TNFAIP3(+)	TNFAIP3	138199875			51	DELETION		6255008	10296	92196	25	NEW_VARIANT
P-0003271-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	-		1079	0	18	6	Exon 8 of TNFAIP3(+)	TNFAIP3	138201318			6	IGR: 42Kb before PERP(-)	PERP	138367567			37	DELETION		166249	10297	4343	18	NEW_VARIANT
P-0003395-T01-IM5		PRECISE		MANUAL_OK	3to5	3to5	-		3095	0	22	21	IGR: 187bp after MX1(+)	MX1	42831327			21	Exon 12 of TMPRSS2(-)	TMPRSS2	42840334			42	DELETION		9007	11159	1494	25	NEW_VARIANT
P-0003466-T01-IM5		PRECISE	Note: The RB1 (NM_000321) rearrangement event results in the deletion of RB1 exons 25-26, potentially disabling the function of the gene.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: out of frame		3728	0	82	13	Intron of RB1(+): 1Kb before exon 25	RB1	49049372			13	Intron of RB1(+): 35bp before exon 27	RB1	49054099			75	DELETION		4727	11609	2639	88	NEW_VARIANT
P-0003540-T01-IM5	c.368+690_c.347del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		822	0	5	13	Intron of FLT3(-): 690bp after exon 3	FLT3	28635314			13	Exon 3 of FLT3(-)	FLT3	28636025			0	DELETION		711	11917	565	9	NEW_VARIANT
P-0003779-T01-IM5	IGF1R (NM_000875) rearrangement: c.954-1844_1009del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		720	1	39	15	Intron of IGF1R(+): 2Kb before exon 4	IGF1R	99438142			15	Exon 4 of IGF1R(+)	IGF1R	99440041			98	DELETION		1899	13423	3432	88	NEW_VARIANT
P-0004285-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-2530:TMPRSS2_c.18+10159:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		52320	0	21	21	Intron of ERG(-): 10Kb after exon 1	ERG	39860128			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872646			22	DELETION		3012518	18651	48473	20	NEW_VARIANT
P-0004401-T01-IM5	ATP8A2 (NM_016529) - LATS2( NM_01457) rearrangement: c.76+23397:ATP8A2_c.2773-21:LATS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (ATP8A2-LATS2)		23502	0	10	13	Intron of LATS2(-): 21bp before exon 8	LATS2	21549524			13	Intron of ATP8A2(+): 23Kb after exon 1	ATP8A2	25969823			20	INVERSION		4420299	19871	31553	9	NEW_VARIANT
P-0004414-T01-IM5	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)	IMPRECISE	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)	MANUAL_OK	5to3	5to3	Protein fusion: in frame (SDC4-ROS1)		0	0	8	20	Intron of SDC4(-): 984bp before exon 5	SDC4	43957039			6	Intron of ROS1(-): 1Kb before exon 32	ROS1	117651952			0	TRANSLOCATION		0	20061	0	8	NEW_VARIANT
P-0004545-T01-IM5	ERBB3 (NM_001982) - SEMA3A (NM_006080) translocation: t(12,7)(q13.2; q21.11) (chr12:g.56481635::chr7:g.83729009)	IMPRECISE	The ERBB3 (NM_001982) - SEMA3A (NM_006080) rearrangement is a translocation, possibly resulting in a truncated ERBB3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	39	12	Exon 6 of ERBB3(+)	ERBB3	56481635			7	Intron of SEMA3A(-): 11Kb after exon 4	SEMA3A	83729009			0	TRANSLOCATION		0	22388	0	39	NEW_VARIANT
P-0004545-T01-IM5	DIS3 (NM_014953) -PIBF1(NM_006346) rearrangement: c.387-54:DIS3_c.672+1677:PIBF1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		7058	0	21	13	Intron of DIS3(-): 54bp before exon 3	DIS3	73352572			13	Intron of PIBF1(+): 2Kb after exon 5	PIBF1	73373841			19	DELETION		21269	22386	7562	20	NEW_VARIANT
P-0004551-T01-IM5	STAT3  (NM_139276) -AACN1(NM_001094) Rearangement : c.556-173146:ACCN1_c.1281+104:STAT3del	PRECISE	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	MANUAL_OK	3to5	3to5	Protein fusion: in frame (STAT3-ACCN1)		336258	0	13	17	Intron of ACCN1(-): 6Kb after exon 1	ACCN1	31612231			17	Intron of STAT3(-): 104bp after exon 14	STAT3	40481324			10	DELETION		8869093	22539	310086	13	NEW_VARIANT
P-0004616-T01-IM5	FH(NM_000143) : Rearrangement : c.740_738+2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1055	0	47	1	Exon 6 of FH(-)	FH	241669467			1	Intron of FH(-): 2bp after exon 5	FH	241671901			51	DELETION		2434	22994	583	47	NEW_VARIANT
P-0004616-T01-IM5	MLL2(NM_003482) Rearrangement : c.10217_7184del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		24530	0	14	12	Exon 34 of MLL2(-)	MLL2	49430922			12	Exon 31 of MLL2(-)	MLL2	49434369			9	DELETION		3447	22992	34175	14	NEW_VARIANT
P-0004659-T01-IM5	NBN (NM_002485) rearrangement: c.1295_c.1914+531dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		4082	0	9	8	Intron of NBN(-): 531bp after exon 12	NBN	90959521			8	Exon 10 of NBN(-)	NBN	90967613			17	DUPLICATION		8092	29237	6446	9	NEW_VARIANT
P-0004860-T01-IM5	ERBB4 (NM_005235) rearrangement: c.235-44962_c.652del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6420	0	31	2	Exon 6 of ERBB4(-)	ERBB4	212589890			2	Intron of ERBB4(-): 45Kb before exon 3	ERBB4	212857303			37	DELETION		267413	39773	6679	31	NEW_VARIANT
P-0004867-T01-IM5	C19orf12 (NM_001031726) - AKT2 (NM_001626) rearrangement: c.193+680:C19orf12_c.709-62:AKT2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (C19orf12-AKT2)		48541	0	35	19	Intron of C19orf12(-): 680bp after exon 2	C19orf12	30198481			19	Intron of AKT2(-): 62bp before exon 9	AKT2	40744060			34	DUPLICATION		10545579	39978	66641	35	NEW_VARIANT
P-0005085-T01-IM5	FUBP1(NM_003902) Rearrangement : chr15:g.23699654_c.1822:FUBP1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		4532	0	13	1	IGR: 137Kb before ST6GALNAC5(+)	ST6GALNAC5	77196025			1	Exon 19 of FUBP1(-)	FUBP1	78414944			23	DUPLICATION		1218919	42872	4652	13	NEW_VARIANT
P-0005091-T01-IM5	CARD11 (NM_032415) rearrangement: c.8-3148_c.684+36dup	PRECISE	The CARD11 (NM_032415) rearrangement is an intragenic duplicaion of exons 3-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		8356	0	5	7	Intron of CARD11(-): 36bp after exon 5	CARD11	2983810			7	Intron of CARD11(-): 3Kb before exon 3	CARD11	2990569			6	DUPLICATION		6759	42930	10297	5	NEW_VARIANT
P-0005106-T01-IM5	CDK12 (NM_016507) rearrangement: c.3096-970_c.3610inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		4935	0	52	17	Intron of CDK12(+): 970bp before exon 12	CDK12	37679957			17	Exon 13 of CDK12(+)	CDK12	37682419			31	INVERSION		2462	43790	15373	48	NEW_VARIANT
P-0005220-T01-IM5	MLL3 (NM_170606) Rearrangement: g.15107551_c.62794inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		135240	0	102	7	3-UTR of NUB1(+): 1Kb after coding stop	NUB1	151075514			7	Exon 36 of MLL3(-)	MLL3	151878666			111	INVERSION		803152	45829	297782	125	NEW_VARIANT
P-0005220-T01-IM5	MLL3 (NM_170606) Rearrangement: c.6102_g.153526905inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		90377	0	102	7	Exon 36 of MLL3(-)	MLL3	151878843			7	IGR: 58Kb before DPP6(+)	DPP6	153526905			183	INVERSION		1648062	45830	51097	399	NEW_VARIANT
P-0005393-T01-IM5	CSMD1 (NM_033225) - CIC (NM_015125) rearrangement: t(8;19)(p23.2;q13.2)(chr8:g.4567111::chr19:g.42792003)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CSMD1-CIC)		0	0	89	19	Exon 6 of CIC(+)	CIC	42792003			8	Intron of CSMD1(-): 72Kb before exon 2	CSMD1	4567111			42	TRANSLOCATION		0	48709	0	84	NEW_VARIANT
P-0005582-T01-IM5	PLK2 (NM_006622) -PDE4D (NM_001104631) rearrangement: c.1625+27: PLK2_c.456-334412:PDE4Ddup	PRECISE	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	MANUAL_OK	5to3	5to3	Protein fusion: in frame (PLK2-PDE4D)		17818	0	38	5	Intron of PLK2(-): 27bp after exon 11	PLK2	57751339			5	Intron of PDE4D(-): 36Kb after exon 1	PDE4D	58846206			50	DUPLICATION		1094867	51196	29549	36	NEW_VARIANT
P-0005613-T01-IM5	PTRPRS (NM_002850) - ACER1 (NM_133492) rearrangement : c.4986:PTPRS_c.93+5133:ACER1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		106252	0	89	19	Exon 23 of PTPRS(-)	PTPRS	5212045			19	Intron of ACER1(-): 5Kb after exon 1	ACER1	6328337			75	INVERSION		1116292	52132	76236	74	NEW_VARIANT
P-0005613-T01-IM5	PTPRS (NM_002850) - UNC5D (NM_080872) rearrangement : t(8;19)(8p12;19p13.3)(chr8:g.35547181::chr19:g.5211611)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (PTPRS-UNC5D)		0	0	102	19	Exon 24 of PTPRS(-)	PTPRS	5211611			8	Intron of UNC5D(+): 3Kb after exon 7	UNC5D	35547181			53	TRANSLOCATION		0	52140	0	127	NEW_VARIANT
P-0005818-T01-IM5	IGF1R (NM_000875)  Rearrangement:  c.640+53564_808dup	PRECISE	Note: The IGF1R (NM_000875)  rearrangement results in the intragenic duplication of exon3 of IGF1R . Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1759	0	10	15	Intron of IGF1R(+): 54Kb after exon 2	IGF1R	99304900			15	Exon 3 of IGF1R(+)	IGF1R	99434721			17	DUPLICATION		129821	62340	2173	10	NEW_VARIANT
P-0005818-T01-IM5	EPHA3 (NM_005233) Rearrangement :  c.267_996dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		5719	0	11	3	Exon 3 of EPHA3(+)	EPHA3	89259123			3	Exon 5 of EPHA3(+)	EPHA3	89390930			11	DUPLICATION		131807	62341	6697	11	NEW_VARIANT
P-0005959-T01-IM5	ZFHX3 (NM_006885) Rearrangement : chr16:g.72795737_c.5172del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74400	0	11	16	IGR: 21Kb before ZFHX3(-)	ZFHX3	72795737			16	Exon 9 of ZFHX3(-)	ZFHX3	72831409			25	DELETION		35672	66659	62013	11	NEW_VARIANT
P-0005985-T01-IM5	PIK3CA (NM_006218) rearrangement: c.1539+3416_c.2324del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5356	0	21	3	Intron of PIK3CA(+): 3Kb after exon 9	PIK3CA	178931769			3	Exon 16 of PIK3CA(+)	PIK3CA	178942517			33	DELETION		10748	66922	3277	19	NEW_VARIANT
P-0006072-T01-IM5	MAP3K14 (NM_003954) rearrangement : c.2741:MAP3K14_chr17:g.48567110inv	PRECISE	Note: The MAP3K14 (NM_003954) rearrangement event results in the inversion of MAP3K14 exons 1-16. One of the breakpoints is within MAP3K14 exon16.	MANUAL_OK	3to3	3to3	-		110966	0	17	17	Exon 16 of MAP3K14(-)	MAP3K14	43342105			17	IGR: 4Kb after RSAD1(+)	RSAD1	48567110			31	INVERSION		5225005	67554	106641	17	NEW_VARIANT
P-0006137-T01-IM5	RARA (NM_000964) - APPBP2 (NM_0063) rearrangement: c.650:RARA_c.139-2641:APPBP2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		215686	0	48	17	Exon 6 of RARA(+)	RARA	38508602			17	Intron of APPBP2(-): 3Kb before exon 2	APPBP2	58580489			127	DELETION		20071887	69091	180402	48	NEW_VARIANT
P-0006221-T02-IM5	MITF (NM_198159) rearrangement : t(3;7)(p13;p22.3)(chr3:g.70008546::chr7:g.1244112)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	23	7	IGR: 29Kb before UNCX(+)	UNCX	1244112			3	Exon 9 of MITF(+)	MITF	70008546			10	TRANSLOCATION		0	119787	0	18	NEW_VARIANT
P-0006245-T02-IM5	BRCA2 (NM_000059) Rearrangement :  c.793+502_1531dup	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5464	0	6	13	Intron of BRCA2(+): 502bp after exon 9	BRCA2	32905669			13	Exon 10 of BRCA2(+)	BRCA2	32907146			2	DELETION		1477	109157	5322	6	NEW_VARIANT
P-0006247-T01-IM5	TMPRSS2 (NM_001135099) Rearrangement : c.56-2170_557-2689inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		43113	0	13	21	Intron of TMPRSS2(-): 3Kb before exon 6	TMPRSS2	42855218			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872286			35	INVERSION		17068	70545	40359	13	NEW_VARIANT
P-0006297-T01-IM5	SMARCA4 (NM_00307) - LDLR (NM_000527) rearrangement : c.4520:SMARCA4_c.1186+572:LDLRdel	PRECISE	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	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (SMARCA4-LDLR)		6075	0	44	19	Exon 29 of SMARCA4(+)	SMARCA4	11169026			19	Intron of LDLR(+): 572bp after exon 8	LDLR	11222887			53	DELETION		53861	71143	3079	33	NEW_VARIANT
P-0006378-T01-IM5	PTEN (NM_000314) Rearrangement :  c.164+31_chr10:g.89738911del	PRECISE	Note: The PTEN (NM_000314) rearrangement  results in the intragenic deletion of exons 3 to 9 of PTEN. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7482	0	13	10	Intron of PTEN(+): 31bp after exon 2	PTEN	89653897			10	IGR: 10Kb after PTEN(+)	PTEN	89738911			18	DELETION		85014	91931	4597	12	NEW_VARIANT
P-0006429-T01-IM5	FGFR3 (NM_000142) -TNIP2 (NM_024309) rearrangement: c.2275-42:FGFR3_c.147:TNIP2inv	IMPRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (FGFR3-TNIP2)		1405	0	19	4	Intron of FGFR3(+): 42bp before exon 18	FGFR3	1808801			4	Exon 1 of TNIP2(-)	TNIP2	2757870			0	INVERSION		949069	92732	1834	19	NEW_VARIANT
P-0006442-T01-IM5	PIK3C2G (NM_004570) rearrangement : c.3779+35:PIK3C2G_chr12:g.18912315del	PRECISE	Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of PIK3C2G exons 28-32.	MANUAL_OK	3to5	3to5	-		8739	0	16	12	Intron of PIK3C2G(+): 35bp after exon 27	PIK3C2G	18716467			12	IGR: 21Kb before CAPZA3(+)	CAPZA3	18912315			18	DELETION		195848	92901	4138	16	NEW_VARIANT
P-0006442-T01-IM5	PAX8 (NM_003466) rearrangement : c.26-11156_1190-2615dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 8 exons: out of frame		65811	0	22	2	Intron of PAX8(-): 3Kb before exon 11	PAX8	113980370			2	Intron of PAX8(-): 11Kb before exon 3	PAX8	114015652			32	DUPLICATION		35282	92903	73900	22	NEW_VARIANT
P-0006644-T01-IM5	STAG2 (NM_001042749) rearrangement : c.158_3054-988dup	PRECISE	Note: The STAG2 (NM_001042749) rearrangement event results in the duplication of STAG2 exons4-29. One of the breakpoints is within STAG2 exon4.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		26524	0	6	X	Exon 4 of STAG2(+)	STAG2	123164845			X	Intron of STAG2(+): 988bp before exon 29	STAG2	123219409			8	DUPLICATION		54564	107785	33276	6	NEW_VARIANT
P-0006670-T01-IM5	ASXL2 (NM_018263) - DNMT3A (NM_022552) Rearrangement: c.2235:ASXL2_c.639+13202:DNMT3Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (ASXL2-DNMT3A)		18443	0	53	2	Intron of DNMT3A(-): 13Kb after exon 6	DNMT3A	25484608			2	Exon 12 of ASXL2(-)	ASXL2	25966971			44	DELETION		482363	108152	12028	52	NEW_VARIANT
P-0006809-T01-IM5	MGA (NM_001164273) Rearrangement :  c.3431-1105_3812dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		7149	1	102	15	Intron of MGA(+): 1Kb before exon 10	MGA	42018273			15	Exon 11 of MGA(+)	MGA	42021516			105	DUPLICATION		3243	109205	8259	151	NEW_VARIANT
P-0006809-T01-IM5	KDM6A (NM_021140) Rearrangement : c.620-274_875+95dup	PRECISE	Note: The KDM6A (NM_021140) Rearrangement results in the duplication of exons 8 to 10. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		6470	0	23	X	Intron of KDM6A(+): 274bp before exon 8	KDM6A	44896626			X	Intron of KDM6A(+): 95bp after exon 10	KDM6A	44913295			34	DUPLICATION		16669	109206	6224	19	NEW_VARIANT
P-0006812-T01-IM5	ERCC5 (NM_000123) Rearrangement :  c.88+1135_1209dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		11640	0	10	13	Intron of ERCC5(+): 1Kb after exon 1	ERCC5	103499839			13	Exon 8 of ERCC5(+)	ERCC5	103514708			10	DUPLICATION		14869	109128	14792	8	NEW_VARIANT
P-0006839-T01-IM5	MLL3 (NM_170606) - RPS29 (NM_001030001) translocation : t(7;14)(q36.1;q21.3)(chr7:g.151873899::chr14:g.50046598)	PRECISE	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	MANUAL_OK	3to3	3to3	-		0	0	81	14	Intron of RPS29(-): 2Kb before exon 3	RPS29	50046598			7	Exon 38 of MLL3(-)	MLL3	151873899			38	TRANSLOCATION		0	109355	0	81	NEW_VARIANT
P-0006842-T01-IM5	DNMT1 (NM_001379) - AP1M2 (NM_005498) rearrangement :  c.1036:DNMT1_c.-2215:AP1M2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (DNMT1-AP1M2)		53777	0	19	19	Exon 15 of DNMT1(-)	DNMT1	10270699			19	Promoter of AP1M2(-): 2Kb from tx start	AP1M2	10700122			16	DUPLICATION		429423	109358	50591	9	NEW_VARIANT
P-0006869-T01-IM5	MDC1 (NM_014641) - C10orf76 (NM_024541) rearrangement: t(6;10)(p21.33;q24.32)(chr6:g.30671699::chr10:g.103741063)	IMPRECISE	The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	24	10	Intron of C10orf76(-): 6Kb before exon 20	C10orf76	103741063			6	Exon 10 of MDC1(-)	MDC1	30671699			0	TRANSLOCATION		0	109489	0	24	NEW_VARIANT
P-0006869-T01-IM5	MDC1 (NM_014641) rearrangement: t(5;6)( q31.1;p21.33)(chr5:g.136020145::chr6:g.30671642)	PRECISE	The MDC1 (NM_014641) rearrangement is a translocation which may result in a truncated MDC1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	15	6	Exon 10 of MDC1(-)	MDC1	30671642			5	IGR: 291Kb before SPOCK1(-)	SPOCK1	136020145			54	TRANSLOCATION		0	109491	0	15	NEW_VARIANT
P-0006869-T01-IM5	MDC1 (NM_014641) rearrangement: c.5400:MDC1_chr6:g.17200957inv	PRECISE	The MDC1 (NM_014641) rearrangement is an inversion (13470603 bp) which may result in a truncated MDC1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		170041	0	20	6	IGR: 81Kb before RBM24(+)	RBM24	17200957			6	Exon 10 of MDC1(-)	MDC1	30671560			30	INVERSION		13470603	109488	167589	20	NEW_VARIANT
P-0006913-T01-IM5	NCOA3 (NM_181659) - ZBP1 (NM_030776) rearrangement : c.1832:NCOA3_c.35-191inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (NCOA3-ZBP1)		51286	0	26	20	Exon 12 of NCOA3(+)	NCOA3	46264962			20	Intron of ZBP1(-): 191bp before exon 2	ZBP1	56191715			59	INVERSION		9926753	109906	56223	26	NEW_VARIANT
P-0006913-T01-IM5	MLL3 (NM_170606) rearrangement : chr7:g.151756949_c.11670+985:MLL3del	PRECISE	Note: MLL3 (NM_170606) rearrangement is a deletion which results in the deletion of exon 45-59 of MLL3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense fusion		28619	0	10	7	5-UTR of GALNT11(+): 34Kb before coding start	GALNT11	151756949			7	Intron of MLL3(-): 985bp after exon 44	MLL3	151854963			16	DELETION		98014	109904	30500	10	NEW_VARIANT
P-0007000-T01-IM5	CREBBP (NM_004380) rearrangement :  c.2159-464_2290del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1601	0	34	16	Exon 13 of CREBBP(-)	CREBBP	3823925			16	Intron of CREBBP(-): 464bp before exon 12	CREBBP	3825158			56	DELETION		1233	112612	1072	34	NEW_VARIANT
P-0007108-T01-IM5	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)	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	85	6	Intron of ROS1(-): 554bp before exon 34	ROS1	117646132			5	Intron of CD74(-): 539bp after exon 6	CD74	149783704			41	TRANSLOCATION		0	113467	0	81	NEW_VARIANT
P-0007114-T01-IM5	CREBBP (NM_004380) rearrangement :  c.2463+552_5173-158del	PRECISE	Note: The CREBBP (NM_004380) rearrangement results in the intragenic deletion of exons 14 to 30. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 17 exons: in frame		49026	0	11	16	Intron of CREBBP(-): 158bp before exon 31	CREBBP	3780033			16	Intron of CREBBP(-): 552bp after exon 13	CREBBP	3823200			13	DELETION		43167	113478	37928	9	NEW_VARIANT
P-0007281-T01-IM5	IRS2 (NM_003749) rearrangement: c.*72_chr13.g.110398923del	PRECISE	The IRS2 (NM_003749) rearrangement is a deletion with a breakpoint within the 3-UTR of IRS2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		591	0	32	13	IGR: 7Kb before IRS2(-)	IRS2	110398923			13	3-UTR of IRS2(-): 72bp after coding stop	IRS2	110408579			23	DELETION		9656	114830	594	30	NEW_VARIANT
P-0007413-T01-IM5	ROS1(NM_002944.2) rearrangement : c.4602_c.4321+3009inv	PRECISE	Note: The ROS1(NM_002944.2) rearrangement is an intragenic inversion involving exon 27-28. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2454	0	54	6	Exon 28 of ROS1(-)	ROS1	117663630			6	Intron of ROS1(-): 3Kb after exon 26	ROS1	117671144			45	INVERSION		7514	115885	2301	51	NEW_VARIANT
P-0007587-T01-IM5	CDK12 (NM_016507) RARA (NM_000964) rearrangement: c.2011:CDK12_c.178+4818:RARAinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		108310	0	6	17	Exon 3 of CDK12(+)	CDK12	37646889			17	Intron of RARA(+): 5Kb after exon 2	RARA	38492466			10	INVERSION		845577	117582	119557	6	NEW_VARIANT
P-0007638-T01-IM5	MTOR (NM_004958) Rearrangement : chr1:g.4431259_c.4747:MTORinv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		125354	0	24	1	IGR: 41Kb before LOC284661(+)	LOC284661	4431259			1	Exon 33 of MTOR(-)	MTOR	11205042			43	INVERSION		6773783	117756	110054	24	NEW_VARIANT
P-0007759-T01-IM5	JAK2 (NM_004972) rearrangement: c.615-1087_c.633del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		716	0	10	9	Intron of JAK2(+): 1Kb before exon 7	JAK2	5053476			9	Exon 7 of JAK2(+)	JAK2	5054581			0	DELETION		1105	118285	789	10	NEW_VARIANT
P-0007870-T02-IM6	ROS1 (NM_002944) Rearrangement :  t(X;6)(p11.23;q22.1)(chrX:g.47262831;chr6:g.117659405)	PRECISE	Note: The ROS1 Rearrangement is a translocation with a breakpoint in intron 30 of ROS1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	16	X	Intron of ZNF157(+):7Kb before exon 2	ZNF157	47262831			6	Intron of ROS1(-):902bp before exon 31	ROS1	117659405			10	TRANSLOCATION		0	203925	0	16	NEW_VARIANT
P-0008168-T01-IM5	GPS2 (NM_004489) rearrangement: c.634+21_chr17:g.439993dup	PRECISE	The GPS2 (NM_004489) rearrangement is a duplication exons 1-7 of GPS2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		18296	0	35	17	Intron of GPS2(-): 21bp after exon 7	GPS2	7216866			17	IGR: 12Kb before TNFSF12(+)	TNFSF12	7439993			39	DUPLICATION		223127	120668	19150	25	NEW_VARIANT
P-0008229-T01-IM5	DCUN1D1 (NM_020640) rearrangement : :c.603+49:DCUN1D1_chr3:g.182650622inv	PRECISE	Note: The DCUN1D1 (NM_020640) rearrangement event results in the inversion of DCUN1D1 exon 6-7.	MANUAL_OK	5to5	5to5	-		3927	0	8	3	IGR: 10Kb before DCUN1D1(-)	DCUN1D1	182650622			3	Intron of DCUN1D1(-): 49bp after exon 5	DCUN1D1	182665289			13	INVERSION		14667	120884	4575	8	NEW_VARIANT
P-0008289-T01-IM5	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	PRECISE	Note: The KIF5B (NM_004521) - RET (NM_020975) fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		97784	0	15	10	Intron of KIF5B(-): 824bp before exon 16	KIF5B	32312788			10	Intron of RET(+): 284bp before exon 12	RET	43611748			37	INVERSION		11298960	121166	81738	15	NEW_VARIANT
P-0008434-T01-IM5	ETV6 (NM_001987) rearrangement : c.464-5719:ETV6_chr12:17005932dup	PRECISE	Note: The ETV6 (NM_001987) rearrangement event is a duplication involving ETV6 exons 5-8.	MANUAL_OK	5to3	5to3	-		170324	0	40	12	Intron of ETV6(+): 6Kb before exon 5	ETV6	12016639			12	IGR: 305Kb before LMO3(-)	LMO3	17005932			48	DUPLICATION		4989293	122150	180468	38	NEW_VARIANT
P-0008434-T01-IM5	ATRX (NM_000489) rearrangement : c.3809+3373_3972del	PRECISE	Note: The ATRX (NM_000489) rearrangement event results in the deletion of ATRX exons 11-12. One of the breakpoints is within ATRX exon12.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3537	0	43	X	Exon 12 of ATRX(-)	ATRX	76919019			X	Intron of ATRX(-): 3Kb after exon 10	ATRX	76928348			41	DELETION		9329	122149	2797	42	NEW_VARIANT
P-0008483-T01-IM5	KDM5C (NM_004187) rearrangement: c.817_c.1746+1318inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		15827	0	14	X	Intron of KDM5C(-): 1Kb after exon 12	KDM5C	53238278			X	Exon 7 of KDM5C(-)	KDM5C	53245123			14	INVERSION		6845	122477	13902	13	NEW_VARIANT
P-0008538-T01-IM5	RB1 (NM_000321) rearrangement : c.381-56_608-3120dup	PRECISE	Note: The RB1 (NM_000321) rearrangement event results in the duplication of exons 4-6 of RB1.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		3048	0	17	13	Intron of RB1(+): 56bp before exon 4	RB1	48919160			13	Intron of RB1(+): 3Kb before exon 7	RB1	48931033			14	DUPLICATION		11873	122585	3542	16	NEW_VARIANT
P-0008669-T01-IM5	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)	IMPRECISE		MANUAL_OK	5to3	5to3	Protein fusion: in frame (TMPRSS2-ETV1)		0	0	7	21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872919			7	Intron of ETV1(-): 18Kb after exon 6	ETV1	13999067			0	TRANSLOCATION		0	123379	0	7	NEW_VARIANT
P-0008840-T01-IM5	ANKRD11 (NM_013275) rearrangement: c.1914_chr16:g.50994355del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		578894	0	11	16	IGR: 176Kb before SALL1(-)	SALL1	50994355			16	Exon 9 of ANKRD11(-)	ANKRD11	89351036			26	DELETION		38356681	124566	515414	11	NEW_VARIANT
P-0008908-T01-IM5	CTNNB1 (NM_001904)  rearrangement: c.-48-1284_c.328del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3168	0	17	3	5-UTR of CTNNB1(+): 1Kb before coding start	CTNNB1	41264228			3	Exon 4 of CTNNB1(+)	CTNNB1	41266531			21	DELETION		2303	124837	3401	16	NEW_VARIANT
P-0008908-T01-IM5	NBN (NM_002485) rearrangement: c.1914+130_chr8:g.116744050inv	PRECISE	Note: The NBN (NM_002485) rearrangement is an inversion of exons 1-12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		23416	0	17	8	Intron of NBN(-): 130bp after exon 12	NBN	90959922			8	IGR: 63Kb after TRPS1(-)	TRPS1	116744050			23	INVERSION		25784128	124839	29457	16	NEW_VARIANT
P-0008948-T01-IM5	NOTCH3 (NM_000435) Rearrangement : t(17;19)(17q24.2;19p13.12)(chr17:g.66644028::chr19:g.15298008)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	37	19	Exon 11 of NOTCH3(-)	NOTCH3	15298008			17	IGR: 47Kb after FAM20A(-)	FAM20A	66644028			0	TRANSLOCATION		0	125121	0	31	NEW_VARIANT
P-0008948-T01-IM5	APC (NM_000038) - MCC (NM_001085377) Rearrangement :  c.8117:APC_c.2449-2146:MCC inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (APC-MCC)		14097	0	27	5	Exon 16 of APC(+)	APC	112179408			5	Intron of MCC(-): 2Kb before exon 14	MCC	112387142			46	INVERSION		207734	125119	15690	26	NEW_VARIANT
P-0009002-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons1-11) : c.56-190:TMPRSS2_c.-150+10247:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		71778	0	38	21	5-UTR of ERG(-): 76Kb before coding start	ERG	40023335			21	Intron of TMPRSS2(-): 190bp before exon 2	TMPRSS2	42870306			36	DELETION		2846971	126098	60088	36	NEW_VARIANT
P-0009109-T01-IM5	RAD50 (NM_005732) rearrangement: chr5:g.131815508_c.2346:RAD50dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		16410	0	12	5	IGR: 2Kb before IRF1(-)	IRF1	131815508			5	Exon 14 of RAD50(+)	RAD50	131939130			26	DUPLICATION		123622	126703	17082	12	NEW_VARIANT
P-0009223-T01-IM5	ERBB4 (NM_005235) rearrangement: c.557-7050_c.991del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6198	0	7	2	Exon 8 of ERBB4(-)	ERBB4	212578266			2	Intron of ERBB4(-): 7Kb before exon 5	ERBB4	212622479			14	DELETION		44213	129313	5395	7	NEW_VARIANT
P-0009307-T01-IM5	EGFR (NM_005228) rearrangement: c.2061+79_c.3115-25dup	PRECISE	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 )	MANUAL_OK	5to3	5to3	Duplication of 8 exons: in frame		17514	0	6	7	Intron of EGFR(+): 79bp after exon 17	EGFR	55240896			7	Intron of EGFR(+): 25bp before exon 26	EGFR	55269403			13	DUPLICATION		28507	130014	22167	6	NEW_VARIANT
P-0009347-T01-IM5	CDKN2B (NM_004936) rearrangement : c.341_chr9:g.22015263inv	PRECISE	Note: The CDKN2B (NM_004936) rearrangement event results in the inversion of CDKN2B exons 1-2. One of the breakpoints is within CDKN2B exon2.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (CDKN2B-CDKN2BAS)		11355	0	24	9	Exon 2 of CDKN2B(-)	CDKN2B	22006062			9	5-UTR of CDKN2BAS(+): 106Kb before coding start	CDKN2BAS	22015263			63	INVERSION		9201	130176	8683	13	NEW_VARIANT
P-0009374-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons1-2 with ERG exon2-10) : c.127-1152:TMPRSS2_c.18+82:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		43466	0	56	21	Intron of ERG(-): 82bp after exon 1	ERG	39870205			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867657			60	DELETION		2997452	153416	40944	55	NEW_VARIANT
P-0009431-T01-IM5	GATA3 (NM_002051) rearrangement : c.192:GATA3_chr10:g.25463753inv	PRECISE	Note: The GATA3 (NM_002051) rearrangement event results in the inversion of GATA3 exons 2-6.	MANUAL_OK	3to3	3to3	-		34322	0	43	10	Exon 2 of GATA3(+)	GATA3	8097810			10	3-UTR of LOC100128811(-): 1Kb after coding stop	LOC100128811	25463753			48	INVERSION		17365943	130623	44442	43	NEW_VARIANT
P-0009448-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel	IMPRECISE	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exons 4-11)  : c.56-670:TMPRSS2_c.40-56969:ERGdel	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		51870	0	7	21	Intron of ERG(-): 57Kb before exon 4	ERG	39874513			21	Intron of TMPRSS2(-): 670bp before exon 2	TMPRSS2	42870786			0	DELETION		2996273	130716	46321	7	NEW_VARIANT
P-0009512-T01-IM5	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.	PRECISE	FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement :  c.2302-914:FGFR2_c.238-9180:BICC1inv	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		311024	0	23	10	Intron of BICC1(+): 9Kb before exon 3	BICC1	60452654			10	Intron of FGFR2(-): 914bp before exon 18	FGFR2	123240449			81	INVERSION		62787795	131066	368684	4	NEW_VARIANT
P-0009542-T01-IM5	TMEM116 (NM_001193531) -SH2B3 (NM_005475) Rearrangement : c.315+1899:TMEM116_ c.540:SH2B3_inv	IMPRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (TMEM116-SH2B3)		30681	0	6	12	Exon 2 of SH2B3(+)	SH2B3	111856489			12	Intron of TMEM116(-): 2Kb after exon 7	TMEM116	112379170			0	INVERSION		522681	131222	30678	6	NEW_VARIANT
P-0009626-T01-IM5	RB1 (NM_000321) Rearrangement : c.1131_1695+23010inv	PRECISE	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,	MANUAL_OK	5to5	5to5	-		7293	0	10	13	Exon 12 of RB1(+)	RB1	48947544			13	Intron of RB1(+): 23Kb after exon 17	RB1	48978589			23	INVERSION		31045	131535	9082	10	NEW_VARIANT
P-0009699-T01-IM5	PLCG2 (NM_002661) Rearrangement : t(5;16)(q21.1;q23.3)(chr5:g.103163734::chr16:g. 81934177)	IMPRECISE	Note: The PLCG2 (NM_002661) Rearrangement  results in the possible truncation of exons 14-33 of PLCG2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	16	Intron of PLCG2(+): 40bp before exon 14	PLCG2	81934177			5	IGR: 279Kb before NUDT12(-)	NUDT12	103163734			0	TRANSLOCATION		0	136084	0	21	NEW_VARIANT
P-0009714-T01-IM5	KEAP1 (NM_203500) Rearrangement: c.1325+658_c.1617del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5836	0	90	19	Exon 5 of KEAP1(-)	KEAP1	10599959			19	Intron of KEAP1(-): 658bp after exon 3	KEAP1	10601595			115	DELETION		1636	136109	4385	90	NEW_VARIANT
P-0009740-T01-IM5	ARID1B (NM_020732) rearrangement: c.1926_c.1926+804del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		78	0	64	6	Exon 4 of ARID1B(+)	ARID1B	157222659			6	Intron of ARID1B(+): 804bp after exon 4	ARID1B	157223463			73	DELETION		804	136241	57	63	NEW_VARIANT
P-0009757-T01-IM5	AGAP3 (NM_031946) - BRAF (NM_004333) rearrangement: c.1222-2154:AGAP3_c.1140+237:BRAFinv	PRECISE	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)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (AGAP3-BRAF)		107911	0	40	7	Intron of BRAF(-): 237bp after exon 8	BRAF	140493871			7	Intron of AGAP3(+): 2Kb before exon 10	AGAP3	150823513			30	INVERSION		10329642	136446	131871	37	NEW_VARIANT
P-0009867-T01-IM5	GPS2 (NM_004489) rearrangement : c.-560_119inv	IMPRECISE	Note: The GPS2 (NM_004489) rearrangement event results in the inversion of GPS2 exons 1-3. One of the breakpoints is within GPS2 exon3.	MANUAL_OK	3to3	3to3	-		2589	0	27	17	Exon 3 of GPS2(-)	GPS2	7217892			17	3-UTR of NEURL4(-): 300bp after coding stop	NEURL4	7219142			0	INVERSION		1250	136930	2787	24	NEW_VARIANT
P-0010071-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		44049	0	17	21	Intron of ERG(-): 18Kb before exon 4	ERG	39835555			21	Intron of TMPRSS2(-): 1Kb after exon 2	TMPRSS2	42869039			27	DELETION		3033484	137851	38597	16	NEW_VARIANT
P-0010071-T01-IM5	TSC1 (NM_000368) Rearrangement :  chr9:g.78358260_c.1964:TSC1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		303752	0	15	9	IGR: 20Kb after MIR548H3(-)	MIR548H3	78358260			9	Exon 15 of TSC1(-)	TSC1	135781001			55	INVERSION		57422741	137852	296453	15	NEW_VARIANT
P-0010126-T01-IM5	FAT1 (NM_005245) rearrangement : c.8570:FAT1_chr4:g.139877853del	PRECISE	Note: The FAT1 rearrangement event results in the deletion of FAT1 exons 10-27. One of the breakpoints is within FAT1 exon10.	MANUAL_OK	3to5	3to5	-		201916	0	41	4	IGR: 59Kb before CCRN4L(+)	CCRN4L	139877853			4	Exon 10 of FAT1(-)	FAT1	187539170			26	DELETION		47661317	144310	124459	30	NEW_VARIANT
P-0010243-T01-IM5	TP53 (NM_000546) Rearrangement :  c.375+81_c.*417del	PRECISE	Note: The TP53  Rearrangement results in the intragenic deletion of exons 4-11 of TP53. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		12504	0	14	17	3-UTR of TP53(-): 417bp after coding stop	TP53	7572510			17	Intron of TP53(-): 81bp after exon 4	TP53	7579231			19	DELETION		6721	144990	10782	12	NEW_VARIANT
P-0010334-T01-IM5	NFE2L2 (NM_006164) rearrangement : c.46-3018_156del	PRECISE	Note: The NFE2L2 rearrangement event results in the intragenic deletion of NFE2L2 exon2. One of the breakpoints is within NFE2L2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		647	0	41	2	Exon 2 of NFE2L2(-)	NFE2L2	178098889			2	Intron of NFE2L2(-): 3Kb before exon 2	NFE2L2	178102017			60	DELETION		3128	145565	566	41	NEW_VARIANT
P-0010512-T01-IM5	JAK1 (NM_002227) rearrangement : c.2403+100:JAK1_chr1:g.76414149inv see note1	PRECISE	Note1: The JAK1 rearrangement event results in the inversion of JAK1 exons 1-17.	MANUAL_OK	5to5	5to5	-		79221	0	13	1	Intron of JAK1(-): 100bp after exon 17	JAK1	65309647			1	IGR: 30Kb before ASB17(-)	ASB17	76414149			22	INVERSION		11104502	146755	66584	13	NEW_VARIANT
P-0010512-T01-IM5	JAK1 (NM_002227) rearrangement : t(1;4)(p31.3;q13.2)(chr1:g.65326020::chr4:g.69246009) see note2	IMPRECISE	Note2: The JAK1 rearrangement is a translocation which results in the truncation of JAK1 exons 9-25.	MANUAL_OK	5to3	5to3	-		0	0	12	4	IGR: 30Kb after YTHDC1(-)	YTHDC1	69246009			1	Intron of JAK1(-): 75bp before exon 9	JAK1	65326020			0	TRANSLOCATION		0	146758	0	12	NEW_VARIANT
P-0010600-T01-IM5	RAB35 (NM_006861) rearrangement: c.14_c.52+1593del	PRECISE	Note: The RAB35 rearrangement is an intragenic deletion of exon1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		402	0	19	12	Intron of RAB35(-): 2Kb after exon 1	RAB35	120552810			12	Exon 1 of RAB35(-)	RAB35	120554441			31	DELETION		1631	147841	109	19	NEW_VARIANT
P-0010704-T01-IM5	ARID2 (NM_152641) Rearrangement :  c.3150_c.4646del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		11491	0	58	12	Exon 15 of ARID2(+)	ARID2	46245056			12	Exon 15 of ARID2(+)	ARID2	46246552			73	DELETION		1496	148376	9859	57	NEW_VARIANT
P-0010711-T01-IM5	MAP3K1 (NM_005921)Rearrangement : t(5;16)(q11.2;q12.1)(chr5:g.56171040::chr16:g.48661649)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	24	16	IGR: 18Kb after N4BP1(-)	N4BP1	48661649			5	Exon 10 of MAP3K1(+)	MAP3K1	56171040			0	TRANSLOCATION		0	148361	0	24	NEW_VARIANT
P-0010740-T01-IM5	KCNC2 (NM_139137) - MLL2 (NM_003482) rearrangement : c.687+77124:KCNC2_c.10355+12:MLL2del	PRECISE	Note: The KCNC2-MLL2 rearrangement event is a deletion which results in the fusion of KCNC2 exons 1-2 with MLL2 exons 36-54.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (KCNC2-MLL2)		361269	0	14	12	Intron of MLL2(-): 12bp after exon 35	MLL2	49428583			12	Intron of KCNC2(-): 77Kb after exon 2	KCNC2	75523953			31	DELETION		26095370	148908	324598	14	NEW_VARIANT
P-0010740-T01-IM5	CREBBP (NM_004380) rearrangement : c.527_798+3835del	PRECISE	Note: The CREBBP rearrangement results in the intragenic deletion of CREBBP exon2. One of the breakpoints is within CREBBP exon2.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3795	0	34	16	Intron of CREBBP(-): 4Kb after exon 2	CREBBP	3896463			16	Exon 2 of CREBBP(-)	CREBBP	3900569			39	DELETION		4106	148909	1334	33	NEW_VARIANT
P-0010811-T01-IM5	ERBB2 (NM_004448) rearrangement : c.3049:ERBB2_chr17:g.37886757del	PRECISE	ERBB2 rearrangement event results in the deletion of ERBB2 exons 25-27. One of the breakpoints is within ERBB2 exon25.	MANUAL_OK	3to5	3to5	Antisense fusion		7368	0	7	17	Exon 25 of ERBB2(+)	ERBB2	37883146			17	5-UTR of C17orf37(-): 9bp before coding start	C17orf37	37886757			14	DELETION		3611	149310	6784	7	NEW_VARIANT
P-0010945-T01-IM5	AGK (NM_018238) - BRAF (NM_004333) rearrangement :  c.101+12646:AGK_c.980+2552:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (AGK-BRAF)		28761	0	11	7	Intron of BRAF(-): 3Kb after exon 7	BRAF	140497610			7	Intron of AGK(+): 13Kb after exon 2	AGK	141268013			12	INVERSION		770403	149864	30557	11	NEW_VARIANT
P-0010989-T01-IM5	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (EZR-ROS1)		261218	0	37	6	Intron of ROS1(-): 763bp after exon 32	ROS1	117649729			6	Intron of EZR(-): 215bp after exon 9	EZR	159191581			57	DELETION		41541852	150010	286690	36	NEW_VARIANT
P-0011183-T01-IM5	MAP4 (NM_002375) - SETD2 (NM_014159) rearrangement: c.2000-9359:MAP4_c.5278-1:SETD2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (MAP4-SETD2)		62276	0	8	3	Intron of SETD2(-): 1bp before exon 11	SETD2	47127805			3	Intron of MAP4(-): 9Kb before exon 9	MAP4	47928372			12	DELETION		800567	151538	58584	8	NEW_VARIANT
P-0011201-T01-IM5	CDC73 (NM_024529) rearrangement : c.926_chr1:192828282del	PRECISE	Note: The CDC73 rearrangement event results in the deletion of CDC73 exons 1-10. One of the breakpoints is within CDC73 exon10.	MANUAL_OK	3to5	3to5	-		16777	0	11	1	IGR: 50Kb before RGS2(+)	RGS2	192828282			1	Exon 10 of CDC73(+)	CDC73	193121528			12	DELETION		293246	151717	14999	11	NEW_VARIANT
P-0011290-T01-IM5	MLL2 (NM_003482) - C7orf60 (NM_152556) rearrangement : t(7;12)(q31.1;q13.12)(chr7:g.112507139::chr12:g.49420106)	IMPRECISE	Note: The MLL2-C7orf60 rearrangement event in a translocation which results in the fusion of MLL2 exons 1-48 with C7orf60 exons 4-5.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (MLL2-C7orf60)		0	0	50	12	Exon 48 of MLL2(-)	MLL2	49420106			7	Intron of C7orf60(-): 28Kb after exon 3	C7orf60	112507139			0	TRANSLOCATION		0	152477	0	42	NEW_VARIANT
P-0011335-T01-IM5	CDH1 (NM_004360) Rearrangement :  chr16:g.46718598_c.391:CDH1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		102759	0	29	16	Intron of VPS35(-): 1Kb before exon 2	VPS35	46718598			16	Exon 4 of CDH1(+)	CDH1	68842330			33	DELETION		22123732	153226	90772	29	NEW_VARIANT
P-0012030-T01-IM5	TMPRSS2 (NM_001135099) - RBPMS2 (NM_194272) rearrangement : t(15;21)(q22.31;q22.3)(chr15:g.65037007::chr21:g.42870183)	IMPRECISE	Note: The TMPRSS2-RBPMS2 rearrangement event is a translocation which results in the fusion of TMPRSS2 exon1 with RBPMS2 exon7.  However, the possibility of a more complex rearrangement  cannot be excluded. An alternative platform (i.e.- Archer FusionPlex) may be valuable if clinically indicated.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-RBPMS2)		0	0	31	21	Intron of TMPRSS2(-): 67bp before exon 2	TMPRSS2	42870183			15	Intron of RBPMS2(-): 4Kb before exon 7	RBPMS2	65037007			0	TRANSLOCATION		0	155940	0	31	NEW_VARIANT
P-0012134-T01-IM5	MYC (NM_002467) rearrangement: c.1245_chr8:g.132081862del	PRECISE	Note: The MYC rearrangement is a deletion of MYC exon 3. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6193	0	53	8	Exon 3 of MYC(+)	MYC	128753084			8	IGR: 29Kb after ADCY8(-)	ADCY8	132081862			55	DELETION		3328778	156367	11413	48	NEW_VARIANT
P-0012271-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-2767:TMPRSS2_c.39+13672:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		72027	0	34	21	Intron of ERG(-): 14Kb after exon 3	ERG	39933914			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872883			49	DELETION		2938969	157056	60910	32	NEW_VARIANT
P-0012288-T01-IM5	NSD1 (NM_022455) - GRK5 (NM_005308) rearrangement: t(5;10)(q35.3; q26.1)(chr5:g.176721806::chr10:g.121033310)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		0	0	47	10	Intron of GRK5(+): 53Kb before exon 2	GRK5	121033310			5	Exon 24 of NSD1(+)	NSD1	176721806			15	TRANSLOCATION		0	156922	0	44	NEW_VARIANT
P-0012306-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: chr9:g.22056567_c.377:CDKN2Ap14ARFdel	PRECISE	Note: The CDKN2Ap14ARF  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.	MANUAL_OK	3to5	3to5			12300		16	9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21971024			9	5-UTR of CDKN2BAS(+): 65Kb before coding start	CDKN2BAS	22056567			21	DELETION		85543	157292	12300		NEW_VARIANT
P-0012306-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.22056567_c.334:CDKN2Ap16INK4Adel	PRECISE	Note: The CDKN2Ap16INK4A  rearrangement is a deletion of exons 2-3. One of the breakpoint is within exon 2.	MANUAL_OK	3to5	3to5			12300		16	9	Exon 2 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21971024			9	5-UTR of CDKN2BAS(+): 65Kb before coding start	CDKN2BAS	22056567			21	DELETION		85543	157291	12300		NEW_VARIANT
P-0012375-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11): c.56-59:TMPRSS2_c.40-58424:ERGdel	PRECISE	Note: The TMPRSS2 - ERG (NM_004449) fusion is a deletion which results in the fusion of TMPRSS2 exon1 with ERG exons 4-11.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		50294	0	3	21	Intron of ERG(-): 58Kb before exon 4	ERG	39875968			21	Intron of TMPRSS2(-): 59bp before exon 2	TMPRSS2	42870175			4	DELETION		2994207	157231	69601	3	NEW_VARIANT
P-0012395-T01-IM5	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1152+27174:SND1_c.1140+581:BRAFinv	PRECISE	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).	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SND1-BRAF)		154620	0	14	7	Intron of SND1(+): 27Kb after exon 10	SND1	127388628			7	Intron of BRAF(-): 581bp after exon 8	BRAF	140493527			24	INVERSION		13104899	157353	189356	13	NEW_VARIANT
P-0012456-T01-IM5	NF2 (NM_000268) Rearrangement : c.1123-129_22:35955753inv	PRECISE	Note: The NF2 Rearrangement results in the inversion of exons 12-16 of NF2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		16279	0	16	22	Intron of NF2(+): 129bp before exon 12	NF2	30069129			22	IGR: 6Kb after RASD2(+)	RASD2	35955753			18	INVERSION		5886624	157553	20443	15	NEW_VARIANT
P-0012557-T01-IM5	TP63 (NM_003722) rearrangement: c.1836_c.*2723del	PRECISE	Note: The TP63 rearrangement is a deletion of a part of exon 14. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	-		506	0	7	3	Exon 14 of TP63(+)	TP63	189612084			3	3-UTR of TP63(+): 3Kb after coding stop	TP63	189615014			23	DELETION		2930	157806	607	7	NEW_VARIANT
P-0012577-T01-IM5	PIK3CD (NM_005026) rearrangement: c.1689+30_c.2234+10inv	IMPRECISE	Note: The PIK3CD rearrangement is an inversion of exons 14-17. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		8730	0	59	1	Intron of PIK3CD(+): 30bp after exon 13	PIK3CD	9780997			1	Intron of PIK3CD(+): 10bp after exon 17	PIK3CD	9782221			0	INVERSION		1224	157894	8778	54	NEW_VARIANT
P-0012587-T01-IM5	NFE2L2 (NM_006164) rearrangement: c.46-6982_c.376del	PRECISE	Note: The NFE2L2 rearrangement is an intragenic deletion of exons 2-3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3899	0	17	2	Exon 3 of NFE2L2(-)	NFE2L2	178098004			2	Intron of NFE2L2(-): 7Kb before exon 2	NFE2L2	178105981			21	DELETION		7977	157933	5113	17	NEW_VARIANT
P-0012648-T01-IM5	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-335:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		80876	0	54	10	Intron of KIF5B(-): 2Kb after exon 15	KIF5B	32315493			10	Intron of RET(+): 335bp before exon 12	RET	43611697			79	INVERSION		11296204	158330	76001	54	NEW_VARIANT
P-0012914-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+935:TMPRSS2_c.18+7096:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		63270	0	91	21	Intron of ERG(-): 7Kb after exon 1	ERG	39863191			21	Intron of TMPRSS2(-): 935bp after exon 2	TMPRSS2	42869111			76	DELETION		3005920	159434	76384	85	NEW_VARIANT
P-0012914-T01-IM5	APC (NM_000038) rearrangement: chr5:g.92746031_c.4532del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		71529	0	22	5	3-UTR of FLJ42709(-): 160Kb after coding stop	FLJ42709	92746031			5	Exon 16 of APC(+)	APC	112175823			18	DELETION		19429792	159436	113118	22	NEW_VARIANT
P-0012930-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-102:TMPRSS2_c.18+5504:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		51849	0	99	21	Intron of ERG(-): 6Kb after exon 1	ERG	39864783			21	Intron of TMPRSS2(-): 102bp before exon 2	TMPRSS2	42870218			71	DELETION		3005435	159487	9284	95	NEW_VARIANT
P-0013077-T01-IM5	AKT1 (NM_001014431) Rearrangement: c.703-18:AKT1_chr14:g.105380826del	PRECISE	Note: The AKT1 Rearrangement results in the deletion of exons 1-8 of AKT1.This includes the kinase domain of AKT1.	MANUAL_OK	3to5	3to5	-		15232	0	9	14	Intron of AKT1(-): 18bp before exon 9	AKT1	105239935			14	IGR: 10Kb before PLD4(+)	PLD4	105380826			9	DELETION		140891	160121	15079	8	NEW_VARIANT
P-0013105-T01-IM5	NCOR1 (NM_006311) - USP8 (NM_020886) rearrangement: t(11;17)(q23.2;p12)(chr11:g.113706887::chr17:g.15968849)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NCOR1-USP28)		0	0	102	17	Exon 33 of NCOR1(-)	NCOR1	15968849			11	Intron of USP28(-): 2Kb before exon 6	USP28	113706887			0	TRANSLOCATION		0	160277	0	98	NEW_VARIANT
P-0013151-T01-IM5	CALR (NM_004343) Rearrangement : c.781:CALR_c.442-131:PBX4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		258131	0	34	19	Exon 6 of CALR(+)	CALR	13051433			19	Intron of PBX4(-): 131bp before exon 4	PBX4	19681239			82	DUPLICATION		6629806	160332	359144	34	NEW_VARIANT
P-0013202-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+2565:EML4_c.3173-784:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		63762	0	69	2	Intron of ALK(-): 784bp before exon 20	ALK	29447178			2	Intron of EML4(+): 3Kb after exon 5	EML4	42494436			65	INVERSION		13047258	160472	57833	68	NEW_VARIANT
P-0013232-T01-IM5	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2449:ANKRD11_c.184-519:SPG7del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		39440	0	25	16	Exon 9 of ANKRD11(-)	ANKRD11	89350501			16	Intron of SPG7(+): 519bp before exon 2	SPG7	89576379			40	DELETION		225878	160603	29023	25	NEW_VARIANT
P-0013401-T01-IM5	JUN (NM_002228) rearrangement: c.912:JUN_chr1:g.59238243inv	PRECISE	Note: The JUN rearrangement is an inversion of a part of exon 1. One of the breakpoint is within exon 1.	MANUAL_OK	5to5	5to5	-		8329	0	78	1	IGR: 8Kb before JUN(-)	JUN	59238243			1	Exon 1 of JUN(-)	JUN	59247831			73	INVERSION		9588	161111	7851	72	NEW_VARIANT
P-0013401-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4108:TMPRSS2_c.19-22056:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		129090	0	100	21	Intron of ERG(-): 22Kb before exon 4	ERG	39839600			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875769			88	DELETION		3036169	161107	54847	105	NEW_VARIANT
P-0013404-T01-IM5	CTNNB1 (NM_001904) Rearrangement : c.13+88_443del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4450	0	35	3	Intron of CTNNB1(+): 88bp after exon 2	CTNNB1	41265660			3	Exon 4 of CTNNB1(+)	CTNNB1	41266646			0	DELETION		986	161147	3173	34	NEW_VARIANT
P-0013598-T01-IM5	PTPRD (NM_002839) rearrangement: c.3414-1949_c.3988+83del	PRECISE	Note: The PTPRD rearrangement is an intragenic inversion of exons 31-34.	MANUAL_OK	5to5	5to5	Antisense fusion		9528	0	12	9	Intron of PTPRD(-): 83bp after exon 34	PTPRD	8449642			9	Intron of PTPRD(-): 2Kb before exon 31	PTPRD	8473034			9	INVERSION		23392	161788	10347	11	NEW_VARIANT
P-0013695-T01-IM5	MET (NM_000245) rearrangement: c.3028+410_c.3420dup	PRECISE	Note: The MET rearrangement is a duplication of exons 15- 17. One of the breakpoints is within exon 17. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		4272	0	68	7	Intron of MET(+): 410bp after exon 14	MET	116412453			7	Exon 17 of MET(+)	MET	116418909			88	DUPLICATION		6456	162040	10916	68	NEW_VARIANT
P-0013810-T01-IM5	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	PRECISE	Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		50123	0	67	21	Intron of ERG(-): 65Kb before exon 4	ERG	39882407			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867882			58	DELETION		2985475	162333	51845	64	NEW_VARIANT
P-0013837-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.55+4832:TMPRSS2_c.-149-29687:ERGdel	PRECISE	Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		115244	0	42	21	5-UTR of ERG(-): 39Kb before coding start	ERG	39986556			21	Intron of TMPRSS2(-): 5Kb after exon 1	TMPRSS2	42875045			34	DELETION		2888489	162386	74051	42	NEW_VARIANT
P-0013928-T01-IM5	EPHA7 (NM_004440) rearrangement: c.98-3:EPHA7_chr6:g.92082925inv	PRECISE	Note: The EPHA7 rearrangement is an inversion of exons 2-17.	MANUAL_OK	3to3	3to3	-		46299	0	17	6	IGR: 858Kb before MAP3K7(-)	MAP3K7	92082925			6	Intron of EPHA7(-): 3bp before exon 2	EPHA7	94124488			43	INVERSION		2041563	162760	51638	10	NEW_VARIANT
P-0014162-T01-IM5	PTEN (NM_000314) rearrangement: c.212_c.492+3506PTENdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1745	0	5	10	Exon 4 of PTEN(+)	PTEN	89690805			10	Intron of PTEN(+): 4Kb after exon 5	PTEN	89696514			14	DELETION		5709	163574	299	5	NEW_VARIANT
P-0014380-T01-IM6	LRRK2 (NM_198578) - ERBB3 (NM_001982) rearrangement: c.1892:LRRK2_c.1786:ERBB2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (LRRK2-ERBB3)		290993	0	46	12	Exon 16 of LRRK2(+)	LRRK2	40668746			12	Exon 15 of ERBB3(+)	ERBB3	56488267			58	DELETION		15819521	164351	229359	46	NEW_VARIANT
P-0014425-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2528:TMPRSS2_c.19-4354:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		61082	0	61	21	Intron of ERG(-): 4Kb before exon 4	ERG	39821898			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42872644			60	DELETION		3050746	164498	65472	61	NEW_VARIANT
P-0014474-T01-IM6	AGO2(NM_012154) Rearrangement : c.23-1240_c.1618del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		23975	0	61	8	Exon 13 of EIF2C2(-)	EIF2C2	141557697			8	Intron of EIF2C2(-): 1Kb before exon 2	EIF2C2	141596650			59	DELETION		38953	164596	18675	60	NEW_VARIANT
P-0014506-T01-IM6	RPTOR (NM_020761) rearrangement: chr17:g.43042059_c.2298:RPTORdel	PRECISE	Note: The RPTOR rearrangement is a deletion of exons 20-34. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	-		362036	0	20	17	Intron of C1QL1(-): 3Kb after exon 1	C1QL1	43042059			17	Exon 20 of RPTOR(+)	RPTOR	78867562			28	DELETION		35825503	164875	399987	20	NEW_VARIANT
P-0014506-T01-IM6	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)	PRECISE	Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CD74-ROS1)		0	0	81	6	Intron of ROS1(-): 14bp before exon 32	ROS1	117650623			5	Exon 7 of CD74(-)	CD74	149782871			44	TRANSLOCATION		0	164879	0	79	NEW_VARIANT
P-0014682-T01-IM6	TP53 (NM_000546) rearrangement: chr17:g.7209489_c.672+10:TP53del	IMPRECISE	Note: The TP53 rearrangement is a deletion of exons 7-11.	MANUAL_OK	3to5	3to5	Antisense fusion		21422	0	13	17	Promoter of EIF5A(+): 829bp from tx start	EIF5A	7209489			17	Intron of TP53(-): 10bp after exon 6	TP53	7578167			0	DELETION		368678	165503	22235	11	NEW_VARIANT
P-0014841-T01-IM6	TMPRSS2 (NM_001135099)  - ERG (NM_004449) fusion (TMPRSS2 exon2 fused to ERG exon 4) : c.56-3050:TMPRSS2_c.39+61126:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		98506	0	82	21	Intron of ERG(-): 61Kb after exon 3	ERG	39886460			21	Intron of TMPRSS2(-): 3Kb before exon 2	TMPRSS2	42873166			61	DELETION		2986706	166046	97155	71	NEW_VARIANT
P-0014874-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.-1835_c.257-76del	PRECISE	Note: The TCF7L2 (NM_001146274) rearrangement is a deletion of TCF7L2 exons 1 and 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		2751	0	9	10	Promoter of TCF7L2(+): 1Kb from tx start	TCF7L2	114708681			10	Intron of TCF7L2(+): 76bp before exon 3	TCF7L2	114711166			12	DELETION		2485	166148	2649	9	NEW_VARIANT
P-0014894-T01-IM6	EP300 (NM_001429) rearrangement: chr22:g.41099971_c.1449del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		16127	0	46	22	IGR: 25Kb before MCHR1(+)	MCHR1	41099971			22	Exon 6 of EP300(+)	EP300	41527558			44	DELETION		427587	166195	10900	46	NEW_VARIANT
P-0015012-T01-IM6	TMPRSS2 (NM_001135099)  rearrangement: t(8;21)(q22.1;q22.3)(chr8:g.96904156::chr21:g.42877101)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	12	21	Intron of TMPRSS2(-): 3Kb after exon 1	TMPRSS2	42877101			8	IGR: 250Kb before GDF6(-)	GDF6	96904156			12	TRANSLOCATION		0	166517	0	11	NEW_VARIANT
P-0015029-T01-IM6	EIF1AX (NM_001412) rearrangement: t(X;20)(p22.12;p12.1)(chrX:g.20156591::chr20:g.12665904)	PRECISE	Note: The EIF1AX rearrangement is a translocation that may result in the truncation of exons 3-7. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	X	Intron of EIF1AX(-): 66bp after exon 2	EIF1AX	20156591			20	IGR: 324Kb before SPTLC3(+)	SPTLC3	12665904			12	TRANSLOCATION		0	166612	0	8	NEW_VARIANT
P-0015039-T01-IM6	ARID1B (NM_020732) rearrangement: c.2038-21549_c.2183del	PRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1407	0	7	6	Intron of ARID1B(+): 22Kb before exon 6	ARID1B	157384247			6	Exon 6 of ARID1B(+)	ARID1B	157405941			7	DELETION		21694	166600	1124	7	NEW_VARIANT
P-0020076-T02-IM6	KMT2B (NM_014727) rearrangement: c.358_c.1686inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		16282	0	6	19	Exon 1 of KMT2B(+)	KMT2B	36209278			19	Exon 3 of KMT2B(+)	KMT2B	36211935			0	INVERSION		2657	185260	44653	6	NEW_VARIANT
P-0020482-T01-IM6	RAD21 (NM_006265) Rearrangement : c.1322-1:RAD21_chr8:g.117833120del	PRECISE	Note: The RAD21 Rearrangement results in the deletion of exons 11-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6824	0	7	8	IGR: 25Kb before RAD21(-)	RAD21	117833120			8	Intron of RAD21(-):1bp before exon 11	RAD21	117864336			10	DELETION		31216	184530	7879	8	NEW_VARIANT
P-0020546-T01-IM6	RHEB (NM_005614) rearrangment: chr7:g.151218860_c.16:RHEBdel	PRECISE	Note: The RHEB rearrangement is a partial deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		477	0	28	7	Exon 1 of RHEB(-)	RHEB	151216582			7	Promoter of RHEB(-):56Kb from tx start	RHEB	151218860			10	DELETION		2278	184744	319	34	NEW_VARIANT
P-0020670-T01-IM6	BCL10 (NM_003921) rearrangement: g.65408657_c.605inv	IMPPRECISE	Note: The BCL10 rearrangement is an inversion of exon 3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		43275	0	11	1	5-UTR of JAK1(-):108Kb before coding start	JAK1	65408657			1	Exon 3 of BCL10(-)	BCL10	85733407			0	INVERSION		20324750	185001	47788	11	NEW_VARIANT
P-0020812-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused with ERG exons 4-11): c.55+3638:TMPRSS2_c.39+63429:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		150589	0	180	21	Intron of ERG(-):63Kb after exon 3	ERG	39884157			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42876239			10	DELETION		2992082	185478	188863	198	NEW_VARIANT
P-0020823-T02-IM6	JAK1 (NM_002227) - MSH4 (NM_002440) rearrangement: c.1860:JAK1_c.244+1113:MSH4del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		42328	0	4	1	Exon 13 of JAK1(-)	JAK1	65313254			1	Intron of MSH4(+):1Kb after exon 1	MSH4	76264027			10	DELETION		10950773	186047	35831	4	NEW_VARIANT
P-0020865-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.281_c.762-1516del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3034	0	35	12	Exon 2 of PIK3C2G(+)	PIK3C2G	18435296			12	Intron of PIK3C2G(+):2Kb before exon 4	PIK3C2G	18442273			10	DELETION		6977	185682	2128	51	NEW_VARIANT
P-0020962-T01-IM6	FLCN (NM_144997) rearrangement: g.16994136_c.1062+33del	PRECISE	Note: The FLCN rearrangement results in the deletion of exons 10-14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		8703	0	9	17	Intron of MPRIP(+):13Kb after exon 3	MPRIP	16994136			17	Intron of FLCN(-):32bp after exon 9	FLCN	17122300			10	DELETION		128164	185842	6956	9	NEW_VARIANT
P-0021063-T01-IM6	CREBBP (NM_004380) -  SLX4 (NM_032444) rearrangement: c.4395-651:CREBBP_c.4637-57:SLX4	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CREBBP:SLX4}		81317	0	12	16	Intron of SLX4(-):57bp before exon 13	SLX4	3634929			16	Intron of CREBBP(-):651bp before exon 27	CREBBP	3787467			10	DELETION		152538	186168	65516	13	NEW_VARIANT
P-0021241-T01-IM6	LYN (NM_002350) rearrangement: c.1050+108_g.137719703del	PRECISE	Note: The LYN rearrangement results in the deletion of exons 11-13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		265190	0	3	8	Intron of LYN(+):108bp after exon 10	LYN	56882460			8	IGR: 699Kb before LOC101927915(-)	LOC101927915	137719703			10	DELETION		80837243	186602	226587	3	NEW_VARIANT
P-0021342-T01-IM6	PIK3CD (NM_005026) rearrangement: c.1287_c.1656inv	PRECISE	Note: The PIK3CD rearrangement is an intragenic inversion of exons 10-13. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		7841	0	3	1	Exon 10 of PIK3CD(+)	PIK3CD	9780023			1	Exon 13 of PIK3CD(+)	PIK3CD	9780934			8	INVERSION		911	186923	9232	3	NEW_VARIANT
P-0021342-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38867	0	58	21	Intron of ERG(-):52Kb after exon 3	ERG	39895890			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868257			10	DELETION		2972367	186921	42589	60	NEW_VARIANT
P-0021476-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.3328-160_g.15396709del	PRECISE	Note: The NOTCH3 rearrangement results in the deletion of exons 1-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		115807	0	5	19	Intron of NOTCH3(-):160bp before exon 21	NOTCH3	15290467			19	IGR: 39Kb before BRD4(-)	BRD4	15396709			10	DELETION		106242	187438	103515	4	NEW_VARIANT
P-0021501-T01-IM6	NOTCH4 (NM_004557) rearrangement: c.74-115:NOTCH4_chr6:g.41754978del	PRECISE	Note: The NOTCH4 rearrangement is a deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		151304	0	21	6	Intron of NOTCH4(-):115bp before exon 2	NOTCH4	32190978			6	3-UTR of PRICKLE4(+):4Kb after coding stop	PRICKLE4	41754978			10	DELETION		9564000	187563	130704	22	NEW_VARIANT
P-0021527-T01-IM6	COL15A1 (NM_001855) -TGFBR1 (NM_004612) rearrangement: c.101-17543:COL15A1_c.98-4C:TGFBR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {COL15A1:TGFBR1}		696	0	44	9	Intron of COL15A1(+):18Kb before exon 3	COL15A1	101730304			9	Intron of TGFBR1(+):3bp before exon 2	TGFBR1	101891133			10	DELETION		160829	187632	393	45	NEW_VARIANT
P-0021550-T01-IM6	ARID1A (NM_006015) rearrangement: c.3866+3_chr1:g.232497627inv	PRECISE	Note: The ARID1A rearrangement results in the inversion of exons 16-20. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		888364	0	7	1	Intron of ARID1A(+):3bp after exon 15	ARID1A	27099990			1	IGR: 36Kb before SIPA1L2(-)	SIPA1L2	232497627			10	INVERSION		205397637	187660	946534	7	NEW_VARIANT
P-0021577-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		41281	0	136	21	Intron of ERG(-):14Kb before exon 2	ERG	39831231			21	Intron of TMPRSS2(-):568bp after exon 2	TMPRSS2	42869477			10	DELETION		3038246	187716	37582	151	NEW_VARIANT
P-0021618-T01-IM6	RUNX1 (NM_001754) rearrangement: t(19;21)(p13.3;q22.12)(chr19:g.6377157::chr21:g.36164635)	PRECISE	Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ALKBH7:RUNX1}		0	0	5	21	Exon 9 of RUNX1(-)	RUNX1	36164635			19	Promoter of ALKBH7(+):5Kb from tx start	ALKBH7	6377157			10	TRANSLOCATION		0	187901	0	5	NEW_VARIANT
P-0021674-T01-IM6	PIK3R2 (NM_005027) - MYO9B (NM_004145) rearrangement: c.206:PIK3R2_c.2219+1922:MYO9Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PIK3R2:MYO9B}		85515	0	31	19	Intron of MYO9B(+):2Kb after exon 14	MYO9B	17288472			19	Exon 2 of PIK3R2(+)	PIK3R2	18266895			10	DUPLICATION		978423	188079	107560	34	NEW_VARIANT
P-0021702-T01-IM6	EPHA7 (NM_004440) rearrangement: g.92924560_c.242del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		25859	0	18	6	IGR: 586Kb before CASC6(-)	CASC6	92924560			6	Exon 3 of EPHA7(-)	EPHA7	94120809			10	DELETION		1196249	188105	22641	18	NEW_VARIANT
P-0021709-T01-IM6	DOT1L (NM_032482) rearrangement: t(8,19)(p23.1,p13.3)(chr8:g.8188507::chr19:g.2226441)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	120	19	Exon 27 of DOT1L(+)	DOT1L	2226441			8	Intron of SGK223(-):3Kb before exon 4	SGK223	8188507			10	TRANSLOCATION		0	188130	0	127	NEW_VARIANT
P-0021772-T01-IM6	PARK2 (NM_004562) rearrangement: c.7+55469_c.271del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2845	0	13	6	Exon 3 of PARK2(-)	PARK2	162683698			6	Intron of PARK2(-):55Kb after exon 1	PARK2	163093225			10	DELETION		409527	188208	1640	11	NEW_VARIANT
P-0021853-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exon4) : c.56-3032:TMPRSS2_c.40-59421:ERGdel	PRECISE	Note: TMPRSS2 is fused with non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		72434	0	51	21	Intron of ERG(-):59Kb before exon 4	ERG	39876965			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873148			10	DELETION		2996183	188354	91971	53	NEW_VARIANT
P-0021879-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		63148	0	8	10	Intron of KIF5B(-):882bp before exon 16	KIF5B	32312846			10	Intron of RET(+):515bp after exon 11	RET	43610699			10	INVERSION		11297853	188441	77234	11	NEW_VARIANT
P-0021927-T01-IM6	ETV6 (NM_001987) rearrangement: t(11;12)(p12;p13.2)(chr11:g.39957491:chr12:g.12017383)	PRECISE	Note: The ETV6 rearrangement is a translocation with a breakpoint within ETV6 intron 4. Multiple ETV6 rearrangements were detected in this sample and we cannot exclude the possibility of a more complex rearrangement resulting in an ETV6 gene fusion. This sample is being considered for the Archer FusionPlex targeted RNAseq assay to help characterize any fusion transcript involving the ETV6 gene. If performed, the results will be reported under a separate case number.	MANUAL_OK	3to3	3to3	-		0	0	18	12	Intron of ETV6(+):5Kb before exon 5	ETV6	12017383			11	IGR: 178Kb before LRRC4C(-)	LRRC4C	39957491			10	TRANSLOCATION		0	188535	0	18	NEW_VARIANT
P-0021927-T01-IM6	APC (NM_000038) rearrangement: c.1312+557_c.1506del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2583	0	5	5	Intron of APC(+):557bp after exon 10	APC	112155598			5	Exon 12 of APC(+)	APC	112162902			10	DELETION		7304	188533	365	5	NEW_VARIANT
P-0021983-T01-IM6	IGF1R (NM_000875) rearrangement: t(6;15)(p23;q26.3)(chr6:g.13582729::chr15:g.99467786)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	16	15	Exon 13 of IGF1R(+)	IGF1R	99467786			6	5-UTR of SIRT5(+):2Kb before coding start	SIRT5	13582729			10	TRANSLOCATION		0	188893	0	17	NEW_VARIANT
P-0021983-T01-IM6	KDM6A (NM_021140) rearrangement: c.225+7397_c.2330del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23519	0	36	X	Intron of KDM6A(+):7Kb after exon 2	KDM6A	44740630			X	Exon 17 of KDM6A(+)	KDM6A	44929230			10	DELETION		188600	188891	8736	37	NEW_VARIANT
P-0021993-T01-IM6	AGO2 (NM_012154) rearrangement: c.768+28_c.23-22677dup	PRECISE	Note: The AGO2 rearrangement results in the in-frame duplication of exons 2-6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : in frame		9656	0	36	8	Intron of AGO2(-):27bp after exon 6	AGO2	141569466			8	Intron of AGO2(-):23Kb before exon 2	AGO2	141618087			10	DUPLICATION		48621	188885	12912	36	NEW_VARIANT
P-0022034-T01-IM6	PIK3R2 (NM_005027) Rearrangement: t(19,20)(p13.11,q13.33)(chr19:g.18271854::chr20:g.62118311)	PRECISE	Note: The PIK3R2 Rearrangement results in the possible truncation of PIK3R2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	20	Promoter of EEF1A2(-):1Kb from tx start	EEF1A2	62118311			19	Intron of PIK3R2(+):9bp before exon 5	PIK3R2	18271854			10	TRANSLOCATION		0	188823	0	13	NEW_VARIANT
P-0022044-T01-IM6	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)	PRECISE	Note: The EWSR1 - FEV fusion is predicted to be in-frame.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EWSR1:FEV}		0	0	56	22	Intron of EWSR1(+):468bp before exon 9	EWSR1	29684126			2	Intron of FEV(-):154bp after exon 2	FEV	219848798			10	TRANSLOCATION		0	189134	0	55	NEW_VARIANT
P-0022060-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.236+78:ERG_c.350-337:TMPRSS2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ERG:TMPRSS2}		26311	0	12	21	Intron of ERG(-):77bp after exon 2	ERG	39817249			21	Intron of TMPRSS2(-):337bp before exon 4	TMPRSS2	42861857			0	DUPLICATION		3044608	189234	10830	18	NEW_VARIANT
P-0022067-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2776:TMPRSS2_c.18+2138:ERGdel	PRECISE		MANUAL_OK	3to3	3to3	-		65597	0	3	21	Intron of ERG(-):2Kb after exon 1	ERG	39868149			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872882			7	INVERSION		3004733	189232	82599	2	NEW_VARIANT
P-0022138-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 fused with ALK exons 20-29): c.2333:EML4_c.3173-190:ALKinv	PRECISE	Note: The EML4 - ALK fusion includes the kinase domain of ALK. One of the breakpoints is within EML4 exon 20. This sample has been nominated for analysis using the Archer targeted RNAseq assay to help further characterize this fusion. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		167919	0	43	2	Intron of ALK(-):190bp before exon 20	ALK	29446584			2	Exon 20 of EML4(+)	EML4	42553384			10	INVERSION		13106800	189717	160288	38	NEW_VARIANT
P-0022174-T01-IM6	BRIP1 (NM_032043) rearrangement: c.1473_c.2098-9262del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6702	0	4	17	Intron of BRIP1(-):9Kb before exon 15	BRIP1	59831214			17	Exon 10 of BRIP1(-)	BRIP1	59870958			6	DELETION		39744	190343	9040	4	NEW_VARIANT
P-0022323-T01-IM6	EZH1 (NM_001991) - BRCA1 (NM_007294) Rearrangement : c.-102-4603:EZH1_c.5194-65:BRCA1dup	IMPPRECISE	Note: The EZH1 - BRCA1 Rearrangement results in the fusion of EZH1 5'UTR region and BRCA1 exon 19-23. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {EZH1:BRCA1}		9183	0	6	17	5-UTR of EZH1(-):33Kb before coding start	EZH1	40887539			17	Intron of BRCA1(-):65bp before exon 19	BRCA1	41209217			0	DUPLICATION		321678	190225	11588	6	NEW_VARIANT
P-0022323-T01-IM6	KMT2C (NM_170606) Rearrangement : t(7;21)(q36.1;p11.1)(chr7:g.151945542::chr21:g.11039050)	IMPPRECISE	Note: The KMT2C Rearrangement results in the possible truncation of KMT2C. One of the breakpoints is within exon14. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	1	14	21	3-UTR of BAGE2(-):11Kb after coding stop	BAGE2	11039050			7	Exon 14 of KMT2C(-)	KMT2C	151945542			0	TRANSLOCATION		0	190227	0	75	NEW_VARIANT
P-0022323-T01-IM6	DGAT1 (NM_012079) - RECQL4 (NM_004260) Rearrangement : c.1069:DGAT1_c.784:RECQL4dup	PRECISE	Note: The DGAT1 - RECQL4 Rearrangement results in the fusion of DGAT1 exon 1-13 with RECQL4 exon 5-22. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DGAT1:RECQL4}		40439	0	38	8	Exon 13 of DGAT1(-)	DGAT1	145541021			8	Exon 5 of RECQL4(-)	RECQL4	145741719			10	DUPLICATION		200698	190224	58831	41	NEW_VARIANT
P-0022346-T01-IM6	ALK (NM_004304) rearrangement: t(2;15)(q23.1;q23)(chr2:g.29448144::chr15:g.71944254)	PRECISE	Note: The ALK rearrangement is a translocation which may result in the truncation of exons 1-19. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	28	15	Intron of THSD4(+):9Kb before exon 7	THSD4	71944254			2	Intron of ALK(-):182bp after exon 19	ALK	29448144			10	TRANSLOCATION		0	190351	0	29	NEW_VARIANT
P-0022424-T01-IM6	ARID1A (NM_006015) - SEPT12 (NM_144605) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.27089562::chr16:g.4838352)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARID1A:SEPT12}		0	0	10	16	5-UTR of SEPT12(-):11Kb before coding start	SEPT12	4838352			1	Exon 8 of ARID1A(+)	ARID1A	27089562			10	TRANSLOCATION		0	190844	0	10	NEW_VARIANT
P-0022424-T01-IM6	PDGFRA (NM_006206) rearrangement: t(4;8)(q12;q22.3)(chr4:g.55130160::chr8:g.103867353)	IMPPRECISE	Note: The PDGFRA rearrangement is a translocation which may result in a truncation of PDGFRA exons 1-3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {PDGFRA:AZIN1}		0	0	7	8	5-UTR of AZIN1(-):27Kb before coding start	AZIN1	103867353			4	Intron of PDGFRA(+):66bp after exon 4	PDGFRA	55130160			0	TRANSLOCATION		0	190842	0	7	NEW_VARIANT
P-0022427-T01-IM6	EGFR (NM_005228) rearrangement: c.2062-378_c.3070del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		29076	0	25	7	Intron of EGFR(+):377bp before exon 18	EGFR	55241236			7	Exon 25 of EGFR(+)	EGFR	55269004			0	DELETION		27768	190831	31369	39	NEW_VARIANT
P-0022470-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2657:TMPRSS2_c.40-63048:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52306	0	184	21	Intron of ERG(-):63Kb before exon 4	ERG	39880592			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872773			10	DELETION		2992181	191027	115108	211	NEW_VARIANT
P-0022558-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.530-1560_c.959del	PRECISE	Note: The TGFBR2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2780	0	10	3	Intron of TGFBR2(+):2Kb before exon 5	TGFBR2	30711570			3	Exon 5 of TGFBR2(+)	TGFBR2	30713559			10	DELETION		1989	191266	3128	10	NEW_VARIANT
P-0022800-T01-IM6	STK11 (NM_000455) - ARID3A (NM_005224) Rearrangement : c.80:STK11_c.-601:ARID3Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {STK11:ARID3A}		1364	0	7	19	Promoter of ARID3A(+):310bp from tx start	ARID3A	925726			19	Exon 1 of STK11(+)	STK11	1206992			10	DUPLICATION		281266	192299	1615	7	NEW_VARIANT
P-0022800-T01-IM6	FCAR (NM_002000) - PTPRS (NM_002850) Rearrangement :  c.71-2885:FCAR_c.265:PTPRSinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {FCAR:PTPRS}		1350156	0	36	19	Exon 4 of PTPRS(-)	PTPRS	5273567			19	Intron of FCAR(+):3Kb before exon 2	FCAR	55393762			10	INVERSION		50120195	192306	1528787	36	NEW_VARIANT
P-0022911-T01-IM6	ERBB2 (NM_004448) rearrangement: c.226-238_c.3557del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		71838	0	16	17	Intron of ERBB2(+):237bp before exon 3	ERBB2	37864336			17	Exon 27 of ERBB2(+)	ERBB2	37884086			10	DELETION		19750	192704	49851	16	NEW_VARIANT
P-0022967-T01-IM6	ATR (NM_001184) Rearrangement : c.2633+72_c.3172-268del	PRECISE	Note: The ATR Rearrangement results in the intragenic deletion of exons 12-15. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		4398	0	17	3	Intron of ATR(-):268bp before exon 16	ATR	142267020			3	Intron of ATR(-):71bp after exon 12	ATR	142272410			10	DELETION		5390	193179	6249	18	NEW_VARIANT
P-0023071-T01-IM6	NF1 (NM_001042492) rearrangement: c.60+26655:NF1_chr17:g.29095928dup	PRECISE	Note: The NF1 rearrangement is a duplication which results in the duplication of exon 1. its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {NF1:SUZ12P1}		4145	0	16	17	5-UTR of SUZ12P1(+):1Kb before coding start	SUZ12P1	29095928			17	Intron of NF1(+):27Kb after exon 1	NF1	29449042			10	DUPLICATION		353114	193832	4926	53	NEW_VARIANT
P-0023091-T01-IM6	KMT2B (NM_014727) rearrangement: c.5276+39:KMT2B_chr19:g.47210279del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		234188	0	11	19	Intron of KMT2B(+):39bp after exon 25	KMT2B	36221556			19	Intron of PRKD2(-):2Kb before exon 5	PRKD2	47210279			10	DELETION		10988723	193997	297467	16	NEW_VARIANT
P-0023091-T01-IM6	NBN (NM_002485) rearrangement: c.1063:NBN_chr8:g.90544955del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10544	0	2	8	IGR: 185Kb before LOC101929709(-)	LOC101929709	90544955			8	Exon 9 of NBN(-)	NBN	90971014			7	DELETION		426059	193996	10178	2	NEW_VARIANT
P-0023102-T01-IM6	BRCA1 (NM_007294) rearrangement: chr17:g.39859920_c.3986inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		162626	0	4	17	IGR: 9Kb before GAST(+)	GAST	39859920			17	Exon 10 of BRCA1(-)	BRCA1	41243562			10	INVERSION		1383642	193954	153414	4	NEW_VARIANT
P-0023119-T01-IM6	RAD21 (NM_006265) - CDH1 (NM_004360) rearrangement: t(8;16)(q24.11;q22.1)(chr8:g.117864146::chr16:g.68852231)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {RAD21:CDH1}		0	0	5	16	Intron of CDH1(+):951bp before exon 11	CDH1	68852231			8	Intron of RAD21(-):40bp after exon 11	RAD21	117864146			10	TRANSLOCATION		0	194100	0	5	NEW_VARIANT
P-0023192-T01-IM6	RNF43 (NM_017763) rearrangement: c.123:RNF43_chr17:g.56511985inv	PRECISE	Note: The RNF43 rearrangement is an inversion with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		686	0	9	17	Exon 2 of RNF43(-)	RNF43	56492816			17	Intron of HSF5(-):12Kb before exon 6	HSF5	56511985			9	INVERSION		19169	194333	699	9	NEW_VARIANT
P-0023192-T01-IM6	KDM5C (NM_004187) rearrangement: c.1851_c.*3936del	PRECISE	Note: The KDM5C rearrangement is a deletion of exons 13-26. One of the breakpoints is within exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		39146	0	31	X	Promoter of KDM5C(-):2Kb from tx start	KDM5C	53218213			X	Exon 13 of KDM5C(-)	KDM5C	53231051			10	DELETION		12838	194331	35753	32	NEW_VARIANT
P-0023273-T01-IM6	INPPL1 (NM_001567) rearrangement: chr11:g.64878485_c.3664:INPPL1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		153370	0	20	11	Intron of VPS51(+):232bp after exon 9	VPS51	64878485			11	Exon 27 of INPPL1(+)	INPPL1	71949197			10	INVERSION		7070712	194545	308470	23	NEW_VARIANT
P-0023324-T01-IM6	FGFR2 (NM_000141) rearrangement: c.*320_chr10:g.123403273inv	PRECISE	Note: The FGFR2 rearrangement results in the inversion of exons 1-18. One of the breakpoints is within the 3' UTR of FGFR2. 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.	MANUAL_OK	5to5	5to5	-		93307	0	21	10	3-UTR of FGFR2(-):319bp after coding stop	FGFR2	123239051			10	IGR: 97Kb before ATE1(-)	ATE1	123403273			10	INVERSION		164222	194732	77523	22	NEW_VARIANT
P-0023324-T01-IM6	CARM1 (NM_199141) - DNM2 (NM_001005361) rearrangement: c.1020+2:CARM1_c.161+4368:DNM2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CARM1:DNM2}		15929	0	8	19	Intron of DNM2(+):4Kb after exon 1	DNM2	10833447			19	Intron of CARM1(+):2bp after exon 8	CARM1	11027455			8	DUPLICATION		194008	194731	12808	8	NEW_VARIANT
P-0023464-T01-IM6	ERBB4 (NM_005235) Rearrangement : chr2:g.212109143_c.997+95del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		37651	0	11	2	IGR: 131Kb before ERBB4(-)	ERBB4	212109143			2	Intron of ERBB4(-):94bp after exon 8	ERBB4	212578165			10	DELETION		469022	195527	35225	11	NEW_VARIANT
P-0023546-T02-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+796_c.55+2609del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		59955	0	63	21	Intron of TMPRSS2(-):795bp after exon 2	TMPRSS2	42869250			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42877268			10	DELETION		8018	195822	41412	70	NEW_VARIANT
P-0023588-T01-IM6	POLD1 (NM_002691) - SIGLECL1(NM_173635) Rearrangement : c.2429:POLD1_c.-191+1669:SIGLECL1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {POLD1:SIGLECL1}		17739	0	27	19	Exon 20 of POLD1(+)	POLD1	50918112			19	5-UTR of SIGLECL1(+):10Kb before coding start	SIGLECL1	51762823			10	DELETION		844711	196067	9213	29	NEW_VARIANT
P-0023588-T01-IM6	APC (NM_000038) Rearrangement : c.4714:APC_chr5:g.112187884del	PRECISE	Note: The APC Rearrangement results in the intragenic deletion of exon16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		22138	0	13	5	Exon 16 of APC(+)	APC	112176005			5	IGR: 9Kb before SRP19(+)	SRP19	112187884			10	DELETION		11879	196066	16957	14	NEW_VARIANT
P-0023603-T01-IM6	TSC1 (NM_000368) rearrangement: t(1;9)(q41,q34.13)(chr1:g.222846177::chr9:g.135779003)	PRECISE	Note: The TSC1 rearrangement is a translocation which may result in the truncation of exons 18-23. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TSC1:AIDA}		0	0	44	9	Intron of TSC1(-):34bp after exon 17	TSC1	135779003			1	Intron of AIDA(-):477bp after exon 8	AIDA	222846177			10	TRANSLOCATION		0	196123	0	44	NEW_VARIANT
P-0023707-T01-IM6	TP53 (NM_000546) - EFNB3 (NM_001406) Rearrangement : c.-28-596:TP53_c.123-693inv	PRECISE	Note: The TP53-EFNB3 Rearrangement results in the fusion of exon1 of TP53 with EFNB3 exons 2-5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {TP53:EFNB3}		1685	0	7	17	5-UTR of TP53(-):8Kb before coding start	TP53	7580536			17	Intron of EFNB3(+):692bp before exon 2	EFNB3	7610583			10	INVERSION		30047	196705	1221	7	NEW_VARIANT
P-0023707-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon 4):c.127-1486:TMPRSS2_c.40-60882:ERGdel	PRECISE	Note: The TMPRSS2  - ERG fusion is an in-frame fusion .	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32972	0	20	21	Intron of ERG(-):61Kb before exon 4	ERG	39878426			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867991			10	DELETION		2989565	196704	21329	20	NEW_VARIANT
P-0023707-T01-IM6	SDHA (NM_004168) Rearrangement : chr5:g.55450_c.1001del	PRECISE	Note: The SDHA Rearrangement results in the deletion of exons 1-8. One of the breakpoints is within exon8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		12084	0	21	5	IGR: 85Kb before PLEKHG4B(+)	PLEKHG4B	55450			5	Exon 8 of SDHA(+)	SDHA	233697			10	DELETION		178247	196703	8171	27	NEW_VARIANT
P-0023821-T01-IM6	ATF7 (NM_006856) - BRAF (NM_004333) Rearrangement :  t(7;12)(q34;q13.13)(chr7:g.140483233::chr12:g. 53913299)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ATF7:BRAF}		0	0	53	12	Intron of ATF7(-):2Kb before exon 12	ATF7	53913299			7	Intron of BRAF(-):276bp before exon 10	BRAF	140483233			10	TRANSLOCATION		0	196971	0	57	NEW_VARIANT
P-0023848-T01-IM6	CDKN1B (NM_004064) Rearrangement : c.167_c.*269del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		1529	0	22	12	Exon 1 of CDKN1B(+)	CDKN1B	12870940			12	3-UTR of CDKN1B(+):3Kb after coding stop	CDKN1B	12874230			10	DELETION		3290	197070	2889	25	NEW_VARIANT
P-0023961-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG re-arrangement is a non-canonical gene fusion.	MANUAL_OK	3to5	3to5	-		37880	0	285	21	3-UTR of ERG(-):83Kb after coding stop	ERG	39950968			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868036			10	DELETION		2917068	197444	35394	316	NEW_VARIANT
P-0023961-T01-IM6	EGFL7 (NM_201446) - TNS1 (NM_022648) rearrangement: t(2;9)(q35;q34.3)(chr2:g.218708823::chr9:g.139566440)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EGFL7:TNS1}		0	0	85	9	Exon 8 of EGFL7(+)	EGFL7	139566440			2	Intron of TNS1(-):3Kb after exon 17	TNS1	218708823			10	TRANSLOCATION		0	197447	0	82	NEW_VARIANT
P-0024095-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.72920652::chr21:g.42874147)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	7	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874147			15	IGR: 26Kb before GOLGA6B(+)	GOLGA6B	72920652			10	TRANSLOCATION		0	198117	0	30	NEW_VARIANT
P-0024263-T01-IM6	RB1 (NM_000321) Rearrangement : c.-1480_c.107del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		505	0	13	13	Promoter of RB1(+):1Kb from tx start	RB1	48876569			13	Exon 1 of RB1(+)	RB1	48878155			10	DELETION		1586	199094	233	13	NEW_VARIANT
P-0024344-T01-IM6	BRD4 (NM_058243) - SORCS1 (NM_001013031) rearrangement: t(10;19)(q25.1;p13.2)(chr10:g.108617375::chr19:g.15355232)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BRD4:SORCS1}		0	0	12	19	Exon 13 of BRD4(-)	BRD4	15355232			10	Intron of SORCS1(-):28Kb before exon 3	SORCS1	108617375			10	TRANSLOCATION		0	199684	0	12	NEW_VARIANT
P-0024406-T01-IM6	FOXP1 (NM_001244814) rearrangement: chr3:g.69943237_c.1443del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		15624	0	2	3	Intron of MITF(+):15Kb after exon 2	MITF	69943237			3	Exon 13 of FOXP1(-)	FOXP1	71026179			6	DELETION		1082942	200033	27529	2	NEW_VARIANT
P-0024488-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+2968:TMPRSS2_c.39+16108:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		109844	0	20	21	Intron of ERG(-):16Kb after exon 3	ERG	39931478			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876909			10	DELETION		2945431	200229	67974	22	NEW_VARIANT
P-0024516-T01-IM6	ROS1 (NM_002944) rearrangement: c.1165-29_c.2496+901dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : in frame		8651	0	43	6	Intron of ROS1(-):900bp after exon 16	ROS1	117703579			6	Intron of ROS1(-):29bp before exon 11	ROS1	117714513			10	DUPLICATION		10934	200515	15935	48	NEW_VARIANT
P-0024526-T01-IM6	CDKN2A (NM_000077) rearrangement: c.457+112:CDKN2A_chr9:g.21814419del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		2342	0	18	9	Intron of MTAP(+):1Kb before exon 2	MTAP	21814419			9	Intron of CDKN2A(-):111bp after exon 2	CDKN2A	21970789			10	DELETION		156370	200641	1327	18	NEW_VARIANT
P-0024614-T01-IM6	ERCC5 (NM_000123) rearrangement: c.3314:ERCC5_chr13:g.88748664inv	PRECISE	Note: The ERCC5 rearrangement is an inversion of exon 1-15. One of the breakpoints is within exon 15. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		25194	0	13	13	IGR: 295Kb before LINC00397(-)	LINC00397	88748664			13	Exon 15 of ERCC5(+)	ERCC5	103528006			10	INVERSION		14779342	200791	43584	13	NEW_VARIANT
P-0024721-T01-IM6	KMT2D (NM_003482) rearrangement: chr12:g.44815829_c.5868-95:KMT2Ddel	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 1-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		127746	0	16	12	IGR: 86Kb before NELL2(-)	NELL2	44815829			12	Intron of KMT2D(-):95bp before exon 28	KMT2D	49436208			10	DELETION		4620379	201136	62906	17	NEW_VARIANT
P-0024848-T01-IM6	PTPRT (NM_133170) - EPB41L1 (NM_012156) rearrangement: c.2281:PTPRT_c.2439+506:EPB41L1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PTPRT:EPB41L1}		49478	0	38	20	Intron of EPB41L1(+):506bp after exon 20	EPB41L1	34808272			20	Exon 15 of PTPRT(-)	PTPRT	40877415			10	INVERSION		6069143	202185	156640	54	NEW_VARIANT
P-0024959-T01-IM6	MSI2 (NM_138962) rearrangement: c.*7:MSI2_chr17:g.46887323del	PRECISE	Note: The MSI2 rearrangement results in the deletion of exons 1-13. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		30545	0	5	17	Intron of TTLL6(-):5Kb before exon 2	TTLL6	46887323			17	3-UTR of MSI2(+):420Kb after coding stop	MSI2	55754396			10	DELETION		8867073	202156	90154	5	NEW_VARIANT
P-0025013-T01-IM6	BCL2L14 (NM_138722) -ETV6 (NM_001987)  Rearrangement :  c.945+502:BCL2L14_c.1009+2450:ETV6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BCL2L14:ETV6}		70419	0	11	12	Intron of ETV6(+):2Kb after exon 5	ETV6	12025353			12	Intron of BCL2L14(+):502bp after exon 5	BCL2L14	12248366			10	DUPLICATION		223013	203106	141838	11	NEW_VARIANT
P-0025013-T01-IM6	SH2B3 (NM_005475) - CUX2(NM_015267) Rearrangement: c.901:SH2B3_c.175-230:CUX2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SH2B3:CUX2}		6029	0	16	12	Intron of CUX2(+):229bp before exon 3	CUX2	111655464			12	Exon 4 of SH2B3(+)	SH2B3	111884812			10	DUPLICATION		229348	203107	11874	16	NEW_VARIANT
P-0025130-T01-IM6	VSIG10 (NM_019086 ) - VTCN1 (NM_024626) Rearrangement :  t(1;12)(p12;q24.22)(chr1:g.117753552; chr12:g.118524554)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {VSIG10:VTCN1}		0	0	7	12	Intron of VSIG10(-):4Kb before exon 3	VSIG10	118524554			1	5-UTR of VTCN1(-):63Kb before coding start	VTCN1	117753552			10	TRANSLOCATION		0	203919	0	7	NEW_VARIANT
P-0025130-T01-IM6	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) Rearrangement:  c.337-451:RAB11FIP4_c.5813-1:NF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RAB11FIP4:NF1}		23303	0	69	17	Exon 40 of NF1(+)	NF1	29661855			17	Intron of RAB11FIP4(+):450bp before exon 4	RAB11FIP4	29844218			10	DUPLICATION		182363	203918	30970	78	NEW_VARIANT
P-0025137-T01-IM6	ASIC2 (NM_001094) - RAD51D (NM_133629) Rearrangement : c.556-520534:ASIC2_c.322:RAD51Ddup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ASIC2:RAD51D}		5694	0	7	17	Intron of ASIC2(-):521Kb before exon 2	ASIC2	31959619			17	Exon 4 of RAD51D(-)	RAD51D	33430482			0	DUPLICATION		1470863	203934	7330	8	NEW_VARIANT
P-0025137-T01-IM6	TMPRSS2 (NM_001135099) -  ERG (NM_182918) Fusion (TMPRSS2 exon 2 fused with ERG exon 3): c.126+367:TMPRSS2_c.237-934:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		41840	0	109	21	Intron of ERG(-):934bp before exon 3	ERG	39796417			21	Intron of TMPRSS2(-):366bp after exon 2	TMPRSS2	42869679			10	DELETION		3073262	203933	36218	119	NEW_VARIANT
P-0025201-T01-IM6	NCOR1 (NM_006311) rearrangement: c.6536+1_c.6955+550del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5518	0	22	17	Intron of NCOR1(-):549bp after exon 44	NCOR1	15942197			17	Exon 41 of NCOR1(-)	NCOR1	15952158			10	DELETION		9961	204834	5617	25	NEW_VARIANT
P-0025319-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-607:TMPRSS2_c.40-55236:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		27053	0	54	21	Promoter of ERG(-):121Kb from tx start	ERG	39872780			21	Intron of TMPRSS2(-):607bp before exon 2	TMPRSS2	42870723			10	DELETION		2997943	205325	27007	59	NEW_VARIANT
P-0025319-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.938_c.794+1011inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1026	0	24	21	Exon 9 of TMPRSS2(-)	TMPRSS2	42845324			21	Intron of TMPRSS2(-):1Kb after exon 7	TMPRSS2	42850088			10	INVERSION		4764	205327	1233	23	NEW_VARIANT
P-0025332-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+4096:TMPRSS2_c.40-55162:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		69982	0	96	21	Promoter of ERG(-):121Kb from tx start	ERG	39872706			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875781			10	DELETION		3003075	205373	67737	106	NEW_VARIANT
P-0025342-T01-IM6	MGAT1 (NM_001114617) - FLT4 (NM_182925) rearrangement: c.-127+1128:MGAT1_c.3097-204:FLT4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {MGAT1:FLT4}		30682	0	3	5	Intron of FLT4(-):204bp before exon 23	FLT4	180043693			5	5-UTR of MGAT1(-):16Kb before coding start	MGAT1	180234520			9	DELETION		190827	205415	47051	3	NEW_VARIANT
P-0025395-T01-IM6	RET (NM_020975) rearrangement: c.626-18:RET_chr10:g.54301305inv	PRECISE	Note: The RET rearrangement is an inversion with a breakpoint in intron 3 and could involve the exons 4-20, which include the kinase domain. 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 RET gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	-		68856	0	33	10	Intron of RET(+):17bp before exon 4	RET	43600382			10	IGR: 91Kb before LINC01468(-)	LINC01468	54301305			10	INVERSION		10700923	205599	114067	43	NEW_VARIANT
P-0025408-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.706:PIK3R3_chr1:g.204357692inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		470171	0	10	1	Exon 6 of PIK3R3(-)	PIK3R3	46527659			1	IGR: 15Kb before PPP1R15B(-)	PPP1R15B	204357692			10	INVERSION		157830033	205624	687341	10	NEW_VARIANT
P-0025414-T01-IM6	FOXO1 (NM_002015) rearrangement: c.1774:FOXO1_chr13:g.105039234inv	PRECISE	Note: The FOXO1 rearrangement is an inversion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		161822	0	25	13	Exon 2 of FOXO1(-)	FOXO1	41133854			13	IGR: 962Kb before LINC01309(+)	LINC01309	105039234			10	INVERSION		63905380	205651	203265	32	NEW_VARIANT
P-0010823-T02-IM6	IKZF1 (NM_006060) Rearrangement : c.1446:IKZF1_chr7:g.52483056inv	PRECISE	Note: The IKZF1 Rearrangement results in the  inversion of exon8.One of the breakpoints is within exon8. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2866	0	14	7	Exon 8 of IKZF1(+)	IKZF1	50468207			7	IGR: 620Kb before POM121L12(+)	POM121L12	52483056			10	INVERSION		2014849	205807	5627	20	NEW_VARIANT
P-0025376-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		105217	0	17	2	Intron of ALK(-):350bp before exon 20	ALK	29446744			2	Intron of EML4(+):6Kb before exon 6	EML4	42502362			10	INVERSION		13055618	205548	162367	17	NEW_VARIANT
P-0025379-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.8197:ZFHX3_chr16:g.72806055del	PRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 9-10. One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		15073	0	70	16	IGR: 11Kb before ZFHX3(-)	ZFHX3	72806055			16	Exon 9 of ZFHX3(-)	ZFHX3	72828384			10	DELETION		22329	205560	3455	141	NEW_VARIANT
P-0025390-T02-IM6	FGFR1 (NM_001174067) - WHSC1L1 (NM_023034) rearrangement: c.1756+74:FGFR1_c.675+3313:WHSC1L1del	IMPPRECISE	Note: The FGFR1 - WHSC1L1 rearrangement is a deletion that results in the fusion of FGFR1 exons 1-13 with WHSC1L1 exon 3-24. The functional significance is undetermined. This is the same fusion that was reported on IMPACT (M17-31956) that was then reflexed to Archer (See M17-34051) for further characterization.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {FGFR1:WHSC1L1}		19107	0	8	8	Intron of WHSC1L1(-):3Kb after exon 2	WHSC1L1	38201702			8	Intron of FGFR1(-):73bp after exon 13	FGFR1	38274750			0	DELETION		73048	206189	139803	8	NEW_VARIANT
P-0025405-T01-IM6	NOTCH1 (NM_017617) - AGPAT2 (NM_006412) rearrangement: c.4396:NOTCH1_c.183-2771:AGPAT2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NOTCH1:AGPAT2}		51507	0	2	9	Exon 25 of NOTCH1(-)	NOTCH1	139399952			9	Intron of AGPAT2(-):3Kb before exon 2	AGPAT2	139574779			10	DUPLICATION		174827	205632	70635	3	NEW_VARIANT
P-0025454-T01-IM6	CSF3R (NM_000760) rearrangement: c.1958+31:CSF3R_chr1:g.208621201inv	PRECISE	Note: The CSF3R rearrangement is an inversion of exons 1-15. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		549709	0	59	1	Intron of CSF3R(-):30bp after exon 15	CSF3R	36933128			1	IGR: 426Kb before PLXNA2(-)	PLXNA2	208621201			10	INVERSION		171688073	206052	785044	79	NEW_VARIANT
P-0025455-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		50895	0	56	21	Intron of ERG(-):2Kb after exon 1	ERG	39868589			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872283			10	DELETION		3003694	206047	53673	61	NEW_VARIANT
P-0025468-T01-IM6	WHSC1L1 (NM_023034) rearrangement: chr8:g.37073664_c.748-1:WHSC1L1inv	PRECISE	Note: The WHSC1L1 rearrangement is an inversion with a breakpoint is intron 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		39063	0	39	8	IGR: 190Kb before LOC100507420(-)	LOC100507420	37073664			8	Intron of WHSC1L1(-):1bp before exon 4	WHSC1L1	38194986			10	INVERSION		1121322	205735	66849	43	NEW_VARIANT
P-0025507-T01-IM6	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)	PRECISE	Note: The ETV6-NTRK3 fusion is predicted to be in-frame and includes the kinase domain of NTRK3.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	31	15	Intron of NTRK3(-):32Kb after exon 14	NTRK3	88544573			12	Intron of ETV6(+):1Kb after exon 5	ETV6	12024078			10	TRANSLOCATION		0	205828	0	29	NEW_VARIANT
P-0025531-T01-IM6	NCOA4 (NM_001145260) RET (NM_020975) fusion: c.619-108NCOA4_c.2137-657RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		14832	0	43	10	Intron of RET(+):656bp before exon 12	RET	43611375			10	Intron of TIMM23B(+):150Kb before exon 7	TIMM23B	51582688			10	DUPLICATION		7971313	205836	30125	44	NEW_VARIANT
P-0025550-T01-IM6	KMT2D (NM_003482) rearrangement: c.840-14_c.10232-1071del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion of exons 7-34. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 28 exons : out of frame		81471	0	5	12	Intron of KMT2D(-):1Kb before exon 35	KMT2D	49429789			12	Intron of KMT2D(-):14bp before exon 7	KMT2D	49447118			10	DELETION		17329	205875	50635	6	NEW_VARIANT
P-0025558-T01-IM6	CDH1(NM_004360) Rearrangement : c.388-1507_c.434del	PRECISE	Note: The CDH1Rearrangement results in the intragenic deletion of exon4 of CDH1. One of the breakpoint is within exon4.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		685	0	22	16	Intron of CDH1(+):2Kb before exon 4	CDH1	68840820			16	Exon 4 of CDH1(+)	CDH1	68842373			10	DELETION		1553	205933	840	22	NEW_VARIANT
P-0025571-T01-IM6	FOXA1 (NM_004496) - MIPOL1 (NM_138731) rearrangement: c.-25:FOXA1_c.1032-12901:MIPOL1dup	PRECISE	Note: The FOXA1 - MIPOL1 rearrangement is a duplication with breakpoints within the FOXA1 5 UTR and MIPOL1 intron 13. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		10412	0	26	14	Intron of MIPOL1(+):13Kb before exon 14	MIPOL1	37956212			14	5-UTR of FOXA1(-):4Kb before coding start	FOXA1	38064202			10	DUPLICATION		107990	205987	12775	44	NEW_VARIANT
P-0025571-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10 ):  c.56-2748:TMPRSS2_c.18+2970:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		65171	0	91	21	Intron of ERG(-):3Kb after exon 1	ERG	39867317			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872864			10	DELETION		3005547	205986	58042	94	NEW_VARIANT
P-0025591-T01-IM6	WHSC1L1 (NM_023034) rearrangement: chr8:g.37147510_c.1986+96inv	PRECISE	Note: The WHSC1L1 rearrangement results in the inversion of exons 11-24. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		24096	0	5	8	IGR: 116Kb before LOC100507420(-)	LOC100507420	37147510			8	Intron of WHSC1L1(-):95bp after exon 10	WHSC1L1	38173334			10	INVERSION		1025824	206158	41034	6	NEW_VARIANT
P-0025595-T01-IM6	PIK3R2 (NM_005027) - RXRB (NM_021976) rearrangement: t(6;19)(p21.32;p13.11)(chr6:g.33164798::chr19:g.18273076)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PIK3R2:RXRB}		0	0	5	19	Exon 8 of PIK3R2(+)	PIK3R2	18273076			6	Intron of RXRB(-):415bp before exon 5	RXRB	33164798			10	TRANSLOCATION		0	206197	0	5	NEW_VARIANT
P-0025603-T01-IM6	CREBBP (NM_004380) rearrangement: c.2965_c.5504del	PRECISE	Note: The CREBBP rearrangement is an intragenic deletion of exons 15-31. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		31962	0	63	16	Exon 31 of CREBBP(-)	CREBBP	3779544			16	Exon 15 of CREBBP(-)	CREBBP	3819270			10	DELETION		39726	206233	30438	73	NEW_VARIANT
P-0025603-T01-IM6	EGFR (NM_005228) rearrangement: c.1201_c.1632-102inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		4864	0	15	7	Exon 10 of EGFR(+)	EGFR	55224519			7	Intron of EGFR(+):101bp before exon 14	EGFR	55231324			10	INVERSION		6805	206234	7479	15	NEW_VARIANT
P-0025609-T01-IM6	SHROOM3 (NM_020859) - RET (NM_020975) rearrangement:  t(4;10)(q21.1;q11.21)(chr4:g.77664882::chr10:g.43611545)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SHROOM3:RET}		0	0	47	10	Intron of RET(+):486bp before exon 12	RET	43611545			4	Intron of SHROOM3(+):2Kb after exon 5	SHROOM3	77664882			10	TRANSLOCATION		0	206229	0	51	NEW_VARIANT
P-0025609-T01-IM6	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.2446+369:TMPRSS9_c.708-36:DOT1Ldup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TMPRSS9:DOT1L}		57676	0	71	19	Intron of DOT1L(+):35bp before exon 9	DOT1L	2202663			19	Intron of TMPRSS9(+):369bp after exon 13	TMPRSS9	2422614			10	DUPLICATION		219951	206224	112634	76	NEW_VARIANT
P-0025609-T01-IM6	FAT1 (NM_005245) rearrangement: c.4323+116_chr4:g.187770197inv	PRECISE	Note: The FAT1 rearrangement is an inversion that includes FAT1 exons  1-7. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		38561	0	18	4	Intron of FAT1(-):115bp after exon 7	FAT1	187554722			4	IGR: 261Kb before FAT1(-)	FAT1	187770197			10	INVERSION		215475	206226	60741	18	NEW_VARIANT
P-0025609-T01-IM6	FGFR4 (NM_213647) - DPP10 (NM_001178034) rearrangement: t(2;5)(q14.1;q35.2)(chr2:g.115223375::chr5:g.176518727)	PRECISE	Note: The FGFR4 - DPP10 rearrangement is a translocation with breakpoints within FGFR4 exon 6 and DPP10 intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	38	5	Exon 6 of FGFR4(+)	FGFR4	176518727			2	Intron of DPP10(+):23Kb after exon 1	DPP10	115223375			10	TRANSLOCATION		0	206228	0	56	NEW_VARIANT
P-0025686-T01-IM6	TP53 (NM_000546) rearrangement: c.994-1104_c.1157del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2113	0	17	17	Exon 11 of TP53(-)	TP53	7572952			17	Intron of TP53(-):1Kb before exon 10	TP53	7575137			10	DELETION		2185	206467	1522	18	NEW_VARIANT
P-0025693-T01-IM6	DNMT1 (NM_001379) rearrangement: t(1;19)(p11.2;p13.2)(chr1:g.121485157::chr19:g.10270971)	PRECISE	Note: The DNMT1 rearrangement is a translocation with a breakpoint within intron DNMT1 intron 13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	22	19	Intron of DNMT1(-):88bp after exon 13	DNMT1	10270971			1	IGR: 224Kb before EMBP1(+)	EMBP1	121485157			10	TRANSLOCATION		0	206483	0	38	NEW_VARIANT
P-0025693-T01-IM6	SMARCA4 (NM_003072) - PLIN4 (NM_001080400) rearrangement: c.1419+91:SMARCA4_c.214-57:PLIN4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SMARCA4:PLIN4}		179376	0	12	19	Intron of PLIN4(-):57bp before exon 3	PLIN4	4513773			19	Intron of SMARCA4(+):91bp after exon 8	SMARCA4	11102090			10	INVERSION		6588317	206481	207831	12	NEW_VARIANT
P-0025693-T01-IM6	DNMT1 (NM_001379) rearrangement: c.843+61_chr19:g.30723700inv	PRECISE	Note: The DNMT1 rearrangement is an inversion that includes DNMT1 exons 1-10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		320730	0	38	19	Intron of DNMT1(-):60bp after exon 10	DNMT1	10277213			19	IGR: 140Kb before ZNF536(+)	ZNF536	30723700			10	INVERSION		20446487	206482	372303	41	NEW_VARIANT
P-0025693-T01-IM6	SMARCA4 (NM_003072) - YJEFN3 (NM_001190328) rearrangement:  c.2859+122:SMARCA4_c.169-43C:YJEFN3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {SMARCA4:YJEFN3}		238146	0	8	19	Intron of SMARCA4(+):122bp after exon 19	SMARCA4	11132765			19	Intron of YJEFN3(+):42bp before exon 3	YJEFN3	19645800			10	DELETION		8513035	206477	265904	8	NEW_VARIANT
P-0025693-T01-IM6	DNAJB13 (NM_153614) - PODNL1 (NM_001146254) rearrangement: c.211+1:DNAJB1_c.18+1046:PODNL1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNAJB1:PODNL1}		11313	0	46	19	Intron of PODNL1(-):1Kb after exon 1	PODNL1	14062885			19	Exon 1 of DNAJB1(-)	DNAJB1	14628950			10	DELETION		566065	206478	11448	50	NEW_VARIANT
P-0025693-T01-IM6	UPF1 (NM_002911) rearrangement: chr19:g.18703364_c.2458-32del	PRECISE	Note: The UPF1 rearrangement is a deletion that includes UPF1 exons 1-17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {C19orf60:UPF1}		21757	0	23	19	Promoter of C19orf60(+):4Kb from tx start	C19orf60	18703364			19	Intron of UPF1(+):31bp before exon 18	UPF1	18972787			10	DELETION		269423	206479	22610	24	NEW_VARIANT
P-0025698-T01-IM6	MTOR (NM_004958) rearrangement: chr1:g.31397626_c.1615del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		154112	0	7	1	Exon 11 of MTOR(-)	MTOR	11300531			1	IGR: 7Kb before PUM1(-)	PUM1	31397626			10	DELETION		20097095	206470	226205	7	NEW_VARIANT
P-0025663-T01-IM6	PRKCI (NM_002740) rearrangement: chr3:g.163003734_c.102-9:PRKCIinv	PRECISE	Note: The PRKCI rearrangement is an inversion with a breakpoint in intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4477	0	6	3	3-UTR of LINC01192(-):17Kb after coding stop	LINC01192	163003734			3	Intron of PRKCI(+):8bp before exon 2	PRKCI	169953009			10	INVERSION		6949275	206354	5408	13	NEW_VARIANT
P-0008504-T03-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion ( CCDC6 exons 1-8 fused to RET exons 12-20): c.1230+499:CCDC6_c.2136+399:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET. 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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		11832	0	39	10	Intron of RET(+):399bp after exon 11	RET	43610583			10	Intron of CCDC6(-):498bp after exon 8	CCDC6	61553732			10	INVERSION		17943149	205865	27097	49	NEW_VARIANT
P-0025637-T01-IM6	SMARCA4 (NM_003072) - CARM1 (NM_199141) Rearrangement : c.1593+9:SMARCA4_c.220+16280:NF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SMARCA4:CARM1}		26546	0	47	19	Intron of CARM1(+):16Kb after exon 1	CARM1	10998878			19	Intron of SMARCA4(+):9bp after exon 9	SMARCA4	11105686			10	DUPLICATION		106808	206276	50726	48	NEW_VARIANT
P-0025642-T01-IM6	EP300 (NM_001429) Rearrangement : c.94+9078_c.3672-121del	PRECISE	Note: The EP300 Rearrangement results in the intragenic deletion of exons 2-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 19 exons : out of frame		33236	0	6	22	Intron of EP300(+):9Kb after exon 1	EP300	41498180			22	Intron of EP300(+):120bp before exon 21	EP300	41558606			8	DELETION		60426	206284	29952	7	NEW_VARIANT
P-0025647-T01-IM6	MAP3K14 (NM_003954) Rearrangement :  t(17;19)(q21.31;p13.3)(chr17:g.43364016::chr19:g.50046598)	PRECISE	Note: The MAP3K14 Rearrangement results in the possible truncation of MAP3K14 with a breakpoint of exon5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MAP3K14:SHC2}		0	0	6	19	Promoter of SHC2(-):2Kb from tx start	SHC2	414516			17	Exon 5 of MAP3K14(-)	MAP3K14	43364016			10	TRANSLOCATION		0	206317	0	7	NEW_VARIANT
P-0025650-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 3) : c.56-2498:TMPRSS2_c.39+45031:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		59463	0	126	21	Intron of ERG(-):45Kb after exon 3	ERG	39902555			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872614			10	DELETION		2970059	206318	89423	137	NEW_VARIANT
P-0025676-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+2967:TMPRSS2_c.39+20578:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		60022	0	44	21	Intron of ERG(-):21Kb after exon 3	ERG	39927008			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876910			10	DELETION		2949902	206418	52131	203	NEW_VARIANT
P-0025677-T01-IM6	CIC (NM_015125) rearrangement: chr19:g.42722240_c.4517dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		33588	0	3	19	3-UTR of DEDD2(-):2Kb after coding stop	DEDD2	42722240			19	Exon 20 of CIC(+)	CIC	42799033			7	DUPLICATION		76793	206423	54418	3	NEW_VARIANT
P-0025683-T01-IM6	ERBB2 (NM_004448) rearrangement: chr17:g.37353947_c.2307+2inv	IMPPRECISE	Note: The ERBB2 rearrangement results in the inversion of exons 20-27. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {ERBB2:CACNB1}		53455	0	5	17	5-UTR of CACNB1(-):20Kb before coding start	CACNB1	37353947			17	Intron of ERBB2(+):2bp after exon 19	ERBB2	37880265			0	INVERSION		526318	206412	67619	5	NEW_VARIANT
P-0025683-T01-IM6	LPO (NM_006151) - HOXB13 (NM_006361) rearrangement: c.1106-623:LPO_c.371:HOXB13inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {LPO:HOXB13}		37532	0	21	17	Exon 1 of HOXB13(-)	HOXB13	46805585			17	Intron of LPO(+):622bp before exon 9	LPO	56331549			0	INVERSION		9525964	206413	39684	22	NEW_VARIANT
P-0025683-T01-IM6	RPTOR (NM_020761) rearrangement: chr17:g.74050297_c.2442dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		33827	0	5	17	Intron of SRP68(-):3Kb after exon 8	SRP68	74050297			17	Exon 21 of RPTOR(+)	RPTOR	78882651			0	DUPLICATION		4832354	206411	53816	5	NEW_VARIANT
P-0025684-T01-IM6	DNMT3A (NM_022552) rearrangement: c.2140_c.1936+32del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2288	0	2	2	Exon 18 of DNMT3A(-)	DNMT3A	25463542			2	Intron of DNMT3A(-):31bp after exon 16	DNMT3A	25466735			9	DELETION		3193	206415	2959	2	NEW_VARIANT
P-0025704-T01-IM6	CDK6 (NM_001145306) rearrangement: c.728_c.699-1995del	PRECISE	Note: The CDK6 rearrangement results in the deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		215	0	42	7	Exon 7 of CDK6(-)	CDK6	92247492			7	Intron of CDK6(-):2Kb before exon 7	CDK6	92249516			10	DELETION		2024	206506	91	42	NEW_VARIANT
P-0020938-T02-IM6	KDM6A (NM_021140) rearrangement: chrX:g.43650588_c.3209+24:KDM6Adel	PRECISE	Note: The KDM6A rearrangement is a deletion of exons 1-21.	MANUAL_OK	3to5	3to5	-		33995	0	3	X	Intron of MAOB(-):2Kb after exon 8	MAOB	43650588			X	Intron of KDM6A(+):24bp after exon 21	KDM6A	44941909			10	DELETION		1291321	206351	46262	3	NEW_VARIANT
P-0025753-T01-IM6	CSNK1E (NM_001894) - NF2 (NM_000268) Rearrangement : c.886-1655:CSNK1E_c.288:NF2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CSNK1E:NF2}		27808	1	29	22	Exon 3 of NF2(+)	NF2	30035126			22	Intron of CSNK1E(-):2Kb before exon 8	CSNK1E	38692195			10	INVERSION		8657069	207047	28688	36	NEW_VARIANT
P-0025761-T01-IM6	CDK12 (NM_016507) Rearrangement : c.1769:CDK12_c.433-135:PGAP3dup	PRECISE	Note: The CDK12 Rearrangement results in the duplication of exons 2-14.One of the breakpoints is within exon2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		24452	0	57	17	Exon 2 of CDK12(+)	CDK12	37627854			17	Intron of PGAP3(-):135bp before exon 4	PGAP3	37831067			10	DUPLICATION		203213	207005	48196	62	NEW_VARIANT
P-0025761-T01-IM6	PAX8 (NM_003466) - PSD4 (NM_012455) Rearrangement : c.1088-192:PAX8_c.1629-1102:PSD4del	PRECISE	Note : The PAX8 - PSD4 Rearrangement results in the fusion of exons 1-10 with PSD4 exons 6-17. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {PAX8:PSD4}		50294	0	3	2	Intron of PSD4(+):1Kb before exon 6	PSD4	113948855			2	Intron of PAX8(-):192bp before exon 10	PAX8	113985025			10	INVERSION		36170	207006	125327	5	NEW_VARIANT
P-0025711-T01-IM6	CREBBP (NM_004380) rearrangement: chr16:g.3238048_c.1470inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		121401	0	31	16	IGR: 16Kb before OR1F1(+)	OR1F1	3238048			16	Exon 6 of CREBBP(-)	CREBBP	3832788			10	INVERSION		594740	207119	145589	50	NEW_VARIANT
P-0025757-T01-IM6	DNAH8 (NM_001206927) - IRF4 (NM_002460) Rearrangement : c.13053+1789:DNAH8_c.1073:IRF4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNAH8:IRF4}		328618	0	10	6	Exon 7 of IRF4(+)	IRF4	401751			6	Intron of DNAH8(+):2Kb after exon 87	DNAH8	38953872			10	DUPLICATION		38552121	206998	427302	11	NEW_VARIANT
P-0025763-T01-IM6	STAG2 (NM_001042749) Rearrangement : t(X;5)(q25;q14.2)(chrX:g.123178980::chr5:g.85708121)	PRECISE	Note: The STAG2 Rearrangement results in the possible translocation of STAG2, the breakpoint in STAG2 is within intron7. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	32	X	Intron of STAG2(+):33bp before exon 8	STAG2	123178980			5	IGR: 130Kb before NBPF22P(+)	NBPF22P	85708121			10	TRANSLOCATION		0	207015	0	34	NEW_VARIANT
P-0025793-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-585:TMPRSS2_c.-1597:ERGinv	PRECISE	Note: The TMPRSS2 - ERG rearrangement is an inversion with breakpoints in TMPRSS2 intron 2 and ERG promoter region. This structural variant was observed in addition to another rearrangements involving TMRPSS2, suggesting a complex event that may not be detected by the IMPACT assay. If clinically indicated, further analysis using the Archer targeted RNAseq assay can be performed.	MANUAL_OK	5to5	5to5	Antisense Fusion		17146	0	56	21	Promoter of ERG(-):120Kb from tx start	ERG	39871901			21	Intron of TMPRSS2(-):585bp before exon 3	TMPRSS2	42867090			10	INVERSION		2995189	207090	26646	59	NEW_VARIANT
P-0025770-T01-IM6	FGFR1 (NM_001174067) rearrangement: t(8;11)(p11.23;p11.12)(chr8:g.38275713::chr11:g.48968445)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	8	11	IGR: 85Kb before TRIM49B(+)	TRIM49B	48968445			8	Intron of FGFR1(-):32bp after exon 11	FGFR1	38275713			10	TRANSLOCATION		0	206977	0	11	NEW_VARIANT
P-0025807-T01-IM6	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	PRECISE	Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		187050	0	17	10	Intron of BICC1(+):35Kb before exon 3	BICC1	60426727			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123242181			10	INVERSION		62815454	207136	291547	24	NEW_VARIANT
P-0025807-T01-IM6	YTHDF3 (NM_152758) - FGFR2 (NM_000141) rearrangement: t(8;10)(q12.3;q26.13)(chr8:g.64081967::chr10:g.123242317)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {YTHDF3:FGFR2}		0	0	29	10	Intron of FGFR2(-):894bp after exon 17	FGFR2	123242317			8	Exon 2 of YTHDF3(+)	YTHDF3	64081967			10	TRANSLOCATION		0	207137	0	28	NEW_VARIANT
P-0025823-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		36206	0	199	21	Intron of ERG(-):2Kb after exon 1	ERG	39867922			21	Intron of TMPRSS2(-):246bp before exon 2	TMPRSS2	42870362			10	DELETION		3002440	207181	95628	220	NEW_VARIANT
P-0025823-T01-IM6	TMPRSS2 (NM_023034) - SIMC1 (NM_001308195) rearrangement: t(5;21)(q35.2;q22.3)(chr5:g.175765852::chr21:g.42870360)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SIMC1:TMPRSS2}		0	0	183	21	Intron of TMPRSS2(-):244bp before exon 2	TMPRSS2	42870360			5	Intron of SIMC1(+):2Kb after exon 8	SIMC1	175765852			10	TRANSLOCATION		0	207192	0	182	NEW_VARIANT
P-0025823-T01-IM6	RHEB (NM_005614) - DNAJB6 (NM_058246) rearrangement: c.380+103:RHEB_c.346+6811:DNAJB6inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {RHEB:DNAJB6}		102884	0	16	7	Intron of RHEB(-):102bp after exon 6	RHEB	151168377			7	Intron of DNAJB6(+):7Kb after exon 5	DNAJB6	157166988			10	INVERSION		5998611	207182	107616	21	NEW_VARIANT
P-0025824-T01-IM6	MEF2B (NM_001145785) rearrangement: c.258+19_chr19:g.23671215inv	IMPPRECISE	Note: The MEF2B rearrangement results in the inversion of exons 13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		5567	0	9	19	Intron of MEF2B(-):18bp after exon 3	MEF2B	19260016			19	IGR: 89Kb before LINC01224(-)	LINC01224	23671215			0	INVERSION		4411199	207224	10865	12	NEW_VARIANT
P-0025880-T01-IM6	DNMT1 (NM_001379) rearrangement: t(1;19)(p36.22;p13.2)(chr1:g.10857423::chr19:g.10265403)	PRECISE	Note: The DNMT1 rearrangement is a translocation with a breakpoint in exon 20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CASZ1:DNMT1}		0	0	6	19	Exon 20 of DNMT1(-)	DNMT1	10265403			1	Promoter of CASZ1(-):161Kb from tx start	CASZ1	10857423			10	TRANSLOCATION		0	207726	0	6	NEW_VARIANT
P-0025921-T01-IM6	KDM5A (NM_001042603) rearrangment t(2;12)(p16.1;p13.33)(chr2:g.56637105::chr12:g.419156)	PRECISE	Note: The KDM5A rearrangement is a translocation that involves exon 22. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	8	12	Intron of KDM5A(-):26bp before exon 22	KDM5A	419156			2	IGR: 226Kb before CCDC85A(+)	CCDC85A	56637105			10	TRANSLOCATION		0	207863	0	8	NEW_VARIANT
P-0025924-T01-IM6	CDKN1B (NM_004064) rearrangement: c.-1037_c.401del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1549	0	4	12	Promoter of CDKN1B(+):466bp from tx start	CDKN1B	12869737			12	Exon 1 of CDKN1B(+)	CDKN1B	12871174			6	DELETION		1437	207866	1715	4	NEW_VARIANT
P-0025924-T01-IM6	MED12 (NM_005120) rearrangement: c.5827-10_c.6267+178del	PRECISE	Note: The MED12 rearrangement results in the intragenic deletion of exons 41 and 42. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		5056	0	7	X	Intron of MED12(+):9bp before exon 41	MED12	70357566			X	Intron of MED12(+):178bp after exon 42	MED12	70360885			10	DELETION		3319	207869	7302	7	NEW_VARIANT
P-0025601-T02-IM6	ETV6 (NM_001987) rearrangement: c.464-6797:ETV6_chr12:g.11225690inv	IMPPRECISE	Note: The ETV6 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		56437	0	19	12	3-UTR of PRH1-PRR4(-):99Kb after coding stop	PRH1-PRR4	11225690			12	Intron of ETV6(+):7Kb before exon 5	ETV6	12015561			0	INVERSION		789871	207254	95484	19	NEW_VARIANT
P-0025835-T01-IM6	FGFR2 (NM_000141) rearrangement: t(3;10)(p24.3;q26.13)(chr3:g.18908797::chr10:g.123240192)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	32	10	Intron of FGFR2(-):657bp before exon 18	FGFR2	123240192			3	IGR: 281Kb before KCNH8(+)	KCNH8	18908797			10	TRANSLOCATION		0	207263	0	31	NEW_VARIANT
P-0025835-T01-IM6	FGFR2 (NM_000141) - FOXP1 (NM_001244814) rearrangement: t(3;10)(p13;q26.13)(chr3:g.71178081::chr10:g.123242260)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	29	10	Intron of FGFR2(-):951bp after exon 17	FGFR2	123242260			3	Intron of FOXP1(-):16Kb before exon 3	FOXP1	71178081			10	TRANSLOCATION		0	207264	0	27	NEW_VARIANT
P-0025838-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in-frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		49955	0	70	10	Intron of KIF5B(-):601bp before exon 16	KIF5B	32312565			10	Intron of RET(+):788bp after exon 11	RET	43610972			10	INVERSION		11298407	207237	50083	106	NEW_VARIANT
P-0025841-T01-IM6	KMT2C (NM_170606) rearrangement: c.8725:KMT2C_chr7:g.105612673del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		336514	0	31	7	Intron of CDHR3(+):3Kb before exon 2	CDHR3	105612673			7	Exon 38 of KMT2C(-)	KMT2C	151873813			10	DELETION		46261140	207239	488400	32	NEW_VARIANT
P-0025928-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		66514	0	114	10	Intron of KIF5B(-):482bp after exon 15	KIF5B	32316873			10	Intron of RET(+):121bp before exon 12	RET	43611910			10	INVERSION		11295037	207972	133363	166	NEW_VARIANT
P-0025935-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.1085:MAP3K1_chr5:g.55920869inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		5644	0	12	5	IGR: 114Kb before LOC101928448(-)	LOC101928448	55920869			5	Exon 5 of MAP3K1(+)	MAP3K1	56161216			10	INVERSION		240347	207992	9393	13	NEW_VARIANT
P-0007343-T02-IM6	INPPL1 (NM_001567) - ANK2 (NM_001148) rearrangement: t(4;11)(q25-q26;q13.4)(chr4:g.113898703::chr11:g.71943348)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {INPPL1:ANK2}		0	0	131	11	Exon 14 of INPPL1(+)	INPPL1	71943348			4	Intron of ANK2(+):73Kb after exon 2	ANK2	113898703			10	TRANSLOCATION		0	207799	0	178	NEW_VARIANT
P-0007343-T02-IM6	TBX3 (NM_016569.3) rearrangement: t(12;19)(q24.21;p13.3)(chr12:g.115112036::chr19:g.13270583)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	212	19	IGR: 9Kb before IER2(+)	IER2	13270583			12	Exon 7 of TBX3(-)	TBX3	115112036			10	TRANSLOCATION		0	207801	0	211	NEW_VARIANT
P-0007343-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+662TMPRSS2_c.39+64787ERGdel.	PRECISE	Note: The TMPRSS2 ERG fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32698	0	255	21	Intron of ERG(-):65Kb after exon 3	ERG	39882799			21	Intron of TMPRSS2(-):661bp after exon 2	TMPRSS2	42869384			10	DELETION		2986585	207796	62707	320	NEW_VARIANT
P-0020845-T02-IM6	SMAD3 (NM_005902) rearrangement: c.207-2606_c.400+4dup	PRECISE	Note: The SMAD3 rearrangement results in the duplication of exon 2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1879	0	111	15	Intron of SMAD3(+):3Kb before exon 2	SMAD3	67454627			15	Intron of SMAD3(+):4bp after exon 2	SMAD3	67457430			10	DUPLICATION		2803	207758	3691	125	NEW_VARIANT
P-0020845-T02-IM6	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373)	PRECISE	Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	26	18	IGR: 195Kb before DLGAP1-AS5(+)	DLGAP1-AS5	4459373			8	Intron of TCEB1(-):3bp before exon 4	TCEB1	74859058			10	TRANSLOCATION		0	207763	0	49	NEW_VARIANT
P-0025895-T01-IM6	KDM6A (NM_021140) rearrangement: chrX:g.44430418_c.3091inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		40300	0	75	X	IGR: 48Kb before FUNDC1(-)	FUNDC1	44430418			X	Exon 20 of KDM6A(+)	KDM6A	44938543			10	INVERSION		508125	207741	30719	80	NEW_VARIANT
P-0018048-T02-IM6	ARID1A (NM_006015) Rearrangement : c.3441_c.3715+147del	PRECISE	Note: The ARID1A Rearrangement results in the intragenic deletion of exon13. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		1872	0	23	1	Exon 13 of ARID1A(+)	ARID1A	27099025			1	Intron of ARID1A(+):147bp after exon 14	ARID1A	27099625			10	DUPLICATION		600	205953	2627	24	NEW_VARIANT
P-0025851-T02-IM6	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	IMPPRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29316	0	24	21	Intron of ERG(-):61Kb before exon 4	ERG	39878297			21	Intron of TMPRSS2(-):748bp after exon 2	TMPRSS2	42869297			0	DELETION		2991000	208151	34627	26	NEW_VARIANT
P-0025988-T01-IM6	TBC1D10C (NM_198517) - CCND1 (NM_053056) fusion (TBC1D10C exons 1-8 with CCND1 exons 1-5): c.839-966TBC1D10C_c.1CCND1del.	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TBC1D10C:CCND1}		23699	0	79	11	Intron of TBC1D10C(+):965bp before exon 9	TBC1D10C	67175484			11	Exon 1 of CCND1(+)	CCND1	69456082			10	DELETION		2280598	208190	46567	83	NEW_VARIANT
P-0025988-T01-IM6	TMPRSS2 (NM_001135099) - BRAF (NM_004333) rearrangement: t(7;21)(q34;q22.3)(chr7:g.140484791::chr21:g.42870515)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	127	21	Intron of TMPRSS2(-):399bp before exon 2	TMPRSS2	42870515			7	Intron of BRAF(-):2Kb before exon 10	BRAF	140484791			10	TRANSLOCATION		0	208194	0	153	NEW_VARIANT
P-0025988-T01-IM6	SETD2 (NM_014159): c.5361SETD2_c.5142+3718dup	PRECISE	Note: The SETD2 rearrangement is a duplication of exons 9-11. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		1965	0	49	3	Exon 11 of SETD2(-)	SETD2	47127721			3	Intron of SETD2(-):4Kb after exon 9	SETD2	47135727			10	DUPLICATION		8006	208191	4400	51	NEW_VARIANT
P-0026009-T01-IM6	GAS7 (NM_201433) - TP53 (NM_000546) rearrangement: c.184-54871:GAS7_c.996:TP53del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GAS7:TP53}		57594	0	39	17	Exon 10 of TP53(-)	TP53	7574031			17	Intron of GAS7(-):55Kb before exon 2	GAS7	9978085			10	DELETION		2404054	208140	66058	40	NEW_VARIANT
P-0026012-T01-IM6	CBFB(NM_022845) - RUFY4 (NM_198483) rearrangement: t(2;16)(q35;q22.1)(chr2:g.218917363::chr16:g.67063596)	PRECISE	Note: The CBFB - RUFY4 rearrangement is a translocation with breakpoints within CBFB intron 1 and RUFY4 intron 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	14	16	Intron of CBFB(+):33bp before exon 2	CBFB	67063596			2	5-UTR of RUFY4(+):38Kb before coding start	RUFY4	218917363			10	TRANSLOCATION		0	208137	0	16	NEW_VARIANT
P-0025974-T01-IM6	B2M (NM_004048) Rearrangement : c.5867-701:SPG1_c.150:B2Mdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2303	0	24	15	Intron of SPG11(-):3Kb before exon 31	SPG11	44867940			15	Exon 2 of B2M(+)	B2M	45007703			10	DELETION		139763	208128	3580	24	NEW_VARIANT
P-0025980-T01-IM6	NOTCH2 (NM_024408) Rearrangement : c.2480-581_c.4880inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		19018	0	13	1	Exon 27 of NOTCH2(-)	NOTCH2	120465381			1	Intron of NOTCH2(-):581bp before exon 16	NOTCH2	120492330			10	INVERSION		26949	208110	39294	13	NEW_VARIANT
P-0025980-T01-IM6	POLE (NM_006231) Rearrangement :  c.2173+1_c.5379-1098del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		32545	0	16	12	Intron of POLE(-):1Kb before exon 40	POLE	133216982			12	Exon 19 of POLE(-)	POLE	133244941			10	DELETION		27959	208108	48510	17	NEW_VARIANT
P-0000541-T03-IM6	MEN1 (NM_000244) Rearrangement : c.1256_1791del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6271	0	37	11	Exon 10 of MEN1(-)	MEN1	64571866			11	Exon 9 of MEN1(-)	MEN1	64572611			0	DELETION		745	180802	3792	38	NEW_VARIANT
P-0000541-T03-IM6	BRCA2 (NM_000059) Rearrangement : c.5355_c.6841+201del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14473	0	58	13	Exon 11 of BRCA2(+)	BRCA2	32913847			13	Intron of BRCA2(+):201bp after exon 11	BRCA2	32915534			10	DELETION		1687	180803	7997	63	NEW_VARIANT
P-0003150-T03-IM6	MYC (NM_002467) Rearrangement : t(6,8)(q27,q24.21)(chr6:g.168309690::chr8:g.128753250)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	43	8	3-UTR of MYC(+):4Kb after coding stop	MYC	128753250			6	Intron of MLLT4(+):2Kb after exon 13	MLLT4	168309690			10	TRANSLOCATION		0	184157	0	40	NEW_VARIANT
P-0003195-T02-IM6	MLL3 (NM_170606) Rearrangement : chr7:g.144838860_c.13395:KMT2Cinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		45654	0	54	7	IGR: 690Kb before TPK1(-)	TPK1	144838860			7	Exon 52 of KMT2C(-)	KMT2C	151845617			10	INVERSION		7006757	180358	48078	53	NEW_VARIANT
P-0003357-T02-IM6	ETV6 (NM_001987) rearrangement: c.463+2187:ETV6_chr12:g.30656812inv	PRECISE	Note: The ETV6 rearrangement is an inversion of exons 5-8, potentially disrupting gene function.	MANUAL_OK	3to3	3to3	-		293644	0	6	12	Intron of ETV6(+):2Kb after exon 4	ETV6	12008682			12	IGR: 125Kb before IPO8(-)	IPO8	30656812			10	INVERSION		18648130	178443	349188	6	NEW_VARIANT
P-0003684-T02-IM6	BRAF (NM_004333) rearrangement: t(7;17)(q34;p13.1)(chr7:g.140486105::chr17:g.7963177)	PRECISE	Note: The BRAF rearrangement is a translocation that may result in the truncation of exons 10-18. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	82	17	IGR: 13Kb before ALOX12B(-)	ALOX12B	7963177			7	Intron of BRAF(-):1Kb after exon 9	BRAF	140486105			10	TRANSLOCATION		0	172113	0	82	NEW_VARIANT
P-0004835-T02-IM6	BRIP1 (NM_032043) - PTRH2 (NM_016077) rearrangement: c.2575+19: BRIP1_c.-1+243: PTRH2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {BRIP1:PTRH2}		21339	0	278	17	5-UTR of PTRH2(-):10Kb before coding start	PTRH2	57784489			17	Intron of BRIP1(-):18bp after exon 18	BRIP1	59770772			10	DELETION		1986283	175887	231444	344	NEW_VARIANT
P-0005445-T03-IM6	MLL3 (NM_170606) Rearrangement : c.250+10968_c.10446dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		105568	0	91	7	Exon 43 of MLL3(-)	MLL3	151860216			7	Intron of MLL3(-): 11Kb after exon 2	MLL3	152044704			85	DUPLICATION		184488	166973	149648	86	NEW_VARIANT
P-0006008-T02-IM6	NOTCH1 (NM_017617) rearrangement: c.3644-7_c.141-7069del	IMPPRECISE	Note: The NOTCH1 rearrangement results in the deletion of exons 3-22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 20 exons : out of frame		81530	0	7	9	Intron of NOTCH1(-):7bp before exon 23	NOTCH1	139401432			9	Intron of NOTCH1(-):7Kb before exon 3	NOTCH1	139425500			0	DELETION		24068	183774	82745	8	NEW_VARIANT
P-0007898-T02-IM6	MAP3K14 (NM_003954) - C17orf104 (NM_001145080) Rearrangement : c.1656+179:MAP3K1_c.360-1358:C17orf104inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {MAP3K14:C17orf104}		11704	0	7	17	Intron of C17orf104(+):1Kb before exon 4	C17orf104	42741394			17	Intron of MAP3K14(-):178bp after exon 9	MAP3K14	43350691			10	INVERSION		609297	176613	23081	7	NEW_VARIANT
P-0008599-T02-IM6	KMT2B (NM_014727) : c.3656_4487inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		17591	0	13	19	Exon 12 of KMT2B(+)	KMT2B	36216393			19	Exon 18 of KMT2B(+)	KMT2B	36218876			10	INVERSION		2483	180815	16893	12	NEW_VARIANT
P-0009056-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-864:TMPRSS2_c.18+12444:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		51662	0	73	21	Intron of ERG(-):12Kb after exon 1	ERG	39857843			21	Intron of TMPRSS2(-):864bp before exon 2	TMPRSS2	42870980			10	DELETION		3013137	176703	27382	76	NEW_VARIANT
P-0009640-T02-IM6	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)	IMPRECISE		MANUAL_OK	5to3	5to3	Protein fusion: out of frame (TMPRSS2-ETV1)		0	0	5	21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867556			7	Intron of ETV1(-): 2Kb after exon 1	ETV1	14024117			0	TRANSLOCATION		0	167877	0	5	NEW_VARIANT
P-0009640-T02-IM6	ABL1 (NM_005157) Rearrangement : c.2658:ABL1_3:c.-70:NUP214inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		3896	0	10	9	Exon 11 of ABL1(+)	ABL1	133760335			9	5-UTR of NUP214(+): 70bp before coding start	NUP214	134001022			18	INVERSION		240687	167876	3622	10	NEW_VARIANT
P-0010796-T02-IM6	MGA (NM_001164273) Rearrangement : c.7139+105_7887del	PRECISE	Note: The MGA rearrangement event results in the intragenic deletion of MGA exons 19-23. One of the breakpoints is within MGA exon23.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8363	0	59	15	Intron of MGA(+):105bp after exon 18	MGA	42046870			15	Exon 23 of MGA(+)	MGA	42057227			10	DELETION		10357	170327	6878	61	NEW_VARIANT
P-0010796-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-1410:TMPRSS2_c.19-20820:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		68803	0	167	21	Intron of ERG(-):21Kb before exon 2	ERG	39838364			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871527			10	DELETION		3033163	170328	52541	208	NEW_VARIANT
P-0010983-T02-IM6	CNOT2 (NM_014515) - STAT3 (NM_139276) Rearrangement : t(12,17)(q15,q21.1)(chr12:g.70671823::chr17:g.40475061)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CNOT2:STAT3}		0	0	40	17	Exon 20 of STAT3(-)	STAT3	40475061			12	5-UTR of CNOT2(+):183bp before coding start	CNOT2	70671823			10	TRANSLOCATION		0	174534	0	40	NEW_VARIANT
P-0010983-T02-IM6	E2F3 (NM_001949) Rearrangement : c.394-36841_c.506-3del	PRECISE	Note: The E2F3 Rearrangement results in the deletion of exon2 of E2F3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2018	0	12	6	Intron of E2F3(+):37Kb before exon 2	E2F3	20443236			6	Intron of E2F3(+):2bp before exon 3	E2F3	20481434			10	DELETION		38198	174533	2125	13	NEW_VARIANT
P-0011198-T02-IM6	TMPRSS2 (NM_001135099) - ETV5 (NM_004454) rearrangement : t(3;21)(q27.2;q22.3)(chr3:g.185827431::chr21:g.42867759)	IMPRECISE	Note: The TMPRSS2-ETV5 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV6 promoter region. PMID: 18172298	MANUAL_OK	5to3	5to3	Transcript fusion (TMPRSS2-ETV5)		0	0	29	21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867759			3	Promoter of ETV5(-): 530bp from tx start	ETV5	185827431			0	TRANSLOCATION		0	168633	0	28	NEW_VARIANT
P-0012109-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.55+4448:TMPRSS2_c.40-56700:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		156946	0	102	21	Intron of ERG(-): 57Kb before exon 4	ERG	39874244			21	Intron of TMPRSS2(-): 4Kb after exon 1	TMPRSS2	42875429			163	DELETION		3001185	168640	73840	329	NEW_VARIANT
P-0012572-T02-IM6	POLE (NM_006231) rearrangement: c.86_c.423+93dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		7466	0	42	12	Intron of POLE(-):92bp after exon 5	POLE	133256447			12	Exon 2 of POLE(-)	POLE	133257842			10	DUPLICATION		1395	177995	7143	47	NEW_VARIANT
P-0012675-T02-IM6	KMT2C (NM_170606) rearrangement: c.9263-84_c.162-23697del	PRECISE	Note: The KMT2C rearrangement results in the deletion of exons 2-38. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 37 exons : out of frame		75073	0	31	7	Intron of KMT2C(-):84bp before exon 39	KMT2C	151871411			7	Intron of KMT2C(-):24Kb before exon 2	KMT2C	152079457			10	DELETION		208046	170810	102145	36	NEW_VARIANT
P-0013613-T02-IM6	MAP3K1 (NM_005921) Rearrangement : c.1966-873_c.2087+125inv	PRECISE	Note: The MAP3K1 Rearrangement results in the intragenic inversion of exon 11 of MAP3K1. Its functional significance is unknown.	MANUAL_OK	3to3	3to3	Antisense Fusion		1137	0	2	5	Intron of MAP3K1(+):872bp before exon 11	MAP3K1	56173934			5	Intron of MAP3K1(+):125bp after exon 11	MAP3K1	56175053			9	INVERSION		1119	171896	2365	2	NEW_VARIANT
P-0013844-T02-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-54335:ERG_c.127-1358:TMPRSS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (ERG-TMPRSS2)		47431	0	37	21	Intron of ERG(-): 54Kb before exon 4	ERG	39871879			21	Intron of TMPRSS2(-): 1Kb before exon 3	TMPRSS2	42867863			44	DUPLICATION		2995984	166946	54327	36	NEW_VARIANT
P-0014305-T02-IM6	GNAS (NM_080425) - REST (NM_001193508) rearrangement: t(4;20)(q12;q13.32)(chr4:g.57789330::chr20:g.57429127)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GNAS:REST}		0	0	28	20	Exon 1 of GNAS(+)	GNAS	57429127			4	Intron of REST(+):3Kb after exon 3	REST	57789330			10	TRANSLOCATION		0	177967	0	35	NEW_VARIANT
P-0014435-T02-IM6	EPAS1 (NM_001430) rearrangement: c.2045+133_c.2366del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6919	0	58	2	Intron of EPAS1(+):133bp after exon 12	EPAS1	46607989			2	Exon 15 of EPAS1(+)	EPAS1	46609642			10	DELETION		1653	178876	2563	61	NEW_VARIANT
P-0015061-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3449-1792_c.4412inv	PRECISE	Note: The ZFHX3 rearrangement is an inversion of exons 5-9. One of the breakpoints is within exon 9. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		10825	0	10	16	Exon 9 of ZFHX3(-)	ZFHX3	72832169			16	Intron of ZFHX3(-): 2Kb before exon 5	ZFHX3	72865550			13	INVERSION		33381	166675	10670	10	NEW_VARIANT
P-0015063-T02-IM6	TP63 (NM_003722) rearrangement: c.368_c.579+2150inv	PRECISE	Note: The TP63 rearrangement is an intragenic inversion of exon 4. One of the breakpoint is within exon 4.	MANUAL_OK	3to3	3to3	Antisense fusion		1488	0	19	3	Exon 4 of TP63(+)	TP63	189526104			3	Intron of TP63(+): 2Kb after exon 4	TP63	189528465			49	INVERSION		2361	168050	1045	15	NEW_VARIANT
P-0015078-T01-IM6	KRAS (NM_033360) rearrangement: chr12:g.25463932_c.267dup	PRECISE	Note: The KRAS rearrangement is a duplication which includes exons 1-3. One of the breakpoints is within exon3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		2686	0	34	12	Exon 3 of KRAS(-)	KRAS	25380191			12	IGR: 60Kb after KRAS(-)	KRAS	25463932			40	DUPLICATION		83741	166747	3628	34	NEW_VARIANT
P-0015084-T01-IM6	FAIM2 (NM_012306) - SMARCD1 (NM_003076) rearrangement: c.211+1026:FAIM2_c.178-116:SMARCD1inv	PRECISE	Note: The FAIM2 - SMARCD1 rearrangement is an inversion which results in the fusion of FAIM2 exon2 to SMARCD1 exon2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (FAIM2-SMARCD1)		4064	0	5	12	Intron of FAIM2(-): 1Kb after exon 2	FAIM2	50293887			12	Intron of SMARCD1(+): 116bp before exon 2	SMARCD1	50479828			9	INVERSION		185941	166720	3795	5	NEW_VARIANT
P-0015084-T01-IM6	FOXA1 (NM_004496) rearrangement: c.1081_chr14:g.38565335del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		11278	0	15	14	Exon 2 of FOXA1(-)	FOXA1	38060908			14	IGR: 112Kb before SSTR1(+)	SSTR1	38565335			18	DELETION		504427	166719	6445	8	NEW_VARIANT
P-0015099-T01-IM6	IRS2 (NM_003749) rearrangement: g.99829420_c.2610del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74547	0	102	13	IGR: 23Kb before UBAC2(+)	UBAC2	99829420			13	Exon 1 of IRS2(-)	IRS2	110435791			36	DELETION		10606371	166776	121091	117	NEW_VARIANT
P-0015102-T01-IM6	PIK3C2G (NM_004570) rearrangement: g.16777242_c.2004-131del	PRECISE	Note: The PIK3C2G (NM_004570) rearrangement results in the deletion of exons 1-14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		26930	0	5	12	IGR: 16Kb after LMO3(-)	LMO3	16777242			12	Intron of PIK3C2G(+): 131bp before exon 15	PIK3C2G	18552462			10	DELETION		1775220	166782	26870	5	NEW_VARIANT
P-0015107-T01-IM6	FAT1 (NM_005245) Rearrangement : c.5921+19840:LRBA_c.5848:FAT1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		130408	0	14	4	Intron of LRBA(-): 20Kb after exon 37	LRBA	151584863			4	Exon 10 of FAT1(-)	FAT1	187541892			34	INVERSION		35957029	166829	100470	14	NEW_VARIANT
P-0015108-T01-IM6	TGFBR1(NM_004612) Rearrangement : chr9:101858947_c.406:TGFBR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3927	0	20	9	IGR: 8Kb before TGFBR1(+)	TGFBR1	101858947			9	Exon 3 of TGFBR1(+)	TGFBR1	101894853			32	DELETION		35906	166823	3020	20	NEW_VARIANT
P-0015110-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exons 1-5 with ALK exons 20-29) : c.668-1726:EML4_c.3173-124:ALKinv	PRECISE	Note: The EML4-ALK fusion is predicted to be in-frame and includes the protein kinase domain of ALK	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		160477	0	73	2	Intron of ALK(-): 124bp before exon 20	ALK	29446518			2	Intron of EML4(+): 2Kb before exon 6	EML4	42506264			39	INVERSION		13059746	166808	131320	72	NEW_VARIANT
P-0015119-T01-IM6	SDHA (NM_004168) rearrangement: c.1794+179:SDHA_g.3790215del	PRECISE	Note: The SDHA (NM_004168) rearrangement results in the deletion of exons 14-15. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		64786	0	13	5	Intron of SDHA(+): 179bp after exon 13	SDHA	251762			5	IGR: 194Kb before IRX1(+)	IRX1	3790215			21	DELETION		3538453	166881	92330	13	NEW_VARIANT
P-0015121-T01-IM6	TMPRSS2 (NM_001135099) rearrangement : g.18174576_c.55+1974:TMPRSS2inv	PRECISE	Note: The TMPRSS2 (NM_001135099) rearrangement results in an inversion of TMPRSS2 exons 2-14 . The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		217206	0	97	21	IGR: 212Kb before MIR125B2(+)	MIR125B2	18174576			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877903			77	INVERSION		24703327	166888	216827	93	NEW_VARIANT
P-0015122-T01-IM6	CSF1R (NM_005211) - GRIA1 (NM_000827) rearrangement: c.1918:CSF1R_c.460+1372:GRIA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense fusion		116399	0	49	5	Exon 14 of CSF1R(-)	CSF1R	149440476			5	Intron of GRIA1(+): 1Kb after exon 3	GRIA1	153028099			56	DUPLICATION		3587623	166869	141054	49	NEW_VARIANT
P-0015123-T01-IM6	SMAD4 (NM_005359) rearrangement: c.904+25_c.1308+1698del	PRECISE	Note: The SMAD4 (NM_005359) rearrangement results in the deletion of exons 8-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons: out of frame		5627	0	19	18	Intron of SMAD4(+): 25bp after exon 7	SMAD4	48584851			18	Intron of SMAD4(+): 2Kb after exon 10	SMAD4	48595255			22	DELETION		10404	166906	4582	19	NEW_VARIANT
P-0015123-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement : g.21929130_c.458-3:CDKN2Ap16iNK4Ainv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1256	0	8	9	IGR: 38Kb before C9orf53(+)	C9orf53	21929130			9	Intron of CDKN2A(-): 3bp before exon 3	CDKN2A	21968244			12	INVERSION		39114	166922	1079	8	NEW_VARIANT
P-0015129-T01-IM6	RXRA (NM_002957) rearrangement : c.1135+988_c.1241+32inv	PRECISE	Note: The RXRA (NM_002957) rearrangement results in an inversion of RXRA exon 9 . The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		2734	0	5	9	Intron of RXRA(+): 988bp after exon 8	RXRA	137324830			9	Intron of RXRA(+): 32bp after exon 9	RXRA	137326085			4	INVERSION		1255	166867	2015	4	NEW_VARIANT
P-0015131-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-52916:ERG_c.127-1540:TMPRSS2inv	PRECISE	Note: The ERG - TMPRSS2 rearrangement results in an inversion of ERG 5UTR, exons 1-3  and TMPRSS2 exons 3-14. The complex rearrangement involving TMPRSS2 and ERG in this tumor suggests a TMPRSS2 - ERG fusion. Confirmatory testing by archer assay is suggested if clinically indicated.	MANUAL_OK	3to3	3to3	-		36627	0	11	21	Intron of ERG(-): 53Kb before exon 4	ERG	39870460			21	Intron of TMPRSS2(-): 2Kb before exon 3	TMPRSS2	42868045			21	INVERSION		2997585	166984	32501	11	NEW_VARIANT
P-0015132-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		28546	0	9	21	Intron of ERG(-): 56Kb before exon 4	ERG	39874000			21	Intron of TMPRSS2(-): 625bp before exon 3	TMPRSS2	42867130			26	DELETION		2993130	166962	22756	9	NEW_VARIANT
P-0015136-T01-IM6	CDKN1B (NM_004064) Rearrangement : c.158:CDKN1B_chr12:5g.1623301inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		430696	0	7	12	Exon 1 of CDKN1B(+)	CDKN1B	12870931			12	IGR: 9Kb before DAZAP2(+)	DAZAP2	51623301			8	INVERSION		38752370	166939	396695	7	NEW_VARIANT
P-0015148-T01-IM6	PIK3C2G (M_004570) rearrangement: c.3658-68_c.3889-8636dup	PRECISE	Note: The PIK3C2G rearrangement is an intragenic duplication of exons 27-28.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		2844	0	23	12	Intron of PIK3C2G(+): 68bp before exon 27	PIK3C2G	18716243			12	Intron of PIK3C2G(+): 9Kb before exon 29	PIK3C2G	18738792			28	DUPLICATION		22549	167032	5491	23	NEW_VARIANT
P-0015152-T02-IM6	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	PRECISE	Note: The EML4-ALK fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		120249	0	36	2	Intron of ALK(-): 685bp before exon 20	ALK	29447079			2	Intron of EML4(+): 127bp after exon 19	EML4	42552821			100	INVERSION		13105742	168080	105749	36	NEW_VARIANT
P-0015184-T01-IM6	RECQL4 (NM_004260) rearrangement: c.665_c.354+27dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		3102	0	27	8	Exon 5 of RECQL4(-)	RECQL4	145741838			8	Intron of RECQL4(-): 27bp after exon 4	RECQL4	145742407			70	DUPLICATION		569	167050	3880	27	NEW_VARIANT
P-0015188-T01-IM6	ETV6 (NM_001987) rearrangement: c.163+11741_c.1010-6437dup	PRECISE	Note: The ETV6 rearrangement is an intragenic duplication of exons 3-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: in frame		221314	0	43	12	Intron of ETV6(+): 12Kb after exon 2	ETV6	11917254			12	Intron of ETV6(+): 6Kb before exon 6	ETV6	12030942			51	DUPLICATION		113688	167103	331692	42	NEW_VARIANT
P-0015191-T01-IM6	BCL10 (NM_003921) - C1orf52 (NM_198077) rearrangement: c.447:BCL10_c.276+231:C1orf52inv	PRECISE	Note: The BCL10 - C1orf52 rearrangement is an inversion with a breakpoint within exon3 of BCL10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		2126	0	7	1	Intron of C1orf52(-): 231bp after exon 1	C1orf52	85724810			1	Exon 3 of BCL10(-)	BCL10	85733565			12	INVERSION		8755	167106	2031	7	NEW_VARIANT
P-0015192-T01-IM6	MLL (NM_001197104) rearrangement: c.286_chr11:g.118294747dup	PRECISE	Note: The MLL rearrangement is a duplication with a breakpoint within exon1 of MLL. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		1542	0	5	11	IGR: 12Kb before MLL(+)	MLL	118294747			11	Exon 1 of MLL(+)	MLL	118307513			10	DUPLICATION		12766	167076	1730	5	NEW_VARIANT
P-0015195-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exon17 fused to TACC3 exon8): c.2275-86:FGFR3_c.1645-28:TACC3dup	PRECISE	Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (FGFR3-TACC3)		48685	0	32	4	Intron of TACC3(+): 28bp before exon 8	TACC3	1737430			4	Intron of FGFR3(+): 86bp before exon 18	FGFR3	1808757			25	DUPLICATION		71327	167093	61511	31	NEW_VARIANT
P-0015197-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 6 fused to ALK exon 20) : c.668-2108:EML4_c.3172+318:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		97127	0	49	2	Intron of ALK(-): 318bp after exon 19	ALK	29448009			2	Intron of EML4(+): 2Kb before exon 6	EML4	42505882			74	INVERSION		13057873	167079	107968	49	NEW_VARIANT
P-0015199-T01-IM6	NF2 (NM_000268) rearrangement: c.1341-75_c.1446+958inv	IMPRECISE	Note: The NF2 rearrangement is an intragenic inversion of exon 13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1962	0	102	22	Intron of NF2(+): 75bp before exon 13	NF2	30070750			22	Intron of NF2(+): 958bp after exon 13	NF2	30071888			0	INVERSION		1138	167119	3079	98	NEW_VARIANT
P-0015204-T01-IM6	STAT5A (NM_003152) - STAT3 (NM_139276) rearrangement: c.1997:STAT5A_c.*1443:STAT3del	PRECISE	Note: The STAT5A rearrangement is a deletion with breakpoints within exon17 of STAT5A and the 3UTR of STAT3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5770	0	9	17	Exon 17 of STAT5A(+)	STAT5A	40460286			17	3-UTR of STAT3(-): 1Kb after coding stop	STAT3	40466320			8	DELETION		6034	167165	6897	9	NEW_VARIANT
P-0015204-T01-IM6	ARID1B (NM_020732) rearrangement: c.3377-2146_c.4720+22	PRECISE	Note: The ARID1B rearrangement is an intragenic duplication of exons 14-18. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: in frame		11653	0	55	6	Intron of ARID1B(+): 2Kb before exon 14	ARID1B	157508630			6	Intron of ARID1B(+): 22bp after exon 18	ARID1B	157522644			46	DUPLICATION		14014	167167	12854	54	NEW_VARIANT
P-0015209-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 fused to ERG exon2): c.55+2192:TMPRSS2_c.18+13090:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		138475	0	55	21	Intron of ERG(-): 13Kb after exon 1	ERG	39857197			21	Intron of TMPRSS2(-): 2Kb after exon 1	TMPRSS2	42877685			58	DELETION		3020488	167152	136393	54	NEW_VARIANT
P-0015215-T01-IM6	TSC2 (NM_000548) - NPW (NM_001099456) rearrangement: c.1101:TSC2_c.-3135:NPWdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (TSC2-NPW)		28740	0	39	16	Promoter of NPW(+): 3Kb from tx start	NPW	2066768			16	Exon 11 of TSC2(+)	TSC2	2110796			65	DUPLICATION		44028	167210	48303	38	NEW_VARIANT
P-0015215-T01-IM6	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)	PRECISE	Note: The CD74-ROS1 fusion includes the kinase domain of ROS1. (PMID: 22327623)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (CD74-ROS1)		0	0	38	6	Intron of ROS1(-): 122bp after exon 32	ROS1	117650370			5	Intron of CD74(-): 182bp before exon 7	CD74	149783057			23	TRANSLOCATION		0	167214	0	37	NEW_VARIANT
P-0015239-T01-IM6	PIK3R1 (NM_181523) rearrangement: (5;6)(q13.1;q25.3)(chr5:g.67591907::chr6:g.158681004)	PRECISE	Note: The PIK3R1 rearrangement is a translocation that may result in the truncation of exons 9-16. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	6	6	IGR: 53Kb before TULP4(+)	TULP4	158681004			5	Intron of PIK3R1(+): 92bp before exon 9	PIK3R1	67591907			3	TRANSLOCATION		0	167271	0	6	NEW_VARIANT
P-0015240-T01-IM6	PLCG2 (NM_002661) rearrangement: t(3;16)(q27.1;q23.3)(chr3:g.184034134::chr16:g.81968167)	PRECISE	Note: The PLCG2 rearrangement is a translocation that may result in the truncation of exons 27-33. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (PLCG2-EIF4G1)		0	0	27	16	Intron of PLCG2(+): 31bp after exon 26	PLCG2	81968167			3	Intron of EIF4G1(+): 128bp after exon 4	EIF4G1	184034134			21	TRANSLOCATION		0	167264	0	27	NEW_VARIANT
P-0015244-T01-IM6	APC (NM_000038) rearrangement: t(5;11)(q22.2;q13.3)(chr5:g.112043596::chr11:g.68605475)	IMPRECISE	Note: The rearrangement is a translocation with a breakpoint within the 5UTR  of APC. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense fusion		0	0	26	11	5-UTR of CPT1A(-): 23Kb before coding start	CPT1A	68605475			5	5-UTR of APC(+): 47Kb before coding start	APC	112043596			0	TRANSLOCATION		0	167384	0	26	NEW_VARIANT
P-0015244-T01-IM6	FBXW7 (NM_033632) - SMAD3 (NM_005902) rearrangement: t(4;15)(q31.3;q22.33)(chr4:g.153290194::chr15:g.67479765)	PRECISE	Note: The FBXW7 rearrangement is a translocation which results in the fusion of FBXW7 exon2 to SMAD3 exon 8. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (FBXW7-SMAD3)		0	0	8	15	Exon 8 of SMAD3(+)	SMAD3	67479765			4	Intron of FBXW7(-): 13Kb after exon 1	FBXW7	153290194			17	TRANSLOCATION		0	167387	0	8	NEW_VARIANT
P-0015250-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exon 2): c.56-4310:TMPRSS2_c.19-20348:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		88176	0	53	21	Intron of ERG(-): 20Kb before exon 4	ERG	39837892			21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42874426			71	DELETION		3036534	167397	63894	53	NEW_VARIANT
P-0015291-T01-IM6	RARA (NM_000964) - SMURF2 (NM_022739) rearrangement: c.179-5342:RARA_c.400+2094:SMURF2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (RARA-SMURF2)		498799	0	55	17	Intron of RARA(+): 107bp after exon 1	RARA	38499226			17	Intron of SMURF2(-): 2Kb after exon 5	SMURF2	62585108			47	INVERSION		24085882	167566	530194	50	NEW_VARIANT
P-0015294-T01-IM6	NFKBIA (NM_020529) rearrangement: c.548-39_chr14:g.35888329del	PRECISE	Note: The NFKBIA rearrangement is a deletion which includes exons 1-3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5804	0	16	14	Intron of NFKBIA(-): 39bp before exon 4	NFKBIA	35872104			14	IGR: 18Kb before NFKBIA(-)	NFKBIA	35888329			3	DELETION		16225	167569	3660	14	NEW_VARIANT
P-0015300-T01-IM6	MLL3 (NM_170606) rearrangement: c.3712+1801_c.6520del	PRECISE	Note: The MLL3 rearrangement is an intragenic deletion of exons 24-36. One of the breakpoints is within exon36. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		27752	0	8	7	Exon 36 of MLL3(-)	MLL3	151878425			7	Intron of MLL3(-): 2Kb after exon 23	MLL3	151915807			25	DELETION		37382	167556	19097	5	NEW_VARIANT
P-0015301-T01-IM6	STAG2 (NM_001042749) rearrangement: c.1417-896_c.2184+26del	PRECISE	Note: The STAG2 rearrangement is an intragenic deletion of exons 16-22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons: in frame		9741	0	12	X	Intron of STAG2(+): 896bp before exon 15	STAG2	123194178			X	Intron of STAG2(+): 26bp after exon 21	STAG2	123200138			15	DELETION		5960	167580	11870	11	NEW_VARIANT
P-0015302-T01-IM6	CDK12 (NM_016507) rearrangement: c.809_c.1047-94del	PRECISE	Note: The CDK12 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1488	0	62	17	Exon 1 of CDK12(+)	CDK12	37619133			17	Intron of CDK12(+): 94bp before exon 2	CDK12	37627038			72	DELETION		7905	167572	989	60	NEW_VARIANT
P-0015310-T02-IM6	RUFY3 (NM_001037442) - RET (NM_020975) rearrangement: t(4;10)(q13.3;q11.21)(chr4:g.71655316::chr10:g.43610427)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (RUFY3-RET)		0	0	49	10	Intron of RET(+): 243bp after exon 11	RET	43610427			4	Intron of RUFY3(+): 7bp after exon 12	RUFY3	71655316			0	TRANSLOCATION		0	168656	0	42	NEW_VARIANT
P-0015321-T01-IM6	IRS2 (NM_003749) rearrangement: chr13:g.30177124_c.4013-5776inv	PRECISE	Note: The IRS2 rearrangement is an inversion of a part of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	5to5	5to5	-		259301	0	9	13	IGR: 7Kb after SLC7A1(-)	SLC7A1	30177124			13	Intron of IRS2(-): 6Kb before exon 2	IRS2	110414431			21	INVERSION		80237307	167643	307581	9	NEW_VARIANT
P-0015321-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.244:CDKN2Ap14ARF_chr9:g.22157561del	PRECISE	Note: The CDKN2Ap14ARF rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.	MANUAL_OK	3to5	3to5	-		0		7	9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21971157			9	IGR: 36Kb after CDKN2BAS(+)	CDKN2BAS	22157561			11	DELETION		186404	168197	11559		NEW_VARIANT
P-0015321-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.201:CDKN2Ap16INK4A_chr9:g.22157561del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement is a deletion of 5UTR and exons 1-2. One of the breakpoint is within exon 2.	MANUAL_OK	3to5	3to5	-		0		7	9	Exon 2 of CDKN2Ap16INK4(-)	CDKN2Ap16INK4A	21971157			9	IGR: 36Kb after CDKN2BAS(+)	CDKN2BAS	22157561			11	DELETION		186404	168198	11559		NEW_VARIANT
P-0015333-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(2;21)(q23.3;q22.3)(chr2:g.151050245::chr21:g.42870305)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	28	21	Intron of TMPRSS2(-): 189bp before exon 2	TMPRSS2	42870305			2	IGR: 274Kb before RND3(-)	RND3	151050245			17	TRANSLOCATION		0	167607	0	26	NEW_VARIANT
P-0015333-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-211_c.795-1208del	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exons 2-7.	MANUAL_OK	5to5	5to5	Antisense fusion		29565	0	19	21	Intron of TMPRSS2(-): 1Kb before exon 8	TMPRSS2	42849755			21	Intron of TMPRSS2(-): 211bp before exon 2	TMPRSS2	42870327			25	INVERSION		20572	167605	30598	19	NEW_VARIANT
P-0015337-T01-IM6	POLE (NM_006231) Rearrangement : chr12:g.133806491_c.802-25:POLEdel	PRECISE	Note: The POLE Rearrangement results in the deletion of exons 1-8  of POLE. Its functional significance is undetermined	MANUAL_OK	3to5	3to5	-		15564	0	7	12	Intron of POLE(-): 25bp before exon 9	POLE	133253264			12	IGR: 48Kb before ZNF268(+)	ZNF268	133806491			8	DELETION		553227	167697	16014	7	NEW_VARIANT
P-0015337-T01-IM6	SMARCA4 (NM_003072) Rearrangement : c.-32+8277_c.222+92del	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		4736	0	60	19	5-UTR of SMARCA4(+): 15Kb before coding start	SMARCA4	11080127			19	Intron of SMARCA4(+): 92bp after exon 1	SMARCA4	11095141			83	INVERSION		15014	167698	4569	59	NEW_VARIANT
P-0015345-T01-IM6	BRAF (NM_004333) Rearrangement : c.138+19968_c.1141-304del	PRECISE	Note: The BRAF Rearrangement results in the intragenic deletion of exons 2-8 of BRAF.	MANUAL_OK	3to5	3to5	Deletion of 7 exons: in frame		147930	0	102	7	Intron of BRAF(-): 304bp before exon 9	BRAF	140487688			7	Intron of BRAF(-): 20Kb after exon 1	BRAF	140604398			116	DELETION		116710	167673	90200	197	NEW_VARIANT
P-0015358-T01-IM6	AGO2 (NM_012154) rearrangement: t(8;19)(q24.3;q13.11)(chr8:g.141566378::chr19:g.33663503)	IMPRECISE	Note: The AGO2 rearrangement involves the truncation of exons 9-19. One of the breakpoints is within exon 9.	MANUAL_OK	5to3	5to3	-		0	0	32	19	Intron of WDR88(+): 157bp after exon 10	WDR88	33663503			8	Exon 9 of EIF2C2(-)	EIF2C2	141566378			0	TRANSLOCATION		0	167744	0	30	NEW_VARIANT
P-0015360-T02-IM6	ETV6 (NM_001987) rearrangement: c.329-3183_c.463+3169dup	PRECISE	Note: The ETV6 (NM_001987) rearrangement results in the duplication of exon 4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		15693	0	9	12	Intron of ETV6(+):3Kb before exon 4	ETV6	12003178			12	Intron of ETV6(+):3Kb after exon 4	ETV6	12009664			10	DUPLICATION		6486	172054	35294	9	NEW_VARIANT
P-0015372-T01-IM6	CAPZB (NM_001206540) -MTOR (NM_004958) rearrangement: c.1492:MTOR_c.4-24545:CAPZBdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (CAPZB-MTOR)		80690	0	20	1	Exon 10 of MTOR(-)	MTOR	11301659			1	Intron of CAPZB(-): 25Kb before exon 2	CAPZB	19770789			42	DELETION		8469130	167811	126521	20	NEW_VARIANT
P-0015378-T01-IM6	PAK7 (NM_177990) rearrangement: c.1153_c.-11-6786del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		7045	0	34	20	Exon 6 of PAK7(-)	PAK7	9546869			20	5-UTR of PAK7(-): 7Kb before coding start	PAK7	9631773			39	DELETION		84904	167850	12676	29	NEW_VARIANT
P-0015411-T01-IM6	PTPRT (NM_133170) Rearrangement : c.1444:PTPRT_c.-903:MAFBinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		41752	0	8	20	Promoter of MAFB(-): 517bp from tx start	MAFB	39318393			20	Exon 8 of PTPRT(-)	PTPRT	41100912			21	INVERSION		1782519	167878	50065	8	NEW_VARIANT
P-0015414-T01-IM6	TRAF7 (NM_032271) Rearrangement : c.6583:PKD1_c.1387-44:TRAF7dup	PRECISE	Note: The TRAF7 Rearrangement results in the duplication of exons 1-15 of TRAF7. its functional significance is undetermined	MANUAL_OK	5to3	5to3	Antisense fusion		37157	0	9	16	Exon 15 of PKD1(-)	PKD1	2158585			16	Intron of TRAF7(+): 44bp before exon 16	TRAF7	2225258			13	DUPLICATION		66673	167967	42650	7	NEW_VARIANT
P-0015430-T01-IM6	EIF2C3 (NM_024852) - STK40 (NM_032017) rearrangement:  c.2274+4567:EIF2C3_c.870:STK40dup	PRECISE	Note: The EIF2C3 - STK40 rearrangement is a duplication with a breakpoint within exon 9 of STK40. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		11471	0	21	1	Intron of EIF2C3(+): 5Kb after exon 15	EIF2C3	36513716			1	Exon 9 of STK40(-)	STK40	36809735			21	DUPLICATION		296019	168028	13496	19	NEW_VARIANT
P-0015430-T01-IM6	VTCN1 (NM_024626) rearrangement: c.540_chr1:g.117841527dup	PRECISE	Note: The VTCN1 rearrangement is a duplication with a breakpoint within exon 4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		8648	0	41	1	Exon 4 of VTCN1(-)	VTCN1	117695897			1	IGR: 69Kb before MAN1A2(+)	MAN1A2	117841527			35	DUPLICATION		145630	168027	10237	40	NEW_VARIANT
P-0015430-T01-IM6	MGA (NM_001164273) rearrangement: t(9;15)(q34.3;q15.1)(chr9:g.140014961::chr15:g.42058234)	IMPRECISE	Note: The MGA rearrangement is a translocation with a breakpoint within exon 24. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	102	15	Exon 23 of MGA(+)	MGA	42058234			9	IGR: 6Kb after DPP7(-)	DPP7	140014961			0	TRANSLOCATION		0	168033	0	97	NEW_VARIANT
P-0015430-T01-IM6	STAT5B (NM_012448) - KEAP1 (NM_203500) rearrangement: t(17;19)(q21.2;p13.2)(chr17:g.:40354329::chr19:g.10615471)	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (STAT5B-KEAP1)		0	0	77	19	Promoter of KEAP1(-): 1Kb from tx start	KEAP1	10615471			17	Intron of STAT5B(-): 29bp after exon 18	STAT5B	40354329			20	TRANSLOCATION		0	168035	0	63	NEW_VARIANT
P-0015432-T01-IM6	FGFR2 (NM_000141) - CAT (NM_001752) rearrangement: t(10;11)(q26.13;p13)(chr10:g.123242534::chr11:g.34467980)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-CAT)		0	0	5	11	Intron of CAT(+): 3Kb before exon 2	CAT	34467980			10	Intron of FGFR2(-): 678bp after exon 16	FGFR2	123242534			2	TRANSLOCATION		0	167998	0	5	NEW_VARIANT
P-0015440-T01-IM6	MSI1 (NM_002442) rearrangement: chr12:g.122241038_c.535-53del	PRECISE	Note: The MSI1 rearrangement is a deletion which includes exons 1-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		46185	0	15	12	Intron of MSI1(-): 53bp before exon 9	MSI1	120794875			12	3-UTR of LOC338799(-): 353bp after coding stop	LOC338799	122241038			19	DELETION		1446163	168019	44365	15	NEW_VARIANT
P-0015445-T01-IM6	MYD88 (NM_002468) - ROBO2 (NM_002942) rearrangement: c.503-189:MYD88_c.3935-874:ROBO2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (MYD88-ROBO2)		362340	0	6	3	Intron of MYD88(+): 189bp before exon 3	MYD88	38181690			3	Intron of ROBO2(+): 874bp before exon 25	ROBO2	77692981			5	DELETION		39511291	168054	309335	4	NEW_VARIANT
P-0015457-T01-IM6	RIMBP2 (NM_015347) - CREBBP (NM_004380) rearrangement: t(12;16)(q24.33;p13.3)(chr12:g.130928970::chr16:g.3779580)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (RIMBP2-CREBBP)		0	0	49	16	Exon 31 of CREBBP(-)	CREBBP	3779580			12	Intron of RIMBP2(-): 735bp after exon 7	RIMBP2	130928970			69	TRANSLOCATION		0	168126	0	48	NEW_VARIANT
P-0015471-T01-IM6	LZTS1 (NM_021020) - RAF1 (NM_002880) rearrangement: t(3;8)(p25.2;p21.3)(chr3:g.12641856::chr8:g.20111180)	IMPRECISE	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	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (LZTS1-RAF1)		0	0	48	8	Intron of LZTS1(-): 84bp before exon 2	LZTS1	20111180			3	Intron of RAF1(-): 31bp after exon 8	RAF1	12641856			0	TRANSLOCATION		0	168181	0	45	NEW_VARIANT
P-0015476-T01-IM6	AGO2 (NM_012154)  - SLX4 (NM_032444) rearrangement: t(8;16)(q24.3;p13.3)(chr8:g.141595171::chr16:g.3654062)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (EIF2C2-BTBD12)		0	0	21	16	Intron of BTBD12(-): 2Kb before exon 4	BTBD12	3654062			8	Intron of EIF2C2(-): 47bp after exon 2	EIF2C2	141595171			11	TRANSLOCATION		0	168195	0	18	NEW_VARIANT
P-0015476-T01-IM6	DNMT3A (NM_022552) rearrangement: c.957_chr2:g.24788000dup	PRECISE	Note: The DNMT3A rearrangement is a duplication with a breakpoint within exon 8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		35918	0	70	2	IGR: 19Kb before NCOA1(+)	NCOA1	24788000			2	Exon 8 of DNMT3A(-)	DNMT3A	25470517			87	DUPLICATION		682517	168191	36191	69	NEW_VARIANT
P-0015482-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon1 fused to ERG exon 2): c.56-1115:TMPRSS2_c.18+11715:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		50061	0	12	21	Intron of ERG(-): 12Kb after exon 1	ERG	39858572			21	Intron of TMPRSS2(-): 1Kb before exon 2	TMPRSS2	42871231			31	DELETION		3012659	168150	41730	12	NEW_VARIANT
P-0015494-T01-IM6	IGF1R (NM_000875) - ROS1 (NM_002944) Rearrangement : t(6,15)(q22.1,q26.3)(chr6:g.117646453::chr15:g.99477638)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (IGF1R-ROS1)		0	0	102	15	Intron of IGF1R(+): 415bp before exon 16	IGF1R	99477638			6	Intron of ROS1(-): 875bp before exon 34	ROS1	117646453			53	TRANSLOCATION		0	168239	0	312	NEW_VARIANT
P-0015510-T01-IM6	CYLD (NM_001042355) Rearrangement : c.248:CYLD_chr16:g.54625586del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		37897	0	31	16	Exon 4 of CYLD(+)	CYLD	50783857			16	IGR: 308Kb before IRX3(-)	IRX3	54625586			31	DELETION		3841729	168301	21911	28	NEW_VARIANT
P-0015518-T01-IM6	NOTCH2 (NM_024408) Rearrangement : t(1,2)(p11.2,q12.1)(chr1:g.120510213::chr2:g.104768940)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	44	2	IGR: 282Kb before LOC150568(+)	LOC150568	104768940			1	Exon 8 of NOTCH2(-)	NOTCH2	120510213			18	TRANSLOCATION		0	168308	0	43	NEW_VARIANT
P-0015531-T01-IM6	TNFRSF14 (NM_003820) - PLCH2 (NM_014638)  rearrangement: c.2547:PLCH2_c.69+32:TNFRSF14dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (TNFRSF14-PLCH2)		1943	0	74	1	Exon 19 of PLCH2(+)	PLCH2	2430635			1	Intron of TNFRSF14(+): 32bp after exon 1	TNFRSF14	2488204			49	DUPLICATION		57569	168329	1760	72	NEW_VARIANT
P-0015558-T01-IM6	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.2)(chr12:g.12019771::chr15:g.97567900)	IMPRECISE	Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 5-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	29	15	IGR: 241Kb before SPATA8(+)	SPATA8	97567900			12	Intron of ETV6(+): 3Kb before exon 5	ETV6	12019771			0	TRANSLOCATION		0	168440	0	25	NEW_VARIANT
P-0015572-T01-IM6	MAP2K4 (NM_003010) - FASN (NM_004104) rearrangement: c.954:MAP2K4_c.4564+7:FASNinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (MAP2K4-FASN)		772246	0	8	17	Exon 9 of MAP2K4(+)	MAP2K4	12032518			17	Intron of FASN(-): 7bp after exon 26	FASN	80042668			18	INVERSION		68010150	168519	706665	7	NEW_VARIANT
P-0015572-T01-IM6	NF1 (NM_001042492) rearrangement: c.1399_c.6921+29dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 13-45. One of the breakpoints is within exon 13.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		40932	0	25	17	Exon 13 of NF1(+)	NF1	29541475			17	Intron of NF1(+): 29bp after exon 45	NF1	29665852			47	DUPLICATION		124377	168518	45914	14	NEW_VARIANT
P-0015588-T01-IM6	C10orf118 (NM_018017) - RET (NM_020975) Rearrangement : c.1326+142:C10orf118_c.2136+124:RETinv	PRECISE	The C10orf118- RET Rearrangement results in the fusion exons 1-7 of C10orf118 with exons 12-20 of RET. This event includes the protein kinase domain of RET. Additional testing will be performed via Archer FusionPlexTM Custom Solid Panel if adequate material is available and the results will be reported in a separate accession number.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (C10orf118-RET)		306304	0	27	10	Intron of RET(+): 124bp after exon 11	RET	43610308			10	Intron of C10orf118(-): 142bp after exon 7	C10orf118	115896803			60	INVERSION		72286495	168532	289067	25	NEW_VARIANT
P-0015589-T01-IM6	BAP1 (NM_004656) Rearrangement : c.932-100:BAP1_c.187-1874:PHF7del	PRECISE	Note: The BAP1 Rearrangement results in the deletion of exons 1-10 of BAP1.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		19306	0	27	3	Intron of BAP1(-): 100bp before exon 11	BAP1	52439410			3	Intron of PHF7(+): 2Kb before exon 5	PHF7	52451975			44	DELETION		12565	168546	842	27	NEW_VARIANT
P-0015600-T01-IM6	TAP1 (NM_000593) Rearrangement : c.*35:TAP1_c.939+214:COL11A2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		40171	0	62	6	3-UTR of TAP1(-): 35bp after coding stop	TAP1	32813321			6	Intron of COL11A2(-): 214bp after exon 6	COL11A2	33152555			72	DUPLICATION		339234	168606	46038	62	NEW_VARIANT
P-0015618-T01-IM6	CDH1 (NM_004360) rearrangement: c.388-223_c.688-75del	PRECISE	Note: The CDH1 rearrangement is a deletion of exons 4-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: in frame		5815	0	48	16	Intron of CDH1(+): 223bp before exon 4	CDH1	68842104			16	Intron of CDH1(+): 75bp before exon 6	CDH1	68844025			40	DELETION		1921	168635	3722	43	NEW_VARIANT
P-0015618-T01-IM6	FOXP1 (NM_001244814) rearrangement: c.1429-3_c.1146+678del	PRECISE	Note: The FOXP1 rearrangement is a deletion of exons 11-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons: in frame		3751	0	100	3	Intron of FOXP1(-): 3bp before exon 17	FOXP1	71026196			3	Intron of FOXP1(-): 678bp after exon 14	FOXP1	71036467			76	DELETION		10271	168636	3220	98	NEW_VARIANT
P-0015628-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-27:TMPSS2_c.18+6821:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		66035	0	93	21	Intron of ERG(-): 7Kb after exon 1	ERG	39863466			21	Intron of TMPRSS2(-): 27bp before exon 2	TMPRSS2	42870143			58	DELETION		3006677	168697	47894	89	NEW_VARIANT
P-0015640-T01-IM6	PPP2R1A (NM_014225) rearrangement: c.652-19_chr19:g.53344778del	PRECISE	Note: The PPP2R1A rearrangement is a deletion of exons 6-15.	MANUAL_OK	3to5	3to5	Antisense fusion		17676	0	102	19	Intron of PPP2R1A(+): 19bp before exon 6	PPP2R1A	52716189			19	Exon 5 of ZNF468(-)	ZNF468	53344778			71	DELETION		628589	168730	22834	104	NEW_VARIANT
P-0015668-T01-IM6	CAPN11 (NM_007058) - VEGFA (NM_001171625) Rearrangement : c.1521:CAPN11_c.423-18:VEGFAdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (CAPN11-VEGFA)		3804	0	25	6	Intron of VEGFA(+): 18bp before exon 6	VEGFA	43748451			6	Exon 14 of CAPN11(+)	CAPN11	44147781			26	DUPLICATION		399330	168774	4886	25	NEW_VARIANT
P-0015675-T01-IM6	MLL3 (NM_170606) rearrangement: c.10306:MLL3_g.159036888inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		92808	0	10	7	Exon 43 of MLL3(-)	MLL3	151860356			7	IGR: 216Kb before VIPR2(-)	VIPR2	159036888			24	INVERSION		7176532	169024	110574	9	NEW_VARIANT
P-0015676-T01-IM6	MLL (NM_001197104) rearrangement : c.6576:MLL_g.118626801dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		48339	0	10	11	Exon 27 of MLL(+)	MLL	118373183			11	Intron of DDX6(-): 168bp after exon 11	DDX6	118626801			34	DUPLICATION		253618	169046	65977	9	NEW_VARIANT
P-0015676-T01-IM6	BAP1 (NM_023034) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52437443::chr9:g.140784264)	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		0	0	43	9	Intron of CACNA1B(+): 7Kb after exon 3	CACNA1B	140784264			3	Exon 13 of BAP1(-)	BAP1	52437443			21	TRANSLOCATION		0	169050	0	42	NEW_VARIANT
P-0015689-T01-IM6	RFWD2 (NM_022457) rearrangement : c.832-26:RFWD2_g.180459257inv	PRECISE	Note: The RFWD2 rearrangement results in an inversion of RFWD2 exons 1-6. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		14048	0	16	1	Intron of RFWD2(-): 26bp before exon 7	RFWD2	176105709			1	Intron of ACBD6(-): 2Kb after exon 3	ACBD6	180459257			19	INVERSION		4353548	168834	18505	15	NEW_VARIANT
P-0015692-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.4970_g.112190339del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		18127	0	18	16	Exon 2 of ZFHX3(-)	ZFHX3	72992241			16	5-UTR of ZFHX3(-): 25Kb before coding start	ZFHX3	73018578			28	DELETION		26337	168817	13409	17	NEW_VARIANT
P-0015699-T01-IM6	SPTBN1 (NM_003128) - ALK (NM_004304) fusion (SPTBN1 exon 7  fused to  ALK exon 20):  c.764-1028:SPTBN1_c.3172+890:ALKinv	PRECISE	Note: The SPTBN1 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK. (PMID: 27496196)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (SPTBN1-ALK)		221572	0	13	2	Intron of ALK(-): 890bp after exon 19	ALK	29447437			2	Intron of SPTBN1(+): 1Kb before exon 8	SPTBN1	54847509			40	INVERSION		25400072	168860	202081	13	NEW_VARIANT
P-0015709-T01-IM6	CDKN1B (NM_004064) rearrangement: c.564_chr12:g.12948373del	PRECISE	Note: The CDKN1B rearrangement is a deletion with a breakpoint within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1701	0	6	12	Exon 2 of CDKN1B(+)	CDKN1B	12871847			12	IGR: 4Kb after APOLD1(+)	APOLD1	12948373			9	DELETION		76526	168889	2403	6	NEW_VARIANT
P-0015711-T01-IM6	BRAF (NM_004333) - CAPZA2 (NM_006136) rearrangement:  c.981-1133:BRAF_c.39+8949:CAPZA2dup	PRECISE	Note: The BRAF - CAPZA2 rearrangement is a duplication (23983747 bp) which includes the kinase domain of BRAF.	MANUAL_OK	5to3	5to3	-		209304	0	39	7	Intron of CAPZA2(+): 9Kb after exon 1	CAPZA2	116511653			7	Intron of BRAF(-): 1Kb before exon 8	BRAF	140495400			55	DUPLICATION		23983747	168899	238664	37	NEW_VARIANT
P-0015713-T01-IM6	RB1 (NM_000321) rearrangement: c.1050-15_c.1216-1620dup	PRECISE	Note: The RB1 rearrangement is an intragenic duplication of exons 11-12. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: out of frame		2100	0	44	13	Intron of RB1(+): 15bp before exon 11	RB1	48942648			13	Intron of RB1(+): 2Kb before exon 13	RB1	48949434			36	DUPLICATION		6786	168910	2435	44	NEW_VARIANT
P-0015726-T01-IM6	ELF3 (NM_004433) rearrangement: chr1:g.24920380_c.599-39:ELF3inv	PRECISE	Note: The ELF3 rearrangement is an inversion which includes exons 1-5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1124844	0	47	1	5-UTR of C1orf130(+): 2Kb before coding start	C1orf130	24920380			1	Intron of ELF3(+): 39bp before exon 6	ELF3	201982036			69	INVERSION		177061656	168957	1106087	40	NEW_VARIANT
P-0015727-T01-IM6	ATM (NM_000051) Rearrangement : c.6198+369_6276del	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		867	0	12	11	Intron of ATM(+): 369bp after exon 42	ATM	108187209			11	Exon 43 of ATM(+)	ATM	108188177			0	DELETION		968	168965	606	12	NEW_VARIANT
P-0015735-T01-IM6	RPTOR (NM_020761) - CEP95 (NM_138363) Rearrangement : c.1212+107:RPTOR_c.256+1803:CEPN5dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (RPTOR-CCDC45)		85092	0	5	17	Intron of CCDC45(+): 2Kb after exon 3	CCDC45	62508201			17	Intron of RPTOR(+): 107bp after exon 10	RPTOR	78811904			15	DUPLICATION		16303703	168963	126719	5	NEW_VARIANT
P-0015742-T01-IM6	TBX3 (NM_016569) rearrangement: chr12:g.115489107_c.718-41del	PRECISE	Note: The TBX3 rearrangement is a deletion of 5UTR and exons 1-3.	MANUAL_OK	3to5	3to5	-		7538	0	27	12	Intron of TBX3(-): 41bp before exon 3	TBX3	115117497			12	IGR: 381Kb before TBX3(-)	TBX3	115489107			39	DELETION		371610	169139	4162	27	NEW_VARIANT
P-0015744-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2  exon 1 fused to ERG exons 4-11): c.56-917:TMPRSS2_c.39+7155:ERGdel	PRECISE	Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		35702	0	20	21	Intron of ERG(-): 7Kb after exon 3	ERG	39940431			21	Intron of TMPRSS2(-): 917bp before exon 2	TMPRSS2	42871033			55	DELETION		2930602	169150	20716	20	NEW_VARIANT
P-0015744-T01-IM6	EWSR1 (NM_013986) - NF2 (NM_000268) rearrangement: c.1180-298:EWSR1_c.1738-1347:NF2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		25698	0	26	22	Intron of EWSR1(+): 298bp before exon 11	EWSR1	29691931			22	Intron of NF2(+): 1Kb before exon 5	NF2	30089394			35	INVERSION		397463	169151	25666	26	NEW_VARIANT
P-0015751-T01-IM6	STAT5A (NM_003152) rearrangement: t(11;17)(q24.1;q21.2)(chr11:g.122871383::chr17:g.40461499)	IMPRECISE	Note: The STAT5A rearrangement is a translocation that may result in a truncation of  exons 19-20. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	19	17	Exon 19 of STAT5A(+)	STAT5A	40461499			11	IGR: 17Kb before LOC341056(+)	LOC341056	122871383			0	TRANSLOCATION		0	169176	0	19	NEW_VARIANT
P-0015759-T01-IM6	MLL2 (NM_003482) Rearrangement : c.14076-10_c.14420del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4445	0	48	12	Exon 46 of MLL2(-)	MLL2	49421887			12	Intron of MLL2(-): 10bp before exon 44	MLL2	49423029			67	DELETION		1142	169204	3820	48	NEW_VARIANT
P-0015764-T01-IM6	NOTCH2 (NM_024408) - PDE4DIP (NM_001198834) Rearrangement : c.3289:NOTCH2_c.-1821:PDE4DIPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NOTCH2-PDE4DIP)		26888	0	11	1	Exon 20 of NOTCH2(-)	NOTCH2	120480528			1	Intron of PDE4DIP(-): 2Kb before exon 4	PDE4DIP	144996552			26	DUPLICATION		24516024	169200	32690	11	NEW_VARIANT
P-0015829-T01-IM6	PDCD1 (NM_005018)  - DNER (NM_139072) rearrangement: c.436+117:PDCD1_c.1855+3458:DNERinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		16818	0	4	2	Intron of DNER(-):3Kb after exon 11	DNER	230249523			2	Intron of PDCD1(-):116bp after exon 2	PDCD1	242794656			10	INVERSION		12545133	169392	17762	5	NEW_VARIANT
P-0015831-T01-IM6	PIK3CD (NM_005026) rearrangement: c.930+139_c.2865-26inv	PRECISE	Note: The PIK3CD rearrangement is an intragenic inversion of exons 8-22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 15 exons : out of frame		28801	1	50	1	Intron of PIK3CD(+):139bp after exon 7	PIK3CD	9777305			1	Intron of PIK3CD(+):25bp before exon 23	PIK3CD	9784836			10	DELETION		7531	169393	51798	54	NEW_VARIANT
P-0015831-T01-IM6		IMPPRECISE		MANUAL_OK	3to5	3to5	-		0		5	10	Intron of GATA3(+):75bp after exon 4	GATA3	8106176			3	IGR:191Kb before LINC01206(+)	LINK01206	181861092			0	TRANSLOCATION		0	172022	0		NEW_VARIANT
P-0015837-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-1324:TMPSS2_c.18+10744:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		64378	0	24	21	Intron of ERG(-):11Kb after exon 1	ERG	39859543			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871440			10	DELETION		3011897	169443	49050	26	NEW_VARIANT
P-0015839-T01-IM6	JAK1 (NM_002227) rearrangement: g.59823362_c.83del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		29000	0	33	1	Intron of FGGY(+):11Kb after exon 4	FGGY	59823362			1	Exon 3 of JAK1(-)	JAK1	65349082			10	DELETION		5525720	169446	46757	35	NEW_VARIANT
P-0015839-T01-IM6	FGFR2 (NM_000141) rearrangement: g.53199568_c.2302-1423dup	PRECISE	Note: The FGFR2 rearrangement results in the duplication of exon 18. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		215705	0	24	10	Intron of PRKG1(+):28Kb before exon 3	PRKG1	53199568			10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240958			10	DUPLICATION		70041390	169448	306360	31	NEW_VARIANT
P-0015850-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 to ERG exon 4): c.55+1034:TMPRSS2_c.39+9192:ERG	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		103415	0	18	21	Intron of ERG(-):9Kb after exon 3	ERG	39938394			21	Intron of TMPRSS2(-):1Kb after exon 1	TMPRSS2	42878843			10	DELETION		2940449	169514	154582	19	NEW_VARIANT
P-0015850-T01-IM6		PRECISE		MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SGMS2:TMPRSS2}		0		49	21	Exon 12 of TMPRSS2(-)	TMPRSS2	42840444			4	Intron of SGMS2(+):1Kb before exon 6	SGMS2	108828375			105	TRANSLOCATION		0	172025	0		NEW_VARIANT
P-0015863-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 8-16): c.2312:FGFR3_c.1644+147:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		29712	0	116	4	Intron of TACC3(+):147bp after exon 7	TACC3	1737199			4	Exon 18 of FGFR3(+)	FGFR3	1808880			10	DUPLICATION		71681	169532	69680	133	NEW_VARIANT
P-0015874-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: chr9:g.21981196_c.150+170del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1734	0	16	9	Exon 1 of CDKN2A(-)	CDKN2A	21974507			9	Intron of CDKN2A(-):10Kb before exon 2	CDKN2A	21981196			10	DELETION		6689	169530	1241	17	NEW_VARIANT
P-0015885-T01-IM6	FLT4 (NM_182925) rearrangement: c.449_c.770del	PRECISE	Note: FLT4 (NM_182925) rearrangement is a intragenic deletion of exon 4-6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3994	5	2	5	Exon 6 of FLT4(-)	FLT4	180056742			5	Exon 4 of FLT4(-)	FLT4	180057289			8	DELETION		547	169550	4150	0	NEW_VARIANT
P-0015896-T01-IM6	KANSL2 (NM_017822) - KMT2D (NM_003482) rearrangement: c.974-729:KANSL2_c.9582dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KANSL2:KMT2D}		39351	0	18	12	Intron of KANSL2(-):729bp before exon 8	KANSL2	49055131			12	Exon 34 of KMT2D(-)	KMT2D	49431557			10	DUPLICATION		376426	169545	80537	19	NEW_VARIANT
P-0015896-T01-IM6	CASP8 (NM_00108012) rearrangement: c.1_c.589dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		5792	0	16	2	Intron of ORC2(-):2Kb before exon 16	ORC2	201780633			2	Exon 6 of CASP8(+)	CASP8	202139650			10	DUPLICATION		359017	169544	12704	16	NEW_VARIANT
P-0015903-T01-IM6	NUF2 (NM_031423) - NOS1AP (NM_014697) rearrangement: c.488:NUF2_c.105+21977:NOS1APdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NUF2:NOS1AP}		27176	0	29	1	Intron of NOS1AP(+):22Kb after exon 1	NOS1AP	162062049			1	Exon 7 of NUF2(+)	NUF2	163307862			10	DUPLICATION		1245813	169598	66794	31	NEW_VARIANT
P-0015903-T01-IM6	DDR2 (NM_006182) rearrangement: c.2018_g.167438149del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		22431	0	14	1	Exon 15 of DDR2(+)	DDR2	162745603			1	Intron of CD247(-):28Kb before exon 2	CD247	167438149			10	DELETION		4692546	169592	54084	14	NEW_VARIANT
P-0015903-T01-IM6	RFWD2 (NM_022457) rearrangement: g.171760607_c.1051dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		13570	0	22	1	Intron of METTL13(+):549bp before exon 6	METTL13	171760607			1	Exon 10 of RFWD2(-)	RFWD2	176055002			10	DUPLICATION		4294395	169600	33657	23	NEW_VARIANT
P-0015937-T01-IM6	CARD11 (NM_032415) Rearrangement : c.1102_c.1178del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1032	0	5	7	Exon 9 of CARD11(-)	CARD11	2976834			7	Exon 8 of CARD11(-)	CARD11	2977582			0	DELETION		748	169674	434	7	NEW_VARIANT
P-0015942-T01-IM6	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exons 1-17 with BICC1 exons 9-21) : c.2302-1485:FGFR2_c.1048-60:BICC1inv	PRECISE	Note: The FGFR2-BICC1 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		162037	0	33	10	Intron of BICC1(+):59bp before exon 9	BICC1	60553184			10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123241020			10	INVERSION		62687836	169741	276990	50	NEW_VARIANT
P-0015959-T01-IM6	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1159:EWSR1_c.1438-1716:AP1B1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		22886	0	42	22	Exon 12 of EWSR1(+)	EWSR1	29688575			22	Intron of AP1B1(-):2Kb before exon 12	AP1B1	29740088			10	DELETION		51513	170239	36905	108	NEW_VARIANT
P-0015962-T01-IM6	SPG11 (NM_025137) - B2M (NM_004048) rearrangement: c.2835-559:SPG11_c.318:B2Mdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2173	0	5	15	Intron of SPG11(-):559bp before exon 16	SPG11	44908323			15	Exon 2 of B2M(+)	B2M	45007871			10	DELETION		99548	169791	4805	5	NEW_VARIANT
P-0015962-T01-IM6	REL (NM_002908) rearrangement: c.1759_chr2:g.236014429inv	PRECISE	Note: The REL rearrangement is an inversion (174864860 bp) with a breakpoint within exon 11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		432360	0	36	2	Exon 11 of REL(+)	REL	61149569			2	IGR: 154Kb before SH3BP4(+)	SH3BP4	236014429			10	INVERSION		174864860	169793	998869	35	NEW_VARIANT
P-0015972-T01-IM6	ARHGAP42 (NM_152432) - PGR (NM_000926)  rearrangement: c.1162+197:ARHGAP42_c.2357+60:PGRdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		5225	0	37	11	Intron of ARHGAP42(+):197bp after exon 12	ARHGAP42	100820884			11	Intron of PGR(-):59bp after exon 5	PGR	100922095			10	DELETION		101211	169804	4550	38	NEW_VARIANT
P-0015972-T01-IM6	EGFR (NM_005228) rearrangement: c.3163-105_chr7:g.55303080del	PRECISE	Note: The EGFR rearrangement is a deletion that includes exons 27-28, occurring within the EGFR carboxyl-terminus domain (CTD).	MANUAL_OK	3to5	3to5	-		6383	0	60	7	Intron of EGFR(+):104bp before exon 27	EGFR	55270105			7	IGR: 3Kb before ELDR(-)	ELDR	55303080			10	DELETION		32975	169803	7059	60	NEW_VARIANT
P-0015973-T01-IM6	INPPL1 (NM_001567) rearrangement: t(3;11)(q29;q13.4)(chr3:g.197336862::chr11:g.71944080)	PRECISE	Note: The INPPL1 rearrangement is a translocation with a breakpoint within intron 16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	11	Intron of INPPL1(+):38bp before exon 17	INPPL1	71944080			3	IGR: 4Kb before LOC220729(-)	LOC220729	197336862			10	TRANSLOCATION		0	170268	0	12	NEW_VARIANT
P-0015980-T01-IM6	RAD21 (NM_006265) rearrangement: t(8;9)(q24.11;p13.3)(chr8:g.117864822::chr9:g.34869851)	PRECISE	Note: The RAD21 rearrangement is a translocation with a breakpoint within exon 10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	38	9	IGR: 40Kb before FAM205BP(-)	FAM205BP	34869851			8	Exon 10 of RAD21(-)	RAD21	117864822			10	TRANSLOCATION		0	170277	0	37	NEW_VARIANT
P-0016006-T01-IM6	KMDT2D (NM_170606) : c.1_310:KMDT2Ddup	PRECISE	Note: The KMDT2D (NM_170606) rearrangement is a duplication of KMDT2D exons 1-3. The functional significance is unknown.	MANUAL_OK	5to3	5to3	-		124875	0	34	12	IGR: 73Kb before AMIGO2(-)	AMIGO2	47396442			12	Exon 3 of KMT2D(-)	KMT2D	49448401			10	DUPLICATION		2051959	169858	126787	39	NEW_VARIANT
P-0016006-T01-IM6	GTF2I:NM_032999 - MET:NM_000245 : c.586+712:GTF2I_c.3029-494:METdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {GTF2I:MET}		120942	0	21	7	Intron of GTF2I(+):712bp after exon 6	GTF2I	74115676			7	Intron of MET(+):493bp before exon 15	MET	116414441			10	DELETION		42298765	169857	96694	94	NEW_VARIANT
P-0016009-T01-IM6	EGFR (NM_005228) - VOPP1 (NM_030796): c.747+36:EGFR_c.55-23161VOPP1inv	PRECISE	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	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EGFR:VOPP1}		58593	0	4	7	Intron of EGFR(+):36bp after exon 6	EGFR	55220393			7	Intron of VOPP1(-):23Kb before exon 2	VOPP1	55611984			9	INVERSION		391591	169860	421394	4	NEW_VARIANT
P-0016012-T01-IM6	KMT2C (NM_170606) rearrangment: chr7:g.151822136_c.13623:KMT2Cinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {GALNT11:KMT2C}		9046	0	20	7	Promoter of GALNT11(+):99Kb from tx start	GALNT11	151822136			7	Exon 52 of KMT2C(-)	KMT2C	151845389			10	INVERSION		23253	169856	17301	20	NEW_VARIANT
P-0016027-T01-IM6	TPM4 (NM_001145160) - SMARCA4 (NM_003072) rearrangement: c.114+683:TPM4_c.356-46:SMARCA4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TPM4:SMARCA4}		176156	0	12	19	Intron of SMARCA4(+):45bp before exon 4	SMARCA4	11096819			19	Intron of TPM4(+):683bp after exon 1	TPM4	16179231			10	DUPLICATION		5082412	169888	352295	12	NEW_VARIANT
P-0016046-T01-IM6	ROS1 (NM_002944) - SLC34A2(NM_006424) fusion: t(4;6) (p15;q22)(chr4:g.25667671::chr6:g.117662059)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {SLC34A2:ROS1}		0	0	28	6	Intron of ROS1(-):238bp after exon 30	ROS1	117662059			4	Intron of SLC34A2(+):78bp before exon 5	SLC34A2	25667671			10	TRANSLOCATION		0	169966	0	27	NEW_VARIANT
P-0016054-T01-IM6	MAP3K14 (NM_003954) rearrangement: c.1151+122:MAP3K14_chr17:g.44162424inv	PRECISE	MAP3K14 (NM_003954) rearrangement results in the inversion of genomic region including exons 1-5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		8954	0	40	17	Intron of MAP3K14(-):121bp after exon 5	MAP3K14	43363676			17	Intron of KANSL1(-):3Kb before exon 5	KANSL1	44162424			10	INVERSION		798748	169954	25015	45	NEW_VARIANT
P-0016087-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 4-11) : c.56-3952:TMPRSS2_c.39+61847:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		71591	0	10	21	Intron of ERG(-):62Kb after exon 3	ERG	39885739			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874068			10	DELETION		2988329	170637	54697	10	NEW_VARIANT
P-0016093-T02-IM6	TEK (NM_000459) - NHSL2 (NM_001013627) rearrangement: t(9;X)(p21.2;q13.1)(chr9:g.27209165::chrX:g.71149521)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	16	X	Intron of NHSL2(+):18Kb after exon 1	NHSL2	71149521			9	Exon 16 of TEK(+)	TEK	27209165			10	TRANSLOCATION		0	171168	0	20	NEW_VARIANT
P-0016117-T01-IM6	ARID1B (NM_020732) rearrangement: c.683_chr6:g.170354686dup	PRECISE	Note: The ARID1B rearrangement is a duplication (13254940 bp) with a breakpoint within exon 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		66813	0	36	6	Exon 1 of ARID1B(+)	ARID1B	157099746			6	IGR: 121Kb before LOC102724511(+)	LOC102724511	170354686			10	DUPLICATION		13254940	170706	78071	38	NEW_VARIANT
P-0016129-T01-IM6	PIK3CD (NM_005026) rearrangement: c.-32-8659_c.2526del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		34358	0	39	1	5-UTR of PIK3CD(+):9Kb before coding start	PIK3CD	9761823			1	Exon 20 of PIK3CD(+)	PIK3CD	9783282			10	DELETION		21459	170811	30569	40	NEW_VARIANT
P-0016134-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.56-393:TMPRSS2_c.18+26221:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		55063	0	25	21	Intron of ERG(-):26Kb after exon 1	ERG	39844066			21	Intron of TMPRSS2(-):393bp before exon 2	TMPRSS2	42870509			10	DELETION		3026443	170797	41540	34	NEW_VARIANT
P-0016175-T01-IM6	DNMT3B (NM_006892) rearrangement:  t(6;20)(q27;q11.21)(chr6:g.165208692::chr20:g.31375366)	PRECISE	Note: The DNMT3B rearrangement is a translocation that involves the truncation of exons 1-6.	MANUAL_OK	3to5	3to5	-		0	0	18	20	Intron of DNMT3B(+):109bp after exon 6	DNMT3B	31375366			6	IGR: 484Kb before C6orf118(-)	C6orf118	165208692			10	TRANSLOCATION		0	171002	0	18	NEW_VARIANT
P-0016175-T01-IM6	ROS1 (NM_002944) rearrangement: g.66194183_c.5557+62:ROS1inv	PRECISE	Note: The ROS1 rearrangement results in an inversion of exons 34-43. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		190062	0	68	6	Intron of EYS(-):6Kb after exon 5	EYS	66194183			6	Intron of ROS1(-):61bp after exon 33	ROS1	117647325			10	INVERSION		51453142	171000	234373	96	NEW_VARIANT
P-0016187-T01-IM6	SMYD3 (NM_001167740) rearrangement : c.1141_chr1:g.245909232del	PRECISE	Note : The SMYD3 (NM_001167740) rearrangement results in the deletion of exons 11-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1494	0	2	1	IGR: 3Kb before SMYD3(-)	SMYD3	245909232			1	Exon 11 of SMYD3(-)	SMYD3	245927387			10	DELETION		18155	170930	2111	13	NEW_VARIANT
P-0016187-T01-IM6	UPF1 (NM_002911) rearrangement : c.2550_c.2811inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		3006	0	18	19	Exon 18 of UPF1(+)	UPF1	18972911			19	Exon 20 of UPF1(+)	UPF1	18975014			10	INVERSION		2103	170931	5276	18	NEW_VARIANT
P-0016190-T01-IM6	MAP3K1 (NM_005921) rearrangement : c.1113:MAP3K1_chr5:g.56348204del	PRECISE	Note: The MAP3K1 (NM_005921) rearrangement event is a deletion MAP3K1 exon 5-20 including kinase domain (exon 15-20)	MANUAL_OK	3to5	3to5	-		24270	0	59	5	Exon 5 of MAP3K1(+)	MAP3K1	56161244			5	IGR: 122Kb before GPBP1(+)	GPBP1	56348204			10	DELETION		186960	170913	12787	68	NEW_VARIANT
P-0016193-T05-IM6	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	PRECISE	Note: STRN-ALK fusion includes the kinase domain of ALK.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STRN:ALK}		49782	0	55	2	Exon 19 of ALK(-)	ALK	29448326			2	Intron of STRN(-):5Kb after exon 3	STRN	37138302			10	DELETION		7689976	174717	49170	59	NEW_VARIANT
P-0016195-T01-IM6	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)	PRECISE	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	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:GAB2}		0	0	111	11	Intron of GAB2(-):39Kb before exon 2	GAB2	78030553			10	Intron of FGFR2(-):399bp after exon 17	FGFR2	123242812			10	TRANSLOCATION		0	170910	0	127	NEW_VARIANT
P-0016213-T01-IM6	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)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	0	62	6	Intron of ROS1(-):705bp after exon 32	ROS1	117649786			5	Intron of CD74(-):543bp before exon 7	CD74	149783418			10	TRANSLOCATION		0	171030	0	63	NEW_VARIANT
P-0016215-T01-IM6	DNMT1 (NM_001379) - RAVER1 (NM_133452) rearrangement: c.4441+115:DNMT1_c.181:RAVER1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNMT1:RAVER1}		40716	0	9	19	Intron of DNMT1(-):114bp after exon 36	DNMT1	10247646			19	Exon 1 of RAVER1(-)	RAVER1	10444054			0	DUPLICATION		196408	171075	104790	9	NEW_VARIANT
P-0016218-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 2 with ERG exons 3-11) : c.126+1542:TMPRSS2_c.-150+37585:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	-		25550	0	47	21	3-UTR of ERG(-):38Kb after coding stop	ERG	39995997			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868504			10	DELETION		2872507	171082	38181	50	NEW_VARIANT
P-0016221-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		50727	0	23	10	Intron of KIF5B(-):274bp after exon 15	KIF5B	32317081			10	Intron of RET(+):763bp before exon 12	RET	43611268			10	INVERSION		11294187	171088	55340	32	NEW_VARIANT
P-0016223-T01-IM6	EGFR (NM_005228) rearrangement: t(7;19)(p11.2;p13.3)(chr7:g.55223210::chr19:g.6053108)	PRECISE	Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 8-28. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	40	19	5-UTR of RFX2(-):58Kb before coding start	RFX2	6053108			7	Intron of EGFR(+):312bp before exon 8	EGFR	55223210			10	TRANSLOCATION		0	171079	0	40	NEW_VARIANT
P-0016236-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exon 4): c.56-2874:TMPRSS2_c.39+13664:ERGdel	IMPPRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		50386	0	16	21	Intron of ERG(-):14Kb after exon 3	ERG	39933922			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872990			0	DELETION		2939068	171173	91042	16	NEW_VARIANT
P-0016244-T01-IM6	BRD4:NM_058243 Rearrangement : t(19;21)(p13.12;q21.3)(chr19:g.15350666::chr21:g.25706468)	PRECISE	Note: The BRD4 Rearrangement results in the possible truncation of exons 16-20. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	72	21	IGR: 30Kb before LOC101927869(-)	LOC101927869	25706468			19	Intron of BRD4(-):34bp before exon 16	BRD4	15350666			10	TRANSLOCATION		0	171205	0	69	NEW_VARIANT
P-0016254-T01-IM6	SMAD3 (NM_005902) - EFCAB13 (NM_001195192) rearrangement: t(15;17)(q22.33;q21.32)(chr15:g.67477157::chr17:g.45465290)	PRECISE	Note: The SMAD3 - EFCAB13 rearrangement is a translocation with a breakpoint within SMAD3 exon 7. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	6	17	Intron of EFCAB13(+):4Kb before exon 13	EFCAB13	45465290			15	Exon 7 of SMAD3(+)	SMAD3	67477157			10	TRANSLOCATION		0	171123	0	11	NEW_VARIANT
P-0016280-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) rearrangement: c.1316-2732:EML4_c.3172+422:ALKinv	PRECISE	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)	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		97280	0	28	2	Intron of ALK(-):421bp after exon 19	ALK	29447905			2	Intron of EML4(+):3Kb before exon 13	EML4	42525649			10	INVERSION		13077744	171743	150371	26	NEW_VARIANT
P-0016293-T01-IM6	MITF (NM_198159) rearrangment : c.104+56625_c.1014-63MITFdel	PRECISE	Note: The MITF rearrangement results in the deletion of exons 2-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : in frame		16286	0	14	3	Intron of MITF(+):57Kb after exon 1	MITF	69845477			3	Intron of MITF(+):62bp before exon 9	MITF	70008361			10	DELETION		162884	171746	19530	15	NEW_VARIANT
P-0016295-T01-IM6	PTEN (NM_000314)  rearrangment : c.-879_c.54PTENdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		606	0	25	10	5-UTR of PTEN(+):878bp before coding start	PTEN	89623348			10	Exon 1 of PTEN(+)	PTEN	89624280			0	DELETION		932	171759	401	30	NEW_VARIANT
P-0016296-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1 with ERG exons 2-10) : c.40-46781:TMPRSS2_c.18+5962:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28434	0	25	21	Intron of ERG(-):6Kb after exon 1	ERG	39864325			21	Intron of TMPRSS2(-):519bp before exon 3	TMPRSS2	42867024			10	DELETION		3002699	171752	33851	25	NEW_VARIANT
P-0016296-T01-IM6	PBRM1 (NM_018313) rearrangement :  chr3:g.52327928_c.237-51:PBRM1dup	PRECISE	Note: The PBRM1 rearrangement is a duplication of PBRM1 exons 1-4. The functional significance is unknown.	MANUAL_OK	5to3	5to3	-		79866	0	8	3	3-UTR of GLYCTK(+):4Kb after coding stop	GLYCTK	52327928			3	Intron of PBRM1(-):51bp before exon 4	PBRM1	52702712			10	DUPLICATION		374784	171753	113766	9	NEW_VARIANT
P-0016307-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 with ERG exons 2-11) : c.56-2505:TMPRSS2_c.-150+535:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	-		67896	0	87	21	3-UTR of ERG(-):657bp after coding stop	ERG	40033047			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872621			10	DELETION		2839574	171839	99873	98	NEW_VARIANT
P-0016311-T01-IM6	TRIOBP (NM_001039141) - EWSR1 (NM_013986) rearrangement: c.255-219:TRIOBP_c.1060+2:EWSR1Ldup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TRIOBP:EWSR1}		43222	0	4	22	Intron of EWSR1(+):2bp after exon 11	EWSR1	29688160			22	Intron of TRIOBP(+):218bp before exon 5	TRIOBP	38108998			10	DUPLICATION		8420838	171824	105471	7	NEW_VARIANT
P-0016313-T01-IM6	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)	PRECISE	this is known	MANUAL_OK	3to5	3to5	Transcript Fusion {SLC45A3:BRAF}		0	0	62	7	Intron of BRAF(-):739bp after exon 9	BRAF	140486608			1	5-UTR of SLC45A3(-):10Kb before coding start	SLC45A3	205638452			10	TRANSLOCATION		0	171809	0	66	NEW_VARIANT
P-0016325-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		23628	0	28	21	Promoter of ERG(-):121Kb from tx start	ERG	39872831			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868979			10	DELETION		2996148	171886	69580	28	NEW_VARIANT
P-0016326-T01-IM6	CHEK2 (NM_007194) - TTC28 (NM_001145418) rearrangement: c.594:CHEK2_c.102+8045:TTC28inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		8751	0	50	22	Intron of TTC28(-):8Kb after exon 1	TTC28	29067565			22	Exon 5 of CHEK2(-)	CHEK2	29115472			10	INVERSION		47907	171867	13843	50	NEW_VARIANT
P-0016358-T01-IM6	TRAF7 (NM_032271) Rearrangement : c.1087-41:TRAF7_chr16:g.30884849dup	PRECISE	Note: The TRAF7 Rearrangement results in the duplication of exons 12-21 of TRAF7. Its functional significance is undetermined,	MANUAL_OK	5to3	5to3	-		265954	0	21	16	Intron of TRAF7(+):40bp before exon 12	TRAF7	2223748			16	Intron of BCL7C(-):15Kb after exon 5	BCL7C	30884849			10	DUPLICATION		28661101	171925	407773	21	NEW_VARIANT
P-0016377-T01-IM6	NDUFA3 (NM_004542) - POLD1 (NM_002691) rearrangement: c.85+584:NDUFA3_c.510:POLD1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NDUFA3:POLD1}		70226	0	3	19	Exon 5 of POLD1(+)	POLD1	50905302			19	Intron of NDUFA3(+):584bp after exon 2	NDUFA3	54607080			10	DUPLICATION		3701778	172007	78188	5	NEW_VARIANT
P-0016378-T01-IM6	PPP4R2 (NM_174907) rearrangement: t(3;20)(p13;q13.31)(chr3:g.73046268::chr20:g.55536538)	PRECISE	Note: The PPP4R2 rearrangement is a translocation with a breakpoint after exon1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	20	IGR: 207Kb before BMP7(-)	BMP7	55536538			3	Intron of PPP4R2(+):46bp after exon 1	PPP4R2	73046268			10	TRANSLOCATION		0	172013	0	12	NEW_VARIANT
P-0016386-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2452854::chr21:g.42872453)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14.	MANUAL_OK	5to5	5to5	Transcript Fusion {TMPRSS2:CHST12}		0	0	29	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872453			7	5-UTR of CHST12(+):19Kb before coding start	CHST12	2452854			10	TRANSLOCATION		0	172057	0	46	NEW_VARIANT
P-0016386-T01-IM6	TMPRSS2 (NM_001135099) - KMT2C (NM_170606) rearrangement: t(7;21)(q36.1;q22.3)(chr7:g.151900703::chr21:g.42872453)	PRECISE	Note: The TMPRSS2 - KMT2C rearrangement is a translocation that may result in a truncation of TMPRSS2 exons 2-14 and KMT2C exons 26-59. The two structural variants in this sample involving TMPRSS2 suggests a more complex rearrangement. If clinically indicated, additional testing by Archer FusionPlexTM Custom Solid Panel assay may be considered.	MANUAL_OK	3to3	3to3	-		0	0	67	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872510			7	Intron of KMT2C(-):554bp before exon 26	KMT2C	151900703			10	TRANSLOCATION		0	172058	0	65	NEW_VARIANT
P-0016388-T01-IM6	DROSHA (NM_013235) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515314::chr9:g.17618123)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	5	9	Intron of SH3GL2(+):39Kb after exon 1	SH3GL2	17618123			5	Exon 7 of DROSHA(-)	DROSHA	31515314			9	TRANSLOCATION		0	172052	0	4	NEW_VARIANT
P-0016391-T01-IM6	TSC2 (NM_000548) - NTHL1 (NM_002528) rearrangement: c.648+2:TSC2_c.379-117:NTHL1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TSC2:NTHL1}		9262	0	35	16	Intron of NTHL1(-):117bp before exon 3	NTHL1	2094918			16	Intron of TSC2(+):2bp after exon 7	TSC2	2106247			10	INVERSION		11329	172041	12203	39	NEW_VARIANT
P-0016396-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+797:TMPRSS2_c.18+1126:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		56300	0	75	21	Intron of ERG(-):1Kb after exon 1	ERG	39869161			21	Intron of TMPRSS2(-):796bp after exon 2	TMPRSS2	42869249			10	DELETION		3000088	172133	36803	79	NEW_VARIANT
P-0016398-T01-IM6	PTPRS (NM_002850) rearrangement: t(19;20)(p13.3;q13.12)(chr19:g.5214669::chr20:g.44361214)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	9	20	IGR: 10Kb before SPINT4(+)	SPINT4	44361214			19	Exon 29 of PTPRS(-)	PTPRS	5214669			0	TRANSLOCATION		0	172138	0	10	NEW_VARIANT
P-0016450-T01-IM6	SPEN (NM_015001) - KAZN (NM_201628) rearrangement: c.2147:SPEN_c.726+4286:KAZNdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:KAZN}		16678	0	46	1	Intron of KAZN(+):4Kb after exon 4	KAZN	15374941			1	Exon 11 of SPEN(+)	SPEN	16254882			10	DUPLICATION		879941	172363	37685	50	NEW_VARIANT
P-0016468-T01-IM6	MAP3K14 (NM_003954) - SRCIN1 (NM_025248) rearrangement: c.1069:MAP3K14_c.3417+1021:SRCIN1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MAP3K14:SRCIN1}		281178	0	40	17	Intron of SRCIN1(-):1Kb after exon 18	SRCIN1	36699037			17	Exon 5 of MAP3K14(-)	MAP3K14	43363880			10	DELETION		6664843	172294	407450	42	NEW_VARIANT
P-0016490-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-57506:ERG_c.127-1164:TMPRSS2inv	IMPPRECISE	The ERG - TMRSSS2 rearrangement results in an inversion of TMPRSS2 exons 3-14 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. Confirmatory testing for a fusion by the Archer FusionPlexTM Custom Solid Panel assay is suggested, if clinically indicated.	MANUAL_OK	3to3	3to3	-		28799	0	5	21	Intron of ERG(-):58Kb before exon 4	ERG	39875050			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867669			0	INVERSION		2992619	172342	44397	6	NEW_VARIANT
P-0016499-T01-IM6	ARID2 (NM_152641) rearrangement: c.638-16_c.705+505inv	PRECISE	Note: The ARID2 rearrangement is an intragenic inversion of exon 6.	MANUAL_OK	5to5	5to5	-		529	0	9	12	Intron of ARID2(+):15bp before exon 6	ARID2	46215187			12	Intron of ARID2(+):505bp after exon 6	ARID2	46215775			10	INVERSION		588	172383	1074	9	NEW_VARIANT
P-0016504-T01-IM6	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)	PRECISE	Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	79	20	Intron of SDC4(-):195bp before exon 3	SDC4	43961904			6	Intron of ROS1(-):72bp before exon 32	ROS1	117650681			10	TRANSLOCATION		0	172384	0	84	NEW_VARIANT
P-0016538-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	-		46688	0	89	21	3-UTR of ERG(-):69Kb after coding stop	ERG	39964209			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871996			10	DELETION		2907787	172493	76804	97	NEW_VARIANT
P-0016545-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.3666+42_c.*5156del	PRECISE	Note: The MAP3K1 rearrangement is an intragenic deletion of exons 15-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		6693	0	19	5	Intron of MAP3K1(+):42bp after exon 14	MAP3K1	56178735			5	Promoter of MAP3K1(+):84Kb from tx start	MAP3K1	56194663			10	DELETION		15928	172524	11703	21	NEW_VARIANT
P-0016548-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-1658_c.556+3387inv	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2-5.	MANUAL_OK	3to3	3to3	-		29748	0	95	21	Intron of TMPRSS2(-):3Kb after exon 5	TMPRSS2	42856934			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871774			10	INVERSION		14840	172558	54096	95	NEW_VARIANT
P-0016548-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.55490150::chr21:g.42876875)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	72	21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876875			15	Promoter of RSL24D1(-):17Kb from tx start	RSL24D1	55490150			10	TRANSLOCATION		0	172560	0	87	NEW_VARIANT
P-0016563-T01-IM6	NF1 (NM_001042492)  rearrangement: t(16;17)(p13.12;q11.2)(chr16:g.14398973::chr17:g.29664922)	PRECISE	Note: The NF1 rearrangement is a translocation that may result in the truncation of exons 1-44. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	7	17	Intron of NF1(+):24bp after exon 44	NF1	29664922			16	Promoter of MIR193B(+):1Kb from tx start	MIR193B	14398973			10	TRANSLOCATION		0	172607	0	7	NEW_VARIANT
P-0016568-T01-IM6	TP53 (NM_000546) rearrangement: c.1059_g.7755275del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		14068	0	12	17	Exon 10 of TP53(-)	TP53	7573968			17	Exon 18 of KDM6B(+)	KDM6B	7755275			10	DELETION		181307	172589	25508	12	NEW_VARIANT
P-0016570-T01-IM6	KMT2B (NM_014727) rearrangement: c.5898_g.37913327dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		18583	0	75	19	Exon 28 of KMT2B(+)	KMT2B	36223348			19	Intron of ZNF569(-):3Kb after exon 5	ZNF569	37913327			10	DUPLICATION		1689979	172608	91339	222	NEW_VARIANT
P-0016575-T01-IM6	CDKN2A (NM_000077) rearrangement: c.151-52_chr9:g.25375257del	PRECISE	Note: The CDKN2A rearrangement is a deletion which includes exon 1 of  both the CDKN2Ap16INK4A (NM_000077) and CDKN2Ap14ARF (NM_058195) isoforms.	MANUAL_OK	3to5	3to5	-		6864	0	10	9	Intron of CDKN2A(-):52bp before exon 2	CDKN2A	21971259			9	IGR: 301Kb before TUSC1(-)	TUSC1	25375257			10	DELETION		3403998	172653	12715	11	NEW_VARIANT
P-0016580-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		77896	0	102	2	Intron of ALK(-):747bp after exon 19	ALK	29447579			2	Intron of EML4(+):2Kb after exon 12	EML4	42524913			10	INVERSION		13077334	172648	125134	102	NEW_VARIANT
P-0016594-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+1418_c.56-2775del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		25393	0	37	21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868628			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872891			10	DELETION		4263	172712	23820	39	NEW_VARIANT
P-0016605-T01-IM6	H3F3C (NM_001013699) rearrangement: g.30188428_c.240del	PRECISE	Note: The H3F3C rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3752	0	29	12	IGR: 535Kb before TMTC1(-)	TMTC1	30188428			12	Exon 1 of H3F3C(-)	H3F3C	31944861			10	DELETION		1756433	172706	10260	51	NEW_VARIANT
P-0016614-T01-IM6	EP300 (NM_001429) rearrangement: c.1744_c.3591-369del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		13219	0	6	22	Exon 8 of EP300(+)	EP300	41533778			22	Intron of EP300(+):368bp before exon 20	EP300	41556277			10	DELETION		22499	173062	27220	6	NEW_VARIANT
P-0016625-T01-IM6	BAP1 (NM_004656) rearrangement: c.*1284_c.1474del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		6411	0	12	3	3-UTR of BAP1(-):1Kb after coding stop	BAP1	52435020			3	Exon 13 of BAP1(-)	BAP1	52437687			10	DELETION		2667	172771	10165	12	NEW_VARIANT
P-0016625-T01-IM6	TAP1 (NM_000593) rearrangement: c.1025-41_c.470del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7547	0	23	6	Intron of TAP1(-):41bp before exon 4	TAP1	32818967			6	Exon 1 of TAP1(-)	TAP1	32821124			10	DELETION		2157	172772	15337	23	NEW_VARIANT
P-0016642-T01-IM6	ATM (NM_000051) - TENM4 (NM_001098816) rearrangement : c.2069:ATM_c.2877-305:TENM4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ATM:TENM4}		100759	0	52	11	Intron of TENM4(-):305bp before exon 21	TENM4	78443927			11	Exon 13 of ATM(+)	ATM	108124711			10	INVERSION		29680784	172860	138575	52	NEW_VARIANT
P-0016643-T01-IM6	TP53 (NM_000546)  rearrangement : chr17:g.7572418_c.994-68:TP53inv	PRECISE	Note: The TP53 rearrangement is an inversion which include TP53 exon10-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1857	0	85	17	3-UTR of TP53(-):508bp after coding stop	TP53	7572418			17	Intron of TP53(-):68bp before exon 10	TP53	7574101			10	INVERSION		1683	172853	3814	85	NEW_VARIANT
P-0016661-T01-IM6	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.3159+7:ERBB2_c.827-3270:IKZF3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		6391	0	13	17	Intron of ERBB2(+):7bp after exon 25	ERBB2	37883263			17	Intron of IKZF3(-):3Kb before exon 7	IKZF3	37926016			10	DELETION		42753	172916	6031	13	NEW_VARIANT
P-0016692-T01-IM6	CD79A (NM_001783) rearrangement: c.649:CD79A_chr19:g.42777278del	IMPPRECISE	Note: The CD79A rearrangement is a deletion of exon 5. One of breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	-		26802	0	13	19	Exon 5 of CD79A(+)	CD79A	42385015			19	IGR: 12Kb before CIC(+)	CIC	42777278			0	DELETION		392263	173239	37372	14	NEW_VARIANT
P-0016696-T01-IM6	ARID1A (NM_006015) rearrangement: c.1137+3955_c.4158del	PRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 2-18. One of the breakpoints is within exon18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		26003	0	6	1	Intron of ARID1A(+):4Kb after exon 1	ARID1A	27027986			1	Exon 18 of ARID1A(+)	ARID1A	27100876			10	DELETION		72890	173255	48533	6	NEW_VARIANT
P-0016697-T01-IM6	RAB35 (NM_006861) - PPFIA2 (NM_003625) rearrangement: c.477+69:RAB35_c.303+64413:PPFIA2del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74661		41	12	Intron of PPFIA2(-):64Kb after exon 3	PPFIA2	82006157			12	Intron of RAB35(-):68bp after exon 5	RAB35	120536546			10	DELETION		38530389	176043	146066		NEW_VARIANT
P-0016698-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2599:TMPRSS2_c.18+9969:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49747	0	11	21	Intron of ERG(-):10Kb after exon 1	ERG	39860318			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872715			10	DELETION		3012397	173272	41812	10	NEW_VARIANT
P-0016714-T01-IM6	ARID5B (NM_032199) Rearrangement : c.847-1236_c.3325del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		23767		10	10	Intron of ARID5B(+):1Kb before exon 6	ARID5B	63815640			10	Exon 10 of ARID5B(+)	ARID5B	63852547			10	DELETION		36907	176582	20759		NEW_VARIANT
P-0016714-T01-IM6	FAT1 (NM_005245) Rearrangement : c.8879-31:FAT1_chr4:g.190223782del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74639		7	4	Intron of FAT1(-):31bp before exon 11	FAT1	187538386			4	IGR: 357Kb before LINC01262(+)	LINC01262	190223782			10	DELETION		2685396	176583	85816		NEW_VARIANT
P-0016733-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		149415	0	66	21	Intron of ERG(-):6Kb before exon 2	ERG	39823695			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873910			10	DELETION		3050215	173499	84629	74	NEW_VARIANT
P-0016746-T01-IM6	AR (NM_000044)  Rearrangement : c.2174-1838_c.2191inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		210	0	17	X	Intron of AR(+):2Kb before exon 5	AR	66935482			X	Exon 5 of AR(+)	AR	66937337			10	INVERSION		1855	173564	305	17	NEW_VARIANT
P-0016747-T01-IM6	ROS1 (NM_002944) Rearrangement : c.5557+603:ROS1_chr6:g.126400977del	PRECISE	Note: The ROS1 Rearrangement results in the deletion of exons 1-33. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		107108	0	26	6	Intron of ROS1(-):602bp after exon 33	ROS1	117646784			6	IGR: 33Kb before MIR5695(-)	MIR5695	126400977			10	DELETION		8754193	173551	232934	28	NEW_VARIANT
P-0016763-T01-IM6	MGA (NM_001164273) rearrangement : g.29907619_c.5357:MGAinv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		122273	0	44	15	IGR: 84Kb before TJP1(-)	TJP1	29907619			15	Exon 16 of MGA(+)	MGA	42040979			10	INVERSION		12133360	173599	97510	72	NEW_VARIANT
P-0016776-T01-IM6	NF1 (NM_001042492) - RAB11FIP4 (NM_032932) rearrangement: c.810:NF1_c.159+14109:RAB11FIP4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NF1:RAB11FIP4}		59968	0	47	17	Exon 8 of NF1(+)	NF1	29509605			17	Intron of RAB11FIP4(+):14Kb after exon 1	RAB11FIP4	29733138			10	DELETION		223533	173641	39687	50	NEW_VARIANT
P-0016777-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.927+476_c.3226dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		26444	0	68	4	Intron of WHSC1(+):476bp after exon 4	WHSC1	1919240			4	Exon 17 of WHSC1(+)	WHSC1	1961438			10	DUPLICATION		42198	173638	56223	75	NEW_VARIANT
P-0016785-T01-IM6	STXBP2 (NM_006949) - STK11 (NM_000455)  rearrangement: c.1107+62:STXBP2_c.291-17:STK11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {STXBP2:STK11}		233914	0	24	19	Intron of STK11(+):16bp before exon 2	STK11	1218399			19	Intron of STXBP2(+):62bp after exon 13	STXBP2	7708193			10	DUPLICATION		6489794	173634	286162	26	NEW_VARIANT
P-0016785-T01-IM6	MST1R (NM_002447) - IQCJ-SCHIP1 (NM_001197113) rearrangement: c.2829:MST1R_c.292-12602:IQCJ-SCHIP1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		407047	0	34	3	Exon 12 of MST1R(-)	MST1R	49933281			3	Intron of SCHIP1(+):126Kb before exon 2	SCHIP1	159356211			10	DELETION		109422930	173632	639762	35	NEW_VARIANT
P-0016792-T01-IM6	STK11 (NM_000455) Rearrangement : c.-1700_c.708del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6095	0	15	19	Promoter of STK11(+):584bp from tx start	STK11	1205213			19	Exon 5 of STK11(+)	STK11	1220690			10	DELETION		15477	173677	7287	16	NEW_VARIANT
P-0016795-T01-IM6	KIT (NM_000222) Rearrangement : c.1231+989_2597-55dup	PRECISE	Note: The KIT Rearrangement results in the intragenic duplication of exons 8-18. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons : in frame		9515	0	18	4	Intron of KIT(+):989bp after exon 7	KIT	55576694			4	Intron of KIT(+):54bp before exon 19	KIT	55602832			10	DUPLICATION		26138	173664	20603	18	NEW_VARIANT
P-0016795-T01-IM6	DDC (NM_000790) - EGFR (NM_005228) Rearrangement : c.435+4059:DDC_c.889+359:EGFRinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {DDC:EGFR}		12348	0	82	7	Intron of DDC(-):4Kb after exon 4	DDC	50601499			7	Intron of EGFR(+):359bp after exon 7	EGFR	55222204			10	INVERSION		4620705	173669	45256	112	NEW_VARIANT
P-0016807-T01-IM6	KMT2D (NM_003482) rearrangement: t(12;16)(q13.12;p13.2)(chr12:g.49444705::chr16:g.9209176)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	24	16	Intron of C16orf72(+):1Kb before exon 4	C16orf72	9209176			12	Exon 10 of KMT2D(-)	KMT2D	49444705			10	TRANSLOCATION		0	173734	0	24	NEW_VARIANT
P-0016812-T01-IM6	RET (NM_020975) rearrangement : c.1760-157_c.2136+377inv	PRECISE	Note: The RET rearrangement results in an inversion of exons 10-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		15559	0	5	10	Intron of RET(+):156bp before exon 10	RET	43608847			10	Intron of RET(+):377bp after exon 11	RET	43610561			10	INVERSION		1714	173713	22435	4	NEW_VARIANT
P-0016812-T01-IM6	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement : t(17;21)(q21.31;q22.3)(chr17:g.41623968::chr21:g.42867167)	PRECISE	Note: The TMPRSS2-ETV4 rearrangement is a translocation which results in the fusion of TMPRSS2 exons 1-2 with ETV4 promoter region. PMID: 16585160	MANUAL_OK	5to3	5to3	Transcript Fusion {TMPRSS2:ETV4}		0	0	40	21	Intron of TMPRSS2(-):662bp before exon 3	TMPRSS2	42867167			17	Promoter of ETV4(-):19Kb from tx start	ETV4	41623968			10	TRANSLOCATION		0	173715	0	41	NEW_VARIANT
P-0016815-T01-IM6	MAP3K1 (NM_005921) rearrangement: g.50161653_c.3819+27:MAP3K1inv	PRECISE	Note: The MAP3K1 rearrangement results in an inversion of exons 1-15. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		23467	0	14	5	IGR: 103Kb before LOC100287592(-)	LOC100287592	50161653			5	Intron of MAP3K1(+):27bp after exon 15	MAP3K1	56179533			10	INVERSION		6017880	173727	47124	12	NEW_VARIANT
P-0016815-T01-IM6	PARK2 (NM_004562) rearrangement: g.158228249_c.1083+84:PARK2inv	PRECISE	Note: The PARK2 rearrangement results in an inversion of exons 10-12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		6501	0	6	6	IGR: 16Kb before SNX9(+)	SNX9	158228249			6	Intron of PARK2(-):83bp after exon 9	PARK2	161969802			10	INVERSION		3741553	173728	9883	6	NEW_VARIANT
P-0016820-T01-IM6	ACVR1 (NM_001111067) Rearrangement : c.543+1130_754dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		1684	0	24	2	Exon 7 of ACVR1(-)	ACVR1	158626916			2	Intron of ACVR1(-):1Kb after exon 5	ACVR1	158633513			10	DUPLICATION		6597	173737	2614	25	NEW_VARIANT
P-0016842-T01-IM6	CSF3R (NM_000760) rearrangement: c.1724-48_chr1:g.25041917del	PRECISE	Note: The CSF3R rearrangement is a deletion which includes exons 14-17 of CSF3R. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		75028	0	14	1	IGR: 30Kb before CLIC4(+)	CLIC4	25041917			1	Intron of CSF3R(-):48bp before exon 14	CSF3R	36933611			10	DELETION		11891694	173767	92040	15	NEW_VARIANT
P-0016877-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(1;21)(p33;q22.3)(chr1:g.46831834::chr21:g.42866769)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 3-14.	MANUAL_OK	3to3	3to3	Transcript Fusion {NSUN4:TMPRSS2}		0	0	14	21	Intron of TMPRSS2(-):264bp before exon 3	TMPRSS2	42866769			1	Promoter of NSUN4(+):26Kb from tx start	NSUN4	46831834			10	TRANSLOCATION		0	173816	0	13	NEW_VARIANT
P-0016883-T01-IM6	TMPRSS2 (NM_001135099) -ERG(NM_004449) Rearrangement : c.56-1115:TMPRSS2_c.-149-1187:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		48236	0	108	21	3-UTR of ERG(-):76Kb after coding stop	ERG	39958056			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871231			10	DELETION		2913175	173831	49004	116	NEW_VARIANT
P-0016895-T01-IM6	EZH1 (NM_001991) - FGF14 (NM_175929) Rearrangement : t(13;17)(q33.1;q21.2)(chr13:g.102490730::chr17:g.40876400)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EZH1:FGF14}		0	0	24	17	Exon 5 of EZH1(-)	EZH1	40876400			13	Intron of FGF14(-):30Kb after exon 3	FGF14	102490730			10	TRANSLOCATION		0	173841	0	24	NEW_VARIANT
P-0016895-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		63746	0	30	21	Intron of ERG(-):14Kb before exon 2	ERG	39831327			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873673			10	DELETION		3042346	173836	104629	30	NEW_VARIANT
P-0016910-T01-IM6	POLE (NM_006231) rearrangement: c.4132:POLE_chr12:g.132997799inv	PRECISE	Note: The POLE rearrangement is an inversion of exons 32-49. One of the breakpoints is within exon 32.	MANUAL_OK	3to3	3to3	-		20461	0	63	12	IGR: 69Kb before FBRSL1(+)	FBRSL1	132997799			12	Exon 32 of POLE(-)	POLE	133225532			10	INVERSION		227733	173878	45604	61	NEW_VARIANT
P-0016911-T01-IM6	BRAF (NM_004333) rearrangement: c.1314+303_c.241-7545del	PRECISE	Note: The BRAF rearrangement results in the deletion of exons 3-10.  The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 8 exons : in frame		101162	0	63	7	Intron of BRAF(-):302bp after exon 10	BRAF	140482518			7	Intron of BRAF(-):8Kb before exon 3	BRAF	140542217			10	DELETION		59699	173885	240819	68	NEW_VARIANT
P-0016912-T01-IM6	NF1 (NM_001042492) - LLGL1 (NM_004140) rearrangement: c.5268+78:NF1_c.-1064: LLGL1dup	PRECISE	Note: The NF1 - LLGL1 rearrangement is a duplication which results in the fusion of NF1 exons 1-37 with LLGL1 promoter region.	MANUAL_OK	5to3	5to3	Transcript Fusion {NF1:LLGL1}		38116	0	6	17	Promoter of LLGL1(+):1Kb from tx start	LLGL1	18127933			17	Intron of NF1(+):78bp after exon 37	NF1	29653348			10	DUPLICATION		11525415	173893	70475	6	NEW_VARIANT
P-0016912-T01-IM6	SPOP (NM_001007228) rearrangement: g.47502627_c.481-35:SPOPinv	PRECISE	Note: The SPOP rearrangement is an inversion of exons 6-10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4789	0	11	17	IGR: 21Kb before PHB(-)	PHB	47502627			17	Intron of SPOP(-):35bp before exon 6	SPOP	47688854			10	INVERSION		186227	173894	9471	11	NEW_VARIANT
P-0016933-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.55+4812:TMPRSS2_c.40-58894:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		69608	0	21	21	Intron of ERG(-):59Kb before exon 4	ERG	39876438			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875065			10	DELETION		2998627	173928	103316	24	NEW_VARIANT
P-0016941-T01-IM6	NCOR1 (NM_006311) rearrangement: c.6956-60_c.6679+487inv	PRECISE	Note: The NCOR1 rearrangement is an inversion of exons 43-44. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3162	0	4	17	Intron of NCOR1(-):60bp before exon 45	NCOR1	15938318			17	Intron of NCOR1(-):486bp after exon 42	NCOR1	15949778			8	INVERSION		11460	174209	5087	4	NEW_VARIANT
P-0016941-T01-IM6	PTPRN2 (NM_002847) - KMT2C (NM_170606) rearrangement: c.164-76166: PTPRN2_c.14535-47: KMT2Cdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PTPRN2:KMT2C}		119541	0	28	7	Intron of KMT2C(-):47bp before exon 58	KMT2C	151836036			7	Intron of PTPRN2(-):76Kb before exon 3	PTPRN2	158185790			10	DELETION		6349754	174206	210588	29	NEW_VARIANT
P-0016946-T01-IM6	NCOR1 (NM_006311) rearrangement : g.15887497_c.5603:NCOR1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		14252	0	8	17	Intron of ZSWIM7(-):3Kb before exon 4	ZSWIM7	15887497			17	Exon 37 of NCOR1(-)	NCOR1	15964993			10	INVERSION		77496	174198	4145	13	NEW_VARIANT
P-0016946-T01-IM6	AXIN2 (NM_004655) rearrangement : c.1201-45: AXIN2_g.77075798del	PRECISE	Note: The AXIN2 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		54332	0	8	17	Intron of AXIN2(-):45bp before exon 6	AXIN2	63533998			17	Intron of ENGASE(+):79bp after exon 4	ENGASE	77075798			10	DELETION		13541800	174197	27528	8	NEW_VARIANT
P-0016946-T01-IM6	CARD11 (NM_032415) rearrangement : c.1376_c.-125-13049del	PRECISE	Note: The CARD11 rearrangement results in the deletion of exons 1-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		15478	0	3	7	Exon 10 of CARD11(-)	CARD11	2974229			7	5-UTR of CARD11(-):65Kb before coding start	CARD11	3011314			10	DELETION		37085	174196	3026	6	NEW_VARIANT
P-0016958-T01-IM6	ZNF691 (NM_015911) - CBL (NM_00518) rearrangement: t(1;11)(p34.2;q23.3)(chr1:g.43315081::chr11:g.119077286)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	70	11	Exon 1 of CBL(+)	CBL	119077286			1	5-UTR of ZNF691(+):248bp before coding start	ZNF691	43315081			10	TRANSLOCATION		0	174080	0	129	NEW_VARIANT
P-0016960-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		138105	0	69	2	Intron of ALK(-):488bp after exon 19	ALK	29447838			2	Intron of EML4(+):7Kb after exon 5	EML4	42499324			10	INVERSION		13051486	174098	139936	70	NEW_VARIANT
P-0016968-T01-IM6	PRDM14 (NM_024504) rearrangement: t(2;8)(p11.2;q13.3)(chr2:g.89832919::chr8:g.70981692)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	7	8	Exon 2 of PRDM14(-)	PRDM14	70981692			2	IGR: 721Kb before MIR4436A(+)	MIR4436A	89832919			10	TRANSLOCATION		0	174178	0	7	NEW_VARIANT
P-0016973-T01-IM6	INSR (NM_000208)rearrangement: t(18;19)(q11.1;p13.2)(chr18:g.18934293::chr19:g.7117210)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	21	19	Exon 22 of INSR(-)	INSR	7117210			18	5-UTR of GREB1L(+):29Kb before coding start	GREB1L	18934293			10	TRANSLOCATION		0	174171	0	22	NEW_VARIANT
P-0016985-T01-IM6	FOXO1 (NM_002015) rearrangement : c.1116:FOXO1_g.107386743inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		140539	0	30	13	Exon 2 of FOXO1(-)	FOXO1	41134512			13	IGR: 81Kb before LINC00443(+)	LINC00443	107386743			10	INVERSION		66252231	174047	181631	30	NEW_VARIANT
P-0016985-T01-IM6	FLCN (NM_144997) rearrangement: t(8;17)(p23.1;p11.2)(chr8:g.11209119::chr17:g.17122551)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	44	17	Intron of FLCN(-):28bp before exon 9	FLCN	17122551			8	5-UTR of TDH(+):17Kb before coding start	TDH	11209119			10	TRANSLOCATION		0	174050	0	46	NEW_VARIANT
P-0016991-T01-IM6	NFKBIA (NM_020529) rearrangement: c.739_c.-1051del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4899	0	3	14	Exon 5 of NFKBIA(-)	NFKBIA	35871767			14	Promoter of NFKBIA(-):4Kb from tx start	NFKBIA	35874901			10	DELETION		3134	174037	10180	3	NEW_VARIANT
P-0017011-T01-IM6	PAX8 (NM_003466) - CCDC141 (NM_173648) Rearrangement : c.1189+3343:PAX8_c.526+1048:CCDC141dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {PAX8:CCDC141}		154845	0	9	2	Intron of PAX8(-):3Kb after exon 10	PAX8	113981389			2	Intron of CCDC141(-):1Kb after exon 4	CCDC141	179838736			10	DUPLICATION		65857347	174132	237654	9	NEW_VARIANT
P-0017011-T01-IM6	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement : c.-533:SEC16A_c.5167+178:NOTCH1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {SEC16A:NOTCH1}		19712	0	11	9	5-UTR of SEC16A(-):42Kb before coding start	SEC16A	139377731			9	Intron of NOTCH1(-):177bp after exon 27	NOTCH1	139397456			10	DUPLICATION		19725	174133	29196	12	NEW_VARIANT
P-0017031-T01-IM6	WDR72 (NM_182758) - TP53BP1 (NM_001141980) rearrangement: c.3149-28073:WDR72_c.956-53:TP53BP1del	PRECISE	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	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {WDR72:TP53BP1}		20397	0	3	15	Intron of TP53BP1(-):53bp before exon 9	TP53BP1	43767945			15	Intron of WDR72(-):28Kb before exon 19	WDR72	53843592			10	DELETION		10075647	174279	40492	3	NEW_VARIANT
P-0017031-T01-IM6	NUP93 (NM_014669) - MT1H (NM_005951) rearrangement: c.489+58:NUP93_c.-820:MT1Hdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {NUP93:MT1H}		4191	0	7	16	Promoter of MT1H(+):748bp from tx start	MT1H	56702977			16	Intron of NUP93(+):58bp after exon 5	NUP93	56839602			10	DUPLICATION		136625	174281	8746	7	NEW_VARIANT
P-0017035-T01-IM6	PTPRS (NM_002850) rearrangement: t(6;19)(q22.32;p13.3)(chr6:g.126811782::chr19:g.5208512)	PRECISE	Note: The PTPRS rearrangement is a translocation that may result in a truncation of exons 36-39. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	49	19	Intron of PTPRS(-):110bp before exon 36	PTPRS	5208512			6	IGR: 151Kb before CENPW(+)	CENPW	126811782			10	TRANSLOCATION		0	174286	0	53	NEW_VARIANT
P-0017043-T01-IM6	NFKBIA (NM_020529) rearrangement: chr14:g.35505911_c.690:NFKBIAdel	PRECISE	Note: The NFKBIA rearrangement is a deletion of exons 5-6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	-		1891	0	19	14	IGR: 8Kb before FAM177A1(+)	FAM177A1	35505911			14	Exon 5 of NFKBIA(-)	NFKBIA	35871816			10	DELETION		365905	174300	2669	57	NEW_VARIANT
P-0017051-T01-IM6	KMT2C (NM_170606) rearrangement: c.13636:KMT2C_chr7:g.154725568inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PAXIP1-AS2:KMT2C}		86227	0	11	7	Exon 52 of KMT2C(-)	KMT2C	151845376			7	5-UTR of PAXIP1-AS2(+):13Kb before coding start	PAXIP1-AS2	154725568			10	INVERSION		2880192	174343	161459	11	NEW_VARIANT
P-0017065-T01-IM6	TMPRSS2 (NM_001135099) - ERG Fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-967:TMPRSS2_c.40-42355:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		51499	0	34	21	Intron of ERG(-):10Kb after exon 1	ERG	39859899			21	Intron of TMPRSS2(-):967bp before exon 2	TMPRSS2	42871083			10	DELETION		3011184	174390	76737	37	NEW_VARIANT
P-0017067-T01-IM6	RARA (NM_000964) Rearrangement : c.252:RARA_chr17:g.41463829inv	PRECISE	Note: The RARA Rearrangement  results in the inversion of exons 3-9. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		141359	0	11	17	Exon 3 of RARA(+)	RARA	38504641			17	3-UTR of LINC00910(-):2Kb after coding stop	LINC00910	41463829			10	INVERSION		2959188	174388	242392	11	NEW_VARIANT
P-0017167-T01-IM6	MCL1 (NM_021960) - ENSA (NM_004436) rearrangement: c.813: MCL1_c.333: ENSAdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MCL1:ENSA}		9518	0	31	1	Exon 2 of MCL1(-)	MCL1	150550843			1	Exon 4 of ENSA(-)	ENSA	150598135			10	DUPLICATION		47292	174699	13378	44	NEW_VARIANT
P-0017168-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_182918) fusion (TMPRSS2 exon 1-2 with ERG exons 2-10) : c.126+1703:TMPRSS2_c.19-17382:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		45990	0	43	21	Intron of ERG(-):17Kb before exon 2	ERG	39834926			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868343			10	DELETION		3033417	174688	31968	45	NEW_VARIANT
P-0017176-T01-IM6	DROSHA (NM_013235) rearrangement : c.1433-63: DROSHA_g.31625311inv	IMPPRECISE	Note: The DROSHA rearrangement results in an inversion of exons 1-9 . The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		18746	0	5	5	Intron of DROSHA(-):63bp before exon 9	DROSHA	31508945			5	IGR: 93Kb before C5orf22(+)	C5orf22	31625311			0	INVERSION		116366	174692	20971	5	NEW_VARIANT
P-0017224-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.3547-818_c.4134del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6592	0	19	19	Intron of SMARCA4(+):817bp before exon 26	SMARCA4	11143148			19	Exon 29 of SMARCA4(+)	SMARCA4	11145772			10	DELETION		2624	174834	5795	21	NEW_VARIANT
P-0017224-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement : c.*102-335:CDKN2Ap14ARF_g.34756956inv	PRECISE	Note: The CDKN2Ap14ARF rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0		14	9	Intron of CDKN2A(-):335bp before exon 3	CDKN2Ap14ARF	21968576			9	IGR: 34Kb before FAM205A(-)	FAM205A	34756956			10	INVERSION		12788380	175337	92736		NEW_VARIANT
P-0017224-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement : c.458-335:CDKN2Ap16INK4A_g.34756956inv	PRECISE	Note: The CDKN2Ap16INK4A rearrangement results in an inversion of exons 1-2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	14	9	Intron of CDKN2A(-):335bp before exon 3	CDKN2Ap16INK4A	21968576			9	IGR: 34Kb before FAM205A(-)	FAM205A	34756956			10	INVERSION		12788380	174835	92736	14	NEW_VARIANT
P-0017235-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1-2 with ERG exon 4-11) : c.56-4295:TMPRSS2_c.39+62371:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		69571	0	40	21	Intron of ERG(-):62Kb after exon 3	ERG	39885215			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874411			10	DELETION		2989196	174839	97136	44	NEW_VARIANT
P-0017245-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon3) : c.55+3273:TMPRSS2_c.237-9598:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		71769	0	5	21	Intron of ERG(-):10Kb before exon 3	ERG	39805081			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876604			10	DELETION		3071523	174845	78986	5	NEW_VARIANT
P-0017262-T01-IM6	SUFU (NM_016169) - CHRNA5 (NM_000745) rearrangement: t(10;15)(q24.32;q25.1)(chr10:g.104359393::chr15:g.78876527)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SUFU:CHRNA5}		0	0	8	15	Intron of CHRNA5(+):2Kb before exon 3	CHRNA5	78876527			10	Intron of SUFU(+):92bp after exon 8	SUFU	104359393			10	TRANSLOCATION		0	174897	0	8	NEW_VARIANT
P-0017262-T01-IM6	PTPRS (NM_00285) - FAM227B (NM_152647) rearrangement: t(15;19)(q21.2;p13.3)(chr15:g.49718958::chr19:g.5216740)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PTPRS:FAM227B}		0	0	45	19	Exon 26 of PTPRS(-)	PTPRS	5216740			15	Intron of FAM227B(-):55Kb before exon 12	FAM227B	49718958			10	TRANSLOCATION		0	174898	0	47	NEW_VARIANT
P-0017262-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		26898	0	3	21	Intron of ERG(-):4Kb after exon 1	ERG	39866100			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868297			10	DELETION		3002197	174895	31417	19	NEW_VARIANT
P-0017262-T01-IM6	MGA (NM_001164273) rearrangement: t(15;22)(q15.1;q13.1)(chr15:g.42042118::chr22:g.37609650)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MGA:SSTR3}		0	0	51	22	Promoter of SSTR3(-):9Kb from tx start	SSTR3	37609650			15	Exon 17 of MGA(+)	MGA	42042118			10	TRANSLOCATION		0	174899	0	49	NEW_VARIANT
P-0017265-T01-IM6	TP53 (NM_000546) rearrangement: c.1159_c.*1673del	PRECISE	Note: The TP53 rearrangement is a deletion of a part of exon 11. One of the breakpoint is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		356	0	19	17	Promoter of TP53(-):465bp from tx start	TP53	7571254			17	Exon 11 of TP53(-)	TP53	7572950			10	DELETION		1696	175659	356	21	NEW_VARIANT
P-0017284-T02-IM5	NOTCH2 (NM_024408) rearrangement: chr1:g.108019818_c.3183+159:NOTCH2del	PRECISE	Note: The NOTCH2 rearrangement is a deletion of exons 20-34.	MANUAL_OK	3to5	3to5	Antisense Fusion		51416	0	3	1	Intron of NTNG1(+):3Kb before exon 6	NTNG1	108019818			1	Intron of NOTCH2(-):158bp after exon 19	NOTCH2	120483019			9	DELETION		12463201	176239	96972	3	NEW_VARIANT
P-0017298-T01-IM6	TSNARE1 (NM_145003) - RECQL4 (NM_004260) rearrangement: c.1446+7353:TSNARE1_c.1278:RECQL4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TSNARE1:RECQL4}		22019	0	27	8	Intron of TSNARE1(-):7Kb after exon 12	TSNARE1	143348789			8	Exon 7 of RECQL4(-)	RECQL4	145740822			10	DUPLICATION		2392033	175027	30054	29	NEW_VARIANT
P-0017312-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 with ERG exon 2) : c.126+1523:TMPRSS2_c.18+7805:ERGdel	PRECISE	Note: The fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		24842	0	45	21	Intron of ERG(-):8Kb after exon 1	ERG	39862482			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868523			10	DELETION		3006041	175076	40573	49	NEW_VARIANT
P-0017317-T01-IM6	HIST1H3C (NM_003531) Rearrangement : c.-715_c.2del	PRECISE	Note: The HIST1H3C Rearrangement results in the partial deletion of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		743	0	27	6	Promoter of HIST1H3C(+):714bp from tx start	HIST1H3C	26044924			6	Exon 1 of HIST1H3C(+)	HIST1H3C	26045640			10	DELETION		716	175083	1189	30	NEW_VARIANT
P-0017325-T01-IM6	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)	PRECISE	Note: The SDC4-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	10	20	Intron of SDC4(-):561bp after exon 2	SDC4	43963860			6	Intron of ROS1(-):4Kb before exon 32	ROS1	117654375			10	TRANSLOCATION		0	175097	0	9	NEW_VARIANT
P-0017325-T01-IM6	NBN (NM_002485) rearrangement: g.90932931_c.994+81:NBNdel	PRECISE	Note: The NBN rearrangement results in the deletion of exons 9-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		7856	0	19	8	Intron of OSGIN2(+):376bp before exon 5	OSGIN2	90932931			8	Intron of NBN(-):80bp after exon 8	NBN	90976557			10	DELETION		43626	175096	19863	19	NEW_VARIANT
P-0017368-T01-IM6	HIST1H2BD (NM_021063) - PTPRK  (NM_001135648) rearrangement : c.226: HIST1H2BD_c.2158-357:PTPRKinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {HIST1H2BD:PTPRK}		577732	0	615	6	Exon 1 of HIST1H2BD(+)	HIST1H2BD	26158623			6	Intron of PTPRK(-):357bp before exon 13	PTPRK	128386296			0	INVERSION		102227673	175209	1397828	762	NEW_VARIANT
P-0017375-T01-IM6	LATS2 (NM_014572) rearrangement: c.1743_c.343-9621del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8774	0	90	13	Exon 4 of LATS2(-)	LATS2	21562176			13	Intron of LATS2(-):10Kb before exon 3	LATS2	21575164			10	DELETION		12988	175214	8090	106	NEW_VARIANT
P-0017376-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2204:TMPRSS2_c.40-61559:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		59878	0	36	21	Intron of ERG(-):62Kb before exon 4	ERG	39879103			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872320			10	DELETION		2993217	175204	77265	38	NEW_VARIANT
P-0017412-T01-IM6	BAP1 (NM_004656) rearrangement: c.37+27:BAP1_chr3:g.52450493del	PRECISE	Note: The BAP1 rearrangement is deletion of BAP1 promoter region and exon 1.	MANUAL_OK	3to5	3to5	-		657	0	6	3	Intron of BAP1(-):26bp after exon 1	BAP1	52443831			3	Intron of PHF7(+):2Kb after exon 4	PHF7	52450493			10	DELETION		6662	175359	1020	6	NEW_VARIANT
P-0017415-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1489_c.1812+903del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 9-11. One of the breakpoint is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2707	0	28	19	Exon 9 of SMARCA4(+)	SMARCA4	11105573			19	Intron of SMARCA4(+):903bp after exon 11	SMARCA4	11108123			10	DELETION		2550	175391	5183	29	NEW_VARIANT
P-0017424-T01-IM6	FGFR2 (NM_000141) - ATE1 (NM_001001976) rearrangement: c.2302-908:FGFR2_c.1379-520:ATE1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {FGFR2:ATE1}		42899	0	83	10	Intron of FGFR2(-):908bp before exon 18	FGFR2	123240443			10	Intron of ATE1(-):520bp before exon 12	ATE1	123503893			10	DUPLICATION		263450	175374	256123	90	NEW_VARIANT
P-0017426-T01-IM6	FANCA (NM_000135) rearrangement: c.2779-717_c.2601+28del	PRECISE	Note: The FANCA rearrangement is an intragenic deletion of exon 28. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		2058	0	10	16	Intron of FANCA(-):717bp before exon 29	FANCA	89829147			16	Intron of FANCA(-):27bp after exon 27	FANCA	89833521			10	DELETION		4374	175437	4311	10	NEW_VARIANT
P-0017428-T01-IM6	CDK12 (NM_016507) rearrangement: c.2632_chr17:g.45272565dup	PRECISE	Note: The CDK12 rearrangement is a duplication which includes exons 7-14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		265312	0	82	17	Exon 7 of CDK12(+)	CDK12	37665980			17	IGR: 14Kb before MYL4(+)	MYL4	45272565			10	DUPLICATION		7606585	175452	577356	116	NEW_VARIANT
P-0017432-T01-IM6	CSF3R (NM_000760) rearrangement: c.1071+36_c.1577-198del	PRECISE	Note: The CSF3R rearrangement is an intragenic deletion of exons 10-12. The function significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		5418	0	26	1	Intron of CSF3R(-):198bp before exon 13	CSF3R	36934020			1	Intron of CSF3R(-):35bp after exon 9	CSF3R	36937631			10	DELETION		3611	175432	10506	26	NEW_VARIANT
P-0017444-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 11-16): c.2296:FGFR3_c.1941+70:TACC3dup	IMPPRECISE		MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		26575	0	39	4	Intron of TACC3(+):70bp after exon 10	TACC3	1739499			4	Exon 18 of FGFR3(+)	FGFR3	1808864			0	DUPLICATION		69365	175489	48689	44	NEW_VARIANT
P-0017448-T01-IM6	RTEL1 (NM_032957) - STAU1 (NM_017453) rearrangement: c.3181+36:RTEL1_c.511-4612:STAU1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RTEL1:STAU1}		76162	0	17	20	Intron of STAU1(-):5Kb before exon 6	STAU1	47757080			20	Intron of RTEL1(+):36bp after exon 31	RTEL1	62325877			10	INVERSION		14568797	175497	276681	17	NEW_VARIANT
P-0017459-T01-IM6	ROS1 (NM_002944) Rearrangement : c.5080-508:ROS1_chr6:g.117776626del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		61252	0	3	6	Intron of ROS1(-):508bp before exon 31	ROS1	117659011			6	IGR: 27Kb before DCBLD1(+)	DCBLD1	117776626			10	DELETION		117615	175571	77399	3	NEW_VARIANT
P-0017470-T01-IM6	KMT2B(NM_014727) Rearrangement : c.4259_c.7160-309dup	PRECISE	Note: The KMT2B Rearrangement results in the duplication of exons 16-30. One of the breakpoints is within exon16. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		22633	0	65	19	Exon 16 of KMT2B(+)	KMT2B	36218480			19	Intron of KMT2B(+):308bp before exon 31	KMT2B	36227282			10	DUPLICATION		8802	175562	75684	73	NEW_VARIANT
P-0017476-T01-IM6	CERS5 (NM_147190) - TSC2 (NM_000548) Rearrangement :  t(12,16)(q13.12,p13.3)(chr12:g.131062050::chr16:g.143130066)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {CERS5:TSC2}		0	0	5	16	Intron of TSC2(+):31bp before exon 37	TSC2	2136162			12	Intron of CERS5(-):97bp after exon 8	CERS5	50529417			10	TRANSLOCATION		0	175596	0	5	NEW_VARIANT
P-0017491-T01-IM6	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	PRECISE		MANUAL_OK	3to3	3to3	-		48749	0	41	21	Intron of ERG(-):14Kb after exon 1	ERG	39855851			21	Intron of TMPRSS2(-):927bp before exon 2	TMPRSS2	42871043			10	INVERSION		3015192	175703	77750	40	NEW_VARIANT
P-0017493-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+512_chr21:g.34285242inv	PRECISE	Note: The TMPRSS2 rearrangement is an inversion which includes exons 3-14 of TMPRSS2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		60070	0	41	21	IGR: 113Kb before OLIG2(+)	OLIG2	34285242			21	Intron of TMPRSS2(-):511bp after exon 2	TMPRSS2	42869534			10	INVERSION		8584292	175790	118544	57	NEW_VARIANT
P-0017509-T01-IM6	NPM1(NM_002520) rearrangement: chr5:g.64521538_c.525-19:NPM1del	IMPPRECISE	Note: The NPM1 rearrangement is a deletion of NPM1 promoter region and exons 1-6.	MANUAL_OK	3to5	3to5	-		264498	0	6	5	Intron of ADAMTS6(-):374bp after exon 16	ADAMTS6	64521538			5	Intron of NPM1(+):18bp before exon 7	NPM1	170827138			0	DELETION		106305600	175853	611919	6	NEW_VARIANT
P-0017509-T01-IM6	PDGFRB (NM_002609) rearrangement: c.1973_c.*4684del	PRECISE	Note: The PDGFRB rearrangement is a deletion of exons 14-23. One of the breakpoints is within exon 14	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11468	0	4	5	Promoter of PDGFRB(-):3Kb from tx start	PDGFRB	149490642			5	Exon 14 of PDGFRB(-)	PDGFRB	149503863			7	DELETION		13221	175854	27095	4	NEW_VARIANT
P-0017529-T01-IM5	MTOR (NM_004958) Rearrangement :  c.1723_c.2208+375del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3712	0	106	1	Intron of MTOR(-):374bp after exon 13	MTOR	11297525			1	Exon 11 of MTOR(-)	MTOR	11300423			10	DELETION		2898	176079	4687	111	NEW_VARIANT
P-0017533-T01-IM5	PIK3R1 (NM_181523) Rearrangement : c.1425+51_c.*547del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		4594	0	12	5	Intron of PIK3R1(+):51bp after exon 11	PIK3R1	67589713			5	3-UTR of PIK3R1(+):71Kb after coding stop	PIK3R1	67593976			10	DELETION		4263	176089	8139	13	NEW_VARIANT
P-0017542-T01-IM5	EXOSC10 (NM_001001998) - MTOR (NM_004958) rearrangement: c.372+1601: EXOSC10_c.6299:MTORdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EXOSC10:MTOR}		17085	0	13	1	Intron of EXOSC10(-):2Kb after exon 3	EXOSC10	11154214			1	Exon 45 of MTOR(-)	MTOR	11187119			10	DUPLICATION		32905	176175	29912	14	NEW_VARIANT
P-0017548-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2838:TMPRSS2_c.40-58598:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		76664	0	50	21	Intron of ERG(-):59Kb before exon 4	ERG	39876142			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872954			10	DELETION		2996812	184175	75812	54	NEW_VARIANT
P-0017551-T01-IM5	PDCD1 (NM_005018) rearrangement: chr2:g.242452335_c.206:PDCD1del	PRECISE	Note: The PDCD1 rearrangement is a deletion of exons 2-5. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		5594	0	20	2	IGR: 18Kb before STK25(-)	STK25	242452335			2	Exon 2 of PDCD1(-)	PDCD1	242795003			10	DELETION		342668	176123	11051	32	NEW_VARIANT
P-0017551-T01-IM5	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused with TACC3 exons 10-16): c.2309:FGFR3_c.1836+8:TACC3dup	PRECISE		MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		22540	0	98	4	Intron of TACC3(+):8bp after exon 9	TACC3	1739063			4	Exon 18 of FGFR3(+)	FGFR3	1808877			10	DUPLICATION		69814	176124	61826	111	NEW_VARIANT
P-0017582-T01-IM5	MGA (NM_001164273) Rearrangement : c.4586-416_c.5920del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17633	0	54	15	Intron of MGA(+):415bp before exon 15	MGA	42034328			15	Exon 17 of MGA(+)	MGA	42041725			10	DELETION		7397	176200	19526	56	NEW_VARIANT
P-0017592-T01-IM5	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	PRECISE	Note: This fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		49556	0	46	2	Intron of ALK(-):778bp after exon 19	ALK	29447548			2	Intron of EML4(+):6Kb before exon 6	EML4	42502027			10	INVERSION		13054479	176183	85320	46	NEW_VARIANT
P-0017653-T01-IM5	POLD1 (NM_002691) - ZNF284 (NM_001037813) rearrangement: c.1892+43: POLD1_c.15+1157: ZNF284dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {POLD1:ZNF284}		60445	0	4	19	Intron of ZNF284(+):1Kb after exon 2	ZNF284	44581714			19	Intron of POLD1(+):43bp after exon 15	POLD1	50912201			10	DUPLICATION		6330487	176419	77051	4	NEW_VARIANT
P-0017656-T01-IM5	CDK12 (NM_016507) rearrangement : g.30096337_c.754:CDK12inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		42021	0	9	17	IGR: 83Kb before COPRS(-)	COPRS	30096337			17	Exon 1 of CDK12(+)	CDK12	37619078			10	INVERSION		7522741	176430	63899	11	NEW_VARIANT
P-0017692-T01-IM6	CSF1R (NM_005211) rearrangement: c.2491_c.*2654del	PRECISE	Note: The CSF1R rearrangement is a deletion of exons 19-21. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5373	0	10	5	Promoter of CSF1R(-):2Kb from tx start	CSF1R	149430978			5	Exon 19 of CSF1R(-)	CSF1R	149435652			10	DELETION		4674	176624	7654	10	NEW_VARIANT
P-0017708-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4676:TMPRSS2_c.40-56300:ERGdel	PRECISE	Note: TMPRSS2 is fused with non-canonical ERG  transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		76244	0	5	21	Intron of ERG(-):56Kb before exon 4	ERG	39873844			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874792			10	DELETION		3000948	176686	43069	6	NEW_VARIANT
P-0017711-T01-IM6	NTRK3 (NM_001012338) rearrangement: t(X;15)(q11.1;q25.3)(chrX:g.62147342::chr15:g.88678407)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	19	X	IGR: 420Kb before SPIN4(-)	SPIN4	62147342			15	Exon 10 of NTRK3(-)	NTRK3	88678407			10	TRANSLOCATION		0	176681	0	23	NEW_VARIANT
P-0017715-T01-IM6	AGO2 (NM_012154) rearrangement: c.655+304_c.816del	PRECISE	Note: The AGO2 rearrangement is an intragenic deletion of exons 6-7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1971	0	8	8	Exon 7 of AGO2(-)	AGO2	141568646			8	Intron of AGO2(-):303bp after exon 5	AGO2	141570169			10	DELETION		1523	176690	3017	8	NEW_VARIANT
P-0017716-T01-IM6	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	PRECISE	Note: The NCOA4 - RET fusion includes the kinase domain of RET.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		26209	0	63	10	Intron of RET(+):859bp before exon 12	RET	43611172			10	Intron of TIMM23B(+):150Kb before exon 7	TIMM23B	51582314			10	DUPLICATION		7971142	176709	35199	67	NEW_VARIANT
P-0017718-T01-IM6	CREBBP (NM_004380) rearrangement: t(12;16)(q15;p13.3)(chr12:g.70017642::chr16:g.3777792)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	23	16	Exon 31 of CREBBP(-)	CREBBP	3777792			12	IGR: 15Kb before LRRC10(-)	LRRC10	70017642			10	TRANSLOCATION		0	176684	0	25	NEW_VARIANT
P-0017718-T01-IM6	TERT (NM_198253) rearrangement: t(5;17)(p15.33;q21.2)(chr5:g.1295225::chr17:g.38475855)	PRECISE	Note: The TERT rearrangement is a translocation with a breakpoint in the TERT promoter region. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	20	17	5-UTR of RARA(+):12Kb before coding start	RARA	38475855			5	Promoter of TERT(-):42Kb from tx start	TERT	1295225			10	TRANSLOCATION		0	176685	0	21	NEW_VARIANT
P-0017723-T01-IM6	IRS2 (NM_003749) - CADM2  (NM_001167674) rearrangement: t(3;13)(p12.1;q34)(chr3:g.86035837::chr13:g.110436835)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {IRS2:CADM2}		0	0	88	13	Exon 1 of IRS2(-)	IRS2	110436835			3	Intron of CADM2(+):7Kb after exon 8	CADM2	86035837			10	TRANSLOCATION		0	176729	0	166	NEW_VARIANT
P-0017724-T01-IM6	RET (NM_020975) rearrangement : g.43149839_c.1264-2:RETdel	PRECISE	Note: The RET rearrangement results in the deletion of exons 1-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14546	0	9	10	IGR: 19Kb before LINC01518(-)	LINC01518	43149839			10	Intron of RET(+):20bp before exon 7	RET	43606634			10	DELETION		456795	176712	13663	9	NEW_VARIANT
P-0017724-T01-IM6	FYN (NM_153047) rearrangement: t(2;6)(q37.3;q21)(chr2:g.239377558::chr6:g.112024156)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	18	6	Exon 5 of FYN(-)	FYN	112024156			2	IGR: 42Kb before LINC01107(-)	LINC01107	239377558			10	TRANSLOCATION		0	176713	0	19	NEW_VARIANT
P-0017730-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-4466:TMPRSS2_c.19-8247:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		92838	0	20	21	Intron of ERG(-):8Kb before exon 2	ERG	39825791			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874582			10	DELETION		3048791	176725	66387	28	NEW_VARIANT
P-0017744-T01-IM6	BRCA2 (NM_000059) Rearrangement : c.316+811_c.426-1del	PRECISE	Note: The BRCA2 Rearrangement results in the deletion of exons  4-5 of BRCA2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1006	0	77	13	Intron of BRCA2(+):811bp after exon 3	BRCA2	32894273			13	Exon 5 of BRCA2(+)	BRCA2	32900237			10	DELETION		5964	176756	1856	81	NEW_VARIANT
P-0017760-T01-IM6	MGA (NM_001164273) Rearrangement : c.7744+1111_c.8913del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6400	0	5	15	Intron of MGA(+):1Kb after exon 22	MGA	42055671			15	Exon 24 of MGA(+)	MGA	42059193			10	DELETION		3522	176821	3031	6	NEW_VARIANT
P-0017760-T01-IM6	SOX9 (NM_000346) Rearrangement : c.1200_chr17:g.70140019del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		5806	0	15	17	Exon 3 of SOX9(+)	SOX9	70120198			17	IGR: 23Kb before SOX9(+)	SOX9	70140019			10	DELETION		19821	176822	3882	15	NEW_VARIANT
P-0017769-T01-IM6	DIS3 (NM_014953) Rearrangement : c.654:DIS3_chr13:g.81632702inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		14652	0	14	13	Exon 4 of DIS3(-)	DIS3	73351558			13	IGR: 40Kb before LINC00377(+)	LINC00377	81632702			10	INVERSION		8281144	176826	38745	23	NEW_VARIANT
P-0017774-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : chr21:g.40091030_c.55+4035:TMPRSS2del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		77663	0	17	21	IGR: 20Kb before LINC00114(-)	LINC00114	40091030			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875842			10	DELETION		2784812	176827	68516	18	NEW_VARIANT
P-0017807-T01-IM6	APC (NM_000038) Rearrangement: c.3925_c.*4057del	PRECISE	Note: APC rearrangement is a deletion which leads to the partial deletion of exon 16, potentially leading to a truncated protein.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		20707	0	7	5	Exon 16 of APC(+)	APC	112175216			5	Promoter of APC(+):110Kb from tx start	APC	112183880			10	DELETION		8664	176865	8100	7	NEW_VARIANT
P-0017817-T01-IM6	GRIN2A (NM_001134407) rearrangement: c.3436_c.4030del	IMPPRECISE	Note: The GRIN2A rearrangement is a deletion (594 bp) within exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2485	0	81	16	Exon 13 of GRIN2A(-)	GRIN2A	9857371			16	Exon 13 of GRIN2A(-)	GRIN2A	9857965			0	DELETION		594	176886	1941	89	NEW_VARIANT
P-0017827-T01-IM6	EGFR (NM_005228) rearrangement: c.3028:EGFR_chr7:g.55336682del	PRECISE	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)	MANUAL_OK	3to3	3to3	-		14586	0	109	7	Exon 25 of EGFR(+)	EGFR	55268962			7	IGR: 31Kb before ELDR(-)	ELDR	55336682			10	INVERSION		67720	176914	456468	106	NEW_VARIANT
P-0017831-T01-IM6	FGFR2 (NM_000141) rearrangement: t(10;16)(q26.13;q12.2)(chr10:g.123241224::chr16:g.55238062)	PRECISE	Note: The FGFR2 rearrangement is a translocation that may result in the truncation of FGFR2 exon 18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	15	16	IGR: 120Kb before IRX6(+)	IRX6	55238062			10	Intron of FGFR2(-):2Kb before exon 18	FGFR2	123241224			10	TRANSLOCATION		0	176924	0	22	NEW_VARIANT
P-0017846-T01-IM6	IL10 (NM_000572) Rearrangement : chr1:g.201374280_c.378+39:IL10del	PRECISE	Note: The IL10 Rearrangement results in the deletion of exons 4-5 of IL10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		37072	0	6	1	3-UTR of TNNI1(-):5Kb after coding stop	TNNI1	201374280			1	Intron of IL10(-):38bp after exon 3	IL10	206944213			10	DELETION		5569933	176925	87278	6	NEW_VARIANT
P-0017846-T01-IM6	SF3B1 (NM_012433) Rearrangement : chr2:g.196301398_c.442:SF3B1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		20468	0	14	2	IGR: 220Kb before SLC39A10(+)	SLC39A10	196301398			2	Exon 5 of SF3B1(-)	SF3B1	198283286			10	INVERSION		1981888	176927	50183	13	NEW_VARIANT
P-0017859-T01-IM6	MAX (NM_002382) rearrangement: c.*3102_c.296-91del	PRECISE	Note: The MAX rearrangement results in the deletion of exon 5. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		932	0	22	14	Promoter of MAX(-):2Kb from tx start	MAX	65540092			14	Intron of MAX(-):91bp before exon 5	MAX	65543472			10	INVERSION		3380	176968	879	20	NEW_VARIANT
P-0017882-T01-IM6	PARK2 (NM_004562) rearrangement: t(6;18)(q26;q21.2)(chr6:g.162170030::chr18:g.48058391)	PRECISE	Note: The PARK2 rearrangement is a translocation that may result in a truncation of exons 8-12. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	26	18	IGR: 28Kb before MAPK4(+)	MAPK4	48058391			6	Intron of PARK2(-):37Kb after exon 7	PARK2	162170030			10	TRANSLOCATION		0	177052	0	27	NEW_VARIANT
P-0017882-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(p13.1;q22.3)(chr17:g.7790479::chr21:g.42870483)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation that may result in a truncation of exons 2-14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	82	21	Intron of TMPRSS2(-):367bp before exon 2	TMPRSS2	42870483			17	Intron of CHD3(+):2Kb after exon 1	CHD3	7790479			10	TRANSLOCATION		0	177053	0	85	NEW_VARIANT
P-0017882-T01-IM6	HDAC9 (NM_178425) - XPO1 (NM_003400) rearrangement: t(2;7)(p15;p21.2)(chr2:g.61721253::chr7:g.18926552)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {HDAC9:XPO1}		0	0	197	7	Intron of HDAC9(+):12Kb after exon 21	HDAC9	18926552			2	Intron of XPO1(-):27bp before exon 12	XPO1	61721253			10	TRANSLOCATION		0	177051	0	195	NEW_VARIANT
P-0017892-T01-IM6	RECQL4 (NM_004260) Rearrangement : c.-1259:PTK2B_c.1132-19:RECQL4	PRECISE	Note: The RECQL4 Rearrangement results in the deletion of exons 6-21 of RECQL4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		491057	0	10	8	5-UTR of PTK2B(+):73Kb before coding start	PTK2B	27181977			8	Intron of RECQL4(-):19bp before exon 6	RECQL4	145741293			10	DELETION		118559316	177232	583569	11	NEW_VARIANT
P-0017899-T01-IM6	APC (NM_000038) Rearrangement: t(5;14)(q22.1;q23.1)(chr5:g.112174171::chr14:g.59220719)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	5	14	IGR: 74Kb before LINC01500(+)	LINC01500	59220719			5	Exon 16 of APC(+)	APC	112174171			10	TRANSLOCATION		0	177239	0	5	NEW_VARIANT
P-0017913-T01-IM6	BRD4 (NM_058243) rearrangement: c.*2094_c.3576+51del	PRECISE	Note: The BRD4 rearrangement results in the deletion of exons 18-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		5482	0	104	19	Promoter of BRD4(-):1Kb from tx start	BRD4	15347094			19	Intron of BRD4(-):50bp after exon 17	BRD4	15350152			10	DELETION		3058	177271	8812	117	NEW_VARIANT
P-0017917-T01-IM6	ZRSR2 (NM_005089) rearrangement: t(12;X)(q15;p22.2)(chr12:g.70367195::chrX:g.15841299)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	31	X	Exon 11 of ZRSR2(+)	ZRSR2	15841299			12	IGR: 194Kb before RAB3IP(+)	RAB3IP	70367195			10	TRANSLOCATION		0	177282	0	96	NEW_VARIANT
P-0017917-T01-IM6	ZRSR2 (NM_005089) rearrangement : c.828_c.*1222inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		5472	0	15	X	Exon 10 of ZRSR2(+)	ZRSR2	15838330			X	Promoter of ZRSR2(+):34Kb from tx start	ZRSR2	15842587			10	INVERSION		4257	177280	15618	46	NEW_VARIANT
P-0017924-T01-IM6	KIF5B (NM_004521) - ALK (NM_004304) fusion: t(2;10)(p23.2;p11.22)(chr2:g.29447945::chr10:g.32305310)	PRECISE	Note: The KIF5B - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {KIF5B:ALK}		0	0	41	10	Intron of KIF5B(-):723bp before exon 25	KIF5B	32305310			2	Intron of ALK(-):381bp after exon 19	ALK	29447945			10	TRANSLOCATION		0	177296	0	46	NEW_VARIANT
P-0017932-T01-IM6	KMT2D (NM_003482) rearrangement: c.16368:KMT2D_chr12:g.49628359del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		146204	0	38	12	Exon 52 of KMT2D(-)	KMT2D	49416107			12	IGR: 31Kb before TUBA1C(+)	TUBA1C	49628359			10	DELETION		212252	177320	205189	46	NEW_VARIANT
P-0017932-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3865-625_c.10608del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		40098	0	49	16	Exon 10 of ZFHX3(-)	ZFHX3	72821567			16	Intron of ZFHX3(-):625bp before exon 8	ZFHX3	72834653			10	DELETION		13086	177321	42919	55	NEW_VARIANT
P-0017978-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		144205	0	15	2	Intron of ALK(-):215bp before exon 20	ALK	29446609			2	Intron of EML4(+):7Kb after exon 5	EML4	42499177			10	INVERSION		13052568	177504	118332	18	NEW_VARIANT
P-0017987-T01-IM6	C1orf112 (NM_018186) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q24.2;q22.3)(chr1:g.169817552::chr21:g.42871817)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {C1orf112:TMPRSS2}		0	0	170	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871817			1	Intron of C1orf112(+):608bp after exon 20	C1orf112	169817552			10	TRANSLOCATION		0	177548	0	169	NEW_VARIANT
P-0017989-T01-IM6	SLC25A21 (NM_030631) - FOXA1 (NM_00449) rearrangement: c.71-139753:SLC25A21_c.320:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC25A21:FOXA1}		10996	0	12	14	Intron of SLC25A21(-):140Kb before exon 2	SLC25A21	37483962			14	Exon 2 of FOXA1(-)	FOXA1	38061669			10	DUPLICATION		577707	177556	14967	12	NEW_VARIANT
P-0017990-T01-IM6	ARID1A (NM_006015) rearrangement: c.6377:ARID1A_chr1:g.41724708inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		136858	0	33	1	Exon 20 of ARID1A(+)	ARID1A	27106766			1	IGR: 103Kb before FOXO6(+)	FOXO6	41724708			10	INVERSION		14617942	177553	130191	33	NEW_VARIANT
P-0018003-T01-IM6	TMPRSS2 (NM_001135099) - LSS (NM_001001438) rearrangement: c.56-147:TMPRSS2_c.1951:LSSdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TMPRSS2:LSS}		143864	0	10	21	Intron of TMPRSS2(-):147bp before exon 2	TMPRSS2	42870263			21	Exon 19 of LSS(-)	LSS	47614442			10	DUPLICATION		4744179	177589	154383	11	NEW_VARIANT
P-0018007-T01-IM6	ERBB2 (NM_004448) rearrangement: c.3412+62:ERBB2_chr17:g.37891043del	PRECISE	Note: The ERBB2 rearrangement is a deletion of exon 27.	MANUAL_OK	3to5	3to5	-		4462	0	14	17	Intron of ERBB2(+):62bp after exon 26	ERBB2	37883862			17	IGR: 3Kb before GRB7(+)	GRB7	37891043			10	DELETION		7181	177594	3784	16	NEW_VARIANT
P-0018016-T01-IM6	DNMT1 (NM_001379) - EIF3G (NM_003755) rearrangement: c.376:DNMT1_c.596-198del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNMT1:EIF3G}		46330	0	29	19	Intron of EIF3G(-):198bp before exon 8	EIF3G	10226948			19	Exon 4 of DNMT1(-)	DNMT1	10291095			10	DELETION		64147	177630	65620	29	NEW_VARIANT
P-0018030-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.chr19:g.25566206_c.936inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {GNG7:SMARCA4}		199402	0	26	19	5-UTR of GNG7(-):51Kb before coding start	GNG7	2566206			19	Exon 6 of SMARCA4(+)	SMARCA4	11098418			10	INVERSION		8532212	177717	304588	35	NEW_VARIANT
P-0018038-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.56-3057:TMPRSS2_c.18+11021:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		94246	0	14	21	Intron of ERG(-):11Kb after exon 1	ERG	39859266			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873173			10	DELETION		3013907	177743	68808	15	NEW_VARIANT
P-0018069-T01-IM6	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.1648+160:RET_c.1915-72:KIF5Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RET:KIF5B}		49281	0	40	10	Intron of KIF5B(-):72bp before exon 17	KIF5B	32311257			10	Intron of RET(+):160bp after exon 8	RET	43607832			10	INVERSION		11296575	177829	46721	40	NEW_VARIANT
P-0018082-T01-IM6	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)	PRECISE	Note: The TFG - NTRK1 fusion is predicted to be in-frame and includes the kinase domain of NTRK1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TFG:NTRK1}		0	0	16	3	Intron of TFG(+):885bp before exon 5	TFG	100450466			1	Intron of NTRK1(+):45bp after exon 8	NTRK1	156843796			10	TRANSLOCATION		0	177852	0	16	NEW_VARIANT
P-0018086-T01-IM6	ERG (NM_182918) rearrangement: t(16;21)(p13.2;q22.2)(chr16:g.8690703::chr21:g.39817374)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	19	21	Exon 2 of ERG(-)	ERG	39817374			16	IGR: 25Kb before METTL22(+)	METTL22	8690703			10	TRANSLOCATION		0	177918	0	22	NEW_VARIANT
P-0018090-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		19005	0	29	21	Intron of ERG(-):2Kb before exon 2	ERG	39819785			21	Intron of TMPRSS2(-):620bp before exon 3	TMPRSS2	42867125			10	DELETION		3047340	177901	30471	30	NEW_VARIANT
P-0018108-T02-IM6	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241667340::chr13:g.42830153)	IMPPRECISE	Note: The FH rearrangement is a translocation that may result in a truncation of exons 8-10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {FH:DGKH}		0	0	25	13	5-UTR of DGKH(+):563bp before coding start	DGKH	42830153			1	Intron of FH(-):1bp after exon 7	FH	241667340			0	TRANSLOCATION		0	178003	0	27	NEW_VARIANT
P-0018109-T01-IM6	BLM (NM_000057) - ANKLE2 (NM_015114) rearrangement: t(12;15)(q24.33;q26.1)(chr12:g.133320386::chr15:g.91358467)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {BLM:ANKLE2}		0	0	29	15	Exon 22 of BLM(+)	BLM	91358467			12	Intron of ANKLE2(-):524bp before exon 6	ANKLE2	133320386			0	TRANSLOCATION		0	177991	0	28	NEW_VARIANT
P-0018112-T01-IM6	RFWD2 (NM_022457) rearrangement: c.408-3437_c.467+23inv	PRECISE	Note: The RFWD2 rearrangement is an intragenic inversion of exon 2, potentially disrupting the gene function.	MANUAL_OK	5to5	5to5	Antisense Fusion		982	0	16	1	Intron of RFWD2(-):22bp after exon 2	RFWD2	176153746			1	Intron of RFWD2(-):3Kb before exon 2	RFWD2	176157265			10	INVERSION		3519	177987	879	22	NEW_VARIANT
P-0018113-T01-IM6	TAP1 (NM_000593) rearrangement: t(6;20)(p21.32;p12.3)(chr6:g.32813483::chr20:g.6891743)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	26	20	IGR: 143Kb before BMP2(+)	BMP2	6891743			6	Exon 11 of TAP1(-)	TAP1	32813483			10	TRANSLOCATION		0	177993	0	26	NEW_VARIANT
P-0018115-T01-IM6	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	PRECISE	Note: The FGFR2 - BICC1 fusion is predicted to in-frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		278349	0	59	10	Intron of BICC1(+):35Kb after exon 2	BICC1	60415608			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241970			10	INVERSION		62826362	177983	420241	77	NEW_VARIANT
P-0018122-T01-IM6	TMPRSS2 (NM_001135099) - ABCG1 (NM_207627) Rearrangement: c.794+15:TMPRSS2_c.48+6119:ABCG1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {TMPRSS2:ABCG1}		115502	0	38	21	Intron of TMPRSS2(-):14bp after exon 7	TMPRSS2	42851084			21	Intron of ABCG1(+):6Kb after exon 2	ABCG1	43627952			10	INVERSION		776868	178058	161419	48	NEW_VARIANT
P-0018127-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Rearrangement: c.126+1404:TMPRSS2_.c.19-4088:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		36498	0	15	21	Intron of ERG(-):4Kb before exon 2	ERG	39821632			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868642			10	INVERSION		3047010	178064	21351	13	NEW_VARIANT
P-0018131-T01-IM6	B2M (NM_004048) Rearrangement : c.67_c.68del	PRECISE	Note: The B2M Rearrangement results in the deletion of exon1-2 of B2M. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1312	0	4	15	Exon 1 of B2M(+)	B2M	45003811			15	Exon 2 of B2M(+)	B2M	45007621			10	DELETION		3810	178735	1118	4	NEW_VARIANT
P-0018131-T01-IM6	BCOR (NM_001123385) Rearrangement : chrX:g.39891617_c.2500:BCORdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		13344	0	3	X	IGR: 19Kb before BCOR(-)	BCOR	39891617			X	Exon 4 of BCOR(-)	BCOR	39932099			8	DELETION		40482	178736	7999	3	NEW_VARIANT
P-0018149-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4) : c.55+3556:TMPRSS2_c.40-56840:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		79998	0	13	21	Intron of ERG(-):57Kb before exon 4	ERG	39874384			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42876321			10	DELETION		3001937	178730	45232	14	NEW_VARIANT
P-0018176-T01-IM6	BRCA1 (NM_007294) rearrangement: c.671-148_c.4359del	PRECISE	Note: The BRCA1 rearrangement is an intragenic deletion of exons 10-13. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		33303	0	49	17	Exon 13 of BRCA1(-)	BRCA1	41228630			17	Intron of BRCA1(-):148bp before exon 10	BRCA1	41247025			10	DELETION		18395	178147	41287	58	NEW_VARIANT
P-0018195-T01-IM6	NTRK2 (NM_006180) rearrangement: t(9;14)(q21.33;q32.11)(chr9:g.87317072::chr14:g.90393239)	PRECISE	Note: The NTRK2 rearrangement is a translocation that may result in the truncation of exons 5-21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	22	14	Intron of EFCAB11(-):5Kb after exon 5	EFCAB11	90393239			9	Intron of NTRK2(+):1bp before exon 5	NTRK2	87317072			10	TRANSLOCATION		0	178309	0	22	NEW_VARIANT
P-0018195-T01-IM6	MAP3K14 (NM_003954) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.43364113::chr22:g.43080364)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	21	22	IGR: 8Kb before A4GALT(-)	A4GALT	43080364			17	Exon 5 of MAP3K14(-)	MAP3K14	43364113			0	TRANSLOCATION		0	178310	0	23	NEW_VARIANT
P-0018216-T01-IM6	TERT (NM_198253) rearrangement: c.-94_chr5:g.10249793del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {FAM173B:TERT}		21630	0	3	5	Promoter of TERT(-):42Kb from tx start	TERT	1295198			5	Intron of FAM173B(-):176bp after exon 1	FAM173B	10249793			9	DELETION		8954595	178335	23287	3	NEW_VARIANT
P-0018222-T01-IM6	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)	PRECISE	Note: The CD74-ROS1 fusion includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	44	6	Intron of ROS1(-):631bp before exon 34	ROS1	117646209			5	Intron of CD74(-):327bp after exon 6	CD74	149783915			10	TRANSLOCATION		0	178313	0	45	NEW_VARIANT
P-0018233-T01-IM6	KMT2D (NM_003482)  rearrangement: c.5867+21_chr12:g.48015840del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		93357	0	42	12	IGR: 40Kb before RPAP3(-)	RPAP3	48015840			12	Intron of KMT2D(-):20bp after exon 27	KMT2D	49436323			10	DELETION		1420483	178356	91714	45	NEW_VARIANT
P-0018233-T01-IM6	WT1 (NM_024426) rearrangement: t(11;21)(p13;q21.2)(chr11:g.32414419::chr21:g.26525604)	PRECISE	Note: The WT1 rearrangement is a translocation with a breakpoint within intron 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	21	IGR: 233Kb before LINC00158(-)	LINC00158	26525604			11	Intron of WT1(-):118bp before exon 8	WT1	32414419			10	TRANSLOCATION		0	178364	0	6	NEW_VARIANT
P-0018235-T01-IM6	GLI1 (NM_005269) rearrangement: c.41_chr12:g.57715760inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1082	0	5	12	IGR: 68Kb before R3HDM2(-)	R3HDM2	57715760			12	Exon 2 of GLI1(+)	GLI1	57857515			10	INVERSION		141755	178351	905	5	NEW_VARIANT
P-0018242-T01-IM6	CSDE1 (NM_001242891) rearrangement:  c.666:CSDE1_chr1:g.90028558del	PRECISE	Note: The CSDE1 rearrangement is a deletion of exons 8 - 21. One of the breakpoints is within exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		42352	0	8	1	5-UTR of LRRC8B(+):20Kb before coding start	LRRC8B	90028558			1	Exon 8 of CSDE1(-)	CSDE1	115277117			10	DELETION		25248559	178444	62416	9	NEW_VARIANT
P-0018242-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		98526	0	126	2	Intron of ALK(-):319bp after exon 19	ALK	29448007			2	Intron of EML4(+):8Kb before exon 6	EML4	42500430			10	INVERSION		13052423	178445	117529	124	NEW_VARIANT
P-0018243-T01-IM6	GPRC5C (NM_018653) - MET (NM_000245) rearrangement: t(7;17)(q31.2;q25.1)(chr7:g.116413793::chr17:g.72439446)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {GPRC5C:MET}		0	0	27	17	Intron of GPRC5C(+):510bp before exon 3	GPRC5C	72439446			7	Intron of MET(+):1Kb before exon 15	MET	116413793			10	TRANSLOCATION		0	178427	0	28	NEW_VARIANT
P-0018271-T01-IM6	DOT1L (NM_032482) rearrangement: c.3390+59_g.17159184del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		448758	0	24	19	Intron of DOT1L(+):59bp after exon 24	DOT1L	2222617			19	Promoter of HAUS8(-):1Kb from tx start	HAUS8	17159184			10	DELETION		14936567	178471	737517	109	NEW_VARIANT
P-0018274-T01-IM6	CREBBP (NM_004380) rearrangement: c.2159-98:CREBBP_g.4179394del	PRECISE	Note: The CREBBP rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14041	0	8	16	Intron of CREBBP(-):98bp before exon 12	CREBBP	3824792			16	IGR: 60Kb before SRL(-)	SRL	4179394			10	DELETION		354602	178479	14305	7	NEW_VARIANT
P-0018280-T01-IM6	EML4 (NM_001145076) - ALK (NM_004304) Fusion (EML4 exon 6 fused with ALK exon 20): c.494-6792:EML4_c.3173-793:ALKinv	PRECISE	Note: The Fusion is predicted to be in-frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		81440	0	17	2	Intron of ALK(-):793bp before exon 20	ALK	29447187			2	Intron of EML4(+):7Kb before exon 6	EML4	42501198			10	INVERSION		13054011	178490	92484	17	NEW_VARIANT
P-0018289-T01-IM6	KMT2C(NM_170606) Rearrangement : c.8688_c.7149+164del	PRECISE	Note: The KMT2C Rearrangement results in the deletion of exons 37-38 of KMT2C. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4417	0	21	7	Exon 38 of KMT2C(-)	KMT2C	151873850			7	Intron of KMT2C(-):163bp after exon 36	KMT2C	151877632			10	DELETION		3782	178507	7729	22	NEW_VARIANT
P-0018294-T01-IM6	PARK2 (NM_004562) rearrangement: c.4970_g.112190339del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		353	0	52	6	Exon 2 of PARK2(-)	PARK2	162864482			6	Intron of PARK2(-):32Kb before exon 2	PARK2	162896705			10	DELETION		32223	178542	382	53	NEW_VARIANT
P-0018297-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.55+3942:TMPRSS2_c.-149-36900:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	-		71808	0	19	21	3-UTR of ERG(-):40Kb after coding stop	ERG	39993769			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875935			10	DELETION		2882166	178549	138085	21	NEW_VARIANT
P-0018302-T01-IM6	SETD2 (NM_014159) rearrangement : c.7533+80:SETD2_g.125048522inv	PRECISE	Note: The SETD2 (NM_014159) rearrangement results in an inversion of exons 1-20. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		258960	0	6	3	Intron of SETD2(-):79bp after exon 20	SETD2	47059048			3	5-UTR of ZNF148(-):97Kb before coding start	ZNF148	125048522			10	INVERSION		77989474	178556	418649	6	NEW_VARIANT
P-0018314-T01-IM6	BRCA1 (NM_007294) rearrangement: c.-19-61:BRCA1_chr17:g.41382277del	PRECISE	Note: The BRCA1 rearrangement is a deletion with a breakpoint in the 5UTR. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {LINC00854:BRCA1}		897	0	8	17	5-UTR of BRCA1(-):78Kb before coding start	BRCA1	41276193			17	Promoter of LINC00854(-):9Kb from tx start	LINC00854	41382277			10	DELETION		106084	178568	266	8	NEW_VARIANT
P-0018315-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		31591	0	69	21	Intron of ERG(-):19Kb after exon 1	ERG	39851526			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868471			10	DELETION		3016945	178582	23506	77	NEW_VARIANT
P-0018316-T01-IM6	KMT2D (NM_003482) rearrangement: c.4020+20:KMT2D_chr12:g.49530496del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		47677	0	2	12	Intron of KMT2D(-):19bp after exon 12	KMT2D	49442868			12	IGR: 9Kb before TUBA1B(-)	TUBA1B	49530496			7	DELETION		87628	178559	29605	2	NEW_VARIANT
P-0018329-T01-IM6	APC (NM_000038) rearrangement: c.3581_c.4458inv	PRECISE	Note: The APC rearrangement is an inversion (877 bp) with both breakpoints within exon 16. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3464	0	7	5	Exon 16 of APC(+)	APC	112174872			5	Exon 16 of APC(+)	APC	112175749			10	INVERSION		877	178625	2568	7	NEW_VARIANT
P-0018351-T01-IM6	CDK8 NM_001260) rearrangement: c.645_c.647-1del	PRECISE	Note: The CDK8 rearrangement is an intragenic deletion with breakpoints in exon 6 and 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		583	0	2	13	Exon 6 of CDK8(+)	CDK8	26959478			13	Exon 7 of CDK8(+)	CDK8	26967503			6	DELETION		8025	178638	391	2	NEW_VARIANT
P-0018351-T01-IM6	CBFB (NM_022845) rearrangement: c.495+30_c.496-1del	PRECISE	Note: The CBFB rearrangement is an intragenic deletion with a breakpoint in exon 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1059	0	5	16	Intron of CBFB(+):30bp after exon 5	CBFB	67116241			16	Exon 6 of CBFB(+)	CBFB	67132612			10	DELETION		16371	178639	758	6	NEW_VARIANT
P-0018374-T01-IM6	FAT1 (NM_005245) Rearrangement : c.5344:FAT1_chr4:g.187311035del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		57932	0	6	4	3-UTR of F11-AS1(-):111Kb after coding stop	F11-AS1	187311035			4	Exon 10 of FAT1(-)	FAT1	187542396			10	DELETION		231361	178710	63623	6	NEW_VARIANT
P-0018378-T01-IM6	ROS1 (NM_002944) Rearrangement : c.1377:ROS1_chr6:g.169216197inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		233533	0	13	6	Exon 12 of ROS1(-)	ROS1	117710895			6	IGR: 359Kb before LOC101929504(-)	LOC101929504	169216197			10	INVERSION		51505302	178789	185676	12	NEW_VARIANT
P-0018395-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2464:TMPRSS2_c.40-54367:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		68841	0	35	21	Promoter of ERG(-):120Kb from tx start	ERG	39871911			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877413			10	DELETION		3005502	178835	75421	37	NEW_VARIANT
P-0018416-T01-IM6	SOX9 (NM_000346) rearrangement: chr17:g.69803812_c.788del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		8421	0	63	17	IGR: 214Kb before LOC102723505(-)	LOC102723505	69803812			17	Exon 3 of SOX9(+)	SOX9	70119786			10	DELETION		315974	178869	10189	68	NEW_VARIANT
P-0018419-T01-IM6	SUFU (NM_016169) rearrangement: c.757-1023_c.894del	PRECISE	Note: The SUFU rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		512	0	17	10	Intron of SUFU(+):1Kb before exon 7	SUFU	104355874			10	Exon 7 of SUFU(+)	SUFU	104357034			10	DELETION		1160	178878	605	19	NEW_VARIANT
P-0018453-T01-IM6	BCL6 (NM_001706) rearrangement : g.108661942_c.1709-28:BCL6inv	IMPPRECISE	Note: The BCL6 rearrangement results in an inversion of exons 8-10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		319284	0	17	3	Intron of GUCA1C(-):10Kb after exon 1	GUCA1C	108661942			3	Intron of BCL6(-):28bp before exon 8	BCL6	187443445			0	INVERSION		78781503	179057	412167	17	NEW_VARIANT
P-0018461-T01-IM6	RB1 (NM_000321) rearrangement : g.45902093_c.791:RB1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		9272	0	75	13	IGR: 6Kb before TPT1(-)	TPT1	45902093			13	Exon 8 of RB1(+)	RB1	48937023			10	INVERSION		3034930	179062	8594	75	NEW_VARIANT
P-0018462-T01-IM6	TP53 (NM_000546) rearrangement: c.397_c.894del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 5-8. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5844	0	37	17	Exon 8 of TP53(-)	TP53	7577044			17	Exon 5 of TP53(-)	TP53	7578533			10	DELETION		1489	179075	7188	40	NEW_VARIANT
P-0018464-T01-IM6	HIST1H3G (NM_003534) rearrangement: c.85_chr6:g.26153113del	PRECISE	Note: The HIST1H3G rearrangement is a deletion of exon 1. One of the breakpoints is within exon.  The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14940	0	24	6	IGR: 3Kb before HIST1H1E(+)	HIST1H1E	26153113			6	Exon 1 of HIST1H3G(-)	HIST1H3G	26271528			10	DELETION		118415	179078	17128	25	NEW_VARIANT
P-0018470-T01-IM6	EP300 (NM_001429) rearrangement: c.3778_c.3807-168del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exon 22. One of the breakpoints is within exon 22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		369	0	39	22	Exon 22 of EP300(+)	EP300	41560106			22	Intron of EP300(+):167bp before exon 23	EP300	41562435			10	DELETION		2329	179069	169	84	NEW_VARIANT
P-0018487-T01-IM6	CYLD (NM_001042355) - SPACA7 (NM_145248) rearrangement: t(13, 16)( q12.1, q34)(chr13:g.113008750::chr16:g.50813791)	PRECISE	Note: The CYLD  rearrangement is the translocation of  CYLD exon 8-18 and SPACA7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	9	16	Exon 8 of CYLD(+)	CYLD	50813791			13	IGR: 22Kb before SPACA7(+)	SPACA7	113008750			10	TRANSLOCATION		0	179144	0	9	NEW_VARIANT
P-0018489-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 2-11): c.56-3860:TMPRSS2_c.40-6101:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66598	0	11	21	Intron of ERG(-):6Kb before exon 2	ERG	39823645			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873976			10	DELETION		3050331	179145	79386	11	NEW_VARIANT
P-0018490-T01-IM6	CDKN2Ap16INK4A(NM_000077) rearrangement: c.406:CDKN2Ap16INK4A_chr9:g.24391640inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		12333	0	45	9	Exon 2 of CDKN2A(-)	CDKN2A	21970952			9	IGR: 152Kb before IZUMO3(-)	IZUMO3	24391640			10	INVERSION		2420688	179152	26485	44	NEW_VARIANT
P-0018498-T01-IM6	NOTCH1 (NM_017617) rearrangement: chr1:g.120484441:NOTCH1_chr1:g.120521890del	PRECISE	Note: The NOTCH1 rearrangement is a deletion of exons 6-17.	MANUAL_OK	3to5	3to5	Deletion of 12 exons : in frame		12578	0	15	1	Intron of NOTCH2(-):64bp before exon 18	NOTCH2	120484441			1	Intron of NOTCH2(-):8Kb after exon 5	NOTCH2	120521890			10	DELETION		37449	179187	17515	17	NEW_VARIANT
P-0018498-T01-IM6	NCOR1 (NM_006311) - KIF26A (NM_01565) rearrangement: t(14, 17)(q32.33, p12)(chr14:g.104672507::chr17:g.15978935)	PRECISE	Note: The NCOR1 rearrangement is a deletion of exons 1-27	MANUAL_OK	3to5	3to5	-		0	0	47	17	Exon 27 of NCOR1(-)	NCOR1	15978935			14	IGR: 67Kb before KIF26A(+)	KIF26A	104672507			10	TRANSLOCATION		0	179188	0	49	NEW_VARIANT
P-0018524-T01-IM6	TMPRSS2 (NM_001135099) - BRAF (NM_004333) Rearrangement : t(21;7)(q22.3;q34)(chr21:g.42873801::chr7:g.140490337)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TMPRSS2:BRAF}		0	0	89	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873801			7	Intron of BRAF(-):3Kb before exon 9	BRAF	140490337			10	TRANSLOCATION		0	179383	0	98	NEW_VARIANT
P-0018536-T01-IM6	KMT2C (NM_170606)  Rearrangement :  t(6;7)(q21;q36.1)(chr6:g.106189129::chr7:g.151891246)	PRECISE	Note: The KMT2C Rearrangement results in the possible truncation of exons 31-59. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	65	7	Intron of KMT2C(-):33bp before exon 31	KMT2C	151891246			6	IGR: 345Kb before PRDM1(+)	PRDM1	106189129			10	TRANSLOCATION		0	179404	0	64	NEW_VARIANT
P-0018537-T01-IM6	NOTCH4 (NM_004557) Rearrangement : c.-578:PEX6_c.4316-77:NOTCH4del	PRECISE	Note: The NOTCH4  Rearrangement results in the deletion of exons 1-23 of NOTCH4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {PEX6:NOTCH4}		131677	0	20	6	Intron of NOTCH4(-):77bp before exon 24	NOTCH4	32166999			6	Promoter of PEX6(-):16Kb from tx start	PEX6	42947466			10	DELETION		10780467	179395	281152	19	NEW_VARIANT
P-0018541-T01-IM6	ALK (NM_004304) - LRP1B (NM_018557) Rearrangement : c.2914+151:ALK_c.344-85984:LRP1Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ALK:LRP1B}		435317	0	2	2	Intron of ALK(-):150bp after exon 17	ALK	29450289			2	Intron of LRP1B(-):86Kb before exon 4	LRP1B	142098194			9	DUPLICATION		112647905	179406	819833	2	NEW_VARIANT
P-0018555-T01-IM6	PPP6C (NM_002721) rearrangements: c.669_c.670del	PRECISE	Note: The PPP6C rearrangement is an intragenic deletion with breakpoints in both exon 6 and 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		395	0	3	9	Exon 7 of PPP6C(-)	PPP6C	127912200			9	Exon 6 of PPP6C(-)	PPP6C	127915812			10	DELETION		3612	179468	236	3	NEW_VARIANT
P-0018556-T01-IM6	ASXL1 (NM_015338) rearrangement: c.252+14450_c.1828dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		9655	0	15	20	Intron of ASXL1(+):14Kb after exon 3	ASXL1	30971376			20	Exon 12 of ASXL1(+)	ASXL1	31022343			10	DUPLICATION		50967	179450	23712	15	NEW_VARIANT
P-0018568-T01-IM6	EZH1 (NM_001991) - STAT3 (NM_139276) rearrangement: c.2098+21:EZH1_c.-23-2339:STAT3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {EZH1:STAT3}		2281	0	54	17	5-UTR of STAT3(-):35Kb before coding start	STAT3	40502896			17	Intron of EZH1(-):20bp after exon 19	EZH1	40855737			10	DELETION		352841	179519	5899	59	NEW_VARIANT
P-0018568-T01-IM6	NOTCH1 (NM_017617) - SEC16A (NM_014866) rearrangement: c.6672:NOTCH1_c.3704+620:SEC16Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NOTCH1:SEC16A}		5712	0	78	9	Intron of SEC16A(-):619bp after exon 4	SEC16A	139365807			9	Exon 34 of NOTCH1(-)	NOTCH1	139391519			10	DELETION		25712	179518	8478	87	NEW_VARIANT
P-0018573-T01-IM6	ALK (NM_004304) - EML4(NM_019063) rearrangement: c.2164_c.1489+1323del	PRECISE	Note: The ALK - EML4 rearrangement results in the deletion of ALK exons 1-12 and EML4 exons 1-13. One of the breakpoints is within ALK exon 12. The functional significance is undetermined. Archer targeted RNAseq assay will be performed for further characterization and reported under M17-7130.	MANUAL_OK	3to5	3to5	-		42482	0	52	2	Exon 12 of ALK(-)	ALK	29474011			2	Intron of EML4(+):1Kb after exon 12	EML4	42523979			10	DELETION		13049968	179510	110249	55	NEW_VARIANT
P-0018575-T01-IM6	NF1 (NM_001042492) - RHOT1 (NM_001033568) rearrangement: c.4953:NF1_c.1958+4664:RHOT1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NF1:RHOT1}		40977	0	55	17	Exon 37 of NF1(+)	NF1	29652955			17	Intron of RHOT1(+):8Kb after exon 18	RHOT1	30542921			10	DELETION		889966	179547	57527	58	NEW_VARIANT
P-0018575-T01-IM6	CDK12 (NM_016507) rearrangement: t(4;17)(p15.1;q12)(chr4:g.35688798::chr17:g.37618733)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	98	17	Exon 1 of CDK12(+)	CDK12	37618733			4	IGR: 379Kb before ARAP2(-)	ARAP2	35688798			10	TRANSLOCATION		0	179549	0	104	NEW_VARIANT
P-0018576-T01-IM6	LYN (NM_002350) rearrangement: t(8;17)(q12.1;q12)(chr8:g.56911063::chr17:g.32040644)	PRECISE	Note: The LYN rearrangement is a translocation that may result in the truncation of exons 12-13. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	6	17	Intron of ASIC2(-):442Kb after exon 1	ASIC2	32040644			8	Intron of LYN(+):5bp after exon 11	LYN	56911063			10	TRANSLOCATION		0	179509	0	6	NEW_VARIANT
P-0018581-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		21703	0	94	21	Intron of ERG(-):9Kb after exon 1	ERG	39861458			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868059			10	DELETION		3006601	179570	23723	100	NEW_VARIANT
P-0018582-T01-IM6	SMIM7 (NM_024104.3) - BRD4 (NM_058243) rearrangement: c.213-1319:SMIM7_c.2235:BRD4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMIM7:BRD4}		18583	0	20	19	Exon 13 of BRD4(-)	BRD4	15355388			19	Intron of SMIM7(-):1Kb before exon 5	SMIM7	16759391			10	DELETION		1404003	179567	63123	19	NEW_VARIANT
P-0018598-T02-IM6	PEPD (NM_000285) - CEBPA (NM_004364) rearrangement: c.504-3890:PEPD_c.856:CEBPAdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PEPD:CEBPA}		5421	0	15	19	Exon 1 of CEBPA(-)	CEBPA	33792465			19	Intron of PEPD(-):4Kb before exon 7	PEPD	33972886			10	DELETION		180421	180235	11706	16	NEW_VARIANT
P-0018598-T02-IM6	CIC (NM_015125) rearrangement: c.3130_c.*806inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		15788	0	13	19	Exon 13 of CIC(+)	CIC	42796573			19	Promoter of CIC(+):11Kb from tx start	CIC	42800149			10	INVERSION		3576	180237	33482	13	NEW_VARIANT
P-0018608-T01-IM6	KMT2B (NM_014727) rearrangement: chr19:g.22025862_c.5076+2:KMT2Binv	PRECISE	Note: The KMT2B rearrangement is an inversion of exons 1-23, potentially disrupting gene function.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {KMT2B:ZNF43}		73856	0	18	19	Intron of ZNF43(-):9Kb after exon 1	ZNF43	22025862			19	Intron of KMT2B(+):2bp after exon 23	KMT2B	36221028			10	INVERSION		14195166	179664	151794	18	NEW_VARIANT
P-0018624-T01-IM6	SMAD3 (NM_005902) rearrangement: g.67152286_c.872-33del	PRECISE	Note: The SMAD3 rearrangement results in the deletion of exons 1-6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		10679	0	7	15	IGR: 158Kb before SMAD6(+)	SMAD6	67152286			15	Intron of SMAD3(+):32bp before exon 7	SMAD3	67477032			10	DELETION		324746	179764	18427	7	NEW_VARIANT
P-0018626-T01-IM6	SH2B3 (NM_005475) rearrangement: t(5;12)(p14.1;q24.12)(chr5:g.27195354::chr12:g.111856053)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	62	12	Exon 2 of SH2B3(+)	SH2B3	111856053			5	IGR: 277Kb before LINC01021(+)	LINC01021	27195354			0	TRANSLOCATION		0	179758	0	69	NEW_VARIANT
P-0018630-T01-IM6	JAK2 (NM_004972) rearrangement: t(9;11)(q24.12;p11.2)(chr9:g.5044464::chr11:g.44939223)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	34	11	Intron of TSPAN18(+):299bp before exon 5	TSPAN18	44939223			9	Exon 5 of JAK2(+)	JAK2	5044464			10	TRANSLOCATION		0	179810	0	46	NEW_VARIANT
P-0018647-T01-IM6	CARM1 (NM_199141) Rearrangement : c.1615+88:CARM1_c.721-981:DOCK6del	PRECISE	Note: The CARM1 Rearrangement results in the deletion of exons 15-16 of CARM1.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		48418	0	16	19	Intron of CARM1(+):88bp after exon 14	CARM1	11031891			19	Intron of DOCK6(-):981bp before exon 7	DOCK6	11359808			10	DELETION		327917	179859	85994	15	NEW_VARIANT
P-0018647-T01-IM6	AMER1 (NM_152424) Rearrangement : chrX:g.63373392_c.1644:AMER1del	PRECISE	Note: The AMER1 Rearrangement results in the partial deletion of exon2. The breakpoint is within exon2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		8952	0	7	X	IGR: 32Kb before AMER1(-)	AMER1	63373392			X	Exon 2 of AMER1(-)	AMER1	63411523			10	DELETION		38131	179860	21638	7	NEW_VARIANT
P-0018660-T01-IM6	RTEL1 (NM_032957) Rearrangement : c.3090:RTEL1_c.392:ARFRP1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		10814	0	12	20	Exon 31 of RTEL1(+)	RTEL1	62325750			20	Exon 5 of ARFRP1(-)	ARFRP1	62333207			10	DELETION		7457	179902	15411	12	NEW_VARIANT
P-0018667-T01-IM6	ARID1A (NM_006015) rearrangement: c.2161+38_g.27852005del	PRECISE	Note: The ARID1A rearrangement results in the deletion of exons 5-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		37033	1	30	1	Intron of ARID1A(+):38bp after exon 5	ARID1A	27087625			1	IGR: 9Kb before AHDC1(-)	AHDC1	27852005			10	DELETION		764380	179955	49504	28	NEW_VARIANT
P-0018668-T01-IM6	POLE (NM_006231) rearrangement: t(12;22)(q24.33;q12.2)(chr12:g.133257281::chr22:g.31791989)	PRECISE	Note: The POLE rearrangement is a translocation that may result in the truncation of exons 3-49. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	28	22	IGR: 4Kb before DRG1(+)	DRG1	31791989			12	Intron of POLE(-):8bp before exon 3	POLE	133257281			10	TRANSLOCATION		0	179960	0	39	NEW_VARIANT
P-0018690-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.2172:MAP3K1_chr5:g.79481066del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		52609	0	23	5	Exon 12 of MAP3K1(+)	MAP3K1	56176622			5	Intron of SERINC5(-):7Kb before exon 3	SERINC5	79481066			10	DELETION		23304444	180003	51926	23	NEW_VARIANT
P-0018693-T01-IM6	EWSR1 (NM_013986) rearrangement: c.103-123_c.1028-91del	PRECISE	Note: The EWSR1 rearrangement is an intragenic deletion of exons 4-10.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : out of frame		34842	0	6	22	Intron of EWSR1(+):122bp before exon 4	EWSR1	29669607			22	Intron of EWSR1(+):90bp before exon 11	EWSR1	29688035			10	DELETION		18428	180009	21822	6	NEW_VARIANT
P-0018700-T01-IM6	KMT2D (NM_003482) rearrangement: chr12:g.43055129_c.7303:KMT2Ddel	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 31-54. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	-		86171	0	10	12	IGR: 46Kb before LOC101927058(-)	LOC101927058	43055129			12	Exon 31 of KMT2D(-)	KMT2D	49434250			10	DELETION		6379121	180030	173191	10	NEW_VARIANT
P-0018704-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.56-2342:TMPRSS2_c.39+63678:ERGdel	PRECISE	Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		50685	0	49	21	Intron of ERG(-):64Kb after exon 3	ERG	39883908			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872458			10	DELETION		2988550	180043	42871	55	NEW_VARIANT
P-0018710-T01-IM6	SMAD4 (NM_005359) rearrangement: chr18:g.48526969_c.1409del	PRECISE	Note: The SMAD4 rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	-		8650	0	17	18	IGR: 30Kb before SMAD4(+)	SMAD4	48526969			18	Exon 11 of SMAD4(+)	SMAD4	48603108			10	DELETION		76139	180029	14526	17	NEW_VARIANT
P-0018713-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMRPSS2 exon 1 fused with ERG exons 4-11): c.127-1426:TMPRSS2_c.40-60631:ERGdel	PRECISE	Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		24855	0	35	21	Intron of ERG(-):61Kb before exon 4	ERG	39878175			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867931			10	DELETION		2989756	180026	35176	35	NEW_VARIANT
P-0018761-T01-IM6	GNAS (NM_000516) Rearrangement : c.938:GNAS_chr20:g.54110650del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		35460	0	10	20	IGR: 71Kb before LINC01440(+)	LINC01440	54110650			20	Exon 11 of GNAS(+)	GNAS	57485104			10	DELETION		3374454	180088	100332	12	NEW_VARIANT
P-0018785-T01-IM6	TET1 (NM_030625) - CTNNA3 (NM_013266) rearrangement: c.2089:TET1_c.2159+6353:CTNNA3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TET1:CTNNA3}		16889	0	88	10	Intron of CTNNA3(-):6Kb after exon 15	CTNNA3	67822713			10	Exon 4 of TET1(+)	TET1	70404575			10	INVERSION		2581862	180151	36620	88	NEW_VARIANT
P-0018785-T01-IM6	FGFR2 (NM_000141) rearrangement: t(10;17)(q26.13;p11.2)(chr10:g.123240775::chr17:g.21369673)	PRECISE	Note: The FGFR2 rearrangement is a translocation that may result in the truncation of exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	213	17	IGR: 61Kb before KCNJ18(+)	KCNJ18	21369673			10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240775			10	TRANSLOCATION		0	180153	0	260	NEW_VARIANT
P-0018791-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exons 1 fused to ERG exons 2-10): c.56-2909:TMPRSS2_c.18+13740:ERGdel	PRECISE		MANUAL_OK	5to5	5to5	Antisense Fusion		65138	0	58	21	Intron of ERG(-):14Kb after exon 1	ERG	39856547			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873025			10	INVERSION		3016478	180175	50060	72	NEW_VARIANT
P-0018798-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2155:TMPRSS2_c.19-19621:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		55597	0	34	21	Intron of ERG(-):20Kb before exon 2	ERG	39837165			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872271			10	DELETION		3035106	180162	66664	35	NEW_VARIANT
P-0018798-T01-IM6	KMT2C (NM_170606) rearrangement : g.151754651_c.14667:KMT2Cinv	PRECISE	Note: The KMT2C rearrangement results in an inversion of exon 59. One of the breakpoints is within exon 59. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {GALNT11:KMT2C}		922	0	21	7	5-UTR of GALNT11(+):37Kb before coding start	GALNT11	151754651			7	Exon 59 of KMT2C(-)	KMT2C	151833986			10	INVERSION		79335	180163	1251	35	NEW_VARIANT
P-0018800-T01-IM6	FGFR2 (NM_000141) rearrangement: g.123006554_c.2378:FGFR2del	PRECISE	Note: The FGFR2 rearrangement results in the deletion of exon 18. One of the breakpoints is within exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1580	0	63	10	IGR: 231Kb before FGFR2(-)	FGFR2	123006554			10	Exon 18 of FGFR2(-)	FGFR2	123239459			10	DELETION		232905	180172	1785	63	NEW_VARIANT
P-0018812-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1654:TMPRSS2_c.19-10716:ERGinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		38809	0	20	21	Intron of ERG(-):11Kb before exon 2	ERG	39828260			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868392			10	INVERSION		3040132	180223	21164	34	NEW_VARIANT
P-0018812-T01-IM6	MAP3K1 (NM_005921) - PDE4D (NM_001104631) rearrangement: c.950:MAP3K1_c.456-148209:PDE4Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		50569	0	17	5	Exon 4 of MAP3K1(+)	MAP3K1	56160676			5	Intron of PDE4D(-):148Kb before exon 4	PDE4D	58660003			10	DUPLICATION		2499327	180219	44461	17	NEW_VARIANT
P-0018812-T01-IM6	NTRK2 (NM_006180)  rearrangement: chr9:g.86817107_c.1444+2176dup	PRECISE	Note: The NTRK2 rearrangement is a duplication (661071 bp) which includes exons 1-15 of NTRK2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		46866	0	10	9	IGR: 74Kb before SLC28A3(-)	SLC28A3	86817107			9	Intron of NTRK2(+):2Kb after exon 15	NTRK2	87478178			10	DUPLICATION		661071	180220	61430	11	NEW_VARIANT
P-0018848-T01-IM6	HGF (NM_000601) Rearrangement : c.483-10_c.865+3831dup	PRECISE	Note: The HGF Rearrangement results in the duplication of exons 5-7 of HGF.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		3768	0	11	7	Intron of HGF(-):4Kb after exon 7	HGF	81368838			7	Intron of HGF(-):10bp before exon 5	HGF	81381588			10	DUPLICATION		12750	180275	7373	11	NEW_VARIANT
P-0018868-T01-IM6	GAS6 (NM_000820) - IRS2 (NM_003749) Rearrangement : c.281-566:GAS6_c.2992:IRS2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GAS6:IRS2}		32094	0	3	13	Exon 1 of IRS2(-)	IRS2	110435409			13	Intron of GAS6(-):566bp before exon 4	GAS6	114550128			10	DELETION		4114719	180370	21658	3	NEW_VARIANT
P-0018870-T01-IM6	EXOSC7 (NM_015004) - CTNNB1 (NM_001904) Rearrangement : c.58-5293:EXOSC7_c.1954+10:CTNNB1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {EXOSC7:CTNNB1}		6410	0	10	3	Intron of CTNNB1(+):10bp after exon 12	CTNNB1	41278000			3	Intron of EXOSC7(+):5Kb before exon 2	EXOSC7	45025339			10	DUPLICATION		3747339	180335	6323	10	NEW_VARIANT
P-0018893-T01-IM6	TGFBR1 (NM_004612) rearrangement: chr9:g.101859374_c.16del	PRECISE	Note: The TGFBR1 rearrangement is a partial deletion of exon 1.	MANUAL_OK	3to5	3to5	-		42	0	5	9	IGR: 8Kb before TGFBR1(+)	TGFBR1	101859374			9	Exon 1 of TGFBR1(+)	TGFBR1	101867503			10	DELETION		8129	180478	79	5	NEW_VARIANT
P-0018896-T01-IM6	ERBB2 (NM_004448) rearrangement: t(11;17)(q22.1;q12)(chr11:g.100478828::chr17:g.37879868)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	37	17	Exon 18 of ERBB2(+)	ERBB2	37879868			11	IGR: 80Kb before ARHGAP42(+)	ARHGAP42	100478828			10	TRANSLOCATION		0	180451	0	89	NEW_VARIANT
P-0018921-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.*2336_c.458-429del	PRECISE	Note:  The CDKN2A rearrangement is a deletion (2778 bp) which includes exon 3 of CDKN2Ap16INK4A. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		971	0	42	9	Promoter of CDKN2A(-):2Kb from tx start	CDKN2A	21965892			9	Intron of CDKN2A(-):429bp before exon 3	CDKN2A	21968670			10	DELETION		2778	180554	802	45	NEW_VARIANT
P-0018925-T01-IM6	TSC2 (NM_000548) rearrangement: c.4663-304C>T_c.4865inv	PRECISE	Note: The TSC2 rearrangement is an inversion of exons 37-38. One of the breakpoints is within exon 38. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2839	0	3	16	Intron of TSC2(+):303bp before exon 37	TSC2	2135890			16	Exon 38 of TSC2(+)	TSC2	2136748			5	INVERSION		858	180565	3352	4	NEW_VARIANT
P-0018926-T01-IM6	EFCAB5 (NM_198529) - RNF43 (NM_017763) rearrangement: c.1201-5046:EFCAB5_c.376-2:RNF43inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EFCAB5:RNF43}		606547	0	20	17	Intron of EFCAB5(+):5Kb before exon 9	EFCAB5	28373090			17	Intron of RNF43(-):2bp before exon 4	RNF43	56440963			10	INVERSION		28067873	180569	1428768	20	NEW_VARIANT
P-0018933-T01-IM6	SYT1 (NM_001135806) - KMT2D (NM_003482) rearrangement: c.-18+8078:SYT1_c.14648:KMT2Dinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SYT1:KMT2D}		303305	0	21	12	Exon 48 of KMT2D(-)	KMT2D	49421101			12	5-UTR of SYT1(+):162Kb before coding start	SYT1	79449220			10	INVERSION		30028119	180578	456822	21	NEW_VARIANT
P-0018969-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-760:EML4_c.3083:ALKinv	PRECISE	Note: The EML4- ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		157939	0	21	2	Exon 19 of ALK(-)	ALK	29448416			2	Intron of EML4(+):759bp before exon 13	EML4	42527621			10	INVERSION		13079205	180673	66199	19	NEW_VARIANT
P-0018985-T01-IM6	DAXX (NM_001141970) rearrangement: c.243+67_c.1396inv	PRECISE	Note: The DAXX rearrangement is an intragenic inversion of exons 3-5. One of the breakpoints is within exon 5.	MANUAL_OK	3to3	3to3	-		7997	0	4	6	Exon 5 of DAXX(-)	DAXX	33287893			6	Intron of DAXX(-):66bp after exon 2	DAXX	33289429			10	INVERSION		1536	180758	8092	4	NEW_VARIANT
P-0018987-T01-IM6	NSD1 (NM_022455) rearrangement: t(X;5)(q21.2;q35.3)(chrX:g.76752806::chr5:g.176638676)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	5	X	IGR: 8Kb before ATRX(-)	ATRX	76752806			5	Exon 5 of NSD1(+)	NSD1	176638676			10	TRANSLOCATION		0	180760	0	4	NEW_VARIANT
P-0019022-T02-IM6	SPEN (NM_015001) - ZCCHC11 (NM_001009881) rearrangement : c.674:SPEN_c.719-3409:ZCCHC11inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SPEN:ZCCHC11}		474661	0	2	1	Exon 3 of SPEN(+)	SPEN	16202966			1	Intron of ZCCHC11(-):3Kb before exon 3	ZCCHC11	52985135			10	INVERSION		36782169	183766	530868	2	NEW_VARIANT
P-0019022-T02-IM6	ARID1A (NM_006015) rearrangement: c.2439_c.3716-77dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		14025	0	59	1	Exon 8 of ARID1A(+)	ARID1A	27089483			1	Intron of ARID1A(+):76bp before exon 15	ARID1A	27099760			10	DUPLICATION		10277	183764	19876	66	NEW_VARIANT
P-0019022-T02-IM6	GRK4 (NM_182982) - FGFR3 (NM_000142) rearrangement: c.339+3191:GRK4_c.44:FGFR3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {GRK4:FGFR3}		95792	0	33	4	Exon 2 of FGFR3(+)	FGFR3	1795705			4	Intron of GRK4(+):3Kb after exon 3	GRK4	2997210			10	DUPLICATION		1201505	183765	112480	40	NEW_VARIANT
P-0019055-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.-48-1056_c.201del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2170	0	25	3	5-UTR of CTNNB1(+):1Kb before coding start	CTNNB1	41264456			3	Exon 3 of CTNNB1(+)	CTNNB1	41266204			10	DELETION		1748	181122	1232	27	NEW_VARIANT
P-0019058-T01-IM6	AXIN1 (NM_003502) rearrangement: c.1255-25_c.878+14756del	PRECISE	Note: The AXIN1 rearrangement results in the deletion of exons 3-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		7261	0	130	16	Intron of AXIN1(-):25bp before exon 6	AXIN1	348276			16	Intron of AXIN1(-):15Kb after exon 2	AXIN1	381392			10	DELETION		33116	181126	1971	175	NEW_VARIANT
P-0019058-T01-IM6	BRIP1 (NM_032043) rearrangement: c.2380-9185_c.1140+101del	PRECISE	Note: The BRIP1 rearrangement results in the in-frame deletion of exons 9-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 8 exons : in frame		16230	0	12	17	Intron of BRIP1(-):9Kb before exon 17	BRIP1	59802609			17	Intron of BRIP1(-):100bp after exon 8	BRIP1	59878513			10	DELETION		75904	181127	9821	13	NEW_VARIANT
P-0019058-T01-IM6	KMT2B (NM_014727) rearrangement: g.36188393_c.5995del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		91701	0	43	19	IGR: 15Kb before ZBTB32(+)	ZBTB32	36188393			19	Exon 28 of KMT2B(+)	KMT2B	36223445			10	DELETION		35052	181128	51334	61	NEW_VARIANT
P-0019058-T01-IM6	AGO2 (NM_012154) rearrangement: c.2472-52_c.23-10801del	PRECISE	Note: The AGO2 rearrangement results in the deletion of exons 2-18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 17 exons : out of frame		36720	0	63	8	Intron of AGO2(-):52bp before exon 19	AGO2	141542303			8	Intron of AGO2(-):11Kb before exon 2	AGO2	141606211			10	DELETION		63908	181125	20829	80	NEW_VARIANT
P-0019062-T01-IM6	AMER1 (NM_152424) rearrangement: c.1984_c.147del	PRECISE	Note: The AMER1 rearrangement results in the deletion of exon 2. Both of the breakpoints are within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9278	0	24	X	Exon 2 of AMER1(-)	AMER1	63411183			X	Exon 2 of AMER1(-)	AMER1	63413020			10	DELETION		1837	181111	5186	26	NEW_VARIANT
P-0019068-T01-IM6	PRDM1 (NM_001198) rearrangement: t(6;12)(q21;q21.31)(chr6:g.106554248::chr12:g.80543892)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	10	12	IGR: 59Kb before OTOGL(+)	OTOGL	80543892			6	Exon 6 of PRDM1(+)	PRDM1	106554248			10	TRANSLOCATION		0	181171	0	10	NEW_VARIANT
P-0019088-T01-IM6	FBXW7 (NM_033632) Rearrangement : c.1123-413_c.1302inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		3293	0	14	4	Exon 9 of FBXW7(-)	FBXW7	153249476			4	Intron of FBXW7(-):413bp before exon 8	FBXW7	153251350			10	INVERSION		1874	181193	2337	14	NEW_VARIANT
P-0019094-T01-IM6	CSDE1 (NM_001242891) Rearrangement : c.1676_c.1892-421del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4215	0	18	1	Intron of CSDE1(-):421bp before exon 17	CSDE1	115267044			1	Exon 15 of CSDE1(-)	CSDE1	115268934			10	DELETION		1890	181192	3880	20	NEW_VARIANT
P-0019108-T01-IM6	NOTCH1 (NM_017617)  Rearrangement : c.141-37_c.4421del	PRECISE	Note: The NOTCH1 Rearrangement results in the inversion of exons 3-25. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		53636	0	7	9	Exon 25 of NOTCH1(-)	NOTCH1	139399927			9	Intron of NOTCH1(-):379bp before exon 3	NOTCH1	139418810			10	INVERSION		18883	181264	45594	7	NEW_VARIANT
P-0019111-T01-IM6	NCOR1 (NM_006311) rearrangement: c.999_c.1083-1302inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		975	0	14	17	Intron of NCOR1(-):1Kb before exon 11	NCOR1	16048312			17	Exon 10 of NCOR1(-)	NCOR1	16049773			10	INVERSION		1461	181269	1054	16	NEW_VARIANT
P-0019111-T01-IM6	ROS1 (NM_002944) - GOPC (NM_020399) rearrangement: c.5642-895:ROS1_c.912+138:GOPCdup	IMPPRECISE	Note: The ROS1-GOPC rearrangement is a duplication that results in an out of frame fusion of ROS1 exons 1-34 with GOPC exons 7-9. This rearrangement is not predicted to include the ROS1 kinase domain. Archer will be performed, if additional material is available, to verify the structure of this rearrangement.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ROS1:GOPC}		175526	0	31	6	Intron of ROS1(-):895bp before exon 35	ROS1	117643452			6	Intron of GOPC(-):137bp after exon 6	GOPC	117891885			0	DUPLICATION		248433	181268	176415	34	NEW_VARIANT
P-0019126-T01-IM6	PARK2 (NM_004562) rearrangement: c.412+119_c.534+7569del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon3. The functional significance is undermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1281	0	6	6	Intron of PARK2(-):8Kb after exon 4	PARK2	162614594			6	Intron of PARK2(-):118bp after exon 3	PARK2	162683438			10	DELETION		68844	181320	579	6	NEW_VARIANT
P-0019129-T01-IM6	NCOA3 (NM_181659) rearrangement: c.-98-33680_c.721+35dup	PRECISE	Note: The NCOA3 rearrangement is an intragenic duplication (78281 bp) of exons 2-7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		8121	0	33	20	5-UTR of NCOA3(+):73Kb before coding start	NCOA3	46178247			20	Intron of NCOA3(+):35bp after exon 7	NCOA3	46256528			10	DUPLICATION		78281	181328	19238	54	NEW_VARIANT
P-0019130-T01-IM6	KDM5A (NM_001042603) rearrangement: c.958_chr12:g.11658386inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		46553	0	21	12	Exon 8 of KDM5A(-)	KDM5A	463313			12	IGR: 43Kb before LINC01252(+)	LINC01252	11658386			10	INVERSION		11195073	181290	38764	19	NEW_VARIANT
P-0019130-T01-IM6	TMPRSS2 (NM_001135099) rearrangement:  chr21:g.35443032_c.150inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TMPRSS2:MRPS6}		72310	0	9	21	Promoter of MRPS6(+):3Kb from tx start	MRPS6	35443032			21	Exon 3 of TMPRSS2(-)	TMPRSS2	42866482			10	INVERSION		7423450	181291	95875	11	NEW_VARIANT
P-0019136-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.1879_c.1881+2559del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		725	0	8	4	Exon 9 of WHSC1(+)	WHSC1	1941503			4	Intron of WHSC1(+):3Kb after exon 9	WHSC1	1944064			10	DELETION		2561	181295	601	10	NEW_VARIANT
P-0019144-T01-IM6	PBRM1 (NM_018313) rearrangement: g.47031659_c.995+68del	PRECISE	Note: The PBRM1 rearrangement results in the deletion of exons 11-30. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		190698	0	3	3	Intron of NBEAL2(+):576bp after exon 6	NBEAL2	47031659			3	Intron of PBRM1(-):67bp after exon 10	PBRM1	52677196			5	DELETION		5645537	181353	307074	3	NEW_VARIANT
P-0019148-T01-IM6	NCOR1 (NM_006311) - USP43 (NM_153210) rearrangement: c.4951+83:NCOR1_c.741-2291:USP43inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {NCOR1:USP43}		38985	0	15	17	Intron of USP43(+):2Kb before exon 4	USP43	9575917			17	Intron of NCOR1(-):82bp after exon 33	NCOR1	15968716			10	INVERSION		6392799	181355	63652	16	NEW_VARIANT
P-0019148-T01-IM6	ERBB4 (NM_005235) rearrangement: g.843212_c.1515:ERBB4del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		916503	0	4	2	3-UTR of LINC01115(-):21Kb after coding stop	LINC01115	843212			2	Exon 13 of ERBB4(-)	ERBB4	212543884			10	DELETION		211700672	181354	1143495	18	NEW_VARIANT
P-0019150-T01-IM6	FUBP1 (NM_003902) rearrangement: c.637-22_c.121-95del	PRECISE	Note: The FUBP1 rearrangement results in the in-frame deletion of exons 2-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : in frame		9144	0	4	1	Intron of FUBP1(-):22bp before exon 9	FUBP1	78430675			1	Intron of FUBP1(-):95bp before exon 2	FUBP1	78435794			8	DELETION		5119	181345	12108	4	NEW_VARIANT
P-0019153-T01-IM6	PALB2 (NM_024675) rearrangement: c.2997-115_g.23726499del	PRECISE	Note: The PALB2 rearrangement results in the deletion of exons 10-13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {ERN2:PALB2}		34106	0	9	16	Intron of PALB2(-):115bp before exon 10	PALB2	23632914			16	Promoter of ERN2(-):25Kb from tx start	ERN2	23726499			10	DELETION		93585	181349	37791	9	NEW_VARIANT
P-0019153-T01-IM6	DDR2 (NM_006182)  rearrangement: t(1;6)(q23.3;q21)(chr1:g.162730897::chr6:g.112896512)	PRECISE	Note: The DDR2 rearrangement is a translocation that may result in the truncation of exons 9-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	7	6	IGR: 228Kb before RFPL4B(+)	RFPL4B	112896512			1	Intron of DDR2(+):103bp before exon 9	DDR2	162730897			10	TRANSLOCATION		0	181352	0	7	NEW_VARIANT
P-0019205-T02-IM6	ROS1 (NM_002944) rearrangement: t(6;20)(q22.1;q13.12)(chr6:g.117654098::chr20:g.43949086)	PRECISE	Note: The ROS1 rearrangement is a translocation with a breakpoint in intron before exon 32. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ROS1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	5	20	Promoter of RBPJL(+):14Kb from tx start	RBPJL	43949086			6	Intron of ROS1(-):3Kb before exon 32	ROS1	117654098			10	TRANSLOCATION		0	182086	0	5	NEW_VARIANT
P-0019222-T01-IM6	BCL6 (NM_001706) rearrangement: c.1540+133_c.*2609inv	PRECISE	Note: The BCL6 rearrangement is an inversion (8378 bp) of exons 7-10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		5022	0	13	3	Promoter of BCL6(-):2Kb from tx start	BCL6	187437637			3	Intron of BCL6(-):132bp after exon 6	BCL6	187446015			10	INVERSION		8378	181470	9943	13	NEW_VARIANT
P-0019222-T01-IM6	NSD1 (NM_022455) rearrangement: c.3922-31_c.5146+1203dup	PRECISE	Note: The NSD1 rearrangement is a duplication (23165 bp) of exons 7-14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 8 exons : out of frame		12234	0	12	5	Intron of NSD1(+):30bp before exon 7	NSD1	176665207			5	Intron of NSD1(+):1Kb after exon 14	NSD1	176688372			10	DUPLICATION		23165	181467	13040	12	NEW_VARIANT
P-0019222-T01-IM6	KMT2C (NM_170606) rearrangement: c.9453+698_c.10274dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		6249	0	57	7	Exon 43 of KMT2C(-)	KMT2C	151860388			7	Intron of KMT2C(-):697bp after exon 40	KMT2C	151867651			10	DUPLICATION		7263	181468	9635	65	NEW_VARIANT
P-0019226-T01-IM6	ETV6 (NM_001987) rearrangement: c.328+6821_c.464-6237del	PRECISE	Note: The ETV6 rearrangement is an intragenic deletion (17062  bp) of exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		82637	0	15	12	Intron of ETV6(+):7Kb after exon 3	ETV6	11999059			12	Intron of ETV6(+):6Kb before exon 5	ETV6	12016121			10	DELETION		17062	181491	90137	16	NEW_VARIANT
P-0019243-T01-IM6	NF1 (NM_001042492) - PRKG1 (NM_001098512) rearrangement: t(10;17)(q21.1;q11.2)(chr10:g.53522352::chr17:g.29422402)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {NF1:PRKG1}		0	0	74	17	Intron of NF1(+):15bp after exon 1	NF1	29422402			10	Intron of PRKG1(+):42Kb before exon 4	PRKG1	53522352			10	TRANSLOCATION		0	181527	0	86	NEW_VARIANT
P-0019262-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.850_c.874+5330del	PRECISE	Note; The NOTCH2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		530	0	4	1	Intron of NOTCH2(-):5Kb after exon 5	NOTCH2	120524253			1	Exon 5 of NOTCH2(-)	NOTCH2	120529607			10	DELETION		5354	181634	493	5	NEW_VARIANT
P-0019262-T01-IM6	ABL1 (NM_005157) - FUBP3 (NM_003934) rearrangement: c.822+6:ABL1_c.191-582:FUBP3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ABL1:FUBP3}		9211	0	14	9	Intron of FUBP3(+):581bp before exon 3	FUBP3	133484759			9	Intron of ABL1(+):6bp after exon 4	ABL1	133738428			10	DUPLICATION		253669	181635	9443	14	NEW_VARIANT
P-0019266-T01-IM6	CDKN2A (NM_058195, NM_000077) rearrangement: c.-453_c.*102-531del	PRECISE	Note: The CDKN2A rearrangement is a deletion of exons 1-2 of the CDKN2Ap14ARF and CDKN2Ap16INK4A isoforms of CDKN2A	MANUAL_OK	3to5	3to5	-		9617	0	64	9	Intron of CDKN2A(-):531bp before exon 3	CDKN2A	21968772			9	Promoter of CDKN2B-AS1(+):6bp from tx start	CDKN2B-AS1	21994783			10	DELETION		26011	181591	4042	67	NEW_VARIANT
P-0019285-T01-IM6	SMAD3 (NM_005902)- IQCH (NM_001031715 Rearrangement : c.1224:SMAD3_c.754-3646:IQCHdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMAD3:IQCH}		580	0	2	15	Exon 9 of SMAD3(+)	SMAD3	67482820			15	Intron of IQCH(+):4Kb before exon 6	IQCH	67660803			5	DELETION		177983	181706	570	3	NEW_VARIANT
P-0019320-T01-IM6	RB1 (NM_000321) rearrangement: c.-51_c.501-1010inv	PRECISE	Note: The RB1 rearrangement is predicted to result in the inversion of exons 1-4. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4177	0	36	13	5-UTR of RB1(+):50bp before coding start	RB1	48877998			13	Intron of RB1(+):1Kb before exon 5	RB1	48920951			10	INVERSION		42953	181875	3752	61	NEW_VARIANT
P-0019320-T01-IM6	EPHA3 (NM_005233) rearrangement: c.1306+1_c.1306+20088del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within intron		267	0	8	3	Intron of EPHA3(+):1bp after exon 5	EPHA3	89391241			3	Intron of EPHA3(+):20Kb after exon 5	EPHA3	89411328			10	DELETION		20087	181874	132	7	NEW_VARIANT
P-0019324-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2067_c.127-919inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		42747	0	61	21	Intron of TMPRSS2(-):919bp before exon 3	TMPRSS2	42867424			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872183			10	INVERSION		4759	181877	31395	73	NEW_VARIANT
P-0019337-T01-IM6	EED (NM_003797) rearrangement: c.228_c.360+1399del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1487	0	46	11	Exon 2 of EED(+)	EED	85961451			11	Intron of EED(+):1Kb after exon 3	EED	85964681			10	DELETION		3230	181818	1279	54	NEW_VARIANT
P-0019337-T01-IM6	CDK12 (NM_016507) rearrangement: c.3761-1245_c.3924inv	PRECISE	Note: The CDK12 rearrangement is an inversion of exon 14. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1148	0	82	17	Intron of CDK12(+):1Kb before exon 14	CDK12	37685612			17	Exon 14 of CDK12(+)	CDK12	37687020			10	INVERSION		1408	181819	2910	113	NEW_VARIANT
P-0019340-T01-IM6	RECQL (NM_032941)  rearrangement: t(12;16)(p12.1;p13.3)(chr12:g.21644586::chr16:g.1564105)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	37	16	Intron of IFT140(-):3Kb before exon 31	IFT140	1564105			12	Exon 4 of RECQL(-)	RECQL	21644586			10	TRANSLOCATION		0	181922	0	38	NEW_VARIANT
P-0019346-T01-IM6	ARID1A (NM_006015) rearrangement: c.1138-11170_c.4852del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		35920	0	3	1	Intron of ARID1A(+):11Kb before exon 2	ARID1A	27044972			1	Exon 18 of ARID1A(+)	ARID1A	27101570			10	DELETION		56598	181919	33747	4	NEW_VARIANT
P-0019346-T01-IM6	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)	PRECISE	known	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CD74:NRG1}		0	0	7	8	Intron of NRG1(+):1Kb before exon 6	NRG1	32584466			5	Exon 7 of CD74(-)	CD74	149782781			10	TRANSLOCATION		0	181921	0	7	NEW_VARIANT
P-0019350-T01-IM6	RARA (NM_000964) - THRA (NM_003250) rearrangement: c.1196:RARA_c.223-1330:THRAdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RARA:THRA}		17971	0	27	17	Intron of THRA(+):1Kb before exon 5	THRA	38238758			17	Exon 9 of RARA(+)	RARA	38512285			10	DUPLICATION		273527	181894	31563	33	NEW_VARIANT
P-0019364-T01-IM6	RASAL2 (NM_170692) - IKBKE(NM_014002) Rearrangement : c.1628-181:RASAL2_c.1076:IKBKEdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RASAL2:IKBKE}		87746	0	11	1	Intron of RASAL2(+):180bp before exon 10	RASAL2	178420525			1	Exon 10 of IKBKE(+)	IKBKE	206652369			10	DELETION		28231844	181937	89266	11	NEW_VARIANT
P-0019370-T01-IM6	ELF3 (NM_004433)  Rearrangement : c.1097_c.*1138del	PRECISE	Note: The ELF3  Rearrangement results in the partial deletion of exon9. One of the breakpoints is within exon9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		534	0	5	1	Exon 9 of ELF3(+)	ELF3	201984432			1	3-UTR of ELF3(+):5Kb after coding stop	ELF3	201985589			10	DELETION		1157	181938	372	5	NEW_VARIANT
P-0019377-T01-IM6	NOTCH2 (NM_024408) rearrangement: t(1;21)(p21;q22.11)(chr1:g.120510065::chr21:g.32851230)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NOTCH2:TIAM1}		0	0	9	21	5-UTR of TIAM1(-):359Kb before coding start	TIAM1	32851230			1	Exon 8 of NOTCH2(-)	NOTCH2	120510065			10	TRANSLOCATION		0	181947	0	9	NEW_VARIANT
P-0019391-T01-IM6	DNMT1 (NM_001379) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.78114433::chr19:g.10251361)	PRECISE	Note: The DNMT1 rearrangement is a translocation that may result in the truncation of exons 32-40. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	7	19	Intron of DNMT1(-):95bp after exon 31	DNMT1	10251361			17	Intron of EIF4A3(-):494bp before exon 5	EIF4A3	78114433			10	TRANSLOCATION		0	182010	0	7	NEW_VARIANT
P-0019407-T01-IM6	KMT2C (NM_170606) rearrangement: c.9887_c.13555del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion with breakpoints in exons 43 and 52.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23867	0	32	7	Exon 52 of KMT2C(-)	KMT2C	151845457			7	Exon 43 of KMT2C(-)	KMT2C	151860775			10	DELETION		15318	182096	29030	33	NEW_VARIANT
P-0019410-T01-IM6	DOT1L (NM_032482 rearrangement:  c.1797+140:DOT1L_chr19:g.42147951del	PRECISE	Note: The DOT1L rearrangement is a deletion of exons 19-28.	MANUAL_OK	3to5	3to5	-		975241	0	6	19	Intron of DOT1L(+):140bp after exon 18	DOT1L	2214125			19	IGR: 23Kb before CEACAM4(-)	CEACAM4	42147951			10	DELETION		39933826	182082	930788	4	NEW_VARIANT
P-0019420-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 2-11):c.56-2768:TMPRSS2_c.-149-9232:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	-		76509	0	96	21	3-UTR of ERG(-):68Kb after coding stop	ERG	39966101			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872884			10	DELETION		2906783	182112	76343	102	NEW_VARIANT
P-0019427-T01-IM6	ETV6 (NM_001987) rearrangement: c.33+23133_c.1009+5549dup	PRECISE	Note: The ETV6 rearrangement is an intragenic duplication of exons 2-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : out of frame		171233	0	6	12	Intron of ETV6(+):23Kb after exon 1	ETV6	11826227			12	Intron of ETV6(+):6Kb after exon 5	ETV6	12028452			10	DUPLICATION		202225	182143	195186	6	NEW_VARIANT
P-0019433-T01-IM6	TCF3 (NM_001136139) rearrangement: chr19:g.489738_c.101:TCF3inv	PRECISE	Note: The TCF3 rearrangement is an inversion of exons 2-13. One of the breakpoints is within exon 2.The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		60821	0	4	19	IGR: 7Kb before MADCAM1(+)	MADCAM1	489738			19	Exon 2 of TCF3(-)	TCF3	1646398			10	INVERSION		1156660	182127	34949	3	NEW_VARIANT
P-0019436-T01-IM6	STK11 (NM_000455) rearrangement: c.-1943_c.122inv	PRECISE	Note: The STK11 rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1410	0	21	19	Promoter of STK11(+):827bp from tx start	STK11	1204970			19	Exon 1 of STK11(+)	STK11	1207034			10	INVERSION		2064	182132	1003	25	NEW_VARIANT
P-0019445-T01-IM6	ETV6 (NM_001987) - GRIN2B (NM_000834) rearrangement: c.463+2758:ETV6_c.-19+13931:GRIN2Bdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		266755	0	51	12	Intron of ETV6(+):3Kb after exon 4	ETV6	12009253			12	5-UTR of GRIN2B(-):403Kb before coding start	GRIN2B	14118931			10	DELETION		2109678	182150	298787	54	NEW_VARIANT
P-0019456-T01-IM6	PTPN11 (NM_002834)  rearrangement: c.854-145_c.1224+538dup	PRECISE	Note: The PTPN11 rearrangement is an intragenic duplication of exons 8-10. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		4861	0	12	12	Intron of PTPN11(+):144bp before exon 8	PTPN11	112915310			12	Intron of PTPN11(+):538bp after exon 10	PTPN11	112920547			10	DUPLICATION		5237	182172	7790	13	NEW_VARIANT
P-0019460-T01-IM6	PPM1D (NM_003620) rearrangement: c.345_chr17:g.75766061inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		168727	0	8	17	Exon 1 of PPM1D(+)	PPM1D	58678120			17	IGR: 47Kb before LOC100132174(-)	LOC100132174	75766061			10	INVERSION		17087941	182195	73979	8	NEW_VARIANT
P-0019460-T01-IM6	NF1 (NM_001042492) rearrangement: t(17;19)(q11.2;p13.2)(chr17:g.29646941::chr19:g.9293069)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint within intron 36. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	19	IGR: 3Kb before OR7D2(+)	OR7D2	9293069			17	Intron of NF1(+):6Kb before exon 37	NF1	29646941			10	TRANSLOCATION		0	182196	0	5	NEW_VARIANT
P-0019471-T01-IM6	CSF3R (NM_000760) Rearrangement : t(1;6)(p34.3;q22.31)(chr1:g.36939288::chr6:g.118964150)	PRECISE	Note: The CSF3R Rearrangement results in the possible truncation of CSF3R. One of the breakpoints is within intron 5. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	31	6	Intron of CEP85L(-):10Kb after exon 2	CEP85L	118964150			1	Intron of CSF3R(-):65bp before exon 6	CSF3R	36939288			10	TRANSLOCATION		0	182241	0	31	NEW_VARIANT
P-0019473-T01-IM6	CD79A (NM_001783) - MRPL36 (NM_032479) Rearrangement : t(5,19)(p15.33,q13.2)(chr5:g.1795958::chr19:g.42384823)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {CD79A:MRPL36}		0	0	12	19	Intron of CD79A(+):18bp after exon 4	CD79A	42384823			5	Promoter of MRPL36(-):3Kb from tx start	MRPL36	1795958			0	TRANSLOCATION		0	182272	0	12	NEW_VARIANT
P-0019489-T01-IM6	ELF3 (NM_004433) - CAPN2 (NM_001748) rearrangement: c.163+125:ELF3_c.1135+1210:CAPN2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {ELF3:CAPN2}		85756	0	3	1	Intron of ELF3(+):125bp after exon 2	ELF3	201980552			1	Intron of CAPN2(+):1Kb after exon 9	CAPN2	223941868			5	DELETION		21961316	182296	86370	3	NEW_VARIANT
P-0019489-T01-IM6	CCND1 (NM_053056) rearrangement: c.574+39_g.71719423del	PRECISE	Note: The CCND1 rearrangement results in the deletion of exons 4-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		34837	0	5	11	Intron of CCND1(+):39bp after exon 3	CCND1	69458798			11	Intron of NUMA1(-):310bp after exon 20	NUMA1	71719423			10	DELETION		2260625	182297	31127	5	NEW_VARIANT
P-0019491-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 with ALK exons 20-29): c.1490-486:EML4_c.3173-202:ALKinv	PRECISE	Note: The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		138467	0	80	2	Intron of ALK(-):202bp before exon 20	ALK	29446596			2	Intron of EML4(+):485bp before exon 13	EML4	42527895			10	INVERSION		13081299	182281	123890	80	NEW_VARIANT
P-0019492-T01-IM6	WHSC1L1 (NM_023034) rearrangement: g.691711_c.1807del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		124250	0	11	8	5-UTR of ERICH1-AS1(+):396Kb before coding start	ERICH1-AS1	691711			8	Exon 8 of WHSC1L1(-)	WHSC1L1	38178592			10	DELETION		37486881	182283	90857	11	NEW_VARIANT
P-0019512-T01-IM6	INPPL1 (NM_001567) rearrangement: c.182+1384_c.605del	PRECISE	Note: The INPPL1 rearrangement is an intragenic deletion of exons 2-5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7164	0	6	11	Intron of INPPL1(+):1Kb after exon 1	INPPL1	71937594			11	Exon 5 of INPPL1(+)	INPPL1	71940220			10	DELETION		2626	182350	6364	6	NEW_VARIANT
P-0019513-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 19-29): c.1489+2278:EML4_c.3096:ALKinv	PRECISE	Note: The EML4 - ALK fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		123269	0	134	2	Exon 19 of ALK(-)	ALK	29448403			2	Intron of EML4(+):2Kb after exon 12	EML4	42524934			10	INVERSION		13076531	182368	152756	130	NEW_VARIANT
P-0019529-T01-IM6	CSDE1 (NM_001242891) rearrangement: c.1779-187_c.1892-394inv	PRECISE	Note: The CSDE1 rearrangement is an inversion (1124  bp) of exon 16. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1539	0	17	1	Intron of CSDE1(-):394bp before exon 17	CSDE1	115267017			1	Intron of CSDE1(-):187bp before exon 16	CSDE1	115268141			10	INVERSION		1124	182590	7313	11	NEW_VARIANT
P-0019529-T01-IM6	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.688+24:RAD21_c.289+29346:EIF3Hdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {RAD21:EIF3H}		11328	0	9	8	Intron of EIF3H(-):29Kb after exon 2	EIF3H	117708909			8	Intron of RAD21(-):23bp after exon 6	RAD21	117869482			10	DELETION		160573	182589	15222	9	NEW_VARIANT
P-0019533-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-6 with ALK exons 20-29): c.667+6837:EML4_c.3173-100:ALKinv	PRECISE	The EML4 - ALK  fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		158246	0	19	2	Intron of ALK(-):100bp before exon 20	ALK	29446494			2	Intron of EML4(+):7Kb after exon 5	EML4	42498708			10	INVERSION		13052214	182595	167095	21	NEW_VARIANT
P-0019535-T02-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		100061	0	79	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32314077			10	Intron of RET(+):118bp before exon 12	RET	43611913			10	INVERSION		11297836	183955	103901	127	NEW_VARIANT
P-0019541-T01-IM6	ALK (NM_004304) - MYO3B (NM_138995) rearrangement: c.3172+534:ALK_c.749+32154:MYO3Bdel	PRECISE	Note: The ALK - MYO3B rearrangement detected by this assay is a deletion (141677007 bp) which includes ALK exons 1-19 and MYO3B exons 1-7. While this rearrangement does not result in an ALK fusion, upon manual review there is evidence of a potential EML4-ALK fusion.   Additional testing by Archer targeted RNAseq assay is being attempted.	MANUAL_OK	3to5	3to5	-		732072	0	20	2	Intron of ALK(-):533bp after exon 19	ALK	29447793			2	Intron of MYO3B(+):32Kb after exon 7	MYO3B	171124800			10	DELETION		141677007	182587	539045	21	NEW_VARIANT
P-0019552-T01-IM6	MTOR (NM_004958) Rearrangement : chr1:g.10998818_c.6764:MTOR	PRECISE	Note: The MTOR Rearrangement results in the duplication of exons 1-48. One of the breakpoints is within exon48. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		14530	0	7	1	IGR: 8Kb before C1orf127(-)	C1orf127	10998818			1	Exon 48 of MTOR(-)	MTOR	11182082			10	DUPLICATION		183264	182634	15965	7	NEW_VARIANT
P-0019564-T01-IM6	CDK4 (NM_000075) - GNB3 (NM_002075) rearrangement : c.71:CDK4_c.-155:GNB3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CDK4:GNB3}		721891	0	2	12	5-UTR of GNB3(+):378bp before coding start	GNB3	6950073			12	Exon 2 of CDK4(-)	CDK4	58145430			6	INVERSION		51195357	182687	676510	2	NEW_VARIANT
P-0019564-T01-IM6	MDM2 (NM_002392) rearrangement: c.1008_g.71085394del	PRECISE	Note: The MDM2 rearrangement results in the deletion of exon 11. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		2705	0	12	12	Exon 11 of MDM2(+)	MDM2	69233143			12	Intron of PTPRR(-):7Kb after exon 8	PTPRR	71085394			10	DELETION		1852251	182685	5133	12	NEW_VARIANT
P-0019580-T01-IM6	TP53 (NM_000546) - FXR2 (NM_004860) rearrangement: c.-28-733:TP53_c.660+186:FXR2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {TP53:FXR2}		21828	0	4	17	Intron of FXR2(-):185bp after exon 7	FXR2	7504541			17	5-UTR of TP53(-):8Kb before coding start	TP53	7580673			10	DELETION		76132	182515	12881	4	NEW_VARIANT
P-0019581-T01-IM6	DNMT3A (NM_022552) rearrangement: c2478_c.2479del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		697	0	2	2	Exon 22 of DNMT3A(-)	DNMT3A	25458694			2	Exon 21 of DNMT3A(-)	DNMT3A	25459805			7	DELETION		1111	182522	284	2	NEW_VARIANT
P-0019584-T01-IM6	KMT2D (NM_003482) rearrangement: c.1139_c.2467del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion (1467 bp) of exons 9-10. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17317	0	40	12	Exon 10 of KMT2D(-)	KMT2D	49444999			12	Exon 9 of KMT2D(-)	KMT2D	49446466			10	DELETION		1467	182526	10021	40	NEW_VARIANT
P-0019584-T01-IM6	INPP4B (NM_001101669) rearrangement: c.1721-4219_c.1894-71del	PRECISE	Note: The INPP4B rearrangement is an intragenic deletion (5493 bp) of exon 19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1621	0	41	4	Intron of INPP4B(-):71bp before exon 20	INPP4B	143044639			4	Intron of INPP4B(-):4Kb before exon 19	INPP4B	143050132			10	DELETION		5493	182524	1234	43	NEW_VARIANT
P-0019600-T01-IM6	NFKBIA (NM_020529) Rearrangement : c.-2947_ c.336+54inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		2311	0	29	14	Intron of NFKBIA(-):53bp after exon 2	NFKBIA	35872842			14	Promoter of NFKBIA(-):6Kb from tx start	NFKBIA	35876797			10	INVERSION		3955	182562	5586	32	NEW_VARIANT
P-0019614-T01-IM6	TCF7L2 (NM_001146274) Rearrangement : c.-2525_c.257-102del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		3174	0	22	10	Promoter of TCF7L2(+):2Kb from tx start	TCF7L2	114707991			10	Intron of TCF7L2(+):101bp before exon 3	TCF7L2	114711140			10	DELETION		3149	182693	1041	22	NEW_VARIANT
P-0019637-T01-IM6	AXIN2 (NM_004655) rearrangement: c.544_c.-116-199del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5377	0	63	17	Exon 2 of AXIN2(-)	AXIN2	63554195			17	5-UTR of AXIN2(-):29Kb before coding start	AXIN2	63555053			10	DELETION		858	182731	1400	66	NEW_VARIANT
P-0019654-T01-IM6	CREBBP (NM_004380) rearrangement: chr16:g.75025150_c.4717inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		377685	0	52	16	Exon 28 of CREBBP(-)	CREBBP	3786048			16	IGR: 8Kb before ZNRF1(+)	ZNRF1	75025150			10	INVERSION		71239102	182755	506045	75	NEW_VARIANT
P-0019654-T01-IM6	NOTCH1 (NM_017617) rearrangement: chr9:g.139622044_c.5250dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		85564	0	11	9	Exon 28 of NOTCH1(-)	NOTCH1	139396858			9	3-UTR of SNHG7(-):592bp after coding stop	SNHG7	139622044			10	DUPLICATION		225186	182754	117426	11	NEW_VARIANT
P-0019659-T01-IM6	FGFR1 (NM_001174067) Rearrangement : c.1417_c.1756+409del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6701	0	23	8	Intron of FGFR1(-):408bp after exon 13	FGFR1	38274415			8	Exon 11 of FGFR1(-)	FGFR1	38275852			10	DELETION		1437	182798	6370	25	NEW_VARIANT
P-0019663-T01-IM6	RET (NM_020975) - ATXN2 (NM_002973) Rearrangement : t(10;12)(q11.21;q24.13)(chr10:g.43608640:chr12:g.111918446)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	42	12	Intron of ATXN2(-):5Kb after exon 18	ATXN2	111918446			10	Intron of RET(+):229bp after exon 9	RET	43608640			10	TRANSLOCATION		0	182788	0	42	NEW_VARIANT
P-0019663-T01-IM6	RET (NM_020975) - LIN52 (NM_001024674) Rearrangement : t(10;14)(p32.1;q12)(chr10:g.43608613:chr14:g.74562750)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RET:LIN52}		0	0	11	14	Intron of LIN52(+):62bp after exon 3	LIN52	74562750			10	Intron of RET(+):202bp after exon 9	RET	43608613			10	TRANSLOCATION		0	182789	0	14	NEW_VARIANT
P-0019676-T01-IM6	FSTL4 (NM_015082) - FLT4 (NM_182925) rearrangement: c.410-1835:FSTL4_c.867:FLT4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FSTL4:FLT4}		279250	0	3	5	Intron of FSTL4(-):2Kb before exon 5	FSTL4	132654179			5	Exon 7 of FLT4(-)	FLT4	180056377			10	DUPLICATION		47402198	182812	435204	3	NEW_VARIANT
P-0019680-T01-IM6	SMYD3 (NM_001167740) rearrangement: t(X;1)(q27.2;q44)(chrX:g.141735629::chr1:g.246518356)	PRECISE	Note: The SMYD3 rearrangement is a translocation that may result in a truncation of  exons 2-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	17	X	IGR: 378Kb before SPANXN4(+)	SPANXN4	141735629			1	Exon 2 of SMYD3(-)	SMYD3	246518356			10	TRANSLOCATION		0	182808	0	18	NEW_VARIANT
P-0019692-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+1604:TMPRSS2_c.40-60431:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		130253	0	50	21	Intron of ERG(-):60Kb before exon 4	ERG	39877975			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42878273			10	DELETION		3000298	182828	74281	52	NEW_VARIANT
P-0019695-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-941:TMPRSS2_c.40-61030:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		74418	0	2	21	Intron of ERG(-):61Kb before exon 4	ERG	39878574			21	Intron of TMPRSS2(-):941bp before exon 2	TMPRSS2	42871057			5	DELETION		2992483	182829	38462	2	NEW_VARIANT
P-0019720-T01-IM6	ARID1B (NM_020732) rearrangement: c.4013+799_c.4766del	PRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exons 17-18. One of the breakpoints is within exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5889	0	80	6	Intron of ARID1B(+):799bp after exon 16	ARID1B	157518248			6	Exon 18 of ARID1B(+)	ARID1B	157522494			10	DELETION		4246	182859	3433	89	NEW_VARIANT
P-0019727-T01-IM6	TCF3 (NM_001136139) rearrangement: c.299-1_g.7615432del	PRECISE	Note: The TCF3 rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		289819	0	93	19	Intron of TCF3(-):1bp before exon 5	TCF3	1627426			19	Exon 19 of PNPLA6(+)	PNPLA6	7615432			10	DELETION		5988006	183018	381481	105	NEW_VARIANT
P-0019731-T01-IM6	ARID1A (NM_006015) rearrangement : c.5337:ARID1A_g.120250048inv	PRECISE	Note: The ARID1A rearrangement results in the inversion of exon 20. One of the breakpoints is within exon 20. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		407016	0	13	1	Exon 20 of ARID1A(+)	ARID1A	27105726			1	IGR: 4Kb before PHGDH(+)	PHGDH	120250048			10	INVERSION		93144322	183007	515714	17	NEW_VARIANT
P-0019748-T01-IM6	GSK3A (NM_019884) - CIC (NM_015125) rearrangement: c.284-416:GSK3A_c.1531:CICdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		26937	0	113	19	Intron of GSK3A(-):416bp before exon 2	GSK3A	42744710			19	Exon 10 of CIC(+)	CIC	42794451			10	DUPLICATION		49741	182910	80775	125	NEW_VARIANT
P-0019761-T01-IM6	FUBP1 (NM_003902) - ZZZ3 (NM_015534) rearrangement: c.250+104:FUBP1_c.-403+14447:ZZZ3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {FUBP1:ZZZ3}		18248	0	4	1	5-UTR of ZZZ3(-):102Kb before coding start	ZZZ3	78133823			1	Intron of FUBP1(-):103bp after exon 3	FUBP1	78433745			6	DELETION		299922	182920	6866	4	NEW_VARIANT
P-0019772-T01-IM6	DNMT3B (NM_006892) rearrangement: c.878_c.1126+76del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3488	0	14	20	Exon 8 of DNMT3B(+)	DNMT3B	31379471			20	Intron of DNMT3B(+):76bp after exon 10	DNMT3B	31381477			10	DELETION		2006	182948	2885	14	NEW_VARIANT
P-0019776-T01-IM6	USP6 (NM_004505) - CDK12 (NM_016507) rearrangement: c.2916-470:USP6_c.2847-101:CDK12del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {USP6:CDK12}		319242	0	29	17	Intron of USP6(+):469bp before exon 25	USP6	5065709			17	Intron of CDK12(+):100bp before exon 10	CDK12	37673592			10	DELETION		32607883	182944	307251	33	NEW_VARIANT
P-0019776-T01-IM6	INSR (NM_000208) rearrangement: c.1484-19_chr19:g.7100343dup	PRECISE	Note: The INSR rearrangement is a duplication (67781  bp) which includes exons 7-22 of INSR. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		31098	0	4	19	IGR: 12Kb before INSR(-)	INSR	7100343			19	Intron of INSR(-):19bp before exon 7	INSR	7168124			10	DUPLICATION		67781	182945	38041	7	NEW_VARIANT
P-0019776-T01-IM6	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.356-254:SMARCA4_c.1334+15:CARM1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SMARCA4:CARM1}		13348	0	9	19	Intron of CARM1(+):15bp after exon 11	CARM1	11031264			19	Intron of SMARCA4(+):253bp before exon 4	SMARCA4	11096611			10	DUPLICATION		65347	182946	14936	9	NEW_VARIANT
P-0019776-T01-IM6	C20orf203 (NM_182584) - DNMT3B (NM_006892) rearrangement: c.*1178-3794:C20orf203_c.551:DNMT3Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		8098	0	21	20	3-UTR of C20orf203(-):6Kb after coding stop	C20orf203	31232283			20	Exon 6 of DNMT3B(+)	DNMT3B	31375154			10	DUPLICATION		142871	182947	9524	21	NEW_VARIANT
P-0019777-T01-IM6	FLT4 (NM_182925) rearrangement: c.1103+333_c.2648-27inv	IMPPRECISE	Note: The FLT4 rearrangement is an inversion of exons 9-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		27664	0	8	5	Intron of FLT4(-):27bp before exon 19	FLT4	180046393			5	Intron of FLT4(-):332bp after exon 8	FLT4	180055549			0	INVERSION		9156	182965	30696	9	NEW_VARIANT
P-0019792-T01-IM6	MDM4 (NM_002393) rearrangement: t(1;2)(q32.1;q31.2)(chr1:g.204518563::chr2:g.178015265)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	17	2	IGR: 62Kb before HNRNPA3(+)	HNRNPA3	178015265			1	Exon 11 of MDM4(+)	MDM4	204518563			10	TRANSLOCATION		0	182992	0	18	NEW_VARIANT
P-0019802-T01-IM6	RET (NM_020975) Rearrangement : t(8;10)(q24.13;q11.21)(chr8:g.125313999::chr10:g.43610696)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	18	10	Intron of RET(+):512bp after exon 11	RET	43610696			8	IGR: 9Kb before TMEM65(-)	TMEM65	125313999			10	TRANSLOCATION		0	183044	0	20	NEW_VARIANT
P-0019836-T01-IM6	ETV6 (NM_001987) - ANKS1B (NM_152788) Rearrangement : c.463+383:ETV6_c.1757-48649:ANKS1Binv	PRECISE	Note: The ETV6  - ANKS1B  Rearrangement results in the fusion of ETV6 exons 1-4 with ANKS1B exon 13-26. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:ANKS1B}		667301	0	5	12	Intron of ETV6(+):383bp after exon 4	ETV6	12006878			12	Intron of ANKS1B(-):49Kb before exon 13	ANKS1B	99689291			10	INVERSION		87682413	183085	742705	4	NEW_VARIANT
P-0019840-T01-IM6	ETV6 (NM_001987) Rearrangement: t(3;12)(p11.1;p13.2)(chr3:g.88996930::chr12:g.12008769)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	87	12	Intron of ETV6(+):2Kb after exon 4	ETV6	12008769			3	IGR: 160Kb before EPHA3(+)	EPHA3	88996930			10	TRANSLOCATION		0	183088	0	87	NEW_VARIANT
P-0019840-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 with ERG exons 2-10) : c.56-4117:TMPRSS2_c.18+11302:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		80339	0	46	21	Intron of ERG(-):11Kb after exon 1	ERG	39858985			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874233			10	DELETION		3015248	183087	76289	52	NEW_VARIANT
P-0019842-T01-IM6	IRS2 (NM_003749) Rearrangement : c.3413:IRS2_chr13:g.106047899del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		16580	0	5	13	IGR: 64Kb before DAOA-AS1(-)	DAOA-AS1	106047899			13	Exon 1 of IRS2(-)	IRS2	110434988			10	DELETION		4387089	183078	10775	5	NEW_VARIANT
P-0019855-T01-IM6	RPS6KB2 (NM_003952)  - CORO1B (NM_020441) rearrangement: c.550:RPS6KB2_c.210:CORO1Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		13781	0	66	11	Exon 7 of RPS6KB2(+)	RPS6KB2	67200242			11	Exon 3 of CORO1B(-)	CORO1B	67209551			10	DUPLICATION		9309	183105	22838	76	NEW_VARIANT
P-0019855-T01-IM6	BRCA1 (NM_007294) - ANKFN1 (NM_153228) rearrangement: c.4986:BRCA2_c.919+13903:ANKFN1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		126116	0	89	17	Exon 15 of BRCA1(-)	BRCA1	41222945			17	Intron of ANKFN1(+):14Kb after exon 7	ANKFN1	54465978			10	DUPLICATION		13243033	183106	164482	99	NEW_VARIANT
P-0019855-T01-IM6	HIST1H3C (NM_003531) rearrangement:  c.494_chr6:g.26049856dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		1358	0	45	6	IGR: 4Kb before HIST1H3C(+)	HIST1H3C	26049856			6	Exon 1 of HIST1H1C(-)	HIST1H1C	26056163			10	DUPLICATION		6307	183104	2432	53	NEW_VARIANT
P-0019855-T01-IM6	KMT2C (NM_170606) rearrangement: c.1902_c.5083-357del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		26198	0	78	7	Intron of KMT2C(-):357bp before exon 35	KMT2C	151880598			7	Exon 14 of KMT2C(-)	KMT2C	151945617			10	DELETION		65019	183102	20943	89	NEW_VARIANT
P-0019868-T01-IM6	RB1 (NM_000321) rearrangement: c.526_c.607+921del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1178	0	23	13	Exon 5 of RB1(+)	RB1	48921986			13	Intron of RB1(+):921bp after exon 6	RB1	48924080			10	DELETION		2094	183128	439	26	NEW_VARIANT
P-0019880-T01-IM6	SMAD4 (NM_005359) rearrangement: chr18:g.48531265_c.37:SMAD4del	PRECISE	Note: The SMAD4 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		273	0	8	18	IGR: 25Kb before SMAD4(+)	SMAD4	48531265			18	Exon 2 of SMAD4(+)	SMAD4	48573453			10	DELETION		42188	183151	168	10	NEW_VARIANT
P-0019883-T01-IM6	ETV6 (NM_001987) rearrangement: c.464-1161_c.1009+1080dup	PRECISE	Note: The ETV6 rearrangement is an intragenic duplication of exon  5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		25615	0	7	12	Intron of ETV6(+):1Kb before exon 5	ETV6	12021197			12	Intron of ETV6(+):1Kb after exon 5	ETV6	12023983			10	DUPLICATION		2786	183149	20534	6	NEW_VARIANT
P-0019918-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-3507_c.349+2123del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		41643	0	12	21	Intron of TMPRSS2(-):2Kb after exon 3	TMPRSS2	42864160			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873623			10	DELETION		9463	183213	20394	12	NEW_VARIANT
P-0019922-T01-IM6	GLI1 (NM_005269) rearrangement: c.2776:GLI1_chr12:g.71730061inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		36966	0	127	12	Exon 12 of GLI1(+)	GLI1	57865299			12	IGR: 103Kb before LGR5(+)	LGR5	71730061			10	INVERSION		13864762	183225	168928	188	NEW_VARIANT
P-0019922-T01-IM6	EGFR (NM_005228) rearrangement: t(7;19)(p22.1;q13.2)(chr7:g.5523893::chr19:g.38806683)	PRECISE	Note: The EGFR rearrangement is a translocation that may result in the truncation of exons 17-28.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	429	19	Promoter of YIF1B(-):12Kb from tx start	YIF1B	38806683			7	Intron of EGFR(+):33bp after exon 16	EGFR	55238939			10	TRANSLOCATION		0	183226	0	578	NEW_VARIANT
P-0019924-T01-IM6	PITHD1 (NM_020362) - ERBB2 (NM_004448) rearrangement: t(1;17)(p36.11;q12)(chr1:g.24108131::chr17:g.37871691)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PITHD1:ERBB2}		0	0	14	17	Intron of ERBB2(+):7bp before exon 11	ERBB2	37871691			1	Intron of PITHD1(+):2Kb after exon 3	PITHD1	24108131			10	TRANSLOCATION		0	183218	0	14	NEW_VARIANT
P-0019930-T01-IM6	CDK12 (NM_016507) rearrangement: c.578_c.1046+2617del	PRECISE	Note: The CDK12 rearrangement is an intragenic deletion of a part of exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4006	0	55	17	Exon 1 of CDK12(+)	CDK12	37618902			17	Intron of CDK12(+):3Kb after exon 1	CDK12	37621987			10	DELETION		3085	183256	4116	59	NEW_VARIANT
P-0019930-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-826:TMPRSS2_c.40-59325:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		63273	0	93	21	Intron of ERG(-):59Kb before exon 4	ERG	39876869			21	Intron of TMPRSS2(-):826bp before exon 2	TMPRSS2	42870942			10	DELETION		2994073	183257	81406	99	NEW_VARIANT
P-0019933-T01-IM6	RUNX1 (NM_001754) rearrangement: t(11;21)(q25;q22.12)(chr11:g.133681309::chr21:g.36259357)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RUNX1:LOC646522}		0	0	41	21	Exon 4 of RUNX1(-)	RUNX1	36259357			11	Promoter of LOC646522(-):28Kb from tx start	LOC646522	133681309			10	TRANSLOCATION		0	183249	0	42	NEW_VARIANT
P-0019933-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion ( TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-4692:TMPRSS2_c.39+60021:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		92894	0	35	21	Intron of ERG(-):60Kb after exon 3	ERG	39887565			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874808			10	DELETION		2987243	183247	99439	36	NEW_VARIANT
P-0019936-T01-IM6	BAP1 (NM_004656) rearrangement: c.1683:BAP1_chr3:g.52454975del	PRECISE	Note: BAP1 rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	-		22431	0	6	3	Exon 13 of BAP1(-)	BAP1	52437478			3	Exon 7 of PHF7(+)	PHF7	52454975			10	DELETION		17497	183253	21197	6	NEW_VARIANT
P-0019937-T01-IM6	BRCA2 (NM_000059) rearrangement: c.2801:BRCA2_chr13:g.35518543inv	PRECISE	Note: The BRCA2 rearrangement is an inversion of exons 11-27. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		70354	0	76	13	Exon 11 of BRCA2(+)	BRCA2	32911293			13	Intron of NBEA(+):1Kb after exon 1	NBEA	35518543			10	INVERSION		2607250	183275	62967	74	NEW_VARIANT
P-0019957-T01-IM6	MAP2K4 (NM_003010) rearrangement: c.1086+11_chr17:g.12465067del	PRECISE	Note: The MAP2K4 rearrangement is a deletion (421855 bp) which includes MAP2K4 exon 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {MAP2K4:LINC00670}		1792	0	17	17	Intron of MAP2K4(+):11bp after exon 10	MAP2K4	12043212			17	5-UTR of LINC00670(+):75Kb before coding start	LINC00670	12465067			10	DELETION		421855	183286	575	61	NEW_VARIANT
P-0019966-T01-IM6	NFE2L2 (NM_006164) rearrangement:  c.45+14986_c.263del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1583	0	20	2	Exon 2 of NFE2L2(-)	NFE2L2	178098782			2	Intron of NFE2L2(-):15Kb after exon 1	NFE2L2	178114274			10	DELETION		15492	183340	1744	21	NEW_VARIANT
P-0019976-T01-IM6	MED12 (NM_005120) Rearrangement : c.736-45:MED12_chrX:g.39187963dup	PRECISE	Note: The MED12 Rearrangement results in the duplication of exons 1-5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		235055	0	8	X	Promoter of LINC01281(-):24Kb from tx start	LINC01281	39187963			X	Intron of MED12(+):44bp before exon 6	MED12	70341132			10	DUPLICATION		31153169	183372	420228	8	NEW_VARIANT
P-0019977-T01-IM6	CREBBP (NM_004380) Rearrangement : c.799-7084_c.1468del	PRECISE	Note: The CREBBP Rearrangement results in the deletion of exons 3-6. One of the breakpoints is within exon6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6986	0	7	16	Exon 6 of CREBBP(-)	CREBBP	3832790			16	Intron of CREBBP(-):7Kb before exon 3	CREBBP	3867864			8	DELETION		35074	183351	7242	6	NEW_VARIANT
P-0019991-T01-IM6	PAX8 (NM_003466) Rearrangement :  t(2;5)(q14.1;p11)(chr2:g.113978655::chr5:g.46376227)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	14	5	IGR: 1Mb before HCN1(-)	HCN1	46376227			2	Intron of PAX8(-):900bp before exon 11	PAX8	113978655			10	TRANSLOCATION		0	183429	0	29	NEW_VARIANT
P-0020007-T01-IM6	NF1 (NM_001042492) - ATP6V1H (NM_015941) rearrangement: t(8;17)(q11.23;q11.2)(chr8:g.54716159::chr17:g.29588857)	PRECISE	Note: The NF1 - ATP6V1H rearrangement is a translocation with breakpoints within NF1 exon 35 and ATP6V1H intron 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	17	Exon 35 of NF1(+)	NF1	29588857			8	Intron of ATP6V1H(-):2Kb before exon 8	ATP6V1H	54716159			10	TRANSLOCATION		0	183466	0	7	NEW_VARIANT
P-0020007-T01-IM6	RHOA (NM_001664) rearrangement: c.277+76_chr3:g.49493880dup	PRECISE	Note: The RHOA rearrangement is a duplication (88095 bp) which includes RHOA exons 1-3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		4817	0	34	3	Intron of RHOA(-):75bp after exon 3	RHOA	49405785			3	IGR: 12Kb before DAG1(+)	DAG1	49493880			10	DUPLICATION		88095	183465	7321	34	NEW_VARIANT
P-0020010-T01-IM6	CDKN2B (NM_004936) - ELAVL2 (NM_004432)  rearrangement: c.156+68:CDKN2B_c.333+6227:ELAVL2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		3512	0	23	9	Intron of CDKN2B(-):67bp after exon 1	CDKN2B	22008729			9	Intron of ELAVL2(-):6Kb after exon 3	ELAVL2	23724793			10	INVERSION		1716064	183449	3234	30	NEW_VARIANT
P-0020013-T01-IM6	TMPRSS2 (NM_001135099) - SEPT11 (NM_018243) rearrangement: t(4;21)(q21.1;q22.3)(chr4:g.77953453::chr21:g.42872227)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {TMPRSS2:SEPT11}		0	0	6	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872227			4	Intron of SEPT11(+):1Kb after exon 9	SEPT11	77953453			10	TRANSLOCATION		0	183458	0	10	NEW_VARIANT
P-0020047-T01-IM6	ZFHX3 (NM_006885) - RASL12 (NM_016563) rearrangement: t(15;16)(q22.31;q22.3)(chr15:g.65351569::chr16:g.72992701)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	10	16	Exon 2 of ZFHX3(-)	ZFHX3	72992701			15	Intron of RASL12(-):113bp after exon 3	RASL12	65351569			10	TRANSLOCATION		0	183505	0	12	NEW_VARIANT
P-0020058-T01-IM6	CBFB (NM_022845) rearrangement: c.282+70:CBFB_chr16:g.67139204del	PRECISE	Note: The CBFB rearrangement is a deletion of exons 4-6.	MANUAL_OK	3to5	3to5	-		4797	0	8	16	Intron of CBFB(+):70bp after exon 3	CBFB	67070728			16	IGR: 5Kb before C16orf70(+)	C16orf70	67139204			10	DELETION		68476	183543	1462	12	NEW_VARIANT
P-0020078-T01-IM6	RET (NM_020975) rearrangement: c.1760-133_c.2136+245inv	PRECISE	Note: The RET rearrangement is an intragenic inversion of exons 10-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		12273	0	4	10	Intron of RET(+):132bp before exon 10	RET	43608871			10	Intron of RET(+):245bp after exon 11	RET	43610429			10	INVERSION		1558	183591	17229	4	NEW_VARIANT
P-0020078-T01-IM6	POLE (NM_006231) rearrangement: chr12:g.131945557_c.801+43del	PRECISE	Note: The POLE rearrangement is a deletion of exons 8-49.	MANUAL_OK	3to5	3to5	-		65160	0	75	12	IGR: 114Kb before LOC338797(+)	LOC338797	131945557			12	Intron of POLE(-):42bp after exon 8	POLE	133253906			10	DELETION		1308349	183584	67816	78	NEW_VARIANT
P-0020078-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-2608:TMPRSS2_c.236+3010:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		63289	0	52	21	Intron of ERG(-):3Kb after exon 2	ERG	39814317			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872724			10	DELETION		3058407	183585	78400	57	NEW_VARIANT
P-0020080-T01-IM6	GATA3 (NM_002051) rearrangement: c.1047+947_c.1179del	PRECISE	Note: The GATA3 rearrangement is an intragenic deletion of a part of exon 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1120	0	34	10	Intron of GATA3(+):947bp after exon 5	GATA3	8112508			10	Exon 6 of GATA3(+)	GATA3	8115833			10	DELETION		3325	183565	1137	33	NEW_VARIANT
P-0020083-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-3084:TMPRSS2_c.18+8091:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		68349	0	28	21	Intron of ERG(-):8Kb after exon 1	ERG	39862196			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873200			10	DELETION		3011004	183566	68381	31	NEW_VARIANT
P-0020086-T01-IM6	GREM1 (NM_013372) rearrangement: t(8;15)(p11.21;q13.3)(chr8:g.42632131::chr15:g.33023043)	IMPPRECISE	Note: The GREM1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	16	15	Exon 2 of GREM1(+)	GREM1	33023043			8	IGR: 24Kb before CHRNA6(-)	CHRNA6	42632131			0	TRANSLOCATION		0	183573	0	5	NEW_VARIANT
P-0020107-T01-IM6	AKT3 (NM_005465) Rearrangement : c.121:AKT3_chr1:g.242740337del	PRECISE	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.	MANUAL_OK	5to3	5to3	-		17335	0	21	1	IGR: 479Kb before LINC01347(-)	LINC01347	242740337			1	Exon 2 of AKT3(-)	AKT3	243858944			10	DUPLICATION		1118607	183602	14435	22	NEW_VARIANT
P-0020111-T01-IM6	INSR (NM_000208) Rearrangement : t(19,21)(p13.2,q22.2)(chr19:g.7126683::chr21:g.:40105340)	PRECISE	Note: The INSR Rearrangement results in the possible truncation of exons 16-22 of INSR. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	39	21	IGR: 6Kb before LINC00114(-)	LINC00114	40105340			19	Intron of INSR(-):21bp before exon 16	INSR	7126683			10	TRANSLOCATION		0	183654	0	38	NEW_VARIANT
P-0020111-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement : c.127-247:TMPRSS2_c.39+4072:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		24392	0	11	21	Intron of ERG(-):4Kb after exon 3	ERG	39943514			21	Intron of TMPRSS2(-):247bp before exon 3	TMPRSS2	42866752			10	INVERSION		2923238	183652	26716	10	NEW_VARIANT
P-0020120-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.942-117_g.56333264del	PRECISE	Note: The PIK3R3 rearrangement results in the inversion of exons 1-7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		88995	0	10	1	Intron of PIK3R3(-):117bp before exon 8	PIK3R3	46512414			1	IGR: 627Kb before PPAP2B(-)	PPAP2B	56333264			10	INVERSION		9820850	183689	109890	9	NEW_VARIANT
P-0020120-T01-IM6	CBL (NM_005188) rearrangement: c.1095+42_c.1431+776del	PRECISE	Note: The CBL rearrangement results in the deletion of exons 8-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		5562	0	23	11	Intron of CBL(+):42bp after exon 7	CBL	119148596			11	Intron of CBL(+):776bp after exon 9	CBL	119150199			10	DELETION		1603	183686	5085	28	NEW_VARIANT
P-0020122-T01-IM6	PPARG (NM_015869) rearrangement: c.1324_g.13048437del	PRECISE	Note: The PPARG rearrangement results in the deletion of exon 7. One of the breakpoints is within exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		34726	0	67	3	Exon 7 of PPARG(+)	PPARG	12475450			3	Intron of IQSEC1(-):65Kb before exon 2	IQSEC1	13048437			10	DELETION		572987	183691	127318	398	NEW_VARIANT
P-0020124-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		113548	0	49	2	Intron of ALK(-):371bp after exon 19	ALK	29447955			2	Intron of EML4(+):879bp after exon 12	EML4	42523535			10	INVERSION		13075580	183690	57623	46	NEW_VARIANT
P-0020132-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38046	0	18	21	Intron of ERG(-):57Kb after exon 3	ERG	39890646			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867623			10	DELETION		2976977	183728	24215	19	NEW_VARIANT
P-0020135-T01-IM6	FGFR2 (NM_000141) - BTBD16 (NM_144587) rearrangement: c.2302-167:FGFR2_c.386-107: BTBD16inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {FGFR2:BTBD16}		97363	0	41	10	Intron of FGFR2(-):167bp before exon 18	FGFR2	123239702			10	Intron of BTBD16(+):106bp before exon 6	BTBD16	124049317			0	INVERSION		809615	183720	2155489	77	NEW_VARIANT
P-0020141-T01-IM6	TMPRSS2 (NM_001135099) - DMD (NM_004006) rearrangement: t(21;X)(q22.3;p21.1)(chr21:g.42839577::chrX:g.32030014)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	44	X	Intron of DMD(-):43Kb before exon 17	DMD	32030014			21	Intron of TMPRSS2(-):83bp after exon 13	TMPRSS2	42839577			10	TRANSLOCATION		0	183714	0	48	NEW_VARIANT
P-0020145-T01-IM6	TSC1 (NM_000368) rearrangement: c.2208+230_c.2392-11del	PRECISE	Note: The TSC1 rearrangement is an intragenic deletion of exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		3359	0	35	9	Intron of TSC1(-):11bp before exon 19	TSC1	135777097			9	Intron of TSC1(-):229bp after exon 17	TSC1	135778808			10	DELETION		1711	183723	1755	39	NEW_VARIANT
P-0020148-T01-IM6	SOX2 (NM_003106) - STEAP4 (NM_024636) rearrangement: t(3;7)(q26.33;q21.12)(chr3:g.181430851::chr7:g.87911114)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SOX2:STEAP4}		0	0	32	7	Intron of STEAP4(-):720bp before exon 5	STEAP4	87911114			3	Exon 1 of SOX2(+)	SOX2	181430851			10	TRANSLOCATION		0	183769	0	31	NEW_VARIANT
P-0020151-T01-IM6	FAT1 (NM_005245) rearrangement: c.2144_c.-18-941inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		19035	0	14	4	Exon 2 of FAT1(-)	FAT1	187628838			4	5-UTR of FAT1(-):122Kb before coding start	FAT1	187631940			10	INVERSION		3102	183772	17971	18	NEW_VARIANT
P-0020157-T01-IM6	FGFR1 (NM_001174067) rearrangement: c.191-1250_c.355del	PRECISE	Note: The FGFR1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1607	0	16	8	Exon 4 of FGFR1(-)	FGFR1	38287302			8	Intron of FGFR1(-):1Kb before exon 4	FGFR1	38288716			10	DELETION		1414	183802	1152	17	NEW_VARIANT
P-0020158-T01-IM6	TG (NM_003235) - NBN (NM_002485) rearrangement: c.7036+2798:TG_c.481-22:NBNinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {TG:NBN}		72113	0	6	8	Intron of NBN(-):22bp before exon 5	NBN	90990573			8	Intron of TG(+):3Kb after exon 40	TG	134037193			10	INVERSION		43046620	183803	86577	6	NEW_VARIANT
P-0020161-T01-IM6	ARID1A (NM_006015) rearrangement: c.2733-42_c.4101+196dup	PRECISE	Note: The ARID1A rearrangement is a an intragenic duplication of exons 9-17. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 9 exons : out of frame		15284	0	58	1	Intron of ARID1A(+):41bp before exon 9	ARID1A	27092670			1	Intron of ARID1A(+):196bp after exon 17	ARID1A	27100585			10	DUPLICATION		7915	183806	20337	60	NEW_VARIANT
P-0020161-T01-IM6	GNAS (NM_000516) rearrangement: c.213-600_c.719-33dup	PRECISE	Note: The GNAS rearrangement is an intragenic duplication of exons 3-9. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 7 exons : out of frame		7329	0	6	20	Intron of GNAS(+):599bp before exon 3	GNAS	57473396			20	Intron of GNAS(+):32bp before exon 10	GNAS	57484706			10	DUPLICATION		11310	183807	14218	6	NEW_VARIANT
P-0020161-T01-IM6	RAD21 (NM_006265) rearrangement: c.-19_c.144+980inv	PRECISE	Note: The RAD21 rearrangement is an inversion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1094	0	9	8	Intron of RAD21(-):979bp after exon 2	RAD21	117877845			8	5-UTR of RAD21(-):19Kb before coding start	RAD21	117878987			10	INVERSION		1142	183809	3500	9	NEW_VARIANT
P-0020167-T01-IM6	MDC1 (NM_014641) rearrangement: c.94_chr6:g.31067025dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		2043	0	20	6	Exon 2 of MDC1(-)	MDC1	30682859			6	IGR: 12Kb before C6orf15(-)	C6orf15	31067025			10	DUPLICATION		384166	183820	4046	20	NEW_VARIANT
P-0020169-T01-IM6	TEK (NM_000459) rearrangement: c.1183-76_c.1624+304dup	PRECISE	Note: The TEK rearrangement is a duplication of exons 9-11. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		6093	0	3	9	Intron of TEK(+):75bp before exon 9	TEK	27185407			9	Intron of TEK(+):304bp after exon 11	TEK	27192925			9	DUPLICATION		7518	183827	4600	3	NEW_VARIANT
P-0020175-T01-IM6	CALR (NM_004343) Rearrangement : c.398-128_c.961-508dup	PRECISE	Note: The CALR Rearrangement results in the duplication of exons4-7 of CALR.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : out of frame		6861	0	4	19	Intron of CALR(+):127bp before exon 4	CALR	13050739			19	Intron of CALR(+):507bp before exon 8	CALR	13053843			10	DUPLICATION		3104	183840	9229	4	NEW_VARIANT
P-0020180-T02-IM6	MTUS2 (NM_001033602) - FANCA (NM_000135) Rearrangement: t(13,16)(q12.3,q24.3)(chr13:g.29866903::chr16:g.89851360)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MTUS2:FANCA}		0	0	112	16	Exon 15 of FANCA(-)	FANCA	89851360			13	Intron of MTUS2(+):11Kb after exon 4	MTUS2	29866903			10	TRANSLOCATION		0	183847	0	111	NEW_VARIANT
P-0020186-T01-IM6	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exon17 fused with BICC1 exon3 ): c.2302-1613:FGFR2_c.237+32254:BICC1inv	PRECISE	Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		272354	0	15	10	Intron of BICC1(+):32Kb after exon 2	BICC1	60412915			10	Intron of FGFR2(-):2Kb before exon 18	FGFR2	123241148			10	INVERSION		62828233	183869	212185	20	NEW_VARIANT
P-0020188-T01-IM6	EZH1(NM_001991) Rearrangement : c.367-292_640del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5042	0	5	17	Exon 7 of EZH1(-)	EZH1	40872315			17	Intron of EZH1(-):292bp before exon 6	EZH1	40875225			10	DELETION		2910	183907	3416	5	NEW_VARIANT
P-0020189-T01-IM6	APC (NM_000038) Rearrangement: t(4,5)(q21.23,q22.1)(chr4:g.85927495::chr5:g.112175197)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {WDFY3-AS2:APC}		0	0	24	5	Exon 16 of APC(+)	APC	112175197			4	5-UTR of WDFY3-AS2(+):673bp before coding start	WDFY3-AS2	85927495			10	TRANSLOCATION		0	183903	0	24	NEW_VARIANT
P-0020218-T01-IM6	TECRL (NM_001010874) - EPHA5 (NM_004439) rearrangement: c.234+7990:TECRL_c.1627:EPHA5dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TECRL:EPHA5}		16871	0	29	4	Intron of TECRL(-):8Kb after exon 1	TECRL	65266846			4	Exon 7 of EPHA5(-)	EPHA5	66280062			10	DUPLICATION		1013216	183926	26043	30	NEW_VARIANT
P-0020223-T01-IM6	NF1 (NM_001042492) - BCAS3 (NM_001099432) rearrangement: c.2850+95:NF1_c.2471-41787:BCAS3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {NF1:BCAS3}		650291	0	17	17	Intron of NF1(+):95bp after exon 21	NF1	29556578			17	Intron of BCAS3(+):42Kb before exon 24	BCAS3	59403901			10	DELETION		29847323	183934	789631	17	NEW_VARIANT
P-0020223-T01-IM6	NDST3 (NM_004784) - SESN1 (NM_014454) rearrangement: t(10;11)(q26;q21)(chr10:g.126280260::chr11:g.17734059)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {NDST3:SESN1}		0	0	41	6	Exon 2 of SESN1(-)	SESN1	109323487			4	Intron of NDST3(+):462bp before exon 6	NDST3	119064248			10	TRANSLOCATION		0	183935	0	41	NEW_VARIANT
P-0020231-T01-IM6	MSH6 (NM_000179) rearrangement: chr2:g.47947631_c.1332:MSH6del	PRECISE	Note: The MSH6 rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11040	0	6	2	IGR: 63Kb before MSH6(+)	MSH6	47947631			2	Exon 4 of MSH6(+)	MSH6	48026454			10	DELETION		78823	183970	12118	5	NEW_VARIANT
P-0020237-T01-IM6	ROS1 (NM_002944) rearrangement: chr6:g.30239323_c.5367-112:ROS1del	IMPPRECISE	Note: The ROS1 rearrangement is a deletion of exons 33-43. 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 ROS1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	-		669509	0	3	6	3-UTR of HCG17(-):55Kb after coding stop	HCG17	30239323			6	Intron of ROS1(-):112bp before exon 33	ROS1	117647689			0	DELETION		87408366	183971	648886	3	NEW_VARIANT
P-0020240-T01-IM6	FOXA1 (NM_004496) rearrangement: chr14:g.38310541_c.979:FOXA1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		8360	0	47	14	Exon 2 of FOXA1(-)	FOXA1	38061010			14	IGR: 252Kb before FOXA1(-)	FOXA1	38310541			10	DELETION		249531	183983	9063	53	NEW_VARIANT
P-0020243-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42653772_c.-56-356:TMPRSS2inv	IMPPRECISE	Note: The TMPRSS2  rearrangement results in an inversion of TMPRSS2 exons 2-14. 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 TMPRSS2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	-		47056	0	36	21	3-UTR of BACE2(+):114Kb after coding stop	BACE2	42653772			21	Intron of TMPRSS2(-):356bp before exon 2	TMPRSS2	42870472			0	INVERSION		216700	183975	44204	47	NEW_VARIANT
P-0020244-T01-IM6	SMARCA4 (NM_003072) - FKBP8 (NM_012181) rearrangement: c.3951+53:SMARCA4_c.293-771:FKBP8del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		298074	0	4	19	Intron of SMARCA4(+):53bp after exon 28	SMARCA4	11144929			19	Intron of FKBP8(-):771bp before exon 3	FKBP8	18651301			10	DELETION		7506372	183979	502797	6	NEW_VARIANT
P-0020245-T01-IM6	APC (NM_000038) rearrangement: c.4021_c.5586del	PRECISE	Note: The APC rearrangement results in the intragenic deletion of exon 16. The breakpoints are within exon 16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7614	0	9	5	Exon 16 of APC(+)	APC	112175312			5	Exon 16 of APC(+)	APC	112176877			10	DELETION		1565	183972	6394	10	NEW_VARIANT
P-0020249-T01-IM6	GRB7 (NM_005310) - ERBB2 (NM_004448) rearrangement: c.-489:GRB7_c.1947-146:ERBB2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {GRB7:ERBB2}		24789	0	26	17	Intron of ERBB2(+):145bp before exon 17	ERBB2	37879426			17	Promoter of GRB7(+):213bp from tx start	GRB7	37893948			0	DUPLICATION		14522	183985	751946	32	NEW_VARIANT
P-0020263-T01-IM6	CLYBL (NM_206808) - ERCC5 (NM_000123) rearrangement: c.187+6723:CYLBL_c.1692:ERCC5del	PRECISE	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	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CLYBL:ERCC5}		18589	0	16	13	Intron of CLYBL(+):7Kb after exon 2	CLYBL	100431987			13	Exon 8 of ERCC5(+)	ERCC5	103515191			10	DELETION		3083204	184028	17452	16	NEW_VARIANT
P-0020263-T01-IM6	CTNNB1 (NM_001904) rearrangement: t(1;3)(q32.1;p22.1)(chr1:g.207117851::chr3:g.41266567)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CTNNB1:PIGR}		0	0	18	3	Exon 4 of CTNNB1(+)	CTNNB1	41266567			1	5-UTR of PIGR(-):14Kb before coding start	PIGR	207117851			0	TRANSLOCATION		0	184029	0	19	NEW_VARIANT
P-0020263-T01-IM6	GALNT12 (NM_024642) - TGFBR1 (NM_004612) rearrangement: c.1606-679:GALNT12_c.156:TGFBR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GALNT12:TGFBR1}		834	0	20	9	Intron of GALNT12(+):678bp before exon 10	GALNT12	101610555			9	Exon 2 of TGFBR1(+)	TGFBR1	101891195			10	DELETION		280640	184027	544	21	NEW_VARIANT
P-0020273-T02-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		81446	0	7	10	Intron of KIF5B(-):130bp after exon 16	KIF5B	32311645			10	Intron of RET(+):212bp before exon 12	RET	43611819			10	INVERSION		11300174	184092	58765	8	NEW_VARIANT
P-0020306-T01-IM6	CARM1 (NM_199141) rearrangement: t(1;19)(p13.2;p13.2)(chr1:g.111953456::chr19:g.11031667)	PRECISE	Note: The CARM1 rearrangement is a translocation that may result in the truncation of exons 14-16. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	19	Intron of CARM1(+):45bp after exon 13	CARM1	11031667			1	IGR: 3Kb before OVGP1(-)	OVGP1	111953456			10	TRANSLOCATION		0	184088	0	13	NEW_VARIANT
P-0020313-T01-IM6	ARID1A (NM_006015) Rearrangement : c.1921-3491_c.2251+69dup	PRECISE	Note: The ARID1A Rearrangement results in the intragenic duplication of exons 5-6 of ARID1A. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		4843	0	42	1	Intron of ARID1A(+):3Kb before exon 5	ARID1A	27083856			1	Intron of ARID1A(+):69bp after exon 6	ARID1A	27088033			10	DUPLICATION		4177	184147	10805	44	NEW_VARIANT
P-0020323-T01-IM6	NFIX (NM_002501) - CALR (NM_004343) Rearrangement : c.27+550:NFIX_c.961-42:CALRdup	PRECISE	Note: The NFIX - CALR Rearrangement results in the fusion of exons of NFIX with exons of CALR. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {NFIX:CALR}		2834	0	14	19	Intron of CALR(+):41bp before exon 8	CALR	13054309			19	Intron of NFIX(+):550bp after exon 1	NFIX	13107228			10	DUPLICATION		52919	184143	2821	14	NEW_VARIANT
P-0020334-T01-IM6	MAX (NM_002382) rearrangement: g.35276358_c.198inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		74888	0	12	14	Intron of BAZ1A(-):298bp after exon 6	BAZ1A	35276358			14	Exon 4 of MAX(-)	MAX	65544728			10	INVERSION		30268370	184169	78556	12	NEW_VARIANT
P-0020334-T01-IM6	TSHR (NM_000369) rearrangement: c.317+1950_c.457inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		2137	0	11	14	Intron of TSHR(+):2Kb after exon 3	TSHR	81536622			14	Exon 5 of TSHR(+)	TSHR	81557477			10	INVERSION		20855	184170	2263	11	NEW_VARIANT
P-0020339-T01-IM6	BRCA1 (NM_007294) - DCXR (NM_016286) Rearrangement : c.2297:BRCA1_c.-1737:DCXR	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BRCA1:DCXR}		358492	0	13	17	Exon 10 of BRCA1(-)	BRCA1	41245251			17	Promoter of DCXR(-):4Kb from tx start	DCXR	79997295			10	DUPLICATION		38752044	184204	362473	15	NEW_VARIANT
P-0020341-T01-IM6	CREBBP (NM_004380) Rearrangement :  chr16:g.3963526_c.-49:CREBBPdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		44	0	30	16	5-UTR of CREBBP(-):152Kb before coding start	CREBBP	3929966			16	IGR: 34Kb before LOC102724927(-)	LOC102724927	3963526			10	DELETION		33560	184179	21	41	NEW_VARIANT
P-0020353-T01-IM6	ABL1 (NM_005157) - COQ4 (NM_016035) rearrangement: c.866:ABL1_c.402+2158:COQ4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ABL1:COQ4}		12477	0	28	9	Intron of COQ4(+):2Kb after exon 4	COQ4	131090318			9	Exon 5 of ABL1(+)	ABL1	133747559			10	DUPLICATION		2657241	184227	17415	32	NEW_VARIANT
P-0020355-T01-IM6	DNAJB1 (NM_006145) - PLVAP (NM_031310) rearrangement: c.774:DNAJB1_c.369+3270:PLVAPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNAJB1:PLVAP}		210592	0	14	19	Exon 2 of DNAJB1(-)	DNAJB1	14627296			19	Intron of PLVAP(-):3Kb after exon 1	PLVAP	17484459			10	DUPLICATION		2857163	184219	169356	16	NEW_VARIANT
P-0020355-T01-IM6	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	PRECISE	Note: The FGFR3 - TACC3 fusion is predicted to be in frame and includes the kinase domain of FGFR3.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		45185	0	2	4	Intron of TACC3(+):311bp before exon 11	TACC3	1741117			4	Intron of FGFR3(+):35bp before exon 18	FGFR3	1808807			10	DUPLICATION		67690	184217	38951	2	NEW_VARIANT
P-0020358-T01-IM6	YWHAE (NM_006761) - NOTCH1 (NM_017617) rearrangement: t(9;17)(q34.3;p13.3)(chr9:g.139397624::chr17:g.1296199)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {YWHAE:NOTCH1}		0	0	108	17	Intron of YWHAE(-):7Kb after exon 1	YWHAE	1296199			9	Intron of NOTCH1(-):9bp after exon 27	NOTCH1	139397624			10	TRANSLOCATION		0	184213	0	115	NEW_VARIANT
P-0020365-T01-IM6	POLE (NM_006231) rearrangement: c.3238_c.2732del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5756	0	15	12	Exon 26 of POLE(-)	POLE	133235918			12	Exon 24 of POLE(-)	POLE	133238245			10	DELETION		2327	184226	4253	18	NEW_VARIANT
P-0020377-T01-IM6	DNMT1 (NM_001379) rearrangement : t(5;19)(q14.3;q13.2)(chr5:g.88595050::chr19:g.10246818)	PRECISE	Note: The DNMT1 rearrangement is a translocation that may result in a truncation of exons 37-40. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	19	Exon 37 of DNMT1(-)	DNMT1	10246818			5	IGR: 410Kb before MEF2C-AS1(+)	MEF2C-AS1	88595050			10	TRANSLOCATION		0	184249	0	7	NEW_VARIANT
P-0020394-T01-IM6	DOT1L (NM_032482) rearrangement: c.4024_c.4606+997inv	IMPPRECISE	Note: The DOT1L rearrangement is an intragenic deletion of a part of exon 27. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		9561	0	7	19	Exon 27 of DOT1L(+)	DOT1L	2226544			19	Intron of DOT1L(+):997bp after exon 27	DOT1L	2228123			0	INVERSION		1579	184271	14002	7	NEW_VARIANT
P-0020395-T01-IM6	RECQL (NM_032941) rearrangement: c.1175:RECQL_chr12:g.24778811del	PRECISE	Note: The RECQL rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		21406	0	9	12	Exon 11 of RECQL(-)	RECQL	21628443			12	IGR: 59Kb before LINC00477(-)	LINC00477	24778811			10	DELETION		3150368	184280	17687	9	NEW_VARIANT
P-0020396-T01-IM6	RB1 (NM_000321) rearrangement: c.1695+33:RB1_chr13:g.61408465del	PRECISE	Note: The RB1 rearrangement is a deletion of exons 18-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		26432	0	62	13	Intron of RB1(+):33bp after exon 17	RB1	48955612			13	IGR: 161Kb before LINC00378(+)	LINC00378	61408465			10	DELETION		12452853	184281	1784	68	NEW_VARIANT
P-0020402-T01-IM6	ETV6 (NM_001987) rearrangement: c.464-5389:ETV6_chr12:g.93097480del	PRECISE	Note: The ETV6 rearrangement is a deletion of exons 5-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {ETV6:C12orf74}		770427	0	13	12	Intron of ETV6(+):5Kb before exon 5	ETV6	12016969			12	5-UTR of C12orf74(+):3Kb before coding start	C12orf74	93097480			10	DELETION		81080511	184302	970149	13	NEW_VARIANT
P-0020402-T01-IM6	SMARCA2 (NM_003070) - EWSR1 (NM_013986) rearragement: t(9;22)(p24.3;q12.2)(chr9:g.2157696::chr22:g.29684038)	PRECISE	Note: The SMARCA2 rearrangement is a translocation that results in the fusion of SMARCA2 exons 1-28 with EWSR1 exons 9-18. 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 EWSR1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SMARCA2:EWSR1}		0	0	16	22	Intron of EWSR1(+):556bp before exon 9	EWSR1	29684038			9	Intron of SMARCA2(+):4Kb before exon 28	SMARCA2	2157696			10	TRANSLOCATION		0	184305	0	16	NEW_VARIANT
P-0020406-T01-IM6	TP53 (NM_000546) rearrangement:  c.994-345_c.*3317del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 10 -11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		3158	0	17	17	Promoter of TP53(-):2Kb from tx start	TP53	7569610			17	Intron of TP53(-):345bp before exon 10	TP53	7574378			10	DELETION		4768	184308	726	65	NEW_VARIANT
P-0020410-T01-IM6	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	PRECISE	Note: The FGFR2 - DDX21 fusion is predicted to be in frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:DDX21}		200665	0	36	10	Intron of DDX21(+):859bp before exon 2	DDX21	70718702			10	Intron of FGFR2(-):163bp after exon 17	FGFR2	123243048			10	INVERSION		52524346	184314	218098	50	NEW_VARIANT
P-0020414-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.-48-534_c.389del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3450	0	23	3	5-UTR of CTNNB1(+):581bp before coding start	CTNNB1	41264978			3	Exon 4 of CTNNB1(+)	CTNNB1	41266592			10	DELETION		1614	184317	2248	23	NEW_VARIANT
P-0020424-T01-IM6	GPS2 (NM_004489) rearrangement: c.95-61_c.-837del	PRECISE	Note: The GPS2 rearrangement results in the deletion of the promoter and exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		2043	0	30	17	Intron of GPS2(-):61bp before exon 3	GPS2	7217977			17	Promoter of GPS2(-):3Kb from tx start	GPS2	7219419			10	DELETION		1442	184356	923	30	NEW_VARIANT
P-0020424-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.55+590:TMPRSS2_c.40-60250:ERGdel	PRECISE	Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		134726	0	22	21	Intron of ERG(-):60Kb before exon 4	ERG	39877794			21	Intron of TMPRSS2(-):589bp after exon 1	TMPRSS2	42879287			10	DELETION		3001493	184357	106351	22	NEW_VARIANT
P-0020430-T01-IM6	TP53 (NM_000546) rearrangement: c.1100+285_c.837del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5439	0	23	17	Intron of TP53(-):284bp after exon 10	TP53	7573642			17	Exon 8 of TP53(-)	TP53	7577101			10	DELETION		3459	184367	4192	23	NEW_VARIANT
P-0018779-T02-IM6	CNNM2 (NM_017649) - SUFU (NM_016169) rearrangement: c.1621+38766:CNNM2_c.91:SUFUdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CNNM2:SUFU}		16052	0	47	10	Exon 1 of SUFU(+)	SUFU	104264000			10	Intron of CNNM2(+):39Kb after exon 1	CNNM2	104718624			10	DUPLICATION		454624	208454	19804	47	NEW_VARIANT
P-0025857-T01-IM6	AXIN1 (NM_003502) rearrangement: t(10;15)(p15.1;p13.3)(chr10:g.5637288::chr16:g.347033)	PRECISE	Note: The AXIN1 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	74	16	Intron of AXIN1(-):22bp after exon 7	AXIN1	347033			10	IGR: 44Kb before ASB13(-)	ASB13	5637288			10	TRANSLOCATION		0	208866	0	84	NEW_VARIANT
P-0025947-T01-IM6	BCL2 (NM_000633) Rearrangement :  c.585+75026:BCL2_c.2475+15186:NFATC1del	PRECISE	Note: The BCL2 Rearrangement results in the deletion of exons 1-2 of BCL2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		15192	0	7	18	Intron of BCL2(-):75Kb after exon 2	BCL2	60910289			18	Intron of NFATC1(+):15Kb after exon 9	NFATC1	77261816			8	DELETION		16351527	208056	11425	7	NEW_VARIANT
P-0025947-T01-IM6	TGFBR2 (NM_001024847) Rearrangement : c.2_c.530-9893inv	PRECISE	Note: The TGFBR2 Rearrangement results in the inversion of exons 1-4.One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3412	0	47	3	Exon 1 of TGFBR2(+)	TGFBR2	30648377			3	Intron of TGFBR2(+):10Kb before exon 5	TGFBR2	30703237			10	INVERSION		54860	208057	2932	64	NEW_VARIANT
P-0025950-T01-IM6	NOTCH2 (NM_024408) Rearrangement : chr1:g.56269765_c.1303inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		146872	0	19	1	IGR: 578Kb before MIR4422(+)	MIR4422	56269765			1	Exon 8 of NOTCH2(-)	NOTCH2	120510206			10	INVERSION		64240441	208067	240869	25	NEW_VARIANT
P-0025950-T01-IM6	KDM6A (NM_021140) Rearrangement : chrX:g.44725131_c.2554del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		9156	0	28	X	IGR: 7Kb before KDM6A(+)	KDM6A	44725131			X	Exon 17 of KDM6A(+)	KDM6A	44929454			10	DELETION		204323	208066	5770	28	NEW_VARIANT
P-0026033-T01-IM6	NFKBIA (NM_020529) rearrangement: c.228-99:NFKBIA_chr14:g.36803740del	IMPPRECISE	Note: The NFKBIA rearrangement is a deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1833	0	5	14	Intron of NFKBIA(-):99bp before exon 2	NFKBIA	35873103			14	IGR: 36Kb before MBIP(-)	MBIP	36803740			0	DELETION		930637	208437	4552	5	NEW_VARIANT
P-0026038-T01-IM6	EPB41L1 (NM_012156) - SRC (NM_198291) rearrangement: c.490+1264:EPB41L1_c.1040-143:SRCdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EPB41L1:SRC}		10198	0	4	20	Intron of EPB41L1(+):1Kb after exon 6	EPB41L1	34767858			20	Intron of SRC(+):142bp before exon 11	SRC	36029862			5	DELETION		1262004	208441	32478	4	NEW_VARIANT
P-0026038-T01-IM6	KMT2C (NM_170606) rearrangement: c.12181_c.*5095del	PRECISE	Note: The KMT2C rearrangement is a deletion of exons 48 - 59. One of the breakpoints is within exon 48. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		12718	0	6	7	IGR: 3Kb before KMT2C(-)	KMT2C	151828822			7	Exon 48 of KMT2C(-)	KMT2C	151851190			10	INVERSION		22368	208443	33342	6	NEW_VARIANT
P-0026039-T01-IM6	MGA (NM_001164273) rearrangement: c.736:MGA_chr15:g.41871206inv	PRECISE	Note: The MGA rearrangement is an inversion of exons 1-2. One of the breakpoints is in exon 2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2894	0	13	15	3-UTR of TYRO3(+):20Kb after coding stop	TYRO3	41871206			15	Exon 2 of MGA(+)	MGA	41961828			10	INVERSION		90622	208464	4133	12	NEW_VARIANT
P-0026072-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 fused to ERG exons 2-11): c.56-3750:TMPRSS2_c.-149-29688:ERG	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74241	0	29	21	3-UTR of ERG(-):47Kb after coding stop	ERG	39986557			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873866			10	DELETION		2887309	209220	61363	149	NEW_VARIANT
P-0026123-T01-IM6	SMAD4 (NM_005359) rearrangement: t(17;18)(q11.1;q21.1)(chr17:g.:25550206::chr18:g.48591841)	PRECISE	Note: The SMAD4 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	11	18	Exon 9 of SMAD4(+)	SMAD4	48591841			17	IGR: 71Kb before MIR4522(-)	MIR4522	25550206			10	TRANSLOCATION		0	209330	0	11	NEW_VARIANT
P-0026123-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: chr21:g.42266771_c.1021inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	-		4039	0	30	21	IGR: 247Kb before LINC00323(-)	LINC00323	42266771			21	Exon 10 of TMPRSS2(-)	TMPRSS2	42843898			0	INVERSION		577127	209329	7548	30	NEW_VARIANT
P-0026200-T01-IM6	SPEN (NM_015001) - SULF2 (NM_018837) rearrangement: t(1;20)(p36.13;q13.12)(chr1:g16265882::chr20:g.46321003)	PRECISE	Note: The SPEN - SULF2 rearrangement is a translocation with breakpoints within SPEN exon 15 and SULF2 intron 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	29	20	Intron of SULF2(-):2Kb before exon 5	SULF2	46321003			1	Exon 15 of SPEN(+)	SPEN	16265882			10	TRANSLOCATION		0	209870	0	29	NEW_VARIANT
P-0026106-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.471_chr9:g.22013106del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		6	9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21971053			9	5-UTR of CDKN2B-AS1(+):108Kb before coding start	CDKN2B-AS1	22013106			10	DELETION		42053	209758	8924		NEW_VARIANT
P-0026106-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.305_chr9:g.22013106del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		6	9	Exon 2 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21971053			9	5-UTR of CDKN2B-AS1(+):108Kb before coding start	CDKN2B-AS1	22013106			10	DELETION		42053	209757	8924		NEW_VARIANT
P-0026108-T01-IM6	ALK (NM_004304) rearrangement: c.3172+208_chr2:g.41387535del	PRECISE	Note: The ALK rearrangement results in the deletion of exons 1-19.	MANUAL_OK	3to5	3to5	-		50582	0	102	2	Intron of ALK(-):207bp after exon 19	ALK	29448119			2	IGR: 717Kb before LOC388942(+)	LOC388942	41387535			10	DELETION		11939416	209269	88438	117	NEW_VARIANT
P-0026152-T01-IM6	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)	PRECISE		MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:ETV1}		0	0	87	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872732			7	Intron of ETV1(-):445bp before exon 5	ETV1	14017550			10	TRANSLOCATION		0	209520	0	91	NEW_VARIANT
P-0026196-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		61499	0	19	21	Intron of ERG(-):63Kb after exon 3	ERG	39884340			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873713			10	DELETION		2989373	209844	59852	19	NEW_VARIANT
P-0026212-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		60356	0	8	21	Intron of ERG(-):57Kb after exon 3	ERG	39890829			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873852			10	DELETION		2983023	209924	42147	9	NEW_VARIANT
P-0026159-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused to ERG exon2) : c.55+2059:TMPRSS2_c.19-16879:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		99415	0	6	21	Intron of ERG(-):9Kb before exon 2	ERG	39826074			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877818			10	DELETION		3051744	209535	69354	7	NEW_VARIANT
P-0026139-T01-IM6	FGFR1 (NM_001174067) Rearrangement : chr8:g.32978873_c.1798del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		53306	0	19	8	IGR: 249Kb before FUT10(-)	FUT10	32978873			8	Exon 14 of FGFR1(-)	FGFR1	38273537			10	DELETION		5294664	209556	52208	20	NEW_VARIANT
P-0026228-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		26185	0	9	21	Intron of ERG(-):8bp after exon 1	ERG	39870278			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868990			10	DELETION		2998712	210040	26049	51	NEW_VARIANT
P-0026245-T01-IM6	KIAA1217 (NM_019590) - RET (NM_020975) fusion (KIAA1217 exons 1-13 fused to RET exons 7-20): c.2390:KIAA1217_c.1275:RETdel	IMPPRECISE	Note: The KIAA1217 - RET fusion includes the kinase domain of RET. This sample has been nominated for analysis using the Archer targeted RNAseq assay to further characterize the structural variant involving the RET gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {KIAA1217:RET}		56858	0	13	10	Exon 13 of KIAA1217(+)	KIAA1217	24810792			10	Exon 7 of RET(+)	RET	43606666			0	DELETION		18795874	210158	117185	13	NEW_VARIANT
P-0026377-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2) :c.56-3439:TMPRSS2_c.18+2268:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53250	0	16	21	Intron of ERG(-):2Kb after exon 1	ERG	39868019			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873555			10	DELETION		3005536	210450	49741	17	NEW_VARIANT
P-0026153-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused to ERG exon4) : c.126+1611:TMPRSS2_c.39+54119:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		33192	0	96	21	Intron of ERG(-):54Kb after exon 3	ERG	39893467			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868435			10	DELETION		2974968	209517	34021	100	NEW_VARIANT
P-0026289-T01-IM6	RB1 (NM_000321) Rearrangement: c.1215+58_c.1332+582	PRECISE	Note: The RB1 rearrangement results in the deletion of exon 13.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		535	0	5	13	Intron of RB1(+):58bp after exon 12	RB1	48947686			13	Intron of RB1(+):582bp after exon 13	RB1	48951752			9	DELETION		4066	210220	738	5	NEW_VARIANT
P-0026272-T01-IM6	FAT1 (NM_005245) rearrangement: c.10658:FAT1_chr4:g.187636565inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		65983	0	10	4	Exon 19 of FAT1(-)	FAT1	187525022			4	5-UTR of FAT1(-):127Kb before coding start	FAT1	187636565			10	INVERSION		111543	210265	28396	10	NEW_VARIANT
P-0026273-T01-IM6	ARID1A (NM_006015) rearrangement: c.1138-883_c.5122dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		35785	0	8	1	Intron of ARID1A(+):882bp before exon 2	ARID1A	27055259			1	Exon 19 of ARID1A(+)	ARID1A	27102196			0	DUPLICATION		46937	210258	19991	8	NEW_VARIANT
P-0026279-T01-IM6	CIC (NM_015125) rearrangement: chr19:g.42764612_c.1756:CICdel	PRECISE	Note: The CIC rearrangement is a deletion of exons 1-10. One of the breakpoints is within exon 10. The functionals significance is undetermined,	MANUAL_OK	3to5	3to5	-		19299	0	11	19	IGR: 13Kb before ERF(-)	ERF	42764612			19	Exon 10 of CIC(+)	CIC	42794676			10	DELETION		30064	210270	17768	12	NEW_VARIANT
P-0026351-T01-IM6	TFE3 (NM_006521) rearrangement: c.885+214_c.1136+665dup	PRECISE	Note: The TFE3 rearrangement is an intragenic duplication of exons 6-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		7297	0	13	X	Intron of TFE3(-):664bp after exon 8	TFE3	48890315			X	Intron of TFE3(-):213bp after exon 5	TFE3	48895321			10	DUPLICATION		5006	210284	14149	14	NEW_VARIANT
P-0026354-T01-IM6	ARHGEF11 (NM_198236) - NTRK1 (NM_002529)  rearrangement: c.4631-285:ARHGEF11_c.1355-128:NTRK1inv	PRECISE	Note: The ARHGEF11 - NTRK1 rearrangement is an inversion that results in an in-frame fusion of ARHGEF11 exons 1-39 to NTRK1 exons 12-17, which include the kinase domain. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the NTRK1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {ARHGEF11:NTRK1}		8509	0	18	1	Intron of NTRK1(+):127bp before exon 12	NTRK1	156845184			1	Intron of ARHGEF11(-):285bp before exon 40	ARHGEF11	156906135			10	INVERSION		60951	210297	16655	21	NEW_VARIANT
P-0026407-T01-IM6	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-18 fused with ALK exons 20-29): c.1981-2450:EML4_c.3175:ALKinv	PRECISE	Note: One of the breakpoints is within ALK exon 20 and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		117036	0	56	2	Exon 20 of ALK(-)	ALK	29446392			2	Intron of EML4(+):2Kb before exon 19	EML4	42550157			10	INVERSION		13103765	210478	123847	53	NEW_VARIANT
P-0026409-T01-IM6	CIC (NM_015125) rearrangement: t(3;19)(p25.2;q13.2)(chr3:g.13023744::chr19:g.42793933)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	89	19	Intron of CIC(+):66bp before exon 9	CIC	42793933			3	Intron of IQSEC1(-):40Kb before exon 2	IQSEC1	13023744			10	TRANSLOCATION		0	210496	0	90	NEW_VARIANT
P-0026409-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+1383:TMPRSS2_c.18+21976:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		124747	0	116	21	Intron of ERG(-):22Kb after exon 1	ERG	39848311			21	Intron of TMPRSS2(-):1Kb after exon 1	TMPRSS2	42878494			10	DELETION		3030183	210482	126590	126	NEW_VARIANT
P-0026151-T01-IM6	IL7R (NM_002185) Rearrangement : chr5:g.22317231_c.318dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		72328	0	11	5	5-UTR of CDH12(-):565Kb before coding start	CDH12	22317231			5	Exon 3 of IL7R(+)	IL7R	35867504			10	DUPLICATION		13550273	209506	98390	13	NEW_VARIANT
P-0026162-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-2434:TMPRSS2_c.40-58863:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53450	0	89	21	Intron of ERG(-):59Kb before exon 4	ERG	39876407			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872550			10	DELETION		2996143	209983	71848	96	NEW_VARIANT
P-0026175-T01-IM6	WWTR1 (NM_001168280) rearrangement: c.841_c.1018+1550inv	PRECISE	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	MANUAL_OK	3to3	3to3	-		2141	0	27	3	Intron of WWTR1(-):2Kb after exon 6	WWTR1	149242250			3	Exon 5 of WWTR1(-)	WWTR1	149245687			10	INVERSION		3437	209998	4167	26	NEW_VARIANT
P-0026175-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.1965+7_c.2087+6del	PRECISE	Note: The MAP3K1 rearrangement is an intragenic deletion of exon 11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		746	0	10	5	Intron of MAP3K1(+):7bp after exon 10	MAP3K1	56171144			5	Intron of MAP3K1(+):6bp after exon 11	MAP3K1	56174934			10	DELETION		3790	209995	1290	10	NEW_VARIANT
P-0026390-T01-IM6	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)	PRECISE	Note: The ETV6-NTRK3 fusion is an in-frame fusion and includes the protein kinase domain of NTRK3.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	38	15	Intron of NTRK3(-):18Kb after exon 13	NTRK3	88651131			12	Intron of ETV6(+):5Kb before exon 5	ETV6	12016863			10	TRANSLOCATION		0	210538	0	38	NEW_VARIANT
P-0026422-T01-IM6	WHSC1L1 rearrangement: t(8;17)(p11.23;q25.1)(chr8:g.38172814::chr17:g.74191825)	PRECISE	Note: The WHSC1L1 rearrangement is a translocation which involves exon 11. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	8	17	Intron of RNF157(-):17Kb after exon 2	RNF157	74191825			8	Intron of WHSC1L1(-):119bp after exon 11	WHSC1L1	38172814			10	TRANSLOCATION		0	210575	0	8	NEW_VARIANT
P-0026430-T01-IM6	ETV6 (NM_001987) - GNB1 (NM_002074) rearrangement: t(1;12)(p36/33;p13.2)(chr1:g.1785936::chr12:g.12019513)	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {ETV6:GNB1}		0	0	200	12	Intron of ETV6(+):3Kb before exon 5	ETV6	12019513			1	5-UTR of GNB1(-):67Kb before coding start	GNB1	1785936			10	TRANSLOCATION		0	210573	0	198	NEW_VARIANT
P-0026448-T01-IM6	FAT1 (NM_005245) rearrangement: c.13139-23_c.3581-5825del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 4-26.	MANUAL_OK	3to5	3to5	Deletion of 23 exons : in frame		74145	0	5	4	Intron of FAT1(-):23bp before exon 27	FAT1	187510397			4	Intron of FAT1(-):6Kb before exon 4	FAT1	187566762			10	DELETION		56365	210634	63408	5	NEW_VARIANT
P-0026449-T01-IM6	EPAS1 (NM_001430) rearrangement: c.739_c.*265inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		25266	0	4	2	Exon 6 of EPAS1(+)	EPAS1	46588189			2	3-UTR of EPAS1(+):87Kb after coding stop	EPAS1	46612064			10	INVERSION		23875	210636	25736	4	NEW_VARIANT
P-0026514-T01-IM6	TMPRSS2 (NM_001135099) - WISP3 (NM_003880) Rearrangement : t(6,21)(q21,q22.2)(chr6:g.112390072::chr21:g.30301865)	PRECISE	Note: The TMPRSS2 - WISP3 Rearrangement results in the fusion of exon 1 of TMPRSS2 with exon 6 of WISP3. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {TMPRSS2:WISP3}		0	0	7	21	Intron of TMPRSS2(-):205bp after exon 1	TMPRSS2	42879671			6	Intron of WISP3(+):469bp before exon 6	WISP3	112390072			10	TRANSLOCATION		0	210861	0	15	NEW_VARIANT
P-0024217-T02-IM6	FLT3 (NM_004119) rearrangement: t(2;13)(p22.2;q12.2)(chr2:g.38136570::chr13:g.28623971)	PRECISE	Note: The FLT3 rearrangement is a translocation involving exon 3. ITs functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	13	13	Intron of FLT3(-):60bp before exon 7	FLT3	28623971			2	IGR: 16Kb before RMDN2(+)	RMDN2	38136570			10	TRANSLOCATION		0	210779	0	13	NEW_VARIANT
P-0024217-T02-IM6	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	PRECISE	Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		67798	0	51	21	Intron of ERG(-):19Kb after exon 3	ERG	39928235			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874589			10	DELETION		2946354	210776	109448	55	NEW_VARIANT
P-0026484-T01-IM6	EP300 (NM_001429) rearrangement: t(19;22)(p13.12;q13.2)(chr19:g.15895130::chr22:g.41573283)	PRECISE	Note: The EP300 rearrangement is a translocation involving exon 31. One of the breakpoints is within exon 31. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	21	22	Exon 31 of EP300(+)	EP300	41573283			19	IGR: 10Kb before OR10H5(+)	OR10H5	15895130			10	TRANSLOCATION		0	210761	0	22	NEW_VARIANT
P-0026485-T01-IM6	PDGFRB (NM_002609) rearrangement: t(5;17)(q32;q23.3)(chr5:g.149497245::chr17:g.62611355)	PRECISE	Note: The PDGFRB rearrangement is a translocation involving exon 22. One of the breakpoints is within exon 22. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	61	17	Intron of SMURF2(-):9Kb before exon 2	SMURF2	62611355			5	Exon 22 of PDGFRB(-)	PDGFRB	149497245			10	TRANSLOCATION		0	210783	0	61	NEW_VARIANT
P-0026485-T01-IM6	PDPK1 (NM_002613)  rearrangement: t(16;19)(p13.3;q13.41)(chr16:g.2645831::chr19:g.51698785)	PRECISE	Note: The PDPK1 rearrangement is a translocation which involves exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	16	19	IGR: 11Kb before MIR8074(-)	MIR8074	51698785			16	Exon 12 of PDPK1(+)	PDPK1	2645831			10	TRANSLOCATION		0	210784	0	15	NEW_VARIANT
P-0026526-T01-IM6	PTPRS (NM_002850) - GLOD4 (NM_016080) rearrangement: t(17;19)(p13.3;p13.3)(chr17:g.666026::chr19:g.5231417)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PTPRS:GLOD4}		0	0	55	19	Exon 14 of PTPRS(-)	PTPRS	5231417			17	Intron of GLOD4(-):3Kb before exon 9	GLOD4	666026			10	TRANSLOCATION		0	210899	0	64	NEW_VARIANT
P-0026526-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.404_c.1065+578del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6147	0	13	8	Intron of WHSC1L1(-):577bp after exon 5	WHSC1L1	38188371			8	Exon 2 of WHSC1L1(-)	WHSC1L1	38205286			10	DELETION		16915	210898	7091	13	NEW_VARIANT
P-0026614-T01-IM6	SPECC1L (NM_001145468) - RET (NM_020975) fusion (SPECC1L exons 1-10 fused to RET exons 12-20): t(10;22)(10q11.21;22q11.23)(chr10:g.43611575::chr22:g.24740413)	PRECISE	Note: The SPECC1L - RET fusion is predicted to be in-frame and includes the RET kinase domain. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the SPECC1L and RET genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {SPECC1L:RET}		0	0	116	22	Intron of SPECC1L(+):3Kb before exon 11	SPECC1L	24740413			10	Intron of RET(+):456bp before exon 12	RET	43611575			10	TRANSLOCATION		0	210915	0	133	NEW_VARIANT
P-0026623-T01-IM6	ETV6 (NM_001987) rearrangement: c.1009+1254:ETV6_chr12:g.12134793inv	PRECISE	Note: The ETV6 rearrangement is an inversion of exons 6-8. This structural variant was observed in addition to other rearrangements involving ETV6, suggesting a complex event that may not be detected by the IMPACT assay. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ETV6 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	-		82454	0	54	12	Intron of ETV6(+):1Kb after exon 5	ETV6	12024157			12	IGR: 89Kb before BCL2L14(+)	BCL2L14	12134793			10	INVERSION		110636	210972	230098	54	NEW_VARIANT
P-0026650-T02-IM6	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	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {ALK:EML4}		96438	0	21	2	Intron of ALK(-):875bp after exon 19	ALK	29447451			2	Intron of EML4(+):7Kb after exon 5	EML4	42499245			10	INVERSION		13051794	211018	142472	29	NEW_VARIANT
P-0026652-T01-IM6	CD276 (NM_001024736) Rearrangement : t(15,16)(q24.1,q24.1)(chr15:g.73995403::chr16:g.85397630)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	32	16	IGR: 58Kb before MIR5093(-)	MIR5093	85397630			15	Exon 4 of CD276(+)	CD276	73995403			10	TRANSLOCATION		0	211071	0	39	NEW_VARIANT
P-0026667-T01-IM6	FGFR4 (NM_213647) - FRAT1 (NM_005479) rearrangement: t(5;10)(q35.2;q24.1)(chr5:g.:176518004::chr10:g.:99079984)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {FRAT1:FGFR4}		0	0	17	10	Exon 1 of FRAT1(+)	FRAT1	99079984			5	Exon 5 of FGFR4(+)	FGFR4	176518004			10	TRANSLOCATION		0	211016	0	18	NEW_VARIANT
P-0026544-T01-IM6	NAB2 (NM_005967) rearrangement: t(12;18)(q13.3;q11.2)(chr12:g.57488056::chr18:g.24061792)	PRECISE	Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	18	Intron of KCTD1(-):5Kb before exon 3	KCTD1	24061792			12	Intron of NAB2(+):338bp before exon 7	NAB2	57488056			10	TRANSLOCATION		0	211226	0	12	NEW_VARIANT
P-0026673-T01-IM6	CDK12 (NM_016507) rearrangement: chr17:g.37297706_c.2847-104del	PRECISE	Note: The CDK12 rearrangement is a deletion of exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		13516	0	11	17	Intron of PLXDC1(-):2Kb before exon 2	PLXDC1	37297706			17	Intron of CDK12(+):103bp before exon 10	CDK12	37673589			10	DELETION		375883	211146	19804	11	NEW_VARIANT
P-0026676-T01-IM6	PIK3R1 (NM_181523) - TMEM117 (NM_032256) rearrangement: t(5;12)(5q13.1;12q12)(chr5:g.67522870::chr12:g.44739711)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PIK3R1:TMEM117}		0	0	6	12	Intron of TMEM117(+):31Kb before exon 7	TMEM117	44739711			5	Intron of PIK3R1(+):33bp after exon 2	PIK3R1	67522870			10	TRANSLOCATION		0	211153	0	6	NEW_VARIANT
P-0026682-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.8814:ZFHX3_chr16:g.72801772del	PRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 1-9. One of the breakpoints is within exon 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		8855	0	3	16	IGR: 15Kb before ZFHX3(-)	ZFHX3	72801772			16	Exon 9 of ZFHX3(-)	ZFHX3	72827767			10	DELETION		25995	211145	10184	3	NEW_VARIANT
P-0026689-T01-IM6	TP63 (NM_003722):c.325-30del_g.177279698	PRECISE	Note: The TP63 rearrangement results in the intergenic deletion of TP63 exons 1-3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {LINC00578:TP63}		101914	0	36	3	5-UTR of LINC00578(+):191Kb before coding start	LINC00578	177279698			3	Intron of TP63(+):29bp before exon 4	TP63	189526031			10	DELETION		12246333	211167	168318	38	NEW_VARIANT
P-0026691-T01-IM6	TCF3 (NM_001136139) - CDKN2Ap14ARF (NM_058195) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0		65	19	Intron of TCF3(-):3Kb before exon 6	TCF3	1619713			9	Intron of CDKN2Ap14ARF(-):1kb before exon 2	CDKN2Ap14ARF	21972496			10	TRANSLOCATION		0	211986	0		NEW_VARIANT
P-0026691-T01-IM6	TCF3 (NM_001136139) - CDKN2Ap16INK4A (NM_000077) rearrangement:t(9;19)(chr9:g.21972496::chr19:g.1619713)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0		65	19	Intron of TCF3(-):3Kb before exon 6	TCF3	1619713			9	Intron of CDKN2Ap16INK4A(-):1kb before exon 2	CDKN2Ap16INK4A	21972496			10	TRANSLOCATION		0	211985	0		NEW_VARIANT
P-0026693-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion:c.2544+156:KIF5_c.2136+327:RETinv.	PRECISE	Note: The KIF58 - RET fusion is predicted to be in frame and it includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		53704	0	17	10	Intron of KIF5B(-):155bp after exon 23	KIF5B	32306824			10	Intron of RET(+):327bp after exon 11	RET	43610511			10	INVERSION		11303687	211162	85056	24	NEW_VARIANT
P-0026696-T01-IM6	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)	PRECISE	The ETV6 - NTRK3 fusion is predicted to be in frame. It includes kinase domain of NTRK3.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	19	15	Intron of NTRK3(-):12Kb after exon 13	NTRK3	88657925			12	Intron of ETV6(+):1Kb after exon 4	ETV6	12007967			10	TRANSLOCATION		0	211194	0	19	NEW_VARIANT
P-0026699-T01-IM6	KMT2D (NM_003482):c.8207_c.7157inv.	PRECISE	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.	MANUAL_OK	3to3	3to3	-		9419	0	4	12	Exon 32 of KMT2D(-)	KMT2D	49433240			12	Exon 31 of KMT2D(-)	KMT2D	49434396			9	INVERSION		1156	211199	21841	4	NEW_VARIANT
P-0026701-T01-IM6	TP53 (NM_000546):c.97-42_c.994-858del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 4 to 9.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		12586	0	18	17	Intron of TP53(-):858bp before exon 10	TP53	7574891			17	Intron of TP53(-):42bp before exon 4	TP53	7579632			10	DELETION		4741	211165	7232	83	NEW_VARIANT
P-0026804-T01-IM6	FBXL7 (NM_012304) - PGR (NM_000926) rearrangement: t(5;11)(p15.1;q22.1)(chr5:g.15611089::chr11:g.100920672)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {FBXL7:PGR}		0	0	7	11	Exon 6 of PGR(-)	PGR	100920672			5	Intron of FBXL7(+):5Kb before exon 2	FBXL7	15611089			10	TRANSLOCATION		0	211965	0	7	NEW_VARIANT
P-0026804-T01-IM6	SHMT1 (NM_005412) - CD79A (NM_001783) rearrangement: t(17;19)(p11.2;q13.2)(chr17:g.18266040::chr19:g.42383410)	PRECISE	Note: The SHMT1 - CD79A rearrangement is a translocation that involves 5-UTR of SHMT1 and intron 2 of CD79A. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	50	19	Intron of CD79A(+):51bp after exon 2	CD79A	42383410			17	5-UTR of SHMT1(-):34Kb before coding start	SHMT1	18266040			10	TRANSLOCATION		0	211966	0	55	NEW_VARIANT
P-0026806-T01-IM6	PTPRS (NM_002850) - XRN2 (NM_012255) rearrangement :t(19;20)(p13.3;p11.22)(chr19:g.5256123::chr20:g.21300045)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PTPRS:XRN2}		0	0	90	20	Intron of XRN2(+):7Kb before exon 2	XRN2	21300045			19	Exon 9 of PTPRS(-)	PTPRS	5256123			10	TRANSLOCATION		0	211968	0	143	NEW_VARIANT
P-0026808-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3722:TMPRSS2_c.19-15805:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		61547	0	91	21	Intron of ERG(-):16Kb before exon 2	ERG	39833349			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873838			10	DELETION		3040489	211962	44236	109	NEW_VARIANT
P-0026763-T01-IM6	ERBB2 (NM_004448) rearrangement: t(11;17)(q14.1;q12)(chr11:g.81026379::chr17:g.37871727)	PRECISE	Note: The ERBB2 rearrangement is a translocation with a breakpoint in exon 11. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	28	17	Exon 11 of ERBB2(+)	ERBB2	37871727			11	IGR: 564Kb before LOC101928944(-)	LOC101928944	81026379			10	TRANSLOCATION		0	212040	0	42	NEW_VARIANT
P-0026768-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-1013:TMPRSS2_c.39+54142:ERGdel	PRECISE	Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		34479	0	99	21	Intron of ERG(-):54Kb after exon 3	ERG	39893444			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871129			10	DELETION		2977685	211995	32014	104	NEW_VARIANT
P-0026768-T01-IM6	KMT2C (NM_170606) rearrangement: c.11460+700_c.10619del	PRECISE	Note: The KMT2C rearrangement results in the deletion of exon 43. One of the breakpoints is within exon 43. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2397	0	30	7	Intron of KMT2C(-):699bp after exon 43	KMT2C	151858502			7	Exon 43 of KMT2C(-)	KMT2C	151860043			10	DELETION		1541	211994	1987	32	NEW_VARIANT
P-0026773-T01-IM6	BRAF (NM_004333) rearrangement: c.1315-604:BRAF_chr7:g.138277426del	PRECISE	Note: The BRAF rearrangement results in the deletion of exons 11-18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {BRAF:SVOPL}		8934	0	22	7	Promoter of SVOPL(-):2Kb from tx start	SVOPL	138277426			7	Intron of BRAF(-):604bp before exon 11	BRAF	140482097			10	DELETION		2204671	212000	20918	24	NEW_VARIANT
P-0026785-T01-IM6	GATA3 (NM_002051) Rearrangement : c.327:GATA3_chr10:g.77209520dup	PRECISE	Note: The GATA3 Rearrangement results in the duplication of exons 3-6. One of the breakpoints is within exon3. Its functional significance is unknown.	MANUAL_OK	5to3	5to3	-		150075	0	3	10	Exon 3 of GATA3(+)	GATA3	8100353			10	IGR: 41Kb before LOC101929234(+)	LOC101929234	77209520			7	DUPLICATION		69109167	211903	185348	3	NEW_VARIANT
P-0026786-T01-IM6	TGFBR2 (NM_001024847) Rearrangement : t(1;3)(q11.2;p23)(chr1:g.66741811::chr3:g.30664833)	PRECISE	Note: The TGFBR2 Rearrangement results in  the possible truncation of TGFBR2.One of the breakpoints is within intron2.Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	15	3	Intron of TGFBR2(+):68bp after exon 2	TGFBR2	30664833			1	Intron of PDE4B(+):10Kb after exon 6	PDE4B	66741811			10	TRANSLOCATION		0	211899	0	15	NEW_VARIANT
P-0026841-T01-IM6	EPCAM (NM_002354) rearrangement: chr2:g.:47489472_c.209del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2107	0	5	2	3-UTR of LOC101927043(-):83Kb after coding stop	LOC101927043	47489472			2	Exon 3 of EPCAM(+)	EPCAM	47600971			10	DELETION		111499	212082	2937	6	NEW_VARIANT
P-0026847-T01-IM6	KDM5A (NM_001042603) rearrangement: c.1317_chr12:g.:648356del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		11424	0	10	12	Exon 11 of KDM5A(-)	KDM5A	443580			12	Intron of B4GALNT3(+):3Kb after exon 3	B4GALNT3	648356			10	DELETION		204776	212084	23782	10	NEW_VARIANT
P-0026854-T01-IM6	LUZP1 (NM_033631) - MPL (NM_005373) Rearrangement : c.-2991:LUZP1_c.1166-11:MPLinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript Fusion {LUZP1:MPL}		165828	0	25	1	Promoter of LUZP1(-):87Kb from tx start	LUZP1	23497958			1	Intron of MPL(+):10bp before exon 8	MPL	43812452			10	INVERSION		20314494	212124	166198	33	NEW_VARIANT
P-0022151-T01-IM6	DOT1L (NM_032482) - ITK (NM_005546) rearrangement: t(5;19)(q33.3;p13.3)(chr5:g.156631381::chr19:g.2193796)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {DOT1L:ITK}		0	0	22	19	Intron of DOT1L(+):14bp after exon 6	DOT1L	2193796			5	Intron of ITK(+):5Kb before exon 2	ITK	156631381			10	TRANSLOCATION		0	189783	0	22	NEW_VARIANT
P-0022151-T01-IM6	APC (NM_000038) rearrangement: chr5:g.98951265_c.7014:APCinv	PRECISE	Note: The APC rearrangement is an inversion with a breakpoint within exon 16. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		42147	0	35	5	IGR: 82Kb before CTD-2151A2.1(+)	CTD-2151A2.1	98951265			5	Exon 16 of APC(+)	APC	112178305			10	INVERSION		13227040	189781	70151	35	NEW_VARIANT
P-0024549-T03-IM6	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+651_c.1196-73inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TPR:NTRK1}		93084	0	46	1	Intron of NTRK1(+):72bp before exon 10	NTRK1	156844290			1	Intron of TPR(-):650bp after exon 21	TPR	186318704			10	INVERSION		29474414	212676	161754	70	NEW_VARIANT
P-0026831-T01-IM6	RAD51B (NM_133509) rearrangement: c.1037-91C:RAD51B_chr14:g.69090674del	PRECISE	Note: The RAD51B rearrangement results in the deletion of exons 1-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		857	0	2	14	Intron of RAD51B(+):90bp before exon 11	RAD51B	69061111			14	IGR: 164Kb before ZFP36L1(-)	ZFP36L1	69090674			10	DELETION		29563	212594	1393	2	NEW_VARIANT
P-0026930-T01-IM6	ARID1A (NM_006015) rearrangement: c.1351-32_c.3866+5dup	PRECISE	Note: The ARID1A rearrangement is an intragenic duplication of exons 3-15.	MANUAL_OK	5to3	5to3	Duplication of 13 exons : out of frame		23231	0	49	1	Intron of ARID1A(+):31bp before exon 3	ARID1A	27057611			1	Intron of ARID1A(+):5bp after exon 15	ARID1A	27099992			10	DUPLICATION		42381	212439	25525	51	NEW_VARIANT
P-0026930-T01-IM6	ADCY1 (NM_021116) - CSF1R (NM_005211) rearrangement: t(5;7)(q32;p12.3)(chr5:g.149452928::chr7:g.45629335)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ADCY1:CSF1R}		0	0	38	7	Intron of ADCY1(+):3Kb before exon 2	ADCY1	45629335			5	Exon 7 of CSF1R(-)	CSF1R	149452928			10	TRANSLOCATION		0	212443	0	38	NEW_VARIANT
P-0026937-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2437_c.2611+842deldel	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1617	0	15	8	Intron of WHSC1L1(-):841bp after exon 14	WHSC1L1	38161263			8	Exon 13 of WHSC1L1(-)	WHSC1L1	38162769			10	DELETION		1506	212427	2017	50	NEW_VARIANT
P-0026937-T01-IM6	NTRK2 (NM_006180) rearrangement: c.1444+18_c.1633+2908dup	PRECISE	Note: The NTRK2 rearrangement is an intragenic duplication of exon 16. 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 NTRK2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		48958	0	47	9	Intron of NTRK2(+):18bp after exon 15	NTRK2	87476020			9	Intron of NTRK2(+):3Kb after exon 16	NTRK2	87485254			10	DUPLICATION		9234	212428	85317	50	NEW_VARIANT
P-0026992-T01-IM6	EMID1 (NM_133455) - EWSR1 (NM_013986) rearrangement: c.320-2287_c.794-10inv.	PRECISE	Note: The EMID1 - EWSR1 rearrangement is an inversion that includes EMID1 exons 1-3 and EWSR1 exons 1-10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		37612	0	3	22	Intron of EMID1(+):2Kb before exon 4	EMID1	29618835			22	Intron of EWSR1(+):9bp before exon 11	EWSR1	29688116			10	INVERSION		69281	212541	43877	4	NEW_VARIANT
P-0009689-T01-IM5	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.365:PPM1D_c.2470+37341:BCAS3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (PPM1D-BCAS3)		28248	0	22	17	Exon 1 of PPM1D(+)	PPM1D	58678140			17	Intron of BCAS3(+): 37Kb after exon 22	BCAS3	59199266			70	DELETION		521126	135967	30435	13	NEW_VARIANT
P-0010689-T01-IM5	PBRM1 (NM_018313) rearrangement: c.1836_c.3312+2164dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		23484	0	39	3	Intron of PBRM1(-): 2Kb after exon 21	PBRM1	52618277			3	Exon 16 of PBRM1(-)	PBRM1	52649455			51	DUPLICATION		31178	148334	25561	37	NEW_VARIANT
P-0011147-T01-IM5	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement : c.790-3028:CUL1_c.2182:EZH2del	PRECISE	Note: The CUL1-EZH2 rearrangement event results in the deletion of EZH2 exons 19-20. One of the breakpoints is within EZH2 exon19.	MANUAL_OK	3to5	3to5	Antisense fusion		3431	0	58	7	Intron of CUL1(+): 3Kb before exon 8	CUL1	148460625			7	Exon 19 of EZH2(-)	EZH2	148506176			61	DELETION		45551	151395	3152	56	NEW_VARIANT
P-0018197-T01-IM6	FGFR1 (NM_001174067) rearrangement : g.33895943_c.1744:FGFR1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		74204	0	4	8	IGR: 447Kb before DUSP26(-)	DUSP26	33895943			8	Exon 13 of FGFR1(-)	FGFR1	38274836			10	INVERSION		4378893	178274	115777	9	NEW_VARIANT
P-0024119-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-1097:TMPRSS2_chr21:g.39992544del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		74733	0	15	21	3-UTR of ERG(-):41Kb after coding stop	ERG	39992544			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871213			10	DELETION		2878669	198336	33223	15	NEW_VARIANT
P-0026974-T01-IM6	FUBP1 (NM_003902) rearrangement: c.1705+69:FUBP1_chr1:g.85991712inv	PRECISE	Note: The FUBP1 rearrangement is an inversion of exons 1-17. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		22841	0	4	1	Intron of FUBP1(-):68bp after exon 17	FUBP1	78422188			1	5-UTR of DDAH1(-):205Kb before coding start	DDAH1	85991712			8	INVERSION		7569524	212501	45352	4	NEW_VARIANT
P-0027021-T01-IM6	TAP1 (NM_000593) - PSMB8 (NM_148919) Rearrangement (TAP1 exon10 with PSMB8 exon5 ) : c.2219:TAP1_c.538-80:PSMB8del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TAP1:PSMB8}		2382	0	12	6	Intron of PSMB8(-):80bp before exon 5	PSMB8	32809592			6	Exon 10 of TAP1(-)	TAP1	32814846			10	DELETION		5254	212638	3719	11	NEW_VARIANT
P-0027073-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3724:TMPRSS2_c.18+19585:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		54635	0	7	21	Intron of ERG(-):20Kb after exon 1	ERG	39850702			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873840			10	DELETION		3023138	212735	59045	8	NEW_VARIANT
P-0027079-T01-IM6	CUL3 (NM_003590) rearrangement: t(2;11)(q36.2;p15.4)(chr2:g.225378244::chr11:g.6857883)	PRECISE	Note: The CUL3 rearrangement is a translocation with a breakpoint within CUL3 exon 5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	33	11	IGR: 9Kb before OR10A5(+)	OR10A5	6857883			2	Exon 5 of CUL3(-)	CUL3	225378244			10	TRANSLOCATION		0	212706	0	37	NEW_VARIANT
P-0027081-T01-IM6	CREBBP (NM_004380) rearrangement: c.1573+53_c.2463+929inv	PRECISE	Note: The CREBBP rearrangement is an inversion of exons 7-13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		7440	0	3	16	Intron of CREBBP(-):928bp after exon 13	CREBBP	3822823			16	Intron of CREBBP(-):52bp after exon 6	CREBBP	3832632			10	INVERSION		9809	212702	10362	10	NEW_VARIANT
P-0027081-T01-IM6	BRCA1 (NM_007294) rearrangement: c.3576_chr17:g.41287037del	PRECISE	Note: The BRCA1 rearrangement is a deletion that includes BRCA1 exons 1-10. One of the breakpoints is within BRCA1 exon 10.	MANUAL_OK	3to5	3to5	-		22723	0	18	17	Exon 10 of BRCA1(-)	BRCA1	41243972			17	5-UTR of NBR2(+):10Kb before coding start	NBR2	41287037			10	DELETION		43065	212699	18664	19	NEW_VARIANT
P-0027082-T01-IM6	KMT2C (NM_170606) rearrangement: chr7:g.150053665_c.13391:KMT2Cdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		16474	0	37	7	IGR: 10Kb before RNU6-33P(+)	RNU6-33P	150053665			7	Exon 52 of KMT2C(-)	KMT2C	151845621			10	DELETION		1791956	212710	24855	38	NEW_VARIANT
P-0027086-T01-IM6	EZH2 (NM_004456) rearrangement: c.105:EZH2_chr7:g.148458308del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		14113	0	5	7	Intron of CUL1(+):720bp after exon 7	CUL1	148458308			7	Exon 2 of EZH2(-)	EZH2	148544286			10	DELETION		85978	212769	19233	5	NEW_VARIANT
P-0027092-T01-IM6	PLEKHH2 (NM_172069) - ALK (NM_004304) rearrangement: c.502+545: PLEKHH2_c.3173-112:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {PLEKHH2:ALK}		99442	0	55	2	Intron of ALK(-):112bp before exon 20	ALK	29446506			2	Intron of PLEKHH2(+):545bp after exon 6	PLEKHH2	43922908			10	INVERSION		14476402	212765	82158	54	NEW_VARIANT
P-0027098-T01-IM6	KMT2B (NM_014727) rearrangement: t(6;19)(p11.2;q13.12)(chr6:g.57161995::chr19:g.36214642)	PRECISE	Note: The KMT2B rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	29	19	Exon 8 of KMT2B(+)	KMT2B	36214642			6	IGR: 18Kb before PRIM2(+)	PRIM2	57161995			10	TRANSLOCATION		0	212779	0	28	NEW_VARIANT
P-0027134-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement:c.56-4414:TMPRSS2_c.39+60150:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		79223	0	64	21	Intron of ERG(-):60Kb after exon 3	ERG	39887436			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874530			10	INVERSION		2987094	212872	90570	59	NEW_VARIANT
P-0027141-T01-IM6	SOX9 (NM_000346) rearrangement: t(4;17)(q21.23;q24.3)(chr4:g.84464806::chr17:g.70120234)	PRECISE	Note: The SOX9 rearrangement is a translocation with a breakpoint within exon 3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	173	17	Exon 3 of SOX9(+)	SOX9	70120234			4	Intron of AGPAT9(+):882bp before exon 2	AGPAT9	84464806			10	TRANSLOCATION		0	212883	0	411	NEW_VARIANT
P-0027161-T01-IM6	RAD21 (NM_006265) rearrangement: c.224_g.117769470del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RAD21:EIF3H}		12239	0	20	8	Promoter of EIF3H(-):112Kb from tx start	EIF3H	117769470			8	Exon 3 of RAD21(-)	RAD21	117875419			10	DELETION		105949	212909	18325	21	NEW_VARIANT
P-0027028-T01-IM6	MAX (NM_002382) rearrangement: chr14:g.:25176242_c.172-6244dup	PRECISE	Note: The MAX rearrangement is a duplication that includes exons 4-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		64726	0	12	14	IGR: 76Kb before GZMB(-)	GZMB	25176242			14	Intron of MAX(-):6Kb before exon 4	MAX	65550998			10	DUPLICATION		40374756	212658	149266	12	NEW_VARIANT
P-0026969-T01-IM6	DTNB (NM_021907) - ASXL2 (NM_018263) rearrangement: c.362+2130:DTNB_c.1705:ASLX2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DTNB:ASXL2}		13771	0	14	2	Intron of DTNB(-):2Kb after exon 4	DTNB	25848910			2	Exon 11 of ASXL2(-)	ASXL2	25972720			10	DUPLICATION		123810	212495	18486	14	NEW_VARIANT
P-0027196-T01-IM6	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.149782321::chr6:g.117650377)	PRECISE	Note: The CD74 - ROS1 fusion includes ROS1 kinase domain. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the CD74 and ROS1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	0	41	6	Intron of ROS1(-):114bp after exon 32	ROS1	117650377			5	Intron of CD74(-):133bp before exon 8	CD74	149782321			10	TRANSLOCATION		0	212972	0	40	NEW_VARIANT
P-0027203-T01-IM6	PLCD3 (NM_133373) - MAP3K14 (NM_003954) rearrangement: c.164-4289_c.1290-7dup	PRECISE	Note: The PLCD3 - MAP3K14 rearrangement is a duplication which involves PLCD3 exon 2- 15 and MAP3K14 exons 1-6. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PLCD3:MAP3K14}		14851	0	10	17	Intron of PLCD3(-):4Kb before exon 2	PLCD3	43203028			17	Intron of MAP3K14(-):7bp before exon 7	MAP3K14	43351967			10	DUPLICATION		148939	212987	25526	10	NEW_VARIANT
P-0027203-T01-IM6	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.197_c.173-1754dup	PRECISE	Note: The CD79A - RPS19 rearrangement is a duplication which involves CD79A exons 2-5 and RPS19 exons 1-3	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CD79A:RPS19}		1735	0	3	19	Intron of RPS19(+):2Kb before exon 4	RPS19	42371347			19	Exon 2 of CD79A(+)	CD79A	42383177			10	DUPLICATION		11830	212988	3460	3	NEW_VARIANT
P-0027210-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-687:TMPRSS2_c.39+51208:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		37416	0	69	21	Intron of ERG(-):51Kb after exon 3	ERG	39896378			21	Intron of TMPRSS2(-):687bp before exon 2	TMPRSS2	42870803			10	DELETION		2974425	212992	43684	74	NEW_VARIANT
P-0027269-T01-IM6	PTPRD (NM_002839) rearrangement: c.692-845_c.680-66dup	PRECISE	Note: The PTPRD rearrangement results in the duplication of PTPRD exon 19. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		503	0	23	9	Intron of PTPRD(-):845bp before exon 20	PTPRD	8522391			9	Intron of PTPRD(-):66bp before exon 19	PTPRD	8523590			10	DUPLICATION		1199	213129	1107	24	NEW_VARIANT
P-0027272-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2470_c.19-26014del	PRECISE	Note: The variant results in TMPRSS2 exon1 fusing with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		47447	0	6	21	Intron of ERG(-):26Kb before exon 2	ERG	39843558			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872586			5	DELETION		3029028	213130	66265	6	NEW_VARIANT
P-0027288-T01-IM6	TCF3 (NM_001136139) rearrangement: chr19:g.1593723_c.1024dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MBD3:TCF3}		12515	0	10	19	Promoter of MBD3(-):17Kb from tx start	MBD3	1593723			19	Exon 12 of TCF3(-)	TCF3	1621036			10	DUPLICATION		27313	213170	11283	10	NEW_VARIANT
P-0026370-T02-IM6	CTNNB1 (NM_001904) rearrangement: c.991:CTNNB1_chr3:g.40674718dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		6005	0	27	3	IGR: 108Kb before ZNF621(+)	ZNF621	40674718			3	Exon 7 of CTNNB1(+)	CTNNB1	41268753			10	DUPLICATION		594035	213207	12167	29	NEW_VARIANT
P-0027185-T01-IM6	GNAQ (NM_002072) rearrangement: c.1054:GNAQ_chr9:g.80320467del	PRECISE	Note: The GNAQ rearrangement is an inversion with a breakpoint in exon 7. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		203	0	15	9	IGR: 11Kb before GNAQ(-)	GNAQ	80320467			9	Exon 7 of GNAQ(-)	GNAQ	80336265			10	INVERSION		15798	212959	309	21	NEW_VARIANT
P-0027300-T01-IM6	LDLR (NM_000527) - SMARCA4 (NM_003072) rearrangement: c.1845+936:LDLR_c.4602:SMARCA4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LDLR:SMARCA4}		5914	0	2	19	Exon 32 of SMARCA4(+)	SMARCA4	11169532			19	Intron of LDLR(+):936bp after exon 12	LDLR	11228610			9	DUPLICATION		59078	213214	7324	2	NEW_VARIANT
P-0027305-T01-IM6	FGFR2 (NM_000141) - CCDC6 (NM_005436) fusion (FGFR2 exons 1-17 fused to CCDC6 exons 4-9): c.2301+1670:FGFR2_c.582+6426:CCDC6del	PRECISE	Note: The FGFR2 - CCDC6 fusion is predicted to be in-frame and includes the kinase domain of FGFR2. Further characterization of this fusion gene is being performed on a RNA level by Archer FusionPlex assay, which will be reported separately (M18-5264).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:CCDC6}		36511	0	3	10	Intron of CCDC6(-):6Kb after exon 3	CCDC6	61585857			10	Intron of FGFR2(-):2Kb after exon 17	FGFR2	123241542			10	DELETION		61655685	213224	330479	3	NEW_VARIANT
P-0027311-T01-IM6	ETV6 (NM_001987) rearrangement: c.1010-268:ETV6_chr12:g.12056304del	PRECISE	Note: The ETV6 rearrangement is a deletion of exons 6-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5204	0	21	12	Intron of ETV6(+):267bp before exon 6	ETV6	12037111			12	3-UTR of RNU6-19P(-):23Kb after coding stop	RNU6-19P	12056304			10	DELETION		19193	213233	7657	22	NEW_VARIANT
P-0027321-T01-IM6	TERT (NM_198253)  rearrangement: t(4;5)(p13;p15.33)(chr4:g.44149829::chr5:g.1295406)	PRECISE	Note: The TERT rearrangement involves the truncation of the promoter. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	8	5	Promoter of TERT(-):42Kb from tx start	TERT	1295406			4	IGR: 26Kb before KCTD8(-)	KCTD8	44149829			10	TRANSLOCATION		0	213326	0	8	NEW_VARIANT
P-0027251-T01-IM6	NKX2-1 (NM_001079668) rearrangement: c.464-11:NKX2-1_chr14:g.37047558del	PRECISE	Note: The NKX2-1 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {NKX2-8:NKX2-1}		5819	0	135	14	Intron of NKX2-1(-):11bp before exon 3	NKX2-1	36987236			14	Promoter of NKX2-8(-):2Kb from tx start	NKX2-8	37047558			10	DELETION		60322	213058	2976	181	NEW_VARIANT
P-0027352-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.-48-1846_c.336del	PRECISE	Note: The CTNNB1 rearrangement is an intragenic deletion which involves CTNNB1 5-UTR region and exon 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2765	0	37	3	5-UTR of CTNNB1(+):2Kb before coding start	CTNNB1	41263666			3	Exon 4 of CTNNB1(+)	CTNNB1	41266539			10	DELETION		2873	213409	3012	40	NEW_VARIANT
P-0027353-T01-IM6	MUTYH (NM_001128425) rearrangement: c.342:MUTYH_g.144950020del	PRECISE	Note: The MUTYH - NBPF20 rearrangement results in the deletion of MUTYH exon 1-3.	MANUAL_OK	3to5	3to5	-		278825	0	9	1	Exon 3 of MUTYH(-)	MUTYH	45799091			1	Intron of NBPF20(+):125Kb after exon 53	NBPF20	144950020			10	DELETION		99150929	213415	460192	26	NEW_VARIANT
P-0027216-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-1525_c.839-18del	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		36987	0	25	21	Intron of TMPRSS2(-):18bp before exon 9	TMPRSS2	42845441			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871641			10	INVERSION		26200	213463	25871	35	NEW_VARIANT
P-0027226-T01-IM6	SPEN (NM_015001) rearrangement: c.5202:SPEN_chr1:g.16148632del	PRECISE	Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	-		33876	0	7	1	IGR: 12Kb before FLJ37453(-)	FLJ37453	16148632			1	Exon 11 of SPEN(+)	SPEN	16257937			10	DELETION		109305	213459	57592	7	NEW_VARIANT
P-0027391-T01-IM6	AXL (NM_021913) rearrangement: t(10;19)(q11.22;q13.2)(chr10:g.48490590::chr19:g.41762374)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	5	19	Exon 18 of AXL(+)	AXL	41762374			10	IGR: 65Kb before GDF10(-)	GDF10	48490590			10	TRANSLOCATION		0	213501	0	6	NEW_VARIANT
P-0027395-T01-IM6	SESN2 (NM_031459) rearrangement: chr1:g.23343226_c.651dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		69448	0	39	1	Promoter of C1orf234(-):6Kb from tx start	C1orf234	23343226			1	Exon 5 of SESN2(+)	SESN2	28599205			10	DUPLICATION		5255979	213503	109175	40	NEW_VARIANT
P-0027075-T01-IM6	FGFR3 (NM_000142) rearrangement:  chr4:g.1504892_c.1204:FGFR3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		15446	0	50	4	IGR: 108Kb before NKX1-1(-)	NKX1-1	1504892			4	Exon 9 of FGFR3(+)	FGFR3	1806185			10	DUPLICATION		301293	212728	11721	49	NEW_VARIANT
P-0027453-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q22.1;q22.3)(chr18:g.62539742::chr21:g.42860348)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	45	21	Exon 5 of TMPRSS2(-)	TMPRSS2	42860348			18	IGR: 659Kb before LINC01538(-)	LINC01538	62539742			10	TRANSLOCATION		0	213640	0	62	NEW_VARIANT
P-0027453-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-2167:TMPRSS2_c.39+56989:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		68499	0	46	21	Intron of ERG(-):57Kb after exon 3	ERG	39890597			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872283			10	DELETION		2981686	213639	70733	96	NEW_VARIANT
P-0027454-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(14;21)(q11.2;q22.3)(chr14:g.23791333::chr21:g.42869346)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	21	Intron of TMPRSS2(-):699bp after exon 2	TMPRSS2	42869346			14	Intron of PABPN1(+):56bp before exon 2	PABPN1	23791333			10	TRANSLOCATION		0	213644	0	7	NEW_VARIANT
P-0027454-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		27075	0	21	21	Intron of ERG(-):9Kb after exon 1	ERG	39861313			21	Intron of TMPRSS2(-):707bp after exon 2	TMPRSS2	42869338			10	DELETION		3008025	213643	46169	23	NEW_VARIANT
P-0027489-T01-IM6	LATS2 (NM_014572) rearrangement: c.1052_c.342+5100del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6325	0	73	13	Exon 4 of LATS2(-)	LATS2	21562867			13	Intron of LATS2(-):5Kb after exon 2	LATS2	21614724			10	DELETION		51857	213725	3852	79	NEW_VARIANT
P-0024546-T01-IM6	MYOD1 (NM_002478): c.64:MYOD1_chr11:g.17737403del	PRECISE	Note: The MYOD1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1259	0	64	11	IGR: 4Kb before MYOD1(+)	MYOD1	17737403			11	Exon 1 of MYOD1(+)	MYOD1	17741393			10	DELETION		3990	200673	435	66	NEW_VARIANT
P-0025688-T01-IM6	ARID1A (NM_006015) - SGK1 (NM_001143676) rearrangement: t(1;6)(p36.11;q23.2)(chr1:g.1:27106417::chr6:g.134562414)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARID1A:SGK1}		0	0	10	6	Intron of SGK1(-):21Kb after exon 2	SGK1	134562414			1	Exon 20 of ARID1A(+)	ARID1A	27106417			10	TRANSLOCATION		0	206458	0	10	NEW_VARIANT
P-0027386-T01-IM6	CDKN2Ap14ARF (NM_058195.3) rearrangement: c.*90_c.194-2311del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		48	9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21970912			9	Intron of CDKN2Ap14ARF(-):2kb before exon 2	CDKN2Ap14ARF	21973518			10	DELETION		2606	213962	1062		NEW_VARIANT
P-0027386-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.446_c.150+1159del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		48	9	Exon 2 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21970912			9	1159bp after exon 1 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21973518			10	DELETION		2606	213961	1062		NEW_VARIANT
P-0027448-T01-IM6	ARHGAP39 (NM_025251) - RECQL4 (NM_004260) rearrangement: c.596+183:ARHGAP39_c.3173:RECQL4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ARHGAP39:RECQL4}		36606	0	6	8	Exon 19 of RECQL4(-)	RECQL4	145737590			8	Intron of ARHGAP39(-):182bp after exon 5	ARHGAP39	145780761			10	DELETION		43171	213645	65039	6	NEW_VARIANT
P-0027417-T01-IM6	KCNMA1 (NM_001161352) -  RET (NM_020975) rearrangement: c.378+15627:KCNMA1_c.1649-143:RET	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {KCNMA1:RET}		142743	0	44	10	Intron of RET(+):142bp before exon 9	RET	43608158			10	Intron of KCNMA1(-):16Kb after exon 1	KCNMA1	79381396			10	INVERSION		35773238	214010	280705	68	NEW_VARIANT
P-0027526-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a non-canonical fusion predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29538	0	39	21	Intron of ERG(-):61Kb before exon 4	ERG	39878354			21	Intron of TMPRSS2(-):293bp after exon 2	TMPRSS2	42869752			10	DELETION		2991398	214057	39533	41	NEW_VARIANT
P-0027530-T01-IM6	KDR  (NM_002253) rearrangement: c.1646-34:KDR_chr4:g.57171503del.	PRECISE	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.	MANUAL_OK	3to5	3to5	-		13789	0	6	4	Intron of KDR(-):34bp before exon 13	KDR	55971185			4	Intron of KIAA1211(+):2Kb before exon 5	KIAA1211	57171503			10	DELETION		1200318	214047	32209	6	NEW_VARIANT
P-0027542-T01-IM6	ARID1A (NM_006015) rearrangement: c.1137+13751_c.3797dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		19992	0	12	1	Intron of ARID1A(+):14Kb after exon 1	ARID1A	27037782			1	Exon 15 of ARID1A(+)	ARID1A	27099918			10	DUPLICATION		62136	213893	11646	12	NEW_VARIANT
P-0027542-T01-IM6	SLC17A3 (NM_001098486) - HIST1H1C (NM_005319) rearrangement: c.92-15:SLC17A3_c.510:HIST1H1Cdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC17A3:HIST1H1C}		8125	0	12	6	Intron of SLC17A3(-):15bp before exon 3	SLC17A3	25862687			6	Exon 1 of HIST1H1C(-)	HIST1H1C	26056147			10	DUPLICATION		193460	213894	10602	12	NEW_VARIANT
P-0027548-T01-IM6	CIC (NM_015125) rearrangement: c.1465-115_c.2152inv	IMPPRECISE	Note: The CIC rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4382	0	6	19	Intron of CIC(+):114bp before exon 10	CIC	42794270			19	Exon 10 of CIC(+)	CIC	42795072			0	INVERSION		802	213880	3258	7	NEW_VARIANT
P-0027548-T01-IM6	HIST1H3E (NM_003532) rearrangement: c.275:HIST1H3E_chr6:g.26132417del	PRECISE	Note: The HIST1H3E rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		8498	0	8	6	IGR: 8Kb before HIST1H2AC(+)	HIST1H2AC	26132417			6	Exon 1 of HIST1H3E(+)	HIST1H3E	26225657			7	DELETION		93240	213840	6818	9	NEW_VARIANT
P-0027553-T01-IM6	KCNK3 (NM_002246) - CENPA (NM_001809) rearrangement: c.283+1043:KCNK3_c.101-62:CENPA	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KCNK3:CENPA}		572	0	4	2	Intron of KCNK3(+):1Kb after exon 1	KCNK3	26917069			2	Intron of CENPA(+):61bp before exon 2	CENPA	27014937			7	DELETION		97868	213895	714	4	NEW_VARIANT
P-0027627-T01-IM6	BAP1(NM_004656) rearrangement: c.604:BAP1_chr3:g.52495299del	PRECISE	Note: The BAP1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	-		8693	0	5	3	Exon 8 of BAP1(-)	BAP1	52440900			3	Intron of NISCH(+):2Kb after exon 3	NISCH	52495299			10	DELETION		54399	214180	6048	5	NEW_VARIANT
P-0027630-T01-IM6	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)	PRECISE	Note: The SDC4 - ROS1 fusion is predicted to be in-frame and includes ROS1 kinase domain.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	16	20	Intron of SDC4(-):720bp before exon 3	SDC4	43962429			6	Intron of ROS1(-):1Kb before exon 32	ROS1	117651891			10	TRANSLOCATION		0	214176	0	36	NEW_VARIANT
P-0027590-T01-IM6	ERCC2 (NM_000400) - EXOC3L2 (NM_138568) rearrangement: c.1581:ERCC2_c.540+265: EXOC3L2 del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ERCC2:EXOC3L2}		9382	0	16	19	Intron of EXOC3L2(-):264bp after exon 6	EXOC3L2	45727771			19	Exon 17 of ERCC2(-)	ERCC2	45858072			10	DELETION		130301	214167	11966	16	NEW_VARIANT
P-0027597-T01-IM6	ASXL1 (NM_015338) rearrangement: c.1719+44:ASXL1_chr20:g.42888843inv	PRECISE	Note: The ASXL1 rearrangement is an inversion of ASXL1 intron 11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		154767	0	49	20	Intron of ASXL1(+):44bp after exon 11	ASXL1	31021764			20	Intron of GDAP1L1(+):2Kb after exon 3	GDAP1L1	42888843			10	INVERSION		11867079	214131	344961	49	NEW_VARIANT
P-0027609-T01-IM6	NCOA3 (NM_181659) rearrangement: c.2707+33_c.3253-806inv	PRECISE	Note: The NCOA3 rearrangement results in the inversion of intron 14 to intron 17. Its functional significance is undetermined,	MANUAL_OK	3to3	3to3	Antisense Fusion		4200	0	11	20	Intron of NCOA3(+):33bp after exon 14	NCOA3	46267979			20	Intron of NCOA3(+):805bp before exon 18	NCOA3	46275011			10	INVERSION		7032	214129	9009	11	NEW_VARIANT
P-0027623-T01-IM6	FGFR2 (NM_000141) rearrangement: t(3;10)(q21.1;q26.13)(chr3:g.123525612::chr10:g.123240959)	PRECISE	Note: The FGFR2 rearrangement is translocation with a breakpoint in intron 17. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Transcript Fusion {FGFR2:MYLK}		0	0	56	10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240959			3	5-UTR of MYLK(-):193Kb before coding start	MYLK	123525612			10	TRANSLOCATION		0	214191	0	61	NEW_VARIANT
P-0027635-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		34946	0	19	21	Intron of ERG(-):18Kb before exon 2	ERG	39835414			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867959			10	DELETION		3032545	214219	29205	20	NEW_VARIANT
P-0027411-T01-IM6	ROS1 (NM_002944) rearrangement: c.6800:ROS1_chr6:g.117287744inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1864	0	4	6	IGR: 89Kb before RFX6(+)	RFX6	117287744			6	Exon 43 of ROS1(-)	ROS1	117609899			10	INVERSION		322155	214007	2083	5	NEW_VARIANT
P-0027414-T01-IM6	GATA1 (NM_002049) rearrangement: c.420_c.818inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		2278	0	65	X	Exon 3 of GATA1(+)	GATA1	48650450			X	Exon 5 of GATA1(+)	GATA1	48651652			10	INVERSION		1202	214017	2878	79	NEW_VARIANT
P-0027593-T01-IM6	PTEN (NM_000314) rearrangement: c.461_c.492+1310del	PRECISE	Note: The PTEN rearrangement results in the deletion of exon 5. One of the breakpoints is within exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		616	0	3	10	Exon 5 of PTEN(+)	PTEN	89692977			10	Intron of PTEN(+):1Kb after exon 5	PTEN	89694318			10	DELETION		1341	214166	277	4	NEW_VARIANT
P-0027606-T01-IM6	ETV6 (NM_001987) rearrangement: c.163+4431_c.464-6577dup.	PRECISE	Note: The ETV6 rearrangement results in the in frame duplication of intron 2 to intron 4. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		62245	0	19	12	Intron of ETV6(+):4Kb after exon 2	ETV6	11909944			12	Intron of ETV6(+):7Kb before exon 5	ETV6	12015781			10	DUPLICATION		105837	214118	79150	19	NEW_VARIANT
P-0027645-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	-		18275	0	12	21	3-UTR of ERG(-):83Kb after coding stop	ERG	39950793			21	Intron of TMPRSS2(-):75bp before exon 3	TMPRSS2	42866580			10	DELETION		2915787	214284	20000	12	NEW_VARIANT
P-0027645-T01-IM6	SHQ1 (NM_018130) rearrangement: c.1182-10735_c.1573inv	PRECISE	Note: The SHQ1 rearrangement results in the inversion of exon 11. One breakpoint is in exon 11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2173	0	27	3	Exon 11 of SHQ1(-)	SHQ1	72799596			3	Intron of SHQ1(-):11Kb before exon 11	SHQ1	72810722			10	INVERSION		11126	214285	2300	26	NEW_VARIANT
P-0027657-T01-IM6	DICER1 (NM_030621) rearrangement: c.4511_chr14:g.58473233inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		54020	0	13	14	Intron of C14orf37(-):1Kb before exon 7	C14orf37	58473233			14	Exon 25 of DICER1(-)	DICER1	95562746			10	INVERSION		37089513	214241	83968	13	NEW_VARIANT
P-0027661-T01-IM6	RNF43 (NM_017763) rearrangement: c.952+96_c.376-534dup	PRECISE	Note: The RNF43 rearrangement results in the duplication of exons 4-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : out of frame		7464	0	35	17	Intron of RNF43(-):95bp after exon 8	RNF43	56437414			17	Intron of RNF43(-):534bp before exon 4	RNF43	56441495			10	DUPLICATION		4081	214229	14422	37	NEW_VARIANT
P-0027664-T01-IM6	FOXL2 (NM_023067) rearrangement: c.1012_c.-84inv	PRECISE	Note: The FOXL2 rearrangement results in the inversion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4304	0	2	3	Exon 1 of FOXL2(-)	FOXL2	138664553			3	5-UTR of FOXL2(-):1Kb before coding start	FOXL2	138665648			7	INVERSION		1095	214244	10676	1	NEW_VARIANT
P-0027685-T01-IM6	RAB5C (NM_001252039) - ALK (NM_004304) fusion: t(2;17)(p23.2;q21.2)(chr2:g.29447944::chr17:g.40279299)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	49	17	Intron of RAB5C(-):433bp before exon 5	RAB5C	40279299			2	Intron of ALK(-):382bp after exon 19	ALK	29447944			10	TRANSLOCATION		0	214380	0	49	NEW_VARIANT
P-0022593-T02-IM6	MSH3 (NM_002439) - TSTA3 (NM_003313) rearrangement: t(5;8)(q14.1;q24.3)(chr5:g.79966005::chr8:g.144698059)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MSH3:TSTA3}		0	0	14	8	Intron of TSTA3(-):216bp after exon 3	TSTA3	144698059			5	Exon 4 of MSH3(+)	MSH3	79966005			0	TRANSLOCATION		0	214431	0	14	NEW_VARIANT
P-0027741-T01-IM6	FGFR2 (NM_000141) rearrangement: t(10;19)(q26.13;q13.2)(chr10:g.123241990::chr19:g.42175729)	PRECISE	Note: The FGFR2 rearrangement is a translocation with a breakpoint in FGFR2 intron 17. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Transcript Fusion {FGFR2:CEACAM7}		0	0	31	19	Promoter of CEACAM7(-):2Kb from tx start	CEACAM7	42175729			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241990			10	TRANSLOCATION		0	214633	0	32	NEW_VARIANT
P-0027741-T01-IM6	ERCC2 (NM_000400) rearrangement: c.1378-33:ERCC2_chr19:g.58327100inv	PRECISE	Note: The ERCC2 rearrangement is an inversion of exons 1-14. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		92963	0	71	19	Intron of ERCC2(-):33bp before exon 15	ERCC2	45860662			19	Promoter of ZNF552(-):9Kb from tx start	ZNF552	58327100			10	INVERSION		12466438	214632	78270	73	NEW_VARIANT
P-0026777-T02-IM6	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	PRECISE	Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		54380	0	41	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32313518			10	Intron of RET(+):533bp after exon 11	RET	43610717			10	INVERSION		11297199	214414	86100	60	NEW_VARIANT
P-0027722-T01-IM6	AR (NM_000044) rearrangement: c.2174-1943_c.2608-51del	PRECISE	Note: The AR rearrangement results in the deletion of exons 5-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		2376	0	64	X	Intron of AR(+):2Kb before exon 5	AR	66935377			X	Intron of AR(+):50bp before exon 8	AR	66943477			10	DELETION		8100	214609	270	66	NEW_VARIANT
P-0027723-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion (KIF5B exons 1-15 fused to RET exons 11-20):c.1725+966:KIF5B_c.2123:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KIF5B:RET}		36970	0	23	10	Intron of KIF5B(-):965bp after exon 15	KIF5B	32316390			10	Exon 11 of RET(+)	RET	43610171			10	INVERSION		11293781	214612	56350	27	NEW_VARIANT
P-0027731-T01-IM6	CDH1 (NM_004360) rearrangement: c.1433:CDH1_chr16:g.68971469inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		8265	0	17	16	Exon 10 of CDH1(+)	CDH1	68849530			16	Intron of TANGO6(+):7Kb after exon 14	TANGO6	68971469			10	INVERSION		121939	214625	10984	19	NEW_VARIANT
P-0027754-T02-IM6	CSDE1 (NM_001242891) rearrangement: c.1188+1_c.1190del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		797	0	5	1	Exon 12 of CSDE1(-)	CSDE1	115273268			1	Exon 11 of CSDE1(-)	CSDE1	115275224			10	DELETION		1956	215095	738	5	NEW_VARIANT
P-0027759-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2302-919:FGFR2_chr10:g.133670877inv	PRECISE	Note: The FGFR2 rearrangement is an inversion with a breakpoint in intron 17. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		57976	0	146	10	Intron of FGFR2(-):919bp before exon 18	FGFR2	123240454			10	IGR: 66Kb before LINC01164(-)	LINC01164	133670877			10	INVERSION		10430423	214667	201178	180	NEW_VARIANT
P-0027764-T01-IM6	RET (NM_020975) rearrangement: t(10;12)(q11.21;p12.2)(chr10:g.43611187::chr12:g.21413909)	PRECISE	Note: The RET rearrangement is a translocation involving exon 12. This involves the kinase domain of RET. Its functional significance is undetermined	MANUAL_OK	3to5	3to5	-		0	0	33	12	IGR: 4Kb before SLCO1A2(-)	SLCO1A2	21413909			10	Intron of RET(+):844bp before exon 12	RET	43611187			10	TRANSLOCATION		0	214701	0	33	NEW_VARIANT
P-0027811-T01-IM6	MTOR (NM_004958) rearrangement: c.3399-24:MTOR_chr1:g.42333975inv	PRECISE	Note: The MTOR rearrangement results in the inversion of exons 1-22. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		317774	0	14	1	Intron of MTOR(-):24bp before exon 23	MTOR	11272555			1	3-UTR of HIVEP3(-):168Kb after coding stop	HIVEP3	42333975			10	INVERSION		31061420	215039	455290	13	NEW_VARIANT
P-0027811-T01-IM6	ARID5B (NM_032199) rearrangement: c.3560:ARID5B_chr10:g.463862183inv	PRECISE	Note: The ARID5B rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		221	0	3	10	Exon 10 of ARID5B(+)	ARID5B	63852782			10	IGR: 53Kb before ARID5B(+)	ARID5B	63862183			7	INVERSION		9401	215040	291	3	NEW_VARIANT
P-0027831-T01-IM6	MAP3K14 (NM_003954) rearrangement: t(12;17)(q14.1;q21.31)(chr12:g.58127459::chr17:g.43362279)	PRECISE	Note: The MAP3K14 rearrangement is a translocation with a breakpoint within exon 6. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	68	17	Exon 6 of MAP3K14(-)	MAP3K14	43362279			12	Intron of AGAP2(-):349bp after exon 5	AGAP2	58127459			10	TRANSLOCATION		0	215090	0	68	NEW_VARIANT
P-0027853-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		90814	0	139	2	Intron of ALK(-):592bp after exon 19	ALK	29447734			2	Intron of EML4(+):156bp before exon 20	EML4	42553137			10	INVERSION		13105403	215181	137721	138	NEW_VARIANT
P-0027991-T01-IM6	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	PRECISE	Note: The KIF5B-RET fusion is an in-frame fusion and includes the protein kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		44166	0	60	10	Intron of KIF5B(-):248bp before exon 25	KIF5B	32304835			10	Intron of RET(+):99bp before exon 9	RET	43608201			10	INVERSION		11303366	215559	60686	68	NEW_VARIANT
P-0004918-T02-IM6	RGS7 (NM_002924) - FH (NM_000143) rearrangement: c.79-95591:RGS7_c.1109-139:FHdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RGS7:FH}		5053	0	24	1	Intron of RGS7(-):96Kb before exon 3	RGS7	241357653			1	Intron of FH(-):139bp before exon 8	FH	241666009			10	DUPLICATION		308356	215244	10354	26	NEW_VARIANT
P-0004918-T02-IM6	STAT3 (NM_139276) rearrangement: t(14;17)(q21.2;q21.2)(chr14:g.44234319::chr17:g.40469176)	PRECISE	Note: The STAT3 rearrangement is a translocation with a breakpoint in exon 22. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	14	17	Intron of STAT3(-):23bp after exon 22	STAT3	40469176			14	IGR: 739Kb before FSCB(-)	FSCB	44234319			10	TRANSLOCATION		0	215250	0	13	NEW_VARIANT
P-0004918-T02-IM6	SOX9 (NM_000346) rearrangement: c.1234:SOX9_chr17:g.78453502inv	PRECISE	Note: The SOX9 rearrangement is an inversion with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		25079	0	187	17	Exon 3 of SOX9(+)	SOX9	70120232			17	IGR: 13Kb before NPTX1(-)	NPTX1	78453502			10	INVERSION		8333270	215248	41680	285	NEW_VARIANT
P-0027540-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.*102-661_c.193+6485del	PRECISE	Note: The CDKN2Ap14ARF rearrangement results in the deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0		15	9	Intron of CDKN2Ap14ARF(-):661bp before exon 3	CDKN2Ap14ARF	21968902			9	Intron of CDKN2Ap14ARF(-):6Kb after exon 1	CDKN2Ap14ARF	21987653			10	DELETION		18751	214350	4219		NEW_VARIANT
P-0027540-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-661_chr9:g.21987653del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exons 1 to 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0		15	9	Intron of CDKN2Ap16INK4A(-):661bp before exon 3	CDKN2Ap16INK4A	21968902			9	IGR: 19Kb before CDKN2Ap16INK4A	CDKN2Ap16INK4A	21987653			10	DELETION		18751	214349	4219		NEW_VARIANT
P-0027757-T01-IM6	SYK (NM_003177) rearrangement: c.578_c.579del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		472	0	3	9	Exon 3 of SYK(+)	SYK	93607876			9	Exon 4 of SYK(+)	SYK	93624488			10	DELETION		16612	214658	471	3	NEW_VARIANT
P-0027874-T01-IM6	ERBB3 (NM_001982) rearrangement: t(10;12)(q22.3;q13.2)(chr10:g.79794131::chr12:g.56494017)	PRECISE	Note: The ERBB3 rearrangement is a translocation involving a breakpoint in exon 26. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	214	12	Exon 26 of ERBB3(+)	ERBB3	56494017			10	Intron of RPS24(+):469bp after exon 1	RPS24	79794131			10	TRANSLOCATION		0	215214	0	214	NEW_VARIANT
P-0027879-T01-IM6	ROS1 (NM_002944) - c.5778-469:ROS1_chr6:g.47344251del	PRECISE	Note: The ROS1 rearrangement is a deletion of exons 36-43. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		142972	0	66	6	IGR: 101Kb before CD2AP(+)	CD2AP	47344251			6	Intron of ROS1(-):469bp before exon 36	ROS1	117641662			10	DELETION		70297411	215202	245705	72	NEW_VARIANT
P-0027889-T01-IM6	ETV6:NM_001987) - APOLD1 (NM_001130415) rearrangement: c.1010-6957:ETV6_c.96+30120:APOLD1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ETV6:APOLD1}		70692	0	9	12	Intron of ETV6(+):7Kb before exon 6	ETV6	12030422			12	Intron of APOLD1(+):30Kb after exon 1	APOLD1	12909150			10	DELETION		878728	215241	89103	10	NEW_VARIANT
P-0027889-T01-IM6	STK11 (NM_000455) rearragement: c.269:STK11_chr19:g.1205538del	PRECISE	Note: The STK11 rearrangement is a deletion with breakpoints in the promoter region and exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2582	0	10	19	Promoter of STK11(+):259bp from tx start	STK11	1205538			19	Exon 1 of STK11(+)	STK11	1207181			10	DELETION		1643	215242	3186	11	NEW_VARIANT
P-0027892-T01-IM6	NSD1 (NM_022455) rearrangment: c.1515_c.3796+4024del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16493	0	18	5	Exon 5 of NSD1(+)	NSD1	176636915			5	Intron of NSD1(+):4Kb after exon 5	NSD1	176643220			10	DELETION		6305	215254	8645	22	NEW_VARIANT
P-0027939-T01-IM6	RNF43 (NM_017763) rearrangement: c.849+65_c.376-68dup	PRECISE	Note: The RNF43 rearrangement results in the duplication of exons 4-7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		5987	0	31	17	Intron of RNF43(-):64bp after exon 7	RNF43	56438079			17	Intron of RNF43(-):68bp before exon 4	RNF43	56441029			10	DUPLICATION		2950	215366	9864	31	NEW_VARIANT
P-0027953-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+20901:CCDC6_c.2137-754:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		28642	0	57	10	Intron of RET(+):753bp before exon 12	RET	43611278			10	Intron of CCDC6(-):21Kb after exon 1	CCDC6	61644979			10	INVERSION		18033701	215399	43394	70	NEW_VARIANT
P-0027989-T01-IM6	ROS1 (NM_002944) rearrangement: t(6;18)(q22.1;q21.1)(chr6:g.117643946::chr18:g.18:46871756)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	5	18	Intron of DYM(-):12Kb before exon 7	DYM	46871756			6	Intron of ROS1(-):1Kb before exon 35	ROS1	117643946			8	TRANSLOCATION		0	215468	0	5	NEW_VARIANT
P-0027995-T01-IM6	ARID1B (NM_020732) rearrangement: c.2961+826:ARID1B_chr6:g.157787825del	PRECISE	Note: The ARID1B rearrangement results in the deletion of ARID1B exons 1-11. One of the breakpoints is within the ARID1B intron 11.	MANUAL_OK	3to5	3to5	-		26481	0	16	6	Intron of ARID1B(+):826bp after exon 11	ARID1B	157496077			6	IGR: 15Kb before ZDHHC14(+)	ZDHHC14	157787825			10	DELETION		291748	215565	25504	17	NEW_VARIANT
P-0027995-T01-IM6	KDM5C (NM_004187) - AMER1 (NM_152424) rearrangement: c.1746+1883:KDM5C_c.1896:AMER1inv.	PRECISE	Note: The KDM5C - AMER1 rearrangement results in the inversion of KDM5C exons 1-12 and AMER1 exon 2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		35478	0	15	X	Intron of KDM5C(-):2Kb after exon 12	KDM5C	53237713			X	Exon 2 of AMER1(-)	AMER1	63411271			10	INVERSION		10173558	215567	43013	26	NEW_VARIANT
P-0028009-T01-IM6	NTHL1 (NM_002528) - ZNF598 (NM_178167) rearrangement: c.275:NTHL1_c.338-17:ZNF598dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		9764	0	60	16	Intron of ZNF598(-):17bp before exon 5	ZNF598	2053138			16	Promoter of TSC2(+):2Kb from tx start	TSC2	2096232			10	DUPLICATION		43094	215579	10321	65	NEW_VARIANT
P-0028009-T01-IM6	AMER1 (NM_152424) - ASB12 (NM_130388) rearrangement: c.31:AMER1_c.-25+170:ASB12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {AMER1:ASB12}		5566	0	18	X	Exon 2 of AMER1(-)	AMER1	63413136			X	5-UTR of ASB12(-):6Kb before coding start	ASB12	63450173			10	DUPLICATION		37037	215580	5133	18	NEW_VARIANT
P-0009301-T02-IM6	FLCN (NM_144997) rearrangement: t(4;17)(p14;p11.2)(chr4:g.39589422::chr17:g.17120488)	PRECISE	Note: The FLCN rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	12	17	Exon 10 of FLCN(-)	FLCN	17120488			4	Intron of SMIM14(-):15Kb before exon 3	SMIM14	39589422			10	TRANSLOCATION		0	215391	0	15	NEW_VARIANT
P-0009301-T02-IM6	MSH6 (NM_000179) rearrangement: c.1202:MSH6_chr2:g.13175938inv	PRECISE	Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		319629	0	24	2	IGR: 69Kb before LOC100506474(-)	LOC100506474	13175938			2	Exon 4 of MSH6(+)	MSH6	48026324			10	INVERSION		34850386	215389	420671	29	NEW_VARIANT
P-0009301-T02-IM6	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	PRECISE	Note: The EML4- ALK fusion is predicted to be in-frame and includes the kinase domain.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		117847	0	45	2	Intron of ALK(-):257bp before exon 20	ALK	29446651			2	Intron of EML4(+):7Kb before exon 6	EML4	42501297			10	INVERSION		13054646	215390	156231	44	NEW_VARIANT
P-0017214-T02-IM6	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	PRECISE	Note: The KIF5B-RET fusion is predicted to be in-frame and includes the protein kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		44566	0	20	10	Intron of KIF5B(-):27bp before exon 24	KIF5B	32306314			10	Intron of RET(+):463bp after exon 11	RET	43610647			10	INVERSION		11304333	215654	80221	23	NEW_VARIANT
P-0017214-T02-IM6	TSC2 (NM_000548): c.4662+217_c.4850-100del	IMPPRECISE	Note: The TSC2 rearrangement is an intragenic deletion of exon 37.	MANUAL_OK	3to3	3to3	Antisense Fusion		1670	0	4	16	Intron of TSC2(+):217bp after exon 36	TSC2	2135540			16	Intron of TSC2(+):99bp before exon 38	TSC2	2136633			0	INVERSION		1093	215656	3132	4	NEW_VARIANT
P-0027307-T02-IM6	PARK2 (NM_004562) rearrangement: c.413-22549_c.413del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion breakpoints in exon 4 and intron 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		251	0	39	6	Exon 4 of PARK2(-)	PARK2	162622284			6	Intron of PARK2(-):23Kb before exon 4	PARK2	162644833			10	DELETION		22549	215641	317	41	NEW_VARIANT
P-0027762-T01-IM6	ZC3HAV1 (NM_020119) - BRAF (NM_004333) rearrangement: c.698-431:ZC3HAV1_c.1177+1402:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ZC3HAV1:BRAF}		29528	0	4	7	Intron of ZC3HAV1(-):431bp before exon 4	ZC3HAV1	138765420			7	Intron of BRAF(-):1Kb after exon 9	BRAF	140485946			5	DUPLICATION		1720526	214696	58413	4	NEW_VARIANT
P-0027823-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+490:TMPRSS2_chr21:g.40053392del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exons 3-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		35900	0	70	21	IGR: 57Kb before LINC00114(-)	LINC00114	40053392			21	Intron of TMPRSS2(-):489bp after exon 2	TMPRSS2	42869556			10	DELETION		2816164	215142	47376	79	NEW_VARIANT
P-0028037-T01-IM6	DOT1L (NM_032482) rearrangement: c.-31:DOT1L_chr19:g.2103210del	PRECISE	Note: The DOT1L rearrangement is a deletion with a breakpoint in the 5UTR of DOT1L. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		116	0	82	19	Intron of AP3D1(-):943bp before exon 30	AP3D1	2103210			19	5-UTR of DOT1L(+):30bp before coding start	DOT1L	2164153			10	DELETION		60943	215643	165	95	NEW_VARIANT
P-0028038-T01-IM6	RAB37 (NM_175738) - EZH1 (NM_001991) rearrangement: c.73-9053:RAB37_c.488-70:EZH1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RAB37:EZH1}		250418	0	7	17	Intron of EZH1(-):70bp before exon 7	EZH1	40872537			17	Intron of RAB37(+):9Kb before exon 2	RAB37	72716342			10	INVERSION		31843805	215644	407829	7	NEW_VARIANT
P-0028118-T01-IM6	MDC1 (NM_014641) rearrangement: c.416:MDC1_chr6:g.58454054inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		221677	0	21	6	Exon 3 of MDC1(-)	MDC1	30681681			6	IGR: 182Kb before GUSBP4(-)	GUSBP4	58454054			10	INVERSION		27772373	216138	401696	39	NEW_VARIANT
P-0021332-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.-48-1976_c.272del	PRECISE	Note: The CTNNB1 rearrangement is a deletion of exons 1-4. One of the breakpoints is within exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3328	0	3	3	5-UTR of CTNNB1(+):2Kb before coding start	CTNNB1	41263536			3	Exon 4 of CTNNB1(+)	CTNNB1	41266475			10	DELETION		2939	186869	2067	3	NEW_VARIANT
P-0022192-T01-IM6	LRP1 (NM_002332) - NAB2 (NM_005967) rearrangement: c.842-2141:LRP1_c.1092-146:NAB2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {LRP1:NAB2}		18980	0	8	12	Intron of NAB2(+):145bp before exon 4	NAB2	57486554			12	Intron of LRP1(+):2Kb before exon 7	LRP1	57545850			10	DUPLICATION		59296	189947	24612	8	NEW_VARIANT
P-0027091-T01-IM6	TET1 (NM_030625) rearrangement: c.5405-202_c.5874del	PRECISE	Note: The TET1 rearrangement is an intragenic deletion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2243	0	16	10	Intron of TET1(+):201bp before exon 12	TET1	70450363			10	Exon 12 of TET1(+)	TET1	70451034			10	DELETION		671	212768	2580	20	NEW_VARIANT
P-0027275-T03-IM6	AMER1 (NM_152424) rearrangement: c.1674:AMER1_chrX:g.65018297inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		18422	0	63	X	Exon 2 of AMER1(-)	AMER1	63411493			X	IGR: 131Kb before MSN(+)	MSN	65018297			10	INVERSION		1606804	216192	18408	62	NEW_VARIANT
P-0027643-T01-IM6	ETV6 (NM_001987) rearrangement: c.329-4344_c.463+7835del	PRECISE	Note: The ETV6 rearrangement results in intragenic deletion of exons 4.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		47407	0	57	12	Intron of ETV6(+):4Kb before exon 4	ETV6	12002017			12	Intron of ETV6(+):8Kb after exon 4	ETV6	12014330			10	DELETION		12313	214256	24819	63	NEW_VARIANT
P-0027647-T01-IM6	APC (NM_000038) rearrangement: c.135+1377_c.6760del	PRECISE	Note: The APC rearrangement results in the deletion of exons 13-16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		24067	0	10	5	Intron of APC(+):1Kb after exon 2	APC	112092099			5	Exon 16 of APC(+)	APC	112178051			10	DELETION		85952	214286	21529	11	NEW_VARIANT
P-0027658-T01-IM6	TP53 (NM_000546) rearrangement: c.143_chr17:g.7581086del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3597	0	49	17	Exon 4 of TP53(-)	TP53	7579544			17	5-UTR of TP53(-):8Kb before coding start	TP53	7581086			10	DELETION		1542	214236	2694	54	NEW_VARIANT
P-0027658-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.*1996_c.5584inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	-		12944	0	25	19	Promoter of NOTCH3(-):966bp from tx start	NOTCH3	15269477			19	Exon 30 of NOTCH3(-)	NOTCH3	15276681			0	INVERSION		7204	214238	20489	24	NEW_VARIANT
P-0028143-T01-IM6	FAM204A (NM_001134672) - TCF7L2 (NM_001146274) rearrangement: c.544-4180:FAM204A_c.1230:TCF7L2	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FAM204A:TCF7L2}		15207	0	45	10	Exon 11 of TCF7L2(+)	TCF7L2	114912160			10	Intron of FAM204A(-):4Kb before exon 7	FAM204A	120075005			10	INVERSION		5162845	216190	21253	50	NEW_VARIANT
P-0028149-T01-IM6	ETV6 (NM_001987) rearrangement: c.163+35894_c.464-6807del	PRECISE	Note: The ETV6 rearrangement results in the in-frame deletion of exons 3-4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		57903	0	32	12	Intron of ETV6(+):36Kb after exon 2	ETV6	11941407			12	Intron of ETV6(+):7Kb before exon 5	ETV6	12015551			10	DELETION		74144	216185	41994	32	NEW_VARIANT
P-0028149-T01-IM6	GRIN2A (NM_001134407) rearrangement: c.4337_c.1007+20851inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		22161	0	5	16	Exon 13 of GRIN2A(-)	GRIN2A	9857064			16	Intron of GRIN2A(-):21Kb after exon 3	GRIN2A	10010965			10	INVERSION		153901	216188	24594	5	NEW_VARIANT
P-0028149-T01-IM6	PREX2 (NM_024870) rearrangement: c.4087+3328_c.4125inv	PRECISE	Note: The PREX2 rearrangement results in the inversion of exon 34. One of the breakpoints is within exon 34. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		451	0	6	8	Intron of PREX2(+):3Kb after exon 33	PREX2	69054080			8	Exon 34 of PREX2(+)	PREX2	69058481			10	INVERSION		4401	216187	583	6	NEW_VARIANT
P-0028155-T01-IM6	FAT1 (NM_005245) rearrangement: c.10_chr4:g.187697960del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		385	0	5	4	Exon 2 of FAT1(-)	FAT1	187630972			4	IGR: 189Kb before FAT1(-)	FAT1	187697960			10	DELETION		66988	216194	527	7	NEW_VARIANT
P-0028160-T01-IM6	FOXA1 (NM_004496) rearrangement: c.1121:FOXA1_chr14:g.38004592dup	PRECISE	Note: The FOXA1 rearrangement results in the duplication of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		5428	0	19	14	Intron of MIPOL1(+):12Kb before exon 15	MIPOL1	38004592			14	Exon 2 of FOXA1(-)	FOXA1	38060868			10	DUPLICATION		56276	216200	4533	21	NEW_VARIANT
P-0028164-T01-IM6	SMAD4 (NM_005359) - AGMO (NM_001004320) rearrangement: t(7;18)(p21;q21.2)(chr7:g.15569155::chr18:g.48581266)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SMAD4:AGMO}		0	0	58	18	Exon 5 of SMAD4(+)	SMAD4	48581266			7	Intron of AGMO(-):15Kb after exon 3	AGMO	15569155			10	TRANSLOCATION		0	216216	0	58	NEW_VARIANT
P-0028195-T01-IM6	BCOR (NM_001123385) rearrangement: c.-40-3515_c.424inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		2387	0	12	X	Exon 4 of BCOR(-)	BCOR	39934175			X	5-UTR of BCOR(-):29Kb before coding start	BCOR	39940737			10	INVERSION		6562	216451	3891	12	NEW_VARIANT
P-0028200-T01-IM6	RXRA (NM_002957) translocation: t(9;14)(q34.2;q31.3)(chr9:g.137321221::chr14:g.85179414)	PRECISE	Note: The RXRA rearrangement is a translocation with a breakpoint within RXRA intron 7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	20	14	IGR: 681Kb before LINC00911(+)	LINC00911	85179414			9	Intron of RXRA(+):135bp after exon 7	RXRA	137321221			10	TRANSLOCATION		0	216430	0	20	NEW_VARIANT
P-0028206-T01-IM6	RB1 (NM_000321) rearrangement: c.2521-250_c.2664-33del	IMPPRECISE	Note: The RB1 rearrangement is a intragenic deletion of exon 25. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1092	0	4	13	Intron of RB1(+):249bp before exon 25	RB1	49050587			13	Intron of RB1(+):32bp before exon 26	RB1	49051458			0	DELETION		871	216456	1622	4	NEW_VARIANT
P-0028250-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.-32+6538_c.1419+169dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 2-8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		15763	0	10	19	5-UTR of SMARCA4(+):16Kb before coding start	SMARCA4	11078388			19	Intron of SMARCA4(+):169bp after exon 8	SMARCA4	11102168			10	DUPLICATION		23780	216549	29554	10	NEW_VARIANT
P-0028254-T01-IM6	XRCC2 (NM_005431) - KMT2C (NM_170606) rearrangement: c.39+1308:XRCC2_c.289:KMT2Cdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {XRCC2:KMT2C}		7816	0	9	7	Exon 3 of KMT2C(-)	KMT2C	152027786			7	Intron of XRCC2(-):1Kb after exon 1	XRCC2	152371818			10	DELETION		344032	216548	10112	9	NEW_VARIANT
P-0015434-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon 13 fused to ALK exon20): c.1489+63:EML4_c.3172+130:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		88769	0	64	2	Intron of ALK(-):129bp after exon 19	ALK	29448197			2	Intron of EML4(+):63bp after exon 12	EML4	42522719			10	INVERSION		13074522	216071	135511	64	NEW_VARIANT
P-0028090-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+8087:ERG_c.127-641:TMPRSS2inv	PRECISE	Note: The ERG - TMPRSS2 rearrangement is an inversion which involves ERG exons 1 with TMPRSS2 exons 3-14. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		21747	0	49	21	Intron of ERG(-):8Kb after exon 1	ERG	39862200			21	Intron of TMPRSS2(-):641bp before exon 3	TMPRSS2	42867146			10	INVERSION		3004946	216072	26091	56	NEW_VARIANT
P-0028093-T01-IM6	FLT1 (NM_002019) rearrangement: c.3814:FLT1_chr13:g.20956827del	PRECISE	Note: The FLT1 rearrangement is a deletion of FLT1 exons 29-30. One breakpoint is within exon 29. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		73108	0	4	13	IGR: 21Kb before CRYL1(-)	CRYL1	20956827			13	Exon 29 of FLT1(-)	FLT1	28880816			10	DELETION		7923989	216070	81684	4	NEW_VARIANT
P-0028094-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.3604:NOTCH3_chr19:g.10091386del	PRECISE	Note: The NOTCH3 rearrangement results in the deletion of NOTCH3 exons 1-22. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NOTCH3:COL5A3}		194777	0	5	19	Intron of COL5A3(-):18bp before exon 35	COL5A3	10091386			19	Exon 22 of NOTCH3(-)	NOTCH3	15289950			10	DELETION		5198564	216075	222753	5	NEW_VARIANT
P-0028098-T01-IM6	CDKN2Ap16INK4A (NM_058195) rearrangement: c.*92_c.194-995del	PRECISE	Note: The CDKN2A rearrangement is a deletion of CDKN2Ap14ARF intron 1 to exon 2. Its functional significance is undetermined,	MANUAL_OK	3to5	3to5	-		0		51	9	Exon 2 of CDKN2Ap14ARF(-)	CDKN2Ap14ARF	21970910			9	Intron of CDKN2A(-):995bp before exon 2	CDKN2Ap14ARF	21972202			10	DELETION		1292	216942	1820		NEW_VARIANT
P-0028098-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.448_c.151-995del	PRECISE	Note: The CDKN2A rearrangement is a deletion of CDKN2Ap16INK4A intron 1 to exon 2. Its functional significance is undetermined,	MANUAL_OK	3to5	3to5	-		0		51	9	Exon 2 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21970910			9	Intron of CDKN2A(-):995bp before exon 2	CDKN2Ap16INK4A	21972202			10	DELETION		1292	216941	1820		NEW_VARIANT
P-0028377-T01-IM6	RAD54L (NM_001142548) rearrangement: c.1169+292:RAD54L_chr1:g.213770090inv	IMPPRECISE	Note: The RAD54L rearrangement is an inversion of exons 12-19. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		570071	0	7	1	Intron of RAD54L(+):292bp after exon 11	RAD54L	46736749			1	IGR: 328Kb before LINC00538(+)	LINC00538	213770090			0	INVERSION		167033341	216995	727087	7	NEW_VARIANT
P-0028378-T01-IM6	FGFR2 (NM_000141) - CTNNA3 (NM_013266) rearrangement: c.2302-1725:FGFR2_c.1732+8711:CTNNA3inv	PRECISE	Note: The FGFR2 - CTNNA3 rearrangement is an inversion with breakpoints in FGFR2 intron 17 and CTNNA3 intron 12. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 and CTNNA3 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	-		181175	0	83	10	Intron of CTNNA3(-):9Kb after exon 12	CTNNA3	68130199			10	Intron of FGFR2(-):2Kb before exon 18	FGFR2	123241260			10	INVERSION		55111061	217004	188181	78	NEW_VARIANT
P-0022291-T02-IM6	ATRX (NM_000489) rearrangement: c.1685_c.3809+5643inv	PRECISE	Note: The ATRX rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12985	0	41	X	Intron of ATRX(-):6Kb after exon 10	ATRX	76926078			X	Exon 9 of ATRX(-)	ATRX	76939063			10	INVERSION		12985	216890	21920	41	NEW_VARIANT
P-0028321-T01-IM6	ELF3 (NM_004433) rearrangement: c.435:ELF3_chr1:g.201971987inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		5118	0	34	1	Intron of RNPEP(+):377bp before exon 9	RNPEP	201971987			1	Exon 4 of ELF3(+)	ELF3	201981521			10	INVERSION		9534	216849	8436	33	NEW_VARIANT
P-0028321-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-14 fused to TACC3 exons 7-16): c.1943:FGFR3_c.1591+377:TACC3dup	PRECISE	Note: The FGFR3 - TACC3 rearrangement is a duplication that results in the fusion of FGFR3 exons 1-14 to TACC3 exons 7-16. One of the breakpoints is within FGFR3 exon 14. The fusion does not include the entire kinase domain of FGFR3. The sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR3 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		23926	0	3	4	Intron of TACC3(+):377bp after exon 6	TACC3	1733405			4	Exon 14 of FGFR3(+)	FGFR3	1807884			6	DUPLICATION		74479	216848	27894	3	NEW_VARIANT
P-0013114-T02-IM6	VTCN1 (NM_024626) rearrangement: t(1;6)(p13.1;q27)(chr1:g.117753496::chr6:g.169564182)	PRECISE	Note: The VTCN1 rearrangement is a translocation that may disrupt the 5UTR region. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	32	6	IGR: 11Kb before LOC101929504(-)	LOC101929504	169564182			1	Intron of VTCN1(-):8bp after exon 1	VTCN1	117753437			10	TRANSLOCATION		0	216978	0	33	NEW_VARIANT
P-0028287-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		67780	0	39	2	Intron of ALK(-):267bp before exon 20	ALK	29446661			2	Intron of EML4(+):3Kb before exon 6	EML4	42505367			10	INVERSION		13058706	216829	101731	39	NEW_VARIANT
P-0028289-T01-IM6	PPM1D (NM_003620) rearrangement: 1;17)(q41;q23.2)(chr1:g.216077920chr17:g.58740285)	PRECISE	Note: The PPM1D rearrangement is a translocation involving exon 6. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	1	92	17	Intron of PPM1D(+):70bp before exon 6	PPM1D	58740285			1	Intron of USH2A(-):4Kb before exon 39	USH2A	216077920			10	TRANSLOCATION		0	216815	0	92	NEW_VARIANT
P-0028295-T01-IM6	MYH9 (NM_002473) - ROS1 (NM_002944) rearrangement: t(6;22)(q22.1;q12.3)(chr6:g.117641564::chr22:g.36691922)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {MYH9:ROS1}		0	0	25	22	Intron of MYH9(-):159bp before exon 26	MYH9	36691922			6	Intron of ROS1(-):371bp before exon 36	ROS1	117641564			10	TRANSLOCATION		0	216816	0	24	NEW_VARIANT
P-0028363-T01-IM6	EWSR1 (NM_013986) rearrangement: c.992+544:EWSR1_chr22:g.29219730del.	PRECISE	Note: The EWSR1 rearrangement results in the deletion of EWSR1 exon 1 to exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17927	0	21	22	IGR: 29Kb before XBP1(-)	XBP1	29219730			22	Intron of EWSR1(+):544bp after exon 9	EWSR1	29685319			10	DELETION		465589	216980	25642	21	NEW_VARIANT
P-0014689-T02-IM6	TPCN2 (NM_139075) - FGF3 (NM_005247) rearrangement: c.1589+280:TPCN2_c.325-1954:FGF3del	IMPPRECISE	Note: The TPCN2 - FGF3 rearrangement is a deletion which involves TPCN2 exons 1-17 and FGF3 exons 1-2.	MANUAL_OK	3to5	3to5	Antisense Fusion		39257	0	23	11	Intron of TPCN2(+):280bp after exon 17	TPCN2	68847631			11	Intron of FGF3(-):2Kb before exon 3	FGF3	69627422			0	DELETION		779791	215547	167592	23	NEW_VARIANT
P-0027119-T03-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		98820	0	188	2	Intron of ALK(-):317bp before exon 20	ALK	29446711			2	Intron of EML4(+):836bp before exon 13	EML4	42527544			10	INVERSION		13080833	217048	141068	187	NEW_VARIANT
P-0027998-T01-IM6	NOTCH2 (NM_024408) fusion: c.3337+43_c.1916-44dup	PRECISE	Note: The NOTCH2 fusion is predicted to be in frame. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 9 exons : in frame		13697	0	48	1	Intron of NOTCH2(-):42bp after exon 20	NOTCH2	120480437			1	Intron of NOTCH2(-):44bp before exon 12	NOTCH2	120502169			10	DUPLICATION		21732	215552	21300	49	NEW_VARIANT
P-0028344-T01-IM6	YAP1 (NM_001130145) rearrangement: t(5;11)(q11.2;q22.1)(chr5:g.58795652::chr11:g.102056674)	PRECISE	Note: The YAP1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	41	11	Intron of YAP1(+):74bp before exon 4	YAP1	102056674			5	Intron of PDE4D(-):284Kb before exon 4	PDE4D	58795652			10	TRANSLOCATION		0	216871	0	41	NEW_VARIANT
P-0028344-T01-IM6	TBX3 (NM_016569) rearrangement: c.960:TBX3_chr12:g.116070739del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		7268	0	79	12	Exon 6 of TBX3(-)	TBX3	115114257			12	IGR: 326Kb before MED13L(-)	MED13L	116070739			10	DELETION		956482	216869	12070	81	NEW_VARIANT
P-0028405-T01-IM6	TNFRSF14 (NM_003820) rearrangement: c.694+62_chr1:g.26512742inv	PRECISE	Note: The TNFRSF14 rearrangement is an inversion that includes TNFRSF14 exons 7-8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		242745	0	20	1	Intron of TNFRSF14(+):62bp after exon 6	TNFRSF14	2493316			1	Intron of CNKSR1(+):916bp before exon 15	CNKSR1	26512742			10	INVERSION		24019426	217096	250684	18	NEW_VARIANT
P-0028414-T01-IM6	RIT1 (NM_006912) rearrangement: t(1;15)(q22;q15.1)(chr1:g.155880302::chr15:g.41171099)	PRECISE	Note: The RIT1 rearrangement is a translocation with a breakpoint within RIT1 intron 2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	90	15	IGR: 7Kb before RHOV(-)	RHOV	41171099			1	Intron of RIT1(-):5bp before exon 3	RIT1	155880302			10	TRANSLOCATION		0	217094	0	92	NEW_VARIANT
P-0006768-T03-IM6	EGFR (NM_005228) Rearrangement : c.89-37152_c.890-499inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		13957	0	23	7	Intron of EGFR(+):37Kb before exon 2	EGFR	55172827			7	Intron of EGFR(+):498bp before exon 8	EGFR	55223024			10	INVERSION		50197	216789	466857	23	NEW_VARIANT
P-0007125-T01-IM5	SMARCA4 (NM_003072) rearrangement: c.-32+11329_c.886del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		17534	0	16	19	5-UTR of SMARCA4(+): 12Kb before coding start	SMARCA4	11083179			19	Exon 5 of SMARCA4(+)	SMARCA4	11098368			43	DELETION		15189	113549	15210	15	NEW_VARIANT
P-0007125-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-14 with ALK exons 20-29) : c.1328:EML4_c.3173-203:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (EML4-ALK)		95649	0	40	2	Intron of ALK(-): 203bp before exon 20	ALK	29446597			2	Exon 13 of EML4(+)	EML4	42528393			26	INVERSION		13081796	113551	91930	38	NEW_VARIANT
P-0021045-T02-IM6	SMARCD1 (NM_003076) - SPATS2 (NM_023071) rearrangement:  c.365+3:SMARCD1_c.-243-34386:SPATS2dup.	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {SMARCD1:SPATS2}		4102	0	45	12	5-UTR of SPATS2(+):35Kb before coding start	SPATS2	49820167			12	Intron of SMARCD1(+):3bp after exon 2	SMARCD1	50480134			10	DUPLICATION		659967	216796	10837	49	NEW_VARIANT
P-0021177-T02-IM6	TCF7L2 (NM_001146274) rearrangement: c.1318+591:TCF7L2_chr10:g.115131344del	PRECISE	Note: The TCF7L2 rearrangement is a deletion of exons 13-14.	MANUAL_OK	3to5	3to5	-		6156	0	13	10	Intron of TCF7L2(+):591bp after exon 12	TCF7L2	114918419			10	IGR: 179Kb before HABP2(+)	HABP2	115131344			10	DELETION		212925	217492	3256	13	NEW_VARIANT
P-0021177-T02-IM6	KMT2D (NM_003482) rearrangement: c.6450:KMT2D_chr12:g.49487152del	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 1-31. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DHH:KMT2D}		61385	0	48	12	Exon 31 of KMT2D(-)	KMT2D	49435103			12	Intron of DHH(-):840bp after exon 1	DHH	49487152			10	DELETION		52049	217493	56740	72	NEW_VARIANT
P-0028302-T01-IM6	BAP1 (NM_004656) rearrangement: c.68-6:BAP1_chr3:g.52450481del	PRECISE	Note: The BAP1 rearrangement is a deletion of BAP1 exons  1-2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1903	0	71	3	Intron of BAP1(-):6bp before exon 3	BAP1	52443630			3	Intron of PHF7(+):2Kb after exon 4	PHF7	52450481			10	DELETION		6851	216775	680	82	NEW_VARIANT
P-0028430-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10).	PRECISE	Note: TMPRSS2 is predicted to form a fusion with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		51714	0	5	21	Intron of ERG(-):59Kb before exon 4	ERG	39876653			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873954			10	DELETION		2997301	217200	61887	5	NEW_VARIANT
P-0028432-T01-IM6	NF1 (NM_001042492) rearrangement: c.4111-120_c.4430+350dup.	PRECISE	Note: The NF1 rearrangement is an intragenic duplications of exons 31-33. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		2579	0	17	17	Intron of NF1(+):119bp before exon 31	NF1	29579836			17	Intron of NF1(+):350bp after exon 33	NF1	29586497			10	DUPLICATION		6661	217205	3313	17	NEW_VARIANT
P-0028433-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.4193:NOTCH3_chr19:g.15441551del	PRECISE	Note: The NOTCH3 rearrangement is a deletion of exons 1-24. One of the breakpoints is within exon 24. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		85340	0	15	19	Exon 24 of NOTCH3(-)	NOTCH3	15288546			19	IGR: 23Kb before AKAP8(-)	AKAP8	15441551			10	DELETION		153005	217211	39558	15	NEW_VARIANT
P-0028470-T01-IM6	ARID2 (NM_152641) - MON2 (NM_015026) rearrangement: c.186+70:ARID2_c.176-4180del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ARID2:MON2}		265021	0	13	12	Intron of ARID2(+):70bp after exon 2	ARID2	46123990			12	Intron of MON2(+):4Kb before exon 3	MON2	62883515			10	DELETION		16759525	217596	266193	14	NEW_VARIANT
P-0003132-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	-		129232	0	27	12	3-UTR of MLL2(-): 2Kb after coding stop	MLL2	49413356			12	Intron of MLL2(-): 8bp after exon 8	MLL2	49446690			43	DELETION		33334	8543	76138	29	NEW_VARIANT
P-0003233-T05-IM6	FGFR4 (NM_213647) rearrangement: c.919-52:FGFR4_chr5:g.168403446dup	PRECISE	Note: The FGFR4 rearrangement results in the duplication of exons 1-7. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		30403	0	21	5	Intron of SLIT3(-):93Kb before exon 5	SLIT3	168403446			5	Intron of FGFR4(+):51bp before exon 8	FGFR4	176519595			10	DUPLICATION		8116149	220381	40560	23	NEW_VARIANT
P-0004094-T02-IM6	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)	PRECISE	Note: The KIAA1468 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KIAA1468:RET}		0	0	53	18	Intron of KIAA1468(+):3Kb before exon 11	KIAA1468	59909399			10	Intron of RET(+):95bp after exon 11	RET	43610279			10	TRANSLOCATION		0	218646	0	54	NEW_VARIANT
P-0004756-T02-IM6	KMT2D (NM_003482) - WHSC1L1 (NM_018013) rearrangement: t(8;12)(p11.22;q13.12)(chr8:g.38151870::chr12:g.32312089)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KMT2D:WHSC1L1}		0	0	173	12	Exon 39 of KMT2D(-)	KMT2D	49425873			8	Intron of WHSC1L1(-):1Kb after exon 16	WHSC1L1	38151870			10	TRANSLOCATION		0	222557	0	181	NEW_VARIANT
P-0004756-T02-IM6	ARFGEF1 (NM_006421) - KMT2D (NM_003482) rearrangement: t(8;12)(q13.2;q13.12)(chr8:g.68111283::chr12:g.49425875)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ARFGEF1:KMT2D}		0	0	54	12	Exon 39 of KMT2D(-)	KMT2D	49425875			8	Exon 39 of ARFGEF1(-)	ARFGEF1	68111283			10	TRANSLOCATION		0	222558	0	56	NEW_VARIANT
P-0004756-T02-IM6	IRS2 (NM_003749) - DOCK9 (NM_015296) rearrangement: c.2538:IRS2_c.130-30138:DOCK9del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {IRS2:DOCK9}		37322	0	100	13	Intron of DOCK9(-):30Kb before exon 2	DOCK9	99637943			13	Exon 1 of IRS2(-)	IRS2	110435863			10	DELETION		10797920	222553	43958	105	NEW_VARIANT
P-0004937-T02-IM6	ATM (NM_000051) - C11orf65 (NM_152587) rearrangement : c.8987+25:ATM_c.*1558:C11orf65del	PRECISE	Note: The ATM (NM_000051) - C11orf65 (NM_152587) rearrangement results in the deletion of ATM exon63.	MANUAL_OK	3to5	3to5	Antisense Fusion		1938	0	58	11	Intron of ATM(+):25bp after exon 62	ATM	108235970			11	Promoter of C11orf65(-):2Kb from tx start	C11orf65	108252191			10	DELETION		16221	217643	1874	61	NEW_VARIANT
P-0004937-T02-IM6	RTEL1 (NM_032957) rearrangement: t(19;20)(p11;q13.33)(chr19:g.24531369::chr20:g.62303901)	PRECISE	Note: The RTEL1 rearrangement is a translocation with a breakpoint after exon 5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	162	20	Intron of RTEL1(+):7bp before exon 9	RTEL1	62303901			19	IGR: 186Kb before HAVCR1P1(-)	HAVCR1P1	24531369			10	TRANSLOCATION		0	217644	0	194	NEW_VARIANT
P-0005502-T03-IM6	RB1 (NM_000321) rearrangement: c.861+125_c.1696-1106del	PRECISE	Note: The RB1 rearrangement results in the in-frame deletion of exons 9-17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 9 exons : in frame		8430	0	3	13	Intron of RB1(+):125bp after exon 8	RB1	48937218			13	Intron of RB1(+):1Kb before exon 18	RB1	49026023			10	DELETION		88805	221296	14583	2	NEW_VARIANT
P-0008082-T01-IM5	BRCA2 (NM_000059) rearrangement: c.4945_c.6841+44del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		12350	0	19	13	Exon 11 of BRCA2(+)	BRCA2	32913437			13	Intron of BRCA2(+): 44bp after exon 11	BRCA2	32915377			33	DELETION		1940	120304	8138	19	NEW_VARIANT
P-0008525-T02-IM6	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exons 1-2 with ERG exons 2-10): c.126+622:TMPRSS2_c.40-44718:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion event involves the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32939	0	121	21	Intron of ERG(-):8Kb after exon 1	ERG	39862262			21	Intron of TMPRSS2(-):621bp after exon 2	TMPRSS2	42869424			10	DELETION		3007162	219151	26424	126	NEW_VARIANT
P-0008525-T02-IM6	CNTRL (NM_007018) - SETD2 (NM_014159) rearrangement: t(3;9)(p21.31;q33.2)(chr3:g.47162787::chr9:g.123913096)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CNTRL:SETD2}		0	0	52	9	Intron of CNTRL(+):335bp after exon 23	CNTRL	123913096			3	Exon 3 of SETD2(-)	SETD2	47162787			10	TRANSLOCATION		0	219153	0	52	NEW_VARIANT
P-0008712-T02-IM6	PAX5 (NM_016734) rearrangement: c.910+60_chr9:g.29168846del	PRECISE	Note: The PAX5 (NM_016734) rearrangement is a deletion of exons 8-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {PAX5:LINGO2}		12655	0	59	9	5-UTR of LINGO2(-):1Mb before coding start	LINGO2	29168846			9	Intron of PAX5(-):59bp after exon 7	PAX5	36923292			10	DELETION		7754446	218123	31281	59	NEW_VARIANT
P-0009687-T02-IM6	TP53 (NM_000546) rearrangement: t(15;17)(q21.1;p13.1)(chr15:g.44943476::chr17:g.7579206)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in intron 4. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	46	17	Intron of TP53(-):102bp after exon 4	TP53	7579209			15	Intron of SPG11(-):214bp after exon 6	SPG11	44943474			10	TRANSLOCATION		0	221487	0	47	NEW_VARIANT
P-0009687-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+3180:TMPRSS2_c.18+6016:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		70398	0	52	21	Intron of ERG(-):6Kb after exon 1	ERG	39864271			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876698			10	DELETION		3012427	221484	113439	54	NEW_VARIANT
P-0009687-T02-IM6	EP300 (NM_001429) rearrangement: c.6795:EP300_chr22:g.18946332dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		207006	0	25	22	IGR: 12Kb before DGCR5(+)	DGCR5	18946332			22	Exon 31 of EP300(+)	EP300	41574510			10	DUPLICATION		22628178	221485	322143	39	NEW_VARIANT
P-0012695-T01-IM5	DENND3 - TMPRSS2 rearrangement: t(8;21)(q24.3;q22.3)(chr8:g.142204112::chr21:g.42873872)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (DENND3-TMPRSS2)		0	0	40	21	Intron of TMPRSS2(-): 4Kb before exon 2	TMPRSS2	42873872			8	Intron of DENND3(+): 20bp before exon 23	DENND3	142204112			34	TRANSLOCATION		0	158600	0	40	NEW_VARIANT
P-0013755-T02-IM6	ERBB2 (NM_004448) Rearrangement :  c.759+36:ERBB2_c.827-2329:IKZF3	PRECISE	Note: The ERBB2 rearrangement results in the duplication of exons 7-27. It includes the kinase domain of ERBB2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		35529	0	6	17	Intron of ERBB2(+):37bp after exon 6	ERBB2	37866491			17	Intron of IKZF3(-):2Kb before exon 7	IKZF3	37925075			10	DUPLICATION		58584	218299	64387	6	NEW_VARIANT
P-0013934-T02-IM6	NOTCH1 (NM_017617) rearrangement: c.*1763_c.3310inv	PRECISE	Note: The NOTCH1 (NM_017617) rearrangement is an inversion of exons 20 - 34. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		48068	0	67	9	Promoter of NOTCH1(-):135bp from tx start	NOTCH1	139388760			9	Exon 20 of NOTCH1(-)	NOTCH1	139402699			10	INVERSION		13939	218103	66946	97	NEW_VARIANT
P-0017365-T03-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.303+25501:CCDC6_c.2137-568:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		37262	0	36	10	Intron of RET(+):567bp before exon 12	RET	43611464			10	Intron of CCDC6(-):26Kb after exon 1	CCDC6	61640379			10	INVERSION		18028915	189824	52389	46	NEW_VARIANT
P-0017365-T03-IM6	PIK3C2G (NM_004570) rearrangement: c.1873-3988_c.2004-111del	PRECISE	Note: The PIK3C2G rearrangement is an intragenic deletion of exon 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1186	0	9	12	Intron of PIK3C2G(+):4Kb before exon 14	PIK3C2G	18540068			12	Intron of PIK3C2G(+):110bp before exon 15	PIK3C2G	18552482			8	DELETION		12414	189822	1375	9	NEW_VARIANT
P-0017365-T03-IM6	CDKN2A (NM_000077) rearrangement: c.458-15_chr9:g.22143651del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		18190	0	6	9	Intron of CDKN2A(-):15bp before exon 3	CDKN2A	21968256			9	IGR: 141Kb before CDKN2B(-)	CDKN2B	22143651			8	DELETION		175395	189821	20649	7	NEW_VARIANT
P-0018046-T02-IM6	LATS1 (NM_004690) Rearrangement: c.2883+965_c.2776+12del	PRECISE	Note: The LATS1 rearrangement is a deletion of LATS1 exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1474	0	3	6	Intron of LATS1(-):964bp after exon 7	LATS1	149996431			6	Intron of LATS1(-):11bp after exon 6	LATS1	149997679			4	DELETION		1248	219714	1868	3	NEW_VARIANT
P-0018583-T02-IM6	SMAD4 (NM_005359) rearrangement: c.1592:SMAD4_chr18:g.48624100del	PRECISE	Note: The SMAD4 rearrangement is a deletion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		505	0	99	18	Exon 12 of SMAD4(+)	SMAD4	48604770			18	IGR: 68Kb before SMAD4(+)	SMAD4	48624100			10	DELETION		19330	217873	108	105	NEW_VARIANT
P-0019246-T03-IM6	SMARCA4 (NM_003072) rearrangement: t(8;19)(p23.2;p13.2)(chr8:g.5383702::chr19:g.11100157)	PRECISE	Note: The SMARCA4 rearrangement is a translocation involving exon 7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	61	19	Intron of SMARCA4(+):38bp after exon 7	SMARCA4	11100157			8	IGR: 877Kb before LOC100287015(-)	LOC100287015	5383702			10	TRANSLOCATION		0	222160	0	62	NEW_VARIANT
P-0019246-T03-IM6	EZH2 (NM_004456) rearrangement: c.670_c.246+4853del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3836	0	35	7	Exon 7 of EZH2(-)	EZH2	148524314			7	Intron of EZH2(-):5Kb after exon 3	EZH2	148538709			10	DELETION		14395	222159	1104	41	NEW_VARIANT
P-0019543-T01-IM6	NF1 (NM_001042492) Rearrangement : c.4111-53_c.4430+537dup	PRECISE	Note: The NF1 Rearrangement results in the duplication of exons 31-33 of NF1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		3640	0	24	17	Intron of NF1(+):52bp before exon 31	NF1	29579903			17	Intron of NF1(+):537bp after exon 33	NF1	29586684			10	DUPLICATION		6781	182631	4998	28	NEW_VARIANT
P-0019543-T01-IM6	NOTCH1 (NM_017617) - NPR2 (NM_003995) Rearrangement: c.1520:NOTCH1_c.-1180:NPR2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NOTCH1:NPR2}		519996	0	30	9	Promoter of NPR2(+):1Kb from tx start	NPR2	35791226			9	Exon 9 of NOTCH1(-)	NOTCH1	139411759			10	INVERSION		103620533	182632	452309	40	NEW_VARIANT
P-0020138-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		155492	0	10	2	Intron of ALK(-):419bp after exon 19	ALK	29447907			2	Intron of EML4(+):3Kb before exon 6	EML4	42504974			10	INVERSION		13057067	183730	110368	16	NEW_VARIANT
P-0020766-T01-IM6	RTEL (NM_032957) - rearrangement: t(5,20)(p14.3,q13.33)(chr5:g.18137294::chr20:g.62322308)	PRECISE	Note: The RTEL rearrangement is a translocation that may result in the truncation of RTEL1 exons 28-35. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	258	20	Intron of RTEL1(+):8bp after exon 27	RTEL1	62322308			5	IGR: 758Kb before LOC401177(-)	LOC401177	18137294			10	TRANSLOCATION		0	185291	0	349	NEW_VARIANT
P-0021693-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		119652	0	99	2	Intron of ALK(-):608bp before exon 20	ALK	29447002			2	Intron of EML4(+):2Kb before exon 13	EML4	42526872			10	INVERSION		13079870	188096	112829	112	NEW_VARIANT
P-0022100-T03-IM6	INPPL1 (NM_001567) Rearrangement: c.2880-103:INPPL1_g.71834974del	PRECISE	Note: The INPPL1 rearrangement results in the deletion of INPPL1 exons 1-25. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		28372	0	8	11	IGR: 12Kb before FOLR3(+)	FOLR3	71834974			11	Intron of INPPL1(+):102bp before exon 26	INPPL1	71948065			10	DELETION		113091	223010	43409	8	NEW_VARIANT
P-0022101-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon18 fused with ALK exon 20): c.2057-510:EML4_c.2057-510:ALKinv	PRECISE	Note: The EML4 -ALK Fusion is an in-frame fusion and includes the protein kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		129281	0	15	2	Intron of ALK(-):567bp after exon 19	ALK	29447759			2	Intron of EML4(+):509bp before exon 18	EML4	42544057			10	INVERSION		13096298	189561	83601	13	NEW_VARIANT
P-0022530-T02-IM6	NOTCH3 (NM_000435) rearrangement: c.4812:NOTCH3_chr19:g.15437650del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		56278	0	12	19	Exon 26 of NOTCH3(-)	NOTCH3	15281561			19	IGR: 27Kb before AKAP8(-)	AKAP8	15437650			10	DELETION		156089	219472	58205	11	NEW_VARIANT
P-0023156-T01-IM6	PBRM1 (NM_018313) Rearrangement : c.-13+371_c.236+173inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		3629	0	4	3	Intron of PBRM1(-):172bp after exon 3	PBRM1	52712343			3	5-UTR of PBRM1(-):137Kb before coding start	PBRM1	52719394			9	INVERSION		7051	194258	2187	4	NEW_VARIANT
P-0024200-T02-IM6	STK11 (NM_000455) rearrangement: c.375-198:STK11_chr19:g.1202435del	PRECISE	Note: The STK11 rearrangement is a deletion of exons 1-2.	MANUAL_OK	3to5	3to5	-		4759	0	4	19	IGR: 3Kb before STK11(+)	STK11	1202435			19	Intron of STK11(+):197bp before exon 3	STK11	1219125			7	DELETION		16690	223281	2555	4	NEW_VARIANT
P-0024229-T01-IM6	NFE2L2 (NM_006164) rearrangement:  c.46-3198_c.73del	PRECISE	Note: The NFE2L2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		257	0	15	2	Exon 2 of NFE2L2(-)	NFE2L2	178098972			2	Intron of NFE2L2(-):3Kb before exon 2	NFE2L2	178102197			10	DELETION		3225	199012	247	16	NEW_VARIANT
P-0024869-T01-IM6	MGA (NM_001164273) rearrangement: c.8484_chr15:g.56553582del	IMPPRECISE	Note: The MGA rearrangement results in the deletion of exon 24. One of the breakpoints is within exon 24. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		71065	0	6	15	Exon 24 of MGA(+)	MGA	42058764			15	IGR: 104Kb before TEX9(+)	TEX9	56553582			0	DELETION		14494818	202428	98737	6	NEW_VARIANT
P-0025349-T03-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion ( CCDC6 exon 1 fused to RET exons 12-20): c.304-10038:CCDC6_c.2137-46:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET. The low read support for this rearrangement suggests that it may be a subclonal event. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the CCDC6 and RET genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		26294	0	2	10	Intron of RET(+):45bp before exon 12	RET	43611986			10	Intron of CCDC6(-):10Kb before exon 2	CCDC6	61622498			10	INVERSION		18010512	218694	35873	2	NEW_VARIANT
P-0028166-T01-IM6	SUFU (NM_016169) rearrangement: c.1297-55_g.103512655del	PRECISE	Note: SUFU (NM_016169) rearrangement results in the deletion of exons 1-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		15208	0	4	10	IGR: 17Kb before FGF8(-)	FGF8	103512655			10	Intron of SUFU(+):54bp before exon 11	SUFU	104386877			8	DELETION		874222	216229	16994	4	NEW_VARIANT
P-0028166-T01-IM6	ATRX (NM_000489) rearrangement: c.4121-11_g.77074225del	PRECISE	Note: ATRX (NM_000489) rearrangement results in the deletion of exons 1-12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14024	0	53	X	Intron of ATRX(-):11bp before exon 13	ATRX	76912154			X	IGR: 8Kb before MAGT1(-)	MAGT1	77074225			10	DELETION		162071	216230	6787	55	NEW_VARIANT
P-0028361-T01-IM6	GLI1 (NM_005269) - YEATS4 (NM_006530) rearrangement: c.912+76:GLI1_c.52-806:YEATS4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {GLI1:YEATS4}		50420	0	5	12	Intron of GLI1(+):76bp after exon 8	GLI1	57860248			12	Intron of YEATS4(+):805bp before exon 2	YEATS4	69755762			10	DELETION		11895514	216963	377730	5	NEW_VARIANT
P-0028420-T01-IM6	ARID1A  (NM_006015) rearrangement: c.1920+13682_c.2420-85del	IMPPRECISE	Note: The ARID1A rearrangement is a deletion of exons 5-7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		5361	0	6	1	Intron of ARID1A(+):14Kb after exon 4	ARID1A	27072965			1	Intron of ARID1A(+):84bp before exon 8	ARID1A	27089379			0	DELETION		16414	217245	5568	6	NEW_VARIANT
P-0028513-T01-IM6	MALT1 (NM_006785) rearrangement: c.403:MALT1_g.56805185dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SEC11C:MALT1}		18055	0	50	18	Exon 3 of MALT1(+)	MALT1	56363624			18	Promoter of SEC11C(+):2Kb from tx start	SEC11C	56805185			10	DUPLICATION		441561	217650	39697	53	NEW_VARIANT
P-0028541-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		116268	0	213	2	Intron of ALK(-):528bp before exon 20	ALK	29446922			2	Intron of EML4(+):5Kb after exon 2	EML4	42477458			10	INVERSION		13030536	217724	158869	212	NEW_VARIANT
P-0028548-T01-IM6	CBFB (NM_022845) rearrangement: c.165+7_c.282+11707del	IMPPRECISE	Note: The CBFB rearrangement is an intragenic deletions of exon 3. Its functional significance is undetermined,	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		781	0	52	16	Intron of CBFB(+):7bp after exon 2	CBFB	67063723			16	Intron of CBFB(+):12Kb after exon 3	CBFB	67082365			0	DELETION		18642	217703	1066	58	NEW_VARIANT
P-0028548-T01-IM6	NSD1 (NM_022455) rearrangement: c.3797-8075_c.5893-134del	PRECISE	Note: The NSD1 rearrangement results in intragenic deletions of exons 6 to 18. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 13 exons : out of frame		17467	0	5	5	Intron of NSD1(+):8Kb before exon 6	NSD1	176654747			5	Intron of NSD1(+):133bp before exon 19	NSD1	176709332			9	DELETION		54585	217702	30731	6	NEW_VARIANT
P-0028551-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-2137:TMPRSS_c.40-54306:ERGdel	PRECISE	Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		66806	0	80	21	Promoter of ERG(-):120Kb from tx start	ERG	39871850			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872253			10	DELETION		3000403	217837	109430	87	NEW_VARIANT
P-0028576-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2758+79:WHSC1L1_chr8:g.32505812del	PRECISE	Note: The WHSC1L1 rearrangement is a deletion of exons 16-24. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		16218	0	42	8	Exon 1 of NRG1(+)	NRG1	32505812			8	Intron of WHSC1L1(-):78bp after exon 15	WHSC1L1	38156883			10	DELETION		5651071	217922	21135	43	NEW_VARIANT
P-0028582-T01-IM6	SH2B3 (NM_005475) rearrangement: t(12;22)(q24.12;q13.2)(chr12:g.111885072::chr22:g.41815856)	PRECISE	Note: The SH2B3 rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	28	22	IGR: 14Kb before TOB2(-)	TOB2	41815856			12	Intron of SH2B3(+):49bp after exon 5	SH2B3	111885072			10	TRANSLOCATION		0	217918	0	30	NEW_VARIANT
P-0028587-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.-56-1085:TMPRSS2_c.18+6551:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52483	0	15	21	Intron of ERG(-):7Kb after exon 1	ERG	39863736			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871201			10	DELETION		3007465	217921	24736	14	NEW_VARIANT
P-0028601-T01-IM6	KDM5C (NM_004187) rearrangement: chrX:g.50303622_c.228+26del	PRECISE	Note: The KDM5C rearrangement is a deletion that includes KDM5C exons 3-26. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		58769	0	20	X	IGR: 31Kb before SHROOM4(-)	SHROOM4	50303622			X	Intron of KDM5C(-):25bp after exon 2	KDM5C	53249995			10	DELETION		2946373	217973	57167	21	NEW_VARIANT
P-0028626-T01-IM6	CDKN2A (NM_000077, NM_058195) rearrangement: c.68:CDKN2A_chr9:g.22153033del.	PRECISE	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.	MANUAL_OK	3to5	3to5	-		8161	0	15	9	Exon 1 of CDKN2A(-)	CDKN2A	21974759			9	IGR: 150Kb before CDKN2B(-)	CDKN2B	22153033			10	DELETION		178274	218579	8841	15	NEW_VARIANT
P-0028631-T01-IM6	FAT (NM_005245) rearrangement: c.8879-94:FAT1_chr4:g.184216350dup	PRECISE	Note: The FAT rearrangement is a duplications of FAT exons 11-27. Its functional significance is undetermined,	MANUAL_OK	5to3	5to3	-		36611	0	12	4	Intron of WWC2(+):6Kb after exon 21	WWC2	184216350			4	Intron of FAT1(-):94bp before exon 11	FAT1	187538449			10	DUPLICATION		3322099	218076	42009	12	NEW_VARIANT
P-0028632-T01-IM6	TSC2 (NM_000548) rearrangement: t(1;16)(p36.11;p13.3)(chr1:g.23695925::chr16:g.2111887)	PRECISE	Note: The TSC2 (NM_000548) rearrangement is a translocation with a breakpoint within exon 12 of TSC2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ZNF436-AS1:TSC2}		0	0	25	16	Exon 12 of TSC2(+)	TSC2	2111887			1	5-UTR of ZNF436-AS1(+):2Kb before coding start	ZNF436-AS1	23695925			10	TRANSLOCATION		0	218088	0	26	NEW_VARIANT
P-0028632-T01-IM6	JAK3 (NM_000215) rearrangement: c.1446:JAK3_chr19:g.14556834dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		111690	0	10	19	Intron of PKN1(+):403bp before exon 4	PKN1	14556834			19	Exon 11 of JAK3(-)	JAK3	17949195			10	DUPLICATION		3392361	218086	197942	11	NEW_VARIANT
P-0028636-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.2563:NOTCH1_chr9:g.103795660del	PRECISE	Note: The NOTCH1 rearrangement is a deletion of exons 16-34. One of the breakpoints is within exon 16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		178443	0	4	9	5-UTR of LPPR1(+):152Kb before coding start	LPPR1	103795660			9	Exon 16 of NOTCH1(-)	NOTCH1	139405628			7	DELETION		35609968	218152	196099	4	NEW_VARIANT
P-0029930-T01-IM6	EPB41L3 (NM_012307) - CRLF2 (NM_022148) rearrangement: t(X;18)(p11.31;p22.33)(chrX:g.1325397::chr18:g.5596405)	PRECISE	Note: The CRLF2 rearrangement is a translocation with a breakpoint in exon 3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {EPB41L3:CRLF2}		0	0	20	X	Exon 3 of CRLF2(-)	CRLF2	1325397			18	5-UTR of EPB41L3(-):202Kb before coding start	EPB41L3	5596405			10	TRANSLOCATION		0	223284	0	20	NEW_VARIANT
P-0029939-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4852:TMPRSS2_c.40-56952:ERG	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		70680	0	46	21	Intron of ERG(-):57Kb before exon 4	ERG	39874496			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875025			10	DELETION		3000529	223356	65284	46	NEW_VARIANT
P-0029943-T01-IM6	ATF1 (NM_005171) - ERBB3 (NM_001982) rearrangement: c.-6-6493:ATF1_c.1818:ERBB3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ATF1:ERBB3}		24864	0	5	12	5-UTR of ATF1(+):6Kb before coding start	ATF1	51167430			12	Exon 15 of ERBB3(+)	ERBB3	56488299			10	DELETION		5320869	223335	36689	5	NEW_VARIANT
P-0029944-T01-IM6	PTCH1 (NM_000264) rearrangement: c.3804+55:PTCH1_chr9:g.98108601del	PRECISE	Note: The PTCH1 rearrangement is a deletion of exons 22-23.	MANUAL_OK	3to5	3to5	-		3399	0	42	9	IGR: 97Kb before PTCH1(-)	PTCH1	98108601			9	Intron of PTCH1(-):54bp after exon 22	PTCH1	98211296			10	DELETION		102695	223345	3295	42	NEW_VARIANT
P-0029971-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-119:EML4_c.3172+520:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		84614	0	76	2	Intron of ALK(-):519bp after exon 19	ALK	29447807			2	Intron of EML4(+):118bp before exon 6	EML4	42507871			10	INVERSION		13060064	223404	152003	76	NEW_VARIANT
P-0029972-T01-IM6	STAT5B (NM_012448) - STAT5A (NM_003152) rearrangement: c.1052:STAT5B_c.1005:STAT5Ainv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {STAT5B:STAT5A}		19804	0	5	17	Exon 9 of STAT5B(-)	STAT5B	40370286			17	Exon 10 of STAT5A(+)	STAT5A	40453308			0	INVERSION		83022	223431	19829	10	NEW_VARIANT
P-0029997-T01-IM6	RET (NM_020975) rearrangement: c.2137-764:RET_chr10:g.92431103del	PRECISE	Note: The RET rearrangement results in the deletion of exons 12-20. The functional significance is undetermined. This case is being considered for further analysis using the Archer targeted RNAseq assay to help characterize this structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number (M18-14743).	MANUAL_OK	3to5	3to5	-		161199	0	27	10	Intron of RET(+):763bp before exon 12	RET	43611268			10	IGR: 69Kb before HTR7(-)	HTR7	92431103			10	DELETION		48819835	223467	99649	27	NEW_VARIANT
P-0030000-T01-IM6	CDKN2A (NM_058195, NM_000077) rearrangement: t(6;9)(q14.3;p21.3)(chr6:g.86363454::chr9:g.21971298)	PRECISE	Note: The CDKN2A rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	42	9	Intron of CDKN2A(-):91bp before exon 2	CDKN2A	21971298			6	IGR: 23Kb before SNHG5(-)	SNHG5	86363454			10	TRANSLOCATION		0	223479	0	42	NEW_VARIANT
P-0030008-T01-IM6	FAM175A (NM_139076) rearrangement: c.476+48_c.179-263dup	PRECISE	Note: The FAM175A rearrangement results in the duplication of exons 3-5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		3090	0	2	4	Intron of FAM175A(-):47bp after exon 5	FAM175A	84391308			4	Intron of FAM175A(-):263bp before exon 3	FAM175A	84398095			4	DUPLICATION		6787	223495	1405	2	NEW_VARIANT
P-0028640-T01-IM6	CDC73 (NM_024529) rearrangement: c.546_c.829-104del	PRECISE	Note: The CDC73 rearrangement is a deletion of exons 7-8. One of the breakpoints is within CDC73 exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1963	0	5	1	Exon 7 of CDC73(+)	CDC73	193111013			1	Intron of CDC73(+):103bp before exon 9	CDC73	193119330			9	DELETION		8317	218133	2509	5	NEW_VARIANT
P-0028640-T01-IM6	ATM (NM_000051) - RAB39A (NM_017516) rearrangement: c.6238:ATM_c.227+7554RAB39Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ATM:RAB39A}		42522	0	22	11	Intron of RAB39A(+):8Kb after exon 1	RAB39A	107807075			11	Exon 43 of ATM(+)	ATM	108188139			10	DUPLICATION		381064	218138	80107	24	NEW_VARIANT
P-0028640-T01-IM6	CREBBP (NM_004380) rearrangement: c.86-6157_c.352del	PRECISE	Note: The CREBBP rearrangement is an intragenic deletion of a part of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1580	0	6	16	Exon 2 of CREBBP(-)	CREBBP	3900744			16	Intron of CREBBP(-):6Kb before exon 2	CREBBP	3907167			6	DELETION		6423	218137	2029	6	NEW_VARIANT
P-0028642-T01-IM6	INPP4B (NM_001101669) rearrangement: c.2249_c.2642+1128del	PRECISE	Note: The INPP4B rearrangement is an intragenic deletion of exons 22-25. One of the breakpoints is within exon 22.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2945	0	23	4	Intron of INPP4B(-):1Kb after exon 25	INPP4B	143002056			4	Exon 22 of INPP4B(-)	INPP4B	143033722			10	DELETION		31666	218145	4547	24	NEW_VARIANT
P-0028658-T01-IM6	MCL1 (NM_021960) Rearrangement: c.49:MCL1_chr1:150348305del	PRECISE	Note: The MCL1 rearrangement results in the deletion of exons 1-3. One breakpoint is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		5766	0	32	1	Intron of RPRD2(+):11Kb after exon 1	RPRD2	150348305			1	Exon 1 of MCL1(-)	MCL1	150551958			10	DELETION		203653	218622	7046	32	NEW_VARIANT
P-0028658-T01-IM6	ERBB2 (NM_004448) - TCAP (NM_003673) Rearrangement:  c.3159+84:ERBB2_c.312:TCAPdup	PRECISE	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	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERBB2:TCAP}		34858	0	11	17	Exon 2 of TCAP(+)	TCAP	37822170			17	Intron of ERBB2(+):84bp after exon 25	ERBB2	37883340			10	DUPLICATION		61170	218625	46879	12	NEW_VARIANT
P-0028678-T01-IM6	KMT2D (NM_003482) rearrangement: c.14644-185:KMT2D_chr12:g.72767423del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		239286	0	23	12	Intron of KMT2D(-):185bp before exon 48	KMT2D	49421290			12	Intron of TRHDE(+):4Kb before exon 3	TRHDE	72767423			10	DELETION		23346133	218251	441981	23	NEW_VARIANT
P-0028689-T01-IM6	RB1 (NM_000321) rearrangement: c.1389+42:RB1_chr13:g.48812170inv	PRECISE	Note: The RB1 rearrangement is an inversion of exons 1-14.	MANUAL_OK	3to3	3to3	Antisense Fusion		10231	0	88	13	Intron of ITM2B(+):5Kb after exon 1	ITM2B	48812170			13	Intron of RB1(+):42bp after exon 14	RB1	48953828			10	INVERSION		141658	218296	16141	86	NEW_VARIANT
P-0028695-T01-IM6	SPEN (NM_015001) - DNAJC16 (NM_015291) rearrangement: c.9879:SPEN_c.234+512:DNAJC16dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:DNAJC16}		71048	0	17	1	Intron of DNAJC16(+):512bp after exon 3	DNAJC16	15861310			1	Exon 11 of SPEN(+)	SPEN	16262614			10	DUPLICATION		401304	218397	52056	18	NEW_VARIANT
P-0028699-T01-IM6	CDKN2B (NM_004936) rearrangement: c.156+143_c.-1067inv	PRECISE	Note: The CDKN2B rearrangement results in the inversion of exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		2566	0	13	9	Intron of CDKN2B(-):142bp after exon 1	CDKN2B	22008654			9	Promoter of CDKN2B(-):7Kb from tx start	CDKN2B	22010019			10	INVERSION		1365	218393	2259	13	NEW_VARIANT
P-0028710-T01-IM6	KATNA1 (NM_007044) - LATS1 (NM_004690) rearrangement: c.644:KATNA1_c.2656:LATS1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KATNA1:LATS1}		6195	0	42	6	Exon 6 of KATNA1(-)	KATNA1	149924489			6	Exon 6 of LATS1(-)	LATS1	149997811			10	DUPLICATION		73322	218402	5878	42	NEW_VARIANT
P-0028712-T01-IM6	ETV6 (NM_001987) rearrangement: t(12;21)(p13.2;q22.3)(chr12:g.11992159::chr21:g.48029480)	PRECISE	Note: The ETV6 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	21	IGR: 11Kb before S100B(-)	S100B	48029480			12	Exon 3 of ETV6(+)	ETV6	11992159			10	TRANSLOCATION		0	218414	0	5	NEW_VARIANT
P-0028715-T01-IM6	DSTYK (NM_015375) - ERBB3 (NM_001982) rearrangement: t(1;12)(q32.1;q13.2)(chr1:g.205142365::chr12:g.56487607)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {DSTYK:ERBB3}		0	0	20	12	Exon 13 of ERBB3(+)	ERBB3	56487607			1	Intron of DSTYK(-):3Kb before exon 3	DSTYK	205142365			0	TRANSLOCATION		0	218517	0	28	NEW_VARIANT
P-0028721-T01-IM6	PTCH1 (NM_000264) rearrangement: c.3550_c.585-138dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		23550	0	19	9	Exon 22 of PTCH1(-)	PTCH1	98211605			9	Intron of PTCH1(-):138bp before exon 4	PTCH1	98244623			10	DUPLICATION		33018	218529	31819	21	NEW_VARIANT
P-0028743-T01-IM6	FGFR3 (NM_000142) rearrangement: c.2274+82:FGFR3_chr4:g.2007790dup	PRECISE	Note: The FGFR3 rearrangement is a duplication of exons 18. This does not include the kinase domain of FGFR3. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		36917	0	37	4	Intron of FGFR3(+):82bp after exon 17	FGFR3	1808743			4	Intron of NELFA(-):3Kb after exon 1	NELFA	2007790			10	DUPLICATION		199047	218561	51927	37	NEW_VARIANT
P-0028745-T01-IM6	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exons 1-12 fused with ALK exons 20-29): c.1523-2563:EML4_c.3172:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		97887	0	134	2	Intron of ALK(-):817bp after exon 19	ALK	29447509			2	Intron of EML4(+):3Kb before exon 13	EML4	42525818			10	INVERSION		13078309	218565	107513	134	NEW_VARIANT
P-0028754-T01-IM6	U2AF1 (NM_006758) rearrangement: t(3;21)(q28-29;q22.3)(chr3:g.192445271::chr21:g.44513280)	PRECISE	Note: The U2AF1 rearrangement is a translocation involving a breakpoint in exon 8. Its functional significance is undetermined	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {FGF12:U2AF1}		0	0	37	21	Exon 8 of U2AF1(-)	U2AF1	44513280			3	5-UTR of FGF12(-):583Kb before coding start	FGF12	192445271			10	TRANSLOCATION		0	218535	0	64	NEW_VARIANT
P-0028759-T01-IM6	FAT1 (NM_005245) rearrangement: c.343:FAT1_chr4:g.190476182del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4528	0	5	4	Exon 2 of FAT1(-)	FAT1	187630639			4	IGR: 105Kb before LINC01262(+)	LINC01262	190476182			10	DELETION		2845543	218531	6346	11	NEW_VARIANT
P-0028761-T01-IM6	PTPRD (NM_002839) rearrangement: c.4387-460_c.4507-118del	PRECISE	Note: The PTPRD rearrangement is an intragenic deletion of exon 38. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1241	0	12	9	Intron of PTPRD(-):118bp before exon 39	PTPRD	8376208			9	Intron of PTPRD(-):460bp before exon 38	PTPRD	8377186			9	DELETION		978	218540	1365	10	NEW_VARIANT
P-0028773-T02-IM6	KMT2A (NM_001197104) rearrangement: chr11:g.60627032_c.946del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		343532	0	9	11	IGR: 8Kb before ZP1(+)	ZP1	60627032			11	Exon 3 of KMT2A(+)	KMT2A	118342820			10	DELETION		57715788	219242	423302	9	NEW_VARIANT
P-0028775-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-1430:TMPRSS2_chr21:g.40053713del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		18446	0	7	21	IGR: 57Kb before LINC00114(-)	LINC00114	40053713			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867935			10	DELETION		2814222	219483	24851	7	NEW_VARIANT
P-0028779-T01-IM6	SZT2 (NM_015284) rearrangement: c.347:SZT2_chr1:g.43175179dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		14246	0	3	1	IGR: 24Kb before CLDN19(-)	CLDN19	43175179			1	Exon 4 of SZT2(+)	SZT2	43870070			7	DUPLICATION		694891	219486	25845	3	NEW_VARIANT
P-0028787-T01-IM6	EWSR1 (NM_013986) rearrangement: t(19;22)(p13.11;q12.2)(chr19:g.17759728::chr22:g.29692321)	PRECISE	Note: The EWSR1 rearrangement is a translocation involving a breakpoint in exon 13 of EWSR1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	22	Exon 13 of EWSR1(+)	EWSR1	29692321			19	Exon 14 of UNC13A(-)	UNC13A	17759728			10	TRANSLOCATION		0	218675	0	6	NEW_VARIANT
P-0028790-T01-IM6	VHL (NM_000551) rearrangement: c.-2662_c.340+1702inv	PRECISE	Note: The VHL rearrangement is an intragenic inversion of exon 1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2986	0	24	3	Promoter of VHL(+):2Kb from tx start	VHL	10180870			3	Intron of VHL(+):2Kb after exon 1	VHL	10185573			10	INVERSION		4703	218634	3613	30	NEW_VARIANT
P-0028842-T01-IM6	APC (NM_000038) rearrangement: c.1743+2529_c.4265dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8291	0	6	5	Intron of APC(+):3Kb after exon 14	APC	112167198			5	Exon 16 of APC(+)	APC	112175556			10	DUPLICATION		8358	218854	6287	6	NEW_VARIANT
P-0028865-T02-IM6	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)	IMPPRECISE	Note: The TPM3 - ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TPM3:ROS1}		0	0	79	6	Intron of ROS1(-):1Kb before exon 35	ROS1	117643589			1	Intron of TPM3(-):3Kb before exon 7	TPM3	154133648			0	TRANSLOCATION		0	220398	0	83	NEW_VARIANT
P-0028892-T01-IM6	KDR (NM_002253) rearrangement: c.1815:KDR_chr4:g.117110034del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		143458	0	2	4	Exon 13 of KDR(-)	KDR	55970982			4	IGR: 111Kb before MIR1973(+)	MIR1973	117110034			7	DELETION		61139052	218988	146491	2	NEW_VARIANT
P-0028915-T01-IM6	PRKCI (NM_002740) rearrangement: c.1068-956_c.1156inv	PRECISE	Note: the PRKCI rearrangement is an intragenic inversion of exon 12. One of the breakpoints is within exon 12. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		291	0	8	3	Intron of PRKCI(+):955bp before exon 12	PRKCI	170001293			3	Exon 12 of PRKCI(+)	PRKCI	170002337			10	INVERSION		1044	219170	403	11	NEW_VARIANT
P-0028918-T01-IM6	HIST1H3I (NM_003533) rearrangement: c.199_chr6:g.27921069del	PRECISE	Note: The HIST1H3I rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3615	0	9	6	Exon 1 of HIST1H3I(-)	HIST1H3I	27839895			6	IGR: 4Kb before OR2B6(+)	OR2B6	27921069			10	DELETION		81174	219227	4453	9	NEW_VARIANT
P-0028933-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.1464:NFE2L2_chr2:g.178089672del.	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		1637	1	72	2	Promoter of HNRNPA3(+):12Kb from tx start	HNRNPA3	178089672			2	Exon 5 of NFE2L2(-)	NFE2L2	178095867			10	DELETION		6195	219305	1865	79	NEW_VARIANT
P-0028933-T01-IM6	EP300 (NM_001429) rearrangement: t(17;22)(q21.31;q13.2)(chr17:g.42537013::chr22:g.41574494)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	165	22	Exon 31 of EP300(+)	EP300	41574494			17	Intron of GPATCH8(-):5Kb after exon 3	GPATCH8	42537013			10	TRANSLOCATION		0	219308	0	174	NEW_VARIANT
P-0028936-T01-IM6	CDK4 (NM_000075) rearrangement: c.354+56_c.-147inv	PRECISE	Note: The CDK4 rearrangement is an inversion of CDK4 exons 1 to 3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		2414	0	4	12	Intron of CDK4(-):55bp after exon 3	CDK4	58144934			12	5-UTR of CDK4(-):4Kb before coding start	CDK4	58146085			8	INVERSION		1151	219299	6474	4	NEW_VARIANT
P-0028937-T01-IM6	POLE (NM_006231) rearrangement: c.3275+23_c.-2875inv	PRECISE	Note: The POLE rearrangement results in the inversion of exons 1-26. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		33169	0	4	12	Intron of POLE(-):22bp after exon 26	POLE	133235858			12	Promoter of POLE(-):66Kb from tx start	POLE	133266776			10	INVERSION		30918	219247	52665	5	NEW_VARIANT
P-0028937-T01-IM6	FGFR1 (NM_001174067) rearrangement: c.2070+59:FGFR1_chr8:g.37619984del	PRECISE	Note: The FGFR1 rearrangement results in the deletion of exons 16-19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		48043	0	20	8	Promoter of PROSC(+):116bp from tx start	PROSC	37619984			8	Intron of FGFR1(-):58bp after exon 15	FGFR1	38272238			10	DELETION		652254	219245	84010	20	NEW_VARIANT
P-0028938-T01-IM6	RASA1 (NM_002890) rearrangement: c.2798:RASA1_chr5:g.42683483inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		103997	0	3	5	Intron of GHR(+):6Kb before exon 3	GHR	42683483			5	Exon 22 of RASA1(+)	RASA1	86681157			4	INVERSION		43997674	219271	236846	3	NEW_VARIANT
P-0028940-T01-IM6	PDGFRA (NM_006206) rearrangement: t(1;4)(p13.1;q12)(chr1:g.116439067::chr4:g.55146618)	PRECISE	Note: The PDGFRA rearrangement is a translocation with a breakpoint in exon 16. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	27	4	Exon 16 of PDGFRA(+)	PDGFRA	55146618			1	IGR: 23Kb before LOC101928995(+)	LOC101928995	116439067			10	TRANSLOCATION		0	219284	0	26	NEW_VARIANT
P-0028941-T01-IM6	CD58 (NM_001779) - VTCN1 (NM_024626) rearrangement: c.364+1033:CD58_c.390:VTCN1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CD58:VTCN1}		3761	0	2	1	Intron of CD58(-):1Kb after exon 2	CD58	117085900			1	Exon 3 of VTCN1(-)	VTCN1	117699251			10	DUPLICATION		613351	219279	7522	5	NEW_VARIANT
P-0028974-T01-IM6	PPP6C (NM_002721) rearrangement: t(5;9)(q14.1;q33.3)(chr5:g.77053105::chr9:g.127951896)	PRECISE	Note: The PPP6C rearrangement is a translocation with a breakpoint within intron 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	84	9	Intron of PPP6C(-):26bp after exon 1	PPP6C	127951896			5	Intron of TBCA(-):19Kb after exon 1	TBCA	77053105			10	TRANSLOCATION		0	219553	0	84	NEW_VARIANT
P-0028995-T01-IM6	TRPC6 (NM_004621) - PGR (NM_000926) rearrangement: c.170+4756:TRPC6_c.2133:PGRdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TRPC6:PGR}		14411	0	18	11	Exon 4 of PGR(-)	PGR	100933257			11	Intron of TRPC6(-):5Kb after exon 1	TRPC6	101449309			0	DELETION		516052	219585	39468	23	NEW_VARIANT
P-0029016-T01-IM6	FANCC (NM_000136) - MAK (NM_001242957) Rearrangement : t(6,9)(p24.2,q22.32)(chr6:g.10809757::chr9:g.97888733)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {FANCC:MAK}		0	0	27	9	Intron of FANCC(-):77bp after exon 9	FANCC	97888733			6	Intron of MAK(-):582bp before exon 6	MAK	10809757			10	TRANSLOCATION		0	219708	0	27	NEW_VARIANT
P-0029016-T01-IM6	ABL1 (NM_005157) Rearrangement : t(7,9)(q31.1,q34.12)(chr7:g.113847210::chr9:g.133710845)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	27	9	Exon 1 of ABL1(+)	ABL1	133710845			7	5-UTR of FOXP2(+):487Kb before coding start	FOXP2	113847210			10	TRANSLOCATION		0	219709	0	40	NEW_VARIANT
P-0029018-T01-IM6	TSC2 (NM_000548) rearrangement: c.1013_c.2246inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		19538	0	4	16	Exon 11 of TSC2(+)	TSC2	2110708			16	Exon 21 of TSC2(+)	TSC2	2122875			10	INVERSION		12167	219704	24980	4	NEW_VARIANT
P-0029022-T01-IM6	SMAD4 (NM_005359) Rearrangement : t(12,18)(q23.1,q21.2)(chr12:g.96912182::chr18:g.48584555)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	12	18	Exon 6 of SMAD4(+)	SMAD4	48584555			12	IGR: 240Kb before CDK17(-)	CDK17	96912182			10	TRANSLOCATION		0	219698	0	12	NEW_VARIANT
P-0029023-T01-IM6	ARID1B (NM_020732) rearrangement: c.3591_chr6:g.67007800del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		395628	0	91	6	IGR: 510Kb before SLC25A51P1(+)	SLC25A51P1	67007800			6	Exon 14 of ARID1B(+)	ARID1B	157510816			10	DELETION		90503016	219732	681507	93	NEW_VARIANT
P-0029024-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2606_c.2243-974inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		2623	0	14	8	Exon 14 of WHSC1L1(-)	WHSC1L1	38162110			8	Intron of WHSC1L1(-):974bp before exon 13	WHSC1L1	38163937			10	INVERSION		1827	219728	5457	16	NEW_VARIANT
P-0029028-T01-IM6	ETV6 (NM_001987) rearrangement: c.33+132_chr12:g.13294731del	PRECISE	Note: The ETV6 rearrangement results in the deletion of exons 2-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		219401	0	13	12	Intron of ETV6(+):132bp after exon 1	ETV6	11803226			12	IGR: 55Kb before EMP1(+)	EMP1	13294731			10	DELETION		1491505	219738	210530	16	NEW_VARIANT
P-0029059-T01-IM6	BRAF (NM_004333) rearrangement: c.1178-1159:BRAF_chr7:g.130724897del	PRECISE	Note: The BRAF rearrangement is a deletion of BRAF exons 1 to 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		26855	0	78	7	3-UTR of LINC-PINT(-):67Kb after coding stop	LINC-PINT	130724897			7	Intron of BRAF(-):1Kb before exon 10	BRAF	140484116			10	DELETION		9759219	219900	35411	78	NEW_VARIANT
P-0029067-T01-IM6	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	PRECISE	Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		166894	0	198	10	Intron of BICC1(+):38Kb before exon 3	BICC1	60423713			10	Intron of FGFR2(-):662bp before exon 18	FGFR2	123240197			10	INVERSION		62816484	219889	166568	234	NEW_VARIANT
P-0029084-T01-IM6	FAT1 (NM_005245) rearrangement:c.5168:FAT1_chr4:g.189982700del	PRECISE	Note: The FAT1 rearrangement is a deletion of exon 10-27. One of the breakpoints is within exon 10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		31152	0	5	4	Exon 10 of FAT1(-)	FAT1	187542572			4	IGR: 598Kb before LINC01262(+)	LINC01262	189982700			10	DELETION		2440128	219973	20390	6	NEW_VARIANT
P-0029091-T01-IM6	RNF43 (NM_017763) rearrangement: c.2309-1047_c.1983del	PRECISE	Note: The RNF43 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4241	0	91	17	Intron of RNF43(-):1Kb before exon 10	RNF43	56433394			17	Exon 9 of RNF43(-)	RNF43	56435154			10	DELETION		1760	219971	3129	98	NEW_VARIANT
P-0029105-T01-IM6	TMPRSS2 (NM_001135099)  - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3000:TMPRSS2_c.18+16661:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		69427	0	67	21	Intron of ERG(-):17Kb after exon 1	ERG	39853626			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873116			10	DELETION		3019490	220279	43842	72	NEW_VARIANT
P-0029141-T01-IM6	SLX4 (NM_032444) rearrangement: c.3651:SLX4_chr16:g.3617116del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		17169	0	24	16	3-UTR of NLRC3(-):10Kb after coding stop	NLRC3	3617116			16	Exon 12 of SLX4(-)	SLX4	3639988			10	DELETION		22872	220438	20172	25	NEW_VARIANT
P-0029152-T01-IM6	RB1 (NM_000321) rearrangement: c.137+44_c.264+1746del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		681	0	36	13	Intron of RB1(+):44bp after exon 1	RB1	48878229			13	Intron of RB1(+):2Kb after exon 2	RB1	48883288			10	DELETION		5059	220417	838	36	NEW_VARIANT
P-0029156-T01-IM6	EGFR (NM_005228) rearrangement: c.2946+126:EGFR_chr7:g.50834558del	PRECISE	Note: The EGFR rearrangement results in the deletion of exons 1-24. The functional significance is undetermined. Of note, no fusion gene transcript involving EGFR was detected by Archer FusionPlex, a targeted RNA assay that was reported separately (M18-11488).	MANUAL_OK	3to5	3to5	-		46325	0	14	7	5-UTR of GRB10(-):174Kb before coding start	GRB10	50834558			7	Intron of EGFR(+):126bp after exon 24	EGFR	55268232			10	DELETION		4433674	220391	70854	14	NEW_VARIANT
P-0029174-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		97945	0	230	2	Intron of ALK(-):262bp before exon 20	ALK	29446656			2	Intron of EML4(+):168bp after exon 19	EML4	42552862			10	INVERSION		13106206	220515	162319	237	NEW_VARIANT
P-0029183-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+4036:TMPRSS2_chr21:g.40098936del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exon 2-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		87271	0	65	21	IGR: 12Kb before LINC00114(-)	LINC00114	40098936			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875841			10	DELETION		2776905	220527	100092	67	NEW_VARIANT
P-0029184-T01-IM6	SMAD3 (NM_005902) - SKOR1 (NM_001258024) rearrangement: c.400+57:SMAD3_c.1585+101:SKOR1del	PRECISE	Note: The SMAD3 - SKOR1 rearrangement is a deletion which results in the fusion of SMAD3 exons 1-2 with SKOR1 exons 7-15	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {SMAD3:SKOR1}		11269	0	65	15	Intron of SMAD3(+):57bp after exon 2	SMAD3	67457483			15	Intron of SKOR1(+):101bp after exon 6	SKOR1	68119531			10	DELETION		662048	220529	4020	68	NEW_VARIANT
P-0029184-T01-IM6	NF1 (NM_001042492) rearrangement: c.5073_c.6006+451del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5987	0	51	17	Exon 37 of NF1(+)	NF1	29653075			17	Intron of NF1(+):451bp after exon 40	NF1	29662500			10	DELETION		9425	220531	2338	56	NEW_VARIANT
P-0029216-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement: c.56-1639:TMPRSS2_chr21:g.40100480del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of TMPRSS2 exons 2 to 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		52341	0	4	21	IGR: 10Kb before LINC00114(-)	LINC00114	40100480			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871755			10	DELETION		2771275	221130	70153	4	NEW_VARIANT
P-0029227-T01-IM6	ARID2 (NM_152641) rearrangement: c.2787:ARDI2_chr12:g.98537965inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		289795	0	7	12	Exon 15 of ARID2(+)	ARID2	46244693			12	IGR: 149Kb before MIR4303(-)	MIR4303	98537965			10	INVERSION		52293272	221141	634369	7	NEW_VARIANT
P-0029254-T01-IM6	CCND2 (NM_001759) rearrangement: t(6;12)(p22.3;p13.32)(chr6:g.21808818::chr12:g.4383256)	PRECISE	Note: The CCND2 rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	22	12	Exon 1 of CCND2(+)	CCND2	4383256			6	5-UTR of CASC15(+):386Kb before coding start	CASC15	21808818			10	TRANSLOCATION		0	221299	0	30	NEW_VARIANT
P-0029273-T01-IM6	NCOR1 (NM_006311) Rearrangement: c.2820+1814_ c.843-78dup	PRECISE	Note: The NCOR1 rearrangement is a duplication of NCOR1 exons 9 to 21. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 13 exons : out of frame		15456	0	18	17	Intron of NCOR1(-):2Kb after exon 21	NCOR1	15999867			17	Intron of NCOR1(-):78bp before exon 9	NCOR1	16052909			10	DUPLICATION		53042	221513	24120	18	NEW_VARIANT
P-0029289-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2302-756:FGFR2_chr10:g.122889706del	IMPPRECISE	Note: The FGFR2 rearrangement is a deletion of FGFR2 exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7647	0	3	10	IGR: 279Kb before WDR11(+)	WDR11	122889706			10	Intron of FGFR2(-):756bp before exon 18	FGFR2	123240291			0	DELETION		350585	221399	11209	3	NEW_VARIANT
P-0029294-T01-IM6	CYLD (NM_001042355) Rearrangement: c.375_c.661del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3028	0	34	16	Exon 3 of CYLD(+)	CYLD	50783984			16	Exon 4 of CYLD(+)	CYLD	50785671			10	DELETION		1687	221392	2737	34	NEW_VARIANT
P-0029294-T01-IM6	LYN (NM_002350) rearrangement: c.1205-100:LYN_chr8:g.57070090inv	PRECISE	Note: The LYN rearrangement is an inversion of LYN exons 12 to 13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4484	0	16	8	Intron of LYN(+):99bp before exon 12	LYN	56911877			8	IGR: 3Kb before PLAG1(-)	PLAG1	57070090			10	INVERSION		158213	221396	4809	16	NEW_VARIANT
P-0029298-T01-IM6	APC (NM_000038) rearrangement: c.3723_c.*2367del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17330	0	73	5	Exon 16 of APC(+)	APC	112175014			5	Promoter of APC(+):109Kb from tx start	APC	112182190			10	DELETION		7176	221402	6565	72	NEW_VARIANT
P-0029299-T01-IM6	NF2 (NM_000268) rearrangement: c.115-3779_c.448-142del	PRECISE	Note: The NF2 rearrangement is an intragenic deletion of NF2 exons 2 to 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		3395	0	9	22	Intron of NF2(+):4Kb before exon 2	NF2	30028961			22	Intron of NF2(+):141bp before exon 5	NF2	30050504			10	DELETION		21543	221406	2152	9	NEW_VARIANT
P-0029315-T02-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12-20): c.304-20462:CCDC6_c.2136+447:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		27715	0	49	10	Intron of RET(+):447bp after exon 11	RET	43610631			10	Intron of CCDC6(-):20Kb before exon 2	CCDC6	61632922			10	INVERSION		18022291	222852	66610	61	NEW_VARIANT
P-0029326-T01-IM6	DIAPH1 (NM_005219) - NTRK1 (NM_002529) rearrangement: t(1;5)(q23.1;q31.3)(chr1:g.156843860::chr5:g.140904837)	PRECISE	Note: The DIAPH1 - NTRK1 rearrangement is a translocation that results in an in-frame fusion of DIAPH1 exons 1-26 with NTRK1 exons 9-17, including the kinase domain of NTRK1.  Additional testing by the Archer targeted RNAseq assay will be performed to further characterize this structural variant if additional material is available; and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {DIAPH1:NTRK1}		0	0	29	5	Intron of DIAPH1(-):767bp after exon 25	DIAPH1	140904837			1	Intron of NTRK1(+):109bp after exon 8	NTRK1	156843860			10	TRANSLOCATION		0	221490	0	30	NEW_VARIANT
P-0029333-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1 - ERG exons 4-11):  c.56-3881:TMPRSS2_c.40-57209:ERG	IMPPRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		47985	0	6	21	Intron of ERG(-):57Kb before exon 4	ERG	39874753			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873997			0	DELETION		2999244	221494	71908	8	NEW_VARIANT
P-0029353-T01-IM6	ATM (NM_000051) Rearrangment: c.8268:ATM_chr11:g.108253231del	PRECISE	Note: The ATM rearrangement is a deletion of exons 56 - 63. One of the breakpoints is within exon 56.  The functional significance is unknown.	MANUAL_OK	3to5	3to5	Antisense Fusion		4967	0	25	11	Exon 56 of ATM(+)	ATM	108206688			11	Promoter of C11orf65(-):495bp from tx start	C11orf65	108253231			10	DELETION		46543	221667	2156	25	NEW_VARIANT
P-0029353-T01-IM6	CARM1 (NM_199141) Rearrangement: c.346+43:CARM1_chr19:g.24480361inv	PRECISE	Note: The CARM1 (NM_199141) rearrangement results the inversion of exons 2-16. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		283487	0	4	19	Intron of CARM1(+):43bp after exon 2	CARM1	11015795			19	IGR: 135Kb before HAVCR1P1(-)	HAVCR1P1	24480361			10	INVERSION		13464566	221668	467830	4	NEW_VARIANT
P-0029354-T01-IM6	ERF (NM_006494) Rearrangement: t(22;19) (2q31.3;19q13.2) (chr2:g.181327407::chr19:g.42754531)	PRECISE	Note: The ERF rearrangement is a translocation involving exon 2. One of the breakpoints is in exon 2. The functional significance is unknown.	MANUAL_OK	5to5	5to5	-		0	0	7	19	Exon 2 of ERF(-)	ERF	42754531			2	IGR: 229Kb before SCHLAP1(+)	SCHLAP1	181327407			10	TRANSLOCATION		0	221648	0	11	NEW_VARIANT
P-0029354-T01-IM6	FGFR1 (NM_001174067) Rearrangment: t(8;19) (8p11.23;19p13.12)(chr8:g.38272399::chr19:g.14765577)	PRECISE	Note: The FGFR1 rearrangment is a translocation involving exon 15. One of the breakpoints is in exon 15. The functional significance is unknown.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	8	19	Intron of EMR3(-):216bp after exon 6	EMR3	14765577			8	Exon 15 of FGFR1(-)	FGFR1	38272399			10	TRANSLOCATION		0	221647	0	15	NEW_VARIANT
P-0029368-T01-IM6	FOXP1 (NM_001244814) rearrangement: c.282+5739_c.1890-27del	PRECISE	Note: The FOXP1 rearrangement is an intragenic deletion of exons 4-16.	MANUAL_OK	3to5	3to5	Deletion of 13 exons : out of frame		9724	0	4	3	Intron of FOXP1(-):27bp before exon 17	FOXP1	71008569			3	Intron of FOXP1(-):6Kb after exon 3	FOXP1	71155948			9	DELETION		147379	221672	14498	4	NEW_VARIANT
P-0029393-T01-IM6	BIRC3 (NM_182962) rearrangement: c.-114+1099_c.519dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2418	0	44	11	5-UTR of BIRC3(+):6Kb before coding start	BIRC3	102189401			11	Exon 3 of BIRC3(+)	BIRC3	102195759			10	DUPLICATION		6358	221700	1879	46	NEW_VARIANT
P-0029393-T01-IM6	FANCA (NM_000135) rearrangement: c.3063_c.*3732del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17139	0	82	16	Promoter of FANCA(-):3Kb from tx start	FANCA	89801277			16	Exon 31 of FANCA(-)	FANCA	89818549			10	DELETION		17272	221699	7868	84	NEW_VARIANT
P-0029393-T01-IM6	RNF43 (NM_017763) - PIBF1 (NM_006346) rearrangement: t(13;17)(q22.1;q22)(chr13:g.73547996::chr17:g.56440469)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {RNF43:PIBF1}		0	0	34	17	Intron of RNF43(-):166bp after exon 5	RNF43	56440469			13	Intron of PIBF1(+):183bp after exon 16	PIBF1	73547996			10	TRANSLOCATION		0	221701	0	34	NEW_VARIANT
P-0029393-T01-IM6	NCOA3 (NM_181659) rearrangement: t(9;20)(p13.3;q13.12)(chr9:g.34739492::chr20:g.46270904)	IMPPRECISE	Note: The NCOA3 rearrangement is a translocation with a breakpoint in intron 16. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	20	Intron of NCOA3(+):52bp before exon 17	NCOA3	46270904			9	IGR: 16Kb before FAM205A(-)	FAM205A	34739492			0	TRANSLOCATION		0	221702	0	11	NEW_VARIANT
P-0029393-T01-IM6	RAD21 (NM_006265) rearrangement: c.-32-1505_c.70del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		423	0	48	8	Exon 2 of RAD21(-)	RAD21	117878899			8	5-UTR of RAD21(-):21Kb before coding start	RAD21	117880505			10	DELETION		1606	221698	795	49	NEW_VARIANT
P-0029398-T01-IM6	PBRM1 (NM_018313) rearrangement: c.139-16_c.-12-459del	PRECISE	Note: The PBRM1 rearrangement results in the deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1105	0	11	3	Intron of PBRM1(-):16bp before exon 3	PBRM1	52712629			3	5-UTR of PBRM1(-):132Kb before coding start	PBRM1	52714198			10	DELETION		1569	221714	1625	12	NEW_VARIANT
P-0029400-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		83225	0	138	2	Intron of ALK(-):658bp after exon 19	ALK	29447668			2	Intron of EML4(+):641bp after exon 12	EML4	42523297			10	INVERSION		13075629	221704	132713	138	NEW_VARIANT
P-0029402-T01-IM6	CSF3R (NM_000760) rearrangement: c.346:CSF3R_chr1:g.33652766inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		39328	0	34	1	IGR: 42Kb before TRIM62(-)	TRIM62	33652766			1	Exon 4 of CSF3R(-)	CSF3R	36940993			10	INVERSION		3288227	221724	62860	45	NEW_VARIANT
P-0029402-T01-IM6	CSF3R (NM_000760) rearrangement: c.1647:CSF3R_chr1:g.33893988inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		24901	0	45	1	IGR: 44Kb before ZSCAN20(+)	ZSCAN20	33893988			1	Exon 13 of CSF3R(-)	CSF3R	36933752			10	INVERSION		3039764	221725	43099	45	NEW_VARIANT
P-0029405-T01-IM6	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	IMPPRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		22613	0	25	21	Intron of ERG(-):21Kb after exon 1	ERG	39849525			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867932			0	DELETION		3018407	221726	35453	25	NEW_VARIANT
P-0029406-T01-IM6	PIK3CB (NM_006219) - KCNAB1 (NM_172160) rearrangement: c.133:PIK3CB_c.275+78559:KCNAB1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PIK3CB:KCNAB1}		89383	0	21	3	Exon 1 of PIK3CB(-)	PIK3CB	138478053			3	Intron of KCNAB1(+):56Kb after exon 1	KCNAB1	155917234			10	INVERSION		17439181	221769	189491	26	NEW_VARIANT
P-0029453-T01-IM6	PTEN (NM_000314) rearrangement: c.203_chr10:g.90743125del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		7945	0	5	10	Exon 3 of PTEN(+)	PTEN	89685308			10	5-UTR of ACTA2(-):48Kb before coding start	ACTA2	90743125			10	DELETION		1057817	221916	3014	6	NEW_VARIANT
P-0029460-T01-IM6	ROS1 (NM_002944) Rearrangement:  c.6178:ROS1_chr6:g.50511502inv	PRECISE	Note: The ROS1 rearrangement in an inversion of exons 39-43.  One breakpoint is in exon 39.  The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		140051	0	4	6	IGR: 170Kb before TFAP2D(+)	TFAP2D	50511502			6	Exon 39 of ROS1(-)	ROS1	117632238			10	INVERSION		67120736	222008	129008	10	NEW_VARIANT
P-0029465-T01-IM6	ARAF (NM_001654) Rearrangment: t(X;2) (Xp11.3;2q22.1-q22.2)(chrX:g.47424257::chr2:g.141622159)	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	21	X	Exon 4 of ARAF(+)	ARAF	47424257			2	Intron of LRP1B(-):3Kb after exon 27	LRP1B	141622159			0	TRANSLOCATION		0	221993	0	21	NEW_VARIANT
P-0029465-T01-IM6	ARAF (NM_001654) Rearrangement: c.554_c.558-3del	PRECISE	Note: The ARAF rearrangement is an intragenic deletion of exon 6.  One of the breakpoints is in exon 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		837	0	24	X	Exon 6 of ARAF(+)	ARAF	47424746			X	Intron of ARAF(+):2bp before exon 7	ARAF	47426035			10	DELETION		1289	221992	778	25	NEW_VARIANT
P-0029542-T01-IM6	RASA1 (NM_002890) rearrangement: c.664:RASA1_chr5:g.89498591del	PRECISE	Note: The RASA1 rearrangement is a deletion of exons  2-25. One of the breakpoints is within exon 2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		20251	0	101	5	Exon 2 of RASA1(+)	RASA1	86627289			5	3-UTR of LINC01339(-):87Kb after coding stop	LINC01339	89498591			10	DELETION		2871302	222143	19249	106	NEW_VARIANT
P-0029550-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		108805	0	12	2	Intron of ALK(-):463bp after exon 19	ALK	29447863			2	Intron of EML4(+):720bp before exon 6	EML4	42507269			10	INVERSION		13059406	222151	145197	11	NEW_VARIANT
P-0029559-T01-IM6	TOP1 (NM_003286) - PTPRG (NM_002841) rearrangement: t(3;20)(p14.2;q12)(chr3:g.61957689::chr20:g.39708821)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TOP1:PTPRG}		0	0	54	20	Intron of TOP1(+):1bp after exon 6	TOP1	39708821			3	Intron of PTPRG(+):18Kb before exon 3	PTPRG	61957689			10	TRANSLOCATION		0	222303	0	54	NEW_VARIANT
P-0029575-T01-IM6	LMO1 (NM_002315) rearrangement: c.-62_chr11:g.6081746inv	PRECISE	Note: The LMO1 rearrangement results in the inversion of the 5' UTR and exons 1-4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		6485	0	87	11	IGR: 34Kb before OR56A1(-)	OR56A1	6081746			11	5-UTR of LMO1(-):39Kb before coding start	LMO1	8284971			10	INVERSION		2203225	222309	8987	87	NEW_VARIANT
P-0029583-T01-IM6	INHBA (NM_002192) rearrangement: c.1178:INHBA_chr7:g.55480357dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		97637	0	5	7	Exon 3 of INHBA(-)	INHBA	41729351			7	Intron of LANCL2(+):575bp after exon 6	LANCL2	55480357			9	DUPLICATION		13751006	222307	161860	5	NEW_VARIANT
P-0029590-T01-IM6	NF2 (NM_000268) - SCUBE1 (NM_173050) rearrangement: c.1737+1355:NF2_c.1084+692:SCUBE1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NF2:SCUBE1}		83349	0	4	22	Intron of NF2(+):1Kb after exon 15	NF2	30078945			22	Intron of SCUBE1(-):691bp after exon 9	SCUBE1	43624386			5	INVERSION		13545441	222382	105246	4	NEW_VARIANT
P-0029594-T01-IM6	TSHR (NM_000369) rearrangement: t(8;14)(q13.3;q31.1)(chr8:g.72056267::chr14:g.81609711)	PRECISE	Note: The TSHR rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	9	14	Exon 10 of TSHR(+)	TSHR	81609711			8	IGR: 53Kb before EYA1(-)	EYA1	72056267			8	TRANSLOCATION		0	222371	0	9	NEW_VARIANT
P-0029597-T01-IM6	DIS3 (NM_014953) rearrangement: c.2128-109:DIS3_chr13:g.73643525del	PRECISE	Note: The DIS3 rearrangement results in the deletion of exons 1-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17006	0	3	13	Intron of DIS3(-):109bp before exon 17	DIS3	73336384			13	Intron of KLF5(+):6Kb after exon 3	KLF5	73643525			9	DELETION		307141	222379	18687	3	NEW_VARIANT
P-0029602-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-5768:CCDC6_c.2137-872:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		41414	0	111	10	Intron of RET(+):871bp before exon 12	RET	43611160			10	Intron of CCDC6(-):6Kb before exon 2	CCDC6	61618228			10	INVERSION		18007068	222421	61286	151	NEW_VARIANT
P-0029604-T01-IM6	POLD1 (NM_002691) rearrangement: c.1494+9_c.1893-26inv	PRECISE	Note: The POLD1 rearrangement results in the inversion of exons 13-15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		5640	0	2	19	Intron of POLD1(+):9bp after exon 12	POLD1	50909783			19	Intron of POLD1(+):25bp before exon 16	POLD1	50912353			6	INVERSION		2570	222408	12089	2	NEW_VARIANT
P-0029617-T02-IM6	MST1R (NM_002447) rearrangement: chr3:g.49859022_c.3065-32dup	PRECISE	Note: The MST1R rearrangement is a duplication that includes MST1R exons 14-20. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		14990	0	25	3	IGR: 7Kb before TRAIP(-)	TRAIP	49859022			3	Intron of MST1R(-):32bp before exon 14	MST1R	49932838			10	DUPLICATION		73816	222453	26209	28	NEW_VARIANT
P-0029644-T01-IM6	ATRX (NM_000489) rearrangement: c.4557+6511_c.4978del	PRECISE	Note: The ATRX rearrangement is an intragenic deletion of exons 16-19. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2256	0	47	X	Exon 19 of ATRX(-)	ATRX	76888851			X	Intron of ATRX(-):7Kb after exon 15	ATRX	76901093			10	DELETION		12242	222477	1451	50	NEW_VARIANT
P-0029645-T01-IM6	EGFR (NM_005228) vIII intragenic deletion: c.89-16253_c.889+66del	PRECISE		MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		10523	0	5	7	Intron of EGFR(+):16Kb before exon 2	EGFR	55193726			7	Intron of EGFR(+):66bp after exon 7	EGFR	55221911			10	DELETION		28185	222456	12894	5	NEW_VARIANT
P-0029723-T01-IM6	TP53BP1 (NM_001141980) rearrangement: c.4514:TP53BP1_chr15:g.100734817inv	PRECISE	Note: The TP53BP1 rearrangement is an inversion of exons 1-21. One of the breakpoints is within exon 21.	MANUAL_OK	5to5	5to5	Antisense Fusion		221459	0	31	15	Exon 21 of TP53BP1(-)	TP53BP1	43712670			15	Intron of ADAMTS17(-):5Kb after exon 8	ADAMTS17	100734817			10	INVERSION		57022147	222751	254831	48	NEW_VARIANT
P-0029726-T01-IM6	FGFR2 (NM_000141) - UBP1 (NM_001128161) fusion: t(3;10)(p22.3;q26.13)(chr3:g.33449450::chr10:g.123240062)	PRECISE	Note: The FGFR2 - UBP1 fusion involves FGFR2 exons 1-17 and UBP1 exons 10-17. The fusion is predicted to be in-frame and includes the kinase domain of FGFR2. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the FGFR2 and UBP1 genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR2:UBP1}		0	0	56	10	Intron of FGFR2(-):527bp before exon 18	FGFR2	123240062			3	Intron of UBP1(-):731bp after exon 9	UBP1	33449450			10	TRANSLOCATION		0	222758	0	56	NEW_VARIANT
P-0029727-T01-IM6	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+12095:SND1_c.1314+564:BRAFinv	PRECISE	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	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SND1:BRAF}		49791	0	93	7	Intron of SND1(+):12Kb after exon 10	SND1	127373549			7	Intron of BRAF(-):563bp after exon 10	BRAF	140482257			10	INVERSION		13108708	222764	69948	93	NEW_VARIANT
P-0029750-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		86506	0	88	2	Intron of ALK(-):266bp before exon 20	ALK	29446660			2	Intron of EML4(+):3Kb before exon 13	EML4	42525807			10	INVERSION		13079147	222842	102772	86	NEW_VARIANT
P-0029756-T01-IM6	HIST1H3H (NM_003536) rearrangement: c.-2156_c.*4452del	PRECISE	Note: The HIST1H3H rearrangement is a deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {HIST1H3H:HIST1H2BM}		2545	0	32	6	Promoter of HIST1H3H(+):2Kb from tx start	HIST1H3H	27775696			6	Promoter of HIST1H2BM(+):107bp from tx start	HIST1H2BM	27782714			10	DELETION		7018	222859	2478	35	NEW_VARIANT
P-0029793-T01-IM6	RECQL4 (NM_004260) rearrangement: t(8;X)(q24.3;p21.2)(chr8:g.145740560::chrX:g.29843951)	IMPPRECISE	Note: The RECQL4 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	5	X	Intron of IL1RAPL1(+):92Kb before exon 7	IL1RAPL1	29843951			8	Exon 8 of RECQL4(-)	RECQL4	145740560			0	TRANSLOCATION		0	223269	0	5	NEW_VARIANT
P-0029796-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3489:TMPRSS2_c.40-58375:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 4-11.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		67392	0	35	21	Intron of ERG(-):58Kb before exon 4	ERG	39875919			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876388			10	DELETION		3000469	223273	70481	36	NEW_VARIANT
P-0029798-T01-IM6	BCL6 (NM_001706) rearrangement: c.2064_chr3:g.168207075inv	PRECISE	Note: The BCL6 rearrangement results in the inversion of exon 10. One of the breakpoints is within exon 10. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EGFEM1P:BCL6}		94934	0	36	3	5-UTR of EGFEM1P(+):341Kb before coding start	EGFEM1P	168207075			3	Exon 10 of BCL6(-)	BCL6	187440303			10	INVERSION		19233228	223267	157729	36	NEW_VARIANT
P-0029801-T01-IM6	FAM193A (NM_003704) - NOTCH4 (NM_004557) rearrangement: t(4;6)(p16.3;p21.32)(chr4:g.2664220::chr6:g.32183122)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {FAM193A:NOTCH4}		0	0	140	6	Exon 12 of NOTCH4(-)	NOTCH4	32183122			4	Intron of FAM193A(+):344bp before exon 9	FAM193A	2664220			10	TRANSLOCATION		0	223263	0	137	NEW_VARIANT
P-0029803-T01-IM6	BAP1 (NM_004656) rearrangement: t(1;3)(p36.22;p21.1)(chr1:g.11870943::chr3:g.52441869)	PRECISE	Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	13	3	Intron of BAP1(-):104bp after exon 5	BAP1	52441869			1	Intron of CLCN6(+):4Kb after exon 2	CLCN6	11870943			10	TRANSLOCATION		0	223264	0	14	NEW_VARIANT
P-0029809-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1-2 with ERG exons 4-10) : c.126+1597:TMPRSS2_c.39+39940:ERGdel	PRECISE	Note: TMPRSS2 is predicted to form fusion with the non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		24776	0	18	21	Intron of ERG(-):40Kb after exon 3	ERG	39907646			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868449			10	DELETION		2960803	222907	26619	19	NEW_VARIANT
P-0029814-T01-IM6	NF1 (NM_001042492) rearrangement: t(8;17)(p12;q11.2)(chr8:g.36189531::chr17:g.29588872)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 35. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	11	17	Exon 35 of NF1(+)	NF1	29588872			8	IGR: 452Kb before KCNU1(+)	KCNU1	36189531			10	TRANSLOCATION		0	222906	0	11	NEW_VARIANT
P-0029819-T01-IM6	ETV6 (NM_001987) rearrangement: c.164-9463_c.463+2991del	PRECISE	Note: The ETV6 rearrangement results in the in-frame deletion of exons 3-4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		17277	0	24	12	Intron of ETV6(+):9Kb before exon 3	ETV6	11982611			12	Intron of ETV6(+):3Kb after exon 4	ETV6	12009486			10	DELETION		26875	222917	21403	25	NEW_VARIANT
P-0029821-T01-IM6	BRD4 (NM_058243) rearrangement: c.3967:BRD4_chr19:g.15337047dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EPHX3:BRD4}		2137	0	4	19	Promoter of EPHX3(-):682bp from tx start	EPHX3	15337047			19	Exon 19 of BRD4(-)	BRD4	15349607			10	DUPLICATION		12560	222938	2890	4	NEW_VARIANT
P-0029823-T01-IM6	ERBB2 (NM_004448) rearrangement: t(11;17)(q13.2;q12)(chr11:g.67137375::chr17:g.37875982)	PRECISE	Note: The ERBB2 rearrangement is a translocation with a breakpoint in intron 15. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	66	17	Intron of ERBB2(+):57bp before exon 16	ERBB2	37875982			11	Intron of CLCF1(-):2Kb before exon 2	CLCF1	67137375			10	TRANSLOCATION		0	222926	0	69	NEW_VARIANT
P-0029835-T01-IM6	YAP1 (NM_001130145) Rearrangement: c.802+5150_c.1276+73dup	PRECISE	Note: The YAP1 rearrangement is an intragenic duplication of exons 5 to 8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		3679	0	8	11	Intron of YAP1(+):5Kb after exon 4	YAP1	102062012			11	Intron of YAP1(+):73bp after exon 8	YAP1	102098385			10	DUPLICATION		36373	222959	7300	8	NEW_VARIANT
P-0029835-T01-IM6	RAD21 (NM_006265) Rearrangement: c.841_c.144+1356del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4296	0	39	8	Exon 8 of RAD21(-)	RAD21	117868501			8	Intron of RAD21(-):1Kb after exon 2	RAD21	117877469			10	DELETION		8968	222958	11075	41	NEW_VARIANT
P-0029843-T01-IM6	SH3BGR (NM_007341) - TMPRSS2 (NM_001135099) rearrangement: c.421-1136:SH3BGR_c.56-2096:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {SH3BGR:TMPRSS2}		39490	0	15	21	Intron of SH3BGR(+):1Kb before exon 3	SH3BGR	40845925			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872212			10	INVERSION		2026287	222997	21227	15	NEW_VARIANT
P-0029849-T01-IM6	B2M (NM_004048) rearrangement: c.67_c.68del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		955	0	9	15	Exon 1 of B2M(+)	B2M	45003811			15	Exon 2 of B2M(+)	B2M	45007621			10	DELETION		3810	222980	1991	11	NEW_VARIANT
P-0029870-T01-IM6	B2M (NM_004048) - TRIM69 (NM_182985) rearrangement: c.67+112:B2M_c.6+8770:TRIM69del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {B2M:TRIM69}		3445	0	3	15	Intron of B2M(+):112bp after exon 1	B2M	45003923			15	Intron of TRIM69(+):9Kb after exon 1	TRIM69	45037678			4	DELETION		33755	223003	2937	5	NEW_VARIANT
P-0029946-T01-IM6	B2M (NM_004048) rearrangement.t(1;15)(p34.1;q21.1)(chr1:g.220072784::chr15:g.45005885)	PRECISE	Note: The B2M rearrangement is a translocation which involves exon 2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	29	15	Intron of B2M(+):2Kb before exon 2	B2M	45005885			1	5-UTR of RNU5F-1(+):220Kb before coding start	RNU5F-1	220072784			10	TRANSLOCATION		0	223352	0	29	NEW_VARIANT
P-0029946-T01-IM6	PLCG2 (NM_002661) rearrangement: c.766-1547_c.1073-108del	PRECISE	Note: The PLCG2 rearrangement is an intragenic deletion of exons 10-12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		3765	0	51	16	Intron of PLCG2(+):2Kb before exon 10	PLCG2	81921230			16	Intron of PLCG2(+):107bp before exon 13	PLCG2	81929304			10	DELETION		8074	223347	1859	51	NEW_VARIANT
P-0029946-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.3402:SMARCA4_chr19:g.11239260inv	PRECISE	Note: The SMARCA4 rearrangement is an inversion of exons 25-35. One of the breakpoints is within exon 25. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		20161	0	128	19	Exon 25 of SMARCA4(+)	SMARCA4	11141425			19	Intron of LDLR(+):499bp after exon 16	LDLR	11239260			10	INVERSION		97835	223349	32763	147	NEW_VARIANT
P-0029946-T01-IM6	EP300 (NM_001429) rearrangement: c.4780-794_c.5476del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5662	0	159	22	Intron of EP300(+):793bp before exon 30	EP300	41571457			22	Exon 31 of EP300(+)	EP300	41573191			10	DELETION		1734	223348	2734	164	NEW_VARIANT
P-0029948-T01-IM6	TRIM33 (NM_015906) - NUF2 (NM_031423) rearrangement: c.1420+682:TRIM33_c.624:NUF2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TRIM33:NUF2}		258820	0	38	1	Intron of TRIM33(-):681bp after exon 8	TRIM33	114969117			1	Exon 9 of NUF2(+)	NUF2	163310171			10	INVERSION		48341054	223342	280919	39	NEW_VARIANT
P-0029948-T01-IM6	CDK6 (NM_001145306) - PPP1R9A (NM_001166161) rearrangement: c.834+73:CDK6_c.1396-13757:PPP1R9Ainv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CDK6:PPP1R9A}		6146	0	5	7	Intron of CDK6(-):72bp after exon 7	CDK6	92247313			7	Intron of PPP1R9A(+):14Kb before exon 2	PPP1R9A	94726814			0	INVERSION		2479501	223344	7180	5	NEW_VARIANT
P-0029956-T01-IM6	PARK2 (NM_004562) Rearrangement : c.535-124_735-37385dup	PRECISE	Note: The PARK2 Rearrangement results in the intragenic duplication of exons 5-6 of PARK2.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		1899	0	8	6	Intron of PARK2(-):37Kb before exon 7	PARK2	162244325			6	Intron of PARK2(-):124bp before exon 5	PARK2	162475330			10	DUPLICATION		231005	223374	3413	8	NEW_VARIANT
P-0029963-T01-IM6	NTRK3 (NM_001012338) Rearrangement : c.836-1619:GABRB3_c.1586-40642:NTRK3inv	PRECISE	Note: The NTRK3 Rearrangement results in the inversion of exons 15-20 of NTRK3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		235499	0	16	15	Intron of GABRB3(-):2Kb before exon 9	GABRB3	26807942			15	Intron of NTRK3(-):41Kb before exon 15	NTRK3	88524626			10	INVERSION		61716684	223378	111523	16	NEW_VARIANT
P-0030029-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement: c.126+73_c.55+4105del	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		31224	0	79	21	Intron of TMPRSS2(-):72bp after exon 2	TMPRSS2	42869973			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875772			10	DELETION		5799	223523	27500	88	NEW_VARIANT
P-0030032-T01-IM6	TSEN2 (NM_001145392) - SETD2 (NM_014159) Rearrangement: c.309-1282:TSEN2_c.6196:SETD2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TSEN2:SETD2}		90318	0	94	3	Intron of TSEN2(+):1Kb before exon 5	TSEN2	12543479			3	Exon 14 of SETD2(-)	SETD2	47103750			10	INVERSION		34560271	223515	176419	94	NEW_VARIANT
P-0030033-T01-IM6	DROSHA (NM_013235) Rearrangement: c.2882+9_c.2821+121inv	IMPPRECISE	Note: The DROSHA rearrangement is an intragenic inversion of exon 22. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		726	0	23	5	Intron of DROSHA(-):8bp after exon 22	DROSHA	31448645			5	Intron of DROSHA(-):120bp after exon 21	DROSHA	31449267			0	INVERSION		622	223525	902	29	NEW_VARIANT
P-0014464-T02-IM6	NF1 (NM_001042492) rearrangement : c.7180_c.7189+2041del	PRECISE	Note: The NF1 rearrangement results in the deletion of exon 48. One of the breakpoints is within exon 48. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		473	0	28	17	Exon 48 of NF1(+)	NF1	29670144			17	Intron of NF1(+):2Kb after exon 48	NF1	29672195			10	DELETION		2051	223324	215	28	NEW_VARIANT
P-0030107-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4157:TMPRSS2_c.40-57456:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		58118	0	11	21	Intron of ERG(-):57Kb before exon 4	ERG	39875000			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874273			10	DELETION		2999273	224427	59204	12	NEW_VARIANT
P-0030109-T01-IM6	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.120-27147:SLC25A21_c.32:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC25A21:FOXA1}		9695	0	4	14	Intron of SLC25A21(-):27Kb before exon 3	SLC25A21	37310353			14	Exon 1 of FOXA1(-)	FOXA1	38064146			8	DUPLICATION		753793	224436	12158	4	NEW_VARIANT
P-0030109-T01-IM6	TP53 (NM_000546) rearrangement: c.375+66:TP53_chr17:g.3605902del	PRECISE	Note: The TP53 rearrangement results in the deletion of exons 5-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		24419	0	27	17	IGR: 12Kb before ITGAE(-)	ITGAE	3605902			17	Intron of TP53(-):65bp after exon 4	TP53	7579246			10	DELETION		3973344	224433	20872	29	NEW_VARIANT
P-0030109-T01-IM6	ASXL1 (NM_015338) rearrangement: c.1627:ASXL1_chr20:g.33684946del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		43198	0	16	20	Exon 11 of ASXL1(+)	ASXL1	31021628			20	IGR: 18Kb before EDEM2(-)	EDEM2	33684946			10	DELETION		2663318	224434	34677	17	NEW_VARIANT
P-0030109-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2838:TMPRSS2_c.40-58598:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		20623	0	8	21	Intron of ERG(-):58Kb before exon 4	ERG	39875207			21	Intron of TMPRSS2(-):703bp before exon 3	TMPRSS2	42867208			10	DELETION		2992001	224435	16413	9	NEW_VARIANT
P-0008431-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused with ERG exons 4-11) : c.56-1980:TMPRSS2_c.40-52619:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		77898	0	9	21	Intron of ERG(-): 124bp after exon 1	ERG	39870163			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872096			9	DELETION		3001933	122128	70234	9	NEW_VARIANT
P-0021526-T02-IM6	KMT2B (NM_014727) rearrangement: c.5460:KMT2B_chr19:g.32548661inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		62874	0	198	19	IGR: 32Kb before LINC01533(+)	LINC01533	32548661			19	Exon 27 of KMT2B(+)	KMT2B	36222831			10	INVERSION		3674170	224024	125005	265	NEW_VARIANT
P-0029892-T04-IM6	PLEKHA6 (NM_014935) - NTRK1 (NM_002529) fusion: c.2032+105:PLEKHA6_c.1195+47:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {PLEKHA6:NTRK1}		150096	0	91	1	Intron of NTRK1(+):47bp after exon 9	NTRK1	156844239			1	Intron of PLEKHA6(-):104bp after exon 14	PLEKHA6	204214638			10	INVERSION		47370399	223477	175077	105	NEW_VARIANT
P-0029892-T04-IM6	PTEN (NM_000314) rearrangement: c.528_c.1027-1146dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3794	0	27	10	Exon 6 of PTEN(+)	PTEN	89711910			10	Intron of PTEN(+):1Kb before exon 9	PTEN	89723898			10	DUPLICATION		11988	223476	2914	28	NEW_VARIANT
P-0030133-T01-IM6	NF2 (NM_000268) rearrangement: c.1300:NF2_chr22:g.20027873inv	IMPPRECISE	Note: The NF2 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		136971	0	5	22	Intron of TANGO2(+):3Kb before exon 3	TANGO2	20027873			22	Exon 12 of NF2(+)	NF2	30069435			0	INVERSION		10041562	224489	197482	6	NEW_VARIANT
P-0030134-T01-IM6	AKT2 (NM_001626) rearrangement: c.640-179:AKT2_chr19:g.40736136inv	PRECISE	Note: The AKT2 rearrangement is an inversion of exons 1-7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12626	0	8	19	Promoter of AKT2(-):87bp from tx start	AKT2	40736136			19	Intron of AKT2(-):179bp before exon 8	AKT2	40745059			10	INVERSION		8923	224483	18625	8	NEW_VARIANT
P-0030135-T01-IM6	ERBB4 (NM_005235) rearrangement: c.422-572_c.549dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		757	0	19	2	Exon 4 of ERBB4(-)	ERBB4	212652757			2	Intron of ERBB4(-):572bp before exon 4	ERBB4	212653456			10	DUPLICATION		699	224475	679	19	NEW_VARIANT
P-0030184-T01-IM6	KMT2D (NM_003482) rearrangement: c.8096:KMT2D_chr12:g.75706091inv	PRECISE	Note: The KMT2D rearrangement is an inversion of exons 1-32. One of the breakpoints is within exon 32. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		219536	0	53	12	Exon 32 of KMT2D(-)	KMT2D	49433351			12	Intron of CAPS2(-):536bp after exon 8	CAPS2	75706091			10	INVERSION		26272740	224604	244765	85	NEW_VARIANT
P-0030184-T01-IM6	PBRM1 (NM_018313) rearrangement:     c.4386:PBRM1_chr3:g.22617724del	PRECISE	Note: The PBRM1 rearrangement is a deletion of exons 29-30. One of the breakpoints is within exon 29. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		227420	0	12	3	IGR: 619Kb before ZNF385D-AS2(+)	ZNF385D-AS2	22617724			3	Exon 29 of PBRM1(-)	PBRM1	52584627			10	DELETION		29966903	224602	238638	13	NEW_VARIANT
P-0030187-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4546:TMPRSS2_c.18+5296:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		70107	0	41	21	Intron of ERG(-):5Kb after exon 1	ERG	39864991			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874662			10	DELETION		3009671	224596	51652	44	NEW_VARIANT
P-0030213-T01-IM6	LIN37 (NM_019104) - KMT2B (NM_014727) rearrangement: c.444+169:LIN37_c.7483:KMT2Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LIN37:KMT2B}		5115	0	58	19	Exon 33 of KMT2B(+)	KMT2B	36228097			19	Intron of LIN37(+):169bp after exon 6	LIN37	36244323			10	DUPLICATION		16226	224679	14845	62	NEW_VARIANT
P-0030261-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4365:TMPRSS2_c.39+58079:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		62988	0	114	21	Intron of ERG(-):58Kb after exon 3	ERG	39889507			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875512			10	DELETION		2986005	224742	58029	115	NEW_VARIANT
P-0030267-T01-IM6	CPM (NM_001005502) - FGFR1 (NM_001174067) rearrangement: t(8;12)(q11.23;q15)(chr8:g.38272053::chr12:g.69274149)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {FGFR1:CPM}		0	0	53	12	Intron of CPM(-):5Kb after exon 3	CPM	69274149			8	Intron of FGFR1(-):23bp after exon 16	FGFR1	38272053			10	TRANSLOCATION		0	224747	0	52	NEW_VARIANT
P-0012630-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 3-11): c.56-1480:TMPRSS2_c.-47-4326:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	-		50141	0	22	21	3-UTR of ERG(-):82Kb after coding stop	ERG	39951997			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871596			10	DELETION		2919599	224831	89736	74	NEW_VARIANT
P-0012630-T02-IM6	PIK3R1 (NM_181523) rearrangement: c.1735_chr5:g.143970832inv	PRECISE	Note: The PIK3R1 rearrangement is an inversion that includes PIK3R1 exons 13-16. One of the breakpoints is within exon 13.	MANUAL_OK	3to3	3to3	-		175876	0	52	5	Exon 13 of PIK3R1(+)	PIK3R1	67591142			5	IGR: 420Kb before KCTD16(+)	KCTD16	143970832			10	INVERSION		76379690	224833	239955	59	NEW_VARIANT
P-0030345-T01-IM6	FLT3 (NM_004119) rearrangement: t(6;13)(q16.1;q12.2)(chr6:g.98003011::chr13:g.:28623849)	PRECISE	Note: The FLT3 rearrangement is a translocation with a breakpoint within FLT3 exon 7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {LOC101927314:FLT3}		0	0	33	13	Exon 7 of FLT3(-)	FLT3	28623849			6	5-UTR of LOC101927314(+):154Kb before coding start	LOC101927314	98003011			10	TRANSLOCATION		0	225403	0	33	NEW_VARIANT
P-0030345-T01-IM6	NCOR1 (NM_006311) rearrangement: c.1353-60_chr17:g.19331269inv	PRECISE	Note: The NCOR1 rearrangement is an inversion that includes NCOR1 exons 1-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		36822	0	24	17	Intron of NCOR1(-):60bp before exon 13	NCOR1	16041586			17	IGR: 17Kb before RNF112(+)	RNF112	19331269			10	DELETION		3289683	225401	67001	26	NEW_VARIANT
P-0015960-T02-IM6	U2AF2 (NM_007279) - HIST1H3B (NM_003537) rearrangement: t(6;19)(p22.2;q13.42)(chr6:g.26032161::chr19:g.56181895)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {U2AF2:HIST1H3B}		0	0	20	19	Intron of U2AF2(+):837bp after exon 11	U2AF2	56181895			6	Exon 1 of HIST1H3B(-)	HIST1H3B	26032161			10	TRANSLOCATION		0	225350	0	61	NEW_VARIANT
P-0015960-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.56-116:TMPRSS2_c.40-64777:ERGdel	PRECISE	Note: The TMPRSS2 is fused with the non-canonical ERG(NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		46214	0	91	21	Intron of ERG(-):65Kb before exon 4	ERG	39882321			21	Intron of TMPRSS2(-):116bp before exon 2	TMPRSS2	42870232			10	DELETION		2987911	225336	46135	150	NEW_VARIANT
P-0015960-T02-IM6	PBRM1 (NM_018313) Rearrangemnet: c.996-371_c.899+68inv	IMPPRECISE	Note: The PBRM1 rearrangement is an intragenic inversion of PBRM1 exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1628	0	3	3	Intron of PBRM1(-):371bp before exon 11	PBRM1	52676432			3	Intron of PBRM1(-):67bp after exon 9	PBRM1	52678652			0	INVERSION		2220	225338	1884	3	NEW_VARIANT
P-0030228-T01-IM6	IGF1 (NM_001111285) - GLT8D2 (NM_031302) rearrangement: c.307:IGF1_c.112+4819:GLT8D2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {IGF1:GLT8D2}		3912	0	2	12	Exon 3 of IGF1(-)	IGF1	102813382			12	Intron of GLT8D2(-):5Kb after exon 4	GLT8D2	104403972			10	DUPLICATION		1590590	225296	5660	2	NEW_VARIANT
P-0030232-T01-IM6	ARID1A (NM_006015) rearrangement: c.1138-12301_c.2252-8del	PRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 2-6.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : out of frame		8957	0	51	1	Intron of ARID1A(+):12Kb before exon 2	ARID1A	27043841			1	Intron of ARID1A(+):7bp before exon 7	ARID1A	27088635			10	DELETION		44794	225284	10470	51	NEW_VARIANT
P-0030289-T01-IM6	INSR (NM_000208) Rearrangement: c.3478_c.2842+540del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6660	0	60	19	Exon 19 of INSR(-)	INSR	7122676			19	Intron of INSR(-):539bp after exon 14	INSR	7131629			10	DELETION		8953	225308	10064	65	NEW_VARIANT
P-0030322-T01-IM6	FOXP1 (NM_001244814) Rearrangement: c.869+11517_c.664+50del	PRECISE	Note: The FOXP1 rearrangement is an intragenic deletion of exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1462	0	25	3	Intron of FOXP1(-):12Kb after exon 7	FOXP1	71078962			3	Intron of FOXP1(-):49bp after exon 6	FOXP1	71096043			10	DELETION		17081	225359	2090	27	NEW_VARIANT
P-0030333-T01-IM6	CCND1 (NM_053056) Rearrangement: c.20_chr11:g.85739851del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		111270	0	24	11	Exon 1 of CCND1(+)	CCND1	69456101			11	Intron of PICALM(-):2Kb before exon 3	PICALM	85739851			10	DELETION		16283750	225369	159932	24	NEW_VARIANT
P-0030333-T01-IM6	MDC1 (NM_014641) rearrangement: t(6;15)(p21.32;q12)(chr6:g.30675950::chr15:g.27671033)	PRECISE	Note: The MDC1 rearrangement is a translocation that may result in a truncation of exons 8-15. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	40	15	Intron of GABRG3(+):55Kb before exon 6	GABRG3	27671033			6	Exon 8 of MDC1(-)	MDC1	30675950			10	TRANSLOCATION		0	225374	0	40	NEW_VARIANT
P-0030333-T01-IM6	ICOSLG (NM_015259) Rearrangement: t(12;21)(q33.3;q22.3)(chr13:g.107684536::chr21:g.45656951)	PRECISE	Note: The ICOSLG rearrangement is a translocation that may result in a truncation of exons 3-7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	49	21	Exon 3 of ICOSLG(-)	ICOSLG	45656951			13	IGR: 136Kb before FAM155A(-)	FAM155A	107684536			10	TRANSLOCATION		0	225375	0	48	NEW_VARIANT
P-0030408-T01-IM6	TCEB2 (NM_207013) - BAP1 (NM_004656) rearrangement: t(3;16)(p21.1;p13.3)(chr3:g.52438638::chr16:g.2824342)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TCEB2:BAP1}		0	0	48	16	Intron of TCEB2(-):1Kb after exon 3	TCEB2	2824342			3	Intron of BAP1(-):36bp before exon 12	BAP1	52438638			10	TRANSLOCATION		0	225802	0	51	NEW_VARIANT
P-0030449-T01-IM6	RUNX1 (NM_001754) rearrangement: t(21;X)(q22.12;p11.3)(chr21:g.36206846::chrX:g.46136512)	PRECISE	Note: The RUNX1 rearrangement is a translocation with a breakpoint in exon 7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	13	X	IGR: 49Kb before LINC01186(-)	LINC01186	46136512			21	Exon 7 of RUNX1(-)	RUNX1	36206846			8	TRANSLOCATION		0	225916	0	13	NEW_VARIANT
P-0030453-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-2396:KIF5B_c.2136+727:RETinv	PRECISE	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. This sample has been nominated for analysis using the Archer targeted RNAseq assay to further characterize the structural variant. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		51349	0	39	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32314360			10	Intron of RET(+):727bp after exon 11	RET	43610911			10	INVERSION		11296551	225907	58966	52	NEW_VARIANT
P-0019765-T02-IM6	NOTCH3 (NM_000435) - LARP4B (NM_015155) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.941664::chr19:g.15275995)	PRECISE	Note: The NOTCH3 - LARP4B rearrangement is a translocation with breakpoints within NOTCH3 intron 31 and LARP4B intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	10	19	Intron of NOTCH3(-):183bp after exon 31	NOTCH3	15275995			10	5-UTR of LARP4B(-):83Kb before coding start	LARP4B	941664			10	TRANSLOCATION		0	225879	0	10	NEW_VARIANT
P-0019765-T02-IM6	BRD4 (NM_058243) - IDI2 (NM_033261) rearrangement: t(10;19)(p15.3;p13.12)(chr10:g.1065652::chr19:g.15376225)	PRECISE	Note: The BRD4 - IDI2 rearrangement is a translocation with breakpoints within BRD4 exon 5 and IDI2 exon 5. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	87	19	Exon 5 of BRD4(-)	BRD4	15376225			10	Exon 5 of IDI2(-)	IDI2	1065652			10	TRANSLOCATION		0	225880	0	87	NEW_VARIANT
P-0027193-T03-IM6	IL20 (NM_018724) - IKBKE (NM_014002) Rearrangement : c.398:IL20_c.2046-146:IKBKE	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {IL20:IKBKE}		7582	0	8	1	Intron of IKBKE(+):145bp before exon 21	IKBKE	206667107			1	Exon 4 of IL20(+)	IL20	207040748			0	DUPLICATION		373641	225513	15406	8	NEW_VARIANT
P-0030303-T01-IM6	BRAF (NM_004333) rearrangement: c.1141-61:BRAF_chr9:g.142397017inv	IMPPRECISE	Note: The BRAF rearrangement results in the inversion of exons 1-8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		92603	0	6	7	Intron of BRAF(-):61bp before exon 9	BRAF	140487445			7	IGR: 23Kb before MTRNR2L6(+)	MTRNR2L6	142397017			0	INVERSION		1909572	226623	100142	6	NEW_VARIANT
P-0030374-T01-IM6	KDM5C (NM_004187) Rearrangement : c.2061+750_c.2226del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1489	0	13	X	Exon 15 of KDM5C(-)	KDM5C	53228176			X	Intron of KDM5C(-):749bp after exon 14	KDM5C	53229982			10	DELETION		1806	225522	1484	13	NEW_VARIANT
P-0030381-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion : c.55+3863:TMPRSS2_c.18+9727:ERGdel	PRECISE	TMPRSS2 exon1 with ERG exon2	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		72459	0	162	21	Intron of ERG(-):10Kb after exon 1	ERG	39860560			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42876014			10	DELETION		3015454	225517	102994	168	NEW_VARIANT
P-0030382-T01-IM6	NCOR1 (NM_006311) - PIGL (NM_004278) Rearrangement : c.1866:NCOR1_c.335+13717:PIGLinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NCOR1:PIGL}		17848	0	6	17	Exon 17 of NCOR1(-)	NCOR1	16022786			17	Intron of PIGL(+):14Kb after exon 2	PIGL	16151101			0	INVERSION		128315	225520	24323	7	NEW_VARIANT
P-0030520-T01-IM6	HIST2H3D (NM_001123375) rearrangement: t(1;11)(q21.2;q14.1)(chr1:g.149785203::chr11:g.82997912)	IMPPRECISE	Note: The HIST2H3D rearrangement is a translocation with a breakpoint within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {HIST2H3D:CCDC90B}		0	0	7	11	Promoter of CCDC90B(-):28Kb from tx start	CCDC90B	82997912			1	Exon 1 of HIST2H3D(-)	HIST2H3D	149785203			0	TRANSLOCATION		0	226528	0	14	NEW_VARIANT
P-0030527-T01-IM6	EDF1 (NM_003792) - TRAF2 (NM_021138) rearrangement: c.291+54:EDF1_c.970:TRAF2del	PRECISE	Note: The EDF1 - TRAF2 rearrangement is a deletion that includes EDF1 exons 1-3 and TRAF2 exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14569	0	8	9	Intron of EDF1(-):107bp after exon 3	EDF1	139757686			9	Exon 9 of TRAF2(+)	TRAF2	139815499			10	DELETION		57813	226527	17355	8	NEW_VARIANT
P-0030528-T01-IM6	ERF (NM_006494) - CIC (NM_015125) rearrangemnet: c.22+337:ERF_c.1018:CICdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10842	0	103	19	Intron of ERF(-):336bp after exon 1	ERF	42758793			19	Exon 7 of CIC(+)	CIC	42793126			10	DELETION		34333	226535	1538	115	NEW_VARIANT
P-0009743-T01-IM5	TP53 (NM_000546)  rearrangement: c.993+582_c.826del	IMPRECISE	Note: The TP53 (NM_000546) rearrangement is a intragenic deletion of exons 8-9. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		6521	0	101	17	Intron of TP53(-): 582bp after exon 9	TP53	7576271			17	Exon 8 of TP53(-)	TP53	7577112			0	DELETION		841	136337	3927	104	NEW_VARIANT
P-0030308-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement : c.*93:_c.193+8893del	PRECISE	Note: The CDKN2Ap14ARF rearrangement results in the deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4161	0	7	9	Exon 2 of CDKN2A(-)	CDKN2A	21970909			9	Intron of CDKN2A(-):9Kb after exon 1	CDKN2A	21985245			10	DELETION		14336	226621	3614	7	NEW_VARIANT
P-0030308-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement : c.449:CDKN2Ap16INK4A_chr9:g.21985245del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0		7	9	Intron of CDKN2Ap16INK4A(-):9Kb after exon 1	CDKN2Ap16INK4A	21970909			9	Intron of ARID4B(-):136bp before exon 13	CDKN2Ap16INK4A	21985245			10	DELETION		14336	226987	3614		NEW_VARIANT
P-0030462-T01-IM6	BRAF (NM_004333) rearrangement: chr7:g.140429032_c.1177+1038dup	PRECISE	Note: The BRAF rearrangement is a duplication that includes BRAF exons 10-18, including the kinase domain.	MANUAL_OK	5to3	5to3	-		51102	0	116	7	IGR: 5Kb before BRAF(-)	BRAF	140429032			7	Intron of BRAF(-):1Kb after exon 9	BRAF	140486310			10	DUPLICATION		57278	226602	92947	123	NEW_VARIANT
P-0030466-T01-IM6	DAXX (NM_001141970) rearrangement: c.2200-20_chr6:g.64186175del	PRECISE	Note: The DAXX rearrangement is a deletion that includes DAXX exons 1-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		91188	0	10	6	Intron of DAXX(-):20bp before exon 8	DAXX	33286599			6	IGR: 96Kb before PTP4A1(+)	PTP4A1	64186175			10	DELETION		30899576	226597	95428	10	NEW_VARIANT
P-0030469-T01-IM6	RAD51D (NM_133629) rearrangement: c.145-32:RAD51D_chr17:g.33433532del	IMPPRECISE	Note: The RAD51D rearrangement is a deletion that includes exons 1-2 of RAD51D. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		298847	0	6	17	Intron of RAD51D(-):32bp before exon 3	RAD51D	33433532			17	IGR: 20Kb before CDK5RAP3(+)	CDK5RAP3	46068807			0	DELETION		12635275	226600	391300	7	NEW_VARIANT
P-0030472-T01-IM6	NEGR1 (NM_173808) rearrangement: c.901_c.940+11245del	PRECISE	Note: The NEGR1 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		511	0	14	1	Intron of NEGR1(-):11Kb after exon 6	NEGR1	72047255			1	Exon 6 of NEGR1(-)	NEGR1	72058539			10	DELETION		11284	226599	340	14	NEW_VARIANT
P-0030580-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.18+1813:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion includes the TMRSS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		57466	0	62	21	Intron of ERG(-):2Kb after exon 1	ERG	39868474			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873112			10	DELETION		3004638	226762	38664	101	NEW_VARIANT
P-0030622-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exons 12 - 20): c.304-5054:CCDC6_c.2136+566:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		33543	0	25	10	Intron of RET(+):566bp after exon 11	RET	43610750			10	Intron of CCDC6(-):5Kb before exon 2	CCDC6	61617514			10	INVERSION		18006764	226923	22407	34	NEW_VARIANT
P-0030593-T01-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.*106:FGFR2_c.2565+1927:TACC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		50807	0	191	10	3-UTR of FGFR2(-):105bp after coding stop	FGFR2	123239265			10	Intron of TACC2(+):4Kb after exon 13	TACC2	123991882			10	INVERSION		752617	226776	298908	213	NEW_VARIANT
P-0030626-T01-IM6	MST1R (NM_002447) - PBRM1 (NM_018313) rearrangement: c.2650-33_c.1924+418dup	PRECISE	Note: The MST1R - PBRM1 rearrangement is a duplication that results in the fusion of MST1R exons 1-10 with PBRM1 exons 17-30.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {MST1R:PBRM1}		68043	0	21	3	Intron of MST1R(-):33bp before exon 11	MST1R	49933573			3	Intron of PBRM1(-):417bp after exon 16	PBRM1	52648949			10	DUPLICATION		2715376	227056	71224	23	NEW_VARIANT
P-0030626-T01-IM6	MDC1 (NM_014641) rearrangement: c.5527_chr6:g.64207942dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		242093	0	8	6	Exon 10 of MDC1(-)	MDC1	30671433			6	IGR: 74Kb before PTP4A1(+)	PTP4A1	64207942			10	DUPLICATION		33536509	227057	258974	9	NEW_VARIANT
P-0030641-T01-IM6	PRKCI (NM_002740) rearrangement: t(3;7)(q26.2;q31.2)(chr3:g.169997993::chr7:g.116889371)	PRECISE	Note: The PRKCI rearrangement is a translocation with a breakpoint within intron 8. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	15	7	IGR: 27Kb before WNT2(-)	WNT2	116889371			3	Intron of PRKCI(+):21bp before exon 9	PRKCI	169997993			10	TRANSLOCATION		0	227019	0	27	NEW_VARIANT
P-0030675-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 5-11): c.55+1904:TMPRSS2_c.40-59905:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		67023	0	48	21	Intron of ERG(-):60Kb before exon 4	ERG	39877449			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877973			10	DELETION		3000524	227107	57788	49	NEW_VARIANT
P-0030717-T01-IM6	EZH1 (NM_001991) rearrangement: c.2098+98:EZH1_chr17:g.40439374del	PRECISE	Note: The EZH1 rearrangement results in the deletion of exons 1-19. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		68863	0	52	17	Promoter of STAT5A(+):190bp from tx start	STAT5A	40439374			17	Intron of EZH1(-):97bp after exon 19	EZH1	40855660			10	DELETION		416286	227261	48665	53	NEW_VARIANT
P-0030721-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.29_c.461del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2146	0	59	3	Exon 3 of CTNNB1(+)	CTNNB1	41266032			3	Exon 4 of CTNNB1(+)	CTNNB1	41266664			10	DELETION		632	227278	1573	65	NEW_VARIANT
P-0002375-T02-IM6	WT1 (NM_024426) - TAPT1 (NM_153365) rearrangement: t(4;11)(p15.32;p13)(chr4:g.16168647::chr11:g.32456161)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {WT1:TAPT1}		0	0	8	11	Intron of WT1(-):84bp after exon 1	WT1	32456161			4	Intron of TAPT1(-):231bp before exon 13	TAPT1	16168647			10	TRANSLOCATION		0	227272	0	8	NEW_VARIANT
P-0002375-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-470:TMPRSS2_c.19-14125:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exons 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		46567	0	27	21	Intron of ERG(-):14Kb before exon 2	ERG	39831669			21	Intron of TMPRSS2(-):470bp before exon 2	TMPRSS2	42870586			0	DELETION		3038917	227270	44320	27	NEW_VARIANT
P-0002901-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		28803	0	27	21	Intron of ERG(-): 4Kb after exon 1	ERG	39866331			21	Intron of TMPRSS2(-): 999bp after exon 2	TMPRSS2	42869047			29	DELETION		3002716	6149	31924	29	NEW_VARIANT
P-0002901-T01-IM3		PRECISE	looks real, but same breakpoint as with erg!	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (NR3C2-TMPRSS2)		0	0	25	21	Intron of TMPRSS2(-): 891bp after exon 2	TMPRSS2	42869155			4	Intron of NR3C2(-): 32Kb before exon 3	NR3C2	149213311			23	TRANSLOCATION		0	6160	0	0	NEW_VARIANT
P-0030719-T01-IM6	ARNTL2 (NM_001248002) - KDM5A (NM_001042603) rearrangement: c.285-4357:ARNTL2_c.1992:KDM5A	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARNTL2:KDM5A}		313237	0	12	12	Exon 15 of KDM5A(-)	KDM5A	432924			12	Intron of ARNTL2(+):4Kb before exon 3	ARNTL2	27528823			10	INVERSION		27095899	227260	396561	12	NEW_VARIANT
P-0030773-T01-IM6	CIC (NM_015125) rearrangement: c.2934:CIC_chr19:g.32449624inv	PRECISE	Note: The CIC rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12.	MANUAL_OK	5to5	5to5	-		203040	0	109	19	IGR: 67Kb before LINC01533(+)	LINC01533	32449624			19	Exon 12 of CIC(+)	CIC	42796285			10	INVERSION		10346661	227364	309503	133	NEW_VARIANT
P-0030745-T01-IM6	POLE (NM_006231) rearrangement: t(8;12)(q12.1;q24.33)(chr8:g.58136160::chr12:g.133256566)	IMPPRECISE	Note: The POLE rearrangement is a translocation with a breakpoint in exon 5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	19	12	Exon 5 of POLE(-)	POLE	133256566			8	5-UTR of LOC100507651(+):9Kb before coding start	LOC100507651	58136160			0	TRANSLOCATION		0	227349	0	19	NEW_VARIANT
P-0030749-T01-IM6	BRCA1 (NM_007294) rearrangement: c.670+105_c.4675+1206del	PRECISE	Note: The BRCA1 rearrangement is an intragenic deletion of exons 10-14.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		23741	0	28	17	Intron of BRCA1(-):1Kb after exon 14	BRCA1	41225142			17	Intron of BRCA1(-):104bp after exon 9	BRCA1	41247758			10	DELETION		22616	227352	15154	29	NEW_VARIANT
P-0030749-T01-IM6	SMAD4 (NM_005359) rearrangement:  c.455-2248_c.1139+85inv	PRECISE	Note: The SMAD4 rearrangement is an intragenic inversion of exons 5-9.	MANUAL_OK	3to3	3to3	Antisense Fusion		4085	0	7	18	Intron of SMAD4(+):2Kb before exon 5	SMAD4	48578903			18	Intron of SMAD4(+):85bp after exon 9	SMAD4	48592061			10	INVERSION		13158	227353	4609	7	NEW_VARIANT
P-0030750-T01-IM6	FGF19 (NM_005117) rearrangement: c.641:FGF19_chr11:g.69526352del	IMPPRECISE	Note: The FGF19 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5287	0	10	11	Exon 3 of FGF19(-)	FGF19	69514040			11	IGR: 13Kb before FGF19(-)	FGF19	69526352			0	DELETION		12312	227356	11317	12	NEW_VARIANT
P-0030750-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.5028_c.7470+1675del	PRECISE	Note: The ANKRD11 rearrangement is an intragenic deletion of a part of exon 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7996	0	114	16	Intron of ANKRD11(-):2Kb after exon 9	ANKRD11	89343805			16	Exon 9 of ANKRD11(-)	ANKRD11	89347922			10	DELETION		4117	227357	18920	118	NEW_VARIANT
P-0030720-T01-IM6	PREX2 (NM_024870) - DCN (NM_133503) rearrangement: t(8;12)(q13.2;q21.33)(chr8:g.68965387::chr12:g.91564661)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PREX2:DCN}		0	0	12	12	Intron of DCN(-):6Kb before exon 3	DCN	91564661			8	Exon 9 of PREX2(+)	PREX2	68965387			10	TRANSLOCATION		0	227267	0	10	NEW_VARIANT
P-0003274-T02-IM6	RARA (NM_000964) Rearrangement : t(5;17)(p14.1;q21.1)(chr5:g.25855191::chr17:g. 38510622)	PRECISE	Note: The RARA Rearrangement is a translocation event with the breakpoint in exon7. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	49	17	Exon 7 of RARA(+)	RARA	38510622			5	IGR: 1Mb before LOC340107(-)	LOC340107	25855191			10	TRANSLOCATION		0	227667	0	51	NEW_VARIANT
P-0003274-T02-IM6	DROSHA (NM_013235) Rearrangement : chr5:g.13054033_c.1555:DROSHAdel	PRECISE	Note: The DROSHA Rearrangement results in the deletion of exons 9-35 of DROSHA. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		55895	0	67	5	IGR: 479Kb before LINC01194(+)	LINC01194	13054033			5	Exon 9 of DROSHA(-)	DROSHA	31508760			10	DELETION		18454727	227649	104600	71	NEW_VARIANT
P-0019819-T02-IM6	EWSR1 (NM_013986) - ZNRF3 (NM_001206998) rearrangement: c.793+1474:EWSR1_c.744+199:ZNRF3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EWSR1:ZNRF3}		8336	0	25	22	Intron of ZNRF3(+):199bp after exon 5	ZNRF3	29441077			22	Exon 9 of EWSR1(+)	EWSR1	29684597			10	DUPLICATION		243520	227769	14442	29	NEW_VARIANT
P-0019819-T02-IM6	ARHGEF38 (NM_001242729) - TET2 (NM_001127208) rearrangement: c.197-16141:ARHGEF38_c.3804-40:TET2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ARHGEF38:TET2}		10578	0	27	4	Intron of TET2(+):39bp before exon 7	TET2	106180736			4	Intron of ARHGEF38(+):16Kb before exon 2	ARHGEF38	106494264			10	DUPLICATION		313528	227766	18385	27	NEW_VARIANT
P-0030792-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement: c.127-1213:TMPRSS2_chr21:g.40102198del	PRECISE	Note: The TMPRSS2 rearrangement is an deletion of TMPRSS2 exons 3 to 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		22710	0	42	21	IGR: 9Kb before LINC00114(-)	LINC00114	40102198			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867718			10	DELETION		2765520	227531	32494	43	NEW_VARIANT
P-0030808-T01-IM6	HMBOX1 (NM_001135726) ALK (NM_004304) Rearrangement : t(2,8)(p23.3,p21.1)(chr2:g.29447713::chr8:g.28904937)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {HMBOX1:ALK}		0	0	115	8	Exon 8 of HMBOX1(+)	HMBOX1	28904937			2	Intron of ALK(-):613bp after exon 19	ALK	29447713			10	TRANSLOCATION		0	227670	0	115	NEW_VARIANT
P-0030812-T01-IM6	PTEN (NM_000314) rearrangement: t(1;10)(q21.3;q23.31)(chr1:g.151714790::chr10:g.89725115)	PRECISE	Note: The PTEN rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	17	10	Exon 9 of PTEN(+)	PTEN	89725115			1	IGR: 17Kb before MRPL9(-)	MRPL9	151714790			10	TRANSLOCATION		0	227678	0	17	NEW_VARIANT
P-0030812-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1054:TMPRSS2_c.40-56880:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		33707	0	20	21	Intron of ERG(-):57Kb before exon 4	ERG	39874424			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867559			10	DELETION		2993135	227677	18920	21	NEW_VARIANT
P-0030845-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.56-579:TMPRSS2_c.40-59079:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		44031	0	70	21	Intron of ERG(-):59Kb before exon 4	ERG	39876623			21	Intron of TMPRSS2(-):579bp before exon 2	TMPRSS2	42870695			10	DELETION		2994072	227715	47653	79	NEW_VARIANT
P-0030847-T01-IM6	SMAD4 (NM_005359) Rearrangement: t(1;18)(q32.1;q21.2)(chr1:g.201465436::chr18:g.48584640)	IMPPRECISE	Note: The SMAD4 rearrangement is a translocation that results in the possible truncation of SMAD4. The functionals significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {SMAD4:CSRP1}		0	0	13	18	Intron of SMAD4(+):26bp after exon 6	SMAD4	48584640			1	5-UTR of CSRP1(-):12Kb before coding start	CSRP1	201465436			0	TRANSLOCATION		0	227730	0	13	NEW_VARIANT
P-0030872-T01-IM6	TET1 (NM_030625) rearrangement: t(3;10)(q25.31;q21.3)(chr3:g.156287710::chr10:g.70446541)	PRECISE	Note: The TET1 rearrangement is a translocation with a breakpoint in intron 11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	18	10	Intron of TET1(+):77bp after exon 11	TET1	70446541			3	IGR: 30Kb before SSR3(-)	SSR3	156287710			10	TRANSLOCATION		0	227774	0	17	NEW_VARIANT
P-0030872-T01-IM6	TPAN4 (NM_001025238) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p15.5;q22.3)(chr11:g.:865773::chr21:g.42867997)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TSPAN4:TMPRSS2}		0	0	16	21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867997			11	Exon 7 of TSPAN4(+)	TSPAN4	865773			10	TRANSLOCATION		0	227775	0	16	NEW_VARIANT
P-0030872-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2562:TMPRSS2_c.18+12161:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		51346	0	8	21	Intron of ERG(-):12Kb after exon 1	ERG	39858126			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872678			10	DELETION		3014552	227772	79428	13	NEW_VARIANT
P-0030872-T01-IM6	MX1 (NM_001178046) - TMPRSS2 (NM_001135099) rearrangement: c.1432+622:MX1_c.56-2534:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {MX1:TMPRSS2}		45819	0	25	21	Intron of MX1(+):4Kb after exon 9	MX1	42821844			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872650			10	INVERSION		50806	227773	71106	25	NEW_VARIANT
P-0030872-T01-IM6	TMPRSS2 (NM_001135099) - POLDIP3 (NM_032311) rearrangement: t(21;22)(q22.3;q13.2)(chr21:g.:42867864::chr22:g.43009989)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:POLDIP3}		0	0	32	22	Intron of POLDIP3(-):815bp after exon 1	POLDIP3	43009989			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867864			10	TRANSLOCATION		0	227776	0	32	NEW_VARIANT
P-0004887-T01-IM5	The NFE2L2 (NM_006164) - ZNF385B (NM_152520) rearrangement: c.123:NFE2L2_c.253+111221:ZNF385Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (NFE2L2-ZNF385B)		9323	0	6	2	Exon 2 of NFE2L2(-)	NFE2L2	178098922			2	Intron of ZNF385B(-): 87Kb after exon 1	ZNF385B	180523009			4	DUPLICATION		2424087	40309	11277	6	NEW_VARIANT
P-0007699-T02-IM5	FOXA1 (NM_004496) rearrangement: chr14:g.38304410_c.341:FOXA1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3712	0	30	14	Exon 2 of FOXA1(-)	FOXA1	38061648			14	IGR: 245Kb before FOXA1(-)	FOXA1	38304410			29	DELETION		242762	119870	1632	30	NEW_VARIANT
P-0012051-T01-IM5	GREM1 (NM_013372) rearrangement : c.*3295_chr15:g.49277656inv	PRECISE	Note: The GREM1 rearrangement event results in the inversion of the 3 UTR of GREM1. The functional significance of this event is uncertain.	MANUAL_OK	3to3	3to3	-		276002	0	26	15	3-UTR of GREM1(+): 3Kb after coding stop	GREM1	33026741			15	IGR: 3Kb before SECISBP2L(-)	SECISBP2L	49277656			36	INVERSION		16250915	156013	220355	26	NEW_VARIANT
P-0030660-T01-IM6	NF1 (NM_001042492) Rearrangement: c.4835+15100_c.5610-70del	IMPPRECISE	Note: The NF1 rearrangement is an intragenic deletion of exons 37 to 38. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		4419	0	5	17	Intron of NF1(+):15Kb after exon 36	NF1	29607457			17	Intron of NF1(+):69bp before exon 39	NF1	29657244			0	DELETION		49787	227101	3292	5	NEW_VARIANT
P-0030876-T01-IM6	ERBB2 (NM_004448) Rearrangement: c.1283_c.1947-13inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		6166	0	33	17	Exon 11 of ERBB2(+)	ERBB2	37871759			17	Intron of ERBB2(+):12bp before exon 17	ERBB2	37879559			10	INVERSION		7800	227790	13763	33	NEW_VARIANT
P-0030897-T01-IM6	HOXB13 (NM_006361) Rearrangement : c.114_c.602-398dup	IMPPRECISE	Note: The HOXB13 Rearrangement results in the intragenic duplication of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3492	0	7	17	Intron of HOXB13(-):398bp before exon 2	HOXB13	46804803			17	Exon 1 of HOXB13(-)	HOXB13	46805842			0	DUPLICATION		1039	227803	4774	8	NEW_VARIANT
P-0030935-T01-IM6	SMARCA4 (NM_003072) rearrangement: t(8;19)(q24.12;p13.2)(chr8:g.121126818::chr19:g.11097142)	PRECISE	Note: The SMARCA4 rearrangement is a translocation involving a breakpoint within exon 4. Its functional significance is undetermined	MANUAL_OK	3to3	3to3	-		0	0	24	19	Exon 4 of SMARCA4(+)	SMARCA4	11097142			8	IGR: 11Kb before COL14A1(+)	COL14A1	121126818			10	TRANSLOCATION		0	228051	0	24	NEW_VARIANT
P-0000122-T02-IM6	STAT3 (NM_139276) rearrangement: c.1056_c.2102-1006dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		18608	0	153	17	Intron of STAT3(-):1Kb before exon 22	STAT3	40470248			17	Exon 11 of STAT3(-)	STAT3	40483543			10	DUPLICATION		13295	227822	37590	172	NEW_VARIANT
P-0030787-T01-IM6	RAD21 (NM_006265) Rearrangement: c.1470+83:RAD21_chr8:g.96518250del	PRECISE	Note: The RAD21 rearrangement is a deletion of exons 12 to 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		13245	0	10	8	5-UTR of C8orf37-AS1(+):304Kb before coding start	C8orf37-AS1	96518250			8	Intron of RAD21(-):82bp after exon 11	RAD21	117864104			10	DELETION		21345854	227520	21223	10	NEW_VARIANT
P-0031044-T01-IM6	FGFR3 (NM_000142) Rearrangement: c.1266+139:FGFR3_chr4:g.15330489del	PRECISE	Note: The FGFR3 rearrangement is a deletion of exons 10-18. Its functional significance is undetermined,	MANUAL_OK	3to5	3to5	-		61176	0	9	4	Intron of FGFR3(+):139bp after exon 9	FGFR3	1806386			4	3-UTR of LOC101929095(-):99Kb after coding stop	LOC101929095	15330489			10	DELETION		13524103	228393	90295	8	NEW_VARIANT
P-0031056-T01-IM6	TCEB1 (NM_005648) rearrangement: t(8;18)(q21.11;p11.31)(chr8:g.74859058::chr18:g.4459373)	PRECISE	Note: The TCEB1 rearrangement is a translocation with a breakpoint in intron 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	5	18	IGR: 195Kb before DLGAP1-AS5(+)	DLGAP1-AS5	4459373			8	Intron of TCEB1(-):3bp before exon 4	TCEB1	74859058			10	TRANSLOCATION		0	228469	0	10	NEW_VARIANT
P-0030958-T01-IM6	EP300 (NM_001429) Rearrangement: c.4780-76_c.6691del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		13669	0	52	22	Intron of EP300(+):75bp before exon 30	EP300	41572175			22	Exon 31 of EP300(+)	EP300	41574406			10	DELETION		2231	228170	15532	56	NEW_VARIANT
P-0030962-T01-IM6	CREBBP (NM_004380) Rearrangement:  t(5;16)(p15.1;p13.3)(chr5:g.15641044::chr16:g.3929765)	PRECISE	Note: The CREBBP rearrangement is a translocation which results in the possible truncation of exons 2-31. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	84	16	Intron of CREBBP(-):67bp after exon 1	CREBBP	3929765			5	Intron of FBXL7(+):25Kb after exon 2	FBXL7	15641044			10	TRANSLOCATION		0	228169	0	84	NEW_VARIANT
P-0030980-T01-IM6	FAT1 (NM_005245) rearrangement: c.3990:FAT1_chr4:g.187948271del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 1-6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	-		18856	0	5	4	Exon 6 of FAT1(-)	FAT1	187557372			4	IGR: 277Kb before LOC339975(-)	LOC339975	187948271			10	DELETION		390899	228226	26349	5	NEW_VARIANT
P-0031082-T01-IM6	PLK2 (NM_006622) Rearrangement : c.969:PLK2_chr5:g.77184889del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24825	0	9	5	Exon 7 of PLK2(-)	PLK2	57753047			5	5-UTR of LOC101929154(+):70Kb before coding start	LOC101929154	77184889			10	DELETION		19431842	228583	25586	9	NEW_VARIANT
P-0031188-T01-IM6	CTCF (NM_006565) rearrangement: t(16;21)(q22.1;q21.1)(chr16:g.:67671612::chr21:g.17465819)	PRECISE	Note: The CTCF rearrangement is a translocation with with a breakpoint within exon 12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MIR99AHG:CTCF}		0	0	108	21	5-UTR of MIR99AHG(+):516Kb before coding start	MIR99AHG	17465819			16	Exon 12 of CTCF(+)	CTCF	67671612			10	TRANSLOCATION		0	228964	0	109	NEW_VARIANT
P-0031189-T01-IM6	TSC2 (NM_00054) rearrangement: t(16;19)(p13.3;q13.32)(chr16:g.2122449::chr19:g.47992744)	PRECISE	Note: The TSC2 rearrangement is a translocation with a breakpoint within intron 20.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	69	19	Intron of NAPA(-):223bp after exon 10	NAPA	47992744			16	Intron of TSC2(+):85bp after exon 20	TSC2	2122449			10	TRANSLOCATION		0	228949	0	71	NEW_VARIANT
P-0031189-T01-IM6	AXL (NM_021913) rearrangement: chr19:g.31603461_c.662inv	IMPPRECISE	Note: The AXL rearrangement is an inversion that includes AXL exons 1-5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		171754	0	34	19	IGR: 162Kb before TSHZ3(-)	TSHZ3	31603461			19	Exon 5 of AXL(+)	AXL	41736947			0	INVERSION		10133486	228946	210878	34	NEW_VARIANT
P-0031202-T01-IM6	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;q22.1)(chr6:g.157505664::chr10:g.73062411)	PRECISE	Note: The ARID1B rearrangement is a translocation with a breakpoint within intron 13.	MANUAL_OK	5to3	5to3	-		0	0	8	10	3-UTR of UNC5B(+):90Kb after coding stop	UNC5B	73062411			6	Intron of ARID1B(+):95bp after exon 13	ARID1B	157505664			10	TRANSLOCATION		0	228745	0	9	NEW_VARIANT
P-0031208-T01-IM6	CBFB (NM_022845) rearrangement: c.165+56_chr16:g.73099214inv	IMPPRECISE	Note: The CBFB rearrangement is an inversion that includes exons 3-6.	MANUAL_OK	3to3	3to3	-		151025	0	8	16	Intron of CBFB(+):56bp after exon 2	CBFB	67063772			16	IGR: 27Kb before HCCAT5(+)	HCCAT5	73099214			0	INVERSION		6035442	228753	132536	8	NEW_VARIANT
P-0015961-T02-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		153951	0	49	2	Intron of ALK(-):132bp before exon 20	ALK	29446526			2	Intron of EML4(+):7Kb before exon 6	EML4	42501324			10	INVERSION		13054798	184380	182979	48	NEW_VARIANT
P-0030981-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.9641_c.10810del	PRECISE	Note: The ZFHX3 rearrangement is an intragenic deletion with both breakpoints in exon 10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3225	0	15	16	Exon 10 of ZFHX3(-)	ZFHX3	72821365			16	Exon 10 of ZFHX3(-)	ZFHX3	72822534			10	DELETION		1169	228233	5701	15	NEW_VARIANT
P-0030981-T01-IM6	EZH2 (NM_004456) rearrangement: c.1088_c.1947+246del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3921	0	25	7	Intron of EZH2(-):245bp after exon 16	EZH2	148508471			7	Exon 10 of EZH2(-)	EZH2	148515121			10	DELETION		6650	228232	4726	25	NEW_VARIANT
P-0030988-T01-IM6	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2349:TRIM24_c.1140+3106:BRAFinv	PRECISE	Note: The TRIM24 - BRAF fusion involves TRIM24 exons 1-15 and BRAF exons 9-18, which include the kinase domain. One of the breakpoints is within TRIM24 exon 15. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the TRIM24 and BRAF genes. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TRIM24:BRAF}		46371	0	25	7	Exon 15 of TRIM24(+)	TRIM24	138264041			7	Intron of BRAF(-):3Kb after exon 8	BRAF	140491002			10	INVERSION		2226961	228244	40876	25	NEW_VARIANT
P-0031131-T01-IM6	KMT2D (NM_003482) Rearrangement: c.4239_c.9112dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		48933	0	19	12	Exon 34 of KMT2D(-)	KMT2D	49432027			12	Exon 15 of KMT2D(-)	KMT2D	49440571			10	DUPLICATION		8544	228613	66968	19	NEW_VARIANT
P-0031135-T01-IM6	C16orf52 (NM_001164579) - ERCC4 (NM_005236) Rearrangement: c.107-5101:C16orf52_c.793-2:ERCC4dup	PRECISE	Note: The C16orf52  - ERCC4 rearrangement is a duplication of C16orf52 exon 1 to ERCC4 eonxs 5 to 11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {C16orf52:ERCC4}		14107	0	7	16	Intron of ERCC4(+):1bp before exon 5	ERCC4	14024565			16	Intron of C16orf52(+):5Kb before exon 2	C16orf52	22081707			10	DUPLICATION		8057142	228614	9037	7	NEW_VARIANT
P-0031153-T01-IM6	ETV6 (NM_001987) Rearrangement: c.1208:ETV6_chr12:g.6833024inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		203377	0	19	12	Promoter of COPS7A(+):424bp from tx start	COPS7A	6833024			12	Exon 7 of ETV6(+)	ETV6	12038915			10	INVERSION		5205891	228664	117256	21	NEW_VARIANT
P-0031155-T01-IM6	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	PRECISE	Note: The FGFR3 - TACC3 fusion is predicted to be in-frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		33729	0	20	4	Intron of TACC3(+):125bp after exon 7	TACC3	1737177			4	Intron of FGFR3(+):54bp after exon 17	FGFR3	1808715			10	DUPLICATION		71538	228669	49489	20	NEW_VARIANT
P-0018493-T01-IM6	NF2 (NM_000268) rearrangement: c.1000-75:NF2_chr22:g.29992870del	PRECISE	Note: The NF2 rearrangement is a deletion of exons 1-11.	MANUAL_OK	3to5	3to5	-		7206	0	14	22	IGR: 7Kb before NF2(+)	NF2	29992870			22	Intron of NF2(+):74bp before exon 11	NF2	30067740			10	DELETION		74870	179162	8079	14	NEW_VARIANT
P-0030545-T02-IM6	MAP2K2 (NM_030662) rearrangement: t(19;22)(p13.3;q13.2)(chr19:g.4095405::chr22:g.41578462)	PRECISE	Note: The MAP2K2 rearrangement is a translocation with breakpoint is exon 9. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	37	22	Promoter of EP300(+):90Kb from tx start	EP300	41578462			19	Exon 9 of MAP2K2(-)	MAP2K2	4095405			10	TRANSLOCATION		0	229124	0	37	NEW_VARIANT
P-0030545-T02-IM6	WHSC1 (NM_001042424) rearrangement: c.3032:WHSC1_chr4:g.1824058del	PRECISE	Note: The WHSC1 rearrangement is a deletion of exons 1-17. One of the breakpoints is within exon 17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		22577	0	39	4	Intron of LETM1(-):19bp before exon 10	LETM1	1824058			4	Exon 17 of WHSC1(+)	WHSC1	1961244			10	DELETION		137186	229122	26479	41	NEW_VARIANT
P-0030964-T01-IM6	VEGFA (NM_001171623) rearrangement: c.-325_c.91del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1403	0	32	6	5-UTR of VEGFA(+):324bp before coding start	VEGFA	43738659			6	Exon 2 of VEGFA(+)	VEGFA	43742102			10	DELETION		3443	229131	2383	32	NEW_VARIANT
P-0030969-T01-IM6	ARID1B (NM_020732) rearrangement: c.2183_c.2282-3671del	PRECISE	Note: The ARID1B rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		603	0	3	6	Exon 6 of ARID1B(+)	ARID1B	157405941			6	Intron of ARID1B(+):4Kb before exon 7	ARID1B	157427935			5	DELETION		21994	229130	778	3	NEW_VARIANT
P-0030976-T01-IM6	KDM6A (NM_021140) rearrangement: t(22;X)(q11.22;p11.3)(chr22:g.22661479::chrX:g.44919395)	PRECISE	Note: The KDM6A rearrangement is a translocation with a breakpoint in exon 13. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	7	X	Exon 13 of KDM6A(+)	KDM6A	44919395			22	5-UTR of BMS1P20(+):16Kb before coding start	BMS1P20	22661479			10	TRANSLOCATION		0	229136	0	40	NEW_VARIANT
P-0031265-T01-IM6	CTNNB1 (NM_001904) Rearrangement: c.-48-6776_c.382del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3473	0	54	3	5-UTR of CTNNB1(+):7Kb before coding start	CTNNB1	41258736			3	Exon 4 of CTNNB1(+)	CTNNB1	41266585			10	DELETION		7849	229287	1878	56	NEW_VARIANT
P-0031241-T01-IM6	STK11 (NM_000455) rearrangement: c.-34_c.290+793del	PRECISE	Note: The STK11 rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript		2478	0	5	19	5-UTR of STK11(+):33bp before coding start	STK11	1206879			19	Intron of STK11(+):793bp after exon 1	STK11	1207995			10	DELETION		1116	228834	1106	5	NEW_VARIANT
P-0000120-T02-IM6	MDM4 (NM_002393) rearrangement: t(1;8)(q32.1;q23.3)(chr1:g.204507560::chr8:g.114388613)	PRECISE	Note: The MDM4 rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	18	8	Intron of CSMD3(-):60Kb after exon 1	CSMD3	114388613			1	Intron of MDM4(+):124bp after exon 7	MDM4	204507560			10	TRANSLOCATION		0	229175	0	18	NEW_VARIANT
P-0003061-T02-IM6	SHQ1 (NM_018130) rearrangement: t(3;7)(p13;p11.2)(chr3:g.72893631::chr7:g.55694452)	PRECISE	Note: The SHQ1 rearrangement is a translocation involving exon 2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	27	7	IGR: 54Kb before FKBP9P1(-)	FKBP9P1	55694452			3	Intron of SHQ1(-):57bp before exon 2	SHQ1	72893631			10	TRANSLOCATION		0	216764	0	27	NEW_VARIANT
P-0003678-T02-IM6	(NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.127-714:TMPRSS2_c.40-61240:ERGdel	PRECISE	Note: The fusion involves the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		27874	0	22	21	Intron of ERG(-):61Kb before exon 4	ERG	39878784			21	Intron of TMPRSS2(-):714bp before exon 3	TMPRSS2	42867219			10	DELETION		2988435	229346	20720	26	NEW_VARIANT
P-0007322-T02-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.454-1512:CCDC6_c.2136+84:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		38944	0	67	10	Intron of RET(+):84bp after exon 11	RET	43610268			10	Intron of CCDC6(-):2Kb before exon 3	CCDC6	61593923			10	INVERSION		17983655	229778	57738	83	NEW_VARIANT
P-0027418-T01-IM6	MSH6 (NM_000179) rearrangement: c.2542:MSH6_chr2:g.32398951inv	PRECISE	Note: The MSH6 rearrangement is an inversion of exons 1-4. One of the breakpoints is within exon 4. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		128590	0	14	2	Intron of SLC30A6(+):180bp before exon 2	SLC30A6	32398951			2	Exon 4 of MSH6(+)	MSH6	48027664			10	INVERSION		15628713	214002	192803	14	NEW_VARIANT
P-0028007-T01-IM6	C12orf56 (NM_001170633) - KDR (NM_002253) rearrangement: t(4;12)(q12;q14.2)(chr4:g.55984933::chr12:g.64672804)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {C12orf56:KDR}		0	0	5	12	Intron of C12orf56(-):1Kb before exon 9	C12orf56	64672804			4	Exon 3 of KDR(-)	KDR	55984933			10	TRANSLOCATION		0	215581	0	5	NEW_VARIANT
P-0028017-T01-IM6	RAD54L (NM_001142548) rearrangement: t(1;16)(p34.1;q22.1)(chr1:g.46714267::chr16:g.67982423)	PRECISE	Note: The RAD54L rearrangement is a translocation with a breakpoint within RD54L exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	1	85	16	Intron of SLC12A4(-):361bp before exon 14	SLC12A4	67982423			1	Exon 3 of RAD54L(+)	RAD54L	46714267			10	TRANSLOCATION		0	215588	0	102	NEW_VARIANT
P-0031030-T02-IM6	PTEN (NM_000314) Rearrangement: c.493-154_c.1027-1433dup	PRECISE	Note: The PTEN rearrangement is an intragenic duplication of exons 6 to 8. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		3386	0	22	10	Intron of PTEN(+):153bp before exon 6	PTEN	89711721			10	Intron of PTEN(+):1Kb before exon 9	PTEN	89723611			10	DUPLICATION		11890	229935	6701	24	NEW_VARIANT
P-0031270-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Rearrangement: c.127-1111:TMPRSS2_c.-149-7749:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		33832	0	44	21	3-UTR of ERG(-):69Kb after coding stop	ERG	39964618			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867616			10	DELETION		2902998	229281	18636	53	NEW_VARIANT
P-0031274-T01-IM6	CDH1 (NM_004360) rearrangement: c.48+112_c.164-22319inv	IMPPRECISE	Note: The CDH1 rearrangement is an intragenic inversion of exon 2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		1924	0	5	16	Intron of CDH1(+):112bp after exon 1	CDH1	68771478			16	Intron of CDH1(+):22Kb before exon 3	CDH1	68813254			0	INVERSION		41776	229302	2827	5	NEW_VARIANT
P-0031406-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-5 with ALK exons 20-29): c.668-2889:EML4_c.3173-31:ALKinv	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		106271	0	84	2	Intron of ALK(-):31bp before exon 20	ALK	29446425			2	Intron of EML4(+):3Kb before exon 6	EML4	42505101			10	INVERSION		13058676	229557	144564	85	NEW_VARIANT
P-0031409-T01-IM6	TP53 (NM_000546) Rearrangement : c.-28-1861_c.811dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		13293	0	19	17	Exon 8 of TP53(-)	TP53	7577127			17	5-UTR of TP53(-):9Kb before coding start	TP53	7581801			10	DUPLICATION		4674	229562	14712	20	NEW_VARIANT
P-0031410-T01-IM6	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) Rearrangement : c.7+117:TP53BP1_c.3770:PPIP5K1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TP53BP1:PPIP5K1}		1300	0	21	15	Intron of TP53BP1(-):116bp after exon 1	TP53BP1	43785118			15	Exon 30 of PPIP5K1(-)	PPIP5K1	43827329			10	DUPLICATION		42211	229581	1050	21	NEW_VARIANT
P-0031412-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.55+3832:TMPRSS2_c.19-22354:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		73552	0	157	21	Intron of ERG(-):22Kb before exon 2	ERG	39839898			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42876045			10	DELETION		3036147	229567	98508	167	NEW_VARIANT
P-0031413-T01-IM6	KIAA1731(NM_033395) -ATM (NM_000051) Rearrangement : c.5750-2662:KIAA1731_ c.5178-173:ATMdel	PRECISE	Note: The KIAA1731 -ATM  Rearrangement results in the fusion of exon18 of  KIAA1731  with ATM exon35. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CEP295:ATM}		119123	0	19	11	Intron of CEP295(+):3Kb before exon 19	CEP295	93451816			11	Intron of ATM(+):172bp before exon 35	ATM	108172202			10	DELETION		14720386	229560	132907	19	NEW_VARIANT
P-0031419-T01-IM6	ETV6 (NM_001987) Rearrangement : t(7,12)(q11.21;p13.2) (chr7:g.62515009::chr7:g.12028600)	PRECISE	Note: The ETV6 rearrangement results is a translocation event that results with a breakpoint in intron 5. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	169	12	Intron of ETV6(+):6Kb after exon 5	ETV6	12028600			7	IGR: 237Kb before ZNF733P(-)	ZNF733P	62515009			10	TRANSLOCATION		0	229619	0	168	NEW_VARIANT
P-0031429-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 fused to ERG exon 2-10) :c.56-2568:TMPRSS2_c.40-46240:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		47214	0	4	21	Intron of ERG(-):7Kb after exon 1	ERG	39863784			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872684			10	DELETION		3008900	229658	20984	12	NEW_VARIANT
P-0031430-T01-IM6	NOTCH3 (NM_000435) Rearrangement: c.*2656_c.3587inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		30237	0	33	19	Promoter of NOTCH3(-):2Kb from tx start	NOTCH3	15268817			19	Exon 22 of NOTCH3(-)	NOTCH3	15289967			10	INVERSION		21150	229652	44776	32	NEW_VARIANT
P-0031431-T01-IM6	DROSHA (NM_013235) rearrangement: t(5;10)(p13.3;q11.21)(chr5:g.31526450::chr10:g.43479900)	PRECISE	Note: The DROSHA rearrangement results in the translocation with breakpoint in exon 4 of DROSHA. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DROSHA:LINC01264}		0	0	47	10	Promoter of LINC01264(-):5Kb from tx start	LINC01264	43479900			5	Exon 4 of DROSHA(-)	DROSHA	31526450			10	TRANSLOCATION		0	229651	0	50	NEW_VARIANT
P-0031431-T01-IM6	NTRK2 (NM_006180) Rearrangement: c.1444+1516_c.1633+3654del	PRECISE	Note: The NTRK2 rearrangement is an intragenic  duplication of exon 16. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		32886	0	54	9	Intron of NTRK2(+):2Kb after exon 15	NTRK2	87477518			9	Intron of NTRK2(+):4Kb after exon 16	NTRK2	87486000			10	DUPLICATION		8482	229650	51204	56	NEW_VARIANT
P-0031438-T01-IM6	PARK2 (NM_004562) Rearrangement: c.471_c.534+6308del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		422	0	5	6	Intron of PARK2(-):6Kb after exon 4	PARK2	162615855			6	Exon 4 of PARK2(-)	PARK2	162622226			0	DELETION		6371	229641	602	5	NEW_VARIANT
P-0031438-T01-IM6	CDKN2A (NM_000077) Rearrangement: c.458-35:CDKN2A_chr9:g.21964007del	PRECISE	Note: The  CDKN2A rearrangement results in the deletion of  CDKN2A exon 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		514	0	13	9	IGR: 3Kb before CDKN2A-AS1(+)	CDKN2A-AS1	21964007			9	Intron of CDKN2A(-):35bp before exon 3	CDKN2A	21968276			10	DELETION		4269	229642	525	13	NEW_VARIANT
P-0031472-T01-IM6	MAPK1 (NM_002745) rearrangement: c.967-77:MAPK1_chr22:g.22766451del	IMPPRECISE	Note: The MAPK1 rearrangement s a deletion of exons 1-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7768	0	10	22	Intron of MAPK1(-):77bp before exon 8	MAPK1	22123686			22	IGR: 72Kb before ZNF280B(-)	ZNF280B	22766451			0	DELETION		642765	229771	7381	11	NEW_VARIANT
P-0031478-T01-IM6	KMT2A (NM_001197104) rearrangement: c.7559_c.8632del	IMPPRECISE	Note: The KMT2A rearrangement in an intragenic deletion with both breakpoints in exon 27.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4061	0	6	11	Exon 27 of KMT2A(+)	KMT2A	118374166			11	Exon 27 of KMT2A(+)	KMT2A	118375239			0	DELETION		1073	229769	5150	6	NEW_VARIANT
P-0031478-T01-IM6	KDM5C (NM_004187) rearrangement: t(X:7)(p11.22;q31.33)(chrX:g.53223929::chr7:g.125243090)	PRECISE	Note: The KDM5C rearrangement is a translocation with breakpoint in intron 22. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	16	X	Intron of KDM5C(-):9bp before exon 23	KDM5C	53223929			7	IGR: 373Kb before LOC101928254(-)	LOC101928254	125243090			10	TRANSLOCATION		0	229770	0	15	NEW_VARIANT
P-0031490-T01-IM6	SPEN (NM_015001) Rearrangement: c.5732:SPEN_chr1:g.15748399inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		37113	0	53	1	Intron of EFHD2(+):4Kb before exon 2	EFHD2	15748399			1	Exon 11 of SPEN(+)	SPEN	16258467			10	INVERSION		510068	229793	44454	61	NEW_VARIANT
P-0031536-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1017:TMPRSS2_c.18+13014:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		36361	0	15	21	Intron of ERG(-):13Kb after exon 1	ERG	39857273			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42869029			10	DELETION		3011756	229992	25582	15	NEW_VARIANT
P-0030907-T01-IM6	MARK4 (NM_001199867) - PIK3CD (NM_005026) rearrangement: t(1;19)(p36.22;q13.32)(chr1:g.9781425::chr19:g.45804589)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {MARK4:PIK3CD}		0	0	10	19	Intron of MARK4(+):1Kb before exon 17	MARK4	45804589			1	Intron of PIK3CD(+):76bp before exon 15	PIK3CD	9781425			10	TRANSLOCATION		0	227835	0	11	NEW_VARIANT
P-0030907-T01-IM6	BAP1 (NM_004656) rearrangement: c.58:BAP1_chr3:g.52445834del	PRECISE	Note: The BAP1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1487	0	37	3	Exon 2 of BAP1(-)	BAP1	52443739			3	Promoter of BAP1(-):11Kb from tx start	BAP1	52445834			10	DELETION		2095	227834	959	39	NEW_VARIANT
P-0030967-T01-IM6	PREX2 (NM_024870) rearrangement: c.142-21913_c.600dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		4953	0	5	8	Intron of PREX2(+):22Kb before exon 2	PREX2	68908168			8	Exon 6 of PREX2(+)	PREX2	68942788			0	DUPLICATION		34620	229138	5437	5	NEW_VARIANT
P-0031038-T01-IM6	ETV6 (NM_001987) Rearrangement: c.1010-4569:ETV6_chr12:g.12219924del	PRECISE	Note: The ETV6 rearrangement is a deletion of ETV6 exons 6 to 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		37709	0	54	12	Intron of ETV6(+):5Kb before exon 6	ETV6	12032810			12	IGR: 4Kb before BCL2L14(+)	BCL2L14	12219924			10	DELETION		187114	228391	28280	57	NEW_VARIANT
P-0031461-T01-IM6	DNMT1 (NM_001379) rearrangement: c.1232+773_c.2673-52del	PRECISE	Note: The DNMT1 rearrangement is an intrangenic deletion of exons 17-26. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 10 exons : in frame		15266	0	21	19	Intron of DNMT1(-):52bp before exon 27	DNMT1	10257252			19	Intron of DNMT1(-):772bp after exon 16	DNMT1	10269561			10	DELETION		12309	229755	18382	22	NEW_VARIANT
P-0031583-T01-IM6	B2M (NM_004048) rearrangement: c.67_c.68del	PRECISE	Note: The B2M rearrangement is an intragenic deletion of exons 1-2. Both breakpoints are within exon.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1320	0	16	15	Exon 1 of B2M(+)	B2M	45003811			15	Exon 2 of B2M(+)	B2M	45007621			10	DELETION		3810	230122	989	21	NEW_VARIANT
P-0026326-T02-IM6	WT1 (NM_024426) rearrangement: c.769+6:WT1_chr11:g.32372352del	PRECISE	Note: The WT1 rearrangement is a deletion of exons 2-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9452	0	3	11	IGR: 37Kb before WT1(-)	WT1	32372352			11	Intron of WT1(-):5bp after exon 2	WT1	32450037			7	DELETION		77685	230242	13746	3	NEW_VARIANT
P-0028529-T01-IM6	ROS1 (NM_002944)  rearrangement: t(6;10)(q22.1;q21.2)(chr6:g.117658271::chr10:g.:61807139)	PRECISE	Note: The ROS1 rearrangement is a translocation with a breakpoint within intron 31 of ROS1. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the ROS1 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to3	3to3	-		0	0	6	10	Intron of ANK3(-):5Kb before exon 43	ANK3	61807139			6	Intron of ROS1(-):63bp after exon 31	ROS1	117658271			10	TRANSLOCATION		0	217660	0	6	NEW_VARIANT
P-0030990-T03-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12-20): c.303+10940:CCDC6_c.2137-151:RETinv	PRECISE	Note: The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		27370	0	85	10	Intron of RET(+):150bp before exon 12	RET	43611881			10	Intron of CCDC6(-):11Kb after exon 1	CCDC6	61654940			10	INVERSION		18043059	229351	45788	125	NEW_VARIANT
P-0030990-T03-IM6	NUP93 (NM_014669) Rearrangement : t(6;16)(p11.1;q13)(chr6:g.57189490::chr16:g.56864649)	PRECISE	Note: The NUP93 rearrangement results in the possible truncation of NOTCH2. One of the breakpoints is within intron 10. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	11	16	Intron of NUP93(+):52bp after exon 10	NUP93	56864649			6	Intron of PRIM2(+):412bp after exon 4	PRIM2	57189490			10	TRANSLOCATION		0	229352	0	11	NEW_VARIANT
P-0031489-T01-IM6	INSR (NM_000208) Rearrangement: c.2286:INSR_chr19:g.18449247inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PGPEP1:INSR}		477020	0	58	19	Exon 12 of INSR(-)	INSR	7143083			19	Promoter of PGPEP1(+):2Kb from tx start	PGPEP1	18449247			10	INVERSION		11306164	229789	552420	55	NEW_VARIANT
P-0031640-T01-IM6	SETD2 (NM_014159) Rearrangement: c.1703:SETD2_chr3:g.47048057del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		39440	0	48	3	Intron of NBEAL2(+):118bp after exon 45	NBEAL2	47048057			3	Exon 3 of SETD2(-)	SETD2	47164423			10	DELETION		116366	230344	39243	50	NEW_VARIANT
P-0031648-T01-IM6	NF1 (NM_001042492) Rearrangement: c.3388_c.3974+6479del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4838	0	25	17	Exon 26 of NF1(+)	NF1	29559791			17	Intron of NF1(+):6Kb after exon 29	NF1	29569518			10	DELETION		9727	230351	469	28	NEW_VARIANT
P-0031657-T01-IM6	APC (NM_000038) rearrangement: c.5226:APC_chr5:g.118822534del	PRECISE	Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:HSD17B4}		32542	0	3	5	Exon 16 of APC(+)	APC	112176517			5	Intron of HSD17B4(+):2Kb before exon 8	HSD17B4	118822534			10	DELETION		6646017	230362	39076	4	NEW_VARIANT
P-0031512-T01-IM6	ATM (NM_000051) rearrangement: c.577_c.3077+423del	PRECISE	Note: The ATM rearrangement is an intragenic deletion of exons 6-20. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		20397	0	10	11	Exon 6 of ATM(+)	ATM	108114760			11	Intron of ATM(+):423bp after exon 20	ATM	108142556			10	DELETION		27796	229863	22532	10	NEW_VARIANT
P-0031512-T01-IM6	VEGFA (NM_001171623) rearrangement: t(6;8)(p21.1;q24.22)(chr6:g.43738643;chr8:g.133498635)	PRECISE	Note: The VEGFA rearrangement is a translocation which involves exon 1. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	99	8	IGR: 74Kb before HPYR1(-)	HPYR1	133498635			6	5-UTR of VEGFA(+):340bp before coding start	VEGFA	43738643			10	TRANSLOCATION		0	229864	0	99	NEW_VARIANT
P-0031512-T01-IM6	ASXL2 (NM_018263) rearrangement: t(2;9)(p22.3;q22.1)(chr2:g.25967196::chr9:g.90960962)	PRECISE	Note: The ASXL2 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	54	9	IGR: 42Kb before SPIN1(+)	SPIN1	90960962			2	Exon 12 of ASXL2(-)	ASXL2	25967196			10	TRANSLOCATION		0	229866	0	60	NEW_VARIANT
P-0031719-T01-IM6	TMPRSS2 (NM_001135099) - ERG(NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon1 )  : c.56-1239.3:TMPRSS2_c.-901:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		58861	0	17	21	Promoter of ERG(-):119Kb from tx start	ERG	39871205			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871355			10	DELETION		3000150	230420	59527	17	NEW_VARIANT
P-0031722-T01-IM6	TERT (NM_198253) Rearrangement :t(1;5)(p21.3;p15.32)(chr1:g.92107307::chr5:g.1295310)	PRECISE	Note: The TERT Rearrangement is a translocation event with the breakpoint in the promoter region of TERT. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	38	5	Promoter of TERT(-):42Kb from tx start	TERT	1295310			1	IGR: 39Kb before TGFBR3(-)	TGFBR3	92107307			10	TRANSLOCATION		0	230432	0	40	NEW_VARIANT
P-0031725-T01-IM6	ETV6 (NM_001987) Rearrangement : t(5;12)(p12;p13.2)(chr5:g.46092989::chr12:g.12028148)	PRECISE	Note: The ETV6 Rearrangement is a translocation event with the breakpoint in intron 5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	39	12	Intron of ETV6(+):5Kb after exon 5	ETV6	12028148			5	IGR: 838Kb before HCN1(-)	HCN1	46092989			10	TRANSLOCATION		0	230430	0	38	NEW_VARIANT
P-0031726-T01-IM6	SEC16A (NM_014866) - NOTCH1 (NM_017617) Rearrangement: c.6448-85:SEC16A_c.5269:NOTCH1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SEC16A:NOTCH1}		32044	0	33	9	Intron of SEC16A(-):85bp before exon 26	SEC16A	139342217			9	Exon 28 of NOTCH1(-)	NOTCH1	139396839			10	DUPLICATION		54622	230423	26905	33	NEW_VARIANT
P-0031514-T01-IM6	BTBD11 (NM_001018072) - ERBB3 (NM_001982) rearrangement: c.1136-66952:BTBD11_c.548-379:ERBB3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {BTBD11:ERBB3}		119792	0	4	12	Intron of ERBB3(+):378bp before exon 5	ERBB3	56480982			12	Intron of BTBD11(+):67Kb before exon 2	BTBD11	107847312			10	DUPLICATION		51366330	229929	357636	4	NEW_VARIANT
P-0031693-T01-IM6	LATS1 (NM_004690) rearrangement: t(6;20)(q25.1;p12.1)(chr6:g.150004589::chr20:g.14939921)	PRECISE	Note: The LATS1 rearrangement is a translocation with a breakpoint within exon 4.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	25	20	Intron of MACROD2(+):271Kb before exon 6	MACROD2	14939921			6	Exon 4 of LATS1(-)	LATS1	150004589			10	TRANSLOCATION		0	230755	0	33	NEW_VARIANT
P-0031712-T01-IM6	TSC2 (NM_000548) - RNPS1 (NM_006711) Rearrangement : c.3610+22:TSC2_c.676+889:RNPS1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TSC2:RNPS1}		55637	0	19	16	Intron of TSC2(+):22bp after exon 30	TSC2	2130400			16	Intron of RNPS1(-):888bp after exon 6	RNPS1	2311390			10	INVERSION		180990	230398	68544	19	NEW_VARIANT
P-0031712-T01-IM6	SRSF2 (NM_003016) Rearrangement : c.-744_c.78:SRSF2del	IMPPRECISE	Note: The SRSF2 Rearrangement results in the deletion of ex	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		764	0	25	17	Exon 1 of SRSF2(-)	SRSF2	74733165			17	Promoter of SRSF2(-):4Kb from tx start	SRSF2	74733986			0	DELETION		821	230397	882	25	NEW_VARIANT
P-0031737-T01-IM6	TEF (NM_003216) - EP300 (NM_001429) rearrangement: c.697-275:TEF_c.6650:EP300dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TEF:EP300}		5711	0	7	22	Exon 31 of EP300(+)	EP300	41574365			22	Intron of TEF(+):274bp before exon 4	TEF	41791474			10	DUPLICATION		217109	230710	6085	7	NEW_VARIANT
P-0031751-T01-IM6	PTPRD (NM_002839) rearrangement: c.5185_c.5380-2407del	PRECISE	Note: The PTPRD rearrangement is an intragenic deletion of exons 42-43. One of the breakpoints is within exon 42.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2466	0	36	9	Intron of PTPRD(-):2Kb before exon 44	PTPRD	8334143			9	Exon 42 of PTPRD(-)	PTPRD	8340411			10	DELETION		6268	230470	1561	36	NEW_VARIANT
P-0031759-T01-IM6	RB1 (NM_000321) rearrangement: c.968:RB1_chr13:g.49280131dup	PRECISE	Note: The RB1 rearrangement is a duplication that includes RB1 exons 10-27. One of the breakpoints is within RB1 exon 10.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CYSLTR2:RB1}		24183	0	16	13	Exon 10 of RB1(+)	RB1	48941658			13	Promoter of CYSLTR2(+):819bp from tx start	CYSLTR2	49280131			10	DUPLICATION		338473	230469	22285	16	NEW_VARIANT
P-0031759-T01-IM6	ZFHX3 (NM_006885) rearrangement: chr16:g.72795012_c.6128del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		31092	0	13	16	IGR: 22Kb before ZFHX3(-)	ZFHX3	72795012			16	Exon 9 of ZFHX3(-)	ZFHX3	72830453			10	DELETION		35441	230466	25266	13	NEW_VARIANT
P-0031759-T01-IM6	FGFR3 (NM_000142) rearrangement: c.1413-15_c.2030+86del	PRECISE	Note: The FGFR3 rearrangement is an intragenic deletion of exons 11-15.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		8033	0	18	4	Intron of FGFR3(+):157bp before exon 11	FGFR3	1806924			4	Intron of FGFR3(+):86bp after exon 15	FGFR3	1808140			10	DELETION		1216	230463	9880	18	NEW_VARIANT
P-0031757-T01-IM6	CCND2 (NM_001759) rearrangement: c.411+131_chr12:g.5215914del	PRECISE	Note: The CCND2 rearrangement is a deletion that includes CCND2 exons 3-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7313	0	36	12	Intron of CCND2(+):131bp after exon 2	CCND2	4385517			12	IGR: 63Kb before KCNA5(+)	KCNA5	5215914			10	DELETION		830397	230481	7009	36	NEW_VARIANT
P-0031844-T01-IM6	MDM2 (NM_002392) - CNOT2 (NM_014515) Rearrangement : c.358+70:MDM2_c.137:CNOT2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MDM2:CNOT2}		9932	0	136	12	Intron of MDM2(+):70bp after exon 5	MDM2	69214224			12	Exon 4 of CNOT2(+)	CNOT2	70704763			10	DELETION		1490539	230976	65657	210	NEW_VARIANT
P-0031868-T01-IM6	CSDE1 (NM_001242891) rearrangement: t(1;5)(p13.2;q12.3)(chr1:g.115282496::chr5:g.66058605)	PRECISE	Note: The CSDE1 rearrangement is a translocation with a breakpoint in exon 4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	23	5	Intron of MAST4(+):3Kb after exon 2	MAST4	66058605			1	Exon 4 of CSDE1(-)	CSDE1	115282496			10	TRANSLOCATION		0	231085	0	22	NEW_VARIANT
P-0031874-T01-IM6	EWSR1 (NM_013986) rearrangement: t(18;22)(p11.31;q12.2)(chr18:g.3359987::chr22:g.29687574)	IMPPRECISE	Note: The EWSR1 rearrangement is a translocation with a breakpoint in exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	34	22	Exon 10 of EWSR1(+)	EWSR1	29687574			18	IGR: 52Kb before TGIF1(+)	TGIF1	3359987			0	TRANSLOCATION		0	231093	0	36	NEW_VARIANT
P-0031881-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.-31-1224_c.4636-12del	PRECISE	Note: The SMARCA4 rearrangement results in the deletion of exons 2-32. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		95261	0	41	19	5-UTR of SMARCA4(+):1Kb before coding start	SMARCA4	11093573			19	Intron of SMARCA4(+):11bp before exon 33	SMARCA4	11170417			10	DELETION		76844	231215	58929	45	NEW_VARIANT
P-0031891-T01-IM6	PTEN (NM_000314) - KCNB2 (NM_004770) rearrangement: t(8;10)(q13.3;q23.31)(chr8:g.73786031::chr10:g.89690932)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PTEN:KCNB2}		0	0	7	10	Intron of PTEN(+):86bp after exon 4	PTEN	89690932			8	Intron of KCNB2(+):62Kb before exon 3	KCNB2	73786031			0	TRANSLOCATION		0	231208	0	7	NEW_VARIANT
P-0031891-T01-IM6	GNAS (NM_000516) rearrangement: c.530_c.531del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		791	0	2	20	Exon 6 of GNAS(+)	GNAS	57480535			20	Exon 7 of GNAS(+)	GNAS	57484217			7	DELETION		3682	231205	1321	2	NEW_VARIANT
P-0031891-T01-IM6	RBM10 (NM_001204468) rearrangement: c.171_c.213-9160del	PRECISE	Note: The RBM10 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		729	0	4	X	Exon 2 of RBM10(+)	RBM10	47006856			X	Intron of RBM10(+):9Kb before exon 3	RBM10	47019554			8	DELETION		12698	231206	947	4	NEW_VARIANT
P-0025017-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(13;21)(q21.31;q22.3)(chr13:g.63655835::chr21:g.42879521)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with one of the breakpoints within intron 1 of TMPRSS2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	8	21	Intron of TMPRSS2(-):355bp after exon 1	TMPRSS2	42879521			13	IGR: 101Kb before LINC00376(-)	LINC00376	63655835			10	TRANSLOCATION		0	231199	0	8	NEW_VARIANT
P-0031852-T01-IM6	KMT2B (NM_014727) Rearrangement: c.235:KMT2B_chr19:g.50354530inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		290364	0	3	19	Exon 1 of KMT2B(+)	KMT2B	36209155			19	3-UTR of PTOV1-AS1(-):403bp after coding stop	PTOV1-AS1	50354530			8	INVERSION		14145375	231187	377298	3	NEW_VARIANT
P-0031860-T01-IM6	WHSC1L1 (NM_023034) Rearrangement: c.521:WHSC1L1_chr8:g.38708526del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		39713	0	61	8	Exon 2 of WHSC1L1(-)	WHSC1L1	38205169			8	3-UTR of TACC1(+):63Kb after coding stop	TACC1	38708526			10	DELETION		503357	231200	27729	217	NEW_VARIANT
P-0031928-T01-IM6	NFKBIA (NM_020529) rearrangement: chr14:g.35810679_c.474dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		4377	0	31	14	IGR: 49Kb before PSMA6(+)	PSMA6	35810679			14	Exon 3 of NFKBIA(-)	NFKBIA	35872429			10	DUPLICATION		61750	231338	8068	37	NEW_VARIANT
P-0031827-T02-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		109847	0	87	2	Intron of ALK(-):252bp before exon 20	ALK	29446646			2	Intron of EML4(+):638bp before exon 13	EML4	42527742			10	INVERSION		13081096	231377	205619	87	NEW_VARIANT
P-0031933-T01-IM6	TP53 (NM_000546) rearrangement: t(1;17)(p22.1;p13.1)(chr1:g.9252773::chr17:g.7576552)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint after exon 9.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	84	17	Intron of TP53(-):300bp after exon 9	TP53	7576552			1	Intron of EPHX4(+):838bp before exon 7	EPHX4	92527773			10	TRANSLOCATION		0	231391	0	87	NEW_VARIANT
P-0031939-T01-IM6	FOXP1 (NM_001244814) rearrangement:c.869+531_ c.1934del	PRECISE	Note: The FOXP1 rearrangement is an intragenic deletion of exons 8-17. One of the breakpoints is within exon 17.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10651	0	18	3	Exon 17 of FOXP1(-)	FOXP1	71008498			3	Intron of FOXP1(-):530bp after exon 7	FOXP1	71089948			10	DELETION		81450	231361	14050	18	NEW_VARIANT
P-0031864-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.151-200:CDKN2Ap16INK4A_chr9:g.22002380del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-200:CDKN2Ap14ARF_chr9:g.22002380del	PRECISE	Note: The CDKN2A rearrangement results in the deletion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {CDKN2B:CDKN2A}		3195	0	9	9	Intron of CDKN2A(-):200bp before exon 2	CDKN2A	21971407			9	Promoter of CDKN2B(-):521bp from tx start	CDKN2B	22002380			10	DELETION		30973	231078	1433	10	NEW_VARIANT
P-0031952-T01-IM6	AXL (NM_021913) Rearrangemnet: c.*16_c.*3769inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		215	0	21	19	3-UTR of AXL(+):41Kb after coding stop	AXL	41765825			19	Promoter of AXL(+):44Kb from tx start	AXL	41769578			10	INVERSION		3753	231454	388	21	NEW_VARIANT
P-0032014-T01-IM6	NTRK3 (NM_001012338) rearrangement: c.1396+73:NTRK3_chr15:g.88406573del	PRECISE	Note: The NTRK3 rearrangement results in the deletion of exons 14-20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17688	0	38	15	IGR: 13Kb before NTRK3(-)	NTRK3	88406573			15	Intron of NTRK3(-):72bp after exon 13	NTRK3	88669429			10	DELETION		262856	231848	20558	38	NEW_VARIANT
P-0032027-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon3 with ERG exon2) : c.303:TMPRSS2_c.19-1548:ERGdel	IMPPRECISE	Note: The TMPRSS2 -ERG fusion results in the fusion of TMPRSS2 exon3 with ERG exon2. The breakpoint in TMPRSS2 is within exon3.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TMPRSS2:ERG}		24700	0	124	21	Intron of ERG(-):2Kb before exon 2	ERG	39819092			21	Exon 3 of TMPRSS2(-)	TMPRSS2	42866329			0	DELETION		3047237	231862	16365	136	NEW_VARIANT
P-0032027-T01-IM6	KMT2C (MLL3) (NM_170606) Rearrangement : c.12139+20:KMT2C_chr7:g.151681695del	PRECISE	Note: The KMT2C (MLL3) Rearrangement results in the deletion of exons 48-59 of KMT2C. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		22349	0	86	7	Intron of GALNTL5(+):1Kb after exon 4	GALNTL5	151681695			7	Intron of KMT2C(-):19bp after exon 47	KMT2C	151851332			10	DELETION		169637	231860	9180	88	NEW_VARIANT
P-0032044-T01-IM6	RFWD2 (NM_022457) rearrangement: c.467_c.468del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		613	0	4	1	Exon 3 of RFWD2(-)	RFWD2	176145143			1	Exon 2 of RFWD2(-)	RFWD2	176153769			10	DELETION		8626	231957	279	7	NEW_VARIANT
P-0032044-T01-IM6	RBM10 (NM_001204468) rearrangement: c.768_c.772-3del	PRECISE	Note: The RBM10 rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1178	0	3	X	Exon 6 of RBM10(+)	RBM10	47034488			X	Intron of RBM10(+):2bp before exon 7	RBM10	47035896			10	DELETION		1408	231958	910	3	NEW_VARIANT
P-0032046-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4862:TMPRSS2_c.40-58959:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		88928	0	4	21	Intron of ERG(-):59Kb before exon 4	ERG	39876503			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875015			10	DELETION		2998512	231962	47573	4	NEW_VARIANT
P-0032033-T01-IM6	FGFR2 (NM_000141) - BICC1 (NM_001080512) Fusion (FGFR2 exon 18 fused with BICC1 exon3) : c.2301+1527:FGFR2_c.237+38877:BICC1inv	PRECISE	Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and doesn't include the protein kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		223758	0	55	10	Intron of BICC1(+):39Kb after exon 2	BICC1	60419538			10	Intron of FGFR2(-):2Kb after exon 17	FGFR2	123241685			10	INVERSION		62822147	231865	225130	65	NEW_VARIANT
P-0018565-T02-IM6	BRCA2 (NM_000059) rearrangement: c.6178_c.6841+879del	PRECISE	Note: The BRCA2 rearrangement is an intragenic deletion of a part of exon 11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3904	0	7	13	Exon 11 of BRCA2(+)	BRCA2	32914670			13	Intron of BRCA2(+):879bp after exon 11	BRCA2	32916212			10	DELETION		1542	231544	4811	9	NEW_VARIANT
P-0031994-T01-IM6	TP53BP1 (NM_001141980) rearrangement: t(14;15)(q31.3;q15.3)(chr14:g.89311583::chr15:g.43739706)	IMPPRECISE	Note: The TP53BP1 rearrangement is a translocation with a breakpoint in TP53BP1 intron 12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	16	15	Intron of TP53BP1(-):23bp before exon 13	TP53BP1	43739706			14	Intron of TTC8(+):4Kb after exon 6	TTC8	89311583			0	TRANSLOCATION		0	231601	0	17	NEW_VARIANT
P-0031996-T01-IM6	RAD51B (NM_133509) rearrangement: c.199-1_c.315+848del	PRECISE	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.	MANUAL_OK	5to5	5to5	-		724	0	15	14	Exon 4 of RAD51B(+)	RAD51B	68301796			14	Intron of RAD51B(+):848bp after exon 4	RAD51B	68302761			10	INVERSION		965	231753	1230	15	NEW_VARIANT
P-0031996-T01-IM6	EWSR1 (NM_013986) rearrangement: t(12;22)(q11;q12.2)(chr12:g.37879543::chr22:g.29684857)	IMPPRECISE	Note: The EWSR1 rearrangement is a translocation with a breakpoint in intron 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	23	22	Intron of EWSR1(+):82bp after exon 9	EWSR1	29684857			12	IGR: 831Kb before ALG10B(+)	ALG10B	37879543			0	TRANSLOCATION		0	231754	0	69	NEW_VARIANT
P-0008954-T01-IM5	TMPRSS2 (NM_00113509) rearrangement: c.56-883:TMPRSS2_chr21:g.40099405del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		65580	0	102	21	IGR: 11Kb before NCRNA00114(-)	NCRNA00114	40099405			21	Intron of TMPRSS2(-): 883bp before exon 2	TMPRSS2	42870999			82	DELETION		2771594	125325	69018	105	NEW_VARIANT
P-0014467-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.350-82:TMPRSS2_chr21:g.38949621dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		63583	0	14	21	IGR: 47Kb before KCNJ6(-)	KCNJ6	38949621			21	Intron of TMPRSS2(-): 82bp before exon 4	TMPRSS2	42861602			27	DUPLICATION		3911981	164562	77509	14	NEW_VARIANT
P-0024797-T02-IM6	SPEN (NM_015001) Rearrangement: t(1;12)(p36.13; q14.3)(chr1:g.16261055::chr12:g.64915315)	PRECISE	Note: The SPEN Rearrangement is a translocation event with the breakpoint in exon11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	37	12	IGR: 69Kb before TBK1(+)	TBK1	64915315			1	Exon 11 of SPEN(+)	SPEN	16261055			10	TRANSLOCATION		0	235367	0	37	NEW_VARIANT
P-0026821-T05-IM6	NOTCH2 (NM_024408) Rearrangement : t(1;16)(p13.1;q12.1)(chr1:g.120464783::chr16:g.47284570)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	14	16	Intron of ITFG1(-):8Kb after exon 12	ITFG1	47284570			1	Intron of NOTCH2(-):75bp after exon 28	NOTCH2	120464783			10	TRANSLOCATION		0	227704	0	14	NEW_VARIANT
P-0026821-T05-IM6	NOTCH3 (NM_000435) Rearrangement: c.3142+73_c.2679inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		6580	0	6	19	Intron of NOTCH3(-):72bp after exon 19	NOTCH3	15291419			19	Exon 17 of NOTCH3(-)	NOTCH3	15292500			0	INVERSION		1081	227701	12730	6	NEW_VARIANT
P-0029640-T01-IM6	TFE3 (NM_006521) rearrangement: c.781-4_chrX:g/48923791dup	PRECISE	Note: The TFE3 rearrangement is a duplication that includes TFE3 exons 1-4. This sample has been nominated for further analysis using the Archer targeted RNAseq assay to help characterize the structural variant involving the TFE3 gene. Assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	5to3	5to3	Antisense Fusion		12318	0	15	X	Intron of TFE3(-):4bp before exon 5	TFE3	48895643			X	Intron of CCDC120(+):415bp after exon 9	CCDC120	48923791			10	DUPLICATION		28148	222476	14925	18	NEW_VARIANT
P-0029657-T01-IM6	KMT2D (NM_003482) rearrangement: c.4813_c.6670del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion with breakpoints in exons 19 and 31.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		21776	0	5	12	Exon 31 of KMT2D(-)	KMT2D	49434883			12	Exon 19 of KMT2D(-)	KMT2D	49438677			10	DELETION		3794	232864	15907	5	NEW_VARIANT
P-0029936-T01-IM6	ACSF2 (NM_025149) - NF1 (NM_001042492) rearrangement: c.1215+229:ACSF2_c.2993:NF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ACSF2:NF1}		410128	0	9	17	Exon 23 of NF1(+)	NF1	29557280			17	Intron of ACSF2(+):2Kb after exon 11	ACSF2	48543946			5	DUPLICATION		18986666	223338	609561	9	NEW_VARIANT
P-0030169-T01-IM6	PTPRS (NM_002850) Rearrangement : t(14;19)(q11.2; p13.3)(chr14:g.22757521::chr19:g.5219993)	PRECISE	Note: The PTPRS Rearrangement results in the possible truncation of PTPRS. The breakpoint in PTPRS is within exon22. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	54	19	Exon 22 of PTPRS(-)	PTPRS	5219993			14	IGR: 276Kb before DAD1(-)	DAD1	22757521			10	TRANSLOCATION		0	224568	0	54	NEW_VARIANT
P-0030396-T02-IM6	DOCK1 (NM_001380) - RET (NM_020975) Rearrangement: c.2515+295:RET_c.1668:RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DOCK1:RET}		270910	0	110	10	Exon 9 of RET(+)	RET	43608320			10	Intron of DOCK1(+):295bp after exon 25	DOCK1	128908913			10	DUPLICATION		85300593	233476	409916	114	NEW_VARIANT
P-0030396-T02-IM6	RBPMS (NM_001008712) - RET (NM_020975) Rearrangement : t(8,10)(p21.1,q11.21)(chr8:g.30412656::chr10:g.43610018)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RBPMS:RET}		0	0	74	10	Exon 11 of RET(+)	RET	43610018			8	Intron of RBPMS(+):4Kb before exon 7	RBPMS	30412656			10	TRANSLOCATION		0	233477	0	73	NEW_VARIANT
P-0030552-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2965:TMRPSS2_chr21:g.43719730inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {ABCG1:TMPRSS2}		39499	0	11	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873081			21	Promoter of ABCG1(+):80Kb from tx start	ABCG1	43719730			10	INVERSION		846649	226706	33598	11	NEW_VARIANT
P-0030893-T01-IM6	BRCA1 (NM_007294) Rearrangement : t(12,17)(p13.32,q21.31)(chr12:g.1952789::chr17:g.41244044)	PRECISE	Note: The BRCA1 Rearrangement is a translocation event with the breakpoint in exon10. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	44	17	Exon 10 of BRCA1(-)	BRCA1	41244044			12	Intron of CACNA2D4(-):778bp after exon 25	CACNA2D4	1952789			10	TRANSLOCATION		0	227811	0	57	NEW_VARIANT
P-0030984-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4741:TMPRSS2_c.40-57465:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves exon 1 of TMPRSS1 and exons 4-11 of the non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52786	0	35	21	Intron of ERG(-):57Kb before exon 4	ERG	39875009			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874857			10	DELETION		2999848	228224	67649	37	NEW_VARIANT
P-0031219-T01-IM6	RAD52 (NM_134424) rearrangement: c.132:RAD52_chr12:g.1055374del	PRECISE	Note: The RAD52 rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2219	0	15	12	Exon 3 of RAD52(-)	RAD52	1040440			12	5-UTR of RAD52(-):33Kb before coding start	RAD52	1055374			10	DELETION		14934	228796	2127	18	NEW_VARIANT
P-0031269-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-737:TMPRSS2_ c.19-13490:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52815	0	47	21	Intron of ERG(-):13Kb before exon 2	ERG	39831034			21	Intron of TMPRSS2(-):737bp before exon 2	TMPRSS2	42870853			10	DELETION		3039819	229288	51591	49	NEW_VARIANT
P-0032065-T01-IM6	HIST3H3 (NM_003493) rearrangement: c.161:HIST3H3_chr1:g.145082149dup	IMPPRECISE	Note: The HIST3H3 rearrangement results in the duplication of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		292637	0	5	1	Intron of NBPF20(+):231Kb before exon 54	NBPF20	145082149			1	Exon 1 of HIST3H3(-)	HIST3H3	228612866			0	DUPLICATION		83530717	231948	377778	5	NEW_VARIANT
P-0032066-T01-IM6	RPTOR (NM_020761) rearrangement: t(11;17)(q12.2;q25.3)(chr11:g.61390991::chr17:g.78765364)	PRECISE	Note: The RPTOR rearrangement is a translocation with a breakpoint in intron 7. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	39	17	Intron of RPTOR(+):55bp after exon 7	RPTOR	78765364			11	5-UTR of RPLP0P2(+):16Kb before coding start	RPLP0P2	61390991			10	TRANSLOCATION		0	231949	0	50	NEW_VARIANT
P-0032067-T01-IM6	NPM1 (NM_002520) rearrangement: c.139-399_c.582+3del	PRECISE	Note: The NPM1 rearrangement results in the in-frame deletion of exons 3-7. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		4300	0	4	5	Intron of NPM1(+):398bp before exon 3	NPM1	170817910			5	Intron of NPM1(+):3bp after exon 7	NPM1	170827217			10	DELETION		9307	231950	6634	4	NEW_VARIANT
P-0032111-T01-IM6	RPS6KB2 (NM_003952) Rearrangement: c.1156-7:RPS6KB2_chr11:g.66096453inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		17808	0	355	11	IGR: 3Kb before RIN1(-)	RIN1	66096453			11	Intron of RPS6KB2(+):6bp before exon 14	RPS6KB2	67202046			10	INVERSION		1105593	232077	22319	696	NEW_VARIANT
P-0032111-T01-IM6	REL (NM_002908) Rearrangement: c.302+833_c.1246del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7146	0	46	2	Intron of REL(+):833bp after exon 3	REL	61122513			2	Exon 11 of REL(+)	REL	61149056			10	DELETION		26543	232076	9824	53	NEW_VARIANT
P-0032131-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2836_c.3231+51inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		4505	0	2	8	Intron of WHSC1L1(-):50bp after exon 18	WHSC1L1	38146860			8	Exon 16 of WHSC1L1(-)	WHSC1L1	38153393			10	INVERSION		6533	232139	5937	2	NEW_VARIANT
P-0032153-T01-IM6	FAT1 (NM_005245) rearrangement: c.13609:FAT1_chr4:g.187509113inv	PRECISE	Note: The FAT1 rearrangement is an inversions with a breakpoint in exon 27. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		594	0	18	4	3-UTR of FAT1(-):632bp after coding stop	FAT1	187509113			4	Exon 27 of FAT1(-)	FAT1	187509904			10	INVERSION		791	232636	562	18	NEW_VARIANT
P-0032170-T01-IM6	RB1 (NM_000321) rearrangement: c.139:RB1_chr13:g.48876391del	PRECISE	Note: The RB1 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		371	0	4	13	Promoter of RB1(+):1Kb from tx start	RB1	48876391			13	Exon 2 of RB1(+)	RB1	48881417			10	DELETION		5026	232209	296	6	NEW_VARIANT
P-0032170-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1822:EML4_c.3172+632:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		99838	0	56	2	Intron of ALK(-):631bp after exon 19	ALK	29447695			2	Intron of EML4(+):2Kb after exon 12	EML4	42524478			10	INVERSION		13076783	232211	75356	54	NEW_VARIANT
P-0032208-T01-IM6	FGFR2 (NM_000141) - MYO18B (NM_032608) rearrangement: t(10;22)(q26.13;q12.2)(chr10:g.123241929::chr22:g.26280218)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:MYO18B}		0	0	5	22	Intron of MYO18B(+):6Kb after exon 25	MYO18B	26280218			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241929			10	TRANSLOCATION		0	232344	0	6	NEW_VARIANT
P-0032215-T01-IM6	BIRC3 (NM_182962) rearrangement: c.854-42_c.954-1149inv	PRECISE	Note: The BIRC3 rearrangement is an intragenic inversion of exon 4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		750	0	12	11	Intron of BIRC3(+):41bp before exon 4	BIRC3	102196155			11	Intron of BIRC3(+):1Kb before exon 5	BIRC3	102197634			10	INVERSION		1479	232341	1351	12	NEW_VARIANT
P-0032229-T01-IM6	ARID1B (NM_020732) rearrangement: c.3135+962:ARID1B_chr6:g.121762939inv	IMPPRECISE	Note: The ARID1B rearrangement results in the inversion of exons 1-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		100431	0	7	6	5-UTR of GJA1(+):5Kb before coding start	GJA1	121762939			6	Intron of ARID1B(+):962bp after exon 11	ARID1B	157496213			0	INVERSION		35733274	233044	144701	7	NEW_VARIANT
P-0032237-T01-IM6	STAT5B (NM_012448) - STAT3 (NM_139276) rearrangement: c.990-166:STAT5B_c.1982:STAT3inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		46291	0	6	17	Intron of STAT5B(-):166bp before exon 9	STAT5B	40370514			17	Exon 21 of STAT3(-)	STAT3	40474419			0	INVERSION		103905	233042	47470	7	NEW_VARIANT
P-0032311-T01-IM6	SMAD3 (NM_005902) rearrangement: c.207-129:SMAD3_chr15:g.67353055del	IMPPRECISE	Note: The SMAD3 rearrangement results in the deletion of exon 1.	MANUAL_OK	3to5	3to5	-		2393	0	7	15	IGR: 5Kb before SMAD3(+)	SMAD3	67353055			15	Intron of SMAD3(+):128bp before exon 2	SMAD3	67457104			0	DELETION		104049	232612	727	7	NEW_VARIANT
P-0032376-T01-IM6	NF1 (NM_001042492) Rearrangement: c.3796_c.4836-21034dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		7674	0	6	17	Exon 28 of NF1(+)	NF1	29562716			17	Intron of NF1(+):21Kb before exon 37	NF1	29631804			10	DUPLICATION		69088	232846	11114	6	NEW_VARIANT
P-0032394-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.45+14851_c.403-223del	PRECISE	Note: The NFE2L2 rearrangement is an intragenic deletion of exons 2-3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		3461	0	3	2	Intron of NFE2L2(-):223bp before exon 4	NFE2L2	178097534			2	Intron of NFE2L2(-):15Kb after exon 1	NFE2L2	178114409			5	DELETION		16875	232862	3959	3	NEW_VARIANT
P-0032407-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+230:KIF5B_c.2137-302:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		58798	0	30	10	Intron of KIF5B(-):229bp after exon 16	KIF5B	32311546			10	Intron of RET(+):301bp before exon 12	RET	43611730			10	INVERSION		11300184	232886	60225	41	NEW_VARIANT
P-0032432-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+13:FGFR3_c.1837-134:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		34856	0	95	4	Intron of TACC3(+):133bp before exon 10	TACC3	1739191			4	Intron of FGFR3(+):13bp after exon 17	FGFR3	1808674			10	DUPLICATION		69483	232976	41862	102	NEW_VARIANT
P-0032432-T01-IM6	TERT (NM_198253) rearrangement: c.-62_chr5:g.10249995del	PRECISE	Note: The TERT rearrangement is a deletion with a breakpoint within the promoter region of TERT. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14730	0	6	5	Promoter of TERT(-):42Kb from tx start	TERT	1295166			5	3-UTR of FAM173B(-):26bp after coding stop	FAM173B	10249995			10	DELETION		8954829	232975	13726	7	NEW_VARIANT
P-0032442-T01-IM6	CDK8 (NM_001260) - EXOSC8 (NM_181503) rearrangement: c.833:CDK8_c.609-51:EXOSC8del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDK8:EXOSC8}		149587	0	6	13	Exon 8 of CDK8(+)	CDK8	26970464			13	Intron of EXOSC8(+):50bp before exon 10	EXOSC8	37582815			7	DELETION		10612351	233097	211519	6	NEW_VARIANT
P-0032445-T01-IM6	CDKN2A (NM_000077) rearrangement: c.70:CDKN2A_chr9:g.21981860del	PRECISE	Note: The CDKN2A rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		113	0	18	9	Exon 1 of CDKN2A(-)	CDKN2A	21974757			9	Intron of CDKN2A(-):11Kb before exon 2	CDKN2A	21981860			10	DELETION		7103	233098	115	18	NEW_VARIANT
P-0032457-T01-IM6	FGFR1 (NM_001174067) Rearrangement: c.2071-39_c.*2020inv	PRECISE	Note: The FGFR1 rearrangement is an intragenic inversion of exons 16-19. The functional significance is undetermined,	MANUAL_OK	3to3	3to3	-		6736	0	22	8	3-UTR of FGFR1(-):2Kb after coding stop	FGFR1	38269126			8	Intron of FGFR1(-):39bp before exon 16	FGFR1	38272186			10	INVERSION		3060	233136	7242	22	NEW_VARIANT
P-0032467-T01-IM6	HOXB3(NM_006361) Rearrangement: c.698:HOXB13_chr17:g.21146664inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	-		475165	0	9	17	Exon 3 of NATD1(-)	NATD1	21146664			17	Exon 2 of HOXB13(-)	HOXB13	46804309			0	INVERSION		25657645	233104	686028	9	NEW_VARIANT
P-0032478-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : t(10;21)(q11.21;q22.2)(chr10:g.45577774::chr21:g.42861302)	PRECISE	Note: The TMPRSS2 Rearrangement is a translocation event with a breakpoint in intron4.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	14	21	Intron of TMPRSS2(-):131bp after exon 4	TMPRSS2	42861302			10	IGR: 17Kb before RSU1P2(-)	RSU1P2	45577774			10	TRANSLOCATION		0	233160	0	15	NEW_VARIANT
P-0032507-T01-IM6	FGFR2 (NM_000141) Rearrangement : c.2301+944:FGFR2_chr10:g.97250518del	PRECISE	Note: The FGFR2 Rearrangement results in the deletion of exon 18 of FGFR2.This does not include the protein kinase domain of FGFR2.	MANUAL_OK	3to5	3to5	Transcript Fusion {FGFR2:SORBS1}		73219	0	10	10	5-UTR of SORBS1(-):176Kb before coding start	SORBS1	97250518			10	Intron of FGFR2(-):943bp after exon 17	FGFR2	123242268			10	DELETION		25991750	233478	82321	10	NEW_VARIANT
P-0032513-T01-IM6	STK11 (NM_000455) Rearrangement : c.122_c.290+2342del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1663	0	16	19	Exon 1 of STK11(+)	STK11	1207034			19	Intron of STK11(+):2Kb after exon 1	STK11	1209544			10	DELETION		2510	233480	1556	21	NEW_VARIANT
P-0032518-T01-IM6	EML4 (NM_001145076) - ALK (NM_004304) fusion: c.1315+2607:EML4_c.3140:ALKinv	PRECISE	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	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		100214	0	68	2	Exon 19 of ALK(-)	ALK	29448359			2	Intron of EML4(+):3Kb after exon 12	EML4	42525263			10	INVERSION		13076904	234156	143148	68	NEW_VARIANT
P-0032550-T01-IM6	MPL (NM_005373) rearrangement: c.853+27:MPL_chr1:g.43822389del	PRECISE	Note: The MPL rearrangement is a deletion of exons 6-12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		12455	0	57	1	Intron of MPL(+):27bp after exon 5	MPL	43805824			1	Promoter of MPL(+):19Kb from tx start	MPL	43822389			10	DELETION		16565	234213	14937	183	NEW_VARIANT
P-0032550-T01-IM6	NKX3-1 (NM_006167) - MYC (NM_002467) rearrangement: c.383:NKX3-1_c.-55:MYCdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		334575	0	17	8	Exon 2 of NKX3-1(-)	NKX3-1	23538831			8	5-UTR of MYC(+):54bp before coding start	MYC	128748785			10	DELETION		105209954	234214	432837	63	NEW_VARIANT
P-0032620-T01-IM6	DOT1L (NM_032482) rearrangement:c.2909:DOT1L_chr19:g.1981791del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CSNK1G2:DOT1L}		51318	0	41	19	Promoter of CSNK1G2(+):41Kb from tx start	CSNK1G2	1981791			19	Exon 24 of DOT1L(+)	DOT1L	2222077			10	DELETION		240286	234459	32674	42	NEW_VARIANT
P-0032682-T01-IM6	PGR (NM_000926) rearrangement: t(9;11)(p24.3;q22.1)(chr9:g.1442340::chr11:g.100999195)	PRECISE	Note: The PGR rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	81	11	Exon 1 of PGR(-)	PGR	100999195			9	IGR: 392Kb before DMRT2(+)	DMRT2	1442340			10	TRANSLOCATION		0	234891	0	81	NEW_VARIANT
P-0032683-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2122:EML4_c.3172+564:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		98060	0	11	2	Intron of ALK(-):563bp after exon 19	ALK	29447763			2	Intron of EML4(+):2Kb before exon 13	EML4	42526259			10	INVERSION		13078496	234882	90366	11	NEW_VARIANT
P-0032686-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2299:KIF5B_c.2137-50:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		66467	0	100	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315057			10	Intron of RET(+):49bp before exon 12	RET	43611982			10	INVERSION		11296925	234868	59981	108	NEW_VARIANT
P-0032686-T01-IM6	PTPRD (NM_002839) rearrangement: c.64+11242_c.352+116dup	IMPPRECISE	Note: The PTPRD rearrangement results in the in-frame duplication of exons 13-14. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		2157	0	16	9	Intron of PTPRD(-):115bp after exon 14	PTPRD	8633201			9	Intron of PTPRD(-):11Kb after exon 12	PTPRD	8722538			0	DUPLICATION		89337	234867	2438	16	NEW_VARIANT
P-0032778-T01-IM6	KLK10 (NM_001077500) - POLD1 (NM_002691) Rearrangement :  c.88+823:KLK10_c.2925:POLD1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KLK10:POLD1}		6388	0	6	19	Exon 23 of POLD1(+)	POLD1	50919757			19	Intron of KLK10(-):822bp after exon 2	KLK10	51521476			10	INVERSION		601719	235410	8805	6	NEW_VARIANT
P-0032702-T01-IM6	NF1 (NM_001042492) rearrangement: c.2001+12:NF1_chr17:g.28678685inv	PRECISE	Note: The NF1 rearrangement results in the inversion of exons 1-17. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		24360	0	12	17	IGR: 27Kb before CPD(+)	CPD	28678685			17	Intron of NF1(+):12bp after exon 17	NF1	29552280			10	INVERSION		873595	234757	29264	12	NEW_VARIANT
P-0032702-T01-IM6	APC (NM_000038) rearrangement: c.1959-245_c.3438del	PRECISE	Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4686	0	3	5	Intron of APC(+):244bp before exon 16	APC	112173005			5	Exon 16 of APC(+)	APC	112174729			6	DELETION		1724	234755	4613	3	NEW_VARIANT
P-0032702-T01-IM6	TEK (NM_000459) rearrangement: t(9;X)(p21.2;q27.2)(chr9:g.27217610::chrX:g.140560188)	PRECISE	Note: The TEK rearrangement is a translocation with a breakpoint in intron 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	14	X	IGR: 31Kb before SPANXA2-OT1(+)	SPANXA2-OT1	140560188			9	Intron of TEK(+):75bp before exon 19	TEK	27217610			10	TRANSLOCATION		0	234758	0	14	NEW_VARIANT
P-0032801-T01-IM6	PTEN (NM_000314) Rearrangement: c.165-132:PTEN_chr10:g.90636313inv	PRECISE	Note: The PTEN rearrangement is an inversion of PTEN exons 3 to 9. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		9444	0	9	10	Intron of PTEN(+):131bp before exon 3	PTEN	89685138			10	IGR: 4Kb before STAMBPL1(+)	STAMBPL1	90636313			10	INVERSION		951175	235416	4995	9	NEW_VARIANT
P-0032801-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-595:TMPRSS2_c.19-12368:ERGdel	PRECISE	Note: The TMRPSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		43262	0	67	21	Intron of ERG(-):12Kb before exon 2	ERG	39829912			21	Intron of TMPRSS2(-):595bp before exon 2	TMPRSS2	42870711			10	DELETION		3040799	235415	19667	73	NEW_VARIANT
P-0032646-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exons 1 fused to ERG exons 2-10): c.56-2331:TMPRSS2_c.18+11761:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		58868	0	106	21	Intron of ERG(-):12Kb after exon 1	ERG	39858526			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872447			10	DELETION		3013921	234693	38920	115	NEW_VARIANT
P-0032650-T01-IM6	ETV6 (NM_001987) rearrangement: chr12:g.7329461_c.163+94inv	PRECISE	Note: The ETV6 rearrangement is an inversion that includes  ETV6 exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3910	0	27	12	IGR: 12Kb before PEX5(+)	PEX5	7329461			12	Intron of ETV6(+):94bp after exon 2	ETV6	11905607			10	INVERSION		4576146	234691	5282	27	NEW_VARIANT
P-0032681-T01-IM6	PIK3CD (NM_005026) - NBPF20 (NM_001278267) rearrangement: c.1689+1:PIK3CD_c.5307-228539:NBPF20del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PIK3CD:NBPF20}		684875	0	4	1	Intron of PIK3CD(+):1bp after exon 13	PIK3CD	9780968			1	Intron of NBPF20(+):229Kb before exon 53	NBPF20	144596166			10	DELETION		134815198	234877	740053	12	NEW_VARIANT
P-0032681-T01-IM6	CDKN1B (NM_004064) rearrangement: t(9;12)(q33.1;p13.1)(chr9:g.117720034::chr12:g.12871086)	PRECISE	Note: The CDKN1B rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	12	Exon 1 of CDKN1B(+)	CDKN1B	12871086			9	IGR: 57Kb before TNFSF8(-)	TNFSF8	117720034			10	TRANSLOCATION		0	234881	0	7	NEW_VARIANT
P-0032681-T01-IM6	PIK3R2 (NM_005027) - PGLS (NM_012088) rearrangement: c.536:PIK3R2_c.640-628:PGLSdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PIK3R2:PGLS}		48890	0	39	19	Intron of PGLS(+):627bp before exon 5	PGLS	17631125			19	Exon 5 of PIK3R2(+)	PIK3R2	18271933			10	DUPLICATION		640808	234879	61508	41	NEW_VARIANT
P-0032687-T01-IM6	BRD4 (NM_058243) rearrangement: c.2158+84:BRD4_chr19:g.8553970inv	IMPPRECISE	Note: The BRD4 rearrangement results in the inversion of exons 12-20. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		300329	0	16	19	3-UTR of HNRNPM(+):44Kb after coding stop	HNRNPM	8553970			19	Intron of BRD4(-):83bp after exon 11	BRD4	15364879			0	INVERSION		6810909	234870	274349	16	NEW_VARIANT
P-0032896-T01-IM6	TSC2 (NM_000548) rearrangement: t(1;16)(q21.1;p13.3)(chr1:g.145721517::chr16:g.2136314)	PRECISE	Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 37.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NBPF20:TSC2}		0	0	17	16	Exon 37 of TSC2(+)	TSC2	2136314			1	Intron of NBPF20(+):357Kb after exon 99	NBPF20	145721517			10	TRANSLOCATION		0	236054	0	17	NEW_VARIANT
P-0032965-T01-IM6	CDK8 (NM_001260) Rearrangement: t(5;13)(q11.2;q12.13)(chr5:g.54146908::chr13:g.26975603)	PRECISE	Note: The CDK8 rearrangement is a translocation involving a breakpoint in exon 12. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	55	13	Exon 12 of CDK8(+)	CDK8	26975603			5	IGR: 127Kb before ESM1(-)	ESM1	54146908			10	TRANSLOCATION		0	236820	0	57	NEW_VARIANT
P-0007065-T01-IM5	PALB2 (NM_024675) rearrangement : c.1451:PALB2_c.118-6342:DCTN5del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		15760	0	20	16	Exon 4 of PALB2(-)	PALB2	23646416			16	Intron of DCTN5(+): 6Kb before exon 3	DCTN5	23663486			29	DELETION		17070	112874	15182	20	NEW_VARIANT
P-0007065-T01-IM5	RNF43 (NM_017763) rearrangement :  c.252+7204_c.1148del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		15314	0	13	17	Exon 9 of RNF43(-)	RNF43	56435989			17	Intron of RNF43(-): 7Kb after exon 2	RNF43	56485483			21	DELETION		49494	112875	13328	13	NEW_VARIANT
P-0032993-T01-IM6	ARID1A (NM_006015) Rearrangement: t(1;5)(p35.3.3;p12)(chr1:g.27092885::chr5:g.42600647)	PRECISE	Note: The ARID1A Rearrangement is a translocation event with the breakpoint in intron9. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	33	5	Intron of GHR(+):28Kb before exon 2	GHR	42600647			1	Intron of ARID1A(+):28bp after exon 9	ARID1A	27092885			10	TRANSLOCATION		0	237163	0	33	NEW_VARIANT
P-0032993-T01-IM6	DLG2 (NM_001142699) -ATRX (NM_000489)  Rearrangement : t(X;11)(q13.3;p21.2)(chrX:g.76888956::chr11:g.83978235)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {DLG2:ATRX}		0	0	54	X	Intron of ATRX(-):84bp before exon 19	ATRX	76888956			11	Intron of DLG2(-):16Kb before exon 8	DLG2	83978235			10	TRANSLOCATION		0	237165	0	52	NEW_VARIANT
P-0033072-T01-IM6	HMGA2 (NM_003483)  - KMT2D (NM_003482) rearrangement: c.249+19827:HMGA2_c.5189-60:KMT2Dinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {HMGA2:KMT2D}		200903	0	7	12	Intron of KMT2D(-):60bp before exon 22	KMT2D	49437841			12	Intron of HMGA2(+):20Kb after exon 3	HMGA2	66252176			9	INVERSION		16814335	237456	250885	6	NEW_VARIANT
P-0033072-T01-IM6	NAB2 (NM_005967) - SRGAP1 (NM_020762) rearrangement: c.1468+356_c.68-8733:SRGAP1inv	PRECISE	Note: The NAB2 rearrangement is an inversion with a breakpoints within NAB2 intron 6 and SRGAP1 intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		57252	0	6	12	Intron of NAB2(+):356bp after exon 6	NAB2	57487737			12	Intron of SRGAP1(+):9Kb before exon 2	SRGAP1	64368994			7	INVERSION		6881257	237457	98765	6	NEW_VARIANT
P-0033078-T01-IM6	RB1 (NM_000321) rearrangement: c.1696-23270_c.1815-127del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 18.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1778	0	51	13	Intron of RB1(+):23Kb before exon 18	RB1	49003859			13	Intron of RB1(+):126bp before exon 19	RB1	49030213			10	DELETION		26354	237494	552	52	NEW_VARIANT
P-0033097-T01-IM6	NKX2-1 (NM_001079668) rearrangement: c.121:NKX2-1_chr14:g.37145781dup	PRECISE	Note: The NKX2-1 rearrangement is a duplication with a breakpoint within NKX2-1 exon 2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		3617	0	8	14	Exon 2 of NKX2-1(-)	NKX2-1	36988532			14	3-UTR of PAX9(+):14Kb after coding stop	PAX9	37145781			10	DUPLICATION		157249	237609	4812	9	NEW_VARIANT
P-0033126-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.56-4414:TMPRSS2_chr21:g.40082965del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		64976	0	52	21	IGR: 28Kb before LINC00114(-)	LINC00114	40082965			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874530			0	DELETION		2791565	237704	94059	54	NEW_VARIANT
P-0018607-T03-IM6	FAT1 (NM_005245) Rearrangement: c.4324-689_c.8287del.	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17993	0	74	4	Exon 10 of FAT1(-)	FAT1	187539453			4	Intron of FAT1(-):689bp before exon 8	FAT1	187550606			10	DELETION		11153	236829	15959	80	NEW_VARIANT
P-0032951-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4118;TMPRSS2_c.-150+11848:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		84588	0	97	21	3-UTR of ERG(-):12Kb after coding stop	ERG	40021734			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875759			10	DELETION		2854025	236799	57654	98	NEW_VARIANT
P-0033136-T01-IM6	ARID1A (NM_006015) Rearrangement: t(1,4)(p36.11; q31.1)(chr1:g.27058209::chr4:g.141107510)	PRECISE	Note: The ARID1A Rearrangement is a translocation event with a breakpoint in intron3.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	15	4	IGR: 71Kb before SCOC(+)	SCOC	141107510			1	Intron of ARID1A(+):114bp after exon 3	ARID1A	27058209			10	TRANSLOCATION		0	237725	0	15	NEW_VARIANT
P-0033136-T01-IM6	HAPLN1 (NM_001884) - RASA1 (NM_002890) Rearrangement : c.2604-38:HAPLN1_c.2604-38:RASA1inv	PRECISE	Note: The HAPLN1 -RASA1 Rearrangement results in the fusion of exon1 of HAPLN1 with exons  20-25 of RASA1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {HAPLN1:RASA1}		20992	0	27	5	5-UTR of HAPLN1(-):66Kb before coding start	HAPLN1	83002855			5	Intron of RASA1(+):37bp before exon 20	RASA1	86676288			10	INVERSION		3673433	237724	22375	27	NEW_VARIANT
P-0033226-T01-IM6	TP53 (NM_000546) Rearrangement : chr17:g.75261748_c.560-35inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		820163	0	26	17	Intron of TP53(-):35bp before exon 6	TP53	7578324			17	IGR: 16Kb before SEPT9(+)	SEPT9	75261748			10	INVERSION		67683424	238574	389052	29	NEW_VARIANT
P-0033226-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon2) : c.56-1088:TMPRSS2_c.40-47540:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		47389	0	44	21	Intron of ERG(-):5Kb after exon 1	ERG	39865084			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871204			10	DELETION		3006120	238571	20474	47	NEW_VARIANT
P-0033178-T01-IM6	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-46812:ST7_c.303:METdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ST7:MET}		54167	0	4	7	Exon 2 of MET(+)	MET	116339441			7	Intron of ST7(+):47Kb before exon 2	ST7	116693004			7	DUPLICATION		353563	238112	71952	4	NEW_VARIANT
P-0033180-T01-IM6	ALK (NM_004304) rearrangement: c.3173-106_c.3516-155inv	PRECISE	Note: The ALK rearrangement is an intragenic inversion of exons 20-22. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		5432	0	71	2	Intron of ALK(-):155bp before exon 23	ALK	29443856			2	Intron of ALK(-):106bp before exon 20	ALK	29446500			10	INVERSION		2644	238100	6420	71	NEW_VARIANT
P-0033181-T01-IM6	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.89-1476:TRAP1_c.5376:CREBBPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TRAP1:CREBBP}		14456	0	25	16	Intron of TRAP1(-):3Kb before exon 2	TRAP1	3742462			16	Exon 31 of CREBBP(-)	CREBBP	3779672			10	DUPLICATION		37210	238106	10070	27	NEW_VARIANT
P-0033193-T01-IM6	DNMT1(NM_001379) Rearrangement:  c.46:DNMT1_chr19:g.58808368inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {DNMT1:ZNF8}		750171	0	40	19	Exon 1 of DNMT1(-)	DNMT1	10305530			19	Promoter of ZNF8(+):18Kb from tx start	ZNF8	58808368			10	INVERSION		48502838	238146	813451	68	NEW_VARIANT
P-0033205-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.106+5198_c.297del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1508	0	3	1	Exon 3 of PIK3R3(-)	PIK3R3	46543204			1	Intron of PIK3R3(-):5Kb after exon 1	PIK3R3	46592321			10	DELETION		49117	238248	1388	3	NEW_VARIANT
P-0021905-T02-IM6	IRS2 (NM_003749) rearrangement: c.2170:IRS2_chr13:g.110468522del	PRECISE	Note: The IRS2 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6166	0	5	13	Exon 1 of IRS2(-)	IRS2	110436231			13	IGR: 62Kb before IRS2(-)	IRS2	110468522			9	DELETION		32291	238096	12239	5	NEW_VARIANT
P-0021905-T02-IM6	NPM1 (NM_002520) - FGF18 (NM_003862) rearrangement: c.582+63:NPM1_c.69+4735:FGF18del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {NPM1:FGF18}		4280	0	21	5	Intron of NPM1(+):63bp after exon 7	NPM1	170827277			5	Intron of FGF18(+):5Kb after exon 2	FGF18	170852182			10	DELETION		24905	238095	5214	23	NEW_VARIANT
P-0033399-T01-IM6	PAXBP1 (NM_013329) - SPOP (NM_001007228) rearrangement: t(17;21)(q21.33;q22.11)(chr17:g.47699480::chr21:g.:34122819)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PAXBP1:SPOP}		0	0	36	21	Intron of PAXBP1(-):408bp after exon 10	PAXBP1	34122819			17	Intron of SPOP(-):51bp before exon 3	SPOP	47699480			10	TRANSLOCATION		0	243045	0	34	NEW_VARIANT
P-0033429-T01-IM6	APC (NM_000038) Rearrangement: t(5;14)(q22.2;q23.1)(chr5:g.112175465::chr14:g.59220602)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	14	14	IGR: 74Kb before LINC01500(+)	LINC01500	59220602			5	Exon 16 of APC(+)	APC	112175465			10	TRANSLOCATION		0	239495	0	17	NEW_VARIANT
P-0033465-T01-IM6	ALOX12B (NM_001139) rearrangement: c.1337_chr17:g.8029057dup	PRECISE	Note: The ALOX12B rearrangement is a duplication that includes ALOX12B exons 1-10. One of the breakpoints is within exon 10.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ALOX12B:HES7}		16436	0	166	17	Exon 10 of ALOX12B(-)	ALOX12B	7980000			17	Promoter of HES7(-):5Kb from tx start	HES7	8029057			10	DUPLICATION		49057	240993	26930	182	NEW_VARIANT
P-0033465-T01-IM6	RYBP (NM_012234) rearrangemnet: t(1;3)(q24.2;p13)(chr1:g.168626981::chr3:g.72455938)	PRECISE	Note: The RYBP rearrangement is a translocation with a breakpoint within intron 1.	MANUAL_OK	5to5	5to5	-		0	0	103	3	Intron of RYBP(-):27Kb before exon 2	RYBP	72455938			1	IGR: 38Kb before DPT(-)	DPT	168626981			10	TRANSLOCATION		0	240994	0	110	NEW_VARIANT
P-0033508-T01-IM6	NOTCH2 (NM_024408) - IGSF3 (NM_001542) rearrangement: c.855:NOTCH2_c.43+10742:IGSF3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NOTCH2:IGSF3}		70433	0	59	1	Intron of IGSF3(-):11Kb after exon 1	IGSF3	117198164			1	Exon 5 of NOTCH2(-)	NOTCH2	120529602			10	DELETION		3331438	241087	80185	66	NEW_VARIANT
P-0033529-T01-IM6	ERBB4 (NM_005235) rearrangement: c.557-16484_c.1125-2del	PRECISE	Note: The ERBB4 rearrangement results in the intragenic deletion of exons 5 to 9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : out of frame		6281	0	5	2	Intron of ERBB4(-):2bp before exon 10	ERBB4	212570118			2	Intron of ERBB4(-):16Kb before exon 5	ERBB4	212631913			7	DELETION		61795	241313	7078	5	NEW_VARIANT
P-0033575-T01-IM6	GPS2 (NM_004489) Rearrangement : c.241:GPS2_chr17:g.7856267del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		26216	0	15	17	Exon 4 of GPS2(-)	GPS2	7217686			17	IGR: 21Kb before CNTROB(+)	CNTROB	7856267			10	DELETION		638581	243325	34068	57	NEW_VARIANT
P-0033575-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-238:TMPRSS2_c.18+8414:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		44557	0	67	21	Intron of ERG(-):8Kb after exon 1	ERG	39861873			21	Intron of TMPRSS2(-):238bp before exon 2	TMPRSS2	42870354			10	DELETION		3008481	243327	54996	70	NEW_VARIANT
P-0033749-T01-IM6	FANCA (NM_000135) rearrangement: c.3408+18:FANCA_chr16:g.87145722del	PRECISE	Note: The FANCA rearrangement is a deletion of exons 35-43. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		65361	0	232	16	IGR: 54Kb before LOC440390(+)	LOC440390	87145722			16	Intron of FANCA(-):17bp after exon 34	FANCA	89813221			10	DELETION		2667499	245134	86795	284	NEW_VARIANT
P-0033615-T01-IM6	GNAS (NM_000516) - CREM (NM_181571) rearrangement: t(10;20)(p11.21;q13.32)(chr10:g.35491448::chr20:g.57479028)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {GNAS:CREM}		0	0	9	20	Intron of GNAS(+):182bp after exon 5	GNAS	57479028			10	Intron of CREM(+):1Kb after exon 2	CREM	35491448			10	TRANSLOCATION		0	243660	0	9	NEW_VARIANT
P-0033766-T01-IM6	IGF1R (NM_000875) rearrangement: c.640+71778_c.2131del	PRECISE	Note: The IGF1R rearrangement is an intragenic deletion of exons 3-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10698	0	22	15	Intron of IGF1R(+):72Kb after exon 2	IGF1R	99323114			15	Exon 10 of IGF1R(+)	IGF1R	99460035			10	DELETION		136921	245546	9851	22	NEW_VARIANT
P-0033766-T01-IM6	AGO2 (NM_012154) rearrangement: c.2271+298_c.2284del	PRECISE	Note: The AGO2 rearrangement is an intragenic deletion of exons 18. One of the breakpoints is within exon 18. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		390	0	22	8	Exon 18 of AGO2(-)	AGO2	141542702			8	Intron of AGO2(-):297bp after exon 17	AGO2	141545269			10	DELETION		2567	245545	464	23	NEW_VARIANT
P-0033789-T01-IM6	RECQL4 (NM_004260) rearrangement: t(1;8)(q31.3;q24.3)(chr1:g.194264448::chr8:g.145739644)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	14	8	Exon 11 of RECQL4(-)	RECQL4	145739644			1	IGR: 991Kb before LINC01031(+)	LINC01031	194264448			10	TRANSLOCATION		0	245601	0	15	NEW_VARIANT
P-0014304-T02-IM6	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	IMPPRECISE	Note: The EZR-ROS1 event results in an in-frame fusion which includes the protein kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EZR:ROS1}		279927	0	28	6	Intron of ROS1(-):371bp before exon 34	ROS1	117645949			6	Intron of EZR(-):78bp after exon 9	EZR	159191717			0	DELETION		41545768	245032	316166	28	NEW_VARIANT
P-0033523-T01-IM6	BIRC3 (NM_182962) - C11orf70 (NM_032930) rearrangement: c.853+38:BIRC3_c.193-1514:C11orf70dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BIRC3:C11orf70}		16012	0	8	11	Intron of C11orf70(+):2Kb before exon 3	C11orf70	101928097			11	Intron of BIRC3(+):38bp after exon 3	BIRC3	102196131			0	DUPLICATION		268034	246911	31774	8	NEW_VARIANT
P-0033523-T01-IM6	PBRM1 (NM_018313) rearrangement: c.2567+498_c.4132+9dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 9 exons : out of frame		12581	0	10	3	Intron of PBRM1(-):8bp after exon 26	PBRM1	52595774			3	Intron of PBRM1(-):497bp after exon 17	PBRM1	52642831			10	DUPLICATION		47057	246910	15502	10	NEW_VARIANT
P-0033810-T01-IM6	ETV6 (NM_001987) -PDE3A (NM_000921) Rearrangement : c.1010-1239:ETV6_c.960+53099:PDE3A	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ETV6:PDE3A}		52592	0	46	12	Intron of ETV6(+):1Kb before exon 6	ETV6	12036140			12	Intron of PDE3A(+):53Kb after exon 1	PDE3A	20576277			10	DELETION		8540137	245697	77639	47	NEW_VARIANT
P-0033832-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1767:TMPRSS2_c.39+62909:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32102	0	16	21	Intron of ERG(-):63Kb after exon 3	ERG	39884677			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868279			10	DELETION		2983602	246118	24237	18	NEW_VARIANT
P-0033925-T01-IM6	ARID1B (NM_020732) rearrangement: c.6115_c.*395inv	PRECISE	Note: The ARID1B rearrangement is an inversion that includes ARID1B exon 20. One of the breakpoints is within exon.	MANUAL_OK	5to5	5to5	-		2976	0	9	6	Exon 20 of ARID1B(+)	ARID1B	157528564			6	3-UTR of ARID1B(+):430Kb after coding stop	ARID1B	157529420			10	INVERSION		856	246844	4333	9	NEW_VARIANT
P-0033975-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.46-4925_c.170del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		538	0	7	2	Exon 2 of NFE2L2(-)	NFE2L2	178098875			2	Intron of NFE2L2(-):5Kb before exon 2	NFE2L2	178103924			9	DELETION		5049	247201	684	7	NEW_VARIANT
P-0016870-T02-IM6	PARP1 (NM_001618) rearrangement: t(1;14)(q42.12;q21.1)(chr1:g.226549636::chr14:g.40515347)	IMPPRECISE	Note: The PARP1 rearrangement is a translocation involving exon 22. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	10	14	IGR: 650Kb before FBXO33(-)	FBXO33	40515347			1	Intron of PARP1(-):33bp after exon 22	PARP1	226549636			0	TRANSLOCATION		0	245609	0	10	NEW_VARIANT
P-0016870-T02-IM6	RICTOR (NM_152756) rearrangement: c.2735_c.4137-197dup	PRECISE	Note: The RICTOR rearrangement is an intragenic duplication of exons 28-31. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8378	0	20	5	Intron of RICTOR(-):197bp before exon 32	RICTOR	38947740			5	Exon 28 of RICTOR(-)	RICTOR	38953618			10	DUPLICATION		5878	245607	15352	21	NEW_VARIANT
P-0033823-T01-IM6	WHSC1L1 (NM_023034) - CHRNB3 (NM_000749) Rearrangement : c.1986+29:WHSC1L1_c.1242+453:CHRNB3inv	PRECISE	Note: The WHSC1L1 - CHRNB3 Rearrangement results in the fusion of exons 1-10 of WHSC1L1 with exon6 of CHRNB3.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {WHSC1L1:CHRNB3}		50084	0	3	8	Intron of WHSC1L1(-):28bp after exon 10	WHSC1L1	38173401			8	Intron of CHRNB3(+):453bp after exon 5	CHRNB3	42588145			9	INVERSION		4414744	245720	68359	3	NEW_VARIANT
P-0028180-T02-IM6	ALK (NM_004304) Rearrangement: c.3068-391:ALK_chr2:g.218382626del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		570466	0	36	2	Intron of ALK(-):391bp before exon 19	ALK	29448822			2	3-UTR of DIRC3(-):239Kb after coding stop	DIRC3	218382626			10	DELETION		188933804	247271	456746	37	NEW_VARIANT
P-0033988-T01-IM6	RB1 (NM_000321) rearrangement: c.256_c.264+965del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		258	7	11	13	Exon 2 of RB1(+)	RB1	48881534			13	Intron of RB1(+):965bp after exon 2	RB1	48882507			9	DELETION		973	247315	226	6	NEW_VARIANT
P-0027600-T01-IM6	TMPRSS2: (NM_001135099) rearrangement: c.556+3086_c.55+2661inv	PRECISE	Note: The TMPRSS2 rearrangement results in the inversion of intron 1 to intron 5. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		73138	0	13	21	Intron of TMPRSS2(-):3Kb after exon 5	TMPRSS2	42857235			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42877216			10	INVERSION		19981	214114	118902	13	NEW_VARIANT
P-0023994-T05-IM6	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exon 10 fused with NTRK1 exon 11) : c.1699-362:LMNA_c.1251+107:NTRK1del	PRECISE	Note: The LMNA-NTRK1 fusion is predicted to be in-frame and includes the protein kinase domain of NTRK1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {LMNA:NTRK1}		44819	0	36	1	Intron of LMNA(+):361bp before exon 10	LMNA	156107917			1	Intron of NTRK1(+):107bp after exon 10	NTRK1	156844525			10	DELETION		736608	237096	56799	36	NEW_VARIANT
P-0032862-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) Fusion(EML4 exon 11 fused to ALK exon20 ): c.1489+671:EML4_c.3172+839:ALK	PRECISE	Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		103215	0	83	2	Intron of ALK(-):838bp after exon 19	ALK	29447488			2	Intron of EML4(+):671bp after exon 12	EML4	42523327			10	INVERSION		13075839	235902	110616	82	NEW_VARIANT
P-0032171-T03-IM6	FGFR2 (NM_000141) - OPTN (NM_021980) rearrangement: c.2302-254:FGFR2_c.553-1543:OPTNinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:OPTN}		343394	0	40	10	Intron of OPTN(+):2Kb before exon 5	OPTN	13156724			10	Intron of FGFR2(-):254bp before exon 18	FGFR2	123239789			10	INVERSION		110083065	249542	376405	48	NEW_VARIANT
P-0033884-T01-IM6	STK11 (NM_000455) rearrangement: c.589_c.920+334del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4680	0	57	19	Exon 4 of STK11(+)	STK11	1220496			19	Intron of STK11(+):334bp after exon 7	STK11	1222339			10	DELETION		1843	248655	1782	127	NEW_VARIANT
P-0034177-T01-IM6	APC (NM_000038) - STARD4 (NM_139164) rearrangement: c.1408+35:APC_c.156-1888:STARD4inv	IMPPRECISE	Note: The APC - STARD4 rearrangement is an inversion that may result in the fusion of APC exons 1-11 with STARD4 exons 4-6.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {APC:STARD4}		16003	0	5	5	Intron of STARD4(-):2Kb before exon 4	STARD4	110839674			5	Intron of APC(+):35bp after exon 11	APC	112157723			0	INVERSION		1318049	249497	21505	5	NEW_VARIANT
P-0034177-T01-IM6	APC (NM_000038 rearrangement: c.1744-727_c.4040del	PRECISE	Note: The APC rearrangement is an intragenic deletion of exons 15-16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11156	0	6	5	Intron of APC(+):726bp before exon 15	APC	112169921			5	Exon 16 of APC(+)	APC	112175331			5	DELETION		5410	249496	14005	6	NEW_VARIANT
P-0034192-T01-IM6	AXIN2 (NM_004655) rearrangement: c.1649_chr17:g.63512989dup	PRECISE	Note: The AXIN2 rearrangement is a duplication that includes AXIN2 exons 6-11. One of the breakpoints is within exon 6.	MANUAL_OK	5to3	5to3	-		11580	0	5	17	IGR: 12Kb before AXIN2(-)	AXIN2	63512989			17	Exon 6 of AXIN2(-)	AXIN2	63533505			8	DUPLICATION		20516	249543	15651	5	NEW_VARIANT
P-0033848-T01-IM6	MSH2 (NM_000251) rearrangement: c.2456_c.2459-2del	PRECISE	Note: The MSH2 rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon 14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		679	0	11	2	Exon 14 of MSH2(+)	MSH2	47705656			2	Intron of MSH2(+):1bp before exon 15	MSH2	47707833			10	DELETION		2177	248115	1022	12	NEW_VARIANT
P-0033848-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.45+9425_c.594+2dup	IMPPRECISE	Note: The NFE2L2 rearrangement is an intragenic duplication of exons 2-4. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		4656	0	8	2	Intron of NFE2L2(-):1bp after exon 4	NFE2L2	178097118			2	Intron of NFE2L2(-):9Kb after exon 1	NFE2L2	178119835			0	DUPLICATION		22717	248121	5564	8	NEW_VARIANT
P-0033848-T01-IM6	DNMT1 (NM_001379) rearrangement: t(19;21)(p13.2;q22.11)(chr19:g.10291039::chr21:g.32247604)	PRECISE	Note: The DNMT1 rearrangement is a translocation involving a breakpoint in exon 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	11	21	IGR: 5Kb before KRTAP11-1(-)	KRTAP11-1	32247604			19	Exon 4 of DNMT1(-)	DNMT1	10291039			10	TRANSLOCATION		0	248124	0	11	NEW_VARIANT
P-0033848-T01-IM6	PBRM1 (NM_018313) rearrangement: c.2780-3432_c.4531del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		19954	0	4	3	Exon 29 of PBRM1(-)	PBRM1	52584482			3	Intron of PBRM1(-):3Kb before exon 19	PBRM1	52626703			4	DELETION		42221	248117	25070	4	NEW_VARIANT
P-0033899-T01-IM6	KMT2A (NM_001197104) - PHC2 (NM_198040) rearrangement: t(1;11)(p35.3;q23.3)(chr1:g.33810963::chr11:g.118342947)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KMT2A:PHC2}		0	0	6	11	Exon 3 of KMT2A(+)	KMT2A	118342947			1	Intron of PHC2(-):9Kb after exon 8	PHC2	33810963			10	TRANSLOCATION		0	248713	0	5	NEW_VARIANT
P-0034092-T01-IM6	FLT1 (NM_002019) rearrangement: c.3742:FLT1_chr13:g.25721451dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		55804	0	4	13	IGR: 14Kb before AMER2(-)	AMER2	25721451			13	Exon 29 of FLT1(-)	FLT1	28880888			9	DUPLICATION		3159437	248724	134251	4	NEW_VARIANT
P-0034140-T01-IM6	NCOR1 (NM_006311) rearrangement: t(4;17)(q31.22;p12)(chr4:g.147071771::chr17:g.15983773)	PRECISE	Note: The NCOR1 rearrangement is a translocation with a breakpoint in exon 25. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	31	17	Exon 25 of NCOR1(-)	NCOR1	15983773			4	IGR: 25Kb before LSM6(+)	LSM6	147071771			10	TRANSLOCATION		0	249393	0	37	NEW_VARIANT
P-0034215-T01-IM6	DOT1L (NM_032482) - CSNK1G2 (NM_001319) rearrangement: c.3752:DOT1L_c.-265-8178:CSNK1G2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DOT1L:CSNK1G2}		58839	0	4	19	5-UTR of CSNK1G2(+):8Kb before coding start	CSNK1G2	1961329			19	Exon 27 of DOT1L(+)	DOT1L	2226272			10	DUPLICATION		264943	249868	56634	4	NEW_VARIANT
P-0034256-T01-IM6	CDH1 (NM_004360) rearrangement: c.1866_chr16:g.73261464inv	PRECISE	Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 12-16. One of the breakpoints is within exon 12.	MANUAL_OK	5to5	5to5	-		98796	0	26	16	Exon 12 of CDH1(+)	CDH1	68856058			16	IGR: 101Kb before C16orf47(-)	C16orf47	73261464			10	INVERSION		4405406	250248	59455	30	NEW_VARIANT
P-0033701-T02-IM6	RB1 (NM_000321) rearrangement: c.1696-6786_c.1726del	PRECISE	Note: The RB1 rearrangement results in the deletion of exon 18. One of the breakpoints is within exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		411	0	50	13	Intron of RB1(+):7Kb before exon 18	RB1	49020343			13	Exon 18 of RB1(+)	RB1	49027159			10	DELETION		6816	250434	270	62	NEW_VARIANT
P-0033701-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3851:TMPRSS2_c.19-2454:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		62983	0	110	21	Intron of ERG(-):2Kb before exon 2	ERG	39819998			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873967			10	DELETION		3053969	250435	106066	116	NEW_VARIANT
P-0033701-T02-IM6	CYP3A43 (NM_022820) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(q22.1;q22.3)(chr7:g.99448887::chr21:g.42873843)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {CYP3A43:TMPRSS2}		0	0	97	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873843			7	Intron of CYP3A43(+):2Kb after exon 7	CYP3A43	99448887			0	TRANSLOCATION		0	250437	0	97	NEW_VARIANT
P-0033701-T02-IM6	PIK3R1 (NM_181523) rearrangement: c.1814+70:PIK3R1_chr5:g.70728320del	PRECISE	Note: The PIK3R1 rearrangement results in the deletion of exons 14-16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1831	0	36	5	Intron of PIK3R1(+):70bp after exon 14	PIK3R1	67591386			5	IGR: 23Kb before BDP1(+)	BDP1	70728320			10	DELETION		3136934	250433	2338	43	NEW_VARIANT
P-0034291-T01-IM6	NPM1 (NM_002520) rearrangement: t(X;5)(q22.1;q35.1)(chrX:g.100027214::chr5:g.170820119)	PRECISE	Note: The NPM1 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	X	IGR: 48Kb before CSTF2(+)	CSTF2	100027214			5	Intron of NPM1(+):137bp after exon 6	NPM1	170820119			10	TRANSLOCATION		0	250272	0	5	NEW_VARIANT
P-0034296-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1303:TMPRSS2_c.40-58938:ERGdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53283	0	7	21	Intron of ERG(-):59Kb before exon 4	ERG	39876482			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871419			0	DELETION		2994937	250275	31758	7	NEW_VARIANT
P-0034296-T01-IM6	PLK2 (NM_006622) rearrangement: c.704:PLK2_chr5:g.57189065del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		11858	0	23	5	3-UTR of LOC101928539(-):6Kb after coding stop	LOC101928539	57189065			5	Exon 5 of PLK2(-)	PLK2	57753920			10	DELETION		564855	250274	4314	23	NEW_VARIANT
P-0034384-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2506:TMPRSS2_c.18+6601:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		48435	0	7	21	Intron of ERG(-):7Kb after exon 1	ERG	39863686			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872622			10	DELETION		3008936	250667	32646	9	NEW_VARIANT
P-0034399-T01-IM6	FGFR2 (NM_000141) rearrangement: t(2;10)(q36.1;q26.13)(chr2:g.225329353::chr10:g.123240519)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	50	10	Intron of FGFR2(-):984bp before exon 18	FGFR2	123240519			2	IGR: 6Kb before CUL3(-)	CUL3	225329353			10	TRANSLOCATION		0	250686	0	51	NEW_VARIANT
P-0034375-T01-IM6	SDHC(NM_003001) - DDR2(NM_006182) Rearrangement: c.179+1155:SDHC_c.1729-181:DDR2inv	PRECISE	Note: The SDHC - DDR2 rearrangement is an inversion of SDHC exons 4-6 and DDR2 14-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		15239	0	7	1	Intron of SDHC(+):1Kb after exon 3	SDHC	161299442			1	Intron of DDR2(+):180bp before exon 14	DDR2	162743078			10	INVERSION		1443636	250633	25145	7	NEW_VARIANT
P-0034418-T01-IM6	RB1 (NM_000321) : c.2664-76_c.*4633inv	PRECISE	Note: The RB1 rearrangement is an inversion that includes RB1 exons 26-27.	MANUAL_OK	5to5	5to5	-		1126	0	17	13	Intron of RB1(+):75bp before exon 26	RB1	49051415			13	Promoter of RB1(+):181Kb from tx start	RB1	49058840			10	INVERSION		7425	250762	1357	17	NEW_VARIANT
P-0034419-T01-IM6	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	PRECISE	Note: The FGFR3 - JAKMIP1 fusion is predicted to be in frame and includes the kinase domain of FGFR3.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {FGFR3:JAKMIP1}		44861	0	349	4	Intron of FGFR3(+):88bp after exon 17	FGFR3	1808749			4	Intron of JAKMIP1(-):9Kb after exon 3	JAKMIP1	6098039			10	INVERSION		4289290	250765	58176	345	NEW_VARIANT
P-0030503-T01-IM6	IDH1 (NM_005896)  rearrangement: t(2;8)(q34;p11.21)(chr2:g.209116140::chr8:g.42635681)	PRECISE	Note: The IDH1 rearrangement is a translocation with the breakpoint in intron 3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	33	8	IGR: 28Kb before CHRNA6(-)	CHRNA6	42635681			2	Intron of IDH1(-):13bp after exon 3	IDH1	209116140			10	TRANSLOCATION		0	236769	0	41	NEW_VARIANT
P-0031352-T01-IM6	PARK2 (NM_004562) rearrangement: c.171+46537_c.47del	PRECISE	Note: The PARK2 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1055	0	8	6	Intron of PARK2(-):47Kb after exon 2	PARK2	162817805			6	Exon 2 of PARK2(-)	PARK2	162864466			8	DELETION		46661	229367	595	8	NEW_VARIANT
P-0031643-T01-IM6	SLX4 (NM_032444) Rearrangement: c.*2394_c.3564del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17812	0	46	16	Promoter of SLX4(-):1Kb from tx start	SLX4	3629949			16	Exon 12 of SLX4(-)	SLX4	3640075			10	DELETION		10126	230346	21804	96	NEW_VARIANT
P-0031790-T01-IM6	BRD4 (NM_058243) rearrangement: c.523_c.849+161del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3179	0	24	19	Intron of BRD4(-):160bp after exon 5	BRD4	15376004			19	Exon 4 of BRD4(-)	BRD4	15378263			0	DELETION		2259	231024	5529	25	NEW_VARIANT
P-0031833-T01-IM6	KMT2C (NM_170606) rearrangement: c.8828:KMT2C_chr7:g.151818189del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		41347	0	8	7	Intron of GALNT11(+):136bp after exon 11	GALNT11	151818189			7	Exon 38 of KMT2C(-)	KMT2C	151873710			10	DELETION		55521	231178	28277	8	NEW_VARIANT
P-0032048-T01-IM6	SMAD4 (NM_005359) rearrangement: c.-127-3807_c.961del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9399	0	70	18	5-UTR of SMAD4(+):4Kb before coding start	SMAD4	48569483			18	Exon 9 of SMAD4(+)	SMAD4	48591798			10	DELETION		22315	231965	1554	72	NEW_VARIANT
P-0032124-T01-IM6	TCF7L2 (NM_001146274) - PPP2CA (NM_002715) Rearrangement : t(5;10)(q31.1;q25.2)(chr5:g.133531112::chr10:g.114920515)	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {TCF7L2:PPP2CA}		0	0	29	10	Intron of TCF7L2(+):65bp after exon 13	TCF7L2	114920515			5	Promoter of PPP2CA(-):1Kb from tx start	PPP2CA	133531112			10	TRANSLOCATION		0	232095	0	28	NEW_VARIANT
P-0032390-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2232:TMPRSS2_c.19-12935:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49674	0	41	21	Intron of ERG(-):13Kb before exon 2	ERG	39830479			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872348			10	DELETION		3041869	232859	53461	42	NEW_VARIANT
P-0032458-T01-IM6	EP300 (NM_001429) Rearrangement: t(16;22)(p13.13;q13.2)(chr16:g.11453170::chr22:g.41573186)	PRECISE	Note: The EP300 rearrangement is a translocation with breakpoints within exon 31 of EP300. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	40	22	Exon 31 of EP300(+)	EP300	41573186			16	IGR: 14Kb before RMI2(+)	RMI2	11453170			10	TRANSLOCATION		0	233132	0	42	NEW_VARIANT
P-0032480-T01-IM6	TMPRSS2 (NM_001135099) - ERG(NM_004449) Rearrangement : c.126+617:TMPRSS2_c.39+41589:ERG	PRECISE	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.	MANUAL_OK	3to3	3to3	-		37792	0	14	21	Intron of ERG(-):42Kb after exon 3	ERG	39905997			21	Intron of TMPRSS2(-):616bp after exon 2	TMPRSS2	42869429			10	INVERSION		2963432	233164	26842	12	NEW_VARIANT
P-0032663-T01-IM6	PAX8 (NM_003466) Rearrangement: c.1087+958:PAX8_chr2:g.114132526del	PRECISE	Note: The PAX8 rearrangement results in the deletion of PAX8 exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7980	0	13	2	Intron of PAX8(-):957bp after exon 9	PAX8	113992013			2	IGR: 63Kb before CBWD2(+)	CBWD2	114132526			10	DELETION		140513	234828	6448	13	NEW_VARIANT
P-0032663-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.55+2322:TMPRSS2_c.18+12726:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		100660	0	12	21	Intron of ERG(-):13Kb after exon 1	ERG	39857561			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877555			10	DELETION		3019994	234830	88355	21	NEW_VARIANT
P-0032819-T01-IM6	NF1 (NM_001042492) rearrangement: c.1845+207_c.3708+50dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 17-27. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons : in frame		14652	0	15	17	Intron of NF1(+):207bp after exon 16	NF1	29550792			17	Intron of NF1(+):50bp after exon 27	NF1	29560281			10	DUPLICATION		9489	235861	11718	17	NEW_VARIANT
P-0032823-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.1307_c.2719+1741del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10597	0	38	16	Intron of ZFHX3(-):2Kb after exon 2	ZFHX3	72989585			16	Exon 2 of ZFHX3(-)	ZFHX3	72992738			10	DELETION		3153	235717	8898	48	NEW_VARIANT
P-0033150-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.-1375_c.346del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-4994_c.389del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3476	0	111	9	Exon 2 of CDKN2A(-)	CDKN2A	21971012			9	Intron of CDKN2A(-):5Kb before exon 2	CDKN2A	21976201			10	DELETION		5189	237794	769	121	NEW_VARIANT
P-0033171-T01-IM6	CIC (NM_015125) rearrangement: c.931+290_c.2481inv	PRECISE	Note: The CIC rearrangement is an intragenic inversion of exons 7-10. One of the breakpoints is within exon 10.	MANUAL_OK	3to3	3to3	Antisense Fusion		14762	0	16	19	Intron of CIC(+):290bp after exon 6	CIC	42792417			19	Exon 10 of CIC(+)	CIC	42795401			10	INVERSION		2984	238015	12800	15	NEW_VARIANT
P-0033171-T01-IM6	PTPRD (NM_002839) rearrangement: chr9:g.8208089_c.3153+55del	PRECISE	Note: The PTPRD rearrangement is a deletion that includes PTPRD exons 30-46.	MANUAL_OK	3to5	3to5	-		26792	0	11	9	IGR: 106Kb before PTPRD(-)	PTPRD	8208089			9	Intron of PTPRD(-):54bp after exon 29	PTPRD	8485172			10	DELETION		277083	238014	22006	11	NEW_VARIANT
P-0033183-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1246-40_c.4636-84del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 8-32.	MANUAL_OK	3to5	3to5	Deletion of 25 exons : in frame		49191	0	38	19	Intron of SMARCA4(+):39bp before exon 8	SMARCA4	11101786			19	Intron of SMARCA4(+):83bp before exon 33	SMARCA4	11170345			10	DELETION		68559	238110	33394	39	NEW_VARIANT
P-0033292-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.9485:ZFHX3_chr16:g.72812219del	PRECISE	Note: The ZFHX3 rearrangement is a deletion of a part of exon 10. One of the breakpoints is in exon 10.	MANUAL_OK	3to5	3to5	-		13687	0	65	16	IGR: 5Kb before ZFHX3(-)	ZFHX3	72812219			16	Exon 10 of ZFHX3(-)	ZFHX3	72822690			10	DELETION		10471	238684	10483	68	NEW_VARIANT
P-0033294-T01-IM6	FANCA (NM_000135) rearrangement: t(1;16)(q32.1;q24.3)(chr1:g.206279359::chr16:g.89877021)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {FANCA:C1orf186}		0	0	6	16	Intron of FANCA(-):93bp after exon 5	FANCA	89877021			1	5-UTR of C1orf186(-):40Kb before coding start	C1orf186	206279359			10	TRANSLOCATION		0	238673	0	51	NEW_VARIANT
P-0033383-T01-IM6	SMAD3 (NM_005902) Rearrangement: c.418:SMAD3_chr15:g.62843216inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		35407	0	37	15	IGR: 86Kb before MGC15885(-)	MGC15885	62843216			15	Exon 3 of SMAD3(+)	SMAD3	67457608			10	INVERSION		4614392	239467	48912	57	NEW_VARIANT
P-0033398-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+805_c.350-33del	IMPPRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		14059	0	18	21	Intron of TMPRSS2(-):33bp before exon 4	TMPRSS2	42861553			21	Intron of TMPRSS2(-):804bp after exon 2	TMPRSS2	42869241			0	DELETION		7688	243043	7338	17	NEW_VARIANT
P-0033548-T01-IM6	MAP3K13 (NM_004721) rearrangement: c.1011-161_chr3:g.193808028inv	PRECISE	Note: The MAP3K13 rearrangement is an inversion that includes MAP3K13 exons 6-14. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		63364	0	30	3	Intron of MAP3K13(+):160bp before exon 6	MAP3K13	185167527			3	IGR: 46Kb before HES1(+)	HES1	193808028			10	INVERSION		8640501	251218	172066	30	NEW_VARIANT
P-0033634-T01-IM6	FGFR2 (NM_000141) rearrangement: t(10;18)(q26.13;q21.32)(chr10:g.123244300::chr18:g.58428114)	PRECISE	Note: The FGFR2 rearrangement is a translocation with a breakpoint within intron 16.  The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	67	18	IGR: 390Kb before MC4R(-)	MC4R	58428114			10	Intron of FGFR2(-):608bp after exon 16	FGFR2	123244300			10	TRANSLOCATION		0	243685	0	65	NEW_VARIANT
P-0033634-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1388_chr19:g.46414845inv	PRECISE	Note: The SMARCA4 rearrangement is an inversion that includes SMARCA4 exons 8-35. One of the breakpoints is within exon 8.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SMARCA4:NANOS2}		728196	0	44	19	Exon 8 of SMARCA4(+)	SMARCA4	11101968			19	Promoter of NANOS2(-):2Kb from tx start	NANOS2	46414845			10	INVERSION		35312877	243684	738882	44	NEW_VARIANT
P-0033634-T01-IM6	NPAS2 (NM_002518) - INPP4A (NM_001134224) rearrangement: c.485-1:NPAS2_c.580-3:INPP4Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NPAS2:INPP4A}		32209	0	9	2	Intron of INPP4A(+):2bp before exon 9	INPP4A	99155351			2	Exon 7 of NPAS2(+)	NPAS2	101565828			10	DUPLICATION		2410477	243683	31092	10	NEW_VARIANT
P-0033634-T01-IM6	ATRX (NM_000489) rearrangement: chrX:g.77051146_c.3089del	PRECISE	Note: The ATRX rearrangement is a deletion that includes ATRX exons 1-9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		28594	0	16	X	Exon 9 of ATRX(-)	ATRX	76937659			X	IGR: 31Kb before MAGT1(-)	MAGT1	77051146			10	DELETION		113487	243682	16517	17	NEW_VARIANT
P-0033742-T01-IM6	TET1 (NM_030625) rearrangement: t(10;22)(q21.3;q12.3)(chr10:g.70427055::chr22:g.36131794)	PRECISE	Note: The TET1 rearrangement is a translocation which involves exon 7. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	7	22	Promoter of RBFOX2(-):3Kb from tx start	RBFOX2	36131794			10	Intron of TET1(+):42bp after exon 7	TET1	70427055			10	TRANSLOCATION		0	245125	0	8	NEW_VARIANT
P-0033845-T01-IM6	RUNX1 (NM_001754) rearrangement: c.352-96:RUNX1_chr21:g.38829898del	PRECISE	Note: The RUNX1 rearrangement is a deletion of exons 1-4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5610	0	15	21	Intron of RUNX1(-):96bp before exon 5	RUNX1	36253106			21	Intron of DYRK1A(+):15Kb before exon 2	DYRK1A	38829898			10	DELETION		2576792	248132	8049	16	NEW_VARIANT
P-0033855-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.582_c.859+185del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 4-5. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3324	1	63	19	Exon 4 of SMARCA4(+)	SMARCA4	11097091			19	Intron of SMARCA4(+):185bp after exon 5	SMARCA4	11097864			10	DELETION		773	248137	1068	76	NEW_VARIANT
P-0034080-T02-IM6	NAB2 (NM_005967) rearrangement: t(12;14)(q13.3;q31.1)(chr12:g.57487449::chr14:g.82091713)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	16	14	Promoter of LINC01467(-):20Kb from tx start	LINC01467	82091713			12	Intron of NAB2(+):68bp after exon 6	NAB2	57487449			0	TRANSLOCATION		0	250754	0	16	NEW_VARIANT
P-0034255-T01-IM6	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.85+112:AXL_c.296-1265:HNRNPUL1inv	PRECISE	Note: The AXL - HNRNPUL1 rearrangement is an inversion that includes AXL exons 2-20 and HNRNPUL1 exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		45138	0	14	19	Intron of AXL(+):112bp after exon 1	AXL	41725494			19	Intron of HNRNPUL1(+):1Kb before exon 2	HNRNPUL1	41772863			10	INVERSION		47369	250257	35915	14	NEW_VARIANT
P-0034289-T01-IM6	APC (NM_000038) rearrangement: c.4324:APC_chr5:g.112194400del	PRECISE	Note: The APC rearrangement is a deletion of a part of exon 16. One of the breakpoint is within exon 16.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		15530	0	35	5	Exon 16 of APC(+)	APC	112175615			5	Promoter of SRP19(+):2Kb from tx start	SRP19	112194400			10	DELETION		18785	250268	6041	35	NEW_VARIANT
P-0034352-T01-IM6	NEGR1 (NM_173808) rearrangement: c.835:NEGR1_chr1:g.145082046inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NEGR1:NBPF20}		193398	0	48	1	Exon 6 of NEGR1(-)	NEGR1	72058605			1	Intron of NBPF20(+):231Kb before exon 54	NBPF20	145082046			10	INVERSION		73023441	250441	247891	56	NEW_VARIANT
P-0034379-T01-IM6	ATR (NM_001184) rearrangement: t(3;12)(q23;q14.3)(chr3:g.142277934::chr12:g.65647870)	PRECISE	Note: The ATR rearrangement is a translocation involving exon 7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	5	12	IGR: 25Kb before MSRB3(+)	MSRB3	65647870			3	Intron of ATR(-):158bp after exon 7	ATR	142277934			10	TRANSLOCATION		0	250643	0	5	NEW_VARIANT
P-0034483-T01-IM6	PALB2 (NM_024675) rearrangement: t(2;16)(q31.1;p12.2)(chr2:g.176432726::chr16:g.23647039)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	135	16	Exon 4 of PALB2(-)	PALB2	23647039			2	IGR: 358Kb before KIAA1715(-)	KIAA1715	176432726			10	TRANSLOCATION		0	251227	0	149	NEW_VARIANT
P-0034540-T01-IM6	EMR3(NM_032571) - MEF2BNB (NM_001145784) Rearrangement :  c.-2027:EMR3_c.337:MEF2BNBdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EMR3:MEF2B}		201845	0	136	19	Promoter of EMR3(-):58Kb from tx start	EMR3	14787609			19	Exon 4 of MEF2B(-)	MEF2B	19258563			10	DUPLICATION		4470954	252314	370907	156	NEW_VARIANT
P-0034540-T01-IM6	JAK2 (NM_004972) Rearrangement : c.2529_c.2762-204del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		932	0	42	9	Exon 19 of JAK2(+)	JAK2	5081819			9	Intron of JAK2(+):203bp before exon 21	JAK2	5090242			10	DELETION		8423	252313	1517	44	NEW_VARIANT
P-0034559-T01-IM6	ROS1 (NM_002944) rearrangement: c.5558-523_c.5642-1074del	PRECISE	Note: The ROS1 rearrangement results in the deletion of exon 34. Further analysis using the Archer targeted RNA seq assay will be performed if additional material is available and results will be reported under a separate accession number.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		16876	0	25	6	Intron of ROS1(-):1Kb before exon 35	ROS1	117643631			6	Intron of ROS1(-):523bp before exon 34	ROS1	117646101			10	DELETION		2470	252079	19017	26	NEW_VARIANT
P-0034643-T01-IM6	TCF3 (NM_001136139) - PRSS57 (NM_214710) rearrangement: c.1450+69:TCF3_c.382-485:PRSSS57del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TCF3:PRSS57}		25185	0	15	19	Intron of PRSS57(-):485bp before exon 4	PRSS57	687673			19	Intron of TCF3(-):68bp after exon 15	TCF3	1619041			10	DELETION		931368	252632	25579	22	NEW_VARIANT
P-0034946-T01-IM6	KMT2C (NM_170606) rearrangement: c.8323_c.13423del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		38900	0	114	7	Exon 52 of KMT2C(-)	KMT2C	151845589			7	Exon 38 of KMT2C(-)	KMT2C	151874215			10	DELETION		28626	254736	42967	118	NEW_VARIANT
P-0034946-T01-IM6	TEK (NM_000459) rearrangement: c.2575+394_c.3119del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10096	0	186	9	Intron of TEK(+):394bp after exon 15	TEK	27207184			9	Exon 21 of TEK(+)	TEK	27220062			10	DELETION		12878	254737	4702	194	NEW_VARIANT
P-0035009-T01-IM6	STK11 (NM_000455) rearrangement: c.222_c.920+359del	PRECISE	Note: The STK11 rearrangement is an intragenic deletion of exons 1-7. One of the breakpoints is within STK11 exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6862	0	82	19	Exon 1 of STK11(+)	STK11	1207134			19	Intron of STK11(+):359bp after exon 7	STK11	1222364			10	DELETION		15230	254987	3233	90	NEW_VARIANT
P-0035013-T01-IM6	STAT3 (NM_139276) rearrangement: c.2102-94:STAT3_chr17:g.55289920del	PRECISE	Note: The STAT3 rearrangement is a deletion of exons 1-21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		175273	0	15	17	Intron of STAT3(-):94bp before exon 22	STAT3	40469336			17	IGR: 44Kb before MSI2(+)	MSI2	55289920			10	DELETION		14820584	254981	242636	15	NEW_VARIANT
P-0035021-T01-IM6	RASA1 (NM_002890) rearrangement: c.1102+114:RASA1_chr5:g.179255094inv	PRECISE	Note: The RASA1 rearrangement is an intragenic inversion of exons 8-25.	MANUAL_OK	3to3	3to3	Antisense Fusion		364345	0	6	5	Intron of RASA1(+):114bp after exon 7	RASA1	86642655			5	Intron of SQSTM1(+):3Kb after exon 6	SQSTM1	179255094			10	INVERSION		92612439	254991	227252	6	NEW_VARIANT
P-0035076-T01-IM6	ATM (NM_000051) rearrangement: c.7515+274_c.8986del	PRECISE	Note: The ATM rearrangement is an intragenic deletion of exon 51-62. One of the breakpoints is within exon 62.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9750	0	4	11	Intron of ATM(+):274bp after exon 50	ATM	108201422			11	Exon 62 of ATM(+)	ATM	108235944			9	DELETION		34522	255513	3160	5	NEW_VARIANT
P-0035082-T01-IM6	ARID1B (NM_020732) rearrangement: t(6;10)(q25.3;p15.3)(chr6:g.57099972::chr10:g.124553)	PRECISE	Note: The ARID1B rearrangement is a translocation with a breakpoint within exon 1.	MANUAL_OK	5to3	5to3	-		0	0	18	10	IGR: 32Kb before TUBB8(-)	TUBB8	124553			6	Exon 1 of ARID1B(+)	ARID1B	157099972			10	TRANSLOCATION		0	255502	0	22	NEW_VARIANT
P-0035082-T01-IM6	COL5A3 (NM_015719) - DNMT1 (NM_001379) rearrangement: c.1587+777:COL5A3_c.4459:DNMT1inv	IMPPRECISE	Note: The COL5A3 - DNMT1 rearrangement is an inversion that includes COL5A3 exons 1-16 and DNMT1 exons 37-40. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		5885	0	60	19	Intron of COL5A3(-):776bp after exon 16	COL5A3	10105463			19	Exon 37 of DNMT1(-)	DNMT1	10246946			0	INVERSION		141483	255501	8380	60	NEW_VARIANT
P-0035085-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		79957	0	5	2	Intron of ALK(-):685bp before exon 20	ALK	29447079			2	Intron of EML4(+):7Kb after exon 5	EML4	42499232			10	INVERSION		13052153	255508	35631	5	NEW_VARIANT
P-0034907-T01-IM6	BRD4 (NM_058243) rearrangement: t(1;19)(q25.3,p13.12)(chr1:g.180481230::chr19:g.15353735)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	130	19	Exon 14 of BRD4(-)	BRD4	15353735			1	IGR: 47Kb before OVAAL(+)	OVAAL	180481230			0	TRANSLOCATION		0	254603	0	146	NEW_VARIANT
P-0034912-T01-IM6	MTOR (NM_004958) rearrangement: c.6663-269_c.6823del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2272	0	3	1	Exon 49 of MTOR(-)	MTOR	11181413			1	Intron of MTOR(-):269bp before exon 48	MTOR	11182452			5	DELETION		1039	254592	3247	3	NEW_VARIANT
P-0034912-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement : c.151-90:CDKN2Ap16INK4A_chr9:g.22060034del CDKN2Ap14ARF (NM_058195) rearrangement : c.194-90:CDKN2Ap14ARF_chr9:g.22060034del	PRECISE	Note: The CDKN2A rearrangement results in the deletion of exon 1 of both the CDKN2Ap16INK4A and CDKN2Ap14ARF isoforms.	MANUAL_OK	3to5	3to5	-		11948	0	40	9	Intron of CDKN2A(-):90bp before exon 2	CDKN2A	21971297			9	5-UTR of CDKN2B-AS1(+):61Kb before coding start	CDKN2B-AS1	22060034			10	DELETION		88737	254593	11689	46	NEW_VARIANT
P-0034916-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.1330-104_c.1471+2213del	PRECISE	Note: The TGFBR2 rearrangement is an intragenic deletion of exon 6. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		898	0	6	3	Intron of TGFBR2(+):103bp before exon 6	TGFBR2	30715493			3	Intron of TGFBR2(+):2Kb after exon 6	TGFBR2	30717951			8	INVERSION		2458	254659	982	6	NEW_VARIANT
P-0035075-T01-IM6	TP53 (NM_000546) rearrangement: c.993+650:TP53_chr17:g.7569521inv	PRECISE	Note: The TP53 rearrangement is an inversion of exons 10-11.	MANUAL_OK	5to5	5to5	Antisense Fusion		3211	0	8	17	Promoter of TP53(-):2Kb from tx start	TP53	7569521			17	Intron of TP53(-):649bp after exon 9	TP53	7576203			10	INVERSION		6682	255441	663	11	NEW_VARIANT
P-0035163-T01-IM6	CD274 (NM_014143) rearrangement: t(9;14)(p24.1;q21.2)(chr9:g.5457150::chr14:g.39459204)	PRECISE	Note: The CD274 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	32	14	IGR: 42Kb before SEC23A(-)	SEC23A	39459204			9	Exon 3 of CD274(+)	CD274	5457150			10	TRANSLOCATION		0	256099	0	35	NEW_VARIANT
P-0035167-T01-IM6	PRKD1 (NM_002742) rearrangement: c.1314+197:PRKD1_chr14:g.26379764inv	PRECISE	Note: The PRKD1 rearrangement is an inversion of exons 9-18. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		21669	0	27	14	IGR: 535Kb before NOVA1(-)	NOVA1	26379764			14	Intron of PRKD1(-):196bp after exon 8	PRKD1	30103427			10	INVERSION		3723663	255904	17438	27	NEW_VARIANT
P-0035167-T01-IM6	AR (NM_000044) rearrangement: c.2173+14:AR_chrX:g.77626841del	PRECISE	Note: The AR rearrangement is a deletion of exons 5-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		118122	0	24	X	Intron of AR(+):14bp after exon 4	AR	66931545			X	IGR: 100Kb before CYSLTR1(-)	CYSLTR1	77626841			10	DELETION		10695296	255902	172979	27	NEW_VARIANT
P-0035211-T01-IM6	POLE (NM_006231) rearrangement: c.4290+5_c.6330+2503del	PRECISE	Note: The POLE rearrangement is an intragenic deletion of exons  34-45.	MANUAL_OK	3to5	3to5	Deletion of 12 exons : in frame		19064	0	81	12	Intron of POLE(-):3Kb after exon 45	POLE	133206398			12	Intron of POLE(-):4bp after exon 33	POLE	133220418			10	DELETION		14020	256900	26692	82	NEW_VARIANT
P-0035211-T01-IM6	FANCA (NM_000135) rearrangement: c.2249_c.2852+338del	PRECISE	Note: The FANCA intragenic deletion involves exons 25-29. One of the breakpoints is within exon 25.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5372	1	221	16	Intron of FANCA(-):337bp after exon 29	FANCA	89828019			16	Exon 25 of FANCA(-)	FANCA	89836641			10	DELETION		8622	256901	2114	242	NEW_VARIANT
P-0022166-T02-IM6	CDC73 (NM_024529) rearrangement: c.132-1234_c.512+123dup	PRECISE	Note: The CDC73 rearrangement results in the intragenic duplication of exons 2-6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : in frame		4161	0	12	1	Intron of CDC73(+):1Kb before exon 2	CDC73	193093008			1	Intron of CDC73(+):123bp after exon 6	CDC73	193107426			10	DUPLICATION		14418	257657	9391	12	NEW_VARIANT
P-0022166-T02-IM6	ATM (NM_000051) rearrangement: t(11;12)(q22.3;q21.32)(chr11:g.108224556::chr12:g.88926122)	PRECISE	Note: The ATM rearrangement is a translocation with a breakpoint in exon 60. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	48	12	Intron of KITLG(-):95bp after exon 3	KITLG	88926122			11	Exon 60 of ATM(+)	ATM	108224556			10	TRANSLOCATION		0	257658	0	49	NEW_VARIANT
P-0022861-T02-IM6	EPHA5 (NM_004439) rearrangement: t(4;12)(q13.1;q14.3)(chr4:g.66201820::chr12:g.67086133)	PRECISE	Note: The EPHA5 rearrangement is a translocation with a breakpoint within exon 16. The  functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	12	IGR: 345Kb before GRIP1(-)	GRIP1	67086133			4	Exon 16 of EPHA5(-)	EPHA5	66201820			10	TRANSLOCATION		0	258062	0	12	NEW_VARIANT
P-0022861-T02-IM6	ATRX (NM_000489) - PPM1H (NM_020700) rearrangement: t(X;12)(q21.1;q14.2)(chrX:g.76907807::chr12:g.63147303)	PRECISE	Note: The ATRX - PPM1H rearrangement is a translocation with breakpoints within ATRX exon 15 and PPM1H intron 4.	MANUAL_OK	3to3	3to3	-		0	0	24	X	Exon 15 of ATRX(-)	ATRX	76907807			12	Intron of PPM1H(-):16Kb before exon 5	PPM1H	63147303			10	TRANSLOCATION		0	258063	0	23	NEW_VARIANT
P-0034569-T02-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		103943	0	57	2	Intron of ALK(-):120bp before exon 20	ALK	29446514			2	Intron of EML4(+):216bp before exon 20	EML4	42553077			10	INVERSION		13106563	258049	116766	56	NEW_VARIANT
P-0035120-T01-IM6	KIT (NM_000222) rearrangement: c.1775-34:KIT_chr4:g.57331639del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {KIT:SRP72}		55247	0	14	4	Intron of KIT(+):33bp before exon 12	KIT	55593955			4	Promoter of SRP72(+):2Kb from tx start	SRP72	57331639			10	DELETION		1737684	257651	94854	18	NEW_VARIANT
P-0035121-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4857:EML4_c.3172+944:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		104302	0	25	2	Intron of ALK(-):943bp after exon 19	ALK	29447383			2	Intron of EML4(+):5Kb before exon 6	EML4	42503133			10	INVERSION		13055750	257675	121303	24	NEW_VARIANT
P-0035122-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.-29-1913_c.629inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		5232	0	2	4	5-UTR of WHSC1(+):2Kb before coding start	WHSC1	1900440			4	Exon 3 of WHSC1(+)	WHSC1	1905974			4	INVERSION		5534	257670	5033	1	NEW_VARIANT
P-0035219-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-1718_c.*1663del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exons 2-14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		35995	0	38	21	Promoter of TMPRSS2(-):71bp from tx start	TMPRSS2	42836406			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871834			10	DELETION		35428	256929	38064	40	NEW_VARIANT
P-0035219-T01-IM6	DROSHA (NM_013235) rearrangement: c.3994+58:DROSHA_chr5:g.32816052inv	PRECISE	Note: The DROSHA rearrangement results in the inversion of exons 1-34. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		37633	0	8	5	Intron of DROSHA(-):57bp after exon 34	DROSHA	31405726			5	IGR: 105Kb before NPR3(+)	NPR3	32816052			10	INVERSION		1410326	256931	53695	8	NEW_VARIANT
P-0035226-T01-IM6	CDH1 (NM_004360) rearrangement: c.2515_c.*636inv	PRECISE	Note: The CDH1 rearrangement results in the inversion of exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	5to5	5to5	-		714	0	21	16	Exon 16 of CDH1(+)	CDH1	68867268			16	3-UTR of CDH1(+):97Kb after coding stop	CDH1	68868038			10	INVERSION		770	256943	1116	30	NEW_VARIANT
P-0035226-T01-IM6	RERE (NM_001042681) - SMAD2 (NM_001003652) rearrangement: t(1;18)(p36.23;q21.1)(chr1:g.8565611::chr18:g.45368323)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RERE:SMAD2}		0	0	8	18	Intron of SMAD2(-):2bp before exon 11	SMAD2	45368323			1	Intron of RERE(-):3Kb after exon 8	RERE	8565611			0	TRANSLOCATION		0	256945	0	8	NEW_VARIANT
P-0035226-T01-IM6	GNAS (NM_000516) rearrangement: c.586-7_c.*4inv	PRECISE	Note: The GNAS rearrangement results in the inversion of exons 8-13. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4055	0	20	20	Intron of GNAS(+):6bp before exon 8	GNAS	57484398			20	3-UTR of GNAS(+):19Kb after coding stop	GNAS	57485888			10	INVERSION		1490	256944	6582	20	NEW_VARIANT
P-0035227-T01-IM6	TP53 (NM_000546) rearrangement: c.673-50_c.993+375inv	PRECISE	Note: The TP53 rearrangement results in the inversion of exons 7-9.	MANUAL_OK	5to5	5to5	Antisense Fusion		4675	0	2	17	Intron of TP53(-):374bp after exon 9	TP53	7576478			17	Intron of TP53(-):50bp before exon 7	TP53	7577658			10	INVERSION		1180	256953	5473	2	NEW_VARIANT
P-0035240-T01-IM6	RARA (NM_000964) rearrangement: c.469+54_chr17:g.38525291del	PRECISE	Note: The RARA rearrangement is a deletion that includes RARA exons 5-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9279	0	21	17	Intron of RARA(+):54bp after exon 4	RARA	38506231			17	IGR: 8Kb before GJD3(-)	GJD3	38525291			10	DELETION		19060	256967	7022	21	NEW_VARIANT
P-0035270-T01-IM6	TMPRSS2:NM_001135099 - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 fused to ERG exons 2-11):	PRECISE		MANUAL_OK	3to5	3to5	-		31248	0	71	21	3-UTR of ERG(-):59Kb after coding stop	ERG	39975032			21	Intron of TMPRSS2(-):127bp after exon 2	TMPRSS2	42869918			10	DELETION		2894886	257358	31723	74	NEW_VARIANT
P-0035283-T01-IM6	ALOX12B (NM_001139) rearrangement: c.1654+71:ALOX12B_chr17:g.6914967del	IMPPRECISE	Note: The ALOX12B rearrangement results in the deletion of exons 13-15. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		48991	0	10	17	3-UTR of ALOX12-AS1(-):686bp after coding stop	ALOX12-AS1	6914967			17	Intron of ALOX12B(-):70bp after exon 12	ALOX12B	7978842			0	DELETION		1063875	257736	50356	10	NEW_VARIANT
P-0035284-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+991:TMPRSS2_c.40-63565:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		31342	0	129	21	Intron of ERG(-):64Kb before exon 4	ERG	39881109			21	Intron of TMPRSS2(-):990bp after exon 2	TMPRSS2	42869055			10	DELETION		2987946	257753	43926	132	NEW_VARIANT
P-0035373-T01-IM6	MGA (NM_001164273) rearrangement: chr15:g.41935537_c.7009-11del	PRECISE	Note: The MGA rearrangement is an intragenic deletion of exons 1 to 17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		63087	0	12	15	IGR: 17Kb before MGA(+)	MGA	41935537			15	Intron of MGA(+):10bp before exon 18	MGA	42046624			10	DELETION		111087	258020	73979	12	NEW_VARIANT
P-0035373-T01-IM6	TSC2 (NM_000548) Rearrangement: c.5195:TSC2_chr16:g.2161814del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		3503	0	9	16	Exon 41 of TSC2(+)	TSC2	2138262			16	Exon 15 of PKD1(-)	PKD1	2161814			10	DELETION		23552	258021	6541	14	NEW_VARIANT
P-0035373-T01-IM6	TP53 (NM_000546) Rearrangement: c.318_c.994-916del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12667	0	9	17	Intron of TP53(-):916bp before exon 10	TP53	7574949			17	Exon 4 of TP53(-)	TP53	7579369			10	DELETION		4420	258022	17402	9	NEW_VARIANT
P-0035373-T01-IM6	BRCA1 (NM_007294) Rearrangement: c.5278-2343_c.5588del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6982	0	4	17	Exon 23 of BRCA1(-)	BRCA1	41197699			17	Intron of BRCA1(-):2Kb before exon 20	BRCA1	41205477			5	DELETION		7778	258023	9958	4	NEW_VARIANT
P-0035373-T01-IM6	SETD2 (NM_014159) Rearrangement: c.71+7073_c.5016-30del	PRECISE	Note: The SETD2 rearrangement is an intragenic deletion of exons 2 to 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : in frame		36191	0	10	3	Intron of SETD2(-):30bp before exon 9	SETD2	47139601			3	Intron of SETD2(-):7Kb after exon 1	SETD2	47198271			10	DELETION		58670	258018	39973	10	NEW_VARIANT
P-0035374-T01-IM6	RAD21 (NM_006265) Rearrangement: c.-32-30_c.938-196del	PRECISE	Note: The RAD21 rearrangement is an intragenic deletion of exons 1 to 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		11080	0	7	8	Intron of RAD21(-):196bp before exon 9	RAD21	117866903			8	5-UTR of RAD21(-):19Kb before coding start	RAD21	117879030			9	DELETION		12127	258044	7973	7	NEW_VARIANT
P-0035375-T01-IM6	TAP1 (NM_000593) Rearrangement: t(6;10)(p21.32;q26.11)(chr6:g.32820038::chr10:g.119130943)	PRECISE	Note: The TAP1 rearrangement is a translocation involving a breakpoint within intron 2 of TAP1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	68	10	Intron of PDZD8(-):3Kb after exon 1	PDZD8	119130943			6	Intron of TAP1(-):22bp before exon 3	TAP1	32820038			10	TRANSLOCATION		0	258015	0	70	NEW_VARIANT
P-0035448-T01-IM6	DNMT1 (NM_001379) rearrangement: c.4441+11:DNMT1_chr19:g.10228347inv	PRECISE	Note: The DNMT1 rearrangement is an inversion of exons 37-40. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		7039	0	11	19	Intron of EIF3G(-):483bp before exon 6	EIF3G	10228347			19	Intron of DNMT1(-):10bp after exon 36	DNMT1	10247750			10	INVERSION		19403	258224	8856	11	NEW_VARIANT
P-0035466-T01-IM6	ATP1A2 (NM_000702) - NTRK1 (NM_002529) rearrangement: c.2563+2:ATP1A2_c.1268:NTRK1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ATP1A2:NTRK1}		26435	0	3	1	Exon 11 of NTRK1(+)	NTRK1	156844714			1	Intron of ATP1A2(+):2bp after exon 18	ATP1A2	160106162			7	DUPLICATION		3261448	258373	23696	3	NEW_VARIANT
P-0035473-T01-IM6	SMAD4 (NM_005359) rearrangement: c.667+761_c.1448-120del	PRECISE	Note: The SMAD4 rearrangement is an intragenic deletion of exons 6-11.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		7835	0	4	18	Intron of SMAD4(+):761bp after exon 5	SMAD4	48582124			18	Intron of SMAD4(+):119bp before exon 12	SMAD4	48604506			10	DELETION		22382	258371	3534	5	NEW_VARIANT
P-0025100-T02-IM6	KIF5B (NM_004521) and RET (NM_020975) Fusion (KIF5B exon 16 fused to RET exon 12): c.1726-2273:KIF5B_c.2137-788:RETinv	PRECISE	Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		59306	0	48	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32314237			10	Intron of RET(+):520bp before exon 12	RET	43611511			10	INVERSION		11297274	255769	92064	54	NEW_VARIANT
P-0025100-T02-IM6	PARK2 (NM_004562) - RAD21 (NM_006265) Rearrangement : t(6;8)(q26;q24.11)(chr6:g.162807539::chr8:g.117875650)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {PARK2:RAD21}		0	0	6	8	Intron of RAD21(-):152bp before exon 3	RAD21	117875650			6	Intron of PARK2(-):57Kb after exon 2	PARK2	162807539			8	TRANSLOCATION		0	255770	0	6	NEW_VARIANT
P-0035576-T01-IM6	CDKN2B (NM_004936)  - CDKN2A (NM_000077) Rearrangement: c.224:CDKN2B_c.153:CDKN2Adel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDKN2B:CDKN2A}		6031	0	41	9	Exon 2 of CDKN2A(-)	CDKN2A	21971205			9	Exon 2 of CDKN2B(-)	CDKN2B	22006179			0	DELETION		34974	259785	4493	60	NEW_VARIANT
P-0020945-T02-IM6	DOT1L (NM_032482) Rearrangement : c.1006-268_c.1558-159del	PRECISE	Note: The DOT1L Rearrangement results in the intragenic deletion of exons 13-16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		6845	0	12	19	Intron of DOT1L(+):267bp before exon 13	DOT1L	2210131			19	Intron of DOT1L(+):158bp before exon 17	DOT1L	2213379			7	DELETION		3248	191567	7838	13	NEW_VARIANT
P-0020945-T02-IM6	MDM4 (NM_002393) Rearrangement : t(1,2)(q12.1,q32.1)(chr1:g.204495627::chr2:g.102872474)	PRECISE	Note : The MDM4 Rearrangement results in the possible truncation of MDM4. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	14	2	IGR: 55Kb before IL1RL1(+)	IL1RL1	102872474			1	Intron of MDM4(+):65bp after exon 3	MDM4	204495627			10	TRANSLOCATION		0	191569	0	16	NEW_VARIANT
P-0022683-T01-IM6	SMAD4 (NM_005359) rearrangement: c.1228_c.1309-3020del	PRECISE	Note: The SMAD4 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		432	0	14	18	Exon 10 of SMAD4(+)	SMAD4	48593477			18	Intron of SMAD4(+):3Kb before exon 11	SMAD4	48599988			10	DELETION		6511	191764	507	18	NEW_VARIANT
P-0022683-T01-IM6	POLRMT (NM_005035) - MAP2K2 (NM_030662) rearrangement: c.823-1775:POLRMT_c.415-84:MAP2K2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {POLRMT:MAP2K2}		184058	0	15	19	Intron of POLRMT(-):2Kb before exon 4	POLRMT	627029			19	Intron of MAP2K2(-):84bp before exon 9	MAP2K2	4095531			10	DUPLICATION		3468502	191765	141346	15	NEW_VARIANT
P-0022871-T01-IM6	CBFB (NM_022845) Rearrangement : c.-616_c.66del	PRECISE	Note: The CBFB Rearrangement results in the intragenic deletion of exon1 of CBFB. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		364	0	80	16	Promoter of CBFB(+):354bp from tx start	CBFB	67062695			16	Exon 1 of CBFB(+)	CBFB	67063376			10	DELETION		681	192897	188	107	NEW_VARIANT
P-0022936-T01-IM6	NTRK1 (NM_002529) rearrangement: c.1847_chr1:g.156855832del	IMPPRECISE	Note: The NTRK1 rearrangement is a deletion of NTRK1 exons 15-17, including the kinase domain. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7878	0	48	1	Exon 15 of NTRK1(+)	NTRK1	156848955			1	IGR: 8Kb before PEAR1(+)	PEAR1	156855832			0	DELETION		6877	193012	6486	52	NEW_VARIANT
P-0022936-T01-IM6	NTRK1 (NM_002529) - STK11 (NM_000455) rearrangement: t(1;19)(;)(chr1:g.56848955::chr19:g.204186)	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NTRK1:STK11}		0	0	5	19	Promoter of STK11(+):2Kb from tx start	STK11	1204186			1	Exon 15 of NTRK1(+)	NTRK1	156848955			0	TRANSLOCATION		0	193018	0	5	NEW_VARIANT
P-0023215-T01-IM6	ETV6 (NM_001987) rearrangement: t(12;15)(p13.2;q26.1)(chr12:g.12035854::chr15:g.90039073)	PRECISE	Note: The ETV6 rearrangement is a translocation that may result in a truncation of exons 7-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	64	15	Intron of RHCG(-):518bp after exon 1	RHCG	90039073			12	Intron of ETV6(+):2Kb before exon 6	ETV6	12035854			10	TRANSLOCATION		0	194368	0	68	NEW_VARIANT
P-0023215-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.194-36:CDKN2Ap14ARF_chr9:g.22734473inv	PRECISE	Note: The CDKN2Ap14ARF rearrangement is an inversion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0		92	9	Intron of CDKN2Ap14ARF:36bp before exon 2	CDKN2Ap14ARF	21971243			9	5-UTR of LINC01239(+):90Kb before coding start	LINC01239	22734473			10	INVERSION		763230	195442	5107		NEW_VARIANT
P-0023215-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.151-36:CDKN2Ap16INK4A_chr9:g.22734473inv	PRECISE	Note: The CDKN2Ap16INK4A rearrangement is an inversion of exon 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0		92	9	Intron of CDKN2Ap16INK4A:36bp before exon 2	CDKN2Ap16INK4A	21971243			9	5-UTR of LINC01239(+):90Kb before coding start	LINC01239	22734473			10	INVERSION		763230	195441	5107		NEW_VARIANT
P-0033407-T01-IM6	RET (NM_020975) Rearrangement: c.2739:RET_chr10:g.38458902inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		84895	0	7	10	IGR: 6Kb before LOC100129055(+)	LOC100129055	38458902			10	Exon 16 of RET(+)	RET	43617402			10	INVERSION		5158500	239337	77442	7	NEW_VARIANT
P-0035502-T01-IM6	DAXX (NM_001141970) rearrangement: c.1416:DAXX_chr6:g.33806571inv	PRECISE	Note: The DAXX rearrangement is an inversion of exons 1-5. One of the breakpoints is within exon 5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		11169	0	8	6	Exon 5 of DAXX(-)	DAXX	33287873			6	IGR: 44Kb before MLN(-)	MLN	33806571			10	INVERSION		518698	258795	14197	8	NEW_VARIANT
P-0035506-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-16831:ERG_c.55+1176:TMPRSS2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ERG:TMPRSS2}		103595	0	7	21	Intron of ERG(-):17Kb before exon 2	ERG	39834375			21	Intron of TMPRSS2(-):1Kb after exon 1	TMPRSS2	42878701			0	DUPLICATION		3044326	258804	32091	8	NEW_VARIANT
P-0035577-T01-IM6	SMAD4 (NM_005359) rearrangement: g.48535585_c.1023del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		9270	0	111	18	IGR: 21Kb before SMAD4(+)	SMAD4	48535585			18	Exon 9 of SMAD4(+)	SMAD4	48591860			10	DELETION		56275	259760	5030	116	NEW_VARIANT
P-0035584-T01-IM6	CHEK2 (NM_007194) Rearrangement: t(17;22)(q23.2;q12.1)(chr17:g.60026179::chr22:g.29115449)	PRECISE	Note: The CHEK2 rearrangement is a translocation with the breakpoint in exon 5 CHEK2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	49	22	Exon 5 of CHEK2(-)	CHEK2	29115449			17	Intron of MED13(-):2Kb before exon 29	MED13	60026179			10	TRANSLOCATION		0	259783	0	48	NEW_VARIANT
P-0035586-T01-IM6	SMAD3 (NM_005902) rearrangement: c.207-26812:SMAD3_chr15:g.67497181del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		12984	0	30	15	Intron of SMAD3(+):27Kb before exon 2	SMAD3	67430421			15	Intron of AAGAB(-):695bp before exon 8	AAGAB	67497181			10	DELETION		66760	259787	13893	30	NEW_VARIANT
P-0004752-T03-IM6	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)	PRECISE	Note: The CD74 - NRG1 fusion is predicted to be in-frame.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CD74:NRG1}		0	0	70	8	Intron of NRG1(+):36Kb before exon 6	NRG1	32549504			5	Intron of CD74(-):89bp before exon 7	CD74	149782964			10	TRANSLOCATION		0	190681	0	88	NEW_VARIANT
P-0015376-T01-IM6	WHSC1L1 (NM_023034) rearrangement: t(8;13)(p11.23;q12.3)(chr8:g.38175374::chr13:g.30470955)	PRECISE	Note: The WHSC1L1 rearrangement is a translocation that may result in a truncation of exons 10-24. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	5	13	IGR: 46Kb after UBL3(-)	UBL3	30470955			8	Intron of WHSC1L1(-): 1Kb after exon 9	WHSC1L1	38175374			6	TRANSLOCATION		0	167795	0	5	NEW_VARIANT
P-0021497-T01-IM6	IGF2 (NM_001127598) rearrangement: c.61:IGF2_chr11:g.2283381inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1872	0	14	11	Exon 2 of IGF2(-)	IGF2	2161466			11	IGR: 6Kb before ASCL2(-)	ASCL2	2283381			10	INVERSION		121915	187567	2509	14	NEW_VARIANT
P-0025764-T01-IM6	STAG2 (NM_001042749) Rearrangement : c.-162-27000_c.2141del	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		17066	0	28	X	5-UTR of STAG2(+):28Kb before coding start	STAG2	123128217			X	Exon 22 of STAG2(+)	STAG2	123200069			10	DUPLICATION		71852	207044	52214	32	NEW_VARIANT
P-0025791-T03-IM6	URAD (NM_001105577) - FLT3 (NM_004119) Rearrangement : c.175+4829:URAD_c.1562:FLT3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {FLT3:URAD}		18154	0	6	13	Intron of URAD(-):5Kb after exon 1	URAD	28557771			13	Exon 12 of FLT3(-)	FLT3	28609667			10	DELETION		51896	233215	20106	6	NEW_VARIANT
P-0027309-T03-IM6	RPS6KA4 (NM_003942) rearrangement: c.1958-26:RPS6KA4_chr11:g.64015463del	PRECISE	Note: The RPS6KA4 rearrangement is a deletion of exons 1-16.	MANUAL_OK	3to5	3to5	-		24025	0	60	11	Promoter of PPP1R14B(-):4Kb from tx start	PPP1R14B	64015463			11	Intron of RPS6KA4(+):25bp before exon 16	RPS6KA4	64138009			10	DELETION		122546	232887	22487	62	NEW_VARIANT
P-0029928-T01-IM6	PARK2 (NM_004562) rearrangement: c.413-24781_c.871+36638del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exons 4-7. Its functional significance is undetermined	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		5087	0	11	6	Intron of PARK2(-):37Kb after exon 7	PARK2	162170166			6	Intron of PARK2(-):25Kb before exon 4	PARK2	162647065			10	DELETION		476899	223278	4343	11	NEW_VARIANT
P-0030526-T01-IM6	KMT2C (NM_170606) rearrangement: c.251-9913_c.4541-31del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 3-30.	MANUAL_OK	3to5	3to5	Deletion of 28 exons : in frame		32365	0	9	7	Intron of KMT2C(-):31bp before exon 31	KMT2C	151891244			7	Intron of KMT2C(-):10Kb before exon 3	KMT2C	152037737			10	DELETION		146493	226530	29181	10	NEW_VARIANT
P-0030526-T01-IM6	KDM6A (NM_021140) rearrangement: c.1194+7_c.1425+613del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 13-14.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		5169	0	27	X	Intron of KDM6A(+):7bp after exon 12	KDM6A	44918718			X	Intron of KDM6A(+):613bp after exon 14	KDM6A	44921277			10	DELETION		2559	226532	4275	29	NEW_VARIANT
P-0031357-T01-IM6	RB1 (NM_000321) rearrangement: c.2160_c.2713+901del	PRECISE	Note: The RB1 rearrangement results in the deletion of exons 21-26. One of the breakpoints is within exon 21.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6049	0	65	13	Exon 21 of RB1(+)	RB1	49037920			13	Intron of RB1(+):901bp after exon 26	RB1	49052441			10	DELETION		14521	229373	3136	69	NEW_VARIANT
P-0034908-T01-IM6	DDR2 (NM_006182) - NOS1AP (NM_014697) rearrangement: c.565+75:DDR2_c.453+397:NOS1APdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {DDR2:NOS1AP}		5818	0	41	1	Intron of NOS1AP(+):397bp after exon 5	NOS1AP	162303312			1	Intron of DDR2(+):75bp after exon 6	DDR2	162725168			0	DUPLICATION		421856	254589	22044	42	NEW_VARIANT
P-0035570-T01-IM6	CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup	PRECISE	CAMK2A (NM_015981) -CD74 (NM_001025159) Rearrangement : c.985-2282:CAMK2A_c.626-237:CD74dup	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CAMK2A:CD74}		1586	0	97	5	Intron of CAMK2A(-):2Kb before exon 14	CAMK2A	149621581			5	Intron of CD74(-):237bp before exon 7	CD74	149783112			10	DUPLICATION		161531	259685	2489	103	NEW_VARIANT
P-0001768-T02-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-734_c.349+1172del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		5026	0	7	21	Intron of TMPRSS2(-):1Kb after exon 3	TMPRSS2	42865111			21	Intron of TMPRSS2(-):734bp before exon 3	TMPRSS2	42867239			10	DELETION		2128	189879	5955	9	NEW_VARIANT
P-0001768-T02-IM6	VEGFA (NM_001171623) - RPS6KC1 (NM_012424) rearrangement: t(1;6)(q32.3;p21.1)(chr1:g.213285654::chr6:g.43741921)	PRECISE	Note: The VEGFA - RPS6KC1 rearrangement is a translocation with breakpoints within VEGFA intron 1 and RPS6KC1 intron 4. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	25	6	Intron of VEGFA(+):156bp before exon 2	VEGFA	43741921			1	Intron of RPS6KC1(+):5Kb before exon 4	RPS6KC1	213285654			10	TRANSLOCATION		0	189888	0	25	NEW_VARIANT
P-0002334-T02-IM6	PBRM1 (NM_018313) rearrangement: c.2675_c.-13+2179del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		26822	0	24	3	Exon 18 of PBRM1(-)	PBRM1	52637641			3	5-UTR of PBRM1(-):136Kb before coding start	PBRM1	52717586			10	DELETION		79945	198850	24118	29	NEW_VARIANT
P-0002334-T02-IM6	HGF (NM_000601) rearrangement: c.1271+90_c.1168+2117inv	PRECISE	Note: The HGF rearrangement results in the inversion of exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1021	0	25	7	Intron of HGF(-):89bp after exon 10	HGF	81349971			7	Intron of HGF(-):2Kb after exon 9	HGF	81353089			10	INVERSION		3118	198854	1427	26	NEW_VARIANT
P-0010920-T02-IM6	SMARCC1 (NM_003074) - SETD2 (NM_014159) rearrangement: c.647-1684:SMARCC1_c.1125:SETD1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMARCC1:SETD2}		9606	0	18	3	Exon 3 of SETD2(-)	SETD2	47165001			3	Intron of SMARCC1(-):2Kb before exon 7	SMARCC1	47763909			10	DELETION		598908	200679	14042	18	NEW_VARIANT
P-0019077-T02-IM6	KDM6A (NM_021140) rearrangement: chrX:g.44666338_c.577del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		7545	1	36	X	IGR: 37Kb before DUSP21(+)	DUSP21	44666338			X	Exon 7 of KDM6A(+)	KDM6A	44894188			10	DELETION		227850	200466	6402	35	NEW_VARIANT
P-0022744-T01-IM6	KMT2B (NM_014727) rearrangement: c.5437+94_c.6008inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		9099	0	40	19	Intron of KMT2B(+):94bp after exon 26	KMT2B	36221862			19	Exon 28 of KMT2B(+)	KMT2B	36223458			10	INVERSION		1596	192150	12767	48	NEW_VARIANT
P-0022746-T01-IM6	BRCA1 (NM_007294) rearrangement: c.593+41_c.670+125del	PRECISE	Note: The BRCA1 rearrangement is an intragenic deletion of exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1528	0	2	17	Intron of BRCA1(-):124bp after exon 9	BRCA1	41247738			17	Intron of BRCA1(-):40bp after exon 8	BRCA1	41249220			9	DELETION		1482	192134	958	2	NEW_VARIANT
P-0022781-T01-IM6	FGFR2 (NM_000141) - PDZRN4 (NM_001164595) rearrangement: t(6;10)(q23.1;q26.1)(chr6:g.130408449::chr10:g.123239680)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:PDZRN4}		0	0	58	12	Intron of PDZRN4(+):97Kb after exon 3	PDZRN4	41685122			10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241997			10	TRANSLOCATION		0	192212	0	66	NEW_VARIANT
P-0022781-T01-IM6	PLCG2 (NM_002661) rearrangement: c.1409:PLCG2_chr16:g.81726043inv	PRECISE	Note: The PLCG2 rearrangement is an inversion of exons 15-33. One of the breakpoints is within exon 15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		22722	0	3	16	Intron of CMIP(+):598bp after exon 11	CMIP	81726043			16	Exon 15 of PLCG2(+)	PLCG2	81939054			10	INVERSION		213011	192210	16096	3	NEW_VARIANT
P-0022782-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		99577	0	46	21	Intron of ERG(-):9Kb after exon 1	ERG	39861233			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874883			10	DELETION		3013650	192195	62169	49	NEW_VARIANT
P-0023037-T01-IM6	FANCA (NM_000135) Rearrangement : t(8,16)(q23.2,q24.2)(chr8:g.111811259::chr16:g.89882953)	PRECISE	Note: The FANCA  Rearrangement results in the possible truncation of FANCA. The breakpoint in FANCA is within exon1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	38	16	Exon 1 of FANCA(-)	FANCA	89882953			8	IGR: 139Kb before LOC101927459(-)	LOC101927459	111811259			10	TRANSLOCATION		0	193589	0	39	NEW_VARIANT
P-0023385-T01-IM6	SMAD4 (NM_005359) rearrangement: c.-128+5079_c.1308+55dup	PRECISE	Note: The SMAD4 rearrangement is a duplication with breakpoints in the 5UTR region and intron 10. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		14554	0	4	18	5-UTR of SMAD4(+):11Kb before coding start	SMAD4	48562072			18	Intron of SMAD4(+):55bp after exon 10	SMAD4	48593612			10	DUPLICATION		31540	194920	12712	4	NEW_VARIANT
P-0024048-T01-IM6	PAX8 (NM_003466) Rearrangement : c.1190-2641:PAX8_chr2:g.149285052del	PRECISE	Note: The PAX8 Rearrangement results in the deletion of exons 1-10 of PAX8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		144085	0	40	2	Intron of PAX8(-):3Kb before exon 11	PAX8	113980396			2	IGR: 118Kb before EPC2(+)	EPC2	149285052			10	DELETION		35304656	197918	113759	43	NEW_VARIANT
P-0024117-T01-IM6	BRD4 (NM_058243) rearrangement: c.2758_c.3169+795inv	PRECISE	Note: The BRD4 rearrangement is an intragenic inversion of exon 14. One of the breakpoints is within exon 14. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3348	0	2	19	Intron of BRD4(-):794bp after exon 14	BRD4	15352916			19	Exon 14 of BRD4(-)	BRD4	15354122			4	INVERSION		1206	198335	3213	2	NEW_VARIANT
P-0024569-T01-IM6	TP53BP1 (NM_001141980) rearrangement: c.4682-1277_c.5746+55dup	PRECISE	Note: The TP53BP1 rearrangement is an intragenic duplication of exons 22-27. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : in frame		14677	0	15	15	Intron of TP53BP1(-):54bp after exon 27	TP53BP1	43700086			15	Intron of TP53BP1(-):1Kb before exon 22	TP53BP1	43709891			10	DUPLICATION		9805	200843	15931	15	NEW_VARIANT
P-0024569-T01-IM6	BRIP1 (NM_032043) rearrangement: c.2459_c.2492+890del	PRECISE	Note: The BRIP1 rearrangement is an intragenic deletion of exon 17. One of the breakpoints is within exon 17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		558	0	55	17	Intron of BRIP1(-):889bp after exon 17	BRIP1	59792422			17	Exon 17 of BRIP1(-)	BRIP1	59793345			10	DELETION		923	200842	180	77	NEW_VARIANT
P-0024640-T01-IM6	BMPR1A (NM_004329) rearrangement: chr10:g.88017504_c.1525:BMPR1Adel	PRECISE	Note: The BMPR1A rearrangement is a deletion of exons 1-13. One of the breakpoints is within exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		20269	0	15	10	Intron of GRID1(-):51Kb before exon 3	GRID1	88017504			10	Exon 13 of BMPR1A(+)	BMPR1A	88683402			10	DELETION		665898	201097	19795	45	NEW_VARIANT
P-0024898-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : t(21;1)(q22.3;q32.1)(chr21:42873896::chr1:205610270)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	35	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873896			1	IGR: 17Kb before SLC45A3(-)	SLC45A3	205610270			10	TRANSLOCATION		0	202649	0	35	NEW_VARIANT
P-0025437-T02-IM6	ATRX (NM_000489) rearrangement: t(X;9)(p22.3;q21.1)(chrX:g.76845379::chr9:g.16558821)	IMPPRECISE	Note: The ATRX rearrangement is a translocation with a breakpoint within exon 27.	MANUAL_OK	3to3	3to3	-		0	0	15	X	Exon 27 of ATRX(-)	ATRX	76845379			9	Intron of BNC2(-):6Kb before exon 5	BNC2	16558821			0	TRANSLOCATION		0	227014	0	16	NEW_VARIANT
P-0028519-T01-IM6	PIK3C3 (NM_002647) rearrangement: c.1484+1813_c.1772dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2655	0	50	18	Intron of PIK3C3(+):2Kb after exon 13	PIK3C3	39602482			18	Exon 16 of PIK3C3(+)	PIK3C3	39613854			10	DUPLICATION		11372	217682	6722	52	NEW_VARIANT
P-0030702-T01-IM6	TP53 (NM_000546) rearrangement: c.-29+2212_c.532dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8940	0	62	17	Exon 5 of TP53(-)	TP53	7578398			17	5-UTR of TP53(-):16Kb before coding start	TP53	7588483			10	DUPLICATION		10085	227167	13167	65	NEW_VARIANT
P-0032459-T01-IM6	NAB2 (NM_005967) Rearrangement: c.1276+90:NAB2_chr12:g.74965141inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		64827	0	11	12	Intron of NAB2(+):90bp after exon 5	NAB2	57487068			12	IGR: 34Kb before ATXN7L3B(+)	ATXN7L3B	74965141			10	INVERSION		17478073	233107	812680	13	NEW_VARIANT
P-0034038-T01-IM6	PPP4R2 (NM_174907) Rearrangement: c.116+22240_c.208del	PRECISE	Note: The PPP4R2 rearrangement is an intragenic deletion of exon3. One of the breakpoint is within exon3 of PPP4R2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		107	0	31	3	Intron of PPP4R2(+):22Kb after exon 2	PPP4R2	73069549			3	Exon 3 of PPP4R2(+)	PPP4R2	73096428			10	DELETION		26879	247812	99	37	NEW_VARIANT
P-0035551-T01-IM6	TERT (NM_198253) Rearrangement :t(1;5)(q34.2;q31.3)(chr1:g.235010251::chr5:g.1295257)	PRECISE	Note: The TERT Rearrangement is a translocation event with a breakpoint in the promoter region of TERT. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	14	5	Promoter of TERT(-):42Kb from tx start	TERT	1295257			1	IGR: 83Kb before LOC101927851(-)	LOC101927851	235010251			10	TRANSLOCATION		0	259665	0	14	NEW_VARIANT
P-0035551-T01-IM6	RICTOR (NM_152756) Rearrangement : c.1715+55_c.-13-9670:OSMRdel	PRECISE	Note: The RICTOR Rearrangement results in the deletion of exons 1-19 of RICTOR. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		25679	0	85	5	5-UTR of OSMR(+):10Kb before coding start	OSMR	38859464			5	Intron of RICTOR(-):54bp after exon 19	RICTOR	38962362			10	DELETION		102898	259664	25480	88	NEW_VARIANT
P-0035710-T01-IM6	PRKD1 (NM_002742) rearrangement: chr14:g.29876388_c.354del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		23572	0	16	14	IGR: 20Kb before MIR548AI(-)	MIR548AI	29876388			14	Exon 2 of PRKD1(-)	PRKD1	30194791			10	DELETION		318403	261141	32118	16	NEW_VARIANT
P-0035712-T01-IM6	ALK (NM_004304) rearrangement: t(1;2)(p36.22;p23.2)(chr1:g.9314150::chr2:g.29462508)	PRECISE	Note: The ALK rearrangement is a translocation with a breakpoint within ALK intron 13. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	43	2	Intron of ALK(-):37bp after exon 13	ALK	29462508			1	Intron of H6PD(+):7Kb after exon 3	H6PD	9314150			10	TRANSLOCATION		0	261137	0	43	NEW_VARIANT
P-0035736-T01-IM6	TP53 (NM_000546) Rearrangement : c.97-17_c.560-23del	PRECISE	Note: The TP53  Rearrangement results in the intragenic deletion of exons 4-5 of TP53. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		5824	0	24	17	Intron of TP53(-):23bp before exon 6	TP53	7578312			17	Intron of TP53(-):17bp before exon 4	TP53	7579607			10	DELETION		1295	261151	7260	29	NEW_VARIANT
P-0035393-T02-IM6	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.771+833:MKRN1_c.1141-1052:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {MKRN1:BRAF}		42575	0	67	7	Intron of MKRN1(-):832bp after exon 4	MKRN1	140157974			7	Intron of BRAF(-):1Kb before exon 9	BRAF	140488436			10	DUPLICATION		330462	260725	59053	72	NEW_VARIANT
P-0035720-T01-IM6	APC (NM_000038) rearrangement: c.87:APC_chr5:g.121241258inv	PRECISE	Note: The APC rearrangement results in the inversion of exons 2-16. One of the breakpoints is within exon 2.	MANUAL_OK	3to3	3to3	-		36617	0	23	5	Exon 2 of APC(+)	APC	112090674			5	IGR: 54Kb before FTMT(+)	FTMT	121241258			10	INVERSION		9150584	261119	50778	23	NEW_VARIANT
P-0035723-T01-IM6	YBX2 (NM_015982) - RTEL1 (NM_032957) rearrangement: t(17;20)(p13.1;q13.33)(chr17:g.7193375::chr20:g.62292480)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {YBX2:RTEL1}		0	0	8	20	Intron of RTEL1(+):170bp before exon 3	RTEL1	62292480			17	Exon 6 of YBX2(-)	YBX2	7193375			10	TRANSLOCATION		0	261111	0	7	NEW_VARIANT
P-0035764-T01-IM6	ZGPAT (NM_032527) - RTEL1 (NM_032957) rearrangement: c.585-8272:ZGPAT_c.2302:RTEL1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ZGPAT:RTEL1}		18462	0	5	20	Exon 25 of RTEL1(+)	RTEL1	62321528			20	Intron of ZGPAT(+):8Kb before exon 3	ZGPAT	62356299			0	DUPLICATION		34771	261442	21287	5	NEW_VARIANT
P-0035772-T01-IM6	STAT3 (NM_139276) rearrangement: c.372+234:STAT3_chr17:g.44240986inv	IMPPRECISE	Note: The STAT3 rearrangement is an inversion of exons 1-4. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		142551	0	8	17	Intron of STAT3(-):233bp after exon 4	STAT3	40497343			17	Intron of KANSL1(-):7Kb after exon 3	KANSL1	44240986			0	INVERSION		3743643	261485	299014	8	NEW_VARIANT
P-0035786-T01-IM6	HIST1H3G (NM_003534) rearrangement: c.171:HIST1H3G_chr6:g.26309900del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		1398	0	38	6	Exon 1 of HIST1H3G(-)	HIST1H3G	26271442			6	IGR: 25Kb before HIST1H4H(-)	HIST1H4H	26309900			10	DELETION		38458	261521	977	39	NEW_VARIANT
P-0035788-T01-IM6	CARM1 (NM_199141) Rearrangement: t(12;19)(p12.1;p13.2)(chr12:g.23564653::chr19:g.11032250)	PRECISE	Note:  The CARM1 rearrangement is a translocation with breakpoint in intron 15 of CARM1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	16	19	Intron of CARM1(+):40bp before exon 16	CARM1	11032250			12	IGR: 121Kb before SOX5(-)	SOX5	23564653			10	TRANSLOCATION		0	261519	0	15	NEW_VARIANT
P-0035793-T01-IM6	ERBB2 (NM_004448) Rearrangement: c.3207_c.*573del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		5954	0	15	17	Exon 26 of ERBB2(+)	ERBB2	37883595			17	3-UTR of ERBB2(+):28Kb after coding stop	ERBB2	37884870			10	DELETION		1275	261524	5739	17	NEW_VARIANT
P-0035868-T01-IM6	ROS1 (NM_002944) rearrangement: c.5641+1040:ROS1_chr6:g.117887080del	PRECISE	Note: The ROS1 rearrangement is a deletion of exons 1-34. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		146004	0	72	6	Intron of ROS1(-):1Kb after exon 34	ROS1	117644455			6	Intron of DCBLD1(+):4Kb before exon 15	DCBLD1	117887080			10	DELETION		242625	262018	107887	77	NEW_VARIANT
P-0013032-T02-IM6	SETD2 (NM_014159) Rearrangement : t(3,12)(p21.31,q14.3)(chr3:g.47084233::chr12:g.68312811)	PRECISE	Note: The SETD2 Rearrangement is a translocation with a breakpoint in intron16. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	33	12	IGR: 10Kb before LINC01479(+)	LINC01479	68312811			3	Intron of SETD2(-):43bp before exon 17	SETD2	47084233			10	TRANSLOCATION		0	261853	0	33	NEW_VARIANT
P-0035854-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+533:TMPRSS2_c.39+11353:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		40960	0	71	21	Intron of ERG(-):11Kb after exon 3	ERG	39936233			21	Intron of TMPRSS2(-):532bp after exon 2	TMPRSS2	42869513			10	DELETION		2933280	261978	37485	168	NEW_VARIANT
P-0035867-T01-IM6	APC (NM_000038) rearrangement: c.4505:APC_chr5:g.112181350del	PRECISE	Note: The APC rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		15403	0	19	5	Exon 16 of APC(+)	APC	112175796			5	3-UTR of APC(+):91Kb after coding stop	APC	112181350			10	DELETION		5554	262022	10858	20	NEW_VARIANT
P-0002372-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2699:TMPRSS2_c.40-60926:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53822	0	75	21	Intron of ERG(-):61Kb before exon 4	ERG	39878470			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872815			10	DELETION		2994345	261464	58561	82	NEW_VARIANT
P-0035767-T01-IM6	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12029143::chr15:g.88505787)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	79	15	Intron of NTRK3(-):22Kb before exon 15	NTRK3	88505787			12	Intron of ETV6(+):6Kb after exon 5	ETV6	12029143			10	TRANSLOCATION		0	261484	0	77	NEW_VARIANT
P-0035768-T01-IM6	KMT2D (NM_003482) rearrangement: t(6;12)(p25.3;q13.12)(chr6:g.238826::chr12:g.49432543)	IMPPRECISE	Note: The KMT2D rearrangement is a translocation involving a breakpoint in exon 34. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	12	Exon 34 of KMT2D(-)	KMT2D	49432543			6	IGR: 53Kb before DUSP22(+)	DUSP22	238826			0	TRANSLOCATION		0	261482	0	5	NEW_VARIANT
P-0035812-T01-IM6	DROSHA (NM_013235) - ADAMTS12 (NM_030955) Rearrangement : c.2241+102:DROSHA_c.4607-3459_ADAMTS12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {DROSHA:ADAMTS12}		24116	0	21	5	Intron of DROSHA(-):101bp after exon 16	DROSHA	31472068			5	Intron of ADAMTS12(-):3Kb before exon 24	ADAMTS12	33530930			10	DUPLICATION		2058862	261795	32124	21	NEW_VARIANT
P-0035812-T01-IM6	PRELID1 (NM_013237) - NSD1 (NM_022455)  Rearrangement :  c.512:PRELID1_c.2220:NSD1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PRELID1:NSD1}		34668	0	8	5	Exon 5 of NSD1(+)	NSD1	176637620			5	Exon 5 of PRELID1(+)	PRELID1	176733423			9	DUPLICATION		95803	261796	39332	8	NEW_VARIANT
P-0035812-T01-IM6	TSC1 (NM_000368) - GBGT1 (NM_021996) Rearrangement : c.2502+9:TSC1_c.360-218:GBGT1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TSC1:GBGT1}		20712	0	21	9	Intron of TSC1(-):8bp after exon 19	TSC1	135776967			9	Intron of GBGT1(-):218bp before exon 6	GBGT1	136029866			0	DUPLICATION		252899	261797	24160	21	NEW_VARIANT
P-0035814-T01-IM6	INPPL1 (NM_001567) Rearrangement : t(11,17)(q13.4,q25.3)(chr11:g.71943225::chr17:g.75802681)	PRECISE	Note: The INPPL1 Rearrangement is a translocation event with a breakpoint in intron13. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	14	17	IGR: 72Kb before FLJ45079(-)	FLJ45079	75802681			11	Intron of INPPL1(+):58bp before exon 14	INPPL1	71943225			10	TRANSLOCATION		0	261818	0	14	NEW_VARIANT
P-0035926-T01-IM6	EGFR (NM_005228) rearrangement: c.2947-91_chr7:g.56436684inv	PRECISE	Note: The EGFR rearrangement results in the inversion of exons 25-28. This includes the carboxyl terminal domain of EGFR.	MANUAL_OK	3to3	3to3	-		17703	0	6	7	Intron of EGFR(+):90bp before exon 25	EGFR	55268790			7	IGR: 55Kb before LOC650226(-)	LOC650226	56436684			10	INVERSION		1167894	262504	27612	7	NEW_VARIANT
P-0035765-T01-IM6	BRCA2 (NM_000059) - VCAN (NM_004385) rearrangement: t(5;13)(q14.3;q13.1)(chr5:g.82844662::chr13:g.32918847)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {BRCA2:VCAN}		0	0	7	13	Intron of BRCA2(+):57bp after exon 12	BRCA2	32918847			5	Intron of VCAN(+):759bp after exon 10	VCAN	82844662			0	TRANSLOCATION		0	261443	0	7	NEW_VARIANT
P-0036007-T01-IM6	TET1 (NM_030625) - CAMTA1 (NM_015215) Rearrangment: c.871:TET1_c.438+35538:CAMTA1	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TET1:CAMTA1}		0	0	64	10	Exon 2 of TET1(+)	TET1	70332966			1	Intron of CAMTA1(+):36Kb after exon 5	CAMTA1	7345224			10	TRANSLOCATION		0	263423	0	66	NEW_VARIANT
P-0036007-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon 1 with ERG exon 2) : c.56-4127:TMPRSS2_c.18+10822:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		80568	0	113	21	Intron of ERG(-):11Kb after exon 1	ERG	39859465			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874243			10	DELETION		3014778	263421	74249	115	NEW_VARIANT
P-0036009-T01-IM6	PTPN11 (NM_002834) Rearrangement: t(4,12)(q21.13,q24.12)(chr4:g.93691193::chr12:g.112926914)	PRECISE	Note: The PTPN11 Rearrangement is a translocation event with the breakpoint in exon13 of PTPN11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	41	12	Exon 13 of PTPN11(+)	PTPN11	112926914			4	Intron of GRID2(+):180Kb after exon 2	GRID2	93691193			10	TRANSLOCATION		0	263434	0	47	NEW_VARIANT
P-0036009-T01-IM6	CDK12 (NM_016507) Rearrangement :  t(8,17)(p13.3,q24.12)(chr8:g.83375277::chr17:g.37673753)	IMPPRECISE	Note: The CDK12 Rearrangement is a translocation event with a breakpoint in exon10 of CDK12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	8	17	Exon 10 of CDK12(+)	CDK12	37673753			8	IGR: 663Kb before SNX16(-)	SNX16	83375277			0	TRANSLOCATION		0	263435	0	8	NEW_VARIANT
P-0036009-T01-IM6	RUNX1 (NM_001754) Rearrangement : c.968-3144_c.976del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		636	0	143	21	Exon 9 of RUNX1(-)	RUNX1	36164899			21	Intron of RUNX1(-):3Kb before exon 9	RUNX1	36168051			10	DELETION		3152	263432	531	144	NEW_VARIANT
P-0036010-T01-IM6	CD79A (NM_001783) - ZNF83 (NM_018300) Rearrangement : c.239:CD79A_c.-658+9171:ZNF83inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ZNF83:CD79A}		236322	0	10	19	Exon 2 of CD79A(+)	CD79A	42383219			19	5-UTR of ZNF83(-):68Kb before coding start	ZNF83	53184525			0	INVERSION		10801306	263427	195729	10	NEW_VARIANT
P-0036010-T01-IM6	CIC (NM_015125) - VRK3 (NM_016440) Rearrangement : c.986:CIC_c.-65+2216:VRK3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CIC:VRK3}		112925	0	28	19	Exon 7 of CIC(+)	CIC	42793094			19	5-UTR of VRK3(-):44Kb before coding start	VRK3	50526308			10	INVERSION		7733214	263428	93383	27	NEW_VARIANT
P-0036015-T01-IM6	BLM (NM_000057) Rearrangement : c.799+331_c.2824-79del	PRECISE	Note: The BLM Rearrangement results in the intragenic deletion of exons 4-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 11 exons : out of frame		18571	0	10	15	Intron of BLM(+):331bp after exon 3	BLM	91293628			15	Intron of BLM(+):78bp before exon 15	BLM	91333800			10	DELETION		40172	263415	22011	10	NEW_VARIANT
P-0036015-T01-IM6	NF1 (NM_001042492) Rearrangement : c.7457+67_c.7970+132dup	PRECISE	Note: The NF1  Rearrangement results in the duplication of exons 51-54 of NF1. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		5921	0	31	17	Intron of NF1(+):67bp after exon 50	NF1	29677403			17	Intron of NF1(+):132bp after exon 54	NF1	29684519			10	DUPLICATION		7116	263417	8987	32	NEW_VARIANT
P-0036015-T01-IM6	EPAS1 (NM_001430) - MSH2 (NM_000251) Rearrangement : c.27-5917:EPAS1_c.1760-90:MSH2	PRECISE	Note: The EPAS1-MSH2 Rearrangement results in the fusion of exon 1of EPAS1 with exons 12-16 of MSH2.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {EPAS1:MSH2}		69933	0	16	2	Intron of EPAS1(+):6Kb before exon 2	EPAS1	46568095			2	Intron of MSH2(+):89bp before exon 12	MSH2	47702074			10	DELETION		1133979	263414	76466	16	NEW_VARIANT
P-0036020-T01-IM6	JAK2 (NM_004972) rearrangement: c.1133_c.3060-1962del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		20194	0	36	9	Exon 9 of JAK2(+)	JAK2	5064959			9	Intron of JAK2(+):2Kb before exon 23	JAK2	5121042			10	DELETION		56083	263365	21446	35	NEW_VARIANT
P-0036028-T01-IM6	NUMA1 (NM_006185) - EGFR (NM_005228) rearrangement: t(7;11)(p11.2;q13.4)(chr7:g.55241128::chr11:g.71728415)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {NUMA1:EGFR}		0	0	65	11	Intron of NUMA1(-):317bp after exon 13	NUMA1	71728415			7	Intron of EGFR(+):311bp after exon 17	EGFR	55241128			10	TRANSLOCATION		0	263458	0	82	NEW_VARIANT
P-0036003-T01-IM6	CIC (NM_015125) Rearrangement: c.3011:CIC_chr19:g.43041838inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		18991	0	46	19	Exon 13 of CIC(+)	CIC	42796454			19	5-UTR of LIPE-AS1(+):115Kb before coding start	LIPE-AS1	43041838			0	INVERSION		245384	262803	18452	43	NEW_VARIANT
P-0036054-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.4530_chr19:g.36346742inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KIRREL2:NOTCH3}		306004	0	10	19	Exon 25 of NOTCH3(-)	NOTCH3	15285085			19	Promoter of KIRREL2(+):1Kb from tx start	KIRREL2	36346742			10	INVERSION		21061657	264482	357095	10	NEW_VARIANT
P-0036054-T01-IM6	CIC (NM_015125) - DEDD2 (NM_133328) rearrangement: c.1465-67:CIC_c.-1266:DEDD2inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		27187	0	16	19	3-UTR of DEDD2(-):1Kb after coding stop	DEDD2	42723011			19	Intron of CIC(+):66bp before exon 10	CIC	42794318			0	INVERSION		71307	264483	32919	18	NEW_VARIANT
P-0036059-T01-IM6	EZH1 (NM_001991) - WNT3 (NM_030753) rearrangement: c.1802:EZH1_c.80+3466:WNT3dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EZH1:WNT3}		94827	0	25	17	Exon 16 of EZH1(-)	EZH1	40858062			17	Intron of WNT3(-):3Kb after exon 1	WNT3	44892418			0	DUPLICATION		4034356	264467	142430	25	NEW_VARIANT
P-0036106-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		118925	0	80	2	Intron of ALK(-):536bp before exon 20	ALK	29446930			2	Intron of EML4(+):2Kb before exon 13	EML4	42526326			10	INVERSION		13079396	264495	112828	79	NEW_VARIANT
P-0031178-T02-IM6	CDH1 (NM_004360) rearrangement: c.388-226_chr16:g.85385815del	PRECISE	Note: The CDH1 rearrangement is an inversion that includes CDH1 exons 4-16.	MANUAL_OK	5to5	5to5	-		184182	0	10	16	Intron of CDH1(+):225bp before exon 4	CDH1	68842101			16	IGR: 46Kb before MIR5093(-)	MIR5093	85385815			10	INVERSION		16543714	264592	152375	10	NEW_VARIANT
P-0031178-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.56-4350:TMPRSS2_c.18+11076:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		79765	0	157	21	Intron of ERG(-):11Kb after exon 1	ERG	39859211			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874466			10	DELETION		3015255	264589	59250	165	NEW_VARIANT
P-0036120-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38166	0	50	21	Intron of ERG(-):13Kb before exon 2	ERG	39830796			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868693			10	DELETION		3037897	264599	9069	61	NEW_VARIANT
P-0027456-T02-IM6	MSI2 (NM_138962) rearrangement: c.185+86_c.312+20657del	IMPPRECISE	Note: The MSI2 rearrangement is an intragenic deletion of exons 4-5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		2314	0	38	17	Intron of MSI2(+):86bp after exon 3	MSI2	55334994			17	Intron of MSI2(+):21Kb after exon 5	MSI2	55360210			0	DELETION		25216	261453	4256	41	NEW_VARIANT
P-0027456-T02-IM6	CTNNB1 (NM_001904) rearrangement: c.1082-1244_c.1719dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3595	0	52	3	Intron of CTNNB1(+):1Kb before exon 8	CTNNB1	41273588			3	Exon 11 of CTNNB1(+)	CTNNB1	41277250			10	DUPLICATION		3662	261457	10242	53	NEW_VARIANT
P-0027456-T02-IM6	MSH6 (NM_000179) rearrangement: t(2;8)(p16.3;p11.21)(chr2:g.48030834::chr8:g.43096828)	IMPPRECISE	Note: The MSH6 rearrangement is a translocation with a breakpoint in intron 5. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	8	IGR: 51Kb before POTEA(+)	POTEA	43096565			2	Intron of MSH6(+):7bp after exon 5	MSH6	48030831			0	TRANSLOCATION		0	261458	0	7	NEW_VARIANT
P-0036261-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1716_chr5:g.5:68233907del	PRECISE	Note: The PIK3R1 rearrangement is a deletion that includes PIK3R1 exons 13-15. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	-		2462	0	12	5	Exon 13 of PIK3R1(+)	PIK3R1	67591123			5	IGR: 156Kb before SLC30A5(+)	SLC30A5	68233907			10	DELETION		642784	266815	3250	14	NEW_VARIANT
P-0036282-T01-IM6	ETV6 (NM_001987) rearrangement: c.164-37058_c.1009+1038del	IMPPRECISE	Note: The ETV6 rearrangement is an intragenic deletion of exons 3-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		129681	0	27	12	Intron of ETV6(+):37Kb before exon 3	ETV6	11955016			12	Intron of ETV6(+):1Kb after exon 5	ETV6	12023941			0	DELETION		68925	266877	144600	27	NEW_VARIANT
P-0036321-T01-IM6	BRCA1 (NM_007294) rearrangement: t(4;17)(p16.1;q21.31)(chr4:g.7544612::chr17:g.41228481)	PRECISE	Note: The BRCA1 rearrangement is a translocation with a breakpoint in intron 13. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	20	17	Intron of BRCA1(-):23bp after exon 13	BRCA1	41228481			4	Intron of SORCS2(+):11Kb after exon 3	SORCS2	7544612			10	TRANSLOCATION		0	268714	0	20	NEW_VARIANT
P-0036321-T01-IM6	RUNX1 (NM_001754) rearrangement: c.208_c.806-9677dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		11173	0	114	21	Intron of RUNX1(-):10Kb before exon 8	RUNX1	36181436			21	Exon 4 of RUNX1(-)	RUNX1	36259283			10	DUPLICATION		77847	268713	18732	126	NEW_VARIANT
P-0036321-T01-IM6	RAF1 (NM_002880) - SATB1 (NM_001131010) rearrangement: c.742:RAF1_c.1576-11367:SATB1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RAF1:SATB1}		15513	0	8	3	Exon 7 of RAF1(-)	RAF1	12645727			3	Intron of SATB1(-):11Kb before exon 10	SATB1	18405054			10	DUPLICATION		5759327	268711	27250	8	NEW_VARIANT
P-0031911-T02-IM6	MET (NM_000245) - PPP1R9A (NM_001166161) rearrangement: c.3632+34:MET_c.2046+10406:PPP1R9Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {MET:PPP1R9A}		91585	0	5	7	Intron of PPP1R9A(+):10Kb after exon 6	PPP1R9A	94865834			7	Intron of MET(+):34bp after exon 18	MET	116422185			9	DUPLICATION		21556351	268131	173790	5	NEW_VARIANT
P-0036305-T01-IM6	FGFR3 - (NM_000142) TACC3 (NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon3) : c.2334:FGFR3_c.274:TACC3dup	PRECISE	Note: The FGFR3 - TACC3 Fusion includes the protein kinase domain of FGFR3. The breakpoints are within exon18 of FGFR3 and exon3 of TACC3.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		36722	0	135	4	Exon 3 of TACC3(+)	TACC3	1725566			4	Exon 18 of FGFR3(+)	FGFR3	1808902			10	DUPLICATION		83336	267243	54873	150	NEW_VARIANT
P-0031395-T01-IM6	NOTCH3 (NM_000435) Rearrangement : c.1192+11_c.2297-104inv	PRECISE	Note: The NOTCH3 Rearrangement results in the intragenic inversion of exons 8-16 of NOTCH3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		20307	0	41	19	Intron of NOTCH3(-):104bp before exon 15	NOTCH3	15295934			19	Intron of NOTCH3(-):10bp after exon 7	NOTCH3	15300073			10	INVERSION		4139	268809	12228	40	NEW_VARIANT
P-0036164-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.-48+1323:ERG_c.56-2136:TMPRSS2del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		56023	0	75	21	3-UTR of ERG(-):78Kb after coding stop	ERG	39955445			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872252			10	DELETION		2916807	264999	53404	79	NEW_VARIANT
P-0036176-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3823:TMPRSS2_c.18+14211:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		85881	0	53	21	Intron of ERG(-):14Kb after exon 1	ERG	39856076			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873939			10	DELETION		3017863	265644	20320	57	NEW_VARIANT
P-0036178-T01-IM6	MDC1 (NM_014641) rearrangement: c.2847:MDC1_chr6:g.30692385del	PRECISE	Note: The MDC1 rearrangement is a deletion of exons 1-8. One of the breakpoints is within exon 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		25353	0	11	6	Exon 8 of MDC1(-)	MDC1	30675509			6	3-UTR of TUBB(+):3Kb after coding stop	TUBB	30692385			10	DELETION		16876	265643	34578	11	NEW_VARIANT
P-0036328-T01-IM6	FLT4 (NM_182925) Rearrangement : c.59-2991_c.1549-50del	PRECISE	Note: The FLT4 Rearrangement results in the intragenic inversion of exons 2-11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		20063	0	63	5	Intron of FLT4(-):50bp before exon 12	FLT4	180049889			5	Intron of FLT4(-):3Kb before exon 2	FLT4	180061769			10	INVERSION		11880	267381	22269	68	NEW_VARIANT
P-0036331-T01-IM6	SMARCA4 (NM_003072) - LDLR (NM_000527) Rearrangement :  c.2859+79:SMARCA4_c.-3015:LDLRdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Transcript Fusion {SMARCA4:LDLR}		26249	0	6	19	Intron of SMARCA4(+):79bp after exon 19	SMARCA4	11132722			19	Promoter of LDLR(+):3Kb from tx start	LDLR	11197210			0	DELETION		64488	267392	30319	8	NEW_VARIANT
P-0036332-T01-IM6	ARID1A (NM_006015) Rearrangement : c.1921-42:ARID1A_c.234+77783:CAMTA1inv	IMPPRECISE	Note: The ARID1A Rearrangement results in the inversion of exons 1-5 of ARID1A. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		284323	0	6	1	Intron of CAMTA1(+):78Kb after exon 3	CAMTA1	6963053			1	Intron of ARID1A(+):41bp before exon 5	ARID1A	27087305			0	INVERSION		20124252	267394	325015	6	NEW_VARIANT
P-0036332-T01-IM6	NF1 (NM_001042492) Rearrangement : c.60+12161_c.541	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4154	0	6	17	Intron of NF1(+):12Kb after exon 1	NF1	29434548			17	Exon 5 of NF1(+)	NF1	29496970			6	DELETION		62422	267393	5807	6	NEW_VARIANT
P-0036332-T01-IM6	PTPRD (NM_002839) Rearrangement : chr9:g.1444584_c.2289inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		82823	0	17	9	IGR: 394Kb before DMRT2(+)	DMRT2	1444584			9	Exon 25 of PTPRD(-)	PTPRD	8499680			10	INVERSION		7055096	267395	103069	18	NEW_VARIANT
P-0036346-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 fused with ERG exon4): c.56-484:TMPRSS2_c.39+15996:ERGdel	PRECISE	Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		46243	0	38	21	Intron of ERG(-):16Kb after exon 3	ERG	39931590			21	Intron of TMPRSS2(-):484bp before exon 2	TMPRSS2	42870600			10	DELETION		2939010	268726	41361	39	NEW_VARIANT
P-0036348-T01-IM6	ANKRD11 (NM_013275) Rearrangement : t(14;16)(p32.31;q24.3)(chr14:g.107133040::chr16:g.89351017)	PRECISE	Note: The ANKRD11 Rearrangement is a translocation event with a breakpoint in exon9. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	115	16	Exon 9 of ANKRD11(-)	ANKRD11	89351017			14	IGR: 126Kb before MIR5195(-)	MIR5195	107133040			10	TRANSLOCATION		0	268798	0	119	NEW_VARIANT
P-0036351-T01-IM6	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) : c.56-2148:TMPRSS2_c.39+62508:ERG del	PRECISE	Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		56713	0	30	21	Intron of ERG(-):63Kb after exon 3	ERG	39885078			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872264			10	DELETION		2987186	268751	31106	35	NEW_VARIANT
P-0036382-T01-IM6	MAX (NM_002382) Rearrangement: c.64-887_c.296-28del	PRECISE	Note: The MAX rearrangement is an intragenic deletion of exons 3 to 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		6567	0	12	14	Intron of MAX(-):28bp before exon 5	MAX	65543409			14	Intron of MAX(-):887bp before exon 3	MAX	65561420			10	DELETION		18011	268236	5792	12	NEW_VARIANT
P-0027019-T01-IM6	GLI1 (NM_005269) - MARS (NM_004990) rearrangement: c.1748:GLI1_c.1294-196:MARSdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GLI1:MARS}		12104	0	10	12	Exon 12 of GLI1(+)	GLI1	57864271			12	Intron of MARS(+):195bp before exon 11	MARS	57897812			10	DELETION		33541	268421	8105	11	NEW_VARIANT
P-0029223-T01-IM6	PLCG2 (NM_002661) rearrangement: c.2254:PLCG2_chr16:g.81159441del	PRECISE	Note: The PLCG2 rearrangement is a deletion of exons 1-21. One of the breakpoints is in exon 21. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		23205	0	8	16	Intron of PKD1L2(-):2Kb after exon 25	PKD1L2	81159441			16	Exon 21 of PLCG2(+)	PLCG2	81954821			10	DELETION		795380	268415	23214	8	NEW_VARIANT
P-0033090-T01-IM6	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)	PRECISE	Note: The KIF5B - MET fusion is predicted to be in frame and includes the kinase domain of MET	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:MET}		0	0	18	10	Intron of KIF5B(-):647bp before exon 25	KIF5B	32305234			7	Intron of MET(+):354bp after exon 14	MET	116412397			10	TRANSLOCATION		0	237622	0	21	NEW_VARIANT
P-0035212-T01-IM6	KMT2A (NM_001197104) rearrangement: t(11;17)(q23.3;q11.2)(chr11:g.118342702::chr17:g.30264018)	PRECISE	Note: The KMT2A rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KMT2A:SUZ12}		0	0	15	17	Promoter of SUZ12(+):25bp from tx start	SUZ12	30264018			11	Exon 3 of KMT2A(+)	KMT2A	118342702			10	TRANSLOCATION		0	256911	0	23	NEW_VARIANT
P-0036200-T01-IM6	ASXL2 (NM_018263) rearrangement: c.505-138:ASXL2_chr2:g.25223246inv	IMPPRECISE	Note: The ASXL2 rearrangement is an inversion of exons 6-12. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {DNAJC27-AS1:ASXL2}		63975	0	7	2	5-UTR of DNAJC27-AS1(+):39Kb before coding start	DNAJC27-AS1	25223246			2	Intron of ASXL2(-):138bp before exon 6	ASXL2	25991875			0	INVERSION		768629	266206	81953	7	NEW_VARIANT
P-0036212-T01-IM6	IGF1R (NM_000875) - TTC23 (NM_001040659) rearrangement: c.2782+28:IGF1R_c.1144-2460:TTC23inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {IGF1R:TTC23}		13415	0	5	15	Intron of IGF1R(+):28bp after exon 13	IGF1R	99467941			15	Intron of TTC23(-):2Kb before exon 11	TTC23	99682064			0	INVERSION		214123	266140	126414	5	NEW_VARIANT
P-0036232-T01-IM6	TSC1 (NM_000368) Rearrangement: c.1571:TSC1_chr9:g.75142084del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		331692	0	18	9	5-UTR of TMC1(+):121Kb before coding start	TMC1	75142084			9	Exon 15 of TSC1(-)	TSC1	135781394			10	DELETION		60639310	266418	314265	18	NEW_VARIANT
P-0036236-T01-IM6	SH2B3 (NM_005475) Rearrangement: t(8;12)(q13.1;q24.11)(chr8:g.67120297::chr12:g.111885689)	IMPPRECISE	Note: The SH2B3 rearrangement is a translocation with a breakpoint in intron 7 of SH2B3. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	12	Intron of SH2B3(+):58bp after exon 7	SH2B3	111885689			8	IGR: 16Kb before LINC00967(+)	LINC00967	67120297			0	TRANSLOCATION		0	266461	0	10	NEW_VARIANT
P-0036236-T01-IM6	DNMT3A (NM_022552) Rearrangement: t(2;4)(p23.1;p16.3(chr2:g.25467463::chr4:g.561524)	PRECISE	Note: The DNMT3A rearrangement is a translocation with a breakpoint in exon 14 of DNMT3A. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	4	IGR: 58Kb before PDE6B(+)	PDE6B	561524			2	Exon 14 of DNMT3A(-)	DNMT3A	25467463			10	TRANSLOCATION		0	266460	0	7	NEW_VARIANT
P-0036244-T01-IM6	MGA (NM_001164273) rearrangement: c.1064+9674_c.7892-53del	PRECISE	Note: The MGA rearrangement is an intragenic deletion of exons 3-22. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 20 exons : out of frame		54631	0	37	15	Intron of MGA(+):10Kb after exon 2	MGA	41971830			15	Intron of MGA(+):52bp before exon 23	MGA	42057031			10	DELETION		85201	266788	39870	39	NEW_VARIANT
P-0036247-T01-IM6	MAP2K4 (NM_003010) rearrangement: c.1041-4430_c.1060del	PRECISE	Note: The MAP2K4 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		229	0	16	17	Intron of MAP2K4(+):4Kb before exon 10	MAP2K4	12038726			17	Exon 10 of MAP2K4(+)	MAP2K4	12043175			10	DELETION		4449	266763	59	17	NEW_VARIANT
P-0036247-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+107:EML4_c.3172+470:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		86156	0	87	2	Intron of ALK(-):469bp after exon 19	ALK	29447857			2	Intron of EML4(+):107bp after exon 12	EML4	42522763			10	INVERSION		13074906	266764	58204	87	NEW_VARIANT
P-0036349-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.56-1371:TMPRSS2_chr21:g.40097824del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		50816	0	127	21	IGR: 13Kb before LINC00114(-)	LINC00114	40097824			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871487			10	DELETION		2773663	268720	31876	142	NEW_VARIANT
P-0036357-T01-IM6	CDK12 (NM_016507) rearrangement: c.3269:CDK12_chr17:g.27096697inv	PRECISE	Note: The CDK12 rearrangement is an inversion of exons 1-12. One of the breakpoints is within exon 12. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FAM222B:CDK12}		133881	0	45	17	5-UTR of FAM222B(-):11Kb before coding start	FAM222B	27096697			17	Exon 12 of CDK12(+)	CDK12	37681100			10	INVERSION		10584403	268072	173655	56	NEW_VARIANT
P-0036368-T01-IM6	RTEL1 (NM_032957) rearrangement: c.1794+42:RTEL1_chr20:g.48618565inv	PRECISE	Note: The RTEL1 rearrangement is an inversion of exons 1-20. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		73786	0	11	20	IGR: 19Kb before SNAI1(+)	SNAI1	48618565			20	Intron of RTEL1(+):42bp after exon 20	RTEL1	62319781			10	INVERSION		13701216	267955	141898	11	NEW_VARIANT
P-0036409-T01-IM6	FLCN (NM_144997) - COPS3 (NM_003653) rearrangement: c.871+334:FLCN_c.55+2283:COPS3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FLCN:COPS3}		12441	0	15	17	Intron of FLCN(-):333bp after exon 8	FLCN	17124517			17	Intron of COPS3(-):2Kb after exon 1	COPS3	17182163			10	DUPLICATION		57646	268418	11080	17	NEW_VARIANT
P-0036411-T01-IM6	RAD50 (NM_005732) - PTDSS1 (NM_014754) rearrangement: t(5;8)(q31.1;q22.1)(chr5:g.131923393::chr8:g.97283528)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RAD50:PTDSS1}		0	0	60	8	Intron of PTDSS1(+):2Kb before exon 2	PTDSS1	97283528			5	Intron of RAD50(+):11bp after exon 6	RAD50	131923393			10	TRANSLOCATION		0	268422	0	60	NEW_VARIANT
P-0036423-T01-IM6	MALT1 (NM_006785) - WDR7 (NM_015285) rearrangement: c.31:MALT1_c.4165-1604:WDR7dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MALT1:WDR7}		3085	0	6	18	Intron of WDR7(+):2Kb before exon 26	WDR7	54686372			18	Exon 1 of MALT1(+)	MALT1	56338906			7	DUPLICATION		1652534	269419	3922	6	NEW_VARIANT
P-0036438-T01-IM6	CPM (NM_001005502) - IDH1 (NM_005896) rearrangement t(2;12)(q34;q15)(chr2:g.209108415::chr12:g.69293886)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CPM:IDH1}		0	0	14	12	Intron of CPM(-):14Kb before exon 3	CPM	69293886			2	Intron of IDH1(-):87bp before exon 6	IDH1	209108415			10	TRANSLOCATION		0	269134	0	14	NEW_VARIANT
P-0036438-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-1144:TMPRSS2_c.18+2770:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		22021	0	38	21	Intron of ERG(-):3Kb after exon 1	ERG	39867517			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867649			10	DELETION		3000132	269133	33249	38	NEW_VARIANT
P-0036441-T01-IM6	PPP2R1A (NM_014225) - ZFC3H1 (NM_144982) rearrangement: t(12;19)(q21.2;q13.41)(chr12:g.72019702::chr19:g.52715868)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {ZFC3H1:PPP2R1A}		0	0	45	19	Intron of PPP2R1A(+):70bp before exon 5	PPP2R1A	52715868			12	Intron of ZFC3H1(-):337bp after exon 22	ZFC3H1	72019702			10	TRANSLOCATION		0	269122	0	48	NEW_VARIANT
P-0036481-T01-IM6	SPEN (NM_015001) rearrangement: c.2132:SPEN_chr1:g.14808094del	PRECISE	Note: The SPEN rearrangement is a deletion of exons 1-11. One of the breakpoints is within SPEN exon 11.	MANUAL_OK	3to5	3to5	-		20545	0	17	1	IGR: 117Kb before KAZN(+)	KAZN	14808094			1	Exon 11 of SPEN(+)	SPEN	16254867			10	DELETION		1446773	269229	26681	18	NEW_VARIANT
P-0036553-T01-IM6	FBXL20 (NM_032875) - CDK12 (NM_016507) rearrangement: c.697-2344:FBXL20_c.738:CDK12inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FBXL20:CDK12}		3209	0	6	17	Intron of FBXL20(-):2Kb before exon 9	FBXL20	37433697			17	Exon 1 of CDK12(+)	CDK12	37619062			8	INVERSION		185365	269787	16513	7	NEW_VARIANT
P-0036553-T01-IM6	BRCA1 (NM_007294) rearrangement: c.1530:BRCA1_chr17:g.37741308inv	IMPPRECISE	Note: The BRCA1 rearrangement results in the deletion of exons 10-23. One of the breakpoints is within exon 10.	MANUAL_OK	5to5	5to5	-		207782	0	12	17	IGR: 19Kb before NEUROD2(-)	NEUROD2	37741308			17	Exon 10 of BRCA1(-)	BRCA1	41246018			0	INVERSION		3504710	269788	437720	18	NEW_VARIANT
P-0036292-T01-IM6	TSC2 (NM_000548) rearrangement: t(7;16)(q22.3;p13.3)(chr7:g.104453296::chr16:g.2138054)	PRECISE	Note: The TSC2 rearrangement is a translocation involving a breakpoint in exon 40.	MANUAL_OK	5to5	5to5	-		0	0	7	16	Exon 40 of TSC2(+)	TSC2	2138054			7	Intron of LHFPL3(+):76Kb after exon 2	LHFPL3	104453296			10	TRANSLOCATION		0	268856	0	14	NEW_VARIANT
P-0036294-T01-IM6	TMPRSS2 (NM_001135099) -  ERG (NM_182918) fusion: c.127-1016:TMPRSS2_c.18+4202:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25452	0	62	21	Intron of ERG(-):4Kb after exon 1	ERG	39866085			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867521			10	DELETION		3001436	268849	30019	65	NEW_VARIANT
P-0036375-T01-IM6	ATP6V1C2 (NM_001039362) - CDK4 (NM_000075) rearrangement: t(2;12)(p25.1;q13.3)(chr2:g.10902938::chr12:g.58144811)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ATP6V1C2:CDK4}		0	0	6	12	Exon 4 of CDK4(-)	CDK4	58144811			2	Intron of ATP6V1C2(+):2Kb before exon 5	ATP6V1C2	10902938			10	TRANSLOCATION		0	268148	0	6	NEW_VARIANT
P-0036531-T01-IM6	RAD21 (NM_006265) rearrangement: c.1704+126:RAD21_chr8:g.117854751del	PRECISE	Note: The RAD21 rearrangement is a deletion of exon 14.  The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1087	0	23	8	IGR: 3Kb before RAD21(-)	RAD21	117854751			8	Intron of RAD21(-):125bp after exon 13	RAD21	117861059			10	DELETION		6308	269690	1253	24	NEW_VARIANT
P-0036545-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-464:TMPRSS2_c.40-59641:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		41876	0	90	21	Intron of ERG(-):60Kb before exon 4	ERG	39877185			21	Intron of TMPRSS2(-):464bp before exon 2	TMPRSS2	42870580			10	DELETION		2993395	269813	28708	92	NEW_VARIANT
P-0036545-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.1963_chr8:g.36081862inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		26581	0	22	8	IGR: 552Kb before LOC101929550(-)	LOC101929550	36081862			8	Exon 10 of WHSC1L1(-)	WHSC1L1	38173453			10	INVERSION		2091591	269814	15607	22	NEW_VARIANT
P-0036573-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.56-537_chr21:g.40068238del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		44258	0	43	21	IGR: 43Kb before LINC00114(-)	LINC00114	40068238			21	Intron of TMPRSS2(-):537bp before exon 2	TMPRSS2	42870653			10	DELETION		2802415	270004	54112	45	NEW_VARIANT
P-0036594-T01-IM6	ARID1A (NM_006015) - MAN1C1 (NM_020379) Rearrangement: c.3763:ARID1A_c.638-26041:MAN1C1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ARID1A:MAN1C1}		26678	0	38	1	Intron of MAN1C1(+):26Kb before exon 3	MAN1C1	26047118			1	Exon 15 of ARID1A(+)	ARID1A	27099884			10	DUPLICATION		1052766	270973	42184	42	NEW_VARIANT
P-0036662-T01-IM6	NTRK1 (NM_002529) rearrangement: t(1;5)(q23.1;p13.2)(chr1:g.156837969::chr5:g.37075787)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	163	5	IGR: 31Kb before C5orf42(-)	C5orf42	37075787			1	Exon 5 of NTRK1(+)	NTRK1	156837969			10	TRANSLOCATION		0	271855	0	203	NEW_VARIANT
P-0036662-T01-IM6	NTRK1 (NM_002529) - SHPRH (NM_001042683) rearrangement: t(1;6)(q231;q24.3)(chr1:g.156831180::chr6:g.146225530)	PRECISE	Note: The NTRK1 - SHPRH rearrangement is a translocation that results in the fusion of NTRK1 exon 1 with SHPRH exons 26-30.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NTRK1:SHPRH}		0	0	8	6	Intron of SHPRH(-):6Kb after exon 25	SHPRH	146225530			1	Intron of NTRK1(+):242bp after exon 1	NTRK1	156831180			6	TRANSLOCATION		0	271857	0	8	NEW_VARIANT
P-0036669-T01-IM6	EWSR1 (NM_013986) - CDADC1 (NM_030911) rearrangement: t(13;22)(q14.2;q12.2)(chr13:g.49835899::chr22:g.29694130)	IMPPRECISE	Note: The EWSR1 - CDADC1 rearrangement is a translocation that results in the fusion of EWSR1 exons 1-14 with CDADC1 exons 5-10.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EWSR1:CDADC1}		0	0	126	22	Intron of EWSR1(+):191bp after exon 14	EWSR1	29694130			13	Intron of CDADC1(+):2Kb after exon 4	CDADC1	49835899			0	TRANSLOCATION		0	271869	0	130	NEW_VARIANT
P-0036669-T01-IM6	EP300 (NM_001429) rearrangement: t(X;22)(q26.3;q13.2)(chrX:g.133828640::chr22:g.41560109)	PRECISE	Note: The EP300 rearrangement is a translocation with a breakpoint within exon 22. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	62	X	IGR: 75Kb before FAM122B(-)	FAM122B	133828640			22	Exon 22 of EP300(+)	EP300	41560109			10	TRANSLOCATION		0	271871	0	64	NEW_VARIANT
P-0024686-T02-IM6	TMPRSS2 (NM_001135099) - PLCD3 (NM_133373) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.43208249::chr21:g.42840366)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	48	21	Exon 12 of TMPRSS2(-)	TMPRSS2	42840366			17	Intron of PLCD3(-):1Kb after exon 1	PLCD3	43208249			10	TRANSLOCATION		0	272589	0	48	NEW_VARIANT
P-0024686-T02-IM6	TMPRSS2 (NM_001135099) - ETV4 (NM_001986) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41615041::chr21:g.42840400)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TMPRSS2:ETV4}		0	0	64	21	Exon 12 of TMPRSS2(-)	TMPRSS2	42840400			17	Intron of ETV4(-):1Kb before exon 5	ETV4	41615041			10	TRANSLOCATION		0	272590	0	69	NEW_VARIANT
P-0028690-T01-IM6	CCND1 (NM_053056) Rearrangement: chr11:g.24441784_c.*93inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		167605	0	17	11	IGR: 77Kb before LUZP2(+)	LUZP2	24441784			11	3-UTR of CCND1(+):10Kb after coding stop	CCND1	69466143			10	INVERSION		45024359	271139	87418	17	NEW_VARIANT
P-0036558-T01-IM6	PRDM14 (NM_024504) rearrangement: t(8;11)(q13.3;p11.2)(chr8:g.70980437::chr11:g.45629910)	PRECISE	Note: The PRDM14 rearrangement is a translocation with a breakpoint in PRDM14 intron 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	222	11	IGR: 39Kb before CHST1(-)	CHST1	45629910			8	Intron of PRDM14(-):27bp after exon 4	PRDM14	70980437			10	TRANSLOCATION		0	272599	0	245	NEW_VARIANT
P-0036574-T01-IM6	CD276 (NM_001024736) Rearrangement:  t(5;15)(q11.2;q24.1)(chr5:g.54239847::chr15:g.73996135)	PRECISE	Note: The CD276 Rearrangement is a translocation event with a breakpoint in exon5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	190	15	Exon 5 of CD276(+)	CD276	73996135			5	IGR: 34Kb before ESM1(-)	ESM1	54239847			10	TRANSLOCATION		0	270020	0	239	NEW_VARIANT
P-0036582-T01-IM6	BRD4 (NM_058243) rearrangement: c.2048-99:BRD4_chr19:g.15405858del	PRECISE	Note: The BRD4 rearrangement is a deletion of exons 1-11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		21293	0	4	19	Intron of BRD4(-):99bp before exon 11	BRD4	15365172			19	IGR: 48Kb before BRD4(-)	BRD4	15405858			9	DELETION		40686	270951	34720	4	NEW_VARIANT
P-0036631-T01-IM6	KDM6A (NM_021140) Rearrangement : c.3921_chrX:g.44979900inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		4156	1	13	X	Exon 27 of KDM6A(+)	KDM6A	44966697			X	IGR: 28Kb before CXorf36(-)	CXorf36	44979900			10	INVERSION		13203	271128	1841	11	NEW_VARIANT
P-0036746-T01-IM6	BRCA1 (NM_007294) - RPL27 (NM_000988) Rearrangement : c.3356:BRCA1_c.252-1051:RPL27inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {BRCA1:RPL27}		25556	0	6	17	Intron of RPL27(+):1Kb before exon 4	RPL27	41153639			17	Exon 10 of BRCA1(-)	BRCA1	41244192			8	INVERSION		90553	272639	31836	6	NEW_VARIANT
P-0020290-T02-IM6	APC (NM_000038) rearrangement: c.4458_chr5:g.112194235del	PRECISE	Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		13344	0	103	5	Exon 16 of APC(+)	APC	112175749			5	Promoter of SRP19(+):3Kb from tx start	SRP19	112194235			10	DELETION		18486	273073	2512	105	NEW_VARIANT
P-0035898-T01-IM6	CASP8 (NM_001080125) rearrangement: chr2:g.201843889_c.1327:CASP8dup	PRECISE	Note: The CASP8 rearrangement is a duplication that includes CASP8 exon 1-8. One of the breakpoints is within exon 8.	MANUAL_OK	5to3	5to3	-		10484	0	6	2	3-UTR of FAM126B(-):2Kb after coding stop	FAM126B	201843889			2	Exon 8 of CASP8(+)	CASP8	202149886			8	DUPLICATION		305997	273511	14365	7	NEW_VARIANT
P-0036613-T01-IM6	MEF2B (NM_001145785) rearrangement: t(8;19)(q24.3;p13.11)(chr8:g.144708079::chr19:g.19256750)	PRECISE	Note: The MEF2B rearrangement is a translocation involving a breakpoint in exon 9. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	19	19	Exon 9 of MEF2B(-)	MEF2B	19256750			8	IGR: 10Kb before ZNF623(+)	ZNF623	144708079			10	TRANSLOCATION		0	271009	0	19	NEW_VARIANT
P-0036677-T01-IM6	KDM6A (NM_021140) rearrangement: t(X;8)(q24.13;p11.3)(chrX:g.44941938::chr8:g.124293775)	PRECISE	Note: The KDM6A rearrangement is a translocation with a breakpoint within intron 21. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	61	X	Intron of KDM6A(+):21bp before exon 22	KDM6A	44941938			8	IGR: 33Kb before ZHX1(-)	ZHX1	124293775			10	TRANSLOCATION		0	271892	0	60	NEW_VARIANT
P-0036717-T01-IM6	SMARCA4 (NM_003072) rearrangement: (17;19)(q25.3;p13.2)(chr17:g.76087542::chr19:g.11141361)	PRECISE	Note: The SMARCA4 intragenic rearrangement is a translocation with a breakpoint in intron 24. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	51	19	Intron of SMARCA4(+):44bp before exon 25	SMARCA4	11141361			17	Exon 15 of TNRC6C(+)	TNRC6C	76087542			10	TRANSLOCATION		0	272350	0	65	NEW_VARIANT
P-0036759-T01-IM6	BCOR (NM_001123385) rearrangement: c.1802_c.2997+287del	PRECISE	Note: The BCOR rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4853	0	27	X	Intron of BCOR(-):286bp after exon 4	BCOR	39931315			X	Exon 4 of BCOR(-)	BCOR	39932797			10	DELETION		1482	272739	3407	28	NEW_VARIANT
P-0036849-T01-IM6	GSK3B (NM_002093) rearrangement: c.813+99_c.1235-7556del	PRECISE	Note: The GSK3B rearrangement is an intragenic deletion of exons 8-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		3207	0	9	3	Intron of GSK3B(-):8Kb before exon 12	GSK3B	119553258			3	Intron of GSK3B(-):98bp after exon 7	GSK3B	119624503			10	DELETION		71245	273060	4844	9	NEW_VARIANT
P-0036920-T01-IM6	ERCC5 (NM_000123) rearrangement: chr13:g.57179785_c.1851del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		52571	0	87	13	IGR: 535Kb before PRR20D(+)	PRR20D	57179785			13	Exon 8 of ERCC5(+)	ERCC5	103515350			10	DELETION		46335565	273504	92855	91	NEW_VARIANT
P-0036698-T01-IM6	ATRX (NM_000489) rearrangement: c.484+2165_c.3170del	PRECISE	Note: The ATRX rearrangement is an intragenic deletion of exons 7-9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5930	0	6	X	Exon 9 of ATRX(-)	ATRX	76937578			X	Intron of ATRX(-):2Kb after exon 6	ATRX	76947148			10	DELETION		9570	272320	9077	6	NEW_VARIANT
P-0036732-T01-IM6	MGA (NM_001164273) Rearrangement: c.2013+14:MGA_chr15:g.42199394del	PRECISE	Note: The MGA rearrangement results in the deletion of MGA exons 4 to 24. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		47171	0	50	15	Intron of MGA(+):14bp after exon 3	MGA	41989235			15	Intron of EHD4(-):3Kb after exon 5	EHD4	42199394			10	DELETION		210159	272381	32875	100	NEW_VARIANT
P-0036810-T01-IM6	STK11 (NM_000455) rearrangement: c.597+30_c.920+31del	PRECISE	Note: The STK11 rearrangement is an intragenic deletion of exons 5-7.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		4643	0	49	19	Intron of STK11(+):30bp after exon 4	STK11	1220534			19	Intron of STK11(+):31bp after exon 7	STK11	1222036			10	DELETION		1502	273038	1848	49	NEW_VARIANT
P-0036892-T01-IM6	APC (NM_000038) Rearrangement : c.4189_c.6465del	PRECISE	Note: The APC Rearrangement results in the intragenic deletion of exon16 of APC. Both the breakpoints are within 16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6443	0	61	5	Exon 16 of APC(+)	APC	112175480			5	Exon 16 of APC(+)	APC	112177756			10	DELETION		2276	273466	5712	62	NEW_VARIANT
P-0036893-T01-IM6	PIK3R2 (NM_005027) Rearrangement : c.1290+57:PIK3R2_c.-2922:RAB8Ainv	PRECISE	Note : The PIK3R2 Rearrangement results in the inversion of exons 1-10 of PIK3R2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		40142	0	23	19	Promoter of RAB8A(+):3Kb from tx start	RAB8A	16219790			19	Intron of PIK3R2(+):57bp after exon 10	PIK3R2	18274014			10	INVERSION		2054224	273476	36561	23	NEW_VARIANT
P-0036895-T01-IM6	NF2 (NM_000268) Rearrangement : t(19,22)(q11,q12.2)(chr19:g.28825367::chr22:g.30079061)	PRECISE	Note: The NF2 Rearrangement is a translocation event with the breakpoint intron 15. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	36	22	Intron of NF2(+):1Kb after exon 15	NF2	30079061			19	IGR: 101Kb before LOC100420587(-)	LOC100420587	28825367			10	TRANSLOCATION		0	273464	0	36	NEW_VARIANT
P-0036766-T01-IM6	ATR (NM_001184) rearrangement: c.1863_c.1885+832del	IMPPRECISE	Note: The ATR rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		271	0	35	3	Intron of ATR(-):831bp after exon 8	ATR	142276634			3	Exon 8 of ATR(-)	ATR	142277488			0	DELETION		854	272712	310	36	NEW_VARIANT
P-0036937-T01-IM6	EXOC4 (NM_021807) - BRAF (NM_004333) fusion: c.1514+93469:EXOC4_c.1141-2857:BRAFinv	PRECISE	Note: The EXOC4 - BRAF fusion involves EXOC4 exons 1-10 and BRAF exons 9-18, including the BRAF kinase domain.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {EXOC4:BRAF}		47730	0	37	7	Intron of EXOC4(+):93Kb after exon 10	EXOC4	133408363			7	Intron of BRAF(-):3Kb before exon 9	BRAF	140490241			10	INVERSION		7081878	275008	35711	34	NEW_VARIANT
P-0037005-T01-IM6	IGF1R (NM_000875) - ITSN1 (NM_003024) rearrangement: t(15;21)(q26.3;q22.11)(chr15:g.99456690::chr21:g.35197921)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {IGF1R:ITSN1}		0	0	6	21	Intron of ITSN1(+):1Kb before exon 26	ITSN1	35197921			15	Intron of IGF1R(+):179bp after exon 8	IGF1R	99456690			5	TRANSLOCATION		0	275027	0	5	NEW_VARIANT
P-0037005-T01-IM6	ATR (NM_001184) rearrangement: t(1;3)(p11.2;q23)(chr1:g.121485434::chr3:g.142184004)	PRECISE	Note: The ATR rearrangement is a translocation with a breakpoint in exon 41. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	14	3	Exon 41 of ATR(-)	ATR	142184004			1	IGR: 225Kb before EMBP1(+)	EMBP1	121485434			10	TRANSLOCATION		0	275025	0	31	NEW_VARIANT
P-0037008-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.936+16:CTNNB1_chr3:g.41368388del	PRECISE	Note: The CTNNB1 rearrangement is a deletion of exons 7-15. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		10982	0	14	3	Intron of CTNNB1(+):16bp after exon 6	CTNNB1	41267368			3	Intron of ULK4(-):71Kb after exon 35	ULK4	41368388			10	DELETION		101020	275023	5349	14	NEW_VARIANT
P-0012649-T02-IM6	STK11 (NM_000455) rearrangement: c.465-120_c.863-89del	IMPPRECISE	Note: The STK11 rearrangement is an intragenic deletion of exons 4-6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		4420	0	9	19	Intron of STK11(+):119bp before exon 4	STK11	1220252			19	Intron of STK11(+):88bp before exon 7	STK11	1221859			0	DELETION		1607	274690	3624	9	NEW_VARIANT
P-0014384-T02-IM6	DNMT3B (NM_006892) Rearrangement : c.1997-115_c.2231+41dup	PRECISE	Note: The DNMT3B Rearrangement results in the duplication of exons 19-20 of DNMT3B. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		2597	0	91	20	Intron of DNMT3B(+):114bp before exon 19	DNMT3B	31388969			20	Intron of DNMT3B(+):41bp after exon 20	DNMT3B	31390317			10	DUPLICATION		1348	205015	4724	92	NEW_VARIANT
P-0015435-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion (CCDC6 exon 1 fused to RET exon 12): c.304-21366:CCDC6_c.2136+785:RETinv	PRECISE	Note; The CCDC6 - RET fusion is predicted to be in frame and includes the kinase domain of RET	MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		56015	0	53	10	Intron of RET(+): 785bp after exon 11	RET	43610969			10	Intron of CCDC6(-): 21Kb before exon 2	CCDC6	61633826			60	INVERSION		18022857	167994	53610	52	NEW_VARIANT
P-0015507-T01-IM6	BRD4 (NM_058243) Rearrangement : c.230:BRD4_c.62-157:PGLYRP2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		1908	0	18	19	Exon 2 of BRD4(-)	BRD4	15383681			19	Intron of PGLYRP2(-): 157bp before exon 2	PGLYRP2	15587576			22	INVERSION		203895	168275	1431	17	NEW_VARIANT
P-0017563-T01-IM5	EPHA7 (NM_004440) rearrangement: t(6;8)(q16.1;q24.23)(chr6:g.93982172::chr8:g.138179021)	PRECISE	Note: The EPHA7 rearrangement is a translocation that may result in a truncation of exons 6-17. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	40	8	IGR: 239Kb before LOC101927915(-)	LOC101927915	138179021			6	Intron of EPHA7(-):32bp before exon 6	EPHA7	93982172			10	TRANSLOCATION		0	176141	0	41	NEW_VARIANT
P-0017900-T01-IM6	CDKN2Ap14ARF (NM_058195) Rearrangement : chr9:g.18389532_c.317-3482:CDKN2Ap14ARFinv	PRECISE	Note: The CDKN2Ap14ARF Rearrangement results in the inversion of exon 2. Its functional significance is undetermined.	MANUAL_OK	3 to 3	3 to 3	-		12566		157	9	IGR: 85Kb before ADAMTSL1	ADAMTSL1	18389532			9	Intron of CDKN2Ap14ARF before exon 2	CDKN2Ap14ARF	21974689			10	INVERSION		3585157	177403	17867		NEW_VARIANT
P-0017900-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : chr9:g.18389532_c.138:CDKN2Ap16INK4Ainv	PRECISE	Note: The CDKN2Ap16INK4A Rearrangement results in the inversion of exons 1-3.The breakpoint in CDKN2Ap16INK4A is within exon1.  Its functional significance is undetermined.	MANUAL_OK	3 to 3	3 to 3	-		12566		157	9	IGR: 85Kb before ADAMTSL1	ADAMTSL1	18389532			9	Exon 1 of CDKN2Ap16INK4A	CDKN2Ap16INK4A	21974689			10	INVERSION		3585157	177402	17867		NEW_VARIANT
P-0018687-T01-IM6	ETV6 (NM_001987) rearrangement: c.329-768_c.464-4544del	PRECISE	Note: The ETV6 rearrangement results in the deletion of exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		61226	0	13	12	Intron of ETV6(+):767bp before exon 4	ETV6	12005593			12	Intron of ETV6(+):5Kb before exon 5	ETV6	12017814			10	DELETION		12221	179979	92683	13	NEW_VARIANT
P-0018886-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMRPSS2 exon 1 fused  with ERG exons 2-10): c.56-2764:TMPRSS2_c.18+8733:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		100064	0	16	21	Intron of ERG(-):9Kb after exon 1	ERG	39861554			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872880			10	DELETION		3011326	180403	54468	17	NEW_VARIANT
P-0018886-T01-IM6	CDC37L1 (NM_017913) - JAK2 (NM_004972) rearrangement: c.635:CDC37L1_c.3060-11016:JAK2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDC37L1:JAK2}		42268	0	10	9	Exon 5 of CDC37L1(+)	CDC37L1	4697767			9	Intron of JAK2(+):11Kb before exon 23	JAK2	5111988			10	DELETION		414221	180400	15250	10	NEW_VARIANT
P-0019347-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2419:TMPRSS2_c.19-7767:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75922	0	59	21	Intron of ERG(-):8Kb before exon 2	ERG	39825311			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872535			10	DELETION		3047224	181892	60449	66	NEW_VARIANT
P-0020159-T01-IM6	INPP4B (NM_001101669) rearrangement: chr4:g.34776389_c.526:INPP4Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		377657	0	33	4	IGR: 878Kb before LOC101928622(-)	LOC101928622	34776389			4	Exon 10 of INPP4B(-)	INPP4B	143191905			10	INVERSION		108415516	183804	291514	31	NEW_VARIANT
P-0020224-T01-IM6	MGA (NM_001164273) - RTF1 (NM_015138) rearrangement: c.5400:MGA_c.663-1603:RTF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MGA:RTF1}		50415	0	4	15	Intron of RTF1(+):2Kb before exon 5	RTF1	41755366			15	Exon 16 of MGA(+)	MGA	42041022			9	DUPLICATION		285656	183917	68003	4	NEW_VARIANT
P-0020433-T01-IM6	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement : c.4823:APC_c.-2279:SRP19del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		18946	0	2	5	Exon 16 of APC(+)	APC	112176114			5	Promoter of SRP19(+):2Kb from tx start	SRP19	112194795			5	DELETION		18681	184440	4147	2	NEW_VARIANT
P-0020459-T01-IM6	ABL1 (NM_005157) rearrangement: chr9:g.78504638_c.79+61:ABL1inv	PRECISE	Note: The ABL1 rearrangement is an inversion of exon 1. The functional significance is undetermined	MANUAL_OK	3to3	3to3	Antisense Fusion		433910	0	12	9	Promoter of PCSK5(+):921bp from tx start	PCSK5	78504638			9	Intron of ABL1(+):61bp after exon 1	ABL1	133710973			10	INVERSION		55206335	184458	129264	12	NEW_VARIANT
P-0020574-T01-IM6	GSK3B (NM_002093) rearrangement: chr3:g.112419488_c.1136-76:GSK3Binv	PRECISE	Note: The GSK3B rearrangement is an inversion of exons 11-12. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		10457	0	5	3	IGR: 36Kb before LOC101929694(-)	LOC101929694	112419488			3	Intron of GSK3B(-):76bp before exon 11	GSK3B	119562276			10	INVERSION		7142788	184765	6416	4	NEW_VARIANT
P-0020713-T01-IM6	INSR (NM_000208) - CRABP2 (NM_001878) rearrangement: t(1,19)(q23.1,p13.2)(chr1:g.156675691::chr19:c.2667)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {INSR:CRABP2}		0	0	16	19	Exon 13 of INSR(-)	INSR	7141703			1	Promoter of CRABP2(-):6Kb from tx start	CRABP2	156675691			10	TRANSLOCATION		0	185119	0	16	NEW_VARIANT
P-0020844-T01-IM6	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	PRECISE	Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32164	0	58	21	Intron of ERG(-):61Kb before exon 4	ERG	39878848			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868131			10	DELETION		2989283	185536	33381	59	NEW_VARIANT
P-0020844-T01-IM6	BRAF (NM_004333) rearrangement: g.116584014_c.1141-745inv	PRECISE	Note: The BRAF rearrangement results in the inversion of exons 9-18 and includes the kinase domain of BRAF. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		109376	0	52	7	IGR: 8Kb before ST7-AS1(-)	ST7-AS1	116584014			7	Intron of BRAF(-):745bp before exon 9	BRAF	140488129			10	INVERSION		23904115	185537	173417	52	NEW_VARIANT
P-0020844-T01-IM6	KMT2C (NM_170606) rearrangement: g.151053870_c.12456del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		30117	0	81	7	Intron of NUB1(+):562bp after exon 7	NUB1	151053870			7	Exon 49 of KMT2C(-)	KMT2C	151849860			10	DELETION		795990	185535	32400	95	NEW_VARIANT
P-0021673-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-3939:TMPRSS2_c.18+2925:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		83457	0	38	21	Intron of ERG(-):3Kb after exon 1	ERG	39867362			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874055			10	DELETION		3006693	188084	72599	40	NEW_VARIANT
P-0023930-T01-IM6	BRCA2 (NM_000059) - KL (NM_004795) rearrangement: c.6841+166:BRCA2_c.819+9933:KLdel	PRECISE	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	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {BRCA2:KL}		37752	0	33	13	Intron of BRCA2(+):166bp after exon 11	BRCA2	32915499			13	Intron of KL(+):10Kb after exon 1	KL	33601330			10	DELETION		685831	197326	21201	34	NEW_VARIANT
P-0023930-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q21.1;q22.3)(chr18:g.46767863::chr21:g.42874721)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	91	21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874721			18	Intron of DYM(-):16Kb after exon 13	DYM	46767863			10	TRANSLOCATION		0	197327	0	99	NEW_VARIANT
P-0026232-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.-31-1296_c.1074dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 2-6. One of the breakpoints is within exon 6.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		13841	0	11	19	5-UTR of SMARCA4(+):1Kb before coding start	SMARCA4	11093501			19	Exon 6 of SMARCA4(+)	SMARCA4	11098556			10	DUPLICATION		5055	263371	16609	12	NEW_VARIANT
P-0026232-T01-IM6	BCL2L11 (NM_138621) rearrangement: c.498+695_c.506del	PRECISE	Note: The BCL2L11 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3296	0	20	2	Intron of BCL2L11(+):695bp after exon 3	BCL2L11	111908419			2	Exon 4 of BCL2L11(+)	BCL2L11	111921717			10	DELETION		13298	263367	4038	22	NEW_VARIANT
P-0026232-T01-IM6	FAM58A (NM_152274) rearrangement: c.111-630_c.177dup	PRECISE	Note: The FAM58A rearrangement is an intragenic duplication of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		928	0	13	X	Exon 2 of FAM58A(-)	FAM58A	152861579			X	Intron of FAM58A(-):630bp before exon 2	FAM58A	152862275			10	DUPLICATION		696	263372	1261	13	NEW_VARIANT
P-0026238-T01-IM6	TP53 (NM_000546) rearrangement: c.673-240_c.965del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 7-9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2181	0	2	17	Exon 9 of TP53(-)	TP53	7576881			17	Intron of TP53(-):240bp before exon 7	TP53	7577848			10	DELETION		967	210146	1731	3	NEW_VARIANT
P-0026238-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.55+4255:TMPRSS2_c.18+13682:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52823	0	30	21	Intron of ERG(-):14Kb after exon 1	ERG	39856605			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875622			10	DELETION		3019017	210147	47750	30	NEW_VARIANT
P-0026384-T01-IM6	SETD2 (NM_014159) Rearrangement : c.4840-828_5142+70dup	PRECISE	Note : The SETD2 Rearrangement results in the intragenic duplication of exons 7-9 of SETD2.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		4030	0	5	3	Intron of SETD2(-):69bp after exon 9	SETD2	47139375			3	Intron of SETD2(-):828bp before exon 7	SETD2	47145741			10	DUPLICATION		6366	210526	5959	5	NEW_VARIANT
P-0026615-T02-IM6	PAK1 (NM_002576) Rearrangement: t(8;11)(p12;q13.5)(chr8:g.32259693::chr11:g.77036046)	PRECISE	Note: The PAK1 rearrangement is a translocation with breakpoints within intron 15 of PAK1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	6	11	Intron of PAK1(-):2Kb before exon 15	PAK1	77036046			8	Intron of NRG1(+):194Kb before exon 2	NRG1	32259693			7	TRANSLOCATION		0	258028	0	5	NEW_VARIANT
P-0028258-T01-IM6	PAK1 (NM_002576) rearrangement: c.1181_chr11:g.76259831dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		6290	0	36	11	Intron of C11orf30(+):1Kb before exon 21	C11orf30	76259831			11	Exon 12 of PAK1(-)	PAK1	77048404			10	DUPLICATION		788573	216536	13197	43	NEW_VARIANT
P-0028298-T01-IM6	ADAMTS16 (NM_139056) - TERT (NM_198253) rearrangement: c.175+1379C:ADAMTS16_c.-237:TERTinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {ADAMTS16:TERT}		7711	0	71	5	Promoter of TERT(-):42Kb from tx start	TERT	1295341			5	Intron of ADAMTS16(+):1Kb after exon 2	ADAMTS16	5142258			0	INVERSION		3846917	216818	10076	70	NEW_VARIANT
P-0028347-T01-IM6	NAB2 (NM_005967) rearrangement: c.1056:NAB2_chr12:g.86871854inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {NAB2:MGAT4C}		65675	0	441	12	Exon 3 of NAB2(+)	NAB2	57486329			12	5-UTR of MGAT4C(-):499Kb before coding start	MGAT4C	86871854			10	INVERSION		29385525	216866	925678	451	NEW_VARIANT
P-0028347-T01-IM6	IRF4 (NM_002460) rearrangement: c.157:IRF4_chr6:g.14202222inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		18656	0	8	6	Exon 2 of IRF4(+)	IRF4	393309			6	IGR: 78Kb before LINC01108(-)	LINC01108	14202222			9	INVERSION		13808913	216864	24566	8	NEW_VARIANT
P-0028538-T01-IM6	FOXA1 (NM_004496) rearrangement: c.1113:FOXA1_chr14:g.37105233dup	IMPPRECISE	Note: The FOXA1 rearrangement is a duplication of exon 2. One of the breakpoints is within FOXA1 exon 2.	MANUAL_OK	5to3	5to3	-		5383	0	6	14	IGR: 22Kb before PAX9(+)	PAX9	37105233			14	Exon 2 of FOXA1(-)	FOXA1	38060876			0	DUPLICATION		955643	217701	2529	6	NEW_VARIANT
P-0028901-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in-frame and contains the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		98210	0	53	2	Intron of ALK(-):213bp before exon 20	ALK	29446607			2	Intron of EML4(+):843bp before exon 13	EML4	42527537			10	INVERSION		13080930	219076	109200	52	NEW_VARIANT
P-0029163-T01-IM6	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	PRECISE	Note: TMPRSS2 is fused to non-canonical ERG transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		43438	0	50	21	Intron of ERG(-):33Kb after exon 3	ERG	39914571			21	Intron of TMPRSS2(-):23bp before exon 2	TMPRSS2	42870139			10	DELETION		2955568	220506	39242	52	NEW_VARIANT
P-0029163-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1703:PIK3R1_chr5:g.67596143del	PRECISE	Note: The PIK3R1 rearrangement is a deletion of exons 13-16. One of the breakpoints is within exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3083	0	8	5	Exon 13 of PIK3R1(+)	PIK3R1	67591110			5	3-UTR of PIK3R1(+):74Kb after coding stop	PIK3R1	67596143			10	DELETION		5033	220504	3625	7	NEW_VARIANT
P-0029377-T01-IM6	FAT1 (NM_005245) rearrangement: c.7492:FAT_chr4:g.182710429inv	PRECISE	Note: The FAT1 rearrangement is an inversion of exons 10-27. One of the breakpoints is within exon 10. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		40786	0	6	4	IGR: 349Kb before LOC90768(-)	LOC90768	182710429			4	Exon 10 of FAT1(-)	FAT1	187540248			10	INVERSION		4829819	221886	60354	12	NEW_VARIANT
P-0029811-T01-IM6	RTEL1 (NM_032957) Rearrangement: c.1421-191_c.2254inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		11605	0	17	20	Intron of RTEL1(+):190bp before exon 17	RTEL1	62318800			20	Exon 25 of RTEL1(+)	RTEL1	62321480			10	INVERSION		2680	222903	19294	17	NEW_VARIANT
P-0029811-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 2 fused to ERG exons 2-10): c.56-1741:TMPRSS2_c.18+17833:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		44403	0	24	21	Intron of ERG(-):18Kb after exon 1	ERG	39852454			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871857			10	DELETION		3019403	222902	44282	25	NEW_VARIANT
P-0030777-T01-IM6	NTRK2 (NM_006180) - COL5A1 (NM_000093) rearrangement: c.359+58:NTRK2_c.5067+932:COL5A1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {NTRK2:COL5A1}		250126	0	17	9	Intron of NTRK2(+):58bp after exon 6	NTRK2	87317392			9	Intron of COL5A1(+):932bp after exon 63	COL5A1	137718682			10	DELETION		50401290	227367	271462	18	NEW_VARIANT
P-0031505-T01-IM6	FGFR1 (NM_001174067) rearrangement: c.1174+39:FGFR1_chr8:g.38270523del	PRECISE	Note: The FGFR1 rearrangement is a deletion of exons 9-19. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		17354	0	8	8	3-UTR of FGFR1(-):622bp after coding stop	FGFR1	38270523			8	Intron of FGFR1(-):38bp after exon 9	FGFR1	38279276			10	DELETION		8753	229839	14111	9	NEW_VARIANT
P-0031599-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4162:TMPRSS2_c.19-26160:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in frame and includes TMPRSS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53542	2	21	21	Intron of ERG(-):26Kb before exon 2	ERG	39843704			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875715			10	DELETION		3032011	244874	47532	20	NEW_VARIANT
P-0031661-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-288:EML4_c.3172+830:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		112799	0	5	2	Intron of ALK(-):829bp after exon 19	ALK	29447497			2	Intron of EML4(+):287bp before exon 13	EML4	42528093			9	INVERSION		13080596	230361	131726	5	NEW_VARIANT
P-0031666-T01-IM6	FLT3 (NM_004119) rearrangement: c.1942+133:FLT3_chr13:g.28028510inv	PRECISE	Note: The FLT3 rearrangement is an inversion of exons 16-24. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		14423	0	23	13	IGR: 19Kb before MTIF3(-)	MTIF3	28028510			13	Intron of FLT3(-):132bp after exon 15	FLT3	28607891			10	INVERSION		579381	230356	18089	23	NEW_VARIANT
P-0032161-T02-IM6	ARID1B (NM_020732) rearrangement: c.2038-30562:c.3990del	PRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exons 6-16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23558	0	6	6	Intron of ARID1B(+):31Kb before exon 6	ARID1B	157375234			6	Exon 16 of ARID1B(+)	ARID1B	157517426			10	DELETION		142192	234204	13579	6	NEW_VARIANT
P-0032490-T01-IM6	PIK3C3 (NM_002647) Rearrangement : c.511_c.1840-1208inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		12377	0	22	18	Exon 4 of PIK3C3(+)	PIK3C3	39550400			18	Intron of PIK3C3(+):1Kb before exon 17	PIK3C3	39616448			10	INVERSION		66048	233178	4702	22	NEW_VARIANT
P-0032543-T01-IM6	RB1 (NM_000321) rearrangement: c.265-6530_c.1013del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 3-10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8285	0	15	13	Intron of RB1(+):7Kb before exon 3	RB1	48910205			13	Exon 10 of RB1(+)	RB1	48941703			10	DELETION		31498	234201	2537	15	NEW_VARIANT
P-0032573-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4: c.126+133:TMPRSS2_c.40-60824:ERGdel	PRECISE	Note: This fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		34510	0	7	21	Intron of ERG(-):61Kb before exon 4	ERG	39878368			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868708			10	DELETION		2990340	234222	26061	8	NEW_VARIANT
P-0032604-T01-IM6	EGFR (NM_005228) - SEPT14 (NM_207366) fusion :  c.2947-110:EGFR_c.1120-1204:SEPT14	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EGFR:SEPT14}		19417	0	140	7	Intron of EGFR(+):109bp before exon 25	EGFR	55268771			7	Intron of SEPT14(-):1Kb before exon 10	SEPT14	55864989			10	INVERSION		596218	234482	142935	141	NEW_VARIANT
P-0032637-T01-IM6	TSC2 (NM_000548) - SLC9A3R2 (NM_001130012) Rearrangement : c.282:TSC2_c.415-442:SLC9A3R2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TSC2:SLC9A3R2}		19480	0	131	16	Intron of SLC9A3R2(+):441bp before exon 3	SLC9A3R2	2085883			16	Exon 4 of TSC2(+)	TSC2	2103399			10	DUPLICATION		17516	234652	42078	140	NEW_VARIANT
P-0032637-T01-IM6	EZH2 (NM_004456) Rearrangement : t(7,18)(q36.1,q23)(chr7:g.148506395::chr18:g.78016098)	PRECISE	Note: The EZH2 Rearrangement is a translocation event with the breakpoint in intron18 of EZH2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	36	18	IGR: 101Kb before PARD6G(-)	PARD6G	78016098			7	Intron of EZH2(-):6bp after exon 18	EZH2	148506395			10	TRANSLOCATION		0	234653	0	53	NEW_VARIANT
P-0032640-T01-IM6	RICTOR (NM_152756) - NIPBL (NM_133433) Rearrangement : c.1542:RICTOR_c.4024:NIPBLinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {RICTOR:NIPBL}		23874	0	32	5	Exon 17 of NIPBL(+)	NIPBL	37006627			5	Exon 17 of RICTOR(-)	RICTOR	38963002			0	INVERSION		1956375	234651	172106	41	NEW_VARIANT
P-0032722-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1. One of the breakpoints is within CD74 exon 7	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CD74:ROS1}		0	0	183	6	Intron of ROS1(-):99bp before exon 34	ROS1	117645677			5	Exon 7 of CD74(-)	CD74	149782874			10	TRANSLOCATION		0	234912	0	190	NEW_VARIANT
P-0032728-T01-IM6	EZH1 (NM_001991) - BCAS3 (NM_001099432) rearrangement:  c.1164:EZH1_c.1486+3919:BCAS3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {EZH1:BCAS3}		198463	0	49	17	Exon 11 of EZH1(-)	EZH1	40865267			17	Intron of BCAS3(+):4Kb after exon 15	BCAS3	59071515			10	INVERSION		18206248	234919	195297	64	NEW_VARIANT
P-0032745-T01-IM6	FH (NM_000143) - RGS7 (NM_002924) rearrangement:  c.738+181:FH_c.386-8492:RGS7del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {FH:RGS7}		8159	0	27	1	Intron of RGS7(-):8Kb before exon 5	RGS7	241041911			1	Intron of FH(-):180bp after exon 5	FH	241671722			10	DELETION		629811	234927	5148	28	NEW_VARIANT
P-0032745-T01-IM6	BAP1 (NM_004656) - PDZRN4 (NM_001164595) rearrangement: t(3;12)(p21.2;q12)(chr3:g.52440343::chr12:g.41663465)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {BAP1:PDZRN4}		0	0	61	12	Intron of PDZRN4(+):75Kb after exon 3	PDZRN4	41663465			3	Exon 9 of BAP1(-)	BAP1	52440343			10	TRANSLOCATION		0	234929	0	68	NEW_VARIANT
P-0032748-T01-IM6	PRKD1 (NM_002742) rearrangement: c.1392+564_c.1906-18del	PRECISE	Note: The PRKD1 rearrangement is an intragenic deletion of exons 10-13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		4723	0	10	14	Intron of PRKD1(-):18bp before exon 14	PRKD1	30069041			14	Intron of PRKD1(-):563bp after exon 9	PRKD1	30101511			10	DELETION		32470	235058	3143	10	NEW_VARIANT
P-0032753-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1323:KIF5B_c.2136+741:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		47414	0	84	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32316033			10	Intron of RET(+):741bp after exon 11	RET	43610925			10	INVERSION		11294892	235045	47634	91	NEW_VARIANT
P-0032753-T01-IM6	ATR (NM_001184) rearrangement: c.7426:ATR_chr3:g.138900546del	PRECISE	Note: The ATR rearrangement is a deletion of exons 44-47. One of the breakpoints is within exon 44.	MANUAL_OK	3to5	3to5	-		5371	0	22	3	IGR: 51Kb before PISRT1(-)	PISRT1	138900546			3	Exon 44 of ATR(-)	ATR	142177877			10	DELETION		3277331	235040	8550	22	NEW_VARIANT
P-0032753-T01-IM6	PRKCI (NM_002740) rearrangement: c.980+288:PRKCI_chr3:g.178665442del	IMPPRECISE	Note: The PRKCI rearrangement is a deletion of exons 11-18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		12127	0	11	3	Intron of PRKCI(+):288bp after exon 10	PRKCI	169999339			3	IGR: 70Kb before ZMAT3(-)	ZMAT3	178665442			0	DELETION		8666103	235041	22855	11	NEW_VARIANT
P-0032799-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11): c.55+815:TMPRSS2_c.39+61431:ERGdel	PRECISE	Note: The TMPRSS2-ERG re-arrangement is a non-canonical fusion.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		88158	0	36	21	Intron of ERG(-):61Kb after exon 3	ERG	39886155			21	Intron of TMPRSS2(-):814bp after exon 1	TMPRSS2	42879062			10	DELETION		2992907	235418	45739	36	NEW_VARIANT
P-0032828-T01-IM6	RAD50 (NM_005732) rearrangement: c.472:RAD50_chr5:g.132029280del	PRECISE	Note: The RAD50 rearrangement is a deletion of exons 4-25. Onee of the breakpoints is within exon 25. The functional significance is undetermined,	MANUAL_OK	3to5	3to5	-		20642	0	50	5	Exon 4 of RAD50(+)	RAD50	131915115			5	3-UTR of KIF3A(-):3Kb after coding stop	KIF3A	132029280			10	DELETION		114165	235703	16145	51	NEW_VARIANT
P-0032851-T01-IM6	DOT1L (NM_032482) Rearrangement : c.1044_c.3391-140dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		25283	0	35	19	Exon 13 of DOT1L(+)	DOT1L	2210437			19	Intron of DOT1L(+):139bp before exon 25	DOT1L	2223140			0	DUPLICATION		12703	235914	35979	36	NEW_VARIANT
P-0032895-T01-IM6	DDR2 (NM_006182) rearrangement: c.1293+41:DDR2_chr1:g.167123216del	IMPPRECISE	Note: The DDR2 rearrangement is a deletion of exons 12-18. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		29280	0	12	1	Intron of DDR2(+):41bp after exon 11	DDR2	162737190			1	IGR: 21Kb before LINC01363(-)	LINC01363	167123216			0	DELETION		4386026	236032	39928	12	NEW_VARIANT
P-0032895-T01-IM6	APC (NM_000038) rearrangement: c.645+794_c.1240del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4124	0	39	5	Intron of APC(+):794bp after exon 6	APC	112117394			5	Exon 10 of APC(+)	APC	112154969			10	DELETION		37575	236033	4338	40	NEW_VARIANT
P-0032962-T01-IM6	AKT2 (NM_001626) Rearrangement: c.1366+231:AKT2_chr19:g.39236036inv	PRECISE	Note: The AKT2 rearrangement results in the inversion of AKT2 exon 14. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1772	0	107	19	Promoter of CAPN12(-):15Kb from tx start	CAPN12	39236036			19	Intron of AKT2(-):230bp after exon 13	AKT2	40740721			10	INVERSION		1504685	236828	4580	120	NEW_VARIANT
P-0032998-T01-IM6	CUX1 (NM_181552) - NCOR1 (NM_006311) rearrangement: t(7;17)(q21.1;p11.2)(chr7:g.101708544::chr17:g.15983467)	PRECISE	Note: The CUX1 - NCOR1 rearrangement is a translocation which may result in the fusion of CUX1 exons 1-3 with NCOR1 exons 26-46.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {CUX1:NCOR1}		0	0	26	17	Intron of NCOR1(-):89bp before exon 26	NCOR1	15983467			7	Intron of CUX1(+):5Kb before exon 4	CUX1	101708544			10	TRANSLOCATION		0	237199	0	26	NEW_VARIANT
P-0032998-T01-IM6	TSC1 (NM_000368) rearrangement: c.2502+103_c.2626-1469del	PRECISE	Note: The TSC1 rearrangement results in the deletion of exon 20. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1263	0	32	9	Intron of TSC1(-):1Kb before exon 21	TSC1	135774466			9	Intron of TSC1(-):102bp after exon 19	TSC1	135776873			10	DELETION		2407	237197	314	32	NEW_VARIANT
P-0033034-T01-IM6	ENOSF1 (NM_017512) - TP53 (NM_000546) Rearrangement: t(17;18)(p13.1;p11.32)(chr17:g.7577544::chr18:g.687063)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ENOSF1:TP53}		0	1	68	18	Intron of ENOSF1(-):1Kb before exon 10	ENOSF1	687063			17	Exon 7 of TP53(-)	TP53	7577544			10	TRANSLOCATION		0	237350	0	69	NEW_VARIANT
P-0033034-T01-IM6	ERBB4 (NM_005235) Rearrangemnet: chr2:g.126960119_c.1198+52:ERBB4inv	PRECISE	Note: The ERBB4 rearrangement is an inversion of ERBB4 exons 11 to 28. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		215959	0	7	2	IGR: 453Kb before GYPC(+)	GYPC	126960119			2	Intron of ERBB4(-):51bp after exon 10	ERBB4	212569991			8	INVERSION		85609872	237349	243518	7	NEW_VARIANT
P-0033083-T01-IM6	MEF2B (NM_001145785) rearrangement: chr19:g.18686772_c.817dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		43194	0	16	19	3-UTR of UBA52(+):3Kb after coding stop	UBA52	18686772			19	Exon 8 of MEF2B(-)	MEF2B	19257146			10	DUPLICATION		570374	237489	69392	16	NEW_VARIANT
P-0033083-T01-IM6	MDC1 (NM_014641) rearrangement: c.5224_chr6:g.30794463dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	-		42078	0	7	6	Exon 10 of MDC1(-)	MDC1	30671736			6	IGR: 56Kb before DDR1(+)	DDR1	30794463			0	DUPLICATION		122727	237487	66456	7	NEW_VARIANT
P-0033083-T01-IM6	BTK (NM_000061) - RPL36A-HNRNPH2 (NM_001199974) rearrangement : c.681:BTK_c.285+5720:RPL36A-HNRNPH2 dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		11510	0	12	X	Exon 8 of BTK(-)	BTK	100615651			X	Intron of RPL36A-HNRNPH2(+):2Kb after exon 4	RPL36A-HNRNPH2	100652530			10	DUPLICATION		36879	237490	15489	12	NEW_VARIANT
P-0033167-T01-IM6	DNMT1 (NM_001379) - CACNA1A (NM_001127222) rearrangement: c.635+105:DNMT1_c.293+21068:CACNA1A dup	PRECISE	Note: The DNMT1 - CACNA1A rearrangement is a duplication that results in the fusion of DNMT1 exons 1-7 with CACNA1A exons 2-47	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {DNMT1:CACNA1A}		139600	0	57	19	Intron of DNMT1(-):104bp after exon 7	DNMT1	10284442			19	Intron of CACNA1A(-):21Kb after exon 1	CACNA1A	13595678			10	DUPLICATION		3311236	238020	288222	59	NEW_VARIANT
P-0033175-T01-IM6	FOXA1 (NM_004496) rearrangement: c.73-32_chr14:g.40100185del	PRECISE	Note: The FOXA1 rearrangement is a deletion that includes FOXA1 exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5224	0	3	14	Intron of FOXA1(-):32bp before exon 2	FOXA1	38061948			14	IGR: 235Kb before FBXO33(-)	FBXO33	40100185			7	DELETION		2038237	237999	8270	3	NEW_VARIANT
P-0033301-T01-IM6	RET (NM_020975) rearrangement: c.2137-171:RET_chr10:g.43288718inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		98040	0	149	10	Intron of BMS1(+):126bp after exon 8	BMS1	43288718			10	Intron of RET(+):170bp before exon 12	RET	43611861			10	INVERSION		323143	238823	87511	178	NEW_VARIANT
P-0033302-T01-IM6	STAG2 (NM_001042749) rearrangement: c.3278-1254_c.3467+25inv	PRECISE	Note: The STAG2 rearrangement is an intragenic inversion of exon 31. The functional significance is undetermined	MANUAL_OK	5to5	5to5	-		2037	0	24	X	Intron of STAG2(+):1Kb before exon 31	STAG2	123223171			X	Intron of STAG2(+):25bp after exon 31	STAG2	123224639			10	INVERSION		1468	238826	2958	24	NEW_VARIANT
P-0033464-T01-IM6	GRIN2A (NM_001134407) rearrangement: c.1778-112_c.2007+1330inv	PRECISE	Note: The GRIN2A rearrangement is an inversion of exon 9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2355	0	53	16	Intron of GRIN2A(-):1Kb after exon 9	GRIN2A	9921950			16	Intron of GRIN2A(-):112bp before exon 9	GRIN2A	9923621			10	INVERSION		1671	240996	7679	53	NEW_VARIANT
P-0033474-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.2411-55_c.2792+25Ginv	PRECISE	Note: The NOTCH3 rearrangement is an intragenic inversion of exons 16-17. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		5406	0	10	19	Intron of NOTCH3(-):24bp after exon 17	NOTCH3	15292362			19	Intron of NOTCH3(-):55bp before exon 16	NOTCH3	15295316			10	INVERSION		2954	240985	6409	12	NEW_VARIANT
P-0033474-T01-IM6	NOTCH3 (NM_000435) - BRD4 (NM_058243) rearrangement: c.2661:NOTCH3_c.1551+151:BRD4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		78006	0	26	19	Exon 17 of NOTCH3(-)	NOTCH3	15292518			19	Intron of BRD4(-):150bp after exon 8	BRD4	15367624			10	INVERSION		75106	240986	97294	26	NEW_VARIANT
P-0033474-T01-IM6	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.793+1788:EWSR1_c.526-940:AP1B1dup	PRECISE	Note: The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 10-18 and AP1B1 exons 6-23. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		66393	0	18	22	Intron of EWSR1(+):136bp after exon 9	EWSR1	29684911			22	Intron of AP1B1(-):940bp before exon 6	AP1B1	29753545			10	DUPLICATION		68634	240984	83446	23	NEW_VARIANT
P-0033554-T01-IM6	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)	PRECISE	Note: The TMPRSS2 - ETV1 fusion is predicted to be in frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:ETV1}		0	0	73	21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871598			7	Intron of ETV1(-):13Kb before exon 6	ETV1	13992250			10	TRANSLOCATION		0	243201	0	74	NEW_VARIANT
P-0033555-T01-IM6	EWSR1 (NM_013986) - AP1B1 (NM_001127) rearrangement: c.1309+253:EWSR1_c.2163+658:AP1B1dup	PRECISE	Note; The EWSR1 - AP1B1 rearrangement is a duplication that includes EWSR1 exons 13-18 and AP1B1 exons 17-23. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		8962	0	122	22	Intron of EWSR1(+):253bp after exon 13	EWSR1	29692611			22	Intron of AP1B1(-):657bp after exon 15	AP1B1	29734321			10	DUPLICATION		41710	243225	20839	126	NEW_VARIANT
P-0033555-T01-IM6	PHF7 (NM_016483) - PBRM1 (NM_018313) rearrangement: c.413+146:PHF7_c.3459-124:PBRM1dup	PRECISE	Note: The PHF7 - PBRM1 rearrangement is a duplication that includes PHF7 exons 7-11 and PBRM1 exons 23-30. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		12705	0	27	3	Intron of PHF7(+):146bp after exon 6	PHF7	52454597			3	Intron of PBRM1(-):124bp before exon 23	PBRM1	52610838			10	DUPLICATION		156241	243223	31395	27	NEW_VARIANT
P-0033597-T01-IM6	SLC2A5 (NM_003039) - PIK3CD (NM_005026) rearrangement: c.294-3232:SLC2A5_c.2830:PIK3CDdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		34125	0	20	1	Intron of SLC2A5(-):3Kb before exon 4	SLC2A5	9111025			1	Exon 22 of PIK3CD(+)	PIK3CD	9784445			10	DELETION		673420	243352	33426	21	NEW_VARIANT
P-0033597-T01-IM6	NF1 (NM_001042492) rearrangement: c.8202_c.8378-604del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exon 57. One of the breakpoints is within exon.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2495	0	12	17	Exon 57 of NF1(+)	NF1	29687546			17	Intron of NF1(+):603bp before exon 58	NF1	29700427			10	DELETION		12881	243354	2372	12	NEW_VARIANT
P-0033602-T01-IM6	CDKN2A (NM_000077) rearrangement: c.-3363_c.225del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2419	0	15	9	Exon 2 of CDKN2A(-)	CDKN2A	21971133			9	Intron of CDKN2A(-):7Kb before exon 2	CDKN2A	21978189			0	DELETION		7056	243341	2916	23	NEW_VARIANT
P-0033630-T01-IM6	RECQL (NM_032941) rearrangement: c.1715_chr12:g.34134949dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		32015	0	4	12	Exon 15 of RECQL(-)	RECQL	21623985			12	IGR: 40Kb before ALG10(+)	ALG10	34134949			10	DUPLICATION		12510964	243704	43566	8	NEW_VARIANT
P-0033630-T01-IM6	NCOR1 (NM_006311) rearrangement: c.909_c.1083-1312inv	IMPPRECISE	Note: The NCOR1 rearrangement is an intragenic inversion of exons 9-10. One of the breakpoints is within exon 9.	MANUAL_OK	5to5	5to5	Antisense Fusion		1737	0	7	17	Intron of NCOR1(-):1Kb before exon 11	NCOR1	16048322			17	Exon 9 of NCOR1(-)	NCOR1	16052765			0	INVERSION		4443	243705	2314	9	NEW_VARIANT
P-0033635-T01-IM6	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangemnet: c.203-15769:LOH12CR1_c.464-2376:ETV6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {LOH12CR1:ETV6}		133132	0	6	12	Intron of ETV6(+):2Kb before exon 5	ETV6	12019982			12	Intron of LOH12CR1(+):16Kb before exon 3	LOH12CR1	12572793			10	DUPLICATION		552811	243677	114862	6	NEW_VARIANT
P-0033690-T01-IM6	KMT2C (NM_170606) rearrangement: c.9570_c.14343+1412dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		29496	0	24	7	Intron of KMT2C(-):1Kb after exon 55	KMT2C	151840386			7	Exon 42 of KMT2C(-)	KMT2C	151864411			10	DUPLICATION		24025	244146	39599	24	NEW_VARIANT
P-0033720-T01-IM6	KMT2B (NM_014727) Rearrangement :chr19:g.35558580_c.364-2:KMT2Bdel	PRECISE	Note: The KMT2B (NM_014727) Rearrangement results in the deletion of exons 1-2 of KMT2B. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1708	0	5	19	3-UTR of HPN-AS1(-):39Kb after coding stop	HPN-AS1	35558580			19	Intron of KMT2B(+):1bp before exon 2	KMT2B	36210369			10	DELETION		651789	245028	1276	7	NEW_VARIANT
P-0033726-T01-IM6	PTEN (NM_000314) Rearrangement : c.165-610_c.621del	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		5896	0	6	10	Intron of PTEN(+):609bp before exon 3	PTEN	89684660			10	Exon 6 of PTEN(+)	PTEN	89712003			0	DUPLICATION		27343	244975	5620	9	NEW_VARIANT
P-0033726-T01-IM6	CREBBP (NM_004380) Rearrangement: c.799-13048_c.1509dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		7681	0	73	16	Exon 6 of CREBBP(-)	CREBBP	3832749			16	Intron of CREBBP(-):13Kb before exon 3	CREBBP	3873828			10	DUPLICATION		41079	244976	11263	79	NEW_VARIANT
P-0033769-T01-IM6	ARID2 (NM_152641) rearrangement: c.4773+767_c.5364-554dup	PRECISE	Note: The ARID2 rearrangement is an intragenic duplication of exons 16-20.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : out of frame		5217	0	3	12	Intron of ARID2(+):767bp after exon 15	ARID2	46247446			12	Intron of ARID2(+):553bp before exon 21	ARID2	46298163			5	DUPLICATION		50717	245551	4982	3	NEW_VARIANT
P-0033798-T01-IM6	SETD8 (NM_020382) rearrangement: c.133-28:SETD8_chr12:g.117582663del	IMPPRECISE	Note: The SETD8 rearrangement is a deletion of exons 1-2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		58557	0	10	12	3-UTR of FBXO21(-):1Kb after coding stop	FBXO21	117582663			12	Intron of SETD8(+):27bp before exon 3	SETD8	123875149			0	DELETION		6292486	245611	46406	14	NEW_VARIANT
P-0033798-T01-IM6	KDM6A (NM_021140) rearrangement: c.3672:KDM6A_chrX:g.46333025inv	PRECISE	Note: The KDM6A rearrangement is an inversion of exons 25-29. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		6221	0	27	X	Exon 25 of KDM6A(+)	KDM6A	44949111			X	3-UTR of KRBOX4(+):23Kb after coding stop	KRBOX4	46333025			10	INVERSION		1383914	245614	8981	36	NEW_VARIANT
P-0033812-T01-IM6	ZFHX3 (NM_006885) Rearrangement : c.6957:ZFHX3_chr16:g.73684489del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		42493	1	22	16	Exon 9 of ZFHX3(-)	ZFHX3	72829624			16	IGR: 264Kb before LINC01568(+)	LINC01568	73684489			10	DELETION		854865	245701	46327	21	NEW_VARIANT
P-0033813-T01-IM6	PTPRD (NM_002839) Rearrangement : c.2322+24:PTPRD_chr9:g.26375496inv	PRECISE	Note: The PTPRD Rearrangement results in the inversion of exons 1-25 of PTPRD.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		43041	0	14	9	Intron of PTPRD(-):23bp after exon 25	PTPRD	8499623			9	IGR: 309Kb before LOC100506422(+)	LOC100506422	26375496			10	INVERSION		17875873	245690	26908	15	NEW_VARIANT
P-0033816-T01-IM6	APC (NM_000038) Rearrangement : c.4549_c.7693del	PRECISE	Note: The APC Rearrangement results in the intragenic  partial deletion of exon16. Both the breakpoints are within exon16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11451	0	48	5	Exon 16 of APC(+)	APC	112175840			5	Exon 16 of APC(+)	APC	112178984			10	DELETION		3144	245721	7041	54	NEW_VARIANT
P-0033821-T01-IM6	TP53 (NM_000546) Rearrangement : t(14,17)(q11.2; q12)(chr14:g.23619168::chr17:g.7578709)	PRECISE	The TP53 (NM_000546) Rearrangement is a translocation event with the breakpoint in intron 4.Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	32	17	Intron of TP53(-):155bp before exon 5	TP53	7578709			14	Intron of SLC7A8(-):7Kb before exon 4	SLC7A8	23619168			10	TRANSLOCATION		0	245712	0	31	NEW_VARIANT
P-0033890-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-616:CDKN2Ap16INK4A_chr9:g.22217818del	PRECISE	Note: The CDKN2A rearrangement is a deletion of exons 1-2. This affects the CDKN2Ap16INK4A (NM_000077) transcript.	MANUAL_OK	3to5	3to5	-		13996	0	47	9	Intron of CDKN2A(-):616bp before exon 3	CDKN2A	21968857			9	IGR: 215Kb before CDKN2B(-)	CDKN2B	22217818			10	DELETION		248961	248665	10403	51	NEW_VARIANT
P-0033934-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+665:TMPRSS2_c.40-58822:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		91987	0	3	21	Intron of ERG(-):59Kb before exon 4	ERG	39876366			21	Intron of TMPRSS2(-):664bp after exon 1	TMPRSS2	42879212			8	DELETION		3002846	246900	96507	3	NEW_VARIANT
P-0033934-T01-IM6	RBM33 (NM_053043) - KMT2C (NM_170606) rearrangement: c.123-2768:RBM33_c.6361:KMT2Cinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {RBM33:KMT2C}		56072	0	4	7	Exon 36 of KMT2C(-)	KMT2C	151878584			7	Intron of RBM33(+):3Kb before exon 3	RBM33	155462793			10	INVERSION		3584209	246902	48363	4	NEW_VARIANT
P-0033937-T01-IM6	RPTOR (NM_020761) rearrangement: c.163-35973_c.3266-132del	PRECISE	Note: The RPTOR rearrangement results in the deletion of exons 2-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 26 exons : out of frame		47462	0	3	17	Intron of RPTOR(+):36Kb before exon 2	RPTOR	78563518			17	Intron of RPTOR(+):131bp before exon 28	RPTOR	78923111			10	DELETION		359593	246904	29268	3	NEW_VARIANT
P-0033953-T01-IM6	DNM3 (NM_015569) - SPEN (NM_015001) rearrangement: c.1770-16871:DNM3_c.8790:SPENdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNM3:SPEN}		718733	0	66	1	Exon 11 of SPEN(+)	SPEN	16261525			1	Intron of DNM3(+):17Kb before exon 16	DNM3	172260997			10	DUPLICATION		155999472	246929	753275	69	NEW_VARIANT
P-0033962-T01-IM6	PLCD3 (NM_133373) - MAP3K14(NM_003954) Rearrangement: c.163+24:PLCD3_c.2611: MAP3K14dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PLCD3:MAP3K14}		3091	0	34	17	Intron of PLCD3(-):23bp after exon 1	PLCD3	43209591			17	Exon 15 of MAP3K14(-)	MAP3K14	43342597			10	DUPLICATION		133006	247270	4158	36	NEW_VARIANT
P-0034025-T01-IM6	ASXL1 (NM_015338) Rearrangement: c.2110:ASXL1_chr20:g.31423707inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		41159	0	19	20	Exon 12 of ASXL1(+)	ASXL1	31022625			20	Intron of MAPRE1(+):732bp before exon 4	MAPRE1	31423707			10	INVERSION		401082	247733	58934	31	NEW_VARIANT
P-0034031-T01-IM6	EWSR1 (NM_013986) - AP1B1 (NM_001127) Rearrangement: c.811+32:EWSR1_c.1437+1202:AP1B1dup	PRECISE	Note: The EWSR1 - AP1B1 rearrangement is a duplication of EWSR1 exons 9 to 18 and AP1B1 exons 12-23. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		57650	0	17	22	Intron of EWSR1(+):32bp after exon 8	EWSR1	29683155			22	Intron of AP1B1(-):1Kb after exon 11	AP1B1	29744005			10	DUPLICATION		60850	247814	103441	17	NEW_VARIANT
P-0034157-T02-IM6	CDK12 (NM_016507) rearrangement: c.3559:CDK12_chr17:g.61753552inv	PRECISE	Note: The CDK12 rearrangement is an inversion of exons 13-14. One of the breakpoints is within exon 13. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		333372	0	59	17	Exon 13 of CDK12(+)	CDK12	37682368			17	Intron of MAP3K3(+):6Kb before exon 7	MAP3K3	61753552			10	INVERSION		24071184	254653	474719	89	NEW_VARIANT
P-0034183-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion (FGFR3 exons 1-18 fused to TACC3 exons 7-16): c.2346:FGFR3_c.1591+1975dup	PRECISE	Note: The FGFR3 -TACC3 fusion includes the kinase domain of FGFR3. One of the breakpoints is within FGFR3 exon 18.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		36599	0	102	4	Intron of TACC3(+):2Kb after exon 6	TACC3	1735003			4	Exon 18 of FGFR3(+)	FGFR3	1808914			10	DUPLICATION		73911	249546	47221	118	NEW_VARIANT
P-0034278-T01-IM6	CIC (NM_015125) rearrangment: c.1019:CIC_chr19:g.45393207inv	PRECISE	Note: The CIC rearrangement is an inversion of exons 7-20. One of the breakpoints is within exon 7.	MANUAL_OK	5to5	5to5	-		35692	0	3	19	Exon 7 of CIC(+)	CIC	42793127			19	Promoter of PVRL2(+):44Kb from tx start	PVRL2	45393207			7	INVERSION		2600080	250284	43634	4	NEW_VARIANT
P-0034298-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2967:TMPRSS2_c.-149-4226:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	-		76186	0	50	21	3-UTR of ERG(-):73Kb after coding stop	ERG	39961095			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873083			10	DELETION		2911988	250420	53655	53	NEW_VARIANT
P-0034356-T01-IM6	CDK12 (NM_016507) rearrangement: c.-1342_c.467del	PRECISE	Note: The CDK12 rearrangement results in the deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1963	0	35	17	Promoter of CDK12(+):780bp from tx start	CDK12	37616983			17	Exon 1 of CDK12(+)	CDK12	37618791			10	DELETION		1808	250423	2292	35	NEW_VARIANT
P-0034431-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-2658:TMPRSS2_c.18+15598:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be out of frame.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		58116	0	134	21	Intron of ERG(-):16Kb after exon 1	ERG	39854689			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872774			10	DELETION		3018085	250774	50906	144	NEW_VARIANT
P-0034450-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon13 fused with ALK exons 20) : c.1641+555:EML4_c.3213:ALKinv	PRECISE	Note: The EML4-ALK fusion includes the protein kinase domain of ALK. The breakpoint in ALK is within exon 20	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		112791	0	55	2	Exon 20 of ALK(-)	ALK	29446354			2	Intron of EML4(+):555bp after exon 13	EML4	42529087			10	INVERSION		13082733	250787	46713	52	NEW_VARIANT
P-0034464-T01-IM6	CDC73 (NM_024529) rearrangement: c.776_c.1031-3046del	PRECISE	Note: The CDC73 rearrangement is an intragenic deletion of exons 8-11. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2340	0	4	1	Exon 8 of CDC73(+)	CDC73	193117043			1	Intron of CDC73(+):3Kb before exon 12	CDC73	193178149			10	DELETION		61106	250813	3719	4	NEW_VARIANT
P-0034464-T01-IM6	FANCA (NM_000135) rearrangement: chr16:g.85711453_c.3066+129del	PRECISE	Note: The FANCA rearrangement is a deletion that includes FANCA exons 32 - 43.	MANUAL_OK	3to5	3to5	-		83136	0	10	16	3-UTR of GINS2(-):364bp after coding stop	GINS2	85711453			16	Intron of FANCA(-):128bp after exon 31	FANCA	89818417			10	DELETION		4106964	250814	107158	10	NEW_VARIANT
P-0034464-T01-IM6	PTCH1 (NM_000264) - UPP2 (NM_001135098) rearrangement: t(2;9)(q24.1;q22.32)(chr2:g.158929185::chr9:g.98212161)	PRECISE	Note: The PTCH1 - UPP2 rearrangement is a translocation with breakpoints within PTCH1 exon 21 and UPP2 intron 2.	MANUAL_OK	3to5	3to5	-		0	0	5	9	Exon 21 of PTCH1(-)	PTCH1	98212161			2	Intron of UPP2(+):29Kb before exon 3	UPP2	158929185			10	TRANSLOCATION		0	250815	0	5	NEW_VARIANT
P-0034506-T01-IM6	ARID2 (NM_152641) rearrangement: c.705+25_chr12:g.47316536del	IMPPRECISE	Note: The ARID2 rearrangement results in the deletion of exons 7-21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		33527	0	6	12	Intron of ARID2(+):25bp after exon 6	ARID2	46215295			12	IGR: 153Kb before AMIGO2(-)	AMIGO2	47316536			0	DELETION		1101241	251422	30596	6	NEW_VARIANT
P-0034515-T01-IM6	NCOR1 (NM_006311) - WASF2 (NM_006990) rearrangement: t(1;17)(p36.11;p12)(chr1:g.27748183::chr17:g.15983299)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NCOR1:WASF2}		0	0	25	17	Exon 26 of NCOR1(-)	NCOR1	15983299			1	Intron of WASF2(-):3Kb before exon 3	WASF2	27748183			10	TRANSLOCATION		0	251509	0	45	NEW_VARIANT
P-0034577-T01-IM6	STK11 (NM_000455) rearrangement: t(16;19)(p13.3;p13.3)(chr16:g.762979::chr19:g.1221857)	IMPPRECISE	Note: The STK11 rearrangement is a translocation with a breakpoint in intron 6. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {METRN:STK11}		0	0	9	19	Intron of STK11(+):90bp before exon 7	STK11	1221857			16	Promoter of METRN(+):2Kb from tx start	METRN	762979			0	TRANSLOCATION		0	252090	0	9	NEW_VARIANT
P-0034609-T01-IM6	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+175:EZR_c.5557+143:ROS1del	PRECISE	Note: The EZR - ROS1 rearrangement is a deletion which forms a fusion of EZR exons 1-9 with ROS1 exons 34-43.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EZR:ROS1}		270871	0	48	6	Intron of ROS1(-):142bp after exon 33	ROS1	117647244			6	Intron of EZR(-):174bp after exon 9	EZR	159191621			10	DELETION		41544377	252456	269575	51	NEW_VARIANT
P-0034620-T01-IM6	CSK (NM_001127190) - TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q24.1;q22.3)(chr15:g.75094115::chr21:g.42875844)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CSK:TMPRSS2}		0	0	9	21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875844			15	Exon 12 of CSK(+)	CSK	75094115			10	TRANSLOCATION		0	252571	0	8	NEW_VARIANT
P-0034620-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3990:TMPRSS2_c.18+9776:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion which forms a fusion of TMPRSS2 exons 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		87488	0	5	21	Intron of ERG(-):10Kb after exon 1	ERG	39860511			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42875887			0	DELETION		3015376	252568	55467	5	NEW_VARIANT
P-0034651-T01-IM6	ARID2 (NM_152641) rearrangement: c.285-34697_c.2302del	PRECISE	Note: The ARID2 rearrangement is an intragenic deletion of exons 4-15. One of the breakpoints is withiin exon 15.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17616	0	43	12	Intron of ARID2(+):35Kb before exon 4	ARID2	46170504			12	Exon 15 of ARID2(+)	ARID2	46244208			10	DELETION		73704	252780	15490	49	NEW_VARIANT
P-0034651-T01-IM6	CDKN1A (NM_078467) rearrangement: c.446-99:CDKN1A_chr6:g.36650568del	IMPPRECISE	Note: The CDKN1A rearrangement is a deletion of exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript		5734	0	62	6	5-UTR of CDKN1A(+):1Kb before coding start	CDKN1A	36650568			6	Intron of CDKN1A(+):98bp before exon 4	CDKN1A	36653429			0	DELETION		2861	252779	5016	63	NEW_VARIANT
P-0034667-T01-IM6	SMAD2 (NM_001003652) Rearrangement: c.655+92_chr18:g.45343181del	PRECISE	Note: The SMAD2 rearrangement is an intragenic deletion of exons 6-11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7274	0	14	18	IGR: 16Kb before SMAD2(-)	SMAD2	45343181			18	Intron of SMAD2(-):91bp after exon 5	SMAD2	45394602			10	DELETION		51421	252905	10743	16	NEW_VARIANT
P-0034684-T01-IM6	KDM2B (NM_032590) Rearrangement : t(6;12)(q21;q24.31)(chr6:g.109330448::chr12:g.121909964)	PRECISE	Note: The KDM2B Rearrangement is a translocation event with a breakpoint in intron12. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	73	12	Intron of KDM2B(-):19Kb before exon 13	KDM2B	121909964			6	Intron of SESN1(-):7Kb before exon 2	SESN1	109330448			10	TRANSLOCATION		0	252879	0	82	NEW_VARIANT
P-0034704-T01-IM6	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)	PRECISE	Note: The TRIM24-RET fusion is predicted to be in-frame and includes the kinase domain of RET	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TRIM24:RET}		0	0	143	10	Intron of RET(+):204bp before exon 12	RET	43611827			7	Intron of TRIM24(+):3Kb after exon 9	TRIM24	138243011			10	TRANSLOCATION		0	253565	0	145	NEW_VARIANT
P-0034708-T01-IM6	KIF13B (NM_015254) - DUSP4 (NM_001394) Rearrangement : c.149+15289:KIF13B_c.433+4346:DUSP4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {KIF13B:DUSP4}		11711	0	14	8	Intron of KIF13B(-):15Kb after exon 2	KIF13B	29087574			8	Intron of DUSP4(-):4Kb after exon 1	DUSP4	29203017			10	DUPLICATION		115443	253570	15519	14	NEW_VARIANT
P-0034727-T01-IM6	PBRM1 (NM_018313) Rearrangement : c.645+2057_c.868del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3447	0	24	3	Exon 9 of PBRM1(-)	PBRM1	52678751			3	Intron of PBRM1(-):2Kb after exon 6	PBRM1	52690158			10	DELETION		11407	253005	1137	25	NEW_VARIANT
P-0034733-T01-IM6	ALK (NM_004304) Rearrangement : c.3172+337_c.3359+71del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		22278	0	49	2	Intron of ALK(-):70bp after exon 20	ALK	29446137			2	Intron of ALK(-):336bp after exon 19	ALK	29447990			10	DELETION		1853	252993	15425	53	NEW_VARIANT
P-0034750-T01-IM6	CCNE1 (NM_001238) rearrangement: c.283:CCNE1_chr19:g.30915262inv	IMPPRECISE	Note: The CCNE1 rearrangement is an inversion of exons 5-12. One of the breakpoints is within exon 5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		11902	0	6	19	Exon 5 of CCNE1(+)	CCNE1	30308146			19	5-UTR of ZNF536(+):19Kb before coding start	ZNF536	30915262			0	INVERSION		607116	253728	12348	6	NEW_VARIANT
P-0034763-T01-IM6	FAT (NM_005245) Rearrangement : c.9853+481_c.10960inv	PRECISE	Note: The FAT Rearrangement results in the inversion of exons 15-19. One of the breakpoints is within exon19. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		10711	0	54	4	Exon 19 of FAT1(-)	FAT1	187524720			4	Intron of FAT1(-):480bp after exon 14	FAT1	187532059			10	INVERSION		7339	253420	12174	55	NEW_VARIANT
P-0034773-T01-IM6	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.812-463:EWSR1_c.1205-1206:EMID1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {EWSR1:EMID1}		5156	0	3	22	Intron of EMID1(+):1Kb before exon 15	EMID1	29653600			22	Intron of EWSR1(+):462bp before exon 9	EWSR1	29684132			10	DUPLICATION		30532	253579	1746	3	NEW_VARIANT
P-0034796-T01-IM6	PMS2 (NM_000535) rearrangement: c.667:PMS2_chr7:g.11273145inv	PRECISE	Note: The PMS2 rearrangement is an inversion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		19688	0	27	7	Exon 6 of PMS2(-)	PMS2	6038777			7	IGR: 137Kb before THSD7A(-)	THSD7A	11273145			10	INVERSION		5234368	253624	30543	28	NEW_VARIANT
P-0034815-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3040:TMPRSS2_c.18+3720:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		58346	0	23	21	Intron of ERG(-):4Kb after exon 1	ERG	39866567			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873156			10	DELETION		3006589	253701	40209	27	NEW_VARIANT
P-0034845-T01-IM6	SND1 (NM_014390) - BRAF (NM_004333) rearrangement: c.1527+3658:SND1_c.1141-1857:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SND1:BRAF}		96441	0	93	7	Intron of SND1(+):4Kb after exon 14	SND1	127548530			7	Intron of BRAF(-):2Kb before exon 9	BRAF	140489241			10	INVERSION		12940711	254263	128974	90	NEW_VARIANT
P-0034865-T01-IM6	OSBPL1A (NM_080597) - TMPRSS2 (NM_001135099) rearrangement: t(18;21)(q11.2;q22.3)(chr18:g.21746075::chr21:g.42874744)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {OSBPL1A:TMPRSS2}		0	0	33	21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874744			18	Intron of OSBPL1A(-):467bp after exon 14	OSBPL1A	21746075			10	TRANSLOCATION		0	254495	0	34	NEW_VARIANT
P-0034865-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4544:TMPRSS2_c.40-63678:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		44130	0	54	21	Intron of ERG(-):64Kb before exon 4	ERG	39881222			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874660			10	DELETION		2993438	254494	58290	59	NEW_VARIANT
P-0034917-T01-IM6	MDC1 (NM_014641) rearrangement: t(6;12)(p21.33;q14.1)(chr6:g.30680394::chr12:g.61245740)	IMPPRECISE	Note: The MDC1 rearrangement is a translocation involving a breakpoint in exon 5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	13	12	IGR: 856Kb before FAM19A2(-)	FAM19A2	61245740			6	Exon 5 of MDC1(-)	MDC1	30680394			0	TRANSLOCATION		0	254641	0	13	NEW_VARIANT
P-0034928-T01-IM6	PRKCI (NM_002740) rearrangement: c.224-1:PRKCI_chr3:g.169756755del	PRECISE	Note: The PRKCI rearrangement is a deletion of exons 1-3. One of the breakpoints is within exon 3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GPR160:PRKCI}		3209	0	16	3	5-UTR of GPR160(+):45Kb before coding start	GPR160	169756755			3	Exon 3 of PRKCI(+)	PRKCI	169977756			10	DELETION		221001	254703	3934	21	NEW_VARIANT
P-0034975-T01-IM6	KDM5A (NM_001042603) rearrangement: c.4139:KDM5A_chr12:g.14309266inv	PRECISE	Note: The KDM5A rearrangement is an inversion of exons 1-25. One of the breakpoints is within exon 25. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		292583	0	6	12	Exon 25 of KDM5A(-)	KDM5A	406302			12	IGR: 209Kb before ATF7IP(+)	ATF7IP	14309266			6	INVERSION		13902964	254885	494020	6	NEW_VARIANT
P-0035065-T01-IM6	NCOR1 (NM_006311) rearrangement: c.1082+54_c.1174-1771del	IMPPRECISE	Note: The NCOR1 rearrangement is an intragenic deletion of exon 11.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		985	0	7	17	Intron of NCOR1(-):2Kb before exon 12	NCOR1	16044271			17	Intron of NCOR1(-):53bp after exon 10	NCOR1	16049636			0	DELETION		5365	255427	1073	7	NEW_VARIANT
P-0035065-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4830:TMPRSS2_c.39+38144:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		76223	0	65	21	Intron of ERG(-):38Kb after exon 3	ERG	39909442			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875047			10	DELETION		2965605	255428	50724	70	NEW_VARIANT
P-0035078-T01-IM6	AGO2 (NM_012154): c.1840-54_chr8: g.142022551del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		24559	0	6	8	Intron of AGO2(-):54bp before exon 15	AGO2	141551511			8	IGR: 116Kb before DENND3(+)	DENND3	142022551			0	DELETION		471040	255517	25136	6	NEW_VARIANT
P-0035093-T01-IM6	YAP1 (NM_001130145) rearrangement: t(1;11)(p12;q22.1)(chr1:g.119374897::chr11:g.102076978)	IMPPRECISE	Note: The YAP1 rearrangement is a translocation with a breakpoint in YAP1 intron 5. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	11	Intron of YAP1(+):173bp after exon 5	YAP1	102076978			1	IGR: 51Kb before TBX15(-)	TBX15	119374897			0	TRANSLOCATION		0	255750	0	7	NEW_VARIANT
P-0035107-T01-IM6	BCL2(NM_000633)  Rearrangement : c.420:BCL2_chr18:g.61340025inv	PRECISE	Note: The BCL2(NM_000633)  Rearrangement results in the inversion of exon2.The breakpoint is within exon2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2756	0	48	18	Exon 2 of BCL2(-)	BCL2	60985480			18	IGR: 18Kb before SERPINB3(-)	SERPINB3	61340025			10	INVERSION		354545	255745	3147	48	NEW_VARIANT
P-0035118-T01-IM6	DCUN1D1 (NM_020640) rearrangement: t(3;6)(q26.33;q16.3)(chr3:g.182683416::chr6:g.100978161)	IMPPRECISE	Note: The DCUN1D1 rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	5	6	Intron of ASCC3(-):10Kb after exon 37	ASCC3	100978161			3	Exon 2 of DCUN1D1(-)	DCUN1D1	182683416			0	TRANSLOCATION		0	257646	0	6	NEW_VARIANT
P-0035118-T01-IM6	KDM6A (NM_021140) rearrangement: c.45:KDM6A_chrX:g.48353211inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		119117	0	23	X	Exon 1 of KDM6A(+)	KDM6A	44732842			X	IGR: 14Kb before PORCN(+)	PORCN	48353211			10	INVERSION		3620369	257645	93143	34	NEW_VARIANT
P-0035151-T01-IM6	APC (NM_000038) Rearrangement : t(5;13)(q22.1;q13.2)(chr5:g.112173891::chr13:g.105759777)	PRECISE	Note: The APC Rearrangement is a translocation event with a breakpoint in exon16. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	9	13	IGR: 352Kb before DAOA-AS1(-)	DAOA-AS1	105759777			5	Exon 16 of APC(+)	APC	112173891			10	TRANSLOCATION		0	255855	0	8	NEW_VARIANT
P-0035160-T01-IM6	POLD1 (NM_002691) rearrangement: c.2155-1243_c.3068-135del	PRECISE	Note: The POLD1 rearrangement is an intragenic deletion of exons 18-24. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : out of frame		12629	0	5	19	Intron of POLD1(+):1Kb before exon 18	POLD1	50915440			19	Intron of POLD1(+):134bp before exon 25	POLD1	50920167			10	DELETION		4727	255887	8040	5	NEW_VARIANT
P-0035160-T01-IM6	TEK (NM_000459) - DDX58 (NM_014314) rearrangement: c.610:TEK_c.1103:DDX58inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TEK:DDX58}		38773	0	9	9	Exon 4 of TEK(+)	TEK	27169609			9	Exon 8 of DDX58(-)	DDX58	32488052			10	INVERSION		5318443	255888	38979	8	NEW_VARIANT
P-0035170-T01-IM6	KDM6A (NM_021140) - PIGL (NM_004278) Rearrangement : t(X,17)(p11.23; p12) (chrX:g.44949188::chr17:g.16127247)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KDM6A:PIGL}		0	0	12	X	Intron of KDM6A(+):13bp after exon 25	KDM6A	44949188			17	Intron of PIGL(+):6Kb after exon 1	PIGL	16127247			10	TRANSLOCATION		0	256117	0	12	NEW_VARIANT
P-0035221-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4689:TMPRSS2_c.39+50100:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52824	0	11	21	Intron of ERG(-):50Kb after exon 3	ERG	39897486			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874805			10	DELETION		2977319	256938	34197	11	NEW_VARIANT
P-0035288-T01-IM6	RICTOR (NM_152756) rearrangement: c.-712_c.4662del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		27839	0	11	5	Exon 35 of RICTOR(-)	RICTOR	38945142			5	Promoter of RICTOR(-):137Kb from tx start	RICTOR	39075191			10	DELETION		130049	257635	21872	11	NEW_VARIANT
P-0035378-T01-IM6	BRCA1 (NM_007294) - CA10 (NM_001082533) rearrangement: c.547+98:BRCA1_c.280-78647:CA10dup	PRECISE	Note: The BRCA1 - CA10 rearrangement is a duplication that may result in the fusion of BRCA1 exons 1-7 with CA10 exons 5-10	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BRCA1:CA10}		92841	0	10	17	Intron of BRCA1(-):97bp after exon 7	BRCA1	41251694			17	Intron of CA10(-):79Kb before exon 4	CA10	49903825			10	DUPLICATION		8652131	258065	57449	10	NEW_VARIANT
P-0035378-T01-IM6	IRAK2 (NM_001570) - VHL (NM_000551) : c.95-834:IRAK2_c.568:VHLdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {IRAK2:VHL}		2676	0	4	3	Exon 3 of VHL(+)	VHL	10191575			3	Intron of IRAK2(+):833bp before exon 2	IRAK2	10218688			10	DUPLICATION		27113	258064	2003	11	NEW_VARIANT
P-0035383-T01-IM6	BAP1 (NM_004656) rearrangement: chr3:g.3:52432893_c.803del	PRECISE	Note: The BAP1 rearrangement is a deletion that includes BAP1 exons 10-17. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14736	0	22	3	Promoter of BAP1(-):2Kb from tx start	BAP1	52432893			3	Exon 10 of BAP1(-)	BAP1	52439909			10	DELETION		7016	258052	5129	23	NEW_VARIANT
P-0035516-T01-IM6	STK11 (NM_000455) rearrangement: c.598-4_c.921-51inv	PRECISE	Note: The ATK11 rearrangement is an intragenic inversion of exons 5-7. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		4634	0	15	19	Intron of STK11(+):3bp before exon 5	STK11	1220576			19	Intron of STK11(+):50bp before exon 8	STK11	1222933			10	INVERSION		2357	258862	6867	15	NEW_VARIANT
P-0035527-T01-IM6	RB1 (NM_000321) rearrangement: c.2656:RB1_chr13:g.34574296inv	PRECISE	Note: The RB1 rearrangement is an inversion of exons 1-25. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		37825	0	55	13	IGR: 182Kb before RFC3(+)	RFC3	34574296			13	Exon 25 of RB1(+)	RB1	49050972			10	INVERSION		14476676	258876	18552	53	NEW_VARIANT
P-0035527-T01-IM6	TP53 (NM_000546) rearrangement: c.920-44:TP53_chr17:g.7581782del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 1-8.	MANUAL_OK	3to5	3to5	Deletion within transcript		12150	0	26	17	Intron of TP53(-):44bp before exon 9	TP53	7576970			17	5-UTR of TP53(-):9Kb before coding start	TP53	7581782			10	DELETION		4812	258874	8566	37	NEW_VARIANT
P-0035528-T01-IM6	RNF43 (NM_017763)  rearrangement: c.253-14455_c.1745del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14966	0	37	17	Exon 9 of RNF43(-)	RNF43	56435392			17	Intron of RNF43(-):14Kb before exon 3	RNF43	56462849			10	DELETION		27457	258879	14230	37	NEW_VARIANT
P-0035552-T01-IM6	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)	PRECISE	Note: The ETV6 - NTRK3 Fusion is predicted to be in-frame and includes the protein kinase domain of NTRK3.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	66	15	Intron of NTRK3(-):18Kb after exon 13	NTRK3	88651251			12	Intron of ETV6(+):1Kb before exon 5	ETV6	12020963			10	TRANSLOCATION		0	259651	0	66	NEW_VARIANT
P-0035563-T01-IM6	SMARCA4 (NM_003072) - PDE4A (NM_001111307) Rearrangement : c.3959:SMARCA4_c.670+11:PDE4Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SMARCA4:PDE4A}		88021	0	6	19	Intron of PDE4A(+):11bp after exon 5	PDE4A	10561339			19	Exon 29 of SMARCA4(+)	SMARCA4	11145597			10	DUPLICATION		584258	259690	131602	6	NEW_VARIANT
P-0035563-T01-IM6	CENPP (NM_001012267) - NTRK2 (NM_006180) Rearrangement : c.468-791:CENPP_c.1765-10:NTRK2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CENPP:NTRK2}		23663	0	3	9	Intron of NTRK2(+):9bp before exon 18	NTRK2	87563367			9	Intron of CENPP(+):790bp before exon 4	CENPP	95141254			8	DUPLICATION		7577887	259689	29595	3	NEW_VARIANT
P-0035642-T01-IM6	EWSR1 (NM_013986) - TTC28 (NM_001145418) rearrangement: c.1179+1655:EWSR1_c.382-16678:TTC28del	PRECISE	Note: The EWSR1- TTC28 rearrangement is a deletion that includes EWSR1 exons 1-12 and TTC28 exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		65752	0	16	22	Intron of TTC28(-):17Kb before exon 3	TTC28	28719309			22	Intron of EWSR1(+):2Kb after exon 12	EWSR1	29690250			10	DELETION		970941	260178	65730	20	NEW_VARIANT
P-0036526-T01-IM6	HIST1H3B (NM_003537) - SIRT5 (NM_012241) rearrangement: c.243:HIST1H3B_c.654:SIRT5inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {HIST1H3B:SIRT5}		18465	0	3	6	Exon 8 of SIRT5(+)	SIRT5	13599300			6	Exon 1 of HIST1H3B(-)	HIST1H3B	26032046			8	INVERSION		12432746	269742	20638	3	NEW_VARIANT
P-0036567-T01-IM6	SND1 (NM_014390) - BRAF (NM_004333) Fusion (SND1 exon10 fused with BRAF exon9) : c.1153-22013:SND1_ c.1140+556:BRAFinv	PRECISE	Note: The SND1-BRAF Fusion is an in-frame fusion and includes the protein kinase domain of BRAF.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SND1:BRAF}		121314	0	16	7	Intron of SND1(+):22Kb before exon 11	SND1	127425525			7	Intron of BRAF(-):555bp after exon 8	BRAF	140493552			10	INVERSION		13068027	269965	191927	16	NEW_VARIANT
P-0036699-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1733:TMPRSS2_c.40-58568:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25663	0	9	21	Intron of ERG(-):59Kb before exon 4	ERG	39876112			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868238			10	DELETION		2992126	272281	16708	9	NEW_VARIANT
P-0036723-T01-IM6	DNM2 (NM_001005361) - SMARCA4 (NM_003072) fusion: c.2543+154:DNM2_c.2644:SMARCA4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNM2:SMARCA4}		53786	0	46	19	Intron of DNM2(+):154bp after exon 19	DNM2	10941208			19	Exon 19 of SMARCA4(+)	SMARCA4	11132428			10	DELETION		191220	272369	61908	46	NEW_VARIANT
P-0036757-T01-IM6	RECQL (NM_032941) rearrangement: c.501+118:RECQL_chr12:g.20757854del	PRECISE	Note: The RECQL rearrangement is a deletion of exons 7-16. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		14187	0	4	12	Intron of PDE3A(+):9Kb before exon 3	PDE3A	20757854			12	Intron of RECQL(-):117bp after exon 6	RECQL	21639295			8	DELETION		881441	272716	19600	4	NEW_VARIANT
P-0036760-T01-IM6	TP53 (NM_000546) rearrangement: c.517_c.993+73del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 5-9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5981	0	34	17	Intron of TP53(-):72bp after exon 9	TP53	7576780			17	Exon 5 of TP53(-)	TP53	7578413			10	DELETION		1633	272741	3659	106	NEW_VARIANT
P-0036791-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3503:TMPRSS2_c.18+1131:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is the result of deletion which fuses TMPRSS2 exon 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53849	0	41	21	Intron of ERG(-):1Kb after exon 1	ERG	39869156			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873619			10	DELETION		3004463	273000	70100	41	NEW_VARIANT
P-0036807-T01-IM6	KEAP1 (NM_203500) rearrangement: c.1455_c.1709-149del	PRECISE	Note: The KEAP1 rearrangement is an intragenic deletion of exons 4-5. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3316	0	130	19	Intron of KEAP1(-):149bp before exon 6	KEAP1	10597643			19	Exon 4 of KEAP1(-)	KEAP1	10600400			10	DELETION		2757	273037	1158	139	NEW_VARIANT
P-0036808-T01-IM6	PTPRD (NM_002839) - SLC1A1 (NM_004170) rearrangement: c.2409:PTPRD_c.92-21484:SLC1A1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		76529	0	9	9	Intron of SLC1A1(+):21Kb before exon 2	SLC1A1	4523083			9	Exon 27 of PTPRD(-)	PTPRD	8492920			10	DUPLICATION		3969837	273036	32596	11	NEW_VARIANT
P-0036814-T01-IM6	FUBP1 (NM_003902) rearrangement: c.474-209_c.1114dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		5380	0	35	1	Exon 13 of FUBP1(-)	FUBP1	78429328			1	Intron of FUBP1(-):209bp before exon 8	FUBP1	78431124			10	DUPLICATION		1796	273028	9782	37	NEW_VARIANT
P-0036827-T01-IM6	AXIN2 (NM_004655) rearrangement: c.-116-866_c.350del	PRECISE	Note: The AXIN2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is mid exon.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1919	0	57	17	Exon 2 of AXIN2(-)	AXIN2	63554389			17	5-UTR of AXIN2(-):30Kb before coding start	AXIN2	63555720			10	DELETION		1331	273307	1226	63	NEW_VARIANT
P-0036827-T01-IM6	APC (NM_000038): c.6528_chr5:g.112190800del	PRECISE	Note: The APC rearrangement is a deletion that includes APC exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	-		6887	0	10	5	Exon 16 of APC(+)	APC	112177819			5	IGR: 6Kb before SRP19(+)	SRP19	112190800			10	DELETION		12981	273305	3684	10	NEW_VARIANT
P-0036828-T01-IM6	NF1 (NM_001042492) rearrangement: c.1845+66_c.2326-115dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 17-19.  The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		4852	0	46	17	Intron of NF1(+):66bp after exon 16	NF1	29550651			17	Intron of NF1(+):114bp before exon 20	NF1	29554426			10	DUPLICATION		3775	273329	5076	51	NEW_VARIANT
P-0036845-T01-IM6	BAP1 (NM_004656) rearrangement: c.934_chr3:g.52446650del	PRECISE	Note: The BAP1 rearrangement is a deletion that includes BAP1 exons 1-11. One of the breakpoints is within BAP1 exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12405	0	169	3	Exon 11 of BAP1(-)	BAP1	52439308			3	Promoter of BAP1(-):12Kb from tx start	BAP1	52446650			10	DELETION		7342	273074	2713	184	NEW_VARIANT
P-0036867-T01-IM6	NKX2-1 (NM_001079668) Rearrangement : c.774_chr14:g.36676003del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3530	0	97	14	IGR: 71Kb before PTCSC3(-)	PTCSC3	36676003			14	Exon 3 of NKX2-1(-)	NKX2-1	36986915			10	DELETION		310912	274764	2829	178	NEW_VARIANT
P-0036871-T01-IM6	NF2 (NM_000268) Rearrangement : c.57_.114+4073del	PRECISE	Note: The NF2 Rearrangement results in the intragenic deletion of exon1. One of the breakpoints is within exon1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		750	0	5	22	Exon 1 of NF2(+)	NF2	30000044			22	Intron of NF2(+):4Kb after exon 1	NF2	30004174			10	DELETION		4130	274769	583	5	NEW_VARIANT
P-0036871-T01-IM6	CDKN2Ap14ARF (NM_058195) Rearrangement : c.194-3351:CDKN2Ap14ARF_chr9:g.22393377del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		11344	0	42	9	Exon 1 of CDKN2A(-)	CDKN2A	21974558			9	IGR: 53Kb before DMRTA1(+)	DMRTA1	22393377			10	DELETION		418819	274767	9364	45	NEW_VARIANT
P-0036887-T01-IM6	EZH1 (NM_001991) rearrangement: t(17;22)(q21.2;q11.23)(chr17:g.40859970::chr22:g.23513917)	PRECISE	Note: The EZH1 rearrangement is a translocation involving exon 15. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	63	22	IGR: 9Kb before BCR(+)	BCR	23513917			17	Intron of EZH1(-):5bp after exon 15	EZH1	40859970			10	TRANSLOCATION		0	275245	0	77	NEW_VARIANT
P-0036911-T01-IM6	B2M (NM_004048) Rearrangement: c.266_c.*406inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		2771	0	10	15	Exon 2 of B2M(+)	B2M	45007819			15	3-UTR of B2M(+):6Kb after coding stop	B2M	45010196			10	INVERSION		2377	273485	3130	12	NEW_VARIANT
P-0036963-T01-IM6	PAX8 (NM_003466) rearrangement: c.1189+92:PAX8_chr2:g.135527206del	PRECISE	Note: The PAX8 rearrangement is a deletion of exons 11-12. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		94172	0	63	2	Intron of PAX8(-):91bp after exon 10	PAX8	113984640			2	IGR: 69Kb before ACMSD(+)	ACMSD	135527206			10	DELETION		21542566	274648	106242	68	NEW_VARIANT
P-0036970-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q33.1;q22.1)(chr5:g.149783480::chr6:g.117650273)	PRECISE	Note: The CD74 - ROS1 rearrangement is a translocation which results in the fusion of CD74 exons 1-6 with ROS1 exons 33-43.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	3	294	6	Intron of ROS1(-):218bp after exon 32	ROS1	117650273			5	Intron of CD74(-):605bp before exon 7	CD74	149783480			10	TRANSLOCATION		0	274680	0	309	NEW_VARIANT
P-0036974-T01-IM6	SMYD3 (NM_001167740) rearrangement: c.845_c.814-6743el	PRECISE	Note: The SMYD3 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		560	0	45	1	Exon 9 of SMYD3(-)	SMYD3	246027157			1	Intron of SMYD3(-):7Kb before exon 9	SMYD3	246033931			10	DELETION		6774	274670	589	46	NEW_VARIANT
P-0036992-T01-IM6	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12015303::chr15:g.88666269)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	16	15	Intron of NTRK3(-):3Kb after exon 13	NTRK3	88666269			12	Intron of ETV6(+):7Kb before exon 5	ETV6	12015303			10	TRANSLOCATION		0	275002	0	13	NEW_VARIANT
P-0036870-T01-IM6	PRIM2 (NM_000947) - BRAF (NM_004333) Rearrangement : t(6;7)(p11.1;q34)(chr6:g.57410815::chr7:g.140493232)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {PRIM2:BRAF}		0	0	13	7	Intron of BRAF(-):875bp after exon 8	BRAF	140493232			6	Intron of PRIM2(+):12Kb after exon 10	PRIM2	57410815			10	TRANSLOCATION		0	274737	0	13	NEW_VARIANT
P-0026589-T02-IM6	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)	PRECISE	Note: The CD74 -ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	19	6	Intron of ROS1(-):454bp before exon 34	ROS1	117646032			5	Intron of CD74(-):115bp before exon 7	CD74	149782990			10	TRANSLOCATION		0	272756	0	19	NEW_VARIANT
P-0035561-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon2 fused with ERG exon2) : c.56-1709:TMPRSS2_c.18+5540:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		43104	0	32	21	Intron of ERG(-):6Kb after exon 1	ERG	39864747			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871825			10	DELETION		3007078	259693	55873	34	NEW_VARIANT
P-0036960-T01-IM6	MFSD4 (NM_181644) - TMPRSS2 (NM_001135099) rearrangement: t(1;21)(q32.1;q22.3)(chr1:g.205560208::chr21:g.42867222)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {MFSD4:TMPRSS2}		0	0	94	21	Intron of TMPRSS2(-):717bp before exon 3	TMPRSS2	42867222			1	Intron of MFSD4(+):1Kb before exon 7	MFSD4	205560208			10	TRANSLOCATION		0	274643	0	94	NEW_VARIANT
P-0036960-T01-IM6	EGFR (NM_005228) rearrangement: c.109_c.889+89dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8179	0	4	7	Exon 2 of EGFR(+)	EGFR	55209999			7	Intron of EGFR(+):89bp after exon 7	EGFR	55221934			10	DUPLICATION		11935	274640	12431	4	NEW_VARIANT
P-0034480-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11 ): c.56-1833:TMPRSS2_c.39+53541:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		55208	0	20	21	Intron of ERG(-):54Kb after exon 3	ERG	39894045			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871949			10	DELETION		2977904	251213	49889	21	NEW_VARIANT
P-0037101-T01-IM6	TLN2 (NM_015059) - RPS6KB2 (NM_003952) rearrangement: t(11;15)(q13.2;q22.2)(chr11:g.67201947::chr15:g.63122011)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TLN2:RPS6KB2}		0	0	82	15	Intron of TLN2(+):4Kb before exon 52	TLN2	63122011			11	Exon 13 of RPS6KB2(+)	RPS6KB2	67201947			10	TRANSLOCATION		0	276258	0	79	NEW_VARIANT
P-0036525-T01-IM6	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.31)(chr1:g.220440791::chr20:g.54958234)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RAB3GAP2:AURKA}		0	0	13	20	Intron of AURKA(-):2bp before exon 5	AURKA	54958234			1	Intron of RAB3GAP2(-):5Kb after exon 1	RAB3GAP2	220440791			0	TRANSLOCATION		0	278502	0	16	NEW_VARIANT
P-0036885-T01-IM6	NRG3 (NM_001010848) - NOTCH4 (NM_004557) rearrangement: t(6;10)(p21.32;q23.1)(chr6:g.32163675::chr10:g.84452811)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {NRG3:NOTCH4}		0	0	45	10	Intron of NRG3(+):46Kb before exon 4	NRG3	84452811			6	Exon 30 of NOTCH4(-)	NOTCH4	32163675			0	TRANSLOCATION		0	275226	0	43	NEW_VARIANT
P-0036885-T01-IM6	TRMT1 (NM_001136035) - BRD4 (NM_058243) rearrangement: c.1583+671_c.4021-35dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TRMT1:BRD4}		102895	0	2	19	Intron of TRMT1(-):670bp after exon 12	TRMT1	13217717			19	Intron of BRD4(-):35bp before exon 20	BRD4	15349291			10	DUPLICATION		2131574	275224	62948	18	NEW_VARIANT
P-0036885-T01-IM6	KMT2B (NM_014727) rearrangement: c.363+60_c.2458-18del	PRECISE	Note: The KMT2B rearrangement is an intragenic deletion of exons 2-3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		19955	0	15	19	Intron of KMT2B(+):60bp after exon 1	KMT2B	36209343			19	Intron of KMT2B(+):17bp before exon 4	KMT2B	36213243			10	DELETION		3900	275223	10492	15	NEW_VARIANT
P-0036886-T01-IM6	GRIN2A (NM_001134407) rearrangement: c.1831_c.2356+6658del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5488	0	30	16	Intron of GRIN2A(-):7Kb after exon 11	GRIN2A	9885476			16	Exon 9 of GRIN2A(-)	GRIN2A	9923456			0	DELETION		37980	275229	5861	32	NEW_VARIANT
P-0036886-T01-IM6	RPTOR (NM_020761) rearrangement: c.731_c.830+1624del	PRECISE	Note: The RPTOR rearrangement is an intragenic deletion of exon 6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1041	0	7	17	Exon 6 of RPTOR(+)	RPTOR	78727886			17	Intron of RPTOR(+):2Kb after exon 6	RPTOR	78729609			10	DELETION		1723	275230	1136	7	NEW_VARIANT
P-0036886-T01-IM6	CUL3 (NM_003590) rearrangement: c.1843-5786_c.2029+8inv	PRECISE	Note: The CUL3 rearrangement is an intragenic inversion of exon 14. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1728	0	67	2	Intron of CUL3(-):7bp after exon 14	CUL3	225346601			2	Intron of CUL3(-):6Kb before exon 14	CUL3	225352581			10	INVERSION		5980	275231	2279	88	NEW_VARIANT
P-0036886-T01-IM6	AGK (NM_018238) - BRAF (NM_004333) rearrangement: c.101+10859:AGK_c.981-42:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {AGK:BRAF}		49543	0	116	7	Intron of BRAF(-):42bp before exon 8	BRAF	140494309			7	Intron of AGK(+):11Kb after exon 2	AGK	141266226			10	INVERSION		771917	275232	54725	116	NEW_VARIANT
P-0036886-T01-IM6	KMT2C (NM_170606) rearrangement: c.9454-766_c.9751-50del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 41-42. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		3524	0	38	7	Intron of KMT2C(-):50bp before exon 43	KMT2C	151860961			7	Intron of KMT2C(-):766bp before exon 41	KMT2C	151867100			10	DELETION		6139	275228	4400	38	NEW_VARIANT
P-0036886-T01-IM6	FAM58A (NM_152274) rearrangement: t(X;8)(q28;q12.3)(chrX:g.152859987::chr8:g.62373134)	PRECISE	Note: The FAM58A rearrangement is a translocation which involves exon 5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	49	X	Intron of FAM58A(-):17bp after exon 3	FAM58A	152859987			8	Intron of CLVS1(+):2Kb after exon 5	CLVS1	62373134			10	TRANSLOCATION		0	275234	0	49	NEW_VARIANT
P-0037370-T01-IM6	APC (NM_000038) rearrangement: c.4544_c.6166del	PRECISE	Note: The APC rearrangement is an intragenic deletion of exon 16. Both breakpoints are within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4217	0	15	5	Exon 16 of APC(+)	APC	112175835			5	Exon 16 of APC(+)	APC	112177457			10	DELETION		1622	278517	4052	17	NEW_VARIANT
P-0037688-T01-IM6	PIK3C2G (NM_004570) -FBXO16 (NM_172366) Rearrangement: t(8,12)(p11.22; q12)(chr8:g.28324745::chr12:g.18552829)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {PIK3C2G:FBXO16}		0	0	32	12	Intron of PIK3C2G(+):48bp after exon 15	PIK3C2G	18552829			8	Intron of FBXO16(-):3Kb before exon 3	FBXO16	28324745			10	TRANSLOCATION		0	281755	0	32	NEW_VARIANT
P-0037688-T01-IM6	STK19 (NM_004197) -C4A( (NM_007293) Rearrangement : c.919:STK19_c.3275:C4Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STK19:C4A}		692	0	4	6	Exon 7 of STK19(+)	STK19	31948448			6	Exon 26 of C4A(+)	C4A	31963776			10	DELETION		15328	281754	597	7	NEW_VARIANT
P-0037767-T01-IM6	CA10 (NM_001082533) - RECQL4 (NM_004260) rearrangement: t(8;17)(q24.3;q21.33)(chr8:g.145742559::chr17:g.50212204)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CA10:RECQL4}		0	0	14	17	Intron of CA10(-):23Kb after exon 1	CA10	50212204			8	Exon 4 of RECQL4(-)	RECQL4	145742559			10	TRANSLOCATION		0	281872	0	14	NEW_VARIANT
P-0037777-T01-IM6	KMT2B (NM_014727) - MLL5 (NM_018682) rearrangement: t(7;19)(q22.3;q13.12)(chr7:g.104695690;chr19:g.36224589)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KMT2B:KMT2E}		0	0	8	19	Intron of KMT2B(+):2bp after exon 29	KMT2B	36224589			7	Intron of KMT2E(+):7Kb before exon 3	MLL5	104695690			0	TRANSLOCATION		0	281870	0	8	NEW_VARIANT
P-0037818-T01-IM6	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2463+8:CREBBP_c.2014-366:SLX4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CREBBP:SLX4}		92312	0	85	16	Intron of SLX4(-):366bp before exon 10	CREBBP	3644966			16	Intron of CREBBP(-):7bp after exon 13	SLX4	3823744			10	DELETION		178778	282126	107265	383	NEW_VARIANT
P-0038013-T01-IM6	TEK (NM_000459) Rearrangment: c.476-100:TEK_chr9:g.16340059inv	PRECISE	Note: The TEK rearrangement results in a inversion with breakpoint within intron 3 of TEK. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		21110	0	34	9	IGR: 69Kb before BNC2(-)	TEK	16340059			9	Intron of TEK(+):99bp before exon 4	TEK	27169375			10	INVERSION		10829316	283433	20747	34	NEW_VARIANT
P-0037803-T01-IM6	CDKN2Ap14ARF (NM_058195) rearrangement: c.317-3302:CDKN2Ap14ARF_chr9:g.22066617del	PRECISE	Note: The CDKN2Ap14ARF rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	-		9860	0	16	9	Exon 1 of CDKN2A(-)	CDKN2Ap14ARF	21974509			9	5-UTR of CDKN2B-AS1(+):54Kb before coding start	CDKN2Ap14ARF	22066617			10	DELETION		92108	281952	3381	17	NEW_VARIANT
P-0037803-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.150+168:CDKN2Ap16INK4A_chr9:g.22066617del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	-		9860	0	16	9	Exon 1 of CDKN2Ap16INK4A(-)	CDKN2Ap16INK4A	21974509			9	5'-UTR of CDKN2B-AS1(+):54Kb before coding start	CDKN2Ap16INK4A	22066617			10	DELETION		92108	284442	3381	17	NEW_VARIANT
P-0004224-T02-IM6	RBM10 (NM_001204468) rearrangement : t(X;6)(Xp11.23;6p22.3)(chrX:g.47034490::chr6:g.21827554)	PRECISE	Note: The RBM10 rearrangement involves a breakpoint in exon 6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RBM10:CASC15}		0	0	217	X	Exon 6 of RBM10(+)	RBM10	47034490			6	5-UTR of CASC15(+):367Kb before coding start	RBM10	21827555			10	TRANSLOCATION		0	280347	0	251	NEW_VARIANT
P-0037914-T01-IM6	TNFRSF14 (NM_003820) - PLXNA2 (NM_025179) rearrangement: c.70-109:TNFRSF14_c.1371+18891:PLXNA2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TNFRSF14:PLXNA2}		1144773	0	3	1	Intron of TNFRSF14(+):108bp before exon 2	TNFRSF14	2489056			1	Intron of PLXNA2(-):19Kb after exon 3	PLXNA2	208364734			5	INVERSION		205875678	282759	1193281	3	NEW_VARIANT
P-0037971-T01-IM6	RICTOR (NM_152756) - TTC33 (NM_012382) rearrangement: c.4399+34:RICTOR_c.304-865:TTC33dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RICTOR:TTC33}		38679	0	4	5	Intron of RICTOR(-):33bp after exon 33	RICTOR	38946536			5	Intron of TTC33(-):865bp before exon 4	TTC33	40729443			9	DUPLICATION		1782907	283075	58052	4	NEW_VARIANT
P-0038012-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+46:TMPRSS2_c.39+11109:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		34488	0	18	21	Intron of ERG(-):11Kb after exon 3	TMPRSS2	39936477			21	Intron of TMPRSS2(-):45bp after exon 2	ERG	42870000			10	DELETION		2933523	283424	34287	18	NEW_VARIANT
P-0037982-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-138:EML4_c.3173-85:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		126499	0	97	2	Intron of ALK(-):85bp before exon 20	EML4	29446479			2	Intron of EML4(+):137bp before exon 13	ALK	42528243			10	INVERSION		13081764	283127	176420	97	NEW_VARIANT
P-0037983-T01-IM6	AR (NM_000044) rearrangement: c.289:AR_chrX:g.66764311del	IMPPRECISE	Note: The AR rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3006	0	64	X	5-UTR of AR(+):677bp before coding start	AR	66764311			X	Exon 1 of AR(+)	AR	66765277			0	DELETION		966	283097	2609	77	NEW_VARIANT
P-0038044-T01-IM6	ERG (NM_182918) rearrangement: t(13;21)(q33.1;q22.2)(chr13:g.104080776::chr21:g.39772291)	PRECISE	Note: The ERG rearrangement is a translocation involving exon 6. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {LINC01309:ERG}		0	0	6	21	Intron of ERG(-):204bp after exon 6	ERG	39772291			13	Promoter of LINC01309(+):3Kb from tx start	ERG	104080776			10	TRANSLOCATION		0	283519	0	6	NEW_VARIANT
P-0038047-T01-IM6	RB1 (NM_000321) rearrangement: c.2510:RB1_chr13:g.49055407del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 24-27. One of the breakpoints is within exon 24.	MANUAL_OK	3to5	3to5	-		3532	0	15	13	Exon 24 of RB1(+)	RB1	49047516			13	3-UTR of RB1(+):177Kb after coding stop	RB1	49055407			10	DELETION		7891	284233	839	15	NEW_VARIANT
P-0038047-T01-IM6	NCOA3 (NM_181659) rearrangement: c.823+2670_c.2602del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12081	0	28	20	Intron of NCOA3(+):3Kb after exon 8	NCOA3	46259437			20	Exon 14 of NCOA3(+)	NCOA3	46267841			10	DELETION		8404	284234	12710	33	NEW_VARIANT
P-0038081-T01-IM6	ATM (NM_000051) rearrangement: c.7308-34:ATM_chr11:g.107979515del	IMPPRECISE	Note: The ATM rearrangement is a deletion of exons 1 - 49.	MANUAL_OK	3to5	3to5	Transcript Fusion {CUL5:ATM}		53408	0	8	11	Promoter of CUL5(+):100Kb from tx start	ATM	107979515			11	Intron of ATM(+):33bp before exon 50	ATM	108200907			0	DELETION		221392	284119	65307	9	NEW_VARIANT
P-0038083-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.530-3362_c.954del	PRECISE	The TGFBR2 rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2528	0	36	3	Intron of TGFBR2(+):3Kb before exon 5	TGFBR2	30709768			3	Exon 5 of TGFBR2(+)	TGFBR2	30713554			10	DELETION		3786	284116	3286	36	NEW_VARIANT
P-0038093-T01-IM6	TMEM132D (NM_133448) - ARID1A (NM_006015)  rearrangement: t(1;12)(p36.11;q24.33)(chr1:g.27023940::chr12:g.130356620)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TMEM132D:ARID1A}		0	0	6	12	Intron of TMEM132D(-):31Kb after exon 1	TMEM132D	130356620			1	Exon 1 of ARID1A(+)	ARID1A	27023940			10	TRANSLOCATION		0	284217	0	9	NEW_VARIANT
P-0038096-T01-IM6	FGFR2 (NM_000141) rearrangement: t(10;17)(q26.13;q24.3)(chr10:g.123274680::chr17:g.67640339)	PRECISE	Note: The FGFR2 rearrangement is a translocation involving a breakpoint in exon 9. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	10	17	5-UTR of LINC01483(+):259Kb before coding start	FGFR2	67640339			10	Exon 9 of FGFR2(-)	FGFR2	123274680			10	TRANSLOCATION		0	284207	0	10	NEW_VARIANT
P-0038096-T01-IM6	RTEL1 (NM_032957) rearrangement: c.1420+809_c.3064+55dup	PRECISE	Note: The RTEL1 rearrangement is an intragenic duplication of exons 17-30. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 14 exons : in frame		24741	0	58	20	Intron of RTEL1(+):809bp after exon 16	RTEL1	62318034			20	Intron of RTEL1(+):55bp after exon 30	RTEL1	62324691			10	DUPLICATION		6657	284206	54480	59	NEW_VARIANT
P-0025990-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1674:TMPRSS2_c.18+4717:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		27230	0	86	21	Intron of ERG(-):5Kb after exon 1	TMPRSS2	39865570			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868372			10	DELETION		3002802	283817	35370	90	NEW_VARIANT
P-0037988-T01-IM6	NF2 (NM_000268) rearrangement: c.447+4860_c.811-48del	PRECISE	Note: The NF2 rearrangement is an intragenic deletion of exons 5-8.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		4978	0	51	22	Intron of NF2(+):5Kb after exon 4	NF2	30043134			22	Intron of NF2(+):47bp before exon 9	NF2	30060931			10	DELETION		17797	283132	1882	53	NEW_VARIANT
P-0037814-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41635815::chr21:g.42873514)	IMPPRECISE	Note: The TMPRSS2 rearrangement is a translocation involving exon 2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873514			17	IGR: 31Kb before ETV4(-)	TMPRSS2	41635815			0	TRANSLOCATION		0	282118	0	11	NEW_VARIANT
P-0038155-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2302-385:FGFR2_chr10:g.123979249dup	PRECISE	Note: The FGFR2 rearrangement is a duplication of exons 1 - 17. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		69548	0	237	10	Intron of FGFR2(-):385bp before exon 18	FGFR2	123239920			10	Intron of TACC2(+):3Kb after exon 10	FGFR2	123979249			10	DUPLICATION		739329	284934	319171	351	NEW_VARIANT
P-0011429-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3735:TMPRSS2_c.18+9727:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		103752	0	211	21	Intron of ERG(-):10Kb after exon 1	TMPRSS2	39860560			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42876142			10	DELETION		3015582	285115	131029	226	NEW_VARIANT
P-0025859-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) rearrangement: c.126:FGFR3_c.1941+33:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		1455	0	16	4	Intron of TACC3(+):33bp after exon 10	FGFR3	1739462			4	Exon 3 of FGFR3(+)	TACC3	1800997			10	DUPLICATION		61535	224721	1393	20	NEW_VARIANT
P-0034813-T03-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3457:TMPRSS2_c.18+4434:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		95585	0	163	21	Intron of ERG(-):4Kb after exon 1	TMPRSS2	39865853			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42876420			10	DELETION		3010567	285125	94564	175	NEW_VARIANT
P-0034813-T03-IM6	CDKN1B (NM_004064) rearrangement: t(12;X)(p13.1;p22.31)(chr12:g.12871320::chrX:g.9499399)	PRECISE	Note: The CDKN1B rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {CDKN1B:TBL1X}		0	0	59	X	5-UTR of TBL1X(+):123Kb before coding start	CDKN1B	9499399			12	Intron of CDKN1B(+):72bp after exon 1	CDKN1B	12871320			10	TRANSLOCATION		0	285128	0	59	NEW_VARIANT
P-0038179-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3703:TMPRSS2_c.40-56593:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		78932	0	76	21	Intron of ERG(-):57Kb before exon 4	TMPRSS2	39874137			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873819			10	DELETION		2999682	285071	70668	82	NEW_VARIANT
P-0038194-T01-IM6	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(q34;q33.2)(chr7:g.140484954::chr9:g.123187156)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CDK5RAP2:BRAF}		0	0	46	9	Intron of CDK5RAP2(-):2Kb before exon 26	CDK5RAP2	123187156			7	Intron of BRAF(-):2Kb before exon 10	BRAF	140484954			10	TRANSLOCATION		0	285104	0	48	NEW_VARIANT
P-0038195-T01-IM6	MAP2K1 (NM_002755) rearrangement: c.656:MAP2K1_chr15:g.50987680inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		25637	0	2	15	IGR: 12Kb before SPPL2A(-)	MAP2K1	50987680			15	Exon 6 of MAP2K1(+)	MAP2K1	66774180			5	INVERSION		15786500	285112	29414	2	NEW_VARIANT
P-0038198-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(1;21)(p33;q22.3)(chr1:g.47143557::chr21:g.42872071)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	120	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872071			1	3-UTR of EFCAB14(-):575bp after coding stop	TMPRSS2	47143557			10	TRANSLOCATION		0	285107	0	136	NEW_VARIANT
P-0038204-T01-IM6	PTPRD (NM_002839) rearrangement: t(9,10)(p24.1;q21.3)(chr9:g.8521187::chr10:g.67541496)	IMPPRECISE	Note: The PTPRD rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	21	10	IGR: 131Kb before CTNNA3(-)	PTPRD	67541496			9	Intron of PTPRD(-):89bp after exon 20	PTPRD	8521187			0	TRANSLOCATION		0	285220	0	21	NEW_VARIANT
P-0038204-T01-IM6	RPS6KB2 (NM_003952) rearrangement: t(11,14)(q13.2;q12)(chr11:g.67200806::chr14:g.32983149)	PRECISE	Note: The RPS6KB2 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	12	14	Intron of AKAP6(+):22Kb before exon 3	RPS6KB2	32983149			11	Intron of RPS6KB2(+):4bp before exon 10	RPS6KB2	67200806			10	TRANSLOCATION		0	285222	0	14	NEW_VARIANT
P-0038238-T01-IM6	DOT1L (NM_032482) rearrangement: c.4576_c.4606+902inv	PRECISE	Note: The DOT1L rearrangement results in the inversion of exon 27. One of the breakpoints is within exon 27. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2445	0	2	19	Exon 27 of DOT1L(+)	DOT1L	2227096			19	Intron of DOT1L(+):902bp after exon 27	DOT1L	2228028			4	INVERSION		932	285250	2695	2	NEW_VARIANT
P-0038238-T01-IM6	EP300 (NM_001429) rearrangement: c.1622_chr22:g.37681407inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		20588	0	9	22	Intron of CYTH4(+):3Kb after exon 1	EP300	37681407			22	Exon 7 of EP300(+)	EP300	41531910			9	INVERSION		3850503	285251	29465	9	NEW_VARIANT
P-0038241-T01-IM6	WHSC1 (NM_001042424) rearrangement: t(4;17)(p16.3;q21.32)(chr4:g.1978321::chr17:g.47043304)	PRECISE	Note: The WHSC1 rearrangement is a translocation with a breakpoint in exon 21. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	21	17	Intron of GIP(-):1Kb after exon 2	WHSC1	47043304			4	Exon 21 of WHSC1(+)	WHSC1	1978321			10	TRANSLOCATION		0	285261	0	21	NEW_VARIANT
P-0038241-T01-IM6	FAT1 (NM_005245) rearrangement: c.11569:FAT1_chr4:g.182881463inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		20004	0	18	4	IGR: 178Kb before LOC90768(-)	FAT1	182881463			4	Exon 21 of FAT1(-)	FAT1	187522494			10	INVERSION		4641031	285260	23388	18	NEW_VARIANT
P-0038251-T01-IM6	BRCA2 (NM_000059) Rearrangement : c.3877_c.5313del	PRECISE	Note: The BRCA2 Rearrangement results in the intragenic deletion of exon11 of BRCA2. Both the breakpoints are within exon11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7403	0	2	13	Exon 11 of BRCA2(+)	BRCA2	32912369			13	Exon 11 of BRCA2(+)	BRCA2	32913805			5	DELETION		1436	285430	4788	1	NEW_VARIANT
P-0038184-T01-IM6	TP53 (NM_000546) Rearrangement: c.672+64_c.783-88del	PRECISE	Note: The TP53 rearrangement results in intragenic deletion of exon 7.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2723	0	68	17	Intron of TP53(-):88bp before exon 8	TP53	7577243			17	Intron of TP53(-):63bp after exon 6	TP53	7578113			10	DELETION		870	285061	1932	70	NEW_VARIANT
P-0038348-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: (TMPRSS2 exon 1 fused to ERG exons 4-11): c.55+3992:TMPRSS2_c.40-59510:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		87369	0	156	21	Intron of ERG(-):60Kb before exon 4	TMPRSS2	39877054			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875885			10	DELETION		2998831	285610	82713	164	NEW_VARIANT
P-0038349-T01-IM6	KMT2D (NM_003482) rearrangement: c.4634_chr12:g.49478928inv	PRECISE	Note: The KMT2D rearrangement is an inversion that includes KMT2D exons 1-17. One of the breakpoints is within exon 17.	MANUAL_OK	3to3	3to3	-		55639	0	52	12	Exon 17 of KMT2D(-)	KMT2D	49439907			12	IGR: 4Kb before DHH(-)	KMT2D	49478928			10	INVERSION		39021	285603	40692	52	NEW_VARIANT
P-0038349-T01-IM6	NTRK3 (NM_001012338) - VPS39 (NM_015289) rearrangement: c.1662:NTRK3_c.961-770:VPS39inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		182850	0	20	15	Intron of VPS39(-):770bp before exon 12	NTRK3	42466820			15	Exon 15 of NTRK3(-)	VPS39	88483908			10	INVERSION		46017088	285605	135266	29	NEW_VARIANT
P-0038349-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: chr21:g.33128749_c.56-4656inv	PRECISE	Note: The TMPRSS2 rearrangement is an inversion that includes TMRSS2 exons 2-14.	MANUAL_OK	5to5	5to5	-		127610	0	6	21	IGR: 85Kb before SCAF4(-)	TMPRSS2	33128749			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874772			10	INVERSION		9746023	285606	44099	7	NEW_VARIANT
P-0038351-T01-IM6	ERRFI1 (NM_018948) rearrangement: t(1;17)(p36.23;q23.3)(chr1:g.8075627::chr17:g.62495243)	PRECISE	Note: The ERRFI1 rearrangement is a translocation with a breakpoint within ERRFI1 exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	15	17	3-UTR of DDX5(-):797bp after coding stop	ERRFI1	62495243			1	Exon 2 of ERRFI1(-)	ERRFI1	8075627			10	TRANSLOCATION		0	285596	0	15	NEW_VARIANT
P-0038352-T01-IM6	MET (NM_000245) rearrangement: c.2731-77_c.3028+772del	PRECISE	Note: The MET rearrangement is an intragenic deletion of MET exons 13-14.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		9716	0	7	7	Intron of MET(+):76bp before exon 13	MET	116411475			7	Intron of MET(+):772bp after exon 14	MET	116412815			10	DELETION		1340	285608	7165	7	NEW_VARIANT
P-0038298-T01-IM6	RECQL4 (NM_004260) Rearrangement: t(8;12)(q11.22;q15)(chr8:g.145738716::chr12:g.69857749)	PRECISE	Note: The RECQL4 rearrangement is a translocation with breakpoint in exon 15 of RECQL4. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	171	12	IGR: 6Kb before FRS2(+)	RECQL4	69857749			8	Exon 15 of RECQL4(-)	RECQL4	145738716			10	TRANSLOCATION		0	285313	0	214	NEW_VARIANT
P-0038299-T01-IM6	STAT5A (NM_003152) - TTC7B (NM_001010854) rearrangement: t(14;17)(q32.11;q21.2)(chr14:g.91189253::chr17:g.40458420)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {STAT5A:TTC7B}		0	0	8	17	Exon 14 of STAT5A(+)	STAT5A	40458420			14	Intron of TTC7B(-):7Kb after exon 5	TTC7B	91189253			10	TRANSLOCATION		0	285552	0	7	NEW_VARIANT
P-0038299-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1050:TMPRSS2_c.39+51237:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		23215	0	5	21	Intron of ERG(-):51Kb after exon 3	TMPRSS2	39896349			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867555			10	DELETION		2971206	285550	10081	5	NEW_VARIANT
P-0038318-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-87:FGFR3_c.1462-57:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		38084	0	75	4	Intron of TACC3(+):56bp before exon 6	FGFR3	1732842			4	Intron of FGFR3(+):86bp before exon 18	TACC3	1808756			10	DUPLICATION		75914	285653	73080	77	NEW_VARIANT
P-0038328-T01-IM6	AXIN1 (NM_003502) rearrangement: c.1498_c.1255-1302inv	PRECISE	Note: The AXIN1 rearrangement is an intragenic inversion of exon 6. One of the breakpoints is within exon 6.	MANUAL_OK	5to5	5to5	Antisense Fusion		2818	0	47	16	Exon 6 of AXIN1(-)	AXIN1	348008			16	Intron of AXIN1(-):1Kb before exon 6	AXIN1	349553			10	INVERSION		1545	285723	3438	77	NEW_VARIANT
P-0038329-T01-IM6	EPHB1 (NM_004441) translocation: t(3;11)(q22.2;q12.1)(chr3:g.134920357::chr11:g.58655556)	PRECISE	Note: The EPHB1 rearrangement is a translocation with a breakpoint within EPHB1 exon 12. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	31	11	IGR: 40Kb before GLYATL1(+)	EPHB1	58655556			3	Exon 12 of EPHB1(+)	EPHB1	134920357			10	TRANSLOCATION		0	285721	0	30	NEW_VARIANT
P-0038394-T01-IM6	SDC4 (NM_002999) - ROS1 (NM_002944) rearrangement: t(6;20)(q22.1;q13.12)(chr6:g.117654360::chr20:g.43961742)	PRECISE	Note: The SDC4 - ROS1 rearrangement is a translocation which may result in the fusion of SDC4 exons 1-2 with ROS1 exons 32-43.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	9	20	Intron of SDC4(-):33bp before exon 3	SDC4	43961742			6	Intron of ROS1(-):4Kb before exon 32	ROS1	117654360			8	TRANSLOCATION		0	286170	0	9	NEW_VARIANT
P-0024325-T02-IM6	DNMT3A (NM_022552) - ASXL2 (NM_018263) rearrangement: c.1294:DNMT3A_c.2054:ASXL2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNMT3A:ASXL2}		38366	0	113	2	Exon 11 of DNMT3A(-)	DNMT3A	25469164			2	Exon 12 of ASXL2(-)	ASXL2	25967152			10	DUPLICATION		497988	287836	74209	115	NEW_VARIANT
P-0038161-T01-IM6	CDH1 (NM_004360) rearrangement: c.99_c.164-14352del	PRECISE	Note: The CDH1 rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1450	0	25	16	Exon 2 of CDH1(+)	CDH1	68772250			16	Intron of CDH1(+):14Kb before exon 3	CDH1	68821221			10	DELETION		48971	287628	980	26	NEW_VARIANT
P-0038162-T01-IM6	AXL (NM_021913) rearrangement: c.783+2381_c.1711+231inv	PRECISE	Note: The AXL rearrangement results in the inversion of exons 7-14. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		16316	0	20	19	Intron of AXL(+):2Kb after exon 6	AXL	41739584			19	Intron of AXL(+):231bp after exon 14	AXL	41754956			10	INVERSION		15372	287627	31267	20	NEW_VARIANT
P-0038166-T01-IM6	NF1 (NM_001042492) rearrangement: c.7457+59_c.7615+1767del	PRECISE	Note: The NF1 rearrangement results in the deletion of exon 51. The functional significance is undetermined	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1450	0	4	17	Intron of NF1(+):59bp after exon 50	NF1	29677395			17	Intron of NF1(+):2Kb after exon 51	NF1	29681199			4	DELETION		3804	287629	1510	4	NEW_VARIANT
P-0038166-T01-IM6	KREMEN1 (NM_032045) - CHEK2 (NM_007194) rearrangement: c.260+797:KREMEN1_c.684-29:CHEK2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {KREMEN1:CHEK2}		9382	0	6	22	Intron of CHEK2(-):29bp before exon 6	KREMEN1	29108034			22	Intron of KREMEN1(+):797bp after exon 2	CHEK2	29491205			10	INVERSION		383171	287631	11492	6	NEW_VARIANT
P-0038166-T01-IM6	MSH3 (NM_002439) rearrangement: c.1049_c.1569-17inv	PRECISE	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	MANUAL_OK	5to5	5to5	-		6148	0	17	5	Exon 7 of MSH3(+)	MSH3	79970823			5	Intron of MSH3(+):16bp before exon 11	MSH3	80037266			10	INVERSION		66443	287630	7226	17	NEW_VARIANT
P-0038369-T01-IM6	TAP1 (NM_000593) rearrangement: c.432:TAP1_chr6:g.27816456inv	PRECISE	Note: The TAP1 rearrangement is an inversion of exons 1-11. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		280271	0	50	6	IGR: 10Kb before HIST1H2BN(+)	TAP1	27816456			6	Exon 1 of TAP1(-)	TAP1	32821162			10	INVERSION		5004706	286091	341665	61	NEW_VARIANT
P-0038374-T01-IM6	DNMT1 (NM_001379) rearrangement: c.683+82:DNMT1_chr19:g.10325900inv	IMPPRECISE	Note: The DNMT1 rearrangement is an inversion of exons 1-7. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		9519	0	5	19	Intron of DNMT1(-):81bp after exon 7	DNMT1	10284465			19	IGR: 6Kb before S1PR2(-)	DNMT1	10325900			0	INVERSION		41435	286095	11312	5	NEW_VARIANT
P-0038374-T01-IM6	BCL2L11 (NM_138621) rearrangement: c.394+3437:BCL2L11_chr2:g.112807418del	IMPPRECISE	Note: The BCL2L11 rearrangement is a deletion of exons 3-4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		13728	0	6	2	Intron of BCL2L11(+):3Kb after exon 2	BCL2L11	111885153			2	IGR: 5Kb before TMEM87B(+)	BCL2L11	112807418			0	DELETION		922265	286092	18580	6	NEW_VARIANT
P-0038381-T01-IM6	PALB2 (NM_024675) - NME6 (NM_005793) rearrangement: t(3;16)(p21.31;p12.2)(chr3:g.48342586::chr16:g.23632769)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PALB2:NME6}		0	0	20	16	Exon 10 of PALB2(-)	PALB2	23632769			3	Intron of NME6(-):199bp after exon 1	NME6	48342586			10	TRANSLOCATION		0	286075	0	20	NEW_VARIANT
P-0021574-T03-IM6	SPEN (NM_015001) Rearrangement :c.10509+10_c.10705-20del	PRECISE	Note: The SPEN Rearrangement results in the intragenic deletion of exon13 of SPEN. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		3037	0	13	1	Intron of SPEN(+):10bp after exon 12	SPEN	16264150			1	Intron of SPEN(+):19bp before exon 14	SPEN	16265193			10	DELETION		1043	286493	3154	13	NEW_VARIANT
P-0036560-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) : c.126+892:TMPRSS2_c.39+3031:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		36589	0	39	21	Intron of ERG(-):3Kb after exon 3	TMPRSS2	39944555			21	Intron of TMPRSS2(-):891bp after exon 2	ERG	42869154			10	INVERSION		2924599	286293	28667	39	NEW_VARIANT
P-0038406-T01-IM6	ELF3 (NM_004433) Rearrangement : c.492_c.1002-71inv	PRECISE	Note: The ELF3 Rearrangement results in the intragenic inversion of exons 5-8 of ELF3. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		12205	0	23	1	Exon 5 of ELF3(+)	ELF3	201981781			1	Intron of ELF3(+):70bp before exon 9	ELF3	201984266			10	INVERSION		2485	286261	9233	24	NEW_VARIANT
P-0038406-T01-IM6	CSF3 (NM_000759) - CDK12 (NM_016507) Rearrangement : c.313-58:CSF3_c.2964-126:CDK12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CSF3:CDK12}		92430	0	6	17	Intron of CDK12(+):125bp before exon 11	CSF3	37676083			17	Intron of CSF3(+):57bp before exon 3	CDK12	38172680			10	DUPLICATION		496597	286260	88436	7	NEW_VARIANT
P-0038406-T01-IM6	KMT2C (NM_170606) Rearrangement : c.1300-3465_c.7647del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		60330	0	5	7	Exon 38 of KMT2C(-)	KMT2C	151874891			7	Intron of KMT2C(-):3Kb before exon 10	KMT2C	151953265			6	DELETION		78374	286259	49601	5	NEW_VARIANT
P-0038414-T01-IM6	ELF3 (NM_004433) rearrangement: c.423:ELF3_chr1:g.16840713inv	PRECISE	Note: The ELF3 rearrangement is an inversion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1084417	0	67	1	IGR: 35Kb before MIR3675(+)	ELF3	16840713			1	Exon 4 of ELF3(+)	ELF3	201981509			10	INVERSION		185140796	286324	1436350	112	NEW_VARIANT
P-0038414-T01-IM6	CSF3R (NM_000760) - KIAA0319L (NM_024874) rearrangement: c.673+224:CSF3R_c.1201+1129:KIAA0319Ldel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CSF3R:KIAA0319L}		62797	0	32	1	Intron of KIAA0319L(-):1Kb after exon 7	CSF3R	35931080			1	Intron of CSF3R(-):223bp after exon 6	KIAA0319L	36938812			10	DELETION		1007732	286318	91363	35	NEW_VARIANT
P-0038414-T01-IM6	RPS6KA4 (NM_003942) rearrangement: c.1219:RPS6KA4_chr11:g.66694825inv	PRECISE	Note: The RPS6KA4 rearrangement is an inversion of exons 11 - 17. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {RPS6KA4:PC}		52301	0	24	11	Exon 11 of RPS6KA4(+)	RPS6KA4	64135958			11	5-UTR of PC(-):78Kb before coding start	RPS6KA4	66694825			10	INVERSION		2558867	286325	76915	24	NEW_VARIANT
P-0038414-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2301:FGFR3_c.1941+974:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		46182	0	271	4	Intron of TACC3(+):974bp after exon 10	FGFR3	1740403			4	Exon 18 of FGFR3(+)	TACC3	1808869			10	DUPLICATION		68466	286322	103720	305	NEW_VARIANT
P-0038415-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+2095:TMPRSS2_c.19-14849:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		126384	0	90	21	Intron of ERG(-):15Kb before exon 2	TMPRSS2	39832393			21	Intron of TMPRSS2(-):2Kb after exon 1	ERG	42877782			10	DELETION		3045389	286326	74397	92	NEW_VARIANT
P-0038415-T01-IM6	MAP3K1 (NM_005921) rearrangement: t(5,7)(q11.2;q21.11)(chr5:g.56184195::chr7:g.79055104)'	IMPPRECISE	Note: The MAP3K1 rearrangement is a translocation with a breakpoint in intron 19. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	5	7	Intron of MAGI2(-):27Kb after exon 1	MAP3K1	79055104			5	Intron of MAP3K1(+):11bp after exon 19	MAP3K1	56184195			0	TRANSLOCATION		0	286328	0	5	NEW_VARIANT
P-0038417-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-64882:ERG_c.56-3214:TMPRSS2inv	PRECISE	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).	MANUAL_OK	3to3	3to3	-		79968	0	18	21	Intron of ERG(-):65Kb before exon 4	ERG	39882426			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42873330			10	INVERSION		2990904	286349	68262	16	NEW_VARIANT
P-0038419-T01-IM6	ZNF598 (NM_178167) - TSC2 (NM_000548) rearrangement: c.2446:ZNF598_c.4850-65:TSC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ZNF598:TSC2}		109971	0	3	16	Exon 14 of ZNF598(-)	ZNF598	2048504			16	Intron of TSC2(+):64bp before exon 38	TSC2	2136668			9	INVERSION		88164	286343	111516	4	NEW_VARIANT
P-0038419-T01-IM6	PBRM1 (NM_018313) rearrangement: c.3617-1469_c.4555del	PRECISE	Note: The PBRM1 rearrangement is an intragenic deletion of exons 24 - 29. One of the breakpoints is within exon 29.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		15008	0	8	3	Exon 29 of PBRM1(-)	PBRM1	52584458			3	Intron of PBRM1(-):1Kb before exon 24	PBRM1	52599718			10	DELETION		15260	286341	12995	8	NEW_VARIANT
P-0033527-T01-IM6	ELF3 (NM_004433) rearrangement: c.261_chr1:g.202003116dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		15870	0	4	1	Exon 3 of ELF3(+)	ELF3	201981182			1	IGR: 23Kb before ELF3(+)	ELF3	202003116			10	DUPLICATION		21934	241307	17518	4	NEW_VARIANT
P-0033527-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2195+509_c.*2131del	PRECISE	Note: The FGFR2 rearrangement results in the deletion of exons 17-18 and includes the kinase domain of FGFR2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		42803	0	26	10	Promoter of FGFR2(-):603bp from tx start	FGFR2	123237240			10	Intron of FGFR2(-):508bp after exon 16	FGFR2	123244400			10	DELETION		7160	241306	50043	27	NEW_VARIANT
P-0038514-T01-IM6	MON1A (NM_032355) - MST1 (NM_020998) rearrangement: c.279-3634:MON1A_c.1420:MST1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MON1A:MST1}		91653	0	3	3	Exon 12 of MST1(-)	MON1A	49722907			3	Intron of MON1A(-):4Kb before exon 2	MST1	49954426			10	DELETION		231519	286818	93562	15	NEW_VARIANT
P-0038514-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2906:WHSC1L1_chr8:g.34562568del	PRECISE	Note: The WHSC1L1 rearrangement is a deletion of exons 16 - 24. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		25619	0	119	8	IGR: 79Kb before LINC01288(+)	WHSC1L1	34562568			8	Exon 16 of WHSC1L1(-)	WHSC1L1	38153323			10	DELETION		3590755	286820	28227	130	NEW_VARIANT
P-0012706-T02-IM6	SDHC (NM_003001) Rearrangement : c.*1834:ITLN1_c.21-152:SDHCdel	PRECISE	Note: The SDHC Rearrangement results in the deletion of exon1 of SDHC. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1398	0	21	1	Promoter of ITLN1(-):2Kb from tx start	SDHC	160844620			1	Intron of SDHC(+):151bp before exon 2	SDHC	161293252			10	DELETION		448632	287979	5348	22	NEW_VARIANT
P-0038426-T01-IM6	HGF (NM_000601) rearrangement: c.1752:HGF_chr7:g.85393601inv	PRECISE	Note: The HGF rearrangement is an inversion of exons 1 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		26001	0	18	7	Exon 15 of HGF(-)	HGF	81335608			7	IGR: 769Kb before SEMA3D(-)	HGF	85393601			10	INVERSION		4057993	286447	19930	21	NEW_VARIANT
P-0038427-T01-IM6	CDK12 (NM_016507) rearrangement: c.672:CDK12_chr17:g.55810160inv	PRECISE	Note: The CDK12 rearrangement is an inversion of exons 1 - 14. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		461360	0	5	17	Exon 1 of CDK12(+)	CDK12	37618996			17	IGR: 12Kb before CCDC182(-)	CDK12	55810160			10	INVERSION		18191164	286471	177649	5	NEW_VARIANT
P-0038428-T02-IM6	MAP3K14 (NM_003954) rearrangement: c.1288-505_c.1550-67inv	PRECISE	Note: The MAP3K14 rearrangement is an intragenic inversion of exons 7 - 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		5642	0	7	17	Intron of MAP3K14(-):67bp before exon 9	MAP3K14	43351041			17	Intron of MAP3K14(-):505bp before exon 7	MAP3K14	43352465			10	INVERSION		1424	286480	5384	11	NEW_VARIANT
P-0038483-T01-IM6	MSH2 (NM_000251) - MSH6 (NM_000179) rearrangement: c.646-879:MSH2_c.3710:MSH6del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MSH2:MSH6}		46390	0	46	2	Intron of MSH2(+):878bp before exon 4	MSH2	47638674			2	Exon 8 of MSH6(+)	MSH6	48033406			10	DELETION		394732	286717	68266	46	NEW_VARIANT
P-0038483-T01-IM6	ERBB4 (NM_005235) rearrangement: c.82+21192_.2774del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		32137	0	45	2	Exon 23 of ERBB4(-)	ERBB4	212288972			2	Intron of ERBB4(-):21Kb after exon 1	ERBB4	213381981			10	DELETION		1093009	286718	48827	46	NEW_VARIANT
P-0038584-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon2 ):c.127-1350:TMPRSS2_c.40-14330:ERGdel	PRECISE	Note: The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		27203	0	50	21	Intron of ERG(-):14Kb before exon 2	TMPRSS2	39831874			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867855			10	DELETION		3035981	287534	29569	50	NEW_VARIANT
P-0038589-T01-IM6	TAP2 (NM_018833) Rearrangement : c.762_c.946-1126dup	PRECISE	Note: The TAP2 Rearrangement results in the intragenic duplication of exon5 of TAP2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		1449	0	16	6	Intron of TAP2(-):1Kb before exon 6	TAP2	32801727			6	Exon 5 of TAP2(-)	TAP2	32803114			10	DUPLICATION		1387	287530	1553	17	NEW_VARIANT
P-0038658-T01-IM6	ZFHX3 (NM_006885) Rearrangement : chr16:g.72810206_c.9037del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		4485	0	5	16	IGR: 7Kb before ZFHX3(-)	ZFHX3	72810206			16	Exon 9 of ZFHX3(-)	ZFHX3	72827544			5	DELETION		17338	287986	8501	5	NEW_VARIANT
P-0038658-T01-IM6	SMAD2 (NM_001003652) Rearrangement : t(18,20)(q21.1; p11.1) (chr12:g.56481635::chr7:g.83729009)	PRECISE	Note: The SMAD2 Rearrangement is a translocation event with a breakpoint  in intron7. Its functional signficance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	15	20	5-UTR of NINL(-):106Kb before coding start	SMAD2	25540026			18	Intron of SMAD2(-):17bp after exon 7	SMAD2	45377627			10	TRANSLOCATION		0	287987	0	15	NEW_VARIANT
P-0038683-T01-IM6	CSF2RA (NM_001161530) - EGFR (NM_005228) rearrangement: t(7;X)(p11.2;p22.33)(chr7:g.55224220::chrX:g.1401662)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CSF2RA:EGFR}		0	0	34	X	Exon 1 of CSF2RA(+)	CSF2RA	1401662			7	Intron of EGFR(+):5bp before exon 9	EGFR	55224220			10	TRANSLOCATION		0	289193	0	39	NEW_VARIANT
P-0004593-T03-IM6	FOXA1 (NM_004496) rearrangement: c.*686_c.1040del	PRECISE	Note: The FOXA1 rearrangement is an intragenic deletion of exon 2. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		6970	0	25	14	3-UTR of FOXA1(-):685bp after coding stop	FOXA1	38059884			14	Exon 2 of FOXA1(-)	FOXA1	38060949			10	DELETION		1065	186837	3360	25	NEW_VARIANT
P-0006490-T01-IM5	ARID1A (NM_006015) rearrangement : chr1:g.26939894_c.2277:ARID1Adel	PRECISE	Note: The ARID1A (NM_006015) rearrangement event results in the deletion of ARID1A exons 1-7. One of the breakpoints is within ARID1A exon7.	MANUAL_OK	3to5	3to5	-		12910	0	5	1	IGR: 59Kb before MIR1976(+)	ARID1A	26939894			1	Exon 7 of ARID1A(+)	ARID1A	27088668			13	DELETION		148774	93675	19235	5	NEW_VARIANT
P-0006960-T01-IM5	VTCN1 (NM_024626) rearrangement : c.517_724+1186del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2034	0	26	1	Intron of VTCN1(-): 1Kb after exon 4	VTCN1	117694527			1	Exon 4 of VTCN1(-)	VTCN1	117695920			46	DELETION		1393	112446	1401	26	NEW_VARIANT
P-0024793-T01-IM6	ZFHX3 (NM_006885) Rearrangement : c.798_c.3217-29283dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		19052	0	12	16	Intron of ZFHX3(-):29Kb before exon 4	ZFHX3	72953144			16	Exon 2 of ZFHX3(-)	ZFHX3	72993247			10	DUPLICATION		40103	201529	15372	13	NEW_VARIANT
P-0024793-T01-IM6	NFE2L2 (NM_006164) Rearrangement : c.46-3658_c.403-50del	IMPPRECISE	Note: The NFE2L2 Rearrangement results in the intragenic deletion of exons 2-3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		3791	0	7	2	Intron of NFE2L2(-):50bp before exon 4	NFE2L2	178097361			2	Intron of NFE2L2(-):4Kb before exon 2	NFE2L2	178102657			0	DELETION		5296	201516	3158	7	NEW_VARIANT
P-0024793-T01-IM6	PARK2 (NM_004562) Rearrangement : c.171+87_c.412+22095del	IMPPRECISE	Note: The PARK2 Rearrangement results in the intragenic deletion of exon3 of PARK2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2386	0	10	6	Intron of PARK2(-):22Kb after exon 3	PARK2	162661462			6	Intron of PARK2(-):86bp after exon 2	PARK2	162864255			0	DELETION		202793	201518	1438	11	NEW_VARIANT
P-0031374-T02-IM6	DNMT3A (NM_022552) - ACVR2A (NM_001616) rearrangement: c.1014+79:DNMT3A_c.816+170:ACVR2Ainv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {DNMT3A:ACVR2A}		724822	0	6	2	Intron of DNMT3A(-):78bp after exon 8	DNMT3A	25470381			2	Intron of ACVR2A(+):170bp after exon 6	ACVR2A	148675165			0	INVERSION		123204784	263604	959744	6	NEW_VARIANT
P-0036253-T01-IM6	PAPSS2 (NM_001015880) - PTEN (NM_000314) rearrangement: c.880+2183:PAPSS2 _c.254-66:PTENdel	PRECISE	Note: The PAPSS2 - PTEN rearrangement is a deletion which results in the fusion of PAPSS2 exons 1-7 with PTEN exons 5-9.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {PAPSS2:PTEN}		3591	0	22	10	Intron of PAPSS2(+):3Kb before exon 8	PAPSS2	89483710			10	Intron of PTEN(+):65bp before exon 5	PTEN	89692704			10	DELETION		208994	266773	395	25	NEW_VARIANT
P-0036253-T01-IM6	CUL1 (NM_003592) - EZH2 (NM_004456) rearrangement: c.1298+434:CUL1_c.1725:EZH2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CUL1:EZH2}		6137	0	85	7	Intron of CUL1(+):434bp after exon 11	CUL1	148481603			7	Exon 15 of EZH2(-)	EZH2	148511177			10	INVERSION		29574	266775	6334	83	NEW_VARIANT
P-0038443-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.3453:NOTCH2_chr1:g.121485135inv	PRECISE	Note: The NOTCH2 rearrangement is an inversion of exons 1-21. One of the breakpoints is within exon 21. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		21919	0	36	1	Exon 21 of NOTCH2(-)	NOTCH2	120479974			1	IGR: 224Kb before EMBP1(+)	NOTCH2	121485135			10	INVERSION		1005161	290767	46041	70	NEW_VARIANT
P-0038444-T01-IM6	PTEN (NM_000314) rearrangement: t(3;10)(p13.13;q23.31)(chr3:g.109517319::chr10:g.89720655)	PRECISE	Note: The PTEN rearrangement is a translocation with a breakpoint in exon 8.	MANUAL_OK	5to5	5to5	-		0	0	27	10	Exon 8 of PTEN(+)	PTEN	89720655			3	IGR: 388Kb before LINC01205(+)	PTEN	109517319			10	TRANSLOCATION		0	290777	0	44	NEW_VARIANT
P-0038500-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1052:SMARCA4_chr19:g.11084276del	PRECISE	Note: The SMARCA4 rearrangement is a deletion of exons 1-6. One of the breakpoints is within exon 6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		13771	0	9	19	5-UTR of SMARCA4(+):11Kb before coding start	SMARCA4	11084276			19	Exon 6 of SMARCA4(+)	SMARCA4	11098534			10	DELETION		14258	286764	9397	10	NEW_VARIANT
P-0038534-T01-IM6	ATM (NM_000051) rearrangement: t(7;11)(q21.1;q22.3)(chr7:g.78322725::chr11:g.108196903)	PRECISE	Note: The ATM rearrangement is a translocation with a breakpoint in exon 47. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	23	11	Exon 47 of ATM(+)	ATM	108196903			7	Intron of MAGI2(-):66Kb before exon 3	ATM	78322725			10	TRANSLOCATION		0	286968	0	23	NEW_VARIANT
P-0038540-T01-IM6	PTPRS (NM_002850) - KDM4B (NM_015015) rearrangement: c.4195-19:PTPRS_c.919-2474:KDM4Binv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {PTPRS:KDM4B}		21715	0	4	19	Intron of KDM4B(+):2Kb before exon 10	PTPRS	5108159			19	Intron of PTPRS(-):19bp before exon 28	KDM4B	5215442			10	INVERSION		107283	286955	15666	4	NEW_VARIANT
P-0038541-T01-IM6	AKT1 (NM_001014431) - CEP128 (NM_152446) rearrangement: c.313:AKT1_c.2856+6472:CEP128del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {AKT1:CEP128}		74765	1	71	14	Intron of CEP128(-):6Kb after exon 19	AKT1	81040246			14	Exon 5 of AKT1(-)	CEP128	105242111			0	DELETION		24201865	286947	103646	72	NEW_VARIANT
P-0038543-T01-IM6	NF1 (NM_001042492) rearrangement: c.655-45_c.1063-152dup	IMPPRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 7-9. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		3529	0	9	17	Intron of NF1(+):44bp before exon 7	NF1	29508683			17	Intron of NF1(+):151bp before exon 10	NF1	29527903			0	DUPLICATION		19220	286962	6089	15	NEW_VARIANT
P-0038718-T01-IM6	ETV6 (NM_001987) rearrangement: chr12:g.3165810_c.463+6994del	PRECISE	Note: The ETV6 rearrangement is a deletion that includes ETV6 exons 1-4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		69904	0	8	12	IGR: 21Kb before TSPAN9(+)	ETV6	3165810			12	Intron of ETV6(+):7Kb after exon 4	ETV6	12013489			10	DELETION		8847679	289674	79854	8	NEW_VARIANT
P-0038718-T01-IM6	IL7R (NM_002185) rearrangement: c.1291_chr5:g.38200461del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		2598	0	6	5	Exon 8 of IL7R(+)	IL7R	35876499			5	IGR: 58Kb before EGFLAM(+)	IL7R	38200461			10	DELETION		2323962	289673	2810	7	NEW_VARIANT
P-0038722-T01-IM6	FLT1 (NM_002019) rearrangement: t(11;13)(p11.12;q12.2)(chr11:g.49412395::chr13:g.28896791)	PRECISE	Note: The FLT1 rearrangement is a translocation with a breakpoint within intron 21. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	29	13	Intron of FLT1(-):135bp after exon 21	FLT1	28896791			11	IGR: 168Kb before LOC440040(+)	FLT1	49412395			10	TRANSLOCATION		0	289707	0	31	NEW_VARIANT
P-0038745-T01-IM6	STAT3 (NM_139276) Rearrangement: c.2102-1867_c.2144+45dup	IMPPRECISE	Note: The STAT3 rearrangement is an intragenic duplication of exon 22. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		813	0	11	17	Intron of STAT3(-):44bp after exon 22	STAT3	40469155			17	Intron of STAT3(-):2Kb before exon 22	STAT3	40471109			0	DUPLICATION		1954	289905	1348	11	NEW_VARIANT
P-0038772-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2341+147:EML4_c.3173-293:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		107451	0	78	2	Intron of ALK(-):293bp before exon 20	EML4	29446687			2	Intron of EML4(+):147bp after exon 20	ALK	42553539			10	INVERSION		13106852	290727	134473	76	NEW_VARIANT
P-0038772-T01-IM6	FNDC3B (NM_022763) - CDKN2A (NM_058195, NM_000077) rearrangement: t(3;9)(q26.31;p21.3)(chr3:g.171854277::chr9:g.21971075)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {FNDC3B:CDKN2A}		0	0	11	9	Exon 2 of CDKN2A(-)	FNDC3B	21971075			3	Intron of FNDC3B(+):3Kb after exon 3	CDKN2A	171854277			10	TRANSLOCATION		0	290728	0	17	NEW_VARIANT
P-0038773-T01-IM6	NF1 (NM_001042492) rearrangement: t(1;22)(q32.1;q12.2)(chr1:g.201159807::chr22:g.30078654)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	43	22	Intron of NF2(+):1Kb after exon 15	NF1	30078654			1	Promoter of IGFN1(+):145bp from tx start	NF1	201159807			10	TRANSLOCATION		0	290736	0	44	NEW_VARIANT
P-0038774-T01-IM6	FLCN (NM_144997) rearrangement: c.397-9:FLCN_chr17:g.17661541del	PRECISE	Note: The FLCN rearrangement results in the deletion of exons 1-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7501	0	19	17	Intron of FLCN(-):9bp before exon 6	FLCN	17127466			17	5-UTR of RAI1(+):35Kb before coding start	FLCN	17661541			10	DELETION		534075	290747	7179	19	NEW_VARIANT
P-0038779-T01-IM6	CARM1 (NM_199141) rearrangement: c.221-5521_c.1615+110inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		22752	0	147	19	Intron of CARM1(+):6Kb before exon 2	CARM1	11010106			19	Intron of CARM1(+):110bp after exon 14	CARM1	11031913			10	INVERSION		21807	290757	21820	145	NEW_VARIANT
P-0038779-T01-IM6	CERKL (NM_201548) - CUL3 (NM_003590) rearrangement: c.482-6652:CERKL_c.1843-74:CUL3dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CERKL:CUL3}		180970	0	21	2	Intron of CERKL(-):14Kb before exon 3	CERKL	182445263			2	Intron of CUL3(-):74bp before exon 14	CUL3	225346869			0	DUPLICATION		42901606	290756	349694	21	NEW_VARIANT
P-0037990-T01-IM6	PEMT (NM_148172) - RNF43 (NM_017763) rearrangement: c.204+11349:PEMT_c.1909:RNF43dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PEMT:RNF43}		473049	0	5	17	Intron of PEMT(-):11Kb after exon 2	PEMT	17468885			17	Exon 9 of RNF43(-)	RNF43	56435228			10	DUPLICATION		38966343	287502	509665	5	NEW_VARIANT
P-0037990-T01-IM6	DNM2 (NM_001005361) - SMARCA4 (NM_003072) rearrangement: c.1671+1967:DNM2_c.3952-14:SMARCA4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {DNM2:SMARCA4}		84115	0	16	19	Intron of DNM2(+):2Kb after exon 14	DNM2	10925020			19	Intron of SMARCA4(+):13bp before exon 29	SMARCA4	11145576			10	DELETION		220556	287501	76435	19	NEW_VARIANT
P-0038133-T02-IM6	NFKBIA (NM_020529) rearrangement: t(12,14)(q14.3;q13.2)(chr12:g.66469859::chr14:g.35873769)	PRECISE	Note: The NFKBIA rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	39	14	Exon 1 of NFKBIA(-)	NFKBIA	35873769			12	IGR: 47Kb before LLPH(-)	NFKBIA	66469859			10	TRANSLOCATION		0	287767	0	39	NEW_VARIANT
P-0038557-T01-IM6	SMAD4 (NM_005359) Rearrangement : chr18:g.48486870_c.455-39del	PRECISE	Note: The SMAD4 Rearrangement results in the deletion of exons 1-5 of SMAD4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2985	0	8	18	IGR: 8Kb before ELAC1(+)	SMAD4	48486870			18	Intron of SMAD4(+):38bp before exon 5	SMAD4	48581112			9	DELETION		94242	292041	951	9	NEW_VARIANT
P-0038568-T01-IM6	NTRK1 (NM_002529) - SEMA4A (NM_001193300) rearrangement: c.850+416:NTRK1_c.301-270:SEMA4Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NTRK1:SEMA4A}		40455	0	18	1	Intron of SEMA4A(+):269bp before exon 4	NTRK1	156127591			1	Intron of NTRK1(+):416bp after exon 7	SEMA4A	156841963			10	DUPLICATION		714372	287509	35240	18	NEW_VARIANT
P-0038625-T01-IM6	TEK (NM_000459) rearrangement: c.1183-843_c.1278inv	PRECISE	Note: The TEK rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		926	0	83	9	Intron of TEK(+):842bp before exon 9	TEK	27184640			9	Exon 9 of TEK(+)	TEK	27185578			10	INVERSION		938	287770	1280	83	NEW_VARIANT
P-0038631-T01-IM6	ERCC2 (NM_000400) - PPP1R13L (NM_006663) rearrangement: c.2157:ERCC2_c.700:PPP1R13Ldup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERCC2:PPP1R13L}		39119	0	34	19	Exon 22 of ERCC2(-)	ERCC2	45855500			19	Exon 4 of PPP1R13L(-)	PPP1R13L	45899815			10	DUPLICATION		44315	287778	41676	34	NEW_VARIANT
P-0038643-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4433:TMPRSS2_c.40-56242:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		79994	0	50	21	Intron of ERG(-):56Kb before exon 4	TMPRSS2	39873786			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875444			10	DELETION		3001658	287866	43902	55	NEW_VARIANT
P-0023614-T02-IM6	BRAF (NM_004333) Rearrangement : chr7:g.97412920_c.1177+1522:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		173525	0	2	7	IGR: 52Kb before TAC1(+)	BRAF	97412920			7	Intron of BRAF(-):2Kb after exon 9	BRAF	140485826			10	INVERSION		43072906	291050	256402	7	NEW_VARIANT
P-0037865-T01-IM6	DNMT1 (NM_001379) Rearrangement : c.117+48:DNMT1_chr19:g.43650244inv	IMPPRECISE	Note: The DNMT1 Rearrangement results in the inversion of exons1-2 of DNMT1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		832987	0	8	19	Intron of DNMT1(-):47bp after exon 2	DNMT1	10292669			19	IGR: 22Kb before PSG5(-)	DNMT1	43650244			0	INVERSION		33357575	286488	795626	12	NEW_VARIANT
P-0038801-T01-IM6	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)	PRECISE	Note: The TFG - MET fusion is predicted to be in frame and includes the kinase domain of MET	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TFG:MET}		0	0	44	7	Intron of MET(+):1Kb before exon 15	TFG	116413541			3	Intron of TFG(+):1Kb after exon 5	MET	100452598			10	TRANSLOCATION		0	290832	0	45	NEW_VARIANT
P-0038808-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) Fusion (TMPRSS2 exon1 fused with ERG exon2) :c.55+3082:TMPRSS2_c.18+25160:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		10603	0	115	21	Intron of ERG(-):25Kb after exon 1	TMPRSS2	39845127			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42876795			10	DELETION		3031668	290964	50363	126	NEW_VARIANT
P-0037866-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2124:TMPRSS2_c.39+60551:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		42296	0	78	21	Intron of ERG(-):61Kb after exon 3	TMPRSS2	39887035			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42872240			10	DELETION		2985205	293011	76144	84	NEW_VARIANT
P-0038901-T01-IM6	ETV6 (NM_001987) rearrangement: c.1010-2332:ETV6_chr12:g.8297469del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		175204	0	38	12	IGR: 11Kb before POU5F1P3(-)	ETV6	8297469			12	Intron of ETV6(+):2Kb before exon 6	ETV6	12035047			10	DELETION		3737578	292294	206936	39	NEW_VARIANT
P-0038901-T01-IM6	PAX8 (NM_003466) rearrangement: c.1088-2327:PAX8_chr2:g.184698547del	PRECISE	Note: The PAX8 rearrangement is a deletion of exons 1 - 9. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		129068	0	38	2	Intron of PAX8(-):2Kb before exon 10	PAX8	113987160			2	IGR: 709Kb before NUP35(+)	PAX8	184698547			10	DELETION		70711387	292293	146158	38	NEW_VARIANT
P-0038970-T01-IM6	CREBBP (NM_004380) rearrangement: c.798+162:CREBBP_chr16:g.48497783inv	PRECISE	Note: The CREBBP rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		183459	0	3	16	Intron of CREBBP(-):161bp after exon 2	CREBBP	3900136			16	IGR: 75Kb before N4BP1(-)	CREBBP	48497783			10	INVERSION		44597647	292830	160052	6	NEW_VARIANT
P-0038970-T01-IM6	CDK12 (NM_016507) rearrangement: c.2249-190_c.2667-159dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		5905	0	5	17	Intron of CDK12(+):189bp before exon 5	CDK12	37650587			17	Intron of CDK12(+):158bp before exon 8	CDK12	37667623			10	DUPLICATION		17036	292829	7109	5	NEW_VARIANT
P-0038990-T01-IM6	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-6760:CDH3_c.164-49:CDH1del	IMPPRECISE	Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exons 3 - 16.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CDH3:CDH1}		3316	0	5	16	Intron of CDH3(+):7Kb before exon 3	CDH3	68703528			16	Intron of CDH1(+):48bp before exon 3	CDH1	68835524			0	DELETION		131996	293081	4061	5	NEW_VARIANT
P-0038990-T01-IM6	CDK12 (NM_016507) - FBXL20 (NM_032875) rearrangement: c.3095+27:CDK12_c.104+18457:FBXL20inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {CDK12:FBXL20}		23333	0	16	17	Intron of FBXL20(-):18Kb after exon 2	CDK12	37480976			17	Intron of CDK12(+):27bp after exon 11	FBXL20	37676367			10	INVERSION		195391	293082	60493	16	NEW_VARIANT
P-0038995-T01-IM6	JAK2 (NM_004972) rearrangement: c.2791_c.3059+880del	PRECISE	Note: The JAK2 rearrangement is an intragenic deletion of exons 21 - 22. One of the breakpoints is within exon 21. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1180	0	4	9	Exon 21 of JAK2(+)	JAK2	5090475			9	Intron of JAK2(+):880bp after exon 22	JAK2	5091791			6	DELETION		1316	293079	697	4	NEW_VARIANT
P-0039070-T01-IM6	BRCA2 (NM_000059) Rearrangement: c.8308_c.8332-974del	PRECISE	Note: The BRAC2 rearrangement is an intragenic deletion of exon 18. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		360	0	38	13	Exon 18 of BRCA2(+)	BRCA2	32937647			13	Intron of BRCA2(+):973bp before exon 19	BRCA2	32943565			10	DELETION		5918	293291	92	40	NEW_VARIANT
P-0038819-T01-IM6	NTRK1 (NM_002529) - RAB25 (NM_020387) Rearrangement :	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NTRK1:RAB25}		49938	0	88	1	Intron of RAB25(+):2Kb after exon 1	NTRK1	156032830			1	Intron of NTRK1(+):40bp after exon 10	RAB25	156844458			10	DUPLICATION		811628	291101	81662	94	NEW_VARIANT
P-0038819-T01-IM6	TP53 (NM_000546) Rearrangement : c.-28-2585_c.672+67dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript		10146	0	8	17	Intron of TP53(-):66bp after exon 6	TP53	7578110			17	5-UTR of TP53(-):10Kb before coding start	TP53	7582525			0	DUPLICATION		4415	291103	12650	8	NEW_VARIANT
P-0038848-T01-IM6	SMYD3 (NM_001167740) Rearrangement : c.532-12038_c.703-62del	IMPPRECISE	Note: The SMYD3 Rearrangement results in the intragenic deletion of exons 6-7 of SMYD3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		2186	0	13	1	Intron of SMYD3(-):62bp before exon 8	SMYD3	246079004			1	Intron of SMYD3(-):12Kb before exon 6	SMYD3	246105277			0	DELETION		26273	292004	2394	15	NEW_VARIANT
P-0038907-T01-IM6	NOTCH3 (NM_000435) - PRKCZ (NM_002744) rearrangement: t(1;19)(p36.33;p13.12)(chr1:g.2026923::chr19:g.15290892)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NOTCH3:PRKCZ}		0	0	23	19	Exon 20 of NOTCH3(-)	NOTCH3	15290892			1	Intron of PRKCZ(+):36Kb after exon 4	PRKCZ	2026923			10	TRANSLOCATION		0	292310	0	35	NEW_VARIANT
P-0038907-T01-IM6	MPL (NM_005373) rearrangement: t(1;9)(p34.2;q33.3)(chr1:g.43814976::chr9:g.128023496)	PRECISE	Note: The MPL rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MPL:GAPVD1}		0	0	12	9	Promoter of GAPVD1(+):576bp from tx start	MPL	128023496			1	Exon 10 of MPL(+)	MPL	43814976			10	TRANSLOCATION		0	292309	0	15	NEW_VARIANT
P-0038937-T01-IM6	FBXL20 (NM_032875) - ERBB2 (NM_004448) fusion: c.105-18648:FBXL20_c.1223-24:ERBB2inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ERBB2:FBXL20}		50776	0	20	17	Intron of FBXL20(-):20Kb before exon 3	FBXL20	37479575			17	Exon 18 of ERBB2(+)	ERBB2	37879824			0	INVERSION		400249	292767	1471786	22	NEW_VARIANT
P-0038937-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.936+16:CTNNB1_chr3:g.40352713inv	PRECISE	Note: The CTNNB1 rearrangement is an inversion of exons 1 - 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		5399	0	18	3	Intron of EIF1B(+):166bp after exon 2	CTNNB1	40352713			3	Intron of CTNNB1(+):16bp after exon 6	CTNNB1	41267368			10	INVERSION		914655	292764	11118	17	NEW_VARIANT
P-0038937-T01-IM6	DAXX (NM_001141970) rearrangement: c.243+38:DAXX_chr6:g.41395990inv	IMPPRECISE	Note: The DAXX rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		27181	0	47	6	Intron of DAXX(-):37bp after exon 2	DAXX	33289458			6	IGR: 74Kb before LINC01276(+)	DAXX	41395990			0	INVERSION		8106532	292765	44708	51	NEW_VARIANT
P-0039001-T01-IM6	DLG1 (NM_004087) - PIK3CA (NM_006218) rearrangement: c.1646-1039:DLG1_c.233:PIK3CAinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {DLG1:PIK3CA}		125314	0	99	3	Exon 2 of PIK3CA(+)	DLG1	178916846			3	Intron of DLG1(-):1Kb before exon 11	PIK3CA	196818936			10	INVERSION		17902090	293123	176951	121	NEW_VARIANT
P-0039003-T01-IM6	PTEN (NM_000314) rearrangement: c.497:PTEN_chr10:g.115299593inv	PRECISE	Note : The PTEN rearrangement is an inversion of exons 6 - 9. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		72464	0	46	10	Exon 6 of PTEN(+)	PTEN	89711879			10	IGR: 11Kb before HABP2(+)	PTEN	115299593			10	INVERSION		25587714	293110	89051	59	NEW_VARIANT
P-0039021-T01-IM6	PRKCE (NM_005400) - ALK (NM_004304) fusion: c.348+43259:PRKCE_c.3173-812:ALKinv	PRECISE	Note : The PRKCE - ALK fusion involves PRKCE exon 1 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {PRKCE:ALK}		81006	0	39	2	Intron of ALK(-):812bp before exon 20	PRKCE	29447206			2	Intron of PRKCE(+):43Kb after exon 1	ALK	45922846			10	INVERSION		16475640	293272	103404	36	NEW_VARIANT
P-0039058-T01-IM6	SKIL (NM_001248008) - PRKCI (NM_002740) rearrangement: c.1099-4405:SKIL_c.1418-3:PRKCIdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SKIL:PRKCI}		3650	0	30	3	Intron of PRKCI(+):2bp before exon 15	SKIL	170013696			3	Intron of SKIL(+):4Kb before exon 4	PRKCI	170094627			10	DUPLICATION		80931	293565	4840	32	NEW_VARIANT
P-0039063-T01-IM6	TP53 (NM_000546) rearrangement: c.189_c.809del	PRECISE	Note : The TP53 rearrangement is an intragenic deletion of exons 4 - 8. The breakpoints are within exon 4 and exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7544	0	56	17	Exon 8 of TP53(-)	TP53	7577129			17	Exon 4 of TP53(-)	TP53	7579498			10	DELETION		2369	293548	6551	60	NEW_VARIANT
P-0039063-T01-IM6	KEAP1 (NM_203500) rearrangement: c.1246:KEAP1_chr19:g.10595435del	PRECISE	Note : The KEAP1 rearrangement is a deletion of exons 3 - 6. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7507	0	15	19	Promoter of KEAP1(-):1Kb from tx start	KEAP1	10595435			19	Exon 3 of KEAP1(-)	KEAP1	10602332			10	DELETION		6897	293549	6818	26	NEW_VARIANT
P-0039064-T01-IM6	MFSD11 (NM_001242532) - NOTCH2 (NM_024408) rearrangement: t(1;17)(p12;q25.1)(chr1:g.120497842::chr17:g.74746935)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MFSD11:NOTCH2}		0	0	36	17	Intron of MFSD11(+):3Kb before exon 9	MFSD11	74746935			1	Exon 13 of NOTCH2(-)	NOTCH2	120497842			10	TRANSLOCATION		0	293562	0	39	NEW_VARIANT
P-0039064-T01-IM6	APC (NM_000038) rearrangement: t(5;21)(q22.2;p11.2)(chr5:g.112151212::chr21:g.10829409)	PRECISE	Note : The APC rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	18	21	IGR: 77Kb before TPTE(-)	APC	10829409			5	Exon 9 of APC(+)	APC	112151212			10	TRANSLOCATION		0	293563	0	19	NEW_VARIANT
P-0016627-T02-IM6	GLI1 (NM_005269) rearrangement: t(1;12)(q31.1;q13.3)(chr1:g.188655289::chr12:g.57857810)	PRECISE	Note: The GLI1 rearrangement is a translocation with breakpoint in exon 3 of GLI1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	174	12	Exon 3 of GLI1(+)	GLI1	57857810			1	IGR: 1Mb before BRINP3(-)	GLI1	188655289			10	TRANSLOCATION		0	293290	0	174	NEW_VARIANT
P-0038857-T01-IM6	PIK3C3 (NM_002647) Rearrangement : chr18:g.6630097_c.2432+13:PIK3C3inv	PRECISE	Note: The PIK3C3 Rearrangement results in the inversion of exons 1-22 of PIK3C3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		43714	0	57	18	IGR: 119Kb before LINC01387(+)	PIK3C3	6630097			18	Intron of PIK3C3(+):13bp after exon 22	PIK3C3	39638028			10	INVERSION		33007931	291987	71817	57	NEW_VARIANT
P-0039045-T01-IM6	KDM5A (NM_001042603) - STAT5A (NM_003152) rearrangement: t(12;17)(p13.33;q21.2)(chr12:g.470840::chr17:g.40459887)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {KDM5A:STAT5A}		0	0	6	17	Intron of STAT5A(+):146bp after exon 16	KDM5A	40459887			12	Intron of KDM5A(-):1Kb after exon 5	STAT5A	470840			6	TRANSLOCATION		0	293418	0	6	NEW_VARIANT
P-0039047-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4233:TMPRSS2_c.18+8075:ERGdel	PRECISE	Note : The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66945	0	47	21	Intron of ERG(-):8Kb after exon 1	TMPRSS2	39862212			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874349			10	DELETION		3012137	293427	69329	47	NEW_VARIANT
P-0039180-T01-IM6	OSBP2 (NM_030758) - EWSR1 (NM_013986) rearrangement: c.853+38356:OSBP2_c.993-1321:EWSR1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {OSBP2:EWSR1}		74490	0	98	22	Intron of EWSR1(+):1Kb before exon 10	OSBP2	29686233			22	Intron of OSBP2(+):38Kb after exon 2	EWSR1	31175712			10	DUPLICATION		1489479	293946	60862	106	NEW_VARIANT
P-0039087-T01-IM6	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	PRECISE	Note: The FGFR2 - BICC1 Fusion is an in-frame fusion and include the protein kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		219056	0	25	10	Intron of BICC1(+):133bp after exon 15	FGFR2	60563135			10	Intron of FGFR2(-):1Kb after exon 17	BICC1	123242059			10	INVERSION		62678924	293406	279324	27	NEW_VARIANT
P-0039094-T01-IM6	CREBBP (NM_004380) Rearrangement: c.435_c.798+6330del	PRECISE	Note: The CREBBP rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2878	0	21	16	Intron of CREBBP(-):6Kb after exon 2	CREBBP	3893968			16	Exon 2 of CREBBP(-)	CREBBP	3900661			10	DELETION		6693	293408	2378	23	NEW_VARIANT
P-0039223-T01-IM6	TRAF7 (NM_032271) rearrangement: t(16;20)(p13.3;q12)(chr16:g.2221580::chr20:g.40221310)	PRECISE	Note: The TRAF7 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TRAF7:CHD6}		0	0	14	20	5-UTR of CHD6(-):188Kb before coding start	TRAF7	40221310			16	Exon 7 of TRAF7(+)	TRAF7	2221580			10	TRANSLOCATION		0	294375	0	14	NEW_VARIANT
P-0039241-T01-IM6	C16orf45 (NM_033201) - TSC2 (NM_000548) rearrangement: c.106+2910:C16orf45_c.1840-5:TSC2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {C16orf45:TSC2}		294633	0	15	16	Intron of TSC2(+):4bp before exon 18	C16orf45	2121506			16	Intron of C16orf45(+):3Kb after exon 1	TSC2	15531526			10	DUPLICATION		13410020	294733	280640	14	NEW_VARIANT
P-0039245-T01-IM6	EWSR1 (NM_013986) rearrangement: c.1309+219:EWSR1_chr22:g.29890022dup	PRECISE	Note: The EWSR1 rearrangement is a duplication of exons 14 - 18. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {NEFH:EWSR1}		9056	0	15	22	Intron of EWSR1(+):219bp after exon 13	EWSR1	29692577			22	Promoter of NEFH(+):14Kb from tx start	EWSR1	29890022			10	DUPLICATION		197445	294739	9747	15	NEW_VARIANT
P-0039245-T01-IM6	PDGFRB (NM_002609) rearrangement: c.1367+75:PDGFRB_chr5:g.152640215inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		36413	0	15	5	Intron of PDGFRB(-):74bp after exon 9	PDGFRB	149510027			5	IGR: 230Kb before GRIA1(+)	PDGFRB	152640215			10	INVERSION		3130188	294740	45838	18	NEW_VARIANT
P-0039297-T01-IM6	PPM1D (NM_003620) rearrangement: c.827-117_c.1017+3546dup	PRECISE	Note: The PPM1D rearrangement is an intragenic duplication of exon 4. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1392	0	12	17	Intron of PPM1D(+):116bp before exon 4	PPM1D	58725136			17	Intron of PPM1D(+):4Kb after exon 4	PPM1D	58728989			10	DUPLICATION		3853	295287	2838	25	NEW_VARIANT
P-0039300-T01-IM6	BTK (NM_000061) rearrangement: c.1908+94:BTK_chrX:g.99466815del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		1925	0	28	X	IGR: 80Kb before PCDH19(-)	BTK	99466815			X	Intron of BTK(-):93bp after exon 18	BTK	100608088			10	DELETION		1141273	295290	3174	37	NEW_VARIANT
P-0039306-T01-IM6	POLE (NM_006231) rearrangement: c.2865-21:POLE_chr12:g.76693286inv	IMPPRECISE	Note: The POLE rearrangement is an inversion of exons 25 - 49. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		163857	0	19	12	IGR: 45Kb before BBS10(-)	POLE	76693286			12	Intron of POLE(-):21bp before exon 25	POLE	133237771			0	INVERSION		56544485	295297	222078	19	NEW_VARIANT
P-0039307-T01-IM6	FOXK1 (NM_001037165) - CARD11 (NM_032415) rearrangement: c.1244+854:FOXK1_c.1342-84:CARD11inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {FOXK1:CARD11}		12116	0	28	7	Intron of CARD11(-):84bp before exon 10	FOXK1	2974347			7	Intron of FOXK1(+):854bp after exon 5	CARD11	4797672			10	INVERSION		1823325	295298	16666	28	NEW_VARIANT
P-0021561-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon2 with ERG exon4) :  c.127-1071:TMPRSS2_c.40-56818:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28535	0	42	21	Intron of ERG(-):57Kb before exon 4	TMPRSS2	39874362			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867576			10	DELETION		2993214	187673	39786	43	NEW_VARIANT
P-0039139-T01-IM6	NAB2 (NM_005967) - KIF5A (NM_004984) rearrangement: c.958-157:NAB2_c.129+5819:KIF5Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {NAB2:KIF5A}		64663	0	62	12	Intron of NAB2(+):156bp before exon 3	NAB2	57486074			12	Intron of KIF5A(+):6Kb after exon 1	KIF5A	57950002			10	DELETION		463928	293751	51034	235	NEW_VARIANT
P-0039229-T01-IM6	UPF1 (NM_002911) rearrangement: c.3019+11:UPF1_chr19:g.16454164inv	PRECISE	Note: The UPF1 rearrangement is an inversion of exons 1 - 21. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		129825	0	5	19	IGR: 12Kb before EPS15L1(-)	UPF1	16454164			19	Intron of UPF1(+):11bp after exon 21	UPF1	18976270			7	INVERSION		2522106	294659	187209	5	NEW_VARIANT
P-0039229-T01-IM6	HIGD1A (NM_001099668) - CTNNB1 (NM_001904) rearrangement: c.139+3968:HIGD1A_c.242-64:CTNNB1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {HIGD1A:CTNNB1}		14449	0	52	3	Intron of CTNNB1(+):63bp before exon 4	HIGD1A	41266381			3	Intron of HIGD1A(-):4Kb after exon 2	CTNNB1	42831681			10	INVERSION		1565300	294658	22713	56	NEW_VARIANT
P-0039234-T01-IM6	ADCY10 (NM_018417) - NUF2 (NM_031423) rearrangement: c.828+205:ADCY10_c.26:NUF2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ADCY10:NUF2}		18108	0	32	1	Exon 2 of NUF2(+)	ADCY10	163295867			1	Intron of ADCY10(-):204bp after exon 5	NUF2	167862886			10	INVERSION		4567019	294674	17519	47	NEW_VARIANT
P-0039234-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2672_c.126+638del	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		23025	0	107	21	Intron of TMPRSS2(-):637bp after exon 2	TMPRSS2	42869408			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872788			10	DELETION		3380	294672	24781	255	NEW_VARIANT
P-0039238-T01-IM6	NF1 (NM_001042492) rearrangement: c.4198:NF1_chr17:g.34951290inv	PRECISE	Note: The NF1 rearrangement is an inversion of exons 32 - 58. One of the breakpoints is within exon 32. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		69570	0	23	17	Exon 32 of NF1(+)	NF1	29585386			17	Intron of DHRS11(+):110bp before exon 2	NF1	34951290			10	INVERSION		5365904	294527	100854	30	NEW_VARIANT
P-0039238-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-480:TMPRSS2_c.18+5750:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		23234	0	6	21	Intron of ERG(-):6Kb after exon 1	TMPRSS2	39864537			21	Intron of TMPRSS2(-):480bp before exon 3	ERG	42866985			0	DELETION		3002448	294525	28409	6	NEW_VARIANT
P-0039291-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.2518+51:WHSC1_chr4:g.28355378del	PRECISE	Note: The WHSC1 rearrangement is a deletion of exons 14 - 22. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		29962	0	13	4	Intron of WHSC1(+):51bp after exon 13	WHSC1	1957118			4	IGR: 466Kb before MIR4275(+)	WHSC1	28355378			10	DELETION		26398260	295495	33918	13	NEW_VARIANT
P-0039295-T01-IM6	INPPL1 (NM_001567) rearrangement: t(3;11)(p11.1;q13.4)(chr3:g.90035582::chr11:g.71936263)	PRECISE	Note: The INPPL1 rearrangement is a translocation with a breakpoint in intron 1.	MANUAL_OK	3to5	3to5	-		0	0	40	11	Intron of INPPL1(+):53bp after exon 1	INPPL1	71936263			3	IGR: 879Kb before EPHA3(+)	INPPL1	90035582			10	TRANSLOCATION		0	295515	0	39	NEW_VARIANT
P-0039320-T01-IM6	ALK (NM_004304) rearrangement: c.2651:ALK_chr2:g.22452824dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		119700	0	54	2	IGR: 307Kb before LOC102723362(+)	ALK	22452824			2	Exon 16 of ALK(-)	ALK	29451914			10	DUPLICATION		6999090	295389	128819	63	NEW_VARIANT
P-0039326-T01-IM6	UPF1 (NM_002911) rearrangement: t(8;19)(p21.2;p13.11)(chr8:g.24400830::chr19:g.18974316)	PRECISE	Note: The UPF1 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	69	19	Exon 19 of UPF1(+)	UPF1	18974316			8	3-UTR of LOC101929294(-):5Kb after coding stop	UPF1	24400830			10	TRANSLOCATION		0	295405	0	74	NEW_VARIANT
P-0001507-T01-IM3	None	PRECISE		MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5797	0	6	17	Intron of MAP2K4(+): 6Kb after exon 2	None	11964668			17	Exon 5 of MAP2K4(+)	None	12011204			26	DELETION		46536	1910	2784	7	NEW_VARIANT
P-0033283-T03-IM6	MEN1 (NM_000244) rearrangement: t(11,18)(q13.1;p11.31)(chr11:g.64574579::chr18:g.4043058)	PRECISE	Note: The MEN1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	49	18	5-UTR of DLGAP1(-):544Kb before coding start	MEN1	4043058			11	Intron of MEN1(-):9bp before exon 6	MEN1	64574579			10	TRANSLOCATION		0	284124	0	48	NEW_VARIANT
P-0039109-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-83:FGFR3_c.162+65:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		28625	0	17	4	Intron of TACC3(+):65bp after exon 2	FGFR3	1725375			4	Intron of FGFR3(+):82bp before exon 18	TACC3	1808760			10	DUPLICATION		83385	293526	32508	17	NEW_VARIANT
P-0039365-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.2491:PIK3C2G_chr12:g.18195353del	PRECISE	Note: The PIK3C2G rearrangement is a deletion of exons 1 - 18. One of the breakpoints is within exon 18. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		25276	0	47	12	IGR: 38Kb before RERGL(-)	PIK3C2G	18195353			12	Exon 18 of PIK3C2G(+)	PIK3C2G	18641492			10	DELETION		446139	296009	24632	50	NEW_VARIANT
P-0039370-T01-IM6	RPAP3 (NM_024604) - FGFR2 (NM_000141) rearrangement: t(10;12)(q26.13;q13.11)(chr10:g.123242832::chr12:g.48092574)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RPAP3:FGFR2}		0	0	59	12	Intron of RPAP3(-):1Kb before exon 4	RPAP3	48092574			10	Intron of FGFR2(-):379bp after exon 17	FGFR2	123242832			10	TRANSLOCATION		0	295991	0	61	NEW_VARIANT
P-0039377-T01-IM6	EIF4A2 (NM_001967) rearrangement: t(2;3)(q31.2;q27.3)(chr2:g.180104857::chr3:g.186505193)	PRECISE	Note: The EIF4A2 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	20	3	Intron of EIF4A2(+):90bp before exon 9	EIF4A2	186505193			2	5-UTR of SESTD1(-):130Kb before coding start	EIF4A2	180104857			10	TRANSLOCATION		0	296008	0	19	NEW_VARIANT
P-0039413-T01-IM6	NUP210L (NM_207308) - PTCH1 (NM_000264) rearrangement: t(1;9)(q21.3;q22.32)(chr1:g.153966858::chr9:g.98209832)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {NUP210L:PTCH1}		0	0	21	9	Intron of PTCH1(-):99bp before exon 23	NUP210L	98209832			1	Intron of NUP210L(-):693bp after exon 36	PTCH1	153966858			10	TRANSLOCATION		0	296199	0	21	NEW_VARIANT
P-0039421-T01-IM6	DOT1L (NM_032482) - ZNF77 (NM_021217) rearrangement: c.4606+1182:DOT1L_c.130+1031:ZNF77inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {DOT1L:ZNF77}		3408	0	34	19	Intron of DOT1L(+):1Kb after exon 27	DOT1L	2228308			19	Intron of ZNF77(-):1Kb after exon 2	ZNF77	2938248			10	INVERSION		709940	296202	4631	34	NEW_VARIANT
P-0039422-T01-IM6	RAD52 (NM_134424) rearrangement: t(1;12)(q32.1;p13.33)(chr1:g.201991943::chr12:g.1025575)	PRECISE	Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 9. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	60	12	Exon 9 of RAD52(-)	RAD52	1025575			1	IGR: 12Kb before ELF3(+)	RAD52	201991943			10	TRANSLOCATION		0	296198	0	62	NEW_VARIANT
P-0039508-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.1010+22:TMPRSS2_c.19-22866:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 9 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		14804	0	30	21	Intron of ERG(-):23Kb before exon 2	TMPRSS2	39840410			21	Intron of TMPRSS2(-):21bp after exon 9	ERG	42845230			10	DELETION		3004820	296498	8464	33	NEW_VARIANT
P-0003167-T01-IM5		PRECISE	Note: The STK11 (NM_000455) rearrangement event results in the intragenic deletion of exons 2-5, potentially disabling the function of the gene.	MANUAL_OK	3to5	3to5	Deletion of 4 exons: in frame		6608	0	20	19	Intron of STK11(+): 3Kb before exon 2	STK11	1215776			19	Intron of STK11(+): 46bp before exon 6	STK11	1221166			46	DELETION		5390	9344	4991	23	NEW_VARIANT
P-0003206-T01-IM5		PRECISE	EML4-ALK Known fusion annotation	MANUAL_OK	3to3	3to3	Protein fusion: mid-exon (EML4-ALK)		62635	0	101	2	Exon 19 of ALK(-)	ALK	29448365			2	Intron of EML4(+): 488bp after exon 5	EML4	42492359			89	INVERSION		13043994	9702	55899	128	NEW_VARIANT
P-0003507-T01-IM5		PRECISE	exon 1 and 2 of ROS1 fuse to exon 4-6 of SLC16A10.  functional significance is undetermined	MANUAL_OK	5to5	5to5	Protein fusion: in frame (ROS1-SLC16A10)		286637	0	9	6	Intron of SLC16A10(+): 10Kb before exon 4	SLC16A10	111518235			6	Intron of ROS1(-): 64bp after exon 2	ROS1	117739561			12	INVERSION		6221326	11938	236297	9	NEW_VARIANT
P-0003560-T01-IM5	c.1726_*7586inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		4065	0	26	5	Exon 7 of PIK3R1(+)	c.1726_*7586inv	67591133			5	IGR: 3Kb after PIK3R1(+)	c.1726_*7586inv	67601015			42	INVERSION		9882	12079	2437	24	NEW_VARIANT
P-0003700-T01-IM5	NOTCH2 (NM_024408) rearrangement: c.1682-62_c.1916-920dup	PRECISE	NOTCH2 (NM_024408) rearrangement event is a duplication which results in the duplication of exons 11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon: in frame		2128	0	5	1	Intron of NOTCH2(-): 920bp before exon 12	NOTCH2	120503045			1	Intron of NOTCH2(-): 62bp before exon 11	NOTCH2	120506492			16	DUPLICATION		3447	12630	2705	5	NEW_VARIANT
P-0004203-T01-IM5	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement: t(7;9)(7q34;9q33.2)(chr7:140491585::chr9:123251876)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (CDK5RAP2-BRAF)		0	0	71	9	Intron of CDK5RAP2(-): 2Kb after exon 13	CDK5RAP2	123251876			7	Intron of BRAF(-): 3Kb after exon 8	BRAF	140491585			25	TRANSLOCATION		0	16703	0	62	NEW_VARIANT
P-0004650-T01-IM5	KDM5C(NM_004187) Rearrangement : chrX:g.42358230_c.1314:KDM5Cinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		153714	0	34	X	IGR: 278Kb before PPP1R2P9(-)	KDM5C	42358230			X	Exon 10 of KDM5C(-)	KDM5C	53240766			39	INVERSION		10882536	28977	160746	32	NEW_VARIANT
P-0004650-T01-IM5	KDM5C(NM_004187) Rearrangement : c.881:KDM5C_chrX:g.53629392inv	PRECISE	Note: The KDM5C(NM_004187) Rearrangement results in the inversion of exons 1 to 7 of KDM5C.The breakpoint is within exon 7.Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		8645	0	21	X	Exon 7 of KDM5C(-)	KDM5C	53245059			X	Intron of HUWE1(-): 133bp after exon 28	KDM5C	53629392			32	INVERSION		384333	28978	9560	21	NEW_VARIANT
P-0039159-T01-IM6	TSC2 (NM_000548) rearrangement: c.1717-2316_c.2082del	PRECISE	Note : The TSC2 rearrangement is an intragenic deletion of exons 17 - 19. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5595	0	68	16	Intron of TSC2(+):2Kb before exon 17	TSC2	2118141			16	Exon 19 of TSC2(+)	TSC2	2121920			10	DELETION		3779	293931	4745	81	NEW_VARIANT
P-0039159-T01-IM6	AGO2 (NM_012154) - PTK2 (NM_005607) rearrangement: c.2169+76:AGO2_c.2208+5073:PTK2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {AGO2:PTK2}		27508	0	40	8	Intron of AGO2(-):75bp after exon 16	AGO2	141549343			8	Intron of PTK2(-):5Kb after exon 23	PTK2	141722624			10	DUPLICATION		173281	293932	48083	41	NEW_VARIANT
P-0039439-T01-IM6	AKAP12 (NM_005100) - E2F3 (NM_001949) rearrangement: c.163-16213:AKAP12_c.1136-225:E2F3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {AKAP12:E2F3}		491919	0	10	6	Intron of E2F3(+):224bp before exon 7	AKAP12	20490174			6	Intron of AKAP12(+):16Kb before exon 3	E2F3	151610669			6	DUPLICATION		131120495	295974	805252	10	NEW_VARIANT
P-0039473-T01-IM6	MSH3 (NM_002439) rearrangement: c.1341-16442_c.2436-132inv	PRECISE	Note: The MSH3 rearrangement is an intragenic inversion of exons 9 - 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		10304	0	13	5	Intron of MSH3(+):16Kb before exon 9	MSH3	80004830			5	Intron of MSH3(+):131bp before exon 18	MSH3	80083252			10	INVERSION		78422	296097	8351	14	NEW_VARIANT
P-0006796-T01-IM5	FAT1 (NM_005245) rearrangement : c.10118_11640+406inv	PRECISE	Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 16-21. One of the breakpoints is within FAT1 exon16.	MANUAL_OK	3to3	3to3	-		23006	0	53	4	Intron of FAT1(-): 406bp after exon 21	FAT1	187522017			4	Exon 16 of FAT1(-)	FAT1	187530425			73	INVERSION		8408	109035	19959	38	NEW_VARIANT
P-0006796-T01-IM5	FAT1 (NM_005245) rearrangement : c.10068+193_11436inv	PRECISE	Note: The FAT1 (NM_005245) rearrangement event results in the inversion of FAT1 exons 16-20. One of the breakpoints is within FAT1 exon20.	MANUAL_OK	5to5	5to5	Antisense fusion		18533	0	34	4	Exon 20 of FAT1(-)	FAT1	187524103			4	Intron of FAT1(-): 193bp after exon 15	FAT1	187530762			82	INVERSION		6659	109036	17357	34	NEW_VARIANT
P-0006856-T02-IM5	TMPRSS2 (NM_001135099) -ERG (NM_004449) fusion (TMPRSS2 exon 1 fused with ERG exons 4-11): c.56-2091:TMPRSS2_c.40-13213:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		87424	0	102	21	Intron of ERG(-): 13Kb before exon 4	TMPRSS2	39830757			21	Intron of TMPRSS2(-): 2Kb before exon 2	ERG	42872207			70	DELETION		3041450	162053	55191	108	NEW_VARIANT
P-0006856-T02-IM5	MAP3K1 (NM_005921) - C5orf64 (NM_173667) rearrangement: c.3454:MAP3K1_c.226-4097:C5orf64del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (MAP3K1-FLJ37543)		47532	0	39	5	Exon 14 of MAP3K1(+)	MAP3K1	56178481			5	Intron of FLJ37543(+): 4Kb before exon 4	C5orf64	60995596			33	DELETION		4817115	162054	30685	27	NEW_VARIANT
P-0007980-T01-IM5	PIM1 (NM_002648) rearrangement: t(6;7)(p21.2;p14.3)(chr6:g.37138620::chr7:g.30811615 )	PRECISE	The PIM1 (NM_002648) rearrangement: is a translocation which may result in a truncated PIM1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	15	7	Intron of FAM188B(+): 443bp after exon 1	PIM1	30811615			6	Exon 2 of PIM1(+)	PIM1	37138620			13	TRANSLOCATION		0	119886	0	14	NEW_VARIANT
P-0010537-T01-IM5	ETV6 (NM_001987) Rearrangement : c.163+31820_463+1139dup	PRECISE	Note: The ETV6 Rearrangement  results in the duplication of exons 3-4 of ETV6. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		13937	0	84	12	Intron of ETV6(+): 32Kb after exon 2	ETV6	11937333			12	Intron of ETV6(+): 1Kb after exon 4	ETV6	12007634			93	DUPLICATION		70301	147573	19109	74	NEW_VARIANT
P-0010537-T01-IM5	PPP2R1A (NM_014225) rearrangement: t(10;19)(q23.33;q13.41)(chr10:g.95055215::chr19:g.52724231)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	40	19	Intron of PPP2R1A(+): 1bp before exon 12	PPP2R1A	52724231			10	IGR: 11Kb before MYOF(-)	PPP2R1A	95055215			48	TRANSLOCATION		0	147578	0	40	NEW_VARIANT
P-0011515-T01-IM5	TMPRSS2 (NM_001135099)  Rearrangement : c.56-954_c.556+505inv	PRECISE	Note: The  TMPRSS2 Rearrangement results in the intragenic inversion of exon2-5 of TMPRSS2. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		35790	0	22	21	Intron of TMPRSS2(-): 505bp after exon 5	TMPRSS2	42859816			21	Intron of TMPRSS2(-): 954bp before exon 2	TMPRSS2	42871070			36	INVERSION		11254	154011	28513	12	NEW_VARIANT
P-0011537-T01-IM5	EGFL7 (NM_201446) rearrangement: t(3;9)(p14.2;q34.3)(chr3:g.59696693::chr9:g.139564655)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	29	9	Exon 7 of EGFL7(+)	EGFL7	139564655			3	IGR: 38Kb before FHIT(-)	EGFL7	59696693			34	TRANSLOCATION		0	154136	0	29	NEW_VARIANT
P-0011555-T01-IM5	SDHAF2 (NM_017841) rearrangement: c.367_c.371-4del	PRECISE	Note: The SDHAF2 rearrangement is an intragenic deletion of a part of exon 3. One of the breakpoint is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		606	0	8	11	Exon 3 of SDHAF2(+)	SDHAF2	61205582			11	Intron of SDHAF2(+): 4bp before exon 4	SDHAF2	61213409			23	DELETION		7827	155613	641	8	NEW_VARIANT
P-0011555-T01-IM5	FAM65B (NM_014722) - SDHAF2 (NM_017841) rearrangement: t(6;11)(p22.3;q12.2)(chr6:g.24806597::chr11:g.61205093)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	5	11	Intron of SDHAF2(+): 4bp before exon 2	FAM65B	61205093			6	3-UTR of FAM65B(-): 4bp after coding stop	SDHAF2	24806597			7	TRANSLOCATION		0	155614	0	5	NEW_VARIANT
P-0012048-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+186:TMPRSS2_c.39+62923:ERGdel	PRECISE	Note: TMPRSS2 is fused with the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		58846	0	48	21	Intron of ERG(-): 63Kb after exon 3	TMPRSS2	39884663			21	Intron of TMPRSS2(-): 186bp after exon 2	ERG	42869860			43	DELETION		2985197	159977	40826	43	NEW_VARIANT
P-0012736-T01-IM5	CDKN2A (NM_000077, NM_058195) rearrangement: c.150+462_c.244del:CDKN2Ap16INK4A ,  c.194-3008_c.287del:CDKN2Ap14ARF	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		373	0	23	9	Exon 2 of CDKN2A(-)	CDKN2A	21971114			9	Intron of CDKN2A(-): 462bp after exon 1	CDKN2A	21974215			29	DELETION		3101	158736	134	20	NEW_VARIANT
P-0013000-T01-IM5	FANCA (NM_000135) Rearrangement :  c.2015-88:FANCA_c.614+201:TCF25del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		48295	0	21	16	Intron of FANCA(-): 88bp before exon 23	FANCA	89838310			16	Intron of TCF25(+): 201bp after exon 5	FANCA	89954326			25	DELETION		116016	159882	34975	18	NEW_VARIANT
P-0013000-T01-IM5	AKAP8 (NM_005858) -NOTCH3  (NM_000435) Rearrangement : c.1623+359:AKAP8_c.4705:NOTCH3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (AKAP8-NOTCH3)		130720	0	54	19	Exon 25 of NOTCH3(-)	AKAP8	15284910			19	Intron of AKAP8(-): 359bp after exon 13	NOTCH3	15469419			66	DELETION		184509	159883	93282	53	NEW_VARIANT
P-0013106-T01-IM5	AXIN1 (NM_003502) rearrangement: chr16:g.331906_c.1116+53:AXIN1del	PRECISE	Note: The AXIN1 rearrangement is a deletion of exons 5-11.	MANUAL_OK	3to5	3to5	Antisense fusion		33490	0	5	16	Exon 2 of ARHGDIG(+)	AXIN1	331906			16	Intron of AXIN1(-): 53bp after exon 4	AXIN1	359920			9	DELETION		28014	160282	31761	5	NEW_VARIANT
P-0013106-T01-IM5	POLD1 (NM_002691) rearrangement: c.1757:POLD1_chr19:g.56784053del	PRECISE	Note: The POLD1 rearrangement is a deletion of exons 14-27. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	-		106010	0	102	19	Exon 14 of POLD1(+)	POLD1	50910654			19	IGR: 51Kb before ZSCAN5A(-)	POLD1	56784053			117	DELETION		5873399	160283	152505	158	NEW_VARIANT
P-0013503-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused with ERG exons 2-10): c.55+4160:TMPRSS2_c.18+11744:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		108634	0	100	21	Intron of ERG(-):12Kb after exon 1	TMPRSS2	39858543			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875718			10	DELETION		3017175	186391	89497	112	NEW_VARIANT
P-0013625-T01-IM5	ARID5B (NM_032199) rearrangement: c.734-289_c.991del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2537	0	10	10	Intron of ARID5B(+): 289bp before exon 5	ARID5B	63810358			10	Exon 6 of ARID5B(+)	ARID5B	63817020			16	DELETION		6662	161855	1667	10	NEW_VARIANT
P-0013625-T01-IM5	CTNNB1 (NM_001904) rearrangement: c.-48-2076_c.844del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		9114	0	42	3	5-UTR of CTNNB1(+): 2Kb before coding start	CTNNB1	41263436			3	Exon 6 of CTNNB1(+)	CTNNB1	41267260			46	DELETION		3824	161857	10974	42	NEW_VARIANT
P-0013831-T01-IM5	CDK12 (NM_016507) rearrangement: chr17:g.37597504_c.1301:CDK12del	PRECISE	Note: The CDK12 rearrangement is a deletion of 5UTR and exons 1-2.	MANUAL_OK	3to5	3to5	-		13536	0	25	17	Intron of MED1(-): 574bp before exon 4	CDK12	37597504			17	Exon 2 of CDK12(+)	CDK12	37627386			40	DELETION		29882	162461	15214	24	NEW_VARIANT
P-0014261-T01-IM6	NF1 (NM_001042492) rearrangement: c.5268+131_c.6155inv	PRECISE	Note: The NF1 rearrangement is an intragenic inversion of exons 36-41. One of the breakpoints is within exon 41.	MANUAL_OK	3to3	3to3	Antisense fusion		8053	0	9	17	Intron of NF1(+): 131bp after exon 36	NF1	29653401			17	Exon 41 of NF1(+)	NF1	29663660			12	INVERSION		10259	163934	6928	9	NEW_VARIANT
P-0014261-T01-IM6	SYK (NM_003177) rearrangement: c.1408:SYK_chr9:g.134211866inv	PRECISE	Note: The SYK rearrangement is an inversion of exons 11-14. One of the breakpoints is within exon 11.	MANUAL_OK	5to5	5to5	-		225482	0	35	9	Exon 10 of SYK(+)	SYK	93641062			9	IGR: 47Kb before PPAPDC3(+)	SYK	134211866			61	INVERSION		40570804	163935	240834	35	NEW_VARIANT
P-0014629-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exon3): c.56-4111:TMPRSS2_c.39+32697:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		91507	0	81	21	Intron of ERG(-): 33Kb after exon 3	TMPRSS2	39914889			21	Intron of TMPRSS2(-): 4Kb before exon 2	ERG	42874227			47	DELETION		2959338	165298	56254	70	NEW_VARIANT
P-0014634-T01-IM6	CIC (NM_015125) Rearrangement : c.3008+26:CIC_chr19:42803409del	PRECISE	Note: The CIC Rearrangement results in the deletion of exon 12 -20 of CIC. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense fusion		23652	0	49	19	Intron of CIC(+): 26bp after exon 12	CIC	42796385			19	Intron of PAFAH1B3(-): 713bp after exon 4	CIC	42803409			56	DELETION		7024	165329	20556	38	NEW_VARIANT
P-0016983-T02-IM6	DNAJB1 (NM_006145) Rearrangement : 19:47623580_c.211+21:DNAJB1inv	PRECISE	Note: The DNAJB1 Rearrangement results in the inversion of exon 1 of DNAJB1. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		591707	0	28	19	Intron of DNAJB1(-):20bp after exon 1	DNAJB1	14628930			19	IGR: 10Kb before SAE1(+)	DNAJB1	47623580			10	INVERSION		32994650	187681	569379	28	NEW_VARIANT
P-0016983-T02-IM6	UPF1 (NM_002911) Rearrangement : c.3045:UPF1_chr19:g.58978895inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		430670	0	31	19	Exon 22 of UPF1(+)	UPF1	18976395			19	5-UTR of ZNF324(+):2Kb before coding start	UPF1	58978895			10	INVERSION		40002500	187682	510797	30	NEW_VARIANT
P-0016983-T02-IM6	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	PRECISE	Note: The TMPRSS2  - ERG fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28469	0	93	21	Intron of ERG(-):15Kb before exon 2	TMPRSS2	39832975			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG fusion	42867872			10	DELETION		3034897	187678	13788	100	NEW_VARIANT
P-0020592-T01-IM6	ROS1 (NM_002944) rearrangement: g.21888762_c.5367-710del	PRECISE	Note: The ROS1 rearrangement results in the deletion of exons 33-43. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		909711	0	43	6	5-UTR of CASC15(+):306Kb before coding start	ROS1	21888762			6	Intron of ROS1(-):710bp before exon 33	ROS1	117648287			10	DELETION		95759525	184772	1093458	44	NEW_VARIANT
P-0020608-T01-IM6	TP53 (NM_000546) rearrangement: t(12:17)(q23.1;p13.1)(chr12:g.98491631::chr17:g.7579685)	PRECISE	Note: The TP53 rearrangement is a translocation that may result in the truncation of TP53 exons 4-11.	MANUAL_OK	5to3	5to3	-		0	0	103	17	Intron of TP53(-):14bp after exon 3	TP53	7579685			12	IGR: 102Kb before MIR4303(-)	TP53	98491631			10	TRANSLOCATION		0	184837	0	115	NEW_VARIANT
P-0020843-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRRS2 exon 1 fused to ERG exons 4-11):c.126+1610:TMPRSS2_c.40-60543:ERGdel	PRECISE	Note: The TMPRSS2-ERG rearrangement is a non-canonical fusion and it is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		46877	0	44	21	Intron of ERG(-):61Kb before exon 4	TMPRSS2	39878087			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868436			10	DELETION		2990349	185544	28818	50	NEW_VARIANT
P-0020950-T01-IM6	EP300 (NM_001429) rearrangement: c.3806+75_c.4553inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		10673	0	67	22	Intron of EP300(+):75bp after exon 22	EP300	41560209			22	Exon 28 of EP300(+)	EP300	41568603			10	INVERSION		8394	185846	3563	66	NEW_VARIANT
P-0020984-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRRS2 exon 1 fused to ERG exons 2-10): c.56-1454:TMPRSS2_c.18+8460:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		65465	0	53	21	Intron of ERG(-):8Kb after exon 1	TMPRSS2	39861827			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871570			10	DELETION		3009743	185947	47999	57	NEW_VARIANT
P-0021179-T01-IM6	PTPN11 (NM_002834) rearrangement: t(12;22)(q24.13;q11.23)(chr12:g.112927045::chr22:g.25404722)	PRECISE	Note: The PTPN11 rearrangement is a translocation that may result in a truncation of PTPN11 exons 14-15. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	37	22	IGR: 19Kb before KIAA1671(+)	PTPN11	25404722			12	Intron of PTPN11(+):66bp after exon 13	PTPN11	112927045			10	TRANSLOCATION		0	186339	0	40	NEW_VARIANT
P-0021297-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) (TMPRSS2 exons 1-2 fused with ERG exons 3-10):c.126+871:TMPRSS2_c.237-7837:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53435	0	27	21	Intron of ERG(-):8Kb before exon 3	TMPRSS2	39803320			21	Intron of TMPRSS2(-):870bp after exon 2	ERG	42869175			10	DELETION		3065855	186815	16854	29	NEW_VARIANT
P-0021310-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.39+53911:ERG_c.126+1319:TMPRSS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ERG:TMPRSS2}		45529	0	108	21	Intron of ERG(-):54Kb after exon 3	ERG	39893675			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868727			10	DUPLICATION		2975052	186835	46875	125	NEW_VARIANT
P-0039132-T01-IM6	ATM (NM_000051) rearrangement: c.186-51:ATM_chr11:g.88962170inv	IMPPRECISE	Note: The ATM rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		87354	0	5	11	Intron of TYR(+):1Kb after exon 3	ATM	88962170			11	Intron of ATM(+):50bp before exon 4	ATM	108099854			0	INVERSION		19137684	293816	151483	5	NEW_VARIANT
P-0039480-T01-IM6	NAB2 (NM_005967) rearrangement: c.850:NAB2_chr12:g.54655657inv	PRECISE	Note: The NAB2 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CBX5:NAB2}		44609	0	818	12	5-UTR of CBX5(-):20Kb before coding start	NAB2	54655657			12	Exon 2 of NAB2(+)	NAB2	57485674			10	INVERSION		2830017	296086	63103	1180	NEW_VARIANT
P-0037712-T01-IM6	ARID1A (NM_006015) - GPATCH3 (NM_022078) rearrangement: c.5053:ARID1A_c.877-1228:GPATCH3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARID1A:GPATCH3}		8827	0	27	1	Exon 19 of ARID1A(+)	ARID1A	27102127			1	Intron of GPATCH3(-):1Kb before exon 3	GPATCH3	27222129			10	INVERSION		120002	281601	9255	26	NEW_VARIANT
P-0037712-T01-IM6	RASA1 (NM_002890) rearrangement: c.539+9413_c.1598dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		6771	0	7	5	Intron of RASA1(+):9Kb after exon 1	RASA1	86574220			5	Exon 11 of RASA1(+)	RASA1	86659309			10	DUPLICATION		85089	281599	5513	7	NEW_VARIANT
P-0037718-T01-IM6	KMT2D (NM_003482) - FAM149B1 (NM_173348) rearrangement: t(10;12)(q22.2;q13.12)(chr10:g.74969560::chr12:g.49446311)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {KMT2D:FAM149B1}		0	0	38	12	Intron of KMT2D(-):35bp after exon 9	KMT2D	49446311			10	Intron of FAM149B1(+):448bp before exon 7	FAM149B1	74969560			10	TRANSLOCATION		0	281579	0	41	NEW_VARIANT
P-0037718-T01-IM6	GATA1 (NM_002049) rearrangement: c.298:GATA1_chrX:g.54291385dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		76927	0	4	X	Exon 3 of GATA1(+)	GATA1	48650328			X	Intron of WNK3(-):6Kb before exon 11	GATA1	54291385			6	DUPLICATION		5641057	281576	73342	4	NEW_VARIANT
P-0026492-T02-IM6	SMO (NM_005631) rearrangement: c.1265-185:SMO_chr7:g.117726946inv	PRECISE	Note: The SMO rearrangement is an inversion of exons 1 - 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		37844	0	9	7	IGR: 97Kb before LSM8(+)	SMO	117726946			7	Intron of SMO(+):184bp before exon 7	SMO	128848415			10	INVERSION		11121469	297576	23425	10	NEW_VARIANT
P-0039584-T01-IM6	FER1L6 (NM_001039112) - AGO2 (NM_012154) rearrangement: c.2589+1237:FER1L6_c.1027-3:AGO2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {FER1L6:AGO2}		50197	0	73	8	Intron of FER1L6(+):1Kb after exon 20	FER1L6	125053484			8	Intron of AGO2(-):3bp before exon 9	AGO2	141566388			10	INVERSION		16512904	297575	74940	72	NEW_VARIANT
P-0039590-T01-IM6	RPTOR (NM_020761) - TRAF7 (NM_032271) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.2226123::chr17:g.78576760)	PRECISE	Note: The RPTOR - TRAF7 rearrangement is a translocation with breakpoints in RPTOR intron 1 and TRAF7 exon 19. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	17	Intron of RPTOR(+):23Kb before exon 2	RPTOR	78576760			16	Exon 19 of TRAF7(+)	TRAF7	2226123			10	TRANSLOCATION		0	297595	0	12	NEW_VARIANT
P-0039594-T01-IM6	RET (NM_020975) rearrangement: t(10;19)(q11.21;p13.2)(chr10:g.43611995::chr19:g.11067799)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	193	19	IGR: 4Kb before SMARCA4(+)	RET	11067799			10	Intron of RET(+):36bp before exon 12	RET	43611995			10	TRANSLOCATION		0	297173	0	209	NEW_VARIANT
P-0039627-T01-IM6	SMARCA4 (NM_003072) - CARM1 (NM_199141) rearrangement: c.3774+61:SMARCA4_c.221-7710:CARM1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SMARCA4:CARM1}		110176	0	31	19	Intron of CARM1(+):8Kb before exon 2	SMARCA4	11007917			19	Intron of SMARCA4(+):61bp after exon 26	CARM1	11144254			10	DUPLICATION		136337	297264	276816	33	NEW_VARIANT
P-0019783-T02-IM6	CDK8 (NM_001260) rearrangement: c.1031+79:CDK8_chr13:g.30676512del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		56524	0	32	13	Intron of CDK8(+):79bp after exon 10	CDK8	26974766			13	IGR: 100Kb before KATNAL1(-)	CDK8	30676512			10	DELETION		3701746	297275	173211	33	NEW_VARIANT
P-0039554-T01-IM6	PTPRT (NM_133170) rearrangement: c.1071_c.1153+5107del	PRECISE	Note: The PTPRT rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		863	0	29	20	Intron of PTPRT(-):5Kb after exon 7	PTPRT	41301399			20	Exon 7 of PTPRT(-)	PTPRT	41306588			10	DELETION		5189	296788	919	29	NEW_VARIANT
P-0039569-T01-IM6	DNMT1 (NM_001379) rearrangement: c.1445-224_c.1721inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		2467	0	65	19	Exon 20 of DNMT1(-)	DNMT1	10265325			19	Intron of DNMT1(-):224bp before exon 19	DNMT1	10265956			10	INVERSION		631	296989	3556	65	NEW_VARIANT
P-0039649-T01-IM6	RB1 (NM_000321) rearrangement: c.2017_c.2211+292del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 20 - 21. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1544	0	73	13	Exon 20 of RB1(+)	RB1	49033880			13	Intron of RB1(+):292bp after exon 21	RB1	49038263			10	DELETION		4383	297355	685	79	NEW_VARIANT
P-0039652-T01-IM6	BLM (NM_000057) rearrangement: c.2091:BLM_chr15:g.90779259del	PRECISE	Note: The BLM rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		14716	0	10	15	3-UTR of CIB1(-):30Kb after coding stop	BLM	90779259			15	Exon 9 of BLM(+)	BLM	91308542			10	DELETION		529283	297361	16680	10	NEW_VARIANT
P-0039680-T01-IM6	EIF4A2 (NM_001967) rearrangement: t(3;10)(q27.3;q25.2)(chr3:g.186506982::chr10:g.113877258)	PRECISE	Note: The EIF4A2 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	10	IGR: 32Kb before GPAM(-)	EIF4A2	113877258			3	Exon 11 of EIF4A2(+)	EIF4A2	186506982			10	TRANSLOCATION		0	297706	0	6	NEW_VARIANT
P-0023958-T02-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-2153:ERG_c.126+1716:TMPRSS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ERG:TMPRSS2}		8367	0	87	21	Intron of ERG(-):2Kb before exon 2	ERG	39819697			21	Intron of TMPRSS2(-):2Kb after exon 2	TMPRSS2	42868330			10	DUPLICATION		3048633	297736	30261	96	NEW_VARIANT
P-0039640-T01-IM6	INSR (NM_000208) rearrangement: t(5;19)(q11.2;p13.2)(chr5:g.53033886::chr19:g.7152854)	PRECISE	Note: The INSR rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	8	19	Exon 10 of INSR(-)	INSR	7152854			5	IGR: 147Kb before ARL15(-)	INSR	53033886			10	TRANSLOCATION		0	297367	0	7	NEW_VARIANT
P-0039698-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-4258:TMPRSS2_c.18+3607:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		88259	0	3	21	Intron of ERG(-):4Kb after exon 1	TMPRSS2	39866680			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874374			10	DELETION		3007694	297904	32619	3	NEW_VARIANT
P-0035722-T02-IM6	JUN (NM_002228) rearrangement: c.826:JUN_chr1:g.61042535inv	PRECISE	Note: The JUN rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		10688	0	3	1	Exon 1 of JUN(-)	JUN	59247917			1	IGR: 83Kb before LOC101926964(-)	JUN	61042535			10	INVERSION		1794618	298325	23901	3	NEW_VARIANT
P-0039657-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41632313::chr21:g.42871753)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	73	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871753			17	IGR: 27Kb before ETV4(-)	TMPRSS2	41632313			10	TRANSLOCATION		0	298280	0	79	NEW_VARIANT
P-0039689-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-203:TMPRSS2_c.19-1128:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		42480	0	11	21	Intron of ERG(-):1Kb before exon 2	TMPRSS2	39818672			21	Intron of TMPRSS2(-):203bp before exon 2	ERG	42870319			10	DELETION		3051647	297727	31644	11	NEW_VARIANT
P-0039805-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.3215+77:SMARCA4_chr19:g.55276048inv	PRECISE	Note: The SMARCA4 rearrangement is an inversion of exons 24 - 35. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1109014	0	33	19	Intron of SMARCA4(+):77bp after exon 23	SMARCA4	11137099			19	IGR: 5Kb before LOC101928804(-)	SMARCA4	55276048			10	INVERSION		44138949	298336	1026394	34	NEW_VARIANT
P-0039805-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2856_c.838+696del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : in frame		63165	0	71	21	Intron of TMPRSS2(-):695bp after exon 8	TMPRSS2	42847808			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872972			10	DELETION		25164	298332	40089	71	NEW_VARIANT
P-0039805-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1985+87:PIK3R1_chr5:g.67667228inv	PRECISE	Note: The PIK3R1 rearrangement is an inversion of exon 16. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1336	0	19	5	Intron of PIK3R1(+):87bp after exon 15	PIK3R1	67592256			5	IGR: 79Kb before PIK3R1(+)	PIK3R1	67667228			10	INVERSION		74972	298334	1503	19	NEW_VARIANT
P-0039808-T01-IM6	ZNF532 (NM_018181) - MALT1 (NM_006785) rearrangement: c.2868+2087:ZNF532_c.1912-112:MALT1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ZNF532:MALT1}		5209	0	24	18	Intron of MALT1(+):111bp before exon 16	ZNF532	56412786			18	Intron of ZNF532(+):2Kb after exon 7	MALT1	56617548			9	DUPLICATION		204762	298339	5419	24	NEW_VARIANT
P-0039808-T01-IM6	MDC1 (NM_014641) rearrangement: c.2282:MDC1_chr6:g.30741532inv	PRECISE	Note: The MDC1 rearrangement is an inversion of exons 1 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		23419	0	20	6	Exon 8 of MDC1(-)	MDC1	30676074			6	IGR: 31Kb before IER3(-)	MDC1	30741532			10	INVERSION		65458	298340	49475	36	NEW_VARIANT
P-0000631-T03-IM6	DNMT1 (NM_001379) rearrangement: c.4736:DNMT1_chr19:g.14487154del	PRECISE	Note: The DNMT1 rearrangement is a deletion of exons 1 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		267002	0	177	19	Exon 39 of DNMT1(-)	DNMT1	10244973			19	IGR: 5Kb before CD97(+)	DNMT1	14487154			10	DELETION		4242181	298479	380928	207	NEW_VARIANT
P-0000631-T03-IM6	CLASP1 (NM_015282) - INSR (NM_000208) rearrangement: t(2;19)(q14.2;p13.2)(chr2:g.122236197::chr19:g.7152997)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CLASP1:INSR}		0	0	9	19	Intron of INSR(-):59bp before exon 10	CLASP1	7152997			2	Intron of CLASP1(-):9Kb before exon 9	INSR	122236197			0	TRANSLOCATION		0	298482	0	59	NEW_VARIANT
P-0000631-T03-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2516:TMPRSS2_c.39+58475:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		77383	0	100	21	Intron of ERG(-):58Kb after exon 3	TMPRSS2	39889111			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872632			10	DELETION		2983521	298480	55278	106	NEW_VARIANT
P-0000631-T03-IM6	ELF3 (NM_004433) rearrangement: t(1;3)(q32.1;q24)(chr1:g.201984440::chr3:g.146132148)	PRECISE	Note: The ELF3 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	12	3	IGR: 19Kb before PLSCR2(-)	ELF3	146132148			1	Exon 9 of ELF3(+)	ELF3	201984440			10	TRANSLOCATION		0	298481	0	14	NEW_VARIANT
P-0010096-T03-IM6	ALK (NM_004304) rearrangement: c.1207_c.1282+881del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		834	0	20	2	Intron of ALK(-):880bp after exon 5	ALK	29605717			2	Exon 5 of ALK(-)	ALK	29606673			10	DELETION		956	298159	763	23	NEW_VARIANT
P-0010096-T03-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2357:FGFR3_c.1941+378:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		38399	0	3	4	Intron of TACC3(+):378bp after exon 10	FGFR3	1739807			4	Exon 18 of FGFR3(+)	TACC3	1808925			7	DUPLICATION		69118	298161	50053	3	NEW_VARIANT
P-0022760-T02-IM6	DOT1L (NM_032482) rearrangement: c.4534_c.4606+847inv	PRECISE	Note: The DOT1L rearrangement is an intragenic inversion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1824	0	2	19	Exon 27 of DOT1L(+)	DOT1L	2227054			19	Intron of DOT1L(+):847bp after exon 27	DOT1L	2227973			8	INVERSION		919	298478	2915	2	NEW_VARIANT
P-0039255-T02-IM6	TP53 (NM_000546) rearrangement: c.116_c.1100+344del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 4 - 10. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		13612	0	12	17	Intron of TP53(-):343bp after exon 10	TP53	7573583			17	Exon 4 of TP53(-)	TP53	7579571			10	DELETION		5988	298082	9974	15	NEW_VARIANT
P-0039255-T02-IM6	EGFR (NM_005228) - SEPT14 (NM_207366) fusion: c.3271+489:EGFR_c.818-3507:SEPT14inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EGFR:SEPT14}		3872	0	12	7	Intron of EGFR(+):489bp after exon 27	EGFR	55270807			7	Intron of SEPT14(-):4Kb before exon 8	SEPT14	55878458			10	INVERSION		607651	298083	15006	4	NEW_VARIANT
P-0039767-T01-IM6	CSF3R (NM_000760) rearrangement: c.1286-39:CSF3R_chr1:g.39179138del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		20480	0	48	1	Intron of CSF3R(-):39bp before exon 11	CSF3R	36935480			1	IGR: 125Kb before RRAGC(-)	CSF3R	39179138			10	DELETION		2243658	298220	30719	55	NEW_VARIANT
P-0039771-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2539:TMPRSS2_c.39+64394:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		63679	0	74	21	Intron of ERG(-):64Kb after exon 3	TMPRSS2	39883192			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872655			10	DELETION		2989463	298233	66250	77	NEW_VARIANT
P-0039799-T01-IM6	AGAP3 (NM_031946) - BRAF (NM_004333) fusion: c.1221+416:AGAP3_c.1314+504:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {AGAP3:BRAF}		189511	0	75	7	Intron of BRAF(-):503bp after exon 10	AGAP3	140482317			7	Intron of AGAP3(+):416bp after exon 9	BRAF	150821389			10	INVERSION		10339072	298299	204027	74	NEW_VARIANT
P-0039811-T01-IM6	BCL2L11 (NM_138621) rearrangement: c.394+1356_c.498+5499del	PRECISE	Note: The BCL2L11 rearrangement is an intragenic deletion of exon 3.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		30940	0	43	2	Intron of BCL2L11(+):1Kb after exon 2	BCL2L11	111883072			2	Intron of BCL2L11(+):5Kb after exon 3	BCL2L11	111913223			10	DELETION		30151	298321	5630	45	NEW_VARIANT
P-0039926-T01-IM6	SRC (NM_198291) - LMX1A (NM_001174069) rearrangement: t(1;20)(q23.3;q11.23)(chr1:g.165259752::chr20:g.36014560)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SRC:LMX1A}		0	0	81	20	Exon 5 of SRC(+)	SRC	36014560			1	Intron of LMX1A(-):41Kb before exon 4	LMX1A	165259752			10	TRANSLOCATION		0	298752	0	80	NEW_VARIANT
P-0039927-T01-IM6	ARID1B (NM_020732) rearrangement: c.3690-20:ARID1B_chr6:g.157631138inv	PRECISE	Note: The ARID1B rearrangement is an inversion of exons 15 - 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		18982	0	6	6	Intron of ARID1B(+):19bp before exon 15	ARID1B	157511152			6	IGR: 79Kb before TMEM242(-)	ARID1B	157631138			10	INVERSION		119986	298741	13555	6	NEW_VARIANT
P-0039927-T01-IM6	KDM6A (NM_021140) rearrangement: c.3144+558_c.3213dup	PRECISE	Note: The KDM6A rearrangement is an intragenic duplication of exons 21 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		745	0	63	X	Intron of KDM6A(+):558bp after exon 20	KDM6A	44939154			X	Exon 22 of KDM6A(+)	KDM6A	44941963			10	DUPLICATION		2809	298740	1774	65	NEW_VARIANT
P-0039978-T01-IM6	KEAP1 (NM_203500) rearrangement: c.775_c.1325+545del	PRECISE	Note: The KEAP1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5181	0	136	19	Intron of KEAP1(-):544bp after exon 3	KEAP1	10601708			19	Exon 3 of KEAP1(-)	KEAP1	10602803			10	DELETION		1095	299208	1401	328	NEW_VARIANT
P-0039980-T01-IM6	NF1 (NM_001042492) rearrangement: t(8;17)(q11.21;q11.2)(chr8:g.50391945::chr17:g.29528649)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	17	Intron of NF1(+):146bp after exon 11	NF1	29528649			8	IGR: 407Kb before C8orf22(+)	NF1	50391945			6	TRANSLOCATION		0	299979	0	6	NEW_VARIANT
P-0001338-T01-IM3		PRECISE		AUTO_OK	3to5	3to5	Protein fusion: mid-exon (DHX35-TOP1)		14544	0	89	20	Intron of DHX35(+): 1Kb before exon 20	DHX35	37658302			20	Exon 11 of TOP1(+)	TOP1	39726899			89	DELETION		2068597	2258	22303	94	NEW_VARIANT
P-0001697-T02-IM3		PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		20571	0	14	21	Intron of ERG(-): 14Kb after exon 1	ERG	39856489			21	Intron of TMPRSS2(-): 2Kb before exon 2	TMPRSS2	42872306			15	DELETION		3015817	4298	22530	15	NEW_VARIANT
P-0001724-T01-IM3	RECQL4 (NM_004260) - MYT1 (NM_004535) Translocation :   t(8;20)(q24.3;q13.33)(chr20:c.3055+13::chr8:c.1-2888)	PRECISE	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.	AUTO_OK	5to5	5to5	Transcript fusion (RECQL4-MYT1)		0	0	11	20	5-UTR of MYT1(+): 3Kb before coding start	RECQL4	62827327			8	Intron of RECQL4(-): 13bp after exon 17	MYT1	145737762			29	TRANSLOCATION		0	1192	0	11	NEW_VARIANT
P-0002039-T01-IM3		PRECISE		AUTO_OK	5to5	5to5	Protein fusion: in frame (FGFR2-RASAL2)		0	0	4	10	Intron of FGFR2(-): 337bp before exon 17	FGFR2	123242028			1	Intron of RASAL2(+): 5Kb after exon 2	RASAL2	178257418			13	TRANSLOCATION		0	2202	0	4	NEW_VARIANT
P-0002039-T01-IM3		PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: out of frame (TACC2-FGFR2)		54899	0	8	10	Intron of FGFR2(-): 439bp before exon 17	FGFR2	123242130			10	Intron of TACC2(+): 6Kb before exon 6	TACC2	123885852			11	INVERSION		643722	2201	53104	8	NEW_VARIANT
P-0002402-T01-IM3		PRECISE		AUTO_OK	3to3	3to3	-		131334	0	16	17	Intron of NCOR1(-): 36bp before exon 44	NCOR1	15943004			17	IGR: 40Kb before MPRIP(+)	MPRIP	16906001			35	INVERSION		962997	3266	165673	15	NEW_VARIANT
P-0002407-T01-IM3		PRECISE	deletion of first 3 exons	AUTO_OK	3to5	3to5	-		5248	0	22	3	Exon 3 of ATR(-)	ATR	142285020			3	IGR: 4Kb after ATR(-)	ATR	142301931			45	DELETION		16911	3273	4405	25	NEW_VARIANT
P-0002408-T01-IM3	EML4 (NM_019063) and ALK (NM_004304) inversion (13096399bp) :  EML4:c.2057-115_ALK:c.3172+274inv	PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		82897	0	37	2	Intron of ALK(-): 274bp after exon 19	EML4	29448053			2	Intron of EML4(+): 115bp before exon 18	EML4	42544452			54	INVERSION		13096399	3279	81915	36	NEW_VARIANT
P-0002469-T01-IM3		PRECISE	slightly amplified but good read support	MANUAL_OK	3to3	3to3	-		11012	0	24	3	Intron of ATR(-): 141bp before exon 16	ATR	142266893			3	Exon 11 of ATR(-)	ATR	142272696			41	INVERSION		5803	3544	10313	23	NEW_VARIANT
P-0002488-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	-		581	0	71	18	Exon 12 of SMAD4(+)	SMAD4	48604772			18	3-UTR of SMAD4(+): 2Kb after coding stop	SMAD4	48606495			99	DELETION		1723	3634	122	122	NEW_VARIANT
P-0002495-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3048	0	8	17	Exon 5 of RNF43(-)	RNF43	56440669			17	Intron of RNF43(-): 14Kb before exon 3	RNF43	56462615			16	DELETION		21946	3655	2659	9	NEW_VARIANT
P-0002497-T01-IM3		PRECISE		MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (ESR1-C6orf97)		2679	0	61	6	Intron of C6orf97(+): 1Kb before exon 5	C6orf97	151868329			6	Exon 3 of ESR1(+)	ESR1	152129362			77	DUPLICATION		261033	3675	4370	68	NEW_VARIANT
P-0002499-T02-IM6	KDM6A (NM_021140) rearrangement: c.385-14612_c.1547dup	PRECISE	Note: The KDM6A rearrangement is an intragenic duplication of exons 5 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		6568	0	3	X	Intron of KDM6A(+):15Kb before exon 5	KDM6A	44855594			X	Exon 16 of KDM6A(+)	KDM6A	44922686			7	DUPLICATION		67092	300384	10662	4	NEW_VARIANT
P-0002526-T01-IM3		PRECISE	deletion of exons 4 to 7	MANUAL_OK	3to5	3to5	-		4155	0	5	19	Exon 4 of GNA11(+)	GNA11	3115025			19	IGR: 699bp after GNA11(+)	GNA11	3122151			12	DELETION		7126	3745	1310	4	NEW_VARIANT
P-0002877-T01-IM3		IMPRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	3	6	Intron of ROS1(-): 292bp before exon 34	ROS1	117645870			5	Intron of CD74(-): 247bp before exon 7	CD74	149782435			0	TRANSLOCATION		0	6024	0	6	NEW_VARIANT
P-0002912-T01-IM3		PRECISE		MANUAL_OK	5to3	5to3	Protein fusion: in frame (ROS1-CD74)		0	0	4	6	Intron of ROS1(-): 748bp before exon 34	ROS1	117646326			5	Intron of CD74(-): 544bp before exon 7	CD74	149783419			10	TRANSLOCATION		0	6187	0	17	NEW_VARIANT
P-0003102-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	-		31185	0	11	19	Intron of AXL(+): 35bp after exon 9	AXL	41745254			19	IGR: 47Kb before PSG5(-)	PSG5	43624654			12	DELETION		1879400	8316	27155	6	NEW_VARIANT
P-0003455-T02-IM5	C19orf26 (NM_152769) - STK11 (NM_000455) rearrangement: c.5:C19orf26_c.1013:STK11inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (C19orf26-STK11)		2245	0	10	19	Exon 8 of STK11(+)	C19orf26	1223076			19	5-UTR of C19orf26(-): 14bp before coding start	STK11	1236095			15	INVERSION		13019	13170	1751	10	NEW_VARIANT
P-0003948-T01-IM3	TP53 (NM_000546) Inversion: c.993+243_g.48892577inv	PRECISE		MANUAL_OK	3to3	3to3	-		565819	0	43	17	Intron of TP53(-): 26bp before exon 6	TP53	7576610			17	IGR: 20Kb before WFIKKN2(+)	TP53	48892577			77	INVERSION		41315967	79544	871993	43	NEW_VARIANT
P-0004454-T01-IM5	TSC2 (NM_000548) rearrangement : chr16:g.2088970_c.2838-64:TSC2del	PRECISE	Note: The TSC2 (NM_000548) rearrangement event results in the deletion of TSC2 exons 1-25.	MANUAL_OK	3to5	3to5	-		30643	0	8	16	3-UTR of SLC9A3R2(+): 985bp after coding stop	TSC2	2088970			16	Intron of TSC2(+): 64bp before exon 26	TSC2	2127535			8	DELETION		38565	21297	26528	8	NEW_VARIANT
P-0005152-T01-IM5	SOX17 (NM_022454) - XKR4 (NM_052898) Rearrangement: c.307+18:SOX17_c.807-118046:XKR4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (SOX17-XKR4)		5929	0	8	8	Intron of SOX17(+): 18bp after exon 1	SOX17	55371023			8	Intron of XKR4(+): 118Kb before exon 2	XKR4	56152192			14	DELETION		781169	44224	8616	8	NEW_VARIANT
P-0005240-T01-IM5	EGFR (NM_005228) Rearrangement :  c.560-2097_889+126del	PRECISE	Note: The EGFR (NM_005228) Rearrangement results in the intragenic deletion of exon5 to exon7 . Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons: in frame		7067	0	36	7	Intron of EGFR(+): 2Kb before exon 5	EGFR	55216890			7	Intron of EGFR(+): 126bp after exon 7	EGFR	55221971			46	DELETION		5081	46101	26850	35	NEW_VARIANT
P-0005461-T02-IM5	CDK5RAP2 (NM_018249) - BRAF (NM_004333) rearrangement : t(7;9)(7q34;9q33.2)(chr7:140481684::chr9:123255452)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (CDK5RAP2-BRAF)		0	0	19	9	Intron of CDK5RAP2(-): 2Kb before exon 13	CDK5RAP2	123255452			7	Intron of BRAF(-): 191bp before exon 11	BRAF	140481684			0	TRANSLOCATION		0	52833	0	19	NEW_VARIANT
P-0005573-T01-IM5	KIF5B (NM_004521) - RET (NM_020975)  Fusion (KIF5B exon15 fused with RET exon12): c.1726-860:KIF5B_c.2136+234:RETinv	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (KIF5B-RET)		60891	0	47	10	Intron of KIF5B(-): 860bp before exon 16	KIF5B	32312824			10	Intron of RET(+): 234bp after exon 11	RET	43610418			94	INVERSION		11297594	50802	60366	46	NEW_VARIANT
P-0005583-T01-IM5	BIRC3 (NM_182962) - SIK3 (NM_025164) rearrangement: c.1159:BIRC3_ c.442+13590:SIK3del	PRECISE	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	MANUAL_OK	3to5	3to5	Antisense fusion		126894	0	64	11	Exon 7 of BIRC3(+)	BIRC3	102201807			11	Intron of SIK3(-): 14Kb after exon 4	SIK3	116784345			84	DELETION		14582538	51168	75428	63	NEW_VARIANT
P-0005743-T02-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-20 with ALK exons 20-29) : c.2243-181:EML4_c.3172+658:ALKinv	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		39513	0	23	2	Intron of ALK(-): 658bp after exon 19	EML4	29447669			2	Intron of EML4(+): 181bp before exon 20	ALK	42553113			44	INVERSION		13105444	64459	35871	23	NEW_VARIANT
P-0005768-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 fused to ERG exons 3-11) : c.56-1181:TMPRSS2_c.-150+10082:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Transcript fusion (TMPRSS2-ERG)		38906	0	36	21	5-UTR of ERG(-): 76Kb before coding start	TMPRSS2	40023500			21	Intron of TMPRSS2(-): 1Kb before exon 2	ERG	42871297			73	DELETION		2847797	65105	26694	36	NEW_VARIANT
P-0005868-T02-IM5	IRS1 (NM_005544) rearrangement : t(2;9)(2q36.3;9p21.3)(chr2:g.227663341::chr9:24948307)	PRECISE	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	MANUAL_OK	5to5	5to5	-		0	0	6	9	IGR: 728Kb before TUSC1(-)	IRS1	24948307			2	Exon 1 of IRS1(-)	IRS1	227663341			10	TRANSLOCATION		0	67833	0	6	NEW_VARIANT
P-0006023-T02-IM5	SOX9 (NM_000346) rearrangement: c.582_c.*1399del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		7197	0	41	17	Exon 2 of SOX9(+)	SOX9	70119010			17	3-UTR of SOX9(+): 1Kb after coding stop	SOX9	70121927			66	DELETION		2917	91114	5837	41	NEW_VARIANT
P-0006112-T02-IM5	GNA11 (NM_002067) rearrangement: c.506:GNA11_chr19:g.4560347del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		25073	0	20	19	Exon 4 of GNA11(+)	GNA11	3114971			19	Promoter of SEMA6B(-): 2Kb from tx start	GNA11	4560347			43	DELETION		1445376	108344	20944	19	NEW_VARIANT
P-0006646-T01-IM5	RAB11FIP1 (NM_001002814) - FGFR1 (NM_001174067) rearrangement : c.2027:RAB11FIP1_c.1378-65:FGFR1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (RAB11FIP1-FGFR1)		19630	0	12	8	Exon 4 of RAB11FIP1(-)	RAB11FIP1	37730293			8	Intron of FGFR1(-): 65bp before exon 9	FGFR1	38275956			22	DUPLICATION		545663	107821	18235	12	NEW_VARIANT
P-0006681-T01-IM5	APC (NM_000038) rearrangement : c.1958+1186_977del	PRECISE	Note: The APC (NM_000038) rearrangement event affects of APC exon16 splice site.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		512	0	33	5	Intron of APC(+): 1Kb after exon 15	APC	112172048			5	Exon 16 of APC(+)	APC	112173268			57	DELETION		1220	108245	123	33	NEW_VARIANT
P-0007078-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2 to 10): c.55+4786G_c.19-20913del	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		145488	0	33	21	Intron of ERG(-): 21Kb before exon 4	TMPRSS2	39838457			21	Intron of TMPRSS2(-): 5Kb after exon 1	ERG	42875091			62	DELETION		3036634	116049	124308	33	NEW_VARIANT
P-0007664-T01-IM5	SMAD2 (NM_001003652) rearrangement: c.520+88_c.731-2898del	PRECISE	The SMAD2 (NM_001003652) rearrangement is an intragenic deletion of exons 5-6. The functional significance is undetermined	MANUAL_OK	3to5	3to5	Deletion of 2 exons: in frame		4753	0	18	18	Intron of SMAD2(-): 3Kb before exon 7	SMAD2	45380596			18	Intron of SMAD2(-): 88bp after exon 4	SMAD2	45395526			28	DELETION		14930	117878	4888	18	NEW_VARIANT
P-0007664-T01-IM5	SMAD2 (NM_001003652) rearrangement: c.237-350_c.417del	PRECISE	The SMAD2 (NM_001003652) rearrangement is an intragenic deletion of exons 3-4. One of the breakpoints within exon 4 of SMAD2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		2813	0	41	18	Exon 4 of SMAD2(-)	SMAD2	45395717			18	Intron of SMAD2(-): 350bp before exon 3	SMAD2	45397285			51	DELETION		1568	117879	2211	41	NEW_VARIANT
P-0007669-T01-IM5	FH (NM_000143) rearrangement: t(1;13)(q43;q14.11)(chr1:g.241661295::chr13:g.42830622 )	IMPRECISE	The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	93	13	IGR: 16Kb before AKAP11(+)	AKAP11	42830622			1	Intron of FH(-): 25bp before exon 10	FH	241661295			0	TRANSLOCATION		0	117923	0	63	NEW_VARIANT
P-0007669-T01-IM5	FH (NM_000143) rearrangement: t(1;7(q43;q22.31)(chr1:g.241661124::chr7:g.94032373  )	PRECISE	The FH (NM_000143) rearrangement is a translocation which may result in the truncation of FH. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	77	7	Intron of COL1A2(+): 1Kb after exon 6	COL1A2	94032373			1	3-UTR of FH(-): 4bp after coding stop	FH	241661124			51	TRANSLOCATION		0	117925	0	75	NEW_VARIANT
P-0007739-T01-IM5	LMNA (NM_170707) - NTRK1 (NM_002529) Fusion (LMNA exons 1-8 fused to NTRK1 exons 12-17):  c.1443:LMNA_c.1354+235:NTRK1	PRECISE	Note: The LMNA (NM_170707) - NTRK1 (NM_002529) Fusion includes the kinase domain of NTRK1.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (LMNA-NTRK1)		31201	0	6	1	Exon 8 of LMNA(+)	LMNA	156106774			1	Intron of NTRK1(+): 235bp after exon 11	NTRK1	156845035			47	DELETION		738261	118272	18575	6	NEW_VARIANT
P-0007883-T01-IM5	FOXP1 (NM_001244814) rearrangement : chr3:g.71594017_c.1652+403:FOXP1del	PRECISE	Note: The FOXP1 (NM_001244814) rearrangement event results in the deletion of FOXP1 exons 1-14.	MANUAL_OK	3to5	3to5	Deletion within transcript		30843	0	30	3	Intron of FOXP1(-): 403bp after exon 18	FOXP1	71021303			3	5-UTR of FOXP1(-): 346Kb before coding start	FOXP1	71594017			53	DELETION		572714	119530	21499	30	NEW_VARIANT
P-0008308-T01-IM5	BARD1 (NM_000465) rearrangement: chr2:g.215687909_c.255del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3383	0	15	2	Exon 3 of BARD1(-)	BARD1	215657130			2	IGR: 13Kb after BARD1(-)	BARD1	215687909			20	DELETION		30779	121283	2671	15	NEW_VARIANT
P-0008488-T02-IM5	IP6K1 (NM_153273) - MST1R (NM_002447) rearrangement: c.-128-18075:IP6K1_c.2003:MST1Rdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (IP6K1-MST1R)		57700	0	18	3	5-UTR of IP6K1(-): 18Kb before coding start	IP6K1	49803676			3	Exon 6 of MST1R(-)	MST1R	49934996			19	DUPLICATION		131320	123103	50942	18	NEW_VARIANT
P-0008536-T02-IM5	RNF43 (NM_017763) rearrangement: c.582+234_c.896del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		3616	0	21	17	Exon 8 of RNF43(-)	RNF43	56437566			17	Intron of RNF43(-): 234bp after exon 5	RNF43	56440402			33	DELETION		2836	125345	2436	21	NEW_VARIANT
P-0008769-T02-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon1 with ERG exons 4-11) : c.56-2251:TMPRSS2_c.40-34826:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		65887	0	47	21	Intron of ERG(-): 18Kb after exon 1	TMPRSS2	39852370			21	Intron of TMPRSS2(-): 2Kb before exon 2	ERG	42872367			41	DELETION		3019997	126102	38696	43	NEW_VARIANT
P-0009324-T02-IM5	ETV6 (NM_001987) Rearrangement :  c.464-1400_chr12:g.12149453del	PRECISE	Note: The ETV6 (NM_001987) Rearrangement  results in the intragenic deletion of exons 5-8 of ETV6.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		73529	0	42	12	Intron of ETV6(+): 1Kb before exon 5	ETV6	12020958			12	IGR: 74Kb before BCL2L14(+)	ETV6	12149453			91	DELETION		128495	130764	58012	42	NEW_VARIANT
P-0009402-T02-IM6	ARID1A (NM_006015) rearrangement: c.1137+5027_c.5984dup	PRECISE	Note: The ARID1A rearrangement is an intragenic duplication of exons 2-20. One of the breakpoints is within exon 20.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		39147	0	43	1	Intron of ARID1A(+):5Kb after exon 1	ARID1A	27029058			1	Exon 20 of ARID1A(+)	ARID1A	27106373			10	DUPLICATION		77315	251521	51547	43	NEW_VARIANT
P-0009741-T01-IM5	APC (NM_000038) rearrangement: c.4583_c.6030del	PRECISE	Note: The APC (NM_000038) rearrangement is a deletion within APC exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		9139	0	17	5	Exon 16 of APC(+)	APC	112175874			5	Exon 16 of APC(+)	APC	112177321			27	DELETION		1447	136351	8376	17	NEW_VARIANT
P-0014014-T01-IM5	EPHA5 (NM_004439) rearrangement: c.181+9039_c.172inv	PRECISE	Note: The EPHA5 (NM_004439) rearrangement is an inversion of EPHA5 exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense fusion		994	0	14	4	Intron of EPHA5(-): 9Kb after exon 1	EPHA5	66526241			4	Exon 1 of EPHA5(-)	EPHA5	66535289			39	INVERSION		9048	166190	512	14	NEW_VARIANT
P-0028935-T02-IM6	SMAD4 (NM_005359) rearrangement: c.454+142_chr18:g.48625572del	IMPPRECISE	Note: The SMAD4 rearrangement is a deletion that includes SMAD4 exons 5-12.	MANUAL_OK	3to5	3to5	-		10204	0	5	18	Intron of SMAD4(+):142bp after exon 4	SMAD4	48575836			18	IGR: 69Kb before SMAD4(+)	SMAD4	48625572			0	DELETION		49736	251215	1068	6	NEW_VARIANT
P-0030874-T01-IM6	KMT2A (NM_001197104) - TMPRSS4 (NM_019894) rearrangement: c.2177:KMT2A_c.441-574:TMPRSS4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KMT2A:TMPRSS4}		8377	0	8	11	Intron of TMPRSS4(+):588bp before exon 6	KMT2A	117977915			11	Exon 3 of KMT2A(+)	TMPRSS4	118344051			10	DUPLICATION		366136	227780	15158	9	NEW_VARIANT
P-0033700-T02-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1454:KIF5B_c.2137-362:RET	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		73947	0	104	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32315902			10	Intron of RET(+):361bp before exon 12	RET	43611670			10	INVERSION		11295768	252560	68880	125	NEW_VARIANT
P-0033700-T02-IM6	JAK3 (NM_000215) rearrangement: c.1702-146:JAK3_chr19:g.10451444inv	PRECISE	Note: The JAK3 rearrangement is an inversion of exons 14-24. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		339998	0	19	19	Promoter of ICAM3(-):7Kb from tx start	JAK3	10451444			19	Intron of JAK3(-):146bp before exon 13	JAK3	17948168			10	INVERSION		7496724	252561	418295	19	NEW_VARIANT
P-0033700-T02-IM6	MAP3K13 (NM_004721) rearrangement: c.1130_c.1644-728del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5985	0	38	3	Exon 6 of MAP3K13(+)	MAP3K13	185167807			3	Intron of MAP3K13(+):727bp before exon 11	MAP3K13	185190035			10	DELETION		22228	252559	7201	61	NEW_VARIANT
P-0034079-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2177:TMPRSS2_c.39+60313:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and includes the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		69570	0	10	21	Intron of ERG(-):60Kb after exon 3	TMPRSS2	39887273			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42872293			10	DELETION		2985020	252723	16172	12	NEW_VARIANT
P-0034112-T01-IM6	CDKN2Ap16INK4A (NM_000077) Rearrangement : c.180_c.*1508del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4254	0	6	9	Promoter of CDKN2A(-):1Kb from tx start	CDKN2Ap16INK4A	21966720			9	Exon 2 of CDKN2A(-)	CDKN2Ap16INK4A	21971178			10	DELETION		4458	251753	2906	6	NEW_VARIANT
P-0034144-T01-IM6	FLCN (NM_144997) rearrangement: c.230:FLCN_chr17:g.14246021del	PRECISE	Note: The FLCN rearrangement is a deletion of exons 4-14. One of the breakpoints is within exon 4. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		79417	0	12	17	Intron of HS3ST3B1(+):2Kb before exon 2	FLCN	14246021			17	Exon 4 of FLCN(-)	FLCN	17131222			10	DELETION		2885201	249397	79520	12	NEW_VARIANT
P-0034357-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1863:KIF5B_c.2137-845:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		62066	0	90	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315493			10	Intron of RET(+):844bp before exon 12	RET	43611187			10	INVERSION		11295694	250426	77995	99	NEW_VARIANT
P-0034357-T01-IM6	RET (NM_020975) rearrangement: t(10;20)(q11.21;p13)(chr10:g.43611134::chr20:g.456852)	PRECISE	Note: The RET rearrangement is a translocation with a breakpoint in intron 11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	32	20	IGR: 6Kb before CSNK2A1(-)	RET	456852			10	Intron of RET(+):897bp before exon 12	RET	43611134			10	TRANSLOCATION		0	250427	0	31	NEW_VARIANT
P-0034357-T01-IM6	RECQL4 (NM_004260) rearrangement: c.355-36:RECQL4_chr8:g.121672884inv	PRECISE	Note: The RECQL4 rearrangement results in the inversion of exons 5-22. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		93897	0	21	8	Intron of SNTB1(-):28Kb before exon 3	RECQL4	121672884			8	Intron of RECQL4(-):36bp before exon 5	RECQL4	145742184			10	INVERSION		24069300	250425	153786	19	NEW_VARIANT
P-0034373-T01-IM6	CDKN2A (NM_000077) Rearrangement: c.143:CDKN2A_chr9:g.25710229del	PRECISE	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.	MANUAL_OK	5to5	5to5	-		8106	0	16	9	Exon 1 of CDKN2A(-)	CDKN2A	21974684			9	IGR: 34Kb before TUSC1(-)	CDKN2A	25710229			10	INVERSION		3735545	250631	4282	19	NEW_VARIANT
P-0034383-T01-IM6	PPM1D (NM_003620) - BCAS3 (NM_001099432) rearrangement: c.1017+49:PPM1D_c.2470+111086:BCAS3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PPM1D:BCAS3}		5936	0	11	17	Intron of PPM1D(+):49bp after exon 4	PPM1D	58725492			17	Intron of BCAS3(+):111Kb after exon 23	BCAS3	59273011			10	DELETION		547519	250651	4480	11	NEW_VARIANT
P-0034425-T01-IM6	NUP93 (NM_014669 ) Rearrangement: c.1910:NUP93_chr16:g.54859823del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		18997	0	30	16	IGR: 93Kb before CRNDE(-)	NUP93	54859823			16	Exon 18 of NUP93(+)	NUP93	56871530			10	DELETION		2011707	250768	22606	30	NEW_VARIANT
P-0034441-T01-IM6	ERRFI1 (NM_018948) Rearrangement : c.276:ERRFI1_chr1:g.8348413inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		4649	0	8	1	Exon 4 of ERRFI1(-)	ERRFI1	8074383			1	IGR: 30Kb before SLC45A1(+)	ERRFI1	8348413			10	INVERSION		274030	250795	10042	8	NEW_VARIANT
P-0034441-T01-IM6	EWSR1 (NM_013986) Rearrangement : t(20;22)(q13.1;q13.1)(chr20:g.51121822::chr22:g.29685243)	PRECISE	Note: The EWSR1 Rearrangement is a translocation event with a breakpoint in intron9. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	427	22	Intron of EWSR1(+):468bp after exon 9	EWSR1	29685243			20	IGR: 116Kb before LINC01524(+)	EWSR1	51121822			10	TRANSLOCATION		0	250796	0	570	NEW_VARIANT
P-0034441-T01-IM6	RHOA (NM_001664) Rearrangement : c.-2-16935_c.305del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3809	0	5	3	Exon 4 of RHOA(-)	RHOA	49400032			3	5-UTR of RHOA(-):32Kb before coding start	RHOA	49429959			10	DELETION		29927	250794	5385	5	NEW_VARIANT
P-0034518-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41636514::chr21:g.:42872555)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint within intron 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	200	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872555			17	IGR: 31Kb before ETV4(-)	TMPRSS2	41636514			10	TRANSLOCATION		0	251526	0	212	NEW_VARIANT
P-0034538-T01-IM6	RNF43 (NM_017763) Rearrangement : c.253-6871_c.2309-7inv	PRECISE	Note: The RNF43 Rearrangement results in the inversion of exons 3-9 of RNF43. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		14873	0	66	17	Intron of RNF43(-):7bp before exon 10	RNF43	56432354			17	Intron of RNF43(-):7Kb before exon 3	RNF43	56455265			10	INVERSION		22911	252310	17542	66	NEW_VARIANT
P-0034538-T01-IM6	KDM6A (NM_021140) Rearrangement :c.3610:KDM6A_c.188-759:EGFL6inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		44201	0	56	X	Intron of EGFL6(+):758bp before exon 3	KDM6A	13612196			X	Exon 25 of KDM6A(+)	KDM6A	44949049			10	INVERSION		31336853	252311	96316	56	NEW_VARIANT
P-0034557-T01-IM6	IGF1R (NM_000875) rearrangement: c.3331:IGF1R_chr15:g.99580663dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		6917	0	2	15	Exon 18 of IGF1R(+)	IGF1R	99482463			15	IGR: 23Kb before LUNAR1(+)	IGF1R	99580663			6	DUPLICATION		98200	252077	11976	2	NEW_VARIANT
P-0034557-T01-IM6	MPL (NM_005373) rearrangement: t(1;8)(p34.2;q24.13)(chr1:g.43803867::chr8:g.124117761)	PRECISE	Note: The MPL rearrangement is a translocation with a breakpoint in exon 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	9	8	Intron of TBC1D31(+):57bp after exon 8	MPL	124117761			1	Exon 2 of MPL(+)	MPL	43803867			10	TRANSLOCATION		0	252078	0	10	NEW_VARIANT
P-0034557-T01-IM6	PREX2 (NM_024870) rearrangement: c.4169:PREX2_chr8:g.141637481dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		104944	0	57	8	Exon 34 of PREX2(+)	PREX2	69058525			8	Intron of AGO2(-):8Kb after exon 1	PREX2	141637481			10	DUPLICATION		72578956	252076	213335	58	NEW_VARIANT
P-0034621-T01-IM6	ABCC2 (NM_000392) - BRAF (NM_004333) rearrangement: t(7;10)(q34;24.2)(chr7:g.140495500::chr10:g.101559038)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ABCC2:BRAF}		0	0	13	10	Exon 8 of ABCC2(+)	ABCC2	101559038			7	Intron of BRAF(-):1Kb before exon 8	BRAF	140495500			10	TRANSLOCATION		0	252562	0	13	NEW_VARIANT
P-0034631-T01-IM6	ARID2 (NM_152641) - SLC2A13 (NM_052885) rearrangement: c.1029:ARID2_c.925+4537:SLC2A13inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARID2:SLC2A13}		12038	0	283	12	Intron of SLC2A13(-):5Kb after exon 3	ARID2	40417566			12	Exon 9 of ARID2(+)	SLC2A13	46231109			10	INVERSION		5813543	252597	103078	264	NEW_VARIANT
P-0034631-T01-IM6	EGFL7 (NM_201446) rearrangement: t(9;12)(q34.3;q14.1)(chr9:g.139565498::chr12:g.58414208)	PRECISE	Note: The EGFL7 rearrangement is a translocation involving exon 7. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	9	12	IGR: 79Kb before XRCC6BP1(+)	EGFL7	58414208			9	Intron of EGFL7(+):32bp after exon 7	EGFL7	139565498			10	TRANSLOCATION		0	252598	0	14	NEW_VARIANT
P-0034642-T01-IM6	DNMT1 (NM_001379) rearrangement: t(1;19)(q21.3;p13.2)(chr1:g.152184933::chr19:g.10271012)	PRECISE	Note: The DNMT1 rearrangement is a translocation with a breakpoint in intron 13. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	19	Intron of DNMT1(-):47bp after exon 13	DNMT1	10271012			1	3-UTR of HRNR(-):618bp after coding stop	DNMT1	152184933			10	TRANSLOCATION		0	252618	0	22	NEW_VARIANT
P-0034676-T01-IM6	SLC25A21(NM_030631) -  FOXA1 (NM_004496) rearrangement: c.70+58700:SLC25A21_c.176:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC25A21:FOXA1}		11413	0	4	14	Intron of SLC25A21(-):59Kb after exon 1	SLC25A21	37582786			14	Exon 2 of FOXA1(-)	FOXA1	38061813			5	DUPLICATION		479027	252912	16570	4	NEW_VARIANT
P-0034686-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon1) : c.55+4815:TMPRSS2_c.40-59886:ERGdel	PRECISE	Note: The fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		70379	0	29	21	Intron of ERG(-):60Kb before exon 4	TMPRSS2	39877430			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875062			10	DELETION		2997632	252888	47511	30	NEW_VARIANT
P-0034694-T01-IM6	APC (NM_000038) rearrangement: c.8002:APC_chr5:g.20611790inv	PRECISE	Note: The APC rearrangement is an inversion of exons 1-16. One of the breakpoints is within exon 16.	MANUAL_OK	5to5	5to5	-		287060	0	9	5	IGR: 848Kb before GUSBP1(+)	APC	20611790			5	Exon 16 of APC(+)	APC	112179293			10	INVERSION		91567503	254155	439444	9	NEW_VARIANT
P-0034781-T01-IM6	GRIPAP1 (NM_020137) - RET (NM_020975) rearrangement: t(X;10)(p11.23q11.21)(chrX:g.48831008::chr10:g.43611853)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {GRIPAP1:RET}		0	0	29	X	Intron of GRIPAP1(-):311bp before exon 26	GRIPAP1	48831008			10	Intron of RET(+):178bp before exon 12	RET	43611853			10	TRANSLOCATION		0	253578	0	31	NEW_VARIANT
P-0034816-T01-IM6	FUBP1 (NM_003902) rearrangement: c.1926+106:FUBP1_chr1:g.78156523del	PRECISE	Note: The FUBP1 rearrangement results in the deletion of exon 20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		625	0	11	1	IGR: 5Kb before USP33(-)	FUBP1	78156523			1	Intron of FUBP1(-):105bp after exon 19	FUBP1	78414734			10	DELETION		258211	253710	823	12	NEW_VARIANT
P-0034816-T01-IM6	TSC2 (NM_000548) rearrangement: t(16;17)(p13.3;p13.1)(chr16:g.2133763::chr17:g.7043177)	PRECISE	Note: The TSC2 rearrangement is a translocation with a breakpoint in exon 33. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	17	IGR: 34Kb before ASGR1(-)	TSC2	7043177			16	Exon 33 of TSC2(+)	TSC2	2133763			10	TRANSLOCATION		0	253719	0	5	NEW_VARIANT
P-0034816-T01-IM6	ALK (NM_004304) rearrangement: c.3844:ALK_chr2:g.28665721dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		8478	0	70	2	IGR: 50Kb before FOSL2(+)	ALK	28665721			2	Exon 26 of ALK(-)	ALK	29430131			10	DUPLICATION		764410	253713	19190	76	NEW_VARIANT
P-0034816-T01-IM6	PBRM1 (NM_018313) rearrangement: t(1;3)(q42.11;p21.1)(chr1:g.224289787::chr3:g.52668594)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	101	3	Intron of PBRM1(-):23bp after exon 12	PBRM1	52668594			1	IGR: 12Kb before FBXO28(+)	PBRM1	224289787			10	TRANSLOCATION		0	253716	0	123	NEW_VARIANT
P-0034816-T01-IM6	STK38 (NM_007271) - MDC1 (NM_014641) rearrangement: c.835-1890:STK38_c.6230:MDC1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STK38:MDC1}		214132	0	50	6	Exon 15 of MDC1(-)	STK38	30668282			6	Intron of STK38(-):2Kb before exon 10	MDC1	36469657			10	DELETION		5801375	253712	306736	50	NEW_VARIANT
P-0034818-T01-IM6	GNA11 (NM_002067) rearrangement: t(6;19)(q22.31;p13.3)(chr6:g.122459052::chr19:g.3119247)	PRECISE	Note: The GNA11 rearrangement is a translocation with a breakpoint in exon 6. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	75	19	Exon 6 of GNA11(+)	GNA11	3119247			6	IGR: 262Kb before HSF2(+)	GNA11	122459052			10	TRANSLOCATION		0	253723	0	75	NEW_VARIANT
P-0034818-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.3221:NOTCH1_chr9:g.140014051dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		75263	0	2	9	Exon 20 of NOTCH1(-)	NOTCH1	139402788			9	IGR: 9Kb before DPP7(-)	NOTCH1	140014051			4	DUPLICATION		611263	253721	103563	2	NEW_VARIANT
P-0034877-T01-IM6	SHOC2 (NM_007373) - TSC22D1 (NM_183422) rearrangement: t(10;13)(q25.2;q14.11)(chr10:g.112769116::chr13:g.45064416)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SHOC2:TSC22D1}		0	0	46	13	Intron of TSC22D1(-):56Kb before exon 2	SHOC2	45064416			10	Exon 7 of SHOC2(+)	TSC22D1	112769116			10	TRANSLOCATION		0	254517	0	46	NEW_VARIANT
P-0034900-T01-IM6	HOOK3 (NM_032410) - RPS6KB2 (NM_003952) rearrangement: t(8;11)(p11.21;q13.2)(chr8:g.42762715::chr11:g.67198652)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {HOOK3:RPS6KB2}		0	0	20	11	Intron of RPS6KB2(+):186bp before exon 5	HOOK3	67198652			8	Intron of HOOK3(+):1Kb after exon 2	RPS6KB2	42762715			10	TRANSLOCATION		0	254542	0	20	NEW_VARIANT
P-0034901-T01-IM6	BAP1 (NM_004656) rearrangement: c.1983+3:BAP1_chr3:g.52406605del	PRECISE	Note: The BAP1 rearrangement results in the deletion of exons 16-17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		3204	0	6	3	Intron of DNAH1(+):202bp after exon 43	BAP1	52406605			3	Intron of BAP1(-):2bp after exon 15	BAP1	52436792			10	DELETION		30187	254543	2693	6	NEW_VARIANT
P-0034944-T01-IM6	STAT3 (NM_139276) - STAT5A (NM_003152) rearrangement: c.1050-680:STAT3_c.2191:STAT5Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {STAT3:STAT5A}		18274	0	52	17	Exon 19 of STAT5A(+)	STAT3	40461471			17	Intron of STAT3(-):680bp before exon 11	STAT5A	40484229			10	INVERSION		22758	254735	32994	71	NEW_VARIANT
P-0039719-T01-IM6	PTPRT (NM_133170) rearrangement: c.2740-3697_c.4037del	IMPPRECISE	Note: The PTPRT rearrangement is an intragenic deletion of exons 19 - 30. One of the breakpoints is within exon 30.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		18109	0	5	20	Exon 30 of PTPRT(-)	PTPRT	40713478			20	Intron of PTPRT(-):4Kb before exon 19	PTPRT	40774339			0	DELETION		60861	298061	24973	5	NEW_VARIANT
P-0022198-T03-IM6	KMT2A (NM_001197104) rearrangement: c.552:KMT2A_chr11:g.114253339inv	PRECISE	Note: The KMT2A rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {LOC101928940:KMT2A}		4570	0	25	11	Promoter of LOC101928940(-):22Kb from tx start	KMT2A	114253339			11	Exon 3 of KMT2A(+)	KMT2A	118342426			10	INVERSION		4089087	298630	7009	32	NEW_VARIANT
P-0036379-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+26500:CCDC6_c.2137-614:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		29179	0	109	10	Intron of RET(+):613bp before exon 12	CCDC6	43611418			10	Intron of CCDC6(-):26Kb after exon 1	RET	61639380			10	INVERSION		18027962	268240	36717	128	NEW_VARIANT
P-0036637-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		71930	0	40	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32313695			10	Intron of RET(+):66bp before exon 12	RET	43611965			10	INVERSION		11298270	271575	74486	46	NEW_VARIANT
P-0036737-T02-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		66392	0	36	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32315869			10	Intron of RET(+):6bp before exon 12	RET	43612025			10	INVERSION		11296156	273478	61166	44	NEW_VARIANT
P-0036737-T02-IM6	DNMT3B (NM_006892): Rearrangement: c.2102:DNMT3B_chr20:g.30803463inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		57981	0	19	20	Intron of POFUT1(+):209bp after exon 3	DNMT3B	30803463			20	Exon 19 of DNMT3B(+)	DNMT3B	31389189			10	INVERSION		585726	273480	56514	18	NEW_VARIANT
P-0037367-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1038:KIF5B_c.2137-158:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		68464	0	25	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32316318			10	Intron of RET(+):157bp before exon 12	RET	43611874			10	INVERSION		11295556	278515	63408	29	NEW_VARIANT
P-0037412-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-11974:CCDC6_c.2136+655:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		36289	0	52	10	Intron of RET(+):655bp after exon 11	CCDC6	43610839			10	Intron of CCDC6(-):12Kb before exon 2	RET	61624434			10	INVERSION		18013595	278828	32133	65	NEW_VARIANT
P-0037494-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) Fusion (KIF5B exon15 fused with RET exon12 ): c.1725+985:KIF5B_c.2137-277:RETinv	PRECISE	Note: The KIF5B-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		51589	0	35	10	Intron of KIF5B(-):984bp after exon 15	KIF5B	32316371			10	Intron of RET(+):276bp before exon 12	RET	43611755			10	INVERSION		11295384	279262	89111	38	NEW_VARIANT
P-0037494-T01-IM6	APC (NM_000038) - SRP19 (NM_001204199) Rearrangement: c.2042:APC_c.-1221:SRP19del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		20804	0	5	5	Exon 16 of APC(+)	APC	112173333			5	Promoter of SRP19(+):1Kb from tx start	SRP19	112195853			0	DELETION		22520	279259	26996	6	NEW_VARIANT
P-0037961-T01-IM6	NCOA4 (NM_001145260) - RET (NM_020975) rearrangement: c.763-360:NCOA4_c.2137-584:RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		25956	0	30	10	Intron of RET(+):583bp before exon 12	NCOA4	43611448			10	Intron of TIMM23B(+):149Kb before exon 7	RET	51584256			10	DUPLICATION		7972808	283044	23162	35	NEW_VARIANT
P-0038257-T01-IM6	CCDC6(NM_005436 ) - RET (NM_020975.4) Fusion (CCDC6 exon1 fused with RET exon12):c.304-2131:CCDC6_c.2136+410:RETinv	PRECISE	Note: The CCDC6-RET Fusion is predicted to be in-frame and includes the protein kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		48814	0	22	10	Intron of RET(+):410bp after exon 11	CCDC6	43610594			10	Intron of CCDC6(-):2Kb before exon 2	RET	61614591			10	INVERSION		18003997	285455	27376	28	NEW_VARIANT
P-0038315-T01-IM6	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.763-415:NCOA4_c.2137-51:RETdup	PRECISE	Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		22709	0	96	10	Intron of RET(+):50bp before exon 12	NCOA4	43611981			10	Intron of TIMM23B(+):149Kb before exon 7	RET	51584201			10	DUPLICATION		7972220	285670	18798	106	NEW_VARIANT
P-0039548-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-9501:CCDC6_c.2136+659:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		36652	0	63	10	Intron of RET(+):659bp after exon 11	CCDC6	43610843			10	Intron of CCDC6(-):10Kb before exon 2	RET	61621961			10	INVERSION		18011118	296780	54647	79	NEW_VARIANT
P-0039881-T01-IM6	MRE11A (NM_005591) rearrangement: c.660-14_c.870inv	PRECISE	Note: The MRE11A rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1495	0	2	11	Exon 9 of MRE11A(-)	MRE11A	94203784			11	Intron of MRE11A(-):14bp before exon 8	MRE11A	94204939			7	INVERSION		1155	298592	1589	1	NEW_VARIANT
P-0039881-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-4590:TMPRSS2_chr21:g.43413131del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ZBTB21:TMPRSS2}		45888	0	14	21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874706			21	Exon 3 of ZBTB21(-)	TMPRSS2	43413131			10	DELETION		538425	298591	34225	29	NEW_VARIANT
P-0039883-T01-IM6	ATM (NM_000051) rearrangement: c.5215_c.5320-357dup	PRECISE	Note: The ATM rearrangement is an intragenic duplication of exon 35. One of the breakpoints is within exon 35. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		569	0	2	11	Exon 35 of ATM(+)	ATM	108172412			11	Intron of ATM(+):356bp before exon 36	ATM	108173223			5	DUPLICATION		811	298596	687	2	NEW_VARIANT
P-0040077-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.3656-80:NOTCH2_chr1:g.222057559del	PRECISE	Note: The NOTCH2 rearrangement is a deletion of exons 1 - 22.	MANUAL_OK	3to5	3to5	-		324303	0	8	1	Intron of NOTCH2(-):80bp before exon 23	NOTCH2	120471915			1	IGR: 57Kb before LOC101929771(-)	NOTCH2	222057559			10	DELETION		101585644	300304	367467	8	NEW_VARIANT
P-0040081-T01-IM6	NCOA3 (NM_181659) rearrangement: c.2512+178:NCOA3_chr20:g.41905066inv	PRECISE	Note: The NCOA3 rearrangement is an inversion of exons 1 - 13. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		14240	0	14	20	IGR: 181Kb before SRSF6(+)	NCOA3	41905066			20	Intron of NCOA3(+):178bp after exon 13	NCOA3	46266705			10	INVERSION		4361639	300296	28923	13	NEW_VARIANT
P-0040082-T01-IM6	KMT2C (NM_170606) rearrangement: c.4092+972_c.5654inv	PRECISE	Note: The KMT2C rearrangement is an intragenic inversion of exons 27 - 36. One of the breakpoints is within exon 36. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		8041	0	17	7	Exon 36 of KMT2C(-)	KMT2C	151879291			7	Intron of KMT2C(-):971bp after exon 26	KMT2C	151899047			10	INVERSION		19756	300301	12265	18	NEW_VARIANT
P-0040019-T01-IM6	CDKN2A (NM_058195) rearrangement: c.348:CDKN2A_chr9:g.21951523del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3801	0	55	9	IGR: 16Kb before CDKN2A-AS1(+)	CDKN2A	21951523			9	Exon 2 of CDKN2A(-)	CDKN2A	21971053			10	DELETION		19530	300054	3255	55	NEW_VARIANT
P-0040184-T01-IM6	CASP8 (NM_001080125) rearrangement: c.313:CASP8_chr2:g.202186808del	PRECISE	Note: The CASP8 rearrangement is a deletion of exons 2 - 9. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		11401	0	9	2	Exon 2 of CASP8(+)	CASP8	202131345			2	Intron of ALS2CR12(-):8Kb after exon 9	CASP8	202186808			10	DELETION		55463	300475	8343	13	NEW_VARIANT
P-0040055-T01-IM6	SPEN (NM_015001) rearrangement: c.10057:SPEN_chr1:g.16281610del	PRECISE	Note: The SPEN rearrangement is a deletion of exons 12 - 15. One of the breakpoints is within exon 12.	MANUAL_OK	3to5	3to5	Antisense Fusion		7003	0	6	1	Exon 12 of SPEN(+)	SPEN	16263688			1	5-UTR of ZBTB17(-):13Kb before coding start	SPEN	16281610			10	DELETION		17922	300173	10940	9	NEW_VARIANT
P-0040116-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.227-170:ANKRD11_chr16:g.89434071del	PRECISE	Note: The ANKRD11 rearrangement is a deletion of exons 1 - 4.	MANUAL_OK	3to5	3to5	Deletion within transcript		4582	0	2	16	Intron of ANKRD11(-):170bp before exon 5	ANKRD11	89357761			16	5-UTR of ANKRD11(-):99Kb before coding start	ANKRD11	89434071			10	DELETION		76310	300381	4248	3	NEW_VARIANT
P-0040116-T01-IM6	EGFR (NM_005228) rearrangement: c.1007-89_c.1723-158dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : out of frame		6289	0	3	7	Intron of EGFR(+):88bp before exon 9	EGFR	55224137			7	Intron of EGFR(+):157bp before exon 15	EGFR	55232815			5	DUPLICATION		8678	300382	8951	3	NEW_VARIANT
P-0040118-T01-IM6	AKT2 (NM_001626) rearrangement: c.200_c.287+4668inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		1064	0	4	19	Intron of AKT2(-):5Kb after exon 4	AKT2	40756397			19	Exon 4 of AKT2(-)	AKT2	40761152			6	INVERSION		4755	300403	1123	4	NEW_VARIANT
P-0040193-T01-IM6	ALK (NM_004304) rearrangement: c.3172+281:ALK_chr2:g.31931590del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		69632	0	82	2	Intron of ALK(-):280bp after exon 19	ALK	29448046			2	IGR: 161Kb before MEMO1(-)	ALK	31931590			10	DELETION		2483544	300601	53768	91	NEW_VARIANT
P-0040338-T01-IM6	EGFR (NM_005228) rearrangement: c.1298+174_c.1919+406del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		7862	0	16	7	Intron of EGFR(+):174bp after exon 11	EGFR	55225620			7	Intron of EGFR(+):406bp after exon 16	EGFR	55239312			10	DELETION		13692	301292	10308	14	NEW_VARIANT
P-0006603-T01-IM5	SETD4 (NM_017438) - TMPRSS2 (NM_001135099) rearrangement: c.169+807:SETD4_c.126+629:TMPRSS2del	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (SETD4-TMPRSS2)		65666	0	78	21	Intron of SETD4(-): 807bp after exon 3	SETD4	37428600			21	Intron of TMPRSS2(-): 629bp after exon 2	TMPRSS2	42869417			62	DUPLICATION		5440817	107322	99122	74	NEW_VARIANT
P-0006603-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exons 1-2 with ERG exons 4-10): c.126+554:TMPRSS2_c.40-2798:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		43363	0	96	21	Intron of ERG(-): 3Kb before exon 4	TMPRSS2	39820342			21	Intron of TMPRSS2(-): 554bp after exon 2	ERG	42869492			64	DELETION		3049150	107319	67013	87	NEW_VARIANT
P-0032012-T01-IM6	NOTCH4 (NM_004557) rearrangement: c.1625-5:NOTCH4_chr6:g.58776688del	PRECISE	Note: The NOTCH4 rearrangement results in the deletion of exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		160461	0	8	6	Intron of NOTCH4(-):5bp before exon 10	NOTCH4	32185048			6	IGR: 505Kb before GUSBP4(-)	NOTCH4	58776688			10	DELETION		26591640	231850	115262	50	NEW_VARIANT
P-0032050-T01-IM6	PIK3CD (NM_005026) rearrangement: c.1977:PIK3CD_chr1:g.10019018inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		14995	0	55	1	Exon 16 of PIK3CD(+)	PIK3CD	9781840			1	5-UTR of NMNAT1(+):13Kb before coding start	PIK3CD	10019018			10	INVERSION		237178	231968	22520	54	NEW_VARIANT
P-0032068-T01-IM6	KMT2D (NM_003482) Rearrangement: c.8644:KMT2D_chr12:g.72507173inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		191931	0	12	12	Exon 34 of KMT2D(-)	KMT2D	49432495			12	IGR: 140Kb before TRHDE-AS1(-)	KMT2D	72507173			10	INVERSION		23074678	231983	241731	13	NEW_VARIANT
P-0032152-T01-IM6	FGFR2 (NM_000141) - KIAA1598 (NM_001127211) fusion: c.2301+1699:FGFR2_c.534+751:KIAA1598	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:KIAA1598}		18254	0	19	10	Intron of KIAA1598(-):750bp after exon 6	FGFR2	118710669			10	Intron of FGFR2(-):2Kb after exon 17	KIAA1598	123241513			10	DELETION		4530844	232630	22304	19	NEW_VARIANT
P-0032152-T01-IM6	MGA (NM_00116427) rearrangement: c.7191+105:MGA_chr15:g.42229443del	PRECISE	Note: The MGA rearrangement is a deletion of exons 20-24.	MANUAL_OK	3to5	3to5	Antisense Fusion		8786	0	35	15	Intron of MGA(+):105bp after exon 19	MGA	42050142			15	Intron of EHD4(-):6Kb after exon 3	MGA	42229443			10	DELETION		179301	232631	10711	34	NEW_VARIANT
P-0032152-T01-IM6	DROSHA (NM_013235) rearrangement: t(5;16)(p13.3;p11.2)(chr5:g.31424707::chr16:g.34383454)	PRECISE	Note: The DROSHA rearrangement is a translocation with a breakpoint in intron 26. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	40	16	IGR: 20Kb before UBE2MP1(-)	DROSHA	34383454			5	Intron of DROSHA(-):129bp before exon 27	DROSHA	31424707			10	TRANSLOCATION		0	232633	0	40	NEW_VARIANT
P-0032155-T01-IM6	NRAS (NM_002524) rearrangement: c.290+1223_c.397inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		671	0	7	1	Exon 4 of NRAS(-)	NRAS	115252243			1	Intron of NRAS(-):1Kb after exon 3	NRAS	115255198			10	INVERSION		2955	232628	926	7	NEW_VARIANT
P-0032187-T01-IM6	NFE2L2 (NM_006164) Rearrangement:  c.106_c.46-2233del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		351	0	40	2	Exon 2 of NFE2L2(-)	NFE2L2	178098939			2	Intron of NFE2L2(-):2Kb before exon 2	NFE2L2	178101232			10	DELETION		2293	232216	516	45	NEW_VARIANT
P-0032187-T01-IM6	CTNNB1 (NM_001904) Rearrangement: t(3;5)(p21.3;p14.3)(chr3:g.41277838::chr5:g.20450107)	IMPPRECISE	Note: The ctnnb1 rearrangement is a translocation with breakpoints in intron 11 of CTNNB1 and an intergenic region on chr5	MANUAL_OK	3to5	3to5	-		0	0	13	5	5-UTR of CDH18(-):977Kb before coding start	CTNNB1	20450107			3	Intron of CTNNB1(+):1bp before exon 12	CTNNB1	41277838			0	TRANSLOCATION		0	232221	0	13	NEW_VARIANT
P-0032227-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2000:KIF5B_c.2137-907:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		57008	0	27	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315356			10	Intron of RET(+):906bp before exon 12	RET	43611125			10	INVERSION		11295769	233038	35707	28	NEW_VARIANT
P-0040143-T01-IM6	CRTC3 (NM_022769) - BLM (NM_000057) rearrangement: c.578-1669:CRTC3_c.3433:BLMdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CRTC3:BLM}		18785	0	44	15	Intron of CRTC3(+):2Kb before exon 7	CRTC3	91156016			15	Exon 18 of BLM(+)	BLM	91346825			10	DELETION		190809	300454	33739	44	NEW_VARIANT
P-0040134-T01-IM6	ROS1 (NM_002944) rearrangement: t(1;6)(q21.3;q22.1)(chr1:g.154135115::chr6:g.117647954)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TPM3:ROS1}		0	0	51	6	Intron of ROS1(-):377bp before exon 33	ROS1	117647954			1	Intron of TPM3(-):5Kb before exon 7	ROS1	154135115			10	TRANSLOCATION		0	300405	0	52	NEW_VARIANT
P-0040292-T01-IM6	CSDE1 (NM_001242891) rearrangement: c.2279:CSDE1_chr1:g.103296617inv	PRECISE	Note: The CSDE1 rearrangement is an inversion of exons 19 - 21. One of the breakpoints is within exon 19. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		15444	0	39	1	IGR: 45Kb before COL11A1(-)	CSDE1	103296617			1	Exon 19 of CSDE1(-)	CSDE1	115262275			10	INVERSION		11965658	300895	11103	53	NEW_VARIANT
P-0040300-T01-IM6	DNAJC8 (NM_014280) - MTOR (NM_004958) rearrangement: c.181-280:DNAJC8_c.7327:MTORdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNAJC8:MTOR}		270575	0	50	1	Exon 54 of MTOR(-)	DNAJC8	11172948			1	Intron of DNAJC8(-):280bp before exon 3	MTOR	28541787			10	DELETION		17368839	300896	541778	54	NEW_VARIANT
P-0040300-T01-IM6	NTRK1 (NM_002529) rearrangement: c.1789:NTRK1_chr1:g.201437190inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		111274	0	106	1	Exon 14 of NTRK1(+)	NTRK1	156846348			1	3-UTR of PHLDA3(-):340bp after coding stop	NTRK1	201437190			10	INVERSION		44590842	300901	165004	106	NEW_VARIANT
P-0040300-T01-IM6	MGA (NM_001164273) rearrangement: c.464:MGA_chr15:g.41846191del	PRECISE	Note: The MGA rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		4598	0	33	15	IGR: 5Kb before TYRO3(+)	MGA	41846191			15	Exon 2 of MGA(+)	MGA	41961556			10	DELETION		115365	300897	5791	36	NEW_VARIANT
P-0040300-T01-IM6	ERF (NM_006494) - CIC (NM_015125) rearrangement: c.913:ERF_c.3009-45:CICdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		46195	0	9	19	Exon 4 of ERF(-)	ERF	42753351			19	Intron of CIC(+):44bp before exon 13	CIC	42796407			10	DELETION		43056	300898	56278	10	NEW_VARIANT
P-0040307-T01-IM6	RAD54L (NM_001142548) rearrangement: c.1610+97:RAD54L_chr1:g.118268672inv	PRECISE	Note: The RAD54L rearrangement is an inversion of exons 16 - 19. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		180697	0	2	1	Intron of RAD54L(+):97bp after exon 15	RAD54L	46739516			1	IGR: 120Kb before FAM46C(+)	RAD54L	118268672			10	INVERSION		71529156	301261	112108	5	NEW_VARIANT
P-0040307-T01-IM6	CCNT1 (NM_001240) - KMT2D (NM_003482) rearrangement: c.373-613:CCNT1_c.7391:KMT2Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CCNT1:KMT2D}		77228	0	10	12	Intron of CCNT1(-):613bp before exon 4	CCNT1	49095469			12	Exon 31 of KMT2D(-)	KMT2D	49434162			10	DUPLICATION		338693	301260	75082	19	NEW_VARIANT
P-0040307-T01-IM6	EP300 (NM_001429) rearrangement: t(3;22)(q26.2;q13.2)(chr3:g.169670000::chr22:g.41545936)	IMPPRECISE	Note: The EP300 rearrangement is a translocation with a breakpoint in exon 14. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	26	22	Exon 14 of EP300(+)	EP300	41545936			3	3-UTR of LOC100128164(-):15Kb after coding stop	EP300	169670000			0	TRANSLOCATION		0	301262	0	25	NEW_VARIANT
P-0040327-T01-IM6	NFE2L2 (NM_006164) rearrangement: c.46-1976_c.313-64del	PRECISE	Note: The NFE2L2 rearrangement is an intragenic deletion of exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1668	0	24	2	Intron of NFE2L2(-):64bp before exon 3	NFE2L2	178098131			2	Intron of NFE2L2(-):2Kb before exon 2	NFE2L2	178100975			10	DELETION		2844	301287	2359	24	NEW_VARIANT
P-0040343-T01-IM6	IL10 (NM_000572) rearrangement: t(1;X)(q32.1;q22.3)(chr1:g.206944654::chrX:g.104497492)	PRECISE	Note: The IL10 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	6	X	Intron of IL1RAPL2(+):15Kb before exon 5	IL10	104497492			1	Intron of IL10(-):46bp after exon 2	IL10	206944654			10	TRANSLOCATION		0	301324	0	6	NEW_VARIANT
P-0040458-T01-IM6	BRCA2 (NM_000059) rearrangement: c.7618-1:BRCA2_chr13:g.33938000dup	PRECISE	Note: The BRCA2 rearrangement is a duplication of exons 16 - 27. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		17926	0	10	13	Exon 16 of BRCA2(+)	BRCA2	32931878			13	Intron of STARD13(-):76Kb after exon 5	BRCA2	33938000			10	DUPLICATION		1006122	301769	21392	11	NEW_VARIANT
P-0008232-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1086:TMPRSS2_c.40-59158:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29935	0	18	21	Intron of ERG(-):59Kb before exon 4	TMPRSS2	39876702			21	Intron of TMPRSS2(-):1Kb after exon 2	ERG	42868960			10	DELETION		2992258	301274	44843	18	NEW_VARIANT
P-0021838-T02-IM6	PTPRS (NM_002850) rearrangement: t(12;19)(q22;p13.3)(chr12:g.93413328::chr19:g.5240169)	PRECISE	Note: The PTPRS rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	22	19	Intron of PTPRS(-):40bp after exon 12	PTPRS	5240169			12	3-UTR of LOC643339(-):358Kb after coding stop	PTPRS	93413328			10	TRANSLOCATION		0	302135	0	22	NEW_VARIANT
P-0040511-T01-IM6	GNAS (NM_000516) - GDPD5 (NM_030792) rearrangement: t(11;20)(q13.4;q13.32)(chr11:g.75150246::chr20:g.57474193)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {GNAS:GDPD5}		0	0	19	20	Intron of GNAS(+):153bp after exon 3	GNAS	57474193			11	Intron of GDPD5(-):677bp after exon 15	GDPD5	75150246			10	TRANSLOCATION		0	302119	0	17	NEW_VARIANT
P-0040519-T01-IM6	KMT2D (NM_003482) rearrangement: c.16549:KMT2D_chr12:g.49412345del	PRECISE	Note: The KMT2D rearrangement is a deletion of exon 54. One of the breakpoints is within exon 54.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		294	0	11	12	Promoter of KMT2D(-):412bp from tx start	KMT2D	49412345			12	Exon 54 of KMT2D(-)	KMT2D	49415628			10	DELETION		3283	302137	339	12	NEW_VARIANT
P-0040519-T01-IM6	FANCA (NM_000135) rearrangement: c.893+227:FANCA_chr16:g.88532673del	PRECISE	Note: The FANCA rearrangement is a deletion of exons 11 - 43.	MANUAL_OK	3to5	3to5	Antisense Fusion		37725	0	14	16	Intron of ZFPM1(+):13Kb after exon 1	FANCA	88532673			16	Intron of FANCA(-):226bp after exon 10	FANCA	89865347			10	DELETION		1332674	302139	90626	17	NEW_VARIANT
P-0040519-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1047:TMPRSS2_c.40-54812:ERGdel	IMPPRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		13067	0	6	21	Promoter of ERG(-):120Kb from tx start	TMPRSS2	39872356			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871163			0	DELETION		2998807	302140	47005	6	NEW_VARIANT
P-0040520-T01-IM6	PBRM1 (NM_018313) rearrangement: t(3;16)(p21.1;q24.1)(chr3:g.52643949::chr16:g.85652741)	PRECISE	Note: The PBRM1 rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	16	16	Intron of GSE1(+):6Kb after exon 1	PBRM1	85652741			3	Exon 17 of PBRM1(-)	PBRM1	52643949			10	TRANSLOCATION		0	302144	0	14	NEW_VARIANT
P-0040443-T02-IM6	MAP3K13 (NM_004721) rearrangement: c.2222_c.2431-1575del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1809	0	25	3	Exon 11 of MAP3K13(+)	MAP3K13	185191341			3	Intron of MAP3K13(+):2Kb before exon 12	MAP3K13	185193539			10	DELETION		2198	301757	1539	40	NEW_VARIANT
P-0040443-T02-IM6	FGFR3 (NM_000142) rearrangement: c.773:FGFR3_chr4:g.1888480del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {FGFR3:WHSC1}		25987	0	3	4	Exon 7 of FGFR3(+)	FGFR3	1803595			4	5-UTR of WHSC1(+):14Kb before coding start	FGFR3	1888480			10	DELETION		84885	301758	17364	3	NEW_VARIANT
P-0017005-T01-IM6	BAZ1A (NM_013448) - DICER1(NM_030621) Rearrangement : c.-1088:BAZ1A_c.5528-8:DICER1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {BAZ1A:DICER1}		63053	0	39	14	Promoter of BAZ1A(-):123Kb from tx start	BAZ1A	35345373			14	Intron of DICER1(-):8bp before exon 28	DICER1	95557454			10	DUPLICATION		60212081	174099	107907	41	NEW_VARIANT
P-0017629-T01-IM5	PDPK1 (NM_002613) rearrangement: c.1402-8:PDPK1_chr16:g.2150327del	PRECISE	Note: The PDPK1 rearrangement is a deletion of exons 1-12.	MANUAL_OK	3to5	3to5	-		20928	0	3	16	Intron of PKD1(-):17bp before exon 28	PDPK1	2150327			16	Intron of PDPK1(+):7bp before exon 13	PDPK1	2647116			10	DELETION		496789	176321	75753	7	NEW_VARIANT
P-0017664-T01-IM5	RAD21 (NM_006265) - ADH7 (NM_001166504) rearrangement: t(4;8)(q23;q24.11)(chr4:g.100338146::chr8:g.117869648)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RAD21:ADH7}		0	0	39	8	Exon 6 of RAD21(-)	RAD21	117869648			4	Intron of ADH7(-):1Kb before exon 8	ADH7	100338146			10	TRANSLOCATION		0	176742	0	45	NEW_VARIANT
P-0018345-T01-IM6	FH (NM_000143) rearrangement: c.267_c.268del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		295	0	16	1	Exon 3 of FH(-)	FH	241677013			1	Exon 2 of FH(-)	FH	241680482			10	DELETION		3469	178634	296	16	NEW_VARIANT
P-0021991-T01-IM6	FLT4 (NM_182925) rearrangement: g.52740102_c.2167+12inv	IMPPRECISE	Note: The FLT4 rearrangement results in the inversion of exons 15-30. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		277981	0	5	5	IGR: 36Kb before FST(+)	FLT4	52740102			5	Intron of FLT4(-):11bp after exon 14	FLT4	180048094			0	INVERSION		127307992	188864	556081	5	NEW_VARIANT
P-0023380-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-4212:TMPRSS2_c.39+64807:ERGdel	PRECISE	Note: TMPRSS2 is fused to the non-canonical ERG (NM_004449) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		62677	0	20	21	Intron of ERG(-):65Kb after exon 3	TMPRSS2	39882779			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874328			10	DELETION		2991549	194897	44152	101	NEW_VARIANT
P-0024146-T01-IM6	PIK3C3 (NM_002647) rearrangement: chr18:g.37483346_c.984+12inv	IMPPRECISE	Note: The PIK3C3 rearrangement results in the inversion of exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		7581	0	8	18	IGR: 163Kb before LINC01477(+)	PIK3C3	37483346			18	Intron of PIK3C3(+):12bp after exon 9	PIK3C3	39576706			0	INVERSION		2093360	198538	13413	7	NEW_VARIANT
P-0024146-T01-IM6	WHSC1 (NM_001042424) - FGFR3 (NM_000142) rearrangement: c.761-178:WHSC1_c.380-60:FGFR3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {WHSC1:FGFR3}		25038	0	16	4	Intron of FGFR3(+):59bp before exon 4	WHSC1	1801414			4	Intron of WHSC1(+):177bp before exon 4	FGFR3	1918420			10	DUPLICATION		117006	198536	48340	16	NEW_VARIANT
P-0024146-T01-IM6	AMER1 (NM_152424) rearrangement: t(X;11)(q11.2;q13.4)(chrX:g.63412860::chr11:g.74289154)	PRECISE	Note: The AMER1 rearrangement is a translocation which involves a breakpoint in exon 2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	14	X	Exon 2 of AMER1(-)	AMER1	63412860			11	IGR: 14Kb before POLD3(+)	AMER1	74289154			10	TRANSLOCATION		0	198539	0	14	NEW_VARIANT
P-0024149-T01-IM6	NF1 (NM_001042492) rearrangement: c.1244_c.4725-907inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		13412	0	9	17	Exon 11 of NF1(+)	NF1	29528487			17	Intron of NF1(+):906bp before exon 36	NF1	29591340			10	INVERSION		62853	198546	16633	9	NEW_VARIANT
P-0025463-T01-IM6	KMT2C (NM_170606) rearrangement: t(7;21)(q36.1;p11.1)(chr7:g.151945554::chr21:g.11039052)	IMPPRECISE	Note: The KMT2C rearrangement is a translocation involving a breakpoint in exon 14. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	14	21	3-UTR of BAGE2(-):11Kb after coding stop	KMT2C	11039052			7	Exon 14 of KMT2C(-)	KMT2C	151945554			0	TRANSLOCATION		0	206025	0	9	NEW_VARIANT
P-0025463-T01-IM6	APC (NM_000038) rearrangement: t(5;9)(q22.2;q31.3)(chr5:g.112177163::chr9:g.111567118)	PRECISE	Note: The APC rearrangement is a translocation involving a breakpoint in exon 16. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	21	9	IGR: 50Kb before ACTL7B(-)	APC	111567118			5	Exon 16 of APC(+)	APC	112177163			10	TRANSLOCATION		0	206022	0	24	NEW_VARIANT
P-0025737-T01-IM6	PGR (NM_000926) - MS4A13 (NM_001012417) rearrangement: c.1637+92:PGR_c.129+2012:MS4A13inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {PGR:MS4A13}		97233	0	6	11	Intron of MS4A13(+):2Kb after exon 3	PGR	60287697			11	Intron of PGR(-):91bp after exon 1	MS4A13	100998073			0	INVERSION		40710376	206532	229855	8	NEW_VARIANT
P-0026636-T01-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.*4:FGFR2_c.7896+636:TACC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		24064	0	14	10	3-UTR of FGFR2(-):3bp after coding stop	FGFR2	123239367			10	Intron of TACC2(+):636bp after exon 13	TACC2	123988159			10	INVERSION		748792	210949	69735	20	NEW_VARIANT
P-0026636-T01-IM6	CDKN2B (NM_004936) rearrangement: c.247:CDKN2B_chr9:g.21910667del	PRECISE	Note: The CDKN2B rearrangement is a deletion with a breakpoint is exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		8088	0	73	9	IGR: 56Kb before CDKN2A-AS1(+)	CDKN2B	21910667			9	Exon 2 of CDKN2B(-)	CDKN2B	22006156			10	DELETION		95489	210948	9960	90	NEW_VARIANT
P-0030304-T01-IM6	DNMT1 (NM_001379) - DOT1L (NM_032482) rearrangement: c.4816+127:DNMT1_c.201-47:DOT1Linv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {DNMT1:DOT1L}		133961	0	10	19	Intron of DOT1L(+):46bp before exon 4	DNMT1	2189684			19	Intron of DNMT1(-):126bp after exon 39	DOT1L	10244766			10	INVERSION		8055082	226618	276772	10	NEW_VARIANT
P-0030304-T01-IM6	DNMT1 (NM_001379) - TYK2 (NM_003331) rearrangement: c.878+94:DNMT1_c.465+110:TYK2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {DNMT1:TYK2}		9199	0	7	19	Intron of DNMT1(-):93bp after exon 11	DNMT1	10273908			19	Intron of TYK2(-):109bp after exon 5	TYK2	10478621			10	DUPLICATION		204713	226616	21726	8	NEW_VARIANT
P-0030304-T01-IM6	MEGF8 (NM_001410) - CIC (NM_015125) rearrangement: c.6703:MEGF8_c.2887-24:CICdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MEGF8:CIC}		12303	0	11	19	Intron of CIC(+):23bp before exon 12	MEGF8	42796214			19	Exon 38 of MEGF8(+)	CIC	42874410			10	DUPLICATION		78196	226617	30338	11	NEW_VARIANT
P-0030304-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(12;21)(q13.13;q22.3)(chr12:g.53196493::chr21:g.42842718)	IMPPRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	5	21	Intron of TMPRSS2(-):48bp before exon 11	TMPRSS2	42842718			12	IGR: 4Kb before KRT4(-)	TMPRSS2	53196493			0	TRANSLOCATION		0	226619	0	5	NEW_VARIANT
P-0030556-T01-IM6	PBRM1 (NM_018313) rearrangement: c.3616+5492_c.3800+52dup	PRECISE	Note: The PBRM1 rearrangement is an intragenic duplication of exon 24. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1102	0	23	3	Intron of PBRM1(-):51bp after exon 24	PBRM1	52598014			3	Intron of PBRM1(-):5Kb after exon 23	PBRM1	52605065			10	DUPLICATION		7051	226668	1942	24	NEW_VARIANT
P-0031041-T01-IM6	RECQL4 (NM_004260) rearrangement: t(10;12)(q22.3;p12.1)(chr10:g.78493482::chr12:g.21628298)	PRECISE	Note: The RECQL4 rearrangement is a translocation with the breakpoint in intron 11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	9	12	Intron of RECQL(-):103bp after exon 11	RECQL4	21628298			10	IGR: 136Kb before KCNMA1(-)	RECQL4	78493482			10	TRANSLOCATION		0	228385	0	9	NEW_VARIANT
P-0033042-T01-IM6	NOTCH2 (NM_024408) Rearrangement: chr1:g.101514328_c.1427:NOTCH2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		48591	0	45	1	5-UTR of LOC102606465(+):39Kb before coding start	NOTCH2	101514328			1	Exon 8 of NOTCH2(-)	NOTCH2	120510082			10	DELETION		18995754	237296	82338	53	NEW_VARIANT
P-0033652-T01-IM6	FGFR2 (NM_000141) - CCDC186(NM_018017) Rearrangement :  c.2302-1295:FGFR2_c.1222-3356:CCDC186del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:CCDC186}		11721	0	60	10	Intron of CCDC186(-):3Kb before exon 7	FGFR2	115900405			10	Intron of FGFR2(-):1Kb before exon 18	CCDC186	123240830			10	DELETION		7340425	243977	22994	106	NEW_VARIANT
P-0034258-T01-IM6	NCOR1 (NM_006311) - DLG2 (NM_001142699) rearrangement: t(11;17)(q14.1;p11.2)(chr11:g.84221683::chr17:g.15952268)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NCOR1:DLG2}		0	0	7	17	Exon 41 of NCOR1(-)	NCOR1	15952268			11	Intron of DLG2(-):24Kb after exon 7	DLG2	84221683			10	TRANSLOCATION		0	250097	0	7	NEW_VARIANT
P-0034784-T01-IM6	FGFR2 (NM_000141) - KIAA1217 (NM_019590) fusion: c.2301+958:FGFR2_c.355-49659:KIAA1217inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:KIAA1217}		211042	0	12	10	Intron of KIAA1217(+):50Kb before exon 4	FGFR2	24620139			10	Intron of FGFR2(-):957bp after exon 17	KIAA1217	123242254			10	INVERSION		98622115	253577	242807	20	NEW_VARIANT
P-0034784-T01-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement : c.251:CDKN2Ap16INK4A_chr9:g.21981088del CDKN2Ap14ARF (NM_058195) rearrangement:c.194-9881_c.294del	PRECISE	Note: The CDKN2A rearrangement results in the deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1893	0	4	9	Exon 2 of CDKN2A(-)	CDKN2Ap16INK4A	21971107			9	Intron of CDKN2A(-):10Kb before exon 2	CDKN2Ap16INK4A	21981088			10	DELETION		9981	253576	1694	17	NEW_VARIANT
P-0034885-T01-IM6	BCAS3 (NM_001099432) - PPM1D (NM_003620) rearrangement: c.585-525:BCAS3_c.1261-173:PPM1Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BCAS3:PPM1D}		3084	0	9	17	Intron of PPM1D(+):172bp before exon 6	BCAS3	58740183			17	Intron of BCAS3(+):524bp before exon 9	PPM1D	58951498			6	DUPLICATION		211315	254505	7804	9	NEW_VARIANT
P-0034885-T01-IM6	HIST1H3B (NM_003537) rearrangement: t(6;20)(p22.2;p12.3)(chr6:g.26031916::chr20:g.5641761)	PRECISE	Note: The HIST1H3B rearrangement is a translocation with a breakpoint in exon 1. The functional significance is undetermined	MANUAL_OK	5to3	5to3	-		0	0	13	20	IGR: 89Kb before C20orf196(+)	HIST1H3B	5641761			6	Exon 1 of HIST1H3B(-)	HIST1H3B	26031916			10	TRANSLOCATION		0	254506	0	13	NEW_VARIANT
P-0036098-T01-IM6	YAP1 (NM_001130145) rearrangement: c.-3159_c.283dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		821	0	24	11	Promoter of YAP1(+):3Kb from tx start	YAP1	101978421			11	Exon 1 of YAP1(+)	YAP1	101981862			10	DUPLICATION		3441	264940	4349	24	NEW_VARIANT
P-0036673-T01-IM6	PGR (NM_000926) - SIK3 (NM_025164) rearrangement: c.2488+212:PGR_c.100-14184:SIK3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PGR:SIK3}		178421	0	6	11	Intron of PGR(-):211bp after exon 6	PGR	100920448			11	Intron of SIK3(-):14Kb before exon 2	SIK3	116841964			9	DUPLICATION		15921516	271831	236742	7	NEW_VARIANT
P-0039908-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.462:ANKRD11_chr16:g.83930601del	PRECISE	Note: The ANKRD11 rearrangement is a deletion of exons 6 - 13. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Antisense Fusion		54219	0	63	16	Promoter of MLYCD(+):2Kb from tx start	ANKRD11	83930601			16	Exon 6 of ANKRD11(-)	ANKRD11	89357172			10	DELETION		5426571	298490	70160	66	NEW_VARIANT
P-0020150-T02-IM6	INPPL1 (NM_001567) rearrangement: c.659+75:INPPL1_chr11:g.71982730del	PRECISE	Note: The INPPL1 rearrangement is a deletion of exons 6 - 28.	MANUAL_OK	3to5	3to5	-		58451	0	55	11	Intron of INPPL1(+):75bp after exon 5	INPPL1	71940349			11	IGR: 21Kb before CLPB(-)	INPPL1	71982730			10	DELETION		42381	302629	28981	64	NEW_VARIANT
P-0020150-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1331:TMPRSS2_c.40-57667:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		33588	0	167	21	Intron of ERG(-):58Kb before exon 4	TMPRSS2	39875211			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867836			10	DELETION		2992625	302631	29399	186	NEW_VARIANT
P-0025699-T02-IM6	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2014+674:TRIM24_c.1177+494:BRAFinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TRIM24:BRAF}		10213	0	12	7	Intron of TRIM24(+):674bp after exon 12	TRIM24	138259061			7	Intron of BRAF(-):493bp after exon 9	BRAF	140486854			0	INVERSION		2227793	302728	45707	10	NEW_VARIANT
P-0026050-T04-IM6	ATR (NM_001184) rearrangement: c.4292_c.4382+1317del	PRECISE	Note: The ATR rearrangement is an intragenic deletion of exon 24. One of the breakpoints is within exon 24.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		492	0	7	3	Intron of ATR(-):1Kb after exon 24	ATR	142237194			3	Exon 24 of ATR(-)	ATR	142238601			5	DELETION		1407	302491	529	7	NEW_VARIANT
P-0026050-T04-IM6	BRAF (NM_004333) rearrangement: c.1084:BRAF_chr7:g.145389205del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		53686	0	129	7	Exon 8 of BRAF(-)	BRAF	140494164			7	IGR: 424Kb before CNTNAP2(+)	BRAF	145389205			10	DELETION		4895041	302496	131413	135	NEW_VARIANT
P-0026050-T04-IM6	BTK (NM_000061) rearrangement: c.392-16:BTK_chrX:g.82536485inv	IMPPRECISE	Note: The BTK rearrangement is an inversion of exons 6 - 19. The rearrangement includes the kinase domain of BTK. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		38829	0	13	X	IGR: 227Kb before POU3F4(+)	BTK	82536485			X	Intron of BTK(-):16bp before exon 6	BTK	100617693			0	INVERSION		18081208	302498	40293	15	NEW_VARIANT
P-0038074-T02-IM6	BRCA2 (NM_000059) rearrangement: c.2017_c.2740del	PRECISE	Note: The BRCA2 rearrangement is an intragenic deletion of exon 11. The breakpoints are within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2924	0	53	13	Exon 11 of BRCA2(+)	BRCA2	32910509			13	Exon 11 of BRCA2(+)	BRCA2	32911232			10	DELETION		723	303001	3298	55	NEW_VARIANT
P-0039994-T03-IM6	NF1 (NM_001042492) rearrangement: t(5;17)(p13.2;q11.2)(chr5:g.37923642::chr17:g.29527467)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	17	Exon 9 of NF1(+)	NF1	29527467			5	IGR: 50Kb before GDNF-AS1(+)	NF1	37923642			10	TRANSLOCATION		0	302673	0	8	NEW_VARIANT
P-0040536-T01-IM6	PBRM1 (NM_018313) rearrangement: c.917_c.1819-402dup	PRECISE	Note: The PBRM1 rearrangement is an intragenic duplication of exons 10 - 15. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8879	0	34	3	Intron of PBRM1(-):402bp before exon 16	PBRM1	52649874			3	Exon 10 of PBRM1(-)	PBRM1	52677342			10	DUPLICATION		27468	302162	13236	35	NEW_VARIANT
P-0040579-T01-IM6	TBC1D24 (NM_001199107) - TSC2 (NM_000548) rearrangement: c.1143-71:TBC1D24_c.3648:TSC2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TBC1D24:TSC2}		69010	0	12	16	Exon 31 of TSC2(+)	TBC1D24	2131633			16	Intron of TBC1D24(+):70bp before exon 5	TSC2	2549287			10	DUPLICATION		417654	302479	50863	13	NEW_VARIANT
P-0040588-T01-IM6	PTPN11 (NM_002834) rearrangement: c.1225-5:PTPN11_chr12:g.115772818del	PRECISE	Note: The PTPN11 rearrangement is a deletion of exons 11 - 15. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		32761	0	3	12	Intron of PTPN11(+):4bp before exon 11	PTPN11	112924274			12	IGR: 624Kb before MED13L(-)	PTPN11	115772818			5	DELETION		2848544	302529	75373	3	NEW_VARIANT
P-0040588-T01-IM6	ATR (NM_001184) rearrangement: c.7042-36:ATR_chr3:g.141768495dup	IMPPRECISE	Note: The ATR rearrangement is a duplication of exons 42 - 47. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TFDP2:ATR}		6564	0	14	3	Intron of TFDP2(-):43Kb after exon 3	ATR	141768495			3	Intron of ATR(-):36bp before exon 42	ATR	142180968			0	DUPLICATION		412473	302530	20030	14	NEW_VARIANT
P-0040595-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-244:TMPRSS2_c.18+1439:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		55452	0	35	21	Intron of ERG(-):1Kb after exon 1	TMPRSS2	39868848			21	Intron of TMPRSS2(-):244bp before exon 2	ERG	42870360			10	DELETION		3001512	302533	23396	39	NEW_VARIANT
P-0040602-T01-IM6	STK11 (NM_000455) rearrangement: c.375-6_c.536inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		1053	0	41	19	Intron of STK11(+):5bp before exon 3	STK11	1219317			19	Exon 4 of STK11(+)	STK11	1220443			10	INVERSION		1126	302646	1710	67	NEW_VARIANT
P-0040684-T01-IM6	AKT3 (NM_005465) rearrangement: c.1040:AKT3_chr1:g.239082557inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		21152	0	24	1	IGR: 439Kb before LINC01139(-)	AKT3	239082557			1	Exon 10 of AKT3(-)	AKT3	243716154			10	INVERSION		4633597	302736	41314	25	NEW_VARIANT
P-0040684-T01-IM6	UNK (NM_001080419) - H3F3B (NM_005324) rearrangement: c.104+1748:UNK_c.325:H3F3Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {UNK:H3F3B}		3331	0	2	17	Exon 4 of H3F3B(-)	UNK	73774762			17	Intron of UNK(+):2Kb after exon 1	H3F3B	73782813			10	INVERSION		8051	302738	5770	4	NEW_VARIANT
P-0040739-T01-IM6	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	PRECISE		MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		24785	0	35	21	Promoter of ERG(-):121Kb from tx start	TMPRSS2	39872529			21	Intron of TMPRSS2(-):848bp after exon 2	ERG	42869197			10	DELETION		2996668	303015	26206	38	NEW_VARIANT
P-0040748-T01-IM6	NF1 (NM_001042492) rearrangement: c.7587:NF1_chr17:g.29662315del	IMPPRECISE	Note: The NF1 rearrangement is a deletion of exons 41 - 51. One of the breakpoints is within exon 51.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9064	0	8	17	Intron of NF1(+):266bp after exon 40	NF1	29662315			17	Exon 51 of NF1(+)	NF1	29679404			0	DELETION		17089	303006	6318	10	NEW_VARIANT
P-0030521-T02-IM6	CNTLN (NM_017738) - FANCC (NM_000136) rearrangement: c.3855+6228:CNTLN_c.687-96:FANCCinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {CNTLN:FANCC}		239609	0	41	9	Intron of CNTLN(+):6Kb after exon 23	CNTLN	17473117			9	Intron of FANCC(-):96bp before exon 8	FANCC	97897880			10	INVERSION		80424763	303115	296986	38	NEW_VARIANT
P-0039523-T02-IM6	ARID1A (NM_006015) rearrangement: t(1;18)(p36.11;q12.3)(chr1:g.27101004::chr18:g.40077260)	IMPPRECISE	Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	123	18	5-UTR of LINC00907(+):194Kb before coding start	ARID1A	40077260			1	Exon 18 of ARID1A(+)	ARID1A	27101004			0	TRANSLOCATION		0	302702	0	122	NEW_VARIANT
P-0021969-T02-IM6	JAK1 (NM_002227) rearrangement: c.651:JAK1_chr1:g.65452897del	PRECISE	Note: The JAK1 rearrangement is a deletion of exons 1 - 7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	-		2298	0	20	1	Exon 7 of JAK1(-)	JAK1	65332888			1	3-UTR of LINC01359(-):15Kb after coding stop	JAK1	65452897			10	DELETION		120009	303044	8160	20	NEW_VARIANT
P-0021969-T02-IM6	MAP3K13 (NM_004721) - TNIK (NM_015028) rearrangement: c.1010+192:MAP3K13_c.4000-268:TNIKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {MAP3K13:TNIK}		18467	0	29	3	Intron of TNIK(-):268bp before exon 30	MAP3K13	170782021			3	Intron of MAP3K13(+):192bp after exon 5	TNIK	185165927			10	INVERSION		14383906	303046	180304	29	NEW_VARIANT
P-0040754-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-201:TMPRSS2_c.40-54954:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		49737	0	114	21	Promoter of ERG(-):121Kb from tx start	TMPRSS2	39872498			21	Intron of TMPRSS2(-):201bp before exon 2	ERG	42870317			10	DELETION		2997819	303062	52074	116	NEW_VARIANT
P-0040947-T01-IM6	PIK3CD (NM_005026) rearrangement: c.3062:PIK3CD_chr1:g.9911454del	PRECISE	Note: The PIK3CD rearrangement is a deletion of exon 24. One of the breakpoints is within exon 24. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		1281	0	11	1	Exon 24 of PIK3CD(+)	PIK3CD	9787031			1	Intron of CTNNBIP1(-):620bp before exon 6	PIK3CD	9911454			10	DELETION		124423	304187	815	19	NEW_VARIANT
P-0038086-T01-IM6	ERBB4 (NM_005235) rearrangement: c.422-39327_c.1321del	PRECISE	Note: The ERBB4 rearrangement is an intragenic deletion of exons 4 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8713	0	14	2	Exon 12 of ERBB4(-)	ERBB4	212566860			2	Intron of ERBB4(-):39Kb before exon 4	ERBB4	212692211			10	DELETION		125351	284122	11406	14	NEW_VARIANT
P-0038086-T01-IM6	GNAQ (NM_002072) rearrangement: c.606-60:GNAQ_chr9:g.80877309del	PRECISE	Note: The GNAQ rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6182	0	51	9	Intron of GNAQ(-):60bp before exon 5	GNAQ	80409568			9	Intron of CEP78(+):513bp before exon 12	GNAQ	80877309			10	DELETION		467741	284123	6135	62	NEW_VARIANT
P-0040643-T01-IM6	RARA (NM_000964) - FER1L5 (NM_001113382) rearrangement: t(2;17)(q11.2;q21.2)(chr2:g.97351976::chr17:g.38504786)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RARA:FER1L5}		0	0	23	17	Intron of RARA(+):70bp after exon 3	RARA	38504786			2	Exon 23 of FER1L5(+)	FER1L5	97351976			10	TRANSLOCATION		0	302703	0	23	NEW_VARIANT
P-0041007-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.2002-1888_c.3774+83dup	PRECISE	Note: The SMARCA4 rearrangement is an intragenic duplication of exons 14 - 26. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 13 exons : in frame		25796	0	45	19	Intron of SMARCA4(+):2Kb before exon 14	SMARCA4	11116690			19	Intron of SMARCA4(+):83bp after exon 26	SMARCA4	11144276			10	DUPLICATION		27586	305285	28838	50	NEW_VARIANT
P-0041032-T01-IM6	PIK3CD (NM_005026) rearrangement: c.1955+71:PIK3CD_chr1:g.20738691del	PRECISE	Note: The PIK3CD rearrangement is a deletion of exons 16 - 24. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		234137	0	4	1	Intron of PIK3CD(+):71bp after exon 15	PIK3CD	9781716			1	3-UTR of LINC01141(-):17Kb after coding stop	PIK3CD	20738691			6	DELETION		10956975	305424	298436	4	NEW_VARIANT
P-0040422-T02-IM6	ROS1 (NM_002944) rearrangement: c.5642-856_c.5777+139inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		4957	0	2	6	Intron of ROS1(-):138bp after exon 35	ROS1	117642283			6	Intron of ROS1(-):856bp before exon 35	ROS1	117643413			10	INVERSION		1130	305542	4586	2	NEW_VARIANT
P-0040995-T01-IM6	KMT2C (NM_170606) rearrangement: c.5021:KMT2C_chr7:g.150477103del	PRECISE	Note: The KMT2C rearrangement is a deletion of exons 34 - 59. One of the breakpoints is within exon 34.	MANUAL_OK	3to5	3to5	-		78468	0	9	7	IGR: 11Kb before TMEM176B(-)	KMT2C	150477103			7	Exon 34 of KMT2C(-)	KMT2C	151882704			10	DELETION		1405601	305133	68279	16	NEW_VARIANT
P-0041103-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.13;q22.3)(chr19:g.38571571::chr21:g.42871994)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	21	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871994			19	5-UTR of SIPA1L3(+):634bp before coding start	TMPRSS2	38571571			10	TRANSLOCATION		0	305850	0	22	NEW_VARIANT
P-0041103-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-1557:TMPRSS2_chr21:g.39961941del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		70370	0	28	21	3-UTR of ERG(-):72Kb after coding stop	TMPRSS2	39961941			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42871673			10	DELETION		2909732	305846	40515	31	NEW_VARIANT
P-0041108-T01-IM6	MAPK3 (NM_002746) rearrangement: c.306:MAPK3_chr16:g.30140007del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3554	0	31	16	Exon 2 of MAPK3(-)	MAPK3	30133192			16	IGR: 12Kb before MAPK3(-)	MAPK3	30140007			10	DELETION		6815	305833	6057	31	NEW_VARIANT
P-0041108-T01-IM6	FGFR3 (NM_000142) rearrangement: t(2;4)(p24.3;p16.3)(chr2:g.16434694::chr4:g.1808368)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	126	4	Exon 16 of FGFR3(+)	FGFR3	1808368			2	IGR: 244Kb before GACAT3(+)	FGFR3	16434694			10	TRANSLOCATION		0	305835	0	131	NEW_VARIANT
P-0023910-T09-IM6	FLT4 (NM_182925) rearrangement: t(5;12)(q35.3;q23.1)(chr5:g.180046682::chr12:g.97517987)	PRECISE	Note: The FLT4 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	88	12	IGR: 217Kb before NEDD1(+)	FLT4	97517987			5	Exon 18 of FLT4(-)	FLT4	180046682			10	TRANSLOCATION		0	305843	0	88	NEW_VARIANT
P-0023910-T09-IM6	FAT1 (NM_005245) rearrangement: c.11482+108:FAT1_chr4:g.29213342inv	PRECISE	Note: The FAT1 rearrangement is an inversion of exons 21 - 27. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		437139	0	76	4	IGR: 392Kb before MIR4275(+)	FAT1	29213342			4	Intron of FAT1(-):107bp after exon 20	FAT1	187523949			10	INVERSION		158310607	305842	294979	76	NEW_VARIANT
P-0040504-T01-IM6	SLIT2 (NM_004787) - ETV6 (NM_001987) rearrangement: t(4;12)(p15.31;p13.2)(chr4:g.20374490::chr12:g.12034059)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SLIT2:ETV6}		0	0	121	12	Intron of ETV6(+):3Kb before exon 6	SLIT2	12034059			4	Intron of SLIT2(+):95Kb before exon 5	ETV6	20374490			10	TRANSLOCATION		0	306117	0	120	NEW_VARIANT
P-0040504-T01-IM6	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.55-5627:BAIAP2_c.3478-165:RPTORdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {BAIAP2:RPTOR}		10296	0	6	17	Intron of RPTOR(+):164bp before exon 30	BAIAP2	78933713			17	Intron of BAIAP2(+):6Kb before exon 2	RPTOR	79021841			5	DUPLICATION		88128	306116	9387	6	NEW_VARIANT
P-0040925-T01-IM6	KMT2B (NM_014727) rearrangement: c.4087:KMT2B_chr19:g.31655075del	PRECISE	Note: The KMT2B rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15.	MANUAL_OK	3to5	3to5	-		57617	0	109	19	IGR: 111Kb before TSHZ3(-)	KMT2B	31655075			19	Exon 15 of KMT2B(+)	KMT2B	36218140			10	DELETION		4563065	304238	70803	119	NEW_VARIANT
P-0040955-T01-IM6	SUGP1 (NM_172231) - MEF2B (NM_001145785) rearrangement: c.585:SUGP1_c.394-2:MEF2Bdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SUGP1:MEF2B}		8096	0	69	19	Intron of MEF2B(-):2bp before exon 5	SUGP1	19257994			19	Exon 5 of SUGP1(-)	MEF2B	19414610			10	DELETION		156616	304165	11729	83	NEW_VARIANT
P-0040965-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-4759:TMPRSS2_chr21:g.39968609del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		80207	0	59	21	3-UTR of ERG(-):65Kb after coding stop	TMPRSS2	39968609			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874875			10	DELETION		2906266	304180	61578	66	NEW_VARIANT
P-0037465-T02-IM6	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.2159-476:CREBBP_c.1280:SLX4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CREBBP:SLX4}		67116	0	84	16	Exon 6 of SLX4(-)	CREBBP	3647884			16	Intron of CREBBP(-):476bp before exon 12	SLX4	3825170			10	DELETION		177286	306079	56700	91	NEW_VARIANT
P-0037465-T02-IM6	NOTCH1 (NM_017617) rearrangement: c.1442-30:NOTCH1_chr9:g.139450872del	PRECISE	Note: The NOTCH1 rearrangement is a deletion of exons 1 - 8.	MANUAL_OK	3to5	3to5	-		19934	0	204	9	Intron of NOTCH1(-):30bp before exon 9	NOTCH1	139411867			9	IGR: 9Kb before LINC01573(+)	NOTCH1	139450872			10	DELETION		39005	306078	16389	229	NEW_VARIANT
P-0008440-T02-IM6	SMO (NM_005631) rearrangement: c.2252:SMO_chr7:g.134549261del	PRECISE	Note: The SMO rearrangement is a deletion of exon 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SMO:CALD1}		2482	0	64	7	Exon 12 of SMO(+)	SMO	128852180			7	5-UTR of CALD1(+):3Kb before coding start	SMO	134549261			10	DELETION		5697081	306280	3618	72	NEW_VARIANT
P-0041192-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+8632:CCDC6_c.2136+387:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		54756	0	33	10	Intron of RET(+):387bp after exon 11	CCDC6	43610571			10	Intron of CCDC6(-):9Kb after exon 1	RET	61657248			10	INVERSION		18046677	306179	31697	55	NEW_VARIANT
P-0041274-T01-IM6	FOXP1 (NM_001244814) rearrangement: c.1299_c.1722+7del	PRECISE	Note: The FOXP1 rearrangement is an intragenic deletion of exons 11 - 15. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2930	0	10	3	Intron of FOXP1(-):6bp after exon 15	FOXP1	71019880			3	Exon 11 of FOXP1(-)	FOXP1	71027028			10	DELETION		7148	306285	4485	10	NEW_VARIANT
P-0000828-T03-IM6	BRAF (NM_004333) - GTF2IRD1 (NM_005685) rearrangement: c.1178-597:BRAF_c.2320+14181:GTF2IRD1inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {BRAF:GTF2IRD1}		183915	0	46	7	Intron of GTF2IRD1(+):14Kb after exon 22	BRAF	73988166			7	Intron of BRAF(-):597bp before exon 10	GTF2IRD1	140483554			0	INVERSION		66495388	306442	327180	48	NEW_VARIANT
P-0041363-T01-IM6	BARD1 (NM_000465) rearrangement: t(2;13)(q35;q21.33)(chr2:g.215610383::chr13:g.69145496)	PRECISE	Note: The BARD1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	20	13	IGR: 290Kb before LINC00550(-)	BARD1	69145496			2	Intron of BARD1(-):62bp after exon 8	BARD1	215610383			10	TRANSLOCATION		0	306411	0	21	NEW_VARIANT
P-0005264-T03-IM6	EIF4A2 (NM_001967) rearrangement: c.409:EIF4A2_chr3:g.186523625inv	IMPPRECISE	Note: The EIF4A2 rearrangement is an inversion of exons 5 - 11. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EIF4A2:RFC4}		5074	0	24	3	Exon 5 of EIF4A2(+)	EIF4A2	186503732			3	5-UTR of RFC4(-):16Kb before coding start	EIF4A2	186523625			0	INVERSION		19893	306338	4094	26	NEW_VARIANT
P-0041289-T01-IM6	FLCN (NM_144997) - SLC38A10 (NM_001037984) rearrangement: c.618+49:FLCN_c.912+1222:SLC38A10dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FLCN:SLC38A10}		630774	0	4	17	Intron of FLCN(-):48bp after exon 6	FLCN	17127187			17	Intron of SLC38A10(-):1Kb after exon 8	SLC38A10	79248547			6	DUPLICATION		62121360	306319	646746	4	NEW_VARIANT
P-0041289-T01-IM6	PTCH1 (NM_000264) rearrangement: c.394+89_c.2212del	PRECISE	Note: The PTCH1 rearrangement is an intragenic deletion of exons 3 - 14. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14884	0	8	9	Exon 14 of PTCH1(-)	PTCH1	98231071			9	Intron of PTCH1(-):88bp after exon 2	PTCH1	98268600			10	DELETION		37529	306317	16013	8	NEW_VARIANT
P-0033315-T03-IM6	KCNMB3 (NM_171828) - PIK3CB (NM_006219) rearrangement: c.62+1284:KCNMB3_c.1421:PIK3CBdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {KCNMB3:PIK3CB}		170283	0	63	3	Exon 9 of PIK3CB(-)	KCNMB3	138426110			3	Intron of KCNMB3(-):1Kb after exon 1	PIK3CB	178983153			10	DELETION		40557043	307014	319371	63	NEW_VARIANT
P-0033315-T03-IM6	KDR (NM_002253) rearrangement: c.1536+23_c.2267-1471del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		6199	0	60	4	Intron of KDR(-):1Kb before exon 16	KDR	55966441			4	Intron of KDR(-):22bp after exon 11	KDR	55972831			10	DELETION		6390	307015	4926	61	NEW_VARIANT
P-0041429-T01-IM6	PTEN (NM_000314) rearrangement: c.209+2425_c.254-108del	PRECISE	Note: The PTEN rearrangement is an intragenic deletion of exon 4.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		891	0	6	10	Intron of PTEN(+):2Kb after exon 3	PTEN	89687739			10	Intron of PTEN(+):107bp before exon 5	PTEN	89692662			10	DELETION		4923	306756	383	6	NEW_VARIANT
P-0041438-T01-IM6	ALK (NM_004304) - TTC27 (NM_017735) rearrangement: c.3172+510:ALK_c.538-4165:TTC27inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {ALK:TTC27}		70778	0	54	2	Intron of ALK(-):509bp after exon 19	ALK	29447817			2	Intron of TTC27(+):4Kb before exon 5	TTC27	32871033			10	INVERSION		3423216	306755	91526	73	NEW_VARIANT
P-0041579-T01-IM6	KMT2D (NM_003482) rearrangement: t(8;12)(q22.2;q13.12)(chr8:g.100297214::chr12:g.49431612)	PRECISE	Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 34. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	6	12	Exon 34 of KMT2D(-)	KMT2D	49431612			8	Intron of VPS13B(+):10Kb after exon 19	KMT2D	100297214			5	TRANSLOCATION		0	307069	0	6	NEW_VARIANT
P-0040610-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2641:TMPRSS2_c.40-59446:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		99728	0	2	21	Intron of ERG(-):59Kb before exon 4	TMPRSS2	39876990			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42877236			6	DELETION		3000246	306795	110036	2	NEW_VARIANT
P-0041482-T01-IM6	INPPL1 (NM_001567) rearrangement: c.183-51:INPPL1_chr11:g.69426341inv	PRECISE	Note: The INPPL1 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		33985	0	32	11	IGR: 30Kb before CCND1(+)	INPPL1	69426341			11	Intron of INPPL1(+):50bp before exon 2	INPPL1	71939183			10	INVERSION		2512842	306804	67497	36	NEW_VARIANT
P-0041610-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+928:TMPRSS2_c.19-15841:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32117	0	135	21	Intron of ERG(-):16Kb before exon 2	TMPRSS2	39833385			21	Intron of TMPRSS2(-):927bp after exon 2	ERG	42869118			10	DELETION		3035733	307091	26401	141	NEW_VARIANT
P-0041658-T01-IM6	WT1 (NM_024426) rearrangement: c.769+60_c.873-2954del	IMPPRECISE	Note: The WT1 rearrangement is an intragenic deletion of exon 3.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2726	0	5	11	Intron of WT1(-):3Kb before exon 4	WT1	32442154			11	Intron of WT1(-):59bp after exon 2	WT1	32449983			0	DELETION		7829	307232	1784	5	NEW_VARIANT
P-0041658-T01-IM6	PPP2R1A (NM_014225) rearrangement: c.169+39:PPP2R1A_chr19:g.54078970inv	PRECISE	Note: The PPP2R1A rearrangement is an inversion of exons 3 - 15. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		25914	0	13	19	Intron of PPP2R1A(+):39bp after exon 2	PPP2R1A	52705326			19	Intron of ZNF331(+):980bp before exon 5	PPP2R1A	54078970			10	INVERSION		1373644	307234	25760	13	NEW_VARIANT
P-0041658-T01-IM6	NF2 (NM_000268) rearrangement: c.886-938_c.1122+20inv	PRECISE	Note: The NF2 rearrangement is an intragenic inversion of exons 10 - 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2329	0	12	22	Intron of NF2(+):937bp before exon 10	NF2	30063384			22	Intron of NF2(+):20bp after exon 11	NF2	30067957			10	INVERSION		4573	307235	2720	12	NEW_VARIANT
P-0025678-T02-IM6	TP53 (NM_000546) rearrangement: c.782+149_c.994-1193del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 9.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		4547	0	10	17	Intron of TP53(-):1Kb before exon 10	TP53	7575226			17	Intron of TP53(-):148bp after exon 7	TP53	7577350			8	DELETION		2124	307122	5386	10	NEW_VARIANT
P-0000068-T01-IM3		35333463-N_bc28		AUTO_OK	3to5	3to5	Transcript fusion (ERBB2-GRB7)		5082	0	6	17	Intron of ERBB2(+): 60bp after exon 26	ERBB2	37883860			17	5-UTR of GRB7(+): 1Kb before coding start	GRB7	37897388			20	DELETION		13528	94072	5915	9	NEW_VARIANT
P-0000377-T03-IM3	KDM5A (NM_001042603) duplication (64425bp): c.672+1652_4234+155dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 20 exons: out of frame		64299	0	5	12	Intron of KDM5A(-): 155bp after exon 25	KDM5A	406052			12	Intron of KDM5A(-): 2Kb after exon 5	KDM5A	470477			20	DUPLICATION		64425	2834	76892	6	NEW_VARIANT
P-0000377-T03-IM3	KDM5D (NM_001146705) inversion (1896bp): c.c.1810-954_2307-34inv	PRECISE	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.	AUTO_OK	3to3	3to3	-		1352	0	17	Y	Intron of KDM5D(-): 34bp before exon 16	KDM5D	21877659			Y	Intron of KDM5D(-): 954bp before exon 13	KDM5D	21879555			23	INVERSION		1896	2848	1962	17	NEW_VARIANT
P-0000425-T01-IM3	RET (NM_020630) - CCDC6 (NM_005436) Inversion (c.2136+266_c.303+19630inv)	PRECISE		AUTO_OK	3to3	3to3	Protein fusion: in frame (RET-CCDC6)		41631	0	10	10	Intron of RET(+): 266bp after exon 11	RET	43610450			10	Intron of CCDC6(-): 20Kb after exon 1	CCDC6	61646250			21	INVERSION		18035800	71419	44935	24	NEW_VARIANT
P-0000889-T01-IM3	RET (NM_020630) - CCDC6 (NM_005436) Reciprocal Inversion:  c.2137-38_c.2137-38inv	PRECISE	Note: RET-CCDC6 fusion has bee reported in papillary thyroid carcinoma  (PMID: 23145146)	AUTO_OK	3to3	3to3	Protein fusion: in frame (RET-CCDC6)		43459	0	70	10	Intron of RET(+): 38bp before exon 12	RET	43611994			10	Intron of CCDC6(-): 19Kb before exon 2	CCDC6	61631872			83	INVERSION		18019878	72075	51575	110	NEW_VARIANT
P-0001100-T01-IM3	ATR     (NM_001184) Duplication (9066bp): c.1659_c.2850dup	PRECISE	Note: ATR intragenic duplication is predicted to be inactivating.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		10145	0	21	3	Exon 14 of ATR(-)	ATR	142269100			3	Exon 7 of ATR(-)	ATR	142278166			34	DUPLICATION		9066	72431	12275	24	NEW_VARIANT
P-0001453-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)		34512	0	16	4	Intron of TACC3(+): 534bp after exon 8	TACC3	1738095			4	Exon 18 of FGFR3(+)	FGFR3	1808946			34	DUPLICATION		70851	2026	33096	14	NEW_VARIANT
P-0001453-T01-IM3		PRECISE		MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR3-TACC3)	60	34512	0	16	7	Intron of TACC3(+): 534bp after exon 8	TACC3	1738095			4	Exon 18 of FGFR3(+)	FGFR3	1808946			34	INSERTION		43444	1	33096	14	NEW_VARIANT
P-0001638-T01-IM3	None	PRECISE		MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-KIAA1217)		479022	0	68	10	Intron of KIAA1217(+): 9Kb before exon 7	None	24752801			10	Intron of FGFR2(-): 373bp after exon 16	None	123242839			76	INVERSION		98490038	1339	491100	103	NEW_VARIANT
P-0001710-T01-IM3	APC (NM_000038) - SRP19 (NM_001204199) deletion: c.5840_c.-3529del	PRECISE	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.	AUTO_OK	3to5	3to5	-		12305	0	5	5	Exon 16 of APC(+)	APC	112177131			5	IGR: 3Kb before SRP19(+)	SRP19	112193545			13	DELETION		16414	1215	5963	5	NEW_VARIANT
P-0002073-T01-IM3	FAT1 (NM_005245) Deletion : c.5963_c.9464-114del	PRECISE		MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		41002	0	7	4	Intron of FAT1(-): 114bp before exon 14	FAT1	187533043			4	Exon 10 of FAT1(-)	FAT1	187541777			22	DELETION		8734	2317	29212	7	NEW_VARIANT
P-0002145-T01-IM3	RET (NM_020975) - PDCD10 (NM_145860) translocation:  t(10,3)(q11.21;q26.1)(chr10:g.43609394::chr3:g.167419184)	PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: out of frame (RET-PDCD10)		0	0	28	10	Intron of RET(+): 271bp after exon 10	RET	43609394			3	Intron of PDCD10(-): 3Kb after exon 3	PDCD10	167419184			54	TRANSLOCATION		0	2475	0	27	NEW_VARIANT
P-0002145-T01-IM3	RET (NM_020975) - TFG (NM_001195478) translocation:  t(10,3)(q11.21;q12.2)(chr10:g.43609437::chr3:g.100450751)	PRECISE		AUTO_OK	5to3	5to3	Protein fusion: in frame (TFG-RET)		0	0	57	10	Intron of RET(+): 314bp after exon 10	RET	43609437			3	Intron of TFG(+): 601bp before exon 5	TFG	100450751			72	TRANSLOCATION		0	2476	0	27	NEW_VARIANT
P-0002584-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Deletion of 3 exons: in frame		10699	0	21	8	Intron of NBN(-): 124bp before exon 11	NBN	90966043			8	Intron of NBN(-): 3Kb after exon 7	NBN	90980052			30	DELETION		14009	4058	8918	19	NEW_VARIANT
P-0002610-T01-IM3		PRECISE	reciprocal event, keeping the FGFR3-JAKMIP1 as it has been reported in literature	MANUAL_OK	3to3	3to3	Protein fusion: in frame (FGFR3-JAKMIP1)		7271	0	35	4	Intron of FGFR3(+): 73bp after exon 17	FGFR3	1808734			4	Intron of JAKMIP1(-): 2Kb before exon 4	JAKMIP1	6089676			49	INVERSION		4280942	4147	7839	56	NEW_VARIANT
P-0002613-T01-IM3		PRECISE		MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		70880	0	5	2	Intron of ALK(-): 805bp before exon 20	ALK	29447199			2	Intron of EML4(+): 182bp before exon 13	EML4	42528199			11	INVERSION		13081000	4199	65945	5	NEW_VARIANT
P-0002671-T01-IM3		PRECISE	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)	MANUAL_OK	3to3	3to3	Protein fusion: in frame (ETV6-NTRK3)		0	0	13	15	Intron of NTRK3(-): 22Kb before exon 14	NTRK3	88505784			12	Intron of ETV6(+): 2Kb before exon 6	ETV6	12035813			20	TRANSLOCATION		0	4595	0	17	NEW_VARIANT
P-0002758-T01-IM3		PRECISE		MANUAL_OK	3to5	3to5	Transcript fusion (STK11-MIDN)		7150	0	10	19	Intron of STK11(+): 8bp after exon 3	STK11	1219420			19	5-UTR of MIDN(+): 1Kb before coding start	MIDN	1249122			28	DELETION		29702	5101	4686	11	NEW_VARIANT
P-0002998-T01-IM3		PRECISE	Note: EGFR deletion is a rearrangement event which results in deletion of part of exon 1 potentially disabling EGFR protein.	MANUAL_OK	3to5	3to5	-		1042	0	10	7	IGR: 19Kb before SEC61G(-)	SEC61G	54839350			7	Exon 1 of EGFR(+)	EGFR	55087025			21	DELETION		247675	7008	1025	11	NEW_VARIANT
P-0003008-T01-IM3		PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 5 exons: out of frame		5135	0	6	18	Intron of SMAD4(+): 27bp after exon 2	SMAD4	48573692			18	Intron of SMAD4(+): 97bp after exon 7	SMAD4	48584923			9	DUPLICATION		11231	7038	3848	6	NEW_VARIANT
P-0003078-T01-IM5		PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4557	0	33	17	Intron of RNF43(-): 1Kb before exon 10	RNF43	56433440			17	Exon 9 of RNF43(-)	RNF43	56435041			34	DELETION		1601	7826	2172	35	NEW_VARIANT
P-0003871-T01-IM5	CNTROB (NM_001037144) - STAT5B (NM_012448) rearrangement (32504650 bp): c.1994-486:CNTROB_c.2078-227:STAT5Binv	PRECISE	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	MANUAL_OK	3to3	3to3	Protein fusion: in frame (CNTROB-STAT5B)		516730	0	10	17	Intron of CNTROB(+): 486bp before exon 14	CNTROB	7850403			17	Intron of STAT5B(-): 227bp before exon 17	STAT5B	40355053			7	INVERSION		32504650	13876	521116	6	NEW_VARIANT
P-0003871-T01-IM5	NCOR1 (NM_006311) rearrangement: c.177:NCOR1_chr17g.77834316inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		912430	0	102	17	Exon 3 of NCOR1(-)	NCOR1	16089933			17	IGR: 27Kb before CBX4(-)	NCOR1	77834316			104	INVERSION		61744383	13875	1096290	153	NEW_VARIANT
P-0003871-T01-IM5	MLL3 (NM_170606) rearrangement: chr7g.19462033_c.11670+154:MLL3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		332153	0	15	7	IGR: 452Kb before KCND2(+)	MLL3	119462033			7	Intron of MLL3(-): 154bp after exon 44	MLL3	151855794			24	INVERSION		32393761	13877	565724	15	NEW_VARIANT
P-0003872-T01-IM5	BRAF (NM_004333) rearrangement: c.711+1013_c.1314+129 :BRAFdel	PRECISE	The BRAF (NM_004333) rearrangement is an intragenic deletion of exons 5-10. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 5 exons: in frame		136977	0	34	7	Intron of BRAF(-): 129bp after exon 10	BRAF	140482692			7	Intron of BRAF(-): 1Kb after exon 5	BRAF	140506747			49	DELETION		24055	13899	98351	39	NEW_VARIANT
P-0003970-T01-IM5	ROS1 (NM_002944) - EZR ( NM_003379 ) rearrangement:  c.1090+142C:EZR_c.5366+794T:ROS1del	PRECISE	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)	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (EZR-ROS1)		268568	0	24	6	Intron of ROS1(-): 794bp after exon 32	ROS1	117649698			6	Intron of EZR(-): 142bp after exon 9	EZR	159191654			35	DELETION		41541956	14527	250331	30	NEW_VARIANT
P-0004174-T01-IM5	RAD52 (NM_134424) rearrangement: c.543+3970_1049inv	PRECISE	Note: The RAD52 (NM_134424) rearrangement event results in the intragenic inversion of exons 8-11. One of the breakpoints is within RAD52 exon11.	MANUAL_OK	5to5	5to5	Antisense fusion		5376	0	5	12	Exon 11 of RAD52(-)	RAD52	1023206			12	Intron of RAD52(-): 4Kb after exon 7	RAD52	1030646			6	INVERSION		7440	16047	5461	5	NEW_VARIANT
P-0004286-T01-IM5	FGFR2 (NM_000141) rearrangement : c.1288-636_2302-755inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		36950	0	102	10	Intron of FGFR2(-): 755bp before exon 18	FGFR2	123240290			10	Intron of FGFR2(-): 636bp before exon 9	FGFR2	123264091			108	INVERSION		23801	18642	76012	242	NEW_VARIANT
P-0004518-T01-IM5	RAD51 (NM_002875) Rearrangement :  c.531-1626_628dup	PRECISE	Note: The RAD51 (NM_002875) Rearrangement results in the intragenic duplication of exon 7.The breakpoint is within exon7.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1271	0	24	15	Intron of RAD51(+): 2Kb before exon 7	RAD51	41019283			15	Exon 7 of RAD51(+)	RAD51	41021006			30	DUPLICATION		1723	22114	1130	24	NEW_VARIANT
P-0004617-T01-IM5	NFE2L2(NM_006164) Rearrangement : c.313-22_46-4138del	PRECISE	Note: The NFE2L2(NM_006164) Rearrangement  results in the intragenic deletion of exon 2 of NFE2L2.Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		3046	0	29	2	Intron of NFE2L2(-): 22bp before exon 3	NFE2L2	178098089			2	Intron of NFE2L2(-): 4Kb before exon 2	NFE2L2	178103137			33	DELETION		5048	23136	2040	29	NEW_VARIANT
P-0004700-T02-IM5	GPATCH8 (NM_001002909) - ERBB2 (NM_004448) Rearrangement :c.492+2954:GPATCH8_c.1565:ERBB2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (GPATCH8-ERBB2)		322698	0	23	17	Exon 13 of ERBB2(+)	GPATCH8	37872605			17	Intron of GPATCH8(-): 3Kb after exon 6	ERBB2	42498763			45	INVERSION		4626158	154004	264260	22	NEW_VARIANT
P-0005493-T01-IM5	PNPLA6 (NM_001166111) - POLD1 (NM_002691) rearrangement: c.1323:PNPLA6_c.2155-56:POLD1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (PNPLA6-POLD1)		1410229	0	102	19	Exon 11 of PNPLA6(+)	PNPLA6	7607490			19	Intron of POLD1(+): 56bp before exon 18	POLD1	50916627			65	DELETION		43309137	49359	1803306	110	NEW_VARIANT
P-0005493-T01-IM5	SMARCA4 (NM_003072) rearrangement (1871506 bp): c.2758:SMARCA4_c.335-249:GCDHinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		65129	0	102	19	Exon 18 of SMARCA4(+)	SMARCA4	11132542			19	Intron of GCDH(+): 249bp before exon 6	SMARCA4	13004048			127	INVERSION		1871506	49362	73406	182	NEW_VARIANT
P-0005493-T01-IM5	CIC (NM_015125) - POLD1 (NM_002691)  rearrangement (8120964 bp): c.2155-838:POLD1_c.1961:CICinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense fusion		242071	0	102	19	Exon 10 of CIC(+)	CIC	42794881			19	Intron of POLD1(+): 838bp before exon 18	POLD1	50915845			78	INVERSION		8120964	49363	323571	99	NEW_VARIANT
P-0005725-T01-IM5	MITF (NM_198159)  Rearrangement: c.666+21_762+497del	PRECISE	Note: The MITF (NM_198159)  rearrangement results in the intragenic deletion of exon5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		1909	0	46	3	Intron of MITF(+): 21bp after exon 4	MITF	69988353			3	Intron of MITF(+): 497bp after exon 5	MITF	69990979			50	DELETION		2626	54401	1383	46	NEW_VARIANT
P-0005748-T01-IM5	NCOA4 (NM_001145260) - RET (NM_020975) fusion : c.763-260:NCOA4_c.2137-707:RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (NCOA4-RET)		23751	0	4	10	Intron of RET(+): 707bp before exon 12	NCOA4	43611325			10	Intron of NCOA4(+): 260bp before exon 9	RET	51584356			48	DUPLICATION		7973031	57428	22857	2	NEW_VARIANT
P-0005970-T03-IM5	DICER1 (NM_030621) rearrangement: c.5364+1G_c.5365del	PRECISE	Note: The DICER1 rearrangement is a intragenic deletion of intron 25 and the first nucleotide of exon 26. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		745	0	78	14	Exon 26 of DICER1(-)	DICER1	95557702			14	Intron of DICER1(-): 1bp after exon 25	DICER1	95560224			77	DELETION		2522	153841	812	75	NEW_VARIANT
P-0006621-T01-IM5	GRIP1 (NM_021150) - TCF7L2 (NM_001146274) rearrangement : t(10;12)(q25.3;q14.3)(chr10:g.114900968::chr12:g.66756235)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (GRIP1-TCF7L2)		0	0	102	12	Intron of GRIP1(-): 9Kb before exon 22	GRIP1	66756235			10	Exon 5 of TCF7L2(+)	TCF7L2	114900968			361	TRANSLOCATION		0	107360	0	598	NEW_VARIANT
P-0006714-T01-IM5	BRAF (NM_004333) rearrangement: c.139-32224_c.1141-1764del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 7 exons: in frame		110576	0	5	7	Intron of BRAF(-): 2Kb before exon 9	BRAF	140489148			7	Intron of BRAF(-): 32Kb before exon 2	BRAF	140582236			6	DELETION		93088	108498	95438	5	NEW_VARIANT
P-0006953-T01-IM5	ETV6 (NM_001987) rearrangement: c.164-2418_c.464-7073dup	PRECISE	The ETV6 (NM_001987) rearrangement is an intragenic duplication of exons 3-4. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons: in frame		103356	0	102	12	Intron of ETV6(+): 2Kb before exon 3	ETV6	11989656			12	Intron of ETV6(+): 7Kb before exon 5	ETV6	12015285			74	DUPLICATION		25629	112107	177498	140	NEW_VARIANT
P-0007755-T02-IM5	TRPM8 (NM_024080) - NTRK1 (NM_002529) rearrangement: t(1;2)(q23.1; q27.1)(chr1:g.156845664::chr2:g.234866124)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TRPM8-NTRK1)		0	0	10	2	Intron of TRPM8(+): 2Kb after exon 11	TRPM8	234866124			1	Intron of NTRK1(+): 206bp after exon 12	NTRK1	156845664			5	TRANSLOCATION		0	163028	0	9	NEW_VARIANT
P-0008080-T01-IM5	IP6K1 (NM_153273) - SETD2 (NM_014159) rearrangement: c.-129+8864:IP6K1_c:6110-1:SETD2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (IP6K1-SETD2)		77495	0	46	3	Intron of SETD2(-): 1bp before exon 14	IP6K1	47103837			3	5-UTR of IP6K1(-): 29Kb before coding start	SETD2	49814923			56	DELETION		2711086	120307	64236	42	NEW_VARIANT
P-0008103-T01-IM5	GATA3 (NM_002051) rearrangement : c.1047+34:GATA3_chr10:g.9186062del	PRECISE	Note: The GATA3 (NM_002051) rearrangement event results in the deletion of GATA3 exon6.	MANUAL_OK	3to5	3to5	-		6202	0	77	10	Intron of GATA3(+): 34bp after exon 5	GATA3	8111595			10	IGR: 1Mb before GATA3(+)	GATA3	9186062			59	DELETION		1074467	120378	3882	75	NEW_VARIANT
P-0008246-T02-IM5	NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement : c.1178-14:NTRK1_c.-192+7124:DDR2inv	PRECISE	Note: The NTRK1 (NM_002529) - DDR2 (NM_006182) rearrangement event is an inversion involving NTRK1 exons 1-9.	MANUAL_OK	3to3	3to3	Antisense fusion		65487	0	42	1	Intron of NTRK1(+): 14bp before exon 9	NTRK1	156844161			1	5-UTR of DDR2(+): 79Kb before coding start	DDR2	162609545			51	INVERSION		5765384	122169	74117	42	NEW_VARIANT
P-0008290-T01-IM5	BTK (NM_000061) rearrangement: c.392-764_c.1682dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		17877	0	32	X	Exon 17 of BTK(-)	BTK	100608926			X	Intron of BTK(-): 764bp before exon 6	BTK	100618441			32	DUPLICATION		9515	121115	21772	29	NEW_VARIANT
P-0008715-T01-IM5	ARID1A (NM_006015) rearrangement: c.3198+1406_c.5892del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		24009	0	80	1	Intron of ARID1A(+): 1Kb after exon 11	ARID1A	27095896			1	Exon 20 of ARID1A(+)	ARID1A	27106281			56	DELETION		10385	123559	13705	75	NEW_VARIANT
P-0008715-T01-IM5	STK11 (NM_000455) rearrangement: c.636_c.921-244del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		4152	0	31	19	Exon 5 of STK11(+)	STK11	1220618			19	Intron of STK11(+): 244bp before exon 8	STK11	1222740			51	DELETION		2122	123558	1852	29	NEW_VARIANT
P-0008928-T01-IM5	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	IMPRECISE		MANUAL_OK	3to5	3to5	Protein fusion: in frame (TMPRSS2-ERG)		54738	0	59	21	Intron of ERG(-): 61Kb after exon 3	TMPRSS2	39886642			21	Intron of TMPRSS2(-): 1Kb before exon 3	ERG	42867842			0	DELETION		2981200	125045	47687	56	NEW_VARIANT
P-0008942-T01-IM5	PTCH1 (NM_000264) - STRN (NM_003162) Rearrangement : t(2;9)(2p25.1;9q22.32)(chr2:g.7116407::chr9:g.98215861)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (PTCH1-STRN)		0	0	17	9	Exon 20 of PTCH1(-)	PTCH1	98215861			2	Intron of STRN(-): 2Kb before exon 8	STRN	37116407			0	TRANSLOCATION		0	125110	0	16	NEW_VARIANT
P-0009563-T01-IM5	C19orf47 (NM_001256441) - AKT2 (NM_001626) Rearrangement : c.19+973:NM_001256441_c.832-15AKT2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Transcript fusion (C19orf47-AKT2)		17618	0	56	19	Intron of AKT2(-): 15bp before exon 10	C19orf47	40742307			19	5-UTR of C19orf47(-): 5Kb before coding start	AKT2	40846773			57	DELETION		104466	131248	12855	52	NEW_VARIANT
P-0009647-T01-IM5	TUBGCP3 (NM_006322) - BRCA2 (NM_000059) rearrangement: c.1745+7:TUBGCP3_c.794-177:BRCA2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: out of frame (TUBGCP3-BRCA2)		437275	0	7	13	Intron of BRCA2(+): 177bp before exon 10	TUBGCP3	32906232			13	Intron of TUBGCP3(-): 7bp after exon 14	BRCA2	113176627			9	INVERSION		80270395	131610	496125	5	NEW_VARIANT
P-0009647-T01-IM5	TP63 (NM_003722) - LEPREL1 (NM_018192) rearrangement: c.324+76:TP63_c.480+38077:LEPREL1inv	IMPRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (TP63-LEPREL1)		29302	0	13	3	Intron of TP63(+): 76bp after exon 3	TP63	189456639			3	Intron of LEPREL1(-): 38Kb after exon 1	LEPREL1	189799964			0	INVERSION		343325	131612	36802	10	NEW_VARIANT
P-0009876-T01-IM5	TGFBR2 (NM_001024847) rearrangement : c.1611:TGFBR2_chr3:g.24649275del	PRECISE	Note: The TGFBR2 (NM_001024847) rearrangement event results in the deletion of TGFBR2 exons 1-8. One of the breakpoints is within TGFBR2 exon8.	MANUAL_OK	3to5	3to5	-		20690	0	27	3	IGR: 491Kb before THRB(-)	TGFBR2	24649275			3	Exon 7 of TGFBR2(+)	TGFBR2	30732923			46	DELETION		6083648	136947	19774	27	NEW_VARIANT
P-0009940-T01-IM5	MTOR (NM_004958) rearrangement: c.1588_c.7016+305del	PRECISE	Note: The MTOR rearrangement is an intragenic deletion of exons 11-50. One of the breakpoints is within exon11. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		105379	0	13	1	Intron of MTOR(-): 305bp after exon 50	MTOR	11176756			1	Exon 11 of MTOR(-)	MTOR	11300558			20	DELETION		123802	137189	87653	13	NEW_VARIANT
P-0012241-T01-IM5	PAX5 (NM_016734) Rearrangement: c.365_c.605-3847inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		4919	0	43	9	Intron of PAX5(-): 4Kb before exon 6	PAX5	36970568			9	Exon 3 of PAX5(-)	PAX5	37015039			48	INVERSION		44471	156805	6022	43	NEW_VARIANT
P-0012400-T01-IM5	SMARCA4 (NM_003072) rearrangement: c.3951+88_c.4170+2065del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exon 29.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: in frame		3035	0	21	19	Intron of SMARCA4(+): 88bp after exon 26	SMARCA4	11144964			19	Intron of SMARCA4(+): 2Kb after exon 27	SMARCA4	11147873			25	DELETION		2909	157367	2330	20	NEW_VARIANT
P-0012400-T01-IM5	LATS1 (NM_004690) - GLIS3 (NM_001042413) rearrangement: t(6;9)(q25.1;p24.2)(chr6:g.150001247::chr9:g.3858763)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (LATS1-GLIS3)		0	0	11	9	Intron of GLIS3(-): 3Kb before exon 9	LATS1	3858763			6	Exon 5 of LATS1(-)	GLIS3	150001247			4	TRANSLOCATION		0	157371	0	10	NEW_VARIANT
P-0012696-T01-IM5	ARID5B (NM_032199) rearrangement: c.-1841_c.-182del	PRECISE	Note: The ARID5B rearrangement is a deletion of the promoter and 5UTR. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		85	0	15	10	Promoter of ARID5B(+): 1Kb from tx start	ARID5B	63659628			10	5-UTR of ARID5B(+): 182bp before coding start	ARID5B	63661287			15	DELETION		1659	158602	150	14	NEW_VARIANT
P-0012696-T01-IM5	TCF3 (NM_001136139) rearrangement: c.550-172_c.1586+396dup	PRECISE	Note: The TCF3 rearrangement is a duplication of exons 8-18. One of the breakpoints is within exon 18. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		26088	0	39	19	Exon 18 of TCF3(-)	TCF3	1615289			19	Intron of TCF3(-): 172bp before exon 8	TCF3	1622586			56	DUPLICATION		7297	158605	26033	38	NEW_VARIANT
P-0012696-T01-IM5	PTPRS (NM_002850) rearrangement: t(8;19)(q12.1;p13.3)(chr8:g.61237662::chr19:g.5210677)	IMPRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	33	19	Intron of PTPRS(-): 13bp after exon 25	PTPRS	5210677			8	IGR: 44Kb after CA8(-)	PTPRS	61237662			0	TRANSLOCATION		0	158607	0	30	NEW_VARIANT
P-0012884-T01-IM5	PWWP2A (NM_001130864) - BRAF(NM_004333) Rearrangement : t(5;7)(q33.3;q34)(chr5:g.159539324::chr7:g.140495243)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (PWWP2A-BRAF)		0	0	47	7	Intron of BRAF(-): 976bp before exon 8	PWWP2A	140495243			5	Intron of PWWP2A(-): 6Kb after exon 1	BRAF	159539324			36	TRANSLOCATION		0	159230	0	35	NEW_VARIANT
P-0012947-T01-IM5	CDKN2Ap14ARF (NM_058195) rearrangement: c.*102-382_c.*3284del	PRECISE	Note: The CDKN2Ap14ARF rearrangement results in the deletion of 3UTR. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1784	0	14	9	Promoter of C9orf53(+): 2Kb from tx start	CDKN2Ap14ARF	21965059			9	Intron of CDKN2Ap14ARF(-): 382bp before exon 3	CDKN2Ap14ARF	21968623			4	INVERSION		3564	159935	1103	11	NEW_VARIANT
P-0012947-T01-IM5	CDKN2Ap16INK4A (NM_000077) rearrangement: c.458-382_c.*3169del	PRECISE	Note: The CDKN2Ap16INK4A rearrangement results in the deletion of exon 3 and 3UTR.	MANUAL_OK	3to5	3to5	-		1784	0	14	9	Promoter of C9orf53(+): 2Kb from tx start	CDKN2Ap16INK4A	21971024			9	Intron of CDKN2Ap16INK4A(-): 382bp before exon 3	CDKN2Ap16INK4A	22056567			4	INVERSION		3564	159936	1103	11	NEW_VARIANT
P-0013025-T01-IM5	TBX3 (NM_016569) rearrangement: chr12:g.124583968_c.211:TBX3inv	PRECISE	Note: The TBX3 rearrangement is an inversion of 5UTR and exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	5to5	5to5	-		56458	0	24	12	Exon 1 of TBX3(-)	TBX3	115120795			12	IGR: 126Kb before ZNF664(+)	TBX3	124583968			41	INVERSION		9463173	159966	45493	24	NEW_VARIANT
P-0013782-T01-IM5	SMARCD1 (NM_003076) rearrangement:c.1130_c.1134-4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		1115	0	7	12	Exon 9 of SMARCD1(+)	SMARCD1	50484370			12	Intron of SMARCD1(+): 4bp before exon 10	SMARCD1	50488216			15	DELETION		3846	162315	1091	6	NEW_VARIANT
P-0013808-T02-IM6	PBRM1 (NM_018313) - SMG1 (NM_015092) rearrangement: t(3;16)(p21.1;p12.3)(chr3:g.52695981::chr16:g.18853678)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PBRM1:SMG1}		0	0	41	16	Exon 40 of SMG1(-)	PBRM1	18853678			3	Intron of PBRM1(-):167bp after exon 5	SMG1	52695981			10	TRANSLOCATION		0	226538	0	41	NEW_VARIANT
P-0013808-T02-IM6	EP300 (NM_001429) rearrangement: chr22:g.41448977_c.6920dup	PRECISE	Note: The EP300 rearrangement is a duplication that includes EP300 exons 1-13. One of the breakpoints is within exon 31.	MANUAL_OK	5to3	5to3	-		71616	0	9	22	IGR: 40Kb before MIR1281(+)	EP300	41448977			22	Exon 31 of EP300(+)	EP300	41574635			10	DUPLICATION		125658	226537	118699	9	NEW_VARIANT
P-0014137-T01-IM5	NF2 (NM_000268) Rearrangement : c.363+6:NF2_chr22:45151093inv	PRECISE	Note: The NF2 Rearrangement results in the inversion of exons 4-16 of NF2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		108541	0	38	22	Intron of NF2(+): 6bp after exon 3	NF2	30035207			22	Intron of PRR5-ARHGAP8(+): 29Kb after exon 4	NF2	45151093			67	INVERSION		15115886	163314	162411	37	NEW_VARIANT
P-0015415-T01-IM6	MLL (NM_001197104) Rearrangement: c.433-2334_c.1347del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		5912	0	37	11	Intron of MLL(+): 2Kb before exon 2	MLL	118337156			11	Exon 3 of MLL(+)	MLL	118343221			36	DELETION		6065	167960	2349	36	NEW_VARIANT
P-0015724-T01-IM6	LOH12CR1 (NM_058169) - ETV6 (NM_001987) rearrangement: c.202+1037:LOH12CR1_c.1010-2951:ETV6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (LOH12CR1-ETV6)		29700	0	3	12	Intron of ETV6(+): 3Kb before exon 6	LOH12CR1	12034428			12	Intron of LOH12CR1(+): 1Kb after exon 2	ETV6	12515320			7	DUPLICATION		480892	168951	57513	3	NEW_VARIANT
P-0015920-T01-IM6	ARID1A (NM_006015) rearrangement: c.2733-1053_c.2958del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1635	0	19	1	Intron of ARID1A(+):1Kb before exon 9	ARID1A	27091659			1	Exon 10 of ARID1A(+)	ARID1A	27093027			10	DELETION		1368	169619	1308	22	NEW_VARIANT
P-0015920-T01-IM6	RAD54L (NM_001142548) rearrangement: c.1342_c.1869+927del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4632	0	13	1	Exon 13 of RAD54L(+)	RAD54L	46738441			1	Intron of RAD54L(+):927bp after exon 17	RAD54L	46741316			10	DELETION		2875	169620	6788	15	NEW_VARIANT
P-0015920-T01-IM6	NCOR1 (NM_006311) rearrangement: c.2120_c.2055+4196del	PRECISE	Note: The NCOR1 rearrangement results in the deletion of exon 19. One of the breakpoints is within exon 19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		517	0	17	17	Exon 19 of NCOR1(-)	NCOR1	16012162			17	Intron of NCOR1(-):4Kb after exon 18	NCOR1	16017006			10	DELETION		4844	169624	380	22	NEW_VARIANT
P-0015984-T01-IM6	TACC3 (NM_006342) - FGFR3 (NM_000142) Rearrangement : c.1645-67:TACC3_c.*18:FGFR3dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	-		29923	0	5	4	Intron of TACC3(+):66bp before exon 8	TACC3	1737391			4	3-UTR of FGFR3(+):13Kb after coding stop	FGFR3	1809007			0	DUPLICATION		71616	169838	46056	5	NEW_VARIANT
P-0016347-T01-IM6	TRIM63 (NM_032588) - NTRK1 (NM_002529) Rearrangement : c.1051+386:TRIM63_c.1178-127:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TRIM63:NTRK1}		620034	0	24	1	Intron of TRIM63(-):385bp after exon 8	TRIM63	26379998			1	Intron of NTRK1(+):126bp before exon 9	NTRK1	156844048			10	INVERSION		130464050	171919	527960	39	NEW_VARIANT
P-0016351-T01-IM6	TP63 (NM_003722) Rearrangement : c.580-11:TP63_c.823+1433:LEPREL1dup	PRECISE	Note: The TP63 Rearrangement results in the duplication of exons 5-14 of TP63. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		17352	0	7	3	Intron of TP63(+):10bp before exon 5	TP63	189582010			3	Intron of LEPREL1(-):1Kb after exon 3	TP63	189710450			10	DUPLICATION		128440	171933	25653	7	NEW_VARIANT
P-0016546-T01-IM6	SPEN (NM_015001) - TMEM51 (NM_018022) rearrangement: c.2173:SPEN_c.-193-17536:TMEM51dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:TMEM51}		18495	0	10	1	5-UTR of TMEM51(+):18Kb before coding start	SPEN	15523855			1	Exon 11 of SPEN(+)	TMEM51	16254908			10	DUPLICATION		731053	172530	39161	10	NEW_VARIANT
P-0017217-T01-IM6	AKT1 (NM_001014431) rearrangement: c.1260_c.1261del	PRECISE	Note: The AKT1 rearrangement is an intragenic deletion with breakpoints on both the exons 12 and 13.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		575	0	8	14	Exon 13 of AKT1(-)	AKT1	105237184			14	Exon 12 of AKT1(-)	AKT1	105238702			10	DELETION		1518	174791	867	8	NEW_VARIANT
P-0017217-T01-IM6	NCOR1 (NM_006311) rearrangement: c.3178-1644_c.3401-128del	PRECISE	Note: The NCOR1 rearrangement is an intragenic deletion of NCOR1 exons 24-25.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		1740	0	6	17	Intron of NCOR1(-):128bp before exon 26	NCOR1	15983506			17	Intron of NCOR1(-):2Kb before exon 24	NCOR1	15985685			10	DELETION		2179	174792	772	6	NEW_VARIANT
P-0019915-T01-IM6	CDKN1A (NM_078467) rearrangement: t(3;6)(q28;p21.2)(chr3:g.191928578::chr6:g.36651921)	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	10	6	Exon 3 of CDKN1A(+)	CDKN1A	36651921			3	Intron of FGF12(-):40Kb before exon 5	CDKN1A	191928578			10	TRANSLOCATION		0	183217	0	10	NEW_VARIANT
P-0020065-T01-IM6	KMT2D (NM_003482) rearrangement : c.8166_c.7194inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		11808	0	2	12	Exon 32 of KMT2D(-)	KMT2D	49433281			12	Exon 31 of KMT2D(-)	KMT2D	49434359			8	INVERSION		1078	184008	15559	2	NEW_VARIANT
P-0020065-T01-IM6	SRC (NM_198291) rearrangement : c.704-116:SRC_g.36481250inv	PRECISE	Note: The SRC rearrangement results in the inversion of exons 9-14. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		15379	0	12	20	Intron of SRC(+):115bp before exon 9	SRC	36025986			20	Intron of CTNNBL1(+):7Kb before exon 14	SRC	36481250			10	INVERSION		455264	184012	22021	12	NEW_VARIANT
P-0020156-T01-IM6	EWSR1 (NM_013986) - EMID1 (NM_133455) rearrangement: c.945+800:EWSR1_c.466-2061:EMID1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {EWSR1:EMID1}		65109	0	29	22	Intron of EMID1(+):2Kb before exon 6	EWSR1	29624948			22	Intron of EWSR1(+):800bp after exon 12	EMID1	29689395			10	DUPLICATION		64447	183783	85245	30	NEW_VARIANT
P-0020694-T01-IM6	B2M (NM_004048) rearrangement: chr15:g.44989687_c.143:B2Mdel	PRECISE	Note: The B2M rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3628	0	35	15	IGR: 14Kb before B2M(+)	B2M	44989687			15	Exon 2 of B2M(+)	B2M	45007696			10	DELETION		18009	185076	1730	36	NEW_VARIANT
P-0020720-T01-IM6	TP53 (NM_000546) rearrangement: c.376-159_c.-28-566del	IMPPRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 1-4.	MANUAL_OK	3to5	3to5	Deletion within transcript		5605	0	84	17	Intron of TP53(-):159bp before exon 5	TP53	7578713			17	5-UTR of TP53(-):8Kb before coding start	TP53	7580506			0	DELETION		1793	185112	1511	87	NEW_VARIANT
P-0021390-T02-IM6	ARID1A (NM_006015) rearrangement: c.1921-1093_c.1949del	IMPPRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exon 5. One of the breakpoints is within exon 5. Its significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		433	0	138	1	Intron of ARID1A(+):1Kb before exon 5	ARID1A	27086311			1	Exon 5 of ARID1A(+)	ARID1A	27087375			0	DELETION		1064	224561	181	220	NEW_VARIANT
P-0021390-T02-IM6	CDKN2Ap16INK4A (NM_000077) rearrangement: c.14_c.-969del	IMPPRECISE	Note: The CDKN2Ap16INK4A rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		33	0	69	9	Exon 1 of CDKN2A(-)	CDKN2Ap16INK4A	21974813			9	Intron of CDKN2A(-):5Kb before exon 2	CDKN2Ap16INK4A	21975795			0	DELETION		982	224562	59	83	NEW_VARIANT
P-0021605-T01-IM6	SHOC2 (NM_007373) Rearrangement : chr10:g.91947785_c.1487:SHOC2del	PRECISE	Note: The SHOC2 Rearrangement results in the deletion of exons 1-8 of SHOC2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		62361	0	8	10	IGR: 214Kb before LOC101926942(-)	SHOC2	91947785			10	Exon 8 of SHOC2(+)	SHOC2	112769535			10	DELETION		20821750	187820	60604	17	NEW_VARIANT
P-0022795-T01-IM6	EWSR1 (NM_013986) Rearrangement : c.260+2008:KREMEN1_c.993-1354:EWSR1inv	PRECISE	Note: The EWSR1 Rearrangement results in the inversion of exons 1-10 of EWSR1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		33267	0	10	22	Intron of KREMEN1(+):2Kb after exon 2	EWSR1	29492416			22	Intron of EWSR1(+):1Kb before exon 10	EWSR1	29686200			10	INVERSION		193784	192295	28971	10	NEW_VARIANT
P-0023249-T02-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2320_c.839-334inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		37793	0	75	21	Intron of TMPRSS2(-):334bp before exon 9	TMPRSS2	42845757			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872436			10	INVERSION		26679	227021	51373	104	NEW_VARIANT
P-0025018-T01-IM6	LANCL2 (NM_018697) - EGFR (NM_005228) rearrangement: c.1259-255:LANCL2_c.2947-344:EGFRdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {LANCL2:EGFR}		17929	0	38	7	Intron of EGFR(+):343bp before exon 25	LANCL2	55268537			7	Intron of LANCL2(+):254bp before exon 9	EGFR	55498664			10	DUPLICATION		230127	203226	49490	38	NEW_VARIANT
P-0025871-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.738:WHSC1L1 _chr8:g.36973437inv	PRECISE	Note: The WHSC1L1 rearrangement is an inversion of exons 3 - 24. One of the breakpoints is within exon 3. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		30026	0	32	8	IGR: 291Kb before LOC100507420(-)	WHSC1L1	36973437			8	Exon 3 of WHSC1L1(-)	WHSC1L1	38196063			10	INVERSION		1222626	207672	38400	37	NEW_VARIANT
P-0025973-T01-IM6	SETD2 (NM_014159) Rearrangement : c.5015+844_c.5142+160dup	PRECISE	Note: The SETD2 (NM_014159) Rearrangement results in the intragenic duplication of exon 9. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1227	0	9	3	Intron of SETD2(-):159bp after exon 9	SETD2	47139285			3	Intron of SETD2(-):843bp after exon 8	SETD2	47142104			10	DUPLICATION		2819	208113	2320	9	NEW_VARIANT
P-0026488-T01-IM6	PRKAR1A (NM_212471) - MYO1D (NM_015194) rearrangement: c.708+36:PRKAR1A_c.1468-2012:MYO1Dinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {PRKAR1A:MYO1D}		456144	0	8	17	Intron of MYO1D(-):2Kb before exon 12	PRKAR1A	31078036			17	Intron of PRKAR1A(+):36bp after exon 7	MYO1D	66522089			10	INVERSION		35444053	210765	1341546	8	NEW_VARIANT
P-0026506-T01-IM6	WT1 (NM_024426) Rearrangement :  t(8;13)(q21.11,p13)(chr8:g.74791141::chr11:g.32414224)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	9	11	Exon 8 of WT1(-)	WT1	32414224			8	Exon 1 of UBE2W(-)	WT1	74791141			10	TRANSLOCATION		0	228372	0	9	NEW_VARIANT
P-0026683-T01-IM6	BRD4 (NM_058243) rearrangement: c.2659:BRD4_chr19:g.15431410del	PRECISE	Note: The BRD4 rearrangement is a deletion of exons 1-14. One of the breakpoints is within exon 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		19183	0	28	19	Exon 14 of BRD4(-)	BRD4	15354221			19	IGR: 33Kb before AKAP8(-)	BRD4	15431410			10	DELETION		77189	211140	25480	31	NEW_VARIANT
P-0027084-T01-IM6	SLX4 (NM_032444) rearrangement: c.4840:SLX4_chr16:g.34647886inv	PRECISE	Note: the SLX4 rearrangement is an inversion of exons 1-14. One of the breakpoints is within exon 14. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		192038	0	47	16	Exon 14 of SLX4(-)	SLX4	3633411			16	IGR: 50Kb before LINC01566(+)	SLX4	34647886			10	INVERSION		31014475	212761	228394	45	NEW_VARIANT
P-0028804-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.1579:NOTCH1_chr9:g.139536999inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		19130	0	131	9	Exon 10 of NOTCH1(-)	NOTCH1	139410523			9	IGR: 16Kb before EGFL7(+)	NOTCH1	139536999			10	INVERSION		126476	218699	16508	127	NEW_VARIANT
P-0029539-T01-IM6	CCNE1 (NM_001238) - ACTN4 (NM_004924) rearrangement: c.463-68:CCNE1_c.2410:ACTN4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CCNE1:ACTN4}		87200	0	4	19	Intron of CCNE1(+):67bp before exon 7	CCNE1	30311541			19	Exon 19 of ACTN4(+)	ACTN4	39218658			9	DELETION		8907117	222138	150112	4	NEW_VARIANT
P-0029539-T01-IM6	RRAS (NM_006270) rearrangement: t(5;19)(p15.2;q13.33)(chr5:g.12569365::chr19:g.50139900)	PRECISE	Note: The RRAS rearrangement is a translocation involving a breakpoint in exon 4. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	28	19	Exon 4 of RRAS(-)	RRAS	50139900			5	IGR: 6Kb before LINC01194(+)	RRAS	12569365			10	TRANSLOCATION		0	222142	0	28	NEW_VARIANT
P-0030023-T01-IM6	KDM5C (NM_004187) Rearrangement: c.1123-944_c.1035del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1223	0	14	X	Intron of KDM5C(-):944bp before exon 9	KDM5C	53242032			X	Exon 8 of KDM5C(-)	KDM5C	53243958			10	DELETION		1926	223524	305	17	NEW_VARIANT
P-0030156-T01-IM6	PREX2 (NM_024870) Rearrangement : c.2715+497_c.3655del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10584	0	35	8	Intron of PREX2(+):497bp after exon 23	PREX2	69012575			8	Exon 30 of PREX2(+)	PREX2	69033215			10	DELETION		20640	224558	16461	36	NEW_VARIANT
P-0030309-T01-IM6	EGFR (NM_005228) rearrangement: chr7:g.52700313_c.3162+189:EGFR_inv	PRECISE	Note: The EGFR rearrangement results in the inversion of exons 1-26. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		67140	0	5	7	IGR: 403Kb before POM121L12(+)	EGFR	52700313			7	Intron of EGFR(+):189bp after exon 26	EGFR	55269664			10	INVERSION		2569351	226629	92319	5	NEW_VARIANT
P-0030384-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1256:TMPRSS2_c.39+13477:ERGdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		54589	0	29	21	Intron of ERG(-):13Kb after exon 3	TMPRSS2	39934109			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871372			0	DELETION		2937263	227276	18612	30	NEW_VARIANT
P-0030645-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion (TMPRSS2 exon 1 fused to ERG exons 4-11): c.56-658:TMPRSS2_c.39+17522:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		38722	0	27	21	Intron of ERG(-):18Kb after exon 3	TMPRSS2	39930064			21	Intron of TMPRSS2(-):658bp before exon 2	ERG	42870774			10	DELETION		2940710	227005	38541	29	NEW_VARIANT
P-0030694-T01-IM6	SUZ12 (NM_015355) rearrangement: t(16;17)(q21;q11.2)(chr16:g.58252801::chr17:g.30320331)	PRECISE	Note: The SUZ12 rearrangement is a translocation involving a breakpoint in exon 11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	25	17	Exon 11 of SUZ12(+)	SUZ12	30320331			16	IGR: 31Kb before CCDC113(+)	SUZ12	58252801			10	TRANSLOCATION		0	227155	0	28	NEW_VARIANT
P-0030738-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.200_c.2975del	PRECISE	Note: The ZFHX3 rearrangement is an intragenic deletion with breakpoints on exons 2 and 3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		18658	0	33	16	Exon 3 of ZFHX3(-)	ZFHX3	72984609			16	Exon 2 of ZFHX3(-)	ZFHX3	72993845			10	DELETION		9236	227318	23919	34	NEW_VARIANT
P-0030844-T01-IM6	PIK3CD (NM_005026) - MTOR (NM_004958) Rearrangement: c.2426+2:PIK3CD_c.4254-479:MTORdel	PRECISE	Note: The PIK3CD - MTRO rearrangement is an deletion of PIK3CD exons 20-24 to MTOR exons 29-58	MANUAL_OK	3to5	3to5	Antisense Fusion		43599	0	14	1	Intron of PIK3CD(+):2bp after exon 19	PIK3CD	9782666			1	Intron of MTOR(-):479bp before exon 29	MTOR	11228053			10	DELETION		1445387	227728	41367	16	NEW_VARIANT
P-0030844-T01-IM6	FGFR2 (NM_000141) - MYH15 (NM_014981) rearrangement: t(3;10)(q13.13;q26.13)(chr3:g.108134575::chr10:g.123240665)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR2:MYH15}		0	0	105	10	Intron of FGFR2(-):1Kb before exon 18	FGFR2	123240665			3	Intron of MYH15(-):1Kb after exon 30	MYH15	108134575			10	TRANSLOCATION		0	227729	0	127	NEW_VARIANT
P-0030943-T01-IM6	BRCA1 (NM_007294) rearrangement: c.-1772_c.726del	PRECISE	Note: The BRCA1 rearrangement is a deletion of exons 1-10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12279	0	50	17	Exon 10 of BRCA1(-)	BRCA1	41246822			17	Promoter of BRCA1(-):83Kb from tx start	BRCA1	41279040			10	DELETION		32218	228047	14253	51	NEW_VARIANT
P-0030943-T01-IM6	ROS1 (NM_002944) rearrangement: c.5080-1093:ROS1_chr6:g.121016948del	PRECISE	Note: The ROS1 rearrangement is a deletion of exons 1-30. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		77863	0	48	6	Intron of ROS1(-):1Kb before exon 31	ROS1	117659596			6	IGR: 384Kb before TBC1D32(-)	ROS1	121016948			10	DELETION		3357352	228046	80048	52	NEW_VARIANT
P-0031008-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3443:TMPRSS2_c.18+19812:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		83149	0	15	21	Intron of ERG(-):20Kb after exon 1	TMPRSS2	39850475			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873559			10	DELETION		3023084	229160	47985	16	NEW_VARIANT
P-0031031-T01-IM6	RTEL1 (NM_032957) Rearrangement: c.3182-48:RTEL1_chr20:g.57400991del	PRECISE	Note: The RTEL1 rearrangement is a deletion of RTEL1 exons 2 to 31. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		67209	0	15	20	3-UTR of GNAS-AS1(-):25Kb after coding stop	RTEL1	57400991			20	Intron of RTEL1(+):47bp before exon 32	RTEL1	62326046			10	DELETION		4925055	228383	103127	15	NEW_VARIANT
P-0031152-T01-IM6	NUF2 (NM_031423) Rearrangement: c.1261-1557_c.*112inv	PRECISE	Note: The NUF2 rearrangement is an intragenic inversion of exon 14. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		920	0	24	1	Intron of NUF2(+):2Kb before exon 14	NUF2	163323568			1	3-UTR of NUF2(+):30Kb after coding stop	NUF2	163325371			10	INVERSION		1803	228658	1649	24	NEW_VARIANT
P-0031232-T01-IM6	CDKN2B (NM_004936) rearrangement: c.156+303:CDKN1B_chr9:g.21962196del	PRECISE	Note: The CDKN2B rearrangement is a deletion of exon 2.	MANUAL_OK	3to5	3to5	-		17134	0	3	9	IGR: 5Kb before CDKN2A-AS1(+)	CDKN2B	21962196			9	Intron of CDKN2B(-):302bp after exon 1	CDKN2B	22008494			5	DELETION		46298	228760	15808	4	NEW_VARIANT
P-0031234-T01-IM6	PAX8 (NM_003466) - USP37 (NM_020935) rearrangement: c.1189+676:PAX8_c.1026-4311:USP37dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PAX8:USP37}		277627	0	3	2	Intron of PAX8(-):675bp after exon 10	PAX8	113984056			2	Intron of USP37(-):4Kb before exon 12	USP37	219367191			10	DUPLICATION		105383135	228831	341390	3	NEW_VARIANT
P-0031824-T01-IM6	FANCA (NM_000135) rearrangement: c.2171:FANCA_chr16:g.89592277dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		29864	0	58	16	Intron of SPG7(+):459bp before exon 5	FANCA	89592277			16	Exon 24 of FANCA(-)	FANCA	89837023			10	DUPLICATION		244746	231168	51834	59	NEW_VARIANT
P-0031824-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.208+2971:EML4_c.2816-19:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		79245	1	167	2	Intron of ALK(-):19bp before exon 17	EML4	29450557			2	Intron of EML4(+):3Kb after exon 2	ALK	42475798			10	INVERSION		13025241	235348	102084	166	NEW_VARIANT
P-0031946-T01-IM6	TP53 (NM_000546) Rearrangement: c.993+155_c.*4475inv	PRECISE	Note: The TP53 rearrangement is an intragenic inversion of exons 10-11. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4667	0	19	17	IGR: 3Kb before TP53(-)	TP53	7568452			17	Intron of TP53(-):154bp after exon 9	TP53	7576698			10	INVERSION		8246	231462	7648	19	NEW_VARIANT
P-0033077-T01-IM6	MSH2 (NM_000251) rearrangement: chr2:g.34164010_c.2635-1del	PRECISE	Note: The MSH2 rearrangement is a deletion that includes MSH2 exons 1-16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {LINC01317:MSH2}		142406	0	17	2	5-UTR of LINC01317(+):359Kb before coding start	MSH2	34164010			2	Exon 16 of MSH2(+)	MSH2	47709917			10	DELETION		13545907	237498	75743	18	NEW_VARIANT
P-0033077-T01-IM6	ROS1 (NM_002944) - SLC35F1 (NM_00102985) rearrangement: c.5249-591:ROS1_c.174-110100:SLC35F1del	PRECISE	Note: The ROS1 - SLC35F1 rearrangement is a deletion that includes ROS1 exons 1-31 and SLC35F1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		101566	0	17	6	Intron of ROS1(-):591bp before exon 32	ROS1	117651200			6	Intron of SLC35F1(+):110Kb before exon 2	SLC35F1	118365508			10	DELETION		714308	237499	62200	17	NEW_VARIANT
P-0033633-T01-IM6	DROSHA (NM_013235) rearrangement: c.1040_c.1317dup	PRECISE	Note: The DROSHA rearrangement is an intragenic duplication of exons 6-8. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3785	0	44	5	Exon 8 of DROSHA(-)	DROSHA	31511257			5	Exon 6 of DROSHA(-)	DROSHA	31515579			10	DUPLICATION		4322	243687	6927	45	NEW_VARIANT
P-0034632-T03-IM6	CDH1 (NM_004360) rearrangement: t(15;16)(q25.1;q22.1)(chr15:g.79195333::chr16:g.68847420)	PRECISE	Note: The CDH1 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	11	16	Intron of CDH1(+):22bp after exon 9	CDH1	68847420			15	IGR: 19Kb before CTSH(-)	CDH1	79195333			10	TRANSLOCATION		0	308164	0	11	NEW_VARIANT
P-0034868-T01-IM6	TLK2 (NM_006852) - BRIP1 (NM_032043) rearrangement: c.1461-1686:TLK2_c.3392:BRIP1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TLK2:BRIP1}		17770	0	9	17	Exon 20 of BRIP1(-)	TLK2	59761015			17	Intron of TLK2(+):2Kb before exon 18	BRIP1	60672260			10	INVERSION		911245	254496	28987	8	NEW_VARIANT
P-0035316-T01-IM6	ERRFI1 (NM_018948) rearrangement: c.679_chr1:g.12117784del	PRECISE	Note: The ERRFI1 rearrangement is a deletion that includes ERRFI1 exon 4.	MANUAL_OK	3to5	3to5	-		132495	0	56	1	Exon 4 of ERRFI1(-)	ERRFI1	8073980			1	IGR: 6Kb before TNFRSF8(+)	ERRFI1	12117784			10	DELETION		4043804	257778	195596	65	NEW_VARIANT
P-0036680-T01-IM6	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)	PRECISE	Note: The KLHL12 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KLHL12:BRAF}		0	0	39	7	Intron of BRAF(-):123bp after exon 8	KLHL12	140493984			1	Intron of KLHL12(-):639bp before exon 5	BRAF	202880970			10	TRANSLOCATION		0	271883	0	42	NEW_VARIANT
P-0038250-T01-IM6	MAP1A (NM_002373) - TP53BP1 (NM_001141980) Rearrangement : c.2178:MAP1A_c.4169:TP53BP1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MAP1A:TP53BP1}		39398	0	62	15	Exon 20 of TP53BP1(-)	MAP1A	43713304			15	Exon 4 of MAP1A(+)	TP53BP1	43815849			10	INVERSION		102545	285429	63642	119	NEW_VARIANT
P-0038250-T01-IM6	ANKRD11 (NM_013275) Rearrangement : c.5765_c.7570-37dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		7901	0	6	16	Intron of ANKRD11(-):37bp before exon 11	ANKRD11	89341402			16	Exon 9 of ANKRD11(-)	ANKRD11	89347185			10	DUPLICATION		5783	285428	11835	7	NEW_VARIANT
P-0038316-T01-IM6	GATA1 (NM_002049) rearrangement: c.838:GATA1_chrX:g.48599163dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		10837	0	128	X	IGR: 21Kb before GLOD5(+)	GATA1	48599163			X	Exon 5 of GATA1(+)	GATA1	48651672			10	DUPLICATION		52509	285655	21414	156	NEW_VARIANT
P-0040452-T01-IM6	AGO2 (NM_012154) rearrangement: c.215+103:AGO2_chr8:g.130712714del	IMPPRECISE	Note: The AGO2 rearrangement is a deletion of exons 3 - 19. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		39453	0	7	8	IGR: 48Kb before GSDMC(-)	AGO2	130712714			8	Intron of AGO2(-):102bp after exon 2	AGO2	141595115			0	DELETION		10882401	301754	55730	7	NEW_VARIANT
P-0041672-T01-IM6	AK9 (NM_001145128) - IGF1R (NM_000875) rearrangement: t(6;15)(q21;q26.3)(chr6:g.109947133::chr15:g.99486197)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {AK9:IGF1R}		0	0	5	15	Exon 19 of IGF1R(+)	AK9	99486197			6	Intron of AK9(-):7Kb before exon 13	IGF1R	109947133			10	TRANSLOCATION		0	307283	0	5	NEW_VARIANT
P-0041855-T01-IM6	FAT1 (NM_005245) rearrangement: c.3266-6560_c.11102del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 19. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		42820	0	35	4	Exon 19 of FAT1(-)	FAT1	187524578			4	Intron of FAT1(-):7Kb before exon 3	FAT1	187591327			10	DELETION		66749	307567	32419	37	NEW_VARIANT
P-0041874-T01-IM6	BCAN (NM_021948) - NTRK1 (NM_002529) fusion: c.92-224:BCAN_c.851-167:NTRK1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {BCAN:NTRK1}		33875	0	9	1	Intron of BCAN(+):223bp before exon 3	BCAN	156616369			1	Intron of NTRK1(+):166bp before exon 8	NTRK1	156843258			10	DELETION		226889	307583	99939	9	NEW_VARIANT
P-0041900-T01-IM6	STK11 (NM_000455) rearrangement: c.93_c.290+4807del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3134	0	16	19	Exon 1 of STK11(+)	STK11	1207005			19	Intron of STK11(+):5Kb after exon 1	STK11	1212009			10	DELETION		5004	307654	1748	17	NEW_VARIANT
P-0041985-T01-IM6	KMT2B (NM_014727) rearrangement: c.291:KMT2B_chr19:g.36208418del	IMPPRECISE	Note: The KMT2B rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		59	0	17	19	Promoter of KMT2B(+):502bp from tx start	KMT2B	36208418			19	Exon 1 of KMT2B(+)	KMT2B	36209211			0	DELETION		793	307771	104	17	NEW_VARIANT
P-0042104-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1056:KIF5B_c.2136+321:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		61839	0	24	10	Intron of KIF5B(-):1Kb before exon 16	KIF5B	32313020			10	Intron of RET(+):321bp after exon 11	RET	43610505			10	INVERSION		11297485	308425	169345	32	NEW_VARIANT
P-0006660-T02-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+17:FGFR3_c.1591+1556:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {FGFR3:TACC3}		40670	0	16	4	Intron of TACC3(+):2Kb after exon 6	FGFR3	1734584			4	Intron of FGFR3(+):17bp after exon 17	TACC3	1808678			10	DUPLICATION		74094	308090	49773	16	NEW_VARIANT
P-0014385-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1890:EML4_c.3172+651:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		109063	0	366	2	Intron of ALK(-):650bp after exon 19	EML4	29447676			2	Intron of EML4(+):2Kb after exon 12	ALK	42524546			10	INVERSION		13076870	308133	163434	364	NEW_VARIANT
P-0042098-T01-IM6	RAB3GAP2 (NM_012414) - AURKA (NM_003600) rearrangement: t(1;20)(q41;q13.2)(chr1:g.220440226::chr20:g.54945391)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RAB3GAP2:AURKA}		0	0	5	20	Exon 9 of AURKA(-)	RAB3GAP2	54945391			1	Intron of RAB3GAP2(-):5Kb after exon 1	AURKA	220440226			10	TRANSLOCATION		0	308268	0	20	NEW_VARIANT
P-0042173-T01-IM6	MDM2 (NM_002392) - CADM3 (NM_021189) rearrangement: t(1;12)(q23.2;q15)(chr1:g.159155314::chr12:g.69233222)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MDM2:CADM3}		0	0	11	12	Exon 11 of MDM2(+)	MDM2	69233222			1	Intron of CADM3(+):4Kb before exon 2	CADM3	159155314			10	TRANSLOCATION		0	308256	0	11	NEW_VARIANT
P-0034921-T02-IM6	PTEN (NM_000314) rearrangement: c.492+129:PTEN_chr10:g.90317365del	PRECISE	Note: The PTEN rearrangement is a deletion of exons 6 - 9.	MANUAL_OK	3to5	3to5	Antisense Fusion		3230	0	3	10	Intron of PTEN(+):129bp after exon 5	PTEN	89693137			10	Intron of RNLS(-):15Kb after exon 4	PTEN	90317365			7	DELETION		624228	309132	4600	4	NEW_VARIANT
P-0035890-T02-IM6	FAM46C (NM_017709) rearrangement: c.370:FAM46C_chr1:g.118247292del	PRECISE	Note: The FAM46C rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5952	0	57	1	Exon 2 of FAM46C(+)	FAM46C	118165860			1	IGR: 99Kb before FAM46C(+)	FAM46C	118247292			10	DELETION		81432	308578	10550	70	NEW_VARIANT
P-0036756-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2587:TMPRSS2_c.19-4454:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		88456	0	12	21	Intron of ERG(-):4Kb before exon 2	TMPRSS2	39821998			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42877290			10	DELETION		3055292	308415	99342	13	NEW_VARIANT
P-0041695-T01-IM6	CCDC30 (NM_001080850) - ROS1 (NM_002944) fusion: t(1;6)(p34.2;q22.1)(chr1:g.43087864::chr6:g.117643359)	PRECISE	Note: The CCDC30 - ROS1 fusion involves CCDC30 exons 1 - 10 and ROS1 exons 35 - 43. The fusion includes the kinase domain of ROS1.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {CCDC30:ROS1}		0	0	172	6	Intron of ROS1(-):802bp before exon 35	CCDC30	117643359			1	Intron of CCDC30(+):11Kb after exon 10	ROS1	43087864			10	TRANSLOCATION		0	307294	0	183	NEW_VARIANT
P-0010250-T02-IM6	RSPRY1 (NM_133368) - NUP93 (NM_014669) rearrangement: c.1273+508:RSPRY1_c.565-4:NUP93dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RSPRY1:NUP93}		22714	0	26	16	Intron of NUP93(+):3bp before exon 7	RSPRY1	56855412			16	Intron of RSPRY1(+):508bp after exon 11	NUP93	57261873			10	DUPLICATION		406461	308237	36118	26	NEW_VARIANT
P-0042167-T01-IM6	KMT2C (NM_170606) rearrangement: c.162-29358_c.8476del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 2 - 38. One of the breakpoints is within exon 38.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		61369	0	34	7	Exon 38 of KMT2C(-)	KMT2C	151874062			7	Intron of KMT2C(-):29Kb before exon 2	KMT2C	152085118			10	DELETION		211056	308174	36412	34	NEW_VARIANT
P-0042346-T01-IM6	PLEKHM3 (NM_001080475) - SF3B1 (NM_012433) rearrangement: c.2109-15321:PLEKHM3_c.416-181:SF3B1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PLEKHM3:SF3B1}		28180	0	15	2	Intron of SF3B1(-):181bp before exon 5	PLEKHM3	198283493			2	Intron of PLEKHM3(-):15Kb before exon 8	SF3B1	208708541			10	DELETION		10425048	309712	31400	18	NEW_VARIANT
P-0042346-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q21.1;q22.3)(chr15:g.45823222::chr21:g.42873873)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	75	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42873873			15	5-UTR of HMGN2P46(+):26Kb before coding start	TMPRSS2	45823222			10	TRANSLOCATION		0	309713	0	84	NEW_VARIANT
P-0032175-T02-IM6	MAP3K13 (NM_004721) rearrangement: c.1897_c.2430+522del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4258	0	3	3	Exon 11 of MAP3K13(+)	MAP3K13	185191016			3	Intron of MAP3K13(+):522bp after exon 11	MAP3K13	185192071			0	DELETION		1055	310058	2465	3	NEW_VARIANT
P-0033300-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1125:TMPRSS2_c.19-12860:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		98446	0	6	21	Intron of ERG(-):13Kb before exon 2	TMPRSS2	39830404			21	Intron of TMPRSS2(-):1Kb after exon 1	ERG	42878752			10	DELETION		3048348	309769	118525	6	NEW_VARIANT
P-0033300-T02-IM6	PIK3R1 (NM_181523) rearrangement: c.1735:PIK3R1_chr5:g.72070476del	PRECISE	Note: The PIK3R1 rearrangement is a deletion of exons 13 - 16. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	-		3447	0	10	5	Exon 13 of PIK3R1(+)	PIK3R1	67591142			5	IGR: 42Kb before TNPO1(+)	PIK3R1	72070476			10	DELETION		4479334	309768	4636	10	NEW_VARIANT
P-0033799-T02-IM6	KMT2A (NM_001197104) rearrangement: t(4;11)(q31.23;q23.3)(chr4:g.150937415::chr11:g.118355175)	IMPPRECISE	Note: The KMT2A rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	11	Intron of KMT2A(+):146bp after exon 9	KMT2A	118355175			4	IGR: 62Kb before DCLK2(+)	KMT2A	150937415			0	TRANSLOCATION		0	309188	0	8	NEW_VARIANT
P-0033799-T02-IM6	TRAP1 (NM_016292) - SLX4 (NM_032444) rearrangement: c.88+228:TRAP1_c.4637-72:SLX4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TRAP1:SLX4}		47242	0	13	16	Intron of SLX4(-):72bp before exon 13	TRAP1	3634944			16	Intron of TRAP1(-):227bp after exon 1	SLX4	3767194			10	DELETION		132250	309186	29887	12	NEW_VARIANT
P-0033799-T02-IM6	MALT1 (NM_006785) rearrangement: c.1594:MALT1_chr18:g.56433959del	PRECISE	Note: The MALT1 rearrangement is a deletion of exons 13 - 17. One of the breakpoints is within exon 13. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		3607	0	7	18	Exon 13 of MALT1(+)	MALT1	56402552			18	IGR: 95Kb before MALT1(+)	MALT1	56433959			8	DELETION		31407	309187	3542	8	NEW_VARIANT
P-0039522-T03-IM6	CTNNB1 (NM_001904) rearrangement: c.141_c.465del	IMPPRECISE	Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3 - 4. The breakpoints are within exon 3 and exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2151	0	21	3	Exon 3 of CTNNB1(+)	CTNNB1	41266144			3	Exon 4 of CTNNB1(+)	CTNNB1	41266668			0	DELETION		524	310297	1026	24	NEW_VARIANT
P-0042558-T01-IM6	FLT1 (NM_002019) rearrangement: t(13;16)(q12.3;p13.3)(chr13:g.29041141::chr16:g.443668)	PRECISE	Note: The FLT1 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {LOC100134368:FLT1}		0	0	9	16	Promoter of LOC100134368(+):11Kb from tx start	FLT1	443668			13	Exon 3 of FLT1(-)	FLT1	29041141			10	TRANSLOCATION		0	310814	0	9	NEW_VARIANT
P-0019351-T03-IM6	PALB2 (NM_024675) rearrangement: c.3201+1_c.3203del	PRECISE	Note: The PALB2 rearrangement is an intragenic deletion of exons 11 - 12. The breakpoints are within exon 11 and exon 12.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		663	0	3	16	Exon 12 of PALB2(-)	PALB2	23619332			16	Exon 11 of PALB2(-)	PALB2	23625324			8	DELETION		5992	309942	389	3	NEW_VARIANT
P-0019351-T03-IM6	STAT5B (NM_012448) rearrangement: c.1776-43_c.1906+1041inv	PRECISE	Note: The STAT5B rearrangement is an intragenic inversion of exon 15. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1056	0	8	17	Intron of STAT5B(-):1Kb after exon 15	STAT5B	40361148			17	Intron of STAT5B(-):43bp before exon 15	STAT5B	40362362			10	INVERSION		1214	309943	912	8	NEW_VARIANT
P-0034774-T03-IM6	HIST1H3A (NM_003529) rearrangement: c.115:HIST1H3A_chr6:g.26042531inv	PRECISE	Note: The HIST1H3A rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {HIST1H3A:HIST1H2BB}		5045	0	4	6	Exon 1 of HIST1H3A(+)	HIST1H3A	26020832			6	Promoter of HIST1H2BB(-):923bp from tx start	HIST1H3A	26042531			9	INVERSION		21699	308267	7490	4	NEW_VARIANT
P-0042332-T01-IM6	BRCA2 (NM_000059) rearrangement: c.8487+123:BRCA2_chr13:g.61534109del	PRECISE	Note: The BRCA2 rearrangement is a deletion of exons 20 - 27.	MANUAL_OK	3to5	3to5	-		63800	0	30	13	Intron of BRCA2(+):123bp after exon 19	BRCA2	32944817			13	IGR: 240Kb before MIR3169(-)	BRCA2	61534109			10	DELETION		28589292	309699	43265	30	NEW_VARIANT
P-0042549-T01-IM6	PTEN (NM_000314) rearrangement: c.80-1356_c.105del	PRECISE	Note: The PTEN rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		111	0	10	10	Intron of PTEN(+):1Kb before exon 2	PTEN	89652426			10	Exon 2 of PTEN(+)	PTEN	89653807			10	DELETION		1381	310817	82	10	NEW_VARIANT
P-0014522-T01-IM6	ABCC4 (NM_005845) -  TMPRSS2 (NM_001135099) Rearrangement : t(13;21)(q32.1;q22.3)(chr13:g.:95689572::chr21:g.42873289)	IMPRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: out of frame (ABCC4-TMPRSS2)		0	0	5	21	Intron of TMPRSS2(-): 3Kb before exon 2	ABCC4	42873289			13	Intron of ABCC4(-): 3Kb before exon 30	TMPRSS2	95689572			0	TRANSLOCATION		0	164834	0	4	NEW_VARIANT
P-0042580-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1619:KIF5B_c.2136+760:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		69016	0	36	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315737			10	Intron of RET(+):760bp after exon 11	RET	43610944			10	INVERSION		11295207	310826	101430	38	NEW_VARIANT
P-0004234-T02-IM6	RAD52 (NM_134424) rearrangement: t(4;12)(p16.1;p13.33)(chr4:g.8469708::chr12:g.1039265)	PRECISE	Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	23	12	Exon 4 of RAD52(-)	RAD52	1039265			4	Exon 9 of TRMT44(+)	RAD52	8469708			10	TRANSLOCATION		0	311024	0	22	NEW_VARIANT
P-0012132-T03-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1525:TMPRSS2_c.18+2872:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38069	0	63	21	Intron of ERG(-):3Kb after exon 1	TMPRSS2	39867415			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868521			10	DELETION		3001106	311016	19964	70	NEW_VARIANT
P-0012132-T03-IM6	FUBP1 (NM_003902) - C4orf45 (NM_152543) rearrangement: t(1;4)(p31.1;q32.1)(chr1:g.78420821::chr4:g.159924443)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FUBP1:C4orf45}		0	0	24	4	Intron of C4orf45(-):30Kb before exon 2	FUBP1	159924443			1	Intron of FUBP1(-):118bp after exon 18	C4orf45	78420821			10	TRANSLOCATION		0	311017	0	24	NEW_VARIANT
P-0042502-T01-IM6	TP53 (NM_000546) rearrangement: c.993+292:TP53_chr17:g.7473200del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 10 - 11.	MANUAL_OK	3to5	3to5	Antisense Fusion		4608	0	108	17	Intron of SENP3(+):473bp before exon 9	TP53	7473200			17	Intron of TP53(-):291bp after exon 9	TP53	7576561			10	DELETION		103361	310458	4782	110	NEW_VARIANT
P-0042672-T01-IM6	CDKN2B (NM_004936) rearrangement: c.156+544:CDKN2B_chr9:g.3627278del	PRECISE	Note: The CDKN2B rearrangement is a deletion of exon 2.	MANUAL_OK	3to5	3to5	-		128325	0	34	9	IGR: 41Kb before RFX3-AS1(+)	CDKN2B	3627278			9	Intron of CDKN2B(-):543bp after exon 1	CDKN2B	22008253			10	DELETION		18380975	311021	60604	33	NEW_VARIANT
P-0022380-T03-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+21810:CCDC6_c.2136+475:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		15534	0	167	10	Intron of RET(+):475bp after exon 11	CCDC6	43610659			10	Intron of CCDC6(-):22Kb after exon 1	RET	61644070			10	INVERSION		18033411	310931	68704	208	NEW_VARIANT
P-0022380-T03-IM6	TMEM25 (NM_032780) - KMT2A (NM_001197104) rearrangement: c.674-97:TMEM25_c.6838:KMT2Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TMEM25:KMT2A}		9375	0	16	11	Exon 27 of KMT2A(+)	TMEM25	118373445			11	Intron of TMEM25(+):96bp before exon 5	KMT2A	118404038			10	DUPLICATION		30593	310929	50476	16	NEW_VARIANT
P-0009024-T02-IM6	MKRN1 (NM_013446) - BRAF (NM_004333) fusion: c.772-185:MKRN1_c.1140+623:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {MKRN1:BRAF}		62454	0	59	7	Intron of MKRN1(-):185bp before exon 5	MKRN1	140156851			7	Intron of BRAF(-):622bp after exon 8	BRAF	140493485			10	DUPLICATION		336634	306342	151971	64	NEW_VARIANT
P-0037052-T02-IM6	CTNNB1 (NM_001904) rearrangement: c.212:CTNNB1_chr3:g.41254099inv	PRECISE	Note: The CTNNB1 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2034	0	17	3	5-UTR of CTNNB1(+):11Kb before coding start	CTNNB1	41254099			3	Exon 3 of CTNNB1(+)	CTNNB1	41266215			10	INVERSION		12116	311515	897	17	NEW_VARIANT
P-0038235-T01-IM6	FGFR2 (NM_000141) - NOL4 (NM_003787) fusion: t(10;18)(q26.13;q12.1)(chr10:g.123240418::chr18:g.31580817)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:NOL4}		0	0	34	18	Intron of NOL4(-):18Kb after exon 6	FGFR2	31580817			10	Intron of FGFR2(-):883bp before exon 18	NOL4	123240418			10	TRANSLOCATION		0	311151	0	34	NEW_VARIANT
P-0038345-T02-IM6	MGA (NM_001164273) rearrangement: c.2014-56:MGA_chr15:g.41942833del	IMPPRECISE	Note: The MGA rearrangement is a deletion of exons 1 - 3.	MANUAL_OK	3to5	3to5	-		6869	0	17	15	IGR: 10Kb before MGA(+)	MGA	41942833			15	Intron of MGA(+):55bp before exon 4	MGA	41991005			0	DELETION		48172	311711	11101	19	NEW_VARIANT
P-0042791-T01-IM6	KMT2C (NM_170606) rearrangement: c.8135:KMT2C_chr7:g.151824873del	PRECISE	Note: The KMT2C rearrangement is a deletion of exons 38 - 59. One of the breakpoints is within exon 38.	MANUAL_OK	3to5	3to5	-		41256	0	59	7	IGR: 7Kb before KMT2C(-)	KMT2C	151824873			7	Exon 38 of KMT2C(-)	KMT2C	151874403			10	DELETION		49530	311387	28579	60	NEW_VARIANT
P-0042865-T01-IM6	BAP1 (NM_004656) rearrangement: t(3;12)(p21.1;q24.23)(chr3:g.52440433::chr12:g.119130791)	PRECISE	Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	12	IGR: 289Kb before SRRM4(+)	BAP1	119130791			3	Intron of BAP1(-):41bp before exon 9	BAP1	52440433			10	TRANSLOCATION		0	311546	0	9	NEW_VARIANT
P-0042865-T01-IM6	JAK3 (NM_000215) rearrangement: t(7;19)(p21.3;p13.11)(chr7:g.12881070::chr19:g.17953169)	PRECISE	Note: The JAK3 rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	19	Exon 6 of JAK3(-)	JAK3	17953169			7	IGR: 154Kb before ARL4A(+)	JAK3	12881070			9	TRANSLOCATION		0	311547	0	11	NEW_VARIANT
P-0042956-T01-IM6	FAT1 (NM_005245) rearrangement: c.3580+1189_c.9614del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 4 - 14. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		37725	0	17	4	Exon 14 of FAT1(-)	FAT1	187532779			4	Intron of FAT1(-):1Kb after exon 3	FAT1	187583264			10	DELETION		50485	311773	42617	17	NEW_VARIANT
P-0031005-T02-IM6	RICTOR (NM_152756) rearrangement: c.3480:RICTOR_chr5:g.44977508del	PRECISE	Note: The RICTOR rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		29301	0	43	5	Exon 31 of RICTOR(-)	RICTOR	38950470			5	IGR: 168Kb before MRPS30(+)	RICTOR	44977508			10	DELETION		6027038	313193	49762	43	NEW_VARIANT
P-0042826-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-740:TMPRSS2_c.18+14519:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49916	0	25	21	Intron of ERG(-):15Kb after exon 1	TMPRSS2	39855768			21	Intron of TMPRSS2(-):740bp before exon 2	ERG	42870856			10	DELETION		3015088	313104	41115	32	NEW_VARIANT
P-0042990-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1517:TMPRSS2_c.39+57418:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		34382	0	74	21	Intron of ERG(-):57Kb after exon 3	TMPRSS2	39890168			21	Intron of TMPRSS2(-):2Kb before exon 3	ERG	42868022			10	DELETION		2977854	312932	22876	77	NEW_VARIANT
P-0042990-T01-IM6	LPA (NM_005577) - HIST1H3H (NM_003536) rearrangement: c.209+271:LPA_c.28:HIST1H3Hinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {LPA:HIST1H3H}		949840	0	17	6	Exon 1 of HIST1H3H(+)	LPA	27777879			6	Intron of LPA(-):270bp after exon 3	HIST1H3H	161071099			10	INVERSION		133293220	312935	1048576	26	NEW_VARIANT
P-0043076-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2358:FGFR3_c.2019-34:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		40581	0	197	4	Intron of TACC3(+):33bp before exon 12	FGFR3	1741652			4	Exon 18 of FGFR3(+)	TACC3	1808926			10	DUPLICATION		67274	313238	74805	225	NEW_VARIANT
P-0038201-T03-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+989:EML4_c.3172+579:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		115280	0	43	2	Intron of ALK(-):578bp after exon 19	EML4	29447748			2	Intron of EML4(+):989bp after exon 12	ALK	42523645			10	INVERSION		13075897	313368	78302	43	NEW_VARIANT
P-0043029-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+1728:TMPRSS2_c.18+13223:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		107925	0	67	21	Intron of ERG(-):13Kb after exon 1	TMPRSS2	39857064			21	Intron of TMPRSS2(-):2Kb after exon 1	ERG	42878149			10	DELETION		3021085	313452	110951	72	NEW_VARIANT
P-0043120-T01-IM6	CSDE1 (NM_001242891) rearrangement: c.337+773_c.720+37inv	PRECISE	Note: The CSDE1 rearrangement is an intragenic inversion of exons 5 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		4446	0	12	1	Intron of CSDE1(-):36bp after exon 8	CSDE1	115277026			1	Intron of CSDE1(-):772bp after exon 4	CSDE1	115281540			10	INVERSION		4514	313329	4495	13	NEW_VARIANT
P-0043120-T01-IM6	DROSHA (NM_013235) rearrangement: c.3261+11_c.3526-1355del	PRECISE	Note: The DROSHA rearrangement is an intragenic deletion of exons 28 - 29. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		3379	0	52	5	Intron of DROSHA(-):1Kb before exon 30	DROSHA	31412349			5	Intron of DROSHA(-):10bp after exon 27	DROSHA	31424523			10	DELETION		12174	313328	2651	53	NEW_VARIANT
P-0043145-T01-IM6	CDKN2A (NM_000077) rearrangement: c.396:CDKN2A_chr9:g.30796986del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		49607	0	28	9	Exon 2 of CDKN2A(-)	CDKN2A	21970962			9	IGR: 408Kb before LINC01242(-)	CDKN2A	30796986			10	DELETION		8826024	313381	55876	28	NEW_VARIANT
P-0043292-T01-IM6	GNAS (NM_000516) rearrangement: c.839+18:GNAS_chr20:g.57486231inv	IMPPRECISE	Note: The GNAS rearrangement is an inversion of exons 11 - 13. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3522	0	45	20	Intron of GNAS(+):18bp after exon 10	GNAS	57484877			20	3-UTR of GNAS(+):19Kb after coding stop	GNAS	57486231			0	INVERSION		1354	313736	4952	44	NEW_VARIANT
P-0031368-T04-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1154:EML4_c.3173-797:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		107906	0	97	2	Intron of ALK(-):797bp before exon 20	EML4	29447191			2	Intron of EML4(+):1Kb before exon 13	ALK	42527227			10	INVERSION		13080036	314071	101192	96	NEW_VARIANT
P-0002675-T01-IM3		PRECISE	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).	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		232043	0	87	10	Intron of BICC1(+): 5Kb before exon 3	BICC1	60456648			10	Intron of FGFR2(-): 2Kb before exon 18	FGFR2	123241096			56	INVERSION		62784448	4601	222775	87	NEW_VARIANT
P-0006885-T01-IM5	FGFR2 (NM_000141) - BICC1 (NM_001080512) rearrangement: c.2302-1052:FGFR2_c.238-5239:BICC1inv	PRECISE	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 .	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		196474	0	77	10	Intron of BICC1(+): 5Kb before exon 3	FGFR2	60456595			10	Intron of FGFR2(-): 1Kb before exon 18	BICC1	123240587			70	INVERSION		62783992	109777	203886	74	NEW_VARIANT
P-0007041-T01-IM5	MAP2K1 (NM_002755) rearrangement :  c.528_568+1908inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		256	0	6	15	Exon 5 of MAP2K1(+)	MAP2K1	66737005			15	Intron of MAP2K1(+): 2Kb after exon 5	MAP2K1	66738953			3	INVERSION		1948	112744	150	5	NEW_VARIANT
P-0007041-T01-IM5	DOT1L (NM_032482) rearrangement :  c.708-727_2158dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		11224	0	6	19	Intron of DOT1L(+): 727bp before exon 9	DOT1L	2201972			19	Exon 20 of DOT1L(+)	DOT1L	2216514			8	DUPLICATION		14542	112742	8880	6	NEW_VARIANT
P-0007205-T01-IM5	SHBG (NM_001040) - TP53 (NM_000546) rearrangement : chr17:g.7522278_c.-28-709:TP53inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript fusion (SHBG-TP53)		27195	0	19	17	5-UTR of SHBG(+): 14Kb before coding start	SHBG	7522278			17	5-UTR of TP53(-): 737bp before coding start	TP53	7580649			15	INVERSION		58371	114585	33075	19	NEW_VARIANT
P-0007520-T01-IM5	RPS6KB2 (NM_003952) - CNIH2 (NM_182553) -  Rearrangement : c.81+215:CNIH2_c.969+56:RPS6KB2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (RPS6KB2-CNIH2)		17126	0	41	11	Intron of CNIH2(+): 215bp after exon 1	RPS6KB2	66046223			11	Intron of RPS6KB2(+): 56bp after exon 11	CNIH2	67201584			39	DUPLICATION		1155361	117082	23907	38	NEW_VARIANT
P-0008286-T01-IM5	SMARCD1 (NM_003076) - PTPRR (NM_002849) rearrangement: c.531+104:SMARCD1_c.1008-6669:PTPRRinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein fusion: out of frame (SMARCD1-PTPRR)		185967	0	10	12	Intron of SMARCD1(+): 104bp after exon 4	SMARCD1	50480765			12	Intron of PTPRR(-): 7Kb before exon 7	PTPRR	71101772			14	INVERSION		20621007	121130	257030	6	NEW_VARIANT
P-0008658-T01-IM5	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2302-1658:FGFR2_c.355-22274:KIAA1217inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-KIAA1217)		437258	0	55	10	Intron of KIAA1217(+): 22Kb before exon 4	FGFR2	24647524			10	Intron of FGFR2(-): 2Kb before exon 18	KIAA1217	123241193			74	INVERSION		98593669	123288	432706	54	NEW_VARIANT
P-0009694-T01-IM5	PRKAR1B (NM_001164758) -BRAF (NM_004333) Rearrangement :  c.892-2551:PRKAR1B_c.1140+2253:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (PRKAR1B-BRAF)		585325	0	25	7	Intron of PRKAR1B(-): 3Kb before exon 10	PRKAR1B	593658			7	Intron of BRAF(-): 2Kb after exon 8	BRAF	140491855			43	DUPLICATION		139898197	136076	747513	25	NEW_VARIANT
P-0010701-T01-IM5	BCL2L11 (NM_138621) Rearrangement : c.-13-1249_c.394+2099del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		7594	0	18	2	5-UTR of BCL2L11(+): 1Kb before coding start	BCL2L11	111880061			2	Intron of BCL2L11(+): 2Kb after exon 2	BCL2L11	111883815			23	DELETION		3754	148444	5926	16	NEW_VARIANT
P-0011329-T01-IM5	FGFR2 (NM_000141) Rearrangement :  chr10:g.65610482_ c.2302-649inv	PRECISE	Note: The FGFR2 Rearrangement results in the inversion of exon 18 of FGFR2.  This involves the kinase domain of FGFR2.	MANUAL_OK	3to3	3to3	-		223257	0	63	10	IGR: 329Kb before REEP3(+)	FGFR2	65610482			10	Intron of FGFR2(-): 649bp before exon 18	FGFR2	123240184			57	INVERSION		57629702	153209	247089	33	NEW_VARIANT
P-0011394-T01-IM5	FGFR2 (NM_000141) - LAMC1 (NM_002293) rearrangment: t(1;10)(q25.3;q26.13)(chr1:g.183109471::chr10:g.123240042 )	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-LAMC1)		0	0	27	10	Intron of FGFR2(-): 507bp before exon 18	FGFR2	123240042			1	Intron of LAMC1(+): 68bp before exon 27	LAMC1	183109471			30	TRANSLOCATION		0	153457	0	27	NEW_VARIANT
P-0011394-T01-IM5	FGFR2 (NM_000141) - RABGAP1L (NM_014857) rearrangement: t(1;10)(q25.1;q26.13)(chr1:g.174863117::chr10:g.123240065 )	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-RABGAP1L)		0	0	102	10	Intron of FGFR2(-): 530bp before exon 18	FGFR2	123240065			1	Intron of RABGAP1L(+): 16Kb after exon 2	RABGAP1L	174863117			87	TRANSLOCATION		0	153458	0	122	NEW_VARIANT
P-0011516-T01-IM5	CTNNA3 (NM_013266) -FGFR2 (NM_000141) Rearrangement : c.1048-8479:CTNNA3_c.2301+1272:FGFR2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (CTNNA3-FGFR2)		285893	0	28	10	Intron of CTNNA3(-): 8Kb before exon 8	CTNNA3	68543761			10	Intron of FGFR2(-): 249bp before exon 17	FGFR2	123241940			33	DUPLICATION		54698179	153982	284478	28	NEW_VARIANT
P-0011516-T01-IM5	FGFR2 (NM_000141) - SH2C (NM_012435) Rearrangement : t(10;19)(q26.13;p13.3)(chr10:g.123243182::chr19:g.447779)	PRECISE	Note: The FGFR2  - SH2C Rearrangement results in the fusion of exons1-16 of FGFR2 and exon2-13 of SH2C. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-SHC2)		0	0	62	19	Intron of SHC2(-): 7Kb before exon 2	FGFR2	447779			10	Intron of FGFR2(-): 30bp after exon 16	SH2C	123243182			33	TRANSLOCATION		0	153986	0	37	NEW_VARIANT
P-0012376-T01-IM5	FGFR2 (NM_000141) rearrangement: t(1;10)(q32.1;q26.13)(chr1:g.205735259::chr10:g.123241306 )	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	79	10	Intron of FGFR2(-): 2Kb before exon 18	FGFR2	123241306			1	IGR: 2Kb before RAB7L1(-)	FGFR2	205735259			67	TRANSLOCATION		0	157232	0	78	NEW_VARIANT
P-0012423-T02-IM6	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)	PRECISE	Note: The FGFR2 - NOL4 fusion is predicted to be in-frame and includes the kinase domain of FGFR2.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:NOL4}		0	0	7	18	Intron of NOL4(-):25Kb before exon 7	FGFR2	31563418			10	Intron of FGFR2(-):1Kb after exon 17	NOL4	123242055			10	TRANSLOCATION		0	178565	0	6	NEW_VARIANT
P-0012639-T01-IM5	FGFR2 (NM_000141) - SEPT10 (NM_144710) rearrangement: t(2;10)(q13;q26.13)(chr2:g.110325395::chr10:g.123240798)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: mid-exon (FGFR2-SEPT10)		0	0	16	10	Intron of FGFR2(-): 1Kb before exon 18	FGFR2	123240798			2	Exon 6 of SEPT10(-)	SEPT10	110325395			18	TRANSLOCATION		0	158338	0	14	NEW_VARIANT
P-0012666-T01-IM5	FGFR2 (NM_000141) - AMOT (NM_001113490) Rearrangement : t(10;X)(q26.13.1;q23)(chr10:g.123241762::chrX:g.112058354)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-AMOT)		0	1	87	X	Intron of AMOT(-): 232bp after exon 3	FGFR2	112058354			10	Intron of FGFR2(-): 71bp before exon 17	AMOT	123241762			36	TRANSLOCATION		0	158442	0	83	NEW_VARIANT
P-0013174-T01-IM5	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion (FGFR2 exons 1-17 with BICC1 exons 16-21): c.2302-588:FGFR2_c.2182-284:BICC1inv	PRECISE	Note: The FGFR2 - BICC1 fusion is predicted to be in frame and includes the kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		263655	0	6	10	Intron of BICC1(+): 284bp before exon 16	FGFR2	60566060			10	Intron of FGFR2(-): 588bp before exon 18	BICC1	123240123			14	INVERSION		62674063	160411	265454	6	NEW_VARIANT
P-0013405-T01-IM5	FGFR2 (NM_000141) - KIAA1217 (NM_019590) Rearrangement: c.2301+1446:FGFR2_c.354+73179:KIAA1217inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-KIAA1217)		524538	0	84	10	Intron of KIAA1217(+): 73Kb after exon 3	FGFR2	24582017			10	Intron of FGFR2(-): 75bp before exon 17	KIAA1217	123241766			114	INVERSION		98659749	161152	506336	77	NEW_VARIANT
P-0020164-T01-IM6	FGFR2 (NM_000141) - ADAM9 (NM_003816) fusion: t(8;10(p11.22;q26.13)(chr8:g.38901161::chr10:g.123242738)	PRECISE	Note: The FGFR2 - ADAM9 fusion is predicted to be in frame and includes the kinase domain of FGFR2	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:ADAM9}		0	0	63	10	Intron of FGFR2(-):473bp after exon 17	FGFR2	123242738			8	Intron of ADAM9(+):2Kb after exon 12	ADAM9	38901161			10	TRANSLOCATION		0	183815	0	90	NEW_VARIANT
P-0026846-T01-IM6	UPF1 (NM_002911) rearrangement: t(9;19)(p21.1;p13.11)(chr9:g.31342057::chr19:g.18974414)	PRECISE	Note: The UPF1 rearrangement is translocation with a breakpoint within UPF1 exon 19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	15	19	Exon 19 of UPF1(+)	UPF1	18974414			9	IGR: 953Kb before LINC01242(-)	UPF1	31342057			10	TRANSLOCATION		0	212088	0	14	NEW_VARIANT
P-0029335-T01-IM6	CIC (NM_015125) rearrangement: chr19:g.42738483_c.3754:CICdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		39993	0	13	19	Intron of GSK3A(-):21bp after exon 6	CIC	42738483			19	Exon 15 of CIC(+)	CIC	42797392			10	DELETION		58909	221499	60051	13	NEW_VARIANT
P-0030378-T01-IM6	PTCH1 (NM_000264) Rearrangement : chr9:g.27937753_c.1425:PTCH1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		143734	0	80	9	IGR: 10Kb before LINGO2(-)	PTCH1	27937753			9	Exon 10 of PTCH1(-)	PTCH1	98239907			10	INVERSION		70302154	225538	235302	80	NEW_VARIANT
P-0043132-T01-IM6	RARA (NM_000964) rearrangement: c.179-5462:RARA_chr17:g.60911308del	PRECISE	Note: The RARA rearrangement is a deletion of exons 3 - 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {RARA:MIR548W}		366268	0	24	17	Intron of RARA(+):5Kb before exon 3	RARA	38499106			17	5-UTR of MIR548W(+):357Kb before coding start	RARA	60911308			10	DELETION		22412202	313361	498296	25	NEW_VARIANT
P-0015479-T02-IM6	TP53 (NM_000546) rearrangement: c.993+243:TP53_chr17:g.62224960inv	PRECISE	Note: The TP53 rearrangement is an inversion of exons 1 - 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		776361	0	106	17	Intron of TP53(-):242bp after exon 9	TP53	7576610			17	3-UTR of TEX2(-):1Kb after coding stop	TP53	62224960			10	INVERSION		54648350	314110	927084	106	NEW_VARIANT
P-0015479-T02-IM6	TMPRSS2 (NM_001135099) rearrangement: c.1425+183:TMPRSS2_chr21:g.42836610del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 13 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2770	0	21	21	3-UTR of TMPRSS2(-):1Kb after coding stop	TMPRSS2	42836610			21	Intron of TMPRSS2(-):182bp after exon 12	TMPRSS2	42840140			9	DELETION		3530	314109	1322	21	NEW_VARIANT
P-0027460-T01-IM6	RPS6KA4 (NM_003942) - MACROD1 (NM_014067) rearrangement: c.1994:RPS6KA4_c.518-47220:MACROD1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {RPS6KA4:MACROD1}		24668	0	15	11	Intron of MACROD1(-):47Kb before exon 4	RPS6KA4	63829973			11	Exon 16 of RPS6KA4(+)	MACROD1	64138071			10	INVERSION		308098	316319	33417	15	NEW_VARIANT
P-0037164-T02-IM6	BAP1 (NM_004656) rearrangement: c.1696:BAP1_chr3:g.52403726del	PRECISE	Note: The BAP1 rearrangement is a deletion of exons 13 - 17. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	Antisense Fusion		7567	0	33	3	Intron of DNAH1(+):114bp before exon 38	BAP1	52403726			3	Exon 13 of BAP1(-)	BAP1	52437465			10	DELETION		33739	315091	6784	77	NEW_VARIANT
P-0042780-T01-IM6	ERBB3 (NM_001982) rearrangement: t(12;16)(q13.2;p13.13)(chr12:g.56493955::chr16:g.11917462)	PRECISE	Note: The ERBB3 rearrangement is a translocation with a breakpoint in intron 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	34	16	3-UTR of BCAR4(-):5Kb after coding stop	ERBB3	11917462			12	Intron of ERBB3(+):2bp before exon 26	ERBB3	56493955			10	TRANSLOCATION		0	314099	0	39	NEW_VARIANT
P-0043181-T01-IM6	EPC1 (NM_025209) - INHBA (NM_002192) rearrangement: t(7;10)(p14.1;p11.22)(chr7:g.41735073::chr10:g.32575797)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {EPC1:INHBA}		0	0	24	10	Intron of EPC1(-):27bp before exon 9	EPC1	32575797			7	Intron of INHBA(-):5Kb after exon 2	INHBA	41735073			10	TRANSLOCATION		0	313441	0	25	NEW_VARIANT
P-0043319-T01-IM6	DROSHA (NM_013235) rearrangement: c.3420-168:DROSHA_chr5:g.31395819dup	PRECISE	Note: The DROSHA rearrangement is a duplication of exons 29 - 35. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		10049	0	3	5	IGR: 5Kb before DROSHA(-)	DROSHA	31395819			5	Intron of DROSHA(-):168bp before exon 29	DROSHA	31421652			6	DUPLICATION		25833	313861	12272	3	NEW_VARIANT
P-0043416-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3800:TMPRSS2_c.19-13761:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66043	0	24	21	Intron of ERG(-):14Kb before exon 2	TMPRSS2	39831305			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873916			10	DELETION		3042611	314122	77485	25	NEW_VARIANT
P-0043422-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-1681_c.350-1608del	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		7452	0	18	21	Intron of TMPRSS2(-):2Kb before exon 4	TMPRSS2	42863128			21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868186			10	DELETION		5058	314104	5624	20	NEW_VARIANT
P-0043556-T01-IM6	FGFR1 (NM_001174067) rearrangement: c.464:FGFR1_chr8:g.30003025inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		80020	0	9	8	3-UTR of MIR548O2(-):105Kb after coding stop	FGFR1	30003025			8	Exon 5 of FGFR1(-)	FGFR1	38285947			10	INVERSION		8282922	314967	91553	9	NEW_VARIANT
P-0043704-T01-IM6	RET (NM_020975) - KIF5B (NM_004521) rearrangement: c.2136+147:RET_c.2545-77:KIF5Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {RET:KIF5B}		47062	0	26	10	Intron of KIF5B(-):77bp before exon 24	RET	32306364			10	Intron of RET(+):147bp after exon 11	KIF5B	43610331			10	INVERSION		11303967	315367	66946	26	NEW_VARIANT
P-0043817-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.1010+73:TMPRSS2_chr21:g.42836304del	IMPPRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 10 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		5576	0	15	21	Promoter of TMPRSS2(-):173bp from tx start	TMPRSS2	42836304			21	Intron of TMPRSS2(-):72bp after exon 9	TMPRSS2	42845179			0	DELETION		8875	316333	3750	15	NEW_VARIANT
P-0043823-T01-IM6	SFTA3 (NM_001101341) - NUF2 (NM_031423) rearrangement: t(1;14)(q23.3;q13.3)(chr1:g.163309186::chr14:g.36956644)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {SFTA3:NUF2}		0	0	5	14	Intron of SFTA3(-):4Kb after exon 2	SFTA3	36956644			1	Exon 8 of NUF2(+)	NUF2	163309186			10	TRANSLOCATION		0	316344	0	6	NEW_VARIANT
P-0043823-T01-IM6	NOTCH3 (NM_000435) rearrangement: t(12;19)(q14.3;p13.12)(chr12:g.66426103::chr19:g.15288174)	PRECISE	Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 24. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	24	19	Intron of NOTCH3(-):161bp after exon 24	NOTCH3	15288174			12	IGR: 9Kb before MIR6074(-)	NOTCH3	66426103			10	TRANSLOCATION		0	316345	0	24	NEW_VARIANT
P-0014310-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+6128:EML4_c.3172+783:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		86932	0	7	2	Intron of ALK(-):782bp after exon 19	EML4	29447544			2	Intron of EML4(+):6Kb after exon 5	ALK	42497999			10	INVERSION		13050455	317324	45484	34	NEW_VARIANT
P-0036062-T02-IM6	ARID1A (NM_006015) rearrangement: c.1631_c.2251+13del	PRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4519	0	65	1	Exon 3 of ARID1A(+)	ARID1A	27057923			1	Intron of ARID1A(+):13bp after exon 6	ARID1A	27087977			10	DELETION		30054	317358	2293	69	NEW_VARIANT
P-0044042-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-1681:EML4_c.3172+600:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		120971	0	28	2	Intron of ALK(-):599bp after exon 19	EML4	29447727			2	Intron of EML4(+):2Kb before exon 6	ALK	42506309			10	INVERSION		13058582	317416	101090	28	NEW_VARIANT
P-0044176-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.696:ZFHX3_chr16:g.72999556inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		5019	0	29	16	Exon 2 of ZFHX3(-)	ZFHX3	72993349			16	5-UTR of ZFHX3(-):178Kb before coding start	ZFHX3	72999556			10	INVERSION		6207	318204	4575	41	NEW_VARIANT
P-0013345-T02-IM6	YES1 (NM_005433) - PTPRM (NM_001105244) rearrangement: c.271+14:YES1_c.197-45137:PTPRMinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {YES1:PTPRM}		4653	0	11	18	Intron of YES1(-):13bp after exon 2	YES1	756543			18	Intron of PTPRM(+):45Kb before exon 3	PTPRM	7842967			10	INVERSION		7086424	318267	11361	12	NEW_VARIANT
P-0025146-T02-IM6	TCF3 (NM_001136139) rearrangement: c.1620:TCF3_chr19:g.1878693inv	PRECISE	Note: The TCF3 rearrangement is an inversion of exons 1 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		33222	0	4	19	Exon 17 of TCF3(-)	TCF3	1612399			19	Intron of ABHD17A(-):1Kb before exon 5	TCF3	1878693			10	INVERSION		266294	318356	41623	35	NEW_VARIANT
P-0044256-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+939:TMPRSS2_c.18+22179:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		35448	0	87	21	Intron of ERG(-):22Kb after exon 1	TMPRSS2	39848108			21	Intron of TMPRSS2(-):938bp after exon 2	ERG	42869107			10	DELETION		3020999	318679	35994	162	NEW_VARIANT
P-0044377-T01-IM6	TP53 (NM_000546) - TLK2 (NM_006852) rearrangement: c.672+231:TP53_c.81+1850:TLK2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TP53:TLK2}		747709	0	16	17	Intron of TP53(-):230bp after exon 6	TP53	7577946			17	Intron of TLK2(+):2Kb after exon 2	TLK2	60560417			10	INVERSION		52982471	319051	1404146	57	NEW_VARIANT
P-0044377-T01-IM6	PDCD1LG2 (NM_025239) rearrangement: c.816+148:PDCD1LG2_chr9:g.24818667inv	PRECISE	Note: The PDCD1LG2 rearrangement is an inversion of exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		75231	0	29	9	Intron of PDCD1LG2(+):148bp after exon 6	PDCD1LG2	5563359			9	IGR: 275Kb before IZUMO3(-)	PDCD1LG2	24818667			10	INVERSION		19255308	319050	78048	29	NEW_VARIANT
P-0005636-T03-IM6	PIK3CD (NM_005026) rearrangement: c.1470+79:PIK3CD_chr1:g.12569292del	PRECISE	Note: The PIK3CD rearrangement is a deletion of exons 12 - 24. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		101373	0	44	1	Intron of PIK3CD(+):79bp after exon 11	PIK3CD	9780379			1	3-UTR of VPS13D(+):275Kb after coding stop	PIK3CD	12569292			10	DELETION		2788913	319160	110721	46	NEW_VARIANT
P-0005636-T03-IM6	MTOR (NM_004958) rearrangement: t(1;15)(p36.22;q14)(chr1:g.11184865:chr15:g.37509514)	PRECISE	Note: The MTOR rearrangement is a translocation with a breakpoint in intron 46. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	15	IGR: 244Kb before MIR8063(-)	MTOR	37509514			1	Intron of MTOR(-):175bp before exon 47	MTOR	11184865			10	TRANSLOCATION		0	319164	0	7	NEW_VARIANT
P-0005636-T03-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4760:TMPRSS2_c.19-17111:ERGdel	PRECISE	The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		64768	0	74	21	Intron of ERG(-):17Kb before exon 2	TMPRSS2	39834655			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875117			10	DELETION		3040462	319161	44097	73	NEW_VARIANT
P-0036499-T03-IM6	NTRK1 (NM_002529) rearrangement: c.1174:NTRK1_chr1:g.201743980inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		158990	0	138	1	Exon 8 of NTRK1(+)	NTRK1	156843748			1	Intron of NAV1(+):6Kb before exon 2	NTRK1	201743980			0	INVERSION		44900232	319176	252401	138	NEW_VARIANT
P-0036499-T03-IM6	IRS2 (NM_003749) rearrangement: t(13;15)(q34;q21.3)(chr13:g.110436723::chr15:g.57613785)	PRECISE	Note: The IRS2 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	66	15	5-UTR of LINC01413(+):3Kb before coding start	IRS2	57613785			13	Exon 1 of IRS2(-)	IRS2	110436723			10	TRANSLOCATION		0	319177	0	70	NEW_VARIANT
P-0044414-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+4617:TMPRSS2_chr21:g.39982152del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		72610	0	11	21	3-UTR of ERG(-):52Kb after coding stop	TMPRSS2	39982152			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875260			10	DELETION		2893108	319099	35062	11	NEW_VARIANT
P-0044432-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2057-576:EML4_c.3155:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		95237	0	40	2	Exon 19 of ALK(-)	EML4	29448344			2	Intron of EML4(+):575bp before exon 18	ALK	42543991			10	INVERSION		13095647	319159	98476	38	NEW_VARIANT
P-0044470-T01-IM6	MAPKAP1 (NM_001006617) rearrangement: t(4;9)(p15.2;q33.3)(chr4:g.23486215::chr9:g.128230200)	PRECISE	Note: The MAPKAP1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	39	9	Intron of MAPKAP1(-):50bp after exon 10	MAPKAP1	128230200			4	IGR: 286Kb before MIR548AJ2(-)	MAPKAP1	23486215			10	TRANSLOCATION		0	319236	0	40	NEW_VARIANT
P-0044536-T01-IM6	NF1 (NM_001042492) rearrangement: c.2850+12:NF1_chr17:g.33639065inv	IMPPRECISE	Note: The NF1 rearrangement is an inversion of exons 22 - 58. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		70531	0	7	17	Intron of NF1(+):12bp after exon 21	NF1	29556495			17	IGR: 38Kb before SLFN11(-)	NF1	33639065			0	INVERSION		4082570	320123	80330	7	NEW_VARIANT
P-0024083-T02-IM6	INHA (NM_002191) rearrangement: c.1085:INHA_chr2:g.37386053inv	PRECISE	Note: The INHA rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {INHA:EIF2AK2}		803813	0	100	2	Promoter of EIF2AK2(-):54Kb from tx start	INHA	37386053			2	Exon 2 of INHA(+)	INHA	220440232			10	INVERSION		183054179	320203	1372241	99	NEW_VARIANT
P-0024083-T02-IM6	LAMA4 (NM_001105206) - ESR1 (NM_001122740) rearrangement: c.4982-618:LAMA4_c.453-83:ESR1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {LAMA4:ESR1}		281635	0	46	6	Intron of LAMA4(-):618bp before exon 36	LAMA4	112437814			6	Intron of ESR1(+):82bp before exon 3	ESR1	152163649			10	INVERSION		39725835	320204	439517	47	NEW_VARIANT
P-0044178-T01-IM6	FGFR3 (NM_000142) rearrangement: c.1265_c.1793inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		9131	0	2	4	Exon 9 of FGFR3(+)	FGFR3	1806246			4	Exon 13 of FGFR3(+)	FGFR3	1807624			7	INVERSION		1378	318238	4100	2	NEW_VARIANT
P-0020986-T01-IM6	PDGFRA (NM_006206) rearrangement: chr4:g.53132170_c.1238-110:PDGFRAdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24790	0	37	4	IGR: 215Kb before SPATA18(+)	PDGFRA	53132170			4	Intron of PDGFRA(+):109bp before exon 9	PDGFRA	55138451			10	DELETION		2006281	185948	50775	41	NEW_VARIANT
P-0021014-T01-IM6	KMT2C (NM_170606) rearrangement: c.9517+80_c.849+2148dup	PRECISE	Note: The KMT2C rearrangement is an intragenic duplication of exons 7-41. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 35 exons : out of frame		75594	0	9	7	Intron of KMT2C(-):79bp after exon 41	KMT2C	151866191			7	Intron of KMT2C(-):2Kb after exon 6	KMT2C	152004903			10	DUPLICATION		138712	186011	99862	9	NEW_VARIANT
P-0044916-T01-IM6	EZH2 (NM_004456) rearrangement: c.118-94:EZH2_chr7:g.148612082inv	PRECISE	Note: The EZH2 rearrangement is an inversion of exons 1 - 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1129	0	6	7	Intron of EZH2(-):94bp before exon 3	EZH2	148543784			7	IGR: 73Kb before GHET1(+)	EZH2	148612082			8	INVERSION		68298	320935	2190	6	NEW_VARIANT
P-0027245-T03-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.18+1582:ERG_c.56-2109:TMPRSS2inv	PRECISE	Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 2 - 14.	MANUAL_OK	3to3	3to3	-		51641	0	110	21	Intron of ERG(-):2Kb after exon 1	ERG	39868705			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872225			10	INVERSION		3003520	320682	80382	109	NEW_VARIANT
P-0039885-T02-IM6	BRIP1 (NM_032043) - DNMT1 (NM_001379) rearrangement: t(17;19)(q23.2;p13.2)(chr17:g.59886338::chr19:g.10288034)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {BRIP1:DNMT1}		0	0	77	19	Exon 5 of DNMT1(-)	BRIP1	10288034			17	Intron of BRIP1(-):220bp before exon 7	DNMT1	59886338			10	TRANSLOCATION		0	321132	0	80	NEW_VARIANT
P-0004339-T04-IM6	KMT2C (NM_170606) rearrangement: t(3;7)(q29;q36.1)(chr3:g.197675580::chr7:g.151860908)	PRECISE	Note: The KMT2C rearrangement is a translocation with a breakpoint in exon 43. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	25	7	Exon 43 of KMT2C(-)	KMT2C	151860908			3	5-UTR of IQCG(-):59Kb before coding start	KMT2C	197675580			10	TRANSLOCATION		0	321358	0	25	NEW_VARIANT
P-0005114-T03-IM6	MET (NM_000245) rearrangement: c.2888-8_c.3029-890del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		8451	0	90	7	Intron of MET(+):7bp before exon 14	MET	116411895			7	Intron of MET(+):889bp before exon 15	MET	116414045			10	DELETION		2150	295695	13180	96	NEW_VARIANT
P-0006365-T01-IM5	ATM (NM_000051) rearrangement: c.5178-47_c.5674+821dup	PRECISE	The ATM (NM_000051) rearrangement is an out of frame intragenic duplication of exons 35-37. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons: out of frame		3604	0	8	11	Intron of ATM(+): 47bp before exon 35	ATM	108172328			11	Intron of ATM(+): 821bp after exon 37	ATM	108176400			23	DUPLICATION		4072	91886	4052	8	NEW_VARIANT
P-0010011-T01-IM5	PAX8 (NM_003466) rearrangement: c.1088-2028_c.25+11587del	PRECISE	Note: The PAX8 rearrangement is a deletion of PAX8 exons 3-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons: out of frame		39049	0	19	2	Intron of PAX8(-): 2Kb before exon 10	PAX8	113986861			2	Intron of PAX8(-): 12Kb after exon 2	PAX8	114024360			33	DELETION		37499	137685	39138	18	NEW_VARIANT
P-0012008-T02-IM6	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)	IMPPRECISE	Note: The SDC4 - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	45	20	Intron of SDC4(-):371bp after exon 2	SDC4	43964050			6	Intron of ROS1(-):1Kb before exon 32	ROS1	117652099			0	TRANSLOCATION		0	252267	0	46	NEW_VARIANT
P-0032357-T01-IM6	IKZF3 (NM_01248) - ERBB2 (NM_004448) rearrangement: c.592+775:IKZF3_c.759+48inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {IKZF3:ERBB2}		32948	0	1001	17	Intron of ERBB2(+):48bp after exon 6	IKZF3	37866502			17	Intron of IKZF3(-):774bp after exon 5	ERBB2	37946894			10	INVERSION		80392	232833	1588854	2179	NEW_VARIANT
P-0032703-T01-IM6	TP53 (NM_000546) rearrangement: t(17;20)(p13.1;q13.13)(chr17:g.7579551::chr20:g.48334484)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in exon 4.	MANUAL_OK	5to3	5to3	-		0	0	31	20	IGR: 85Kb before B4GALT5(-)	TP53	48334484			17	Exon 4 of TP53(-)	TP53	7579551			10	TRANSLOCATION		0	234759	0	32	NEW_VARIANT
P-0033545-T04-IM6	SMAD3 (NM_005902) rearrangement: c.207-25590_c.719del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8697	0	47	15	Intron of SMAD3(+):26Kb before exon 2	SMAD3	67431643			15	Exon 6 of SMAD3(+)	SMAD3	67473639			10	DELETION		41996	284218	5745	51	NEW_VARIANT
P-0034876-T01-IM6	DICER1 (NM_030621) rearrangement: c.4207-1271_c.4231del	PRECISE	Note: The DICER1 rearrangement results in the deletion of exon 25. One of the breakpoints is within exon 25. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		292	0	2	14	Exon 25 of DICER1(-)	DICER1	95563026			14	Intron of DICER1(-):1Kb before exon 25	DICER1	95564321			5	DELETION		1295	254518	193	2	NEW_VARIANT
P-0034876-T01-IM6	PAXBP1 (NM_016631) - TMPRSS2 (NM_001135099) rearrangement: c.649+322:PAXBP1_c.127-629:TMPRSS2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PAXBP1:TMPRSS2}		64091	0	4	21	Intron of PAXBP1(-):321bp after exon 3	PAXBP1	34136337			21	Intron of TMPRSS2(-):629bp before exon 3	TMPRSS2	42867134			10	DUPLICATION		8730797	254520	50637	5	NEW_VARIANT
P-0036013-T01-IM6	RIT1 (NM_006912) Rearrangement : c.474:RIT1_c.1632-961:ARHGEF2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		7708	0	110	1	Exon 6 of RIT1(-)	RIT1	155870365			1	Intron of ARHGEF2(-):961bp before exon 14	RIT1	155925721			10	INVERSION		55356	263412	16485	115	NEW_VARIANT
P-0036013-T01-IM6	PBRM1 (NM_018313) Rearrangement :  c.-141:NT5DC2_c.1924+202:PBRMinv	PRECISE	Note: The PBRM1 Rearrangement results in the inversion of exons 17-30 of PBRM1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		31186	0	5	3	5-UTR of NT5DC2(-):10Kb before coding start	PBRM1	52568810			3	Intron of PBRM1(-):201bp after exon 16	PBRM1	52649165			10	INVERSION		80355	263413	58301	5	NEW_VARIANT
P-0036013-T01-IM6	AMER1 (NM_152424)  Rearrangement : chrX:g.63280801_c.950del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		22994	0	3	X	IGR: 124Kb before AMER1(-)	AMER1	63280801			X	Exon 2 of AMER1(-)	AMER1	63412217			10	DELETION		131416	263411	27400	6	NEW_VARIANT
P-0036233-T01-IM6	PREX2 (NM_024870) Rearrangement: c.1093+73:PREX2_chr8:g.69483080inv	IMPPRECISE	Note: The PREX2 rearrangement is an inversion with the breakpoint in intron 9 of PREX2. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		47162	0	9	8	Intron of PREX2(+):73bp after exon 9	PREX2	68965554			8	Intron of C8orf34(+):38Kb after exon 7	PREX2	69483080			0	INVERSION		517526	266427	86897	9	NEW_VARIANT
P-0036302-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon2 fused with ERG exon4) : c.40-59382:TMPRSS2_c.127-1153:ERGdel	PRECISE	Note: The TMPRSS2 -ERG Fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		24232	0	31	21	Intron of ERG(-):59Kb before exon 4	TMPRSS2	39876926			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867658			10	DELETION		2990732	267254	19819	31	NEW_VARIANT
P-0037070-T01-IM6	IGF2 (NM_001127598) rearrangement: c.69:IGF2_chr11:g.121451136del	PRECISE	Note: The IGF2 rearrangement is a deletion of exons 1-2. One of the breakpoints is within exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		582317	0	51	11	Exon 2 of IGF2(-)	IGF2	2161458			11	Intron of SORL1(+):3Kb after exon 25	IGF2	121451136			10	DELETION		119289678	276136	452664	58	NEW_VARIANT
P-0037291-T01-IM6	DNAJB1 (NM_006145) - PRKACA (NM_002730) fusion (DNAJB1 exon 1 fused to PRKACA exons 2-10): c.212-523:DNAJB1_ c.46+3770:PRKACAdel	PRECISE	Note: The DNAJB1 - PRKACA fusion is predicted to be in frame and includes the kinase domain of PRKACA	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {DNAJB1:PRKACA}		13875	0	8	19	Intron of PRKACA(-):401bp after exon 1	DNAJB1	14224544			19	Intron of DNAJB1(-):523bp before exon 2	PRKACA	14628381			10	DELETION		403837	277436	7494	9	NEW_VARIANT
P-0037293-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1238:TMPRSS2_c.40-57682:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		61137	0	137	21	Intron of ERG(-):58Kb before exon 4	TMPRSS2	39875226			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871354			10	INVERSION		2996128	277443	71525	133	NEW_VARIANT
P-0037369-T01-IM6	NAV1 (NM_020443) - ELF3 (NM_004433) rearrangement: c.758-744:NAV1_c.806-120:ELF3del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {NAV1:ELF3}		10793	0	12	1	Intron of NAV1(+):743bp before exon 2	NAV1	201681201			1	Intron of ELF3(+):119bp before exon 8	ELF3	201982837			0	DELETION		301636	278509	15147	12	NEW_VARIANT
P-0037462-T01-IM6	WNT1 (NM_005430) - KMT2D (NM_003482) rearrangement: c.625-20:WNT1_c.5989:KMT2Dinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {WNT1:KMT2D}		79110	0	50	12	Intron of WNT1(+):19bp before exon 4	WNT1	49374915			12	Exon 28 of KMT2D(-)	KMT2D	49435992			10	INVERSION		61077	279031	79402	49	NEW_VARIANT
P-0037462-T01-IM6	PBRM1 (NM_018313) rearrangement: c.1613_1925-1558dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2782	0	30	3	Intron of PBRM1(-):2Kb before exon 17	PBRM1	52645529			3	Exon 15 of PBRM1(-)	PBRM1	52651483			10	DUPLICATION		5954	279030	3391	30	NEW_VARIANT
P-0037478-T01-IM6	ABL1 (NM_005157) -PIP5K1B(NM_003558) Rearrangement : c.2716:ABL1_c.454:PIP5K1Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ABL1:PIP5K1B}		287483	0	36	9	Exon 7 of PIP5K1B(+)	ABL1	71504032			9	Exon 11 of ABL1(+)	PIP5K1B	133760393			10	DUPLICATION		62256361	279339	345602	37	NEW_VARIANT
P-0037484-T01-IM6	LMLN (NM_001136049) - TSC2 (NM_000548) Rearrangement : t(3,16)(q29; p13.3) (chr3:g.197695630::chr16:g.2121541)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LMLN:TSC2}		0	0	77	16	Exon 18 of TSC2(+)	LMLN	2121541			3	Intron of LMLN(+):6Kb before exon 2	TSC2	197695630			10	TRANSLOCATION		0	279267	0	82	NEW_VARIANT
P-0037484-T01-IM6	UPF1 (NM_002911) Rearrangement : c.372-593_c.810+133dup	PRECISE	Note: The UPF1 Rearrangement results in the intragenic duplication of exons3-5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		4718	0	41	19	Intron of UPF1(+):592bp before exon 3	UPF1	18957960			19	Intron of UPF1(+):133bp after exon 5	UPF1	18961810			10	DUPLICATION		3850	279266	10708	43	NEW_VARIANT
P-0037620-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+982:TMPRSS2_c.236+9086:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves exons TMPRSS2 exons 1-2 and ERG exons 3-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		28486	0	3	21	Intron of ERG(-):9Kb after exon 2	TMPRSS2	39808241			21	Intron of TMPRSS2(-):981bp after exon 2	ERG	42869064			6	DELETION		3060823	280725	46858	3	NEW_VARIANT
P-0037810-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.107-17501_c.621+33dup	PRECISE	Note: The PIK3R3 rearrangement is a duplication of exons 2-5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : out of frame		4068	0	27	1	Intron of PIK3R3(-):32bp after exon 5	PIK3R3	46531693			1	Intron of PIK3R3(-):18Kb before exon 2	PIK3R3	46563923			10	DUPLICATION		32230	281967	6915	27	NEW_VARIANT
P-0037891-T01-IM6	MAP3K13 (NM_004721) - IGF1R (NM_000875) rearrangement: t(3,15)(q27.2;q26.3)(chr3:g.185040460::chr15:g.99500351)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MAP3K13:IGF1R}		0	0	32	15	Exon 21 of IGF1R(+)	MAP3K13	99500351			3	Intron of MAP3K13(+):37Kb after exon 2	IGF1R	185040460			10	TRANSLOCATION		0	282534	0	33	NEW_VARIANT
P-0037904-T01-IM6	IRS1 (NM_005544) rearrangement: c.648:IRS1_chr2:g.227329627dup	PRECISE	Note: The IRS1 rearrangement results in the duplication of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		18000	0	4	2	IGR: 194Kb before MIR5702(-)	IRS1	227329627			2	Exon 1 of IRS1(-)	IRS1	227662807			9	DUPLICATION		333180	282685	21555	5	NEW_VARIANT
P-0037909-T01-IM6	RTEL1 (NM_032957) rearrangement: c.3724+83:RTEL1_chr20:g.62425706del	PRECISE	Note: The RTEL1 rearrangement results in the deletion of exon 35. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		2559	0	5	20	Intron of RTEL1(+):83bp after exon 34	RTEL1	62326916			20	5-UTR of ZBTB46(-):47Kb before coding start	RTEL1	62425706			10	DELETION		98790	282688	2522	5	NEW_VARIANT
P-0037909-T01-IM6	STAG2 (NM_001042749) rearrangement: c.-163+13306_c.44+20inv	PRECISE	Note: The STAG2 rearrangement results in the inversion of exons 1-3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		332	0	3	X	5-UTR of STAG2(+):48Kb before coding start	STAG2	123108022			X	Intron of STAG2(+):20bp after exon 3	STAG2	123156541			5	INVERSION		48519	282689	224	3	NEW_VARIANT
P-0037919-T01-IM6	PTPRT (NM_133170) rearrangement: c.4329+44:PTPRT_chr20:g.34150608del	PRECISE	Note: The PTPRT rearrangement is a deletion of of exon 32.	MANUAL_OK	3to5	3to5	-		52791	0	3	20	3-UTR of FER1L4(-):45Kb after coding stop	PTPRT	34150608			20	Intron of PTPRT(-):43bp after exon 31	PTPRT	40710478			7	DELETION		6559870	282751	53990	3	NEW_VARIANT
P-0037920-T01-IM6	HLA-DMB (NM_002118) - TAP1 (NM_000593) rearrangement: c.622+404:HLA-DMB_c.1884:TAP1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {HLA-DMB:TAP1}		24823	0	4	6	Exon 8 of TAP1(-)	HLA	32815732			6	Intron of HLA-DMB(-):403bp after exon 3	DMB	32904545			10	DELETION		88813	282748	35913	4	NEW_VARIANT
P-0037962-T01-IM6	NEGR1 (NM_173808) rearrangement: c.177-153640_c.410-89del	PRECISE	Note: The NEGR1 rearrangement is an intragenic deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1787	0	6	1	Intron of NEGR1(-):89bp before exon 3	NEGR1	72242069			1	Intron of NEGR1(-):154Kb before exon 2	NEGR1	72554634			10	DELETION		312565	283053	2304	6	NEW_VARIANT
P-0038253-T01-IM6	FGFR3 (NM_000142)  -TACC3( NM_006342) Fusion (FGFR3 exon18 fused with TACC3 exon8) : c.2284:FGFR3_c.1644+106:TACC3dup	PRECISE	Note: The FGFR3-TACC3 Fusion includes the protein kinase domain of FGFR3 and the breakpoint in FGFR3 is within exon18.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		34652	0	60	4	Intron of TACC3(+):106bp after exon 7	FGFR3	1737158			4	Exon 18 of FGFR3(+)	TACC3	1808852			10	DUPLICATION		71694	285431	47513	61	NEW_VARIANT
P-0039172-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.5762:NOTCH2_chr1:g.120336534del	PRECISE	Note : The NOTCH2 rearrangement is a deletion of exons 31 - 34. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NOTCH2:REG4}		12342	0	3	1	Promoter of REG4(-):106bp from tx start	NOTCH2	120336534			1	Exon 31 of NOTCH2(-)	NOTCH2	120461954			6	DELETION		125420	293922	17401	3	NEW_VARIANT
P-0039227-T01-IM6	RB1 (NM_000321) rearrangement: c.1388_c.1695+10356del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 17. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1480	0	82	13	Exon 14 of RB1(+)	RB1	48953785			13	Intron of RB1(+):10Kb after exon 17	RB1	48965935			10	DELETION		12150	294363	450	90	NEW_VARIANT
P-0039289-T01-IM6	NDE1 (NM_017668) - BLM (NM_000057) rearrangement: t(15;16)(q26.1;p13.11)(chr15:g.91310060::chr16:g.15795773)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {NDE1:BLM}		0	0	23	16	Intron of NDE1(+):5Kb after exon 9	NDE1	15795773			15	Intron of BLM(+):79bp before exon 10	BLM	91310060			10	TRANSLOCATION		0	295493	0	23	NEW_VARIANT
P-0039752-T01-IM6	FAT1 (NM_005245) rearrangement: c.3265+12120_c.7874del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23962	0	20	4	Exon 10 of FAT1(-)	FAT1	187539866			4	Intron of FAT1(-):12Kb after exon 2	FAT1	187615597			10	DELETION		75731	298080	15844	21	NEW_VARIANT
P-0039935-T01-IM6	MEF2B (NM_001145785) rearrangement: c.1079:MEF2B_chr19:g.19253625dup	PRECISE	Note: The MEF2B rearrangement is a duplication of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		749	0	5	19	Promoter of MEF2B(-):3Kb from tx start	MEF2B	19253625			19	Exon 9 of MEF2B(-)	MEF2B	19256634			10	DUPLICATION		3009	298745	594	7	NEW_VARIANT
P-0039965-T01-IM6	MGAT4A (NM_012214) - INPP4A (NM_001134224) rearrangement: c.1469-2119:MGAT4A_c.2622:INPP4Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {MGAT4A:INPP4A}		5392	0	38	2	Exon 24 of INPP4A(+)	MGAT4A	99189366			2	Intron of MGAT4A(-):2Kb before exon 12	INPP4A	99244417			10	INVERSION		55051	299176	40544	56	NEW_VARIANT
P-0040084-T01-IM6	UBE2W (NM_001001481) - TEK (NM_000459) rearrangement: t(8;9)(q21.11;p21.2)(chr8:g.74735893::chr9:g.27180309)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {UBE2W:TEK}		0	0	54	9	Exon 7 of TEK(+)	UBE2W	27180309			8	Intron of UBE2W(-):1Kb after exon 3	TEK	74735893			10	TRANSLOCATION		0	300300	0	60	NEW_VARIANT
P-0040154-T01-IM6	TSC2 (NM_000548) rearrangement: c.225+60_c.4849+25dup	PRECISE	Note: The TSC2 rearrangement is an intragenic duplication of exons 4 - 37. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 34 exons : out of frame		54331	0	2	16	Intron of TSC2(+):60bp after exon 3	TSC2	2100547			16	Intron of TSC2(+):25bp after exon 37	TSC2	2136405			8	DUPLICATION		35858	300445	46510	2	NEW_VARIANT
P-0040281-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.483-5377_c.1153-69del	PRECISE	Note: The MAP3K1 rearrangement is an intragenic deletion of exons 2 - 5. The rearrangement does not include the kinase domain of MAP3K1.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		5232	0	7	5	Intron of MAP3K1(+):5Kb before exon 2	MAP3K1	56147050			5	Intron of MAP3K1(+):68bp before exon 6	MAP3K1	56161587			10	DELETION		14537	300881	5204	14	NEW_VARIANT
P-0040335-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.557-1097:TMPRSS2_c.40-52915:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		14868	0	7	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39870459			21	Intron of TMPRSS2(-):1Kb before exon 6	ERG	42853626			10	DELETION		2983167	301283	15625	7	NEW_VARIANT
P-0040461-T01-IM6	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140488218::chr12:g.122833264)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CLIP1:BRAF}		0	0	9	12	Intron of CLIP1(-):1Kb before exon 9	CLIP1	122833264			7	Intron of BRAF(-):834bp before exon 9	BRAF	140488218			10	TRANSLOCATION		0	301776	0	9	NEW_VARIANT
P-0040618-T01-IM6	MALT1 (NM_006785) rearrangement: c.1604-3055_c.2343del	PRECISE	Note: The MALT1 rearrangement is an intragenic deletion of exons 14 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4703	0	4	18	Intron of MALT1(+):3Kb before exon 14	MALT1	56406042			18	Exon 17 of MALT1(+)	MALT1	56414942			8	DELETION		8900	302679	3712	4	NEW_VARIANT
P-0040618-T01-IM6	THSD4 (NM_024817) - EWSR1 (NM_013986) rearrangement: t(15;22)(q23;q12.2)(chr15:g.71660057::chr22:g.29684202)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {THSD4:EWSR1}		0	0	13	22	Intron of EWSR1(+):392bp before exon 9	THSD4	29684202			15	Intron of THSD4(+):44Kb before exon 6	EWSR1	71660057			10	TRANSLOCATION		0	302680	0	16	NEW_VARIANT
P-0040855-T01-IM6	BCL2L14 (NM_138723) - ETV6 (NM_001987) rearrangement: c.434-2555:BCL2L14_c.1009+5088:ETV6dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {BCL2L14:ETV6}		61512	0	34	12	Intron of ETV6(+):5Kb after exon 5	BCL2L14	12027991			12	Intron of BCL2L14(+):3Kb before exon 3	ETV6	12237592			10	DUPLICATION		209601	304036	95411	34	NEW_VARIANT
P-0041285-T01-IM6	BRCA1 (NM_007294) rearrangement: c.441+1741_c.3289del	PRECISE	Note: The BRCA1 rearrangement is an intragenic deletion of exons 7 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		24166	0	21	17	Exon 10 of BRCA1(-)	BRCA1	41244259			17	Intron of BRCA1(-):2Kb after exon 6	BRCA1	41254398			10	DELETION		10139	306294	20915	32	NEW_VARIANT
P-0041285-T01-IM6	BRCA1 (NM_007294) rearrangement: c.547+430_c.1093del	PRECISE	Note: The BRCA1 rearrangement is an intragenic deletion of exons 8 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5569	0	11	17	Exon 10 of BRCA1(-)	BRCA1	41246455			17	Intron of BRCA1(-):429bp after exon 7	BRCA1	41251362			10	DELETION		4907	306295	4330	14	NEW_VARIANT
P-0041345-T01-IM6	EP300 (NM_001429) - GUCD1 (NM_031444) rearrangement: c.6779:EP300_c.128+261:GUCD1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EP300:GUCD1}		167103	0	16	22	Intron of GUCD1(-):260bp after exon 2	EP300	24944624			22	Exon 31 of EP300(+)	GUCD1	41574494			10	INVERSION		16629870	306400	225051	16	NEW_VARIANT
P-0041659-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1474:TMPRSS2_c.40-62694:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32103	0	52	21	Intron of ERG(-):63Kb before exon 4	TMPRSS2	39880238			21	Intron of TMPRSS2(-):1Kb after exon 2	ERG	42868572			10	DELETION		2988334	307239	23423	54	NEW_VARIANT
P-0042153-T01-IM6	KIF13A (NM_022113) - RET (NM_020975) fusion: t(6;10)(p22.3;q11.21)(chr6:g.17806558::chr10:g.43610510)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF13A:RET}		0	0	415	10	Intron of RET(+):326bp after exon 11	KIF13A	43610510			6	Intron of KIF13A(-):712bp before exon 19	RET	17806558			10	TRANSLOCATION		0	308219	0	669	NEW_VARIANT
P-0042153-T01-IM6	BRCA1 (NM_007294) rearrangement: t(9;17)(q34.3;q21.31)(chr9:g.140583654::chr17:g.41244909)	PRECISE	Note: The BRCA1 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	6	17	Exon 10 of BRCA1(-)	BRCA1	41244909			9	Intron of EHMT1(+):22Kb before exon 2	BRCA1	140583654			6	TRANSLOCATION		0	308220	0	6	NEW_VARIANT
P-0043229-T01-IM6	FAT1 (NM_005245) rearrangement: c.3266-11620_c.3704del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 3 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3068	0	8	4	Exon 5 of FAT1(-)	FAT1	187558007			4	Intron of FAT1(-):12Kb before exon 3	FAT1	187596387			10	DELETION		38380	313664	3219	8	NEW_VARIANT
P-0043229-T01-IM6	PTPRD (NM_002839) rearrangement: c.352+36549_c.2926del	PRECISE	Note: The PTPRD rearrangement is an intragenic deletion of exons 15 - 28. One of the breakpoints is within exon 28.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		20937	0	4	9	Exon 28 of PTPRD(-)	PTPRD	8485891			9	Intron of PTPRD(-):37Kb after exon 14	PTPRD	8596768			6	DELETION		110877	313665	29806	5	NEW_VARIANT
P-0043240-T01-IM6	RASA1 (NM_002890) rearrangement: c.137:RASA1_chr5:g.86555625del	PRECISE	Note: The RASA1 rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	-		1148	0	53	5	IGR: 8Kb before RASA1(+)	RASA1	86555625			5	Exon 1 of RASA1(+)	RASA1	86564405			10	DELETION		8780	313689	323	59	NEW_VARIANT
P-0043241-T01-IM6	ID3 (NM_002167) rearrangement: c.300+17:ID3_chr1:g.38197642inv	PRECISE	Note: The ID3 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		140284	0	39	1	Intron of ID3(-):16bp after exon 1	ID3	23885601			1	Intron of EPHA10(-):388bp before exon 7	ID3	38197642			10	INVERSION		14312041	313614	344831	39	NEW_VARIANT
P-0043241-T01-IM6	GNL2 (NM_013285) - MAPK1 (NM_002745) rearrangement: t(1;22)(p34.3;q11.21)(chr1:g.38056295::chr22:g.22143180)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {GNL2:MAPK1}		0	0	7	22	Intron of MAPK1(-):83bp before exon 5	GNL2	22143180			1	Intron of GNL2(-):11bp after exon 4	MAPK1	38056295			0	TRANSLOCATION		0	313618	0	7	NEW_VARIANT
P-0043241-T01-IM6	CCDC171 (NM_173550) - PTPRD (NM_002839) rearrangement: c.352+5531:CCDC171_c.3876-4804:PTPRDinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {CCDC171:PTPRD}		33157	0	5	9	Intron of PTPRD(-):5Kb before exon 34	CCDC171	8454641			9	Intron of CCDC171(+):6Kb after exon 4	PTPRD	15584552			0	INVERSION		7129911	313615	15167	5	NEW_VARIANT
P-0043567-T01-IM6	NCOR1 (NM_006311) rearrangement: t(16;17)(q21;p11.2)(chr16:g.59600624::chr17:g.16041505)	PRECISE	Note: The NCOR1 rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	17	Exon 13 of NCOR1(-)	NCOR1	16041505			16	IGR: 187Kb before APOOP5(-)	NCOR1	59600624			10	TRANSLOCATION		0	314943	0	6	NEW_VARIANT
P-0043581-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-686:TMPRSS2_c.39+8942:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		26663	0	10	21	Intron of ERG(-):9Kb after exon 3	TMPRSS2	39938644			21	Intron of TMPRSS2(-):686bp before exon 3	ERG	42867191			10	DELETION		2928547	314995	21060	10	NEW_VARIANT
P-0045030-T01-IM6	KMT2B (NM_014727) rearrangement: c.4810_c.5252del	PRECISE	Note: The KMT2B rearrangement is an intragenic deletion of exons 22 - 25. The breakpoints are within exon 22 and exon 25.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4729	0	6	19	Exon 22 of KMT2B(+)	KMT2B	36220090			19	Exon 25 of KMT2B(+)	KMT2B	36221493			8	DELETION		1403	321367	7969	6	NEW_VARIANT
P-0045030-T01-IM6	PTPRT (NM_133170) rearrangement: c.2176+75:PTPRT_chr20:g.53084718inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		49961	0	19	20	Intron of PTPRT(-):74bp after exon 13	PTPRT	40911054			20	IGR: 7Kb before DOK5(+)	PTPRT	53084718			0	INVERSION		12173664	321370	108720	22	NEW_VARIANT
P-0045030-T01-IM6	CARD11 (NM_032415) rearrangement: t(3;7)(q13.12;p22.2)(chr3:g.106730609::chr7:g.2959073)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	9	7	Exon 18 of CARD11(-)	CARD11	2959073			3	IGR: 98Kb before LINC00882(-)	CARD11	106730609			8	TRANSLOCATION		0	321372	0	9	NEW_VARIANT
P-0045031-T01-IM6	IKBKE (NM_014002) rearrangement: c.88-463_c.1155del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12179	0	6	1	Intron of IKBKE(+):462bp before exon 4	IKBKE	206647211			1	Exon 10 of IKBKE(+)	IKBKE	206652448			10	DELETION		5237	321362	17821	6	NEW_VARIANT
P-0045032-T01-IM6	AMPH (NM_001635) - KMT2C (NM_170606) rearrangement: c.1398+5667:AMPH_c.9907:KMT2Cdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {AMPH:KMT2C}		430330	0	6	7	Intron of AMPH(-):10Kb after exon 16	AMPH	38451758			7	Exon 43 of KMT2C(-)	KMT2C	151860755			10	DUPLICATION		113408997	321377	256129	7	NEW_VARIANT
P-0045039-T01-IM6	TMPRSS2 (NM_001135099) - SH3GL3 (NM_003027) rearrangement: t(15;21)(q25.2;q22.3)(chr15:g.84263952::chr21:g.42872075)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TMPRSS2:SH3GL3}		0	0	17	21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872075			15	Intron of SH3GL3(+):6Kb after exon 11	SH3GL3	84263952			10	TRANSLOCATION		0	321351	0	17	NEW_VARIANT
P-0045042-T01-IM6	TSC2 (NM_000548) rearrangement: c.1840-60:TSC2_chr16:g.2052248del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		34979	0	6	16	Exon 7 of ZNF598(-)	TSC2	2052248			16	Intron of TSC2(+):59bp before exon 18	TSC2	2121451			5	DELETION		69203	321353	18780	7	NEW_VARIANT
P-0045047-T01-IM6	SHOC2 (NM_007373) rearrangement: c.779:SHOC2_chr10:g.104144408del	PRECISE	Note: The SHOC2 rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GBF1:SHOC2}		26961	0	11	10	Promoter of GBF1(+):139Kb from tx start	SHOC2	104144408			10	Exon 3 of SHOC2(+)	SHOC2	112745461			10	DELETION		8601053	321355	37679	12	NEW_VARIANT
P-0045047-T01-IM6	SHOC2 (NM_007373) rearrangement: t(6;10)(q23.2;q25.2)(chr6:g.132792537::chr10:g.112745448)	PRECISE	Note: The SHOC2 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	10	10	Exon 3 of SHOC2(+)	SHOC2	112745448			6	Intron of STX7(-):64bp after exon 5	SHOC2	132792537			10	TRANSLOCATION		0	321357	0	10	NEW_VARIANT
P-0045047-T01-IM6	ALOX12B (NM_001139) rearrangement: c.1384_c.1654+804dup	PRECISE	Note: The ALOX12B rearrangement is an intragenic duplication of exons 11 - 12. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2259	0	8	17	Intron of ALOX12B(-):803bp after exon 12	ALOX12B	7978109			17	Exon 11 of ALOX12B(-)	ALOX12B	7979641			10	DUPLICATION		1532	321356	3078	8	NEW_VARIANT
P-0045096-T01-IM6	GATA1 (NM_002049) - HDAC6 (NM_006044) rearrangement: c.61:GATA1_c.807-307:HDAC6del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GATA1:HDAC6}		11762	0	4	X	Exon 2 of GATA1(+)	GATA1	48649577			X	Intron of HDAC6(+):306bp before exon 11	HDAC6	48672540			6	DELETION		22963	321542	4170	4	NEW_VARIANT
P-0045101-T01-IM6	SF3B1 (NM_012433) rearrangement: c.904+126:SF3B1_chr2:g.196075812inv	PRECISE	Note: The SF3B1 rearrangement is an inversion of exons 8 - 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		22648	0	34	2	IGR: 446Kb before SLC39A10(+)	SF3B1	196075812			2	Intron of SF3B1(-):125bp after exon 7	SF3B1	198274368			10	INVERSION		2198556	321549	45453	36	NEW_VARIANT
P-0045101-T01-IM6	FANCC (NM_000136) rearrangement: c.30:FANCC_chr9:g.98021717inv	IMPPRECISE	Note: The FANCC rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		354	0	11	9	Exon 2 of FANCC(-)	FANCC	98011544			9	5-UTR of FANCC(-):158Kb before coding start	FANCC	98021717			0	INVERSION		10173	321550	564	18	NEW_VARIANT
P-0045124-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.1252:MAP3K1_chr5:g.53706086del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {LINC01033:MAP3K1}		6340	0	6	5	5-UTR of LINC01033(+):5Kb before coding start	MAP3K1	53706086			5	Exon 6 of MAP3K1(+)	MAP3K1	56161755			5	DELETION		2455669	321835	11679	6	NEW_VARIANT
P-0044943-T02-IM6	ARID1A (NM_006015) rearrangement: c.1471:ARID1A_chr1:g.27198047del	PRECISE	Note: The ARID1A rearrangement is a deletion of exons 3 - 20. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	-		50467	0	18	1	Exon 3 of ARID1A(+)	ARID1A	27057763			1	IGR: 8Kb before GPN2(-)	ARID1A	27198047			10	DELETION		140284	322111	44013	20	NEW_VARIANT
P-0045019-T02-IM6	CDKN2B (NM_004936) - CDKN2A (NM_058195) rearrangement: c.338:CDKN2B_c.303:CDKN2Adel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDKN2B:CDKN2A}		8289	0	39	9	Exon 2 of CDKN2A(-)	CDKN2B	21971098			9	Exon 2 of CDKN2B(-)	CDKN2A	22006065			0	DELETION		34967	321858	5500	46	NEW_VARIANT
P-0045104-T01-IM6	SETD2 (NM_014159) rearrangement: t(3;12)(p21.31;p13.33)(chr3:g.47098917::chr12:g.1531949)	PRECISE	Note: The SETD2 rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	8	12	Intron of ERC1(+):15Kb after exon 16	SETD2	1531949			3	Exon 15 of SETD2(-)	SETD2	47098917			10	TRANSLOCATION		0	321803	0	8	NEW_VARIANT
P-0045139-T01-IM6	KMT2B (NM_014727) rearrangement: c.264:KMT2B_chr19:g.36206971del	PRECISE	Note: The KMT2B rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		168	0	4	19	Promoter of KMT2B(+):2Kb from tx start	KMT2B	36206971			19	Exon 1 of KMT2B(+)	KMT2B	36209184			10	DELETION		2213	321861	234	4	NEW_VARIANT
P-0045141-T01-IM6	BRAF (NM_004333) rearrangement: c.1177+527:BRAF_chr7:g.140421701dup	PRECISE	Note: The BRAF rearrangement is a duplication of exons 10 - 18. The rearrangement includes the kinase domain of BRAF. Functional significance is undetermined .	MANUAL_OK	5to3	5to3	-		26618	0	14	7	IGR: 12Kb before BRAF(-)	BRAF	140421701			7	Intron of BRAF(-):526bp after exon 9	BRAF	140486821			10	DUPLICATION		65120	321869	36476	15	NEW_VARIANT
P-0045146-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon2 fused with ERG exon2): c.126+343:TMPRSS2_c.18+8891:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32286	0	223	21	Intron of ERG(-):9Kb after exon 1	TMPRSS2	39861396			21	Intron of TMPRSS2(-):342bp after exon 2	ERG	42869703			10	DELETION		3008307	321867	55590	337	NEW_VARIANT
P-0045153-T01-IM6	BABAM1 (NM_001033549) rearrangement: c.341:BABAM1_chr19:g.8834399inv	PRECISE	Note: The BABAM1 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		369489	0	7	19	IGR: 7Kb before OR2Z1(+)	BABAM1	8834399			19	Exon 3 of BABAM1(+)	BABAM1	17382461			10	INVERSION		8548062	321925	485944	8	NEW_VARIANT
P-0045153-T01-IM6	PARK2 (NM_004562) rearrangement: c.8-27690_c.65del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		577	0	3	6	Exon 2 of PARK2(-)	PARK2	162864448			6	Intron of PARK2(-):28Kb before exon 2	PARK2	162892195			10	DELETION		27747	321923	630	4	NEW_VARIANT
P-0045156-T01-IM6	ARID1A (NM_006015) rearrangement: c.742:ARID1A_chr1:g.27021996del	PRECISE	Note: The ARID1A rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2625	0	142	1	Promoter of ARID1A(+):525bp from tx start	ARID1A	27021996			1	Exon 1 of ARID1A(+)	ARID1A	27023636			10	DELETION		1640	321918	138	159	NEW_VARIANT
P-0045158-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4406:TMPRSS2_c.39+51706:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		59905	0	14	21	Intron of ERG(-):52Kb after exon 3	TMPRSS2	39895880			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874522			10	DELETION		2978642	321911	35648	15	NEW_VARIANT
P-0045158-T01-IM6	SYN3 (NM_003490) - RAC2 (NM_002872) rearrangement: c.712-9002:SYN3_c.108-27:RAC2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SYN3:RAC2}		11073	0	3	22	Intron of SYN3(-):9Kb before exon 6	SYN3	33001724			22	Intron of RAC2(-):27bp before exon 3	RAC2	37628985			10	DUPLICATION		4627261	321914	8780	3	NEW_VARIANT
P-0045158-T01-IM6	RICTOR (NM_152756) rearrangement: t(3;5)(q26.33;p13.1)(chr3:g.182061807::chr5:g.39074350)	PRECISE	Note: The RICTOR rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	5	Intron of RICTOR(-):80bp after exon 1	RICTOR	39074350			3	IGR: 103Kb before FLJ46066(-)	RICTOR	182061807			10	TRANSLOCATION		0	321916	0	9	NEW_VARIANT
P-0045181-T01-IM6	SHQ1 (NM_018130) rearrangement: c.1182-15003:SHQ1_chr3:g.89156692inv	PRECISE	Note: The SHQ1 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {SHQ1:EPHA3}		25212	0	9	3	Intron of SHQ1(-):15Kb before exon 11	SHQ1	72814990			3	5-UTR of EPHA3(+):206bp before coding start	SHQ1	89156692			10	INVERSION		16341702	321966	32483	9	NEW_VARIANT
P-0045185-T01-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-479:FGFR2_c.8128-2249:TACC2inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:TACC2}		52335	0	12	10	Intron of FGFR2(-):479bp before exon 18	FGFR2	123240014			10	Intron of TACC2(+):2Kb before exon 14	TACC2	123994661			0	INVERSION		754647	321962	326624	19	NEW_VARIANT
P-0045188-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.1208+177_c.2003+2920del	PRECISE	Note: The PIK3C2G rearrangement is an intragenic deletion of exons 8 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : in frame		7884	0	3	12	Intron of PIK3C2G(+):177bp after exon 7	PIK3C2G	18474143			12	Intron of PIK3C2G(+):3Kb after exon 14	PIK3C2G	18547106			9	DELETION		72963	321960	8054	3	NEW_VARIANT
P-0045188-T01-IM6	CREBBP (NM_004380) rearrangement: t(16;X)(p13.3;p22.12)(chr16:g.3843591::chrX:g.19329205)	PRECISE	Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	X	IGR: 33Kb before PDHA1(+)	CREBBP	19329205			16	Exon 4 of CREBBP(-)	CREBBP	3843591			9	TRANSLOCATION		0	321961	0	6	NEW_VARIANT
P-0045189-T01-IM6	AXL (NM_021913) rearrangement: c.125:AXL_chr19:g.42248893del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		41775	0	25	19	Exon 2 of AXL(+)	AXL	41726580			19	IGR: 11Kb before CEACAM6(+)	AXL	42248893			10	DELETION		522313	321956	53254	26	NEW_VARIANT
P-0045189-T01-IM6	MSH6 (NM_000179) rearrangement: c.261-1982_c.587dup	PRECISE	Note: The MSH6 rearrangement is an intragenic duplication of exons 2 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2696	0	10	2	Intron of MSH6(+):2Kb before exon 2	MSH6	48016084			2	Exon 3 of MSH6(+)	MSH6	48023162			10	DUPLICATION		7078	321957	4401	10	NEW_VARIANT
P-0045190-T01-IM6	FLCN (NM_144997) rearrangement: c.1147:FLCN_chr17:g.17116943del	PRECISE	Note: The FLCN rearrangement is a deletion of exons 10 - 14. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	-		7622	0	81	17	3-UTR of FLCN(-):25bp after coding stop	FLCN	17116943			17	Exon 10 of FLCN(-)	FLCN	17120412			10	DELETION		3469	321949	7920	83	NEW_VARIANT
P-0045245-T01-IM6	BRAF (NM_004333) rearrangement: c.1177+1757_c.1694+3327del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		21759	0	26	7	Intron of BRAF(-):3Kb after exon 13	BRAF	140473385			7	Intron of BRAF(-):2Kb after exon 9	BRAF	140485591			10	DELETION		12206	322096	6489	27	NEW_VARIANT
P-0045250-T01-IM6	SOS1 (NM_005633) rearrangement: c.721-40:SOS1_chr2:g.131846662inv	PRECISE	Note: The SOS1 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		437822	0	6	2	Intron of SOS1(-):40bp before exon 6	SOS1	39278468			2	5-UTR of FAM168B(-):36Kb before coding start	SOS1	131846662			10	INVERSION		92568194	322090	334170	8	NEW_VARIANT
P-0045252-T01-IM6	FLT4 (NM_182925) rearrangement: c.1421+1_c.1658-373del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5001	0	20	5	Intron of FLT4(-):373bp before exon 13	FLT4	180049277			5	Exon 10 of FLT4(-)	FLT4	180052868			10	DELETION		3591	322094	4165	20	NEW_VARIANT
P-0045275-T01-IM6	MAP2K4 (NM_003010) rearrangement: c.685+1323_c.1134del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4456	0	7	17	Intron of MAP2K4(+):1Kb after exon 6	MAP2K4	12015066			17	Exon 11 of MAP2K4(+)	MAP2K4	12044511			0	DELETION		29445	322109	4836	8	NEW_VARIANT
P-0045280-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.1319-504:TCF7L2_chr10:g.116507504del	PRECISE	Note: The TCF7L2 rearrangement is a deletion of exons 13 - 14.	MANUAL_OK	3to5	3to5	-		9103	0	18	10	Intron of TCF7L2(+):503bp before exon 13	TCF7L2	114919874			10	IGR: 17Kb before LOC101927692(+)	TCF7L2	116507504			10	DELETION		1587630	322110	5310	21	NEW_VARIANT
P-0045225-T01-IM6	MUM1 (NM_032853) - STK11 (NM_000455) rearrangement: c.2078+1394:MUM1_c.304:STK11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {MUM1:STK11}		16402	0	18	19	Exon 2 of STK11(+)	MUM1	1218429			19	Intron of MUM1(+):1Kb after exon 13	STK11	1374553			10	DUPLICATION		156124	322029	21034	18	NEW_VARIANT
P-0045225-T01-IM6	RECQL4 (NM_004260) rearrangement: c.2815:RECQL4_chr8:g.145061684inv	PRECISE	Note: The RECQL4 rearrangement is an inversion of exons 17 - 22. One of the breakpoints is within exon 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {RECQL4:GRINA}		11597	0	15	8	Promoter of GRINA(+):3Kb from tx start	RECQL4	145061684			8	Exon 17 of RECQL4(-)	RECQL4	145738095			10	INVERSION		676411	322030	17613	20	NEW_VARIANT
P-0045243-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-3064:EML4_c.3172+29:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		104724	0	31	2	Intron of ALK(-):28bp after exon 19	EML4	29448298			2	Intron of EML4(+):3Kb before exon 6	ALK	42504926			10	INVERSION		13056628	322054	80935	40	NEW_VARIANT
P-0044066-T01-IM6	RAD52 (NM_134424) rearrangement: t(3;12)(p14.2;p13.33)(chr3:g.63578870::chr12:g.1022740)	PRECISE	Note: The RAD52 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	12	Intron of RAD52(-):122bp before exon 12	RAD52	1022740			3	Intron of SYNPR(+):16Kb before exon 5	RAD52	63578870			10	TRANSLOCATION		0	317381	0	6	NEW_VARIANT
P-0044365-T01-IM6	CDK4 (NM_000075) rearrangement: c.727:CDK4_chr12:g.25188035inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		287780	0	66	12	IGR: 17Kb before LRMP(+)	CDK4	25188035			12	Exon 7 of CDK4(-)	CDK4	58143057			10	INVERSION		32955022	318834	365305	83	NEW_VARIANT
P-0044365-T01-IM6	KMT2B (NM_014727) rearrangement: c.3424:KMT2B_chr19:g.41160688del	PRECISE	Note: The KMT2B rearrangement is a deletion of exons 9 - 37. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		82489	0	30	19	Exon 9 of KMT2B(+)	KMT2B	36215627			19	IGR: 11Kb before NUMBL(-)	KMT2B	41160688			10	DELETION		4945061	318833	115162	32	NEW_VARIANT
P-0045111-T01-IM6	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.2257-760:TRIM24_c.1141-665:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TRIM24:BRAF}		51713	0	24	7	Intron of TRIM24(+):759bp before exon 15	TRIM24	138263189			7	Intron of BRAF(-):665bp before exon 9	BRAF	140488049			10	INVERSION		2224860	321577	48667	24	NEW_VARIANT
P-0045313-T01-IM6	RAD52 (NM_134424) rearrangement: t(12;18)(p13.33;q22.1)(chr12:g.1025842::chr18:g.62012153)	PRECISE	Note: The RAD52 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	131	18	5-UTR of LOC284294(+):79Kb before coding start	RAD52	62012153			12	Exon 8 of RAD52(-)	RAD52	1025842			10	TRANSLOCATION		0	322358	0	134	NEW_VARIANT
P-0045318-T01-IM6	CARD11 (NM_032415) rearrangement: c.8-106_c.803del	PRECISE	Note: The CARD11 rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8100	0	4	7	Exon 6 of CARD11(-)	CARD11	2979444			7	Intron of CARD11(-):106bp before exon 3	CARD11	2987527			6	DELETION		8083	322349	12884	4	NEW_VARIANT
P-0045341-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4434:EML4_c.3172+407:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		58665	0	102	2	Intron of ALK(-):406bp after exon 19	EML4	29447920			2	Intron of EML4(+):4Kb before exon 6	ALK	42503556			10	INVERSION		13055636	322393	116428	101	NEW_VARIANT
P-0045344-T01-IM6	PARK2 (NM_004562) rearrangement: c.412+92_c.534+40671del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon 4.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		899	0	10	6	Intron of PARK2(-):41Kb after exon 4	PARK2	162581492			6	Intron of PARK2(-):91bp after exon 3	PARK2	162683465			10	DELETION		101973	322392	899	10	NEW_VARIANT
P-0045213-T01-IM6	TP53 (NM_000546) rearrangement: t(6;17)(q22.1;p13.1)(chr6:g.116160774::chr17:g.7579873)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	28	17	Exon 2 of TP53(-)	TP53	7579873			6	IGR: 102Kb before FRK(-)	TP53	116160774			10	TRANSLOCATION		0	322026	0	42	NEW_VARIANT
P-0045221-T01-IM6	PARK2 (NM_004562) rearrangement: c.172-73931_c.172del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		219	0	27	6	Exon 3 of PARK2(-)	PARK2	162683797			6	Intron of PARK2(-):74Kb before exon 3	PARK2	162757728			10	DELETION		73931	322009	223	27	NEW_VARIANT
P-0045256-T02-IM6	ARID2 (NM_152641) rearrangement: c.5364-509:ARID2_chr12:g.46304714del	IMPPRECISE	Note: The ARID2 rearrangement is a deletion of exon 21.	MANUAL_OK	3to5	3to5	Deletion within transcript		935	0	5	12	Intron of ARID2(+):508bp before exon 21	ARID2	46298208			12	Promoter of ARID2(+):181Kb from tx start	ARID2	46304714			0	DELETION		6506	322163	1189	5	NEW_VARIANT
P-0045286-T01-IM6	ERBB3 (NM_001982) rearrangement: t(1;12)(p32.3;q13.2)(chr1:g.51595284::chr12:g.56486803)	PRECISE	Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	13	12	Exon 11 of ERBB3(+)	ERBB3	56486803			1	Intron of C1orf185(+):11Kb after exon 3	ERBB3	51595284			10	TRANSLOCATION		0	322158	0	13	NEW_VARIANT
P-0045286-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1624:TMPRSS2_c.19-13251:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32144	0	68	21	Intron of ERG(-):13Kb before exon 2	TMPRSS2	39830795			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868422			10	DELETION		3037627	322154	30974	71	NEW_VARIANT
P-0045288-T01-IM6	HIST1H1C (NM_005319) rearrangement: c.122:HIST1H1C_chr6:g.26121429del	PRECISE	Note: The HIST1H1C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2657	0	11	6	Exon 1 of HIST1H1C(-)	HIST1H1C	26056535			6	Promoter of HIST1H2AC(+):3Kb from tx start	HIST1H1C	26121429			10	DELETION		64894	322159	2734	11	NEW_VARIANT
P-0045291-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4177:TMPRSS2_c.18+8298:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		81780	0	63	21	Intron of ERG(-):8Kb after exon 1	TMPRSS2	39861989			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875700			10	DELETION		3013711	322144	67006	65	NEW_VARIANT
P-0045434-T01-IM6	NTHL1 (NM_002528) - TSC2 (NM_000548) rearrangement: c.815+35:NTHL1_c.3815-318:TSC2del	PRECISE	Note: The NTHL1 - TSC2 rearrangement is a deletion of NTHL1 exons 1 - 5 and TSC2 exons 1 - 31.	MANUAL_OK	3to5	3to5	-		91983	0	41	16	Intron of NTHL1(-):34bp after exon 5	NTHL1	2090099			16	Intron of TSC2(+):317bp before exon 32	TSC2	2132119			10	DELETION		42020	322797	132610	41	NEW_VARIANT
P-0044245-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4498:TMPRSS2_c.40-53757:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		36886	0	83	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39871301			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874614			10	DELETION		3003313	319791	58690	86	NEW_VARIANT
P-0045300-T01-IM6	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+63480:SLC25A21_c.872:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC25A21:FOXA1}		8810	0	14	14	Intron of SLC25A21(-):63Kb after exon 1	SLC25A21	37578006			14	Exon 2 of FOXA1(-)	FOXA1	38061117			10	DUPLICATION		483111	322199	10113	14	NEW_VARIANT
P-0045300-T01-IM6	RAD21 (NM_006265) rearrangement: c.275-483_c.1161+134dup	PRECISE	Poor read support Note: The RAD21 rearrangement is an intragenic duplication of exons 4 - 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : out of frame		9297	0	8	8	Intron of RAD21(-):133bp after exon 9	RAD21	117866350			8	Intron of RAD21(-):483bp before exon 4	RAD21	117874662			6	DUPLICATION		8312	322198	11327	8	NEW_VARIANT
P-0045300-T01-IM6	AGO2 (NM_012154) rearrangement: c.23-23327_c.1788del	PRECISE	Note: The AGO2 rearrangement is an intragenic deletion of exons 2 - 14. One of the breakpoints is within exon 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		31030	0	9	8	Exon 14 of AGO2(-)	AGO2	141554363			8	Intron of AGO2(-):23Kb before exon 2	AGO2	141618737			10	DELETION		64374	322197	31682	9	NEW_VARIANT
P-0045304-T01-IM6	STK11 (NM_000455) - MIDN (NM_177401) rearrangement: c.960:STK11_c.1130-7:MIDNdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STK11:MIDN}		4381	0	8	19	Exon 8 of STK11(+)	STK11	1223023			19	Intron of MIDN(+):6bp before exon 8	MIDN	1256987			10	DELETION		33964	322196	4543	9	NEW_VARIANT
P-0045408-T01-IM6	FGFR2 (NM_000141) rearrangement: t(7;10)(q21.13;q26.13)(chr7:g.88585840::chr10:g.123240135)	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	59	10	Intron of FGFR2(-):600bp before exon 18	FGFR2	123240135			7	Intron of ZNF804B(+):196Kb after exon 1	FGFR2	88585840			10	TRANSLOCATION		0	322656	0	58	NEW_VARIANT
P-0042711-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-543:TMPRSS2_c.40-59085:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		39606	0	70	21	Intron of ERG(-):59Kb before exon 4	TMPRSS2	39876629			21	Intron of TMPRSS2(-):543bp before exon 2	ERG	42870659			10	DELETION		2994030	322939	33269	72	NEW_VARIANT
P-0045382-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2335:FGFR3_c.1942-101:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		49325	0	77	4	Intron of TACC3(+):100bp before exon 11	FGFR3	1741328			4	Exon 18 of FGFR3(+)	TACC3	1808903			10	DUPLICATION		67575	322624	98272	78	NEW_VARIANT
P-0045399-T01-IM6	PTPRD (NM_002839) rearrangement: c.64+52:PTPRD_chr9:g.10203900inv	PRECISE	Note: The PTPRD rearrangement is an inversion of exons 1 - 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1428	0	10	9	Intron of PTPRD(-):51bp after exon 12	PTPRD	8733728			9	5-UTR of PTPRD(-):2Mb before coding start	PTPRD	10203900			10	INVERSION		1470172	322657	1093	10	NEW_VARIANT
P-0045400-T01-IM6	TAP2 (NM_018833) rearrangement: c.1273-1_c.1795+168inv	IMPPRECISE	Note: The TAP2 rearrangement is an intragenic inversion of exons 8 - 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4170	0	152	6	Intron of TAP2(-):167bp after exon 10	TAP2	32797539			6	Intron of TAP2(-):1bp before exon 8	TAP2	32798584			0	INVERSION		1045	322660	21983	151	NEW_VARIANT
P-0045411-T01-IM6	KIT (NM_000222) rearrangement: c.564_c.756+33del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1438	0	2	4	Exon 3 of KIT(+)	KIT	55564676			4	Intron of KIT(+):33bp after exon 4	KIT	55565965			3	DELETION		1289	322715	454	2	NEW_VARIANT
P-0045412-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+3275:TMPRSS2_chr21:g.39987066del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		62400	0	60	21	3-UTR of ERG(-):47Kb after coding stop	TMPRSS2	39987066			21	Intron of TMPRSS2(-):3Kb after exon 1	TMPRSS2	42876602			10	DELETION		2889536	322733	39483	164	NEW_VARIANT
P-0045414-T01-IM6	PBRM1 (NM_018313) rearrangement: c.2780-4270_c.3312+97dup	IMPPRECISE	Note: The PBRM1 rearrangement is an intragenic duplication of exons 19 - 21. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		3866	0	17	3	Intron of PBRM1(-):96bp after exon 21	PBRM1	52620344			3	Intron of PBRM1(-):4Kb before exon 19	PBRM1	52627541			0	DUPLICATION		7197	322707	7440	17	NEW_VARIANT
P-0045416-T01-IM6	EP300 (NM_001429) rearrangement: c.4149:EP300_chr22:g.42369335inv	PRECISE	Note: The EP300 rearrangement is an inversion of exons 25 - 31. One of the breakpoints is within exon 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		25278	0	21	22	Exon 25 of EP300(+)	EP300	41564848			22	IGR: 4Kb before SEPT3(+)	EP300	42369335			10	INVERSION		804487	322722	32841	26	NEW_VARIANT
P-0045466-T01-IM6	RET (NM_020975) rearrangement: c.2136+60:RET_chr10:g.51588788dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		35835	0	48	10	Intron of RET(+):60bp after exon 11	RET	43610244			10	Intron of TIMM23B(+):144Kb before exon 7	RET	51588788			10	DUPLICATION		7978544	322920	20386	49	NEW_VARIANT
P-0045466-T01-IM6	IRS2 (NM_003749) rearrangement: c.4017:IRS2_chr13:g.113369567del	PRECISE	Note: The IRS2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		36731	0	16	13	Exon 2 of IRS2(-)	IRS2	110408651			13	Intron of ATP11A(+):25Kb after exon 1	IRS2	113369567			10	DELETION		2960916	322919	23380	15	NEW_VARIANT
P-0045468-T01-IM6	RTEL1 (NM_032957) rearrangement: c.772-58:RTEL1_chr20:g.22755561inv	PRECISE	Note: The RTEL1 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		272794	0	31	20	IGR: 187Kb before LINC01384(-)	RTEL1	22755561			20	Intron of RTEL1(+):57bp before exon 9	RTEL1	62303851			10	INVERSION		39548290	322934	277099	37	NEW_VARIANT
P-0045469-T01-IM6	MET (NM_000245) rearrangement: c.2583+1379_c.3028+1168del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		9409	0	47	7	Intron of MET(+):1Kb after exon 11	MET	116404701			7	Intron of MET(+):1Kb after exon 14	MET	116413211			10	DELETION		8510	322930	11096	48	NEW_VARIANT
P-0045462-T01-IM6	FOXP1 (NM_001244814) rearrangement: t(3;7)(p13;q11.22)(chr3:g.71027118::chr7:g.68292852)	PRECISE	Note: The FOXP1 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	18	7	IGR: 768Kb before LOC100507468(-)	FOXP1	68292852			3	Exon 11 of FOXP1(-)	FOXP1	71027118			10	TRANSLOCATION		0	322883	0	18	NEW_VARIANT
P-0045496-T01-IM6	PDGFRB (NM_002609) rearrangement: c.2024-491_c.2900inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		8283	0	21	5	Exon 21 of PDGFRB(-)	PDGFRB	149498314			5	Intron of PDGFRB(-):491bp before exon 15	PDGFRB	149503255			10	INVERSION		4941	323080	10158	24	NEW_VARIANT
P-0045507-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+72:FGFR3_c.1942-413:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		31760	0	244	4	Intron of TACC3(+):412bp before exon 11	FGFR3	1741016			4	Intron of FGFR3(+):72bp after exon 17	TACC3	1808733			10	DUPLICATION		67717	323230	83841	271	NEW_VARIANT
P-0045517-T01-IM6	STAT3 (NM_139276) rearrangement: c.2258-32:STAT3_chr17:g.42887976inv	PRECISE	Note: The STAT3 rearrangement is an inversion of exons 1 - 23. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		102304	0	47	17	Intron of STAT3(-):32bp before exon 24	STAT3	40467850			17	5-UTR of GJC1(-):6Kb before coding start	STAT3	42887976			10	INVERSION		2420126	323223	136886	46	NEW_VARIANT
P-0045517-T01-IM6	INPP4B (NM_001101669) rearrangement: c.837-5974_c.2488-24del	PRECISE	Note: The INPP4B rearrangement is an intragenic deletion of exons 13 - 24.	MANUAL_OK	3to5	3to5	Deletion of 12 exons : out of frame		12160	0	13	4	Intron of INPP4B(-):24bp before exon 25	INPP4B	143003362			4	Intron of INPP4B(-):6Kb before exon 13	INPP4B	143136153			10	DELETION		132791	323222	13330	13	NEW_VARIANT
P-0045531-T01-IM6	LGR5 (NM_003667) - NAB2 (NM_005967) rearrangement: c.285-7692:LGR5_c.1532:NAB2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LGR5:NAB2}		54085	0	35	12	Exon 7 of NAB2(+)	LGR5	57488458			12	Intron of LGR5(+):8Kb before exon 3	NAB2	71910494			10	DUPLICATION		14422036	323306	64626	35	NEW_VARIANT
P-0045535-T01-IM6	PAX8 (NM_003466) - PPARG (NM_015869) rearrangement: t(2;3)(q13;p25.2)(chr2:g.113992616::chr3:g.12399709)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {PAX8:PPARG}		0	0	80	3	Intron of PPARG(+):7Kb after exon 1	PAX8	12399709			2	Intron of PAX8(-):354bp after exon 9	PPARG	113992616			10	TRANSLOCATION		0	323310	0	87	NEW_VARIANT
P-0045191-T01-IM6	CIC (NM_015125) rearrangement: c.3008+35_c.4297del	PRECISE	Note: The CIC rearrangement is an intragenic deletion of exons 13 - 18. One of the breakpoints is within exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8172	1	2	19	Intron of CIC(+):35bp after exon 12	CIC	42796394			19	Exon 18 of CIC(+)	CIC	42798426			10	DELETION		2032	321952	23085	1	NEW_VARIANT
P-0045224-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-3570:CDKN2A_chr9:g.36781788inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		55102	0	6	9	Exon 1 of CDKN2A(-)	CDKN2A	21974777			9	IGR: 42Kb before MIR4475(-)	CDKN2A	36781788			10	INVERSION		14807011	322018	15377	6	NEW_VARIANT
P-0045557-T01-IM6	ALK (NM_004304) rearrangement: t(2;4)(p23.2;q22.1)(chr2:g.29447286::chr4:g.90210936)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {GPRIN3:ALK}		0	0	94	4	5-UTR of GPRIN3(-):42Kb before coding start	ALK	90210936			2	Intron of ALK(-):892bp before exon 20	ALK	29447286			10	TRANSLOCATION		0	323351	0	95	NEW_VARIANT
P-0045578-T01-IM6	INPPL1 (NM_001567) - FOLR2 (NM_001113536) rearrangement: c.397+99:INPPL1_c.151-191:FOLR2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {INPPL1:FOLR2}		4071	0	7	11	Intron of FOLR2(+):190bp before exon 3	INPPL1	71931723			11	Intron of INPPL1(+):99bp after exon 3	FOLR2	71939641			9	DUPLICATION		7918	323401	6722	6	NEW_VARIANT
P-0045578-T01-IM6	CDK12 (NM_016507) rearrangement: c.932:CDK12_chr17:g.71208276del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		456883	0	83	17	Exon 1 of CDK12(+)	CDK12	37619256			17	Intron of FAM104A(-):2Kb before exon 3	CDK12	71208276			10	DELETION		33589020	323400	642149	121	NEW_VARIANT
P-0045583-T01-IM6	PMAIP1 (NM_021127) rearrangement: c.57:PMAIP1_chr18:g.60612888inv	PRECISE	Note: The PMAIP1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3712	0	2	18	Exon 1 of PMAIP1(+)	PMAIP1	57567466			18	Intron of PHLPP1(+):384bp after exon 12	PMAIP1	60612888			5	INVERSION		3045422	323394	9120	2	NEW_VARIANT
P-0045583-T01-IM6	EGFR (NM_005228) rearrangement: c.89-8942_c.889+168inv	IMPPRECISE	Note: The EGFR rearrangement is a vIII alteration.	MANUAL_OK	3to3	3to3	Antisense Fusion		8630	0	4	7	Intron of EGFR(+):9Kb before exon 2	EGFR	55201037			7	Intron of EGFR(+):168bp after exon 7	EGFR	55222013			0	INVERSION		20976	323392	53908	4	NEW_VARIANT
P-0045566-T01-IM6	ZFPM2 (NM_012082) - ALK (NM_004304) fusion: t(2;8)(p23.2;q23.1)(chr2:g.29447902::chr8:g.106384092)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ZFPM2:ALK}		0	0	29	8	Intron of ZFPM2(+):47Kb before exon 2	ZFPM2	106384092			2	Intron of ALK(-):424bp after exon 19	ALK	29447902			10	TRANSLOCATION		0	323367	0	29	NEW_VARIANT
P-0045613-T01-IM6	BRAF (NM_004333) rearrangement: c.1315-14:BRAF_chr7:g.140429365dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		7629	0	3	7	IGR: 4Kb before BRAF(-)	BRAF	140429365			7	Intron of BRAF(-):14bp before exon 11	BRAF	140481507			5	DUPLICATION		52142	323438	9952	4	NEW_VARIANT
P-0045616-T01-IM6	CDKN2B (NM_004936) - SLC24A2 (NM_020344) rearrangement: c.113:CDKN2B_c.931-51322:SLC24A2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDKN2B:SLC24A2}		13863	0	22	9	Intron of SLC24A2(-):51Kb before exon 2	CDKN2B	19673619			9	Exon 1 of CDKN2B(-)	SLC24A2	22008840			10	DELETION		2335221	323444	14678	25	NEW_VARIANT
P-0045617-T01-IM6	NEGR1 (NM_173808) rearrangement: c.536-132:NEGR1_chr1:g.63091106inv	PRECISE	Note: The NEGR1 rearrangement is an inversion of exons 4 - 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		33614	0	54	1	Intron of DOCK7(-):34bp before exon 12	NEGR1	63091106			1	Intron of NEGR1(-):132bp before exon 4	NEGR1	72163954			10	INVERSION		9072848	323439	41732	54	NEW_VARIANT
P-0045617-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.6530:NOTCH2_chr1:g.96486979inv	PRECISE	Note: The NOTCH2 rearrangement is an inversion of exon 34. One of the breakpoints is within exon 34. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {LOC102723661:NOTCH2}		56093	0	29	1	5-UTR of LOC102723661(+):1Kb before coding start	NOTCH2	96486979			1	Exon 34 of NOTCH2(-)	NOTCH2	120458815			10	INVERSION		23971836	323440	77709	29	NEW_VARIANT
P-0045617-T01-IM6	KMT2A (NM_001197104) rearrangement: c.3953:KMT2A_chr11:g.133388889inv	PRECISE	Note: The KMT2A rearrangement is an inversion of exons 7 - 36. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KMT2A:OPCML}		75609	0	20	11	Exon 7 of KMT2A(+)	KMT2A	118352748			11	Intron of OPCML(-):13Kb after exon 1	KMT2A	133388889			10	INVERSION		15036141	323441	103512	20	NEW_VARIANT
P-0045619-T01-IM6	TP53 (NM_000546) rearrangement: t(2;17)(p11.2;p13.1)(chr2:g.86353784::chr17:g.7576703)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	21	17	Intron of TP53(-):149bp after exon 9	TP53	7576703			2	Intron of PTCD3(+):499bp before exon 13	TP53	86353784			10	TRANSLOCATION		0	323435	0	21	NEW_VARIANT
P-0045623-T01-IM6	EZH2 (NM_004456) rearrangement: c.2029+32:EZH2_chr7:g.148423587del	PRECISE	Note: The EZH2 rearrangement is a deletion of exons 18 - 20.	MANUAL_OK	3to5	3to5	Antisense Fusion		3261	0	4	7	5-UTR of CUL1(+):4Kb before coding start	EZH2	148423587			7	Intron of EZH2(-):31bp after exon 17	EZH2	148507393			5	DELETION		83806	323434	4765	4	NEW_VARIANT
P-0045728-T01-IM6	NF1 (NM_001042492) rearrangement: c.5610-73:NF1_chr17:g.25695654inv	IMPPRECISE	Note: The NF1 rearrangement is an inversion of exons 1 - 38. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		38901	0	6	17	IGR: 49Kb before TBC1D3P5(+)	NF1	25695654			17	Intron of NF1(+):72bp before exon 39	NF1	29657241			0	INVERSION		3961587	323652	32152	6	NEW_VARIANT
P-0045740-T01-IM6	TP53 (NM_000546) - UNC13D (NM_199242) rearrangement: c.993+53:TP53_c.1056-60:UNC13Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TP53:UNC13D}		541574	0	5	17	Intron of TP53(-):52bp after exon 9	TP53	7576800			17	Intron of UNC13D(-):60bp before exon 13	UNC13D	73833059			10	DUPLICATION		66256259	323632	638667	6	NEW_VARIANT
P-0045633-T01-IM6	TP53 (NM_000546) rearrangement: c.993+1071_c.1059del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exon 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		511	0	32	17	Exon 10 of TP53(-)	TP53	7573968			17	Intron of TP53(-):1Kb after exon 9	TP53	7575782			10	DELETION		1814	323466	424	33	NEW_VARIANT
P-0045643-T01-IM6	IGF1R (NM_000875) rearrangement: c.641-37313_c.807dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		1641	0	7	15	Intron of IGF1R(+):37Kb before exon 3	IGF1R	99397241			15	Exon 3 of IGF1R(+)	IGF1R	99434720			8	DUPLICATION		37479	323505	2288	7	NEW_VARIANT
P-0045669-T01-IM6	EWSR1 (NM_013986) rearrangement: c.600-78_c.811+623inv	PRECISE	Note: The EWSR1 rearrangement is an intragenic inversion of exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3420	0	2	22	Intron of EWSR1(+):77bp before exon 8	EWSR1	29682834			22	Intron of EWSR1(+):623bp after exon 8	EWSR1	29683746			9	INVERSION		912	323531	2506	2	NEW_VARIANT
P-0045670-T01-IM6	RB1 (NM_000321) rearrangement: c.2211+135_c.2325+17del	IMPPRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 22.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		845	0	3	13	Intron of RB1(+):135bp after exon 21	RB1	49038106			13	Intron of RB1(+):17bp after exon 22	RB1	49039264			0	DELETION		1158	323533	632	3	NEW_VARIANT
P-0045773-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2247:KIF5B_c.2137-99:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		63221	0	20	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315109			10	Intron of RET(+):98bp before exon 12	RET	43611933			10	INVERSION		11296824	323876	54184	23	NEW_VARIANT
P-0045821-T01-IM6	ELF3 (NM_004433) rearrangement: c.386-26:ELF3_chr1:g.201992796del	PRECISE	Note: The ELF3 rearrangement is a deletion of exons 4 - 9.	MANUAL_OK	3to5	3to5	-		14164	0	17	1	Intron of ELF3(+):25bp before exon 4	ELF3	201981446			1	IGR: 13Kb before ELF3(+)	ELF3	201992796			10	DELETION		11350	323946	10703	18	NEW_VARIANT
P-0045832-T01-IM6	ETV6 (NM_001987) rearrangement: c.464-5415:ETV6_chr12:g.97487697inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		597173	0	73	12	Intron of ETV6(+):5Kb before exon 5	ETV6	12016943			12	IGR: 186Kb before NEDD1(+)	ETV6	97487697			10	INVERSION		85470754	323962	686536	81	NEW_VARIANT
P-0045832-T01-IM6	MDM2 (NM_002392) - GNPTAB (NM_024312) rearrangement: c.523+59:MDM2_c.118-14879:GNPTABinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {MDM2:GNPTAB}		16824	0	11	12	Intron of MDM2(+):59bp after exon 7	MDM2	69218490			12	Intron of GNPTAB(-):15Kb before exon 2	GNPTAB	102205419			0	INVERSION		32986929	323963	57486	11	NEW_VARIANT
P-0045832-T01-IM6	CSF1R (NM_005211) - CPM (NM_001005502) rearrangement: t(5;12)(q32;q15)(chr5:g.149449803::chr12:g.69319777)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CSF1R:CPM}		0	0	83	12	Intron of CPM(-):7Kb after exon 2	CSF1R	69319777			5	Exon 9 of CSF1R(-)	CPM	149449803			10	TRANSLOCATION		0	323968	0	84	NEW_VARIANT
P-0045836-T01-IM6	RFWD2 (NM_022457) rearrangement: c.79_c.642+114del	PRECISE	Note: The RFWD2 rearrangement is an intragenic deletion of exons 1 - 4. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4174	0	32	1	Intron of RFWD2(-):113bp after exon 4	RFWD2	176132837			1	Exon 1 of RFWD2(-)	RFWD2	176176036			10	DELETION		43199	323960	4315	33	NEW_VARIANT
P-0045875-T01-IM6	PBRM1 (NM_018313) rearrangement: c.3161_c.3313-593del	PRECISE	Note: The PBRM1 rearrangement is an intragenic deletion of exon 21. One of the breakpoints is within exon 21.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1048	0	21	3	Intron of PBRM1(-):593bp before exon 22	PBRM1	52613808			3	Exon 21 of PBRM1(-)	PBRM1	52620592			10	DELETION		6784	324091	1078	21	NEW_VARIANT
P-0045878-T01-IM6	TCF3 (NM_001136139) rearrangement: c.1893:TCF3_chr19:g.1412534del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		1741	0	99	19	Intron of DAZAP1(+):5Kb after exon 1	TCF3	1412534			19	Exon 18 of TCF3(-)	TCF3	1611769			10	DELETION		199235	324095	1986	108	NEW_VARIANT
P-0045881-T01-IM6	EGFL7 (NM_201446) rearrangement: c.80+43:EGFL7_chr9:g.139685238dup	PRECISE	Note: The EGFL7 rearrangement is a duplication of exons 3 - 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {TMEM141:EGFL7}		14990	0	21	9	Intron of EGFL7(+):43bp after exon 2	EGFL7	139562857			9	Promoter of TMEM141(+):538bp from tx start	EGFL7	139685238			10	DUPLICATION		122381	324090	22614	22	NEW_VARIANT
P-0045508-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2301+1436:FGFR2_chr10:g.130925993inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		38187	0	45	10	Intron of FGFR2(-):1Kb after exon 17	FGFR2	123241776			10	IGR: 339Kb before MGMT(+)	FGFR2	130925993			10	INVERSION		7684217	323224	67062	46	NEW_VARIANT
P-0045626-T01-IM6	KMT2D (NM_003482) - RILPL1 (NM_178314) rearrangement: c.14051:KMT2D_c.461-4396:RILPL1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KMT2D:RILPL1}		461105	0	15	12	Exon 43 of KMT2D(-)	KMT2D	49423208			12	Intron of RILPL1(-):4Kb before exon 3	RILPL1	123988479			10	DUPLICATION		74565271	323464	402598	58	NEW_VARIANT
P-0026774-T02-IM6	ZFHX3 (NM_006885) rearrangement: c.8262:ZFHX3_chr16:g.73087045del	PRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		63219	0	7	16	Exon 9 of ZFHX3(-)	ZFHX3	72828319			16	5-UTR of ZFHX3(-):266Kb before coding start	ZFHX3	73087045			9	DELETION		258726	324139	90502	7	NEW_VARIANT
P-0029401-T02-IM6	BABAM1 (NM_001033549) - DNAH14 (NM_001373) rearrangement: t(1;19)(q42.12;p13.11)(chr1:g.225434872::chr19:g.17386670)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {BABAM1:DNAH14}		0	0	6	19	Intron of BABAM1(+):36bp after exon 6	BABAM1	17386670			1	Intron of DNAH14(+):3Kb before exon 43	DNAH14	225434872			10	TRANSLOCATION		0	323587	0	6	NEW_VARIANT
P-0045460-T01-IM6	SMYD3 (NM_001167740) rearrangement: c.968:SMYD3_chr1:g.245806197del	PRECISE	Note: The SMYD3 rearrangement is a deletion of exons 10 - 12. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		3495	0	4	1	Intron of KIF26B(+):3Kb before exon 10	SMYD3	245806197			1	Exon 10 of SMYD3(-)	SMYD3	246021906			8	DELETION		215709	322885	4210	4	NEW_VARIANT
P-0045460-T01-IM6	RET (NM_020975) rearrangement: c.2136+101:RET_chr10:g.51588385dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		37973	0	106	10	Intron of RET(+):101bp after exon 11	RET	43610285			10	Intron of TIMM23B(+):144Kb before exon 7	RET	51588385			10	DUPLICATION		7978100	322887	43537	115	NEW_VARIANT
P-0045713-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.552+13197_c.1318+655dup	PRECISE	Note: The TCF7L2 rearrangement is an intragenic duplication of exons 6 - 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 7 exons : out of frame		8964	0	5	10	Intron of TCF7L2(+):13Kb after exon 5	TCF7L2	114813082			10	Intron of TCF7L2(+):655bp after exon 12	TCF7L2	114918483			6	DUPLICATION		105401	323589	9942	5	NEW_VARIANT
P-0045724-T01-IM6	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.764-456:SPTBN1_c.3173-402:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SPTBN1:ALK}		171072	0	63	2	Intron of ALK(-):402bp before exon 20	SPTBN1	29446796			2	Intron of SPTBN1(+):455bp before exon 8	ALK	54848081			10	INVERSION		25401285	323601	166309	63	NEW_VARIANT
P-0045847-T01-IM6	BCL2L14 (NM_138723) - CDKN1B (NM_004064) rearrangement: c.608-223:BCL2L14_c.572:CDKN1Bdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {BCL2L14:CDKN1B}		3138	0	5	12	Intron of BCL2L14(+):222bp before exon 4	BCL2L14	12243490			12	Exon 2 of CDKN1B(+)	CDKN1B	12871855			0	DELETION		628365	324055	3086	8	NEW_VARIANT
P-0045858-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2011:WHSC1L1_chr8:g.9352182inv	PRECISE	Note: The WHSC1L1 rearrangement is an inversion of exons 11 - 24. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		49748	0	7	8	IGR: 61Kb before TNKS(+)	WHSC1L1	9352182			8	Exon 11 of WHSC1L1(-)	WHSC1L1	38173038			10	INVERSION		28820856	324086	58036	7	NEW_VARIANT
P-0045861-T01-IM6	ANKRD11 (NM_013275) rearrangement: t(10;16)(q25.3;q24.3)(chr10:g.116181365::chr16:g.89350468)	PRECISE	Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	17	16	Exon 9 of ANKRD11(-)	ANKRD11	89350468			10	IGR: 10Kb before ABLIM1(-)	ANKRD11	116181365			10	TRANSLOCATION		0	324087	0	19	NEW_VARIANT
P-0045862-T01-IM6	ERBB4 (NM_005235) rearrangement: c.1125-403_c.1199-19del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		797	0	4	2	Intron of ERBB4(-):19bp before exon 11	ERBB4	212568938			2	Intron of ERBB4(-):403bp before exon 10	ERBB4	212570519			5	DELETION		1581	324084	696	4	NEW_VARIANT
P-0045890-T01-IM6	NF1 (NM_001042492) rearrangement: c.5947_c.7190-2234dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 40 - 48. One of the breakpoints is within exon 40. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		8461	0	4	17	Exon 40 of NF1(+)	NF1	29661990			17	Intron of NF1(+):2Kb before exon 49	NF1	29673904			10	DUPLICATION		11914	324111	11105	9	NEW_VARIANT
P-0045898-T01-IM6	STAT5A (NM_003152) rearrangement: c.1361:STAT5A_chr17:g.61466676inv	PRECISE	Note: The STAT5A rearrangement is an inversion of exons 12 - 20. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		250600	0	20	17	Exon 12 of STAT5A(+)	STAT5A	40456651			17	Exon 15 of TANC2(+)	STAT5A	61466676			10	INVERSION		21010025	324106	409752	22	NEW_VARIANT
P-0045902-T01-IM6	EGFLAM (NM_001205301) - RICTOR (NM_152756) rearrangement: c.1350-1227:EGFLAM_c.4914-37:RICTORinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EGFLAM:RICTOR}		1627	0	20	5	Intron of EGFLAM(+):1Kb before exon 11	EGFLAM	38411379			5	Intron of RICTOR(-):37bp before exon 37	RICTOR	38943110			10	INVERSION		531731	324129	2365	28	NEW_VARIANT
P-0026158-T04-IM6	MAD1L1 (NM_001013837) - BRAF (NM_004333) fusion: c.1417-9863:MAD1L1_c.1140+2359:BRAFdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {MAD1L1:BRAF}		556329	0	325	7	Intron of MAD1L1(-):10Kb before exon 15	MAD1L1	2030039			7	Intron of BRAF(-):2Kb after exon 8	BRAF	140491749			10	DUPLICATION		138461710	324397	505445	342	NEW_VARIANT
P-0026158-T04-IM6	ATRX (NM_000489) rearrangement: c.5448+29:ATRX_chrX:g.76117797del	IMPPRECISE	Note: The ATRX rearrangement is a deletion of exons 22 - 35.	MANUAL_OK	3to5	3to5	-		10082	0	6	X	3-UTR of MIR325HG(-):117Kb after coding stop	ATRX	76117797			X	Intron of ATRX(-):28bp after exon 21	ATRX	76874245			0	DELETION		756448	324396	1963	7	NEW_VARIANT
P-0045651-T01-IM6	ARID2 (NM_152641) rearrangement: t(12;13)(q12;q22.2)(chr12:g.46245145::chr13:g.77149393)	PRECISE	Note: The ARID2 rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	44	13	IGR: 305Kb before KCTD12(-)	ARID2	77149393			12	Exon 15 of ARID2(+)	ARID2	46245145			10	TRANSLOCATION		0	323520	0	44	NEW_VARIANT
P-0045651-T01-IM6	WHSC1 (NM_001042424) - TACC3 (NM_006342) rearrangement: c.597+105:WHSC1_c.2224-399:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {WHSC1:TACC3}		40794	0	27	4	Intron of TACC3(+):398bp before exon 14	WHSC1	1745846			4	Intron of WHSC1(+):105bp after exon 2	TACC3	1903083			10	DUPLICATION		157237	323519	54034	30	NEW_VARIANT
P-0045660-T01-IM6	APC (NM_000038) rearrangement: c.4203_c.7685del	PRECISE	Note: The APC rearrangement is an intragenic deletion of exon 16. The breakpoints are within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9153	0	21	5	Exon 16 of APC(+)	APC	112175494			5	Exon 16 of APC(+)	APC	112178976			10	DELETION		3482	323513	3514	22	NEW_VARIANT
P-0045661-T01-IM6	APC (NM_000038) rearrangement: c.1268:APC_chr5:g.77595801inv	PRECISE	Note: The APC rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		57215	0	55	5	IGR: 59Kb before SCAMP1-AS1(-)	APC	77595801			5	Exon 10 of APC(+)	APC	112154997			10	INVERSION		34559196	323514	74210	59	NEW_VARIANT
P-0045709-T01-IM6	BAP1 (NM_004656) rearrangement: t(3;13)(p21.1;q33.3)(chr3:g.52442050::chr13:g.108262196)	PRECISE	Note: The BAP1 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	32	13	Intron of FAM155A(-):256Kb after exon 1	BAP1	108262196			3	Exon 5 of BAP1(-)	BAP1	52442050			10	TRANSLOCATION		0	323595	0	34	NEW_VARIANT
P-0045918-T01-IM6	INPP4A (NM_001134224) rearrangement: c.671-15:INPP4A_chr2:g.98539823del	PRECISE	Note: The INPP4A rearrangement is a deletion of exons 1 - 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9375	0	27	2	Intron of TMEM131(-):4Kb after exon 2	INPP4A	98539823			2	Intron of INPP4A(+):14bp before exon 10	INPP4A	99155976			10	DELETION		616153	324178	9904	27	NEW_VARIANT
P-0045919-T01-IM6	FUBP1 (NM_003902) rearrangement: c.1889:FUBP1_chr1:g.78408581del	PRECISE	Note: The FUBP1 rearrangement is a deletion of exons 19 - 20. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	-		815	0	8	1	3-UTR of NEXN(+):27Kb after coding stop	FUBP1	78408581			1	Exon 19 of FUBP1(-)	FUBP1	78414877			10	DELETION		6296	324177	723	8	NEW_VARIANT
P-0045926-T01-IM6	NSRP1 (NM_032141) - BRCA1 (NM_007294) rearrangement: c.114+6366:NSRP1_c.4097-188:BRCA1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NSRP1:BRCA1}		311546	0	4	17	Intron of NSRP1(+):6Kb after exon 2	NSRP1	28451557			17	Intron of BRCA1(-):188bp before exon 11	BRCA1	41243237			10	INVERSION		12791680	324183	391404	3	NEW_VARIANT
P-0046005-T01-IM6	DNMT1 (NM_001379) rearrangement: c.2148:DNMT1_chr19:g.10214783inv	PRECISE	Note: The DNMT1 rearrangement is an inversion of exons 23 - 40. One of the breakpoints is within exon 23. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PPAN-P2RY11:DNMT1}		30675	0	7	19	Promoter of PPAN-P2RY11(+):2Kb from tx start	DNMT1	10214783			19	Exon 23 of DNMT1(-)	DNMT1	10262143			10	INVERSION		47360	324361	27502	8	NEW_VARIANT
P-0046008-T01-IM6	KMT2D (NM_003482) rearrangement: c.5631_c.6235-13del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion of exons 25 - 30. One of the breakpoints is within exon 25.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7374	0	2	12	Intron of KMT2D(-):13bp before exon 31	KMT2D	49435331			12	Exon 25 of KMT2D(-)	KMT2D	49436872			6	DELETION		1541	324362	7581	2	NEW_VARIANT
P-0009432-T02-IM6	DOT1L (NM_032482) rearrangement: t(11;19)(q14.1;p13.3)(chr11:g.79148763::chr19:g.2208868)	PRECISE	Note: The DOT1L rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {TENM4:DOT1L}		0	0	48	19	Intron of DOT1L(+):65bp before exon 12	DOT1L	2208868			11	5-UTR of TENM4(-):780Kb before coding start	DOT1L	79148763			10	TRANSLOCATION		0	324659	0	60	NEW_VARIANT
P-0009432-T02-IM6	PTPRS (NM_002850) rearrangement: c.4097-179:PTPRS_chr19:g.3987676inv	PRECISE	Note: The PTPRS rearrangement is an inversion of exons 27 - 38. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		46944	0	12	19	Promoter of EEF2(-):12Kb from tx start	PTPRS	3987676			19	Intron of PTPRS(-):179bp before exon 27	PTPRS	5215785			10	INVERSION		1228109	324658	46269	12	NEW_VARIANT
P-0014808-T03-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1764:KIF5B_c.2136+872:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		54626	0	72	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315592			10	Intron of RET(+):872bp after exon 11	RET	43611056			10	INVERSION		11295464	324652	35120	95	NEW_VARIANT
P-0014808-T03-IM6	RET (NM_020975) - ERCC6 (NM_000124) rearrangement: c.2137-816:RET_c.1397+6822:ERCC6inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RET:ERCC6}		22881	0	77	10	Intron of RET(+):815bp before exon 12	RET	43611216			10	Intron of ERCC6(-):7Kb after exon 5	ERCC6	50725257			10	INVERSION		7114041	324653	16818	71	NEW_VARIANT
P-0019263-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.106+25450_c.198del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		908	0	5	1	Exon 2 of PIK3R3(-)	PIK3R3	46546331			1	Intron of PIK3R3(-):25Kb after exon 1	PIK3R3	46572069			10	DELETION		25738	181623	671	5	NEW_VARIANT
P-0022907-T01-IM6	ARID1B (NM_020732) rearrangement: c.5147_c.*1269del	PRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exon 20. One of the breakpoints is within exon 20. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		12299	0	29	6	Exon 20 of ARID1B(+)	ARID1B	157527422			6	3-UTR of ARID1B(+):431Kb after coding stop	ARID1B	157530294			10	DELETION		2872	192688	3211	32	NEW_VARIANT
P-0024221-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.2438+1723_c.2860-101del	PRECISE	Note: The SMARCA4 rearrangement results in the deletion of exons 17-19. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		8841	0	15	19	Intron of SMARCA4(+):2Kb after exon 16	SMARCA4	11125511			19	Intron of SMARCA4(+):100bp before exon 20	SMARCA4	11134093			10	DELETION		8582	198860	4189	16	NEW_VARIANT
P-0027735-T01-IM6	TP53 (NM_000546) rearrangement: c.75-2_c.994-1dup	PRECISE	Note: The TP53 rearrangement is an intragenic duplication of exons 3-9.	MANUAL_OK	5to3	5to3	Duplication of 7 exons : out of frame		11696	0	71	17	Intron of TP53(-):1bp before exon 10	TP53	7574034			17	Intron of TP53(-):28bp before exon 3	TP53	7579749			10	DUPLICATION		5715	214628	21567	91	NEW_VARIANT
P-0027735-T01-IM6	NF1 (NM_001042492) rearrangement: t(2;17)(p12;q11.2)(chr2:g.80131260::chr17:g.29664530)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 43.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	83	17	Exon 43 of NF1(+)	NF1	29664530			2	Intron of CTNNA2(+):5Kb before exon 7	NF1	80131260			10	TRANSLOCATION		0	214629	0	82	NEW_VARIANT
P-0036844-T02-IM6	BCL2L11 (NM_138621) rearrangement: c.394+3733_c.498+3185del	PRECISE	Note: The BCL2L11 rearrangement is an intragenic deletion of exon 3.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		8518	0	33	2	Intron of BCL2L11(+):4Kb after exon 2	BCL2L11	111885449			2	Intron of BCL2L11(+):3Kb after exon 3	BCL2L11	111910909			10	DELETION		25460	324450	12933	34	NEW_VARIANT
P-0045171-T01-IM6	TERT (NM_198253) Rearrangement : chr5:g.1295249_c.41-346:PCDH1inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		313693	0	8	5	Promoter of TERT(-):42Kb from tx start	TERT	1295249			5	Intron of PCDH1(-):346bp before exon 2	TERT	141249342			0	INVERSION		139954093	324393	448735	8	NEW_VARIANT
P-0045691-T01-IM6	SOX9 (NM_000346) rearrangement: c.202:SOX9_chr17:g.72219596inv	PRECISE	Note: The SOX9 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		12678	0	13	17	Exon 1 of SOX9(+)	SOX9	70117734			17	Intron of TTYH2(+):800bp after exon 2	SOX9	72219596			10	INVERSION		2101862	323579	10271	16	NEW_VARIANT
P-0045691-T01-IM6	SOX9 (NM_000346) rearrangement: t(8;17)(q24.3;q24.3)(chr8:g.141408932::chr17:g.70117921)	PRECISE	Note: The SOX9 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	21	17	Exon 1 of SOX9(+)	SOX9	70117921			8	Intron of TRAPPC9(-):1Kb before exon 7	SOX9	141408932			10	TRANSLOCATION		0	323580	0	22	NEW_VARIANT
P-0045947-T01-IM6	JUN (NM_002228) rearrangement: c.753:JUN_chr1:g.59240840del	PRECISE	Note: The JUN rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4496	0	12	1	IGR: 6Kb before JUN(-)	JUN	59240840			1	Exon 1 of JUN(-)	JUN	59247990			10	DELETION		7150	324255	4716	12	NEW_VARIANT
P-0045959-T01-IM6	MSH3 (NM_002439) rearrangement: c.792+611_c.910-63del	PRECISE	Note: The MSH3 rearrangement is an intragenic deletion of exon 5.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1260	0	14	5	Intron of MSH3(+):611bp after exon 4	MSH3	79966739			5	Intron of MSH3(+):62bp before exon 6	MSH3	79968497			10	DELETION		1758	324276	1208	15	NEW_VARIANT
P-0045964-T01-IM6	TP53 (NM_000546) rearrangement: c.75-3_c.375+218del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 4.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3147	0	19	17	Intron of TP53(-):217bp after exon 4	TP53	7579094			17	Intron of TP53(-):3bp before exon 3	TP53	7579724			10	DELETION		630	324320	3320	19	NEW_VARIANT
P-0045987-T01-IM6	SUZ12 (NM_015355) rearrangement: c.387-2091_c.1595+6dup	PRECISE	Note: The SUZ12 rearrangement is an intragenic duplication of exons 4 - 13. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 10 exons : in frame		7918	0	9	17	Intron of SUZ12(+):2Kb before exon 4	SUZ12	30272545			17	Intron of SUZ12(+):6bp after exon 13	SUZ12	30321746			10	DUPLICATION		49201	324324	8763	44	NEW_VARIANT
P-0045994-T01-IM6	TRAF7 (NM_032271) rearrangement: c.81+182_c.348+4dup	PRECISE	Note: The TRAF7 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : in frame		4733	0	30	16	Intron of TRAF7(+):182bp after exon 2	TRAF7	2214184			16	Intron of TRAF7(+):4bp after exon 5	TRAF7	2220735			10	DUPLICATION		6551	324334	5653	42	NEW_VARIANT
P-0045996-T01-IM6	MGA (NM_001164273) rearrangement: c.3844-499_c.4568del	PRECISE	Note: The MGA rearrangement is an intragenic deletion of exons 12 - 14. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4548	0	10	15	Intron of MGA(+):498bp before exon 12	MGA	42026221			15	Exon 14 of MGA(+)	MGA	42032384			10	DELETION		6163	324331	1685	10	NEW_VARIANT
P-0046020-T01-IM6	UNC13A (NM_001080421) - RAD50 (NM_005732) rearrangement: t(5;19)(q31.1;p13.11)(chr5:g.131915030::chr19:g.17752171)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {UNC13A:RAD50}		0	0	48	19	Intron of UNC13A(-):30bp after exon 20	UNC13A	17752171			5	Exon 4 of RAD50(+)	RAD50	131915030			10	TRANSLOCATION		0	324381	0	54	NEW_VARIANT
P-0046026-T01-IM6	PNRC1 (NM_006813) rearrangement: c.540+1121:PNRC1_chr6:g.89780366del	PRECISE	Note: The PNRC1 rearrangement is a deletion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5475	0	2	6	IGR: 10Kb before PNRC1(+)	PNRC1	89780366			6	Intron of PNRC1(+):1Kb after exon 1	PNRC1	89792274			8	DELETION		11908	324383	6710	2	NEW_VARIANT
P-0046069-T01-IM6	FOXA1 (NM_004496) rearrangement: c.821:FOXA1_chr14:g.38055116del	PRECISE	Note: The FOXA1 rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		7329	0	101	14	IGR: 4Kb before FOXA1(-)	FOXA1	38055116			14	Exon 2 of FOXA1(-)	FOXA1	38061168			10	DELETION		6052	324411	4865	116	NEW_VARIANT
P-0046069-T01-IM6	ERCC6L2 (NM_001010895) - TSC1 (NM_000368) rearrangement: c.1880+1309:ERCC6L2_c.474:TSC1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ERCC6L2:TSC1}		151036	0	7	9	Intron of ERCC6L2(+):1Kb after exon 12	ERCC6L2	98705140			9	Exon 6 of TSC1(-)	TSC1	135798769			10	INVERSION		37093629	324412	120341	7	NEW_VARIANT
P-0046083-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+986:EML4_c.3173-271:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		98463	0	73	2	Intron of ALK(-):271bp before exon 20	EML4	29446665			2	Intron of EML4(+):986bp after exon 12	ALK	42523642			10	INVERSION		13076977	324422	211559	73	NEW_VARIANT
P-0046083-T01-IM6	FLT4 (NM_182925) rearrangement: c.58+2307_c.1039inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		14821	0	287	5	Exon 8 of FLT4(-)	FLT4	180055946			5	Intron of FLT4(-):2Kb after exon 1	FLT4	180074181			0	INVERSION		18235	324423	60239	583	NEW_VARIANT
P-0046092-T01-IM6	WHSC1L1 (NM_023034) - ADAM32 (NM_145004) rearrangement: c.611:WHSC1L1_c.1902+1372:ADAM32inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {WHSC1L1:ADAM32}		49609	0	7	8	Exon 2 of WHSC1L1(-)	WHSC1L1	38205079			8	Intron of ADAM32(+):1Kb after exon 17	ADAM32	39105057			10	INVERSION		899978	324446	14386	10	NEW_VARIANT
P-0046098-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.106+2442:PIK3R3_chr1:g.46597663inv	IMPPRECISE	Note: The PIK3R3 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		948	0	14	1	Intron of PIK3R3(-):2Kb after exon 1	PIK3R3	46595077			1	5-UTR of PIK3R3(-):88Kb before coding start	PIK3R3	46597663			0	INVERSION		2586	324448	1138	14	NEW_VARIANT
P-0046106-T01-IM6	BBC3 (NM_001127240) rearrangement: t(2;19)(q33.2;q13.32)(chr2:g.204419521::chr19:g.47729968)	PRECISE	Note: The BBC3 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	23	19	Exon 3 of BBC3(-)	BBC3	47729968			2	IGR: 113Kb before RAPH1(-)	BBC3	204419521			10	TRANSLOCATION		0	324490	0	31	NEW_VARIANT
P-0046108-T01-IM6	AXIN2 (NM_004655) rearrangement: c.815+3064_c.1067del	PRECISE	Note: The AXIN2 rearrangement is an intragenic deletion of exons 3 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1756	0	57	17	Exon 5 of AXIN2(-)	AXIN2	63534454			17	Intron of AXIN2(-):3Kb after exon 2	AXIN2	63550860			10	DELETION		16406	324489	2555	60	NEW_VARIANT
P-0046110-T01-IM6	RB1 (NM_000321) rearrangement: c.607+9_c.940-284del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 7 - 9.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		1409	0	65	13	Intron of RB1(+):9bp after exon 6	RB1	48923168			13	Intron of RB1(+):283bp before exon 10	RB1	48941346			10	DELETION		18178	324480	228	67	NEW_VARIANT
P-0046151-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-124:CDKN2A_chr9:g.22691184inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {LINC01239:CDKN2A}		10421	0	25	9	Intron of CDKN2A(-):124bp before exon 2	CDKN2A	21971331			9	5-UTR of LINC01239(+):133Kb before coding start	CDKN2A	22691184			10	INVERSION		719853	324631	10359	25	NEW_VARIANT
P-0046153-T01-IM6	CDKN1B (NM_004064) rearrangement: t(8;12)(q21.3;p13.1)(chr8:g.87279220::chr12:g.12870997)	PRECISE	Note: The CDKN1B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	38	12	Exon 1 of CDKN1B(+)	CDKN1B	12870997			8	IGR: 53Kb before SLC7A13(-)	CDKN1B	87279220			10	TRANSLOCATION		0	324619	0	38	NEW_VARIANT
P-0046160-T01-IM6	TP63 (NM_003722) rearrangement: c.2026:TP63_chr3:g.189715390del	PRECISE	Note: The TP63 rearrangement is a deletion of exon 14. One of the breakpoints is within exon 14.	MANUAL_OK	3to5	3to5	Antisense Fusion		272	0	20	3	Exon 14 of TP63(+)	TP63	189612274			3	Intron of LEPREL1(-):2Kb before exon 2	TP63	189715390			10	DELETION		103116	324637	365	20	NEW_VARIANT
P-0004871-T01-IM5	BRAF (NM_004333) rearrangement : c.1140+1724:BRAF_chr7:g.156140327inv	PRECISE	Note: The BRAF (NM_004333) rearrangement event results in the inversion of BRAF exons 1-8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		275326	0	18	7	Intron of BRAF(-): 2Kb after exon 8	BRAF	140492384			7	IGR: 193Kb before NCRNA00244(+)	BRAF	156140327			22	INVERSION		15647943	39968	279421	18	NEW_VARIANT
P-0005201-T02-IM6	RPTOR (NM_020761) rearrangement: chr17:g.50212445_c.3226:RPTORdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		288318	0	20	17	Intron of CA10(-):23Kb after exon 1	RPTOR	50212445			17	Exon 27 of RPTOR(+)	RPTOR	78921112			10	DELETION		28708667	188281	278189	21	NEW_VARIANT
P-0007293-T01-IM5	CTNNB1 (NM_001904) rearrangement : t(3;4)(p22.1;q34.3)(chr3:g.41267307::chr4:g.177727721)	PRECISE	Note: The CTNNB1 (NM_001904) rearrangement event is a translocation which results in a truncated CTNNB1. One of the breakpoints is within CTBBN1 exon6.	MANUAL_OK	5to5	5to5	-		0	0	27	4	IGR: 14Kb after VEGFC(-)	CTNNB1	177727721			3	Exon 6 of CTNNB1(+)	CTNNB1	41267307			15	TRANSLOCATION		0	115277	0	26	NEW_VARIANT
P-0007690-T02-IM6	SMARCA4 (NM_003072) rearrangement: c.4912-106:SMARCA4_chr19:g.10684923del	IMPPRECISE	Note: The SMARCA4 rearrangement is a deletion of exon 35. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		97398	0	7	19	Intron of AP1M2(-):169bp after exon 11	SMARCA4	10684923			19	Intron of SMARCA4(+):105bp before exon 35	SMARCA4	11172354			0	DELETION		487431	277674	81503	8	NEW_VARIANT
P-0015717-T02-IM6	PTPRD (NM_002839) - ATP10A (NM_024490) rearrangement: t(9;15)(p24.1;q12)(chr9:g.8331699::chr15:g.26029000)	PRECISE	Note: The PTPRD - ATP10A rearrangement is a translocation with breakpoints within PTPRD exon 44 and ATP10A intron 1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	177	15	Intron of ATP10A(-):3Kb before exon 2	PTPRD	26029000			9	Exon 44 of PTPRD(-)	ATP10A	8331699			10	TRANSLOCATION		0	172083	0	177	NEW_VARIANT
P-0015717-T02-IM6	RICTOR (NM_152756) rearrangement: c.746_chr5:g.17010344inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		102096	0	123	5	IGR: 120Kb before LOC285696(-)	RICTOR	17010344			5	Exon 8 of RICTOR(-)	RICTOR	38981977			10	INVERSION		21971633	172064	452635	251	NEW_VARIANT
P-0015717-T02-IM6	DROSHA (NM_01323) - SH3GL2 (NM_003026) rearrangement: t(5;9)(p13.3;p22.2)(chr5:g.31515270::chr9:g.17618065)	PRECISE	Note:  The DROSHA - SH3GL2 rearrangement is a translocation with breakpoints within DROSHA exon 7 and SH3GL2 intron 1. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	221	9	Intron of SH3GL2(+):39Kb after exon 1	DROSHA	17618065			5	Exon 7 of DROSHA(-)	SH3GL2	31515270			10	TRANSLOCATION		0	172081	0	301	NEW_VARIANT
P-0021198-T01-IM6	GSK3B (NM_002093) rearrangement: c.948+12_c.910-742inv	PRECISE	Note: The GSK3B rearrangement is an inversion of exon 9. Its significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		897	0	3	3	Intron of GSK3B(-):11bp after exon 9	GSK3B	119585425			3	Intron of GSK3B(-):742bp before exon 9	GSK3B	119586217			10	INVERSION		792	186408	282	3	NEW_VARIANT
P-0023323-T01-IM6	YES1 (NM_005433) rearrangement: c.1343_chr18:g.803969inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		21374	0	67	18	Exon 11 of YES1(-)	YES1	732914			18	5-UTR of YES1(-):80Kb before coding start	YES1	803969			10	INVERSION		71055	194742	32802	95	NEW_VARIANT
P-0045456-T01-IM6	MGA (NM_001164273) rearrangement: c.3431-11:MGA_chr15:g.36457287del	PRECISE	Note: The MGA rearrangement is a deletion of exons 1 - 9.	MANUAL_OK	3to5	3to5	-		57673	0	4	15	IGR: 238Kb before MIR4510(+)	MGA	36457287			15	Intron of MGA(+):10bp before exon 10	MGA	42019367			9	DELETION		5562080	322879	68644	4	NEW_VARIANT
P-0023378-T01-IM6	BRAF (NM_004333) - AGK (NM_018238) rearrangement: c.980+1800:BRAF_c.101+14574:AGKinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {BRAF:AGK}		23189	0	8	7	Intron of BRAF(-):2Kb after exon 7	BRAF	140498362			7	Intron of AGK(+):15Kb after exon 2	AGK	141269941			0	INVERSION		771579	194906	26447	11	NEW_VARIANT
P-0025561-T01-IM6	BRAF (NM_004333) - AGK (NM_018238) Rearrangement: c.980+1288:BRAF_c.101+772:AGKinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {BRAF:AGK}		19988	0	30	7	Intron of BRAF(-):1Kb after exon 7	BRAF	140498874			7	Intron of AGK(+):772bp after exon 2	AGK	141256139			10	INVERSION		757265	205951	24265	31	NEW_VARIANT
P-0028078-T01-IM6	MDM4 (NM_002393) rearrangement: c.288-137:MDM4_chr1:g.248451616inv	PRECISE	Note: The MDM4 rearrangement is an inversion of exons 5-11. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		143238	0	5	1	Intron of MDM4(+):136bp before exon 5	MDM4	204501182			1	IGR: 6Kb before OR2T12(-)	MDM4	248451616			10	INVERSION		43950434	216048	205859	5	NEW_VARIANT
P-0028707-T01-IM6	STK11 (NM_000455) rearrangement: c.597+28:STK11_chr19:g.1279387del	PRECISE	Note: The STK11 rearrangement results in the deletion of exons 5-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {STK11:C19orf24}		10943	0	2	19	Intron of STK11(+):28bp after exon 4	STK11	1220532			19	Promoter of C19orf24(+):4Kb from tx start	STK11	1279387			3	DELETION		58855	218410	13279	2	NEW_VARIANT
P-0032812-T01-IM6	FYN (NM_153047) rearrangement: t(q21;p12.3)(chr6:g.112020748::chr12:g.16974089	PRECISE	Note: The FYN rearrangement is a translocation involving a breakpoint in exon 6. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	6	12	IGR: 168Kb before SKP1P2(+)	FYN	16974089			6	Exon 6 of FYN(-)	FYN	112020748			7	TRANSLOCATION		0	235850	0	7	NEW_VARIANT
P-0032812-T01-IM6	PREX2 (NM_024870) rearrangement: c.1929:PREX2_chr8:g.57326304inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		29975	0	22	8	IGR: 27Kb before PENK(-)	PREX2	57326304			8	Exon 18 of PREX2(+)	PREX2	68995525			10	INVERSION		11669221	235849	53718	22	NEW_VARIANT
P-0034168-T01-IM6	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	PRECISE	Note: The SND1 - BRAF fusion is predicted to be in frame and includes the kinase domain of BRAF	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SND1:BRAF}		103559	0	118	7	Intron of SND1(+):7Kb after exon 10	SND1	127368426			7	Intron of BRAF(-):2Kb before exon 9	BRAF	140489421			10	INVERSION		13120995	249561	153291	116	NEW_VARIANT
P-0034370-T01-IM6	LATS2 (NM_014572) Rearrangement: t(9;13)(q34.3;q12.11)(chr9:g.139825979::chr13:g.21555688)	PRECISE	Note: The LATS2 rearrangement is a translocation with breakpoint in exon 6 of LATS2. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	25	13	Exon 6 of LATS2(-)	LATS2	21555688			9	IGR: 9Kb before FBXW5(-)	LATS2	139825979			10	TRANSLOCATION		0	250628	0	25	NEW_VARIANT
P-0034710-T01-IM6	TP53BP1 (NM_001141980) Rearrangement :  t(15;20)(q11.21;p11.21)(chr15:g.43713243::chr20:g.22803318)	PRECISE	Note: The TP53BP1 Rearrangement is a translocation event with the breakpoint in exon20. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	23	20	IGR: 213Kb before SSTR4(+)	TP53BP1	22803318			15	Exon 20 of TP53BP1(-)	TP53BP1	43713243			10	TRANSLOCATION		0	253561	0	23	NEW_VARIANT
P-0034710-T01-IM6	TFAP2B (NM_003221) - DAXX (NM_001141970)  Rearrangement : c.82-509:TFAP2B_c.193:DAXXinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TFAP2B:DAXX}		58421	0	11	6	Exon 2 of DAXX(-)	TFAP2B	33289546			6	Intron of TFAP2B(+):508bp before exon 2	DAXX	50790611			10	INVERSION		17501065	253560	83433	13	NEW_VARIANT
P-0036240-T01-IM6	PTEN (NM_000314) rearrangement: c.209+85:PTEN_chr10:g.96615851inv	PRECISE	Note: The PTEN rearrangement is an inversion of exons 4-9. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		13287	0	25	10	Intron of PTEN(+):85bp after exon 3	PTEN	89685399			10	Promoter of CYP2C19(+):93Kb from tx start	PTEN	96615851			10	INVERSION		6930452	266784	10958	27	NEW_VARIANT
P-0036862-T01-IM6	AXIN1 (NM_003502) Rearrangement : c.41_c.1020-2030del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4041	0	100	16	Intron of AXIN1(-):2Kb before exon 4	AXIN1	362099			16	Exon 2 of AXIN1(-)	AXIN1	396985			10	DELETION		34886	274730	6925	104	NEW_VARIANT
P-0036862-T01-IM6	SAE1 (NM_005500) - NOTCH2 (NM_024408) Rearrangement : t(1;19)(p11.2;q13.1)(chr1:g.120458500::chr19:g.47633732)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SAE1:NOTCH2}		0	0	32	19	Promoter of SAE1(+):347bp from tx start	SAE1	47633732			1	Exon 34 of NOTCH2(-)	NOTCH2	120458500			10	TRANSLOCATION		0	274733	0	32	NEW_VARIANT
P-0038799-T01-IM6	RFWD2 (NM_022457) rearrangement: c.1530+9_c.1612+6576del	PRECISE	Note: The RFWD2 rearrangement is an intragenic deletion of exon 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1244	0	28	1	Intron of RFWD2(-):7Kb after exon 14	RFWD2	176005746			1	Intron of RFWD2(-):8bp after exon 13	RFWD2	176012837			10	DELETION		7091	290828	958	32	NEW_VARIANT
P-0039162-T01-IM6	MPL (NM_005373) - PDZRN3 (NM_015009) rearrangement: t(1;3)(p34.2;p13)(chr1:g.43806209::chr3:g.73597756)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {MPL:PDZRN3}		0	0	7	3	Intron of PDZRN3(-):54Kb after exon 3	MPL	73597756			1	Intron of MPL(+):25bp after exon 6	PDZRN3	43806209			10	TRANSLOCATION		0	293916	0	9	NEW_VARIANT
P-0039162-T01-IM6	ARID1B (NM_020732) rearrangement: t(5;6)(p15.1;q25.3)(chr5:g.15008789::chr6:g.157099879)	PRECISE	Note : The ARID1B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	30	6	Exon 1 of ARID1B(+)	ARID1B	157099879			5	IGR: 183Kb before MIR4637(-)	ARID1B	15008789			10	TRANSLOCATION		0	293917	0	31	NEW_VARIANT
P-0039162-T01-IM6	ZFHX3 (NM_006885) rearrangement: t(7;16)(p14.3;q22.2)(chr7:g.30224334::chr16:g.72821085)	PRECISE	Note : The ZFHX3 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	40	16	Exon 10 of ZFHX3(-)	ZFHX3	72821085			7	IGR: 50Kb before MTURN(+)	ZFHX3	30224334			10	TRANSLOCATION		0	293919	0	41	NEW_VARIANT
P-0039629-T01-IM6	MITF (NM_198159) rearrangement: t(3;16)(p13;q12.2)(chr3:g.69928477::chr16:g.56183319)	IMPPRECISE	Note: The MITF rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	20	16	3-UTR of LOC283856(-):42Kb after coding stop	MITF	56183319			3	Exon 2 of MITF(+)	MITF	69928477			0	TRANSLOCATION		0	297286	0	20	NEW_VARIANT
P-0040246-T01-IM6	ALDOA (NM_001243177) - IRS1 (NM_005544) rearrangement: t(2;16)(q36.3;p11.2)(chr2:g.227660770::chr16:g.30081156)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ALDOA:IRS1}		0	0	12	16	Exon 8 of ALDOA(+)	ALDOA	30081156			2	Exon 1 of IRS1(-)	IRS1	227660770			0	TRANSLOCATION		0	300731	0	14	NEW_VARIANT
P-0040246-T01-IM6	IRS1 (NM_005544) rearrangement: t(2;22)(q36.3;q13.31)(chr2:g.227660594::chr22:g.47611716)	PRECISE	Note: The IRS1 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	37	22	IGR: 245Kb before LL22NC03-75H12.2(-)	IRS1	47611716			2	Exon 1 of IRS1(-)	IRS1	227660594			10	TRANSLOCATION		0	300733	0	41	NEW_VARIANT
P-0043860-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-980:EML4_c.3173-537:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		94568	0	64	2	Intron of ALK(-):537bp before exon 20	EML4	29446931			2	Intron of EML4(+):979bp before exon 13	ALK	42527401			10	INVERSION		13080470	325104	159574	134	NEW_VARIANT
P-0046112-T01-IM6	PDGFRA (NM_006206) rearrangement: c.266:PDGFRA_chr4:g.43764201del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		25128	0	13	4	IGR: 412Kb before KCTD8(-)	PDGFRA	43764201			4	Exon 3 of PDGFRA(+)	PDGFRA	55127478			10	DELETION		11363277	324485	20127	13	NEW_VARIANT
P-0046202-T01-IM6	UBA2 (NM_005499) - CEBPA (NM_004364) rearrangement: c.293+574:UBA2_c.1007:CEBPAinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {UBA2:CEBPA}		7648	0	537	19	Exon 1 of CEBPA(-)	UBA2	33792314			19	Intron of UBA2(+):574bp after exon 3	CEBPA	34923410			10	INVERSION		1131096	324799	11189	537	NEW_VARIANT
P-0046202-T01-IM6	SMAD4 (NM_005359) - TTC28 (NM_001145418) rearrangement: t(18;22)(q21.2;q12.1)(chr18:g.48592015::chr22:g.29065731)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {SMAD4:TTC28}		0	0	11	22	Intron of TTC28(-):10Kb after exon 1	SMAD4	29065731			18	Intron of SMAD4(+):39bp after exon 9	TTC28	48592015			0	TRANSLOCATION		0	324803	0	11	NEW_VARIANT
P-0046212-T01-IM6	NF1 (NM_001042492) rearrangement: c.4836-6260:NF1_chr17:g.30703505inv	IMPPRECISE	Note: The NF1 rearrangement is an inversion of exons 37 - 58. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		39708	0	5	17	Intron of NF1(+):6Kb before exon 37	NF1	29646578			17	IGR: 26Kb before ZNF207(+)	NF1	30703505			0	INVERSION		1056927	324746	46404	6	NEW_VARIANT
P-0046219-T01-IM6	AXL (NM_021913) rearrangement: c.2196+24:AXL_chr19:g.48678698del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {AXL:C19orf68}		149039	0	12	19	Intron of AXL(+):24bp after exon 18	AXL	41762540			19	Intron of C19orf68(+):3Kb after exon 2	AXL	48678698			10	DELETION		6916158	324927	158138	12	NEW_VARIANT
P-0046235-T01-IM6	BAP1 (NM_004656) rearrangement: c.2098:BAP1_chr3:g.51914799inv	PRECISE	Note: The BAP1 rearrangement is an inversion of exon 17. One of the breakpoints is within exon 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1577	0	31	3	IGR: 7Kb before IQCF5(-)	BAP1	51914799			3	Exon 17 of BAP1(-)	BAP1	52436396			10	INVERSION		521597	324830	2033	43	NEW_VARIANT
P-0046236-T01-IM6	CDKN2A (NM_000077) rearrangement: c.458-18:CDKN2A_chr9:g.21966591del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		454	0	28	9	Promoter of CDKN2A(-):1Kb from tx start	CDKN2A	21966591			9	Intron of CDKN2A(-):18bp before exon 3	CDKN2A	21968259			10	DELETION		1668	324829	100	29	NEW_VARIANT
P-0046243-T01-IM6	RB1 (NM_000321) rearrangement: c.1:RB1_chr13:g.52414371inv	PRECISE	Note: The RB1 rearrangement is an inversion of exons 1 - 27. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		33931	0	24	13	Exon 1 of RB1(+)	RB1	48878049			13	3-UTR of LINC00282(-):5Kb after coding stop	RB1	52414371			10	INVERSION		3536322	324952	29632	41	NEW_VARIANT
P-0046246-T01-IM6	AXL (NM_021913) - ACPP (NM_001134194) rearrangement: t(3;19)(q22.1;q13.2)(chr3:g.132075952::chr19:g.41745897)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {AXL:ACPP}		0	0	23	19	Intron of AXL(+):272bp after exon 10	AXL	41745897			3	Intron of ACPP(+):253bp after exon 10	ACPP	132075952			10	TRANSLOCATION		0	324941	0	22	NEW_VARIANT
P-0046250-T01-IM6	RUNX1 (NM_001754) rearrangement: c.59-16671_c.805+11inv	PRECISE	Note: The RUNX1 rearrangement is an intragenic inversion of exons 3 - 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		7727	0	3	21	Intron of RUNX1(-):10bp after exon 7	RUNX1	36206696			21	Intron of RUNX1(-):17Kb before exon 3	RUNX1	36281931			7	INVERSION		75235	324940	6209	3	NEW_VARIANT
P-0046253-T01-IM6	PBRM1 (NM_018313) rearrangement: t(3;22)(p21.1;q13.2)(chr3:g.52668553::chr22:g.41866350)	IMPPRECISE	Note: The PBRM1 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	9	22	Intron of ACO2(+):1Kb after exon 1	PBRM1	41866350			3	Intron of PBRM1(-):64bp after exon 12	PBRM1	52668553			0	TRANSLOCATION		0	324951	0	9	NEW_VARIANT
P-0046254-T01-IM6	KMT2D (NM_003482) rearrangement: t(12;X)(q13.12;q26.2)(chr12:g.49435733::chrX:g.133357229)	PRECISE	Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 29. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	X	IGR: 14Kb before CCDC160(+)	KMT2D	133357229			12	Exon 29 of KMT2D(-)	KMT2D	49435733			10	TRANSLOCATION		0	324953	0	9	NEW_VARIANT
P-0046259-T01-IM6	ANKRD11 (NM_013275) - PIEZO1 (NM_001142864) rearrangement: c.7923:ANKRD11_c.65-13589:PIEZO1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ANKRD11:PIEZO1}		1018	0	19	16	Intron of PIEZO1(-):14Kb before exon 2	ANKRD11	88829476			16	Exon 13 of ANKRD11(-)	PIEZO1	89334955			10	DELETION		505479	324972	846	26	NEW_VARIANT
P-0046259-T01-IM6	NCOA3 (NM_181659) rearrangement: t(9;20)(q21.12;q13.12)(chr9:g.72660473::chr20:g.46279928)	PRECISE	Note: The NCOA3 rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	26	20	Exon 20 of NCOA3(+)	NCOA3	46279928			9	Intron of MAMDC2(+):860bp after exon 2	NCOA3	72660473			10	TRANSLOCATION		0	324973	0	33	NEW_VARIANT
P-0046260-T01-IM6	ALG9 (NM_001077690) - KMT2A (NM_001197104) rearrangement: c.1714-9207:ALG9_c.11072-27:KMT2Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {ALG9:KMT2A}		72562	0	4	11	Intron of ALG9(-):9Kb before exon 16	ALG9	111666451			11	Intron of KMT2A(+):26bp before exon 31	KMT2A	118382639			10	INVERSION		6716188	324971	33616	5	NEW_VARIANT
P-0046261-T01-IM6	MAP3K1 (NM_005921) rearrangement: t(5;12)(q11.2;p13.32)(chr5:g.56179537::chr12:g.4987480)	PRECISE	Note: The MAP3K1 rearrangement is a translocation with a breakpoint in intron 15.Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	10	12	IGR: 32Kb before KCNA1(+)	MAP3K1	4987480			5	Intron of MAP3K1(+):31bp after exon 15	MAP3K1	56179537			10	TRANSLOCATION		0	324968	0	10	NEW_VARIANT
P-0046296-T01-IM6	RET (NM_020975) rearrangement: t(10;13)(q11.21;q12.11)(chr10:g.43611791::chr13:g.22535936)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	5	13	IGR: 89Kb before LINC00424(-)	RET	22535936			10	Intron of RET(+):240bp before exon 12	RET	43611791			10	TRANSLOCATION		0	325054	0	5	NEW_VARIANT
P-0046298-T01-IM6	ARID1A (NM_006015) rearrangement: c.1137+7077_c.4276del	PRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 2 - 18. One of the breakpoints is within exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		30602	0	7	1	Intron of ARID1A(+):7Kb after exon 1	ARID1A	27031108			1	Exon 18 of ARID1A(+)	ARID1A	27100994			10	DELETION		69886	325048	27366	7	NEW_VARIANT
P-0046298-T01-IM6	ATP6V0A1 (NM_001130020) - STAT5A (NM_003152) rearrangement: c.424-2307:ATP6V0A1_c.1713:STAT5Adup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ATP6V0A1:STAT5A}		38725	0	11	17	Exon 15 of STAT5A(+)	ATP6V0A1	40459452			17	Intron of ATP6V0A1(+):2Kb before exon 6	STAT5A	40627350			10	DUPLICATION		167898	325049	41401	12	NEW_VARIANT
P-0046315-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+1172:TMPRSS2_c.40-61021:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		84968	0	24	21	Intron of ERG(-):61Kb before exon 4	TMPRSS2	39878565			21	Intron of TMPRSS2(-):1Kb after exon 1	ERG	42878705			10	DELETION		3000140	325091	45854	24	NEW_VARIANT
P-0046321-T01-IM6	STK11 (NM_000455) rearrangement: t(18;19)(q12.2;p13.3)(chr18:g.32923566::chr19:g.1220489)	PRECISE	Note: The STK11 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {STK11:ZNF24}		0	0	73	19	Exon 4 of STK11(+)	STK11	1220489			18	5-UTR of ZNF24(-):6Kb before coding start	STK11	32923566			10	TRANSLOCATION		0	325093	0	72	NEW_VARIANT
P-0004226-T03-IM6	INPPL1 (NM_001567) - FCHSD2 (NM_014824) rearrangement: c.2415+83:INPPL1_c.705+16440:FCHSD2inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {INPPL1:FCHSD2}		24603	0	20	11	Intron of INPPL1(+):83bp after exon 21	INPPL1	71945742			11	Intron of FCHSD2(-):16Kb after exon 8	FCHSD2	72678693			0	INVERSION		732951	325674	48146	20	NEW_VARIANT
P-0046401-T01-IM6	NF1 (NM_001042492) rearrangement: c.4836-1907_c.5762dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 37 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		4541	0	118	17	Intron of NF1(+):2Kb before exon 37	NF1	29650931			17	Exon 39 of NF1(+)	NF1	29657466			10	DUPLICATION		6535	325482	8806	122	NEW_VARIANT
P-0043747-T02-IM6	AGO2 (NM_012154) rearrangement: c.2402:AGO2_chr8:g.141541880inv	PRECISE	Note: The AGO2 rearrangement is an inversion of exons 18 - 19. One of the breakpoints is within exon 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2116	0	3	8	3-UTR of AGO2(-):262bp after coding stop	AGO2	141541880			8	Exon 18 of AGO2(-)	AGO2	141542584			8	INVERSION		704	325694	2524	3	NEW_VARIANT
P-0046463-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4822:TMPRSS2_c.40-53654:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		64501	0	90	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39871198			21	Intron of TMPRSS2(-):5Kb before exon 2	ERG	42874938			10	DELETION		3003740	325735	51270	94	NEW_VARIANT
P-0046467-T01-IM6	KDM5A (NM_001042603) rearrangement: c.4359_c.4455+1117del	PRECISE	Note: The KDM5A rearrangement is an intragenic deletion of exon 26. One of the breakpoints is within exon 26. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		683	0	29	12	Intron of KDM5A(-):1Kb after exon 26	KDM5A	403622			12	Exon 26 of KDM5A(-)	KDM5A	404835			10	DELETION		1213	325722	978	28	NEW_VARIANT
P-0046480-T01-IM6	PPM1D (NM_003620) rearrangement: c.473-16:PPM1D_chr17:g.58662102del	IMPPRECISE	Note: The PPM1D rearrangement is a deletion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {LOC388406:PPM1D}		4053	0	6	17	5-UTR of LOC388406(+):2Kb before coding start	PPM1D	58662102			17	Intron of PPM1D(+):15bp before exon 2	PPM1D	58700866			0	DELETION		38764	325742	3352	6	NEW_VARIANT
P-0046552-T01-IM6	RICTOR (NM_152756) rearrangement: t(5;20)(p13.1;q13.2)(chr5:g.39074150::chr20:g.50693085)	PRECISE	Note: The RICTOR rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	20	IGR: 7Kb before ZFP64(-)	RICTOR	50693085			5	Intron of RICTOR(-):62bp after exon 2	RICTOR	39074150			8	TRANSLOCATION		0	325890	0	6	NEW_VARIANT
P-0046306-T01-IM6	PTEN (NM_000314) rearrangement: c.210-71_c.405dup	PRECISE	Note: The PTEN rearrangement is an intragenic duplication of exons 4 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		429	0	20	10	Intron of PTEN(+):70bp before exon 4	PTEN	89690732			10	Exon 5 of PTEN(+)	PTEN	89692921			10	DUPLICATION		2189	325452	1433	38	NEW_VARIANT
P-0046342-T01-IM6	NSD1 (NM_022455) rearrangement: c.928-87:NSD1_chr5:g.175874680del	PRECISE	Note: The NSD1 rearrangement is a deletion of exons 1 - 2.	MANUAL_OK	3to5	3to5	Transcript Fusion {FAF2:NSD1}		34762	0	34	5	Promoter of FAF2(+):675bp from tx start	NSD1	175874680			5	Intron of NSD1(+):86bp before exon 3	NSD1	176618798			10	DELETION		744118	325368	26914	36	NEW_VARIANT
P-0046360-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.2716:ZFHX3_chr16:g.65619132del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		116557	0	52	16	IGR: 301Kb before LINC00922(-)	ZFHX3	65619132			16	Exon 2 of ZFHX3(-)	ZFHX3	72991329			10	DELETION		7372197	325427	330208	97	NEW_VARIANT
P-0046362-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2088:TMPRSS2_c.40-58426:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		86337	0	47	21	Intron of ERG(-):58Kb before exon 4	TMPRSS2	39875970			21	Intron of TMPRSS2(-):2Kb after exon 1	ERG	42877789			10	DELETION		3001819	325441	85361	52	NEW_VARIANT
P-0046495-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.6069:ZFHX3_chr16:g.72804103del	IMPPRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		41521	0	44	16	IGR: 13Kb before ZFHX3(-)	ZFHX3	72804103			16	Exon 9 of ZFHX3(-)	ZFHX3	72830512			0	DELETION		26409	325806	40066	44	NEW_VARIANT
P-0046527-T01-IM6	PREX2 (NM_024870) rearrangement: t(8;16)(q13.2;q12.1)(chr8:g.69021796::chr16:g.50865290)	PRECISE	Note: The PREX2 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	47	16	IGR: 89Kb before CYLD(+)	PREX2	50865290			8	Exon 25 of PREX2(+)	PREX2	69021796			10	TRANSLOCATION		0	325867	0	54	NEW_VARIANT
P-0046527-T01-IM6	NBN (NM_002485) rearrangement: c.111_c.333inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		1319	0	15	8	Exon 4 of NBN(-)	NBN	90993109			8	Exon 2 of NBN(-)	NBN	90995010			10	INVERSION		1901	325866	2853	15	NEW_VARIANT
P-0046527-T01-IM6	ATRX (NM_000489) rearrangement: t(8;X)(q21.3;q21.1)(chr8:g.89361199::chrX:g.76776451)	PRECISE	Note: The ATRX rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	8	X	Intron of ATRX(-):57bp before exon 34	ATRX	76776451			8	IGR: 312Kb before MMP16(-)	ATRX	89361199			7	TRANSLOCATION		0	325868	0	8	NEW_VARIANT
P-0028499-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.1652_c.1952-139del	PRECISE	Note: The NOTCH3 rearrangement is an intragenic deletion of exons 11 - 12. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4263	0	87	19	Intron of NOTCH3(-):139bp before exon 13	NOTCH3	15296629			19	Exon 11 of NOTCH3(-)	NOTCH3	15298104			10	DELETION		1475	326051	2900	89	NEW_VARIANT
P-0046404-T01-IM6	RAC2 (NM_002872) - ATP6V0A4 (NM_130841) rearrangement: t(7;22)(q34;q13.1)(chr7:g.138393574::chr22:g.37637553)	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RAC2:ATP6V0A4}		0	0	70	22	Intron of RAC2(-):73bp after exon 2	RAC2	37637553			7	Intron of ATP6V0A4(-):794bp after exon 20	ATP6V0A4	138393574			0	TRANSLOCATION		0	325485	0	69	NEW_VARIANT
P-0046576-T01-IM6	CASP8 (NM_001080125) rearrangement: c.588+53_c.772+743inv	IMPPRECISE	Note: The CASP8 rearrangement is an intragenic inversion of exons 4 - 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2263	0	6	2	Intron of CASP8(+):53bp after exon 3	CASP8	202136397			2	Intron of CASP8(+):743bp after exon 5	CASP8	202138408			0	INVERSION		2011	325933	3022	6	NEW_VARIANT
P-0046579-T01-IM6	PIK3C2G (NM_004570) rearrangement: t(12;19)(p12.3;q13.2)(chr12:g.18524131::chr19:g.41278692)	PRECISE	Note: The PIK3C2G rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MIA-RAB4B:PIK3C2G}		0	0	8	19	Promoter of MIA-RAB4B(+):3Kb from tx start	PIK3C2G	41278692			12	Exon 12 of PIK3C2G(+)	PIK3C2G	18524131			10	TRANSLOCATION		0	325931	0	9	NEW_VARIANT
P-0046580-T01-IM6	ATF6 (NM_007348) - NUF2 (NM_031423) rearrangement: c.1719+11445:ATF6_c.1261-58:NUF2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {ATF6:NUF2}		36834	0	8	1	Intron of ATF6(+):11Kb after exon 14	ATF6	161844547			1	Intron of NUF2(+):57bp before exon 14	NUF2	163325067			6	DELETION		1480520	325934	48394	8	NEW_VARIANT
P-0046582-T01-IM6	STAG2 (NM_001042749) rearrangement: c.1240:STAG2_chrX:g.122976403inv	PRECISE	Note: The STAG2 rearrangement is an inversion of exons 1 - 14. One of the breakpoints is within exon 14. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		24312	0	25	X	IGR: 17Kb before XIAP(+)	STAG2	122976403			X	Exon 14 of STAG2(+)	STAG2	123190021			10	INVERSION		213618	325932	38357	30	NEW_VARIANT
P-0046594-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+2217:EML4_c.3173-51:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		110484	0	9	2	Intron of ALK(-):51bp before exon 20	EML4	29446445			2	Intron of EML4(+):2Kb after exon 5	ALK	42494088			7	INVERSION		13047643	326054	112468	9	NEW_VARIANT
P-0046612-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.4425-6750_c.4534del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 31 - 32. One of the breakpoints is within exon 32.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1912	0	12	19	Intron of SMARCA4(+):7Kb before exon 31	SMARCA4	11162181			19	Exon 32 of SMARCA4(+)	SMARCA4	11169464			10	DELETION		7283	326022	1059	11	NEW_VARIANT
P-0046612-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.2206:WHSC1_chr4:g.1817511dup	PRECISE	Note: The WHSC1 rearrangement is a duplication of exons 1 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		20291	0	11	4	Exon 13 of LETM1(-)	WHSC1	1817511			4	Exon 12 of WHSC1(+)	WHSC1	1955119			10	DUPLICATION		137608	326024	16359	11	NEW_VARIANT
P-0046623-T01-IM6	RAC2 (NM_002872) rearrangement: c.108-318:RAC2_chr22:g.36088023inv	PRECISE	Note: The RAC2 rearrangement is an inversion of exons 3 - 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12408	0	9	22	IGR: 26Kb before APOL5(+)	RAC2	36088023			22	Intron of RAC2(-):318bp before exon 3	RAC2	37629276			10	INVERSION		1541253	326083	15401	11	NEW_VARIANT
P-0046624-T01-IM6	SPATA2L (NM_152339) - FANCA (NM_000135) rearrangement: c.304-596:SPATA2L_c.736:FANCAdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPATA2L:FANCA}		61572	0	12	16	Intron of SPATA2L(-):596bp before exon 3	SPATA2L	89765309			16	Exon 8 of FANCA(-)	FANCA	89869723			10	DUPLICATION		104414	326099	59956	21	NEW_VARIANT
P-0046624-T01-IM6	NCOR1 (NM_006311) rearrangement: c.1853-34:NCOR1_chr17:g.16345142del	PRECISE	Note:The NCOR1 rearrangement is a deletion of exons 1 - 16.	MANUAL_OK	3to5	3to5	-		21415	0	13	17	Intron of NCOR1(-):34bp before exon 17	NCOR1	16022833			17	5-UTR of LRRC75A-AS1(+):29Kb before coding start	NCOR1	16345142			10	DELETION		322309	326098	38475	13	NEW_VARIANT
P-0046628-T01-IM6	APC (NM_000038) rearrangement: c.1626+197_c.6225del	PRECISE	Note:The APC rearrangement is an intragenic deletion of exons 14 - 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		18636	0	13	5	Intron of APC(+):197bp after exon 13	APC	112163900			5	Exon 16 of APC(+)	APC	112177516			10	DELETION		13616	326076	14635	13	NEW_VARIANT
P-0046629-T01-IM6	CDKN2A (NM_058195, NM_000077) rearrangement: c.458-28:NM_000077_c.193+1786:NM_058195del	PRECISE	Note:The CDKN2A rearrangement is a deletion of CDKN2A exons 1 - 2. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		4231	0	11	9	Intron of CDKN2A(-):28bp before exon 3	CDKN2A	21968269			9	Intron of CDKN2A(-):2Kb after exon 1	CDKN2A	21992352			10	DELETION		24083	326080	5699	11	NEW_VARIANT
P-0046629-T01-IM6	KDM6A (NM_021140) rearrangement: c.1269:KDM6A_chrX:g.44623978del	PRECISE	Note: The KDM6A rearrangement is a deletion of exons 1 - 13. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	-		5468	0	5	X	IGR: 79Kb before DUSP21(+)	KDM6A	44623978			X	Exon 13 of KDM6A(+)	KDM6A	44919341			10	DELETION		295363	326081	9635	11	NEW_VARIANT
P-0021937-T03-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+886:KIF5B_c.2137-477:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		68419	0	188	10	Intron of KIF5B(-):885bp after exon 15	KIF5B	32316470			10	Intron of RET(+):476bp before exon 12	RET	43611555			10	INVERSION		11295085	325973	112303	265	NEW_VARIANT
P-0034062-T02-IM6	ATRX (NM_000489) rearrangement: t(11;X)(q24.3;q21.1)(chr11:g.129873889::chrX:g.76907888)	PRECISE	Note: The ATRX rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {LINC00167:ATRX}		0	0	7	X	Intron of ATRX(-):45bp before exon 15	ATRX	76907888			11	5-UTR of LINC00167(+):1Kb before coding start	ATRX	129873889			10	TRANSLOCATION		0	325965	0	7	NEW_VARIANT
P-0046564-T01-IM6	KDM5C (NM_004187) rearrangement: c.98:KDM5C_chrX:g.53255881del	PRECISE	Note: The KDM5C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		610	0	25	X	Exon 1 of KDM5C(-)	KDM5C	53253974			X	Promoter of KDM5C(-):35Kb from tx start	KDM5C	53255881			10	DELETION		1907	325943	228	29	NEW_VARIANT
P-0046569-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+526:TMPRSS2_c.19-19800:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32358	0	23	21	Intron of ERG(-):20Kb before exon 2	TMPRSS2	39837344			21	Intron of TMPRSS2(-):525bp after exon 2	ERG	42869520			10	DELETION		3032176	325942	23136	23	NEW_VARIANT
P-0046601-T01-IM6	PAX8 (NM_003466) rearrangement: c.1190-2363:PAX8_chr2:g.160291186inv	PRECISE	Note: The PAX8 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		181010	0	5	2	Intron of PAX8(-):2Kb before exon 11	PAX8	113980118			2	Intron of BAZ2B(-):1Kb before exon 9	PAX8	160291186			5	INVERSION		46311068	325983	200255	5	NEW_VARIANT
P-0046601-T01-IM6	CD74 (NM_001025159) rearrangement: c.442-58:CD74_chr5:g.149771672del	PRECISE	Note: The CD74 rearrangement is a deletion of exons 5 - 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		12626	0	197	5	Exon 20 of TCOF1(+)	CD74	149771672			5	Intron of CD74(-):58bp before exon 5	CD74	149784801			10	DELETION		13129	325982	7999	211	NEW_VARIANT
P-0045809-T02-IM6	SUFU (NM_016169) rearrangement: t(3;10)(p12.1;q24.32)(chr3:g.85786435::chr10:g.104389884)	PRECISE	Note: The SUFU rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	5	10	Exon 12 of SUFU(+)	SUFU	104389884			3	Intron of CADM2(+):65Kb before exon 2	SUFU	85786435			10	TRANSLOCATION		0	325373	0	6	NEW_VARIANT
P-0045809-T02-IM6	RET (NM_020975) - FBXL7 (NM_012304) fusion: t(5;10)(p15.1;q11.21)(chr5:g.15556734::chr10:g.43622269)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {RET:FBXL7}		0	0	5	10	Intron of RET(+):99bp after exon 19	RET	43622269			5	Intron of FBXL7(+):56Kb after exon 1	FBXL7	15556734			0	TRANSLOCATION		0	325372	0	5	NEW_VARIANT
P-0046563-T01-IM6	NTRK3 (NM_001012338) rearrangement: c.395+7789_c.623-25del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3465	0	28	15	Intron of NTRK3(-):25bp before exon 8	NTRK3	88679865			15	Intron of NTRK3(-):8Kb after exon 5	NTRK3	88718860			10	DELETION		38995	325944	2468	28	NEW_VARIANT
P-0046563-T01-IM6	NF1 (NM_001042492) rearrangement: t(4;17)(p12;q11.2)(chr4:g.45420174::chr17:g.29661961)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 40. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	11	17	Exon 40 of NF1(+)	NF1	29661961			4	IGR: 618Kb before GABRG1(-)	NF1	45420174			10	TRANSLOCATION		0	325945	0	13	NEW_VARIANT
P-0046474-T02-IM6	SMAD4 (NM_005359) rearrangement: c.357:SMAD4_chr18:g.61422486inv	PRECISE	Note: The SMAD4 rearrangement is an inversion of exons 3 - 12. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		42056	0	11	18	Exon 3 of SMAD4(+)	SMAD4	48575163			18	5-UTR of SERPINB7(+):27Kb before coding start	SMAD4	61422486			10	INVERSION		12847323	326270	11613	12	NEW_VARIANT
P-0046689-T01-IM6	BAP1 (NM_004656) rearrangement: t(3;17)(p21.1;q21.31)(chr3:g.52439384::chr17:g.42111278)	PRECISE	Note: The BAP1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	36	17	Promoter of LSM12(-):724bp from tx start	BAP1	42111278			3	Intron of BAP1(-):74bp before exon 11	BAP1	52439384			10	TRANSLOCATION		0	326441	0	35	NEW_VARIANT
P-0046693-T01-IM6	EWSR1 (NM_013986) - FLI1 (NM_002017) fusion: t(11;22)(q24.3;q12.2)(chr11:g.128656732::chr22:g.29683940)	IMPPRECISE	Note: The EWSR1 - FLI1 fusion involves EWSR1 exons 1 - 8 and FLI1 exons 6 - 9. The fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EWSR1:FLI1}		0	0	16	22	Intron of EWSR1(+):654bp before exon 9	EWSR1	29683940			11	Intron of FLI1(+):5Kb after exon 5	FLI1	128656732			0	TRANSLOCATION		0	326433	0	14	NEW_VARIANT
P-0046711-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.1369_c.1567+22inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		1426	0	18	1	Intron of NOTCH2(-):21bp after exon 9	NOTCH2	120508977			1	Exon 8 of NOTCH2(-)	NOTCH2	120510140			10	INVERSION		1163	326725	1119	29	NEW_VARIANT
P-0046713-T01-IM6	ALOX12B (NM_001139) rearrangement: t(11;17)(q13.1;p13.1)(chr11:g.65317075::chr17:g.7976987)	PRECISE	Note: The ALOX12B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	5	17	Exon 13 of ALOX12B(-)	ALOX12B	7976987			11	Intron of LTBP3(-):2Kb after exon 11	ALOX12B	65317075			10	TRANSLOCATION		0	326444	0	11	NEW_VARIANT
P-0046713-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-342:TMPRSS2_c.40-57445:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		39726	0	7	21	Intron of ERG(-):57Kb before exon 4	TMPRSS2	39874989			21	Intron of TMPRSS2(-):342bp before exon 2	ERG	42870458			10	DELETION		2995469	326443	25273	8	NEW_VARIANT
P-0046736-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-576:ERG_c.56-554:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		41381	0	14	21	Intron of ERG(-):576bp before exon 2	ERG	39818120			21	Intron of TMPRSS2(-):554bp before exon 2	TMPRSS2	42870670			10	INVERSION		3052550	326762	29261	12	NEW_VARIANT
P-0046736-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-4000_c.350-2072inv	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		39457	0	12	21	Intron of TMPRSS2(-):2Kb before exon 4	TMPRSS2	42863592			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874116			10	INVERSION		10524	326763	31687	12	NEW_VARIANT
P-0026710-T02-IM6	HOXB13 (NM_006361) rearrangement: c.602-198:HOXB13_chr17:g.48898867del	PRECISE	Note: The HOXB13 rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	-		15878	0	12	17	Intron of HOXB13(-):198bp before exon 2	HOXB13	46804603			17	IGR: 14Kb before WFIKKN2(+)	HOXB13	48898867			9	DELETION		2094264	326877	25811	12	NEW_VARIANT
P-0026710-T02-IM6	ASXL1 (NM_015338) - TBCD (NM_005993) rearrangement: t(17;20)(q25.3;q11.21)(chr17:g.80876983::chr20:g.31023295)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ASXL1:TBCD}		0	0	40	20	Exon 12 of ASXL1(+)	ASXL1	31023295			17	Intron of TBCD(+):1Kb before exon 24	TBCD	80876983			10	TRANSLOCATION		0	326878	0	40	NEW_VARIANT
P-0033566-T02-IM6	CD74 (NM_001025159) - PDE6A (NM_000440) rearrangement: c.442-141:CD74_c.2135+2556:PDE6Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:PDE6A}		92008	0	433	5	Intron of PDE6A(-):3Kb after exon 17	CD74	149260436			5	Intron of CD74(-):141bp before exon 5	PDE6A	149784884			10	DELETION		524448	326287	467743	1635	NEW_VARIANT
P-0044109-T02-IM6	PTEN (NM_000314) rearrangement: c.80-4310_c.164+116inv	PRECISE	Note: The PTEN rearrangement is an intragenic inversion of exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		835	0	24	10	Intron of PTEN(+):4Kb before exon 2	PTEN	89649472			10	Intron of PTEN(+):116bp after exon 2	PTEN	89653982			10	INVERSION		4510	326309	580	23	NEW_VARIANT
P-0046366-T01-IM6	NCOR1 (NM_006311) rearrangement: t(13;17)(q34;p12)(chr13:g.110777086::chr17:g.15968666)	PRECISE	Note: The NCOR1 rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	17	Intron of NCOR1(-):132bp after exon 33	NCOR1	15968666			13	IGR: 24Kb before COL4A1(-)	NCOR1	110777086			8	TRANSLOCATION		0	325424	0	8	NEW_VARIANT
P-0046660-T01-IM6	GATA1 (NM_002049) rearrangement: c.929:GATA1_chrX:g.48664112inv	PRECISE	Note: The GATA1 rearrangement is an inversion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2686	0	12	X	Exon 6 of GATA1(+)	GATA1	48652258			X	Intron of HDAC6(+):34bp after exon 6	GATA1	48664112			10	INVERSION		11854	326276	2870	12	NEW_VARIANT
P-0046676-T01-IM6	CARM1 (NM_199141) rearrangement: c.558+32:CARM1_chr19:g.11085632del	PRECISE	Note: The CARM1 rearrangement is a deletion of exons 5 - 16. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {CARM1:SMARCA4}		21869	0	40	19	Intron of CARM1(+):32bp after exon 4	CARM1	11019915			19	5-UTR of SMARCA4(+):9Kb before coding start	CARM1	11085632			10	DELETION		65717	326307	8447	43	NEW_VARIANT
P-0046720-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1641+1:EML4_c.3173-275:ALKinv	PRECISE	Note: The EML4 - ALK fusion involves EML4 exons 1 - 13 and ALK exons 20 - 29. The fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {EML4:ALK}		106995	0	16	2	Intron of ALK(-):275bp before exon 20	EML4	29446669			2	Intron of EML4(+):1bp after exon 13	ALK	42528533			10	INVERSION		13081864	326749	34035	16	NEW_VARIANT
P-0046725-T01-IM6	KDM6A (NM_021140) rearrangement: c.748+97:KDM6A_chrX:g.40408262inv	PRECISE	Note: The KDM6A rearrangement is an inversion of exons 1 - 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		4517	0	22	X	IGR: 32Kb before ATP6AP2(+)	KDM6A	40408262			X	Intron of KDM6A(+):97bp after exon 9	KDM6A	44911144			10	INVERSION		4502882	326738	10709	22	NEW_VARIANT
P-0046755-T01-IM6	RAD52 (NM_134424) rearrangement: c.187-67:RAD52_chr12:g.20234604inv	PRECISE	Note: The RAD52 rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {LOC100506393:RAD52}		245467	0	73	12	Intron of RAD52(-):67bp before exon 4	RAD52	1039377			12	5-UTR of LOC100506393(+):17Kb before coding start	RAD52	20234604			10	INVERSION		19195227	326809	133999	69	NEW_VARIANT
P-0046757-T01-IM6	DNMT1 (NM_001379) rearrangement: c.4817-119:DNMT1_chr19:g.18537515del	PRECISE	Note: The DNMT1 rearrangement is a deletion of exons 1 - 39. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		480668	0	25	19	Intron of DNMT1(-):119bp before exon 40	DNMT1	10244496			19	Intron of SSBP4(+):645bp before exon 2	DNMT1	18537515			10	DELETION		8293019	326808	534527	27	NEW_VARIANT
P-0046758-T01-IM6	FGFR3 (NM_000142) rearrangement: t(4;15)(p16.3;q15.1)(chr4:g.1807488::chr15:g.40834741)	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	10	15	Intron of C15orf57(-):10Kb before exon 4	FGFR3	40834741			4	Exon 13 of FGFR3(+)	FGFR3	1807488			10	TRANSLOCATION		0	326815	0	11	NEW_VARIANT
P-0046758-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.1410+4547_c.1751del	PRECISE	Note: The WHSC1 rearrangement is an intragenic deletion of exons 6 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3317	0	25	4	Intron of WHSC1(+):5Kb after exon 5	WHSC1	1924897			4	Exon 8 of WHSC1(+)	WHSC1	1940254			10	DELETION		15357	326814	3416	26	NEW_VARIANT
P-0046775-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-620_c.349+2051del	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		3124	0	8	21	Intron of TMPRSS2(-):2Kb after exon 3	TMPRSS2	42864232			21	Intron of TMPRSS2(-):620bp before exon 3	TMPRSS2	42867125			10	DELETION		2893	326880	2225	9	NEW_VARIANT
P-0046777-T01-IM6	IRS2 (NM_003749) rearrangement: c.4012+90:IRS2_chr13:g.110441644dup	PRECISE	Note: The IRS2 rearrangement is a duplication of exon 1. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		23520	0	4	13	Intron of IRS2(-):89bp after exon 1	IRS2	110434299			13	Promoter of IRS2(-):35Kb from tx start	IRS2	110441644			10	DUPLICATION		7345	326884	32386	4	NEW_VARIANT
P-0046790-T01-IM6	RET (NM_020975) - UXS1 (NM_001253875) rearrangement: t(2;10)(q12.2;q11.21)(chr2:g.106728260::chr10:g.43600430)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {RET:UXS1}		0	0	5	10	Exon 4 of RET(+)	RET	43600430			2	Intron of UXS1(-):841bp after exon 10	UXS1	106728260			10	TRANSLOCATION		0	326842	0	5	NEW_VARIANT
P-0046790-T01-IM6	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.225+207:ERBB2_c.1932-6773:CDK12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ERBB2:CDK12}		18797	0	8	17	Intron of CDK12(+):7Kb before exon 3	ERBB2	37640037			17	Intron of ERBB2(+):207bp after exon 2	CDK12	37863601			10	DUPLICATION		223564	326840	24574	8	NEW_VARIANT
P-0046793-T01-IM6	AXIN2 (NM_004655) rearrangement: c.703:AXIN2_chr17:g.63555989del	PRECISE	Note: The AXIN2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3149	0	37	17	Exon 2 of AXIN2(-)	AXIN2	63554036			17	5-UTR of AXIN2(-):30Kb before coding start	AXIN2	63555989			10	DELETION		1953	326826	3488	38	NEW_VARIANT
P-0046798-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+2826:TMPRSS2_c.40-53504:ERGdel	IMPPRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		81488	0	5	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39871048			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42877051			0	DELETION		3006003	326867	41438	5	NEW_VARIANT
P-0046837-T01-IM6	FGFR3 (NM_000142) rearrangement: t(4;11)(p16.3;p15.5)(chr4:g.1807338::chr11:g.2505245)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	7	11	Intron of KCNQ1(+):39Kb after exon 1	FGFR3	2505245			4	Exon 12 of FGFR3(+)	FGFR3	1807338			10	TRANSLOCATION		0	326984	0	7	NEW_VARIANT
P-0046837-T01-IM6	CREBBP (NM_004380) rearrangement: t(3;16)(p21.31;p13.3)(chr3:g.50188271::chr16:g.3900582)	PRECISE	Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	16	Exon 2 of CREBBP(-)	CREBBP	3900582			3	IGR: 5Kb before SEMA3F(+)	CREBBP	50188271			10	TRANSLOCATION		0	326985	0	12	NEW_VARIANT
P-0046838-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-319:TMPRSS2_c.19-18320:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		35877	0	69	21	Intron of ERG(-):18Kb before exon 2	TMPRSS2	39835864			21	Intron of TMPRSS2(-):319bp before exon 2	ERG	42870435			10	DELETION		3034571	326988	53506	71	NEW_VARIANT
P-0046665-T01-IM6	BBC3 (NM_001127240) rearrangement: c.229_c.568+589del	PRECISE	Note: The BBC3 rearrangement is an intragenic deletion of exons 2 - 3. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2305	0	13	19	Intron of BBC3(-):588bp after exon 3	BBC3	47729232			19	Exon 2 of BBC3(-)	BBC3	47731563			10	DELETION		2331	326269	2063	13	NEW_VARIANT
P-0046796-T01-IM6	ERBB2 (NM_004448) - IKZF3 (NM_012481) rearrangement: c.1314-49:ERBB2_c.164-10105:IKZF3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ERBB2:IKZF3}		25223	0	8	17	Intron of ERBB2(+):48bp before exon 12	ERBB2	37871944			17	Intron of IKZF3(-):10Kb before exon 4	IKZF3	37959291			10	INVERSION		87347	326862	781554	7	NEW_VARIANT
P-0046856-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.190-120:TCF7L2_chr10:g.114979136del	PRECISE	Note: The TCF7L2 rearrangement is a deletion of exons 2 - 14.	MANUAL_OK	3to5	3to5	-		21396	0	9	10	Intron of TCF7L2(+):119bp before exon 2	TCF7L2	114710846			10	IGR: 269Kb before TCF7L2(+)	TCF7L2	114979136			10	DELETION		268290	326960	25784	9	NEW_VARIANT
P-0046857-T01-IM6	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1169+665:ACOXL_c.394+4550:BCL2L11del	PRECISE	Note: The ACOXL - BCL2L11 rearrangement is a deletion that results in a fusion of ACOXL exons 1 - 13 to BCL2L11 exons 3 - 4.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ACOXL:BCL2L11}		14658	0	57	2	Intron of ACOXL(+):665bp after exon 13	ACOXL	111745459			2	Intron of BCL2L11(+):5Kb after exon 2	BCL2L11	111886266			10	DELETION		140807	326958	24502	59	NEW_VARIANT
P-0044707-T03-IM6	RTEL1 (NM_032957) - CDH4 (NM_001794) rearrangement: c.991+225:RTEL1_c.170-168444:CDH4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RTEL1:CDH4}		16058	0	27	20	Intron of CDH4(+):76Kb after exon 1	RTEL1	60150175			20	Intron of RTEL1(+):225bp after exon 10	CDH4	62305671			10	DUPLICATION		2155496	327161	50684	28	NEW_VARIANT
P-0046864-T01-IM6	BRCA1 (NM_007294) rearrangement: c.2944_c.4185+13inv	PRECISE	Note: The BRCA1 rearrangement is an intragenic inversion of exons 10 - 11. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		6512	0	2	17	Intron of BRCA1(-):12bp after exon 11	BRCA1	41242948			17	Exon 10 of BRCA1(-)	BRCA1	41244604			7	INVERSION		1656	327165	7127	2	NEW_VARIANT
P-0046870-T01-IM6	RAC1 (NM_018890) rearrangement: c.108-1748_c.174del	PRECISE	Note: The RAC1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		306	0	5	7	Intron of RAC1(+):2Kb before exon 3	RAC1	6429807			7	Exon 3 of RAC1(+)	RAC1	6431621			8	DELETION		1814	327166	360	6	NEW_VARIANT
P-0046875-T01-IM6	DOT1L (NM_032482) rearrangement: c.3860_c.4606+432inv	IMPPRECISE	Note: The DOT1L rearrangement is an intragenic inversion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		7024	0	3	19	Exon 27 of DOT1L(+)	DOT1L	2226380			19	Intron of DOT1L(+):432bp after exon 27	DOT1L	2227558			0	INVERSION		1178	327177	10875	3	NEW_VARIANT
P-0046881-T01-IM6	STAT3 (NM_139276) rearrangement: t(7;17)(q36.1;q21.2)(chr7:g.151490268::chr17:g.40477132)	PRECISE	Note: The STAT3 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	112	17	Intron of STAT3(-):53bp before exon 16	STAT3	40477132			7	Intron of PRKAG2(-):7Kb before exon 2	STAT3	151490268			10	TRANSLOCATION		0	327184	0	110	NEW_VARIANT
P-0046881-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+2519:TMPRSS2_c.18+14885:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75920	0	194	21	Intron of ERG(-):15Kb after exon 1	TMPRSS2	39855402			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42877358			10	DELETION		3021956	327180	137441	210	NEW_VARIANT
P-0046884-T01-IM6	TCF3 (NM_001136139) rearrangement: c.73-30_c.145+6490dup	PRECISE	Note: The TCF3 rearrangement is an intragenic duplication of exon 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1676	0	94	19	Intron of TCF3(-):6Kb after exon 2	TCF3	1639864			19	Intron of TCF3(-):30bp before exon 2	TCF3	1646456			10	DUPLICATION		6592	327186	2036	99	NEW_VARIANT
P-0046887-T01-IM6	POLE (NM_006231) rearrangement: c.4150-2330_c.4517inv	PRECISE	Note: The POLE rearrangement is an intragenic inversion of exons 33 - 35. One of the breakpoints is within exon 35. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		4508	0	75	12	Exon 35 of POLE(-)	POLE	133219844			12	Intron of POLE(-):2Kb before exon 33	POLE	133222893			10	INVERSION		3049	327175	7151	96	NEW_VARIANT
P-0014496-T03-IM6	AKT1 (NM_001014431) rearrangement: c.1212:AKT1_chr14:g.99512393del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		8284	0	33	14	IGR: 123Kb before BCL11B(-)	AKT1	99512393			14	Exon 12 of AKT1(-)	AKT1	105238750			10	DELETION		5726357	327193	8081	34	NEW_VARIANT
P-0046489-T01-IM6	HGF (NM_000601) rearrangement: t(7;22)(q21.11;q12.3)(chr7:g.81355058::chr22:g.34966766)	PRECISE	Note: The HGF rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	8	22	IGR: 495Kb before ISX(+)	HGF	34966766			7	Intron of HGF(-):147bp after exon 9	HGF	81355058			10	TRANSLOCATION		0	328480	0	8	NEW_VARIANT
P-0046868-T01-IM6	CEBPA (NM_004364) rearrangement: c.29:CEBPA_chr19:g.41809503del	PRECISE	Note: The CEBPA rearrangement is a deletion within exon 1.	MANUAL_OK	3to5	3to5	-		161675	0	31	19	Exon 1 of CEBPA(-)	CEBPA	33793292			19	Intron of HNRNPUL1(+):373bp before exon 13	CEBPA	41809503			10	DELETION		8016211	327172	201063	36	NEW_VARIANT
P-0046906-T01-IM6	SOCS1 (NM_003745) rearrangement: c.129:SOCS1_chr16:g.762649inv	PRECISE	Note: The SOCS1 rearrangement is an inversion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {SOCS1:METRN}		365770	0	162	16	Promoter of METRN(+):3Kb from tx start	SOCS1	762649			16	Exon 2 of SOCS1(-)	SOCS1	11349207			10	INVERSION		10586558	328477	296907	206	NEW_VARIANT
P-0046910-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.23_c.410del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2419	0	53	3	Exon 3 of CTNNB1(+)	CTNNB1	41266026			3	Exon 4 of CTNNB1(+)	CTNNB1	41266613			10	DELETION		587	328485	1722	56	NEW_VARIANT
P-0046931-T02-IM6	AURKA (NM_003600) rearrangement: c.42+114:AURKA_chr20:g.54729689del	IMPPRECISE	Note: The AURKA rearrangement is a deletion of exons 3 - 9. The rearrangement includes the kinase domain of AURKA. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11522	0	16	20	IGR: 94Kb before MC3R(+)	AURKA	54729689			20	Intron of AURKA(-):113bp after exon 2	AURKA	54963098			0	DELETION		233409	328571	24667	16	NEW_VARIANT
P-0046951-T01-IM6	BCOR (NM_001123385) - IL1RAPL2 (NM_017416) rearrangement: c.2997+49:BCOR_c.83-155811:IL1RAPL2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {BCOR:IL1RAPL2}		277202	0	24	X	Intron of BCOR(-):48bp after exon 4	BCOR	39931553			X	Intron of IL1RAPL2(+):156Kb before exon 3	IL1RAPL2	104284346			10	INVERSION		64352793	328580	316911	41	NEW_VARIANT
P-0046952-T01-IM6	AKT3 (NM_005465) rearrangement: c.900_c.948+1841del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		514	0	8	1	Intron of AKT3(-):2Kb after exon 9	AKT3	243725181			1	Exon 9 of AKT3(-)	AKT3	243727070			10	DELETION		1889	328573	185	9	NEW_VARIANT
P-0046957-T01-IM6	KMT2B (NM_014727) rearrangement: t(12;19)(q14.2;q13.12)(chr12:g.64138499::chr19:g.36229383)	PRECISE	Note: The KMT2B rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	11	19	Exon 37 of KMT2B(+)	KMT2B	36229383			12	IGR: 35Kb before TMEM5(+)	KMT2B	64138499			10	TRANSLOCATION		0	328578	0	13	NEW_VARIANT
P-0017386-T04-IM6	STK40 (NM_032017) rearrangement: c.1008:STK40_chr1:g.121485036del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		448061	0	12	1	Exon 11 of STK40(-)	STK40	36809046			1	IGR: 224Kb before EMBP1(+)	STK40	121485036			10	DELETION		84675990	329407	657619	55	NEW_VARIANT
P-0017386-T04-IM6	MGA (NM_001164273) rearrangement: c.2189-23_c.3431-2986dup	PRECISE	Note: The MGA rearrangement is an intragenic duplication of exons 6 - 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		7395	0	63	15	Intron of MGA(+):22bp before exon 6	MGA	41999903			15	Intron of MGA(+):3Kb before exon 10	MGA	42016392			10	DUPLICATION		16489	329409	12104	63	NEW_VARIANT
P-0039285-T02-IM6	DUSP4 (NM_001394) rearrangement: c.580-163:DUSP4_chr8:g.29044779inv	PRECISE	Note: The DUSP4 rearrangement is an inversion of exons 3 - 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		7429	0	6	8	Intron of KIF13B(-):790bp before exon 6	DUSP4	29044779			8	Intron of DUSP4(-):163bp before exon 3	DUSP4	29196181			10	INVERSION		151402	329327	10031	6	NEW_VARIANT
P-0043094-T02-IM6	FOXO1 (NM_002015) rearrangement: c.630+78:FOXO1_chr13:g.49932326inv	IMPPRECISE	Note: The FOXO1 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		28429	0	5	13	Intron of FOXO1(-):77bp after exon 1	FOXO1	41239642			13	Intron of CAB39L(-):2Kb after exon 4	FOXO1	49932326			0	INVERSION		8692684	328708	21563	5	NEW_VARIANT
P-0046940-T01-IM6	SPEN (NM_015001) rearrangement: c.404+294_c.10866del	PRECISE	Note: The SPEN rearrangement is an intragenic deletion of exons 3 - 15. One of the breakpoints is within exon 15.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		49514	0	43	1	Intron of SPEN(+):294bp after exon 2	SPEN	16199925			1	Exon 15 of SPEN(+)	SPEN	16265793			10	DELETION		65868	328678	51407	45	NEW_VARIANT
P-0046940-T01-IM6	ARID2 (NM_152641) - SIPA1L3 (NM_015073) rearrangement: t(12;19)(q12;q13.13)(chr12:g.46123998::chr19:g.38692821)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ARID2:SIPA1L3}		0	0	26	19	Intron of SIPA1L3(+):184bp after exon 20	ARID2	38692821			12	Intron of ARID2(+):78bp after exon 2	SIPA1L3	46123998			10	TRANSLOCATION		0	328679	0	28	NEW_VARIANT
P-0046943-T01-IM6	GLI1 (NM_005269) rearrangement: c.389+14:GLI1_chr12:g.116180623inv	PRECISE	Note: The GLI1 rearrangement is an inversion of exons 5 - 12. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		103966	0	14	12	Intron of GLI1(+):14bp after exon 4	GLI1	57858665			12	IGR: 216Kb before MED13L(-)	GLI1	116180623			10	INVERSION		58321958	328682	142446	14	NEW_VARIANT
P-0046943-T01-IM6	NOTCH3 (NM_000435) rearrangement: t(9;19)(q22.31;p13.12)(chr9:g.95511808::chr19:g.15299695)	PRECISE	Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	12	19	Intron of NOTCH3(-):104bp after exon 8	NOTCH3	15299695			9	Intron of BICD2(-):15Kb after exon 1	NOTCH3	95511808			10	TRANSLOCATION		0	328683	0	12	NEW_VARIANT
P-0046943-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+477:TMPRSS2_chr21:g.40030286del	PRECISE	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).	MANUAL_OK	3to5	3to5	-		72918	0	55	21	3-UTR of ERG(-):3Kb after coding stop	TMPRSS2	40030286			21	Intron of TMPRSS2(-):476bp after exon 1	TMPRSS2	42879400			10	DELETION		2849114	328681	65010	55	NEW_VARIANT
P-0046945-T01-IM6	FAT1 (NM_005245) rearrangement: c.3265+2110_c.3643-66inv	PRECISE	Note: The FAT1 rearrangement is an intragenic inversion of exons 3 - 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1740	0	12	4	Intron of FAT1(-):66bp before exon 5	FAT1	187558134			4	Intron of FAT1(-):2Kb after exon 2	FAT1	187625607			10	INVERSION		67473	328672	3057	12	NEW_VARIANT
P-0046985-T01-IM6	PAWR (NM_002583) - ERBB3 (NM_001982) rearrangement: c.516+27255:PAWR_c.3251:ERBB3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PAWR:ERBB3}		74846	0	14	12	Exon 27 of ERBB3(+)	PAWR	56494894			12	Intron of PAWR(-):27Kb after exon 2	ERBB3	80056254			10	INVERSION		23561360	328597	59788	17	NEW_VARIANT
P-0046988-T01-IM6	TERT (NM_198253) rearrangement: c.2419_c.2970+250inv	IMPPRECISE	Note: The TERT rearrangement is an intragenic inversion of exons 8 - 12. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		6136	0	3	5	Intron of TERT(-):249bp after exon 12	TERT	1260339			5	Exon 8 of TERT(-)	TERT	1271283			0	INVERSION		10944	328599	5584	3	NEW_VARIANT
P-0047009-T01-IM6	PIK3CD (NM_005026) rearrangement: c.780+70_c.1243-55del	PRECISE	Note: The PIK3CD rearrangement is an intragenic deletion of exons 7 - 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		7173	0	3	1	Intron of PIK3CD(+):70bp after exon 6	PIK3CD	9776747			1	Intron of PIK3CD(+):54bp before exon 10	PIK3CD	9779924			8	DELETION		3177	328705	7118	3	NEW_VARIANT
P-0047009-T01-IM6	ARID1A (NM_006015) - SLC17A8 (NM_139319) rearrangement: t(1;12)(p36.11;q23.1)(chr1:g.27100005::chr12:g.100779582)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ARID1A:SLC17A8}		0	0	5	12	Intron of SLC17A8(+):5Kb after exon 2	ARID1A	100779582			1	Intron of ARID1A(+):18bp after exon 15	SLC17A8	27100005			8	TRANSLOCATION		0	328706	0	5	NEW_VARIANT
P-0047080-T01-IM6	KMT2B (NM_014727) rearrangement: c.3886-92:KMT2B_chr19:g.57191978inv	PRECISE	Note: The KMT2B rearrangement is an inversion of exons 14 - 37. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		393196	0	70	19	Intron of KMT2B(+):91bp before exon 14	KMT2B	36217045			19	IGR: 18Kb before ZNF835(-)	KMT2B	57191978			10	INVERSION		20974933	329493	515731	100	NEW_VARIANT
P-0047124-T01-IM6	EP300 (NM_001429) rearrangement: c.5458:EP300_chr22:g.45672535del	PRECISE	Note: The EP300 rearrangement is a deletion of exon 31. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	-		19749	0	14	22	Exon 31 of EP300(+)	EP300	41573173			22	IGR: 8Kb before UPK3A(+)	EP300	45672535			10	DELETION		4099362	329509	24804	14	NEW_VARIANT
P-0018869-T03-IM6	FGFR2 (NM_000141) - ABLIM1 (NM_002313) fusion: c.2301+611:FGFR2_c.895-12244:ABLIM1del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {FGFR2:ABLIM1}		20534	0	8	10	Intron of ABLIM1(-):12Kb before exon 7	FGFR2	116263881			10	Intron of FGFR2(-):610bp after exon 17	ABLIM1	123242601			0	DELETION		6978720	329339	24297	8	NEW_VARIANT
P-0046950-T01-IM6	NFKBIA (NM_020529) rearrangement: t(1;14)(p36.12;q13.2)(chr1:g.22271508::chr14:g.35871855)	PRECISE	Note: The NFKBIA rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	18	14	Exon 5 of NFKBIA(-)	NFKBIA	35871855			1	IGR: 32Kb before CELA3B(+)	NFKBIA	22271508			10	TRANSLOCATION		0	328585	0	20	NEW_VARIANT
P-0046969-T01-IM6	NRAS (NM_002524) rearrangement: t(1;19)(p13.2;q13.33)(chr1:g.115256393::chr19:g.49258664)	IMPPRECISE	Note: The NRAS rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {NRAS:FGF21}		0	0	5	19	Promoter of FGF21(+):679bp from tx start	NRAS	49258664			1	Intron of NRAS(-):27bp after exon 3	NRAS	115256393			0	TRANSLOCATION		0	328634	0	6	NEW_VARIANT
P-0047149-T01-IM6	NF1 (NM_001042492) rearrangement: c.4836-22676_c.5812+36dup	IMPPRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 37 - 39. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		5944	0	9	17	Intron of NF1(+):23Kb before exon 37	NF1	29630162			17	Intron of NF1(+):36bp after exon 39	NF1	29657552			0	DUPLICATION		27390	329614	6832	9	NEW_VARIANT
P-0047149-T01-IM6	DOT1L (NM_032482) rearrangement: c.1466-107:DOT1L_chr19:g.2163961del	PRECISE	Note: The DOT1L rearrangement is a deletion of exons 1 - 15. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		30293	0	3	19	Promoter of DOT1L(+):186bp from tx start	DOT1L	2163961			19	Intron of DOT1L(+):106bp before exon 16	DOT1L	2211643			5	DELETION		47682	329613	38087	3	NEW_VARIANT
P-0047152-T01-IM6	AXIN2 (NM_004655) rearrangement: c.1156:AXIN2_chr17:g.63760602inv	PRECISE	Note: The AXIN2 rearrangement is an inversion of exons 1 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		9295	0	2	17	Exon 5 of AXIN2(-)	AXIN2	63534365			17	Intron of CEP112(-):14Kb before exon 20	AXIN2	63760602			5	INVERSION		226237	329610	14579	3	NEW_VARIANT
P-0047156-T01-IM6	ARID1A (NM_006015) rearrangement: c.1920+4680_c.3867-20dup	PRECISE	Note: The ARID1A rearrangement is an intragenic duplication of exons 5 - 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 11 exons : out of frame		16854	0	43	1	Intron of ARID1A(+):5Kb after exon 4	ARID1A	27063963			1	Intron of ARID1A(+):19bp before exon 16	ARID1A	27100051			10	DUPLICATION		36088	329617	24741	45	NEW_VARIANT
P-0047202-T01-IM6	KEAP1 (NM_203500) rearrangement: c.1532-89_c.1708+772del	IMPPRECISE	Note: The KEAP1 rearrangement is an intragenic deletion of exon 5.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		2590	0	12	19	Intron of KEAP1(-):771bp after exon 5	KEAP1	10599096			19	Intron of KEAP1(-):89bp before exon 5	KEAP1	10600133			0	DELETION		1037	330164	964	18	NEW_VARIANT
P-0047203-T01-IM6	KMT2D (NM_003482) rearrangement: c.5982:KMT2D_chr12:g.45466650inv	IMPPRECISE	Note: The KMT2D rearrangement is an inversion of exons 28 - 54. One of the breakpoints is within exon 28. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		141983	0	24	12	IGR: 10Kb before RACGAP1P(-)	KMT2D	45466650			12	Exon 28 of KMT2D(-)	KMT2D	49435999			0	INVERSION		3969349	330153	169711	24	NEW_VARIANT
P-0047206-T01-IM6	ARAF (NM_001654) - SCML2 (NM_006089) rearrangement: c.96+47:ARAF_c.487-4683:SCML2inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ARAF:SCML2}		132506	0	5	X	Intron of SCML2(-):5Kb before exon 7	ARAF	18328018			X	Intron of ARAF(+):47bp after exon 2	SCML2	47422509			0	INVERSION		29094491	330166	297721	5	NEW_VARIANT
P-0034561-T01-IM6	MGA (NM_001164273) rearrangement: t(14;15)(q24.3;q15.1)(chr14:g.74523162::chr15:g.42049853)	PRECISE	Note: The MGA rearrangement is a translocation with a breakpoint in intron 18. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CCDC176:MGA}		0	0	11	15	Intron of MGA(+):132bp before exon 19	MGA	42049853			14	Intron of CCDC176(+):446bp before exon 10	MGA	74523162			10	TRANSLOCATION		0	330128	0	11	NEW_VARIANT
P-0046331-T01-IM6	KDM5A (NM_001042603) rearrangement: t(9;12)(p13.2;p13.33)(chr9:g.37548328::chr12:g.465623)	PRECISE	Note: The KDM5A rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	30	12	Exon 6 of KDM5A(-)	KDM5A	465623			9	5-UTR of FBXO10(-):36Kb before coding start	KDM5A	37548328			10	TRANSLOCATION		0	325110	0	41	NEW_VARIANT
P-0046331-T01-IM6	PLCG2 (NM_002661) rearrangement: t(14;16)(q32.12;q23.3)(chr14:g.92264481::chr16:g.81904561)	IMPPRECISE	Note: The PLCG2 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	6	16	Intron of PLCG2(+):21bp after exon 7	PLCG2	81904561			14	Intron of TC2N(-):161bp after exon 7	PLCG2	92264481			0	TRANSLOCATION		0	325111	0	6	NEW_VARIANT
P-0046331-T01-IM6	TRAP1 (NM_016292) - CREBBP (NM_004380) rearrangement: c.2014-255:TRAP1_c.4281-135:CREBBPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TRAP1:CREBBP}		25580	0	13	16	Intron of TRAP1(-):255bp before exon 17	TRAP1	3708486			16	Intron of CREBBP(-):135bp before exon 26	CREBBP	3788808			10	DUPLICATION		80322	325109	35977	14	NEW_VARIANT
P-0046331-T01-IM6	ATR (NM_001184) rearrangement: c.481:ATR_chr3:g.125082265del	PRECISE	Note: The ATR rearrangement is a deletion of exons 4 - 47. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ATR:ZNF148}		134807	0	40	3	5-UTR of ZNF148(-):131Kb before coding start	ATR	125082265			3	Exon 4 of ATR(-)	ATR	142281763			10	DELETION		17199498	325107	157738	41	NEW_VARIANT
P-0047139-T01-IM6	CSDE1 (NM_001242891) rearrangement: c.1778_c.1779del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		641	0	6	1	Exon 16 of CSDE1(-)	CSDE1	115267954			1	Exon 15 of CSDE1(-)	CSDE1	115268832			10	DELETION		878	329970	1128	6	NEW_VARIANT
P-0047139-T01-IM6	CDC73 (NM_024529) rearrangement: c.829-60:CDC73_chr1:g.193002339del	PRECISE	Note: The CDC73 rearrangement is a deletion of exons 1 - 8.	MANUAL_OK	3to5	3to5	-		5550	0	3	1	Intron of UCHL5(-):4Kb before exon 4	CDC73	193002339			1	Intron of CDC73(+):59bp before exon 9	CDC73	193119374			5	DELETION		117035	329972	10244	5	NEW_VARIANT
P-0047211-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+3935:TMPRSS2_c.18+1778:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75644	0	56	21	Intron of ERG(-):2Kb after exon 1	TMPRSS2	39868509			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875942			10	DELETION		3007433	330136	29807	58	NEW_VARIANT
P-0047213-T01-IM6	ARID2 (NM_152641) rearrangement: c.1581-39_c.2420del	PRECISE	Note: The ARID2 rearrangement is an intragenic deletion of exons 13 - 15. One of the breakpoints is within exon 15.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2712	0	11	12	Intron of ARID2(+):38bp before exon 13	ARID2	46242580			12	Exon 15 of ARID2(+)	ARID2	46244326			10	DELETION		1746	330135	4697	11	NEW_VARIANT
P-0047313-T01-IM6	JAK3 (NM_000215) rearrangement: t(8;19)(q23.1;p13.11)(chr8:g.110031275::chr19:g.17945774)	PRECISE	Note: The JAK3 rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	19	19	Exon 16 of JAK3(-)	JAK3	17945774			8	IGR: 68Kb before TRHR(+)	JAK3	110031275			10	TRANSLOCATION		0	330311	0	26	NEW_VARIANT
P-0047338-T01-IM6	NUF2 (NM_031423) rearrangement: c.338-270:NUF2_chr1:g.163266615inv	PRECISE	Note: The NUF2 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {RGS5:NUF2}		5012	0	13	1	5-UTR of RGS5(-):149Kb before coding start	NUF2	163266615			1	Intron of NUF2(+):269bp before exon 6	NUF2	163306271			10	INVERSION		39656	330381	15906	13	NEW_VARIANT
P-0047343-T01-IM6	ARID1A (NM_006015) rearrangement: c.1137+13428_c.2732+57dup	PRECISE	Note: The ARID1A rearrangement is an intragenic duplication of exons 2 - 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 7 exons : out of frame		18253	0	25	1	Intron of ARID1A(+):13Kb after exon 1	ARID1A	27037459			1	Intron of ARID1A(+):57bp after exon 8	ARID1A	27089833			10	DUPLICATION		52374	330372	23328	25	NEW_VARIANT
P-0047102-T01-IM6	EZH1 (NM_001991) rearrangement: t(6;17)(q24.1;q21.2)(chr6:g.140038690::chr17:g.40870395)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	28	17	Intron of EZH1(-):76bp after exon 9	EZH1	40870395			6	IGR: 54Kb before LOC100132735(+)	EZH1	140038690			10	TRANSLOCATION		0	329500	0	28	NEW_VARIANT
P-0047287-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-710:TMPRSS2_c.18+11070:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25718	0	14	21	Intron of ERG(-):11Kb after exon 1	TMPRSS2	39859217			21	Intron of TMPRSS2(-):710bp before exon 3	ERG	42867215			10	DELETION		3007998	330277	21379	14	NEW_VARIANT
P-0047304-T01-IM6	RB1 (NM_000321) - CYSLTR2 (NM_020377) rearrangement: c.2490-1057:RB1_c.884:CYSLTR2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RB1:CYSLTR2}		13395	0	76	13	Intron of RB1(+):1Kb before exon 24	RB1	49046439			13	Exon 1 of CYSLTR2(+)	CYSLTR2	49281837			10	DELETION		235398	330306	1138	79	NEW_VARIANT
P-0047304-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-380:TMPRSS2_chr21:g.27694846inv	PRECISE	Note: The TMPRSS2 rearrangement is an inversion of exons 3 - 14. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		69144	0	8	21	IGR: 144Kb before CYYR1(-)	TMPRSS2	27694846			21	Intron of TMPRSS2(-):380bp before exon 3	TMPRSS2	42866885			10	INVERSION		15172039	330307	70245	8	NEW_VARIANT
P-0047306-T01-IM6	MET (NM_000245) rearrangement: c.3799-1570_c.3840inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		383	0	43	7	Intron of MET(+):2Kb before exon 20	MET	116434139			7	Exon 20 of MET(+)	MET	116435750			10	INVERSION		1611	330308	1100	47	NEW_VARIANT
P-0047332-T01-IM6	ANKRD11 (NM_013275) rearrangement: t(2;16)(p11.2;q24.3)(chr2:g.83471575::chr16:g.89357093)	PRECISE	Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	16	Exon 6 of ANKRD11(-)	ANKRD11	89357093			2	IGR: 388Kb before LOC1720(+)	ANKRD11	83471575			10	TRANSLOCATION		0	330454	0	22	NEW_VARIANT
P-0047355-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+925:EML4_c.3173-215:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		86908	0	30	2	Intron of ALK(-):215bp before exon 20	EML4	29446609			2	Intron of EML4(+):925bp after exon 5	ALK	42492796			10	INVERSION		13046187	330401	87151	30	NEW_VARIANT
P-0047358-T01-IM6	MDC1 (NM_014641) - DNAH8 (NM_001206927) rearrangement: c.484:MDC1_c.3523+2614:DNAH8inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {MDC1:DNAH8}		190692	0	20	6	Exon 3 of MDC1(-)	MDC1	30681613			6	Intron of DNAH8(+):3Kb after exon 26	DNAH8	38786047			10	INVERSION		8104434	330391	317077	20	NEW_VARIANT
P-0047359-T01-IM6	MBIP (NM_016586) - RET (NM_020975) fusion: t(10;14)(q11.21;q13.3)(chr10:g.43610084::chr14:g.36773155)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {MBIP:RET}		0	0	8	14	Intron of MBIP(-):3Kb before exon 8	MBIP	36773155			10	Exon 11 of RET(+)	RET	43610084			10	TRANSLOCATION		0	330398	0	9	NEW_VARIANT
P-0047290-T01-IM6	FGFR3 (NM_000142) rearrangement: c.2274+67:FGFR3_chr4:g.1809658inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		2753	0	3	4	Intron of FGFR3(+):67bp after exon 17	FGFR3	1808728			4	3-UTR of FGFR3(+):14Kb after coding stop	FGFR3	1809658			10	INVERSION		930	330263	2016	3	NEW_VARIANT
P-0047395-T01-IM6	ETV6 (NM_001987) rearrangement: c.463+178:ETV6_chr12:g.12275489del	PRECISE	Note: The ETV6 rearrangement is a deletion of exons 5 - 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		218630	0	54	12	Intron of ETV6(+):178bp after exon 4	ETV6	12006673			12	Intron of LRP6(-):1Kb before exon 23	ETV6	12275489			10	DELETION		268816	330487	296894	56	NEW_VARIANT
P-0047438-T01-IM6	ARID1A (NM_006015) rearrangement: c.3809_c.4269del	IMPPRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 15 - 18. The breakpoints are within exon 15 and exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4988	0	79	1	Exon 15 of ARID1A(+)	ARID1A	27099930			1	Exon 18 of ARID1A(+)	ARID1A	27100987			0	DELETION		1057	330761	4530	81	NEW_VARIANT
P-0047450-T01-IM6	RPTOR (NM_020761) rearrangement: c.3692+40_c.3939+180del	PRECISE	Note: The RPTOR rearrangement is an intragenic deletion of exons 32 - 33. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		4798	0	188	17	Intron of RPTOR(+):40bp after exon 31	RPTOR	78935320			17	Intron of RPTOR(+):180bp after exon 33	RPTOR	78937037			10	DELETION		1717	330743	4013	204	NEW_VARIANT
P-0047465-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.6940:NOTCH3_chr19:g.15393284del	IMPPRECISE	Note: The NOTCH3 rearrangement is a deletion of exons 1 - 33. One of the breakpoints is within exon 33.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {BRD4:NOTCH3}		142566	0	5	19	Exon 33 of NOTCH3(-)	NOTCH3	15271499			19	Promoter of BRD4(-):45Kb from tx start	NOTCH3	15393284			0	DELETION		121785	330773	187810	5	NEW_VARIANT
P-0047565-T01-IM6	HIST1H3D (NM_003530) rearrangement: c.84:HIST1H3D_chr6:g.26116722del	PRECISE	Note: The HIST1H3D rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11094	0	20	6	IGR: 7Kb before HIST1H2BC(-)	HIST1H3D	26116722			6	Exon 2 of HIST1H3D(-)	HIST1H3D	26197395			10	DELETION		80673	330951	11746	21	NEW_VARIANT
P-0040655-T02-IM6	PIK3CG (NM_002649) rearrangement: c.3256:PIK3CG_chr7:g.147785722inv	PRECISE	Note: The PIK3CG rearrangement is an inversion of exon 11. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		311668	0	18	7	Exon 11 of PIK3CG(+)	PIK3CG	106545779			7	Intron of CNTNAP2(+):29Kb before exon 16	PIK3CG	147785722			10	INVERSION		41239943	330850	273399	18	NEW_VARIANT
P-0040655-T02-IM6	CTTNBP2 (NM_033427) - KMT2C (NM_170606) rearrangement: c.82-950:CTTNBP2_c.1690:KMT2Cdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CTTNBP2:KMT2C}		385237	0	6	7	Intron of CTTNBP2(-):950bp before exon 2	CTTNBP2	117502320			7	Exon 12 of KMT2C(-)	KMT2C	151947983			6	DUPLICATION		34445663	330848	342627	6	NEW_VARIANT
P-0032400-T02-IM6	NCOA3 (NM_181659) - MDM2 (NM_002392) rearrangement: t(12;20)(q15;q13.12)(chr12:g.69227313::chr20:g.46265559)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {NCOA3:MDM2}		0	0	38	20	Intron of NCOA3(+):53bp after exon 12	NCOA3	46265559			12	Intron of MDM2(+):2Kb before exon 9	MDM2	69227313			10	TRANSLOCATION		0	328703	0	39	NEW_VARIANT
P-0046827-T02-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1305:KIF5B_c.2136+705:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		85223	0	54	10	Intron of KIF5B(-):1Kb before exon 16	KIF5B	32313269			10	Intron of RET(+):705bp after exon 11	RET	43610889			10	INVERSION		11297620	331217	98857	67	NEW_VARIANT
P-0046827-T02-IM6	SMARCD1 (NM_003076) rearrangement: c.177+27:SMARCD1_chr12:g.46300876inv	PRECISE	Note: The SMARCD1 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		239541	0	150	12	3-UTR of ARID2(+):177Kb after coding stop	SMARCD1	46300876			12	Intron of SMARCD1(+):27bp after exon 1	SMARCD1	50479356			10	INVERSION		4178480	331218	358162	150	NEW_VARIANT
P-0047317-T01-IM6	PPARG (NM_015869) rearrangement: t(3;4)(p25.2;p15.1)(chr3:g.12475518::chr4:g.34763475)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	45	4	IGR: 866Kb before LOC101928622(-)	PPARG	34763475			3	Exon 7 of PPARG(+)	PPARG	12475518			10	TRANSLOCATION		0	330334	0	44	NEW_VARIANT
P-0047317-T01-IM6	MDC1 (NM_014641) rearrangement: c.99:MDC1_chr6:g.30684389del	PRECISE	Note: The MDC1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1012	0	5	6	Exon 2 of MDC1(-)	MDC1	30682854			6	5-UTR of MDC1(-):16Kb before coding start	MDC1	30684389			7	DELETION		1535	330331	1494	5	NEW_VARIANT
P-0047610-T01-IM6	MALT1 (NM_006785) rearrangement: c.1222+2438_c.1476-21del	PRECISE	Note: The MALT1 rearrangement is an intragenic deletion of exons 11 - 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		2644	0	5	18	Intron of MALT1(+):2Kb after exon 10	MALT1	56392921			18	Intron of MALT1(+):20bp before exon 13	MALT1	56402413			10	DELETION		9492	331210	2118	5	NEW_VARIANT
P-0047614-T01-IM6	FUT10 (NM_032664) - WHSC1L1 (NM_023034) rearrangement: c.81+3371:FUT10_c.2116-177:WHSC1L1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FUT10:WHSC1L1}		25273	0	44	8	Intron of FUT10(-):3Kb after exon 2	FUT10	33315519			8	Intron of WHSC1L1(-):177bp before exon 12	WHSC1L1	38172468			10	DUPLICATION		4856949	331207	198118	49	NEW_VARIANT
P-0047603-T01-IM6	ERCC3 (NM_000122) rearrangement: c.1635:ERCC3_chr2:g.128053922inv	PRECISE	Note: The ERCC3 rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		20829	0	26	2	Exon 10 of ERCC3(-)	ERCC3	128036844			2	Promoter of ERCC3(-):39Kb from tx start	ERCC3	128053922			10	INVERSION		17078	331163	37037	26	NEW_VARIANT
P-0047604-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+31:FGFR3_c.1941+484:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		37721	0	163	4	Intron of TACC3(+):484bp after exon 10	FGFR3	1739913			4	Intron of FGFR3(+):31bp after exon 17	TACC3	1808692			10	DUPLICATION		68779	331154	64688	180	NEW_VARIANT
P-0047618-T01-IM6	RUNX1 (NM_001754) rearrangement: c.967+81_c.1255del	IMPPRECISE	Note: The RUNX1 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3182	0	6	21	Exon 9 of RUNX1(-)	RUNX1	36164620			21	Intron of RUNX1(-):80bp after exon 8	RUNX1	36171517			0	DELETION		6897	331224	389	12	NEW_VARIANT
P-0047183-T02-IM6	HGF (NM_000601) rearrangement: c.2104:HGF_chr7:g.81330692inv	PRECISE	Note: The HGF rearrangement is an inversion of exon 18. One of the breakpoints is within exon 18. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		339	0	17	7	Promoter of HGF(-):751bp from tx start	HGF	81330692			7	Exon 18 of HGF(-)	HGF	81331980			10	INVERSION		1288	330923	491	19	NEW_VARIANT
P-0047544-T01-IM6	ELF3 (NM_004433) rearrangement: c.137:ELF3_chr1:g.202099757del	PRECISE	Note: The ELF3 rearrangement is a deletion of exons 2 - 9. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		18091	0	73	1	Exon 2 of ELF3(+)	ELF3	201980401			1	Promoter of ARL8A(-):3Kb from tx start	ELF3	202099757			10	DELETION		119356	330927	14787	80	NEW_VARIANT
P-0047546-T01-IM6	ANKRD11 (NM_013275) - SPG7 (NM_003119) rearrangement: c.2114:ANKRD11_c.1553-19:SPG7inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ANKRD11:SPG7}		26522	0	31	16	Exon 9 of ANKRD11(-)	ANKRD11	89350836			16	Intron of SPG7(+):18bp before exon 12	SPG7	89614392			10	INVERSION		263556	330926	20307	36	NEW_VARIANT
P-0047573-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2276:FGFR3_c.1942-892:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		52667	0	68	4	Intron of TACC3(+):891bp before exon 11	FGFR3	1740537			4	Exon 18 of FGFR3(+)	TACC3	1808844			10	DUPLICATION		68307	330900	58081	73	NEW_VARIANT
P-0047575-T01-IM6	RAD21 (NM_006265) rearrangement: c.1322-126:RAD21_chr8:g.117879554del	PRECISE	Note: The RAD21 rearrangement is a deletion of exons 1 - 10.	MANUAL_OK	3to5	3to5	Deletion within transcript		8800	0	6	8	Intron of RAD21(-):126bp before exon 11	RAD21	117864461			8	5-UTR of RAD21(-):20Kb before coding start	RAD21	117879554			5	DELETION		15093	330895	9984	7	NEW_VARIANT
P-0026989-T03-IM6	CDK12 (NM_016507) rearrangement: c.2964-115:CDK12_chr17:g.36372477del	PRECISE	Note: The CDK12 rearrangement is a deletion of exons 1 - 10. The rearrangement includes a part of the kinase domain of CDK12.	MANUAL_OK	3to5	3to5	-		17986	0	5	17	3-UTR of LOC440434(-):41Kb after coding stop	CDK12	36372477			17	Intron of CDK12(+):114bp before exon 11	CDK12	37676094			10	DELETION		1303617	331286	29179	15	NEW_VARIANT
P-0026989-T03-IM6	KDM6A (NM_021140) rearrangement: c.225+20377_c.3548+113dup	PRECISE	Note: The KDM6A rearrangement is an intragenic duplication of exons 3 - 24. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 22 exons : out of frame		12616	0	17	X	Intron of KDM6A(+):20Kb after exon 2	KDM6A	44753610			X	Intron of KDM6A(+):113bp after exon 24	KDM6A	44945337			10	DUPLICATION		191727	331289	26746	18	NEW_VARIANT
P-0046745-T01-IM6	FGFR3 (NM_000142) rearrangement: t(4;10)(p16.3;q26.11)(chr4:g.1808988::chr10:g.119935563)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	36	10	5-UTR of CASC2(+):34Kb before coding start	FGFR3	119935563			4	Exon 18 of FGFR3(+)	FGFR3	1808988			10	TRANSLOCATION		0	331246	0	35	NEW_VARIANT
P-0046745-T01-IM6	KCND2 (NM_012281) - BRAF (NM_004333) fusion: c.1115+91797:KCND2_c.1177+1481:BRAFinv	PRECISE	Note: The KCND2 - BRAF fusion involves KCND2 exon 1 and BRAF exons 10 - 18. The fusion includes the kinase domain of BRAF.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {KCND2:BRAF}		60060	0	8	7	Intron of KCND2(+):92Kb after exon 1	KCND2	120007598			7	Intron of BRAF(-):1Kb after exon 9	BRAF	140485867			10	INVERSION		20478269	331245	51764	8	NEW_VARIANT
P-0047471-T02-IM6	PIK3R2 (NM_005027) rearrangement: t(1;19)(q23.3;p13.11)(chr1:g.161137226::chr19:g.18271152)	PRECISE	Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	12	19	Intron of PIK3R2(+):128bp before exon 3	PIK3R2	18271152			1	Exon 4 of PPOX(+)	PIK3R2	161137226			10	TRANSLOCATION		0	331262	0	12	NEW_VARIANT
P-0047634-T01-IM6	ETV6 (NM_001987) rearrangement: c.34-29588_c.464-5154del	PRECISE	Note: The ETV6 rearrangement is an intragenic deletion of exons 2 - 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		63080	0	49	12	Intron of ETV6(+):30Kb before exon 2	ETV6	11875796			12	Intron of ETV6(+):5Kb before exon 5	ETV6	12017204			10	DELETION		141408	331266	80273	49	NEW_VARIANT
P-0047636-T01-IM6	TP53 (NM_000546) rearrangement: c.813:TP53_chr17:g.7569417del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 8 - 11. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6433	0	61	17	Promoter of TP53(-):2Kb from tx start	TP53	7569417			17	Exon 8 of TP53(-)	TP53	7577125			10	DELETION		7708	331271	3383	66	NEW_VARIANT
P-0047637-T01-IM6	BRAF (NM_004333) rearrangement: c.853:BRAF_chr7:g.142196577inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		5419	0	17	7	Exon 6 of BRAF(-)	BRAF	140501219			7	IGR: 178Kb before MTRNR2L6(+)	BRAF	142196577			10	INVERSION		1695358	331264	10593	28	NEW_VARIANT
P-0047648-T01-IM6	KMT2D (NM_003482) rearrangement: c.1576:KMT2D_chr12:g.69859324del	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 1 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	-		145705	0	46	12	Exon 10 of KMT2D(-)	KMT2D	49445890			12	IGR: 5Kb before FRS2(+)	KMT2D	69859324			10	DELETION		20413434	331240	230439	48	NEW_VARIANT
P-0047648-T01-IM6	RTEL1 (NM_032957) - VRK3 (NM_016440) rearrangement: t(19;20)(q13.33;q13.33)(chr19:g.50499591::chr20:g.62325880)	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {RTEL1:VRK3}		0	0	30	20	Intron of RTEL1(+):39bp after exon 31	RTEL1	62325880			19	Intron of VRK3(-):1Kb before exon 8	VRK3	50499591			0	TRANSLOCATION		0	331242	0	34	NEW_VARIANT
P-0047648-T01-IM6	CSF1R (NM_005211) rearrangement: c.1875_c.2132+478del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2792	0	9	5	Intron of CSF1R(-):477bp after exon 15	CSF1R	149438785			5	Exon 14 of CSF1R(-)	CSF1R	149440519			10	DELETION		1734	331239	3337	11	NEW_VARIANT
P-0047650-T01-IM6	CLSPN (NM_022111) - CSF3R (NM_000760) rearrangement: c.134-84:CLSPN_c.362-86:CSF3Rdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CLSPN:CSF3R}		48951	0	5	1	Intron of CLSPN(-):84bp before exon 3	CLSPN	36230399			1	Intron of CSF3R(-):86bp before exon 5	CSF3R	36939574			0	DUPLICATION		709175	331248	65751	5	NEW_VARIANT
P-0047673-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3791:ZFHX3_chr16:g.72505498inv	PRECISE	Note: The ZFHX3 rearrangement is an inversion of exons 7 - 10. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		44526	0	32	16	3-UTR of LINC01572(-):193Kb after coding stop	ZFHX3	72505498			16	Exon 7 of ZFHX3(-)	ZFHX3	72845549			10	INVERSION		340051	331291	51306	31	NEW_VARIANT
P-0047673-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3449-17445_c.3663+21inv	PRECISE	Note: The ZFHX3 rearrangement is an intragenic inversion of exons 5 - 6. Functional significance is undetermined. Multiple structural variants involving ZFHX3 suggests the presence of a more complex rearrangement in ZFHX3.	MANUAL_OK	5to5	5to5	Antisense Fusion		2432	0	56	16	Intron of ZFHX3(-):20bp after exon 6	ZFHX3	72845783			16	Intron of ZFHX3(-):17Kb before exon 5	ZFHX3	72881203			10	INVERSION		35420	331292	3036	58	NEW_VARIANT
P-0021823-T02-IM6	ETV1 (NM_001163147) rearrangement: t(7;14)(p21.2;q11.2)(chr7:g.14026320::chr14:g.21735813)	PRECISE	Note: The ETV1 rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {HNRNPC:ETV1}		0	0	40	14	5-UTR of HNRNPC(-):56Kb before coding start	ETV1	21735813			7	Intron of ETV1(-):10bp before exon 4	ETV1	14026320			10	TRANSLOCATION		0	331460	0	40	NEW_VARIANT
P-0043100-T02-IM6	TP53 (NM_000546) rearrangement: c.902_c.993+1134inv	PRECISE	Note: The TP53 rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2427	0	20	17	Intron of TP53(-):1Kb after exon 9	TP53	7575719			17	Exon 8 of TP53(-)	TP53	7577036			10	INVERSION		1317	331454	1709	28	NEW_VARIANT
P-0047760-T01-IM6	CREBBP (NM_004380) rearrangement: c.761:CREBBP_chr16:g.3573904del	PRECISE	Note: The CREBBP rearrangement is a deletion of exons 2 - 31. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		105419	0	21	16	Intron of CLUAP1(+):605bp after exon 8	CREBBP	3573904			16	Exon 2 of CREBBP(-)	CREBBP	3900335			10	DELETION		326431	331456	82878	22	NEW_VARIANT
P-0047760-T01-IM6	RBM10 (NM_001204468) rearrangement: c.1436_c.2145+1288inv	PRECISE	Note: The RBM10 rearrangement is an intragenic inversion of exons 12 - 17. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3943	0	47	X	Exon 12 of RBM10(+)	RBM10	47039898			X	Intron of RBM10(+):1Kb after exon 17	RBM10	47043013			10	INVERSION		3115	331458	8296	52	NEW_VARIANT
P-0047697-T01-IM6	YAP1 (NM_001130145) rearrangement: c.321+26:YAP1_chr11:g.42257177inv	PRECISE	Note: The YAP1 rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		325655	0	44	11	3-UTR of LOC100507205(-):18Kb after coding stop	YAP1	42257177			11	Intron of YAP1(+):26bp after exon 1	YAP1	101981926			10	INVERSION		59724749	331389	314926	44	NEW_VARIANT
P-0047709-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.3393_c.7714-147del	PRECISE	Note: The ANKRD11 rearrangement is an intragenic deletion of exons 9 - 11. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		36734	0	39	16	Intron of ANKRD11(-):147bp before exon 12	ANKRD11	89337464			16	Exon 9 of ANKRD11(-)	ANKRD11	89349557			10	DELETION		12093	331386	37906	39	NEW_VARIANT
P-0047710-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.3942:WHSC1_chr4:g.1981450del	PRECISE	Note: The WHSC1 rearrangement is a deletion of exon 22. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1442	0	8	4	Exon 22 of WHSC1(+)	WHSC1	1980480			4	3-UTR of WHSC1(+):79Kb after coding stop	WHSC1	1981450			10	DELETION		970	331416	2328	8	NEW_VARIANT
P-0047710-T01-IM6	TGFBR1 (NM_004612) rearrangement: c.1131-339_c.1314del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1189	0	20	9	Intron of TGFBR1(+):338bp before exon 7	TGFBR1	101908428			9	Exon 8 of TGFBR1(+)	TGFBR1	101909994			10	DELETION		1566	331417	1509	20	NEW_VARIANT
P-0047716-T01-IM6	POLE (NM_006231) rearrangement: c.5861_c.6159del	PRECISE	Note: The POLE rearrangement is an intragenic deletion of exons 43 - 45. The breakpoints are within exon 43 and exon 45.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3509	0	17	12	Exon 45 of POLE(-)	POLE	133209072			12	Exon 43 of POLE(-)	POLE	133210915			10	DELETION		1843	331411	2729	17	NEW_VARIANT
P-0047719-T01-IM6	AKAP8L (NM_014371) - BRD4 (NM_058243) rearrangement: c.1536+6695:AKAP8L_c.964:BRD4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {AKAP8L:BRD4}		8278	0	3	19	Exon 6 of BRD4(-)	AKAP8L	15375463			19	Intron of AKAP8L(-):7Kb after exon 12	BRD4	15501266			8	DELETION		125803	331415	10616	3	NEW_VARIANT
P-0047737-T01-IM6	KRAS (NM_033360) - PIKFYVE (NM_015040) rearrangement: t(2;12)(q34;p12.1)(chr2:g.209141988::chr12:g.25398161)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KRAS:PIKFYVE}		0	0	5	12	Intron of KRAS(-):46bp after exon 2	KRAS	25398161			2	Intron of PIKFYVE(+):272bp before exon 5	PIKFYVE	209141988			0	TRANSLOCATION		0	331433	0	5	NEW_VARIANT
P-0047741-T01-IM6	MAOA (NM_000240) - KDM6A (NM_021140) rearrangement: c.307-1775:MAOA_c.2942:KDM6Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MAOA:KDM6A}		27252	0	13	X	Intron of MAOA(+):2Kb before exon 4	MAOA	43569344			X	Exon 20 of KDM6A(+)	KDM6A	44938394			10	DELETION		1369050	331442	26934	14	NEW_VARIANT
P-0047743-T01-IM6	HIST1H3B (NM_003537) rearrangement: t(2;6)(q22.1;p22.2)(chr2:g.137043939::chr6:g.26032075)	PRECISE	Note: The HIST1H3B rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	34	6	Exon 1 of HIST1H3B(-)	HIST1H3B	26032075			2	IGR: 172Kb before CXCR4(-)	HIST1H3B	137043939			10	TRANSLOCATION		0	331436	0	34	NEW_VARIANT
P-0047748-T01-IM6	MGA (NM_001164273) rearrangement: c.3430+3672_c.3843+55inv	IMPPRECISE	Note: The MGA rearrangement is an intragenic inversion of exons 10 - 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		3463	0	18	15	Intron of MGA(+):4Kb after exon 9	MGA	42009366			15	Intron of MGA(+):55bp after exon 11	MGA	42021602			0	INVERSION		12236	331449	4821	17	NEW_VARIANT
P-0016624-T02-IM6	ALK (NM_004304) rearrangement: c.1282+92:ALK_chr2:g.13865654del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		182637	0	12	2	IGR: 503Kb before LINC00276(-)	ALK	13865654			2	Intron of ALK(-):91bp after exon 5	ALK	29606506			10	DELETION		15740852	331784	180595	12	NEW_VARIANT
P-0047576-T01-IM6	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.3568-31:SEC16A_c.1455:NOTCH1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SEC16A:NOTCH1}		106387	0	2	9	Intron of SEC16A(-):31bp before exon 4	SEC16A	139366594			9	Exon 9 of NOTCH1(-)	NOTCH1	139411824			8	DUPLICATION		45230	330894	20575	2	NEW_VARIANT
P-0047878-T01-IM6	NTRK1 (NM_002529) rearrangement: c.851-206:NTRK1_chr1:g.156997988del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		28551	0	6	1	Intron of NTRK1(+):205bp before exon 8	NTRK1	156843219			1	Intron of ARHGEF11(-):16Kb after exon 1	NTRK1	156997988			10	DELETION		154769	331732	27513	6	NEW_VARIANT
P-0047878-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.1985+199:PIK3R1_chr5:g.136534380del	PRECISE	Note: The PIK3R1 rearrangement is a deletion of exon 16.	MANUAL_OK	3to5	3to5	Antisense Fusion		117870	0	8	5	Intron of PIK3R1(+):199bp after exon 15	PIK3R1	67592368			5	Intron of SPOCK1(-):58Kb before exon 4	PIK3R1	136534380			10	DELETION		68942012	331733	175001	8	NEW_VARIANT
P-0047880-T01-IM6	RECQL4 (NM_004260) - ARHGAP39 (NM_025251) rearrangement: c.3393+28:RECQL4_c.2615-555:ARHGAP39dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RECQL4:ARHGAP39}		32177	0	5	8	Intron of RECQL4(-):27bp after exon 20	RECQL4	145737266			8	Intron of ARHGAP39(-):555bp before exon 9	ARHGAP39	145760141			10	DUPLICATION		22875	331730	42895	5	NEW_VARIANT
P-0047882-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+1349_c.556+2440dup	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		9917	0	46	21	Intron of TMPRSS2(-):2Kb after exon 5	TMPRSS2	42857881			21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868697			10	DUPLICATION		10816	331731	17370	47	NEW_VARIANT
P-0047889-T01-IM6	RPS6KB2 (NM_003952) rearrangement: c.2_c.309+873inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		3683	0	4	11	Exon 1 of RPS6KB2(+)	RPS6KB2	67196018			11	Intron of RPS6KB2(+):873bp after exon 4	RPS6KB2	67197939			10	INVERSION		1921	331774	5584	4	NEW_VARIANT
P-0047890-T01-IM6	KDM6A (NM_021140) rearrangement: c.385-9047_c.1528-173del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 5 - 15.	MANUAL_OK	3to5	3to5	Deletion of 11 exons : in frame		4823	0	9	X	Intron of KDM6A(+):9Kb before exon 5	KDM6A	44861159			X	Intron of KDM6A(+):172bp before exon 16	KDM6A	44922494			4	DELETION		61335	331736	1730	12	NEW_VARIANT
P-0047892-T01-IM6	MET (NM_000245) rearrangement: t(7;8)(q31.2;p23.1)(chr7:g.116435712::chr8:g.11529165)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	346	8	IGR: 33Kb before GATA4(+)	MET	11529165			7	Exon 20 of MET(+)	MET	116435712			10	TRANSLOCATION		0	331773	0	536	NEW_VARIANT
P-0047902-T01-IM6	JAK1 (NM_002227) rearrangement: t(1;3)(p31.3;q21.3)(chr1:g.65309773::chr3:g.129135343)	PRECISE	Note: The JAK1 rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {JAK1:EFCAB12}		0	0	5	3	Intron of EFCAB12(-):1Kb before exon 4	JAK1	129135343			1	Exon 17 of JAK1(-)	JAK1	65309773			10	TRANSLOCATION		0	331779	0	5	NEW_VARIANT
P-0047905-T01-IM6	ETV6 (NM_001987) rearrangement: c.463+4669:ETV6_chr12:g.15129970del	PRECISE	Note: The ETV6 rearrangement is a deletion of exons 5 - 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {ETV6:PDE6H}		160936	0	17	12	Intron of ETV6(+):5Kb after exon 4	ETV6	12011164			12	5-UTR of PDE6H(+):976bp before coding start	ETV6	15129970			10	DELETION		3118806	331781	206836	17	NEW_VARIANT
P-0047905-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2275-41:FGFR3_c.1837-96:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		38449	0	108	4	Intron of TACC3(+):95bp before exon 10	FGFR3	1739229			4	Intron of FGFR3(+):40bp before exon 18	TACC3	1808802			10	DUPLICATION		69573	331782	76609	111	NEW_VARIANT
P-0047715-T01-IM6	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement: c.8233:SPEN_c.60+9907:PLEKHM2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:PLEKHM2}		36467	0	36	1	Intron of PLEKHM2(+):10Kb after exon 1	SPEN	16021020			1	Exon 11 of SPEN(+)	PLEKHM2	16260968			0	DUPLICATION		239948	331422	68376	38	NEW_VARIANT
P-0047715-T01-IM6	KMT2D (NM_003482) rearrangement: c.4741+60:KMT2D_chr12:g.99540965inv	IMPPRECISE	Note: The KMT2D rearrangement is an inversion of exons 1 - 18. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		175494	0	111	12	Intron of KMT2D(-):59bp after exon 18	KMT2D	49439643			12	Intron of ANKS1B(-):7Kb after exon 15	KMT2D	99540965			0	INVERSION		50101322	331423	238164	138	NEW_VARIANT
P-0047883-T01-IM6	PLCD3(NM_133373) - MAP3K14 (NM_003954) rearrangement : c.1126:PLCD3_.3:c.2325+63dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PLCD3:MAP3K14}		5481	0	6	17	Exon 7 of PLCD3(-)	PLCD3	43195495			17	Intron of MAP3K14(-):62bp after exon 12	MAP3K14	43344710			10	DUPLICATION		149215	331727	8179	6	NEW_VARIANT
P-0047883-T01-IM6	CHEK2 (NM_007194) rearrangement: c.592+2639_c.1461+23inv	PRECISE	Note: The CHEK2 rearrangement is an intragenic inversion of exons 5 - 13. The rearrangement includes the kinase domain of CHEK2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		6613	0	19	22	Intron of CHEK2(-):22bp after exon 13	CHEK2	29089997			22	Intron of CHEK2(-):3Kb after exon 4	CHEK2	29118326			10	INVERSION		28329	331729	10983	59	NEW_VARIANT
P-0032986-T02-IM6	BRAF (NM_004333) rearrangement: t(7;8)(q34;p23.1)(chr7:g.140500362::chr8:g.11716338)	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {CTSB:BRAF}		0	0	26	8	5-UTR of CTSB(-):14Kb before coding start	BRAF	11716338			7	Intron of BRAF(-):81bp before exon 7	BRAF	140500362			10	TRANSLOCATION		0	331815	0	28	NEW_VARIANT
P-0047795-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+4806_c.557-3057inv	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 5. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		42156	0	45	21	Intron of TMPRSS2(-):3Kb before exon 6	TMPRSS2	42855586			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875071			10	INVERSION		19485	331810	38431	56	NEW_VARIANT
P-0047797-T01-IM6	CCND1 (NM_053056) rearrangement: c.807:CCND1_chr11:g.69469425del	PRECISE	Note: The CCND1 rearrangement is a deletion of exon 5. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1562	0	69	11	Exon 5 of CCND1(+)	CCND1	69465969			11	Promoter of CCND1(+):14Kb from tx start	CCND1	69469425			10	DELETION		3456	331817	1198	76	NEW_VARIANT
P-0047797-T01-IM6	ERBB4 (NM_005235) rearrangement: c.1871+28_c.2301+5882del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		4152	0	20	2	Intron of ERBB4(-):6Kb after exon 19	ERBB4	212478020			2	Intron of ERBB4(-):27bp after exon 15	ERBB4	212530020			10	DELETION		52000	331816	4003	21	NEW_VARIANT
P-0047806-T01-IM6	ATM (NM_000051) rearrangement: c.335:ATM_chr11:g.108096596del	IMPPRECISE	Note: The ATM rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1499	0	6	11	5-UTR of ATM(+):2Kb before coding start	ATM	108096596			11	Exon 5 of ATM(+)	ATM	108106400			0	DELETION		9804	331811	1404	6	NEW_VARIANT
P-0047937-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-1482_c.557-1600dup	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic duplication of exons 3 - 5. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 3 exons : out of frame		7247	0	72	21	Intron of TMPRSS2(-):2Kb before exon 6	TMPRSS2	42854129			21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867987			10	DUPLICATION		13858	331924	8557	78	NEW_VARIANT
P-0047937-T01-IM6	PIK3R1 (NM_181523) rearrangement: t(5;6)(q13.1;q14.1)(chr5:g.67591383::chr6:g.76642727)	PRECISE	Note: The PIK3R1 rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	23	6	Intron of IMPG1(-):2Kb before exon 15	PIK3R1	76642727			5	Intron of PIK3R1(+):67bp after exon 14	PIK3R1	67591383			10	TRANSLOCATION		0	331926	0	23	NEW_VARIANT
P-0048007-T01-IM6	FANCC (NM_000136) rearrangement: t(9;22)(q22.32;q13.31)(chr9:g.97864041::chr22:g.44300238)	PRECISE	Note: The FANCC rearrangement is a translocation with a breakpoint in exon 15. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	16	22	IGR: 19Kb before PNPLA3(+)	FANCC	44300238			9	Exon 15 of FANCC(-)	FANCC	97864041			10	TRANSLOCATION		0	332072	0	23	NEW_VARIANT
P-0047982-T01-IM6	PTEN (NM_000314) rearrangement: t(5;10)(q11.2;q23.31)(chr5:g.55280572::chr10:g.89624398)	IMPPRECISE	Note: The PTEN rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	10	Intron of PTEN(+):93bp after exon 1	PTEN	89624398			5	3-UTR of IL6ST(-):10Kb after coding stop	PTEN	55280572			0	TRANSLOCATION		0	331994	0	14	NEW_VARIANT
P-0047827-T02-IM6	WIZ (NM_021241) - BRD4 (NM_058243) rearrangement: c.529+3652:WIZ_c.2212-31:BRD4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {WIZ:BRD4}		29450	0	42	19	Intron of BRD4(-):31bp before exon 13	WIZ	15355442			19	Intron of WIZ(-):4Kb after exon 3	BRD4	15543965			10	DELETION		188523	332416	25265	43	NEW_VARIANT
P-0047827-T02-IM6	EGFR (NM_005228) rearrangement: c.2061+304_c.3163-183dup	PRECISE	Note: The EGFR rearrangement is a kinase domain duplication (KDD) alteration.	MANUAL_OK	5to3	5to3	Duplication of 9 exons : in frame		28150	0	87	7	Intron of EGFR(+):304bp after exon 17	EGFR	55241121			7	Intron of EGFR(+):182bp before exon 27	EGFR	55270027			10	DUPLICATION		28906	332417	51925	91	NEW_VARIANT
P-0047959-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1555:TMPRSS2_c.18+174:ERGdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29235	0	39	21	Intron of ERG(-):173bp after exon 1	TMPRSS2	39870113			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868491			0	DELETION		2998378	331939	11449	43	NEW_VARIANT
P-0048004-T01-IM6	FOXP1 (NM_001244814) rearrangement: c.283-20627_c.298del	PRECISE	Note: The FOXP1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		270	0	10	3	Exon 4 of FOXP1(-)	FOXP1	71102909			3	Intron of FOXP1(-):21Kb before exon 4	FOXP1	71123551			10	DELETION		20642	332073	205	11	NEW_VARIANT
P-0048033-T01-IM6	BAIAP2 (NM_017451) - RPTOR (NM_020761) rearrangement: c.489+2583:BAIAP2_c.2243-52:RPTORdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {BAIAP2:RPTOR}		26219	0	2	17	Intron of RPTOR(+):51bp before exon 20	BAIAP2	78867455			17	Intron of BAIAP2(+):3Kb after exon 6	RPTOR	79062963			4	DUPLICATION		195508	332204	30765	3	NEW_VARIANT
P-0048038-T01-IM6	CD274 (NM_014143) rearrangement: t(9;20)(p24.1;p11.21)(chr9:g.5463221::chr20:g.22314553)	PRECISE	Note: The CD274 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	13	20	IGR: 54Kb before LINC01427(-)	CD274	22314553			9	Intron of CD274(+):100bp after exon 4	CD274	5463221			10	TRANSLOCATION		0	332198	0	13	NEW_VARIANT
P-0048041-T01-IM6	TSC1 (NM_000368) - AK8 (NM_152572) rearrangement: c.2813+18:TSC1_c.979+5282:AK8del	PRECISE	Note: The TSC1 - AK8 rearrangement is a deletion that results in a fusion of TSC1 exons 1 - 21 to AK8 exons 11 - 13.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TSC1:AK8}		4075	0	22	9	Intron of AK8(-):5Kb after exon 10	TSC1	135684743			9	Intron of TSC1(-):17bp after exon 21	AK8	135772792			10	DELETION		88049	332200	4288	22	NEW_VARIANT
P-0048072-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2:TMPRSS2_c.39+59528:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		41981	0	29	21	Intron of ERG(-):60Kb after exon 3	TMPRSS2	39888058			21	Intron of TMPRSS2(-):2bp before exon 2	ERG	42870118			10	DELETION		2982060	332224	34802	31	NEW_VARIANT
P-0048115-T01-IM6	DIS3 (NM_014953) rearrangement: c.1755+84:DIS3_chr13:g.32297113del	IMPPRECISE	Note: The DIS3 rearrangement is a deletion of exons 14 - 21. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		115528	0	15	13	IGR: 17Kb before RXFP2(+)	DIS3	32297113			13	Intron of DIS3(-):83bp after exon 13	DIS3	73344958			0	DELETION		41047845	332366	350367	15	NEW_VARIANT
P-0048115-T01-IM6	FAT1 (NM_005245) rearrangement: c.4462:FAT1_chr4:g.187335856del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 8 - 27. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	-		45460	0	25	4	3-UTR of F11-AS1(-):86Kb after coding stop	FAT1	187335856			4	Exon 8 of FAT1(-)	FAT1	187549779			10	DELETION		213923	332365	62922	25	NEW_VARIANT
P-0048159-T01-IM6	BRAF (NM_004333) rearrangement: c.609-233_c.1177+2191dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : out of frame		73764	0	9	7	Intron of BRAF(-):2Kb after exon 9	BRAF	140485157			7	Intron of BRAF(-):233bp before exon 5	BRAF	140508095			10	DUPLICATION		22938	332425	66328	9	NEW_VARIANT
P-0048161-T01-IM6	SMAD4 (NM_005359) rearrangement: c.1231:SMAD4_chr18:g.48835676inv	PRECISE	Note: The SMAD4 rearrangement is an inversion of exons 10 - 12. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2583	0	34	18	Exon 10 of SMAD4(+)	SMAD4	48593480			18	IGR: 83Kb before LOC100287225(+)	SMAD4	48835676			10	INVERSION		242196	332424	1629	32	NEW_VARIANT
P-0048169-T01-IM6	RB1 (NM_000321) rearrangement: c.1332+101_c.1960+133del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 19.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : out of frame		3725	0	31	13	Intron of RB1(+):101bp after exon 13	RB1	48951271			13	Intron of RB1(+):133bp after exon 19	RB1	49030618			10	DELETION		79347	332414	473	31	NEW_VARIANT
P-0048141-T01-IM6	ESR1 (NM_001122740) rearrangement: c.1433:ESR1_chr6:g.126953648inv	PRECISE	Note: The ESR1 rearrangement is an inversion of exons 1 - 8. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		77159	0	39	6	IGR: 293Kb before CENPW(+)	ESR1	126953648			6	Exon 8 of ESR1(+)	ESR1	152415583			10	INVERSION		25461935	332406	88359	40	NEW_VARIANT
P-0048144-T01-IM6	KMT2A (NM_001197104) rearrangement: t(1;11)(p36.12;q23.3)(chr1:g.23703057::chr11:g.118367285)	PRECISE	Note: The KMT2A rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	8	11	Intron of KMT2A(+):203bp after exon 20	KMT2A	118367285			1	IGR: 4Kb before TCEA3(-)	KMT2A	23703057			10	TRANSLOCATION		0	332397	0	7	NEW_VARIANT
P-0048174-T01-IM6	FAT1 (NM_005245) rearrangement: c.648_c.2756del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exon 2. The breakpoints are within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10717	0	2	4	Exon 2 of FAT1(-)	FAT1	187628226			4	Exon 2 of FAT1(-)	FAT1	187630334			10	DELETION		2108	332449	9739	2	NEW_VARIANT
P-0039030-T03-IM6	MAP3K1 (NM_005921) rearrangement: t(5;9)(q11.2;p21.3)(chr5:g.56111607::chr9:g.24253800)	PRECISE	Note: The MAP3K1 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	25	9	IGR: 289Kb before IZUMO3(-)	MAP3K1	24253800			5	Exon 1 of MAP3K1(+)	MAP3K1	56111607			10	TRANSLOCATION		0	331219	0	25	NEW_VARIANT
P-0042796-T02-IM6	NOTCH4 (NM_004557) rearrangement: t(6;19)(p21.32;p13.3)(chr6:g.32166201::chr19:g.3281852)	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	21	19	Intron of CELF5(+):271bp before exon 7	NOTCH4	3281852			6	Exon 26 of NOTCH4(-)	NOTCH4	32166201			10	TRANSLOCATION		0	331722	0	21	NEW_VARIANT
P-0047579-T02-IM6	APC (NM_000038) rearrangement: c.5580:APC_chr5:g.112190648del	PRECISE	Note: The APC rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	-		8753	0	9	5	Exon 16 of APC(+)	APC	112176871			5	IGR: 6Kb before SRP19(+)	APC	112190648			10	DELETION		13777	331837	4730	9	NEW_VARIANT
P-0047762-T01-IM6	SF3B1 (NM_012433) rearrangement: c.3622:SF3B1_chr2:g.198794918dup	PRECISE	Note: The SF3B1 rearrangement is a duplication of exons 1 - 24. One of the breakpoints is within exon 24. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		27942	0	4	2	Exon 24 of SF3B1(-)	SF3B1	198257830			2	Intron of PLCL1(+):125Kb after exon 1	SF3B1	198794918			10	DUPLICATION		537088	331822	26483	4	NEW_VARIANT
P-0047789-T01-IM6	DNMT3A (NM_022552) rearrangement: c.2322+1_c.2324del	PRECISE	Note: The DNMT3A rearrangement is an intragenic deletion of exons 19 - 20. The breakpoints are within exon 19 and exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		718	0	3	2	Exon 20 of DNMT3A(-)	DNMT3A	25462083			2	Exon 19 of DNMT3A(-)	DNMT3A	25463170			6	DELETION		1087	331839	893	3	NEW_VARIANT
P-0047823-T01-IM6	DUSP4 (NM_001394) rearrangement: c.579+18:DUSP4_chr8:g.28791503inv	PRECISE	Note: The DUSP4 rearrangement is an inversion of exons 3 - 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {DUSP4:HMBOX1}		9998	0	97	8	5-UTR of HMBOX1(+):30Kb before coding start	DUSP4	28791503			8	Intron of DUSP4(-):17bp after exon 2	DUSP4	29197597			10	INVERSION		406094	331804	8286	117	NEW_VARIANT
P-0047856-T01-IM6	PARP1 (NM_001618) rearrangement: c.2688:PARP1_chr1:g.226446443inv	PRECISE	Note: The PARP1 rearrangement is an inversion of exons 20 - 23. One of the breakpoints is within exon 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2865	0	30	1	Intron of LIN9(-):7Kb after exon 10	PARP1	226446443			1	Exon 20 of PARP1(-)	PARP1	226551742			10	INVERSION		105299	331701	3452	33	NEW_VARIANT
P-0047859-T01-IM6	DNMT1 (NM_001379) - CAMTA1 (NM_015215) rearrangement: t(1;19)(p36.31;p13.2)(chr1:g.6958300::chr19:g.10291323)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {DNMT1:CAMTA1}		0	0	5	19	Intron of DNMT1(-):78bp before exon 4	DNMT1	10291323			1	Intron of CAMTA1(+):73Kb after exon 3	CAMTA1	6958300			10	TRANSLOCATION		0	331698	0	6	NEW_VARIANT
P-0023366-T03-IM6	FLT4 (NM_182925) - REL (NM_002908) rearrangement: t(2;5)(p16.1;q35.3)(chr2:g.61127034::chr5:g.180056861)	PRECISE	Note: The FLT4 - REL rearrangement is a translocation with breakpoints in FLT4 intron 5 and REL intron 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	43	5	Intron of FLT4(-):26bp before exon 6	FLT4	180056861			2	Intron of REL(+):1Kb before exon 4	REL	61127034			10	TRANSLOCATION		0	332777	0	45	NEW_VARIANT
P-0047763-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-671:TMPRSS2_c.18+16055:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		27211	0	25	21	Intron of ERG(-):16Kb after exon 1	TMPRSS2	39854232			21	Intron of TMPRSS2(-):671bp before exon 3	ERG	42867176			10	DELETION		3012944	331821	16088	26	NEW_VARIANT
P-0047811-T01-IM6	MDC1 (NM_014641) rearrangement: t(6;13)(p21.33;q14.2)(chr6:g.30671876::chr13:g.49335769)	PRECISE	Note: The MDC1 rearrangement is a translocation with a breakpoint in exon 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	90	13	IGR: 55Kb before CYSLTR2(+)	MDC1	49335769			6	Exon 10 of MDC1(-)	MDC1	30671876			10	TRANSLOCATION		0	331830	0	123	NEW_VARIANT
P-0047811-T01-IM6	SOX17 (NM_022454) rearrangement: c.300:SOX17_chr8:g.72866321del	PRECISE	Note: The SOX17 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SOX17:LOC100132891}		84807	0	67	8	Exon 1 of SOX17(+)	SOX17	55370998			8	5-UTR of LOC100132891(+):102Kb before coding start	SOX17	72866321			10	DELETION		17495323	331829	86271	70	NEW_VARIANT
P-0047818-T01-IM6	SESN3 (NM_144665) rearrangement: c.1247+33:SESN3_chr11:g.45757807del	PRECISE	Note: The SESN3 rearrangement is a deletion of exons 9 - 10.	MANUAL_OK	3to5	3to5	-		225075	0	15	11	IGR: 14Kb before LOC100507384(+)	SESN3	45757807			11	Intron of SESN3(-):32bp after exon 8	SESN3	94910850			10	DELETION		49153043	331828	324099	15	NEW_VARIANT
P-0047961-T01-IM6	YAP1 (NM_001130145) rearrangement: c.1241:YAP1_chr11:g.108597375inv	PRECISE	Note: The YAP1 rearrangement is an inversion of exons 8 - 9. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		69677	0	10	11	Exon 8 of YAP1(+)	YAP1	102098277			11	Intron of DDX10(+):3Kb after exon 13	YAP1	108597375			10	INVERSION		6499098	331941	91762	11	NEW_VARIANT
P-0007266-T02-IM6	CLIP1 (NM_001247997) - BRAF (NM_004333) fusion: t(7;12)(q34;q24.31)(chr7:g.140495673::chr12:g.122767026)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {CLIP1:BRAF}		0	0	67	12	Intron of CLIP1(-):3Kb before exon 21	CLIP1	122767026			7	Intron of BRAF(-):1Kb before exon 8	BRAF	140495673			10	TRANSLOCATION		0	332850	0	70	NEW_VARIANT
P-0048241-T01-IM6	BMP1 (NM_006129) - MTOR (NM_004958) rearrangement: t(1;8)(p36.22;p21.3)(chr1:g.11259667::chr8:g.22041165)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {BMP1:MTOR}		0	0	53	8	Intron of BMP1(+):3Kb after exon 8	BMP1	22041165			1	Exon 27 of MTOR(-)	MTOR	11259667			10	TRANSLOCATION		0	332744	0	53	NEW_VARIANT
P-0048268-T01-IM6	EPHB1 (NM_004441) rearrangement: c.962-3651_c.1601del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7005	0	3	3	Intron of EPHB1(+):4Kb before exon 5	EPHB1	134847905			3	Exon 8 of EPHB1(+)	EPHB1	134884825			5	DELETION		36920	332789	5617	3	NEW_VARIANT
P-0048269-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.9353:ZFHX3_chr16:g.72597392del	PRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		11725	0	6	16	3-UTR of LINC01572(-):102Kb after coding stop	ZFHX3	72597392			16	Exon 9 of ZFHX3(-)	ZFHX3	72827228			9	DELETION		229836	332779	13241	6	NEW_VARIANT
P-0048272-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-5636_c.194-3554del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		214	0	33	9	Exon 1 of CDKN2A(-)	CDKN2A	21974761			9	Intron of CDKN2A(-):6Kb before exon 2	CDKN2A	21976843			10	DELETION		2082	332788	174	34	NEW_VARIANT
P-0047008-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.126+1704:TMPRSS2_c.39+10262:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		26982	0	74	21	Intron of ERG(-):10Kb after exon 3	TMPRSS2	39937324			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868342			10	DELETION		2931018	332770	31435	79	NEW_VARIANT
P-0048251-T01-IM6	FH (NM_000143) rearrangement: c.1390+166:FH_chr1:g.185113306inv	PRECISE	Note: The FH rearrangement is an inversion of exon 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		174968	0	14	1	Intron of TRMT1L(-):145bp before exon 6	TRMT1L	185113306			1	Intron of FH(-):165bp after exon 9	FH	241663571			10	INVERSION		56550265	332761	271655	18	NEW_VARIANT
P-0048251-T01-IM6	BRIP1 (NM_032043) rearrangement: c.1473+29:BRIP1_chr17:g.69421263inv	PRECISE	Note: The BRIP1 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		67586	0	49	17	Intron of BRIP1(-):28bp after exon 10	BRIP1	59870929			17	IGR: 327Kb before CASC17(-)	BRIP1	69421263			10	INVERSION		9550334	332763	124818	50	NEW_VARIANT
P-0048320-T01-IM6	MDM4 (NM_002393) - EFCAB6 (NM_022785) rearrangement: t(1;22)(q32.1;q13.2)(chr1:g.204516048::chr22:g.44039483)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {MDM4:EFCAB6}		0	0	23	22	Intron of EFCAB6(-):8Kb before exon 18	MDM4	44039483			1	Intron of MDM4(+):43bp after exon 10	EFCAB6	204516048			10	TRANSLOCATION		0	332813	0	23	NEW_VARIANT
P-0028732-T02-IM6	SMARCA4 (NM_003072) rearrangement: c.1419+1659_c.4171-101del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 9 - 29.	MANUAL_OK	3to5	3to5	Deletion of 21 exons : in frame		46789	0	44	19	Intron of SMARCA4(+):2Kb after exon 8	SMARCA4	11103658			19	Intron of SMARCA4(+):100bp before exon 30	SMARCA4	11151882			10	DELETION		48224	332839	23007	45	NEW_VARIANT
P-0047991-T02-IM6	NCOA4 (NM_001145260) - RET  (NM_020975) fusion: c.762+537:NCOA4_c.2137-494:RETdup	PRECISE	Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		24118	0	163	10	Intron of RET(+):493bp before exon 12	NCOA4	43611538			10	Intron of TIMM23B(+):149Kb before exon 7	RET	51583476			10	DUPLICATION		7971938	332808	22147	170	NEW_VARIANT
P-0048293-T01-IM6	KMT2D (NM_003482) rearrangement: c.4390_c.4741+351del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion of exons 15 - 18. One of the breakpoints is within exon 15.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4146	0	18	12	Intron of KMT2D(-):350bp after exon 18	KMT2D	49439352			12	Exon 15 of KMT2D(-)	KMT2D	49440420			10	DELETION		1068	332844	4971	20	NEW_VARIANT
P-0048296-T01-IM6	CDKN2A (NM_000077) rearrangement: c.458-568_c.193+7281del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		6378	0	43	9	Intron of CDKN2A(-):568bp before exon 3	CDKN2A	21968809			9	Intron of CDKN2A(-):7Kb after exon 1	CDKN2A	21986857			10	DELETION		18048	332842	2841	43	NEW_VARIANT
P-0048306-T02-IM6	RER1 (NM_007033) - ARID1A (NM_006015) rearrangement: c.187-285:RER1_c.1471:ARID1Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RER1:ARID1A}		312212	0	140	1	Intron of RER1(+):284bp before exon 4	RER1	2330569			1	Exon 3 of ARID1A(+)	ARID1A	27057763			10	DELETION		24727194	332814	294652	150	NEW_VARIANT
P-0048353-T01-IM6	BRCA1 (NM_007294) rearrangement: c.5332+82:BRCA1_chr17:g.41122482del	PRECISE	Note: The BRCA1 rearrangement is a deletion of exons 21 - 23.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {BRCA1:PTGES3L}		3726	0	14	17	Intron of PTGES3L(-):123bp before exon 5	BRCA1	41122482			17	Intron of BRCA1(-):81bp after exon 20	BRCA1	41202998			10	DELETION		80516	332982	5593	15	NEW_VARIANT
P-0048354-T01-IM6	NOTCH1 (NM_017617) rearrangement: t(8;9)(p23.2;q34.3)(chr8:g.6125999::chr9:g.139403489)	IMPPRECISE	Note: The NOTCH1 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	13	9	Exon 19 of NOTCH1(-)	NOTCH1	139403489			8	IGR: 135Kb before LOC100287015(-)	NOTCH1	6125999			0	TRANSLOCATION		0	332978	0	26	NEW_VARIANT
P-0048355-T01-IM6	FGFR3 (NM_000142) rearrangement: c.2274+60:FGFR3_chr4:g.6711492inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {FGFR3:MRFAP1L1}		42096	0	44	4	Intron of FGFR3(+):60bp after exon 17	FGFR3	1808721			4	5-UTR of MRFAP1L1(-):520bp before coding start	FGFR3	6711492			10	INVERSION		4902771	332981	49104	44	NEW_VARIANT
P-0048357-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41638942::chr21:g.42867694)	PRECISE	Note: The TMPRSS2 structural variant translocates the first 2 exons of TMPRSS2 to the intergenic region before ETV4.	MANUAL_OK	5to3	5to3	-		0	0	73	21	Intron of TMPRSS2(-):1Kb before exon 3	TMPRSS2	42867694			17	IGR: 34Kb before ETV4(-)	TMPRSS2	41638942			10	TRANSLOCATION		0	332969	0	73	NEW_VARIANT
P-0048373-T01-IM6	TOP1 (NM_003286) rearrangement: c.976-24_c.2090del	PRECISE	Note: The TOP1 rearrangement is an intragenic deletion of exons 12 - 20. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7520	0	5	20	Intron of TOP1(+):23bp before exon 12	TOP1	39728672			20	Exon 20 of TOP1(+)	TOP1	39750690			9	DELETION		22018	333005	10553	6	NEW_VARIANT
P-0048408-T01-IM6	MGA (NM_001164273) rearrangement: t(5;15)(p13.3;q15.1)(chr5:g.30242172::chr15:g.41989094)	IMPPRECISE	Note: The MGA rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	29	15	Exon 3 of MGA(+)	MGA	41989094			5	IGR: 862Kb before LOC101929681(-)	MGA	30242172			0	TRANSLOCATION		0	333016	0	30	NEW_VARIANT
P-0048434-T01-IM6	PTPN11 (NM_002834) rearrangement: c.1245:PTPN11_chr12:g.92988526del	PRECISE	Note: The PTPN11 rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		45693	0	22	12	IGR: 108Kb before C12orf74(+)	PTPN11	92988526			12	Exon 11 of PTPN11(+)	PTPN11	112924299			10	DELETION		19935773	333104	62545	22	NEW_VARIANT
P-0048473-T01-IM6	NSD1 (NM_022455) rearrangement: t(5;15)(q35.3;q26.3)(chr5:g.176637022::chr15:g.102521137)	PRECISE	Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	33	15	Promoter of DDX11L9(-):4Kb from tx start	NSD1	102521137			5	Exon 5 of NSD1(+)	NSD1	176637022			10	TRANSLOCATION		0	333148	0	40	NEW_VARIANT
P-0048473-T01-IM6	STAT3 (NM_139276) rearrangement: t(3;17)(p22.1;q21.2)(chr3:g.39726709::chr17:g.40474483)	PRECISE	Note: The STAT3 rearrangement is a translocation with a breakpoint in exon 21. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	17	Exon 21 of STAT3(-)	STAT3	40474483			3	IGR: 124Kb before MYRIP(+)	STAT3	39726709			10	TRANSLOCATION		0	333149	0	11	NEW_VARIANT
P-0048473-T01-IM6	TAP2 (NM_018833) rearrangement: c.1796-139:TAP2_chr6:g.32938006inv	PRECISE	Note: The TAP2 rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {BRD2:TAP2}		63838	0	17	6	Intron of TAP2(-):139bp before exon 11	TAP2	32797452			6	5-UTR of BRD2(+):3Kb before coding start	TAP2	32938006			10	INVERSION		140554	333147	48443	17	NEW_VARIANT
P-0048484-T01-IM6	NOTCH4 (NM_004557) rearrangement: t(6;13)(p21.32;q12.13)(chr6:g.32171958::chr13:g.27435738)	PRECISE	Note: The NOTCH4 rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	28	13	IGR: 106Kb before GPR12(-)	NOTCH4	27435738			6	Exon 19 of NOTCH4(-)	NOTCH4	32171958			10	TRANSLOCATION		0	333159	0	29	NEW_VARIANT
P-0048484-T01-IM6	STK19 (NM_004197) - MRPS31 (NM_005830) rearrangement: t(6;13)(p21.33;q14.11)(chr6:g.31948577::chr13:g.41339661)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {STK19:MRPS31}		0	0	37	13	Intron of MRPS31(-):1Kb after exon 2	STK19	41339661			6	Exon 7 of STK19(+)	MRPS31	31948577			10	TRANSLOCATION		0	333160	0	73	NEW_VARIANT
P-0048484-T01-IM6	NSD1 (NM_022455) rearrangement: t(5;6)(q35.2;p21.33)(chr5:g.176562282::chr6:g.31617932)	PRECISE	Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	61	6	Intron of BAG6(-):528bp before exon 3	NSD1	31617932			5	Exon 2 of NSD1(+)	NSD1	176562282			10	TRANSLOCATION		0	333158	0	62	NEW_VARIANT
P-0028057-T02-IM6	ERBB4 (NM_005235) rearrangement: c.422-20667_c.883+57dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		5334	0	9	2	Intron of ERBB4(-):56bp after exon 7	ERBB4	212587061			2	Intron of ERBB4(-):21Kb before exon 4	ERBB4	212673551			10	DUPLICATION		86490	333445	6494	17	NEW_VARIANT
P-0047470-T02-IM6	KMT2C (NM_170606) - PRKAG2 (NM_016203) rearrangement: c.12774+74:KMT2C_c.466+46558:PRKAG2del	IMPPRECISE	Note: The KMT2C - PRKAG2 rearrangement is a deletion that results in a fusion of KMT2C exons 1 - 51 to PRKAG2 exons 4 - 16.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {KMT2C:PRKAG2}		13505	0	6	7	Intron of PRKAG2(-):47Kb after exon 3	KMT2C	151431680			7	Intron of KMT2C(-):73bp after exon 51	PRKAG2	151847911			0	DELETION		416231	333180	13384	7	NEW_VARIANT
P-0048452-T01-IM6	AURKA (NM_003600) rearrangement: t(20;21)(q13.2;q22.3)(chr20:g.54958225::chr21:g.46653413)	PRECISE	Note: The AURKA rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	5	21	IGR: 30Kb before POFUT2(-)	AURKA	46653413			20	Exon 5 of AURKA(-)	AURKA	54958225			6	TRANSLOCATION		0	333132	0	5	NEW_VARIANT
P-0048454-T01-IM6	BRD4 (NM_058243) rearrangement: c.16_c.1342-263del	PRECISE	Note: The BRD4 rearrangement is an intragenic deletion of exons 2 - 7. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12226	0	5	19	Intron of BRD4(-):263bp before exon 8	BRD4	15368247			19	Exon 2 of BRD4(-)	BRD4	15383895			10	DELETION		15648	333135	6806	7	NEW_VARIANT
P-0048454-T01-IM6	EPHB1 (NM_004441) rearrangement: c.2496+386_c.2522del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		486	0	20	3	Intron of EPHB1(+):386bp after exon 13	EPHB1	134960525			3	Exon 14 of EPHB1(+)	EPHB1	134967183			10	DELETION		6658	333134	242	21	NEW_VARIANT
P-0048525-T01-IM6	YAP1 (NM_001130145) rearrangement: c.803-105:YAP1_chr11:g.91175282del	PRECISE	Note: The YAP1 rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		63471	0	14	11	IGR: 886Kb before MIR4490(-)	YAP1	91175282			11	Intron of YAP1(+):104bp before exon 5	YAP1	102076519			10	DELETION		10901237	333242	53159	16	NEW_VARIANT
P-0048530-T01-IM6	DERA (NM_015954) - GLI1 (NM_005269) rearrangement: c.508+217:DERA_c.3081:GLI1del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DERA:GLI1}		397667	0	33	12	Intron of DERA(+):217bp after exon 5	DERA	16116098			12	Exon 12 of GLI1(+)	GLI1	57865604			0	DELETION		41749506	333239	357989	33	NEW_VARIANT
P-0048531-T01-IM6	YAP1 (NM_001130145) - MAML2 (NM_032427) rearrangement: c.54:YAP1_c.513+33265:MAML2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {YAP1:MAML2}		29536	0	9	11	Intron of MAML2(-):33Kb after exon 1	YAP1	96041282			11	Exon 1 of YAP1(+)	MAML2	101981633			10	INVERSION		5940351	333245	27883	9	NEW_VARIANT
P-0048586-T01-IM6	CSDE1 (NM_001242891) rearrangement: t(1;14)(p13.2;q21.2)(chr1:g.115280412::chr14:g.45909793)	PRECISE	Note: The CSDE1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	12	14	IGR: 237Kb before MIS18BP1(-)	CSDE1	45909793			1	Intron of CSDE1(-):171bp after exon 5	CSDE1	115280412			10	TRANSLOCATION		0	333439	0	12	NEW_VARIANT
P-0048586-T01-IM6	PHOX2B (NM_003924) rearrangement: c.558:PHOX2B_chr4:g.41740029del	PRECISE	Note: The PHOX2B rearrangement is a deletion of exon 3. One of the breakpoints is within exon 3.. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1455	0	2	4	IGR: 6Kb before PHOX2B(-)	PHOX2B	41740029			4	Exon 3 of PHOX2B(-)	PHOX2B	41748211			5	DELETION		8182	333436	4880	2	NEW_VARIANT
P-0048593-T01-IM6	SLX4 (NM_032444) rearrangement: t(16;17)(p13.3;p13.3)(chr16:g.3652199::chr17:g.1815214)	PRECISE	Note: The SLX4 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	34	17	IGR: 23Kb before RTN4RL1(-)	SLX4	1815214			16	Exon 4 of SLX4(-)	SLX4	3652199			10	TRANSLOCATION		0	333450	0	34	NEW_VARIANT
P-0048593-T01-IM6	BRD4 (NM_058243) rearrangement: c.2316:BRD4_chr19:g.15425839del	PRECISE	Note: The BRD4 rearrangement is a deletion of exons 1 - 13. One of the breakpoints is within exon 13. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		32649	0	12	19	Exon 13 of BRD4(-)	BRD4	15355307			19	IGR: 38Kb before AKAP8(-)	BRD4	15425839			10	DELETION		70532	333447	36055	17	NEW_VARIANT
P-0048593-T01-IM6	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1370-816:ACOXL_c.394+3154:BCL2L11del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {ACOXL:BCL2L11}		17855	0	10	2	Intron of ACOXL(+):815bp before exon 16	ACOXL	111805979			2	Intron of BCL2L11(+):3Kb after exon 2	BCL2L11	111884870			10	DELETION		78891	333446	20942	10	NEW_VARIANT
P-0043891-T05-IM6	ELF3 (NM_004433) rearrangement: c.806-155:ELF3_chr1:g.201980127del	PRECISE	Note: The ELF3 rearrangement is a deletion of exons 1 - 7.	MANUAL_OK	3to5	3to5	Deletion within transcript		9911	0	9	1	5-UTR of ELF3(+):137bp before coding start	ELF3	201980127			1	Intron of ELF3(+):154bp before exon 8	ELF3	201982802			10	DELETION		2675	333186	5944	9	NEW_VARIANT
P-0048500-T01-IM6	FAT1 (NM_005245) rearrangement: c.9967:FAT1_chr4:g.187868727del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15.	MANUAL_OK	3to5	3to5	-		34470	0	40	4	Exon 15 of FAT1(-)	FAT1	187531056			4	IGR: 357Kb before LOC339975(-)	FAT1	187868727			10	DELETION		337671	333221	48894	41	NEW_VARIANT
P-0048507-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-999:TMPRSS2_c.39+51321:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		19877	0	15	21	Intron of ERG(-):51Kb after exon 3	TMPRSS2	39896265			21	Intron of TMPRSS2(-):999bp before exon 3	ERG	42867504			10	DELETION		2971239	333227	18774	15	NEW_VARIANT
P-0048510-T01-IM6	MGA (NM_001164273) rearrangement: c.7191+34:MGA_chr15:g.41775137inv	PRECISE	Note: The MGA rearrangement is an inversion of exons 1 - 19. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		34524	0	38	15	3-UTR of RTF1(+):66Kb after coding stop	MGA	41775137			15	Intron of MGA(+):34bp after exon 19	MGA	42050071			10	INVERSION		274934	333225	56463	38	NEW_VARIANT
P-0048510-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-148:TMPRSS2_c.-149-32518:ERGdel	PRECISE	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	MANUAL_OK	3to5	3to5	-		28442	0	76	21	3-UTR of ERG(-):44Kb after coding stop	TMPRSS2	39989387			21	Intron of TMPRSS2(-):148bp before exon 2	ERG	42870264			10	DELETION		2880877	333224	25436	78	NEW_VARIANT
P-0048551-T01-IM6	APC (NM_000038) - SRP19 (NM_001204199) rearrangement: c.7278:APC_c.301+454:SRP19del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		3453	0	4	5	Exon 16 of APC(+)	APC	112178569			5	Intron of SRP19(+):454bp after exon 4	SRP19	112200883			4	DELETION		22314	333259	3801	4	NEW_VARIANT
P-0048554-T01-IM6	TBX3 (NM_016569) rearrangement: c.1868:TBX3_chr12:g.117884190del	PRECISE	Note: The TBX3 rearrangement is a deletion of exons 1 - 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	-		18052	0	42	12	Exon 8 of TBX3(-)	TBX3	115110010			12	IGR: 7Kb before KSR2(-)	TBX3	117884190			10	DELETION		2774180	333255	18969	42	NEW_VARIANT
P-0048558-T01-IM6	CD79A (NM_001783) - RPS19 (NM_001022) rearrangement: c.309:CD79A_c.172+326:RPS19dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {CD79A:RPS19}		3305	0	72	19	Intron of RPS19(+):326bp after exon 3	CD79A	42365607			19	Exon 2 of CD79A(+)	RPS19	42383289			10	DUPLICATION		17682	333257	5971	75	NEW_VARIANT
P-0048608-T01-IM6	BRCA2 (NM_000059) rearrangement: c.6193:BRCA2_chr13:g.38945399del	PRECISE	Note: The BRCA2 rearrangement is a deletion of exons 11 - 27. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	-		40091	0	10	13	Exon 11 of BRCA2(+)	BRCA2	32914685			13	IGR: 21Kb before UFM1(+)	BRCA2	38945399			10	DELETION		6030714	333612	58405	11	NEW_VARIANT
P-0048610-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.349+100:TMPRSS2_c.40-56888:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		29152	0	20	21	Intron of ERG(-):57Kb before exon 4	TMPRSS2	39874432			21	Intron of TMPRSS2(-):99bp after exon 3	ERG	42866183			10	DELETION		2991751	333613	15718	20	NEW_VARIANT
P-0048611-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+12938:CCDC6_c.2137-795:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		40961	0	39	10	Intron of RET(+):794bp before exon 12	CCDC6	43611237			10	Intron of CCDC6(-):13Kb after exon 1	RET	61652942			10	INVERSION		18041705	333611	35472	47	NEW_VARIANT
P-0048613-T01-IM6	ERBB3 (NM_001982) rearrangement: t(12;20)(q13.2;p11.23)(chr12:g.56490271::chr20:g.19043904)	PRECISE	The ERBB3 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	16	20	IGR: 149Kb before SLC24A3(+)	ERBB3	19043904			12	Intron of ERBB3(+):15bp before exon 18	ERBB3	56490271			10	TRANSLOCATION		0	333569	0	17	NEW_VARIANT
P-0048437-T01-IM6	NKX2-1 (NM_001079668) - KIAA0391 (NM_014672) rearrangement: c.260:NKX2-1_c.1276-10713:KIAA0391inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NKX2-1:KIAA0391}		17354	0	17	14	Intron of KIAA0391(+):11Kb before exon 4	NKX2	35725220			14	Exon 2 of NKX2-1(-)	NKX2-1	36988393			10	INVERSION		1263173	333101	106107	63	NEW_VARIANT
P-0048437-T01-IM6	IKZF1 (NM_006060) Rearrangement: c.1312:IKZF1_chr7:g.25970278inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	-		34075	0	9	7	IGR: 19Kb before MIR148A(-)	IKZF1	25970278			7	Exon 8 of IKZF1(+)	IKZF1	50468073			0	INVERSION		24497795	333100	34495	9	NEW_VARIANT
P-0048597-T01-IM6	TMPRSS2 exon 2 with ERG exon 4	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		44460	0	28	21	Intron of ERG(-):65Kb after exon 3	TMPRSS2 exon 2 with ERG exon 4	39882599			21	Intron of TMPRSS2(-):351bp after exon 2	TMPRSS2 exon 2 with ERG exon 4	42869694			10	DELETION		2987095	333502	32008	28	NEW_VARIANT
P-0048504-T01-IM6	TMPRSS2 (NM_001135099) fusion: t(17;21)(q21.31;q22.3)(chr17:g.41633928::chr21:g.42866665)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	11	21	Intron of TMPRSS2(-):160bp before exon 3	TMPRSS2	42866665			17	IGR: 29Kb before ETV4(-)	TMPRSS2	41633928			10	TRANSLOCATION		0	333233	0	11	NEW_VARIANT
P-0048621-T01-IM6	ALK (NM_004304) rearrangement: c.2915-159:ALK_chr2:g.16609882del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		122254	0	6	2	IGR: 121Kb before FAM49A(-)	ALK	16609882			2	Intron of ALK(-):159bp before exon 18	ALK	29450099			9	DELETION		12840217	333645	192512	6	NEW_VARIANT
P-0048622-T01-IM6	CEBPA (NM_004364) rearrangement: c.156:CEBPA_chr19:g.33735782inv	PRECISE	Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		7965	0	36	19	IGR: 36Kb before SLC7A10(-)	CEBPA	33735782			19	Exon 1 of CEBPA(-)	CEBPA	33793165			10	INVERSION		57383	333646	14349	37	NEW_VARIANT
P-0048624-T01-IM6	ETV6 (NM_001987) rearrangement: t(12;19)(p13.2;p13.12)(chr12:g.12020310::chr19:g.14528519)	PRECISE	Note: The ETV6 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	37	19	3-UTR of DDX39A(-):2Kb after coding stop	ETV6	14528519			12	Intron of ETV6(+):2Kb before exon 5	ETV6	12020310			10	TRANSLOCATION		0	333642	0	38	NEW_VARIANT
P-0048671-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783869::chr6:g.117647250)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	153	6	Intron of ROS1(-):136bp after exon 33	CD74	117647250			5	Intron of CD74(-):373bp after exon 6	ROS1	149783869			10	TRANSLOCATION		0	333669	0	156	NEW_VARIANT
P-0048098-T02-IM6	ARID1A (NM_006015) rearrangement: t(1;5)(p36.11;q35.2)(chr1:g.27101346::chr5:g.175351720)	PRECISE	Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	5	IGR: 35Kb before THOC3(-)	ARID1A	175351720			1	Exon 18 of ARID1A(+)	ARID1A	27101346			10	TRANSLOCATION		0	333734	0	12	NEW_VARIANT
P-0048650-T01-IM6	ERCC2 (NM_000400) - NKPD1 (NM_198478) rearrangement: c.1119-74:ERCC2_c.409:NKPD1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ERCC2:NKPD1}		19392	0	8	19	Exon 2 of NKPD1(-)	ERCC2	45662041			19	Intron of ERCC2(-):74bp before exon 12	NKPD1	45864974			10	DELETION		202933	333656	23156	8	NEW_VARIANT
P-0048655-T01-IM6	AGXT2 (NM_031900) - TERT (NM_198253) rearrangement: c.487-607:AGXT2_c.3037:TERTdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {AGXT2:TERT}		118437	0	13	5	Exon 14 of TERT(-)	AGXT2	1255522			5	Intron of AGXT2(-):607bp before exon 5	TERT	35036028			10	DELETION		33780506	333652	96457	15	NEW_VARIANT
P-0048657-T01-IM6	SMAD3 (NM_005902) rearrangement: c.872-6_c.1154+588dup	PRECISE	Note: The SMAD3 rearrangement is an intragenic duplication of exons 7 - 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		3087	0	6	15	Intron of SMAD3(+):5bp before exon 7	SMAD3	67477059			15	Intron of SMAD3(+):588bp after exon 8	SMAD3	67480435			10	DUPLICATION		3376	333651	3760	7	NEW_VARIANT
P-0048660-T01-IM6	PLK2 (NM_006622) rearrangement: c.914:PLK2_chr5:g.57749444del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7385	0	32	5	Promoter of PLK2(-):365bp from tx start	PLK2	57749444			5	Exon 7 of PLK2(-)	PLK2	57753102			10	DELETION		3658	333659	10707	35	NEW_VARIANT
P-0048696-T01-IM6	PMS1 (NM_000534) rearrangement: c.1856+3301_c.2473+34dup	PRECISE	Note: The PMS1 rearrangement is an intragenic duplication of exons 10 - 11. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		2919	0	15	2	Intron of PMS1(+):3Kb after exon 9	PMS1	190723155			2	Intron of PMS1(+):34bp after exon 11	PMS1	190732689			10	DUPLICATION		9534	333735	4180	15	NEW_VARIANT
P-0048750-T01-IM6	MGA (NM_001164273) rearrangement: t(3;15)(p24.1;q15.1)(chr3:g.29948992::chr15:g.42042391)	PRECISE	The MGA rearrangement is a translocation with a breakpoint in exon 17. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	5	15	Exon 17 of MGA(+)	MGA	42042391			3	Intron of RBMS3(+):8Kb after exon 10	MGA	29948992			10	TRANSLOCATION		0	333818	0	5	NEW_VARIANT
P-0012045-T03-IM6	BRAF (NM_004333) rearrangement: c.1141-152:BRAF_chr7:g.141759418del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		72134	0	26	7	Intron of BRAF(-):152bp before exon 9	BRAF	140487536			7	Intron of MGAM(+):18bp after exon 32	BRAF	141759418			10	DELETION		1271882	333756	62253	28	NEW_VARIANT
P-0045906-T02-IM6	TP53 (NM_000546) rearrangement: t(5;17)(p14.1;p13.1)(chr5:g.25413095::chr17:g.7578033)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	15	17	Intron of TP53(-):143bp after exon 6	TP53	7578033			5	IGR: 578Kb before LOC340107(-)	TP53	25413095			10	TRANSLOCATION		0	333759	0	15	NEW_VARIANT
P-0048596-T01-IM6	RARA (NM_000964) rearrangement: t(17;20)(q21.2;q12)(chr17:g.38512345::chr20:g.39591760)	PRECISE	Note: The RARA rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	63	20	IGR: 66Kb before TOP1(+)	RARA	39591760			17	Exon 9 of RARA(+)	RARA	38512345			10	TRANSLOCATION		0	333501	0	63	NEW_VARIANT
P-0048596-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.1303_c.1330-684del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		718	0	34	3	Exon 5 of TGFBR2(+)	TGFBR2	30713903			3	Intron of TGFBR2(+):683bp before exon 6	TGFBR2	30714913			0	DELETION		1010	333500	333	38	NEW_VARIANT
P-0048702-T01-IM6	STIP1 (NM_006819) - RPS6KA4 (NM_003942) rearrangement: c.1024-379:STIP1_c.1765:RPS6KA4del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STIP1:RPS6KA4}		22828	0	58	11	Intron of STIP1(+):378bp before exon 9	STIP1	63967033			11	Exon 14 of RPS6KA4(+)	RPS6KA4	64137333			10	DELETION		170300	333730	23983	68	NEW_VARIANT
P-0048708-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.127-1452:TMPRSS2_c.39+39917:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		14388	0	26	21	Intron of ERG(-):40Kb after exon 3	TMPRSS2	39907669			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867957			10	DELETION		2960288	333742	31506	26	NEW_VARIANT
P-0048709-T01-IM6	MTOR (NM_004958) rearrangement: c.1116+6:MTOR_chr1:g.11492685inv	PRECISE	Note: The MTOR rearrangement is an inversion of exons 1 - 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		9811	0	5	1	Intron of MTOR(-):5bp after exon 7	MTOR	11307870			1	IGR: 47Kb before PTCHD2(+)	MTOR	11492685			7	INVERSION		184815	333738	9868	5	NEW_VARIANT
P-0048755-T01-IM6	INSR (NM_000208) rearrangement: c.2267+139:INSR_chr19:g.5461998inv	IMPPRECISE	Note: The INSR rearrangement is an inversion of exons 12 - 22. The rearrangement includes the kinase domain of INSR. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		19236	0	18	19	IGR: 7Kb before ZNRF4(+)	INSR	5461998			19	Intron of INSR(-):138bp after exon 11	INSR	7150369			0	INVERSION		1688371	333806	21114	19	NEW_VARIANT
P-0048755-T01-IM6	PARK2 (NM_004562) rearrangement: c.85_c.171+6891del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		554	0	51	6	Intron of PARK2(-):7Kb after exon 2	PARK2	162857451			6	Exon 2 of PARK2(-)	PARK2	162864428			10	DELETION		6977	333805	558	56	NEW_VARIANT
P-0048756-T01-IM6	KDM5A (NM_001042603) rearrangement: t(12;14)(p13.33;q32.32)(chr12:g.461291::chr14:g.103256288)	IMPPRECISE	Note: The KDM5A rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {KDM5A:TRAF3}		0	0	11	14	5-UTR of TRAF3(+):80Kb before coding start	KDM5A	103256288			12	Intron of KDM5A(-):79bp after exon 9	KDM5A	461291			0	TRANSLOCATION		0	333804	0	14	NEW_VARIANT
P-0048763-T01-IM6	VTCN1 (NM_024626) rearrangement: c.446-3:VTCN1_chr1:g.81533670inv	PRECISE	Note: The VTCN1 rearrangement is an inversion of exons 4 - 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		53590	0	103	1	IGR: 427Kb before LOC101927412(+)	VTCN1	81533670			1	Intron of VTCN1(-):3bp before exon 4	VTCN1	117695994			10	INVERSION		36162324	333808	106516	103	NEW_VARIANT
P-0048772-T01-IM6	STAT3 (NM_139276) rearrangement: c.1465-8:STAT3_chr17:g.40636770dup	PRECISE	Note: The STAT3 rearrangement is a duplication of exons 1 - 16. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		14921	0	38	17	Intron of STAT3(-):8bp before exon 17	STAT3	40476872			17	Intron of ATP6V0A1(+):2Kb after exon 9	STAT3	40636770			10	DUPLICATION		159898	334320	31102	38	NEW_VARIANT
P-0048772-T01-IM6	STAT5B (NM_012448) rearrangement: t(6;17)(q25.3;q21.2)(chr6:g.159208883::chr17:g.40364046)	PRECISE	Note: The STAT5B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	34	17	Exon 13 of STAT5B(-)	STAT5B	40364046			6	Intron of EZR(-):648bp before exon 3	STAT5B	159208883			10	TRANSLOCATION		0	334321	0	40	NEW_VARIANT
P-0048773-T01-IM6	CREBBP (NM_004380) rearrangement: c.799-11521_c.3610-95inv	PRECISE	Note: The CREBBP rearrangement is an intragenic inversion of exons 3 - 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		25402	0	47	16	Intron of CREBBP(-):95bp before exon 19	CREBBP	3807472			16	Intron of CREBBP(-):12Kb before exon 3	CREBBP	3872301			10	INVERSION		64829	334305	30239	47	NEW_VARIANT
P-0048776-T01-IM6	TSC1 (NM_000368) rearrangement: c.2502+66:TSC1_chr9:g.73622510inv	PRECISE	Note: The TSC1 rearrangement is an inversion of exons 20 - 23. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		322338	0	7	9	Intron of TRPM3(-):114Kb after exon 1	TSC1	73622510			9	Intron of TSC1(-):65bp after exon 19	TSC1	135776910			8	INVERSION		62154400	334319	280344	7	NEW_VARIANT
P-0048786-T01-IM6	HIST1H3E (NM_003532) rearrangement: c.39:HIST1H3E_chr6:g.26032289inv	IMPPRECISE	Note: The HIST1H3E rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {HIST1H3E:HIST1H3B}		17802	0	6	6	Promoter of HIST1H3B(-):473bp from tx start	HIST1H3E	26032289			6	Exon 1 of HIST1H3E(+)	HIST1H3E	26225421			0	INVERSION		193132	334054	22175	15	NEW_VARIANT
P-0048828-T01-IM6	TP53 (NM_000546) rearrangement: c.376-62:TP53_chr17:g.7581327del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 1 - 4.	MANUAL_OK	3to5	3to5	Deletion within transcript		5632	0	57	17	Intron of TP53(-):62bp before exon 5	TP53	7578616			17	5-UTR of TP53(-):8Kb before coding start	TP53	7581327			10	DELETION		2711	334262	5725	64	NEW_VARIANT
P-0048829-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+948:KIF5B_c.2136+432:RETinv	IMPPRECISE	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	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		48855	0	41	10	Intron of KIF5B(-):947bp after exon 15	KIF5B	32316408			10	Intron of RET(+):432bp after exon 11	RET	43610616			0	INVERSION		11294208	334258	52220	44	NEW_VARIANT
P-0048846-T01-IM6	NOTCH1 (NM_017617) rearrangement: t(9;20)(q34.3;q13.12)(chr9:g.139405807::chr20:g.42802904)	PRECISE	Note: The NOTCH1 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	50	20	Intron of JPH2(-):12Kb after exon 1	NOTCH1	42802904			9	Intron of NOTCH1(-):84bp before exon 16	NOTCH1	139405807			10	TRANSLOCATION		0	334252	0	50	NEW_VARIANT
P-0048802-T01-IM6	TERT (NM_198253) rearrangement: t(5;18)(p15.33;q22.3)(chr5:g.1295313::chr18:g.71923116)	PRECISE	Note: The TERT rearrangement is a translocation with a breakpoint in the promoter region. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	45	18	Intron of CYB5A(-):106bp before exon 3	TERT	71923116			5	Promoter of TERT(-):42Kb from tx start	TERT	1295313			10	TRANSLOCATION		0	334293	0	45	NEW_VARIANT
P-0048806-T01-IM6	MDM4 (NM_002393) rearrangement: c.512-105:MDM4_chr1:g.151223675inv	PRECISE	Note: The MDM4 rearrangement is an inversion of exons 1 - 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		158602	0	3	1	Promoter of PIP5K1A(+):53Kb from tx start	MDM4	151223675			1	Intron of MDM4(+):104bp before exon 8	MDM4	204511807			6	INVERSION		53288132	334290	239001	3	NEW_VARIANT
P-0048815-T01-IM6	TNFRSF14 (NM_003820) rearrangement: c.694+36:TNFRSF14_chr1:g.78601774del	PRECISE	Note: The TNFRSF14 rearrangement is a deletion of exons 7 - 8.	MANUAL_OK	3to5	3to5	-		646541	1	41	1	Intron of TNFRSF14(+):36bp after exon 6	TNFRSF14	2493290			1	3-UTR of GIPC2(+):90Kb after coding stop	TNFRSF14	78601774			10	DELETION		76108484	334285	442443	44	NEW_VARIANT
P-0048815-T01-IM6	ASB17 (NM_080868) - FUBP1 (NM_003902) rearrangement: c.682-1387:ASB17_c.100:FUBP1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ASB17:FUBP1}		18280	2	27	1	Intron of ASB17(-):1Kb before exon 3	ASB17	76386230			1	Exon 1 of FUBP1(-)	FUBP1	78444589			10	DUPLICATION		2058359	334286	14591	25	NEW_VARIANT
P-0048887-T01-IM6	THSD4 (NM_024817) - VTCN1 (NM_024626) rearrangement: t(1;15)(p13.1;q23)(chr1:g.117695948::chr15:g.72060483)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {THSD4:VTCN1}		0	0	148	15	Intron of THSD4(+):3Kb before exon 16	THSD4	72060483			1	Exon 4 of VTCN1(-)	VTCN1	117695948			10	TRANSLOCATION		0	334405	0	158	NEW_VARIANT
P-0048887-T01-IM6	TAP2 (NM_018833) - CYP21A2 (NM_000500) rearrangement: c.283:TAP2_c.871:CYP21A2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TAP2:CYP21A2}		85240	0	20	6	Exon 7 of CYP21A2(+)	TAP2	32007914			6	Exon 2 of TAP2(-)	CYP21A2	32805728			10	INVERSION		797814	334403	197425	98	NEW_VARIANT
P-0048893-T01-IM6	SPTBN1 (NM_003128) - ALK (NM_004304) fusion: c.763+1517:SPTBN1_c.3153:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SPTBN1:ALK}		184256	0	97	2	Exon 19 of ALK(-)	SPTBN1	29448346			2	Intron of SPTBN1(+):2Kb after exon 7	ALK	54846847			10	INVERSION		25398501	334362	307176	97	NEW_VARIANT
P-0048898-T01-IM6	PAK7 (NM_177990) - RB1 (NM_000321) rearrangement: t(13;20)(q14.2;p12.2)(chr13:g.48909327::chr20:g.9525034)	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	100	20	Exon 8 of PAK7(-)	PAK7	9525034			13	Intron of RB1(+):7Kb before exon 3	RB1	48909327			10	TRANSLOCATION		0	334357	0	100	NEW_VARIANT
P-0041118-T03-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782265::chr6:g.117647424)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CD74:ROS1}		0	0	36	6	Exon 33 of ROS1(-)	CD74	117647424			5	Intron of CD74(-):77bp before exon 8	ROS1	149782265			10	TRANSLOCATION		0	334771	0	36	NEW_VARIANT
P-0048904-T01-IM6	ERBB3 (NM_001982) rearrangement: t(12;18)(q13.2;q21.32)(chr12:g.56493685::chr18:g.57428632)	PRECISE	Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	27	18	IGR: 139Kb before PMAIP1(+)	ERBB3	57428632			12	Exon 25 of ERBB3(+)	ERBB3	56493685			10	TRANSLOCATION		0	334524	0	30	NEW_VARIANT
P-0048904-T01-IM6	CCNE1 (NM_001238) rearrangement: c.638:CCNE1_chr19:g.42157013del	PRECISE	Note: The CCNE1 rearrangement is a deletion of exons 8 - 12. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		169245	0	16	19	Exon 8 of CCNE1(+)	CCNE1	30312657			19	IGR: 20Kb before CEACAM7(-)	CCNE1	42157013			10	DELETION		11844356	334520	207005	17	NEW_VARIANT
P-0048904-T01-IM6	AXL (NM_021913) - EPN1 (NM_001130071) rearrangement: c.704:AXL_c.1300:EPN1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {AXL:EPN1}		233919	0	30	19	Exon 6 of AXL(+)	AXL	41737124			19	Exon 7 of EPN1(+)	EPN1	56203399			10	DELETION		14466275	334521	287895	32	NEW_VARIANT
P-0048904-T01-IM6	PDGFRA (NM_006206) rearrangement: c.1365:PDGFRA_chr4:g.33633229del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		42347	0	3	4	IGR: 265Kb before LOC101928622(-)	PDGFRA	33633229			4	Exon 10 of PDGFRA(+)	PDGFRA	55139704			5	DELETION		21506475	334519	56298	3	NEW_VARIANT
P-0048909-T01-IM6	PTPRS (NM_002850) rearrangement: c.4620:PTPRS_chr19:g.5295751del	PRECISE	Note: The PTPRS rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		48024	0	4	19	Exon 31 of PTPRS(-)	PTPRS	5212497			19	5-UTR of PTPRS(-):89Kb before coding start	PTPRS	5295751			10	DELETION		83254	334512	53037	4	NEW_VARIANT
P-0048923-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.2118:PIK3R1_chr5:g.83476610del	PRECISE	Note: The PIK3R1 rearrangement is a deletion of exon 16. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	Antisense Fusion		42234	0	25	5	Exon 16 of PIK3R1(+)	PIK3R1	67593372			5	Intron of EDIL3(-):271bp before exon 4	PIK3R1	83476610			10	DELETION		15883238	334540	41916	25	NEW_VARIANT
P-0048968-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1914+211:KIF5B_c.2137-223:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		48199	0	46	10	Intron of KIF5B(-):210bp after exon 16	KIF5B	32311565			10	Intron of RET(+):222bp before exon 12	RET	43611809			10	INVERSION		11300244	334774	71766	57	NEW_VARIANT
P-0048977-T01-IM6	TET1 (NM_030625) - SUPV3L1 (NM_003171) rearrangement: c.4914+152:TET1_c.1518+735:SUPV3L1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TET1:SUPV3L1}		8516	0	12	10	Intron of TET1(+):152bp after exon 9	TET1	70441397			10	Intron of SUPV3L1(+):735bp after exon 12	SUPV3L1	70960990			7	DELETION		519593	334715	13574	12	NEW_VARIANT
P-0030266-T01-IM6	PREX2 (NM_024870) rearrangement: c.706-33:PREX2_chr8:g.68615664del	PRECISE	Note: The PREX2 rearrangement is a deletion of exons 1 - 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		7658	0	32	8	Intron of CPA6(-):43Kb after exon 1	PREX2	68615664			8	Intron of PREX2(+):32bp before exon 7	PREX2	68950361			10	DELETION		334697	335000	10541	32	NEW_VARIANT
P-0048920-T01-IM6	CUL5 (NM_003478) - ATM (NM_000051) rearrangement: c.780+381:CUL5_c.6096-43:ATMdel	IMPPRECISE	Note: The CUL5 - ATM rearrangement is a deletion that results in a fusion of CUL5 exons 1 - 7 to ATM exons 42 - 63.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CUL5:ATM}		50754	0	6	11	Intron of CUL5(+):381bp after exon 7	CUL5	107926063			11	Intron of ATM(+):42bp before exon 42	ATM	108186695			0	DELETION		260632	334550	33952	10	NEW_VARIANT
P-0048925-T01-IM6	RASA1 (NM_002890) rearrangement: c.2345-27:RASA1_chr5:g.86547885del	PRECISE	Note: The RASA1 rearrangement is a deletion of exons 1 - 17.	MANUAL_OK	3to5	3to5	-		17199	0	4	5	IGR: 16Kb before RASA1(+)	RASA1	86547885			5	Intron of RASA1(+):26bp before exon 18	RASA1	86674186			6	DELETION		126301	334535	31597	4	NEW_VARIANT
P-0048936-T01-IM6	SMARCD1 (NM_003076) rearrangement: t(6;12)(q21;q13.12)(chr6:g.106876550::chr12:g.50484218)	PRECISE	Note: The SMARCD1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	68	12	Intron of SMARCD1(+):33bp after exon 8	SMARCD1	50484218			6	IGR: 83Kb before AIM1(+)	SMARCD1	106876550			10	TRANSLOCATION		0	334698	0	67	NEW_VARIANT
P-0048936-T01-IM6	ALG14 (NM_144988) - RB1 (NM_000321) rearrangement: t(1;13)(p21.3;q14.2)(chr1:g.95496402::chr13:g.49051408)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {ALG14:RB1}		0	0	36	13	Intron of RB1(+):82bp before exon 26	ALG14	49051408			1	Intron of ALG14(-):4Kb before exon 3	RB1	95496402			10	TRANSLOCATION		0	334701	0	36	NEW_VARIANT
P-0048936-T01-IM6	ERBB3 (NM_001982) - KPNA3 (NM_002267) rearrangement: t(12;13)(q13.2;q14.2)(chr12:g.56489142::chr13:g.50346188)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ERBB3:KPNA3}		0	0	69	13	Intron of KPNA3(-):20Kb after exon 1	ERBB3	50346188			12	Intron of ERBB3(+):48bp after exon 16	KPNA3	56489142			10	TRANSLOCATION		0	334702	0	69	NEW_VARIANT
P-0048936-T01-IM6	ROS1 (NM_002944) rearrangement: t(1;6)(p22.1;q22.1)(chr1:g.93761577::chr6:g.117646467)	PRECISE	Note: The ROS1 rearrangement is a translocation with a breakpoint in intron 33. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	104	6	Intron of ROS1(-):889bp before exon 34	ROS1	117646467			1	IGR: 14Kb before LOC100131564(-)	ROS1	93761577			10	TRANSLOCATION		0	334696	0	106	NEW_VARIANT
P-0048936-T01-IM6	LMOD1 (NM_012134) - IFNGR1 (NM_000416) rearrangement: t(1;6)(q32.1;q23.3)(chr1:g.201913481::chr6:g.137519310)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {LMOD1:IFNGR1}		0	0	44	6	Exon 7 of IFNGR1(-)	LMOD1	137519310			1	Intron of LMOD1(-):2Kb after exon 1	IFNGR1	201913481			10	TRANSLOCATION		0	334697	0	47	NEW_VARIANT
P-0048950-T01-IM6	SND1 (NM_014390) - BRAF (NM_004333) fusion: c.1152+30037:SND1_c.1140+2075:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SND1:BRAF}		98474	0	99	7	Intron of SND1(+):30Kb after exon 10	SND1	127391491			7	Intron of BRAF(-):2Kb after exon 8	BRAF	140492033			10	INVERSION		13100542	334683	140429	97	NEW_VARIANT
P-0048954-T01-IM6	TOP1 (NM_003286) rearrangement: c.335+156_c.1951-1168del	PRECISE	Note: The TOP1 rearrangement is an intragenic deletion of exons 6 - 18.	MANUAL_OK	3to5	3to5	Deletion of 13 exons : out of frame		14151	0	3	20	Intron of TOP1(+):156bp after exon 5	TOP1	39706433			20	Intron of TOP1(+):1Kb before exon 19	TOP1	39749168			7	DELETION		42735	334677	19653	3	NEW_VARIANT
P-0048955-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1067:TMPRSS2_c.237-4991:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		31412	0	34	21	Intron of ERG(-):5Kb before exon 3	TMPRSS2	39800474			21	Intron of TMPRSS2(-):1Kb after exon 2	ERG	42868979			10	DELETION		3068505	334673	50752	35	NEW_VARIANT
P-0048958-T01-IM6	PARK2 (NM_004562) rearrangement: c.172-16_c.412+24205dup	IMPPRECISE	Note: The PARK2 rearrangement is an intragenic duplication of exon 3. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		1803	0	8	6	Intron of PARK2(-):24Kb after exon 3	PARK2	162659352			6	Intron of PARK2(-):16bp before exon 3	PARK2	162683813			0	DUPLICATION		24461	334675	2981	9	NEW_VARIANT
P-0048980-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(17;21)(q21.31;q22.3)(chr17:g.41631175::chr21:g.42868674)	PRECISE	Note: The TMPRSS2 rearrangement involves intron 2.	MANUAL_OK	5to3	5to3	-		0	0	89	21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868674			17	IGR: 26Kb before ETV4(-)	TMPRSS2	41631175			10	TRANSLOCATION		0	334792	0	94	NEW_VARIANT
P-0048996-T01-IM6	NF1 (NM_001042492) rearrangement: c.2409+635_c.2664inv	PRECISE	Note: The NF1 rearrangement is an intragenic inversion of exon 21. One of the breakpoints is within exon 21. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1096	0	2	17	Intron of NF1(+):635bp after exon 20	NF1	29555259			17	Exon 21 of NF1(+)	NF1	29556297			7	INVERSION		1038	334814	587	2	NEW_VARIANT
P-0048998-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2754:TMPRSS2_c.19-3127:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		52798	0	9	21	Intron of ERG(-):3Kb before exon 2	TMPRSS2	39820671			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872870			10	DELETION		3052199	334811	62319	9	NEW_VARIANT
P-0049127-T01-IM6	EP300 (NM_001429) rearrangement: c.6587:EP300_chr22:g.41577834dup	PRECISE	Note: The EP300 rearrangement is a duplication of exon 31. One of the breakpoints is within exon 31. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		5926	0	2	22	Exon 31 of EP300(+)	EP300	41574302			22	Promoter of EP300(+):89Kb from tx start	EP300	41577834			10	DUPLICATION		3532	335008	5301	2	NEW_VARIANT
P-0049006-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.3837+208_c.5400del	PRECISE	Note: The NOTCH3 rearrangement is an intragenic deletion of exons 24 - 30. One of the breakpoints is within exon 30.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16038	0	15	19	Exon 30 of NOTCH3(-)	NOTCH3	15276865			19	Intron of NOTCH3(-):207bp after exon 23	NOTCH3	15289426			10	DELETION		12561	334836	10222	16	NEW_VARIANT
P-0049006-T01-IM6	SOS1 (NM_005633) - FBXO11 (NM_001190274) rearrangement: c.1074+104:SOS1_c.2006+820:FBXO11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SOS1:FBXO11}		110558	0	4	2	Intron of SOS1(-):103bp after exon 8	SOS1	39262249			2	Intron of FBXO11(-):819bp after exon 16	FBXO11	48045098			10	DUPLICATION		8782849	334837	136070	7	NEW_VARIANT
P-0049006-T01-IM6	RASA1 (NM_002890) rearrangement: c.2604-73_c.3061-69del	PRECISE	Note: The RASA1 rearrangement is an intragenic deletion of exons 20 - 24.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : out of frame		3623	0	15	5	Intron of RASA1(+):72bp before exon 20	RASA1	86676253			5	Intron of RASA1(+):68bp before exon 25	RASA1	86686548			10	DELETION		10295	334835	4458	15	NEW_VARIANT
P-0024088-T02-IM6	TCF3 (NM_001136139) rearrangement: c.1586+307:TCF3_chr19:g.1918294dup	PRECISE	Note: The TCF3 rearrangement is a duplication of exons 1 - 16. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		26927	0	37	19	Intron of TCF3(-):306bp after exon 16	TCF3	1615378			19	Intron of SCAMP4(+):12bp after exon 4	TCF3	1918294			10	DUPLICATION		302916	335442	26770	37	NEW_VARIANT
P-0024088-T02-IM6	ATRX (NM_000489) rearrangement: c.4585_c.5134+1603inv	PRECISE	Note: The ATRX rearrangement is an intragenic inversion of exons 16 - 19. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1865	0	20	X	Intron of ATRX(-):2Kb after exon 19	ATRX	76887092			X	Exon 16 of ATRX(-)	ATRX	76891520			10	INVERSION		4428	335444	813	20	NEW_VARIANT
P-0046175-T02-IM6	RCN1 (NM_002901) - TMPRSS2 (NM_001135099) rearrangement: t(11;21)(p13;q22.3)(chr11:g.32114150::chr21:g.42875275)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RCN1:TMPRSS2}		0	0	19	21	Intron of TMPRSS2(-):5Kb after exon 1	RCN1	42875275			11	Intron of RCN1(+):1Kb after exon 1	TMPRSS2	32114150			10	TRANSLOCATION		0	334893	0	19	NEW_VARIANT
P-0046175-T02-IM6	FAT1 (NM_005245) rearrangement: c.112:FAT1_chr4:g.188179915inv	PRECISE	Note: The FAT1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		750	0	7	4	Exon 2 of FAT1(-)	FAT1	187630870			4	IGR: 45Kb before LOC339975(-)	FAT1	188179915			10	INVERSION		549045	334892	1036	7	NEW_VARIANT
P-0046175-T02-IM6	AR (NM_000044) rearrangement: t(6;X)(p24.3;q12)(chr6:g.7324070::chrX:g.66931498)	PRECISE	Note: The AR rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {AR:CAGE1}		0	0	19	X	Exon 4 of AR(+)	AR	66931498			6	Promoter of CAGE1(-):3Kb from tx start	CAGE1	7324070			10	TRANSLOCATION		0	334894	0	19	NEW_VARIANT
P-0047840-T02-IM6	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117645871::chr20:g.43955947)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SDC4:ROS1}		0	0	13	20	Exon 5 of SDC4(-)	SDC4	43955947			6	Intron of ROS1(-):293bp before exon 34	ROS1	117645871			10	TRANSLOCATION		0	334884	0	13	NEW_VARIANT
P-0048861-T01-IM6	EP300 (NM_001429) rearrangement: c.938_c.1529-1999del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4224	0	12	22	Exon 4 of EP300(+)	EP300	41523522			22	Intron of EP300(+):2Kb before exon 7	EP300	41529818			10	DELETION		6296	334992	5667	12	NEW_VARIANT
P-0049029-T01-IM6	RELA (NM_021975) rearrangement: t(7;11)(q21.11;q13.1)(chr7:g.79622169::chr11:g.65429657)	PRECISE	Note: The RELA rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	11	Exon 2 of RELA(-)	RELA	65429657			7	IGR: 142Kb before GNAI1(+)	RELA	79622169			10	TRANSLOCATION		0	334862	0	7	NEW_VARIANT
P-0049048-T01-IM6	BAP1 (NM_004656) rearrangement: c.122+101_c.627del	PRECISE	Note: The BAP1 rearrangement is an intragenic deletion of exons 4 - 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4592	0	138	3	Exon 8 of BAP1(-)	BAP1	52440877			3	Intron of BAP1(-):100bp after exon 3	BAP1	52443469			10	DELETION		2592	334864	3403	139	NEW_VARIANT
P-0049057-T01-IM6	TBX3 (NM_016569) rearrangement: c.1771-85:TBX3_chr12:g.55866104inv	PRECISE	Note: The TBX3 rearrangement is an inversion of exon 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		174493	0	29	12	Promoter of OR6C70(-):3Kb from tx start	TBX3	55866104			12	Intron of TBX3(-):85bp before exon 8	TBX3	115110192			10	INVERSION		59244088	334881	327385	29	NEW_VARIANT
P-0049061-T01-IM6	KMT2D (NM_003482) rearrangement: c.6771:KMT2D_chr12:g.49468612del	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 1 - 31. One of the breakpoints is within exon 31.	MANUAL_OK	3to5	3to5	-		54927	0	4	12	Exon 31 of KMT2D(-)	KMT2D	49434782			12	IGR: 10Kb before RHEBL1(-)	KMT2D	49468612			9	DELETION		33830	334886	96950	4	NEW_VARIANT
P-0049068-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-736:TMPRSS2_c.18+1656:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		24348	0	5	21	Intron of ERG(-):2Kb after exon 1	TMPRSS2	39868631			21	Intron of TMPRSS2(-):736bp before exon 3	ERG	42867241			6	DELETION		2998610	335142	36157	4	NEW_VARIANT
P-0049068-T01-IM6	KMT2C (NM_170606) rearrangement: c.850-15790_c.7779dup	PRECISE	Note: The KMT2C rearrangement is an intragenic duplication of exons 7 - 38. One of the breakpoints is within exon 38. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		41338	0	9	7	Exon 38 of KMT2C(-)	KMT2C	151874759			7	Intron of KMT2C(-):16Kb before exon 7	KMT2C	151986742			10	DUPLICATION		111983	335143	68807	11	NEW_VARIANT
P-0049087-T01-IM6	SPOP (NM_001007228) rearrangement: c.837+52:SPOP_chr17:g.49150995inv	PRECISE	Note: The SPOP rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		7364	0	15	17	Intron of SPOP(-):51bp after exon 8	SPOP	47684560			17	Intron of SPAG9(-):6Kb after exon 2	SPOP	49150995			10	INVERSION		1466435	335286	11590	15	NEW_VARIANT
P-0049091-T01-IM6	CDKN2A (NM_000077) rearrangement: c.457_c.458del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1738	0	3	9	Exon 3 of CDKN2A(-)	CDKN2A	21968241			9	Exon 2 of CDKN2A(-)	CDKN2A	21970901			8	DELETION		2660	335290	2301	3	NEW_VARIANT
P-0049200-T01-IM6	PTP4A1 (NM_003463) rearrangement: t(1;6)(q25.2;q12)(chr1:g.176585817::chr6:g.64286894)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	7	6	Intron of PTP4A1(+):4bp after exon 2	PTP4A1	64286894			1	Intron of PAPPA2(+):21Kb after exon 3	PTP4A1	176585817			10	TRANSLOCATION		0	335308	0	13	NEW_VARIANT
P-0049247-T01-IM6	PLCG2 (NM_002661) - AP1G1 (NM_001128) rearrangement: c.1257:PLCG2_c.202-1294:AP1G1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PLCG2:AP1G1}		88588	0	9	16	Intron of AP1G1(-):1Kb before exon 3	PLCG2	71809789			16	Exon 14 of PLCG2(+)	AP1G1	81934280			10	INVERSION		10124491	335413	76234	9	NEW_VARIANT
P-0049247-T01-IM6	MLH1 (NM_000249) rearrangement: c.206_c.208-1del	PRECISE	Note: The MLH1 rearrangement is an intragenic deletion of exons 2 - 3. The breakpoints are within exon 2 and exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		432	0	4	3	Exon 2 of MLH1(+)	MLH1	37038199			3	Exon 3 of MLH1(+)	MLH1	37042445			10	DELETION		4246	335408	160	4	NEW_VARIANT
P-0049247-T01-IM6	MLH1 (NM_000249) rearrangement: c.304_c.307-2del	PRECISE	Note: The MLH1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		677	0	2	3	Exon 3 of MLH1(+)	MLH1	37042542			3	Intron of MLH1(+):1bp before exon 4	MLH1	37045890			10	DELETION		3348	335409	326	2	NEW_VARIANT
P-0049247-T01-IM6	MLH1 (NM_000249) rearrangement: c.378_c.381-2del	PRECISE	Note: The MLH1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		592	0	2	3	Exon 4 of MLH1(+)	MLH1	37045963			3	Intron of MLH1(+):1bp before exon 5	MLH1	37048480			10	DELETION		2517	335410	241	3	NEW_VARIANT
P-0049247-T01-IM6	MLH1 (NM_000249) rearrangement: c.452_c.454-1del	PRECISE	Note: The MLH1 rearrangement is an intragenic deletion of exons 5 - 6. The breakpoints are within exon 5 and exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		586	0	3	3	Exon 5 of MLH1(+)	MLH1	37048553			3	Exon 6 of MLH1(+)	MLH1	37050304			10	DELETION		1751	335411	283	4	NEW_VARIANT
P-0049248-T01-IM6	ZCCHC14 (NM_015144) - FANCA (NM_000135) rearrangement: c.429+45:ZCCHC14_c.3935-98:FANCAdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {ZCCHC14:FANCA}		65778	0	14	16	Intron of ZCCHC14(-):44bp after exon 4	ZCCHC14	87457371			16	Intron of FANCA(-):98bp before exon 40	FANCA	89806059			0	DUPLICATION		2348688	335421	98838	14	NEW_VARIANT
P-0049248-T01-IM6	BAP1 (NM_004656) rearrangement: c.2176:BAP1_chr3:g.52719537dup	PRECISE	Note: The BAP1 rearrangement is a duplication of exons 1 - 17. One of the breakpoints is within exon 17. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BAP1:PBRM1}		66124	0	89	3	Exon 17 of BAP1(-)	BAP1	52436318			3	5-UTR of PBRM1(-):137Kb before coding start	BAP1	52719537			10	DUPLICATION		283219	335420	121863	90	NEW_VARIANT
P-0049262-T01-IM6	NCOA3 (NM_181659) rearrangement: c.4203:NCOA3_chr20:g.46285828del	PRECISE	Note: The NCOA3 rearrangement is a deletion of exons 22 - 23. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1587	0	7	20	Exon 22 of NCOA3(+)	NCOA3	46281756			20	Promoter of NCOA3(+):155Kb from tx start	NCOA3	46285828			10	DELETION		4072	335440	2051	8	NEW_VARIANT
P-0049263-T01-IM6	ARID2 (NM_152641) rearrangement: c.5147+98:ARID2_chr12:g.64444814inv	PRECISE	Note: The ARID2 rearrangement is an inversion of exons 19 - 21. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		247590	0	7	12	Intron of ARID2(+):98bp after exon 18	ARID2	46285977			12	Intron of SRGAP1(+):7Kb after exon 6	ARID2	64444814			9	INVERSION		18158837	335429	370117	10	NEW_VARIANT
P-0049269-T01-IM6	TAF4 (NM_003185) - RTEL1 (NM_032957) rearrangement: c.1360+15853:TAF4_c.1980:RTEL1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TAF4:RTEL1}		36755	0	13	20	Intron of TAF4(-):16Kb after exon 1	TAF4	60623654			20	Exon 23 of RTEL1(+)	RTEL1	62320884			10	INVERSION		1697230	335500	47510	17	NEW_VARIANT
P-0049270-T01-IM6	IRF4 (NM_002460) - IFNGR1 (NM_000416) rearrangement: c.144:IRF4_c.862-1030:IFNGR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		882285	0	33	6	Exon 2 of IRF4(+)	IRF4	393296			6	Intron of IFNGR1(-):1Kb before exon 7	IFNGR1	137520806			10	DELETION		137127510	335496	987932	33	NEW_VARIANT
P-0049337-T01-IM6	ERBB3 (NM_001982) rearrangement: c.614-7:ERBB3_chr12:g.69067301del	PRECISE	Note: The ERBB3 rearrangement is a deletion of exons 6 - 28. The rearrangement includes the kinase domain of ERBB3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		110521	0	4	12	Intron of ERBB3(+):6bp before exon 6	ERBB3	56481572			12	Promoter of LOC100507250(-):849bp from tx start	ERBB3	69067301			8	DELETION		12585729	335698	114551	4	NEW_VARIANT
P-0049346-T01-IM6	PIP5K1A (NM_001135638) - PIK3CD (NM_005026) rearrangement: c.157-70:PIP5K1A_c.2865-64:PIK3CDdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PIP5K1A:PIK3CD}		817756	0	16	1	Intron of PIK3CD(+):63bp before exon 23	PIP5K1A	9784798			1	Intron of PIP5K1A(+):69bp before exon 3	PIK3CD	151199726			0	DUPLICATION		141414928	335679	918181	17	NEW_VARIANT
P-0049346-T01-IM6	DNMT3B (NM_006892) rearrangement: t(14;20)(q11.2;q11.21)(chr14:g.23983015::chr20:g.31384948)	IMPPRECISE	Note: The DNMT3B rearrangement is a translocation with a breakpoint in intron 13. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	10	20	Intron of DNMT3B(+):44bp before exon 14	DNMT3B	31384948			14	5-UTR of THTPA(+):46Kb before coding start	DNMT3B	23983015			0	TRANSLOCATION		0	335680	0	10	NEW_VARIANT
P-0049346-T01-IM6	ASXL1 (NM_015338) rearrangement: c.253-11072_c.719-260del	PRECISE	Note: The ASXL1 rearrangement is an intragenic deletion of exons 4 - 7.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		5603	0	16	20	Intron of ASXL1(+):11Kb before exon 4	ASXL1	31004859			20	Intron of ASXL1(+):259bp before exon 8	ASXL1	31018864			10	DELETION		14005	335678	9197	16	NEW_VARIANT
P-0049348-T01-IM6	ATR (NM_001184) rearrangement: c.3435:ATR_chr3:g.71998222del	PRECISE	Note: The ATR rearrangement is a deletion of exons 17 - 47. One of the breakpoints is within exon 17.	MANUAL_OK	3to5	3to5	-		146737	0	28	3	IGR: 86Kb before LINC00877(-)	ATR	71998222			3	Exon 17 of ATR(-)	ATR	142261522			10	DELETION		70263300	335675	241412	30	NEW_VARIANT
P-0049436-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.95-3598_c.1591del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		9931	0	5	3	Intron of TGFBR2(+):4Kb before exon 2	TGFBR2	30661093			3	Exon 7 of TGFBR2(+)	TGFBR2	30729995			0	DELETION		68902	335959	14350	5	NEW_VARIANT
P-0049439-T01-IM6	KLK3 (NM_001648) - TMPRSS2 (NM_001135099) rearrangement: t(19;21)(q13.33;q22.3)(chr19:g.51359165::chr21:g.42843855)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KLK3:TMPRSS2}		0	1	63	21	Exon 10 of TMPRSS2(-)	KLK3	42843855			19	Intron of KLK3(+):330bp before exon 2	TMPRSS2	51359165			10	TRANSLOCATION		0	335954	0	60	NEW_VARIANT
P-0049457-T01-IM6	RAD51B (NM_133509) rearrangement: c.497_c.756+4846del	IMPPRECISE	Note: The RAD51B rearrangement is an intragenic deletion of exons 6 - 7. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1649	0	6	14	Exon 6 of RAD51B(+)	RAD51B	68352630			14	Intron of RAD51B(+):5Kb after exon 7	RAD51B	68358767			0	DELETION		6137	335933	1778	6	NEW_VARIANT
P-0049457-T01-IM6	TP53 (NM_000546) rearrangement: c.75-16:TP53_chr17:g.7549007del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 3 - 11.	MANUAL_OK	3to5	3to5	-		16971	0	87	17	IGR: 5Kb before ATP1B2(+)	TP53	7549007			17	Intron of TP53(-):16bp before exon 3	TP53	7579737			10	DELETION		30730	335934	12027	90	NEW_VARIANT
P-0047538-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.2465_c.3216+13961del	PRECISE	Note: The ZFHX3 rearrangement is an intragenic deletion of exons 2 - 3. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5976	0	15	16	Intron of ZFHX3(-):14Kb after exon 3	ZFHX3	72970407			16	Exon 2 of ZFHX3(-)	ZFHX3	72991580			10	DELETION		21173	335839	8864	15	NEW_VARIANT
P-0049292-T01-IM6	FGFR2 (NM_000141) rearrangement: c.110-136:FGFR2_chr10:g.122834769inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		59696	0	26	10	IGR: 224Kb before WDR11(+)	FGFR2	122834769			10	Intron of FGFR2(-):136bp before exon 3	FGFR2	123325354			10	INVERSION		490585	335544	2899573	26	NEW_VARIANT
P-0049292-T01-IM6	CARM1 (NM_199141) - SMARCA4 (NM_003072) rearrangement: c.346+1276:CARM1_c.4171-2015:SMARCA4inv	PRECISE	The CARM1 - SMARCA4 rearrangement is an inversion of CARM1 exons 3 - 16 and SMARCA4 exons 1 - 29. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		87458	0	5	19	Intron of CARM1(+):1Kb after exon 2	CARM1	11017028			19	Intron of SMARCA4(+):2Kb before exon 30	SMARCA4	11149968			10	INVERSION		132940	335545	168522	5	NEW_VARIANT
P-0049438-T01-IM6	INPPL1 (NM_001567) rearrangement: c.3553-113:INPPL1_chr11:g.71956569del	PRECISE	Note: The INPPL1 rearrangement is a deletion of exons 27 - 28.	MANUAL_OK	3to5	3to5	Antisense Fusion		4248	0	4	11	Intron of INPPL1(+):112bp before exon 27	INPPL1	71948973			11	Promoter of PHOX2A(-):6Kb from tx start	INPPL1	71956569			8	DELETION		7596	335955	1505	4	NEW_VARIANT
P-0049438-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(3;21)(q27.2;q22.3)(chr3:g.185825058::chr21:g.42861570)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation which involves intron 3.Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Transcript Fusion {ETV5:TMPRSS2}		0	0	11	21	Intron of TMPRSS2(-):50bp before exon 4	TMPRSS2	42861570			3	5-UTR of ETV5(-):59Kb before coding start	TMPRSS2	185825058			10	TRANSLOCATION		0	335956	0	11	NEW_VARIANT
P-0049355-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.1453+42:NOTCH2_chr1:g.144545453inv	PRECISE	Note: The NOTCH2 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {NOTCH2:NBPF20}		8911	0	7	1	Intron of NOTCH2(-):41bp after exon 8	NOTCH2	120510014			1	Intron of NBPF20(+):279Kb before exon 53	NOTCH2	144545453			10	INVERSION		24035439	335728	16368	11	NEW_VARIANT
P-0049355-T01-IM6	H3F3B (NM_005324) - UNK (NM_001080419) rearrangement: c.326:H3F3B_c.105-8656:UNKinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {H3F3B:UNK}		3077	0	24	17	Exon 4 of H3F3B(-)	H3F3B	73774761			17	Intron of UNK(+):9Kb before exon 2	UNK	73797185			10	INVERSION		22424	335729	6066	29	NEW_VARIANT
P-0049366-T01-IM6	NOTCH4 (NM_004557) rearrangement: c.4041:NOTCH4_chr6:g.23089705inv	PRECISE	Note: The NOTCH4 rearrangement is an inversion of exons 22 - 30. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		215197	0	87	6	IGR: 520Kb before HDGFL1(+)	NOTCH4	23089705			6	Exon 22 of NOTCH4(-)	NOTCH4	32168992			10	INVERSION		9079287	335752	267223	105	NEW_VARIANT
P-0049375-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1166:EML4_c.3173-338:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		78666	0	118	2	Intron of ALK(-):338bp before exon 20	EML4	29446732			2	Intron of EML4(+):1Kb after exon 5	ALK	42493037			10	INVERSION		13046305	335744	130875	116	NEW_VARIANT
P-0049381-T01-IM6	KDM6A (NM_021140) rearrangement: t(2;X)(q24.2;p11.3)(chr2:g.163611887::chrX:g.44918272)	PRECISE	Note: The KDM6A rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	58	X	Exon 11 of KDM6A(+)	KDM6A	44918272			2	Intron of KCNH7(-):81Kb after exon 2	KDM6A	163611887			10	TRANSLOCATION		0	335714	0	83	NEW_VARIANT
P-0049383-T01-IM6	RB1 (NM_000321) - DIAPH3 (NM_001042517) rearrangement: c.2489+7:RB1_c.2608-5833:DIAPH3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RB1:DIAPH3}		14590	0	79	13	Intron of RB1(+):7bp after exon 23	RB1	49039511			13	Intron of DIAPH3(-):6Kb before exon 21	DIAPH3	60441503			10	INVERSION		11401992	335719	22656	79	NEW_VARIANT
P-0049385-T01-IM6	FANCA (NM_000135) rearrangement: c.3951_c.4261-20del	IMPPRECISE	Note: The FANCA rearrangement is an intragenic deletion of exons 40 - 42. One of the breakpoints is within exon 40.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3013	0	12	16	Intron of FANCA(-):20bp before exon 43	FANCA	89805136			16	Exon 40 of FANCA(-)	FANCA	89805945			0	DELETION		809	335707	4066	12	NEW_VARIANT
P-0049385-T01-IM6	RAD50 (NM_005732) rearrangement: c.3478_c.3924inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		2232	0	5	5	Exon 23 of RAD50(+)	RAD50	131973775			5	Exon 25 of RAD50(+)	RAD50	131978041			0	INVERSION		4266	335709	4095	6	NEW_VARIANT
P-0049407-T01-IM6	PTEN (NM_000314) rearrangement: t(10;17)(q23.31;q21.33)(chr10:g.89711879::chr17:g.49865374)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	38	17	Intron of CA10(-):40Kb before exon 4	PTEN	49865374			10	Exon 6 of PTEN(+)	PTEN	89711879			10	TRANSLOCATION		0	335846	0	44	NEW_VARIANT
P-0049411-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1217:TMPRSS2_c.18+11245:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		41058	0	21	21	Intron of ERG(-):11Kb after exon 1	TMPRSS2	39859042			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871333			10	DELETION		3012291	335848	38317	21	NEW_VARIANT
P-0012098-T06-IM6	WNT2 (NM_003391) - CARD11 (NM_032415) rearrangement: c.84-902:WNT2_c.2608-24:CARD11del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {WNT2:CARD11}		334121	0	35	7	Intron of CARD11(-):24bp before exon 20	WNT2	2957043			7	Intron of WNT2(-):902bp before exon 2	CARD11	116961749			0	DELETION		114004706	335903	685752	35	NEW_VARIANT
P-0049417-T01-IM6	FUBP1 (NM_003902) rearrangement: c.459_c.1576+1058del	IMPPRECISE	Note: The FUBP1 rearrangement is an intragenic deletion of exons 7 - 16. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6204	0	5	1	Intron of FUBP1(-):1Kb after exon 16	FUBP1	78424811			1	Exon 7 of FUBP1(-)	FUBP1	78432392			0	DELETION		7581	335886	5850	8	NEW_VARIANT
P-0049427-T01-IM6	ALS2CR12 (NM_001127391) - CASP8 (NM_001080125) rearrangement: c.676-5456:ALS2CR12_c.589-79:CASP8inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {ALS2CR12:CASP8}		6697	0	45	2	Intron of CASP8(+):78bp before exon 4	ALS2CR12	202137282			2	Intron of ALS2CR12(-):5Kb before exon 10	CASP8	202179429			10	INVERSION		42147	335911	13882	88	NEW_VARIANT
P-0049427-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3573:TMPRSS2_c.39+64657:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49375	0	100	21	Intron of ERG(-):65Kb after exon 3	TMPRSS2	39882929			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873689			10	DELETION		2990760	335910	42213	105	NEW_VARIANT
P-0049505-T01-IM6	JAK3 (NM_000215) rearrangement: c.1914+21_c.2351-26del	PRECISE	Note: The JAK3 rearrangement is an intragenic deletion of exons 15 - 17. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		5585	0	53	19	Intron of JAK3(-):26bp before exon 18	JAK3	17943764			19	Intron of JAK3(-):20bp after exon 14	JAK3	17946712			10	DELETION		2948	335992	5525	57	NEW_VARIANT
P-0049542-T01-IM6	RUNX1 (NM_001754) rearrangement: c.168_c.351+2077del	PRECISE	Note: The RUNX1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1433	0	2	21	Intron of RUNX1(-):2Kb after exon 4	RUNX1	36257063			21	Exon 4 of RUNX1(-)	RUNX1	36259323			10	DELETION		2260	336075	1966	2	NEW_VARIANT
P-0049542-T01-IM6	ATRX (NM_000489) rearrangement: c.1733:ATRX_chrX:g.74625189inv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 9 - 35. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		50424	0	8	X	Intron of ZDHHC15(-):12Kb after exon 9	ATRX	74625189			X	Exon 9 of ATRX(-)	ATRX	76939015			8	INVERSION		2313826	336076	74054	8	NEW_VARIANT
P-0049543-T01-IM6	RTEL1 (NM_032957) rearrangement: t(14;20)(q22.1;q13.33)(chr14:g.51787212::chr20:g.62305625)	PRECISE	Note: The RTEL1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	13	20	Intron of RTEL1(+):179bp after exon 10	RTEL1	62305625			14	IGR: 13Kb before LINC00640(+)	RTEL1	51787212			10	TRANSLOCATION		0	336078	0	12	NEW_VARIANT
P-0049543-T01-IM6	EPHA5 (NM_004439) rearrangement: t(4;7)(q13.1;q34)(chr4:g.66217161::chr7:g.140209842)	PRECISE	Note: The EPHA5 rearrangement is a translocation with a breakpoint in exon 14. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	32	7	IGR: 8Kb before DENND2A(-)	EPHA5	140209842			4	Exon 14 of EPHA5(-)	EPHA5	66217161			10	TRANSLOCATION		0	336077	0	32	NEW_VARIANT
P-0048875-T03-IM6	RET (NM_020975) rearrangement: c.2136:RET_chr10:g.56155858del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		53575	0	79	10	Exon 11 of RET(+)	RET	43610184			10	Intron of PCDH15(-):17Kb before exon 5	RET	56155858			10	DELETION		12545674	335972	64318	206	NEW_VARIANT
P-0048875-T03-IM6	RICTOR (NM_152756) - FYB (NM_001243093) rearrangement: c.97+4:RICTOR_c.1166-21065:FYBdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RICTOR:FYB}		1223	0	56	5	Intron of RICTOR(-):3bp after exon 2	RICTOR	39074209			5	Intron of FYB(-):21Kb before exon 3	FYB	39174771			10	DUPLICATION		100562	335973	4935	57	NEW_VARIANT
P-0049483-T01-IM6	YAP1 (NM_001130145) rearrangement: t(11;13)(q22.1;q21.33)(chr11:g.102098052::chr13:g.72715658)	PRECISE	Note: The YAP1 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	11	13	IGR: 567Kb before MZT1(-)	YAP1	72715658			11	Intron of YAP1(+):147bp before exon 8	YAP1	102098052			10	TRANSLOCATION		0	336006	0	11	NEW_VARIANT
P-0049483-T01-IM6	BRD4 (NM_058243) rearrangement: c.640:BRD4_chr19:g.15246720del	PRECISE	Note: The BRD4 rearrangement is a deletion of exons 5 - 20. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		129609	0	7	19	IGR: 21Kb before ILVBL(-)	BRD4	15246720			19	Exon 5 of BRD4(-)	BRD4	15376374			10	DELETION		129654	336005	394037	8	NEW_VARIANT
P-0049516-T01-IM6	TMPRSS9 (NM_182973) - DOT1L (NM_032482) rearrangement: c.412+824:TMPRSS9_c.4606+1197:DOT1Ldup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS9:DOT1L}		2611	0	18	19	Intron of DOT1L(+):1Kb after exon 27	TMPRSS9	2228323			19	Intron of TMPRSS9(+):824bp after exon 3	DOT1L	2400015			10	DUPLICATION		171692	336045	3665	20	NEW_VARIANT
P-0049516-T01-IM6	ATRX (NM_000489) rearrangement: t(18;X)(p11.31;q21.1)(chr18:g.5234240::chrX:g.76876077)	PRECISE	Note: The ATRX rearrangement is a translocation with a breakpoint in intron 19. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	50	X	Intron of ATRX(-):77bp before exon 20	ATRX	76876077			18	Promoter of LINC00526(-):2Kb from tx start	ATRX	5234240			10	TRANSLOCATION		0	336048	0	50	NEW_VARIANT
P-0049516-T01-IM6	ATRX (NM_000489) rearrangement: c.5566+72:ATRX_chrX:g.56493169inv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 23 - 35. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		160751	0	56	X	IGR: 97Kb before UBQLN2(+)	ATRX	56493169			X	Intron of ATRX(-):71bp after exon 22	ATRX	76872009			10	INVERSION		20378840	336046	272993	59	NEW_VARIANT
P-0049519-T01-IM6	PPP2R1A (NM_014225) rearrangement: t(8;19)(q23.2;q13.41)(chr8:g.110514912::chr19:g.52714414)	PRECISE	Note: The PPP2R1A rearrangement is a translocation with a breakpoint in intron 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	10	19	Intron of PPP2R1A(+):98bp before exon 4	PPP2R1A	52714414			8	Intron of PKHD1L1(+):2Kb before exon 68	PPP2R1A	110514912			10	TRANSLOCATION		0	336057	0	10	NEW_VARIANT
P-0049520-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-4799:TMPRSS2_chr21:g.40822873inv	PRECISE	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	MANUAL_OK	3to3	3to3	Transcript Fusion {SH3BGR:TMPRSS2}		57942	0	11	21	5-UTR of SH3BGR(+):12Kb before coding start	TMPRSS2	40822873			21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874915			9	INVERSION		2052042	336055	86183	11	NEW_VARIANT
P-0049520-T01-IM6	TP63 (NM_003722) rearrangement: c.88:TP63_chr3:g.190865940del	PRECISE	Note: The TP63 rearrangement is a deletion of exons 2 - 14. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		19248	0	7	3	Exon 2 of TP63(+)	TP63	189455554			3	IGR: 64Kb before OSTN(+)	TP63	190865940			7	DELETION		1410386	336053	29441	7	NEW_VARIANT
P-0049560-T01-IM6	DNMT3A (NM_022552) - DTNB (NM_021907) rearrangement: c.1880:DNMT3A_c.1554+3558:DTNBdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DNMT3A:DTNB}		28885	0	44	2	Exon 16 of DNMT3A(-)	DNMT3A	25466823			2	Intron of DTNB(-):4Kb after exon 14	DTNB	25646846			10	DUPLICATION		180023	336346	52741	45	NEW_VARIANT
P-0049560-T01-IM6	PTPRD (NM_002839) rearrangement: c.961+360_c.5126+181dup	PRECISE	Note: The PTPRD rearrangement is an intragenic duplication of exons 21 - 41. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 21 exons : out of frame		24739	0	6	9	Intron of PTPRD(-):180bp after exon 41	PTPRD	8340909			9	Intron of PTPRD(-):359bp after exon 20	PTPRD	8520917			10	DUPLICATION		180008	336347	51925	6	NEW_VARIANT
P-0018669-T02-IM6	ARHGAP40 (NM_001164431) - TOP1 (NM_003286) rearrangement: c.338-1687:ARHGAP40_c.432-137:TOP1del	PRECISE	Note: The ARHGAP40 - TOP1 rearrangement is a deletion that results in a fusion of ARHGAP40 exons 1 - 2 to TOP1 exons 7 - 21.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ARHGAP40:TOP1}		5026	0	17	20	Intron of ARHGAP40(+):2Kb before exon 3	ARHGAP40	37253954			20	Intron of TOP1(+):136bp before exon 7	TOP1	39709668			10	DELETION		2455714	336948	14360	17	NEW_VARIANT
P-0044017-T02-IM6	CDKN2A (NM_058195) rearrangement: c.194-3159:CDKN2A_chr9:g.21958116del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		8555	0	131	9	IGR: 9Kb before CDKN2A-AS1(+)	CDKN2A	21958116			9	Intron of CDKN2A(-):3Kb before exon 2	CDKN2A	21974366			10	DELETION		16250	336943	4460	159	NEW_VARIANT
P-0048102-T02-IM6	STRN (NM_003162) - ALK (NM_004304) fusion: c.412+2761:STRN_c.3173-662:ALKdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {STRN:ALK}		46475	0	39	2	Intron of ALK(-):662bp before exon 20	STRN	29447056			2	Intron of STRN(-):3Kb after exon 3	ALK	37140460			10	DELETION		7693404	334989	65613	40	NEW_VARIANT
P-0049522-T01-IM6	SESN2 (NM_031459) rearrangement: c.90+1115_c.1020+90inv	PRECISE	Note: The SESN2 rearrangement is an intragenic inversion of exons 2 - 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		11442	0	4	1	Intron of SESN2(+):1Kb after exon 1	SESN2	28587563			1	Intron of SESN2(+):90bp after exon 7	SESN2	28600759			8	INVERSION		13196	336041	20775	4	NEW_VARIANT
P-0049522-T01-IM6	SESN2 (NM_031459) rearrangement: c.1211+9:SESN2_chr1:g.30977575inv	PRECISE	Note: The SESN2 rearrangement is an inversion of exons 9 - 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		6870	0	2	1	Intron of SESN2(+):9bp after exon 8	SESN2	28601535			1	IGR: 207Kb before MATN1(-)	SESN2	30977575			10	INVERSION		2376040	336042	12809	3	NEW_VARIANT
P-0049522-T01-IM6	WHSC1 (NM_001042424) - KALRN (NM_001024660) rearrangement: t(3;4)(q21.2;p16.3)(chr3:g.124313742::chr4:g.1954066)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {WHSC1:KALRN}		0	0	6	4	Intron of WHSC1(+):108bp after exon 11	WHSC1	1954066			3	Intron of KALRN(+):10Kb after exon 1	KALRN	124313742			8	TRANSLOCATION		0	336044	0	6	NEW_VARIANT
P-0049524-T01-IM6	KMT2D (NM_003482) rearrangement: c.950_c.5468-78del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion of exons 7 - 23. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		45394	0	50	12	Intron of KMT2D(-):78bp before exon 24	KMT2D	49437289			12	Exon 7 of KMT2D(-)	KMT2D	49446994			10	DELETION		9705	336027	37806	54	NEW_VARIANT
P-0049524-T01-IM6	SOX9 (NM_000346) rearrangement: c.560_c.1369del	PRECISE	Note: The SOX9 rearrangement is an intragenic deletion of exons 2 - 3. The breakpoints are within exon 2 and exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4844	0	49	17	Exon 2 of SOX9(+)	SOX9	70118988			17	Exon 3 of SOX9(+)	SOX9	70120367			10	DELETION		1379	336028	3817	51	NEW_VARIANT
P-0049524-T01-IM6	KEAP1 (NM_203500) rearrangement: c.1591:KEAP1_chr19:g.10612345del	PRECISE	Note: The KEAP1 rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16327	0	35	19	Exon 5 of KEAP1(-)	KEAP1	10599985			19	5-UTR of KEAP1(-):15Kb before coding start	KEAP1	10612345			10	DELETION		12360	336029	12676	38	NEW_VARIANT
P-0049524-T01-IM6	ASXL2 (NM_018263) rearrangement: c.975_c.1037-368del	PRECISE	Note: The ASXL2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		652	0	29	2	Intron of ASXL2(-):368bp before exon 10	ASXL2	25976876			2	Exon 9 of ASXL2(-)	ASXL2	25978948			10	DELETION		2072	336026	598	31	NEW_VARIANT
P-0049532-T01-IM6	MED12 (NM_005120) rearrangement: c.1348+59:MED12_chrX:g.64807314del	PRECISE	Note: The MED12 rearrangement is a deletion of exons 1 - 9.	MANUAL_OK	3to5	3to5	-		41696	0	3	X	IGR: 37Kb before FRMD8P1(-)	MED12	64807314			X	Intron of MED12(+):59bp after exon 9	MED12	70342516			9	DELETION		5535202	336035	21003	3	NEW_VARIANT
P-0049541-T01-IM6	KEAP1 (NM_203500) rearrangement: t(16;19)(p11.2;p13.2)(chr16:g.33840009::chr19:g.10597674)	PRECISE	Note: The KEAP1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	10	19	Intron of KEAP1(-):180bp before exon 6	KEAP1	10597674			16	IGR: 121Kb before LINC00273(-)	KEAP1	33840009			10	TRANSLOCATION		0	336079	0	11	NEW_VARIANT
P-0049590-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+11:TMPRSS2_chr21:g.42433155dup	PRECISE	Note: The TMPRSS2 rearrangement is a duplication of exons 2 - 14. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		118120	0	73	21	IGR: 80Kb before LINC00323(-)	TMPRSS2	42433155			21	Intron of TMPRSS2(-):10bp after exon 1	TMPRSS2	42879866			10	DUPLICATION		446711	336436	233181	81	NEW_VARIANT
P-0049597-T01-IM6	BRD4 (NM_058243) rearrangement: t(19;X)(p13.12;q26.3)(chr19:g.15350005::chrX:g.137085626)	PRECISE	Note: The BRD4 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	8	X	IGR: 437Kb before ZIC3(+)	BRD4	137085626			19	Exon 18 of BRD4(-)	BRD4	15350005			10	TRANSLOCATION		0	336447	0	7	NEW_VARIANT
P-0049598-T01-IM6	NF1 (NM_001042492) rearrangement: t(4;17)(q35.1;q11.2)(chr4:g.185552772::chr17:g.29422420)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	23	17	Intron of NF1(+):33bp after exon 1	NF1	29422420			4	Intron of CASP3(-):146bp after exon 6	NF1	185552772			10	TRANSLOCATION		0	336446	0	25	NEW_VARIANT
P-0049598-T01-IM6	KMT2B (NM_014727) rearrangement: c.5276+36_c.6259inv	PRECISE	Note: The KMT2B rearrangement is an intragenic inversion of exons 26 - 28. One of the breakpoints is within exon 28. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		17345	0	37	19	Intron of KMT2B(+):36bp after exon 25	KMT2B	36221553			19	Exon 28 of KMT2B(+)	KMT2B	36223709			10	INVERSION		2156	336445	16004	36	NEW_VARIANT
P-0049618-T01-IM6	RARA (NM_000964) rearrangement: c.1012+25:RARA_chr17:g.58915279inv	PRECISE	Note: The RARA rearrangement is an inversion of exons 8 - 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		332054	0	89	17	Intron of RARA(+):25bp after exon 7	RARA	38510783			17	Intron of BCAS3(+):30Kb after exon 7	RARA	58915279			10	INVERSION		20404496	336879	271319	111	NEW_VARIANT
P-0049618-T01-IM6	NCOA3 (NM_181659) rearrangement: c.129:NCOA3_chr20:g.52041710del	PRECISE	Note: The NCOA3 rearrangement is a deletion of exons 4 - 23. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		33127	0	4	20	Exon 4 of NCOA3(+)	NCOA3	46252700			20	3-UTR of TSHZ2(+):240Kb after coding stop	NCOA3	52041710			8	DELETION		5789010	336878	49481	4	NEW_VARIANT
P-0049633-T01-IM6	RNF43 (NM_017763) rearrangement: c.246_c.252+2378del	PRECISE	Note: The RNF43 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		249	0	75	17	Intron of RNF43(-):2Kb after exon 2	RNF43	56490309			17	Exon 2 of RNF43(-)	RNF43	56492693			10	DELETION		2384	336853	228	77	NEW_VARIANT
P-0049637-T01-IM6	KANK1 (NM_015158) - MET (NM_000245) fusion: t(7;9)(q31.2;p24.3)(chr7:g.116413312::chr9:g.725428)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {KANK1:MET}		0	0	47	9	Intron of KANK1(+):5Kb before exon 8	KANK1	725428			7	Intron of MET(+):1Kb after exon 14	MET	116413312			10	TRANSLOCATION		0	336848	0	52	NEW_VARIANT
P-0049638-T01-IM6	CTNNB1 (NM_001904) - ANKRD28 (NM_015199) rearrangement: c.1559:CTNNB1_c.112-7220:ANKRD28inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CTNNB1:ANKRD28}		65306	0	15	3	Intron of ANKRD28(-):7Kb before exon 3	CTNNB1	15815039			3	Exon 10 of CTNNB1(+)	ANKRD28	41275664			10	INVERSION		25460625	336842	82556	14	NEW_VARIANT
P-0049640-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149782214::chr6:g.117650417)	PRECISE	Note: The CD74 - ROS1 fusion involves CD74 exons 1 - 7 and ROS1 exons 33 - 43. The fusion includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	0	16	6	Intron of ROS1(-):74bp after exon 32	CD74	117650417			5	Intron of CD74(-):26bp before exon 8	ROS1	149782214			10	TRANSLOCATION		0	336845	0	16	NEW_VARIANT
P-0049640-T01-IM6	CDKN2B (NM_004936) rearrangement: c.96:CDKN2B_chr9:g.21895095del	PRECISE	Note: The CDKN2B rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	-		15543	0	28	9	IGR: 72Kb before CDKN2A-AS1(+)	CDKN2B	21895095			9	Exon 1 of CDKN2B(-)	CDKN2B	22008857			10	DELETION		113762	336844	17455	28	NEW_VARIANT
P-0049684-T01-IM6	KMT2C (NM_170606) rearrangement: c.7103:KMT2C_chr7:g.116254326del	PRECISE	Note: The KMT2C rearrangement is a deletion of exons 36 - 59. One of the breakpoints is within exon 36.	MANUAL_OK	3to5	3to5	-		210562	0	13	7	3-UTR of LINC01510(-):548bp after coding stop	KMT2C	116254326			7	Exon 36 of KMT2C(-)	KMT2C	151877842			10	DELETION		35623516	336970	134560	15	NEW_VARIANT
P-0049461-T02-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-3450:CCDC6_c.2137-327:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		33942	0	71	10	Intron of RET(+):326bp before exon 12	CCDC6	43611705			10	Intron of CCDC6(-):3Kb before exon 2	RET	61615910			10	INVERSION		18004205	337132	22553	83	NEW_VARIANT
P-0049588-T01-IM6	RET (NM_020975) - CCDC6 (NM_005436) rearrangement: c.1879+314:RET_c.304-15222:CCDC6inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {RET:CCDC6}		53759	0	46	10	Intron of RET(+):314bp after exon 10	RET	43609437			10	Intron of CCDC6(-):15Kb before exon 2	CCDC6	61627682			10	INVERSION		18018245	336409	55775	47	NEW_VARIANT
P-0049588-T01-IM6	RET (NM_020975) rearrangement: t(9;10)(p21.3;q11.21)(chr9:g.20531517::chr10:g.43610683)	PRECISE	Note: The RET rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	66	10	Intron of RET(+):499bp after exon 11	RET	43610683			9	Intron of MLLT3(-):75Kb before exon 3	RET	20531517			10	TRANSLOCATION		0	336410	0	68	NEW_VARIANT
P-0049734-T01-IM6	ABL1 (NM_005157) - VAV3 (NM_006113) rearrangement: t(1;9)(p13.3;q24.12)(chr1:g.108439901::chr9:g.133589782)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ABL1:VAV3}		0	0	34	9	Exon 1 of ABL1(+)	ABL1	133589782			1	Intron of VAV3(-):22Kb before exon 2	VAV3	108439901			10	TRANSLOCATION		0	337126	0	34	NEW_VARIANT
P-0049763-T01-IM6	EZH1 (NM_001991) rearrangement: t(12;17)(q23.3;q21.2)(chr12:g.108659733::chr17:g.40865300)	PRECISE	Note: The EZH1 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	64	17	Exon 11 of EZH1(-)	EZH1	40865300			12	IGR: 22Kb before CMKLR1(-)	EZH1	108659733			10	TRANSLOCATION		0	337105	0	66	NEW_VARIANT
P-0049763-T01-IM6	CDKN2B (NM_004936) rearrangement: c.156+526:CDKN2B_chr9:g.22033412inv	IMPPRECISE	Note: The CDKN2B rearrangement is an inversion of exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {CDKN2B:CDKN2B-AS1}		3889	0	19	9	Intron of CDKN2B(-):525bp after exon 1	CDKN2B	22008271			9	5-UTR of CDKN2B-AS1(+):88Kb before coding start	CDKN2B	22033412			0	INVERSION		25141	337103	6439	23	NEW_VARIANT
P-0049767-T01-IM6	IRS2 (NM_003749) rearrangement: c.1678:IRS2_chr13:g.110406534del	PRECISE	Note: The IRS2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		24338	0	27	13	3-UTR of IRS2(-):2Kb after coding stop	IRS2	110406534			13	Exon 1 of IRS2(-)	IRS2	110436723			10	DELETION		30189	337099	37204	27	NEW_VARIANT
P-0049776-T01-IM6	ERBB4 (NM_005235) rearrangement: c.421+70885_c.1883del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		14300	0	37	2	Exon 16 of ERBB4(-)	ERBB4	212522542			2	Intron of ERBB4(-):71Kb after exon 3	ERBB4	212741270			10	DELETION		218728	337095	8833	38	NEW_VARIANT
P-0049782-T01-IM6	DNMT1 (NM_001379) - TMC8 (NM_152468) rearrangement: t(17;19)(q25.3;p13.2)(chr17:g.76130996::chr19:g.10260454)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {DNMT1:TMC8}		0	0	54	19	Intron of DNMT1(-):74bp after exon 24	DNMT1	10260454			17	Exon 9 of TMC8(+)	TMC8	76130996			10	TRANSLOCATION		0	337093	0	56	NEW_VARIANT
P-0049795-T01-IM6	RAD54L (NM_001142548) rearrangement: t(1;17)(p34.1;q21.31)(chr1:g.46738180::chr17:g.42742114)	PRECISE	Note: The RAD54L rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	40	17	Intron of C17orf104(+):637bp before exon 4	RAD54L	42742114			1	Exon 12 of RAD54L(+)	RAD54L	46738180			10	TRANSLOCATION		0	337502	0	51	NEW_VARIANT
P-0049795-T01-IM6	TP53 (NM_000546) rearrangement: t(17;22)(p13.1;q13.31)(chr17:g.7579139::chr22:g.45835284)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	22	IGR: 26Kb before RIBC2(+)	TP53	45835284			17	Intron of TP53(-):172bp after exon 4	TP53	7579139			10	TRANSLOCATION		0	337503	0	6	NEW_VARIANT
P-0049799-T01-IM6	EED (NM_003797) rearrangement: c.114+98:EED_chr11:g.86488383del	PRECISE	Note: The EED rearrangement is a deletion of exons 2 - 12.	MANUAL_OK	3to5	3to5	-		11842	0	20	11	Intron of EED(+):98bp after exon 1	EED	85956483			11	IGR: 14Kb before PRSS23(+)	EED	86488383			10	DELETION		531900	337508	11642	21	NEW_VARIANT
P-0049807-T01-IM6	TERT (NM_198253) rearrangement: c.2383-182:TERT_chr5:g.7735518del	PRECISE	Note: The TERT rearrangement is a deletion of exons 1 - 7. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		38057	0	10	5	Intron of TERT(-):182bp before exon 8	TERT	1271501			5	Intron of ADCY2(+):8Kb after exon 14	TERT	7735518			5	DELETION		6464017	337510	38079	10	NEW_VARIANT
P-0049789-T01-IM6	PREX2 (NM_024870) rearrangement: t(8;11)(q13.2;q11)(chr8:g.69009227::chr11:g.55663374)	PRECISE	Note: The PREX2 rearrangement is a translocation with a breakpoint in intron 21. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	67	11	IGR: 13Kb before TRIM51(+)	PREX2	55663374			8	Intron of PREX2(+):24bp before exon 22	PREX2	69009227			10	TRANSLOCATION		0	337341	0	75	NEW_VARIANT
P-0049789-T01-IM6	IGHMBP2 (NM_002180) - FGFR1 (NM_001174067) fusion: t(8;11)(p11.23;q13.3)(chr8:g.38275857::chr11:g.68697608)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {IGHMBP2:FGFR1}		0	0	148	11	Intron of IGHMBP2(+):783bp after exon 8	IGHMBP2	68697608			8	Exon 11 of FGFR1(-)	FGFR1	38275857			10	TRANSLOCATION		0	337342	0	152	NEW_VARIANT
P-0046749-T02-IM6	TSC1 (NM_000368) rearrangement: c.211-103:TSC1_chr9:g.135810074del	PRECISE	Note: The TSC1 rearrangement is a deletion of exons 1 - 4.	MANUAL_OK	3to5	3to5	Deletion within transcript		1772	0	5	9	Intron of TSC1(-):103bp before exon 5	TSC1	135801229			9	5-UTR of TSC1(-):38Kb before coding start	TSC1	135810074			7	DELETION		8845	336400	1810	5	NEW_VARIANT
P-0048569-T02-IM6	NTHL1 (NM_002528) rearrangement: t(12;16)(q13.13;p13.3)(chr12:g.53347002::chr16:g.2093677)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NTHL1:KRT18}		0	0	31	16	Exon 4 of NTHL1(-)	NTHL1	2093677			12	Promoter of KRT18(+):4Kb from tx start	NTHL1	53347002			0	TRANSLOCATION		0	336908	0	46	NEW_VARIANT
P-0049565-T01-IM6	THOP1 (NM_003249) - CALR (NM_004343) rearrangement: c.750+630:THOP1_c.845:CALRdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {THOP1:CALR}		331257	0	6	19	Intron of THOP1(+):630bp after exon 6	THOP1	2805804			19	Exon 7 of CALR(+)	CALR	13051586			10	DELETION		10245782	336398	283305	6	NEW_VARIANT
P-0049566-T01-IM6	BCOR (NM_001123385) rearrangement: c.166-131_c.1719del	PRECISE	Note: The BCOR rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4819	0	5	X	Exon 4 of BCOR(-)	BCOR	39932880			X	Intron of BCOR(-):131bp before exon 4	BCOR	39934564			8	DELETION		1684	336404	5165	5	NEW_VARIANT
P-0049600-T01-IM6	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.1889:NCOA4_c.2137-419:RETdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NCOA4:RET}		18426	0	53	10	Intron of RET(+):418bp before exon 12	NCOA4	43611613			10	Exon 11 of NCOA4(+)	RET	51586611			10	DUPLICATION		7974998	336490	28540	60	NEW_VARIANT
P-0049601-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.557-301_c.1101inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		7009	0	43	21	Exon 10 of TMPRSS2(-)	TMPRSS2	42843818			21	Intron of TMPRSS2(-):301bp before exon 6	TMPRSS2	42852830			10	INVERSION		9012	336485	7357	55	NEW_VARIANT
P-0049677-T01-IM6	KMT2D (NM_003482) rearrangement: c.3907-52:KMT2D_chr12:g.51463325inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		61751	0	43	12	Intron of KMT2D(-):52bp before exon 12	KMT2D	49443053			12	Intron of CSRNP2(-):2Kb before exon 4	KMT2D	51463325			10	INVERSION		2020272	336904	72348	43	NEW_VARIANT
P-0049679-T01-IM6	RNF43 (NM_017763) rearrangement: c.2199:RNF43_chr17:g.56419522del	PRECISE	Note: The RNF43 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Antisense Fusion		4669	0	63	17	5-UTR of BZRAP1-AS1(+):12Kb before coding start	RNF43	56419522			17	Exon 9 of RNF43(-)	RNF43	56434938			10	DELETION		15416	336899	5094	66	NEW_VARIANT
P-0030151-T02-IM6	KMT2A (NM_001197104) rearrangement: c.3570-306_c.10613dup	PRECISE	Note: The KMT2A rearrangement is an intragenic duplication of exons 6 - 27. One of the breakpoints is within exon 27. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		38976	0	3	11	Intron of KMT2A(+):305bp before exon 6	KMT2A	118350583			11	Exon 27 of KMT2A(+)	KMT2A	118377220			5	DUPLICATION		26637	337751	36255	3	NEW_VARIANT
P-0045231-T02-IM6	THSD4 (NM_024817) - CTCF (NM_006565) rearrangement: t(15;16)(q23;q22.1)(chr15:g.71907219::chr16:g.67654689)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {THSD4:CTCF}		0	0	13	16	Exon 6 of CTCF(+)	THSD4	67654689			15	Intron of THSD4(+):46Kb before exon 7	CTCF	71907219			10	TRANSLOCATION		0	337828	0	13	NEW_VARIANT
P-0045231-T02-IM6	KDM6A (NM_021140) rearrangement: c.226-31834_c.975-49del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 3 - 11.	MANUAL_OK	3to5	3to5	Deletion of 9 exons : out of frame		7257	0	4	X	Intron of KDM6A(+):32Kb before exon 3	KDM6A	44788695			X	Intron of KDM6A(+):48bp before exon 12	KDM6A	44918443			10	DELETION		129748	337826	4823	4	NEW_VARIANT
P-0047193-T02-IM6	CD276 (NM_001024736) rearrangement: c.1582+191:CD276_chr15:g.89160814inv	PRECISE	Note: The CD276 rearrangement is an inversion of exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		37696	0	7	15	Intron of CD276(+):191bp after exon 9	CD276	74003702			15	IGR: 4Kb before AEN(+)	CD276	89160814			10	INVERSION		15157112	337832	52391	7	NEW_VARIANT
P-0048433-T01-IM6	NEGR1 (NM_173808) rearrangement: c.410-5_c.536-13165dup	PRECISE	Note: The NEGR1 rearrangement is an intragenic duplication of exon 3. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		610	0	5	1	Intron of NEGR1(-):13Kb before exon 4	NEGR1	72176987			1	Intron of NEGR1(-):5bp before exon 3	NEGR1	72241985			10	DUPLICATION		64998	333103	477	5	NEW_VARIANT
P-0049545-T02-IM6	CTNNB1 (NM_001904) rearrangement: c.374:CTNNB1_chr3:g.41264962del	PRECISE	Note: The CTNNB1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2300	0	77	3	5-UTR of CTNNB1(+):597bp before coding start	CTNNB1	41264962			3	Exon 4 of CTNNB1(+)	CTNNB1	41266577			10	DELETION		1615	337672	2251	83	NEW_VARIANT
P-0049846-T01-IM6	RAD21 (NM_006265) rearrangement: c.145-10:RAD21_chr8:g.118200891del	PRECISE	Note: The RAD21 rearrangement is a deletion of exons 1 - 2.	MANUAL_OK	3to5	3to5	-		1060	0	42	8	Intron of RAD21(-):10bp before exon 3	RAD21	117875508			8	IGR: 54Kb before SLC30A8(+)	RAD21	118200891			10	DELETION		325383	337669	1225	43	NEW_VARIANT
P-0049869-T01-IM6	CDKN1B (NM_004064) rearrangement: c.379:CDKN1B_chr12:g.12875422inv	PRECISE	Note: The CDKN1B rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1955	0	4	12	Exon 1 of CDKN1B(+)	CDKN1B	12871152			12	Promoter of CDKN1B(+):5Kb from tx start	CDKN1B	12875422			10	INVERSION		4270	337680	3253	6	NEW_VARIANT
P-0049886-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3880:TMPRSS2_c.18+26025:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53952	0	62	21	Intron of ERG(-):26Kb after exon 1	TMPRSS2	39844262			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873996			10	DELETION		3029734	337741	62242	63	NEW_VARIANT
P-0049938-T01-IM6	RECQL (NM_032941) rearrangement: t(1;12)(p31.1;p12.1)(chr1:g.84517611::chr12:g.21627727)	PRECISE	Note: The RECQL rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	31	12	Intron of RECQL(-):47bp after exon 12	RECQL	21627727			1	IGR: 26Kb before PRKACB(+)	RECQL	84517611			10	TRANSLOCATION		0	337798	0	31	NEW_VARIANT
P-0049939-T01-IM6	KIT (NM_000222) rearrangement: t(1;4)(q42.2;q12)(chr1:g.234269491::chr4:g.55604661)	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	12	4	Exon 21 of KIT(+)	KIT	55604661			1	Intron of SLC35F3(+):98Kb before exon 3	KIT	234269491			10	TRANSLOCATION		0	337800	0	12	NEW_VARIANT
P-0049943-T01-IM6	EFNA2 (NM_001405) - STK11 (NM_000455) rearrangement: c.455-1105:EFNA2_c.465-73:STK11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {EFNA2:STK11}		13468	0	14	19	Intron of STK11(+):72bp before exon 4	EFNA2	1220299			19	Intron of EFNA2(+):1Kb before exon 3	STK11	1297445			10	DUPLICATION		77146	337783	22989	14	NEW_VARIANT
P-0049951-T01-IM6	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2610+187:TPR_c.1252-38:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TPR:NTRK1}		121565	0	87	1	Intron of NTRK1(+):37bp before exon 11	TPR	156844660			1	Intron of TPR(-):186bp after exon 20	NTRK1	186320275			10	INVERSION		29475615	337816	139319	152	NEW_VARIANT
P-0049954-T01-IM6	BRCA2 (NM_000059) rearrangement: c.7806-79_c.8283del	PRECISE	Note: The BRCA2 rearrangement is an intragenic deletion of exons 17 - 18. One of the breakpoints is within exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3127	0	10	13	Intron of BRCA2(+):78bp before exon 17	BRCA2	32936581			13	Exon 18 of BRCA2(+)	BRCA2	32937622			10	DELETION		1041	337810	2205	10	NEW_VARIANT
P-0049957-T01-IM6	ATRX (NM_000489) rearrangement: c.371-527_c.409del	PRECISE	Note: The ATRX rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		181	0	4	X	Exon 6 of ATRX(-)	ATRX	76949388			X	Intron of ATRX(-):527bp before exon 6	ATRX	76949953			8	DELETION		565	337808	170	4	NEW_VARIANT
P-0049959-T01-IM6	MEF2B (NM_001145785) rearrangement: t(12;19)(q13.11;p13.11)(chr12:g.46501152::chr19:g.19257680)	PRECISE	Note: The MEF2B rearrangement is a translocation with a breakpoint in exon 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	193	19	Exon 6 of MEF2B(-)	MEF2B	19257680			12	IGR: 76Kb before SLC38A1(-)	MEF2B	46501152			10	TRANSLOCATION		0	337811	0	190	NEW_VARIANT
P-0049966-T01-IM6	TMPRSS2 (NM_001135099) - ETV1 (NM_001163147) fusion: t(7;21)(p21.2;q22.3)(chr7:g.14007075::chr21:g.42872833)	IMPPRECISE	Note: The TMPRSS2 - ETV1 fusion involves TMPRSS2 exon 1 and ETV1 exons 6 - 12. The fusion is predicted to be in frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:ETV1}		0	0	27	21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872833			7	Intron of ETV1(-):10Kb after exon 5	ETV1	14007075			0	TRANSLOCATION		0	337830	0	28	NEW_VARIANT
P-0049968-T01-IM6	CSF1R (NM_005211) rearrangement: c.308-24:CSF1R_chr5:g.149479340del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		5608	0	20	5	Intron of CSF1R(-):24bp before exon 4	CSF1R	149459923			5	5-UTR of CSF1R(-):46Kb before coding start	CSF1R	149479340			10	DELETION		19417	337829	4467	22	NEW_VARIANT
P-0049970-T01-IM6	NOTCH2 (NM_024408) rearrangement: c.1201_c.1265del	IMPPRECISE	Note: The NOTCH2 rearrangement is an intragenic deletion of exons 7 - 8. The breakpoints are within exon 7 and exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1124	0	10	1	Exon 8 of NOTCH2(-)	NOTCH2	120510244			1	Exon 7 of NOTCH2(-)	NOTCH2	120510763			0	DELETION		519	337831	847	10	NEW_VARIANT
P-0033244-T03-IM6	RRAS (NM_006270) rearrangement: c.199:RRAS_chr19:g.50130834inv	IMPPRECISE	Note: The RRAS rearrangement is an inversion of exons 2 - 6. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PRR12:RRAS}		7625	0	5	19	Promoter of PRR12(+):36Kb from tx start	RRAS	50130834			19	Exon 2 of RRAS(-)	RRAS	50140342			0	INVERSION		9508	337700	7197	5	NEW_VARIANT
P-0049777-T01-IM6	ALK (NM_004304) rearrangement: c.2356-27:ALK_chr2:g.55625130inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		162855	0	5	2	Intron of ALK(-):27bp before exon 14	ALK	29456589			2	Intron of CCDC88A(-):9Kb before exon 3	ALK	55625130			7	INVERSION		26168541	337088	221379	5	NEW_VARIANT
P-0049777-T01-IM6	HIST1H3E (NM_003532) rearrangement: c.259:HIST1H3E_chr6:g.10278247del	PRECISE	Note: The HIST1H3E rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		46556	0	5	6	IGR: 119Kb before TFAP2A(-)	HIST1H3E	10278247			6	Exon 1 of HIST1H3E(+)	HIST1H3E	26225641			10	DELETION		15947394	337087	66495	5	NEW_VARIANT
P-0049870-T01-IM6	STAG2 (NM_001042749) rearrangement: c.1305-474_c.1916del	PRECISE	Note: The STAG2 rearrangement is an intragenic deletion of exons 15 - 20. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2052	0	3	X	Intron of STAG2(+):473bp before exon 15	STAG2	123191242			X	Exon 20 of STAG2(+)	STAG2	123197792			7	DELETION		6550	337688	2981	4	NEW_VARIANT
P-0005873-T02-IM6	ROS1 (NM_002944) rearrangement: c.5641+318:ROS1_chr6:g.117541165del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		36346	0	23	6	IGR: 46Kb before VGLL2(+)	ROS1	117541165			6	Intron of ROS1(-):317bp after exon 34	ROS1	117645177			10	DELETION		104012	339092	34172	23	NEW_VARIANT
P-0019607-T06-IM6	CALR (NM_004343) rearrangement: t(2;19)(q12.1;p13.2)(chr2:g.105170597::chr19:g.13054653)	PRECISE	Note: The CALR rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	41	19	Exon 9 of CALR(+)	CALR	13054653			2	IGR: 66Kb before LINC01103(-)	CALR	105170597			10	TRANSLOCATION		0	339474	0	42	NEW_VARIANT
P-0019607-T06-IM6	NOTCH4 (NM_004557) rearrangement: c.2680+88:NOTCH4_chr6:g.31401460inv	IMPPRECISE	Note: The NOTCH4 rearrangement is an inversion of exons 18 - 30. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		65810	0	11	6	IGR: 29Kb before HCP5(+)	NOTCH4	31401460			6	Intron of NOTCH4(-):87bp after exon 17	NOTCH4	32180163			0	INVERSION		778703	339473	92543	13	NEW_VARIANT
P-0019607-T06-IM6	HGF (NM_000601) rearrangement: c.997_c.1040+591del	IMPPRECISE	Note: The HGF rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		553	1	8	7	Intron of HGF(-):590bp after exon 8	HGF	81358330			7	Exon 8 of HGF(-)	HGF	81358964			0	DELETION		634	339472	689	7	NEW_VARIANT
P-0030465-T02-IM6	ERBB4 (NM_005235) rearrangement: c.1872-136:ERBB4_chr2:g.188632702inv	PRECISE	Note: The ERBB4 rearrangement is an inversion of exons 16 - 28. The rearrangement includes the kinase domain of ERBB4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		116711	0	6	2	IGR: 268Kb before LINC01090(-)	ERBB4	188632702			2	Intron of ERBB4(-):136bp before exon 16	ERBB4	212522689			10	INVERSION		23889987	339087	124684	6	NEW_VARIANT
P-0031015-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+2384:TMPRSS2_c.40-63530:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		74198	0	17	21	Intron of ERG(-):64Kb before exon 4	TMPRSS2	39881074			21	Intron of TMPRSS2(-):2Kb after exon 1	ERG	42877493			10	DELETION		2996419	339478	79484	25	NEW_VARIANT
P-0049308-T02-IM6	TERT (NM_198253) rearrangement: c.2655-14:TERT_chr5:g.20081454inv	PRECISE	Note: The TERT rearrangement is an inversion of exons 1 - 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		62094	0	11	5	Intron of TERT(-):14bp before exon 11	TERT	1264721			5	5-UTR of CDH18(-):608Kb before coding start	TERT	20081454			10	INVERSION		18816733	339094	51472	11	NEW_VARIANT
P-0049919-T01-IM6	NOTCH4 (NM_004557) rearrangement: c.3643:NOTCH4_chr6:g.32929127del	PRECISE	Note: The NOTCH4 rearrangement is a deletion of exons 1 - 21. One of the breakpoints is within exon 21.	MANUAL_OK	3to5	3to5	-		101508	0	98	6	Exon 21 of NOTCH4(-)	NOTCH4	32169965			6	IGR: 7Kb before BRD2(+)	NOTCH4	32929127			10	DELETION		759162	337894	97506	107	NEW_VARIANT
P-0049921-T01-IM6	CARM1 (NM_199141) rearrangement: c.1787:CARM1_chr19:g.10959120del	PRECISE	Note: The CARM1 rearrangement is a deletion of exons 1 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {C19orf38:CARM1}		25927	0	23	19	5-UTR of C19orf38(+):64bp before coding start	CARM1	10959120			19	Exon 16 of CARM1(+)	CARM1	11032393			10	DELETION		73273	337900	37628	23	NEW_VARIANT
P-0049921-T01-IM6	CARD11 (NM_032415) rearrangement: c.2510+153_c.2703+260del	PRECISE	Note: The CARD11 rearrangement is an intragenic deletion of exons 19 - 20. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3604	0	21	7	Intron of CARD11(-):259bp after exon 20	CARD11	2956664			7	Intron of CARD11(-):152bp after exon 18	CARD11	2958853			10	DELETION		2189	337899	2092	21	NEW_VARIANT
P-0049933-T01-IM6	B2M (NM_004048) rearrangement: c.68-1537_c.346+83del	PRECISE	Note: The B2M rearrangement is an intragenic deletion of exon 2.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1810	0	3	15	Intron of B2M(+):2Kb before exon 2	B2M	45006084			15	Intron of B2M(+):83bp after exon 2	B2M	45007982			4	DELETION		1898	337773	3006	3	NEW_VARIANT
P-0049933-T01-IM6	DUSP4 (NM_001394) rearrangement: t(6;8)(q23.2;p12)(chr6:g.132934535::chr8:g.29207538)	PRECISE	Note: The DUSP4 rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	71	8	Exon 1 of DUSP4(-)	DUSP4	29207538			6	IGR: 4Kb before TAAR2(-)	DUSP4	132934535			10	TRANSLOCATION		0	337774	0	71	NEW_VARIANT
P-0049963-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2618_c.557-1792inv	PRECISE	Note: The TMPRSS2 rearrangement is an intragenic inversion of exons 2 - 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		39387	0	4	21	Intron of TMPRSS2(-):2Kb before exon 6	TMPRSS2	42854321			21	Intron of TMPRSS2(-):3Kb before exon 2	TMPRSS2	42872734			10	INVERSION		18413	339095	18635	4	NEW_VARIANT
P-0049979-T01-IM6	DAXX (NM_001141970) rearrangement: t(1;6)(q23.1;p21.32)(chr1:g.156682800::chr6:g.33286569)	PRECISE	Note: The DAXX rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	86	6	Exon 8 of DAXX(-)	DAXX	33286569			1	IGR: 10Kb before ISG20L2(-)	DAXX	156682800			10	TRANSLOCATION		0	337836	0	93	NEW_VARIANT
P-0049985-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4790:TMPRSS2_c.19-24695:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		74981	0	14	21	Intron of ERG(-):25Kb before exon 2	TMPRSS2	39842239			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875087			10	DELETION		3032848	337847	80459	15	NEW_VARIANT
P-0049986-T01-IM6	STAT5B (NM_012448) rearrangement: t(3;17)(p21.31;q21.2)(chr3:g.45058637::chr17:g.40384144)	PRECISE	Note: The STAT5B rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	11	17	Exon 2 of STAT5B(-)	STAT5B	40384144			3	IGR: 9Kb before CLEC3B(+)	STAT5B	45058637			10	TRANSLOCATION		0	337860	0	11	NEW_VARIANT
P-0049988-T01-IM6	NEGR1 (NM_173808) rearrangement: t(1;16)(p31.1;p13.13)(chr1:g.71924675::chr16:g.11348618)	PRECISE	Note: The NEGR1 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	15	16	3-UTR of SOCS1(-):81bp after coding stop	NEGR1	11348618			1	Intron of NEGR1(-):51Kb before exon 7	NEGR1	71924675			10	TRANSLOCATION		0	337853	0	15	NEW_VARIANT
P-0050058-T01-IM6	FOXP1 (NM_001244814) rearrangement: t(3;5)(p13;q15)(chr3:g.71026977::chr5:g.96973852)	PRECISE	Note: The FOXP1 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	48	5	5-UTR of LINC01340(+):33Kb before coding start	FOXP1	96973852			3	Intron of FOXP1(-):1bp after exon 11	FOXP1	71026977			10	TRANSLOCATION		0	338459	0	48	NEW_VARIANT
P-0050065-T01-IM6	SETD2 (NM_014159) rearrangement: c.7662:SETD2_chr3:g.47058024inv	PRECISE	Note: The SETD2 rearrangement is an inversion of exon 21. One of the breakpoints is within exon 21. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		611	0	12	3	3-UTR of SETD2(-):558bp after coding stop	SETD2	47058024			3	Exon 21 of SETD2(-)	SETD2	47058616			10	INVERSION		592	338455	1020	12	NEW_VARIANT
P-0050067-T01-IM6	RPS6KA4 (NM_003942) - SLC22A9 (NM_080866) rearrangement: c.1957+74:RPS6KA4_c.1073+9725:SLC22A9dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RPS6KA4:SLC22A9}		29391	0	107	11	Intron of SLC22A9(+):10Kb after exon 6	RPS6KA4	63159474			11	Intron of RPS6KA4(+):74bp after exon 15	SLC22A9	64137930			10	DUPLICATION		978456	338458	55172	116	NEW_VARIANT
P-0050086-T01-IM6	ERG (NM_182918) rearrangement: c.18+43:ERG_chr21:g.28329679inv	PRECISE	Note: The ERG rearrangement is an inversion of exons 2 - 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		47587	0	12	21	Intron of ADAMTS5(-):2Kb before exon 2	ERG	28329679			21	Intron of ERG(-):42bp after exon 1	ERG	39870244			10	INVERSION		11540565	338491	58810	15	NEW_VARIANT
P-0050112-T01-IM6	FAT1 (NM_005245) rearrangement: c.3266-1343_c.3378inv	IMPPRECISE	Note: The FAT1 rearrangement is an intragenic inversion of exon 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		591	0	43	4	Exon 3 of FAT1(-)	FAT1	187584655			4	Intron of FAT1(-):1Kb before exon 3	FAT1	187586110			0	INVERSION		1455	338578	558	44	NEW_VARIANT
P-0050114-T01-IM6	ARID1A (NM_006015) rearrangement: c.3928:ARID1A_chr1:g.235098599del	PRECISE	Note: The ARID1A rearrangement is a deletion of exons 16 - 20. One of the breakpoints is within exon 16.	MANUAL_OK	3to5	3to5	-		795813	0	24	1	Exon 16 of ARID1A(+)	ARID1A	27100132			1	3-UTR of LOC101927851(-):1Kb after coding stop	ARID1A	235098599			10	DELETION		207998467	338580	591764	24	NEW_VARIANT
P-0050121-T01-IM6	YWHAZ (NM_001135699) - CTNNB1 (NM_001904) rearrangement: t(3;8)(p22.1;q22.3)(chr3:g.41266706::chr8:g.101953077)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {YWHAZ:CTNNB1}		0	0	10	8	Intron of YWHAZ(-):8Kb after exon 2	YWHAZ	101953077			3	Intron of CTNNB1(+):8bp after exon 4	CTNNB1	41266706			10	TRANSLOCATION		0	338671	0	10	NEW_VARIANT
P-0050123-T01-IM6	MAP2K4 (NM_003010) rearrangement: c.393+199_c.813+183dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		3870	0	17	17	Intron of MAP2K4(+):199bp after exon 3	MAP2K4	11985046			17	Intron of MAP2K4(+):183bp after exon 7	MAP2K4	12016860			9	DUPLICATION		31814	338668	5562	16	NEW_VARIANT
P-0050123-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.127-704:TMPRSS2_chr21:g.40094251del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 3 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		26779	0	28	21	IGR: 17Kb before LINC00114(-)	TMPRSS2	40094251			21	Intron of TMPRSS2(-):704bp before exon 3	TMPRSS2	42867209			10	DELETION		2772958	338667	24223	36	NEW_VARIANT
P-0050148-T01-IM6	FANCA (NM_000135) rearrangement: c.2778+178_c.2981+713del	PRECISE	Note: The FANCA rearrangement is an intragenic deletion of exons 29 - 30.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3141	0	8	16	Intron of FANCA(-):712bp after exon 30	FANCA	89824272			16	Intron of FANCA(-):177bp after exon 28	FANCA	89831120			10	DELETION		6848	338855	2866	8	NEW_VARIANT
P-0050148-T01-IM6	ERBB4 (NM_005235) rearrangement: c.1666_c.2487+14740del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8955	0	18	2	Intron of ERBB4(-):15Kb after exon 20	ERBB4	212411888			2	Exon 14 of ERBB4(-)	ERBB4	212537939			10	DELETION		126051	338854	8868	19	NEW_VARIANT
P-0050153-T01-IM6	TP53 (NM_000546) rearrangement: c.919+18:TP53_chr17:g.7581384inv	PRECISE	Note: The TP53 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		15318	0	15	17	Intron of TP53(-):17bp after exon 8	TP53	7577001			17	5-UTR of TP53(-):8Kb before coding start	TP53	7581384			10	INVERSION		4383	338851	17803	22	NEW_VARIANT
P-0050187-T01-IM6	SOX17 (NM_022454) rearrangement: c.307+1:SOX17_chr8:g.55373335del	PRECISE	Note: The SOX17 rearrangement is a deletion of exon 2.	MANUAL_OK	3to5	3to5	-		7680	0	36	8	Intron of SOX17(+):1bp after exon 1	SOX17	55371006			8	3-UTR of SOX17(+):3Kb after coding stop	SOX17	55373335			10	DELETION		2329	338875	9813	38	NEW_VARIANT
P-0050196-T01-IM6	DBI (NM_001178017) - BRAF (NM_004333) fusion: t(2;7)(q14.2;q34)(chr2:g.120128894::chr7:g.140486284)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {DBI:BRAF}		0	1	229	7	Intron of BRAF(-):1Kb after exon 9	DBI	140486284			2	Intron of DBI(+):516bp after exon 3	BRAF	120128894			10	TRANSLOCATION		0	338893	0	224	NEW_VARIANT
P-0050209-T01-IM6	RAD51 (NM_002875) rearrangement: c.700:RAD51_chr15:g.40606005del	PRECISE	Note: The RAD51 rearrangement is a deletion of exons 1 - 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	-		22926	0	22	15	IGR: 10Kb before INAFM2(+)	RAD51	40606005			15	Exon 8 of RAD51(+)	RAD51	41021758			10	DELETION		415753	338912	25456	22	NEW_VARIANT
P-0050234-T01-IM6	RB1 (NM_000321) rearrangement: c.500+75_c.607+1688del	IMPPRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 5 - 6.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		508	0	12	13	Intron of RB1(+):75bp after exon 4	RB1	48919410			13	Intron of RB1(+):2Kb after exon 6	RB1	48924847			0	DELETION		5437	339483	463	12	NEW_VARIANT
P-0050249-T01-IM6	PTEN (NM_000314) rearrangement: c.210-94:PTEN_chr10:g.88753165inv	PRECISE	Note: The PTEN rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1763	0	14	10	5-UTR of AGAP11(+):8Kb before coding start	PTEN	88753165			10	Intron of PTEN(+):93bp before exon 4	PTEN	89690709			10	INVERSION		937544	339107	3367	15	NEW_VARIANT
P-0050249-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+989:TMPRSS2_c.19-20075:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		85523	0	58	21	Intron of ERG(-):20Kb before exon 2	TMPRSS2	39837619			21	Intron of TMPRSS2(-):988bp after exon 1	ERG	42878888			10	DELETION		3041269	339106	101891	60	NEW_VARIANT
P-0050250-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-4532_c.294del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3689	0	12	9	Exon 2 of CDKN2A(-)	CDKN2A	21971107			9	Intron of CDKN2A(-):5Kb before exon 2	CDKN2A	21975739			10	DELETION		4632	339103	3298	16	NEW_VARIANT
P-0050253-T01-IM6	ETV6 (NM_001987) rearrangement: c.329-315_c.464-3483dup	PRECISE	Note: The ETV6 rearrangement is an intragenic duplication of exon 4. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		68257	0	33	12	Intron of ETV6(+):314bp before exon 4	ETV6	12006046			12	Intron of ETV6(+):3Kb before exon 5	ETV6	12018875			10	DUPLICATION		12829	339111	94023	37	NEW_VARIANT
P-0050257-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.4936:ZFHX3_chr16:g.72795899del	IMPPRECISE	Note: The ZFHX3 rearrangement is a deletion of exons 9 - 10. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		41051	0	5	16	IGR: 21Kb before ZFHX3(-)	ZFHX3	72795899			16	Exon 9 of ZFHX3(-)	ZFHX3	72831645			0	DELETION		35746	339129	43026	5	NEW_VARIANT
P-0050260-T01-IM6	STAG2 (NM_001042749) rearrangement: c.408_c.2775+203dup	PRECISE	Note: The STAG2 rearrangement is an intragenic duplication of exons 7 - 27. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		7963	0	53	X	Exon 7 of STAG2(+)	STAG2	123176441			X	Intron of STAG2(+):203bp after exon 27	STAG2	123212111			10	DUPLICATION		35670	339128	20126	54	NEW_VARIANT
P-0050264-T01-IM6	JAK3 (NM_000215) rearrangement: t(1;19)(p36.22;p13.11)(chr1:g.9448228::chr19:g.17952430)	PRECISE	Note: The JAK3 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	9	19	Intron of JAK3(-):18bp after exon 7	JAK3	17952430			1	IGR: 37Kb before LOC100506022(-)	JAK3	9448228			10	TRANSLOCATION		0	339134	0	10	NEW_VARIANT
P-0050285-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-146:TMPRSS2_c.39+53629:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		40383	0	45	21	Intron of ERG(-):54Kb after exon 3	TMPRSS2	39893957			21	Intron of TMPRSS2(-):146bp before exon 2	ERG	42870262			10	DELETION		2976305	339160	26223	45	NEW_VARIANT
P-0050286-T01-IM6	FLT4 (NM_182925) rearrangement: c.3611:FLT4_chr5:g.144857146inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		241326	0	13	5	IGR: 279Kb before PRELID2(-)	FLT4	144857146			5	Exon 27 of FLT4(-)	FLT4	180038406			10	INVERSION		35181260	339163	263130	15	NEW_VARIANT
P-0050289-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-2621:TMPRSS2_c.40-59203:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		54324	0	73	21	Intron of ERG(-):59Kb before exon 4	TMPRSS2	39876747			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872737			10	DELETION		2995990	339444	72899	74	NEW_VARIANT
P-0050309-T01-IM6	NAB2 (NM_005967) rearrangement: t(2;12)(p24.2;q13.3)(chr2:g.17948133::chr12:g.57487915)	IMPPRECISE	Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	257	12	Intron of NAB2(+):479bp before exon 7	NAB2	57487915			2	Intron of GEN1(+):177bp after exon 5	NAB2	17948133			0	TRANSLOCATION		0	339549	0	366	NEW_VARIANT
P-0050350-T01-IM6	NKX3-1 (NM_006167) rearrangement: t(8;17)(p21.2;q21.31)(chr8:g.23539161::chr17:g.41654143)	PRECISE	Note: The NKX3-1 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	17	IGR: 49Kb before ETV4(-)	NKX3	41654143			8	Intron of NKX3-1(-):9bp before exon 2	NKX3-1	23539161			10	TRANSLOCATION		0	339679	0	8	NEW_VARIANT
P-0050351-T01-IM6	ETV6 (NM_001987) rearrangement: c.1009+1555:ETV6_chr12:g.22933086inv	IMPPRECISE	Note: The ETV6 rearrangement is an inversion of exons 6 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		154319	0	6	12	Intron of ETV6(+):2Kb after exon 5	ETV6	12024458			12	IGR: 155Kb before ETNK1(+)	ETV6	22933086			0	INVERSION		10908628	339672	167203	7	NEW_VARIANT
P-0050351-T01-IM6	CLEC1A (NM_016511) - CCNE1 (NM_001238) rearrangement: t(12;19)(p13.2;q12)(chr12:g.10234241::chr19:g.30314505)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {CLEC1A:CCNE1}		0	0	9	19	Intron of CCNE1(+):56bp before exon 12	CLEC1A	30314505			12	Intron of CLEC1A(-):229bp before exon 3	CCNE1	10234241			10	TRANSLOCATION		0	339676	0	9	NEW_VARIANT
P-0050351-T01-IM6	PTPRS (NM_002850) rearrangement: c.4770-34:PTPRS_chr19:g.5198769inv	PRECISE	Note: The PTPRS rearrangement is an inversion of exons 32 - 38. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		14657	0	10	19	IGR: 7Kb before PTPRS(-)	PTPRS	5198769			19	Intron of PTPRS(-):34bp before exon 32	PTPRS	5212295			10	INVERSION		13526	339673	20140	11	NEW_VARIANT
P-0050351-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.2562:NOTCH3_chr19:g.43041943inv	IMPPRECISE	Note: The NOTCH3 rearrangement is an inversion of exons 1 - 16. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NOTCH3:LIPE-AS1}		547297	0	5	19	Exon 16 of NOTCH3(-)	NOTCH3	15295110			19	5-UTR of LIPE-AS1(+):115Kb before coding start	NOTCH3	43041943			0	INVERSION		27746833	339674	893723	5	NEW_VARIANT
P-0050351-T01-IM6	MYC (NM_002467) rearrangement: c.444:MYC_chr8:g.129109519del	PRECISE	Note: The MYC rearrangement is a deletion of exons 2 - 3. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MYC:PVT1}		6835	0	6	8	Exon 2 of MYC(+)	MYC	128750907			8	5-UTR of PVT1(+):4Kb before coding start	MYC	129109519			10	DELETION		358612	339669	31078	6	NEW_VARIANT
P-0050352-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4572:TMPRSS2_c.39+11100:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		28529	0	20	21	Intron of ERG(-):11Kb after exon 3	TMPRSS2	39936486			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875305			10	DELETION		2938819	339682	66405	20	NEW_VARIANT
P-0050392-T01-IM6	GSK3B (NM_002093) rearrangement: c.910-751_c.927inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		381	0	2	3	Exon 9 of GSK3B(-)	GSK3B	119585458			3	Intron of GSK3B(-):751bp before exon 9	GSK3B	119586226			7	INVERSION		768	339856	178	3	NEW_VARIANT
P-0050395-T01-IM6	NBN (NM_002485) rearrangement: c.585-2804_c.1124+91dup	PRECISE	Note: The NBN rearrangement is an intragenic duplication of exons 6 - 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : in frame		3264	0	22	8	Intron of NBN(-):90bp after exon 9	NBN	90970862			8	Intron of NBN(-):3Kb before exon 6	NBN	90986322			10	DUPLICATION		15460	339858	5549	23	NEW_VARIANT
P-0050415-T01-IM6	FOXA1 (NM_004496) rearrangement: c.745:FOXA1_chr14:g.38101340del	PRECISE	Note: The FOXA1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		7054	0	61	14	Exon 2 of FOXA1(-)	FOXA1	38061244			14	IGR: 43Kb before FOXA1(-)	FOXA1	38101340			10	DELETION		40096	339890	8035	62	NEW_VARIANT
P-0050433-T01-IM6	FGFR4 (NM_213647) - EYS (NM_001142800) rearrangement: t(5;6)(q35.2;q12)(chr5:g.176523102::chr6:g.65813208)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {FGFR4:EYS}		0	0	30	6	Intron of EYS(-):46Kb before exon 13	FGFR4	65813208			5	Exon 14 of FGFR4(+)	EYS	176523102			10	TRANSLOCATION		0	339913	0	30	NEW_VARIANT
P-0050433-T01-IM6	BCOR (NM_001123385) rearrangement: c.276:BCOR_chrX:g.39909892inv	PRECISE	Note: The BCOR rearrangement is an inversion of exons 4 - 15. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		40074	0	10	X	Promoter of BCOR(-):606bp from tx start	BCOR	39909892			X	Exon 4 of BCOR(-)	BCOR	39934323			10	INVERSION		24431	339912	49886	10	NEW_VARIANT
P-0050435-T01-IM6	RARA (NM_000964) rearrangement: c.328-35:RARA_chr17:g.48311315inv	PRECISE	Note: The RARA rearrangement is an inversion of exons 4 - 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		257827	0	79	17	Intron of RARA(+):34bp before exon 4	RARA	38506001			17	IGR: 19Kb before LOC101927230(+)	RARA	48311315			10	INVERSION		9805314	339910	324238	86	NEW_VARIANT
P-0050445-T01-IM6	FANCA (NM_000135) rearrangement: c.284-420:FANCA_chr16:g.50248117del	PRECISE	Note: The FANCA rearrangement is a deletion of exons 4 - 43.	MANUAL_OK	3to5	3to5	Antisense Fusion		333867	0	33	16	Intron of PAPD5(+):14bp before exon 4	FANCA	50248117			16	Intron of FANCA(-):420bp before exon 4	FANCA	89877899			10	DELETION		39629782	340014	146188	33	NEW_VARIANT
P-0050445-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-4720:TMPRSS2_c.18+6052:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		58625	0	9	21	Intron of ERG(-):6Kb after exon 1	TMPRSS2	39864235			21	Intron of TMPRSS2(-):5Kb before exon 2	ERG	42874836			0	DELETION		3010601	340015	34170	10	NEW_VARIANT
P-0036748-T02-IM6	NCOR1 (NM_006311) rearrangement: t(17;20)(p12;p13)(chr17:g.15983421::chr20:g.2327385)	PRECISE	Note: The NCOR1 rearrangement is a translocation with a breakpoint in intron 25. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	20	IGR: 34Kb before TGM6(+)	NCOR1	2327385			17	Intron of NCOR1(-):43bp before exon 26	NCOR1	15983421			10	TRANSLOCATION		0	340231	0	22	NEW_VARIANT
P-0049848-T01-IM6	RB1 (NM_000321) rearrangement: c.265-51_c.501-802dup	PRECISE	Note: The RB1 rearrangement is an intragenic duplication of exons 3 - 4. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		1032	0	94	13	Intron of RB1(+):50bp before exon 3	RB1	48916684			13	Intron of RB1(+):801bp before exon 5	RB1	48921159			10	DUPLICATION		4475	337677	2480	97	NEW_VARIANT
P-0049848-T01-IM6	INPP4B (NM_001101669) rearrangement: c.373-28621_c.403del	PRECISE	Note: The INPP4B rearrangement is an intragenic deletion of exon 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		205	0	23	4	Exon 8 of INPP4B(-)	INPP4B	143235885			4	Intron of INPP4B(-):29Kb before exon 8	INPP4B	143264536			10	DELETION		28651	337675	199	24	NEW_VARIANT
P-0050452-T01-IM6	DNMT3B (NM_006892) rearrangement: c.1126+793_c.1529dup	PRECISE	Note: The DNMT3B rearrangement is an intragenic duplication of exons 11 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		5136	0	33	20	Intron of DNMT3B(+):793bp after exon 10	DNMT3B	31382194			20	Exon 15 of DNMT3B(+)	DNMT3B	31386304			10	DUPLICATION		4110	340002	11864	37	NEW_VARIANT
P-0050454-T01-IM6	CD79B (NM_001039933) rearrangement: c.678:CD79B_chr17:g.62005175del	PRECISE	Note: The CD79B rearrangement is a deletion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		442	0	7	17	Promoter of CD79B(-):922bp from tx start	CD79B	62005175			17	Exon 6 of CD79B(-)	CD79B	62006601			10	DELETION		1426	340011	176	7	NEW_VARIANT
P-0050488-T01-IM6	NSD1 (NM_022455) rearrangement: t(1;5)(p11.2;q35.3)(chr1:g.121484679::chr5:g.176678821)	PRECISE	Note: The NSD1 rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	13	5	Exon 12 of NSD1(+)	NSD1	176678821			1	IGR: 224Kb before EMBP1(+)	NSD1	121484679			10	TRANSLOCATION		0	340215	0	13	NEW_VARIANT
P-0050495-T01-IM6	SHQ1 (NM_018130) rearrangement: t(3;8)(p13;p11.21)(chr3:g.72861734::chr8:g.42218035)	IMPPRECISE	Note: The SHQ1 rearrangement is a translocation with a breakpoint in intron 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	13	8	Intron of POLB(+):777bp before exon 10	SHQ1	42218035			3	Intron of SHQ1(-):87bp after exon 9	SHQ1	72861734			0	TRANSLOCATION		0	340234	0	12	NEW_VARIANT
P-0050499-T01-IM6	GOLPH3L (NM_018178) - PBRM1 (NM_018313) rearrangement: t(1;3)(q21.3;p21.1)(chr1:g.150659882::chr3:g.52582106)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GOLPH3L:PBRM1}		0	0	6	3	Exon 30 of PBRM1(-)	GOLPH3L	52582106			1	Intron of GOLPH3L(-):7Kb after exon 2	PBRM1	150659882			10	TRANSLOCATION		0	340275	0	7	NEW_VARIANT
P-0050515-T01-IM6	BAP1 (NM_004656) rearrangement: t(3;12)(p21.1;q24.23)(chr3:g.52439888::chr12:g.120555325)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	76	12	Promoter of RAB35(-):22Kb from tx start	BAP1	120555325			3	Exon 10 of BAP1(-)	BAP1	52439888			10	TRANSLOCATION		0	340326	0	76	NEW_VARIANT
P-0050529-T01-IM6	CDH1 (NM_004360) rearrangement: c.49-148:CDH1_chr16:g.68767896del	PRECISE	Note: The CDH1 rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	-		933	0	35	16	IGR: 3Kb before CDH1(+)	CDH1	68767896			16	Intron of CDH1(+):147bp before exon 2	CDH1	68772052			10	DELETION		4156	340449	858	37	NEW_VARIANT
P-0050534-T01-IM6	DDX6 (NM_004397) - TCF3 (NM_001136139) rearrangement: t(11;19)(q23.3;p13.3)(chr11:g.118643584::chr19:g.1615424)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {DDX6:TCF3}		0	0	48	19	Intron of TCF3(-):260bp after exon 16	DDX6	1615424			11	Intron of DDX6(-):5Kb before exon 5	TCF3	118643584			10	TRANSLOCATION		0	340452	0	49	NEW_VARIANT
P-0050541-T01-IM6	GRIN2A (NM_001134407) rearrangement: c.646:GRIN2A_chr16:g.27280740inv	PRECISE	Note: The GRIN2A rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {GRIN2A:FLJ21408}		59577	0	18	16	Exon 3 of GRIN2A(-)	GRIN2A	10032177			16	5-UTR of FLJ21408(+):21Kb before coding start	GRIN2A	27280740			10	INVERSION		17248563	340460	100577	20	NEW_VARIANT
P-0050541-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-55175:ERG_c.838+32:TMPRSS2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		13031	0	29	21	Promoter of ERG(-):121Kb from tx start	ERG	39872719			21	Intron of TMPRSS2(-):31bp after exon 8	TMPRSS2	42848472			10	INVERSION		2975753	340461	20861	30	NEW_VARIANT
P-0050548-T01-IM6	ETV1 (NM_001163147) - PTK2 (NM_005607) rearrangement: t(7;8)(p21.2;q24.3)(chr7:g.13975429::chr8:g.141762207)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ETV1:PTK2}		0	0	21	8	Intron of PTK2(-):123bp after exon 17	ETV1	141762207			7	Exon 7 of ETV1(-)	PTK2	13975429			10	TRANSLOCATION		0	340464	0	21	NEW_VARIANT
P-0050566-T01-IM6	PLIN5 (NM_001013706) - PTPRS (NM_002850) rearrangement: c.61-544:PLIN5_c.719-11:PTPRSdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PLIN5:PTPRS}		64005	0	7	19	Intron of PLIN5(-):544bp before exon 3	PLIN5	4532378			19	Intron of PTPRS(-):11bp before exon 10	PTPRS	5246067			10	DUPLICATION		713689	341063	71740	7	NEW_VARIANT
P-0050566-T01-IM6	MET (NM_000245) rearrangement: t(1;7)(p33;q31.2)(chr1:g.47763737::chr7:g.116411552)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	54	7	Exon 13 of MET(+)	MET	116411552			1	Intron of STIL(-):2Kb after exon 6	MET	47763737			10	TRANSLOCATION		0	341065	0	55	NEW_VARIANT
P-0050442-T01-IM6	BRAF (NM_004333) rearrangement: c.981-233_c.1141-1349del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		35240	0	10	7	Intron of BRAF(-):1Kb before exon 9	BRAF	140488733			7	Intron of BRAF(-):233bp before exon 8	BRAF	140494500			10	DELETION		5767	339968	39163	10	NEW_VARIANT
P-0050536-T01-IM6	RPS6KB2 (NM_003952) - WDR37 (NM_014023) rearrangement: t(10;11)(p15.3;q13.2)(chr10:g.1153634::chr11:g.67198895)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RPS6KB2:WDR37}		0	0	26	11	Exon 5 of RPS6KB2(+)	RPS6KB2	67198895			10	Intron of WDR37(+):2Kb after exon 11	WDR37	1153634			10	TRANSLOCATION		0	340442	0	25	NEW_VARIANT
P-0050552-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2863:TMPRSS2_c.18+17272:ERGdel	IMPPRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		69842	0	59	21	Intron of ERG(-):17Kb after exon 1	TMPRSS2	39853015			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872979			0	DELETION		3019964	340500	46447	63	NEW_VARIANT
P-0050553-T01-IM6	WIBG (NM_032345) - ERBB3 (NM_001982) rearrangement: c.37+7302:WIBG_c.2617-73:ERBB3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {WIBG:ERBB3}		43837	0	5	12	Intron of WIBG(-):7Kb after exon 1	WIBG	56314207			12	Intron of ERBB3(+):72bp before exon 22	ERBB3	56492211			7	INVERSION		178004	340498	21902	5	NEW_VARIANT
P-0050553-T01-IM6	ERBB4 (NM_005235) - PLCL1 (NM_006226) rearrangement: c.2079+117:ERBB4_c.241-50815:PLCL1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {ERBB4:PLCL1}		71644	0	23	2	Intron of PLCL1(+):51Kb before exon 2	ERBB4	198897667			2	Intron of ERBB4(-):116bp after exon 17	PLCL1	212495070			10	INVERSION		13597403	340497	61438	23	NEW_VARIANT
P-0050527-T01-IM6	IL7R (NM_002185) rearrangement: t(5;19)(p13.2;q13.11)(chr5:g.35873544::chr19:g.35201559)	PRECISE	Note: The IL7R rearrangement is a translocation with a breakpoint in intron 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	1	74	19	IGR: 24Kb before ZNF181(+)	IL7R	35201559			5	Intron of IL7R(+):37bp before exon 5	IL7R	35873544			10	TRANSLOCATION		0	340448	0	89	NEW_VARIANT
P-0003018-T01-IM3		PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (FOXO4-MED12)		22452	0	55	X	Promoter of FOXO4(+): 1Kb from tx start	FOXO4	70314996			X	Exon 12 of MED12(+)	MED12	70343467			69	DELETION		28471	7199	15273	72	NEW_VARIANT
P-0003576-T01-IM5	None	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		14756	0	7	17	Exon 9 of FLCN(-)	None	17122405			17	5-UTR of FLCN(-): 3Kb before coding start	None	17134202			16	DELETION		11797	12098	13286	6	NEW_VARIANT
P-0050471-T01-IM6	NF1 (NM_001042492) rearrangement: c.2936_c.3198-479del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exons 22 - 24. One of the breakpoints is within exon 22.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1664			17	Exon 22 of NF1(+)	NF1	29556938			17	Intron of NF1(+):478bp before exon 25	NF1	29558612				DELETION		1674	342750	1948		NEW_VARIANT
P-0050471-T01-IM6	PLCG2 (NM_002661) rearrangement: t(16;21)(q23.3;q21.2)(chr16:g.81927563::chr21:g.26566180)	PRECISE	Note: The PLCG2 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0			21	IGR: 192Kb before LINC00158(-)	PLCG2	26566180			16	Intron of PLCG2(+):164bp after exon 12	PLCG2	81927563				TRANSLOCATION		0	342751	0		NEW_VARIANT
P-0049071-T01-IM6	NRG3 (NM_001010848) - FGFR2 (NM_000141) rearrangement: c.823+108972:NRG3_c.2195+27:FGFR2inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NRG3:FGFR2}		148365	0	11	10	Intron of NRG3(+):107Kb after exon 1	NRG3	83744891			10	Intron of FGFR2(-):26bp after exon 16	FGFR2	123244882			0	INVERSION		39499991	335140	110761	11	NEW_VARIANT
P-0049071-T01-IM6	KLF4 (NM_004235) rearrangement: c.631:KLF4_chr9:g.110231435del	PRECISE	Note: The KLF4 rearrangement is a deletion of exons 3 - 5. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {KLF4:LINC01509}		9341	0	5	9	Promoter of LINC01509(-):49Kb from tx start	KLF4	110231435			9	Exon 3 of KLF4(-)	KLF4	110250044			10	DELETION		18609	335139	6999	6	NEW_VARIANT
P-0010083-T01-IM5	PARP12 (NM_022750) - BRAF (NM_004333) rearrangement: c.327-1194:PARP12_c.1140+2871;BRAFinv.	PRECISE	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.	MANUAL_OK	3to3	3to3	-		97873	0	12	7	Intron of PARP12(-): 1Kb before exon 2	PARP12	139759028			7	Intron of BRAF(-): 3Kb after exon 8	BRAF	140491237			13	INVERSION		732209	137888	120079	12	NEW_VARIANT
P-0025739-T01-IM6	ARID5B (NM_032199) rearrangement: c.277-3447_c.430del	PRECISE	Note: The ARID5B rearrangement is an intragenic deletion of exon 3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		637	0	6	10	Intron of ARID5B(+):3Kb before exon 3	ARID5B	63696495			10	Exon 3 of ARID5B(+)	ARID5B	63700095			10	DELETION		3600	206551	645	6	NEW_VARIANT
P-0038853-T01-IM6	KMT2C(NM_170606) Rearrangement: c.7568_c.13372dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		29439	0	62	7	Exon 52 of KMT2C(-)	KMT2C	151845640			7	Exon 38 of KMT2C(-)	KMT2C	151874970			10	DUPLICATION		29330	292013	42074	64	NEW_VARIANT
P-0015914-T01-IM6	MSI2 (NM_138962) rearrangement: t(17;17)(p13.1;q22)(chr17:g.117316023::chr17:g.55334155)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0		54	17	Exon 1 of MSI2(+)	MSI2	55334155			17	IGR: 19Kb before CD2(+)	MSI2	117316023			10	TRANSLOCATION		0	169978	0		NEW_VARIANT
P-0019560-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-16 with ALK exons 20-29): c.1968-2879:EML4_c.3172+375:ALKinv	PRECISE	Note: The EML4 - ALK fusion includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {EML4:ALK}		131596	0	93	2	Intron of ALK(-):374bp after exon 19	EML4	29447952			2	Intron of EML4(+):3Kb before exon 17	ALK	42540223			10	INVERSION		13092271	182652	92928	94	NEW_VARIANT
P-0022650-T01-IM6	RB1 (NM_000321) rearrangement: c.2106+1354_c.2212-148del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 21. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1258	0	35	13	Intron of RB1(+):1Kb after exon 20	RB1	49035323			13	Intron of RB1(+):147bp before exon 22	RB1	49038986			10	DELETION		3663	191615	116	40	NEW_VARIANT
P-0044573-T01-IM6	KDM5C (NM_004187) rearrangement: c.1122+188:KDM5C_chrX:g.56088205inv	PRECISE	Note: The KDM5C rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		14507	0	2	X	Intron of KDM5C(-):187bp after exon 8	KDM5C	53243683			X	IGR: 171Kb before KLF8(+)	KDM5C	56088205			8	INVERSION		2844522	320130	14526	5	NEW_VARIANT
P-0049511-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2242+9:EML4_c.3173-597:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		81486	0	58	2	Intron of ALK(-):597bp before exon 20	EML4	29446991			2	Intron of EML4(+):9bp after exon 19	ALK	42552703			10	INVERSION		13105712	336052	129840	58	NEW_VARIANT
P-0050353-T01-IM6	ZFHX3 (NM_006885) rearrangement: t(12;16)(q14.3;q22.2)(chr12:g.66396352::chr16:g.72994092)	IMPPRECISE	Note: The ZFHX3 rearrangement is a translocation with a breakpoint in 5-UTR region of ZFHX3. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	5	16	5-UTR of ZFHX3(-):173Kb before coding start	ZFHX3	72994092			12	IGR: 21Kb before MIR6074(-)	ZFHX3	66396352			0	TRANSLOCATION		0	339688	0	5	NEW_VARIANT
P-0017046-T01-IM6	IGSF21 (NM_032880) - PIK3R3 (NM_003629) rearrangement: c.306-17554:IGSF21_c.216-2:PIK3R3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0		53	1	Intron of IGSF21(+):18Kb before exon 4	IGSF21	18643832			1	Intron of PIK3R3(-):2bp before exon 3	PIK3R3	46543287			10	INVERSION		27899455	176578	53		NEW_VARIANT
P-0017046-T01-IM6	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	PRECISE	None	MANUAL_OK	5to3	5to3	-		0		21	4	Intron of TACC3(+):881bp after exon 10	FGFR3	1740310			4	Intron of FGFR3(+):10bp after exon 17	TACC3	1808671			10	DUPLICATION		68361	176577	22		NEW_VARIANT
P-0017046-T01-IM6	FGFR1 (NM_001174067) rearrangement: c.348:FGFR1_chr8:g.36454836inv	PRECISE	Note: The FGFR1 rearrangement is an inversion of exons 4 - 19, potentially disrupting gene function.	MANUAL_OK	5to5	5to5	-		0		95	8	IGR: 187Kb before KCNU1(+)	FGFR1	36454836			8	Exon 4 of FGFR1(-)	FGFR1	38287309			10	INVERSION		1832473	176579	128		NEW_VARIANT
P-0021421-T01-IM6	NF1 (NM_001042492) rearrangement: c.2990+21_c.3198-2del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exons 23-24.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		2233	0	8	17	Intron of NF1(+):21bp after exon 22	NF1	29557013			17	Intron of NF1(+):1bp before exon 25	NF1	29559089			10	DELETION		2076	187129	636	63	NEW_VARIANT
P-0021421-T01-IM6	ASXL2 (NM_018263) rearrangement: c.144-18272_c.2044del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		17733	0	11	2	Exon 12 of ASXL2(-)	ASXL2	25967162			2	Intron of ASXL2(-):18Kb before exon 3	ASXL2	26047478			10	DELETION		80316	187128	18359	14	NEW_VARIANT
P-0032269-T01-IM6	APC (NM_000038) rearrangement: c.4489_chr5:g.112196053del	PRECISE	Note: The APC rearrangement results in the deletion of exon 16. One of the breakpoints is within exon 16. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {APC:SRP19}		10841	0	49	5	Exon 16 of APC(+)	APC	112175780			5	Promoter of SRP19(+):831bp from tx start	APC	112196053			10	DELETION		20273	232681	6224	52	NEW_VARIANT
P-0032569-T02-IM6	GNAS (NM_000516) rearrangement: c.312+3:GNAS_chr20:g.55438526inv	PRECISE	Note: The GNAS rearrangement is an inversion of exons 1 - 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		23109	0	66	20	IGR: 234Kb before TFAP2C(+)	GNAS	55438526			20	Intron of GNAS(+):3bp after exon 4	GNAS	57478643			10	INVERSION		2040117	325088	57244	66	NEW_VARIANT
P-0032569-T02-IM6	TRIM24 (NM_015905) - BRAF (NM_004333) fusion: c.1878+791:TRIM24_c.1141-552:BRAFinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {TRIM24:BRAF}		31089	0	86	7	Intron of TRIM24(+):791bp after exon 11	TRIM24	138256539			7	Intron of BRAF(-):552bp before exon 9	BRAF	140487936			10	INVERSION		2231397	325086	60599	85	NEW_VARIANT
P-0034036-T03-IM6	PARK2 (NM_004562) rearrangement: c.412+91_c.618+29764del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exons 4 - 5.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		1602	0	15	6	Intron of PARK2(-):30Kb after exon 5	PARK2	162445359			6	Intron of PARK2(-):90bp after exon 3	PARK2	162683466			10	DELETION		238107	325058	1590	19	NEW_VARIANT
P-0037571-T01-IM6	KMT2D (NM_003482) rearrangement: c.4237-484_c.6720del	PRECISE	Note: The KMT2D intragenic deletion involves exons 15-31	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		32928	0	4	12	Exon 31 of KMT2D(-)	KMT2D	49434833			12	Intron of KMT2D(-):484bp before exon 15	KMT2D	49441057			10	DELETION		6224	281444	33428	4	NEW_VARIANT
P-0037673-T01-IM6	APC (NM_000038) rearrangement: t(5;22)(q22.2;q12.1)(chr5:g.112175871::chr22:g.29065471)	PRECISE	Note: The APC rearrangement is a translocation with a breakpoint in exon 16.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	19	22	Intron of TTC28(-):10Kb after exon 1	APC	29065471			5	Exon 16 of APC(+)	APC	112175871			10	TRANSLOCATION		0	281161	0	20	NEW_VARIANT
P-0040601-T01-IM6	SPRYD3 (NM_032840) - KMT2D (NM_003482) rearrangement: c.901+391:SPRYD3_c.14350:KMT2Ddel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SPRYD3:KMT2D}		152495	0	37	12	Exon 45 of KMT2D(-)	SPRYD3	49422643			12	Intron of SPRYD3(-):390bp after exon 8	KMT2D	53461041			10	DELETION		4038398	302643	235157	37	NEW_VARIANT
P-0044143-T01-IM6	APC (NM_000038) rearrangement: t(5;22)(q22.2;q12.1)(chr5:g.112173427::chr22:g.29065511)	IMPPRECISE	Note: The APC rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	31	22	Intron of TTC28(-):10Kb after exon 1	APC	29065511			5	Exon 16 of APC(+)	APC	112173427			0	TRANSLOCATION		0	317479	0	31	NEW_VARIANT
P-0045253-T01-IM6	CREBBP (NM_004380) - TRAP1 (NM_016292) rearrangement: c.6286:CREBBP_c.88+22:TRAP1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CREBBP:TRAP1}		11636	0	26	16	Intron of TRAP1(-):21bp after exon 1	CREBBP	3767400			16	Exon 31 of CREBBP(-)	TRAP1	3778762			10	DELETION		11362	322093	8020	26	NEW_VARIANT
P-0045717-T01-IM6	RAD54L (NM_001142548) rearrangement: c.1033:RAD54L_chr1:g.60351411inv	PRECISE	Note: The RAD54L rearrangement is an inversion of exons 10 - 19. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		32201	0	41	1	Exon 10 of RAD54L(+)	RAD54L	46733272			1	IGR: 8Kb before CYP2J2(-)	RAD54L	60351411			10	INVERSION		13618139	323600	32010	41	NEW_VARIANT
P-0046055-T01-IM6	ALOX12B (NM_001139) rearrangement: t(8;17)(q24.3;p13.1)(chr8:g.144092736::chr17:g.7977072)	PRECISE	Note: The ALOX12B rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	17	Exon 13 of ALOX12B(-)	ALOX12B	7977072			8	3-UTR of LOC100133669(-):7Kb after coding stop	ALOX12B	144092736			10	TRANSLOCATION		0	324402	0	7	NEW_VARIANT
P-0046055-T01-IM6	ACTN4 (NM_004924) - CIC (NM_015125) rearrangement: c.912+17:ACTN4_c.3957:CICdel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ACTN4:CIC}		170216	0	23	19	Intron of ACTN4(+):17bp after exon 9	ACTN4	39205218			19	Exon 16 of CIC(+)	CIC	42797905			0	DELETION		3592687	324400	196812	25	NEW_VARIANT
P-0047197-T01-IM6	LATS1 (NM_004690) rearrangement: t(6;10)(q25.1;q24.31)(chr6:g.149983086::chr10:g.102418032)	PRECISE	Note: The LATS1 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	32	10	IGR: 87Kb before PAX2(+)	LATS1	102418032			6	Exon 8 of LATS1(-)	LATS1	149983086			10	TRANSLOCATION		0	330161	0	32	NEW_VARIANT
P-0047833-T02-IM6	LRBA (NM_001199282) - BRAF (NM_004333) fusion: t(4;7)(q31.3;q34)(chr4:g.151502269::chr7:g.140493444)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {LRBA:BRAF}		0	0	128	7	Intron of BRAF(-):663bp after exon 8	LRBA	140493444			4	Intron of LRBA(-):7Kb after exon 40	BRAF	151502269			10	TRANSLOCATION		0	338891	0	134	NEW_VARIANT
P-0047833-T02-IM6	AR (NM_000044) rearrangement: c.2174-2789_c.2567del	PRECISE	Note: The AR rearrangement is an intragenic deletion of exons 5 - 7. One of the breakpoints is within exon 7. This represents an ARv567es.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2160	0	48	X	Intron of AR(+):3Kb before exon 5	AR	66934531			X	Exon 7 of AR(+)	AR	66942786			10	DELETION		8255	338889	1821	48	NEW_VARIANT
P-0048063-T01-IM6	TCF3 (NM_001136139) - SBNO2 (NM_014963) rearrangement: c.24:TCF3_c.93+1074:SBNO2del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {TCF3:SBNO2}		60783	0	13	19	Intron of SBNO2(-):1Kb after exon 2	TCF3	1153109			19	Exon 1 of TCF3(-)	SBNO2	1650224			0	DELETION		497115	332238	43930	14	NEW_VARIANT
P-0048170-T01-IM6	RUNX1 (NM_001754) rearrangement: c.806-152:RUNX1_chr21:g.20859351inv	IMPPRECISE	Note: The RUNX1 rearrangement is an inversion of exons 8 - 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		11530	0	5	21	IGR: 926Kb before LOC101927797(-)	RUNX1	20859351			21	Intron of RUNX1(-):152bp before exon 8	RUNX1	36171911			0	INVERSION		15312560	332423	13405	5	NEW_VARIANT
P-0048658-T01-IM6	CDK12 (NM_016507) rearrangement: c.160:CDK12_chr17:g.37615359del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1000	0	8	17	Promoter of CDK12(+):2Kb from tx start	CDK12	37615359			17	Exon 1 of CDK12(+)	CDK12	37618484			10	DELETION		3125	333658	850	8	NEW_VARIANT
P-0049065-T01-IM6	RAD21 (NM_006265) - EIF3H (NM_003756) rearrangement: c.446:RAD21_c.133-12565:EIF3Hdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RAD21:EIF3H}		9376	0	9	8	Intron of EIF3H(-):13Kb before exon 2	RAD21	117750976			8	Exon 5 of RAD21(-)	EIF3H	117870626			10	DELETION		119650	334882	12156	9	NEW_VARIANT
P-0049078-T01-IM6	TPM3 (NM_001278190) - NTRK1 (NM_002529)  fusion: c.395-6179:TPM3_ c.963:NTRK1inv	PRECISE	Note: The TPM3 -NTRK1 fusion includes the kinase domain of NTRK1. One of the breakpoints is within NTRK1 exon 8.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TPM3:NTRK1}		45998	0	5	1	Intron of TPM3(-):6Kb before exon 7	TPM3	154136376			1	Exon 8 of NTRK1(+)	NTRK1	156843537			10	INVERSION		2707161	334897	50828	6	NEW_VARIANT
P-0049956-T01-IM6	KMT2C (NM_170606) rearrangement: c.4794-35_c.14344-1615del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 33 - 55.	MANUAL_OK	3to5	3to5	Deletion of 23 exons : out of frame		57043	0	13	7	Intron of KMT2C(-):2Kb before exon 56	KMT2C	151838491			7	Intron of KMT2C(-):35bp before exon 33	KMT2C	151884596			10	DELETION		46105	337812	81749	13	NEW_VARIANT
P-0050143-T01-IM6	TP53 (NM_000546) rearrangement: c.994-4:TP53_chr17:g.8374380del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 1 - 9.	MANUAL_OK	3to5	3to5	-		54800	0	32	17	Intron of TP53(-):4bp before exon 10	TP53	7574037			17	Promoter of NDEL1(+):35Kb from tx start	TP53	8374380			10	DELETION		800343	338843	70221	34	NEW_VARIANT
P-0050152-T01-IM6	TP53 (NM_000546) rearrangement: c.673-86:TP53_chr17:g.7582323del	IMPPRECISE	Note: The TP53 rearrangement is a deletion of exons 1 - 6.	MANUAL_OK	3to5	3to5	Deletion within transcript		11077	0	15	17	Intron of TP53(-):86bp before exon 7	TP53	7577694			17	5-UTR of TP53(-):9Kb before coding start	TP53	7582323			0	DELETION		4629	338853	8035	22	NEW_VARIANT
P-0050437-T01-IM6	NCOR1 (NM_006311) rearrangement: c.1634+2329_c.1769inv	PRECISE	Note: The NCOR1 rearrangement is an intragenic inversion of exon 16. One of the breakpoints is within exon 16. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		1349	0	8	17	Exon 16 of NCOR1(-)	NCOR1	16024449			17	Intron of NCOR1(-):2Kb after exon 15	NCOR1	16027067			9	INVERSION		2618	339976	1239	9	NEW_VARIANT
P-0050437-T01-IM6	PIK3R2 (NM_005027) rearrangement: t(8;19)(p12;p13.11)(chr8:g.35063141::chr19:g.18273183)	PRECISE	Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	19	Intron of PIK3R2(+):34bp before exon 9	PIK3R2	18273183			8	IGR: 30Kb before UNC5D(+)	PIK3R2	35063141			10	TRANSLOCATION		0	339977	0	11	NEW_VARIANT
P-0050437-T01-IM6	EPHA7 (NM_004440) rearrangement: c.1634-602_c.1743-219del	PRECISE	Note: The EPHA7 rearrangement is an intragenic deletion of exon 8. The rearrangement does not include the kinase domain of EPHA7.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1473	0	6	6	Intron of EPHA7(-):219bp before exon 9	EPHA7	93973852			6	Intron of EPHA7(-):602bp before exon 8	EPHA7	93975022			10	DELETION		1170	339974	253	6	NEW_VARIANT
P-0050516-T01-IM6	TP53 (NM_000546) rearrangement: c.75-6_c.920-2del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 8.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : out of frame		9391	0	88	17	Intron of TP53(-):2bp before exon 9	TP53	7576928			17	Intron of TP53(-):6bp before exon 3	TP53	7579727			10	DELETION		2799	340323	10871	95	NEW_VARIANT
P-0001036-T01-IM3		PRECISE		AUTO_OK	5to3	5to3	Protein fusion: in frame (MKRN1-BRAF)		14735	0	6	7	Intron of MKRN1(-): 392bp after exon 4	MKRN1	140158415			7	Intron of BRAF(-): 571bp after exon 10	BRAF	140482250			14	DUPLICATION		323835	2256	17357	9	NEW_VARIANT
P-0013641-T01-IM5	SPOCK3 (NM_016950) - MLL (NM_001197104) rearrangement: t(4;11)(11q23.3;4q32.3)(chr11:g.118373285::chr4:g.168136694)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: mid-exon (SPOCK3-MLL)		0	0	28	11	Exon 27 of MLL(+)	SPOCK3	118373285			4	Intron of SPOCK3(-): 18Kb after exon 2	MLL	168136694			23	TRANSLOCATION		0	161899	0	27	NEW_VARIANT
P-0013641-T01-IM5	EIF3H (NM_003756) - RAD21 (NM_006265)  rearrangement: c.132+13079:EIF3H_c.1471-37:RAD21dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: in frame (EIF3H-RAD21)		8440	0	18	8	Intron of EIF3H(-): 13Kb after exon 1	EIF3H	117754826			8	Intron of RAD21(-): 37bp before exon 12	RAD21	117863043			29	DUPLICATION		108217	161898	11795	18	NEW_VARIANT
P-0020006-T01-IM6	DOT1L (NM_032482) rearrangement: c.1660_chr19:g.15241142inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		392054	0	11	19	Exon 18 of DOT1L(+)	DOT1L	2213848			19	IGR: 15Kb before ILVBL(-)	DOT1L	15241142			10	INVERSION		13027294	183463	360839	13	NEW_VARIANT
P-0020118-T01-IM6	DNMT1 (NM_001379) - RANBP3 (NM_007322) rearrangement: c.1705:DNMT1_c.22+8490:RANBP3del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {DNMT1:RANBP3}		121570	0	14	19	Intron of RANBP3(-):8Kb after exon 1	DNMT1	5969582			19	Exon 20 of DNMT1(-)	RANBP3	10265341			10	DELETION		4295759	183698	101184	16	NEW_VARIANT
P-0022397-T01-IM6	KMT2C (NM_170606): t(4;7)(q35.2;q36.1)(chr4:g.188268934::chr7:g.151878590)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	61	7	Exon 36 of KMT2C(-)	KMT2C	151878590			4	3-UTR of LOC339975(-):158Kb after coding stop	KMT2C	188268934			10	TRANSLOCATION		0	190535	0	60	NEW_VARIANT
P-0022507-T01-IM6	FLT3 (NM_004119) Rearrangement : chr13:g.29588123_c.742+49:FLT3inv	PRECISE	Note: The FLT3 Rearrangement results in the inversion of exons 1-6 of FLT3. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		60431	0	17	13	Intron of FLT3(-):48bp after exon 6	FLT3	28624183			13	IGR: 11Kb before MTUS2(+)	FLT3	29588123			10	INVERSION		963940	191037	46112	18	NEW_VARIANT
P-0023560-T01-IM6	AXL (NM_021913) Rearrangement : chr19:g.35782298_c.586+33:AXLdel	PRECISE	Note: The AXL Rearrangement results in the inversion of exons 1-4. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		155227	0	15	19	Promoter of MAG(+):690bp from tx start	AXL	35782298			19	Intron of AXL(+):33bp after exon 4	AXL	41727994			10	INVERSION		5945696	195910	132644	15	NEW_VARIANT
P-0023767-T01-IM6	KMT2D (NM_003482) rearrangement: chr12:g.49348815_c.12025inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		24318	0	10	12	5-UTR of ARF3(-):16Kb before coding start	KMT2D	49348815			12	Exon 39 of KMT2D(-)	KMT2D	49426463			10	INVERSION		77648	196908	20395	10	NEW_VARIANT
P-0023767-T01-IM6	AXIN1 (NM_003502) rearrangement: t(1;16)(p36.22;p13.3)(chr1:g.10744557::chr16:g.360175)	PRECISE	Note: The AXIN1 rearrangement is a translocation which involves exons 4-11. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	5	16	Intron of AXIN1(-):106bp before exon 4	AXIN1	360175			1	Intron of CASZ1(-):9Kb after exon 4	AXIN1	10744557			9	TRANSLOCATION		0	196909	0	4	NEW_VARIANT
P-0024365-T01-IM6	PAK7 (NM_177990) Rearrangement : c.434:PAK7_chr20:g.11058657inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		3567	0	5	20	Exon 4 of PAK7(-)	PAK7	9561348			20	IGR: 189Kb before LOC339593(-)	PAK7	11058657			10	INVERSION		1497309	199982	4160	5	NEW_VARIANT
P-0024365-T01-IM6	RIN2 (NM_001242581) -RTEL1 (NM_032957) Rearrangement : c.2348-1384:RIN2_c.2338-6:RTEL1	PRECISE	Note: The RIN2 -RTEL1 Rearrangement results in the fusion of RIN2 exons 1-10 with RTEL1 exons 26-35. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RIN2:RTEL1}		282928	0	13	20	Intron of RIN2(+):1Kb before exon 10	RIN2	19975939			20	Intron of RTEL1(+):5bp before exon 26	RTEL1	62321641			10	DELETION		42345702	199981	305680	14	NEW_VARIANT
P-0024726-T01-IM6	EP300 (NM_001429) rearrangement: chr22:g.41442701_c.6996:EP300del	PRECISE	Note: The EP300 rearrangement is a deletion of exons 1-30. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		76104	0	19	22	IGR: 46Kb before MIR1281(+)	EP300	41442701			22	Exon 31 of EP300(+)	EP300	41574711			10	DELETION		132010	201129	41288	21	NEW_VARIANT
P-0024726-T01-IM6	XRCC2 (NM_005431) rearrangement: chr7:g.151369240_c.416:XRCC2inv	PRECISE	Note: The XRCC2 rearrangement is an inversion with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		127117	0	4	7	Intron of PRKAG2(-):3Kb after exon 4	XRCC2	151369240			7	Exon 3 of XRCC2(-)	XRCC2	152346154			10	INVERSION		976914	201130	125038	4	NEW_VARIANT
P-0024740-T01-IM6	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.753+11588:ACOXL_c.394+1521:BCL2L11del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ACOXL:BCL2L11}		1246	0	12	2	Intron of ACOXL(+):12Kb after exon 9	ACOXL	111574560			2	Intron of BCL2L11(+):2Kb after exon 2	BCL2L11	111883237			10	DELETION		308677	201280	2748	13	NEW_VARIANT
P-0025026-T01-IM6	EP300 (NM_001429) rearrangement: c.4240_c.4779+1208dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		4030	0	23	22	Exon 26 of EP300(+)	EP300	41565574			22	Intron of EP300(+):1Kb after exon 29	EP300	41570996			10	DUPLICATION		5422	203224	5185	23	NEW_VARIANT
P-0029267-T03-IM6	NTRK3 (NM_001012338) rearrangement: c.1432:NTRK3_chr15:g.85411017del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		19496	0	7	15	Intron of ALPK3(+):324bp before exon 14	NTRK3	85411017			15	Exon 14 of NTRK3(-)	NTRK3	88576241			10	DELETION		3165224	298626	4426	7	NEW_VARIANT
P-0029267-T03-IM6	ERBB2 (NM_004448) rearrangement: c.2208+78:ERBB2_chr17:g.43293842del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		257624	0	9	17	Intron of ERBB2(+):78bp after exon 18	ERBB2	37879991			17	IGR: 5Kb before FMNL1(+)	ERBB2	43293842			0	DELETION		5413851	298627	228664	9	NEW_VARIANT
P-0037553-T01-IM6	SETD8 (NM_020382) rearrangement: t(10;12)(q21.3;q24.31)(chr10:g.69599715::chr12:g.123891871)	PRECISE	Note: The SETD8 rearrangement is a translocation involving exon 8. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {DNAJC12:SETD8}		0	0	7	12	Intron of SETD8(+):168bp before exon 8	SETD8	123891871			10	Promoter of DNAJC12(-):43Kb from tx start	SETD8	69599715			10	TRANSLOCATION		0	280331	0	9	NEW_VARIANT
P-0038649-T01-IM6	PDPK1 (NM_002613) rearrangement: t(4,16)(q32.2;p13.3)(chr4:g.163884492::chr16:g.2647209)	PRECISE	Note: The PDPK1 rearrangement is a translocation with a breakpoint in exon 13. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	36	16	Exon 13 of PDPK1(+)	PDPK1	2647209			4	IGR: 163Kb before NAF1(-)	PDPK1	163884492			10	TRANSLOCATION		0	287851	0	39	NEW_VARIANT
P-0038960-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.3965-98:PIK3C2G_chr12:g.11089445inv	PRECISE	Note: The PIK3C2G rearrangement is an inversion of exons 1 - 29. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {PRH1:PIK3C2G}		237726	0	27	12	Intron of PRH1(-):37Kb after exon 3	PIK3C2G	11089445			12	Intron of PIK3C2G(+):97bp before exon 30	PIK3C2G	18762371			10	INVERSION		7672926	292808	423817	27	NEW_VARIANT
P-0038960-T01-IM6	BRD4 (NM_058243) rearrangement: t(14;19)(q24.3;p13.12)(chr14:g.75937499::chr19:g.15364419)	PRECISE	Note: The BRD4 rearrangement is a translocation with a breakpoint in intron 11. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	89	19	Intron of BRD4(-):543bp after exon 11	BRD4	15364419			14	3-UTR of JDP2(+):38Kb after coding stop	BRD4	75937499			10	TRANSLOCATION		0	292810	0	89	NEW_VARIANT
P-0039012-T01-IM6	EPCAM (NM_002354) rearrangement: c.78_c.468dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3302	0	2	2	Exon 2 of EPCAM(+)	EPCAM	47600603			2	Exon 4 of EPCAM(+)	EPCAM	47602415			5	DUPLICATION		1812	293114	2382	2	NEW_VARIANT
P-0039685-T01-IM6	PAX8 (NM_003466) rearrangement: c.1088-1971:PAX8_chr2:g.116993803del	PRECISE	Note: The PAX8 rearrangement is a deletion of exons 1 - 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		27296	0	17	2	Intron of PAX8(-):2Kb before exon 10	PAX8	113986804			2	IGR: 1Mb before DPP10(+)	PAX8	116993803			10	DELETION		3006999	297744	37819	45	NEW_VARIANT
P-0039798-T01-IM6	NPM1 (NM_002520) rearrangement: c.165_c.524+2207del	PRECISE	Note: The NPM1 rearrangement is an intragenic deletion of exons 3 - 6. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4598	0	17	5	Exon 3 of NPM1(+)	NPM1	170818335			5	Intron of NPM1(+):2Kb after exon 6	NPM1	170822189			10	DELETION		3854	298311	4488	17	NEW_VARIANT
P-0039798-T01-IM6	PPP6C (NM_002721) rearrangement: c.75+714:PPP6C_chr9:g.127962827del	PRECISE	Note: The PPP6C rearrangement is a deletion of exon 1.	MANUAL_OK	3to5	3to5	-		2497	0	67	9	Intron of PPP6C(-):713bp after exon 1	PPP6C	127951209			9	5-UTR of RABEPK(+):2Kb before coding start	PPP6C	127962827			10	DELETION		11618	298312	1725	77	NEW_VARIANT
P-0044349-T01-IM6	DNMT1 (NM_001379) rearrangement: t(1;19)(q42.2;p13.2)(chr1:g.231871724::chr19:g.10273346)	IMPPRECISE	Note: The DNMT1 rearrangement is a translocation with a breakpoint in exon 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	12	19	Exon 12 of DNMT1(-)	DNMT1	10273346			1	Intron of DISC1(+):14Kb before exon 3	DNMT1	231871724			0	TRANSLOCATION		0	319008	0	12	NEW_VARIANT
P-0044349-T01-IM6	ERBB4 (NM_005235) rearrangement: c.2487+102:ERBB4_chr2:g.211981994del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		10485	0	5	2	IGR: 258Kb before ERBB4(-)	ERBB4	211981994			2	Intron of ERBB4(-):101bp after exon 20	ERBB4	212426526			5	DELETION		444532	319003	13468	5	NEW_VARIANT
P-0044349-T01-IM6	BCOR (NM_001123385) rearrangement: c.3239-2441_c.3568del	PRECISE	Note: The BCOR rearrangement is an intragenic deletion of exons 7 - 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4007	0	12	X	Exon 8 of BCOR(-)	BCOR	39923140			X	Intron of BCOR(-):2Kb before exon 7	BCOR	39926293			10	DELETION		3153	319006	2688	12	NEW_VARIANT
P-0044349-T01-IM6	BTK (NM_000061) rearrangement: c.392-121:BTK_chrX:g.121586039del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		23986	0	12	X	Intron of BTK(-):121bp before exon 6	BTK	100617798			X	IGR: 732Kb before GRIA3(+)	BTK	121586039			8	DELETION		20968241	319007	23894	13	NEW_VARIANT
P-0044451-T01-IM6	GPS2 (NM_004489) rearrangement: c.850:GPS2_chr17:g.7214985del	PRECISE	Note: The GPS2 rearrangement is a deletion of exons 10 - 11. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1727	0	168	17	Promoter of GPS2(-):992bp from tx start	GPS2	7214985			17	Exon 10 of GPS2(-)	GPS2	7216398			10	DELETION		1413	319172	1080	191	NEW_VARIANT
P-0045544-T01-IM6	RFWD2 (NM_022457) rearrangement: c.566-2043_c.617del	PRECISE	Note: The RFWD2 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		311	0	19	1	Exon 4 of RFWD2(-)	RFWD2	176132976			1	Intron of RFWD2(-):2Kb before exon 4	RFWD2	176135070			10	DELETION		2094	323320	471	19	NEW_VARIANT
P-0045544-T01-IM6	ATR (NM_001184) rearrangement: c.292+96:ATR_chr3:g.132133790del	IMPPRECISE	Note: The ATR rearrangement is a deletion of exons 4 - 47.	MANUAL_OK	3to5	3to5	Antisense Fusion		105664	0	7	3	Promoter of DNAJC13(+):3Kb from tx start	ATR	132133790			3	Intron of ATR(-):95bp after exon 3	ATR	142284867			0	DELETION		10151077	323321	184983	7	NEW_VARIANT
P-0006124-T01-IM5	FANCA (NM_000135) rearrangement: c.1627-1039_1603del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		840	0	38	16	Intron of FANCA(-): 1Kb before exon 18	FANCA	89847404			16	Exon 17 of FANCA(-)	FANCA	89849290			50	DELETION		1886	68993	740	38	NEW_VARIANT
P-0006124-T01-IM5	None	PRECISE		MANUAL_OK	3to5	3to5	Deletion within transcript: mid-exon		122	0	27	21	Exon 6 of RUNX1(-)	None	36164873			21	Intron of RUNX1(-): 2Kb before exon 6	None	36167165			64	DELETION		2292	68994	66	27	NEW_VARIANT
P-0040386-T01-IM6	TSC1 (NM_000368) rearrangement: t(9;10)(q34.13;q26.11)(chr9:g.135797351::chr10:g.120090828)	PRECISE	Note: The TSC1 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	7	10	Intron of FAM204A(-):4Kb after exon 5	TSC1	120090828			9	Exon 7 of TSC1(-)	TSC1	135797351			10	TRANSLOCATION		0	301865	0	9	NEW_VARIANT
P-0040386-T01-IM6	ABL1 (NM_005157) rearrangement: c.823-69_c.2132del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		15745	0	11	9	Intron of ABL1(+):68bp before exon 5	ABL1	133747447			9	Exon 11 of ABL1(+)	ABL1	133759809			10	DELETION		12362	301864	8613	11	NEW_VARIANT
P-0037474-T01-IM6	TSC2 (NM_000548) Rearrangement : c.1885_c.3814+31dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		35837	0	186	16	Exon 18 of TSC2(+)	TSC2	2121556			16	Intron of TSC2(+):31bp after exon 31	TSC2	2131830			10	DUPLICATION		10274	279337	39022	208	NEW_VARIANT
P-0010497-T01-IM5	EP300 (NM_001429) rearrangement : c.1996:EP300_chr22:g.41694128del	PRECISE	Note: The EP300 rearrangement event results in the deletion of EP300 exons 10-31. One of the breakpoints is within EP300 exon10.	MANUAL_OK	3to5	3to5	-		52613	0	6	22	Exon 10 of EP300(+)	EP300	41537169			22	IGR: 3Kb before ZC3H7B(+)	EP300	41694128			13	DELETION		156959	146818	43861	6	NEW_VARIANT
P-0014908-T01-IM6	RPS6KA4 (NM_003942) Rearrangement : c.188-3737:BAD_ c.1593:RPS6KA4dup	PRECISE	Note: The RPS6KA4 Rearrangement results in the duplication of exons1-13. One of the breakpoints is within exon 13. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense fusion		20900	0	29	11	Intron of BAD(-): 4Kb before exon 2	RPS6KA4	64043012			11	Exon 13 of RPS6KA4(+)	RPS6KA4	64137082			81	DUPLICATION		94070	166121	24345	29	NEW_VARIANT
P-0033800-T01-IM6	SPEN (NM_015001) - DDI2 (NM_032341) rearrangement: c.2992:SPEN_c.760+1876:DDI2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:DDI2}		20661	0	5	1	Intron of DDI2(+):2Kb after exon 5	SPEN	15966805			1	Exon 11 of SPEN(+)	DDI2	16255727			10	DUPLICATION		288922	245616	27565	6	NEW_VARIANT
P-0004901-T01-IM5	CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion (CCDC6 exon1 with RET exons 12-20) : :CCDC6_:RETinv	PRECISE	Note: The CCDC6 (NM_005436) - RET (NM_020975) reciprocal fusion includes the kinase domain of RET gene.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (CCDC6-RET)		58166	0	102	10	Intron of RET(+): 303bp before exon 12	CCDC6	43611729			10	Intron of CCDC6(-): 13Kb after exon 1	RET	61653032			115	INVERSION		18041303	40355	58372	144	NEW_VARIANT
P-0014595-T01-IM6	RB1 (NM_000321) rearrangement: t(13;17)(q14.2;q13.1)(chr13:g.48916736::chr17:g.7541457)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	36	17	IGR: 5Kb after SHBG(+)	RB1	7541457			13	Exon 3 of RB1(+)	RB1	48916736			14	TRANSLOCATION		0	165054	0	35	NEW_VARIANT
P-0014595-T01-IM6	MITF (NM_198159) rearrangement: c.587_c.762+1035inv	PRECISE	Note: The MITF (NM_198159) rearrangement is an inversion of exons 4-5. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense fusion		1259	0	6	3	Exon 4 of MITF(+)	MITF	69988253			3	Intron of MITF(+): 1Kb after exon 5	MITF	69991517			19	INVERSION		3264	165051	1435	6	NEW_VARIANT
P-0015058-T03-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-451:TMPRSS2_c.18+8534:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		34660	0	173	21	Intron of ERG(-):9Kb after exon 1	TMPRSS2	39861753			21	Intron of TMPRSS2(-):451bp before exon 2	ERG	42870567			10	DELETION		3008814	282582	42623	178	NEW_VARIANT
P-0015058-T03-IM6	CENPE (NM_001813) - FAM175A (NM_139076) rearrangement: c.7541-96:CENPE_c.477-36:FAM175Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CENPE:FAM175A}		15179	0	52	4	Intron of FAM175A(-):36bp before exon 6	CENPE	84390340			4	Intron of CENPE(-):96bp before exon 45	FAM175A	104032264			10	DELETION		19641924	282581	18536	61	NEW_VARIANT
P-0016886-T01-IM6	SETD2 (NM_014159) - GNB4 (NM_021629) Rearrangement : c.5128:SETD2_c.-43+6699:GNB4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SETD2:GNB4}		474245	0	25	3	Exon 9 of SETD2(-)	SETD2	47139459			3	5-UTR of GNB4(-):43Kb before coding start	GNB4	179162435			10	DUPLICATION		132022976	173844	739780	27	NEW_VARIANT
P-0027293-T02-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-426:TMPRSS2_c.39+52928:ERGinv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		44326	0	47	21	Intron of ERG(-):53Kb after exon 3	TMPRSS2	39894658			21	Intron of TMPRSS2(-):426bp before exon 2	ERG	42870542			10	INVERSION		2975884	278977	47544	46	NEW_VARIANT
P-0031217-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.597_c.3382+1300del	PRECISE	Note: The SMARCA4 rearrangement is a deletion of exons 4-24. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		48851	0	18	19	Exon 4 of SMARCA4(+)	SMARCA4	11097106			19	Intron of SMARCA4(+):1Kb after exon 24	SMARCA4	11139926			10	DELETION		42820	229630	58043	20	NEW_VARIANT
P-0031217-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.2002:NOTCH3_chr19:g.12995615del	PRECISE	Note: The NOTCH3 rearrangement is a deletion of exons 13-33. One of the breakpoints is within exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		103885	0	146	19	3-UTR of KLF1(-):83bp after coding stop	NOTCH3	12995615			19	Exon 13 of NOTCH3(-)	NOTCH3	15296440			10	DELETION		2300825	229631	140780	160	NEW_VARIANT
P-0031217-T01-IM6	BRD4 (NM_058243) rearrangement: c.850-131:BRD4_chr19:g.15386105del	PRECISE	Note: The BRD4 rearrangement is a deletion of exons 1-5. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		9957	0	12	19	Intron of BRD4(-):131bp before exon 6	BRD4	15375708			19	5-UTR of BRD4(-):37Kb before coding start	BRD4	15386105			10	DELETION		10397	229632	14633	12	NEW_VARIANT
P-0032339-T01-IM6	NAB2(NM_005967) - STAT6(NM_003153) Rearrangement: c.*434:NAB2_c.1512+724:STAT6inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		2152	0	51	12	3-UTR of NAB2(+):6Kb after coding stop	NAB2	57488938			12	Intron of STAT6(-):723bp after exon 13	STAT6	57495349			10	INVERSION		6411	232761	2927	108	NEW_VARIANT
P-0032339-T01-IM6	SMARCA4(NM_003072) Rearrangement: c.-89_c.2002-30del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 1-13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		21661	0	21	19	5-UTR of SMARCA4(+):23Kb before coding start	SMARCA4	11071791			19	Intron of SMARCA4(+):89bp before exon 14	SMARCA4	11118488			10	DELETION		46697	232759	3499	21	NEW_VARIANT
P-0032352-T01-IM6	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	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28518	0	50	21	Intron of ERG(-):20Kb after exon 1	TMPRSS2	39849794			21	Intron of TMPRSS2(-):413bp after exon 2	ERG	42869632			10	DELETION		3019838	232827	38703	51	NEW_VARIANT
P-0033856-T01-IM6	SOX9 (NM_000346) rearrangement: c.1496:SOX9_chr17:g.70485069del	PRECISE	Note: The SOX9 rearrangement is a deletion of exon 3. One of the breakpoints is within exon 3. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2486	0	5	17	Exon 3 of SOX9(+)	SOX9	70120494			17	3-UTR of LINC00673(-):104Kb after coding stop	SOX9	70485069			8	DELETION		364575	248111	4652	5	NEW_VARIANT
P-0033879-T01-IM6	RPS6KB2 (NM_003952) rearrangement: c.857_c.*516del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11113	0	8	11	Exon 10 of RPS6KB2(+)	RPS6KB2	67200869			11	Promoter of RPS6KB2(+):7Kb from tx start	RPS6KB2	67203156			10	DELETION		2287	277446	11263	8	NEW_VARIANT
P-0037022-T01-IM6	HRAS (NM_001130442) rearrangement: t(9;11)(q33.2;p15.5)(chr9:g.124685061::chr11:g.533931)	PRECISE	Note: The HRAS rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	6	11	Exon 3 of HRAS(-)	HRAS	533931			9	Intron of TTLL11(-):51Kb after exon 6	HRAS	124685061			10	TRANSLOCATION		0	275617	0	6	NEW_VARIANT
P-0037022-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-2103:TMPRSS2_c.39+59657:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 4-11. The fusion involves the non-canonical ERG transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		61023	0	52	21	Intron of ERG(-):60Kb after exon 3	TMPRSS2	39887929			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42872219			10	DELETION		2984290	275614	82972	54	NEW_VARIANT
P-0037022-T01-IM6	LACE1 (NM_145315) - ROS1 (NM_002944) rearrangement: c.808-19179:LACE1_c.5079+1435:ROS1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {LACE1:ROS1}		171434	0	3	6	Intron of LACE1(+):19Kb before exon 8	LACE1	108749238			6	Intron of ROS1(-):1Kb after exon 30	ROS1	117660863			10	INVERSION		8911625	275615	201457	4	NEW_VARIANT
P-0037028-T01-IM6	SMAD3 (NM_005902) rearrangement: c.401-37:SMAD3_chr15:g.67333415del	PRECISE	Note: The SMAD3 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4809	0	72	15	IGR: 25Kb before SMAD3(+)	SMAD3	67333415			15	Intron of SMAD3(+):36bp before exon 3	SMAD3	67457554			10	DELETION		124139	275645	5071	74	NEW_VARIANT
P-0037105-T01-IM6	PARK2 (NM_004562) rearrangement: c.618+20977_c.670del	PRECISE	Note: The PARK2 rearrangement results in the deletion of exon 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		458	0	17	6	Exon 6 of PARK2(-)	PARK2	162394398			6	Intron of PARK2(-):21Kb after exon 5	PARK2	162454146			10	DELETION		59748	276244	196	18	NEW_VARIANT
P-0037120-T01-IM6	DROSHA (NM_013235) rearrangement: t(5;8)(p13.3;q22.1)(chr5:g.31485128::chr8:g.97865366)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	42	8	Intron of CPQ(+):18Kb after exon 3	DROSHA	97865366			5	Intron of DROSHA(-):59bp before exon 14	DROSHA	31485128			10	TRANSLOCATION		0	276299	0	45	NEW_VARIANT
P-0037167-T01-IM6	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2553:ERBB2_c.2864:CDK12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERBB2:CDK12}		45704	0	93	17	Exon 10 of CDK12(+)	ERBB2	37673710			17	Exon 21 of ERBB2(+)	CDK12	37881361			10	DUPLICATION		207651	276732	70457	98	NEW_VARIANT
P-0037307-T01-IM6	ARID2 (NM_152641) - TWF1 (NM_001242397) rearrangement: c.5096:ARID2_c.283-514:TWF1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {ARID2:TWF1}		25923	0	55	12	Intron of TWF1(-):514bp before exon 4	ARID2	44194847			12	Exon 18 of ARID2(+)	TWF1	46285828			10	INVERSION		2090981	277582	33994	55	NEW_VARIANT
P-0037392-T01-IM6	TSC2 (NM_000548) rearrangement: c.2356-81_c.2742+74del	PRECISE	Note: The TSC2 rearrangement results in the in-frame intragenic deletion of exons 22 to 24.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		4957	0	22	16	Intron of TSC2(+):80bp before exon 22	TSC2	2124120			16	Intron of TSC2(+):74bp after exon 24	TSC2	2126245			10	DELETION		2125	278943	2998	24	NEW_VARIANT
P-0037409-T01-IM6	ARID5B (NM_032199) - KDM2B (NM_032590) rearrangement: t(10;12)(q21.2;q24.31)(chr10:g.63760134::chr12:g.121894267)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ARID5B:KDM2B}		0	0	38	12	Intron of KDM2B(-):3Kb before exon 13	ARID5B	121894267			10	Intron of ARID5B(+):54bp after exon 4	KDM2B	63760134			10	TRANSLOCATION		0	278863	0	37	NEW_VARIANT
P-0037409-T01-IM6	DOT1L (NM_032482) rearrangement: t(19;22)(p13.3;q13.1)(chr19:g.2217933::chr22:g.37994256)	IMPPRECISE	Note: The DOT1L rearrangement is a translocation involving exon 22. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	22	IGR: 10Kb before GGA1(+)	DOT1L	37994256			19	Intron of DOT1L(+):16bp after exon 22	DOT1L	2217933			0	TRANSLOCATION		0	278866	0	5	NEW_VARIANT
P-0037409-T01-IM6	ST7 (NM_021908) - MET (NM_000245) rearrangement: c.152-654:ST7_c.3029-571:METdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {ST7:MET}		12274	0	6	7	Intron of MET(+):570bp before exon 15	ST7	116414364			7	Intron of ST7(+):653bp before exon 2	MET	116739162			10	DUPLICATION		324798	278860	15081	7	NEW_VARIANT
P-0037461-T01-IM6	ASXL1 (NM_015338) rearrangement: c.1335:ASXL1_chr20:g.31472710del	PRECISE		MANUAL_OK	3to5	3to5	-		41800	0	85	20	Exon 11 of ASXL1(+)	ASXL1	31021336			20	IGR: 65Kb before MAPRE1(+)	ASXL1	31472710			10	DELETION		451374	279033	41937	90	NEW_VARIANT
P-0037461-T01-IM6	EZH2 (NM_004456) rearrangement: c.456:EZH2_chr7:g.148410813del	PRECISE		MANUAL_OK	3to5	3to5	Antisense Fusion		14684	0	9	7	5-UTR of CUL1(+):16Kb before coding start	EZH2	148410813			7	Exon 5 of EZH2(-)	EZH2	148526848			10	DELETION		116035	279032	28005	9	NEW_VARIANT
P-0037461-T01-IM6	APOOL (NM_198450) - ATRX (NM_000489) rearrangement: c.16-7781:APOOL_c.190-138:ATRXinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {APOOL:ATRX}		3645	0	20	X	Intron of ATRX(-):138bp before exon 4	APOOL	76953261			X	Intron of APOOL(+):8Kb before exon 2	ATRX	84293671			10	INVERSION		7340410	279036	6074	20	NEW_VARIANT
P-0037664-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-300_c.556+2378inv	PRECISE	Note: The TMPRSS2 rearrangement results in the inversion of exons 2-5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		17320	0	74	21	Intron of TMPRSS2(-):2Kb after exon 5	TMPRSS2	42857943			21	Intron of TMPRSS2(-):300bp before exon 2	TMPRSS2	42870416			10	INVERSION		12473	281167	22317	80	NEW_VARIANT
P-0039149-T01-IM6	PAK1 (NM_002576) rearrangement: c.191-2797_c.598-16del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		5606	0	9	11	Intron of PAK1(-):16bp before exon 7	PAK1	77066903			11	Intron of PAK1(-):3Kb before exon 3	PAK1	77093836			10	DELETION		26933	293747	3465	14	NEW_VARIANT
P-0039149-T01-IM6	POLE (NM_006231) rearrangement: t(1;12)(q21.1;q24.33)(chr1:g.145089130::chr12:g.133248890)	PRECISE	Note: The POLE rearrangement is a translocation with a breakpoint in exon 16. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	68	12	Exon 16 of POLE(-)	POLE	133248890			1	Intron of NBPF20(+):224Kb before exon 54	POLE	145089130			10	TRANSLOCATION		0	293749	0	71	NEW_VARIANT
P-0039149-T01-IM6	SPEN (NM_015001) rearrangement: t(1;17)(p36.13;q25.1)(chr1:g.16202815::chr17:g.74507875)	PRECISE	Note: The SPEN rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	50	17	IGR: 16Kb before CYGB(-)	SPEN	74507875			1	Exon 3 of SPEN(+)	SPEN	16202815			10	TRANSLOCATION		0	293750	0	49	NEW_VARIANT
P-0039725-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.1164:WHSC1L1_chr8:g.37538799inv	PRECISE	Note: The WHSC1L1 rearrangement is an inversion of exons 6 - 24. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		39075	0	30	8	IGR: 15Kb before ZNF703(+)	WHSC1L1	37538799			8	Exon 6 of WHSC1L1(-)	WHSC1L1	38187313			10	INVERSION		648514	298049	44323	33	NEW_VARIANT
P-0039734-T01-IM6	NF1 (NM_001042492) rearrangement: c.60+6317_c.1063-65del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exons 2 - 9.	MANUAL_OK	3to5	3to5	Deletion of 8 exons : in frame		4754	0	30	17	Intron of NF1(+):6Kb after exon 1	NF1	29428704			17	Intron of NF1(+):64bp before exon 10	NF1	29527990			10	DELETION		99286	297940	1965	38	NEW_VARIANT
P-0040180-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3769:TMPRSS2_c.19-1393:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		55697	0	3	21	Intron of ERG(-):1Kb before exon 2	TMPRSS2	39818937			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873885			10	DELETION		3054948	300471	43700	4	NEW_VARIANT
P-0040259-T01-IM6	DIS3 (NM_014953) rearrangement: c.1239+8:DIS3_chr13:g.75899289inv	PRECISE	Note: The DIS3 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		10102	0	8	13	Intron of DIS3(-):7bp after exon 8	DIS3	73347814			13	Intron of TBC1D4(-):752bp before exon 11	DIS3	75899289			10	INVERSION		2551475	300858	8528	8	NEW_VARIANT
P-0040561-T02-IM6	SETD2 (NM_014159) - PHF7 (NM_016483) rearrangement: c.310:SETD2_c.681-15:PHF7inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {SETD2:PHF7}		131197	0	51	3	Exon 3 of SETD2(-)	SETD2	47165816			3	Intron of PHF7(+):14bp before exon 9	PHF7	52456223			10	INVERSION		5290407	307601	56767	61	NEW_VARIANT
P-0040815-T01-IM6	CDK4 (NM_000075) - DCC (NM_005215) rearrangement: t(12;18)(q14.1;q21.2)(chr12:g.58145295::chr18:g.50434781)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CDK4:DCC}		0	0	18	18	Intron of DCC(+):2Kb after exon 3	CDK4	50434781			12	Exon 2 of CDK4(-)	DCC	58145295			10	TRANSLOCATION		0	303104	0	16	NEW_VARIANT
P-0040985-T01-IM6	NOTCH2 (NM_024408) rearrangement: t(1;6)(p12;q12)(chr1:g.120497534::chr6:g.64352374)	PRECISE	Note: The NOTCH2 rearrangement is a translocation with a breakpoint in intron 13. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {NOTCH2:PHF3}		0	0	11	6	5-UTR of PHF3(+):38Kb before coding start	NOTCH2	64352374			1	Intron of NOTCH2(-):128bp after exon 13	NOTCH2	120497534			10	TRANSLOCATION		0	305110	0	12	NEW_VARIANT
P-0041149-T01-IM6	EGFR (NM_005228) - RAD51 (NM_002875) fusion: t(7;15)(p11.2;q15.1)(chr7:g.55268799::chr15:g.40996189)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {EGFR:RAD51}		0	0	16	15	Intron of RAD51(+):2Kb before exon 4	EGFR	40996189			7	Intron of EGFR(+):81bp before exon 25	RAD51	55268799			10	TRANSLOCATION		0	306061	0	16	NEW_VARIANT
P-0041211-T01-IM6	TSC1 (NM_000368) rearrangement: t(9;14)(q34.13;q23.1)(chr9:g.135787874::chr14:g.59220977)	IMPPRECISE	Note: The TSC1 rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	9	14	IGR: 74Kb before LINC01500(+)	TSC1	59220977			9	Intron of TSC1(-):30bp before exon 9	TSC1	135787874			0	TRANSLOCATION		0	306214	0	9	NEW_VARIANT
P-0041308-T02-IM6	RRBP1 (NM_004587) - BRAF (NM_004333) fusion: t(7;20)(q34;p12.1)(chr7:g.140485917::chr20:g.17634546)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RRBP1:BRAF}		0	0	49	20	Intron of RRBP1(-):5Kb after exon 3	RRBP1	17634546			7	Intron of BRAF(-):1Kb after exon 9	BRAF	140485917			10	TRANSLOCATION		0	320480	0	49	NEW_VARIANT
P-0041372-T01-IM6	HIVEP3 (NM_001127714) - BRD4 (NM_058243) rearrangement: t(1;19)(p34.2;p13.12)(chr1:g.41995508::chr19:g.15378399)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {HIVEP3:BRD4}		0	0	21	19	Intron of BRD4(-):37bp before exon 4	HIVEP3	15378399			1	Intron of HIVEP3(-):5Kb before exon 6	BRD4	41995508			0	TRANSLOCATION		0	306434	0	21	NEW_VARIANT
P-0041386-T01-IM6	TAP2 (NM_018833) rearrangement: c.1932+570:TAP2_chr6:g.27423075inv	IMPPRECISE	Note: The TAP2 rearrangement is an inversion of exon 12. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		244664	0	6	6	Intron of ZNF184(-):2Kb after exon 5	TAP2	27423075			6	Intron of TAP2(-):569bp after exon 11	TAP2	32796607			0	INVERSION		5373532	306534	408125	6	NEW_VARIANT
P-0041461-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1651:TMPRSS2_c.18+15743:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		29691	0	34	21	Intron of ERG(-):16Kb after exon 1	TMPRSS2	39854544			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868395			10	DELETION		3013851	306780	48976	35	NEW_VARIANT
P-0041464-T01-IM6	KMT2C (NM_170606) rearrangement: c.9453+372_c.10376del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 41 - 43. One of the breakpoints is within exon 43.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		6885	0	18	7	Exon 43 of KMT2C(-)	KMT2C	151860286			7	Intron of KMT2C(-):371bp after exon 40	KMT2C	151867977			10	DELETION		7691	306789	3882	19	NEW_VARIANT
P-0041472-T01-IM6	URI1 (NM_003796) - KMT2B (NM_014727) rearrangement: c.118-14115:URI1_c.2457+43:KMT2Bdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {URI1:KMT2B}		36615	0	99	19	Intron of URI1(+):14Kb before exon 2	URI1	30447985			19	Intron of KMT2B(+):43bp after exon 3	KMT2B	36212749			10	DELETION		5764764	306814	30249	109	NEW_VARIANT
P-0041602-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+4147:TMPRSS2_c.39+6989:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 4 - 11 and involves the ERG non-canonical transcript (NM_004449).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		75837	0	87	21	Intron of ERG(-):7Kb after exon 3	TMPRSS2	39940597			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875730			10	DELETION		2935133	307053	87930	88	NEW_VARIANT
P-0041616-T01-IM6	ERI3 (NM_024066) - PARP1 (NM_001618) rearrangement: c.931+10191:ERI3_c.3021:PARP1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERI3:PARP1}		600465	0	20	1	Intron of ERI3(-):10Kb after exon 7	ERI3	44703420			1	Exon 23 of PARP1(-)	PARP1	226549185			10	DUPLICATION		181845765	307104	687118	21	NEW_VARIANT
P-0041698-T01-IM6	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.337-2647:RAB11FIP4_c.7402:NF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RAB11FIP4:NF1}		11370	0	7	17	Exon 50 of NF1(+)	RAB11FIP4	29677281			17	Intron of RAB11FIP4(+):3Kb before exon 4	NF1	29842022			10	DUPLICATION		164741	307291	13747	7	NEW_VARIANT
P-0041702-T01-IM6	RGS11 (NM_183337) - AXIN1 (NM_003502) rearrangement: c.506+22:RGS11_c.2192:AXIN1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RGS11:AXIN1}		6603	0	5	16	Intron of RGS11(-):21bp after exon 7	RGS11	323738			16	Exon 9 of AXIN1(-)	AXIN1	341292			0	DUPLICATION		17554	307287	7237	5	NEW_VARIANT
P-0041957-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+1817:TMPRSS2_chr21:g.39964163del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		100608	0	32	21	3-UTR of ERG(-):70Kb after coding stop	TMPRSS2	39964163			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42878060			10	DELETION		2913897	307755	71399	32	NEW_VARIANT
P-0042018-T01-IM6	SMAD4 (NM_005359) rearrangement: c.454+193_c.956-2252del	PRECISE	Note: The SMAD4 rearrangement is an intragenic deletion of exons 5 - 8.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : in frame		4391	0	9	18	Intron of SMAD4(+):193bp after exon 4	SMAD4	48575887			18	Intron of SMAD4(+):2Kb before exon 9	SMAD4	48589541			8	DELETION		13654	308068	2319	8	NEW_VARIANT
P-0042082-T01-IM6	PREX2 (NM_024870) rearrangement: c.3421+2_c.3440del	PRECISE	Note: The PREX2 rearrangement is an intragenic deletion of exon 28. One of the breakpoints is within exon 28. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		939	0	2	8	Intron of PREX2(+):2bp after exon 27	PREX2	69030881			8	Exon 28 of PREX2(+)	PREX2	69031685			5	DELETION		804	308260	299	2	NEW_VARIANT
P-0042270-T01-IM6	ANKRD36 (NM_001164315) - NTRK1 (NM_002529) fusion: t(1;2)(q23.1;q11.2)(chr1:g.156844593::chr2:g.97835462)	PRECISE	Note: The ANKRD36 - NTRK1 fusion involves ANKRD36 exons 1 - 22 and NTRK1 exons 11 - 17. The fusion includes the kinase domain of NTRK1.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {ANKRD36:NTRK1}		0	0	5	2	Intron of ANKRD36(+):2Kb after exon 22	ANKRD36	97835462			1	Intron of NTRK1(+):104bp before exon 11	NTRK1	156844593			10	TRANSLOCATION		0	309604	0	6	NEW_VARIANT
P-0042342-T01-IM6	XPO1 (NM_003400) - USP34 (NM_014709) rearrangement: c.3069+76:XPO1_c.3013+938:USP34del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {XPO1:USP34}		1076	0	5	2	Intron of USP34(-):937bp after exon 21	XPO1	61551572			2	Intron of XPO1(-):75bp after exon 24	USP34	61708244			10	DELETION		156672	309685	1651	5	NEW_VARIANT
P-0042610-T01-IM6	CBFB (NM_022845) - CDH3 (NM_001793) rearrangement: c.4:CBFB_c.45+57:CDH3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		29314	0	2	16	Exon 1 of CBFB(+)	CBFB	67063310			16	Intron of CDH3(+):57bp after exon 1	CDH3	68679384			10	INVERSION		1616074	310882	39545	4	NEW_VARIANT
P-0042696-T01-IM6	CDH1 (NM_004360) rearrangement: c.1138-504_c.2164+44dup	PRECISE	Note: The CDH1 rearrangement is an intragenic duplication of exons 9 - 13. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 5 exons : out of frame		10259	0	8	16	Intron of CDH1(+):503bp before exon 9	CDH1	68846712			16	Intron of CDH1(+):44bp after exon 13	CDH1	68857573			10	DUPLICATION		10861	311147	12001	8	NEW_VARIANT
P-0042814-T01-IM6	NF2 (NM_000268) rearrangement: c.114+3348_c.675+206dup	PRECISE	Note: The NF2 rearrangement is an intragenic duplication of exons 2 - 7. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 6 exons : in frame		7155	0	21	22	Intron of NF2(+):3Kb after exon 1	NF2	30003449			22	Intron of NF2(+):206bp after exon 7	NF2	30054459			10	DUPLICATION		51010	311443	10859	22	NEW_VARIANT
P-0042971-T01-IM6	PTEN (NM_000314) rearrangement: c.14:PTEN_chr10:g.9509369inv	PRECISE	Note: The PTEN rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		223217	0	5	10	IGR: 192Kb before LINC00709(+)	PTEN	9509369			10	Exon 1 of PTEN(+)	PTEN	89624240			10	INVERSION		80114871	311830	149111	5	NEW_VARIANT
P-0042971-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-4095:TMPRSS2_chr21:g.40014900del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		71898	0	86	21	3-UTR of ERG(-):19Kb after coding stop	TMPRSS2	40014900			21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2	42874211			10	DELETION		2859311	311829	55833	91	NEW_VARIANT
P-0042974-T01-IM6	NOTCH3 (NM_000435) rearrangement: t(1;19)(p31.1;p13.12)(chr1:g.81334562::chr19:g.15296585)	PRECISE	Note: The NOTCH3 rearrangement is a translocation with a breakpoint in intron 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	17	19	Intron of NOTCH3(-):95bp before exon 13	NOTCH3	15296585			1	IGR: 228Kb before LOC101927412(+)	NOTCH3	81334562			10	TRANSLOCATION		0	311810	0	17	NEW_VARIANT
P-0042986-T01-IM6	DOT1L (NM_032482) rearrangement: t(8;19)(p23.2;p13.3)(chr8:g.3679668::chr19:g.2229723)	PRECISE	Note: The DOT1L rearrangement is a translocation with a breakpoint in intron 27. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	105	19	Intron of DOT1L(+):60bp before exon 28	DOT1L	2229723			8	Intron of CSMD1(-):68Kb before exon 6	DOT1L	3679668			10	TRANSLOCATION		0	312922	0	113	NEW_VARIANT
P-0042986-T01-IM6	BAP1 (NM_004656) rearrangement: c.1117-130:BAP1_chr3:g.52253450dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Transcript Fusion {TLR9:BAP1}		14318	0	23	3	Promoter of TLR9(-):2Kb from tx start	BAP1	52253450			3	Intron of BAP1(-):130bp before exon 12	BAP1	52438732			10	DUPLICATION		185282	312919	12892	23	NEW_VARIANT
P-0042986-T01-IM6	INPP4B (NM_001101669) rearrangement: c.2176_c.2277-1036del	PRECISE	Note: The INPP4B rearrangement is an intragenic deletion of exon 22. One of the breakpoints is within exon 22.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		840	0	24	4	Intron of INPP4B(-):1Kb before exon 23	INPP4B	143030379			4	Exon 22 of INPP4B(-)	INPP4B	143033795			10	DELETION		3416	312917	267	26	NEW_VARIANT
P-0043158-T01-IM6	TP53 (NM_000546) rearrangement: c.993+21:TP53_chr17:g.1926474inv	PRECISE	Note: The TP53 rearrangement is an inversion of exons 10 - 11. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		24135	0	59	17	Intron of RTN4RL1(-):2Kb after exon 1	TP53	1926474			17	Intron of TP53(-):20bp after exon 9	TP53	7576832			10	INVERSION		5650358	313417	17572	70	NEW_VARIANT
P-0043159-T01-IM6	VTCN1 (NM_024626) rearrangement: c.510_c.724+2536del	PRECISE	Note: The VTCN1 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2045	0	10	1	Intron of VTCN1(-):3Kb after exon 4	VTCN1	117693177			1	Exon 4 of VTCN1(-)	VTCN1	117695927			8	DELETION		2750	313418	2164	10	NEW_VARIANT
P-0043489-T01-IM6	BRIP1 (NM_032043) rearrangement: t(17;20)(q23.2;q13.31)(chr17:g.59886002::chr20:g.55040117)	PRECISE	Note: The BRIP1 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	88	20	IGR: 4Kb before RTFDC1(+)	BRIP1	55040117			17	Exon 7 of BRIP1(-)	BRIP1	59886002			10	TRANSLOCATION		0	314463	0	90	NEW_VARIANT
P-0043489-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.126+1361:TMPRSS2_c.18+110:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		28046	0	66	21	Intron of ERG(-):109bp after exon 1	TMPRSS2	39870177			21	Intron of TMPRSS2(-):1Kb after exon 2	ERG	42868685			10	DELETION		2998508	314462	26188	70	NEW_VARIANT
P-0043532-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.1855+93_c.2242+1298del	PRECISE	Note: The WHSC1L1 rearrangement is an intragenic deletion of exons 10 - 12. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		3084	0	16	8	Intron of WHSC1L1(-):1Kb after exon 12	WHSC1L1	38170867			8	Intron of WHSC1L1(-):92bp after exon 9	WHSC1L1	38176320			10	DELETION		5453	314917	4930	19	NEW_VARIANT
P-0043587-T01-IM6	CREBBP (NM_004380) rearrangement: c.4395-17_c.4728+335dup	PRECISE	Note: The CREBBP rearrangement is an intragenic duplication of exons 27 - 28. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		3283	0	35	16	Intron of CREBBP(-):334bp after exon 28	CREBBP	3785702			16	Intron of CREBBP(-):17bp before exon 27	CREBBP	3786833			10	DUPLICATION		1131	318762	5398	40	NEW_VARIANT
P-0043587-T01-IM6	NF1 (NM_001042492) rearrangement: c.61-29266_c.288+96dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 2 - 3. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		1460	0	8	17	Intron of NF1(+):29Kb before exon 2	NF1	29453735			17	Intron of NF1(+):96bp after exon 3	NF1	29486207			10	DUPLICATION		32472	318763	1558	8	NEW_VARIANT
P-0043591-T01-IM6	ARID1B (NM_020732) rearrangement: c.3112:ARID1B_chr6:g.119442122del	PRECISE	Note: The ARID1B rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	-		123141	0	26	6	5-UTR of FAM184A(-):161Kb before coding start	ARID1B	119442122			6	Exon 11 of ARID1B(+)	ARID1B	157495228			10	DELETION		38053106	315064	201443	28	NEW_VARIANT
P-0043789-T01-IM6	NF1 (NM_001042492) rearrangement: c.61-8307_c.2251+56dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 2 - 18. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 17 exons : out of frame		15801	0	48	17	Intron of NF1(+):8Kb before exon 2	NF1	29474694			17	Intron of NF1(+):56bp after exon 18	NF1	29553758			10	DUPLICATION		79064	316303	25203	72	NEW_VARIANT
P-0043789-T01-IM6	EP300 (NM_001429) rearrangement: c.730-1474_c.5798dup	PRECISE	Note: The EP300 rearrangement is an intragenic duplication of exons 3 - 31. One of the breakpoints is within exon 31. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		42535	0	3	22	Intron of EP300(+):1Kb before exon 3	EP300	41520394			22	Exon 31 of EP300(+)	EP300	41573513			7	DUPLICATION		53119	316304	54584	3	NEW_VARIANT
P-0043929-T01-IM6	ERF (NM_006494) - DNAJC4 (NM_005528) rearrangement: t(11;19)(q13.1;q13.2)(chr11:g.64001339::chr19:g.42752786)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ERF:DNAJC4}		0	0	54	19	Exon 4 of ERF(-)	ERF	42752786			11	Intron of DNAJC4(+):26bp before exon 6	DNAJC4	64001339			10	TRANSLOCATION		0	316653	0	65	NEW_VARIANT
P-0043935-T01-IM6	PIK3R1 (NM_181523) rearrangement: c.916+5568_c.1379del	PRECISE	Note: The PIK3R1 rearrangement is an intragenic deletion of exons 8 - 11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2753	0	27	5	Intron of PIK3R1(+):6Kb after exon 7	PIK3R1	67582402			5	Exon 11 of PIK3R1(+)	PIK3R1	67589616			10	DELETION		7214	316978	2963	27	NEW_VARIANT
P-0044150-T01-IM6	CACNA1A (NM_001127222) - CARM1 (NM_199141) rearrangement: c.5732-2757:CACNA1A_c.49:CARM1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CACNA1A:CARM1}		126088	0	22	19	Exon 1 of CARM1(+)	CACNA1A	10982427			19	Intron of CACNA1A(-):3Kb before exon 39	CARM1	13328179			10	INVERSION		2345752	318132	99840	30	NEW_VARIANT
P-0044204-T01-IM6	WHSC1 (NM_001042424) rearrangement: t(1;4)(q21.3;p16.3)(chr1:g.153840676::chr4:g.1978453)	PRECISE	Note: The WHSC1 rearrangement is a translocation with a breakpoint in intron 21. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {WHSC1:GATAD2B}		0	0	6	4	Intron of WHSC1(+):47bp after exon 21	WHSC1	1978453			1	5-UTR of GATAD2B(-):58Kb before coding start	WHSC1	153840676			8	TRANSLOCATION		0	318304	0	6	NEW_VARIANT
P-0044288-T01-IM6	TMPRSS2 (NM_001135099) - MPP5 (NM_022474) rearrangement: t(14;21)(q23.3;q22.3)(chr14:g.67791033::chr21:g.42869498)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TMPRSS2:MPP5}		0	0	201	21	Intron of TMPRSS2(-):547bp after exon 2	TMPRSS2	42869498			14	Intron of MPP5(+):504bp after exon 14	MPP5	67791033			10	TRANSLOCATION		0	318774	0	251	NEW_VARIANT
P-0044288-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4464:TMPRSS2_c.18+3461:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		60146	0	132	21	Intron of ERG(-):3Kb after exon 1	TMPRSS2	39866826			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875413			10	DELETION		3008587	318772	119414	141	NEW_VARIANT
P-0044305-T01-IM6	DOT1L (NM_032482) rearrangement: c.4068_c.4606+865del	PRECISE	Note: The DOT1L rearrangement is an intragenic deletion of exon 27. One of the breakpoints is within exon 27. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3846	0	37	19	Exon 27 of DOT1L(+)	DOT1L	2226588			19	Intron of DOT1L(+):865bp after exon 27	DOT1L	2227991			10	DELETION		1403	319027	3772	40	NEW_VARIANT
P-0044465-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783638::chr6:g.117646909)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	81	6	Intron of ROS1(-):477bp after exon 33	CD74	117646909			5	Intron of CD74(-):604bp after exon 6	ROS1	149783638			10	TRANSLOCATION		0	319260	0	81	NEW_VARIANT
P-0044659-T01-IM6	FAM172A (NM_032042) - NPM1 (NM_002520) rearrangement: c.1109-62102:FAM172A_c.525:NPM1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FAM172A:NPM1}		223376	0	2	5	Intron of FAM172A(-):62Kb before exon 9	FAM172A	93018937			5	Exon 7 of NPM1(+)	NPM1	170827157			9	INVERSION		77808220	320336	259789	2	NEW_VARIANT
P-0044905-T01-IM6	TSC2 (NM_000548) - HAGH (NM_005326) rearrangement: c.2742+122:TSC2_c.76+165:HAGHinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {TSC2:HAGH}		57788	0	3	16	Intron of HAGH(-):164bp after exon 1	TSC2	1876548			16	Intron of TSC2(+):122bp after exon 24	HAGH	2126293			10	INVERSION		249745	320884	95111	3	NEW_VARIANT
P-0044905-T01-IM6	RAB11FIP4 (NM_032932) - NF1 (NM_001042492) rearrangement: c.159+10486:RAB11FIP4_c.4286:NF1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RAB11FIP4:NF1}		28655	0	6	17	Exon 32 of NF1(+)	RAB11FIP4	29585474			17	Intron of RAB11FIP4(+):10Kb after exon 1	NF1	29729515			10	DUPLICATION		144041	320883	50557	15	NEW_VARIANT
P-0044999-T01-IM6	IDUA (NM_000203) - LATS1 (NM_004690) rearrangement: t(4;6)(p16.3;q25.1)(chr4:g.981090::chr6:g.149983308)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {IDUA:LATS1}		0	0	22	6	Exon 8 of LATS1(-)	IDUA	149983308			4	Intron of IDUA(+):60bp after exon 1	LATS1	981090			10	TRANSLOCATION		0	321142	0	22	NEW_VARIANT
P-0045222-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2243-30:EML4_c.3172+839:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		107271	0	24	2	Intron of ALK(-):838bp after exon 19	EML4	29447488			2	Intron of EML4(+):29bp before exon 20	ALK	42553264			10	INVERSION		13105776	322006	94276	24	NEW_VARIANT
P-0047119-T01-IM6	CDK12 (NM_016507) rearrangement: c.682:CDK12_chr17:g.37554870del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		4115	0	24	17	Intron of FBXL20(-):3Kb after exon 1	CDK12	37554870			17	Exon 1 of CDK12(+)	CDK12	37619006			10	DELETION		64136	329506	5000	134	NEW_VARIANT
P-0048791-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-23334:ERG_c.56-1202:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		44279	0	7	21	Intron of ERG(-):23Kb before exon 2	ERG	39840878			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871318			10	INVERSION		3030440	334228	16298	11	NEW_VARIANT
P-0000505-T02-IM6	FOXA1 (NM_004496) Rearrangement : c.700:FOXA1_chr14:g.40011548dup	IMPPRECISE	Note: The FOXA1 Rearrangement results in the duplication of exon2 of FOXA1. One of the breakpoints is within exon2. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		9133	0	98	14	Exon 2 of FOXA1(-)	FOXA1	38061289			14	IGR: 146Kb before FBXO33(-)	FOXA1	40011548			0	DUPLICATION		1950259	276705	17359	103	NEW_VARIANT
P-0008099-T01-IM5	KDM5A (NM_001042603) rearrangement : c.4455+404_4798inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		4495	0	42	12	Exon 27 of KDM5A(-)	KDM5A	401993			12	Intron of KDM5A(-): 404bp after exon 26	KDM5A	404335			60	INVERSION		2342	120334	5319	40	NEW_VARIANT
P-0008404-T02-IM5	MSH2 (NM_00025) rearrangement: c.1387-6599_c.1511-124del	PRECISE	Note: The MSH2 (NM_00025) rearrangement is an intragenic deletion of exon9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		2706	0	13	2	Intron of MSH2(+): 7Kb before exon 9	MSH2	47683571			2	Intron of MSH2(+): 124bp before exon 10	MSH2	47693673			21	DELETION		10102	130425	1485	11	NEW_VARIANT
P-0021532-T01-IM6	ALK (NM_004304) rearrangement c.2432_c.2356-1311del	PRECISE	Note: The ALK rearrangement is an intragenic deletion of exon 14. One of the breakpoints is within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1206	0	31	2	Exon 14 of ALK(-)	ALK	29456486			2	Intron of ALK(-):1Kb before exon 14	1311del	29457873			10	DELETION		1387	187633	1246	31	NEW_VARIANT
P-0022097-T02-IM6	CIC (NM_015125) Rearrangement: c.1606:CIC_chr19:g.42738021del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	-		44149	0	5	19	Intron of GSK3A(-):483bp after exon 6	CIC	42738021			19	Exon 10 of CIC(+)	CIC	42794526			0	DELETION		56505	229932	53862	5	NEW_VARIANT
P-0030121-T01-IM6	RASA1 (NM_002890) rearrangement: c.426_c.540-27225del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2467	0	17	5	Exon 1 of RASA1(+)	RASA1	86564694			5	Intron of RASA1(+):27Kb before exon 2	RASA1	86599940			10	DELETION		35246	224468	3126	17	NEW_VARIANT
P-0032256-T01-IM6	OXCT1 (NM_00043) - MAP3K1 (NM_005921) Rearrangement : c.415-379:OXCT1_c.3998:MAP3K1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {OXCT1:MAP3K1}		22811	0	33	5	Intron of OXCT1(-):379bp before exon 5	OXCT1	41850660			5	Exon 17 of MAP3K1(+)	MAP3K1	56181774			10	INVERSION		14331114	232459	15589	37	NEW_VARIANT
P-0035825-T01-IM6	TP53 (NM_000546) Rearrangement : t(11,17)(p11.2,p13.1)(chr11:g.48110744::chr17:g.7578421)	PRECISE	Note: The TP53 Rearrangement is a translocation event with a breakpoint in exon5. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		0	0	47	17	Exon 5 of TP53(-)	TP53	7578421			11	Intron of PTPRJ(+):21Kb before exon 2	TP53	48110744			10	TRANSLOCATION		0	261855	0	48	NEW_VARIANT
P-0036092-T01-IM6	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	PRECISE	Note: The KIF5B - RET fusion is predicted to be in frame and includes the kinase domain of RET.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		55373	1	181	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32316218			10	Intron of RET(+):229bp after exon 11	RET	43610413			10	INVERSION		11294195	269240	34843	225	NEW_VARIANT
P-0036826-T01-IM6	AURKA (NM_003600) - FAM114A2 (NM_018691) rearrangement: t(5;20)(q33.2;q13.2)(chr5:g.153381607::chr20:g.54945351)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {AURKA:FAM114A2}		0	0	16	20	Exon 9 of AURKA(-)	AURKA	54945351			5	Intron of FAM114A2(-):203bp after exon 11	FAM114A2	153381607			10	TRANSLOCATION		0	273315	0	18	NEW_VARIANT
P-0036826-T01-IM6	TMPRSS2 (NM_001135099) - ZCCHC6 (NM_024617) rearrangement: t(9;21)(q21.33;q22.3)(chr9:g.88940236::chr21:g.42869032)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	17	21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42869032			9	Intron of ZCCHC6(-):12bp after exon 12	ZCCHC6	88940236			10	TRANSLOCATION		0	273316	0	21	NEW_VARIANT
P-0037021-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+1323:TMPRSS2_chr21:g.43538595del	PRECISE	Note: The TMPRSS2 rearrangement results in the deletion of exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		74913	0	30	21	Intron of TMPRSS2(-):1Kb after exon 2	TMPRSS2	42868723			21	Intron of UMODL1(+):625bp before exon 15	TMPRSS2	43538595			10	DELETION		669872	275625	75787	31	NEW_VARIANT
P-0037151-T01-IM6	MAPK3 (NM_002746) Rearrangement : c.354-685_c.907+9dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : out of frame		4645	0	3	16	Intron of MAPK3(-):8bp after exon 6	MAPK3	30128466			16	Intron of MAPK3(-):685bp before exon 3	MAPK3	30130544			3	DUPLICATION		2078	276589	5590	3	NEW_VARIANT
P-0037151-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (TMPRSS2 exon1 with ERG exon2): c.55+3777:TMPRSS2_c.40-18163::ERGdel	PRECISE	Note: The TMPRSS2-ERG Fusion includes the non-canaonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		57361	0	56	21	Intron of ERG(-):18Kb before exon 2	TMPRSS2	39835707			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42876100			10	DELETION		3040393	276587	52755	62	NEW_VARIANT
P-0037171-T01-IM6	ABL1 (NM_005157) rearrangement: c.914:ABL1_chr9:g.133517056inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		9459	0	15	9	IGR: 15Kb before MIR6856(+)	ABL1	133517056			9	Exon 6 of ABL1(+)	ABL1	133748253			10	INVERSION		231197	276740	14704	19	NEW_VARIANT
P-0037177-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1678:TMPRSS2_c.19-9161:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is predicted to be in-frame and involves TMPRSS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		53807	0	56	21	Intron of ERG(-):9Kb before exon 2	TMPRSS2	39826705			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42871794			10	DELETION		3045089	276847	27932	57	NEW_VARIANT
P-0037198-T01-IM6	PARP1 (NM_001618) - NVL (NM_002533) rearrangement: c.1941+185:PARP1_c.1180+599:NVLdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PARP1:NVL}		17644	0	12	1	Intron of NVL(-):598bp after exon 9	PARP1	224483604			1	Intron of PARP1(-):184bp after exon 13	NVL	226564624			10	DELETION		2081020	276863	26940	13	NEW_VARIANT
P-0037198-T01-IM6	UPF1 (NM_002911) - ATAT1 (NM_001031722) rearrangement: t(6;19)(p21.33;p13.11)(chr6:g.30606726::chr19:g.18971862)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {UPF1:ATAT1}		0	0	61	19	Intron of UPF1(+):71bp after exon 17	UPF1	18971862			6	Intron of ATAT1(+):1Kb before exon 7	ATAT1	30606726			10	TRANSLOCATION		0	276867	0	68	NEW_VARIANT
P-0037268-T01-IM6	RET (NM_020975) rearrangement: c.338-29_chr10:g.43148631del	PRECISE	Note: The RET rearrangement is a deletion that includes RET exons 1-2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4565	0	9	10	IGR: 20Kb before LINC01518(-)	RET	43148631			10	Intron of RET(+):28bp before exon 3	RET	43597761			9	DELETION		449130	277275	4231	9	NEW_VARIANT
P-0037268-T01-IM6	RASA1 (NM_002890) rearrangement: chr5:g.86060945_c.1809del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		20834	0	66	5	IGR: 18Kb before LOC100505878(+)	RASA1	86060945			5	Exon 14 of RASA1(+)	RASA1	86670012			10	DELETION		609067	277274	11669	69	NEW_VARIANT
P-0037373-T01-IM6	MTOR (NM_004958) - KAZN (NM_201628) rearrangement: c.4253+84:MTOR_c.419-17412:KAZNinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {MTOR:KAZN}		41756	0	6	1	Intron of MTOR(-):83bp after exon 28	MTOR	11259231			1	Intron of KAZN(+):17Kb before exon 3	KAZN	15343833			0	INVERSION		4084602	278525	41895	6	NEW_VARIANT
P-0037373-T01-IM6	PPP1R18 (NM_001134870) - MDC1 (NM_014641) rearrangement: c.1611+927:PPP1R18_c.3830:MDC1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PPP1R18:MDC1}		19671	1	80	6	Intron of PPP1R18(-):926bp after exon 2	PPP1R18	30651258			6	Exon 10 of MDC1(-)	MDC1	30673130			10	DUPLICATION		21872	278523	58911	88	NEW_VARIANT
P-0037375-T01-IM6	BRCA2 (NM_000059) rearrangement: c.67+800_c.2040del	PRECISE	Note: The BRCA2 rearrangement is an intragenic deletion of exons 3-11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11401	0	37	13	Intron of BRCA2(+):800bp after exon 2	BRCA2	32891464			13	Exon 11 of BRCA2(+)	BRCA2	32910532			10	DELETION		19068	278508	9052	40	NEW_VARIANT
P-0037529-T01-IM6	BCL2L1 (NM_138578) rearrangement: c.374_c.565-15091:inv	PRECISE	Note: The BCL2L1 rearrangement is an intragenic deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to3	3to3	-		4760	0	114	20	Intron of BCL2L1(-):15Kb before exon 3	BCL2L1	30268980			20	Exon 2 of BCL2L1(-)	BCL2L1	30309648			10	INVERSION		40668	279839	5844	114	NEW_VARIANT
P-0037751-T01-IM6	TMPRSS2 (NM_001135099) - ERG(NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon 4 - 10) : c.56-2526:TMPRSS2_c.39+6198:ERG del	PRECISE	Note:The TMPRSS2-ERG Fusion includes the non-canonical transcript of ERG.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		83269	1	113	21	Intron of ERG(-):6Kb after exon 3	TMPRSS2	39941388			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872642			10	DELETION		2931254	281929	60109	163	NEW_VARIANT
P-0037751-T01-IM6	ST7 (NM_021908) - MET (NM_000245) Rearrangement: c.235-3291:ST7_c.2347:METdel	PRECISE	Note: The ST7 - MET rearrangement is a duplication of ST7 exons 3-16 and MET exons 10-21. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ST7:MET}		57740	0	51	7	Exon 10 of MET(+)	ST7	116399527			7	Intron of ST7(+):3Kb before exon 3	MET	116756324			10	DUPLICATION		356797	281931	102002	52	NEW_VARIANT
P-0039513-T01-IM6	WHSC1 (NM_001042424) - WASF3 (NM_006646) rearrangement: t(4;13)(p16.3;q12.13)(chr4:g.1941497::chr13:g.27230973)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {WHSC1:WASF3}		0	0	13	13	Intron of WASF3(+):8Kb before exon 4	WHSC1	27230973			4	Exon 9 of WHSC1(+)	WASF3	1941497			10	TRANSLOCATION		0	296490	0	13	NEW_VARIANT
P-0039794-T01-IM6	EGFR (NM_005228) rearrangement: c.88+21179_c.890-376del	PRECISE	Note: The EGFR rearrangement is a vIII alteration.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		14484	0	19	7	Intron of EGFR(+):21Kb after exon 1	EGFR	55108237			7	Intron of EGFR(+):375bp before exon 8	EGFR	55223147			10	DELETION		114910	298247	17152	20	NEW_VARIANT
P-0039794-T01-IM6	KDM6A (NM_021140) rearrangement: c.384+16262_c.1476dup	PRECISE	Note: The KDM6A rearrangement is an intragenic duplication of exons 5 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		9028	0	25	X	Intron of KDM6A(+):16Kb after exon 4	KDM6A	44850222			X	Exon 15 of KDM6A(+)	KDM6A	44921942			10	DUPLICATION		71720	298256	15111	25	NEW_VARIANT
P-0039932-T01-IM6	CREBBP (NM_004380) rearrangement: t(16;19)(p13.3;p13.12)(chr16:g.3781315::chr19:g.15859804)	PRECISE	Note: The CREBBP rearrangement is a translocation with a breakpoint in exon 30. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	170	19	IGR: 8Kb before OR10H3(+)	CREBBP	15859804			16	Exon 30 of CREBBP(-)	CREBBP	3781315			10	TRANSLOCATION		0	298738	0	187	NEW_VARIANT
P-0040698-T01-IM6	PIK3R3 (NM_003629) - MEGF6 (NM_001409) rearrangement: c.949:PIK3R3_c.3223+61:MEGF6del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {PIK3R3:MEGF6}		591357	0	7	1	Intron of MEGF6(-):60bp after exon 25	PIK3R3	3415201			1	Exon 8 of PIK3R3(-)	MEGF6	46512290			0	DELETION		43097089	302775	529457	7	NEW_VARIANT
P-0040698-T01-IM6	MTOR (NM_004958) rearrangement: c.6381:MTOR_chr1:g.47367819inv	PRECISE	Note: The MTOR rearrangement is an inversion of exons 1 - 46. One of the breakpoints is within exon 46. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		543080	0	15	1	Exon 46 of MTOR(-)	MTOR	11186824			1	Promoter of CYP4Z2P(-):59Kb from tx start	MTOR	47367819			10	INVERSION		36180995	302776	486042	17	NEW_VARIANT
P-0040700-T01-IM6	ELF3 (NM_004433) rearrangement: c.427_c.1002-401inv	PRECISE	Note: The ELF3 rearrangement is an intragenic inversion of exons 4 - 8. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		10857	0	2	1	Exon 4 of ELF3(+)	ELF3	201981513			1	Intron of ELF3(+):400bp before exon 9	ELF3	201983936			10	INVERSION		2423	302764	7679	4	NEW_VARIANT
P-0040755-T01-IM6	NTRK1 (NM_002529) rearrangement: c.360-562:NTRK1_chr1:g.157625604del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		70715	0	118	1	Intron of NTRK1(+):561bp before exon 4	NTRK1	156836140			1	IGR: 22Kb before FCRL3(-)	NTRK1	157625604			10	DELETION		789464	303066	82533	206	NEW_VARIANT
P-0040755-T01-IM6	NF1 (NM_001042492) rearrangement: t(3;17)(q21.3;q11.2)(chr3:g.125890858::chr17:g.29664297)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 42 resulting in truncation of gene and corresponding intragenic deletion.	MANUAL_OK	5to3	5to3	-		0	0	41	17	Intron of NF1(+):88bp before exon 43	NF1	29664297			3	Intron of ALDH1L1(-):9Kb after exon 1	NF1	125890858			10	TRANSLOCATION		0	303068	0	41	NEW_VARIANT
P-0040783-T01-IM6	BRIP1 (NM_032043) rearrangement: c.1629-16:BRIP1_chr17:g.59757201inv	PRECISE	Note: The BRIP1 rearrangement is an inversion of exons 12 - 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		14735	0	9	17	3-UTR of BRIP1(-):3Kb after coding stop	BRIP1	59757201			17	Intron of BRIP1(-):16bp before exon 12	BRIP1	59858382			10	INVERSION		101181	303080	19402	9	NEW_VARIANT
P-0040854-T01-IM6	SLC25A21 (NM_030631) - FOXA1 (NM_004496) rearrangement: c.70+91433:SLC25A21_c.73-76:FOXA1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {SLC25A21:FOXA1}		13533	0	63	14	Intron of SLC25A21(-):91Kb after exon 1	SLC25A21	37550053			14	Intron of FOXA1(-):76bp before exon 2	FOXA1	38061992			10	DUPLICATION		511939	304023	24060	65	NEW_VARIANT
P-0041412-T01-IM6	CDK12 (NM_016507) rearrangement: c.2768+110_c.4004del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11737	0	7	17	Intron of CDK12(+):110bp after exon 8	CDK12	37667993			17	Exon 14 of CDK12(+)	CDK12	37687100			10	DELETION		19107	306538	13428	7	NEW_VARIANT
P-0041420-T01-IM6	MTUS2 (NM_001033602) - BRCA2 (NM_000059) rearrangement: c.2936-3366:MTUS2_c.8205:BRCA2del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MTUS2:BRCA2}		48478	0	25	13	Intron of MTUS2(+):3Kb before exon 6	MTUS2	29930033			13	Exon 18 of BRCA2(+)	BRCA2	32937544			10	DELETION		3007511	306548	89505	25	NEW_VARIANT
P-0041420-T01-IM6	ATR (NM_001184) rearrangement: c.4152+7_c.4154del	PRECISE	Note: The ATR rearrangement is an intragenic deletion of exon 23. One of the breakpoints is within exon 23.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		504	0	2	3	Exon 23 of ATR(-)	ATR	142241682			3	Intron of ATR(-):6bp after exon 22	ATR	142242828			7	DELETION		1146	306547	175	2	NEW_VARIANT
P-0041549-T01-IM6	NF1 (NM_001042492) rearrangement: c.587-126:NF1_chr17:g.7263421del	PRECISE	Note: The NF1 rearrangement is a deletion of exons 1 - 5.	MANUAL_OK	3to5	3to5	Transcript Fusion {TMEM95:NF1}		182931	0	8	17	Promoter of TMEM95(+):5Kb from tx start	NF1	7263421			17	Intron of NF1(+):125bp before exon 6	NF1	29508314			10	DELETION		22244893	307018	177713	12	NEW_VARIANT
P-0041549-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.127-606:TMPRSS2_c.18+16516:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 2 - 10. The fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25707	0	40	21	Intron of ERG(-):17Kb after exon 1	TMPRSS2	39853771			21	Intron of TMPRSS2(-):606bp before exon 3	ERG	42867111			10	DELETION		3013340	307019	13573	41	NEW_VARIANT
P-0041945-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.127-660:TMPRSS2_c.18+1836:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		21399	0	8	21	Intron of ERG(-):2Kb after exon 1	TMPRSS2	39868451			21	Intron of TMPRSS2(-):660bp before exon 3	ERG	42867165			10	DELETION		2998714	307726	23777	8	NEW_VARIANT
P-0042084-T01-IM6	FOXA1 (NM_004496) rearrangement: c.812:FOXA1_chr14:g.38056065del	PRECISE	Note: The FOXA1 rearrangement is a deletion of exon 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7771	0	8	14	Promoter of FOXA1(-):3Kb from tx start	FOXA1	38056065			14	Exon 2 of FOXA1(-)	FOXA1	38061177			10	DELETION		5112	308258	9150	12	NEW_VARIANT
P-0042310-T01-IM6	SMAD3 (NM_005902) rearrangement: c.1242:SMAD3_chr15:g.67506410del	PRECISE	Note: The SMAD3 rearrangement is a deletion of exon 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Antisense Fusion		677	0	79	15	Exon 9 of SMAD3(+)	SMAD3	67482838			15	Intron of AAGAB(-):5Kb before exon 6	SMAD3	67506410			10	DELETION		23572	309626	512	81	NEW_VARIANT
P-0042588-T01-IM6	ARID1A (NM_006015) rearrangement: t(1;15)(p36.11;q24.3)(chr1:g.27107174::chr15:g.78248444)	PRECISE	Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	46	15	IGR: 37Kb before LOC91450(-)	ARID1A	78248444			1	Exon 20 of ARID1A(+)	ARID1A	27107174			10	TRANSLOCATION		0	310823	0	50	NEW_VARIANT
P-0042656-T01-IM6	ERCC2 (NM_000400) rearrangement: c.1238-75:ERCC2_chr19:g.45903488del	PRECISE	Note: The ERCC2 rearrangement is a deletion of exons 1 - 12.	MANUAL_OK	3to5	3to5	Transcript Fusion {PPP1R13L:ERCC2}		15876	0	5	19	Intron of ERCC2(-):75bp before exon 13	ERCC2	45861032			19	5-UTR of PPP1R13L(-):20Kb before coding start	ERCC2	45903488			10	DELETION		42456	310945	25831	5	NEW_VARIANT
P-0042656-T01-IM6	EZH2 (NM_004456) rearrangement: c.857:EZH2_chr7:g.148415342del	PRECISE	Note: The EZH2 rearrangement is a deletion of exons 8 - 20. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Antisense Fusion		5026	0	21	7	5-UTR of CUL1(+):12Kb before coding start	EZH2	148415342			7	Exon 8 of EZH2(-)	EZH2	148523596			10	DELETION		108254	310944	14545	21	NEW_VARIANT
P-0042823-T01-IM6	MSI2 (NM_138962) rearrangement: t(2;17)(p11.2;q22)(chr2:g.83485930::chr17:g.55339568)	PRECISE	Note: The MSI2 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	5	17	Intron of MSI2(+):15bp after exon 5	MSI2	55339568			2	IGR: 402Kb before LOC1720(+)	MSI2	83485930			10	TRANSLOCATION		0	313101	0	5	NEW_VARIANT
P-0042965-T01-IM6	TPR (NM_003292) - NTRK1 (NM_002529) fusion: c.2776+531:TPR_c.1129:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {TPR:NTRK1}		135870	0	101	1	Exon 8 of NTRK1(+)	TPR	156843703			1	Intron of TPR(-):530bp after exon 21	NTRK1	186318824			10	INVERSION		29475121	311818	129900	127	NEW_VARIANT
P-0043039-T01-IM6	RNF43 (NM_017763) rearrangement: c.655_c.688-139del	PRECISE	Note: The RNF43 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		793	0	176	17	Intron of RNF43(-):139bp before exon 7	RNF43	56438444			17	Exon 6 of RNF43(-)	RNF43	56439937			10	DELETION		1493	313118	333	195	NEW_VARIANT
P-0043160-T01-IM6	RCBTB2 (NM_001268) - RB1 (NM_000321) rearrangement: c.350-1065:RCBTB2_c.2137:RB1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {RCBTB2:RB1}		6729	0	46	13	Exon 21 of RB1(+)	RCBTB2	49037897			13	Intron of RCBTB2(-):1Kb before exon 7	RB1	49088096			10	INVERSION		50199	313411	3821	53	NEW_VARIANT
P-0043201-T01-IM6	MAP3K13 (NM_004721) rearrangement: c.451_c.475+3909inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		456	0	16	3	Exon 2 of MAP3K13(+)	MAP3K13	185146820			3	Intron of MAP3K13(+):4Kb after exon 2	MAP3K13	185150753			10	INVERSION		3933	313564	738	18	NEW_VARIANT
P-0043233-T01-IM6	MDC1 (NM_014641) rearrangement: c.3798:MDC1_chr6:g.30704580inv	PRECISE	Note: The MDC1 rearrangement is an inversion of exons 1 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		35768	0	6	6	Exon 10 of MDC1(-)	MDC1	30673162			6	Intron of FLOT1(-):3Kb after exon 8	MDC1	30704580			10	INVERSION		31418	313679	57527	17	NEW_VARIANT
P-0043237-T01-IM6	PGR (NM_000926) rearrangement: c.2730:PGR_chr11:g.100908756inv	PRECISE	Note: The PGR rearrangement is an inversion of exon 8. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		420	0	2	11	3-UTR of PGR(-):1Kb after coding stop	PGR	100908756			11	Exon 8 of PGR(-)	PGR	100909919			5	INVERSION		1163	313688	186	2	NEW_VARIANT
P-0043415-T01-IM6	KMT2A (NM_001197104) rearrangement: c.11441:KMT2A_chr11:g.116498477del	PRECISE	Note: The KMT2A rearrangement is a deletion of exons 1 - 34. One of the breakpoints is within exon 34.	MANUAL_OK	3to5	3to5	-		60525	0	91	11	IGR: 120Kb before BUD13(-)	KMT2A	116498477			11	Exon 34 of KMT2A(+)	KMT2A	118391528			10	DELETION		1893051	314125	72274	97	NEW_VARIANT
P-0043727-T01-IM6	CSDE1 (NM_001242891) - FAM46C (NM_017709) rearrangement: c.976-217:CSDE1_c.710:FAM46Cdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		24713	0	40	1	Intron of CSDE1(-):217bp before exon 11	CSDE1	115275654			1	Exon 2 of FAM46C(+)	FAM46C	118166200			10	DELETION		2890546	315391	39647	42	NEW_VARIANT
P-0043904-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-113:TMPRSS2_c.236+10174:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		37324	0	8	21	Intron of ERG(-):10Kb after exon 2	TMPRSS2	39807153			21	Intron of TMPRSS2(-):113bp before exon 2	ERG	42870229			0	DELETION		3063076	316745	34025	8	NEW_VARIANT
P-0043950-T01-IM6	UPF1 (NM_002911) rearrangement: c.2182+204_c.2857+108inv	PRECISE	Note: The UPF1 rearrangement is an intragenic inversion of exons 16 - 20. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		8118	0	13	19	Intron of UPF1(+):204bp after exon 15	UPF1	18968546			19	Intron of UPF1(+):108bp after exon 20	UPF1	18975168			10	INVERSION		6622	317254	9395	11	NEW_VARIANT
P-0044025-T01-IM6	NCOR1 (NM_006311) rearrangement: c.2690+1303_c.3671-1del	PRECISE	Note: The NCOR1 rearrangement is an intragenic deletion of exons 21 - 27.	MANUAL_OK	3to5	3to5	Deletion of 7 exons : out of frame		6825	0	29	17	Intron of NCOR1(-):1bp before exon 28	NCOR1	15976884			17	Intron of NCOR1(-):1Kb after exon 20	NCOR1	16003261			10	DELETION		26377	317332	7533	28	NEW_VARIANT
P-0044084-T01-IM6	PAK1 (NM_002576) rearrangement: c.1116+20:PAK1_chr11:g.77030392del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript		7754	0	16	11	Promoter of PAK1(-):3Kb from tx start	PAK1	77030392			11	Intron of PAK1(-):19bp after exon 11	PAK1	77051671			10	DELETION		21279	317389	11439	19	NEW_VARIANT
P-0044166-T01-IM6	PIK3CD (NM_005026) rearrangement: c.2718+22:PIK3CD_chr1:g.9744256dup	PRECISE	Note: The PIK3CD rearrangement is a duplication of exons 1 - 21. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript		43122	0	27	1	5-UTR of PIK3CD(+):26Kb before coding start	PIK3CD	9744256			1	Intron of PIK3CD(+):22bp after exon 21	PIK3CD	9784172			10	DUPLICATION		39916	318191	52450	29	NEW_VARIANT
P-0044166-T01-IM6	EIF4E (NM_001130678) - SHROOM3 (NM_020859) rearrangement: c.459+782:EIF4E_c.5623-561:SHROOM3inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {EIF4E:SHROOM3}		21191	0	6	4	Intron of SHROOM3(+):560bp before exon 11	EIF4E	77699401			4	Intron of EIF4E(-):781bp after exon 5	SHROOM3	99807448			0	INVERSION		22108047	318194	27919	8	NEW_VARIANT
P-0044224-T01-IM6	EPCAM (NM_002354) rearrangement: c.76+47:EPCAM_chr2:g.47615051del	PRECISE	Note: The EPCAM rearrangement is a deletion of exons 2 - 9.	MANUAL_OK	3to5	3to5	Deletion within transcript		9529	0	71	2	Intron of EPCAM(+):47bp after exon 1	EPCAM	47596767			2	Promoter of EPCAM(+):19Kb from tx start	EPCAM	47615051			10	DELETION		18284	318278	5999	79	NEW_VARIANT
P-0044224-T01-IM6	MSH2 (NM_000251) rearrangement: c.367-385_c.793-51del	IMPPRECISE	Note: The MSH2 rearrangement is an intragenic deletion of exons 3 - 4.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		4068	0	5	2	Intron of MSH2(+):384bp before exon 3	MSH2	47636848			2	Intron of MSH2(+):50bp before exon 5	MSH2	47641357			0	DELETION		4509	318279	2592	5	NEW_VARIANT
P-0044255-T01-IM6	NF1 (NM_001042492) rearrangement: c.1393-80_c.4577+42dup	PRECISE	Note: The NF1 rearrangement is an intragenic duplication of exons 13 - 34. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 22 exons : out of frame		22629	0	8	17	Intron of NF1(+):79bp before exon 13	NF1	29541389			17	Intron of NF1(+):42bp after exon 34	NF1	29587575			10	DUPLICATION		46186	318675	13142	12	NEW_VARIANT
P-0044255-T01-IM6	DNMT1 (NM_001379) rearrangement: c.105:DNMT1_chr19:g.8770811inv	PRECISE	Note: The DNMT1 rearrangement is an inversion of exons 2 - 40. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		61588	0	7	19	IGR: 37Kb before ACTL9(-)	DNMT1	8770811			19	Exon 2 of DNMT1(-)	DNMT1	10292729			7	INVERSION		1521918	318677	41012	8	NEW_VARIANT
P-0044255-T01-IM6	KDR (NM_002253) rearrangement: c.926_c.976+798inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		617	0	17	4	Intron of KDR(-):797bp after exon 7	KDR	55978673			4	Exon 7 of KDR(-)	KDR	55979521			10	INVERSION		848	318676	2340	17	NEW_VARIANT
P-0044325-T01-IM6	KMT2A (NM_001197104) rearrangement: c.3359:KMT2A_chr11:g.117628118del	PRECISE	Note: The KMT2A rearrangement is a deletion of exons 1 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	-		15231	0	55	11	Intron of DSCAML1(-):19Kb after exon 3	KMT2A	117628118			11	Exon 5 of KMT2A(+)	KMT2A	118348706			10	DELETION		720588	318794	25052	55	NEW_VARIANT
P-0044366-T01-IM6	FGFR2 (NM_000141) rearrangement: c.2301+1825:FGFR2_chr10:g.125122504del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		41527	0	14	10	Intron of FGFR2(-):2Kb after exon 17	FGFR2	123241387			10	IGR: 209Kb before BUB3(+)	FGFR2	125122504			10	DELETION		1881117	318828	65349	15	NEW_VARIANT
P-0044366-T01-IM6	RECQL4 (NM_004260) - CYHR1 (NM_138496) rearrangement: c.2885+16:RECQL4_c.247-3269:CYHR1del	PRECISE	Note: The RECQL4 - CYHR1 rearrangement is a deletion that results in a fusion of RECQL4 exons 1 - 17 to CYHR1 exons 3 - 5.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RECQL4:CYHR1}		8046	0	5	8	Intron of CYHR1(-):3Kb before exon 3	RECQL4	145682112			8	Intron of RECQL4(-):15bp after exon 17	CYHR1	145738009			7	DELETION		55897	318827	15700	5	NEW_VARIANT
P-0044600-T01-IM6	TET1 (NM_030625) rearrangement: c.1969-3454_c.5533dup	PRECISE	Note: The TET1 rearrangement is an intragenic duplication of exons 4 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		35000	0	33	10	Intron of TET1(+):3Kb before exon 4	TET1	70401001			10	Exon 12 of TET1(+)	TET1	70450693			10	DUPLICATION		49692	320201	38041	39	NEW_VARIANT
P-0044647-T01-IM6	NF1 (NM_001042492) rearrangement: c.480-1412_c.680inv	PRECISE	Note: The NF1 rearrangement is an intragenic inversion of exons 5 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		1760	0	7	17	Intron of NF1(+):1Kb before exon 5	NF1	29495497			17	Exon 7 of NF1(+)	NF1	29508753			10	INVERSION		13256	320313	313	6	NEW_VARIANT
P-0044647-T01-IM6	NF1 (NM_001042492) rearrangement: t(2;17)(p15;q11.2)(chr2:g.63115460::chr17:g.29546080)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 14. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	58	17	Exon 14 of NF1(+)	NF1	29546080			2	Intron of EHBP1(+):14Kb after exon 10	NF1	63115460			10	TRANSLOCATION		0	320314	0	58	NEW_VARIANT
P-0044784-T01-IM6	STAG2 (NM_001042749) rearrangement: c.1017+48_c.2265+79del	PRECISE	Note: The STAG2 rearrangement is an intragenic deletion of exons 12 - 23.	MANUAL_OK	3to5	3to5	Deletion of 12 exons : in frame		11882	0	4	X	Intron of STAG2(+):48bp after exon 11	STAG2	123184207			X	Intron of STAG2(+):79bp after exon 23	STAG2	123200365			5	DELETION		16158	320577	8647	4	NEW_VARIANT
P-0044856-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.783:TGFBR2_chr3:g.30808859del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		4708	0	8	3	Exon 5 of TGFBR2(+)	TGFBR2	30713383			3	Intron of GADL1(-):11Kb after exon 14	TGFBR2	30808859			7	DELETION		95476	320692	7977	8	NEW_VARIANT
P-0044955-T01-IM6	POLE (NM_006231) rearrangement: c.487:POLE_chr12:g.128462756inv	PRECISE	Note: The POLE rearrangement is an inversion of exons 6 - 49. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		94341	0	166	12	3-UTR of LINC00508(-):6Kb after coding stop	POLE	128462756			12	Exon 6 of POLE(-)	POLE	133256174			10	INVERSION		4793418	320981	96861	166	NEW_VARIANT
P-0045046-T01-IM6	STK11 (NM_000455) rearrangement: t(19;X)(p13.3;q28)(chr19:g.1207210::chrX:g.155259729)	IMPPRECISE	Note: The STK11 rearrangement is a translocation with a breakpoint in intron 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {STK11:DDX11L16}		0	0	28	X	Promoter of DDX11L16(-):4Kb from tx start	STK11	155259729			19	Intron of STK11(+):8bp after exon 1	STK11	1207210			0	TRANSLOCATION		0	321352	0	59	NEW_VARIANT
P-0045257-T02-IM6	PAX5 (NM_016734) rearrangement: c.475+126_c.604+11920del	PRECISE	Note: The PAX5 rearrangement is an intragenic deletion of exon 5.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1274	0	6	9	Intron of PAX5(-):12Kb after exon 5	PAX5	36990725			9	Intron of PAX5(-):125bp after exon 4	PAX5	37006344			8	DELETION		15619	324076	1001	6	NEW_VARIANT
P-0047286-T01-IM6	KMT2D (NM_003482) - ACSS3 (NM_024560) rearrangement: c.14539:KMT2D_c.780+1040:ACSS3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KMT2D:ACSS3}		320632	0	41	12	Exon 47 of KMT2D(-)	KMT2D	49421690			12	Intron of ACSS3(+):1Kb after exon 4	ACSS3	81534084			10	INVERSION		32112394	330273	966497	41	NEW_VARIANT
P-0014026-T01-IM5	APC(NM_000038) - REEP5(NM_005669)  rearrangement: c.4364:APC_c.352-7191:REEP5del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense fusion		47108	0	86	5	Exon 16 of APC(+)	APC	112175655			5	Intron of REEP5(-): 7Kb before exon 4	REEP5	112230071			103	DELETION		54416	163077	27367	84	NEW_VARIANT
P-0017479-T02-IM6	GRIN2A (NM_001134407) Rearrangement: c.2270_c.2357-2819dup	PRECISE	Note: The GRIN2A rearrangement is an intragenic duplication of exon 11. One breakpoint is in exon 11. The significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		868	0	58	16	Intron of GRIN2A(-):3Kb before exon 12	GRIN2A	9865765			16	Exon 11 of GRIN2A(-)	GRIN2A	9892220			10	DUPLICATION		26455	221981	2203	59	NEW_VARIANT
P-0024513-T01-IM6	APC (NM_000038) rearrangement: c.313:APC_chr5:g.113610357del	PRECISE	Note: The APC rearrangement is a deletion of exons 4-16. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	-		45947	0	5	5	Exon 4 of APC(+)	APC	112102978			5	IGR: 88Kb before KCNN2(+)	APC	113610357			10	DELETION		1507379	200523	33516	5	NEW_VARIANT
P-0029336-T01-IM6	BRCA2 (NM_000059) rearrangement: c.1670_chr13:g.51658908	PRECISE	Note: The BRCA2 rearrangement is an inversion that includes BRCA2 exons 10-27. One of the breakpoints is within exon 10.	MANUAL_OK	3to3	3to3	-		105986	0	38	13	Exon 10 of BRCA2(+)	BRCA2	32907285			13	3-UTR of LINC00371(-):87Kb after coding stop	BRCA2	51658908			10	INVERSION		18751623	221501	80651	38	NEW_VARIANT
P-0029585-T01-IM6	CREBBP (NM_004380) rearrangement: c.1309:CREBBP_chr16:g.3619041del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		108601	0	9	16	3-UTR of NLRC3(-):8Kb after coding stop	CREBBP	3619041			16	Exon 5 of CREBBP(-)	CREBBP	3842003			8	DELETION		222962	222312	157533	9	NEW_VARIANT
P-0032092-T01-IM6	TRAIP (NM_005879) - MST1R (NM_002447) rearrangement: c.240+1000:TRAIP_c.1548+73:MST1Rdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TRAIP:MST1R}		34901	0	5	3	Intron of TRAIP(-):999bp after exon 3	TRAIP	49883958			3	Intron of MST1R(-):72bp after exon 3	MST1R	49936227			6	DUPLICATION		52269	232054	38332	5	NEW_VARIANT
P-0032336-T01-IM6	EP300 (NM_001429) Rearrangement: t(16;22)(p11.2;q13.2)(chr16:g.30001065::chr22:g.41574417)	PRECISE	Note: The EP300 rearrangement results in the translocation with breakpoint in exon 31 of EP300. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	90	22	Exon 31 of EP300(+)	EP300	41574417			16	Exon 17 of TAOK2(+)	EP300	30001065			10	TRANSLOCATION		0	232756	0	101	NEW_VARIANT
P-0032336-T01-IM6	HIST1H3D(NM_003530) - HIST1H3E(NM_003532) Rearrangement: c.407:HIST1H3D_c.*1927:HIST1H3Edel	PRECISE	Note: The HIST1H3D-HIST1H3E rearrangement results in the deletion of HIST1H3D and HIST1H3E. One of the breakpoints is in HIST1H3D exon2.	MANUAL_OK	3to5	3to5	-		3206	0	4	6	Exon 2 of HIST1H3D(-)	HIST1H3D	26197072			6	Promoter of HIST1H3E(+):2Kb from tx start	HIST1H3E	26227720			10	DELETION		30648	232754	3057	4	NEW_VARIANT
P-0032342-T01-IM6	DROSHA(NM_013235) Rearrangement: c.3415:DROSHA_chr5:g.30226624inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		7681	0	65	5	IGR: 846Kb before LOC101929681(-)	DROSHA	30226624			5	Exon 28 of DROSHA(-)	DROSHA	31422898			10	INVERSION		1196274	232810	14996	93	NEW_VARIANT
P-0032342-T01-IM6	PDCD1LG2(NM_025239) - PTPRD(NM_002839) Rearrangement: c.766+12:PDCD1LG2_c.-545+115685:PTPRDdel	PRECISE	Note The PDCD1LG2 - PTPRD rearrangement results in the deletion of PDCD1LG2 exon 5-6 and the entire PTPRD gene. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		46610	0	80	9	Intron of PDCD1LG2(+):12bp after exon 5	PDCD1LG2	5557764			9	5-UTR of PTPRD(-):2Mb before coding start	PTPRD	10225278			10	DELETION		4667514	232805	49599	87	NEW_VARIANT
P-0033710-T01-IM6	JAK1 (NM_002227) rearrangement: c.3369+182:JAK1_chr1:g.69521361inv	PRECISE	Note: The JAK1 rearrangement is an inversion of exons 1-24. This includes the kinase domain of JAK1. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		34965	0	6	1	Intron of JAK1(-):181bp after exon 24	JAK1	65300897			1	IGR: 559Kb before DEPDC1-AS1(+)	JAK1	69521361			10	INVERSION		4220464	246327	128520	6	NEW_VARIANT
P-0036358-T01-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) fusion: c.2302-208:FGFR2_c.7344+468:TACC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:TACC2}		51646	0	23	10	Intron of FGFR2(-):208bp before exon 18	FGFR2	123239743			10	Intron of TACC2(+):468bp after exon 9	TACC2	123975434			10	INVERSION		735691	267970	61955	29	NEW_VARIANT
P-0037087-T01-IM6	RPS6KB2 (NM_003952) Rearrangement : c.457+289_c.1083del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		7135	0	22	11	Intron of RPS6KB2(+):289bp after exon 5	RPS6KB2	67199275			11	Exon 13 of RPS6KB2(+)	RPS6KB2	67201883			10	DELETION		2608	276269	6747	22	NEW_VARIANT
P-0037087-T01-IM6	ASXL1 (NM_015338) Rearrangement: c.57+1790_c.252+50dup	IMPPRECISE	Note: The ASXL1 Rearrangement results in the intragenic duplication of exons 2-3 of ASXL1.Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		2416	0	8	20	Intron of ASXL1(+):2Kb after exon 1	ASXL1	30948425			20	Intron of ASXL1(+):50bp after exon 3	ASXL1	30956976			0	DUPLICATION		8551	276270	4382	8	NEW_VARIANT
P-0037126-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2310:FGFR3_c.1837-16:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {FGFR3:TACC3}		34673	0	20	4	Intron of TACC3(+):15bp before exon 10	FGFR3	1739309			4	Exon 18 of FGFR3(+)	TACC3	1808878			10	DUPLICATION		69569	276301	18264	21	NEW_VARIANT
P-0037160-T01-IM6	KRAS (NM_033360) Rearrangement: c.450+3814_c.*58dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		1533	0	7	12	3-UTR of KRAS(-):6Kb after coding stop	KRAS	25362792			12	Intron of KRAS(-):4Kb after exon 4	KRAS	25374734			10	DUPLICATION		11942	276708	1107	7	NEW_VARIANT
P-0037180-T01-IM6	PLEKHA7 (NM_175058) - RPS6KA4 (NM_003942) rearrangement: c.222-55887:PLEKHA7_c.625:RPS6KA4inv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PLEKHA7:RPS6KA4}		94435	0	6	11	Intron of PLEKHA7(-):56Kb before exon 4	PLEKHA7	16948616			11	Exon 6 of RPS6KA4(+)	RPS6KA4	64128995			0	INVERSION		47180379	276853	109164	7	NEW_VARIANT
P-0037180-T01-IM6	PARK2 (NM_004562) rearrangement: c.171+7616_c.256del	PRECISE	Note: The PARK2 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		862	0	20	6	Exon 3 of PARK2(-)	PARK2	162683713			6	Intron of PARK2(-):8Kb after exon 2	PARK2	162856726			10	DELETION		173013	276851	624	20	NEW_VARIANT
P-0037180-T01-IM6	RECQL4 (NM_004260) - CPSF1 (NM_013291) rearrangement: c.2487:RECQL4_c.219:CPSF1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RECQL4:CPSF1}		13040	0	45	8	Exon 4 of CPSF1(-)	RECQL4	145626911			8	Exon 16 of RECQL4(-)	CPSF1	145738498			10	DELETION		111587	276852	13219	46	NEW_VARIANT
P-0037253-T01-IM6	RICTOR (NM_152756) rearrangement: c.889+6:RICTOR_chr5:g.49952642del	PRECISE	Note: The RICTOR rearrangement is a deletion of exons 1-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11444	0	13	5	Intron of RICTOR(-):5bp after exon 10	RICTOR	38975633			5	IGR: 9Kb before PARP8(+)	RICTOR	49952642			10	DELETION		10977009	277210	15778	13	NEW_VARIANT
P-0037257-T01-IM6	RRAS (NM_006270) rearrangement: c.58:RRAS_chr19:g.50572777del	IMPPRECISE	Note: The RRAS rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		477	0	5	19	Exon 1 of RRAS(-)	RRAS	50143298			19	Promoter of FLJ26850(+):19Kb from tx start	RRAS	50572777			0	DELETION		429479	277209	875	5	NEW_VARIANT
P-0037263-T01-IM6	DICER1 (NM_030621) rearrangement: t(14;15)(q32.13;q14)(chr14:g.95572446::chr15:g.35039509)	PRECISE	Note: The DICER1 rearrangement is a translocation with a breakpoint in exon 20. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	25	15	IGR: 5Kb before GJD2(-)	DICER1	35039509			14	Exon 20 of DICER1(-)	DICER1	95572446			10	TRANSLOCATION		0	277224	0	24	NEW_VARIANT
P-0037283-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon 1 fused to ERG exons 2-10): c.56-2450:TMPRSS2_c.19-5937:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		65011	0	15	21	Intron of ERG(-):6Kb before exon 2	TMPRSS2	39823481			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42872457			10	DELETION		3048976	277367	53142	17	NEW_VARIANT
P-0037545-T01-IM6	PPP6C (NM_002721) rearrangement: t(9;10)(q33.3;q25.3)(chr9:g.127951728::chr10:g.111892246)	PRECISE	Note: The PPP6C rearrangement is a translocation involving exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	8	10	Intron of ADD3(+):837bp before exon 14	PPP6C	111892246			9	Intron of PPP6C(-):194bp after exon 1	PPP6C	127951728			10	TRANSLOCATION		0	280482	0	8	NEW_VARIANT
P-0037545-T01-IM6	EYA1 (NM_172058) - WHSC1L1 (NM_023034) rearrangement: c.826+5510:EYA1_c.622:WHSC1L1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {EYA1:WHSC1L1}		168139	0	38	8	Exon 2 of WHSC1L1(-)	EYA1	38205068			8	Intron of EYA1(-):6Kb after exon 9	WHSC1L1	72205772			10	DELETION		34000704	280480	151140	46	NEW_VARIANT
P-0037548-T01-IM6	BCOR (NM_001123385) rearrangement: t(X;8)(p11.4;q13.1)(chrX:g.39930104::chr8:g.66508332)	PRECISE	Note: The BCOR rearrangement is a translocation involving exon 6. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	21	X	Intron of BCOR(-):121bp after exon 6	BCOR	39930104			8	IGR: 6Kb before ARMC1(-)	BCOR	66508332			10	TRANSLOCATION		0	280499	0	22	NEW_VARIANT
P-0037834-T01-IM6	DNMT1 (NM_001379) rearrangement: c.1325:DNMT1_chr19:g.53065226del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		1131604	0	5	19	Exon 17 of DNMT1(-)	DNMT1	10267093			19	IGR: 8Kb before ZNF701(+)	DNMT1	53065226			10	DELETION		42798133	282195	1926645	5	NEW_VARIANT
P-0037834-T01-IM6	NPAS1 (NM_002517) - BBC3 (NM_001127240) rearrangement: c.359-497:NPAS1_c.569-2141:BBC3inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {NPAS1:BBC3}		6709	0	21	19	Intron of NPAS1(+):496bp before exon 3	NPAS1	47535039			19	Intron of BBC3(-):2Kb before exon 4	BBC3	47727316			10	INVERSION		192277	282198	13376	24	NEW_VARIANT
P-0037834-T01-IM6	KDM6A (NM_021140) rearrangement: c.225+28705_c.3878+32dup	PRECISE	Note: The KDM6A rearrangement results in the intragenic duplication of exons 3-26. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 24 exons : out of frame		22970	0	57	X	Intron of KDM6A(+):29Kb after exon 2	KDM6A	44761938			X	Intron of KDM6A(+):32bp after exon 26	KDM6A	44950141			10	DUPLICATION		188203	282197	39050	57	NEW_VARIANT
P-0037960-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.126+1742:TMPRSS2_c.39+36464:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38009	0	70	21	Intron of ERG(-):36Kb after exon 3	TMPRSS2	39911122			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868304			10	DELETION		2957182	283046	53663	73	NEW_VARIANT
P-0039051-T01-IM6	EXOC4 (NM_021807) - SMO (NM_005631) rearrangement: c.1514+40892:EXOC4_c.587:SMOdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {EXOC4:SMO}		20733	0	77	7	Exon 3 of SMO(+)	EXOC4	128845093			7	Intron of EXOC4(+):41Kb after exon 10	SMO	133355786			10	DUPLICATION		4510693	293422	27400	83	NEW_VARIANT
P-0039753-T01-IM6	GLI1 (NM_005269) rearrangement: c.2126:GLI1_chr12:g.59094643inv	PRECISE	Note: The GLI1 rearrangement is an inversion of exon 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		19689	0	77	12	Exon 12 of GLI1(+)	GLI1	57864649			12	3-UTR of LOC101927653(-):81Kb after coding stop	GLI1	59094643			10	INVERSION		1229994	298093	16740	75	NEW_VARIANT
P-0039753-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-1241:TMPRSS2_c.39+60112:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		44262	0	49	21	Intron of ERG(-):60Kb after exon 3	TMPRSS2	39887474			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871357			10	DELETION		2983883	298092	38723	51	NEW_VARIANT
P-0039804-T01-IM6	EPHA3 (NM_005233) rearrangement: c.2691-22:EPHA3_chr3:g.88907146inv	PRECISE	Note: The EPHA3 rearrangement is an inversion of exons 1 - 15. The rearrangement includes the kinase domain of EPHA3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		29078	0	50	3	IGR: 250Kb before EPHA3(+)	EPHA3	88907146			3	Intron of EPHA3(+):21bp before exon 16	EPHA3	89521592			10	INVERSION		614446	298296	17688	68	NEW_VARIANT
P-0040119-T01-IM6	KMT2D (NM_003482) - TUBA1B (NM_006082) rearrangement: c.3297:KMT2D_c.434:TUBA1Bdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KMT2D:TUBA1B}		26141	0	5	12	Exon 11 of KMT2D(-)	KMT2D	49444074			12	Exon 4 of TUBA1B(-)	TUBA1B	49522663			0	DUPLICATION		78589	300380	56430	46	NEW_VARIANT
P-0040355-T01-IM6	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12036111::chr15:g.88497191)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	84	15	Intron of NTRK3(-):13Kb before exon 15	ETV6	88497191			12	Intron of ETV6(+):1Kb before exon 6	NTRK3	12036111			10	TRANSLOCATION		0	301336	0	81	NEW_VARIANT
P-0040611-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1208:TMPRSS2_c.39+5853:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		25237	0	36	21	Intron of ERG(-):6Kb after exon 3	TMPRSS2	39941733			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867713			10	DELETION		2925980	302652	27935	37	NEW_VARIANT
P-0040803-T01-IM6	KMT2C (NM_170606) rearrangement: c.681_c.11461-1464del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of exons 5 - 43. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		74602	0	32	7	Intron of KMT2C(-):1Kb before exon 44	KMT2C	151857621			7	Exon 5 of KMT2C(-)	KMT2C	152008941			10	DELETION		151320	303096	43316	35	NEW_VARIANT
P-0040817-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.1491:NOTCH1_chr9:g.139456931del	IMPPRECISE	Note: The NOTCH1 rearrangement is a deletion of exons 1 - 9. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		24230	0	35	9	Exon 9 of NOTCH1(-)	NOTCH1	139411788			9	IGR: 15Kb before LINC01573(+)	NOTCH1	139456931			0	DELETION		45143	303107	18745	39	NEW_VARIANT
P-0041541-T01-IM6	ARID1B (NM_020732) rearrangement: c.1926+6815_c.4111-128del	IMPPRECISE	Note: The ARID1B rearrangement is an intragenic deletion of exons 5 - 17.	MANUAL_OK	3to5	3to5	Deletion of 13 exons : in frame		25624	0	5	6	Intron of ARID1B(+):7Kb after exon 4	ARID1B	157229474			6	Intron of ARID1B(+):127bp before exon 18	ARID1B	157521711			0	DELETION		292237	306927	18693	5	NEW_VARIANT
P-0041618-T01-IM6	APC (NM_000038) rearrangement: c.834+4289_c.1136del	PRECISE	Note: The APC rearrangement is an intragenic deletion of exons 9 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2170	0	26	5	Intron of APC(+):4Kb after exon 8	APC	112141369			5	Exon 10 of APC(+)	APC	112154865			10	DELETION		13496	307118	760	79	NEW_VARIANT
P-0042120-T01-IM6	CSF1R (NM_005211) rearrangement: c.592+51:CSF1R_chr5:g.55036856del	PRECISE	Note: The CSF1R rearrangement is a deletion of exons 5 - 22. The rearrangement includes the kinase domain of CSF1R. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		302441	0	2	5	Intron of DDX4(+):2Kb after exon 2	CSF1R	55036856			5	Intron of CSF1R(-):50bp after exon 4	CSF1R	149459564			4	DELETION		94422708	308456	166285	2	NEW_VARIANT
P-0042120-T01-IM6	KDM6A (NM_021140) rearrangement: c.655-6333_c.2939-29del	PRECISE	Note: The KDM6A rearrangement is an intragenic deletion of exons 9 - 19.	MANUAL_OK	3to5	3to5	Deletion of 11 exons : out of frame		13522	0	7	X	Intron of KDM6A(+):6Kb before exon 9	KDM6A	44904621			X	Intron of KDM6A(+):28bp before exon 20	KDM6A	44938362			8	DELETION		33741	308457	8924	7	NEW_VARIANT
P-0042152-T01-IM6	TSHR (NM_000369) rearrangement: t(3;14)(p11.1;q31.1)(chr3:g.88275067::chr14:g.81574993)	PRECISE	Note: The TSHR rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	12	14	Intron of TSHR(+):197bp after exon 8	TSHR	81574993			3	IGR: 76Kb before C3orf38(+)	TSHR	88275067			10	TRANSLOCATION		0	308242	0	10	NEW_VARIANT
P-0042152-T01-IM6	AXIN2 (NM_004655) rearrangement: c.956+117_c.1087del	PRECISE	Note: The AXIN2 rearrangement is an intragenic deletion of exons 4 - 5. One of the breakpoints is within exon 5.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2590	0	14	17	Exon 5 of AXIN2(-)	AXIN2	63534434			17	Intron of AXIN2(-):116bp after exon 3	AXIN2	63545521			10	DELETION		11087	308238	887	15	NEW_VARIANT
P-0042152-T01-IM6	PRDM14 (NM_024504) rearrangement: c.701-4_c.912+614inv	PRECISE	Note: The PRDM14 rearrangement is an intragenic inversion of exons 3 - 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3086	0	2	8	Intron of PRDM14(-):613bp after exon 4	PRDM14	70979851			8	Intron of PRDM14(-):4bp before exon 3	PRDM14	70980771			4	INVERSION		920	308241	1416	2	NEW_VARIANT
P-0042341-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4078:TMPRSS2_c.40-62578:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		57355	0	46	21	Intron of ERG(-):63Kb before exon 4	TMPRSS2	39880122			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874194			10	DELETION		2994072	309687	26785	47	NEW_VARIANT
P-0042358-T01-IM6	ARID1A (NM_006015) rearrangement: c.2315:ARID1A_chr1:g.26904763del	PRECISE	Note: The ARID1A rearrangement is a deletion of exons 1 - 7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	-		17007	0	31	1	IGR: 24Kb before MIR1976(+)	ARID1A	26904763			1	Exon 7 of ARID1A(+)	ARID1A	27088706			10	DELETION		183943	309708	22405	31	NEW_VARIANT
P-0042583-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.126+124:TMPRSS2_chr21:g.39962828del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		41065	0	37	21	3-UTR of ERG(-):71Kb after coding stop	TMPRSS2	39962828			21	Intron of TMPRSS2(-):123bp after exon 2	TMPRSS2	42869922			10	DELETION		2907094	310819	22977	40	NEW_VARIANT
P-0042595-T03-IM6	CDKN2A (NM_000077) rearrangement: c.406_c.194-1084del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1489	0	13	9	Exon 2 of CDKN2A(-)	CDKN2A	21970952			9	Intron of CDKN2A(-):1Kb before exon 2	CDKN2A	21972291			10	DELETION		1339	325900	1055	14	NEW_VARIANT
P-0042647-T01-IM6	NOTCH3 (NM_000435) - ZNF30 (NM_001099437) rearrangement: c.4379:NOTCH3_c.160+258:ZNF30inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NOTCH3:ZNF30}		341707	0	32	19	Exon 24 of NOTCH3(-)	NOTCH3	15288360			19	Intron of ZNF30(+):258bp after exon 3	ZNF30	35423155			10	INVERSION		20134795	310951	398775	49	NEW_VARIANT
P-0042662-T01-IM6	AXIN1 (NM_003502) rearrangement: c.1117-2251_c.1269del	PRECISE	Note: The AXIN1 rearrangement is an intragenic deletion of exons 5 - 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3525	0	12	16	Exon 6 of AXIN1(-)	AXIN1	348237			16	Intron of AXIN1(-):2Kb before exon 5	AXIN1	356692			10	DELETION		8455	311043	1495	13	NEW_VARIANT
P-0042680-T01-IM6	TMPRSS2 (NM_001135099) - GCOM1 (NM_001018090) rearrangement: t(15;21)(q21.3;q22.3)(chr15:g.57940741::chr21:g.42877616)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {TMPRSS2:GCOM1}		0	0	48	21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42877616			15	Intron of GCOM1(+):9Kb after exon 10	GCOM1	57940741			10	TRANSLOCATION		0	311059	0	58	NEW_VARIANT
P-0042880-T01-IM6	RET (NM_020975) rearrangement: c.2136+836:RET_chr10:g.51588973del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RET:TIMM23B}		25606	0	58	10	Intron of RET(+):836bp after exon 11	RET	43611020			10	Intron of TIMM23B(+):144Kb before exon 7	RET	51588973			10	DELETION		7977953	311559	32533	60	NEW_VARIANT
P-0042960-T01-IM6	MALT1 (NM_006785) - ETV4 (NM_001986) rearrangement: t(17;18)(q21.31;q21.32)(chr17:g.41612825::chr18:g.56367894)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {MALT1:ETV4}		0	0	8	18	Intron of MALT1(+):71bp after exon 4	MALT1	56367894			17	Intron of ETV4(-):968bp after exon 5	ETV4	41612825			10	TRANSLOCATION		0	311783	0	13	NEW_VARIANT
P-0042985-T01-IM6	CNTRL (NM_007018) - CDKN2B (NM_004936) rearrangement: c.1455+1114:CNTRL_c.156+547:CDKN2Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {CNTRL:CDKN2B}		316647	0	7	9	Intron of CDKN2B(-):546bp after exon 1	CNTRL	22008250			9	Intron of CNTRL(+):1Kb after exon 9	CDKN2B	123878592			9	INVERSION		101870342	312916	385214	7	NEW_VARIANT
P-0043128-T01-IM6	BCOR (NM_001123385) rearrangement: c.4429-79:BCOR_chrX:g.39699662dup	PRECISE	Note: The BCOR rearrangement is a duplication of exons 11 - 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		4472	0	15	X	IGR: 211Kb before BCOR(-)	BCOR	39699662			X	Intron of BCOR(-):79bp before exon 11	BCOR	39916653			10	DUPLICATION		216991	313358	8960	15	NEW_VARIANT
P-0043135-T01-IM6	ALK (NM_004304) rearrangement: c.2990_c.3836+951del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		39633	0	4	2	Intron of ALK(-):950bp after exon 25	ALK	29431701			2	Exon 18 of ALK(-)	ALK	29449865			7	DELETION		18164	313348	48481	4	NEW_VARIANT
P-0043336-T01-IM6	TET1 (NM_030625) rearrangement: t(1;10)(p36.22;q21.3)(chr1:g.9933952::chr10:g.70360699)	PRECISE	Note: The TET1 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	58	10	Intron of TET1(+):38bp before exon 3	TET1	70360699			1	5-UTR of CTNNBIP1(-):23Kb before coding start	TET1	9933952			10	TRANSLOCATION		0	313868	0	57	NEW_VARIANT
P-0043336-T01-IM6	ALK (NM_004304) rearrangement: t(1;2)(q32.1;p23.2)(chr1:g.205559556::chr2:g.29450227)	PRECISE	Note: The ALK rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	165	2	Intron of ALK(-):212bp after exon 17	ALK	29450227			1	Intron of MFSD4(+):2Kb before exon 7	ALK	205559556			10	TRANSLOCATION		0	313867	0	178	NEW_VARIANT
P-0043336-T01-IM6	SRC (NM_198291) rearrangement: c.703+225:SRC_chr20:g.36135046del	PRECISE	Note: The SRC rearrangement is a deletion of exons 9 - 14. The rearrangement includes the kinase domain of SRC. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		11875	0	13	20	Intron of SRC(+):225bp after exon 8	SRC	36024939			20	IGR: 11Kb before BLCAP(-)	SRC	36135046			7	DELETION		110107	313864	12917	14	NEW_VARIANT
P-0043336-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+4684:TMPRSS2_c.19-14284:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		73859	0	165	21	Intron of ERG(-):14Kb before exon 2	TMPRSS2	39831828			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875193			10	DELETION		3043365	313865	90154	171	NEW_VARIANT
P-0043661-T01-IM6	TGFBR2 (NM_001024847) rearrangement: c.1271_c.1471+1007del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1562	0	24	3	Exon 5 of TGFBR2(+)	TGFBR2	30713871			3	Intron of TGFBR2(+):1Kb after exon 6	TGFBR2	30716745			10	DELETION		2874	315189	2176	24	NEW_VARIANT
P-0043914-T01-IM6	JAK1 (NM_002227) rearrangement: c.163_c.991-585inv	PRECISE	Note: The JAK1 rearrangement is an intragenic inversion of exons 3 - 7. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		5173	0	3	1	Intron of JAK1(-):585bp before exon 8	JAK1	65331240			1	Exon 3 of JAK1(-)	JAK1	65349002			10	INVERSION		17762	316751	7726	3	NEW_VARIANT
P-0043914-T01-IM6	EIF4A2 (NM_001967) rearrangement: c.808:EIF4A2_chr3:g.195046321dup	PRECISE	Note: The EIF4A2 rearrangement is a duplication of exons 8 - 11. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		43067	0	24	3	Exon 8 of EIF4A2(+)	EIF4A2	186504952			3	Intron of ACAP2(-):1Kb after exon 9	EIF4A2	195046321			10	DUPLICATION		8541369	316750	66432	25	NEW_VARIANT
P-0043914-T01-IM6	ESR1 (NM_001122740) rearrangement: c.453-90_c.643+11644inv	PRECISE	Note: The ESR1 rearrangement is an intragenic inversion of exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		1336	0	16	6	Intron of ESR1(+):89bp before exon 3	ESR1	152163642			6	Intron of ESR1(+):12Kb after exon 3	ESR1	152175566			10	INVERSION		11924	316753	1966	16	NEW_VARIANT
P-0044185-T01-IM6	IDH1 (NM_005896) rearrangement: c.612:IDH1_chr2:g.209116629dup	PRECISE	Note: The IDH1 rearrangement is a duplication of exons 1 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		4600	0	2	2	Exon 6 of IDH1(-)	IDH1	209108237			2	5-UTR of IDH1(-):15Kb before coding start	IDH1	209116629			5	DUPLICATION		8392	318222	2746	2	NEW_VARIANT
P-0044185-T01-IM6	EWSR1 (NM_013986) rearrangement: c.811+579_c.998del	PRECISE	Note: The EWSR1 rearrangement is an intragenic deletion of exons 9 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		33918	0	6	22	Intron of EWSR1(+):579bp after exon 8	EWSR1	29683702			22	Exon 10 of EWSR1(+)	EWSR1	29687559			10	DELETION		3857	318221	14690	6	NEW_VARIANT
P-0044212-T01-IM6	NF1 (NM_001042492) rearrangement: c.6148-20:NF1_chr17:g.29355827del	PRECISE	Note: The NF1 rearrangement is a deletion of exons 1 - 41.	MANUAL_OK	3to5	3to5	-		43513	0	15	17	IGR: 53Kb before DPRXP4(+)	NF1	29355827			17	Intron of NF1(+):19bp before exon 42	NF1	29663633			10	DELETION		307806	318314	45260	16	NEW_VARIANT
P-0044219-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.431:WHSC1L1_chr8:g.27323508inv	PRECISE	Note: The WHSC1L1 rearrangement is an inversion of exons 2 - 24. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		68981	0	88	8	Intron of CHRNA2(-):1Kb after exon 5	WHSC1L1	27323508			8	Exon 2 of WHSC1L1(-)	WHSC1L1	38205259			10	INVERSION		10881751	318273	54013	125	NEW_VARIANT
P-0044333-T01-IM6	NOTCH1 (NM_017617) - GNL3 (NM_014366) rearrangement: t(3;9)(p21.1;q34.3)(chr3:g.52723317::chr9:g.139397753)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NOTCH1:GNL3}		0	0	8	9	Exon 27 of NOTCH1(-)	NOTCH1	139397753			3	Intron of GNL3(+):95bp after exon 6	GNL3	52723317			9	TRANSLOCATION		0	318821	0	9	NEW_VARIANT
P-0044376-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-4624:TMPRSS2_c.39+51402:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		76434	0	80	21	Intron of ERG(-):51Kb after exon 3	TMPRSS2	39896184			21	Intron of TMPRSS2(-):5Kb before exon 2	ERG	42874740			10	DELETION		2978556	319614	46315	86	NEW_VARIANT
P-0044397-T01-IM6	KIAA1324L (NM_001142749) - NOTCH2 (NM_024408) rearrangement: t(1;7)(p12;q21.12)(chr1:g.120465401::chr7:g.86589695)	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {KIAA1324L:NOTCH2}		0	0	99	7	Intron of KIAA1324L(-):5Kb after exon 2	KIAA1324L	86589695			1	Exon 27 of NOTCH2(-)	NOTCH2	120465401			0	TRANSLOCATION		0	319119	0	253	NEW_VARIANT
P-0044793-T01-IM6	ERBB2 (NM_004448) rearrangement: c.2970+32:ERBB2_chr17:g.27068786inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		183940	0	6	17	Intron of NEK8(+):190bp before exon 15	ERBB2	27068786			17	Intron of ERBB2(+):32bp after exon 24	ERBB2	37882944			10	INVERSION		10814158	320596	159778	6	NEW_VARIANT
P-0044907-T01-IM6	MET (NM_000245) rearrangement: c.263_c.1702-6554dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		9134	0	3	7	Exon 2 of MET(+)	MET	116339401			7	Intron of MET(+):7Kb before exon 6	MET	116388855			10	DUPLICATION		49454	320881	12293	4	NEW_VARIANT
P-0044907-T01-IM6	MED12 (NM_005120) - NLGN3 (NM_181303) rearrangement: c.2226+15:MED12_c.728-587:NLGN3del	PRECISE	Note: The MED12 - NLGN3 rearrangement is a deletion that results in a fusion of MED12 exons 1 - 15 to NLGN3 exons 4 - 8.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {MED12:NLGN3}		63829	0	92	X	Intron of MED12(+):15bp after exon 15	MED12	70345011			X	Intron of NLGN3(+):586bp before exon 4	NLGN3	70383406			10	DELETION		38395	320880	60308	101	NEW_VARIANT
P-0044915-T01-IM6	JAK1 (NM_002227) rearrangement: c.3370-4:JAK1_chr1:g.67621368del	PRECISE	Note: The JAK1 rearrangement is a deletion of exons 1 - 24.	MANUAL_OK	3to5	3to5	-		34511	0	6	1	Intron of JAK1(-):4bp before exon 25	JAK1	65300344			1	IGR: 11Kb before IL23R(+)	JAK1	67621368			10	DELETION		2321024	320943	20026	6	NEW_VARIANT
P-0045358-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3497:TMPRSS2_c.237-3947:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 3 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66940	0	95	21	Intron of ERG(-):4Kb before exon 3	TMPRSS2	39799430			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873613			10	DELETION		3074183	322594	70364	98	NEW_VARIANT
P-0045546-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-401:TMPRSS2_c.40-57469:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		31765	0	30	21	Intron of ERG(-):57Kb before exon 4	TMPRSS2	39875013			21	Intron of TMPRSS2(-):401bp before exon 2	ERG	42870517			10	DELETION		2995504	323311	29212	32	NEW_VARIANT
P-0047087-T01-IM6	SUFU (NM_016169) - PPAPDC1A (NM_001030059) rearrangement: c.1136:SUFU_c.445+5423:PPAPDC1Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {SUFU:PPAPDC1A}		64058	0	14	10	Exon 9 of SUFU(+)	SUFU	104375138			10	Intron of PPAPDC1A(+):5Kb after exon 5	PPAPDC1A	122286030			10	DELETION		17910892	329482	68932	14	NEW_VARIANT
P-0049133-T02-IM6	FGFR2 (NM_000141) - BICC1 (NM_001080512) fusion: c.2301+1114:FGFR2_c.237+29879:BICC1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		202778	0	48	10	Intron of BICC1(+):30Kb after exon 2	FGFR2	60410540			10	Intron of FGFR2(-):1Kb after exon 17	BICC1	123242098			10	INVERSION		62831558	336034	183768	54	NEW_VARIANT
P-0005596-T01-IM5	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion (TMPRSS2 exon1 with ERG exons 2-10): c.56-2228:TMPRSS2_c.19-8779:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein fusion: out of frame (TMPRSS2-ERG)		86704	0	102	21	Intron of ERG(-): 9Kb before exon 4	TMPRSS2	39826323			21	Intron of TMPRSS2(-): 2Kb before exon 2	ERG	42872344			72	DELETION		3046021	51256	88870	130	NEW_VARIANT
P-0011252-T01-IM5	PTEN (NM_000314) rearrangement: c.1026+87:PTEN_chr10:g.90177234del	PRECISE	Note: The PTEN rearrangement is a deletion of exon 9.	MANUAL_OK	3to5	3to5	Antisense fusion		1061	0	17	10	Intron of PTEN(+): 87bp after exon 8	PTEN	89720962			10	Intron of RNLS(-): 55Kb before exon 5	PTEN	90177234			21	DELETION		456272	151997	363	12	NEW_VARIANT
P-0017272-T01-IM6	MGA (NM_001164273) rearrangement: chr15:g.28511764_c.8260:MGAdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		100559	0	41	15	Intron of HERC2(-):644bp before exon 13	MGA	28511764			15	Exon 24 of MGA(+)	MGA	42058540			10	DELETION		13546776	175687	178636	43	NEW_VARIANT
P-0020088-T01-IM6	CIC (NM_015125) rearrangement: c.3255:CIC_chr19:g.48885780inv	PRECISE	Note: The CIC rearrangement is an inversion of exons 14-20.  One of the breakpoints is in exon 14. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CIC:KDELR1}		67310	0	45	19	Exon 14 of CIC(+)	CIC	42796797			19	Promoter of KDELR1(-):46bp from tx start	CIC	48885780			10	INVERSION		6088983	183564	117873	45	NEW_VARIANT
P-0020450-T01-IM6	ALK (NM_004304) rearrangement: c.3172+142:ALK_chr2:g.123228344del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		715480	0	17	2	Intron of ALK(-):141bp after exon 19	ALK	29448185			2	IGR: 715Kb before TSN(+)	ALK	123228344			10	DELETION		93780159	184456	683038	17	NEW_VARIANT
P-0021318-T01-IM6	TP53 (NM_000546) rearrangement: c.*520_c.1030del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 10-11. One of the breakpoints is within exon 10. Its significance is undetermined.	MANUAL_OK	3to5	3to5	-		2600	0	43	17	3-UTR of TP53(-):519bp after coding stop	TP53	7572407			17	Exon 10 of TP53(-)	TP53	7573997			10	DELETION		1590	186865	1777	46	NEW_VARIANT
P-0024150-T01-IM6	PTPN11 (NM_002834) rearrangement: c.1767_chr12:g.113053952inv	PRECISE	Note: The PTPN11 rearrangement results in the inversion of exon 15. One of the breakpoints is within exon 15. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		544	0	2	12	Exon 15 of PTPN11(+)	PTPN11	112942553			12	IGR: 176Kb before RPH3A(+)	PTPN11	113053952			9	INVERSION		111399	198549	797	3	NEW_VARIANT
P-0024831-T01-IM6	TFE3 (NM_006521) rearrangement: c.886-702:TFE3_chrX:g.45846839inv	PRECISE	Note: The TFE3 rearrangement results in the inversion of exons 6-10. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		100971	0	299	X	IGR: 139Kb before LOC401585(-)	TFE3	45846839			X	Intron of TFE3(-):702bp before exon 6	TFE3	48892468			10	INVERSION		3045629	201915	165745	295	NEW_VARIANT
P-0025479-T01-IM6	BRCA1 (NM_007294) rearrangement: t(15;17)(q22.2;q21.31)(chr15:g.62705905::chr17:g.41223156)	PRECISE	Note: The BRCA1 rearrangement is a translocation with a breakpoint in exon 15. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	26	17	Exon 15 of BRCA1(-)	BRCA1	41223156			15	IGR: 71Kb before MIR6085(+)	BRCA1	62705905			10	TRANSLOCATION		0	205767	0	26	NEW_VARIANT
P-0027130-T01-IM6	SMAD4 (NM_005359) rearrangement: c.1447+25:SMAD4_chr18:g.48624512del	PRECISE	Note: The SMAD4 rearrangement results in the deletion of exons 11-12. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1457	0	11	18	Intron of SMAD4(+):25bp after exon 11	SMAD4	48603171			18	IGR: 68Kb before SMAD4(+)	SMAD4	48624512			10	DELETION		21341	212857	1836	11	NEW_VARIANT
P-0027130-T01-IM6	PLK2 (NM_006622) - PDE4D (NM_001104631) rearrangement: c.1156+14:PLK2_c.922-15282:PDE4Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {PLK2:PDE4D}		10441	0	10	5	Intron of PLK2(-):13bp after exon 8	PLK2	57752758			5	Intron of PDE4D(-):15Kb before exon 9	PDE4D	58304574			10	DUPLICATION		551816	212858	17290	10	NEW_VARIANT
P-0028066-T01-IM6	BCL6 (NM_001706) rearrangement: c.1540+111:BCL6_chr3:g.187103059del	PRECISE	Note: The BCL6 rearrangement is a rearrangement is a deletion of exons 7-10. its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5221	0	3	3	IGR: 17Kb before RTP4(+)	BCL6	187103059			3	Intron of BCL6(-):110bp after exon 6	BCL6	187446037			7	DELETION		342978	216016	8390	3	NEW_VARIANT
P-0028080-T01-IM6	CDKN1B (NM_004064) rearrangement: c.-9_c.476-73del	IMPPRECISE	Note: The CDKN1B rearrangement is a deletion of exon 1. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1572	0	7	12	5-UTR of CDKN1B(+):8bp before coding start	CDKN1B	12870765			12	Intron of CDKN1B(+):72bp before exon 2	CDKN1B	12871686			0	DELETION		921	216058	2220	8	NEW_VARIANT
P-0028080-T01-IM6	PRKAR1A (NM_212471) rearrangement: c.503-76:PRKAR1A_chr17:g.65890416inv	PRECISE	Note: The PRKAR1A rearrangement is an inversion of exons 1-5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4316	0	9	17	Intron of BPTF(+):135bp after exon 9	PRKAR1A	65890416			17	Intron of PRKAR1A(+):75bp before exon 6	PRKAR1A	66520977			10	INVERSION		630561	216060	7229	11	NEW_VARIANT
P-0028080-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4857:TMPRSS2_c.18+9341:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion is a deletion which results in the fusion of TMPRSS2 exon 1 with ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66104	0	23	21	Intron of ERG(-):9Kb after exon 1	TMPRSS2	39860946			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875020			10	DELETION		3014074	216059	80132	23	NEW_VARIANT
P-0028328-T01-IM6	NF1 (NM_001042492) rearrangement: t(1;17)(q24.3;q11.2)(chr1:g.171191499::chr17:g.29486091)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in exon 3, and may result in truncation of the gene.	MANUAL_OK	3to5	3to5	-		0	0	37	17	Exon 3 of NF1(+)	NF1	29486091			1	IGR: 26Kb before FMO1(+)	NF1	171191499			10	TRANSLOCATION		0	216897	0	37	NEW_VARIANT
P-0030380-T01-IM6	BMPR1A (NM_004329) Rearrangement : c.530+286_c.1342+81dup	IMPPRECISE	Note: The BMPR1A Rearrangement results in the intragenic duplication of exons 8-11. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 4 exons : out of frame		7014	0	10	10	Intron of BMPR1A(+):286bp after exon 7	BMPR1A	88660169			10	Intron of BMPR1A(+):81bp after exon 11	BMPR1A	88681533			0	DUPLICATION		21364	225539	12597	11	NEW_VARIANT
P-0031582-T01-IM6	GREB1L (NM_001142966) - LMO1 (NM_002315) rearrangement: t(11;18)(p15.4;q11.1)(chr11:g.8246318::chr18:g.18956391)	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {GREB1L:LMO1}		0	0	13	18	5-UTR of GREB1L(+):7Kb before coding start	GREB1L	18956391			11	Intron of LMO1(-):50bp before exon 4	LMO1	8246318			10	TRANSLOCATION		0	230117	0	14	NEW_VARIANT
P-0032335-T01-IM6	LIN37(NM_019104) - KMT2B(NM_014727) fusion: c.445-100:LIN37_c.5463:KMT2Bdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LIN37:KMT2B}		24039	0	8	19	Exon 27 of KMT2B(+)	LIN37	36222834			19	Intron of LIN37(+):99bp before exon 7	KMT2B	36244818			10	DUPLICATION		21984	232753	69555	8	NEW_VARIANT
P-0033924-T01-IM6	SUZ12 (NM_015355) rearrangement: c.274+107_chr17:g.34136244inv	PRECISE	Note: The SUZ12 rearrangement is an inversion that includes exons 1-16. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		41717	0	27	17	Intron of SUZ12(+):107bp after exon 1	SUZ12	30264646			17	Promoter of TAF15(+):214bp from tx start	SUZ12	34136244			10	INVERSION		3871598	246848	77270	35	NEW_VARIANT
P-0035993-T01-IM6	PAX8 (NM_003466) - POLR1B (NM_019014) rearrangement: c.1189+1007:PAX8_c.177+886:POLR1Binv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {PAX8:POLR1B}		47244	0	33	2	Intron of POLR1B(+):886bp after exon 1	PAX8	113301134			2	Intron of PAX8(-):1Kb after exon 10	POLR1B	113983725			10	INVERSION		682591	308416	63665	34	NEW_VARIANT
P-0037023-T01-IM6	CPNE4 (NM_130808) - CASP8 (NM_001080125) rearrangement: t(2;3)(q33.1;q22.1)(chr2:g.202131409::chr3:g.131752452)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CPNE4:CASP8}		0	0	8	3	Intron of CPNE4(-):4Kb after exon 2	CPNE4	131752452			2	Exon 2 of CASP8(+)	CASP8	202131409			10	TRANSLOCATION		0	275624	0	8	NEW_VARIANT
P-0037608-T01-IM6	PGM5 (NM_021965) - TMPRSS2 (NM_001135099) rearrangement: t(9;21)(q21.11;q22.3)(chr9:g.71138173::chr21:g.42869299)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {PGM5:TMPRSS2}		0	0	40	21	Intron of TMPRSS2(-):746bp after exon 2	PGM5	42869299			9	Intron of PGM5(+):6Kb before exon 11	TMPRSS2	71138173			10	TRANSLOCATION		0	280703	0	40	NEW_VARIANT
P-0037612-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: (17;21)(q21.31;q22.3)(chr17:g.41635523::chr21:g.42868077)	PRECISE	Note: The TMPRSS2 rearrangement is a translocation involving exon 3. Its functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	24	21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868077			17	IGR: 30Kb before ETV4(-)	TMPRSS2	41635523			10	TRANSLOCATION		0	280710	0	33	NEW_VARIANT
P-0037867-T01-IM6	CASP8 (NM_001080125) rearrangement: c.925:CASP8_chr2:g.202108480del	PRECISE	Note: The CASP8 rearrangement results in the deletion of exons 1-7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8162	0	30	2	5-UTR of CASP8(+):23Kb before coding start	CASP8	202108480			2	Exon 7 of CASP8(+)	CASP8	202141637			10	DELETION		33157	282997	5115	33	NEW_VARIANT
P-0037969-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+662:TMPRSS2_c.18+6989:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1 - 2 and ERG exons 2 - 10. The fusion is predicted to be in frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		38942	0	19	21	Intron of ERG(-):7Kb after exon 1	TMPRSS2	39863298			21	Intron of TMPRSS2(-):661bp after exon 2	ERG	42869384			10	DELETION		3006086	283064	20927	19	NEW_VARIANT
P-0039939-T01-IM6	MAOB (NM_000898) - KDM6A (NM_021140) rearrangement: c.280-6009:MAOB_c.1330-47:KDM6Ainv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {MAOB:KDM6A}		8327	0	8	X	Intron of MAOB(-):6Kb before exon 4	MAOB	43668660			X	Intron of KDM6A(+):46bp before exon 14	KDM6A	44920522			10	INVERSION		1251862	298810	7206	9	NEW_VARIANT
P-0040111-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.304-13873:CCDC6_c.1919:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {CCDC6:RET}		45188	0	44	10	Exon 11 of RET(+)	CCDC6	43609967			10	Intron of CCDC6(-):14Kb before exon 2	RET	61626333			10	INVERSION		18016366	300370	53462	52	NEW_VARIANT
P-0040340-T01-IM6	KMT2D (NM_003482) - ADCY6 (NM_015270) rearrangement: c.13095:KMT2D_c.865-567:ADCY6del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {KMT2D:ADCY6}		38195	0	11	12	Intron of ADCY6(-):567bp before exon 2	KMT2D	49172607			12	Exon 39 of KMT2D(-)	ADCY6	49425393			10	DELETION		252786	301281	52745	11	NEW_VARIANT
P-0040593-T01-IM6	PRKCI (NM_002740) rearrangement: c.882+63_c.1204-3176inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		3426	0	9	3	Intron of PRKCI(+):63bp after exon 9	PRKCI	169998254			3	Intron of PRKCI(+):3Kb before exon 13	PRKCI	170006466			0	INVERSION		8212	302537	4126	9	NEW_VARIANT
P-0040673-T01-IM6	KCNMA1 (NM_001161352) - ATM (NM_000051) rearrangement: t(10;11)(q22.3;q22.3)(chr10:g.79012810::chr11:g.108100016)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KCNMA1:ATM}		0	0	18	11	Exon 4 of ATM(+)	KCNMA1	108100016			10	Intron of KCNMA1(-):2Kb before exon 3	ATM	79012810			10	TRANSLOCATION		0	302730	0	21	NEW_VARIANT
P-0040742-T01-IM6	CDKN1A (NM_078467) rearrangement: t(6;10)(p21.2;q24.1)(chr6:g.36652108::chr10:g.97688301)	PRECISE	Note: The CDKN1A rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	36	10	Intron of C10orf131(+):1Kb after exon 7	CDKN1A	97688301			6	Exon 3 of CDKN1A(+)	CDKN1A	36652108			10	TRANSLOCATION		0	303012	0	61	NEW_VARIANT
P-0040742-T01-IM6	PIEZO1 (NM_001142864) - ANKRD11 (NM_013275) rearrangement: c.64+10713:PIEZO1_c.4215:ANKRD11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PIEZO1:ANKRD11}		26858	0	3	16	Intron of PIEZO1(-):11Kb after exon 1	PIEZO1	88840596			16	Exon 9 of ANKRD11(-)	ANKRD11	89348735			10	DUPLICATION		508139	303009	20441	3	NEW_VARIANT
P-0040742-T01-IM6	FANCA (NM_000135) rearrangement: c.523-242:FANCA_chr16:g.89845570del	IMPPRECISE	Note: The FANCA rearrangement is a deletion of exons 6 - 43.	MANUAL_OK	3to5	3to5	Deletion of 13 exons : out of frame		18826	0	5	16	Intron of FANCA(-):159bp before exon 19	FANCA	89845570			16	Intron of FANCA(-):242bp before exon 6	FANCA	89875017			0	DELETION		29447	303008	11895	5	NEW_VARIANT
P-0040858-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.5638+146_c.7460del	PRECISE	Note: The NOTCH1 rearrangement is an intragenic deletion of exons 31 - 34. One of the breakpoints is within exon 34.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		21122	0	12	9	Exon 34 of NOTCH1(-)	NOTCH1	139390731			9	Intron of NOTCH1(-):145bp after exon 30	NOTCH1	139396054			10	DELETION		5323	304044	24341	12	NEW_VARIANT
P-0041191-T01-IM6	NF1 (NM_001042492) rearrangement: t(6;17)(p21.31;q11.2)(chr6:g.34639847::chr17:g.29486248)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 3. This could potentially lead to loss of function of NF1.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	14	17	Intron of NF1(+):137bp after exon 3	NF1	29486248			6	Intron of C6orf106(-):17Kb before exon 2	NF1	34639847			10	TRANSLOCATION		0	306180	0	14	NEW_VARIANT
P-0041236-T01-IM6	KMT2A (NM_001197104) rearrangement: c.5665-631_c.7580inv	PRECISE	Note: The KMT2A rearrangement is an intragenic inversion of exons 21 - 27. One of the breakpoints is within exon 27. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		12364	0	17	11	Intron of KMT2A(+):630bp before exon 21	KMT2A	118368020			11	Exon 27 of KMT2A(+)	KMT2A	118374187			10	INVERSION		6167	306259	21181	23	NEW_VARIANT
P-0041479-T01-IM6	NCOA3 (NM_181659) rearrangement: c.2752:NCOA3_chr20:g.30868436del	PRECISE	Note: The NCOA3 rearrangement is a deletion of exons 1 - 15. One of the breakpoints is within exon 15. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {KIF3B:NCOA3}		170589	0	18	20	5-UTR of KIF3B(+):29Kb before coding start	NCOA3	30868436			20	Exon 15 of NCOA3(+)	NCOA3	46268365			10	DELETION		15399929	306798	319141	23	NEW_VARIANT
P-0041514-T01-IM6	MYCN (NM_005378) - NBAS (NM_015909) rearrangement: c.1140:MYCN_c.3704-2157:NBASinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MYCN:NBAS}		13008	0	32	2	Intron of NBAS(-):2Kb before exon 32	MYCN	15508974			2	Exon 3 of MYCN(+)	NBAS	16085964			10	INVERSION		576990	306924	246510	32	NEW_VARIANT
P-0041556-T02-IM6	NF1 (NM_001042492) rearrangement: c.5604:NF1_chr17:g.29865551del	PRECISE	Note: The NF1 rearrangement is a deletion of exons 38 - 58. One of the breakpoints is within exon 38.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {NF1:RAB11FIP4}		23248	0	49	17	Exon 38 of NF1(+)	NF1	29654852			17	Promoter of RAB11FIP4(+):147Kb from tx start	NF1	29865551			10	DELETION		210699	313415	20527	53	NEW_VARIANT
P-0041663-T01-IM6	BRCA1 (NM_007294) rearrangement: t(12;17)(q21.31;q21.31)(chr12:g.85813278::chr17:g.41256332)	PRECISE	Note: The BRCA1 rearrangement is a translocation with a breakpoint in intron 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	20	17	Intron of BRCA1(-):54bp before exon 6	BRCA1	41256332			12	IGR: 139Kb before ALX1(+)	BRCA1	85813278			10	TRANSLOCATION		0	307241	0	20	NEW_VARIANT
P-0041865-T01-IM6	CREBBP (NM_004380) - CLUAP1 (NM_015041) rearrangement: c.4560+81:CREBBP_c.856-1144:CLUAP1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CREBBP:CLUAP1}		104770	0	8	16	Intron of CLUAP1(+):1Kb before exon 9	CREBBP	3575268			16	Intron of CREBBP(-):80bp after exon 27	CLUAP1	3786570			10	INVERSION		211302	307591	86718	9	NEW_VARIANT
P-0041865-T01-IM6	CLUAP1 (NM_015041) - SLX4 (NM_032444) rearrangement: c.856-1082:CLUAP1_c.1795:SLX4inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {CLUAP1:SLX4}		48465	0	8	16	Intron of CLUAP1(+):1Kb before exon 9	CLUAP1	3575330			16	Exon 8 of SLX4(-)	SLX4	3646283			10	INVERSION		70953	307592	41791	8	NEW_VARIANT
P-0041865-T01-IM6	CREBBP (NM_004380) - SLX4 (NM_032444) rearrangement: c.4560+81:CREBBP_c.1793:SLX4del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CREBBP:SLX4}		56274	0	8	16	Exon 8 of SLX4(-)	CREBBP	3646285			16	Intron of CREBBP(-):80bp after exon 27	SLX4	3786570			0	DELETION		140285	307590	44891	8	NEW_VARIANT
P-0041944-T01-IM6	RB1 (NM_000321) rearrangement: c.1216-894_c.1242del	IMPPRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 13. One of the breakpoints is within exon 13.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		163	0	41	13	Intron of RB1(+):893bp before exon 13	RB1	48950160			13	Exon 13 of RB1(+)	RB1	48951080			0	DELETION		920	307724	43	80	NEW_VARIANT
P-0041944-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-1755:TMPRSS2_c.40-52948:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		38850	0	65	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39870492			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42871871			10	DELETION		3001379	307725	40858	65	NEW_VARIANT
P-0041955-T01-IM6	AR (NM_000044) rearrangement: c.2063:AR_chrX:g.67117287del	PRECISE	Note: The AR rearrangement is a deletion of exons 4 - 8. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		4415	0	76	X	Exon 4 of AR(+)	AR	66931421			X	IGR: 145Kb before OPHN1(-)	OPHN1	67117287			10	DELETION		185866	307760	6577	78	NEW_VARIANT
P-0042144-T01-IM6	ASXL2 (NM_018263) rearrangement: c.404-492_c.567del	PRECISE	Note: The ASXL2 rearrangement is an intragenic deletion of exons 5 - 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1720	0	6	2	Exon 6 of ASXL2(-)	ASXL2	25991675			2	Intron of ASXL2(-):492bp before exon 5	ASXL2	25994901			10	DELETION		3226	308196	1520	6	NEW_VARIANT
P-0042144-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+3863_c.56-4726del	IMPPRECISE	Note: The TMPRSS2 rearrangement is an intragenic deletion with breakpoints in intron 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within intron		9321	0	30	21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874842			21	Intron of TMPRSS2(-):4Kb after exon 1	TMPRSS2	42876014			0	DELETION		1172	308197	7291	32	NEW_VARIANT
P-0042157-T02-IM6	TRAF7 (NM_032271) rearrangement: t(16;17)(p13.3;q25.3)(chr16:g.2223408::chr17:g.75302737)	IMPPRECISE	Note: The TRAF7 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	51	17	Intron of SEPT9(+):485bp before exon 2	TRAF7	75302737			16	Intron of TRAF7(+):8bp after exon 10	TRAF7	2223408			0	TRANSLOCATION		0	311298	0	51	NEW_VARIANT
P-0042157-T02-IM6	NCOR1 (NM_006311) - TANC2 (NM_025185) rearrangement: c.788:NCOR1_c.2829+1417:TANC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NCOR1:TANC2}		547486	0	32	17	Exon 7 of NCOR1(-)	NCOR1	16056654			17	Intron of TANC2(+):1Kb after exon 15	TANC2	61468322			10	INVERSION		45411668	311297	1160627	36	NEW_VARIANT
P-0042157-T02-IM6	SMARCA4 (NM_003072) rearrangement: c.1593+167_c.4170+2954del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exons 10 - 29.	MANUAL_OK	3to5	3to5	Deletion of 20 exons : in frame		34318	0	12	19	Intron of SMARCA4(+):167bp after exon 9	SMARCA4	11105844			19	Intron of SMARCA4(+):3Kb after exon 29	SMARCA4	11148762			6	DELETION		42918	311295	39197	11	NEW_VARIANT
P-0042157-T02-IM6	DNMT3B (NM_006892) rearrangement: c.45:DNMT3B_chr20:g.31576096del	PRECISE	Note: The DNMT3B rearrangement is a deletion of exons 2 - 23. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		30231	0	5	20	Exon 2 of DNMT3B(+)	DNMT3B	31368174			20	Intron of SUN5(-):515bp before exon 10	DNMT3B	31576096			7	DELETION		207922	311296	41636	5	NEW_VARIANT
P-0042157-T02-IM6	FAT1 (NM_005245) rearrangement: c.3580+5962_c.4049del	PRECISE	Note: The FAT1 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2794	0	13	4	Exon 6 of FAT1(-)	FAT1	187557313			4	Intron of FAT1(-):6Kb after exon 3	FAT1	187578491			10	DELETION		21178	311294	3461	13	NEW_VARIANT
P-0042162-T01-IM6	RB1 (NM_000321) rearrangement: t(13;19)(q14.2;p13.3)(chr13:g.49050895::chr19:g.4443302)	PRECISE	Note: The RB1 rearrangement is a translocation with a breakpoint in exon 25. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	32	19	3-UTR of CHAF1A(+):41Kb after coding stop	RB1	4443302			13	Exon 25 of RB1(+)	RB1	49050895			10	TRANSLOCATION		0	308180	0	34	NEW_VARIANT
P-0042252-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3404:TMPRSS2_c.19-24065:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		38082	0	10	21	Intron of ERG(-):24Kb before exon 2	TMPRSS2	39841609			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873520			0	DELETION		3031911	309159	79740	11	NEW_VARIANT
P-0042281-T01-IM6	ALK (NM_004304) rearrangement: c.3172+234:ALK_chr2:g.240030513inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		833073	0	5	2	Intron of ALK(-):233bp after exon 19	ALK	29448093			2	Intron of HDAC4(-):634bp before exon 15	ALK	240030513			10	INVERSION		210582420	309595	307299	5	NEW_VARIANT
P-0042489-T01-IM6	PTEN (NM_000314) rearrangement: c.573:PTEN_chr10:g.89858758del	PRECISE	Note: The PTEN rearrangement is a deletion of exons 6 - 9. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	-		4284	0	14	10	Exon 6 of PTEN(+)	PTEN	89711955			10	IGR: 175Kb before RNLS(-)	PTEN	89858758			10	DELETION		146803	310436	3141	14	NEW_VARIANT
P-0042503-T01-IM6	ETV6 (NM_001987) - NTRK3 (NM_001012338) fusion: t(12;15)(p13.2;q25.3)(chr12:g.12032802::chr15:g.88556067)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	245	15	Intron of NTRK3(-):20Kb after exon 14	ETV6	88556067			12	Intron of ETV6(+):5Kb before exon 6	NTRK3	12032802			10	TRANSLOCATION		0	310457	0	244	NEW_VARIANT
P-0042548-T01-IM6	ARID1A (NM_006015) rearrangement: c.5676:ARID1A_chr1:g.29532886del	PRECISE	Note: The ARID1A rearrangement is a deletion of exon 20. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Antisense Fusion		33098	0	37	1	Exon 20 of ARID1A(+)	ARID1A	27106065			1	Intron of MECR(-):387bp after exon 4	ARID1A	29532886			10	DELETION		2426821	310615	18112	37	NEW_VARIANT
P-0042591-T01-IM6	CARD11 (NM_032415) rearrangement: c.685-259_c.2876inv	IMPPRECISE	Note: The CARD11 rearrangement is an intragenic inversion of exons 6 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		32286	0	7	7	Exon 22 of CARD11(-)	CARD11	2953064			7	Intron of CARD11(-):259bp before exon 6	CARD11	2979821			0	INVERSION		26757	310870	36478	7	NEW_VARIANT
P-0042654-T01-IM6	SEC16A (NM_014866) - NOTCH1 (NM_017617) rearrangement: c.6478:SEC16A_c.749:NOTCH1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SEC16A:NOTCH1}		107118	1	136	9	Exon 26 of SEC16A(-)	SEC16A	139342102			9	Exon 5 of NOTCH1(-)	NOTCH1	139414011			10	DUPLICATION		71909	310941	147491	153	NEW_VARIANT
P-0042741-T01-IM6	MSH2 (NM_000251) rearrangement: c.367-659_c.646-71inv	PRECISE	Note: The MSH2 rearrangement is an intragenic inversion of exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		2047	0	4	2	Intron of MSH2(+):658bp before exon 3	MSH2	47636574			2	Intron of MSH2(+):70bp before exon 4	MSH2	47639482			3	INVERSION		2908	311301	2143	4	NEW_VARIANT
P-0042741-T01-IM6	PBRM1 (NM_018313) rearrangement: c.3126_c.3617-3352dup	PRECISE	Note: The PBRM1 rearrangement is an intragenic duplication of exons 21 - 23. One of the breakpoints is within exon 21. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		3333	0	43	3	Intron of PBRM1(-):3Kb before exon 24	PBRM1	52601601			3	Exon 21 of PBRM1(-)	PBRM1	52620627			10	DUPLICATION		19026	311299	4434	45	NEW_VARIANT
P-0042818-T01-IM6	DNMT3A (NM_022552) rearrangement: c.1474+76_c.1554+22inv	PRECISE	Note: The DNMT3A rearrangement is an intragenic inversion of exon 13. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		2310	0	7	2	Intron of DNMT3A(-):21bp after exon 13	DNMT3A	25468100			2	Intron of DNMT3A(-):75bp after exon 12	DNMT3A	25468813			10	INVERSION		713	313095	2886	7	NEW_VARIANT
P-0043381-T02-IM6	KMT2A (NM_001197104) - YAP1 (NM_001130145) rearrangement: c.3634+100:KMT2A_c.1277-339:YAP1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {KMT2A:YAP1}		101647	0	48	11	Intron of YAP1(+):338bp before exon 9	KMT2A	102100094			11	Intron of KMT2A(+):100bp after exon 6	YAP1	118351053			10	DUPLICATION		16250959	319234	87718	50	NEW_VARIANT
P-0043706-T01-IM6	ERBB2 (NM_004448) - CDK12 (NM_016507) rearrangement: c.2293:ERBB2_c.2768+237:CDK12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ERBB2:CDK12}		39943	0	17	17	Intron of CDK12(+):237bp after exon 8	ERBB2	37668120			17	Exon 19 of ERBB2(+)	CDK12	37880249			10	DUPLICATION		212129	315371	44051	17	NEW_VARIANT
P-0044075-T01-IM6	ERBB4 (NM_005235) rearrangement: c.2529:ERBB4_chr2:g.144181408del	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		139800	0	5	2	Intron of ARHGAP15(+):12Kb before exon 7	ERBB4	144181408			2	Exon 21 of ERBB4(-)	ERBB4	212295784			10	DELETION		68114376	317394	179031	6	NEW_VARIANT
P-0044122-T01-IM6	RAD51 (NM_002875) rearrangement: c.226:RAD51_chr15:g.40878263del	PRECISE	Note: The RAD51 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	-		4055	0	2	15	IGR: 8Kb before CASC5(+)	RAD51	40878263			15	Exon 4 of RAD51(+)	RAD51	40998375			4	DELETION		120112	317448	4881	2	NEW_VARIANT
P-0044136-T01-IM6	CALR (NM_004343) rearrangement: t(19;22)(p13.2;q11.21)(chr19:g.13054505::chr22:g.20098581)	PRECISE	Note: The CALR rearrangement is a translocation with a breakpoint in intron 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	63	22	3-UTR of DGCR8(+):25Kb after coding stop	CALR	20098581			19	Intron of CALR(+):21bp before exon 9	CALR	13054505			10	TRANSLOCATION		0	317464	0	64	NEW_VARIANT
P-0044137-T01-IM6	MDC1 (NM_014641) rearrangement: c.2222-907_c.4545inv	IMPPRECISE	Note: The MDC1 rearrangement is an intragenic inversion of exons 8 - 10. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		21010	0	9	6	Exon 10 of MDC1(-)	MDC1	30672415			6	Intron of MDC1(-):907bp before exon 8	MDC1	30677041			0	INVERSION		4626	317466	25197	9	NEW_VARIANT
P-0044146-T01-IM6	PBRM1 (NM_018313) rearrangement: c.995+93:PBRM1_chr3:g.51878023del	PRECISE	Note: The PBRM1 rearrangement is a deletion of exons 11 - 30.	MANUAL_OK	3to5	3to5	-		58186	0	29	3	IGR: 17Kb before IQCF3(+)	PBRM1	51878023			3	Intron of PBRM1(-):92bp after exon 10	PBRM1	52677171			10	DELETION		799148	317486	52012	30	NEW_VARIANT
P-0044188-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.126_c.495+11del	IMPPRECISE	Note: The CTNNB1 rearrangement is an intragenic deletion of exons 3 - 4. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2275	0	18	3	Exon 3 of CTNNB1(+)	CTNNB1	41266129			3	Intron of CTNNB1(+):11bp after exon 4	CTNNB1	41266709			0	DELETION		580	318225	1970	20	NEW_VARIANT
P-0044216-T01-IM6	UBE2W (NM_001001481) - TCEB1 (NM_005648) rearrangement: c.331-2118:UBE2W_c.5-72:TCEB1dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {UBE2W:TCEB1}		3580	0	9	8	Intron of UBE2W(-):2Kb before exon 4	UBE2W	74724982			8	Intron of TCEB1(-):72bp before exon 3	TCEB1	74868361			0	DUPLICATION		143379	318285	6618	14	NEW_VARIANT
P-0044258-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.55+3295:TMPRSS2_c.39+20043:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		83627	0	6	21	Intron of ERG(-):20Kb after exon 3	TMPRSS2	39927543			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42876582			10	DELETION		2949039	319742	93040	6	NEW_VARIANT
P-0044291-T01-IM6	ETV6 (NM_001987) rearrangement: c.34-69:ETV6_chr12:g.3781481del	PRECISE	Note: The ETV6 rearrangement is a deletion of exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		19853	0	11	12	Intron of CRACR2A(-):1Kb after exon 7	ETV6	3781481			12	Intron of ETV6(+):68bp before exon 2	ETV6	11905315			10	DELETION		8123834	318761	26712	11	NEW_VARIANT
P-0044415-T01-IM6	FGFR3 (NM_000142) rearrangement: c.1745:FGFR3_chr4:g.1774446del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		26176	0	151	4	IGR: 21Kb before FGFR3(+)	FGFR3	1774446			4	Exon 13 of FGFR3(+)	FGFR3	1807576			10	DELETION		33130	319100	13693	164	NEW_VARIANT
P-0044482-T01-IM6	ATRX (NM_000489) rearrangement: c.2352:ATRX_chrX:g.72451668inv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 9 - 35. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		49106	0	27	X	IGR: 20Kb before NAP1L2(-)	ATRX	72451668			X	Exon 9 of ATRX(-)	ATRX	76938396			10	INVERSION		4486728	319241	38601	35	NEW_VARIANT
P-0044568-T01-IM6	PRKCI (NM_002740) rearrangement: c.1324:PRKCI_chr3:g.169921961inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		11333	0	25	3	IGR: 18Kb before PRKCI(+)	PRKCI	169921961			3	Exon 14 of PRKCI(+)	PRKCI	170011203			10	INVERSION		89242	320145	21203	30	NEW_VARIANT
P-0044782-T01-IM6	TP53 (NM_000546) rearrangement: c.782+109_c.994-1104del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 9.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3865	0	25	17	Intron of TP53(-):1Kb before exon 10	TP53	7575137			17	Intron of TP53(-):108bp after exon 7	TP53	7577390			10	DELETION		2253	320578	3587	26	NEW_VARIANT
P-0044801-T01-IM6	TSPAN9 (NM_001168320) - TEK (NM_000459) rearrangement: t(9;12)(p21.2;p13.32)(chr9:g.27192473::chr12:g.3328633)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TSPAN9:TEK}		0	0	5	12	Intron of TSPAN9(+):18Kb after exon 2	TSPAN9	3328633			9	Intron of TEK(+):13bp before exon 11	TEK	27192473			0	TRANSLOCATION		0	320586	0	5	NEW_VARIANT
P-0045298-T01-IM6	KMT2A (NM_001197104) rearrangement: c.9366:KMT2A_chr11:g.80166458del	PRECISE	Note: The KMT2A rearrangement is a deletion of exons 1 - 27. One of the breakpoints is within exon 27.	MANUAL_OK	3to5	3to5	-		314951	0	87	11	IGR: 296Kb before LOC101928944(-)	KMT2A	80166458			11	Exon 27 of KMT2A(+)	KMT2A	118375973			10	DELETION		38209515	322316	225118	93	NEW_VARIANT
P-0048585-T03-IM6	ARID1A (NM_006015) rearrangement: t(1;10)(p36.11;q21.3)(chr1:g.27088668::chr10:g.70533678)	PRECISE	Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	40	10	Intron of CCAR1(+):822bp after exon 19	ARID1A	70533678			1	Exon 7 of ARID1A(+)	ARID1A	27088668			10	TRANSLOCATION		0	335937	0	81	NEW_VARIANT
P-0048585-T03-IM6	CIC (NM_015125) rearrangement: t(9;19)(q34.11;q13.2)(chr9:g.130456657::chr19:g.42793014)	PRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	86	19	Intron of CIC(+):25bp before exon 7	CIC	42793014			9	Promoter of STXBP1(+):82Kb from tx start	CIC	130456657			10	TRANSLOCATION		0	335939	0	97	NEW_VARIANT
P-0048761-T01-IM6	TMPRSS2 exon 1 to ETV5 exon 6	PRECISE	Note: The TMPRSS2 - ETV5 fusion involves TMPRSS2 exon 1 and ETV5 exons 6 - 13. The fusion is predicted to be in frame.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TMPRSS2:ETV5}		0	0	11	21	Intron of TMPRSS2(-):4Kb before exon 2	TMPRSS2 exon 1 to ETV5 exon 6	42873899			3	Intron of ETV5(-):1Kb before exon 6	TMPRSS2 exon 1 to ETV5 exon 6	185800235			10	TRANSLOCATION		0	333801	0	12	NEW_VARIANT
P-0049188-T01-IM6	TP53 (NM_000546) rearrangement: c.1065:TP53_chr17:g.8205033del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 1 - 10. One of the breakpoints is within exon 10.	MANUAL_OK	3to5	3to5	-		75640	0	82	17	Exon 10 of TP53(-)	TP53	7573962			17	IGR: 9Kb before ARHGEF15(+)	TP53	8205033			10	DELETION		631071	335265	77255	106	NEW_VARIANT
P-0049188-T01-IM6	MAD1L1 (NM_001013837) - TMPRSS2 (NM_001135099) rearrangement: t(7;21)(p22.3;q22.3)(chr7:g.2217379::chr21:g.42874884)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {MAD1L1:TMPRSS2}		0	0	56	21	Intron of TMPRSS2(-):5Kb before exon 2	MAD1L1	42874884			7	Intron of MAD1L1(-):29Kb before exon 11	TMPRSS2	2217379			10	TRANSLOCATION		0	335266	0	57	NEW_VARIANT
P-0004863-T01-IM5	LDLR (NM_000527)  - SMARCA4 (NM_003072) rearrangement : c.940+53:LDLR_c.4171-1958:SMARCA4dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein fusion: out of frame (LDLR-SMARCA4)		14957	0	6	19	Intron of SMARCA4(+): 109bp before exon 30	LDLR	11150025			19	Intron of LDLR(+): 535bp after exon 6	SMARCA4	11218725			3	DUPLICATION		68700	39784	14608	6	NEW_VARIANT
P-0009748-T01-IM5	ERBB2 (NM_004448) - SHC1 (NM_001130041) rearrangement: t(1;17)(q21.3;q12)(chr1:g.154946879::chr17:g.37883375)	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript fusion (ERBB2-SHC1)		0	0	32	17	Intron of ERBB2(+): 119bp after exon 25	ERBB2	37883375			1	5-UTR of SHC1(-): 4Kb before coding start	SHC1	154946879			17	TRANSLOCATION		0	136348	0	25	NEW_VARIANT
P-0014640-T01-IM6	FAT1 (NM_005245) Rearrangement :  t(4;16)(q35.2;q24.1)(chr4:g.187630430::chr16:g.:84263298)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense fusion		0	0	21	16	Intron of KCNG4(-): 7Kb before exon 3	FAT1	84263298			4	Exon 2 of FAT1(-)	FAT1	187630430			16	TRANSLOCATION		0	165325	0	21	NEW_VARIANT
P-0014640-T01-IM6	FAT1 (NM_005245) Rearrangement : t(1;4)(p21.1;q35.2)(chr1:g.103194060::chr4:g.187630550)	PRECISE	Note: The FAT1 Rearrangement is a translocation event which results in the possible truncation of exons 1-2 of FAT1. One of the breakpoints is within exon2. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	25	4	Exon 2 of FAT1(-)	FAT1	187630550			1	IGR: 148Kb before COL11A1(-)	FAT1	103194060			24	TRANSLOCATION		0	165327	0	25	NEW_VARIANT
P-0016989-T02-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+57:FGFR3_c.1645-139:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		36098	0	111	4	Intron of TACC3(+):138bp before exon 8	FGFR3	1737319			4	Intron of FGFR3(+):57bp after exon 17	TACC3	1808718			10	DUPLICATION		71399	280332	59013	117	NEW_VARIANT
P-0031769-T01-IM6	KMT2C (NM_170606) rearrangement: c.13948_c.14032-558del	PRECISE	Note: The KMT2C rearrangement is an intragenic deletion of a part of exon 53. One of the breakpoints is within exon 53.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		435	0	17	7	Intron of KMT2C(-):558bp before exon 54	KMT2C	151842938			7	Exon 53 of KMT2C(-)	KMT2C	151843767			10	DELETION		829	231009	693	18	NEW_VARIANT
P-0033066-T01-IM6	STRN (NM_003162) - ALK (NM_004304) fusion( STRN exons 1-3 fused to ALK exons 19-29): c.413-1084:STRN_c.3134:ALKdel	PRECISE	Note: The STRN - ALK fusion includes the kinase domain of ALK. One of the breakpoints is within ALK exon 19.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {STRN:ALK}		48833	0	71	2	Exon 19 of ALK(-)	STRN	29448365			2	Intron of STRN(-):1Kb before exon 4	ALK	37133845			10	DELETION		7685480	237465	45642	83	NEW_VARIANT
P-0034063-T01-IM6	STAT3(NM_139276) Rearrangement: c.372+1_c.1282-1423	PRECISE	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	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		8881	0	22	17	Intron of STAT3(-):1Kb before exon 15	STAT3	40479640			17	Exon 4 of STAT3(-)	STAT3	40497576			10	DELETION		17936	248152	8183	22	NEW_VARIANT
P-0034131-T01-IM6	ETV6 (NM_001987) rearrangement: t(6;12)(p21.32;p13.2)(chr6:g.32990236::chr12:g.12030529)	PRECISE	Note: The ETV6 rearrangement is translocation with a breakpoint in intron 5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	36	12	Intron of ETV6(+):7Kb before exon 6	ETV6	12030529			6	IGR: 18Kb before HLA-DOA(-)	ETV6	32990236			10	TRANSLOCATION		0	248895	0	39	NEW_VARIANT
P-0034897-T01-IM6	ERG (NM_004449) - TMPRSS2 (NM_001135099) rearrangement: c.40-56487:ERG_c.56-1366:TMPRSS2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		42374	0	36	21	Intron of ERG(-):56Kb before exon 4	ERG	39874031			21	Intron of TMPRSS2(-):1Kb before exon 2	TMPRSS2	42871482			10	INVERSION		2997451	254537	40626	36	NEW_VARIANT
P-0036175-T01-IM6	RB1 (NM_000321) rearrangement: c.1726:RB1_chr13:g.48827936inv	PRECISE	Note: The RB1 rearrangement is an inversion of exons 1-18. One of the breakpoints is within exon 18. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		19531	0	16	13	Intron of ITM2B(+):7bp before exon 2	RB1	48827936			13	Exon 18 of RB1(+)	RB1	49027159			10	INVERSION		199223	265624	13259	15	NEW_VARIANT
P-0037381-T01-IM6	FLT3 (NM_004119) rearrangement: c.1309+105:FLT3_chr13:g.28496734del	PRECISE	Note: The FLT3 rearrangement results in the deletion of exons 11-24. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		15362	0	12	13	Intron of PDX1(+):2Kb before exon 2	FLT3	28496734			13	Intron of FLT3(-):104bp after exon 10	FLT3	28611217			8	DELETION		114483	278603	20842	12	NEW_VARIANT
P-0037535-T01-IM6	SRC (NM_198291) - RPN2 (NM_002951) rearrangement: c.989:SRC_c.986+998:RPN2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SRC:RPN2}		12354	0	21	20	Intron of RPN2(+):998bp after exon 7	SRC	35839566			20	Exon 10 of SRC(+)	RPN2	36028647			10	DUPLICATION		189081	279868	19721	27	NEW_VARIANT
P-0037535-T01-IM6	MST1R (NM_002447) rearrangement: c.1231-1449_c.2474:del	PRECISE	Note: MST1R rearrangement is an intragenic deletion of exons 2-10. One of the breakpoints is within exon 10. The functionals significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		16309	0	36	3	Exon 10 of MST1R(-)	MST1R	49933803			3	Intron of MST1R(-):1Kb before exon 2	MST1R	49938145			10	DELETION		4342	279865	13888	36	NEW_VARIANT
P-0037541-T01-IM6	DNMT3B (NM_006892) rearrangement: c.814-51:DNMT3B_chr20:g.36490825inv	PRECISE	Note: The DNMT3B rearrangement is an inversion of exons 8-23. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		47241	0	24	20	Intron of DNMT3B(+):50bp before exon 8	DNMT3B	31379356			20	Intron of CTNNBL1(+):2Kb after exon 15	DNMT3B	36490825			10	INVERSION		5111469	280469	62107	25	NEW_VARIANT
P-0037610-T01-IM6	ETV6 (NM_001987) - NTRK3 (NM_001012338) rearrangement: t(12;15)(p13.2;q25.3)(chr12:g.12014663::chr15:g.88594532)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ETV6:NTRK3}		0	0	29	15	Intron of NTRK3(-):18Kb before exon 14	ETV6	88594532			12	Intron of ETV6(+):8Kb before exon 5	NTRK3	12014663			10	TRANSLOCATION		0	280697	0	28	NEW_VARIANT
P-0037750-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+3617:TMPRSS2_c.18+9142:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exon 1 and ERG exons 2-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		107912	0	18	21	Intron of ERG(-):9Kb after exon 1	TMPRSS2	39861145			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42876260			10	DELETION		3015115	281948	38570	19	NEW_VARIANT
P-0037968-T01-IM6	RPTOR (NM_020761) rearrangement: c.3074_c.3370+2706del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4442	0	5	17	Exon 26 of RPTOR(+)	RPTOR	78919515			17	Intron of RPTOR(+):3Kb after exon 28	RPTOR	78926053			0	DELETION		6538	283072	6074	5	NEW_VARIANT
P-0038498-T01-IM6	NCOR1 (NM_006311) - CENPV (NM_181716) rearrangement: c.1534:NCOR1_c.579+1344:CENPVdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NCOR1:CENPV}		18514	0	8	17	Exon 15 of NCOR1(-)	NCOR1	16029496			17	Intron of CENPV(-):1Kb after exon 3	CENPV	16250586			9	DUPLICATION		221090	286776	19687	8	NEW_VARIANT
P-0039666-T02-IM6	RAD51C (NM_058216) rearrangement: t(5;17)(q31.3;q22)(chr5:g.142325223::chr17:g.56772289)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	-		0	0	17	17	Intron of RAD51C(+):2bp before exon 2	RAD51C	56772289			5	Intron of ARHGAP26(+):14Kb after exon 11	RAD51C	142325223			0	TRANSLOCATION		0	315359	0	23	NEW_VARIANT
P-0040447-T01-IM6	RB1 (NM_000321) rearrangement: c.1696-28342_c.1960+118dup	PRECISE	Note: The RB1 rearrangement is an intragenic duplication of exons 18 - 19. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		1715	0	10	13	Intron of RB1(+):28Kb before exon 18	RB1	48998787			13	Intron of RB1(+):118bp after exon 19	RB1	49030603			8	DUPLICATION		31816	301743	2120	10	NEW_VARIANT
P-0040447-T01-IM6	DOT1L (NM_032482) rearrangement: c.4606+1220:DOT1L_chr19:g.2067589del	PRECISE	Note: The DOT1L rearrangement is a deletion of exons 1 - 27. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		68072	0	27	19	IGR: 3Kb before MOB3A(-)	DOT1L	2067589			19	Intron of DOT1L(+):1Kb after exon 27	DOT1L	2228346			10	DELETION		160757	301742	73193	29	NEW_VARIANT
P-0040532-T01-IM6	SLC24A3 (NM_020689) - BCL2L11 (NM_138621) rearrangement: t(2;20)(q13;p11.23)(chr2:g.111887601::chr20:g.19507624)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {SLC24A3:BCL2L11}		0	0	5	20	Intron of SLC24A3(+):11Kb after exon 3	SLC24A3	19507624			2	Intron of BCL2L11(+):6Kb after exon 2	BCL2L11	111887601			0	TRANSLOCATION		0	302169	0	5	NEW_VARIANT
P-0040532-T01-IM6	NUF2 (NM_031423) rearrangement: t(1;8)(q23.3;q21.11)(chr1:g.163307802::chr8:g.78255575)	PRECISE	Note: The NUF2 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	23	8	IGR: 107Kb before LOC102724874(+)	NUF2	78255575			1	Intron of NUF2(+):7bp before exon 7	NUF2	163307802			10	TRANSLOCATION		0	302168	0	22	NEW_VARIANT
P-0040533-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.1187+33:PIK3R3_chr1:g.46508673del	PRECISE	Note: The PIK3R3 rearrangement is a deletion of exon 10.	MANUAL_OK	3to5	3to5	-		2289	0	35	1	3-UTR of PIK3R3(-):671bp after coding stop	PIK3R3	46508673			1	Intron of PIK3R3(-):32bp after exon 9	PIK3R3	46511557			10	DELETION		2884	302164	2225	39	NEW_VARIANT
P-0040533-T01-IM6	ELF3 (NM_004433) rearrangement: t(1;6)(q32.1;p22.3)(chr1:g.201982527::chr6:g.21341871)	IMPPRECISE	Note: The ELF3 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	33	6	IGR: 144Kb before LINC00581(-)	ELF3	21341871			1	Intron of ELF3(+):101bp after exon 7	ELF3	201982527			0	TRANSLOCATION		0	302165	0	33	NEW_VARIANT
P-0040846-T01-IM6	KMT2D (NM_003482) rearrangement: t(8;12)(q24.22;q13.12)(chr8:g.131599592::chr12:g.49443721)	PRECISE	Note: The KMT2D rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	75	12	Exon 11 of KMT2D(-)	KMT2D	49443721			8	IGR: 193Kb before ADCY8(-)	KMT2D	131599592			10	TRANSLOCATION		0	304021	0	99	NEW_VARIANT
P-0040853-T01-IM6	APC (NM_000038) rearrangement: c.1351:APC_chr5:g.150062097del	IMPPRECISE	Note: The APC rearrangement is a deletion of exons 11 - 16. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	-		203972	0	7	5	Exon 11 of APC(+)	APC	112157631			5	IGR: 8Kb before RBM22(-)	APC	150062097			0	DELETION		37904466	304032	213878	7	NEW_VARIANT
P-0040973-T01-IM6	ATRX (NM_000489) rearrangement: c.1339_c.5135-6053del	PRECISE	Note: The ATRX rearrangement is an intragenic deletion of exons 9 - 19. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12018	0	66	X	Intron of ATRX(-):6Kb before exon 20	ATRX	76882053			X	Exon 9 of ATRX(-)	ATRX	76939409			10	DELETION		57356	305087	2376	69	NEW_VARIANT
P-0041027-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4212:TMPRSS2_c.18+1068:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		61551	0	105	21	Intron of ERG(-):1Kb after exon 1	TMPRSS2	39869219			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875665			10	DELETION		3006446	305372	55310	106	NEW_VARIANT
P-0041234-T01-IM6	NRXN2 (NM_015080) - MEN1 (NM_000244) rearrangement: c.3848-706:NRXN2_c.1365+92:MEN1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NRXN2:MEN1}		4656	0	171	11	Intron of NRXN2(-):706bp before exon 21	NRXN2	64391256			11	Intron of MEN1(-):91bp after exon 9	MEN1	64572414			10	DUPLICATION		181158	306262	15053	194	NEW_VARIANT
P-0041234-T01-IM6	RECQL (NM_032941) rearrangement: c.1216+238_c.1668-86del	PRECISE	Note: The RECQL rearrangement is an intragenic deletion of exons 12 - 14.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		3892	0	6	12	Intron of RECQL(-):86bp before exon 15	RECQL	21624118			12	Intron of RECQL(-):237bp after exon 11	RECQL	21628164			10	DELETION		4046	306261	4090	11	NEW_VARIANT
P-0041234-T01-IM6	EP300 (NM_001429) rearrangement: t(14;22)(q32.33;q13.2)(chr14:g.107283261::chr22:g.41548197)	PRECISE	Note: The EP300 rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	7	22	Intron of EP300(+):12bp before exon 16	EP300	41548197			14	IGR: 24Kb before MIR5195(-)	EP300	107283261			10	TRANSLOCATION		0	306263	0	35	NEW_VARIANT
P-0041235-T01-IM6	NHSL2 (NM_001013627) - MED12 (NM_005120) rearrangement: c.281-101040:NHSL2_c.6021:MED12dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NHSL2:MED12}		7695	0	7	X	Exon 41 of MED12(+)	NHSL2	70357770			X	Intron of NHSL2(+):101Kb before exon 2	MED12	71250889			10	DUPLICATION		893119	306255	4238	7	NEW_VARIANT
P-0041326-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2260:TMPRSS2_chr21:g.37538498del	PRECISE	Note: The TMPRSS2 rearrangement is a deletion of exons 2 - 14. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		60317	0	35	21	Intron of DOPEY2(+):1Kb after exon 2	TMPRSS2	37538498			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872376			10	DELETION		5333878	306363	66398	38	NEW_VARIANT
P-0041432-T01-IM6	TP53 (NM_000546) rearrangement: c.1173:TP53_chr17:g.687501del	PRECISE	Note: The TP53 rearrangement is a deletion of exon 11. One of the breakpoints is within exon 11.	MANUAL_OK	3to5	3to5	Antisense Fusion		21894	0	122	17	Intron of RNMTL1(+):934bp after exon 2	TP53	687501			17	Exon 11 of TP53(-)	TP53	7572936			10	DELETION		6885435	306750	29314	130	NEW_VARIANT
P-0041547-T01-IM6	NOTCH2 (NM_024408) rearrangement: t(1;18)(p12;q12.1)(chr1:g.120462071::chr18:g.27255333)	PRECISE	Note: The NOTCH2 rearrangement is a translocation with a breakpoint in exon 31. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	53	18	IGR: 624Kb before MIR302F(+)	NOTCH2	27255333			1	Exon 31 of NOTCH2(-)	NOTCH2	120462071			10	TRANSLOCATION		0	307013	0	53	NEW_VARIANT
P-0041584-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) (TMPRSS2 exon 1 fused to ERG exon 2-11): c.56-236:TMPRSS2_c.-150+5808:ERGdel	IMPPRECISE		MANUAL_OK	3to5	3to5	-		31671	0	23	21	3-UTR of ERG(-):6Kb after coding stop	TMPRSS2	40027774			21	Intron of TMPRSS2(-):236bp before exon 2	ERG	42870352			0	DELETION		2842578	307033	54552	24	NEW_VARIANT
P-0041639-T01-IM6	RB1 (NM_000321) rearrangement: c.1050-139:RB1_chr13:g.51785980inv	PRECISE	Note: The RB1 rearrangement is an inversion of exons 11 - 27. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		24744	0	7	13	Intron of RB1(+):138bp before exon 11	RB1	48942524			13	IGR: 10Kb before FAM124A(+)	RB1	51785980			10	INVERSION		2843456	307199	25061	7	NEW_VARIANT
P-0041836-T01-IM6	FGFR3 (NM_000142) rearrangement: c.930+627_c.1267-143del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		8245	0	4	4	Intron of FGFR3(+):627bp after exon 7	FGFR3	1804379			4	Intron of FGFR3(+):142bp before exon 10	FGFR3	1806408			10	DELETION		2029	307543	8114	4	NEW_VARIANT
P-0042035-T01-IM6	PIK3R2 (NM_005027) rearrangement: c.1979+40:PIK3R2_chr19:g.18529061inv	PRECISE	Note: The PIK3R2 rearrangement is an inversion of exon 16. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		2108	0	11	19	Intron of PIK3R2(+):40bp after exon 15	PIK3R2	18279746			19	Promoter of SSBP4(+):1Kb from tx start	PIK3R2	18529061			10	INVERSION		249315	308099	2579	11	NEW_VARIANT
P-0042036-T01-IM6	BRAF (NM_004333) rearrangement: c.1314+573:BRAF_chr7:g.114530920del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		140119	0	8	7	IGR: 31Kb before MDFIC(+)	BRAF	114530920			7	Intron of BRAF(-):572bp after exon 10	BRAF	140482248			10	DELETION		25951328	308082	78111	10	NEW_VARIANT
P-0042064-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.13+185_c.242-54del	PRECISE	Note: The CTNNB1 rearrangement is an intragenic deletion of exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1823	0	113	3	Intron of CTNNB1(+):185bp after exon 2	CTNNB1	41265757			3	Intron of CTNNB1(+):53bp before exon 4	CTNNB1	41266391			10	DELETION		634	308159	1065	118	NEW_VARIANT
P-0042065-T01-IM6	UPF1 (NM_002911) rearrangement: c.133:UPF1_chr19:g.19928130inv	PRECISE	Note: The UPF1 rearrangement is an inversion of exons 1 - 23. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {UPF1:ZNF506}		72102	0	20	19	Exon 1 of UPF1(+)	UPF1	18943151			19	Intron of ZNF506(-):4Kb after exon 1	UPF1	19928130			10	INVERSION		984979	308166	53255	26	NEW_VARIANT
P-0042166-T01-IM6	APC (NM_000038) rearrangement: c.1006_c.1313dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		2827	0	55	5	Exon 10 of APC(+)	APC	112154735			5	Exon 11 of APC(+)	APC	112157593			10	DUPLICATION		2858	308169	4582	56	NEW_VARIANT
P-0042174-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449)rearrangement: c.55+3407:TMPRSS2_ c.-48+2714:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	-		93085	0	29	21	3-UTR of ERG(-):80Kb after coding stop	TMPRSS2	39954054			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42876470			10	DELETION		2922416	308248	94164	31	NEW_VARIANT
P-0042223-T01-IM6	FUBP1 (NM_003902) - GIPC2 (NM_017655) rearrangement: c.1024:FUBP1_c.241-9922:GIPC2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FUBP1:GIPC2}		12204	0	25	1	Exon 12 of FUBP1(-)	FUBP1	78429764			1	Intron of GIPC2(+):10Kb before exon 2	GIPC2	78536437			10	INVERSION		106673	309122	14270	27	NEW_VARIANT
P-0042223-T01-IM6	TP53 (NM_000546) rearrangement: c.75-44_c.799del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 3 - 8. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		11720	0	51	17	Exon 8 of TP53(-)	TP53	7577139			17	Intron of TP53(-):44bp before exon 3	TP53	7579765			10	DELETION		2626	309121	8113	54	NEW_VARIANT
P-0042378-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.55+1935:TMPRSS2_c.18+16715:ERGdel	PRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		94492	0	16	21	Intron of ERG(-):17Kb after exon 1	TMPRSS2	39853572			21	Intron of TMPRSS2(-):2Kb after exon 1	ERG	42877942			10	DELETION		3024370	309773	58996	20	NEW_VARIANT
P-0042507-T01-IM6	WWTR1 (NM_001168280) rearrangement: c.905+478_c.961del	PRECISE	Note: The WWTR1 rearrangement is an intragenic deletion of exon 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		712	0	6	3	Exon 6 of WWTR1(-)	WWTR1	149243857			3	Intron of WWTR1(-):477bp after exon 5	WWTR1	149245145			7	DELETION		1288	310448	1087	6	NEW_VARIANT
P-0042907-T01-IM6	EZH2 (NM_004456) rearrangement: c.2029+29:EZH2_chr7:g.148447872del	PRECISE	Note: The EZH2 rearrangement is a deletion of exons 18 - 20.	MANUAL_OK	3to5	3to5	Antisense Fusion		2704	0	11	7	Intron of CUL1(+):3Kb before exon 3	EZH2	148447872			7	Intron of EZH2(-):28bp after exon 17	EZH2	148507396			8	DELETION		59524	311657	3691	12	NEW_VARIANT
P-0043041-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+1782:EML4_c.3173-203:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		104260	0	58	2	Intron of ALK(-):203bp before exon 20	EML4	29446597			2	Intron of EML4(+):2Kb after exon 12	ALK	42524438			10	INVERSION		13077841	313119	116313	58	NEW_VARIANT
P-0043077-T01-IM6	NCOA4 (NM_001145260) - RET (NM_020975) fusion: c.762+608:NCOA4_c.2137-452:RETdup	PRECISE	Note: The NCOA4 - RET fusion involves NCOA4 exons 1-8 with RET exons 12-20 and includes the kinase domain of RET.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TIMM23B:RET}		25900	0	106	10	Intron of RET(+):451bp before exon 12	NCOA4	43611580			10	Intron of TIMM23B(+):149Kb before exon 7	RET	51583547			10	DUPLICATION		7971967	313240	24789	115	NEW_VARIANT
P-0043253-T01-IM6	FAT1 (NM_005245) rearrangement: c.472:FAT1_chr4:g.186320655del	PRECISE	Note: The FAT1 rearrangement is a deletion of exons 2 - 27. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	Antisense Fusion		79780	0	30	4	Intron of ANKRD37(+):68bp before exon 4	FAT1	186320655			4	Exon 2 of FAT1(-)	FAT1	187630510			10	DELETION		1309855	313592	76388	31	NEW_VARIANT
P-0043290-T01-IM6	BAI3 (NM_001704) - CDKN2A (NM_000077) rearrangement: t(6;9)(q12;p21.3)(chr6:g.69608821::chr9:g.21968952)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {BAI3:CDKN2A}		0	0	14	9	Intron of CDKN2A(-):711bp before exon 3	BAI3	21968952			6	Intron of BAI3(+):32Kb before exon 4	CDKN2A	69608821			10	TRANSLOCATION		0	313735	0	14	NEW_VARIANT
P-0043334-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.1016+102:PIK3R3_chr1:g.98035591inv	PRECISE	Note: The PIK3R3 rearrangement is an inversion of exons 1 - 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		169253	0	33	1	Intron of PIK3R3(-):101bp after exon 8	PIK3R3	46512121			1	Intron of DPYD(-):4Kb after exon 11	PIK3R3	98035591			10	INVERSION		51523470	313869	286659	34	NEW_VARIANT
P-0043334-T01-IM6	CEBPA (NM_004364) rearrangement: c.241:CEBPA_chr19:g.39308775inv	PRECISE	Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		105912	0	39	19	Exon 1 of CEBPA(-)	CEBPA	33793080			19	Intron of ECH1(-):560bp before exon 4	CEBPA	39308775			10	INVERSION		5515695	313870	200809	39	NEW_VARIANT
P-0043417-T01-IM6	TP53 (NM_000546) rearrangement: c.85_c.672+43inv	IMPPRECISE	Note: The TP53 rearrangement is an intragenic inversion of exons 3 - 6. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		7171	0	113	17	Intron of TP53(-):42bp after exon 6	TP53	7578134			17	Exon 3 of TP53(-)	TP53	7579711			0	INVERSION		1577	314132	18686	382	NEW_VARIANT
P-0043417-T01-IM6	CTC1 (NM_025099) - AURKB (NM_004217) rearrangement: c.34-1646:CTC1_c.1035:AURKBdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CTC1:AURKB}		13787	0	29	17	Exon 9 of AURKB(-)	CTC1	8108189			17	Intron of CTC1(-):2Kb before exon 2	AURKB	8148112			10	DELETION		39923	314131	72441	29	NEW_VARIANT
P-0043491-T01-IM6	BCL2 (NM_000633) rearrangement: c.586-54070:BCL2_chr18:g.28860403inv	IMPPRECISE	Note: The BCL2 rearrangement is an inversion of exon 3. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		79460	0	5	18	IGR: 38Kb before DSG1(+)	BCL2	28860403			18	Intron of BCL2(-):54Kb before exon 3	BCL2	60850062			0	INVERSION		31989659	314458	136197	5	NEW_VARIANT
P-0043565-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: t(15;21)(q14;q22.3)(chr15:g.37245374::chr21:g.42874936)	PRECISE	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.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	63	21	Intron of TMPRSS2(-):5Kb before exon 2	TMPRSS2	42874936			15	Intron of MEIS2(-):3Kb before exon 9	TMPRSS2	37245374			10	TRANSLOCATION		0	314950	0	72	NEW_VARIANT
P-0043568-T01-IM6	KDM6A (NM_021140) rearrangement: c.620-810_c.654+57dup	PRECISE	Note: The KDM6A rearrangement is an intragenic duplication of exon 8. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : out of frame		457	0	20	X	Intron of KDM6A(+):809bp before exon 8	KDM6A	44896090			X	Intron of KDM6A(+):57bp after exon 8	KDM6A	44896991			10	DUPLICATION		901	314941	351	20	NEW_VARIANT
P-0043571-T01-IM6	EIF4A2 (NM_001967) rearrangement: c.1025:EIF4A2_chr3:g.186552349del	PRECISE	Note: The EIF4A2 rearrangement is a deletion of exons 10 - 11. One of the breakpoints is within exon 10. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		1336	0	13	3	Exon 10 of EIF4A2(+)	EIF4A2	186505617			3	IGR: 8Kb before ADIPOQ(+)	EIF4A2	186552349			10	DELETION		46732	314942	1522	13	NEW_VARIANT
P-0043634-T01-IM6	ERCC2 (NM_000400) rearrangement: c.184-11:ERCC2_chr19:g.45882309inv	PRECISE	Note: The ERCC2 rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		4898	0	9	19	Intron of ERCC2(-):11bp before exon 4	ERCC2	45872261			19	Promoter of PPP1R13L(-):582bp from tx start	ERCC2	45882309			10	INVERSION		10048	315113	4176	11	NEW_VARIANT
P-0043634-T01-IM6	WHSC1L1 (NM_023034) rearrangement: c.2361_c.2443del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		995	0	20	8	Exon 14 of WHSC1L1(-)	WHSC1L1	38162273			8	Exon 13 of WHSC1L1(-)	WHSC1L1	38162845			0	DELETION		572	315112	1169	24	NEW_VARIANT
P-0043838-T01-IM6	SLC5A5 (NM_000453) - PIK3R2 (NM_005027) rearrangement: c.970-823:SLC5A5_c.1560-134:PIK3R2del	PRECISE	Note: The SLC5A5 - PIK3R2 rearrangement is a deletion that results in a fusion of SLC5A5 exons 1 - 7 to PIK3R2 exons 13 - 16.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {SLC5A5:PIK3R2}		20658	0	14	19	Intron of SLC5A5(+):822bp before exon 8	SLC5A5	17990851			19	Intron of PIK3R2(+):133bp before exon 13	PIK3R2	18277806			10	DELETION		286955	316457	20313	16	NEW_VARIANT
P-0043870-T01-IM6	BRIP1 (NM_032043) rearrangement: c.839:BRIP1_chr17:g.59109530del	PRECISE	Note: The BRIP1 rearrangement is a deletion of exons 7 - 20. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	Antisense Fusion		17586	0	2	17	Intron of BCAS3(+):2Kb before exon 18	BRIP1	59109530			17	Exon 7 of BRIP1(-)	BRIP1	59885907			5	DELETION		776377	316493	25991	2	NEW_VARIANT
P-0043953-T01-IM6	TFAP2E (NM_178548) - CSF3R (NM_000760) rearrangement: c.1047-1011:TFAP2E_c.1291:CSF3Rinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {TFAP2E:CSF3R}		30505	0	6	1	Intron of TFAP2E(+):1Kb before exon 7	TFAP2E	36058984			1	Exon 11 of CSF3R(-)	CSF3R	36935436			10	INVERSION		876452	317258	52481	6	NEW_VARIANT
P-0043953-T01-IM6	RAD54L (NM_001142548) rearrangement: c.766+40_c.891+2361inv	PRECISE	Note: The RAD54L rearrangement is an intragenic inversion of exon 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		1359	0	6	1	Intron of RAD54L(+):40bp after exon 8	RAD54L	46726727			1	Intron of RAD54L(+):2Kb after exon 9	RAD54L	46729418			7	INVERSION		2691	317259	2609	6	NEW_VARIANT
P-0043953-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.4058:WHSC1_chr4:g.4885490inv	IMPPRECISE	Note: The WHSC1 rearrangement is an inversion of exon 22. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		1268	0	5	4	Exon 22 of WHSC1(+)	WHSC1	1980596			4	IGR: 24Kb before MSX1(+)	WHSC1	4885490			0	INVERSION		2904894	317260	1975	5	NEW_VARIANT
P-0044041-T01-IM6	NF1 (NM_001042492) rearrangement: t(3;17)(p21.1;q11.2)(chr3:g.54146314::chr17:g.29548812)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 14. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	22	17	Intron of NF1(+):55bp before exon 15	NF1	29548812			3	IGR: 10Kb before CACNA2D3(+)	NF1	54146314			10	TRANSLOCATION		0	317424	0	27	NEW_VARIANT
P-0044041-T01-IM6	ALK (NM_004304) rearrangement: c.2381_c.3646-1833del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		64326	0	22	2	Intron of ALK(-):2Kb before exon 24	ALK	29438780			2	Exon 14 of ALK(-)	ALK	29456537			10	DELETION		17757	317422	57546	22	NEW_VARIANT
P-0044041-T01-IM6	XPO1 (NM_003400) rearrangement: c.270:XPO1_chr2:g.61780951del	PRECISE	Note: The XPO1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		2606	0	17	2	Exon 4 of XPO1(-)	XPO1	61749777			2	IGR: 76Kb before XPO1(-)	XPO1	61780951			10	DELETION		31174	317423	2062	18	NEW_VARIANT
P-0044210-T01-IM6	B2M (NM_004048) rearrangement: c.164:B2M_chr15:g.45009747del	PRECISE	Note: The B2M rearrangement is a deletion of exons 2 - 3. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		1364	0	7	15	Exon 2 of B2M(+)	B2M	45007717			15	3-UTR of B2M(+):6Kb after coding stop	B2M	45009747			10	DELETION		2030	318310	2101	7	NEW_VARIANT
P-0044296-T01-IM6	TP53 (NM_000546) rearrangement: c.782+137_c.1101-252del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 8 - 10.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		4793	0	28	17	Intron of TP53(-):252bp before exon 11	TP53	7573260			17	Intron of TP53(-):136bp after exon 7	TP53	7577362			10	DELETION		4102	318769	3638	29	NEW_VARIANT
P-0044301-T01-IM6	SMARCB1 (NM_003073) rearrangement: c.359_c.362+3471del	PRECISE	Note: The SMARCB1 rearrangement is an intragenic deletion of exon 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		336	0	2	22	Exon 3 of SMARCB1(+)	SMARCB1	24135872			22	Intron of SMARCB1(+):3Kb after exon 3	SMARCB1	24139346			10	DELETION		3474	319029	645	4	NEW_VARIANT
P-0044346-T01-IM6	INPP4A (NM_001134224) rearrangement: t(2;3)(q11.2;q26.31)(chr2:g.99182038::chr3:g.174056638)	PRECISE	Note: The INPP4A rearrangement is a translocation with a breakpoint in intron 20. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	14	3	IGR: 428Kb before NLGN1-AS1(-)	INPP4A	174056638			2	Intron of INPP4A(+):64bp before exon 21	INPP4A	99182038			10	TRANSLOCATION		0	319018	0	14	NEW_VARIANT
P-0044391-T01-IM6	ARID1A (NM_006015) rearrangement: c.6522:ARID1A_chr1:g.27109427del	PRECISE	Note: The ARID1A rearrangement is a deletion of exon 20. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1889	0	7	1	Exon 20 of ARID1A(+)	ARID1A	27106911			1	Promoter of ARID1A(+):87Kb from tx start	ARID1A	27109427			9	DELETION		2516	319110	2222	8	NEW_VARIANT
P-0044391-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3217-489_c.3409del	PRECISE	Note: The ZFHX3 rearrangement is an intragenic deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1521	0	13	16	Exon 4 of ZFHX3(-)	ZFHX3	72923669			16	Intron of ZFHX3(-):489bp before exon 4	ZFHX3	72924350			10	DELETION		681	319111	1415	12	NEW_VARIANT
P-0044391-T01-IM6	ARID1A (NM_006015) rearrangement: t(1;4)(p36.11;q32.2)(chr1:g.27023724::chr4:g.163326089)	PRECISE	Note: The ARID1A rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	11	4	IGR: 382Kb before LOC101928052(+)	ARID1A	163326089			1	Exon 1 of ARID1A(+)	ARID1A	27023724			10	TRANSLOCATION		0	319113	0	11	NEW_VARIANT
P-0044393-T01-IM6	NOTCH1 (NM_017617) - PNPLA7 (NM_001098537) rearrangement: c.5018+48:NOTCH1_c.748-7350:PNPLA7dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NOTCH1:PNPLA7}		83668	0	7	9	Intron of NOTCH1(-):47bp after exon 26	NOTCH1	139399077			9	Intron of PNPLA7(-):7Kb before exon 9	PNPLA7	140424659			10	DUPLICATION		1025582	319108	107070	7	NEW_VARIANT
P-0044499-T01-IM6	CBL (NM_005188) rearrangement: c.1096-156_c.1431+1123del	PRECISE	Note: The CBL rearrangement is an intragenic deletion of exons 8 - 9.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : in frame		2867	0	9	11	Intron of CBL(+):155bp before exon 8	CBL	119148720			11	Intron of CBL(+):1Kb after exon 9	CBL	119150546			10	DELETION		1826	319281	4585	9	NEW_VARIANT
P-0044499-T01-IM6	POLE (NM_006231) rearrangement: c.2314:POLE_chr12:g.131958142del	PRECISE	Note: The POLE rearrangement is a deletion of exons 20 - 49. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	-		52686	0	9	12	IGR: 126Kb before LOC338797(+)	POLE	131958142			12	Exon 20 of POLE(-)	POLE	133244094			10	DELETION		1285952	319282	84134	9	NEW_VARIANT
P-0044499-T01-IM6	TP53BP1 (NM_001141980) rearrangement: t(14;15)(q21.1;q15.3)(chr14:g.38880416::chr15:g.43720289)	PRECISE	Note: The TP53BP1 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	17	15	Exon 18 of TP53BP1(-)	TP53BP1	43720289			14	IGR: 157Kb before CLEC14A(-)	TP53BP1	38880416			10	TRANSLOCATION		0	319284	0	17	NEW_VARIANT
P-0044499-T01-IM6	RNF43 (NM_017763) rearrangement: c.376-862_c.673del	PRECISE	Note: The RNF43 rearrangement is an intragenic deletion of exons 4 - 6. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4137	0	28	17	Exon 6 of RNF43(-)	RNF43	56439919			17	Intron of RNF43(-):862bp before exon 4	RNF43	56441823			10	DELETION		1904	319283	3071	29	NEW_VARIANT
P-0044499-T01-IM6	DNMT3B (NM_006892) rearrangement: t(12;20)(q24.33;q11.21)(chr12:g.130228060::chr20:g.31383141)	PRECISE	Note: The DNMT3B rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	20	Intron of DNMT3B(+):73bp before exon 11	DNMT3B	31383141			12	Intron of TMEM132D(-):43Kb before exon 2	DNMT3B	130228060			10	TRANSLOCATION		0	319285	0	8	NEW_VARIANT
P-0044607-T01-IM6	ATR (NM_001184) - NAV3 (NM_014903) rearrangement: t(3;12)(q23;q21.2)(chr3:g.142281699::chr12:g.78469330)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ATR:NAV3}		0	0	74	12	Intron of NAV3(+):16Kb after exon 12	ATR	78469330			3	Exon 4 of ATR(-)	NAV3	142281699			10	TRANSLOCATION		0	320178	0	112	NEW_VARIANT
P-0044607-T01-IM6	NTRK2 (NM_006180) - PRUNE2 (NM_015225) rearrangement: c.1445-2036:NTRK2_c.756+13664:PRUNE2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {NTRK2:PRUNE2}		52773	0	6	9	Intron of PRUNE2(-):14Kb after exon 6	NTRK2	79424884			9	Intron of NTRK2(+):2Kb before exon 16	PRUNE2	87480122			10	INVERSION		8055238	320176	64147	6	NEW_VARIANT
P-0044811-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.55+4610:TMPRSS2_c.236+920:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 3 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		77771	0	3	21	Intron of ERG(-):919bp after exon 2	TMPRSS2	39816407			21	Intron of TMPRSS2(-):5Kb after exon 1	ERG	42875267			7	DELETION		3058860	320601	80906	3	NEW_VARIANT
P-0044819-T01-IM6	PPAP2A (NM_176895) - BRAF (NM_004333) fusion: t(5;7)(q11.2;q34)(chr5:g.54789192::chr7:g.140482123)	PRECISE	Note: The PPAP2A - BRAF fusion involves PPAP2A exon 1 and BRAF exons 11 - 18. The fusion includes the kinase domain of BRAF.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {PPAP2A:BRAF}		0	0	38	7	Intron of BRAF(-):630bp before exon 11	PPAP2A	140482123			5	Intron of PPAP2A(-):18Kb before exon 2	BRAF	54789192			10	TRANSLOCATION		0	320603	0	40	NEW_VARIANT
P-0044968-T01-IM6	AIG1 (NM_016108) - TNFAIP3 (NM_006290) rearrangement: c.516-18946:AIG1_c.994:TNFAIP3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {AIG1:TNFAIP3}		10671	0	9	6	Exon 7 of TNFAIP3(+)	AIG1	138199576			6	Intron of AIG1(+):19Kb before exon 5	TNFAIP3	143635473			10	DUPLICATION		5435897	321010	19852	9	NEW_VARIANT
P-0047316-T01-IM6	ERG (NM_182918) rearrangement: t(17;21)(p13.1;q22.2)(chr17:g.7965049::chr21:g.39870294)	PRECISE	Note: The ERG rearrangement is a translocation with a breakpoint in exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	5	21	Exon 1 of ERG(-)	ERG	39870294			17	IGR: 11Kb before ALOX12B(-)	ERG	7965049			10	TRANSLOCATION		0	330344	0	5	NEW_VARIANT
P-0005459-T02-IM6	ATR (NM_001184) rearrangement: t(3;13)(q23;q12.11)(chr3:g.142279020::chr13:g.20695257)	PRECISE	Note: The ATR rearrangement is a translocation involving exon 6. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	19	13	IGR: 17Kb before GJA3(-)	ATR	20695257			3	Intron of ATR(-):84bp after exon 6	ATR	142279020			10	TRANSLOCATION		0	246325	0	19	NEW_VARIANT
P-0005459-T02-IM6	TMPRSS2 (NM_001135099) - DSCAM (NM_001389) rearrangement: c.127-1405:TMPRSS2_c.3562+3890:DSCAMdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:DSCAM}		21753	0	30	21	Intron of DSCAM(-):4Kb after exon 19	TMPRSS2	41501891			21	Intron of TMPRSS2(-):1Kb before exon 3	DSCAM	42867910			10	DELETION		1366019	246323	35664	168	NEW_VARIANT
P-0006847-T01-IM5	PGR (NM_000926) Rearrangement :  c.469_chr11:g.58736058inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		213617	0	14	11	IGR: 25Kb before GLYATL1(+)	PGR	58736058			11	Exon 1 of PGR(-)	PGR	100999333			75	INVERSION		42263275	109434	194179	14	NEW_VARIANT
P-0009524-T01-IM5	AXL (NM_021913) - HNRNPUL1 (NM_007040) rearrangement: c.1369:AXL_c.1000-5031:HNRNPUL1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: mid-exon (AXL-HNRNPUL1)		27502	0	15	19	Exon 10 of AXL(+)	AXL	41748844			19	Intron of HNRNPUL1(+): 5Kb before exon 8	HNRNPUL1	41793119			18	DELETION		44275	131116	25415	14	NEW_VARIANT
P-0009524-T01-IM5	PTPRD (NM_002839) rearrangement: c.65-36596_c.210+2del	PRECISE	Note: The PTPRD (NM_002839) rearrangement is an intragenic deletion of exon 13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon: out of frame		1384	0	15	9	Intron of PTPRD(-): 2bp after exon 13	PTPRD	8636697			9	Intron of PTPRD(-): 37Kb before exon 13	PTPRD	8673440			17	DELETION		36743	131117	1004	15	NEW_VARIANT
P-0009791-T01-IM5	INPP4B (NM_001101669)  Rearrangement: chr4:g.133235766_ c.881:INPP4Binv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		33763	0	18	4	IGR: 835Kb before PCDH10(+)	INPP4B	133235766			4	Exon 14 of INPP4B(-)	INPP4B	143130135			59	INVERSION		9894369	136521	30101	19	NEW_VARIANT
P-0009791-T01-IM5	PPP6C (NM_002721) Rearrangement :  c.460-26:PPP6C_chr9:g.133439773inv	PRECISE	Note: The PPP6C (NM_002721) Rearrangement results in the inversion of exons1-5 of PPP6C.Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		19204	0	7	9	Intron of PPP6C(-): 26bp before exon 6	PPP6C	127916047			9	IGR: 13Kb before LOC100272217(-)	PPP6C	133439773			6	INVERSION		5523726	136522	18660	7	NEW_VARIANT
P-0011025-T01-IM5	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)	PRECISE	Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	67	6	Intron of ROS1(-): 311bp before exon 34	CD74	117645889			5	Intron of CD74(-): 488bp after exon 6	ROS1	149783755			36	TRANSLOCATION		0	150420	0	65	NEW_VARIANT
P-0012114-T03-IM6	DOT1L (NM_032482) Rearrangement: c.1006-245_c.3390+36dup	PRECISE	Note: The DOT1L rearrangement is an intragenic duplication of exons 13-24. The functional significance us undetermined.	MANUAL_OK	5to3	5to3	Duplication of 12 exons : in frame		40624	0	32	19	Intron of DOT1L(+):244bp before exon 13	DOT1L	2210154			19	Intron of DOT1L(+):36bp after exon 24	DOT1L	2222594			10	DUPLICATION		12440	238676	60572	33	NEW_VARIANT
P-0012114-T03-IM6	MET (NM_000245) - MYH15 (NM_014981) rearrangement: t(3;7)(q13.3;q31.2)(chr3:g.108193597::chr7:g.116412012)	PRECISE	Note: The MET - MYH15 rearrangement is a translocation that results in a fusion of MET exons 1-14 to MYH15 exons 14-42.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {MET:MYH15}		0	0	35	7	Exon 14 of MET(+)	MET	116412012			3	Intron of MYH15(-):2Kb after exon 13	MYH15	108193597			10	TRANSLOCATION		0	238677	0	35	NEW_VARIANT
P-0012114-T03-IM6	CD47 (NM_001777) - MET (NM_000245) rearrangement: t(3;7)(q13.12;q31.2)(chr3:g.107772171::chr7:g.116412066)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CD47:MET}		0	0	28	7	Intron of MET(+):23bp after exon 14	CD47	116412066			3	Intron of CD47(-):1Kb before exon 8	MET	107772171			10	TRANSLOCATION		0	238678	0	30	NEW_VARIANT
P-0015437-T01-IM6	FGFR2 (NM_000141) - HSPA12A (NM_025015) rearrangement: c.2301+621:FGFR2_c.663+3346:HSPA12Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (FGFR2-HSPA12A)		35167	0	18	10	Intron of HSPA12A(-): 3Kb after exon 6	FGFR2	118448516			10	Intron of FGFR2(-): 621bp after exon 16	HSPA12A	123242591			17	DELETION		4794075	168018	36439	18	NEW_VARIANT
P-0019995-T01-IM6	PBRM1 (NM_018313) Rearrangement :  c.385-2621_c.2522del	PRECISE	Note: The PBRM1 Rearrangement results in the deletion of exon 5-17. One of the breakpoints is within exon17. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		23091	0	5	3	Exon 17 of PBRM1(-)	PBRM1	52643374			3	Intron of PBRM1(-):3Kb before exon 5	PBRM1	52698913			10	DELETION		55539	183431	20122	5	NEW_VARIANT
P-0020970-T01-IM6	RFWD2 (NM_022457) rearrangement: c.920_c.642+31del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4227	0	45	1	Exon 8 of RFWD2(-)	RFWD2	176104194			1	Intron of RFWD2(-):30bp after exon 4	RFWD2	176132920			10	DELETION		28726	185882	3114	45	NEW_VARIANT
P-0021147-T01-IM6	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	PRECISE	Note: The GOPC - ROS1 fusion is predicted to be in-frame and includes the protein kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {GOPC:ROS1}		185598	0	53	6	Intron of ROS1(-):508bp before exon 36	GOPC	117641701			6	Intron of GOPC(-):735bp before exon 5	ROS1	117895530			10	DELETION		253829	186300	102079	62	NEW_VARIANT
P-0021782-T01-IM6	TMPRSS2 (NM_001135099) -ERG (NM_004449) Fusion (TMPRSS2 exon 1 with ERG exon4) : c.56-2752:TMPRSS2_c.39+30375:ERGdel	PRECISE		MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		80541	0	125	21	Intron of ERG(-):30Kb after exon 3	TMPRSS2	39917211			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42872868			10	DELETION		2955657	188218	93088	138	NEW_VARIANT
P-0023364-T03-IM6	FGFR2 (NM_000141) - TACC2 (NM_206862) rearrangement: c.2301+1625:FGFR2_c.34-5469:TACC2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		53329	0	35	10	Intron of FGFR2(-):2Kb after exon 17	FGFR2	123241587			10	Intron of TACC2(+):5Kb before exon 3	TACC2	123804484			0	DUPLICATION		562897	310807	664187	35	NEW_VARIANT
P-0027049-T04-IM6	FOXA1 (NM_004496) rearrangement: c.1148_c.-2851del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5193	0	54	14	Exon 2 of FOXA1(-)	FOXA1	38060841			14	Promoter of FOXA1(-):8Kb from tx start	FOXA1	38067028			10	DELETION		6187	275621	7354	58	NEW_VARIANT
P-0027662-T01-IM6	NOTCH2 (NM_024408) rearrangement: t(1;6)(p12;q21)(chr1:g.120462040::chr6:g.109700010)	PRECISE	Note: The NOTCH2 rearrangement is a translocation with a breakpoint in exon 31. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	21	6	Intron of CD164(-):771bp after exon 2	NOTCH2	109700010			1	Exon 31 of NOTCH2(-)	NOTCH2	120462040			10	TRANSLOCATION		0	214233	0	21	NEW_VARIANT
P-0028283-T03-IM6	MET (NM_000245) rearrangement: c.1701+657_c.2937del	PRECISE	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).	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		12755	0	162	7	Intron of MET(+):657bp after exon 5	MET	116381736			7	Exon 14 of MET(+)	MET	116411952			10	DELETION		30216	320317	13690	165	NEW_VARIANT
P-0031772-T01-IM6	ARID1A (NM_006015) rearrangement: c.3887:ARID1A_chr1:g.2350666inv	PRECISE	Note: The ARID1A rearrangement is an inversion of exons 16. One of the breakpoints is within exon 16.	MANUAL_OK	5to5	5to5	-		294127	0	12	1	IGR: 14Kb before PEX10(-)	ARID1A	2350666			1	Exon 16 of ARID1A(+)	ARID1A	27100091			10	INVERSION		24749425	231002	447842	14	NEW_VARIANT
P-0032093-T01-IM6	MPL (NM_005373) rearrangement: c.80-39:MPL_chr1:g.44094042inv	PRECISE	Note: The MPL rearrangement is an inversion of exons 2-12. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		29123	0	59	1	Intron of MPL(+):38bp before exon 2	MPL	43803731			1	IGR: 22Kb before KDM4A(+)	MPL	44094042			10	INVERSION		290311	232061	47723	73	NEW_VARIANT
P-0032093-T01-IM6	AXIN1 (NM_003502) - CREBBP (NM_004380) rearrangement: c.879-4862:AXIN1_c.2161:CREBBPdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {AXIN1:CREBBP}		272166	0	103	16	Intron of AXIN1(-):5Kb before exon 3	AXIN1	369545			16	Exon 12 of CREBBP(-)	CREBBP	3824692			10	DUPLICATION		3455147	232060	483925	105	NEW_VARIANT
P-0032956-T01-IM6	SF3B1 (NM_012433) Rearrangement: c.495+9:SF3B1_chr2:g.42597820inv	PRECISE	Note: The SF3B1 rearrangement results in the inversion of SF3B1 exons 6 - 25. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		492152	0	5	2	IGR: 20Kb before COX7A2L(-)	SF3B1	42597820			2	Intron of SF3B1(-):8bp after exon 5	SF3B1	198283224			10	INVERSION		155685404	236826	503438	6	NEW_VARIANT
P-0035891-T01-IM6	B2M (NM_004048) rearrangement: t(5;15)(q12.1;q21.1)(chr5:g.61772023::chr15:g.45007799)	PRECISE	Note: The B2M rearrangement is a translocation with a breakpoint in exon 2.	MANUAL_OK	5to5	5to5	-		0	0	6	15	Exon 2 of B2M(+)	B2M	45007799			5	Intron of IPO11(+):486bp before exon 9	B2M	61772023			7	TRANSLOCATION		0	264208	0	6	NEW_VARIANT
P-0035891-T01-IM6	MST1 (NM_020998) rearrangement: c.1236:MST1_chr3:g.49629637dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		11559	0	2	3	Intron of BSN(+):33Kb before exon 2	MST1	49629637			3	Exon 10 of MST1(-)	MST1	49723307			10	DUPLICATION		93670	264206	16359	5	NEW_VARIANT
P-0035891-T01-IM6	MAP3K1 (NM_005921) rearrangement: c.482+17975_c.1966-44del	PRECISE	Note: The MAP3K1 rearrangement results in the deletion of exons 2-10. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 9 exons : out of frame		8961	0	2	5	Intron of MAP3K1(+):18Kb after exon 1	MAP3K1	56129857			5	Intron of MAP3K1(+):43bp before exon 11	MAP3K1	56174763			7	DELETION		44906	264203	8587	3	NEW_VARIANT
P-0036235-T01-IM6	FOXA1 (NM_004496) rearrangement: c.-34:FOXA1_chr14:g.37143996inv	PRECISE	Note: The FOXA1 rearrangement is an inversion with breakpoint in region upstream of FOXA1. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	Transcript Fusion {PAX9:FOXA1}		11438	0	149	14	Intron of PAX9(+):1Kb before exon 5	FOXA1	37143996			14	5-UTR of FOXA1(-):4Kb before coding start	FOXA1	38064211			10	INVERSION		920215	266428	13322	148	NEW_VARIANT
P-0036235-T01-IM6	KLK2 (NM_005551) - ETV1(NM_001163147) rearrangement: t(7;19)(p21.2;q13.33)(chr7:g.13975427::chr19:g.51377605)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KLK2:ETV1}		0	0	95	19	Intron of KLK2(+):371bp before exon 2	KLK2	51377605			7	Exon 7 of ETV1(-)	ETV1	13975427			10	TRANSLOCATION		0	266429	0	94	NEW_VARIANT
P-0037029-T01-IM6	SYT16 (NM_031914) - AKT1 (NM_001014431) rearrangement: c.1625-4528:SYT16_c.169:AKT1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SYT16:AKT1}		150651	0	34	14	Intron of SYT16(+):5Kb before exon 6	SYT16	62562584			14	Exon 3 of AKT1(-)	AKT1	105246431			10	INVERSION		42683847	275629	161490	34	NEW_VARIANT
P-0037029-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+1715:TMPRSS2_c.19-11583:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRRS2 exons 1-2 and ERG exons 2-10. The fusion is predicted to be in-frame.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		36730	0	101	21	Intron of ERG(-):12Kb before exon 2	TMPRSS2	39829127			21	Intron of TMPRSS2(-):2Kb after exon 2	ERG	42868331			10	DELETION		3039204	275628	31157	115	NEW_VARIANT
P-0037098-T01-IM6	MDC1 (NM_014641) rearrangement: c.5738:MDC1_chr6:g.54282565dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		324827	0	18	6	Exon 12 of MDC1(-)	MDC1	30671008			6	IGR: 109Kb before TINAG(+)	MDC1	54282565			10	DUPLICATION		23611557	276242	361895	18	NEW_VARIANT
P-0037132-T01-IM6	IDH1 (NM_005896) rearrangement: c.414+737_c.768del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4369	0	4	2	Exon 7 of IDH1(-)	IDH1	209106800			2	Intron of IDH1(-):736bp after exon 4	IDH1	209112356			10	DELETION		5556	276332	3298	5	NEW_VARIANT
P-0037132-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.56-2141_c.127-1737inv	PRECISE	Note: The TMPRSS2 rearrangement results in the inversion of exon 2. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		30060	0	4	21	Intron of TMPRSS2(-):2Kb before exon 3	TMPRSS2	42868242			21	Intron of TMPRSS2(-):2Kb before exon 2	TMPRSS2	42872257			10	INVERSION		4015	276333	29504	4	NEW_VARIANT
P-0037423-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-2996:TMPRSS2_c.237-9913:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRRS2 exon 1 and ERG exons 3-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		71140	0	16	21	Intron of ERG(-):10Kb before exon 3	TMPRSS2	39805396			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873112			10	DELETION		3067716	278997	38792	16	NEW_VARIANT
P-0037617-T01-IM6	BICC1 (NM_001080512) - FGFR2 (NM_000141) rearrangement: c.238-34060:BICC1_c.2302-1767:FGFR2inv	PRECISE	Note: The BICC1 - FGFR2 rearrangement is translocation that results in a fusion of BICC1 exons 1-2 to FGFR2 exon 18.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {BICC1:FGFR2}		166316	0	104	10	Intron of BICC1(+):34Kb before exon 3	BICC1	60427774			10	Intron of FGFR2(-):2Kb before exon 18	FGFR2	123241302			10	INVERSION		62813528	280718	323317	104	NEW_VARIANT
P-0037666-T01-IM6	SOX2 (NM_003106) -PIK3C2G (NM_004570) rearrangement: t(3;12)(q26.33;p12.3)(chr3:g.181430991::chr12:g.18665844)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SOX2:PIK3C2G}		0	0	36	12	Intron of PIK3C2G(+):7Kb after exon 23	SOX2	18665844			3	Exon 1 of SOX2(+)	PIK3C2G	181430991			10	TRANSLOCATION		0	281162	0	37	NEW_VARIANT
P-0037668-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2742:EML4_c.3172+696:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		73539	0	39	2	Intron of ALK(-):695bp after exon 19	EML4	29447631			2	Intron of EML4(+):3Kb before exon 13	ALK	42525639			10	INVERSION		13078008	281158	47503	39	NEW_VARIANT
P-0037668-T01-IM6	EGFR (NM_005228) rearrangement: c.2469+67:EGFR_chr7:g.84278082del	PRECISE	Note: The EGFR rearrangement results in the deletion of exons 21-28. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		62470	0	15	7	Intron of EGFR(+):67bp after exon 20	EGFR	55249238			7	IGR: 116Kb before LOC101927378(+)	EGFR	84278082			10	DELETION		29028844	281157	49579	15	NEW_VARIANT
P-0037682-T01-IM6	FAT1 (NM_005245) - PCGF3 (NM_006315) Rearrangement : c.12441:FAT1_c.600+1304:PCGF3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {FAT1:PCGF3}		276829	0	4	4	Intron of PCGF3(+):1Kb after exon 9	FAT1	756508			4	Exon 25 of FAT1(-)	PCGF3	187518253			9	INVERSION		186761745	281362	355127	4	NEW_VARIANT
P-0037698-T01-IM6	IDH2 (NM_002168) rearrangement: c.1012:IDH2_chr15:g.90523585del	PRECISE	Note: The IDH2 rearrangement is a deletion of exons 8-11. One of the breakpoints is within exon 8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		5828	0	4	15	IGR: 21Kb before ZNF710(+)	IDH2	90523585			15	Exon 8 of IDH2(-)	IDH2	90628575			10	DELETION		104990	281445	10056	4	NEW_VARIANT
P-0037701-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.126+524:TMPRSS2_c.237-2747:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exons 1-2 and ERG exons 3-10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		43754	0	62	21	Intron of ERG(-):3Kb before exon 3	TMPRSS2	39798230			21	Intron of TMPRSS2(-):523bp after exon 2	ERG	42869522			0	DELETION		3071292	281447	45067	65	NEW_VARIANT
P-0038256-T01-IM6	ERC1 (NM_178040) - RET (NM_020975) Rearrangement : t(10;12)(q11.1; p13.32)(chr10:g.43609964::chr12:g.1264106)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ERC1:RET}		0	0	99	12	Intron of ERC1(+):13Kb after exon 7	ERC1	1264106			10	Exon 11 of RET(+)	RET	43609964			10	TRANSLOCATION		0	285451	0	99	NEW_VARIANT
P-0038720-T01-IM6	SPRED1 (NM_152594) rearrangement: c.1328_c.*805	PRECISE	Note: The SPRED1 rearrangement is an intragenic deletion of exon 7. One of the breakpoints is within exon 7.	MANUAL_OK	3to5	3to5	-		625	0	12	15	Exon 7 of SPRED1(+)	SPRED1	38643858			15	3-UTR of SPRED1(+):99Kb after coding stop	SPRED1	38644670			10	DELETION		812	289688	1085	12	NEW_VARIANT
P-0038720-T01-IM6	BAP1 (NM_004656) rearrangement: c.931+135_c.*24del	IMPPRECISE	Note: The BAP1 rearrangement is an intragenic deletion of BAP1 exons 11-17.	MANUAL_OK	3to5	3to5	-		16954	0	14	3	3-UTR of BAP1(-):23bp after coding stop	BAP1	52436280			3	Intron of BAP1(-):134bp after exon 10	BAP1	52439646			0	DELETION		3366	289685	3276	17	NEW_VARIANT
P-0038793-T01-IM6	BAP1 (NM_004656) -  PHF7 (NM_016483) rearrangement: c.-22:BAP1_c.186+1887:PHF7del	PRECISE	Note: The BAP1 - PHF7 rearrangement is a deletion with a breakpoint within the 5'UTR of BAP1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		304	0	42	3	5-UTR of BAP1(-):8Kb before coding start	BAP1	52443916			3	Intron of PHF7(+):2Kb after exon 4	PHF7	52450490			10	DELETION		6574	290781	220	45	NEW_VARIANT
P-0038803-T01-IM6	BCOR (NM_001123385) rearrangement: chrX:g.14000773_c.3484dup	PRECISE	Note: The BCOR rearrangement is a duplication that includes BCOR exons 7-15. One of the breakpoints is within exon 7.	MANUAL_OK	5to3	5to3	-		26150	0	9	X	IGR: 24Kb before GEMIN8(-)	BCOR	14000773			X	Exon 7 of BCOR(-)	BCOR	39923607			10	DUPLICATION		25922834	290834	49697	11	NEW_VARIANT
P-0039448-T01-IM6	NOTCH4 (NM_004557) rearrangement: c.1802:NOTCH4_chr6:g.32202804inv	PRECISE	Note: The NOTCH4 rearrangement is an inversion of exons 1 - 11. One of the breakpoints is within exon 11. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		25356	0	12	6	Exon 11 of NOTCH4(-)	NOTCH4	32184781			6	IGR: 40Kb before NOTCH4(-)	NOTCH4	32202804			10	INVERSION		18023	296261	53948	12	NEW_VARIANT
P-0039829-T01-IM6	ELF3 (NM_004433) rearrangement: c.478+59:ELF3_chr1:g.201984748del	PRECISE	Note: The ELF3 rearrangement is a deletion of exons 5 - 9.	MANUAL_OK	3to5	3to5	-		10243	0	26	1	Intron of ELF3(+):59bp after exon 4	ELF3	201981623			1	3-UTR of ELF3(+):4Kb after coding stop	ELF3	201984748			10	DELETION		3125	298281	5968	26	NEW_VARIANT
P-0039901-T01-IM6	ELF3 (NM_004433) rearrangement: c.681:ELF3_chr1:g.201990452del	PRECISE	Note: The ELF3 rearrangement is a deletion of exons 6 - 9. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	-		4780	0	5	1	Exon 6 of ELF3(+)	ELF3	201982157			1	IGR: 11Kb before ELF3(+)	ELF3	201990452			10	DELETION		8295	298493	6941	5	NEW_VARIANT
P-0040007-T01-IM6	GATA3 (NM_002051) rearrangement: t(6;10)(q22.31;p14)(chr6:g.121274074::chr10:g.8106070)	PRECISE	Note: The GATA3 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	18	10	Exon 4 of GATA3(+)	GATA3	8106070			6	IGR: 127Kb before TBC1D32(-)	GATA3	121274074			10	TRANSLOCATION		0	300003	0	19	NEW_VARIANT
P-0040032-T01-IM6	ALK (NM_004304) rearrangement: c.3067+637_c.3173-299del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		24179	0	41	2	Intron of ALK(-):299bp before exon 20	ALK	29446693			2	Intron of ALK(-):636bp after exon 18	ALK	29449151			10	DELETION		2458	300052	20965	43	NEW_VARIANT
P-0040032-T01-IM6	CDKN2A (NM_000077) rearrangement: c.388:CDKN2A_chr9:g.21981057	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		3798	0	4	9	Exon 2 of CDKN2A(-)	CDKN2A	21970970			9	Intron of CDKN2A(-):10Kb before exon 2	CDKN2A	21981057			10	DELETION		10087	300053	3076	5	NEW_VARIANT
P-0040094-T01-IM6	CALR (NM_004343) rearrangement: t(1;19)(p34.3;p13.2)(chr1:g.36624367::chr19:g.13050882)	PRECISE	Note: The CALR rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	31	19	Exon 4 of CALR(+)	CALR	13050882			1	Intron of MAP7D1(+):2Kb after exon 1	CALR	36624367			10	TRANSLOCATION		0	300325	0	56	NEW_VARIANT
P-0040121-T01-IM6	AGO2 (NM_012154) rearrangement: c.501_c.1269+1124del	PRECISE	Note: The AGO2 rearrangement is an intragenic deletion of exons 4 - 10. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		10583	0	11	8	Intron of AGO2(-):1Kb after exon 10	AGO2	141564871			8	Exon 4 of AGO2(-)	AGO2	141572569			10	DELETION		7698	300387	7994	12	NEW_VARIANT
P-0040248-T01-IM6	EGFR (NM_005228) rearrangement: c.1879_c.1881-1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		4403	0	2	7	Exon 15 of EGFR(+)	EGFR	55233129			7	Exon 16 of EGFR(+)	EGFR	55238867			10	DELETION		5738	300737	2014	2	NEW_VARIANT
P-0040444-T01-IM6	PMAIP1 (NM_021127) rearrangement: c.55_c.59-3del	PRECISE	Note: The PMAIP1 rearrangement is an intragenic deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1025	0	5	18	Exon 1 of PMAIP1(+)	PMAIP1	57567464			18	Intron of PMAIP1(+):2bp before exon 2	PMAIP1	57569876			9	DELETION		2412	301746	1220	5	NEW_VARIANT
P-0040509-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-4323:TMPRSS2_c.39+6430:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		54467	0	48	21	Intron of ERG(-):6Kb after exon 3	TMPRSS2	39941156			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42874439			10	DELETION		2933283	302124	59984	54	NEW_VARIANT
P-0040518-T01-IM6	PTPRS (NM_002850) rearrangement: t(12;19)(q24.21;p13.3)(chr12:g.114898875::chr19:g.5222209)	PRECISE	Note: The PTPRS rearrangement is a translocation with a breakpoint in exon 19. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	19	Exon 19 of PTPRS(-)	PTPRS	5222209			12	IGR: 53Kb before TBX5-AS1(+)	PTPRS	114898875			10	TRANSLOCATION		0	306077	0	11	NEW_VARIANT
P-0040545-T01-IM6	FLT3 (NM_004119) - PDX1 (NM_000209) rearrangement: c.2418+171:FLT3_c.407-1761:PDX1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {FLT3:PDX1}		5074	0	7	13	Intron of PDX1(+):2Kb before exon 2	FLT3	28496632			13	Intron of FLT3(-):170bp after exon 19	PDX1	28597316			7	INVERSION		100684	302198	55126	7	NEW_VARIANT
P-0040587-T01-IM6	ERCC5 (NM_000123) rearrangement: c.1234:ERCC5_chr13:g.103600469inv	PRECISE	Note: The ERCC5 rearrangement is an inversion of exons 8 - 15. One of the breakpoints is within exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		13888	0	25	13	Exon 8 of ERCC5(+)	ERCC5	103514733			13	IGR: 68Kb before METTL21EP(+)	ERCC5	103600469			10	INVERSION		85736	302387	26974	26	NEW_VARIANT
P-0040587-T01-IM6	E4F1 (NM_004424) - TRAF7 (NM_032271) rearrangement: c.310-104:E4F1_c.1292:TRAF7dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {E4F1:TRAF7}		15665	0	21	16	Exon 14 of TRAF7(+)	E4F1	2224280			16	Intron of E4F1(+):103bp before exon 3	TRAF7	2279467			10	DUPLICATION		55187	302386	19904	22	NEW_VARIANT
P-0040669-T01-IM6	TP53BP1 (NM_001141980) rearrangement: c.3829-1967_c.4229inv	PRECISE	Note: The TP53BP1 rearrangement is an intragenic inversion of exons 19 - 20. One of the breakpoints is within exon 20. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		4004	0	27	15	Exon 20 of TP53BP1(-)	TP53BP1	43713244			15	Intron of TP53BP1(-):2Kb before exon 19	TP53BP1	43716291			10	INVERSION		3047	302731	5264	29	NEW_VARIANT
P-0040672-T01-IM6	ARID1B (NM_020732) rearrangement: c.3135+743:ARID1B_chr6:g.158764567inv	PRECISE	Note: The ARID1B rearrangement is an inversion of exons 12 - 20. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		33417	0	62	6	Intron of ARID1B(+):743bp after exon 11	ARID1B	157495994			6	Intron of TULP4(+):29Kb after exon 1	ARID1B	158764567			10	INVERSION		1268573	302723	37858	71	NEW_VARIANT
P-0040749-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.127-1065:TMPRSS2_c.39+63388:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {TMPRSS2:ERG}		32086	0	10	21	Intron of ERG(-):63Kb after exon 3	TMPRSS2	39884198			21	Intron of TMPRSS2(-):1Kb before exon 3	ERG	42867570			10	DELETION		2983372	303043	9450	10	NEW_VARIANT
P-0040752-T01-IM6	CDK12 (NM_016507) - C6orf203 (NM_016487) rearrangement: t(6;17)(q21;q12)(chr6:g.107368450::chr17:g.37687160)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CDK12:C6orf203}		0	0	18	17	Exon 14 of CDK12(+)	CDK12	37687160			6	Intron of C6orf203(+):3Kb after exon 3	C6orf203	107368450			10	TRANSLOCATION		0	303056	0	18	NEW_VARIANT
P-0040752-T01-IM6	PIK3R3 (NM_003629) rearrangement: t(1;2)(p34.1;q35)(chr1:g.46532639::chr2:g.218631120)	PRECISE	Note: The PIK3R3 rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	18	2	IGR: 33Kb before TNS1(-)	PIK3R3	218631120			1	Exon 4 of PIK3R3(-)	PIK3R3	46532639			10	TRANSLOCATION		0	303054	0	18	NEW_VARIANT
P-0040956-T01-IM6	KMT2D (NM_003482) rearrangement: c.10232-879_c.13531-32del	PRECISE	Note: The KMT2D rearrangement is an intragenic deletion of exons 35 - 39.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : out of frame		28023	0	31	12	Intron of KMT2D(-):32bp before exon 40	KMT2D	49424848			12	Intron of KMT2D(-):879bp before exon 35	KMT2D	49429597			10	DELETION		4749	304172	16910	31	NEW_VARIANT
P-0040956-T01-IM6	NOTCH1 (NM_017617) - FH (NM_000143) rearrangement: t(1;9)(q43;q34.3)(chr1:g.241672198::chr9:g.139417940)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {NOTCH1:FH}		0	0	10	9	Intron of NOTCH1(-):228bp after exon 3	NOTCH1	139417940			1	Intron of FH(-):113bp before exon 5	FH	241672198			10	TRANSLOCATION		0	304173	0	8	NEW_VARIANT
P-0040975-T01-IM6	SYNRG (NM_007247) - ERBB2 (NM_004448) fusion: c.2608+2066:SYNRG_c.1899-372:ERBB2inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {SYNRG:ERBB2}		57977	0	47	17	Intron of SYNRG(-):2Kb after exon 13	SYNRG	35911151			17	Intron of ERBB2(+):371bp before exon 16	ERBB2	37875668			10	INVERSION		1964517	305091	289941	47	NEW_VARIANT
P-0041034-T01-IM6	TRAF7 (NM_032271) rearrangement: c.231+167:TRAF7_chr16:g.145124del	PRECISE	Note: The TRAF7 rearrangement is a deletion of exons 1 - 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		144888	0	2	16	Intron of NPRL3(-):2Kb before exon 7	TRAF7	145124			16	Intron of TRAF7(+):167bp after exon 4	TRAF7	2218336			4	DELETION		2073212	305426	94151	2	NEW_VARIANT
P-0041034-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1526:TMPRSS2_c.18+3778:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		49833	0	138	21	Intron of ERG(-):4Kb after exon 1	TMPRSS2	39866509			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42871642			10	DELETION		3005133	305427	31617	146	NEW_VARIANT
P-0041122-T01-IM6	CDKN2A (NM_058195) rearrangement: c.275:CDKN2A_chr9:g.22045861del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		12936	0	10	9	Exon 2 of CDKN2A(-)	CDKN2A	21971126			9	5-UTR of CDKN2B-AS1(+):75Kb before coding start	CDKN2A	22045861			10	DELETION		74735	306006	14330	11	NEW_VARIANT
P-0041144-T01-IM6	KRAS (NM_033360) rearrangement: t(10;12)(p11.21;p12.1)(chr10:g.36334124::chr12:g.25378602)	IMPPRECISE	Note: The KRAS rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	7	12	Exon 4 of KRAS(-)	KRAS	25378602			10	IGR: 267Kb before LINC01452(+)	KRAS	36334124			0	TRANSLOCATION		0	306066	0	7	NEW_VARIANT
P-0041176-T01-IM6	PDGFRA (NM_006206) - ZNF536 (NM_014717) rearrangement: t(4;19)(q12;q12)(chr4:g.55130148::chr19:g.30956498)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {PDGFRA:ZNF536}		0	0	8	19	Intron of ZNF536(+):20Kb after exon 2	PDGFRA	30956498			4	Intron of PDGFRA(+):54bp after exon 4	ZNF536	55130148			10	TRANSLOCATION		0	306073	0	7	NEW_VARIANT
P-0041196-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.55+4101:TMPRSS2_c.40-60529:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		79649	0	6	21	Intron of ERG(-):61Kb before exon 4	TMPRSS2	39878073			21	Intron of TMPRSS2(-):4Kb after exon 1	ERG	42875776			10	DELETION		2997703	306176	91903	7	NEW_VARIANT
P-0041196-T01-IM6	GATA2 (NM_032638) rearrangement: c.6:GATA2_chr3:g.177218975del	PRECISE	Note: The GATA2 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		193050	0	22	3	Exon 2 of GATA2(-)	GATA2	128205869			3	5-UTR of LINC00578(+):252Kb before coding start	GATA2	177218975			10	DELETION		49013106	306175	238842	24	NEW_VARIANT
P-0041295-T01-IM6	STK11 (NM_000455) rearrangement: c.324:STK11_chr19:g.1111056del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		3271	0	23	19	Exon 25 of SBNO2(-)	STK11	1111056			19	Exon 2 of STK11(+)	STK11	1218449			10	DELETION		107393	306315	1421	24	NEW_VARIANT
P-0041298-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.2766:SMARCA4_chr19:g.11086045del	PRECISE	Note: The SMARCA4 rearrangement is a deletion of exons 1 - 19. One of the breakpoints is within exon 19.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		32355	0	8	19	5-UTR of SMARCA4(+):9Kb before coding start	SMARCA4	11086045			19	Exon 19 of SMARCA4(+)	SMARCA4	11132550			7	DELETION		46505	306316	24616	8	NEW_VARIANT
P-0041309-T01-IM6	MAP2K4 (NM_003010) rearrangement: c.219-6453_c.220del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		273	0	7	17	Intron of MAP2K4(+):6Kb before exon 3	MAP2K4	11978220			17	Exon 3 of MAP2K4(+)	MAP2K4	11984674			10	DELETION		6454	308126	89	16	NEW_VARIANT
P-0041327-T01-IM6	TERT (NM_198253) rearrangement: t(1;5)(p21.2;p15.3)(chr1:g.99836853::chr5:g.1295277)	PRECISE	Note: The TERT rearrangement is a translocation with a breakpoint in the TERT promoter region. The functional significance of this variant is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	66	5	Promoter of TERT(-):42Kb from tx start	TERT	1295277			1	IGR: 101Kb before LOC101928270(-)	TERT	99836853			10	TRANSLOCATION		0	306360	0	102	NEW_VARIANT
P-0041343-T01-IM6	NOTCH1 (NM_017617) rearrangement: c.5257:NOTCH1_chr9:g.139239051del	PRECISE	Note: The NOTCH1 rearrangement is a deletion of exons 28 - 34. One of the breakpoints is within exon 28.	MANUAL_OK	3to5	3to5	Antisense Fusion		23885	0	36	9	Intron of GPSM1(+):4Kb after exon 9	NOTCH1	139239051			9	Exon 28 of NOTCH1(-)	NOTCH1	139396851			10	DELETION		157800	306398	22638	40	NEW_VARIANT
P-0041646-T01-IM6	TSC2 (NM_000548) rearrangement: c.3611-8:TSC2_chr16:g.63844236inv	PRECISE	Note: The TSC2 rearrangement is an inversion of exons 31 - 42. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		384526	0	7	16	Intron of TSC2(+):7bp before exon 31	TSC2	2131588			16	IGR: 1Mb before CDH11(-)	TSC2	63844236			10	INVERSION		61712648	307200	386609	7	NEW_VARIANT
P-0041837-T01-IM6	TMEM117 (NM_032256) - RECQL (NM_032941) rearrangement: c.411-22932:TMEM117_c.950-6:RECQLinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {TMEM117:RECQL}		32603	0	3	12	Intron of RECQL(-):6bp before exon 10	TMEM117	21628764			12	Intron of TMEM117(+):23Kb before exon 4	RECQL	44514396			6	INVERSION		22885632	307564	42300	2	NEW_VARIANT
P-0042108-T01-IM6	ANKRD11 (NM_013275) rearrangement: t(16;17)(q24.3;q25.1)(chr16:g.89350931::chr17:g.73285392)	PRECISE	Note: The ANKRD11 rearrangement is a translocation with a breakpoint in exon 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ANKRD11:SLC25A19}		0	0	11	17	5-UTR of SLC25A19(-):16Kb before coding start	ANKRD11	73285392			16	Exon 9 of ANKRD11(-)	ANKRD11	89350931			10	TRANSLOCATION		0	308424	0	11	NEW_VARIANT
P-0042108-T01-IM6	DNMT1 (NM_001379) rearrangement: c.2539-14_c.2847-607dup	PRECISE	Note: The DNMT1 rearrangement is an intragenic duplication of exons 26 - 27. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		2864	0	8	19	Intron of DNMT1(-):607bp before exon 28	DNMT1	10255270			19	Intron of DNMT1(-):14bp before exon 26	DNMT1	10259707			10	DUPLICATION		4437	308422	3980	8	NEW_VARIANT
P-0042156-T01-IM6	EP300 (NM_001429) rearrangement: c.4453-821_c.4642del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exons 28 - 29. One of the breakpoints is within exon 29.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1805	0	55	22	Intron of EP300(+):820bp before exon 28	EP300	41567682			22	Exon 29 of EP300(+)	EP300	41569651			10	DELETION		1969	308191	921	61	NEW_VARIANT
P-0042200-T01-IM6	CARM1 (NM_199141) rearrangement: t(4;19)(q13.1;p13.2)(chr4:g.65841314::chr19:g.11018608)	PRECISE	Note: The CARM1 rearrangement is a translocation with a breakpoint in intron 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	6	19	Intron of CARM1(+):106bp before exon 3	CARM1	11018608			4	3-UTR of LOC401134(-):29Kb after coding stop	CARM1	65841314			8	TRANSLOCATION		0	308587	0	6	NEW_VARIANT
P-0042215-T01-IM6	ACOXL (NM_001142807) - BCL2L11 (NM_138621) rearrangement: c.1441-12512:ACOXL_c.233:BCL2L11del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ACOXL:BCL2L11}		1546	0	2	2	Intron of ACOXL(+):13Kb before exon 17	ACOXL	111837930			2	Exon 2 of BCL2L11(+)	BCL2L11	111881555			7	DELETION		43625	308473	2003	3	NEW_VARIANT
P-0042238-T01-IM6	BRCA2 (NM_000059) rearrangement: c.9257-5239_c.9844dup	PRECISE	Note: The BRCA2 rearrangement is an intragenic duplication of exons 25 - 27. One of the breakpoints is within exon 27.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		4100	0	42	13	Intron of BRCA2(+):5Kb before exon 25	BRCA2	32963587			13	Exon 27 of BRCA2(+)	BRCA2	32972494			10	DUPLICATION		8907	309139	6289	44	NEW_VARIANT
P-0042238-T01-IM6	CBFB (NM_022845) rearrangement: c.399+89:CBFB_chr16:g.1667825inv	PRECISE	Note: The CBFB rearrangement is an inversion of exons 1 - 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		606501	0	16	16	Intron of CRAMP1L(+):3Kb after exon 1	CBFB	1667825			16	Intron of CBFB(+):89bp after exon 4	CBFB	67100790			10	INVERSION		65432965	309140	482439	15	NEW_VARIANT
P-0042276-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-2913:TMPRSS2_c.18+14783:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		59680	0	89	21	Intron of ERG(-):15Kb after exon 1	TMPRSS2	39855504			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873029			10	DELETION		3017525	309601	67766	93	NEW_VARIANT
P-0042373-T01-IM6	PBRM1 (NM_018313) rearrangement: c.714+37_c.1087+3010del	PRECISE	Note: The PBRM1 rearrangement is an intragenic deletion of exons 8 - 11.	MANUAL_OK	3to5	3to5	Deletion of 4 exons : out of frame		4700	0	9	3	Intron of PBRM1(-):3Kb after exon 11	PBRM1	52672960			3	Intron of PBRM1(-):36bp after exon 7	PBRM1	52685721			10	DELETION		12761	309770	3625	9	NEW_VARIANT
P-0042476-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.6087:ZFHX3_chr16:g.72733095inv	PRECISE	Note: The ZFHX3 rearrangement is an inversion of exons 9 - 10. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		39993	0	101	16	IGR: 84Kb before ZFHX3(-)	ZFHX3	72733095			16	Exon 9 of ZFHX3(-)	ZFHX3	72830494			10	INVERSION		97399	310427	71888	124	NEW_VARIANT
P-0042476-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.3864+2874_c.6098inv	PRECISE	Note: The ZFHX3 rearrangement is an intragenic inversion of exons 8 - 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		16620	0	26	16	Exon 9 of ZFHX3(-)	ZFHX3	72830483			16	Intron of ZFHX3(-):3Kb after exon 7	ZFHX3	72842602			10	INVERSION		12119	310428	29288	26	NEW_VARIANT
P-0042663-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3014:TMPRSS2_c.18+20952:ERGdel	PRECISE	Note: The TMPRSS2-ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		63547	0	73	21	Intron of ERG(-):21Kb after exon 1	TMPRSS2	39849335			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873130			10	DELETION		3023795	311042	47884	77	NEW_VARIANT
P-0042830-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) fusion: c.56-3008:TMPRSS2_c.40-53644:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Transcript Fusion {TMPRSS2:ERG}		68269	0	23	21	Promoter of ERG(-):119Kb from tx start	TMPRSS2	39871188			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873124			10	DELETION		3001936	313196	14157	26	NEW_VARIANT
P-0042958-T01-IM6	PSMA5 (NM_002790) - SMYD3 (NM_001167740) rearrangement: c.648+1286:PSMA5_c.904:SMYD3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PSMA5:SMYD3}		546014	0	2	1	Intron of PSMA5(-):1Kb after exon 8	PSMA5	109951264			1	Exon 10 of SMYD3(-)	SMYD3	246021970			5	DUPLICATION		136070706	311767	405106	2	NEW_VARIANT
P-0042958-T01-IM6	TOP1 (NM_003286) rearrangement: t(13;20)(q12.2;q12)(chr13:g.28121662::chr20:g.39658076)	PRECISE	Note: The TOP1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	26	20	Exon 2 of TOP1(+)	TOP1	39658076			13	3-UTR of LNX2(-):809bp after coding stop	TOP1	28121662			10	TRANSLOCATION		0	311768	0	25	NEW_VARIANT
P-0043108-T01-IM6	AXIN1 (NM_003502) rearrangement: c.879-6318_c.1255-4del	PRECISE	Note: The AXIN1 rearrangement is an intragenic deletion of exons 3 - 5.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : out of frame		7645	0	7	16	Intron of AXIN1(-):4bp before exon 6	AXIN1	348255			16	Intron of AXIN1(-):6Kb before exon 3	AXIN1	371001			10	DELETION		22746	313306	9086	7	NEW_VARIANT
P-0043113-T01-IM6	BRCA2 (NM_000059) rearrangement: t(2;13)(q37.3;q13.1)(chr2:g.241343675::chr13:g.32914249)	PRECISE	Note: The BRCA2 rearrangement is a translocation with a breakpoint in exon 11. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	13	Exon 11 of BRCA2(+)	BRCA2	32914249			2	IGR: 31Kb before GPC1(+)	BRCA2	241343675			10	TRANSLOCATION		0	313304	0	11	NEW_VARIANT
P-0043246-T01-IM6	PAN3 (NM_175854) - FLT1 (NM_002019) rearrangement: c.691-7254:PAN3_c.2954-141:FLT1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {PAN3:FLT1}		11369	0	13	13	Intron of PAN3(+):7Kb before exon 5	PAN3	28764068			13	Intron of FLT1(-):141bp before exon 22	FLT1	28896637			10	INVERSION		132569	313622	16647	13	NEW_VARIANT
P-0043404-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-164:CDKN2A_chr9:g.11836214inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		9897	0	6	9	IGR: 857Kb before TYRP1(+)	CDKN2A	11836214			9	Intron of CDKN2A(-):164bp before exon 2	CDKN2A	21971371			6	INVERSION		10135157	314088	14166	6	NEW_VARIANT
P-0043413-T01-IM6	ERG (NM_182918) - TMPRSS2 (NM_001135099) rearrangement: c.19-4013:ERG_c.127-228:TMPRSS2inv	PRECISE	Note: The ERG - TMPRSS2 rearrangement is an inversion of ERG exon 1 and TMPRSS2 exons 3 - 14. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		27846	0	29	21	Intron of ERG(-):4Kb before exon 2	ERG	39821557			21	Intron of TMPRSS2(-):228bp before exon 3	TMPRSS2	42866733			10	INVERSION		3045176	314134	33317	29	NEW_VARIANT
P-0043472-T01-IM6	RBM10 (NM_001204468) - PLXNA3 (NM_017514) rearrangement: c.2361+33:RBM10_c.5156+49:PLXNA3del	PRECISE	Note: The RBM10 - PLXNA3 rearrangement is a deletion that results in a fusion of RBM10 exons 1 - 19 to PLXNA3 exons 31 - 33.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {RBM10:PLXNA3}		449220	0	31	X	Intron of RBM10(+):33bp after exon 19	RBM10	47044799			X	Intron of PLXNA3(+):49bp after exon 30	PLXNA3	153699003			10	DELETION		106654204	314433	409488	32	NEW_VARIANT
P-0043583-T01-IM6	BRCA1 (NM_007294) rearrangement: c.671-35:BRCA1_chr17:g.42410005del	PRECISE	Note: The BRCA1 rearrangement is a deletion of exons 1 - 9.	MANUAL_OK	3to5	3to5	-		6717	0	63	17	Intron of BRCA1(-):35bp before exon 10	BRCA1	41246912			17	IGR: 12Kb before GRN(+)	BRCA1	42410005			10	DELETION		1163093	314991	21119	67	NEW_VARIANT
P-0043583-T01-IM6	ADHFE1 (NM_144650) - TMPRSS2 (NM_001135099) rearrangement: t(8;21)(q13.1;q22.3)(chr8:g.67354656::chr21:g.42875000)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ADHFE1:TMPRSS2}		0	0	30	21	Intron of TMPRSS2(-):5Kb after exon 1	ADHFE1	42875000			8	Intron of ADHFE1(+):376bp before exon 3	TMPRSS2	67354656			10	TRANSLOCATION		0	314994	0	33	NEW_VARIANT
P-0043615-T01-IM6	SMARCB1 (NM_003073) rearrangement: t(8;22)(q22.2;q11.23)(chr8:g.101422122::chr22:g.24175790)	IMPPRECISE	Note: The SMARCB1 rearrangement is a translocation with a breakpoint in exon 8. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	19	22	Exon 8 of SMARCB1(+)	SMARCB1	24175790			8	IGR: 27Kb before MIR4471(+)	SMARCB1	101422122			0	TRANSLOCATION		0	315083	0	36	NEW_VARIANT
P-0043633-T01-IM6	MDC1 (NM_014641) rearrangement: c.84:MDC1_chr6:g.30666783del	PRECISE	Note: The MDC1 rearrangement is a deletion of exons 2 - 15. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		50938	0	27	6	Promoter of MDC1(-):800bp from tx start	MDC1	30666783			6	Exon 2 of MDC1(-)	MDC1	30682869			10	DELETION		16086	315111	48393	28	NEW_VARIANT
P-0043660-T01-IM6	ARID1B (NM_020732) - CDKN2A (NM_000077) rearrangement: t(6;9)(q25.3;p21.3)(chr6:g.157398404::chr9:g.21968863)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ARID1B:CDKN2A}		0	0	14	9	Intron of CDKN2A(-):622bp before exon 3	ARID1B	21968863			6	Intron of ARID1B(+):7Kb before exon 6	CDKN2A	157398404			10	TRANSLOCATION		0	315188	0	14	NEW_VARIANT
P-0043671-T01-IM6	TMPRSS2 (NM_001135099) rearrangement: c.55+1504:TMPRSS2_chr21:g.40039999del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		105048	0	47	21	IGR: 71Kb before LINC00114(-)	TMPRSS2	40039999			21	Intron of TMPRSS2(-):2Kb after exon 1	TMPRSS2	42878373			10	DELETION		2838374	315227	61549	50	NEW_VARIANT
P-0043698-T01-IM6	TP53 (NM_000546) - SUPT3H (NM_003599) rearrangement: t(6;17)(p21.1;p13.1)(chr6:g.45270502::chr17:g.7579660)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {TP53:SUPT3H}		0	0	28	17	Intron of TP53(-):39bp after exon 3	TP53	7579660			6	Intron of SUPT3H(-):19Kb after exon 4	SUPT3H	45270502			10	TRANSLOCATION		0	315354	0	28	NEW_VARIANT
P-0043868-T01-IM6	TET2 (NM_001127208) rearrangement: c.5582:TET2_chr4:g.105889922del	PRECISE	Note: The TET2 rearrangement is a deletion of exons 1 - 11. One of the breakpoints is within exon 11.Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		23947	0	5	4	IGR: 177Kb before TET2(+)	TET2	105889922			4	Exon 11 of TET2(+)	TET2	106197249			6	DELETION		307327	316485	22563	5	NEW_VARIANT
P-0044010-T01-IM6	RRAS2 (NM_012250) rearrangement: c.528-8:RRAS2_chr11:g.45787087inv	PRECISE	Note: The RRAS2 rearrangement is an inversion of exons 1 - 5. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		58071	0	13	11	Intron of RRAS2(-):8bp before exon 6	RRAS2	14300978			11	IGR: 6Kb before DKFZp779M0652(+)	RRAS2	45787087			10	INVERSION		31486109	317438	100751	21	NEW_VARIANT
P-0044010-T01-IM6	ABCC1 (NM_004996) - HNF1A (NM_000545) rearrangement: t(12;16)(q24.31;p13.11)(chr12:g.121416656::chr16:g.16232122)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {ABCC1:HNF1A}		0	0	5	16	Intron of ABCC1(+):98bp before exon 30	ABCC1	16232122			12	Exon 1 of HNF1A(+)	HNF1A	121416656			6	TRANSLOCATION		0	317439	0	5	NEW_VARIANT
P-0044065-T01-IM6	CSDE1 (NM_001242891) rearrangement: t(1;4)(p13.2;q31.21)(chr1:g.115263350::chr4:g.146051831)	PRECISE	Note: The CSDE1 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Transcript Fusion {OTUD4:CSDE1}		0	0	26	4	Promoter of OTUD4(-):3Kb from tx start	CSDE1	146051831			1	Intron of CSDE1(-):12bp before exon 18	CSDE1	115263350			10	TRANSLOCATION		0	317372	0	26	NEW_VARIANT
P-0044065-T01-IM6		PRECISE		MANUAL_OK	3to5	3to5	-		770	0	19	4	5-UTR of EIF4E(-):48Kb before coding start	EIF4E	99850164			4	IGR: 55Kb before METAP1(+)	METAP1	99861763			10	DELETION		11599	317370	500	22	NEW_VARIANT
P-0044218-T01-IM6	OSBPL2 (NM_144498) - TMPRSS2 (NM_001135099) rearrangement: t(20;21)(q13.33;q22.3)(chr20:g.60866051::chr21:g.42872237)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {OSBPL2:TMPRSS2}		0	0	12	21	Intron of TMPRSS2(-):2Kb before exon 2	OSBPL2	42872237			20	Intron of OSBPL2(+):707bp before exon 13	TMPRSS2	60866051			10	TRANSLOCATION		0	318283	0	15	NEW_VARIANT
P-0044218-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-1670:TMPRSS2_c.18+6374:ERGdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		50586	0	22	21	Intron of ERG(-):6Kb after exon 1	TMPRSS2	39863913			21	Intron of TMPRSS2(-):2Kb before exon 2	ERG	42871786			10	DELETION		3007873	318281	63483	25	NEW_VARIANT
P-0044503-T01-IM6	KDM5A (NM_001042603) rearrangement: t(7;12)(q31.33;p13.33)(chr7:g.125904725::chr12:g.465570)	IMPPRECISE	Note: The KDM5A rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	6	12	Intron of KDM5A(-):27bp after exon 6	KDM5A	465570			7	IGR: 174Kb before GRM8(-)	KDM5A	125904725			0	TRANSLOCATION		0	319291	0	6	NEW_VARIANT
P-0044548-T01-IM6	KMT2B (NM_014727) rearrangement: c.6537_c.7160-962inv	PRECISE	Note: The KMT2B rearrangement is an intragenic inversion of exons 28 - 30. One of the breakpoints is within exon 28. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		6143	0	7	19	Exon 28 of KMT2B(+)	KMT2B	36223987			19	Intron of KMT2B(+):961bp before exon 31	KMT2B	36226629			10	INVERSION		2642	320103	7191	10	NEW_VARIANT
P-0044579-T01-IM6	MAP3K1 (NM_005921) rearrangement: t(1;5)(p12;q11.2)(chr1:g.120024255::chr5:g.56152501)	PRECISE	Note: The MAP3K1 rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	5	Exon 2 of MAP3K1(+)	MAP3K1	56152501			1	IGR: 26Kb before HSD3B1(+)	MAP3K1	120024255			10	TRANSLOCATION		0	320159	0	9	NEW_VARIANT
P-0044579-T01-IM6	CDKN2A (NM_058195) rearrangement: c.-36G>A:CDKN2Ap14ARF_chr9.g:22070476del	PRECISE	Note: The CDKN2Ap14ARF rearrangement is a deletion with breakpoint in the 5UTR. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		9976	0	11	9	5-UTR of CDKN2A(-):23Kb before coding start	CDKN2A	21994489			9	5-UTR of CDKN2B-AS1(+):51Kb before coding start	CDKN2A	22070476			10	DELETION		75987	320157	8895	11	NEW_VARIANT
P-0044808-T01-IM6	KMT2D (NM_003482) rearrangement: c.14030_c.16336dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		22588	0	160	12	Exon 51 of KMT2D(-)	KMT2D	49416375			12	Exon 43 of KMT2D(-)	KMT2D	49423229			10	DUPLICATION		6854	320602	41174	176	NEW_VARIANT
P-0044862-T01-IM6	GLI1 (NM_005269) - KIF5A (NM_004984) rearrangement: c.861:GLI1_c.1293+360:KIF5Adel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GLI1:KIF5A}		24169	0	2	12	Exon 8 of GLI1(+)	GLI1	57860121			12	Intron of KIF5A(+):360bp after exon 12	KIF5A	57964305			9	DELETION		104184	320687	16801	2	NEW_VARIANT
P-0044919-T01-IM6	TSC1 (NM_000368) rearrangement: t(9;11)(q34.13;p14.1)(chr9:g.135778054::chr11:g.30603418)	PRECISE	Note: The TSC1 rearrangement is a translocation with a breakpoint in exon 18. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	34	11	5-UTR of MPPED2(-):193Kb before coding start	TSC1	30603418			9	Exon 18 of TSC1(-)	TSC1	135778054			10	TRANSLOCATION		0	320932	0	41	NEW_VARIANT
P-0045237-T01-IM6	TBX3 (NM_016569) rearrangement: c.1265:TBX3_chr12:g.116583171inv	PRECISE	Note: The TBX3 rearrangement is an inversion of exons 1 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12508	0	10	12	Exon 7 of TBX3(-)	TBX3	115112475			12	Intron of MED13L(-):34Kb before exon 3	TBX3	116583171			10	INVERSION		1470696	322050	14034	10	NEW_VARIANT
P-0045237-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) rearrangement: c.56-3428:TMPRSS2_c.18+5115:ERGdel	IMPPRECISE	Note: The TMPRSS2 - ERG rearrangement is a deletion that results in a fusion of TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		60055	0	5	21	Intron of ERG(-):5Kb after exon 1	TMPRSS2	39865172			21	Intron of TMPRSS2(-):3Kb before exon 2	ERG	42873544			0	DELETION		3008372	322049	72919	5	NEW_VARIANT
P-0046024-T01-IM6	ARID1A (NM_006015) rearrangement: c.1137+5964_c.5571del	PRECISE	Note: The ARID1A rearrangement is an intragenic deletion of exons 2 - 20. One of the breakpoints is within exon 20.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		35793	0	55	1	Intron of ARID1A(+):6Kb after exon 1	ARID1A	27029995			1	Exon 20 of ARID1A(+)	ARID1A	27105960			10	DELETION		75965	324377	10319	62	NEW_VARIANT
P-0047736-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.284:CTNNB1_chr3:g.41264128del	PRECISE	Note: The CTNNB1 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1874	0	5	3	5-UTR of CTNNB1(+):1Kb before coding start	CTNNB1	41264128			3	Exon 4 of CTNNB1(+)	CTNNB1	41266487			10	DELETION		2359	331431	890	5	NEW_VARIANT
P-0007687-T02-IM6	NTRK1 (NM_002529) rearrangement: c.145:NTRK1_chr1:g.218470640inv	PRECISE	Note: The NTRK1 rearrangement is an inversion with a breakpoint in exon 1. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		251303	0	12	1	Exon 1 of NTRK1(+)	NTRK1	156830871			1	Intron of RRP15(+):5Kb before exon 2	NTRK1	218470640			10	INVERSION		61639769	232340	333497	15	NEW_VARIANT
P-0007687-T02-IM6	SMYD3 (NM_001167740) rearrangement: c.532-49350_c.771del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2993	0	22	1	Exon 8 of SMYD3(-)	SMYD3	246078874			1	Intron of SMYD3(-):49Kb before exon 6	SMYD3	246142589			10	DELETION		63715	232336	3852	22	NEW_VARIANT
P-0012084-T01-IM5	NEGR1 (NM_173808) rearrangement: c.139_c.176+96526dup	PRECISE	Note: The NEGR1 rearrangement is an intragenic duplication of a part of exon 1.	MANUAL_OK	5to3	5to3	Duplication within transcript: mid-exon		1562	0	8	1	Intron of NEGR1(-): 97Kb after exon 1	NEGR1	72651476			1	Exon 1 of NEGR1(-)	NEGR1	72748039			20	DUPLICATION		96563	156182	978	7	NEW_VARIANT
P-0012521-T01-IM5	BAP1 (NM_004656) rearrangement: c.2097_chr3:g.52436397inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		218124	0	23	3	IGR: 2Kb before CCR1(-)	BAP1	46240702			3	Exon 17 of BAP1(-)	BAP1	52436397			42	INVERSION		6195695	157630	200877	23	NEW_VARIANT
P-0021327-T01-IM6	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	PRECISE	Note: The FGFR2 - BICC1 fusion is  predicted to be in-frame and includes the protein kinase domain of FGFR2.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:BICC1}		294516	0	28	10	Intron of BICC1(+):644bp before exon 16	FGFR2	60565699			10	Intron of FGFR2(-):809bp before exon 18	BICC1	123240344			10	INVERSION		62674645	186904	220470	31	NEW_VARIANT
P-0021776-T01-IM6	ERBB2 (NM_004448) rearrangement: t(17;21)(q12;q21.2)(chr17:g.37881392::chr21:g.21176072)	PRECISE	Note: The ERBB2 rearrangement is  a translocation that may result in the truncation of exons 21-27. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	45	21	IGR: 939Kb before LINC00320(-)	ERBB2	21176072			17	Exon 21 of ERBB2(+)	ERBB2	37881392			10	TRANSLOCATION		0	188203	0	53	NEW_VARIANT
P-0021776-T01-IM6	ATRX (NM_000489) rearrangement: chrX:g.37033335_c.4809+130:ATRXinv	PRECISE	Note: The ATRX rearrangement is an inversion of exons 18-35 that may potentially disrupt the gene function.	MANUAL_OK	5to5	5to5	-		329881	0	7	X	IGR: 7Kb before FAM47C(+)	ATRX	37033335			X	Intron of ATRX(-):129bp after exon 17	ATRX	76889955			10	INVERSION		39856620	188202	382752	7	NEW_VARIANT
P-0025675-T01-IM6	NOTCH3 (NM_000435) rearrangement: c.6189_chr19:g.38926895dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Antisense Fusion		313673	0	26	19	Exon 33 of NOTCH3(-)	NOTCH3	15272250			19	Intron of RYR1(+):2Kb after exon 1	NOTCH3	38926895			10	DUPLICATION		23654645	206378	550627	32	NEW_VARIANT
P-0029548-T01-IM6	PIK3CD (NM_005026) - CLSTN1 (NM_001009566) rearrangement: c.957:PIK3CD_c.1356+861:CLSTN1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PIK3CD:CLSTN1}		28205	0	5	1	Exon 8 of PIK3CD(+)	PIK3CD	9777621			1	Intron of CLSTN1(-):860bp after exon 9	CLSTN1	9803081			10	INVERSION		25460	222156	72581	5	NEW_VARIANT
P-0029548-T01-IM6	BIRC3 (NM_182962) rearrangement: c.-49-281_c.1033-6del	PRECISE	Note: The BIRC3 rearrangement is an intragenic deletion of exons 1-5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		5505	0	113	11	5-UTR of BIRC3(+):329bp before coding start	BIRC3	102194911			11	Intron of BIRC3(+):5bp before exon 6	BIRC3	102199622			10	DELETION		4711	222155	14960	133	NEW_VARIANT
P-0035498-T01-IM6	SESN3 (NM_144665) Rearrangement: c.1392+102_c.*7865del	PRECISE	Note: The SESN3 rearrangement is an intragenic deletion of exons 1-9. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1321	0	9	11	Promoter of SESN3(-):122bp from tx start	SESN3	94898554			11	Intron of SESN3(-):101bp after exon 9	SESN3	94908560			10	DELETION		10006	258810	2007	11	NEW_VARIANT
P-0035498-T01-IM6	PAX 8 (NM_003466) Rearrangement: t(2;17)(q13;p13.2)(chr2:g.113987958::chr17:g.4414421)	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		0	0	111	17	Intron of SPNS2(+):2Kb before exon 2	PAX 8	4414421			2	Intron of PAX8(-):3Kb before exon 10	PAX 8	113987958			0	TRANSLOCATION		0	258819	0	112	NEW_VARIANT
P-0036117-T01-IM6	KMT2B (NM_014727) rearrangement: c.4625_chr19:g.36379015inv	PRECISE	Note: The KMT2B rearrangement is an inversion that includes KMT2B exons 20-37. One of the breakpoints is within exon 20.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {NFKBID:KMT2B}		18758	0	26	19	Exon 20 of KMT2B(+)	KMT2B	36219728			19	Promoter of NFKBID(-):127bp from tx start	KMT2B	36379015			10	INVERSION		159287	264598	55010	43	NEW_VARIANT
P-0043514-T01-IM6	PIK3C2G (NM_004570) rearrangement: c.3888:PIK3C2G_chr12:g.22631196del	PRECISE	Note: The PIK3C2G rearrangement is a deletion of exons 28 - 32. One of the breakpoints is within exon 28. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		22837	0	48	12	Exon 28 of PIK3C2G(+)	PIK3C2G	18719991			12	Intron of C2CD5(-):50bp after exon 15	PIK3C2G	22631196			10	DELETION		3911205	314902	24312	48	NEW_VARIANT
P-0045731-T01-IM6	NOS1AP (NM_014697) - NTRK1 (NM_002529) fusion: c.1106-363:NOS1AP_c.881:NTRK1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NOS1AP:NTRK1}		38328	0	156	1	Exon 8 of NTRK1(+)	NOS1AP	156843455			1	Intron of NOS1AP(+):362bp before exon 10	NTRK1	162336479			10	DUPLICATION		5493024	323646	92318	161	NEW_VARIANT
P-0046877-T02-IM6	TPM3 (NM_152263) - NTRK1 (NM_002529) fusion: c.776-357:TPM3_c.1177+60:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {TPM3:NTRK1}		47621	0	51	1	Intron of TPM3(-):357bp before exon 9	TPM3	154142216			1	Intron of NTRK1(+):60bp after exon 8	NTRK1	156843811			10	INVERSION		2701595	331951	26796	69	NEW_VARIANT
P-0048150-T01-IM6	ALOX12B (NM_001139) rearrangement: c.754+71:ALOX12B_chr17:g.6943000del	PRECISE	Note: The ALOX12B rearrangement is a deletion of exons 7 - 15. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		52201	0	19	17	Intron of SLC16A13(+):81bp before exon 4	ALOX12B	6943000			17	Intron of ALOX12B(-):70bp after exon 6	ALOX12B	7983482			10	DELETION		1040482	332442	29894	19	NEW_VARIANT
P-0049942-T01-IM6	HIST1H3F (NM_021018) rearrangement: c.339:HIST1H3F_chr6:g.26131239del	PRECISE	Note: The HIST1H3F rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		14172	0	16	6	IGR: 7Kb before HIST1H2AC(+)	HIST1H3F	26131239			6	Exon 1 of HIST1H3F(-)	HIST1H3F	26250495			10	DELETION		119256	337784	18458	17	NEW_VARIANT
P-0005786-T01-IM5	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exons 1-18 with ALK exons 20-29) : c.2057-186:EML4_c.3172+88:ALKinv	PRECISE	Note: The EML4 (NM_019063) - ALK (NM_004304) fusion is predicted to be in-frame.	MANUAL_OK	3to3	3to3	Protein fusion: in frame (EML4-ALK)		44815	0	17	2	Intron of ALK(-): 88bp after exon 19	EML4	29448239			2	Intron of EML4(+): 186bp before exon 18	ALK	42544381			24	INVERSION		13096142	62095	38605	17	NEW_VARIANT
P-0014129-T03-IM6	KMT2C (NM_170606) rearrangement: c.8306_chr7:g.152299391dup	PRECISE	Note: The KMT2C rearrangement is a duplication that includes KMT2C exons 1-38. One of the breakpoints is within exon 38.	MANUAL_OK	5to3	5to3	-		67805	0	26	7	Exon 38 of KMT2C(-)	KMT2C	151874232			7	IGR: 44Kb before XRCC2(-)	KMT2C	152299391			10	DUPLICATION		425159	277564	66280	31	NEW_VARIANT
P-0015825-T01-IM6	TNFRSF14 (NM_003820) rearrangement: c.764_chr1:g.173990228inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		839694	0	7	1	Exon 8 of TNFRSF14(+)	TNFRSF14	2494624			1	IGR: 90Kb before RC3H1(-)	TNFRSF14	173990228			10	INVERSION		171495604	169394	1910321	8	NEW_VARIANT
P-0017158-T05-IM6	ZCCHC7 (NM_032226) - TEK (NM_000459) Fusion(ZCCHC7 exon1-2 fused with TEK exons 11-23) : c.611-20860:ZCCHC7_c.1540:TEK	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {ZCCHC7:TEK}		38727	0	7	9	Exon 11 of TEK(+)	ZCCHC7	27192537			9	Intron of ZCCHC7(+):21Kb before exon 3	TEK	37281325			0	DUPLICATION		10088788	232463	37673	7	NEW_VARIANT
P-0021722-T01-IM6	ASXL2 (NM_018263) rearrangement: c.140+46_c.1795del	PRECISE	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	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		18264	0	9	2	Exon 11 of ASXL2(-)	ASXL2	25972630			2	Intron of ASXL2(-):45bp after exon 2	ASXL2	26068304			10	DELETION		95674	188140	10633	13	NEW_VARIANT
P-0022811-T01-IM6	KMT2C (NM_170606) rearrangement: t(1;7)(p36.33;q36.1)(chr1:g.1500228:chr7:g.151902162)	PRECISE	Note: The KMT2C rearrangement is a translocation that may result in a truncation of exons 26-59. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		0	0	13	7	Intron of KMT2C(-):28bp after exon 25	KMT2C	151902162			1	Exon 2 of SSU72(-)	KMT2C	1500228			10	TRANSLOCATION		0	192351	0	25	NEW_VARIANT
P-0023439-T01-IM6	ETV6 (NM_001987) rearrangement: chr12:g.10974606_c.1009+48inv	PRECISE	Note: The ETV6 rearrangement is an inversion (1048345 bp) that includes ETV6 exons 1-5. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		114103	0	101	12	IGR: 3Kb before TAS2R10(-)	ETV6	10974606			12	Intron of ETV6(+):48bp after exon 5	ETV6	12022951			10	INVERSION		1048345	195186	108127	127	NEW_VARIANT
P-0023788-T01-IM6	CAMK4 (NM_001744) - APC (NM_000038) Rearrangement : c.241-906:CAMK4_c.6561:APCdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {CAMK4:APC}		25240	0	5	5	Intron of CAMK4(+):905bp before exon 3	CAMK4	110709642			5	Exon 16 of APC(+)	APC	112177852			7	DELETION		1468210	196946	39210	5	NEW_VARIANT
P-0024559-T01-IM6	RET (NM_020975) rearrangement: chr10:g.32186894_c.2136+598del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		73668	0	32	10	Intron of ARHGAP12(-):10Kb after exon 3	RET	32186894			10	Intron of RET(+):598bp after exon 11	RET	43610782			10	DELETION		11423888	200473	56855	32	NEW_VARIANT
P-0032284-T01-IM6	NOTCH2 (NM_024408) rearrangement: t(1;17)(p12;q24.3)(chr1:g.120510237::chr17:g.68563463)	PRECISE	Note: The NOTCH2 rearrangement is a translocation which involves a breakpoint in exon 8. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	7	17	IGR: 398Kb before KCNJ2(+)	NOTCH2	68563463			1	Exon 8 of NOTCH2(-)	NOTCH2	120510237			10	TRANSLOCATION		0	232480	0	7	NEW_VARIANT
P-0032351-T01-IM6	BRD4(NM_058243) - EPHX3(NM_024794) Fusion:  c.2673:BRD4_c.616+1381:EPHX3del	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {BRD4:EPHX3}		13007	0	5	19	Intron of EPHX3(-):1Kb after exon 4	BRD4	15340392			19	Exon 14 of BRD4(-)	EPHX3	15354207			0	DELETION		13815	232821	23936	5	NEW_VARIANT
P-0032351-T01-IM6	BRD4(NM_058243) - PLEKHA2(NM_021623) Fusion: t(8;19)(p11.23;p13.13)(chr8:g.38789930::chr19:g.15354210)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {BRD4:PLEKHA2}		0	0	117	19	Exon 14 of BRD4(-)	BRD4	15354210			8	Intron of PLEKHA2(+):4Kb before exon 3	PLEKHA2	38789930			10	TRANSLOCATION		0	232823	0	172	NEW_VARIANT
P-0034132-T01-IM6	SMAD4 (NM_005359) rearrangement: c.-127-6115_c.*50inv	PRECISE	Note: The SMAD4 rearrangement is an inversion with breakpoints in SMAD4 5UTR and 3UTR. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12443	0	6	18	5-UTR of SMAD4(+):6Kb before coding start	SMAD4	48567175			18	3-UTR of SMAD4(+):31Kb after coding stop	SMAD4	48604887			10	INVERSION		37712	248901	10497	6	NEW_VARIANT
P-0037143-T01-IM6	PAX8 (NM_003466) Rearrangement : c.1189+1224:PAX8_chr2:g.118870847inv	PRECISE	Note: The PAX8 Rearrangement results in the inversion of exons1-10 of PAX8. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		63743	0	106	2	Intron of PAX8(-):1Kb after exon 10	PAX8	113983508			2	IGR: 25Kb before INSIG2(+)	PAX8	118870847			10	INVERSION		4887339	276592	80067	106	NEW_VARIANT
P-0037172-T01-IM6	RTEL1 (NM_032957) rearrangement: t(10;20)(q24.3;q13.33)(chr10:g.114961946::chr20:g.62321521)	PRECISE	Note: The RTEL1 rearrangement is a translocation with a breakpoint in RTEL1 exon 25. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	8	20	Exon 25 of RTEL1(+)	RTEL1	62321521			10	IGR: 252Kb before TCF7L2(+)	RTEL1	114961946			10	TRANSLOCATION		0	276855	0	8	NEW_VARIANT
P-0037284-T01-IM6	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	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {DCTN1:ALK}		250249	0	5	2	Intron of ALK(-):435bp after exon 19	DCTN1	29447891			2	Intron of DCTN1(-):375bp before exon 24	ALK	74590929			10	DELETION		45143038	277345	357751	5	NEW_VARIANT
P-0037448-T01-IM6	ATP5G2 (NM_005176) - BRCA2 (NM_000059) rearrangement: t(12;13)(q13.13;q13.1)(chr12:g.54062814::chr13:g.32918654)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: out of frame  {ATP5G2:BRCA2}		0	0	22	13	Intron of BRCA2(+):40bp before exon 12	ATP5G2	32918654			12	Intron of ATP5G2(-):117bp after exon 4	BRCA2	54062814			10	TRANSLOCATION		0	279082	0	22	NEW_VARIANT
P-0037491-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) Fusion (EML4 exon12 fused with ALK exon20): c.1490-1120:EML4_c.3173-392:ALKinv	PRECISE	Note: The EML4-ALK Fusion is predicted to be in-frame and includes the protein kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		91798	0	122	2	Intron of ALK(-):392bp before exon 20	EML4	29446786			2	Intron of EML4(+):1Kb before exon 13	ALK	42527261			10	INVERSION		13080475	279242	152107	122	NEW_VARIANT
P-0037601-T01-IM6	PIK3CB (NM_006219) rearrangement: c.179:PIK3CB_chr3:g.137751528inv	PRECISE	Note: The PIK3CB rearrangement  is an inversion of exons 2-22. One of the breakpoints is within exon 2. Its functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		33161	0	23	3	3-UTR of CLDN18(+):22Kb after coding stop	PIK3CB	137751528			3	Exon 2 of PIK3CB(-)	PIK3CB	138474814			10	INVERSION		723286	280704	54211	23	NEW_VARIANT
P-0037642-T01-IM6	RECQL4 (NM_004260) rearrangement: c.783:RECQL4_chr8:g.143647141del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		44898	0	11	8	IGR: 45Kb before ARC(-)	RECQL4	143647141			8	Exon 5 of RECQL4(-)	RECQL4	145741720			10	DELETION		2094579	281052	49604	11	NEW_VARIANT
P-0037643-T01-IM6	MET (NM_000245) rearrangement: c.2887+42_c.3029-506del	PRECISE	Note: The MET rearrangement results in the in-frame deletion of exon 14. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		31921	0	83	7	Intron of MET(+):42bp after exon 13	MET	116411750			7	Intron of MET(+):505bp before exon 15	MET	116414429			10	DELETION		2679	281048	12820	90	NEW_VARIANT
P-0037692-T01-IM6	ELF3 (NM_004433) Rearrangement : c.-9+151_c.688+24inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		9611	0	17	1	5-UTR of ELF3(+):279bp before coding start	ELF3	201979985			1	Intron of ELF3(+):24bp after exon 6	ELF3	201982188			10	INVERSION		2203	281764	12732	17	NEW_VARIANT
P-0037693-T01-IM6	ROS1 (NM_002944) Rearrangement : c.229-417_c.374inv	PRECISE	Note: The ROS1 Rearrangement results in the inversion of exon5 of ROS1. One of the breakpoints is within exon5. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		2682	0	25	6	Exon 5 of ROS1(-)	ROS1	117725507			6	Intron of ROS1(-):417bp before exon 4	ROS1	117731222			10	INVERSION		5715	281768	2830	26	NEW_VARIANT
P-0037925-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4634:EML4_c.3173-128:ALKinv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		137364	0	14	2	Intron of ALK(-):128bp before exon 20	EML4	29446522			2	Intron of EML4(+):5Kb after exon 5	ALK	42496505			0	INVERSION		13049983	282743	126224	14	NEW_VARIANT
P-0037925-T01-IM6	OXSR1 (NM_005109) - MYD88 (NM_002468) rearrangement: c.70+6690:OXSR1_c.684-85:MYD88dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {OXSR1:MYD88}		2827	0	53	3	Intron of MYD88(+):84bp before exon 4	OXSR1	38182163			3	Intron of OXSR1(+):7Kb after exon 1	MYD88	38214127			10	DUPLICATION		31964	282741	3075	55	NEW_VARIANT
P-0039219-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1813-3045_c.1920del	PRECISE	Note: The SMARCA4 rearrangement is an intragenic deletion of exon 12. One of the breakpoints is within exon 12.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1159	0	21	19	Intron of SMARCA4(+):3Kb before exon 12	SMARCA4	11110660			19	Exon 12 of SMARCA4(+)	SMARCA4	11113812			10	DELETION		3152	294359	901	23	NEW_VARIANT
P-0039219-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783535::chr6:g.117646339)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	156	6	Intron of ROS1(-):761bp before exon 34	CD74	117646339			5	Intron of CD74(-):660bp before exon 7	ROS1	149783535			10	TRANSLOCATION		0	294362	0	159	NEW_VARIANT
P-0039257-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+1132:KIF5B_c.2012:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KIF5B:RET}		46813	0	68	10	Intron of KIF5B(-):1Kb after exon 15	KIF5B	32316224			10	Exon 11 of RET(+)	RET	43610060			10	INVERSION		11293836	295239	56346	73	NEW_VARIANT
P-0039257-T01-IM6	B2M (NM_004048) rearrangement: c.21:B2M_chr15:g.45002849del	IMPPRECISE	Note: The B2M rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		558	0	32	15	Promoter of B2M(+):835bp from tx start	B2M	45002849			15	Exon 1 of B2M(+)	B2M	45003765			0	DELETION		916	295237	572	34	NEW_VARIANT
P-0039853-T01-IM6	LZTR1 (NM_006767) - CRKL (NM_005207) rearrangement: c.321-170:LZTR1_c.375:CRKLdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {LZTR1:CRKL}		7310	0	5	22	Exon 2 of CRKL(+)	LZTR1	21288130			22	Intron of LZTR1(+):169bp before exon 4	CRKL	21341623			6	DUPLICATION		53493	298484	12506	8	NEW_VARIANT
P-0039853-T01-IM6	STK19 (NM_004197) rearrangement: c.901+34:STK19_chr6:g.31981147del	PRECISE	Note: The STK19 rearrangement is a deletion of exons 7 - 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1052	85	64	6	Intron of STK19(+):34bp after exon 6	STK19	31948359			6	Promoter of STK19(+):370bp from tx start	STK19	31981147			10	DELETION		32788	298483	1669	168	NEW_VARIANT
P-0039998-T01-IM6	CDKN2A (NM_000077) rearrangement: c.423_c.194-2195del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1404	0	51	9	Exon 2 of CDKN2A(-)	CDKN2A	21970935			9	Intron of CDKN2A(-):2Kb before exon 2	CDKN2A	21973402			10	DELETION		2467	300439	1387	52	NEW_VARIANT
P-0040095-T01-IM6	C20orf194 (NM_001009984) - CDKN2A (NM_000077) rearrangement: t(9;20)(p21.3;p13)(chr9:g.21968295::chr20:g.3271180)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {C20orf194:CDKN2A}		0	0	53	20	Intron of C20orf194(-):317bp before exon 26	C20orf194	3271180			9	Intron of CDKN2A(-):54bp before exon 3	CDKN2A	21968295			10	TRANSLOCATION		0	300357	0	53	NEW_VARIANT
P-0040544-T01-IM6	NFE2L2 (NM_006164) rearrangement: t(2;13)(q31.2;q21.31)(chr2:g.178096192::chr13:g.63941965)	PRECISE	Note: The NFE2L2 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	7	13	IGR: 185Kb before LINC00376(-)	NFE2L2	63941965			2	Exon 5 of NFE2L2(-)	NFE2L2	178096192			10	TRANSLOCATION		0	302180	0	7	NEW_VARIANT
P-0040553-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+30:EML4_c.3173-661:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		88231	0	10	2	Intron of ALK(-):661bp before exon 20	EML4	29447055			2	Intron of EML4(+):30bp after exon 12	ALK	42522686			10	INVERSION		13075631	302181	62844	9	NEW_VARIANT
P-0040577-T01-IM6	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)	PRECISE	Note: The CD74-ROS1 fusion is predicted to be in-frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	0	54	6	Intron of ROS1(-):332bp after exon 32	CD74	117650159			5	Intron of CD74(-):566bp before exon 7	ROS1	149783441			10	TRANSLOCATION		0	302357	0	53	NEW_VARIANT
P-0040811-T01-IM6	RB1 (NM_000321) rearrangement: t(13;18)(q14.2;q12.1)(chr13:g.49027014::chr18:g.29737371)	PRECISE	Note: The RB1 rearrangement is a translocation with a breakpoint in intron 17. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	1	19	18	IGR: 33Kb before MEP1B(+)	RB1	29737371			13	Intron of RB1(+):114bp before exon 18	RB1	49027014			10	TRANSLOCATION		0	303105	0	18	NEW_VARIANT
P-0040821-T01-IM6	ASXL1 (NM_015338) rearrangement: c.1638_c.1730del	IMPPRECISE	Note: The ASXL1 rearrangement is an intragenic deletion of exons 11 - 12. The breakpoints are within exon 11 and exon 12.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1356	0	5	20	Exon 11 of ASXL1(+)	ASXL1	31021639			20	Exon 12 of ASXL1(+)	ASXL1	31022245			0	DELETION		606	303118	1470	6	NEW_VARIANT
P-0040869-T01-IM6	CD74 (NM_001025159) - ROS1 (NM_002944) fusion: t(5;6)(q32;q22.1)(chr5:g.149783792::chr6:g.117647263)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {CD74:ROS1}		0	0	67	6	Intron of ROS1(-):123bp after exon 33	CD74	117647263			5	Intron of CD74(-):450bp after exon 6	ROS1	149783792			10	TRANSLOCATION		0	304037	0	64	NEW_VARIANT
P-0040894-T01-IM6	TP53BP1 (NM_001141980) - PPIP5K1 (NM_014659) rearrangement: c.286+88:TP53BP1_c.3311-2129:PPIP5K1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {TP53BP1:PPIP5K1}		3035	0	17	15	Intron of TP53BP1(-):87bp after exon 3	TP53BP1	43784112			15	Intron of PPIP5K1(-):2Kb before exon 28	PPIP5K1	43833910			10	DUPLICATION		49798	304084	3786	18	NEW_VARIANT
P-0041310-T01-IM6	PBRM1 (NM_018313) rearrangement: c.1087+28:PBRM1_chr3:g.39820565del	PRECISE	Note: The PBRM1 rearrangement is a deletion of exons 12 - 30.	MANUAL_OK	3to5	3to5	-		196115	0	30	3	IGR: 30Kb before MYRIP(+)	PBRM1	39820565			3	Intron of PBRM1(-):27bp after exon 11	PBRM1	52675942			10	DELETION		12855377	306336	214269	47	NEW_VARIANT
P-0041418-T01-IM6	KMT2D (NM_003482) rearrangement: c.12670:KMT2D_chr12:g.49607473dup	PRECISE	Note: The KMT2D rearrangement is a duplication of exons 1 - 39. One of the breakpoints is within exon 39. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		127461	0	3	12	Exon 39 of KMT2D(-)	KMT2D	49425818			12	IGR: 29Kb before TUBA1A(-)	KMT2D	49607473			6	DUPLICATION		181655	306551	122308	3	NEW_VARIANT
P-0041471-T01-IM6	DNMT3B (NM_006892) rearrangement: c.592:DNMT3B_chr20:g.31363836inv	PRECISE	Note: The DNMT3B rearrangement is an inversion of exons 1 - 6. One of the breakpoints is within exon 6. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		9258	0	6	20	5-UTR of DNMT3B(+):4Kb before coding start	DNMT3B	31363836			20	Exon 6 of DNMT3B(+)	DNMT3B	31375195			10	INVERSION		11359	306811	11910	6	NEW_VARIANT
P-0041611-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.3152_c.6606del	PRECISE	Note: The ANKRD11 rearrangement is an intragenic deletion of exon 9. The breakpoints are within exon 9.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		28079	0	44	16	Exon 9 of ANKRD11(-)	ANKRD11	89346344			16	Exon 9 of ANKRD11(-)	ANKRD11	89349798			10	DELETION		3454	307101	28511	51	NEW_VARIANT
P-0041637-T01-IM6	PDGFRB (NM_002609) rearrangement: c.403:PDGFRB_chr5:g.67335726inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		243271	0	89	5	IGR: 150Kb before LOC102467655(+)	PDGFRB	67335726			5	Exon 4 of PDGFRB(-)	PDGFRB	149514541			10	INVERSION		82178815	307149	427146	89	NEW_VARIANT
P-0041866-T01-IM6	ELF3 (NM_004433) - CSAD (NM_001244705) rearrangement: t(1;12)(q32.1;q13.13)(chr1:g.201981995::chr12:g.53556508)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: out of frame  {ELF3:CSAD}		0	0	15	12	Intron of CSAD(-):1Kb before exon 2	ELF3	53556508			1	Intron of ELF3(+):79bp before exon 6	CSAD	201981995			10	TRANSLOCATION		0	307588	0	16	NEW_VARIANT
P-0041866-T01-IM6	RASAL3 (NM_022904) - AXL (NM_021913) rearrangement: c.2683:RASAL3_c.1538-93:AXLinv	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {RASAL3:AXL}		415702	0	12	19	Exon 16 of RASAL3(-)	RASAL3	15563614			19	Intron of AXL(+):92bp before exon 13	AXL	41754326			0	INVERSION		26190712	307587	471781	12	NEW_VARIANT
P-0041866-T01-IM6	SLC34A1 (NM_003052) - NSD1 (NM_022455) rearrangement: c.936+1867:SLC34A1_c.7929:NSD1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SLC34A1:NSD1}		1227	0	2	5	Exon 23 of NSD1(+)	SLC34A1	176722298			5	Intron of SLC34A1(+):2Kb after exon 8	NSD1	176817240			9	DUPLICATION		94942	307585	988	2	NEW_VARIANT
P-0041967-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+447:EML4_c.3172+180:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		84398	0	39	2	Intron of ALK(-):179bp after exon 19	EML4	29448147			2	Intron of EML4(+):447bp after exon 12	ALK	42523103			10	INVERSION		13074956	307731	58923	39	NEW_VARIANT
P-0042214-T01-IM6	FOXO1 (NM_002015) rearrangement: c.631-8518_c.1277inv	PRECISE	Note: The FOXO1 rearrangement is an intragenic inversion of exon 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		2857	0	7	13	Exon 2 of FOXO1(-)	FOXO1	41134351			13	Intron of FOXO1(-):9Kb before exon 2	FOXO1	41143515			5	INVERSION		9164	308472	3106	7	NEW_VARIANT
P-0042214-T01-IM6	STAT5A (NM_003152) - GAST (NM_000805) rearrangement: c.669:STAT5A_c.212-26:GASTdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {STAT5A:GAST}		43120	0	17	17	Intron of GAST(+):25bp before exon 3	STAT5A	39872004			17	Exon 7 of STAT5A(+)	GAST	40451887			10	DUPLICATION		579883	308471	48480	24	NEW_VARIANT
P-0042596-T02-IM6	DNMT3A (NM_022552) rearrangement: c.1279+153:DNMT3A_chr2:g.10625811inv	PRECISE	Note: The DNMT3A rearrangement is an inversion of exons 11 - 23. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		42606	0	12	2	IGR: 36Kb before LOC101929715(+)	DNMT3A	10625811			2	Intron of DNMT3A(-):152bp after exon 10	DNMT3A	25469336			10	INVERSION		14843525	311648	50086	12	NEW_VARIANT
P-0042596-T02-IM6	SQSTM1 (NM_003900) - ALK (NM_004304) fusion: t(2;5)(p23.2;q35.3)(chr2:g.29446511::chr5:g.179254603)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {SQSTM1:ALK}		0	0	34	5	Intron of SQSTM1(+):2Kb after exon 6	SQSTM1	179254603			2	Intron of ALK(-):117bp before exon 20	ALK	29446511			10	TRANSLOCATION		0	311650	0	39	NEW_VARIANT
P-0042713-T01-IM6	TNFAIP3 (NM_006290) rearrangement: c.805+2:TNFAIP3_chr6:g.138203304del	PRECISE	Note: The TNFAIP3 rearrangement is a deletion of exons 6 - 9.	MANUAL_OK	3to5	3to5	-		11107	0	19	6	Intron of TNFAIP3(+):2bp after exon 5	TNFAIP3	138197305			6	3-UTR of TNFAIP3(+):11Kb after coding stop	TNFAIP3	138203304			10	DELETION		5999	311156	11950	21	NEW_VARIANT
P-0042736-T01-IM6	RPGRIP1L (NM_015272) - FANCA (NM_000135) rearrangement: c.231-767:RPGRIP1L_c.1901-65:FANCAdup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {RPGRIP1L:FANCA}		280811	0	10	16	Intron of RPGRIP1L(-):767bp before exon 4	RPGRIP1L	53727043			16	Intron of FANCA(-):65bp before exon 22	FANCA	89839857			0	DUPLICATION		36112814	311290	121484	10	NEW_VARIANT
P-0042800-T01-IM6	RPTOR (NM_020761) - MAP3K3 (NM_002401) rearrangement: c.2101+230:RPTOR_c.5-4456:MAP3K3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RPTOR:MAP3K3}		144251	0	6	17	Intron of MAP3K3(+):4Kb before exon 2	RPTOR	61705585			17	Intron of RPTOR(+):230bp after exon 18	MAP3K3	78865867			10	DUPLICATION		17160282	311416	179438	6	NEW_VARIANT
P-0042801-T01-IM6	KCNK13 (NM_022054) - AKT1 (NM_001014431) rearrangement: c.334+4464:KCNK13_c.924:AKT1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {KCNK13:AKT1}		58747	0	60	14	Intron of KCNK13(+):4Kb after exon 1	KCNK13	90533347			14	Exon 10 of AKT1(-)	AKT1	105239621			10	INVERSION		14706274	311417	46819	57	NEW_VARIANT
P-0042863-T01-IM6	RHEB (NM_005614) rearrangement: c.50_c.462+196inv	PRECISE	Note: The RHEB rearrangement is an intragenic inversion of exons 1 - 7. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		6313	0	3	7	Intron of RHEB(-):195bp after exon 7	RHEB	151167461			7	Exon 1 of RHEB(-)	RHEB	151216548			8	INVERSION		49087	311544	4763	5	NEW_VARIANT
P-0042874-T01-IM6	EGFR (NM_005228) rearrangement: t(7;17)(p11.2;p11.2)(chr7:g.55241239::chr17:g.19540903)	PRECISE	Note: The EGFR rearrangement is a translocation with a breakpoint in intron 17. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	6	17	IGR: 11Kb before ALDH3A2(+)	EGFR	19540903			7	Intron of EGFR(+):374bp before exon 18	EGFR	55241239			8	TRANSLOCATION		0	311557	0	6	NEW_VARIANT
P-0042874-T01-IM6	PAK7 (NM_177990) rearrangement: t(18;20)(q23;p12.2)(chr18:g.75150951::chr20:g.9546741)	PRECISE	Note: The PAK7 rearrangement is a translocation with a breakpoint in exon 5. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	12	20	Exon 5 of PAK7(-)	PAK7	9546741			18	IGR: 189Kb before GALR1(+)	PAK7	75150951			10	TRANSLOCATION		0	311558	0	13	NEW_VARIANT
P-0042912-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-3467:CDKN2A_chr9:g.22055601del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		6562	0	13	9	Exon 1 of CDKN2A(-)	CDKN2A	21974674			9	5-UTR of CDKN2B-AS1(+):65Kb before coding start	CDKN2A	22055601			10	DELETION		80927	311646	4433	17	NEW_VARIANT
P-0042935-T01-IM6	MET (NM_000245) rearrangement: t(1;7)(p36.33;q31.2)(chr1:g.1138847::chr7:g.116412969)	PRECISE	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.	MANUAL_OK	5to5	5to5	Transcript Fusion {TNFRSF18:MET}		0	0	37	7	Intron of MET(+):926bp after exon 14	MET	116412969			1	Promoter of TNFRSF18(-):40bp from tx start	MET	1138847			10	TRANSLOCATION		0	311716	0	45	NEW_VARIANT
P-0043242-T01-IM6	H3F3C (NM_001013699) rearrangement: c.310:H3F3C_chr12:g.25464235del	PRECISE	Note: The H3F3C rearrangement is a deletion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		6224	0	9	12	IGR: 107Kb before KRAS(-)	H3F3C	25464235			12	Exon 1 of H3F3C(-)	H3F3C	31944791			10	DELETION		6480556	313611	9095	16	NEW_VARIANT
P-0043350-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-4017:EML4_c.3172+814:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		97789	0	64	2	Intron of ALK(-):813bp after exon 19	EML4	29447513			2	Intron of EML4(+):4Kb before exon 6	ALK	42503973			10	INVERSION		13056460	313910	118498	63	NEW_VARIANT
P-0043612-T01-IM6	CTNNB1 (NM_001904) rearrangement: c.242-61:CTNNB1_chr3:g.41259809del	PRECISE	Note: The CTNNB1 rearrangement is a deletion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1452	0	20	3	5-UTR of CTNNB1(+):6Kb before coding start	CTNNB1	41259809			3	Intron of CTNNB1(+):60bp before exon 4	CTNNB1	41266384			10	DELETION		6575	315087	2326	20	NEW_VARIANT
P-0043628-T01-IM6	CDKN2A (NM_000077) rearrangement: c.457+413_c.194-3286inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		3608	0	4	9	Intron of CDKN2A(-):412bp after exon 2	CDKN2A	21970488			9	Exon 1 of CDKN2A(-)	CDKN2A	21974493			10	INVERSION		4005	315100	4196	4	NEW_VARIANT
P-0043938-T01-IM6	SDC4 (NM_002999) - ROS1 (NM_002944) fusion: t(6;20)(q22.1;q13.12)(chr6:g.117651208::chr20:g.43962372)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SDC4:ROS1}		0	0	8	20	Intron of SDC4(-):663bp before exon 3	SDC4	43962372			6	Intron of ROS1(-):599bp before exon 32	ROS1	117651208			10	TRANSLOCATION		0	316979	0	17	NEW_VARIANT
P-0044335-T01-IM6	RASA1 (NM_002890) rearrangement: c.2012-145:RASA1_chr5:g.82942092del	PRECISE	Note: The RASA1 rearrangement is a deletion of exons 1 - 15.	MANUAL_OK	3to5	3to5	-		12327	0	15	5	Intron of HAPLN1(-):2Kb before exon 4	RASA1	82942092			5	Intron of RASA1(+):144bp before exon 16	RASA1	86672065			10	DELETION		3729973	318816	12128	15	NEW_VARIANT
P-0044335-T01-IM6	PTPRD (NM_002839) rearrangement: c.2467+792_c.3153+150dup	PRECISE	Note: The PTPRD rearrangement is an intragenic duplication of exons 28 - 29. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : out of frame		2932	0	18	9	Intron of PTPRD(-):149bp after exon 29	PTPRD	8485077			9	Intron of PTPRD(-):791bp after exon 27	PTPRD	8492070			10	DUPLICATION		6993	318818	4384	20	NEW_VARIANT
P-0044441-T01-IM6	RB1 (NM_000321) rearrangement: c.1333-906_c.1421+25del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exons 14 - 15.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		472	0	97	13	Intron of RB1(+):905bp before exon 14	RB1	48952824			13	Intron of RB1(+):25bp after exon 15	RB1	48954245			10	DELETION		1421	319174	40	100	NEW_VARIANT
P-0044475-T01-IM6	TP53 (NM_000546) rearrangement: c.672+142_c.993+1324del	PRECISE	Note: The TP53 rearrangement is an intragenic deletion of exons 7 - 9.	MANUAL_OK	3to5	3to5	Deletion of 3 exons : in frame		6462	0	13	17	Intron of TP53(-):1Kb after exon 9	TP53	7575529			17	Intron of TP53(-):141bp after exon 6	TP53	7578035			10	DELETION		2506	319229	5119	13	NEW_VARIANT
P-0044475-T01-IM6	BCL6 (NM_001706) rearrangement: t(3;22)(q27.3;q12.3)(chr3:g.187444650::chr22:g.34770793)	PRECISE	Note: The BCL6 rearrangement is a translocation with a breakpoint in exon 7. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	9	22	IGR: 650Kb before LARGE-AS1(+)	BCL6	34770793			3	Exon 7 of BCL6(-)	BCL6	187444650			10	TRANSLOCATION		0	319231	0	8	NEW_VARIANT
P-0044475-T01-IM6	EPHA3 (NM_005233) rearrangement: c.1502:EPHA3_chr3:g.106473529inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		16556	0	10	3	Exon 7 of EPHA3(+)	EPHA3	89448538			3	IGR: 355Kb before LINC00882(-)	EPHA3	106473529			10	INVERSION		17024991	319230	16165	12	NEW_VARIANT
P-0044771-T01-IM6	KMT2D (NM_003482) rearrangement: c.16228:KMT2D_chr12:g.49330097del	PRECISE	Note: The KMT2D rearrangement is a deletion of exons 51 - 54. One of the breakpoints is within exon 51.	MANUAL_OK	3to5	3to5	-		3744	0	7	12	3-UTR of ARF3(-):3Kb after coding stop	KMT2D	49330097			12	Exon 51 of KMT2D(-)	KMT2D	49416483			10	DELETION		86386	320505	1910	7	NEW_VARIANT
P-0044827-T01-IM6	SMAD3 (NM_005902) - ASPSCR1 (NM_001251888) rearrangement: t(15;17)(q22.33;q25.3)(chr15:g.67482866::chr17:g.79944678)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SMAD3:ASPSCR1}		0	0	55	17	Intron of ASPSCR1(+):1Kb after exon 4	SMAD3	79944678			15	Exon 9 of SMAD3(+)	ASPSCR1	67482866			10	TRANSLOCATION		0	320671	0	54	NEW_VARIANT
P-0000840-T01-IM3	ROS1 (NM_002944) - CD74 (NM_001025158) Translocation:  t(6;5)(q22.1;q32)(chr6:g.117646938::chr5:g.149783508)	PRECISE		AUTO_OK	3to5	3to5	Protein fusion: in frame (CD74-ROS1)		0	0	3	6	Intron of ROS1(-): 449bp after exon 33	ROS1	117646938			5	Intron of CD74(-): 633bp before exon 7	CD74	149783508			5	TRANSLOCATION		0	72036	0	9	NEW_VARIANT
P-0004934-T01-IM5	TAOK1 (NM_020791) - NF1 (NM_001042492) rearrangement : c.133-769:TAOK1_c.889-21:NF1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein fusion: in frame (TAOK1-NF1)		19477	0	5	17	Intron of TAOK1(+): 769bp before exon 3	TAOK1	27793394			17	Intron of NF1(+): 21bp before exon 9	NF1	29527419			4	DELETION		1734025	41035	22841	5	NEW_VARIANT
P-0006921-T01-IM5	ROS1 (NM_002944) - SLC34A2(NM_006424) rearrangement : t(4;6) (p15;q22)(chr4:g.25679037::chr6:g.117648517)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	51	6	Intron of ROS1(-): 940bp before exon 33	ROS1	117648517			4	3-UTR of SLC34A2(+): 666bp after coding stop	SLC34A2	25679037			34	TRANSLOCATION		0	109881	0	50	NEW_VARIANT
P-0006921-T01-IM5	FAM135B (NM_015912) - ROS1 (NM_002944) rearrangement : t(6;8)(q22;q24)(chr6:g.117648534::chr8:g.138220899)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	67	8	IGR: 921Kb before FAM135B(-)	FAM135B	138220899			6	Intron of ROS1(-): 957bp before exon 33	ROS1	117648534			21	TRANSLOCATION		0	109885	0	66	NEW_VARIANT
P-0014932-T01-IM6	FGFR1 (NM_001174067) Rearrangement : c.1756+611_c.2142-18del	PRECISE	Note: The FGFR1 Rearrangement results in the deletion of exons 14-16.This includes the protein kinase domain of FGFR1.	MANUAL_OK	3to5	3to5	Deletion of 3 exons: out of frame		5698	0	43	8	Intron of FGFR1(-): 18bp before exon 15	FGFR1	38271825			8	Intron of FGFR1(-): 611bp after exon 11	FGFR1	38274213			47	DELETION		2388	166236	5204	37	NEW_VARIANT
P-0018245-T01-IM6	RAD51B (NM_133509) rearrangement: c.780_c.853+1794inv	PRECISE	Note: The RAD51B is an intragenic inversion of a part of exon 8, potentially disrupting gene function.	MANUAL_OK	3to3	3to3	Antisense Fusion		559	0	7	14	Exon 8 of RAD51B(+)	RAD51B	68758624			14	Intron of RAD51B(+):2Kb after exon 8	RAD51B	68760491			10	INVERSION		1867	178437	860	7	NEW_VARIANT
P-0018245-T01-IM6	KMT2B (NM_014727) rearrangement: t(19;20)(q13.12;p11.23)(chr19:g.36216347::chr20:g.19374059)	PRECISE	Note: The KMT2B rearrangement is a translocation that may result in a truncation of KMT2B exons 12-37. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	11	20	Intron of SLC24A3(+):112Kb after exon 2	KMT2B	19374059			19	Intron of KMT2B(+):32bp before exon 12	KMT2B	36216347			10	TRANSLOCATION		0	178440	0	20	NEW_VARIANT
P-0018916-T01-IM6	CDKN2Ap16INK4A (NM_000077) - CDKN2B (NM_004936) rearrangement: c.457+275:CDKN2Ap16INK4A_c.156+2:CDKN2Binv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		10694	0	7	9	Intron of CDKN2A(-):274bp after exon 2	CDKN2Ap16INK4A	21970626			9	Intron of CDKN2B(-):1bp after exon 1	CDKN2B	22008795			10	INVERSION		38169	180520	16094	7	NEW_VARIANT
P-0019303-T02-IM6	STAT5B (NM_012448) rearrangement: c.2077+32:STAT5B_chr17:g.37367870inv	PRECISE	Note: The STAT5B rearrangement is an inversion of exons 17-19. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		132115	0	39	17	3-UTR of STAC2(-):674bp after coding stop	STAT5B	37367870			17	Intron of STAT5B(-):31bp after exon 16	STAT5B	40359544			10	INVERSION		2991674	282046	241252	40	NEW_VARIANT
P-0021839-T01-IM6	CDK12 (NM_016507) Rearrangement : t(7,17)(p22.1,q12)(chr7:g.4787537::chr17:g.37681073)	PRECISE	Note : The CDK12 Rearrangement possible results in the possible truncation of CDK12.One of the breakpoints is within exon12. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	11	17	Exon 12 of CDK12(+)	CDK12	37681073			7	Intron of FOXK1(+):7Kb before exon 3	CDK12	4787537			10	TRANSLOCATION		0	188300	0	15	NEW_VARIANT
P-0024556-T01-IM6	ZFHX3 (NM_006885) Rearrangement: chr16:g.72718236_c.416:ZFHX3del	PRECISE	Note: The ZFHX3 Rearrangement results in the deletion of exons 2-10. One of the breakpoints is within exon2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		76018	0	4	16	IGR: 99Kb before ZFHX3(-)	ZFHX3	72718236			16	Exon 2 of ZFHX3(-)	ZFHX3	72993629			10	DELETION		275393	198740	112721	4	NEW_VARIANT
P-0024556-T01-IM6	KMT2C (NM_170606) Rearrangement : c.403-41051:CNTNAP2_c.9820:KMT2Cdel	PRECISE	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.	MANUAL_OK	3to5	3to5	Antisense Fusion		75816	0	39	7	Intron of CNTNAP2(+):41Kb before exon 4	KMT2C	146699948			7	Exon 43 of KMT2C(-)	KMT2C	151860842			10	DELETION		5160894	198738	96355	40	NEW_VARIANT
P-0025040-T01-IM6	EML4 (NM_001145076) - ALK (NM_004304) fusion (EML4 exon 12 fused to ALK exon 20) :  c.1316-1940:EML4_c.3173-758:ALKinv	PRECISE	Note: The EML4 -ALK fusion is an in-frame fusion and includes the protein kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		90732	0	56	2	Intron of ALK(-):758bp before exon 20	EML4	29447152			2	Intron of EML4(+):2Kb before exon 13	ALK	42526441			10	INVERSION		13079289	203275	59663	56	NEW_VARIANT
P-0025714-T03-IM6	NOS1AP (NM_014697) - MCL1 (NM_021960) rearrangement: c.345-15882:NOS1AP_c.470:MCL1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {NOS1AP:MCL1}		80674	0	20	1	Exon 1 of MCL1(-)	NOS1AP	150551537			1	Intron of NOS1AP(+):16Kb before exon 5	MCL1	162286925			10	INVERSION		11735388	248904	75391	20	NEW_VARIANT
P-0026022-T01-IM6	DOT1L (NM_032482) rearrangement: c.2874_chr19:g.2362078dup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		19374	0	27	19	Exon 24 of DOT1L(+)	DOT1L	2222042			19	IGR: 28Kb before TMPRSS9(+)	DOT1L	2362078			10	DUPLICATION		140036	208254	30271	28	NEW_VARIANT
P-0028081-T01-IM6	EZR (NM_003379) - ROS1 (NM_002944) fusion: c.1090+285:EZR_c.5557+112:ROS1del	PRECISE	Note: The EZR - ROS1 fusion is predicted to be in frame and includes the kinase domain of ROS1.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {EZR:ROS1}		223664	0	45	6	Intron of ROS1(-):111bp after exon 33	EZR	117647275			6	Intron of EZR(-):284bp after exon 9	ROS1	159191511			10	DELETION		41544236	216047	151312	45	NEW_VARIANT
P-0028917-T01-IM6	SPEN (NM_015001) - PLEKHM2 (NM_015164) rearrangement:  c.6123:SPEN_c.61-10330:PLEKHM2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SPEN:PLEKHM2}		49299	0	5	1	Intron of PLEKHM2(+):10Kb before exon 2	SPEN	16032402			1	Exon 11 of SPEN(+)	PLEKHM2	16258858			10	DUPLICATION		226456	219225	48352	5	NEW_VARIANT
P-0029225-T01-IM6	AXL (NM_021913) Rearrangement: c.252:AXL_chr19:g.18915509del	PRECISE	Note: The AXL rearrangement is a deletion of AXL exons 1 to 2. One of the breakpoints is within AXL exon 2.	MANUAL_OK	3to5	3to5	-		203481	0	56	19	IGR: 22Kb before COMP(-)	AXL	18915509			19	Exon 2 of AXL(+)	AXL	41726707			10	DELETION		22811198	221103	264756	69	NEW_VARIANT
P-0030471-T01-IM6	TCF7L2 (NM_001146274) rearrangement: c.876-947_c.937del	PRECISE	Note: The TCF7L2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		760	0	9	10	Intron of TCF7L2(+):946bp before exon 9	TCF7L2	114909810			10	Exon 9 of TCF7L2(+)	TCF7L2	114910818			10	DELETION		1008	226604	1069	9	NEW_VARIANT
P-0030471-T01-IM6	KDM5C (NM_004187) rearrangement: chrX:g.:11024795_c.1867-2inv	PRECISE	Note: The KDM5C rearrangement is an inversion that includes KDM5C exons 14-26.	MANUAL_OK	5to5	5to5	-		286437	0	4	X	IGR: 105Kb before HCCS(+)	KDM5C	11024795			X	Intron of KDM5C(-):2bp before exon 14	KDM5C	53230928			10	INVERSION		42206133	226606	461772	5	NEW_VARIANT
P-0032211-T02-IM6	TPH2 (NM_173353) -  MDM2 (NM_002392) Rearrangement : c.256-415:TPH2_c.248:MDM2dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {TPH2:MDM2}		12815	0	19	12	Exon 4 of MDM2(+)	TPH2	69210665			12	Intron of TPH2(+):414bp before exon 3	MDM2	72337659			0	DUPLICATION		3126994	253436	69213	24	NEW_VARIANT
P-0034334-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4909:EML4_c.3173-176:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		140173	0	100	2	Intron of ALK(-):176bp before exon 20	EML4	29446570			2	Intron of EML4(+):5Kb after exon 5	ALK	42496780			10	INVERSION		13050210	250514	127181	99	NEW_VARIANT
P-0035694-T01-IM6	EPYC (NM_004950) - KEAP1 (NM_203500) rearrangement: t(12;19)(q21.33;p13.2)(chr12:g.91372652::chr19:g.10600151)	PRECISE	Note: The EPYC - KEAP1 rearrangement is a translocation that results in the fusion of EPYC exons 1-2 with KEAP1 exons 5-6.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {EPYC:KEAP1}		0	0	138	19	Intron of KEAP1(-):107bp before exon 5	EPYC	10600151			12	Intron of EPYC(-):613bp before exon 3	KEAP1	91372652			10	TRANSLOCATION		0	260736	0	154	NEW_VARIANT
P-0035694-T01-IM6	INSR (NM_000208) - TYK2 (NM_003331) rearrangement: c.3112:INSR_c.2617+238:TYK2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {INSR:TYK2}		98504	0	40	19	Exon 17 of INSR(-)	INSR	7125440			19	Intron of TYK2(-):237bp after exon 18	TYK2	10467006			10	DUPLICATION		3341566	260735	504683	49	NEW_VARIANT
P-0035694-T01-IM6	BRD9 (NM_023924) - TERT (NM_198253) rearrangement: c.47:BRD9_c.-56:TERTdup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {BRD9:TERT}		34739	0	9	5	Exon 1 of BRD9(-)	BRD9	892726			5	5-UTR of TERT(-):41Kb before coding start	TERT	1295160			10	DUPLICATION		402434	260734	119856	13	NEW_VARIANT
P-0037082-T01-IM6	TMPRSS2 (NM_001135099) Rearrangement : c.55+4876:TMPRSS2_chr21:g.40091831del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		56217	0	30	21	IGR: 19Kb before LINC00114(-)	TMPRSS2	40091831			21	Intron of TMPRSS2(-):5Kb after exon 1	TMPRSS2	42875001			10	DELETION		2783170	276274	43523	33	NEW_VARIANT
P-0037226-T01-IM6	PIK3R3 (NM_003629) rearrangement: c.622-1177:PIK3R3_chr1:g.46598399del	PRECISE	Note: The PIK3R3 rearrangement is a deletion of exons 1-5. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		7899	0	140	1	Intron of PIK3R3(-):1Kb before exon 6	PIK3R3	46528920			1	Promoter of PIK3R3(-):93Kb from tx start	PIK3R3	46598399			10	DELETION		69479	277144	7359	152	NEW_VARIANT
P-0037236-T01-IM6	PAX5 (NM_016734) rearrangement: t(9;17)(p13.2;p13.1)(chr9:g.36923458::chr17:g.8339095)	PRECISE	Note: The PAX5 rearrangement is a translocation involving a breakpoint in exon 7. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {PAX5:NDEL1}		0	0	50	17	Promoter of NDEL1(+):74bp from tx start	PAX5	8339095			9	Exon 7 of PAX5(-)	PAX5	36923458			10	TRANSLOCATION		0	277189	0	61	NEW_VARIANT
P-0037238-T01-IM6	PRKCI (NM_002740) - MECOM (NM_004991) rearrangement: c.581:PRKCI_c.376-48366:MEMCOMinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {PRKCI:MECOM}		9404	0	11	3	Intron of MECOM(-):48Kb before exon 3	PRKCI	168909986			3	Exon 6 of PRKCI(+)	MECOM	169988339			10	INVERSION		1078353	277190	26490	18	NEW_VARIANT
P-0037404-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+4963:EML4_c.3172+455:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		106044	0	33	2	Intron of ALK(-):454bp after exon 19	EML4	29447872			2	Intron of EML4(+):5Kb after exon 5	ALK	42496834			10	INVERSION		13048962	278836	76121	31	NEW_VARIANT
P-0037477-T01-IM6	GNAI2 (NM_002070) - MYD88 (NM_002468) Rearrangement : c.465-109:GNAI2_c.540:MYD88dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {GNAI2:MYD88}		160872	0	9	3	Exon 3 of MYD88(+)	GNAI2	38181916			3	Intron of GNAI2(+):108bp before exon 5	MYD88	50293515			10	DUPLICATION		12111599	279334	263264	14	NEW_VARIANT
P-0037577-T01-IM6	ETV6 (NM_001987) rearrangement: c.1010-5036:ETV6_chr12:g.18819650del	PRECISE	Note: The ETV6 rearrangement is a deletion of exons 6-8. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		85010	0	8	12	Intron of ETV6(+):5Kb before exon 6	ETV6	12032343			12	IGR: 16Kb before PLCZ1(-)	ETV6	18819650			10	DELETION		6787307	280358	95477	8	NEW_VARIANT
P-0037729-T01-IM6	ZFHX3 (NM_006885) rearrangement: c.7061:ZFHX3_chr16:g.72798880del	PRECISE	Note: The ZFHX3 rearrangement results in the deletion of exons 9-10. One of the breakpoints is within exon 9.	MANUAL_OK	3to5	3to5	-		24987	0	20	16	IGR: 18Kb before ZFHX3(-)	ZFHX3	72798880			16	Exon 9 of ZFHX3(-)	ZFHX3	72829520			10	DELETION		30640	281672	24261	20	NEW_VARIANT
P-0037729-T01-IM6	ETV1 (NM_001163147) rearrangement: c.181+548:ETV1_chr7:g.6669540del	IMPPRECISE	Note: The ETV1 rearrangement results in the deletion of exons 5-12. The functional significance is unknown.	MANUAL_OK	3to5	3to5	-		20465	0	5	7	IGR: 7Kb before ZNF316(+)	ETV1	6669540			7	Intron of ETV1(-):547bp after exon 4	ETV1	14025715			0	DELETION		7356175	281667	28072	6	NEW_VARIANT
P-0038972-T01-IM6	WHSC1 (NM_001042424) rearrangement: c.1556-183:WHSC1_chr4:g.119207del	PRECISE	Note: The WHSC1 rearrangement is a deletion of exons 1 - 6. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Protein Fusion: in frame  {ZNF718:WHSC1}		61371	0	7	4	Intron of ZNF718(+):35Kb before exon 5	WHSC1	119207			4	Intron of WHSC1(+):182bp before exon 7	WHSC1	1936688			10	DELETION		1817481	292822	95480	7	NEW_VARIANT
P-0039604-T01-IM6	RET (NM_020975) rearrangement: c.2137-515:RET_chr10:g.54088195inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		30186	0	10	10	Intron of RET(+):514bp before exon 12	RET	43611517			10	IGR: 14Kb before DKK1(+)	RET	54088195			10	INVERSION		10476678	297147	33240	11	NEW_VARIANT
P-0039604-T01-IM6	DNMT3B (NM_006892) rearrangement: t(16;20)(p13.13;q11.21)(chr16:g.11628924::chr20:g.31390225)	PRECISE	Note: The DNMT3B rearrangement is a translocation with a breakpoint in exon 20. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	75	20	Exon 20 of DNMT3B(+)	DNMT3B	31390225			16	IGR: 13Kb before LITAF(-)	DNMT3B	11628924			10	TRANSLOCATION		0	297150	0	92	NEW_VARIANT
P-0039604-T01-IM6	EGFR (NM_005228) rearrangement: c.2062-394_c.3115-18dup	PRECISE	Note: The EGFR rearrangement is a kinase domain duplication (KDD) alteration, involving exons 18-25.	MANUAL_OK	5to3	5to3	Duplication of 8 exons : in frame		24242	0	480	7	Intron of EGFR(+):393bp before exon 18	EGFR	55241220			7	Intron of EGFR(+):17bp before exon 26	EGFR	55269410			10	DUPLICATION		28190	297145	67860	527	NEW_VARIANT
P-0039941-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1725+2040:KIF5B_c.2137-693:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		72157	0	45	10	Intron of KIF5B(-):2Kb after exon 15	KIF5B	32315316			10	Intron of RET(+):692bp before exon 12	RET	43611339			10	INVERSION		11296023	298812	76746	51	NEW_VARIANT
P-0040258-T01-IM6	ERRFI1 (NM_018948) rearrangement: c.1205:ERRFI1_chr1:g.8060312del	PRECISE	Note: The ERRFI1 rearrangement is a deletion of exon 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	-		1199	0	3	1	IGR: 11Kb before ERRFI1(-)	ERRFI1	8060312			1	Exon 4 of ERRFI1(-)	ERRFI1	8073454			8	DELETION		13142	300849	1677	4	NEW_VARIANT
P-0040313-T01-IM6	INPPL1 (NM_001567) rearrangement: c.269:INPPL1_chr11:g.81893992inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		76732	0	47	11	Exon 3 of INPPL1(+)	INPPL1	71939414			11	3-UTR of LOC101928989(-):221Kb after coding stop	INPPL1	81893992			10	INVERSION		9954578	301273	200270	52	NEW_VARIANT
P-0040571-T01-IM6	Note: The FAT1 rearrangement is a deletion of exons 13 - 27.	PRECISE	FAT1 (NM_005245) rearrangement: c.9229+44:FAT1_chr4:g.186619246del	MANUAL_OK	3to5	3to5	Transcript Fusion {FAT1:SORBS2}		34804	0	11	4	5-UTR of SORBS2(-):110Kb before coding start	Note	186619246			4	Intron of FAT1(-):43bp after exon 12	Note	187535301			10	DELETION		916055	302348	32775	12	NEW_VARIANT
P-0040576-T01-IM6	Note: The NF1 rearrangement is an inversion of exons 47 - 58. Functional significance is undetermined.	IMPPRECISE	NF1 (NM_001042492) rearrangement: c.6921+26:NF1_chr17:g.29751233inv	MANUAL_OK	3to3	3to3	Antisense Fusion		16295	0	5	17	Intron of NF1(+):26bp after exon 46	Note	29665849			17	Intron of RAB11FIP4(+):8Kb before exon 2	Note	29751233			0	INVERSION		85384	302350	13782	5	NEW_VARIANT
P-0040576-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion (EML4 exon5 fused with ALK exon20) : c.668-821:EML4_c.3173-927:ALKinv	PRECISE	Note: The EML4-ALK fusion results in an in-frame fusion and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		117282	0	121	2	Intron of ALK(-):927bp before exon 20	EML4	29447321			2	Intron of EML4(+):820bp before exon 6	ALK	42507169			10	INVERSION		13059848	302349	93121	120	NEW_VARIANT
P-0040732-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1832:EML4_c.3173-242:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		151577	0	110	2	Intron of ALK(-):242bp before exon 20	EML4	29446636			2	Intron of EML4(+):2Kb before exon 13	ALK	42526549			10	INVERSION		13079913	306065	99614	108	NEW_VARIANT
P-0040990-T01-IM6	CALR (NM_004343) rearrangement: c.397+48:CALR_chr19:g.10884675inv	PRECISE	Note: The CALR rearrangement is an inversion of exons 1 - 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		114787	0	3	19	Intron of DNM2(+):1Kb after exon 3	CALR	10884675			19	Intron of CALR(+):48bp after exon 3	CALR	13050493			6	INVERSION		2165818	305127	159958	3	NEW_VARIANT
P-0041052-T01-IM6	GLI1 (NM_005269) rearrangement: c.442:GLI1_chr12:g.45085414dup	PRECISE	Note: The GLI1 rearrangement is a duplication of exons 1 - 5. One of the breakpoints is within exon 5. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Antisense Fusion		276691	0	386	12	Intron of NELL2(-):12Kb after exon 12	GLI1	45085414			12	Exon 5 of GLI1(+)	GLI1	57858946			10	DUPLICATION		12773532	305549	425127	479	NEW_VARIANT
P-0041210-T01-IM6	MET (NM_000245) rearrangement: c.1201-6894_c.1966-9del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion of 5 exons : in frame		7729	0	8	7	Intron of MET(+):7Kb before exon 3	MET	116364828			7	Intron of MET(+):8bp before exon 8	MET	116397683			5	DELETION		32855	306205	11056	8	NEW_VARIANT
P-0041256-T02-IM6	CDK4 (NM_000075) rearrangement: t(5;12)(p14.2;q14.1)(chr5:g.23876068::chr12:g.58143197)	PRECISE	Note: The CDK4 rearrangement is a translocation with a breakpoint in intron 6. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	26	12	Intron of CDK4(-):39bp after exon 6	CDK4	58143197			5	IGR: 368Kb before PRDM9(+)	CDK4	23876068			10	TRANSLOCATION		0	306809	0	26	NEW_VARIANT
P-0041269-T01-IM6	NF1 (NM_001042492) rearrangement: c.2159_c.3828dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		11259	0	53	17	Exon 18 of NF1(+)	NF1	29553610			17	Exon 28 of NF1(+)	NF1	29562748			10	DUPLICATION		9138	306277	10353	80	NEW_VARIANT
P-0041269-T01-IM6	RECQL4 (NM_004260) - LRRC24 (NM_001024678) rearrangement: c.1620+1:RECQL4_c.608-173:LRRC24dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {RECQL4:LRRC24}		15530	0	100	8	Exon 9 of RECQL4(-)	RECQL4	145740319			8	Intron of LRRC24(-):173bp before exon 5	LRRC24	145748966			10	DUPLICATION		8647	306276	44515	112	NEW_VARIANT
P-0041387-T01-IM6	MYEF2 (NM_016132) - CALR (NM_004343) rearrangement: t(15;19)(q21.1;p13.2)(chr15:g.48457161::chr19:g.13054420)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {MYEF2:CALR}		0	0	17	19	Exon 8 of CALR(+)	MYEF2	13054420			15	Intron of MYEF2(-):968bp after exon 5	CALR	48457161			10	TRANSLOCATION		0	306529	0	26	NEW_VARIANT
P-0041459-T01-IM6	BLM (NM_000057) rearrangement: c.231:BLM_chr15:g.83638536del	PRECISE	Note: The BLM rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	-		46599	0	12	15	IGR: 16Kb before FAM103A1(+)	BLM	83638536			15	Exon 3 of BLM(+)	BLM	91292729			10	DELETION		7654193	306766	45920	12	NEW_VARIANT
P-0041484-T01-IM6	NTRK1 (NM_002529) rearrangement: c.1109:NTRK1_chr1:g.156627355inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		38885	0	116	1	Intron of BCAN(+):111bp before exon 11	NTRK1	156627355			1	Exon 8 of NTRK1(+)	NTRK1	156843683			10	INVERSION		216328	306816	70442	134	NEW_VARIANT
P-0041535-T01-IM6	PAK1 (NM_002576) rearrangement: c.191-650_c.439+11dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Duplication of 2 exons : in frame		2432	0	36	11	Intron of PAK1(-):10bp after exon 4	PAK1	77090275			11	Intron of PAK1(-):650bp before exon 3	PAK1	77091689			10	DUPLICATION		1414	306947	2952	37	NEW_VARIANT
P-0041624-T01-IM6	GLG1 (NM_012201) - CDH1 (NM_004360) rearrangement: c.438+30436:GLG1_c.2026:CDH1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {GLG1:CDH1}		92718	1	82	16	Exon 13 of CDH1(+)	GLG1	68857391			16	Intron of GLG1(-):30Kb after exon 1	CDH1	74610119			10	INVERSION		5752728	307107	119488	116	NEW_VARIANT
P-0041624-T01-IM6	MDC1 (NM_014641) - PPP1R10 (NM_002714) rearrangement: c.4358:MDC1_c.854-290:PPP1R10del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {MDC1:PPP1R10}		18557	0	45	6	Intron of PPP1R10(-):290bp before exon 11	MDC1	30573161			6	Exon 10 of MDC1(-)	PPP1R10	30672602			10	DELETION		99441	307105	21919	104	NEW_VARIANT
P-0041852-T02-IM6	RAD51D (NM_133629) - SPAG9 (NM_001130528) rearrangement: c.82+31:RAD51D_c.3700+200:SPAG9dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {RAD51D:SPAG9}		341549	0	25	17	Intron of RAD51D(-):30bp after exon 1	RAD51D	33446520			17	Intron of SPAG9(-):199bp after exon 27	SPAG9	49051932			0	DUPLICATION		15605412	307751	582519	25	NEW_VARIANT
P-0041875-T01-IM6	CEBPA (NM_004364) rearrangement: c.274:CEBPA_chr19:g.33469519inv	PRECISE	Note: The CEBPA rearrangement is an inversion of exon 1. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		7185	0	30	19	3-UTR of RHPN2(-):1Kb after coding stop	CEBPA	33469519			19	Exon 1 of CEBPA(-)	CEBPA	33793047			10	INVERSION		323528	307579	11130	37	NEW_VARIANT
P-0042048-T01-IM6	ASXL2 (NM_018263) rearrangement: c.404-6653_c.3872inv	PRECISE	Note: The ASXL2 rearrangement is an intragenic inversion of exons 5 - 12. One of the breakpoints is within exon 12. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		26378	0	14	2	Exon 12 of ASXL2(-)	ASXL2	25965334			2	Intron of ASXL2(-):7Kb before exon 5	ASXL2	26001062			10	INVERSION		35728	308132	25571	13	NEW_VARIANT
P-0042048-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) rearrangement: c.56-3652:TMPRSS2_c.39+59577:ERGdel	PRECISE	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).	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		72171	0	28	21	Intron of ERG(-):60Kb after exon 3	TMPRSS2	39888009			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873768			10	DELETION		2985759	308131	56462	34	NEW_VARIANT
P-0042241-T01-IM6	FGFR2 (NM_000141) - ZMYM4 (NM_005095) fusion: t(1;10)(p34.3;q26.13)(chr1:g.35833702::chr10:g.123242889)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {FGFR2:ZMYM4}		0	0	128	10	Intron of FGFR2(-):322bp after exon 17	FGFR2	123242889			1	Intron of ZMYM4(+):2Kb before exon 6	ZMYM4	35833702			10	TRANSLOCATION		0	309136	0	167	NEW_VARIANT
P-0042407-T01-IM6	ARID5B (NM_032199) rearrangement: c.276+19:ARID5B_chr10:g.63644443dup	PRECISE	Note: The ARID5B rearrangement is a duplication of exons 1 - 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		2475	0	33	10	IGR: 17Kb before ARID5B(+)	ARID5B	63644443			10	Intron of ARID5B(+):19bp after exon 2	ARID5B	63662191			10	DUPLICATION		17748	309798	2947	36	NEW_VARIANT
P-0042407-T01-IM6	ANKRD11 (NM_013275) rearrangement: c.5442_c.7714-136dup	PRECISE	Note: The ANKRD11 rearrangement is an intragenic duplication of exons 9 - 11. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		15274	0	40	16	Intron of ANKRD11(-):136bp before exon 12	ANKRD11	89337453			16	Exon 9 of ANKRD11(-)	ANKRD11	89347508			10	DUPLICATION		10055	309799	15873	43	NEW_VARIANT
P-0042407-T01-IM6	RICTOR (NM_152756) rearrangement: t(5;X)(p13.1;q26.1)(chr5:g.38943061::chrX:g.129248290)	PRECISE	Note: The RICTOR rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	20	X	IGR: 15Kb before AIFM1(-)	RICTOR	129248290			5	Exon 37 of RICTOR(-)	RICTOR	38943061			10	TRANSLOCATION		0	309800	0	19	NEW_VARIANT
P-0042620-T01-IM6	WIPI2 (NM_016003) - CALR (NM_004343) rearrangement: t(7;19)(p22.1;p13.2)(chr7:g.5268169::chr19:g.13049530)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {WIPI2:CALR}		0	0	11	19	Exon 1 of CALR(+)	WIPI2	13049530			7	Intron of WIPI2(+):327bp after exon 11	CALR	5268169			10	TRANSLOCATION		0	310908	0	11	NEW_VARIANT
P-0042664-T01-IM6	MAP3K13 (NM_004721) rearrangement: c.1291_c.1643+1219del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		2953	0	4	3	Exon 8 of MAP3K13(+)	MAP3K13	185181350			3	Intron of MAP3K13(+):1Kb after exon 10	MAP3K13	185185970			7	DELETION		4620	311045	2505	4	NEW_VARIANT
P-0042755-T01-IM6	ERBB3 (NM_001982) rearrangement: t(8;12)(q12.1;q13.2)(chr8:g.56386721::chr12:g.56494888)	PRECISE	Note: The ERBB3 rearrangement is a translocation with a breakpoint in exon 27. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	24	12	Exon 27 of ERBB3(+)	ERBB3	56494888			8	Intron of XKR4(+):49Kb before exon 3	ERBB3	56386721			10	TRANSLOCATION		0	311323	0	24	NEW_VARIANT
P-0043000-T02-IM6	MED12 (NM_005120) rearrangement: t(13;X)(q14.3;q13.1)(chr13:g.53230412::chrX:g.70356437)	PRECISE	Note: The MED12 rearrangement is a translocation with a breakpoint in exon 37. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	8	X	Exon 37 of MED12(+)	MED12	70356437			13	Intron of SUGT1(+):1Kb before exon 3	MED12	53230412			10	TRANSLOCATION		0	319326	0	11	NEW_VARIANT
P-0043007-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.2544+168:KIF5B_c.2136+629:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		53567	0	37	10	Intron of KIF5B(-):167bp after exon 23	KIF5B	32306812			10	Intron of RET(+):629bp after exon 11	RET	43610813			10	INVERSION		11304001	313022	57422	46	NEW_VARIANT
P-0043153-T01-IM6	STK11 (NM_000455) rearrangement: c.291-18:STK11_chr19:g.1202211del	PRECISE	Note: The STK11 rearrangement is a deletion of exon 1. The rearrangement includes a part of the kinase domain of STK11.	MANUAL_OK	3to5	3to5	-		4429	0	57	19	IGR: 4Kb before STK11(+)	STK11	1202211			19	Intron of STK11(+):17bp before exon 2	STK11	1218398			10	DELETION		16187	313410	3039	60	NEW_VARIANT
P-0043250-T01-IM6	STK19 (NM_004197) rearrangement: c.901+5:STK19_chr6:g.31981147del	PRECISE	Note: The STK19 rearrangement is a deletion of exons 7 - 8. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		1029	68	38	6	Intron of STK19(+):5bp after exon 6	STK19	31948330			6	Promoter of STK19(+):370bp from tx start	STK19	31981147			10	DELETION		32817	313598	847	80	NEW_VARIANT
P-0043277-T01-IM6	PAK1 (NM_002576) rearrangement: c.885+1210_c.1018del	PRECISE	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.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1920	0	3	11	Exon 11 of PAK1(-)	PAK1	77051789			11	Intron of PAK1(-):1Kb after exon 9	PAK1	77059074			8	DELETION		7285	313716	3275	3	NEW_VARIANT
P-0043277-T01-IM6	KEAP1 (NM_203500) rearrangement: c.1:KEAP1_chr19:g.10618964del	PRECISE	Note: The KEAP1 rearrangement is a deletion of exons 1 - 2. One of the breakpoints is within exon 2.	MANUAL_OK	3to5	3to5	-		561	0	22	19	Exon 2 of KEAP1(-)	KEAP1	10610709			19	IGR: 4Kb before S1PR5(-)	KEAP1	10618964			10	DELETION		8255	313717	414	26	NEW_VARIANT
P-0043277-T01-IM6	POLD1 (NM_002691) rearrangement: c.84:POLD1_chr19:g.50186003inv	PRECISE	Note: The POLD1 rearrangement is an inversion of exons 1 - 2. One of the breakpoints is within exon 2. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		1365	0	49	19	Intron of PRMT1(+):487bp after exon 4	POLD1	50186003			19	Exon 2 of POLD1(+)	POLD1	50902192			10	INVERSION		716189	313718	1895	49	NEW_VARIANT
P-0043314-T02-IM6	SUFU (NM_016169) rearrangement: c.455-917_c.684-60del	PRECISE	Note: The SUFU rearrangement is an intragenic deletion of exons 4 - 5.	MANUAL_OK	3to5	3to5	Deletion of 2 exons : out of frame		3910	0	3	10	Intron of SUFU(+):916bp before exon 4	SUFU	104351422			10	Intron of SUFU(+):59bp before exon 6	SUFU	104353690			7	DELETION		2268	320701	3209	3	NEW_VARIANT
P-0043314-T02-IM6	EGFR (NM_005228) rearrangement: c.88+53282_c.890-398del	PRECISE	Note: The EGFR rearrangement is a vIII alteration.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		15639	0	10	7	Intron of EGFR(+):53Kb after exon 1	EGFR	55140340			7	Intron of EGFR(+):397bp before exon 8	EGFR	55223125			10	DELETION		82785	320699	27432	10	NEW_VARIANT
P-0043374-T01-IM6	ESR1 (NM_001122740) rearrangement: c.1236-8227_c.1298inv	PRECISE	Note: The ESR1 rearrangement is an intragenic inversion of exon 7. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		374	0	55	6	Intron of ESR1(+):8Kb before exon 7	ESR1	152373899			6	Exon 7 of ESR1(+)	ESR1	152382188			10	INVERSION		8289	313956	287	62	NEW_VARIANT
P-0043502-T02-IM6	MED12 (NM_005120) rearrangement: c.3524:MED12_chrX:g.68183411inv	IMPPRECISE	Note: The MED12 rearrangement is an inversion of exons 1 - 25. One of the breakpoints is within exon 25. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		36158	0	6	X	IGR: 135Kb before EFNB1(+)	MED12	68183411			X	Exon 25 of MED12(+)	MED12	70349012			0	INVERSION		2165601	316980	40501	7	NEW_VARIANT
P-0043699-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-1064:TMPRSS2_c.18+19751:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 and ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		38245	0	21	21	Intron of ERG(-):20Kb after exon 1	TMPRSS2	39850536			21	Intron of TMPRSS2(-):1Kb before exon 2	ERG	42871180			10	DELETION		3020644	315345	22428	22	NEW_VARIANT
P-0043699-T01-IM6	MITF (NM_198159) rearrangement: c.1161+99:MITF_chr3:g.188085953inv	PRECISE	Note: The MITF rearrangement is an inversion of exon 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		320430	0	4	3	Intron of MITF(+):99bp after exon 9	MITF	70008670			3	5-UTR of LPP(+):38Kb before coding start	MITF	188085953			10	INVERSION		118077283	315347	223353	4	NEW_VARIANT
P-0043854-T01-IM6	KIF5B (NM_004521) - MET (NM_000245) fusion: t(7;10)(q31.2;p11.22)(chr7:g.116412098::chr10:g.32304904)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:MET}		0	0	13	10	Intron of KIF5B(-):317bp before exon 25	KIF5B	32304904			7	Intron of MET(+):55bp after exon 14	MET	116412098			10	TRANSLOCATION		0	316471	0	13	NEW_VARIANT
P-0043869-T02-IM6	EP300 (NM_001429) rearrangement: c.3728+63_c.3806+571del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exon 22.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		908	0	9	22	Intron of EP300(+):63bp after exon 21	EP300	41558846			22	Intron of EP300(+):571bp after exon 22	EP300	41560705			10	DELETION		1859	316489	505	34	NEW_VARIANT
P-0044108-T02-IM6	STK11 (NM_000455) rearrangement: c.451:STK11_chr19:g.1142410del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		5108	0	3	19	Intron of SBNO2(-):5Kb after exon 4	STK11	1142410			19	Exon 3 of STK11(+)	STK11	1219399			10	DELETION		76989	319106	2432	4	NEW_VARIANT
P-0044140-T01-IM6	TERT (NM_198253) rearrangement: t(3;5)(q22.2;p15.33)(chr3:g.3:134091986::chr5:g.1295406)	IMPPRECISE	Note: The TERT rearrangement is a translocation with a breakpoint in the promoter region. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	31	5	Promoter of TERT(-):42Kb from tx start	TERT	1295406			3	Intron of AMOTL2(-):2Kb before exon 2	TERT	134091986			0	TRANSLOCATION		0	317475	0	31	NEW_VARIANT
P-0044207-T01-IM6	FGFR4 (NM_213647) rearrangement: c.2399:FGFR4_chr5:g.51357750inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		322935	0	9	5	IGR: 679Kb before ISL1(+)	FGFR4	51357750			5	Exon 18 of FGFR4(+)	FGFR4	176524667			10	INVERSION		125166917	318311	481435	9	NEW_VARIANT
P-0044328-T01-IM6	KLF4 (NM_004235) rearrangement: c.1199:KLF4_chr9:g.108890966inv	PRECISE	Note: The KLF4 rearrangement is an inversion of exons 4 - 5. One of the breakpoints is within exon 4. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4451	0	6	9	IGR: 434Kb before TMEM38B(+)	KLF4	108890966			9	Exon 4 of KLF4(-)	KLF4	110249374			10	INVERSION		1358408	318820	6883	6	NEW_VARIANT
P-0044518-T01-IM6	COL15A1 (NM_001855) - TGFBR1 (NM_004612) rearrangement: c.804+1113:COL15A1_c.596:TGFBR1del	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {COL15A1:TGFBR1}		2906	0	27	9	Intron of COL15A1(+):1Kb after exon 5	COL15A1	101752653			9	Exon 4 of TGFBR1(+)	TGFBR1	101900162			10	DELETION		147509	319335	1015	27	NEW_VARIANT
P-0044885-T01-IM6	TERT(NM_198253) rearrangement: t(5;12)(p15.33;q14.1)(chr5:g.1295424::chr12:g.58874633)	PRECISE	Note: The TERT rearrangement is a translocation with breakpoint within promoter region of TERT. The functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	11	12	IGR: 85Kb before LOC101927653(-)	TERT	58874633			5	Promoter of TERT(-):42Kb from tx start	TERT	1295424			10	TRANSLOCATION		0	320858	0	11	NEW_VARIANT
P-0045005-T01-IM6	PTPRT (NM_133170) rearrangement: t(6;20)(p23;q12)(chr6:g.14960811::chr20:g.40727119)	PRECISE	Note: The PTPRT rearrangement is a translocation with a breakpoint in exon 28. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	16	20	Exon 28 of PTPRT(-)	PTPRT	40727119			6	IGR: 285Kb before JARID2(+)	PTPRT	14960811			10	TRANSLOCATION		0	321136	0	16	NEW_VARIANT
P-0046454-T01-IM6	BABAM1 (NM_001033549) rearrangement: c.545-696_c.698inv	PRECISE	Note: The BABAM1 rearrangement is an intragenic inversion of exons 6 - 7. One of the breakpoints is within exon 7. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		3315	0	22	19	Intron of BABAM1(+):695bp before exon 6	BABAM1	17385914			19	Exon 7 of BABAM1(+)	BABAM1	17387432			10	INVERSION		1518	325703	4529	23	NEW_VARIANT
P-0006713-T01-IM5	ERRFI1 (NM_018948) rearrangement: t(1;17)(p36.23;p13.1)(chr1:g.8085068::chr17:g.7619057)	PRECISE	The ERRFI1 (NM_018948) rearrangement is a translocation which results in a truncated ERRFI1. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	94	17	IGR: 4Kb before DNAH2(+)	ERRFI1	7619057			1	5-UTR of ERRFI1(-): 9Kb before coding start	ERRFI1	8085068			32	TRANSLOCATION		0	108469	0	90	NEW_VARIANT
P-0007966-T02-IM6	MAP2K1 (NM_002755) rearrangement : c.80+29:MAP2K1_chr15:g.67250578del	PRECISE	Note: The MAP2K1 rearrangement is a deletion of exons 2-11. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		18753	0	27	15	Intron of MAP2K1(+):29bp after exon 1	MAP2K1	66679794			15	IGR: 108Kb before SMAD3(+)	MAP2K1	67250579			10	DELETION		570785	280350	20819	27	NEW_VARIANT
P-0013299-T02-IM6	EML4 (NM_019063) -ALK (NM_004304) Fusion(EML4 exon5 fused with ALK exon20) : c.667+1302:EML4_c.3173-644:ALKinv	PRECISE	Note: The EML4-ALK Fusion is predicted to be in -frame and includes the protein kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		72500	0	94	2	Intron of ALK(-):644bp before exon 20	EML4	29447038			2	Intron of EML4(+):1Kb after exon 5	ALK	42493173			10	INVERSION		13046135	281372	99609	93	NEW_VARIANT
P-0013299-T02-IM6	TSC1 (NM_000368) - COL5A1 (NM_000093) rearrangement: c.17:TSC1_c.2899-203:COL5A1del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		15812	0	72	9	Exon 3 of TSC1(-)	TSC1	135804243			9	Intron of COL5A1(+):201bp before exon 37	COL5A1	137690052			10	DELETION		1885809	281370	27702	75	NEW_VARIANT
P-0021785-T01-IM6	ERBB3 (NM_001982) - ZCRB1 (NM_033114) Rearrangement : c.3201+46:ERBB3_c.333+785:ZCRB1inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {ERBB3:ZCRB1}		349517	0	11	12	Intron of ZCRB1(-):784bp after exon 5	ERBB3	42710357			12	Intron of ERBB3(+):46bp after exon 26	ZCRB1	56494075			10	INVERSION		13783718	188235	243037	11	NEW_VARIANT
P-0021788-T01-IM6	VPS26A (NM_004896) - FGFR2 (NM_000141) Rearrangement : c.4-1035:VPS26A_c.2301+986:FGFR2inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {VPS26A:FGFR2}		168576	0	88	10	Intron of VPS26A(+):1Kb before exon 2	VPS26A	70891619			10	Intron of FGFR2(-):985bp after exon 17	FGFR2	123242226			10	INVERSION		52350607	188231	228966	88	NEW_VARIANT
P-0022184-T01-IM6	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	PRECISE	Note: The EML4 - ALK fusion is predicted to be in frame and includes the kinase domain of ALK.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		115766	0	51	2	Intron of ALK(-):641bp before exon 20	EML4	29447035			2	Intron of EML4(+):1Kb after exon 12	ALK	42524042			10	INVERSION		13077007	189876	134288	49	NEW_VARIANT
P-0022184-T01-IM6	APC (NM_000038) rearrangement: c.2529_c.6192del	IMPPRECISE	Note: The APC rearrangement is an intragenic deletion of exon 16. Both breakpoints are within exon. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		15693	0	6	5	Exon 16 of APC(+)	APC	112173820			5	Exon 16 of APC(+)	APC	112177483			0	DELETION		3663	189874	11886	6	NEW_VARIANT
P-0024572-T01-IM6	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)	PRECISE	Note: The CD74 - ROS1 fusion includes the kinase domain of ROS1	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CD74:ROS1}		0	0	142	6	Intron of ROS1(-):733bp after exon 32	CD74	117649758			5	Intron of CD74(-):659bp after exon 6	ROS1	149783583			10	TRANSLOCATION		0	200840	0	149	NEW_VARIANT
P-0025917-T02-IM6	STK11 (NM_000455) rearrangement: c.862+268_c.921-34del	PRECISE	Note: The STK11 rearrangement is an intragenic deletion of exon 7. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		828	0	25	19	Intron of STK11(+):268bp after exon 6	STK11	1221607			19	Intron of STK11(+):33bp before exon 8	STK11	1222950			10	DELETION		1343	210198	573	25	NEW_VARIANT
P-0026906-T02-IM6	EGFL7 (NM_201446) rearrangement: c.636+258_c.*49inv	PRECISE	Note: The EGFL7 rearrangement results in the inversion of exons 7-9. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		3305	0	2	9	Intron of EGFL7(+):258bp after exon 7	EGFL7	139565724			9	3-UTR of EGFL7(+):4Kb after coding stop	EGFL7	139566787			10	INVERSION		1063	215022	5815	1	NEW_VARIANT
P-0029514-T01-IM6	RIT1 (NM_006912) - GON4L (NM_001037533) rearrangement: c.376:RIT1_c.4726+352:GON4Ldel	IMPPRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {RIT1:GON4L}		1298	0	46	1	Intron of GON4L(-):351bp after exon 22	RIT1	155732751			1	Exon 5 of RIT1(-)	GON4L	155874155			0	DELETION		141404	222805	2012	73	NEW_VARIANT
P-0031449-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_004449) Fusion (fTMPRSS2 exon 1 with ERG exons 4-10): c.55+3413:TMPRSS2_c.c.40-62452:ERGdel	PRECISE	Note: The TMPRSS2 is fused with the non-canonical ERG (NM_00444) transcript.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		66602	0	6	21	Intron of ERG(-):62Kb before exon 4	TMPRSS2	39879996			21	Intron of TMPRSS2(-):3Kb after exon 1	ERG	42876464			10	DELETION		2996468	229674	89612	6	NEW_VARIANT
P-0036932-T01-IM6	CDKN1B (NM_004064) rearrangement: c.475+58:CDKN1B_chr12:g.14676500del	PRECISE	Note: The CDKN1B rearrangement is a deletion of exon 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	Antisense Fusion		3587	0	6	12	Intron of CDKN1B(+):58bp after exon 1	CDKN1B	12871306			12	Intron of PLBD1(-):12Kb before exon 7	CDKN1B	14676500			10	DELETION		1805194	276721	3297	10	NEW_VARIANT
P-0037229-T01-IM6	FOXP1 (NM_001244814) rearrangement: c.1652+397:FOXP1_chr3:g.71306509del	PRECISE	Note: The FOXP1 rearrangement is a deletion of exons 1-14. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript		23497	0	26	3	Intron of FOXP1(-):396bp after exon 14	FOXP1	71021309			3	5-UTR of FOXP1(-):298Kb before coding start	FOXP1	71306509			10	DELETION		285200	277143	19046	28	NEW_VARIANT
P-0037230-T01-IM6	RB1 (NM_000321) rearrangement: c.1498+78_c.1695+10859del	PRECISE	Note: The RB1 rearrangement is an intragenic deletion of exon 17. Its functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1782	0	37	13	Intron of RB1(+):78bp after exon 16	RB1	48954455			13	Intron of RB1(+):11Kb after exon 17	RB1	48966438			10	DELETION		11983	277141	66	46	NEW_VARIANT
P-0037297-T01-IM6	CHEK2 (NM_007194) rearrangement: c.1264_chr22:g.29592609del	PRECISE	Note: The CHEK2 rearrangement is a deletion that includes CHEK2 exons 1-12. One of the breakpoints is within exon 12.	MANUAL_OK	3to5	3to5	-		21008	0	47	22	Exon 12 of CHEK2(-)	CHEK2	29091226			22	IGR: 9Kb before EMID1(+)	CHEK2	29592609			10	DELETION		501383	277439	11763	77	NEW_VARIANT
P-0037322-T01-IM6	DDR2 (NM_006182) rearrangement: t(1;2)(q23.3;q37.3)(chr1:g.162740087::chr2:g.240384262)	PRECISE	Note: The DDR2 rearrangement is a translocation with a breakpoint within DDR2 intron 11. The functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	20	2	IGR: 111Kb before MIR2467(-)	DDR2	240384262			1	Intron of DDR2(+):4bp before exon 12	DDR2	162740087			10	TRANSLOCATION		0	277594	0	22	NEW_VARIANT
P-0037338-T01-IM6	DEPDC7 (NM_001077242) - SMARCB1 (NM_003073) rearrangement: t(11;22)(p13;q11.23)(chr11:g.33040227::chr22:g.24133958)	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {DEPDC7:SMARCB1}		0	0	13	22	Exon 2 of SMARCB1(+)	DEPDC7	24133958			11	Intron of DEPDC7(+):2Kb after exon 1	SMARCB1	33040227			0	TRANSLOCATION		0	277710	0	13	NEW_VARIANT
P-0037338-T01-IM6	YES1 (NM_005433) - ADRBK2 (NM_005160) rearrangement: t(18;22)(p11.32;q12.1)(chr18:g.742917::chr22:g.26044366)	IMPPRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {YES1:ADRBK2}		0	0	24	22	Intron of ADRBK2(+):4Kb after exon 3	YES1	26044366			18	Exon 8 of YES1(-)	ADRBK2	742917			0	TRANSLOCATION		0	277717	0	42	NEW_VARIANT
P-0037556-T02-IM6	ANKRD11 (NM_013275) rearrangement: c.226+62:ANKRD11_chr16:g.64001177inv	PRECISE	Note: The ANKRD11 rearrangement is an inversion of exons 5-13. Its functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		301650	0	77	16	IGR: 980Kb before CDH11(-)	ANKRD11	64001177			16	Intron of ANKRD11(-):61bp after exon 4	ANKRD11	89371552			10	INVERSION		25370375	280355	215504	84	NEW_VARIANT
P-0037639-T01-IM6	UPF1 (NM_002911) - ZC3H7B (NM_017590) rearrangement: t(19,22)(p13.11;q13.2)(chr19:g.18976550::chr22:g.41744573)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {UPF1:ZC3H7B}		0	0	41	22	Intron of ZC3H7B(+):402bp after exon 15	UPF1	41744573			19	Exon 22 of UPF1(+)	ZC3H7B	18976550			10	TRANSLOCATION		0	281467	0	43	NEW_VARIANT
P-0037674-T01-IM6	SPEN (NM_015001) rearrangement: c.6550:SPEN_chr1:g.5804200inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		129343	0	13	1	IGR: 119Kb before MIR4689(-)	SPEN	5804200			1	Exon 11 of SPEN(+)	SPEN	16259285			10	INVERSION		10455085	281149	210318	13	NEW_VARIANT
P-0037728-T01-IM6	PAK1 (NM_002576) rearrangement: c.1413+172:PAK1_chr11:g.97205904del	PRECISE	Note: The PAK1  rearrangement results in the deletion of exons 1-13. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		69012	0	5	11	Intron of PAK1(-):171bp after exon 13	PAK1	77046959			11	IGR: 285Kb before MIR7976(-)	PAK1	97205904			9	DELETION		20158945	281695	86765	5	NEW_VARIANT
P-0037728-T01-IM6	BIRC3 (NM_182962) rearrangement: t(11;12)(q22.2;q21.1)(chr11:g.102195780::chr12:g.74859022)	PRECISE	Note: The BIRC3 rearrangement is a translocation with a breakpoint in exon 3. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	313	12	IGR: 73Kb before ATXN7L3B(+)	BIRC3	74859022			11	Exon 3 of BIRC3(+)	BIRC3	102195780			10	TRANSLOCATION		0	281696	0	291	NEW_VARIANT
P-0037728-T01-IM6	NAB2 (NM_005967) rearrangement: t(12;X)(q13.3;p22.11)(chr12:g.57486173::chrX:g.23509870)	PRECISE	Note: The NAB2 rearrangement is a translocation with a breakpoint in intron 2. The functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		0	0	45	X	IGR: 157Kb before PTCHD1(+)	NAB2	23509870			12	Intron of NAB2(+):57bp before exon 3	NAB2	57486173			10	TRANSLOCATION		0	281697	0	46	NEW_VARIANT
P-0037728-T01-IM6	TBX3 (NM_016569) rearrangement: t(12;Y)(q24.21;q11.223)(chr12:g.115109879::chrY:g.22716517)	PRECISE	Note: The TBX3 rearrangement is a translocation with a breakpoint in exon 8. The functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	10	Y	IGR: 21Kb before EIF1AY(+)	TBX3	22716517			12	Exon 8 of TBX3(-)	TBX3	115109879			10	TRANSLOCATION		0	281698	0	9	NEW_VARIANT
P-0037901-T01-IM6	EPS15 (NM_001981) - NTRK1 (NM_002529) rearrangement: c.2119+1240:EPS15_c.1195+20:NTRK1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {EPS15:NTRK1}		234520	0	157	1	Intron of EPS15(-):1Kb after exon 21	EPS15	51858813			1	Intron of NTRK1(+):20bp after exon 9	NTRK1	156844212			10	INVERSION		104985399	282683	332731	184	NEW_VARIANT
P-0038398-T03-IM6	PIK3CA (NM_006218) - NAALADL2 (NM_207015) rearrangement: c.3190:PIK3CA_c.43+3905:NAALADL2dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PIK3CA:NAALADL2}		26376	0	7	3	Intron of NAALADL2(+):4Kb after exon 1	PIK3CA	174581145			3	Exon 21 of PIK3CA(+)	NAALADL2	178952135			10	DUPLICATION		4370990	311776	52154	8	NEW_VARIANT
P-0038961-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-293:KIF5B_c.2136+591:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		60438	0	55	10	Intron of KIF5B(-):293bp before exon 16	KIF5B	32312257			10	Intron of RET(+):591bp after exon 11	RET	43610775			10	INVERSION		11298518	292815	95835	67	NEW_VARIANT
P-0039650-T01-IM6	STK11 (NM_000455) rearrangement: c.920+90_c.1108+1006del	IMPPRECISE	Note: The STK11 rearrangement is an intragenic deletion of exon 8. The rearrangement includes a part of the kinase domain of STK11.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		2871	0	13	19	Intron of STK11(+):90bp after exon 7	STK11	1222095			19	Intron of STK11(+):1Kb after exon 8	STK11	1224177			0	DELETION		2082	297357	1975	13	NEW_VARIANT
P-0039992-T01-IM6	TSC1 (NM_000368) rearrangement: c.2892:TSC1_chr9:g.135804870dup	PRECISE	Note: The TSC1 rearrangement is a duplication of exons 1 - 22. One of the breakpoints is within exon 22. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication within transcript : mid-exon		29347	0	24	9	Exon 22 of TSC1(-)	TSC1	135772654			9	5-UTR of TSC1(-):33Kb before coding start	TSC1	135804870			10	DUPLICATION		32216	306256	39151	25	NEW_VARIANT
P-0040261-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-1340:EML4_c.3173-709:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		86570	0	102	2	Intron of ALK(-):709bp before exon 20	EML4	29447103			2	Intron of EML4(+):1Kb before exon 13	ALK	42527041			10	INVERSION		13079938	300860	158842	108	NEW_VARIANT
P-0040309-T01-IM6	ALK (NM_004304) rearrangement: c.3172+946:ALK_chr2:g.34064604inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Transcript Fusion {LINC01317:ALK}		55333	0	55	2	Intron of ALK(-):945bp after exon 19	ALK	29447381			2	5-UTR of LINC01317(+):458Kb before coding start	ALK	34064604			10	INVERSION		4617223	301266	62048	54	NEW_VARIANT
P-0040382-T01-IM6	RICTOR (NM_152756) rearrangement: c.1400+110:RICTOR_chr5:g.45655385inv	PRECISE	Note: The RICTOR rearrangement is an inversion of exons 1 - 16. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		16277	0	12	5	Intron of RICTOR(-):109bp after exon 16	RICTOR	38964784			5	Intron of HCN1(-):10Kb before exon 2	RICTOR	45655385			10	INVERSION		6690601	301863	35952	12	NEW_VARIANT
P-0040570-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.668-2504:EML4_c.3172+167:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		105000	0	4	2	Intron of ALK(-):166bp after exon 19	EML4	29448160			2	Intron of EML4(+):3Kb before exon 6	ALK	42505486			9	INVERSION		13057326	302363	117079	4	NEW_VARIANT
P-0040596-T01-IM6	AXIN2 (NM_004655) rearrangement: c.1495:AXIN2_chr17:g.63504771del	PRECISE	Note: The AXIN2 rearrangement is a deletion of exons 6 - 11. One of the breakpoints is within exon 6.	MANUAL_OK	3to5	3to5	-		15921	0	12	17	IGR: 20Kb before AXIN2(-)	AXIN2	63504771			17	Exon 6 of AXIN2(-)	AXIN2	63533659			10	DELETION		28888	302531	16315	13	NEW_VARIANT
P-0040600-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.667+1795:EML4_c.3172+639:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		93801	0	58	2	Intron of ALK(-):638bp after exon 19	EML4	29447688			2	Intron of EML4(+):2Kb after exon 5	ALK	42493666			10	INVERSION		13045978	302641	73952	58	NEW_VARIANT
P-0041037-T01-IM6	CDH3 (NM_001793) - CDH1 (NM_004360) rearrangement: c.161-14482:CDH3_c.2440-54:CDH1del	PRECISE	Note: The CDH3 - CDH1 rearrangement is a deletion that results in a fusion of CDH3 exons 1 - 2 to CDH1 exon 16.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {CDH3:CDH1}		29770	0	5	16	Intron of CDH3(+):14Kb before exon 3	CDH3	68695806			16	Intron of CDH1(+):53bp before exon 16	CDH1	68867139			8	DELETION		171333	305423	22516	5	NEW_VARIANT
P-0041037-T01-IM6	ROS1 (NM_002944) rearrangement: c.5080-420:ROS1_chr6:g.119045740del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		66656	0	7	6	Intron of ROS1(-):420bp before exon 31	ROS1	117658923			6	IGR: 58Kb before LOC100287632(+)	ROS1	119045740			10	DELETION		1386817	305422	61176	7	NEW_VARIANT
P-0041247-T01-IM6	MYOM1 (NM_003803) - CRLF2 (NM_022148) rearrangement: t(18;X)(p11.31;p22.33)(chr18:g.3191087::chrX:g.1315073)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {MYOM1:CRLF2}		0	0	32	X	Intron of CRLF2(-):59bp before exon 6	MYOM1	1315073			18	Intron of MYOM1(-):2Kb before exon 4	CRLF2	3191087			10	TRANSLOCATION		0	306269	0	35	NEW_VARIANT
P-0041247-T01-IM6	ATRX (NM_000489) rearrangement: c.2160_c.3736+115inv	PRECISE	Note: The ATRX rearrangement is an intragenic inversion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Antisense Fusion		7175	0	8	X	Intron of ATRX(-):114bp after exon 9	ATRX	76936897			X	Exon 9 of ATRX(-)	ATRX	76938588			10	INVERSION		1691	306267	5706	9	NEW_VARIANT
P-0041422-T01-IM6	ETV6 (NM_001987) rearrangement: t(12;14)(p13.2;q32.33)(chr12:g.12030747::chr14:g.106257006)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	10	14	IGR: 121Kb before ELK2AP(-)	ETV6	106257006			12	Intron of ETV6(+):7Kb before exon 6	ETV6	12030747			10	TRANSLOCATION		0	306546	0	10	NEW_VARIANT
P-0041513-T01-IM6	KMT2D (NM_003482) - IRAK3 (NM_007199) rearrangement: c.6888:KMT2D_c.316+2751:IRAK3inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {KMT2D:IRAK3}		372896	0	262	12	Exon 31 of KMT2D(-)	KMT2D	49434665			12	Intron of IRAK3(+):3Kb after exon 2	IRAK3	66600424			10	INVERSION		17165759	306899	368421	388	NEW_VARIANT
P-0041513-T01-IM6	ABCC4 (NM_005845) - MDM2 (NM_002392) rearrangement: t(12;13)(q15;q32.1)(chr12:g.69229720::chr13:g.95779735)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {ABCC4:MDM2}		0	0	15	13	Intron of ABCC4(-):11Kb before exon 19	ABCC4	95779735			12	Exon 9 of MDM2(+)	MDM2	69229720			10	TRANSLOCATION		0	306900	0	30	NEW_VARIANT
P-0041623-T01-IM6	TSC2 (NM_000548) rearrangement: t(4;16)(q23;p13.3)(chr4:g.99223910::chr16:g.2126001)	PRECISE	Note: The TSC2 rearrangement is a translocation with a breakpoint in intron 23. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	Antisense Fusion		0	0	11	16	Intron of TSC2(+):67bp before exon 24	TSC2	2126001			4	Intron of RAP1GDS1(+):9Kb after exon 2	TSC2	99223910			10	TRANSLOCATION		0	307115	0	11	NEW_VARIANT
P-0041623-T01-IM6	PIK3CG (NM_002649) rearrangement: t(7;20)(q22.3;p11.23)(chr7:g.106508538::chr20:g.19014680)	PRECISE	Note: The PIK3CG rearrangement is a translocation with a breakpoint in exon 2. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	-		0	0	5	20	IGR: 179Kb before SLC24A3(+)	PIK3CG	19014680			7	Exon 2 of PIK3CG(+)	PIK3CG	106508538			10	TRANSLOCATION		0	307116	0	6	NEW_VARIANT
P-0041640-T01-IM6	EGFR (NM_005228) rearrangement: c.89-41093_c.889+652del	PRECISE	Note: The EGFR rearrangement is a vIII alteration.	MANUAL_OK	3to5	3to5	Deletion of 6 exons : in frame		14181	0	11	7	Intron of EGFR(+):41Kb before exon 2	EGFR	55168886			7	Intron of EGFR(+):652bp after exon 7	EGFR	55222497			10	DELETION		53611	307198	20439	12	NEW_VARIANT
P-0042121-T01-IM6	SMYD3 (NM_001167740) rearrangement: c.164+19:SMYD3_chr1:g.247310040dup	PRECISE	Note: The SMYD3 rearrangement is a duplication of exon 1. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {SMYD3:ZNF124}		1751	0	9	1	Intron of SMYD3(-):18bp after exon 1	SMYD3	246670337			1	Intron of ZNF124(-):12Kb after exon 3	SMYD3	247310040			10	DUPLICATION		639703	308462	1167	9	NEW_VARIANT
P-0042121-T01-IM6	NOTCH3 (NM_000435) - EPHX3 (NM_024794) rearrangement: c.736:NOTCH3_c.616+979:EPHX3dup	IMPPRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {NOTCH3:EPHX3}		10225	0	7	19	Exon 5 of NOTCH3(-)	NOTCH3	15302622			19	Intron of EPHX3(-):978bp after exon 4	EPHX3	15340794			0	DUPLICATION		38172	308463	3558	7	NEW_VARIANT
P-0042222-T01-IM6	BCL2 (NM_000633) rearrangement: c.585+35197:BCL2_chr18:g.59604842inv	PRECISE	Note: The BCL2 rearrangement is an inversion of exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		4414	0	18	18	IGR: 107Kb before PIGN(-)	BCL2	59604842			18	Intron of BCL2(-):35Kb after exon 2	BCL2	60950118			10	INVERSION		1345276	309127	5747	18	NEW_VARIANT
P-0042222-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.3215+5:SMARCA4_chr19:g.11066021del	PRECISE	Note: The SMARCA4 rearrangement is a deletion of exons 1 - 23.	MANUAL_OK	3to5	3to5	-		58617	0	12	19	IGR: 6Kb before SMARCA4(+)	SMARCA4	11066021			19	Intron of SMARCA4(+):5bp after exon 23	SMARCA4	11137027			10	DELETION		71006	309125	80093	12	NEW_VARIANT
P-0042222-T01-IM6	TP53 (NM_000546) rearrangement: t(17;20)(p13.1;q13.13)(chr17:g.7579702::chr20:g.48337428)	PRECISE	Note: The TP53 rearrangement is a translocation with a breakpoint in exon 3. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	49	20	IGR: 88Kb before B4GALT5(-)	TP53	48337428			17	Exon 3 of TP53(-)	TP53	7579702			10	TRANSLOCATION		0	309130	0	56	NEW_VARIANT
P-0042334-T01-IM6	GNAS (NM_000516) rearrangement: t(1;20)(q32.2;q13.32)(chr1:g.209041232::chr20:g.57484747)	PRECISE	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.	MANUAL_OK	5to3	5to3	-		0	0	27	20	Exon 10 of GNAS(+)	GNAS	57484747			1	IGR: 561Kb before MIR205HG(+)	GNAS	209041232			10	TRANSLOCATION		0	309683	0	28	NEW_VARIANT
P-0042334-T01-IM6	CDKN2A (NM_058195) rearrangement: c.194-3668:CDKN2A_chr9:g.22187864del	PRECISE	Note: The CDKN2A rearrangement is a deletion of exon 1. This variant affects both CDKN2Ap14ARF (NM_058195) and CDKN2Ap16INK4A (NM_000077) isoforms.	MANUAL_OK	3to5	3to5	-		6889	0	10	9	Intron of CDKN2A(-):4Kb before exon 2	CDKN2A	21974875			9	IGR: 185Kb before CDKN2B(-)	CDKN2A	22187864			10	DELETION		212989	309680	4060	12	NEW_VARIANT
P-0042355-T01-IM6	CIC (NM_015125) rearrangement: t(10;19)(q11.21;q13.2)(chr10:g.42389428::chr19:g.42797695)	PRECISE	Note: The CIC rearrangement is a translocation with a breakpoint in intron 15. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		0	0	5	19	Intron of CIC(+):48bp before exon 16	CIC	42797695			10	IGR: 438Kb before LOC441666(-)	CIC	42389428			10	TRANSLOCATION		0	309707	0	9	NEW_VARIANT
P-0042355-T01-IM6	AKT2 (NM_001626) rearrangement: c.441+77:AKT2_chr19:g.13268475inv	PRECISE	Note: The AKT2 rearrangement is an inversion of exons 6 - 14. The rearrangement includes the kinase domain of AKT2. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	Transcript Fusion {AKT2:IER2}		411130	0	5	19	Promoter of IER2(+):7Kb from tx start	AKT2	13268475			19	Intron of AKT2(-):76bp after exon 5	AKT2	40748364			7	INVERSION		27479889	309705	520789	5	NEW_VARIANT
P-0042402-T01-IM6	NF1 (NM_001042492) rearrangement: c.4836-18716_c.5021del	PRECISE	Note: The NF1 rearrangement is an intragenic deletion of exon 37. One of the breakpoints is within exon 37.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		853	0	24	17	Intron of NF1(+):19Kb before exon 37	NF1	29634122			17	Exon 37 of NF1(+)	NF1	29653023			10	DELETION		18901	309796	724	29	NEW_VARIANT
P-0042417-T01-IM6	CCDC6 (NM_005436) - RET (NM_020975) fusion: c.303+16388:CCDC6_c.2136+213:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {CCDC6:RET}		36222	0	67	10	Intron of RET(+):213bp after exon 11	CCDC6	43610397			10	Intron of CCDC6(-):16Kb after exon 1	RET	61649492			10	INVERSION		18039095	309945	35906	75	NEW_VARIANT
P-0042608-T01-IM6	KIF5B (NM_004521) - RET (NM_020975) fusion: c.1726-1670:KIF5B_c.2137-230:RETinv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: in frame  {KIF5B:RET}		87443	0	87	10	Intron of KIF5B(-):2Kb before exon 16	KIF5B	32313634			10	Intron of RET(+):229bp before exon 12	RET	43611802			10	INVERSION		11298168	310886	92173	107	NEW_VARIANT
P-0042608-T01-IM6	WNT10B (NM_003394) - KMT2D (NM_003482) rearrangement: c.338-881:WNT10B_c.11911:KMT2Ddup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {WNT10B:KMT2D}		55186	0	13	12	Intron of WNT10B(-):881bp before exon 4	WNT10B	49362983			12	Exon 39 of KMT2D(-)	KMT2D	49426577			10	DUPLICATION		63594	310884	59877	13	NEW_VARIANT
P-0042612-T01-IM6	PIK3R2 (NM_005027) rearrangement: t(19;20)(p13.11;p11.1)(chr19:g.18272932::chr20:g.25673697)	IMPPRECISE	Note: The PIK3R2 rearrangement is a translocation with a breakpoint in intron 7. Functional significance is undetermined. low read support, no split on PIK3R2	MANUAL_OK	3to3	3to3	Transcript Fusion {PIK3R2:ZNF337}		0	0	7	20	5-UTR of ZNF337(-):18Kb before coding start	PIK3R2	25673697			19	Intron of PIK3R2(+):71bp after exon 7	PIK3R2	18272932			0	TRANSLOCATION		0	310883	0	7	NEW_VARIANT
P-0043170-T01-IM6	CIC (NM_015125) rearrangement: c.1464+93:CIC_chr19:g.42785275del	PRECISE	Note: The CIC rearrangement is a deletion of exons 1 - 9.	MANUAL_OK	3to5	3to5	-		19563	0	56	19	IGR: 4Kb before CIC(+)	CIC	42785275			19	Intron of CIC(+):93bp after exon 9	CIC	42794196			10	DELETION		8921	313398	23359	56	NEW_VARIANT
P-0043234-T01-IM6	CCND2 (NM_001759) - RAD51B (NM_133509) rearrangement: t(12;14)(p13.32;q24.1)(chr12:g.4388092::chr14:g.68610135)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: out of frame  {CCND2:RAD51B}		0	0	5	14	Intron of RAD51B(+):148Kb before exon 8	CCND2	68610135			12	Intron of CCND2(+):7bp after exon 3	RAD51B	4388092			10	TRANSLOCATION		0	313686	0	5	NEW_VARIANT
P-0043243-T01-IM6	STAT3 (NM_139276) rearrangement: c.273+433_c.373-14del	PRECISE	Note: The STAT3 rearrangement is an intragenic deletion of exon 4. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : in frame		1891	0	6	17	Intron of STAT3(-):14bp before exon 5	STAT3	40491441			17	Intron of STAT3(-):432bp after exon 3	STAT3	40498154			10	DELETION		6713	313609	2799	6	NEW_VARIANT
P-0043243-T01-IM6	SIRT2 (NM_012237) - ANKRD11 (NM_013275) rearrangement: t(16;19)(q24.3;q13.2)(chr16:g.89351636::chr19:g.39372774)	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {SIRT2:ANKRD11}		0	0	9	19	Intron of SIRT2(-):643bp before exon 10	SIRT2	39372774			16	Exon 9 of ANKRD11(-)	ANKRD11	89351636			10	TRANSLOCATION		0	313610	0	9	NEW_VARIANT
P-0043363-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.2254:EML4_c.3172+226:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {EML4:ALK}		101225	0	73	2	Intron of ALK(-):225bp after exon 19	EML4	29448101			2	Exon 20 of EML4(+)	ALK	42553305			10	INVERSION		13105204	313894	111654	73	NEW_VARIANT
P-0043498-T02-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1490-2142:EML4_c.3173-569:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		108481	0	50	2	Intron of ALK(-):569bp before exon 20	EML4	29446963			2	Intron of EML4(+):2Kb before exon 13	ALK	42526239			10	INVERSION		13079276	316492	86404	49	NEW_VARIANT
P-0043632-T01-IM6	GLI1 (NM_005269) - ZFAND3 (NM_021943) rearrangement: t(6;12)(p21.2;q13.3)(chr6:g.38088525::chr12:g.57859454)	PRECISE	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.	MANUAL_OK	3to5	3to5	Protein Fusion: mid-exon  {GLI1:ZFAND3}		0	0	7	12	Exon 6 of GLI1(+)	GLI1	57859454			6	Intron of ZFAND3(+):4Kb after exon 5	ZFAND3	38088525			10	TRANSLOCATION		0	315108	0	8	NEW_VARIANT
P-0043696-T01-IM6	JAK2 (NM_004972) rearrangement: c.1057-1491_c.1165del	PRECISE	Note: The JAK2 rearrangement is an intragenic deletion of exon 9. One of the breakpoints is within exon 9. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		318	0	6	9	Intron of JAK2(+):1Kb before exon 9	JAK2	5063392			9	Exon 9 of JAK2(+)	JAK2	5064991			10	DELETION		1599	315350	406	6	NEW_VARIANT
P-0043711-T01-IM6	EP300 (NM_001429) rearrangement: c.3261+838_c.3405del	PRECISE	Note: The EP300 rearrangement is an intragenic deletion of exon 18. One of the breakpoints is within exon 18.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		950	0	101	22	Intron of EP300(+):838bp after exon 17	EP300	41551955			22	Exon 18 of EP300(+)	EP300	41553316			10	DELETION		1361	315365	276	103	NEW_VARIANT
P-0043829-T01-IM6	CBL (NM_005188) rearrangement: c.1214_c.1431+2134del	PRECISE	Note: The CBL rearrangement is an intragenic deletion of exons 8 - 9. One of the breakpoints is within exon 8.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		1947	0	63	11	Exon 8 of CBL(+)	CBL	119148994			11	Intron of CBL(+):2Kb after exon 9	CBL	119151557			10	DELETION		2563	316347	2021	66	NEW_VARIANT
P-0043867-T01-IM6	TP53 (NM_000546) rearrangement: c.227:TP53_chr17:g.7582510del	PRECISE	Note: The TP53 rearrangement is a deletion of exons 1 - 4. One of the breakpoints is within exon 4.	MANUAL_OK	3to5	3to5	Deletion within transcript : mid-exon		5200	0	111	17	Exon 4 of TP53(-)	TP53	7579460			17	5-UTR of TP53(-):10Kb before coding start	TP53	7582510			10	DELETION		3050	316484	1637	124	NEW_VARIANT
P-0044057-T01-IM6	FGFR3 (NM_000142) - TACC3 (NM_006342) fusion: c.2274+53:FGFR3_c.1645-189:TACC3dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: in frame  {FGFR3:TACC3}		24249	0	12	4	Intron of TACC3(+):188bp before exon 8	FGFR3	1737269			4	Intron of FGFR3(+):53bp after exon 17	TACC3	1808714			10	DUPLICATION		71445	317379	33769	12	NEW_VARIANT
P-0044077-T01-IM6	PXN (NM_001080855) - MSI1 (NM_002442) rearrangement: c.14-9946:PXN_c.709:MSI1dup	PRECISE	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.	MANUAL_OK	5to3	5to3	Protein Fusion: mid-exon  {PXN:MSI1}		7973	0	23	12	Intron of PXN(-):10Kb before exon 2	PXN	120672126			12	Exon 10 of MSI1(-)	MSI1	120791126			10	DUPLICATION		119000	317391	10591	27	NEW_VARIANT
P-0044100-T02-IM6	EGFR (NM_005228) rearrangement: c.89-28860_c.1705inv	PRECISE	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.	MANUAL_OK	3to3	3to3	Antisense Fusion		30960	0	48	7	Intron of EGFR(+):29Kb before exon 2	EGFR	55181119			7	Exon 14 of EGFR(+)	EGFR	55231499			10	INVERSION		50380	321156	46280	47	NEW_VARIANT
P-0044100-T02-IM6	EGFR (NM_005228) rearrangement: c.424+960_c.2072inv	PRECISE	Note: The EGFR rearrangement is an intragenic inversion of exons 4 - 18. One of the breakpoints is within exon 18. The rearrangement does not include the kinase domain of EGFR. Functional significance is undetermined.	MANUAL_OK	5to5	5to5	-		45634	0	31	7	Intron of EGFR(+):960bp after exon 3	EGFR	55212141			7	Exon 18 of EGFR(+)	EGFR	55241624			10	INVERSION		29483	321157	65911	32	NEW_VARIANT
P-0044246-T01-IM6	SMARCA4 (NM_003072) rearrangement: c.1593+12:SMARCA4_chr19:g.32708379del	PRECISE	Note: The SMARCA4 rearrangement is a deletion of exons 10 - 35.	MANUAL_OK	3to5	3to5	-		340810	0	147	19	Intron of SMARCA4(+):12bp after exon 9	SMARCA4	11105689			19	IGR: 115Kb before LOC101927411(-)	SMARCA4	32708379			10	DELETION		21602690	318337	458251	416	NEW_VARIANT
P-0044246-T01-IM6	SIPA1L3 (NM_015073) - KDM5C (NM_004187) rearrangement: t(19;X)(q13.13;p11.22)(chr19:g.38649964::chrX:g.53231096)	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: mid-exon  {SIPA1L3:KDM5C}		0	0	17	X	Exon 13 of KDM5C(-)	SIPA1L3	53231096			19	Intron of SIPA1L3(+):3Kb before exon 14	KDM5C	38649964			10	TRANSLOCATION		0	318339	0	18	NEW_VARIANT
P-0044380-T02-IM6	RET (NM_020975) rearrangement: t(7;10)(q21.13;q11.21)(chr7:g.89052378::chr10:g.43607734)	PRECISE	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.	MANUAL_OK	3to5	3to5	-		0	0	88	10	Intron of RET(+):62bp after exon 8	RET	43607734			7	IGR: 459Kb before STEAP2-AS1(-)	RET	89052378			10	TRANSLOCATION		0	321106	0	89	NEW_VARIANT
P-0044402-T01-IM6	ERF (NM_006494) rearrangement: t(2;19)(p12;q13.2)(chr2:g.76279515::chr19:g.42752863)	PRECISE	Note: The ERF rearrangement is a translocation with a breakpoint in exon 4. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	27	19	Exon 4 of ERF(-)	ERF	42752863			2	IGR: 351Kb before GCFC2(-)	ERF	76279515			10	TRANSLOCATION		0	319071	0	26	NEW_VARIANT
P-0044575-T01-IM6	PDCD1LG2 (NM_025239) rearrangement: c.134:PDCD1LG2_chr9:g.19387023del	PRECISE	Note: The PDCD1LG2 rearrangement is a deletion of exons 3 - 7. One of the breakpoints is within exon 3. Functional significance is undetermined.	MANUAL_OK	3to5	3to5	-		44460	0	25	9	Exon 3 of PDCD1LG2(+)	PDCD1LG2	5534823			9	IGR: 11Kb before RPS6(-)	PDCD1LG2	19387023			10	DELETION		13852200	320131	74129	26	NEW_VARIANT
P-0044656-T01-IM6	SOX9 (NM_000346) rearrangement: c.366:SOX9_chr17:g.70359850inv	PRECISE	Note: The SOX9 rearrangement is an inversion of exons 1 - 3. One of the breakpoints is within exon 1. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		12203	0	2	17	Exon 1 of SOX9(+)	SOX9	70117898			17	IGR: 40Kb before LINC00673(-)	SOX9	70359850			9	INVERSION		241952	320346	15276	2	NEW_VARIANT
P-0044656-T01-IM6	TMPRSS2 (NM_001135099) - ERG (NM_182918) fusion: c.56-3702:TMPRSS2_c.18+1310:ERGdel	PRECISE	Note: The TMPRSS2 - ERG fusion involves TMPRSS2 exon 1 to ERG exons 2 - 10.	MANUAL_OK	3to5	3to5	Protein Fusion: out of frame  {TMPRSS2:ERG}		64815	0	79	21	Intron of ERG(-):1Kb after exon 1	TMPRSS2	39868977			21	Intron of TMPRSS2(-):4Kb before exon 2	ERG	42873818			10	DELETION		3004841	320345	57129	81	NEW_VARIANT
P-0044661-T01-IM6	SBF2 (NM_030962) - EPAS1 (NM_001430) rearrangement: t(2;11)(p21;p15.4)(chr2:g.46605894::chr11:g.9929559)	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein Fusion: mid-exon  {SBF2:EPAS1}		0	0	25	11	Intron of SBF2(-):12Kb before exon 17	SBF2	9929559			2	Exon 11 of EPAS1(+)	EPAS1	46605894			10	TRANSLOCATION		0	320328	0	27	NEW_VARIANT
P-0044902-T01-IM6	DAXX (NM_001141970) rearrangement: c.288:DAXX_chr6:g.37277191del	PRECISE	Note: The DAXX rearrangement is a deletion of exons 1 - 3. One of the breakpoints is within exon 3.	MANUAL_OK	3to5	3to5	-		25804	0	25	6	Exon 3 of DAXX(-)	DAXX	33289300			6	Intron of TBC1D22B(+):4Kb before exon 9	DAXX	37277191			10	DELETION		3987891	320868	37377	26	NEW_VARIANT
P-0044969-T01-IM6	PRKD1 (NM_002742) rearrangement: c.535+269_c.697-39inv	IMPPRECISE	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.	MANUAL_OK	3to3	3to3	-		1514	0	5	14	Intron of PRKD1(-):39bp before exon 5	PRKD1	30108149			14	Intron of PRKD1(-):268bp after exon 3	PRKD1	30135014			0	INVERSION		26865	321012	2979	5	NEW_VARIANT
P-0044969-T01-IM6	NF1 (NM_001042492) rearrangement: t(7;17)(q11.22;q11.2)(chr7:g.68108423::chr17:g.29528219)	PRECISE	Note: The NF1 rearrangement is a translocation with a breakpoint in intron 10. Functional significance is undetermined.	MANUAL_OK	3to3	3to3	-		0	0	6	17	Intron of NF1(+):42bp after exon 10	NF1	29528219			7	IGR: 623Kb before LOC102723427(+)	NF1	68108423			8	TRANSLOCATION		0	321014	0	7	NEW_VARIANT
P-0044988-T01-IM6	EML4 (NM_019063) - ALK (NM_004304) fusion: c.1489+2670:EML4_c.3172+533:ALKinv	PRECISE	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.	MANUAL_OK	3to3	3to3	Protein Fusion: in frame  {EML4:ALK}		79103	0	18	2	Intron of ALK(-):532bp after exon 19	EML4	29447794			2	Intron of EML4(+):3Kb after exon 12	ALK	42525326			10	INVERSION		13077532	321104	90000	18	NEW_VARIANT
P-0049880-T01-IM6	PTEN (NM_000314) rearrangement: c.635-1359_c.802-28del	IMPPRECISE	Note: The PTEN rearrangement is an intragenic deletion of exon 7.	MANUAL_OK	3to5	3to5	Deletion of 1 exon : out of frame		1783	0	5	10	Intron of PTEN(+):1Kb before exon 7	PTEN	89716251			10	Intron of PTEN(+):27bp before exon 8	PTEN	89720623			0	DELETION		4372	337706	2341	7	NEW_VARIANT
P-0001716-T01-IM3	RPS6KB2 (NM_003952) - ANO5 (NM_213599) duplication:  c.970-59_c.1333-371dup	PRECISE	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	AUTO_OK	5to3	5to3	Protein fusion: in frame (RPS6KB2-ANO5)		189284	0	15	11	Intron of ANO5(+): 371bp before exon 14	RPS6KB2	22278855			11	Intron of RPS6KB2(+): 59bp before exon 12	ANO5	67201610			38	DUPLICATION		44922755	1221	197743	17	NEW_VARIANT
P-0004520-T01-IM5	FGFR2(NM_000141) - BICC1( NM_001080512) Fusion (FGFR2 exon 17 fused with exon 10 of BICC1) :  c.2302-734:FGFR2_c.1180-924:BICC1inv	PRECISE	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.	MANUAL_OK	5to5	5to5	Protein fusion: in frame (FGFR2-BICC1)		272533	0	56	10	Intron of BICC1(+): 924bp before exon 10	FGFR2	60555176			10	Intron of FGFR2(-): 734bp before exon 18	BICC1	123240269			56	INVERSION		62685093	22146	252191	52	NEW_VARIANT
P-0025754-T01-IM6	ATR (NM_001184) Rearrangement : chr3:g.119493103_c.5381-35:ATRdup	PRECISE	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.	MANUAL_OK	5to3	5to3	-		107910	0	319	3	IGR: 6Kb before NR1I2(+)	ATR	119493103			3	Intron of ATR(-):35bp before exon 32	ATR	142217651			10	DUPLICATION		22724548	207038	158415	441	NEW_VARIANT
P-0032991-T01-IM6	CDKN2A (NM_000077) Rearrangement:  chr9:g.21675509_c.-44inv	PRECISE	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.	MANUAL_OK	3to3	3to3	-		6121	0	11	9	IGR: 127Kb before MTAP(+)	CDKN2A	21675509			9	Intron of CDKN2A(-):4Kb before exon 2	CDKN2A	21974870			10	INVERSION		299361	237175	3207	11	NEW_VARIANT
P-0047553-T01-IM6	AGO2 (NM_012154) rearrangement: c.1147-2_c.1269+1696dup	PRECISE	Note: The AGO2 rearrangement is an intragenic duplication of exon 10. Functional significance is undetermined.	MANUAL_OK	5to3	5to3	Duplication of 1 exon : in frame		1336	0	48	8	Intron of AGO2(-):2Kb after exon 10	AGO2	141564299			8	Intron of AGO2(-):2bp before exon 10	AGO2	141566119			10	DUPLICATION		1820	330931	1862	50	NEW_VARIANT
P-0048544-T01-IM6	EGFR (NM_005228) rearrangement: c.560-95:EGFR_chr7:g.55081300del	PRECISE	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.	MANUAL_OK	3to5	3to5	-		4611	0	11	7	IGR: 5Kb before EGFR(+)	EGFR	55081300			7	Intron of EGFR(+):94bp before exon 5	EGFR	55218892			10	DELETION		137592	333252	5546	12	NEW_VARIANT
P-0028912-T01-IM6	XPO1 (NM_003400) rearrangement: c.1135:XPO1_chr2:g.57754879inv	PRECISE	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.	MANUAL_OK	5to5	5to5	-		15123	0	15	2	IGR: 380Kb before VRK2(+)	XPO1	57754879			2	Exon 12 of XPO1(-)	XPO1	61721139			10	INVERSION		3966260	219163	51290	20	NEW_VARIANT
P-0028912-T01-IM6	PTPRT (NM_133170) rearrangement: t(10;20)(p15.1;q12)(chr10:g.3968862::chr20:g.40733369)	PRECISE	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.	MANUAL_OK	3to3	3to3	-		0	0	41	20	Intron of PTPRT(-):11bp before exon 26	PTPRT	40733369			10	IGR: 64Kb before MIR6078(+)	PTPRT	3968862			10	TRANSLOCATION		0	219166	0	41	NEW_VARIANT
