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["Table e3. Predicted functional annotations of variants at the 13q34 region detected from the GOCHA and ERICH dataset "]
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{"sheet":"Table. e4","index":1,"n_rows":3836,"n_cols":51,"rows_kept":1125,"cut":true,"bounds":{"rows_first":500,"rows_last":125,"rows_between":500,"halvings":2}}
["Table e4. Predicted functional annotations of variants at the 13q34 region detected from the LINCHPIN dataset"]
[]
["Location","Allele","Consequence","IMPACT","SYMBOL","Gene","Feature_type","Feature","BIOTYPE","EXON","INTRON","HGVSc","HGVSp","cDNA_position","CDS_position","Protein_position","Amino_acids","Codons","Existing_variation","DISTANCE","STRAND","FLAGS","SYMBOL_SOURCE","HGNC_ID","TSL","APPRIS","CCDS","SIFT","PolyPhen","gnomAD_AF","gnomAD_AFR_AF","gnomAD_AMR_AF","gnomAD_ASJ_AF","gnomAD_EAS_AF","gnomAD_FIN_AF","gnomAD_NFE_AF","gnomAD_OTH_AF","gnomAD_SAS_AF","CLIN_SIG","SOMATIC","PHENO","PUBMED","MOTIF_NAME","MOTIF_POS","HIGH_INF_POS","MOTIF_SCORE_CHANGE","CADD_PHRED","CADD_RAW","LoFtool","ada_score","rf_score"]
["13:110813633-110813633","A","stop_gained","HIGH","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","49/52","-","-","-",4668,4546,1516,"R/*","Cga/Tga","COSM5842153,COSM5842154","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-","-","-","-","-","-","-","-","-","-","-","1,1","1,1","-","-","-","-","-",37,11.295958,0.0123,"-","-"]
["13:110804809-110804809","A","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","51/52","-","-","-",4922,4800,1600,"S","tcC/tcT","rs650724","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.1129,0.2076,0.2273,0.1216,0.003306,0.08481,0.09692,0.1137,0.07774,"benign","-",1,"25741868,21527998","-","-","-","-",8.951,0.71894,0.0123,"-","-"]
["13:110813531-110813531","T","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","49/51","-","-","-","-","-","-","-","rs117566874","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.005701,0.007776,0.00399,0.01675,0,1.794E-3,7.358E-3,0.007474,2.696E-3,"likely_benign","-",1,"-","-","-","-","-",7.336,0.487683,0.0123,"7.69804235104544E-5",0]
["13:110813532-110813532","A","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","49/51","-","-","-","-","-","-","-","rs2275843","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.1661,0.1175,0.1804,0.1686,0.3045,0.1075,0.1551,0.1821,0.1758,"benign","-",1,"25741868,21527998","-","-","-","-",0.793,-0.265658,0.0123,"1.04993150462405E-5",0.004]
["13:110813709-110813709","A","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","49/52","-","-","-",4592,4470,1490,"A","gcC/gcT","rs1133219","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.3348,0.3665,0.2109,0.3528,0.2051,0.4313,0.3557,0.3304,0.377,"benign","-",1,"25741868,21527998","-","-","-","-",11.57,1.167089,0.0123,"-","-"]
["13:110822943-110822943","T","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","42/52","-","-","-",3815,3693,1231,"T","acG/acA","rs117738194","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.02199,0.002247,0.1046,0.005222,0.08276,1.381E-4,1.23E-3,0.01791,0.0009352,"benign","-",1,25741868,"-","-","-","-",16.01,1.967208,0.0123,"-","-"]
["13:110827574-110827574","A","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","37/52","-","-","-",3311,3189,1063,"R","cgA/cgT","rs874203","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.354,0.2781,0.392,0.3144,0.2946,0.3515,0.363,0.3445,0.3673,"benign","-",1,"25741868,21527998,22144573","-","-","-","-",2.125,-0.050745,0.0123,"-","-"]
["13:110827580-110827580","T","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","37/52","-","-","-",3305,3183,1061,"G","ggG/ggA","rs874204","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.3541,0.278,0.3924,0.3144,0.2944,0.3514,0.363,0.3438,0.3674,"benign","-",1,"25741868,21527998","-","-","-","-",10.25,0.929579,0.0123,"-","-"]
["13:110830496-110830496","C","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","32/52","-","-","-",2663,2541,847,"A","gcT/gcG","-","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-","-",0.029,-0.878422,0.0123,"-","-"]
["13:110833702-110833702","T","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","29/52","-","-","-",2252,2130,710,"P","ccG/ccA","rs16975492","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.3506,0.2403,0.3896,0.3154,0.2904,0.3507,0.36,0.3387,0.3761,"benign","-",1,"25741868,20452482,21527998","-","-","-","-",8.077,0.588605,0.0123,"-","-"]
["13:110838814-110838814","G","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","26/52","-","-","-",1937,1815,605,"P","ccT/ccC","rs61749897","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.08259,0.08925,0.1255,0.01548,0.1363,0.08879,0.06925,0.06648,0.07012,"benign","-",1,"25741868,21527998","-","-","-","-",0.866,-0.248136,0.0123,"-","-"]
["13:110844637-110844637","A","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","23/51","-","-","-","-","-","-","-","rs183563055","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.001548,0.0003923,1.817E-3,0.006503,0,8.97e-05,0.00207,2.918E-3,3.25e-05,"uncertain_significance,likely_benign","-",1,"-","-","-","-","-",1.823,-0.087723,0.0123,2.0613044203369E-5,0]
["13:110844637-110844637","A","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","-","23/24","-","-","-","-","-","-","-","rs183563055","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.001548,0.0003923,1.817E-3,0.006503,0,8.97e-05,0.00207,2.918E-3,3.25e-05,"uncertain_significance,likely_benign","-",1,"-","-","-","-","-",1.823,-0.087723,0.0123,2.0613044203369E-5,0]
["13:110850842-110850842","G","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","21/52","-","-","-",1379,1257,419,"P","ccT/ccC","rs995224","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.2608,0.2212,0.3331,0.2408,0.04506,0.3287,0.276,0.2673,0.2234,"benign","-",1,"25741868,21527998","-","-","-","-",0.039,-0.817812,0.0123,"-","-"]
["13:110850842-110850842","G","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","21/25","-","-","-",1361,1257,419,"P","ccT/ccC","rs995224","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.2608,0.2212,0.3331,0.2408,0.04506,0.3287,0.276,0.2673,0.2234,"benign","-",1,"25741868,21527998","-","-","-","-",0.039,-0.817812,0.0123,"-","-"]
["13:110859069-110859069","C","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","14/51","-","-","-","-","-","-","-","rs9588116","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.37,0.4623,0.4985,0.2994,0.2368,0.3921,0.3573,0.3686,0.3116,"benign","-",1,"25741868,21527998","-","-","-","-",0.044,-0.79575,0.0123,"1.47138069197762E-4",0.008]
["13:110859069-110859069","C","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","-","14/24","-","-","-","-","-","-","-","rs9588116","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.37,0.4623,0.4985,0.2994,0.2368,0.3921,0.3573,0.3686,0.3116,"benign","-",1,"25741868,21527998","-","-","-","-",0.044,-0.79575,0.0123,"1.47138069197762E-4",0.008]
["13:110859743-110859743","T","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","13/51","-","-","-","-","-","-","-","rs598893","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.6207,0.4136,0.4953,0.7006,0.7582,0.6073,0.6423,0.6264,0.6881,"benign","-",1,"25741868,20452482,20617897,21527998","-","-","-","-",3.229,0.064126,0.0123,"7.06341561599038E-6",0]
["13:110859743-110859743","T","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","-","13/24","-","-","-","-","-","-","-","rs598893","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.6207,0.4136,0.4953,0.7006,0.7582,0.6073,0.6423,0.6264,0.6881,"benign","-",1,"25741868,20452482,20617897,21527998","-","-","-","-",3.229,0.064126,0.0123,"7.06341561599038E-6",0]
["13:110864225-110864225","T","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","7/52","-","-","-",554,432,144,"A","gcT/gcA","rs532625","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.4669,0.3692,0.4046,0.5277,0.4967,0.4137,0.4657,0.4621,0.5909,"benign","-",1,"25741868,21527998","-","-","-","-",0.052,-0.76032,0.0123,"-","-"]
["13:110864225-110864225","T","synonymous_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","7/25","-","-","-",536,432,144,"A","gcT/gcA","rs532625","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.4669,0.3692,0.4046,0.5277,0.4967,0.4137,0.4657,0.4621,0.5909,"benign","-",1,"25741868,21527998","-","-","-","-",0.052,-0.76032,0.0123,"-","-"]
["13:110866265-110866265","A","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000375820","protein_coding","-","3/51","-","-","-","-","-","-","-","rs9521650","-",-1,"-","HGNC",2202,"-","-","CCDS9511.1","-","-",0.1412,0.08906,0.09541,0.1453,0.2514,0.1322,0.1611,0.1557,0.08576,"benign","-",1,"25741868,21527998","-","-","-","-",2.969,0.038838,0.0123,"2.69673633934422E-5",0]
["13:110866265-110866265","A","splice_region_variant,intron_variant","LOW","COL4A1","ENSG00000187498","Transcript","ENST00000543140","protein_coding","-","3/24","-","-","-","-","-","-","-","rs9521650","-",-1,"-","HGNC",2202,"-","-","-","-","-",0.1412,0.08906,0.09541,0.1453,0.2514,0.1322,0.1611,0.1557,0.08576,"benign","-",1,"25741868,21527998","-","-","-","-",2.969,0.038838,0.0123,"2.69673633934422E-5",0]
["13:111077197-111077197","A","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","5/48","-","-","-",603,297,99,"T","acG/acA","rs4238272","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.9643,0.8538,0.9808,0.9812,0.9999,0.9852,0.961,0.9728,0.9716,"benign","-",1,21527998,"-","-","-","-",8.688,0.678835,0.0908,"-","-"]
["13:111077197-111077197","A","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000400163","protein_coding","5/5","-","-","-",473,297,99,"T","acG/acA","rs4238272","-",1,"cds_end_NF","HGNC",2203,"-","-","-","-","-",0.9643,0.8538,0.9808,0.9812,0.9999,0.9852,0.961,0.9728,0.9716,"benign","-",1,21527998,"-","-","-","-",8.688,0.678835,0.0908,"-","-"]
["13:111098226-111098226","T","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","17/48","-","-","-",1314,1008,336,"P","ccC/ccT","rs4103","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.5106,0.3967,0.4942,0.4253,0.5245,0.4987,0.5373,0.4909,0.52,"benign","-",1,"21527998,26982741","-","-","-","-",9.866,0.866272,0.0908,"-","-"]
["13:111102042-111102042","A","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","19/48","-","-","-",1401,1095,365,"P","ccG/ccA","rs76425569","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.3084,0.1202,0.1732,0.2765,0.2644,0.4043,0.3718,0.2826,0.3256,"benign","-",1,21527998,"-","-","-","-",13.89,1.606983,0.0908,"-","-"]
["13:111102126-111102126","T","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","19/48","-","-","-",1485,1179,393,"I","atC/atT","rs74941798","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.3303,0.1242,0.1892,0.294,0.2537,0.4558,0.402,0.3118,0.3373,"benign","-",1,21527998,"-","-","-","-",12.89,1.418619,0.0908,"-","-"]
["13:111111173-111111173","A","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","22/48","-","-","-",1794,1488,496,"P","ccG/ccA","rs7990214","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.5208,0.6355,0.3848,0.6668,0.2306,0.4441,0.603,0.5474,0.4808,"benign","-",1,21527998,"-","-","-","-",9.52,0.809169,0.0908,"-","-"]
["13:111114731-111114731","T","splice_region_variant,synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","24/48","-","-","-",2082,1776,592,"P","ccC/ccT","rs767094122,COSM3688614","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",3.771e-05,0.0001424,0,0,0,0,5.577e-05,0,3.25e-05,"-","0,1","0,1","-","-","-","-","-",4.901,0.221218,0.0908,"6.98679917122492E-5",0.042]
["13:111117745-111117745","T","splice_region_variant,intron_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","-","24/47","-","-","-","-","-","-","-","rs3803236","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.53,0.6545,0.4105,0.6504,0.2981,0.442,0.5996,0.5405,0.4774,"benign","-",1,21527998,"-","-","-","-",5.638,0.294236,0.0908,"2.15636947441856E-4",2E-3]
["13:111118344-111118344","T","splice_region_variant,intron_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","-","25/47","-","-","-","-","-","-","-","rs190632602","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.004526,1.439E-3,0.003845,0.002844,0,0.006817,0.006797,0.003652,0.00013,"likely_benign","-",1,"-","-","-","-","-",6.894,0.432745,0.0908,"9.21333742245411E-6",0.012]
["13:111130408-111130408","C","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","30/48","-","-","-",2790,2484,828,"P","ccT/ccC","rs181706751","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",1.745E-3,0,3.044E-5,0,0,0.01425,0.0008581,1.864E-3,0,"likely_benign","-",1,"-","-","-","-","-",0.059,-0.739108,0.0908,"-","-"]
["13:111130519-111130519","T","splice_region_variant,intron_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","-","30/47","-","-","-","-","-","-","-","rs2281974","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.3745,0.5437,0.3817,0.3798,0.4904,0.2935,0.3144,0.3411,0.5016,"benign","-",1,21527998,"-","-","-","-",5.561,0.286388,0.0908,"4.79314207206413E-5",0]
["13:111130519-111130519","T","splice_region_variant,intron_variant,non_coding_transcript_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000483683","processed_transcript","-","1/4","-","-","-","-","-","-","-","rs2281974","-",1,"-","HGNC",2203,"-","-","-","-","-",0.3745,0.5437,0.3817,0.3798,0.4904,0.2935,0.3144,0.3411,0.5016,"benign","-",1,21527998,"-","-","-","-",5.561,0.286388,0.0908,"4.79314207206413E-5",0]
["13:111134858-111134858","C","splice_region_variant,intron_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","-","31/47","-","-","-","-","-","-","-","rs3803228","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",0.1722,0.2356,0.1237,0.1293,0.2042,0.1358,0.1774,0.1726,0.1972,"benign","-",1,21527998,"-","-","-","-",9.85,0.863615,0.0908,"1.32442894718479E-4",0.006]
["13:111134858-111134858","C","splice_region_variant,intron_variant,non_coding_transcript_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000483683","processed_transcript","-","2/4","-","-","-","-","-","-","-","rs3803228","-",1,"-","HGNC",2203,"-","-","-","-","-",0.1722,0.2356,0.1237,0.1293,0.2042,0.1358,0.1774,0.1726,0.1972,"benign","-",1,21527998,"-","-","-","-",9.85,0.863615,0.0908,"1.32442894718479E-4",0.006]
["13:111138063-111138063","T","synonymous_variant","LOW","COL4A2","ENSG00000134871","Transcript","ENST00000360467","protein_coding","34/48","-","-","-",3393,3087,1029,"P","ccC/ccT","rs201630262","-",1,"-","HGNC",2203,"-","-","CCDS41907.1","-","-",1.761E-4,0.0002619,0,0,0,8.97e-05,3.279E-4,0.0001831,0,"uncertain_significance","-",1,"-","-","-","-","-",12.99,1.438021,0.0908,"-","-"]
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