Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID COSMIC_Codon COSMIC_Gene Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm CPSF3L 54973 hgsc.bcm.edu hg19 1 1248221 1248221 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . CPSF3L NM_001256456 exon14 c.C1258T p.H420Y CGCCATGCACCAG . 40.0 17.0 74.0 0.0 . 33 . . . none . . PASS Atlas-SNP CROCC 9696 hgsc.bcm.edu hg19 1 17287328 17287328 + Silent SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . CROCC NM_014675 exon27 c.C4108T p.L1370L GGCTCCCTGGAGG . 7.0 5.0 14.0 0.0 . 185 . . . none . . PASS Atlas-SNP ZBTB40 9923 hgsc.bcm.edu hg19 1 22816649 22816649 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZBTB40 NM_001083621 exon3 c.G208A p.E70K CCCGAGGAGTTTG . 88.0 33.0 92.0 0.0 . 87 . . . none . . PASS Atlas-SNP RUNX3 864 hgsc.bcm.edu hg19 1 25229150 25229150 + Silent SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RUNX3 NM_001031680 exon6 c.G753A p.S251S CAGTTCCGAGGTG . 117.0 12.0 129.0 0.0 . 72 . . . none . . PASS Atlas-SNP ZMYM6 9204 hgsc.bcm.edu hg19 1 35453543 35453543 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZMYM6 NM_007167 exon16 c.C3140T p.S1047L ATACGTGAATTTA . 123.0 48.0 172.0 0.0 . 110 . . . none . . PASS Atlas-SNP RASAL2 9462 hgsc.bcm.edu hg19 1 178063786 178063786 + Silent SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RASAL2 NM_170692 exon1 c.T159C p.L53L GATCCTTCTGGAG . 193.0 79.0 221.0 0.0 . 334 . . . none . . PASS Atlas-SNP CDC73 79577 hgsc.bcm.edu hg19 1 193119495 193119495 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . CDC73 NM_024529 exon9 c.G890C p.R297T AGGAAAGATTCAA . 90.0 32.0 93.0 0.0 . 163 . . . none . . PASS Atlas-SNP DISP1 84976 hgsc.bcm.edu hg19 1 223176848 223176848 + Silent SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DISP1 NM_032890 exon10 c.A2109G p.R703R ATCTCGAATTTTT . 106.0 58.0 104.0 0.0 . 145 . . . none . . PASS Atlas-SNP DISC1 27185 hgsc.bcm.edu hg19 1 232094574 232094574 + Missense_Mutation SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DISC1 NM_001164537 exon11 c.A2078G p.E693G CCCCAGAAACAAG . 141.0 77.0 118.0 0.0 . 207 . . . none . . PASS Atlas-SNP C2orf70 339778 hgsc.bcm.edu hg19 2 26798881 26798881 + Silent SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . C2orf70 NM_001105519 exon2 c.T186C p.T62T CCACACTCCCTTC . 86.0 44.0 106.0 0.0 . 26 . . . none . . PASS Atlas-SNP MTA3 57504 hgsc.bcm.edu hg19 2 42931435 42931435 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MTA3 NM_020744 exon12 c.G1127A p.G376E TCTTAGGGAGAGC . 118.0 48.0 140.0 0.0 . 39 . . . none . . PASS Atlas-SNP ABCG8 64241 hgsc.bcm.edu hg19 2 44100948 44100948 + Nonsense_Mutation SNP C C T rs137852991 bycluster TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 ABCG8,NS,carcinoma,0,1 ABCG8 NM_022437 exon9 c.C1234T p.R412X GACTTCCGAGACC . 58.0 3.0 60.0 0.0 . 98 . . . weak . . PASS Atlas-SNP WDR33 55339 hgsc.bcm.edu hg19 2 128482691 128482691 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . WDR33 NM_018383 exon9 c.T950G p.I317S TTTCTGATATCAA . 116.0 48.0 142.0 0.0 . 136 . . . none . . PASS Atlas-SNP MBD5 55777 hgsc.bcm.edu hg19 2 149243320 149243320 + Missense_Mutation SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MBD5 NM_018328 exon11 c.C2855T p.S952L ATATGTCATCAAT . 133.0 47.0 159.0 0.0 . 164 . . . none . . PASS Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179606399 179606399 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TTN NM_001267550 exon48 c.T11561A p.F3854Y TTAAAGAACCACT . 124.0 41.0 168.0 0.0 . 18412 . . . none . . PASS Atlas-SNP UNC80 285175 hgsc.bcm.edu hg19 2 210824431 210824431 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . UNC80 NM_032504 exon50 c.G7607C p.R2536T ACATGAGGTACTG . 87.0 34.0 104.0 0.0 . 280 . . . none . . PASS Atlas-SNP UGT1A9 54600 hgsc.bcm.edu hg19 2 234581095 234581095 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . UGT1A9 NM_021027 exon1 c.T515C p.I172T GGGGAATACTTTG . 86.0 38.0 117.0 0.0 . 79 . . . none . . PASS Atlas-SNP ZNF660 285349 hgsc.bcm.edu hg19 3 44636593 44636593 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF660 NM_173658 exon3 c.A908T p.K303I CCTATAAATGTAG . 243.0 151.0 228.0 0.0 . 28 . . . none . . PASS Atlas-SNP ITIH1 3697 hgsc.bcm.edu hg19 3 52822035 52822035 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ITIH1 NM_002215 exon17 c.C1958A p.T653N CTCCTACTCATTC . 173.0 41.0 194.0 0.0 . 108 . . . none . . PASS Atlas-SNP DNAH12 201625 hgsc.bcm.edu hg19 3 57419454 57419454 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DNAH12 NM_178504 exon31 c.A4688G p.E1563G ACCTTTTCTTCCT . 92.0 9.0 82.0 0.0 . 182 . . . none . . PASS Atlas-SNP ZNF717 100131827 hgsc.bcm.edu hg19 3 75786895 75786895 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 .,1 ZNF717 NM_001128223 exon5 c.A1879C p.T627P GAAAGGTTTTTCC . 46.0 4.0 54.0 0.0 . 160 . . . none . . PASS Atlas-SNP EPHA6 285220 hgsc.bcm.edu hg19 3 97311466 97311466 + Silent SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . EPHA6 NM_001080448 exon12 c.G2397A p.P799P CTTCCCGGCCATT . 119.0 33.0 117.0 0.0 . 439 . . . none . . PASS Atlas-SNP MBNL1 4154 hgsc.bcm.edu hg19 3 152132779 152132779 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MBNL1 NM_207292 exon3 c.T224C p.L75S CACATTTAAAAAC . 191.0 115.0 135.0 0.0 . 100 . . . none . . PASS Atlas-SNP TNFSF10 8743 hgsc.bcm.edu hg19 3 172224318 172224318 + Silent SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TNFSF10 NM_003810 exon5 c.T810C p.H270H GGCTTCATGGTCC . 275.0 175.0 262.0 0.0 . 30 . . . none . . PASS Atlas-SNP EHHADH 1962 hgsc.bcm.edu hg19 3 184947277 184947277 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . EHHADH NM_001966 exon4 c.A406G p.T136A GCTGGGTTCCTCT . 90.0 36.0 60.0 0.0 . 73 . . . none . . PASS Atlas-SNP TMEM156 80008 hgsc.bcm.edu hg19 4 38990469 38990469 + Splice_Site SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TMEM156 NM_024943 exon5 c.739+2T>G . ATACTTACTCTGC . 61.0 30.0 72.0 0.0 . 31 . . . none . . PASS Atlas-SNP RASGEF1B 153020 hgsc.bcm.edu hg19 4 82369435 82369435 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RASGEF1B NM_152545 exon5 c.A442G p.T148A TGTATGTCTGCTA . 79.0 23.0 96.0 0.0 . 44 . . . none . . PASS Atlas-SNP WDFY3 23001 hgsc.bcm.edu hg19 4 85731169 85731169 + Nonsense_Mutation SNP G G T rs79515377 bycluster TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . WDFY3 NM_014991 exon14 c.C2216A p.S739X GTATTTGAGGGGA . 155.0 61.0 154.0 0.0 . 314 . . . weak . . PASS Atlas-SNP ANK2 287 hgsc.bcm.edu hg19 4 114153415 114153415 + Silent SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ANK2 NM_001148 exon5 c.G483A p.E161E TACAGAGGTAAGA . 55.0 23.0 74.0 0.0 . 576 . . . none . . PASS Atlas-SNP CCNA2 890 hgsc.bcm.edu hg19 4 122740067 122740067 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . CCNA2 NM_001237 exon6 c.T1004G p.F335C CCCAAAAACTGGA . 151.0 65.0 158.0 0.0 . 30 . . . none . . PASS Atlas-SNP ZNF827 152485 hgsc.bcm.edu hg19 4 146686704 146686704 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF827 NM_178835 exon12 c.A3047G p.E1016G CCTTTCTCTGGCT . 57.0 29.0 58.0 0.0 . 102 . . . none . . PASS Atlas-SNP SLC45A2 51151 hgsc.bcm.edu hg19 5 33954590 33954590 + Nonsense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SLC45A2 NM_016180 exon4 c.T908A p.L303X GACTTTAATGTCA . 86.0 39.0 114.0 0.0 . 100 . . . none . . PASS Atlas-SNP DAB2 1601 hgsc.bcm.edu hg19 5 39383191 39383191 + Silent SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DAB2 NM_001343 exon10 c.T870C p.P290P AGGATTAGGGGTG . 135.0 51.0 162.0 0.0 . 124 . . . none . . PASS Atlas-SNP FTMT 94033 hgsc.bcm.edu hg19 5 121187742 121187742 + Silent SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FTMT NM_177478 exon1 c.C84A p.L28L CGCGCTCCCGCTG . 26.0 12.0 33.0 0.0 . 71 . . . none . . PASS Atlas-SNP PCDHGB3 56102 hgsc.bcm.edu hg19 5 140751854 140751854 + Silent SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PCDHGB3 NM_018924 exon1 c.C1893A p.T631T GCGTACCTTGGGC . 58.0 25.0 66.0 0.0 . 168 . . . none . . PASS Atlas-SNP WWC1 23286 hgsc.bcm.edu hg19 5 167812372 167812372 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . WWC1 NM_015238 exon3 c.A386T p.Q129L AGTACCAGCAACT . 68.0 34.0 92.0 0.0 . 98 . . . none . . PASS Atlas-SNP MCM3 4172 hgsc.bcm.edu hg19 6 52141273 52141273 + Silent SNP T T A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MCM3 NM_002388 exon9 c.A1302T p.G434G GCGCTCTCCTGGG . 68.0 56.0 88.0 0.0 . 63 . . . none . . PASS Atlas-SNP KIAA1586 57691 hgsc.bcm.edu hg19 6 56917572 56917572 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . KIAA1586 NM_020931 exon4 c.A275C p.E92A ATAATGAAGTGAG . 176.0 144.0 233.0 0.0 . 59 . . . none . . PASS Atlas-SNP HBS1L 10767 hgsc.bcm.edu hg19 6 135358037 135358037 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 HBS1L_ENST00000367822,NS,carcinoma,0,1 HBS1L NM_001145207 exon5 c.C1558G p.L520V AACTTAGAACTTT . 120.0 97.0 97.0 0.0 . 75 . . . none . . PASS Atlas-SNP PCLO 27445 hgsc.bcm.edu hg19 7 82578940 82578940 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PCLO NM_014510 exon6 c.A10964C p.K3655T AGTACTTTCTGTG . 150.0 75.0 111.0 0.0 . 1506 . . . none . . PASS Atlas-SNP SLC4A2 6522 hgsc.bcm.edu hg19 7 150773188 150773188 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SLC4A2 NM_003040 exon22 c.T3560C p.L1187P CCTCCCTGGCCTT . 84.0 41.0 44.0 0.0 . 98 . . . none . . PASS Atlas-SNP AP3M2 10947 hgsc.bcm.edu hg19 8 42015584 42015584 + Silent SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . AP3M2 NM_001134296 exon4 c.C399T p.L133L AGAACTCATAAAG . 90.0 35.0 101.0 0.0 . 41 . . . none . . PASS Atlas-SNP ARMC1 55156 hgsc.bcm.edu hg19 8 66517664 66517664 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ARMC1 NM_018120 exon5 c.A575C p.K192T TCAGCTTTCAAAT . 201.0 86.0 209.0 0.0 . 22 . . . none . . PASS Atlas-SNP TLN1 7094 hgsc.bcm.edu hg19 9 35697810 35697810 + Nonsense_Mutation SNP G G T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TLN1 NM_006289 exon57 c.C7604A p.S2535X AGCTCTGAAGGCA . 84.0 45.0 97.0 0.0 . 185 . . . none . . PASS Atlas-SNP C9orf3 84909 hgsc.bcm.edu hg19 9 97522664 97522664 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . C9orf3 NM_001193331 exon2 c.G599C p.R200T GTTGGAGGGAGCA . 52.0 19.0 73.0 0.0 . 100 . . . none . . PASS Atlas-SNP TTLL11 158135 hgsc.bcm.edu hg19 9 124751966 124751966 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TTLL11 NM_001139442 exon4 c.C1047G p.I349M GAGGTAGATTCCA . 78.0 27.0 109.0 0.0 . 67 . . . none . . PASS Atlas-SNP DNA2 1763 hgsc.bcm.edu hg19 10 70182647 70182647 + Missense_Mutation SNP G G T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DNA2 NM_001080449 exon15 c.C2209A p.L737I CTATAAGCTAAAA . 170.0 108.0 138.0 0.0 . 76 . . . none . . PASS Atlas-SNP TET1 80312 hgsc.bcm.edu hg19 10 70432683 70432683 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TET1 NM_030625 exon8 c.G4705C p.E1569Q GATCCAGAGACTT . 96.0 54.0 89.0 0.0 . 255 . . . none . . PASS Atlas-SNP NEUROG3 50674 hgsc.bcm.edu hg19 10 71332496 71332496 + Missense_Mutation SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . NEUROG3 NM_020999 exon2 c.G304A p.A102T CCAGTGCCGAGTT . 103.0 53.0 124.0 0.0 . 33 . . . none . . PASS Atlas-SNP DUPD1 338599 hgsc.bcm.edu hg19 10 76818209 76818209 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DUPD1 NM_001003892 exon1 c.C64T p.P22S TCTTCGGCGACAG . 79.0 45.0 56.0 0.0 . 30 . . . none . . PASS Atlas-SNP BTRC 8945 hgsc.bcm.edu hg19 10 103294516 103294516 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . BTRC NM_033637 exon10 c.G1196C p.C399S TGACCTGCTCCAA . 133.0 35.0 128.0 0.0 . 64 . . . none . . PASS Atlas-SNP FTH1 2495 hgsc.bcm.edu hg19 11 61732247 61732247 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FTH1 NM_002032 exon4 c.A504C p.E168D GAGATATTCCGCC . 289.0 114.0 343.0 0.0 . 18 . . . none . . PASS Atlas-SNP MRPL49 740 hgsc.bcm.edu hg19 11 64892052 64892052 + Missense_Mutation SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MRPL49 NM_004927 exon2 c.C157T p.P53S CTGTTACCGGCTA . 129.0 61.0 169.0 0.0 . 5 . . . none . . PASS Atlas-SNP C11orf54 28970 hgsc.bcm.edu hg19 11 93494797 93494797 + Silent SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . C11orf54 NM_014039 exon8 c.A741G p.A247A ACCTGCAGAGTTT . 104.0 45.0 123.0 0.0 . 23 . . . none . . PASS Atlas-SNP GPR19 2842 hgsc.bcm.edu hg19 12 12814283 12814283 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . GPR19 NM_006143 exon4 c.C1100G p.A367G TTTTTGGCCATCC . 125.0 41.0 120.0 0.0 . 47 . . . none . . PASS Atlas-SNP IPO8 10526 hgsc.bcm.edu hg19 12 30792466 30792466 + Silent SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . IPO8 NM_006390 exon21 c.T2472C p.D824D ATCTGTATCATTC . 184.0 62.0 166.0 0.0 . 105 . . . none . . PASS Atlas-SNP GTF3A 2971 hgsc.bcm.edu hg19 13 28006937 28006937 + Missense_Mutation SNP C C G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 GTF3A,NS,carcinoma,0,1 GTF3A NM_002097 exon5 c.C558G p.H186Q GGCCCACGAGGGT . 140.0 54.0 155.0 0.0 . 11 . . . none . . PASS Atlas-SNP TOX4 9878 hgsc.bcm.edu hg19 14 21961062 21961062 + Silent SNP T T A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 TOX4,NS,carcinoma,0,2 TOX4 NM_014828 exon7 c.T1287A p.A429A AGCAGCTGCTGCT . 64.0 3.0 75.0 1.0 . 50 . . . none . . PASS Atlas-SNP DHRS4 10901 hgsc.bcm.edu hg19 14 24424419 24424419 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DHRS4 NM_021004 exon2 c.A304T p.T102S GTGGCCACGGTGA . 170.0 76.0 202.0 0.0 . 22 . . . none . . PASS Atlas-SNP TTC7B 145567 hgsc.bcm.edu hg19 14 91142993 91142993 + Silent SNP G G A rs149388931 TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 TTC7B,NS,carcinoma,0,1 TTC7B NM_001010854 exon9 c.C1026T p.D342D CACAGCGTCCCGG . 48.0 15.0 47.0 0.0 . 93 . . . weak G|1.000;A|0.000 0.000 PASS Atlas-SNP MAPKBP1 23005 hgsc.bcm.edu hg19 15 42109123 42109123 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MAPKBP1 NM_001128608 exon15 c.C1619A p.A540E TGCTAGCATCGGC . 42.0 16.0 70.0 0.0 . 120 . . . none . . PASS Atlas-SNP RCN2 5955 hgsc.bcm.edu hg19 15 77227974 77227974 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RCN2 NM_002902 exon3 c.G358C p.D120H ACTTGGGATGAAT . 103.0 43.0 145.0 0.0 . 16 . . . none . . PASS Atlas-SNP AMDHD2 51005 hgsc.bcm.edu hg19 16 2577574 2577574 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . AMDHD2 NM_001145815 exon4 c.A373C p.I125L CCTCAGATCCCTG . 56.0 14.0 82.0 0.0 . 33 . . . none . . PASS Atlas-SNP ABCC6 368 hgsc.bcm.edu hg19 16 16267179 16267179 + Nonsense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ABCC6 NM_001171 exon21 c.G2749T p.G917X GCCATCCTGCCCT . 101.0 35.0 117.0 0.0 . 110 . . . none . . PASS Atlas-SNP TAOK2 9344 hgsc.bcm.edu hg19 16 29998173 29998173 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TAOK2 NM_016151 exon16 c.C2580A p.S860R GAGGAGCATTGTT . 166.0 111.0 140.0 0.0 . 142 . . . none . . PASS Atlas-SNP HYDIN 54768 hgsc.bcm.edu hg19 16 71101222 71101222 + Silent SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . HYDIN NM_001198542 exon15 c.A2127G p.E709E CACCTCTTCTCCG . 58.0 16.0 44.0 0.0 . 788 . . . none . . PASS Atlas-SNP DNAAF1 123872 hgsc.bcm.edu hg19 16 84189316 84189316 + Missense_Mutation SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DNAAF1 NM_178452 exon5 c.C703T p.P235S AGTGACCCGGAGA . 130.0 28.0 95.0 0.0 . 81 . . . none . . PASS Atlas-SNP USP10 9100 hgsc.bcm.edu hg19 16 84778731 84778731 + Missense_Mutation SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . USP10 NM_001272075 exon5 c.C656T p.S219F AGAACTCCACAGA . 137.0 35.0 157.0 0.0 . 51 . . . none . . PASS Atlas-SNP ZNF469 84627 hgsc.bcm.edu hg19 16 88503562 88503562 + Silent SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF469 NM_001127464 exon2 c.G9600C p.L3200L CCTTCTGAACAGC . 114.0 31.0 120.0 0.0 . 121 . . . none . . PASS Atlas-SNP MYH4 4622 hgsc.bcm.edu hg19 17 10366192 10366192 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MYH4 NM_017533 exon11 c.T998A p.M333K GTGGCCATCAGCT . 94.0 36.0 65.0 0.0 . 349 . . . none . . PASS Atlas-SNP RNF112 7732 hgsc.bcm.edu hg19 17 19315946 19315946 + Nonsense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RNF112 NM_007148 exon3 c.C231A p.C77X CTTCTGCATACGG . 65.0 22.0 79.0 0.0 . 37 . . . none . . PASS Atlas-SNP SRCIN1 80725 hgsc.bcm.edu hg19 17 36708714 36708714 + Missense_Mutation SNP C C T rs370322301 TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 SRCIN1,NS,carcinoma,0,1 SRCIN1 NM_025248 exon13 c.G2449A p.G817R TGACCCCGCGGCA . 113.0 33.0 114.0 0.0 . 66 . . . weak . . PASS Atlas-SNP NBR1 4077 hgsc.bcm.edu hg19 17 41343586 41343586 + Missense_Mutation SNP C C G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . NBR1 NM_031862 exon10 c.C1061G p.S354C TCCAGTCTAATAC . 281.0 76.0 213.0 0.0 . 55 . . . none . . PASS Atlas-SNP MAP3K3 4215 hgsc.bcm.edu hg19 17 61767096 61767096 + Splice_Site SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MAP3K3 NM_203351 exon12 c.1156+1G>A . CCAAGTGTGAGGA . 99.0 20.0 108.0 0.0 . 56 . . . none . . PASS Atlas-SNP QRICH2 84074 hgsc.bcm.edu hg19 17 74288747 74288747 + Silent SNP C C T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . QRICH2 NM_032134 exon4 c.G1563A p.Q521Q GCCAGGCTGATAT . 90.0 5.0 87.0 0.0 . 143 . . . none . . PASS Atlas-SNP FSCN2 25794 hgsc.bcm.edu hg19 17 79503808 79503808 + Silent SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FSCN2 NM_001077182 exon4 c.G1338A p.R446R CTACCGGATCCGA . 441.0 128.0 368.0 0.0 . 35 . . . none . . PASS Atlas-SNP ROCK1 6093 hgsc.bcm.edu hg19 18 18624118 18624118 + Missense_Mutation SNP T T A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ROCK1 NM_005406 exon6 c.A620T p.D207V GATTTATCCAGCA . 108.0 29.0 81.0 0.0 . 162 . . . none . . PASS Atlas-SNP DCC 1630 hgsc.bcm.edu hg19 18 50589777 50589777 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DCC NM_005215 exon6 c.A1088C p.N363T CTGTGAATTGGAT . 143.0 76.0 113.0 0.0 . 360 . . . none . . PASS Atlas-SNP RAX 30062 hgsc.bcm.edu hg19 18 56936510 56936510 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RAX NM_013435 exon3 c.C767G p.A256G TGCAGCGCCGTGG . 77.0 50.0 59.0 0.0 . 19 . . . none . . PASS Atlas-SNP FSD1 79187 hgsc.bcm.edu hg19 19 4306010 4306010 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FSD1 NM_024333 exon2 c.C83A p.S28Y TCTACTCCCTGAA . 82.0 34.0 118.0 0.0 . 51 . . . none . . PASS Atlas-SNP CATSPERD 257062 hgsc.bcm.edu hg19 19 5739405 5739405 + Silent SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . . NM_152784 exon7 c.A528T p.S176S TTATTCAAATACT . 67.0 20.0 81.0 0.0 . . . . . none . . PASS Atlas-SNP MUC16 94025 hgsc.bcm.edu hg19 19 9068211 9068211 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MUC16 NM_024690 exon3 c.A19235G p.Q6412R GTGCCTTGGATGG . 146.0 6.0 165.0 0.0 . 4315 . . . none . . PASS Atlas-SNP IL12RB1 3594 hgsc.bcm.edu hg19 19 18180414 18180414 + Silent SNP G G A rs371543581 TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . IL12RB1 NM_005535 exon10 c.C1131T p.D377D GCCCCCGTCCTGG . 20.0 10.0 39.0 0.0 . 92 . . . weak . . PASS Atlas-SNP NCAN 1463 hgsc.bcm.edu hg19 19 19338444 19338444 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . NCAN NM_004386 exon8 c.C2015A p.A672D CCCCTGCTGCAGA . 46.0 19.0 71.0 0.0 . 277 . . . none . . PASS Atlas-SNP ZNF737 100129842 hgsc.bcm.edu hg19 19 20728068 20728068 + Missense_Mutation SNP T T G rs146757334 by1000genomes;alternate_allele TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF737 NM_001159293 exon4 c.A941C p.K314T TCACATTTGTAGG . 67.0 29.0 91.0 0.0 . 50 . . . alt T|0.998;C|0.002 . PASS Atlas-SNP RYR1 6261 hgsc.bcm.edu hg19 19 38949843 38949843 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RYR1 NM_001042723 exon19 c.T2225G p.V742G AAGACGTGATCAG . 51.0 17.0 62.0 0.0 . 708 . . . none . . PASS Atlas-SNP SUPT5H 6829 hgsc.bcm.edu hg19 19 39964953 39964953 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SUPT5H NM_003169 exon26 c.T2731C p.Y911H CAGAGCTACCACC . 168.0 59.0 282.0 0.0 . 119 . . . none . . PASS Atlas-SNP ZNF324B 388569 hgsc.bcm.edu hg19 19 58966867 58966867 + Missense_Mutation SNP G G T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF324B NM_207395 exon4 c.G556T p.G186W GTGCCTGGGAGGC . 51.0 24.0 89.0 0.0 . 58 . . . none . . PASS Atlas-SNP ZNFX1 57169 hgsc.bcm.edu hg19 20 47865692 47865692 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNFX1 NM_021035 exon14 c.T3869A p.L1290Q CAGGGCAGGCTGC . 145.0 86.0 125.0 0.0 . 194 . . . none . . PASS Atlas-SNP SLC9A8 23315 hgsc.bcm.edu hg19 20 48429466 48429466 + Missense_Mutation SNP G G C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SLC9A8 NM_001260491 exon1 c.G7C p.E3Q ATGGGGGAGAAGA . 29.0 19.0 29.0 0.0 . 63 . . . none . . PASS Atlas-SNP CTCFL 140690 hgsc.bcm.edu hg19 20 56099187 56099187 + Silent SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 .,1 CTCFL NM_001269044 exon1 c.A75G p.K25K CAGGCCTTTTTCC . 54.0 3.0 49.0 0.0 . 97 . . . none . . PASS Atlas-SNP DONSON 29980 hgsc.bcm.edu hg19 21 34951869 34951869 + Splice_Site SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . DONSON NM_017613 exon10 c.1351-1G>T . CCGTGCCTTCATG . 66.0 26.0 116.0 0.0 . 34 . . . none . . PASS Atlas-SNP NIPSNAP1 8508 hgsc.bcm.edu hg19 22 29957632 29957632 + Missense_Mutation SNP A A T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . NIPSNAP1 NM_003634 exon6 c.T442A p.Y148N CCAGGTACTCCTG . 30.0 19.0 49.0 0.0 . 17 . . . none . . PASS Atlas-SNP SMTN 6525 hgsc.bcm.edu hg19 22 31486118 31486118 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SMTN NM_001207018 exon7 c.C985A p.P329T GAGACCCCTGCTG . 101.0 37.0 152.0 0.0 . 219 . . . none . . PASS Atlas-SNP PKDREJ 10343 hgsc.bcm.edu hg19 22 46656408 46656408 + Missense_Mutation SNP C C A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PKDREJ NM_006071 exon1 c.G2812T p.D938Y CGTTATCTGCAAC . 89.0 4.0 128.0 0.0 . 195 . . . none . . PASS Atlas-SNP TBC1D22A 25771 hgsc.bcm.edu hg19 22 47290719 47290719 + Missense_Mutation SNP A A C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TBC1D22A NM_014346 exon7 c.A877C p.I293L GCGTTGATCCTGC . 76.0 26.0 105.0 0.0 . 54 . . . none . . PASS Atlas-SNP KDM6A 7403 hgsc.bcm.edu hg19 X 44937747 44937747 + Missense_Mutation SNP T T G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . KDM6A NM_021140 exon19 c.T2935G p.L979V CTTAAGTTAGGTA . 340.0 283.0 437.0 0.0 . 274 . . . none . . PASS Atlas-SNP HDAC6 10013 hgsc.bcm.edu hg19 X 48661330 48661330 + Missense_Mutation SNP A A G novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . HDAC6 NM_006044 exon3 c.A146G p.E49G TAGCGGAGGTAAA . 149.0 120.0 202.0 0.0 . 111 . . . none . . PASS Atlas-SNP AMER1 139285 hgsc.bcm.edu hg19 X 63412149 63412149 + Missense_Mutation SNP T T C novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . . NM_152424 exon2 c.A1018G p.M340V CTGTCATACTGTC . 27.0 27.0 53.0 0.0 . . . . . none . . PASS Atlas-SNP ND4 0 hgsc.bcm.edu hg19 MT 11126 11126 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . . ENST00000361381 exon1 c.G367A p.E123K TTCTTCGAAACCA . 73.0 29.0 39.0 0.0 . . . . . none . . PASS Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 12838 12838 + Missense_Mutation SNP G G A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . . ENST00000361567 exon1 c.G502A p.A168T ACAGCAGCCATTC . 63.0 16.0 30.0 0.0 . . . . . none . . PASS Atlas-SNP PPOX 5498 hgsc.bcm.edu hg19 1 161140540 161140541 + Frame_Shift_Ins INS - - CTTGGTCCATCTA novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PPOX NM_001122764 exon11 c.1229_1230insCTTGGTCCATCTA p.C410fs . . 60.0 10.0 78.0 0.0 . 34 . 0.166667 0 none . . PASS Atlas-Indel,Pindel PYROXD2 84795 hgsc.bcm.edu hg19 10 100152221 100152222 + Frame_Shift_Ins INS - - T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PYROXD2 NM_032709 exon10 c.1030_1031insA p.P344fs . . 67.0 45.0 60.0 0.0 . 43 . 0.671642 0 none . . PASS Atlas-Indel,Pindel MYO1B 4430 hgsc.bcm.edu hg19 2 192206229 192206230 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . MYO1B NM_012223 exon5 c.389_390insA p.G130fs . . 86.0 32.0 154.0 0.0 . 160 . 0.372093 0 none . . PASS Atlas-Indel,Pindel PALB2 79728 hgsc.bcm.edu hg19 16 23641617 23641624 + Frame_Shift_Del DEL CAAAGTCT CAAAGTCT - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 CAAAGTCT CAAAGTCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . PALB2 NM_024675 exon5 c.1852_1859del p.618_620del . . 201.0 102.0 207.0 0.0 . 108 . 0.507463 0 none . . PASS Atlas-Indel,Pindel ZNF490 57474 hgsc.bcm.edu hg19 19 12693708 12693709 + Frame_Shift_Ins INS - - T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZNF490 NM_020714 exon4 c.306_307insA p.D102fs . . 79.0 32.0 108.0 0.0 . 42 . 0.405063 0 none . . PASS Atlas-Indel,Pindel SLC23A1 9963 hgsc.bcm.edu hg19 5 138716053 138716054 + Frame_Shift_Ins INS - - T novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SLC23A1 NM_152685 exon6 c.503_504insA p.S168fs . . 94.0 33.0 110.0 0.0 . 51 . 0.351064 0 none . . PASS Atlas-Indel,Pindel ANKIB1 54467 hgsc.bcm.edu hg19 7 92021609 92021609 + Splice_Site DEL A A - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ANKIB1 NM_019004 exon17 c.2283+2A>- . . . 200.0 74.0 127.0 0.0 . 92 . 0.37 0 none . . PASS Atlas-Indel,Pindel ZBTB25 7597 hgsc.bcm.edu hg19 14 64957106 64957106 + Frame_Shift_Del DEL A A - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZBTB25 NM_006977 exon2 c.147delC p.F49fs . . 285.0 113.0 364.0 0.0 . 27 . 0.396491 0 none . . PASS Atlas-Indel,Pindel JHDM1D 80853 hgsc.bcm.edu hg19 7 139818990 139818990 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . JHDM1D NM_030647 exon9 c.1170delA p.T390fs . . 221.0 95.0 128.0 0.0 . 54 . 0.429864 0 none . . PASS Atlas-Indel,Pindel APBA2 321 hgsc.bcm.edu hg19 15 29346965 29346966 + Frame_Shift_Ins INS - - CT novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . APBA2 NM_005503 exon3 c.878_879insCT p.P293fs . . 26.0 10.0 32.0 0.0 . 132 . 0.384615 0 none . . PASS Atlas-INDEL ELL2 22936 hgsc.bcm.edu hg19 5 95234239 95234240 + Frame_Shift_Ins INS - - AGGTCTTG novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ELL2 NM_012081 exon8 c.1230_1231insCAAGACCT p.L410fs . . 137.0 32.0 170.0 0.0 . 63 . 0.233577 0 none . . PASS Atlas-Indel,Pindel IGSF22 283284 hgsc.bcm.edu hg19 11 18738437 18738444 + Frame_Shift_Del DEL ACTTCCAC ACTTCCAC - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 ACTTCCAC ACTTCCAC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . IGSF22 NM_173588 exon10 c.1078_1085del p.360_362del . . 101.0 23.0 159.0 0.0 . 211 . 0.227723 0 none . . PASS Atlas-Indel,Pindel FAM71F2 346653 hgsc.bcm.edu hg19 7 128315824 128315824 + Frame_Shift_Del DEL T T - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FAM71F2 NM_001012454 exon2 c.275delA p.N92fs . . 69.0 34.0 50.0 0.0 . 19 . 0.492754 0 none . . PASS Atlas-INDEL ZFC3H1 196441 hgsc.bcm.edu hg19 12 72017305 72017306 + Frame_Shift_Ins INS - - CCATG novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . ZFC3H1 NM_144982 exon24 c.4579_4580insCATGG p.L1527fs . . 204.0 77.0 106.0 0.0 . 172 . 0.377451 0 none . . PASS Atlas-Indel,Pindel CREB3 10488 hgsc.bcm.edu hg19 9 35736483 35736484 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . CREB3 NM_006368 exon9 c.876_877insA p.H292fs . . 44.0 19.0 77.0 0.0 . 24 . 0.431818 0 none . . PASS Atlas-Indel,Pindel HIC2 23119 hgsc.bcm.edu hg19 22 21799452 21799458 + Frame_Shift_Del DEL TCCACAG TCCACAG - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 TCCACAG TCCACAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . HIC2 NM_015094 exon3 c.267_273del p.89_91del . . 40.0 11.0 72.0 0.0 . 42 . 0.275 0 none . . PASS Atlas-INDEL KRT19 3880 hgsc.bcm.edu hg19 17 39684113 39684113 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . KRT19 NM_002276 exon1 c.388delT p.Y130fs . . 76.0 28.0 93.0 0.0 . 41 . 0.368421 0 none . . PASS Atlas-Indel,Pindel RNF123 63891 hgsc.bcm.edu hg19 3 49740161 49740162 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . RNF123 NM_022064 exon20 c.1725_1726insA p.S575fs . . 68.0 14.0 65.0 0.0 . 100 . 0.205882 0 none . . PASS Atlas-Indel,Pindel TNRC18 84629 hgsc.bcm.edu hg19 7 5352663 5352665 + In_Frame_Del DEL GAT GAT - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 GAT GAT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . TNRC18 NM_001080495 exon27 c.7858_7860del p.2620_2620del . . 18.0 11.0 8.0 0.0 . 311 . 0.611111 0 none . . PASS Atlas-INDEL FAM71F2 346653 hgsc.bcm.edu hg19 7 128315818 128315818 + Frame_Shift_Del DEL C C - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . FAM71F2 NM_001012454 exon2 c.269delT p.L90fs . . 65.0 10.0 52.0 0.0 . 19 . 0.154 . none . . PASS Pindel COL4A3 1285 hgsc.bcm.edu hg19 2 228176530 228176530 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . COL4A3 NM_000091 exon52 c.4956delT p.A1652fs . . 502.0 112.0 642.0 0.0 . 293 . 0.223 . none . . PASS Pindel SPTLC1 10558 hgsc.bcm.edu hg19 9 94821586 94821604 + In_Frame_Del DEL TATCTCTGCAAGGAAAAGA TATCTCTGCAAGGAAAAGA - novel TCGA-SX-A7SS-01A-11D-A35Z-10 TCGA-SX-A7SS-10A-01D-A35Z-10 TATCTCTGCAAGGAAAAGA TATCTCTGCAAGGAAAAGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 8a5b9c2f-52f8-4f4c-864e-288f4a31f85f b78095c0-dd7d-406b-9d5c-0e0a56f03118 . SPTLC1 NM_006415 exon7 c.561_566del p.187_189del . . 52.0 10.0 82.0 0.0 . 42 . 0.192 . none . . PASS Pindel