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 ATP13A2 23400 hgsc.bcm.edu hg19 1 17322884 17322884 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ATP13A2 NM_022089 exon13 c.C1303A p.L435M CACCCAGGACAGA . 90.0 35.0 97.0 0.0 . 85 . . . none . . PASS Atlas-SNP CACNA1S 779 hgsc.bcm.edu hg19 1 201030589 201030589 + Missense_Mutation SNP A A G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CACNA1S NM_000069 exon25 c.T3061C p.Y1021H CCTTGTACAGCAG . 83.0 17.0 54.0 0.0 . 249 . . . none . . PASS Atlas-SNP NAV1 89796 hgsc.bcm.edu hg19 1 201781618 201781618 + Nonsense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NAV1 NM_020443 exon27 c.G5050T p.E1684X AACGTGGAGCCAG . 182.0 84.0 107.0 0.0 . 143 . . . none . . PASS Atlas-SNP PLEKHA6 22874 hgsc.bcm.edu hg19 1 204236626 204236626 + Missense_Mutation SNP T T A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PLEKHA6 NM_014935 exon5 c.A257T p.D86V CAGCGATCCACCA . 125.0 40.0 73.0 0.0 . 115 . . . none . . PASS Atlas-SNP KIAA1804 0 hgsc.bcm.edu hg19 1 233518317 233518317 + Missense_Mutation SNP A A G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . KIAA1804 NM_032435 exon10 c.A2971G p.R991G AAGGAGAGAACTA . 149.0 39.0 94.0 0.0 . 129 . . . none . . PASS Atlas-SNP TBCE 6905 hgsc.bcm.edu hg19 1 235599915 235599915 + Missense_Mutation SNP A A C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . TBCE NM_003193 exon11 c.A955C p.I319L AATCAGATATCAC . 158.0 34.0 126.0 0.0 . 40 . . . none . . PASS Atlas-SNP TFCP2L1 29842 hgsc.bcm.edu hg19 2 121991738 121991738 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . TFCP2L1 NM_014553 exon12 c.G1127A p.C376Y TCCTGACAGACAT . 87.0 32.0 90.0 0.0 . 54 . . . none . . PASS Atlas-SNP CNPPD1 27013 hgsc.bcm.edu hg19 2 220039577 220039577 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CNPPD1 NM_015680 exon5 c.A433C p.N145H CGTCGTTGAAGAC . 91.0 31.0 77.0 0.0 . 22 . . . none . . PASS Atlas-SNP AGXT 189 hgsc.bcm.edu hg19 2 241808770 241808770 + Missense_Mutation SNP G G A rs180177208 alternate_allele TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . AGXT NM_000030 exon2 c.G349A p.E117K ATCGGGGAGCGCA . 87.0 32.0 82.0 0.0 . 50 . . . alt . . PASS Atlas-SNP PASK 23178 hgsc.bcm.edu hg19 2 242065794 242065794 + Missense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PASK NM_015148 exon10 c.C2536T p.H846Y GAACGTGTCCTGG . 165.0 59.0 132.0 0.0 . 230 . . . none . . PASS Atlas-SNP ZNF502 91392 hgsc.bcm.edu hg19 3 44763320 44763320 + Missense_Mutation SNP C C G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ZNF502 NM_001134440 exon4 c.C1011G p.N337K GGCAAACCTCTCT . 117.0 79.0 124.0 0.0 . 58 . . . none . . PASS Atlas-SNP NBEAL2 23218 hgsc.bcm.edu hg19 3 47032943 47032943 + Silent SNP G G T rs181297174 bycluster;by1000genomes;alternate_allele TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NBEAL2 NM_015175 exon8 c.G690T p.L230L CCTGCTGAGTGTG . 29.0 22.0 20.0 0.0 . 267 . . . alt G|1.000;C|0.000 . PASS Atlas-SNP SETD2 29072 hgsc.bcm.edu hg19 3 47143047 47143047 + Splice_Site SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 SETD2_ENST00000409792,NS,carcinoma,0,2 SETD2 NM_014159 exon9 c.4918-2A>G . GTCCACTGAGATG . 139.0 102.0 115.0 0.0 . 721 . . . none . . PASS Atlas-SNP NPHP3 27031 hgsc.bcm.edu hg19 3 132410108 132410108 + Missense_Mutation SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NPHP3 NM_153240 exon18 c.A2498G p.E833G AGGTACTCCAATC . 308.0 175.0 251.0 0.0 . 110 . . . none . . PASS Atlas-SNP STX18 53407 hgsc.bcm.edu hg19 4 4436571 4436571 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . STX18 NM_016930 exon7 c.G628A p.E210K GTGTTTCAGCCAA . 71.0 18.0 88.0 0.0 . 16 . . . none . . PASS Atlas-SNP YTHDC1 91746 hgsc.bcm.edu hg19 4 69185877 69185877 + Missense_Mutation SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . YTHDC1 NM_001031732 exon12 c.A1648G p.R550G CAATCCTTGGTTT . 81.0 25.0 113.0 0.0 . 81 . . . none . . PASS Atlas-SNP ELOVL6 79071 hgsc.bcm.edu hg19 4 111119479 111119479 + Missense_Mutation SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ELOVL6 NM_001130721 exon2 c.G13T p.V5L TCAACACTGACAT . 147.0 45.0 204.0 0.0 . 27 . . . none . . PASS Atlas-SNP INPP4B 8821 hgsc.bcm.edu hg19 4 143181690 143181690 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 INPP4B,NS,carcinoma,0,1 INPP4B NM_003866 exon12 c.C643A p.P215T TTTCCGGGGCTGT . 52.0 16.0 47.0 0.0 . 132 . . . none . . PASS Atlas-SNP TIGD4 201798 hgsc.bcm.edu hg19 4 153691640 153691640 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . TIGD4 NM_145720 exon2 c.G517A p.D173N GATAATCATTTAA . 56.0 18.0 87.0 0.0 . 53 . . . none . . PASS Atlas-SNP SORBS2 8470 hgsc.bcm.edu hg19 4 186545113 186545113 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . SORBS2 NM_001270771 exon16 c.C1758T p.H586H GTCCTTGTGCTGC . 117.0 49.0 106.0 0.0 . 300 . . . none . . PASS Atlas-SNP SORBS2 8470 hgsc.bcm.edu hg19 4 186545114 186545114 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . SORBS2 NM_001270771 exon16 c.A1757C p.H586P TCCTTGTGCTGCT . 114.0 49.0 108.0 0.0 . 300 . . . none . . PASS Atlas-SNP MROH2B 133558 hgsc.bcm.edu hg19 5 41048530 41048530 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . . NM_173489 exon16 c.G1580A p.G527E CCAGCCCCACGTA . 58.0 31.0 63.0 0.0 . . . . . none . . PASS Atlas-SNP KLHL3 26249 hgsc.bcm.edu hg19 5 136975648 136975648 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . KLHL3 NM_017415 exon9 c.G922A p.G308S CCTGGCCGCCAAC . 90.0 20.0 78.0 0.0 . 54 . . . none . . PASS Atlas-SNP FAM13B 51306 hgsc.bcm.edu hg19 5 137289855 137289855 + Missense_Mutation SNP C C G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . FAM13B NM_001101800 exon14 c.G1652C p.R551T ATATACCTAGTAA . 77.0 17.0 64.0 0.0 . 46 . . . none . . PASS Atlas-SNP GABRA1 2554 hgsc.bcm.edu hg19 5 161281260 161281260 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . GABRA1 NM_001127643 exon4 c.G171A p.L57L TCGCCTGAGACCA . 112.0 23.0 73.0 0.0 . 132 . . . none . . PASS Atlas-SNP TNXB 7148 hgsc.bcm.edu hg19 6 32049190 32049190 + Missense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 TNXB_ENST00000375247,NS,carcinoma,0,2 TNXB NM_019105 exon10 c.C3997T p.R1333C TGCCACGAAGCCC . 8.0 5.0 5.0 0.0 . 553 . . . none . . PASS Atlas-SNP SCUBE3 222663 hgsc.bcm.edu hg19 6 35213120 35213120 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . SCUBE3 NM_152753 exon19 c.G2517A p.K839K ACCCAAGCGCAAG . 122.0 39.0 117.0 0.0 . 99 . . . none . . PASS Atlas-SNP PEX6 5190 hgsc.bcm.edu hg19 6 42932546 42932546 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PEX6 NM_000287 exon16 c.G2788A p.V930I CATGAACCCTGCG . 148.0 54.0 143.0 0.0 . 44 . . . none . . PASS Atlas-SNP PKHD1 5314 hgsc.bcm.edu hg19 6 51882414 51882414 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PKHD1 NM_170724 exon34 c.C5394T p.F1798F ACACAGGAAGGCC . 103.0 42.0 102.0 0.0 . 927 . . . none . . PASS Atlas-SNP ENPP1 5167 hgsc.bcm.edu hg19 6 132206107 132206107 + Missense_Mutation SNP A A C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ENPP1 NM_006208 exon23 c.A2348C p.K783T TGCGAAAGTATGC . 96.0 34.0 84.0 0.0 . 108 . . . none . . PASS Atlas-SNP TNFAIP3 7128 hgsc.bcm.edu hg19 6 138200458 138200458 + Missense_Mutation SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 .,1 TNFAIP3 NM_001270507 exon7 c.C1876A p.L626M TGCACACTGTGTT . 52.0 32.0 85.0 0.0 . 340 . . . none . . PASS Atlas-SNP LRWD1 222229 hgsc.bcm.edu hg19 7 102110042 102110042 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . LRWD1 NM_152892 exon10 c.T1250G p.I417S AGCGGATCATCCT . 127.0 26.0 143.0 0.0 . 41 . . . none . . PASS Atlas-SNP LRWD1 222229 hgsc.bcm.edu hg19 7 102110043 102110043 + Silent SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . LRWD1 NM_152892 exon10 c.C1251A p.I417I GCGGATCATCCTC . 127.0 27.0 144.0 0.0 . 41 . . . none . . PASS Atlas-SNP CSMD1 64478 hgsc.bcm.edu hg19 8 3216707 3216707 + Missense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CSMD1 NM_033225 exon21 c.C3271T p.R1091C ACACACGGCGGCC . 120.0 33.0 117.0 0.0 . 1469 . . . none . . PASS Atlas-SNP ADAM7 8756 hgsc.bcm.edu hg19 8 24357759 24357759 + Missense_Mutation SNP A A C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ADAM7 NM_003817 exon18 c.A1992C p.L664F AACCTTACATGTT . 66.0 26.0 43.0 0.0 . 165 . . . none . . PASS Atlas-SNP ADAM7 8756 hgsc.bcm.edu hg19 8 24357760 24357760 + Missense_Mutation SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ADAM7 NM_003817 exon18 c.C1993A p.H665N ACCTTACATGTTA . 68.0 26.0 43.0 0.0 . 165 . . . none . . PASS Atlas-SNP SPATA31D1 389763 hgsc.bcm.edu hg19 9 84608073 84608073 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . . NM_001001670 exon4 c.T2688G p.S896R CCTTAGTTCCAAC . 66.0 26.0 56.0 0.0 . . . . . none . . PASS Atlas-SNP TXN 7295 hgsc.bcm.edu hg19 9 113013695 113013695 + Silent SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . TXN NM_001244938 exon2 c.A72G p.V24V GTCAACTACTACA . 46.0 12.0 41.0 0.0 . 6 . . . none . . PASS Atlas-SNP MVB12B 89853 hgsc.bcm.edu hg19 9 129143362 129143362 + Missense_Mutation SNP G G C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . . NM_001011703 exon3 c.G224C p.G75A CAGATGGTGTGGA . 93.0 28.0 103.0 0.0 . . . . . none . . PASS Atlas-SNP CYP2C18 1562 hgsc.bcm.edu hg19 10 96443672 96443672 + Silent SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CYP2C18 NM_000772 exon1 c.C96A p.G32G GTCTGGCCCCACT . 78.0 9.0 52.0 0.0 . 79 . . . none . . PASS Atlas-SNP DMBT1 1755 hgsc.bcm.edu hg19 10 124351862 124351862 + Silent SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . DMBT1 NM_007329 exon20 c.C2251A p.R751R CTATACCGAGGCT . 437.0 141.0 397.0 1.0 . 677 . . . none . . PASS Atlas-SNP CD81 975 hgsc.bcm.edu hg19 11 2417109 2417109 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CD81 NM_004356 exon6 c.G470T p.C157F ACTGCTGTGGCTC . 75.0 32.0 70.0 0.0 . 11 . . . none . . PASS Atlas-SNP NELL1 4745 hgsc.bcm.edu hg19 11 21581738 21581738 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NELL1 NM_006157 exon17 c.T1790G p.I597S CAGACATTGATGA . 144.0 60.0 181.0 0.0 . 179 . . . none . . PASS Atlas-SNP SLC5A12 159963 hgsc.bcm.edu hg19 11 26742996 26742996 + Missense_Mutation SNP A A T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . SLC5A12 NM_178498 exon1 c.T266A p.L89Q ACAAATAGGTAAG . 66.0 28.0 81.0 0.0 . 134 . . . none . . PASS Atlas-SNP FLRT1 23769 hgsc.bcm.edu hg19 11 63884401 63884401 + Missense_Mutation SNP T T A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . FLRT1 NM_013280 exon2 c.T662A p.L221H AGGGCCTCAACAG . 44.0 13.0 50.0 0.0 . 46 . . . none . . PASS Atlas-SNP PITPNM1 9600 hgsc.bcm.edu hg19 11 67265787 67265787 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PITPNM1 NM_001130848 exon11 c.C1491T p.S497S GTAAGGGCTCAGG . 23.0 8.0 24.0 0.0 . 84 . . . none . . PASS Atlas-SNP WNK1 65125 hgsc.bcm.edu hg19 12 977170 977170 + Missense_Mutation SNP C C T rs200794710 bycluster TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . WNK1 NM_213655 exon10 c.C2533T p.R845C CAGCGGCGTAAGA . 148.0 7.0 101.0 0.0 . 403 . . . weak . . PASS Atlas-SNP KCNC2 3747 hgsc.bcm.edu hg19 12 75441966 75441966 + Missense_Mutation SNP A A C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . KCNC2 NM_139137 exon4 c.T1747G p.Y583D ACGTGTAATCACC . 286.0 108.0 284.0 0.0 . 239 . . . none . . PASS Atlas-SNP NUAK1 9891 hgsc.bcm.edu hg19 12 106460987 106460987 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NUAK1 NM_014840 exon7 c.C1579A p.H527N TGCTGTGTTTCAA . 121.0 53.0 113.0 0.0 . 196 . . . none . . PASS Atlas-SNP RNF17 56163 hgsc.bcm.edu hg19 13 25352542 25352542 + Silent SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . RNF17 NM_001184993 exon4 c.T427C p.L143L GTAATGTTGGTAT . 197.0 60.0 171.0 0.0 . 259 . . . none . . PASS Atlas-SNP CSPG4 1464 hgsc.bcm.edu hg19 15 75981607 75981607 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CSPG4 NM_001897 exon3 c.G1799A p.G600D GGGAGGCCAGAGG . 49.0 23.0 47.0 0.0 . 175 . . . none . . PASS Atlas-SNP MCTP2 55784 hgsc.bcm.edu hg19 15 94884070 94884070 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . MCTP2 NM_001159643 exon6 c.G886T p.D296Y CTGGAAGATCCAA . 56.0 25.0 63.0 0.0 . 122 . . . none . . PASS Atlas-SNP PRSS21 10942 hgsc.bcm.edu hg19 16 2868724 2868724 + Missense_Mutation SNP C C G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PRSS21 NM_144957 exon4 c.C304G p.Q102E TTTGGCCAGCTGA . 184.0 35.0 98.0 0.0 . 32 . . . none . . PASS Atlas-SNP ZNF597 146434 hgsc.bcm.edu hg19 16 3487524 3487524 + Missense_Mutation SNP G G C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 ZNF597,NS,malignant_melanoma,0,1 ZNF597 NM_152457 exon4 c.C175G p.P59A TCTCAGGCTTGCC . 145.0 91.0 82.0 0.0 . 41 . . . none . . PASS Atlas-SNP USP31 57478 hgsc.bcm.edu hg19 16 23083424 23083424 + Silent SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . USP31 NM_020718 exon15 c.C2430A p.T810T CAGGGAGGTGCGT . 232.0 20.0 134.0 0.0 . 122 . . . none . . PASS Atlas-SNP NUP93 9688 hgsc.bcm.edu hg19 16 56792502 56792502 + Silent SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . NUP93 NM_014669 exon3 c.T232C p.L78L CAGCGATTGGAGA . 98.0 37.0 112.0 0.0 . 75 . . . none . . PASS Atlas-SNP COG8 84342 hgsc.bcm.edu hg19 16 69368791 69368791 + Missense_Mutation SNP C C G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . COG8 NM_032382 exon3 c.G1046C p.C349S TACATGCACTGGC . 93.0 34.0 103.0 0.0 . 32 . . . none . . PASS Atlas-SNP ZNF778 197320 hgsc.bcm.edu hg19 16 89294017 89294017 + Nonsense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ZNF778 NM_001201407 exon7 c.C1321T p.R441X CACGTACGAACAC . 80.0 23.0 71.0 0.0 . 67 . . . none . . PASS Atlas-SNP DEF8 54849 hgsc.bcm.edu hg19 16 90015887 90015887 + Missense_Mutation SNP C C A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . DEF8 NM_207514 exon2 c.C14A p.S5Y TCCTGTCCCTGCG . 90.0 31.0 86.0 0.0 . 28 . . . none . . PASS Atlas-SNP KDM6B 23135 hgsc.bcm.edu hg19 17 7755372 7755372 + Silent SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . KDM6B NM_001080424 exon18 c.T4269G p.A1423A CAGCGCTTTCTGT . 63.0 19.0 57.0 0.0 . 95 . . . none . . PASS Atlas-SNP ABCA9 10350 hgsc.bcm.edu hg19 17 66981100 66981100 + Silent SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ABCA9 NM_080283 exon34 c.C4305T p.I1435I CCCCAGGATGCTC . 174.0 31.0 116.0 0.0 . 192 . . . none . . PASS Atlas-SNP ABCA10 10349 hgsc.bcm.edu hg19 17 67170778 67170778 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ABCA10 NM_080282 exon25 c.C3018A p.F1006L AAGCTGGAATCCC . 231.0 71.0 143.0 0.0 . 209 . . . none . . PASS Atlas-SNP FASN 2194 hgsc.bcm.edu hg19 17 80050833 80050833 + Missense_Mutation SNP G G A rs200752265 alternate_allele TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . FASN NM_004104 exon6 c.C718T p.R240W CCCGCCGGGCCAG . 37.0 12.0 24.0 0.0 . 154 . . . alt G|0.998;T|0.002 . PASS Atlas-SNP MED16 10025 hgsc.bcm.edu hg19 19 879943 879943 + Missense_Mutation SNP G G C rs76403059 bycluster TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 MED16,colon,carcinoma,0,1 MED16 NM_005481 exon8 c.C1347G p.H449Q CTTCCCGTGGCTG . 19.0 2.0 15.0 1.0 . 61 . . . weak . . PASS Atlas-SNP CD97 976 hgsc.bcm.edu hg19 19 14513447 14513447 + Missense_Mutation SNP A A G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . CD97 NM_078481 exon12 c.A1222G p.T408A AACATGACGACAT . 91.0 4.0 121.0 0.0 . 86 . . . none . . PASS Atlas-SNP PPP1R15A 23645 hgsc.bcm.edu hg19 19 49379135 49379135 + Missense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PPP1R15A NM_014330 exon3 c.G1930A p.V644I TCCCCAGTCCAGA . 284.0 91.0 247.0 0.0 . 48 . . . none . . PASS Atlas-SNP ZNF773 374928 hgsc.bcm.edu hg19 19 58018434 58018434 + Missense_Mutation SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . ZNF773 NM_198542 exon4 c.T971C p.V324A AGAGAGTTCACAC . 200.0 47.0 219.0 0.0 . 62 . . . none . . PASS Atlas-SNP PLCB1 23236 hgsc.bcm.edu hg19 20 8741054 8741054 + Missense_Mutation SNP G G T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PLCB1 NM_015192 exon25 c.A2657T p.Q886L TTACAGGTTCTGT . 69.0 21.0 71.0 0.0 . 394 . . . none . . PASS Atlas-SNP KCNS1 3787 hgsc.bcm.edu hg19 20 43726464 43726464 + Missense_Mutation SNP A A T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . KCNS1 NM_002251 exon4 c.T949A p.Y317N TGAGATAGAAGGG . 29.0 16.0 32.0 0.0 . 30 . . . none . . PASS Atlas-SNP WFDC2 10406 hgsc.bcm.edu hg19 20 44108666 44108666 + Missense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . WFDC2 NM_006103 exon3 c.G308A p.C103Y GCCAGTGTCCTGG . 181.0 74.0 217.0 0.0 . 8 . . . none . . PASS Atlas-SNP DNTTIP1 116092 hgsc.bcm.edu hg19 20 44424050 44424050 + Missense_Mutation SNP A A G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . DNTTIP1 NM_052951 exon4 c.A340G p.I114V CAGCTGATCCAGG . 18.0 7.0 29.0 0.0 . 23 . . . none . . PASS Atlas-SNP PSMA7 5688 hgsc.bcm.edu hg19 20 60714841 60714841 + Missense_Mutation SNP T T G novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PSMA7 NM_002792 exon3 c.A344C p.K115T ACCTGCTTCAGAC . 64.0 21.0 59.0 0.0 . 13 . . . none . . PASS Atlas-SNP PRPF6 24148 hgsc.bcm.edu hg19 20 62642772 62642772 + Silent SNP G G C rs199552405 by1000genomes;alternate_allele TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PRPF6 NM_012469 exon11 c.G1440C p.T480T GAACACGCAGATG . 46.0 12.0 52.0 0.0 . 88 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP SON 6651 hgsc.bcm.edu hg19 21 34925625 34925625 + Missense_Mutation SNP C C T novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . SON NM_032195 exon3 c.C4088T p.S1363L AGTCTTCGGCTGT . 68.0 17.0 54.0 0.0 . 343 . . . none . . PASS Atlas-SNP STAG2 10735 hgsc.bcm.edu hg19 X 123200037 123200037 + Silent SNP T T C novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . STAG2 NM_001042749 exon22 c.T2109C p.L703L TGACCTTTCAAAG . 65.0 44.0 76.0 0.0 . 309 . . . none . . PASS Atlas-SNP ND4 0 hgsc.bcm.edu hg19 MT 10971 10971 + Nonsense_Mutation SNP G G A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . . ENST00000361381 exon1 c.G212A p.W71X CTACCTGACTCCT . 141.0 127.0 51.0 0.0 . . . . . none . . PASS Atlas-SNP PBRM1 55193 hgsc.bcm.edu hg19 3 52696272 52696272 + Frame_Shift_Del DEL T T - novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . PBRM1 NM_018313 exon5 c.406delG p.A136fs . . 91.0 61.0 149.0 0.0 . 1252 . 0.67033 0 none . . PASS Atlas-INDEL HOXA2 3199 hgsc.bcm.edu hg19 7 27140389 27140390 + Frame_Shift_Ins INS - - A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . HOXA2 NM_006735 exon2 c.1087_1088insT p.T363fs . . 177.0 23.0 177.0 0.0 . 56 . 0.129944 0 none . . PASS Atlas-INDEL COL14A1 7373 hgsc.bcm.edu hg19 8 121219275 121219276 + Frame_Shift_Ins INS - - A novel TCGA-BQ-5890-01A-11D-1589-08 TCGA-BQ-5890-11A-01D-1589-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c6938c32-20f1-4d04-9939-0c3d217b7c81 7d6403bb-f48a-43e1-9a32-feb3bb9de789 . COL14A1 NM_021110 exon10 c.1133_1134insA p.G378fs . . 59.0 19.0 49.0 0.0 . 292 . 0.322034 0 none . . PASS Atlas-INDEL