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 dbSNP_AF Algorithm C1orf111 284680 hgsc.bcm.edu hg19 1 162343882 162343882 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . C1orf111 NM_182581 exon3 c.G742A p.E248K GGTGTTCAGCAGG . 117.0 28.0 108.0 0.0 . 26 . . Atlas-SNP LYST 1130 hgsc.bcm.edu hg19 1 235955200 235955200 + Missense_Mutation SNP G G C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . LYST NM_000081 exon12 c.C4342G p.L1448V ATGAAAGCAGCCG . 164.0 30.0 137.0 0.0 . 370 . . Atlas-SNP GPR137B 7107 hgsc.bcm.edu hg19 1 236306038 236306038 + Missense_Mutation SNP C C A rs199613305 alternate_allele TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . GPR137B NM_003272 exon1 c.C116A p.P39H TGCCCCCCTACGT . 104.0 31.0 67.0 0.0 . 57 . C|0.999;T|0.001 Atlas-SNP RYR2 6262 hgsc.bcm.edu hg19 1 237774131 237774131 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . RYR2 NM_001035 exon36 c.C4753T p.R1585C CCCCCGCGCCTCC . 133.0 55.0 135.0 0.0 . 1273 . . Atlas-SNP APOB 338 hgsc.bcm.edu hg19 2 21229749 21229749 + Missense_Mutation SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . APOB NM_000384 exon26 c.A9991G p.I3331V CAGGAATAAAAAT . 147.0 55.0 229.0 0.0 . 761 . . Atlas-SNP AGBL5 60509 hgsc.bcm.edu hg19 2 27282078 27282078 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . AGBL5 NM_021831 exon11 c.C1895A p.S632Y CCTGCTCCGAAAA . 152.0 68.0 235.0 0.0 . 126 . . Atlas-SNP EML6 400954 hgsc.bcm.edu hg19 2 55185121 55185121 + Missense_Mutation SNP G G T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . EML6 NM_001039753 exon32 c.G4681T p.V1561L CTCTCCGTGGCCT . 30.0 11.0 52.0 0.0 . 85 . . Atlas-SNP SULT1C3 442038 hgsc.bcm.edu hg19 2 108872149 108872149 + Missense_Mutation SNP G G C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 SULT1C3,NS,carcinoma,0,1 SULT1C3 NM_001008743 exon4 c.G521C p.G174A TGTCCGGAAAAGG . 37.0 20.0 74.0 0.0 . 53 . . Atlas-SNP SCN9A 6335 hgsc.bcm.edu hg19 2 167163101 167163101 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . SCN9A NM_002977 exon4 c.G386T p.S129I AGCATGCTGAATA . 59.0 24.0 65.0 0.0 . 296 . . Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179544702 179544702 + Missense_Mutation SNP C C G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TTN NM_001267550 exon140 c.G33499C p.V11167L CTTCTACAAGATA . 85.0 24.0 150.0 0.0 . 18412 . . Atlas-SNP AOX1 316 hgsc.bcm.edu hg19 2 201527688 201527688 + Missense_Mutation SNP A A G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . AOX1 NM_001159 exon31 c.A3539G p.H1180R GGGATCATAAGGT . 54.0 24.0 89.0 0.0 . 152 . . Atlas-SNP EPHA4 2043 hgsc.bcm.edu hg19 2 222428734 222428734 + Silent SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . EPHA4 NM_004438 exon3 c.G540A p.G180G GTAAAACCCCTTT . 49.0 23.0 92.0 0.0 . 263 . . Atlas-SNP SSUH2 51066 hgsc.bcm.edu hg19 3 8665330 8665330 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . . NM_001256748 exon11 c.G886A p.V296M AGTCCACGATGGG . 35.0 9.0 64.0 0.0 . . . . Atlas-SNP LAMB2 3913 hgsc.bcm.edu hg19 3 49162918 49162918 + Splice_Site SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . LAMB2 NM_002292 exon20 c.2489-1G>T . GGCAGGCTAGGAG . 121.0 39.0 150.0 0.0 . 156 . . Atlas-SNP DNAH1 25981 hgsc.bcm.edu hg19 3 52361949 52361949 + Missense_Mutation SNP A A G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . DNAH1 NM_015512 exon6 c.A790G p.M264V ATCAACATGGGCT . 126.0 67.0 200.0 0.0 . 534 . . Atlas-SNP ACOX2 8309 hgsc.bcm.edu hg19 3 58520174 58520174 + Missense_Mutation SNP G G T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ACOX2 NM_003500 exon3 c.C236A p.A79D ATGGCAGCCTTAT . 116.0 50.0 160.0 0.0 . 53 . . Atlas-SNP ACOX2 8309 hgsc.bcm.edu hg19 3 58520175 58520175 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ACOX2 NM_003500 exon3 c.G235A p.A79T TGGCAGCCTTATA . 118.0 50.0 159.0 0.0 . 53 . . Atlas-SNP CBLB 868 hgsc.bcm.edu hg19 3 105459455 105459455 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CBLB NM_170662 exon7 c.G866T p.C289F CGAGTGCAACTTA . 54.0 21.0 93.0 0.0 . 118 . . Atlas-SNP PCDHA10 56139 hgsc.bcm.edu hg19 5 140237151 140237151 + Silent SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PCDHA10 NM_031859 exon1 c.C1518T p.Y506Y GAGCTACGTGTCG . 63.0 32.0 92.0 0.0 . 358 . . Atlas-SNP PCDHB8 56128 hgsc.bcm.edu hg19 5 140558018 140558018 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PCDHB8 NM_019120 exon1 c.C403A p.L135M GTATTTCTGGACA . 963.0 126.0 1554.0 1.0 . 199 . . Atlas-SNP BTNL2 56244 hgsc.bcm.edu hg19 6 32370894 32370894 + Missense_Mutation SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . BTNL2 NM_019602 exon3 c.A527G p.Y176C TCCCAATACACCT . 170.0 100.0 151.0 0.0 . 50 . . Atlas-SNP CUL9 23113 hgsc.bcm.edu hg19 6 43160821 43160821 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CUL9 NM_015089 exon9 c.C2263T p.L755F CGCCTCCTTTACC . 87.0 54.0 75.0 0.0 . 248 . . Atlas-SNP MEP1A 4224 hgsc.bcm.edu hg19 6 46797206 46797206 + Missense_Mutation SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . MEP1A NM_005588 exon10 c.T1042C p.Y348H TTTTTCTATAAAA . 120.0 34.0 131.0 0.0 . 93 . . Atlas-SNP C6orf58 352999 hgsc.bcm.edu hg19 6 127899881 127899881 + Missense_Mutation SNP G G C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . C6orf58 NM_001010905 exon2 c.G352C p.D118H TCTGGAGATCATA . 65.0 28.0 99.0 0.0 . 35 . . Atlas-SNP GRM8 2918 hgsc.bcm.edu hg19 7 126173751 126173751 + Missense_Mutation SNP G G C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . GRM8 NM_000845 exon8 c.C1685G p.P562R ATGTTGGGTCTCT . 110.0 62.0 186.0 0.0 . 377 . . Atlas-SNP CNTNAP2 26047 hgsc.bcm.edu hg19 7 146825914 146825914 + Nonsense_Mutation SNP G G T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CNTNAP2 NM_014141 exon7 c.G1069T p.E357X AAATTAGAGCCCT . 115.0 32.0 179.0 0.0 . 392 . . Atlas-SNP PSD3 23362 hgsc.bcm.edu hg19 8 18730005 18730005 + Silent SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PSD3 NM_015310 exon3 c.C369T p.L123L TTCCTTGAGATGA . 73.0 35.0 91.0 0.0 . 142 . . Atlas-SNP ATP6V1B2 526 hgsc.bcm.edu hg19 8 20068787 20068787 + Missense_Mutation SNP A A C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ATP6V1B2 NM_001693 exon6 c.A563C p.K188T GGCAGAAAATTCC . 55.0 25.0 86.0 0.0 . 34 . . Atlas-SNP ZNF703 80139 hgsc.bcm.edu hg19 8 37553564 37553564 + Missense_Mutation SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ZNF703 NM_025069 exon1 c.G67A p.G23S GGCGGCGGCGGGA . 39.0 27.0 65.0 0.0 . 16 . . Atlas-SNP PREX2 80243 hgsc.bcm.edu hg19 8 69030794 69030794 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PREX2 NM_024870 exon27 c.C3336A p.N1112K CTGCAACAGCAAT . 50.0 24.0 69.0 0.0 . 614 . . Atlas-SNP TRPA1 8989 hgsc.bcm.edu hg19 8 72975718 72975718 + Missense_Mutation SNP A A T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TRPA1 NM_007332 exon5 c.T641A p.M214K ATTTCCATGCATT . 41.0 25.0 69.0 0.0 . 256 . . Atlas-SNP RECQL4 9401 hgsc.bcm.edu hg19 8 145742465 145742465 + Missense_Mutation SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . RECQL4 NM_004260 exon4 c.G323T p.R108L TTGAGCCGCTGCC . 57.0 4.0 86.0 0.0 . 75 . . Atlas-SNP TUBAL3 79861 hgsc.bcm.edu hg19 10 5437418 5437418 + Missense_Mutation SNP G G T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TUBAL3 NM_024803 exon3 c.C268A p.H90N AACGGTGCTGGCC . 98.0 38.0 123.0 0.0 . 54 . . Atlas-SNP GLYAT 10249 hgsc.bcm.edu hg19 11 58477472 58477472 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . GLYAT NM_201648 exon6 c.G658A p.D220N TTAGATCCCAGCA . 70.0 32.0 107.0 0.0 . 53 . . Atlas-SNP ALG9 79796 hgsc.bcm.edu hg19 11 111724383 111724383 + Missense_Mutation SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ALG9 NM_001077690 exon8 c.A778G p.I260V ATAGTATGAGGGC . 170.0 37.0 292.0 0.0 . 77 . . Atlas-SNP CHD4 1108 hgsc.bcm.edu hg19 12 6701152 6701152 + Missense_Mutation SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CHD4 NM_001273 exon20 c.C3020T p.S1007F AGCAGAGACACCT . 83.0 41.0 133.0 0.0 . 539 . . Atlas-SNP STYK1 55359 hgsc.bcm.edu hg19 12 10783658 10783658 + Missense_Mutation SNP A A G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . STYK1 NM_018423 exon5 c.T437C p.L146P GCCTTGAGAATAA . 87.0 13.0 151.0 0.0 . 55 . . Atlas-SNP ACACB 32 hgsc.bcm.edu hg19 12 109637211 109637211 + Silent SNP C C A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ACACB NM_001093 exon17 c.C2632A p.R878R AGTTACCGAATTA . 80.0 42.0 115.0 0.0 . 330 . . Atlas-SNP RB1 5925 hgsc.bcm.edu hg19 13 48953788 48953788 + Splice_Site SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . RB1 NM_000321 exon14 c.1389+2T>C . AATCAGTAAGTTA . 72.0 49.0 310.0 0.0 . 1068 . . Atlas-SNP VIPAS39 63894 hgsc.bcm.edu hg19 14 77895420 77895420 + Missense_Mutation SNP T T G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . . NM_001193314 exon18 c.A1285C p.N429H CCAGATTGACATA . 42.0 17.0 81.0 0.0 . . . . Atlas-SNP CDH1 999 hgsc.bcm.edu hg19 16 68849486 68849486 + Silent SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CDH1 NM_004360 exon10 c.G1389A p.E463E TTTTGAGGTCTCT . 73.0 34.0 154.0 0.0 . 535 . . Atlas-SNP ZFHX3 463 hgsc.bcm.edu hg19 16 72821615 72821615 + Silent SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 ZFHX3,NS,carcinoma,0,1 ZFHX3 NM_006885 exon10 c.C10560T p.G3520G GCCGCCGCCACCG . 10.0 5.0 6.0 0.0 . 404 . . Atlas-SNP KIAA0100 9703 hgsc.bcm.edu hg19 17 26970215 26970215 + Silent SNP G G C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . KIAA0100 NM_014680 exon4 c.C363G p.S121S GCTGAAGGACAGT . 51.0 21.0 81.0 0.0 . 175 . . Atlas-SNP NF1 4763 hgsc.bcm.edu hg19 17 29592294 29592294 + Missense_Mutation SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . NF1 NM_001042492 exon36 c.G4772A p.S1591N CGTTAAGTATTTT . 90.0 34.0 148.0 0.0 . 1586 . . Atlas-SNP TAF15 8148 hgsc.bcm.edu hg19 17 34149836 34149836 + Missense_Mutation SNP A A C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TAF15 NM_139215 exon6 c.A483C p.Q161H CACACAAGGTAAG . 144.0 55.0 264.0 0.0 . 46 . . Atlas-SNP POTEC 388468 hgsc.bcm.edu hg19 18 14537872 14537872 + Silent SNP A A G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . POTEC NM_001137671 exon3 c.T738C p.A246A GTGGACAGCATAG . 178.0 81.0 319.0 0.0 . 129 . . Atlas-SNP GATA6 2627 hgsc.bcm.edu hg19 18 19756976 19756976 + Missense_Mutation SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . GATA6 NM_005257 exon3 c.C1196T p.P399L AGACGCCGCTGTG . 35.0 14.0 36.0 0.0 . 35 . . Atlas-SNP CREB3L3 84699 hgsc.bcm.edu hg19 19 4171379 4171379 + Splice_Site SNP G G A rs112561919 bycluster TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . CREB3L3 NM_001271995 exon9 c.973-1G>A . CCACCAGGTCCTG . 115.0 27.0 96.0 0.0 . 53 . C|1.000 Atlas-SNP ANO8 57719 hgsc.bcm.edu hg19 19 17442017 17442017 + Silent SNP G G T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ANO8 NM_020959 exon7 c.C711A p.I237I ATCACAGATGTCA . 43.0 22.0 59.0 0.0 . 67 . . Atlas-SNP ZNF257 113835 hgsc.bcm.edu hg19 19 22271464 22271464 + Silent SNP T T C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ZNF257 NM_033468 exon4 c.T912C p.T304T CCTTACTCAACAT . 95.0 52.0 114.0 0.0 . 156 . . Atlas-SNP ZNF350 59348 hgsc.bcm.edu hg19 19 52468329 52468329 + Silent SNP C C T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ZNF350 NM_021632 exon5 c.G1377A p.G459G AGTCGCCCCGTTA . 76.0 10.0 100.0 0.0 . 48 . . Atlas-SNP ITSN1 6453 hgsc.bcm.edu hg19 21 35258604 35258604 + Silent SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ITSN1 NM_003024 exon39 c.G4857A p.P1619P CAACCCGTACTGT . 113.0 51.0 166.0 0.0 . 166 . . Atlas-SNP PWP2 5822 hgsc.bcm.edu hg19 21 45534063 45534063 + Missense_Mutation SNP G G A novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PWP2 NM_005049 exon4 c.G230A p.G77D CAGGGGGCGATGC . 22.0 14.0 46.0 0.0 . 64 . . Atlas-SNP VSIG4 11326 hgsc.bcm.edu hg19 X 65244890 65244890 + Missense_Mutation SNP A A G novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . VSIG4 NM_001257403 exon6 c.T917C p.L306P CGACAGAGCATGA . 269.0 58.0 456.0 0.0 . 54 . . Atlas-SNP REV3L 5980 hgsc.bcm.edu hg19 6 111694495 111694495 + Frame_Shift_Del DEL C C - novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . REV3L NM_002912 exon13 c.5064delA p.G1688fs . . 61.0 22.0 114.0 0.0 . 386 . . Atlas-Indel,Pindel PCLO 27445 hgsc.bcm.edu hg19 7 82390054 82390055 + Frame_Shift_Ins INS - - T novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . PCLO NM_033026 exon24 c.15189_15190insA p.K5063fs . . 196.0 73.0 325.0 0.0 . 1506 . . Atlas-Indel,Pindel TTN 7273 hgsc.bcm.edu hg19 2 179544684 179544699 + Frame_Shift_Del DEL ACTCTTCTTCTTCTTC ACTCTTCTTCTTCTTC - novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 ACTCTTCTTCTTCTTC ACTCTTCTTCTTCTTC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TTN NM_001267550 exon140 c.33503_33518del p.11168_11173del . . 80.0 22.0 130.0 0.0 . 18412 . . Atlas-INDEL GTF2B 2959 hgsc.bcm.edu hg19 1 89318944 89318944 + Frame_Shift_Del DEL A A - novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . GTF2B NM_001514 exon7 c.904delA p.T302fs . . 40.0 12.0 73.0 0.0 . 32 . . Atlas-Indel,Pindel FBXO42 54455 hgsc.bcm.edu hg19 1 16577608 16577609 + Frame_Shift_Ins INS - - C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . FBXO42 NM_018994 exon10 c.1711_1712insG p.P571fs . . 31.0 23.0 91.0 0.0 . 53 . . Atlas-Indel,Pindel ATG16L1 55054 hgsc.bcm.edu hg19 2 234198547 234198548 + Frame_Shift_Ins INS - - C novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . ATG16L1 NM_030803 exon13 c.1251_1252insC p.L417fs . . 76.0 30.0 87.0 0.0 . 83 . . Pindel TTN 7273 hgsc.bcm.edu hg19 2 179544684 179544702 + Frame_Shift_Del DEL ACTCTTCTTCTTCTTCTAC ACTCTTCTTCTTCTTCTAC - novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 ACTCTTCTTCTTCTTCTAC ACTCTTCTTCTTCTTCTAC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . TTN NM_001267550 exon140 c.33500_33518del p.11167_11173del . . 88.0 23.0 140.0 0.0 . 18412 . . Pindel RERGL 79785 hgsc.bcm.edu hg19 12 18241889 18242060 + In_Frame_Del DEL GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC - novel TCGA-RC-A7S9-01A-11D-A33Q-10 TCGA-RC-A7S9-10A-02D-A33Q-10 GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC GGCTGCAAAGCAAACAATCTAGATTTAGGGCTGTTATATTTTAGGAAACAGCTAATTTGGTTATGTGCATAAGGCTTTAGTTCTTAAACCAAAAATATTCAAGAATTAATAAAGACTTTAAAATTAGACCAAATTCTGTTCTAAATAGTAGTTAACAATATTTCCATGGTAC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 51aa8270-daf2-45af-b4a7-b80b053bada3 0a31c7e6-f1af-4ff5-8011-67d8e91a85d6 . RERGL NM_024730 exon3 c.56_58del p.19_20del . . 57.0 12.0 95.0 0.0 . 66 . . Pindel