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 TAS1R3 83756 hgsc.bcm.edu hg19 1 1267767 1267767 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TAS1R3 NM_152228 exon3 c.T856C p.Y286H TTCAACTACAGCA . 54.0 19.0 133.0 0.0 . 39 . . . none . . PASS Atlas-SNP LEPR 3953 hgsc.bcm.edu hg19 1 66088612 66088612 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . LEPR NM_001003680 exon19 c.A2621G p.D874G GGGAAGATGTTCC . 92.0 32.0 59.0 0.0 . 284 . . . none . . PASS Atlas-SNP PRCC 5546 hgsc.bcm.edu hg19 1 156767106 156767106 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PRCC NM_005973 exon6 c.A1362C p.K454N GCGGAAACACCAG . 118.0 44.0 77.0 0.0 . 39 . . . none . . PASS Atlas-SNP SOAT1 6646 hgsc.bcm.edu hg19 1 179310206 179310206 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . SOAT1 NM_003101 exon7 c.T541G p.F181V GGCAAATTTCCTA . 85.0 41.0 57.0 0.0 . 53 . . . none . . PASS Atlas-SNP SMG7 9887 hgsc.bcm.edu hg19 1 183495889 183495889 + Silent SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . SMG7 NM_201569 exon5 c.C471T p.H157H CGTCCACCTTGGA . 59.0 24.0 51.0 0.0 . 165 . . . none . . PASS Atlas-SNP IRF2BP2 359948 hgsc.bcm.edu hg19 1 234743069 234743069 + Silent SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . IRF2BP2 NM_182972 exon2 c.G1578C p.S526S CTTGTGCGAAGGG . 64.0 29.0 115.0 0.0 . 37 . . . none . . PASS Atlas-SNP DESI2 51029 hgsc.bcm.edu hg19 1 244849928 244849928 + Silent SNP T T A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . . NM_016076 exon2 c.T72A p.I24I ATCCATTGGAATT . 37.0 10.0 46.0 0.0 . . . . . none . . PASS Atlas-SNP CAD 790 hgsc.bcm.edu hg19 2 27456276 27456276 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CAD NM_004341 exon20 c.C3088A p.Q1030K CATCGGCAGCAGT . 88.0 4.0 53.0 0.0 . 199 . . . none . . PASS Atlas-SNP POLR1A 25885 hgsc.bcm.edu hg19 2 86272888 86272888 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . POLR1A NM_015425 exon20 c.C2738T p.S913L AGGCACGAGATCT . 337.0 96.0 183.0 0.0 . 137 . . . none . . PASS Atlas-SNP PAX8 7849 hgsc.bcm.edu hg19 2 114000281 114000281 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PAX8 NM_013952 exon5 c.C464A p.P155H TGTCCGGGACTCA . 155.0 39.0 126.0 0.0 . 42 . . . none . . PASS Atlas-SNP HOXD1 3231 hgsc.bcm.edu hg19 2 177054137 177054137 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . HOXD1 NM_024501 exon1 c.G608T p.S203I CCTTCAGCACGTT . 152.0 91.0 258.0 0.0 . 33 . . . none . . PASS Atlas-SNP CAPN7 23473 hgsc.bcm.edu hg19 3 15287046 15287046 + Silent SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CAPN7 NM_014296 exon17 c.A1878G p.P626P ACCTCCATACATT . 86.0 27.0 64.0 0.0 . 63 . . . none . . PASS Atlas-SNP UBE2K 3093 hgsc.bcm.edu hg19 4 39779353 39779353 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . UBE2K NM_005339 exon6 c.G451A p.V151M GCACATGTGTATG . 181.0 52.0 144.0 0.0 . 16 . . . none . . PASS Atlas-SNP EPHA5 2044 hgsc.bcm.edu hg19 4 66535302 66535302 + Silent SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . EPHA5 NM_004439 exon1 c.C159A p.L53L GGCCAGGAGGGTC . 183.0 120.0 275.0 0.0 . 315 . . . none . . PASS Atlas-SNP FAT4 79633 hgsc.bcm.edu hg19 4 126239708 126239708 + Silent SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . FAT4 NM_024582 exon1 c.T2142C p.T714T TGCCACTGACCCA . 120.0 30.0 84.0 0.0 . 1752 . . . none . . PASS Atlas-SNP POU5F2 134187 hgsc.bcm.edu hg19 5 93076747 93076747 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . POU5F2 NM_153216 exon1 c.G523A p.A175T TGTTGGCGACGCT . 44.0 26.0 31.0 0.0 . 10 . . . none . . PASS Atlas-SNP GLRA1 2741 hgsc.bcm.edu hg19 5 151231003 151231003 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . GLRA1 NM_000171 exon7 c.C860T p.T287I AGCACAGTGGTGA . 155.0 39.0 83.0 0.0 . 61 . . . none . . PASS Atlas-SNP NEDD9 4739 hgsc.bcm.edu hg19 6 11185765 11185765 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . NEDD9 NM_001142393 exon8 c.A2135G p.Y712C TGGTCATAGTAGA . 56.0 25.0 54.0 0.0 . 191 . . . none . . PASS Atlas-SNP SYNE1 23345 hgsc.bcm.edu hg19 6 152497619 152497619 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . SYNE1 NM_182961 exon130 c.C23537T p.A7846V TGGCTGGCTTTAG . 82.0 29.0 65.0 0.0 . 3227 . . . none . . PASS Atlas-SNP BUD31 8896 hgsc.bcm.edu hg19 7 99008752 99008752 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . BUD31 NM_003910 exon3 c.G37A p.D13N CCCCCAGATGGCT . 148.0 90.0 136.0 0.0 . 12 . . . none . . PASS Atlas-SNP MBLAC1 255374 hgsc.bcm.edu hg19 7 99725163 99725163 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MBLAC1 NM_203397 exon2 c.C145T p.P49S GTCCTACCCCAGA . 94.0 31.0 169.0 0.0 . 13 . . . none . . PASS Atlas-SNP KLHDC10 23008 hgsc.bcm.edu hg19 7 129760626 129760626 + Silent SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . KLHDC10 NM_014997 exon4 c.T513C p.G171G TGGAGGTACGGGC . 164.0 51.0 96.0 0.0 . 36 . . . none . . PASS Atlas-SNP ESYT2 57488 hgsc.bcm.edu hg19 7 158528197 158528197 + Silent SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ESYT2 NM_020728 exon20 c.C2583T p.G861G TACTTTGCCAAGG . 50.0 10.0 69.0 0.0 . 70 . . . none . . PASS Atlas-SNP RB1CC1 9821 hgsc.bcm.edu hg19 8 53596456 53596456 + Silent SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . RB1CC1 NM_001083617 exon4 c.T189C p.S63S CCCAGCACTGTAG . 61.0 17.0 47.0 0.0 . 163 . . . none . . PASS Atlas-SNP TLN1 7094 hgsc.bcm.edu hg19 9 35714845 35714845 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TLN1 NM_006289 exon22 c.C2783A p.A928D TGTGTGGCTGAGG . 21.0 6.0 29.0 0.0 . 185 . . . none . . PASS Atlas-SNP ANKS6 203286 hgsc.bcm.edu hg19 9 101546386 101546386 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ANKS6 NM_173551 exon4 c.T961G p.L321V TGACCAAGTTCAC . 27.0 6.0 49.0 0.0 . 59 . . . none . . PASS Atlas-SNP FAM102A 399665 hgsc.bcm.edu hg19 9 130742371 130742371 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . FAM102A NM_001035254 exon1 c.T46G p.F16V GGGTGAAAGTAGT . 93.0 30.0 183.0 0.0 . 32 . . . none . . PASS Atlas-SNP C9orf96 169436 hgsc.bcm.edu hg19 9 136253234 136253234 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . C9orf96 NM_153710 exon5 c.T298G p.S100A CAGATCTCTTCTC . 68.0 30.0 109.0 0.0 . 77 . . . none . . PASS Atlas-SNP ARID5B 84159 hgsc.bcm.edu hg19 10 63829547 63829547 + Missense_Mutation SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ARID5B NM_032199 exon8 c.A1190G p.H397R GCAGACATTATGA . 100.0 53.0 53.0 0.0 . 125 . . . none . . PASS Atlas-SNP DPYSL4 10570 hgsc.bcm.edu hg19 10 134011925 134011925 + Nonsense_Mutation SNP A A T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . DPYSL4 NM_006426 exon7 c.A628T p.K210X GAGCAGAAGCGGT . 41.0 25.0 63.0 0.0 . 91 . . . none . . PASS Atlas-SNP FRG2B 441581 hgsc.bcm.edu hg19 10 135438923 135438923 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . FRG2B NM_001080998 exon4 c.A517G p.K173E AGCTTTTTCGAAT . 293.0 127.0 303.0 0.0 . 47 . . . none . . PASS Atlas-SNP KCNQ1 3784 hgsc.bcm.edu hg19 11 2608884 2608884 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . KCNQ1 NM_000218 exon9 c.C1213G p.L405V CACACTCTGCTGT . 65.0 23.0 122.0 0.0 . 60 . . . none . . PASS Atlas-SNP OR4A5 81318 hgsc.bcm.edu hg19 11 51411524 51411524 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . OR4A5 NM_001005272 exon1 c.T872G p.M291R TTTCTCATCTCTG . 104.0 45.0 39.0 0.0 . 116 . . . none . . PASS Atlas-SNP PCNXL3 399909 hgsc.bcm.edu hg19 11 65395000 65395000 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PCNXL3 NM_032223 exon22 c.C3649G p.L1217V CCGCGCCTCTCCC . 25.0 10.0 72.0 0.0 . 140 . . . none . . PASS Atlas-SNP KIAA1377 57562 hgsc.bcm.edu hg19 11 101829047 101829047 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . KIAA1377 NM_020802 exon5 c.C655G p.L219V CTTAAACTGGAGG . 102.0 32.0 68.0 0.0 . 111 . . . none . . PASS Atlas-SNP VWF 7450 hgsc.bcm.edu hg19 12 6103203 6103203 + Silent SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . VWF NM_000552 exon37 c.C6423A p.V2141V GAGGAGGACCTGG . 141.0 40.0 62.0 0.0 . 338 . . . none . . PASS Atlas-SNP KLHL42 57542 hgsc.bcm.edu hg19 12 27950834 27950834 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . . NM_020782 exon3 c.T1253A p.V418E TCACCGTGCAGTC . 264.0 86.0 91.0 0.0 . . . . . none . . PASS Atlas-SNP SMAGP 57228 hgsc.bcm.edu hg19 12 51639787 51639787 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . SMAGP NM_001031628 exon4 c.G232A p.A78T CGATGGCACTGGG . 198.0 113.0 82.0 0.0 . 7 . . . none . . PASS Atlas-SNP CUX2 23316 hgsc.bcm.edu hg19 12 111729279 111729279 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CUX2 NM_015267 exon5 c.G359A p.S120N CCCCCAGCTTTGA . 133.0 20.0 100.0 0.0 . 145 . . . none . . PASS Atlas-SNP MSI1 4440 hgsc.bcm.edu hg19 12 120795647 120795647 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MSI1 NM_002442 exon8 c.T506A p.I169N AAATGAATTTCAC . 143.0 29.0 125.0 0.0 . 40 . . . none . . PASS Atlas-SNP PAN3 255967 hgsc.bcm.edu hg19 13 28794514 28794514 + Silent SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PAN3 NM_175854 exon6 c.A999G p.P333P AGCGCCAGGTAAG . 55.0 24.0 38.0 0.0 . 123 . . . none . . PASS Atlas-SNP FRY 10129 hgsc.bcm.edu hg19 13 32808840 32808840 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . FRY NM_023037 exon42 c.T5657C p.L1886S ATGCCTTATCTGA . 104.0 14.0 71.0 0.0 . 312 . . . none . . PASS Atlas-SNP SAV1 60485 hgsc.bcm.edu hg19 14 51111608 51111608 + Missense_Mutation SNP A A T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . SAV1 NM_021818 exon3 c.T660A p.H220Q TGTGTTATGATCT . 58.0 27.0 46.0 0.0 . 18 . . . none . . PASS Atlas-SNP ARHGAP11A 9824 hgsc.bcm.edu hg19 15 32928491 32928491 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ARHGAP11A NM_014783 exon12 c.T1517C p.L506S AAACCTTACTAAC . 90.0 33.0 88.0 0.0 . 84 . . . none . . PASS Atlas-SNP TP53BP1 7158 hgsc.bcm.edu hg19 15 43769942 43769942 + Silent SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TP53BP1 NM_001141980 exon8 c.T804G p.P268P GCTAAAAGGCATG . 62.0 21.0 89.0 0.0 . 157 . . . none . . PASS Atlas-SNP MEX3B 84206 hgsc.bcm.edu hg19 15 82336360 82336360 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MEX3B NM_032246 exon2 c.A851G p.Y284C TTGCGGTAGCTAG . 25.0 10.0 45.0 0.0 . 50 . . . none . . PASS Atlas-SNP GTF3C1 2975 hgsc.bcm.edu hg19 16 27523094 27523094 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . GTF3C1 NM_001520 exon7 c.A1102G p.M368V TGAGCATATCCCG . 103.0 55.0 79.0 0.0 . 210 . . . none . . PASS Atlas-SNP ZNF629 23361 hgsc.bcm.edu hg19 16 30795034 30795034 + Silent SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ZNF629 NM_001080417 exon3 c.C615T p.P205P CTTGTAGGGCTTC . 60.0 39.0 132.0 0.0 . 44 . . . none . . PASS Atlas-SNP IRX6 79190 hgsc.bcm.edu hg19 16 55359021 55359021 + Missense_Mutation SNP T T G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . IRX6 NM_024335 exon1 c.T18G p.F6L ACACTTTGGACAC . 50.0 25.0 96.0 0.0 . 66 . . . none . . PASS Atlas-SNP KARS 3735 hgsc.bcm.edu hg19 16 75674216 75674216 + Missense_Mutation SNP T T C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . KARS NM_001130089 exon4 c.A338G p.H113R AGCTGATGAATTG . 76.0 46.0 58.0 0.0 . 77 . . . none . . PASS Atlas-SNP TMEM88 92162 hgsc.bcm.edu hg19 17 7758984 7758984 + Silent SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TMEM88 NM_203411 exon2 c.C432G p.A144A CCGGGCCTCACCA . 36.0 8.0 87.0 0.0 . 6 . . . none . . PASS Atlas-SNP AOC2 314 hgsc.bcm.edu hg19 17 41002294 41002294 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . AOC2 NM_009590 exon4 c.C2200T p.P734S ATCAATCCTGTGG . 76.0 43.0 84.0 0.0 . 61 . . . none . . PASS Atlas-SNP FZD2 2535 hgsc.bcm.edu hg19 17 42636200 42636200 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . FZD2 NM_001466 exon1 c.G1144A p.V382I CCGGCCGTCAAGA . 48.0 13.0 80.0 0.0 . 81 . . . none . . PASS Atlas-SNP MYL12A 10627 hgsc.bcm.edu hg19 18 3254019 3254019 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MYL12A NM_006471 exon3 c.C314T p.A105V GAAATGCCTTTGC . 199.0 73.0 223.0 0.0 . 12 . . . none . . PASS Atlas-SNP LAMA1 284217 hgsc.bcm.edu hg19 18 7016662 7016662 + Silent SNP A A G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . LAMA1 NM_005559 exon21 c.T2817C p.Y939Y CCCATAATAGCCA . 42.0 14.0 21.0 0.0 . 458 . . . none . . PASS Atlas-SNP DUS3L 56931 hgsc.bcm.edu hg19 19 5786483 5786483 + Silent SNP A A T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . DUS3L NM_020175 exon10 c.T1557A p.I519I CCGGGCAATCATG . 28.0 12.0 74.0 0.0 . 42 . . . none . . PASS Atlas-SNP ZNF565 147929 hgsc.bcm.edu hg19 19 36674230 36674230 + Missense_Mutation SNP T T A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ZNF565 NM_001042474 exon5 c.A638T p.H213L CTCTGATGCTGAA . 56.0 22.0 58.0 0.0 . 46 . . . none . . PASS Atlas-SNP MYH14 79784 hgsc.bcm.edu hg19 19 50747513 50747513 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MYH14 NM_001077186 exon11 c.G1129A p.V377I CGGATGGTCTCAG . 66.0 30.0 125.0 0.0 . 261 . . . none . . PASS Atlas-SNP PTPRT 11122 hgsc.bcm.edu hg19 20 40713469 40713469 + Missense_Mutation SNP C C T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PTPRT NM_133170 exon30 c.G4046A p.R1349H ACTATACGATAAC . 109.0 43.0 39.0 0.0 . 372 . . . none . . PASS Atlas-SNP PARD6B 84612 hgsc.bcm.edu hg19 20 49354557 49354557 + Missense_Mutation SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PARD6B NM_032521 exon2 c.A230C p.N77T ATGATAATTATCA . 244.0 87.0 132.0 0.0 . 31 . . . none . . PASS Atlas-SNP KRTAP27-1 643812 hgsc.bcm.edu hg19 21 31709386 31709386 + Missense_Mutation SNP C C A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . KRTAP27-1 NM_001077711 exon1 c.G601T p.G201C GAGAACCACCAGT . 166.0 35.0 59.0 0.0 . 53 . . . none . . PASS Atlas-SNP BCL2L13 23786 hgsc.bcm.edu hg19 22 18138483 18138483 + Silent SNP G G C rs144712899 byfrequency;alternate_allele TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f BCL2L13,NS,adenocarcinoma,0,2 BCL2L13 NM_001270732 exon2 c.G6C p.A2A AATGGCGTCCTCT . 58.0 26.0 69.0 1.0 . 27 . . . alt G|1.000;A|0.000 . PASS Atlas-SNP RANBP1 5902 hgsc.bcm.edu hg19 22 20109854 20109854 + Missense_Mutation SNP G G T novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . RANBP1 NM_002882 exon3 c.G220T p.D74Y ACTGGTGACGTCA . 84.0 29.0 132.0 0.0 . 19 . . . none . . PASS Atlas-SNP CSNK1E 1454 hgsc.bcm.edu hg19 22 38690505 38690505 + Missense_Mutation SNP C C G novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CSNK1E NM_001894 exon8 c.G921C p.E307D TCGCCGCTCCCGG . 52.0 24.0 146.0 0.0 . 143 . . . none . . PASS Atlas-SNP MOV10L1 54456 hgsc.bcm.edu hg19 22 50591546 50591546 + Silent SNP A A C novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . MOV10L1 NM_018995 exon22 c.A2965C p.R989R TACCACAGGGAAC . 79.0 32.0 163.0 0.0 . 238 . . . none . . PASS Atlas-SNP DCAF8L2 347442 hgsc.bcm.edu hg19 X 27765728 27765728 + Missense_Mutation SNP G G A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . DCAF8L2 NM_001136533 exon1 c.G716A p.R239H ACCAGCGTGGCAC . 83.0 69.0 45.0 0.0 . 79 . . . none . . PASS Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 6955 6955 + Missense_Mutation SNP G G A rs11510102 TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . . ENST00000361624 exon1 c.G1052A p.G351D CCGTAGGTGGCCT . 22.0 13.0 3.0 0.0 . . . . . weak . . PASS Atlas-SNP PHF3 23469 hgsc.bcm.edu hg19 6 64421622 64421622 + Frame_Shift_Del DEL A A - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PHF3 NM_015153 exon15 c.4137delT p.D1379fs . . 185.0 76.0 86.0 0.0 . 191 . 0.410811 0 none . . PASS Atlas-Indel,Pindel AHCTF1 25909 hgsc.bcm.edu hg19 1 247081550 247081560 + Splice_Site DEL TTATGTTTACC TTATGTTTACC - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 TTATGTTTACC TTATGTTTACC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . AHCTF1 . . . . . . 139.0 25.0 147.0 0.0 . 187 . 0.179856 0 none . . PASS Atlas-Indel,Pindel USH1G 124590 hgsc.bcm.edu hg19 17 72919094 72919094 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . USH1G NM_173477 exon1 c.76delA p.N26fs . . 123.0 41.0 192.0 0.0 . 40 . 0.333333 0 none . . PASS Atlas-INDEL GGH 8836 hgsc.bcm.edu hg19 8 63936714 63936714 + Frame_Shift_Del DEL A A - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . GGH NM_003878 exon6 c.532delC p.P178fs . . 248.0 61.0 111.0 0.0 . 32 . 0.245968 0 none . . PASS Atlas-Indel,Pindel ASPN 54829 hgsc.bcm.edu hg19 9 95237024 95237025 + In_Frame_Ins INS - - TCCTCA rs111419727 bycluster;byfrequency;alternate_allele TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f .,2 ASPN NM_001193335 exon2 c.156_157insTGAGGA p.E52delinsDEE . . 67.0 24.0 49.0 0.0 . 52 . 0.358209 0 alt -|0.500;TCA|0.500 . PASS Atlas-INDEL PHF16 9767 hgsc.bcm.edu hg19 X 46918210 46918210 + Frame_Shift_Del DEL A A - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PHF16 NM_014735 exon11 c.2202delG p.V734fs . . 45.0 36.0 28.0 0.0 . 72 . 0.8 0 none . . PASS Atlas-INDEL DNAH1 25981 hgsc.bcm.edu hg19 3 52392687 52392687 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . DNAH1 NM_015512 exon25 c.4199delA p.E1400fs . . 131.0 62.0 216.0 0.0 . 534 . 0.473282 0 none . . PASS Atlas-Indel,Pindel CEP95 90799 hgsc.bcm.edu hg19 17 62518864 62518864 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CEP95 NM_138363 exon8 c.759delA p.L253fs . . 141.0 75.0 89.0 0.0 . 103 . 0.531915 0 none . . PASS Atlas-Indel,Pindel VTA1 51534 hgsc.bcm.edu hg19 6 142491530 142491530 + Frame_Shift_Del DEL T T - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . VTA1 NM_016485 exon4 c.382delA p.I128X . . 28.0 10.0 15.0 0.0 . 29 . 0.357143 0 none . . PASS Atlas-INDEL ROCK1 6093 hgsc.bcm.edu hg19 18 18600173 18600174 + Frame_Shift_Del DEL TA TA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 TA TA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ROCK1 NM_005406 exon12 c.1300_1301del p.434_434del . . 20.0 10.0 40.0 0.0 . 162 . 0.5 0 none . . PASS Atlas-INDEL CEP290 80184 hgsc.bcm.edu hg19 12 88523531 88523532 + Frame_Shift_Ins INS - - AAAA novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CEP290 NM_025114 exon10 c.792_793insTTTT p.V264fs . . 145.0 12.0 56.0 0.0 . 195 . 0.0827586 0 none . . PASS Atlas-INDEL LIAS 11019 hgsc.bcm.edu hg19 4 39465225 39465225 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . LIAS NM_194451 exon4 c.392delT p.M131fs . . 53.0 40.0 50.0 0.0 . 26 . 0.754717 0 none . . PASS Atlas-Indel,Pindel TPR 7175 hgsc.bcm.edu hg19 1 186289494 186289494 + Frame_Shift_Del DEL G G - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f TPR_ENST00000367478,NS,carcinoma,0,2 TPR NM_003292 exon46 c.6519delA p.P2173fs . . 85.0 38.0 53.0 0.0 . 441 . 0.447059 0 none . . PASS Atlas-Indel,Pindel TMPRSS7 344805 hgsc.bcm.edu hg19 3 111799843 111799844 + Frame_Shift_Del DEL GA GA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 GA GA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TMPRSS7 NM_001042575 exon16 c.2065_2066del p.689_689del . . 147.0 43.0 197.0 0.0 . 126 . 0.292517 0 none . . PASS Atlas-INDEL CEP290 80184 hgsc.bcm.edu hg19 12 88523533 88523534 + Frame_Shift_Ins INS - - A novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CEP290 NM_025114 exon10 c.790_791insT p.V264fs . . 144.0 12.0 56.0 0.0 . 195 . 0.0833333 0 none . . PASS Atlas-INDEL ZNF540 163255 hgsc.bcm.edu hg19 19 38102608 38102609 + Frame_Shift_Del DEL AA AA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 AA AA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . ZNF540 NM_152606 exon5 c.426_427del p.142_143del . . 137.0 55.0 127.0 0.0 . 75 . 0.40146 0 none . . PASS Atlas-Indel,Pindel TMPRSS7 344805 hgsc.bcm.edu hg19 3 111799843 111799845 + In_Frame_Del DEL GAA GAA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 GAA GAA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . TMPRSS7 NM_001042575 exon16 c.2065_2067del p.689_689del . . 148.0 36.0 200.0 0.0 . 126 . 0.243 . none . . PASS Pindel PHF16 9767 hgsc.bcm.edu hg19 X 46918210 46918211 + Frame_Shift_Del DEL AA AA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 AA AA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . PHF16 NM_014735 exon11 c.2202_2203del p.734_735del . . 45.0 26.0 28.0 0.0 . 72 . 0.578 . none . . PASS Pindel USH1G 124590 hgsc.bcm.edu hg19 17 72919094 72919095 + Frame_Shift_Del DEL CA CA - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 CA CA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . USH1G NM_173477 exon1 c.75_76del p.25_26del . . 127.0 30.0 194.0 0.0 . 40 . 0.236 . none . . PASS Pindel CEP290 80184 hgsc.bcm.edu hg19 12 88523533 88523533 + Frame_Shift_Del DEL C C - novel TCGA-2Z-A9JG-01A-11D-A42J-10 TCGA-2Z-A9JG-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 7c8dab16-b1ab-45d2-b73f-239d8a74c8c3 c6173f98-c359-458d-a604-779cc45d612f . CEP290 NM_025114 exon10 c.791delT p.V264fs . . 145.0 12.0 56.0 0.0 . 195 . 0.083 . none . . PASS Pindel