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 PTCHD2 57540 hgsc.bcm.edu hg19 1 11561256 11561256 + Silent SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PTCHD2 NM_020780 exon2 c.C207T p.T69T CTTCACCAATCCG . 75.0 29.0 76.0 0.0 . 193 . . . none . . PASS Atlas-SNP KLHDC7A 127707 hgsc.bcm.edu hg19 1 18808064 18808064 + Missense_Mutation SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . KLHDC7A NM_152375 exon1 c.C589T p.P197S GAGCATCCAGGAC . 27.0 6.0 37.0 0.0 . 60 . . . none . . PASS Atlas-SNP SNRNP40 9410 hgsc.bcm.edu hg19 1 31744229 31744229 + Missense_Mutation SNP T T A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SNRNP40 NM_004814 exon6 c.A772T p.T258S TACCTGTATTGTC . 31.0 7.0 29.0 0.0 . 18 . . . none . . PASS Atlas-SNP WDR65 149465 hgsc.bcm.edu hg19 1 43649431 43649431 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . WDR65 NM_152498 exon4 c.C644A p.T215N TTGGCACTGACAC . 95.0 36.0 112.0 0.0 . 76 . . . none . . PASS Atlas-SNP BTBD19 149478 hgsc.bcm.edu hg19 1 45278737 45278737 + Splice_Site SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . BTBD19 NM_001136537 exon5 c.483+1G>T . AGCCAGGTACTGC . 50.0 14.0 67.0 0.0 . 16 . . . none . . PASS Atlas-SNP HMGCS2 3158 hgsc.bcm.edu hg19 1 120300026 120300026 + Nonsense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HMGCS2 NM_005518 exon5 c.C886T p.Q296X TGTACTGTAAATC . 74.0 20.0 92.0 0.0 . 58 . . . none . . PASS Atlas-SNP PEAR1 375033 hgsc.bcm.edu hg19 1 156876561 156876561 + Missense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PEAR1 NM_001080471 exon6 c.G533T p.C178F AGCCCTGTACCCC . 101.0 39.0 132.0 0.0 . 118 . . . none . . PASS Atlas-SNP TADA1 117143 hgsc.bcm.edu hg19 1 166838685 166838685 + Missense_Mutation SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TADA1 NM_053053 exon3 c.C229G p.P77A TACCTGGTGTAGA . 60.0 25.0 77.0 0.0 . 32 . . . none . . PASS Atlas-SNP ADCY10 55811 hgsc.bcm.edu hg19 1 167871039 167871039 + Missense_Mutation SNP A A T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ADCY10 NM_018417 exon5 c.T297A p.D99E CAGTGCATCACCT . 62.0 18.0 59.0 0.0 . 175 . . . none . . PASS Atlas-SNP PRRC2C 23215 hgsc.bcm.edu hg19 1 171526383 171526383 + Missense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . NM_015172 exon19 c.G5126T p.W1709L AGGTCTGGAACAA . 71.0 22.0 119.0 0.0 . . . . . none . . PASS Atlas-SNP ARPC5 10092 hgsc.bcm.edu hg19 1 183604774 183604774 + Silent SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ARPC5 NM_005717 exon1 c.G21T p.S7S GGCCGACGACACT . 71.0 20.0 69.0 0.0 . 6 . . . none . . PASS Atlas-SNP HMCN1 83872 hgsc.bcm.edu hg19 1 186101461 186101461 + Missense_Mutation SNP A A C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HMCN1 NM_031935 exon86 c.A13232C p.N4411T CATAGAATGAAGA . 61.0 18.0 73.0 0.0 . 797 . . . none . . PASS Atlas-SNP TMCC2 9911 hgsc.bcm.edu hg19 1 205211011 205211011 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TMCC2 NM_014858 exon2 c.C586A p.H196N AGCCCTCACCTGC . 25.0 12.0 32.0 0.0 . 89 . . . none . . PASS Atlas-SNP TSPYL6 388951 hgsc.bcm.edu hg19 2 54482228 54482228 + Missense_Mutation SNP A A T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TSPYL6 NM_001003937 exon1 c.T1061A p.F354Y TCTGAAAACCAGG . 73.0 25.0 87.0 0.0 . 54 . . . none . . PASS Atlas-SNP FANCL 55120 hgsc.bcm.edu hg19 2 58425781 58425781 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . FANCL NM_018062 exon7 c.C488T p.P163L TAATCTGGTGATT . 181.0 51.0 207.0 0.0 . 35 . . . none . . PASS Atlas-SNP EHBP1 23301 hgsc.bcm.edu hg19 2 63175859 63175859 + Silent SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . EHBP1 NM_015252 exon14 c.A1983G p.G661G CTCTGGAAGGACT . 87.0 24.0 105.0 0.0 . 127 . . . none . . PASS Atlas-SNP RNF181 51255 hgsc.bcm.edu hg19 2 85823986 85823986 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . RNF181 NM_016494 exon3 c.G259A p.E87K GAGGAGGAGACTG . 46.0 14.0 92.0 0.0 . 10 . . . none . . PASS Atlas-SNP RNF181 51255 hgsc.bcm.edu hg19 2 85823987 85823987 + Missense_Mutation SNP A A C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . RNF181 NM_016494 exon3 c.A260C p.E87A AGGAGGAGACTGC . 46.0 14.0 92.0 0.0 . 10 . . . none . . PASS Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179426840 179426840 + Missense_Mutation SNP T T A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TTN NM_001267550 exon326 c.A84019T p.T28007S CTCTAGTTGTCTC . 85.0 21.0 90.0 0.0 . 18412 . . . none . . PASS Atlas-SNP PMS1 5378 hgsc.bcm.edu hg19 2 190717495 190717495 + Missense_Mutation SNP A A T rs375164425 alternate_allele TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PMS1 NM_001128144 exon7 c.A814T p.I272F AAAGATATCTTAA . 190.0 69.0 226.0 0.0 . 78 . . . alt . . PASS Atlas-SNP GLS 2744 hgsc.bcm.edu hg19 2 191797508 191797508 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . GLS NM_001256310 exon15 c.A1717G p.K573E GTATGGAAAAAAG . 50.0 16.0 73.0 0.0 . 47 . . . none . . PASS Atlas-SNP STAT1 6772 hgsc.bcm.edu hg19 2 191873805 191873805 + Missense_Mutation SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . STAT1 NM_007315 exon4 c.G157C p.A53P TGGTGGCAAATGA . 69.0 16.0 78.0 0.0 . 93 . . . none . . PASS Atlas-SNP DNPEP 23549 hgsc.bcm.edu hg19 2 220251040 220251040 + Missense_Mutation SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DNPEP NM_012100 exon5 c.G427A p.D143N TCAGGTCACGGTC . 85.0 21.0 79.0 0.0 . 40 . . . none . . PASS Atlas-SNP SLC19A3 80704 hgsc.bcm.edu hg19 2 228566972 228566972 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SLC19A3 NM_025243 exon2 c.A63G p.L21L ACCAAATAAGCAG . 77.0 27.0 59.0 0.0 . 62 . . . none . . PASS Atlas-SNP UGT1A5 54579 hgsc.bcm.edu hg19 2 234622288 234622288 + Silent SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . UGT1A5 NM_019078 exon1 c.T651G p.P217P CTACCCTCTGGCC . 102.0 39.0 108.0 0.0 . 66 . . . none . . PASS Atlas-SNP CNTN6 27255 hgsc.bcm.edu hg19 3 1337389 1337389 + Missense_Mutation SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CNTN6 NM_014461 exon6 c.G559C p.E187Q AAAGTGGAACCAT . 116.0 39.0 120.0 0.0 . 245 . . . none . . PASS Atlas-SNP PLXNB1 5364 hgsc.bcm.edu hg19 3 48463585 48463585 + Silent SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PLXNB1 NM_001130082 exon6 c.T1449C p.A483A GTGCTGAGCACAG . 65.0 26.0 71.0 0.0 . 150 . . . none . . PASS Atlas-SNP ROBO2 6092 hgsc.bcm.edu hg19 3 77626674 77626674 + Missense_Mutation SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ROBO2 NM_002942 exon15 c.T2237C p.L746P CTGTACTGACAGT . 216.0 77.0 202.0 0.0 . 527 . . . none . . PASS Atlas-SNP ABCC5 10057 hgsc.bcm.edu hg19 3 183639163 183639163 + Silent SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ABCC5 NM_005688 exon30 c.C4239G p.V1413V CAGAAGGACCGAT . 160.0 55.0 206.0 0.0 . 142 . . . none . . PASS Atlas-SNP HGFAC 3083 hgsc.bcm.edu hg19 4 3447058 3447058 + Nonsense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HGFAC NM_001528 exon9 c.C1083A p.Y361X GGAGTACTGCCGC . 91.0 38.0 107.0 0.0 . 69 . . . none . . PASS Atlas-SNP RBM47 54502 hgsc.bcm.edu hg19 4 40440004 40440004 + Missense_Mutation SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . RBM47 NM_001098634 exon4 c.G907A p.G303S CAGTGCCGTTGAG . 44.0 21.0 49.0 0.0 . 146 . . . none . . PASS Atlas-SNP KLHL8 57563 hgsc.bcm.edu hg19 4 88091657 88091657 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . KLHL8 NM_020803 exon7 c.G1319T p.W440L GTACTCCACTGAT . 337.0 82.0 358.0 0.0 . 51 . . . none . . PASS Atlas-SNP ETFDH 2110 hgsc.bcm.edu hg19 4 159627888 159627888 + Missense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ETFDH NM_004453 exon12 c.G1576T p.G526C CTGAGTGGTACTA . 60.0 18.0 63.0 0.0 . 57 . . . none . . PASS Atlas-SNP GALNT7 51809 hgsc.bcm.edu hg19 4 174213365 174213365 + Missense_Mutation SNP A A C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . GALNT7 NM_017423 exon3 c.A694C p.K232Q GTAATTAAAAGGA . 151.0 53.0 176.0 0.0 . 61 . . . none . . PASS Atlas-SNP PPIP5K2 23262 hgsc.bcm.edu hg19 5 102509564 102509564 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PPIP5K2 NM_015216 exon20 c.A2417G p.Y806C TTAGGTATTCTAG . 36.0 12.0 38.0 0.0 . 98 . . . none . . PASS Atlas-SNP IK 3550 hgsc.bcm.edu hg19 5 140034273 140034273 + Nonsense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . IK NM_006083 exon8 c.G598T p.E200X AAAGATGAGGATC . 277.0 105.0 362.0 1.0 . 46 . . . none . . PASS Atlas-SNP RANBP9 10048 hgsc.bcm.edu hg19 6 13639868 13639868 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . RANBP9 NM_005493 exon9 c.A1452G p.P484P CATACTTGGACTA . 86.0 36.0 97.0 0.0 . 42 . . . none . . PASS Atlas-SNP FAM8A1 51439 hgsc.bcm.edu hg19 6 17601243 17601243 + Silent SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . FAM8A1 NM_016255 exon1 c.C603A p.G201G CGCGGGCCTGGGA . 23.0 8.0 21.0 0.0 . 26 . . . none . . PASS Atlas-SNP KDM1B 221656 hgsc.bcm.edu hg19 6 18166565 18166565 + Missense_Mutation SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . KDM1B NM_153042 exon6 c.C373G p.P125A ACCGAACCTAGTC . 124.0 50.0 132.0 0.0 . 58 . . . none . . PASS Atlas-SNP HIST1H2BB 3018 hgsc.bcm.edu hg19 6 26043884 26043884 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HIST1H2BB NM_021062 exon1 c.T2C p.M1T TCAGGCATTGCTA . 34.0 15.0 40.0 0.0 . 20 . . . none . . PASS Atlas-SNP ZNF391 346157 hgsc.bcm.edu hg19 6 27368767 27368767 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZNF391 NM_001076781 exon3 c.T618C p.T206T AAGCACTAACCTT . 48.0 20.0 61.0 0.0 . 90 . . . none . . PASS Atlas-SNP SLC22A7 10864 hgsc.bcm.edu hg19 6 43266308 43266308 + Missense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f SLC22A7,NS,carcinoma,0,1 SLC22A7 NM_006672 exon1 c.G212T p.R71L TTCCCCGGGAGCC . 24.0 11.0 46.0 0.0 . 69 . . . none . . PASS Atlas-SNP DDO 8528 hgsc.bcm.edu hg19 6 110726039 110726039 + Silent SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DDO NM_003649 exon4 c.T480C p.F160F CTGACCAAACACA . 105.0 47.0 145.0 0.0 . 51 . . . none . . PASS Atlas-SNP CCDC170 80129 hgsc.bcm.edu hg19 6 151907203 151907203 + Silent SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . NM_025059 exon7 c.C1272T p.N424N AGACAACTTGAAT . 66.0 24.0 72.0 0.0 . . . . . none . . PASS Atlas-SNP MAS1 4142 hgsc.bcm.edu hg19 6 160328746 160328746 + Missense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . MAS1 NM_002377 exon1 c.G759T p.E253D CTATGAGTATTGG . 110.0 47.0 110.0 0.0 . 42 . . . none . . PASS Atlas-SNP IGF2BP3 10643 hgsc.bcm.edu hg19 7 23352352 23352352 + Splice_Site SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . IGF2BP3 NM_006547 exon15 c.1641+2C>T . CCACTTGCCTGGC . 237.0 117.0 185.0 0.0 . 71 . . . none . . PASS Atlas-SNP IGF2BP3 10643 hgsc.bcm.edu hg19 7 23352353 23352353 + Splice_Site SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . IGF2BP3 NM_006547 exon15 c.1641+1G>A . CACTTGCCTGGCA . 237.0 120.0 184.0 0.0 . 71 . . . none . . PASS Atlas-SNP GATS 352954 hgsc.bcm.edu hg19 7 99821281 99821281 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . GATS NM_178831 exon4 c.C452T p.S151L TCTGATGACAACG . 408.0 90.0 378.0 0.0 . 18 . . . none . . PASS Atlas-SNP SRRT 51593 hgsc.bcm.edu hg19 7 100482162 100482162 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SRRT NM_001128853 exon7 c.G931A p.D311N AAGGAAGACGGCA . 234.0 62.0 163.0 0.0 . 108 . . . none . . PASS Atlas-SNP CPED1 79974 hgsc.bcm.edu hg19 7 120935571 120935571 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . NM_024913 exon23 c.T2946C p.Y982Y AAGATATTTCAGC . 117.0 31.0 114.0 0.0 . . . . . none . . PASS Atlas-SNP DLGAP2 9228 hgsc.bcm.edu hg19 8 1626467 1626467 + Silent SNP G G T rs149482724 bycluster;byfrequency;by1000genomes;alternate_allele TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DLGAP2 NM_004745 exon9 c.G2136T p.T712T CACCACGGAGGAC . 98.0 9.0 96.0 0.0 . 292 . . . alt G|0.999;A|0.001 . PASS Atlas-SNP SPAG11B 10407 hgsc.bcm.edu hg19 8 7308713 7308713 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SPAG11B NM_016512 exon3 c.T223C p.S75P GGTGAGAGATGTG . 507.0 146.0 420.0 0.0 . 32 . . . none . . PASS Atlas-SNP ENTPD4 9583 hgsc.bcm.edu hg19 8 23305329 23305329 + Silent SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ENTPD4 NM_004901 exon4 c.G276C p.V92V GTCCACCACGATC . 153.0 77.0 110.0 0.0 . 56 . . . none . . PASS Atlas-SNP ZNF395 55893 hgsc.bcm.edu hg19 8 28206326 28206326 + Missense_Mutation SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZNF395 NM_018660 exon10 c.G1452C p.K484N GCACTTCTTAGCC . 82.0 21.0 86.0 0.0 . 54 . . . none . . PASS Atlas-SNP ADAM32 203102 hgsc.bcm.edu hg19 8 39080665 39080665 + Missense_Mutation SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ADAM32 NM_145004 exon14 c.T1433G p.I478S CTTTAATCAATGG . 87.0 27.0 66.0 0.0 . 70 . . . none . . PASS Atlas-SNP C9orf152 401546 hgsc.bcm.edu hg19 9 112963539 112963539 + Nonsense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . C9orf152 NM_001012993 exon2 c.C409T p.Q137X GTACTTGATGACT . 30.0 11.0 62.0 0.0 . 20 . . . none . . PASS Atlas-SNP OR1L1 26737 hgsc.bcm.edu hg19 9 125424669 125424669 + Silent SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . OR1L1 NM_001005236 exon1 c.T675G p.V225V CACTGTTCTGAAG . 80.0 31.0 113.0 0.0 . 54 . . . none . . PASS Atlas-SNP PHYHD1 254295 hgsc.bcm.edu hg19 9 131702760 131702760 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PHYHD1 NM_174933 exon9 c.C548A p.S183Y GTTCATCCCTGGC . 61.0 26.0 58.0 0.0 . 29 . . . none . . PASS Atlas-SNP ZNF22 7570 hgsc.bcm.edu hg19 10 45499114 45499114 + Nonsense_Mutation SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZNF22 NM_006963 exon2 c.C298T p.Q100X CTCATTCAGCATC . 32.0 8.0 42.0 0.0 . 28 . . . none . . PASS Atlas-SNP ADK 132 hgsc.bcm.edu hg19 10 75911070 75911070 + Missense_Mutation SNP A A C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ADK NM_001202450 exon1 c.A34C p.K12Q CCCAAAAAGCTGA . 105.0 32.0 81.0 0.0 . 28 . . . none . . PASS Atlas-SNP CCSER2 54462 hgsc.bcm.edu hg19 10 86185593 86185593 + Missense_Mutation SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CCSER2 NM_018999 exon5 c.T1812G p.H604Q GGAGCATTACCAC . 60.0 19.0 100.0 0.0 . 7 . . . none . . PASS Atlas-SNP RBM20 282996 hgsc.bcm.edu hg19 10 112572059 112572059 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . RBM20 NM_001134363 exon9 c.C1904A p.S635Y CGCGGTCTCGTAG . 28.0 12.0 32.0 0.0 . 50 . . . none . . PASS Atlas-SNP FCHSD2 9873 hgsc.bcm.edu hg19 11 72552500 72552500 + Silent SNP G G A rs201269620 TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f FCHSD2_ENST00000409418,NS,carcinoma,0,6 FCHSD2 NM_014824 exon18 c.C2055T p.N685N CTTACCGTTTGCT . 78.0 32.0 100.0 0.0 . 106 . . . weak G|0.998;A|0.002 0.002 PASS Atlas-SNP PCF11 51585 hgsc.bcm.edu hg19 11 82877707 82877707 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f PCF11_ENST00000298281,NS,carcinoma,0,2 PCF11 NM_015885 exon5 c.A1768G p.S590G TGGCAAAGTTCCA . 159.0 38.0 192.0 0.0 . 220 . . . none . . PASS Atlas-SNP VAMP1 6843 hgsc.bcm.edu hg19 12 6574108 6574108 + Splice_Site SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f VAMP1,NS,carcinoma,0,1 VAMP1 NM_016830 exon5 c.289-1G>A . CATCATCTGAGGA . 30.0 12.0 35.0 0.0 . 6 . . . none . . PASS Atlas-SNP ATF7IP 55729 hgsc.bcm.edu hg19 12 14577946 14577946 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ATF7IP NM_018179 exon2 c.A1097G p.E366G CTCCTGAAAATGA . 58.0 33.0 56.0 0.0 . 136 . . . none . . PASS Atlas-SNP PDZRN4 29951 hgsc.bcm.edu hg19 12 41967250 41967250 + Missense_Mutation SNP A A C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PDZRN4 NM_001164595 exon10 c.A2669C p.K890T AATGGAAGGTGAA . 51.0 31.0 37.0 0.0 . 346 . . . none . . PASS Atlas-SNP PPHLN1 51535 hgsc.bcm.edu hg19 12 42768782 42768782 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . PPHLN1 NM_201515 exon6 c.T438C p.D146D AAAGGATTCTCCA . 201.0 108.0 152.0 0.0 . 101 . . . none . . PASS Atlas-SNP SLC38A2 54407 hgsc.bcm.edu hg19 12 46756297 46756297 + Missense_Mutation SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SLC38A2 NM_018976 exon14 c.G1304C p.R435T ATATCCCTAATAG . 210.0 55.0 157.0 0.0 . 36 . . . none . . PASS Atlas-SNP TBC1D15 64786 hgsc.bcm.edu hg19 12 72274296 72274296 + Silent SNP T T C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TBC1D15 NM_001146214 exon5 c.T276C p.G92G AAGAGGTCATCGA . 224.0 111.0 158.0 0.0 . 99 . . . none . . PASS Atlas-SNP COL4A2 1284 hgsc.bcm.edu hg19 13 111090980 111090980 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f COL4A2,NS,carcinoma,0,1 COL4A2 NM_001846 exon15 c.G877A p.G293R TTGAAGGGAGAAG . 66.0 20.0 83.0 0.0 . 178 . . . none . . PASS Atlas-SNP ZFP36L1 677 hgsc.bcm.edu hg19 14 69259682 69259682 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZFP36L1 NM_001244701 exon2 c.C181T p.R61C AGGGGCGAGGATC . 26.0 13.0 26.0 0.0 . 47 . . . none . . PASS Atlas-SNP ATG2B 55102 hgsc.bcm.edu hg19 14 96783528 96783528 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ATG2B NM_018036 exon20 c.T3164C p.L1055P TTCAGAAGAACTG . 97.0 41.0 108.0 0.0 . 169 . . . none . . PASS Atlas-SNP EID1 23741 hgsc.bcm.edu hg19 15 49170567 49170567 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . EID1 NM_014335 exon1 c.C194A p.P65Q CCCAGCCAATGGC . 49.0 14.0 60.0 0.0 . 16 . . . none . . PASS Atlas-SNP MYO5C 55930 hgsc.bcm.edu hg19 15 52517329 52517329 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . MYO5C NM_018728 exon27 c.T3308C p.M1103T TCTGACATCTTTT . 45.0 17.0 70.0 0.0 . 162 . . . none . . PASS Atlas-SNP CCDC64B 146439 hgsc.bcm.edu hg19 16 3078253 3078253 + Missense_Mutation SNP C C G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CCDC64B NM_001103175 exon9 c.G1381C p.G461R GCTGCCCGATCAC . 10.0 6.0 0.0 0.0 . 19 . . . none . . PASS Atlas-SNP SPIRE2 84501 hgsc.bcm.edu hg19 16 89929899 89929899 + Missense_Mutation SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . SPIRE2 NM_032451 exon11 c.G1591A p.V531M CACCCCGTGGAGA . 39.0 23.0 40.0 0.0 . 63 . . . none . . PASS Atlas-SNP DHRS13 147015 hgsc.bcm.edu hg19 17 27229847 27229847 + Missense_Mutation SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DHRS13 NM_144683 exon1 c.C116G p.A39G ACCACGGCCGTGC . 6.0 5.0 2.0 0.0 . 22 . . . none . . PASS Atlas-SNP HGS 9146 hgsc.bcm.edu hg19 17 79663907 79663907 + Silent SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HGS NM_004712 exon18 c.C1761A p.A587A ACCAGCCAGCTTC . 43.0 15.0 29.0 0.0 . 54 . . . none . . PASS Atlas-SNP ARHGDIA 396 hgsc.bcm.edu hg19 17 79827786 79827786 + Silent SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ARHGDIA NM_004309 exon2 c.A21C p.T7T CTCGGCTGTGGGC . 50.0 14.0 45.0 0.0 . 14 . . . none . . PASS Atlas-SNP TEX19 400629 hgsc.bcm.edu hg19 17 80320408 80320408 + Nonsense_Mutation SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TEX19 NM_207459 exon2 c.G382T p.E128X CCTCAGGAGGCTG . 91.0 37.0 77.0 0.0 . 17 . . . none . . PASS Atlas-SNP NEDD4L 23327 hgsc.bcm.edu hg19 18 56050535 56050535 + Nonsense_Mutation SNP A A T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NEDD4L NM_001144967 exon25 c.A2410T p.K804X GAAAACAAAAGGG . 62.0 22.0 61.0 0.0 . 126 . . . none . . PASS Atlas-SNP ARRDC5 645432 hgsc.bcm.edu hg19 19 4891365 4891365 + Missense_Mutation SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ARRDC5 NM_001080523 exon3 c.G722A p.R241Q GACCGCCGCTCTG . 24.0 9.0 21.0 0.0 . 19 . . . none . . PASS Atlas-SNP TSSK6 83983 hgsc.bcm.edu hg19 19 19625679 19625679 + Silent SNP G G T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TSSK6 NM_032037 exon1 c.C558A p.I186I GTAGGGGATGCCC . 21.0 7.0 14.0 0.0 . 32 . . . none . . PASS Atlas-SNP ZNF681 148213 hgsc.bcm.edu hg19 19 23927682 23927682 + Missense_Mutation SNP T T G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZNF681 NM_138286 exon4 c.A670C p.K224Q ACGATTTCTCTCC . 31.0 13.0 34.0 0.0 . 76 . . . none . . PASS Atlas-SNP CD3EAP 10849 hgsc.bcm.edu hg19 19 45912507 45912507 + Silent SNP G G A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CD3EAP NM_012099 exon3 c.G1281A p.K427K GAAGAAGAAAGAG . 85.0 30.0 90.0 0.0 . 27 . . . none . . PASS Atlas-SNP NFAM1 150372 hgsc.bcm.edu hg19 22 42781205 42781205 + Missense_Mutation SNP C C A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NFAM1 NM_145912 exon6 c.G775T p.D259Y CATCATCTTCGAA . 37.0 14.0 62.0 0.0 . 12 . . . none . . PASS Atlas-SNP CXorf38 159013 hgsc.bcm.edu hg19 X 40496278 40496278 + Missense_Mutation SNP A A G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CXorf38 NM_144970 exon4 c.T602C p.V201A GAGTATACTGCCA . 86.0 66.0 98.0 0.0 . 29 . . . none . . PASS Atlas-SNP TSPYL2 64061 hgsc.bcm.edu hg19 X 53112145 53112145 + Silent SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . TSPYL2 NM_022117 exon1 c.G465C p.A155A GTGGGCGCCCCAG . 54.0 43.0 77.0 0.0 . 53 . . . none . . PASS Atlas-SNP AR 367 hgsc.bcm.edu hg19 X 66765164 66765164 + Missense_Mutation SNP A A T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . AR NM_000044 exon1 c.A176T p.Q59L TGCAGCAGCAGCA . 66.0 13.0 71.0 0.0 . 249 . . . none . . PASS Atlas-SNP ND5 0 hgsc.bcm.edu hg19 MT 12980 12980 + Missense_Mutation SNP G G C novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . ENST00000361567 exon1 c.G644C p.G215A TACTAGGCCTCCT . 167.0 146.0 11.0 0.0 . . . . . none . . PASS Atlas-SNP CYTB 0 hgsc.bcm.edu hg19 MT 14752 14752 + Silent SNP C C T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . ENST00000361789 exon1 c.C6T p.T2T AATGACCCCAATA . 288.0 236.0 120.0 0.0 . . . . . none . . PASS Atlas-SNP DLGAP2 9228 hgsc.bcm.edu hg19 8 1626467 1626468 + Frame_Shift_Ins INS - - GAGGACT novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DLGAP2 NM_004745 exon9 c.2136_2137insGAGGACT p.T712fs . . 98.0 18.0 96.0 0.0 . 292 . 0.183673 0 none . . PASS Atlas-Indel,Pindel KIAA0586 9786 hgsc.bcm.edu hg19 14 58965662 58965663 + Frame_Shift_Ins INS - - T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . KIAA0586 NM_001244189 exon29 c.4311_4312insT p.Q1437fs . . 60.0 26.0 66.0 0.0 . 180 . 0.433333 0 none . . PASS Atlas-Indel,Pindel HIVEP1 3096 hgsc.bcm.edu hg19 6 12125716 12125716 + Frame_Shift_Del DEL G G - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HIVEP1 NM_002114 exon4 c.5687delA p.K1896fs . . 58.0 16.0 62.0 0.0 . 242 . 0.275862 0 none . . PASS Atlas-Indel,Pindel NEDD4 4734 hgsc.bcm.edu hg19 15 56207818 56207818 + Frame_Shift_Del DEL A A - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NEDD4 NM_198400 exon1 c.1213delA p.K405fs . . 98.0 37.0 119.0 0.0 . 167 . 0.377551 0 none . . PASS Atlas-Indel,Pindel DIP2C 22982 hgsc.bcm.edu hg19 10 459927 459927 + Frame_Shift_Del DEL C C - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . DIP2C NM_014974 exon8 c.984delC p.G328fs . . 39.0 14.0 40.0 0.0 . 195 . 0.358974 0 none . . PASS Atlas-Indel,Pindel NIPBL 25836 hgsc.bcm.edu hg19 5 37024711 37024728 + In_Frame_Del DEL AGAGTAATAAAGATTCTC AGAGTAATAAAGATTCTC - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 AGAGTAATAAAGATTCTC AGAGTAATAAAGATTCTC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NIPBL NM_015384 exon30 c.5598_5615del p.1866_1872del . . 168.0 24.0 235.0 0.0 . 513 . 0.142857 0 none . . PASS Atlas-Indel,Pindel NBPF6 653149 hgsc.bcm.edu hg19 1 108995872 108995873 + Frame_Shift_Del DEL GA GA - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 GA GA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NBPF6 NM_001143987 exon4 c.347_348del p.116_116del . . 208.0 33.0 247.0 0.0 . 4 . 0.158654 0 none . . PASS Atlas-Indel,Pindel ZFP64 55734 hgsc.bcm.edu hg19 20 50701317 50701318 + Frame_Shift_Ins INS - - G novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . ZFP64 NM_199427 exon9 c.1717_1718insC p.K573fs . . 27.0 12.0 52.0 0.0 . 240 . 0.444444 0 none . . PASS Atlas-INDEL NUP43 348995 hgsc.bcm.edu hg19 6 150059828 150059828 + Frame_Shift_Del DEL T T - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NUP43 NM_198887 exon5 c.590delT p.I197fs . . 76.0 30.0 51.0 0.0 . 32 . 0.394737 0 none . . PASS Atlas-Indel,Pindel HIPK1 204851 hgsc.bcm.edu hg19 1 114483624 114483626 + In_Frame_Del DEL TGC TGC - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 TGC TGC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . HIPK1 NM_152696 exon2 c.618_620del p.206_207del . . 35.0 10.0 55.0 0.0 . 195 . 0.285714 0 none . . PASS Atlas-INDEL MRPL23 6150 hgsc.bcm.edu hg19 11 1972132 1972133 + Frame_Shift_Del DEL CC CC - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 CC CC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . MRPL23 NM_021134 exon2 c.20_21del p.7_7del . . 51.0 14.0 51.0 0.0 . 14 . 0.27451 0 none . . PASS Atlas-Indel,Pindel KIAA1109 84162 hgsc.bcm.edu hg19 4 123277058 123277059 + Frame_Shift_Ins INS - - A novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . KIAA1109 NM_015312 exon81 c.14413_14414insA p.E4805fs . . 92.0 35.0 101.0 0.0 . 424 . 0.380435 0 none . . PASS Atlas-Indel,Pindel MED13L 23389 hgsc.bcm.edu hg19 12 116418708 116418709 + Frame_Shift_Ins INS - - T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . MED13L NM_015335 exon23 c.5211_5212insA p.K1737fs . . 93.0 18.0 53.0 0.0 . 193 . 0.193548 0 none . . PASS Atlas-Indel,Pindel EMC4 51234 hgsc.bcm.edu hg19 15 34519983 34519983 + Frame_Shift_Del DEL C C - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . . NM_016454 exon3 c.290delT p.F97fs . . 84.0 21.0 98.0 0.0 . . . 0.25 0 none . . PASS Atlas-Indel,Pindel CXorf22 170063 hgsc.bcm.edu hg19 X 35994031 35994032 + Splice_Site INS - - T novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . CXorf22 NM_152632 exon15 c.2713+1->T . . . 35.0 18.0 39.0 0.0 . 272 . 0.514 . none . . PASS Pindel NBPF4 148545 hgsc.bcm.edu hg19 1 108783712 108783713 + Frame_Shift_Del DEL TC TC - novel TCGA-SX-A71U-01A-12D-A33Q-10 TCGA-SX-A71U-10A-01D-A33Q-10 TC TC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 3d451356-8c58-451d-a6cf-223e76cae191 2c6bb397-d986-49b1-b1dc-1151c8aae19f . NBPF4 NM_001143989 exon4 c.353_354del p.118_118del . . 266.0 33.0 273.0 0.0 . 4 . 0.124 . none . . PASS Pindel