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 PHF13 148479 hgsc.bcm.edu hg19 1 6681657 6681657 + Missense_Mutation SNP A A G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PHF13 NM_153812 exon4 c.A863G p.N288S GTTCCAACCGCTC . 110.0 6.0 156.0 0.0 . 24 . . Atlas-SNP FBXO2 26232 hgsc.bcm.edu hg19 1 11710798 11710798 + Missense_Mutation SNP T T G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 FBXO2,NS,carcinoma,0,1 FBXO2 NM_012168 exon2 c.A116C p.E39A GCCGCCTCCTCCT . 16.0 2.0 25.0 0.0 . 25 . . Atlas-SNP TNFRSF8 943 hgsc.bcm.edu hg19 1 12169683 12169683 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TNFRSF8 NM_001243 exon5 c.C482T p.A161V CCTGTGCCAGCCC . 68.0 4.0 85.0 0.0 . 70 . . Atlas-SNP PADI2 11240 hgsc.bcm.edu hg19 1 17410314 17410314 + Silent SNP C C T rs141844952 TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PADI2 NM_007365 exon9 c.G957A p.L319L CAGGAACAGGTAA . 67.0 30.0 93.0 0.0 . 72 . C|1.000;T|0.000 Atlas-SNP FAM110D 79927 hgsc.bcm.edu hg19 1 26487902 26487902 + Missense_Mutation SNP G G T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . . NM_024869 exon2 c.G120T p.E40D ACAGGAGCCAGCC . 92.0 33.0 149.0 0.0 . . . . Atlas-SNP IPP 3652 hgsc.bcm.edu hg19 1 46195357 46195357 + Missense_Mutation SNP T T G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . IPP NM_001145349 exon4 c.A809C p.K270T CAAAACTTGTTCT . 247.0 52.0 294.0 0.0 . 66 . . Atlas-SNP CA14 23632 hgsc.bcm.edu hg19 1 150235583 150235583 + Missense_Mutation SNP G G T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . CA14 NM_012113 exon7 c.G705T p.Q235H GTCCCAGATTTCA . 211.0 11.0 165.0 0.0 . 37 . . Atlas-SNP TADA1 117143 hgsc.bcm.edu hg19 1 166826920 166826920 + Missense_Mutation SNP C C G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TADA1 NM_053053 exon8 c.G892C p.A298P TAAGAGCATAGAC . 172.0 59.0 152.0 0.0 . 32 . . Atlas-SNP HMCN1 83872 hgsc.bcm.edu hg19 1 186047303 186047303 + Silent SNP T T A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . HMCN1 NM_031935 exon55 c.T8550A p.A2850A TGTGGCTGTGAAT . 214.0 32.0 179.0 0.0 . 797 . . Atlas-SNP PGBD5 79605 hgsc.bcm.edu hg19 1 230492809 230492809 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 PGBD5,rectum,carcinoma,-1,1 PGBD5 NM_001258311 exon2 c.G590A p.R197H AGGCTGCGGTTGC . 134.0 6.0 134.0 0.0 . 73 . . Atlas-SNP LRPPRC 10128 hgsc.bcm.edu hg19 2 44152227 44152227 + Missense_Mutation SNP A A G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . LRPPRC NM_133259 exon27 c.T2875C p.Y959H GATTGTAGTACAT . 63.0 13.0 95.0 0.0 . 105 . . Atlas-SNP ANTXR1 84168 hgsc.bcm.edu hg19 2 69408989 69408989 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ANTXR1 NM_032208 exon15 c.C1161T p.G387G GAGAGGCGTTGGA . 96.0 23.0 154.0 0.0 . 128 . . Atlas-SNP DPP4 1803 hgsc.bcm.edu hg19 2 162894911 162894911 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . DPP4 NM_001935 exon8 c.A514G p.I172V CATAAATGTCATT . 186.0 19.0 271.0 0.0 . 90 . . Atlas-SNP ANKRD44 91526 hgsc.bcm.edu hg19 2 197948233 197948233 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ANKRD44 NM_001195144 exon14 c.G1317A p.R439R AGGGGTCCTGAAA . 74.0 11.0 88.0 0.0 . 281 . . Atlas-SNP SIAH2 6478 hgsc.bcm.edu hg19 3 150480232 150480232 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . SIAH2 NM_005067 exon1 c.G405A p.L135L GGGAAACAGGACT . 52.0 23.0 94.0 0.0 . 33 . . Atlas-SNP ATP13A3 79572 hgsc.bcm.edu hg19 3 194140666 194140666 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ATP13A3 NM_024524 exon30 c.A3344G p.Y1115C AAAATATATAAAA . 620.0 30.0 717.0 0.0 . 94 . . Atlas-SNP ALB 213 hgsc.bcm.edu hg19 4 74280793 74280793 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ALB NM_000477 exon9 c.T1100C p.V367A ACTCTGTCGTGCT . 80.0 34.0 132.0 0.0 . 132 . . Atlas-SNP PDHA2 5161 hgsc.bcm.edu hg19 4 96761441 96761441 + Missense_Mutation SNP G G T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PDHA2 NM_005390 exon1 c.G140T p.G47V AAGAGGGTCCCCC . 137.0 25.0 183.0 0.0 . 118 . . Atlas-SNP CDKN2AIP 55602 hgsc.bcm.edu hg19 4 184367702 184367702 + Nonsense_Mutation SNP G G T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . CDKN2AIP NM_017632 exon3 c.G865T p.E289X GAGATCGAGGTGC . 159.0 39.0 172.0 0.0 . 31 . . Atlas-SNP ANKRD55 79722 hgsc.bcm.edu hg19 5 55422893 55422893 + Missense_Mutation SNP T T G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ANKRD55 NM_024669 exon8 c.A653C p.H218P CCCTGGTGATGGC . 187.0 57.0 150.0 0.0 . 70 . . Atlas-SNP DOCK2 1794 hgsc.bcm.edu hg19 5 169507279 169507279 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . DOCK2 NM_004946 exon50 c.C5279A p.T1760N TGCCTACCATCCC . 91.0 26.0 78.0 0.0 . 389 . . Atlas-SNP DOCK2 1794 hgsc.bcm.edu hg19 5 169507280 169507280 + Silent SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . DOCK2 NM_004946 exon50 c.C5280A p.T1760T GCCTACCATCCCA . 90.0 27.0 77.0 0.0 . 389 . . Atlas-SNP PKHD1 5314 hgsc.bcm.edu hg19 6 51910977 51910977 + Missense_Mutation SNP A A G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PKHD1 NM_170724 exon24 c.T2417C p.V806A ATTTGTACAGGGA . 105.0 11.0 151.0 0.0 . 927 . . Atlas-SNP COL12A1 1303 hgsc.bcm.edu hg19 6 75847218 75847218 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . COL12A1 NM_004370 exon31 c.A5329G p.S1777G GACCACTAGCAGG . 99.0 33.0 125.0 0.0 . 385 . . Atlas-SNP PRDM13 59336 hgsc.bcm.edu hg19 6 100057092 100057092 + Missense_Mutation SNP G G T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PRDM13 NM_021620 exon3 c.G306T p.Q102H CGTCCAGCCAGGG . 99.0 37.0 114.0 0.0 . 65 . . Atlas-SNP PCLO 27445 hgsc.bcm.edu hg19 7 82545902 82545902 + Silent SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 PCLO_ENST00000333891,right_upper_lobe,carcinoma,0,2 PCLO NM_014510 exon7 c.C11400T p.Y3800Y TTCCAGGTATCGT . 129.0 9.0 144.0 0.0 . 1506 . . Atlas-SNP DPP6 1804 hgsc.bcm.edu hg19 7 154667719 154667719 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . DPP6 NM_130797 exon20 c.C1987T p.R663C GACGGCCGTGGCA . 94.0 16.0 106.0 0.0 . 383 . . Atlas-SNP ANGPT1 284 hgsc.bcm.edu hg19 8 108315574 108315574 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ANGPT1 NM_001146 exon5 c.G830T p.R277I TCCTCTCTTTTTC . 141.0 8.0 99.0 0.0 . 111 . . Atlas-SNP COL22A1 169044 hgsc.bcm.edu hg19 8 139601631 139601631 + Silent SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . COL22A1 NM_152888 exon65 c.C4746T p.G1582G TTGAGGGCCAGGG . 338.0 33.0 233.0 0.0 . 390 . . Atlas-SNP TOPORS 10210 hgsc.bcm.edu hg19 9 32543499 32543499 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TOPORS NM_005802 exon3 c.C1024T p.P342S AAAATGGTCTTAA . 69.0 15.0 68.0 0.0 . 127 . . Atlas-SNP TRPM3 80036 hgsc.bcm.edu hg19 9 73213415 73213415 + Missense_Mutation SNP T T A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TRPM3 NM_001007471 exon20 c.A2932T p.I978F AGTAAATGATGTT . 183.0 29.0 179.0 0.0 . 700 . . Atlas-SNP TRIM32 22954 hgsc.bcm.edu hg19 9 119460448 119460448 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TRIM32 NM_012210 exon2 c.G427A p.E143K GCAGCTGAGGAGC . 106.0 50.0 110.0 0.0 . 67 . . Atlas-SNP ATRNL1 26033 hgsc.bcm.edu hg19 10 117278802 117278802 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ATRNL1 NM_207303 exon25 c.G3684A p.M1228I AATCATGGACCTT . 96.0 42.0 102.0 0.0 . 219 . . Atlas-SNP FOXI2 399823 hgsc.bcm.edu hg19 10 129537185 129537185 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 FOXI2_ENST00000388920,NS,carcinoma,0,2 FOXI2 NM_207426 exon2 c.C913T p.R305C GGCTTCCGCCTCA . 72.0 6.0 63.0 0.0 . 35 . . Atlas-SNP MUC6 4588 hgsc.bcm.edu hg19 11 1031883 1031883 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . MUC6 NM_005961 exon3 c.C286T p.R96W TGATCCGCGAGAT . 73.0 9.0 63.0 0.0 . 408 . . Atlas-SNP MUC5B 727897 hgsc.bcm.edu hg19 11 1251007 1251007 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . MUC5B NM_002458 exon10 c.G1190A p.G397D GCCCGGGCACCTC . 45.0 14.0 41.0 0.0 . 473 . . Atlas-SNP TCIRG1 10312 hgsc.bcm.edu hg19 11 67815394 67815394 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TCIRG1 NM_006019 exon13 c.C1509T p.N503N TCCCAACGTCACC . 118.0 36.0 140.0 0.0 . 40 . . Atlas-SNP CCDC60 160777 hgsc.bcm.edu hg19 12 119978493 119978493 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . CCDC60 NM_178499 exon14 c.C1626T p.P542P CATACCCATTGGG . 57.0 18.0 72.0 0.0 . 84 . . Atlas-SNP COG3 83548 hgsc.bcm.edu hg19 13 46085912 46085912 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . COG3 NM_031431 exon16 c.C1732A p.Q578K GTGTTCCAAGGAT . 83.0 9.0 82.0 0.0 . 52 . . Atlas-SNP FAM179B 23116 hgsc.bcm.edu hg19 14 45496671 45496671 + Silent SNP A A G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . FAM179B NM_015091 exon9 c.A3498G p.E1166E GAATGAAAAAGAT . 167.0 39.0 210.0 0.0 . 115 . . Atlas-SNP ZFP36L1 677 hgsc.bcm.edu hg19 14 69256295 69256295 + Silent SNP T T G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ZFP36L1 NM_001244701 exon3 c.A1179C p.S393S GCGTCTTGAGTTG . 73.0 11.0 105.0 0.0 . 47 . . Atlas-SNP GABRA5 2558 hgsc.bcm.edu hg19 15 27193200 27193200 + Silent SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . GABRA5 NM_001165037 exon11 c.C1209A p.V403V CTCAGTCTCAGTA . 427.0 180.0 395.0 0.0 . 127 . . Atlas-SNP PARP6 56965 hgsc.bcm.edu hg19 15 72541642 72541642 + Missense_Mutation SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PARP6 NM_020214 exon19 c.C1505T p.A502V CCATAGGCTGCTC . 70.0 31.0 58.0 0.0 . 44 . . Atlas-SNP BAIAP3 8938 hgsc.bcm.edu hg19 16 1396324 1396324 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . BAIAP3 NM_003933 exon25 c.C2560T p.R854W CTGCAACGGGAGG . 153.0 50.0 171.0 0.0 . 88 . . Atlas-SNP TP53 7157 hgsc.bcm.edu hg19 17 7577538 7577538 + Missense_Mutation SNP C C T rs11540652 bycluster TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 TP53_ENST00000545858,NS,adenocarcinoma,0,4 TP53 NM_000546 exon7 c.G743A p.R248Q GGCCTCCGGTTCA . 86.0 18.0 98.0 0.0 . 33396 . . Atlas-SNP SOX9 6662 hgsc.bcm.edu hg19 17 70120053 70120053 + Missense_Mutation SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . SOX9 NM_000346 exon3 c.C1055T p.A352V CACAGGCCCCGCC . 61.0 23.0 135.0 0.0 . 91 . . Atlas-SNP UNK 85451 hgsc.bcm.edu hg19 17 73805893 73805893 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . UNK NM_001080419 exon2 c.T157C p.C53R CACAAATGCACGC . 124.0 29.0 154.0 0.0 . 87 . . Atlas-SNP ZNF91 7644 hgsc.bcm.edu hg19 19 23542679 23542679 + Silent SNP G G A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ZNF91 NM_003430 exon4 c.C3102T p.S1034S CTTTGAGGATCGA . 50.0 4.0 38.0 0.0 . 349 . . Atlas-SNP KLK10 5655 hgsc.bcm.edu hg19 19 51520439 51520439 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . KLK10 NM_145888 exon3 c.G196T p.G66C AGAGGCCGTTGAA . 120.0 7.0 125.0 0.0 . 32 . . Atlas-SNP ZNF665 79788 hgsc.bcm.edu hg19 19 53668097 53668097 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ZNF665 NM_024733 exon4 c.A1646G p.K549R AAGACCTTGCCGC . 96.0 22.0 121.0 0.0 . 136 . . Atlas-SNP VSTM1 284415 hgsc.bcm.edu hg19 19 54545432 54545432 + Missense_Mutation SNP G G C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 VSTM1,NS,carcinoma,0,1 VSTM1 NM_198481 exon6 c.C506G p.S169C TTGGTGGATTCCT . 101.0 36.0 147.0 0.0 . 30 . . Atlas-SNP LILRA3 11026 hgsc.bcm.edu hg19 19 54802132 54802132 + Missense_Mutation SNP C C G novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . LILRA3 NM_006865 exon6 c.G1056C p.M352I AGTGTGCATCCCT . 88.0 34.0 93.0 0.0 . 65 . . Atlas-SNP LENG8 114823 hgsc.bcm.edu hg19 19 54967900 54967900 + Nonsense_Mutation SNP A A T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . LENG8 NM_052925 exon11 c.A1531T p.K511X AAGCAGAAGCGGG . 123.0 5.0 127.0 0.0 . 73 . . Atlas-SNP U2AF2 11338 hgsc.bcm.edu hg19 19 56180129 56180129 + Missense_Mutation SNP G G C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . U2AF2 NM_001012478 exon9 c.G916C p.E306Q TTCTGTGAGTACG . 73.0 19.0 72.0 0.0 . 62 . . Atlas-SNP PREX1 57580 hgsc.bcm.edu hg19 20 47267479 47267479 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PREX1 NM_020820 exon23 c.G2770T p.D924Y TGGTGTCACAGAT . 77.0 16.0 63.0 0.0 . 441 . . Atlas-SNP PREX1 57580 hgsc.bcm.edu hg19 20 47267528 47267528 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PREX1 NM_020820 exon23 c.G2721A p.L907L GCTGCTCAGGGCC . 92.0 17.0 74.0 0.0 . 441 . . Atlas-SNP PREX1 57580 hgsc.bcm.edu hg19 20 47267976 47267976 + Silent SNP C C T novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . PREX1 NM_020820 exon22 c.G2613A p.E871E GATCTTCTCCAGC . 112.0 14.0 85.0 0.0 . 441 . . Atlas-SNP TSHZ2 128553 hgsc.bcm.edu hg19 20 51870809 51870809 + Missense_Mutation SNP C C A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 TSHZ2,NS,carcinoma,0,1 TSHZ2 NM_173485 exon2 c.C812A p.A271D AGGATGCTCAAAA . 281.0 12.0 207.0 1.0 . 209 . . Atlas-SNP CCT8L2 150160 hgsc.bcm.edu hg19 22 17071949 17071949 + Missense_Mutation SNP T T C novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . CCT8L2 NM_014406 exon1 c.A1492G p.I498V TGACTATTAGGGT . 156.0 68.0 165.0 0.0 . 150 . . Atlas-SNP RYR1 6261 hgsc.bcm.edu hg19 19 38964339 38964340 + In_Frame_Ins INS - - GGG novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . RYR1 NM_001042723 exon28 c.4088_4089insGGG p.A1363delinsAG . . 357.0 32.0 367.0 0.0 . 708 . . Atlas-INDEL ZNF800 168850 hgsc.bcm.edu hg19 7 127014205 127014205 + Frame_Shift_Del DEL T T - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . ZNF800 NM_176814 exon5 c.1186delG p.G396fs . . 155.0 24.0 135.0 0.0 . 78 . . Atlas-INDEL NKX2-2 4821 hgsc.bcm.edu hg19 20 21493051 21493065 + In_Frame_Del DEL GACTCGTCGGCCGAG GACTCGTCGGCCGAG - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 GACTCGTCGGCCGAG GACTCGTCGGCCGAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . NKX2-2 NM_002509 exon2 c.319_333del p.107_111del . . 55.0 25.0 54.0 0.0 . 49 . . Atlas-INDEL NLGN4Y 22829 hgsc.bcm.edu hg19 Y 16941993 16942000 + Frame_Shift_Del DEL GTGTCCAA GTGTCCAA - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 GTGTCCAA GTGTCCAA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . NLGN4Y NM_014893 exon5 c.1194_1201del p.398_401del . . 223.0 36.0 290.0 0.0 . 44 . . Atlas-INDEL NLGN4Y 22829 hgsc.bcm.edu hg19 Y 16942005 16942017 + Frame_Shift_Del DEL GTGGACAACCTTT GTGGACAACCTTT - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 GTGGACAACCTTT GTGGACAACCTTT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . NLGN4Y NM_014893 exon5 c.1206_1218del p.402_406del . . 225.0 36.0 270.0 0.0 . 44 . . Atlas-INDEL UPF3B 65109 hgsc.bcm.edu hg19 X 118975107 118975108 + Frame_Shift_Ins INS - - A novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . UPF3B NM_023010 exon7 c.739_740insT p.I247fs . . 53.0 33.0 40.0 0.0 . 74 . . Atlas-INDEL ALB 213 hgsc.bcm.edu hg19 4 74272459 74272459 + Frame_Shift_Del DEL A A - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 .,1 ALB NM_000477 exon3 c.250delG p.E84fs . . 75.0 12.0 92.0 0.0 . 132 . . Atlas-INDEL TBX18 9096 hgsc.bcm.edu hg19 6 85446692 85446699 + Frame_Shift_Del DEL TGGTTAGT TGGTTAGT - novel TCGA-WQ-AB4B-01A-11D-A40P-10 TCGA-WQ-AB4B-10A-01D-A40P-10 TGGTTAGT TGGTTAGT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq d1df28a1-65e0-4a10-b05b-7e20735cf012 3fa70dca-15c8-4428-978e-0c1403b4f704 . TBX18 NM_001080508 exon8 c.1529_1536del p.510_512del . . 129.0 28.0 174.0 0.0 . 131 . . Atlas-INDEL