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 C1orf86 199990 hgsc.bcm.edu hg19 1 2125123 2125123 + Missense_Mutation SNP G G T rs200185087 bycluster;alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . C1orf86 NM_001256946 exon3 c.C425A p.A142E AGGGCCGCGGCAC . 102.0 42.0 88.0 0.0 . 20 . . . alt . . PASS Atlas-SNP C1orf127 148345 hgsc.bcm.edu hg19 1 11009850 11009850 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . C1orf127 NM_001170754 exon11 c.C1121T p.A374V GTTGAGGCAGGCG . 102.0 40.0 96.0 0.0 . 134 . . . none . . PASS Atlas-SNP PRDM2 7799 hgsc.bcm.edu hg19 1 14105779 14105779 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PRDM2 NM_015866 exon8 c.A1489G p.N497D CATACTAATATGA . 299.0 12.0 273.0 0.0 . 147 . . . none . . PASS Atlas-SNP OTUD3 23252 hgsc.bcm.edu hg19 1 20220906 20220906 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . OTUD3 NM_015207 exon3 c.T416C p.I139T ATGCAATTGTAGC . 73.0 35.0 69.0 0.0 . 25 . . . none . . PASS Atlas-SNP OTUD3 23252 hgsc.bcm.edu hg19 1 20220910 20220910 + Silent SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . OTUD3 NM_015207 exon3 c.A420G p.V140V AATTGTAGCCTTT . 75.0 37.0 72.0 0.0 . 25 . . . none . . PASS Atlas-SNP USP48 84196 hgsc.bcm.edu hg19 1 22041910 22041910 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . USP48 NM_032236 exon15 c.T1935A p.N645K ATTAAAATTTAAT . 512.0 200.0 502.0 1.0 . 91 . . . none . . PASS Atlas-SNP SZT2 23334 hgsc.bcm.edu hg19 1 43906920 43906920 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SZT2 NM_015284 exon52 c.A7209T p.K2403N CCCCAAAACAACT . 112.0 54.0 114.0 0.0 . 383 . . . none . . PASS Atlas-SNP BTBD19 149478 hgsc.bcm.edu hg19 1 45278689 45278689 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . BTBD19 NM_001136537 exon5 c.G436A p.G146R GGCCTGGGGCAGC . 102.0 39.0 67.0 0.0 . 16 . . . none . . PASS Atlas-SNP RPRD2 23248 hgsc.bcm.edu hg19 1 150337371 150337371 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . RPRD2 NM_015203 exon1 c.C181A p.H61N GTCTATCATTGGA . 136.0 46.0 129.0 0.0 . 189 . . . none . . PASS Atlas-SNP CACNA1E 777 hgsc.bcm.edu hg19 1 181765855 181765855 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CACNA1E NM_001205293 exon47 c.A6260C p.K2087T GATCAAAAGAGCG . 128.0 47.0 115.0 0.0 . 778 . . . none . . PASS Atlas-SNP USH2A 7399 hgsc.bcm.edu hg19 1 215853630 215853630 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . USH2A NM_206933 exon62 c.T12155G p.I4052S CTTAAAATTTCTC . 98.0 46.0 129.0 0.0 . 1168 . . . none . . PASS Atlas-SNP OBSCN 84033 hgsc.bcm.edu hg19 1 228525744 228525744 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . OBSCN NM_001271223 exon78 c.G19771A p.A6591T CTGGATGCAGCCC . 58.0 16.0 53.0 0.0 . 2142 . . . none . . PASS Atlas-SNP NUP133 55746 hgsc.bcm.edu hg19 1 229606482 229606482 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NUP133 NM_018230 exon15 c.T1921A p.C641S GCTCACAGAGCAA . 138.0 65.0 171.0 0.0 . 111 . . . none . . PASS Atlas-SNP SH3YL1 26751 hgsc.bcm.edu hg19 2 253096 253096 + Silent SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 SH3YL1_ENST00000405430,NS,carcinoma,0,2 SH3YL1 NM_001159597 exon2 c.C21T p.S7S CAAATTGGAAGGT . 64.0 24.0 51.0 0.0 . 49 . . . none . . PASS Atlas-SNP GPR113 165082 hgsc.bcm.edu hg19 2 26537464 26537464 + Missense_Mutation SNP T T A rs148640513 bycluster;by1000genomes;alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GPR113 NM_001145168 exon7 c.A950T p.Q317L AAGCCCTGGGCCT . 167.0 70.0 160.0 0.0 . 134 . . . alt T|1.000;C|0.000 . PASS Atlas-SNP C2orf71 388939 hgsc.bcm.edu hg19 2 29296881 29296881 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . C2orf71 NM_001029883 exon1 c.T247G p.S83A TGCCTGAAGCAGG . 158.0 56.0 137.0 0.0 . 146 . . . none . . PASS Atlas-SNP PCBP1 5093 hgsc.bcm.edu hg19 2 70315518 70315518 + Nonsense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 PCBP1,NS,carcinoma,0,1 PCBP1 NM_006196 exon1 c.G643T p.E215X GACCTGGAGGGAC . 120.0 57.0 101.0 0.0 . 28 . . . none . . PASS Atlas-SNP SESTD1 91404 hgsc.bcm.edu hg19 2 179997038 179997038 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SESTD1 NM_178123 exon10 c.A965C p.Q322P CTGTGCTGGCTCT . 61.0 23.0 65.0 0.0 . 66 . . . none . . PASS Atlas-SNP CERKL 375298 hgsc.bcm.edu hg19 2 182468798 182468798 + Nonsense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CERKL NM_001160277 exon2 c.A247T p.K83X CATACTTAGAATC . 109.0 48.0 81.0 0.0 . 138 . . . none . . PASS Atlas-SNP TRIP12 9320 hgsc.bcm.edu hg19 2 230633435 230633435 + Silent SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TRIP12 NM_004238 exon40 c.T5679C p.S1893S AGCCCGACTATAA . 84.0 35.0 64.0 0.0 . 207 . . . none . . PASS Atlas-SNP TRIP12 9320 hgsc.bcm.edu hg19 2 230663701 230663701 + Silent SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TRIP12 NM_004238 exon22 c.A3147G p.T1049T TCCCCATGTTTTT . 95.0 44.0 94.0 0.0 . 207 . . . none . . PASS Atlas-SNP PER2 8864 hgsc.bcm.edu hg19 2 239167228 239167228 + Missense_Mutation SNP C C G rs202103918 by1000genomes;alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PER2 NM_022817 exon15 c.G1685C p.S562T CCCAGGCTGTCCT . 84.0 39.0 81.0 0.0 . 85 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP THAP4 51078 hgsc.bcm.edu hg19 2 242541346 242541346 + Silent SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . THAP4 NM_015963 exon5 c.A1579C p.R527R AGATCCTGGCGAT . 42.0 17.0 50.0 0.0 . 27 . . . none . . PASS Atlas-SNP THAP4 51078 hgsc.bcm.edu hg19 2 242541347 242541347 + Silent SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . THAP4 NM_015963 exon5 c.C1578G p.A526A GATCCTGGCGATG . 41.0 16.0 50.0 0.0 . 27 . . . none . . PASS Atlas-SNP CNTN6 27255 hgsc.bcm.edu hg19 3 1424987 1424987 + Silent SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CNTN6 NM_014461 exon19 c.G2412A p.L804L TCAACTGGCCCCA . 203.0 45.0 135.0 0.0 . 245 . . . none . . PASS Atlas-SNP ZNF385D 79750 hgsc.bcm.edu hg19 3 21478596 21478596 + Missense_Mutation SNP C C T rs368223028 alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZNF385D NM_024697 exon5 c.G539A p.S180N GTTGGGCTTTTTT . 136.0 35.0 96.0 0.0 . 93 . . . alt . . PASS Atlas-SNP AMT 275 hgsc.bcm.edu hg19 3 49456530 49456530 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . AMT NM_001164712 exon7 c.C751G p.P251A CCTCTGGGTTTTT . 167.0 98.0 121.0 0.0 . 22 . . . none . . PASS Atlas-SNP GNAI2 2771 hgsc.bcm.edu hg19 3 50294444 50294444 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GNAI2 NM_002070 exon7 c.C799A p.L267I ATCATCCTCTTCC . 106.0 78.0 105.0 0.0 . 42 . . . none . . PASS Atlas-SNP STAB1 23166 hgsc.bcm.edu hg19 3 52551367 52551367 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . STAB1 NM_015136 exon43 c.C4521T p.G1507G CGGGGGCTGCCAC . 213.0 61.0 162.0 0.0 . 178 . . . none . . PASS Atlas-SNP ZBTB11 27107 hgsc.bcm.edu hg19 3 101371385 101371385 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZBTB11 NM_014415 exon10 c.T2599G p.F867V GAGTGAATTTTCT . 157.0 74.0 107.0 0.0 . 77 . . . none . . PASS Atlas-SNP ZBTB11 27107 hgsc.bcm.edu hg19 3 101371390 101371390 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZBTB11 NM_014415 exon10 c.G2594A p.R865K AATTTTCTTCCAC . 159.0 75.0 106.0 0.0 . 77 . . . none . . PASS Atlas-SNP ACAP2 23527 hgsc.bcm.edu hg19 3 195000100 195000100 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ACAP2 NM_012287 exon23 c.C2294A p.P765Q TTCTCTGGATTAT . 284.0 79.0 186.0 0.0 . 72 . . . none . . PASS Atlas-SNP MUC4 4585 hgsc.bcm.edu hg19 3 195512378 195512378 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MUC4 NM_018406 exon2 c.G6073T p.A2025S TGGATGCTGAGGA . 115.0 7.0 74.0 0.0 . 1505 . . . none . . PASS Atlas-SNP LRRC66 339977 hgsc.bcm.edu hg19 4 52861134 52861134 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . LRRC66 NM_001024611 exon4 c.A2054T p.E685V ACTGGTTCCTTGT . 48.0 21.0 38.0 0.0 . 128 . . . none . . PASS Atlas-SNP MOB1B 92597 hgsc.bcm.edu hg19 4 71844887 71844887 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . . NM_001244766 exon6 c.T467C p.I156T AAACTATACTCAA . 96.0 36.0 83.0 0.0 . . . . . none . . PASS Atlas-SNP SHROOM3 57619 hgsc.bcm.edu hg19 4 77680809 77680809 + Silent SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SHROOM3 NM_020859 exon9 c.G5310T p.V1770V AGAAGTGAATGAG . 171.0 82.0 167.0 0.0 . 134 . . . none . . PASS Atlas-SNP FRAS1 80144 hgsc.bcm.edu hg19 4 79188585 79188585 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . FRAS1 NM_001166133 exon9 c.G980T p.R327L GTGCCCGGGTAAG . 122.0 48.0 123.0 0.0 . 779 . . . none . . PASS Atlas-SNP USP53 54532 hgsc.bcm.edu hg19 4 120189437 120189437 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . USP53 NM_019050 exon13 c.G1150A p.V384I AAGCCTGTAATTC . 350.0 132.0 373.0 1.0 . 69 . . . none . . PASS Atlas-SNP KIAA1109 84162 hgsc.bcm.edu hg19 4 123159421 123159421 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . KIAA1109 NM_015312 exon26 c.A3749T p.K1250M GTGAAAAGGAAAG . 115.0 48.0 99.0 0.0 . 424 . . . none . . PASS Atlas-SNP GZMK 3003 hgsc.bcm.edu hg19 5 54327207 54327207 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GZMK NM_002104 exon4 c.A379G p.K127E GCCGCAAAACTCA . 177.0 77.0 160.0 0.0 . 39 . . . none . . PASS Atlas-SNP MAST4 375449 hgsc.bcm.edu hg19 5 66448607 66448607 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MAST4 NM_001164664 exon25 c.T3438A p.S1146R CCACAGTTCGGGG . 121.0 48.0 126.0 0.0 . 218 . . . none . . PASS Atlas-SNP AGGF1 55109 hgsc.bcm.edu hg19 5 76326724 76326724 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . AGGF1 NM_018046 exon1 c.G133A p.E45K GTGCGGGAGATCG . 916.0 356.0 979.0 1.0 . 71 . . . none . . PASS Atlas-SNP APC 324 hgsc.bcm.edu hg19 5 112177639 112177639 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . APC NM_001127510 exon17 c.T6348G p.H2116Q TTTACATCAAGCT . 111.0 50.0 84.0 0.0 . 4158 . . . none . . PASS Atlas-SNP FAM217A 222826 hgsc.bcm.edu hg19 6 4073537 4073537 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . . NM_173563 exon6 c.C274G p.L92V CATTAAGAGGACA . 167.0 72.0 141.0 0.0 . . . . . none . . PASS Atlas-SNP HIST1H4E 8367 hgsc.bcm.edu hg19 6 26204932 26204932 + Silent SNP T T C rs147263244 alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . HIST1H4E NM_003545 exon1 c.T60C p.R20R TCACCGTAAGGTC . 104.0 46.0 92.0 0.0 . 22 . . . alt T|1.000;A|0.000 . PASS Atlas-SNP GTF2H4 2968 hgsc.bcm.edu hg19 6 30877807 30877807 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GTF2H4 NM_001517 exon4 c.T341A p.F114Y CCATTTTCCGCCA . 77.0 22.0 75.0 0.0 . 38 . . . none . . PASS Atlas-SNP SPDEF 25803 hgsc.bcm.edu hg19 6 34508841 34508841 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SPDEF NM_001252294 exon3 c.C554T p.A185V GACATGGCGCACA . 57.0 23.0 68.0 0.0 . 34 . . . none . . PASS Atlas-SNP GPR110 266977 hgsc.bcm.edu hg19 6 46973599 46973599 + Silent SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GPR110 NM_153840 exon13 c.G2547T p.L849L GTTGAACAGAAGT . 75.0 29.0 69.0 0.0 . 102 . . . none . . PASS Atlas-SNP ARHGAP18 93663 hgsc.bcm.edu hg19 6 129963090 129963090 + Silent SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ARHGAP18 NM_033515 exon2 c.C187A p.R63R TTGATCGATCAAA . 98.0 6.0 90.0 0.0 . 52 . . . none . . PASS Atlas-SNP UTRN 7402 hgsc.bcm.edu hg19 6 144744729 144744729 + Silent SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . UTRN NM_007124 exon4 c.C279A p.V93V TAACGTCAACAGA . 73.0 27.0 80.0 0.0 . 327 . . . none . . PASS Atlas-SNP SCAF8 22828 hgsc.bcm.edu hg19 6 155153549 155153549 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SCAF8 NM_014892 exon20 c.A2836G p.I946V CCTGGAATTCCAC . 83.0 31.0 115.0 0.0 . 122 . . . none . . PASS Atlas-SNP MAGI2 9863 hgsc.bcm.edu hg19 7 77885345 77885345 + Silent SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MAGI2 NM_012301 exon10 c.A1962T p.V654V GTTCTGTACATTC . 71.0 34.0 73.0 0.0 . 246 . . . none . . PASS Atlas-SNP SEMA3E 9723 hgsc.bcm.edu hg19 7 83023614 83023614 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SEMA3E NM_012431 exon13 c.G1499T p.R500L CTTACCCGCTTTG . 74.0 25.0 48.0 0.0 . 125 . . . none . . PASS Atlas-SNP GATAD1 57798 hgsc.bcm.edu hg19 7 92085728 92085728 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GATAD1 NM_021167 exon5 c.T662A p.F221Y TGGAATTTGTTTG . 70.0 33.0 73.0 0.0 . 10 . . . none . . PASS Atlas-SNP CUX1 1523 hgsc.bcm.edu hg19 7 101891877 101891877 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CUX1 NM_001202543 exon24 c.A4106T p.Q1369L AGTCTCAGGGAGA . 38.0 14.0 50.0 0.0 . 253 . . . none . . PASS Atlas-SNP HIPK2 28996 hgsc.bcm.edu hg19 7 139305300 139305300 + Silent SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . HIPK2 NM_022740 exon7 c.A1629G p.S543S GAAACATGATTTG . 98.0 43.0 73.0 0.0 . 192 . . . none . . PASS Atlas-SNP DPP6 1804 hgsc.bcm.edu hg19 7 154684050 154684050 + Missense_Mutation SNP C C A rs186233086 by1000genomes;alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . DPP6 NM_130797 exon26 c.C2458A p.P820T ATTTACCCGGACG . 115.0 49.0 99.0 0.0 . 383 . . . alt C|1.000;T|0.000 . PASS Atlas-SNP DLC1 10395 hgsc.bcm.edu hg19 8 12957624 12957624 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 DLC1,bladder,carcinoma,0,3 DLC1 NM_182643 exon9 c.G2222C p.S741T CTGCTGCTGGTCT . 63.0 6.0 51.0 0.0 . 411 . . . none . . PASS Atlas-SNP DUSP4 1846 hgsc.bcm.edu hg19 8 29195962 29195962 + Silent SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . DUSP4 NM_001394 exon3 c.C636T p.A212A TCTCCGGGCAGCA . 74.0 27.0 77.0 0.0 . 58 . . . none . . PASS Atlas-SNP COL14A1 7373 hgsc.bcm.edu hg19 8 121170481 121170481 + Silent SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . COL14A1 NM_021110 exon3 c.T201A p.T67T TCCAACTTCAGGT . 100.0 48.0 109.0 0.0 . 292 . . . none . . PASS Atlas-SNP TTC39B 158219 hgsc.bcm.edu hg19 9 15211355 15211355 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TTC39B NM_001168340 exon5 c.A523G p.I175V CCACAATGGTACT . 123.0 47.0 129.0 0.0 . 83 . . . none . . PASS Atlas-SNP FOCAD 54914 hgsc.bcm.edu hg19 9 20740261 20740261 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . . NM_017794 exon7 c.T314G p.I105S AAGCCATTATGCA . 449.0 185.0 357.0 0.0 . . . . . none . . PASS Atlas-SNP ZFP37 7539 hgsc.bcm.edu hg19 9 115805449 115805449 + Silent SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZFP37 NM_003408 exon4 c.T1449C p.H483H CTTAGTATGAGTT . 71.0 18.0 60.0 0.0 . 93 . . . none . . PASS Atlas-SNP PHYHD1 254295 hgsc.bcm.edu hg19 9 131689459 131689459 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PHYHD1 NM_001100877 exon2 c.A176G p.E59G AAGAGGAGCAGCT . 71.0 37.0 67.0 0.0 . 29 . . . none . . PASS Atlas-SNP DOLK 22845 hgsc.bcm.edu hg19 9 131708203 131708203 + Silent SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . DOLK NM_014908 exon1 c.C1380A p.T460T CCCCATGGTGCTA . 111.0 39.0 115.0 0.0 . 39 . . . none . . PASS Atlas-SNP UPF2 26019 hgsc.bcm.edu hg19 10 11998440 11998440 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . UPF2 NM_080599 exon13 c.A2453T p.N818I TTCACATTCCAGA . 90.0 39.0 84.0 0.0 . 111 . . . none . . PASS Atlas-SNP UPF2 26019 hgsc.bcm.edu hg19 10 11998442 11998442 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . UPF2 NM_080599 exon13 c.G2451T p.W817C CACATTCCAGATG . 87.0 39.0 84.0 0.0 . 111 . . . none . . PASS Atlas-SNP MYPN 84665 hgsc.bcm.edu hg19 10 69918255 69918255 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MYPN NM_032578 exon7 c.T1330A p.L444M CAAAATTTGTCAG . 91.0 34.0 84.0 0.0 . 189 . . . none . . PASS Atlas-SNP TET1 80312 hgsc.bcm.edu hg19 10 70451494 70451494 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TET1 NM_030625 exon12 c.T6334G p.L2112V TTAACATTAACCC . 92.0 36.0 96.0 0.0 . 255 . . . none . . PASS Atlas-SNP C10orf11 83938 hgsc.bcm.edu hg19 10 77795776 77795776 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . C10orf11 NM_032024 exon2 c.G58A p.G20R CTGGAAGGACTGA . 53.0 17.0 83.0 0.0 . 19 . . . none . . PASS Atlas-SNP PIK3AP1 118788 hgsc.bcm.edu hg19 10 98380246 98380246 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PIK3AP1 NM_152309 exon12 c.A1804G p.T602A CTGGCGTTTTCAT . 100.0 41.0 104.0 0.0 . 111 . . . none . . PASS Atlas-SNP TDRD1 56165 hgsc.bcm.edu hg19 10 115964611 115964611 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TDRD1 NM_198795 exon10 c.A1256T p.E419V AAGAGGAAGTGGT . 139.0 53.0 114.0 0.0 . 126 . . . none . . PASS Atlas-SNP CALCA 796 hgsc.bcm.edu hg19 11 14991618 14991618 + Silent SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CALCA NM_001033953 exon3 c.T90A p.S30S CAGGGCAGACCTG . 226.0 86.0 210.0 0.0 . 30 . . . none . . PASS Atlas-SNP CPSF7 79869 hgsc.bcm.edu hg19 11 61183972 61183972 + Silent SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CPSF7 NM_024811 exon6 c.T699C p.H233H TCGGGAATGGGCC . 89.0 32.0 94.0 0.0 . 46 . . . none . . PASS Atlas-SNP PAAF1 80227 hgsc.bcm.edu hg19 11 73602239 73602239 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PAAF1 NM_025155 exon4 c.C275T p.T92I TTCATACAAAGAG . 70.0 24.0 55.0 0.0 . 39 . . . none . . PASS Atlas-SNP SLCO2B1 11309 hgsc.bcm.edu hg19 11 74915579 74915579 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SLCO2B1 NM_007256 exon14 c.T2084C p.L695S AGCAATTGCTAGT . 78.0 27.0 91.0 0.0 . 84 . . . none . . PASS Atlas-SNP BIRC3 330 hgsc.bcm.edu hg19 11 102195478 102195478 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . BIRC3 NM_001165 exon2 c.G238T p.D80Y AGAGGAGACAGTC . 100.0 11.0 137.0 0.0 . 56 . . . none . . PASS Atlas-SNP ATM 472 hgsc.bcm.edu hg19 11 108236079 108236079 + Silent SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ATM NM_000051 exon63 c.A9015T p.V3005V CAAAGTAGCTGAA . 67.0 48.0 113.0 0.0 . 1657 . . . none . . PASS Atlas-SNP JAM3 83700 hgsc.bcm.edu hg19 11 134014786 134014786 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . JAM3 NM_032801 exon5 c.A509C p.H170P GGCCTCACTACAG . 136.0 58.0 154.0 0.0 . 41 . . . none . . PASS Atlas-SNP CNTN1 1272 hgsc.bcm.edu hg19 12 41387017 41387017 + Missense_Mutation SNP C C G rs377022967 alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CNTN1 NM_001843 exon17 c.C2059G p.L687V AATACACTGGGTA . 127.0 44.0 145.0 0.0 . 207 . . . alt . . PASS Atlas-SNP KRT3 3850 hgsc.bcm.edu hg19 12 53188110 53188110 + Silent SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . KRT3 NM_057088 exon2 c.G651T p.R217R CAGGAACCGCACC . 98.0 45.0 122.0 0.0 . 65 . . . none . . PASS Atlas-SNP ATP5G2 517 hgsc.bcm.edu hg19 12 54059109 54059109 + Missense_Mutation SNP A A G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ATP5G2 NM_005176 exon5 c.T586C p.F196L TGGCAAAGAGGAT . 167.0 60.0 128.0 0.0 . 16 . . . none . . PASS Atlas-SNP TBK1 29110 hgsc.bcm.edu hg19 12 64860793 64860793 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TBK1 NM_013254 exon5 c.T471G p.D157E CACAGATTTTGGT . 94.0 31.0 93.0 0.0 . 149 . . . none . . PASS Atlas-SNP GLTP 51228 hgsc.bcm.edu hg19 12 110295370 110295370 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GLTP NM_016433 exon3 c.C257T p.P86L ACTTTGGGCCACT . 51.0 30.0 63.0 0.0 . 15 . . . none . . PASS Atlas-SNP HNF1A 6927 hgsc.bcm.edu hg19 12 121434509 121434509 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . HNF1A NM_000545 exon6 c.A1273C p.T425P GGTCCTACGTTCA . 104.0 36.0 80.0 0.0 . 302 . . . none . . PASS Atlas-SNP SETD1B 23067 hgsc.bcm.edu hg19 12 122260973 122260973 + Silent SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SETD1B NM_015048 exon12 c.G4359T p.A1453A TCGTGCGCCCACC . 41.0 14.0 31.0 0.0 . 105 . . . none . . PASS Atlas-SNP PSMD9 5715 hgsc.bcm.edu hg19 12 122340948 122340948 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PSMD9 NM_002813 exon4 c.T490A p.S164T TTCGGCTCTGTGA . 148.0 90.0 113.0 0.0 . 8 . . . none . . PASS Atlas-SNP RILPL1 353116 hgsc.bcm.edu hg19 12 123984011 123984011 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . RILPL1 NM_178314 exon3 c.G533A p.R178H TTGGCGCGGATCT . 87.0 43.0 59.0 0.0 . 23 . . . none . . PASS Atlas-SNP NCOR2 9612 hgsc.bcm.edu hg19 12 124887084 124887084 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NCOR2 NM_006312 exon16 c.G1506A p.Q502Q CTGCTGCTGCTGC . 57.0 6.0 29.0 0.0 . 475 . . . none . . PASS Atlas-SNP RIMBP2 23504 hgsc.bcm.edu hg19 12 130921476 130921476 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . RIMBP2 NM_015347 exon10 c.C1966A p.L656M GTGGCAGGATGCG . 100.0 60.0 92.0 0.0 . 220 . . . none . . PASS Atlas-SNP PGAM5 192111 hgsc.bcm.edu hg19 12 133291557 133291557 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PGAM5 NM_138575 exon2 c.T305A p.L102H TCTTCCTCATCAG . 162.0 40.0 105.0 0.0 . 18 . . . none . . PASS Atlas-SNP MDP1 145553 hgsc.bcm.edu hg19 14 24683307 24683307 + Nonsense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MDP1 NM_001199821 exon5 c.C314G p.S105X ACCCTTGACTTAG . 77.0 38.0 77.0 0.0 . 13 . . . none . . PASS Atlas-SNP COQ6 51004 hgsc.bcm.edu hg19 14 74426189 74426189 + Silent SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . COQ6 NM_182476 exon8 c.T855C p.D285D CATGGATGAGGAA . 103.0 46.0 102.0 0.0 . 27 . . . none . . PASS Atlas-SNP PPP4R4 57718 hgsc.bcm.edu hg19 14 94722854 94722854 + Silent SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PPP4R4 NM_058237 exon17 c.T1923C p.D641D TGCTGATAAGCAT . 81.0 35.0 88.0 0.0 . 107 . . . none . . PASS Atlas-SNP TP53BP1 7158 hgsc.bcm.edu hg19 15 43714077 43714077 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TP53BP1 NM_001141980 exon19 c.C4076G p.S1359C CCTCGGGAGCTGG . 79.0 39.0 86.0 0.0 . 157 . . . none . . PASS Atlas-SNP POLG 5428 hgsc.bcm.edu hg19 15 89861981 89861981 + Splice_Site SNP C C G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . POLG NM_002693 exon22 c.3274-1G>C . CATAAACTGGGAA . 44.0 13.0 30.0 0.0 . 75 . . . none . . PASS Atlas-SNP RGMA 56963 hgsc.bcm.edu hg19 15 93595536 93595536 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . RGMA NM_001166283 exon3 c.G356C p.S119T TGCTGGCTCATGA . 37.0 16.0 41.0 0.0 . 49 . . . none . . PASS Atlas-SNP SMPD3 55512 hgsc.bcm.edu hg19 16 68405641 68405641 + Silent SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SMPD3 NM_018667 exon3 c.A444G p.Q148Q CCGCGCTTGGGTG . 86.0 42.0 73.0 0.0 . 52 . . . none . . PASS Atlas-SNP SMPD3 55512 hgsc.bcm.edu hg19 16 68405649 68405649 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SMPD3 NM_018667 exon3 c.A436C p.N146H GGGTGTTAAAAAG . 85.0 45.0 69.0 0.0 . 52 . . . none . . PASS Atlas-SNP PKD1L2 114780 hgsc.bcm.edu hg19 16 81219237 81219237 + Silent SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PKD1L2 NM_001076780 exon11 c.G1857T p.L619L AACCACCAGCTCC . 112.0 64.0 76.0 0.0 . 361 . . . none . . PASS Atlas-SNP SPNS3 201305 hgsc.bcm.edu hg19 17 4343008 4343008 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SPNS3 NM_182538 exon2 c.G255C p.L85F TGGTTTGCTTCAG . 42.0 14.0 45.0 0.0 . 52 . . . none . . PASS Atlas-SNP MED9 55090 hgsc.bcm.edu hg19 17 17380470 17380470 + Missense_Mutation SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MED9 NM_018019 exon1 c.C115T p.P39S CCGGTCCCTGCGC . 103.0 48.0 69.0 0.0 . 11 . . . none . . PASS Atlas-SNP MYO18A 399687 hgsc.bcm.edu hg19 17 27447772 27447772 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MYO18A NM_078471 exon7 c.G1590A p.E530E CCACTTCTCCACT . 102.0 27.0 96.0 0.0 . 217 . . . none . . PASS Atlas-SNP GPR179 440435 hgsc.bcm.edu hg19 17 36482812 36482812 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GPR179 NM_001004334 exon11 c.A6640T p.M2214L TTCCCATGCTGCC . 83.0 48.0 63.0 0.0 . 170 . . . none . . PASS Atlas-SNP TEX2 55852 hgsc.bcm.edu hg19 17 62271048 62271048 + Silent SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TEX2 NM_018469 exon4 c.C2047A p.R683R GATCTCGCTGGCT . 180.0 116.0 107.0 0.0 . 89 . . . none . . PASS Atlas-SNP ABCA8 10351 hgsc.bcm.edu hg19 17 66918423 66918423 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ABCA8 NM_007168 exon11 c.A1461C p.K487N ATATTCTTTTGTA . 253.0 75.0 164.0 0.0 . 213 . . . none . . PASS Atlas-SNP SMCHD1 23347 hgsc.bcm.edu hg19 18 2728547 2728547 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SMCHD1 NM_015295 exon23 c.G2866A p.E956K TTAGATGAATCAG . 103.0 47.0 115.0 0.0 . 88 . . . none . . PASS Atlas-SNP CABLES1 91768 hgsc.bcm.edu hg19 18 20815956 20815956 + Missense_Mutation SNP T T C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CABLES1 NM_001100619 exon6 c.T1283C p.L428P GTAACCTGAGCCA . 76.0 23.0 63.0 0.0 . 32 . . . none . . PASS Atlas-SNP TTR 7276 hgsc.bcm.edu hg19 18 29178600 29178600 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 TTR,NS,carcinoma,0,1 TTR NM_000371 exon4 c.T406G p.Y136D TACTCCTATTCCA . 60.0 20.0 71.0 2.0 . 21 . . . none . . PASS Atlas-SNP WDR18 57418 hgsc.bcm.edu hg19 19 984377 984377 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . WDR18 NM_024100 exon1 c.C24T p.A8A GGTGGCCGTGTGT . 179.0 8.0 157.0 0.0 . 20 . . . none . . PASS Atlas-SNP DOT1L 84444 hgsc.bcm.edu hg19 19 2216297 2216297 + Silent SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . DOT1L NM_032482 exon20 c.A1941T p.L647L GGAGCTAGAGAAG . 64.0 30.0 60.0 0.0 . 205 . . . none . . PASS Atlas-SNP RANBP3 8498 hgsc.bcm.edu hg19 19 5921298 5921298 + Missense_Mutation SNP G G A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . RANBP3 NM_007322 exon14 c.C1244T p.S415L GACTGTGAGGTCT . 55.0 23.0 92.0 0.0 . 36 . . . none . . PASS Atlas-SNP MUC16 94025 hgsc.bcm.edu hg19 19 9049050 9049050 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MUC16 NM_024690 exon5 c.T32581G p.S10861A AACTGGATTCTGC . 125.0 49.0 115.0 0.0 . 4315 . . . none . . PASS Atlas-SNP ZNF490 57474 hgsc.bcm.edu hg19 19 12693704 12693704 + Missense_Mutation SNP C C G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZNF490 NM_020714 exon4 c.G310C p.D104H CAATATCCTGGTC . 90.0 10.0 56.0 0.0 . 42 . . . none . . PASS Atlas-SNP UPF1 5976 hgsc.bcm.edu hg19 19 18960968 18960968 + Missense_Mutation SNP G G T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . UPF1 NM_002911 exon4 c.G546T p.E182D CCTGGAGTGCTAC . 61.0 29.0 68.0 0.0 . 88 . . . none . . PASS Atlas-SNP ZNF529 57711 hgsc.bcm.edu hg19 19 37038652 37038652 + Missense_Mutation SNP T T A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZNF529 NM_001145649 exon6 c.A808T p.T270S GTGGAGTAACTTT . 77.0 36.0 72.0 0.0 . 82 . . . none . . PASS Atlas-SNP ZNF585B 92285 hgsc.bcm.edu hg19 19 37677880 37677880 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZNF585B NM_152279 exon5 c.A559C p.K187Q TGCACTTATAGGG . 91.0 39.0 80.0 0.0 . 91 . . . none . . PASS Atlas-SNP PLEKHA4 57664 hgsc.bcm.edu hg19 19 49364695 49364695 + Missense_Mutation SNP C C T rs201822487 TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PLEKHA4 NM_001161354 exon5 c.G329A p.G110E CCCGGCCCATCTG . 98.0 51.0 56.0 0.0 . 70 . . . weak C|0.999;T|0.001 0.001 PASS Atlas-SNP AP2A1 160 hgsc.bcm.edu hg19 19 50304776 50304776 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . AP2A1 NM_130787 exon13 c.C1683T p.G561G CCAGGGCGTCCTG . 156.0 20.0 138.0 0.0 . 108 . . . none . . PASS Atlas-SNP ZNF749 388567 hgsc.bcm.edu hg19 19 57955392 57955392 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZNF749 NM_001023561 exon3 c.C876T p.L292L GATTCTCAGTAGA . 123.0 49.0 118.0 0.0 . 75 . . . none . . PASS Atlas-SNP NINL 22981 hgsc.bcm.edu hg19 20 25460838 25460838 + Missense_Mutation SNP T T G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NINL NM_025176 exon15 c.A1876C p.K626Q GCTCCTTTACCTG . 132.0 48.0 97.0 0.0 . 148 . . . none . . PASS Atlas-SNP EDEM2 55741 hgsc.bcm.edu hg19 20 33730267 33730267 + Silent SNP G G T rs375028628 alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . EDEM2 NM_018217 exon4 c.C273A p.V91V TTCTGAGACATTC . 103.0 55.0 56.0 0.0 . 46 . . . alt . . PASS Atlas-SNP TOMM34 10953 hgsc.bcm.edu hg19 20 43580553 43580553 + Silent SNP C C T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TOMM34 NM_006809 exon4 c.G471A p.R157R ATTCCACCTCTTC . 73.0 29.0 71.0 0.0 . 16 . . . none . . PASS Atlas-SNP NRIP1 8204 hgsc.bcm.edu hg19 21 16337481 16337481 + Missense_Mutation SNP A A T novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NRIP1 NM_003489 exon4 c.T3033A p.S1011R AGTAGGACTCACA . 53.0 26.0 35.0 0.0 . 103 . . . none . . PASS Atlas-SNP NRIP1 8204 hgsc.bcm.edu hg19 21 16337482 16337482 + Missense_Mutation SNP C C A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NRIP1 NM_003489 exon4 c.G3032T p.S1011I GTAGGACTCACAG . 52.0 25.0 34.0 0.0 . 103 . . . none . . PASS Atlas-SNP MORC3 23515 hgsc.bcm.edu hg19 21 37732306 37732306 + Missense_Mutation SNP A A C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MORC3 NM_015358 exon11 c.A1262C p.K421T GGCGGAAATTACC . 142.0 55.0 171.0 0.0 . 78 . . . none . . PASS Atlas-SNP TBC1D22A 25771 hgsc.bcm.edu hg19 22 47507468 47507468 + Missense_Mutation SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TBC1D22A NM_014346 exon12 c.G1394C p.R465T GATGGAGGAAGGA . 101.0 34.0 107.0 0.0 . 54 . . . none . . PASS Atlas-SNP BRD1 23774 hgsc.bcm.edu hg19 22 50187854 50187854 + Missense_Mutation SNP G G C rs369329207 alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . BRD1 NM_014577 exon6 c.C2187G p.C729W CATAGCGCAGGTG . 61.0 30.0 69.0 0.0 . 144 . . . alt . . PASS Atlas-SNP ZRSR2 8233 hgsc.bcm.edu hg19 X 15841227 15841227 + Silent SNP G G C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZRSR2 NM_005089 exon11 c.G1311C p.R437R GGGCCGGGGCAGC . 338.0 14.0 334.0 0.0 . 78 . . . none . . PASS Atlas-SNP ZRSR2 8233 hgsc.bcm.edu hg19 X 15841260 15841260 + Silent SNP C C G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZRSR2 NM_005089 exon11 c.C1344G p.R448R GAGCCGCAGGAGC . 336.0 18.0 328.0 0.0 . 78 . . . none . . PASS Atlas-SNP MAGEC3 139081 hgsc.bcm.edu hg19 X 140967157 140967157 + Missense_Mutation SNP A A G rs200403296 TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MAGEC3 NM_138702 exon3 c.A455G p.Y152C CAGGCTACACCCT . 271.0 13.0 261.0 0.0 . 228 . . . weak . . PASS Atlas-SNP AGPAT2 10555 hgsc.bcm.edu hg19 9 139568332 139568332 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . AGPAT2 NM_006412 exon6 c.710delC p.T237fs . . 96.0 34.0 97.0 0.0 . 17 . 0.354167 0 none . . PASS Atlas-Indel,Pindel NPM1 4869 hgsc.bcm.edu hg19 5 170818328 170818329 + Frame_Shift_Ins INS - - A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NPM1 NM_199185 exon3 c.158_159insA p.A53fs . . 26.0 12.0 29.0 0.0 . 5003 . 0.461538 0 none . . PASS Atlas-INDEL CDH10 1008 hgsc.bcm.edu hg19 5 24535913 24535913 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . CDH10 NM_006727 exon4 c.546delC p.V182fs . . 45.0 28.0 67.0 0.0 . 391 . 0.622222 0 none . . PASS Atlas-Indel,Pindel ARHGEF37 389337 hgsc.bcm.edu hg19 5 149006771 149006772 + In_Frame_Ins INS - - TGGCCA novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ARHGEF37 NM_001001669 exon11 c.1597_1598insTGGCCA p.V533delinsVAM . . 94.0 22.0 97.0 0.0 . 45 . 0.234043 0 none . . PASS Atlas-Indel,Pindel MED13 9969 hgsc.bcm.edu hg19 17 60033103 60033103 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MED13 NM_005121 exon25 c.5721delT p.P1907fs . . 291.0 24.0 186.0 0.0 . 181 . 0.0824742 0 none . . PASS Atlas-Indel,Pindel C1orf127 148345 hgsc.bcm.edu hg19 1 11008797 11008797 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . C1orf127 NM_001170754 exon12 c.1396delC p.P466fs . . 69.0 25.0 69.0 0.0 . 134 . 0.362319 0 none . . PASS Atlas-Indel,Pindel NDST4 64579 hgsc.bcm.edu hg19 4 115749045 115749046 + Frame_Shift_Ins INS - - G novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . NDST4 NM_022569 exon14 c.2546_2547insC p.L849fs . . 55.0 30.0 65.0 0.0 . 193 . 0.545455 0 none . . PASS Atlas-Indel,Pindel EPHA4 2043 hgsc.bcm.edu hg19 2 222321422 222321422 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . EPHA4 NM_004438 exon7 c.1515delT p.P505fs . . 96.0 44.0 98.0 0.0 . 263 . 0.458333 0 none . . PASS Atlas-Indel,Pindel SLC32A1 140679 hgsc.bcm.edu hg19 20 37356467 37356468 + Frame_Shift_Ins INS - - C novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SLC32A1 NM_080552 exon2 c.763_764insC p.A255fs . . 73.0 30.0 84.0 0.0 . 81 . 0.410959 0 none . . PASS Atlas-Indel,Pindel TUBB4B 10383 hgsc.bcm.edu hg19 9 140137032 140137033 + Frame_Shift_Ins INS - - A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . . NM_006088 exon4 c.362_363insA p.R121fs . . 61.0 18.0 78.0 0.0 . . . 0.295082 0 none . . PASS Atlas-Indel,Pindel COL6A2 1292 hgsc.bcm.edu hg19 21 47545869 47545879 + Frame_Shift_Del DEL CTCATCAAGGA CTCATCAAGGA - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 CTCATCAAGGA CTCATCAAGGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . COL6A2 NM_058175 exon26 c.2139_2149del p.713_717del . . 131.0 31.0 190.0 0.0 . 351 . 0.236641 0 none . . PASS Atlas-INDEL MAPRE1 22919 hgsc.bcm.edu hg19 20 31413759 31413764 + In_Frame_Del DEL CAGTGA CAGTGA - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 CAGTGA CAGTGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MAPRE1 NM_012325 exon2 c.25_30del p.9_10del . . 80.0 42.0 62.0 0.0 . 17 . 0.525 0 none . . PASS Atlas-Indel,Pindel F9 2158 hgsc.bcm.edu hg19 X 138643733 138643760 + Frame_Shift_Del DEL ATTCGAATTATTCCTCACCACAACTACA ATTCGAATTATTCCTCACCACAACTACA - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 ATTCGAATTATTCCTCACCACAACTACA ATTCGAATTATTCCTCACCACAACTACA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . F9 NM_000133 exon8 c.888_915del p.296_305del . . 190.0 44.0 184.0 0.0 . 107 . 0.231579 0 none . . PASS Atlas-Indel,Pindel GOLGA6A 342096 hgsc.bcm.edu hg19 15 74367333 74367333 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GOLGA6A NM_001038640 exon11 c.858delA p.P286fs . . 40.0 22.0 85.0 0.0 . 28 . 0.55 0 none . . PASS Atlas-INDEL COL6A2 1292 hgsc.bcm.edu hg19 21 47545867 47545867 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 COL6A2_ENST00000357838,NS,carcinoma,0,5 COL6A2 NM_058175 exon26 c.2137delC p.R713fs . . 136.0 31.0 192.0 0.0 . 351 . 0.227941 0 none . . PASS Atlas-INDEL ZSWIM2 151112 hgsc.bcm.edu hg19 2 187703706 187703706 + Frame_Shift_Del DEL C C - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ZSWIM2 NM_182521 exon4 c.475delC p.L159fs . . 50.0 26.0 52.0 0.0 . 119 . 0.52 0 none . . PASS Atlas-Indel,Pindel SLC3A2 6520 hgsc.bcm.edu hg19 11 62648555 62648556 + Frame_Shift_Ins INS - - A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . SLC3A2 NM_001012662 exon4 c.366_367insA p.E122fs . . 129.0 49.0 127.0 0.0 . 55 . 0.379845 0 none . . PASS Atlas-Indel,Pindel GOLGA6A 342096 hgsc.bcm.edu hg19 15 74367328 74367328 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GOLGA6A NM_001038640 exon11 c.863delT p.L288fs . . 45.0 23.0 86.0 0.0 . 28 . 0.511111 0 none . . PASS Atlas-INDEL PRKCA 5578 hgsc.bcm.edu hg19 17 64728827 64728827 + Frame_Shift_Del DEL G G - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . PRKCA NM_002737 exon9 c.939delT p.A313fs . . 215.0 65.0 145.0 0.0 . 82 . 0.302326 0 none . . PASS Atlas-Indel,Pindel MLL3 58508 hgsc.bcm.edu hg19 7 151874432 151874433 + Frame_Shift_Del DEL TT TT - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 TT TT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . MLL3 NM_170606 exon38 c.8106_8107del p.2702_2703del . . 88.0 33.0 86.0 0.0 . 1564 . 0.375 0 none . . PASS Atlas-Indel,Pindel ERCC6 2074 hgsc.bcm.edu hg19 10 50679145 50679146 + Frame_Shift_Ins INS - - A novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ERCC6 NM_000124 exon17 c.2946_2947insT p.T982fs . . 70.0 34.0 72.0 0.0 . 162 . 0.485714 0 none . . PASS Atlas-Indel,Pindel A4GALT 53947 hgsc.bcm.edu hg19 22 43089135 43089143 + In_Frame_Del DEL CGCGGCAGG CGCGGCAGG - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 CGCGGCAGG CGCGGCAGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . A4GALT NM_017436 exon3 c.816_824del p.272_275del . . 46.0 11.0 57.0 0.0 . 35 . 0.23913 0 none . . PASS Atlas-Indel,Pindel ANK2 287 hgsc.bcm.edu hg19 4 114279656 114279656 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . ANK2 NM_001148 exon38 c.9881delA p.N3294fs . . 101.0 50.0 91.0 0.0 . 576 . 0.49505 0 none . . PASS Atlas-Indel,Pindel FBXO38 81545 hgsc.bcm.edu hg19 5 147806844 147806844 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . FBXO38 NM_030793 exon15 c.1986delG p.Q662fs . . 259.0 124.0 248.0 0.0 . 115 . 0.478764 0 none . . PASS Atlas-Indel,Pindel R3HDM1 23518 hgsc.bcm.edu hg19 2 136396355 136396355 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . R3HDM1 NM_015361 exon13 c.987delA p.I329fs . . 133.0 52.0 89.0 0.0 . 84 . 0.390977 0 none . . PASS Atlas-Indel,Pindel IMMP1L 196294 hgsc.bcm.edu hg19 11 31454087 31454087 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . IMMP1L NM_144981 exon7 c.462delA p.L154fs . . 400.0 141.0 374.0 0.0 . 16 . 0.3525 0 none . . PASS Atlas-Indel,Pindel TM9SF2 9375 hgsc.bcm.edu hg19 13 100172311 100172311 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . TM9SF2 NM_004800 exon3 c.260delC p.S87X . . 119.0 10.0 108.0 0.0 . 52 . 0.084 . none . . PASS Pindel COL6A2 1292 hgsc.bcm.edu hg19 21 47545867 47545879 + Frame_Shift_Del DEL GCCTCATCAAGGA GCCTCATCAAGGA - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 GCCTCATCAAGGA GCCTCATCAAGGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 COL6A2_ENST00000357838,NS,carcinoma,0,5 COL6A2 NM_058175 exon26 c.2137_2149del p.713_717del . . 145.0 33.0 184.0 0.0 . 351 . 0.228 . none . . PASS Pindel USP4 7375 hgsc.bcm.edu hg19 3 49315762 49315762 + Frame_Shift_Del DEL A A - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . USP4 NM_003363 exon22 c.2857delG p.G953fs . . 112.0 43.0 68.0 0.0 . 72 . 0.384 . none . . PASS Pindel TENM2 57451 hgsc.bcm.edu hg19 5 167622284 167622285 + Frame_Shift_Ins INS - - CCCGCCAGGATGGCACGTGAGT novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . . NM_001122679 exon15 c.2857_2858insCCCGCCAGGATGGCACGTGAGT p.T953_R954delinsTRQDGTX . . 88.0 21.0 84.0 0.0 . . . 0.239 . none . . PASS Pindel OR2T2 401992 hgsc.bcm.edu hg19 1 248616710 248616734 + Frame_Shift_Del DEL CGTGCTGATGCTGCTTATCCCTCTA CGTGCTGATGCTGCTTATCCCTCTA - rs72452004 bycluster;alternate_allele TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 CGTGCTGATGCTGCTTATCCCTCTA CGTGCTGATGCTGCTTATCCCTCTA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . OR2T2 NM_001004136 exon1 c.611_635del p.204_212del . . 218.0 21.0 261.0 0.0 . 73 . 0.096 . alt . . PASS Pindel GOLGA6A 342096 hgsc.bcm.edu hg19 15 74367333 74367334 + Frame_Shift_Del DEL GG GG - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 GG GG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . GOLGA6A NM_001038640 exon11 c.857_858del p.286_286del . . 40.0 11.0 84.0 0.0 . 28 . 0.275 . none . . PASS Pindel KRT86 3892 hgsc.bcm.edu hg19 12 52702335 52702335 + Frame_Shift_Del DEL T T - novel TCGA-UZ-A9PS-01A-11D-A42J-10 TCGA-UZ-A9PS-10A-01D-A42M-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq acba931b-e52d-4487-b13a-7d8c91981263 57691588-0681-41ba-b333-4d612c7f0542 . KRT86 NM_002284 exon9 c.1426delG p.V476fs . . 21.0 12.0 9.0 0.0 . 33 . 0.571 . none . . PASS Pindel