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 PRAMEF12 390999 hgsc.bcm.edu hg19 1 12837407 12837407 + Missense_Mutation SNP A A T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PRAMEF12 NM_001080830 exon3 c.A1117T p.S373C GCCCTGAGCCGCT . 737.0 215.0 505.0 0.0 . 69 . . . none . . PASS Atlas-SNP SPEN 23013 hgsc.bcm.edu hg19 1 16257911 16257911 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SPEN NM_015001 exon11 c.G5176A p.D1726N TCAGGTGACCAGC . 152.0 16.0 149.0 0.0 . 374 . . . none . . PASS Atlas-SNP CADM3 57863 hgsc.bcm.edu hg19 1 159170698 159170698 + Nonsense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a CADM3,NS,malignant_melanoma,0,1 CADM3 NM_021189 exon10 c.G1285T p.E429X AAGAAGGAATATT . 239.0 25.0 183.0 0.0 . 118 . . . none . . PASS Atlas-SNP MROH9 80133 hgsc.bcm.edu hg19 1 170965712 170965712 + Missense_Mutation SNP C C G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . . NM_025063 exon14 c.C1402G p.L468V ATTACTCTAATGA . 138.0 32.0 128.0 0.0 . . . . . none . . PASS Atlas-SNP LYST 1130 hgsc.bcm.edu hg19 1 235872510 235872510 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . LYST NM_000081 exon44 c.C10024T p.R3342W CCTGCCGATGGAT . 291.0 82.0 275.0 0.0 . 370 . . . none . . PASS Atlas-SNP NCOA1 8648 hgsc.bcm.edu hg19 2 24929447 24929447 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . NCOA1 NM_147223 exon11 c.G1108A p.G370R CACAGTGGGCTTT . 70.0 24.0 71.0 0.0 . 210 . . . none . . PASS Atlas-SNP C2orf81 388963 hgsc.bcm.edu hg19 2 74642884 74642884 + Silent SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . C2orf81 NM_001145054 exon3 c.C429T p.P143P CAGCACGGGCACT . 169.0 55.0 82.0 0.0 . 23 . . . none . . PASS Atlas-SNP FN1 2335 hgsc.bcm.edu hg19 2 216274676 216274676 + Missense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . FN1 NM_212476 exon14 c.C2103A p.S701R GCTGGTGCTGGTG . 506.0 121.0 398.0 0.0 . 521 . . . none . . PASS Atlas-SNP PDCD6IP 10015 hgsc.bcm.edu hg19 3 33840351 33840351 + Missense_Mutation SNP A A C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PDCD6IP NM_013374 exon1 c.A131C p.E44A CGGCGGAGGAGCT . 111.0 28.0 61.0 0.0 . 62 . . . none . . PASS Atlas-SNP ARHGEF3 50650 hgsc.bcm.edu hg19 3 56766301 56766301 + Missense_Mutation SNP C C A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ARHGEF3 NM_001128615 exon12 c.G1289T p.G430V AGGGAGCCACCCA . 202.0 46.0 133.0 0.0 . 128 . . . none . . PASS Atlas-SNP SPON2 10417 hgsc.bcm.edu hg19 4 1164263 1164263 + Missense_Mutation SNP C C A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SPON2 NM_012445 exon5 c.G738T p.Q246H GGGGCTCTGTCGC . 124.0 46.0 58.0 0.0 . 22 . . . none . . PASS Atlas-SNP KIAA1239 57495 hgsc.bcm.edu hg19 4 37447380 37447380 + Missense_Mutation SNP T T G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . KIAA1239 NM_001144990 exon7 c.T3770G p.F1257C CTGTGTTTTTTTG . 261.0 22.0 232.0 0.0 . 79 . . . none . . PASS Atlas-SNP KLB 152831 hgsc.bcm.edu hg19 4 39435931 39435931 + Silent SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . KLB NM_175737 exon2 c.G927T p.R309R AAACCGGTCGGAA . 373.0 119.0 307.0 0.0 . 95 . . . none . . PASS Atlas-SNP GABRG1 2565 hgsc.bcm.edu hg19 4 46043272 46043272 + Splice_Site SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . GABRG1 NM_173536 exon10 c.1132-1G>A . AGTCATCTGAGCA . 70.0 17.0 66.0 0.0 . 172 . . . none . . PASS Atlas-SNP FAT4 79633 hgsc.bcm.edu hg19 4 126239108 126239108 + Silent SNP T T C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . FAT4 NM_024582 exon1 c.T1542C p.I514I CAGCATTGTCTCT . 147.0 55.0 150.0 0.0 . 1752 . . . none . . PASS Atlas-SNP HAND2 9464 hgsc.bcm.edu hg19 4 174450317 174450317 + Missense_Mutation SNP A A T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . HAND2 NM_021973 exon1 c.T124A p.Y42N GGAAGTAGGGGTT . 29.0 7.0 17.0 0.0 . 25 . . . none . . PASS Atlas-SNP WDR17 116966 hgsc.bcm.edu hg19 4 177056301 177056301 + Missense_Mutation SNP G G A rs140987021 TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . WDR17 NM_170710 exon9 c.G1213A p.D405N CCTGACGATCCTA . 190.0 62.0 213.0 0.0 . 198 . . . weak G|1.000;A|0.000 0.000 PASS Atlas-SNP ANKHD1 54882 hgsc.bcm.edu hg19 5 139876316 139876316 + Silent SNP A A G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ANKHD1 NM_017747 exon15 c.A2457G p.E819E AGAAGAACTTAAA . 61.0 29.0 80.0 0.0 . 233 . . . none . . PASS Atlas-SNP FAT2 2196 hgsc.bcm.edu hg19 5 150921871 150921871 + Missense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . FAT2 NM_001447 exon9 c.C8817A p.N2939K CTGCCTGTTCTGC . 104.0 30.0 91.0 0.0 . 465 . . . none . . PASS Atlas-SNP KIF4B 285643 hgsc.bcm.edu hg19 5 154395501 154395501 + Silent SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . KIF4B NM_001099293 exon1 c.G2082A p.Q694Q CTTCCAGAAACAA . 320.0 79.0 302.0 0.0 . 307 . . . none . . PASS Atlas-SNP CASP8AP2 9994 hgsc.bcm.edu hg19 6 90577520 90577520 + Missense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . CASP8AP2 NM_001137667 exon8 c.G4511T p.S1504I CAAGCAGTAAATC . 156.0 44.0 142.0 0.0 . 108 . . . none . . PASS Atlas-SNP FBXO30 84085 hgsc.bcm.edu hg19 6 146126628 146126628 + Missense_Mutation SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a FBXO30,NS,carcinoma,0,1 FBXO30 NM_032145 exon2 c.G914A p.G305D GAATCACCATGTA . 84.0 16.0 77.0 0.0 . 56 . . . none . . PASS Atlas-SNP ABCB4 5244 hgsc.bcm.edu hg19 7 87037472 87037472 + Missense_Mutation SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ABCB4 NM_018849 exon25 c.G3160A p.G1054R TCAGCCCCTGAAG . 150.0 30.0 93.0 0.0 . 177 . . . none . . PASS Atlas-SNP LRRD1 401387 hgsc.bcm.edu hg19 7 91794441 91794441 + Missense_Mutation SNP A A T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . LRRD1 NM_001161528 exon1 c.T76A p.S26T TCATTGACTGTGA . 72.0 37.0 48.0 0.0 . 35 . . . none . . PASS Atlas-SNP TECPR1 25851 hgsc.bcm.edu hg19 7 97847037 97847037 + Silent SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TECPR1 NM_015395 exon25 c.G3351A p.E1117E CTTGGGCTCGTGA . 68.0 20.0 15.0 0.0 . 77 . . . none . . PASS Atlas-SNP MEPCE 56257 hgsc.bcm.edu hg19 7 100030705 100030705 + Missense_Mutation SNP T T A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . MEPCE NM_019606 exon2 c.T1835A p.I612N GGGGCATCCTGGT . 367.0 83.0 219.0 0.0 . 52 . . . none . . PASS Atlas-SNP ELP3 55140 hgsc.bcm.edu hg19 8 28047190 28047190 + Missense_Mutation SNP G G C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ELP3 NM_018091 exon15 c.G1592C p.R531T ATTATAGAAAGAT . 82.0 28.0 78.0 0.0 . 36 . . . none . . PASS Atlas-SNP CSMD3 114788 hgsc.bcm.edu hg19 8 113516202 113516202 + Missense_Mutation SNP T T C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . CSMD3 NM_198123 exon30 c.A4900G p.S1634G CTATGCTAAAACT . 32.0 10.0 51.0 0.0 . 2325 . . . none . . PASS Atlas-SNP CSMD3 114788 hgsc.bcm.edu hg19 8 113516207 113516207 + Splice_Site SNP C C G rs76670724 bycluster;alternate_allele TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . CSMD3 NM_052900 exon30 c.4584-1G>C . CTAAAACTGAAAA . 25.0 9.0 42.0 0.0 . 2325 . . . alt . . PASS Atlas-SNP ZNF79 7633 hgsc.bcm.edu hg19 9 130206739 130206739 + Missense_Mutation SNP T T C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ZNF79 NM_007135 exon5 c.T760C p.C254R AGTGAATGTGGAA . 129.0 35.0 93.0 0.0 . 47 . . . none . . PASS Atlas-SNP ACBD5 91452 hgsc.bcm.edu hg19 10 27529275 27529275 + Missense_Mutation SNP T T G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ACBD5 NM_145698 exon2 c.A154C p.K52Q TCACCTTCACGGC . 136.0 39.0 127.0 0.0 . 75 . . . none . . PASS Atlas-SNP MUC5B 727897 hgsc.bcm.edu hg19 11 1264092 1264092 + Silent SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . MUC5B NM_002458 exon31 c.C5982T p.R1994R GACCCGCCTATCA . 1304.0 383.0 785.0 0.0 . 473 . . . none . . PASS Atlas-SNP NAV2 89797 hgsc.bcm.edu hg19 11 19890497 19890497 + Missense_Mutation SNP T T A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . NAV2 NM_145117 exon4 c.T465A p.N155K CTTGAATTTCCTG . 53.0 16.0 59.0 0.0 . 255 . . . none . . PASS Atlas-SNP GAS2 2620 hgsc.bcm.edu hg19 11 22759307 22759307 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . GAS2 NM_177553 exon5 c.G466A p.A156T CGGATTGCAGCCA . 210.0 60.0 143.0 0.0 . 46 . . . none . . PASS Atlas-SNP SLC43A3 29015 hgsc.bcm.edu hg19 11 57182446 57182446 + Missense_Mutation SNP G G C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SLC43A3 NM_017611 exon10 c.C903G p.N301K CAAGGAGTTGAGA . 69.0 21.0 55.0 0.0 . 54 . . . none . . PASS Atlas-SNP KBTBD3 143879 hgsc.bcm.edu hg19 11 105925034 105925034 + Missense_Mutation SNP A A T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . KBTBD3 NM_152433 exon3 c.T382A p.L128M ATGACAACTGGAA . 107.0 34.0 95.0 0.0 . 59 . . . none . . PASS Atlas-SNP ESAM 90952 hgsc.bcm.edu hg19 11 124623587 124623587 + Silent SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ESAM NM_138961 exon7 c.G1128A p.V376V CACAGGCACAGCA . 84.0 7.0 55.0 0.0 . 31 . . . none . . PASS Atlas-SNP NTM 50863 hgsc.bcm.edu hg19 11 132180102 132180102 + Missense_Mutation SNP T T C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . NTM NM_001144059 exon5 c.T758C p.F253S CAGAATTCCAGTG . 307.0 91.0 229.0 0.0 . 253 . . . none . . PASS Atlas-SNP EXOSC8 11340 hgsc.bcm.edu hg19 13 37583387 37583387 + Missense_Mutation SNP A A G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . EXOSC8 NM_181503 exon11 c.A782G p.E261G ACAAAGAAGTTAA . 138.0 29.0 146.0 0.0 . 16 . . . none . . PASS Atlas-SNP VWA8 23078 hgsc.bcm.edu hg19 13 42293875 42293875 + Missense_Mutation SNP A A G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a KIAA0564,rectum,carcinoma,+2,1 . NM_015058 exon26 c.T2968C p.F990L TCGGAAATTTCTG . 62.0 30.0 62.0 0.0 . . . . . none . . PASS Atlas-SNP TIMM9 26520 hgsc.bcm.edu hg19 14 58878635 58878635 + Missense_Mutation SNP T T C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TIMM9 NM_012460 exon4 c.A29G p.Q10R TTTATCTGATCAG . 75.0 35.0 121.0 0.0 . 7 . . . none . . PASS Atlas-SNP PLEKHD1 400224 hgsc.bcm.edu hg19 14 69994009 69994009 + Silent SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PLEKHD1 NM_001161498 exon11 c.G1161A p.E387E TAAGGAGAAGGAG . 174.0 52.0 158.0 0.0 . 24 . . . none . . PASS Atlas-SNP WDR72 256764 hgsc.bcm.edu hg19 15 53815462 53815462 + Missense_Mutation SNP A A G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . WDR72 NM_182758 exon19 c.T3206C p.V1069A TCCTCCACGTCTT . 70.0 14.0 57.0 0.0 . 177 . . . none . . PASS Atlas-SNP TLN2 83660 hgsc.bcm.edu hg19 15 63097959 63097959 + Missense_Mutation SNP T T A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TLN2 NM_015059 exon48 c.T6638A p.V2213E AAGCCGTGTCAGA . 196.0 56.0 154.0 0.0 . 253 . . . none . . PASS Atlas-SNP MEGF11 84465 hgsc.bcm.edu hg19 15 66190397 66190397 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . MEGF11 NM_032445 exon23 c.C3010T p.H1004Y AGTTATGACCGCA . 139.0 34.0 142.0 0.0 . 70 . . . none . . PASS Atlas-SNP IL21R 50615 hgsc.bcm.edu hg19 16 27459983 27459983 + Silent SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a IL21R_ENST00000395754,NS,carcinoma,0,1 IL21R NM_181079 exon10 c.G1062T p.T354T GCTCACGGAGCTA . 259.0 65.0 94.0 1.0 . 95 . . . none . . PASS Atlas-SNP POLR2C 5432 hgsc.bcm.edu hg19 16 57503976 57503976 + Silent SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . POLR2C NM_032940 exon7 c.G543A p.G181G TGCAGGGGTGGCT . 337.0 182.0 185.0 0.0 . 24 . . . none . . PASS Atlas-SNP KLHDC4 54758 hgsc.bcm.edu hg19 16 87760467 87760467 + Silent SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . KLHDC4 NM_017566 exon7 c.G663A p.L221L CGGGGACAGCTTG . 269.0 142.0 102.0 0.0 . 45 . . . none . . PASS Atlas-SNP ZNF469 84627 hgsc.bcm.edu hg19 16 88496091 88496091 + Missense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ZNF469 NM_001127464 exon1 c.G2213T p.R738L GTGACCGCAACTA . 58.0 4.0 13.0 0.0 . 121 . . . none . . PASS Atlas-SNP WDR81 124997 hgsc.bcm.edu hg19 17 1630178 1630178 + Missense_Mutation SNP C C G novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . WDR81 NM_001163809 exon1 c.C1925G p.P642R CCACTCCCTGTGA . 99.0 42.0 61.0 0.0 . 180 . . . none . . PASS Atlas-SNP C17orf104 284071 hgsc.bcm.edu hg19 17 42744034 42744034 + Missense_Mutation SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . C17orf104 NM_001145080 exon5 c.C755T p.T252I TTCAGACAAATGA . 190.0 12.0 112.0 0.0 . 75 . . . none . . PASS Atlas-SNP PPM1E 22843 hgsc.bcm.edu hg19 17 56833454 56833454 + Silent SNP G G A rs77856248 TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a PPM1E,colon,carcinoma,0,1 PPM1E NM_014906 exon1 c.G96A p.E32E GCCGGAGCCGGAA . 39.0 9.0 17.0 0.0 . 97 . . . weak . . PASS Atlas-SNP PPM1E 22843 hgsc.bcm.edu hg19 17 56833457 56833457 + Silent SNP G G C rs74256772 TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a PPM1E,colon,carcinoma,0,1 PPM1E NM_014906 exon1 c.G99C p.P33P GGAGCCGGAACCC . 44.0 16.0 17.0 0.0 . 97 . . . weak . . PASS Atlas-SNP RNF152 220441 hgsc.bcm.edu hg19 18 59483369 59483369 + Missense_Mutation SNP G G C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . RNF152 NM_173557 exon2 c.C328G p.R110G GCGCACGCTCCTT . 78.0 26.0 28.0 0.0 . 37 . . . none . . PASS Atlas-SNP PSG11 5680 hgsc.bcm.edu hg19 19 43519496 43519496 + Missense_Mutation SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PSG11 NM_002785 exon4 c.C736A p.P246T CTGAAGGGAAAAT . 102.0 46.0 102.0 0.0 . 57 . . . none . . PASS Atlas-SNP ZNF415 55786 hgsc.bcm.edu hg19 19 53612760 53612760 + Missense_Mutation SNP T T A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ZNF415 NM_018355 exon4 c.A538T p.I180L AAATTATTTGGGG . 80.0 29.0 87.0 0.0 . 68 . . . none . . PASS Atlas-SNP SEL1L2 80343 hgsc.bcm.edu hg19 20 13868446 13868446 + Silent SNP G G T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SEL1L2 NM_001271539 exon8 c.C714A p.A238A ACTTAGGGCAACT . 83.0 21.0 98.0 0.0 . 103 . . . none . . PASS Atlas-SNP TRPC4AP 26133 hgsc.bcm.edu hg19 20 33623074 33623074 + Silent SNP A A C novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TRPC4AP NM_199368 exon8 c.T903G p.L301L TTTGCAAAGCCGC . 90.0 26.0 115.0 0.0 . 64 . . . none . . PASS Atlas-SNP TRPC4AP 26133 hgsc.bcm.edu hg19 20 33623099 33623099 + Missense_Mutation SNP C C A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TRPC4AP NM_199368 exon8 c.G878T p.S293I GGAATGCTGAGAA . 75.0 20.0 93.0 0.0 . 64 . . . none . . PASS Atlas-SNP PCK1 5105 hgsc.bcm.edu hg19 20 56140806 56140806 + Silent SNP C C A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PCK1 NM_002591 exon10 c.C1815A p.P605P CCTCCCCTGTGAA . 151.0 50.0 114.0 0.0 . 95 . . . none . . PASS Atlas-SNP ZGPAT 84619 hgsc.bcm.edu hg19 20 62366740 62366740 + Silent SNP T T A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . ZGPAT NM_032527 exon6 c.T1281A p.P427P GGCTCCTGGGGCC . 61.0 20.0 58.0 0.0 . 57 . . . none . . PASS Atlas-SNP LGALS2 3957 hgsc.bcm.edu hg19 22 37966307 37966307 + Missense_Mutation SNP C C T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . LGALS2 NM_006498 exon4 c.G362A p.G121D AACCCGCCCCTTA . 174.0 10.0 138.0 0.0 . 16 . . . none . . PASS Atlas-SNP PNPLA3 80339 hgsc.bcm.edu hg19 22 44333050 44333050 + Missense_Mutation SNP G G A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . PNPLA3 NM_025225 exon6 c.G877A p.A293T GCCTTGGCTGTGA . 133.0 44.0 106.0 0.0 . 53 . . . none . . PASS Atlas-SNP RGMB 285704 hgsc.bcm.edu hg19 5 98115590 98115591 + Frame_Shift_Del DEL GG GG - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 GG GG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . RGMB NM_001012761 exon4 c.565_566del p.189_189del . . 204.0 65.0 174.0 0.0 . 29 . 0.318627 0 none . . PASS Atlas-Indel,Pindel ATP13A1 57130 hgsc.bcm.edu hg19 19 19762514 19762515 + Frame_Shift_Ins INS - - TGCAGGA novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a ATP13A1,NS,carcinoma,0,1 ATP13A1 NM_020410 exon17 c.2319_2320insTCCTGCA p.Q773fs . . 241.0 36.0 169.0 0.0 . 82 . 0.149378 0 none . . PASS Atlas-Indel,Pindel TTL 150465 hgsc.bcm.edu hg19 2 113260589 113260589 + Frame_Shift_Del DEL A A - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TTL NM_153712 exon5 c.705delC p.D235fs . . 126.0 31.0 130.0 0.0 . 27 . 0.246032 0 none . . PASS Atlas-Indel,Pindel NEFH 4744 hgsc.bcm.edu hg19 22 29885400 29885417 + In_Frame_Del DEL GAGGCAAAGTCACCGGCT GAGGCAAAGTCACCGGCT - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 GAGGCAAAGTCACCGGCT GAGGCAAAGTCACCGGCT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . NEFH NM_021076 exon4 c.1770_1787del p.590_596del . . 264.0 22.0 182.0 0.0 . 178 . 0.0833333 0 none . . PASS Atlas-INDEL NUP88 4927 hgsc.bcm.edu hg19 17 5312151 5312152 + Frame_Shift_Ins INS - - A novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . NUP88 NM_002532 exon5 c.759_760insT p.L253fs . . 254.0 61.0 162.0 0.0 . 47 . 0.240157 0 none . . PASS Atlas-Indel,Pindel TUT1 64852 hgsc.bcm.edu hg19 11 62343357 62343370 + Frame_Shift_Del DEL GTAAAGGGATCGGC GTAAAGGGATCGGC - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 GTAAAGGGATCGGC GTAAAGGGATCGGC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TUT1 NM_022830 exon9 c.1936_1949del p.646_650del . . 130.0 27.0 145.0 0.0 . 122 . 0.207692 0 none . . PASS Atlas-Indel,Pindel SEL1L3 23231 hgsc.bcm.edu hg19 4 25819805 25819806 + Frame_Shift_Ins INS - - T novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SEL1L3 NM_015187 exon9 c.1519_1520insA p.H507fs . . 198.0 49.0 175.0 0.0 . 62 . 0.247475 0 none . . PASS Atlas-Indel,Pindel TRIM55 84675 hgsc.bcm.edu hg19 8 67064722 67064722 + Frame_Shift_Del DEL T T - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . TRIM55 NM_033058 exon8 c.1095delG p.E365fs . . 44.0 17.0 55.0 0.0 . 91 . 0.386364 0 none . . PASS Atlas-Indel,Pindel SLC25A40 55972 hgsc.bcm.edu hg19 7 87466048 87466048 + Frame_Shift_Del DEL A A - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . SLC25A40 NM_018843 exon11 c.902delC p.S301X . . 112.0 21.0 103.0 0.0 . 32 . 0.1875 0 none . . PASS Atlas-Indel,Pindel GAD1 2571 hgsc.bcm.edu hg19 2 171705820 171705820 + Frame_Shift_Del DEL A A - novel TCGA-HE-A5NL-01A-11D-A26P-10 TCGA-HE-A5NL-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq a441697c-4ca0-4eab-9b01-b9cb50223ce2 49cd5084-c2b5-47d4-b921-2f2316afe33a . GAD1 NM_000817 exon12 c.1143delC p.L381fs . . 138.0 50.0 128.0 0.0 . 79 . 0.362319 0 none . . PASS Atlas-Indel,Pindel