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 EPHB2 2048 hgsc.bcm.edu hg19 1 23234542 23234542 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 EPHB2,NS,carcinoma,-1,1 EPHB2 NM_004442 exon12 c.C2236A p.R746S GTTCACCGTGACC . 140.0 6.0 199.0 1.0 . 257 . . . none . . PASS Atlas-SNP AGL 178 hgsc.bcm.edu hg19 1 100346675 100346675 + Missense_Mutation SNP C C G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . AGL NM_000644 exon15 c.C1943G p.S648C TTGTTTCTATGGC . 96.0 44.0 104.0 0.0 . 137 . . . none . . PASS Atlas-SNP PRRC2C 23215 hgsc.bcm.edu hg19 1 171535917 171535917 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . . NM_015172 exon22 c.G6487A p.E2163K GTCTCAGAAATGT . 37.0 11.0 49.0 0.0 . . . . . none . . PASS Atlas-SNP AGT 183 hgsc.bcm.edu hg19 1 230841797 230841797 + Missense_Mutation SNP A A T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . AGT NM_000029 exon3 c.T1006A p.F336I CAGTGAAGGGCAC . 126.0 57.0 146.0 0.0 . 62 . . . none . . PASS Atlas-SNP PUM2 23369 hgsc.bcm.edu hg19 2 20518349 20518349 + Missense_Mutation SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . PUM2 NM_015317 exon2 c.G109A p.G37S ATATGCCTTTTTG . 91.0 35.0 108.0 0.0 . 91 . . . none . . PASS Atlas-SNP ANKRD44 91526 hgsc.bcm.edu hg19 2 197986231 197986231 + Missense_Mutation SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ANKRD44 NM_153697 exon8 c.A731G p.H244R GCGATGTGAAGCG . 50.0 18.0 54.0 0.0 . 281 . . . none . . PASS Atlas-SNP FZD5 7855 hgsc.bcm.edu hg19 2 208632800 208632800 + Missense_Mutation SNP A A G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . FZD5 NM_003468 exon2 c.T664C p.C222R GGTAGCAGGGTAC . 24.0 11.0 25.0 0.0 . 22 . . . none . . PASS Atlas-SNP CCDC13 152206 hgsc.bcm.edu hg19 3 42777251 42777251 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . CCDC13 NM_144719 exon10 c.G1319T p.R440L GCCTCCCGCTCAG . 207.0 11.0 154.0 0.0 . 71 . . . none . . PASS Atlas-SNP ALS2CL 259173 hgsc.bcm.edu hg19 3 46713506 46713506 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ALS2CL NM_001190707 exon24 c.G2552T p.R851L TTCTCCCGTGGGT . 185.0 10.0 160.0 0.0 . 78 . . . none . . PASS Atlas-SNP KIAA1407 57577 hgsc.bcm.edu hg19 3 113721375 113721375 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . KIAA1407 NM_020817 exon12 c.G1989T p.E663D TGCTCTCTCTTCC . 108.0 34.0 51.0 0.0 . 80 . . . none . . PASS Atlas-SNP POLQ 10721 hgsc.bcm.edu hg19 3 121217327 121217327 + Missense_Mutation SNP T T G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . POLQ NM_199420 exon13 c.A2150C p.K717T TACCTTTTATGGA . 221.0 118.0 170.0 0.0 . 273 . . . none . . PASS Atlas-SNP IQCJ 654502 hgsc.bcm.edu hg19 3 158980472 158980472 + Silent SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 IQCJ-SCHIP1,NS,carcinoma,0,2 IQCJ NM_001042705 exon4 c.C291A p.P97P CACACCCGTGAGT . 172.0 7.0 151.0 0.0 . 28 . . . none . . PASS Atlas-SNP SEC62 7095 hgsc.bcm.edu hg19 3 169706125 169706125 + Silent SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SEC62 NM_003262 exon7 c.C708T p.A236A TGTAGCCAGTATT . 180.0 49.0 150.0 0.0 . 27 . . . none . . PASS Atlas-SNP ACAP2 23527 hgsc.bcm.edu hg19 3 195006526 195006526 + Silent SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ACAP2 NM_012287 exon22 c.A2235G p.P745P TTGACCTGGCTGT . 81.0 15.0 63.0 0.0 . 72 . . . none . . PASS Atlas-SNP LMLN 89782 hgsc.bcm.edu hg19 3 197687145 197687145 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . LMLN NM_001136049 exon1 c.G53A p.G18D GAGTGGGTTACTC . 61.0 13.0 47.0 0.0 . 53 . . . none . . PASS Atlas-SNP TET2 54790 hgsc.bcm.edu hg19 4 106157461 106157461 + Nonsense_Mutation SNP G G T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 TET2,NS,haematopoietic_neoplasm,0,2 TET2 NM_001127208 exon3 c.G2362T p.E788X CATGGTGAAAATC . 49.0 24.0 43.0 0.0 . 1762 . . . none . . PASS Atlas-SNP FAT1 2195 hgsc.bcm.edu hg19 4 187530418 187530418 + Silent SNP T T A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . FAT1 NM_005245 exon16 c.A10125T p.I3375I GCCATCTATAATT . 82.0 32.0 73.0 0.0 . 500 . . . none . . PASS Atlas-SNP AGGF1 55109 hgsc.bcm.edu hg19 5 76344781 76344781 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . AGGF1 NM_018046 exon8 c.C1334A p.T445N AACATACTCTCCG . 179.0 82.0 150.0 0.0 . 71 . . . none . . PASS Atlas-SNP NME5 8382 hgsc.bcm.edu hg19 5 137474385 137474385 + Nonsense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 NME5,NS,carcinoma,0,1 NME5 NM_003551 exon2 c.G85T p.E29X GTATCTCCTCCTC . 66.0 33.0 67.0 2.0 . 15 . . . none . . PASS Atlas-SNP NME5 8382 hgsc.bcm.edu hg19 5 137474386 137474386 + Missense_Mutation SNP C C G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . NME5 NM_003551 exon2 c.G84C p.E28D TATCTCCTCCTCT . 66.0 33.0 67.0 0.0 . 15 . . . none . . PASS Atlas-SNP PCDH12 51294 hgsc.bcm.edu hg19 5 141336615 141336615 + Missense_Mutation SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 PCDH12,bladder,carcinoma,0,2 PCDH12 NM_016580 exon1 c.G802A p.A268T CTGTGGCGGTCAG . 97.0 37.0 76.0 0.0 . 133 . . . none . . PASS Atlas-SNP AGXT2L2 85007 hgsc.bcm.edu hg19 5 177642285 177642285 + Silent SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . AGXT2L2 NM_153373 exon9 c.G1074A p.G358G GACATCCCCGACG . 53.0 27.0 62.0 0.0 . 51 . . . none . . PASS Atlas-SNP KCTD20 222658 hgsc.bcm.edu hg19 6 36454734 36454734 + Missense_Mutation SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . KCTD20 NM_173562 exon8 c.C1042T p.R348C GTACAACGCCCCT . 119.0 45.0 182.0 0.0 . 37 . . . none . . PASS Atlas-SNP ULBP1 80329 hgsc.bcm.edu hg19 6 150289835 150289835 + Missense_Mutation SNP C C A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ULBP1 NM_025218 exon2 c.C178A p.P60T GAAAGGCCTTTTC . 192.0 90.0 213.0 0.0 . 25 . . . none . . PASS Atlas-SNP MLLT4 4301 hgsc.bcm.edu hg19 6 168344092 168344092 + Missense_Mutation SNP T T A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . MLLT4 NM_001040000 exon24 c.T3155A p.L1052Q GACGTCTAGCTGC . 250.0 105.0 233.0 0.0 . 351 . . . none . . PASS Atlas-SNP C7orf26 79034 hgsc.bcm.edu hg19 7 6639834 6639834 + Missense_Mutation SNP T T G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . C7orf26 NM_024067 exon4 c.T955G p.F319V ATCCTCTTCGACC . 46.0 29.0 48.0 0.0 . 33 . . . none . . PASS Atlas-SNP ASB4 51666 hgsc.bcm.edu hg19 7 95125264 95125264 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ASB4 NM_016116 exon2 c.G382A p.D128N CTCTGTGATCGTG . 112.0 23.0 101.0 0.0 . 52 . . . none . . PASS Atlas-SNP NRCAM 4897 hgsc.bcm.edu hg19 7 107808822 107808822 + Silent SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . NRCAM NM_001037132 exon26 c.C3213T p.S1071S AAGATTGCTGATC . 81.0 27.0 66.0 0.0 . 267 . . . none . . PASS Atlas-SNP CHD7 55636 hgsc.bcm.edu hg19 8 61654762 61654762 + Silent SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . CHD7 NM_017780 exon2 c.T771C p.H257H GTTCCATCACCAC . 218.0 89.0 258.0 1.0 . 534 . . . none . . PASS Atlas-SNP GTF3C5 9328 hgsc.bcm.edu hg19 9 135917679 135917679 + Missense_Mutation SNP T T A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . GTF3C5 NM_012087 exon2 c.T359A p.I120N CCACCATTTACAA . 97.0 36.0 120.0 0.0 . 46 . . . none . . PASS Atlas-SNP GTF3C5 9328 hgsc.bcm.edu hg19 9 135917680 135917680 + Silent SNP T T A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . GTF3C5 NM_012087 exon2 c.T360A p.I120I CACCATTTACAAA . 94.0 35.0 119.0 0.0 . 46 . . . none . . PASS Atlas-SNP CACNA1B 774 hgsc.bcm.edu hg19 9 140943670 140943670 + Silent SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . CACNA1B NM_001243812 exon24 c.T3613C p.L1205L ATCGACTTGGGAC . 88.0 38.0 89.0 0.0 . 266 . . . none . . PASS Atlas-SNP DIP2C 22982 hgsc.bcm.edu hg19 10 375449 375449 + Missense_Mutation SNP A A T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . DIP2C NM_014974 exon30 c.T3677A p.V1226D TCTCGGACTTTGT . 54.0 24.0 32.0 0.0 . 195 . . . none . . PASS Atlas-SNP ZEB1 6935 hgsc.bcm.edu hg19 10 31812949 31812949 + Missense_Mutation SNP G G T rs35653460 bycluster;alternate_allele TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 ZEB1,rectum,carcinoma,0,1 ZEB1 NM_001174096 exon8 c.G2693T p.R898L AAATGCGGAAGAC . 147.0 59.0 140.0 0.0 . 173 . . . alt G|0.987;A|0.013 . PASS Atlas-SNP SEC23IP 11196 hgsc.bcm.edu hg19 10 121692658 121692658 + Missense_Mutation SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SEC23IP NM_007190 exon17 c.T2900C p.L967P TCGCTCTTCAGAG . 152.0 68.0 128.0 0.0 . 100 . . . none . . PASS Atlas-SNP DOCK1 1793 hgsc.bcm.edu hg19 10 128788791 128788791 + Missense_Mutation SNP C C G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . DOCK1 NM_001380 exon6 c.C397G p.L133V CAAATTCTTTCTG . 29.0 12.0 48.0 0.0 . 188 . . . none . . PASS Atlas-SNP OR56A1 120796 hgsc.bcm.edu hg19 11 6048449 6048449 + Silent SNP A A G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . OR56A1 NM_001001917 exon1 c.T486C p.L162L TGCAGTAAGAAGC . 125.0 56.0 148.0 0.0 . 73 . . . none . . PASS Atlas-SNP VWF 7450 hgsc.bcm.edu hg19 12 6143881 6143881 + Silent SNP G G T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . VWF NM_000552 exon20 c.C2658A p.P886P CTCCCCGGGGAAC . 129.0 6.0 105.0 0.0 . 338 . . . none . . PASS Atlas-SNP MLF2 8079 hgsc.bcm.edu hg19 12 6859057 6859057 + Silent SNP C C A rs201104363 bycluster;by1000genomes;alternate_allele TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 MLF2,NS,carcinoma,0,1 MLF2 NM_005439 exon7 c.G516T p.T172T GTCCCCCGTGCGA . 131.0 6.0 109.0 0.0 . 26 . . . alt C|0.999;T|0.001 . PASS Atlas-SNP C2CD5 9847 hgsc.bcm.edu hg19 12 22623804 22623804 + Silent SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . . NM_014802 exon21 c.G2400A p.Q800Q TAAAGCCTGATTT . 93.0 27.0 78.0 0.0 . . . . . none . . PASS Atlas-SNP ITGB7 3695 hgsc.bcm.edu hg19 12 53586547 53586547 + Missense_Mutation SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ITGB7 NM_000889 exon13 c.A1874G p.Q625R AAGCACTGGCAGC . 106.0 65.0 75.0 0.0 . 60 . . . none . . PASS Atlas-SNP SHMT2 6472 hgsc.bcm.edu hg19 12 57625342 57625342 + Missense_Mutation SNP A A G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SHMT2 NM_005412 exon3 c.A310G p.R104G GGCAAGAGGTGAG . 92.0 4.0 58.0 0.0 . 40 . . . none . . PASS Atlas-SNP FSCB 84075 hgsc.bcm.edu hg19 14 44975261 44975261 + Silent SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . FSCB NM_032135 exon1 c.G930A p.A310A ATTCTCCGCAACT . 88.0 38.0 88.0 0.0 . 173 . . . none . . PASS Atlas-SNP TDP1 55775 hgsc.bcm.edu hg19 14 90429932 90429932 + Silent SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . TDP1 NM_018319 exon3 c.G474A p.L158L CATGCTGGATAAA . 125.0 51.0 137.0 0.0 . 47 . . . none . . PASS Atlas-SNP SRRM2 23524 hgsc.bcm.edu hg19 16 2814253 2814253 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SRRM2 NM_016333 exon11 c.G3724A p.V1242I GAGGTGGTAGAGA . 303.0 72.0 221.0 0.0 . 263 . . . none . . PASS Atlas-SNP SRCAP 10847 hgsc.bcm.edu hg19 16 30735227 30735227 + Silent SNP A A C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SRCAP NM_006662 exon25 c.A4482C p.A1494A CTTGGCACCATCT . 165.0 8.0 133.0 0.0 . 298 . . . none . . PASS Atlas-SNP C16orf86 388284 hgsc.bcm.edu hg19 16 67702137 67702137 + Nonsense_Mutation SNP C C G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . C16orf86 NM_001012984 exon4 c.C588G p.Y196X CCAGTACGTCAAC . 32.0 18.0 25.0 0.0 . 20 . . . none . . PASS Atlas-SNP SCARF1 8578 hgsc.bcm.edu hg19 17 1538231 1538231 + Missense_Mutation SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SCARF1 NM_003693 exon11 c.A2314G p.R772G CTGGTCTGACTGC . 87.0 51.0 75.0 0.0 . 46 . . . none . . PASS Atlas-SNP CAMKK1 84254 hgsc.bcm.edu hg19 17 3788622 3788622 + Missense_Mutation SNP C C G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . CAMKK1 NM_032294 exon2 c.G360C p.E120D ACCAACCTCTGCA . 46.0 14.0 39.0 0.0 . 70 . . . none . . PASS Atlas-SNP ZNF232 7775 hgsc.bcm.edu hg19 17 5009512 5009512 + Silent SNP A A G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ZNF232 NM_014519 exon5 c.T942C p.Y314Y TGAGTTATAAATG . 188.0 47.0 136.0 0.0 . 42 . . . none . . PASS Atlas-SNP SENP3 26168 hgsc.bcm.edu hg19 17 7468055 7468055 + Missense_Mutation SNP G G T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SENP3 NM_015670 exon3 c.G829T p.G277W AGCATCGGGGACC . 129.0 7.0 92.0 0.0 . 18 . . . none . . PASS Atlas-SNP SLC13A2 9058 hgsc.bcm.edu hg19 17 26818545 26818545 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SLC13A2 NM_001145975 exon5 c.G812A p.S271N GCATGAGCCTGTG . 150.0 46.0 131.0 0.0 . 125 . . . none . . PASS Atlas-SNP SPAG5 10615 hgsc.bcm.edu hg19 17 26919846 26919846 + Missense_Mutation SNP T T C novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SPAG5 NM_006461 exon3 c.A416G p.Q139R TGTTGCTGCCCCA . 253.0 145.0 185.0 0.0 . 92 . . . none . . PASS Atlas-SNP CTAGE1 64693 hgsc.bcm.edu hg19 18 19997258 19997258 + Missense_Mutation SNP G G A rs372127240 TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 CTAGE1_ENST00000391403,colon,carcinoma,0,2 CTAGE1 NM_172241 exon1 c.C517T p.R173W CCAACCGTTCTTC . 169.0 71.0 253.0 0.0 . 146 . . . weak . . PASS Atlas-SNP LGI4 163175 hgsc.bcm.edu hg19 19 35617247 35617247 + Missense_Mutation SNP A A G novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . LGI4 NM_139284 exon8 c.T1226C p.V409A GCATAGACATCCT . 36.0 17.0 30.0 0.0 . 32 . . . none . . PASS Atlas-SNP ZNF546 339327 hgsc.bcm.edu hg19 19 40520846 40520846 + Missense_Mutation SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ZNF546 NM_178544 exon7 c.G1669A p.E557K TGTAAGGAATGTG . 84.0 45.0 74.0 0.0 . 93 . . . none . . PASS Atlas-SNP EGLN2 112398 hgsc.bcm.edu hg19 19 41306603 41306603 + Nonsense_Mutation SNP T T A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . EGLN2 NM_053046 exon2 c.T126A p.C42X GCCCTGTCCCCTG . 52.0 15.0 56.0 0.0 . 31 . . . none . . PASS Atlas-SNP SLC24A3 57419 hgsc.bcm.edu hg19 20 19665982 19665982 + Missense_Mutation SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SLC24A3 NM_020689 exon12 c.C1301T p.P434L AAGGACCGTACAC . 106.0 41.0 102.0 0.0 . 92 . . . none . . PASS Atlas-SNP ARFGEF2 10564 hgsc.bcm.edu hg19 20 47641990 47641990 + Silent SNP C C T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . ARFGEF2 NM_006420 exon36 c.C4896T p.Y1632Y CAATTACGAGCAG . 66.0 27.0 90.0 0.0 . 160 . . . none . . PASS Atlas-SNP KRTAP10-3 386682 hgsc.bcm.edu hg19 21 45978008 45978008 + Silent SNP G G A novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . KRTAP10-3 NM_198696 exon1 c.C591T p.L197L GCAGAGGAGGGAC . 33.0 16.0 68.0 0.0 . 17 . . . none . . PASS Atlas-SNP BNC2 54796 hgsc.bcm.edu hg19 9 16552614 16552615 + In_Frame_Ins INS - - GAA novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 BNC2,NS,carcinoma,0,1 BNC2 NM_017637 exon5 c.583_584insTTC p.S195delinsFS . . 77.0 17.0 90.0 0.0 . 166 . 0.220779 0 none . . PASS Atlas-INDEL SMARCB1 6598 hgsc.bcm.edu hg19 22 24175838 24175839 + Frame_Shift_Ins INS - - T novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . SMARCB1 NM_003073 exon8 c.1066_1067insT p.L356fs . . 111.0 91.0 149.0 0.0 . 586 . 0.81982 0 none . . PASS Atlas-INDEL NME5 8382 hgsc.bcm.edu hg19 5 137474383 137474383 + Frame_Shift_Del DEL C C - novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . NME5 NM_003551 exon2 c.88delA p.I30fs . . 63.0 32.0 64.0 0.0 . 15 . 0.507937 0 none . . PASS Atlas-INDEL FRYL 285527 hgsc.bcm.edu hg19 4 48598002 48598003 + Frame_Shift_Del DEL TT TT - novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 TT TT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . FRYL NM_015030 exon14 c.1051_1052del p.351_351del . . 64.0 18.0 54.0 0.0 . 242 . 0.28125 0 none . . PASS Atlas-INDEL FAM20A 54757 hgsc.bcm.edu hg19 17 66538845 66538846 + Frame_Shift_Del DEL AA AA - novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 AA AA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . FAM20A NM_017565 exon6 c.918_919del p.306_307del . . 131.0 30.0 102.0 0.0 . 35 . 0.229008 0 none . . PASS Atlas-INDEL VPS9D1 9605 hgsc.bcm.edu hg19 16 89775318 89775318 + Frame_Shift_Del DEL G G - novel TCGA-GL-6846-01A-11D-1961-08 TCGA-GL-6846-10A-01D-1962-08 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 98a51f37-1d5f-4db0-b785-b751168bf46e 631ce65b-a92f-4c3c-b0eb-c2e13249edd7 . . NM_004913 exon13 c.1645delA p.T549fs . . 29.0 12.0 27.0 0.0 . . . 0.413793 0 none . . PASS Atlas-INDEL