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 CELA2A 63036 hgsc.bcm.edu hg19 1 15789342 15789342 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CELA2A NM_033440 exon4 c.C342A p.N114K CTCCAACCAAATC . 72.0 21.0 111.0 0.0 . 32 . . . none . . PASS Atlas-SNP MAN1C1 57134 hgsc.bcm.edu hg19 1 26109142 26109142 + Missense_Mutation SNP C C G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MAN1C1 NM_020379 exon11 c.C1717G p.P573A AGCACCCCCAACC . 62.0 28.0 83.0 0.0 . 48 . . . none . . PASS Atlas-SNP PPP1R8 5511 hgsc.bcm.edu hg19 1 28157385 28157385 + Silent SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PPP1R8 NM_014110 exon1 c.G39C p.L13L CCCGCTGTTCGAC . 65.0 19.0 81.0 0.0 . 17 . . . none . . PASS Atlas-SNP LURAP1 541468 hgsc.bcm.edu hg19 1 46685818 46685818 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . NM_001013615 exon2 c.G646A p.D216N CCAGAGGATGAGA . 35.0 13.0 30.0 0.0 . . . . . none . . PASS Atlas-SNP SSX2IP 117178 hgsc.bcm.edu hg19 1 85116084 85116084 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . SSX2IP NM_001166417 exon14 c.C1631T p.S544L AAGTCTGAAGTGG . 103.0 6.0 99.0 0.0 . 53 . . . none . . PASS Atlas-SNP DNTTIP2 30836 hgsc.bcm.edu hg19 1 94341887 94341887 + Missense_Mutation SNP T T A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . DNTTIP2 NM_014597 exon2 c.A1604T p.H535L TCGTCATGGTCTG . 265.0 73.0 294.0 0.0 . 59 . . . none . . PASS Atlas-SNP HAO2 51179 hgsc.bcm.edu hg19 1 119925589 119925589 + Silent SNP A A G rs199672779 alternate_allele TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . HAO2 NM_001005783 exon4 c.A183G p.R61R CACCAGAACCACA . 43.0 4.0 32.0 0.0 . 62 . . . alt A|0.999;C|0.001 . PASS Atlas-SNP OBSCN 84033 hgsc.bcm.edu hg19 1 228558813 228558813 + Silent SNP A A G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . OBSCN NM_001271223 exon105 c.A23205G p.V7735V CGGCGTAGCCCGG . 56.0 20.0 76.0 0.0 . 2142 . . . none . . PASS Atlas-SNP HEATR5B 54497 hgsc.bcm.edu hg19 2 37255868 37255868 + Missense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd HEATR5B,NS,carcinoma,0,1 HEATR5B NM_019024 exon23 c.C3557G p.S1186C CAATGAGAAAGTT . 154.0 53.0 177.0 0.0 . 185 . . . none . . PASS Atlas-SNP MAP3K19 80122 hgsc.bcm.edu hg19 2 135744888 135744888 + Silent SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . NM_025052 exon7 c.C1554T p.V518V TATGTTGACACTA . 233.0 89.0 295.0 0.0 . . . . . none . . PASS Atlas-SNP TTN 7273 hgsc.bcm.edu hg19 2 179615537 179615537 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TTN NM_133379 exon46 c.G11590T p.V3864L CATATACTTCCTC . 138.0 47.0 167.0 0.0 . 18412 . . . none . . PASS Atlas-SNP ANKMY1 51281 hgsc.bcm.edu hg19 2 241463492 241463492 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ANKMY1 NM_016552 exon7 c.G1375T p.G459C GACTGCCCCGGTC . 39.0 13.0 42.0 0.0 . 112 . . . none . . PASS Atlas-SNP MUC4 4585 hgsc.bcm.edu hg19 3 195505828 195505828 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MUC4 NM_018406 exon2 c.C12623A p.P4208H GGAAGAGGGGTGG . 45.0 6.0 67.0 0.0 . 1505 . . . none . . PASS Atlas-SNP MUC4 4585 hgsc.bcm.edu hg19 3 195509071 195509071 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MUC4 NM_018406 exon2 c.C9380A p.S3127Y GCTGAGGAAGTGT . 61.0 6.0 55.0 0.0 . 1505 . . . none . . PASS Atlas-SNP ZFYVE28 57732 hgsc.bcm.edu hg19 4 2337512 2337512 + Missense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ZFYVE28 NM_020972 exon6 c.C621G p.D207E CCCGAAGTCCAGG . 40.0 15.0 32.0 0.0 . 79 . . . none . . PASS Atlas-SNP NOP14 8602 hgsc.bcm.edu hg19 4 2946954 2946954 + Silent SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . NOP14 NM_003703 exon12 c.C1638T p.L546L ATAAATGAGCTGG . 45.0 20.0 51.0 0.0 . 69 . . . none . . PASS Atlas-SNP TNIP3 79931 hgsc.bcm.edu hg19 4 122085296 122085296 + Silent SNP T T A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TNIP3 NM_001244764 exon4 c.A216T p.P72P TTTTCCTGGAGTC . 83.0 33.0 79.0 0.0 . 58 . . . none . . PASS Atlas-SNP BHMT2 23743 hgsc.bcm.edu hg19 5 78375253 78375253 + Missense_Mutation SNP T T A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . BHMT2 NM_017614 exon3 c.T228A p.F76L TACCTTTTCTGCC . 49.0 14.0 40.0 0.0 . 44 . . . none . . PASS Atlas-SNP FEM1C 56929 hgsc.bcm.edu hg19 5 114860849 114860849 + Missense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . FEM1C NM_020177 exon3 c.C1010G p.T337S TAAGAGGTATCAG . 84.0 32.0 114.0 0.0 . 50 . . . none . . PASS Atlas-SNP GRAMD3 65983 hgsc.bcm.edu hg19 5 125807996 125807996 + Missense_Mutation SNP A A G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . GRAMD3 NM_001146319 exon4 c.A427G p.S143G AAGCAAAGTAAGT . 102.0 39.0 106.0 0.0 . 30 . . . none . . PASS Atlas-SNP PCDHGA1 56114 hgsc.bcm.edu hg19 5 140710446 140710446 + Silent SNP C C G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PCDHGA1 NM_018912 exon1 c.C195G p.R65R AGTCCGCATCGTC . 74.0 27.0 62.0 0.0 . 397 . . . none . . PASS Atlas-SNP CLK4 57396 hgsc.bcm.edu hg19 5 178032332 178032332 + Missense_Mutation SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CLK4 NM_020666 exon11 c.A1186G p.I396V GTGGTATGGGTCC . 105.0 29.0 137.0 0.0 . 103 . . . none . . PASS Atlas-SNP GFPT2 9945 hgsc.bcm.edu hg19 5 179743447 179743447 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . GFPT2 NM_005110 exon13 c.G1167T p.L389F TTCCTCCAAAACT . 96.0 49.0 72.0 0.0 . 74 . . . none . . PASS Atlas-SNP GLI3 2737 hgsc.bcm.edu hg19 7 42187973 42187973 + Silent SNP C C T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . GLI3 NM_000168 exon3 c.G219A p.E73E AGGTTCCTCACTG . 201.0 84.0 196.0 0.0 . 312 . . . none . . PASS Atlas-SNP DBF4 10926 hgsc.bcm.edu hg19 7 87530188 87530188 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . DBF4 NM_006716 exon10 c.G919A p.E307K GATCTAGAAACTG . 58.0 27.0 52.0 0.0 . 67 . . . none . . PASS Atlas-SNP MUC17 140453 hgsc.bcm.edu hg19 7 100674406 100674406 + Missense_Mutation SNP A A T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MUC17 NM_001040105 exon2 c.A88T p.S30C GACCTCAGTGTGA . 125.0 43.0 171.0 0.0 . 804 . . . none . . PASS Atlas-SNP TMEM229A 730130 hgsc.bcm.edu hg19 7 123672485 123672485 + Silent SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TMEM229A NM_001136002 exon1 c.A573G p.Q191Q CTGCTGTTGCTGC . 17.0 8.0 7.0 0.0 . 31 . . . none . . PASS Atlas-SNP VPS37A 137492 hgsc.bcm.edu hg19 8 17142073 17142073 + Missense_Mutation SNP A A G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . VPS37A NM_152415 exon10 c.A1061G p.E354G TCTTGGAGGGAAA . 116.0 42.0 117.0 0.0 . 22 . . . none . . PASS Atlas-SNP KIF13B 23303 hgsc.bcm.edu hg19 8 28980929 28980929 + Missense_Mutation SNP T T G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . KIF13B NM_015254 exon28 c.A3433C p.M1145L GGACCATCACCGC . 36.0 9.0 30.0 0.0 . 192 . . . none . . PASS Atlas-SNP TMEM245 23731 hgsc.bcm.edu hg19 9 111819564 111819564 + Silent SNP C C T rs201566707 bycluster;alternate_allele TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . NM_032012 exon12 c.G1761A p.L587L GACATGCAACTTC . 81.0 34.0 105.0 0.0 . . . . . alt C|0.999;A|0.001 . PASS Atlas-SNP USP20 10868 hgsc.bcm.edu hg19 9 132638511 132638511 + Silent SNP C C T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . USP20 NM_001008563 exon22 c.C2403T p.F801F CACCTTCATCAAG . 62.0 25.0 65.0 0.0 . 186 . . . none . . PASS Atlas-SNP TUBAL3 79861 hgsc.bcm.edu hg19 10 5443030 5443030 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TUBAL3 NM_024803 exon2 c.C24A p.H8Q ACCGATGTGGATG . 48.0 17.0 54.0 0.0 . 54 . . . none . . PASS Atlas-SNP PALD1 27143 hgsc.bcm.edu hg19 10 72324203 72324203 + Missense_Mutation SNP T T G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd KIAA1274,NS,haematopoietic_neoplasm,0,3 . NM_014431 exon19 c.T2346G p.I782M CCTGATTCTCTTC . 99.0 40.0 86.0 0.0 . . . . . none . . PASS Atlas-SNP KAT6B 23522 hgsc.bcm.edu hg19 10 76788653 76788653 + Silent SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . NM_012330 exon18 c.G4071A p.E1357E GGAGGAGGAGGAG . 24.0 5.0 33.0 0.0 . . . . . none . . PASS Atlas-SNP KIF20B 9585 hgsc.bcm.edu hg19 10 91479191 91479191 + Missense_Mutation SNP A A T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . KIF20B NM_016195 exon13 c.A1450T p.T484S CCAGACACTTTAA . 91.0 37.0 132.0 0.0 . 191 . . . none . . PASS Atlas-SNP CD151 977 hgsc.bcm.edu hg19 11 836827 836827 + Missense_Mutation SNP A A G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CD151 NM_139030 exon4 c.A335G p.Y112C TCGCCTACGCCTA . 63.0 25.0 98.0 0.0 . 7 . . . none . . PASS Atlas-SNP ARFIP2 23647 hgsc.bcm.edu hg19 11 6500088 6500088 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ARFIP2 NM_001242854 exon5 c.G516T p.K172N CTCATACTTGCGC . 70.0 30.0 53.0 0.0 . 23 . . . none . . PASS Atlas-SNP KIAA1731 85459 hgsc.bcm.edu hg19 11 93461858 93461858 + Silent SNP T T A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . KIAA1731 NM_033395 exon25 c.T7173A p.T2391T AGAAACTGGCCAT . 33.0 12.0 31.0 0.0 . 173 . . . none . . PASS Atlas-SNP SIK3 23387 hgsc.bcm.edu hg19 11 116729011 116729011 + Missense_Mutation SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . SIK3 NM_025164 exon20 c.A2852G p.Q951R TGCTGCTGTTGCT . 96.0 18.0 89.0 0.0 . 112 . . . none . . PASS Atlas-SNP PRPF40B 25766 hgsc.bcm.edu hg19 12 50025231 50025231 + Silent SNP C C G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PRPF40B NM_001031698 exon3 c.C132G p.P44P GCTACCCCCCATG . 161.0 40.0 143.0 0.0 . 83 . . . none . . PASS Atlas-SNP UNG 7374 hgsc.bcm.edu hg19 12 109536367 109536367 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . UNG NM_080911 exon2 c.G263A p.R88H CGGCCCGCAACGT . 119.0 67.0 110.0 0.0 . 30 . . . none . . PASS Atlas-SNP HECTD4 283450 hgsc.bcm.edu hg19 12 112622150 112622150 + Silent SNP C C G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . NM_001109662 exon61 c.G10218C p.L3406L GCTGCACAGGGAA . 41.0 21.0 30.0 0.0 . . . . . none . . PASS Atlas-SNP RILPL1 353116 hgsc.bcm.edu hg19 12 124017929 124017929 + Missense_Mutation SNP A A G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . RILPL1 NM_178314 exon1 c.T101C p.V34A TGGCCCACAAGCG . 50.0 29.0 52.0 0.0 . 23 . . . none . . PASS Atlas-SNP COG3 83548 hgsc.bcm.edu hg19 13 46054390 46054390 + Missense_Mutation SNP C C G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . COG3 NM_031431 exon4 c.C514G p.L172V GGAACCCTACATG . 123.0 37.0 100.0 0.0 . 52 . . . none . . PASS Atlas-SNP NALCN 259232 hgsc.bcm.edu hg19 13 101760142 101760142 + Splice_Site SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . NALCN NM_052867 exon22 c.2365-2A>G . GAATGCTAGAAAT . 217.0 94.0 222.0 0.0 . 431 . . . none . . PASS Atlas-SNP NIN 51199 hgsc.bcm.edu hg19 14 51273464 51273464 + Missense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . NIN NM_020921 exon4 c.C256G p.Q86E GTTCTTGAAAGTG . 39.0 14.0 63.0 0.0 . 475 . . . none . . PASS Atlas-SNP HIF1A 3091 hgsc.bcm.edu hg19 14 62207303 62207303 + Silent SNP T T G novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . HIF1A NM_001243084 exon11 c.T1689G p.L563L AAAACTTTTTGCT . 101.0 36.0 84.0 0.0 . 120 . . . none . . PASS Atlas-SNP C15orf57 90416 hgsc.bcm.edu hg19 15 40846226 40846226 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . C15orf57 NM_001080791 exon4 c.C529T p.P177S CCACTGGCTTCTC . 94.0 41.0 84.0 0.0 . 20 . . . none . . PASS Atlas-SNP RPL4 6124 hgsc.bcm.edu hg19 15 66791910 66791910 + Silent SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . RPL4 NM_000968 exon10 c.C1119A p.G373G CTTCTTGCCTGCA . 105.0 40.0 107.0 0.0 . 29 . . . none . . PASS Atlas-SNP DNAJA4 55466 hgsc.bcm.edu hg19 15 78566592 78566592 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . DNAJA4 NM_018602 exon5 c.G559T p.G187W GGGCGGGGGATGC . 53.0 20.0 50.0 0.0 . 63 . . . none . . PASS Atlas-SNP EME2 197342 hgsc.bcm.edu hg19 16 1823269 1823269 + Missense_Mutation SNP A A G rs372940829 TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . EME2 NM_001257370 exon1 c.A41G p.Q14R CTTGCCAGGGCCG . 13.0 6.0 5.0 0.0 . 40 . . . weak . . PASS Atlas-SNP MYLK3 91807 hgsc.bcm.edu hg19 16 46771758 46771758 + Missense_Mutation SNP G G A rs374905189 TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MYLK3 NM_182493 exon3 c.C866T p.S289L CTGGACGATGCTC . 34.0 8.0 48.0 0.0 . 82 . . . weak . . PASS Atlas-SNP KCTD19 146212 hgsc.bcm.edu hg19 16 67337132 67337132 + Missense_Mutation SNP C C A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . KCTD19 NM_001100915 exon4 c.G560T p.S187I ACTAGGCTGGGAT . 51.0 21.0 80.0 0.0 . 82 . . . none . . PASS Atlas-SNP ESRP2 80004 hgsc.bcm.edu hg19 16 68265766 68265766 + Missense_Mutation SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ESRP2 NM_024939 exon10 c.A1238G p.K413R ATGCCCTTGTGCC . 63.0 26.0 85.0 0.0 . 118 . . . none . . PASS Atlas-SNP FXR2 9513 hgsc.bcm.edu hg19 17 7506290 7506290 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . FXR2 NM_004860 exon6 c.C480A p.F160L TTTCTTGAACTCT . 52.0 17.0 82.0 0.0 . 44 . . . none . . PASS Atlas-SNP TBCD 6904 hgsc.bcm.edu hg19 17 80858535 80858535 + Missense_Mutation SNP T T A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TBCD NM_005993 exon18 c.T1658A p.I553N TGTTTATTGCCGG . 166.0 70.0 233.0 0.0 . 94 . . . none . . PASS Atlas-SNP MIER2 54531 hgsc.bcm.edu hg19 19 327981 327981 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MIER2 NM_017550 exon4 c.C252A p.D84E GGGCATGTCGTTG . 40.0 9.0 57.0 0.0 . 51 . . . none . . PASS Atlas-SNP ZNF442 79973 hgsc.bcm.edu hg19 19 12460640 12460640 + Missense_Mutation SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ZNF442 NM_030824 exon6 c.C1759T p.L587F CTCGAAGGAAACG . 98.0 37.0 133.0 0.0 . 102 . . . none . . PASS Atlas-SNP EPHX3 79852 hgsc.bcm.edu hg19 19 15342598 15342598 + Silent SNP G G A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . EPHX3 NM_001142886 exon3 c.C318T p.F106F CTCAGGGAAGCCG . 46.0 21.0 40.0 0.0 . 22 . . . none . . PASS Atlas-SNP RABAC1 10567 hgsc.bcm.edu hg19 19 42461049 42461049 + Missense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . RABAC1 NM_006423 exon5 c.C507G p.F169L CTGGTGGAAGGCA . 91.0 39.0 96.0 0.0 . 6 . . . none . . PASS Atlas-SNP TPRX1 284355 hgsc.bcm.edu hg19 19 48305603 48305603 + Missense_Mutation SNP G G A rs199739873 TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd TPRX1,NS,carcinoma,0,1 TPRX1 NM_198479 exon2 c.C665T p.P222L GGGATCGGGCCTG . 42.0 21.0 52.0 0.0 . 46 . . . weak . . PASS Atlas-SNP SLC12A5 57468 hgsc.bcm.edu hg19 20 44670004 44670004 + Silent SNP T T C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . SLC12A5 NM_001134771 exon8 c.T960C p.H320H TCGCCATGGCTTT . 77.0 17.0 75.0 0.0 . 181 . . . none . . PASS Atlas-SNP DNAJC5 80331 hgsc.bcm.edu hg19 20 62560863 62560863 + Silent SNP C C T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . DNAJC5 NM_025219 exon3 c.C306T p.S102S GCTGTCCAGCTGG . 21.0 9.0 25.0 0.0 . 16 . . . none . . PASS Atlas-SNP SOX18 54345 hgsc.bcm.edu hg19 20 62680619 62680619 + Missense_Mutation SNP C C T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . SOX18 NM_018419 exon1 c.G251A p.R84H CGGATGCGCGACT . 39.0 19.0 41.0 0.0 . 5 . . . none . . PASS Atlas-SNP MCM3AP 8888 hgsc.bcm.edu hg19 21 47665020 47665020 + Missense_Mutation SNP A A C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MCM3AP NM_003906 exon23 c.T4739G p.I1580S TGGCCAATCCCGT . 60.0 22.0 58.0 0.0 . 146 . . . none . . PASS Atlas-SNP CENPI 2491 hgsc.bcm.edu hg19 X 100402791 100402791 + Missense_Mutation SNP G G T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CENPI NM_006733 exon18 c.G1866T p.L622F TGAGTTGGTACAA . 136.0 90.0 162.0 0.0 . 70 . . . none . . PASS Atlas-SNP ND6 0 hgsc.bcm.edu hg19 MT 14569 14569 + Nonsense_Mutation SNP G G C novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . . ENST00000361681 exon1 c.C105G p.S35X CACACCGCTAACA . 77.0 73.0 31.0 0.0 . . . . . none . . PASS Atlas-SNP MUC17 140453 hgsc.bcm.edu hg19 7 100674408 100674408 + Frame_Shift_Del DEL T T - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MUC17 NM_001040105 exon2 c.89delG p.S30fs . . 124.0 44.0 169.0 0.0 . 804 . 0.354839 0 none . . PASS Atlas-INDEL CLCN5 1184 hgsc.bcm.edu hg19 X 49851346 49851347 + In_Frame_Ins INS - - TAA novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CLCN5 NM_001127898 exon11 c.1376_1377insTAA p.F459delinsFN . . 58.0 38.0 75.0 0.0 . 137 . 0.655172 0 none . . PASS Atlas-Indel,Pindel GNL2 29889 hgsc.bcm.edu hg19 1 38039944 38039951 + Frame_Shift_Del DEL CTGGGGGG CTGGGGGG - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 CTGGGGGG CTGGGGGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . GNL2 NM_013285 exon12 c.1410_1416del p.470_472del . . 44.0 16.0 45.0 0.0 . 58 . 0.363636 0 none . . PASS Atlas-Indel,Pindel RRBP1 6238 hgsc.bcm.edu hg19 20 17602147 17602148 + Frame_Shift_Del DEL GT GT - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 GT GT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . RRBP1 NM_001042576 exon17 c.2071_2072del p.691_691del . . 26.0 10.0 28.0 0.0 . 157 . 0.384615 0 none . . PASS Atlas-INDEL PGLYRP4 57115 hgsc.bcm.edu hg19 1 153320386 153320386 + Frame_Shift_Del DEL A A - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PGLYRP4 NM_020393 exon2 c.24delC p.F8fs . . 96.0 40.0 117.0 0.0 . 45 . 0.416667 0 none . . PASS Atlas-Indel,Pindel TRIP4 9325 hgsc.bcm.edu hg19 15 64710865 64710867 + In_Frame_Del DEL TGG TGG - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 TGG TGG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TRIP4 NM_016213 exon9 c.1295_1297del p.432_433del . . 104.0 34.0 99.0 0.0 . 43 . 0.326923 0 none . . PASS Atlas-Indel,Pindel ARID2 196528 hgsc.bcm.edu hg19 12 46244757 46244758 + Frame_Shift_Del DEL CC CC - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 CC CC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . ARID2 NM_152641 exon15 c.2850_2851del p.950_951del . . 115.0 21.0 75.0 0.0 . 311 . 0.182609 0 none . . PASS Atlas-Indel,Pindel SETD2 29072 hgsc.bcm.edu hg19 3 47165283 47165286 + Frame_Shift_Del DEL TTTT TTTT - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 TTTT TTTT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . SETD2 NM_014159 exon3 c.841_844del p.281_282del . . 166.0 109.0 162.0 0.0 . 721 . 0.656627 0 none . . PASS Atlas-Indel,Pindel VPS13A 23230 hgsc.bcm.edu hg19 9 79955390 79955390 + Frame_Shift_Del DEL T T - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . VPS13A NM_001018038 exon50 c.6949delA p.I2317fs . . 190.0 67.0 198.0 0.0 . 735 . 0.352632 0 none . . PASS Atlas-Indel,Pindel POLR2D 5433 hgsc.bcm.edu hg19 2 128610641 128610642 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . POLR2D NM_004805 exon2 c.112_113insT p.H38fs . . 116.0 46.0 127.0 0.0 . 13 . 0.396552 0 none . . PASS Atlas-Indel,Pindel PHF20L1 51105 hgsc.bcm.edu hg19 8 133851799 133851799 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PHF20L1 NM_016018 exon18 c.2358delC p.H786fs . . 54.0 21.0 50.0 0.0 . 129 . 0.388889 0 none . . PASS Atlas-Indel,Pindel CNOT1 23019 hgsc.bcm.edu hg19 16 58608632 58608633 + Frame_Shift_Ins INS - - A novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . CNOT1 NM_001265612 exon16 c.1860_1861insT p.L620fs . . 44.0 12.0 55.0 0.0 . 359 . 0.272727 0 none . . PASS Atlas-INDEL AIM1L 55057 hgsc.bcm.edu hg19 1 26664849 26664849 + Frame_Shift_Del DEL A A - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . AIM1L NM_001039775 exon7 c.3465delG p.M1155fs . . 44.0 10.0 45.0 0.0 . 98 . 0.227273 0 none . . PASS Atlas-INDEL PLEKHA5 54477 hgsc.bcm.edu hg19 12 19408098 19408100 + In_Frame_Del DEL GAG GAG - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 GAG GAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . PLEKHA5 NM_001256470 exon5 c.430_432del p.144_144del . . 54.0 14.0 37.0 0.0 . 198 . 0.259259 0 none . . PASS Atlas-Indel,Pindel STAT1 6772 hgsc.bcm.edu hg19 2 191874648 191874649 + Frame_Shift_Del DEL TG TG - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 TG TG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . STAT1 NM_007315 exon3 c.82_83del p.28_28del . . 186.0 68.0 208.0 0.0 . 93 . 0.365591 0 none . . PASS Atlas-Indel,Pindel TLN2 83660 hgsc.bcm.edu hg19 15 63073341 63073341 + Frame_Shift_Del DEL G G - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . TLN2 NM_015059 exon41 c.5516delT p.L1839fs . . 36.0 14.0 54.0 0.0 . 253 . 0.388889 0 none . . PASS Atlas-Indel,Pindel FNIP2 57600 hgsc.bcm.edu hg19 4 159812799 159812800 + Splice_Site INS - - T novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . FNIP2 NM_020840 exon15 c.3150+1->T . . . 90.0 20.0 93.0 0.0 . 90 . 0.222 . none . . PASS Pindel MUC17 140453 hgsc.bcm.edu hg19 7 100674406 100674408 + In_Frame_Del DEL AGT AGT - novel TCGA-SX-A7SM-01A-11D-A34Z-10 TCGA-SX-A7SM-10A-01D-A34Z-10 AGT AGT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq e6a336f0-67fb-4b2b-b9fd-c5a0fb5d699e bab99f69-b881-4371-88d4-ffdd35a761fd . MUC17 NM_001040105 exon2 c.87_89del p.29_30del . . 125.0 33.0 169.0 0.0 . 804 . 0.264 . none . . PASS Pindel