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 SNIP1 79753 hgsc.bcm.edu hg19 1 38005993 38005993 + Missense_Mutation SNP C C G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SNIP1 NM_024700 exon3 c.G691C p.A231P GAAGTGCCCCAGA . 118.0 63.0 113.0 0.0 . 44 . . . none . . PASS Atlas-SNP CRTC2 200186 hgsc.bcm.edu hg19 1 153926765 153926765 + Missense_Mutation SNP A A G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . CRTC2 NM_181715 exon4 c.T400C p.Y134H ATAAGTAGGCAGG . 46.0 16.0 70.0 0.0 . 58 . . . none . . PASS Atlas-SNP C1orf27 54953 hgsc.bcm.edu hg19 1 186355194 186355194 + Silent SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . C1orf27 NM_001164245 exon4 c.T309C p.D103D AAATGATTTTCAA . 84.0 37.0 117.0 0.0 . 41 . . . none . . PASS Atlas-SNP ERCC3 2071 hgsc.bcm.edu hg19 2 128051097 128051097 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ERCC3 NM_000122 exon2 c.C226A p.L76I CCCAGAGGGGCCT . 51.0 18.0 59.0 0.0 . 73 . . . none . . PASS Atlas-SNP CHL1 10752 hgsc.bcm.edu hg19 3 383612 383612 + Missense_Mutation SNP C C A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . CHL1 NM_001253388 exon5 c.C526A p.Q176K ATCGAACAAGATG . 190.0 89.0 199.0 0.0 . 242 . . . none . . PASS Atlas-SNP FYCO1 79443 hgsc.bcm.edu hg19 3 46000087 46000087 + Nonsense_Mutation SNP G G C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . FYCO1 NM_024513 exon13 c.C3612G p.Y1204X GCAGTAGTAACAG . 117.0 62.0 146.0 0.0 . 115 . . . none . . PASS Atlas-SNP CELSR3 1951 hgsc.bcm.edu hg19 3 48699894 48699894 + Silent SNP G G A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . CELSR3 NM_001407 exon1 c.C174T p.G58G GGCTCCGCCACCG . 36.0 17.0 61.0 0.0 . 237 . . . none . . PASS Atlas-SNP FRMD4B 23150 hgsc.bcm.edu hg19 3 69230503 69230503 + Missense_Mutation SNP G G A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . FRMD4B NM_015123 exon21 c.C2398T p.P800S AAGACGGTGGCTC . 102.0 6.0 72.0 0.0 . 90 . . . none . . PASS Atlas-SNP AFAP1 60312 hgsc.bcm.edu hg19 4 7783233 7783233 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . AFAP1 NM_001134647 exon13 c.C1652A p.P551H TCAGCAGGAGAGT . 106.0 40.0 121.0 0.0 . 93 . . . none . . PASS Atlas-SNP CTNND2 1501 hgsc.bcm.edu hg19 5 10992734 10992734 + Missense_Mutation SNP C C T rs367931998 TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb CTNND2,mucosal,malignant_melanoma,0,1 CTNND2 NM_001332 exon19 c.G3140A p.R1047Q CTTTGCCGGTCCC . 49.0 25.0 47.0 0.0 . 289 . . . weak . . PASS Atlas-SNP HGC6.3 0 hgsc.bcm.edu hg19 6 168377288 168377288 + Silent SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . . NM_001129895 exon1 c.A45G p.G15G GGTCATTCCCCCT . 129.0 34.0 164.0 0.0 . . . . . none . . PASS Atlas-SNP MEOX2 4223 hgsc.bcm.edu hg19 7 15725797 15725797 + Silent SNP A A G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb MEOX2,rectum,carcinoma,0,2 MEOX2 NM_005924 exon1 c.T231C p.H77H GTGGTGATGGTGG . 69.0 7.0 41.0 0.0 . 68 . . . none . . PASS Atlas-SNP MEOX2 4223 hgsc.bcm.edu hg19 7 15725800 15725800 + Silent SNP G G A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MEOX2 NM_005924 exon1 c.C228T p.H76H GTGATGGTGGTGG . 35.0 9.0 11.0 0.0 . 68 . . . none . . PASS Atlas-SNP DFNA5 1687 hgsc.bcm.edu hg19 7 24784199 24784199 + Missense_Mutation SNP A A T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . DFNA5 NM_001127453 exon3 c.T386A p.I129N TCTCTGATGAGCT . 66.0 12.0 70.0 0.0 . 51 . . . none . . PASS Atlas-SNP POR 5447 hgsc.bcm.edu hg19 7 75615290 75615290 + Silent SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . POR NM_000941 exon14 c.T1719C p.D573D CTCGGATGAGGAC . 81.0 18.0 58.0 0.0 . 46 . . . none . . PASS Atlas-SNP ATP5J2-PTCD1 100526740 hgsc.bcm.edu hg19 7 99022430 99022430 + Silent SNP G G A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . . NM_001198879 exon7 c.C1872T p.L624L GTCTGTGAGAAGC . 30.0 9.0 35.0 0.0 . . . . . none . . PASS Atlas-SNP CTSB 1508 hgsc.bcm.edu hg19 8 11705226 11705226 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . CTSB NM_147780 exon9 c.C638A p.P213H TAGCCAGGCTCAC . 53.0 24.0 62.0 0.0 . 24 . . . none . . PASS Atlas-SNP DCAF4L2 138009 hgsc.bcm.edu hg19 8 88885869 88885869 + Missense_Mutation SNP C C G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . DCAF4L2 NM_152418 exon1 c.G331C p.E111Q GGAGCTCAGGGGT . 85.0 32.0 88.0 0.0 . 187 . . . none . . PASS Atlas-SNP PHYHIPL 84457 hgsc.bcm.edu hg19 10 60936661 60936661 + Silent SNP C C A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . PHYHIPL NM_032439 exon1 c.C48A p.P16P CAGCCCCTGTGAG . 46.0 17.0 40.0 0.0 . 44 . . . none . . PASS Atlas-SNP MRPL11 65003 hgsc.bcm.edu hg19 11 66204727 66204727 + Missense_Mutation SNP C C G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MRPL11 NM_170739 exon4 c.G321C p.E107D TGCCACCTCTTTC . 41.0 22.0 38.0 0.0 . 25 . . . none . . PASS Atlas-SNP MTL5 9633 hgsc.bcm.edu hg19 11 68518126 68518126 + Missense_Mutation SNP C C A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MTL5 NM_001039656 exon2 c.G3T p.M1I CTCCTCCATGGCG . 33.0 18.0 33.0 0.0 . 37 . . . none . . PASS Atlas-SNP SRGAP1 57522 hgsc.bcm.edu hg19 12 64377795 64377795 + Missense_Mutation SNP C C T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SRGAP1 NM_020762 exon2 c.C136T p.L46F CAGCTTCTCCAGG . 59.0 24.0 84.0 0.0 . 146 . . . none . . PASS Atlas-SNP ARL1 400 hgsc.bcm.edu hg19 12 101799660 101799660 + Missense_Mutation SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ARL1 NM_001177 exon2 c.A104G p.Y35C AATCTGTACAAAA . 83.0 39.0 123.0 0.0 . 12 . . . none . . PASS Atlas-SNP USP30 84749 hgsc.bcm.edu hg19 12 109490532 109490532 + Missense_Mutation SNP A A T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . USP30 NM_032663 exon1 c.A49T p.I17F AGGGCCATCCAGC . 55.0 26.0 72.0 0.0 . 48 . . . none . . PASS Atlas-SNP BRCA2 675 hgsc.bcm.edu hg19 13 32972588 32972588 + Missense_Mutation SNP A A C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . BRCA2 NM_000059 exon27 c.A9938C p.K3313T CCATAAAGAAAAA . 125.0 51.0 104.0 0.0 . 812 . . . none . . PASS Atlas-SNP SPRY2 10253 hgsc.bcm.edu hg19 13 80911824 80911824 + Missense_Mutation SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SPRY2 NM_005842 exon2 c.A17G p.Q6R CCACTCTGAGCTC . 32.0 17.0 13.0 0.0 . 28 . . . none . . PASS Atlas-SNP ITPK1 3705 hgsc.bcm.edu hg19 14 93408247 93408247 + Missense_Mutation SNP A A T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ITPK1 NM_001142593 exon11 c.T904A p.Y302N CCTCGTAGCCTGG . 31.0 18.0 42.0 0.0 . 53 . . . none . . PASS Atlas-SNP WDR20 91833 hgsc.bcm.edu hg19 14 102675840 102675840 + Missense_Mutation SNP A A G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . WDR20 NM_001242417 exon4 c.A1426G p.S476G GCTGGCAGCAAAA . 73.0 31.0 78.0 0.0 . 35 . . . none . . PASS Atlas-SNP GLCE 26035 hgsc.bcm.edu hg19 15 69548696 69548696 + Missense_Mutation SNP T T C novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . GLCE NM_015554 exon3 c.T551C p.V184A TGGAAGTCCGAGA . 46.0 16.0 58.0 0.0 . 48 . . . none . . PASS Atlas-SNP MYO9A 4649 hgsc.bcm.edu hg19 15 72190184 72190184 + Missense_Mutation SNP C C G novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MYO9A NM_006901 exon25 c.G4660C p.V1554L TCTCTACTCTTTG . 93.0 42.0 76.0 0.0 . 203 . . . none . . PASS Atlas-SNP TMEM202 338949 hgsc.bcm.edu hg19 15 72698982 72698982 + Missense_Mutation SNP T T A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . TMEM202 NM_001080462 exon3 c.T377A p.V126D TCTCTGTCTTTAC . 115.0 55.0 124.0 0.0 . 40 . . . none . . PASS Atlas-SNP SCAMP5 192683 hgsc.bcm.edu hg19 15 75309011 75309011 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SCAMP5 NM_001178111 exon5 c.G214T p.G72C AACTTTGGCCTCG . 39.0 17.0 47.0 0.0 . 34 . . . none . . PASS Atlas-SNP LCAT 3931 hgsc.bcm.edu hg19 16 67976796 67976796 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . LCAT NM_000229 exon3 c.C395A p.S132Y TCCACAGAGTAGG . 29.0 12.0 40.0 0.0 . 31 . . . none . . PASS Atlas-SNP TMEM104 54868 hgsc.bcm.edu hg19 17 72781730 72781730 + Missense_Mutation SNP T T A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . TMEM104 NM_017728 exon3 c.T155A p.L52Q TGTTCCTGGGCTT . 60.0 34.0 52.0 0.0 . 49 . . . none . . PASS Atlas-SNP ACER1 125981 hgsc.bcm.edu hg19 19 6312214 6312214 + Missense_Mutation SNP C C T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ACER1 NM_133492 exon3 c.G296A p.G99D CTATAGCCACTGC . 68.0 24.0 87.0 0.0 . 38 . . . none . . PASS Atlas-SNP C21orf2 755 hgsc.bcm.edu hg19 21 45750162 45750162 + Missense_Mutation SNP C C A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . C21orf2 NM_001271441 exon7 c.G1047T p.E349D CAGCCCCTCTGCA . 55.0 23.0 46.0 0.0 . 10 . . . none . . PASS Atlas-SNP MN1 4330 hgsc.bcm.edu hg19 22 28192976 28192976 + Missense_Mutation SNP C C T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MN1 NM_002430 exon1 c.G3556A p.A1186T CGACGGCGCACTC . 35.0 16.0 26.0 0.0 . 122 . . . none . . PASS Atlas-SNP MID1IP1 58526 hgsc.bcm.edu hg19 X 38664368 38664368 + Missense_Mutation SNP G G T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . MID1IP1 NM_021242 exon2 c.G169T p.G57C GAGGTAGGCGGCA . 151.0 74.0 151.0 0.0 . 12 . . . none . . PASS Atlas-SNP RPA4 29935 hgsc.bcm.edu hg19 X 96139635 96139635 + Missense_Mutation SNP G G A novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . RPA4 NM_013347 exon1 c.G326A p.G109D GGTTTGGTAGAGA . 61.0 33.0 70.0 0.0 . 29 . . . none . . PASS Atlas-SNP RBMX2 51634 hgsc.bcm.edu hg19 X 129546641 129546641 + Missense_Mutation SNP A A T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . RBMX2 NM_016024 exon6 c.A788T p.K263M AAGAAAAGACCAG . 201.0 91.0 233.0 1.0 . 46 . . . none . . PASS Atlas-SNP FCGR1B 2210 hgsc.bcm.edu hg19 1 120927211 120927212 + Frame_Shift_Del DEL GC GC - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 GC GC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . FCGR1B NM_001017986 exon5 c.769_770del p.257_257del . . 508.0 66.0 611.0 0.0 . 14 . 0.129921 0 none . . PASS Atlas-INDEL SERPINI2 5276 hgsc.bcm.edu hg19 3 167189524 167189526 + In_Frame_Del DEL AAG AAG - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 AAG AAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SERPINI2 NM_001012303 exon3 c.128_130del p.43_44del . . 75.0 35.0 89.0 0.0 . 85 . 0.466667 0 none . . PASS Atlas-INDEL ADD1 118 hgsc.bcm.edu hg19 4 2930230 2930232 + In_Frame_Del DEL AAG AAG - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 AAG AAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ADD1 NM_014189 exon15 c.2286_2288del p.762_763del . . 117.0 50.0 157.0 0.0 . 56 . 0.42735 0 none . . PASS Atlas-Indel,Pindel RPS2 6187 hgsc.bcm.edu hg19 16 2014483 2014484 + In_Frame_Ins INS - - CGGCCT novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . RPS2 NM_002952 exon2 c.144_145insAGGCCG p.R48delinsRGR . . 59.0 19.0 55.0 0.0 . 18 . 0.322034 0 none . . PASS Atlas-INDEL LARS 51520 hgsc.bcm.edu hg19 5 145547749 145547751 + In_Frame_Del DEL TCC TCC - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 TCC TCC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . LARS NM_020117 exon5 c.373_375del p.125_125del . . 88.0 28.0 105.0 0.0 . 100 . 0.318182 0 none . . PASS Atlas-Indel,Pindel PCDHGC5 56097 hgsc.bcm.edu hg19 5 140870632 140870633 + Frame_Shift_Ins INS - - T novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . PCDHGC5 NM_018929 exon1 c.1825_1826insT p.L609fs . . 38.0 19.0 40.0 0.0 . 199 . 0.5 0 none . . PASS Atlas-Indel,Pindel FCGR1A 2209 hgsc.bcm.edu hg19 1 149762998 149762999 + Frame_Shift_Del DEL GC GC - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 GC GC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . FCGR1A NM_000566 exon6 c.1049_1050del p.350_350del . . 416.0 26.0 431.0 0.0 . 27 . 0.0625 0 none . . PASS Atlas-INDEL ACSBG2 81616 hgsc.bcm.edu hg19 19 6165945 6165945 + Frame_Shift_Del DEL G G - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . ACSBG2 NM_030924 exon7 c.656delA p.Q219fs . . 56.0 18.0 70.0 0.0 . 83 . 0.321429 0 none . . PASS Atlas-Indel,Pindel SERPINI2 5276 hgsc.bcm.edu hg19 3 167189524 167189527 + Frame_Shift_Del DEL AAGA AAGA - novel TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 AAGA AAGA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb . SERPINI2 NM_001012303 exon3 c.127_130del p.43_44del . . 79.0 30.0 87.0 0.0 . 85 . 0.380 . none . . PASS Pindel BCL6B 255877 hgsc.bcm.edu hg19 17 6928020 6928031 + In_Frame_Del DEL CAGCAGCAGCAG CAGCAGCAGCAG - rs146207245 bycluster;by1000genomes;alternate_allele TCGA-B1-A654-01A-11D-A31X-10 TCGA-B1-A654-10A-01D-A31X-10 CAGCAGCAGCAG CAGCAGCAGCAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq de661caf-c510-4b30-860a-a6b90ce03bdb d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb .,22 BCL6B NM_181844 exon4 c.701_712del p.234_238del . . 67.0 23.0 64.0 0.0 . 85 . 0.343 . alt . . PASS Pindel