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 AGRN 375790 hgsc.bcm.edu hg19 1 957703 957703 + Silent SNP C C A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . AGRN NM_198576 exon2 c.C324A p.S108S GGTGTCCACTGGG . 216.0 38.0 160.0 0.0 . 110 . . . none . . PASS Atlas-SNP OTUD3 23252 hgsc.bcm.edu hg19 1 20233031 20233031 + Silent SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . OTUD3 NM_015207 exon7 c.T942C p.N314N CTTAAATGAAGGC . 138.0 23.0 136.0 0.0 . 25 . . . none . . PASS Atlas-SNP KANK4 163782 hgsc.bcm.edu hg19 1 62739262 62739262 + Missense_Mutation SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . KANK4 NM_181712 exon3 c.G1514A p.G505D TCAGTGCCTGCTT . 133.0 18.0 96.0 0.0 . 135 . . . none . . PASS Atlas-SNP SYDE2 84144 hgsc.bcm.edu hg19 1 85648463 85648463 + Missense_Mutation SNP A A T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SYDE2 NM_032184 exon3 c.T1862A p.L621H TCACTAAGGTAAC . 84.0 13.0 85.0 0.0 . 135 . . . none . . PASS Atlas-SNP NTRK1 4914 hgsc.bcm.edu hg19 1 156851384 156851384 + Silent SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . NTRK1 NM_002529 exon17 c.C2341T p.L781L GCCCGGCTGCAAG . 19.0 4.0 18.0 0.0 . 287 . . . none . . PASS Atlas-SNP ERMN 57471 hgsc.bcm.edu hg19 2 158178038 158178038 + Missense_Mutation SNP T T A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ERMN NM_001009959 exon4 c.A639T p.E213D TCGAACTTCATCT . 73.0 12.0 61.0 0.0 . 31 . . . none . . PASS Atlas-SNP UBR3 130507 hgsc.bcm.edu hg19 2 170762609 170762609 + Missense_Mutation SNP T T A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . UBR3 NM_172070 exon10 c.T1714A p.F572I GCTGCCTTTGCTG . 101.0 29.0 73.0 0.0 . 182 . . . none . . PASS Atlas-SNP OBSL1 23363 hgsc.bcm.edu hg19 2 220416332 220416332 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . OBSL1 NM_015311 exon20 c.C5602A p.H1868N CGTCATGGATGAC . 209.0 53.0 151.0 0.0 . 120 . . . none . . PASS Atlas-SNP SNED1 25992 hgsc.bcm.edu hg19 2 242026825 242026825 + Silent SNP A A T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SNED1 NM_001080437 exon30 c.A4140T p.R1380R CTACCGAGTTCAC . 196.0 70.0 151.0 0.0 . 76 . . . none . . PASS Atlas-SNP SRGAP3 9901 hgsc.bcm.edu hg19 3 9100033 9100033 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SRGAP3 NM_014850 exon7 c.C925A p.L309M AATCCAGGTTGTC . 178.0 29.0 173.0 0.0 . 146 . . . none . . PASS Atlas-SNP TBC1D5 9779 hgsc.bcm.edu hg19 3 17550057 17550057 + Silent SNP A A G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TBC1D5 NM_014744 exon3 c.T6C p.Y2Y GGAATGATACATT . 109.0 32.0 106.0 0.0 . 69 . . . none . . PASS Atlas-SNP STAG1 10274 hgsc.bcm.edu hg19 3 136060303 136060303 + Missense_Mutation SNP T T A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . STAG1 NM_005862 exon31 c.A3537T p.R1179S TCCAGTTCTCACT . 115.0 31.0 77.0 0.0 . 135 . . . none . . PASS Atlas-SNP VWA5B2 90113 hgsc.bcm.edu hg19 3 183955086 183955086 + Missense_Mutation SNP A A T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . VWA5B2 NM_138345 exon11 c.A1606T p.T536S CCCGACACTGTGG . 140.0 22.0 93.0 0.0 . 47 . . . none . . PASS Atlas-SNP UBE2K 3093 hgsc.bcm.edu hg19 4 39757353 39757353 + Missense_Mutation SNP A A G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . UBE2K NM_005339 exon4 c.A293G p.D98G TGAAAGATCAATG . 57.0 8.0 43.0 0.0 . 16 . . . none . . PASS Atlas-SNP OCIAD2 132299 hgsc.bcm.edu hg19 4 48887522 48887522 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . OCIAD2 NM_001014446 exon7 c.C444A p.D148E CTGAGAGTCTCCC . 195.0 42.0 158.0 0.0 . 16 . . . none . . PASS Atlas-SNP ADH1B 125 hgsc.bcm.edu hg19 4 100231924 100231924 + Silent SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ADH1B NM_000668 exon8 c.A1101G p.K367K CTACCTTTTCCCA . 90.0 13.0 100.0 0.0 . 68 . . . none . . PASS Atlas-SNP SLC6A3 6531 hgsc.bcm.edu hg19 5 1394869 1394869 + Missense_Mutation SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 SLC6A3,NS,carcinoma,0,1 SLC6A3 NM_001044 exon15 c.G1844A p.R615H CAGTGGCGGAGCT . 83.0 5.0 66.0 0.0 . 102 . . . none . . PASS Atlas-SNP MED10 84246 hgsc.bcm.edu hg19 5 6378594 6378594 + Missense_Mutation SNP C C A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . MED10 NM_032286 exon1 c.G3T p.M1I CTCCGCCATCGCC . 47.0 10.0 29.0 0.0 . 7 . . . none . . PASS Atlas-SNP MEGF10 84466 hgsc.bcm.edu hg19 5 126790286 126790286 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . MEGF10 NM_032446 exon24 c.G3009T p.M1003I CTATATGGGAAAA . 26.0 4.0 18.0 0.0 . 152 . . . none . . PASS Atlas-SNP ADAM19 8728 hgsc.bcm.edu hg19 5 156908922 156908922 + Missense_Mutation SNP C C A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ADAM19 NM_033274 exon22 c.G2580T p.K860N GAGTGCCTTCTGG . 64.0 16.0 71.0 0.0 . 216 . . . none . . PASS Atlas-SNP UNC5CL 222643 hgsc.bcm.edu hg19 6 41000635 41000635 + Missense_Mutation SNP A A G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . UNC5CL NM_173561 exon4 c.T937C p.Y313H AGATGTACGTGAG . 77.0 10.0 77.0 0.0 . 52 . . . none . . PASS Atlas-SNP DEFB110 245913 hgsc.bcm.edu hg19 6 49986835 49986835 + Missense_Mutation SNP T T G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . DEFB110 NM_001037497 exon2 c.A59C p.K20T TTCTTTTTGGCTG . 102.0 6.0 70.0 0.0 . 5 . . . none . . PASS Atlas-SNP SERINC1 57515 hgsc.bcm.edu hg19 6 122766258 122766258 + Missense_Mutation SNP C C G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SERINC1 NM_020755 exon10 c.G1293C p.W431C GCCAATCCAACTG . 92.0 19.0 68.0 0.0 . 39 . . . none . . PASS Atlas-SNP DUSP26 78986 hgsc.bcm.edu hg19 8 33454873 33454873 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . DUSP26 NM_024025 exon2 c.C161A p.T54K TTGCCTGTGTAGA . 93.0 16.0 94.0 0.0 . 42 . . . none . . PASS Atlas-SNP CA13 377677 hgsc.bcm.edu hg19 8 86162972 86162972 + Missense_Mutation SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . CA13 NM_198584 exon2 c.C41T p.P14L AAGGTCCTATTCA . 91.0 11.0 105.0 0.0 . 26 . . . none . . PASS Atlas-SNP ADCY8 114 hgsc.bcm.edu hg19 8 132002781 132002781 + Missense_Mutation SNP G G A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ADCY8 NM_001115 exon2 c.C968T p.A323V GCCTGGGCCACAA . 91.0 8.0 70.0 0.0 . 291 . . . none . . PASS Atlas-SNP RMI1 80010 hgsc.bcm.edu hg19 9 86617525 86617525 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . RMI1 NM_024945 exon3 c.G1624T p.D542Y TATCTAGATGTAG . 97.0 19.0 110.0 0.0 . 50 . . . none . . PASS Atlas-SNP LPAR1 1902 hgsc.bcm.edu hg19 9 113704022 113704022 + Missense_Mutation SNP G G A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 LPAR1,colon,carcinoma,0,1 LPAR1 NM_001401 exon3 c.C472T p.R158W TCATCCGTGTGTG . 180.0 28.0 154.0 0.0 . 48 . . . none . . PASS Atlas-SNP SPTAN1 6709 hgsc.bcm.edu hg19 9 131362363 131362363 + Missense_Mutation SNP A A T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SPTAN1 NM_003127 exon27 c.A3548T p.E1183V AGGATGAAACTGA . 94.0 9.0 108.0 0.0 . 266 . . . none . . PASS Atlas-SNP LCN10 414332 hgsc.bcm.edu hg19 9 139633991 139633991 + Missense_Mutation SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . LCN10 NM_001001712 exon6 c.A589G p.T197A GGATGGTGTGTGT . 196.0 24.0 140.0 0.0 . 21 . . . none . . PASS Atlas-SNP CUBN 8029 hgsc.bcm.edu hg19 10 16941145 16941145 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . CUBN NM_001081 exon54 c.C8448G p.I2816M GGATCTGATTGTA . 100.0 4.0 92.0 0.0 . 515 . . . none . . PASS Atlas-SNP NUDT13 25961 hgsc.bcm.edu hg19 10 74879794 74879794 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . NUDT13 NM_015901 exon3 c.G102T p.K34N ACTGAAGGAAGAT . 43.0 15.0 51.0 0.0 . 16 . . . none . . PASS Atlas-SNP LZTS2 84445 hgsc.bcm.edu hg19 10 102763858 102763858 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . LZTS2 NM_032429 exon3 c.G1003C p.D335H CTCCGAGACCGGG . 156.0 33.0 122.0 0.0 . 57 . . . none . . PASS Atlas-SNP TIAL1 7073 hgsc.bcm.edu hg19 10 121338280 121338280 + Missense_Mutation SNP A A C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TIAL1 NM_001033925 exon7 c.T565G p.W189G TGGCCCAATTGGT . 183.0 39.0 173.0 0.0 . 47 . . . none . . PASS Atlas-SNP WDR11 55717 hgsc.bcm.edu hg19 10 122664157 122664157 + Splice_Site SNP G G A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . WDR11 NM_018117 exon25 c.3028-1G>A . TTACTAGACAGAC . 98.0 15.0 93.0 0.0 . 95 . . . none . . PASS Atlas-SNP C11orf40 143501 hgsc.bcm.edu hg19 11 4592781 4592781 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . C11orf40 NM_144663 exon4 c.C526G p.R176G CAGTGCGGTCCAA . 86.0 14.0 67.0 0.0 . 37 . . . none . . PASS Atlas-SNP DCHS1 8642 hgsc.bcm.edu hg19 11 6646473 6646473 + Missense_Mutation SNP C C G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . DCHS1 NM_003737 exon19 c.G7102C p.D2368H TGACATCCTCCAC . 136.0 20.0 97.0 0.0 . 277 . . . none . . PASS Atlas-SNP LRP4 4038 hgsc.bcm.edu hg19 11 46898795 46898795 + Missense_Mutation SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . LRP4 NM_002334 exon23 c.A3232G p.I1078V TGGTAATGTTGAT . 176.0 25.0 183.0 0.0 . 160 . . . none . . PASS Atlas-SNP AMOTL1 154810 hgsc.bcm.edu hg19 11 94533391 94533391 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . AMOTL1 NM_130847 exon3 c.G1035T p.M345I CGAGATGGTCAAG . 127.0 22.0 121.0 0.0 . 95 . . . none . . PASS Atlas-SNP TMBIM4 51643 hgsc.bcm.edu hg19 12 66546147 66546147 + Silent SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TMBIM4 NM_016056 exon3 c.A216G p.L72L CAAAATTAAGGCA . 123.0 20.0 114.0 0.0 . 47 . . . none . . PASS Atlas-SNP ZNF140 7699 hgsc.bcm.edu hg19 12 133683062 133683062 + Missense_Mutation SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ZNF140 NM_003440 exon5 c.T1199C p.L400P TTTCCCTCATTCT . 47.0 7.0 21.0 0.0 . 18 . . . none . . PASS Atlas-SNP KCTD12 115207 hgsc.bcm.edu hg19 13 77460122 77460122 + Silent SNP C C G rs371800969 TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . KCTD12 NM_138444 exon1 c.G162C p.S54S GGGCACCGACACC . 6.0 4.0 2.0 0.0 . 11 . . . weak . . PASS Atlas-SNP TEP1 7011 hgsc.bcm.edu hg19 14 20845648 20845648 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TEP1 NM_007110 exon41 c.C5879A p.S1960Y CCCTGGGAACCTA . 76.0 17.0 79.0 0.0 . 224 . . . none . . PASS Atlas-SNP CDH24 64403 hgsc.bcm.edu hg19 14 23524349 23524349 + Nonsense_Mutation SNP T T A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . CDH24 NM_022478 exon3 c.A415T p.K139X GCACTTTGATGAT . 138.0 23.0 118.0 0.0 . 129 . . . none . . PASS Atlas-SNP NYNRIN 57523 hgsc.bcm.edu hg19 14 24885037 24885037 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . NYNRIN NM_025081 exon9 c.G4082T p.G1361V CCTGCGGCCTGGA . 85.0 27.0 66.0 0.0 . 120 . . . none . . PASS Atlas-SNP ATXN3 4287 hgsc.bcm.edu hg19 14 92549507 92549507 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ATXN3 NM_004993 exon7 c.C571G p.L191V CAATAAGTTTTGG . 47.0 7.0 42.0 0.0 . 46 . . . none . . PASS Atlas-SNP TLE3 7090 hgsc.bcm.edu hg19 15 70368460 70368460 + Missense_Mutation SNP T T A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TLE3 NM_001105192 exon5 c.A272T p.Q91L ATGATCTGTGCTA . 57.0 7.0 56.0 0.0 . 104 . . . none . . PASS Atlas-SNP UACA 55075 hgsc.bcm.edu hg19 15 70961458 70961458 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . UACA NM_018003 exon16 c.C1565G p.A522G TTAAGGGCAAGAA . 84.0 4.0 92.0 0.0 . 235 . . . none . . PASS Atlas-SNP CYP11A1 1583 hgsc.bcm.edu hg19 15 74640247 74640247 + Missense_Mutation SNP A A T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . CYP11A1 NM_000781 exon2 c.T419A p.L140Q TTCAACAGGACTC . 102.0 15.0 120.0 0.0 . 54 . . . none . . PASS Atlas-SNP E4F1 1877 hgsc.bcm.edu hg19 16 2285002 2285002 + Missense_Mutation SNP G G T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . E4F1 NM_004424 exon12 c.G1935T p.E645D CATCGAGGTGGGT . 108.0 5.0 98.0 0.0 . 53 . . . none . . PASS Atlas-SNP SRCAP 10847 hgsc.bcm.edu hg19 16 30734928 30734928 + Silent SNP T T C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SRCAP NM_006662 exon25 c.T4183C p.L1395L GCCCCCTTGACCA . 123.0 30.0 109.0 0.0 . 298 . . . none . . PASS Atlas-SNP SLC12A3 6559 hgsc.bcm.edu hg19 16 56919183 56919183 + Missense_Mutation SNP A A C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SLC12A3 NM_001126108 exon15 c.A1832C p.N611T AGGTAAATTGGGG . 99.0 35.0 68.0 0.0 . 99 . . . none . . PASS Atlas-SNP KIAA0753 9851 hgsc.bcm.edu hg19 17 6526336 6526336 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . KIAA0753 NM_014804 exon6 c.C970G p.R324G CCCCTCGGTCAGT . 256.0 68.0 178.0 0.0 . 63 . . . none . . PASS Atlas-SNP SHBG 6462 hgsc.bcm.edu hg19 17 7534128 7534128 + Missense_Mutation SNP C C G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SHBG NM_001040 exon3 c.C334G p.H112D CACAATCACTGGG . 202.0 59.0 143.0 0.0 . 21 . . . none . . PASS Atlas-SNP SOCS7 30837 hgsc.bcm.edu hg19 17 36508826 36508826 + Silent SNP C C A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SOCS7 NM_014598 exon1 c.C699A p.T233T TGGGACCGGCAAG . 47.0 10.0 18.0 0.0 . 22 . . . none . . PASS Atlas-SNP KRTAP4-7 100132476 hgsc.bcm.edu hg19 17 39240796 39240796 + Missense_Mutation SNP G G C rs199957151 TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . KRTAP4-7 NM_033061 exon1 c.G338C p.S113T GCCCCAGCTGCTG . 14.0 9.0 12.0 0.0 . 49 . . . weak . . PASS Atlas-SNP TOB1 10140 hgsc.bcm.edu hg19 17 48940734 48940734 + Missense_Mutation SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TOB1 NM_005749 exon2 c.C645G p.D215E CAAGAGGTCATTC . 230.0 64.0 135.0 0.0 . 40 . . . none . . PASS Atlas-SNP TOMM40 10452 hgsc.bcm.edu hg19 19 45397281 45397281 + Missense_Mutation SNP G G A novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TOMM40 NM_001128917 exon5 c.G601A p.A201T TTCACAGCAGCCG . 106.0 12.0 75.0 0.0 . 13 . . . none . . PASS Atlas-SNP NKX2-2 4821 hgsc.bcm.edu hg19 20 21492814 21492814 + Missense_Mutation SNP T T G novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . NKX2-2 NM_002509 exon2 c.A569C p.K190T ATACCTTTCTCGG . 48.0 5.0 29.0 0.0 . 49 . . . none . . PASS Atlas-SNP SETD4 54093 hgsc.bcm.edu hg19 21 37408418 37408418 + Silent SNP G G C novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . SETD4 NM_017438 exon11 c.C1320G p.T440T AAATCAGGTAAAA . 65.0 13.0 78.0 0.0 . 37 . . . none . . PASS Atlas-SNP MCM3AP 8888 hgsc.bcm.edu hg19 21 47664760 47664760 + Missense_Mutation SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . MCM3AP NM_003906 exon23 c.G4999A p.G1667R GGAACCCGAGCAC . 138.0 32.0 152.0 0.0 . 146 . . . none . . PASS Atlas-SNP PI4KA 5297 hgsc.bcm.edu hg19 22 21119517 21119517 + Nonsense_Mutation SNP C C T novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . PI4KA NM_058004 exon21 c.G2445A p.W815X TTCTGGCCAGAGT . 145.0 28.0 145.0 0.0 . 313 . . . none . . PASS Atlas-SNP ARHGEF4 50649 hgsc.bcm.edu hg19 2 131801154 131801154 + Frame_Shift_Del DEL A A - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ARHGEF4 NM_032995 exon11 c.1596delG p.K532fs . . 202.0 54.0 126.0 0.0 . 89 . 0.267327 0 none . . PASS Atlas-Indel,Pindel CTNNA1 1495 hgsc.bcm.edu hg19 5 138118896 138118897 + Frame_Shift_Del DEL GG GG - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 GG GG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . CTNNA1 NM_001903 exon3 c.135_136del p.45_46del . . 104.0 18.0 72.0 0.0 . 114 . 0.173077 0 none . . PASS Atlas-Indel,Pindel AEBP1 165 hgsc.bcm.edu hg19 7 44150535 44150535 + Frame_Shift_Del DEL G G - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . AEBP1 NM_001129 exon13 c.1508delA p.K503fs . . 105.0 30.0 73.0 0.0 . 102 . 0.285714 0 none . . PASS Atlas-Indel,Pindel FAT4 79633 hgsc.bcm.edu hg19 4 126408614 126408614 + Frame_Shift_Del DEL A A - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 FAT4_ENST00000394329,right_upper_lobe,carcinoma,0,2 FAT4 NM_024582 exon16 c.12930delG p.G4310fs . . 65.0 15.0 54.0 0.0 . 1752 . 0.230769 0 none . . PASS Atlas-Indel,Pindel TG 7038 hgsc.bcm.edu hg19 8 133899726 133899727 + Frame_Shift_Ins INS - - TA novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . TG NM_003235 exon9 c.2109_2110insTA p.C703fs . . 497.0 91.0 416.0 0.0 . 416 . 0.183099 0 none . . PASS Atlas-Indel,Pindel MLH3 27030 hgsc.bcm.edu hg19 14 75516201 75516205 + Frame_Shift_Del DEL TGAAC TGAAC - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 TGAAC TGAAC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . MLH3 NM_014381 exon2 c.155_159del p.52_53del . . 172.0 22.0 157.0 0.0 . 200 . 0.127907 0 none . . PASS Atlas-Indel,Pindel ZW10 9183 hgsc.bcm.edu hg19 11 113619115 113619115 + Frame_Shift_Del DEL T T - novel TCGA-HE-A5NF-01A-11D-A26P-10 TCGA-HE-A5NF-10A-01D-A26P-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq c14407ad-670e-4d1e-9417-2b76f4810fff fcfc53c2-52b3-44d1-ae32-76375e3a0836 . ZW10 NM_004724 exon8 c.954delT p.N318fs . . 67.0 10.0 62.0 0.0 . 49 . 0.149 . none . . PASS Pindel