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 Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut HLA-DQB2 3120 broad.mit.edu 37 6 32725567 32725567 + Missense_Mutation SNP C C T rs114234640 byFrequency TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr6:32725567C>T ENST00000435145.2 - 4 801 c.740G>A c.(739-741)cGt>cAt p.R247H HLA-DQB2_ENST00000437316.2_Missense_Mutation_p.R247H|HLA-DQB2_ENST00000411527.1_Intron Q5SR06 Q5SR06_HUMAN major histocompatibility complex, class II, DQ beta 2 216 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response integral to membrane|MHC class II protein complex endometrium(1)|kidney(1)|lung(1)|prostate(2) 5 ACCCCTGTGACGGATGATAAG 0.552000 3 23 0 0 1 0 0 TREM2 54209 broad.mit.edu 37 6 41126487 41126487 + Missense_Mutation SNP T T A TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr6:41126487T>A ENST00000338469.3 - 4 617 c.514A>T c.(514-516)Agg>Tgg p.R172W TREM2_ENST00000373122.4_3'UTR|TREM2_ENST00000373113.3_3'UTR NM_001271821.1 NP_001258750.1 Q9NZC2 TREM2_HUMAN triggering receptor expressed on myeloid cells 2 162 axon guidance|humoral immune response extracellular region|integral to membrane|plasma membrane receptor activity breast(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1) 11 Ovarian(28;0.0418)|Colorectal(47;0.196) GGGCTTTTCCTCCCATCATCT 0.592000 4 61 0 0 1 0 0 CHIAP2 149620 broad.mit.edu 37 1 111826023 111826023 + RNA SNP C C G rs6688201 by1000genomes TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr1:111826023C>G ENST00000369743.4 + 0 1388 NR_003928.1 CAACGCCTACCTCAATGTGGT 0.502000 5 51 0 0 1 0 0 NBPF10 100132406 broad.mit.edu 37 1 145367767 145367767 + Missense_Mutation SNP G G A rs77484671 TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr1:145367767G>A ENST00000342960.5 + 83 10398 c.10363G>A c.(10363-10365)Gaa>Aaa p.E3455K NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron NM_001039703.4 NP_001034792.4 A6NDV3 A6NDV3_HUMAN neuroblastoma breakpoint family, member 10 3455 p.E3455K(5) NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2) 73 all_hematologic(923;0.032) Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258) atcaaagaaggaaagaagaag 0.423000 5 51 0 0 1 0 0 DNM1P47 100216544 broad.mit.edu 37 15 102304772 102304772 + RNA SNP T T C TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr15:102304772T>C ENST00000561463.1 + 0 12818 CACAGCGGCGTGACGAGACTC 0.587000 11 27 0 0 1 0 0 NBPF10 100132406 broad.mit.edu 37 1 145367739 145367739 + Silent SNP A A G rs146714035 by1000genomes TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr1:145367739A>G ENST00000342960.5 + 83 10370 c.10335A>G c.(10333-10335)aaA>aaG p.K3445K NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron NM_001039703.4 NP_001034792.4 A6NDV3 A6NDV3_HUMAN neuroblastoma breakpoint family, member 10 3445 p.K3445K(4) NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2) 73 all_hematologic(923;0.032) Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258) ggaaggggaaaaaaagaaggg 0.413000 4 70 0 0 1 0 0 HLA-DQB2 3120 broad.mit.edu 37 6 32725572 32725572 + Silent SNP G G A rs116284473 byFrequency TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr6:32725572G>A ENST00000435145.2 - 4 796 c.735C>T c.(733-735)atC>atT p.I245I HLA-DQB2_ENST00000437316.2_Silent_p.I245I|HLA-DQB2_ENST00000411527.1_Intron Q5SR06 Q5SR06_HUMAN major histocompatibility complex, class II, DQ beta 2 216 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response integral to membrane|MHC class II protein complex endometrium(1)|kidney(1)|lung(1)|prostate(2) 5 TGTGACGGATGATAAGGCCCA 0.557000 3 23 0 0 1 0 0 UBR7 55148 broad.mit.edu 37 14 93685006 93685006 + Silent SNP G G A TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr14:93685006G>A ENST00000013070.6 + 7 971 c.735G>A c.(733-735)aaG>aaA p.K245K UBR7_ENST00000416753.1_Silent_p.K169K NM_175748.3 NP_786924.2 Q8N806 UBR7_HUMAN ubiquitin protein ligase E3 component n-recognin 7 (putative) 245 ubiquitin-protein ligase activity|zinc ion binding breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1) 19 AACAGGGAAAGGATGATGTCC 0.453000 6 99 0 0 1 0 0 RPL23AP53 644128 broad.mit.edu 37 8 163387 163387 + RNA SNP C C T rs3008286 by1000genomes TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr8:163387C>T ENST00000606975.1 - 0 534 CACAGCCTGTCTGATCTGGTG 0.468000 4 32 0 0 1 0 0 NOTCH2 4853 broad.mit.edu 37 1 120612003 120612004 + Frame_Shift_Del DEL GG GG - TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr1:120612003_120612004delGG ENST00000256646.2 - 1 236_237 c.17_18delCC c.(16-18)cfs p.P6fs NM_024408.3 NP_077719.2 Q04721 NOTC2_HUMAN notch 2 6 anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity p.P6fs*27(2) breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 158 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) ACAGCAGAGCGGGGCGCAGGGC 0.762 """N, F, Mis""" """marginal zone lymphoma, DLBCL""" Alagille Syndrome 7 21 --- --- --- --- ALMS1 7840 broad.mit.edu 37 2 73613070 73613071 + In_Frame_Ins INS - - GGA rs13009043 TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr2:73613070_73613071insGGA ENST00000264448.6 + 1 185_186 c.74_75insGGA c.(73-75)gga>gGGAga p.25_26insR ALMS1_ENST00000377715.1_In_Frame_Ins_p.25_26insR|ALMS1_ENST00000409009.1_In_Frame_Ins_p.25_26insR NM_015120.4 NP_055935.4 Q8TCU4 ALMS1_HUMAN Alstrom syndrome 1 25 Glu-rich. G2/M transition of mitotic cell cycle centrosome|cilium|cytosol|microtubule basal body|spindle pole breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2) 147 gaggaggaggaagaggaggagg 0.683 2 4 --- --- --- --- AC073321.4 0 broad.mit.edu 37 2 217474994 217474994 + RNA DEL T T - rs71401155 TCGA-86-A4P8-01A-11D-A24P-08 TCGA-86-A4P8-10A-01D-A24P-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3130eca3-86d7-479e-8608-baa388710d20 802a6332-0b85-4512-965b-6a6ed7b50d56 g.chr2:217474994delT ENST00000441803.1 + 0 195 tctttctttcttttttttttt 0.393 3 3 --- --- --- ---