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	---	---	---	---					
