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	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_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	ACHILLES_Lineage_Results_Top_Genes	CGC_CancerGermlineMut	CGC_CancerMolecularGenetics	CGC_CancerSomaticMut	CGC_CancerSyndrome	CGC_Chr	CGC_ChrBand	CGC_GeneID	CGC_Name	CGC_OtherGermlineMut	CGC_TissueType	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	annotation_transcript	bcgsc	broad	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	entrez_gene_id	external_id_capture	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	hgsc	igv_bad	ucsc	t_alt_count	t_ref_count	n_alt_count	n_ref_count	validation_judgement_rna	validation_power_rna	validation_tumor_alt_count_rna	validation_tumor_ref_count_rna	validation_normal_alt_count_rna	validation_normal_ref_count_rna	min_val_count_rna	validation_judgement_targeted	validation_power_targeted	validation_tumor_alt_count_targeted	validation_tumor_ref_count_targeted	validation_normal_alt_count_targeted	validation_normal_ref_count_targeted	min_val_count_targeted	validation_judgement_localAssembly	validation_power_localAssembly	t_alt_count_localAssembly	t_ref_count_localAssembly	n_alt_count_localAssembly	n_ref_count_localAssembly	min_val_count_localAssembly	validation_judgement_KRAS	validation_power_KRAS	t_alt_count_KRAS	t_ref_count_KRAS	n_alt_count_KRAS	n_ref_count_KRAS	min_val_count_KRAS	pon_loglike	pon_pass_loglike	localAssembly_detected	ExAC_AN	ExAC_AC	ExAC_LQ	passExAC	SCNA_NA	SCNA_NB	SCNA_q_hat	SCNA_tau	IS_SCNA	purity	ploidy	dna_fraction_in_tumor	CCF_hat	CCF_CI95_low	CCF_CI95_high	CCF_mode	CCF_mean	CCF_median	clonal	CCF_CI_low	CCF_CI_high
FBXW7	55294	broad.mit.edu	37	4	153253860	153253861	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			AT	-	AT	AT		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:153253860_153253861delAT	ENST00000281708.4	-	6	2101_2102	c.872_873delAT	c.(871-873)tatfs	p.Y291fs	FBXW7_ENST00000296555.5_Frame_Shift_Del_p.Y173fs|FBXW7_ENST00000263981.5_Frame_Shift_Del_p.Y211fs|FBXW7_ENST00000603841.1_Frame_Shift_Del_p.Y291fs|FBXW7_ENST00000393956.3_Frame_Shift_Del_p.Y115fs|FBXW7_ENST00000603548.1_Frame_Shift_Del_p.Y291fs	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	p.?(1)		462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)			ATGAAAGCACATAGAGTGCCAA	0.347000			Mis, N, D, F		colorectal, endometrial, T-ALL										Rec	yes		4	4q31.3	55294	F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)		E, L	1	Unknown(1)						SO:0001589	frameshift_variant			ENST00000281708.4	1	1	hg19	CCDS3777.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1	1	0	0	67	197	0	46	0	7.085031e-01	1	8	0	46	2	1	1	90	234	0	179	2	1	1.000000	68	196	0	46	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.680000	5.500000e-01	0.830000	0.690000	0.697328	0.680000	0	6.100000e-01	7.700000e-01
XPNPEP1	7511	broad.mit.edu	37	10	111635301	111635301	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:111635301G>A	ENST00000502935.1	-	15	1495	c.1376C>T	c.(1375-1377)tCg>tTg	p.S459L	XPNPEP1_ENST00000322238.8_Intron|XPNPEP1_ENST00000369680.4_Missense_Mutation_p.S416L|XPNPEP1_ENST00000369683.1_Missense_Mutation_p.S345L					X-prolyl aminopeptidase (aminopeptidase P) 1, soluble			31		Breast(234;0.174)			TTGAGCACCCGAGTCAATAAG	0.448000																								0							SO:0001583	missense			ENST00000502935.1	1	1	hg19	CCDS7560.2	.	.	.	.	.	.	.	.	.	.	G	31	5.070360	0.93950	.	.	ENSG00000108039	ENST00000502935;ENST00000369683;ENST00000369680	T;T;T	0.74737	-0.87;-0.87;-0.87	5.43	5.43	0.79202	Peptidase M24, structural domain (3);	0.000000	0.85682	D	0.000000	D	0.88640	0.6491	M	0.88031	2.925	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90341	0.4359	10	0.87932	D	0	-11.0405	17.7889	0.88547	0.0:0.0:1.0:0.0	.	416	Q9NQW7	XPP1_HUMAN	L	459;345;416	ENSP00000421566:S459L;ENSP00000358697:S345L;ENSP00000358694:S416L	ENSP00000358694:S416L	S	-	2	0	XPNPEP1	111625291	1.000000	0.71417	0.977000	0.42913	0.987000	0.75469	9.101000	0.94219	2.698000	0.92095	0.655000	0.94253	TCG		TCGA-LB-A7SX-01A-11D-A33T-08	XPNPEP1-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050264.2	0	0	0	11	255	0	27	1	9.861251e-01	11	160	0	27	2		0	0	0	0	0	2	1	0.998292	10	252	0	26	2	0	0	0	0	0	0		-3.192990	1	1	121412	1	25	1	0	2	2	2.265393	1	0.640000	1.650000	0.640000	0.130000	6.000000e-02	1.000000	0.130000	0.241806	0.130000	0	9.000000e-02	2.100000e-01
ABLIM1	3983	broad.mit.edu	37	10	116331054	116331054	+	Splice_Site	SNP	A	A	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:116331054A>C	ENST00000277895.5	-	4	771		c.e4+1		ABLIM1_ENST00000533213.2_Splice_Site|ABLIM1_ENST00000369252.4_Splice_Site	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1			30		Colorectal(252;0.0373)|Breast(234;0.231)			CGGGGCACTTACTGCTGGAGA	0.527000																								0							SO:0001630	splice_region_variant			ENST00000277895.5	1	0	hg19	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.702615	0.88924	.	.	ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000392955;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369256;ENST00000369260;ENST00000277895	.	.	.	5.97	5.97	0.96955	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0319	0.71713	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ABLIM1	116321044	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.069000	0.93967	2.288000	0.76882	0.533000	0.62120	.		TCGA-LB-A7SX-01A-11D-A33T-08	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3	1	0	1	77	338	0	29	1	4.569672e-01	7	1	0	29	2		0	0	0	0	0	2	1	1.000000	76	338	0	28	2	0	0	0	0	0	0		-2.976506	1	1	0	0		1						0.640000	1.650000									0	0
CUBN	8029	broad.mit.edu	37	10	16918924	16918924	+	Silent	SNP	G	G	A	rs140524729	byFrequency	TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:16918924G>A	ENST00000377833.4	-	57	9143	c.9078C>T	c.(9076-9078)ttC>ttT	p.F3026F		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)			241				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACTTGAATCCGAAGTCTGTGA	0.443000																								0							SO:0001819	synonymous_variant			ENST00000377833.4	1	0	hg19	CCDS7113.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	1	0	0	91	383	0	57	0	0	0	1	0	57	2		0	0	0	0	0	2	1	1.000000	91	379	0	57	2	0	0	0	0	0	0		-20.000000	1	1	121412	32	50	1	0	1	1	2.243644	0	0.640000	1.650000	0.638844	0.590000	4.800000e-01	0.710000	0.600000	0.601341	0.590000	0	5.300000e-01	6.600000e-01
KIF5B	3799	broad.mit.edu	37	10	32310006	32310006	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:32310006G>A	ENST00000302418.4	-	19	2605	c.2148C>T	c.(2146-2148)atC>atT	p.I716I	KIF5B_ENST00000493889.1_5'UTR	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B		KIF5B/ALK(8)|KIF5B/RET(79)	35		Prostate(175;0.0137)			TCAAACTACTGATCTGTTTTT	0.358000			T	RET, ALK	NSCLC										Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	0							SO:0001819	synonymous_variant			ENST00000302418.4	1	1	hg19	CCDS7171.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	0	0	0	18	513	0	50	1	9.527299e-01	2	145	0	50	2		0	0	0	0	0	2	1	0.999982	18	511	0	50	2	0	0	0	0	0	0		-3.405940	1	1	0	0		1	0	1	1	2.243644	0	0.640000	1.650000	0.638844	0.100000	5.000000e-02	0.160000	0.100000	0.110924	0.100000	0	7.000000e-02	1.400000e-01
C10orf71	118461	broad.mit.edu	37	10	50531971	50531971	+	Missense_Mutation	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:50531971G>C	ENST00000374144.3	+	3	1669	c.1381G>C	c.(1381-1383)Gac>Cac	p.D461H	C10orf71_ENST00000323868.4_Missense_Mutation_p.D461H			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71			1					GGATTCAGCAGACAGCCAGCC	0.542000																								0							SO:0001583	missense			ENST00000374144.3	1	1	hg19	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	G	1.808	-0.475281	0.04414	.	.	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.16897	2.31;3.44	5.3	0.937	0.19494	.	1.161450	0.06649	N	0.762440	T	0.18882	0.0453	L	0.57536	1.79	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.34601	-0.9822	10	0.72032	D	0.01	.	6.9192	0.24378	0.2294:0.1223:0.6483:0.0	.	461	Q711Q0-3	.	H	461	ENSP00000318713:D461H;ENSP00000363259:D461H	ENSP00000318713:D461H	D	+	1	0	C10orf71	50201977	0.884000	0.30299	0.000000	0.03702	0.001000	0.01503	3.496000	0.53288	-0.096000	0.12329	0.650000	0.86243	GAC		TCGA-LB-A7SX-01A-11D-A33T-08	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	0	0	1	77	236	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	76	235	0	49	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.209438	0	0.640000	1.650000	0.635332	0.750000	6.100000e-01	0.900000	0.760000	0.762476	0.750000	0	6.800000e-01	8.300000e-01
PCDH15	65217	broad.mit.edu	37	10	56128948	56128948	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:56128948C>A	ENST00000320301.6	-	5	800	c.406G>T	c.(406-408)Gtg>Ttg	p.V136L	PCDH15_ENST00000395433.1_Missense_Mutation_p.V114L|PCDH15_ENST00000373965.2_Missense_Mutation_p.V136L|PCDH15_ENST00000395430.1_Missense_Mutation_p.V136L|PCDH15_ENST00000373957.3_Missense_Mutation_p.V114L|PCDH15_ENST00000395440.1_Missense_Mutation_p.V136L|PCDH15_ENST00000395446.1_Missense_Mutation_p.V136L|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.V136L|PCDH15_ENST00000361849.3_Missense_Mutation_p.V136L|PCDH15_ENST00000437009.1_Missense_Mutation_p.V136L|PCDH15_ENST00000395445.1_Missense_Mutation_p.V136L|PCDH15_ENST00000395442.1_Missense_Mutation_p.V136L|PCDH15_ENST00000395432.2_Missense_Mutation_p.V136L|PCDH15_ENST00000373955.1_Missense_Mutation_p.V136L|PCDH15_ENST00000414778.1_Missense_Mutation_p.V141L	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15			237		Melanoma(3;0.117)|Lung SC(717;0.238)			TCTCTCACCACTATTCGCACT	0.438000										HNSCC(58;0.16)														0							SO:0001583	missense			ENST00000320301.6	1	1	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.386402	0.82902	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395442;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57436	0.5;0.55;0.5;0.48;0.5;0.78;0.68;0.4;0.42;0.47;0.41;0.42;0.42;0.48;0.56	5.52	5.52	0.82312	Cadherin (1);Cadherin conserved site (1);	.	.	.	.	T	0.60792	0.2296	N	0.20986	0.625	0.45118	D	0.998131	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.992;0.999;0.998;0.974;0.992;0.998;0.992;0.996;0.994;0.989;0.999;0.999;1.0;1.0;0.999	D;D;D;P;D;D;D;D;D;P;D;D;D;D;D	0.87578	0.989;0.954;0.928;0.809;0.992;0.928;0.989;0.992;0.928;0.874;0.954;0.954;0.998;0.995;0.97	T	0.57207	-0.7851	9	0.27785	T	0.31	.	19.0325	0.92963	0.0:1.0:0.0:0.0	.	114;136;136;141;136;136;136;136;136;136;136;141;136;114;136	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	L	136;141;136;136;136;136;136;136;136;136;114;114;136;136;141;136;136	ENSP00000363076:V136L;ENSP00000410304:V141L;ENSP00000378826:V136L;ENSP00000378832:V136L;ENSP00000378833:V136L;ENSP00000378829:V136L;ENSP00000378827:V136L;ENSP00000378820:V136L;ENSP00000354950:V136L;ENSP00000378821:V114L;ENSP00000363068:V114L;ENSP00000322604:V136L;ENSP00000378818:V136L;ENSP00000412628:V136L;ENSP00000363066:V136L	ENSP00000322604:V136L	V	-	1	0	PCDH15	55798954	1.000000	0.71417	0.960000	0.40013	0.977000	0.68977	4.754000	0.62191	2.590000	0.87494	0.585000	0.79938	GTG		TCGA-LB-A7SX-01A-11D-A33T-08	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	1	0	1	80	193	0	29		0	0	0	0	29	2		0	0	0	0	0	2	1	1.000000	79	192	0	29	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.279394	0	0.640000	1.650000	0.641148	0.910000	7.500000e-01	1.000000	1.000000	0.912666	0.910000	1	8.300000e-01	1
GDI2	2665	broad.mit.edu	37	10	5810230	5810230	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:5810230C>T	ENST00000380191.4	-	8	1227	c.937G>A	c.(937-939)Gat>Aat	p.D313N	GDI2_ENST00000479928.1_5'UTR|GDI2_ENST00000380132.4_Missense_Mutation_p.D317N|GDI2_ENST00000380181.3_Missense_Mutation_p.D268N	NM_001115156.1|NM_001494.3	NP_001108628.1|NP_001485.2	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2			10					GAGTTGGCATCATTGGTGTTC	0.453000																								0							SO:0001583	missense			ENST00000380191.4	0	1	hg19	CCDS7071.1	.	.	.	.	.	.	.	.	.	.	C	14.60	2.583007	0.46006	.	.	ENSG00000057608	ENST00000380191;ENST00000380153;ENST00000447751;ENST00000380132;ENST00000380181	D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09	5.84	5.84	0.93424	.	0.042131	0.85682	D	0.000000	T	0.81079	0.4748	N	0.17922	0.545	0.80722	D	1	B;B;B	0.14805	0.001;0.011;0.0	B;B;B	0.24269	0.012;0.052;0.008	T	0.73675	-0.3908	10	0.22109	T	0.4	-34.1661	19.7341	0.96195	0.0:1.0:0.0:0.0	.	317;268;313	E7EU23;Q5SX88;P50395	.;.;GDIB_HUMAN	N	313;146;141;317;268	ENSP00000369538:D313N;ENSP00000387565:D141N;ENSP00000369475:D317N;ENSP00000369528:D268N	ENSP00000369475:D317N	D	-	1	0	GDI2	5850236	1.000000	0.71417	0.969000	0.41365	0.856000	0.48823	6.019000	0.70818	2.764000	0.94973	0.655000	0.94253	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	GDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046580.1	1	0	1	94	358	0	42	1	1	161	329	0	42	2		0	0	0	0	0	2	1	1.000000	94	354	0	45	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.208544	0	0.640000	1.650000	0.635332	0.630000	5.200000e-01	0.760000	0.640000	0.644723	0.630000	0	5.800000e-01	7.000000e-01
TACR2	6865	broad.mit.edu	37	10	71164771	71164771	+	Silent	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:71164771G>C	ENST00000373306.4	-	5	1551	c.1008C>G	c.(1006-1008)ctC>ctG	p.L336L	TACR2_ENST00000373307.1_Silent_p.L124L	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2			11					GAGTCAGCTCGAGCTTATCTT	0.612000																								0							SO:0001819	synonymous_variant			ENST00000373306.4	1	1	hg19	CCDS7293.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1	0	0	0	12	464	0	67	0	1.964199e-02	0	8	0	67	2		0	0	0	0	0	2	1	0.999114	12	462	0	66	2	0	0	0	0	0	0		-2.864965	1	1	0	0		1	0	0	0	2.160179	0	0.640000	1.650000	0.623116	0.070000	3.000000e-02	0.130000	0.080000	0.081075	0.070000	0	5.000000e-02	1.000000e-01
H2AFY2	55506	broad.mit.edu	37	10	71859992	71859992	+	Missense_Mutation	SNP	A	A	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr10:71859992A>C	ENST00000373255.4	+	7	981	c.717A>C	c.(715-717)aaA>aaC	p.K239N	AIFM2_ENST00000373248.1_Intron	NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2			15					CTGGGGGAAAAGAGTTCTTGG	0.478000																								0							SO:0001583	missense			ENST00000373255.4	1	1	hg19	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124489	0.77436	.	.	ENSG00000099284	ENST00000373255;ENST00000395046;ENST00000455786	T;T	0.24908	1.83;1.83	5.8	-2.77	0.05877	Appr-1-p processing (2);	0.099386	0.64402	D	0.000002	T	0.32164	0.0820	M	0.73372	2.23	0.80722	D	1	P	0.45348	0.856	P	0.48166	0.569	T	0.36407	-0.9749	10	0.87932	D	0	.	11.8874	0.52610	0.612:0.0:0.388:0.0	.	239	Q9P0M6	H2AW_HUMAN	N	239;173;173	ENSP00000362352:K239N;ENSP00000404584:K173N	ENSP00000362352:K239N	K	+	3	2	H2AFY2	71529998	0.598000	0.26882	0.903000	0.35520	0.992000	0.81027	-0.087000	0.11215	-0.424000	0.07382	0.533000	0.62120	AAA		TCGA-LB-A7SX-01A-11D-A33T-08	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	1	0	1	43	109	0	12	1	9.999999e-01	27	43	0	12	2		0	0	0	0	0	2	1	1.000000	43	108	0	12	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.160179	0	0.640000	1.650000	0.623116	0.840000	6.400000e-01	1.000000	1.000000	0.844914	0.840000	0	7.300000e-01	9.500000e-01
RNF26	79102	broad.mit.edu	37	11	119206987	119206987	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:119206987C>T	ENST00000311413.4	+	1	1751	c.1155C>T	c.(1153-1155)gaC>gaT	p.D385D	RP11-334E6.10_ENST00000501918.2_RNA|C1QTNF5_ENST00000525657.1_5'Flank	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26			12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)			TCTGCCAGGACCAGAGCAAGA	0.597000																								0							SO:0001819	synonymous_variant			ENST00000311413.4	1	1	hg19	CCDS8419.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	0	0	0	16	422	0	44	1	8.805467e-01	3	98	0	44	2		0	0	0	0	0	2	1	0.999927	16	415	0	43	2	0	0	0	0	0	0		-15.793170	1	1	0	0		1	0	0	0	2.216782	0	0.640000	1.650000	0.635332	0.110000	6.000000e-02	0.180000	0.120000	0.119040	0.110000	0	8.000000e-02	1.500000e-01
THY1	7070	broad.mit.edu	37	11	119290857	119290857	+	Missense_Mutation	SNP	C	C	T	rs142564004		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:119290857C>T	ENST00000284240.5	-	3	1316	c.277G>A	c.(277-279)Gcc>Acc	p.A93T	THY1_ENST00000527590.1_5'UTR|USP2-AS1_ENST00000498979.2_RNA|THY1_ENST00000580275.1_Missense_Mutation_p.A76T|USP2-AS1_ENST00000500970.1_RNA|RP11-334E6.12_ENST00000578216.1_RNA|THY1_ENST00000528522.1_Missense_Mutation_p.A93T|USP2-AS1_ENST00000530002.1_RNA|USP2-AS1_ENST00000578923.1_RNA	NM_006288.3	NP_006279.2	P04216	THY1_HUMAN	Thy-1 cell surface antigen			12		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)			CTAGTGAAGGCGGATAAGTAG	0.562000																								0							SO:0001583	missense			ENST00000284240.5	1	1	hg19	CCDS8424.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.945019	0.34283	2.27E-4	1.16E-4	ENSG00000154096	ENST00000284240;ENST00000528522;ENST00000524970;ENST00000524659	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.94	-3.71	0.04424	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.566810	0.03175	N	0.171259	T	0.10637	0.0260	N	0.08118	0	0.09310	N	1	B	0.25441	0.126	B	0.23275	0.045	T	0.28138	-1.0053	10	0.42905	T	0.14	-7.3332	7.1224	0.25453	0.1288:0.2015:0.0:0.6697	.	93	P04216	THY1_HUMAN	T	93	ENSP00000284240:A93T;ENSP00000431301:A93T;ENSP00000432808:A93T;ENSP00000435753:A93T	ENSP00000284240:A93T	A	-	1	0	THY1	118796067	0.000000	0.05858	0.028000	0.17463	0.953000	0.61014	-0.396000	0.07278	-0.677000	0.05231	0.591000	0.81541	GCC		TCGA-LB-A7SX-01A-11D-A33T-08	THY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388370.2	0	0	0	17	492	0	70	0	9.834774e-01	0	195	0	70	2		0	0	0	0	0	2	1	0.999965	17	490	0	68	2	0	0	0	0	0	0		-3.041657	1	1	121412	4	39	1	0	0	0	2.216782	0	0.640000	1.650000	0.635332	0.100000	5.000000e-02	0.160000	0.100000	0.108550	0.100000	0	7.000000e-02	1.300000e-01
OR6X1	390260	broad.mit.edu	37	11	123625215	123625215	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:123625215G>A	ENST00000327930.2	-	1	38	c.12C>T	c.(10-12)ggC>ggT	p.G4G		NM_001005188.1	NP_001005188.1	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X, member 1			23		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)			TGATTACTGTGCCATTTCTCA	0.398000																								0							SO:0001819	synonymous_variant			ENST00000327930.2	1	1	hg19	CCDS31695.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	OR6X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387436.1	1	0	1	135	507	0	81		0	0	0	0	81	2		0	0	0	0	0	2	1	1.000000	134	504	0	80	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.222305	0	0.640000	1.650000	0.635332	0.640000	5.500000e-01	0.740000	0.650000	0.650911	0.640000	0	5.900000e-01	7.000000e-01
OR8B12	219858	broad.mit.edu	37	11	124413456	124413456	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:124413456C>T	ENST00000306842.2	-	1	119	c.95G>A	c.(94-96)gGt>gAt	p.G32D		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12			31		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)			CGTGTAGAAACCCAGAAACAG	0.512000																								0							SO:0001583	missense			ENST00000306842.2	1	1	hg19	CCDS31711.1	.	.	.	.	.	.	.	.	.	.	C	8.799	0.932336	0.18131	.	.	ENSG00000170953	ENST00000306842	T	0.00441	7.41	3.89	1.92	0.25849	.	0.739643	0.12351	N	0.476555	T	0.00412	0.0013	M	0.64676	1.99	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.34104	-0.9842	10	0.35671	T	0.21	.	9.0627	0.36444	0.2929:0.5648:0.1422:0.0	.	32	Q8NGG6	OR8BC_HUMAN	D	32	ENSP00000307159:G32D	ENSP00000307159:G32D	G	-	2	0	OR8B12	123918666	0.000000	0.05858	0.075000	0.20258	0.874000	0.50279	0.248000	0.18198	0.550000	0.28991	0.650000	0.86243	GGT		TCGA-LB-A7SX-01A-11D-A33T-08	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1	0	0	0	16	502	0	68		0	0	0	0	68	2		0	0	0	0	0	2	1	0.999925	16	493	0	67	2	0	0	0	0	0	0		-14.378900	1	1	0	0		1	0	0	0	2.222305	0	0.640000	1.650000	0.635332	0.090000	5.000000e-02	0.150000	0.100000	0.100746	0.090000	0	7.000000e-02	1.200000e-01
ARHGAP32	9743	broad.mit.edu	37	11	128844270	128844270	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:128844270G>A	ENST00000310343.9	-	20	2779	c.2780C>T	c.(2779-2781)tCa>tTa	p.S927L	ARHGAP32_ENST00000524655.1_Missense_Mutation_p.S853L|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.S578L|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.S578L	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32			60					TGTGGTATTTGAGACTGTACC	0.438000																								0							SO:0001583	missense			ENST00000310343.9	1	1	hg19	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	1.539	-0.542366	0.04053	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000524655;ENST00000457677;ENST00000527272	T;T;T;T	0.19532	2.14;2.14;2.14;2.14	5.81	5.81	0.92471	.	0.685457	0.14496	N	0.316057	T	0.19005	0.0456	L	0.47716	1.5	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.09422	-1.0675	10	0.27082	T	0.32	.	9.239	0.37484	0.0747:0.0:0.7798:0.1455	.	861;927	Q86T64;A7KAX9	.;RHG32_HUMAN	L	927;578;853;861;578	ENSP00000310561:S927L;ENSP00000376425:S578L;ENSP00000432468:S853L;ENSP00000432862:S578L	ENSP00000310561:S927L	S	-	2	0	ARHGAP32	128349480	0.439000	0.25610	0.010000	0.14722	0.962000	0.63368	3.889000	0.56212	2.745000	0.94114	0.655000	0.94253	TCA		TCGA-LB-A7SX-01A-11D-A33T-08	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	1	0	1	91	345	0	67	1	9.938018e-01	11	21	0	67	2		0	0	0	0	0	2	1	1.000000	91	343	0	67	2	0	0	0	0	0	0		-3.653061	1	1	0	0		1	0	0	0	2.222305	0	0.640000	1.650000	0.635332	0.640000	5.200000e-01	0.760000	0.640000	0.647141	0.640000	0	5.800000e-01	7.100000e-01
BARX2	8538	broad.mit.edu	37	11	129321169	129321169	+	Nonsense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:129321169C>T	ENST00000281437.4	+	4	808	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	BARX2_ENST00000526127.1_Nonsense_Mutation_p.Q93*|BARX2_ENST00000531946.1_Nonsense_Mutation_p.Q116*	NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2			20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)			GGAGCCCTCTCAGGGGCAGGA	0.582000																								0							SO:0001587	stop_gained			ENST00000281437.4	0	1	hg19	CCDS8481.1	.	.	.	.	.	.	.	.	.	.	C	37	6.365625	0.97507	.	.	ENSG00000043039	ENST00000281437;ENST00000526127;ENST00000531946	.	.	.	5.51	-0.263	0.12954	.	1.403330	0.03992	N	0.294986	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	7.0817	0.25235	0.1156:0.3683:0.445:0.0712	.	.	.	.	X	238;93;116	.	ENSP00000281437:Q238X	Q	+	1	0	BARX2	128826379	0.053000	0.20554	0.001000	0.08648	0.008000	0.06430	0.707000	0.25704	0.268000	0.21939	0.655000	0.94253	CAG		TCGA-LB-A7SX-01A-11D-A33T-08	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386153.1	0	0	0	7	369	0	55	1	8.707947e-01	7	187	0	55	2		0	0	0	0	0	2	1	0.980471	7	367	0	55	2	0	0	0	0	0	0		-3.277555	1	1	0	0		1	0	0	0	2.222305	0	0.640000	1.650000	0.635332	0.050000	2.000000e-02	0.110000	0.060000	0.065222	0.050000	0	3.000000e-02	9.000000e-02
ADAMTS15	170689	broad.mit.edu	37	11	130332572	130332572	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:130332572G>T	ENST00000299164.2	+	4	1439	c.1439G>T	c.(1438-1440)tGc>tTc	p.C480F		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15			36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)			CAGATGGTGTGCCAGACCCGC	0.627000																								0							SO:0001583	missense			ENST00000299164.2	0	1	hg19	CCDS8488.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754975	0.89843	.	.	ENSG00000166106	ENST00000299164	T	0.68765	-0.35	5.48	5.48	0.80851	.	.	.	.	.	D	0.87962	0.6310	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91263	0.5038	9	0.87932	D	0	.	19.3471	0.94367	0.0:0.0:1.0:0.0	.	480	Q8TE58	ATS15_HUMAN	F	480	ENSP00000299164:C480F	ENSP00000299164:C480F	C	+	2	0	ADAMTS15	129837782	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.566000	0.86566	0.655000	0.94253	TGC		TCGA-LB-A7SX-01A-11D-A33T-08	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	0	0	0	10	523	0	69	0	0	0	1	0	69	2		0	0	0	0	0	2	1	0.996557	10	512	0	69	2	0	0	0	0	0	0		-3.352012	1	1	0	0		1	0	0	0	2.222305	0	0.640000	1.650000	0.635332	0.050000	2.000000e-02	0.100000	0.060000	0.063348	0.050000	0	3.000000e-02	8.000000e-02
CYP2R1	120227	broad.mit.edu	37	11	14913531	14913531	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:14913531C>G	ENST00000334636.5	-	1	267	c.221G>C	c.(220-222)gGa>gCa	p.G74A	CYP2R1_ENST00000532378.1_5'Flank|CYP2R1_ENST00000526489.1_5'Flank	NM_024514.4	NP_078790.2	Q6VVX0	CP2R1_HUMAN	cytochrome P450, family 2, subfamily R, polypeptide 1			14				Cholecalciferol(DB00169)|Ergocalciferol(DB00153)	CTGTACCTCTCCGTACACCTG	0.682000													NSCLC(173;1584 2058 26117 29365 41534)											0							SO:0001583	missense			ENST00000334636.5	1	1	hg19	CCDS7818.1	.	.	.	.	.	.	.	.	.	.	C	34	5.301978	0.95601	.	.	ENSG00000186104	ENST00000334636	D	0.86230	-2.09	5.12	5.12	0.69794	.	0.053179	0.85682	D	0.000000	D	0.95730	0.8611	H	0.95079	3.62	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96785	0.9578	10	0.87932	D	0	.	18.7483	0.91802	0.0:1.0:0.0:0.0	.	74	Q6VVX0	CP2R1_HUMAN	A	74	ENSP00000334592:G74A	ENSP00000334592:G74A	G	-	2	0	CYP2R1	14870107	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.224000	0.65288	2.665000	0.90641	0.462000	0.41574	GGA		TCGA-LB-A7SX-01A-11D-A33T-08	CYP2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386985.1	1	0	0	56	86	0	34	1	3.470320e-01	2	1	0	34	2		0	0	0	0	0	2	1	1.000000	56	86	0	34	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.757469	1	0.640000	1.650000	0.530271	0.930000	7.500000e-01	1.000000	1.000000	0.925546	0.930000	1	8.400000e-01	1
ABTB2	25841	broad.mit.edu	37	11	34182562	34182562	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:34182562G>A	ENST00000435224.2	-	11	2709	c.2285C>T	c.(2284-2286)tCg>tTg	p.S762L	ABTB2_ENST00000298992.2_Missense_Mutation_p.S576L	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2			25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)			CTGCACCACCGAGTACCGCGA	0.612000																								0							SO:0001583	missense			ENST00000435224.2	0	1	hg19	CCDS7890.2	.	.	.	.	.	.	.	.	.	.	G	17.15	3.314888	0.60524	.	.	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.60424	0.19;0.19	5.15	5.15	0.70609	.	0.192066	0.46442	D	0.000289	T	0.50514	0.1620	L	0.53249	1.67	0.45852	D	0.998714	P	0.45672	0.864	B	0.31495	0.131	T	0.60652	-0.7221	10	0.54805	T	0.06	-16.6682	18.6197	0.91317	0.0:0.0:1.0:0.0	.	576	Q8N961	ABTB2_HUMAN	L	762;576	ENSP00000410157:S762L;ENSP00000298992:S576L	ENSP00000298992:S576L	S	-	2	0	ABTB2	34139138	1.000000	0.71417	0.977000	0.42913	0.995000	0.86356	4.222000	0.58580	2.401000	0.81631	0.561000	0.74099	TCG		TCGA-LB-A7SX-01A-11D-A33T-08	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	0	0	0	5	139	0	30	0	5.489195e-02	0	9	0	30	2		0	0	0	0	0	2	1	0.935165	5	136	0	30	2	0	0	0	0	0	0		-7.661898	1	1	0	0		1	0	1	1	1.757469	1	0.640000	1.650000	0.530271	0.080000	3.000000e-02	0.180000	0.080000	0.097824	0.080000	0	5.000000e-02	1.300000e-01
AGBL2	79841	broad.mit.edu	37	11	47721004	47721004	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:47721004C>A	ENST00000525123.1	-	8	973	c.688G>T	c.(688-690)Gat>Tat	p.D230Y	AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000298861.4_Missense_Mutation_p.D230Y|AGBL2_ENST00000528244.1_Missense_Mutation_p.D192Y|AGBL2_ENST00000357610.3_Missense_Mutation_p.D230Y	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2			34					ATACCTGAATCTAATTGATAG	0.323000																								0							SO:0001583	missense			ENST00000525123.1	1	1	hg19	CCDS7944.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240985	0.39598	.	.	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244;ENST00000532595;ENST00000420784	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.22	4.28	0.50868	.	0.515698	0.23114	N	0.051766	T	0.27419	0.0673	L	0.59436	1.845	0.32047	N	0.597485	B;B;B	0.28208	0.203;0.129;0.129	B;B;B	0.28784	0.094;0.043;0.043	T	0.38887	-0.9640	10	0.72032	D	0.01	-14.9865	4.6077	0.12385	0.0:0.606:0.1987:0.1952	.	192;192;230	F6U0I4;B4DZS1;Q5U5Z8	.;.;CBPC2_HUMAN	Y	230;230;230;192;174;174	ENSP00000435582:D230Y;ENSP00000350228:D230Y;ENSP00000298861:D230Y;ENSP00000436630:D192Y;ENSP00000436063:D174Y	ENSP00000298861:D230Y	D	-	1	0	AGBL2	47677580	0.997000	0.39634	1.000000	0.80357	0.930000	0.56654	0.984000	0.29565	1.168000	0.42723	0.393000	0.25936	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	0	0	0	9	249	0	43	0	1.620984e-03	1	1	0	43	2		0	0	0	0	0	2	1	0.994143	9	246	0	43	2	0	0	0	0	0	0		-10.428710	1	1	0	0		1	0	1	1	1.757469	1	0.640000	1.650000	0.530271	0.080000	3.000000e-02	0.150000	0.080000	0.091800	0.080000	0	5.000000e-02	1.200000e-01
OR51B2	79345	broad.mit.edu	37	11	5344684	5344684	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:5344684G>A	ENST00000328813.2	-	1	898	c.844C>T	c.(844-846)Cct>Tct	p.P282S	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_033180.4	NP_149420.4	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B, member 2			35		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)			ATTAAAGGAGGAAAGAGGAAG	0.373000																								0							SO:0001583	missense			ENST00000328813.2	1	1	hg19	CCDS31377.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185866	0.78789	.	.	ENSG00000184881	ENST00000328813	T	0.35048	1.33	4.38	4.38	0.52667	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38272	U	0.001743	T	0.66636	0.2809	M	0.90252	3.1	0.45118	D	0.998133	D	0.89917	1.0	D	0.79784	0.993	T	0.75720	-0.3219	10	0.87932	D	0	.	15.8595	0.79012	0.0:0.0:1.0:0.0	.	282	Q9Y5P1	O51B2_HUMAN	S	282	ENSP00000327540:P282S	ENSP00000327540:P282S	P	-	1	0	OR51B2	5301260	1.000000	0.71417	0.897000	0.35233	0.988000	0.76386	5.480000	0.66820	2.306000	0.77630	0.638000	0.83543	CCT		TCGA-LB-A7SX-01A-11D-A33T-08	OR51B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142983.1	1	0	1	47	313	0	73		0	0	0	0	73	2		0	0	0	0	0	2	1	1.000000	47	308	0	73	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.757469	1	0.640000	1.650000	0.530271	0.300000	2.300000e-01	0.400000	0.310000	0.316791	0.300000	0	2.600000e-01	3.600000e-01
OR52N5	390075	broad.mit.edu	37	11	5799446	5799446	+	Missense_Mutation	SNP	C	C	T	rs144845456		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:5799446C>T	ENST00000317093.2	-	1	451	c.419G>A	c.(418-420)cGt>cAt	p.R140H	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5			33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)			GGTAGCATAACGCAAAGGGTA	0.502000																								0							SO:0001583	missense			ENST00000317093.2	1	1	hg19	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	C	8.537	0.872434	0.17322	0.0	1.22E-4	ENSG00000181009	ENST00000317093	T	0.00669	5.9	3.7	0.61	0.17580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.27294	U	0.020040	T	0.00608	0.0020	N	0.21508	0.67	0.23966	N	0.996326	B	0.16166	0.016	B	0.10450	0.005	T	0.47971	-0.9075	10	0.34782	T	0.22	.	5.9492	0.19235	0.0:0.6557:0.1568:0.1875	.	140	Q8NH56	O52N5_HUMAN	H	140	ENSP00000322866:R140H	ENSP00000322866:R140H	R	-	2	0	OR52N5	5756022	0.000000	0.05858	0.025000	0.17156	0.722000	0.41435	-0.692000	0.05127	0.025000	0.15241	0.494000	0.49563	CGT		TCGA-LB-A7SX-01A-11D-A33T-08	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	1	0	0	32	88	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	1.000000	31	88	0	38	2	0	0	0	0	0	0		-19.999990	1	1	115844	1	39	1	0	1	1	1.757469	1	0.640000	1.650000	0.530271	0.630000	4.500000e-01	0.820000	0.630000	0.643078	0.630000	0	5.400000e-01	7.300000e-01
ASRGL1	80150	broad.mit.edu	37	11	62159721	62159721	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:62159721G>A	ENST00000415229.2	+	7	1107	c.892G>A	c.(892-894)Gat>Aat	p.D298N	CTD-2531D15.5_ENST00000526045.1_RNA|ASRGL1_ENST00000301776.5_Missense_Mutation_p.D298N	NM_001083926.1	NP_001077395.1	Q7L266	ASGL1_HUMAN	asparaginase like 1			7				L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	CTTCGGAATTGATCCTGACGA	0.527000											OREG0021023	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000415229.2	1	1	hg19	CCDS8019.1	.	.	.	.	.	.	.	.	.	.	G	7.665	0.685751	0.14973	.	.	ENSG00000162174	ENST00000415229;ENST00000301776	D;D	0.94650	-3.48;-3.48	5.24	0.102	0.14522	.	0.502864	0.23382	N	0.048795	D	0.86781	0.6015	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.73733	-0.3890	10	0.31617	T	0.26	-12.1929	3.3361	0.07102	0.3163:0.0:0.3911:0.2926	.	298	Q7L266	ASGL1_HUMAN	N	298	ENSP00000400057:D298N;ENSP00000301776:D298N	ENSP00000301776:D298N	D	+	1	0	ASRGL1	61916297	0.065000	0.20965	0.001000	0.08648	0.066000	0.16364	0.483000	0.22292	0.210000	0.20664	0.655000	0.94253	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	ASRGL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394865.1	1	0	1	72	330	0	55	1	9.999915e-01	6	74	0	55	2		0	0	0	0	0	2	1	1.000000	70	329	0	54	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.219709	0	0.640000	1.650000	0.635332	0.540000	4.300000e-01	0.670000	0.550000	0.556645	0.540000	0	4.900000e-01	6.100000e-01
SIPA1	6494	broad.mit.edu	37	11	65413984	65413984	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:65413984C>T	ENST00000394224.3	+	8	1775	c.1479C>T	c.(1477-1479)ggC>ggT	p.G493G	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000394227.3_Silent_p.G493G|SIPA1_ENST00000534313.1_Silent_p.G493G|SIPA1_ENST00000527525.1_Silent_p.G493G	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1			10					TGCCTGCTGGCGGAGGCCCCT	0.716000																								0							SO:0001819	synonymous_variant			ENST00000394224.3	0	1	hg19	CCDS8108.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	1	0	1	10	73	0	10	1	9.637290e-01	5	40	0	10	2		0	0	0	0	0	2	1	0.996945	10	70	0	10	2	0	0	0	0	0	0		-17.535090	1	1	118984	2	22	1	0	0	0	2.218506	0	0.640000	1.650000	0.635332	0.380000	1.900000e-01	0.620000	0.370000	0.396507	0.380000	0	2.800000e-01	5.000000e-01
ANKRD42	338699	broad.mit.edu	37	11	82921451	82921451	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr11:82921451G>A	ENST00000393392.2	+	4	518	c.356G>A	c.(355-357)cGa>cAa	p.R119Q	ANKRD42_ENST00000260047.6_Missense_Mutation_p.R147Q|ANKRD42_ENST00000526731.1_Missense_Mutation_p.R147Q|ANKRD42_ENST00000533342.1_Missense_Mutation_p.R147Q|RP11-727A23.7_ENST00000531869.1_RNA|ANKRD42_ENST00000393389.3_Missense_Mutation_p.R147Q|ANKRD42_ENST00000531895.1_Missense_Mutation_p.R147Q|ANKRD42_ENST00000528722.1_Missense_Mutation_p.R34Q	NM_182603.2	NP_872409.2	Q8N9B4	ANR42_HUMAN	ankyrin repeat domain 42			18					ATAATGCTCCGAAGTGGAGTG	0.408000																								0							SO:0001583	missense			ENST00000393392.2	0	1	hg19	CCDS8265.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806293	0.70682	.	.	ENSG00000137494	ENST00000545672;ENST00000393389;ENST00000528722;ENST00000260047;ENST00000526731;ENST00000531895;ENST00000393392;ENST00000533342	T;D;T;T;T;T;T	0.81996	-0.06;-1.56;-0.06;-0.06;-0.06;-0.06;-0.06	5.89	4.98	0.66077	Ankyrin repeat-containing domain (4);	0.112713	0.39615	N	0.001304	T	0.71298	0.3323	N	0.13272	0.32	0.36543	D	0.871416	P;P;P;P;D	0.53745	0.838;0.88;0.927;0.906;0.962	B;B;B;B;B	0.43103	0.319;0.213;0.36;0.408;0.319	T	0.75274	-0.3375	9	.	.	.	-0.8612	14.0266	0.64590	0.0734:0.0:0.9266:0.0	.	147;147;412;238;119	E9PIL2;Q8N9B4-2;A1DRY3;A1XPJ0;Q8N9B4	.;.;.;.;ANR42_HUMAN	Q	466;147;34;147;147;147;119;147	ENSP00000377049:R147Q;ENSP00000432375:R34Q;ENSP00000260047:R147Q;ENSP00000433585:R147Q;ENSP00000434666:R147Q;ENSP00000377051:R119Q;ENSP00000435790:R147Q	.	R	+	2	0	ANKRD42	82599099	0.993000	0.37304	1.000000	0.80357	0.996000	0.88848	4.787000	0.62432	1.501000	0.48654	0.655000	0.94253	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	ANKRD42-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000392934.1	0	0	0	12	622	0	77	0	7.047108e-02	1	20	0	77	2		0	0	0	0	0	2	1	0.999089	12	618	0	76	2	0	0	0	0	0	0		-2.463851	0	1	121412	1	31	1	0	0	0	2.218506	0	0.640000	1.650000	0.635332	0.050000	2.000000e-02	0.100000	0.060000	0.062964	0.050000	0	3.000000e-02	8.000000e-02
STAC3	246329	broad.mit.edu	37	12	57642585	57642585	+	Splice_Site	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr12:57642585G>A	ENST00000332782.2	-	4	537	c.336C>T	c.(334-336)ctC>ctT	p.L112L	STAC3_ENST00000554578.1_Splice_Site_p.L73L|STAC3_ENST00000546246.2_Intron	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3			18					ACTTGTTGTTGACTTGGGAAA	0.463000																								0							SO:0001630	splice_region_variant			ENST00000332782.2	1	0	hg19	CCDS8936.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	1	0	0	443	456	0	179	1	9.609328e-01	4	4	0	179	2		0	0	0	0	0	2	1	1.000000	436	450	0	178	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	2	2	1.902695	1	0.640000	1.650000	0.640000	0.990000	9.900000e-01	1.000000	1.000000	1.000000	0.990000	1	9.900000e-01	1
SRGAP1	57522	broad.mit.edu	37	12	64536271	64536271	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr12:64536271G>A	ENST00000355086.3	+	22	3601	c.3077G>A	c.(3076-3078)cGt>cAt	p.R1026H	SRGAP1_ENST00000357825.3_Missense_Mutation_p.R1003H|SRGAP1_ENST00000543397.1_Missense_Mutation_p.R963H	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1			65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)		CAGATTCGACGTAGCACGAGC	0.562000																								0							SO:0001583	missense			ENST00000355086.3	1	1	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.412989	0.83449	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.34667	1.35;1.35;1.35	6.04	6.04	0.98038	.	0.000000	0.34002	U	0.004357	T	0.50667	0.1629	M	0.62723	1.935	0.80722	D	1	P;D	0.64830	0.757;0.994	B;P	0.51415	0.095;0.669	T	0.37220	-0.9715	9	.	.	.	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	1026;963	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	H	1026;1003;963	ENSP00000347198:R1026H;ENSP00000350480:R1003H;ENSP00000437948:R963H	.	R	+	2	0	SRGAP1	62822538	1.000000	0.71417	0.527000	0.27925	0.080000	0.17528	6.584000	0.74057	2.873000	0.98535	0.563000	0.77884	CGT		TCGA-LB-A7SX-01A-11D-A33T-08	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1	1	0	0	22	366	0	76	0	3.180678e-02	1	4	0	76	2		0	0	0	0	0	2	1	0.999999	22	359	0	76	2	0	0	0	0	0	0		-6.053502	1	1	121412	5	42	1	0	2	2	1.902695	1	0.640000	1.650000	0.640000	0.190000	1.100000e-01	1.000000	0.180000	0.365736	0.190000	0	1.400000e-01	1
WIF1	11197	broad.mit.edu	37	12	65471603	65471603	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr12:65471603C>G	ENST00000286574.4	-	3	694	c.320G>C	c.(319-321)cGc>cCc	p.R107P		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1			21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)		ATCCAGGGAGCGCAAGGACAG	0.498000			T	HMGA2	pleomorphic salivary gland adenoma								Esophageal Squamous(148;1595 1816 48559 49439 49664)		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	0							SO:0001583	missense			ENST00000286574.4	1	1	hg19	CCDS8971.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383858	0.82792	.	.	ENSG00000156076	ENST00000286574;ENST00000546001	T;T	0.45276	0.9;0.9	5.35	5.35	0.76521	WIF domain (4);	0.000000	0.85682	D	0.000000	T	0.50769	0.1635	L	0.36672	1.1	0.80722	D	1	D	0.67145	0.996	D	0.63283	0.913	T	0.37407	-0.9707	9	.	.	.	.	14.6498	0.68789	0.0:0.928:0.0:0.072	.	107	Q9Y5W5	WIF1_HUMAN	P	107;45	ENSP00000286574:R107P;ENSP00000442063:R45P	.	R	-	2	0	WIF1	63757870	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.581000	0.46077	2.689000	0.91719	0.650000	0.86243	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2	1	0	1	56	74	0	28	1	9.651849e-01	10	0	0	28	2		0	0	0	0	0	2	1	1.000000	56	73	0	28	2	0	0	0	0	0	0		-12.366650	1	1	0	0		1	0	2	2	1.902695	1	0.640000	1.650000	0.640000	0.990000	9.900000e-01	1.000000	1.000000	0.999876	0.990000	1	9.900000e-01	1
ATP12A	479	broad.mit.edu	37	13	25272886	25272886	+	Missense_Mutation	SNP	A	A	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:25272886A>G	ENST00000381946.3	+	12	1770	c.1603A>G	c.(1603-1605)Acc>Gcc	p.T535A	ATP12A_ENST00000218548.6_Missense_Mutation_p.T541A			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide			74		Lung SC(185;0.0225)|Breast(139;0.077)			GAAATGCAGCACCATCATGAT	0.602000													Pancreas(156;1582 1935 18898 22665 26498)											0							SO:0001583	missense			ENST00000381946.3	1	1	hg19	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040502	0.55003	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.79845	-1.31;-1.31	6.08	6.08	0.98989	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.87680	0.6238	L	0.60845	1.875	0.58432	D	0.999993	B;D	0.62365	0.415;0.991	B;D	0.76071	0.271;0.987	D	0.88592	0.3144	10	0.87932	D	0	.	14.5959	0.68407	1.0:0.0:0.0:0.0	.	541;535	P54707-2;P54707	.;AT12A_HUMAN	A	541;535	ENSP00000218548:T541A;ENSP00000371372:T535A	ENSP00000218548:T541A	T	+	1	0	ATP12A	24170886	1.000000	0.71417	1.000000	0.80357	0.261000	0.26267	5.917000	0.69989	2.333000	0.79357	0.533000	0.62120	ACC		TCGA-LB-A7SX-01A-11D-A33T-08	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	1	0	0	31	490	2	77		0	0	0	2	77	2		0	0	0	0	0	2	1	0.643472	31	487	2	77	29	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.734799	1	0.640000	1.650000	0.539877	0.140000	9.000000e-02	0.200000	0.150000	0.149355	0.140000	0	1.100000e-01	1.700000e-01
LRCH1	23143	broad.mit.edu	37	13	47266759	47266759	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:47266759G>A	ENST00000389798.3	+	8	1300	c.1103G>A	c.(1102-1104)cGc>cAc	p.R368H	LRCH1_ENST00000311191.6_Missense_Mutation_p.R368H|LRCH1_ENST00000389797.3_Missense_Mutation_p.R368H	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1			26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)		TCGTGCCATCGCCTTAGCCCC	0.408000																								0							SO:0001583	missense			ENST00000389798.3	1	1	hg19	CCDS31972.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.771346	0.31320	.	.	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.51574	0.7;0.75;0.76	5.93	0.948	0.19561	.	0.393039	0.29225	N	0.012771	T	0.32406	0.0828	L	0.41961	1.31	0.26342	N	0.977352	B;B;B;B	0.21905	0.037;0.002;0.062;0.006	B;B;B;B	0.17979	0.009;0.002;0.02;0.001	T	0.14727	-1.0462	10	0.33940	T	0.23	-16.3864	4.6171	0.12432	0.4322:0.0:0.4239:0.1439	.	368;368;368;368	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	H	368	ENSP00000308493:R368H;ENSP00000374448:R368H;ENSP00000374447:R368H	ENSP00000308493:R368H	R	+	2	0	LRCH1	46164760	0.001000	0.12720	0.894000	0.35097	0.754000	0.42855	-0.287000	0.08388	-0.140000	0.11394	-0.136000	0.14681	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	1	0	0	77	257	0	46	1	9.603416e-01	5	15	0	46	2		0	0	0	0	0	2	1	1.000000	77	254	0	46	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.329466	0	0.640000	1.650000	0.647887	0.730000	5.900000e-01	1.000000	0.740000	0.754951	0.730000	0	6.600000e-01	8.300000e-01
SUGT1	10910	broad.mit.edu	37	13	53227075	53227075	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:53227075G>A	ENST00000343788.6	+	1	102	c.20G>A	c.(19-21)gGa>gAa	p.G7E	SUGT1_ENST00000310528.8_Missense_Mutation_p.G7E|SUGT1_ENST00000483074.1_3'UTR|SUGT1_ENST00000535397.1_5'UTR	NM_001130912.1	NP_001124384.1	Q9Y2Z0	SUGT1_HUMAN	SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae)			8		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)			gctgcagcagGAACTGCAACA	0.542000											OREG0022432	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000343788.6	1	1	hg19	CCDS45050.1	.	.	.	.	.	.	.	.	.	.	G	8.714	0.912663	0.17907	.	.	ENSG00000165416	ENST00000343788;ENST00000310528	T;T	0.22134	1.97;1.98	4.02	2.14	0.27477	.	0.421812	0.21072	N	0.080645	T	0.10252	0.0251	N	0.08118	0	0.27126	N	0.962025	P;B	0.37781	0.608;0.447	B;B	0.34824	0.131;0.19	T	0.14476	-1.0471	10	0.87932	D	0	-3.5695	10.3823	0.44119	0.0:0.3812:0.6188:0.0	.	7;7	Q9Y2Z0;Q9Y2Z0-2	SUGT1_HUMAN;.	E	7	ENSP00000367208:G7E;ENSP00000308067:G7E	ENSP00000308067:G7E	G	+	2	0	SUGT1	52125076	0.135000	0.22499	0.864000	0.33941	0.730000	0.41778	-0.029000	0.12329	0.873000	0.35799	0.467000	0.42956	GGA		TCGA-LB-A7SX-01A-11D-A33T-08	SUGT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045104.2	1	0	1	61	191	0	36	1	1	46	60	0	36	2		0	0	0	0	0	2	1	1.000000	61	188	0	35	2	0	0	0	0	0	0		-20.000000	1	1	121412	1	24	1	1	2	3	2.329466	0	0.640000	1.650000	0.647887	0.770000	6.100000e-01	1.000000	0.770000	0.790366	0.770000	0	6.900000e-01	8.800000e-01
PCDH9	5101	broad.mit.edu	37	13	67799612	67799612	+	Missense_Mutation	SNP	A	A	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:67799612A>C	ENST00000377865.2	-	1	3095	c.2961T>G	c.(2959-2961)agT>agG	p.S987R	PCDH9_ENST00000456367.1_Missense_Mutation_p.S987R|PCDH9_ENST00000544246.1_Missense_Mutation_p.S987R|PCDH9_ENST00000328454.5_Missense_Mutation_p.S987R|PCDH9_ENST00000377861.3_Missense_Mutation_p.S987R			Q9HC56	PCDH9_HUMAN	protocadherin 9			103		Hepatocellular(98;0.0906)|Breast(118;0.107)			AGTGATCTGAACTAGTGGAAG	0.493000																								0							SO:0001583	missense			ENST00000377865.2	1	1	hg19	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	13.51	2.258886	0.39896	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454;ENST00000377861	T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28	5.63	5.63	0.86233	Protocadherin (1);	0.000000	0.85682	D	0.000000	T	0.57417	0.2052	L	0.61218	1.895	0.58432	D	0.999993	D;D;D;D	0.71674	0.998;0.996;0.998;0.998	D;D;D;D	0.74023	0.982;0.955;0.969;0.982	T	0.57797	-0.7749	10	0.49607	T	0.09	.	15.8249	0.78690	1.0:0.0:0.0:0.0	.	987;987;987;987	B7ZM79;Q5VT82;Q9HC56-2;Q9HC56	.;.;.;PCDH9_HUMAN	R	987	ENSP00000442186:S987R;ENSP00000367096:S987R;ENSP00000401699:S987R;ENSP00000332060:S987R;ENSP00000367092:S987R	ENSP00000332060:S987R	S	-	3	2	PCDH9	66697613	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.163000	0.50763	2.142000	0.66516	0.533000	0.62120	AGT		TCGA-LB-A7SX-01A-11D-A33T-08	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	1	0	1	133	307	0	58	0	0	0	1	0	58	2		0	0	0	0	0	2	1	1.000000	131	305	0	58	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.329466	0	0.640000	1.650000	0.647887	0.960000	8.200000e-01	1.000000	1.000000	0.955251	0.960000	1	8.900000e-01	1
KLHL1	57626	broad.mit.edu	37	13	70681816	70681816	+	Nonsense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:70681816G>A	ENST00000377844.4	-	1	775	c.16C>T	c.(16-18)Cga>Tga	p.R6*	KLHL1_ENST00000545028.1_5'Flank|ATXN8OS_ENST00000424524.1_RNA|ATXN8OS_ENST00000414504.2_RNA	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1			84		Breast(118;0.000162)			AAGTCTTTTCGCCCAGAGCCT	0.647000																								0							SO:0001587	stop_gained			ENST00000377844.4	0	1	hg19	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	G	44	11.251559	0.99537	.	.	ENSG00000150361	ENST00000377844	.	.	.	5.18	-3.56	0.04626	.	0.000000	0.36703	N	0.002455	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8523	0.52417	0.0:0.0873:0.1916:0.7211	.	.	.	.	X	6	.	ENSP00000367075:R6X	R	-	1	2	KLHL1	69579817	0.596000	0.26866	0.966000	0.40874	0.997000	0.91878	0.042000	0.13949	-0.483000	0.06772	0.655000	0.94253	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	1	0	0	57	121	0	26		0	0	0	0	26	2		0	0	0	0	0	2	1	1.000000	57	120	0	26	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.329466	0	0.640000	1.650000	0.647887	0.990000	8.100000e-01	1.000000	1.000000	0.969645	0.990000	1	9.100000e-01	1
DACH1	1602	broad.mit.edu	37	13	72049296	72049296	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr13:72049296G>A	ENST00000359684.2	-	11	2221	c.2222C>T	c.(2221-2223)aCa>aTa	p.T741I	DACH1_ENST00000305425.4_Missense_Mutation_p.T689I|DACH1_ENST00000354591.4_Missense_Mutation_p.T487I|DACH1_ENST00000313174.7_Missense_Mutation_p.T541I			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1			41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)			TTCAGCATCTGTTCTGCCGCC	0.423000																								0							SO:0001583	missense			ENST00000359684.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	21.6	4.172072	0.78452	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	T;T;T;T	0.34072	1.41;1.42;1.42;1.38	5.62	5.62	0.85841	.	0.051334	0.85682	D	0.000000	T	0.57975	0.2090	M	0.62723	1.935	0.42123	D	0.991431	D;D;D	0.69078	0.977;0.997;0.978	P;D;P	0.66602	0.787;0.945;0.815	T	0.53968	-0.8363	10	0.40728	T	0.16	-6.4987	19.6611	0.95871	0.0:0.0:1.0:0.0	.	485;539;687	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	I	689;541;487;741;741	ENSP00000304994:T689I;ENSP00000318506:T541I;ENSP00000346604:T487I;ENSP00000352712:T741I	ENSP00000304994:T689I	T	-	2	0	DACH1	70947297	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.229000	0.95273	2.643000	0.89663	0.655000	0.94253	ACA		TCGA-LB-A7SX-01A-11D-A33T-08	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	1	0	1	80	241	0	41	0	6.346749e-02	0	2	0	41	2		0	0	0	0	0	2	1	1.000000	80	241	0	40	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.329466	0	0.640000	1.650000	0.647887	0.790000	6.400000e-01	1.000000	0.790000	0.810863	0.790000	0	7.200000e-01	9.000000e-01
TRAF3	7187	broad.mit.edu	37	14	103372120	103372120	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:103372120G>A	ENST00000560371.1	+	11	1923	c.1706G>A	c.(1705-1707)tGa>tAa	p.*569*	TRAF3_ENST00000347662.4_Silent_p.*544*|TRAF3_ENST00000539721.1_Silent_p.*486*|TRAF3_ENST00000351691.5_Silent_p.*544*|TRAF3_ENST00000392745.2_Silent_p.*569*	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3			30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)			CCCGATCCCTGATAAGTAGCT	0.453000																								0							SO:0001819	synonymous_variant			ENST00000560371.1	0	1	hg19	CCDS9975.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	1	0	1	44	98	0	32	1	8.605275e-01	4	6	0	32	2		0	0	0	0	0	2	1	1.000000	43	96	0	32	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.688785	1	0.640000	1.650000	0.498886	0.680000	5.200000e-01	0.860000	0.690000	0.696625	0.680000	0	6.000000e-01	7.800000e-01
OR4Q3	441669	broad.mit.edu	37	14	20215850	20215850	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:20215850G>A	ENST00000331723.1	+	1	264	c.264G>A	c.(262-264)caG>caA	p.Q88Q		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3			47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)		ATTTCCTACAGCAGGGCAAGA	0.453000																								0							SO:0001819	synonymous_variant			ENST00000331723.1	1	1	hg19	CCDS32020.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2	1	0	1	162	558	0	132		0	0	0	0	132	2		0	0	0	0	0	2	1	1.000000	147	509	0	134	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.329939	0	0.640000	1.650000	0.646782	0.710000	6.100000e-01	1.000000	0.720000	0.731727	0.710000	0	6.600000e-01	7.800000e-01
NGDN	25983	broad.mit.edu	37	14	23945486	23945486	+	Nonsense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:23945486C>T	ENST00000408901.3	+	8	611	c.583C>T	c.(583-585)Cga>Tga	p.R195*	NGDN_ENST00000397154.3_Nonsense_Mutation_p.R195*|NGDN_ENST00000556580.1_5'UTR	NM_001042635.1|NM_015514.1	NP_001036100.1|NP_056329.1	Q8NEJ9	NGDN_HUMAN	neuroguidin, EIF4E binding protein			12	all_cancers(95;0.000251)				GCGTCTAGAACGAGCCAAGAG	0.473000																								0							SO:0001587	stop_gained			ENST00000408901.3	0	1	hg19	CCDS41926.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.410545|5.410545	0.96072|0.96072	.|.	.|.	ENSG00000129460|ENSG00000129460	ENST00000408901;ENST00000397154|ENST00000556483	.|.	.|.	.|.	5.89|5.89	4.98|4.98	0.66077|0.66077	.|.	0.211551|.	0.40728|.	N|.	0.001026|.	.|T	.|0.70762	.|0.3261	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.70103	.|-0.4964	.|4	0.02654|.	T|.	1|.	-19.2174|-19.2174	14.907|14.907	0.70727|0.70727	0.149:0.851:0.0:0.0|0.149:0.851:0.0:0.0	.|.	.|.	.|.	.|.	X|M	195|142	.|.	ENSP00000380340:R195X|.	R|T	+|+	1|2	2|0	NGDN|NGDN	23015326|23015326	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	3.550000|3.550000	0.53691|0.53691	1.440000|1.440000	0.47531|0.47531	0.563000|0.563000	0.77884|0.77884	CGA|ACG		TCGA-LB-A7SX-01A-11D-A33T-08	NGDN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413782.3	1	0	0	16	206	0	36	0	9.977730e-01	0	132	0	36	2		0	0	0	0	0	2	1	0.999941	16	205	0	36	2	0	0	0	0	0	0		-3.222086	1	1	0	0		1	0	1	1	1.663670	1	0.640000	1.650000	0.470588	0.150000	8.000000e-02	0.230000	0.150000	0.160452	0.150000	0	1.100000e-01	2.000000e-01
LRRC16B	90668	broad.mit.edu	37	14	24530760	24530760	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:24530760C>T	ENST00000342740.5	+	27	2513	c.2359C>T	c.(2359-2361)Cgg>Tgg	p.R787W	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	p.R787W(3)		52					TGTGGCCATGCGGGTGGCCGA	0.612000																								3	Substitution - Missense(3)						SO:0001583	missense			ENST00000342740.5	0	1	hg19	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955757	0.53293	.	.	ENSG00000186648	ENST00000342740	T	0.15718	2.4	5.27	3.36	0.38483	.	0.174329	0.40144	N	0.001165	T	0.21962	0.0529	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	P	0.62014	0.897	T	0.03166	-1.1065	10	0.87932	D	0	-14.9968	10.8426	0.46724	0.3396:0.6604:0.0:0.0	.	787	Q8ND23	LR16B_HUMAN	W	787	ENSP00000340467:R787W	ENSP00000340467:R787W	R	+	1	2	LRRC16B	23600600	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.748000	0.26305	1.430000	0.47334	-0.182000	0.12963	CGG		TCGA-LB-A7SX-01A-11D-A33T-08	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	0	0	0	6	170	1	35		0	0	0	1	35	2		0	0	0	0	0	2	0	0.021931	6	170	1	35	16	0	0	0	0	0	0		-2.835470	1	1	0	0		1	0	1	1	1.639950	1	0.640000	1.650000	0.475524	0.070000	2.000000e-02	0.150000	0.070000	0.083829	0.070000	0	4.000000e-02	1.100000e-01
NID2	22795	broad.mit.edu	37	14	52507535	52507535	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:52507535G>A	ENST00000216286.5	-	8	1859	c.1860C>T	c.(1858-1860)ttC>ttT	p.F620F	NID2_ENST00000541773.1_Silent_p.F567F	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)			87	Breast(41;0.0639)|all_epithelial(31;0.123)				CTCCCGGGTAGAATGTAACTT	0.463000																								0							SO:0001819	synonymous_variant			ENST00000216286.5	1	1	hg19	CCDS9706.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1	1	0	1	140	266	0	71	0	5.621700e-01	0	5	0	71	2		0	0	0	0	0	2	1	1.000000	139	260	0	71	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.685420	1	0.640000	1.650000	0.489796	0.750000	6.500000e-01	0.860000	0.760000	0.760070	0.750000	0	7.000000e-01	8.100000e-01
ZFYVE26	23503	broad.mit.edu	37	14	68275942	68275942	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr14:68275942C>G	ENST00000347230.4	-	4	476	c.338G>C	c.(337-339)gGt>gCt	p.G113A	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.G113A	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26			94					TGGAATGTCACCTTGGAGGTC	0.458000																								0							SO:0001583	missense			ENST00000347230.4	1	1	hg19	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	C	9.232	1.036094	0.19590	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26373	1.89;1.74	6.06	1.78	0.24846	.	0.933364	0.09213	N	0.832992	T	0.17831	0.0428	L	0.44542	1.39	0.09310	N	1	B;B;B	0.27068	0.065;0.167;0.022	B;B;B	0.24269	0.036;0.052;0.006	T	0.34279	-0.9835	10	0.09084	T	0.74	-5.0E-4	6.2815	0.21009	0.0:0.5186:0.0:0.4814	.	113;113;113	Q68DK2-4;G3V2D8;Q68DK2	.;.;ZFY26_HUMAN	A	113	ENSP00000251119:G113A;ENSP00000450603:G113A	ENSP00000251119:G113A	G	-	2	0	ZFYVE26	67345695	0.064000	0.20934	0.854000	0.33618	0.991000	0.79684	1.535000	0.36061	0.457000	0.26962	0.655000	0.94253	GGT		TCGA-LB-A7SX-01A-11D-A33T-08	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	0	0	0	13	406	0	70	0	1.182020e-03	0	2	0	70	2		0	0	0	0	0	2	1	0.999535	13	404	0	70	2	0	0	0	0	0	0		-3.493247	1	1	0	0		1	0	1	1	1.685420	1	0.640000	1.650000	0.489796	0.060000	3.000000e-02	0.110000	0.070000	0.073141	0.060000	0	4.000000e-02	9.000000e-02
SECISBP2L	9728	broad.mit.edu	37	15	49304939	49304939	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr15:49304939G>A	ENST00000559471.1	-	12	1900	c.1637C>T	c.(1636-1638)aCa>aTa	p.T546I	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.T501I	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like			46					ATTAAAGGATGTCAAACAGGG	0.348000																								0							SO:0001583	missense			ENST00000559471.1	1	1	hg19	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.384582	0.42308	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.72394	-0.65	5.76	4.84	0.62591	.	0.433340	0.26248	N	0.025473	T	0.60405	0.2266	L	0.39147	1.195	0.30747	N	0.745561	B;B	0.20988	0.012;0.05	B;B	0.18561	0.006;0.022	T	0.62115	-0.6922	10	0.54805	T	0.06	.	9.5017	0.39022	0.0802:0.2533:0.6665:0.0	.	546;501	Q93073;Q93073-2	SBP2L_HUMAN;.	I	501;546	ENSP00000261847:T501I	ENSP00000261847:T501I	T	-	2	0	SECISBP2L	47092231	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.936000	0.48971	1.433000	0.47394	0.650000	0.86243	ACA		TCGA-LB-A7SX-01A-11D-A33T-08	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	0	0	0	19	514	0	86	0	7.373527e-02	1	11	0	86	2		0	0	0	0	0	2	1	0.999990	19	507	0	86	2	0	0	0	0	0	0		-3.873308	1	1	121410	1	35	1	0	1	1	1.982783	1	0.640000	1.650000	0.582560	0.090000	5.000000e-02	0.150000	0.100000	0.100609	0.090000	0	7.000000e-02	1.200000e-01
MEGF11	84465	broad.mit.edu	37	15	66210374	66210374	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr15:66210374G>A	ENST00000409699.2	-	16	2188	c.2016C>T	c.(2014-2016)aaC>aaT	p.N672N	MEGF11_ENST00000395614.1_De_novo_Start_OutOfFrame|MEGF11_ENST00000395625.2_Silent_p.N597N|MEGF11_ENST00000360698.4_Silent_p.N672N|MEGF11_ENST00000288745.3_Silent_p.N597N|MEGF11_ENST00000422354.1_Silent_p.N672N			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11			19					TGCAGGTCCCGTTGTTGGCAC	0.612000																								0							SO:0001819	synonymous_variant			ENST00000409699.2	1	0	hg19	CCDS10213.2																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	1	0	1	48	202	0	32	0	0	0	1	0	32	2		0	0	0	0	0	2	1	1.000000	48	202	0	32	2	0	0	0	0	0	0		-20.000000	1	1	121408	2	31	1	0	1	1	1.982783	1	0.640000	1.650000	0.582560	0.510000	3.900000e-01	0.650000	0.520000	0.522531	0.510000	0	4.500000e-01	5.900000e-01
LOXL1	4016	broad.mit.edu	37	15	74239478	74239478	+	Missense_Mutation	SNP	G	G	A	rs141057976		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr15:74239478G>A	ENST00000261921.7	+	4	1746	c.1420G>A	c.(1420-1422)Gag>Aag	p.E474K		NM_005576.2	NP_005567.2	Q08397	LOXL1_HUMAN	lysyl oxidase-like 1			10					GAAGGTGGCCGAGGGCCACAA	0.577000																								0							SO:0001583	missense			ENST00000261921.7	1	1	hg19	CCDS10253.1	.	.	.	.	.	.	.	.	.	.	G	34	5.372594	0.95923	0.0	1.16E-4	ENSG00000129038	ENST00000261921;ENST00000395162	T	0.40225	1.04	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.71668	0.3367	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.79940	-0.1591	10	0.87932	D	0	.	16.4684	0.84092	0.0:0.0:1.0:0.0	.	474	Q08397	LOXL1_HUMAN	K	474;336	ENSP00000261921:E474K	ENSP00000261921:E474K	E	+	1	0	LOXL1	72026531	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	9.569000	0.98170	2.222000	0.72286	0.462000	0.41574	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	LOXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268995.2	1	0	1	53	225	0	39	1	9.999346e-01	3	61	0	39	2		0	0	0	0	0	2	1	1.000000	53	224	0	38	2	0	0	0	0	0	0		-20.000000	1	1	121412	19	43	1	0	1	1	1.966388	0	0.640000	1.650000	0.585635	0.510000	3.900000e-01	0.640000	0.510000	0.522280	0.510000	0	4.500000e-01	5.800000e-01
ADAMTSL3	57188	broad.mit.edu	37	15	84652038	84652038	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr15:84652038C>T	ENST00000286744.5	+	21	3882	c.3658C>T	c.(3658-3660)Ccc>Tcc	p.P1220S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P1220S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3			130			BRCA - Breast invasive adenocarcinoma(143;0.211)		CCTTATTACCCCCAGTGAGGC	0.348000																								0							SO:0001583	missense			ENST00000286744.5	1	1	hg19	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.748472	0.00669	.	.	ENSG00000156218	ENST00000286744	T	0.11821	2.74	5.13	2.9	0.33743	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.674572	0.12270	N	0.483872	T	0.05960	0.0155	N	0.11651	0.15	0.09310	N	1	B;B	0.17268	0.004;0.021	B;B	0.16289	0.007;0.015	T	0.39078	-0.9631	10	0.06236	T	0.91	.	7.8817	0.29627	0.244:0.4028:0.3532:0.0	.	1220;1220	P82987-2;P82987	.;ATL3_HUMAN	S	1220	ENSP00000286744:P1220S	ENSP00000286744:P1220S	P	+	1	0	ADAMTSL3	82443042	0.003000	0.15002	0.046000	0.18839	0.277000	0.26821	1.060000	0.30530	1.245000	0.43885	0.557000	0.71058	CCC		TCGA-LB-A7SX-01A-11D-A33T-08	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	0	0	0	21	779	1	109	0	0	0	1	1	109	2		0	0	0	0	0	2	0	0.436028	21	778	1	109	23	0	0	0	0	0	0		-2.023224	0	1	0	0		1	0	1	1	1.960586	1	0.640000	1.650000	0.582560	0.060000	3.000000e-02	0.110000	0.070000	0.073850	0.060000	0	5.000000e-02	9.000000e-02
XYLT1	64131	broad.mit.edu	37	16	17353277	17353277	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:17353277C>G	ENST00000261381.6	-	3	565	c.481G>C	c.(481-483)Gag>Cag	p.E161Q		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I			67					TCGACATTCTCAAAGTCTTTG	0.502000																								0							SO:0001583	missense			ENST00000261381.6	1	1	hg19	CCDS10569.1	.	.	.	.	.	.	.	.	.	.	C	32	5.171543	0.94807	.	.	ENSG00000103489	ENST00000261381	T	0.07688	3.17	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.24586	0.0596	L	0.59436	1.845	0.80722	D	1	D	0.62365	0.991	P	0.60236	0.871	T	0.00045	-1.2218	10	0.66056	D	0.02	-38.7384	18.8353	0.92159	0.0:1.0:0.0:0.0	.	161	Q86Y38	XYLT1_HUMAN	Q	161	ENSP00000261381:E161Q	ENSP00000261381:E161Q	E	-	1	0	XYLT1	17260778	1.000000	0.71417	0.997000	0.53966	0.978000	0.69477	7.328000	0.79160	2.688000	0.91661	0.655000	0.94253	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	1	0	1	151	477	0	70	1	8.213282e-01	6	6	0	70	2		0	0	0	0	0	2	1	1.000000	150	475	0	69	2	0	0	0	0	0	0		-5.363877	1	1	0	0		1	1	2	3	2.316346	0	0.640000	1.650000	0.645669	0.760000	6.500000e-01	1.000000	0.760000	0.774273	0.760000	0	7.000000e-01	8.300000e-01
ITPRIPL2	162073	broad.mit.edu	37	16	19126379	19126379	+	Missense_Mutation	SNP	T	T	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:19126379T>A	ENST00000381440.3	+	1	1126	c.596T>A	c.(595-597)cTg>cAg	p.L199Q	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2			9					GAGCCAGCGCTGGCCCCGGCC	0.701000											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001583	missense			ENST00000381440.3	0	1	hg19	CCDS32395.1	.	.	.	.	.	.	.	.	.	.	T	8.250	0.808707	0.16467	.	.	ENSG00000205730	ENST00000381440	T	0.19250	2.16	4.91	3.81	0.43845	.	1.686950	0.05100	U	0.486938	T	0.25158	0.0611	N	0.19112	0.55	0.29438	N	0.859323	D	0.71674	0.998	P	0.61800	0.894	T	0.15292	-1.0442	10	0.11182	T	0.66	-8.1361	6.7379	0.23419	0.0:0.0837:0.1545:0.7618	.	199	Q3MIP1	IPIL2_HUMAN	Q	199	ENSP00000370849:L199Q	ENSP00000370849:L199Q	L	+	2	0	ITPRIPL2	19033880	0.524000	0.26282	0.167000	0.22817	0.046000	0.14306	1.512000	0.35812	1.829000	0.53265	0.533000	0.62120	CTG		TCGA-LB-A7SX-01A-11D-A33T-08	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	0	0	0	9	231	0	27	0	1.581884e-01	0	16	0	27	2		0	0	0	0	0	2	1	0.994029	9	227	0	27	2	0	0	0	0	0	0		-14.936160	1	1	0	0		1	1	2	3	2.316346	0	0.640000	1.650000	0.645669	0.120000	5.000000e-02	1.000000	0.120000	0.163901	0.120000	0	8.000000e-02	1.800000e-01
SH2B1	25970	broad.mit.edu	37	16	28877903	28877903	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:28877903G>A	ENST00000322610.8	+	4	927	c.488G>A	c.(487-489)cGa>cAa	p.R163Q	SH2B1_ENST00000359285.5_Missense_Mutation_p.R163Q|SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000395532.4_Missense_Mutation_p.R163Q|SH2B1_ENST00000337120.5_Missense_Mutation_p.R163Q|SH2B1_ENST00000545570.1_Intron|SH2B1_ENST00000538342.1_Intron			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1			25					CGCTCTGTCCGAGGCTCAGTC	0.652000																								0							SO:0001583	missense			ENST00000322610.8	1	1	hg19	CCDS53996.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663858	0.67700	.	.	ENSG00000178188	ENST00000322610;ENST00000359285;ENST00000395532;ENST00000337120	T;T;T;T	0.51325	0.71;0.72;0.73;0.73	3.95	3.95	0.45737	.	0.218237	0.26692	N	0.022987	T	0.40979	0.1139	N	0.14661	0.345	0.41978	D	0.990788	D;D;D	0.63880	0.991;0.974;0.993	P;P;P	0.51079	0.658;0.565;0.546	T	0.44711	-0.9310	10	0.46703	T	0.11	-31.1346	14.9215	0.70841	0.0:0.0:1.0:0.0	.	163;163;163	Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;SH2B1_HUMAN	Q	163	ENSP00000321221:R163Q;ENSP00000352232:R163Q;ENSP00000378903:R163Q;ENSP00000337163:R163Q	ENSP00000321221:R163Q	R	+	2	0	SH2B1	28785404	0.996000	0.38824	0.972000	0.41901	0.952000	0.60782	2.673000	0.46858	2.055000	0.61198	0.455000	0.32223	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	SH2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000432666.1	1	0	1	174	535	0	69	1	1	44	89	0	69	2		0	0	0	0	0	2	1	1.000000	155	466	0	60	2	0	0	0	0	0	0		-5.761218	1	1	0	0		1	1	2	3	2.310551	0	0.640000	1.650000	0.644550	0.770000	6.700000e-01	1.000000	0.780000	0.784783	0.770000	0	7.200000e-01	8.400000e-01
RAB11FIP3	9727	broad.mit.edu	37	16	476687	476687	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:476687C>T	ENST00000262305.4	+	1	1069	c.681C>T	c.(679-681)ttC>ttT	p.F227F	RAB11FIP3_ENST00000457159.1_Silent_p.F227F	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)			12		Hepatocellular(16;0.0218)			TCGAGGACTTCATCCAGTTTG	0.706000													Melanoma(160;2366 2595 4474 8099)											0							SO:0001819	synonymous_variant			ENST00000262305.4	0	1	hg19	CCDS32351.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	0	0	0	5	209	0	26	0	2.062573e-01	0	30	0	26	2		0	0	0	0	0	2	1	0.936730	5	207	0	26	2	0	0	0	0	0	0		-6.411320	1	0	0	0		1	1	2	3	2.325029	0	0.640000	1.650000	0.645669	0.080000	2.000000e-02	1.000000	0.080000	0.122601	0.080000	0	4.000000e-02	1.300000e-01
FAM86A	196483	broad.mit.edu	37	16	5141882	5141882	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:5141882G>A	ENST00000427587.4	-	4	323	c.255C>T	c.(253-255)caC>caT	p.H85H	FAM86A_ENST00000458008.4_Intron|FAM86A_ENST00000587133.1_Intron	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A			12					AAGGCTCTGTGTGGACAGCCT	0.547000																								0							SO:0001819	synonymous_variant			ENST00000427587.4	1	1	hg19	CCDS10529.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	1	0	1	88	241	0	50	1	9.996957e-01	10	26	0	50	2		0	0	0	0	0	2	1	1.000000	86	231	0	53	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.325029	0	0.640000	1.650000	0.645669	0.840000	7.000000e-01	1.000000	0.850000	0.856910	0.840000	0	7.700000e-01	9.400000e-01
PIGQ	9091	broad.mit.edu	37	16	633027	633027	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:633027C>A	ENST00000026218.5	+	10	1764	c.1676C>A	c.(1675-1677)gCa>gAa	p.A559E	PIGQ_ENST00000321878.5_Missense_Mutation_p.Q580K|PIGQ_ENST00000409527.2_Missense_Mutation_p.Q580K	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q			13		Hepatocellular(780;0.00335)			AGGGGACAAGCAGGACTGAGG	0.667000																								0							SO:0001583	missense			ENST00000026218.5	1	1	hg19	CCDS10411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.93|12.93	2.085822|2.085822	0.36758|0.36758	.|.	.|.	ENSG00000007541|ENSG00000007541	ENST00000026218|ENST00000409527;ENST00000321878;ENST00000540241	T|T;T	0.22945|0.44482	1.93|0.92;0.92	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	1.882170|.	0.02546|.	N|.	0.095120|.	T|T	0.28995|0.28995	0.0720|0.0720	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D;P|B	0.89917|0.23249	1.0;0.506|0.082	D;B|B	0.76575|0.24269	0.988;0.044|0.052	T|T	0.12656|0.12656	-1.0539|-1.0539	10|9	0.72032|0.62326	D|D	0.01|0.03	-6.9865|-6.9865	18.0399|18.0399	0.89316|0.89316	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	129;559|580	B3KRR7;Q9BRB3|Q9BRB3-2	.;PIGQ_HUMAN|.	E|K	559|580;580;138	ENSP00000026218:A559E|ENSP00000386760:Q580K;ENSP00000326674:Q580K	ENSP00000026218:A559E|ENSP00000326674:Q580K	A|Q	+|+	2|1	0|0	PIGQ|PIGQ	573028|573028	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.878000|0.878000	0.50629|0.50629	1.786000|1.786000	0.38694|0.38694	2.618000|2.618000	0.88619|0.88619	0.462000|0.462000	0.41574|0.41574	GCA|CAG		TCGA-LB-A7SX-01A-11D-A33T-08	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	1	0	0	27	551	0	87	1	9.848813e-01	5	132	0	87	2		0	0	0	0	0	2	1	1.000000	28	543	0	85	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.325029	0	0.640000	1.650000	0.645669	0.140000	9.000000e-02	1.000000	0.150000	0.185290	0.140000	0	1.100000e-01	1.900000e-01
CNTNAP4	85445	broad.mit.edu	37	16	76572111	76572111	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:76572111C>T	ENST00000476707.1	+	18	3242	c.3103C>T	c.(3103-3105)Cat>Tat	p.H1035Y	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.H959Y|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.H983Y|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.H1031Y			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4			64					TGCTTCATTTCATGGTGATAT	0.368000																								0							SO:0001583	missense			ENST00000476707.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	C	7.133	0.580282	0.13686	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.35	5.35	0.76521	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.42821	D	0.000643	T	0.25195	0.0612	.	.	.	0.37798	D	0.927591	B;B;B	0.14805	0.001;0.001;0.011	B;B;B	0.15052	0.002;0.002;0.012	T	0.12630	-1.0540	9	0.09338	T	0.73	.	12.9629	0.58468	0.0:0.9168:0.0:0.0832	.	959;1035;1032	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	Y	1031;983;959;1035	ENSP00000306893:H1031Y;ENSP00000439733:H983Y;ENSP00000418741:H959Y;ENSP00000417628:H1035Y	ENSP00000306893:H1031Y	H	+	1	0	CNTNAP4	75129612	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.793000	0.47845	2.769000	0.95229	0.655000	0.94253	CAT		TCGA-LB-A7SX-01A-11D-A33T-08	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	1	0	0	86	237	0	47		0	0	0	0	47	2		0	0	0	0	0	2	1	1.000000	86	234	0	46	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.297942	0	0.640000	1.650000	0.642289	0.830000	6.800000e-01	1.000000	0.840000	0.841318	0.830000	0	7.500000e-01	9.200000e-01
IL17C	27189	broad.mit.edu	37	16	88706381	88706381	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr16:88706381C>T	ENST00000244241.4	+	3	544	c.495C>T	c.(493-495)cgC>cgT	p.R165R		NM_013278.3	NP_037410.1	Q9P0M4	IL17C_HUMAN	interleukin 17C			2					CCTGCTCCCGCGACGGCTCGG	0.701000																								0							SO:0001819	synonymous_variant			ENST00000244241.4	1	1	hg19	CCDS42217.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	IL17C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422575.1	0	0	0	12	384	0	48	0	3.386817e-01	0	37	0	48	2		0	0	0	0	0	2	1	0.999078	12	379	0	48	2	0	0	0	0	0	0		-3.550582	1	1	120482	2	31	1	1	2	3	2.297942	0	0.640000	1.650000	0.642289	0.090000	4.000000e-02	0.170000	0.100000	0.111369	0.090000	0	6.000000e-02	1.300000e-01
PIP4K2B	8396	broad.mit.edu	37	17	36940505	36940505	+	Silent	SNP	C	C	T	rs143351168	by1000genomes	TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr17:36940505C>T	ENST00000269554.3	-	3	825	c.345G>A	c.(343-345)caG>caA	p.Q115Q	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta			19					CCTGGTAATCCTGATCATCAA	0.502000																								0							SO:0001819	synonymous_variant			ENST00000269554.3	0	1	hg19	CCDS11329.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	0	0	0	5	245	0	25	0	3.207214e-01	1	48	0	25	2		0	0	0	0	0	2	1	0.937505	5	244	0	25	2	0	0	0	0	0	0		-3.320245	1	1	121412	2	28	1	1	2	3	2.292176	0	0.640000	1.650000	0.642289	0.060000	1.000000e-02	0.150000	0.060000	0.083774	0.060000	0	3.000000e-02	1.100000e-01
MED1	5469	broad.mit.edu	37	17	37571341	37571341	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr17:37571341G>A	ENST00000394287.3	-	16	1642	c.1437C>T	c.(1435-1437)ctC>ctT	p.L479L	MED1_ENST00000300651.6_Silent_p.L479L			O95243	MBD4_HUMAN	mediator complex subunit 1	p.L479L(1)		59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)		GCCCTTTGTAGAGTTTACAGC	0.408000										HNSCC(31;0.082)			Pancreas(21;279 768 2492 4877 24026)											1	Substitution - coding silent(1)						SO:0001819	synonymous_variant			ENST00000394287.3	1	1	hg19																																																																																					TCGA-LB-A7SX-01A-11D-A33T-08	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	0	0	0	40	1232	0	174	1	1.807887e-01	4	20	0	174	2		0	0	0	0	0	2	1	1.000000	40	1218	0	173	2	0	0	0	0	0	0		-2.564702	1	1	0	0		1	1	2	3	2.292176	0	0.640000	1.650000	0.642289	0.090000	6.000000e-02	0.140000	0.100000	0.109961	0.090000	0	7.000000e-02	1.200000e-01
AOC2	314	broad.mit.edu	37	17	40997985	40997985	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr17:40997985G>A	ENST00000253799.3	+	1	1369	c.1342G>A	c.(1342-1344)Ggt>Agt	p.G448S	AOC2_ENST00000452774.2_Missense_Mutation_p.G448S	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)			30		Breast(137;0.000143)			TTTCTATGGTGGTTTGGCCAG	0.517000																								0							SO:0001583	missense			ENST00000253799.3	1	1	hg19	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.767027	0.49574	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.03580	3.88;3.88	5.46	4.5	0.54988	Copper amine oxidase, C-terminal (3);	0.056784	0.64402	D	0.000001	T	0.15262	0.0368	M	0.82630	2.6	0.80722	D	1	D;D	0.71674	0.995;0.998	D;D	0.81914	0.995;0.987	T	0.34179	-0.9839	10	0.05351	T	0.99	-21.9121	14.1903	0.65635	0.0723:0.0:0.9277:0.0	.	448;448	O75106;O75106-2	AOC2_HUMAN;.	S	448	ENSP00000253799:G448S;ENSP00000406134:G448S	ENSP00000253799:G448S	G	+	1	0	AOC2	38251511	1.000000	0.71417	0.968000	0.41197	0.044000	0.14063	9.556000	0.98127	1.308000	0.44962	-0.229000	0.12294	GGT		TCGA-LB-A7SX-01A-11D-A33T-08	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	1	0	1	147	328	0	55		0	0	0	0	55	2		0	0	0	0	0	2	1	1.000000	145	323	0	55	2	0	0	0	0	0	0		-11.081750	1	1	0	0		1	1	2	3	2.271010	0	0.640000	1.650000	0.641148	0.960000	8.300000e-01	1.000000	1.000000	0.956660	0.960000	1	9.000000e-01	1
TP53	7157	broad.mit.edu	37	17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532000		111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	GRCh37	CM951226	TP53	M		SO:0001587	stop_gained	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ENST00000269305.4	0	1	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	0	86	91	0	39	1	9.999766e-01	9	13	0	39	2	1	1	411	553	2	1355	6	1	1.000000	84	91	0	38	2	0	0	0	0	0	0		-20.000000	1	1	121412	1	30	1	0	1	1	1.630120	1	0.640000	1.650000	0.473068	0.960000	8.400000e-01	1.000000	1.000000	0.955904	0.960000	1	9.000000e-01	1
ALOXE3	59344	broad.mit.edu	37	17	8017832	8017832	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr17:8017832G>A	ENST00000448843.2	-	6	990	c.650C>T	c.(649-651)aCg>aTg	p.T217M	ALOXE3_ENST00000318227.3_Missense_Mutation_p.T349M|ALOXE3_ENST00000380149.1_Missense_Mutation_p.T373M	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3			31					CAGCGAGATCGTCTTGGTGGC	0.547000																								0							SO:0001583	missense			ENST00000448843.2	1	1	hg19	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.606478	0.46527	2.27E-4	0.0	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	D;D;D	0.89681	-2.55;-2.55;-2.55	5.22	4.24	0.50183	Lipoxygenase, C-terminal (2);	0.286741	0.39985	N	0.001219	D	0.85932	0.5812	L	0.40543	1.245	0.41066	D	0.985412	P;D;D	0.56746	0.782;0.977;0.977	B;P;P	0.47915	0.189;0.561;0.561	D	0.86119	0.1567	10	0.51188	T	0.08	-16.8023	11.1503	0.48455	0.0899:0.0:0.91:0.0	.	349;217;217	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	M	373;349;217	ENSP00000369494:T373M;ENSP00000314879:T349M;ENSP00000400581:T217M	ENSP00000314879:T349M	T	-	2	0	ALOXE3	7958557	0.997000	0.39634	0.954000	0.39281	0.709000	0.40893	2.843000	0.48238	2.578000	0.87016	0.655000	0.94253	ACG		TCGA-LB-A7SX-01A-11D-A33T-08	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1	1	0	0	17	300	0	64	0	0	0	1	0	64	2		0	0	0	0	0	2	1	0.999963	17	294	0	62	2	0	0	0	0	0	0		-18.834910	1	1	121412	14	46	1	0	1	1	1.630120	1	0.640000	1.650000	0.473068	0.110000	6.000000e-02	0.170000	0.110000	0.120044	0.110000	0	8.000000e-02	1.500000e-01
ZNF521	25925	broad.mit.edu	37	18	22804704	22804704	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr18:22804704G>T	ENST00000361524.3	-	4	3326	c.3178C>A	c.(3178-3180)Cac>Aac	p.H1060N	ZNF521_ENST00000538137.2_Missense_Mutation_p.H1060N|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Missense_Mutation_p.H840N	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521			149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)				TTTTGGACGTGCTGGCCCCGC	0.502000			T	PAX5	ALL										Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	0							SO:0001583	missense			ENST00000361524.3	1	1	hg19	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	G	9.539	1.112986	0.20795	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.07800	3.18;3.16	5.98	5.98	0.97165	.	0.156557	0.56097	D	0.000023	T	0.05227	0.0139	N	0.08118	0	0.36885	D	0.889578	B	0.02656	0.0	B	0.04013	0.001	T	0.47573	-0.9107	10	0.20519	T	0.43	-31.416	15.2044	0.73165	0.0:0.0:0.8593:0.1407	.	1060	Q96K83	ZN521_HUMAN	N	1060;1094;1060	ENSP00000354794:H1060N;ENSP00000382352:H1060N	ENSP00000354794:H1060N	H	-	1	0	ZNF521	21058702	1.000000	0.71417	0.996000	0.52242	0.976000	0.68499	7.500000	0.81588	2.835000	0.97688	0.650000	0.86243	CAC		TCGA-LB-A7SX-01A-11D-A33T-08	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	1	0	0	14	298	0	53	0	6.801184e-02	0	9	0	53	2		0	0	0	0	0	2	1	0.999744	14	293	0	52	2	0	0	0	0	0	0		-15.234970	1	1	0	0		1	0	2	2	2.158518	1	0.640000	1.650000	0.640000	0.140000	7.000000e-02	1.000000	0.140000	0.272767	0.140000	0	1.000000e-01	2.400000e-01
CLUL1	27098	broad.mit.edu	37	18	641458	641458	+	Nonsense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr18:641458G>T	ENST00000400606.2	+	7	1271	c.1126G>T	c.(1126-1128)Gag>Tag	p.E376*	CLUL1_ENST00000540035.1_Nonsense_Mutation_p.E428*|C18orf56_ENST00000585033.1_Intron|CLUL1_ENST00000338387.7_Nonsense_Mutation_p.E376*|CLUL1_ENST00000579494.1_Nonsense_Mutation_p.E376*|CLUL1_ENST00000581619.1_Nonsense_Mutation_p.E401*	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)			24					CTATCTGGTGGAGAAGATGAG	0.493000																								0							SO:0001587	stop_gained			ENST00000400606.2	0	1	hg19	CCDS42405.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.116170	0.77323	.	.	ENSG00000079101	ENST00000400606;ENST00000540035;ENST00000338387	.	.	.	5.59	2.63	0.31362	.	0.469100	0.24352	N	0.039263	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	-1.5628	3.4341	0.07440	0.1012:0.307:0.4344:0.1574	.	.	.	.	X	376;428;376	.	ENSP00000341128:E376X	E	+	1	0	CLUL1	631458	0.995000	0.38212	0.832000	0.32986	0.062000	0.15995	0.684000	0.25364	0.676000	0.31285	0.563000	0.77884	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1	0	0	0	9	506	0	69	0	0	0	1	0	69	2		0	0	0	0	0	2	1	0.993981	10	498	0	68	2	0	0	0	0	0	0		-2.971753	1	1	120872	1	32	1	0	2	2	2.158518	1	0.640000	1.650000	0.640000	0.050000	2.000000e-02	1.000000	0.060000	0.197043	0.050000	0	3.000000e-02	1.100000e-01
CD97	976	broad.mit.edu	37	19	14515219	14515219	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:14515219G>A	ENST00000242786.5	+	13	1554	c.1474G>A	c.(1474-1476)Gag>Aag	p.E492K	CD97_ENST00000357355.3_Missense_Mutation_p.E443K|CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000358600.3_Missense_Mutation_p.E399K	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule			30					GCCACGGCAGGAGCTGCTCTG	0.642000																								0							SO:0001583	missense			ENST00000242786.5	1	1	hg19	CCDS32929.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118085	0.56505	.	.	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.70399	-0.48;-0.38;-0.0	5.22	4.19	0.49359	GPS domain (2);	.	.	.	.	T	0.68668	0.3026	L	0.35487	1.065	0.19775	N	0.999955	D;D;B	0.69078	0.987;0.997;0.176	P;P;B	0.61592	0.814;0.891;0.122	T	0.57004	-0.7885	9	0.02654	T	1	.	11.2011	0.48741	0.0884:0.0:0.9116:0.0	.	399;443;492	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	K	492;443;399;442	ENSP00000242786:E492K;ENSP00000349918:E443K;ENSP00000351413:E399K	ENSP00000242786:E492K	E	+	1	0	CD97	14376219	0.983000	0.35010	0.187000	0.23214	0.280000	0.26924	1.237000	0.32695	1.435000	0.47434	0.655000	0.94253	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	1	0	1	209	416	0	113	1	1	46	20	0	113	2		0	0	0	0	0	2	1	1.000000	207	410	0	111	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.574139	1	0.640000	1.650000	0.470588	0.700000	6.200000e-01	0.780000	0.710000	0.710448	0.700000	0	6.600000e-01	7.500000e-01
SLC7A10	56301	broad.mit.edu	37	19	33699875	33699875	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:33699875G>A	ENST00000253188.4	-	11	1640	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	CTD-2540B15.13_ENST00000609744.1_RNA	NM_019849.2	NP_062823.1	Q9NS82	AAA1_HUMAN	solute carrier family 7 (neutral amino acid transporter light chain, asc system), member 10			18	Esophageal squamous(110;0.137)				CTTCGGGGGCGTCCTGGGGGT	0.602000																								0							SO:0001819	synonymous_variant			ENST00000253188.4	1	1	hg19	CCDS12431.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	SLC7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450846.2	1	0	1	69	169	0	23		0	0	0	0	23	2		0	0	0	0	0	2	1	1.000000	65	157	0	21	2	0	0	0	0	0	0		-20.000000	1	1	121404	1	31	1	0	0	0	2.256350	0	0.640000	1.650000	0.640000	0.900000	7.200000e-01	1.000000	1.000000	0.901115	0.900000	1	8.100000e-01	1
FFAR2	2867	broad.mit.edu	37	19	35941517	35941517	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:35941517C>T	ENST00000599180.2	+	2	981	c.901C>T	c.(901-903)Cgc>Tgc	p.R301C	FFAR2_ENST00000246549.2_Missense_Mutation_p.R301C|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2			22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		CCTGTTGGGACGCAGAGGCAA	0.567000													GBM(40;139 809 9833 23358 48736)											0							SO:0001583	missense			ENST00000599180.2	1	1	hg19	CCDS12461.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.037193	0.35893	.	.	ENSG00000126262	ENST00000246549	T	0.69040	-0.37	4.85	-0.293	0.12835	.	0.444083	0.19863	N	0.104381	T	0.52041	0.1710	L	0.51422	1.61	0.09310	N	0.999996	B	0.10296	0.003	B	0.04013	0.001	T	0.41805	-0.9488	10	0.48119	T	0.1	-3.8436	3.8897	0.09113	0.1696:0.4716:0.0:0.3588	.	301	O15552	FFAR2_HUMAN	C	301	ENSP00000246549:R301C	ENSP00000246549:R301C	R	+	1	0	FFAR2	40633357	0.000000	0.05858	0.002000	0.10522	0.282000	0.26991	0.054000	0.14205	-0.091000	0.12440	0.563000	0.77884	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	1	0	1	219	469	0	79	1	5.097691e-01	2	3	0	79	2		0	0	0	0	0	2	1	1.000000	218	465	0	79	2	0	0	0	0	0	0		-20.000000	1	1	121412	12	43	1	0	0	0	2.256350	0	0.640000	1.650000	0.640000	0.980000	8.800000e-01	1.000000	1.000000	0.975398	0.980000	1	9.300000e-01	1
PRX	57716	broad.mit.edu	37	19	40900573	40900573	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:40900573C>T	ENST00000324001.7	-	7	3956	c.3686G>A	c.(3685-3687)cGa>cAa	p.R1229Q	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin			47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		CTGTGCCTCTCGGCTTAGCCC	0.677000																								0							SO:0001583	missense			ENST00000324001.7	1	1	hg19	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.616264	0.28801	.	.	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01043	5.41	4.99	1.46	0.22682	.	0.789709	0.10820	N	0.630577	T	0.01124	0.0037	L	0.36672	1.1	0.09310	N	0.999995	P	0.51791	0.948	B	0.39503	0.301	T	0.54450	-0.8292	10	0.34782	T	0.22	-0.1423	6.6701	0.23064	0.0:0.5058:0.0:0.4942	.	1229	Q9BXM0	PRAX_HUMAN	Q	1229;1164	ENSP00000326018:R1229Q	ENSP00000326018:R1229Q	R	-	2	0	PRX	45592413	0.011000	0.17503	0.566000	0.28421	0.631000	0.37964	0.073000	0.14640	0.529000	0.28599	0.561000	0.74099	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	0	0	0	15	486	0	63	0	4.771301e-02	0	11	0	63	2		0	0	0	0	0	2	1	0.999849	14	475	0	59	2	0	0	0	0	0	0		-3.393076	1	1	121394	1	35	1	1	2	3	2.336264	0	0.640000	1.650000	0.646782	0.090000	4.000000e-02	1.000000	0.100000	0.143410	0.090000	0	7.000000e-02	1.300000e-01
PSG7	5676	broad.mit.edu	37	19	43430840	43430840	+	RNA	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:43430840G>C	ENST00000406070.2	-	0	834				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)					Prostate(69;0.00682)			TTAAGTTATTGATGGTGATGT	0.463000																								0											ENST00000406070.2	1	1	hg19																																																																																					TCGA-LB-A7SX-01A-11D-A33T-08	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	0	0	0	52	1438	0	196		0	0	0	0	196	2		0	0	0	0	0	2	1	1.000000	52	1422	0	193	2	0	0	0	0	0	0		-3.798021	1	1	0	0		1	2	2	4	2.359799	0	0.640000	1.650000	0.657534	0.110000	7.000000e-02	1.000000	0.110000	0.173489	0.110000	0	9.000000e-02	1.400000e-01
CADM4	199731	broad.mit.edu	37	19	44129317	44129317	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:44129317G>A	ENST00000222374.2	-	7	889	c.841C>T	c.(841-843)Ctg>Ttg	p.L281L	CADM4_ENST00000593506.1_5'UTR	NM_145296.1	NP_660339.1	Q8NFZ8	CADM4_HUMAN	cell adhesion molecule 4			12		Prostate(69;0.0199)			GCGGATACCAGACCCGGCAGC	0.622000																								0							SO:0001819	synonymous_variant			ENST00000222374.2	1	1	hg19	CCDS12627.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	CADM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463352.1	0	0	0	12	290	0	39	1	9.552211e-01	12	118	0	39	2		0	0	0	0	0	2	1	0.999131	11	289	0	39	2	0	0	0	0	0	0		-13.319810	1	1	0	0		1	1	2	3	2.341294	0	0.640000	1.650000	0.646782	0.130000	6.000000e-02	1.000000	0.130000	0.176532	0.130000	0	9.000000e-02	1.800000e-01
FLT3LG	2323	broad.mit.edu	37	19	49983561	49983561	+	Nonsense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:49983561C>G	ENST00000594009.1	+	6	567	c.488C>G	c.(487-489)tCa>tGa	p.S163*	FLT3LG_ENST00000600429.1_Nonsense_Mutation_p.S163*|FLT3LG_ENST00000204637.2_Nonsense_Mutation_p.S81*|FLT3LG_ENST00000595510.1_Nonsense_Mutation_p.S81*|FLT3LG_ENST00000597551.1_Nonsense_Mutation_p.S163*|CTD-3148I10.9_ENST00000599536.1_Intron|FLT3LG_ENST00000596435.1_Nonsense_Mutation_p.S145*|CTD-3148I10.15_ENST00000595815.1_RNA	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand			10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)			CCAGACTCCTCAACCCTGCCA	0.667000																								0							SO:0001587	stop_gained			ENST00000594009.1	0	1	hg19	CCDS12767.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446390	0.84101	.	.	ENSG00000090554	ENST00000204637	.	.	.	3.68	3.68	0.42216	.	0.299782	0.30901	N	0.008656	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-13.2738	11.0942	0.48134	0.0:1.0:0.0:0.0	.	.	.	.	X	163	.	ENSP00000204637:S163X	S	+	2	0	FLT3LG	54675373	0.062000	0.20869	0.847000	0.33407	0.441000	0.31987	3.315000	0.51951	2.042000	0.60477	0.561000	0.74099	TCA		TCGA-LB-A7SX-01A-11D-A33T-08	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1	0	0	0	6	190	0	21	0	2.110806e-01	0	24	0	21	2		0	0	0	0	0	2	1	0.965132	6	189	0	21	2	0	0	0	0	0	0		-3.643210	1	1	0	0		1	1	2	3	2.341294	0	0.640000	1.650000	0.646782	0.100000	3.000000e-02	1.000000	0.100000	0.153980	0.100000	0	6.000000e-02	1.600000e-01
NLRP5	126206	broad.mit.edu	37	19	56538857	56538857	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:56538857G>A	ENST00000390649.3	+	7	1258	c.1258G>A	c.(1258-1260)Gag>Aag	p.E420K		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5			25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)			GCTCAAGTCAGAGGTCGTGTC	0.547000																								0							SO:0001583	missense			ENST00000390649.3	0	1	hg19	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	8.718	0.913767	0.17907	.	.	ENSG00000171487	ENST00000390649	T	0.78003	-1.14	3.35	-6.7	0.01766	.	2.074330	0.02664	N	0.107849	T	0.55847	0.1946	N	0.04508	-0.205	0.09310	N	1	B	0.24092	0.097	B	0.33568	0.166	T	0.54596	-0.8270	10	0.48119	T	0.1	.	2.0967	0.03669	0.2778:0.3996:0.1358:0.1869	.	420	P59047	NALP5_HUMAN	K	420	ENSP00000375063:E420K	ENSP00000375063:E420K	E	+	1	0	NLRP5	61230669	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.837000	0.01689	-3.908000	0.00092	-0.967000	0.02615	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	0	0	0	6	145	0	24		0	0	0	0	24	2		0	0	0	0	0	2	1	0.965222	6	144	0	24	2	0	0	0	0	0	0		-8.978947	1	1	0	0		1	1	2	3	2.331647	0	0.640000	1.650000	0.646782	0.130000	5.000000e-02	1.000000	0.120000	0.185340	0.130000	0	8.000000e-02	2.100000e-01
ZFP28	140612	broad.mit.edu	37	19	57051065	57051065	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:57051065G>A	ENST00000301318.3	+	2	351	c.280G>A	c.(280-282)Gaa>Aaa	p.E94K	AC005498.3_ENST00000593218.1_lincRNA|ZFP28_ENST00000591844.1_Missense_Mutation_p.E94K|ZFP28_ENST00000594386.1_3'UTR	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein			35		Colorectal(82;0.000256)|Ovarian(87;0.243)			GACAGGAATTGAACCTAAAGC	0.468000													Ovarian(124;554 1662 19430 21141 52494)											0							SO:0001583	missense			ENST00000301318.3	0	1	hg19	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.927546	0.00493	.	.	ENSG00000196867	ENST00000301318	T	0.04862	3.54	3.15	-2.26	0.06867	.	1.302900	0.05857	N	0.622289	T	0.02494	0.0076	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42378	-0.9455	10	0.06236	T	0.91	.	3.6521	0.08208	0.4893:0.2061:0.3046:0.0	.	94;94	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	K	94	ENSP00000301318:E94K	ENSP00000301318:E94K	E	+	1	0	ZFP28	61742877	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-0.068000	0.11561	-0.378000	0.07918	0.462000	0.41574	GAA		TCGA-LB-A7SX-01A-11D-A33T-08	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	0	0	0	10	267	0	38		0	0	0	0	38	2		0	0	0	0	0	2	1	0.996614	10	260	0	38	2	0	0	0	0	0	0		-11.263180	1	1	0	0		1	1	2	3	2.331647	0	0.640000	1.650000	0.646782	0.110000	5.000000e-02	1.000000	0.120000	0.166402	0.110000	0	8.000000e-02	1.700000e-01
ZNF606	80095	broad.mit.edu	37	19	58490523	58490523	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:58490523C>T	ENST00000341164.4	-	7	2145	c.1525G>A	c.(1525-1527)Gag>Aag	p.E509K	ZNF606_ENST00000536132.1_Missense_Mutation_p.E419K	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606			26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)			AAAGGTTTCTCTCCTGTATGA	0.393000																								0							SO:0001583	missense			ENST00000341164.4	1	1	hg19	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.343802	0.61073	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.24350	1.86;1.86	4.41	4.41	0.53225	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46758	D	0.000271	T	0.37265	0.0997	L	0.37630	1.12	0.53688	D	0.999973	D	0.60575	0.988	D	0.63793	0.918	T	0.13282	-1.0515	10	0.87932	D	0	.	12.7365	0.57228	0.0:0.833:0.167:0.0	.	509	Q8WXB4	ZN606_HUMAN	K	509;419	ENSP00000343617:E509K;ENSP00000445624:E419K	ENSP00000343617:E509K	E	-	1	0	ZNF606	63182335	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.550000	0.60733	2.446000	0.82766	0.561000	0.74099	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	0	0	0	8	278	0	32	0	2.585587e-02	1	7	0	32	2		0	0	0	0	0	2	1	0.989337	8	276	0	32	2	0	0	0	0	0	0		-3.437894	1	1	0	0		1	1	2	3	2.331647	0	0.640000	1.650000	0.646782	0.090000	3.000000e-02	1.000000	0.090000	0.141638	0.090000	0	6.000000e-02	1.400000e-01
MUC16	94025	broad.mit.edu	37	19	9064306	9064306	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr19:9064306G>A	ENST00000397910.4	-	3	23343	c.23140C>T	c.(23140-23142)Ccc>Tcc	p.P7714S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated			590					ACAGGAAGGGGAGAGGGGGGG	0.532000																								0							SO:0001583	missense			ENST00000397910.4	1	1	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.343	-0.134144	0.06711	.	.	ENSG00000181143	ENST00000397910	T	0.20598	2.06	2.11	-3.35	0.04928	.	.	.	.	.	T	0.09113	0.0225	N	0.14661	0.345	.	.	.	P	0.35456	0.502	B	0.27887	0.084	T	0.18903	-1.0322	8	0.87932	D	0	.	6.4736	0.22022	0.6167:0.0:0.3833:0.0	.	7714	B5ME49	.	S	7714	ENSP00000381008:P7714S	ENSP00000381008:P7714S	P	-	1	0	MUC16	8925306	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.693000	0.01917	-0.722000	0.04922	-1.051000	0.02340	CCC		TCGA-LB-A7SX-01A-11D-A33T-08	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	1	0	1	49	280	0	70		0	0	0	0	70	2		0	0	0	0	0	2	1	1.000000	47	274	0	69	2	0	0	0	0	0	0		-19.999750	1	1	0	0		1	0	1	1	1.574451	1	0.640000	1.650000	0.470588	0.310000	2.300000e-01	0.400000	0.320000	0.319899	0.310000	0	2.700000e-01	3.600000e-01
DBT	1629	broad.mit.edu	37	1	100701025	100701025	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:100701025C>G	ENST00000370132.4	-	3	231	c.218G>C	c.(217-219)gGa>gCa	p.G73A	DBT_ENST00000370131.3_Missense_Mutation_p.G73A	NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2			19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)			AATCCCTTCTCCAATGTCTGA	0.289000																								0							SO:0001583	missense			ENST00000370132.4	1	1	hg19	CCDS767.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843596	0.91197	.	.	ENSG00000137992	ENST00000370132;ENST00000370131	T;T	0.73681	-0.77;-0.77	5.62	5.62	0.85841	Single hybrid motif (1);Biotin/lipoyl attachment (2);	0.000000	0.85682	D	0.000000	D	0.88709	0.6510	M	0.91818	3.245	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.90103	0.4186	10	0.87932	D	0	-22.3909	20.0205	0.97499	0.0:1.0:0.0:0.0	.	73	P11182	ODB2_HUMAN	A	73	ENSP00000359151:G73A;ENSP00000359150:G73A	ENSP00000359150:G73A	G	-	2	0	DBT	100473613	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.982000	0.76173	2.801000	0.96364	0.650000	0.86243	GGA		TCGA-LB-A7SX-01A-11D-A33T-08	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030101.2	1	0	1	73	328	0	70	1	7.527027e-01	7	7	0	70	2		0	0	0	0	0	2	1	1.000000	72	327	0	70	2	0	0	0	0	0	0		-3.015423	1	1	0	0		1	0	2	2	2.229829	0	0.640000	1.650000	0.640000	0.570000	4.500000e-01	1.000000	0.570000	0.607553	0.570000	0	5.100000e-01	6.600000e-01
ADORA3	140	broad.mit.edu	37	1	112033386	112033386	+	Splice_Site	SNP	T	T	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:112033386T>C	ENST00000369716.4	-	2	484		c.e2-2		RNU6-792P_ENST00000363490.1_RNA|ADORA3_ENST00000369717.4_Splice_Site	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor			12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	ATTCTGAATCTGTTTAAGGGA	0.448000																								0							SO:0001630	splice_region_variant			ENST00000369716.4	0	1	hg19	CCDS838.1	.	.	.	.	.	.	.	.	.	.	T	11.30	1.598438	0.28445	.	.	ENSG00000121933	ENST00000369717;ENST00000369716	.	.	.	3.49	3.49	0.39957	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.718	0.34423	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADORA3	111834909	1.000000	0.71417	0.980000	0.43619	0.179000	0.23085	2.961000	0.49168	1.847000	0.53656	0.459000	0.35465	.		TCGA-LB-A7SX-01A-11D-A33T-08	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	0	0	0	6	256	0	39		0	0	0	0	39	2		0	0	0	0	0	2	1	0.964211	6	253	0	39	2	0	0	0	0	0	0		-7.665525	1	1	121412	4	34	1	0	0	0	2.193149	0	0.640000	1.650000	0.630542	0.070000	2.000000e-02	0.140000	0.070000	0.080570	0.070000	0	4.000000e-02	1.100000e-01
OTUD7B	56957	broad.mit.edu	37	1	149916371	149916371	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:149916371G>A	ENST00000369135.4	-	12	2211	c.1917C>T	c.(1915-1917)ttC>ttT	p.F639F		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B			39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)		GTTCTGCCAGGAATCTCTCCT	0.517000																								0							SO:0001819	synonymous_variant			ENST00000369135.4	1	1	hg19	CCDS41389.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	1	0	1	157	642	0	114	1	9.627152e-01	6	18	0	114	2		0	0	0	0	0	2	1	1.000000	156	633	0	112	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.179166	0	0.640000	1.650000	0.628099	0.580000	5.000000e-01	0.680000	0.590000	0.596251	0.580000	0	5.400000e-01	6.400000e-01
CLK2	1196	broad.mit.edu	37	1	155233761	155233761	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	G	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:155233761C>G	ENST00000368361.4	-	12	1612	c.1297G>C	c.(1297-1299)Gag>Cag	p.E433Q	CLK2_ENST00000361168.5_Missense_Mutation_p.E432Q|SCAMP3_ENST00000302631.3_5'Flank|CLK2_ENST00000536801.1_Missense_Mutation_p.E433Q|CLK2_ENST00000497188.1_5'UTR|CLK2_ENST00000355560.4_Missense_Mutation_p.E431Q|SCAMP3_ENST00000355379.3_5'Flank			P49760	CLK2_HUMAN	CDC-like kinase 2			22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		TTGCAGTTCTCACGAACATAG	0.542000								Other conserved DNA damage response genes																0							SO:0001583	missense			ENST00000368361.4	1	1	hg19		.	.	.	.	.	.	.	.	.	.	.	18.88	3.717852	0.68844	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000424156;ENST00000536801	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	4.2	4.2	0.49525	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.100176	0.64402	D	0.000002	T	0.09905	0.0243	N	0.21324	0.655	0.80722	D	1	B;B	0.31174	0.114;0.311	B;B	0.35770	0.093;0.21	T	0.11421	-1.0588	10	0.54805	T	0.06	.	15.6036	0.76646	0.0:1.0:0.0:0.0	.	433;432	P49760;P49760-3	CLK2_HUMAN;.	Q	432;433;431;205;433	ENSP00000354856:E432Q;ENSP00000357345:E433Q;ENSP00000347759:E431Q;ENSP00000441023:E433Q	ENSP00000347759:E431Q	E	-	1	0	CLK2	153500385	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.607000	0.82883	2.334000	0.79466	0.561000	0.74099	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	1	0	1	141	591	0	98	1	1	34	148	0	98	2		0	0	0	0	0	2	1	1.000000	137	584	0	98	2	0	0	0	0	0	0		-3.089265	1	1	0	0		1	0	0	0	2.179166	0	0.640000	1.650000	0.628099	0.570000	4.900000e-01	0.670000	0.580000	0.584745	0.570000	0	5.300000e-01	6.300000e-01
MNDA	4332	broad.mit.edu	37	1	158812091	158812091	+	Missense_Mutation	SNP	G	G	T	rs140390501		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:158812091G>T	ENST00000368141.4	+	2	409	c.148G>T	c.(148-150)Gat>Tat	p.D50Y	MNDA_ENST00000491210.1_3'UTR	NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen			65	all_hematologic(112;0.0378)				TAAGATTACAGATTTGATGGA	0.338000																								0							SO:0001583	missense			ENST00000368141.4	1	1	hg19	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.856515	0.32791	.	.	ENSG00000163563	ENST00000368141	T	0.55052	0.54	3.51	-0.707	0.11245	Pyrin (2);	.	.	.	.	T	0.50599	0.1625	M	0.69358	2.11	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.35822	-0.9773	9	0.87932	D	0	-0.51	6.1692	0.20408	0.5109:0.0:0.4891:0.0	.	50	P41218	MNDA_HUMAN	Y	50	ENSP00000357123:D50Y	ENSP00000357123:D50Y	D	+	1	0	MNDA	157078715	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.547000	0.23299	-0.025000	0.13918	-0.259000	0.10710	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	0	0	0	15	405	0	57	0	1.523758e-03	0	2	0	57	2		0	0	0	0	0	2	1	0.999863	14	400	0	57	2	0	0	0	0	0	0		-3.917358	1	1	0	0		1	0	0	0	2.179166	0	0.640000	1.650000	0.628099	0.100000	5.000000e-02	0.170000	0.110000	0.114525	0.100000	0	8.000000e-02	1.400000e-01
GNB1	2782	broad.mit.edu	37	1	1722012	1722012	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:1722012C>T	ENST00000378609.4	-	9	852	c.521G>A	c.(520-522)gGc>gAc	p.G174D		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1			12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)			CGTCTGCTGGCCGGTCTCGAT	0.542000																								0							SO:0001583	missense			ENST00000378609.4	0	1	hg19	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.6|26.6	4.753994|4.753994	0.89843|0.89843	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000424622|ENST00000378609;ENST00000455156;ENST00000378606	.|T	.|0.01613	.|4.73	5.11|5.11	5.11|5.11	0.69529|0.69529	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.11024|0.11024	0.0269|0.0269	M|M	0.82056|0.82056	2.57|2.57	0.80722|0.80722	D|D	1|1	.|D	.|0.61697	.|0.99	.|D	.|0.66351	.|0.943	T|T	0.00353|0.00353	-1.1795|-1.1795	5|10	.|0.87932	.|D	.|0	-24.5913|-24.5913	17.5387|17.5387	0.87841|0.87841	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174	.|P62873	.|GBB1_HUMAN	T|D	32|174;74;174	.|ENSP00000367872:G174D	.|ENSP00000367869:G174D	A|G	-|-	1|2	0|0	GNB1|GNB1	1711872|1711872	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.586000|7.586000	0.82596|0.82596	2.374000|2.374000	0.81015|0.81015	0.655000|0.655000	0.94253|0.94253	GCC|GGC		TCGA-LB-A7SX-01A-11D-A33T-08	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	1	0	0	9	188	0	24	1	9.999979e-01	21	676	0	24	2		0	0	0	0	0	2	1	0.994415	9	187	0	24	2	0	0	0	0	0	0		-11.422060	1	1	0	0		1	0	0	0	2.151466	0	0.640000	1.650000	0.623116	0.130000	6.000000e-02	0.240000	0.130000	0.149542	0.130000	0	9.000000e-02	1.900000e-01
CROCC	9696	broad.mit.edu	37	1	17271988	17271988	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:17271988C>T	ENST00000375541.5	+	15	2092	c.2023C>T	c.(2023-2025)Cgc>Tgc	p.R675C	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin			62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)			GGAAGGGAAGCGCTCAGTCCT	0.642000																								0							SO:0001583	missense			ENST00000375541.5	0	1	hg19	CCDS30616.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.885565	0.51908	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.10382	2.88	5.01	4.02	0.46733	.	.	.	.	.	T	0.25717	0.0626	L	0.57536	1.79	0.48511	D	0.999665	D;D	0.89917	1.0;1.0	D;P	0.64410	0.925;0.878	T	0.00206	-1.1920	9	0.46703	T	0.11	.	13.6849	0.62511	0.1552:0.8448:0.0:0.0	.	538;675	A1L0S8;Q5TZA2	.;CROCC_HUMAN	C	675;556	ENSP00000364691:R675C	ENSP00000364691:R675C	R	+	1	0	CROCC	17144575	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.659000	0.37387	2.712000	0.92718	0.561000	0.74099	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	0	0	0	11	164	0	23	0	1.964007e-01	0	12	0	23	2		0	0	0	0	0	2	0	0.278376	9	143	1	39	13	0	0	0	0	0	0		-5.283819	1	1	121314	11	29	1	0	1	1	2.183241	0	0.640000	1.650000	0.625624	0.190000	1.000000e-01	0.320000	0.190000	0.203032	0.190000	0	1.400000e-01	2.600000e-01
XPR1	9213	broad.mit.edu	37	1	180793903	180793903	+	Nonsense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:180793903G>T	ENST00000367590.4	+	8	976	c.778G>T	c.(778-780)Gaa>Taa	p.E260*	XPR1_ENST00000367589.3_Nonsense_Mutation_p.E260*	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1			35					ATTTAAACTTGAAACAGATAG	0.328000																								0							SO:0001587	stop_gained			ENST00000367590.4	0	1	hg19	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	G	35	5.511924	0.96402	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	.	.	.	5.3	4.33	0.51752	.	0.675652	0.14013	N	0.347315	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-5.9541	4.9217	0.13872	0.0811:0.1489:0.6162:0.1538	.	.	.	.	X	260	.	ENSP00000356561:E260X	E	+	1	0	XPR1	179060526	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.435000	0.44811	2.489000	0.83994	0.650000	0.86243	GAA		TCGA-LB-A7SX-01A-11D-A33T-08	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	1	0	1	94	293	0	42	0	9.261044e-01	1	15	0	42	2		0	0	0	0	0	2	1	1.000000	94	286	0	42	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.179166	0	0.640000	1.650000	0.628099	0.730000	6.000000e-01	0.860000	0.740000	0.737623	0.730000	0	6.600000e-01	8.000000e-01
RHCE	6006	broad.mit.edu	37	1	25717263	25717263	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:25717263G>A	ENST00000294413.7	-	5	836	c.778C>T	c.(778-780)Cac>Tac	p.H260Y	RHCE_ENST00000349438.4_Missense_Mutation_p.H260Y|RHCE_ENST00000346452.4_Intron|RHCE_ENST00000425135.1_Missense_Mutation_p.H260Y|RHCE_ENST00000243186.6_Missense_Mutation_p.H260Y|RHCE_ENST00000340849.4_Intron|RHCE_ENST00000349320.3_Missense_Mutation_p.H244Y|RHCE_ENST00000413854.1_Missense_Mutation_p.H260Y|RHCE_ENST00000374352.2_Missense_Mutation_p.H244Y|RHCE_ENST00000455194.1_Intron	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens			17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)			CTTTGGGGGTGAGCCAAGGAT	0.537000																								0							SO:0001583	missense			ENST00000294413.7	1	1	hg19	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	g	10.01	1.233543	0.22626	.	.	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000349320;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T	0.23754	1.89;1.89;1.89;1.89;1.89;1.89;1.89	4.23	3.3	0.37823	Ammonium transporter AmtB-like (3);	0.534254	0.19648	N	0.109285	T	0.50222	0.1603	M	0.83953	2.67	0.19300	N	0.999972	D;D;D	0.69078	0.988;0.997;0.964	D;D;D	0.77004	0.916;0.943;0.989	T	0.37709	-0.9694	10	0.87932	D	0	-2.9623	9.4703	0.38837	0.0:0.0:0.7883:0.2117	.	244;260;260	Q5VSJ9;Q5VSJ8;P18577	.;.;RHCE_HUMAN	Y	260;202;244;260;260;244;260;260;260	ENSP00000415417:H260Y;ENSP00000363472:H244Y;ENSP00000243186:H260Y;ENSP00000392809:H260Y;ENSP00000311185:H244Y;ENSP00000294413:H260Y;ENSP00000334570:H260Y	ENSP00000243186:H260Y	H	-	1	0	RHCE	25589850	0.912000	0.30974	0.077000	0.20336	0.051000	0.14879	2.349000	0.44054	1.106000	0.41623	0.591000	0.81541	CAC		TCGA-LB-A7SX-01A-11D-A33T-08	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	1	0	0	58	564	0	77	0	0	0	1	0	77	2		0	0	0	0	0	2	1	1.000000	58	561	0	77	2	0	0	0	0	0	0		-3.075755	1	1	0	0		1	0	1	1	2.183241	0	0.640000	1.650000	0.625624	0.270000	2.100000e-01	0.350000	0.280000	0.283852	0.270000	0	2.400000e-01	3.200000e-01
JAK1	3716	broad.mit.edu	37	1	65310517	65310517	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:65310517C>T	ENST00000342505.4	-	16	2419	c.2171G>A	c.(2170-2172)cGt>cAt	p.R724H	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1			120				Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GATGCCCTCACGGGCCAGGAG	0.542000			Mis		ALL										Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	0							SO:0001583	missense			ENST00000342505.4	1	1	hg19	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.762736	0.89932	.	.	ENSG00000162434	ENST00000342505	D	0.82893	-1.66	5.0	4.09	0.47781	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.87509	0.6195	M	0.71036	2.16	0.51767	D	0.999936	D	0.89917	1.0	D	0.91635	0.999	D	0.89235	0.3580	9	0.72032	D	0.01	-5.0492	13.6915	0.62549	0.0:0.9256:0.0:0.0744	.	724	P23458	JAK1_HUMAN	H	724	ENSP00000343204:R724H	ENSP00000343204:R724H	R	-	2	0	JAK1	65083105	1.000000	0.71417	0.864000	0.33941	0.849000	0.48306	7.239000	0.78182	1.347000	0.45714	0.563000	0.77884	CGT		TCGA-LB-A7SX-01A-11D-A33T-08	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	1	0	1	15	315	0	41	1	9.823398e-01	15	127	0	41	2		0	0	0	0	0	2	1	0.999863	15	309	0	40	2	0	0	0	0	0	0		-16.096030	1	1	0	0		1	0	1	1	2.183241	0	0.640000	1.650000	0.625624	0.130000	7.000000e-02	0.220000	0.130000	0.144553	0.130000	0	1.000000e-01	1.800000e-01
NEGR1	257194	broad.mit.edu	37	1	72400859	72400859	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:72400859C>G	ENST00000357731.5	-	2	551	c.312G>C	c.(310-312)caG>caC	p.Q104H	NEGR1_ENST00000306821.3_5'UTR|NEGR1_ENST00000467479.1_5'UTR|NEGR1_ENST00000434200.1_Missense_Mutation_p.Q102H	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1			32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)			CATTCTGTATCTGGAGGCTGT	0.443000																								0							SO:0001583	missense			ENST00000357731.5	1	1	hg19	CCDS661.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.725868	0.69074	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.27557	1.66;1.66	5.71	4.8	0.61643	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.055508	0.85682	D	0.000000	T	0.10723	0.0262	L	0.35644	1.08	0.58432	D	0.999997	B;B	0.21452	0.017;0.056	B;B	0.23018	0.026;0.043	T	0.06552	-1.0820	10	0.09590	T	0.72	-5.4874	14.4709	0.67517	0.0:0.9295:0.0:0.0705	.	102;104	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	H	104;102	ENSP00000350364:Q104H;ENSP00000413294:Q102H	ENSP00000350364:Q104H	Q	-	3	2	NEGR1	72173447	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.217000	0.51184	1.423000	0.47198	0.655000	0.94253	CAG		TCGA-LB-A7SX-01A-11D-A33T-08	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	0	0	0	11	333	0	55	0	1.198114e-02	0	5	0	55	2		0	0	0	0	0	2	1	0.998292	11	329	0	54	2	0	0	0	0	0	0		-11.303760	1	1	0	0		1	0	1	1	2.183241	0	0.640000	1.650000	0.625624	0.090000	4.000000e-02	0.160000	0.100000	0.104038	0.090000	0	6.000000e-02	1.300000e-01
COL24A1	255631	broad.mit.edu	37	1	86313406	86313406	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr1:86313406G>T	ENST00000370571.2	-	39	3770	c.3404C>A	c.(3403-3405)cCt>cAt	p.P1135H	COL24A1_ENST00000436319.1_Missense_Mutation_p.P1135H	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1			101					TTTTCCAGGAGGACCTCTGCT	0.428000																								0							SO:0001583	missense			ENST00000370571.2	1	1	hg19	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	G	4.161	0.028325	0.08054	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.98701	-5.08;-5.08	5.53	4.62	0.57501	.	0.000000	0.38058	N	0.001839	D	0.96898	0.8987	M	0.80982	2.52	0.22552	N	0.998991	B;B	0.25904	0.137;0.042	B;B	0.38683	0.279;0.007	D	0.95224	0.8336	10	0.48119	T	0.1	.	7.2398	0.26090	0.081:0.0:0.6546:0.2643	.	1135;1135	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	H	1135	ENSP00000359603:P1135H;ENSP00000392531:P1135H	ENSP00000359603:P1135H	P	-	2	0	COL24A1	86085994	0.874000	0.30092	0.978000	0.43139	0.377000	0.30045	3.233000	0.51311	1.343000	0.45638	-0.224000	0.12420	CCT		TCGA-LB-A7SX-01A-11D-A33T-08	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	1	0	1	186	378	0	77	0	2.557379e-01	1	2	0	77	2		0	0	0	0	0	2	1	1.000000	185	373	0	76	2	0	0	0	0	0	0		-15.627090	1	1	0	0		1	0	1	1	2.183241	0	0.640000	1.650000	0.625624	0.980000	8.700000e-01	1.000000	1.000000	0.971796	0.980000	1	9.200000e-01	1
NFS1	9054	broad.mit.edu	37	20	34262340	34262340	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr20:34262340G>A	ENST00000374092.4	-	10	1138	c.1068C>T	c.(1066-1068)ctC>ctT	p.L356L	NFS1_ENST00000540053.1_Silent_p.L154L|RP1-309K20.6_ENST00000541176.2_Missense_Mutation_p.S16F|NFS1_ENST00000397425.1_Silent_p.L296L|NFS1_ENST00000374085.1_Silent_p.L296L|NFS1_ENST00000498084.1_5'Flank|NFS1_ENST00000541387.1_Silent_p.L305L	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase			18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)	L-Alanine(DB00160)|L-Cysteine(DB00151)	ATGCAAAGGAGAGGTTGATAC	0.522000																								0							SO:0001819	synonymous_variant			ENST00000374092.4	0	1	hg19	CCDS13262.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078936.4	0	0	0	8	606	0	70	1	4.542917e-01	4	104	0	70	2		0	0	0	0	0	2	1	0.989003	8	600	0	70	2	0	0	0	0	0	0		-3.141534	1	1	0	0		1	2	2	4	2.383269	0	0.640000	1.650000	0.659607	0.040000	0	1.000000	0.040000	0.117614	0.040000	0	2.000000e-02	7.000000e-02
CDH22	64405	broad.mit.edu	37	20	44828152	44828152	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr20:44828152C>G	ENST00000372262.3	-	7	1733	c.1333G>C	c.(1333-1335)Gat>Cat	p.D445H	CDH22_ENST00000537909.1_Missense_Mutation_p.D445H	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2			44		Myeloproliferative disorder(115;0.0122)			GTGTCCGCATCGATATCGAAG	0.637000																								0							SO:0001583	missense			ENST00000372262.3	0	1	hg19	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.183686	0.57800	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.65732	-0.17;-0.17	5.0	4.06	0.47325	Cadherin (4);Cadherin-like (1);	0.054615	0.64402	D	0.000001	T	0.78142	0.4237	M	0.83118	2.625	0.53688	D	0.999977	D	0.89917	1.0	D	0.97110	1.0	T	0.78494	-0.2182	10	0.42905	T	0.14	.	11.1009	0.48174	0.0:0.9137:0.0:0.0863	.	445	Q9UJ99	CAD22_HUMAN	H	445	ENSP00000361336:D445H;ENSP00000437790:D445H	ENSP00000361336:D445H	D	-	1	0	CDH22	44261559	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.606000	0.61126	1.228000	0.43614	0.555000	0.69702	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	1	0	1	13	165	0	14	1	5.933198e-01	4	22	0	14	2		0	0	0	0	0	2	1	0.999565	13	163	0	14	2	0	0	0	0	0	0		-17.635650	1	1	0	0		1	2	2	4	2.392574	0	0.640000	1.650000	0.661654	0.250000	1.300000e-01	1.000000	0.240000	0.317910	0.250000	0	1.900000e-01	3.500000e-01
PREX1	57580	broad.mit.edu	37	20	47324868	47324868	+	Missense_Mutation	SNP	T	T	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr20:47324868T>C	ENST00000371941.3	-	6	735	c.713A>G	c.(712-714)aAt>aGt	p.N238S	PREX1_ENST00000396220.1_Missense_Mutation_p.N238S	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1			110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		CTTGGTCTCATTGATGTTGGA	0.627000																								0							SO:0001583	missense			ENST00000371941.3	1	1	hg19	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.898230	0.91962	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.75589	-0.95;-0.95	5.64	5.64	0.86602	Dbl homology (DH) domain (5);	0.000000	0.64402	U	0.000019	D	0.88250	0.6386	H	0.98089	4.145	0.80722	D	1	P	0.39551	0.678	P	0.47075	0.536	D	0.91608	0.5300	10	0.87932	D	0	.	15.8578	0.78994	0.0:0.0:0.0:1.0	.	238	Q8TCU6	PREX1_HUMAN	S	238	ENSP00000361009:N238S;ENSP00000379522:N238S	ENSP00000361009:N238S	N	-	2	0	PREX1	46758275	1.000000	0.71417	0.970000	0.41538	0.997000	0.91878	7.698000	0.84413	2.147000	0.66899	0.533000	0.62120	AAT		TCGA-LB-A7SX-01A-11D-A33T-08	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	1	0	1	438	934	0	158	1	9.095388e-01	4	7	0	158	2		0	0	0	0	0	2	1	1.000000	432	917	0	156	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.392574	0	0.640000	1.650000	0.661654	0.990000	9.700000e-01	1.000000	1.000000	0.998775	0.990000	1	9.900000e-01	1
ZNF217	7764	broad.mit.edu	37	20	52192921	52192921	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr20:52192921C>T	ENST00000371471.2	-	4	2807	c.2382G>A	c.(2380-2382)caG>caA	p.Q794Q	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Silent_p.Q794Q			O75362	ZN217_HUMAN	zinc finger protein 217			50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)		CAGGAGGGCTCTGCTTCCCCT	0.562000																								0							SO:0001819	synonymous_variant			ENST00000371471.2	1	1	hg19	CCDS13443.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	1	0	1	140	319	0	70	1	9.996587e-01	8	22	0	70	2		0	0	0	0	0	2	1	1.000000	140	318	0	66	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.378692	0	0.640000	1.650000	0.659607	0.990000	8.600000e-01	1.000000	1.000000	0.977937	0.990000	1	9.300000e-01	1
TMPRSS15	5651	broad.mit.edu	37	21	19666604	19666604	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr21:19666604G>A	ENST00000284885.3	-	21	2502	c.2469C>T	c.(2467-2469)gcC>gcT	p.A823A		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15			85					CGCAGTGTGCGGCGGACACCA	0.582000																								0							SO:0001819	synonymous_variant			ENST00000284885.3	1	1	hg19	CCDS13571.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	0	0	1	49	254	1	65		0	0	0	1	65	2		0	0	0	0	0	2	1	1.000000	49	250	0	65	2	0	0	0	0	0	0		-3.164906	1	1	121410	1	29	1	0	1	1	1.505065	1	0.640000	1.650000	0.473068	0.340000	2.500000e-01	0.430000	0.340000	0.348718	0.340000	0	2.900000e-01	3.900000e-01
B3GALT5	10317	broad.mit.edu	37	21	41032648	41032648	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr21:41032648G>A	ENST00000380620.4	+	5	754	c.162G>A	c.(160-162)caG>caA	p.Q54Q	B3GALT5_ENST00000398714.2_Silent_p.Q54Q|B3GALT5_ENST00000343118.4_Silent_p.Q54Q|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000380618.1_Silent_p.Q54Q			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5			16		Prostate(19;2.55e-06)			ACTGCAGGCAGACACCTCCCT	0.502000																								0							SO:0001819	synonymous_variant			ENST00000380620.4	1	1	hg19	CCDS13667.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	1	0	1	84	326	0	74	1	9.454756e-01	10	11	0	74	2		0	0	0	0	0	2	1	1.000000	84	323	0	73	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.078603	0	0.640000	1.650000	0.610052	0.580000	4.700000e-01	0.700000	0.590000	0.594281	0.580000	0	5.300000e-01	6.500000e-01
MCM3AP	8888	broad.mit.edu	37	21	47686068	47686068	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr21:47686068C>T	ENST00000397708.1	-	12	3056	c.2802G>A	c.(2800-2802)ctG>ctA	p.L934L	MCM3AP_ENST00000291688.1_Silent_p.L934L			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein			72	Breast(49;0.112)				CAGACCGGTTCAGCTCCACAC	0.567000																								0							SO:0001819	synonymous_variant			ENST00000397708.1	1	1	hg19	CCDS13734.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	0	0	0	36	1144	0	195	1	7.427446e-01	8	78	0	195	2		0	0	0	0	0	2	1	1.000000	38	1132	0	193	2	0	0	0	0	0	0		-2.902265	1	1	0	0		1	0	0	0	2.053198	0	0.640000	1.650000	0.604569	0.080000	5.000000e-02	0.120000	0.090000	0.089021	0.080000	0	6.000000e-02	1.000000e-01
IGLL5	100423062	broad.mit.edu	37	22	23237723	23237723	+	Missense_Mutation	SNP	A	A	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			A	C	A	A		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:23237723A>C	ENST00000526893.1	+	3	768	c.494A>C	c.(493-495)aAa>aCa	p.K165T	IGLL5_ENST00000532223.2_Missense_Mutation_p.K166T|IGLC1_ENST00000390321.2_RNA|IGLL5_ENST00000531372.1_3'UTR|IGLJ1_ENST00000390320.2_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5			7					GAGACCACCAAACCCTCCAAA	0.602000																								0							SO:0001583	missense			ENST00000526893.1	0	1	hg19	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.289688	0.00248	.	.	ENSG00000254709	ENST00000532223;ENST00000526893	T;T	0.00603	6.28;6.28	3.54	-2.51	0.06365	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.728791	0.12593	N	0.455429	T	0.00241	0.0007	.	.	.	0.09310	N	0.999998	B	0.06786	0.001	B	0.15052	0.012	T	0.40098	-0.9581	9	0.02654	T	1	.	2.1258	0.03738	0.4304:0.2973:0.1611:0.1113	.	165	B9A064	IGLL5_HUMAN	T	166;165	ENSP00000436353:K166T;ENSP00000431254:K165T	ENSP00000431254:K165T	K	+	2	0	IGLL5	21567723	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.399000	0.07250	-1.086000	0.03084	-5.509000	0.00000	AAA		TCGA-LB-A7SX-01A-11D-A33T-08	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	0	0	0	11	383	0	29	0	1	1	2707	0	29	2		0	0	0	0	0	2	1	0.998216	4	383	0	29	2	0	0	0	0	0	0		-11.295330	1	0	121348	25	42	1						0.640000	1.650000									0	0
SEZ6L	23544	broad.mit.edu	37	22	26688941	26688941	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:26688941G>A	ENST00000248933.6	+	2	759	c.664G>A	c.(664-666)Ggg>Agg	p.G222R	SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G222R|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G222R|SEZ6L_ENST00000343706.4_Missense_Mutation_p.G222R|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G222R|SEZ6L_ENST00000402979.1_5'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	p.G222K(1)		80					GCCAGAACCCGGGGAGCCTGG	0.642000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000248933.6	1	1	hg19	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.552259	0.27739	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706	T;T;T;T;T	0.26373	1.98;2.1;2.18;1.98;1.74	4.21	3.17	0.36434	.	0.807228	0.10049	U	0.722474	T	0.16085	0.0387	N	0.14661	0.345	0.09310	N	0.999994	B;B;B;B;B;B	0.28667	0.047;0.047;0.219;0.219;0.01;0.01	B;B;B;B;B;B	0.22880	0.013;0.008;0.042;0.042;0.003;0.003	T	0.19386	-1.0307	10	0.36615	T	0.2	.	12.2	0.54319	0.0:0.3302:0.6698:0.0	.	222;222;222;222;222;222	B7ZLJ8;B7ZLJ6;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;SE6L1_HUMAN	R	222	ENSP00000384772:G222R;ENSP00000437037:G222R;ENSP00000354185:G222R;ENSP00000248933:G222R;ENSP00000342661:G222R	ENSP00000248933:G222R	G	+	1	0	SEZ6L	25018941	0.138000	0.22547	0.016000	0.15963	0.054000	0.15201	0.882000	0.28186	0.870000	0.35726	0.405000	0.27470	GGG		TCGA-LB-A7SX-01A-11D-A33T-08	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3	0	0	0	18	430	0	88		0	0	0	0	88	2		0	0	0	0	0	2	1	0.999979	17	423	0	87	2	0	0	0	0	0	0		-2.529767	1	1	121392	12	41	1	0	1	1	1.690318	1	0.640000	1.650000	0.470588	0.080000	4.000000e-02	0.130000	0.090000	0.089489	0.080000	0	6.000000e-02	1.100000e-01
EIF3D	8664	broad.mit.edu	37	22	36915498	36915498	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:36915498C>T	ENST00000216190.8	-	8	1035	c.665G>A	c.(664-666)cGc>cAc	p.R222H	EIF3D_ENST00000541106.1_Missense_Mutation_p.R173H|EIF3D_ENST00000405442.1_Missense_Mutation_p.R222H	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D			15					GTGGAAGATGCGCTTGATGCT	0.567000																								0							SO:0001583	missense			ENST00000216190.8	1	1	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	C	36	5.693888	0.96793	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000455547	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.85788	0.5778	M	0.88906	2.99	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.976;0.99	D	0.86823	0.2006	9	0.72032	D	0.01	0.1102	20.5792	0.99380	0.0:1.0:0.0:0.0	.	173;222	B4DVY1;O15371	.;EIF3D_HUMAN	H	222;207;173;222;222	.	ENSP00000216190:R222H	R	-	2	0	EIF3D	35245444	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.419000	0.80179	2.873000	0.98535	0.561000	0.74099	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1	1	0	1	159	420	0	76	1	1	289	389	0	76	2		0	0	0	0	0	2	1	1.000000	159	416	0	76	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.428286	1	0.640000	1.650000	0.665676	0.920000	8.000000e-01	1.000000	1.000000	0.929541	0.920000	1	8.600000e-01	1
PHF5A	84844	broad.mit.edu	37	22	41863571	41863571	+	Missense_Mutation	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:41863571G>C	ENST00000216252.3	-	3	195	c.124C>G	c.(124-126)Ctg>Gtg	p.L42V	PHF5A_ENST00000491254.1_5'UTR|ACO2_ENST00000396512.3_5'Flank|ACO2_ENST00000216254.4_5'Flank	NM_032758.3	NP_116147.1	Q7RTV0	PHF5A_HUMAN	PHD finger protein 5A			4					ATGCGCACCAGAGTGCAGGGA	0.493000													Ovarian(15;130 571 1826 2981 46141)											0							SO:0001583	missense			ENST00000216252.3	0	1	hg19	CCDS14016.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064935	0.55432	.	.	ENSG00000100410	ENST00000216252	.	.	.	5.54	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	M	0.72353	2.195	0.80722	D	1	B	0.30664	0.289	B	0.40940	0.344	T	0.65957	-0.6042	9	0.41790	T	0.15	-12.734	11.3569	0.49621	0.1449:0.0:0.8551:0.0	.	42	Q7RTV0	PHF5A_HUMAN	V	42	.	ENSP00000216252:L42V	L	-	1	2	PHF5A	40193517	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.705000	0.54823	1.476000	0.48215	0.655000	0.94253	CTG		TCGA-LB-A7SX-01A-11D-A33T-08	PHF5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320686.1	0	0	0	7	404	0	57	1	8.260086e-01	9	178	0	57	2		0	0	0	0	0	2	1	0.980810	7	404	0	57	2	0	0	0	0	0	0		-6.536546	1	1	0	0		1	2	2	4	2.428428	1	0.640000	1.650000	0.665676	0.060000	2.000000e-02	1.000000	0.060000	0.155533	0.060000	0	3.000000e-02	1.000000e-01
CERK	64781	broad.mit.edu	37	22	47087589	47087589	+	Silent	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:47087589G>T	ENST00000216264.8	-	11	1324	c.1212C>A	c.(1210-1212)ccC>ccA	p.P404P	CERK_ENST00000471929.1_5'UTR|CERK_ENST00000541677.1_Silent_p.P206P	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase			20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)			AGAGGCCCCTGGGGCTCCGGC	0.557000																								0							SO:0001819	synonymous_variant			ENST00000216264.8	1	1	hg19	CCDS14077.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	1	0	1	71	314	0	41	1	9.999997e-01	41	58	0	41	2		0	0	0	0	0	2	1	1.000000	71	310	0	40	2	0	0	0	0	0	0		-3.435703	1	1	121408	3	34	1	2	2	4	2.923040	1	0.640000	1.650000	0.728589	0.790000	6.100000e-01	1.000000	0.760000	0.825973	0.790000	0	6.900000e-01	1
ZBED4	9889	broad.mit.edu	37	22	50279764	50279764	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr22:50279764C>T	ENST00000216268.5	+	2	2931	c.2454C>T	c.(2452-2454)aaC>aaT	p.N818N		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4			44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)			AGACGCTGAACGAGGGGGAGC	0.622000																								0							SO:0001819	synonymous_variant			ENST00000216268.5	1	1	hg19	CCDS33677.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	1	0	0	8	178	0	26	1	5.997546e-01	3	41	0	26	2		0	0	0	0	0	2	1	0.989846	8	178	0	26	2	0	0	0	0	0	0		-10.991430	1	1	116610	6	33	1	2	2	4	2.375485	0	0.640000	1.650000	0.659607	0.150000	6.000000e-02	1.000000	0.150000	0.219025	0.150000	0	1.000000e-01	2.300000e-01
AFF3	3899	broad.mit.edu	37	2	100623429	100623429	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:100623429G>T	ENST00000409236.2	-	5	650	c.538C>A	c.(538-540)Cag>Aag	p.Q180K	AFF3_ENST00000356421.2_Missense_Mutation_p.Q205K|AFF3_ENST00000409579.1_Missense_Mutation_p.Q205K|AFF3_ENST00000317233.4_Missense_Mutation_p.Q180K			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3			86					GCCCGAGGCTGCTGTCTGCCA	0.582000																								0							SO:0001583	missense			ENST00000409236.2	1	1	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.375513	0.24857	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.36	4.48	0.54585	.	0.250032	0.28317	N	0.015799	T	0.53077	0.1774	N	0.08118	0	0.26248	N	0.978761	B;B;D;B;B	0.59357	0.425;0.372;0.985;0.425;0.372	B;B;D;B;B	0.73708	0.192;0.085;0.981;0.192;0.121	T	0.48258	-0.9051	10	0.06236	T	0.91	.	8.8744	0.35337	0.0751:0.0:0.7765:0.1484	.	334;334;180;180;205	B7Z4I6;C9JXV5;A8K353;P51826;P51826-2	.;.;.;AFF3_HUMAN;.	K	180;205;205;180;180;334;205	ENSP00000317421:Q180K;ENSP00000348793:Q205K;ENSP00000386834:Q205K;ENSP00000387207:Q180K	ENSP00000317421:Q180K	Q	-	1	0	AFF3	99989861	1.000000	0.71417	0.988000	0.46212	0.886000	0.51366	6.148000	0.71788	1.259000	0.44117	0.585000	0.79938	CAG		TCGA-LB-A7SX-01A-11D-A33T-08	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	1	0	0	22	364	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	0.999999	22	359	0	49	2	0	0	0	0	0	0		-19.999960	1	1	0	0		1	0	1	1	2.102294	1	0.640000	1.650000	0.603175	0.160000	1.000000e-01	0.240000	0.160000	0.167767	0.160000	0	1.200000e-01	2.000000e-01
RANBP2	5903	broad.mit.edu	37	2	109367778	109367778	+	Nonsense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:109367778G>A	ENST00000283195.6	+	10	1458	c.1332G>A	c.(1330-1332)tgG>tgA	p.W444*		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2		RANBP2/ALK(34)	129					GCTTACAGTGGAATTCATTGC	0.388000																								0							SO:0001587	stop_gained			ENST00000283195.6	0	1	hg19	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	G	39	7.400347	0.98262	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6229	18.8314	0.92141	0.0:0.0:1.0:0.0	.	.	.	.	X	444	.	ENSP00000283195:W444X	W	+	3	0	RANBP2	108734210	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.957000	0.93082	2.521000	0.84997	0.650000	0.86243	TGG		TCGA-LB-A7SX-01A-11D-A33T-08	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	0	0	0	222	561	0	134	0	3.198684e-01	0	4	0	134	2		0	0	0	0	0	2	1	1.000000	65	115	0	175	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.102294	1	0.640000	1.650000	0.603175	0.790000	7.100000e-01	0.890000	0.800000	0.804680	0.790000	0	7.500000e-01	8.500000e-01
NCKAP5	344148	broad.mit.edu	37	2	133887563	133887563	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:133887563G>T	ENST00000409261.1	-	6	701	c.328C>A	c.(328-330)Cag>Aag	p.Q110K	NCKAP5_ENST00000317721.6_Missense_Mutation_p.Q110K|NCKAP5_ENST00000405974.3_Missense_Mutation_p.Q110K|NCKAP5_ENST00000409213.1_Missense_Mutation_p.Q110K	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5			118					GAGAACTGCTGCTGCAAGCTA	0.488000																								0							SO:0001583	missense			ENST00000409261.1	1	1	hg19	CCDS46418.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.69|15.69	2.909250|2.909250	0.52439|0.52439	.|.	.|.	ENSG00000176771|ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834|ENST00000427594	T;T;T;T|.	0.44083|.	2.93;0.93;2.93;0.93|.	6.17|6.17	2.06|2.06	0.26882|0.26882	.|.	.|.	.|.	.|.	.|.	T|T	0.22513|0.22513	0.0543|0.0543	N|N	0.24115|0.24115	0.695|0.695	0.23120|0.23120	N|N	0.998262|0.998262	B;B;B;B|.	0.29988|.	0.017;0.082;0.264;0.242|.	B;B;B;B|.	0.31101|.	0.031;0.032;0.124;0.055|.	T|T	0.21793|0.21793	-1.0235|-1.0235	9|5	0.49607|.	T|.	0.09|.	.|.	4.4369|4.4369	0.11555|0.11555	0.0791:0.2901:0.4811:0.1497|0.0791:0.2901:0.4811:0.1497	.|.	110;85;110;110|.	F5GYX5;O14513-3;O14513-2;O14513|.	.;.;.;NCKP5_HUMAN|.	K|R	110;110;110;110;110;85|105	ENSP00000387128:Q110K;ENSP00000386952:Q110K;ENSP00000380603:Q110K;ENSP00000385692:Q110K|.	ENSP00000380603:Q110K|.	Q|S	-|-	1|3	0|2	NCKAP5|NCKAP5	133604033|133604033	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	1.743000|1.743000	0.38258|0.38258	0.433000|0.433000	0.26313|0.26313	0.655000|0.655000	0.94253|0.94253	CAG|AGC		TCGA-LB-A7SX-01A-11D-A33T-08	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	1	0	1	22	62	0	10		0	0	0	0	10	2		0	0	0	0	0	2	1	1.000000	22	62	0	9	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.096084	1	0.640000	1.650000	0.604569	0.740000	5.000000e-01	1.000000	1.000000	0.752593	0.740000	0	6.100000e-01	8.800000e-01
IFIH1	64135	broad.mit.edu	37	2	163144827	163144827	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:163144827C>T	ENST00000263642.2	-	5	1308	c.913G>A	c.(913-915)Gaa>Aaa	p.E305K		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1			39					AGCTGGAGTTCTGGCTCCGGG	0.478000																								0							SO:0001583	missense			ENST00000263642.2	1	1	hg19	CCDS2217.1	.	.	.	.	.	.	.	.	.	.	C	18.62	3.663722	0.67700	.	.	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.53640	0.61	6.03	5.16	0.70880	DEAD-like helicase (1);	0.117044	0.56097	D	0.000030	T	0.45955	0.1368	L	0.38838	1.175	0.43054	D	0.994663	P	0.48162	0.906	P	0.48738	0.588	T	0.49293	-0.8955	10	0.72032	D	0.01	-17.0742	10.9061	0.47081	0.0:0.8028:0.1295:0.0677	.	305	Q9BYX4	IFIH1_HUMAN	K	305	ENSP00000263642:E305K	ENSP00000263642:E305K	E	-	1	0	IFIH1	162853073	1.000000	0.71417	0.971000	0.41717	0.967000	0.64934	3.203000	0.51075	1.562000	0.49601	0.557000	0.71058	GAA		TCGA-LB-A7SX-01A-11D-A33T-08	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	1	0	1	92	246	0	49	1	9.999131e-01	15	25	0	49	2		0	0	0	0	0	2	1	1.000000	92	246	0	49	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.096084	1	0.640000	1.650000	0.604569	0.760000	6.400000e-01	0.900000	0.770000	0.776669	0.760000	0	7.000000e-01	8.400000e-01
COL3A1	1281	broad.mit.edu	37	2	189868505	189868505	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:189868505G>A	ENST00000304636.3	+	38	2823	c.2653G>A	c.(2653-2655)Ggt>Agt	p.G885S	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1			126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)	Collagenase(DB00048)	TGGTCCTCCTGGTAGTAATGT	0.363000																								0							SO:0001583	missense			ENST00000304636.3	1	1	hg19	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087492	0.76642	.	.	ENSG00000168542	ENST00000304636	D	0.99607	-6.27	5.5	5.5	0.81552	.	0.000000	0.52532	D	0.000071	D	0.99718	0.9891	H	0.97077	3.935	0.80722	D	1	D	0.67145	0.996	D	0.63597	0.916	D	0.97479	1.0046	10	0.87932	D	0	.	13.6693	0.62416	0.0738:0.0:0.9262:0.0	.	885	P02461	CO3A1_HUMAN	S	885	ENSP00000304408:G885S	ENSP00000304408:G885S	G	+	1	0	COL3A1	189576750	1.000000	0.71417	0.983000	0.44433	0.893000	0.52053	7.914000	0.87478	2.590000	0.87494	0.551000	0.68910	GGT		TCGA-LB-A7SX-01A-11D-A33T-08	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	0	0	0	14	376	0	47	0	9.999997e-01	0	844	0	47	2		0	0	0	0	0	2	1	0.999752	14	373	0	47	2	0	0	0	0	0	0		-2.879242	1	1	0	0		1	0	1	1	2.096084	1	0.640000	1.650000	0.604569	0.100000	5.000000e-02	0.160000	0.100000	0.108683	0.100000	0	7.000000e-02	1.400000e-01
PNKD	25953	broad.mit.edu	37	2	219204548	219204548	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:219204548C>T	ENST00000273077.4	+	3	330	c.279C>T	c.(277-279)taC>taT	p.Y93Y	AC021016.8_ENST00000411433.1_RNA|PNKD_ENST00000436005.2_Silent_p.Y33Y|PNKD_ENST00000258362.3_Silent_p.Y69Y	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia			10		Renal(207;0.0474)			ACCTCTTCTACCGACAGCAGC	0.607000																								0							SO:0001819	synonymous_variant			ENST00000273077.4	1	1	hg19	CCDS2411.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2	1	0	1	8	186	0	22	1	3.488304e-01	6	21	0	22	2		0	0	0	0	0	2	1	0.989822	8	186	0	21	2	0	0	0	0	0	0		-10.443830	1	1	0	0		1	0	1	1	2.096084	1	0.640000	1.650000	0.604569	0.120000	5.000000e-02	0.220000	0.120000	0.130200	0.120000	0	8.000000e-02	1.700000e-01
ARMC9	80210	broad.mit.edu	37	2	232104753	232104753	+	Splice_Site	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:232104753C>T	ENST00000349938.4	+	9	1072	c.878C>T	c.(877-879)aCg>aTg	p.T293M	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9			22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)			AGGCCTGGGACGGTGAGGCTC	0.522000																								0							SO:0001630	splice_region_variant			ENST00000349938.4	1	0	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.581425	0.65992	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000444285	T;T	0.45276	2.08;0.9	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.62986	0.2473	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.66148	-0.5996	10	0.62326	D	0.03	-19.4815	16.518	0.84306	0.0:1.0:0.0:0.0	.	293	Q7Z3E5	ARMC9_HUMAN	M	293;293;47	ENSP00000258417:T293M;ENSP00000407146:T47M	ENSP00000258417:T293M	T	+	2	0	ARMC9	231812997	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.989000	0.76219	2.309000	0.77851	0.561000	0.74099	ACG		TCGA-LB-A7SX-01A-11D-A33T-08	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	1	0	0	50	61	0	19	1	9.983015e-01	6	10	0	19	2		0	0	0	0	0	2	1	1.000000	49	60	0	19	2	0	0	0	0	0	0		-20.000000	1	1	121410	8	33	1	0	1	1	2.096084	1	0.640000	1.650000	0.604569	0.990000	9.900000e-01	1.000000	1.000000	0.999256	0.990000	1	9.900000e-01	1
SH3BP4	23677	broad.mit.edu	37	2	235949825	235949825	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:235949825G>A	ENST00000409212.1	+	4	919	c.412G>A	c.(412-414)Gag>Aag	p.E138K	SH3BP4_ENST00000392011.2_Missense_Mutation_p.E138K|SH3BP4_ENST00000344528.4_Missense_Mutation_p.E138K			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4			44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)			GGTAGCCAAGGAGCTGGAGCT	0.507000																								0							SO:0001583	missense			ENST00000409212.1	1	1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.080730	0.76528	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000409212;ENST00000344528;ENST00000446904	T;T;T;T	0.34275	2.74;2.74;2.74;1.37	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.50411	0.1614	L	0.34521	1.04	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.72338	0.977;0.977	T	0.49485	-0.8935	10	0.54805	T	0.06	-0.3903	17.7288	0.88371	0.0:0.0:1.0:0.0	.	138;138	A8K594;Q9P0V3	.;SH3B4_HUMAN	K	138	ENSP00000375867:E138K;ENSP00000386862:E138K;ENSP00000340237:E138K;ENSP00000415391:E138K	ENSP00000340237:E138K	E	+	1	0	SH3BP4	235614564	1.000000	0.71417	0.953000	0.39169	0.031000	0.12232	9.549000	0.98106	2.519000	0.84933	0.655000	0.94253	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1	0	0	1	45	351	0	67	1	9.960359e-01	17	51	0	67	2		0	0	0	0	0	2	1	1.000000	45	346	0	66	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.029684	1	0.640000	1.650000	0.601770	0.310000	2.300000e-01	0.410000	0.320000	0.325962	0.310000	0	2.700000e-01	3.700000e-01
SPDYA	245711	broad.mit.edu	37	2	29052132	29052132	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:29052132C>T	ENST00000334056.5	+	6	688	c.499C>T	c.(499-501)Ctc>Ttc	p.L167F	SPDYA_ENST00000462832.1_3'UTR|SPDYA_ENST00000379579.4_Missense_Mutation_p.L167F	NM_182756.3	NP_877433.2			speedy/RINGO cell cycle regulator family member A			9	Acute lymphoblastic leukemia(172;0.155)				AAGGGACCAGCTCTGGGATAG	0.348000																								0							SO:0001583	missense			ENST00000334056.5	0	1	hg19	CCDS1767.2	.	.	.	.	.	.	.	.	.	.	C	15.93	2.978601	0.53720	.	.	ENSG00000163806	ENST00000379579;ENST00000334056	.	.	.	5.35	5.35	0.76521	.	0.096409	0.43579	U	0.000554	T	0.62295	0.2416	N	0.25031	0.7	0.58432	D	0.999999	D;D	0.67145	0.996;0.995	P;P	0.61477	0.889;0.823	T	0.59852	-0.7376	9	0.32370	T	0.25	0.5219	19.4215	0.94723	0.0:1.0:0.0:0.0	.	167;167	Q5MJ70;Q5MJ70-1	SPDYA_HUMAN;.	F	167	.	ENSP00000335628:L167F	L	+	1	0	SPDYA	28905636	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.309000	0.59135	2.664000	0.90586	0.563000	0.77884	CTC		TCGA-LB-A7SX-01A-11D-A33T-08	SPDYA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157171.1	0	0	0	9	364	0	56	0	7.801418e-04	0	2	0	56	2		0	0	0	0	0	2	1	0.994285	9	363	0	56	2	0	0	0	0	0	0		-3.482211	1	1	0	0		1	0	0	0	2.096230	0	0.640000	1.650000	0.612737	0.060000	2.000000e-02	0.130000	0.070000	0.077331	0.060000	0	4.000000e-02	1.000000e-01
EIF2AK2	5610	broad.mit.edu	37	2	37365423	37365423	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:37365423G>A	ENST00000233057.4	-	8	999	c.677C>T	c.(676-678)tCg>tTg	p.S226L	EIF2AK2_ENST00000395127.2_Missense_Mutation_p.S226L|EIF2AK2_ENST00000405334.1_Missense_Mutation_p.S226L	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2			22		all_hematologic(82;0.248)			CATAAGCAACGAAGAACTGTT	0.358000																								0							SO:0001583	missense			ENST00000233057.4	1	1	hg19	CCDS1786.1	.	.	.	.	.	.	.	.	.	.	G	9.576	1.122371	0.20877	.	.	ENSG00000055332	ENST00000233057;ENST00000395127;ENST00000405334;ENST00000379156	T;T;T	0.76448	-0.99;-0.99;-1.02	2.93	-0.132	0.13489	.	2.710630	0.01408	N	0.013874	T	0.75102	0.3804	M	0.71581	2.175	0.09310	N	1	B;B;B;B	0.14805	0.011;0.011;0.003;0.003	B;B;B;B	0.09377	0.004;0.002;0.002;0.002	T	0.45101	-0.9284	10	0.26408	T	0.33	0.431	6.4738	0.22024	0.3144:0.0:0.6856:0.0	.	226;226;226;226	Q8IW76;B7ZKK7;P19525;E9PC80	.;.;E2AK2_HUMAN;.	L	226	ENSP00000233057:S226L;ENSP00000378559:S226L;ENSP00000385014:S226L	ENSP00000233057:S226L	S	-	2	0	EIF2AK2	37218927	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.674000	0.05233	-0.052000	0.13311	0.557000	0.71058	TCG		TCGA-LB-A7SX-01A-11D-A33T-08	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	1	0	0	24	299	0	40	0	7.584051e-01	1	35	0	40	2		0	0	0	0	0	2	1	1.000000	24	294	0	40	2	0	0	0	0	0	0		-3.017760	1	1	121410	1	30	1	0	1	1	2.090964	1	0.640000	1.650000	0.604569	0.210000	1.300000e-01	0.300000	0.210000	0.218403	0.210000	0	1.700000e-01	2.600000e-01
SMYD5	10322	broad.mit.edu	37	2	73451115	73451115	+	Missense_Mutation	SNP	T	T	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			T	G	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:73451115T>G	ENST00000389501.4	+	10	969	c.924T>G	c.(922-924)ttT>ttG	p.F308L		NM_006062.2	NP_006053.2	Q6GMV2	SMYD5_HUMAN	SMYD family member 5			13					CTGGCCTCTTTGTGCTTCAGA	0.478000																								0							SO:0001583	missense			ENST00000389501.4	1	1	hg19	CCDS33221.2	.	.	.	.	.	.	.	.	.	.	T	17.98	3.521334	0.64747	.	.	ENSG00000135632	ENST00000389501	T	0.81415	-1.49	4.77	2.14	0.27477	SET domain (2);	0.218148	0.48767	D	0.000176	T	0.73125	0.3547	L	0.45581	1.43	0.40606	D	0.981624	B	0.29481	0.245	B	0.35182	0.197	T	0.70594	-0.4829	10	0.66056	D	0.02	-8.2184	6.1113	0.20102	0.0:0.5224:0.0:0.4776	.	308	Q6GMV2	SMYD5_HUMAN	L	308	ENSP00000374152:F308L	ENSP00000374152:F308L	F	+	3	2	SMYD5	73304623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.888000	0.28268	0.815000	0.34398	0.533000	0.62120	TTT		TCGA-LB-A7SX-01A-11D-A33T-08	SMYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318301.1	1	0	1	84	629	0	114	1	9.989949e-01	15	62	0	114	2		0	0	0	0	0	2	1	1.000000	83	626	0	114	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.090964	1	0.640000	1.650000	0.604569	0.330000	2.600000e-01	0.400000	0.330000	0.337908	0.330000	0	2.900000e-01	3.700000e-01
DGUOK	1716	broad.mit.edu	37	2	74154141	74154141	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:74154141G>A	ENST00000264093.4	+	1	189	c.104G>A	c.(103-105)gGg>gAg	p.G35E	DGUOK_ENST00000356837.6_Missense_Mutation_p.G35E|DGUOK_ENST00000348222.1_Missense_Mutation_p.G35E|DGUOK_ENST00000462685.1_3'UTR	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase			8				Nelarabine(DB01280)	CTGCACGCGGGGCGCGGGCCC	0.672000																								0							SO:0001583	missense			ENST00000264093.4	0	1	hg19	CCDS1931.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.016699	0.54468	.	.	ENSG00000114956	ENST00000264093;ENST00000348222;ENST00000356837;ENST00000347161	D;D;D	0.99832	-5.27;-4.72;-7.02	4.19	1.14	0.20703	.	0.757041	0.13116	N	0.412588	D	0.98438	0.9480	L	0.38838	1.175	0.24671	N	0.99342	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	D	0.99942	1.1420	10	0.07175	T	0.84	-3.3064	5.3436	0.15996	0.4514:0.0:0.5486:0.0	.	35;35	E5KSL6;Q16854	.;DGUOK_HUMAN	E	35	ENSP00000264093:G35E;ENSP00000306964:G35E;ENSP00000349294:G35E	ENSP00000264093:G35E	G	+	2	0	DGUOK	74007649	0.784000	0.28713	0.720000	0.30636	0.681000	0.39784	0.699000	0.25586	0.222000	0.20900	0.655000	0.94253	GGG		TCGA-LB-A7SX-01A-11D-A33T-08	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252050.1	0	0	0	6	454	0	61	1	8.522890e-01	6	258	0	61	2		0	0	0	0	0	2	1	0.963254	6	446	0	60	2	0	0	0	0	0	0		-5.032479	1	0	0	0		1	0	1	1	2.090964	1	0.640000	1.650000	0.604569	0.030000	0	0.080000	0.040000	0.043006	0.030000	0	2.000000e-02	6.000000e-02
INPP4A	3631	broad.mit.edu	37	2	99169316	99169316	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr2:99169316G>A	ENST00000523221.1	+	13	1246	c.1246G>A	c.(1246-1248)Gcc>Acc	p.A416T	INPP4A_ENST00000545415.1_Missense_Mutation_p.A416T|INPP4A_ENST00000409851.3_Missense_Mutation_p.A411T|INPP4A_ENST00000409540.3_Missense_Mutation_p.A416T|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Missense_Mutation_p.A416T|INPP4A_ENST00000074304.5_Missense_Mutation_p.A416T			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa			43					GGAGATCATCGCCCAGATCAA	0.517000																								0							SO:0001583	missense			ENST00000523221.1	0	1	hg19	CCDS46369.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.847369	0.91277	.	.	ENSG00000040933	ENST00000409016;ENST00000409851;ENST00000074304;ENST00000545415;ENST00000409540;ENST00000523221	T;T;T;T;T;T	0.19105	2.17;2.17;2.17;2.17;2.17;2.17	5.03	5.03	0.67393	.	0.054882	0.64402	D	0.000001	T	0.25644	0.0624	L	0.40543	1.245	0.54753	D	0.999988	D;D;D;D	0.58268	0.959;0.978;0.982;0.982	B;B;P;P	0.47864	0.357;0.378;0.559;0.559	T	0.00790	-1.1565	10	0.36615	T	0.2	-24.8771	17.5362	0.87832	0.0:0.0:1.0:0.0	.	416;416;416;411	Q96PE3-2;Q96PE3-4;Q96PE3;Q96PE3-3	.;.;INP4A_HUMAN;.	T	416;411;416;416;416;416	ENSP00000386704:A416T;ENSP00000386777:A411T;ENSP00000074304:A416T;ENSP00000442149:A416T;ENSP00000387294:A416T;ENSP00000427722:A416T	ENSP00000074304:A416T	A	+	1	0	INPP4A	98535748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.492000	0.81482	2.608000	0.88229	0.655000	0.94253	GCC		TCGA-LB-A7SX-01A-11D-A33T-08	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	1	0	0	8	140	0	15	0	5.558005e-01	1	31	0	15	2		0	0	0	0	0	2	1	0.989996	8	140	0	15	2	0	0	0	0	0	0		-4.455787	1	1	0	0		1	0	1	1	2.102294	1	0.640000	1.650000	0.603175	0.150000	7.000000e-02	0.280000	0.150000	0.169347	0.150000	0	1.100000e-01	2.200000e-01
ATP2B2	491	broad.mit.edu	37	3	10442753	10442753	+	Missense_Mutation	SNP	A	A	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:10442753A>G	ENST00000352432.4	-	4	734	c.665T>C	c.(664-666)cTc>cCc	p.L222P	ATP2B2_ENST00000397077.1_Missense_Mutation_p.L222P|ATP2B2_ENST00000383800.4_Missense_Mutation_p.L222P|ATP2B2_ENST00000360273.2_Missense_Mutation_p.L222P|ATP2B2_ENST00000343816.4_Missense_Mutation_p.L222P			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2			74					GTCGGCAGGGAGGAGGTCACC	0.567000													Ovarian(125;1619 1709 15675 19819 38835)											0							SO:0001583	missense			ENST00000352432.4	1	1	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314875	0.81358	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.6	5.6	0.85130	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.95516	0.8543	M	0.82716	2.605	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.998	D	0.96098	0.9067	10	0.87932	D	0	-32.0976	15.7913	0.78367	1.0:0.0:0.0:0.0	.	222;234;222	Q01814-7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	P	222;222;222;222;222;188;109;222	ENSP00000324172:L222P;ENSP00000373311:L222P;ENSP00000380267:L222P;ENSP00000353414:L222P;ENSP00000344677:L222P;ENSP00000414854:L109P	ENSP00000342954:L222P	L	-	2	0	ATP2B2	10417753	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	9.313000	0.96297	2.124000	0.65301	0.528000	0.53228	CTC		TCGA-LB-A7SX-01A-11D-A33T-08	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	0	0	0	7	168	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	0.980068	7	165	0	30	2	0	0	0	0	0	0		-9.546685	1	1	0	0		1	0	1	1	1.597415	1	0.640000	1.650000	0.470588	0.080000	3.000000e-02	0.160000	0.080000	0.095423	0.080000	0	5.000000e-02	1.300000e-01
CD96	10225	broad.mit.edu	37	3	111286413	111286413	+	Missense_Mutation	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:111286413G>C	ENST00000283285.5	+	3	593	c.462G>C	c.(460-462)gaG>gaC	p.E154D	CD96_ENST00000438817.2_Missense_Mutation_p.E154D|CD96_ENST00000352690.4_Missense_Mutation_p.E154D	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule			35					TAGAAATAGAGATAAATCAGA	0.368000									Opitz Trigonocephaly syndrome															0							SO:0001583	missense	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	ENST00000283285.5	1	1	hg19	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.628223	0.28978	.	.	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.66099	1.65;-0.19;1.65	5.37	2.35	0.29111	Immunoglobulin subtype (1);	0.968819	0.08496	N	0.937108	T	0.42381	0.1200	L	0.27053	0.805	0.20563	N	0.999889	P;P;P;B	0.37781	0.608;0.557;0.608;0.421	B;B;B;B	0.34242	0.115;0.178;0.115;0.086	T	0.21895	-1.0232	10	0.19590	T	0.45	-0.5288	4.485	0.11785	0.2025:0.1855:0.6119:0.0	.	154;154;154;154	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	D	154	ENSP00000342040:E154D;ENSP00000283285:E154D;ENSP00000389801:E154D	ENSP00000283285:E154D	E	+	3	2	CD96	112769103	1.000000	0.71417	0.973000	0.42090	0.941000	0.58515	2.051000	0.41307	0.812000	0.34326	-0.157000	0.13467	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2	1	0	0	13	254	0	41	0	4.983202e-02	0	7	0	41	2		0	0	0	0	0	2	1	0.999500	13	248	0	41	2	0	0	0	0	0	0		-15.416020	1	1	0	0		1	1	2	3	2.293641	0	0.640000	1.650000	0.642289	0.150000	8.000000e-02	0.270000	0.160000	0.171535	0.150000	0	1.100000e-01	2.100000e-01
GPR156	165829	broad.mit.edu	37	3	119962536	119962536	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:119962536G>A	ENST00000464295.1	-	3	629	c.184C>T	c.(184-186)Ctg>Ttg	p.L62L	GPR156_ENST00000461057.1_Silent_p.L62L|GPR156_ENST00000315843.3_Silent_p.L62L			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156			32					AGTATCAGCAGAAGTCCACAG	0.428000																								0							SO:0001819	synonymous_variant			ENST00000464295.1	1	1	hg19	CCDS2997.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	1	0	1	178	348	0	57	0	0	1	0	0	57	2		0	0	0	0	0	2	1	1.000000	176	343	0	57	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.990000	9.300000e-01	1.000000	1.000000	0.994216	0.990000	1	9.900000e-01	1
STXBP5L	9515	broad.mit.edu	37	3	120957910	120957910	+	Missense_Mutation	SNP	T	T	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:120957910T>C	ENST00000273666.6	+	13	1548	c.1277T>C	c.(1276-1278)aTt>aCt	p.I426T	STXBP5L_ENST00000497029.1_Missense_Mutation_p.I426T|STXBP5L_ENST00000492541.1_Missense_Mutation_p.I426T|STXBP5L_ENST00000471454.1_Missense_Mutation_p.I426T|STXBP5L_ENST00000472879.1_Missense_Mutation_p.I426T	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like			68					CCGGATTTGATTCTAGTACTG	0.313000																								0							SO:0001583	missense			ENST00000273666.6	1	1	hg19	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586545	0.46110	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.39229	1.78;1.78;1.58;1.09;1.58;1.79	4.97	4.97	0.65823	WD40 repeat-like-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.61590	0.2359	M	0.64997	1.995	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.83275	0.996;0.996	T	0.64381	-0.6421	10	0.59425	D	0.04	-30.5866	14.8108	0.69994	0.0:0.0:0.0:1.0	.	426;426	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	T	426	ENSP00000273666:I426T;ENSP00000420019:I426T;ENSP00000419627:I426T;ENSP00000420287:I426T;ENSP00000420666:I426T;ENSP00000420167:I426T	ENSP00000273666:I426T	I	+	2	0	STXBP5L	122440600	1.000000	0.71417	1.000000	0.80357	0.013000	0.08279	7.827000	0.86722	2.088000	0.63022	0.533000	0.62120	ATT		TCGA-LB-A7SX-01A-11D-A33T-08	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3	0	0	0	8	239	0	31		0	0	0	0	31	2		0	0	0	0	0	2	1	0.989701	8	239	0	31	2	0	0	0	0	0	0		-9.775703	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.100000	4.000000e-02	0.200000	0.100000	0.113059	0.100000	0	7.000000e-02	1.500000e-01
ADCY5	111	broad.mit.edu	37	3	123010065	123010065	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:123010065G>A	ENST00000462833.1	-	18	4434	c.3222C>T	c.(3220-3222)ttC>ttT	p.F1074F	ADCY5_ENST00000309879.5_Silent_p.F724F|ADCY5_ENST00000491190.1_Silent_p.F732F	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	p.F1074L(1)		60					CGATGGAGGCGAACATGACCG	0.577000																								1	Substitution - Missense(1)						SO:0001819	synonymous_variant			ENST00000462833.1	1	1	hg19	CCDS3022.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	1	0	1	81	332	0	61	0	9.807758e-01	1	27	0	61	2		0	0	0	0	0	2	1	1.000000	81	330	0	61	2	0	0	0	0	0	0		-3.474703	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.610000	4.900000e-01	0.740000	0.620000	0.618607	0.610000	0	5.500000e-01	6.800000e-01
ADCY5	111	broad.mit.edu	37	3	123021988	123021988	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:123021988G>A	ENST00000462833.1	-	14	3850	c.2638C>T	c.(2638-2640)Cac>Tac	p.H880Y	ADCY5_ENST00000309879.5_Missense_Mutation_p.H530Y|ADCY5_ENST00000491190.1_Missense_Mutation_p.H513Y	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5			60					TCCGCCACGTGACACGCGTTG	0.642000																								0							SO:0001583	missense			ENST00000462833.1	0	1	hg19	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.819575	0.32145	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.04	5.04	0.67666	.	0.066645	0.64402	D	0.000016	T	0.44074	0.1276	M	0.61703	1.905	0.48135	D	0.999599	B;B	0.14438	0.01;0.001	B;B	0.10450	0.005;0.001	T	0.47045	-0.9147	10	0.02654	T	1	.	18.5817	0.91174	0.0:0.0:1.0:0.0	.	880;513	O95622;B3KWA8	ADCY5_HUMAN;.	Y	880;513;530;439	ENSP00000419361:H880Y;ENSP00000418537:H513Y;ENSP00000308685:H530Y;ENSP00000420082:H439Y	ENSP00000308685:H530Y	H	-	1	0	ADCY5	124504678	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	7.719000	0.84751	2.619000	0.88677	0.561000	0.74099	CAC		TCGA-LB-A7SX-01A-11D-A33T-08	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	0	0	0	6	277	0	30	0	2.618954e-02	0	10	0	30	2		0	0	0	0	0	2	1	0.964652	6	275	0	30	2	0	0	0	0	0	0		-7.222277	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.060000	2.000000e-02	0.140000	0.060000	0.076866	0.060000	0	4.000000e-02	1.100000e-01
XRN1	54464	broad.mit.edu	37	3	142142485	142142485	+	Splice_Site	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:142142485C>T	ENST00000264951.4	-	6	745		c.e6-1		XRN1_ENST00000463916.1_Splice_Site|XRN1_ENST00000544157.1_Splice_Site|XRN1_ENST00000392981.2_Splice_Site	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1			61					CAAGCATAATCTGTTGAAAAA	0.279000																								0							SO:0001630	splice_region_variant			ENST00000264951.4	1	1	hg19	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.363755	0.82353	.	.	ENSG00000114127	ENST00000264951;ENST00000392981;ENST00000463916;ENST00000477237	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4475	0.94854	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	XRN1	143625175	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.568000	0.82369	2.609000	0.88269	0.460000	0.39030	.		TCGA-LB-A7SX-01A-11D-A33T-08	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	1	0	1	54	215	0	33		0	0	0	0	33	2		0	0	0	0	0	2	1	1.000000	54	215	0	32	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.620000	4.800000e-01	0.790000	0.630000	0.634935	0.620000	0	5.500000e-01	7.100000e-01
ECT2	1894	broad.mit.edu	37	3	172480552	172480552	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:172480552C>A	ENST00000392692.3	+	10	1137	c.961C>A	c.(961-963)Ctt>Att	p.L321I	ECT2_ENST00000417960.1_Missense_Mutation_p.L289I|ECT2_ENST00000232458.5_Missense_Mutation_p.L290I|ECT2_ENST00000427830.1_Missense_Mutation_p.L290I|ECT2_ENST00000441497.2_Missense_Mutation_p.L290I|ECT2_ENST00000540509.1_Missense_Mutation_p.L321I	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2			37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)		AGTAAAAGATCTTCCCTTTGA	0.333000																								0							SO:0001583	missense			ENST00000392692.3	1	1	hg19	CCDS58860.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.769443	0.31320	.	.	ENSG00000114346	ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	5.84	3.99	0.46301	BRCT (2);	0.123450	0.53938	D	0.000041	T	0.71600	0.3359	L	0.43701	1.375	0.52099	D	0.999947	B;B;B;B	0.16166	0.0;0.016;0.008;0.001	B;B;B;B	0.19666	0.005;0.026;0.017;0.012	T	0.63184	-0.6694	10	0.31617	T	0.26	-13.9281	8.7265	0.34471	0.3898:0.5435:0.0:0.0666	.	321;321;290;289	Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	ECT2_HUMAN;.;.;.	I	290;321;290;289;290;321	ENSP00000232458:L290I;ENSP00000376457:L321I;ENSP00000401910:L290I;ENSP00000415876:L289I;ENSP00000412259:L290I;ENSP00000443160:L321I	ENSP00000232458:L290I	L	+	1	0	ECT2	173963246	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.884000	0.48562	0.744000	0.32741	-0.282000	0.10007	CTT		TCGA-LB-A7SX-01A-11D-A33T-08	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	1	0	1	104	213	0	37	1	9.999156e-01	15	17	0	37	2		0	0	0	0	0	2	1	1.000000	102	212	0	37	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.277020	0	0.640000	1.650000	0.641148	0.990000	8.600000e-01	1.000000	1.000000	0.980082	0.990000	1	9.400000e-01	1
FBXO45	200933	broad.mit.edu	37	3	196304578	196304578	+	Silent	SNP	T	T	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:196304578T>C	ENST00000311630.6	+	2	870	c.573T>C	c.(571-573)agT>agC	p.S191S	FBXO45_ENST00000440469.1_Silent_p.S12S	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45			7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)		TGCTGGGCAGTGATGACCAGA	0.517000																								0							SO:0001819	synonymous_variant			ENST00000311630.6	1	1	hg19	CCDS46985.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2	1	0	1	54	114	0	28	1	7.129333e-01	2	5	0	28	2		0	0	0	0	0	2	1	1.000000	54	113	0	28	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	0	0	2.236930	0	0.640000	1.650000	0.637681	0.990000	7.800000e-01	1.000000	1.000000	0.956297	0.990000	1	8.800000e-01	1
CHL1	10752	broad.mit.edu	37	3	367698	367698	+	Missense_Mutation	SNP	G	G	A	rs150837773		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:367698G>A	ENST00000256509.2	+	4	790	c.148G>A	c.(148-150)Gat>Aat	p.D50N	CHL1_ENST00000397491.2_Missense_Mutation_p.D50N	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like			93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)			CTTTCCCTTCGATGAGTATTT	0.333000																								0							SO:0001583	missense			ENST00000256509.2	1	1	hg19	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724427	0.89298	0.0	1.16E-4	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;D	0.95885	-0.27;-0.27;0.19;-0.27;-0.27;-3.84	5.67	5.67	0.87782	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.182770	0.46145	D	0.000309	D	0.96719	0.8929	L	0.45744	1.44	0.53688	D	0.999976	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.87578	0.808;0.998;0.995	D	0.96379	0.9280	10	0.45353	T	0.12	.	17.9886	0.89162	0.0:0.0:1.0:0.0	.	50;50;50	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	N	50	ENSP00000256509:D50N;ENSP00000380628:D50N;ENSP00000403311:D50N;ENSP00000413628:D50N;ENSP00000397445:D50N;ENSP00000390440:D50N	ENSP00000256509:D50N	D	+	1	0	CHL1	342698	1.000000	0.71417	0.950000	0.38849	0.738000	0.42128	7.870000	0.87175	2.669000	0.90835	0.551000	0.68910	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	1	0	0	7	212	0	47	0	0	0	1	0	47	2		0	0	0	0	0	2	1	0.980147	7	209	0	47	2	0	0	0	0	0	0		-3.092964	1	1	121370	3	37	1						0.640000	1.650000									0	0
CTNNB1	1499	broad.mit.edu	37	3	41266124	41266124	+	Missense_Mutation	SNP	A	A	G	rs121913412		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			A	G	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:41266124A>G	ENST00000349496.5	+	3	401	c.121A>G	c.(121-123)Acc>Gcc	p.T41A	CTNNB1_ENST00000405570.1_Missense_Mutation_p.T41A|CTNNB1_ENST00000396183.3_Missense_Mutation_p.T41A|CTNNB1_ENST00000453024.1_Missense_Mutation_p.T34A|CTNNB1_ENST00000396185.3_Missense_Mutation_p.T41A	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	p.T41A(550)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.T41P(6)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T41S(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.T40_L46del(1)|p.A20_N141del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_T41del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.A39_T42del(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	3893					TGGTGCCACTACCACAGCTCC	0.507000	T41A(CCK81_LARGE_INTESTINE)	15	H, Mis, T	PLAG1	colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma				Pilomatrixoma, Familial Clustering of				Colon(6;3 56 14213 18255)		Dom	yes		3	3p22-p21.3	1499	catenin (cadherin-associated protein), beta 1		E, M, O	681	Substitution - Missense(559)|Deletion - In frame(96)|Complex - deletion inframe(17)|Unknown(7)|Deletion - Frameshift(2)						SO:0001583	missense	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ENST00000349496.5	1	1	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449381	0.84101	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.63117	0.2484	M	0.79258	2.445	0.80722	D	1	P	0.50943	0.94	P	0.52267	0.694	T	0.68561	-0.5376	10	0.87932	D	0	-8.9189	16.3453	0.83126	1.0:0.0:0.0:0.0	.	41	P35222	CTNB1_HUMAN	A	34;41;41;41;41;34;41;41;41	ENSP00000400508:T34A;ENSP00000385604:T41A;ENSP00000412219:T41A;ENSP00000379486:T41A;ENSP00000344456:T41A;ENSP00000411226:T34A;ENSP00000379488:T41A;ENSP00000409302:T41A;ENSP00000401599:T41A	ENSP00000344456:T41A	T	+	1	0	CTNNB1	41241128	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	ACC		TCGA-LB-A7SX-01A-11D-A33T-08	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	1	0	1	106	114	0	37	1	1	219	67	0	37	2		0	0	0	0	0	2	1	1.000000	104	114	0	36	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.608223	1	0.640000	1.650000	0.473068	0.960000	8.500000e-01	1.000000	1.000000	0.959743	0.960000	1	9.100000e-01	1
SCAP	22937	broad.mit.edu	37	3	47455391	47455391	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:47455391C>T	ENST00000265565.5	-	23	4205	c.3793G>A	c.(3793-3795)Gag>Aag	p.E1265K	SCAP_ENST00000441517.2_Missense_Mutation_p.E1009K|SCAP_ENST00000545718.1_Missense_Mutation_p.E872K	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone			26					AGGCTGAGCTCACTGCCAAAG	0.617000													Pancreas(149;978 1908 29304 37806 46700)											0							SO:0001583	missense			ENST00000265565.5	1	1	hg19	CCDS2755.2	.	.	.	.	.	.	.	.	.	.	C	33	5.230099	0.95207	.	.	ENSG00000114650	ENST00000339815;ENST00000360832;ENST00000265565;ENST00000441517;ENST00000545718	T;T;T	0.81078	-1.45;-1.41;0.74	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.82061	0.4955	L	0.29908	0.895	0.80722	D	1	D;D	0.65815	0.995;0.985	P;P	0.57152	0.814;0.718	D	0.84115	0.0403	10	0.62326	D	0.03	-31.3009	18.0736	0.89421	0.0:1.0:0.0:0.0	.	1009;1265	F8W921;Q12770	.;SCAP_HUMAN	K	757;891;1265;1009;872	ENSP00000265565:E1265K;ENSP00000416847:E1009K;ENSP00000438956:E872K	ENSP00000265565:E1265K	E	-	1	0	SCAP	47430395	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.427000	0.66483	2.596000	0.87737	0.655000	0.94253	GAG		TCGA-LB-A7SX-01A-11D-A33T-08	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246872.2	1	0	0	44	942	0	209	1	9.975529e-01	16	176	0	209	2		0	0	0	0	0	2	1	1.000000	42	933	0	208	2	0	0	0	0	0	0		-4.718108	1	1	0	0		1	0	1	1	1.608223	1	0.640000	1.650000	0.473068	0.090000	6.000000e-02	0.130000	0.100000	0.097126	0.090000	0	7.000000e-02	1.100000e-01
BSN	8927	broad.mit.edu	37	3	49690204	49690204	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:49690204G>A	ENST00000296452.4	+	5	3329	c.3215G>A	c.(3214-3216)cGc>cAc	p.R1072H		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein			106					AGCACGGCCCGCAAGACCCGG	0.652000																								0							SO:0001583	missense			ENST00000296452.4	0	1	hg19	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.313063	0.60414	.	.	ENSG00000164061	ENST00000296452	T	0.24151	1.87	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.50257	0.1605	M	0.68952	2.095	0.50171	D	0.999851	D	0.89917	1.0	D	0.71656	0.974	T	0.54476	-0.8288	10	0.72032	D	0.01	.	18.0791	0.89437	0.0:0.0:1.0:0.0	.	1072	Q9UPA5	BSN_HUMAN	H	1072	ENSP00000296452:R1072H	ENSP00000296452:R1072H	R	+	2	0	BSN	49665208	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	9.807000	0.99171	2.357000	0.79964	0.561000	0.74099	CGC		TCGA-LB-A7SX-01A-11D-A33T-08	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	0	0	0	5	197	1	38		0	0	0	1	38	2		0	0	0	0	0	2	0	0.005750	4	193	1	36	17	0	0	0	0	0	0		-6.521200	1	0	0	0		1	0	1	1	1.608223	1	0.640000	1.650000	0.473068	0.050000	1.000000e-02	0.120000	0.050000	0.062453	0.050000	0	3.000000e-02	9.000000e-02
PBRM1	55193	broad.mit.edu	37	3	52610715	52610715	+	Splice_Site	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr3:52610715C>T	ENST00000296302.7	-	22	3535		c.e22-1		PBRM1_ENST00000409114.3_Splice_Site|PBRM1_ENST00000409767.1_Splice_Site|PBRM1_ENST00000410007.1_Splice_Site|PBRM1_ENST00000409057.1_Splice_Site|PBRM1_ENST00000337303.4_Splice_Site|PBRM1_ENST00000356770.4_Splice_Site|PBRM1_ENST00000394830.3_Splice_Site|SMIM4_ENST00000476842.1_Intron			Q86U86	PB1_HUMAN	polybromo 1	p.?(6)		335					TTTTTCAATTCTTGGGGAGGA	0.343000			Mis, N, F, S, D, O		clear cell renal carcinoma, breast										Rec	yes		3	3p21	55193	polybromo 1		E	6	Unknown(6)						SO:0001630	splice_region_variant			ENST00000296302.7	0	1	hg19		.	.	.	.	.	.	.	.	.	.	C	24.8	4.568252	0.86439	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3907	0.94581	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PBRM1	52585755	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.720000	0.84759	2.664000	0.90586	0.591000	0.81541	.		TCGA-LB-A7SX-01A-11D-A33T-08	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	0	0	0	6	170	0	33		0	0	0	0	33	2	1	9.986524e-01	19	386	0	459	2	1	0.963252	6	167	0	33	2	0	0	0	0	0	0		-8.272936	1	1	0	0		1	0	1	1	1.592792	1	0.640000	1.650000	0.473068	0.070000	2.000000e-02	0.150000	0.070000	0.083432	0.070000	0	4.000000e-02	1.100000e-01
TACR3	6870	broad.mit.edu	37	4	104640521	104640521	+	Silent	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:104640521G>C	ENST00000304883.2	-	1	452	c.312C>G	c.(310-312)ctC>ctG	p.L104L		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3			51		Hepatocellular(203;0.217)			AGATGACGATGAGATTTCCCA	0.592000																								0							SO:0001819	synonymous_variant			ENST00000304883.2	1	1	hg19	CCDS3664.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	1	0	0	24	411	0	67		0	0	0	0	67	2		0	0	0	0	0	2	1	1.000000	24	405	0	62	2	0	0	0	0	0	0		-3.142967	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.140000	9.000000e-02	0.220000	0.150000	0.156213	0.140000	0	1.200000e-01	1.900000e-01
PAPSS1	9061	broad.mit.edu	37	4	108641321	108641321	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:108641321C>T	ENST00000265174.4	-	1	287	c.15G>A	c.(13-15)ggG>ggA	p.G5G	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1			16		Hepatocellular(203;0.217)			TGCACAGGCTCCCGGGGATCT	0.677000																								0							SO:0001819	synonymous_variant			ENST00000265174.4	1	1	hg19	CCDS3676.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2	1	0	0	115	321	0	61	1	1	47	42	0	61	2		0	0	0	0	0	2	1	1.000000	114	320	0	60	2	0	0	0	0	0	0		-6.166117	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.710000	6.000000e-01	0.830000	0.720000	0.723180	0.710000	0	6.600000e-01	7.800000e-01
HADH	3033	broad.mit.edu	37	4	108940775	108940775	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:108940775G>A	ENST00000309522.3	+	4	648	c.499G>A	c.(499-501)Gct>Act	p.A167T	HADH_ENST00000603302.1_Missense_Mutation_p.A167T|HADH_ENST00000454409.2_Missense_Mutation_p.A171T|HADH_ENST00000505878.1_Missense_Mutation_p.A171T|HADH_ENST00000403312.1_Missense_Mutation_p.A226T	NM_005327.4	NP_005318	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase			15		Hepatocellular(203;0.217)			AGACCGATTCGCTGGCCTCCA	0.498000																								0							SO:0001583	missense			ENST00000309522.3	1	1	hg19	CCDS3678.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.731123	0.89390	.	.	ENSG00000138796	ENST00000403312;ENST00000309522;ENST00000505878;ENST00000454409	T;T;T	0.76968	-1.06;-1.06;-1.06	5.37	4.53	0.55603	3-hydroxyacyl-CoA dehydrogenase, NAD binding (1);NAD(P)-binding domain (1);	0.153383	0.56097	D	0.000023	D	0.84370	0.5457	M	0.84846	2.72	0.38132	D	0.938196	P;D;P	0.56035	0.941;0.974;0.953	B;P;P	0.50708	0.419;0.648;0.555	D	0.87171	0.2221	10	0.42905	T	0.14	-16.0779	15.4449	0.75223	0.0:0.0:0.8599:0.1401	.	226;171;167	Q16836-2;E9PF18;Q16836	.;.;HCDH_HUMAN	T	167;167;171;171	ENSP00000312288:A167T;ENSP00000425952:A171T;ENSP00000395167:A171T	ENSP00000312288:A167T	A	+	1	0	HADH	109160224	1.000000	0.71417	0.073000	0.20177	0.941000	0.58515	6.776000	0.75023	1.244000	0.43870	0.655000	0.94253	GCT		TCGA-LB-A7SX-01A-11D-A33T-08	HADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254750.2	1	0	1	271	483	0	97	1	1	160	146	0	97	2		0	0	0	0	0	2	1	1.000000	267	475	0	95	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.970000	8.800000e-01	1.000000	1.000000	0.971177	0.970000	1	9.200000e-01	1
OTUD4	54726	broad.mit.edu	37	4	146073752	146073752	+	Silent	SNP	T	T	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:146073752T>A	ENST00000447906.2	-	11	1096	c.909A>T	c.(907-909)gcA>gcT	p.A303A	Y_RNA_ENST00000459374.1_RNA|OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Silent_p.A238A			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4			33	all_hematologic(180;0.151)				CTTGAACATCTGCATTCAAAA	0.363000																								0							SO:0001819	synonymous_variant			ENST00000447906.2	1	1	hg19																																																																																					TCGA-LB-A7SX-01A-11D-A33T-08	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	1	0	1	48	189	0	24	1	9.504278e-01	4	18	0	24	2		0	0	0	0	0	2	1	1.000000	48	186	0	24	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.550000	4.200000e-01	0.690000	0.550000	0.559086	0.550000	0	4.800000e-01	6.300000e-01
PDGFC	56034	broad.mit.edu	37	4	157689125	157689125	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:157689125G>A	ENST00000502773.1	-	5	1211	c.721C>T	c.(721-723)Cta>Tta	p.L241L	PDGFC_ENST00000541126.1_Silent_p.L78L|PDGFC_ENST00000542208.1_Silent_p.L86L|PDGFC_ENST00000422544.2_Silent_p.L241L|PDGFC_ENST00000504672.1_5'UTR	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C			19	all_hematologic(180;0.24)	Renal(120;0.0458)			TCCTCTGTTAGAAGGTTCAGA	0.383000																								0							SO:0001819	synonymous_variant			ENST00000502773.1	1	1	hg19	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	G	8.399	0.841530	0.16963	.	.	ENSG00000145431	ENST00000543489	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	T	0.74703	0.3751	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73830	-0.3859	5	0.40728	T	0.16	-7.46	18.7512	0.91816	0.0:0.0:1.0:0.0	.	.	.	.	F	155	.	ENSP00000446162:S155F	S	-	2	0	PDGFC	157908575	1.000000	0.71417	0.747000	0.31113	0.955000	0.61496	5.667000	0.68067	2.434000	0.82447	0.655000	0.94253	TCT		TCGA-LB-A7SX-01A-11D-A33T-08	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1	0	0	0	28	683	0	111	0	5.996003e-01	1	49	0	111	2		0	0	0	0	0	2	1	1.000000	28	676	0	109	2	0	0	0	0	0	0		-3.260869	1	1	0	0		1	0	1	1	2.052406	1	0.640000	1.650000	0.588665	0.100000	6.000000e-02	0.150000	0.110000	0.111134	0.100000	0	8.000000e-02	1.300000e-01
PCDH7	5099	broad.mit.edu	37	4	30724130	30724130	+	Missense_Mutation	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:30724130G>C	ENST00000361762.2	+	1	2094	c.1086G>C	c.(1084-1086)gaG>gaC	p.E362D	PCDH7_ENST00000543491.1_Missense_Mutation_p.E362D	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7			55					GCCTTGACGAGACGTCCGGCT	0.692000																								0							SO:0001583	missense			ENST00000361762.2	0	1	hg19	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.56|11.56	1.676129|1.676129	0.29783|0.29783	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.53640	.|0.61;0.61	5.69|5.69	2.56|2.56	0.30785|0.30785	.|Cadherin (5);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.51160|0.51160	0.1658|0.1658	L|L	0.48935|0.48935	1.535|1.535	0.45607|0.45607	D|D	0.998546|0.998546	.|P;P;P	.|0.45212	.|0.823;0.823;0.853	.|P;P;P	.|0.53102	.|0.595;0.595;0.718	T|T	0.43458|0.43458	-0.9390|-0.9390	5|9	.|0.35671	.|T	.|0.21	.|.	11.5739|11.5739	0.50850|0.50850	0.2318:0.0:0.7682:0.0|0.2318:0.0:0.7682:0.0	.|.	.|362;315;362	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	H|D	52|362;362;315	.|ENSP00000355243:E362D;ENSP00000441802:E362D	.|ENSP00000330302:E315D	D|E	+|+	1|3	0|2	PCDH7|PCDH7	30333228|30333228	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.003000|0.003000	0.03518|0.03518	3.394000|3.394000	0.52551|0.52551	0.742000|0.742000	0.32697|0.32697	-0.136000|-0.136000	0.14681|0.14681	GAC|GAG		TCGA-LB-A7SX-01A-11D-A33T-08	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	0	0	0	7	328	0	40	1	7.808060e-02	2	17	0	40	2		0	0	0	0	0	2	1	0.979825	7	323	0	40	2	0	0	0	0	0	0		-7.657125	1	1	0	0		1	0	1	1	1.983207	1	0.640000	1.650000	0.585635	0.050000	2.000000e-02	0.110000	0.060000	0.064318	0.050000	0	3.000000e-02	9.000000e-02
JAKMIP1	152789	broad.mit.edu	37	4	6107248	6107248	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:6107248G>A	ENST00000282924.5	-	3	1061	c.576C>T	c.(574-576)gaC>gaT	p.D192D	JAKMIP1_ENST00000410077.2_Intron|JAKMIP1_ENST00000409831.1_Silent_p.D192D|JAKMIP1_ENST00000409021.3_Silent_p.D192D|JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000409371.3_Intron	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1			42					GGTGCACCTCGTCTTGGTGCG	0.701000																								0							SO:0001819	synonymous_variant			ENST00000282924.5	1	1	hg19	CCDS3385.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	1	0	1	33	57	0	14	0	0	0	1	0	14	2		0	0	0	0	0	2	1	1.000000	33	56	0	13	2	0	0	0	0	0	0		-20.000000	1	1	121248	4	27	1	0	1	1	1.983207	1	0.640000	1.650000	0.585635	0.980000	7.300000e-01	1.000000	1.000000	0.943839	0.980000	1	8.500000e-01	1
ADAMTS3	9508	broad.mit.edu	37	4	73205309	73205309	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr4:73205309C>T	ENST00000286657.4	-	5	799	c.763G>A	c.(763-765)Gat>Aat	p.D255N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3			76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		ATATTGTAATCGTTTTCTCCC	0.498000													NSCLC(168;1941 2048 2918 13048 43078)											0							SO:0001583	missense			ENST00000286657.4	1	1	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109068	0.56398	.	.	ENSG00000156140	ENST00000286657	T	0.61274	0.12	5.31	5.31	0.75309	Metallopeptidase, catalytic domain (1);	0.059999	0.64402	D	0.000005	T	0.59128	0.2171	M	0.68593	2.085	0.80722	D	1	B	0.30542	0.284	B	0.28232	0.087	T	0.59836	-0.7379	10	0.48119	T	0.1	.	19.1722	0.93583	0.0:1.0:0.0:0.0	.	255	O15072	ATS3_HUMAN	N	255	ENSP00000286657:D255N	ENSP00000286657:D255N	D	-	1	0	ADAMTS3	73424173	0.998000	0.40836	0.992000	0.48379	0.181000	0.23173	3.879000	0.56138	2.763000	0.94921	0.563000	0.77884	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2	0	0	0	32	1107	0	189	0	0	0	1	0	189	2		0	0	0	0	0	2	1	1.000000	31	1098	0	188	2	0	0	0	0	0	0		-2.439103	0	1	0	0		1	0	1	1	2.033537	1	0.640000	1.650000	0.588665	0.070000	4.000000e-02	0.110000	0.080000	0.079041	0.070000	0	5.000000e-02	9.000000e-02
PCDHAC1	56135	broad.mit.edu	37	5	140308195	140308195	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr5:140308195C>T	ENST00000253807.2	+	1	1718	c.1718C>T	c.(1717-1719)tCt>tTt	p.S573F	PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.S573F|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1			65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GTGCCCCGCTCTGCCAGGACT	0.488000																								0							SO:0001583	missense			ENST00000253807.2	0	1	hg19	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	C	4.946	0.175719	0.09391	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.60920	0.15;0.15	5.95	1.95	0.26073	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.61400	0.2344	M	0.83483	2.645	0.22226	N	0.999273	B;B	0.31209	0.313;0.043	B;B	0.41236	0.351;0.047	T	0.59101	-0.7517	9	0.49607	T	0.09	.	2.6964	0.05136	0.2432:0.478:0.1188:0.1601	.	573;573	Q9H158;Q9H158-2	PCDC1_HUMAN;.	F	573	ENSP00000386356:S573F;ENSP00000253807:S573F	ENSP00000253807:S573F	S	+	2	0	PCDHAC1	140288379	0.000000	0.05858	1.000000	0.80357	0.993000	0.82548	0.405000	0.21015	0.376000	0.24707	0.563000	0.77884	TCT		TCGA-LB-A7SX-01A-11D-A33T-08	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	0	0	0	10	535	0	109		0	0	0	0	109	2		0	0	0	0	0	2	1	0.996841	10	532	0	107	2	0	0	0	0	0	0		-2.517518	1	1	0	0		1	0	1	1	1.643100	1	0.640000	1.650000	0.522293	0.040000	1.000000e-02	0.080000	0.040000	0.047301	0.040000	0	2.000000e-02	6.000000e-02
MRPS30	10884	broad.mit.edu	37	5	44815301	44815301	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr5:44815301C>T	ENST00000507110.1	+	5	1355	c.1317C>T	c.(1315-1317)aaC>aaT	p.N439N		NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30			20	Lung NSC(6;8.08e-07)				TGTTGGAAAACTGAAAAAGCA	0.294000																								0							SO:0001819	synonymous_variant			ENST00000507110.1	1	1	hg19	CCDS3951.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	0	0	0	9	277	0	32	1	8.857023e-01	4	117	0	32	2		0	0	0	0	0	2	1	0.994237	9	275	0	32	2	0	0	0	0	0	0		-10.146630	1	1	0	0		1	2	2	4	2.716313	1	0.640000	1.650000	0.702774	0.130000	5.000000e-02	1.000000	0.110000	0.316554	0.130000	0	9.000000e-02	1
ADAMTS16	170690	broad.mit.edu	37	5	5182355	5182355	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr5:5182355C>A	ENST00000274181.7	+	4	838	c.700C>A	c.(700-702)Cac>Aac	p.H234N	ADAMTS16_ENST00000511368.1_Missense_Mutation_p.H234N	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16			107					TCAACCCCTGCACAGCAGCGA	0.532000																								0							SO:0001583	missense			ENST00000274181.7	1	1	hg19	CCDS43299.1	.	.	.	.	.	.	.	.	.	.	C	8.922	0.961376	0.18583	.	.	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.61392	0.19;0.11	5.04	-2.03	0.07365	.	0.772006	0.11949	N	0.513896	T	0.41627	0.1167	L	0.45581	1.43	0.09310	N	1	B;B;B	0.17038	0.011;0.004;0.02	B;B;B	0.17098	0.011;0.009;0.017	T	0.29488	-1.0010	10	0.15952	T	0.53	.	5.9596	0.19293	0.3613:0.5011:0.0:0.1375	.	234;234;234	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	N	234	ENSP00000274181:H234N;ENSP00000421631:H234N	ENSP00000274181:H234N	H	+	1	0	ADAMTS16	5235355	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.111000	0.15458	-0.120000	0.11809	-0.188000	0.12872	CAC		TCGA-LB-A7SX-01A-11D-A33T-08	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	1	0	1	159	300	0	66		0	0	0	0	66	2		0	0	0	0	0	2	1	1.000000	159	299	0	65	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	1	2	3	2.629439	1	0.640000	1.650000	0.684432	0.990000	9.900000e-01	1.000000	1.000000	0.999983	0.990000	1	9.900000e-01	1
ZDHHC11	79844	broad.mit.edu	37	5	837564	837564	+	Silent	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr5:837564G>T	ENST00000283441.8	-	6	1199	c.816C>A	c.(814-816)ctC>ctA	p.L272L	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Silent_p.L272L	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11			21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)		GGTTATTAATGAGATACTCAA	0.493000																								0							SO:0001819	synonymous_variant			ENST00000283441.8	0	1	hg19	CCDS3857.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	0	0	0	17	943	0	103	0	5.238575e-03	0	6	0	103	2		0	0	0	0	0	2	1	0.999959	16	930	0	113	2	0	0	0	0	0	0		-2.448733	0	1	0	0		1	1	2	3	2.629439	1	0.640000	1.650000	0.684432	0.060000	2.000000e-02	1.000000	0.070000	0.289419	0.060000	0	4.000000e-02	1
POPDC3	64208	broad.mit.edu	37	6	105609437	105609437	+	Silent	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr6:105609437G>A	ENST00000254765.3	-	2	626	c.348C>T	c.(346-348)ttC>ttT	p.F116F	POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369120.2_RNA|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3			26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)			CCAGGGGCTGGAAAAGGGAGC	0.443000																								0							SO:0001819	synonymous_variant			ENST00000254765.3	1	1	hg19	CCDS5052.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	1	0	1	316	354	0	128	1	4.576972e-01	3	0	0	128	2		0	0	0	0	0	2	1	1.000000	314	351	0	127	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.626020	1	0.640000	1.650000	0.473068	0.970000	9.100000e-01	1.000000	1.000000	0.976485	0.970000	1	9.400000e-01	1
FAM184A	79632	broad.mit.edu	37	6	119285893	119285893	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr6:119285893G>A	ENST00000338891.7	-	16	3520	c.3077C>T	c.(3076-3078)aCt>aTt	p.T1026I	FAM184A_ENST00000521531.1_Intron|FAM184A_ENST00000368475.4_Intron|FAM184A_ENST00000352896.5_Missense_Mutation_p.T857I|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A			52					GTTGAAGTTAGTTTCTCGATT	0.303000																								0							SO:0001583	missense			ENST00000338891.7	1	1	hg19	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087818	0.76642	.	.	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368472	T;T;T	0.52057	2.35;2.29;0.68	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.64238	0.2580	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.60520	-0.7247	10	0.41790	T	0.15	-12.1337	19.9925	0.97371	0.0:0.0:1.0:0.0	.	857;1026	F8W8D6;Q8NB25	.;F184A_HUMAN	I	1026;857;87	ENSP00000342604:T1026I;ENSP00000326608:T857I;ENSP00000357457:T87I	ENSP00000342604:T1026I	T	-	2	0	FAM184A	119327592	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.655000	0.74392	2.721000	0.93114	0.655000	0.94253	ACT		TCGA-LB-A7SX-01A-11D-A33T-08	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	1	0	1	12	114	0	32	0	8.585599e-02	0	5	0	32	2		0	0	0	0	0	2	1	0.999233	12	113	0	32	2	0	0	0	0	0	0		-18.289750	1	1	0	0		1	0	1	1	1.626020	1	0.640000	1.650000	0.473068	0.200000	1.100000e-01	0.330000	0.200000	0.214934	0.200000	0	1.500000e-01	2.700000e-01
GRM1	2911	broad.mit.edu	37	6	146350993	146350993	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr6:146350993G>A	ENST00000282753.1	+	1	575	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	GRM1_ENST00000492807.2_Missense_Mutation_p.V114M|GRM1_ENST00000355289.4_Missense_Mutation_p.V114M|GRM1_ENST00000507907.1_Missense_Mutation_p.V114M|GRM1_ENST00000361719.2_Missense_Mutation_p.V114M|GRM1_ENST00000392299.2_Missense_Mutation_p.V114M			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1			126		Ovarian(120;0.0387)			GCACTCTTCCGTGGCTCTGGA	0.567000																								0							SO:0001583	missense			ENST00000282753.1	1	1	hg19	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.326441	0.81690	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.69	5.69	0.88448	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	T	0.71904	0.3395	L	0.49126	1.545	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.998;0.997	T	0.71593	-0.4546	10	0.54805	T	0.06	.	19.8011	0.96507	0.0:0.0:1.0:0.0	.	114;114;109;114	F8W805;Q13255;Q59HC2;Q13255-2	.;GRM1_HUMAN;.;.	M	114	ENSP00000354896:V114M;ENSP00000376119:V114M;ENSP00000424095:V114M;ENSP00000282753:V114M;ENSP00000347437:V114M;ENSP00000425599:V114M	ENSP00000282753:V114M	V	+	1	0	GRM1	146392686	1.000000	0.71417	0.978000	0.43139	0.966000	0.64601	9.869000	0.99810	2.679000	0.91253	0.561000	0.74099	GTG		TCGA-LB-A7SX-01A-11D-A33T-08	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	1	0	1	21	155	0	41	0	0	0	1	0	41	2		0	0	0	0	0	2	1	0.999998	20	153	0	40	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	1.615513	1	0.640000	1.650000	0.473068	0.250000	1.600000e-01	0.360000	0.250000	0.262215	0.250000	0	2.000000e-01	3.100000e-01
PRL	5617	broad.mit.edu	37	6	22290545	22290545	+	Missense_Mutation	SNP	C	C	T	rs139327343	byFrequency	TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr6:22290545C>T	ENST00000306482.1	-	4	868	c.350G>A	c.(349-351)cGa>cAa	p.R117Q	RP3-404K8.2_ENST00000561912.1_RNA	NM_000948.5|NM_001163558.2	NP_000939.1|NP_001157030.1	P01236	PRL_HUMAN	prolactin			16	Ovarian(93;0.163)				ATTCCAGGATCGCAATATGCT	0.423000																								0							SO:0001583	missense			ENST00000306482.1	1	1	hg19	CCDS4548.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.55	1.972820	0.34848	6.81E-4	0.0	ENSG00000172179	ENST00000306482;ENST00000438606	D	0.87650	-2.28	5.87	4.05	0.47172	Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.376195	0.34088	N	0.004279	T	0.68311	0.2987	L	0.42245	1.32	0.38772	D	0.954562	B;P	0.42556	0.148;0.783	B;B	0.34873	0.023;0.191	T	0.66468	-0.5916	10	0.26408	T	0.33	1.517	10.4581	0.44563	0.135:0.7953:0.0:0.0697	.	117;118	P01236;Q5I0G2	PRL_HUMAN;.	Q	117;86	ENSP00000302150:R117Q	ENSP00000302150:R117Q	R	-	2	0	PRL	22398524	0.993000	0.37304	0.907000	0.35723	0.318000	0.28184	2.575000	0.46025	0.887000	0.36136	0.655000	0.94253	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	PRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043327.1	1	0	1	162	172	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	162	172	0	49	2	0	0	0	0	0	0		-20.000000	1	1	121412	9	41	1	0	1	1	1.604606	1	0.640000	1.650000	0.470588	0.960000	8.800000e-01	1.000000	0.990000	0.965731	0.960000	1	9.300000e-01	1
HIST1H2AL	8332	broad.mit.edu	37	6	27833264	27833264	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr6:27833264C>T	ENST00000357320.2	+	1	231	c.132C>T	c.(130-132)gtC>gtT	p.V44V		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al			9					CTGAGCGGGTCGGGGCCGGCG	0.692000																								0							SO:0001819	synonymous_variant			ENST00000357320.2	1	1	hg19	CCDS4634.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	0	0	0	31	508	0	112	0	1.984773e-02	0	4	0	112	2		0	0	0	0	0	2	1	1.000000	32	506	0	108	2	0	0	0	0	0	0		-6.492383	1	1	121366	1	39	1	0	1	1	1.642223	1	0.640000	1.650000	0.473068	0.110000	8.000000e-02	0.170000	0.120000	0.126019	0.110000	0	9.000000e-02	1.500000e-01
RINT1	60561	broad.mit.edu	37	7	105182892	105182892	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:105182892G>A	ENST00000257700.2	+	4	542	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1			22					AAAAGAATTCGAAGTGCCTTA	0.328000																								0							SO:0001583	missense			ENST00000257700.2	1	1	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	G	2.986	-0.209338	0.06140	.	.	ENSG00000135249	ENST00000257700;ENST00000493041	T	0.20463	2.07	4.63	3.47	0.39725	.	0.315890	0.35179	N	0.003399	T	0.04497	0.0123	N	0.00268	-1.735	0.19300	N	0.99998	B	0.02656	0.0	B	0.01281	0.0	T	0.39057	-0.9632	10	0.09843	T	0.71	-1.5379	10.271	0.43483	0.9205:0.0:0.0795:0.0	.	104	Q6NUQ1	RINT1_HUMAN	Q	104;73	ENSP00000257700:R104Q	ENSP00000257700:R104Q	R	+	2	0	RINT1	104970128	1.000000	0.71417	0.986000	0.45419	0.841000	0.47740	4.133000	0.57983	0.606000	0.29965	-0.959000	0.02639	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	1	0	0	40	385	0	53	1	4.920891e-01	6	11	0	53	2		0	0	0	0	0	2	1	1.000000	39	383	0	53	2	0	0	0	0	0	0		-3.142702	1	1	0	0		1	2	2	4	2.375626	0	0.640000	1.650000	0.659607	0.310000	2.200000e-01	1.000000	0.310000	0.366626	0.310000	0	2.600000e-01	3.800000e-01
CASP2	835	broad.mit.edu	37	7	143002066	143002066	+	Missense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:143002066G>T	ENST00000310447.5	+	11	1502	c.1261G>T	c.(1261-1263)Gct>Tct	p.A421S	CASP2_ENST00000493642.1_3'UTR	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase			21	Melanoma(164;0.059)				GGAAGGTTATGCTCCTGGCAC	0.552000																								0							SO:0001583	missense			ENST00000310447.5	1	1	hg19	CCDS5879.1	.	.	.	.	.	.	.	.	.	.	G	33	5.219130	0.95104	.	.	ENSG00000106144	ENST00000310447	T	0.29142	1.58	5.27	5.27	0.74061	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.000000	0.85682	D	0.000000	T	0.32406	0.0828	N	0.11789	0.175	0.80722	D	1	D	0.59357	0.985	P	0.62560	0.904	T	0.03887	-1.0995	10	0.06494	T	0.89	.	18.9739	0.92728	0.0:0.0:1.0:0.0	.	421	P42575	CASP2_HUMAN	S	421	ENSP00000312664:A421S	ENSP00000312664:A421S	A	+	1	0	CASP2	142712188	1.000000	0.71417	0.963000	0.40424	0.944000	0.59088	9.394000	0.97261	2.478000	0.83669	0.650000	0.86243	GCT		TCGA-LB-A7SX-01A-11D-A33T-08	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	1	0	1	96	238	0	36	1	9.999999e-01	25	37	0	36	2		0	0	0	0	0	2	1	1.000000	95	235	0	36	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.375626	0	0.640000	1.650000	0.659607	0.950000	7.900000e-01	1.000000	1.000000	0.942577	0.950000	1	8.700000e-01	1
HDAC9	9734	broad.mit.edu	37	7	18788739	18788739	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:18788739C>A	ENST00000432645.2	+	13	2012	c.2012C>A	c.(2011-2013)aCt>aAt	p.T671N	HDAC9_ENST00000441542.2_Missense_Mutation_p.T674N|HDAC9_ENST00000401921.1_Missense_Mutation_p.T630N|HDAC9_ENST00000406451.4_Missense_Mutation_p.T671N	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9			82	all_lung(11;0.187)			Valproic Acid(DB00313)	CTGCAAGAAACTGGGCTGCTA	0.438000																								0							SO:0001583	missense			ENST00000432645.2	1	1	hg19	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.884382	0.51908	.	.	ENSG00000048052	ENST00000406451;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000341009	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	5.3	5.3	0.74995	Histone deacetylase domain (2);	0.000000	0.64402	D	0.000010	T	0.70894	0.3276	M	0.65975	2.015	0.80722	D	1	B;P;P;P;P;P;P	0.43885	0.001;0.82;0.64;0.64;0.69;0.64;0.69	B;B;B;B;B;B;B	0.41666	0.01;0.328;0.248;0.248;0.363;0.248;0.279	T	0.74973	-0.3481	10	0.56958	D	0.05	-19.3258	15.5062	0.75743	0.0:0.8616:0.1384:0.0	.	671;583;630;674;671;671;649	Q9UKV0-4;Q9UKV0-2;Q9UKV0-6;Q9UKV0-7;Q9UKV0;Q9UKV0-5;Q8N879	.;.;.;.;HDAC9_HUMAN;.;.	N	671;630;671;674;583	ENSP00000384657:T671N;ENSP00000383912:T630N;ENSP00000410337:T671N;ENSP00000408617:T674N	ENSP00000339165:T583N	T	+	2	0	HDAC9	18755264	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.797000	0.55514	2.756000	0.94617	0.563000	0.77884	ACT		TCGA-LB-A7SX-01A-11D-A33T-08	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1	1	0	1	34	100	0	15	0	0	0	1	0	15	2		0	0	0	0	0	2	1	1.000000	34	100	0	15	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.385000	0	0.640000	1.650000	0.659607	0.850000	6.100000e-01	1.000000	1.000000	0.851703	0.850000	1	7.200000e-01	1
GLI3	2737	broad.mit.edu	37	7	42018283	42018283	+	Nonsense_Mutation	SNP	G	G	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:42018283G>T	ENST00000395925.3	-	11	1646	c.1562C>A	c.(1561-1563)tCa>tAa	p.S521*	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3			112					CTGCTCTCTTGAGCAGTCCAG	0.453000									Pallister-Hall syndrome;Greig Cephalopolysyndactyly															0							SO:0001587	stop_gained	Familial Cancer Database	;	ENST00000395925.3	0	1	hg19	CCDS5465.1	.	.	.	.	.	.	.	.	.	.	G	41	8.584889	0.98872	.	.	ENSG00000106571	ENST00000395925	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1381	0.98040	0.0:0.0:1.0:0.0	.	.	.	.	X	521	.	ENSP00000379258:S521X	S	-	2	0	GLI3	41984808	1.000000	0.71417	0.965000	0.40720	0.998000	0.95712	7.817000	0.86213	2.763000	0.94921	0.650000	0.86243	TCA		TCGA-LB-A7SX-01A-11D-A33T-08	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	1	0	0	154	279	0	41	0	1.274913e-01	0	2	0	41	2		0	0	0	0	0	2	1	1.000000	154	275	0	41	2	0	0	0	0	0	0		-16.819040	1	1	0	0		1	1	2	3	2.343501	0	0.640000	1.650000	0.647887	0.990000	9.900000e-01	1.000000	1.000000	0.999243	0.990000	1	9.900000e-01	1
ABCA13	154664	broad.mit.edu	37	7	48431547	48431547	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:48431547C>T	ENST00000435803.1	+	38	11708	c.11684C>T	c.(11683-11685)aCt>aTt	p.T3895I		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13			270					CACCCTCCCACTTCTGGAACC	0.522000																								0							SO:0001583	missense			ENST00000435803.1	0	1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.749632	0.49257	.	.	ENSG00000179869	ENST00000435803	D	0.94330	-3.4	4.95	4.03	0.46877	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.178832	0.26016	U	0.026841	D	0.97018	0.9026	M	0.92412	3.305	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.74674	0.968;0.984	D	0.97391	0.9989	10	0.87932	D	0	.	12.1583	0.54089	0.0:0.7004:0.2996:0.0	.	1597;3895	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	I	3895	ENSP00000411096:T3895I	ENSP00000411096:T3895I	T	+	2	0	ABCA13	48402093	0.183000	0.23186	0.451000	0.26982	0.445000	0.32107	1.741000	0.38238	2.296000	0.77279	0.467000	0.42956	ACT		TCGA-LB-A7SX-01A-11D-A33T-08	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	0	0	0	5	196	0	22	0	0	0	1	0	22	2		0	0	0	0	0	2	1	0.938320	5	196	0	22	2	0	0	0	0	0	0		-7.417472	1	1	0	0		1	1	2	3	2.343501	0	0.640000	1.650000	0.647887	0.080000	2.000000e-02	1.000000	0.080000	0.144679	0.080000	0	5.000000e-02	1.400000e-01
PCLO	27445	broad.mit.edu	37	7	82585369	82585369	+	Missense_Mutation	SNP	C	C	T	rs75707968	by1000genomes	TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:82585369C>T	ENST00000333891.9	-	5	5237	c.4900G>A	c.(4900-4902)Gat>Aat	p.D1634N	PCLO_ENST00000423517.2_Missense_Mutation_p.D1634N	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein			259					AATGCTTCATCGTCTTCATCA	0.428000																								0							SO:0001583	missense			ENST00000333891.9	1	0	hg19	CCDS47630.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	12.57	1.979136	0.34942	0.00222	0.0	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20332	2.08;2.09	5.32	5.32	0.75619	.	.	.	.	.	T	0.26955	0.0660	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.65773	0.938;0.938	T	0.11131	-1.0600	9	0.87932	D	0	.	18.9962	0.92813	0.0:1.0:0.0:0.0	.	1634;1634	Q9Y6V0-5;Q9Y6V0-6	.;.	N	1565;1634;1634	ENSP00000334319:D1634N;ENSP00000388393:D1634N	ENSP00000334319:D1634N	D	-	1	0	PCLO	82423305	1.000000	0.71417	0.638000	0.29380	0.917000	0.54804	5.333000	0.65917	2.483000	0.83821	0.655000	0.94253	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	1	0	1	207	797	0	169		0	0	0	0	169	2		0	0	0	0	0	2	1	1.000000	206	792	0	169	2	0	0	0	0	0	0		-3.298910	1	1	120956	40	53	1	2	2	4	2.375626	0	0.640000	1.650000	0.659607	0.680000	5.900000e-01	1.000000	0.680000	0.706043	0.680000	0	6.300000e-01	7.400000e-01
C7orf43	55262	broad.mit.edu	37	7	99755385	99755385	+	Splice_Site	SNP	T	T	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr7:99755385T>A	ENST00000316937.3	-	3	693	c.508A>T	c.(508-510)Att>Ttt	p.I170F	C7orf43_ENST00000419841.1_5'Flank|C7orf43_ENST00000498638.1_5'Flank|C7orf43_ENST00000457641.1_5'UTR|MIR4658_ENST00000584344.1_RNA|C7orf43_ENST00000394035.2_5'Flank	NM_018275.3	NP_060745.3	Q8WVR3	CG043_HUMAN	chromosome 7 open reading frame 43			10	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				GTCACTACAATCTGTCAAGAG	0.527000											OREG0018198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)												0							SO:0001630	splice_region_variant			ENST00000316937.3	1	0	hg19	CCDS5687.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.035638|4.035638	0.75617|0.75617	.|.	.|.	ENSG00000146826|ENSG00000146826	ENST00000456769|ENST00000316937	.|T	.|0.33216	.|1.42	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.072818	.|0.56097	.|D	.|0.000030	T|T	0.31544|0.31544	0.0800|0.0800	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D	.|0.58268	.|0.982	.|P	.|0.51866	.|0.682	T|T	0.10730|0.10730	-1.0617|-1.0617	5|10	.|0.72032	.|D	.|0.01	-9.3115|-9.3115	14.1012|14.1012	0.65056|0.65056	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|170	.|Q8WVR3	.|CG043_HUMAN	V|F	75|170	.|ENSP00000324741:I170F	.|ENSP00000324741:I170F	D|I	-|-	2|1	0|0	C7orf43|C7orf43	99593321|99593321	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	3.517000|3.517000	0.53443|0.53443	2.217000|2.217000	0.71921|0.71921	0.379000|0.379000	0.24179|0.24179	GAT|ATT		TCGA-LB-A7SX-01A-11D-A33T-08	C7orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337395.2	1	0	1	173	569	0	108	1	9.999998e-01	23	51	0	108	2		0	0	0	0	0	2	1	1.000000	170	562	0	108	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	2	2	4	2.375626	0	0.640000	1.650000	0.659607	0.770000	6.600000e-01	1.000000	0.770000	0.788956	0.770000	0	7.100000e-01	8.400000e-01
FBXO43	286151	broad.mit.edu	37	8	101153416	101153416	+	Nonsense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:101153416G>A	ENST00000428847.2	-	2	1382	c.1066C>T	c.(1066-1068)Caa>Taa	p.Q356*		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43			31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)		AGTAGTTCTTGAAAAGAACCC	0.463000																								0							SO:0001587	stop_gained			ENST00000428847.2	0	1	hg19	CCDS47904.1	.	.	.	.	.	.	.	.	.	.	G	37	6.453024	0.97581	.	.	ENSG00000156509	ENST00000428847	.	.	.	5.57	4.68	0.58851	.	0.342235	0.34314	N	0.004079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-1.0291	16.6488	0.85183	0.0:0.13:0.87:0.0	.	.	.	.	X	356	.	ENSP00000403293:Q356X	Q	-	1	0	FBXO43	101222592	1.000000	0.71417	0.989000	0.46669	0.445000	0.32107	7.277000	0.78572	1.444000	0.47605	0.655000	0.94253	CAA		TCGA-LB-A7SX-01A-11D-A33T-08	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	1	0	1	156	440	0	99	0	1.710510e-01	0	3	0	99	2		0	0	0	0	0	2	1	1.000000	154	436	0	98	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.110200	1	0.640000	1.650000	0.608696	0.740000	6.400000e-01	0.850000	0.750000	0.753995	0.740000	0	6.900000e-01	8.000000e-01
TRMT12	55039	broad.mit.edu	37	8	125463295	125463295	+	Missense_Mutation	SNP	T	T	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:125463295T>G	ENST00000328599.3	+	1	248	c.127T>G	c.(127-129)Ttt>Gtt	p.F43V	TRMT12_ENST00000521443.1_3'UTR	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)			15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)		GCAGAAACTCTTTGATACACA	0.557000																								0							SO:0001583	missense			ENST00000328599.3	0	1	hg19	CCDS6349.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.980463	0.34942	.	.	ENSG00000183665	ENST00000328599	T	0.40225	1.04	5.14	-3.63	0.04529	.	0.071623	0.56097	D	0.000028	T	0.17450	0.0419	N	0.08118	0	0.24462	N	0.994434	B	0.12630	0.006	B	0.06405	0.002	T	0.06303	-1.0834	10	0.66056	D	0.02	-6.7128	6.8676	0.24102	0.0:0.362:0.1226:0.5154	.	43	Q53H54	TYW2_HUMAN	V	43	ENSP00000329858:F43V	ENSP00000329858:F43V	F	+	1	0	TRMT12	125532476	0.057000	0.20700	0.842000	0.33263	0.587000	0.36485	-0.847000	0.04331	-0.876000	0.04017	-0.375000	0.07067	TTT		TCGA-LB-A7SX-01A-11D-A33T-08	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	0	0	0	6	353	0	59	0	4.571259e-02	0	17	0	59	2		0	0	0	0	0	2	1	0.964693	6	351	0	59	2	0	0	0	0	0	0		-6.606910	1	1	0	0		1	0	1	1	2.110200	1	0.640000	1.650000	0.608696	0.040000	1.000000e-02	0.100000	0.050000	0.055655	0.040000	0	2.000000e-02	8.000000e-02
GRINA	2907	broad.mit.edu	37	8	145066090	145066090	+	Silent	SNP	G	G	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			G	C	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:145066090G>C	ENST00000313269.5	+	4	815	c.537G>C	c.(535-537)acG>acC	p.T179T	GRINA_ENST00000395068.4_Silent_p.T179T	NM_000837.1	NP_000828.1	Q7Z429	LFG1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding)			9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		CCCTGTCCACGGTGTCTGTGT	0.572000																								0							SO:0001819	synonymous_variant			ENST00000313269.5	1	1	hg19	CCDS34961.1	.	.	.	.	.	.	.	.	.	.	G	9.085	1.000167	0.19121	.	.	ENSG00000178719	ENST00000534791;ENST00000527194	.	.	.	4.7	-4.37	0.03633	.	.	.	.	.	T	0.38506	0.1043	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36817	-0.9732	4	.	.	.	-16.3463	2.2111	0.03948	0.1049:0.2036:0.2433:0.4482	.	.	.	.	R	103;35	.	.	G	+	1	0	GRINA	145138078	0.001000	0.12720	0.911000	0.35937	0.983000	0.72400	-1.702000	0.01901	-0.701000	0.05063	0.650000	0.86243	GGT		TCGA-LB-A7SX-01A-11D-A33T-08	GRINA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384048.1	1	0	1	194	690	0	136	1	1	83	276	0	136	2		0	0	0	0	0	2	1	1.000000	193	684	0	135	2	0	0	0	0	0	0		-3.741634	1	1	0	0		1	0	1	1	2.087693	1	0.640000	1.650000	0.601770	0.610000	5.300000e-01	0.690000	0.620000	0.621291	0.610000	0	5.700000e-01	6.600000e-01
PRKDC	5591	broad.mit.edu	37	8	48691183	48691183	+	Missense_Mutation	SNP	A	A	C			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08			A	C	A	A		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:48691183A>C	ENST00000314191.2	-	84	11743	c.11687T>G	c.(11686-11688)tTc>tGc	p.F3896C	PRKDC_ENST00000338368.3_Missense_Mutation_p.F3865C|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide			147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)		Caffeine(DB00201)	GAGCGCCAGGAAAGCCTCAGG	0.562000								Non-homologous end-joining					Esophageal Squamous(79;1091 1253 12329 31680 40677)											0							SO:0001583	missense			ENST00000314191.2	1	1	hg19		.	.	.	.	.	.	.	.	.	.	A	18.53	3.644011	0.67244	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	D;D	0.83250	-1.7;-1.7	5.52	5.52	0.82312	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.92838	0.7722	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.987	D	0.94371	0.7596	10	0.87932	D	0	.	15.6454	0.77046	1.0:0.0:0.0:0.0	.	3865;3897	E7EUY0;P78527	.;PRKDC_HUMAN	C	3896;3865	ENSP00000313420:F3896C;ENSP00000345182:F3865C	ENSP00000313420:F3896C	F	-	2	0	PRKDC	48853736	1.000000	0.71417	1.000000	0.80357	0.140000	0.21249	8.843000	0.92142	2.084000	0.62774	0.533000	0.62120	TTC		TCGA-LB-A7SX-01A-11D-A33T-08	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		0	0	1	27	110	0	23	1	1	21	125	0	23	2		0	0	0	0	0	2	1	1.000000	27	110	0	23	2	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.111336	1	0.640000	1.650000	0.608696	0.560000	3.900000e-01	0.760000	0.560000	0.576437	0.560000	0	4.700000e-01	6.700000e-01
EFCAB1	79645	broad.mit.edu	37	8	49643125	49643125	+	Missense_Mutation	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:49643125C>A	ENST00000262103.3	-	3	373	c.293G>T	c.(292-294)cGa>cTa	p.R98L	EFCAB1_ENST00000521002.1_Intron|EFCAB1_ENST00000523092.1_Missense_Mutation_p.R46L|EFCAB1_ENST00000433756.1_Missense_Mutation_p.R46L	NM_024593.3	NP_078869.1	Q9HAE3	EFCB1_HUMAN	EF-hand calcium binding domain 1			14		all_epithelial(80;0.0134)|Lung NSC(129;0.0207)|all_lung(136;0.0464)			CAAAGATCCTCGAAGAAACAG	0.343000																								0							SO:0001583	missense			ENST00000262103.3	0	1	hg19	CCDS6145.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489315	0.84962	.	.	ENSG00000034239	ENST00000433756;ENST00000262103;ENST00000450553;ENST00000523092	T;T;T	0.68025	-0.3;-0.29;-0.3	4.44	4.44	0.53790	EF-hand-like domain (1);	0.060216	0.64402	D	0.000002	D	0.84638	0.5516	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.962	D	0.88273	0.2931	10	0.87932	D	0	.	14.9317	0.70919	0.0:1.0:0.0:0.0	.	46;98	Q9HAE3-2;Q9HAE3	.;EFCB1_HUMAN	L	46;98;98;46	ENSP00000400873:R46L;ENSP00000262103:R98L;ENSP00000430765:R46L	ENSP00000262103:R98L	R	-	2	0	EFCAB1	49805678	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	6.789000	0.75110	2.441000	0.82636	0.563000	0.77884	CGA		TCGA-LB-A7SX-01A-11D-A33T-08	EFCAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377778.1	1	0	1	21	138	0	20		0	0	0	0	20	2		0	0	0	0	0	2	1	0.999998	21	138	0	20	2	0	0	0	0	0	0		-3.082581	1	1	0	0		1	0	1	1	2.111336	1	0.640000	1.650000	0.608696	0.380000	2.400000e-01	0.540000	0.380000	0.391279	0.380000	0	3.000000e-01	4.700000e-01
DCAF4L2	138009	broad.mit.edu	37	8	88885210	88885210	+	Silent	SNP	C	C	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:88885210C>A	ENST00000319675.3	-	1	1086	c.990G>T	c.(988-990)gcG>gcT	p.A330A		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2			83					GGCCCACGGCCGCCACGACTC	0.567000																								0							SO:0001819	synonymous_variant			ENST00000319675.3	1	1	hg19	CCDS6245.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	0	0	0	12	411	0	52		0	0	0	0	52	2		0	0	0	0	0	2	1	0.999037	11	404	0	52	2	0	0	0	0	0	0		-3.324949	1	1	0	0		1	0	1	1	2.111336	1	0.640000	1.650000	0.608696	0.080000	3.000000e-02	0.140000	0.080000	0.087813	0.080000	0	5.000000e-02	1.100000e-01
KIAA1429	25962	broad.mit.edu	37	8	95538657	95538657	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr8:95538657C>T	ENST00000297591.5	-	8	1890	c.1815G>A	c.(1813-1815)gtG>gtA	p.V605V	KIAA1429_ENST00000421249.2_Silent_p.V605V|KIAA1429_ENST00000437199.1_Silent_p.V605V	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429			66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)		TAGAAGCTTCCACCTCATTTT	0.383000																								0							SO:0001819	synonymous_variant			ENST00000297591.5	1	1	hg19	CCDS34923.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	1	0	0	38	701	0	105	0	1.861928e-01	0	15	0	105	2		0	0	0	0	0	2	1	1.000000	38	695	0	105	2	0	0	0	0	0	0		-2.878750	1	1	0	0		1	0	1	1	2.110200	1	0.640000	1.650000	0.608696	0.140000	1.000000e-01	0.200000	0.150000	0.151189	0.140000	0	1.200000e-01	1.700000e-01
OR13C2	392376	broad.mit.edu	37	9	107367328	107367328	+	Missense_Mutation	SNP	T	T	C	rs74954118		TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr9:107367328T>C	ENST00000542196.1	-	1	623	c.581A>G	c.(580-582)gAc>gGc	p.D194G		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2			22					GAACTCATTGTCTGAGATGTC	0.388000																								0							SO:0001583	missense			ENST00000542196.1	1	1	hg19	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	T	5.601	0.295593	0.10622	.	.	ENSG00000257019	ENST00000542196	T	0.00076	8.76	3.52	-3.12	0.05282	GPCR, rhodopsin-like superfamily (1);	0.807899	0.10032	N	0.724612	T	0.00073	0.0002	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01337	-1.1381	10	0.26408	T	0.33	.	3.4954	0.07653	0.4312:0.2306:0.0:0.3382	.	194	Q8NGS9	O13C2_HUMAN	G	194	ENSP00000438815:D194G	ENSP00000438815:D194G	D	-	2	0	OR13C2	106407149	0.000000	0.05858	0.006000	0.13384	0.702000	0.40608	-0.856000	0.04290	-0.430000	0.07318	-0.415000	0.06103	GAC		TCGA-LB-A7SX-01A-11D-A33T-08	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	0	0	0	18	569	0	110		0	0	0	0	110	2		0	0	0	0	0	2	1	0.999981	17	567	0	110	2	0	0	0	0	0	0		-3.314926	1	1	0	0		1	0	1	1	1.683794	1	0.640000	1.650000	0.494382	0.060000	3.000000e-02	0.100000	0.070000	0.071663	0.060000	0	4.000000e-02	9.000000e-02
PTPRD	5789	broad.mit.edu	37	9	8341947	8341947	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chr9:8341947C>T	ENST00000381196.4	-	37	5236	c.4693G>A	c.(4693-4695)Gtc>Atc	p.V1565I	PTPRD_ENST00000355233.5_Missense_Mutation_p.V1159I|PTPRD_ENST00000360074.4_Missense_Mutation_p.V1552I|PTPRD_ENST00000358503.5_Missense_Mutation_p.V1543I|PTPRD_ENST00000356435.5_Missense_Mutation_p.V1565I|PTPRD_ENST00000537002.1_Missense_Mutation_p.V1155I|PTPRD_ENST00000397606.3_Missense_Mutation_p.V1158I|PTPRD_ENST00000397617.3_Missense_Mutation_p.V1158I|PTPRD_ENST00000540109.1_Missense_Mutation_p.V1565I|PTPRD_ENST00000397611.3_Missense_Mutation_p.V1155I|PTPRD_ENST00000486161.1_Missense_Mutation_p.V1158I	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	p.V1565I(1)		168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)			GCATCTATGACGATGAAGCAA	0.358000										TSP Lung(15;0.13)														1	Substitution - Missense(1)						SO:0001583	missense			ENST00000381196.4	1	1	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.619525	0.46736	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	6.07	5.17	0.71159	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	M	0.92367	3.3	0.58432	D	0.999999	B;B;B;B;D;B;D;P;D	0.89917	0.137;0.137;0.137;0.137;0.979;0.113;1.0;0.918;1.0	B;B;B;B;P;B;D;B;D	0.74348	0.047;0.047;0.047;0.047;0.532;0.028;0.983;0.38;0.981	T	0.75895	-0.3156	9	.	.	.	.	16.7686	0.85531	0.1302:0.8698:0.0:0.0	.	1158;1149;1158;1159;1155;1155;1552;1565;1565	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	I	1565;1565;1552;1543;1159;1158;1155;1155;1036;1565;1158;1158	ENSP00000370593:V1565I;ENSP00000348812:V1565I;ENSP00000353187:V1552I;ENSP00000351293:V1543I;ENSP00000347373:V1159I;ENSP00000380741:V1158I;ENSP00000380735:V1155I;ENSP00000440515:V1155I;ENSP00000438164:V1565I;ENSP00000417093:V1158I;ENSP00000380731:V1158I	.	V	-	1	0	PTPRD	8331947	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	7.445000	0.80570	1.559000	0.49555	-0.181000	0.13052	GTC		TCGA-LB-A7SX-01A-11D-A33T-08	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3	0	0	0	10	269	0	58		0	0	0	0	58	2		0	0	0	0	0	2	1	0.996738	10	264	0	56	2	0	0	0	0	0	0		-11.270790	1	1	0	0		1	0	1	1	1.617199	1	0.640000	1.650000	0.475524	0.070000	3.000000e-02	0.130000	0.080000	0.083637	0.070000	0	5.000000e-02	1.100000e-01
TBC1D8B	54885	broad.mit.edu	37	X	106111641	106111641	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:106111641C>T	ENST00000357242.5	+	18	2921	c.2747C>T	c.(2746-2748)tCt>tTt	p.S916F	TBC1D8B_ENST00000276175.3_Missense_Mutation_p.S910F	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)			47					GAAGTGAAATCTAAGGATGCT	0.343000																								0							SO:0001583	missense			ENST00000357242.5	1	1	hg19	CCDS14522.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.514460	0.27123	.	.	ENSG00000133138	ENST00000357242;ENST00000276175;ENST00000394972	T;T	0.08720	3.06;3.06	5.88	2.91	0.33838	EF-hand-like domain (1);	0.641843	0.14963	N	0.288267	T	0.07818	0.0196	L	0.59436	1.845	0.25619	N	0.986428	B	0.15473	0.013	B	0.17979	0.02	T	0.47058	-0.9146	10	0.09338	T	0.73	1.5005	5.2383	0.15458	0.1503:0.6334:0.1307:0.0856	.	916	Q0IIM8	TBC8B_HUMAN	F	916;910;178	ENSP00000349781:S916F;ENSP00000276175:S910F	ENSP00000276175:S910F	S	+	2	0	TBC1D8B	105998297	0.551000	0.26497	0.029000	0.17559	0.958000	0.62258	1.060000	0.30530	0.140000	0.18849	0.600000	0.82982	TCT		TCGA-LB-A7SX-01A-11D-A33T-08	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	0	0	0	11	258	0	47	1	7.260425e-02	3	7	0	47	2		0	0	0	0	0	2	1	0.998397	11	257	0	47	2	0	0	0	0	0	0		-12.409540	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.120000	6.000000e-02	0.220000	0.130000	0.138071	0.120000	0	9.000000e-02	1.800000e-01
RGAG1	57529	broad.mit.edu	37	X	109697313	109697313	+	Silent	SNP	A	A	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:109697313A>G	ENST00000465301.2	+	3	3714	c.3468A>G	c.(3466-3468)gaA>gaG	p.E1156E	RGAG1_ENST00000540313.1_Silent_p.E1156E	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1			73					AAGAGCAGGAAGCAGCCCGGG	0.512000																								0							SO:0001819	synonymous_variant			ENST00000465301.2	1	1	hg19	CCDS14552.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	1	0	1	47	390	0	94	0	0	0	1	0	94	2		0	0	0	0	0	2	1	1.000000	46	386	0	92	2	0	0	0	0	0	0		-16.566330	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.330000	2.400000e-01	0.430000	0.340000	0.341234	0.330000	0	2.800000e-01	3.900000e-01
IL9R	3581	broad.mit.edu	37	X	155239804	155239804	+	Missense_Mutation	SNP	C	C	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:155239804C>G	ENST00000244174.5	+	9	1475	c.1296C>G	c.(1294-1296)agC>agG	p.S432R	IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000424344.3_Missense_Mutation_p.S411R|IL9R_ENST00000540897.1_3'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor			23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				gcaggagcagcagcagcagca	0.627000																								0							SO:0001583	missense			ENST00000244174.5	0	1	hg19	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	c	9.402	1.078258	0.20227	.	.	ENSG00000124334	ENST00000244174;ENST00000424344	T;T	0.10860	2.83;2.83	0.195	0.195	0.15151	.	3.852910	0.00870	N	0.002015	T	0.14356	0.0347	.	.	.	0.09310	N	1	P	0.42518	0.782	P	0.46110	0.504	T	0.20806	-1.0264	8	0.48119	T	0.1	-15.0951	.	.	.	.	432	Q01113	IL9R_HUMAN	R	432;411	ENSP00000244174:S432R;ENSP00000388918:S411R	ENSP00000244174:S432R	S	+	3	2	IL9R	154892998	0.001000	0.12720	0.005000	0.12908	0.005000	0.04900	-0.363000	0.07593	0.283000	0.22279	0.287000	0.19450	AGC		TCGA-LB-A7SX-01A-11D-A33T-08	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	0	0	0	5	79	0	14		0	0	0	0	14	2		0	0	0	0	0	2	1	0.937548	5	78	0	12	2	0	0	0	0	0	0		-2.451345	0	1	115670	13	29	1	0	1	1			0.640000	1.650000	0.640000	0.200000	7.000000e-02	0.390000	0.180000	0.216565	0.200000	0	1.200000e-01	3.000000e-01
ZNF645	158506	broad.mit.edu	37	X	22292031	22292031	+	Missense_Mutation	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:22292031C>T	ENST00000323684.1	+	1	967	c.923C>T	c.(922-924)tCg>tTg	p.S308L		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645			27					ACTCCTAACTCGGTTCGTAGC	0.448000																								0							SO:0001583	missense			ENST00000323684.1	1	1	hg19	CCDS14205.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.552333	0.00918	.	.	ENSG00000175809	ENST00000323684	T	0.30182	1.54	2.42	-1.52	0.08637	.	0.974552	0.08262	N	0.972933	T	0.07773	0.0195	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34800	-0.9814	10	0.07030	T	0.85	.	6.635	0.22877	0.0:0.4115:0.0:0.5885	.	308	Q8N7E2	ZN645_HUMAN	L	308	ENSP00000323348:S308L	ENSP00000323348:S308L	S	+	2	0	ZNF645	22201952	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	2.686000	0.46968	-0.498000	0.06632	-0.366000	0.07423	TCG		TCGA-LB-A7SX-01A-11D-A33T-08	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	0	0	0	26	632	0	93		0	0	0	0	93	2		0	0	0	0	0	2	1	1.000000	26	628	0	91	2	0	0	0	0	0	0		-3.067490	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.120000	7.000000e-02	0.180000	0.120000	0.127714	0.120000	0	9.000000e-02	1.500000e-01
MAGEB4	4115	broad.mit.edu	37	X	30260943	30260943	+	Missense_Mutation	SNP	G	G	A			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:30260943G>A	ENST00000378982.2	+	1	887	c.691G>A	c.(691-693)Gat>Aat	p.D231N	MAGEB1_ENST00000378981.3_5'Flank|MAGEB1_ENST00000397550.1_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4			27					GGGGATCTATGATGGAAAGAG	0.473000																								0							SO:0001583	missense			ENST00000378982.2	1	1	hg19	CCDS14221.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209960	0.39003	.	.	ENSG00000120289	ENST00000378982	T	0.05025	3.51	3.31	1.44	0.22558	.	0.365804	0.22917	U	0.054080	T	0.22282	0.0537	M	0.88181	2.935	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05632	-1.0873	10	0.48119	T	0.1	.	3.927	0.09269	0.1458:0.2453:0.609:0.0	.	231	O15481	MAGB4_HUMAN	N	231	ENSP00000368266:D231N	ENSP00000368266:D231N	D	+	1	0	MAGEB4	30170864	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.003000	0.12901	0.252000	0.21531	-0.192000	0.12808	GAT		TCGA-LB-A7SX-01A-11D-A33T-08	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	0	0	0	12	440	0	62		0	0	0	0	62	2		0	0	0	0	0	2	1	0.999078	12	435	0	62	2	0	0	0	0	0	0		-3.362688	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.080000	4.000000e-02	0.140000	0.080000	0.089354	0.080000	0	5.000000e-02	1.100000e-01
SHROOM4	57477	broad.mit.edu	37	X	50377159	50377159	+	Silent	SNP	A	A	G			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:50377159A>G	ENST00000289292.7	-	4	2197	c.1914T>C	c.(1912-1914)tcT>tcC	p.S638S	SHROOM4_ENST00000460112.3_Silent_p.S522S|SHROOM4_ENST00000376020.2_Silent_p.S638S			Q9ULL8	SHRM4_HUMAN	shroom family member 4			52	Ovarian(276;0.236)				AAGATAGAAGAGATGTGTTAG	0.522000																								0							SO:0001819	synonymous_variant			ENST00000289292.7	1	1	hg19	CCDS35277.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	1	0	1	44	368	0	58	0	1.727114e-01	0	7	0	58	2		0	0	0	0	0	2	1	1.000000	42	366	0	58	2	0	0	0	0	0	0		-15.636670	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.330000	2.400000e-01	0.430000	0.340000	0.339198	0.330000	0	2.800000e-01	3.900000e-01
TRO	7216	broad.mit.edu	37	X	54956406	54956406	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:54956406C>T	ENST00000173898.7	+	12	3361	c.3249C>T	c.(3247-3249)gtC>gtT	p.V1083V	TRO_ENST00000420798.2_Silent_p.V614V|TRO_ENST00000375022.4_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Silent_p.V686V|TRO_ENST00000319167.8_Intron|SNORA11_ENST00000408823.1_RNA	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin			37					GTGGTGCTGTCAGCACCAGTG	0.592000																								0							SO:0001819	synonymous_variant			ENST00000173898.7	1	1	hg19	CCDS43959.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	0	0	0	10	261	0	58		0	0	0	0	58	2		0	0	0	0	0	2	1	0.996917	9	260	0	58	2	0	0	0	0	0	0		-11.431290	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.110000	5.000000e-02	0.200000	0.120000	0.125638	0.110000	0	8.000000e-02	1.600000e-01
HDAC8	55869	broad.mit.edu	37	X	71788701	71788701	+	Silent	SNP	C	C	T			TCGA-LB-A7SX-01A-11D-A33T-08	TCGA-LB-A7SX-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	a4b53f23-f5e7-431d-b4f7-05291a2a2817	1812ab16-427e-4d05-896f-58697b0f3805	g.chrX:71788701C>T	ENST00000373573.3	-	3	539	c.198G>A	c.(196-198)gaG>gaA	p.E66E	HDAC8_ENST00000373561.4_Silent_p.E66E|HDAC8_ENST00000373583.1_Intron|HDAC8_ENST00000439122.2_Silent_p.E66E|HDAC8_ENST00000373556.3_Silent_p.E66E|HDAC8_ENST00000478743.1_5'UTR|HDAC8_ENST00000429103.2_5'UTR|HDAC8_ENST00000373571.1_Silent_p.E66E|HDAC8_ENST00000373559.4_Intron|HDAC8_ENST00000373589.4_Intron|HDAC8_ENST00000373560.2_Silent_p.E66E|HDAC8_ENST00000373554.1_Silent_p.E66E	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8			10	Renal(35;0.156)			Vorinostat(DB02546)	AGGTGGCCATCTCCTCCATGG	0.483000																								0							SO:0001819	synonymous_variant			ENST00000373573.3	0	1	hg19	CCDS14420.1																																																																																				TCGA-LB-A7SX-01A-11D-A33T-08	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	0	0	0	5	145	0	31	1	1.099400e-01	4	10	0	31	2		0	0	0	0	0	2	1	0.938608	5	145	0	31	2	0	0	0	0	0	0		-8.322308	1	1	0	0		1	0	1	1			0.640000	1.650000	0.640000	0.110000	3.000000e-02	0.230000	0.100000	0.122880	0.110000	0	6.000000e-02	1.700000e-01
