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
C16orf72	29035	broad.mit.edu	37	16	9210640	9210640	+	Frame_Shift_Del	DEL	T	T	-			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr16:9210640delT	ENST00000327827.7	+	4	1096	c.699delT	c.(697-699)gatfs	p.D233fs		NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72			8					ATGATGTCGATTTGAACACTT	0.478000																								0							SO:0001589	frameshift_variant			ENST00000327827.7	1	0	hg19	CCDS10538.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	1	0	0	85	845	0	87	1	9.758052e-01	2	58	0	87	2	0	0	0	0	0	0		1	1.000000	112	838	1	87	32	0	0	0	0	0	0		-20.000000	1	1	0	0		1	0	1	1	2.024092	0	0.150000	1.820000	0.146158	0.990000	0.970000	1.000000	1.000000	0.998483	0.990000	1	0.990000	1.000000
ANXA11	311	broad.mit.edu	37	10	81930573	81930573	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr10:81930573C>A	ENST00000438331.1	-	5	636	c.154G>T	c.(154-156)Gac>Tac	p.D52Y	ANXA11_ENST00000372231.3_Missense_Mutation_p.D52Y|ANXA11_ENST00000463657.1_5'Flank|ANXA11_ENST00000422982.3_Missense_Mutation_p.D52Y|ANXA11_ENST00000535999.1_Missense_Mutation_p.D52Y|ANXA11_ENST00000360615.4_Missense_Mutation_p.D52Y|ANXA11_ENST00000537102.1_Missense_Mutation_p.D19Y|ANXA11_ENST00000265447.4_Missense_Mutation_p.D52Y	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11			17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)		GAGAGATAGTCCTGGTTGAAC	0.652000																								0							SO:0001583	missense			ENST00000438331.1	1	1	hg19	CCDS7364.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.29|12.29	1.893491|1.893491	0.33442|0.33442	.|.	.|.	ENSG00000122359|ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000537102;ENST00000445524;ENST00000437799|ENST00000424188	T;T;T;T;T;T;T|.	0.02140|.	4.5;4.5;4.5;4.5;4.5;4.5;4.43|.	4.69|4.69	3.77|3.77	0.43336|0.43336	.|.	1.397770|.	0.04356|.	N|.	0.356611|.	T|T	0.38612|0.38612	0.1047|0.1047	L|L	0.36672|0.36672	1.1|1.1	0.27665|0.27665	N|N	0.946935|0.946935	D;P;P|.	0.58970|.	0.984;0.826;0.826|.	P;B;B|.	0.54372|.	0.75;0.367;0.367|.	T|T	0.31971|0.31971	-0.9924|-0.9924	10|6	0.52906|0.87932	T|D	0.07|0	.|.	7.2398|7.2398	0.26090|0.26090	0.0:0.7252:0.1762:0.0986|0.0:0.7252:0.1762:0.0986	.|.	152;52;52|.	B7Z6L0;Q5T0G8;P50995|.	.;.;ANX11_HUMAN|.	Y|S	52;52;52;52;52;52;52;19;52;52|7	ENSP00000361305:D52Y;ENSP00000404412:D52Y;ENSP00000398610:D52Y;ENSP00000353827:D52Y;ENSP00000265447:D52Y;ENSP00000441748:D52Y;ENSP00000441400:D19Y|.	ENSP00000265447:D52Y|ENSP00000410826:R7S	D|R	-|-	1|3	0|2	ANXA11|ANXA11	81920553|81920553	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.671000|0.671000	0.39405|0.39405	1.595000|1.595000	0.36708|0.36708	2.326000|2.326000	0.78906|0.78906	0.443000|0.443000	0.29094|0.29094	GAC|AGG		TCGA-HZ-A49G-01A-11D-A26I-08	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	1	0	1	19	331	0	52	1	9.999999e-01	55	504	0	52	2		0	0	0	0	0	2	1	0.999992	19	331	0	52	2		0	0	0	0	52	2	-19.935120	1	1	119964	1	29	1	0	0	0	1.944076	0	0.150000	1.820000	0.109948	0.680000	0.430000	1.000000	1.000000	0.703896	0.680000	0	0.540000	0.850000
CTR9	9646	broad.mit.edu	37	11	10785352	10785352	+	Missense_Mutation	SNP	A	A	C			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr11:10785352A>C	ENST00000361367.2	+	9	1546	c.1120A>C	c.(1120-1122)Aat>Cat	p.N374H		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component			40					TTATCCTAATAATTACGAAAC	0.358000																								0							SO:0001583	missense			ENST00000361367.2	1	1	hg19	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.294603	0.81025	.	.	ENSG00000198730	ENST00000361367	T	0.52983	0.64	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72811	0.3507	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.74833	-0.3530	10	0.33940	T	0.23	-32.6144	16.1172	0.81314	1.0:0.0:0.0:0.0	.	374	Q6PD62	CTR9_HUMAN	H	374	ENSP00000355013:N374H	ENSP00000355013:N374H	N	+	1	0	CTR9	10741928	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.156000	0.94705	2.266000	0.75297	0.533000	0.62120	AAT		TCGA-HZ-A49G-01A-11D-A26I-08	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	1	0	0	28	504	0	46	1	5.503940e-01	4	30	0	46	2		0	0	0	0	0	2	1	1.000000	28	503	0	46	2		0	0	0	0	46	2	-20.000000	1	1	0	0		1	0	0	0	1.947351	0	0.150000	1.820000	0.111343	0.660000	0.450000	0.920000	0.670000	0.681717	0.660000	0	0.550000	0.800000
CD44	960	broad.mit.edu	37	11	35227738	35227738	+	Silent	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr11:35227738C>T	ENST00000428726.2	+	11	1485	c.1362C>T	c.(1360-1362)ttC>ttT	p.F454F	CD44_ENST00000433354.2_Silent_p.F455F|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Silent_p.F411F|CD44_ENST00000434472.2_Intron|CD44_ENST00000437706.2_Silent_p.F454F|CD44_ENST00000263398.6_Intron|CD44_ENST00000415148.2_Silent_p.F411F|CD44_ENST00000433892.2_Intron|CD44_ENST00000278386.6_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)			23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)	Hyaluronan(DB08818)	CTGATTTCTTCAACCCAATCT	0.468000																								0							SO:0001819	synonymous_variant			ENST00000428726.2	1	1	hg19	CCDS7897.1	.	.	.	.	.	.	.	.	.	.	C	0.021	-1.427132	0.01117	.	.	ENSG00000026508	ENST00000526553	.	.	.	4.76	-4.84	0.03151	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.0397	6.5665	0.22515	0.0:0.3178:0.3143:0.3678	.	.	.	.	X	107	.	.	Q	+	1	0	CD44	35184314	0.015000	0.18098	0.007000	0.13788	0.000000	0.00434	-1.469000	0.02348	-1.229000	0.02564	-0.797000	0.03246	CAA		TCGA-HZ-A49G-01A-11D-A26I-08	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	1	0	1	51	609	0	56	1	9.200194e-01	9	44	0	56	2		0	0	0	0	0	2	1	1.000000	51	599	0	54	2		0	0	0	0	56	2	-11.898880	1	0	0	0		1	0	0	0	1.947351	0	0.150000	1.820000	0.111343	0.970000	0.740000	1.000000	1.000000	0.942136	0.970000	1	0.850000	1.000000
CKAP5	9793	broad.mit.edu	37	11	46782199	46782199	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr11:46782199G>A	ENST00000529230.1	-	33	4403	c.4357C>T	c.(4357-4359)Cgc>Tgc	p.R1453C	SNORD67_ENST00000516618.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1453C|CKAP5_ENST00000415402.1_Missense_Mutation_p.R1453C|SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1453C			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	p.R1453C(1)		43					GGTCCCTTGCGTAACATGTTG	0.483000													Ovarian(4;85 273 2202 4844 13323)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000529230.1	0	1	hg19	CCDS31477.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.7|20.7	4.036557|4.036557	0.75617|0.75617	.|.	.|.	ENSG00000175216|ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876|ENST00000527333	T;T;T;T|.	0.51071|.	0.72;0.74;0.74;0.74|.	6.03|6.03	5.12|5.12	0.69794|0.69794	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.56455|0.56455	0.1986|0.1986	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	D;B;B|.	0.89917|.	1.0;0.004;0.002|.	D;B;B|.	0.72625|.	0.978;0.001;0.0|.	T|T	0.52866|0.52866	-0.8518|-0.8518	10|5	0.59425|.	D|.	0.04|.	-10.0088|-10.0088	15.5956|15.5956	0.76578|0.76578	0.0658:0.0:0.9342:0.0|0.0658:0.0:0.9342:0.0	.|.	1453;1453;1453|.	Q14008-3;Q14008-2;Q14008|.	.;.;CKAP5_HUMAN|.	C|M	1453;1453;1453;1453;176|1	ENSP00000432768:R1453C;ENSP00000395302:R1453C;ENSP00000310227:R1453C;ENSP00000346566:R1453C|.	ENSP00000310227:R1453C|.	R|T	-|-	1|2	0|0	CKAP5|CKAP5	46738775|46738775	1.000000|1.000000	0.71417|0.71417	0.939000|0.939000	0.37840|0.37840	0.997000|0.997000	0.91878|0.91878	5.506000|5.506000	0.66993|0.66993	1.556000|1.556000	0.49512|0.49512	0.655000|0.655000	0.94253|0.94253	CGC|ACG		TCGA-HZ-A49G-01A-11D-A26I-08	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	1	0	0	36	307	1	38	1	4.285205e-01	7	33	1	38	5		0	0	0	0	0	2	1	0.939787	35	304	1	38	25		0	0	0	1	38	2	-13.585080	1	1	121410	2	36	1	0	0	0	1.947351	0	0.150000	1.820000	0.111343	0.990000	0.920000	1.000000	1.000000	0.995795	0.990000	1	0.990000	1.000000
CNGA4	1262	broad.mit.edu	37	11	6262838	6262838	+	Silent	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr11:6262838G>A	ENST00000379936.2	+	5	1210	c.1095G>A	c.(1093-1095)caG>caA	p.Q365Q	CNGA4_ENST00000533426.1_Silent_p.Q134Q	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4			40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)			TGAAGCTGCAGCCCCAGACCT	0.567000																								0							SO:0001819	synonymous_variant			ENST00000379936.2	1	1	hg19	CCDS31408.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	0	0	0	59	1013	1	155		0	0	0	1	155	2		0	0	0	0	0	2	1	0.999993	59	1005	1	155	22		0	0	0	1	155	2	-8.088550	1	1	121412	1	36	1	0	0	0	1.947351	0	0.150000	1.820000	0.111343	0.690000	0.530000	0.880000	0.700000	0.707134	0.690000	0	0.610000	0.790000
RTN3	10313	broad.mit.edu	37	11	63486571	63486571	+	Silent	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr11:63486571G>A	ENST00000377819.5	+	3	751	c.597G>A	c.(595-597)ttG>ttA	p.L199L	RTN3_ENST00000354497.4_Intron|RTN3_ENST00000540798.1_Silent_p.L87L|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Silent_p.L180L|RTN3_ENST00000341307.2_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3			20					AAACTGCATTGGATGCTGATG	0.413000																								0							SO:0001819	synonymous_variant			ENST00000377819.5	0	1	hg19	CCDS58141.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	0	0	0	8	387	0	28		0	0	0	0	28	2		0	0	0	0	0	2	1	0.989425	8	387	0	28	2		0	0	0	0	28	2	-4.117064	1	0	0	0		1	0	0	0	1.936465	0	0.150000	1.820000	0.105734	0.260000	0.120000	0.470000	0.250000	0.281170	0.260000	0	0.180000	0.370000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	KRAS_deep			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	0	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-HZ-A49G-01A-11D-A26I-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	0	12	131	0	15	1	2.264209e-01	3	7	0	15	2	1	1	36	467	0	424	2	1	0.999217	12	130	0	15	2	1	1	575	7461	0	15	2	-6.683395	1	1	121404	2	44	1	0	0	0	2.008939	0	0.150000	1.820000	0.138368	0.990000	0.610000	1.000000	1.000000	0.938882	0.990000	1	0.820000	1.000000
LRRK2	120892	broad.mit.edu	37	12	40677757	40677757	+	Silent	SNP	G	G	A	rs146103273	byFrequency	TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr12:40677757G>A	ENST00000298910.7	+	19	2380	c.2322G>A	c.(2320-2322)gcG>gcA	p.A774A	LRRK2_ENST00000343742.2_Silent_p.A774A	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2			181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)			TACGAAAAGCGTTGACGATAA	0.433000																								0							SO:0001819	synonymous_variant			ENST00000298910.7	1	1	hg19	CCDS31774.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	1	0	1	70	555	0	52	0	6.637305e-02	0	4	0	52	2		0	0	0	0	0	2	1	1.000000	70	553	0	52	2		0	0	0	0	52	2	-11.715160	1	1	121412	43	50	1	0	0	0	2.008939	0	0.150000	1.820000	0.138368	0.990000	0.990000	1.000000	1.000000	0.999975	0.990000	1	0.990000	1.000000
TPP2	7174	broad.mit.edu	37	13	103299607	103299607	+	Silent	SNP	A	A	G			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr13:103299607A>G	ENST00000376065.4	+	21	2577	c.2541A>G	c.(2539-2541)ttA>ttG	p.L847L	TPP2_ENST00000376052.3_Silent_p.L847L	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II			52	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)				GTGAACTATTATATGAATCTG	0.368000																								0							SO:0001819	synonymous_variant			ENST00000376065.4	0	1	hg19	CCDS9502.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2	1	0	0	21	217	0	19	0	7.241644e-01	1	27	0	19	2		0	0	0	0	0	2	1	0.999998	21	216	0	19	2		0	0	0	0	19	2	-20.000000	1	1	0	0		1	1	2	3	2.031075	0	0.150000	1.820000	0.154439	0.990000	0.760000	1.000000	1.000000	0.977263	0.990000	1	0.960000	1.000000
TM9SF1	10548	broad.mit.edu	37	14	24659700	24659700	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr14:24659700G>A	ENST00000261789.4	-	5	1671	c.1313C>T	c.(1312-1314)gCc>gTc	p.A438V	IPO4_ENST00000354464.6_5'Flank|TM9SF1_ENST00000528669.1_Missense_Mutation_p.A438V|TM9SF1_ENST00000530611.1_Missense_Mutation_p.A647V|TM9SF1_ENST00000556387.1_Missense_Mutation_p.A647V|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000524835.1_Missense_Mutation_p.A351V|TM9SF1_ENST00000396854.4_Missense_Mutation_p.A438V	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1			24					AAAGGGGCTGGCGTTGTTCTT	0.577000																								0							SO:0001583	missense			ENST00000261789.4	1	1	hg19	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	G	33	5.206576	0.95033	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000530611	T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87	5.02	5.02	0.67125	.	0.056859	0.64402	D	0.000001	T	0.51381	0.1671	M	0.66297	2.02	0.80722	D	1	P;P	0.43662	0.599;0.814	P;P	0.47346	0.472;0.544	T	0.55909	-0.8066	10	0.56958	D	0.05	-4.0085	15.8364	0.78801	0.0:0.0:1.0:0.0	.	438;438	Q86SZ6;O15321	.;TM9S1_HUMAN	V	438;438;647;351;438;647	ENSP00000261789:A438V;ENSP00000432997:A438V;ENSP00000451949:A647V;ENSP00000434387:A351V;ENSP00000380063:A438V;ENSP00000433967:A647V	ENSP00000433967:A647V	A	-	2	0	TM9SF1;RP11-468E2.1	23729540	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	8.286000	0.89916	2.317000	0.78254	0.655000	0.94253	GCC		TCGA-HZ-A49G-01A-11D-A26I-08	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	1	0	0	38	443	0	74	1	9.999918e-01	17	188	0	74	2		0	0	0	0	0	2	1	1.000000	36	441	0	74	2		0	0	0	0	74	2	-20.000000	1	1	0	0		1	1	2	3	2.027927	0	0.150000	1.820000	0.153808	0.990000	0.760000	1.000000	1.000000	0.966413	0.990000	1	0.900000	1.000000
WWP2	11060	broad.mit.edu	37	16	69973005	69973005	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr16:69973005G>A	ENST00000359154.2	+	22	2520	c.2419G>A	c.(2419-2421)Ggg>Agg	p.G807R	WWP2_ENST00000542271.1_Missense_Mutation_p.G691R|WWP2_ENST00000356003.2_Missense_Mutation_p.G807R|WWP2_ENST00000568684.1_Missense_Mutation_p.G368R|WWP2_ENST00000448661.1_Missense_Mutation_p.G807R|WWP2_ENST00000544162.1_3'UTR	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2			42					CCTGCCCGTCGGGGGATTTGC	0.597000																								0							SO:0001583	missense			ENST00000359154.2	0	1	hg19	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.058259	0.76074	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.60424	0.19;0.19;0.19;0.19	5.16	5.16	0.70880	HECT (4);	0.000000	0.85682	D	0.000000	T	0.81250	0.4783	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84898	0.0840	9	.	.	.	.	18.6562	0.91455	0.0:0.0:1.0:0.0	.	807	O00308	WWP2_HUMAN	R	807;807;807;694;691	ENSP00000352069:G807R;ENSP00000396871:G807R;ENSP00000348283:G807R;ENSP00000445616:G691R	.	G	+	1	0	WWP2	68530506	1.000000	0.71417	0.969000	0.41365	0.092000	0.18411	9.824000	0.99380	2.410000	0.81850	0.561000	0.74099	GGG		TCGA-HZ-A49G-01A-11D-A26I-08	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	1	0	1	8	72	0	9	1	9.940835e-01	11	78	0	9	2	1	9.999997e-01	65	770	1	721	6	1	0.988401	8	68	0	9	2		0	0	0	0	9	2	-13.546480	1	1	121280	1	21	1	1	2	3	2.029334	0	0.150000	1.820000	0.153808	0.990000	0.650000	1.000000	1.000000	0.965599	0.990000	1	0.940000	1.000000
TP53	7157	broad.mit.edu	37	17	7577114	7577114	+	Missense_Mutation	SNP	C	C	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			C	A	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr17:7577114C>A	ENST00000269305.4	-	8	1013	c.824G>T	c.(823-825)tGt>tTt	p.C275F	TP53_ENST00000445888.2_Missense_Mutation_p.C275F|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C275F|TP53_ENST00000420246.2_Missense_Mutation_p.C275F|TP53_ENST00000359597.4_Missense_Mutation_p.C275F|TP53_ENST00000413465.2_Intron	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.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(1)		24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		Acetylsalicylic acid(DB00945)	AGGACAGGCACAAACACGCAC	0.552000		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	115	Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	GRCh37	CM076568|CM951234	TP53	M		SO:0001583	missense	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	.	.	.	.	.	.	.	.	.	.	C	24.5	4.536533	0.85812	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.97110	0.993;1.0;0.993;0.993	D	0.96317	0.9233	10	0.87932	D	0	-17.2181	15.662	0.77193	0.0:1.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	F	275;275;275;275;275;264;143	ENSP00000352610:C275F;ENSP00000269305:C275F;ENSP00000398846:C275F;ENSP00000391127:C275F;ENSP00000391478:C275F;ENSP00000425104:C143F	ENSP00000269305:C275F	C	-	2	0	TP53	7517839	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	TGT		TCGA-HZ-A49G-01A-11D-A26I-08	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	1	0	1	16	199	0	18	1	9.403865e-01	13	49	0	18	2	1	1	91	869	0	1155	2	1	0.999934	16	195	0	18	2		0	0	0	0	18	2	-19.955830	1	1	0	0		1	0	1	1	1.873034	1	0.150000	1.820000	0.081081	0.810000	0.510000	0.990000	0.880000	0.803128	0.810000	0	0.660000	0.940000
S1PR2	9294	broad.mit.edu	37	19	10334708	10334708	+	Missense_Mutation	SNP	T	T	C			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr19:10334708T>C	ENST00000590320.1	-	2	984	c.874A>G	c.(874-876)Agc>Ggc	p.S292G	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2			15					AGGTCCCGGCTGCGCCACGTG	0.687000													Pancreas(194;229 3020 15179 45747)											0							SO:0001583	missense			ENST00000590320.1	1	1	hg19	CCDS12229.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.765117	0.90020	.	.	ENSG00000175898	ENST00000317726	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.66287	0.2774	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.69412	-0.5152	9	0.66056	D	0.02	.	14.5692	0.68200	0.0:0.0:0.0:1.0	.	292	O95136	S1PR2_HUMAN	G	292	.	ENSP00000322049:S292G	S	-	1	0	S1PR2	10195708	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.040000	0.89188	2.091000	0.63221	0.454000	0.30748	AGC		TCGA-HZ-A49G-01A-11D-A26I-08	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1	0	0	0	10	244	0	41	0	2.448993e-01	0	22	0	41	2		0	0	0	0	0	2	1	0.996663	10	238	0	41	2		0	0	0	0	41	2	-16.196770	1	1	0	0		1	0	0	0	1.952993	0	0.150000	1.820000	0.114122	0.510000	0.260000	0.850000	0.490000	0.532538	0.510000	0	0.370000	0.680000
TMEM145	284339	broad.mit.edu	37	19	42821981	42821981	+	Missense_Mutation	SNP	T	T	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr19:42821981T>A	ENST00000301204.3	+	12	1062	c.1021T>A	c.(1021-1023)Ttt>Att	p.F341I	TMEM145_ENST00000598766.1_Missense_Mutation_p.F365I	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145			27		Prostate(69;0.00682)			ACTGCGACACTTTCCTGAGAA	0.587000																								0							SO:0001583	missense			ENST00000301204.3	1	1	hg19	CCDS12603.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.875924	0.72180	.	.	ENSG00000167619	ENST00000301204	T	0.42900	0.96	4.55	4.55	0.56014	Rhodopsin-like GPCR transmembrane domain (1);	0.406915	0.23626	N	0.046195	T	0.38639	0.1048	L	0.50333	1.59	0.40337	D	0.978994	B	0.33413	0.411	B	0.37015	0.239	T	0.21690	-1.0238	10	0.23302	T	0.38	-16.4936	12.1572	0.54083	0.0:0.0:0.0:1.0	.	341	Q8NBT3	TM145_HUMAN	I	341	ENSP00000301204:F341I	ENSP00000301204:F341I	F	+	1	0	TMEM145	47513821	1.000000	0.71417	0.998000	0.56505	0.944000	0.59088	6.453000	0.73488	1.832000	0.53329	0.482000	0.46254	TTT		TCGA-HZ-A49G-01A-11D-A26I-08	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463737.1	1	0	0	59	584	0	89	0	0	0	1	0	89	2		0	0	0	0	0	2	1	1.000000	59	576	0	88	2		0	0	0	0	89	2	-16.310760	1	1	0	0		1	1	2	3	2.102529	1	0.150000	1.820000	0.168704	0.990000	0.970000	1.000000	1.000000	0.998313	0.990000	1	0.990000	1.000000
PSG8	440533	broad.mit.edu	37	19	43268187	43268187	+	Missense_Mutation	SNP	T	T	C			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr19:43268187T>C	ENST00000306511.4	-	2	408	c.311A>G	c.(310-312)aAt>aGt	p.N104S	PSG8_ENST00000404209.4_Missense_Mutation_p.N104S|PSG8_ENST00000406636.3_Intron|PSG8_ENST00000401467.2_Missense_Mutation_p.N104S	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8			40		Prostate(69;0.00899)			CAGGGATGCATTGGAATATAT	0.423000																								0							SO:0001583	missense			ENST00000306511.4	1	1	hg19	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	t	12.62	1.993629	0.35131	.	.	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.01963	4.53;4.53;4.53	1.35	1.35	0.21983	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.11965	0.0291	M	0.89534	3.04	0.09310	N	1	D;D;D;P;P	0.71674	0.998;0.971;0.963;0.908;0.925	D;P;D;P;P	0.75020	0.985;0.831;0.945;0.716;0.813	T	0.06356	-1.0831	9	0.87932	D	0	.	4.8841	0.13694	0.0:0.0:0.0:1.0	.	104;104;104;104;104	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	S	104	ENSP00000385869:N104S;ENSP00000386090:N104S;ENSP00000305005:N104S	ENSP00000305005:N104S	N	-	2	0	PSG8	47960027	0.108000	0.22018	0.088000	0.20740	0.189000	0.23516	0.679000	0.25291	0.879000	0.35944	0.155000	0.16302	AAT		TCGA-HZ-A49G-01A-11D-A26I-08	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1	1	0	0	232	2551	0	270		0	0	0	0	270	2		0	0	0	0	0	2	1	1.000000	232	2539	0	268	2		0	0	0	0	270	2	-20.000000	1	1	121408	4	44	1	1	2	3	2.102529	1	0.150000	1.820000	0.168704	0.990000	0.990000	1.000000	1.000000	0.999533	0.990000	1	0.990000	1.000000
LIG1	3978	broad.mit.edu	37	19	48654515	48654515	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr19:48654515G>A	ENST00000263274.7	-	7	967	c.548C>T	c.(547-549)aCg>aTg	p.T183M	LIG1_ENST00000599165.1_5'UTR|LIG1_ENST00000427526.2_Missense_Mutation_p.T152M|LIG1_ENST00000536218.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent			44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		Bleomycin(DB00290)	CTTGGGAGGCGTGGTGGGCTG	0.567000								Nucleotide excision repair (NER)																0							SO:0001583	missense			ENST00000263274.7	1	1	hg19	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	G	9.371	1.070591	0.20147	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000542460	T;T;T	0.58060	0.49;0.36;3.03	4.54	-0.526	0.11913	.	1.498560	0.03481	N	0.215059	T	0.47600	0.1454	L	0.51422	1.61	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.10450	0.005;0.005	T	0.39231	-0.9624	10	0.52906	T	0.07	-0.0148	7.3598	0.26739	0.4529:0.0:0.5471:0.0	.	152;183	B4DTU4;P18858	.;DNLI1_HUMAN	M	183;214;152;151	ENSP00000263274:T183M;ENSP00000442841:T152M;ENSP00000445928:T151M	ENSP00000263274:T183M	T	-	2	0	LIG1	53346327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.084000	0.12595	-0.254000	0.11334	ACG		TCGA-HZ-A49G-01A-11D-A26I-08	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	1	0	0	66	1124	0	128	1	4.873682e-01	3	26	0	128	2		0	0	0	0	0	2	1	1.000000	65	1110	0	125	2		0	0	0	0	128	2	-8.585160	1	1	121412	8	45	1	1	2	3	2.112060	1	0.150000	1.820000	0.170529	0.780000	0.590000	1.000000	0.750000	0.814782	0.780000	0	0.680000	1.000000
C3	718	broad.mit.edu	37	19	6710823	6710823	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			G	A	G	G		Inconclusive	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr19:6710823G>A	ENST00000245907.6	-	13	1605	c.1513C>T	c.(1513-1515)Cgc>Tgc	p.R505C		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3			72				Intravenous Immunoglobulin(DB00028)	CGCACCTGGCGTCCCGCCTTC	0.652000																								0							SO:0001583	missense			ENST00000245907.6	1	1	hg19	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	G	15.92	2.976535	0.53720	.	.	ENSG00000125730	ENST00000245907	T	0.65178	-0.14	5.31	3.14	0.36123	Alpha-2-macroglobulin, N-terminal 2 (1);	0.050520	0.85682	N	0.000000	T	0.78477	0.4289	M	0.92026	3.265	0.19300	N	0.999976	D	0.89917	1.0	D	0.97110	1.0	T	0.68085	-0.5502	10	0.59425	D	0.04	.	3.8203	0.08833	0.082:0.1398:0.5074:0.2707	.	505	P01024	CO3_HUMAN	C	505	ENSP00000245907:R505C	ENSP00000245907:R505C	R	-	1	0	C3	6661823	0.662000	0.27439	0.008000	0.14137	0.008000	0.06430	1.347000	0.33975	0.608000	0.30000	0.655000	0.94253	CGC		TCGA-HZ-A49G-01A-11D-A26I-08	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	0	0	0	13	362	0	64	0	9.999999e-01	0	981	0	64	2		0	0	0	0	0	2	1	0.999494	13	355	0	63	2		0	0	0	0	64	2	-13.084040	1	1	121408	1	24	1	0	0	0	1.952993	0	0.150000	1.820000	0.114122	0.440000	0.250000	0.710000	0.440000	0.465264	0.440000	0	0.330000	0.580000
FCGR2B	2213	broad.mit.edu	37	1	161645099	161645099	+	Missense_Mutation	SNP	A	A	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr1:161645099A>T	ENST00000358671.5	+	6	894	c.813A>T	c.(811-813)aaA>aaT	p.K271N	RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367961.4_Missense_Mutation_p.K264N|FCGR2B_ENST00000236937.9_Intron|FCGR2B_ENST00000367960.5_Missense_Mutation_p.K264N|FCGR2B_ENST00000367962.4_Missense_Mutation_p.K271N	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)				all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TCCCTGAGAAACCAGGTGAGT	0.602000			T	?	ALL										Dom	yes		1	1q23	2213	Fc fragment of IgG, low affinity IIb, receptor for (CD32)		L	0							SO:0001583	missense			ENST00000358671.5	0	1	hg19	CCDS30924.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.579357	0.28180	.	.	ENSG00000072694	ENST00000367962;ENST00000367960;ENST00000367961;ENST00000358671	T;T;T;T	0.32272	4.59;1.46;1.46;4.59	5.06	-5.67	0.02444	.	7.541930	0.00550	N	0.000242	T	0.03220	0.0094	N	0.08118	0	0.24714	N	0.993181	B;P	0.35011	0.063;0.48	B;B	0.21917	0.037;0.026	T	0.11108	-1.0601	10	0.38643	T	0.18	.	3.0765	0.06248	0.2125:0.2573:0.4044:0.1258	.	264;271	P31994-3;P31994	.;FCG2B_HUMAN	N	271;264;264;271	ENSP00000356939:K271N;ENSP00000356937:K264N;ENSP00000356938:K264N;ENSP00000351497:K271N	ENSP00000351497:K271N	K	+	3	2	FCGR2B	159911723	0.000000	0.05858	0.213000	0.23690	0.463000	0.32649	-1.239000	0.02916	-1.009000	0.03400	-0.466000	0.05196	AAA		TCGA-HZ-A49G-01A-11D-A26I-08	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	1	0	0	11	81	0	9	0	7.100932e-01	0	20	0	9	2		0	0	0	0	0	2	1	0.996539	9	68	0	11	2		0	0	0	0	9	2	-18.203790	1	1	0	0		1	1	2	3	2.030952	0	0.150000	1.820000	0.154439	0.990000	0.850000	1.000000	1.000000	0.991478	0.990000	1	0.990000	1.000000
SOAT1	6646	broad.mit.edu	37	1	179320574	179320574	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr1:179320574C>T	ENST00000367619.3	+	15	1716	c.1573C>T	c.(1573-1575)Cgt>Tgt	p.R525C	SOAT1_ENST00000540564.1_Missense_Mutation_p.R467C|SOAT1_ENST00000539888.1_Missense_Mutation_p.R460C|SOAT1_ENST00000535686.1_Missense_Mutation_p.R261C	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1			20				Ezetimibe(DB00973)|Hesperetin(DB01094)	ATGGTATGCACGTCAGCACTG	0.433000																								0							SO:0001583	missense			ENST00000367619.3	1	1	hg19	CCDS1330.1	.	.	.	.	.	.	.	.	.	.	C	31	5.067359	0.93898	.	.	ENSG00000057252	ENST00000539888;ENST00000540564;ENST00000535686;ENST00000367619	T;T;T;T	0.37058	1.25;1.24;1.31;1.22	5.58	5.58	0.84498	.	0.175782	0.53938	N	0.000049	T	0.61726	0.2370	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.953;0.988	T	0.64753	-0.6333	10	0.87932	D	0	-6.7329	17.0671	0.86562	0.0:1.0:0.0:0.0	.	467;525	A8K3P4;P35610	.;SOAT1_HUMAN	C	460;467;261;525	ENSP00000441356:R460C;ENSP00000445315:R467C;ENSP00000442503:R261C;ENSP00000356591:R525C	ENSP00000356591:R525C	R	+	1	0	SOAT1	177587197	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.572000	0.60886	2.618000	0.88619	0.563000	0.77884	CGT		TCGA-HZ-A49G-01A-11D-A26I-08	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	1	0	0	86	905	0	83	1	9.999957e-01	7	173	0	83	2		0	0	0	0	0	2	1	1.000000	86	902	0	83	2		0	0	0	0	83	2	-19.841640	1	1	121412	1	35	1	1	2	3	2.030952	0	0.150000	1.820000	0.154439	0.990000	0.940000	1.000000	1.000000	0.996612	0.990000	1	0.990000	1.000000
ALDH4A1	8659	broad.mit.edu	37	1	19212958	19212958	+	Splice_Site	SNP	C	C	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr1:19212958C>A	ENST00000375341.3	-	4	554	c.297G>T	c.(295-297)aaG>aaT	p.K99N	ALDH4A1_ENST00000290597.5_Splice_Site_p.K99N|ALDH4A1_ENST00000538309.1_Splice_Site_p.K39N|ALDH4A1_ENST00000538839.1_Splice_Site_p.K99N|ALDH4A1_ENST00000454547.1_5'Flank|RP13-279N23.2_ENST00000494072.3_3'UTR	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1			15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)			GCTCACTCACCTTGTCTGCAT	0.587000																								0							SO:0001630	splice_region_variant			ENST00000375341.3	1	0	hg19	CCDS188.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.006620	0.93287	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375334	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.71	5.71	0.89125	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.046947	0.85682	D	0.000000	D	0.87676	0.6237	M	0.83852	2.665	0.80722	D	1	D	0.59357	0.985	P	0.61477	0.889	D	0.88178	0.2869	9	.	.	.	-28.641	16.5735	0.84631	0.0:1.0:0.0:0.0	.	99	P30038	AL4A1_HUMAN	N	99;99;99;39;39	ENSP00000290597:K99N;ENSP00000364490:K99N;ENSP00000446071:K99N;ENSP00000442988:K39N	.	K	-	3	2	ALDH4A1	19085545	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.798000	0.75155	2.686000	0.91538	0.655000	0.94253	AAG		TCGA-HZ-A49G-01A-11D-A26I-08	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1	1	0	0	22	208	0	26	0	4.419896e-01	0	15	0	26	2		0	0	0	0	0	2	1	0.999999	22	207	0	26	2		0	0	0	0	26	2	-2.879466	1	1	0	0		1	0	1	1	2.022039	0	0.150000	1.820000	0.145514	0.990000	0.820000	1.000000	1.000000	0.986918	0.990000	1	0.990000	1.000000
USP48	84196	broad.mit.edu	37	1	22030753	22030753	+	Splice_Site	SNP	A	A	G			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr1:22030753A>G	ENST00000308271.9	-	20	3164		c.e20+1		USP48_ENST00000529637.1_Splice_Site|USP48_ENST00000374732.3_Splice_Site|USP48_ENST00000400301.1_Splice_Site	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48			42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)			ATGAAAACTTACTGGGCTCAG	0.368000																								0							SO:0001630	splice_region_variant			ENST00000308271.9	1	1	hg19	CCDS30623.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.969098	0.74131	.	.	ENSG00000090686	ENST00000400301;ENST00000308271;ENST00000374732;ENST00000529637	.	.	.	5.52	5.52	0.82312	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8242	0.70097	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	USP48	21903340	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	7.561000	0.82288	2.094000	0.63399	0.533000	0.62120	.		TCGA-HZ-A49G-01A-11D-A26I-08	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	1	0	0	36	417	0	33	1	1.909166e-02	3	0	0	33	2		0	0	0	0	0	2	1	1.000000	36	412	0	33	2		0	0	0	0	33	2	-20.000000	1	1	0	0		1	1	2	3	2.043071	0	0.150000	1.820000	0.156955	0.990000	0.770000	1.000000	1.000000	0.969413	0.990000	1	0.910000	1.000000
MACF1	23499	broad.mit.edu	37	1	39749752	39749752	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			G	T	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr1:39749752G>T	ENST00000372915.3	+	9	1032	c.945G>T	c.(943-945)agG>agT	p.R315S	MACF1_ENST00000564288.1_Missense_Mutation_p.R310S|MACF1_ENST00000361689.2_Missense_Mutation_p.R315S|MACF1_ENST00000539005.1_Missense_Mutation_p.R315S|MACF1_ENST00000567887.1_Missense_Mutation_p.R347S|MACF1_ENST00000317713.7_Missense_Mutation_p.R315S|MACF1_ENST00000545844.1_Missense_Mutation_p.R315S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1			203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		TGGACTCCAGGTGGCAAGAAT	0.443000																								0							SO:0001583	missense			ENST00000372915.3	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.69	3.192152	0.58017	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.4	4.48	0.54585	.	.	.	.	.	T	0.64516	0.2605	L	0.35249	1.045	0.80722	D	1	B;D	0.62365	0.066;0.991	B;P	0.54026	0.041;0.74	T	0.66995	-0.5782	9	0.87932	D	0	.	9.0036	0.36097	0.0793:0.1485:0.7721:0.0	.	315;280	F8W8Q1;Q9UPN3-3	.;.	S	315;315;315;331;315;315;273;464;475	ENSP00000439537:R315S;ENSP00000362006:R315S;ENSP00000354573:R315S;ENSP00000313438:R315S;ENSP00000444364:R315S;ENSP00000435070:R273S;ENSP00000437059:R464S	ENSP00000313438:R315S	R	+	3	2	MACF1	39522339	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.617000	0.24359	1.249000	0.43950	0.561000	0.74099	AGG		TCGA-HZ-A49G-01A-11D-A26I-08	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	1	0	0	28	527	0	55	0	6.274117e-02	0	8	0	55	2	1	1	23	563	0	612	2	1	1.000000	28	524	0	55	2		0	0	0	0	55	2	-20.000000	1	0	0	0		1	1	2	3	2.038492	0	0.150000	1.820000	0.155699	0.690000	0.460000	1.000000	0.670000	0.713810	0.690000	0	0.560000	0.860000
PAX1	5075	broad.mit.edu	37	20	21689881	21689881	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr20:21689881G>A	ENST00000398485.2	+	4	1135	c.1081G>A	c.(1081-1083)Gtg>Atg	p.V361M	PAX1_ENST00000460221.1_3'UTR|PAX1_ENST00000444366.2_Missense_Mutation_p.V337M	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1			38					CCTCTCTGCCGTGGGCGGCTT	0.697000																								0							SO:0001583	missense			ENST00000398485.2	1	1	hg19	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	G	14.29	2.491158	0.44249	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.98862	-4.78;-5.19	5.66	4.71	0.59529	.	0.070054	0.64402	D	0.000019	D	0.97704	0.9247	M	0.73962	2.25	0.37476	D	0.915822	D;P;D	0.57257	0.968;0.852;0.979	B;B;P	0.44518	0.332;0.079;0.452	D	0.97965	1.0340	10	0.54805	T	0.06	.	11.8979	0.52665	0.1451:0.0:0.8549:0.0	.	337;267;361	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	M	361;337	ENSP00000381499:V361M;ENSP00000410355:V337M	ENSP00000381499:V361M	V	+	1	0	PAX1	21637881	0.998000	0.40836	0.888000	0.34837	0.476000	0.33039	3.037000	0.49775	1.392000	0.46585	0.462000	0.41574	GTG		TCGA-HZ-A49G-01A-11D-A26I-08	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3	0	0	0	47	1318	0	153		0	0	0	0	153	2		0	0	0	0	0	2	1	1.000000	47	1299	0	148	2		0	0	0	0	153	2	-3.596617	1	1	121296	1	37	1	1	5	6	2.668018	1	0.150000	1.820000	0.346154	0.590000	0.430000	0.780000	0.600000	0.607781	0.590000	0	0.510000	0.690000
GGTLC1	92086	broad.mit.edu	37	20	23966551	23966551	+	Missense_Mutation	SNP	C	C	T	rs143742821	byFrequency	TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr20:23966551C>T	ENST00000335694.4	-	4	569	c.365G>A	c.(364-366)cGg>cAg	p.R122Q	GGTLC1_ENST00000278765.4_Missense_Mutation_p.R122Q|GGTLC1_ENST00000286890.4_Missense_Mutation_p.R122Q	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1			15					CACCACCATCCGGACCTGGCC	0.662000																								0							SO:0001583	missense			ENST00000335694.4	1	1	hg19	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	c	12.08	1.830751	0.32329	0.005956	0.0	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.08370	3.1;3.1;3.1	0.844	0.844	0.18943	.	0.384153	0.26627	N	0.023330	T	0.04815	0.0130	M	0.62016	1.91	0.27078	N	0.96317	B	0.31581	0.329	B	0.25291	0.059	T	0.22347	-1.0219	10	0.38643	T	0.18	-48.6079	3.7845	0.08694	0.0:0.6622:0.0:0.3378	.	122	Q9BX51	GGTL1_HUMAN	Q	122	ENSP00000286890:R122Q;ENSP00000278765:R122Q;ENSP00000337587:R122Q	ENSP00000278765:R122Q	R	-	2	0	GGTLC1	23914551	1.000000	0.71417	0.178000	0.23040	0.195000	0.23768	1.410000	0.34691	0.088000	0.17205	0.089000	0.15464	CGG		TCGA-HZ-A49G-01A-11D-A26I-08	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	0	0	0	57	851	0	132	0	1.184031e-02	0	3	0	132	2		0	0	0	0	0	2	1	1.000000	49	774	0	139	2		0	0	0	0	132	2	-2.841672	1	1	121398	71	52	1	0	1	1	2.015068	0	0.150000	1.820000	0.144224	0.820000	0.630000	1.000000	1.000000	0.834756	0.820000	0	0.720000	0.940000
PTPRT	11122	broad.mit.edu	37	20	41101179	41101179	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr20:41101179C>T	ENST00000373187.1	-	8	1176	c.1177G>A	c.(1177-1179)Gtg>Atg	p.V393M	PTPRT_ENST00000373198.4_Missense_Mutation_p.V393M|PTPRT_ENST00000356100.2_Missense_Mutation_p.V393M|PTPRT_ENST00000373184.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373201.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373190.1_Missense_Mutation_p.V393M|PTPRT_ENST00000373193.3_Missense_Mutation_p.V393M			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T			176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)			ACGATTTCCACGTTCTGTGGG	0.562000																								0							SO:0001583	missense			ENST00000373187.1	1	1	hg19	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.577402	0.86645	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4;0.4	5.71	5.71	0.89125	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.67135	0.2861	L	0.51422	1.61	0.80722	D	1	D;D	0.69078	0.997;0.994	P;P	0.61722	0.893;0.674	T	0.67684	-0.5607	10	0.66056	D	0.02	.	19.8432	0.96699	0.0:1.0:0.0:0.0	.	393;393	O14522-1;O14522	.;PTPRT_HUMAN	M	393	ENSP00000362286:V393M;ENSP00000362283:V393M;ENSP00000362289:V393M;ENSP00000348408:V393M;ENSP00000362294:V393M;ENSP00000362280:V393M;ENSP00000362297:V393M	ENSP00000348408:V393M	V	-	1	0	PTPRT	40534593	0.998000	0.40836	0.965000	0.40720	0.815000	0.46073	3.895000	0.56258	2.700000	0.92200	0.462000	0.41574	GTG		TCGA-HZ-A49G-01A-11D-A26I-08	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1	1	0	0	13	291	0	43	0	0	0	1	0	43	2		0	0	0	0	0	2	1	0.999523	13	287	0	42	2		0	0	0	0	43	2	-14.273810	1	1	121006	1	25	1	0	1	1	2.015068	0	0.150000	1.820000	0.144224	0.570000	0.320000	0.900000	0.550000	0.593292	0.570000	0	0.430000	0.740000
PRAME	23532	broad.mit.edu	37	22	22892513	22892513	+	Missense_Mutation	SNP	A	A	C			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr22:22892513A>C	ENST00000398741.1	-	5	894	c.588T>G	c.(586-588)atT>atG	p.I196M	PRAME_ENST00000543184.1_Missense_Mutation_p.I196M|PRAME_ENST00000424204.2_Missense_Mutation_p.I180M|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000398743.2_Missense_Mutation_p.I196M|PRAME_ENST00000402697.1_Missense_Mutation_p.I196M|PRAME_ENST00000405655.3_Missense_Mutation_p.I196M|PRAME_ENST00000539862.1_Missense_Mutation_p.I180M	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma			36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)			TCACTTTCTCAATGAGGTAGG	0.458000													Melanoma(73;1707 1838 15168 27201)											0							SO:0001583	missense			ENST00000398741.1	1	1	hg19	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	.	4.313	0.057476	0.08339	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106	T;T;T;T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45	3.24	-5.23	0.02798	.	1.278720	0.05507	N	0.559414	T	0.10337	0.0253	N	0.17800	0.525	0.09310	N	1	B	0.28208	0.203	B	0.28465	0.09	T	0.30119	-0.9989	10	0.39692	T	0.17	.	7.634	0.28255	0.3112:0.508:0.1808:0.0	.	196	P78395	PRAME_HUMAN	M	196;196;196;196;180;196;180;196	ENSP00000381728:I196M;ENSP00000445675:I196M;ENSP00000381726:I196M;ENSP00000384343:I196M;ENSP00000445097:I180M;ENSP00000385198:I196M;ENSP00000407342:I180M;ENSP00000407320:I196M	ENSP00000381726:I196M	I	-	3	3	PRAME	21222513	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.489000	0.02306	-2.030000	0.00929	-1.256000	0.01477	ATT		TCGA-HZ-A49G-01A-11D-A26I-08	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	1	0	0	48	719	0	80		0	0	0	0	80	2		0	0	0	0	0	2	1	1.000000	47	717	0	80	2		0	0	0	0	80	2	-20.000000	1	1	0	0		1	0	0	0	2.005901	0	0.150000	1.820000	0.137056	0.810000	0.610000	1.000000	1.000000	0.825545	0.810000	0	0.710000	0.940000
NR4A2	4929	broad.mit.edu	37	2	157186342	157186342	+	Silent	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr2:157186342C>T	ENST00000339562.4	-	3	719	c.357G>A	c.(355-357)tcG>tcA	p.S119S	NR4A2_ENST00000539077.1_Silent_p.S130S|NR4A2_ENST00000429376.1_Silent_p.S56S|NR4A2_ENST00000426264.1_Silent_p.S56S|NR4A2_ENST00000409108.2_Silent_p.S119S|NR4A2_ENST00000409572.1_Silent_p.S119S	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2			40					TGTAGTAAACCGACCCGGAGT	0.612000																								0							SO:0001819	synonymous_variant			ENST00000339562.4	1	1	hg19	CCDS2201.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2	1	0	0	47	549	0	64	0	5.539818e-02	0	5	0	64	2		0	0	0	0	0	2	1	1.000000	44	543	0	64	2		0	0	0	0	64	2	-2.920853	1	1	0	0		1	0	0	0	2.001073	0	0.150000	1.820000	0.135740	0.990000	0.770000	1.000000	1.000000	0.961683	0.990000	1	0.890000	1.000000
TTN	7273	broad.mit.edu	37	2	179476557	179476557	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr2:179476557G>A	ENST00000591111.1	-	218	45780	c.45556C>T	c.(45556-45558)Cgg>Tgg	p.R15186W	TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R14259W|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R7762W|TTN_ENST00000589042.1_Missense_Mutation_p.R16827W|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R7954W|TTN_ENST00000359218.5_Missense_Mutation_p.R7887W|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	p.R7762W(1)|p.R7954W(1)|p.R14259W(1)|p.R7887W(1)		1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		TTTTCAGCCCGAACCTGAAAC	0.458000																								4	Substitution - Missense(4)						SO:0001583	missense			ENST00000591111.1	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	8.954	0.968839	0.18659	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.97	3.08	0.35506	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72285	0.3441	M	0.78801	2.425	0.43988	D	0.996681	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.69654	0.965;0.965;0.965;0.965	T	0.73924	-0.3829	9	0.87932	D	0	.	10.0401	0.42153	0.0646:0.0:0.6758:0.2596	.	7762;7887;7954;15186	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	W	14259;7762;7954;7887;7762	ENSP00000343764:R14259W;ENSP00000434586:R7762W;ENSP00000340554:R7954W;ENSP00000352154:R7887W	ENSP00000340554:R7954W	R	-	1	2	TTN	179184802	1.000000	0.71417	0.997000	0.53966	0.895000	0.52256	2.635000	0.46537	0.784000	0.33661	-0.188000	0.12872	CGG		TCGA-HZ-A49G-01A-11D-A26I-08	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	1	0	0	39	695	0	73	0	3.023420e-03	0	2	0	73	2		0	0	0	0	0	2	1	1.000000	39	688	0	73	2		0	0	0	0	73	2	-3.221342	1	1	120840	3	35	1	0	0	0	2.012295	0	0.150000	1.820000	0.139676	0.690000	0.500000	0.920000	0.690000	0.709599	0.690000	0	0.590000	0.810000
SH3BP4	23677	broad.mit.edu	37	2	235949561	235949561	+	Missense_Mutation	SNP	A	A	C	rs138775253		TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr2:235949561A>C	ENST00000409212.1	+	4	655	c.148A>C	c.(148-150)Aac>Cac	p.N50H	SH3BP4_ENST00000392011.2_Missense_Mutation_p.N50H|SH3BP4_ENST00000344528.4_Missense_Mutation_p.N50H			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)			GCTCGTAGACAACCCCACACC	0.532000																								0							SO:0001583	missense			ENST00000409212.1	1	1	hg19	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.481890	0.44147	.	.	ENSG00000130147	ENST00000392011;ENST00000420127;ENST00000416021;ENST00000409212;ENST00000344528;ENST00000444916;ENST00000446904;ENST00000454947	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	5.44	4.25	0.50352	Src homology-3 domain (1);	0.509628	0.23624	N	0.046211	T	0.17704	0.0425	N	0.14661	0.345	0.39020	D	0.959721	P;P	0.41041	0.736;0.604	B;B	0.36885	0.235;0.235	T	0.06303	-1.0834	10	0.54805	T	0.06	0.9174	10.559	0.45133	0.8552:0.0:0.0:0.1448	.	50;50	A8K594;Q9P0V3	.;SH3B4_HUMAN	H	50	ENSP00000375867:N50H;ENSP00000403251:N50H;ENSP00000386862:N50H;ENSP00000340237:N50H;ENSP00000415391:N50H	ENSP00000340237:N50H	N	+	1	0	SH3BP4	235614300	0.997000	0.39634	0.976000	0.42696	0.823000	0.46562	3.448000	0.52943	0.859000	0.35456	0.533000	0.62120	AAC		TCGA-HZ-A49G-01A-11D-A26I-08	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1	1	0	0	33	512	0	68	1	7.556374e-01	4	40	0	68	2		0	0	0	0	0	2	1	1.000000	33	506	0	68	2		0	0	0	0	68	2	-20.000000	1	1	0	0		1	0	0	0	2.012295	0	0.150000	1.820000	0.139676	0.790000	0.560000	1.000000	1.000000	0.803479	0.790000	0	0.670000	0.940000
CLIP4	79745	broad.mit.edu	37	2	29404502	29404502	+	Missense_Mutation	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr2:29404502G>A	ENST00000320081.5	+	16	2116	c.1861G>A	c.(1861-1863)Gtg>Atg	p.V621M	CLIP4_ENST00000401617.2_Missense_Mutation_p.V514M|CLIP4_ENST00000481628.1_3'UTR|CLIP4_ENST00000404424.1_Missense_Mutation_p.V621M	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4			26	Acute lymphoblastic leukemia(172;0.155)				TGAAGGGAGCGTGAAGCTGCA	0.542000																								0							SO:0001583	missense			ENST00000320081.5	1	1	hg19	CCDS1770.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664449	0.88251	.	.	ENSG00000115295	ENST00000401617;ENST00000404424;ENST00000402240;ENST00000320081;ENST00000379543;ENST00000530644	T;T;T	0.77358	-1.09;-0.82;-0.82	5.6	5.6	0.85130	Cytoskeleton-associated protein, Gly-rich domain (2);	0.206120	0.41097	D	0.000956	T	0.80497	0.4634	L	0.29908	0.895	0.80722	D	1	D	0.67145	0.996	P	0.57846	0.828	T	0.80538	-0.1338	10	0.46703	T	0.11	.	19.6109	0.95606	0.0:0.0:1.0:0.0	.	621	Q8N3C7	CLIP4_HUMAN	M	514;621;623;621;639;581	ENSP00000385148:V514M;ENSP00000385594:V621M;ENSP00000327009:V621M	ENSP00000327009:V621M	V	+	1	0	CLIP4	29258006	1.000000	0.71417	0.904000	0.35570	0.887000	0.51463	7.111000	0.77077	2.653000	0.90120	0.491000	0.48974	GTG		TCGA-HZ-A49G-01A-11D-A26I-08	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	0	0	0	11	389	0	42	1	4.698757e-01	2	52	0	42	2		0	0	0	0	0	2	1	0.998385	11	389	0	42	2		0	0	0	0	42	2	-10.247660	1	1	121412	4	39	1	0	0	0	1.990868	0	0.150000	1.820000	0.130435	0.360000	0.190000	0.600000	0.350000	0.382585	0.360000	0	0.270000	0.490000
CEP70	80321	broad.mit.edu	37	3	138289266	138289266	+	Missense_Mutation	SNP	T	T	C	rs143423470		TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr3:138289266T>C	ENST00000264982.3	-	6	625	c.359A>G	c.(358-360)gAa>gGa	p.E120G	CEP70_ENST00000542237.1_Missense_Mutation_p.E100G|CEP70_ENST00000464035.1_Missense_Mutation_p.E120G|CEP70_ENST00000481834.1_Missense_Mutation_p.E120G|CEP70_ENST00000489254.1_Intron|CEP70_ENST00000484888.1_Missense_Mutation_p.E120G|CEP70_ENST00000478673.1_5'UTR	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa			24					TTTCACACTTTCCATAATTTG	0.363000																								0							SO:0001583	missense			ENST00000264982.3	1	1	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	T	11.18	1.563176	0.27915	0.0	1.16E-4	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035	T;T;T;T;T;T;T;T	0.55052	1.18;1.19;1.18;1.19;1.17;0.6;0.59;0.54	4.98	3.83	0.44106	.	0.414678	0.25897	N	0.027597	T	0.42086	0.1187	L	0.47716	1.5	0.27515	N	0.95157	P;P;P	0.42692	0.787;0.787;0.787	B;B;B	0.39379	0.23;0.298;0.23	T	0.33979	-0.9847	10	0.41790	T	0.15	-4.5495	7.2698	0.26250	0.0:0.0985:0.0:0.9015	.	100;120;120	F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;CEP70_HUMAN	G	120;100;120;102;120;99;100;120	ENSP00000264982:E120G;ENSP00000444128:E100G;ENSP00000419231:E120G;ENSP00000419833:E102G;ENSP00000417465:E120G;ENSP00000418131:E99G;ENSP00000417819:E100G;ENSP00000419743:E120G	ENSP00000264982:E120G	E	-	2	0	CEP70	139771956	1.000000	0.71417	0.999000	0.59377	0.202000	0.24057	4.295000	0.59049	0.932000	0.37266	-0.256000	0.11100	GAA		TCGA-HZ-A49G-01A-11D-A26I-08	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	1	0	1	104	520	0	47	1	7.044918e-01	3	11	0	47	2		0	0	0	0	0	2	1	1.000000	103	518	0	47	2		0	0	0	0	47	2	-20.000000	1	1	0	0		1	0	1	1	2.002839	1	0.150000	1.820000	0.081081	0.980000	0.930000	1.000000	0.990000	0.987383	0.980000	1	0.960000	1.000000
ZFYVE28	57732	broad.mit.edu	37	4	2341323	2341323	+	Silent	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr4:2341323C>T	ENST00000290974.2	-	4	717	c.378G>A	c.(376-378)ccG>ccA	p.P126P	ZFYVE28_ENST00000509171.1_Silent_p.P79P|ZFYVE28_ENST00000515312.1_Silent_p.P56P|ZFYVE28_ENST00000503000.1_Silent_p.P126P|ZFYVE28_ENST00000515169.1_Silent_p.P56P|ZFYVE28_ENST00000511071.1_Silent_p.P126P|ZFYVE28_ENST00000505421.1_5'Flank	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28			31					CCTTGGCCAGCGGGCGCATGG	0.692000																								0							SO:0001819	synonymous_variant			ENST00000290974.2	0	1	hg19	CCDS33942.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	1	0	0	5	72	0	13	0	2.879646e-01	1	13	0	13	2		0	0	0	0	0	2	1	0.939687	5	72	0	13	2		0	0	0	0	13	2	-9.421114	1	1	121252	11	36	1	0	1	1	2.024131	0	0.150000	1.820000	0.146158	0.880000	0.350000	1.000000	1.000000	0.818086	0.880000	1	0.570000	1.000000
SLIT3	6586	broad.mit.edu	37	5	168199801	168199801	+	Missense_Mutation	SNP	T	T	C			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr5:168199801T>C	ENST00000519560.1	-	14	1863	c.1444A>G	c.(1444-1446)Aag>Gag	p.K482E	SLIT3_ENST00000404867.3_Missense_Mutation_p.K482E|SLIT3_ENST00000332966.8_Missense_Mutation_p.K482E	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)			100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		CAGCGGAACTTCTTGCTCTTG	0.612000													Ovarian(29;311 847 10864 17279 24903)											0							SO:0001583	missense			ENST00000519560.1	1	1	hg19	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135148	0.77662	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.76060	-0.99;-0.97;-0.97	5.49	5.49	0.81192	Cysteine-rich flanking region, C-terminal (2);	0.091877	0.64402	D	0.000001	T	0.66277	0.2773	L	0.28608	0.87	0.80722	D	1	P;P;P	0.50528	0.936;0.738;0.627	B;B;B	0.42245	0.381;0.195;0.369	T	0.71906	-0.4451	10	0.66056	D	0.02	.	15.5931	0.76554	0.0:0.0:0.0:1.0	.	482;482;482	O75094-2;O75094-3;O75094	.;.;SLIT3_HUMAN	E	482	ENSP00000430333:K482E;ENSP00000332164:K482E;ENSP00000384890:K482E	ENSP00000332164:K482E	K	-	1	0	SLIT3	168132379	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.033000	0.88852	2.075000	0.62263	0.459000	0.35465	AAG		TCGA-HZ-A49G-01A-11D-A26I-08	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	0	0	0	10	363	0	53	0	2.730107e-01	0	35	0	53	2		0	0	0	0	0	2	1	0.996934	10	362	0	53	2		0	0	0	0	53	2	-10.322950	1	1	0	0		1	1	2	3	2.032889	0	0.150000	1.820000	0.154439	0.370000	0.190000	1.000000	0.350000	0.421559	0.370000	0	0.270000	0.530000
LACE1	246269	broad.mit.edu	37	6	108768484	108768484	+	Missense_Mutation	SNP	G	G	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr6:108768484G>T	ENST00000368977.4	+	8	1061	c.875G>T	c.(874-876)gGa>gTa	p.G292V		NM_145315.3	NP_660358.2	Q8WV93	LACE1_HUMAN	lactation elevated 1			15		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)			CCTGCTGCAGGAAAACTCTAC	0.323000																								0							SO:0001583	missense			ENST00000368977.4	0	1	hg19	CCDS5067.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.55|13.55	2.270717|2.270717	0.40194|0.40194	.|.	.|.	ENSG00000135537|ENSG00000135537	ENST00000421954|ENST00000368977	.|.	.|.	.|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.44582	.|0.1300	L|L	0.55990|0.55990	1.75|1.75	0.80722|0.80722	D|D	1|1	.|P	.|0.36837	.|0.571	.|B	.|0.38921	.|0.285	.|T	.|0.53844	.|-0.8381	.|9	.|0.66056	.|D	.|0.02	-13.3981|-13.3981	13.1411|13.1411	0.59436|0.59436	0.0731:0.0:0.9269:0.0|0.0731:0.0:0.9269:0.0	.|.	.|292	.|Q8WV93	.|LACE1_HUMAN	X|V	160|292	.|.	.|ENSP00000357973:G292V	E|G	+|+	1|2	0|0	LACE1|LACE1	108875177|108875177	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.690000|4.690000	0.61731|0.61731	2.693000|2.693000	0.91896|0.91896	0.655000|0.655000	0.94253|0.94253	GAA|GGA		TCGA-HZ-A49G-01A-11D-A26I-08	LACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041719.4	1	0	0	23	263	0	20	1	1.408413e-01	3	5	0	20	2		0	0	0	0	0	2	1	0.999999	23	257	0	20	2		0	0	0	0	20	2	-20.000000	1	1	0	0		1	0	0	0	1.869586	1	0.150000	1.820000	0.073569	0.800000	0.570000	0.900000	0.890000	0.789551	0.800000	0	0.690000	0.870000
PDE10A	10846	broad.mit.edu	37	6	165832222	165832222	+	Missense_Mutation	SNP	A	A	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr6:165832222A>T	ENST00000366882.1	-	12	1023	c.869T>A	c.(868-870)tTc>tAc	p.F290Y	PDE10A_ENST00000354448.4_Missense_Mutation_p.F290Y|PDE10A_ENST00000539869.2_Missense_Mutation_p.F300Y			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A			71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	GTCCACCTGGAAAAGCGCACA	0.388000													Esophageal Squamous(22;308 615 5753 12038 40624)											0							SO:0001583	missense			ENST00000366882.1	0	1	hg19		.	.	.	.	.	.	.	.	.	.	A	26.7	4.762878	0.89932	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69561	-0.41;-0.41	5.03	5.03	0.67393	GAF (2);	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.63428	1.95	0.80722	D	1	D;D	0.62365	0.991;0.988	D;D	0.76071	0.982;0.987	T	0.76887	-0.2793	10	0.54805	T	0.06	.	14.784	0.69787	1.0:0.0:0.0:0.0	.	300;290	Q9ULW9;Q9Y233	.;PDE10_HUMAN	Y	290;318;300;290;289	ENSP00000355847:F290Y;ENSP00000346435:F290Y	ENSP00000341187:F300Y	F	-	2	0	PDE10A	165752212	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	8.749000	0.91619	1.903000	0.55091	0.459000	0.35465	TTC		TCGA-HZ-A49G-01A-11D-A26I-08	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1	1	0	1	30	270	0	17	0	1.578555e-01	0	7	0	17	2		0	0	0	0	0	2	1	1.000000	30	267	0	17	2		0	0	0	0	17	2	-20.000000	1	1	0	0		1	0	0	0	1.855863	1	0.150000	1.820000	0.065934	0.750000	0.620000	1.000000	0.790000	0.758965	0.750000	0	0.690000	0.790000
COL9A1	1297	broad.mit.edu	37	6	70935662	70935662	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr6:70935662C>T	ENST00000357250.6	-	37	2712	c.2554G>A	c.(2554-2556)Ggt>Agt	p.G852S	COL9A1_ENST00000320755.7_Missense_Mutation_p.G609S|COL9A1_ENST00000370499.4_Missense_Mutation_p.G609S|RP1-149L1.1_ENST00000522264.1_RNA|COL9A1_ENST00000489611.1_5'UTR	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1			80					CCAGGCAAACCGTTGGGACCT	0.428000																								0							SO:0001583	missense			ENST00000357250.6	1	1	hg19	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304275	0.81136	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.99329	-5.75;-5.75;-5.75	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.96777	3.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97485	1.0050	10	0.87932	D	0	.	19.2294	0.93831	0.0:1.0:0.0:0.0	.	852;609;401	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	S	852;609;609	ENSP00000349790:G852S;ENSP00000315252:G609S;ENSP00000359530:G609S	ENSP00000315252:G609S	G	-	1	0	COL9A1	70992383	1.000000	0.71417	0.999000	0.59377	0.950000	0.60333	7.313000	0.78978	2.557000	0.86248	0.591000	0.81541	GGT		TCGA-HZ-A49G-01A-11D-A26I-08	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2	0	0	0	19	453	0	47	0	2.471478e-02	0	6	0	47	2		0	0	0	0	0	2	1	0.999990	19	449	0	46	2		0	0	0	0	47	2	-2.675507	1	1	0	0		1	1	2	3	2.029128	0	0.150000	1.820000	0.153808	0.550000	0.340000	1.000000	0.530000	0.579224	0.550000	0	0.430000	0.710000
ABCB5	340273	broad.mit.edu	37	7	20768012	20768012	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr7:20768012C>T	ENST00000404938.2	+	23	3453	c.2801C>T	c.(2800-2802)gCg>gTg	p.A934V	ABCB5_ENST00000258738.6_Missense_Mutation_p.A489V	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	p.A489V(1)		77					TTTGCCTATGCGGCAGGGTTT	0.423000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000404938.2	1	1	hg19	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.306909	0.81247	0.0	1.16E-4	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90133	-2.62;-2.62	3.91	3.91	0.45181	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.52532	D	0.000062	D	0.95689	0.8598	M	0.91300	3.195	0.51012	D	0.999903	D;D;D	0.89917	0.999;1.0;0.995	D;P;P	0.67103	0.949;0.904;0.899	D	0.96323	0.9238	10	0.87932	D	0	.	14.2264	0.65863	0.0:1.0:0.0:0.0	.	934;112;489	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	V	934;489	ENSP00000384881:A934V;ENSP00000258738:A489V	ENSP00000258738:A489V	A	+	2	0	ABCB5	20734537	1.000000	0.71417	0.943000	0.38184	0.979000	0.70002	5.943000	0.70211	2.472000	0.83506	0.655000	0.94253	GCG		TCGA-HZ-A49G-01A-11D-A26I-08	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	1	0	0	53	531	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	53	529	0	44	2		0	0	0	0	44	2	-3.318794	1	1	121410	1	37	1	1	2	3	2.032143	0	0.150000	1.820000	0.154439	0.990000	0.920000	1.000000	1.000000	0.995868	0.990000	1	0.990000	1.000000
DPYS	1807	broad.mit.edu	37	8	105456665	105456665	+	Splice_Site	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr8:105456665C>T	ENST00000351513.2	-	4	736	c.604G>A	c.(604-606)Gga>Aga	p.G202R		NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase			41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)		TTCTTTGCTCCCTAAAAAGAC	0.478000																								0							SO:0001630	splice_region_variant			ENST00000351513.2	1	0	hg19	CCDS6302.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.578794	0.65878	.	.	ENSG00000147647	ENST00000351513;ENST00000521573	D;D	0.89485	-2.52;-2.15	5.67	5.67	0.87782	Amidohydrolase 1 (1);	0.171294	0.49916	D	0.000126	D	0.84701	0.5530	N	0.16130	0.375	0.58432	D	0.999998	P	0.44816	0.844	P	0.51453	0.67	T	0.81309	-0.0991	10	0.13108	T	0.6	-10.9332	14.9731	0.71249	0.0:0.9298:0.0:0.0702	.	202	Q14117	DPYS_HUMAN	R	202;149	ENSP00000276651:G202R;ENSP00000430246:G149R	ENSP00000276651:G202R	G	-	1	0	DPYS	105525841	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.482000	0.60257	2.666000	0.90696	0.655000	0.94253	GGA		TCGA-HZ-A49G-01A-11D-A26I-08	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	1	0	0	13	209	0	29	0	0	0	1	0	29	2		0	0	0	0	0	2	1	0.999568	13	208	0	28	2		0	0	0	0	29	2	-3.322268	1	1	0	0		1	1	2	3	2.050686	0	0.150000	1.820000	0.158207	0.830000	0.450000	1.000000	1.000000	0.815817	0.830000	0	0.620000	1.000000
SPATC1	375686	broad.mit.edu	37	8	145096207	145096207	+	Missense_Mutation	SNP	A	A	G			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr8:145096207A>G	ENST00000377470.3	+	4	1483	c.1381A>G	c.(1381-1383)Atc>Gtc	p.I461V	SPATC1_ENST00000447830.2_Intron	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1			15	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;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)		CCTGTCCAGCATCTTCCCAGA	0.632000																								0							SO:0001583	missense			ENST00000377470.3	1	1	hg19	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	A	15.33	2.802272	0.50315	.	.	ENSG00000186583	ENST00000377470	T	0.39056	1.1	4.48	4.48	0.54585	.	0.219834	0.35615	N	0.003091	T	0.40932	0.1137	L	0.42581	1.335	0.80722	D	1	P	0.42584	0.784	P	0.48166	0.569	T	0.12734	-1.0536	10	0.20519	T	0.43	-18.189	10.4401	0.44460	1.0:0.0:0.0:0.0	.	461	Q76KD6	SPERI_HUMAN	V	461	ENSP00000366690:I461V	ENSP00000366690:I461V	I	+	1	0	SPATC1	145168195	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.117000	0.41939	1.794000	0.52575	0.379000	0.24179	ATC		TCGA-HZ-A49G-01A-11D-A26I-08	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	1	0	0	18	194	0	36	0	8.182601e-03	0	2	0	36	2		0	0	0	0	0	2	1	0.999983	18	191	0	36	2		0	0	0	0	36	2	-19.999980	1	1	0	0		1	1	2	3	2.050686	0	0.150000	1.820000	0.158207	0.990000	0.720000	1.000000	1.000000	0.968298	0.990000	1	0.920000	1.000000
CDKN2A	1029	broad.mit.edu	37	9	21971003	21971003	+	Missense_Mutation	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr9:21971003C>T	ENST00000304494.5	-	2	625	c.355G>A	c.(355-357)Gag>Aag	p.E119K	CDKN2A_ENST00000530628.2_Silent_p.*133*|CDKN2A_ENST00000498124.1_Missense_Mutation_p.E119K|CDKN2A_ENST00000579755.1_Silent_p.*133*|CDKN2A_ENST00000494262.1_Missense_Mutation_p.E68K|CDKN2A_ENST00000497750.1_Missense_Mutation_p.E68K|CDKN2A_ENST00000578845.2_Missense_Mutation_p.E68K|CDKN2A_ENST00000446177.1_Missense_Mutation_p.E119K|CDKN2A_ENST00000361570.3_Silent_p.*174*|CDKN2A_ENST00000498628.2_Missense_Mutation_p.E68K|CDKN2A_ENST00000579122.1_Missense_Mutation_p.E119K|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.E68K	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	p.0?(1315)|p.?(44)|p.E119*(4)|p.E119Q(2)|p.0(1)|p.A118fs*10(1)|p.A118fs*27(1)|p.*174L(1)		4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)			CCCAGCTCCTCAGCCAGGTCC	0.726000		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)														1369	Whole gene deletion(1316)|Unknown(44)|Substitution - Nonsense(4)|Substitution - Missense(2)|Deletion - Frameshift(1)|Complex - frameshift(1)|Nonstop extension(1)						SO:0001583	missense			ENST00000304494.5	1	1	hg19	CCDS6510.1	.	.	.	.	.	.	.	.	.	.	C	9.497	1.102324	0.20632	.	.	ENSG00000147889	ENST00000304494;ENST00000446177	T;T	0.64085	-0.08;-0.08	5.93	2.91	0.33838	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.69504	0.3118	.	.	.	0.21220	N	0.999751	D	0.71674	0.998	D	0.74023	0.982	T	0.56498	-0.7969	8	0.20519	T	0.43	-4.2732	8.4897	0.33093	0.0:0.4925:0.4233:0.0842	.	119	P42771	CD2A1_HUMAN	K	119	ENSP00000307101:E119K;ENSP00000394932:E119K	ENSP00000307101:E119K	E	-	1	0	CDKN2A	21961003	0.002000	0.14202	0.998000	0.56505	0.865000	0.49528	0.628000	0.24522	0.816000	0.34421	0.655000	0.94253	GAG		TCGA-HZ-A49G-01A-11D-A26I-08	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	1	0	1	22	206	0	30	1	4.120908e-01	3	11	0	30	2	1	1	44	434	0	441	2	1	0.999999	22	204	0	30	2		0	0	0	0	30	2	-9.131699	1	1	0	0		1	0	1	1	1.867881	1	0.150000	1.820000	0.081081	0.900000	0.660000	1.000000	0.990000	0.889158	0.900000	1	0.790000	0.980000
INSL4	3641	broad.mit.edu	37	9	5233847	5233847	+	Silent	SNP	C	C	T			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chr9:5233847C>T	ENST00000239316.4	+	2	495	c.390C>T	c.(388-390)gaC>gaT	p.D130D		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)			6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)			TAATTTGTGACGATGGAACTT	0.378000																								0							SO:0001819	synonymous_variant			ENST00000239316.4	0	1	hg19	CCDS6459.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	1	0	0	12	193	0	18		0	0	0	0	18	2		0	0	0	0	0	2	1	0.999127	11	191	0	18	2		0	0	0	0	18	2	-5.147433	1	1	121400	12	39	1	0	1	1	1.867881	1	0.150000	1.820000	0.081081	0.680000	0.380000	0.960000	0.690000	0.694832	0.680000	0	0.520000	0.860000
BEX2	84707	broad.mit.edu	37	X	102564742	102564742	+	Missense_Mutation	SNP	G	G	A	rs149711551	byFrequency	TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chrX:102564742G>A	ENST00000372677.3	-	3	430	c.163C>T	c.(163-165)Cgg>Tgg	p.R55W	BEX2_ENST00000372674.1_Missense_Mutation_p.R55W|BEX2_ENST00000536889.1_Missense_Mutation_p.R87W	NM_032621.3	NP_116010.1	Q9BXY8	BEX2_HUMAN	brain expressed X-linked 2			3					ACGCGGAACCGCCTACGGTTT	0.478000																								0							SO:0001583	missense			ENST00000372677.3	1	1	hg19	CCDS14505.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.672757	0.47781	.	.	ENSG00000133134	ENST00000372677;ENST00000536889;ENST00000372674;ENST00000449185	T;T;T;T	0.12361	2.69;2.69;2.69;2.69	4.01	-1.23	0.09465	.	0.689247	0.12748	N	0.442385	T	0.26810	0.0656	M	0.81497	2.545	0.09310	N	1	D;D	0.76494	0.999;0.999	P;D	0.63488	0.828;0.915	T	0.18713	-1.0328	10	0.87932	D	0	.	0.4238	0.00460	0.2149:0.1628:0.2858:0.3364	.	55;87	Q9BXY8;F5H7H5	BEX2_HUMAN;.	W	55;87;55;55	ENSP00000361762:R55W;ENSP00000442521:R87W;ENSP00000361759:R55W;ENSP00000394915:R55W	ENSP00000361759:R55W	R	-	1	2	BEX2	102451398	0.766000	0.28496	0.031000	0.17742	0.715000	0.41141	0.716000	0.25836	-0.425000	0.07371	0.600000	0.82982	CGG		TCGA-HZ-A49G-01A-11D-A26I-08	BEX2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057702.1	0	0	0	43	932	1	98	0	3.461783e-01	0	66	1	98	4		0	0	0	0	0	2	1	0.961286	44	924	1	98	29		0	0	0	1	98	2	-4.948481	1	1	121410	129	55	1	0	1	1			0.150000	1.820000	0.150000	0.580000	0.430000	0.770000	0.580000	0.596982	0.580000	0	0.500000	0.680000
ARX	170302	broad.mit.edu	37	X	25033684	25033684	+	Silent	SNP	G	G	A			TCGA-HZ-A49G-01A-11D-A26I-08	TCGA-HZ-A49G-10A-01D-A26I-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b69d58f0-e51c-470b-bcb3-743fb4cede11	6b9bda12-72ab-4d91-a3e5-df702e7cf48e	g.chrX:25033684G>A	ENST00000379044.4	-	1	381	c.171C>T	c.(169-171)cgC>cgT	p.R57R		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox			4					CCGGGTCGGCGCGGCTGGTCA	0.627000																								0							SO:0001819	synonymous_variant			ENST00000379044.4	0	1	hg19	CCDS14215.1																																																																																				TCGA-HZ-A49G-01A-11D-A26I-08	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056109.1	1	0	1	13	97	0	19		0	0	0	0	19	2		0	0	0	0	0	2	1	0.999621	13	96	0	19	2		0	0	0	0	19	2	-19.897360	1	1	0	0		1	0	1	1			0.150000	1.820000	0.150000	0.990000	0.870000	1.000000	1.000000	0.992853	0.990000	1	0.990000	1.000000
