Datasets:

bedylmz
/

missense-variant-effects

Chrom stringclasses 24 values	Position int64 47.3k 249M	Ref Base stringclasses 17 values	Alt Base stringclasses 20 values	Gene stringlengths 2 15	Sequence Ontology stringclasses 5 values	Exon Number float64 1 347 ⌀	cDNA change stringlengths 6 92	Protein Change stringlengths 9 13 ⌀	End Position int64 47.3k 249M	Tags stringlengths 6 16	1000 Genomes AF float64 0 1	1000 Genomes AFR AF float64 0 1	1000 Genomes AMR AF float64 0 1	1000 Genomes EAS AF float64 0 1	1000 Genomes EUR AF float64 0 1	1000 Genomes SAS AF float64 0 1	CADD Exome Score float64 -4.09 13.2	CADD Exome Phred float64 0 63	ESP6500 European American AF float64 0 1	ESP6500 African American AF float64 0 1	ExAC Gene and CNV pLI float64 0 1 ⌀	ExAC Gene and CNV pLI (Hom) float64 0 1 ⌀	ExAC Gene and CNV pLT float64 0 1 ⌀	ExAC Gene and CNV pLI NonTCGA float64 0 1 ⌀	ExAC Gene and CNV pLI (Hom) NonTCGA float64 0 1 ⌀	ExAC Gene and CNV pLT NonTCGA float64 0 1 ⌀	ExAC Gene and CNV pLI Nonpsych float64 0 1 ⌀	ExAC Gene and CNV pLI (Hom) Nonpsych float64 0 1 ⌀	ExAC Gene and CNV pLT Nonpsych float64 0 1 ⌀	ExAC Gene and CNV Del Int Z-Score float64 -2.62 3.81 ⌀	ExAC Gene and CNV Dup Int Z-Score float64 -2.53 2.74 ⌀	ExAC Gene and CNV CNV Int Z-Score float64 -2.47 3.02 ⌀	ExAC Gene and CNV CNV Bias/Noise stringclasses 2 values	Extra VCF INFO Annotations VCF Ref Allele stringclasses 23 values	Extra VCF INFO Annotations VCF Alt Allele stringclasses 25 values	Flanking Sequence Ref Sequence stringlengths 11 11	Flanking Sequence Alt Sequence stringlengths 11 11	GERP++ Neutral Rate float64 0 6.17	GERP++ RS Score float64 -12.3 6.17	GERP++ RS Ranked Score float64 0 1 ⌀	Grantham Scores Score int64 0 215	PhyloP Vert Score float64 -20 10	PhyloP Vert Ranked Score float64 0 1 ⌀	PhyloP Mamm Score float64 -20 11.9	PhyloP Mamm Ranked Score float64 0 1 ⌀	PhyloP Primate Score float64 -8.41 0.76 ⌀	PhyloP Primate Ranked Score float64 0 0.94 ⌀	PolyPhen-2 HDIV Prediction stringclasses 3 values	PolyPhen-2 HVAR Prediction stringclasses 3 values	PolyPhen-2 HDIV Rank Score float64 0 0.91	PolyPhen-2 HVAR Rank Score float64 0 0.97 ⌀	REVEL Score float64 0 1	REVEL Rank Score float64 0 1 ⌀	SIFT Prediction stringclasses 2 values	SIFT Confidence stringclasses 2 values	SIFT Score float64 0 1	SIFT Rank Score float64 0 1 ⌀	SIFT Median Info float64 2 4.32 ⌀	SIFT Seqs at Position float64 2 399 ⌀	SiPhy Stationary Distribution stringlengths 15 27 ⌀	SiPhy Score float64 0 27.7	SiPhy Rank Score float64 0 1 ⌀	Pathologic/Benign stringclasses 2 values	Flanking Sequence 5aa stringlengths 6 11 ⌀	Ref_AA stringclasses 21 values	Alt_AA stringclasses 21 values	Physico Change stringclasses 17 values	Source_Genome stringclasses 2 values
chr14	50,621,885	A	G	ATL1	missense_variant	10	c.1033A>G	p.Lys345Glu	50,621,885	AlleleID_4642958	0	0	0	0	0	0	3.53542	24.8	0	0	0.992118	0.007882	0	0.99706	0.00294	0	0.996669	0.003331	0	0.289127	-0.159186	0.026145	N	A	G	ATCCCAAATCC	ATCCCGAATCC	5.73	5.73	0.8969	56	9.325	0.96006	11.252	0.90779	0.756	0.94297	B	B	0.24313	0.34839	0.46	0.75755	Damaging	High	0.037	0.963037	2.72	68	1.0;0.0;0.0;0.0	15.2001	0.72697	Pathogenic	ELPHPKSMLQA	Lys	Glu	Basic to Acidic	hg38
chr1	216,422,138	A	C	USH2A	missense_variant	2	c.199T>G	p.Cys67Gly	216,422,138	rs2102788868	0	0	0	0	0	0	3.767267	25.7	0	0	0	0.999989	0.000011	0	0.999992	0.000008	0	0.999999	0.000001	-2.22771	-0.343251	-0.833268	N	A	C	GTGACAAAAAG	GTGACCAAAAG	5.27	5.27	0.73696	159	7.298	0.78152	11.053	0.85327	0.691	0.84096	D	D	0.90584	0.92359	0.654	0.86986	Damaging	Low	0	1	3.48	15	1.0;0.0;0.0;0.0	15.1859	0.72568	Pathogenic	DRSTFCHSSAA	Cys	Gly	Nonpolar to Nonpolar	hg19
chr17	43,091,680	T	C	BRCA1	missense_variant	10	c.3851A>G	p.His1284Arg	43,091,680	rs80357499	0	0	0	0	0	0	1.251804	14.03	0	0	0	0.106035	0.893965	0	0.987832	0.012168	0	0.039737	0.960263	-1.804717	0.372233	-0.541889	N	T	C	TAAGGTGATGT	TAAGGCGATGT	5.01	2.72	0.31038	29	-0.335	0.07917	0.398	0.17967	0.609	0.47794	P	B	0.4774	0.3554	0.608	0.84613	Damaging	High	0.047	0.953047	2.79	21	0.1401;0.0;0.2919;0.568	6.9814	0.23731	Benign	ASQEHHLSEET	His	Arg	Basic to Basic	hg38
chr9	135,771,075	A	G	KCNT1	missense_variant	18	c.1988A>G	p.His663Arg	135,771,075	rs1285595185	0	0	0	0	0	0	1.63013	16.57	0	0	0.005349	0.994649	0.000002	0.008504	0.991492	0.000005	0.821183	0.178817	0	0.603067	0.434602	0.560655	N	A	G	CGTGCACAGCA	CGTGCGCAGCA	3.62	3.62	0.40451	29	5.103	0.64415	6.785	0.56592	0.65	0.52971	P	B	0.40811	0.44119	0.263	0.57612	Tolerated	High	0.062	0.938062	3.06	88	1.0;0.0;0.0;0.0	12.3839	0.5447	Benign	QGTEHRPTQSG	His	Arg	Basic to Basic	hg19
chr14	105,367,372	A	G	PACS2	missense_variant	5	c.583A>G	p.Thr195Ala	105,367,372	AlleleID_3578313	0	0	0	0	0	0	1.199843	13.63	0.000116	0	0.999325	0.000675	0	0.999693	0.000307	0	0.999621	0.000379	0	1.003845	-1.364332	-0.777085	N	A	G	AGTCCACGGGT	AGTCCGCGGGT	4.37	4.37	0.51663	58	1.461	0.34866	-0.325	0.09934	0.691	0.84096	B	B	0.02946	0.04355	0.106	0.3013	Tolerated	High	0.509	0.491508	2.5	66	1.0;0.0;0.0;0.0	12.3851	0.54477	Benign	PKAKSTDNYSE	Thr	Ala	Polar to Nonpolar	hg38
chr1	237,628,052	G	A	RYR2	missense_variant	41	c.6412G>A	p.Glu2138Lys	237,628,052	rs1553531703	0	0	0	0	0	0	4.364054	31	0	0	1	0	0	1	0	0	0.999999	0.000001	0	-0.168246	-0.426883	-0.404698	N	G	A	AAGAAGAAGAG	AAGAAAAAGAG	5.47	5.47	0.8027	56	0	null	0	null	null	null	D	D	0.90584	0.92359	0.839	0.94952	null	null	0.015	null	null	null	0.0;0.0;1.0;0.0	19.6715	0.95891	Pathogenic	RMGKEEEKLMI	Glu	Lys	Acidic to Basic	hg38
chr14	105,383,456	C	G	PACS2	missense_variant	16	c.1723C>G	p.Leu575Val	105,383,456	rs2544819538	0	0	0	0	0	0	3.559706	24.9	0	0	0.999325	0.000675	0	0.999693	0.000307	0	0.999621	0.000379	0	1.003845	-1.364332	-0.777085	N	C	G	AGCAGCTGTCC	AGCAGGTGTCC	4.17	3.25	0.36208	32	2.661	0.46423	2.034	0.30268	0.599	0.4025	D	D	0.90584	0.92359	0.375	0.69358	Damaging	High	0.006	0.994006	2.55	66	0.0;0.9023;0.0;0.0977	11.5352	0.49698	Benign	QLSHKTPDWLG	Leu	Val	Nonpolar to Nonpolar	hg19
chr8	38,145,313	G	A	STAR	missense_variant	6	c.653C>T	p.Ala218Val	38,145,313	rs137852690	0	0	0	0	0	0	3.081036	23.6	0	0	0	0.177592	0.822408	0.000015	0.409941	0.590045	0.000102	0.548936	0.450962	0.551749	-0.077883	0.19073	N	G	A	GCTCCGCCCTG	GCTCCACCCTG	5.86	4.06	0.46402	64	3.357	0.51997	8.314	0.76952	0.672	0.70159	D	P	0.65571	0.46548	0.758	0.91753	Damaging	High	0.006	0.994006	3.21	36	0.0;0.5105;0.4895;0.0	17.295	0.86994	Pathogenic	VSYFSHELGFK	Ala	Val	Nonpolar to Nonpolar	hg38
chr7	94,409,805	G	C	COL1A2	missense_variant	19	c.1019G>C	p.Gly340Ala	94,409,805	AlleleID_4188053	0	0	0	0	0	0	4.263564	29.3	0	0	0.999755	0.000245	0	0.999728	0.000272	0	0.999908	0.000092	0	-0.85644	-0.537773	-0.576131	N	G	C	TACTGGTGCCA	TACTGCTGCCA	5.7	5.7	0.88645	60	9.574	0.97344	11.912	0.99606	0.676	0.7674	D	D	0.77913	0.88582	0.965	0.99518	Damaging	High	0.002	0.998002	2.63	138	0.0;0.0;1.0;0.0	20.2246	0.98333	Pathogenic	AAGATGARGLV	Gly	Ala	Nonpolar to Nonpolar	hg19
chr14	104,943,836	A	G	AHNAK2	missense_variant	7	c.11615T>C	p.Leu3872Pro	104,943,836	AlleleID_3674999	0.0002	0	0	0	0	0.001022	0.217209	3.322	0	0	null	null	null	null	null	null	null	null	null	null	null	null	null	A	G	CCTCCAGGAGT	CCTCCGGGAGT	4.28	-2.03	0.0692	98	1.427	0.34489	-4.092	0.02347	-0.194	0.09177	B	B	0.02946	0.01387	0.027	0.05988	Tolerated	High	0.371	0.629371	3.18	12	0.3492;0.0;0.5195;0.1313	7.2986	0.2542	Benign	VDMKLLEGHVP	Leu	Pro	Nonpolar to Nonpolar	hg38
chr21	33,552,853	G	A	SON	missense_variant	3	c.3622G>A	p.Val1208Ile	33,552,853	rs1480721717	0	0	0	0	0	0	2.361105	21.9	0	0	1	0	0	1	0	0	1	0	0	0.531859	0.188915	0.424614	N	G	A	AGTCTGTATCG	AGTCTATATCG	5.12	4.23	0.49151	29	3.26	0.51225	3.99	0.4098	0.676	0.7674	P	P	0.46109	0.47948	0.074	0.21613	Tolerated	High	0.088	0.912088	3.1	25	0.0;0.153;0.847;0.0	13.9291	0.63333	Benign	PSEESVSQPEP	Val	Ile	Nonpolar to Nonpolar	hg19
chr13	32,363,390	G	C	BRCA2	missense_variant	18	c.8188G>C	p.Ala2730Pro	32,363,390	rs80359066	0	0	0	0	0	0	3.435181	24.5	0	0.000227	0	0.999975	0.000025	0	0.999999	0.000001	0	0.999886	0.000114	-0.587781	1.061048	0.429504	N	G	C	TTAAGGCCCAG	TTAAGCCCCAG	5.49	5.49	0.80949	27	6.514	0.73657	7.498	0.59452	0.618	0.50648	null	null	0.60381	null	0.711	0.89696	Damaging	High	0.008	0.992008	2.69	30	0.0;0.0;1.0;0.0	19.3535	0.94365	Pathogenic	WYAVKAQLDPP	Ala	Pro	Nonpolar to Nonpolar	hg19
chr5	36,035,886	C	T	UGT3A2	missense_variant	7	c.1384G>A	p.Val462Ile	36,035,886	AlleleID_3632555	0.0002	0	0	0	0	0.001022	0.173641	2.828	0	0	0	0.082048	0.917952	0.000001	0.514018	0.485981	0	0.036273	0.963727	0.083219	1.303234	0.917599	N	C	T	GAGGACGTGGT	GAGGATGTGGT	2.74	-1.18	0.09071	29	0.808	0.26813	0.762	0.21323	-0.917	0.02218	B	B	0.19556	0.087	0.121	0.3358	Tolerated	High	1	0.000999	2.63	46	0.0;0.3223;0.0;0.6777	7.3078	0.2547	Benign	GWIDHVLQTGG	Val	Ile	Nonpolar to Nonpolar	hg38
chr13	51,944,230	C	G	ATP7B	missense_variant	14	c.3122G>C	p.Arg1041Pro	51,944,230	rs2547628381	0	0	0	0	0	0	3.391973	24.4	0	0	0	0.005483	0.994517	0	0.013689	0.986311	0	0.075685	0.924315	-2.09996	-0.354683	-1.030212	N	C	G	GCACCCGCATG	GCACCGGCATG	5.43	5.43	0.78925	103	2.11	0.41497	3.3	0.37375	0.599	0.4025	D	D	0.90584	0.88582	0.827	0.94503	Damaging	High	0.01	0.99001	2.52	86	0.0;1.0;0.0;0.0	19.2349	0.93815	Pathogenic	VPRVMRVLLLG	Arg	Pro	Basic to Nonpolar	hg38
chr20	63,444,737	C	A	KCNQ2	missense_variant	4	c.612G>T	p.Gln204His	63,444,737	rs796052625	0	0	0	0	0	0	3.114848	23.7	0	0	0.999356	0.000644	0	0.998668	0.001332	0	0.998459	0.001541	0	-2.35173	-2.122308	-2.141488	N	C	A	AGAATCTGCAG	AGAATATGCAG	3.88	0.661	0.16971	24	2.136	0.41744	0.737	0.21131	0.533	0.24879	D	D	0.77913	0.92359	0.778	0.92583	Damaging	High	0.001	0.999001	2.56	96	0.0;0.675;0.1488;0.1762	6.4735	0.21083	Pathogenic	SLRFLQILRMI	Gln	His	Polar to Basic	hg19
chr7	44,220,084	G	A	CAMK2B	missense_variant	23	c.1979C>T	p.Ala660Val	44,220,084	rs778590827	0	0	0	0	0	0	4.199904	28.7	0	0	0.46862	0.53137	0.000009	0.982524	0.017476	0	0.633765	0.366221	0.000015	0.290507	1.167926	0.986324	N	G	A	CAGGCGCGCCC	CAGGCACGCCC	4.32	4.32	0.5073	64	9.535	0.97135	11.749	0.95364	0.676	0.7674	D	D	0.90584	0.92359	0.346	0.66769	Damaging	Low	0.003	0.997003	3.26	124	0.0;0.0;1.0;0.0	15.7149	0.77321	Benign	FHCSGAPVAPL	Ala	Val	Nonpolar to Nonpolar	hg19
chr7	30,451,816	C	T	NOD1	missense_variant	6	c.1601G>A	p.Arg534Lys	30,451,816	AlleleID_3562977	0	0	0	0	0	0	-1.177848	0.003	0	0	0	0.051794	0.948206	0	0.32976	0.67024	0	0.033411	0.966589	0.259461	-0.012367	0.103611	Y	C	T	CCACCCTGTCG	CCACCTTGTCG	5.52	-2.53	0.05926	26	0.192	0.16902	-1.455	0.05401	-1.021	0.01731	B	B	0.02946	0.01387	0.129	0.35316	Tolerated	Low	1	0.000999	3.32	17	0.0;0.5202;0.0;0.4798	13.2462	0.59283	Benign	LVLDDRVGTQE	Arg	Lys	Basic to Basic	hg19
chr1	161,307,338	A	C	MPZ	missense_variant	2	c.154T>G	p.Phe52Val	161,307,338	rs1558154644	0	0	0	0	0	0	4.243336	29.1	0	0	0.691716	0.304225	0.00406	0.905785	0.093448	0.000767	0.648819	0.343867	0.007314	0.179726	0.033038	0.121092	N	A	C	CCAGAAGGAGC	CCAGACGGAGC	5.29	5.29	0.74331	50	8.19	0.89672	11.175	0.88104	0.756	0.94297	D	D	0.90584	0.97372	0.897	0.97097	Damaging	High	0	1	2.57	34	1.0;0.0;0.0;0.0	13.1777	0.58888	Pathogenic	TLHCSFWSSEW	Phe	Val	Nonpolar to Nonpolar	hg38
chr12	102,855,183	T	G	PAH	missense_variant	6	c.659A>C	p.His220Pro	102,855,183	rs1592954413	0	0	0	0	0	0	1.620873	16.51	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	T	G	CTTCATGGAAG	CTTCAGGGAAG	5.47	0.833	0.17934	77	0.186	0.16787	0.597	0.19884	-0.126	0.13398	B	B	0.02946	0.04355	0.397	0.71163	Tolerated	High	0.088	0.912088	2.48	179	0.0;0.4269;0.0;0.5731	10.7465	0.45192	Pathogenic	KYCGFHEDNIP	His	Pro	Basic to Nonpolar	hg19
chr3	15,644,557	C	A	BTD	missense_variant	4	c.641C>A	p.Thr214Asn	15,644,557	AlleleID_4858582	0	0	0	0	0	0	3.033992	23.5	0	0	0.000001	0.210972	0.789026	0.000001	0.162044	0.837955	0.000001	0.139845	0.860155	-0.583177	-0.472238	-0.550575	N	C	A	TGATACCCCCT	TGATAACCCCT	5.73	5.73	0.8969	65	7.905	0.86479	7.705	0.66497	0.549	0.26987	D	D	0.90584	0.97372	0.833	0.94728	Damaging	High	0.002	0.998002	2.68	68	0.0;1.0;0.0;0.0	19.8778	0.9687	Pathogenic	LITFDTPFAGR	Thr	Asn	Polar to Polar	hg38
chr11	121,158,084	T	C	TECTA	missense_variant	14	c.4549T>C	p.Cys1517Arg	121,158,084	rs2496973735	0	0	0	0	0	0	4.247247	29.1	0	0	0	0.99999	0.00001	0	0.999993	0.000007	0	0.999998	0.000002	-0.551815	0.753261	0.26467	N	T	C	CCATCTGCCAG	CCATCCGCCAG	5.67	5.67	0.87626	180	6.248	0.72374	7.881	0.72509	0.661	0.55757	D	D	0.90584	0.92359	0.758	0.91753	Damaging	Low	0	1	3.8	12	0.0;0.0;0.0;1.0	15.9165	0.79218	Pathogenic	VLSTICQKLPD	Cys	Arg	Nonpolar to Basic	hg38
chr7	44,150,015	C	T	GCK	missense_variant	5	c.533G>A	p.Gly178Glu	44,150,015	rs886039380	0	0	0	0	0	0	3.895088	26.3	0	0	0.204306	0.793691	0.002003	0.466617	0.532243	0.00114	0.957282	0.042692	0.000026	0.35147	0.176415	0.290779	N	C	T	TGTTCCCTTCT	TGTTCTCTTCT	5.83	5.83	0.93035	98	7.905	0.86479	7.605	0.61698	0.599	0.4025	D	D	0.90584	0.97372	0.964	0.9949	Damaging	High	0.01	0.99001	2.6	122	0.0;1.0;0.0;0.0	19.7478	0.96237	Pathogenic	GTPYWMAPEVA	Gly	Glu	Nonpolar to Acidic	hg38
chr17	43,124,027	A	G	BRCA1	missense_variant	2	c.70T>C	p.Cys24Arg	43,124,027	rs80357410	0	0	0	0	0	0	4.115228	27.9	0	0	0	0.106035	0.893965	0	0.987832	0.012168	0	0.039737	0.960263	-1.804717	0.372233	-0.541889	N	A	G	GGGACACTCTA	GGGACGCTCTA	3.83	3.83	0.43117	180	4.168	0.58007	11.085	0.85821	0.634	0.51959	D	D	0.90584	0.97372	0.94	0.98708	Damaging	Low	0	1	3.41	19	1.0;0.0;0.0;0.0	8.9255	0.3461	Pathogenic	QKILECPICLE	Cys	Arg	Nonpolar to Basic	hg19
chr17	43,045,732	C	A	BRCA1	missense_variant	23	c.5538G>T	p.Gln1846His	43,045,732	rs80356849	0	0	0	0	0	0	3.110928	23.7	0	0	0	0.106035	0.893965	0	0.987832	0.012168	0	0.039737	0.960263	-1.804717	0.372233	-0.541889	N	C	A	TGGCACTGGTA	TGGCAATGGTA	5.32	1.19	0.20025	24	0.535	0.22822	0.096	0.14582	0.599	0.4025	D	P	0.68779	0.54713	0.645	0.86536	Damaging	Low	0.003	0.997003	4.12	21	0.0;0.6708;0.0;0.3292	7.4699	0.26349	Benign	SVALYQCQELD	Gln	His	Polar to Basic	hg38
chr12	101,753,518	G	T	GNPTAB	missense_variant	19	c.3456C>A	p.Asp1152Glu	101,753,518	rs1594204203	0	0	0	0	0	0	3.558679	24.9	0	0	0.000004	0.999978	0.000018	0.000032	0.999944	0.000023	0.000126	0.999854	0.00002	0.747111	-2.531252	-2.471628	N	G	T	ATGTTGTCATT	ATGTTTTCATT	5.45	3.62	0.40451	45	3.819	0.55386	3.411	0.3819	0.608	0.46601	D	D	0.90584	0.82059	0.776	0.92501	Damaging	High	0	1	2.3	34	0.2276;0.0;0.7724;0.0	8.8049	0.33906	Pathogenic	FVCLNDNIDHN	Asp	Glu	Acidic to Acidic	hg19
chr19	919,563	T	C	KISS1R	missense_variant	3	c.443T>C	p.Leu148Ser	919,563	rs28939719	0	0	0	0	0	0	3.814421	25.9	0	0	0.003971	0.647047	0.348982	0.114766	0.778594	0.10664	0.003296	0.576677	0.420027	null	null	null	null	T	C	CCCGTTGCGCG	CCCGTCGCGCG	3.96	3.96	0.44926	145	2.048	0.40903	5.845	0.50284	0.556	0.28261	D	D	0.7322	0.72001	0.484	0.77335	Damaging	High	0.001	0.999001	3.19	69	0.0;0.0;0.0;1.0	10.7939	0.4546	Pathogenic	VTVFPLRALHR	Leu	Ser	Nonpolar to Polar	hg38
chr17	43,124,025	A	C	BRCA1	missense_variant	2	c.72T>G	p.Cys24Trp	43,124,025	rs1597923232	0	0	0	0	0	0	4.222076	28.9	0	0	0	0.106035	0.893965	0	0.987832	0.012168	0	0.039737	0.960263	-1.804717	0.372233	-0.541889	N	A	C	ATGGGACACTC	ATGGGCCACTC	3.83	2.74	0.3121	215	2.718	0.46904	4.628	0.44104	-0.206	0.08541	D	D	0.90584	0.97372	0.886	0.96688	Damaging	Low	0	1	3.41	19	0.8758;0.0;0.1242;0.0	5.7399	0.17238	Pathogenic	QKILECPICLE	Cys	Trp	Nonpolar to Nonpolar	hg38
chr17	43,115,729	C	G	BRCA1	missense_variant	3	c.131G>C	p.Cys44Ser	43,115,729	rs80357446	0	0	0	0	0	0	3.658958	25.3	0	0	0	0.106035	0.893965	0	0.987832	0.012168	0	0.039737	0.960263	-1.804717	0.372233	-0.541889	N	C	G	ACTTGCAAAAT	ACTTGGAAAAT	5.97	5.97	0.96923	112	3.475	0.529	7.6	0.61533	0.599	0.4025	D	D	0.90584	0.92359	0.925	0.98154	Damaging	Low	0	1	3.32	22	0.0;1.0;0.0;0.0	15.9389	0.79435	Pathogenic	CDHIFCKFCML	Cys	Ser	Nonpolar to Polar	hg19
chr9	35,825,795	T	C	FAM221B	missense_variant	2	c.367A>G	p.Thr123Ala	35,825,795	rs1435819903	0	0	0	0	0	0	-1.516045	0.001	0	0	0.000004	0.214728	0.785268	0.000025	0.312178	0.687796	0.000024	0.280133	0.719843	0.339709	0.36816	0.503047	N	T	C	CAGAGTATCAG	CAGAGCATCAG	4.19	-5.66	0.02242	58	-2.791	0.00837	-2.677	0.03477	-0.352	0.05559	B	B	0.02946	0.04355	0.002	0.00045	Tolerated	Low	0.143	0.857143	3.42	11	0.2475;0.2091;0.1218;0.4215	0.947	0.01269	Benign	LSSSDTLKEDL	Thr	Ala	Polar to Nonpolar	hg38
chrX	41,346,394	T	G	DDX3X	missense_variant	13	c.1481T>G	p.Ile494Ser	41,346,394	rs1064796924	0	0	0	0	0	0	4.219069	28.8	0	0	0.99893	0.00107	0	0.997965	0.002034	0	0.997976	0.002024	0	null	null	null	null	T	G	CCCAATTTTAG	CCCAAGTTTAG	5.1	5.1	0.68795	142	7.969	0.87564	7.911	0.7403	0.665	0.62972	D	D	0.90584	0.92359	0.881	0.96502	Damaging	High	0	1	2.53	154	0.0;0.0;0.0;1.0	14.0517	0.64111	Pathogenic	SGKSPILVATA	Ile	Ser	Nonpolar to Polar	hg38
chr7	117,480,087	G	C	CFTR	5_prime_UTR_variant	1	c.-8G>C	null	117,480,087	rs1800501	0.027356	0.002269	0.012968	0.060516	0.048708	0.015337	1.417793	15.2	0.055465	0.011575	0	0.000005	0.999995	0	0.00012	0.99988	0	0.000012	0.999988	-2.623544	-0.857439	-1.552174	N	G	C	CGCCCGAGAGA	CGCCCCAGAGA	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg19
chr12	49,040,100	G	A	KMT2D	missense_variant	32	c.7670C>T	p.Pro2557Leu	49,040,100	rs189888707	0.008586	0.012859	0.008646	0	0.00497	0.015337	2.824758	23.1	0.00702	0.014033	1	0	0	1	0	0	1	0	0	0.934218	1.422585	1.338016	Y	G	A	GTGGCGGGAGA	GTGGCAGGAGA	5.3	4.42	0.52608	98	3.75	0.54874	8.578	0.77634	0.618	0.50648	B	B	0.09854	0.06944	0.317	0.63904	null	null	0.015	null	null	null	0.0828;0.0;0.9172;0.0	12.3413	0.5424	Benign	PQPGLPPPHGI	Pro	Leu	Nonpolar to Nonpolar	hg19
chr10	104,034,280	C	T	COL17A1	missense_variant	52	c.3821G>A	p.Gly1274Glu	104,034,280	rs749093771	0	0	0	0	0	0	3.887119	26.3	0	0	0	1	0	0	1	0	0	1	0	0.487246	-0.17196	0.079216	N	C	T	GGGGTCCCTGC	GGGGTTCCTGC	4.98	4.98	0.65545	98	5.707	0.68023	7.56	0.60459	0.524	0.24156	D	D	0.90584	0.78396	0.898	0.97135	Damaging	High	0.001	0.999001	2.69	72	0.0;1.0;0.0;0.0	16.4329	0.83627	Pathogenic	PPGPQGPPGDS	Gly	Glu	Nonpolar to Acidic	hg38
chr13	26,382,824	A	G	CDK8	missense_variant	5	c.467A>G	p.Asn156Ser	26,382,824	AlleleID_3883778	0	0	0	0	0	0	3.950371	26.6	0	0	0.946653	0.053346	0	0.892023	0.107976	0.000002	0.877706	0.122291	0.000003	1.123911	-0.388815	0.123675	N	A	G	TGCTAATATTT	TGCTAGTATTT	5.87	5.87	0.94246	46	8.639	0.90787	11.176	0.88137	0.756	0.94297	D	D	0.90584	0.97372	0.884	0.96614	Damaging	High	0	1	2.52	108	1.0;0.0;0.0;0.0	16.5764	0.84463	Pathogenic	DLKPANILVMG	Asn	Ser	Polar to Polar	hg38
chr6	7,727,238	C	T	BMP6	missense_variant	1	c.283C>T	p.Pro95Ser	7,727,238	rs199518216	0.0002	0	0.001441	0	0	0	3.184522	23.8	0.000871	0	0.895082	0.104876	0.000042	null	null	null	0.841013	0.158832	0.000155	0.878657	0.736755	0.988115	N	C	T	CCCGGCCCCTG	CCCGGTCCCTG	3.34	1.46	0.21665	74	5.342	0.6574	4.507	0.43632	0.505	0.23025	D	D	0.7322	0.75477	0.373	0.69188	Damaging	High	0.037	0.963037	2.51	70	0.0;0.7402;0.1636;0.0962	7.8176	0.28262	Benign	PHRPRPLHGLQ	Pro	Ser	Nonpolar to Polar	hg19
chr1	161,306,759	G	C	MPZ	missense_variant	3	c.397C>G	p.Pro133Ala	161,306,759	rs1553259648	0	0	0	0	0	0	3.862733	26.1	0	0	0.691716	0.304225	0.00406	0.905785	0.093448	0.000767	0.648819	0.343867	0.007314	0.179726	0.033038	0.121092	N	G	C	GTCTGGAGGGT	GTCTGCAGGGT	4.76	4.76	0.60037	27	9.006	0.93125	9.926	0.82543	0.654	0.53741	P	P	0.52645	0.55225	0.685	0.8849	Damaging	High	0	1	2.6	34	0.0;0.0;1.0;0.0	15.3148	0.73658	Pathogenic	DVKNPPDIVGK	Pro	Ala	Nonpolar to Nonpolar	hg19
chr3	52,349,202	C	G	DNAH1	missense_variant	14	c.2308C>G	p.Gln770Glu	52,349,202	rs74363541	0.020767	0.073374	0.010086	0	0	0	1.020992	11.89	0	0.0489	0	1	0	0	1	0	0	1	0	0.718312	0.663116	0.682978	N	C	G	CCTACCAGACG	CCTACGAGACG	5.13	4.2	0.48646	29	1.087	0.30476	4.627	0.441	0.599	0.4025	null	null	0.60381	null	0.117	0.32689	Tolerated	High	1	0.000999	2.52	41	0.0;0.7866;0.2134;0.0	15.744	0.77588	Benign	FLKTYQTQGLL	Gln	Glu	Polar to Acidic	hg19
chr15	92,978,284	G	T	CHD2	missense_variant	21	c.2628G>T	p.Leu876Phe	92,978,284	rs772889877	0	0	0	0	0	0	4.002048	27	0	0	1	0	0	1	0	0	1	0	0	0.935566	-0.558162	-0.082395	N	G	T	AATTTGGCTTC	AATTTTGCTTC	5.82	5.82	0.92715	22	5.721	0.68126	5.14	0.47705	0.676	0.7674	D	D	0.90584	0.97372	0.76	0.91837	Damaging	High	0	1	3.13	395	0.0;0.0;1.0;0.0	20.1001	0.97861	Pathogenic	GLGINLASADT	Leu	Phe	Nonpolar to Nonpolar	hg19
chr12	102,843,736	T	C	PAH	missense_variant	11	c.1109A>G	p.Glu370Gly	102,843,736	rs1592947508	0	0	0	0	0	0	3.668312	25.3	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	T	C	TCTTCTCCAGC	TCTTCCCCAGC	5.24	5.24	0.72756	98	5.089	0.64326	7.87	0.71911	0.609	0.47794	B	B	0.35387	0.43568	0.744	0.91155	Tolerated	High	0.147	0.853147	2.49	179	0.0;0.0;0.0;1.0	15.1404	0.72163	Pathogenic	LPLELEKTAIQ	Glu	Gly	Acidic to Nonpolar	hg38
chr12	57,572,100	C	T	KIF5A	missense_variant	14	c.1402C>T	p.Arg468Trp	57,572,100	rs771021589	0	0	0	0	0	0	2.814013	23	0	0	0.99998	0.00002	0	0.999917	0.000083	0	0.999977	0.000023	0	0.355654	-0.493358	-0.199356	N	C	T	TCCAGCGGGAG	TCCAGTGGGAG	4.93	4.01	0.4565	101	-0.135	0.10399	3.297	0.37352	0.599	0.4025	P	B	0.42206	0.30104	0.287	0.60574	Damaging	High	0.012	0.988012	2.57	73	0.3191;0.6809;0.0;0.0	11.7509	0.5093	Benign	NEKVQRELSHL	Arg	Trp	Basic to Nonpolar	hg19
chr6	32,049,456	C	T	TNXB	missense_variant	28	c.9571G>A	p.Gly3191Ser	32,049,456	rs60738846	0.00619	0.021936	0.002882	0	0	0	1.633977	16.59	0	0.028922	0.774154	0.224204	0.001642	0.730464	0.266814	0.002722	0.732107	0.264643	0.00325	null	null	null	null	C	T	GCGGCCCTGGG	GCGGCTCTGGG	4.39	4.39	0.52044	56	0	null	0	null	null	null	null	null	0.60381	null	0.185	0.45933	Damaging	Low	0	1	3.6	24	0.0;1.0;0.0;0.0	13.9491	0.63457	Benign	WTVPQGRFDSF	Gly	Ser	Nonpolar to Polar	hg19
chr12	102,848,500	T	C	PAH	intron_variant	null	c.913-1549A>G	null	102,848,500	rs34213541	0	0	0	0	0	0	0	0	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	T	C	AGAGGTTGAGG	AGAGGCTGAGG	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg38
chrX	154,861,810	C	G	F8	missense_variant	24	c.6631G>C	p.Ala2211Pro	154,861,810	rs137852468	0	0	0	0	0	0	3.660486	25.3	0	0	1	0	0	0.999999	0.000001	0	1	0	0	null	null	null	null	C	G	TGAAGCAGTAA	TGAAGGAGTAA	5.6	5.6	0.84939	27	6.09	0.71042	7.284	0.58032	0.596	0.33519	D	D	0.90584	0.92359	0.978	0.99822	Damaging	High	0	1	2.85	37	0.0;1.0;0.0;0.0	15.8026	0.78144	Pathogenic	DAQITASSYFT	Ala	Pro	Nonpolar to Nonpolar	hg19
chr5	44,305,072	C	T	FGF10	missense_variant	3	c.550G>A	p.Gly184Arg	44,305,072	rs1554035469	0	0	0	0	0	0	4.089173	27.7	0	0	0.858815	0.139003	0.002182	0.839804	0.157163	0.003033	0.844805	0.151818	0.003377	0.610144	0.880893	1.042124	N	C	T	AGCTCCTTTTC	AGCTCTTTTTC	5.87	5.87	0.94246	125	7.905	0.86479	7.717	0.67122	0.599	0.4025	D	D	0.90584	0.97372	0.966	0.99545	Damaging	High	0	1	2.7	64	0.0;1.0;0.0;0.0	20.2013	0.98255	Pathogenic	ALNGKGAPRRG	Gly	Arg	Nonpolar to Basic	hg38
chr6	87,256,408	A	C	ZNF292	missense_variant	8	c.2779A>C	p.Thr927Pro	87,256,408	AlleleID_4103405	0	0	0	0	0	0	1.313442	14.48	0.000121	0	0.999977	0.000023	0	null	null	null	0.999975	0.000025	0	-0.55578	0.028848	-0.164887	N	A	C	CTACTACTCCT	CTACTCCTCCT	5.77	2.02	0.25519	38	1.041	0.29901	0.241	0.16308	0.691	0.84096	P	B	0.4011	0.33484	0.047	0.12962	Tolerated	High	0.167	0.833167	2.77	17	0.641;0.0;0.359;0.0	8.176	0.30268	Benign	ENPATTPLLQS	Thr	Pro	Polar to Nonpolar	hg38
chr12	102,853,660	G	A	PAH	intron_variant	null	c.707-710C>T	null	102,853,660	rs539981875	0.000599	0.002269	0	0	0	0	0	0	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	G	A	AAATCGCTCAA	AAATCACTCAA	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg38
chr12	102,894,758	G	A	PAH	missense_variant	3	c.329C>T	p.Ser110Leu	102,894,758	rs199475627	0	0	0	0	0	0	3.789471	25.8	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	G	A	CTCGTGAAAGC	CTCGTAAAAGC	6.17	6.17	0.99706	145	8.899	0.92172	11.681	0.94222	0.676	0.7674	D	D	0.67487	0.66095	0.717	0.89966	Tolerated	High	0.062	0.938062	2.65	40	0.0;0.0;1.0;0.0	20.8794	0.99869	Pathogenic	TVHELSRDKKK	Ser	Leu	Polar to Nonpolar	hg38
chr15	48,229,307	G	C	SLC12A1	missense_variant	6	c.843G>C	p.Glu281Asp	48,229,307	rs886039870	0	0	0	0	0	0	3.223959	23.9	0	0	0	0.999053	0.000946	0.000003	0.99909	0.000908	0.00001	0.999249	0.000741	0.213787	-0.627819	-0.347008	N	G	C	GCTGAGACTGT	GCTGACACTGT	5.81	2.85	0.32189	45	2.321	0.43465	2.556	0.33289	0.676	0.7674	D	D	0.62325	0.71341	0.725	0.90324	Tolerated	High	0.078	0.922078	2.6	106	0.3667;0.1574;0.4759;0.0	4.4291	0.10864	Pathogenic	VVGFAETVVDL	Glu	Asp	Acidic to Acidic	hg38
chr3	129,528,915	T	A	RHO	missense_variant	1	c.182T>A	p.Val61Asp	129,528,915	AlleleID_3407850	0	0	0	0	0	0	4.100422	27.8	0	0	0.000557	0.704297	0.295147	0.000402	0.634846	0.364752	0.000379	0.591471	0.40815	0.461193	-0.026407	0.175684	N	T	A	CTACGTCACCG	CTACGACACCG	5.52	5.52	0.82084	152	8.012	0.88211	7.902	0.73606	0.609	0.47794	D	D	0.90584	0.92359	0.804	0.93621	Damaging	High	0.001	0.999001	2.74	306	0.0;0.0;0.0;1.0	15.3042	0.73568	Pathogenic	FLTLYVTVQHK	Val	Asp	Nonpolar to Acidic	hg38
chr14	73,192,712	G	T	PSEN1	missense_variant	7	c.617G>T	p.Gly206Val	73,192,712	rs63750082	0	0	0	0	0	0	4.060323	27.4	0	0	0.997601	0.002399	0	0.996102	0.003898	0	0.995825	0.004174	0	1.018537	1.21179	1.445078	N	G	T	TTTTGGTGTGG	TTTTGTTGTGG	5.6	5.6	0.84939	109	9.828	0.98316	11.667	0.94056	0.509	0.23192	D	D	0.90584	0.97372	0.934	0.98489	Damaging	High	0.002	0.998002	2.75	92	0.0;0.0;1.0;0.0	19.604	0.9555	Pathogenic	LIWNFGVVGMI	Gly	Val	Nonpolar to Nonpolar	hg19
chr13	32,337,117	T	A	BRCA2	missense_variant	11	c.2762T>A	p.Ile921Asn	32,337,117	AlleleID_3421270	0	0	0	0	0	0	0.258702	3.806	0	0	0	0.999975	0.000025	0	0.999999	0.000001	0	0.999886	0.000114	-0.587781	1.061048	0.429504	N	T	A	ACCCATTTTCA	ACCCAATTTCA	5.98	0.624	0.1676	149	0.41	0.20819	0.126	0.14982	-0.229	0.07765	null	null	0.60381	null	0.074	0.21613	Tolerated	High	0.136	0.864136	2.77	23	0.3841;0.066;0.1126;0.4374	2.9443	0.05444	Benign	CVNEPIFKNST	Ile	Asn	Nonpolar to Polar	hg19
chr5	163,483,272	G	A	HMMR	missense_variant	15	c.1690G>A	p.Ala564Thr	163,483,272	rs774072548	0	0	0	0	0	0	0.562964	7.148	0	0	0	0.071729	0.928271	0	0.19579	0.80421	0	0.133882	0.866118	0.996021	0.822746	1.10806	N	G	A	GAAAAGCTGAA	GAAAAACTGAA	5.55	-6.84	0.01519	58	0.148	0.16042	-0.434	0.09203	-0.777	0.03376	B	B	0.16609	0.12992	0.026	0.05648	Tolerated	High	0.653	0.347652	2.39	27	0.3126;0.0;0.1075;0.5799	7.3138	0.25502	Benign	EGRKAEKENTT	Ala	Thr	Nonpolar to Polar	hg38
chr5	159,320,326	C	T	IL12B	missense_variant	5	c.677G>A	p.Ser226Asn	159,320,326	rs55661460	0.004393	0	0	0.021825	0	0	2.733632	22.9	0.000233	0.000227	0.000223	0.745319	0.254458	0.005517	0.897063	0.09742	0.000912	0.775265	0.223824	0.521935	0.861169	0.988121	N	C	T	AGAAGCTGCTG	AGAAGTTGCTG	5.28	4.4	0.52235	46	3.135	0.50241	4.093	0.41817	0.549	0.26987	B	B	0.32073	0.27542	0.101	0.28911	Damaging	Low	0.027	0.973027	3.35	30	0.0;0.8999;0.0;0.1001	8.8428	0.34127	Benign	ENYTSSFFIRD	Ser	Asn	Polar to Polar	hg19
chr7	33,109,356	C	A	RP9	missense_variant	1	c.17G>T	p.Gly6Val	33,109,356	rs1242766014	0	0	0	0	0	0	1.974671	19.06	0	0	0.174163	0.812652	0.013185	0.137338	0.842458	0.020204	0.45625	0.536499	0.007251	0.317649	-2.531252	-2.471628	Y	C	A	CGCGCCCAGGC	CGCGCACAGGC	1.71	1.71	0.23316	109	0.577	0.23461	0.433	0.18345	0.288	0.18739	B	B	0.25437	0.23986	0.23	0.53062	Tolerated	High	0.184	0.816184	3.15	11	0.0;0.7862;0.0;0.2138	4.1329	0.09555	Benign	MSSRPGREDVG	Gly	Val	Nonpolar to Nonpolar	hg38
chr12	102,841,578	A	G	PAH	intron_variant	null	c.1200-1063T>C	null	102,841,578	rs568781447	0.000998	0	0	0	0.000994	0.00409	0	0	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	A	G	CTGTTATACTA	CTGTTGTACTA	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg38
chrX	80,024,064	C	T	TBX22	missense_variant	4	c.358C>T	p.Arg120Trp	80,024,064	AlleleID_4013023	0	0	0	0	0	0	3.394104	24.4	0	0	0.974752	0.025219	0.000028	0.964791	0.035145	0.000065	0.96648	0.033451	0.00007	null	null	null	null	C	T	ACAGGCGGATG	ACAGGTGGATG	4.71	1.66	0.2297	101	0.449	0.21459	-0.012	0.13046	0.599	0.4025	D	D	0.90584	0.97372	0.883	0.96576	Damaging	High	0	1	2.53	53	0.7044;0.2956;0.0;0.0	11.7981	0.51199	Pathogenic	TKAGRRMFPSV	Arg	Trp	Basic to Nonpolar	hg38
chr6	52,035,662	C	G	PKHD1	missense_variant	28	c.3157G>C	p.Gly1053Arg	52,035,662	rs1322231013	0	0	0	0	0	0	3.640218	25.2	0	0	0	1	0	0	1	0	0	1	0	-2.12908	-1.35998	-1.361559	N	C	G	AGATCCAAATA	AGATCGAAATA	5.69	5.69	0.88301	125	5.239	0.65196	6.004	0.52535	0.599	0.4025	D	D	0.90584	0.92359	0.936	0.98563	Damaging	Low	0.006	0.994006	3.29	17	0.0;1.0;0.0;0.0	18.7853	0.91882	Pathogenic	SLILFGSYSCA	Gly	Arg	Nonpolar to Basic	hg38
chr12	49,046,668	G	T	KMT2D	missense_variant	16	c.4359C>A	p.His1453Gln	49,046,668	rs767737749	0	0	0	0	0	0	2.984896	23.4	0	0	1	0	0	1	0	0	1	0	0	0.934218	1.422585	1.338016	Y	G	T	TATGTGTGGTA	TATGTTTGGTA	5.23	3.36	0.3742	24	2.603	0.4593	0.571	0.19607	0.676	0.7674	D	D	0.90584	0.92359	0.832	0.94691	null	null	0.015	null	null	null	0.1539;0.0;0.8461;0.0	11.3881	0.48851	Pathogenic	CDISYHTYCLD	His	Gln	Basic to Polar	hg19
chr20	18,162,673	G	A	KAT14	missense_variant	7	c.1396G>A	p.Glu466Lys	18,162,673	rs771882905	0	0	0	0	0	0	4.185953	28.5	0	0	0	0.802379	0.197621	0	0.767055	0.232945	0	0.697597	0.302403	0.661979	-0.117292	0.189845	N	G	A	TCTACGAGGAA	TCTACAAGGAA	6.17	6.17	0.99706	56	9.441	0.96742	11.808	0.96852	0.676	0.7674	D	D	0.90584	0.76113	0.35	0.67142	Damaging	High	0.009	0.991009	2.58	23	0.0;0.0;1.0;0.0	20.8794	0.99869	Pathogenic	TPVSIYEEKLL	Glu	Lys	Acidic to Basic	hg38
chr12	102,843,673	C	G	PAH	missense_variant	11	c.1172G>C	p.Ser391Thr	102,843,673	rs869312997	0	0	0	0	0	0	3.194796	23.9	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	C	G	TAAAACTCTCT	TAAAAGTCTCT	5.34	5.34	0.75888	58	6.085	0.70992	7.699	0.66186	0.549	0.26987	P	P	0.40281	0.48197	0.883	0.96576	Damaging	High	0.023	0.977023	2.52	171	0.0;0.8546;0.1454;0.0	14.6353	0.68148	Pathogenic	YYVAESFNDAK	Ser	Thr	Polar to Polar	hg19
chr2	121,367,677	G	A	CLASP1	missense_variant	36	c.3860C>T	p.Pro1287Leu	121,367,677	rs376007044	0.000399	0.000756	0.001441	0	0	0	3.315808	24.2	0	0.000246	1	0	0	1	0	0	1	0	0	1.44111	0.945971	1.291803	N	G	A	GGTACGGGTTG	GGTACAGGTTG	5.47	3.52	0.39253	98	6.818	0.75047	9.931	0.8258	0.618	0.50648	B	B	0.16609	0.11217	0.222	0.51872	Damaging	Low	0.001	0.999001	3.42	50	0.0797;0.1329;0.7874;0.0	10.2442	0.42316	Benign	KEAVFDDDMEQ	Pro	Leu	Nonpolar to Nonpolar	hg19
chr18	23,539,866	A	T	NPC1	missense_variant	18	c.2740T>A	p.Cys914Ser	23,539,866	rs2511213538	0	0	0	0	0	0	4.212326	28.8	0	0	0.000213	0.999785	0.000002	0.000297	0.999698	0.000005	0.005827	0.994171	0.000002	0.884271	0.355697	0.623525	N	A	T	GTTGCAGCCCA	GTTGCTGCCCA	5.52	5.52	0.82084	112	9.24	0.94518	11.116	0.86435	0.756	0.94297	D	D	0.67487	0.7382	0.977	0.99803	Damaging	High	0	1	2.6	49	1.0;0.0;0.0;0.0	15.9238	0.79291	Pathogenic	CGGMGCNNDSL	Cys	Ser	Nonpolar to Polar	hg38
chr5	177,212,121	G	C	NSD1	missense_variant	5	c.3722G>C	p.Ser1241Thr	177,212,121	rs138641637	0.000998	0	0.004323	0	0.001988	0	0.941166	10.89	0.000814	0	1	0	0	1	0	0	1	0	0	1.442036	0.955283	1.314084	N	G	C	ATCCAGTGCCA	ATCCACTGCCA	4.12	0.125	0.13957	58	0.519	0.2257	-0.964	0.06769	0.676	0.7674	B	B	0.2048	0.22909	0.049	0.13647	Tolerated	High	0.288	0.712288	2.91	7	0.4277;0.1929;0.3793;0.0	4.2443	0.1004	Benign	VCDKSSASIGD	Ser	Thr	Polar to Polar	hg38
chr15	48,432,917	A	G	FBN1	missense_variant	55	c.6688T>C	p.Cys2230Arg	48,432,917	rs1555394906	0	0	0	0	0	0	4.304587	29.6	0	0	1	0	0	1	0	0	1	0	0	1.134817	0.390334	0.692566	N	A	G	TTTGCATTCAT	TTTGCGTTCAT	6.06	6.06	0.98334	180	9.325	0.96006	11.187	0.88524	0.756	0.94297	null	null	0.60381	null	0.989	0.99969	Damaging	High	0	1	2.65	82	1.0;0.0;0.0;0.0	16.2708	0.82366	Pathogenic	YGSYECKCPVG	Cys	Arg	Nonpolar to Basic	hg38
chr16	20,348,984	C	T	UMOD	missense_variant	3	c.317G>A	p.Cys106Tyr	20,348,984	rs398123697	0	0	0	0	0	0	3.604314	25.1	0	0	0	0.517029	0.482971	0	0.522275	0.477725	0.000001	0.634611	0.365388	-0.463947	0.194158	-0.040778	N	C	T	CTGTGCAGCCG	CTGTGTAGCCG	5.45	5.45	0.79612	194	4.135	0.57758	7.303	0.58097	0.597	0.34315	D	D	0.90584	0.92359	0.883	0.96576	Damaging	High	0	1	2.97	62	0.0;1.0;0.0;0.0	16.7695	0.85327	Pathogenic	SPGLGCTDVDE	Cys	Tyr	Nonpolar to Nonpolar	hg38
chr12	102,843,422	G	A	PAH	intron_variant	null	c.1199+224C>T	null	102,843,422	rs189287704	0.000998	0.003782	0	0	0	0	0	0	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	G	A	GTTGCGTTGAA	GTTGCATTGAA	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg19
chr2	215,362,057	C	T	FN1	missense_variant	45	c.7274G>A	p.Arg2425His	215,362,057	rs148505961	0.0002	0	0	0	0.000994	0	4.084324	27.6	0.001279	0	0.064442	0.935558	0	0.086219	0.913781	0	0.184188	0.815812	0	0.846928	1.028008	1.068277	N	C	T	GTCTGCGGCAG	GTCTGTGGCAG	5.97	4.19	0.48476	29	3.677	0.54354	1.417	0.26331	0.599	0.4025	D	D	0.90584	0.92359	0.16	0.41473	Damaging	Low	0.003	0.997003	3.41	36	0.0;0.8668;0.0;0.1332	12.6251	0.55805	Benign	RCDNCRRPGGE	Arg	His	Basic to Basic	hg38
chr2	190,995,205	G	A	STAT1	missense_variant	10	c.800C>T	p.Ala267Val	190,995,205	rs387906759	0	0	0	0	0	0	3.812137	25.9	0	0	0.999994	0.000006	0	0.999985	0.000015	0	0.99998	0.00002	0	-0.482792	-0.406478	-0.40535	N	G	A	TCTCCGCAACT	TCTCCACAACT	5.66	5.66	0.87243	64	6.563	0.73858	11.676	0.94162	0.676	0.7674	D	P	0.77913	0.58514	0.514	0.79217	Damaging	High	0.04	0.96004	2.54	77	0.0;0.0;1.0;0.0	19.7589	0.96286	Pathogenic	WFTIVAESLQQ	Ala	Val	Nonpolar to Nonpolar	hg38
chr17	42,536,502	T	G	NAGLU	missense_variant	1	c.230T>G	p.Val77Gly	42,536,502	rs1599253805	0	0	0	0	0	0	3.87854	26.2	0	0	0.000404	0.990706	0.00889	0.000227	0.980048	0.019724	0.005898	0.988493	0.005608	0.220705	1.009256	0.856509	N	T	G	GCGGGTGCGCG	GCGGGGGCGCG	4.56	3.49	0.38904	109	2.457	0.44662	7.336	0.58227	0.551	0.28136	P	P	0.45051	0.48072	0.837	0.94877	Damaging	High	0.002	0.998002	2.6	41	0.0;0.0894;0.0;0.9106	8.9506	0.34762	Pathogenic	AARVRVRGSTG	Val	Gly	Nonpolar to Nonpolar	hg19
chr1	21,561,127	G	C	ALPL	missense_variant	4	c.212G>C	p.Arg71Pro	21,561,127	rs121918003	0	0	0	0	0	0	4.412285	31	0	0	0.001106	0.988604	0.01029	0.003425	0.986605	0.00997	0.003146	0.983204	0.01365	null	null	null	null	G	C	TGCCCGCATCC	TGCCCCCATCC	5.29	5.29	0.74331	103	9.602	0.97623	11.804	0.96737	0.676	0.7674	D	D	0.90584	0.97372	0.992	0.99986	Damaging	High	0	1	2.51	106	0.0;0.0;1.0;0.0	17.4801	0.87507	Pathogenic	TVTAARILKGQ	Arg	Pro	Basic to Nonpolar	hg38
chr6	56,618,549	G	C	DST	intron_variant	null	c.4930-4065C>G	null	56,618,549	rs79943354	0.011781	0.043116	0.002882	0	0	0	0.913979	10.58	0.000116	0.036995	1	0	0	1	0	0	1	0	0	2.01357	1.989394	2.011044	N	G	C	TTTCTGACATT	TTTCTCACATT	5.21	4.33	0.50915	0	2.415	0.44289	5.165	0.47806	0.676	0.7674	B	B	0.09854	0.12133	0.045	0.12272	Tolerated	Low	0.797	0.203796	3.54	21	0.0818;0.0;0.7595;0.1587	9.0196	0.35166	Benign	null	-	-	No_Change	hg38
chr1	237,783,980	C	T	RYR2	missense_variant	90	c.12268C>T	p.Pro4090Ser	237,783,980	rs794728782	0	0	0	0	0	0	3.793737	25.8	0	0	1	0	0	1	0	0	0.999999	0.000001	0	-0.168246	-0.426883	-0.404698	N	C	T	ACGAACCTGCG	ACGAATCTGCG	5.85	5.85	0.93642	74	0	null	0	null	null	null	D	D	0.90584	0.86255	0.664	0.87479	null	null	0.015	null	null	null	0.0;1.0;0.0;0.0	20.1577	0.98114	Pathogenic	KRFHEPAKDIG	Pro	Ser	Nonpolar to Polar	hg38
chr10	13,188,941	C	T	MCM10	missense_variant	10	c.1276C>T	p.Arg426Cys	13,188,941	rs746874909	0	0	0	0	0	0	3.12046	23.7	0	0	0	0.9399	0.0601	0	0.886296	0.113704	0.000002	0.997853	0.002145	0.115119	1.331338	0.971518	N	C	T	CAAAGCGTGCG	CAAAGTGTGCG	5.87	3.89	0.43927	180	1.85	0.38968	2.659	0.33867	0.599	0.4025	D	D	0.90584	0.97372	0.755	0.91626	Damaging	Low	0	1	3.33	23	0.3495;0.6505;0.0;0.0	15.3498	0.73972	Pathogenic	KKLSAKRADLQ	Arg	Cys	Basic to Nonpolar	hg38
chr13	48,261,174	A	G	ITM2B	missense_variant	6	c.751A>G	p.Ile251Val	48,261,174	rs139394220	0.0002	0	0	0	0	0.001022	3.706352	25.4	0	0.000227	0.715127	0.281665	0.003208	0.670091	0.324931	0.004978	0.914919	0.084361	0.00072	-1.802697	0.515663	-0.540274	N	A	G	TCGCAATTCGG	TCGCAGTTCGG	5.84	5.84	0.93351	29	8.571	0.9054	11.264	0.91177	0.756	0.94297	D	D	0.67487	0.76113	0.394	0.70924	Damaging	High	0	1	2.79	53	1.0;0.0;0.0;0.0	15.3919	0.7436	Benign	SNCFAIRHFEN	Ile	Val	Nonpolar to Nonpolar	hg19
chr9	34,648,395	A	C	GALT	missense_variant	7	c.626A>C	p.Tyr209Ser	34,648,395	rs111033744	0	0	0	0	0	0	3.38738	24.4	0	0	0.001191	0.989528	0.009282	0.003663	0.987268	0.009069	0.000637	0.972731	0.026632	-2.623544	-0.256425	-1.622835	N	A	C	GGCCTATAAGA	GGCCTCTAAGA	4.94	3.78	0.42461	144	2.642	0.46262	6.978	0.57115	0.756	0.94297	D	P	0.56768	0.54942	0.81	0.93854	Damaging	High	0.001	0.999001	2.58	209	0.8146;0.0;0.0;0.1854	7.7815	0.28063	Pathogenic	RSQQAYKSQHG	Tyr	Ser	Nonpolar to Polar	hg19
chr12	102,852,533	C	T	PAH	intron_variant	null	c.842+282G>A	null	102,852,533	rs76256705	0.029553	0.105144	0.011527	0	0	0.001022	0	0	0	0	0	0.307449	0.692551	0	0.449969	0.550031	0	0.35993	0.64007	0.848617	1.120173	1.303993	N	C	T	AACTTCGTAGC	AACTTTGTAGC	0	0	null	0	0	null	0	null	null	null	B	B	0	0	0	0	Tolerated	null	1	0	null	null	null	0	null	Benign	null	-	-	No_Change	hg19
chr4	113,356,450	A	G	ANK2	missense_variant	38	c.7832A>G	p.Tyr2611Cys	113,356,450	rs1246829809	0	0	0	0	0	0	1.14623	13.19	0	0	1	0	0	1	0	0	1	0	0	0.708018	1.23804	1.151525	N	A	G	GGACTACAAAA	GGACTGCAAAA	6.01	-1.63	0.07854	194	0.054	0.14087	0.01	0.13426	0.756	0.94297	null	null	0.60381	null	0.075	0.21907	Tolerated	High	0.208	0.792208	2.74	31	0.5063;0.0;0.4937;0.0	12.0947	0.52865	Benign	KQKRDYKKEPK	Tyr	Cys	Nonpolar to Nonpolar	hg19
chrX	119,105,125	C	T	KIAA1210	missense_variant	6	c.515G>A	p.Arg172Gln	119,105,125	rs373503324	0	0	0	0	0	0	-0.104737	0.811	0	0	0.090793	0.909192	0.000015	0.160752	0.839221	0.000027	0.161286	0.838681	0.000032	null	null	null	null	C	T	TGAGTCGGCGT	TGAGTTGGCGT	4.55	0.993	0.18861	43	-0.159	0.10043	0.396	0.17945	-0.343	0.05659	B	B	0.25173	0.11217	0.005	0.00259	Tolerated	High	0.643	0.357642	2.88	8	0.0;0.431;0.0;0.569	5.5468	0.16243	Benign	FKALKSFFVKK	Arg	Gln	Basic to Polar	hg38
chr9	135,778,781	G	C	KCNT1	missense_variant	23	c.2688G>C	p.Met896Ile	135,778,781	rs797044544	0	0	0	0	0	0	3.375286	24.3	0	0	0.005349	0.994649	0.000002	0.008504	0.991492	0.000005	0.821183	0.178817	0	0.603067	0.434602	0.560655	N	G	C	TACATGGCGGA	TACATCGCGGA	4.5	4.5	0.54218	10	9.65	0.97854	11.504	0.92975	0.674	0.70861	P	B	0.43566	0.42942	0.662	0.87381	Damaging	High	0.012	0.988012	3.07	95	0.0;0.0;1.0;0.0	17.1945	0.86708	Pathogenic	RLFPSLSITTE	Met	Ile	Nonpolar to Nonpolar	hg19
chr22	28,725,070	C	T	CHEK2	missense_variant	4	c.499G>A	p.Gly167Arg	28,725,070	rs72552322	0	0	0	0	0	0	3.976642	26.8	0.000116	0	0	0.005519	0.994481	0	0.005228	0.994772	0	0.035819	0.964181	null	null	null	null	C	T	GGTTCCATTGC	GGTTCTATTGC	5.87	5.87	0.94246	125	5.652	0.67632	7.537	0.60015	0.549	0.26987	D	D	0.90584	0.97372	0.955	0.99221	Damaging	High	0	1	2.54	39	0.0;1.0;0.0;0.0	19.2001	0.93667	Pathogenic	DHSGNGTFVNT	Gly	Arg	Nonpolar to Basic	hg38
chrX	136,877,915	C	A	RBMX	missense_variant	4	c.388G>T	p.Asp130Tyr	136,877,915	rs2522767271	0	0	0	0	0	0	4.961014	33	0	0	0.9483	0.051666	0.000034	0.923069	0.076837	0.000094	0.926241	0.073657	0.000103	null	null	null	null	C	A	ATTACCCATGT	ATTACACATGT	4.02	4.02	0.45797	160	4.748	0.61842	7.597	0.61435	0.594	0.325	B	B	0.25173	0.23986	0.43	0.73662	Damaging	High	0.004	0.996004	2.95	23	0.0;1.0;0.0;0.0	14.5816	0.67749	Pathogenic	RGGHMDDGGYS	Asp	Tyr	Acidic to Nonpolar	hg19
chr7	117,603,665	T	C	CFTR	missense_variant	17	c.2791T>C	p.Phe931Leu	117,603,665	AlleleID_3425462	0	0	0	0	0	0	-0.468847	0.138	0	0	0	0.000005	0.999995	0	0.00012	0.99988	0	0.000012	0.999988	-2.623544	-0.857439	-1.552174	N	T	C	TGGGATTCTTC	TGGGACTCTTC	5.76	-11.5	0.00057	22	-2.963	0.00736	-7.065	0.0124	0.609	0.47794	B	B	0.02946	0.06944	0.465	0.76089	Tolerated	Low	0.344	0.656344	3.61	29	0.5139;0.1461;0.0543;0.2857	5.1153	0.14067	Benign	LLAMGFFRGLP	Phe	Leu	Nonpolar to Nonpolar	hg19
chr13	23,334,577	G	T	SACS	missense_variant	10	c.9299C>A	p.Ser3100Tyr	23,334,577	rs150615169	0.001797	0	0	0.008929	0	0	1.745434	17.34	0	0	0	1	0	0	1	0	0	1	0	-1.203293	-1.815881	-1.563224	Y	G	T	AAAAAGATCTG	AAAAATATCTG	5.75	5.75	0.90354	144	2.039	0.40815	5.825	0.50115	0.676	0.7674	B	B	0.25173	0.22546	0.242	0.54781	Damaging	Low	0.048	0.952048	4.32	8	0.0811;0.0;0.7657;0.1531	8.6082	0.32765	Benign	PADIRSFLMTF	Ser	Tyr	Polar to Nonpolar	hg19

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Genetic Variant Pathogenicity Dataset

Dataset Description

This dataset contains annotated genetic variants (mutations) designed for tabular binary classification tasks. The objective is to predict whether a given genetic variant is Pathogenic (disease-causing) or Benign (harmless) based on a rich set of bioinformatics annotations, evolutionary conservation scores, and functional prediction tools.

Task: Binary Classification
Target Column: Pathologic/Benign

Dataset Structure

The dataset is pre-split into train and test sets, making it ready for immediate machine learning modeling. The class distribution is highly balanced.

Split	Number of Rows	Benign Count	Pathogenic Count
Train	7,856	3,940	3,916
Test	4,910	2,460	2,450

Key Features

The dataset consists of 69 columns. While it includes extensive biological data, some of the most critical feature categories include:

Variant Identifiers: Chrom, Position, Ref Base, Alt Base, Gene
Molecular Consequences: Sequence Ontology (e.g., missense_variant), cDNA change, Protein Change
Population Frequencies: Allele frequencies from the 1000 Genomes Project and ESP6500.
Functional Prediction Scores: CADD Exome Score, PolyPhen-2, SIFT, REVEL Score
Conservation Scores: GERP++, PhyloP, SiPhy
Target Label: Pathologic/Benign (Values: "Benign" or "Pathogenic")

Usage

You can easily load and explore this dataset using the Hugging Face datasets library:

from datasets import load_dataset

# Load the dataset (replace 'your-username' with your actual Hugging Face username)
dataset = load_dataset("your-username/genetic-variant-pathogenicity")

# View the dataset structure
print(dataset)

# Convert the train split to a Pandas DataFrame for easy manipulation
df_train = dataset['train'].to_pandas()
print(df_train['Pathologic/Benign'].value_counts())

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