T-REx

Variant location (GRCh37) chrX:2835863

Variant class : SNV
Alleles : G/T
Existing ID : rs78034736&COSM1319458

Quality score : 22142.27
Filter : PASS

Annotations

Consequence	Impact	Gene	HGVSg	HGVSc	HGVSp	cDNA position	CDS position	Protein position	Codons	Amino acids	SIFT score	PolyPhen score
missense_variant	MODERATE	ARSD	chrX:g.2835863G>T	NM_001669.3:c.845C>A	NP_001660.2:p.Ala282Asp	945/5183	845/1782	282/593	gCt/gAt	A/D	deleterious(0)	probably_damaging(0.963)

Allele frequencies

Subpopulation	Allele count	Allele number	Allele frequency
Group A	13	160	T:0.081
Group B	11	126	T:0.087
Group C	28	436	T:0.064
Group D	43	662	T:0.065
Group E	9	146	T:0.062
Group X	7	97	T:0.072
All Thais	111	1627	T:0.068

Other Population frequencies from gnomAD

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Exomes
Genomes

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African		0	10057	0	0.0
Ashkenazi Jewish		0	5145	0	0.0
European (non-Finnish)
	Southern European	0	2943	0	0.0
	North-western European	1	19764	0	5.0597e-05
	Bulgarian	0	1310	0	0.0
East Asian		1	9326	0	0.000107227
	Japanese	0	92	0	0.0
	Korean	1	1961	0	0.000509944
	Other East Asian	1	9326	0	0.000107227
European (Finnish)		0	10357	0	0.0
South Asian		2	7939	0	0.000251921
Other		0	2984	0	0.0

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African		2	3702	0	0.000540249
Ashkenazi Jewish		0	84	0	0.0
European (non-Finnish)
	Southern European	0	47	0	0.0
	North-western European	1	3655	0	0.000273598
	Bulgarian
East Asian		0	540	0	0.0
	Japanese
	Korean
	Other East Asian	0	540	0	0.0
European (Finish)		0	1845	0	0.0
South Asian
Other		0	570	0	0.0

Genotype Quality Metrics

Site Quality Metrics

Metric
BaseQRankSum	-1.718
ClippingRankSum	0.000
DP	28476
FS	2.087
InbreedingCoeff	-0.020
MQ	77.930
MQRankSum	0.000
QD	4.880
ReadPosRankSum	0.473
SiteQuality	22142.27
SOR	0.509
VQSLOD	N/A