T-REx

Variant location (GRCh37) chr14:65234545

Variant class : SNV
Alleles : A/G
Existing ID : rs121918648&CM951194

Quality score : 9722.7
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	SPTB	chr14:g.65234545A>G	NM_001024858.2:c.6055T>C	NP_001020029.1:p.Ser2019Pro	6109/10064	6055/6987	2019/2328	Tct/Cct	S/P	tolerated(0.09)	benign(0.157)

Allele frequencies

Subpopulation	Allele count	Allele number	Allele frequency
Group A	0	228	G:0.000e+00
Group B	1	170	G:0.006
Group C	9	588	G:0.015
Group D	1	872	G:0.001
Group E	6	198	G:0.030
Group X	0	128	G:0.000e+00
All Thais	17	2184	G:0.008

Other Population frequencies from gnomAD

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Exomes
Genomes

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African
Ashkenazi Jewish
European (non-Finnish)
	Southern European
	North-western European
	Bulgarian
East Asian
	Japanese
	Korean
	Other East Asian
European (Finnish)
South Asian
Other

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African
Ashkenazi Jewish
European (non-Finnish)
	Southern European
	North-western European
	Bulgarian
East Asian
	Japanese
	Korean
	Other East Asian
European (Finish)
South Asian
Other

Genotype Quality Metrics

Site Quality Metrics

Metric
BaseQRankSum	-1.489
ClippingRankSum	0.000
DP	35515
FS	1.284
InbreedingCoeff	-0.006
MQ	60.000
MQRankSum	0.000
QD	13.260
ReadPosRankSum	0.190
SiteQuality	9722.70
SOR	0.537
VQSLOD	6.660