T-REx

Variant location (GRCh37) chr11:5248200

Variant class : SNV
Alleles : T/A
Existing ID : rs33986703&CM790002&HbVar.800

Quality score : 3021.37
Filter : PASS

Annotations

Consequence	Impact	Gene	HGVSg	HGVSc	HGVSp	cDNA position	CDS position	Protein position	Codons	Amino acids	SIFT score	PolyPhen score
stop_gained	HIGH	HBB	chr11:g.5248200T>A	NM_000518.4:c.52A>T	NP_000509.1:p.Lys18Ter	102/626	52/444	18/147	Aag/Tag	K/*

Allele frequencies

Subpopulation	Allele count	Allele number	Allele frequency
Group A	0	228	A:0.000e+00
Group B	0	170	A:0.000e+00
Group C	0	588	A:0.000e+00
Group D	1	872	A:0.001
Group E	1	198	A:0.005
Group X	1	128	A:0.008
All Thais	3	2184	A:0.001

Other Population frequencies from gnomAD

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Exomes
Genomes

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African		0	16256	0	0.0
Ashkenazi Jewish		0	10078	0	0.0
European (non-Finnish)
	Southern European	0	11488	0	0.0
	North-western European	0	42118	0	0.0
	Bulgarian	0	2668	0	0.0
East Asian		14	18376	0	0.000761863
	Japanese	0	152	0	0.0
	Korean	0	3800	0	0.0
	Other East Asian	14	18376	0	0.000761863
European (Finnish)		0	21642	0	0.0
South Asian		0	30616	0	0.0
Other		0	6132	0	0.0

Population		Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
African		0	8716	0	0.0
Ashkenazi Jewish		0	290	0	0.0
European (non-Finnish)
	Southern European	0	106	0	0.0
	North-western European	0	8596	0	0.0
	Bulgarian
East Asian		2	1560	0	0.00128205
	Japanese
	Korean
	Other East Asian	2	1560	0	0.00128205
European (Finish)		0	3476	0	0.0
South Asian
Other		0	1088	0	0.0

Genotype Quality Metrics

Site Quality Metrics

Metric
BaseQRankSum	0.167
ClippingRankSum	0.000
DP	58092
FS	5.818
InbreedingCoeff	-0.001
MQ	68.210
MQRankSum	0.000
QD	13.800
ReadPosRankSum	-0.597
SiteQuality	3021.37
SOR	1.070
VQSLOD	4.520