• T-REx Database

Variant location (GRCh37) chr11:5246862

  • Variant class : SNV
  • Alleles : C/T
  • Existing ID : rs33949486&CM024482&HbVar.548
  • Quality score : 1395.68
  • 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 HBB chr11:g.5246862C>T NM_000518.4:c.410G>A NP_000509.1:p.Gly137Asp 460/626 410/444 137/147 gGt/gAt G/D tolerated(0.5) possibly_damaging(0.865)

Allele frequencies

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

Other Population frequencies from gnomAD

  • Exomes
  • Genomes
Population Allele Count Allele Number Number of Homozygotes Allele Frequency
African 3 16256 0 0.000184547
Ashkenazi Jewish 0 10074 0 0.0
European (non-Finnish)
Southern European 0 11492 0 0.0
North-western European 0 42182 0 0.0
Bulgarian 0 2670 0 0.0
East Asian 0 18388 0 0.0
Japanese 0 152 0 0.0
Korean 0 3812 0 0.0
Other East Asian 0 18388 0 0.0
European (Finnish) 0 21640 0 0.0
South Asian 0 30616 0 0.0
Other 0 6130 0 0.0
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

  • Genotype quality
  • Depth
  • Allele balance for heterozygotes

Site Quality Metrics

Metric
BaseQRankSum -2.472
ClippingRankSum 0.000
DP 39201
FS 0.000
InbreedingCoeff -0.001
MQ 60.000
MQRankSum 0.000
QD 10.340
ReadPosRankSum -1.132
SiteQuality 1395.68
SOR 0.674
VQSLOD 6.320


Logo
Logo
Logo
Logo
Logo
Logo
Logo
Logo
Copyright © 2020, NBT, NSTDA.