chr11:67586499:T>C Detail (hg38) (GSTP1)

Information

Genome

Assembly Position
hg19 chr11:67,353,970-67,353,970 View the variant detail on this assembly version.
hg38 chr11:67,586,499-67,586,499

HGVS

[No Data.]
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.143
ToMMo:0.140
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.178

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-06-09 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Carcinoma of lung When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplo... BeFree 24786234 Detail
<0.001 Malignant neoplasm of lung When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplo... BeFree 24786234 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000852.4(GSTP1):c.555T>C (p.Ser185=) AND not provided ClinVar Detail
When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplotype CACA (rs749174+... DisGeNET Detail
When Phase 2 software was used to reconstruct the haplotype for GSTP1, the haplotype CACA (rs749174+... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4891 dbSNP
Genome
hg38
Position
chr11:67,586,499-67,586,499
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
181.76
Standard deviation of sample read depth (HGVD)
81.64
Number of reference allele (HGVD)
2074
Number of alternative allele (HGVD)
346
Allele Frequency (HGVD)
0.14297520661157026
Gene Symbol (HGVD)
GSTP1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs4891
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1402
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2349
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
Homozygous Counts in All Race (ExAC)
7626
East Asian Chromosome Counts (ExAC)
8602
East Asian Allele Counts (ExAC)
1527
East Asian Heterozygous Counts (ExAC)
1235
East Asian Homozygous Counts (ExAC)
146
East Asian Allele Frequency (ExAC)
0.17751685654498953
Chromosome Counts in All Race (ExAC)
120310
Allele Counts in All Race (ExAC)
40954
Heterozygous Counts in All Race (ExAC)
25702
Allele Frequency in All Race (ExAC)
0.3404039564458482
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