chr8:143762932:G>A Detail (hg19) (PSCA)

Information

Genome

Assembly Position
hg19 chr8:143,762,932-143,762,932
hg38 chr8:142,681,514-142,681,514 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_005672.4:c.133+80G>A
Ensemble ENST00000301258.5:c.133+80G>A
ENST00000513264.1:c.*48G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.641
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.309

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 602470 OMIM
HGNC 9500 HGNC
Ensembl ENSG00000167653 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv35049253 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 gastritis Herein, we aimed to evaluate associations between PSCA (C&gt;T, rs2294008; G&gt;... BeFree 25503145 Detail
0.002 Malignant neoplasm of stomach The results of subgroup analyses (according to histopathology, countries and sou... BeFree 22155405 Detail
0.008 gastritis Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are asso... BeFree 25503145 Detail
0.002 stomach carcinoma The results of subgroup analyses (according to histopathology, countries and sou... BeFree 22155405 Detail
<0.001 gastritis Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are asso... BeFree 25503145 Detail
<0.001 gastric adenocarcinoma Two SNPs of rs2294008 (C&gt;T) and rs2976392 (G&gt;A) were identified to be asso... BeFree 26006239 Detail
Annotation

Annotations

DescrptionSourceLinks
Herein, we aimed to evaluate associations between PSCA (C&gt;T, rs2294008; G&gt;A, rs2976392), MUC1 ... DisGeNET Detail
The results of subgroup analyses (according to histopathology, countries and sources of controls) in... DisGeNET Detail
Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are associated with GC and H... DisGeNET Detail
The results of subgroup analyses (according to histopathology, countries and sources of controls) in... DisGeNET Detail
Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are associated with GC and H... DisGeNET Detail
Two SNPs of rs2294008 (C&gt;T) and rs2976392 (G&gt;A) were identified to be associated with GAC risk... 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
rs2976392 dbSNP
Genome
hg19
Position
chr8:143,762,932-143,762,932
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs2976392
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6415
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10749
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
538
East Asian Allele Counts (ExAC)
166
East Asian Heterozygous Counts (ExAC)
108
East Asian Homozygous Counts (ExAC)
29
East Asian Allele Frequency (ExAC)
0.30855018587360594
Chromosome Counts in All Race (ExAC)
16714
Allele Counts in All Race (ExAC)
7698
Heterozygous Counts in All Race (ExAC)
4154
Homozygous Counts in All Race (ExAC)
1772
Allele Frequency in All Race (ExAC)
0.46057197558932633
Genome browser