chr9:125143792:C>A Detail (hg19) (PTGS1)

Information

Genome

Assembly Position
hg19 chr9:125,143,792-125,143,792
hg38 chr9:122,381,513-122,381,513 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000962.3:c.639C>A NP_000953.2:p.Gly213=
NM_001271367.1:c.639C>A NP_001258296.1:p.Gly213=
NM_080591.2:c.639C>A NP_542158.1:p.Gly213=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.028
ToMMo:0.024
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.047

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 176805 OMIM
HGNC 9604 HGNC
Ensembl ENSG00000095303 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv37534366 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
0.107 colorectal cancer Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8... BeFree 18992148 Detail
0.026 colorectal cancer Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8... BeFree 18992148 Detail
0.011 colorectal cancer Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8... BeFree 18992148 Detail
Annotation

Annotations

DescrptionSourceLinks
Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8 c.-352T>A, and M... DisGeNET Detail
Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8 c.-352T>A, and M... DisGeNET Detail
Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8 c.-352T>A, and M... 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
-
Genome
hg19
Position
chr9:125,143,792-125,143,792
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
102.19
Standard deviation of sample read depth (HGVD)
48.63
Number of reference allele (HGVD)
2351
Number of alternative allele (HGVD)
67
Allele Frequency (HGVD)
0.027708850289495452
Gene Symbol (HGVD)
PTGS1
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))
rs5788
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0241
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
404
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
406
East Asian Heterozygous Counts (ExAC)
380
East Asian Homozygous Counts (ExAC)
13
East Asian Allele Frequency (ExAC)
0.046936416184971096
Chromosome Counts in All Race (ExAC)
121368
Allele Counts in All Race (ExAC)
20641
Heterozygous Counts in All Race (ExAC)
14663
Homozygous Counts in All Race (ExAC)
2989
Allele Frequency in All Race (ExAC)
0.1700695405708259
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