chr1:186643541:C>T Detail (hg19) (PTGS2)

Information

Genome

Assembly Position
hg19 chr1:186,643,541-186,643,541
hg38 chr1:186,674,409-186,674,409 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000963.3:c.1759G>A NP_000954.1:p.Gly587Arg
Ensemble ENST00000367468.10:c.1759G>A ENST00000367468.10:p.Gly587Arg
ENST00000680451.1:c.1759G>A ENST00000680451.1:p.Gly587Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.012
ToMMo:0.013
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.023

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600262 OMIM
HGNC 9605 HGNC
Ensembl ENSG00000073756 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv4103074 TogoVar
COSMIC COSM3689211 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.127 Squamous cell carcinoma of esophagus Cyclooxygenase-2 Gly587Arg variant is associated with differential enzymatic act... BeFree 19347867 Detail
Annotation

Annotations

DescrptionSourceLinks
Cyclooxygenase-2 Gly587Arg variant is associated with differential enzymatic activity and risk of es... 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
chr1:186,643,541-186,643,541
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
82.78
Standard deviation of sample read depth (HGVD)
37.91
Number of reference allele (HGVD)
2391
Number of alternative allele (HGVD)
29
Allele Frequency (HGVD)
0.011983471074380166
Gene Symbol (HGVD)
PTGS2
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))
rs3218625
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0126
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
211
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
201
East Asian Heterozygous Counts (ExAC)
197
East Asian Homozygous Counts (ExAC)
2
East Asian Allele Frequency (ExAC)
0.023231622746185853
Chromosome Counts in All Race (ExAC)
121292
Allele Counts in All Race (ExAC)
204
Heterozygous Counts in All Race (ExAC)
200
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
0.0016818916334135805
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