chr9:122381513:C>A Detail (hg38) (PTGS1)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr9:125,143,792-125,143,792 View the variant detail on this assembly version. |
hg38 | chr9:122,381,513-122,381,513 |
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 |
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
Descrption | Source | Links |
---|---|---|
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
- hg38
- Position
- chr9:122,381,513-122,381,513
- 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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