chr20:48140682:C>T Detail (hg19) (PTGIS)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr20:48,140,682-48,140,682 |
| hg38 | chr20:49,524,145-49,524,145 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000961.3:c.768G>A | NP_000952.1:p.Leu256= |
| Ensemble | ENST00000244043.5:c.768G>A | ENST00000244043.5:p.Leu256= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.063 |
| ToMMo:0.065 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.093 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000151) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2019-10-21 | criteria provided, single submitter | PTGIS-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.003 | Ischemic Cerebrovascular Accident | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.002 | Ischemic Cerebrovascular Accident | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.003 | Ischemic stroke | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.001 | Ischemic Cerebrovascular Accident | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.002 | Ischemic stroke | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.001 | Ischemic stroke | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.004 | Ischemic Cerebrovascular Accident | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
| 0.009 | Ischemic stroke | To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid bios... | BeFree | 21816595 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000961.4(PTGIS):c.768G>A (p.Leu256=) AND PTGIS-related disorder | ClinVar | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) of eicosanoid biosynthesis genes are a... | 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
- chr20:48,140,682-48,140,682
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 148.72
- Standard deviation of sample read depth (HGVD)
- 70.15
- Number of reference allele (HGVD)
- 2268
- Number of alternative allele (HGVD)
- 152
- Allele Frequency (HGVD)
- 0.0628099173553719
- Gene Symbol (HGVD)
- PTGIS
- 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))
- rs5628
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0648
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1086
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 800
- East Asian Heterozygous Counts (ExAC)
- 724
- East Asian Homozygous Counts (ExAC)
- 38
- East Asian Allele Frequency (ExAC)
- 0.09250693802035152
- Chromosome Counts in All Race (ExAC)
- 121364
- Allele Counts in All Race (ExAC)
- 9849
- Heterozygous Counts in All Race (ExAC)
- 8907
- Homozygous Counts in All Race (ExAC)
- 471
- Allele Frequency in All Race (ExAC)
- 0.08115256583500874
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