chr2:202050677:A>G Detail (hg19) (CASP10)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:202,050,677-202,050,677 |
| hg38 | chr2:201,185,954-201,185,954 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001230.4:c.177A>G | NP_001221.2:p.Ser59= |
| NM_032977.3:c.177A>G | NP_116759.2:p.Ser59= | |
| NM_032974.4:c.177A>G | NP_116756.2:p.Ser59= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.181 |
| ToMMo:0.160 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.221 |
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
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | autoimmune lymphoproliferative syndrome type 2A |
germline
|
Detail |
|
Benign
|
2023-11-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2015-03-03 | criteria provided, single submitter | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.008 | Lymphoma, Non-Hodgkin | We investigated five single nucleotide polymorphisms in four key caspase genes, ... | BeFree | 17071630 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_032977.4(CASP10):c.177A>G (p.Ser59=) AND Autoimmune lymphoproliferative syndrome type 2A | ClinVar | Detail |
| NM_032977.4(CASP10):c.177A>G (p.Ser59=) AND not specified | ClinVar | Detail |
| NM_032977.4(CASP10):c.177A>G (p.Ser59=) AND not provided | ClinVar | Detail |
| We investigated five single nucleotide polymorphisms in four key caspase genes, CASP3 [Ex8-280C>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
- -
- dbSNP
- rs3900115 dbSNP
- Genome
- hg19
- Position
- chr2:202,050,677-202,050,677
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1199
- Mean of sample read depth (HGVD)
- 46.39
- Standard deviation of sample read depth (HGVD)
- 21.08
- Number of reference allele (HGVD)
- 1965
- Number of alternative allele (HGVD)
- 433
- Allele Frequency (HGVD)
- 0.1805671392827356
- Gene Symbol (HGVD)
- CASP10
- 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))
- rs3900115
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1601
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2684
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8616
- East Asian Allele Counts (ExAC)
- 1907
- East Asian Heterozygous Counts (ExAC)
- 1509
- East Asian Homozygous Counts (ExAC)
- 199
- East Asian Allele Frequency (ExAC)
- 0.22133240482822655
- Chromosome Counts in All Race (ExAC)
- 121082
- Allele Counts in All Race (ExAC)
- 54778
- Heterozygous Counts in All Race (ExAC)
- 28866
- Homozygous Counts in All Race (ExAC)
- 12956
- Allele Frequency in All Race (ExAC)
- 0.4524041558613171
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