chr2:189066418:A>G Detail (hg38) (COL5A2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:189,931,144-189,931,144 View the variant detail on this assembly version. |
| hg38 | chr2:189,066,418-189,066,418 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000393.3:c.1535T>C | NP_000384.2:p.Val512Ala |
| Ensemble | ENST00000374866.9:c.1535T>C | ENST00000374866.9:p.Val512Ala |
| ENST00000618828.1:c.374T>C | ENST00000618828.1:p.Val125Ala |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.005 |
| ToMMo:0.008 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely 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
|
2012-12-11 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Ehlers-Danlos syndrome, classic type, 1 |
germline
|
Detail |
|
Likely benign
|
2016-06-14 | criteria provided, single submitter | Ehlers-Danlos syndrome type 7A |
germline
|
Detail |
|
Benign
|
2024-04-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2023-11-10 | criteria provided, multiple submitters, no conflicts | Ehlers-Danlos syndrome, classic type, 2 |
germline
|
Detail |
|
Benign
|
2022-07-16 | criteria provided, single submitter | Ehlers-Danlos syndrome |
germline
|
Detail |
|
Benign
|
2015-08-07 | criteria provided, single submitter | Familial thoracic aortic aneurysm and aortic dissection |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND not specified | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND Ehlers-Danlos syndrome, classic type, 1 | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND Ehlers-Danlos syndrome type 7A | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND not provided | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND Ehlers-Danlos syndrome, classic type, 2 | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND Ehlers-Danlos syndrome | ClinVar | Detail |
| NM_000393.5(COL5A2):c.1535T>C (p.Val512Ala) AND Familial thoracic aortic aneurysm and aortic dissect... | ClinVar | 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
- rs35852101 dbSNP
- Genome
- hg38
- Position
- chr2:189,066,418-189,066,418
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 122.23
- Standard deviation of sample read depth (HGVD)
- 63.16
- Number of reference allele (HGVD)
- 2408
- Number of alternative allele (HGVD)
- 12
- Allele Frequency (HGVD)
- 0.0049586776859504135
- Gene Symbol (HGVD)
- COL5A2
- 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))
- rs35852101
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0076
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 127
- 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)
- 6
- East Asian Heterozygous Counts (ExAC)
- 6
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 6.934812760055479E-4
- Chromosome Counts in All Race (ExAC)
- 121386
- Allele Counts in All Race (ExAC)
- 2213
- Heterozygous Counts in All Race (ExAC)
- 2145
- Homozygous Counts in All Race (ExAC)
- 34
- Allele Frequency in All Race (ExAC)
- 0.01823109749064966
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