chr2:189009011:A>G Detail (hg38) (COL3A1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:189,873,737-189,873,737 View the variant detail on this assembly version. |
| hg38 | chr2:189,009,011-189,009,011 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000090.3:c.3613A>G | NP_000081.1:p.Ile1205Val |
| Ensemble | ENST00000304636.9:c.3613A>G | ENST00000304636.9:p.Ile1205Val |
| ENST00000450867.2:c.3514A>G | ENST00000450867.2:p.Ile1172Val |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.100 |
| ToMMo:0.097 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.056 |
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
|
2015-06-05 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-05 | criteria provided, multiple submitters, no conflicts | Ehlers-Danlos syndrome, type 4 |
germline
|
Detail |
|
Benign
|
2023-11-21 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2018-03-15 | criteria provided, multiple submitters, no conflicts | Familial thoracic aortic aneurysm and aortic dissection |
germline
|
Detail |
|
Benign
|
2021-09-03 | criteria provided, single submitter | Ehlers-Danlos syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Chronic Kidney Diseases | The Chi-square test, multivariable logistic regression analysis with adjustment ... | BeFree | 19424605 | Detail |
| <0.001 | Chronic Kidney Diseases | The Chi-square test, multivariable logistic regression analysis with adjustment ... | BeFree | 19424605 | Detail |
| <0.001 | Chronic Kidney Diseases | The Chi-square test, multivariable logistic regression analysis with adjustment ... | BeFree | 19424605 | Detail |
| 0.002 | Chronic Kidney Diseases | The Chi-square test, multivariable logistic regression analysis with adjustment ... | BeFree | 19424605 | Detail |
| 0.002 | Chronic Kidney Diseases | The Chi-square test, multivariable logistic regression analysis with adjustment ... | BeFree | 19424605 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000090.4(COL3A1):c.3613A>G (p.Ile1205Val) AND not specified | ClinVar | Detail |
| NM_000090.4(COL3A1):c.3613A>G (p.Ile1205Val) AND Ehlers-Danlos syndrome, type 4 | ClinVar | Detail |
| NM_000090.4(COL3A1):c.3613A>G (p.Ile1205Val) AND not provided | ClinVar | Detail |
| NM_000090.4(COL3A1):c.3613A>G (p.Ile1205Val) AND Familial thoracic aortic aneurysm and aortic dissec... | ClinVar | Detail |
| NM_000090.4(COL3A1):c.3613A>G (p.Ile1205Val) AND Ehlers-Danlos syndrome | ClinVar | Detail |
| The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... | DisGeNET | Detail |
| The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... | DisGeNET | Detail |
| The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... | DisGeNET | Detail |
| The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... | DisGeNET | Detail |
| The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... | 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
- rs2271683 dbSNP
- Genome
- hg38
- Position
- chr2:189,009,011-189,009,011
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 55.80
- Standard deviation of sample read depth (HGVD)
- 23.12
- Number of reference allele (HGVD)
- 2177
- Number of alternative allele (HGVD)
- 241
- Allele Frequency (HGVD)
- 0.09966914805624483
- Gene Symbol (HGVD)
- COL3A1
- 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))
- rs2271683
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0966
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1619
- 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)
- 482
- East Asian Heterozygous Counts (ExAC)
- 466
- East Asian Homozygous Counts (ExAC)
- 8
- East Asian Allele Frequency (ExAC)
- 0.055722543352601156
- Chromosome Counts in All Race (ExAC)
- 121402
- Allele Counts in All Race (ExAC)
- 543
- Heterozygous Counts in All Race (ExAC)
- 527
- Homozygous Counts in All Race (ExAC)
- 8
- Allele Frequency in All Race (ExAC)
- 0.004472743447389664
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