chr7:94043239:C>G Detail (hg19) (COL1A2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr7:94,043,239-94,043,239 |
| hg38 | chr7:94,413,927-94,413,927 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000089.3:c.1645C>G | NP_000080.2:p.Pro549Ala |
| Ensemble | ENST00000297268.11:c.1645C>G | ENST00000297268.11:p.Pro549Ala |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.971 |
| ToMMo:0.959 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.915 |
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
|
2017-07-26 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, multiple submitters, no conflicts | Ehlers-danlos syndrome, arthrochalasia type, 2 |
germline
|
Detail |
|
Benign
|
2022-07-18 | criteria provided, multiple submitters, no conflicts | osteogenesis imperfecta |
germline
|
Detail |
|
Benign
|
2019-05-28 | criteria provided, single submitter | Ehlers-Danlos syndrome, classic type |
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Ehlers-Danlos syndrome, classic type, 1,Osteogenesis imperfecta type I |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Ehlers-Danlos syndrome, classic type, 1,Osteogenesis imperfecta type I |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, single submitter | Osteogenesis imperfecta type III |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, single submitter | Osteogenesis imperfecta with normal sclerae, dominant form |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, single submitter | Osteogenesis imperfecta, perinatal lethal |
germline
|
Detail |
|
Benign
|
2023-11-30 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2022-07-16 | criteria provided, single submitter | Ehlers-Danlos syndrome |
germline
|
Detail |
|
Benign
|
2018-12-04 | criteria provided, single submitter |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.014 | intracranial aneurysm | A coding polymorphism (rs42524) in COL1A2 has previously been associated with in... | BeFree | 19426706 | Detail |
| 0.014 | intracranial aneurysm | In this study, we investigated the association of rs42524 in the alpha-2 type I ... | BeFree | 22815632 | Detail |
| 0.014 | intracranial aneurysm | [Polymorphism rs42524 of COL1A2 and sporadic intracranial aneurysms in the Chine... | GAD | 19035720 | Detail |
| 0.014 | intracranial aneurysm | Polymorphism rs42524 of COL1A2 and sporadic intracranial aneurysms in the Chines... | BeFree | 19035720 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND not specified | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Ehlers-danlos syndrome, arthrochalasia type, 2 | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Osteogenesis imperfecta | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Ehlers-Danlos syndrome, classic type | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND multiple conditions | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND multiple conditions | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Osteogenesis imperfecta type III | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Osteogenesis imperfecta with normal sclerae, dominan... | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Osteogenesis imperfecta, perinatal lethal | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND not provided | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Ehlers-Danlos syndrome | ClinVar | Detail |
| NM_000089.4(COL1A2):c.1645C>G (p.Pro549Ala) AND Cardiovascular phenotype | ClinVar | Detail |
| A coding polymorphism (rs42524) in COL1A2 has previously been associated with intracranial aneurysms... | DisGeNET | Detail |
| In this study, we investigated the association of rs42524 in the alpha-2 type I collagen (COL1A2) ge... | DisGeNET | Detail |
| [Polymorphism rs42524 of COL1A2 and sporadic intracranial aneurysms in the Chinese population.] | DisGeNET | Detail |
| Polymorphism rs42524 of COL1A2 and sporadic intracranial aneurysms in the Chinese population. | 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
- rs42524 dbSNP
- Genome
- hg19
- Position
- chr7:94,043,239-94,043,239
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1192
- Mean of sample read depth (HGVD)
- 73.64
- Standard deviation of sample read depth (HGVD)
- 31.52
- Number of reference allele (HGVD)
- 68
- Number of alternative allele (HGVD)
- 2304
- Allele Frequency (HGVD)
- 0.9713322091062394
- Gene Symbol (HGVD)
- COL1A2
- 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))
- rs42524
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.9593
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16076
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 7919
- East Asian Heterozygous Counts (ExAC)
- 675
- East Asian Homozygous Counts (ExAC)
- 3622
- East Asian Allele Frequency (ExAC)
- 0.9150681765657499
- Chromosome Counts in All Race (ExAC)
- 121334
- Allele Counts in All Race (ExAC)
- 93340
- Heterozygous Counts in All Race (ExAC)
- 20825
- Homozygous Counts in All Race (ExAC)
- 36256
- Allele Frequency in All Race (ExAC)
- 0.7692814874643545
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