chr1:102888582:A>G Detail (hg38) (COL11A1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:103,354,138-103,354,138 View the variant detail on this assembly version. |
| hg38 | chr1:102,888,582-102,888,582 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001190709.1:c.4486T>C | NP_001177638.1:p.Ser1496Pro |
| NM_080629.2:c.4639T>C | NP_542196.2:p.Ser1547Pro | |
| NM_001854.3:c.4603T>C | NP_001845.3:p.Ser1535Pro |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.713 |
| ToMMo:0.675 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.730 |
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 |
|---|---|---|---|---|---|
risk factor
|
2007-12-01 | no assertion criteria provided | Lumbar disk herniation, susceptibility to |
germline
|
Detail |
|
Benign
|
2016-09-29 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, multiple submitters, no conflicts | Stickler syndrome type 2 |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, multiple submitters, no conflicts | fibrochondrogenesis 1 |
germline
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, single submitter | Hearing loss, autosomal dominant 37 |
germline
|
Detail |
|
Benign
|
2021-07-22 | criteria provided, single submitter | Marshall syndrome |
germline
|
Detail |
|
Benign
|
2022-07-18 | criteria provided, single submitter | Connective tissue disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.120 | LUMBAR DISC HERNIATION, SUSCEPTIBILITY TO | NA | CLINVAR | Detail | |
| <0.001 | Headache | One single-nucleotide polymorphism for the α 1 chain of collagen type XI (COL11A... | BeFree | 24025612 | Detail |
| 0.120 | Angle Closure Glaucoma | Our study suggests that rs1676486 and rs12138977 in COL11A1 as well as rs216489 ... | BeFree | 24854855 | Detail |
| 0.120 | Angle Closure Glaucoma | Our study suggests that rs1676486 and rs12138977 in COL11A1 as well as rs216489 ... | BeFree | 24854855 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Lumbar disk herniation, susceptibility to | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND not specified | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Stickler syndrome type 2 | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Fibrochondrogenesis 1 | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND not provided | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Hearing loss, autosomal dominant 37 | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Marshall syndrome | ClinVar | Detail |
| NM_001854.4(COL11A1):c.4603T>C (p.Ser1535Pro) AND Connective tissue disorder | ClinVar | Detail |
| NA | DisGeNET | Detail |
| One single-nucleotide polymorphism for the α 1 chain of collagen type XI (COL11A1-rs1676486) gene wa... | DisGeNET | Detail |
| Our study suggests that rs1676486 and rs12138977 in COL11A1 as well as rs216489 and rs11024102 in PL... | DisGeNET | Detail |
| Our study suggests that rs1676486 and rs12138977 in COL11A1 as well as rs216489 and rs11024102 in PL... | 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
- rs1676486 dbSNP
- Genome
- hg38
- Position
- chr1:102,888,582-102,888,582
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1057
- Mean of sample read depth (HGVD)
- 23.70
- Standard deviation of sample read depth (HGVD)
- 13.31
- Number of reference allele (HGVD)
- 606
- Number of alternative allele (HGVD)
- 1508
- Allele Frequency (HGVD)
- 0.7133396404919584
- Gene Symbol (HGVD)
- COL11A1
- 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))
- rs1676486
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.6752
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 11316
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8626
- East Asian Allele Counts (ExAC)
- 6300
- East Asian Heterozygous Counts (ExAC)
- 1668
- East Asian Homozygous Counts (ExAC)
- 2316
- East Asian Allele Frequency (ExAC)
- 0.7303501043357292
- Chromosome Counts in All Race (ExAC)
- 120994
- Allele Counts in All Race (ExAC)
- 96088
- Heterozygous Counts in All Race (ExAC)
- 19256
- Homozygous Counts in All Race (ExAC)
- 38416
- Allele Frequency in All Race (ExAC)
- 0.7941550820701853
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