chr21:44480616:G>A Detail (hg19) (CBS)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr21:44,480,616-44,480,616 |
| hg38 | chr21:43,060,506-43,060,506 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001178008.2:c.1080C>T | NP_001171479.1:p.Ala360= |
| NM_001320298.1:c.1080C>T | NP_001307227.1:p.Ala360= | |
| NM_001178009.2:c.1080C>T | NP_001171480.1:p.Ala360= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.583 |
| ToMMo:0.532 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.621 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2014-03-12 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-07-14 | criteria provided, multiple submitters, no conflicts | Classic homocystinuria |
germline
|
Detail |
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED |
germline
|
Detail |
|
Benign
|
2014-11-24 | criteria provided, single submitter | Familial thoracic aortic aneurysm and aortic dissection |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.128 | Lymphoma, Non-Hodgkin | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Non-Hodgkin | A borderline significantly increased risk of NHL was also observed for CBS (rs18... | BeFree | 23913011 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000071.3(CBS):c.1080C>T (p.Ala360=) AND not specified | ClinVar | Detail |
| NM_000071.3(CBS):c.1080C>T (p.Ala360=) AND Classic homocystinuria | ClinVar | Detail |
| NM_000071.3(CBS):c.1080C>T (p.Ala360=) AND not provided | ClinVar | Detail |
| NM_000071.3(CBS):c.1080C>T (p.Ala360=) AND HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED | ClinVar | Detail |
| NM_000071.3(CBS):c.1080C>T (p.Ala360=) AND Familial thoracic aortic aneurysm and aortic dissection | ClinVar | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | DisGeNET | Detail |
| A borderline significantly increased risk of NHL was also observed for CBS (rs1801181, Ex13+41C>T... | 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
- rs1801181 dbSNP
- Genome
- hg19
- Position
- chr21:44,480,616-44,480,616
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 976
- Mean of sample read depth (HGVD)
- 18.27
- Standard deviation of sample read depth (HGVD)
- 9.50
- Number of reference allele (HGVD)
- 814
- Number of alternative allele (HGVD)
- 1138
- Allele Frequency (HGVD)
- 0.5829918032786885
- Gene Symbol (HGVD)
- CBS
- 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))
- rs1801181
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5323
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8920
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 8410
- East Asian Allele Counts (ExAC)
- 5220
- East Asian Heterozygous Counts (ExAC)
- 1990
- East Asian Homozygous Counts (ExAC)
- 1615
- East Asian Allele Frequency (ExAC)
- 0.6206896551724138
- Chromosome Counts in All Race (ExAC)
- 116306
- Allele Counts in All Race (ExAC)
- 39329
- Heterozygous Counts in All Race (ExAC)
- 24127
- Homozygous Counts in All Race (ExAC)
- 7601
- Allele Frequency in All Race (ExAC)
- 0.3381510842088972
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