chr1:11863038:G>A Detail (hg19) (MTHFR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:11,863,038-11,863,038 |
| hg38 | chr1:11,802,981-11,802,981 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005957.4:c.136C>T | NP_005948.3:p.Arg46Trp |
| Ensemble | ENST00000376592.6:c.136C>T | ENST00000376592.6:p.Arg46Trp |
| ENST00000641407.1:c.136C>T | ENST00000641407.1:p.Arg46Trp |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.003 |
| ToMMo:0.003 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.003 |
Prediction
ClinVar
| Clinical Significance |
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Likely benign
|
2024-01-29 | criteria provided, single submitter | Homocystinuria due to methylene tetrahydrofolate reductase deficiency |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.362 | HOMOCYSTINURIA DUE TO DEFICIENCY OF N(5,10)-METHYLENETETRAHYDROFOLATE REDUCTASE ACTIVITY | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_005957.5(MTHFR):c.136C>T (p.Arg46Trp) AND Homocystinuria due to methylene tetrahydrofolate reduct... | ClinVar | Detail |
| NA | 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
- rs138189536 dbSNP
- Genome
- hg19
- Position
- chr1:11,863,038-11,863,038
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 217.95
- Standard deviation of sample read depth (HGVD)
- 95.87
- Number of reference allele (HGVD)
- 2413
- Number of alternative allele (HGVD)
- 7
- Allele Frequency (HGVD)
- 0.002892561983471074
- Gene Symbol (HGVD)
- MTHFR
- 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))
- rs138189536
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.003
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 50
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8640
- East Asian Allele Counts (ExAC)
- 23
- East Asian Heterozygous Counts (ExAC)
- 23
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.002662037037037037
- Chromosome Counts in All Race (ExAC)
- 119772
- Allele Counts in All Race (ExAC)
- 27
- Heterozygous Counts in All Race (ExAC)
- 27
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 2.254283137962128E-4
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