chr5:7878424:T>A Detail (hg19) (MTRR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:7,878,424-7,878,424 |
| hg38 | chr5:7,878,311-7,878,311 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002454.2:c.850T>A | NP_002445.2:p.Ser284Thr |
| NM_024010.2:c.850T>A | NP_076915.2:p.Ser284Thr | |
| NR_134480.1:c.850T>A |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.110 |
| ToMMo:0.108 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.111 |
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, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2018-01-13 | criteria provided, single submitter | Disorders of Intracellular Cobalamin Metabolism |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Methylcobalamin deficiency type cblE |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Adenoma of large intestine | In addition, the methionine synthase reductase (MTRR) Arg415Cys and MTRR Ser284T... | BeFree | 17389618 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002454.3(MTRR):c.769T>A (p.Ser257Thr) AND not specified | ClinVar | Detail |
| NM_002454.3(MTRR):c.769T>A (p.Ser257Thr) AND Disorders of Intracellular Cobalamin Metabolism | ClinVar | Detail |
| NM_002454.3(MTRR):c.769T>A (p.Ser257Thr) AND Methylcobalamin deficiency type cblE | ClinVar | Detail |
| In addition, the methionine synthase reductase (MTRR) Arg415Cys and MTRR Ser284Thr variant carriers,... | 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
- rs2303080 dbSNP
- Genome
- hg19
- Position
- chr5:7,878,424-7,878,424
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 147.48
- Standard deviation of sample read depth (HGVD)
- 75.02
- Number of reference allele (HGVD)
- 2154
- Number of alternative allele (HGVD)
- 266
- Allele Frequency (HGVD)
- 0.10991735537190082
- Gene Symbol (HGVD)
- MTRR
- 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))
- rs2303080
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1078
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 1807
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- Homozygous Counts in All Race (ExAC)
- 146
- East Asian Chromosome Counts (ExAC)
- 8600
- East Asian Allele Counts (ExAC)
- 951
- East Asian Heterozygous Counts (ExAC)
- 873
- East Asian Homozygous Counts (ExAC)
- 39
- East Asian Allele Frequency (ExAC)
- 0.11058139534883721
- Chromosome Counts in All Race (ExAC)
- 120990
- Allele Counts in All Race (ExAC)
- 4919
- Heterozygous Counts in All Race (ExAC)
- 4627
- Allele Frequency in All Race (ExAC)
- 0.040656252582858085
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