chr5:7878079:T>C Detail (hg38) (MTRR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:7,878,192-7,878,192 View the variant detail on this assembly version. |
| hg38 | chr5:7,878,079-7,878,079 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002454.2:c.618T>C | NP_002445.2:p.Leu206= |
| NM_024010.2:c.618T>C | NP_076915.2:p.Leu206= | |
| NR_134480.1:c.618T>C |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.153 |
| ToMMo:0.144 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.182 |
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
|
2013-05-29 | 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, multiple submitters, no conflicts | Methylcobalamin deficiency type cblE |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Lymphoma, Large-Cell, Follicular | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
| 0.006 | Lymphoma, Non-Hodgkin | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Large-Cell, Follicular | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
| <0.001 | Lymphoma, Non-Hodgkin | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
| 0.006 | Lymphoma, Non-Hodgkin | A significantly reduced risk of NHL was associated with the homozygous TT genoty... | BeFree | 23913011 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002454.3(MTRR):c.537T>C (p.Leu179=) AND not specified | ClinVar | Detail |
| NM_002454.3(MTRR):c.537T>C (p.Leu179=) AND Disorders of Intracellular Cobalamin Metabolism | ClinVar | Detail |
| NM_002454.3(MTRR):c.537T>C (p.Leu179=) AND Methylcobalamin deficiency type cblE | ClinVar | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | DisGeNET | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | DisGeNET | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | DisGeNET | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | DisGeNET | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | DisGeNET | Detail |
| A significantly reduced risk of NHL was associated with the homozygous TT genotype in CBS (rs234706,... | 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
- rs161870 dbSNP
- Genome
- hg38
- Position
- chr5:7,878,079-7,878,079
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 89.06
- Standard deviation of sample read depth (HGVD)
- 39.95
- Number of reference allele (HGVD)
- 2050
- Number of alternative allele (HGVD)
- 370
- Allele Frequency (HGVD)
- 0.15289256198347106
- 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))
- rs161870
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.144
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2413
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8610
- East Asian Allele Counts (ExAC)
- 1567
- East Asian Heterozygous Counts (ExAC)
- 1283
- East Asian Homozygous Counts (ExAC)
- 142
- East Asian Allele Frequency (ExAC)
- 0.18199767711962833
- Chromosome Counts in All Race (ExAC)
- 121268
- Allele Counts in All Race (ExAC)
- 20744
- Heterozygous Counts in All Race (ExAC)
- 15714
- Homozygous Counts in All Race (ExAC)
- 2515
- Allele Frequency in All Race (ExAC)
- 0.17105914173565986
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