chr5:7891506:C>G Detail (hg19) (MTRR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:7,891,506-7,891,506 |
| hg38 | chr5:7,891,393-7,891,393 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002454.2:c.1430C>G | NP_002445.2:p.Pro477Arg |
| NM_024010.2:c.1430C>G | NP_076915.2:p.Pro477Arg | |
| NR_134480.1:c.1430C>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.147 |
| ToMMo:0.167 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.185 |
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
|
2014-01-23 | 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 |
|---|---|---|---|---|---|
| 0.112 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.004 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.033 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.015 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.036 | colorectal cancer | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| <0.001 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
| 0.002 | colorectal carcinoma | Statistically significant associations were observed between CRC risk and functi... | BeFree | 26108676 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002454.3(MTRR):c.1349C>G (p.Pro450Arg) AND not specified | ClinVar | Detail |
| NM_002454.3(MTRR):c.1349C>G (p.Pro450Arg) AND Disorders of Intracellular Cobalamin Metabolism | ClinVar | Detail |
| NM_002454.3(MTRR):c.1349C>G (p.Pro450Arg) AND Methylcobalamin deficiency type cblE | ClinVar | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | DisGeNET | Detail |
| Statistically significant associations were observed between CRC risk and functionally defined candi... | 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
- rs16879334 dbSNP
- Genome
- hg19
- Position
- chr5:7,891,506-7,891,506
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1140
- Mean of sample read depth (HGVD)
- 103.15
- Standard deviation of sample read depth (HGVD)
- 44.77
- Number of reference allele (HGVD)
- 1945
- Number of alternative allele (HGVD)
- 335
- Allele Frequency (HGVD)
- 0.14692982456140352
- 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))
- rs16879334
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1669
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2797
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- Homozygous Counts in All Race (ExAC)
- 306
- East Asian Chromosome Counts (ExAC)
- 8612
- East Asian Allele Counts (ExAC)
- 1593
- East Asian Heterozygous Counts (ExAC)
- 1351
- East Asian Homozygous Counts (ExAC)
- 121
- East Asian Allele Frequency (ExAC)
- 0.18497445424988387
- Chromosome Counts in All Race (ExAC)
- 121002
- Allele Counts in All Race (ExAC)
- 6657
- Heterozygous Counts in All Race (ExAC)
- 6045
- Allele Frequency in All Race (ExAC)
- 0.055015619576535925
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