chr5:7885959:A>G Detail (hg19) (MTRR)

Information

Genome

Assembly Position
hg19 chr5:7,885,959-7,885,959
hg38 chr5:7,885,846-7,885,846 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002454.2:c.1130A>G NP_002445.2:p.Lys377Arg
NM_024010.2:c.1130A>G NP_076915.2:p.Lys377Arg
NR_134480.1:c.1130A>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.123
ToMMo:0.144
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.181

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602568 OMIM
HGNC 7473 HGNC
Ensembl ENSG00000124275 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20178483 TogoVar
COSMIC
MONDO
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
Uncertain significance no assertion criteria provided gastrointestinal stromal tumor germline Detail
Benign 2018-01-12 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
0.020 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.010 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.008 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
0.005 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
<0.001 spina bifida With respect to spina bifida, we observed ORs with 95% confidence intervals that... BeFree 19493349 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) AND not specified ClinVar Detail
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) AND Gastrointestinal stromal tumor ClinVar Detail
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) AND Disorders of Intracellular Cobalamin Metabolism ClinVar Detail
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) AND Methylcobalamin deficiency type cblE ClinVar Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... DisGeNET Detail
With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0... 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
rs162036 dbSNP
Genome
hg19
Position
chr5:7,885,959-7,885,959
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1109
Mean of sample read depth (HGVD)
41.80
Standard deviation of sample read depth (HGVD)
25.25
Number of reference allele (HGVD)
1945
Number of alternative allele (HGVD)
273
Allele Frequency (HGVD)
0.12308385933273219
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))
rs162036
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))
2414
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
1566
East Asian Heterozygous Counts (ExAC)
1282
East Asian Homozygous Counts (ExAC)
142
East Asian Allele Frequency (ExAC)
0.18104046242774566
Chromosome Counts in All Race (ExAC)
121316
Allele Counts in All Race (ExAC)
20754
Heterozygous Counts in All Race (ExAC)
15726
Homozygous Counts in All Race (ExAC)
2514
Allele Frequency in All Race (ExAC)
0.1710738896765472
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