chr5:7878179:C>T Detail (hg19) (MTRR)

Information

Genome

Assembly Position
hg19 chr5:7,878,179-7,878,179
hg38 chr5:7,878,066-7,878,066 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002454.2:c.605C>T NP_002445.2:p.Ser202Leu
NM_024010.2:c.605C>T NP_076915.2:p.Ser202Leu
NR_134480.1:c.605C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.105
ToMMo:0.103
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.157

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 tgv20178120 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-08-26 criteria provided, single submitter not specified germline Detail
Uncertain significance no assertion criteria provided gastrointestinal stromal tumor germline Detail
Benign 2018-03-06 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
0.003 breast carcinoma Viable cell growth, MDI, and polymorphism frequency in MTRR (A66G and C524T) and... BeFree 18842997 Detail
0.016 congenital heart defects A66G and C524T polymorphisms of the methionine synthase reductase gene are assoc... BeFree 22057956 Detail
0.017 Malignant neoplasm of breast Viable cell growth, MDI, and polymorphism frequency in MTRR (A66G and C524T) and... BeFree 18842997 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) AND not specified ClinVar Detail
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) AND Gastrointestinal stromal tumor ClinVar Detail
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) AND Disorders of Intracellular Cobalamin Metabolism ClinVar Detail
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) AND Methylcobalamin deficiency type cblE ClinVar Detail
Viable cell growth, MDI, and polymorphism frequency in MTRR (A66G and C524T) and MTHFR (A1298C and A... DisGeNET Detail
A66G and C524T polymorphisms of the methionine synthase reductase gene are associated with congenita... DisGeNET Detail
Viable cell growth, MDI, and polymorphism frequency in MTRR (A66G and C524T) and MTHFR (A1298C and A... 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
rs1532268 dbSNP
Genome
hg19
Position
chr5:7,878,179-7,878,179
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
82.00
Standard deviation of sample read depth (HGVD)
36.72
Number of reference allele (HGVD)
2165
Number of alternative allele (HGVD)
255
Allele Frequency (HGVD)
0.10537190082644628
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))
rs1532268
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1027
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1721
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)
1355
East Asian Heterozygous Counts (ExAC)
1151
East Asian Homozygous Counts (ExAC)
102
East Asian Allele Frequency (ExAC)
0.15737514518002324
Chromosome Counts in All Race (ExAC)
121204
Allele Counts in All Race (ExAC)
38236
Heterozygous Counts in All Race (ExAC)
25352
Homozygous Counts in All Race (ExAC)
6442
Allele Frequency in All Race (ExAC)
0.3154681363651365
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