chr5:7889304:C>T Detail (hg19) (MTRR)

Information

Genome

Assembly Position
hg19 chr5:7,889,304-7,889,304
hg38 chr5:7,889,191-7,889,191 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002454.2:c.1324C>T NP_002445.2:p.Arg442Cys
NM_024010.2:c.1324C>T NP_076915.2:p.Arg442Cys
NR_134480.1:c.1324C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.158
ToMMo:0.167
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.187

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 tgv20178624 TogoVar
COSMIC
MONDO
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
<0.001 Adenoma of large intestine In addition, the methionine synthase reductase (MTRR) Arg415Cys and MTRR Ser284T... BeFree 17389618 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
<0.001 liver carcinoma Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTH... BeFree 25318605 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002454.3(MTRR):c.1243C>T (p.Arg415Cys) AND not specified ClinVar Detail
NM_002454.3(MTRR):c.1243C>T (p.Arg415Cys) AND Disorders of Intracellular Cobalamin Metabolism ClinVar Detail
NM_002454.3(MTRR):c.1243C>T (p.Arg415Cys) AND Methylcobalamin deficiency type cblE ClinVar Detail
In addition, the methionine synthase reductase (MTRR) Arg415Cys and MTRR Ser284Thr variant carriers,... DisGeNET Detail
Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... DisGeNET Detail
Results showed that six SNPs (MTHFR rs1801133, MTRR rs2287780, MTRR rs10380, FTHFD rs1127717, GART r... 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
rs2287780 dbSNP
Genome
hg19
Position
chr5:7,889,304-7,889,304
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1152
Mean of sample read depth (HGVD)
36.67
Standard deviation of sample read depth (HGVD)
18.46
Number of reference allele (HGVD)
1939
Number of alternative allele (HGVD)
365
Allele Frequency (HGVD)
0.1584201388888889
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))
rs2287780
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1667
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2794
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
1617
East Asian Heterozygous Counts (ExAC)
1357
East Asian Homozygous Counts (ExAC)
130
East Asian Allele Frequency (ExAC)
0.18710946540152743
Chromosome Counts in All Race (ExAC)
121386
Allele Counts in All Race (ExAC)
6870
Heterozygous Counts in All Race (ExAC)
6192
Homozygous Counts in All Race (ExAC)
339
Allele Frequency in All Race (ExAC)
0.056596312589590234
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