chr5:7900599:G>A Detail (hg38) (MTRR)

Information

Genome

Assembly Position
hg19 chr5:7,900,712-7,900,712 View the variant detail on this assembly version.
hg38 chr5:7,900,599-7,900,599

HGVS

Type Transcript Protein
RefSeq NM_002454.2:c.*541G>A
NM_024010.2:c.*541G>A
NR_134480.1:c.*541G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.121
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

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 tgv20179178 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-13 criteria provided, single submitter Disorders of Intracellular Cobalamin Metabolism 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.*541G>A AND Disorders of Intracellular Cobalamin Metabolism 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
rs9332 dbSNP
Genome
hg38
Position
chr5:7,900,599-7,900,599
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs9332
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1214
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2035
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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