chr5:80149981:A>G Detail (hg19) (MSH3)

Information

Genome

Assembly Position
hg19 chr5:80,149,981-80,149,981
hg38 chr5:80,854,162-80,854,162 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002439.4:c.2846A>G NP_002430.3:p.Gln949Arg
Ensemble ENST00000265081.7:c.2846A>G ENST00000265081.7:p.Gln949Arg
ENST00000658259.1:c.2678A>G ENST00000658259.1:p.Gln893Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.999
ToMMo:1.000
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.999

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600887 OMIM
HGNC 7326 HGNC
Ensembl ENSG00000113318 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21677920 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-02-27 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002439.5(MSH3):c.2846A>G (p.Gln949Arg) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_002439.5(MSH3):c.2846A>G (p.Gln949Arg) AND not provided ClinVar Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... 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
rs184967 dbSNP
Genome
hg19
Position
chr5:80,149,981-80,149,981
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
42.43
Standard deviation of sample read depth (HGVD)
20.42
Number of reference allele (HGVD)
3
Number of alternative allele (HGVD)
2413
Allele Frequency (HGVD)
0.9987582781456954
Gene Symbol (HGVD)
MSH3
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))
rs184967
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Homozygous Counts in All Race (ExAC)
46317
East Asian Chromosome Counts (ExAC)
8636
East Asian Allele Counts (ExAC)
8630
East Asian Heterozygous Counts (ExAC)
6
East Asian Homozygous Counts (ExAC)
4312
East Asian Allele Frequency (ExAC)
0.9993052339045855
Chromosome Counts in All Race (ExAC)
121224
Allele Counts in All Race (ExAC)
105841
Heterozygous Counts in All Race (ExAC)
13207
Allele Frequency in All Race (ExAC)
0.8731026859367782
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