chr2:47637246:A>G Detail (hg19) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,637,246-47,637,246
hg38 chr2:47,410,107-47,410,107 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.380A>G NP_000242.1:p.Asn127Ser
NM_001258281.1:c.182A>G NP_001245210.1:p.Asn61Ser
Ensemble ENST00000406134.5:c.380A>G ENST00000406134.5:p.Asn127Ser
Summary

MGeND

Clinical significance Benign
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609309 OMIM
HGNC 7325 HGNC
Ensembl ENSG00000095002 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6780378 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2021/03/19 control germline MGS000047
(TMGS000111) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Benign 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Conflicting interpretations of pathogenicity 2023-07-07 criteria provided, conflicting interpretations Lynch syndrome 1 germline Detail
Benign 2020-02-06 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Benign 2023-11-28 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Likely benign 2022-04-23 criteria provided, single submitter Mismatch repair cancer syndrome 2,Muir-Torré syndrome,Lynch syndrome 1 unknown Detail
Likely benign 2022-04-23 criteria provided, single submitter Mismatch repair cancer syndrome 2,Muir-Torré syndrome,Lynch syndrome 1 unknown Detail
Likely benign 2022-04-23 criteria provided, single submitter Mismatch repair cancer syndrome 2,Muir-Torré syndrome,Lynch syndrome 1 unknown Detail
Benign 2021-07-02 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Triple Negative Breast Neoplasms Gly322Asp and Asn127Ser single nucleotide polymorphisms (SNPs) of hMSH2 mismatch... BeFree 25134804 Detail
0.365 Turcot syndrome (disorder) Our data demonstrate that MSH2 N127S and G322D per se are not sufficient to trig... BeFree 18470917 Detail
0.144 colorectal cancer The role of one of the most frequently reported MMR gene VUS, MSH2 c.380A&gt;G (... BeFree 22581703 Detail
0.320 Colorectal cancer, hereditary nonpolyposis, type 1 Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in ... UNIPROT 22581703 Detail
0.002 Tumor Progression We performed a case-control study to test the association between two polymorphi... BeFree 16252083 Detail
0.063 colorectal carcinoma The role of one of the most frequently reported MMR gene VUS, MSH2 c.380A&gt;G (... BeFree 22581703 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND Lynch syndrome ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND not specified ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND not provided ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND multiple conditions ClinVar Detail
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) AND Breast and/or ovarian cancer ClinVar Detail
Gly322Asp and Asn127Ser single nucleotide polymorphisms (SNPs) of hMSH2 mismatch repair gene and the... DisGeNET Detail
Our data demonstrate that MSH2 N127S and G322D per se are not sufficient to trigger MMR deficiency. DisGeNET Detail
The role of one of the most frequently reported MMR gene VUS, MSH2 c.380A&gt;G (p.Asn127Ser), is esp... DisGeNET Detail
Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients. DisGeNET Detail
We performed a case-control study to test the association between two polymorphisms in the hMSH2 gen... DisGeNET Detail
The role of one of the most frequently reported MMR gene VUS, MSH2 c.380A&gt;G (p.Asn127Ser), is esp... 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
rs17217772 dbSNP
Genome
hg19
Position
chr2:47,637,246-47,637,246
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs17217772
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
848
Heterozygous Counts in All Race (ExAC)
794
Homozygous Counts in All Race (ExAC)
27
Allele Frequency in All Race (ExAC)
0.006985288060758826
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