chr2:47403195:G>A Detail (hg38) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,630,334-47,630,334 View the variant detail on this assembly version.
hg38 chr2:47,403,195-47,403,195

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.4G>A NP_000242.1:p.Ala2Thr
NM_001258281.1:c.-31+20G>A
Ensemble ENST00000233146.7:c.4G>A ENST00000233146.7:p.Ala2Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Likely 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
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2021-11-03 criteria provided, conflicting interpretations not provided germline unknown Detail
Likely benign 2018-06-13 reviewed by expert panel Lynch syndrome 1 germline unknown Detail
Likely benign 2022-01-01 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Likely benign 2023-08-15 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Likely benign 2018-02-01 criteria provided, single submitter Lynch syndrome germline Detail
Likely benign 2024-01-31 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Uncertain significance 2019-01-01 criteria provided, single submitter breast carcinoma unknown Detail
Uncertain significance no assertion criteria provided unknown Detail
Uncertain significance 2021-10-08 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
Likely benign 2021-01-28 criteria provided, single submitter MSH2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.332 Hereditary Nonpolyposis Colorectal Cancer NA CLINVAR Detail
0.121 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND not provided ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND not specified ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Lynch syndrome ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Breast carcinoma ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Malignant tumor of breast ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND Breast and/or ovarian cancer ClinVar Detail
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) AND MSH2-related disorder ClinVar Detail
NA DisGeNET Detail
NA 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
rs63750466 dbSNP
Genome
hg38
Position
chr2:47,403,195-47,403,195
Variant Type
snv
Reference Allele
G
Alternative Allele
A
East Asian Chromosome Counts (ExAC)
2862
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)
38072
Allele Counts in All Race (ExAC)
15
Heterozygous Counts in All Race (ExAC)
15
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.939903341038033E-4
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