chr2:47480696:G>A Detail (hg38) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,707,835-47,707,835 View the variant detail on this assembly version.
hg38 chr2:47,480,696-47,480,696

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.2459G>A NP_000242.1:p.Gly820Asp
NM_001258281.1:c.2261G>A NP_001245210.1:p.Gly754Asp
Ensemble ENST00000233146.7:c.2459G>A ENST00000233146.7:p.Gly820Asp
Summary

MGeND

Clinical significance
Variant entry
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:[No Data.]

Prediction

ClinVar

Clinical Significance Uncertain significance
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 tgv6784765 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2023-03-17 criteria provided, multiple submitters, no conflicts Lynch syndrome 1 unknown Detail
Uncertain significance 2023-11-05 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
Uncertain significance 2023-05-09 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Uncertain significance 2018-07-02 criteria provided, single submitter Lynch syndrome unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.320 Colorectal cancer, hereditary nonpolyposis, type 1 NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.2459G>A (p.Gly820Asp) AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.2459G>A (p.Gly820Asp) AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.2459G>A (p.Gly820Asp) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.2459G>A (p.Gly820Asp) AND Lynch syndrome ClinVar 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
rs794729229 dbSNP
Genome
hg38
Position
chr2:47,480,696-47,480,696
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))
rs794729229
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))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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