chr2:47630213:T>C Detail (hg19) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,630,213-47,630,213
hg38 chr2:47,403,074-47,403,074 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001258281.1:c.-132T>C
Ensemble ENST00000543555.6:c.-132T>C
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.136
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 609309 OMIM
HGNC 7325 HGNC
Ensembl ENSG00000095002 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6779631 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2013-09-05 reviewed by expert panel Lynch syndrome germline Detail
Benign 2021-05-19 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign criteria provided, single submitter not specified germline Detail
Benign 2023-11-08 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Lynch syndrome 1 germline unknown Detail
Benign 2024-01-29 criteria provided, single submitter Hereditary nonpolyposis colorectal neoplasms germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.019 Malignant neoplasm of lung In the present case-control study, we investigated the promoter polymorphisms of... BeFree 25252909 Detail
0.002 Carcinoma of lung In the present case-control study, we investigated the promoter polymorphisms of... BeFree 25252909 Detail
0.014 Malignant neoplasm of lung In the present case-control study, we investigated the promoter polymorphisms of... BeFree 25252909 Detail
0.002 Carcinoma of lung In the present case-control study, we investigated the promoter polymorphisms of... BeFree 25252909 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.2(MSH2):c.-118T>C AND Lynch syndrome ClinVar Detail
NM_000251.2(MSH2):c.-118T>C AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.2(MSH2):c.-118T>C AND not specified ClinVar Detail
NM_000251.2(MSH2):c.-118T>C AND not provided ClinVar Detail
NM_000251.2(MSH2):c.-118T>C AND Lynch syndrome 1 ClinVar Detail
NM_000251.2(MSH2):c.-118T>C AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
In the present case-control study, we investigated the promoter polymorphisms of selected mismatch r... DisGeNET Detail
In the present case-control study, we investigated the promoter polymorphisms of selected mismatch r... DisGeNET Detail
In the present case-control study, we investigated the promoter polymorphisms of selected mismatch r... DisGeNET Detail
In the present case-control study, we investigated the promoter polymorphisms of selected mismatch r... 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
rs2303425 dbSNP
Genome
hg19
Position
chr2:47,630,213-47,630,213
Variant Type
snv
Reference Allele
T
Alternative Allele
C
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))
rs2303425
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1359
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2277
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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