chr2:47403411:C>G Detail (hg38) (MSH2)

Information

Genome

Assembly Position
hg19 chr2:47,630,550-47,630,550 View the variant detail on this assembly version.
hg38 chr2:47,403,411-47,403,411

HGVS

Type Transcript Protein
RefSeq NM_000251.2:c.211+9C>G
NM_001258281.1:c.13+9C>G
Ensemble ENST00000233146.7:c.211+9C>G
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.747
ToMMo:0.746
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.805

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 tgv6779950 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 2015-05-27 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Lynch syndrome 1 germline Detail
Benign 2020-10-19 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 no assertion criteria provided Carcinoma of colon unknown Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
0.001 gallbladder carcinoma Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
<0.001 Malignant neoplasm of gallbladder Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&... BeFree 21283657 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000251.3(MSH2):c.211+9C>G AND Lynch syndrome ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND not specified ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND Lynch syndrome 1 ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND Hereditary nonpolyposis colorectal neoplasms ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND Carcinoma of colon ClinVar Detail
NM_000251.3(MSH2):c.211+9C>G AND not provided ClinVar Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&gt;C (rs2303426), ER... DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2303426 dbSNP
Genome
hg38
Position
chr2:47,403,411-47,403,411
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
805
Mean of sample read depth (HGVD)
5.67
Standard deviation of sample read depth (HGVD)
4.47
Number of reference allele (HGVD)
407
Number of alternative allele (HGVD)
1203
Allele Frequency (HGVD)
0.7472049689440994
Gene Symbol (HGVD)
MSH2
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))
rs2303426
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7464
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12495
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16740
East Asian Chromosome Counts (ExAC)
6418
East Asian Allele Counts (ExAC)
5166
East Asian Heterozygous Counts (ExAC)
1069
East Asian Homozygous Counts (ExAC)
2047
East Asian Allele Frequency (ExAC)
0.8049236522281085
Chromosome Counts in All Race (ExAC)
80162
Allele Counts in All Race (ExAC)
40457
Heterozygous Counts in All Race (ExAC)
20372
Homozygous Counts in All Race (ExAC)
10041
Allele Frequency in All Race (ExAC)
0.5046905017339887
Genome browser