chr2:47630550:C>A Detail (hg19) (MSH2)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

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

HGVS

MSH2

Type	Transcript	Protein
RefSeq	NM_000251.2:c.211+9C>A
	NM_001258281.1:c.13+9C>A
Ensemble	ENST00000233146.7:c.211+9C>A
	ENST00000406134.5:c.211+9C>A
	ENST00000543555.6:c.13+9C>A
	ENST00000645506.1:c.211+9C>A
	ENST00000713854.1:c.211+9C>A
	ENST00000713860.1:c.211+9C>A
	ENST00000713861.1:c.211+9C>A
	ENST00000713919.1:c.211+9C>A

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
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Links

MSH2

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
Likely benign	2024-01-25	criteria provided, single submitter	Hereditary nonpolyposis colorectal neoplasms	germline	Detail
Likely benign	2017-02-21	criteria provided, single submitter	Hereditary cancer-predisposing syndrome	germline	Detail
Likely benign	2017-01-31	criteria provided, single submitter	not specified	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

Descrption	Source	Links
NM_000251.3(MSH2):c.211+9C>A AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000251.3(MSH2):c.211+9C>A AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.211+9C>A AND not specified	ClinVar	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs2303426 dbSNP
Genome: hg19
Position: chr2:47,630,550-47,630,550
Variant Type: snv
Reference Allele: C
Alternative Allele: A
East Asian Chromosome Counts (ExAC): 6418
East Asian Allele Counts (ExAC): 3
East Asian Heterozygous Counts (ExAC): 0
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 4.6743533811156125E-4
Chromosome Counts in All Race (ExAC): 80162
Allele Counts in All Race (ExAC): 3
Heterozygous Counts in All Race (ExAC): 0
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 3.7424215962675585E-5

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