chr2:47641560:A>T 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	chr2:47,641,560-47,641,560
hg38	chr2:47,414,421-47,414,421 View the variant detail on this assembly version.

HGVS

MSH2

Type	Transcript	Protein
RefSeq	NM_001258281.1:c.744+3A>T
	NM_000251.2:c.942+3A>T
Ensemble	ENST00000543555.6:c.744+3A>T
	ENST00000233146.7:c.942+3A>T
	ENST00000406134.5:c.942+3A>T
	ENST00000645506.1:c.942+3A>T
	ENST00000713854.1:c.792+1861A>T
	ENST00000713860.1:c.942+3A>T
	ENST00000713861.1:c.942+3A>T
	ENST00000713919.1:c.663+3A>T

Summary

MGeND

Clinical significance	Likely pathogenic Pathogenic
Variant entry	16
GWAS entry
Disease area statistics	Show details

Frequency

[No Data.]

Prediction

ClinVar

Clinical Significance	Pathogenic
Review star
Show details

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	tgv6781069	TogoVar
	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation	Comment	Image
Pathogenic		gastric cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Pathogenic		small intestinal cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Pathogenic		Ovarian cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Pathogenic		renal pelvis cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Pathogenic		Endometrial cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Pathogenic		colorectal cancer	germline	MGS000060 (TMGS000107)	Hitoshi Nakagama	National Cancer Center Japan
Likely pathogenic	2018/11/02	colorectal cancer, hereditary nonpolyposis	germline	MGS000016 (TMGS000059)	Masashi Mizokami	Shinshu University
Pathogenic		colorectal cancer, hereditary nonpolyposis	germline	MGS000001 (TMGS000138)	Kenjiro Kosaki	Keio University
Pathogenic		colorectal cancer, hereditary nonpolyposis	germline	MGS000001 (TMGS000138)	Kenjiro Kosaki	Keio University
Pathogenic		colorectal cancer, hereditary nonpolyposis	germline	MGS000001 (TMGS000162)	Kenjiro Kosaki	Keio University

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Conflicting interpretations of pathogenicity	2024-03-25	criteria provided, conflicting interpretations	Lynch syndrome 1	germline unknown	Detail
Pathogenic	2013-09-05	reviewed by expert panel	Lynch syndrome	germline	Detail
Pathogenic	2023-02-22	criteria provided, multiple submitters, no conflicts	Hereditary cancer-predisposing syndrome	germline	Detail
Pathogenic	2023-11-27	criteria provided, multiple submitters, no conflicts	not provided	germline unknown	Detail
Pathogenic	2024-01-22	criteria provided, single submitter	Hereditary nonpolyposis colorectal neoplasms	germline	Detail
Pathogenic	2019-07-01	no assertion criteria provided	Lynch-like syndrome	somatic	Detail
Pathogenic		no assertion criteria provided	Carcinoma of colon	unknown	Detail
Pathogenic	2021-08-21	no assertion criteria provided	breast carcinoma	germline	Detail
Pathogenic	2021-09-08	criteria provided, single submitter	Hereditary nonpolyposis colon cancer	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.332	Hereditary Nonpolyposis Colorectal Cancer	NA	CLINVAR		Detail
0.320	Colorectal cancer, hereditary nonpolyposis, type 1	NA	CLINVAR		Detail
0.121	Neoplastic Syndromes, Hereditary	NA	CLINVAR		Detail

Annotation

Annotations

Descrption	Source	Links
NM_000251.3(MSH2):c.942+3A>T AND Lynch syndrome 1	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Lynch syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND not provided	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Lynch-like syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Carcinoma of colon	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Breast carcinoma	ClinVar	Detail
NM_000251.3(MSH2):c.942+3A>T AND Hereditary nonpolyposis colon cancer	ClinVar	Detail
NA	DisGeNET	Detail
NA	DisGeNET	Detail
NA	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs193922376 dbSNP
Genome: hg19
Position: chr2:47,641,560-47,641,560
Variant Type: snv
Reference Allele: A
Alternative Allele: T

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