chr2:47475051:AAT> Detail (hg38) (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	chr2:47,702,190-47,702,192
hg38	chr2:47,475,051-47,475,053

HGVS

MSH2

Type	Transcript	Protein
RefSeq	NM_000251.2:c.1786_1788delAAT	NP_000242.1:p.Asn596del
	NM_001258281.1:c.1588_1590delAAT	NP_001245210.1:p.Asn530del
Ensemble	ENST00000233146.7:c.1786_1788delAAT	ENST00000233146.7:p.Asn596del
	ENST00000406134.5:c.1786_1788delAAT	ENST00000406134.5:p.Asn596del
	ENST00000543555.6:c.1588_1590delAAT	ENST00000543555.6:p.Asn530del
	ENST00000645506.1:c.1786_1788delAAT	ENST00000645506.1:p.Asn596del
	ENST00000713854.1:c.1636_1638delAAT	ENST00000713854.1:p.Asn546del
	ENST00000713919.1:c.1507_1509delAAT	ENST00000713919.1:p.Asn503del

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	Pathogenic
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
Pathogenic	2023-10-17	criteria provided, multiple submitters, no conflicts	Lynch syndrome 1	germline unknown	Detail
Pathogenic	2013-09-05	reviewed by expert panel	Lynch syndrome	germline	Detail
Pathogenic	2023-11-09	criteria provided, multiple submitters, no conflicts	Hereditary cancer-predisposing syndrome	germline	Detail
Pathogenic	2024-02-06	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		no assertion criteria provided	Carcinoma of colon	unknown	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.1786_1788del (p.Asn596del) AND Lynch syndrome 1	ClinVar	Detail
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) AND Lynch syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) AND not provided	ClinVar	Detail
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) AND Hereditary nonpolyposis colorectal neoplasms	ClinVar	Detail
NM_000251.3(MSH2):c.1786_1788del (p.Asn596del) AND Carcinoma of colon	ClinVar	Detail
NA	DisGeNET	Detail
NA	DisGeNET	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: rs63749831 dbSNP
Genome: hg38
Position: chr2:47,475,051-47,475,053
Variant Type: snv
Reference Allele: AAT
Alternative Allele: -
East Asian Chromosome Counts (ExAC): 8648
East Asian Allele Counts (ExAC): 0
East Asian Heterozygous Counts (ExAC): 0
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.0
Chromosome Counts in All Race (ExAC): 121166
Allele Counts in All Race (ExAC): 1
Heterozygous Counts in All Race (ExAC): 1
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 8.253140319891718E-6

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