NM_000251.3(MSH2):c.792+1G>A AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 4, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001588899.3

Allele description [Variation Report for NM_000251.3(MSH2):c.792+1G>A]

NM_000251.3(MSH2):c.792+1G>A

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.792+1G>A

HGVS:

NC_000002.12:g.47412561G>A
NG_007110.2:g.14438G>A
NM_000251.3:c.792+1G>AMANE SELECT
NM_001258281.1:c.594+1G>A
NM_001406631.1:c.792+1G>A
NM_001406632.1:c.792+1G>A
NM_001406633.1:c.792+1G>A
NM_001406634.1:c.792+1G>A
NM_001406635.1:c.792+1G>A
NM_001406636.1:c.792+1G>A
NM_001406637.1:c.792+1G>A
NM_001406638.1:c.792+1G>A
NM_001406639.1:c.792+1G>A
NM_001406640.1:c.792+1G>A
NM_001406641.1:c.792+1G>A
NM_001406642.1:c.792+1G>A
NM_001406643.1:c.792+1G>A
NM_001406644.1:c.792+1G>A
NM_001406645.1:c.792+1G>A
NM_001406646.1:c.792+1G>A
NM_001406647.1:c.792+1G>A
NM_001406648.1:c.792+1G>A
NM_001406649.1:c.792+1G>A
NM_001406650.1:c.792+1G>A
NM_001406651.1:c.792+1G>A
NM_001406652.1:c.792+1G>A
NM_001406653.1:c.732+1G>A
NM_001406654.1:c.372+1G>A
NM_001406655.1:c.792+1G>A
NM_001406656.1:c.-204+1G>A
NM_001406657.1:c.792+1G>A
NM_001406658.1:c.-527+1G>A
NM_001406659.1:c.-677+1G>A
NM_001406660.1:c.-874+1G>A
NM_001406661.1:c.-829+1G>A
NM_001406662.1:c.-746+1G>A
NM_001406666.1:c.792+1G>A
NM_001406669.1:c.-677+1G>A
NM_001406672.1:c.792+1G>A
NM_001406674.1:c.792+1G>A
LRG_218t1:c.792+1G>A
LRG_218:g.14438G>A
NC_000002.11:g.47639700G>A
NM_000251.1:c.792+1G>A
NM_000251.2:c.792+1G>A

Links:

dbSNP: rs267607934

NCBI 1000 Genomes Browser:

rs267607934

Molecular consequence:

NM_000251.3:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001258281.1:c.594+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406631.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406632.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406633.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406634.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406635.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406636.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406637.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406638.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406639.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406640.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406641.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406642.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406643.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406644.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406645.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406646.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406647.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406648.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406649.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406650.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406651.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406652.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406653.1:c.732+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406654.1:c.372+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406655.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406656.1:c.-204+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406657.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406658.1:c.-527+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406659.1:c.-677+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406660.1:c.-874+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406661.1:c.-829+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406662.1:c.-746+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406666.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406669.1:c.-677+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406672.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406674.1:c.792+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001822507	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jan 4, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001822507

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jan 4, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV001822507.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Canonical splice site variant predicted to result in an in-frame deletion of the critical connector domains (Lutzen 2008, Kansikas 2011); Not observed in large population cohorts (Lek 2016); Reported in individuals with colon cancer with concordant mismatch repair immunohistochemistry results reported to result in skipping of exon 4 (Cunningham 2001, Casey 2005, Rosty 2014).; This variant is associated with the following publications: (PMID: 32390703, 11524701, 23752102, 25117503, 15713769, 25525159)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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