NM_000251.3(MSH2):c.793-1G>T AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 10, 2022
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:: RCV002416796.2

Allele description [Variation Report for NM_000251.3(MSH2):c.793-1G>T]

NM_000251.3(MSH2):c.793-1G>T

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.793-1G>T

HGVS:

NC_000002.12:g.47414268G>T
NG_007110.2:g.16145G>T
NM_000251.3:c.793-1G>TMANE SELECT
NM_001258281.1:c.595-1G>T
NM_001406631.1:c.793-1G>T
NM_001406632.1:c.793-1G>T
NM_001406633.1:c.793-1G>T
NM_001406634.1:c.793-1G>T
NM_001406635.1:c.793-1G>T
NM_001406636.1:c.793-34G>T
NM_001406637.1:c.793-1G>T
NM_001406638.1:c.793-1G>T
NM_001406639.1:c.793-1G>T
NM_001406640.1:c.793-1G>T
NM_001406641.1:c.793-1G>T
NM_001406642.1:c.793-1G>T
NM_001406643.1:c.793-1G>T
NM_001406644.1:c.793-1G>T
NM_001406645.1:c.793-1G>T
NM_001406646.1:c.793-1G>T
NM_001406647.1:c.792+1708G>T
NM_001406648.1:c.793-1G>T
NM_001406649.1:c.792+1708G>T
NM_001406650.1:c.792+1708G>T
NM_001406651.1:c.792+1708G>T
NM_001406652.1:c.792+1708G>T
NM_001406653.1:c.733-1G>T
NM_001406654.1:c.373-1G>T
NM_001406655.1:c.793-1G>T
NM_001406656.1:c.-105-1G>T
NM_001406657.1:c.793-1G>T
NM_001406658.1:c.-527+1708G>T
NM_001406659.1:c.-676-1G>T
NM_001406660.1:c.-873-1G>T
NM_001406661.1:c.-828-1G>T
NM_001406662.1:c.-745-1G>T
NM_001406666.1:c.793-1G>T
NM_001406669.1:c.-676-1G>T
NM_001406672.1:c.792+1708G>T
NM_001406674.1:c.793-1G>T
LRG_218:g.16145G>T
NC_000002.11:g.47641407G>T
NM_000251.1:c.793-1G>T

Molecular consequence:

NM_001406636.1:c.793-34G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406647.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406649.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406650.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406651.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406652.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406658.1:c.-527+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001406672.1:c.792+1708G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000251.3:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258281.1:c.595-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406631.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406632.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406633.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406634.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406635.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406637.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406638.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406639.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406640.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406641.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406642.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406643.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406644.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406645.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406646.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406648.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406653.1:c.733-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406654.1:c.373-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406655.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406656.1:c.-105-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406657.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406659.1:c.-676-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406660.1:c.-873-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406661.1:c.-828-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406662.1:c.-745-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406666.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406669.1:c.-676-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406674.1:c.793-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002679551	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Jun 10, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002679551

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Jun 10, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV002679551.2

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

Description

The c.793-1G>T intronic variant results from a G to T substitution one nucleotide before coding exon 5 of the MSH2 gene. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

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

Last Updated: Sep 29, 2024

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