NM_000251.3(MSH2):c.212-2del AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 22, 2020
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:: RCV002418383.9

Allele description [Variation Report for NM_000251.3(MSH2):c.212-2del]

NM_000251.3(MSH2):c.212-2del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.212-2del

HGVS:

NC_000002.12:g.47408399del
NG_007110.2:g.10276del
NM_000251.3:c.212-2delMANE SELECT
NM_001258281.1:c.14-2del
NM_001406631.1:c.212-2del
NM_001406632.1:c.212-2del
NM_001406633.1:c.212-2del
NM_001406634.1:c.212-2del
NM_001406635.1:c.212-2del
NM_001406636.1:c.212-2del
NM_001406637.1:c.212-2del
NM_001406638.1:c.212-2del
NM_001406639.1:c.212-2del
NM_001406640.1:c.212-2del
NM_001406641.1:c.212-2del
NM_001406642.1:c.212-2del
NM_001406643.1:c.212-2del
NM_001406644.1:c.212-2del
NM_001406645.1:c.212-2del
NM_001406646.1:c.212-2del
NM_001406647.1:c.212-2del
NM_001406648.1:c.212-2del
NM_001406649.1:c.212-2del
NM_001406650.1:c.212-2del
NM_001406651.1:c.212-2del
NM_001406652.1:c.212-2del
NM_001406653.1:c.212-62del
NM_001406654.1:c.-129-82del
NM_001406655.1:c.212-2del
NM_001406656.1:c.-784-2del
NM_001406657.1:c.212-2del
NM_001406658.1:c.-1107-2del
NM_001406659.1:c.-1257-2del
NM_001406660.1:c.-1454-2del
NM_001406661.1:c.-1409-2del
NM_001406662.1:c.-1326-2del
NM_001406666.1:c.212-2del
NM_001406669.1:c.-1257-2del
NM_001406672.1:c.212-2del
NM_001406674.1:c.212-2del
LRG_218:g.10276del
NC_000002.11:g.47635537del
NC_000002.11:g.47635538del
NM_000251.1:c.212-2delA
NM_000251.2:c.212-2delA

Links:

dbSNP: rs1060502007

NCBI 1000 Genomes Browser:

rs1060502007

Molecular consequence:

NM_001406653.1:c.212-62del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406654.1:c.-129-82del - intron variant - [Sequence Ontology: SO:0001627]
NM_000251.3:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258281.1:c.14-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406631.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406632.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406633.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406634.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406635.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406636.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406637.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406638.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406639.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406640.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406641.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406642.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406643.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406644.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406645.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406646.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406647.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406648.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406649.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406650.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406651.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406652.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406655.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406656.1:c.-784-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406657.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406658.1:c.-1107-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406659.1:c.-1257-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406660.1:c.-1454-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406661.1:c.-1409-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406662.1:c.-1326-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406666.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406669.1:c.-1257-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406672.1:c.212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406674.1:c.212-2del - 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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LOC105900348 [Clupea harengus]
LOC105900348 [Clupea harengus]
Gene ID:105900348

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002729926	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 22, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002729926

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 22, 2020)

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, SCV002729926.2

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

Description

The c.212-2delA intronic variant, located in intron 1 of the MSH2 gene, results from a deletion of one nucleotide within intron 1 of the MSH2 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: Oct 13, 2024

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