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NM_007194.4(CHEK2):c.909-1G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 15, 2024
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:
RCV000567556.5

Allele description [Variation Report for NM_007194.4(CHEK2):c.909-1G>A]

NM_007194.4(CHEK2):c.909-1G>A

Gene:
CHEK2:checkpoint kinase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.1
Genomic location:
Preferred name:
NM_007194.4(CHEK2):c.909-1G>A
HGVS:
  • NC_000022.11:g.28699938C>T
  • NG_008150.2:g.46929G>A
  • NM_001005735.2:c.1038-1G>A
  • NM_001257387.2:c.246-1G>A
  • NM_001349956.2:c.708-1G>A
  • NM_007194.4:c.909-1G>AMANE SELECT
  • NM_145862.2:c.909-1G>A
  • LRG_302t1:c.909-1G>A
  • LRG_302:g.46929G>A
  • NC_000022.10:g.29095926C>T
  • NM_007194.3:c.909-1G>A
Links:
dbSNP: rs886039721
NCBI 1000 Genomes Browser:
rs886039721
Molecular consequence:
  • NM_001005735.2:c.1038-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001257387.2:c.246-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001349956.2:c.708-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_007194.4:c.909-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_145862.2:c.909-1G>A - 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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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000661759Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(May 15, 2024) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV000661759.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.909-1G>A intronic variant results from a G to A substitution one nucleotide upstream from coding exon 8 of the CHEK2 gene. 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; however direct evidence is insufficient (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024