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NM_007194.4(CHEK2):c.908+1493_1095+388del AND Predisposition to cancer

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 22, 2023
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:
RCV003325286.1

Allele description [Variation Report for NM_007194.4(CHEK2):c.908+1493_1095+388del]

NM_007194.4(CHEK2):c.908+1493_1095+388del

Gene:
CHEK2:checkpoint kinase 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q12.1
Genomic location:
Preferred name:
NM_007194.4(CHEK2):c.908+1493_1095+388del
HGVS:
  • NC_000022.11:g.28696516_28702015del
  • NG_008150.2:g.44855_50354del
  • NM_001005735.2:c.1037+1493_1224+388del
  • NM_001257387.2:c.245+1493_432+388del
  • NM_001349956.2:c.707+1493_894+388del
  • NM_007194.4:c.908+1493_1095+388delMANE SELECT
  • NM_145862.2:c.908+1493_1009-640del
  • LRG_302t1:c.908+1493_1095+388del
  • LRG_302:g.44855_50354del
  • NC_000022.10:g.29092504_29098003del
Molecular consequence:
  • NM_001005735.2:c.1037+1493_1224+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001257387.2:c.245+1493_432+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001349956.2:c.707+1493_894+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_007194.4:c.908+1493_1095+388del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_145862.2:c.908+1493_1009-640del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001005735.2:c.1037+1493_1224+388del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001257387.2:c.245+1493_432+388del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001349956.2:c.707+1493_894+388del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_007194.4:c.908+1493_1095+388del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_145862.2:c.908+1493_1009-640del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Predisposition to cancer
Identifiers:

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004031206St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Pathogenic
(Jun 22, 2023) 		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 St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV004031206.1

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

Description

The CHEK2 c.908+1493_1095+388del variant is a gross deletion of the genomic region encompassing exons 9-10 of the CHEK2 gene. The 5' end is likely confined to intron 8. The 3' end of this event is likely confined to intron 10. This deletion is expected to result in an absent or disrupted protein product. A deletion of this region has been reported in individuals with breast cancer, prostate cancer, thrombocythemia, thyroid cancer, medulloblastoma, and renal cell carcinoma (PMID: 16551709, 17085682, 21876083, 22058216, 25583358, 29753700, 29978187). Of note, this deletion is also referred to as del5395, and is reported to be a Slavic founder variant. In summary, this variant meets criteria to be classified as pathogenic.

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

Last Updated: Sep 3, 2023