VCV002577900.1 - ClinVar

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

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

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

Variation ID: 2577900 Accession: VCV002577900.1

Type and length

Deletion, 5,500 bp

Location

Cytogenetic: 22q12.1 22: 28696513-28702012 (GRCh38) [ NCBI UCSC ] 22: 29092501-29098000 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Sep 3, 2023	Sep 3, 2023	Jun 22, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_007194.4:c.908+1493_1095+388del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice acceptor splice donor
NM_001005735.2:c.1037+1493_1224+388del		splice acceptor splice donor
NM_001257387.2:c.245+1493_432+388del		splice acceptor splice donor
NM_001349956.2:c.707+1493_894+388del		splice acceptor splice donor
NM_145862.2:c.908+1493_1009-640del		splice acceptor splice donor
NC_000022.11:g.28696516_28702015del
NC_000022.10:g.29092504_29098003del
NG_008150.2:g.44855_50354del
LRG_302:g.44855_50354del
LRG_302t1:c.908+1493_1095+388del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CHEK2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	4053	4109

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Predisposition to cancer	Pathogenic (1)	criteria provided, single submitter	Jun 22, 2023	RCV003325286.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jun 22, 2023)	criteria provided, single submitter (St. Jude Assertion Criteria 2020) Method: clinical testing	Predisposition to cancer Affected status: unknown Allele origin: germline	St. Jude Molecular Pathology, St. Jude Children's Research Hospital Accession: SCV004031206.1 First in ClinVar: Sep 03, 2023 Last updated: Sep 03, 2023	Comment: 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 … (more) 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. (less)

Comment:

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.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 03, 2023

ClinVar Genomic variation as it relates to human health

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

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...