NM_007194.4(CHEK2):c.1009-2A>G AND Familial cancer of breast

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Jun 27, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000699758.10

Allele description [Variation Report for NM_007194.4(CHEK2):c.1009-2A>G]

NM_007194.4(CHEK2):c.1009-2A>G

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.1009-2A>G

HGVS:

NC_000022.11:g.28696989T>C
NG_008150.2:g.49878A>G
NM_001005735.2:c.1138-2A>G
NM_001257387.2:c.346-2A>G
NM_001349956.2:c.808-2A>G
NM_007194.4:c.1009-2A>GMANE SELECT
NM_145862.2:c.1009-1116A>G
LRG_302t1:c.1009-2A>G
LRG_302:g.49878A>G
NC_000022.10:g.29092977T>C
NM_007194.3:c.1009-2A>G

Links:

dbSNP: rs766158073

NCBI 1000 Genomes Browser:

rs766158073

Molecular consequence:

NM_145862.2:c.1009-1116A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001005735.2:c.1138-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001257387.2:c.346-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001349956.2:c.808-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_007194.4:c.1009-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

Observations:

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

Recent activity

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mesoderm-specific transcript homolog protein isoform c [Homo sapiens]
mesoderm-specific transcript homolog protein isoform c [Homo sapiens]
gi|359806886|ref|NP_001240829.1|

Protein
Homo sapiens MAGUK p55 scaffold protein 3 (MPP3), transcript variant 6, non-codi...
Homo sapiens MAGUK p55 scaffold protein 3 (MPP3), transcript variant 6, non-coding RNA
gi|1890351119|ref|NR_148343.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000828483	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jun 5, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 21876083, 24713400, 28492532
SCV002588973	BRCAlab, Lund University	no assertion criteria provided	Likely pathogenic (Aug 26, 2022)	germline	clinical testing
SCV004043490	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Jun 27, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000828483

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jun 5, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV002588973

BRCAlab, Lund University

no assertion criteria provided

Likely pathogenic
(Aug 26, 2022)

germline

clinical testing

SCV004043490

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Jun 27, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Risk of breast cancer in women with a CHEK2 mutation with and without a family history of breast cancer.

Cybulski C, Wokołorczyk D, Jakubowska A, Huzarski T, Byrski T, Gronwald J, Masojć B, Deebniak T, Górski B, Blecharz P, Narod SA, Lubiński J.

J Clin Oncol. 2011 Oct 1;29(28):3747-52. doi: 10.1200/JCO.2010.34.0778. Epub 2011 Aug 29.

PubMed [citation]

PMID:: 21876083

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000828483.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 9 of the CHEK2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CHEK2 are known to be pathogenic (PMID: 21876083, 24713400). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 428913). This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. This variant is present in population databases (rs766158073, gnomAD 0.0009%).

#	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

From BRCAlab, Lund University, SCV002588973.1

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

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

From Myriad Genetics, Inc., SCV004043490.2

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

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

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

Last Updated: Sep 29, 2024

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