NM_007194.4(CHEK2):c.52_84del (p.Cys18_Ser28del) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 23, 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:: RCV001207833.9

Allele description [Variation Report for NM_007194.4(CHEK2):c.52_84del (p.Cys18_Ser28del)]

NM_007194.4(CHEK2):c.52_84del (p.Cys18_Ser28del)

Gene:

CHEK2:checkpoint kinase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.52_84del (p.Cys18_Ser28del)

HGVS:

NC_000022.11:g.28734640_28734672del
NG_008150.2:g.12197_12229del
NM_001005735.2:c.52_84del
NM_001257387.2:c.-726_-694del
NM_001349956.2:c.52_84del
NM_007194.4:c.52_84delMANE SELECT
NM_145862.2:c.52_84del
NP_001005735.1:p.Cys18_Ser28del
NP_001336885.1:p.Cys18_Ser28del
NP_009125.1:p.Cys18_Ser28del
NP_665861.1:p.Cys18_Ser28del
LRG_302t1:c.52_84del
LRG_302:g.12197_12229del
LRG_302p1:p.Cys18_Ser28del
NC_000022.10:g.29130626_29130658del
NC_000022.10:g.29130628_29130660del
NG_008150.1:g.12165_12197del
NM_007194.3:c.52_84del
NM_007194.3:c.52_84del33

Links:

dbSNP: rs876658857

NCBI 1000 Genomes Browser:

rs876658857

Molecular consequence:

NM_001257387.2:c.-726_-694del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001005735.2:c.52_84del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001349956.2:c.52_84del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_007194.4:c.52_84del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_145862.2:c.52_84del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001379200	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 23, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001379200

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 23, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001379200.5

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

Description

This variant, c.52_84del, results in the deletion of 11 amino acid(s) of the CHEK2 protein (p.Cys18_Ser28del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with CHEK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 230943). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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