NM_007194.4(CHEK2):c.87A>G (p.Gln29=) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Nov 21, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000567579.5

Allele description [Variation Report for NM_007194.4(CHEK2):c.87A>G (p.Gln29=)]

NM_007194.4(CHEK2):c.87A>G (p.Gln29=)

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.87A>G (p.Gln29=)

HGVS:

NC_000022.11:g.28734635T>C
NG_008150.2:g.12232A>G
NM_001005735.2:c.87A>G
NM_001257387.2:c.-691A>G
NM_001349956.2:c.87A>G
NM_007194.4:c.87A>GMANE SELECT
NM_145862.2:c.87A>G
NP_001005735.1:p.Gln29=
NP_001336885.1:p.Gln29=
NP_009125.1:p.Gln29=
NP_665861.1:p.Gln29=
LRG_302t1:c.87A>G
LRG_302:g.12232A>G
LRG_302p1:p.Gln29=
NC_000022.10:g.29130623T>C
NG_008150.1:g.12200A>G
NM_007194.3:c.87A>G

Links:

dbSNP: rs951525447

NCBI 1000 Genomes Browser:

rs951525447

Molecular consequence:

NM_001257387.2:c.-691A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001005735.2:c.87A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001349956.2:c.87A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_007194.4:c.87A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_145862.2:c.87A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000669286	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 26, 2017)	germline	clinical testing	Citation Link,
SCV004361416	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 21, 2022)	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

SCV000669286

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 26, 2017)

germline

clinical testing

Citation Link,

SCV004361416

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Nov 21, 2022)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ambry Genetics, SCV000669286.5

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

Description

The c.87A>G variant (also known as p.Q29Q), located in coding exon 1, results from an A to G substitution at nucleotide position 87 of the CHEK2 gene. This nucleotide substitution does not change the amino acid at codon 29. This nucleotide position is poorly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is predicted to create a new alternate splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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 Color Diagnostics, LLC DBA Color Health, SCV004361416.1

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

#	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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