NM_007194.4(CHEK2):c.*2dup AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 26, 2016
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:: RCV000164412.9

Allele description [Variation Report for NM_007194.4(CHEK2):c.*2dup]

NM_007194.4(CHEK2):c.*2dup

Gene:

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

Variant type:

Duplication

Cytogenetic location:

22q12.1

Genomic location:

Preferred name:

NM_007194.4(CHEK2):c.*2dup

HGVS:

NC_000022.11:g.28687895dup
NG_008150.2:g.58972dup
NM_001005735.2:c.*2dup
NM_001257387.2:c.*2dup
NM_001349956.2:c.*2dup
NM_007194.4:c.*2dupMANE SELECT
NM_145862.2:c.*2dup
LRG_302t1:c.*2dup
LRG_302:g.58972dup
NC_000022.10:g.29083883dup
NG_008150.1:g.58940dup
NM_007194.3:c.*2dupC

Links:

dbSNP: rs749257861

NCBI 1000 Genomes Browser:

rs749257861

Molecular consequence:

NM_001005735.2:c.*2dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001257387.2:c.*2dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001349956.2:c.*2dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_007194.4:c.*2dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_145862.2:c.*2dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

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
SCV000215049	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 22, 2016)	germline	clinical testing	Citation Link,
SCV000902792	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 26, 2016)	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

SCV000215049

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 22, 2016)

germline

clinical testing

Citation Link,

SCV000902792

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Oct 26, 2016)

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, SCV000215049.7

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

Description

The c.*2dupC variant is located in the 3' untranslated region (3’UTR) of the CHEK2 gene. This variant results from the duplication of C two nucleotides after the termination codon of the CHEK2 gene. This alteration occurs within the non-coding region of the gene and may not interfere with gene function; however, since supporting evidence is limited at this time, the clinical significance of this variant 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, SCV000902792.1

#	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: May 1, 2024

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