NM_000059.4(BRCA2):c.2695A>G (p.Asn899Asp) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Feb 9, 2024
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:: RCV000219179.7

Allele description [Variation Report for NM_000059.4(BRCA2):c.2695A>G (p.Asn899Asp)]

NM_000059.4(BRCA2):c.2695A>G (p.Asn899Asp)

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.2695A>G (p.Asn899Asp)

HGVS:

NC_000013.11:g.32337050A>G
NG_012772.3:g.26571A>G
NM_000059.4:c.2695A>GMANE SELECT
NP_000050.2:p.Asn899Asp
NP_000050.3:p.Asn899Asp
LRG_293t1:c.2695A>G
LRG_293:g.26571A>G
LRG_293p1:p.Asn899Asp
NC_000013.10:g.32911187A>G
NM_000059.3:c.2695A>G

Protein change:

N899D

Links:

dbSNP: rs564197624

NCBI 1000 Genomes Browser:

rs564197624

Molecular consequence:

NM_000059.4:c.2695A>G - missense variant - [Sequence Ontology: SO:0001583]

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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Chain A, Cytoplasmic protein NCK1
Chain A, Cytoplasmic protein NCK1
gi|1808735688|pdb|5QU4|A

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000277976	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 9, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV003850075	University of Washington Department of Laboratory Medicine, University of Washington	criteria provided, single submitter (Dines et al. (Genet Med. 2020))	Likely benign (Mar 23, 2023)	germline	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000277976

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 9, 2024)

germline

clinical testing

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

Citation Link,

SCV003850075

University of Washington Department of Laboratory Medicine, University of Washington

criteria provided, single submitter

(Dines et al. (Genet Med. 2020))

Likely benign
(Mar 23, 2023)

germline

curation

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, curation

Citations

PubMed

Hereditary variants of unknown significance in African American women with breast cancer.

McDonald JT, Ricks-Santi LJ.

PLoS One. 2022;17(10):e0273835. doi: 10.1371/journal.pone.0273835.

PubMed [citation]

PMID:: 36315513
PMCID:: PMC9621418

Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".

Dines JN, Shirts BH, Slavin TP, Walsh T, King MC, Fowler DM, Pritchard CC.

Genet Med. 2020 May;22(5):825-830. doi: 10.1038/s41436-019-0740-6. Epub 2020 Jan 8.

PubMed [citation]

PMID:: 31911673
PMCID:: PMC7200594

Details of each submission

From Ambry Genetics, SCV000277976.5

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

Description

The p.N899D variant (also known as c.2695A>G), located in coding exon 10 of the BRCA2 gene, results from an A to G substitution at nucleotide position 2695. The asparagine at codon 899 is replaced by aspartic acid, an amino acid with highly similar properties. this alteration was identified in an individual diagnosed with breast cancer (McDonald JT et al. PLoS One, 2022 Oct;17:e0273835). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, 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 University of Washington Department of Laboratory Medicine, University of Washington, SCV003850075.1

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

Description

Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).

#	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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