NM_000465.4(BARD1):c.339T>A (p.Asn113Lys) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 14, 2020
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:: RCV001372069.7

Allele description [Variation Report for NM_000465.4(BARD1):c.339T>A (p.Asn113Lys)]

NM_000465.4(BARD1):c.339T>A (p.Asn113Lys)

Gene:

BARD1:BRCA1 associated RING domain 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q35

Genomic location:

Preferred name:

NM_000465.4(BARD1):c.339T>A (p.Asn113Lys)

HGVS:

NC_000002.12:g.214792322A>T
NG_012047.3:g.22390T>A
NM_000465.4:c.339T>AMANE SELECT
NM_001282543.2:c.282T>A
NM_001282545.2:c.215+4739T>A
NM_001282548.2:c.158+17090T>A
NM_001282549.2:c.339T>A
NP_000456.2:p.Asn113Lys
NP_001269472.1:p.Asn94Lys
NP_001269478.1:p.Asn113Lys
LRG_297t1:c.339T>A
LRG_297:g.22390T>A
LRG_297p1:p.Asn113Lys
NC_000002.11:g.215657046A>T
NR_104216.2:n.453T>A

Protein change:

N113K

Links:

dbSNP: rs2106134527

NCBI 1000 Genomes Browser:

rs2106134527

Molecular consequence:

NM_001282545.2:c.215+4739T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001282548.2:c.158+17090T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000465.4:c.339T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282543.2:c.282T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282549.2:c.339T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104216.2:n.453T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial
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
SCV001568657	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 14, 2020)	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

SCV001568657

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 14, 2020)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001568657.4

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

Description

This variant is not present in population databases (ExAC no frequency). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with BARD1-related conditions. This sequence change replaces asparagine with lysine at codon 113 of the BARD1 protein (p.Asn113Lys). The asparagine residue is highly conserved and there is a moderate physicochemical difference between asparagine and lysine.

#	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: Mar 5, 2024

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