NM_000465.4(BARD1):c.403G>A (p.Asp135Asn) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 6, 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:: RCV000528607.7

Allele description [Variation Report for NM_000465.4(BARD1):c.403G>A (p.Asp135Asn)]

NM_000465.4(BARD1):c.403G>A (p.Asp135Asn)

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.403G>A (p.Asp135Asn)

HGVS:

NC_000002.12:g.214781471C>T
NG_012047.3:g.33241G>A
NM_000465.2:c.403G>A
NM_000465.4:c.403G>AMANE SELECT
NM_001282543.2:c.346G>A
NM_001282545.2:c.215+15590G>A
NM_001282548.2:c.158+27941G>A
NM_001282549.2:c.364+10826G>A
NP_000456.2:p.Asp135Asn
NP_001269472.1:p.Asp116Asn
LRG_297t1:c.403G>A
LRG_297:g.33241G>A
LRG_297p1:p.Asp135Asn
NC_000002.11:g.215646195C>T
NG_012047.2:g.33234G>A
NM_000465.3:c.403G>A
NR_104212.2:n.368G>A
NR_104215.2:n.311G>A

Protein change:

D116N

Links:

dbSNP: rs747455698

NCBI 1000 Genomes Browser:

rs747455698

Molecular consequence:

NM_001282545.2:c.215+15590G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001282548.2:c.158+27941G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001282549.2:c.364+10826G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000465.4:c.403G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001282543.2:c.346G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104212.2:n.368G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104215.2:n.311G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000633035	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 6, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33933153, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000633035

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 6, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient.

Zheng Y, Li B, Pan D, Cao J, Zhang J, Wang X, Li X, Hou W, Bao D, Ren L, Yang J, Wang S, Qiu Y, Zhou F, Liu Z, Zhu S, Zhang L, Qing T, Wang Y, Yu Y, Wu J, Hu X, et al.

Breast Cancer Res. 2021 May 1;23(1):53. doi: 10.1186/s13058-021-01428-5.

PubMed [citation]

PMID:: 33933153
PMCID:: PMC8088670

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, SCV000633035.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 135 of the BARD1 protein (p.Asp135Asn). This variant is present in population databases (rs747455698, gnomAD 0.006%). This missense change has been observed in individual(s) with breast cancer (PMID: 33933153). ClinVar contains an entry for this variant (Variation ID: 460748). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change affects BARD1 function (PMID: 33933153). 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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