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NM_000465.4(BARD1):c.860A>T (p.Glu287Val) AND Hereditary cancer-predisposing syndrome

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jan 2, 2020
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:
RCV001181265.6

Allele description [Variation Report for NM_000465.4(BARD1):c.860A>T (p.Glu287Val)]

NM_000465.4(BARD1):c.860A>T (p.Glu287Val)

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.860A>T (p.Glu287Val)
HGVS:
  • NC_000002.12:g.214781014T>A
  • NG_012047.3:g.33698A>T
  • NM_000465.4:c.860A>TMANE SELECT
  • NM_001282543.2:c.803A>T
  • NM_001282545.2:c.215+16047A>T
  • NM_001282548.2:c.158+28398A>T
  • NM_001282549.2:c.364+11283A>T
  • NP_000456.2:p.Glu287Val
  • NP_001269472.1:p.Glu268Val
  • LRG_297t1:c.860A>T
  • LRG_297:g.33698A>T
  • LRG_297p1:p.Glu287Val
  • NC_000002.11:g.215645738T>A
  • NG_012047.2:g.33691A>T
  • NM_000465.2:c.860A>T
  • NR_104212.2:n.825A>T
  • NR_104215.2:n.768A>T
Protein change:
E268V
Links:
dbSNP: rs1197692311
NCBI 1000 Genomes Browser:
rs1197692311
Molecular consequence:
  • NM_001282545.2:c.215+16047A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282548.2:c.158+28398A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282549.2:c.364+11283A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000465.4:c.860A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282543.2:c.803A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_104212.2:n.825A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104215.2:n.768A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001346366Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jan 2, 2020)
germlineclinical testing

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

SCV002676389Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Uncertain significance
(Oct 21, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Color Diagnostics, LLC DBA Color Health, SCV001346366.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Ambry Genetics, SCV002676389.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.E287V variant (also known as c.860A>T), located in coding exon 4 of the BARD1 gene, results from an A to T substitution at nucleotide position 860. The glutamic acid at codon 287 is replaced by valine, an amino acid with dissimilar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6500 samples (13000 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.002% (greater than 65000 alleles tested) in our clinical cohort. This amino acid position is not well conserved however, valine is a reference amino acid in several species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of p.E287V remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024