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NM_000059.4(BRCA2):c.8699A>T (p.Asp2900Val) AND Malignant tumor of breast

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 8, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001005030.4

Allele description [Variation Report for NM_000059.4(BRCA2):c.8699A>T (p.Asp2900Val)]

NM_000059.4(BRCA2):c.8699A>T (p.Asp2900Val)

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.8699A>T (p.Asp2900Val)
HGVS:
  • NC_000013.11:g.32376736A>T
  • NG_012772.3:g.66257A>T
  • NM_000059.4:c.8699A>TMANE SELECT
  • NP_000050.2:p.Asp2900Val
  • NP_000050.3:p.Asp2900Val
  • LRG_293t1:c.8699A>T
  • LRG_293:g.66257A>T
  • LRG_293p1:p.Asp2900Val
  • NC_000013.10:g.32950873A>T
  • NM_000059.3:c.8699A>T
Nucleotide change:
8927A>T
Protein change:
D2900V
Links:
dbSNP: rs398122712
NCBI 1000 Genomes Browser:
rs398122712
Molecular consequence:
  • NM_000059.4:c.8699A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000987289Center of Medical Genetics and Primary Health Care
no assertion criteria provided
Uncertain significance
(Apr 8, 2020) 		germlineresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedresearch

Details of each submission

From Center of Medical Genetics and Primary Health Care, SCV000987289.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedresearchnot provided

Description

ACMG Guidelines 2015 criteria PM1 Pathogenic Moderate: 2 functional domains - a nucleic acid-binding OB-fold (R2669-3184L aa), which functions as ssDNA binding and nucleic acid recognition site; and the Tower domain (M2831-2967T aa) with a major role in tumor suppression and DNA binding. Hot-spot has 27 non-VUS coding variants (17 pathogenic and 10 benign), pathogenicity = 63.0%, proximity score 7.148 > threshold 2.472. PM2 Pathogenic Moderate: GnomAD exomes allele frequency = 0.00000398 < 0.0001 threshold for recessive gene BRCA2. Variant not found in GnomAD genomes. PP3 Pathogenic Supporting: 7 pathogenic predictions from DANN, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationTaster and SIFT vs 2 benign predictions from PrimateAI and REVEL. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 20, 2024