ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.5610C>G (p.Phe1870Leu)

dbSNP: rs1060504598
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000510119 SCV000608226 uncertain significance Hereditary cancer-predisposing syndrome 2016-10-11 criteria provided, single submitter clinical testing The p.F1870L variant (also known as c.5610C>G or 5838C>G), located in coding exon 10 of the BRCA2 gene, results from a C to G substitution at nucleotide position 5610. The phenylalanine at codon 1870 is replaced by leucine, an amino acid with highly similar 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 6502 samples (13004 alleles) with coverage of 6502 at this position. To date, this alteration has been detected with an allele frequency of approximately 0.0007% (greater than 300000 alleles tested) in our clinical cohort. This amino acid position is poorly conserved in available vertebrate 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 this alteration remains unclear.
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State RCV002222187 SCV002026122 likely benign Hereditary breast ovarian cancer syndrome 2021-11-16 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002222187 SCV002594661 uncertain significance Hereditary breast ovarian cancer syndrome 2022-08-20 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA2 protein function. ClinVar contains an entry for this variant (Variation ID: 441502). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1870 of the BRCA2 protein (p.Phe1870Leu).
University of Washington Department of Laboratory Medicine, University of Washington RCV000510119 SCV003848952 likely benign Hereditary cancer-predisposing syndrome 2023-03-23 criteria provided, single submitter curation Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).

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