Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_007294.4(BRCA1):c.811G>C(p.Val271Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,459,460 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V271A) has been classified as Likely benign.
BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
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PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP6
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BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-43094720-C-G is Benign according to our data. Variant chr17-43094720-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 55721.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=5, Benign=1, Likely_benign=1}. Variant chr17-43094720-C-G is described in Lovd as [Likely_benign].
Uncertain significance, criteria provided, single submitter
clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano
Feb 12, 2019
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Likely benign, no assertion criteria provided
clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
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Likely benign, no assertion criteria provided
clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute
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Uncertain significance, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Dec 19, 2016
Variant summary: The BRCA1 c.811G>C (p.Val271Leu) variant involves the alteration of a non-conserved nucleotide. 2/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant is absent in 120990 control chromosomes. This variant has been reported in affected individuals without strong evidence of causality. Variant was predicted to be deleterious based comparative evolution analysis (Pavlicek_HMG_2004), and was predicted to be neutral via cisplatin sensitivity assay and HR activity (Bouwman_Cancer Discovery_2013). In addition, multiple clinical diagnostic laboratories/reputable databases as well as literature reports classified this variant as uncertain significance. Taken together, this variant is classified as VUS. -
Uncertain significance, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Sep 30, 2020
This missense variant replaces valine with leucine at codon 271 of the BRCA1 protein. This variant is also known as 930G>C in the literature. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). A functional study has reported that the variant protein supported growth and resistance to DNA damaging agent in mouse BRCA1-null ES cells (PMID: 23867111). This variant has been reported in two individuals affected with breast cancer (PMID: 15955690, 22476429) and a suspected hereditary breast and ovarian cancer family (PMID: 9333265). This variant has been identified in 1/250228 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely benign, criteria provided, single submitter
curation
University of Washington Department of Laboratory Medicine, University of Washington
Mar 23, 2023
Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673). -
Uncertain significance, criteria provided, single submitter
clinical testing
Ambry Genetics
Dec 30, 2021
The p.V271L variant (also known as c.811G>C), located in coding exon 9 of the BRCA1 gene, results from a G to C substitution at nucleotide position 811. The valine at codon 271 is replaced by leucine, an amino acid with highly similar properties. This alteration has been identified in multiple individuals diagnosed with breast and/or ovarian cancer (Shattuck-Eidens D et al. JAMA. 1997 Oct 15;278(15):1242-50; Wárlám-Rodenhuis CC et al. Eur. J. Cancer, 2005 Jul;41:1409-15; Lu W et al. Fam. Cancer, 2012 Sep;11:381-5). A cDNA-based functional assay that tested the ability of BRCA1 variants to complement BRCA1 deficient mouse embryonic stem cells classified this variant as neutral based on both the ability to support proliferation and cisplatin response (Bouwman P et al. Cancer Discov, 2013 Oct;3:1142-55). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Breast-ovarian cancer, familial, susceptibility to, 1 Uncertain:1
Uncertain significance, no assertion criteria provided
clinical testing
Breast Cancer Information Core (BIC) (BRCA1)
Feb 20, 2004
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Malignant tumor of breast Uncertain:1
Uncertain significance, no assertion criteria provided
clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System
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The p.Val271Leu variant was identified in dbSNP (ID: rs80357244), Exome Aggregation Consortium (ExAC) database, the ClinVar database (classified as a uncertain significance variant by the BIC and CHEO), GeneInsight VariantWire database (1X, classified as “IARC 3” by a clinical laboratory) and the BIC database (3X with unknown clinical importance). This variant was identified in the 1000 Genomes Project in 1 of 5000 chromosomes (frequency: 0.0002), the Exome Aggregation Consortium (ExAC) database in 12 of 8652 chromosomes (frequency: 0.001) from a population of East Asian individuals, increasing the likelihood this may be a low frequency benign variant in this population of origin. The p.Val271 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein. However, this information is not predictive enough to rule out pathogenicity. Another variant at this same position, c.811G>A (p.Val271Met) was previously classified by our laboratory as predicted benign, increasing the likelihood that this residue may not be functionally important.The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a difference in splicing in 1 of 5 programs. However, a functional study by Bouwman et al (2013) classified the variant as neutral based on cisplatin response. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance. -
Hereditary breast ovarian cancer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Invitae
Oct 27, 2022
This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 271 of the BRCA1 protein (p.Val271Leu). 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. Experimental studies have shown that this missense change does not substantially affect BRCA1 function (PMID: 23867111, 25823446). 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 BRCA1 protein function. ClinVar contains an entry for this variant (Variation ID: 55721). This variant is also known as c.930G>C. This missense change has been observed in individual(s) with a personal or family history of breast and/or ovarian cancer (PMID: 9333265, 15955690, 22476429). This variant is not present in population databases (gnomAD no frequency). -