13-32340636-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000059.4(BRCA2):āc.6281A>Gā(p.Tyr2094Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,606,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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BRCA2 | ENST00000380152.8 | c.6281A>G | p.Tyr2094Cys | missense_variant | Exon 11 of 27 | 5 | NM_000059.4 | ENSP00000369497.3 | ||
BRCA2 | ENST00000530893.7 | c.5912A>G | p.Tyr1971Cys | missense_variant | Exon 11 of 27 | 1 | ENSP00000499438.2 | |||
BRCA2 | ENST00000614259.2 | n.6281A>G | non_coding_transcript_exon_variant | Exon 10 of 26 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000821 AC: 2AN: 243716Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131924
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454558Hom.: 0 Cov.: 45 AF XY: 0.00000415 AC XY: 3AN XY: 723438
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:3
Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with a personal or family history including breast and other cancers (Jakubowska 2002, Wong-Brown 2015); This variant is associated with the following publications: (PMID: 26269718, 25682074, 12373604) -
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BRCA2: PM2, BP1, BP4 -
Hereditary cancer-predisposing syndrome Uncertain:2Benign:1
The p.Y2094C variant (also known as c.6281A>G), located in coding exon 10 of the BRCA2 gene, results from an A to G substitution at nucleotide position 6281. The tyrosine at codon 2094 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been detected in a family with early-onset breast and stomach cancers (Jakubowska A et al. Br J Cancer. 2002 Oct 7;87(8):888-91). This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this variant remains unclear. -
Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673). -
This missense variant replaces tyrosine with cysteine at codon 2094 of the BRCA2 protein. Computational prediction suggests that this variant may not impact protein structure and function. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in three individuals affected with breast cancer (PMID 12373604, 25682074, 30040829), and a multifactorial analysis has reported a likelihood ratio based on personal and family history for 1 carrier of 0.807 from log(LR)=-0.093155861 (PMID: 31853058). This variant has been identified in 3/275116 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. -
Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:2
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not specified Uncertain:1
Variant summary: BRCA2 c.6281A>G (p.Tyr2094Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8.2e-06 in 243916 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.6281A>G has been reported in the literature in an individual affected with breast cancer and in her unaffected sister, and in an individual affected with epithelial ovarian cancer, all without evidence of causality (e.g. Jakubowska_2002, Richau_2024). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. Co-occurrences with other pathogenic variants have been reported (BRCA1 c.1504_1508delTTAAA, p.Leu502AlafsX2 (UMD); BRCA1 c.5152+5G>A (internal sample)), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 12373604, 25682074, 38308422). ClinVar contains an entry for this variant (Variation ID: 52046). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -
Fanconi anemia complementation group D1 Uncertain:1
ACMG classification criteria: PS4 supporting, PM2 moderated, BP4 supporting -
Hereditary breast ovarian cancer syndrome Uncertain:1
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 2094 of the BRCA2 protein (p.Tyr2094Cys). This variant is present in population databases (rs397507838, gnomAD 0.003%). This missense change has been observed in individual(s) with breast and pancreatic cancer (PMID: 12373604, 25682074, 30040829). ClinVar contains an entry for this variant (Variation ID: 52046). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt BRCA2 protein function with a negative predictive value of 95%. 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. -
Familial cancer of breast;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at