13-32379812-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_000059.4(BRCA2):āc.9016T>Gā(p.Tyr3006Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.9016T>G | p.Tyr3006Asp | missense_variant | Exon 23 of 27 | 5 | NM_000059.4 | ENSP00000369497.3 | ||
BRCA2 | ENST00000530893.7 | c.8647T>G | p.Tyr2883Asp | missense_variant | Exon 23 of 27 | 1 | ENSP00000499438.2 | |||
BRCA2 | ENST00000614259.2 | n.*1074T>G | non_coding_transcript_exon_variant | Exon 22 of 26 | 2 | ENSP00000506251.1 | ||||
BRCA2 | ENST00000614259 | n.*1074T>G | 3_prime_UTR_variant | Exon 22 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460052Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726464
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Published functional studies demonstrate a damaging effect: defective homology-directed repair activity and sensitivity to PARP inhibitors (PMID: 32377563, 32444794, 33609447, 35665744, 35736817); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as 9244T>G; This variant is associated with the following publications: (PMID: 25722345, 32377563, 35736817, 33609447, 32444794, 29884841, 35665744, 28569743, 31911673, 31853058, 12228710) -
The BRCA2 c.9016T>G (p.Tyr3006Asp) variant has been reported in the published literature in an individual who underwent multigene panel testing (PMID: 31853058 (2020)), and has been reported in an individual with breast cancer (GeneDx, personal communications). Experimental studies have demonstrated this variant is damaging to BRCA2 protein function (PMID: 32444794 (2020), 33609447 (2021), 35736817 (2022)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as likely pathogenic. -
Hereditary breast ovarian cancer syndrome Pathogenic:2
This sequence change replaces tyrosine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 3006 of the BRCA2 protein (p.Tyr3006Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with prostate cancer and breast cancer (internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 38202). Invitae Evidence Modeling incorporating data from in vitro experimental studies (PMID: 33609447) indicates that this missense variant is expected to disrupt BRCA2 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects BRCA2 function (PMID: 32444794, 33609447). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
Variant summary: BRCA2 c.9016T>G (p.Tyr3006Asp) results in a non-conservative amino acid change located in the BRCA2, OB2 domain (IPR048262) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250700 control chromosomes. c.9016T>G has been reported in the literature in a setting of multi-gene panel testing in at least one individual with personal or family history of cancer (e.g. Li_2020). This report does not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. At least two publications report experimental evidence evaluating an impact on protein function showing moderate disruption of BRCA2 function in HDR assay (e.g. Richardson_2021) and sensitivity to PARP inhibitors in vitro (e.g. Yamazawa_2023). ClinVar contains an entry for this variant (Variation ID: 38202). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Hereditary cancer-predisposing syndrome Pathogenic:1Uncertain:1
The p.Y3006D variant (also known as c.9016T>G), located in coding exon 22 of the BRCA2 gene, results from a T to G substitution at nucleotide position 9016. The tyrosine at codon 3006 is replaced by aspartic acid, an amino acid with highly dissimilar properties. This alteration is non functional in multiple assays including a homology-directed, DNA repair assay and multiple drug sensitivity assays (Richardson ME et al. Am J Hum Genet, 2021 03;108:458-468; Ikegami M et al. Nat Commun, 2020 05;11:2573). Based on internal structural analysis, this variant is anticipated to result in a significant decrease in structural stability (Ambry internal data; Yang H et al. Science, 2002 Sep;297:1837-48). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
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Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:1
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Familial cancer of breast Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at