BRCA2 c.3762G>T, p.Glu1254Asp
NM_000059.4:c.3762G>T
Variant of Uncertain Significance (VUS)
BRCA2 c.3762G>T (p.E1254D) is classified as Likely Benign based on two strong benign criteria (BS1: allele frequency exceeds gene-specific threshold; BP1: missense outside critical domains with no splicing impact) and no pathogenic criteria met under VCEP guidelines.
ACMG/AMP Criteria Applied
BS1
BP1
Genetic Information
Gene & Transcript Details
Gene
BRCA2
Transcript
NM_000059.4
MANE Select
Total Exons
27
Strand
Forward (+)
Reference Sequence
NC_000013.10
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_000059.2 | Alternative | 27 exons | Forward |
| NM_000059.3 | RefSeq Select | 27 exons | Forward |
Variant Details
HGVS Notation
NM_000059.4:c.3762G>T
Protein Change
E1254D
Location
Exon 11
(Exon 11 of 27)
5'Exon Structure (27 total)3'
Functional Consequence
Loss of Function
Related Variants
No evidence of other pathogenic variants at position 1254 in gene BRCA2
Variant interpretation based on transcript NM_000059.4
Genome Browser
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HGVS InputNM_000059:c.3762G>T
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Clinical Data
Global Frequency
0.000407%
Extremely Rare
Highest in Population
European (non-Finnish)
0.000897%
Very Rare
Global: 0.000407%
European (non-Finnish): 0.000897%
0%
0.05%
0.1%
1%
5%
10%+
Allele Information
Total: 245818Alt: 1Homozygotes: 0
ACMG Criteria Applied
PM2
This variant is present in gnomAD (MAF= 0.000407%, 1/245818 alleles, homozygotes = 0) and at a higher frequency in the European (non-Finnish) population (MAF= 0.000897%, 1/111512 alleles, homozygotes = 0). The variant is rare (MAF < 0.1%), supporting PM2 criterion application.
Classification
5 publications
Uncertain Significance (VUS)
Based on 8 submitter reviews in ClinVar
Submitter Breakdown
5 VUS
3 LB
Pathogenic
Likely Path.
VUS
Likely Benign
Benign
Publications (5)
Variant summary: BRCA2 c.3762G>T (p.Glu1254Asp) results in a 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 4.1e-06 in 245818 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.3762G>T has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome without strong evidence for causality (Ozcelik_2012, Loizidou_2017, Incorvaia_2020). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Breast And Ovarian Cancer Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Five submitters classified the variant as VUS while one classified as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
This missense variant replaces glutamic acid with aspartic acid at codon 1254 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 reported for this variant. This variant has been reported in individuals affected with breast or ovarian cancer (PMID: 22874498, 27882536, 32380732). In a large breast cancer case-control meta-analysis conducted by the BRIDGES consortium, this variant was reported in 3/60466 cases and 6/53461 controls (PMID: 33471991; Leiden Open Variation Database DB-ID BRCA2_007348). This variant has been identified in 1/245818 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.
This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 1254 of the BRCA2 protein (p.Glu1254Asp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with breast and/or ovarian cancer (PMID: 22874498, 27882536, 32380732, 34178674). This variant is also known as 3990G>T. ClinVar contains an entry for this variant (Variation ID: 234481). 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.
Clinical Statement
This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Likely benign (3 clinical laboratories) and as Uncertain Significance (1 clinical laboratories).
Functional Impact
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain (0 mutations).
Related Variants in This Domain
No evidence of other pathogenic variants at position 1254 in gene BRCA2
Computational Analysis
Pathogenicity Predictions
Predictor Consensus
Mixed/VUS
PP3 Applied
No
Additional Predictors
Benign:
CADD: 0.93polyphen_prediction: benignmetasvm: Tmetalr: Tprimateai: T
Neutral: Show all
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific) VCEP Guidelines
PVS1
PVS1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PVS1 is: "Very Strong Null variant (nonsense, frameshift, splice site (donor/acceptor +/-1,2), initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease." The evidence for this variant shows: it is a missense change (E1254D), not a null variant. Therefore, this criterion is not applied because the variant does not meet the null‐variant requirement.
PS1
PS1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PS1 is: "Strong Apply PS1, for predicted missense substitutions, where a previously classified pathogenic variant is considered to act via protein change (no confirmed or predicted effect on mRNA splicing (SpliceAI≤0.1))." The evidence for this variant shows: there is no previously established pathogenic variant with the same amino acid change (E1254). Therefore, this criterion is not applied because no matching pathogenic protein change exists.
PS2
PS2 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PS2 is: "De novo (both maternity and paternity confirmed) in a patient with the disease and no family history." The evidence for this variant shows: no data on de novo occurrence. Therefore, this criterion is not applied because de novo status is unconfirmed.
PS3
PS3 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PS3 is: "Strong Well-established in vitro or in vivo functional studies supportive of a damaging effect. Apply PS3 for assays measuring effect via protein only OR mRNA and protein combined..." The evidence for this variant shows: no functional studies have been performed. Therefore, this criterion is not applied because functional impact has not been assessed.
PS4
PS4 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PS4 is: "Strong The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Case-control studies; p-value ≤0.05 and OR ≥4..." The evidence for this variant shows: no case-control or enrichment data. Therefore, this criterion is not applied because there is no evidence of increased prevalence in affected individuals.
PM1
PM1 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM1 is: "Located in a mutational hot spot and/or critical and well-established functional domain, without benign variation." The evidence for this variant shows: E1254D lies outside known critical domains (PALB2-binding aa 10–40; DNA-binding aa 2481–3186). Therefore, this criterion is not applied because the variant is not in a recognized hotspot or critical domain.
PM2
PM2 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PM2 is: "Supporting Absent from controls in an outbred population, from gnomAD v2.1 (non-cancer, exome only subset) and gnomAD v3.1 (non-cancer)..." The evidence for this variant shows: it is present in gnomAD with MAF=0.000407%. Therefore, this criterion is not applied because the variant is observed in controls at a frequency above zero.
PM3
PM3 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PM3 is: "Supporting Apply for patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi Anemia (FA), and co-occurrent variants in the same gene..." The evidence for this variant shows: no Fanconi Anemia phenotype or trans‐occurrence data. Therefore, this criterion is not applied for lack of FA‐related evidence.
PM4
PM4 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM4 is: "Protein length changes as a result of in-frame deletions/insertions in a non-repeat region or stop-loss variants." The evidence for this variant shows: E1254D is a missense change without length alteration. Therefore, this criterion is not applied because there is no protein length change.
PM5
PM5 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PM5 is: "Strong Protein termination codon (PTC) variant in an exon where a different proven pathogenic PTC variant has been seen before..." The evidence for this variant shows: it is a missense substitution, not a PTC. Therefore, this criterion is not applied because it does not involve a termination codon.
PM6
PM6 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM6 is: "Assumed de novo, but without confirmation of paternity and maternity." The evidence for this variant shows: no de novo data. Therefore, this criterion is not applied because de novo status is unverified.
PP1
PP1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PP1 is: "Strong Co-segregation with disease in multiple affected family members..." The evidence for this variant shows: no family segregation data. Therefore, this criterion is not applied due to lack of segregation evidence.
PP2
PP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PP2 is: "Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease." The evidence for this variant shows: insufficient data on the overall missense constraint in BRCA2 for this specific position. Therefore, this criterion is not applied.
PP3
PP3 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PP3 is: "Supporting Apply PP3 for missense or in-frame insertion, deletion or delins variants inside a clinically important functional domain and predicted impact via protein change (BayesDel no-AF ≥0.30) or predicted splicing (SpliceAI ≥0.2)..." The evidence for this variant shows: BayesDel no-AF <0.30 and SpliceAI = 0. Therefore, this criterion is not applied because in silico predictions do not meet the pathogenicity thresholds.
PP4
PP4 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PP4 is: "Strong Breast cancer is very common and has a high degree of genetic heterogeneity... Use ONLY to capture combined LR towards pathogenicity..." The evidence for this variant shows: no multifactorial likelihood data available. Therefore, this criterion is not applied.
PP5
PP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PP5 is: "Reputable source recently reports variant as pathogenic but the evidence is not available to the laboratory to perform an independent evaluation." The evidence for this variant shows: ClinVar entries are predominantly VUS or likely benign. Therefore, this criterion is not applied because no reputable source reports it as pathogenic.
BA1
BA1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BA1 is: "Stand Alone Filter allele frequency (FAF) is above 0.1% (FAF > 0.001) in gnomAD..." The evidence for this variant shows: MAF=0.000407% (<0.001). Therefore, this criterion is not applied because the allele frequency does not exceed the BA1 threshold.
BS1
BS1 (Strong)
According to VCEP guidelines, the rule for BS1 is: "Strong Filter allele frequency (FAF) is above 0.01% (FAF > 0.0001) in gnomAD..." The evidence for this variant shows: MAF=0.000407% in gnomAD (non-cancer) and 0.000897% in the European (non-Finnish) subset, both >0.0001. Therefore, this criterion is applied at Strong strength because the allele frequency exceeds the gene-specific benign threshold.
BS2
BS2 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BS2 is: "Strong Applied in absence of features of recessive disease, namely Fanconi Anemia phenotype..." The evidence for this variant shows: no information on absence of FA phenotype in carriers. Therefore, this criterion is not applied due to lack of clinical phenotype data.
BS3
BS3 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BS3 is: "Strong Well-established in vitro or in vivo functional studies shows no damaging effect on protein function..." The evidence for this variant shows: no functional assays have been performed. Therefore, this criterion is not applied because no benign functional evidence is available.
BS4
BS4 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BS4 is: "Strong Lack of segregation in affected members of a family, as measured by a quantitative co-segregation analysis method..." The evidence for this variant shows: no segregation studies. Therefore, this criterion is not applied.
BP1
BP1 (Strong) Strength Modified
According to VCEP guidelines, the rule for BP1 is: "Strong Apply BP1_Strong for silent substitution, missense or in-frame insertion, deletion or delins variants outside a (potentially) clinically important functional domain AND no splicing predicted (SpliceAI ≤0.1)." The evidence for this variant shows: E1254D is a missense change outside the PALB2-binding (aa 10-40) and DNA-binding (aa 2481-3186) domains, and SpliceAI score = 0. Therefore, this criterion is applied at Strong strength because the variant lies outside critical domains with no predicted splicing impact.
BP2
BP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for BP2 is: "Observed in trans with a pathogenic variant for a fully penetrant dominant gene/dominant or X-linked inheritance." The evidence for this variant shows: no trans‐cohort data available. Therefore, this criterion is not applied.
BP3
BP3 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for BP3 is: "In-frame deletions/insertions in a repetitive region without a known function." The evidence for this variant shows: it is a single amino acid substitution, not an in-frame indel. Therefore, this criterion is not applied.
BP4
BP4 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BP4 is: "Supporting Missense or in-frame insertion, deletion or delins variants inside a (potentially) clinically important functional domain, and no predicted impact via protein change or splicing (BayesDel no-AF score ≤0.18 AND SpliceAI ≤0.1)." The evidence for this variant shows: E1254D lies outside the specified functional domains. Therefore, this criterion is not applied because the variant is not within a defined critical domain.
BP5
BP5 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BP5 is: "Strong Use ONLY to capture combined LR against pathogenicity, based on multifactorial likelihood clinical data..." The evidence for this variant shows: no multifactorial clinical data. Therefore, this criterion is not applied.
BP6
BP6 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for BP6 is: "Reputable source recently reports variant as benign but the evidence is not available to the laboratory to perform an independent evaluation." The evidence for this variant shows: ClinVar submissions are VUS or likely benign without detailed evidence. Therefore, this criterion is not applied.
BP7
BP7 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for BP7 is: "Supporting Silent variant inside a potentially clinically important functional domain if BP4 met; intronic variants outside conserved splice sites if BP4 met." The evidence for this variant shows: it is a missense substitution. Therefore, this criterion is not applied.