About BRCA2
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.
Likely benign.A likely benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen BRCA2 VCEP v1.2. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
NM_000059.4:c.8039A>G is absent from gnomAD v2.1 (non-cancer, exome only subset), satisfying the ENIGMA BRCA2 VCEP PM2_Supporting rule for absence from an outbred population control dataset.
The ENIGMA BRCA2 VCEP Table 9 assigns BS3 (Strong) to NM_000059.4:c.8039A>G (p.Asp2680Gly). One calibrated study (Richardson 2021, PMID:33609447) reports that this variant exhibits protein function similar to benign control variants in a validated functional assay of BRCA2 homologous recombination activity.
ENIGMA BRCA2 VCEP v1.2 point-based scoring system applied to conflicting pathogenic and benign evidence: BS3_Strong (-4) + PM2_Supporting (+1) = -3 points, which maps to the Likely Benign range (-6 to -2). The ENIGMA framework explicitly directs use of the point system when both pathogenic and benign criteria are met.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 14 / 1,614,090 alleles. Recorded AF 8.67362e-06. Recorded homozygote count 0.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.010. Refer to the recorded PP3/BP4 rationale for interpretation.
6 Uncertain significance · 1 Uncertain Significance · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2, with the data and sources behind each one.
26 criteria with recorded statuses: 2 met · 13 not met · 0 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_000059.4:c.8039A>G (p.Asp2680Gly) is a missense variant in exon 18 of BRCA2, located within the DNA binding domain (aa 2481-3186).
The ENIGMA BRCA2 VCEP Table 9 assigns BS3 (Strong) to this variant based on calibrated functional assay data from Richardson et al. 2021 (PMID:33609447), which demonstrates that p.Asp2680Gly exhibits homologous recombination activity similar to benign control variants.
The variant is absent from gnomAD v2.1 and ultra-rare in gnomAD v4.1 (AF 8.67e-06, grpmax FAF 5.42e-06), satisfying PM2_Supporting per ENIGMA VCEP criteria.
In silico predictors do not meet ENIGMA VCEP thresholds for PP3 (BayesDel 0.285 < 0.30) or BP4 (BayesDel 0.285 > 0.18). SpliceAI predicts no splicing impact (delta 0.01).
No case-control, segregation, or clinical-history LR data are available to support PS4, PP1, PP4, BS4, or BP5.
Applying the ENIGMA point system: BS3_Strong (-4) + PM2_Supporting (+1) = -3 points, which falls in the Likely Benign range (-6 to -2).
No criteria match.
No further detail was recorded.
Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Remaining individuals2 / 62,506 | 3.2e-05 |
| European (non-Finnish)12 / 1,179,974 | 1e-05 |
This variant is present in gnomAD v4.1 (AF= 8.67362e-06; MAF= 0.00087%, 14/1614090 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.19969e-05; MAF= 0.00320%, 2/62506 alleles, homozygotes = 0); grpmax FAF= 5.42e-06.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.849. BayesDel score = 0.285282.
7 paper records listed. 1 cited in the classification.
Reported by one calibrated study to exhibit protein function similar to benign control variants (PMID:33609447) (BS3 met).
Location Cited by ENIGMA VCEP Table 9; specific variant listed in Supplementary Table 13 (ST13) as NoImpact
Context Validated homologous recombination assay, mammalian cells
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 8.67362e-06; MAF= 0.00087%, 14/1614090 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.19969e-05; MAF= 0.00320%, 2/62506 alleles, homozygotes = 0); grpmax FAF= 5.42e-06.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 52482)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.849. BayesDel score = 0.285282.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.