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Variant interpretation report

BRCA2 c.8039A>G, p.(Asp2680Gly)

NM_000059.4:c.8039A>G NP_000050.3:p.(Asp2680Gly) View identifiers
Classification
Likely benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About BRCA2

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 1 Benign evidence criteria: 1
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting

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.

Benign criteria applied · 1
BS3Strong
BS3 · strong

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.

Recorded classification: Likely benign

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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.010 maximum delta

Recorded SpliceAI maximum delta score: 0.010. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
8 reported laboratory submissions

6 Uncertain significance · 1 Uncertain Significance · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.

COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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).

Met · 2

PM2 SupportingNM_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. Details ▾Hide ▴
Evidence considered
  • Absent from gnomAD v2.1
  • gnomAD v4.1 AF 8.67e-06 (14/1
  • 614
  • 090 alleles)
  • grpmax FAF 5.42e-06
Sources
BS3 StrongThe 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. Details ▾Hide ▴
Evidence considered
  • VCEP Table 9: BS3_Strong assigned
  • Richardson 2021 (PMID:33609447): Neutral functional result
  • SuppT4: No functional impact
  • Hart 2018: Neutral
  • HDR ratio 3.53
  • SuppT13: No functional impact category (NoImpact)
Sources
vcep_specifications_table9_v1_2_2024_11_18PMID:33609447 ↗vcep_supplementarytables_v1_2_2024_11_18

Not met · 13 · evaluated, threshold not reached

PS1 No previously classified pathogenic missense variant at the same amino acid residue (Asp2680) was identified. No comparator variant satisfying the ENIGMA BRCA2 PS1 rule (same residue, pathogenic classification, SpliceAI ≤0.1) is available. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta 0.01 confirms no splicing impact
  • No pathogenic comparator at codon 2680 in ClinVar or VCEP reference sets
Sources
PS3 The ENIGMA BRCA2 VCEP Table 9 assigns BS3 (Strong) to this variant based on calibrated functional data from Richardson 2021 (PMID:33609447), reporting protein function similar to benign control variants. No evidence of a damaging functional effect; PS3 is not met. Details ▾Hide ▴
Evidence considered
  • VCEP Table 9 pre-assigned code: BS3_Strong
  • Richardson 2021 reports p.Asp2680Gly exhibits protein function similar to benign controls
Sources
vcep_specifications_table9_v1_2_2024_11_18PMID:33609447 ↗
PS4 No case-control data demonstrating significantly increased prevalence of NM_000059.4:c.8039A>G in affected individuals compared to controls is available. The variant is ultra-rare (gnomAD v4.1 AF 8.67e-06). Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 AF 8.67e-06 (14/1
  • 614
  • 090 alleles)
Still missing
  • No case-control study available for this variant
Sources
PP1 No co-segregation data is available for NM_000059.4:c.8039A>G. No quantitative co-segregation analysis (LR ≥2.08 required for PP1_Supporting) has been performed. Details ▾Hide ▴
Still missing
  • No segregation analysis data available
PP3 Although p.Asp2680Gly is located within the BRCA2 DNA binding domain (aa 2481-3186), the ENIGMA VCEP PP3 rule requires BayesDel no-AF score ≥0.30. The observed BayesDel score is 0.285, falling below the threshold. SpliceAI delta is 0.01 (≤0.20). No in silico prediction meets the VCEP PP3 thresholds. Details ▾Hide ▴
Evidence considered
  • BayesDel no-AF = 0.285 (<0.30 threshold)
  • SpliceAI max delta = 0.01 (<0.20 threshold)
  • REVEL = 0.849 (not a VCEP PP3 criterion)
  • Align-GVGD C15 (not strongly pathogenic per VCEP ST11)
Sources
bayesdelspliceai ↗revelvcep_supplementarytables_v1_2_2024_11_18
PP4 The variant is absent from the Li et al. 2020 (PMID:31853058) clinical-history LR table. The combined multifactorial LR from Parsons et al. 2019 (SuppT1 of HUMU-40-1557-s001) is 0.84, which falls in the neutral zone (>0.48 and <2.08). Neither PP4 nor BP5 thresholds are met. Details ▾Hide ▴
Evidence considered
  • Not present in Li et al. 2020 clinical-history LR table
  • Combined multifactorial LR = 0.84 (neutral zone
  • PP4 requires LR ≥2.08)
Sources
vcep_pmid_31853058_brca2_clinical_history_lrvcep_humu_40_1557_s001PMID:31853058 ↗
BA1 The ENIGMA BRCA2 VCEP BA1 rule requires filter allele frequency >0.1% (FAF >0.001). The observed grpmax FAF in gnomAD v4.1 is 5.42e-06 (0.000542%), far below the BA1 threshold. The variant is absent from gnomAD v2.1. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF = 5.42e-06 (0.000542%)
  • Absent from gnomAD v2.1
Sources
BS1 The ENIGMA BRCA2 VCEP BS1_Supporting threshold requires FAF >0.002% (FAF >0.00002). The observed grpmax FAF in gnomAD v4.1 is 5.42e-06 (0.000542%), which is below the BS1_Supporting threshold of 0.002%. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF = 5.42e-06 (<0.002% BS1_Supporting threshold)
  • Absent from gnomAD v2.1
Sources
BS2 BS2 requires proband-level data to assess absence of Fanconi Anemia features, scored per the ENIGMA Specifications Table 8 point system. No proband clinical data are available for this assessment. Details ▾Hide ▴
Still missing
  • No proband clinical phenotype data available
BS4 No lack-of-segregation data are available for NM_000059.4:c.8039A>G. BS4 requires quantitative co-segregation analysis showing LR ≤0.48 (Supporting). Details ▾Hide ▴
Still missing
  • No segregation analysis data available
BP4 The ENIGMA BRCA2 VCEP BP4 rule for missense variants inside a clinically important functional domain requires BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1. While SpliceAI delta is 0.01 (≤0.1), the BayesDel no-AF score is 0.285, exceeding the 0.18 threshold. Details ▾Hide ▴
Evidence considered
  • BayesDel no-AF = 0.285 (>0.18 threshold)
  • SpliceAI max delta = 0.01 (≤0.1
  • met but insufficient alone)
Sources
BP5 The variant is absent from the Li et al. 2020 (PMID:31853058) clinical-history LR table. The combined multifactorial LR from Parsons et al. 2019 is 0.84, which falls in the neutral zone (>0.48 and <2.08). BP5_Supporting requires LR ≤0.48. Details ▾Hide ▴
Evidence considered
  • Not present in Li et al. 2020 clinical-history LR table
  • Combined multifactorial LR = 0.84 (neutral zone
  • BP5 requires LR ≤0.48)
Sources
vcep_pmid_31853058_brca2_clinical_history_lrvcep_humu_40_1557_s001
BP7 BP7 applies to mRNA assay data showing no damaging effect. The ENIGMA VCEP Table 9 assigned BS3 (protein-level functional data) rather than BP7 (mRNA-level). No mRNA-specific assay demonstrating no splicing impact has been identified for this variant beyond the SpliceAI prediction (delta 0.01, no splicing predicted). BP7 requires experimental mRNA evidence per Figure 1B of the specification. Details ▾Hide ▴
Evidence considered
  • SpliceAI predicts no splicing impact (delta 0.01)
  • No mRNA-specific experimental assay data available for BP7
Sources
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_000059.4:c.8039A>G is a missense substitution (p.Asp2680Gly), not a null variant (nonsense, frameshift, or canonical splice site). PVS1 is applicable only to null variants per the ENIGMA BRCA2 VCEP v1.2 framework. Details ▾Hide ▴

No further detail was recorded.

PS2 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. Details ▾Hide ▴
Sources
PM1 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. Details ▾Hide ▴
Sources
PM5 N/AThe ENIGMA BRCA2 VCEP repurposes PM5 for PTC (protein termination codon) variants only. NM_000059.4:c.8039A>G is a missense substitution, not a truncating variant. Details ▾Hide ▴
Sources
pm5_candidatescspec ↗
PM6 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. Details ▾Hide ▴
Sources
PP2 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. Details ▾Hide ▴
Sources
PP5 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. ClinVar review status is 'criteria provided, single submitter' (1-star), which does not meet the 3-star expert panel threshold for the PP5 override rule. Details ▾Hide ▴
Evidence considered
  • ClinVar submission: criteria provided
  • single submitter (1-star)
  • override threshold (3-star EP) not met
Sources
BP1 N/ABP1 applies to missense variants outside a clinically important functional domain. p.Asp2680Gly is located within the BRCA2 DNA binding domain (aa 2481-3186), a (potentially) clinically important functional domain per ENIGMA VCEP v1.2 Appendix J. Details ▾Hide ▴
Evidence considered
  • Amino acid position 2680 is within the BRCA2 DNA binding domain (aa 2481-3186)
Sources
BP2 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. Details ▾Hide ▴
Sources
BP6 VCEPMarked Not Applicable by the ENIGMA BRCA2 VCEP v1.2 specification. ClinVar review status is 'criteria provided, single submitter' (1-star), which does not meet the 3-star expert panel threshold for the BP6 override rule. Details ▾Hide ▴
Evidence considered
  • ClinVar submission: criteria provided
  • single submitter (1-star)
  • override threshold (3-star EP) not met
Sources
PS5 N/APS5 is not a standalone criterion in the ENIGMA BRCA2 VCEP v1.2 framework. Details ▾Hide ▴
Sources

Identifiers

Gene
BRCA2
Transcript
NM_000059.4
Coding (HGVS c.)
NM_000059.4:c.8039A>G
Protein (HGVS p.)
NP_000050.3:p.(Asp2680Gly)
GRCh38
chr13:32363241 A>G
GRCh37
chr13:32937378 A>G
ClinVar
52482

Gene diagram

Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.

BRCA2NM_000059.4
Fetching transcript structure from UCSC…
gnomAD v4.1 14 / 1,614,090 alleles AF 8.67e-06 · 0 homozygotes · FAF 5.42e-06
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 8.7e-06 · 14 / 1,614,090 alleles · 0 hom · FAF 5.4e-06
Remaining individuals2 / 62,506 3.2e-05
European (non-Finnish)12 / 1,179,974 1e-05
0 alternate alleles recorded in 8 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

Statements

gnomAD v4.1

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.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -62 bp
0.010
SpliceAI acceptor gainat +129 bp
0.000
SpliceAI donor lossat +292 bp
0.000
SpliceAI donor gainat -17 bp
0.000
Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000

Other predictors

REVEL
0.849
BayesDel
0.285

How the predictions were used

PP3 Although p.Asp2680Gly is located within the BRCA2 DNA binding domain (aa 2481-3186), the ENIGMA VCEP PP3 rule requires BayesDel no-AF score ≥0.30. The observed BayesDel score is 0.285, falling below the threshold. SpliceAI delta is 0.01 (≤0.20). No in silico prediction meets the VCEP PP3 thresholds. Details ▾Hide ▴
Evidence considered
  • BayesDel no-AF = 0.285 (<0.30 threshold)
  • SpliceAI max delta = 0.01 (<0.20 threshold)
  • REVEL = 0.849 (not a VCEP PP3 criterion)
  • Align-GVGD C15 (not strongly pathogenic per VCEP ST11)
Sources
bayesdelspliceai ↗revelvcep_supplementarytables_v1_2_2024_11_18
BP4 The ENIGMA BRCA2 VCEP BP4 rule for missense variants inside a clinically important functional domain requires BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1. While SpliceAI delta is 0.01 (≤0.1), the BayesDel no-AF score is 0.285, exceeding the 0.18 threshold. Details ▾Hide ▴
Evidence considered
  • BayesDel no-AF = 0.285 (>0.18 threshold)
  • SpliceAI max delta = 0.01 (≤0.1
  • met but insufficient alone)
Sources
BP7 BP7 applies to mRNA assay data showing no damaging effect. The ENIGMA VCEP Table 9 assigned BS3 (protein-level functional data) rather than BP7 (mRNA-level). No mRNA-specific assay demonstrating no splicing impact has been identified for this variant beyond the SpliceAI prediction (delta 0.01, no splicing predicted). BP7 requires experimental mRNA evidence per Figure 1B of the specification. Details ▾Hide ▴
Evidence considered
  • SpliceAI predicts no splicing impact (delta 0.01)
  • No mRNA-specific experimental assay data available for BP7
Sources

Statement

In silico

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.

Cited in the classification

  • Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance.
    Richardson ME et al. · 2021 Mar 4
    Richardson et al. 2021 performed functional assessment of BRCA2 DNA-binding domain variants using a validated homologous recombination assay. p.Asp2680Gly (c.8039A>G) was classified as Neutral, exhibiting HR activity similar to benign control variants.
    → BS3 Names this variant
    PMID 33609447 ↗
    Source detail
    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

Other recorded publications

  • Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.
    Guidugli L et al. · 2018
    Guidugli et al. 2018 assessed the clinical relevance of BRCA2 missense variants in the C-terminal DNA binding domain using functional and computational approaches. NM_000059.4:c.8039A>G was not identified in the abstract or available information.
    Does not name this variant
    PMID 29394989 ↗
  • Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study.
    Borg A et al. · 2010
    Borg et al. 2010 (WECARE study) characterized BRCA1/2 variants in unilateral and bilateral breast cancer. NM_000059.4:c.8039A>G was not identified in the abstract-level available content.
    Does not name this variant
    PMID 20104584 ↗
  • Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
    Phillips et al. 2013 examined tamoxifen and contralateral breast cancer risk in BRCA1/2 mutation carriers. NM_000059.4:c.8039A>G was not identified in the abstract-level content.
    Does not name this variant
    PMID 23918944 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    Richards et al. 2015 published the ACMG/AMP standards and guidelines for sequence variant interpretation. This is a methodological framework document and does not discuss NM_000059.4:c.8039A>G.
    Does not name this variant
    PMID 25741868 ↗
  • Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models.
    Hart SN et al. · 2019
    Hart et al. 2019 developed functionally validated sequence-based computational prediction models for BRCA1 and BRCA2 missense variants. The variant is present in VCEP Supplementary Tables (ST4, ST11) with 'No functional impact' and 'Neutral' classification, but direct variant mention in the publication text could not be confirmed from abstract-level review.
    Does not name this variant
    PMID 29884841 ↗
  • Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors.
    Berliner et al. 2007 published NSGC practice recommendations for hereditary breast and ovarian cancer risk assessment and genetic counseling. This is a clinical guidance document and does not discuss NM_000059.4:c.8039A>G.
    Does not name this variant
    PMID 17508274 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

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.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

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)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.849. BayesDel score = 0.285282.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.