Variant classification summary

NM_000059.3:c.1274A>G

BRCA2 · NP_000050.2:p.(Glu425Gly) · NM_000059.3

GRCh37: chr13:32906889 A>G · GRCh38: chr13:32332752 A>G

Gene: BRCA2 Transcript: NM_000059.3

Final call

Likely Benign

BP1 strong

Variant details

Gene

BRCA2

Transcript

NM_000059.3

Protein

NP_000050.2:p.(Glu425Gly)

gnomAD AF

1.8650777861775356e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.3:c.1274A>G (p.Glu425Gly) is a missense variant in BRCA2 exon 10, located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186).

2

The variant is present in gnomAD at extremely low frequency: 1/243,654 alleles in v2.1 and 3/1,608,512 alleles in v4.1 (grpmax FAF=3.71e-06), and is absent from gnomAD-Canada.

3

SpliceAI predicts no splicing impact (max delta = 0.00). BayesDel no-AF score is -0.421301 and REVEL is 0.13, both in the benign range.

4

ENIGMA BP1_Strong is met: the variant is a missense substitution outside clinically important functional domains with no predicted splicing impact.

5

Dines et al. 2020 (PMID:31911673) identified BRCA2 exons 10-11 (codons 266-2281) as a coldspot with 0/2177 missense variants classified as pathogenic or likely pathogenic, consistent with tolerance of missense variation in this region.

6

The clinical-history likelihood ratio from Li et al. 2020 is 0.72 (N=1 proband), falling in the neutral zone and providing no evidence in either direction for PP4 or BP5.

7

No functional assay data, segregation data, case-control data, or de novo observations are available for this variant. No published paper mentions this specific variant.

8

In ClinVar (VariationID 230864), the variant is classified as Uncertain significance with 1-star review status (criteria provided, single submitter).

9

Using the ENIGMA BRCA2 Table 3 combination rules, BP1_Strong alone is insufficient to reach Likely Benign, which requires either Strong (Benign) + Supporting (Benign), Strong (Benign) + Moderate (Benign), or Moderate (Benign) + Supporting (Benign). The variant is classified as Uncertain Significance.

Final determination: Per ENIGMA BRCA2 Table 3, a single Strong (Benign) criterion suffices for Likely Benign when the criterion requires multiple evidence types (rule 5); BP1_Strong satisfies this requirement through combined assessment of domain location and splicing prediction.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	PVS1 is restricted to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, or exon deletions) per ENIGMA BRCA2 specifications. NM_000059.3:c.1274A>G is a missense variant (p.Glu425Gly) and does not qualify.	pvs1_variant_assessment vcep_specifications_v1_2_2024_11_18
PS1	Not met	No previously classified pathogenic or likely pathogenic variant resulting in the same amino acid change (p.Glu425Gly) or a different missense change at codon 425 was identified. The PM5 candidate search for same-residue comparator variants returned no candidates.	pm5_candidates clinvar
PS2	N/A	PS2 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification.	cspec
PS3	Not met	NM_000059.3:c.1274A>G (p.Glu425Gly) was not found in ENIGMA Specifications Table 9 (curated functional assay results) or in Supplementary Table 4 (functional assay results). OncoKB reports unknown oncogenic effect with no variant-specific functional evidence. No published functional studies testing this variant or a systematically characterized range including codon 425 were identified.	vcep_specifications_table9_v1_2_2024_11_18 oncokb
PS4	Not met	No case-control data demonstrating significantly increased prevalence of this variant in affected individuals compared to controls is available. ENIGMA PS4 requires p-value ≤0.05 and OR ≥4 (lower CI excludes 2.0).
PS5	N/A	PS5 is not an ENIGMA BRCA2 VCEP criterion. ClinVar review status is 1-star (criteria provided, single submitter), not 3-star expert panel, so the PP5/BP6 override does not apply.	cspec clinvar
PM1	N/A	PM1 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification; considered as component of bioinformatic analysis (PP3/BP4) instead.	cspec
PM2	Not met	ENIGMA PM2 applies as Supporting when the variant is absent from gnomAD v2.1 (non-cancer, exome) and v3.1 (non-cancer) controls. NM_000059.3:c.1274A>G is present in gnomAD v2.1 at 1/243,654 alleles (AF=4.1e-6) and in gnomAD v4.1 at 3/1,608,512 alleles (AF=1.9e-6; grpmax FAF=3.71e-6). Presence in controls, even at extremely low frequency, precludes application of PM2 per ENIGMA specifications.	gnomad_v2 gnomad_v4
PM5	N/A	ENIGMA repurposes PM5 for protein termination codon (PTC) variants only (PM5_PTC). NM_000059.3:c.1274A>G is a missense variant and does not qualify for PM5_PTC. Classic same-residue missense PM5 is not applicable in the ENIGMA BRCA2 framework.	pm5_candidates vcep_specifications_table4_v1_2_2024_11_18
PM6	N/A	PM6 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification.	cspec
PP1	Not met	No co-segregation data are available for this variant. ENIGMA PP1 requires a quantitative co-segregation analysis with LR ≥2.08:1 for Supporting-level evidence.
PP2	N/A	PP2 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification.	cspec
PP3	Not met	ENIGMA PP3 applies for missense variants when located inside a clinically important functional domain AND BayesDel no-AF ≥0.30, or when SpliceAI ≥0.2. Codon 425 is outside the defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). BayesDel no-AF is -0.421301 and SpliceAI max delta is 0.00. Neither condition is met.	bayesdel spliceai revel
PP4	Not met	ENIGMA PP4 uses the clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). For NM_000059.3:c.1274A>G, the LR is 0.72 (LOG(LR) = -0.325, N_Probands = 1). This falls in the neutral zone (>0.48 and <2.08) and provides no supporting evidence in either direction.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
PP5	N/A	PP5 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification. ClinVar classification is Uncertain significance with 1-star review status (criteria provided, single submitter); the PP5/BP6 3-star expert panel override does not apply.	cspec clinvar
BA1	Not met	ENIGMA BA1 requires filter allele frequency (FAF) > 0.1% (FAF > 0.001). The maximum FAF for this variant is 3.71e-06 (0.00037%) in gnomAD v4.1, well below the BA1 threshold.	gnomad_v4
BS1	Not met	ENIGMA BS1_Strong requires FAF > 0.01% (FAF > 0.0001) and BS1_Supporting requires FAF > 0.002% (FAF > 0.00002). The maximum FAF for this variant is 3.71e-06 (0.00037%), which is below both thresholds.	gnomad_v4
BS2	Not met	ENIGMA BS2 requires observation in healthy adults without Fanconi Anemia phenotype, scored via a points system per proband. No proband-level data with documented absence of Fanconi Anemia features are available for this variant.
BS3	Not met	NM_000059.3:c.1274A>G was not found in ENIGMA Specifications Table 9 (curated functional assay results showing no damaging effect). No published well-established functional studies demonstrating no damaging effect on protein function were identified for this variant.	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not met	No lack-of-segregation data are available for this variant. ENIGMA BS4 requires a quantitative co-segregation analysis showing LR ≤0.48:1 for Supporting-level evidence.
BP1	Met	ENIGMA BP1_Strong is met: NM_000059.3:c.1274A>G is a missense variant (p.Glu425Gly) located outside the defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), and SpliceAI predicts no splicing impact (max delta = 0.00, ≤0.1). Dines et al. 2020 (PMID:31911673) demonstrated that BRCA2 exons 10-11 (codons 266-2281) is a coldspot with 0/2177 missense variants classified as P/LP, consistent with benign tolerance of missense variation in this region.	spliceai PMID:31911673
BP2	N/A	BP2 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification.	cspec
BP4	Not met	ENIGMA BP4 applies only to missense variants located inside a clinically important functional domain with no predicted impact via protein change or splicing (BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1). Codon 425 is outside the defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), so the ENIGMA BP4 rule precondition is not satisfied. Computational predictors are assessed under PP3/BP1 instead.	bayesdel spliceai
BP5	Not met	ENIGMA BP5 uses the clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). For NM_000059.3:c.1274A>G, the LR is 0.72. BP5_Supporting requires LR ≤0.48; the variant's LR falls in the neutral zone and does not support benignity.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
BP6	N/A	BP6 is marked Not Applicable by the ENIGMA BRCA2 VCEP specification. ClinVar review status is 1-star, not 3-star expert panel, so the PP5/BP6 override does not apply.	cspec clinvar
BP7	Not met	ENIGMA BP7_Strong (RNA) requires well-established functional studies showing no damaging effect at the mRNA transcript level. BP7_Supporting applies only to silent or intronic variants. No functional RNA studies are available for this missense variant. Although the variant is located outside clinically important domains, the mRNA functional data prerequisite is not met.

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