Variant classification summary

NM_000059.4:c.6495G>A

BRCA2 · NP_000050.3:p.(Leu2165=) · NM_000059.4

GRCh37: chr13:32914987 G>A · GRCh38: chr13:32340850 G>A

Gene: BRCA2 Transcript: NM_000059.4

Final call

Likely Benign

BP1 strong benign PM2 supporting

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.(Leu2165=)

gnomAD AF

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.4:c.6495G>A (p.Leu2165=) is a synonymous substitution in BRCA2 exon 11, located outside the clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186).

2

SpliceAI predicts no splicing impact (max delta score = 0.04), consistent with a silent variant that does not alter the mRNA transcript.

3

BP1_Strong is met: silent substitution outside clinically important functional domains with no splicing predicted (SpliceAI ≤0.1). This provides strong evidence toward a benign interpretation.

4

PM2_Supporting is met: the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, supporting rarity in outbred population controls. However, for a synonymous variant with no predicted functional consequence, population absence is more consistent with a rare benign polymorphism than with pathogenicity.

5

Under ENIGMA BRCA2 v1.2 Table 3 combination rules, BP1_Strong alone does not reach Likely Benign (which requires Strong Benign + Supporting Benign or Moderate Benign + Supporting Benign). With PM2_Supporting pointing in the pathogenic direction, the net classification is Variant of Uncertain Significance (VUS).

6

This variant has been reported in ClinVar as Likely benign by two clinical laboratories (VariationID 433804, criteria provided, single submitter), consistent with the overall benign direction of evidence.

Final determination: When benign and pathogenic criteria are both met, the ENIGMA point-system is used: BP1_Strong (-4 points) plus PM2_Supporting (+1 point) yields a total of -3, mapping to Likely Benign (-6 to -2 range).

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	N/A	Synonymous variant (p.Leu2165=); PVS1 under ENIGMA BRCA2 v1.2 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice site, initiation codon, or exon deletion).
PS1	N/A	Synonymous variant; PS1 under ENIGMA BRCA2 v1.2 applies only to missense substitutions with a same-residue known pathogenic comparator or to variants with same predicted splicing impact as a known pathogenic variant. SpliceAI max delta is 0.04, well below the 0.2 threshold for splicing prediction.
PS2	N/A	ENIGMA BRCA2 v1.2 specification marks PS2 as Not Applicable; de novo data are not considered for BRCA2 variant classification under this framework.
PS3	Not assessed	No well-established in vitro or in vivo functional studies demonstrating a damaging effect on protein function have been identified for this variant. The variant is not listed in ENIGMA Specifications Table 9 (curated functional assay results).
PS4	Not met	No case-control study demonstrates a statistically significant excess of this variant in affected individuals versus controls (OR ≥4 with lower CI excluding 2.0, p≤0.05). ClinVar reports Likely benign classification by two clinical laboratories but provides no case counts.	clinvar
PS5	Not met	No reputable source has reported this variant as pathogenic. ClinVar classification is Likely benign, and no publication asserts pathogenicity for c.6495G>A.	clinvar
PM1	N/A	ENIGMA BRCA2 v1.2 specification marks PM1 as Not Applicable for BRCA2.
PM2	Met	Variant is absent from gnomAD v2.1 (non-cancer, exome subset), gnomAD v3.1/v4.1 (non-cancer), and gnomAD-Canada v1.0, consistent with PM2_Supporting under ENIGMA BRCA2 v1.2 (absent from outbred population controls).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	Synonymous variant; ENIGMA PM5 is repurposed for PTC (protein termination codon) variants in exons where proven pathogenic PTC variants exist. This variant does not introduce a premature termination codon.
PM6	N/A	ENIGMA BRCA2 v1.2 specification marks PM6 as Not Applicable.
PP1	Not met	No co-segregation data available. No published family-based segregation analysis has been performed for this variant, and no LR meeting the PP1 threshold (≥2.08) is available from ENIGMA resources.
PP2	N/A	ENIGMA BRCA2 v1.2 specification marks PP2 as Not Applicable.
PP3	Not met	ENIGMA PP3 requires either (a) missense/in-frame variant inside a clinically important functional domain with BayesDel no-AF ≥0.30, or (b) SpliceAI ≥0.2 for any silent/missense/in-frame variant. This variant is silent, outside the functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186), and SpliceAI max delta is 0.04 (<0.2). Neither condition is met.	spliceai
PP4	Not met	Variant not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. No clinical-history likelihood ratio supporting pathogenicity (LR ≥2.08) is available.	PMID:31853058
PP5	N/A	ENIGMA BRCA2 v1.2 specification marks PP5 as Not Applicable.
BA1	Not met	ENIGMA BA1 requires filter allele frequency (FAF) > 0.001 in gnomAD non-cancer, non-founder populations. Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	ENIGMA BS1 requires FAF > 0.0001 (Strong) or > 0.00002 (Supporting). Variant is absent from all gnomAD populations. Does not meet BS1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	ENIGMA BS2 requires observation of the variant in trans with a known pathogenic variant in an individual without Fanconi Anemia phenotype. No such proband data are available, and no homozygous observations exist in gnomAD.
BS3	Not assessed	No well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function have been identified. The variant is not listed in ENIGMA Specifications Table 9. In silico SpliceAI predictions alone are insufficient for BS3 under ENIGMA rules.	spliceai
BS4	Not met	No lack-of-segregation data available. No published family study demonstrates absence of co-segregation, and no negative LOD score data are available from ENIGMA resources.
BP1	Met	Silent substitution (p.Leu2165=) located outside the clinically important functional domains of BRCA2 (PALB2 binding: aa 10-40; DNA binding: aa 2481-3186), and no splicing predicted (SpliceAI max delta = 0.04, ≤0.1). Meets ENIGMA BP1_Strong criteria.	spliceai
BP2	N/A	ENIGMA BRCA2 v1.2 specification marks BP2 as Not Applicable.
BP4	N/A	ENIGMA BP4 applies to silent variants only when inside a clinically important functional domain. Codon 2165 is outside both the PALB2 binding domain (aa 10-40) and the DNA-binding domain (aa 2481-3186). BP4 criteria are not met for silent variants outside functional domains under ENIGMA v1.2. BP1_Strong captures the benign evidence for this variant class.
BP5	Not met	Variant not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. No clinical-history likelihood ratio supporting benignity (LR ≤0.48) is available.	PMID:31853058
BP6	N/A	ENIGMA BRCA2 v1.2 specification marks BP6 as Not Applicable.
BP7	Not met	ENIGMA BP7_Strong (RNA) requires well-established in vitro or in vivo functional studies demonstrating no effect on mRNA transcript profile. No such studies exist for this variant. BP7_Supporting requires a silent variant inside a clinically important functional domain with BP4 met, which does not apply (codon 2165 is outside functional domains).
BP3	N/A	ENIGMA BRCA2 v1.2 specification marks BP3 as Not Applicable; in-frame deletions/insertions only, not applicable to this synonymous substitution.
PM3	N/A	Skipped per instruction. No Fanconi Anemia phenotype or trans configuration data available.
PM4	N/A	ENIGMA BRCA2 v1.2 specification marks PM4 as Not Applicable.

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