Variant classification summary

NM_000059.4:c.241T>C

BRCA2 · NP_000050.3:p.(Phe81Leu) · NM_000059.4

GRCh37: chr13:32893387 T>C · GRCh38: chr13:32319250 T>C

Gene: BRCA2 Transcript: NM_000059.4

Final call

Likely Benign

BP1 strong PM2 supporting

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.(Phe81Leu)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

BP1_Strong is met: the missense variant p.Phe81Leu (c.241T>C) lies outside both ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40 and DNA binding domain aa 2481-3186), and SpliceAI predicts no splicing impact (max delta = 0.00).

2

PM2_Supporting is met: the variant is absent from gnomAD v2.1 and v4.1 in outbred, non-cancer populations.

3

The sister variant c.241T>G (p.Phe81Val) is classified as Likely Benign by Parsons et al. 2019 multifactorial analysis (posterior probability 0.0066, IARC class 2), consistent with the BP1_Strong assignment for this position.

4

Katagiri et al. 1998 (PMID:9609997) observed c.241T>C in Family #32, a Japanese breast cancer family with 3 affected individuals (ages 35, 44, 58). The authors noted this was a novel missense alteration but did not perform segregation or functional analysis, and stated such analyses are needed to confirm pathogenicity.

5

No functional data (PS3/BS3), case-control data (PS4), clinical history LR (PP4/BP5), co-segregation data (PP1/BS4), or proband-level data (BS2) are available for this variant.

6

Under ENIGMA Table 3 combining rules: BP1_Strong (benign) and PM2_Supporting (pathogenic) are conflicting. Likely Benign requires 1 Strong Benign + 1 Supporting Benign; Likely Pathogenic requires substantially more pathogenic evidence. The evidence supports assignment as a Variant of Uncertain Significance (VUS) with conflicting evidence.

Final determination: ENIGMA BRCA2 conflicting-evidence point system: PM2_Supporting (+1) plus BP1_Strong (-4) yields total -3, placing the variant in the Likely Benign range (-6 to -2).

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	Missense variant (p.Phe81Leu); PVS1 requires a null variant (nonsense, frameshift, canonical splice, initiation codon, or exon deletion) or mRNA assay evidence (PVS1 RNA pathway). Neither applies.	vcep_specifications_table4_v1_2_2024_11_18
PS1	Not met	No known pathogenic or likely pathogenic missense variant at the same amino acid residue (p.Phe81) in BRCA2. The sister variant c.241T>G (p.Phe81Val) is classified as Likely Benign by Parsons 2019 multifactorial analysis (posterior probability 0.0066). SpliceAI max delta = 0.00, so no splicing concern for a PS1 splicing-based comparison.	vcep_humu_40_1557_s001 spliceai cspec
PS2	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0).	cspec
PS3	Not met	Not present in ENIGMA Table 9 (curated PS3/BS3 functional assay assignments). Not found in the Dace & Findlay interim report. No variant-specific functional data identified in the literature. OncoKB reports no variant-specific reviewed functional evidence.	vcep_specifications_table9_v1_2_2024_11_18 oncokb
PS4	Not assessed	No case-control data meeting ENIGMA thresholds (p≤0.05, OR≥4 with lower CI excluding 2.0) available for this variant. The single family observation in Katagiri et al. 1998 (1/78 Japanese breast cancer families) is an observational report, not a case-control study. Not present in the SupplementaryTables ST7 reference set posterior probability table.
PS5	N/A	Not defined in the ENIGMA BRCA2 VCEP framework (version 1.2.0). The ClinVar classification is Uncertain significance with 1-star review status (single submitter).	cspec clinvar
PM1	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0). Additionally, position 81 is outside both ENIGMA-defined clinically important functional domains (PALB2 binding: aa 10-40; DNA binding: aa 2481-3186).	cspec vcep_appendices_v1_2_2024_11_18
PM2	Met	Absent from gnomAD v2.1 (non-cancer, exome subset) and gnomAD v4.1 in outbred populations. Per ENIGMA BRCA2 specifications, PM2 is applied at Supporting strength when absent from population databases. Coverage at this position appears adequate based on sister variant c.241T>G being observed (2 alleles in gnomAD v2.1).	gnomad_v2 gnomad_v4 cspec
PM5	N/A	ENIGMA PM5 is repurposed for protein termination codon (PTC) variants in exons where proven pathogenic PTC variants exist. This is a missense variant (p.Phe81Leu), not a PTC. Per pm5_candidates.json, PM5 is in PTC/truncating logic mode and classic same-residue missense PM5 is not applicable.	pm5_candidates cspec vcep_specifications_table4_v1_2_2024_11_18
PM6	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0).	cspec
PP1	Not assessed	No quantitative co-segregation analysis data available. Katagiri et al. 1998 (PMID:9609997) observed this variant in a family with 3 breast cancers (ages 35, 44, 58) but did not perform segregation analysis, and the authors explicitly stated that segregation analysis is needed to confirm pathogenicity. Does not meet ENIGMA PP1 LR thresholds (Supporting: LR≥2.08).
PP2	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0).	cspec
PP3	Not met	Position 81 is outside both ENIGMA-defined clinically important functional domains (PALB2 binding: aa 10-40; DNA binding: aa 2481-3186), so the domain-based PP3 rule (BayesDel ≥0.30 inside domain) does not apply. SpliceAI max delta score is 0.00, which is below the 0.20 threshold for the splicing-based PP3 rule. Neither PP3 condition is met.	spliceai bayesdel revel cspec
PP4	Not assessed	c.241T>C was not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical history likelihood ratio spreadsheet. Only the sister variant c.241T>G (LOG(LR) = -0.255, LR = 0.775, N=1) is present. No clinical-history LR data available to assess PP4.	vcep_pmid_31853058_brca2_clinical_history_lr
PP5	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0). Additionally, ClinVar classification is Uncertain significance with 1-star review status (criteria provided, single submitter), which would not meet the 3-star expert panel threshold for PP5 even under generic ACMG/AMP.	cspec clinvar
BA1	Not met	Filter allele frequency is below the ENIGMA BA1 threshold (FAF > 0.001, i.e., >0.1%). The variant is absent from gnomAD v2.1 and v4.1 in non-cancer, non-founder populations.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	Filter allele frequency is below both ENIGMA BS1 thresholds: BS1_Strong requires FAF > 0.01% (FAF > 0.0001) and BS1_Supporting requires FAF > 0.002% (FAF > 0.00002). The variant is absent from gnomAD v2.1 and v4.1.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	ENIGMA BS2 requires proband-level data with absence of Fanconi Anemia features for a point-based scoring system across multiple observations. No proband-level data are available in this case.
BS3	Not met	Not present in ENIGMA Table 9 for BS3 assignments. No calibrated functional studies demonstrate a benign effect for this variant. The Katagiri 1998 paper contains no functional data.	vcep_specifications_table9_v1_2_2024_11_18 oncokb
BS4	Not assessed	No quantitative lack-of-segregation data available. ENIGMA BS4 requires a co-segregation Bayes score with LR ≤0.48 (Supporting), ≤0.23 (Moderate), or ≤0.05 (Strong). No such data exist for this variant.
BP1	Met	Missense variant (p.Phe81Leu) located outside both ENIGMA-defined clinically important functional domains (PALB2 binding: aa 10-40; DNA binding: aa 2481-3186). SpliceAI max delta score is 0.00 (≤0.10). Per ENIGMA BP1_Strong rule: missense variant outside a clinically important functional domain with no splicing predicted.	cspec spliceai vcep_appendices_v1_2_2024_11_18
BP2	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0).	cspec
BP4	N/A	ENIGMA BP4 requires the variant to be inside a clinically important functional domain (PALB2 binding aa 10-40 or DNA binding aa 2481-3186) with no predicted impact (BayesDel ≤0.18 AND SpliceAI ≤0.10). Position 81 is outside both domains; BP4 is not applicable.	cspec bayesdel spliceai
BP5	Not assessed	c.241T>C was not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical history likelihood ratio spreadsheet. Only the sister variant c.241T>G is present (LR = 0.775, neutral zone). No LR data against pathogenicity available.	vcep_pmid_31853058_brca2_clinical_history_lr
BP6	N/A	Marked Not Applicable by the ENIGMA BRCA2 VCEP (version 1.2.0).	cspec
BP7	N/A	ENIGMA BP7 Strong (RNA) requires well-established mRNA assay evidence of no damaging effect. BP7 Supporting applies to silent variants inside domains (when BP4 is met) or intronic variants outside conserved splice positions (when BP4 is met). This is a missense variant with no RNA assay data; none of the BP7 pathways apply.	cspec spliceai

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