Variant classification summary

NM_000059.3:c.9117+2T>C

BRCA2 · NP_000050.2:p.? · NM_000059.3

GRCh37: chr13:32954052 T>C · GRCh38: chr13:32379915 T>C

Gene: BRCA2 Transcript: NM_000059.3

Final call

Likely Pathogenic

PVS1 very strong PM2 supporting

Variant details

Gene

BRCA2

Transcript

NM_000059.3

Protein

NP_000050.2:p.?

gnomAD AF

ClinVar

Pathogenic

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.3:c.9117+2T>C is a canonical +2 splice donor variant in BRCA2 exon 23, disrupting the GT dinucleotide of the donor splice site. ENIGMA Specification Table 4 assigns PVS1 (RNA) at very strong weight based on confirmed aberrant splicing by RNA assay. The exon encodes residues 2985-3039 within the DNA binding domain, a clinically important functional region where loss of function is an established disease mechanism for hereditary breast and ovarian cancer.

2

The variant is absent from gnomAD v2.1 and v4.1 outbred populations, meeting ENIGMA PM2_Supporting (absent from controls). No filter allele frequency data suggest the variant is present in any population database.

3

No formal case-control study (PS4), co-segregation analysis (PP1), or clinical-history likelihood ratio (PP4/BP5) meeting ENIGMA quantitative thresholds is available. The variant is not listed in the Li et al. 2020 BRCA2 clinical-history LR table (PMID:31853058). ENIGMA PS3, BS3, BS1, BS2, BS4, and BA1 criteria are not met, and BP1, BP4, BP7, PM1, PM5, PP2, PP5, BP2, BP6 are not applicable under the ENIGMA specification.

4

Under ENIGMA Table 3 combining rules, one Very Strong criterion (PVS1) and one Supporting criterion (PM2) is sufficient for a Likely Pathogenic classification.

Final determination: Under ENIGMA BRCA1/BRCA2 VCEP Specification Table 3, one Very Strong criterion (PVS1) and one Supporting criterion (PM2) satisfies the Likely Pathogenic combination rule.

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	Met	NM_000059.3:c.9117+2T>C is a canonical +2 splice donor variant in BRCA2 exon 23, which encodes residues within the DNA binding domain (aa 2985-3039). Loss of function is an established disease mechanism for BRCA2 hereditary breast and ovarian cancer. ENIGMA Specification Table 4 assigns PVS1 (RNA) to this variant, indicating that RNA assay data confirm aberrant splicing leading to a null allele. The exon is within a clinically important functional domain and PVS1 is applied at full (very strong) weight per the ENIGMA PVS1 decision framework.	vcep_specifications_table4_v1_2_2024_11_18 cspec pvs1_gene_context pvs1_variant_assessment
PS1	Not assessed	No comparator splice variant at the same position with a confirmed (likely) pathogenic classification was identified in the case materials. ENIGMA PS1 rules for splicing variants require a previously classified (likely) pathogenic variant with the same predicted splicing impact; no such comparator was evaluated.
PS2	N/A	De novo criterion not applicable — no de novo testing data for this variant was provided or identified.
PS3	Not assessed	Under the ENIGMA framework, well-established functional studies measuring effect on mRNA transcript profile are applied as PVS1 (RNA), not PS3. PS3 is reserved for protein-level functional assays. This variant is not listed in ENIGMA Specification Table 9 (curated protein-level functional assay results). The mRNA splicing evidence is captured under PVS1 (RNA).	cspec vcep_specifications_table9_v1_2_2024_11_18
PS4	Not met	ENIGMA PS4 requires a formal case-control study with p≤0.05 and odds ratio ≥4 (lower CI excludes 2.0). No such study was identified. The variant has been submitted to ClinVar as Pathogenic by one clinical laboratory (ClinVar ID 267714, single submitter, criteria provided), but this does not satisfy the ENIGMA PS4 case-control threshold. The exploratory search identified evidence of multiple clinical submitters reporting the variant in probands, but no peer-reviewed case-control study with OR and confidence intervals is available.	clinvar
PS5	N/A	PS5 is not applicable — this is a splice variant, not a missense variant at a residue where a different pathogenic missense has been reported.
PM1	N/A	PM1 is not applicable under the ENIGMA BRCA2 VCEP specification. The criterion is considered a component of bioinformatic analysis captured by PP3/BP4 rather than applied independently.	cspec
PM2	Met	This variant is absent from gnomAD v2.1 (non-cancer, exome subset) and gnomAD v4.1 (non-cancer) outbred populations, meeting the ENIGMA PM2_Supporting threshold (absent from controls in outbred populations). Under the ENIGMA specification, PM2 is only applicable at Supporting strength; the default ACMG Moderate strength is not used.	gnomad_v2 gnomad_v4
PM5	N/A	Under ENIGMA, PM5 is repurposed as PM5_PTC for protein termination codon (nonsense/frameshift) variants annotated as PVS1 in exons where a different proven pathogenic PTC variant has been observed. NM_000059.3:c.9117+2T>C is a canonical splice donor variant, not a direct PTC variant (nonsense/frameshift). Although it is predicted to produce a PTC via aberrant splicing and has PVS1 (RNA) weight per Table 4, PM5_PTC is reserved for variants that are themselves PTCs. Classic same-residue PM5 also does not apply as this is not a missense variant.	cspec pm5_candidates vcep_specifications_table4_v1_2_2024_11_18
PM6	N/A	PM6 is not applicable under the ENIGMA BRCA2 VCEP specification.	cspec
PP1	Not met	No formal quantitative co-segregation analysis with likelihood ratio meeting ENIGMA thresholds (LR ≥2.08 for Supporting) was identified. Exploratory search found indirect indications of familial segregation in ClinVar and BIC database annotations, but no peer-reviewed pedigree analysis or computed LOD score is available.
PP2	N/A	PP2 is not applicable under the ENIGMA BRCA2 VCEP specification.	cspec
PP3	Not met	Under ENIGMA rules, PP3 for predicted splicing (SpliceAI ≥0.2) is applicable for silent, missense, in-frame, and intronic variants outside donor/acceptor ±1,2 positions. This variant is at the canonical +2 donor position and PVS1 has already been applied for the splice disruption mechanism. Per ENIGMA guidance, PP3 is not double-counted when PVS1 captures the same splice-effect evidence. Additionally, SpliceAI returned a max delta score of 0.00, which does not meet the PP3 threshold for splice prediction.	cspec spliceai
PP4	Not met	No ENIGMA PP4 clinical-history likelihood ratio is available. The variant (c.9117+2T>C) was not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. No other multifactorial likelihood data supporting pathogenicity via phenotype specificity was identified.	vcep_pmid_31853058_brca2_clinical_history_lr
PP5	N/A	PP5 is not applicable under the ENIGMA BRCA2 VCEP specification (criterion not for use as recommended by the ClinGen SVI VCEP Review Committee).	cspec
BA1	Not met	Variant is absent from gnomAD v2.1 and v4.1. ENIGMA BA1 requires filter allele frequency (FAF) >0.1% (FAF > 0.001) in gnomAD non-founder populations. The variant does not meet this threshold.	gnomad_v2 gnomad_v4
BS1	Not met	Variant is absent from gnomAD v2.1 and v4.1. ENIGMA BS1_Strong requires FAF >0.01% (FAF > 0.0001) in gnomAD non-founder populations. The variant does not meet this threshold.	gnomad_v2 gnomad_v4
BS2	Not met	No evidence of observation in healthy adults without features of Fanconi anemia phenotype was identified. ENIGMA BS2 requires co-observation with a pathogenic variant in the same gene in the absence of recessive disease features, with points assigned per proband. No such data are available.
BS3	Not met	No well-established in vitro or in vivo functional studies showing no damaging effect on protein function were identified. The variant is not listed in ENIGMA Specification Table 9. The available splicing evidence instead demonstrates a damaging effect, supporting PVS1 (RNA).	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not met	No evidence of lack of segregation in affected family members (non-segregation) was identified. ENIGMA BS4 requires quantitative co-segregation analysis with LR ≤0.48 for Supporting weight. No such data are available.
BP1	N/A	BP1 applies to missense, silent, or in-frame variants outside clinically important functional domains with no splicing predicted. NM_000059.3:c.9117+2T>C is a canonical splice donor variant at the +2 position; BP1 is not applicable to splice site variants.	cspec
BP2	N/A	BP2 is not applicable under the ENIGMA BRCA2 VCEP specification.	cspec
BP3	N/A	BP3 is not applicable — the variant is not an in-frame deletion/insertion in a repetitive region without known function.
BP4	N/A	ENIGMA BP4 applies to intronic variants outside native donor and acceptor splice sites (±1,2 positions) with no predicted splicing impact. This variant is at the canonical +2 donor position, within the native splice site, and ENIGMA Table 4 confirms aberrant splicing via RNA assay data (PVS1 (RNA)). BP4 is not applicable.	cspec vcep_specifications_table4_v1_2_2024_11_18
BP5	Not met	No ENIGMA BP5 clinical-history likelihood ratio supporting benignity is available. The variant (c.9117+2T>C) was not found in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history LR table. No other multifactorial likelihood data supporting benignity was identified.	vcep_pmid_31853058_brca2_clinical_history_lr
BP6	N/A	BP6 is not applicable under the ENIGMA BRCA2 VCEP specification.	cspec
BP7	N/A	ENIGMA BP7 (RNA) applies to intronic and silent variants where RNA assay shows no splicing impact. This variant has confirmed splicing impact per ENIGMA Table 4 (assigned PVS1 (RNA)), demonstrating aberrant splicing. BP7 is not applicable.	cspec vcep_specifications_table4_v1_2_2024_11_18
PM3	N/A	Skipped per case directive — trivially not applicable.
PM4	N/A	Skipped per case directive — trivially not applicable.

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