Variant classification summary

NM_000059.4:c.8633-24T>G

BRCA2 · NP_000050.3:p.? · NM_000059.4

GRCh37: chr13:32950783 T>G · GRCh38: chr13:32376646 T>G

Gene: BRCA2 Transcript: NM_000059.4

Final call

VUS

PM2 supporting BP4 supporting benign BP7 supporting benign

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.?

gnomAD AF

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.4:c.8633-24T>G is an intronic variant in BRCA2 located at position -24 of intron 20. This variant is absent from gnomAD v2.1 (exomes) and v4.1 (genomes) across all populations, meeting PM2 at Supporting strength per ENIGMA BRCA2 VCEP v1.2.0 (pending read depth confirmation at this intronic position).

2

SpliceAI predicts no splicing impact (max delta score 0.00). Combined with its location outside the canonical +/-1,2 splice consensus and beyond the conserved acceptor motif (position -24, beyond -21), this meets BP4_Supporting and BP7_Supporting per ENIGMA BRCA2 VCEP v1.2.0.

3

The variant is not present in ClinVar and has not been reported in the published literature. No functional assay data, case-control studies, segregation data, or clinical-history likelihood ratios are available for this specific variant.

4

Per ENIGMA BRCA1 and BRCA2 VCEP Table 3 combining rules, two Supporting Benign criteria (BP4 + BP7) meet the threshold for Likely Benign. The classification is provisional pending confirmation of gnomAD read depth at position c.8633-24.

Final determination: Conflicting evidence rule from ENIGMA BRCA1/BRCA2 VCEP v1.2.0 Table 3: when both pathogenic and benign criteria are met, a point system is used where total score -1 falls in the Uncertain Significance range (-1 to 5).

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	c.8633-24T>G is an intronic variant at position -24 of intron 20, outside the canonical donor/acceptor +/-1,2 splice consensus. It is not a null variant (nonsense, frameshift, canonical splice site, initiation codon, or exon deletion) and no RNA functional studies demonstrating a damaging effect on mRNA transcript profile are available. PVS1 is not met per ENIGMA BRCA2 VCEP v1.2.0 rules.	cspec pvs1_generic_framework
PS1	Not met	No previously classified pathogenic variant at the same nucleotide position with the same predicted splicing effect is available for comparison. SpliceAI predicts no splicing impact (max delta 0.00), and there is no comparator variant to support PS1 per ENIGMA BRCA2 VCEP v1.2.0.	cspec spliceai
PS2	N/A	PS2 is not applicable per ENIGMA BRCA2 VCEP v1.2.0 specifications.	cspec
PS3	Not assessed	No functional assay data available for NM_000059.4:c.8633-24T>G. The variant is not listed in ENIGMA Table 9 (curated BRCA2 functional assay results) and no published functional studies were identified.	vcep_specifications_table9_v1_2_2024_11_18
PS4	Not assessed	No case-control study data available for this variant. The variant is absent from ClinVar and gnomAD, precluding prevalence comparison between affected individuals and controls.	clinvar gnomad_v2 gnomad_v4
PS5	N/A	PS5 is not part of the ENIGMA BRCA2 VCEP v1.2.0 specification.	cspec
PM1	N/A	PM1 is not applicable per ENIGMA BRCA2 VCEP v1.2.0; mutational hotspot and functional domain evidence is folded into bioinformatic analysis under PP3/BP4.	cspec
PM2	Met	NM_000059.4:c.8633-24T>G is absent from gnomAD v2.1 (exomes, non-cancer) and gnomAD v4.1 (genomes, non-cancer) across all populations. Per ENIGMA BRCA2 VCEP v1.2.0, PM2 is applied at Supporting strength when a variant is absent from controls in outbred populations. Read depth at this intronic position should be confirmed as ≥25x per VCEP requirements.	gnomad_v2 gnomad_v4 gnomad_canada cspec
PM5	N/A	PM5 is repurposed for PTC/truncating variant logic per ENIGMA BRCA2 VCEP v1.2.0 (PM5_PTC). c.8633-24T>G is an intronic substitution, not a protein termination codon variant. PM5_PTC does not apply.	cspec vcep_specifications_table4_v1_2_2024_11_18
PM6	N/A	PM6 is not applicable per ENIGMA BRCA2 VCEP v1.2.0 specifications.	cspec
PP1	Not assessed	No co-segregation data available for this variant. No family studies or likelihood ratio analyses for co-segregation were identified.
PP2	N/A	PP2 is not applicable per ENIGMA BRCA2 VCEP v1.2.0 specifications.	cspec
PP3	Not met	SpliceAI predicts no significant splicing impact (max delta score 0.00, below the ≥0.2 threshold). The variant is intronic and BayesDel/REVEL are not applicable (no protein change). PP3 is not met per ENIGMA BRCA2 VCEP v1.2.0.	spliceai cspec
PP4	Not assessed	The variant NM_000059.4:c.8633-24T>G is not present in the ENIGMA clinical-history likelihood ratio dataset (PMID:31853058, Li et al. 2020). No combined LR from multifactorial clinical data is available to support PP4.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
PP5	N/A	PP5 is not applicable per ENIGMA BRCA2 VCEP v1.2.0; this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	The variant is absent from gnomAD v2.1 and v4.1 across all populations. Filter allele frequency does not exceed 0.1% (FAF > 0.001). BA1 is not met per ENIGMA BRCA2 VCEP v1.2.0.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	The variant is absent from gnomAD v2.1 and v4.1 across all populations. Filter allele frequency does not exceed the BS1_Strong threshold of 0.01% (FAF > 0.0001) or the BS1_Supporting threshold of 0.002% (FAF > 0.00002). BS1 is not met per ENIGMA BRCA2 VCEP v1.2.0.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	No proband data available to assess absence of Fanconi Anemia phenotype features. BS2 per ENIGMA BRCA2 VCEP v1.2.0 requires point-based assessment of co-occurrence with a second pathogenic variant in the absence of recessive disease features.	cspec
BS3	Not assessed	No functional assay data showing no damaging effect is available for this variant. The variant is not listed in ENIGMA Table 9 (curated BRCA2 functional assay results).	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not assessed	No co-segregation data available to assess lack of segregation in affected family members. BS4 requires quantitative co-segregation analysis per ENIGMA BRCA2 VCEP v1.2.0.	cspec
BP1	N/A	BP1 per ENIGMA BRCA2 VCEP v1.2.0 applies only to silent substitutions, missense variants, or in-frame insertions/deletions/delins outside clinically important functional domains. c.8633-24T>G is an intronic substitution and does not fall within the specified variant types for BP1.	cspec
BP2	N/A	BP2 is not applicable per ENIGMA BRCA2 VCEP v1.2.0 specifications.	cspec
BP4	Met	c.8633-24T>G is an intronic variant located outside the native donor and acceptor splice sites (position -24, beyond +/-1,2) with no predicted impact on splicing (SpliceAI max delta score 0.00, ≤0.1). BP4 is met at Supporting strength per ENIGMA BRCA2 VCEP v1.2.0.	spliceai cspec
BP5	Not assessed	The variant NM_000059.4:c.8633-24T>G is not present in the ENIGMA clinical-history likelihood ratio dataset (PMID:31853058, Li et al. 2020). No combined LR against pathogenicity from multifactorial clinical data is available to support BP5.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058
BP6	N/A	BP6 is not applicable per ENIGMA BRCA2 VCEP v1.2.0 specifications.	cspec
BP7	Met	c.8633-24T>G is located at intron 20 position -24, which is beyond the conserved acceptor splice motif (beyond -21). BP4 is met (SpliceAI max delta 0.00). BP7 is met at Supporting strength per ENIGMA BRCA2 VCEP v1.2.0, which applies to intronic variants outside conserved donor/acceptor motif positions when BP4 criteria are satisfied.	spliceai cspec

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