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BRCA2
Final classification
VUS
BRCA2 c.8633-24T>G · p.?
BRCA2

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).

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.8633-24T>G
Consequence
N/A
GRCh38
chr13:32376646 T>G
GRCh37
chr13:32950783 T>G
Basis ENIGMA BRCA1/BRCA2 VCEP v1.2.0 Table 3 conflicting evidence point system: PM2 (Supporting, +1) vs BP4 (Supporting Benign, -1) + BP7 (Supporting Benign, -1). Total score = -1, which falls in the 'Uncertain Significance' range (-1 to 5). Both pathogenic and benign criteria are met, so the point system takes precedence over the non-conflicting likely_benign rule (2 Supporting Benign).
ENIGMA BRCA1/BRCA2 VCEP v1.2.0 Table 3 conflicting evidence point system: PM2 (Supporting, +1) vs BP4 (Supporting Benign, -1) + BP7 (Supporting Benign, -1). Total score = -1, which falls in the 'Uncertain Significance' range (-1 to 5). Both pathogenic and benign criteria are met, so the point system takes precedence over the non-conflicting likely_benign rule (2 Supporting Benign).
Classification rationale
PM2 BP4BP7 VUS
BRCA2 c.8633-24T>G

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).1 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 v1.2.0.2 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.3 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.8633-24.4

PM2 + BP4 + BP7 VUS
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC