Starting
Initialising…
0%
BRCA2
Final classification
Likely Benign
BRCA2 c.1909+11_1909+12del · p.?
BRCA2

NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.1909+11_1909+12del
Consequence
N/A
GRCh38
chr13:32333396 GTC>G
GRCh37
chr13:32907533 GTC>G
Basis ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3: two Supporting (Benign) criteria (BP4_Supporting, BP7_Supporting) met, zero pathogenic criteria met. Matches the likely_benign rule requiring >=2 Supporting (Benign) criteria.
ENIGMA BRCA1/BRCA2 Specification v1.2 Table 3: two Supporting (Benign) criteria (BP4_Supporting, BP7_Supporting) met, zero pathogenic criteria met. Matches the likely_benign rule requiring >=2 Supporting (Benign) criteria.
Classification rationale
BP4BP7 Likely Benign
BRCA2 c.1909+11_1909+12del

NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the native donor splice consensus (+/-1,2). SpliceAI predicts no splicing impact (max delta = 0.00). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.1 The variant is located at intronic position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI ≤0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J.2 No pathogenic criteria are met. PVS1 is not met (outside canonical +/-1,2 splice consensus; does not qualify as a null variant per ENIGMA PVS1 criteria). PM2 is explicitly not applicable for deletion variants per ENIGMA specification. PP3 is not met (SpliceAI max delta = 0.00 < 0.2). Two supporting benign criteria are met (BP4_Supporting, BP7_Supporting). Per ENIGMA Table 3 combining rules, ≥2 Supporting (Benign) criteria supports classification as Likely Benign.3

BP4 + BP7 Likely Benign
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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 · supports benign
      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
      This variant is absent from gnomAD-Canada.
      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
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC