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
Final classification
Likely Benign
BP4BP7
BRCA2
c.1909+11_1909+12del
p.?
This variant
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.
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
BP4 + BP7
→
Likely Benign
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
Gene diagram
· NM_000059.4 · variants mapped to exon structure
BRCA2
NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
BP4
supporting
Benign
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, ≤0.1). BP4_Supporting is met per ENIGMA BRCA2 specification Figure 1A.
SpliceAI max delta = 0.00 ≤ 0.1Intronic deletion at +11/+12outside canonical +/-1
BP7
supporting
Benign
The intronic deletion is located at position +11, outside the conserved donor motif (beyond +7). BP4 is met (SpliceAI max delta = 0.00 ≤ 0.1). BP7_Supporting is met per ENIGMA BRCA2 specification Figure 1A and Appendix J.
Intronic variant at +11 positionoutside conserved donor motif (beyond +7)BP4 met (SpliceAI max delta = 0.00 ≤ 0.1)
Assessed · not applied
· 5 not met · 8 not assessed
Pathogenic
PVS1
NM_000059.4:c.1909+11_1909+12del is an intronic deletion at positions +11 and +12 of intron 10, outside the canonical donor splice consensus (+/-1,2).
PS1
SpliceAI predicts no splicing impact (max delta = 0.00).
PS3
No functional assay data available for this intronic deletion variant in ENIGMA Specifications Table 9 or published literature.
PS4
Variant is absent from ClinVar and COSMIC.
PP1
No co-segregation data available for quantitative analysis per ENIGMA PP1 specification.
PP3
SpliceAI predicts no significant splice impact (max delta = 0.00), well below the ENIGMA PP3 threshold of SpliceAI ≥0.2 for intronic variants outside donor/acceptor +/-1,2 sites.
PP4
Variant is not listed in the Li et al.
Benign
BA1
Variant is absent from gnomAD v2.1 and v4.1.
BS1
Variant is absent from gnomAD v2.1 and v4.1.
BS2
No proband-level data available to evaluate for BS2 points under ENIGMA Specifications Table 8 (absence of Fanconi Anemia phenotype).
BS3
No functional assay data available for this intronic deletion variant in ENIGMA Specifications Table 9 or published literature.
BS4
No segregation data available for quantitative BS4 likelihood-ratio analysis per ENIGMA specification.
BP5
Variant is not listed in the Li et al.
N/A · 12
PS2 · PM1 · PM2 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
Research & evidence
Population frequency · supports benign
gnomAD v4.1
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
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
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.
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.
Sources & reference links