Analysis in progress
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complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
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 applied · 13 assessed
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
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 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