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LYFE SCIENCES
Project: HERA
NM_000059.4:c.9014_9015del
p.Arg3005IlefsTer12  ·  BRCA2
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Legacy Engine
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Classification rationale
1

The BRCA2 c.9014_9015del (p.Arg3005IlefsTer12) variant has not been observed in COSMIC and has been reported in ClinVar as pathogenic, including ENIGMA expert panel review.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, although ENIGMA does not apply PM2_Supporting to insertion, deletion, or delins variants.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

ENIGMA BRCA2 null-variant guidance supports full-strength PVS1 for truncating variants in exon 23 and assigns PM5_PTC Strong to this exon, consistent with a deleterious premature termination event.

cspec ↗
4

SpliceAI predicts possible splice impact with a maximum delta score of 0.23.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
—
Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (4 clinical laboratories) and as pathogenic (1 clinical laboratory) and as Pathogenic by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel).
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Likely Oncogenic
OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.23).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueR3005
Hotspots ↗