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LYFE SCIENCES
Project: HERA
NM_007294.4:c.3271C>G
p.Pro1091Ala  ·  BRCA1
Starting
Initialising…
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Legacy Engine
Processing…
Classification rationale
1

The BRCA1 c.3271C>G (p.Pro1091Ala; p.P1091A) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar.

clinvar ↗
2

This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, supporting rarity, although the ENIGMA BRCA1 PM2_Supporting rule was not applied because the required specified-control-set and coverage documentation were not identified here.

gnomad_v2 ↗ gnomad_v4 ↗ gnomad_canada ↗ cspec ↗
3

SpliceAI predicts no significant splice effect (maximum delta score 0.01, below the ENIGMA 0.1 and 0.2 splice thresholds); BayesDel no-AF is -0.072 and REVEL is 0.572, and because p.Pro1091Ala lies outside the BRCA1 RING, coiled-coil, and BRCT domains, the ENIGMA BRCA1 missense rules support BP1_Strong and do not support PP3.

spliceai ↗ cspec ↗
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
—
—
Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
—
Research and evidence
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.572. BayesDel score = -0.0721595.
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.
ResidueP1091
Hotspots ↗