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LYFE SCIENCES
Project: HERA
NM_000059.3:c.7961T>C
p.Leu2654Pro  ·  BRCA2
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Classification rationale
1

The BRCA2 c.7961T>C (p.Leu2654Pro) variant has been reported in ClinVar with an expert-panel classification of uncertain significance and mixed submitter assertions.

clinvar ↗
2

This variant is present at very low frequency in population databases, including 1/31,406 alleles in gnomAD v2.1 and 3/1,614,066 alleles in gnomAD v4.1, which argues against PM2 and does not reach BA1 or BS1 thresholds.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

In the ENIGMA BRCA2 curated functional dataset, this variant has discordant calibrated assay results, so the available functional evidence does not support either PS3 or BS3.

PMID:29884841 ↗
4

Computational evidence supports a damaging protein effect because the variant lies in the BRCA2 DNA-binding domain, BayesDel no-AF is 0.314702 above the PP3 threshold of 0.30, REVEL is 0.82, and SpliceAI predicts no significant splice effect with a max delta score of 0.02.

cspec ↗ 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
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Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This variant is present in gnomAD v2.1 (AF= 3.1841e-05; MAF= 0.00318%, 1/31406 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000114784; MAF= 0.01148%, 1/8712 alleles, homozygotes = 0).
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 1.85866e-06; MAF= 0.00019%, 3/1614066 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.66894e-05; MAF= 0.00267%, 2/74936 alleles, homozygotes = 0); grpmax FAF= 4.43e-06.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory) and as Uncertain Significance by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 52448)
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.82. BayesDel score = 0.314702.
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.
ResidueL2654
Hotspots ↗