Back
LYFE SCIENCES
Project: HERA
NM_024675.4:c.154G>A
p.Val52Ile  ·  PALB2
Starting
Initialising…
0%
Legacy Engine
Ready
View Legacy →
Classification rationale
1

The PALB2 c.154G>A (p.Val52Ile) variant has been reported in ClinVar with conflicting single-submitter interpretations of uncertain significance and likely benign.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and is present at very low overall frequency in gnomAD v4.1 (3/1,614,050 alleles; 0.00019%), but the highest observed subpopulation frequency is 0.00160% (1/62,510 alleles), which is above the PALB2 PM2 threshold exception and remains below the BS1 and BA1 population thresholds.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts no significant splice impact (max delta score 0.01), and REVEL (0.045) and BayesDel (-0.518425) are low; however, the PALB2 VCEP does not use PP3 or BP4 for missense variants, while BP1 is applicable to all PALB2 missense variants.

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
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1Absent from gnomAD v2.1.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 1.85868e-06; MAF= 0.00019%, 3/1614050 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.59974e-05; MAF= 0.00160%, 1/62510 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory).
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. PALB2, a scaffolding protein involved in DNA repair, is altered in various cancers.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.045. BayesDel score = -0.518425.
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.
ResidueV52
Hotspots ↗