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LYFE SCIENCES
Project: HERA
NM_024675.3:c.109C>A
p.Arg37Ser  ·  PALB2
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Classification rationale
1

The PALB2 c.109C>A (p.Arg37Ser; p.R37S) variant has been reported in ClinVar with an expert-panel classification of uncertain significance, alongside additional clinical laboratory submissions of uncertain significance and likely benign.

clinvar ↗
2

This variant is present in gnomAD v4.1 at 16/1,612,736 alleles (AF 0.00099%), with a highest observed African/African American subpopulation frequency of 0.01603%, which is above the PALB2 BS1 threshold of 0.01% and below the BA1 threshold of 0.1%.

gnomad_v4 ↗ cspec ↗
3

SpliceAI predicts no meaningful splice effect for this variant (max delta score 0.00), which does not meet the PALB2 PP3 splicing threshold of 0.2 and does not support RNA-based PVS1 application.

spliceai ↗ cspec ↗
4

REVEL (0.195) and BayesDel (0.120598) were noted, but the PALB2 VCEP does not use missense protein predictors for PP3 or BP4, while BP1 is applied to PALB2 missense variants under this framework.

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
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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= 1.59074e-05; MAF= 0.00159%, 4/251456 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000123047; MAF= 0.01230%, 2/16254 alleles, homozygotes = 0); grpmax FAF= 2.132e-05.
gnomAD v4.1This variant is present in gnomAD v4.1 (AF= 9.92103e-06; MAF= 0.00099%, 16/1612736 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000160291; MAF= 0.01603%, 12/74864 alleles, homozygotes = 0); grpmax FAF= 9.22e-05.
gnomAD v2 ↗ gnomAD v4 ↗
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Uncertain significance (12 clinical laboratories) and as Likely benign (1 clinical laboratory) and as Uncertain Significance by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel).
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 = 0.00). REVEL score = 0.195. BayesDel score = 0.120598.
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.
ResidueR37
Hotspots ↗