Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PALB2
Final classification
Likely Benign
PALB2 c.928A>G · p.Ser310Gly
PALB2

NM_024675.4:c.928A>G (p.Ser310Gly) is a missense variant in PALB2, a gene in which primarily truncating variants are known to cause disease and missense pathogenic variation is not yet confirmed as a disease mechanism (VCEP v1.2.0).

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.928A>G
Consequence
N/A
GRCh38
chr16:23635618 T>C
GRCh37
chr16:23646939 T>C
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: BS1 strong, BP1 supporting benign; maps to Likely Benign.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: BS1 strong, BP1 supporting benign; maps to Likely Benign.
Classification rationale
BS1BP1 Likely Benign
PALB2 c.928A>G

NM_024675.4:c.928A>G (p.Ser310Gly) is a missense variant in PALB2, a gene in which primarily truncating variants are known to cause disease and missense pathogenic variation is not yet confirmed as a disease mechanism (VCEP v1.2.0).1 The variant is present in gnomAD v4.1 at an overall allele frequency of 0.01276% (206/1,614,002 alleles, 0 homozygotes) with a grpmax filtering AF of 0.015106% in the European (non-Finnish) population. This exceeds the PALB2 VCEP BS1 threshold of >0.01%, supporting a benign interpretation at Strong strength.2 SpliceAI predicts no significant splice impact (max delta score = 0.02), consistent with a missense change without cryptic splice effects.3 REVEL score is 0.034 and BayesDel score is -0.732, consistent with a benign in silico profile, though computational predictors have not been validated for PALB2 missense variant functional outcome per the VCEP.4 BP1 (Supporting) is applied per the PALB2 VCEP, which assigns this code to all missense variants given the very low prior probability that PALB2 missense variants are pathogenic.5 Combining BS1 (Strong benign) with BP1 (Supporting benign) yields a classification of Likely Benign per the ACMG/AMP combination rules adopted by the PALB2 VCEP (Rule 20: ≥1 Benign Strong criterion).6

BS1 + BP1 Likely Benign
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 6 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
BS1 strong Benign
PALB2 VCEP assigns BS1 (Strong) when grpmax Filtering AF >0.01% in gnomAD v4. The grpmax FAF in gnomAD v4.1 is 0.015106%, which exceeds the VCEP threshold. The variant is observed in 206/1,614,002 alleles (AF=0.01276%) in gnomAD v4.1, predominantly in the European (non-Finnish) population (201/1,179,992 alleles).
gnomAD v4.1: grpmax FAF = 0.015106% (>0.01% VCEP threshold for BS1 Strong). 206 total alleles observed0 homozygotes.
BP1 supporting Benign
PALB2 VCEP assigns BP1 (Supporting) to all missense variants in PALB2, given the very low likelihood that missense variants in this gene are pathogenic. NM_024675.4:c.928A>G (p.Ser310Gly) is a missense variant.
VCEP BP1: 'Apply to all missense variants' at Supporting strength. This is a missense variant (p.Ser310Gly).
Assessed · not applied
Pathogenic
PS4 PALB2 VCEP requires case-control studies with p≤0.05 AND (OR≥3 OR lower 95% CI≥1.5).
PM2 PALB2 VCEP assigns PM2_Supporting when gnomAD v4 frequency ≤0.000333% (1/300,000).
PP1 No segregation data (LOD score or co-occurrence in affected relatives) has been published for NM_024675.4:c.928A>G.
Benign
BA1 PALB2 VCEP requires grpmax Filtering AF >0.1% in gnomAD v4.
BS2 PALB2 VCEP BS2 applies to Fanconi Anemia (recessive) probands observed in trans with a pathogenic variant without meeting FA phenotype.
BS4 PALB2 VCEP requires quantitative co-segregation analysis (LOD score or Bayes Factor) demonstrating lack of segregation.
N/A · 17 PVS1 · PS1 · PS2 · PS3 · PM1 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP4 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0.000127633; MAF= 0.01276%, 206/1614002 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00017034; MAF= 0.01703%, 201/1179992 alleles, homozygotes = 0); grpmax FAF= 0.00015106.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.77753e-05; MAF= 0.00478%, 12/251176 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000105619; MAF= 0.01056%, 12/113616 alleles, homozygotes = 0); grpmax FAF= 6.019e-05.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.013% · 206 / 1,614,002
0 hom · FAF 0.015%
European (non-Finnish)
201 / 1,179,992
0.017%
Remaining individuals
5 / 62,480
0.008%
+ 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0048% · 12 / 251,176
0 hom · FAF 0.006%
European (non-Finnish)
12 / 113,616
0.011%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (8 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 128149)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.034. BayesDel score = -0.732133.
Functional / OncoKB screenshot
Functional 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 ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55167149, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
26635394 ↗ RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins. CLINVAR
15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
17200668 ↗ PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. CLINVAR
17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
20301425 ↗ PMID:20301425 CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR