Classification rationale

PM2 BP1 Uncertain Significance - Conflicting Evidence

PALB2 c.871G>A

The PALB2 NM_024675.3:c.871G>A (NP_078951.2:p.(Ala291Thr), p.(A291T)) variant has been reported in ClinVar, where the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel classified it as uncertain significance.¹ This variant is absent from gnomAD v4.1 (0/1613968 alleles; AF 0%), which is below the PALB2 PM2_Supporting threshold of 0.000333% and far below the BS1 and BA1 benign frequency thresholds.² SpliceAI predicts no significant splice impact (max delta score 0.00), and available computational scores are low for missense deleteriousness (REVEL 0.068; BayesDel -0.616818); under the PALB2 specification, PP3 and BP4 are not used for missense variants, while BP1 applies to all missense variants.³

PM2 + BP1 → Uncertain Significance - Conflicting Evidence

1 clinvar ↗

2 gnomad_v4 ↗cspec ↗

3 spliceai ↗revelbayesdelcspec ↗

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

Gene diagram · NM_024675.3 · variants mapped to exon structure

PALB2 NM_024675.3

Fetching transcript structure from UCSC…

Applied criteria · 2 applied · 9 assessed

MetEvidence satisfies this criterion.

Not metEvaluated against available evidence; threshold not reached.

Not assessedApplies in principle, but no evidence was found to evaluate it.

N/ADoesn't apply to this variant type.

Applied · 2

Strength Supporting Moderate Strong Very strong

PM2 supporting review Pathogenic

This variant is absent from gnomAD v4.1 (0/1613968 alleles, AF 0%), which is below the PALB2 PM2_Supporting threshold of 1/300,000 (0.000333%), so PM2_Supporting is met.

gnomAD v4.1 total AC 0 / AN 1613968AF 0.0%.PALB2 PM2 threshold is <=1/300

cspec ↗gnomad_v4 ↗

BP1 supporting review Benign

This is a missense variant, and the PALB2 specification applies BP1_Supporting to all missense variants, so BP1 is met at supporting strength.

Variant consequence is missense: p.(Ala291Thr)/p.(A291T).PALB2 BP1 rule: apply to all missense variants.

cspec ↗

Assessed · not applied · 4 not met · 5 not assessed

Pathogenic

PVS1 This missense variant does not fall into the PALB2 loss-of-function PVS1 framework, and SpliceAI predicts no significant splice impact (max delta score 0.00), so PVS1 is not supported.

PS1 No evidence was identified that this variant produces the same RNA effect as an established pathogenic PALB2 variant, and no splice effect is predicted, so PS1 is not supported.

PS4 No case-control study or exact-variant enrichment data were identified to show that this variant is significantly more common in affected individuals than in controls, so PS4 cannot be applied.

PM3 No report was identified showing this variant in trans with a pathogenic PALB2 variant in a recessive Fanconi anemia context, so PM3 cannot be applied.

PP1 No segregation data were identified for this variant, so PP1 cannot be applied.

Benign

BA1 This variant is absent from gnomAD v4.1 (AF 0%), which is below the PALB2 BA1 threshold of greater than 0.1%, so BA1 is not met.

BS1 This variant is absent from gnomAD v4.1 (AF 0%), which is below the PALB2 BS1 threshold of greater than 0.01%, so BS1 is not met.

BS2 No point-based evidence in unaffected individuals was identified for this variant, so BS2 cannot be applied.

BS4 No non-segregation data or quantitative evidence against cosegregation were identified for this variant, so BS4 cannot be applied.

N/A · 17 PS2 · PS3 · PM1 · PM4 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1613968 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/75000 alleles, homozygotes = 0).

v2.1

This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/251366 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16244 alleles, homozygotes = 0).

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

Absent · 0 / 1,613,968
0 hom

Not observed in any ancestry group.

+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))

gnomAD v2.1

Absent · 0 / 251,366
0 hom

Not observed in any ancestry group.

+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)

gnomAD v4 ↗ gnomAD v2 ↗

ClinVar

This variant has been reported in ClinVar as Uncertain significance (3 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). (ClinVarID = 241572)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.068. BayesDel score = -0.616818.

SpliceAI ↗

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

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

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

34242744 ↗ Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021. CLINVAR

15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. 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 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR

24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR

24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR

28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR

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