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PALB2
Final classification
Uncertain Significance - Conflicting Evidence
PALB2 c.2580G>T · p.Glu860Asp
PALB2

NM_024675.4:c.2580G>T (p.Glu860Asp) is a missense variant in PALB2, a gene where loss of function is an established mechanism of disease but missense pathogenicity is not yet confirmed.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.2580G>T
Consequence
N/A
GRCh38
chr16:23629210 C>A
GRCh37
chr16:23640531 C>A
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP1 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP1 Uncertain Significance - Conflicting Evidence
PALB2 c.2580G>T

NM_024675.4:c.2580G>T (p.Glu860Asp) is a missense variant in PALB2, a gene where loss of function is an established mechanism of disease but missense pathogenicity is not yet confirmed.1 The variant is absent from gnomAD v2.1 and v4.1, meeting the VCEP PM2_Supporting criterion (frequency ≤ 0.000333%).2 Per VCEP PALB2 specification, BP1_Supporting is applied to all missense variants given the very low likelihood that missense variants in PALB2 are pathogenic.3 Multiple VCEP criteria are not applicable to missense variants in PALB2: PVS1, PS1, PM1, PM5, PP2, PP3, BP4. Additional criteria (PS3, BS3, PS2, PM6, PP4, PP5, BP2, BP5, BP6) are not applicable per VCEP specification.4 SpliceAI predicts no splice impact (max delta 0.01). REVEL score (0.021) and BayesDel score (-0.521846) are consistent with a benign computational prediction for the missense change, though not formally applied as criteria per VCEP rules.5 ClinVar reports this variant as Uncertain significance (4 clinical laboratories) and Likely benign (1 clinical laboratory). No expert panel classification is available.6 With PM2_Supporting (1 pathogenic supporting point) and BP1_Supporting (1 benign supporting point), the variant falls into the Uncertain Significance category per ACMG/AMP 2015 combination rules (Rule 31: conflicting supporting evidence).7

PM2 + BP1 Uncertain Significance - Conflicting Evidence
5 spliceai ↗revelbayesdel
7 generic_acmg_combination_rules
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
PM2 supporting Pathogenic
Variant is absent from gnomAD v2.1 (exomes) and gnomAD v4.1 (exomes). Meets VCEP PM2_Supporting threshold (frequency ≤ 0.000333% in gnomAD v4).
Absent from gnomAD v2.1absent from gnomAD v4.1frequency 0% ≤ 0.000333% VCEP threshold.
BP1 supporting Benign
VCEP PALB2 specification: BP1 applies to all missense variants at supporting benign strength. PALB2 has a low rate of missense variants that are non-functional in relevant assays, and true missense pathogenic variants are thought to be exceedingly rare.
VCEP rule: 'Apply to all missense variants.' NM_024675.4:c.2580G>T is a missense variant (p.Glu860Asp).
Assessed · not applied
Pathogenic
PS4 VCEP requires case-control studies with p≤0.05 AND (OR≥3 OR lower 95% CI ≥1.5).
PP1 No co-segregation data available for this variant.
Benign
BA1 Variant is absent from gnomAD v4.1.
BS1 Variant is absent from gnomAD v4.1.
BS2 VCEP BS2 requires Fanconi Anemia proband points from BS2 tables.
BS4 VCEP BS4 requires quantitative co-segregation analysis (LOD scores or Bayes Factors).
N/A · 18 PVS1 · PS1 · PS2 · PS3 · PM1 · PM5 · PM6 · PP2 · PP3 · PP4 · PP5 · BS3 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 (4 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 484223)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.021. BayesDel score = -0.521846.
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 not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. 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
24432435 ↗ PMID 24432435 CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint co CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification crite CLINVAR
31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer CLINVAR
31479213 ↗ PMID 31479213 CLINVAR