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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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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