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PALB2
Final classification
Uncertain Significance - Conflicting Evidence
PALB2 c.1432T>C · p.Ser478Pro
PALB2

The PALB2 c.1432T>C (p.Ser478Pro) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar with conflicting germline submissions, including uncertain significance and likely benign interpretations.

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.1432T>C
Consequence
N/A
GRCh38
chr16:23635114 A>G
GRCh37
chr16:23646435 A>G
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; 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; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP1 Uncertain Significance - Conflicting Evidence
PALB2 c.1432T>C

The PALB2 c.1432T>C (p.Ser478Pro) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar with conflicting germline submissions, including uncertain significance and likely benign interpretations.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1; the observed frequency is therefore below the PALB2 PM2_Supporting threshold of ≤0.000333% and below the benign population thresholds for BS1 and BA1.2 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.01, which is below the PALB2 splice thresholds used for PP3 (≥0.2) and BP4 (≤0.1), although PP3 and BP4 are not applied to missense variants under the PALB2 specification.3 Under the PALB2 expert specification, BP1_Supporting is met because this is a missense variant in a gene where disease is primarily associated with truncating variants, while PVS1 is not met because this variant is not a qualifying loss-of-function change.4

PM2 + BP1 Uncertain Significance - Conflicting Evidence
4 cspec ↗pvs1_gene_contextpvs1_variant_assessment
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.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories) and as Likely benign (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: 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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots