Starting
Initialising…
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POLE
Final classification
VUS
POLE c.1708C>A · p.Leu570Met
POLE

NM_006231.4:c.1708C>A (p.Leu570Met) is a missense variant in POLE, located at residue 570 outside the exonuclease domain in the polymerase domain.

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.1708C>A
Consequence
N/A
GRCh38
chr12:132672301 G>T
GRCh37
chr12:133248887 G>T
Basis The León-Castillo et al. 2020 custom POLE framework (gene_framework) was applied. Only one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met. No pathogenic, likely pathogenic, benign, or likely benign combination rule is satisfied. Per the framework (which mirrors generic ACMG/AMP 2015 combination logic), all other combinations default to Uncertain Significance.
The León-Castillo et al. 2020 custom POLE framework (gene_framework) was applied. Only one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met. No pathogenic, likely pathogenic, benign, or likely benign combination rule is satisfied. Per the framework (which mirrors generic ACMG/AMP 2015 combination logic), all other combinations default to Uncertain Significance.
Classification rationale
PM2 BP4 VUS
POLE c.1708C>A

NM_006231.4:c.1708C>A (p.Leu570Met) is a missense variant in POLE, located at residue 570 outside the exonuclease domain in the polymerase domain. The variant is absent from gnomAD v2.1 (exomes) and v4.1 (exomes) population databases, meeting PM2 at moderate strength (PM2_Moderate).1 Multiple in silico tools predict a benign impact: REVEL score 0.267 (benign-leaning, below the 0.5 pathogenic threshold), BayesDel score -0.221 (benign), and SpliceAI max delta 0.06 (no splice impact). This meets BP4 at supporting benign strength (BP4_Supporting).2 The variant has been reported in ClinVar as Uncertain significance by 4 clinical laboratories (Variation ID 405767). It is not among the established POLE exonuclease-domain hotspot mutations identified by León-Castillo et al. 2020, and is absent from COSMIC and Cancer Hotspots.3 With one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4), the net evidence is equivocal. The variant is classified as Variant of Uncertain Significance (VUS) under the León-Castillo et al. 2020 custom POLE framework and generic ACMG/AMP 2015 combination rules.4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
3 clinvar ↗vcep_path_250_323_s002
4 final_classification_frameworkgeneric_acmg_combination_rules
Gene diagram · NM_006231.4 · variants mapped to exon structure
POLE NM_006231.4
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
      This variant is absent from gnomAD-Canada.
      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). (ClinVarID = 405767)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06). REVEL score = 0.267. BayesDel score = -0.220802.
      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. POLE, the catalytic subunit of DNA polymerase epsilon, is an enzyme involved in DNA replication and repair. Select POLE mutations lead to ultra-high m
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 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
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR