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POLE
Final classification
VUS
POLE c.4735C>T · p.Arg1579Cys
POLE

NM_006231.3:c.4735C>T (p.Arg1579Cys) is a missense variant in the C-terminal polymerase domain of POLE, distant from the exonuclease domain (residues 1-466) where established pathogenic missense variants cluster.

Gene
POLE
Transcript
NM_006231.3
HGVS · transcript:coding
NM_006231.3:c.4735C>T
Consequence
N/A
GRCh38
chr12:132642723 G>A
GRCh37
chr12:133219309 G>A
Basis Only PM2 is met at supporting strength. No PVS1, no Strong (PS), no additional Moderate (PM), and no other Supporting pathogenic criteria are met. No benign criteria are met. Under both the León-Castillo et al. 2020 custom POLE framework and generic ACMG/AMP 2015 combination rules, a single supporting criterion is insufficient to classify as Pathogenic, Likely Pathogenic, Benign, or Likely Benign. The variant defaults to VUS.
Only PM2 is met at supporting strength. No PVS1, no Strong (PS), no additional Moderate (PM), and no other Supporting pathogenic criteria are met. No benign criteria are met. Under both the León-Castillo et al. 2020 custom POLE framework and generic ACMG/AMP 2015 combination rules, a single supporting criterion is insufficient to classify as Pathogenic, Likely Pathogenic, Benign, or Likely Benign. The variant defaults to VUS.
Classification rationale
PM2 VUS
POLE c.4735C>T

NM_006231.3:c.4735C>T (p.Arg1579Cys) is a missense variant in the C-terminal polymerase domain of POLE, distant from the exonuclease domain (residues 1-466) where established pathogenic missense variants cluster.1 This variant is present at very low frequency in population databases: gnomAD v2.1 at 0.00319% (1/31,386 alleles), gnomAD v4.1 at 0.00050% (8/1,613,270 alleles), and absent from gnomAD-Canada, meeting PM2 at supporting strength.2 Under the León-Castillo et al. 2020 custom POLE framework, this variant does not qualify for PM1 (not an exonuclease-domain hotspot), PS4 (not a recurrent pathogenic variant in endometrial carcinoma cohorts), PP3 (absent from supplementary in silico tables), or BP4 (absent from supplementary in silico tables).3 Computational predictors are mixed and do not converge on a pathogenic signal: REVEL 0.412 (intermediate), BayesDel 0.071 (benign-leaning), SpliceAI max delta 0.20 (borderline). PP3 and BP4 are not met.4 This variant is reported in ClinVar (VariationID 405672) as 'Uncertain significance' by three clinical laboratories. The associated publications (PMID:25394175, a cancer genetics referral guideline, and PMID:28492532, the Sherloc classification framework) do not provide variant-specific evidence for NM_006231.3:c.4735C>T.5 No functional studies, segregation data, de novo observations, or case-control studies are available for this variant. All remaining pathogenic criteria (PS1-PS5, PM1, PM5-PM6, PP1-PP5) and benign criteria (BA1, BS1-BS4, BP1-BP6) are either not met or not applicable.6 With only PM2_Supporting met, the overall classification is Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines: insufficient evidence to classify as pathogenic or benign.7

PM2 VUS
1 vcep_path_250_323pvs1_variant_assessment
3 vcep_path_250_323_s002vcep_path_250_323_s003vcep_path_250_323_s004final_classification_framework
4 revelbayesdelspliceai ↗
6 oncokb ↗pm5_candidates
7 generic_acmg_combination_rules
Gene diagram · NM_006231.3 · variants mapped to exon structure
POLE NM_006231.3
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      This variant is present in gnomAD v4.1 (AF= 4.95887e-06; MAF= 0.00050%, 8/1613270 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.78165e-06; MAF= 0.00068%, 8/1179654 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.18613e-05; MAF= 0.00319%, 1/31386 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.48593e-05; MAF= 0.00649%, 1/15418 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0005% · 8 / 1,613,270
      0 hom · FAF 0.00029%
      European (non-Finnish)
      8 / 1,179,654
      0.00068%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0032% · 1 / 31,386
      0 hom
      European (non-Finnish)
      1 / 15,418
      0.0065%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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 (3 clinical laboratories). (ClinVarID = 405672)
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.20). REVEL score = 0.412. BayesDel score = 0.0712825.
      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 previously been reported in somatic cancers (COSMIC; COSV57690476, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 1 PMID not cited in assessment
      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