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POLE
Final classification
VUS
POLE c.3959G>A · p.Arg1320Gln
POLE

NM_006231.4:c.3959G>A (p.Arg1320Gln) in POLE is classified as a Variant of Uncertain Significance (VUS).

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.3959G>A
Consequence
N/A
GRCh38
chr12:132649352 C>T
GRCh37
chr12:133225938 C>T
Basis The adjudicated criteria yield exactly one pathogenic supporting criterion (PM2) and one benign supporting criterion (BP4). No pathogenic criteria reach moderate, strong, or very-strong strength, and no benign criteria reach strong or standalone strength. Under the Leon-Castillo et al. 2020 custom POLE framework (which defers to standard ACMG/AMP 2015 final-combination thresholds), the evidence is insufficient for any classification other than Uncertain Significance. Conflicting supporting-level evidence on both sides confirms VUS.
The adjudicated criteria yield exactly one pathogenic supporting criterion (PM2) and one benign supporting criterion (BP4). No pathogenic criteria reach moderate, strong, or very-strong strength, and no benign criteria reach strong or standalone strength. Under the Leon-Castillo et al. 2020 custom POLE framework (which defers to standard ACMG/AMP 2015 final-combination thresholds), the evidence is insufficient for any classification other than Uncertain Significance. Conflicting supporting-level evidence on both sides confirms VUS.
Classification rationale
PM2 BP4 VUS
POLE c.3959G>A

NM_006231.4:c.3959G>A (p.Arg1320Gln) in POLE is classified as a Variant of Uncertain Significance (VUS).1 This variant is a missense substitution in exon 31 of 49, located in the C-terminal region of POLE, far outside the well-characterized exonuclease domain (residues ~268-471).2 The variant is present at very low frequency in population databases: gnomAD v2.1 allele frequency 0.0032% (8/249,426 alleles) and v4.1 allele frequency 0.0016% (25/1,613,522 alleles), with no homozygotes observed (PM2_Supporting).3 Multiple in silico tools predict a benign effect: REVEL score 0.225, BayesDel score -0.2976, and SpliceAI max delta 0.02 (BP4_Supporting).4 The variant is not one of the five established pathogenic POLE exonuclease-domain hotspot mutations (P286R, V411L, S297F, A456P, S459F) and is absent from the recurrent variant list in the Leon-Castillo et al. 2020 endometrial carcinoma cohort analysis.5 ClinVar classifies this variant as Uncertain Significance with 5 clinical laboratory submissions and review status 'criteria provided, single submitter' (1-star). No expert panel review has been performed.6 No functional studies, segregation data, de novo observations, or case-control data are available for this variant. The reviewed literature (Karbassi et al. 2016, PMID:26467025; Hampel et al. 2015, PMID:25394175; Nykamp et al. 2017, PMID:28492532) consists of variant classification methodology papers that do not mention this variant.7 The net evidence balance is one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), resulting in a classification of Uncertain Significance under the ACMG/AMP 2015 framework.8

PM2 + BP4 VUS
2 vcep_path_250_323
4 revelbayesdelspliceai ↗
5 vcep_path_250_323_s002
8 generic_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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_006231.4:c.3959G>A is present at extremely low frequency in population databases. In gnomAD v2.1, the allele frequency is 3.21e-05 (0.0032%, 8/249,426 alleles, 0 homozygotes; grpmax FAF=8.51e-05). In gnomAD v4.1, the frequency is 1.55e-05 (0.0016%, 25/1,613,522 alleles, 0 homozygotes; grpmax FAF=1.10e-04). Both are well below the 0.1% PM2 threshold. The variant is absent from gnomAD-Canada v1.0. Highest subpopulation frequency is in South Asians (v2.1: 0.020%, v4.1: 0.018%).
gnomAD v2.1 AF=3.21e-05 (0.0032%)8/249426 alleles
BP4 supporting Benign
Under the Leon-Castillo et al. 2020 custom POLE framework, BP4_Supporting applies when the variant appears in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in silico results. R1320Q is absent from both tables, so the custom rule does not apply. Under generic fallback, multiple lines of computational evidence predict no impact: REVEL score 0.225 (below 0.5, benign-leaning), BayesDel score -0.2976 (negative, predicting benign), and SpliceAI max delta 0.02 (no splicing impact). These results support a lack of deleterious effect at the supporting evidence level.
REVEL score: 0.225 (below pathogenic thresholdbenign-leaning).BayesDel score: -0.2976 (negative
Assessed · not applied
Pathogenic
PS1 No evidence is available regarding a different pathogenic nucleotide change at the same amino acid position (Arg1320).
PS2 No de novo data are available for this variant.
PS3 No functional data exist for NM_006231.4:c.3959G>A or a systematically characterized range that includes position 1320.
PS4 Under the Leon-Castillo et al.
PM1 Under the Leon-Castillo et al.
PM6 No de novo data are available for this variant.
PP1 No segregation data are available for this variant.
PP2 PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common mechanism of disease.
PP3 Under the Leon-Castillo et al.
PP4 No patient phenotype or family history data are provided for this case.
PP5 ClinVar reports this variant as Uncertain Significance with review status 'criteria provided, single submitter' (1-star).
Benign
BA1 The variant is present at very low frequency in gnomAD.
BS1 The variant is present at very low frequency in gnomAD.
BS2 No data are available regarding homozygous or hemizygous observations of this variant in healthy individuals.
BS3 No functional studies have been performed on this variant to demonstrate a benign effect.
BS4 No segregation data are available for this variant.
BP1 BP1 is not met.
BP2 No data are available regarding observations of this variant in trans with a known pathogenic variant.
BP5 No data are available regarding an alternate molecular basis for disease in this case.
BP6 ClinVar reports this variant as Uncertain Significance with review status 'criteria provided, single submitter' (1-star).
N/A · 3 PVS1 · PM5 · BP7
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= 1.54941e-05; MAF= 0.00155%, 25/1613522 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000175647; MAF= 0.01756%, 16/91092 alleles, homozygotes = 0); grpmax FAF= 0.00010969.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.20736e-05; MAF= 0.00321%, 8/249426 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 0.000196053; MAF= 0.01961%, 6/30604 alleles, homozygotes = 0); grpmax FAF= 8.513e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0015% · 25 / 1,613,522
0 hom · FAF 0.011%
South Asian
16 / 91,092
0.018%
Middle Eastern
1 / 6,084
0.016%
Remaining individuals
3 / 62,486
0.0048%
African/African American
1 / 74,950
0.0013%
European (non-Finnish)
4 / 1,180,050
0.00034%
+ 5 not observed (Admixed American, European (Finnish), Amish, East Asian, Ashkenazi Jewish)
gnomAD v2.1
0.0032% · 8 / 249,426
0 hom · FAF 0.0085%
South Asian
6 / 30,604
0.02%
Remaining individuals
1 / 6,108
0.016%
European (non-Finnish)
1 / 112,312
0.00089%
+ 5 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish))
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 (5 clinical laboratories). (ClinVarID = 240494)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.225. BayesDel score = -0.297636.
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
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. 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