NM_006231.4:c.6766G>A (p.Gly2256Arg) meets BA1 (stand-alone benign) based on gnomAD grpmax filtering allele frequency of 1.22% in v2.1 and 1.29% in v4.1, exceeding the 1% BA1 threshold, with 4–8 homozygotes observed across datasets.1 The variant meets BS1 (strong benign) with a grpmax allele frequency of 1.22% in gnomAD and an African/African American subpopulation frequency of 1.35%, far exceeding the 0.3% BS1 threshold for a disorder with this prevalence.2 The variant meets BS2 (strong benign): 4 homozygotes are observed in gnomAD v2.1 and 8 homozygotes in gnomAD v4.1, all in the African/African American population, which is incompatible with a fully penetrant autosomal dominant cancer predisposition syndrome.3 The variant meets BP4 (supporting benign): multiple computational tools concordantly predict a benign effect (REVEL 0.048, BayesDel -0.759, SpliceAI delta 0.01).4 The variant is absent from the León-Castillo et al. 2020 POLE recurrent variant tables (Supplementary Tables S1–S3), is not in COSMIC, and lies in the C-terminal region (position 2256) outside the exonuclease domain (residues 268–471), so the custom POLE PM1, PS4, and PP3 criteria do not apply.5 BA1 alone is sufficient for a Benign classification per ACMG/AMP 2015 combination rules. The additional BS1, BS2, and BP4 criteria provide further supportive benign evidence.6
POLE
Final classification
Benign
POLE c.6766G>A · p.Gly2256Arg
POLE
NM_006231.4:c.6766G>A (p.Gly2256Arg) meets BA1 (stand-alone benign) based on gnomAD grpmax filtering allele frequency of 1.22% in v2.1 and 1.29% in v4.1, exceeding the 1% BA1 threshold, with 4–8 homozygotes observed across datasets.
BA1 (stand-alone benign) is met: gnomAD grpmax filtering allele frequency of 1.22% (v2.1) / 1.29% (v4.1) exceeds the 1% BA1 threshold, with 4–8 homozygotes observed. BA1 alone is sufficient for Benign classification under both the local custom POLE framework (León-Castillo et al. 2020) and generic ACMG/AMP 2015 rules. Additional criteria BS1 (strong benign, AF >0.3%), BS2 (strong benign, homozygotes in population), and BP4 (supporting benign, concordant in silico benign predictions) provide further supportive evidence.
Classification rationale
BA1BS1BS2BP4
Benign
POLE c.6766G>A
BA1 + BS1 + BS2 + BP4
→
Benign
4
revelbayesdelspliceai ↗
5
vcep_path_250_323vcep_path_250_323_s002vcep_path_250_323_s003vcep_path_250_323_s004
Gene diagram
· NM_006231.4 · variants mapped to exon structure
POLE
NM_006231.4
Fetching transcript structure from UCSC…
Applied criteria · 4 applied · 19 assessed
Applied · 4
Strength
Supporting
Moderate
Strong
Very strong
✓
BA1
stand-alone
Benign
The gnomAD grpmax filtering allele frequency (FAF) is 1.22% in v2.1 and 1.29% in v4.1, exceeding the 1% BA1 threshold. The African/African American subpopulation allele frequency is 1.35% in both gnomAD versions, with 4 homozygotes in v2.1 and 8 homozygotes in v4.1. This population frequency far exceeds what would be expected for a pathogenic variant in POLE-associated disorders.
gnomAD v2.1 grpmax FAF = 1.22% (>1% BA1 threshold)gnomAD v4.1 grpmax FAF = 1.29%African/African American AF = 1.35%
✓
BS1
strong
Benign
The gnomAD population allele frequency exceeds the 0.3% BS1 threshold. The grpmax FAF is 1.22% (v2.1) and 1.29% (v4.1), and the African/African American subpopulation frequency is 1.35%. This is substantially greater than expected for a pathogenic variant in POLE-associated hereditary cancer syndromes and is superseded by the BA1 criterion.
gnomAD grpmax FAF = 1.22% (>0.3% BS1 threshold)African/African American subpopulation AF = 1.35%
✓
BS2
strong
Benign
The variant is observed in the homozygous state in gnomAD population databases: 4 homozygotes in v2.1 (exomes + genomes, primarily in African/African American population) and 8 homozygotes in v4.1. Observation of homozygosity for a variant in a gene where pathogenic variants are associated with an autosomal dominant cancer predisposition syndrome (POLE-associated colorectal and endometrial cancer) constitutes strong evidence for a benign effect, as homozygous loss of function would be expected to be lethal or cause severe early-onset disease.
4 homozygotes in gnomAD v2.1 (exomes + genomes)8 homozygotes in gnomAD v4.1All homozygotes found in African/African American population
✓
BP4
supporting
Benign
Multiple lines of computational evidence predict a benign effect. REVEL score is 0.048 (benign), BayesDel score is -0.759 (strongly benign), and SpliceAI delta score is 0.01 (no predicted splicing impact). The variant is absent from the León-Castillo et al. supplementary tables, so the custom POLE BP4 rule is not triggered; the generic in silico assessment applies. All available computational tools agree on a benign prediction.
REVEL score = 0.048 (benign range)BayesDel score = -0.759 (strongly benign)SpliceAI max delta = 0.01 (no splice impact)
Assessed · not applied
Pathogenic
PVS1
NM_006231.4:c.6766G>A is a missense variant (p.Gly2256Arg) in exon 49 of POLE.
PS1
No evidence of a different nucleotide change at codon 2256 producing the same p.Gly2256Arg missense change that is established as pathogenic.
PS2
No de novo occurrence data available for this variant.
PS3
No variant-specific functional studies were identified for NM_006231.4:c.6766G>A (p.Gly2256Arg).
PS4
The variant does not meet the custom POLE framework PS4_Supporting criteria: it is absent from the León-Castillo et al.
PM1
The variant does not meet any tier of the custom POLE PM1 framework.
PM2
gnomAD v2.1 total allele frequency is 0.127% (359/281,910 alleles), exceeding the 0.1% PM2 threshold.
PM5
No same-residue comparator variants were identified for PM5 assessment.
PM6
No de novo occurrence data available for this variant.
PP1
No segregation data are available for this variant.
PP2
PP2 requires that missense variants are a common disease mechanism in the gene AND benign missense variation is low.
PP3
The variant is absent from the León-Castillo et al.
PP4
No patient phenotype data are available for this case.
Benign
BS3
No well-established in vitro or in vivo functional studies demonstrating no damaging effect of NM_006231.4:c.6766G>A were identified.
BS4
No segregation data are available.
BP1
BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease.
BP2
No evidence that this variant has been observed in trans with a known pathogenic POLE variant.
BP5
No alternative molecular cause for the patient's phenotype has been identified.
BP6
While ClinVar reports this variant as Benign by 9 clinical laboratories and Likely benign by 1 laboratory, the aggregate review status is 1-star (criteria provided, single submitter), not 3-star expert panel.
N/A · 2
PP5 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 0.000723005; MAF= 0.07230%, 1166/1612714 alleles, homozygotes = 8) and has highest observed frequency in the African/African American population (AF= 0.0135845; MAF= 1.35845%, 1019/75012 alleles, homozygotes = 8); grpmax FAF= 0.0128916.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.00127346; MAF= 0.12735%, 359/281910 alleles, homozygotes = 4) and has highest observed frequency in the African/African American population (AF= 0.0134745; MAF= 1.34745%, 336/24936 alleles, homozygotes = 4); grpmax FAF= 0.0121994.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.0005971769815418024, 11/18420 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.072%
· 1166 / 1,612,714
8 hom · FAF 1.3%
8 hom · FAF 1.3%
African/African American 1019 / 75,012 |
1.4% 8 hom |
Remaining individuals 60 / 62,474 |
0.096% |
Admixed American 45 / 60,036 |
0.075% |
Middle Eastern 3 / 6,062 |
0.049% |
East Asian 3 / 44,888 |
0.0067% |
South Asian 6 / 91,060 |
0.0066% |
European (non-Finnish) 30 / 1,178,650 |
0.0025% |
+ 3 not observed (European (Finnish), Amish, Ashkenazi Jewish)
gnomAD v2.1
0.13%
· 359 / 281,910
4 hom · FAF 1.2%
4 hom · FAF 1.2%
African/African American 336 / 24,936 |
1.3% 4 hom |
Admixed American 17 / 35,436 |
0.048% |
Remaining individuals 2 / 7,220 |
0.028% |
East Asian 3 / 19,952 |
0.015% |
European (non-Finnish) 1 / 128,270 |
0.00078% |
+ 3 not observed (Ashkenazi Jewish, European (Finnish), South Asian)
gnomAD Canada 🇨🇦
0.06%
· 11 / 18,420
0 hom · FAF 0.53%
0 hom · FAF 0.53%
African/African American 10 / 1,018 |
0.98% |
European (non-Finnish) 1 / 11,742 |
0.0085% |
+ 7 not observed (Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
ClinVar
This variant has been reported in ClinVar as Benign (9 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 381926)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.048. BayesDel score = -0.758792.
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
COSMIC
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
Triaged references · 6 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
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
26389258 ↗
Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR