NM_006231.4:c.6766G>A

POLE · NP_006222.2:p.(Gly2256Arg) · NM_006231.4

GRCh37: chr12:133201378 C>T · GRCh38: chr12:132624792 C>T

Gene: POLE Transcript: NM_006231.4

Final call

Benign

BA1 stand-alone benign BS1 strong benign BS2 strong benign BP4 supporting benign

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.(Gly2256Arg)

gnomAD AF

0.0007230048229258256 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

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.

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.

The variant meets BP4 (supporting benign): multiple computational tools concordantly predict a benign effect (REVEL 0.048, BayesDel -0.759, SpliceAI delta 0.01).

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.

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.

Final determination: BA1 alone is sufficient for a Benign classification; the local custom POLE framework (León-Castillo et al. 2020) and generic ACMG/AMP 2015 rules both specify that a single stand-alone benign criterion (BA1) independently classifies a variant as Benign.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	NM_006231.4:c.6766G>A is a missense variant (p.Gly2256Arg) in exon 49 of POLE. It does not fall into the null-variant categories (nonsense, frameshift, canonical ±1,2 splice) required for PVS1 application under the ClinGen SVI PVS1 decision tree (PMC6185798). PVS1 is not applicable to missense variants.	pvs1_generic_framework pvs1_gene_context pvs1_variant_assessment
PS1	Not met	No evidence of a different nucleotide change at codon 2256 producing the same p.Gly2256Arg missense change that is established as pathogenic. No same-codon comparator variants were identified in ClinVar or the literature.
PS2	Not met	No de novo occurrence data available for this variant. No published reports of de novo POLE c.6766G>A were identified.
PS3	Not met	No variant-specific functional studies were identified for NM_006231.4:c.6766G>A (p.Gly2256Arg). The variant is absent from the León-Castillo et al. 2020 supplementary tables and is not listed in OncoKB with reviewed functional evidence. Position 2256 lies in the C-terminal region of POLE, far outside the exonuclease domain (residues 268–471), and no functional characterization of this region or variant was found.	oncokb vcep_path_250_323
PS4	Not met	The variant does not meet the custom POLE framework PS4_Supporting criteria: it is absent from the León-Castillo et al. Supplementary Table S1 (recurrent variants in COSMIC/TCGA endometrial carcinoma cohorts), not present in COSMIC, and does not belong to the established pathogenic hotspot set. No germline case-control data are available. The custom framework PS4_Supporting requires exact-variant recurrence in both COSMIC and TCGA with combined EC count ≥10, which this variant does not satisfy.	vcep_path_250_323_s002 clinvar
PS5	Not met	No alternative pathogenic missense variant at codon 2256 of POLE has been identified. No ClinVar entries or literature reports describe a different missense change at this codon classified as pathogenic.	clinvar
PM1	Not met	The variant does not meet any tier of the custom POLE PM1 framework. It is not one of the five established exonuclease-domain hotspots (P286R, V411L, S297F, A456P, S459F), not one of the non-hotspot recurrent pathogenic variants (F367S, L424I, M295R, P436R, M444K, D368Y), and not in the uncertain-tier set (A465V, L424V, T278M, A428T). Position 2256 is in the C-terminal region, far from the exonuclease domain (residues 268–471). Cancerhotspots.org does not identify this as a significant hotspot residue. No functional domain at position 2256 has been characterized as critical in the literature.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Not met	gnomAD v2.1 total allele frequency is 0.127% (359/281,910 alleles), exceeding the 0.1% PM2 threshold. gnomAD v4.1 total frequency is 0.072% (1,166/1,612,714 alleles). The variant is present at appreciable frequency in population databases, particularly in the African/African American population (1.347% in v2.1, 1.358% in v4.1).	gnomad_v2 gnomad_v4
PM5	Not met	No same-residue comparator variants were identified for PM5 assessment. The automated PM5 candidate harvest found zero candidates at codon 2256. No alternative pathogenic missense change at the same amino acid position is known.	pm5_candidates
PM6	Not met	No de novo occurrence data available for this variant. No published reports of a de novo POLE c.6766G>A event were identified in the literature or ClinVar submissions.
PP1	Not met	No segregation data are available for this variant. No published family studies or co-segregation analyses involving NM_006231.4:c.6766G>A were identified.
PP2	Not met	PP2 requires that missense variants are a common disease mechanism in the gene AND benign missense variation is low. While pathogenic POLE missense variants in the exonuclease domain are a known mechanism, the C-terminal region (position 2256) tolerates substantial benign missense variation: this variant itself is present at 0.13% overall and 1.35% in the African population with homozygotes, indicating high tolerance of missense changes in this region. PP2 does not apply.	gnomad_v2 gnomad_v4
PP3	Not met	The variant is absent from the León-Castillo et al. Supplementary Tables S2 and S3, so the custom POLE PP3_Supporting rule does not apply. Falling back to generic in silico assessment: REVEL score is 0.048 (benign-leaning), BayesDel score is -0.759 (strongly benign), and SpliceAI delta score is 0.01 (no splice impact). Multiple lines of computational evidence predict a benign effect, contradicting PP3 application.	revel bayesdel spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not met	No patient phenotype data are available for this case. PP4 requires that the variant is identified in a patient with a phenotype highly specific for the gene/disease, which cannot be assessed without clinical phenotype information.
PP5	N/A	PP5 requires a reputable source reporting the variant as pathogenic. ClinVar classification for this variant is Benign (9 clinical laboratories) and Likely benign (1 clinical laboratory). With a benign classification, PP5 is not applicable.	clinvar
BA1	Met	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 gnomad_v4
BS1	Met	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_v2 gnomad_v4
BS2	Met	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.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrating no damaging effect of NM_006231.4:c.6766G>A were identified. In silico predictions alone do not satisfy BS3 requirements.
BS4	Not met	No segregation data are available. BS4 requires lack of segregation in affected family members, which cannot be assessed without family studies.
BP1	Not met	BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease. For POLE, the established pathogenic mechanism includes missense variants in the exonuclease domain (e.g., P286R, V411L, S297F, A456P, S459F). Missense variants are a recognized disease mechanism for POLE, so BP1 does not apply even though this specific variant falls outside the exonuclease domain.	vcep_path_250_323
BP2	Not met	No evidence that this variant has been observed in trans with a known pathogenic POLE variant. The gnomAD homozygote observations are in population controls, not in the context of a confirmed pathogenic variant in trans.
BP4	Met	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 bayesdel spliceai
BP5	Not met	No alternative molecular cause for the patient's phenotype has been identified. BP5 requires that an alternative cause is found, which is not documented for this case.
BP6	Not met	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. Under the adjudication framework, BP6 at supporting strength requires ClinVar 3-star expert panel status. The 1-star review status does not meet this threshold for formal BP6 application.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted splicing impact. NM_006231.4:c.6766G>A is a missense variant (p.Gly2256Arg), not a synonymous variant. BP7 is not applicable.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.