NM_006231.4:c.1708C>A

POLE · NP_006222.2:p.(Leu570Met) · NM_006231.4

GRCh37: chr12:133248887 G>T · GRCh38: chr12:132672301 G>T

Gene: POLE Transcript: NM_006231.4

Final call

VUS

PM2 moderate BP4 supporting benign

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.(Leu570Met)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

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).

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).

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.

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.

Final determination: With 1 moderate pathogenic criterion (PM2) and 1 supporting benign criterion (BP4), no pathogenic, likely pathogenic, benign, or likely benign combination rule is satisfied; under the León-Castillo et al. 2020 custom POLE framework (which follows ACMG/AMP 2015 final-combination logic), all other combinations default to Uncertain Significance.

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	N/A	NM_006231.4:c.1708C>A is a missense variant (p.Leu570Met). PVS1 applies only to null variants (nonsense, frameshift, canonical splice ±1,2). This variant does not fall into any PVS1 bucket under PMC6185798.	pvs1_generic_framework
PS1	Not met	No established pathogenic variant with a different nucleotide change producing the same amino acid substitution (p.Leu570Met) has been identified at this codon.
PS2	Not assessed	No de novo data available for this variant.
PS3	Not met	No well-established in vitro or in vivo functional studies have been identified for NM_006231.4:c.1708C>A (p.Leu570Met). The variant is absent from COSMIC and OncoKB reports Unknown Oncogenic Effect with no variant-specific functional evidence.	oncokb
PS4	Not met	NM_006231.4:c.1708C>A (p.Leu570Met) is absent from both the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1 of León-Castillo et al. 2020. The custom POLE framework PS4_Supporting threshold (combined EC count >=10, belonging to established pathogenic set) is not met. Variant is not recurrent in available somatic datasets.	vcep_path_250_323_s002
PS5	Not assessed	No data available regarding detection of this variant in trans with a pathogenic variant for a recessive disorder.
PM1	Not met	p.Leu570Met (residue 570) is not one of the five established POLE exonuclease-domain hotspot variants (P286R, V411L, S297F, A456P, S459F) per the León-Castillo et al. 2020 custom framework. It is not among the PM1_Moderate variants (F367S, L424I, M295R, P436R, M444K, D368Y) or PM1_Supporting variants (A465V, L424V, T278M, A428T). Residue 570 lies outside the exonuclease domain (~268-471) in the polymerase domain. No mutational hotspot or critical functional domain has been established at this position.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	NM_006231.4:c.1708C>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0, meeting the PM2 criterion (allele frequency <0.1% in large population databases).	gnomad_v2 gnomad_v4
PM5	Not met	No pathogenic missense variant at the same codon (Leu570) with a different amino acid change was identified through ClinVar candidate harvesting or the León-Castillo supplementary tables.	pm5_candidates
PM6	Not assessed	No de novo data available for this variant. PM6 cannot be assessed without a confirmed de novo observation.
PP1	Not assessed	No co-segregation data available for this variant in affected families.
PP2	Not assessed	No HCI prior probability score or gene-level missense constraint metrics (z-score, pLI) are available for POLE to evaluate the rate of benign missense variation. PP2 cannot be reliably applied without these data.
PP3	Not met	The variant is absent from Supplementary Tables S2 and S3 of León-Castillo et al. 2020, so the custom POLE PP3 rule does not apply. Under generic ACMG/AMP, REVEL score is 0.267 (below the 0.5 pathogenic threshold) and BayesDel score is -0.221 (negative, benign-leaning). SpliceAI max delta score is 0.06, predicting no splice impact. Multiple computational tools do not support a deleterious effect.	revel bayesdel spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not assessed	No patient-specific phenotype or family history data are available for this case. PP4 cannot be evaluated without clinical context.
PP5	Not met	No reputable source has classified NM_006231.4:c.1708C>A as pathogenic. ClinVar reports this variant as Uncertain significance (Variation ID 405767, 4 clinical laboratories, criteria provided single submitter). OncoKB reports Unknown Oncogenic Effect. None of the reviewed literature sources classify this variant as pathogenic.	clinvar oncokb
BA1	Not met	NM_006231.4:c.1708C>A is absent from gnomAD v2.1 and v4.1. The BA1 threshold of >1% allele frequency in population databases is not met.	gnomad_v2 gnomad_v4
BS1	Not met	NM_006231.4:c.1708C>A is absent from gnomAD v2.1 and v4.1. The BS1 threshold of >0.3% allele frequency in population databases is not met.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available regarding observation of this variant in healthy adult individuals. The variant is absent from gnomAD, so no homozygous or hemizygous counts are available for BS2 evaluation.
BS3	Not assessed	No well-established in vitro or in vivo functional studies have been identified showing no damaging effect for NM_006231.4:c.1708C>A. Absent from COSMIC, and OncoKB shows no variant-specific functional evidence.	oncokb
BS4	Not assessed	No segregation data are available to evaluate lack of co-segregation with disease.
BP1	N/A	BP1 applies to missense variants in genes where primarily truncating variants cause disease. In POLE, both missense variants (particularly in the exonuclease domain) and truncating variants are established mechanisms of disease, and the gene is known to harbor pathogenic missense variants. BP1 is therefore not applicable.
BP2	Not assessed	No data available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product: REVEL score is 0.267 (below the 0.5 pathogenic threshold, in benign-leaning range), BayesDel score is -0.221 (negative, predicting benign impact), and SpliceAI predicts no splicing alteration (max delta score 0.06). The variant is absent from Supplementary Tables S2 and S3 of León-Castillo et al. 2020, so the custom POLE BP4 rule does not apply; this assessment uses the generic ACMG/AMP BP4 criterion based on the converging in silico evidence.	revel bayesdel spliceai
BP5	Not assessed	No data available regarding identification of an alternate molecular basis for disease in a case carrying this variant.
BP6	Not met	No reputable source has classified NM_006231.4:c.1708C>A as benign. ClinVar reports this variant as Uncertain significance (Variation ID 405767). BP6 requires a reputable source to report the variant as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. NM_006231.4:c.1708C>A is a missense variant (p.Leu570Met), not synonymous.

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