León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
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POLE encodes the catalytic subunit of DNA polymerase epsilon, the enzyme that replicates the leading strand of DNA during cell division and participates in DNA repair. It contains a proofreading domain that corrects replication errors, keeping the accumulation of mutations in check. Germline mutations in POLE cause polyposis and predispose to colorectal cancer, and are also linked to a rare syndrome of facial dysmorphism, immunodeficiency, livedo, and short stature. Somatic mutations, particularly in the proofreading domain, occur in colorectal and endometrial cancers, where they drive an ultra-mutated tumor phenotype and are associated with better responses to immune checkpoint inhibitors.
This variant
POLE germline variants predispose to polyposis and colorectal cancer, with pathogenic missense changes concentrated in the exonuclease proofreading domain. This intronic variant is absent from population databases but predicted to have no splice impact, so no evidence links it to POLE disease mechanisms; it remains a variant of uncertain significance pending functional splicing and clinical data.
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.286-8C>G
GRCh38
chr12:132680230 G>C
GRCh37
chr12:133256816 G>C
VUS: one pathogenic-supporting criterion (PM2, absent from gnomAD) and one benign-supporting (BP4, SpliceAI 0.08) meet no qualifying ACMG combination rule.
Classification rationale
PM2BP4VUS
POLE c.286-8C>G
PM2 (Supporting): absent from gnomAD v2.1 and v4.1 (AF=0), consistent with a rare disease-associated allele. BP4 (Supporting): SpliceAI max delta 0.08, below the 0.1 threshold, predicts no significant splice impact. Final classification: VUS — one pathogenic-supporting and one benign-supporting criterion satisfy no qualifying ACMG combination rule.
PM2 + BP4→VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
Gene diagram
· NM_006231.4 · variants mapped to exon structure
POLENM_006231.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in POLE—click a row to locate it on the plot · use the link column to open its page
Protein
Location
Classification
Link
Applied criteria · 2 applied · 18 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
✓
PM2supportingPathogenic
Met (supporting): absent from gnomAD v2.1 and v4.1 (AF=0), below the <0.1% ultra-rare threshold.
Absent (AF=0) in gnomAD v2.1 (GRCh37) and gnomAD v4.1 (GRCh38); AF=0 < project non-VCEP PM2 threshold of 0.1% (user profile convention).Base rule: ACMG/AMP 2015 PM2 (PMID 25741868) - absent in controls or extremely low frequency.PM2 supporting-strength calibration: Whiffin N et al., 'Using high-resolution variant frequencies to empower clinical genome interpretation', Genet Med 2017 (PMID 28518168), recommending PM2 at supporting strength for absence/ultra-rareness in population databases.
Met (supporting): SpliceAI max delta 0.08, below the 0.1 threshold; no significant splice impact predicted.
SpliceAI Lookup (spliceai): max delta 0.08 (DS_AG 0.0, DS_AL 0.08, DS_DG 0.0, DS_DL 0.04) - SpliceAI predicts no significant splice impact; below the BP4 threshold.Generic in-silico operating thresholds (generic_acmg_combination_rules, source PMID 25741868): for intronic/synonymous/non-canonical-splice-position variants evaluate SpliceAI only; SpliceAI max delta <0.1 -> BP4 supporting, per SVI-recommended thresholds (Walker et al. 2023, ClinGen SVI Splicing Subgroup report, PMID 37442131). Max delta 0.08 is <0.1, so BP4 supporting is met.Custom POLE BP4 rule (final_classification_framework; vcep_path_250_323_s003 / vcep_path_250_323_s004): applies only to exact missense variants listed in Supplementary Tables S2/S3; c.286-8C>G is intronic and absent, so the framework falls back to the generic in-silico workflow.