Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
This variantScenario
BenignPathogenic
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
About POLE
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.
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01The reasoning
How it was classified
The recorded framework is León-Castillo et al. 2020 custom POLE framework. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Met (Supporting): gnomAD v4.1 total allele frequency 9.3e-06, far below the 0.1% PM2 cap, with zero homozygotes.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
VUS: the only met criterion is PM2_Supporting (gnomAD v4.1 total AF 9.3e-06, 0 homozygotes), which alone satisfies no ACMG/AMP 2015 combination rule.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
15 / 1,613,766 alleles
gnomAD v4.1: 15 / 1,613,766 alleles. Recorded AF 9.29503e-06. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 8.04538e-06; MAF= 0.00080%, 2/248590 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.00016415; MAF= 0.01641%, 1/6092 alleles, homozygotes = 0).
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
ACMG/AMP criteria under León-Castillo et al. 2020 custom POLE framework, with the data and sources behind each one.
28 criteria with recorded statuses: 1 met · 11 not met · 12 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Governing framework: no official ClinGen CSPEC/VCEP specification exists for POLE. The local custom POLE framework (León-Castillo et al. 2020, 'leon-castillo-2020-custom-framework-v1') customizes only PM1, PS4, PP3, and BP4; per its own fallback notes, PVS1, PM4, and BP3 were adjudicated under generic ACMG/AMP 2015 (PMID 25741868), with the ClinGen SVI PVS1 specification (PMC6185798) governing PVS1 scope.
Variant consequence: NM_006231.4:c.4501G>A is a single-nucleotide missense substitution NP_006222.2:p.(Gly1501Arg) in exon 35 of 49. Normalization (Mutalyzer/VariantValidator) confirms a single amino acid substitution with no protein length change, and the variant is not at a canonical splice consensus position.
Splice context: SpliceAI max delta score 0.01 indicates no significant splice impact, providing no basis for a loss-of-function or reading-frame consequence.
PVS1: not applicable - the variant is not a null variant (no nonsense, frameshift, canonical splice, initiation-loss, or deletion consequence).
PM4: not applicable - no in-frame indel and no stop-loss variant; no protein length change.
BP3: not applicable - the variant is a missense substitution, not an in-frame indel in a repeat region.
PS1 not_met: p.Gly1501Arg is not established as pathogenic through any nucleotide change - ClinVar VCV000473668 is VUS (2 clinical labs, no expert panel), COSMIC absent, OncoKB unknown oncogenic effect, and no residue-1501 record in the León-Castillo package.
PM1 not_met: p.Gly1501Arg is not among the exact exonuclease-domain hotspot/recurrent substitutions of the custom PM1 tiers (Strong/Moderate/Supporting), and generic PM1 is not met because residue 1501 lies outside the exonuclease domain (hotspots at residues 286-459) and is not a statistically significant hotspot (CancerHotspots no result; COSMIC absent; non-EDM mutations largely non-pathogenic per the paper).
PM5 not_assessed: no same-residue (p.Gly1501X) comparator variants were collected (pm5_candidates found=false, mode 'unknown') and none appear in ClinVar, COSMIC, OncoKB, or the León-Castillo tables; the dedicated same-residue search was skipped, so a pathogenic comparator cannot be confirmed or excluded.
PP2 not_assessed: gene-level missense constraint (low rate of benign missense variation) for POLE cannot be evaluated - no gnomAD gene constraint metrics, no HCI prior, no VCEP/PP2 specification in the case bundle.
BP1 not_met: missense variants in the POLE exonuclease domain are an established, common germline disease mechanism (five pathogenic hotspots per León-Castillo et al. 2020; OncoKB germline curation), so the 'primarily truncating' premise of BP1 is false.
PS2: not_assessed — no de novo occurrence of c.4501G>A with confirmed parentage is documented in any source (ClinVar submissions carry only PM2/PP3 signals; no case report exists in the literature packet).
PM6: not_assessed — no de novo occurrence at all (confirmed or assumed) is documented; parentage status of carriers is unknown.
PP1: not_assessed — zero informative meioses; no family segregation testing data exist for this variant.
BS4: not_assessed — no affected family member has been tested and reported as a non-carrier; gnomAD carrier counts are population evidence, not family non-segregation, and were not applied.
All four criteria fall back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868) because the governing local custom POLE framework (León-Castillo et al. 2020, PATH-250-323 package) specifies rules only for PM1/PS4/PP3/BP4.
The complete absence of proband, parental, and family testing data means none of these criteria can be met, refuted, or marked applicable/not-applicable on the evidence available; segregation/de novo evidence would need to be supplied from external family-testing data to change any of these assessments.
Governing framework: no ClinGen CSPEC found for POLE (cspec.found=false); the local custom framework (León-Castillo et al. 2020, J Pathol 250:323-335, precedence_rank 2) specifies only PM1/PS4/PP3/BP4. PS3 and BS3 therefore fall back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868).
PS3 not_assessed: no well-established functional study showing a deleterious effect of p.Gly1501Arg exists in any collected source; OncoKB explicitly reports no variant-specific reviewed functional evidence, ClinVar submissions cite no functional criteria, and the León-Castillo functional/hotspot evidence is confined to five exonuclease-domain hotspots (P286R, V411L, S297F, A456P, S459F) that do not include this variant.
BS3 not_assessed: no well-established functional study showing no damaging effect exists; SpliceAI (max delta 0.01), REVEL (0.492) and BayesDel are in silico predictions and cannot substitute for BS3, and the León-Castillo non-EDM cohort observation is not a variant-specific functional assay.
Neither PS3 nor BS3 contributes to the ACMG/AMP tally for this case; both remain open evidence gaps requiring variant-specific functional assay data for p.Gly1501Arg.
PS4 not_met: the governing POLE custom framework (León-Castillo et al. 2020) requires exact-variant recurrence in both COSMIC and TCGA EC cohorts (Supplementary Table S1) with combined count >=10 among the established set (P286R, V411L, A456P, S297F); p.Gly1501Arg is absent from S1, absent from the COSMIC lookup, and absent from the paper text, so the rule fails deterministically. No germline case-control data exists for generic ACMG PS4.
PP4 not_assessed: no proband phenotype or family-history data for carriers of c.4501G>A is present anywhere in the case bundle (ClinVar conditions empty or 'not provided'); a clinical phenotype report would be required.
PP5 not_met: ClinVar VCV000473668 is Uncertain significance from two non-expert clinical laboratories; no expert-panel classification exists, and the PP5/BP6 restriction rule forbids applying PP5 from ordinary laboratory or aggregate labels.
BP5 not_assessed: no case-level information documenting an alternate molecular basis of disease in a carrier of this variant is available.
BP6 not_met: ClinVar VCV000473668 is Uncertain significance from two non-expert clinical laboratories; no expert-panel classification exists, and the PP5/BP6 restriction rule forbids applying BP6 from ordinary laboratory or aggregate labels.
PM3 not_assessed: the case bundle contains no proband-level allelic data (no zygosity, no phase, no second POLE variant, no family genotyping), so a pathogenic variant in trans cannot be documented; the generic ACMG/AMP 2015 PM3 rule (PMID 25741868) governs because the custom POLE framework does not specify PM3.
BP2 not_assessed: no cis/trans configuration can be established from available evidence (ClinVar VUS submissions without co-occurrence assertions, no publications with variant-level observations); the generic ACMG/AMP 2015 BP2 rule (PMID 25741868) governs because the custom POLE framework does not specify BP2.
Both allelic criteria are driven by the same data gap: absence of proband genotyping, phase, and second-variant information. Neither criterion is met, and neither can be refuted, from the evidence bundle alone; resolving PM3/BP2 requires clinical family data outside this case.
Governing framework: local custom gene framework for POLE (León-Castillo et al. 2020, J Pathol 250:323-335 package); no official ClinGen CSPEC/VCEP for POLE was found (cspec.found=false). The custom framework's PP3/BP4 rules are table-based (exact variant in Supplementary Tables S2/S3 with specific REVEL class and benign-count criteria).
Variant lookup in the framework's own computational tables: c.4501G>A / p.Gly1501R is absent from both Table S2 (PATH-250-323-s003.xlsx, TCGA EC in-silico results) and Table S3 (PATH-250-323-s004.xlsx, non-TCGA EC in-silico results); per the framework's explicit guardrail, the custom PP3/BP4 rules are not applied and the generic in-silico workflow governs.
PP3 not met: REVEL 0.492 is below the PP3 supporting threshold >=0.644 (Pejaver et al. 2022, PMID 36413997); SpliceAI max delta 0.01 is below the 0.2 high-sensitivity cutoff (Jaganathan et al. 2019, PMID 30661751), indicating no splice impact; BayesDel uncalibrated (no verified published threshold) and not usable.
BP4 not met: REVEL 0.492 is far above the BP4 supporting threshold <=0.016 (Pejaver et al. 2022, PMID 36413997); a low SpliceAI score alone does not constitute multiple lines of benign computational evidence; no other calibrated benign-supporting predictor was available.
BP7 not applicable: the variant is missense (p.Gly1501Arg), not synonymous.
The paper underlying the framework (León-Castillo et al. 2020) itself states in silico tools are 'sensitive but not specific' for pathogenic POLE exonuclease-domain mutations, supporting conservative use of computational evidence for POLE; consistent with not assigning PP3/BP4 from uncalibrated or inconclusive predictions.
No ClinGen CSPEC exists for POLE (cspec.found=false). The local custom POLE framework (León-Castillo 2020) customizes only PM1/PS4/PP3/BP4 and explicitly falls back to generic ACMG/AMP outside those rules, so BA1/BS1/BS2/PM2 are adjudicated under generic ACMG/AMP 2015 (Richards et al., PMID 25741868; combination rules per generic_acmg_combination_rules).
BA1 not met: highest observed AF anywhere is 1.641e-04 (0.0164%, single allele in gnomAD v2.1 OTH) and 5.339e-05 (0.00534%, AFR, gnomAD v4.1) - ~300-1000x below the >=5% stand-alone benign threshold.
BS1 not met: total AF 9.295e-06 (0.00093%) and max subpopulation AF 5.339e-05 are far below both the >1% generic threshold and the more lenient >0.3% non-VCEP convention.
BS2 not met: 0 homozygotes in gnomAD v2.1 and v4.1; for this autosomal dominant, adult-onset, reduced-penetrance cancer syndrome, heterozygous carriers in unscreened reference cohorts cannot satisfy BS2.
PM2 met at Supporting: variant is ultra-rare (gnomAD v4.1 AF 9.295e-06, grpmax FAF 1.746e-05, 0 homozygotes; absent in gnomAD-Canada), well below the 0.1% PM2 cap; strength held at Supporting per generic ACMG/AMP 2015 since no gene-specific rule upgrades it.
Net population-group contribution: no benign criteria (BA1/BS1/BS2); PM2_Supporting in favor of pathogenicity.
No criteria match.
Met · 1
PM2SupportingMet (Supporting): gnomAD v4.1 total allele frequency 9.3e-06, far below the 0.1% PM2 cap, with zero homozygotes.
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Reasoning
PM2_Supporting is met. The variant is present at extremely low frequency: gnomAD v4.1 total AF 9.295e-06 (0.00093%, 15/1,613,766 alleles), highest subpopulation (AFR) AF 5.339e-05 (0.00534%), joint grpmax FAF 1.746e-05, 0 homozygotes; gnomAD v2.1 total AF 8.045e-06 (0.00080%, 2/248,590 alleles); absent from gnomAD-Canada v1.0. Every observed AF is far below the 0.1% (0.001) non-VCEP gnomAD PM2 cap and consistent with the ACMG/AMP 2015 PM2 definition of absent or extremely low frequency in population databases (Richards et al. 2015, PMID 25741868). ClinVar submission SCV000653294 (Labcorp) independently flagged PM2 (population database presence) - corroborating only, not the basis for this adjudication. Strength is capped at Supporting under generic ACMG/AMP 2015 because no VCEP/POLE-specific rule was retrieved that could upgrade PM2.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PM2 - absent in controls or at extremely low frequency in population databases; operationalized for non-VCEP gnomAD as AF <0.1% (0.001). gnomAD v4.1 AF 9.295e-06 and max subpopulation AF 5.339e-05 are both far below the cap - met at Supporting.
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 9.295e-06 (0.00093%), 15/1,613,766 alleles, 0 homozygotes; AFR subpopulation AF 5.339e-05 (0.00534%); joint grpmax FAF 1.746e-05 - all far below 0.1% PM2 cap
gnomAD v2.1 (gnomad_v2): total AF 8.045e-06 (0.00080%), 2/248,590 alleles, 0 homozygotes
PM2 definition (absent or extremely low frequency) per Richards et al. 2015 (PMID 25741868); operational 0.1% (0.001) non-VCEP gnomAD cap per project convention - observed max AF 5.339e-05 is ~19x below cap
ClinVar (clinvar): SCV000653294 lists PM2 among its applied criteria (corroboration only; not used as the adjudication basis)
Still missing
PM2 capped at Supporting under generic ACMG/AMP 2015; no ClinGen CSPEC or POLE-specific VCEP population rule retrieved that could adjust PM2 strength or applicability for this dominant cancer gene.
PS1Not met: no pathogenic record of p.Gly1501Arg via a different nucleotide change exists; ClinVar classifies this variant as Uncertain significance.
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Reasoning
PS1 requires the same amino acid change (p.Gly1501Arg) to have been established as pathogenic via a different nucleotide change. No such evidence exists in any consulted source: ClinVar VCV000473668 classifies NM_006231.4:c.4501G>A (p.Gly1501Arg) as Uncertain significance with 2 clinical laboratory submissions and no expert panel; COSMIC has no record for POLE c.4501G>A; OncoKB reports 'Unknown Oncogenic Effect' with no variant-specific reviewed evidence; and the variant is absent from the León-Castillo et al. 2020 recurrent-variant and in silico supplementary tables. The amino acid change p.Gly1501Arg is therefore not established as pathogenic through any nucleotide change, so PS1 is not met. Note: the conclusion rests on curated databases and the framework package; a dedicated literature search for alternate-nucleotide records producing p.Gly1501Arg was not performed.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PS1 - 'Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.' Not customized by the León-Castillo POLE framework (which customizes only PM1, PS4, PP3, BP4).
Evidence considered
ClinVar VCV000473668: NM_006231.4(POLE):c.4501G>A (p.Gly1501Arg) classified Uncertain significance; 2 clinical laboratory submissions (Labcorp/Invitae SCV000653294, Ambry SCV005928726); 0 expert panel submissions; cited PMID 28492532 is the Sherloc methods paper, not variant evidence.
COSMIC search 'POLE c.4501G>A': no result found; variant not previously reported in somatic cancers.
León-Castillo et al. 2020 (PATH-250-323.pdf and supplementary tables S1-S3): no mention of residue 1501 or p.Gly1501Arg; no established-pathogenic same-amino-acid record.
Still missing
No dedicated literature search for alternate nucleotide changes producing p.Gly1501Arg was performed; determination is based on ClinVar (VUS, 2 labs, no expert panel), COSMIC (absent), OncoKB (unknown oncogenic effect), and León-Castillo supplementary tables (absent).
PS4Not met: the variant is absent from the Leon-Castillo recurrent-variant table and COSMIC, failing the somatic-recurrence rule.
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Reasoning
Governing framework is the local custom POLE framework (León-Castillo et al. 2020, J Pathol 250:323-335; framework label 'leon-castillo-2020-custom-framework-v1'), which customizes PS4 as a somatic-recurrence adaptation capped at Supporting. Its rule requires the exact variant to be recurrent in BOTH the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, with combined EC count >=10, and membership in the established/pathogenic set (p.P286R, p.V411L, p.A456P, p.S297F). NM_006231.4:c.4501G>A (p.Gly1501Arg) is absent from Supplementary Table S1 in its entirety (the table lists >100 recurrent POLE variants with counts and G1501R is not among them), absent from the COSMIC search (no_result), absent from the main paper text (grep of full text for 1501/4501: no hits), and is not one of the five established exonuclease-domain hotspots. The framework rule is therefore not met. Generic ACMG/AMP 2015 PS4 (germline case-control enrichment) could not be evaluated: no germline case-control study, no proband counts, and no publication reporting this variant were identified in the case bundle; the only full-text paper (PMID:25394175, an ACMG/NSGC referral-indications guideline) does not mention the variant, and the PMID cited in the Labcorp ClinVar submission (28492532, Sherloc) is a criteria-refinement methods paper with no variant-specific data. No PS4 evidence exists for this variant.
Rule
Custom POLE framework (León-Castillo et al. 2020) PS4 rule: 'Apply PS4_Supporting only when the exact POLE missense variant is recurrent in both the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, has a combined EC count >=10, and belongs to the established/pathogenic set (p.P286R, p.V411L, p.A456P, p.S297F)'; capped at Supporting. Generic ACMG/AMP 2015 PS4 (PMID 25741868) as fallback for germline case-control enrichment.
Evidence considered
POLE custom framework PS4 rule (León-Castillo et al. 2020): Supporting only, requires exact-variant recurrence in both COSMIC and TCGA EC cohorts (Supplementary Table S1), combined EC count >=10, established set p.P286R/p.V411L/p.A456P/p.S297F.
Supplementary Table S1 (PATH-250-323-s002.xlsx): p.Gly1501Arg / c.4501G>A absent from the full recurrent-variant list (top entries p.P286R c.857C>G 160+21=181; p.V411L c.1231G>T 101+13=114).
León-Castillo et al. 2020 main text (PATH-250-323.pdf): full-text search for 1501/4501 returned no hits; variant not among the five hotspot POLE mutations.
ClinVar VCV000473668: Uncertain significance, 2 clinical-laboratory submissions; no case-control or case-count data.
PMID:25394175 (ACMG/NSGC referral guideline): full text checked; no mention of POLE or this variant; provides no PS4 support.
Still missing
No germline case-control dataset (affected vs. control allele counts) for POLE c.4501G>A / p.Gly1501Arg was identified; generic ACMG PS4 cannot be assessed from available evidence.
No publication reporting this exact variant in affected individuals was found in the case bundle.
PM1Not met: residue 1501 lies outside the exonuclease proofreading domain (residues 286-459) containing all established hotspots.
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Reasoning
The governing custom POLE framework (León-Castillo et al. 2020) specifies PM1 only for exact substitutions: Strong tier = p.P286R, p.V411L, p.S297F, p.A456P, p.S459F (established exonuclease-domain hotspots); Moderate tier = p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y (POLE-score >=4 / pathogenic tier); Supporting tier = p.A465V, p.L424V, p.T278M, p.A428T (POLE-score 3 / uncertain tier). p.Gly1501Arg is not in any tier, so generic ACMG/AMP 2015 PM1 applies. Residue 1501 lies far outside the POLE exonuclease (proofreading) domain, which spans the N-terminal region containing the hotspots (residues 286-459); the paper states 'Only 1/23 (4%) tumours with non-EDM showed these genomic alterations, indicating that a large majority of mutations outside the exonuclease domain are not pathogenic.' CancerHotspots reports no statistically significant hotspot for POLE G1501, COSMIC has no entry for this variant, and ClinVar contains no supporting pathogenic record. PM1 (mutational hotspot and/or critical well-established functional domain) is therefore not met.
Rule
León-Castillo custom PM1 (exact substitutions only): Strong = P286R, V411L, S297F, A456P, S459F; Moderate = F367S, L424I, M295R, P436R, M444K, D368Y; Supporting = A465V, L424V, T278M, A428T. G1501R not listed -> fallback generic ACMG/AMP 2015 (PMID 25741868) PM1: 'Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation.'
Evidence considered
León-Castillo et al. 2020 PDF: five established pathogenic exonuclease-domain hotspot missense variants (P286R, V411L, S297F, A456P, S459F); non-exonuclease-domain mutations largely not pathogenic (1/23 = 4% of non-EDM tumors showed the POLE-ultramutated signature).
Supplementary Table S1: recurrent POLE variants with COSMIC/TCGA EC counts; G1501R absent from the entire table (no residue-1501 entry); nearest polymerase-region entries are singletons (e.g., V1514A n=2).
Supplementary Table S2 (TCGA in silico results) and Table S3 (non-TCGA EC in silico results): no residue-1501 / G1501 entry (0 hits for '1501').
CancerHotspots query 'POLE G1501': no statistically significant hotspot (found=false).
COSMIC: no somatic report for POLE c.4501G>A, providing no recurrence support for hotspot status.
ClinVar: only record at residue 1501 is this variant, VUS; no pathogenic hotspot assignment.
Still missing
Precise exonuclease-domain residue boundaries are not stated numerically in the framework package; the conclusion relies on the hotspot residue range (286-459) in the paper and its explicit statement that mutations outside the exonuclease domain are largely non-pathogenic.
PP3Not met: REVEL 0.492 falls below the supporting threshold of 0.644, and SpliceAI max delta 0.01 shows no splice impact.
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Reasoning
Governing framework is the local custom gene framework for POLE ('León-Castillo et al. 2020 custom POLE framework'; no official ClinGen CSPEC for POLE was found). Its PP3_Supporting rule applies only when the exact missense variant appears in Supplementary Table S2 (PATH-250-323-s003.xlsx) or S3 (PATH-250-323-s004.xlsx) with REVEL class 'likely disease causing' and <=1 benign in-silico result. Direct inspection of both tables shows c.4501G>A / p.Gly1501Arg is NOT present, so the custom rule is not applicable and the framework's stated fallback (generic in-silico workflow) governs. Under the generic workflow, the only calibrated missense predictor available is REVEL = 0.492, which is below the PP3 supporting threshold of >=0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997), so the missense path does not support PP3. The splice path (SpliceAI Lookup) gives max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.0), far below the 0.2 high-sensitivity cutoff recommended in the SpliceAI publication (Jaganathan et al., Cell 2019, PMID 30661751), so there is no predicted splice impact supporting PP3. BayesDel score 0.0694247 was retrieved but has no verified published PP3/BP4 threshold available to this pipeline, so it is treated as insufficiently calibrated and contributes nothing. No line of computational evidence supports a deleterious effect; PP3 not met.
Rule
Custom POLE framework PP3 (León-Castillo et al. 2020): PP3_Supporting if exact variant in Table S2/S3 with REVEL class 'likely disease causing' and benign in-silico count <=1; if absent from tables, fall back to generic in-silico workflow (REVEL >=0.644 supporting, PMID 36413997; splice path via SpliceAI >=0.2, PMID 30661751).
Evidence considered
REVEL score 0.492 (source_registry key 'revel'; local REVEL v1.3 lookup at chr12:132643274 C>T, GRCh38); PP3 supporting threshold >=0.644 per Pejaver et al. 2022, Am J Hum Genet 109:2163-2178 (PMID 36413997, ClinGen SVI missense calibration); 0.492 is below the threshold, so REVEL does not support PP3.
SpliceAI max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.0; source_registry key 'spliceai'; SpliceAI Lookup for NM_006231.4:c.4501G>A, GRCh37, distance=500); below the 0.2 high-sensitivity cutoff recommended in Jaganathan et al., Cell 2019;176:535-548 (PMID 30661751); no predicted splice impact, does not support PP3.
BayesDel score 0.0694247 (source_registry key 'bayesdel'; BayesDel_170824_noAF_chr12.gz lookup at chr12:133219860 C>T, GRCh37); no verified published PP3/BP4 threshold available to this pipeline, therefore treated as insufficiently calibrated / not available; not used for PP3.
Custom POLE framework PP3 rule (León-Castillo et al. 2020, J Pathol 250:323-335; vcep_path_250_323 package): PP3_Supporting only when the exact variant appears in Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in-silico result; c.4501G>A (p.Gly1501Arg) is absent from both tables, so the custom rule is inapplicable and the generic in-silico workflow governs (per framework guardrail).
Still missing
BayesDel score (0.0694247) unusable: no verified published threshold (treated as not_available per calibration policy).
Only one calibrated missense predictor (REVEL) was retrieved; other tools (SIFT, PolyPhen2, PROVEAN, PANTHER, SNAP2, aGVGD) were not independently run for this variant in this case.
Variant absent from León-Castillo Supplementary Tables S2/S3, so the custom POLE PP3 rule (table-based) could not be applied; generic fallback used.
PP5Not met: ClinVar classifies this variant as Uncertain significance with no expert-panel submission.
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Reasoning
PP5 may be applied only for an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. An exact-match ClinVar record exists (VCV000473668, NM_006231.4(POLE):c.4501G>A p.Gly1501Arg), but the classification is Uncertain significance (2 clinical-laboratory submissions: Labcorp Genetics/Invitae SCV000653294 and Ambry Genetics SCV005928726, both 'criteria provided, single submitter'), with expert_panel_submissions = 0 and an empty expert_panels map. There is no expert-panel classification for this variant, so PP5 is not met. The ClinVar-tagged candidate paper PMID:25394175 is a general ACMG/NSGC referral guideline with no variant-specific assertion and cannot substitute for an expert-panel classification.
Rule
PP5/BP6 restriction rule: apply PP5 only for an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic (supporting strength); ordinary laboratory submissions and aggregate ClinVar labels never trigger PP5.
Submission audit: SCV000653294 and SCV005928726 both is_expert_panel = false, trust_tier 'single_submitter'.
PMID:25394175: full text contains no POLE or variant mention; no expert assertion for this variant.
Still missing
No ClinGen expert-panel (VCEP) classification exists for this variant; PP5 can only be applied if a Pathogenic/Likely pathogenic expert-panel classification is later submitted to ClinVar.
BA1Not met: highest observed allele frequency 0.00534% is roughly 300-fold below the 5% BA1 threshold.
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Reasoning
Highest observed allele frequency for NM_006231.4:c.4501G>A (p.Gly1501Arg) is 5.339e-05 (0.00534%, 4/74,924 alleles) in African/African American in gnomAD v4.1 and 1.641e-04 (0.01641%, 1/6,092 alleles, single allele) in Remaining individuals in gnomAD v2.1; overall gnomAD v4.1 AF is 9.295e-06 (0.00093%, 15/1,613,766 alleles). The highest observed AF is roughly 300x below the generic ACMG/AMP BA1 threshold of AF >=5% (0.05; Richards et al. 2015, PMID 25741868; ClinGen SVI recommendation Ghosh et al. 2018, PMID 30311386), so BA1 (stand-alone benign) is not met by several orders of magnitude. No ClinGen CSPEC exists for POLE and the local custom POLE framework (León-Castillo 2020) specifies population rules for none of BA1/BS1/BS2/PM2, so the generic ACMG/AMP fallback governs these criteria.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BA1 stand-alone benign requires allele frequency >=5% (0.05) in a reference population. Not met - max observed AF 1.641e-04 (0.0164%, single OTH allele, gnomAD v2.1).
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 9.295e-06 (15/1,613,766 alleles), 0 homozygotes; AFR subpopulation AF 5.339e-05 (4/74,924 alleles); joint grpmax FAF 1.746e-05
gnomAD v2.1 (gnomad_v2): total AF 8.045e-06 (2/248,590 alleles), 0 homozygotes; OTH subpopulation AF 1.641e-04 (1/6,092 alleles)
BA1 threshold AF >=5% (0.05) per Richards et al. 2015 (PMID 25741868) and ClinGen SVI (Ghosh et al. 2018, PMID 30311386); highest observed AF 1.641e-04 is ~300x below threshold
Still missing
No ClinGen CSPEC or POLE-specific VCEP population-frequency rule was retrieved; BA1 adjudicated under generic ACMG/AMP 2015 fallback thresholds only.
BS1Not met: gnomAD v4.1 frequency 0.00093% is about 1,000-fold below the 1% threshold and 60-100x below the 0.3% convention.
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Reasoning
BS1 requires an allele frequency greater than expected for the disorder (generic ACMG/AMP 2015, Richards et al. 2015, typically >1% (0.01); project non-VCEP gnomAD convention >0.3%). Observed frequencies are 9.295e-06 (0.00093%) overall in gnomAD v4.1 and 5.339e-05 (0.00534%) in the highest subpopulation (AFR) - roughly 60-100x below the most lenient 0.3% convention and ~1,000x below 1%. BS1 is not met.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS1 requires AF >1% (0.01) in a reference population (project non-VCEP gnomAD convention >0.3%). Not met - max observed AF 1.641e-04 (0.0164%).
Evidence considered
gnomAD v4.1 (gnomad_v4): total AF 9.295e-06 (0.00093%); max subpopulation (AFR) AF 5.339e-05 (0.00534%)
gnomAD v2.1 (gnomad_v2): total AF 8.045e-06 (0.00080%); max subpopulation (OTH) AF 1.641e-04 (0.0164%, 1 allele)
BS1 threshold >1% (0.01) per Richards et al. 2015 (PMID 25741868); project non-VCEP gnomAD convention >0.3% also not approached (max AF 0.0164%)
BS2Not met: zero homozygotes in gnomAD v2.1 and v4.1, and reference cohorts are not cancer-screened.
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Reasoning
BS2 requires observation in a healthy adult in the homozygous state for an autosomal dominant disorder. POLE-associated hereditary cancer predisposition (colorectal polyposis and cancer, endometrial cancer risk) is autosomal dominant, adult-onset, and incompletely penetrant. gnomAD v2.1 (2/248,590 alleles) and gnomAD v4.1 (15/1,613,766 alleles) both report 0 homozygotes; all carriers are heterozygous. Additionally, heterozygous carriers in gnomAD cannot satisfy BS2 for this dominant adult-onset cancer syndrome because reference cohorts are not screened for cancer phenotype and penetrance is reduced. BS2 is not met.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS2 requires observation in a healthy adult in the homozygous state for a dominant disorder. 0 homozygotes in gnomAD v2.1 and v4.1 - not met.
Evidence considered
gnomAD v4.1 (gnomad_v4): total homozygote count 0 across 15 alleles
gnomAD v2.1 (gnomad_v2): total homozygote count 0 across 2 alleles
BP1Not met: missense in the POLE exonuclease domain is an established disease mechanism, not primarily truncating variants.
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Reasoning
BP1 (missense variant in a gene for which primarily truncating variants are known to cause disease) is contradicted by the established biology of POLE. The governing framework package is built on pathogenic missense: León-Castillo et al. 2020 define five established pathogenic exonuclease-domain hotspot missense variants (P286R, V411L, S297F, A456P, S459F) causing the POLE-ultramutated phenotype, and OncoKB gene-level curation notes that germline heterozygous mutations in the POLE exonuclease/proofreading domain cause polyposis and colorectal cancer predisposition, with proofreading deficiency driving ultra-mutated tumors. Missense (particularly in the exonuclease domain) is therefore a well-established disease mechanism for POLE, not a gene with primarily truncating causation, so BP1 is not met.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): BP1 - 'Missense variant in a gene for which primarily truncating variants are known to cause disease.' No gene-specific BP1 customization in the León-Castillo framework.
Evidence considered
León-Castillo et al. 2020 PDF: five established pathogenic exonuclease-domain missense hotspots (P286R, V411L, S297F, A456P, S459F) are the core pathogenic variant class in POLE-ultramutated endometrial carcinoma - demonstrates missense is a common disease mechanism.
OncoKB POLE gene-level curated context: 'Select POLE mutations lead to ultra-high mutation rates, most frequently in endometrial and colorectal cancer'; germline exonuclease-domain mutations cause polyposis and predispose to colorectal cancer; alterations within the exonuclease domain result in the ultra-mutated phenotype.
gene_context summary: 'Germline mutations in POLE cause polyposis and predispose to colorectal cancer' with the proofreading (exonuclease) domain central to disease mechanism.
BP4Not met: REVEL 0.492 is far above the benign supporting threshold of 0.016.
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Reasoning
The custom POLE framework BP4_Supporting rule requires the exact missense variant to appear in Supplementary Table S2 or S3 with REVEL class 'Likely benign'/'Likely-benign' and >=4 benign in-silico results; direct inspection of both tables shows c.4501G>A / p.Gly1501Arg is absent, so the custom rule does not apply and the generic in-silico workflow governs. Under the generic workflow, REVEL = 0.492 is far above the BP4 supporting threshold of <=0.016 (Pejaver et al. 2022, PMID 36413997), so the single calibrated missense predictor actively argues against a benign computational profile. SpliceAI max delta 0.01 shows no splice impact, but a low splice score alone is not multiple independent lines of evidence that the gene product is unaffected (and the variant is missense, so the missense prediction is the primary path). BayesDel is uncalibrated (no verified published threshold) and contributes nothing. No line of calibrated computational evidence supports a benign effect; BP4 not met.
Rule
Custom POLE framework BP4 (León-Castillo et al. 2020): BP4_Supporting if exact variant in Table S2/S3 with REVEL class 'Likely benign' and benign in-silico count >=4; if absent from tables, fall back to generic in-silico workflow (REVEL <=0.016 supporting, PMID 36413997; multiple lines required).
Evidence considered
REVEL score 0.492 (source_registry key 'revel'; local REVEL v1.3 lookup at chr12:132643274 C>T, GRCh38); BP4 supporting threshold <=0.016 per Pejaver et al. 2022, Am J Hum Genet 109:2163-2178 (PMID 36413997, ClinGen SVI missense calibration); 0.492 is far above the threshold, so REVEL does not support BP4.
SpliceAI max delta score 0.01 (source_registry key 'spliceai'; SpliceAI Lookup for NM_006231.4:c.4501G>A, GRCh37, distance=500); consistent with no splice impact (below 0.2 high-sensitivity cutoff, Jaganathan et al., Cell 2019;176:535-548, PMID 30661751), but a single low splice score is not by itself multiple lines of computational evidence that the gene product is unaffected; not counted toward BP4.
BayesDel score 0.0694247 (source_registry key 'bayesdel'); no verified published PP3/BP4 threshold available to this pipeline, therefore treated as insufficiently calibrated / not available; not used for BP4.
Custom POLE framework BP4 rule (León-Castillo et al. 2020, J Pathol 250:323-335; vcep_path_250_323 package): BP4_Supporting only when the exact variant appears in Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in-silico results; c.4501G>A (p.Gly1501Arg) is absent from both tables, so the custom rule is inapplicable and the generic in-silico workflow governs (per framework guardrail).
Still missing
BayesDel score (0.0694247) unusable: no verified published threshold (treated as not_available per calibration policy).
Only one calibrated missense predictor (REVEL) was retrieved; additional benign-supporting tools (e.g., SIFT, PolyPhen2, PROVEAN, aGVGD) would be needed to establish 'multiple lines' of benign computational evidence.
Variant absent from León-Castillo Supplementary Tables S2/S3, so the custom POLE BP4 rule (table-based) could not be applied; generic fallback used.
BP6Not met: ClinVar classifies this variant as Uncertain significance with no expert-panel benign classification.
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Reasoning
BP6 may be applied only for an exact-variant ClinVar expert-panel classification of Benign/Likely benign; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. The exact-match ClinVar record VCV000473668 is classified Uncertain significance by two ordinary clinical laboratories (Labcorp Genetics/Invitae, Ambry Genetics; both single submitter), with expert_panel_submissions = 0 and empty expert_panels. No expert-panel classification exists for this variant, so BP6 is not met.
Rule
PP5/BP6 restriction rule: apply BP6 only for an exact-variant ClinVar expert-panel classification of Benign/Likely benign (supporting strength); ordinary laboratory submissions and aggregate ClinVar labels never trigger BP6.
Submission audit: both SCVs is_expert_panel = false.
Still missing
No ClinGen expert-panel (VCEP) classification exists for this variant; BP6 can only be applied if a Benign/Likely benign expert-panel classification is later submitted to ClinVar.
PS2Not assessed: no de novo occurrence of this variant in a tested proband is documented in any source.
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Reasoning
PS2 (de novo pathogenic, strong) requires a documented de novo occurrence of the variant in a proband with both parents tested and maternity/paternity confirmed. No de novo observation for NM_006231.4:c.4501G>A (p.Gly1501Arg) is documented in any source in this case record: the ClinVar submission audit (VCV000473668; Labcorp SCV000653294 and Ambry SCV005928726, both germline clinical testing, both VUS) extracted only PM2 (population) and PP3 (in silico) signals, with no de novo assertion; the literature packet contains no case report or proband study mentioning this variant; and the only full-text paper (PMID:25394175) is an ACMG/NSGC referral-indications guideline with no variant-specific content. No proband/parental testing data exist to even begin PS2 evaluation. Criterion falls back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868) because the governing local POLE custom framework (León-Castillo et al. 2020, PATH-250-323 package) customizes only PM1/PS4/PP3/BP4 and contains no segregation/de novo specification.
Rule
Generic ACMG/AMP 2015 PS2: de novo variant (confirmed maternity and paternity) in a patient with the disease and no family history — Richards et al. 2015, PMID 25741868 (no gene-specific PS2 rule in the governing POLE framework)
Evidence considered
ClinVar VCV000473668 submission audit: 2 germline clinical-testing submissions (Labcorp SCV000653294, Ambry SCV005928726), both Uncertain significance, single-submitter review status; evidence signals present are PM2 and PP3 only — no PS2/de novo assertion
Full text of PMID:25394175 reviewed (grep for c.4501G>A, p.Gly1501Arg, G1501R, segregation, de novo): zero matches; paper is an ACMG/NSGC referral-indications practice guideline, not a case report
Governing framework check: final_classification_framework.json (Leon-castillo-2020-custom-framework-v1) customizes PM1/PS4/PP3/BP4 only; PS2 falls back to generic ACMG/AMP 2015 (PMID 25741868)
Still missing
No proband case report with parental testing results is available; de novo status of c.4501G>A has never been assessed or reported
Maternity/paternity confirmation data (or lack thereof) not available for any carrier
No literature case series or segregation study mentioning this exact variant was retrieved
PS3Not assessed: no variant-specific functional study of p.Gly1501Arg exists; OncoKB reports no functional evidence.
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Reasoning
Governing framework: no ClinGen CSPEC exists for POLE (cspec.found=false); the local custom framework (León-Castillo et al. 2020, precedence_rank 2) customizes only PM1/PS4/PP3/BP4 and contains no PS3 specification, so PS3 falls back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PS3 (Strong) requires well-established functional studies demonstrating a deleterious effect. No variant-specific functional study of p.Gly1501Arg exists in any collected source. OncoKB explicitly states it did not identify variant-specific reviewed functional evidence for this variant (classification 'Unknown Oncogenic Effect', is_variant_specific=false, not_reviewed=true). ClinVar (VCV000473668, 2 clinical-lab submissions, both VUS) cites no functional criteria in either submission (evidence signals are PM2 population and PP3 in silico only). COSMIC has no entry and Cancer Hotspots has no row for this variant — both are somatic-recurrence observations, not functional assays. The León-Castillo package (vcep_path_250_323) confirms functional pathogenicity (causality for tumour ultramutation) only for the five exonuclease-domain hotspot mutations P286R, V411L, S297F, A456P, S459F; p.Gly1501Arg is absent from that paper (0 occurrences of 1501/4501/G1501) and lies in exon 35 of the C-terminal polymerase region, outside the exonuclease domain, so the paper's hotspot/ultramutation functional evidence cannot be applied to this variant. SpliceAI (max delta 0.01), REVEL (0.492) and BayesDel are in silico predictions, not functional assays, and cannot satisfy PS3. Evidence is insufficient to adjudicate; the criterion is returned as not_assessed with the gap identified.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PS3 (Strong) — well-established functional studies show a deleterious effect. No POLE-specific PS3 specification exists in the local custom framework (León-Castillo et al. 2020), which customizes only PM1/PS4/PP3/BP4.
Evidence considered
oncokb: explicitly reports no variant-specific reviewed functional evidence for POLE G1501R (Unknown Oncogenic Effect)
clinvar: VCV000473668 two VUS submissions; neither cites functional (PS3/BS3) criteria — PM2 and PP3 signals only; VUS classifications not used as evidence
spliceai: in silico splice prediction only (max delta 0.01); not a functional assay, cannot satisfy PS3
revel: in silico missense prediction (score 0.492); not functional evidence
vcep_path_250_323: León-Castillo et al. 2020 — functional confirmation restricted to five exonuclease-domain hotspots; p.Gly1501Arg absent from paper
PMID:25394175: full text reviewed; referral-indications practice guideline with no variant or functional data
generic_acmg_combination_rules: generic ACMG/AMP 2015 fallback (PMID 25741868) governing PS3 since no gene-specific PS3 rule exists
Still missing
No variant-specific well-established functional study for p.Gly1501Arg exists in any collected source (no polymerase activity/proofreading-fidelity assay, no replication-error or ultramutation phenotype assay, no yeast/complementation assay)
OncoKB confirms absence of variant-specific reviewed functional evidence; ClinVar submissions cite no functional criteria; the literature packet contains no functional paper for this variant
PM3Not assessed: no proband genotyping or phase data exist to test for a variant in trans with a pathogenic allele.
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Reasoning
PM3 requires (a) a recessive disorder context and (b) documentation that this variant is detected in trans with a pathogenic variant (or is homozygous). The governing framework for this case is the local custom POLE framework derived from Leon-Castillo et al. 2020 (vcep_path_250_323), which customizes only PM1, PS4, PP3, and BP4; PM3 is not specified there, so the generic ACMG/AMP 2015 rule (generic_acmg_combination_rules, PMID 25741868) applies. No proband-level evidence is available in this case bundle: no zygosity of c.4501G>A in any proband, no phase information, no second POLE variant, and no parental/family genotyping anywhere in ClinVar (VCV000473668, 2 clinical laboratories, both 'Uncertain significance', no expert panel), the literature packet, or the VCEP materials. POLE is associated with both dominant (polymerase proofreading-associated polyposis / hereditary cancer-predisposing syndrome) and recessive (FILS syndrome) phenotypes, so a recessive biallelic mechanism cannot be categorically excluded; however, no variant in trans (or homozygous observation) is documented to trigger PM3. The two ClinVar-cited PMIDs are a referral-indications guideline (25394175) and a criteria methodology paper (Sherloc, 28492532); neither contains variant-level or allelic observations and neither was used as evidence. Evidence insufficient: PM3 cannot be adjudicated without proband genotyping/phase data.
Rule
PM3 (ACMG/AMP 2015, Richards et al., PMID 25741868): For recessive disorders, detected in trans with a pathogenic variant.
Evidence considered
clinvar - VCV000473668 (2 submissions, both Uncertain significance, germline origin, single-submitter review status, no expert panel) contains no zygosity, phase, second-variant, or family data relevant to PM3
generic_acmg_combination_rules - source PMID 25741868 (Richards et al. 2015) provides the governing PM3 definition used here because the custom POLE framework does not specify PM3
final_classification_framework - local custom POLE framework (Leon-Castillo 2020) customizes PM1/PS4/PP3/BP4 only; PM3 and BP2 fall back to generic ACMG/AMP 2015
PMID:25394175 - full text checked; ACMG/NSGC referral-indications guideline with no variant-level or allelic content; not usable for PM3
Still missing
No proband zygosity data for c.4501G>A (heterozygous vs homozygous)
No second POLE variant identified in any proband to test trans/cis configuration
No parental testing or family phase/segregation data
No explicit recessive (biallelic) disease context established for the proband in this case bundle
PM5Not assessed: no pathogenic comparator at residue 1501 was found, though its absence is not comprehensively confirmed.
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Reasoning
PM5 requires a different missense change at residue 1501 (e.g., p.Gly1501X) previously determined pathogenic. The pipeline's PM5 candidate artifact (pm5_candidates.json) reports found=false, pm5_mode 'unknown', eligible_for_classic_pm5_search=false, and 0 same-residue candidates, with recommendation level 'not_applicable' and an instruction not to apply PM5 from the artifact alone. Consistent with that, no different missense at residue 1501 appears in any consulted source: ClinVar contains only this variant (VUS) at residue 1501, COSMIC has no record, OncoKB has no variant-specific evidence, and the León-Castillo supplementary tables contain no residue-1501 entries (0 hits). Because the dedicated same-residue comparator search was skipped, absence of a pathogenic comparator at residue 1501 is not comprehensively established, so PM5 is recorded as not_assessed pending review rather than not_met.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): PM5 - 'Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.' No gene-specific PM5 customization in the León-Castillo framework.
ClinVar VCV000473668: the only variant at residue 1501 is c.4501G>A (p.Gly1501Arg), classified VUS; no other missense at residue 1501 with a pathogenic classification.
COSMIC: no record for this variant; no other residue-1501 variants reported in the searched records.
Supplementary Table S1: no variant at residue 1501 in the recurrent POLE variant list (nearest recurrent variant is p.V1514A at residue 1514, n=2).
Still missing
Automatic same-residue (p.Gly1501X) comparator search was skipped by the pipeline (pm5_candidates: mode 'unknown', eligible_for_classic_pm5_search=false). No pathogenic different missense at residue 1501 was identified in ClinVar, COSMIC, OncoKB, or the León-Castillo supplementary tables; a dedicated same-residue literature/database search is needed before PM5 can be adjudicated.
PM6Not assessed: no de novo occurrence is documented with or without parentage confirmation.
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Reasoning
PM6 (assumed de novo, moderate) applies to a de novo occurrence without confirmation of maternity/paternity. No de novo occurrence of NM_006231.4:c.4501G>A is reported anywhere in this case record, with or without parentage confirmation: neither ClinVar submission asserts de novo origin, no proband report exists in the literature packet, and the only available full-text paper (PMID:25394175) contains no variant-specific data. Because no de novo event is documented at all, PM6 cannot be applied. Adjudicated under generic ACMG/AMP 2015 (PMID 25741868); the governing POLE custom framework provides no PM6 specification.
Rule
Generic ACMG/AMP 2015 PM6: assumed de novo, without confirmation of paternity and maternity — Richards et al. 2015, PMID 25741868 (no gene-specific PM6 rule in the governing POLE framework)
Evidence considered
ClinVar VCV000473668 submission audit: no de novo or PM6 evidence signal in either submission (only PM2 and PP3 extracted)
Full text of PMID:25394175 reviewed: no mention of c.4501G>A, p.Gly1501Arg, or de novo occurrence
Governing framework check: final_classification_framework.json customizes PM1/PS4/PP3/BP4 only; PM6 falls back to generic ACMG/AMP 2015 (PMID 25741868)
Still missing
No de novo occurrence documented for this variant in any proband (confirmed or assumed)
Parental testing results unavailable for any observed carrier
No case-level literature (e.g., exome/tumor-susceptibility cohort reports) mentioning this exact variant was retrieved
PP1Not assessed: no segregation or family-testing data document any informative meiosis.
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Reasoning
PP1 (co-segregation with disease in affected family members, supporting) requires at least one informative meiosis demonstrating that affected relatives carry the variant. No segregation study, pedigree, or family testing data for NM_006231.4:c.4501G>A exist in this case record: no affected relatives are reported as tested in either ClinVar submission, no segregation paper was retrieved by the literature pass (criteria_index lists only PP5/PS4 candidates, and no segregation-themed paper exists), and the single full-text paper (PMID:25394175) is a referral guideline with no variant content. With zero informative meioses documented, PP1 is not assessable. Adjudicated under generic ACMG/AMP 2015 (PMID 25741868); the governing POLE custom framework has no PP1 specification.
Rule
Generic ACMG/AMP 2015 PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease — Richards et al. 2015, PMID 25741868 (no gene-specific PP1 rule in the governing POLE framework)
Evidence considered
ClinVar VCV000473668 submission audit: no segregation or family-testing assertion in either submission
literature_pass.json: total 2 PMIDs, none segregation-themed; criteria_index maps only PP5 and PS4 candidates; no PP1 candidate papers
Full text of PMID:25394175 reviewed: no segregation data relevant to this variant
Governing framework check: final_classification_framework.json customizes PM1/PS4/PP3/BP4 only; PP1 falls back to generic ACMG/AMP 2015 (PMID 25741868)
Still missing
No family segregation testing data (affected relatives not tested or not reported) for this variant
Zero informative meioses available to support or refute co-segregation
No segregation-focused publication mentioning c.4501G>A was identified in the literature pass
PP2Not assessed: no gene-level missense constraint data (e.g., gnomAD Z-score) are available to evaluate this rule.
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Reasoning
PP2 requires a gene with (a) a low rate of benign missense variation and (b) missense as a common mechanism of disease. While POLE missense in the exonuclease domain is a known germline disease mechanism (polymerase proofreading-associated polyposis), the case bundle contains no gene-level missense constraint data (no gnomAD gene missense Z-score or observed/expected metric, no HCI prior - hci_prior found=false, reason 'gene_not_supported'), no official ClinGen CSPEC/VCEP for POLE, and the custom León-Castillo framework does not specify PP2 (it customizes PM1, PS4, PP3, BP4 only). The 'low rate of benign missense variation' gene-level requirement therefore cannot be evaluated from available evidence, so PP2 is not_assessed.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): PP2 - 'Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease.' No gene-specific PP2 customization in the León-Castillo framework.
Evidence considered
No usable gene-level missense constraint evidence available in the case bundle for POLE (hci_prior: found=false, gene_not_supported; no gnomAD gene constraint metrics included; custom framework has no PP2 rule).
Still missing
No gene-level missense constraint data (e.g., gnomAD gene missense Z-score / missense observed-expected ratio) present in the case bundle; no official VCEP PP2 specification; HCI prior not available (gene_not_supported).
PP4Not assessed: no phenotype or family-history data for any carrier are available.
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Reasoning
PP4 (phenotype or family history highly specific for a disease with a single genetic etiology) requires proband phenotype and family-history data. The case bundle contains no phenotype information for any carrier of POLE c.4501G>A / p.Gly1501Arg: ClinVar submissions carry no condition labels (API conditions lists are empty for both SCVs; one record lists 'not provided'), no proband description, no tumor/age-at-onset details, and no family history are present in prefetch.json, evidence.json, case_summary.json, or the literature. The custom POLE framework does not define a PP4 rule, so generic ACMG/AMP 2015 applies, but the underlying data are absent. PP4 is therefore not assessable from available evidence.
Rule
Generic ACMG/AMP 2015 PP4 (PMID 25741868): 'Phenotype or family history highly specific for a disease with a single genetic etiology'; no custom POLE framework rule defined for PP4.
Evidence considered
ClinVar VCV000473668: conditions for both submissions empty ('not provided' on one record); no phenotype detail captured.
Evidence bundle scan: no phenotype, family-history, or proband descriptors present in any bundled file.
Still missing
No proband phenotype or personal cancer history data for carriers of this variant.
No family history / pedigree data available.
No ClinVar condition-specific phenotype mapping (conditions empty or 'not provided').
BS3Not assessed: no well-established functional study shows a lack of damaging effect for p.Gly1501Arg.
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Reasoning
Governing framework: no ClinGen CSPEC exists for POLE; the local custom framework (León-Castillo et al. 2020) contains no BS3 specification, so BS3 falls back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS3 (Strong) requires well-established functional studies showing no damaging effect on protein function or splicing. No such study exists for p.Gly1501Arg. SpliceAI predicts no significant splice impact (max delta 0.01), but this is an in silico prediction, not a well-established functional study, and cannot satisfy BS3 on its own. OncoKB reports no variant-specific functional evidence; neither ClinVar submission cites a functional criterion. The León-Castillo paper's observation that most non-exonuclease-domain POLE mutations lack the ultramutated genomic phenotype ('Only 1/23 (4%) tumours with non-EDMs showed these genomic alterations, indicating that a large majority of mutations outside the exonuclease domain are not pathogenic') is a cohort-level contextual finding and is not a functional assay of G1501R; it cannot be used as BS3 evidence. REVEL (0.492) and BayesDel are in silico and likewise cannot substitute for a functional assay. Evidence is insufficient to adjudicate; the criterion is returned as not_assessed with the gap identified.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS3 (Strong) — well-established functional studies show no damaging effect on protein function or splicing. No POLE-specific BS3 specification exists in the local custom framework (León-Castillo et al. 2020), which customizes only PM1/PS4/PP3/BP4.
Evidence considered
oncokb: no variant-specific functional evidence identified; nothing to support a benign functional effect
clinvar: VCV000473668 two VUS submissions; no functional criteria cited (PM2 and PP3 signals only)
spliceai: in silico splice prediction (max delta 0.01); insufficient alone for BS3, which requires well-established functional studies
revel: in silico missense prediction (score 0.492); not functional evidence
vcep_path_250_323: non-EDM cohort observation is contextual and variant-agnostic; not a functional assay of G1501R
PMID:25394175: full text reviewed; no functional data relevant to BS3
generic_acmg_combination_rules: generic ACMG/AMP 2015 fallback (PMID 25741868) governing BS3 since no gene-specific BS3 rule exists
Still missing
No well-established functional study demonstrating normal function for p.Gly1501Arg (no enzyme-activity/fidelity assay showing wild-type-like function, no complementation assay)
SpliceAI max delta 0.01 indicates no predicted splice impact but is computational; a published functional assay would be required to support BS3
BS4Not assessed: no affected relative has been tested and shown not to carry the variant.
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Reasoning
BS4 (non-segregation with disease in affected family members, benign supporting) requires an affected family member who does NOT carry the variant, establishing absence of segregation. No family non-segregation data exist for NM_006231.4:c.4501G>A: no affected relatives have been tested and reported as variant-negative in either ClinVar submission, and no segregation study was retrieved. Population carrier counts (gnomAD v2.1: 2/248,590 alleles, 0 homozygotes; gnomAD v4.1: 15/1,613,766 alleles, 0 homozygotes) are population-frequency evidence relevant to BS1/BA1/PM2 and cannot substitute for family non-segregation, so they were deliberately not used for BS4. Adjudicated under generic ACMG/AMP 2015 (PMID 25741868); the governing POLE custom framework has no BS4 specification.
Rule
Generic ACMG/AMP 2015 BS4: non-segregation with disease in affected family members — Richards et al. 2015, PMID 25741868 (no gene-specific BS4 rule in the governing POLE framework)
Evidence considered
ClinVar VCV000473668 submission audit: no BS4/non-segregation assertion in either submission
Full text of PMID:25394175 reviewed: no family non-segregation data relevant to this variant
gnomAD v2.1 and v4.1 reviewed for context only: carrier alleles present (0 homozygotes) — noted as population-frequency evidence, explicitly NOT applied to BS4
Governing framework check: final_classification_framework.json customizes PM1/PS4/PP3/BP4 only; BS4 falls back to generic ACMG/AMP 2015 (PMID 25741868)
Still missing
No affected family members tested and reported as non-carriers for this variant
No family segregation/non-segregation study available for c.4501G>A
Cannot distinguish BS4 (family non-segregation) from population-frequency arguments without pedigree data
BP2Not assessed: no second POLE variant or phase data exist to establish cis/trans configuration.
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Reasoning
BP2 requires a documented allelic configuration: observed in trans with a pathogenic variant for a fully dominant disorder, or observed in cis with a pathogenic variant in any inheritance pattern. The custom POLE framework (vcep_path_250_323) does not specify BP2, so the generic ACMG/AMP 2015 definition (generic_acmg_combination_rules, PMID 25741868) applies. No allelic configuration data exists in this case bundle: there is no proband observation at all (no zygosity, no co-occurring POLE variant, no phase), ClinVar (VCV000473668) provides only VUS classifications with no cis/trans assertions, and no publication in the case contains variant-level observations (the only full text available, PMID 25394175, is a referral guideline; the other ClinVar-cited PMID 28492532 is the Sherloc methodology paper). With no second variant and no phase data, neither the trans-with-pathogenic-variant (dominant) nor the cis-with-pathogenic-variant arm of BP2 can be evaluated. Evidence insufficient: BP2 cannot be adjudicated without proband genotyping/phase data.
Rule
BP2 (ACMG/AMP 2015, Richards et al., PMID 25741868): Observed in trans with a pathogenic variant for a fully dominant disease/disorder; or observed in cis with a pathogenic variant in any inheritance pattern.
Evidence considered
clinvar - VCV000473668 submissions (Labcorp SCV000653294; Ambry SCV005928726) assert no cis/trans or co-occurrence observations; not usable for BP2
generic_acmg_combination_rules - source PMID 25741868 (Richards et al. 2015) provides the governing BP2 definition used here because the custom POLE framework does not specify BP2
final_classification_framework - local custom POLE framework (Leon-Castillo 2020) customizes PM1/PS4/PP3/BP4 only; PM3 and BP2 fall back to generic ACMG/AMP 2015
PMID:25394175 - full text checked; no variant-level or allelic content; not usable for BP2
Still missing
No proband observation documenting the variant's allelic configuration
No second POLE variant to establish cis/trans relationship
No family segregation or parental phase data
No documentation that the disorder in this case is fully dominant (needed for the trans arm of BP2)
BP5Not assessed: no case-level information documents an alternate molecular basis in a carrier.
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Reasoning
BP5 (variant found in a case with an alternate molecular basis for disease) requires case-level evidence of a second, distinct molecular diagnosis in a carrier of this variant. No case-level information of any kind is available for POLE c.4501G>A / p.Gly1501Arg in the case bundle: no proband descriptions, no co-occurring pathogenic variants, no alternate-diagnosis reports in ClinVar (conditions empty/'not provided'), and no literature describing a carrier. The custom POLE framework defines no BP5 rule. BP5 is therefore not assessable from available evidence.
Rule
Generic ACMG/AMP 2015 BP5 (PMID 25741868): 'Variant found in a case with an alternate molecular basis for disease'; no custom POLE framework rule defined for BP5.
Evidence considered
Evidence bundle scan: no carrier case descriptions or alternate molecular diagnoses present in any bundled file.
Still missing
No proband case data documenting an alternate molecular basis of disease in a carrier of this variant.
No co-occurrence / multi-gene panel data for carriers of c.4501G>A.
Not applicable · 4· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: this is a missense substitution, not a null variant, so the loss-of-function criterion does not apply.
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Reasoning
PVS1 is scoped to null variants (nonsense, frameshift, canonical +/-1/2 splice-site, initiation codon, or single/multi-exon deletion) in a gene where loss of function is a known mechanism of disease (ClinGen SVI PVS1 recommendations, PMC6185798). NM_006231.4:c.4501G>A is a single-nucleotide substitution predicted to produce the missense change NP_006222.2:p.(Gly1501Arg); pvs1_variant_assessment records consequence_class 'missense', variant_bucket 'other', canonical_splice_consensus false, and apply_generic_pvs1_framework false, i.e. the variant does not fall into any default generic PVS1 null-variant bucket. SpliceAI predicts no significant splice impact (max delta 0.01), so no alternative splice-based loss-of-function mechanism is supported. Because the variant is a missense substitution rather than a null variant, PVS1 is not applicable and no PVS1 evidence is scored. The gene-level PVS1 eligibility question (lof_mechanism_supported) is moot for this variant class.
Rule
PVS1: null variant (nonsense, frameshift, canonical +/-1/2 splice-site, initiation codon, single/multi-exon deletion) in a gene where LOF is a known mechanism (ClinGen SVI PVS1, PMC6185798).
Evidence considered
pvs1_variant_assessment: consequence_class 'missense', variant_bucket 'other', canonical_splice_consensus false, apply_generic_pvs1_framework false - variant excluded from the generic PVS1 null-variant buckets
spliceai: max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.0) - no significant predicted splice impact
pvs1_generic_framework (PMC6185798): PVS1 null-variant scope definition used as the governing rule for this criterion
generic_acmg_combination_rules (ACMG/AMP 2015, PMID 25741868): governing fallback rule set, since the local POLE custom framework does not customize PVS1
PM4N/ANot applicable: single-nucleotide missense with no protein length change, so the in-frame indel/stop-loss criterion does not apply.
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Reasoning
PM4 (ACMG/AMP 2015, PMID 25741868) requires a protein length change resulting from an in-frame insertion/deletion in a non-repeat region or a stop-loss variant. NM_006231.4:c.4501G>A is a single-nucleotide substitution producing one amino acid change, NP_006222.2:p.(Gly1501Arg); transcript normalization (Mutalyzer) confirms no length alteration (position_last_original = position_last_predicted = 1501, i.e. translation continues to the same final residue), and the variant is not a stop-loss (the wild-type Gly1501 is not the termination codon). No in-frame indel and no stop-loss consequence is present, so PM4 is not applicable.
Rule
PM4: protein length changes as a result of in-frame insertion/deletion in a non-repeat region or stop-loss variants (ACMG/AMP 2015, PMID 25741868).
Evidence considered
generic_acmg_combination_rules (ACMG/AMP 2015, PMID 25741868): PM4 definition - protein length change from in-frame indel in a non-repeat region or stop-loss; governing fallback rule set since the local POLE custom framework does not customize PM4
pvs1_variant_assessment: variant classified as missense (NP_006222.2:p.(Gly1501Arg)), no indel or stop-loss consequence recorded
spliceai: max delta score 0.01 - no splice-altering consequence that could shift the reading frame or protein length
BP3N/ANot applicable: the variant is a missense substitution, not an in-frame insertion/deletion.
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Reasoning
BP3 (ACMG/AMP 2015, PMID 25741868) applies only to in-frame insertions/deletions located in repeat regions without known function. The queried variant is a single-nucleotide missense substitution (c.4501G>A, p.Gly1501Arg) in exon 35 of NM_006231.4, not an in-frame indel, and no functionally silent repeat-region context has been established at this locus. Because the variant is not an in-frame indel, BP3 is not applicable.
Rule
BP3: in-frame insertions/deletions in a repeat region without known function (ACMG/AMP 2015, PMID 25741868).
Evidence considered
generic_acmg_combination_rules (ACMG/AMP 2015, PMID 25741868): BP3 definition - in-frame indels in a repeat region without known function; governing fallback rule set since the local POLE custom framework does not customize BP3
pvs1_variant_assessment: variant is a missense substitution (p.(Gly1501Arg)), not an in-frame insertion/deletion
BP7N/ANot applicable: the variant is missense, not a synonymous change.
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Reasoning
BP7 applies to synonymous (silent) variants for which computational evidence suggests no impact on splicing or the gene product. NM_006231.4:c.4501G>A is a missense variant (NP_006222.2:p.(Gly1501Arg)) in exon 35 (c.4445-4551), not a synonymous change. BP7 is therefore not applicable to this variant, regardless of the low SpliceAI max delta score (0.01).
Rule
Generic ACMG/AMP BP7: synonymous variant (or intronic variant not at conserved splice sites) with no predicted splice impact; requires a synonymous variant - not applicable to missense p.(Gly1501Arg).
Evidence considered
Variant consequence established as missense: NM_006231.4:c.4501G>A -> NP_006222.2:p.(Gly1501Arg) (variant normalization); BP7 is defined for synonymous variants with no predicted splice impact, so it is not applicable here.
SpliceAI max delta 0.01 (source_registry key 'spliceai') confirms no predicted splice impact, but this is only relevant to BP7 for synonymous variants; the variant is missense, so BP7 remains not applicable.
AF 9.3e-06 · 15 / 1,613,766 alleles · 0 hom · FAF 1.7e-05
African/African American4 / 74,924
5.3e-05
Remaining individuals1 / 62,482
1.6e-05
European (Finnish)1 / 63,716
1.6e-05
South Asian1 / 91,094
1.1e-05
European (non-Finnish)8 / 1,180,044
6.8e-06
0 alternate alleles recorded in 5 other groups: Admixed American, Amish, East Asian, Middle Eastern, Ashkenazi Jewish.
gnomAD v2.1
AF 8e-06 · 2 / 248,590 alleles · 0 hom
Remaining individuals1 / 6,092
0.00016
South Asian1 / 30,584
3.3e-05
0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish).
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 9.29503e-06; MAF= 0.00093%, 15/1613766 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33874e-05; MAF= 0.00534%, 4/74924 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 8.04538e-06; MAF= 0.00080%, 2/248590 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.00016415; MAF= 0.01641%, 1/6092 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat +18 bp
0.010
SpliceAI acceptor gainat +442 bp
0.000
SpliceAI donor lossat +224 bp
0.000
SpliceAI donor gainat +443 bp
0.000
Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000
Other predictors
REVEL
0.492
BayesDel
0.069
How the predictions were used
PP3Not met: REVEL 0.492 falls below the supporting threshold of 0.644, and SpliceAI max delta 0.01 shows no splice impact.
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Reasoning
Governing framework is the local custom gene framework for POLE ('León-Castillo et al. 2020 custom POLE framework'; no official ClinGen CSPEC for POLE was found). Its PP3_Supporting rule applies only when the exact missense variant appears in Supplementary Table S2 (PATH-250-323-s003.xlsx) or S3 (PATH-250-323-s004.xlsx) with REVEL class 'likely disease causing' and <=1 benign in-silico result. Direct inspection of both tables shows c.4501G>A / p.Gly1501Arg is NOT present, so the custom rule is not applicable and the framework's stated fallback (generic in-silico workflow) governs. Under the generic workflow, the only calibrated missense predictor available is REVEL = 0.492, which is below the PP3 supporting threshold of >=0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997), so the missense path does not support PP3. The splice path (SpliceAI Lookup) gives max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.0), far below the 0.2 high-sensitivity cutoff recommended in the SpliceAI publication (Jaganathan et al., Cell 2019, PMID 30661751), so there is no predicted splice impact supporting PP3. BayesDel score 0.0694247 was retrieved but has no verified published PP3/BP4 threshold available to this pipeline, so it is treated as insufficiently calibrated and contributes nothing. No line of computational evidence supports a deleterious effect; PP3 not met.
Rule
Custom POLE framework PP3 (León-Castillo et al. 2020): PP3_Supporting if exact variant in Table S2/S3 with REVEL class 'likely disease causing' and benign in-silico count <=1; if absent from tables, fall back to generic in-silico workflow (REVEL >=0.644 supporting, PMID 36413997; splice path via SpliceAI >=0.2, PMID 30661751).
Evidence considered
REVEL score 0.492 (source_registry key 'revel'; local REVEL v1.3 lookup at chr12:132643274 C>T, GRCh38); PP3 supporting threshold >=0.644 per Pejaver et al. 2022, Am J Hum Genet 109:2163-2178 (PMID 36413997, ClinGen SVI missense calibration); 0.492 is below the threshold, so REVEL does not support PP3.
SpliceAI max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.0; source_registry key 'spliceai'; SpliceAI Lookup for NM_006231.4:c.4501G>A, GRCh37, distance=500); below the 0.2 high-sensitivity cutoff recommended in Jaganathan et al., Cell 2019;176:535-548 (PMID 30661751); no predicted splice impact, does not support PP3.
BayesDel score 0.0694247 (source_registry key 'bayesdel'; BayesDel_170824_noAF_chr12.gz lookup at chr12:133219860 C>T, GRCh37); no verified published PP3/BP4 threshold available to this pipeline, therefore treated as insufficiently calibrated / not available; not used for PP3.
Custom POLE framework PP3 rule (León-Castillo et al. 2020, J Pathol 250:323-335; vcep_path_250_323 package): PP3_Supporting only when the exact variant appears in Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in-silico result; c.4501G>A (p.Gly1501Arg) is absent from both tables, so the custom rule is inapplicable and the generic in-silico workflow governs (per framework guardrail).
Still missing
BayesDel score (0.0694247) unusable: no verified published threshold (treated as not_available per calibration policy).
Only one calibrated missense predictor (REVEL) was retrieved; other tools (SIFT, PolyPhen2, PROVEAN, PANTHER, SNAP2, aGVGD) were not independently run for this variant in this case.
Variant absent from León-Castillo Supplementary Tables S2/S3, so the custom POLE PP3 rule (table-based) could not be applied; generic fallback used.
BP4Not met: REVEL 0.492 is far above the benign supporting threshold of 0.016.
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Reasoning
The custom POLE framework BP4_Supporting rule requires the exact missense variant to appear in Supplementary Table S2 or S3 with REVEL class 'Likely benign'/'Likely-benign' and >=4 benign in-silico results; direct inspection of both tables shows c.4501G>A / p.Gly1501Arg is absent, so the custom rule does not apply and the generic in-silico workflow governs. Under the generic workflow, REVEL = 0.492 is far above the BP4 supporting threshold of <=0.016 (Pejaver et al. 2022, PMID 36413997), so the single calibrated missense predictor actively argues against a benign computational profile. SpliceAI max delta 0.01 shows no splice impact, but a low splice score alone is not multiple independent lines of evidence that the gene product is unaffected (and the variant is missense, so the missense prediction is the primary path). BayesDel is uncalibrated (no verified published threshold) and contributes nothing. No line of calibrated computational evidence supports a benign effect; BP4 not met.
Rule
Custom POLE framework BP4 (León-Castillo et al. 2020): BP4_Supporting if exact variant in Table S2/S3 with REVEL class 'Likely benign' and benign in-silico count >=4; if absent from tables, fall back to generic in-silico workflow (REVEL <=0.016 supporting, PMID 36413997; multiple lines required).
Evidence considered
REVEL score 0.492 (source_registry key 'revel'; local REVEL v1.3 lookup at chr12:132643274 C>T, GRCh38); BP4 supporting threshold <=0.016 per Pejaver et al. 2022, Am J Hum Genet 109:2163-2178 (PMID 36413997, ClinGen SVI missense calibration); 0.492 is far above the threshold, so REVEL does not support BP4.
SpliceAI max delta score 0.01 (source_registry key 'spliceai'; SpliceAI Lookup for NM_006231.4:c.4501G>A, GRCh37, distance=500); consistent with no splice impact (below 0.2 high-sensitivity cutoff, Jaganathan et al., Cell 2019;176:535-548, PMID 30661751), but a single low splice score is not by itself multiple lines of computational evidence that the gene product is unaffected; not counted toward BP4.
BayesDel score 0.0694247 (source_registry key 'bayesdel'); no verified published PP3/BP4 threshold available to this pipeline, therefore treated as insufficiently calibrated / not available; not used for BP4.
Custom POLE framework BP4 rule (León-Castillo et al. 2020, J Pathol 250:323-335; vcep_path_250_323 package): BP4_Supporting only when the exact variant appears in Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in-silico results; c.4501G>A (p.Gly1501Arg) is absent from both tables, so the custom rule is inapplicable and the generic in-silico workflow governs (per framework guardrail).
Still missing
BayesDel score (0.0694247) unusable: no verified published threshold (treated as not_available per calibration policy).
Only one calibrated missense predictor (REVEL) was retrieved; additional benign-supporting tools (e.g., SIFT, PolyPhen2, PROVEAN, aGVGD) would be needed to establish 'multiple lines' of benign computational evidence.
Variant absent from León-Castillo Supplementary Tables S2/S3, so the custom POLE BP4 rule (table-based) could not be applied; generic fallback used.
BP7N/ANot applicable: the variant is missense, not a synonymous change.
Details ▾Hide ▴
Reasoning
BP7 applies to synonymous (silent) variants for which computational evidence suggests no impact on splicing or the gene product. NM_006231.4:c.4501G>A is a missense variant (NP_006222.2:p.(Gly1501Arg)) in exon 35 (c.4445-4551), not a synonymous change. BP7 is therefore not applicable to this variant, regardless of the low SpliceAI max delta score (0.01).
Rule
Generic ACMG/AMP BP7: synonymous variant (or intronic variant not at conserved splice sites) with no predicted splice impact; requires a synonymous variant - not applicable to missense p.(Gly1501Arg).
Evidence considered
Variant consequence established as missense: NM_006231.4:c.4501G>A -> NP_006222.2:p.(Gly1501Arg) (variant normalization); BP7 is defined for synonymous variants with no predicted splice impact, so it is not applicable here.
SpliceAI max delta 0.01 (source_registry key 'spliceai') confirms no predicted splice impact, but this is only relevant to BP7 for synonymous variants; the variant is missense, so BP7 remains not applicable.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.492. BayesDel score = 0.0694247.
1 paper record listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
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.
Hampel H et al. · 2015
ACMG/NSGC practice guideline defining personal and family history referral indications for cancer genetic consultation. It is a methodology/guideline document, not a case report or segregation study. Systematic screen of the full text for the queried variant (c.4501G>A, p.Gly1501Arg, G1501R) and for segregation/de novo/parental-testing content returned zero matches, so it provides no evidence for or against PS2, PM6, PP1, or BS4. It was consulted solely to rule out hidden variant-specific family data and does not support any criterion in this group.
the purpose of this practice guideline is to present a single set of comprehensive personal and family history criteria to facilitate identification and maximize appropriate referral of at-risk individuals for cancer genetic consultation.
Full text (publications/25394175.txt), introduction, lines 17-20; document header 'ACMG Practice Guidelines'
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.115 / 1,613,766 recorded allelesOpen source ↗
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 9.29503e-06; MAF= 0.00093%, 15/1613766 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33874e-05; MAF= 0.00534%, 4/74924 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 8.04538e-06; MAF= 0.00080%, 2/248590 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.00016415; MAF= 0.01641%, 1/6092 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 473668)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.492. BayesDel score = 0.0694247.
Functional
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
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
This variant was interpreted by pipeline 7.1.0.
The current version is 11.0.07.
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