POLE c.590G>T, p.(Arg197Met)

Reasoning

PM2 is met at Supporting strength because the exact POLE variant NM_006231.4:c.590G>T (p.Arg197Met) was absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. The database extracts report absence but do not provide coverage, ancestry-specific counts, or sample denominators, so the result should not be upgraded beyond Supporting without review of those details and the relevant disease prevalence and penetrance model.

Rule

Generic ACMG/AMP PM2, applied at Supporting strength: the variant is absent from or extremely rare in population databases appropriate for the disease context. No applicable POLE-specific PM2 specification was retrieved; the local POLE framework customizes PM1, PS4, PP3, and BP4 only.

Evidence considered

• The case bundle reports the exact variant as absent from gnomAD v2.1.
• The case bundle reports the exact variant as absent from gnomAD v4.1.
• The case bundle reports the exact variant as absent from gnomAD-Canada v1.0.
• This supports rarity in population reference datasets, but absence alone does not establish disease mechanism, penetrance, or a disease-specific maximum credible allele frequency.

Still missing

• Allele-count, allele-number, coverage, and ancestry-stratified details were not included in the database extracts.
• The disease-specific maximum credible allele frequency and penetrance model were not provided.

Sources

Reasoning

BP4_Supporting is met by calibrated missense computational evidence. The variant is p.Arg197Met and is absent from the local POLE supplementary tables, so no local pre-assigned BP4 code applies. REVEL is 0.224, below the ClinGen SVI BP4 supporting threshold of 0.290. PP3 is not concurrently applied.

Rule

Local POLE BP4 rule did not apply because the exact variant is absent from Supplementary Table S2 and S3; generic missense REVEL calibration supports BP4_Supporting at REVEL <=0.290 (PMID:36413997).

Evidence considered

• No ClinGen CSPEC was retrieved for POLE. The applicable local POLE BP4 rule requires the exact missense variant to appear in Supplementary Table S2 or S3 with REVEL class 'Likely benign'/'Likely-benign' and at least four benign in-silico results; direct review found p.Arg197Met/c.590G>T absent from both tables, requiring generic fallback.
• The case REVEL lookup reports 0.224 for NM_006231.4:c.590G>T (p.Arg197Met).
• ClinGen SVI's calibrated REVEL thresholds (PMID:36413997) use REVEL <=0.290 for BP4 supporting evidence; 0.224 meets this threshold.
• SpliceAI maximum delta is 0.068, but it is not combined with the missense REVEL result and was not used to duplicate BP4 evidence.
• BayesDel score -0.460088 was not used because this pipeline has no verified published BayesDel calibration threshold.

Sources

Reasoning

NM_006231.4:c.590G>T is a MANE Select exonic missense substitution, predicting p.(Arg197Met), not a nonsense, frameshift, or canonical ±1/2 splice variant. It therefore does not meet the generic PVS1 null-variant entry criteria.

Rule

Generic ACMG/AMP PVS1 with ClinGen SVI PVS1 decision framework: PVS1 is restricted to predicted loss-of-function variant classes after gene- and transcript-level assessment.

Evidence considered

• Variant normalization identifies NM_006231.4:c.590G>T as NP_006222.2:p.(Arg197Met), a missense consequence in exon 7 of the MANE Select transcript.
• The generic ClinGen SVI PVS1 assessment scaffold places this variant in the 'other' bucket and states that it is not a default PVS1 null-variant type.
• Although the local PVS1 gene-context artifact labels POLE eligible for generic PVS1 assessment, that gate cannot make a missense substitution a loss-of-function variant.

Sources

Reasoning

The applicable local POLE framework permits PS4_Supporting only for an exact variant that is recurrent in both COSMIC and TCGA endometrial-carcinoma cohorts, has a combined count of at least 10, and is in the established/pathogenic set. POLE p.(Arg197Met) is not in that set and the case evidence reports no COSMIC result; no case-control enrichment data are available.

Rule

Local POLE PS4_Supporting requires exact-variant recurrence in both COSMIC and TCGA endometrial-carcinoma cohorts, combined count >=10, and membership in the established/pathogenic set; otherwise PS4 is not met.

Evidence considered

• The local POLE PS4 rule is limited to p.P286R, p.V411L, p.A456P, and p.S297F after requiring recurrence in both specified endometrial-carcinoma cohorts and a combined count of at least 10.
• The queried exact variant is POLE NM_006231.4:c.590G>T, p.(Arg197Met); it is not among the framework's eligible established/pathogenic variants.
• OncoKB reports no variant-specific reviewed evidence for POLE R197M, and the case literature packet contains no PMIDs.

Still missing

• No germline case-control cohort data or exact-variant case series were provided.

Sources

Reasoning

The applicable local POLE framework specifies PM1 only for exact listed exonuclease-domain hotspot or recurrent variants. p.Arg197Met is not one of the five established hotspot substitutions or the listed recurrent non-hotspot substitutions, and the case-specific hotspot search was negative. Therefore PM1 is not met under the governing custom framework.

Rule

Local POLE PM1 rule: apply only to the explicitly listed exact exonuclease-domain hotspot or recurrent substitutions, with the specified strength; do not generalize to all substitutions at a codon or throughout the domain.

Evidence considered

• The governing local framework lists PM1_Strong for p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F; PM1_Moderate for p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y; and PM1_Supporting for p.A465V, p.L424V, p.T278M, and p.A428T.
• The queried protein change is p.Arg197Met and does not match any exact variant in those PM1 rule sets.
• The Cancer Hotspots search returned no statistically significant hotspot for POLE R197.
• The local POLE package is contextual and not an official ClinGen CSPEC/VCEP specification; its explicit exact-variant PM1 rules nevertheless govern this case because no higher-priority specification was available.

Sources

Reasoning

The variant is a single-nucleotide missense substitution, p.(Arg197Met), with no change in protein length. It is neither an in-frame insertion/deletion nor a stop-loss variant and therefore does not meet PM4.

Rule

Generic ACMG/AMP PM4: apply only for protein length changes from in-frame insertions/deletions in a non-repeat region or stop-loss variants.

Evidence considered

• The normalized consequence is p.(Arg197Met); the reference and predicted protein sequences retain the same terminal residue position (197 for the affected amino acid comparison), consistent with a substitution rather than a protein-length alteration.

Sources

Reasoning

PP3 is not met. The variant is missense (p.Arg197Met), so the generic missense computational path uses REVEL rather than SpliceAI. p.Arg197Met was absent from both POLE supplementary in-silico tables and therefore has no pre-assigned local-framework PP3 result. Its REVEL score of 0.224 is below the pathogenic supporting calibration threshold.

Rule

Local POLE PP3 rule did not apply because the exact variant is absent from Supplementary Table S2 and S3; generic missense REVEL calibration was used (PMID:36413997).

Evidence considered

• No ClinGen CSPEC was retrieved for POLE. The applicable local POLE framework assigns PP3 only when the exact missense variant is present in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and no more than one benign in-silico result; direct review found p.Arg197Met/c.590G>T absent from both tables, requiring generic fallback.
• The case REVEL lookup reports 0.224 for NM_006231.4:c.590G>T (p.Arg197Met).
• ClinGen SVI's calibrated REVEL thresholds (PMID:36413997) use REVEL >=0.644 for pathogenic supporting computational evidence; 0.224 does not meet that threshold.
• SpliceAI maximum delta is 0.068, but this score is not independently used for a missense variant under the one-mechanism generic computational workflow.
• BayesDel score -0.460088 was not used because this pipeline has no verified published BayesDel calibration threshold.

Sources

Reasoning

The exact variant is absent from ClinVar. Consequently, there is no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification to support PP5.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar search for POLE NM_006231.4:c.590G>T returned no result and no matched variation ID.

Sources

Reasoning

BA1 is not met. NM_006231.4:c.590G>T (POLE p.Arg197Met) was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; no population frequency remotely approaches a stand-alone benign threshold.

Rule

Generic ACMG/AMP BA1: a population allele frequency is sufficiently high for a benign stand-alone criterion. No applicable POLE-specific population rule was retrieved.

Evidence considered

• The case bundle reports the exact variant as absent from gnomAD v2.1.
• The case bundle reports the exact variant as absent from gnomAD v4.1.
• The case bundle reports the exact variant as absent from gnomAD-Canada v1.0.
• Because the variant is absent rather than observed at a high allele frequency, BA1 cannot be applied.

Sources

Reasoning

BS1 is not met. The variant was absent from all three queried population resources, so there is no observed allele frequency above the disease-expected maximum credible frequency or other benign frequency threshold.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for a disorder. No applicable POLE-specific population rule was retrieved.

Evidence considered

• The case bundle reports no gnomAD v2.1 observation for the exact genomic variant.
• The case bundle reports no gnomAD v4.1 observation for the exact genomic variant.
• The case bundle reports no gnomAD-Canada v1.0 observation for the exact genomic variant.
• An absent variant cannot satisfy BS1, which requires an allele frequency that is higher than expected for the disorder.

Sources

Reasoning

BP3 is not met because p.(Arg197Met) is a missense substitution, not an in-frame insertion/deletion. Repeat-region context cannot satisfy BP3 in the absence of an in-frame protein-length change.

Rule

Generic ACMG/AMP BP3: apply only to an in-frame insertion/deletion in a repetitive region without a known function.

Evidence considered

• Variant normalization identifies an exonic missense substitution, p.(Arg197Met), with no insertion or deletion.

Sources

Reasoning

The exact variant is absent from ClinVar. Consequently, there is no exact-variant ClinVar expert-panel Benign or Likely benign classification to support BP6.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar search for POLE NM_006231.4:c.590G>T returned no result and no matched variation ID.

Sources

Reasoning

PS1 cannot be established because the case bundle contains no confirmed pathogenic variant producing the same amino-acid substitution p.Arg197Met through a different nucleotide change. The exact variant is absent from ClinVar, and no literature PMIDs or extracted paper findings were available for comparison.

Rule

Generic ACMG/AMP PS1: same amino-acid change as an established pathogenic variant caused by a different nucleotide change; apply only when the comparator pathogenicity is independently established.

Evidence considered

• The normalized variant is NP_006222.2:p.(Arg197Met) from NM_006231.4:c.590G>T.
• The case-specific ClinVar search returned no result for the exact variant.
• The literature pass found zero PMIDs and paper_extracts.json was empty, so no same-amino-acid pathogenic comparator could be verified.

Still missing

• A confirmed pathogenic p.Arg197Met variant caused by a different nucleotide change is not documented in the available evidence.

Sources

Reasoning

No proband-level de novo evidence or documented confirmed parental testing is present in the case-evidence bundle. PS2 cannot be assessed without verified maternity and paternity and demonstration that the variant is absent in both biological parents, with appropriate consideration of parental identity, mosaicism, and phenotype consistency.

Rule

Generic ACMG/AMP PS2: de novo occurrence in the affected proband with confirmed maternity and paternity; strength may depend on confirmation and phenotype consistency.

Evidence considered

• The consolidated case-evidence bundle contains no proband, parental-testing, parentage, or de novo observation data for NM_006231.4:c.590G>T (NP_006222.2:p.(Arg197Met)).
• The available case records report the variant as absent from ClinVar and population databases, but those observations do not establish a de novo event and were not used for PS2.

Still missing

• Proband phenotype and disease-context details
• Confirmed biological parentage
• Parental test results demonstrating absence of NM_006231.4:c.590G>T
• Testing methodology, coverage, and assessment for parental mosaicism

Reasoning

No validated disease-relevant functional assay data for POLE NM_006231.4:c.590G>T (NP_006222.2:p.Arg197Met) were identified in the case-evidence bundle. The available OncoKB result reports no variant-specific reviewed functional evidence, and no relevant paper extraction or PMID was available. Therefore PS3 cannot be applied or calibrated for strength.

Evidence considered

• The case bundle identifies the variant as NM_006231.4:c.590G>T, NP_006222.2:p.(Arg197Met), a missense substitution.
• OncoKB reports no variant-specific reviewed functional evidence for this variant; the available information is gene-level context rather than an assay result.
• The literature pass contains zero PMIDs and paper_extracts.json is empty, so no published functional study was available for review.
• The POLE local framework customizes PM1, PS4, PP3, and BP4 only; it provides no PS3 or BS3-specific assay rule. Generic ACMG/AMP functional evidence therefore requires direct, appropriately validated assay data.

Still missing

• A disease-relevant functional assay directly testing p.Arg197Met is needed.
• The assay should include appropriate wild-type, known pathogenic, and benign or functionally neutral controls, with quantitative results and reproducible methodology.
• The assay's biological relevance to POLE catalytic or proofreading function and its validation against clinically classified variants are not available.

Sources

Reasoning

No applicable POLE-specific PM3 rule was provided. Under generic ACMG/AMP, PM3 requires the variant to be observed in trans with a pathogenic or likely pathogenic variant in an affected individual for a recessive disorder, with strength determined by the quality and number of such observations. The case-evidence bundle contains no affected-proband observations, parental testing, phase determination, second pathogenic allele, or inheritance-mode evidence for this variant.

Rule

Generic ACMG/AMP PM3: apply only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive condition; assign strength according to the number and quality of independent, phase-confirmed observations.

Evidence considered

• The governing local POLE framework is explicitly limited to PM1, PS4, PP3, and BP4; it does not specify PM3, so generic ACMG/AMP PM3 semantics were used.
• The consolidated case-evidence bundle reports no literature PMIDs and provides no affected-proband, family-segregation, parental-phase, or second-allele observations relevant to PM3.

Still missing

• Affected-proband case observations are unavailable.
• No pathogenic or likely pathogenic second allele is documented.
• No parental testing or experimentally established cis/trans phase is documented.
• The relevant POLE inheritance mode for this case is not established in the bundle.

Reasoning

PM5 cannot be assessed because no independently established pathogenic missense comparator at residue Arg197 was identified. The case PM5 artifact reports zero collected same-residue candidates and explicitly states that classic PM5 semantics could not be safely confirmed.

Rule

Generic ACMG/AMP PM5: a novel missense change at a residue where a different missense change is established as pathogenic; the comparator must be independently classified and not merely reported as present.

Evidence considered

• The case-specific PM5 candidate artifact reports zero total candidates and zero same-residue candidates.
• That artifact recommends skipping automatic candidate harvesting and requires review of comparator pathogenicity before applying PM5.
• ClinVar returned no exact record for the queried variant, and the literature pass contained zero PMIDs.

Still missing

• A validated database or literature record for a different pathogenic missense substitution at POLE residue Arg197 is needed.

Sources

Reasoning

No unconfirmed de novo observations are documented in the case-evidence bundle. PM6 cannot be assessed without a reported de novo occurrence and supporting phenotype and family information when parentage or parental testing is incomplete.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in an affected individual when maternity and paternity are not confirmed and/or parental testing is unavailable or incomplete; supporting phenotype and case documentation are required.

Evidence considered

• The consolidated case-evidence bundle contains no case report, pedigree, proband observation, or parental result documenting a de novo NM_006231.4:c.590G>T event.
• No literature papers were identified in literature_pass.json, and paper_extracts.json is empty; therefore no publication-based de novo evidence was available for PM6.

Still missing

• Reported de novo occurrence in the proband
• Phenotype consistency with a POLE-associated disorder
• Available parentage and parental testing information
• Testing methodology and limitations

Reasoning

No familial pedigree, affected relatives, meioses, or variant-status observations in relatives are provided. Segregation cannot be assessed without informative relatives, phenotype classification, and confirmed testing results.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members; strength can be increased according to the number and informativeness of observed meioses under an applicable segregation framework.

Evidence considered

• The consolidated case-evidence bundle contains no family history, pedigree, segregation table, relative testing results, or meiosis count for NM_006231.4:c.590G>T.
• Population absence and database absence do not constitute cosegregation evidence and were not used for PP1.

Still missing

• Pedigree and number of informative meioses
• Phenotypes and diagnostic status of relatives
• Variant testing results in affected and unaffected relatives
• Assessment of phenocopies and reduced penetrance

Reasoning

PP2 cannot be assessed from this bundle. No applicable POLE-specific missense-mechanism rule or validated gene-level quantitative evidence demonstrating that pathogenic missense variation is common and benign missense variation is uncommon was provided. The available local HCI prior was unavailable, and the contextual POLE package does not establish a germline PP2 rule.

Rule

Generic ACMG/AMP PP2: missense variation is a common mechanism of disease in the gene and benign missense variation is uncommon; gene-level evidence must support both components.

Evidence considered

• The local POLE framework customizes PM1, PS4, PP3, and BP4, but does not provide a POLE-specific PP2 rule.
• The HCI prior was not available for POLE.
• Absence of the individual variant from gnomAD does not establish the gene-level PP2 requirement and was not used for PP2.

Still missing

• A validated POLE-specific or generic gene-level missense mechanism assessment with appropriate benign-variation context is needed.

Sources

Reasoning

No proband phenotype, diagnosis, family history, or phenotype-specificity assessment was provided. Therefore, it cannot be determined whether the phenotype is highly specific for a POLE-related condition.

Rule

Generic ACMG/AMP PP4: apply only when the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The consolidated case-evidence bundle contains variant and database evidence but no patient phenotype or diagnostic information.

Still missing

• Proband phenotype and clinical diagnosis.
• Assessment of phenotype specificity and differential diagnoses for the relevant POLE-associated condition.

Reasoning

BS2 cannot be assessed from the available evidence. The bundle provides population-database absence only; it does not document unaffected healthy adult carriers, homozygotes, or individuals with a phenotype incompatible with the relevant POLE disease mechanism.

Rule

Generic ACMG/AMP BS2: observation in healthy adults, including homozygous observation for a dominant disorder or hemizygous observation for an X-linked disorder, when incompatible with the disease model. No applicable POLE-specific population rule was retrieved.

Evidence considered

• gnomAD absence is not equivalent to observation of the variant in healthy adults and does not establish BS2.
• No case-level healthy-carrier, homozygote, penetrance, or phenotype-incompatibility data were present in the consolidated evidence bundle.

Still missing

• No documented unaffected healthy adult carriers or homozygous individuals were provided.
• No phenotype- or inheritance-specific assessment of an observed carrier was provided.

Reasoning

No validated disease-relevant functional assay demonstrating a normal effect for POLE NM_006231.4:c.590G>T (NP_006222.2:p.Arg197Met) was identified in the case-evidence bundle. The available OncoKB result reports no variant-specific reviewed functional evidence, and no relevant paper extraction or PMID was available. Therefore BS3 cannot be applied or calibrated for strength.

Evidence considered

• The case bundle identifies the variant as NM_006231.4:c.590G>T, NP_006222.2:p.(Arg197Met), a missense substitution.
• OncoKB reports no variant-specific reviewed functional evidence for this variant; absence of a reviewed assay does not establish a normal functional effect.
• The literature pass contains zero PMIDs and paper_extracts.json is empty, so no published functional study was available for review.
• The POLE local framework customizes PM1, PS4, PP3, and BP4 only; it provides no PS3 or BS3-specific assay rule. Generic ACMG/AMP functional evidence therefore requires direct, appropriately validated assay data.

Still missing

• A disease-relevant functional assay directly testing p.Arg197Met is needed to establish a normal functional effect.
• The assay should include appropriate wild-type, known pathogenic, and benign or functionally neutral controls, with quantitative results and reproducible methodology.
• Evidence that the tested assay endpoint is sufficiently sensitive and specific for POLE dysfunction is not available.

Sources

Reasoning

No informative affected or unaffected relatives with documented genotype and phenotype are available. Absence of segregation cannot be established from the case-evidence bundle, so BS4 is not assessable.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected family members, or presence in unaffected members when disease status and penetrance make that observation informative; adequate family data are required.

Evidence considered

• The consolidated case-evidence bundle provides no non-segregation observations, family pedigree, or genotype-phenotype data for relatives of the proband.
• The variant's absence from ClinVar and population databases does not demonstrate non-segregation and was not used for BS4.

Still missing

• Informative relatives tested for the variant
• Reliable disease phenotyping of those relatives
• Pedigree structure and expected inheritance model
• Evaluation for reduced penetrance, age-dependent expression, and phenocopies

Reasoning

BP1 cannot be assessed because the bundle does not provide a validated POLE-specific benign missense rule or sufficient evidence that POLE disease is predominantly caused by truncating variants while missense variation is not an established disease mechanism. The available material includes contextual missense-domain/hotspot discussion but no germline BP1 framework.

Rule

Generic ACMG/AMP BP1: missense variants are known to be a benign mechanism in a gene for which loss-of-function variants are the known disease-causing mechanism; apply only when the gene-level premise is established.

Evidence considered

• The governing local POLE framework does not specify BP1.
• The available POLE package discusses recurrent missense variants and exonuclease-domain hotspots in a somatic endometrial-carcinoma context, but does not establish the germline gene-level premise required for BP1.
• No gene-specific BP1 rule or validated benign missense-mechanism analysis was included in the case bundle.

Still missing

• A validated gene-specific assessment showing a primarily truncating disease mechanism with little or no established pathogenic missense mechanism is needed.

Sources

Reasoning

No applicable POLE-specific BP2 rule was provided. Under generic ACMG/AMP, BP2 requires observation of the variant in trans with a pathogenic variant for a fully penetrant dominant disorder or in cis with a pathogenic variant for a recessive disorder, as applicable. The case-evidence bundle contains no genotype-level observations, parental testing, phase determination, pathogenic comparator allele, or inheritance-mode evidence to evaluate BP2.

Rule

Generic ACMG/AMP BP2: apply only when the variant is observed in trans with a pathogenic variant in a fully penetrant dominant disorder or in cis with a pathogenic variant in a recessive disorder, with the applicable inheritance model and phase established.

Evidence considered

• The governing local POLE framework is explicitly limited to PM1, PS4, PP3, and BP4; it does not specify BP2, so generic ACMG/AMP BP2 semantics were used.
• The consolidated case-evidence bundle reports no literature PMIDs and provides no individual-level genotype, phase, parental, segregation, or inheritance observations relevant to BP2.

Still missing

• No documented cis/trans phase information is available.
• No pathogenic comparator variant is documented in the same individual or family.
• No affected/unaffected status or inheritance model is available to determine the applicable BP2 scenario.

Reasoning

No proband phenotype or independent molecular diagnosis was provided, so it is not possible to assess whether an alternate cause fully explains the presentation.

Rule

Generic ACMG/AMP BP5: consider only when a variant is found in a case with an alternate molecular basis for disease.

Evidence considered

• The consolidated case-evidence bundle contains no patient-level phenotype or co-occurring molecular-diagnosis information.

Still missing

• Proband phenotype and complete diagnostic workup.
• Results establishing or excluding an alternate molecular diagnosis that fully explains the phenotype.