POLE c.1794+19G>T, p.?

Reasoning

PM2 is met at Supporting strength because the variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and is only exceptionally rare in gnomAD v4.1 (2/1,568,238 alleles; total AF 1.27532e-06; maximum reported subpopulation AF 3.28267e-05), with no homozygotes. The frequency is below the generic rare-variant threshold of 0.1%.

Rule

PM2: absent or sufficiently rare in population databases for the disorder; applied here at Supporting strength for AF <0.1% under the generic operating rule.

Evidence considered

• The variant is absent from gnomAD v2.1.
• gnomAD v4.1 reports 2/1,568,238 total alleles, total AF 1.27532e-06, 0 homozygotes, and maximum reported subpopulation AF 3.28267e-05 from 2/60,926 alleles.
• The variant is absent from gnomAD-Canada v1.0.
• Generic PM2 operating threshold used: allele frequency below 0.1%; the observed total and maximum subpopulation frequencies are below this threshold.

Sources

Reasoning

The intronic variant has SpliceAI maximum delta 0.031, below the generic non-missense BP4 threshold (<0.1), predicting no significant splice impact. BP4_Supporting is met.

Rule

Generic ACMG non-missense BP4 fallback: SpliceAI maximum delta <0.1; local POLE missense-table rule not applicable.

Evidence considered

• The local POLE BP4 rule applies only to exact missense variants represented in Supplementary Table S2 or S3. The queried c.1794+19G>T intronic variant is absent from both reviewed tables, so the generic non-missense pathway applies.
• SpliceAI reports a maximum delta of 0.031 (DS_DG 0.031), below the generic BP4 threshold of 0.1 for intronic, synonymous, or non-canonical splice-position variants.

Sources

Reasoning

NM_006231.4:c.1794+19G>T is a deep intronic single-nucleotide substitution, not a predicted nonsense, frameshift, or canonical splice-site (±1/2) variant. It has no defined protein consequence (p.?), and SpliceAI maximum delta is 0.031, providing no prediction of a splice alteration that would create loss of function. PVS1 is not met.

Rule

Generic ClinGen SVI PVS1 framework: loss-of-function evidence requires a predicted or demonstrated null consequence; a non-canonical intronic substitution without predicted or observed splice disruption does not meet PVS1.

Evidence considered

• The local POLE framework does not specify PVS1; generic ClinGen SVI PVS1 guidance therefore applies.
• Variant normalization identifies c.1794+19G>T as intronic, 19 nucleotides from the donor-side exon boundary, with predicted protein consequence p.?.
• The PVS1 variant assessment identifies this as a non-canonical intronic variant outside the default null-variant buckets and does not recommend generic PVS1 application.
• SpliceAI reports maximum delta 0.031 (DS_DG), predicting no significant splice impact; no RNA evidence of aberrant splicing or NMD is present in the case evidence.

Sources

Reasoning

The variant is intronic (c.1794+19G>T), so the generic non-missense splice-prediction pathway applies after the local POLE missense-only lookup rule was not applicable. SpliceAI maximum delta is 0.031, below the PP3 threshold (>0.2); PP3 is not met.

Rule

Generic ACMG non-missense PP3 fallback: SpliceAI maximum delta >0.2; local POLE missense-table rule not applicable.

Evidence considered

• The local POLE framework limits its PP3 rule to an exact missense variant present in Supplementary Table S2 or S3 with the specified REVEL class and benign-tool count. The queried c.1794+19G>T intronic variant is not a missense substitution and is absent from both reviewed tables.
• Under the generic non-missense computational pathway, SpliceAI max delta >0.2 supports PP3; the observed maximum delta is 0.031 (DS_DG), which does not meet that threshold.

Sources

Reasoning

The exact ClinVar record has no expert-panel submission. Its sole submission is a single clinical laboratory assertion and is not eligible for PP5.

Rule

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

Evidence considered

• ClinVar submission audit: exact match NM_006231.4(POLE):c.1794+19G>T; one Labcorp clinical-testing submission, Likely benign, marked is_expert_panel=false; expert_panel_submissions=0.

Sources

Reasoning

The variant does not meet the generic population-frequency threshold for BA1. The highest observed allele frequency is 3.28267e-05 in the gnomAD v4.1 Remaining individuals population, far below the 1% BA1 threshold.

Rule

BA1: allele frequency is sufficiently high in a population database to establish benignity; generic operating threshold is >1%.

Evidence considered

• gnomAD v4.1 reports 2/1,568,238 total alleles, total AF 1.27532e-06, with 0 homozygotes.
• The highest reported subpopulation frequency is 2/60,926 alleles (AF 3.28267e-05; 0 homozygotes) in Remaining individuals.
• The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0.
• Generic BA1 threshold used: allele frequency greater than 1%; the observed frequency is well below this threshold.

Sources

Reasoning

The observed population frequency is not greater than the disease-specific benign threshold used for BS1. The maximum reported allele frequency is 3.28267e-05, below the operating BS1 threshold of 0.3%.

Rule

BS1: allele frequency is greater than expected for the disorder; generic operating threshold is >0.3% when no disease-specific maximum credible allele frequency is available.

Evidence considered

• gnomAD v4.1 reports a total AF of 1.27532e-06 from 2/1,568,238 alleles.
• The highest reported subpopulation frequency is AF 3.28267e-05 from 2/60,926 alleles in Remaining individuals; all reported homozygote counts are 0.
• The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0.
• Generic BS1 threshold used: allele frequency greater than 0.3%; the observed frequency is well below this threshold. Disease prevalence, penetrance, and an established POLE-specific maximum credible allele frequency were not provided, so no lower disease-specific threshold was substituted.

Sources

Reasoning

The exact ClinVar record has no expert-panel submission. The single Likely benign laboratory submission cannot trigger BP6.

Rule

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

Evidence considered

• ClinVar submission audit: exact match NM_006231.4(POLE):c.1794+19G>T; one Labcorp clinical-testing submission, Likely benign, marked is_expert_panel=false; expert_panel_submissions=0.

Sources

Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. There is no parental testing result establishing that NM_006231.4:c.1794+19G>T is absent from both biological parents, and no evidence addressing maternity/paternity or mosaicism.

Rule

Generic ACMG/AMP PS2 requires a confirmed de novo variant in an affected individual with confirmed maternity and paternity; no applicable POLE-specific PS2 specification was available.

Evidence considered

• The case summary identifies the variant as NM_006231.4:c.1794+19G>T in POLE but contains no proband or parental segregation/de novo observations.
• The consolidated bundle contains no family-study, trio-testing, or parental-genotype evidence for this variant.

Still missing

• Proband phenotype and clinical indication
• Confirmed biological parentage
• Parental genotypes for the exact variant
• Assessment for parental mosaicism

Reasoning

No validated functional assay evidence for NM_006231.4:c.1794+19G>T was identified in the case-evidence bundle. The available record is a non-canonical intronic variant with no reported RNA, protein, cellular, biochemical, or other disease-relevant functional assay demonstrating a damaging effect. The POLE local custom framework specifies PM1, PS4, PP3, and BP4 only and provides no PS3 rule; therefore PS3 cannot be applied.

Evidence considered

• The consolidated bundle identifies the variant as NM_006231.4:c.1794+19G>T in POLE and reports no variant-specific functional assay evidence.
• The bundle's paper_extracts.json and fulltext_map.json are empty; literature_pass.json contains only PMID:28492532 as background review with no candidate functional criteria.
• The retrieved POLE custom framework is explicitly limited to PM1, PS4, PP3, and BP4 and does not define PS3 or BS3.

Still missing

• No variant-specific functional assay with appropriate controls and biologically relevant readout was identified.
• No variant-specific RNA or splicing assay was identified to establish abnormal transcript processing or loss of function.

Reasoning

The POLE local framework's PS4 adaptation applies only to specified recurrent POLE missense hotspot variants with combined COSMIC and TCGA endometrial-cancer count at least 10. NM_006231.4:c.1794+19G>T is intronic and is not eligible for that exact-variant missense rule. No germline case-control or other enrichment dataset for this variant is provided for generic PS4 assessment.

Rule

POLE local PS4 rule applies only to qualifying exact recurrent missense variants; otherwise generic ACMG/AMP PS4 requires statistically increased prevalence in affected individuals versus controls.

Evidence considered

• The governing local POLE framework limits its PS4_Supporting somatic-recurrence adaptation to exact recurrent POLE missense hotspot variants and caps the strength at Supporting; it directs generic ACMG/AMP fallback outside that explicit rule.

Still missing

• A variant-specific germline case-control dataset with case and control counts, phenotype definition, and statistical enrichment analysis is needed for generic PS4 assessment.

Sources

Reasoning

PM3 cannot be assessed from the available case bundle. The bundle provides no affected-proband observations, no confirmed pathogenic or likely pathogenic allele in the same gene, and no phase information establishing the tested variant in trans with such an allele. The POLE-specific framework does not define a PM3 rule, so generic ACMG/AMP logic would require these missing allelic and inheritance data.

Rule

Generic PM3: pathogenic or likely pathogenic variants observed in trans with the variant under assessment in affected individuals support a recessive mechanism; strength depends on the number and quality of informative observations and phase confirmation.

Evidence considered

• The case bundle identifies the variant as NM_006231.4:c.1794+19G>T in POLE and contains no family-study, affected-proband, compound-heterozygote, or phase observations.
• The available POLE custom framework specifies PM1, PS4, PP3, and BP4 only; it provides no gene-specific PM3 specification.

Still missing

• No affected-proband case observations attributable to this variant were provided.
• No pathogenic or likely pathogenic variant in POLE was reported in the same proband.
• No parental testing or other phasing evidence was provided to establish trans configuration.
• The inheritance model and whether a recessive disease context applies to this case are not documented.

Reasoning

No suspected de novo occurrence is documented for the variant. The available case evidence does not report parental testing, phenotype concordance, or other information that could support a de novo inference without molecular confirmation.

Rule

Generic ACMG/AMP PM6 concerns a suspected but unconfirmed de novo occurrence; no applicable POLE-specific PM6 specification was available and the case lacks the required family context.

Evidence considered

• The consolidated bundle provides no report of suspected de novo status, parental testing, or a family history relevant to this variant.
• A ClinVar single-submitter likely-benign classification is not de novo evidence and was not used to infer PM6.

Still missing

• Proband phenotype and clinical indication
• Parental genotypes or a documented basis for suspecting de novo origin
• Confirmed biological parentage
• Independent case-level de novo observations

Reasoning

No affected or unaffected relatives, meioses, pedigree, or genotype-phenotype segregation data are reported. Therefore, concordant segregation cannot be evaluated and no PP1 strength can be assigned.

Rule

Generic ACMG/AMP PP1 requires co-segregation of the variant with disease in affected family members; no applicable POLE-specific PP1 specification was available.

Evidence considered

• The case-evidence bundle contains no pedigree, family genotypes, affected-relative observations, unaffected-relative observations, or segregation analysis.
• Population frequency, splice prediction, and the ClinVar submission do not provide family segregation evidence and were not used for PP1.

Still missing

• Pedigree and number of informative meioses
• Phenotypes of relatives
• Genotypes of affected and unaffected relatives
• Variant phase and segregation across informative branches

Reasoning

No individual phenotype, tumor phenotype, or phenotype-specificity evidence for the carrier is supplied. Therefore, a phenotype highly specific for a POLE-related disorder cannot be established.

Rule

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

Evidence considered

• The consolidated case-evidence bundle contains no phenotype or case-observation dataset for the individual carrying NM_006231.4:c.1794+19G>T.

Still missing

• Detailed proband phenotype and indication for testing.
• Evidence that the observed phenotype is highly specific to a POLE-related disorder and that alternative etiologies have been evaluated.

Reasoning

No BS2 evidence is established. gnomAD reports no homozygotes, but the available population records do not document that any carrier was a phenotypically healthy adult or provide disease-specific penetrance information. Therefore, absence of homozygotes and rare heterozygote observations cannot be converted into BS2.

Rule

BS2: the variant is observed in a healthy adult individual for a disorder with full penetrance expected by the relevant inheritance model; population allele counts alone are insufficient without phenotype confirmation.

Evidence considered

• gnomAD v4.1 contains 2 variant alleles among 1,568,238 total alleles and reports 0 homozygotes; the highest subpopulation also reports 0 homozygotes.
• gnomAD v2.1 and gnomAD-Canada v1.0 report the variant as absent.
• These data establish rarity but do not establish the required healthy-adult phenotype observation for BS2.

Still missing

• No documented healthy adult carriers or phenotype-linked population observations were supplied.
• No disease-specific penetrance and inheritance context sufficient to assess BS2 was supplied.

Sources

Reasoning

No validated functional assay evidence showing a normal or benign effect for NM_006231.4:c.1794+19G>T was identified in the case-evidence bundle. The ClinVar record is a single-submitter Likely benign classification and is not itself functional evidence; the cited background publication does not provide a variant-specific assay result in the available evidence. The POLE local custom framework specifies PM1, PS4, PP3, and BP4 only and provides no BS3 rule; therefore BS3 cannot be applied.

Evidence considered

• The consolidated bundle reports only a single-submitter ClinVar Likely benign classification for the exact variant and does not report a variant-specific functional assay result.
• The bundle's paper_extracts.json and fulltext_map.json are empty; literature_pass.json contains only PMID:28492532 as background review with no candidate functional criteria.
• The retrieved POLE custom framework is explicitly limited to PM1, PS4, PP3, and BP4 and does not define PS3 or BS3.

Still missing

• No variant-specific functional assay with validated normal controls and a biologically relevant normal readout was identified.
• No quantitative assay data or assay calibration sufficient for benign-strength assignment was identified.

Reasoning

No unaffected relatives known to carry the variant, no informative non-segregating meioses, and no family genotype-phenotype data are documented. Consequently, absence of segregation cannot be assessed.

Rule

Generic ACMG/AMP BS4 concerns lack of segregation in affected family members or presence in unaffected relatives when informative; no applicable POLE-specific BS4 specification was available.

Evidence considered

• The consolidated bundle contains no data on unaffected relatives carrying NM_006231.4:c.1794+19G>T or on any other non-segregating family observations.
• The absence of reported family data is insufficient to establish BS4 and was treated as an assessment gap rather than evidence against pathogenicity.

Still missing

• Pedigree and disease status of relatives
• Genotypes of unaffected relatives
• Informative non-segregation observations
• Phenotype ascertainment and age-related penetrance assessment

Reasoning

BP2 cannot be assessed from the available case bundle. No unaffected individual or affected individual with an established alternative explanation was documented as carrying this variant together with a pathogenic or likely pathogenic variant, and no cis/trans phase information was provided. The POLE-specific framework does not define a BP2 rule, so generic ACMG/AMP logic would require missing co-occurrence and phase data.

Rule

Generic BP2: the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual, or in cis with a pathogenic variant in an unaffected individual, when the inheritance model and phase make the observation informative; apply only with adequate clinical and phasing evidence.

Evidence considered

• The case bundle contains no family segregation data, unaffected-carrier data, co-occurring pathogenic-variant data, or phase observations relevant to BP2.
• The available POLE custom framework specifies PM1, PS4, PP3, and BP4 only; it provides no gene-specific BP2 specification.

Still missing

• No co-occurrence observation with a pathogenic or likely pathogenic variant was provided.
• No clinical status or alternative molecular explanation for any carrier was provided.
• No parental testing or other phasing evidence was provided to establish cis or trans configuration.
• No inheritance-mode context was provided to determine whether the observed co-occurrence would be informative.

Reasoning

No carrier-level genotype, phenotype, or diagnostic information is supplied to show that the phenotype is explained by an alternative molecular diagnosis.

Rule

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

Evidence considered

• The consolidated case-evidence bundle contains no co-occurring diagnostic variant or alternative molecular diagnosis for the carrier.

Still missing

• Individual-level testing and phenotype data documenting an alternative molecular cause that fully explains the observed phenotype.