POLD1 c.2959del, p.(Asp987ThrfsTer58)

Reasoning

NM_002691.4:c.2959del is a single-nucleotide frameshift deletion predicted to produce NP_002682.2:p.(Asp987ThrfsTer58), introducing a premature termination codon 58 codons downstream of the frameshift start, well before the native stop at residue 1107. No official POLD1 CSPEC/VCEP PVS1 specification exists in this case bundle, so the generic ClinGen SVI PVS1 decision tree (PMC6185798) was applied as the governing framework, consistent with the case's framework_mode of generic_acmg. Germline loss-of-function is an established disease mechanism for POLD1 (targeted literature review found disease-associated germline POLD1 alterations, and the gene-level PVS1 gate was assessed as eligible), satisfying the prerequisite for applying PVS1 to a truncating/frameshift variant in this gene. The frameshift truncates roughly the terminal ~11% of the 1107-residue protein and disrupts the region encompassing the conserved C-terminal metal-binding/PCNA-interaction motifs of the POLD1 catalytic subunit, consistent with removal of functionally important sequence rather than a biologically inert distal tail. The premature termination codon falls well upstream of the final exon-exon junction region expected for a transcript of this length, consistent with a variant predicted to trigger nonsense-mediated decay (NMD) rather than escape it, supporting Very Strong strength under the generic frameshift/nonsense PVS1 pathway.

Rule

PVS1 (generic ACMG/AMP fallback via ClinGen SVI PVS1 recommendations, PMC6185798) applied because no POLD1 CSPEC/VCEP-specific PVS1 rule was available in this case.

Evidence considered

• pvs1_gene_context.json: targeted germline literature review classified POLD1 loss-of-function as an eligible germline disease mechanism ('lof_mechanism_supported': true, 'pvs1_gene_gate': 'eligible'), enabling generic PVS1 framework application in the absence of an official CSPEC/VCEP source.
• pvs1_variant_assessment.json: classifies NM_002691.4:c.2959del as consequence_class='frameshift'/variant_bucket='frameshift', cites the ClinGen SVI PVS1 recommendations (PMC6185798) as the governing generic framework, and flags downgrade_considerations around confirming transcript relevance, NMD escape, and exon-level biological importance before finalizing full-strength PVS1.
• case_summary.json normalization block confirms the predicted protein consequence as NP_002682.2:p.(Asp987ThrfsTer58) (single-nucleotide deletion causing a frameshift with a new stop 58 codons downstream), truncating the protein well before its native 1107-residue length.
• ClinVar (variation ID 935838) lists this exact variant as classified Uncertain significance with a single-submitter review status; ClinVar's own classification was not used to infer this PVS1 call, but the ClinVar record was reviewed to confirm the transcript/protein annotation used for the PVS1 assessment matches the submitted variant.

Still missing

• The case bundle's own pvs1_variant_assessment left the exon number null and did not independently confirm the distance of the premature termination codon from the final exon-exon junction, so exact NMD prediction (versus escape with retained partial function) has not been locked down against a verified exon map for NM_002691.4.
• No official POLD1-specific VCEP PVS1 decision tree was available to confirm whether this specific C-terminal region is formally designated as functionally critical or is instead flagged as a region tolerant of population-observed loss-of-function variation; this should be re-checked if a POLD1 VCEP specification becomes available.
• Recommend human review to confirm the exon/NMD call before finalizing strength at Very Strong versus a Strong downgrade per the downgrade_considerations noted in the variant assessment scaffold.

Sources

Reasoning

PM2 is met at supporting level because the variant is extremely rare in population databases: overall AF is 5.77e-06 in gnomAD v4.1 and 5.55e-05 in gnomAD v2.1, with zero homozygotes in both datasets, and it is absent from gnomAD-Canada. The strongest available population signal remains far below 0.1%. Human review is requested because the ClinVar evidence bundle contains a submitter comment that frequency data at this position may be unreliable due to gnomAD data-quality metrics, although the large gnomAD v4.1 allele denominator and concordant observations support rarity.

Rule

Generic non-VCEP PM2: apply rare/absent population evidence when allele frequency is below 0.1% and there is no homozygote observation, subject to assessment of database quality and disease prevalence/penetrance; this case meets the frequency component but retains a quality caveat.

Evidence considered

• gnomAD v4.1 reports 9/1,558,756 alleles, AF 5.77384e-06, zero homozygotes, and grpmax FAF 9.36e-06; the highest subgroup AF is 5.53301e-05 in Finnish individuals.
• gnomAD v2.1 reports 9/162,082 alleles, AF 5.55274e-05, zero homozygotes, and grpmax FAF 1.988e-05; the highest subgroup AF is 2.67762e-04 in Finnish individuals.
• The variant is absent from gnomAD-Canada v1.0.
• A ClinVar submission's evidence signal states that population-frequency data for this variant may be unreliable because of poor data-quality metrics at the position in gnomAD; this is treated as a review caveat rather than as a final classification.
• The generic non-VCEP operating threshold applied here for PM2 is AF below 0.1% with no homozygotes; the observed frequencies satisfy the rarity component in both gnomAD releases.

Still missing

• The supplied bundle does not include the underlying gnomAD site-level quality metrics needed to independently resolve the ClinVar submitter's data-quality concern.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar variation 935838 has two exact-match clinical laboratory submissions, both Uncertain significance, with review status criteria provided by single submitters and zero expert-panel submissions. Therefore PP5 is not triggered; the ordinary laboratory submissions and their aggregate VUS label are not eligible evidence for PP5.

Rule

PP5_override: apply only for exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification

Evidence considered

• ClinVar exact-match record NM_002691.3(POLD1):c.2959del reports Uncertain significance, criteria provided by single submitters, with two submissions and zero expert-panel submissions.
• The ClinVar submission audit identifies no exact-variant expert-panel Pathogenic or Likely pathogenic classification.

Sources

Reasoning

BA1 is not met. The maximum observed population frequency is 5.53e-05 in the Finnish subgroup in gnomAD v4.1, with overall allele frequency 5.77e-06; these values are far below the generic benign stand-alone threshold of 1% used for this non-VCEP assessment.

Rule

Generic non-VCEP BA1: apply stand-alone benign evidence when population allele frequency exceeds 1%; this variant does not meet that threshold.

Evidence considered

• gnomAD v4.1 reports 9/1,558,756 alleles, overall AF 5.77384e-06, no homozygotes, and the highest subgroup AF of 5.53301e-05 in Finnish individuals (3/54,220 alleles).
• gnomAD v2.1 independently reports 9/162,082 alleles, overall AF 5.55274e-05, no homozygotes, and the highest subgroup AF of 2.67762e-04 in Finnish individuals (3/11,204 alleles).
• The generic non-VCEP operating threshold applied here for BA1 is population AF greater than 1%; the observed frequencies do not approach this threshold.

Sources

Reasoning

BS1 is not met. The maximum observed frequency is 5.53e-05 in gnomAD v4.1 Finnish individuals, which is far below the generic non-VCEP threshold of 0.3% for a benign frequency exceeding the disease-compatible maximum.

Rule

Generic non-VCEP BS1: apply benign supporting evidence when population allele frequency exceeds 0.3% or the disease-compatible maximum; no such excess frequency is observed.

Evidence considered

• gnomAD v4.1 reports an overall AF of 5.77384e-06 and maximum reported subgroup AF of 5.53301e-05 in the Finnish population; no homozygotes were observed.
• gnomAD v2.1 reports an overall AF of 5.55274e-05 and maximum reported subgroup AF of 2.67762e-04 in the Finnish population; no homozygotes were observed.
• The generic non-VCEP operating threshold applied here for BS1 is population AF greater than 0.3%; the observed frequencies are below this threshold.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar variation 935838 has two exact-match clinical laboratory submissions, both Uncertain significance, with review status criteria provided by single submitters and zero expert-panel submissions. Therefore BP6 is not triggered; ordinary laboratory submissions and the aggregate ClinVar label are not eligible evidence for BP6.

Rule

BP6_override: apply only for exact-variant ClinVar expert-panel Benign or Likely benign classification

Evidence considered

• ClinVar exact-match record NM_002691.3(POLD1):c.2959del reports Uncertain significance, criteria provided by single submitters, with two submissions and zero expert-panel submissions.
• The ClinVar submission audit identifies no exact-variant expert-panel Benign or Likely benign classification.

Sources

Reasoning

No case-specific documentation was provided showing that NM_002691.4:c.2959del was confirmed de novo in an affected proband. The evidence bundle contains no proband/parent genotype comparison, parental testing result, maternity/paternity confirmation, or de novo observation suitable for PS2.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no confirmed family history, with maternity and paternity confirmed as applicable; case-specific parental testing evidence is required.

Evidence considered

• The case bundle identifies the variant as NM_002691.4:c.2959del in POLD1 but provides no family-based de novo evidence.
• No applicable POLD1-specific CSPEC/VCEP framework was retrieved; generic ACMG/AMP fallback applies.

Still missing

• Documented proband genotype and confirmed parental genotypes are needed.
• Maternity and paternity should be established before interpreting an apparent de novo finding.
• Phenotype consistency and testing quality for the proband and both parents are not available.

Reasoning

No ClinGen VCEP-specific POLD1 framework is available for this case (vcep_materials.json notes no cspec URL and final_classification_framework falls back to generic_acmg_fallback), so generic ACMG/AMP PS3 criteria apply. No validated functional/biochemical assay data (e.g., polymerase proofreading exonuclease activity assay, yeast complementation, mutation-rate reporter assay) addressing this specific variant, NM_002691.4:c.2959del (p.Asp987ThrfsTer58), were identified anywhere in the evidence bundle. OncoKB explicitly found no variant-specific reviewed functional evidence (biological_effect empty, is_variant_specific false). The one ClinVar-linked publication tagged 'theme: functional' (PMID:23263490) performed fission-yeast Pol3 mutation-rate assays only for the missense exonuclease-domain variants POLE L424V and POLD1 S478N (and structural modeling of P327L, S370R, G426S); it contains no data, assay, or discussion of this frameshift variant, which truncates the protein at residue 987, well outside the POLD1 exonuclease domain (codons ~304-517) that paper characterizes. No other source in the bundle (evidence.json, literature_pass.json, vcep_materials.json) reports a functional assay for this variant.

Evidence considered

• OncoKB record for POLD1 D987Tfs*58 explicitly states no variant-specific reviewed functional evidence and classifies biological effect as unknown.
• PMID:23263490 full text describes fission-yeast Pol3 mutation-rate fluctuation assays only for POLD1 S478N (equivalent to Pol3-C462N) and structural/functional characterization of exonuclease-domain missense variants (L424V analog, P327L, S370R, G426S); no mention of residue 987 or a truncating/frameshift POLD1 variant.
• No cspec/VCEP-specific PS3 assay framework is present for POLD1 in this case (vcep_materials.json: no cspec url available, final_classification_framework source generic_acmg_fallback).

Still missing

• No POLD1-specific VCEP functional assay framework (thresholds, validated assay list) available in this case to calibrate PS3 strength.
• No functional/biochemical assay (polymerase proofreading, complementation, reporter) has been performed or reported for NM_002691.4:c.2959del specifically.
• PMID:23263490 functional data pertain only to missense exonuclease-domain variants (S478N, L424V, P327L) and are not applicable to this truncating variant outside that domain.

Sources

Reasoning

PS4 requires statistically significant enrichment of the exact variant in affected individuals versus controls, or an appropriately specified case-series framework. The bundle provides no exact-variant case-control counts, odds ratio, statistical test, or qualifying case series for NM_002691.4:c.2959del (NP_002682.2:p.(Asp987ThrfsTer58)). The reviewed POLD1 literature describes other variants, not this exact variant, so it cannot establish PS4 for this variant.

Rule

generic_acmg_2015_PS4: case-control enrichment or validated case-series evidence for the exact variant

Evidence considered

• ClinVar-linked publication PMID:23263490 reports a different POLD1 variant, S478N (NM_002691:c.G1433A), in affected families and does not report NM_002691.4:c.2959del.
• PMID:23447401 summarizes POLD1 germline variants p.Ser478Asn and p.Pro327Leu and does not report NM_002691.4:c.2959del.
• The case bundle contains no exact-variant case-control dataset or qualifying PS4 case-series count.

Still missing

• Exact-variant affected-case and control counts are unavailable.
• No variant-specific enrichment statistic or validated case-series threshold is available.
• The exact variant is not reported in the reviewed publications.

Sources

Reasoning

No case-specific documentation was provided for an assumed de novo occurrence of NM_002691.4:c.2959del. There is no report of parental testing, confirmed maternity/paternity, or a clinical presentation supporting an assumed de novo event for this proband.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in a patient with the disease and no family history, without confirmation of paternity and maternity; the assumption must be supported by case-specific clinical and family evidence.

Evidence considered

• The evidence bundle contains no assumed-de-novo case observation for this variant.
• No applicable POLD1-specific CSPEC/VCEP framework was retrieved; generic ACMG/AMP fallback applies.

Still missing

• Parental testing results are absent.
• Maternity and paternity confirmation are absent.
• The proband phenotype and family history needed to judge an assumed de novo event are absent.

Reasoning

No affected relatives carrying NM_002691.4:c.2959del, informative meioses, pedigree, or phenotype-segregation data are documented. The available literature records are not an exact-variant family segregation report and cannot establish PP1 for this case.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength depends on the number and informativeness of meioses and the phenotype specificity.

Evidence considered

• The case bundle provides no family segregation results for NM_002691.4:c.2959del.
• The reviewed POLD1 publications discuss other reported variants or broader disease context, but do not document segregation of this exact variant.

Still missing

• A pedigree with affected and unaffected relatives is not available.
• Genotypes and phenotypes of informative relatives are not available.
• The number of informative meioses and segregation consistency cannot be determined.

Sources

Reasoning

PP4 requires a highly specific phenotype or family history that is characteristic of the disease associated with the gene. The case-evidence bundle does not provide patient-level phenotype, family-history, or a phenotype-specific diagnostic assessment for this variant. Gene-level descriptions of colorectal adenomas and colorectal cancer in publications cannot substitute for the phenotype of this individual case.

Rule

generic_acmg_2015_PP4: highly specific phenotype or family history consistent with the gene-associated disorder

Evidence considered

• The case bundle contains no patient-level phenotype or family-history evidence sufficient to assess PP4.
• Published gene-level disease descriptions were not used as a proxy for this patient's phenotype.

Still missing

• Patient-level phenotype and family-history details are unavailable.
• No phenotype-specific disease matching assessment is provided.

Reasoning

BS2 cannot be established from the available evidence. gnomAD reports zero homozygotes, but provides no phenotype-confirmed healthy-adult observation for this specific variant, and absence of homozygotes is not itself evidence that the variant is present in healthy adults in a manner incompatible with the POLD1 disease model.

Rule

Generic ACMG/AMP BS2 requires observation of the variant in healthy adults at an age and with a phenotype expected to exclude the relevant disease; population-database homozygote counts alone do not establish this criterion.

Evidence considered

• gnomAD v4.1 reports zero observed homozygotes, but the supplied population record does not provide clinical phenotype or age-of-onset information for carriers.
• gnomAD v2.1 also reports zero observed homozygotes, but this is insufficient by itself to satisfy BS2.

Still missing

• No phenotype-confirmed healthy-adult carriers or disease-penetrance analysis is available for this exact variant.
• No disease-specific cohort establishes that heterozygous or homozygous carriers remain unaffected beyond the relevant age of risk.

Sources

Reasoning

No ClinGen VCEP-specific POLD1 framework is available for this case, so generic ACMG/AMP BS3 criteria apply. No functional assay data of any kind (well-established or otherwise) addressing this specific variant, NM_002691.4:c.2959del (p.Asp987ThrfsTer58), were identified in the evidence bundle that would show normal/benign functional impact. OncoKB reports no variant-specific reviewed functional evidence. PMID:23263490's fission-yeast complementation/mutation-rate assays are restricted to missense exonuclease-domain variants and are not applicable to this out-of-domain frameshift/truncating variant, so they cannot be used to argue lack of functional impact either.

Evidence considered

• OncoKB record for POLD1 D987Tfs*58 explicitly states no variant-specific reviewed functional evidence and classifies biological effect as unknown.
• PMID:23263490 full text functional assays cover only missense exonuclease-domain variants and are not applicable to this truncating variant located outside the exonuclease domain.

Still missing

• No functional assay (of any outcome) has been performed or reported for NM_002691.4:c.2959del specifically.
• No POLD1-specific VCEP framework available to define an applicable BS3 assay or strength calibration.

Sources

Reasoning

No tested unaffected relatives, genotype-negative affected relatives, or other informative non-segregation observations are documented for NM_002691.4:c.2959del. Therefore BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; application requires adequately phenotyped and appropriately tested informative relatives.

Evidence considered

• The case bundle contains no non-segregation or genotype-negative affected-relative evidence for this variant.
• No applicable POLD1-specific CSPEC/VCEP framework was retrieved; generic ACMG/AMP fallback applies.

Still missing

• Genotypes and phenotypes of unaffected relatives are absent.
• The number of informative relatives and their ages/phenotype ascertainment are absent.
• No documented non-segregation observation is available.

Reasoning

No applicable POLD1-specific VCEP framework was retrieved, so the generic ACMG/AMP definition is used. BP2 requires observation of the variant in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant. The case bundle contains no additional variant, phase, family, or affected-proband data demonstrating either configuration; BP2 cannot be applied.

Rule

Generic ACMG/AMP BP2: variant observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant.

Evidence considered

• The consolidated case bundle provides no phase-resolved family data, no additional pathogenic variant in the tested individual, and no cis/trans observation for NM_002691.4:c.2959del.
• The literature materials available for this case were not used to infer BP2 because they do not document the exact variant in a cis or trans configuration with another pathogenic variant.

Still missing

• No second variant in the relevant individual is documented.
• No validated cis/trans phase information is available.
• No family-based or affected-proband observation supports BP2.

Reasoning

BP5 requires a well-established alternative molecular basis for the patient's phenotype that excludes the tested variant as the cause. The bundle provides no alternative pathogenic molecular diagnosis for the patient and no phenotype-level evidence establishing an alternative cause. The absence of such information does not support BP5.

Rule

generic_acmg_2015_BP5: alternate molecular basis established for the phenotype

Evidence considered

• The case bundle contains no documented alternative molecular cause for the patient's phenotype.

Still missing

• No alternative pathogenic molecular diagnosis is documented.
• No patient-level phenotype and molecular-correlation assessment is available.