c.266_267del

Reasoning

Variant normalization failed for this case: VariantValidator returned a critical error (HTTP 422 / gene symbol not resolved to a valid reference sequence) and Mutalyzer also errored. Gene, transcript, coding HGVS consequence, exon location, reading-frame effect, and NMD-relevance could not be determined. pvs1_gene_context.json and pvs1_variant_assessment.json both explicitly flag this as unresolved ('pvs1_gene_gate': 'manual_review_required', 'apply_generic_pvs1_framework': false). No CSPEC/VCEP framework was retrieved (cspec fetch skipped: 'no gene'). Without a resolved transcript and confirmed frameshift/reading-frame consequence, PVS1 cannot be adjudicated from this bundle.

Evidence considered

• prefetch.json records a CRITICAL error: VariantValidator unavailable and no coordinate cache found; normalization incomplete, gene/coords are None.
• pvs1_gene_context.json: germline_disease_context_found is false, official_source_type is 'none', lof_mechanism_supported is false, pvs1_gene_gate is 'manual_review_required' due to incomplete literature retrieval.
• pvs1_variant_assessment.json: transcript_hgvs, variant_class, exon, and consequence_class are all empty/unknown; apply_generic_pvs1_framework is false.

Still missing

• Re-run VariantValidator with an explicit transcript (e.g. NM_000546.6) to resolve TP53:c.266_267del to a proper HGVS coding/protein consequence.
• Determine reading-frame effect of the 2-bp deletion (frameshift vs in-frame) and resulting premature termination codon position relative to the last exon/NMD boundary.
• Retrieve the TP53 ClinGen VCEP PVS1 specification once gene/transcript is resolved, since TP53 has a published ClinGen VCEP framework that should govern PVS1 application (LOF mechanism is disease-relevant for TP53 germline Li-Fraumeni syndrome, but exon-specific and NMD caveats apply per VCEP).

Reasoning

Variant normalization failed for this case (VariantValidator unavailable, no coordinate cache; prefetch.errors: 'CRITICAL: VariantValidator unavailable and no coord cache found. Normalization incomplete — gene/coords are None.'). Gene, transcript, and protein consequence are all empty strings/null throughout case_summary.json, evidence.json, and prefetch.json. TP53:c.266_267del is a 2-bp coding deletion, which produces a frameshift rather than a single defined amino-acid substitution, so classic PS1 (same amino-acid change as an established pathogenic variant via a different nucleotide change) does not apply to this variant class even in principle. No gene-specific TP53 VCEP framework content was retrievable (vcep_materials.json is empty, cspec lookup was skipped for lack of gene).

Evidence considered

• prefetch.json records normalization failure: mutalyzer HTTP 422 and VariantValidator returned only a syntax warning listing candidate transcripts, with gene_symbol, hgvs_predicted_protein_consequence, and primary_assembly_loci all empty.
• case_summary.json compact_evidence.normalization has protein_3l, protein_1l, and variant_class all null; cspec.found is null.

Still missing

• Protein consequence (p.HGVS) was never resolved due to VariantValidator failure; without it PS1 applicability cannot be confirmed even as not_applicable with certainty.
• No TP53 VCEP CSpec document was retrieved for this case.

Reasoning

No proband-level or parental-testing evidence is available in the case-evidence bundle. De novo status cannot be assessed, and the variant could not be normalized to a transcript for case-level verification.

Rule

Generic PS2 requires a confirmed de novo occurrence in the proband with confirmed maternity and paternity; strength depends on the quality and completeness of parental testing and phenotype consistency.

Evidence considered

• The case-evidence bundle reports no applicable VCEP or gene-specific framework and falls back to generic ACMG/AMP.
• The bundle contains no proband, parental, trio, or de novo testing observations.
• Normalization failed for TP53:c.266_267del; gene and coordinates remain unresolved in the bundle.

Still missing

• Proband phenotype and indication
• Testing results for both biological parents
• Confirmation that the variant is absent in both parents
• Variant normalization to a defined transcript

Reasoning

Case-level normalization failed (VariantValidator unavailable, no coordinate cache found), so gene, transcript, and CSPEC/VCEP context could not be resolved. No functional/validated-assay evidence, literature, or VCEP-specific PS3 rule was retrievable in prefetch.json, evidence.json, literature_pass.json, vcep_materials.json, fulltext_map.json, or paper_extracts.json for this case, all of which are empty or skipped due to the upstream normalization failure.

Still missing

• Rerun prefetch/normalization once VariantValidator is available to resolve gene (TP53) and transcript context.
• No functional assay data (e.g., transactivation assays, cell-based reporter assays) was retrieved or searched for this variant; literature_pass.json and paper_extracts.json contain zero PMIDs.
• TP53 VCEP CSPEC PS3 rule (if applicable) could not be consulted because cspec retrieval was skipped (no gene resolved).

Reasoning

PS4 cannot be assessed because the case bundle contains no normalized exact variant, affected-case count, control count, or case-control enrichment analysis.

Rule

Generic ACMG/AMP PS4: apply only with statistically supported enrichment of the exact variant in affected individuals compared with controls.

Evidence considered

• The available framework is the generic ACMG/AMP fallback because no TP53 VCEP specification was retrieved into this case.
• The prefetch record reports critical incomplete normalization: gene and genomic coordinates are unavailable, and literature retrieval found no PMIDs.

Still missing

• Normalize the submitted HGVS to a transcript and genomic allele.
• Provide exact-variant case and control counts, phenotype definition, ascertainment, and a statistical enrichment analysis.

Sources

Reasoning

PM1 (mutational hotspot/functional domain) requires a resolved protein position and domain/hotspot annotation. Neither is available: gene is empty, protein consequence is null, and hotspots.found/source_data in case_summary.json are all null/empty due to upstream normalization failure. No TP53 DNA-binding domain hotspot data (e.g., codon 175/248/273 mutational hotspot resources) could be checked against this variant's actual residue position.

Evidence considered

• case_summary.json compact_evidence.hotspots: found=null, evidence_sentence=null, source_data={} — no hotspot data retrieved.
• case_summary.json compact_evidence.cosmic: found=null — no COSMIC data retrieved.

Still missing

• Protein position/residue not resolved.
• No hotspot or domain annotation source (cosmic/hotspots) was queried because gene resolution failed upstream.

Reasoning

No applicable VCEP or gene-specific framework was retrieved, so generic ACMG/AMP population evidence rules are the fallback. PM2 cannot be assessed because the case bundle contains no reliable population allele count or frequency data; the empty gnomAD result is attributable to failed normalization and cannot establish absence from population databases.

Rule

Generic PM2: apply only when the variant is absent or extremely rare in appropriate population databases after confirming correct variant normalization, coverage/callability, ancestry, and database quality.

Evidence considered

• The consolidated bundle reports failed normalization, no genomic coordinates, and an empty gnomAD result.
• Database non-observation cannot be distinguished from lookup failure or insufficient coverage in this case, so PM2 is not established.

Still missing

• Validated transcript-level or genomic representation of TP53:c.266_267del
• Reliable allele counts and frequencies from appropriate population databases
• Coverage and callability review for the variant locus
• Ancestry-stratified data and evaluation of database-specific thresholds or recurrent technical artifacts

Reasoning

PM3 could not be assessed. The case bundle contains no affected-proband observations, no segregation or parental-phase information, and no documented pathogenic variant in trans. Variant normalization failed, and no applicable VCEP or gene-specific framework was available; therefore no allelic evidence can be established.

Evidence considered

• The consolidated case-evidence bundle reports no literature PMIDs and no paper extracts.
• The bundle reports incomplete normalization because the gene-only HGVS input could not be resolved; no proband or phase data are present in the available evidence.
• No pathogenic variant in trans, affected individual, or inheritance-mode observation is documented in the available case evidence.

Still missing

• Affected-proband observations are absent.
• Phase information is absent; a pathogenic variant in trans has not been documented.
• Parental testing and inheritance information are absent.
• The submitted variant was not normalized to a transcript-level HGVS representation.
• No applicable VCEP or gene-specific PM3 specification was available.

Reasoning

PM4 requires assessing protein length change from an in-frame deletion/insertion or stop-loss. Whether c.266_267del is in-frame or frameshift cannot be determined without a resolved transcript-level HGVS consequence, which normalization failed to produce for this case.

Evidence considered

• prefetch.json and pvs1_variant_assessment.json show no resolved protein-level consequence (protein_1l/protein_3l fields empty, consequence_class 'unknown').

Still missing

• Resolve HGVS protein consequence for TP53:c.266_267del (likely frameshift given a 2-bp deletion, which would make PM4 inapplicable in favor of PVS1 pathway, but this must be confirmed, not assumed).
• If in-frame, determine number of residues affected and whether it falls in a non-repeat, functionally important region.

Reasoning

pm5_candidates.json summary in case_summary.json explicitly flags pm5_mode as 'unknown' and eligible_for_classic_pm5_search as false, with recommendation.level 'not_applicable' and instruction: 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting.' total_candidates_seen is 0. Additionally this variant is a 2-bp deletion causing a frameshift rather than a missense substitution at a single residue, so the classic PM5 concept (a different missense change at the same residue already established as pathogenic) is not a natural fit for this variant class, but this cannot be confirmed as not_applicable without a resolved protein consequence.

Evidence considered

• case_summary.json pm5_candidates_summary: pm5_mode='unknown', eligible_for_classic_pm5_search=false, recommendation.level='not_applicable', candidate_summary.total_candidates_seen=0.

Still missing

• No resolved protein consequence to confirm whether this variant even produces a codon-level substitution amenable to PM5 logic.
• PM5 candidate harvesting was skipped entirely per pm5_candidates_summary; zero candidates were seen.

Reasoning

No clinical report or family-level observation documenting an assumed de novo occurrence is available. PM6 cannot be assessed without evidence that the variant arose de novo when parental maternity and/or paternity was not fully confirmed.

Rule

Generic PM6 applies to an assumed de novo occurrence without confirmed maternity and/or paternity; it is weaker than PS2 and requires documented case evidence.

Evidence considered

• The case-evidence bundle contains no PMIDs, literature findings, ClinVar submissions, or family observations relevant to de novo status.
• The bundle does not provide parental identity or testing information.

Still missing

• A documented de novo observation in the proband
• Parental testing details and identity confirmation
• Clinical report or publication supporting the observation
• Variant normalization to a defined transcript

Reasoning

No affected relatives, unaffected relatives, informative meioses, or genotype-phenotype segregation data are present. Familial segregation cannot be assessed.

Rule

Generic PP1 requires co-segregation of the variant with disease in affected family members, with strength determined by the number and informativeness of meioses and the consistency of the phenotype.

Evidence considered

• The case-evidence bundle contains no pedigree, family segregation results, or phenotype data.
• No literature papers were identified or extracted for this case.

Still missing

• Pedigree and number of informative meioses
• Genotypes of affected relatives
• Genotypes and phenotypes of unaffected relatives
• Phenotype definition and consistency with the relevant disorder
• Variant normalization to a defined transcript

Reasoning

PP2 requires establishing that missense variants are a common mechanism of disease in this gene and that this variant is missense. Gene identity itself is unresolved (empty string throughout all source files), so gene missense-mechanism eligibility cannot be evaluated. Furthermore, TP53:c.266_267del is a 2-bp deletion producing a frameshift, not a missense substitution, so PP2 (which is specific to missense variants) would not apply to this variant type regardless of gene, but this cannot be formally confirmed as not_applicable without a resolved variant_class field (currently null in case_summary.json compact_evidence.normalization).

Evidence considered

• case_summary.json compact_evidence.normalization.variant_class is null; protein_3l/protein_1l are null.

Still missing

• variant_class was never resolved (null) due to normalization failure, preventing formal confirmation that this variant is non-missense.
• No TP53-specific PP2 applicability determination (TP53 VCEP specifications typically do not use PP2) could be retrieved since vcep_materials.json is empty.

Reasoning

Variant normalization failed for this case (VariantValidator unavailable, no coordinate cache found; gene/coords resolved to null). SpliceAI, REVEL, and BayesDel were all skipped upstream ("not snv or no coords" / "no gene"), and no cspec/VCEP-specific PP3/BP4 lookup spreadsheet could be retrieved since the cspec lookup was also skipped for lack of a gene. No calibrated computational prediction (splice or missense) is available to evaluate PP3. Note the variant is a 2-bp coding deletion (TP53:c.266_267del), which is in-frame or frameshift depending on exact positioning — not a missense or synonymous substitution — so classic missense predictors (REVEL/BayesDel) would not be the primary applicable path regardless; a splice-impact (SpliceAI) assessment would require successful transcript/coordinate normalization, which did not occur.

Evidence considered

• prefetch.json step 'normalize' failed: VariantValidator returned a validation warning requiring an explicit transcript selection; Mutalyzer returned HTTP 422; no coordinate cache was found, so gene and genomic coordinates were never resolved (extracted.gene = "", chrom/pos/ref/alt all null).
• prefetch.json step 'revel' and 'bayesdel' were both explicitly skipped with reason 'not snv or no coords'.
• prefetch.json step 'cspec' was skipped with reason 'no gene', so no VCEP-specific PP3/BP4 lookup spreadsheet could be checked.
• evidence.json confirms revel result is also skipped with reason 'not snv or no coords' and manifest.revel.ok is false; spliceai/bayesdel are not present in evidence.json results at all.

Still missing

• Variant/gene normalization must succeed (VariantValidator or equivalent) before SpliceAI or any splice-impact scores can be retrieved.
• No TP53-specific VCEP PP3/BP4 lookup table was retrieved (cspec fetch skipped for lack of gene); rerun once normalization succeeds to check for a pre-assigned code.
• Confirm exact variant consequence (in-frame vs frameshift) once transcript context is available, to determine whether PP3/BP4 in-silico missense path even applies.

Reasoning

PP4 cannot be assessed because no individual phenotype, disease diagnosis, or phenotype-specificity evidence is present, and the exact variant was not normalized.

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

• No TP53-specific VCEP framework was retrieved; generic ACMG/AMP fallback is the governing framework for this case.
• The consolidated bundle contains no phenotype or diagnostic data for an affected individual.

Still missing

• Normalize the submitted HGVS to a transcript and genomic allele.
• Provide the proband phenotype and evidence that it is highly specific for a TP53-related disorder with a single genetic etiology.

Sources

Reasoning

PP5 cannot be assessed because ClinVar lookup was skipped after failed normalization; there is no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion.

Rule

Apply PP5 at supporting strength only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; do not use laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• The prefetch record states that ClinVar was skipped because no gene was available after normalization failed.
• No ClinVar submissions or expert-panel assertion are present in the consolidated bundle.

Still missing

• Normalize the submitted HGVS and retrieve the exact-variant ClinVar record and submission-level review status.
• Confirm a Pathogenic or Likely pathogenic assertion from a ClinVar expert panel for the exact normalized variant.

Sources

Reasoning

No applicable VCEP or gene-specific framework was retrieved, so generic ACMG/AMP population evidence rules are the fallback. BA1 cannot be assessed because the case bundle contains no allele frequency, ancestry-stratified frequency, or validated variant identifier, and normalization failed for the gene-level HGVS input.

Rule

Generic BA1: apply only when a reliable population frequency is greater than the established benign stand-alone threshold, accounting for disease prevalence, penetrance, ancestry, and artifacts.

Evidence considered

• The governing framework artifacts report no retrieved VCEP/gene-specific specification and identify generic ACMG/AMP as the fallback.
• The consolidated bundle reports failed normalization, no genomic coordinates, no gene-resolved evidence, and an empty gnomAD result.
• The bundle contains no source showing a population frequency at or above a BA1 threshold.

Still missing

• Validated transcript-level or genomic representation of TP53:c.266_267del
• Reliable population allele frequency and allele count data
• Ancestry-stratified frequency data and assessment of possible technical or recurrent-artifact effects
• A disease-prevalence and penetrance-based maximum credible allele-frequency threshold, if needed

Reasoning

No applicable VCEP or gene-specific framework was retrieved, so generic ACMG/AMP population evidence rules are the fallback. BS1 cannot be assessed because the case bundle contains no usable population frequency, ancestry data, disease prevalence or penetrance model, and no validated variant identifier for database lookup.

Rule

Generic BS1: apply when the observed population frequency is greater than expected for a pathogenic variant, using disease prevalence, penetrance, genetic heterogeneity, ancestry, and artifact controls.

Evidence considered

• The governing framework artifacts report no retrieved VCEP/gene-specific specification and identify generic ACMG/AMP as the fallback.
• The consolidated bundle reports failed normalization, no genomic coordinates, no gene-resolved evidence, and an empty gnomAD result.
• The bundle contains no source showing an allele frequency higher than expected for a pathogenic variant in the relevant disease context.

Still missing

• Validated transcript-level or genomic representation of TP53:c.266_267del
• Reliable population allele frequency and allele count data
• Ancestry-stratified frequency data
• Disease prevalence, penetrance, and a defensible maximum credible allele-frequency threshold

Reasoning

No applicable VCEP or gene-specific framework was retrieved, so generic ACMG/AMP population evidence rules are the fallback. BS2 cannot be assessed because the case bundle contains no population homozygote observations and no disease-status or ascertainment information for any carriers.

Rule

Generic BS2: apply only when the variant is observed in an appropriate population in healthy adults or in unaffected homozygous individuals, with ascertainment, age, penetrance, and technical quality considered.

Evidence considered

• The consolidated bundle reports no gene-resolved population dataset and no homozygote observations.
• No source in the bundle provides unaffected-carrier or disease-status information that could support BS2.

Still missing

• Population observations for the validated variant representation
• Homozygote counts and genotype-quality/technical-artifact review
• Disease status, age, phenotype, and ascertainment information for observed carriers
• Assessment of penetrance and whether unaffected status is informative

Reasoning

Case-level normalization failed (VariantValidator unavailable, no coordinate cache found), so gene, transcript, and CSPEC/VCEP context could not be resolved. No functional/validated-assay evidence, literature, or VCEP-specific BS3 rule was retrievable in prefetch.json, evidence.json, literature_pass.json, vcep_materials.json, fulltext_map.json, or paper_extracts.json for this case, all of which are empty or skipped due to the upstream normalization failure.

Still missing

• Rerun prefetch/normalization once VariantValidator is available to resolve gene (TP53) and transcript context.
• No functional assay data (e.g., transactivation assays, cell-based reporter assays) was retrieved or searched for this variant; literature_pass.json and paper_extracts.json contain zero PMIDs.
• TP53 VCEP CSPEC BS3 rule (if applicable) could not be consulted because cspec retrieval was skipped (no gene resolved).

Reasoning

No family members with known genotypes and phenotypes are reported, so absence of segregation cannot be evaluated. BS4 must not be applied from the absence of family data alone.

Rule

Generic BS4 requires the variant to fail to segregate with disease in informative affected or unaffected family members, after considering penetrance, age, phenocopies, and phenotype ascertainment.

Evidence considered

• The case-evidence bundle contains no non-segregation observations or family testing results.
• No evidence supports applying BS4, and missing family data cannot be treated as evidence against segregation.

Still missing

• Pedigree with informative affected and unaffected relatives
• Genotypes for relatives
• Reliable phenotype status for each tested relative
• Assessment of whether non-segregation is informative rather than attributable to age, penetrance, or phenocopy

Reasoning

BP1 (missense variant in a gene where truncating variants are the primary disease mechanism) requires the same gene-mechanism and variant-class determinations as PP2, neither of which is available. TP53:c.266_267del is a 2-bp deletion/frameshift, not a missense variant, so BP1 as classically defined would not apply, but this cannot be confirmed formally given the unresolved variant_class field.

Evidence considered

• case_summary.json compact_evidence.normalization.variant_class is null.

Still missing

• variant_class unresolved (null), preventing formal confirmation of non-missense status.
• No gene-level mechanism data (missense vs truncating primary mechanism) retrieved for this case.

Reasoning

BP2 could not be assessed. The case bundle contains no documented observation of the variant in cis with a pathogenic variant or in trans with a benign variant, and no phase or inheritance data are available. Variant normalization also failed, so the allelic relationship cannot be evaluated reliably.

Evidence considered

• The consolidated case-evidence bundle reports no literature PMIDs and no paper extracts.
• The bundle contains no cis/trans observations involving this variant and no inheritance or phase information.
• The submitted gene-only HGVS expression could not be normalized, preventing reliable allelic evaluation.

Still missing

• No cis observation with a pathogenic variant is documented.
• No trans observation with a benign variant is documented.
• Phase information is absent.
• Parental testing and inheritance information are absent.
• The submitted variant was not normalized to a transcript-level HGVS representation.
• No applicable VCEP or gene-specific BP2 specification was available.

Reasoning

BP3 requires confirming an in-frame deletion/insertion lies in a repetitive region without known function. Since the reading-frame consequence and exon/domain location of c.266_267del are unresolved, repeat-region context cannot be evaluated.

Still missing

• Resolve transcript/protein consequence and determine if variant is in-frame before repeat-region context can be assessed.
• If in-frame, check for overlap with a low-complexity/repetitive region without established function in TP53's DNA-binding or tetramerization domains.

Reasoning

Same root cause as PP3: normalization failure means no SpliceAI, REVEL, or BayesDel scores were computed, and no VCEP-specific PP3/BP4 lookup table could be consulted. There is no computational evidence of any kind (benign-direction or otherwise) available to evaluate BP4.

Evidence considered

• prefetch.json step 'normalize' failed (VariantValidator warning, Mutalyzer HTTP 422, no coordinate cache); gene and coordinates unresolved.
• prefetch.json revel and bayesdel steps skipped with reason 'not snv or no coords'; cspec step skipped with reason 'no gene'.
• evidence.json revel result skipped ('not snv or no coords'), manifest.revel.ok false; no spliceai or bayesdel entries present in evidence.json results.

Still missing

• Variant/gene normalization must succeed before any splice or missense in-silico prediction can be retrieved.
• No TP53-specific VCEP PP3/BP4 lookup table was retrieved; rerun once normalization succeeds.
• Confirm variant consequence class once transcript context is available.

Reasoning

BP5 cannot be assessed because the bundle contains no affected individual, phenotype, or evidence of an alternative molecular diagnosis that fully explains a reported phenotype.

Rule

Generic ACMG/AMP BP5: apply only when a variant is found in a case with an alternate molecular basis for disease that fully explains the phenotype.

Evidence considered

• The consolidated bundle contains no phenotype, molecular diagnosis, or dual-diagnosis information.

Still missing

• Provide the proband phenotype and molecular diagnostic workup.
• Provide evidence that an alternative molecular cause fully explains the phenotype in the affected individual.

Sources

Reasoning

BP6 cannot be assessed because ClinVar lookup was skipped after failed normalization; there is no exact-variant ClinVar expert-panel Benign or Likely benign assertion.

Rule

Apply BP6 at supporting strength only for an exact-variant ClinVar expert-panel Benign or Likely benign classification; do not use laboratory submissions, aggregate labels, or non-expert assertions.

Evidence considered

• The prefetch record states that ClinVar was skipped because no gene was available after normalization failed.
• No ClinVar submissions or expert-panel assertion are present in the consolidated bundle.

Still missing

• Normalize the submitted HGVS and retrieve the exact-variant ClinVar record and submission-level review status.
• Confirm a Benign or Likely benign assertion from a ClinVar expert panel for the exact normalized variant.

Sources