CREBBP c.7299C>A, p.(Asp2433Glu)

Reasoning

PM2 supporting is met because NM_004380.2:c.7299C>A (CREBBP p.Asp2433Glu) is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. The concordant absence supports rarity in population controls, although numeric allele-number and coverage details are not included in the bundle.

Rule

Generic ACMG/AMP PM2: variant absent from population databases or present at an extremely low frequency; applied at supporting strength for concordant absence across the queried population datasets.

Evidence considered

• The case bundle explicitly reports absence of the variant from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• This is population rarity evidence only; no disease prevalence, penetrance estimate, or homozygote observation was supplied to refine the interpretation.
• Because the bundle provides categorical absence without allele-number and coverage details, PM2 is retained at supporting strength with moderate confidence and human review flagged for population-data audit.

Still missing

• The bundle lacks numeric allele counts, allele numbers, coverage metrics, and ancestry-specific sample sizes needed to quantify the strength of the absence observation.
• No gene-specific CREBBP population-frequency specification was retrieved; generic ACMG/AMP fallback is therefore used.

Sources

Reasoning

NM_004380.2:c.7299C>A (p.(Asp2433Glu)) is a missense substitution; no CSPEC/VCEP-specific PP3/BP4 lookup material is available for CREBBP (framework_mode = generic_acmg, cspec.found = false, vcep_materials note = 'no cspec url available'), so generic calibrated computational thresholds apply. REVEL score = 0.597, which falls in the intermediate/indeterminate zone between the ClinGen SVI-calibrated benign-supporting threshold (<=0.290) and pathogenic-supporting threshold (>=0.644) established by Pejaver et al. (PMID:36413997), so REVEL does not reach the supporting threshold required for PP3. BayesDel score (0.0478) is available in prefetch data but no verified published calibration threshold for BayesDel is available to this pipeline, so it is treated as not_available and cannot be used to invoke PP3. SpliceAI max delta score = 0.003 (DS_AG 0.001, DS_AL 0.0, DS_DG 0.003, DS_DL 0.001), far below any splice-impact threshold; the variant is not in a canonical splice consensus region and is annotated as a missense/exonic substitution (canonical_splice_consensus = false), so this negligible score does not support a splice-disruption prediction and therefore cannot support PP3 via the splice-impact path either. No aGVGD data is present in the bundle. Variant is not synonymous, so BP7 does not apply.

Rule

ACMG/AMP 2015 generic PP3 (REVEL calibration per PMID:36413997; SpliceAI splice-impact path)

Evidence considered

• REVEL score 0.597 (source_registry key 'revel', local REVEL v1.3 lookup) falls between the ClinGen SVI-calibrated benign-supporting cutoff (<=0.290) and pathogenic-supporting cutoff (>=0.644) per Pejaver et al., PMID:36413997, so it does not meet the threshold required to apply PP3.
• SpliceAI max delta score = 0.003 (source_registry key 'spliceai') is negligible and does not support a splice-disruption prediction for this missense variant.
• BayesDel score 0.0477783 is present (source_registry key 'bayesdel') but excluded from consideration because no verified published calibration threshold for BayesDel is available to this pipeline.

Still missing

• REVEL 0.597 sits in the calibrated intermediate zone and cannot support PP3 at any strength.
• No verified BayesDel threshold is available to this pipeline, so BayesDel score cannot be used for PP3.
• No gene-specific CREBBP VCEP PP3/BP4 lookup material was available to override the generic calibration.

Sources

Reasoning

BA1 is not met because NM_004380.2:c.7299C>A (CREBBP p.Asp2433Glu) is absent from the queried population datasets; no allele frequency remotely approaches a benign-alone threshold.

Rule

Generic ACMG/AMP BA1: allele frequency is sufficiently high for a benign-alone criterion; not met because the variant is absent from the queried population datasets.

Evidence considered

• The bundle reports the variant as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore the BA1 frequency threshold is not reached.
• No population frequency, ancestry-specific enrichment, or threshold artifact supports BA1.

Still missing

• The case bundle does not provide numeric allele counts, allele number, or ancestry-stratified coverage metrics for the absent records, although the categorical absence results are concordant across datasets.

Sources

Reasoning

BS1 is not met because the variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no observed frequency exceeds the expected-disease-prevalence threshold.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; not met because no population observation or elevated frequency is reported.

Evidence considered

• All three queried population resources report categorical absence of NM_004380.2:c.7299C>A; thus there is no frequency signal supporting BS1.
• No disease-prevalence, penetrance, ancestry, or population-frequency artifact changes this conclusion.

Still missing

• The bundle does not provide numeric allele counts, allele number, or ancestry-stratified coverage metrics for the absent records.

Sources

Reasoning

Using the same generic calibrated thresholds (no CREBBP-specific VCEP PP3/BP4 lookup is available), REVEL score = 0.597 also fails to reach the benign-supporting threshold (<=0.290) from Pejaver et al. (PMID:36413997), so it cannot support BP4 either -- the score sits in the indeterminate zone, not the benign-predicted zone. BayesDel score (0.0478) is present but is treated as not_available for this pipeline because no verified published calibration threshold has been confirmed, so it cannot be used to invoke BP4. SpliceAI max delta score = 0.003 is very low and consistent with no predicted splice disruption, but this variant is a missense substitution with no canonical splice consensus involvement (canonical_splice_consensus = false) and no indication that a splicing mechanism is plausible for this exonic change; the low SpliceAI score therefore does not constitute an independent affirmative in-silico benign prediction relevant to this variant's primary (missense) consequence, and applying BP4 solely on an uninvoked splice-impact path would not be a genuine, mechanism-relevant application of that sub-path. Variant is not synonymous, so BP7 does not apply.

Rule

ACMG/AMP 2015 generic BP4 (REVEL calibration per PMID:36413997; SpliceAI splice-impact path not mechanistically applicable)

Evidence considered

• REVEL score 0.597 (source_registry key 'revel') does not reach the benign-supporting threshold of <=0.290 from the ClinGen SVI REVEL calibration (Pejaver et al., PMID:36413997), so BP4 cannot be applied via the missense in-silico path.
• SpliceAI max delta score = 0.003 (source_registry key 'spliceai') indicates no predicted splice disruption but is not applied toward BP4 because the variant is missense with no plausible splicing mechanism (not in canonical splice consensus).
• BayesDel score 0.0477783 is present (source_registry key 'bayesdel') but excluded from consideration because no verified published calibration threshold for BayesDel is available to this pipeline.

Still missing

• REVEL 0.597 sits in the calibrated intermediate zone and cannot support BP4 at any strength.
• No verified BayesDel threshold is available to this pipeline, so BayesDel score cannot be used for BP4.
• SpliceAI's negligible score is not being invoked for BP4 because splicing is not a plausible mechanism for this missense, non-splice-region variant.
• No gene-specific CREBBP VCEP PP3/BP4 lookup material was available to override the generic calibration.

Sources

Reasoning

No ClinGen CREBBP VCEP or local gene-specific framework is available for this case (cspec.found=false, framework_mode=generic_acmg), so PS1 falls back to generic ACMG/AMP guidance requiring a known pathogenic variant that produces the identical amino acid change (p.Asp2433Glu) via a different nucleotide substitution. ClinVar returned no result for this variant and no candidate same-residue/same-amino-acid comparator variants were surfaced anywhere in the bundle (literature_pass.json is empty with 0 PMIDs, and pm5_candidates explicitly notes candidate harvesting was skipped). There is no evidence in this bundle of any other pathogenic variant at codon 2433 producing Glu, so PS1 cannot be met, but the absence of a comparator search result (rather than a confirmed absence of any pathogenic p.Asp2433Glu report in the literature/ClinVar at large) means this should be treated as not_assessed pending a dedicated ClinVar/literature search for p.(Asp2433Glu) reports.

Rule

PS1 (generic ACMG/AMP, no applicable CSPEC/VCEP framework found): same amino acid change (p.Asp2433Glu) as an established pathogenic variant, arising from a different nucleotide substitution, with no evidence the alternate change affects splicing.

Evidence considered

• ClinVar search for CREBBP c.7299C>A and NM_004380.2:c.7299C>A returned no_result / found=false, confirming this exact variant is absent from ClinVar and yielding no immediate comparator for the same amino acid change.
• literature_pass.json reports total_pmids=0 with note 'No PMIDs found across evidence sources', so no literature-derived same-amino-acid-change comparator was identified for review.

Still missing

• No ClinVar record for this variant or any same-amino-acid-change comparator at codon 2433
• No literature search results (0 PMIDs) to check for reports of p.(Asp2433Glu) as pathogenic via an alternate nucleotide change
• No CREBBP-specific VCEP PS1 rule available to define required strength or exceptions

Sources

Reasoning

No case-level evidence is provided for a confirmed de novo occurrence in the proband. The evidence bundle contains no proband pedigree details, parental test results, maternity/paternity confirmation, or phenotype-linked de novo observation for NM_004380.2:c.7299C>A.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in an affected individual with confirmed maternity and paternity, with phenotype consistent with the disease; strength depends on the quality and completeness of de novo evidence.

Evidence considered

• The consolidated case-evidence bundle provides no proband, parental testing, maternity/paternity, or de novo evidence for this variant.
• No relevant literature PMIDs were identified in the literature pass, and no publication was reviewed for this criterion.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP fallback was therefore used for the criterion definition only.

Still missing

• Documented proband phenotype and diagnosis
• Variant testing results in both biological parents
• Confirmation of maternity and paternity or equivalent relationship testing
• Assessment for parental mosaicism where relevant

Sources

Reasoning

No CSPEC/VCEP is available for CREBBP in this case (cspec.found=false; final_classification_framework.found=false, generic ACMG fallback), so no gene-specific PS3 functional-assay framework exists. The evidence bundle (review_manifest, case_summary, source_registry, prefetch, evidence, literature_pass, vcep_materials, fulltext_map) contains no functional/enzymatic/reporter/complementation assay data for NM_004380.2:c.7299C>A (p.Asp2433Glu). No PMID or source in this case describes a validated functional assay, well-established in vitro or in vivo study, or assay controls addressing this specific variant.

Still missing

• No functional assay data (biochemical, cell-based, animal model, or high-throughput) identified for this variant anywhere in the evidence bundle.
• No CREBBP-specific VCEP PS3 framework (assay validation tiers, control requirements) is available for this case.

Reasoning

No affected-case series, case-control enrichment analysis, or statistically significant excess of this exact variant was provided. The available bundle contains no literature PMIDs or case-level phenotype evidence sufficient to assess PS4.

Rule

Generic ACMG/AMP PS4: assess statistically significant enrichment of the variant in affected individuals compared with controls or a sufficiently compelling affected-case series; do not infer PS4 from the gene or disease association alone.

Evidence considered

• The case bundle reports no PMIDs across evidence sources and provides no affected-case or control cohort data for NM_004380.2:c.7299C>A.
• PS4 requires evidence that the variant is enriched in affected individuals relative to controls; that evidence is unavailable here.

Still missing

• Affected-case counts and an appropriate control comparison for the exact variant are unavailable.
• No validated case-control enrichment statistic or phenotype-specific case series is available.

Reasoning

No ClinGen CREBBP VCEP framework or local gene-specific mutational hotspot/domain map is present in this bundle (cspec.found=false; gene_vcep_dir=null). CREBBP is a large multidomain transcriptional co-activator (KIX, bromodomain, HAT catalytic domain, ZZ-type zinc finger, TAZ2, NCBD), but this bundle contains no residue-level structural/domain annotation pinpointing where codon 2433 falls relative to those domains, and no mutational-hotspot statistics (cancer hotspot search returned no significant hotspot at D2433, but that resource is somatic-cancer-oriented and not a substitute for a germline critical-domain determination). Without a domain/hotspot source specifically covering residue 2433, PM1 cannot be confidently assessed either way under generic ACMG/AMP guidance.

Rule

PM1 (generic ACMG/AMP, no applicable CSPEC/VCEP framework found): variant located in a mutational hotspot or well-established functional/structural domain without benign variation.

Evidence considered

• case_summary.json compact_evidence.hotspots reports 'This variant does not lie in a statistically significant hotspot' from cancerhotspots.org, a somatic-cancer mutational hotspot resource that does not directly establish or exclude germline functional-domain criticality for PM1 purposes.

Still missing

• No CREBBP VCEP or gene-specific critical-domain/hotspot map available in this case bundle
• No structural/domain annotation resource confirming whether residue 2433 lies within a defined functional domain (e.g., TAZ2, NCBD) or a low-complexity/unstructured region
• Somatic cancer hotspot databases (cancerhotspots.org) are not a validated proxy for germline PM1 domain criticality in Rubinstein-Taybi syndrome

Reasoning

No affected-proband observations, phase information, or identified pathogenic/likely pathogenic variant in trans were provided for NM_004380.2:c.7299C>A (NP_004371.2:p.(Asp2433Glu)). Therefore, the generic PM3 criterion cannot be assessed.

Rule

Generic PM3: evidence that the variant is observed in trans with a pathogenic variant in an affected individual supports pathogenicity; strength depends on the number and quality of informative observations.

Evidence considered

• The case-evidence bundle contains no family segregation, affected-proband, parental-testing, or cis/trans-phase evidence for this variant.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP criteria were therefore considered.

Still missing

• Affected-proband observations are unavailable.
• Parental testing and phase information are unavailable.
• No pathogenic or likely pathogenic variant in trans has been documented.

Reasoning

The pm5_candidates.json artifact explicitly reports pm5_mode='unknown' and eligible_for_classic_pm5_search=false, with the recommendation stating the pipeline could not confirm classic same-residue PM5 semantics safely and therefore skipped automatic comparator harvesting (total_candidates_seen=0). ClinVar itself returned no result for this variant or gene/residue query pattern. No other same-codon (residue 2433) missense comparator variants with pathogenic/likely pathogenic classifications were surfaced anywhere in the evidence bundle, so there is no basis to assess whether a different amino acid substitution at this codon has been classified as pathogenic.

Rule

PM5 (generic ACMG/AMP, no applicable CSPEC/VCEP framework found): a different missense change at the same residue has been established as pathogenic.

Evidence considered

• pm5_candidates.json recommendation: 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting' with candidate_summary showing total_candidates_seen=0 and same_residue_candidates=0.
• ClinVar search for this variant/gene returned search_status='no_result', found=false, providing no comparator variant data at codon 2433.

Still missing

• Automated PM5 comparator candidate harvesting was explicitly skipped by the pipeline (pm5_mode=unknown, eligible_for_classic_pm5_search=false)
• No confirmed pathogenic/likely pathogenic ClinVar variants at codon 2433 with an alternate amino acid change were identified
• A manual ClinVar/literature search specifically for other missense substitutions at residue Asp2433 has not been performed in this bundle

Sources

Reasoning

No case-level evidence is provided for an assumed de novo occurrence. There are no documented parental test results, pedigree observations, or other evidence establishing that NM_004380.2:c.7299C>A arose de novo without confirmed maternity and paternity.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in an affected individual when maternity and paternity are not confirmed; evidence is weaker than confirmed de novo evidence and must be supported by a consistent phenotype and credible parental-origin data.

Evidence considered

• The consolidated case-evidence bundle contains no assumed-de-novo or parental-origin information for this variant.
• No relevant literature PMIDs were identified in the literature pass, and no publication was reviewed for this criterion.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP fallback was therefore used for the criterion definition only.

Still missing

• Documented affected proband and phenotype consistency
• Evidence that the variant is absent from tested parents or other de novo support
• Maternity and paternity confirmation
• Information on parental mosaicism and assay sensitivity

Sources

Reasoning

No segregation data are available. The evidence bundle does not identify informative affected or unaffected relatives, the number of informative meioses, genotype/phenotype results, or a consistent pattern of co-segregation for NM_004380.2:c.7299C>A.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene definitively associated with the disease; strength may increase with multiple informative meioses when justified by the applicable framework.

Evidence considered

• The consolidated case-evidence bundle contains no family segregation observations or informative meiosis count for this variant.
• No relevant literature PMIDs were identified in the literature pass, and no publication was reviewed for this criterion.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP fallback was therefore used for the criterion definition only.

Still missing

• Pedigree containing affected and unaffected relatives
• Genotype results for informative relatives
• Phenotype status and diagnostic criteria for each relative
• Number of informative meioses and segregation analysis

Sources

Reasoning

No ClinGen CREBBP VCEP framework is available to specify PP2 applicability or thresholds for this gene. Generic ACMG/AMP PP2 requires that missense variants are a common mechanism of disease in the gene AND that the gene shows a low rate of benign missense variation. The pvs1_gene_context artifact establishes that CREBBP-related Rubinstein-Taybi syndrome is predominantly a loss-of-function/haploinsufficiency disorder (mechanism_rationale confirms LOF as the supported germline mechanism), while one cited cohort study found missense variants accounted for only 4/17 (24%) of pathogenic CREBBP/EP300 findings versus predominance of frameshift, nonsense, splice-site, and CNV LOF events. This bundle contains no gene-level missense constraint metric (e.g., missense Z-score or o/e ratio) or a formal statement that missense is a 'common mechanism' of CREBBP disease as required to affirmatively meet PP2, so the criterion cannot be confidently resolved as met or not met from the data present.

Rule

PP2 (generic ACMG/AMP, no applicable CSPEC/VCEP framework found): missense variant in a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• pvs1_gene_context.json mechanism_rationale: 'Targeted germline literature review identified disease-focused publications supporting CREBBP loss of function as a germline disease mechanism,' indicating LOF/haploinsufficiency, not missense gain/dominant-negative effect, is the primary established CREBBP disease mechanism.
• pvs1_gene_context.json supporting literature (PMID:41153422 abstract snippet) reports pathogenic CREBBP/EP300 variant types in a 17-patient RSTS cohort as frameshift indels (6/17, 35%), missense (4/17, 24%), nonsense (3/17, 18%), splice-site (2/17, 12%), and gross deletions (2/17, 12%), showing missense variants are a real but minority mechanism relative to truncating/LOF events.

Still missing

• No CREBBP-specific VCEP PP2 rule or benign-missense-rate threshold available
• No gene-level missense constraint metric (e.g., gnomAD missense Z-score/o:e) present in this bundle
• Available literature context (via pvs1_gene_context) indicates LOF/haploinsufficiency is the primary supported disease mechanism, with missense variants a minority of reported pathogenic events, which weighs against but does not conclusively resolve PP2 applicability

Sources

Reasoning

No patient phenotype, clinical feature set, or disease-specific phenotype comparison was supplied for the variant. Phenotype specificity therefore cannot be assessed.

Rule

Generic ACMG/AMP PP4: apply only when the patient's phenotype or family history is highly specific for a disease with a single-gene etiology; gene-level disease knowledge alone is insufficient.

Evidence considered

• The consolidated bundle contains no case phenotype description and no literature evidence tied to this exact variant.
• PP4 cannot be applied from CREBBP gene membership or a general disease association without a documented, highly specific patient phenotype.

Still missing

• Individual clinical phenotype and diagnostic phenotype details are unavailable.
• No comparison of the observed phenotype with the highly specific phenotype of a CREBBP-related disorder is available.

Reasoning

BS2 cannot be established from this case bundle. The population resources report absence of the variant, but do not provide observations of unaffected healthy adults, homozygotes, or a validated penetrance context.

Rule

Generic ACMG/AMP BS2: observation in healthy adults, including homozygotes for a recessive disorder, for a fully penetrant early-onset disorder; not assessable without such observations and phenotype/penetrance context.

Evidence considered

• The queried population datasets report the variant as absent rather than documenting unaffected carriers or homozygotes.
• Absence from population databases is not evidence that the variant occurs in healthy adults and therefore cannot satisfy BS2.

Still missing

• No healthy-adult carrier observations are reported.
• No homozygote observations are reported.
• No phenotype, age, ascertainment, or penetrance data are available to evaluate whether an observed carrier would be unaffected despite a fully penetrant early-onset disorder.

Sources

Reasoning

No CSPEC/VCEP is available for CREBBP in this case (cspec.found=false; final_classification_framework.found=false, generic ACMG fallback), so no gene-specific BS3 functional-assay framework exists. The evidence bundle contains no functional/enzymatic/reporter/complementation assay data showing normal or near-normal function for NM_004380.2:c.7299C>A (p.Asp2433Glu). No PMID or source in this case describes a validated functional assay demonstrating no functional impact for this specific variant.

Still missing

• No functional assay data (biochemical, cell-based, animal model, or high-throughput) identified for this variant anywhere in the evidence bundle.
• No CREBBP-specific VCEP BS3 framework (assay validation tiers, control requirements) is available for this case.

Reasoning

No non-segregation evidence is available. The evidence bundle does not report unaffected relatives who carry NM_004380.2:c.7299C>A, nor does it provide phenotype evaluations, age-related penetrance information, or informative meioses sufficient to assess lack of segregation.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected family members, or presence of the variant in appropriately evaluated unaffected relatives, when the family is informative and penetrance/phenocopy considerations are addressed.

Evidence considered

• The consolidated case-evidence bundle contains no unaffected carrier observations or other non-segregation data for this variant.
• No relevant literature PMIDs were identified in the literature pass, and no publication was reviewed for this criterion.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP fallback was therefore used for the criterion definition only.

Still missing

• Genotype results in clinically well-characterized unaffected relatives
• Age and phenotype assessment adequate for expected penetrance
• Pedigree structure and informative meioses
• Assessment for reduced penetrance, phenocopy, or variable expressivity

Sources

Reasoning

No affected-proband or family observations demonstrate NM_004380.2:c.7299C>A in cis or trans with a pathogenic variant, and no phase information is available. Therefore, the generic BP2 criterion cannot be assessed.

Rule

Generic BP2: the variant is observed in trans with a pathogenic variant for a fully penetrant dominant disorder or in cis with a pathogenic variant for a recessive disorder, supporting a benign interpretation when the inheritance and phase context are informative.

Evidence considered

• The case-evidence bundle contains no family segregation, affected-proband, parental-testing, or cis/trans-phase evidence relevant to BP2.
• No CREBBP-specific VCEP/CSPEC framework was available; generic ACMG/AMP criteria were therefore considered.

Still missing

• Evidence for occurrence with another pathogenic variant in cis or trans is unavailable.
• Parental testing and phase information are unavailable.
• No informative affected or unaffected individual observations are documented.

Reasoning

No evidence was provided that an affected individual has an alternative molecular diagnosis that explains the phenotype and thereby argues against this variant as the cause. BP5 cannot be assessed from the absence of ClinVar, population data, or gene-level information.

Rule

Generic ACMG/AMP BP5: apply only when an affected individual has a molecular diagnosis that provides an alternative explanation for the phenotype; do not infer BP5 from a negative database search or from another variant's classification alone.

Evidence considered

• The case bundle contains no alternative molecular diagnosis or phenotype-linked competing variant for the patient.
• BP5 requires a documented alternative molecular basis for the phenotype; no such evidence is available.

Still missing

• The patient's molecular workup and any confirmed alternative molecular diagnosis are unavailable.
• No evidence links an alternative molecular cause to the patient's phenotype.