CCNE1 c.617A>G, p.(Tyr206Cys)

Reasoning

PM2 is met at supporting strength. Although present in population databases, the highest observed AF is 0.05612% in gnomAD v2.1 African/African American samples; gnomAD v4.1 overall AF is 0.03094% and its grpmax FAF is 0.034706%. All are below the generic PM2 rarity threshold of 0.1%.

Rule

Generic ACMG/AMP population-frequency fallback: PM2_supporting applies when the variant is absent or has an AF <0.1% in population databases; no CCNE1-specific modification was retrieved.

Evidence considered

• gnomAD v2.1: 62/282,496 alleles (AF 0.02195%), highest African/African American AF 0.05612%, zero homozygotes.
• gnomAD v4.1: 496/1,602,884 alleles (AF 0.03094%), highest African/African American AF 0.04547%, grpmax FAF 0.034706%, zero homozygotes.
• gnomAD-Canada v1.0: 2/18,422 alleles (AF 0.01086%), zero homozygotes.

Sources

Reasoning

No CCNE1 VCEP specification exists, so generic ACMG/AMP computational evidence rules apply. SpliceAI predicts no splice impact for NM_001238.4:c.617A>G (max delta score = 0.011 across DS_AG/DS_AL/DS_DG/DS_DL), well below the ~0.2 high-recall splice-altering cutoff established by Jaganathan et al. (Cell 2019, PMID 30661751), supporting the absence of a splicing mechanism and warranting BP4 at supporting strength. The REVEL missense score (0.465) is indeterminate under the Pejaver et al. calibrated thresholds (PMID 36413997) -- it does not cross the <=0.290 benign-supporting cutoff, so it neither adds to nor withholds this BP4 call, which is driven by the splicing-negative SpliceAI result. BayesDel (0.115237) has no verified published threshold available to this pipeline and is excluded from consideration per policy.

Rule

generic_acmg_fallback

Evidence considered

• SpliceAI max delta score = 0.011 (all four component scores DS_AG/DS_AL/DS_DG/DS_DL <= 0.011), interpreted against the ~0.2 high-recall splice-altering threshold from Jaganathan K et al., Cell 2019, PMID 30661751, indicating no predicted splicing impact.
• REVEL score 0.465 (local REVEL v1.3 lookup) does not cross the ClinGen SVI-calibrated BP4-supporting threshold (<=0.290) from Pejaver V et al., PMID 36413997, so it is indeterminate and not independently used to support BP4.
• BayesDel score 0.115237 reported in evidence.json/prefetch.json but excluded because no verified published calibration threshold for BayesDel is available to this pipeline.

Still missing

• REVEL score alone is indeterminate and does not independently corroborate a benign missense computational signal.
• No verified BayesDel threshold available to add a second concordant missense in-silico line of evidence.

Sources

Reasoning

PM1 requires the variant to fall in a well-established mutational hotspot or critical functional domain without benign variation. Cancerhotspots.org was queried directly for CCNE1 Y206 and returned no result, i.e. this residue is not a statistically significant hotspot in the surveyed cancer cohorts. OncoKB likewise has no variant-specific reviewed functional/oncogenic evidence for Y206C (classification 'Unknown Oncogenic Effect', not_reviewed=true), only generic gene-level context that CCNE1 is a cell-cycle regulator amplified in various cancers. No structural/domain annotation (e.g., Pfam cyclin_N/cyclin_C boundaries) was retrieved in this case's evidence to establish that residue 206 lies in a critical, invariant functional domain. Given the explicit negative hotspot finding and lack of any positive domain-criticality evidence, PM1 is not met on the evidence available, though the absence of domain-mapping data means this should be confirmed by a reviewer with UniProt/Pfam domain boundaries for CCNE1 before finalizing.

Evidence considered

• cancerhotspots.org query for 'CCNE1 Y206' returned no_result / not found, with evidence_sentence: 'This variant does not lie in a statistically significant hotspot.' (source not present as a source_registry key in this case bundle, so not citable via evidence_refs).
• OncoKB page for CCNE1 Y206C found but not_reviewed=true, is_variant_specific=false, classification 'Unknown Oncogenic Effect'; only gene-level summary available ('CCNE1, a regulator of the cell cycle, is amplified in various cancer types').

Still missing

• No UniProt/Pfam/InterPro domain boundary data for CCNE1 was retrieved to confirm or exclude residue 206 from a cyclin-fold functional domain
• cancerhotspots.org source key is not present in this case's source_registry, so the negative hotspot finding is documented narratively rather than cited by key

Sources

Reasoning

CCNE1 has no governing VCEP/gene-specific specification (gene_vcep_dir null, vcep_materials.json empty, final_classification_framework falls back to generic ACMG/AMP 2015); no gene-specific PP3/BP4 lookup table is available to pre-assign a code. NM_001238.4:c.617A>G (p.Tyr206Cys) is a missense substitution, so the missense in-silico path applies. REVEL score = 0.465 (local REVEL v1.3 lookup), which falls between the calibrated ClinGen SVI benign-supporting threshold (<=0.290) and pathogenic-supporting threshold (>=0.644) established by Pejaver et al. (PMID 36413997); this is an indeterminate zone and does not meet the PP3 threshold. BayesDel score (0.115237) is available in prefetch/evidence data but no verified published calibration threshold for BayesDel is available to this pipeline, so it is treated as not_available and cannot support PP3. SpliceAI max delta score = 0.011, far below any published splice-altering threshold (Jaganathan et al., PMID 30661751, ~0.2 high-recall cutoff), so splicing evidence does not support PP3 either. No computational evidence line meets the PP3 threshold.

Rule

generic_acmg_fallback

Evidence considered

• REVEL score 0.465 (local REVEL v1.3 predictor lookup) falls in the indeterminate zone between the ClinGen SVI-calibrated BP4-supporting threshold (<=0.290) and PP3-supporting threshold (>=0.644) from Pejaver V et al., 'Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria', PMID 36413997.
• BayesDel score 0.115237 reported in evidence.json/prefetch.json, but no named published calibration threshold for BayesDel is available to this pipeline, so it is treated as not_available for PP3/BP4 per policy.
• SpliceAI scores: DS_AG=0.002, DS_AL=0.001, DS_DG=0.011, DS_DL=0.001, max_delta_score=0.011 (SpliceAI Lookup), well below the ~0.2 high-recall splice-altering threshold established in Jaganathan K et al., 'Predicting Splicing from Primary Sequence with Deep Learning', Cell 2019, PMID 30661751; this argues against a splicing mechanism, not for one.

Still missing

• No verified published BayesDel threshold available to this pipeline to independently corroborate or refute PP3 for the missense change.
• No gene/VCEP-specific PP3/BP4 lookup spreadsheet exists for CCNE1.

Sources

Reasoning

BA1 is not met. The highest observed population AF is 0.05612% in gnomAD v2.1 African/African American samples (14/24,946 alleles); gnomAD v4.1 overall AF is 0.03094% (496/1,602,884 alleles), with maximum ancestry-group AF 0.04547% in African/African American samples (34/74,774 alleles). These values are far below the generic 5% BA1 threshold.

Rule

Generic ACMG/AMP population-frequency fallback: BA1 requires AF >=5%.

Evidence considered

• No CCNE1 VCEP or gene-specific specification was retrieved; the generic ACMG/AMP fallback applies.
• gnomAD v2.1: total AF 0.02195% (62/282,496 alleles), highest ancestry-group AF 0.05612% in African/African American samples, and zero homozygotes.
• gnomAD v4.1: total AF 0.03094% (496/1,602,884 alleles), highest ancestry-group AF 0.04547% in African/African American samples, and zero homozygotes.

Sources

Reasoning

BS1 is not met. The highest observed ancestry-group AF, 0.05612% in gnomAD v2.1 African/African American samples, and gnomAD v4.1 grpmax FAF, 0.034706%, are below the generic 0.3% BS1 threshold.

Rule

Generic ACMG/AMP population-frequency fallback: BS1 requires AF >0.3%.

Evidence considered

• gnomAD v2.1 reports an African/African American AF of 0.05612% (14/24,946 alleles) and a grpmax FAF of 0.037677%.
• gnomAD v4.1 reports an African/African American AF of 0.04547% (34/74,774 alleles) and a grpmax FAF of 0.034706%.

Sources

Reasoning

BS2 is not met. gnomAD v2.1 and v4.1 each report zero homozygotes, and the supplied population records do not identify any qualifying healthy adult carriers with phenotype and age data sufficient for BS2.

Rule

Generic ACMG/AMP BS2 requires observation in healthy adult individual(s) for a fully penetrant early-onset disorder; frequency observations without qualifying health and age data do not satisfy BS2.

Evidence considered

• gnomAD v2.1 reports zero homozygotes among 282,496 alleles.
• gnomAD v4.1 reports zero homozygotes among 1,602,884 alleles.
• gnomAD-Canada v1.0 reports 2/18,422 alleles and zero homozygotes; this frequency dataset alone does not establish healthy adult carrier status.

Still missing

• No phenotype-ascertained healthy-adult carrier cohort or disease-specific age/penetrance framework was provided.

Sources

Reasoning

PS1 requires a previously established pathogenic variant that produces the identical amino acid change (p.Tyr206Cys) via a different nucleotide substitution. No cspec/VCEP is defined for CCNE1 (generic ACMG fallback), ClinVar has no entry for NM_001238.4:c.617A>G itself, and no systematic search for alternate codon-206 changes to Cys with an established pathogenic classification was captured in this case's evidence bundle (no PMIDs, no literature_pass hits, empty pm5_candidates harvest). There is therefore no positive or negative evidence to adjudicate PS1.

Evidence considered

• ClinVar search for CCNE1 c.617A>G returned no result ('This variant is absent from ClinVar'), providing no direct or comparator classification to invoke PS1.
• pm5_candidates.json (same underlying comparator-variant harvesting process used for PS1/PM5) reports zero total candidates seen and explicitly recommends against automated application because classic same-residue semantics could not be confirmed safely.

Still missing

• No comparator search results for other nucleotide substitutions producing p.Tyr206Cys with an established pathogenic/likely pathogenic classification
• No ClinVar record for this variant to anchor a same-change comparison
• No CCNE1-specific VCEP/cspec available to define PS1 usage for this gene

Sources

Reasoning

No proband-level result, parental genotypes, parentage confirmation, phenotype information, or de novo observation is provided. PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in an affected individual with maternity and paternity confirmed.

Evidence considered

• No CCNE1 VCEP specification was retrieved; the case is designated for generic ACMG/AMP fallback.
• The supplied evidence bundle contains no proband or parental testing data and no documented de novo occurrence for NM_001238.4:c.617A>G (p.Tyr206Cys).

Still missing

• Obtain the proband genotype and phenotype.
• Obtain testing of both biological parents with parentage confirmation and assess phenotype consistency.

Sources

Reasoning

No validated functional/biochemical assay data (e.g., cyclin E1-CDK2 kinase activity, degradation/stability assays, cell cycle progression assays) for NM_001238.4:c.617A>G (p.Tyr206Cys) were identified in any source. No CCNE1 ClinGen VCEP specification exists (framework_mode: generic_acmg; no cspec found), so no gene-specific PS3 assay calibration is available either. OncoKB explicitly reports no variant-specific reviewed functional evidence for this variant. The literature search returned zero PMIDs overall, and no functional-study publications were retrieved or reviewed for this variant.

Still missing

• No functional assay publication identified that tests this specific variant (p.Tyr206Cys) in CCNE1.
• No CCNE1-specific VCEP functional assay framework available to calibrate assay validity/strength.
• OncoKB and other evidence sources returned no variant-specific functional data.

Reasoning

No qualifying case-control or cohort enrichment data for CCNE1 c.617A>G (p.Tyr206Cys) were retrieved.

Rule

Generic ACMG/AMP PS4: the variant must be significantly enriched in affected individuals compared with controls.

Evidence considered

• The consolidated literature pass reports zero PMIDs and no high- or medium-priority papers for this exact variant.
• No applicable CCNE1 VCEP/ClinGen gene-specific specification was retrieved; generic ACMG/AMP assessment applies.

Still missing

• A controlled case series or case-control study reporting this exact variant in a defined CCNE1-associated phenotype, with adequate control data and ascertainment details.

Reasoning

No applicable CCNE1 VCEP/gene-specific specification was retrieved. Under the generic ACMG/AMP framework, there is no documented affected proband with NM_001238.4:c.617A>G in trans with a pathogenic or likely pathogenic allele, and no phase or segregation data. PM3 cannot be assessed.

Rule

Generic ACMG/AMP PM3; no applicable gene-specific specification was retrieved.

Evidence considered

• The case bundle reports no CCNE1 CSPEC/VCEP material and designates generic ACMG/AMP fallback.
• The case bundle contains no literature records, affected-proband observations, second alleles, phase data, or inheritance/segregation data for NM_001238.4:c.617A>G.

Still missing

• Affected-proband genotype data for a relevant recessive CCNE1-associated condition.
• Classification of any second allele and confirmed trans phase by parental testing or other validated phasing method.

Reasoning

PM5 requires a different missense change at the same residue (codon 206) previously established as pathogenic. The case's own pm5_candidates harvesting step reports pm5_mode 'unknown', eligible_for_classic_pm5_search=false, zero total candidates seen, zero same-residue candidates, and explicitly instructs that PM5 should not be applied from this artifact alone because classic same-residue semantics could not be confirmed safely. No other source in the bundle (ClinVar, literature_pass, OncoKB) surfaces an alternate codon-206 missense variant with an established pathogenic classification. There is insufficient evidence to assess PM5 in either direction.

Evidence considered

• pm5_candidates.json summary: total_candidates_seen=0, same_residue_candidates=0, recommendation level='not_applicable', summary: 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting.'
• ClinVar search for CCNE1 c.617A>G returned no_result, and no separate codon-206 comparator search was captured in this case's evidence.

Still missing

• No confirmed harvesting of alternate p.Tyr206X missense variants with pathogenic/likely pathogenic classification was performed
• ClinVar returned no entries for this gene/codon region to check for comparator classifications

Sources

Reasoning

No affected proband with absence of the variant in parents, or other presumed de novo observation, is documented. PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence without confirmed maternity and paternity.

Evidence considered

• No CCNE1 VCEP specification was retrieved; the case is designated for generic ACMG/AMP fallback.
• The supplied evidence bundle contains no proband or parental testing data and no documented de novo occurrence for NM_001238.4:c.617A>G (p.Tyr206Cys).

Still missing

• Obtain the proband genotype and phenotype.
• Obtain parental testing or a documented presumed de novo report, including the basis for absent parentage confirmation.

Sources

Reasoning

No pedigree, affected or unaffected relative genotypes, phenotype assignments, or informative meioses are provided. PP1 cannot be assessed.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No CCNE1 VCEP specification was retrieved; the case is designated for generic ACMG/AMP fallback.
• The supplied evidence bundle contains no familial genotype-phenotype segregation data for NM_001238.4:c.617A>G (p.Tyr206Cys).

Still missing

• Obtain a pedigree with genotypes and phenotype status for informative relatives.
• Document informative segregations and meioses, including penetrance- and age-related considerations.

Sources

Reasoning

PP2 requires that missense variants be a common mechanism of disease in this gene and that benign missense variation be uncommon. No CCNE1-specific VCEP/cspec is available (framework_mode='generic_acmg', cspec.found=false), and no gene-level missense-vs-benign constraint data, ClinGen gene curation, or disease-mechanism statement was captured in this case's evidence bundle. Available context (OncoKB gene summary) characterizes CCNE1 as a cell-cycle regulator that is amplified (copy-number gain) in various cancers -- an amplification/gain-of-function oncogene mechanism -- rather than describing missense variation as an established disease mechanism for a Mendelian condition. This is insufficient, and of an inconsistent type, to support or refute PP2.

Evidence considered

• OncoKB gene-level summary states CCNE1 'is amplified in various cancer types', consistent with an oncogene/copy-number-gain mechanism rather than an established missense-disease mechanism; no missense-constraint or gene curation data was otherwise available in this case's evidence bundle.

Still missing

• No ClinGen gene-disease validity or missense constraint (e.g., gnomAD missense Z-score, domain-level tolerance) data retrieved for CCNE1
• No statement establishing missense variation (versus amplification/LOF) as the primary pathogenic mechanism for CCNE1 in a defined Mendelian phenotype

Sources

Reasoning

No proband phenotype, phenotype-to-gene specificity assessment, or exact-variant clinical case evidence was retrieved for this case.

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 literature pass reports zero PMIDs for the exact variant.
• No applicable CCNE1 VCEP/ClinGen gene-specific specification was retrieved; generic ACMG/AMP assessment applies.

Still missing

• A documented patient phenotype and evidence that the phenotype is highly specific for a CCNE1-associated condition, with alternative genetic causes reasonably excluded.

Reasoning

The exact variant is absent from ClinVar; therefore no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is available.

Rule

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

Evidence considered

• ClinVar search returned no result for CCNE1 c.617A>G; no expert-panel assertion was present.

Still missing

• An exact-variant ClinVar submission from an expert panel classifying the variant as Pathogenic or Likely pathogenic.

Sources

Reasoning

No functional/biochemical assay data showing normal or near-normal activity for NM_001238.4:c.617A>G (p.Tyr206Cys) were identified in any source. No CCNE1 ClinGen VCEP specification exists to calibrate BS3 assay validity, and no functional-study publications were retrieved (literature search returned zero PMIDs). OncoKB explicitly reports no variant-specific reviewed functional evidence for this variant.

Still missing

• No functional assay publication identified that tests this specific variant and shows benign/wild-type-like function.
• No CCNE1-specific VCEP functional assay framework available to calibrate assay validity/strength.
• No functional evidence source (OncoKB, literature) returned variant-specific data.

Reasoning

No informative non-segregation observation is provided, such as a well-phenotyped affected non-carrier or an unaffected carrier assessed in the context of penetrance and age. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family.

Evidence considered

• No CCNE1 VCEP specification was retrieved; the case is designated for generic ACMG/AMP fallback.
• The supplied evidence bundle contains no familial non-segregation data for NM_001238.4:c.617A>G (p.Tyr206Cys).

Still missing

• Obtain genotypes and phenotype status for informative affected and unaffected relatives.
• Evaluate any apparent non-segregation against disease definition, penetrance, age of onset, and phenocopy risk.

Sources

Reasoning

BP1 requires that the gene's disease mechanism is predominantly loss-of-function/truncating, such that a missense variant would be less likely pathogenic. No CCNE1-specific VCEP/cspec is available and no gene-level mechanism data (truncating-variant enrichment, ClinGen curation) was captured in this case's evidence bundle to support or refute this. Insufficient evidence to assess.

Still missing

• No gene-level curation data establishing whether truncating variants are the predominant disease mechanism for CCNE1

Reasoning

No applicable CCNE1 VCEP/gene-specific specification was retrieved. The case bundle provides no observation of NM_001238.4:c.617A>G in cis with a pathogenic or likely pathogenic variant, nor a documented alternative molecular diagnosis in an affected individual. BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2; no applicable gene-specific specification was retrieved.

Evidence considered

• The case bundle reports no CCNE1 CSPEC/VCEP material and designates generic ACMG/AMP fallback.
• The case bundle contains no literature records, co-occurring pathogenic variants, phase data, affected-proband observations, or inheritance/segregation data for NM_001238.4:c.617A>G.

Still missing

• A documented individual carrying NM_001238.4:c.617A>G together with a pathogenic or likely pathogenic allele, with validated cis phase.
• Phenotype and inheritance information sufficient to determine whether the co-occurrence is informative for the relevant disease mechanism.

Reasoning

No affected individual, phenotype, or independent molecular diagnosis was provided to establish an alternative genetic cause for the phenotype.

Rule

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

Evidence considered

• No case-level phenotype or alternative molecular diagnosis is present in the consolidated evidence bundle.
• No applicable CCNE1 VCEP/ClinGen gene-specific specification was retrieved; generic ACMG/AMP assessment applies.

Still missing

• Case-level phenotype and molecular testing evidence demonstrating a well-established alternative genetic cause for the affected individual's phenotype.

Reasoning

The exact variant is absent from ClinVar; therefore no exact-variant ClinVar expert-panel Benign or Likely benign assertion is available.

Rule

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

Evidence considered

• ClinVar search returned no result for CCNE1 c.617A>G; no expert-panel assertion was present.

Still missing

• An exact-variant ClinVar submission from an expert panel classifying the variant as Benign or Likely benign.

Sources