FBXW7 c.608C>T, p.(Ser203Leu)

Reasoning

PM2 is met at Moderate strength under the generic ACMG/AMP 2015 fallback. The variant is extremely rare in population data: gnomAD v4.1 has AF 3.74361e-06 (6/1,602,732 alleles), NFE AF 5.10018e-06, and grpmax FAF 1.83e-06; no homozygotes were observed. The higher, older gnomAD v2.1 observation remains rare (1/28,686 alleles; NFE AF 7.03631e-05). It is also absent from gnomAD-Canada v1.0.

Rule

Generic ACMG/AMP 2015 fallback: PM2 applies to a variant absent from controls or present at extremely low frequency when compatible with the disease model.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification was retrieved; the case framework therefore designates generic ACMG/AMP 2015 fallback.
• gnomAD v4.1: total AC/AN 6/1,602,732 (AF 3.74361e-06), NFE AC/AN 6/1,176,428 (AF 5.10018e-06), grpmax FAF 1.83e-06, and zero homozygotes.
• gnomAD v2.1: total AC/AN 1/28,686 (AF 3.48602e-05), NFE AC/AN 1/14,212 (AF 7.03631e-05), and zero homozygotes.
• gnomAD-Canada v1.0 reports the variant absent.

Sources

Reasoning

No governing VCEP/gene-specific PP3/BP4 lookup table exists for FBXW7, so generic ACMG in-silico evidence applies. Missense path: REVEL score = 0.076 falls below the benign-moderate threshold (REVEL <=0.183) from the ClinGen SVI-endorsed calibration (Pejaver et al., PMID 36413997), supporting BP4 at Moderate strength. Splice path: SpliceAI max delta score = 0.012 is far below the standard 0.2 splice-altering threshold (Jaganathan et al., PMID 30661751), consistent with no predicted splicing disruption and providing additional corroborating evidence of a benign computational profile, though it is not separately scored to avoid double-counting the same prediction. BayesDel score is present in the data but is not used because no verified published threshold/citation for BayesDel is available to this pipeline.

Rule

generic_acmg_BP4_missense_REVEL_moderate

Evidence considered

• REVEL score = 0.076 for NM_033632.3:c.608C>T (NP_361014.1:p.(Ser203Leu)); ClinGen SVI-recommended REVEL calibration (Pejaver et al., PMID 36413997) sets benign-moderate threshold at REVEL <=0.183 - met, supporting BP4 at Moderate strength.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.012), consistent with a benign computational profile using the standard 0.2 threshold associated with the SpliceAI algorithm (Jaganathan et al., PMID 30661751); not separately scored to avoid double-counting against the REVEL-based BP4 call.

Still missing

• No gene-specific VCEP calibration for FBXW7 to confirm or adjust the generic REVEL-based BP4 strength.
• BayesDel score exists but excluded pending a verified published threshold/citation.

Sources

Reasoning

FBXW7 p.Ser203L falls in the N-terminal region of the protein, upstream of the F-box domain (~aa 263-310) and the WD40 substrate-recognition repeats (~aa 420-707). Automated cancerhotspots.org lookup for 'FBXW7 S203' found no statistically significant somatic mutational hotspot at this residue, and COSMIC recorded only 2 somatic occurrences (COSV55914039), well below a threshold consistent with a recurrent hotspot. Germline neurodevelopmental-syndrome literature (reviewed while establishing PVS1 gene context) explicitly states that the majority of disease-associated FBXW7 germline variants cluster in the WD40 domain and disrupt substrate recognition, a region that does not include residue 203. No mutational hotspot or established critical functional domain boundary places residue 203 within a PM1-eligible region.

Rule

generic_acmg_pm1_hotspot_or_functional_domain

Evidence considered

• cancerhotspots.org lookup for 'FBXW7 S203' returned no_result: 'This variant does not lie in a statistically significant hotspot.'
• COSMIC reports this variant (COSV55914039) with a somatic count of only 2, well below levels seen at recognized FBXW7 hotspot codons.
• Literature reviewed for FBXW7 germline disease mechanism (PMID:42111496 abstract, via pvs1_gene_context) states germline NDD variants cluster predominantly in the WD40 domain (~aa 420-707) and disrupt substrate recognition; residue 203 lies outside this domain and outside the F-box domain.

Still missing

• No formal residue-by-residue functional domain map (e.g. UniProt domain boundaries) was retrieved in this bundle to definitively confirm residue 203 lies outside all annotated functional domains
• No gene-specific PM1 hotspot/domain rule from a VCEP CSPEC is available for FBXW7 (cspec.found=false); assessment relies on generic cancer-hotspot and literature domain-clustering data

Sources

Reasoning

No governing VCEP/gene-specific PP3/BP4 lookup table exists for FBXW7 (cspec.found=false, vcep_materials.json empty, framework_mode=generic_acmg), so generic ACMG in-silico evidence applies. This is a missense variant (NP_361014.1:p.(Ser203Leu)); the missense computational path is assessed via REVEL, the only predictor with a pipeline-verified published calibration (PMID 36413997). REVEL score = 0.076, which falls well below the pathogenic-supporting threshold (>=0.644) established in that calibration, so REVEL provides no support for a deleterious effect. SpliceAI (max delta score = 0.012, all four DS values <0.01-0.012) is also far below the widely used 0.2 splice-altering threshold (per the SpliceAI publication, PMID 30661751), so there is no computational splicing evidence to support PP3 either. BayesDel score (-0.296435) is available in prefetch data but is excluded from consideration because no verified published threshold/PMID for BayesDel is available to this pipeline. No basis to apply PP3 from either the missense or splice sub-path.

Rule

generic_acmg_PP3_missense_and_splice

Evidence considered

• REVEL score = 0.076 for NM_033632.3:c.608C>T (NP_361014.1:p.(Ser203Leu)); ClinGen SVI-recommended REVEL calibration (Pejaver et al., PMID 36413997) sets pathogenic-supporting threshold at REVEL >=0.644 - not met.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.012; DS_AG=0.001, DS_AL=0.012, DS_DG=0.002, DS_DL=0.009), far below the standard 0.2 delta-score threshold used with the SpliceAI algorithm (Jaganathan et al., PMID 30661751).

Still missing

• No gene-specific VCEP PP3/BP4 lookup table available for FBXW7 to override generic calibration.
• BayesDel score exists but cannot be used for PP3/BP4 pending a verified published threshold/citation.

Sources

Reasoning

The exact variant is absent from ClinVar; therefore, no exact-variant pathogenic or likely pathogenic ClinVar expert-panel assertion exists to support PP5.

Rule

Exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion required for PP5.

Evidence considered

• ClinVar search for FBXW7 c.608C>T / NM_033632.3:c.608C>T returned no exact result: "This variant is absent from ClinVar."

Sources

Reasoning

BA1 is not met. The highest reliable population frequency is gnomAD v2.1 NFE AF 7.03631e-05 (1/14,212 alleles); gnomAD v4.1 reports a substantially lower overall AF of 3.74361e-06 (6/1,602,732 alleles), NFE AF 5.10018e-06, and grpmax FAF 1.83e-06. These frequencies are far below the generic ACMG/AMP BA1 stand-alone benign threshold.

Rule

Generic ACMG/AMP 2015 fallback: BA1 requires an allele frequency greater than 5%.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification was retrieved; the case framework therefore designates generic ACMG/AMP 2015 fallback.
• gnomAD v2.1: total AC/AN 1/28,686 (AF 3.48602e-05); highest reported NFE AF 7.03631e-05 (1/14,212).
• gnomAD v4.1: total AC/AN 6/1,602,732 (AF 3.74361e-06), highest reported NFE AF 5.10018e-06 (6/1,176,428), and grpmax FAF 1.83e-06.

Sources

Reasoning

BP1 applies to missense variants in genes where disease is caused primarily by truncating (loss-of-function) variants, such that a missense change is unlikely to be pathogenic. Literature reviewed for FBXW7 germline disease mechanism explicitly documents that reported germline disease-causing variants include missense, frameshift, splice-site, and larger structural variants, with germline missense variants specifically shown (via functional studies) to impair FBXW7-mediated substrate ubiquitination/degradation. Because missense variants are an established, non-trivial mechanism of FBXW7 germline disease (not merely truncating variants), BP1 does not apply.

Evidence considered

• Literature reviewed while establishing PVS1 gene context (PMID:42111496) states: 'Reported germline variants include missense, frameshift, splice-site, and larger structural variants, with the majority clustering in the WD40 domain and disrupting substrate recognition. Functional studies confirm impaired degradation of critical regulators...' -- demonstrating missense variants are an accepted, non-truncating-exclusive FBXW7 germline disease mechanism.

Still missing

• No VCEP/CSPEC-specific BP1 rule available for FBXW7 to confirm a gene-specific threshold

Sources

Reasoning

The exact variant is absent from ClinVar; therefore, no exact-variant benign or likely benign ClinVar expert-panel assertion exists to support BP6.

Rule

Exact-variant ClinVar expert-panel Benign or Likely benign assertion required for BP6.

Evidence considered

• ClinVar search for FBXW7 c.608C>T / NM_033632.3:c.608C>T returned no exact result: "This variant is absent from ClinVar."

Sources

Reasoning

PS1 requires an established pathogenic variant causing the same amino acid change (p.Ser203Leu) via a different nucleotide substitution. ClinVar was queried but only for this exact variant (c.608C>T) and returned no result ('This variant is absent from ClinVar'); no broader search for other codon changes producing p.Ser203Leu was performed in this bundle, and no VCEP/CSPEC framework is available for FBXW7 (cspec.found=false). literature_pass.json and fulltext_map.json contain no PMIDs. There is no source in this evidence bundle confirming or excluding an established pathogenic p.Ser203Leu comparator.

Evidence considered

• ClinVar search for FBXW7 NM_033632.3:c.608C>T returned no result ('This variant is absent from ClinVar'), meaning this exact variant record does not exist; this does not constitute a search for other codon changes producing the same amino acid substitution.

Still missing

• No comparator search performed for alternate nucleotide changes producing the identical amino acid substitution p.Ser203Leu
• No ClinVar-wide or literature search targeting p.Ser203Leu across other transcripts/submissions

Sources

Reasoning

No case-level proband phenotype, parental genotype, parentage confirmation, or inheritance testing result is present. De novo occurrence therefore cannot be established.

Rule

Generic ACMG/AMP 2015 PS2: confirmed de novo occurrence in a patient with the disease and no family history.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification is available in the case evidence; generic ACMG/AMP assessment applies.
• The consolidated evidence contains no family-based testing or phenotype information for this proband.

Still missing

• Obtain validated testing results for the proband and both biological parents, including confirmation of parentage.
• Document the proband phenotype and its consistency with an FBXW7-related disorder.

Sources

Reasoning

No functional/experimental assay data for NM_033632.3:c.608C>T (p.Ser203Leu) in FBXW7 was found in this case's evidence bundle. There is no ClinGen VCEP specification for FBXW7 (cspec.found=false; vcep_materials.json notes no cspec url available), literature_pass.json returned zero PMIDs (total_pmids=0, note: 'No PMIDs found across evidence sources'), and fulltext_map.json is empty, so no publications describing validated functional/degradation/ubiquitination assays for this variant were available to review. OncoKB provides only gene-level, not variant-specific, functional context ('Unknown Oncogenic Effect', is_variant_specific=false) and explicitly states no reviewed variant-specific functional evidence was identified.

Evidence considered

• evidence.json oncokb result: 'OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up.' is_variant_specific=false, not_reviewed=true, classification='Unknown Oncogenic Effect'.
• literature_pass.json: total_pmids=0, high_priority_papers=[], medium_priority_papers=[], note='No PMIDs found across evidence sources.'
• vcep_materials.json: note='no cspec url available'; final_classification_framework.found=false, source='generic_acmg_fallback', framework_mode=null — no FBXW7-specific functional evidence framework exists in this case.

Still missing

• No functional assay publications (e.g., substrate degradation, ubiquitination, cyclin E/c-Myc turnover assays) identified for this specific variant
• No FBXW7-specific VCEP functional criteria specification available to define assay validation requirements
• OncoKB and other databases only offer gene-level, not variant-specific, functional annotation

Sources

Reasoning

No affected-case series, case-control study, or other quantitative enrichment data for FBXW7 c.608C>T (p.Ser203Leu) were retrieved; PS4 cannot be assessed.

Rule

ACMG/AMP 2015 generic fallback: PS4 requires statistically increased prevalence in affected individuals compared with controls.

Evidence considered

• No FBXW7-specific VCEP/CSPEC or local gene-specific framework was retrieved, so generic ACMG/AMP evidence assessment applies.
• The literature pass reports no PMIDs from the available evidence sources and no case-control or case-series evidence for this exact variant was supplied.

Still missing

• Variant-specific affected and control counts from an appropriately phenotyped cohort, with a defined statistical comparison.

Reasoning

PM3 cannot be assessed: no affected-proband observation of c.608C>T with a pathogenic or likely pathogenic FBXW7 variant in confirmed trans is provided. No FBXW7 gene-specific specification is available; generic ACMG/AMP evidence requirements are used.

Rule

Generic ACMG/AMP PM3: in a recessive disorder, the variant is detected in trans with a pathogenic variant.

Evidence considered

• No ClinGen VCEP/case-level gene-specific specification or local FBXW7 framework was retrieved; the case is designated generic_acmg fallback.
• The bundle provides no affected-proband observations, no second FBXW7 variant, and no phase data for c.608C>T.
• The germline FBXW7 context in the bundle describes heterozygous loss-of-function variants as causative for a neurodevelopmental syndrome, while inheritance is not formally specified; it supplies no evidence for a recessive biallelic presentation involving this variant.

Still missing

• Affected-proband genotype data identifying any second FBXW7 variant.
• Phase evidence establishing trans configuration if a second variant is present.
• Confirmed recessive disease attribution for the relevant phenotype, if PM3 is to be considered.

Sources

Reasoning

The dedicated pm5_candidates.json artifact explicitly flags that classic same-residue PM5 semantics could not be safely confirmed for this case and that automatic comparator harvesting was skipped ('Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting'), with 0 total candidates seen. No alternate amino-acid-change variant at residue 203 (e.g. p.Ser203Pro, p.Ser203Phe) with an established pathogenic classification was identified anywhere in this bundle (ClinVar absent for this variant; literature_pass and fulltext_map both empty).

Evidence considered

• pm5_candidates.json recommendation level = 'not_applicable' with instruction: 'Review whether any collected same-residue comparator variants satisfy the governing PM5 rule; do not apply PM5 from this artifact alone.' total_candidates_seen = 0.

Still missing

• No same-residue comparator variants (different amino acid substitutions at codon 203) have been searched in ClinVar or literature
• pm5_candidates artifact recommends manual review before any PM5 application

Sources

Reasoning

No case-level parental testing result is present; a presumed de novo occurrence cannot be established.

Rule

Generic ACMG/AMP 2015 PM6: assumed de novo occurrence without confirmation of paternity and maternity.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification is available in the case evidence; generic ACMG/AMP assessment applies.
• The consolidated evidence contains no parental genotypes, parental phenotypes, or de novo assertion for this case.

Still missing

• Obtain parental testing results; if one or both parents cannot be tested, document the basis for a presumed de novo assessment.
• Document the proband phenotype and its consistency with an FBXW7-related disorder.

Sources

Reasoning

No informative relatives, genotypes, phenotypes, pedigree, or meiosis count is available; cosegregation cannot be evaluated.

Rule

Generic ACMG/AMP 2015 PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification is available in the case evidence; generic ACMG/AMP assessment applies.
• The consolidated evidence contains no segregation data for this variant.

Still missing

• Provide a pedigree with affected and unaffected relatives, their variant testing results, phenotype status, and the number of informative meioses.

Sources

Reasoning

PP2 requires that the gene have a low rate of benign missense variation and that missense variants are a common mechanism of disease. Reviewed FBXW7 germline-disease literature (used to establish PVS1 gene context) confirms missense variants are among the reported germline disease mechanisms for FBXW7-related neurodevelopmental syndrome, alongside frameshift, splice-site, and structural variants. However, no quantitative gene-level missense constraint metric (e.g. gnomAD missense Z-score or observed/expected ratio) is present anywhere in this evidence bundle, and no VCEP/CSPEC framework is available for FBXW7 to supply a gene-specific PP2 rule. Qualitative literature support for missense as a disease mechanism is insufficient alone to confirm the 'low rate of benign missense variation' component of PP2.

Evidence considered

• Literature reviewed while establishing PVS1 gene context (PMID:42111496, PMID:35395208) reports that germline FBXW7 variants causing neurodevelopmental syndrome include missense variants clustering in the WD40 domain and disrupting substrate recognition, alongside frameshift, splice-site, and structural variants -- indicating missense is a recognized but not exclusive disease mechanism.

Still missing

• Gene-level missense constraint metric (gnomAD missense Z-score / o-e ratio) not present in this evidence bundle
• No VCEP/CSPEC-specific PP2 rule available for FBXW7

Sources

Reasoning

No proband phenotype, diagnostic workup, or phenotype-to-FBXW7 specificity evidence was supplied for this exact variant; PP4 cannot be assessed.

Rule

ACMG/AMP 2015 generic fallback: PP4 requires a highly specific patient phenotype or family history for a disease with a single genetic etiology.

Evidence considered

• No FBXW7-specific VCEP/CSPEC or local gene-specific framework was retrieved, so generic ACMG/AMP evidence assessment applies.
• Available case materials identify the molecular variant and general FBXW7 context but contain no phenotype for the individual carrying c.608C>T (p.Ser203Leu).

Still missing

• Proband-level phenotype and exclusion testing sufficient to determine whether the presentation is highly specific for FBXW7-related disease.

Reasoning

BS1 is not assessed because no FBXW7 disease-specific maximum credible allele-frequency threshold, supported by disease prevalence, inheritance, penetrance, and allelic heterogeneity, was provided. The observed frequencies are very low and do not independently establish that the allele frequency is greater than expected for the relevant disorder.

Rule

Generic ACMG/AMP BS1 requires an allele frequency greater than expected for the disorder; no disorder-specific threshold is available in this case.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification was retrieved; the case framework designates generic ACMG/AMP 2015 fallback.
• The highest observed frequency is gnomAD v2.1 NFE AF 7.03631e-05 (1/14,212); gnomAD v4.1 overall AF is 3.74361e-06 with grpmax FAF 1.83e-06.

Still missing

• A disease-specific maximum credible allele-frequency calculation or applicable VCEP specification for FBXW7 is needed to assess BS1.

Sources

Reasoning

BS2 is not assessed. gnomAD v2.1 and v4.1 report zero homozygotes, and the population data do not document unaffected adult individuals with a phenotype and age distribution incompatible with the relevant FBXW7-associated condition.

Rule

Generic ACMG/AMP BS2 requires observation in healthy adult individual(s) for a fully penetrant early-onset disorder; population allele counts without phenotype and age data do not satisfy this rule.

Evidence considered

• gnomAD v2.1 reports zero homozygotes among 28,686 alleles.
• gnomAD v4.1 reports zero homozygotes among 1,602,732 alleles.

Still missing

• Well-phenotyped unaffected adult observations, with genotype and relevant disease ascertainment, would be required for BS2.

Sources

Reasoning

No functional/experimental assay data was found demonstrating normal/wild-type-like function for NM_033632.3:c.608C>T (p.Ser203Leu) in FBXW7. As with PS3, there is no FBXW7 VCEP specification, zero PMIDs surfaced by the literature pass, and no full-text papers to review. OncoKB's gene-level entry does not constitute a validated functional assay result for this variant in either direction.

Evidence considered

• evidence.json oncokb result: gene-level only, is_variant_specific=false, not_reviewed=true — no assay evidence of normal function.
• literature_pass.json: total_pmids=0 — no functional assay publications identified.
• vcep_materials.json: no cspec/VCEP framework available for FBXW7 functional criteria.

Still missing

• No functional assay data (variant-specific) available showing normal function/activity
• No FBXW7-specific VCEP functional criteria specification to guide assay validation and strength calibration

Sources

Reasoning

No informative non-segregation observation is available; the variant cannot be assessed for lack of segregation with disease.

Rule

Generic ACMG/AMP 2015 BS4: lack of segregation in affected members of a family.

Evidence considered

• No FBXW7 VCEP/ClinGen gene-specific specification is available in the case evidence; generic ACMG/AMP assessment applies.
• The consolidated evidence contains no family non-segregation data for this variant.

Still missing

• Provide genotype and phenotype data for informative relatives, including any affected non-carriers or unaffected carriers, with age and penetrance context.

Sources

Reasoning

BP2 cannot be assessed: no observation places c.608C>T in cis with a pathogenic or likely pathogenic FBXW7 variant, nor in trans with such a variant in an established dominant disorder. No FBXW7 gene-specific specification is available; generic ACMG/AMP evidence requirements are used.

Rule

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

Evidence considered

• No ClinGen VCEP/case-level gene-specific specification or local FBXW7 framework was retrieved; the case is designated generic_acmg fallback.
• The bundle provides no co-occurring FBXW7 variant and no phase or affected-status data for an individual with c.608C>T.
• The available germline FBXW7 context does not document a cis or trans observation involving c.608C>T and a pathogenic or likely pathogenic comparator variant.

Still missing

• Genotype data identifying any co-occurring pathogenic or likely pathogenic FBXW7 variant.
• Phase evidence demonstrating cis configuration, or trans configuration in a confirmed dominant-disorder context.
• Phenotype and inheritance information for the individual carrying both variants.

Sources

Reasoning

No affected individual, phenotype, or independent molecular diagnosis was supplied; BP5 cannot be assessed.

Rule

ACMG/AMP 2015 generic fallback: BP5 requires an alternate molecular basis for disease in an affected individual.

Evidence considered

• No proband-level clinical or molecular diagnostic data were included in the case-evidence bundle.

Still missing

• Proband-level phenotype and a confirmed alternate molecular diagnosis that fully explains the phenotype.