CTNNB1 c.134C>A, p.(Ser45Tyr)

Reasoning

Ser45 is one of four conserved N-terminal phospho-residues (S33, S37, T41, S45) of the CTNNB1/beta-catenin destruction-complex degron. Functional literature establishes that CK1 phosphorylates beta-catenin specifically at S45, creating an obligatory priming site for subsequent GSK3-beta phosphorylation of T41/S37/S33 and beta-TrCP-mediated degradation; loss of this phospho-priming event is a well-characterized mechanism by which N-terminal beta-catenin substitutions stabilize the protein and drive oncogenic Wnt-pathway activation. OncoKB independently curates this exact residue/gene context (CTNNB1 S45) as biologically Gain-of-function with a Likely Oncogenic label. This constitutes a well-established critical functional residue within a domain (the N-terminal phosphodegron) lacking benign variation, supporting PM1 at moderate strength.

Evidence considered

• case_summary.json/evidence.json report that this variant lies in a statistically significant mutational hotspot per cancerhotspots.org (CTNNB1 S45 query), and COSMIC lists 55 independent somatic occurrences at this exact substitution (COSV62689938) -- both corroborating recurrence at this residue, though the underlying hotspots/COSMIC tools have no source_registry key to cite formally.
• PMID:12000790 (Amit et al. 2002) shows via mass spectrometry and phosphopeptide antibodies that an axin-CKI complex phosphorylates beta-catenin specifically at serine 45, and that this CKI phosphorylation event is necessary and sufficient to initiate the destruction cascade -- establishing S45 as a functionally indispensable residue.
• PMID:11955436 (Liu et al. 2002) identifies S33, S37, T41 and S45 as the conserved N-terminal phospho-degron residues whose mutation is the recurrent mechanism of beta-catenin stabilization in human cancers.
• PMID:41629672 states that the phospho-regulatory cascade involves CK1 priming at S45 followed by GSK3-beta phosphorylation at T41/S37/S33 enabling beta-TrCP docking, within the exon 3 degron motif that is among the most commonly mutated regions in CTNNB1-driven tumors.
• OncoKB (oncokb) curates CTNNB1 S45Y specifically as Gain-of-function / Likely Oncogenic.

Still missing

• Cancer-hotspot statistical-significance data (cancerhotspots.org) and COSMIC recurrence counts corroborate this residue as a recurrent mutational hotspot, but neither has a corresponding source_registry citation key, so that supporting detail is documented only in evidence_used, not evidence_refs.
• No formal ClinGen/VCEP PM1 hotspot-domain specification exists for CTNNB1 in this case (cspec.found = false), so this assessment relies on generic ACMG PM1 reasoning rather than a gene-specific calibrated hotspot rule.

Sources

Reasoning

CTNNB1 NM_001904.4:c.134C>A (p.Ser45Tyr) is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. In the absence of a CTNNB1-specific specification, this satisfies generic ACMG/AMP PM2 (absent from population controls).

Rule

Generic ACMG/AMP PM2 (Richards et al., 2015): absent from controls (or at extremely low frequency if recessive) supports pathogenicity at moderate strength.

Evidence considered

• The normalized CTNNB1 NM_001904.4:c.134C>A (p.Ser45Tyr) variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• No CTNNB1-specific VCEP/ClinGen specification was retrieved; generic ACMG/AMP assessment is applicable.

Still missing

• Allele number and ancestry-stratified coverage metrics were not supplied for the negative queries; review them if a quantitative coverage audit is required.

Sources

Reasoning

No governing VCEP/CSPEC was found for CTNNB1 (cspec.found=false; framework_mode=generic_acmg; vcep_materials contains no gene-specific PP3/BP4 lookup spreadsheet), so generic calibrated computational thresholds were applied. NM_001904.4:c.134C>A is a missense variant (NP_001895.1:p.(Ser45Tyr)). SpliceAI predicts no splice impact (DS_AG=0.00, DS_AL=0.002, DS_DG=0.00, DS_DL=0.002; max delta score = 0.002), far below any calibrated SpliceAI threshold used for PP3, so the splice-impact path does not support PP3. On the missense path, REVEL score = 0.353 (Ensembl/dbNSFP REVEL v1.3 local lookup), which falls in the indeterminate zone between the ClinGen SVI/Pejaver et al. (PMID:36413997) calibrated BP4_supporting cutoff (REVEL <= 0.290) and PP3_supporting cutoff (REVEL >= 0.644); it therefore does not reach the PP3 threshold. A BayesDel score (0.104857) is available from a local lookup, but per pipeline policy no verified published calibration threshold for BayesDel is available to this pipeline, so it is treated as not_available/insufficiently calibrated evidence and cannot be used to support PP3. No aGVGD data is present in the bundle. Overall, no calibrated computational evidence (splice or missense) meets the threshold required for PP3.

Rule

Generic ACMG (no CTNNB1 CSPEC/VCEP found); ClinGen SVI calibrated REVEL thresholds (Pejaver et al., PMID:36413997) for missense; SpliceAI for splice-impact path

Evidence considered

• SpliceAI evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).' with detailed scores DS_AG=0.0, DS_AL=0.002, DS_DG=0.0, DS_DL=0.002 (source_registry key: spliceai)
• REVEL score 0.353 from local REVEL v1.3 lookup (source_registry key: revel), compared against ClinGen SVI/Pejaver et al. 2022 (PMID:36413997) calibrated thresholds (BP4_supporting <=0.290, PP3_supporting >=0.644) — 0.353 falls in the indeterminate zone, satisfying neither
• BayesDel score 0.104857 from local BayesDel_170824_noAF lookup (source_registry key: bayesdel) noted but not usable for PP3/BP4 because no verified published calibration threshold/PMID for this BayesDel version is available to this pipeline

Still missing

• REVEL score (0.353) falls in the indeterminate zone and cannot itself support PP3 or BP4
• BayesDel score is present but excluded because no verified published calibration threshold/PMID is available to this pipeline
• No aGVGD score available
• No CTNNB1-specific VCEP PP3/BP4 lookup table was found to override the generic calibration

Sources

Reasoning

The variant is absent from the queried gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 datasets; it therefore cannot meet the stand-alone high-frequency benign criterion BA1.

Rule

Generic ACMG/AMP BA1: a population allele frequency above the stand-alone benign threshold is required; absence does not satisfy BA1.

Evidence considered

• The normalized CTNNB1 NM_001904.4:c.134C>A (p.Ser45Tyr) variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• No CTNNB1-specific VCEP/ClinGen specification was retrieved; generic ACMG/AMP assessment is applicable.

Still missing

• No allele count, allele number, or ancestry-stratified coverage metrics were supplied for the negative gnomAD queries; these would not change the conclusion that BA1 is not met from the available data.

Sources

Reasoning

The variant is absent from the queried gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 datasets, so there is no population frequency exceeding that expected for a CTNNB1-associated disorder and BS1 is not met.

Rule

Generic ACMG/AMP BS1: an allele frequency greater than expected for the disorder is required; no such frequency is present.

Evidence considered

• The normalized CTNNB1 NM_001904.4:c.134C>A (p.Ser45Tyr) variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
• No CTNNB1-specific VCEP/ClinGen specification was retrieved; generic ACMG/AMP assessment is applicable.

Still missing

• A disease-specific prevalence, penetrance, and maximum credible allele-frequency calculation was not supplied; the observed absence precludes BS1 regardless.

Sources

Reasoning

BP1 would apply if this were a missense variant in a gene where primarily truncating variants cause disease, with no other evidence of missense pathogenicity at this residue. While pvs1_gene_context.json does identify loss-of-function as the supported germline CTNNB1 disease mechanism, that gene-level default is directly contradicted for this specific residue: Ser45 is a well-documented recurrent oncogenic hotspot within the essential N-terminal phosphodegron, supported by functional literature establishing S45 as an indispensable CK1 phosphorylation-priming site, OncoKB's Gain-of-function/Likely Oncogenic curation of this exact residue, and hotspot/recurrence data in the bundle. Given this direct, residue-specific functional and clinical evidence of a missense-driven pathogenic mechanism, BP1 is not met.

Evidence considered

• Functional literature (PMID:12000790, PMID:11955436, PMID:41629672) and OncoKB's Gain-of-function/Likely Oncogenic curation of CTNNB1 S45Y directly demonstrate a missense-driven pathogenic/oncogenic mechanism at this specific residue, overriding the gene-level loss-of-function default noted for germline CTNNB1 disease and precluding application of BP1.

Sources

Reasoning

No governing VCEP/CSPEC was found for CTNNB1 (cspec.found=false; framework_mode=generic_acmg; vcep_materials contains no gene-specific PP3/BP4 lookup spreadsheet), so generic calibrated computational thresholds were applied. SpliceAI max delta score of 0.002 shows no predicted splice impact, but this variant's primary consequence is missense (p.Ser45Tyr), not a splice-region/intronic change, so the very low SpliceAI score is expected background noise rather than informative benign splice evidence on its own. On the missense path, REVEL = 0.353 falls between the calibrated BP4_supporting cutoff (REVEL <= 0.290, ClinGen SVI/Pejaver et al., PMID:36413997) and the PP3_supporting cutoff (REVEL >= 0.644), i.e. in the indeterminate zone, so it does not reach the threshold required for BP4. BayesDel (0.104857) is excluded per pipeline policy because no verified published calibration threshold/PMID is available for this pipeline. No aGVGD data is present. Overall, no calibrated computational evidence meets the threshold required for BP4.

Rule

Generic ACMG (no CTNNB1 CSPEC/VCEP found); ClinGen SVI calibrated REVEL thresholds (Pejaver et al., PMID:36413997) for missense; SpliceAI for splice-impact path

Evidence considered

• SpliceAI evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).' with detailed scores DS_AG=0.0, DS_AL=0.002, DS_DG=0.0, DS_DL=0.002 (source_registry key: spliceai); variant is missense (p.Ser45Tyr), not intronic/splice-region, so this near-zero score is not treated as independently sufficient benign splice evidence
• REVEL score 0.353 from local REVEL v1.3 lookup (source_registry key: revel), compared against ClinGen SVI/Pejaver et al. 2022 (PMID:36413997) calibrated thresholds (BP4_supporting <=0.290, PP3_supporting >=0.644) — 0.353 falls in the indeterminate zone, satisfying neither
• BayesDel score 0.104857 from local BayesDel_170824_noAF lookup (source_registry key: bayesdel) noted but not usable for PP3/BP4 because no verified published calibration threshold/PMID for this BayesDel version is available to this pipeline

Still missing

• REVEL score (0.353) falls in the indeterminate zone and cannot itself support PP3 or BP4
• BayesDel score is present but excluded because no verified published calibration threshold/PMID is available to this pipeline
• No aGVGD score available
• No CTNNB1-specific VCEP PP3/BP4 lookup table was found to override the generic calibration

Sources

Reasoning

PS1 requires that the identical amino-acid change, p.(Ser45Tyr), has already been independently established as pathogenic/oncogenic when produced by a different nucleotide substitution. No such independently-classified variant with the same resulting amino-acid change was located in the case bundle (source_registry, ClinVar record, literature). The only ClinVar record identified (VCV004530134) IS this variant itself, so it cannot be used as the independent comparator required by PS1.

Evidence considered

• case_summary.json / clinvar record shows only one ClinVar variation (4530134) corresponding to this exact NM_001904.4:c.134C>A / p.(Ser45Tyr) change; no separate codon change giving the identical amino-acid substitution was located to serve as an independent PS1 comparator.

Still missing

• No second, distinct nucleotide change producing p.(Ser45Tyr) with its own independent pathogenic/oncogenic classification was found in the bundle; PS1 same-amino-acid-change comparison could not be completed.

Reasoning

No germline proband phenotype or parental testing data are provided for this CTNNB1 variant; de novo occurrence with confirmed maternity and paternity cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in an affected individual requires confirmed parental relationships and a phenotype consistent with the relevant disorder.

Evidence considered

• No CTNNB1 CSPEC/VCEP framework was retrieved; the case designates generic ACMG/AMP fallback.
• The available ClinVar record is a somatic submission for rhabdomyosarcoma and contains no parental testing or germline de novo evidence.

Still missing

• Obtain germline testing results for the proband and both biological parents, including confirmation of maternity and paternity.
• Document the proband phenotype and its consistency with the relevant CTNNB1-associated germline disorder.

Sources

Reasoning

No CTNNB1-specific VCEP/CSPEC functional-evidence framework was found for this case (framework_mode = generic_acmg, cspec.found = false), so generic ACMG/AMP PS3 principles apply: a well-validated functional assay must show the specific variant abolishes or grossly alters protein function, with appropriate positive/negative controls, before PS3 can be applied. A directly relevant, well-validated assay system exists in the literature: a saturation genome editing (SGE) screen (PMID:41629672) systematically measured mutational effect scores (MES) for all 19 possible amino acid substitutions at each residue of the CTNNB1 exon-3 degron hotspot (codons 31-48, which includes Ser45) using an endogenous-locus CRISPR HDR knock-in reporter system in mouse ES cells with built-in positive controls (GSK3beta inhibitor CHIR99021) and orthogonal validation (RNA-seq of endogenous beta-catenin target genes, human fetal liver organoid RNA-seq, and two independent TCGA HCC cohorts). However, the retrieved full text and abstract discuss position S45 and other hotspot residues only in aggregate/positional terms (e.g., 'S45 mutations activate weakly') and do not explicitly name or report a quantitative result for the p.Ser45Tyr (S45Y) substitution itself anywhere in the extracted text; the per-substitution MES values are stored in a Supplementary Table not present in the retrieved bundle. Per the strict citation-grounding requirement, a paper can only be cited for a criterion if the exact variant is named in the reviewed text, so this SGE dataset cannot be used to assert a specific functional consequence for c.134C>A/p.(Ser45Tyr) at this time. OncoKB's 'Likely Oncogenic' / 'Gain-of-function' curation is a database-level aggregate classification citing gene/position-level literature (PMID:9419974, PMID:16909133, PMID:25190313, PMID:41629672), not a primary, variant-specific, quantitative functional assay report with visible controls, and therefore does not itself satisfy PS3's evidentiary bar. No other variant-specific degradation, phosphorylation, ubiquitination, TOPFlash/TCF-LEF reporter, or beta-catenin stability assay result naming S45Y or c.134C>A was found in the case bundle or the retrieved full-text publications. PS3 is therefore not assessed pending either (a) direct access to the SGE Supplementary Table 2 entry for the S45Y substitution with its MES value and calibration, or (b) another variant-specific functional publication.

Evidence considered

• PMID:41629672 describes a saturation genome editing (SGE) assay quantifying mutational effect scores (MES) for all 19 possible amino acid substitutions at each CTNNB1 exon 3 hotspot codon (31-48, including Ser45), using CRISPR HDR knock-in at the endogenous mouse Ctnnb1 locus with GSK3beta inhibitor (CHIR99021) as a positive control and validation via RNA-seq of beta-catenin target genes, human fetal liver organoids, and two independent TCGA HCC cohorts; the retrieved text states position-level findings only (e.g., 'S45 mutations generally produced weaker activation than mutations in the docking motif' and 'strong activating S45 mutations are theoretically possible (for example, S45M, S45K) but are rarely observed in cancer') without naming or quantifying the S45Y substitution specifically in the accessible full text.
• OncoKB (accessed via case bundle) classifies CTNNB1 p.S45Y as 'Likely Oncogenic' with biological effect 'Gain-of-function', citing PMID:9419974, PMID:16909133, PMID:25190313, and PMID:41629672 as supporting literature, but this is a curated aggregate classification rather than a directly reported, variant-specific functional assay result with visible experimental controls.
• PMID:11955436 and PMID:12000790 characterize the CK1/GSK3beta phosphorylation cascade at Ser45/Thr41/Ser37/Ser33 and beta-TrCP-mediated degradation using alanine-substitution and other engineered mutants (e.g., S45F, S45A composite mutants), establishing the general biological mechanism by which loss of Ser45 phosphorylation stabilizes beta-catenin, but neither paper reports a functional assay result for the specific S45Y substitution.

Still missing

• The SGE saturation mutagenesis study (PMID:41629672) covers all substitutions at codon 45 including presumably S45Y, but its per-variant MES score for S45Y specifically is in a Supplementary Table not available in this case bundle/full-text extract, so the variant-specific quantitative result could not be confirmed or quoted.
• No other published assay (degradation, ubiquitination, phosphorylation-cascade reconstitution, or reporter assay) explicitly names p.Ser45Tyr or c.134C>A.
• No CTNNB1 VCEP-specific PS3 calibration/strength framework is available; generic ACMG PS3 strength calibration would need to be applied once variant-specific validated assay data is obtained.

Sources

Reasoning

No applicable CTNNB1 VCEP specification was retrieved, so generic ACMG/AMP was used. The available record provides no case-control comparison, affected-case count, control count, or statistical enrichment analysis for the exact variant.

Rule

Generic ACMG/AMP PS4: prevalence in affected individuals must be significantly increased compared with controls.

Evidence considered

• No CTNNB1-specific VCEP/CSPEC framework was available; generic ACMG/AMP criteria apply.
• The available exact-variant ClinVar record is a single somatic laboratory submission and does not provide case-control enrichment data.

Still missing

• A phenotype-defined case-control or statistically evaluable cohort study of CTNNB1 p.(Ser45Tyr), including affected and control allele counts, is required.

Reasoning

No affected individual with a second pathogenic/likely pathogenic allele is documented, and no phase data establish the queried CTNNB1 variant in trans with such an allele. PM3 therefore cannot be assessed under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP PM3: for a recessive disorder, pathogenic/likely pathogenic alleles observed in trans in an affected individual may support PM3; trans phase and the companion allele must be documented.

Evidence considered

• The available ClinVar record is a single somatic submission for rhabdomyosarcoma and supplies no affected-proband germline genotype, second-allele, or phase information.
• No CTNNB1 allelic observations relevant to PM3 were provided in the consolidated case-evidence bundle.

Still missing

• Affected-proband genotype data identifying any second pathogenic/likely pathogenic allele.
• Phase evidence demonstrating that the queried variant and any qualifying second allele are in trans.
• The relevant germline disease indication and inheritance mode for the evaluated individual.

Sources

Reasoning

PM5 requires an independently-established pathogenic/oncogenic missense change at the same residue (a different amino acid substitution at Ser45) to compare against. The dedicated pm5_candidates.json artifact for this case explicitly reports pm5_mode = 'unknown' and eligible_for_classic_pm5_search = false, stating that automatic same-residue comparator harvesting was skipped because classic PM5 semantics could not be safely confirmed for this variant, and lists zero candidates. No manual literature/ClinVar identification of an alternate S45 substitution (e.g., S45P, S45F, S45del) with its own independent classification was found elsewhere in the bundle.

Evidence considered

• pm5_candidates.json: 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting,' with candidate_summary showing zero same-residue candidates identified.

Still missing

• pm5_candidates.json harvesting was explicitly skipped; no same-residue comparator variant with an independent pathogenic/oncogenic classification could be confirmed from the available bundle.

Sources

Reasoning

No reported de novo occurrence is available, and no parental genotypes are supplied. The unconfirmed-parentage de novo criterion cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence may be considered only when a relevant affected proband and parental testing evidence are reported but parental relationships are not confirmed.

Evidence considered

• No CTNNB1 CSPEC/VCEP framework was retrieved; the case designates generic ACMG/AMP fallback.
• The available ClinVar record is a somatic submission for rhabdomyosarcoma and contains no parental testing or germline de novo evidence.

Still missing

• Obtain germline testing results for the proband and both biological parents.
• If parental relationships cannot be confirmed, provide evidence that the variant is de novo in a proband with phenotype consistent with the relevant CTNNB1-associated germline disorder.

Sources

Reasoning

No family pedigree, affected-relative genotypes, phenotype data, or informative meioses are provided. Co-segregation cannot be evaluated.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members requires family-level genotype and phenotype data.

Evidence considered

• No CTNNB1 CSPEC/VCEP framework was retrieved; the case designates generic ACMG/AMP fallback.
• The available case evidence contains no family segregation observations or informative meioses.

Still missing

• Provide a pedigree with variant genotypes and disease status for informative relatives.
• Provide the number of informative meioses and phenotype definitions used for segregation analysis.

Sources

Reasoning

No applicable CTNNB1 VCEP specification was retrieved, so generic ACMG/AMP was used. No individual-level phenotype, diagnostic workup, or evidence that the reported phenotype is highly specific for a CTNNB1-related germline disorder is available for this variant.

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

• ClinVar lists rhabdomyosarcoma for the exact variant, but the only reported submission is somatic and lacks individual-level phenotype and differential-diagnosis information.

Still missing

• Individual-level clinical phenotype and evaluation for alternative diagnoses are required to assess phenotype specificity.

Sources

Reasoning

The exact-variant ClinVar record has no expert-panel assertion. Its only submission is a single somatic laboratory assertion, which cannot support PP5 under the required expert-panel-only rule.

Rule

PP5 is applicable only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar reports review status 'criteria provided, single submitter'; the submission audit identifies zero expert-panel submissions.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is required.

Sources

Reasoning

Absence from population datasets is not evidence of observation in healthy adult individuals. No unaffected adult carrier or homozygote observations, with phenotype and age information, were supplied; BS2 cannot be assessed.

Rule

Generic ACMG/AMP BS2 requires observation in a healthy adult individual for a disorder expected to be fully penetrant at an early age.

Evidence considered

• The queried population datasets report the variant absent and provide no healthy-adult carrier or homozygote observation.
• No CTNNB1-specific VCEP/ClinGen specification was retrieved; generic ACMG/AMP assessment is applicable.

Still missing

• Documented unaffected adult heterozygote or homozygote observations with adequate age and phenotype information, interpreted in the relevant CTNNB1 disease and penetrance context.

Sources

Reasoning

No CTNNB1-specific VCEP/CSPEC framework for BS3 was found (framework_mode = generic_acmg, cspec.found = false); generic ACMG/AMP BS3 requires a well-validated functional assay explicitly showing no damaging effect (normal function) for this specific variant. No source in the case bundle or reviewed full-text publications reports a functional assay result, of any kind, for p.Ser45Tyr (S45Y)/c.134C>A that would support a benign/neutral functional conclusion. On the contrary, all available gene- and position-level functional context (OncoKB Gain-of-function/Likely Oncogenic curation, the S45 phospho-degron mechanism literature, hotspot/COSMIC recurrence, and the CTNNB1 saturation genome editing assay) points toward this hotspot residue's involvement in disrupting beta-catenin destruction-complex-mediated degradation, which is inconsistent with a benign functional signal, though none of this constitutes a variant-specific quantitative assay result that meets the grounding requirement for direct citation. BS3 is not assessed because no qualifying evidence exists in either direction for this specific variant.

Evidence considered

• No source located in the case bundle or reviewed publications reports a functional assay result consistent with normal/benign beta-catenin function for the p.Ser45Tyr substitution specifically; all available gene/position-level functional and oncogenicity context (OncoKB Gain-of-function/Likely Oncogenic label, COSMIC hotspot recurrence n=55, and the CTNNB1 exon-3 degron phospho-regulation mechanism literature) instead points toward a hotspot missense mutation rather than a benign one, though this is not itself a variant-specific assay result usable for direct BS3 citation.

Still missing

• No variant-specific functional assay data (of any polarity) naming p.Ser45Tyr or c.134C>A was located in the reviewed full-text sources.
• If the SGE Supplementary Table 2 (PMID:41629672) MES value for S45Y becomes available and falls within a range calibrated as functionally neutral, BS3 could be revisited.

Sources

Reasoning

No unaffected carriers, affected non-carriers, or other informative non-segregation observations are provided. Lack of segregation cannot be evaluated.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members requires informative family genotype-phenotype data.

Evidence considered

• No CTNNB1 CSPEC/VCEP framework was retrieved; the case designates generic ACMG/AMP fallback.
• The available case evidence contains no family non-segregation observations.

Still missing

• Provide pedigree-level genotypes and phenotypes, including ages and disease-status ascertainment for unaffected relatives.
• Document any affected relatives confirmed not to carry the variant or unaffected relatives who carry it, with penetrance and age-of-onset context.

Sources

Reasoning

No observation of the queried variant in cis with a pathogenic/likely pathogenic variant, or in trans with one for a dominant disorder, is documented. BP2 therefore cannot be assessed under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP BP2: a variant observed in cis with a pathogenic/likely pathogenic variant, or in trans with one for a dominant disorder, may support BP2 when phase and disease context are documented.

Evidence considered

• The available ClinVar record is a single somatic submission for rhabdomyosarcoma and supplies no co-occurring-variant or phase information.
• No CTNNB1 allelic observations relevant to BP2 were provided in the consolidated case-evidence bundle.

Still missing

• A documented co-occurring pathogenic/likely pathogenic variant in the same individual.
• Phase evidence establishing cis or trans configuration with the queried CTNNB1 variant.
• For a trans observation, confirmation that the relevant disease mechanism is dominant and that the observation is clinically applicable.

Sources

Reasoning

No applicable CTNNB1 VCEP specification was retrieved, so generic ACMG/AMP was used. The bundle contains no individual-level evidence of a molecular diagnosis that fully explains a phenotype in a carrier of this variant.

Rule

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

Evidence considered

• No reported individual-level molecular diagnostic findings were available in the evidence bundle.

Still missing

• Individual-level phenotype and confirmed alternative molecular diagnosis information are required.

Reasoning

The exact-variant ClinVar record has no expert-panel assertion. The available single somatic laboratory submission is not an expert-panel Benign or Likely benign classification and cannot support BP6.

Rule

BP6 is applicable only to an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar reports review status 'criteria provided, single submitter'; the submission audit identifies zero expert-panel submissions.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign classification is required.

Sources