AXIN2 c.1365A>T, p.(Pro455=)

Reasoning

PM2 (absent from controls / very low frequency in population databases) applies at supporting strength per the ClinGen SVI 2020 recommendation to downgrade PM2, using a threshold of <= 0.0001 (PMID:25741868). No ClinGen CSPEC, VCEP, or local AXIN2 framework exists, so the generic threshold and the all-comers gnomAD v2.1/v4.1 totals are the default source; the gnomAD v2.1 non-cancer (exome-only) and gnomAD v3.1 non-cancer (genome-only) subsets were also checked and are likewise negative, so the conclusion is unchanged under either source-selection rule. NM_004655.4:c.1365A>T is absent: gnomAD v4.1 total AC=0 of 1,559,354 alleles (AF=0.000000), exome AC=0 of 1,407,484 alleles, homozygotes=0, with AF=0 in every ancestry group (largest, European non-Finnish, 1,153,178 alleles); gnomAD v2.1 exomes, gnomAD v2.1 non-cancer, gnomAD v3.1 non-cancer (genomes) and gnomAD-Canada v1.0 report absence. These are genuine not-observed results (search_status result_found/absent with empty error lists), not failed retrievals misread as absence, and the exome coverage of >1.4 million alleles rules out a sampling artifact. The observed frequency of 0 is below the 0.0001 supporting threshold, so PM2 is met at supporting strength. Caveat for the final classification: PM2 is weak supporting evidence and cannot outweigh the conflicting benign-direction population and ClinVar data seen in this case; noting also that for this gene the disease is incompletely penetrant, so absence from population cohorts carries no additional weight beyond the supporting tier.

Rule

AF <= 0.0001 -> PM2 supporting (ClinGen SVI 2020 downgrade, PMID:25741868); observed AF = 0

Evidence considered

• gnomAD v4.1 (v4.1.0, GRCh38 chr17-65537671-T-A): total AC=0/AN=1,559,354 (AF=0.000000), homozygotes=0; exome AC=0/AN=1,407,484; genome AC=0 with genome AN=0 in the fetched figures; every ancestry group AF=0 (European non-Finnish AN=1,153,178; African/African American AN=73,968; South Asian AN=86,292; Admixed American AN=51,594).
• gnomAD v2.1 (GRCh37 17-63533789-T-A, exomes): absent, search_status absent with no errors recorded.
• gnomAD v2.1 non-cancer (exomes-only figures) absent and gnomAD v3.1 non-cancer (genomes-only) absent; neither subset is a standalone source_registry key, so they are documented here instead of being cited in evidence_refs.
• gnomAD-Canada v1.0 (HostSeq genomes): variant absent.
• Threshold used: PM2 at supporting strength with AF <= 0.0001 (ClinGen SVI 2020 recommendation to downgrade PM2, PMID:25741868).
• Threshold used: BA1 stand-alone >= 0.05 and BS1 strong >= 0.01 (Richards et al. 2015 PMID:25741868; Whiffin et al. 2017 PMID:28518168) — both far above the observed 0 and therefore not met.
• Data-quality check: gnomAD v4.1 returned a populated record (search_status result_found) with all ancestry-level allele numbers present, so AC=0 reflects a true non-observation rather than a failed or empty retrieval.

Still missing

• gnomAD v4.1 genome AN was recorded as 0, so the joint figure is exome-dominated; genome-level absence relies on the gnomAD v3.1 non-cancer subset.
• No AXIN2-specific PM2 threshold or population source is specified by any VCEP because none exists for this gene.

Sources

Reasoning

Scope, as for PP3: NM_004655.4:c.1365A>T (NP_004646.3:p.(Pro455=)) is a synonymous substitution in AXIN2 exon 6, so BP4 is taken from the splice-prediction path (SpliceAI) only. The REVEL missense path is not used - there is no amino-acid substitution for it to score and REVEL is recorded as not found (a missing missense score is not evidence and does not license reaching across to the splice score in reverse); BayesDel is not used because no generic ACMG-strength calibration exists and no VCEP supplies an AXIN2 cutoff. No AXIN2 CSPEC/VCEP specification exists, so the generic published SpliceAI calibration applies. SpliceAI Lookup for this exact variant returns DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000 with a maximum delta score of 0.001, and Pangolin agrees (splice-gain 0.002, splice-loss -0.001). That maximum delta is at or below the recommended SpliceAI no-impact cutoff of <= 0.1, which is the published BP4 (supporting) calibration for splice predictors (Jaganathan et al. 2019, Cell; PMID:30661751). The prediction is internally consistent with the variant's location: c.1365 is not at a splice consensus position (canonical_splice_consensus = false) and lies well inside exon 6 rather than in a splice region, and the nearest predicted cryptic sites are distant (nearest acceptor gain 104 bp, nearest donor gain 482 bp; DP_AG 104, DP_AL 75, DP_DG 482, DP_DL -418), so no donor or acceptor is gained, strengthened, or created. The single SpliceAI/Pangolin result is credited once, here, and is not counted again under BP7; that restriction is noted because both criteria would otherwise rest on this identical prediction. BP4 is met at supporting strength.

Rule

Generic ACMG/AMP in-silico splice path: SpliceAI max delta <= 0.1 -> BP4 (supporting) (Jaganathan et al. 2019, Cell; PMID:30661751). Met: max delta 0.001.

Evidence considered

• Consequence type fixed first: NM_004655.4:c.1365A>T / NP_004646.3:p.(Pro455=) is synonymous, so BP4 is assessed on the SpliceAI splice path only; the REVEL missense path does not apply (REVEL not found for this variant) and BayesDel has no generic ACMG-strength calibration.
• SpliceAI Lookup for NM_004655.4:c.1365A>T / 17-63533789-T-A: max delta score 0.001 (DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000), DP_AG 104, DP_AL 75, DP_DG 482, DP_DL -418; Pangolin SG 0.002, SL -0.001.
• Threshold applied verbatim from the supplied generic ACMG/ClinGen-SVI calibration: SpliceAI max delta <= 0.1 -> BP4 (supporting) (Jaganathan et al. 2019, Cell; PMID:30661751). 0.001 satisfies it.
• No governing VCEP/CSPEC specification for AXIN2 (ClinGen CSPEC not found; vcep_materials.json empty; final_classification_framework = generic_acmg_fallback, framework_complete = false), so the generic published splice-predictor calibration was applied and no gene-specific lookup code pre-assigned BP4.
• The variant is not in a canonical splice site (canonical_splice_consensus = false) and sits well inside exon 6, consistent with the null splice prediction; the prediction, not the position, is the basis for the criterion.
• The single SpliceAI/Pangolin result is the only benign-direction computational evidence for this variant and is credited once, under BP4; crediting it again under BP7 would double-count one prediction (see BP7 rationale).

Sources

Reasoning

PS3 requires well-established functional studies demonstrating a damaging effect on the gene or gene product (Richards et al. 2015, PMID:25741868). No AXIN2-specific VCEP/ClinGen CSPEC specification or local custom framework exists for this gene, so the generic ACMG/AMP 2015 specification governs this assessment. NM_004655.4:c.1365A>T is a synonymous substitution predicted to yield NP_004646.3:p.(Pro455=); functional evidence for such a variant would normally come from an RNA-splicing assay (e.g., minigene or RT-PCR of patient RNA) or a protein/reporter assay, and none exists in any consulted source. The four germline ClinVar submissions on the exact variant (GeneDx SCV001830735, Ambry SCV002696054, Myriad SCV005407601, Labcorp/Invitae SCV001665177; ClinVar variation 1128484) cite no functional study at all, and the only PMID trails attached to that record are a referral-practice guideline (PMID:25394175) and a criteria-refinement methods paper (PMID:28492532), neither of which is an assay. The single full-text paper retrieved for this case (PMID:25394175) never mentions AXIN2 or this variant, so it supplies no functional data. OncoKB returned only gene-level, non-variant-specific context (oncogenicity label 'Unknown Oncogenic Effect', is_variant_specific=false), which is not functional evidence for this specific nucleotide change. The variant is also absent from gnomAD v2.1 and has 0 alleles in 1,559,354 in gnomAD v4.1 - population data, not functional data. SpliceAI max delta 0.001 is a computational prediction rather than a functional study and belongs to the in-silico predictor criteria, so it cannot be counted toward PS3. Because no validated functional assay interrogates this variant, the evidential prerequisite for PS3 is absent and no strength (supporting/moderate/strong) can be assigned.

Evidence considered

• PS3 definition applied: 'well-established functional studies show a damaging effect on the gene or gene product' (Richards et al. 2015, PMID:25741868); no AXIN2-specific VCEP/CSPEC or local custom framework exists (case framework_mode = generic_acmg, framework_complete = false), so the generic ACMG/AMP 2015 specification governs.
• No functional assay evidence for AXIN2 c.1365A>T (p.Pro455=) appears in any consulted source: no minigene, RT-PCR/RNA-splicing, protein-expression, stability, or reporter assay is reported.
• ClinVar variation 1128484: four germline submissions (GeneDx, Ambry Genetics, Myriad Genetics, Labcorp/Invitae) classify the variant Benign/Likely benign, but none cites a functional assay; the PMID trails attached to the record are a referral-practice guideline (PMID:25394175) and a criteria-refinement methods paper (PMID:28492532). ClinVar's own classification was not used as functional evidence - only the absence of any cited assay was noted.
• The only full-text paper retrieved for this case, PMID:25394175 (ACMG/NSGC referral-indications practice guideline), was checked for AXIN2 or variant content and contains neither; it is not a functional study and contributes no assay data.
• PMID:28492532 (Sherloc criteria refinement) was available only at title/abstract level; it is a methods paper on ACMG-AMP criteria usage and reports no functional assay of this variant.
• OncoKB returned only gene-level, non-variant-specific context for AXIN2 P455= (listed oncogenicity label 'Unknown Oncogenic Effect'; is_variant_specific = false; no citation PMIDs), so it does not constitute variant-level functional evidence.
• COSMIC returned no record for AXIN2 c.1365A>T and Cancer Hotspots found no significant hotspot at residue P455; absence of somatic recurrence is not a functional assay.
• SpliceAI max delta score for this variant is 0.001 (DS_AG 0.0, DS_AL 0.001, DS_DG 0.001, DS_DL 0.0; Pangolin SG 0.002, SL -0.001). This is a computational splice prediction, not a functional study, and is adjudicated by the in-silico predictor criteria; it was not counted toward PS3.
• Population data are not functional evidence: variant absent from gnomAD v2.1, and gnomAD v4.1 reports AF 0 (0/1,559,354 alleles, 0 homozygotes).

Still missing

• No functional assay interrogating AXIN2 c.1365A>T (minigene or patient-RNA splicing assay, protein-expression or reporter assay) was identified in any consulted source; such an assay is required before PS3 could be met at any strength.
• Literature retrieval for this case covered only two PMIDs (PMID:25394175 full text, which does not mention AXIN2; PMID:28492532 abstract only). A targeted functional-literature search for this specific synonymous variant was therefore not exhausted; a variant-level functional publication could still exist.
• No AXIN2-specific VCEP specification is available, so no gene-specific PS3 evidence weighting or assay-acceptability (calibration) rules could be applied; the generic 2015 framework was used.

Sources

Reasoning

PS4 requires case-control or case-enrichment evidence, i.e. a statistically increased prevalence of the variant in affected individuals compared with controls (Richards et al. 2015, PMID:25741868). No AXIN2-specific ClinGen CSPEC/VCEP specification and no local gene-specific framework were retrieved for this case (cspec found=false; vcep_materials.json contains no summaries, files, or domain tables; final_classification_framework found=false with source='generic_acmg_fallback'), so the generic ACMG/AMP 2015 framework governs and no gene-specific PS4 odds-ratio or likelihood-ratio threshold is defined for AXIN2. Because no numeric threshold applies to PS4 here, there was no inequality to evaluate and consequently no comparison direction to select for this criterion; nothing was carried over from any neighbouring criterion in this group. The available evidence contains no case-control or affected-cohort data at all. The only literature lead auto-triaged to PS4 (PMID:25394175, theme 'case_observation') is the ACMG/NSGC practice guideline on referral indications for cancer predisposition assessment; its extracted full text does not mention AXIN2 or this variant (paper_extracts.json: variant_mentioned=false, searched_for included 'c.1365A>T' and 'AXIN2'). No proband carrying NM_004655.4:c.1365A>T (NP_004646.3:p.(Pro455=)) was identified in any case report, cohort, or ClinVar submission. The variant is also absent from gnomAD v2.1 and present at total AF 0.0 (0/1,559,354 alleles) in gnomAD v4.1, which is population-frequency evidence relevant to PM2/BS1/BA1 rather than to PS4 and does not supply the affected-vs-control contrast PS4 requires. PS4 is therefore not met.

Evidence considered

• Framework: no AXIN2 CSPEC/VCEP or local gene framework was retrieved (cspec found=false; gene_vcep_dir=null; vcep_materials.json empty; final_classification_framework found=false, framework_complete=false), so generic ACMG/AMP 2015 (PMID:25741868) applies. The generic framework defines no numeric PS4 threshold, so no numeric comparison and no comparison direction was evaluated for PS4.
• ClinVar variation 1128484 (exact match for NM_004655.4:c.1365A>T, p.Pro455=): 4 submissions, 3 'Likely benign' plus 1 'Benign', all from ordinary clinical laboratories; no case-level records, no case-control data, no odds ratio in the record.
• gnomAD v2.1 (exome): variant absent at 17-63533789-T-A.
• gnomAD v4.1: total AF 0.0 (0/1,559,354 alleles; exome AN 1,407,484); highest observed subpopulation AFR AF 0.0 (0/73,968 alleles). Used here only to establish that no population-based enrichment argument exists; these frequencies bear on PM2/BS1/BA1, not on PS4.
• Literature: PMID:25394175, the only paper triaged to PS4, is an ACMG/NSGC referral-indications practice guideline; the pre-computed full-text extraction found no mention of AXIN2 or of this variant, so it supplies no PS4-bearing case or case-control data.
• No ClinVar expert-panel submission, no case series, and no genotype-phenotype cohort for this variant was present anywhere in the case evidence.

Still missing

• No case-control, case-enrichment, or affected-cohort dataset reporting NM_004655.4:c.1365A>T exists in this case's evidence; no odds ratio or equivalent statistic is available.
• No published proband (with or without phenotype) carrying this exact variant was identified, so even an observational case-enrichment argument cannot be constructed.

Sources

Reasoning

Scope was settled before any predictor score was read. NM_004655.4:c.1365A>T normalises to NP_004646.3:p.(Pro455=) (Mutalyzer/VariantValidator in prefetch.json; NC_000017.10:g.63533789T>A / NC_000017.11:g.65537671T>A), i.e. a synonymous substitution in AXIN2 exon 6 - not a missense change, and not a frameshift, nonsense or other protein-length-changing variant. PP3 for this variant therefore comes from the splice-prediction path (SpliceAI) only; the REVEL missense protein-impact path does not apply, because a synonymous change has no amino-acid substitution to score (REVEL is recorded as not found for this variant, and a missing missense score is not a reason to substitute a splice score, nor the reverse). BayesDel is likewise unusable: no generic ACMG-strength calibration exists for it and no VCEP supplies an AXIN2 cutoff (score also not found in this case). No ClinGen CSPEC and no AXIN2 VCEP/gene-specific specification exists (cspec found=false; final classification framework resolved to the generic ACMG/AMP 2015 fallback, framework_complete=false; vcep_materials.json contains no rules, domain tables or index guidance), so the generic published calibration governs. SpliceAI Lookup for this exact variant is available and reports DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000, with maximum delta score 0.001, alongside Pangolin splice-gain 0.002 / splice-loss -0.001; the nearest predicted cryptic acceptor gain is 104 bp away and the nearest donor gain 482 bp away (DP_AG 104, DP_AL 75, DP_DG 482, DP_DL -418). A maximum delta score of 0.001 is far below both published SpliceAI PP3 cutoffs - supporting >= 0.2 and moderate >= 0.5 (Jaganathan et al. 2019, Cell; PMID:30661751) - so no computational evidence supports a deleterious effect. The case contains no other splice-relevant predictor result (no VarSeak/CADD-type output), and the low SpliceAI value here is consistent with the variant's position, which is not at a splice consensus site (canonical_splice_consensus = false) and lies well inside exon 6 rather than in a splice region. PP3 is not met at any strength.

Rule

Generic ACMG/AMP in-silico splice path: SpliceAI max delta >= 0.2 -> PP3 (supporting); >= 0.5 -> PP3 (moderate) (Jaganathan et al. 2019, Cell; PMID:30661751). Not met: max delta 0.001.

Evidence considered

• Variant identity and consequence type were fixed first: NM_004655.4:c.1365A>T = NP_004646.3:p.(Pro455=) (prefetch.json Mutalyzer/VariantValidator normalisation; ClinVar variation 1128484 name 'NM_004655.4(AXIN2):c.1365A>T (p.Pro455=)'), a synonymous substitution, so the applicable PP3 path is SpliceAI (splice impact), not REVEL (missense protein impact).
• SpliceAI Lookup (spliceailookup.broadinstitute.org, hg37, basic, distance 500) for NM_004655.4:c.1365A>T / 17-63533789-T-A: DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000; max delta score 0.001; DP_AG 104, DP_AL 75, DP_DG 482, DP_DL -418; Pangolin SG 0.002, SL -0.001; spliceai_available = true; variant_consequence 'sequence_variant'.
• Thresholds applied verbatim from the supplied generic ACMG/ClinGen-SVI calibration: SpliceAI max delta >= 0.5 -> PP3 (moderate); >= 0.2 -> PP3 (supporting) (Jaganathan et al. 2019, Cell; PMID:30661751). 0.001 reaches neither band.
• No governing VCEP/CSPEC specification exists for AXIN2 (ClinGen CSPEC not found; review_manifest gene_vcep_files = []; vcep_materials.json empty; final_classification_framework source = generic_acmg_fallback, framework_complete = false), so no gene-specific PP3 lookup code is available and the generic published calibration was applied.
• REVEL is not applicable to this variant (synonymous; no amino-acid substitution to score) and is recorded as not found; BayesDel is likewise unused because no generic ACMG-strength calibration exists for it and no VCEP supplies one.
• No other computational evidence bearing on splice impact exists for this variant in the case (no VarSeak/CADD-type predictor output), and the variant is not at a splice consensus position (canonical_splice_consensus = false).

Sources

Reasoning

PP5 requires a reputable, exact-variant assertion that the variant is pathogenic (Richards et al. 2015, PMID:25741868). Under the governing rule for this case, only an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic may trigger PP5; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. ClinVar variation 1128484 is an exact match for NM_004655.4:c.1365A>T (p.Pro455=), so the exact-variant record was found and checked, but it contains 4 submissions, all from ordinary clinical laboratories (GeneDx SCV001830735 'Likely benign'; Ambry Genetics SCV002696054 'Likely benign'; Myriad Genetics SCV005407601 'Benign'; Labcorp Genetics/Invitae SCV001665177 'Likely benign'). expert_panel_submissions = 0, no expert panel is listed in the ClinVar API record (expert_panels = {}), and the record's review status is 'criteria provided, multiple submitters, no conflicts' (2 stars), not expert-panel reviewed. The aggregate label is Benign/Likely benign, which is not a pathogenic assertion in any case. The one submission with a validated PMID trail (SCV001665177) cites PMID:28492532, 'Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria' - a generic criteria-refinement methodology paper, not an expert-panel assertion about this variant - and the only full-text paper screened for PP5 (PMID:25394175) does not mention AXIN2 or the variant. Because the exact-variant record exists and was examined, this is a substantive not_met rather than not_assessed: the triggering condition was tested against the exact-variant record and failed. No AXIN2 CSPEC/VCEP exists, so generic ACMG/AMP applies and PP5 carries no numeric threshold; no numeric comparison or comparison direction was evaluated.

Evidence considered

• ClinVar variation 1128484 is an exact variant match (NM_004655.4(AXIN2):c.1365A>T (p.Pro455=); matched_by transcript_hgvs). Review status 'criteria provided, multiple submitters, no conflicts' (clinvar_api review_stars = 2); expert panel listing is empty (expert_panels = {}) and submission_audit counts give expert_panel_submissions = 0.
• All four submissions are ordinary clinical laboratories: GeneDx (SCV001830735, Likely benign), Ambry Genetics (SCV002696054, Likely benign), Myriad Genetics, Inc. (SCV005407601, Benign), Labcorp Genetics (formerly Invitae) (SCV001665177, Likely benign). None is designated an expert-panel submission.
• The aggregate ClinVar label (Benign/Likely benign) and the individual non-expert submissions were deliberately not used to trigger PP5, per the exact-variant expert-panel requirement; the aggregate label is not a pathogenic assertion in any case.
• The only submission with a validated PMID trail, SCV001665177, cites PMID:28492532 (Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria), a generic criteria-refinement paper rather than an expert-panel assertion about this variant.
• PMID:25394175, the only full-text paper available and the paper triaged to PP5, does not mention AXIN2 or this variant (pre-computed extraction: variant_mentioned = false).
• Framework: no AXIN2 CSPEC/VCEP or local gene framework was retrieved, so generic ACMG/AMP 2015 (PMID:25741868) applies; generic PP5 is qualitative with no numeric threshold, so no numeric comparison or comparison direction was evaluated.

Still missing

• No ClinGen/VCEP expert panel (for example InSiGHT or a hereditary-cancer VCEP) has issued a classification for this exact variant; if one is published later, PP5 must be re-evaluated against it.

Sources

Reasoning

BA1 (stand-alone benign) requires an allele frequency of at least 0.05 (Richards et al. 2015, PMID:25741868). No ClinGen CSPEC, VCEP, or local gene-specific framework exists for AXIN2 (vcep_materials.json file set is empty; final_classification_framework found=false, framework_complete=false), so the generic ACMG/AMP 2015 fallback applies and the all-comers gnomAD v2.1/v4.1 totals are the default population source. NM_004655.4:c.1365A>T was observed zero times in every queried population source: gnomAD v4.1 reports total AC=0 of 1,559,354 alleles (AF=0.000000, homozygotes=0; exome AC=0/1,407,484), it is absent from gnomAD v2.1 exomes, absent from the gnomAD v2.1 non-cancer (exome-only figures) and gnomAD v3.1 non-cancer (genome-only) subsets, and absent from gnomAD-Canada v1.0. Every gnomAD v4.1 ancestry group shows AF=0, including the largest, European (non-Finnish), at 1,153,178 alleles. With an observed frequency of 0, the 0.05 stand-alone threshold is not approached, and there is no ancestry-specific or homozygote signal that could support stand-alone benign classification.

Rule

AF >= 0.05 -> BA1 stand-alone benign (generic ACMG/AMP 2015, PMID:25741868); observed AF = 0

Evidence considered

• gnomAD v4.1 (GRCh38 chr17-65537671-T-A): total AC=0/AN=1,559,354 (AF=0.000000), homozygotes=0; exome AC=0/AN=1,407,484; genome AC=0 with genome AN=0 in the fetched figures; all ancestry groups AF=0, largest group European (non-Finnish) AN=1,153,178.
• gnomAD v2.1 (GRCh37 17-63533789-T-A, exomes): variant absent.
• gnomAD v2.1 non-cancer (exome-only figures) and gnomAD v3.1 non-cancer (genome-only) both reported absent; these non-cancer subsets are not registered as standalone source_registry keys, so they are described here rather than listed in evidence_refs.
• gnomAD-Canada v1.0 (HostSeq genomes, GRCh38): variant absent.
• No ClinGen CSPEC or VCEP/gene-specific framework for AXIN2; generic ACMG/AMP 2015 fallback used, with all-comers gnomAD totals as the default frequency source.
• Threshold used: BA1 stand-alone benign >= 0.05 (Richards et al. 2015, PMID:25741868).

Sources

Reasoning

BS1 (strong benign) requires an allele frequency greater than expected for the disorder; the generic SVI default is >= 0.01, with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168). No CSPEC/VCEP or gene-specific AXIN2 framework exists, and no per-gene BS1 threshold can be derived from an all-zero frequency observation, so the generic 0.01 default is used. The variant was not observed at all: gnomAD v4.1 total AC=0 of 1,559,354 alleles (AF=0.000000), gnomAD v2.1 absent, gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets absent, gnomAD-Canada v1.0 absent, and all gnomAD v4.1 ancestry groups (including European non-Finnish at 1,153,178 alleles and African/African American at 73,968 alleles) AF=0. Even the most common ancestry-specific frequency is 0, which is two orders of magnitude below the 0.01 strong benign threshold; the criterion is not met.

Rule

AF >= 0.01 -> BS1 strong benign (generic SVI default, Whiffin et al. 2017 PMID:28518168); observed AF = 0

Evidence considered

• gnomAD v4.1: total AC=0/AN=1,559,354 (AF=0.000000); best-populated ancestry group African/African American AC=0/AN=73,968; no group-frequency or grpmax FAF above 0.
• gnomAD v2.1 (exomes) absent; gnomAD v2.1 non-cancer (exome-only) and gnomAD v3.1 non-cancer (genome-only) absent; gnomAD-Canada v1.0 absent.
• Threshold used: BS1 strong benign >= 0.01 (generic SVI default; per-gene derivation preferred per Whiffin et al. 2017, PMID:28518168). No AXIN2-specific BS1 calibration exists in any governing specification.
• The single fetched full-text publication (PMID:25394175) contains no AXIN2 or population-frequency content and contributed nothing to this criterion.

Sources

Reasoning

BS2 (strong benign) requires observation of the variant in a healthy adult individual, i.e. homozygotes for a recessive disorder, heterozygotes for a dominant disorder expected to be fully penetrant at an early age, or hemizygotes for an X-linked disorder. The variant's structural prerequisite is not restricted by consequence class, so a synonymous change can be evaluated; the obstacle here is observational, not structural. NM_004655.4:c.1365A>T was observed zero times in any population cohort: gnomAD v4.1 reports AC=0 with homozygote count 0 (0/1,559,354 alleles), and the variant is absent from gnomAD v2.1 exomes, the gnomAD v2.1 non-cancer (exome-only) and gnomAD v3.1 non-cancer (genome-only) subsets, and gnomAD-Canada v1.0. With no carriers and no homozygotes documented in any adult population dataset, there is no healthy-adult observation to support BS2, and the criterion is not met.

Rule

Requires observed healthy-adult homozygote/hemizygote (recessive/X-linked) or heterozygote (dominant, early-onset fully penetrant); observed carrier count = 0 in all population sources

Evidence considered

• gnomAD v4.1 homozygote count = 0 and total AC = 0 of 1,559,354 alleles; no carrier or homozygote observation exists to evaluate.
• gnomAD v2.1 (exomes) absent; gnomAD v2.1 non-cancer (exome-only) and gnomAD v3.1 non-cancer (genome-only) absent; gnomAD-Canada v1.0 absent.
• AXIN2 disease context (attenuated adenomatous polyposis / oligodontia-colorectal cancer syndrome) is autosomal dominant with variable expression; BS2 semantics for a dominant disorder require observed healthy adult heterozygotes, of which there are none.

Still missing

• gnomAD v4.1 genome AN was recorded as 0, so the joint figures are exome-dominated; genome-level absence rests on the gnomAD v3.1 non-cancer subset rather than on v4.1 genomes.

Sources

Reasoning

BS3 requires well-established functional studies demonstrating no damaging effect on the gene or gene product (Richards et al. 2015, PMID:25741868). No AXIN2-specific VCEP/ClinGen CSPEC specification or local custom framework exists for this gene, so the generic ACMG/AMP 2015 specification governs. NM_004655.4:c.1365A>T (NP_004646.3:p.(Pro455=)) is a synonymous substitution, and a benign functional determination for such a variant would require a validated assay of RNA splicing (minigene or patient-RNA RT-PCR, ideally with a splicing-competent control series) or of protein output; no such assay is reported in any consulted source. Codon-level reasoning is not a substitute: a synonymous change is not intrinsically benign, because it can create or destroy exonic splice elements, which is precisely why this criterion demands assay data rather than inference. The only functional-adjacent data available for this variant is a computational predictor result - SpliceAI max delta 0.001 (DS_AG 0.0, DS_AL 0.001, DS_DG 0.001, DS_DL 0.0; Pangolin SG 0.002, SL -0.001), i.e. no predicted splice impact - and a predictor score, however clean, is not a functional study under BS3; that SpliceAI result is instead the province of the in-silico splice-predictor criteria. Likewise the Benign/Likely benign classifications from the four ClinVar germline submitters (GeneDx, Ambry, Myriad, Labcorp/Invitae) and the absence of a COSMIC record or hotspot signal are not assay-based evidence of normal function and were not used as such. With no assay demonstrating preserved splicing or protein function, BS3 is not satisfied at any strength.

Evidence considered

• BS3 definition applied: 'well-established functional studies show no damaging effect on the gene or gene product' (Richards et al. 2015, PMID:25741868); no AXIN2-specific VCEP/CSPEC or local custom framework exists (framework_mode = generic_acmg), so the generic ACMG/AMP 2015 specification governs.
• SpliceAI Lookup for NM_004655.4:c.1365A>T returned max delta score 0.001 (DS_AG 0.0, DS_AL 0.001, DS_DG 0.001, DS_DL 0.0; Pangolin SG 0.002, SL -0.001), i.e. no predicted splice impact. This is a computational prediction, not a functional assay, and therefore cannot satisfy BS3, which requires assay-based evidence of a non-damaging effect; the score belongs to the in-silico splice-predictor criteria path.
• No minigene, patient-RNA RT-PCR, protein-expression, stability, or reporter assay interrogating AXIN2 c.1365A>T was found in any consulted source.
• ClinVar variation 1128484: four germline submissions (GeneDx, Ambry Genetics, Myriad Genetics, Labcorp/Invitae) give Benign/Likely benign classifications and cite no functional assay; these are other submitters' final classifications and were not converted into BS3 evidence.
• The single retrieved full-text paper, PMID:25394175 (ACMG/NSGC referral-indications practice guideline), does not mention AXIN2 or this variant and contains no assay data.
• PMID:28492532 (Sherloc criteria refinement) was available only at title/abstract level and is a methods paper, not a functional study.
• OncoKB listed AXIN2 P455= as 'Unknown Oncogenic Effect' with no variant-specific citations; this is neither damaging nor non-damaging functional evidence and was not used either way.
• Absence from gnomAD v2.1 and 0 alleles in 1,559,354 in gnomAD v4.1, no COSMIC record, and no Cancer Hotspots residue signal are population/somatic-recurrence observations and are not functional assay evidence for BS3.

Still missing

• No RNA-splicing or protein-function assay (minigene, RT-PCR on patient RNA, protein expression/stability) demonstrating preserved function of AXIN2 c.1365A>T was identified in any consulted source, so the evidence required to satisfy BS3 does not exist for this variant.
• The only splicing-relevant data are computational (SpliceAI max delta 0.001; Pangolin SG 0.002, SL -0.001). If a validated splicing assay were performed and confirmed normal splicing, BS3 could be reconsidered within the in-silico/splicing evidence pathway.
• No AXIN2-specific VCEP specification is available, so no gene-specific assay-acceptability or BS3 calibration rules could be applied; the generic 2015 framework was used.

Sources

Reasoning

BP2 (Richards et al. 2015, PMID:25741868) is met when the variant is observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant under any inheritance model. NM_004655.4:c.1365A>T (NP_004646.3:p.(Pro455=)) is reported only as an isolated heterozygous synonymous change: the case contains no proband, no family members, no second AXIN2 variant and no genotype or phase data, and none of the four ClinVar submissions (SCV001830735 GeneDx, SCV002696054 Ambry Genetics, SCV005407601 Myriad Genetics, SCV001665177 Labcorp Genetics) reports the variant in cis or in trans with a pathogenic allele. The one criterion-lead submission (SCV001665177) cites only PMID:28492532, a general ACMG/AMP criteria-refinement paper for which no full text or extraction exists in this case, and the only fetched full text (PMID:25394175) is an ACMG/NSGC cancer-referral practice guideline that never mentions AXIN2 or the variant. Because no cis or trans observation with a pathogenic variant exists in any collected source, BP2 is not met; no VCEP/CSPEC specification governs AXIN2, so the generic ACMG/AMP 2015 definition was applied.

Rule

generic ACMG/AMP 2015 BP2: observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or observed in cis with a pathogenic variant in any inheritance pattern - no cis/trans observation available (generic_acmg_combination_rules fallback, framework_complete=false)

Evidence considered

• All four ClinVar submissions for VCV001128484 (SCV001830735 GeneDx, SCV002696054 Ambry Genetics, SCV005407601 Myriad Genetics, SCV001665177 Labcorp Genetics) are single-submitter records with no reported cis/trans phase, no second AXIN2 variant and no segregation data; three classify Likely benign and one Benign.
• The variant is a synonymous substitution (NP_004646.3:p.(Pro455=)) in exon 6 of AXIN2, reported only as an isolated heterozygous finding, with no co-occurring AXIN2 pathogenic allele documented anywhere in the case record.
• PMID:25394175 is an ACMG/NSGC practice guideline on referral indications for cancer predisposition assessment; its fetched full text contains no mention of AXIN2, c.1365A>T or p.(Pro455=), so it provides no cis/trans observation for this variant.
• PMID:28492532 (Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria) is registered in this case only as the background citation of ClinVar submission SCV001665177; no full text or pre-computed extraction is present, so no variant-specific cis/trans evidence can be obtained from it.
• No proband, parental genotypes or family members are present in the case record, so the variant could not be observed in cis or in trans with any pathogenic variant.

Still missing

• No proband or parental genotypes are available in this case, so the variant could not be phased against any pathogenic AXIN2 allele from primary data.
• PMID:28492532 (Sherloc), cited by ClinVar submission SCV001665177, has no fetched full text or pre-computed extraction in this case, so its exact BP2 wording/usage could not be verified from source.
• No AXIN2 CSPEC/VCEP specification is available; BP2 was assessed with the generic ACMG/AMP 2015 definition.

Sources

Reasoning

BP6 requires a reputable, exact-variant assertion that the variant is benign (Richards et al. 2015, PMID:25741868). Under the governing rule for this case, only an exact-variant ClinVar expert-panel classification of Benign or Likely benign may trigger BP6; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. ClinVar variation 1128484 is an exact match for NM_004655.4:c.1365A>T (p.Pro455=) and its aggregate label is Benign/Likely benign (clinvar_api classification 'Benign/Likely benign', review status 'criteria provided, multiple submitters, no conflicts', 2 stars), but no expert-panel classification underlies that label: all four submissions are ordinary clinical laboratories (GeneDx, Ambry Genetics, Myriad Genetics, Labcorp/Invitae), expert_panels is empty in the ClinVar API record, and submission_audit counts give expert_panel_submissions = 0. The benign-leaning aggregate label is therefore an aggregate of non-expert assertions and is explicitly excluded from triggering BP6. The only cited publication in the record (PMID:28492532, cited by SCV001665177) is a generic ACMG-AMP criteria-refinement paper, not an expert-panel benign assertion, and the only available full-text paper (PMID:25394175) does not mention AXIN2 or this variant. Because the exact-variant record was found and checked, this is a substantive not_met rather than not_assessed: the trigger condition was tested and failed. No AXIN2 CSPEC/VCEP exists, so generic ACMG/AMP applies and BP6 carries no numeric threshold; no numeric comparison or comparison direction was evaluated.

Evidence considered

• ClinVar variation 1128484 is an exact variant match (NM_004655.4(AXIN2):c.1365A>T (p.Pro455=)); aggregate label Benign/Likely benign with review status 'criteria provided, multiple submitters, no conflicts' (2 stars), i.e. not expert-panel reviewed.
• expert_panel_submissions = 0 and the ClinVar API expert_panels object is empty; all four submissions are ordinary clinical laboratories (GeneDx SCV001830735, Ambry Genetics SCV002696054, Myriad Genetics SCV005407601, Labcorp/Invitae SCV001665177).
• The aggregate benign label and the non-expert submissions were deliberately not used to trigger BP6, per the exact-variant expert-panel requirement.
• PMID:28492532 (cited by SCV001665177) is 'Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria', a generic criteria methodology paper, not an expert-panel benign assertion about this exact variant.
• Framework: no AXIN2 CSPEC/VCEP or local framework was retrieved, so generic ACMG/AMP 2015 (PMID:25741868) applies; generic BP6 is qualitative with no numeric threshold, so no numeric comparison or comparison direction was evaluated.

Still missing

• No ClinGen/VCEP expert panel has issued a benign or likely benign classification for this exact variant; BP6 must be re-evaluated if such a classification is published.

Sources

Reasoning

Scope: BP7 applies only to a synonymous variant, and NM_004655.4:c.1365A>T (NP_004646.3:p.(Pro455=)) is synonymous, so the criterion is in scope and was evaluated rather than dismissed. BP7 as defined in the ACMG/AMP 2015 framework (Richards et al., PMID:25741868) requires a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site, and for which the nucleotide is not highly conserved. The first element is supported by the only splice prediction in the case: SpliceAI maximum delta score 0.001 (DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000) with Pangolin splice-gain 0.002 / splice-loss -0.001, i.e. no predicted splice impact. That identical prediction, however, is the evidence already credited to BP4 at supporting strength for this variant (SpliceAI max delta <= 0.1). The ACMG/AMP framework treats predictions from different in-silico tools as a single piece of evidence rather than independent pieces of evidence, and this group's scope forbids double-counting one prediction across PP3/BP4/BP7; crediting the same SpliceAI/Pangolin result under both BP4 and BP7 would count one prediction twice and inflate the benign evidence for this variant. The second element cannot be established at all: no nucleotide-conservation metric for c.1365 (phyloP, GERP, PhastCons or equivalent) is present anywhere in the case evidence, so the 'not highly conserved' requirement of BP7 is unverified. BP7 is therefore not counted as an independent benign criterion here; the prediction that would support it has already been applied once, under BP4.

Rule

BP7 (Richards et al. 2015, PMID:25741868): synonymous variant with no predicted impact on the splice consensus sequence or creation of a new splice site, and the nucleotide not highly conserved. Not credited here because the only supporting prediction is already counted under BP4 and the conservation element is unverified.

Evidence considered

• Consequence type confirmed as synonymous before scoring: NM_004655.4:c.1365A>T = NP_004646.3:p.(Pro455=) (prefetch.json Mutalyzer/VariantValidator normalisation; ClinVar variation 1128484), so BP7 is the criterion scoped to this variant type.
• BP7 definition taken from the ACMG/AMP 2015 standards (Richards et al., PMID:25741868; operationalised generically in this case's framework): synonymous variant with no predicted impact on the splice consensus sequence or creation of a new splice site, and a nucleotide that is not highly conserved.
• SpliceAI/Pangolin result for this exact variant (max delta 0.001; DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, DS_DL 0.000; Pangolin SG 0.002, SL -0.001) predicts no splice impact, but it is the same single prediction already used for BP4 at supporting strength; in-silico predictions are treated as one piece of evidence and this group prohibits counting one prediction across PP3/BP4/BP7.
• Richards et al. (PMID:25741868) warn that in-silico predictions from different programs should be treated as a single piece of evidence rather than independent evidence and should not be the sole source of a clinical assertion - the basis for declining to credit this prediction twice.
• No conservation data (phyloP/GERP/PhastCons or equivalent) for c.1365 appears in any case file, so the second element of BP7 could not be checked.
• No CSPEC/VCEP specification for AXIN2 exists (cspec found=false; framework generic_acmg_fallback, framework_complete=false) to specify gene-level BP7 handling.

Still missing

• No nucleotide-conservation metric for AXIN2 c.1365 (phyloP, GERP, PhastCons or equivalent) appears in any case file (prefetch.json, evidence.json, case_summary.json, literature_pass.json, paper_extracts.json all lack conservation data), so the 'nucleotide is not highly conserved' element of BP7 could not be verified.
• BP7 and BP4 would rest on the same single in-silico prediction for this variant (SpliceAI max delta 0.001; Pangolin SG 0.002 / SL -0.001); only one of the two may be credited, and BP4 was selected because it carries an explicit published calibration (SpliceAI <= 0.1) in this case's governing generic framework.
• No gene-specific (VCEP/CSPEC) BP7 rule for AXIN2 exists to resolve which of the two synonymous-variant codes is preferred (ClinGen CSPEC not found; generic ACMG/AMP 2015 fallback, framework_complete = false).

Sources

Reasoning

PS2 (Richards et al. 2015, PMID:25741868) requires a de novo occurrence confirmed by parental testing - both parents shown to be non-carriers with parentage confirmed - in a patient whose phenotype is consistent with the gene. No gene-specific specification exists for AXIN2 (no ClinGen CSPEC/VCEP; framework_complete=false, so the generic ACMG/AMP 2015 fallback governs), therefore the generic requirement applies in full. This case contains no proband-level information at all: no clinical phenotype, testing indication, age/sex or sample context is recorded in case_summary.json, prefetch.json or evidence.json, and no parental genotypes, trio data, Sanger confirmation or parentage information exists anywhere in the case (a case-wide search for de novo, parental, proband, mother, father, pedigree, meioses and segregation terms returns zero matches). The ClinVar record (ClinVarID 1128484, VCV001128484) lists four germline-labelled submissions with condition terms but no family members and no parental testing, so it neither establishes nor excludes a de novo event; its classification was not used as evidence for this criterion. The one paper retrieved in full text (PMID:25394175) contains no AXIN2 content. PS2 is therefore unassessable. Gap: a proband phenotype plus parental genotype testing (ideally a confirmed trio) for NM_004655.4:c.1365A>T.

Rule

PS2: de novo occurrence (both parents tested, non-carriers, parentage confirmed) in a patient with disease and phenotype consistent with the gene

Evidence considered

• Governing framework check: no ClinGen CSPEC/VCEP specification for AXIN2 (cspec found=false in the case summary; gene_vcep_dir=null; vcep_materials.json contains no summaries, files or domain tables), so the generic ACMG/AMP 2015 criterion definitions were applied via the generic_acmg_combination_rules source.
• PS2 as defined in Richards et al. 2015 (PMID:25741868): de novo occurrence (both parents tested and confirmed non-carriers, parentage confirmed) in a patient with the disease and a phenotype consistent with the gene.
• Case-wide search of the case directory for de novo, segregation, co-segregation, pedigree, proband, parental, mother, father, family history, inheritance pattern and meioses: zero matches, i.e. no family or trio evidence exists in this case.
• ClinVar (ClinVarID 1128484): four submissions (GeneDx, Ambry Genetics, Myriad Genetics, Labcorp/Invitae), germline origin for three, classifications Likely benign x3 and Benign x1 with conditions 'Hereditary cancer-predisposing syndrome', 'Oligodontia-cancer predisposition syndrome' and 'not provided'; no family members, no parental genotypes, no segregation data.
• Literature check: the only full-text paper retrieved for this case (PMID:25394175, ACMG/NSGC practice guideline on referral indications for cancer predisposition assessment) contains zero occurrences of 'AXIN2' and reports no variant, family or segregation data; the other packet PMID (PMID:28492532, Sherloc) is a general criteria-refinement methods paper and was not retrieved as full text.
• Variant context: NM_004655.4:c.1365A>T is a synonymous substitution (NP_004646.3:p.(Pro455=)); no functional or splice-supporting evidence for a damaging de novo occurrence is part of this group's evidence.

Still missing

• No proband is defined in the case: no clinical phenotype, indication for testing, age/sex or disease context is recorded, so the 'phenotype consistent with the gene' element of PS2 cannot be evaluated.
• No parental testing data: no maternal/paternal genotypes, trio data, Sanger confirmation or parentage confirmation for NM_004655.4:c.1365A>T exists in any case file.
• ClinVar has no family or segregation-level information (no proband genotype, no parents), only submitter classifications.

Sources

Reasoning

PM6 (Richards et al. 2015, PMID:25741868) applies to an assumed de novo occurrence in a proband with a phenotype consistent with the gene when parentage has not been confirmed - it still requires a proband, a clinical phenotype and knowledge that parents were not tested (or that testing was uninformative). No gene-specific specification governs AXIN2 (no CSPEC/VCEP; generic ACMG/AMP 2015 fallback). This case provides no proband (no phenotype, indication, age/sex or clinical narrative in case_summary.json, prefetch.json or evidence.json), no family history, and no documentation of parental testing status; the ClinVar submissions (VCV001128484) are germline-labelled but carry no proband or family information. PM6 is therefore unassessable. Gap: a proband with a phenotype consistent with AXIN2-associated disease, plus explicit documentation of whether the parents were tested.

Rule

PM6: assumed de novo occurrence, no confirmation of parentage, in a patient with disease and phenotype consistent with the gene

Evidence considered

• Governing framework check: no ClinGen CSPEC/VCEP specification for AXIN2 (cspec found=false; vcep_materials.json empty of gene-specific criteria), so generic ACMG/AMP 2015 definitions were applied via the generic_acmg_combination_rules source.
• PM6 as defined in Richards et al. 2015 (PMID:25741868): assumed de novo occurrence with no confirmation of parentage, in a patient with the disease and a phenotype consistent with the gene.
• Case files (case_summary.json, prefetch.json, evidence.json) contain no clinical narrative for any individual; nothing states who was tested, whether parents were available, or whether the variant arose de novo.
• ClinVar (ClinVarID 1128484) records four germline submissions with no proband, parental or segregation annotations; classification-level assertions were not converted into evidence for PM6.
• Literature check: the sole full-text paper for this case (PMID:25394175) does not mention AXIN2 or this variant; PMID:28492532 (Sherloc, cited by one ClinVar submission) was not retrieved as full text and is a general criteria-refinement paper.

Still missing

• No proband phenotype or disease context is recorded, so the required 'phenotype consistent with the gene' element of PM6 is missing.
• Parental testing status is entirely undocumented (neither untested-parents nor unconfirmed-parentage information exists).
• No case-level or published report of this variant as a de novo occurrence in an affected individual was found in any consulted source.

Sources

Reasoning

PP1 (Richards et al. 2015, PMID:25741868) requires co-segregation of the variant with disease in multiple affected family members, which presupposes a pedigree containing genotyped affected (and ideally unaffected) relatives and a countable number of informative meioses. No applicable gene-specific specification exists for AXIN2 (no CSPEC/VCEP; generic ACMG/AMP 2015 fallback). This case contains no pedigree, no family structure, no relative genotypes and no meioses information of any kind; the variant is a synonymous substitution (NP_004646.3:p.(Pro455=)) and no affected carrier family for NM_004655.4:c.1365A>T is reported in any consulted source. Consequently no segregation framework threshold (meioses count or LOD) is applicable, because there is no segregation data to score. PP1 is unassessable. Gap: a family study with genotyped affected and unaffected relatives, or published family co-segregation data for this variant.

Rule

PP1: co-segregation with disease in multiple affected family members (pedigree with genotyped relatives)

Evidence considered

• Governing framework check: no ClinGen CSPEC/VCEP specification for AXIN2 (cspec found=false; no gene VCEP directory, no guideline files), so generic ACMG/AMP 2015 PP1 semantics were applied via the generic_acmg_combination_rules source.
• PP1 as defined in Richards et al. 2015 (PMID:25741868): co-segregation with disease in multiple affected family members; no gene-specific meiosis count or LOD threshold is available for AXIN2, and none is needed here because no segregation data exists.
• Case-wide search of the case directory for segregation, co-segregation, pedigree, proband, family history, inheritance pattern, mother, father and meioses returned zero matches: no family data is present in sequence, variant or literature inputs.
• ClinVar (ClinVarID 1128484) provides no family members and no segregation annotation for this variant.
• Literature check: PMID:25394175 (the only paper retrieved in full text; ACMG/NSGC referral-indications guideline) contains no AXIN2 content; the remaining PMID:28492532 (Sherloc) was not retrieved as full text.

Still missing

• No pedigree or family structure is documented in any case file.
• No genotype for any relative (affected or unaffected) of an index case is available, so no informatively meioses can be counted.
• No published family study reporting segregation of NM_004655.4:c.1365A>T was found; the only full-text paper retrieved does not mention AXIN2.

Sources

Reasoning

PP4 requires that the patient's phenotype or family history be highly specific for a disease with a single genetic etiology (Richards et al. 2015, PMID:25741868). Assessing it requires a proband-level clinical description against which specificity can be judged. No proband phenotype, HPO term set, family history, or clinical narrative appears anywhere in the case evidence (review_manifest.json, case_summary.json, source_registry.json, evidence.json, literature_pass.json, vcep_materials.json, fulltext_map.json, paper_extracts.json) or in prefetch.json, and no published case report describing a proband with NM_004655.4:c.1365A>T was identified in the literature pass. The only phenotype-adjacent information in the case is the whole-record ClinVar condition list for variation 1128484 ('Hereditary cancer-predisposing syndrome', 'Oligodontia-cancer predisposition syndrome', 'not provided'), which is a record-level label set, not a proband phenotype, and cannot establish specificity for any single-gene etiology. AXIN2 additionally spans more than one phenotypic context (adenomatous/attenuated polyposis and colorectal cancer predisposition, and oligodontia-colorectal cancer syndrome), so a specificity argument would in any case have to be made against the actual clinical presentation. No AXIN2-specific VCEP exists (cspec found=false), so generic ACMG/AMP applies; PP4 is qualitative there and carries no numeric threshold, hence no comparison or comparison direction arises. With no proband phenotype available, PP4 is not_assessed; the gap is a proband-level clinical description, not a missing source.

Evidence considered

• Case evidence contains no proband phenotype, HPO annotation, family history, or clinical narrative; the case files carry only variant-level, population, in-silico, and database records, plus literature metadata.
• ClinVar variation 1128484 condition labels for this exact variant are 'Hereditary cancer-predisposing syndrome', 'Oligodontia-cancer predisposition syndrome', and 'not provided' - whole-record labels, not a proband phenotype.
• No published proband carrying NM_004655.4:c.1365A>T was identified; the only full-text paper available (PMID:25394175) does not mention AXIN2 or this variant.
• Framework: no AXIN2-specific CSPEC/VCEP or local framework was retrieved, so generic ACMG/AMP 2015 (PMID:25741868) applies; generic PP4 is qualitative and defines no numeric threshold, so no numeric comparison or comparison direction was evaluated.

Still missing

• No proband phenotype, HPO terms, family history, or clinical description is present anywhere in the case evidence or in prefetch.json; PP4 can only be evaluated once a clinical presentation is supplied.
• No published case report for this exact variant (with phenotype) was identified to substitute for a local proband description.

Sources

Reasoning

BS4 (Richards et al. 2015, PMID:25741868) requires affirmative evidence of non-segregation: multiple affected family members who do not carry the variant, i.e. a genotyped family from which lack of segregation can be demonstrated. No applicable gene-specific specification exists for AXIN2 (no CSPEC/VCEP; generic ACMG/AMP 2015 fallback). This case records no family members, no pedigree and no relative genotypes, so non-segregation cannot be demonstrated; the ClinVar record (ClinVarID 1128484, Likely benign/Benign across four submitters) contains no family-level data, and classification-level assertions were deliberately not converted into segregation evidence, since a criterion is never inferred from another source's final classification. The single full-text paper retrieved (PMID:25394175) contains no AXIN2 content. BS4 is therefore unassessable rather than met. Gap: genotypes from multiple affected relatives of an index case (or published non-segregation data) for NM_004655.4:c.1365A>T.

Rule

BS4: lack of segregation in affected members of a family (multiple affected non-carriers genotyped)

Evidence considered

• Governing framework check: no ClinGen CSPEC/VCEP specification for AXIN2 (cspec found=false; vcep_materials.json contains no gene-specific criteria or domain tables), so generic ACMG/AMP 2015 semantics were applied via the generic_acmg_combination_rules source.
• BS4 as defined in Richards et al. 2015 (PMID:25741868): lack of segregation in affected members of a family - a positive finding requiring genotyped affected relatives, not merely absence of a segregation report.
• Case-wide search of the case directory for segregation, pedigree, proband, family history, inheritance pattern, mother, father and meioses returned zero matches: no family genotype data exists to test non-segregation.
• ClinVar (ClinVarID 1128484): four submissions (Likely benign x3, Benign x1) with no family or segregation annotations and no expert-panel review; used only to confirm that no family-level data is available, never as a substitute classification for this criterion.
• Literature check: PMID:25394175 (only paper retrieved in full text) contains no AXIN2 content; PMID:28492532 (Sherloc) was not retrieved as full text.

Still missing

• No family members or pedigree are recorded in any case file, so lack of segregation cannot be shown.
• ClinVar (ClinVarID 1128484) reports no family-level data; the benign/likely benign classifications cannot be relabelled as BS4 evidence.
• The one full-text paper retrieved (PMID:25394175) does not mention AXIN2 or this variant.

Sources

Reasoning

BP5 applies when the variant is found in a case that has an alternate molecular basis for the disease, i.e. proband-level genotyping evidence showing that a different variant (typically pathogenic) already explains the observed phenotype (Richards et al. 2015, PMID:25741868). That requires case-level molecular data: a proband genotype, co-occurring variant findings, or a case report in which another gene's pathogenic variant accounts for disease. No such data exists in this case. The case evidence and prefetch.json contain no patient genotype, no co-occurring variant report, and no case-level records; ClinVar variation 1128484 provides whole-record condition labels only ('Hereditary cancer-predisposing syndrome', 'Oligodontia-cancer predisposition syndrome', 'not provided'), with no molecular co-findings at case level; and the literature pass identified no case report mentioning this variant at all (the only retrieved full-text paper, PMID:25394175, does not mention AXIN2). The specific evidence type BP5 requires was never collected or reported, so BP5 is not_assessed rather than not_met. No AXIN2 CSPEC/VCEP or local framework was retrieved, so generic ACMG/AMP applies; generic BP5 is qualitative and defines no likelihood-ratio or other numeric threshold, so no numeric comparison and no comparison direction was evaluated for this criterion.

Evidence considered

• Case evidence and prefetch.json contain no patient genotype, no co-occurring variant findings, and no case-level records of any kind.
• ClinVar variation 1128484 (exact match) supplies condition labels only; no case-level alternate-molecular-basis information is recorded in the submission audit.
• No published case report describing a proband carrying NM_004655.4:c.1365A>T was identified; the only retrieved full-text paper (PMID:25394175) does not mention AXIN2 or this variant.
• Framework: no AXIN2-specific CSPEC/VCEP or local framework was retrieved, so generic ACMG/AMP 2015 (PMID:25741868) applies; generic BP5 is qualitative with no likelihood-ratio or numeric threshold, so no numeric comparison or comparison direction was evaluated.

Still missing

• No proband-level genotyping data (co-occurring variant findings, or a case report documenting an alternate molecular cause of disease in a carrier of this variant) exists in the case evidence; BP5 cannot be evaluated without it.

Sources