AXIN2 c.1713-18G>A, p.?

Reasoning

BP4 is applicable because NM_004655.4:c.1713-18G>A is an intronic variant, so the SpliceAI path is used exclusively. SpliceAI reports a maximum delta score of 0.06. Under the supplied generic SpliceAI calibration, BP4 supporting applies at a maximum delta score of <=0.1; 0.06 meets this threshold, so BP4 is met at supporting strength. REVEL is not applicable to this intronic variant, and the SpliceAI prediction is not reused as BP7.

Rule

intronic_or_splice_region_spliceai_only; BP4 supporting <=0.1

Evidence considered

• NM_004655.4:c.1713-18G>A is an intronic variant; therefore SpliceAI is the sole applicable PP3/BP4 computational path.
• SpliceAI reports a maximum delta score of 0.06.
• The supplied generic SpliceAI calibration assigns BP4 supporting at <=0.1; the maximum delta score of 0.06 meets BP4.

Sources

Reasoning

No AXIN2-specific VCEP/CSPEC specification is available, so the generic ClinGen SVI PVS1 framework applies. NM_004655.4:c.1713-18G>A is an intronic variant outside the canonical ±1,2 splice positions, has no assigned protein consequence (NP_004646.3:p.?), and is not a nonsense or frameshift variant. SpliceAI predicts no significant splice impact with a maximum delta score of 0.06, below the published 0.2 recommended threshold for a predicted splice effect. Therefore, the variant does not meet a generic PVS1 null-variant category, and there is no validated NMD, exon-importance, or functional RNA/protein evidence establishing a loss-of-function consequence.

Rule

Generic ClinGen SVI PVS1 framework (PMC6185798): default PVS1 categories include nonsense, frameshift, and canonical ±1,2 splice variants; noncanonical intronic variants require evidence of a loss-of-function effect.

Evidence considered

• The generic ClinGen SVI PVS1 framework limits default PVS1 assessment to established loss-of-function variant classes; this variant is intronic at c.1713-18G>A rather than a nonsense, frameshift, or canonical ±1,2 splice variant.
• The variant-level assessment records no protein consequence, no exon assignment, and no applicable generic PVS1 null-variant bucket.
• SpliceAI reports DS_AG 0.06, DS_AL 0.001, DS_DG 0.011, and DS_DL 0.0, with a maximum delta score of 0.06; the published SpliceAI recommended cutoff for a predicted splice effect is 0.2 (Jaganathan et al. 2019, PMID:30661751).
• The ACMG/AMP guidance states that splice-site variants can alter exon usage or intronic sequence inclusion, but predicted null effects require confirmation by RNA or protein analysis; no such variant-specific confirmation is available here.

Still missing

• No variant-specific RNA or protein assay demonstrates abnormal splicing or loss of AXIN2 function.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the supplied generic SVI PM2 supporting threshold of allele frequency <=0.0001 applies. The variant is present in gnomAD v2.1 at AF 0.00155232 and gnomAD v4.1 at AF 0.00158351, with gnomAD-Canada AF 0.00141166. The lowest relevant ancestry-specific value does not rescue PM2 because the variant is clearly present at substantially higher overall frequency, and the maximum ancestry-specific frequencies are 0.00282280 in v2.1 and 0.00618132 in v4.1. Therefore PM2 is not met.

Rule

Generic ClinGen SVI PM2: absence or allele frequency <=0.0001 supports PM2 at supporting strength; no applicable AXIN2-specific VCEP rule was identified.

Evidence considered

• The supplied generic ClinGen SVI PM2 supporting threshold is allele frequency <=0.0001 (Richards et al. 2015, PMID:25741868).
• gnomAD v2.1 all-comers reports AF 0.00155232 (394/253814 alleles), and its highest ancestry-specific AF is 0.00282280.
• gnomAD v4.1 all-comers reports AF 0.00158351 (2529/1597080 alleles), and its highest ancestry-specific AF is 0.00618132.
• gnomAD-Canada reports AF 0.00141166 (26/18418 alleles).

Sources

Reasoning

PP3 is applicable because NM_004655.4:c.1713-18G>A is an intronic variant, so the SpliceAI path is used exclusively. SpliceAI reports a maximum delta score of 0.06. Under the supplied generic SpliceAI calibration, PP3 requires a maximum delta score of at least 0.2 for supporting strength or at least 0.5 for moderate strength; 0.06 meets neither threshold, so PP3 is not met. REVEL is not applicable to this intronic variant, and no other computational predictor is used.

Rule

intronic_or_splice_region_spliceai_only; PP3 supporting >=0.2, moderate >=0.5

Evidence considered

• NM_004655.4:c.1713-18G>A is an intronic variant; therefore SpliceAI is the sole applicable PP3/BP4 computational path.
• SpliceAI reports DS_AG 0.06 as the maximum delta score, with DS_AL 0.001, DS_DG 0.011, and DS_DL 0.0.
• The supplied generic SpliceAI calibration assigns PP3 supporting at >=0.2 and moderate at >=0.5; the maximum delta score of 0.06 does not meet PP3.

Sources

Reasoning

PP5 is not met. The exact variant NM_004655.4:c.1713-18G>A is present in ClinVar variation 136485, but the record contains only laboratory submissions classified as Benign or Likely benign and reports zero expert-panel submissions. Therefore, there is no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification that can support PP5; ordinary submissions and aggregate labels are excluded.

Rule

exact_variant_clinvar_expert_panel_pathogenic_or_likely_pathogenic_only

Evidence considered

• ClinVar variation 136485 is an exact match for NM_004655.4(AXIN2):c.1713-18G>A.
• The ClinVar submission audit reports expert_panel_submissions = 0.
• ClinVar submissions report Benign or Likely benign classifications from individual laboratories; these are not expert-panel assertions and cannot trigger PP5.
• PP5 requires an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; no such assertion is present.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the supplied generic ACMG/AMP stand-alone BA1 threshold of allele frequency >=0.05 applies. The variant's all-comers gnomAD v2.1 frequency is 0.00155232 (394/253814 alleles), and gnomAD v4.1 frequency is 0.00158351 (2529/1597080 alleles), both far below 0.05. The highest reported ancestry-specific frequencies are 0.00282280 in gnomAD v2.1 Admixed American and 0.00618132 in gnomAD v4.1 Middle Eastern, also below the threshold. Therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: allele frequency >=0.05 is stand-alone benign evidence; no applicable AXIN2-specific VCEP rule was identified.

Evidence considered

• The case has no applicable AXIN2-specific VCEP specification; the supplied generic ACMG/AMP BA1 stand-alone threshold is allele frequency >=0.05 (Richards et al. 2015, PMID:25741868).
• gnomAD v2.1 all-comers reports AF 0.00155232 (394/253814 alleles), with highest ancestry-specific AF 0.00282280 in Admixed American.
• gnomAD v4.1 all-comers reports AF 0.00158351 (2529/1597080 alleles), with highest ancestry-specific AF 0.00618132 in Middle Eastern individuals.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the supplied generic SVI BS1 threshold of allele frequency >=0.01 applies. The variant's all-comers gnomAD v2.1 frequency is 0.00155232 and gnomAD v4.1 frequency is 0.00158351; the maximum ancestry-specific frequency is 0.00618132 in gnomAD v4.1 Middle Eastern individuals. These values are below 0.01, and gnomAD-Canada reports AF 0.00141166. Therefore BS1 is not met.

Rule

Generic SVI BS1: allele frequency >=0.01 is strong benign evidence; no applicable AXIN2-specific VCEP rule was identified.

Evidence considered

• The supplied generic SVI BS1 threshold is allele frequency >=0.01, with per-gene derivation preferred; the cited derivation publication is Whiffin et al. 2017 (PMID:28518168).
• gnomAD v2.1 all-comers reports AF 0.00155232 and maximum ancestry-specific AF 0.00282280 in Admixed American.
• gnomAD v4.1 all-comers reports AF 0.00158351 and maximum ancestry-specific AF 0.00618132 in Middle Eastern individuals.
• gnomAD-Canada reports AF 0.00141166 (26/18418 alleles), below 0.01.

Sources

Reasoning

BP6 is not met. The exact variant NM_004655.4:c.1713-18G>A is present in ClinVar variation 136485, but the record contains no expert-panel submission and no exact-variant ClinVar expert-panel Benign or Likely benign classification. The available Benign and Likely benign assertions are ordinary laboratory submissions and cannot trigger BP6.

Rule

exact_variant_clinvar_expert_panel_benign_or_likely_benign_only

Evidence considered

• ClinVar variation 136485 is an exact match for NM_004655.4(AXIN2):c.1713-18G>A.
• The ClinVar submission audit reports expert_panel_submissions = 0.
• The record contains Benign and Likely benign laboratory submissions, but no exact-variant expert-panel Benign or Likely benign assertion.
• BP6 requires an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions and aggregate labels are excluded.

Sources

Reasoning

Generic ACMG/AMP criteria apply because no AXIN2-specific VCEP or CSPEC specification is available. PS2 requires a confirmed de novo occurrence in the proband with maternity and paternity confirmed, together with appropriate phenotype consistency. The available case evidence contains no proband-level de novo observation, parental genotypes, maternity or paternity confirmation, or phenotype documentation for this variant, so PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in a patient with the disease and no family history, with maternity and paternity confirmed; phenotype should be consistent with the disease.

Evidence considered

• No case-level evidence documents that NM_004655.4:c.1713-18G>A is de novo in a proband.
• No parental testing results or maternity/paternity confirmation are provided.
• No phenotype information is provided to evaluate phenotype consistency.

Still missing

• Proband-level variant observation and clinical phenotype
• Maternal and paternal genotypes
• Confirmation of maternity and paternity

Reasoning

No validated AXIN2-specific functional assay was identified for NM_004655.4:c.1713-18G>A. The available evidence consists of generic ACMG guidance and a SpliceAI prediction (maximum delta 0.06), neither of which demonstrates an abnormal experimental functional effect. PS3 therefore cannot be applied at any strength.

Evidence considered

• No variant-specific AXIN2 RNA, protein, cellular, or other validated functional assay result was identified.
• SpliceAI maximum delta score is 0.06, which is a computational prediction rather than experimental functional evidence and was not used to assign PS3.
• The ACMG/AMP guidance states that predicted splice effects require confirmation by functional RNA or protein analysis; it reports no AXIN2-specific assay for this variant.

Still missing

• A validated variant-specific functional assay with appropriate controls and biologically relevant readout is needed to assess PS3.

Sources

Reasoning

PS4 could not be assessed because the available case evidence contains no disease-case versus control comparison, case count, enrichment statistic, odds ratio, or other validated case-control prevalence data for NM_004655.4:c.1713-18G>A. No applicable AXIN2 VCEP specification was available, so no gene-specific PS4 threshold could be applied.

Rule

case_control_enrichment_required; no applicable AXIN2-specific threshold available

Evidence considered

• No case-control comparison or variant-specific prevalence/enrichment statistic was identified for NM_004655.4:c.1713-18G>A.
• No applicable AXIN2 VCEP or ClinGen specification was available; generic ACMG/AMP fallback does not supply a numeric PS4 threshold for this case.

Still missing

• Case-control cohort data with affected-case and control counts or an applicable enrichment statistic.
• A governing AXIN2-specific PS4 threshold, if one exists.

Reasoning

No applicable AXIN2 VCEP or gene-specific framework was available, so generic ACMG/AMP logic was considered. PM3 requires evidence that the variant is in trans with a pathogenic or likely pathogenic variant in an affected individual for a recessive disorder. The available case evidence documents neither affected-proband observations nor a second pathogenic variant, phase, segregation, or a definitive inheritance mode; therefore PM3 cannot be assessed.

Evidence considered

• The case evidence identifies the variant as NM_004655.4:c.1713-18G>A in AXIN2 but provides no affected-proband genotype, second pathogenic allele, phase, or segregation result.
• Generic ACMG/AMP PM3 logic was used because vcep_materials.json reports that no applicable gene-specific framework was found.

Still missing

• Affected-proband clinical and molecular observations are not documented.
• No pathogenic or likely pathogenic second allele is documented.
• Phase of any second allele is not documented.
• Inheritance mode for the relevant AXIN2 disorder is not definitively documented in the case evidence.

Reasoning

Generic ACMG/AMP criteria apply because no AXIN2-specific VCEP or CSPEC specification is available. PM6 concerns a presumed de novo occurrence when maternity and/or paternity has not been confirmed, and therefore requires a documented proband observation, a relevant phenotype, and evidence that the variant was absent from the tested parent or parents. The available case evidence contains no proband-level de novo report, parental test results, parentage information, or phenotype documentation, so PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence in a patient with the disease, without confirmation of maternity and/or paternity; the variant should be absent from tested parent(s) and the phenotype should be consistent.

Evidence considered

• No case-level evidence documents a presumed de novo occurrence of NM_004655.4:c.1713-18G>A.
• No parental testing results demonstrate variant absence in either parent.
• No phenotype information is provided to evaluate disease consistency.

Still missing

• Proband-level variant observation and clinical phenotype
• Parental genotype results demonstrating absence in tested parent(s)
• Parentage information

Reasoning

Generic ACMG/AMP criteria apply because no AXIN2-specific VCEP or CSPEC specification is available. PP1 requires co-segregation of the variant with disease in affected family members, with strength dependent on the amount and informativeness of segregation data, including informative meioses. The available case evidence contains no family pedigree, affected relatives, carrier genotypes, phenotype assessments, or meiosis count, so PP1 cannot be assessed.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members; strength depends on the number and informativeness of meioses and the quality of phenotype ascertainment.

Evidence considered

• No family segregation data are reported for NM_004655.4:c.1713-18G>A.
• No affected-relative genotypes or phenotype concordance data are provided.
• No informative meioses are documented, preventing determination of PP1 strength.

Still missing

• Pedigree and affected-relative information
• Variant genotypes for relatives
• Phenotype status of relatives
• Informative meiosis count

Reasoning

PP4 could not be assessed because no patient phenotype, clinical diagnosis, or sufficiently specific phenotype pattern linked to NM_004655.4:c.1713-18G>A is provided. General AXIN2 disease descriptions do not establish the phenotype of this individual or its specificity for the gene-related disorder.

Rule

highly_specific_patient_phenotype_required

Evidence considered

• The available case materials identify the variant as an intronic AXIN2 variant but do not provide the tested patient's phenotype or diagnosis.
• Gene-level descriptions of AXIN2-associated colorectal cancer and tooth agenesis are insufficient by themselves to apply PP4 to this patient.

Still missing

• Documented patient phenotype and clinical diagnosis.
• Evidence that the phenotype is highly specific for an AXIN2-related disorder rather than a nonspecific presentation.

Reasoning

The variant is observed in homozygous individuals in gnomAD v2.1 (2 homozygotes) and gnomAD v4.1 (8 homozygotes), including the non-cancer v2.1 exome subset (2 homozygotes). However, these aggregate population records do not document the homozygotes' ages, oligodontia status, cancer history, ascertainment, or unaffected status. Because BS2 requires observation in healthy adults or an appropriately unaffected homozygous individual, and AXIN2-associated disease has phenotype and penetrance considerations, the available data are insufficient to apply BS2.

Rule

Generic ACMG/AMP BS2 requires observation of the variant in healthy adults for a dominant condition or in an unaffected homozygous individual for a recessive condition; phenotype and age must be established.

Evidence considered

• gnomAD v2.1 all-comers reports 2 homozygotes among 394 alternate alleles; its non-cancer exome subset also reports 2 homozygotes.
• gnomAD v4.1 all-comers reports 8 homozygotes among 2529 alternate alleles, including 7 exome and 1 genome homozygotes.
• The available population records provide aggregate counts but do not establish that the homozygotes were healthy adults or unaffected for AXIN2-associated oligodontia and cancer predisposition.

Still missing

• Individual-level age and phenotype information for the reported homozygotes is unavailable.
• The oligodontia and cancer-predisposition penetrance status of the homozygous individuals is unavailable.

Sources

Reasoning

No validated AXIN2-specific functional assay was identified for NM_004655.4:c.1713-18G>A. The available evidence does not show a normal experimental result with suitable controls, and the SpliceAI maximum delta score of 0.06 is computational rather than functional evidence. BS3 therefore cannot be applied at any strength.

Evidence considered

• No variant-specific AXIN2 RNA, protein, cellular, or other validated functional assay result was identified.
• SpliceAI maximum delta score is 0.06, which is a computational prediction rather than experimental functional evidence and was not used to assign BS3.
• The ACMG/AMP guidance states that predicted splice effects require confirmation by functional RNA or protein analysis; it reports no AXIN2-specific assay for this variant.

Still missing

• A validated variant-specific functional assay with appropriate controls and biologically relevant readout is needed to assess BS3.

Sources

Reasoning

Generic ACMG/AMP criteria apply because no AXIN2-specific VCEP or CSPEC specification is available. BS4 requires lack of segregation in affected members of a family, or demonstrated non-segregation with the disease phenotype, and must account for age, penetrance, and phenotype ascertainment. The available case evidence contains no family data, affected or unaffected relative genotypes, phenotype assessments, or penetrance information, so BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; interpretation requires reliable family phenotypes, genotypes, and consideration of age-dependent penetrance and phenocopies.

Evidence considered

• No non-segregation observation is reported for NM_004655.4:c.1713-18G>A.
• No affected or unaffected relative genotypes are provided.
• No age, penetrance, or phenotype-ascertainment information is available.

Still missing

• Family pedigree and phenotype ascertainment
• Genotypes of affected and unaffected relatives
• Age and penetrance information for relatives

Reasoning

No applicable AXIN2 VCEP or gene-specific framework was available, so generic ACMG/AMP logic was considered. BP2 requires a documented pathogenic or likely pathogenic allele in the appropriate phase relationship—typically in trans for a dominant disorder or in cis for a recessive disorder. The available case evidence contains no pathogenic comparator allele, affected-proband observation, phase determination, or definitive inheritance mode; therefore BP2 cannot be assessed.

Evidence considered

• The case evidence identifies ClinVar variation 136485 and population records but contains no documented pathogenic comparator allele or cis/trans phase result.
• Generic ACMG/AMP BP2 logic was used because vcep_materials.json reports that no applicable gene-specific framework was found.

Still missing

• No pathogenic or likely pathogenic comparator allele is documented.
• No cis/trans phase determination is documented.
• Affected-proband context for an allelic observation is not documented.
• Inheritance mode for the relevant AXIN2 disorder is not definitively documented in the case evidence.

Reasoning

BP5 could not be assessed because the available materials do not document a patient with NM_004655.4:c.1713-18G>A who has a confirmed alternate molecular explanation for the relevant phenotype. The presence of the variant in ClinVar or in population databases does not establish an alternate molecular diagnosis in a patient.

Rule

patient_with_relevant_phenotype_and_confirmed_alternate_molecular_explanation_required

Evidence considered

• No patient-level alternate pathogenic molecular finding is reported in the available case evidence.
• ClinVar laboratory classifications and population observations do not independently satisfy BP5's alternate-molecular-explanation requirement.

Still missing

• Patient-level phenotype and diagnostic context.
• A confirmed alternative pathogenic molecular finding explaining that phenotype.