AXIN2 c.1059+8C>T, p.?

Reasoning

The variant is annotated as a splice-region variant, so BP4 is evaluated only through SpliceAI. The maximum SpliceAI delta is 0.001 (DS_AL and DS_DG), which is <=0.1 and meets the supplied generic supporting BP4 threshold from the Jaganathan et al. 2019 calibration (PMID:30661751).

Rule

Splice-region/intronic variant: SpliceAI max delta <=0.1 supports BP4 at supporting strength.

Evidence considered

• SpliceAI reports DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, and DS_DL 0.000 for NM_004655.4:c.1059+8C>T; the maximum delta is 0.001.
• The supplied generic SpliceAI calibration assigns BP4 supporting strength at max delta <=0.1, from Jaganathan et al. 2019, Cell (PMID:30661751).

Sources

Reasoning

No AXIN2-specific VCEP or CSPEC specification was available, so the generic ClinGen SVI PVS1 framework applies. NM_004655.4:c.1059+8C>T is a noncanonical intronic variant outside the canonical ±1,2 splice consensus sites, with no established protein consequence (NP_004646.3:p.?), no exon assignment or demonstrated exon loss, and SpliceAI max delta 0.001. The generic framework therefore does not support PVS1 for this variant; the available splice prediction does not establish a loss-of-function transcript or NMD-triggering consequence.

Rule

ClinGen SVI generic PVS1 framework: noncanonical intronic variants are not assigned PVS1 without evidence establishing a loss-of-function splice consequence.

Evidence considered

• The applicable generic ClinGen SVI PVS1 framework is PMC6185798 because no AXIN2-specific VCEP or CSPEC specification was found.
• The variant is NM_004655.4:c.1059+8C>T, a noncanonical intronic substitution; the case normalization reports NP_004646.3:p.? and no exon or protein consequence.
• SpliceAI reports DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, and DS_DL 0.000, with max delta 0.001; this does not establish a splice-disrupting loss-of-function effect.
• ACMG/AMP guidance states that splice-related null effects require confirmation by RNA or protein analysis, including for deeper intronic variants (PMID:25741868).

Still missing

• No RNA or other functional assay establishes abnormal splicing, exon loss, or NMD for this variant.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the supplied generic PM2 supporting threshold of allele frequency <=0.0001 applies. The default all-comers gnomAD v2.1 and v4.1 datasets show overall allele frequencies of 0.000318163 and 0.000270314, and their highest observed ancestry-specific frequencies are 0.00617284 and 0.00770843, respectively. Because the variant exceeds 0.0001 in the overall and ancestry-specific data, PM2 is not met.

Rule

Generic PM2: allele frequency <=0.0001 for supporting evidence; no applicable AXIN2-specific VCEP rule identified.

Evidence considered

• No governing AXIN2 VCEP specification was available; generic ACMG/AMP criteria were therefore used.
• gnomAD v2.1 all-comers reports AF 0.000318163 (90/282874 alleles) and Ashkenazi Jewish AF 0.00617284 (64/10368 alleles).
• gnomAD v4.1 all-comers reports AF 0.000270314 (435/1609242 alleles) and Ashkenazi Jewish AF 0.00770843 (228/29578 alleles; 3 homozygotes).
• The supplied generic PM2 supporting threshold is AF <=0.0001 under the ClinGen SVI recommendation (PMID:25741868).

Sources

Reasoning

The variant is annotated as a splice-region variant, so PP3 is evaluated only through SpliceAI. The maximum SpliceAI delta is 0.001 (DS_AL and DS_DG), below the generic supporting PP3 threshold of >=0.2 from the Jaganathan et al. 2019 calibration (PMID:30661751); therefore PP3 is not met.

Rule

Splice-region/intronic variant: SpliceAI max delta >=0.2 for PP3 supporting; lower values do not meet PP3.

Evidence considered

• SpliceAI reports DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, and DS_DL 0.000 for NM_004655.4:c.1059+8C>T; the maximum delta is 0.001.
• The supplied generic SpliceAI calibration assigns PP3 supporting strength at max delta >=0.2, from Jaganathan et al. 2019, Cell (PMID:30661751).

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar variation 136475 exactly matches NM_004655.4(AXIN2):c.1059+8C>T, but the record reports zero expert-panel submissions and only single-submitter laboratory classifications of Benign or Likely benign; therefore PP5 is not met.

Rule

Apply PP5 only when an exact-variant ClinVar expert panel classifies the variant as Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar variation 136475 is an exact transcript-level match to NM_004655.4:c.1059+8C>T, with expert_panel_submissions = 0.
• The exact-variant ClinVar submissions are single-submitter laboratory assertions classified as Benign or Likely benign; aggregate labels and non-expert assertions are excluded from PP5 by the adjudication rule.

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the generic ACMG/AMP stand-alone threshold of allele frequency >=0.05 from Richards et al. 2015 (PMID:25741868) applies. The highest observed ancestry-specific frequency in the default all-comers gnomAD datasets is 0.00770843 in gnomAD v4.1 Ashkenazi Jewish individuals; gnomAD v2.1 reports 0.00617284, and all are below 0.05. Therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: allele frequency >=0.05; no applicable AXIN2-specific VCEP rule identified.

Evidence considered

• No governing AXIN2 VCEP specification was available; generic ACMG/AMP criteria were therefore used.
• gnomAD v2.1 all-comers reports overall AF 0.000318163 and highest observed Ashkenazi Jewish AF 0.00617284 (64/10368 alleles).
• gnomAD v4.1 all-comers reports overall AF 0.000270314 and highest observed Ashkenazi Jewish AF 0.00770843 (228/29578 alleles; 3 homozygotes).
• The generic BA1 threshold is AF >=0.05 under ACMG/AMP 2015 (PMID:25741868).

Sources

Reasoning

No applicable AXIN2-specific VCEP specification was identified, so the supplied generic BS1 threshold of allele frequency >=0.01 applies. The highest observed ancestry-specific frequency in the default all-comers gnomAD datasets is 0.00770843 in gnomAD v4.1 Ashkenazi Jewish individuals; gnomAD v2.1 reports 0.00617284. These frequencies remain below 0.01, so BS1 is not met.

Rule

Generic BS1: allele frequency >=0.01; no applicable AXIN2-specific VCEP rule identified.

Evidence considered

• No governing AXIN2 VCEP specification was available; generic ACMG/AMP criteria were therefore used.
• gnomAD v2.1 all-comers reports highest observed Ashkenazi Jewish AF 0.00617284 (64/10368 alleles).
• gnomAD v4.1 all-comers reports highest observed Ashkenazi Jewish AF 0.00770843 (228/29578 alleles; 3 homozygotes).
• The supplied generic BS1 threshold is AF >=0.01, with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar variation 136475 exactly matches NM_004655.4(AXIN2):c.1059+8C>T, but the record reports zero expert-panel submissions; its Benign and Likely benign assertions are from single submitters, so BP6 is not met.

Rule

Apply BP6 only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar variation 136475 is an exact transcript-level match to NM_004655.4:c.1059+8C>T, with expert_panel_submissions = 0.
• The exact-variant ClinVar record reports Benign and Likely benign classifications from single-submitter clinical laboratories; aggregate labels and non-expert assertions are excluded from BP6 by the adjudication rule.

Sources

Reasoning

No proband-level parental testing data are provided for NM_004655.4:c.1059+8C>T. Therefore, a confirmed de novo occurrence, including maternity and paternity confirmation and exclusion of parental mosaicism where relevant, cannot be established.

Evidence considered

• The available case evidence contains no proband-specific trio data, parental genotypes, or confirmed de novo observation for this variant.
• The variant is an intronic splice-region SNV, but consequence prediction and population observations do not establish de novo status.

Still missing

• Documented proband genotype and phenotype
• Maternal and paternal test results showing absence of the variant
• Confirmation of maternity and paternity
• Assessment for parental mosaicism if clinically relevant

Reasoning

No variant-specific functional assay was identified for NM_004655.4:c.1059+8C>T. The available literature consists of generic ACMG/AMP guidance and a general scoring framework; neither reports an AXIN2 RNA, protein, cellular, or other validated assay result for this intronic variant. Therefore, the evidence required to establish a damaging functional effect and apply PS3 is unavailable.

Rule

Generic ACMG/AMP PS3 requires well-established functional studies appropriate to the variant and disease mechanism; no variant-specific functional result is available here.

Evidence considered

• The ACMG/AMP guidance states that splice-related effects should be confirmed by RNA or protein analysis, including mRNA-level assays for deeper intronic variants, but does not report an assay for this variant.
• The reviewed variant-scoring study describes general use of splice prediction and functional evidence but contains no AXIN2-specific assay or result for c.1059+8C>T.

Still missing

• A validated variant-specific functional assay with appropriate positive, negative, and assay-quality controls is needed.
• For this intronic variant, variant-specific RNA evidence addressing splicing or transcript processing is not available.

Sources

Reasoning

No variant-level case series, case-control enrichment analysis, affected-case count, control comparison, odds ratio, likelihood ratio, or other quantitative prevalence evidence for NM_004655.4:c.1059+8C>T was identified. The retrieved publication screened for PS4 is a general referral guideline and does not mention AXIN2 or this exact variant, so PS4 cannot be assessed.

Rule

Generic ACMG/AMP PS4: prevalence is significantly increased in affected individuals compared with controls; no applicable gene-specific framework was found.

Evidence considered

• PMID:25394175 was screened for exact-variant case observations and PS4 evidence; its extraction states that AXIN2 and c.1059+8C>T are not mentioned and no variant-level case data are provided.

Still missing

• Exact-variant affected-case and control counts or a validated enrichment statistic are unavailable.

Sources

Reasoning

PM3 cannot be assessed from the available evidence. No affected proband observation, pathogenic or likely pathogenic variant in trans, phase determination, family segregation, or inheritance-mode-specific compound-heterozygous evidence is documented for NM_004655.4:c.1059+8C>T. The available case data do not establish a recessive AXIN2 context in which PM3 would be applicable, and no source provides the required allelic observation.

Evidence considered

• The case evidence documents NM_004655.4:c.1059+8C>T but contains no affected-proband report, second pathogenic AXIN2 allele, phase result, or segregation data.
• The reviewed literature extraction contains no AXIN2-specific observation or co-occurrence/phase evidence for this variant.

Still missing

• Affected-proband clinical and molecular observation for this variant
• A second pathogenic or likely pathogenic AXIN2 variant identified in the same proband
• Validated phase showing the variants are in trans
• Disease inheritance mode applicable to the evaluated phenotype

Sources

Reasoning

No report documents NM_004655.4:c.1059+8C>T as presumed de novo without parental testing. The available evidence does not provide a proband phenotype, a meiosis context, or sufficient parental information to support PM6.

Evidence considered

• The reviewed variant-specific literature does not mention AXIN2 c.1059+8C>T and provides no case observation, parental data, or de novo assessment for it.
• ClinVar records classifications but do not provide usable proband-level presumed de novo evidence for this criterion.

Still missing

• A published or clinical case report identifying the variant in a proband
• Phenotype consistency with an AXIN2-related disorder
• Evidence that parental testing was unavailable or incomplete
• Relevant meiosis and family context

Reasoning

No informative affected relatives, unaffected relatives, variant-carrier relatives, non-carrier relatives, or meioses are documented. Consequently, there is no segregation dataset from which to assign PP1 or a strength level.

Evidence considered

• The available case evidence contains no family pedigree, familial genotypes, or segregation counts for NM_004655.4:c.1059+8C>T.
• General AXIN2 literature identified in the broader case materials is not evidence that this exact variant segregates in a family.

Still missing

• Pedigree or family structure
• Number of informative meioses
• Variant status of affected and unaffected relatives
• Phenotype assessments for tested relatives

Reasoning

The case materials provide no patient phenotype, clinical presentation, or phenotype-to-disease matching information for the individual carrying NM_004655.4:c.1059+8C>T. Therefore, the specificity of the phenotype for an AXIN2-related disorder cannot be evaluated and PP4 is not assessed.

Rule

Generic ACMG/AMP PP4: patient phenotype or family history is highly specific for a disease with a single-gene etiology; no applicable gene-specific framework was found.

Evidence considered

• The case evidence materials contain no patient-level phenotype or clinical presentation for this exact variant.

Still missing

• Patient-level phenotype and clinical diagnosis are unavailable.

Reasoning

The variant is observed in homozygous individuals in population datasets, including 3 homozygotes in gnomAD v4.1 and 1 homozygote in the gnomAD v3.1 non-cancer genome subset. However, these records do not establish that the homozygotes are clinically unaffected, and no AXIN2-specific penetrance or age-dependent disease assessment is available. Because BS2 requires observation in healthy adults for a sufficiently penetrant disease context, the available population counts alone are insufficient to apply BS2.

Rule

Generic BS2 requires observation of the variant in healthy adults for a sufficiently penetrant disease; no AXIN2-specific rule was identified.

Evidence considered

• gnomAD v4.1 all-comers reports 3 homozygotes among 435 alternate alleles and 1,609,242 total alleles.
• The gnomAD v3.1 non-cancer genome subset reports 1 homozygote among 37 alternate alleles and 147,854 total alleles.
• Population homozygote counts do not by themselves demonstrate that carriers were healthy adults or resolve AXIN2 penetrance, so BS2 cannot be applied from these data alone.

Still missing

• Clinical phenotype, age, and disease-status information for the observed homozygotes are unavailable.
• AXIN2 disease penetrance and an applicable BS2-specific threshold or specification are unavailable.

Sources

Reasoning

No variant-specific functional assay was identified for NM_004655.4:c.1059+8C>T showing normal or benign function. The available literature provides only general ACMG/AMP guidance and a general variant-scoring framework, with no AXIN2 RNA, protein, cellular, or other validated assay result and no documented assay controls for this variant. Therefore, BS3 cannot be applied.

Rule

Generic ACMG/AMP BS3 requires well-established functional studies showing no damaging effect, with results appropriate to the variant and disease mechanism; no such result is available here.

Evidence considered

• The ACMG/AMP guidance describes functional studies as relevant to PS3/BS3 but does not report a normal-function assay for this variant.
• The reviewed variant-scoring study contains no AXIN2-specific functional result, control data, or benign-function assessment for c.1059+8C>T.

Still missing

• A validated variant-specific functional assay demonstrating normal or benign function with appropriate controls is needed.
• Assay-specific control performance and quantitative results are unavailable.

Sources

Reasoning

No affected individual known to carry the variant is reported with an unaffected relative who was tested and shown not to carry it. Without phenotype- and genotype-confirmed relatives, non-segregation cannot be evaluated.

Evidence considered

• No non-segregation observation, unaffected tested relative, or family-level genotype-phenotype comparison is documented for this exact variant.
• Population observations and ClinVar classifications cannot substitute for family-based non-segregation evidence.

Still missing

• Affected-relative phenotype and genotype data
• Unaffected-relative phenotype and genotype data
• Family structure and informative meioses
• Assessment of age-dependent penetrance and phenocopies

Reasoning

BP2 cannot be assessed from the available evidence. No report documents this variant in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder; no affected-proband genotype, phase result, co-occurrence observation, or relevant inheritance context is provided.

Evidence considered

• The case evidence contains no co-occurrence, phase, family, or proband-level genotype information that could support or refute BP2.
• The reviewed literature extraction provides no AXIN2-specific cis/trans observation for NM_004655.4:c.1059+8C>T.

Still missing

• Affected-proband genotype and clinical context
• Documented pathogenic or likely pathogenic allele co-occurring with this variant
• Phase determination establishing cis or trans configuration
• Inheritance model for the relevant AXIN2 phenotype

Sources

Reasoning

No exact-variant clinical or family evidence documents NM_004655.4:c.1059+8C>T occurring in cis with a pathogenic variant that explains the relevant phenotype. ClinVar laboratory classifications and population observations do not establish co-occurrence, so BP5 is not assessed.

Rule

Generic ACMG/AMP BP5: variant found in a case with an alternate molecular basis for the disease; no applicable gene-specific framework was found.

Evidence considered

• The case evidence materials contain no phasing, family co-occurrence, or in-cis pathogenic-variant observation for NM_004655.4:c.1059+8C>T.

Still missing

• Phasing and co-occurrence data with a pathogenic variant are unavailable.