APC c.7594C>T, p.(His2532Tyr)

Reasoning

The APC InSiGHT VCEP specifies BS1 at gnomAD Popmax Filtering Allele Frequency >=0.00001 (0.001%). The applicable all-comers gnomAD v4.1 Popmax FAF is 1.064e-05 (0.001064%), which exceeds the threshold; BS1 is met at strong strength.

Rule

APC VCEP BS1: gnomAD Popmax Filtering AF >=0.00001 (0.001%).

Evidence considered

• The APC InSiGHT VCEP specifies BS1 as gnomAD Popmax Filtering Allele Frequency >=0.00001 (0.001%).
• gnomAD v4.1 reports a Popmax filtering allele frequency of 1.064e-05 (0.001064%), exceeding the VCEP threshold.

Sources

Reasoning

The APC VCEP applies BP1 to APC missense variants except those in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035. This missense variant is p.(His2532Tyr), at residue 2532, outside that exception; therefore BP1 Supporting is met.

Rule

BP1 Supporting applies to APC except missense variants in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035.

Evidence considered

• The APC VCEP rule states that BP1 is applicable except for missense variants located in codons 1021-1035, the first 15-amino-acid repeat of the beta-catenin-binding domain.
• The assessed missense variant is NP_001120982.1:p.(His2532Tyr), placing the altered residue at codon 2532, outside the exception.

Sources

Reasoning

The APC VCEP permits PS1 for a missense variant producing the same amino-acid change as a previously established pathogenic or likely pathogenic variant. This variant is p.(His2532Tyr), whereas the VCEP identifies only p.(Asn1026Ser) and p.(Ser1028Arg) as currently likely pathogenic APC missense variants, and neither has the same amino-acid change. No established pathogenic same-amino-acid comparator was identified.

Rule

Same amino-acid change as a previously established pathogenic or likely pathogenic APC variant; the VCEP-listed likely pathogenic missense changes are p.(Asn1026Ser) and p.(Ser1028Arg).

Evidence considered

• The APC VCEP specifies PS1 for the same amino-acid change as a previously established pathogenic or likely pathogenic APC variant.
• The VCEP lists only c.3077A>G p.(Asn1026Ser) and c.3084T>A p.(Ser1028Arg) as currently likely pathogenic APC missense variants; neither matches p.(His2532Tyr).
• The collected PM5 comparator record contains no verified same-residue or same-amino-acid comparator for p.(His2532Tyr).

Sources

Reasoning

The APC InSiGHT VCEP defines PM2 Supporting as allele frequency <=0.000003 when allele count is >1, or <0.00001 when allele count is <=1. In the specified non-cancer exome subset, the variant has allele count 3 and AF 1.27043e-05, exceeding the applicable 0.000003 threshold; the all-comers gnomAD datasets are also above that threshold. PM2 is not met.

Rule

APC VCEP PM2 Supporting: AF <=0.000003 if allele count >1, or AF <0.00001 if allele count <=1.

Evidence considered

• The APC InSiGHT VCEP defines PM2 Supporting as AF <=0.000003 (0.0003%) when allele count is greater than 1, or AF <0.00001 (0.001%) when allele count is 1 or less.
• The specified gnomAD v2.1 non-cancer exome subset reports 3/236,140 alleles, AF 1.27043e-05 (0.00127043%), and 0 homozygotes; because allele count is 3, the applicable threshold is 0.000003 and the observed AF exceeds it.
• For comparison, all-comers gnomAD v2.1 reports AF 1.7725845e-05 and all-comers gnomAD v4.1 reports AF 1.3637034e-05, both also above 0.000003.

Sources

Reasoning

The variant is missense, NM_001127510.3:c.7594C>T (p.His2532Tyr), so PP3/BP4 computational evidence is taken from the missense REVEL path only. REVEL is 0.452, below the generic ClinGen SVI supporting PP3 threshold of >=0.644 from the supplied Pejaver et al. 2022 calibration (PMID:36413997). The APC VCEP specifies PP3 as supporting when computational evidence supports a deleterious effect, but this REVEL result does not meet the supplied calibrated threshold; SpliceAI is not used for this missense PP3 assessment.

Rule

APC VCEP PP3: missense variants should not use conservation or evolutionary computational models; in silico splicing predictors may be used for presumed missense variants to reveal possible splicing effects. Applied here with the instructed missense REVEL path and supplied REVEL calibration.

Evidence considered

• The APC ClinGen InSiGHT VCEP specification assigns PP3 at supporting strength when computational evidence supports a deleterious effect.
• The variant is annotated as missense, p.(His2532Tyr), and the applicable missense predictor is REVEL; the recorded REVEL score is 0.452.
• The supplied ClinGen SVI REVEL calibration gives a supporting PP3 threshold of >=0.644 (Pejaver et al. 2022, PMID:36413997), which the score 0.452 does not reach.

Sources

Reasoning

The APC InSiGHT VCEP specifies BA1 at gnomAD Popmax Filtering Allele Frequency >=0.001 (0.1%). The highest applicable all-comers gnomAD v4.1 Popmax FAF is 1.064e-05 (0.001064%), far below 0.001; therefore BA1 is not met.

Rule

APC VCEP BA1: gnomAD Popmax Filtering AF >=0.001 (0.1%).

Evidence considered

• The APC InSiGHT VCEP specifies BA1 as gnomAD Popmax Filtering Allele Frequency >=0.001 (0.1%).
• gnomAD v4.1 reports a maximum population filtering allele frequency of 1.064e-05 (0.001064%), with 22/1,613,254 total alleles and no homozygotes.

Sources

Reasoning

The APC InSiGHT VCEP assigns PS2 strength by de novo scores: >=4 scores is Very Strong, 2-3.5 is Strong, and 1-1.5 is Moderate. The available evidence contains no proband-level de novo observation, maternity or paternity confirmation, parental testing result, or phenotype-based de novo score for NM_001127510.3:c.7594C>T; PS2 cannot be assessed.

Rule

PS2: >=4 de novo scores = Very Strong; 2-3.5 de novo scores = Strong; 1-1.5 de novo score = Moderate. De novo score curation uses the APC VCEP Tables 1 and 2.

Evidence considered

• The governing APC InSiGHT VCEP specifies PS2 Very Strong for >=4 de novo scores, Strong for 2-3.5 scores, and Moderate for 1-1.5 scores, with de novo scoring based on Tables 1 and 2.
• The available case evidence identifies NM_001127510.3:c.7594C>T (p.His2532Tyr) but reports no proband-level parental testing, confirmed parental relationships, or phenotype-based de novo score.

Still missing

• No documented proband-level de novo observation for NM_001127510.3:c.7594C>T.
• No maternity or paternity confirmation and no parental genotype results are available.
• No APC VCEP phenotype-point or de novo-score calculation is available for the proband.

Sources

Reasoning

The applicable APC InSiGHT VCEP specifies PS3 Very Strong through Strong for defined RNA findings involving a premature stop codon or in-frame skipping of exon 13 or 14 with absent or less than 10% full-length transcript, PS3 Moderate for specified RNA abnormalities, and PS3 Supporting for other defined RNA abnormalities or increased β-catenin-regulated transcription activity/decreased β-catenin binding by surface plasmon resonance. The variant is the missense change NM_001127510.3:c.7594C>T, p.(His2532Tyr), and the available case evidence contains no variant-specific RNA or protein functional assay result. The VCEP protein-assay route is restricted to the β-catenin-binding domain at APC codons 959–2129, whereas this variant affects codon 2532. OncoKB likewise reports no variant-specific reviewed functional evidence. Therefore, no PS3 strength can be assigned.

Rule

RNA assays show a premature stop codon or in-frame skipping of exon 13 or 14 with the specified full-length transcript effects, or other specified RNA abnormalities; protein assays show increased β-catenin-regulated transcription activity and/or decreased binding to β-catenin by surface plasmon resonance, only for variants within APC codons 959–2129.

Evidence considered

• The APC InSiGHT VCEP PS3 specification defines strength-specific RNA assay findings and a supporting protein assay showing increased β-catenin-regulated transcription activity or decreased β-catenin binding by surface plasmon resonance.
• The VCEP limits the protein-assay route to APC codons 959–2129; the variant is p.(His2532Tyr) at codon 2532.
• OncoKB reports no variant-specific reviewed functional evidence for this variant.
• No variant-specific functional assay result, assay controls, quantitative activity measurement, RNA transcript measurement, or reproducibility information is present in the reviewed evidence.

Still missing

• A validated variant-specific RNA assay or an applicable protein functional assay with appropriate controls and quantitative comparison to wild type is not available.

Sources

Reasoning

The APC InSiGHT VCEP specifies PS4 as applicable and assigns strength by phenotype points: >=16 points is Very Strong, 4-15.5 Strong, 2-3.5 Moderate, and 1-1.5 Supporting. The available evidence does not provide a curated phenotype-point total for this exact variant, a case-control enrichment estimate, or sufficient unrelated affected-person phenotype data; therefore PS4 cannot be assessed. No numeric comparison is available to perform.

Rule

PS4 is applicable. >= 16 phenotype points = Very Strong; 4-15.5 phenotype points = Strong; 2-3.5 phenotype points = Moderate; 1-1.5 phenotype point = Supporting. For phenotype points curation see Table 1.

Evidence considered

• The governing APC InSiGHT VCEP states: PS4 Very Strong requires >= 16 phenotype points; Strong requires 4-15.5; Moderate requires 2-3.5; Supporting requires 1-1.5 phenotype points, with phenotype curation in Table 1.
• The case materials identify the exact variant as NM_001127510.3:c.7594C>T (p.His2532Tyr) but provide no curated phenotype-point total or variant-specific case-control enrichment result.

Still missing

• Curated APC VCEP phenotype points for affected probands carrying NM_001127510.3:c.7594C>T are unavailable.
• No variant-specific case-control prevalence, odds ratio, relative risk, or confidence interval is available.

Sources

Reasoning

The APC VCEP allows PM5 when a different missense change at the same residue is established as pathogenic or likely pathogenic, with the required Grantham-distance comparison. The available comparator collection found no same-residue candidates, but retrieval ended with HTTP 429 and therefore does not establish that no qualifying p.His2532 comparator exists.

Rule

Different missense change at the same amino-acid residue established as pathogenic or likely pathogenic, with an equal or higher Grantham distance for the assessed variant; APC-specific PM5 strength rules apply.

Evidence considered

• The APC VCEP requires a different missense change at the same residue that is pathogenic or likely pathogenic; PM5 strength also requires the assessed variant's Grantham distance to be at least that of the comparator.
• The collected PM5 comparator record reports zero same-residue candidates and zero expert-panel or non-expert majority pathogenic/likely pathogenic candidates.
• The comparator collection records HTTP 429, so the absence of a qualifying p.His2532 comparator cannot be treated as definitive.

Still missing

• A reliable search for independently classified missense variants at APC residue His2532, including their VCEP-compatible classifications and Grantham distances, is still required.

Sources

Reasoning

The APC InSiGHT VCEP assigns PM6 strength by de novo score: 2-3.5 scores is Strong, 1-1.5 is Moderate, and 0.5 is Supporting. The available evidence contains no assumed-de-novo observation, parental genotype information, confirmed or unconfirmed parental relationship status, or phenotype-based de novo score; PM6 cannot be assessed.

Rule

PM6: 2-3.5 de novo scores = Strong; 1-1.5 de novo scores = Moderate; 0.5 de novo score = Supporting. De novo score curation uses the APC VCEP Tables 1 and 2.

Evidence considered

• The governing APC InSiGHT VCEP specifies PM6 Strong for 2-3.5 de novo scores, Moderate for 1-1.5 scores, and Supporting for 0.5 score, with de novo scoring based on Tables 1 and 2.
• The available case evidence reports no parental testing, no parental relationship assessment, and no phenotype-based de novo score for this variant.

Still missing

• No documented assumed-de-novo observation for NM_001127510.3:c.7594C>T.
• No parental genotype results or parental relationship status are available.
• No APC VCEP phenotype-point or de novo-score calculation is available for the proband.

Sources

Reasoning

The APC InSiGHT VCEP assigns PP1 strength by informative meioses: segregation in >=7 meioses across >=2 families is Strong, 5-6 meioses in >=1 family is Moderate, and 3-4 meioses in >=1 family is Supporting. The available evidence provides no affected relatives, family pedigrees, variant-positive relatives, or informative meiosis count; PP1 cannot be assessed.

Rule

PP1: segregation in >=7 meioses in >=2 families = Strong; 5-6 meioses in >=1 family = Moderate; 3-4 meioses in >=1 family = Supporting.

Evidence considered

• The governing APC InSiGHT VCEP specifies PP1 Strong for segregation in >=7 meioses in >=2 families, Moderate for 5-6 meioses in >=1 family, and Supporting for 3-4 meioses in >=1 family.
• The available case evidence contains no pedigree, affected-relative genotypes, phenotype-consistent segregation observations, or informative meiosis count for this variant.

Still missing

• No family pedigree or affected-relative testing results are available.
• No variant-positive affected relatives or informative meioses are documented.
• No family count or phenotype-consistent segregation assessment is available.

Sources

Reasoning

The APC InSiGHT VCEP permits BS2 at strong strength for at least 10 healthy-individual points or at least 2 observations in the homozygous state, and at supporting strength for at least 3 healthy-individual points. gnomAD v4.1 and v2.1 report zero homozygotes, but the available aggregate population records do not provide the individual-level age, colonoscopy, indication, or phenotype information needed to calculate healthy-individual points. The criterion therefore cannot be fully assessed.

Rule

APC VCEP BS2: strong at >=10 healthy-individual points or >=2 homozygotes; supporting at >=3 healthy-individual points.

Evidence considered

• The APC InSiGHT VCEP defines BS2 as at least 10 healthy-individual points or at least 2 homozygous observations for strong evidence, and at least 3 healthy-individual points for supporting evidence.
• gnomAD v2.1 reports 0 homozygotes among 282,074 alleles and gnomAD v4.1 reports 0 homozygotes among 1,613,254 alleles.
• Neither aggregate gnomAD record supplies the individual-level clinical information required for the VCEP healthy-individual point system.

Still missing

• Individual-level healthy-control observations with age, testing indication, colonoscopy findings, and APC-relevant phenotype are unavailable; homozygote absence alone does not satisfy the VCEP BS2 threshold.

Sources

Reasoning

The applicable APC InSiGHT VCEP specifies BS3 Strong for a constitutional RNA assay showing no mRNA aberration together with demonstrated biallelic expression and/or nonsense-mediated decay inhibition. BS3 Supporting can be used for a qualifying RNA assay without those controls or for a protein assay showing β-catenin-regulated transcription activity comparable to wild type, but the protein route is limited to APC codons 959–2129. The variant is NM_001127510.3:c.7594C>T, p.(His2532Tyr), at codon 2532, and no variant-specific RNA assay, protein assay, quantitative wild-type comparison, or relevant assay controls are available. Therefore, BS3 cannot be assigned at any strength.

Rule

RNA assay of a synonymous or intronic variant in a constitutional patient sample demonstrates no mRNA aberration with biallelic expression and/or nonsense-mediated decay inhibition for strong evidence; without those controls, or with protein assay showing β-catenin-regulated transcription comparable to wild type, supporting evidence applies only within APC codons 959–2129.

Evidence considered

• The APC InSiGHT VCEP BS3 specification requires a no-aberration constitutional RNA result with defined control requirements for strong evidence, or a qualifying protein assay showing β-catenin-regulated transcription comparable to wild type for supporting evidence.
• The VCEP limits the protein-assay route to APC codons 959–2129; the variant is p.(His2532Tyr) at codon 2532.
• OncoKB reports no variant-specific reviewed functional evidence for this variant.
• No variant-specific benign functional assay, quantitative wild-type comparison, biallelic-expression assessment, nonsense-mediated-decay control, or other assay validation data is present in the reviewed evidence.

Still missing

• A validated variant-specific benign RNA or applicable protein assay with appropriate controls, including transcript integrity or quantitative wild-type comparison, is not available.

Sources

Reasoning

The APC InSiGHT VCEP assigns BS4 Strong when an affected member without the variant has at least 1 phenotype point or when at least two affected noncarriers each have at least 0.5 phenotype points; Supporting requires one affected noncarrier with at least 0.5 phenotype points. The available evidence identifies no affected noncarrier or phenotype-point score, so BS4 cannot be assessed.

Rule

BS4: Strong requires an affected member without the variant with >=1 phenotype point or at least two such members each with >=0.5 points; Supporting requires one affected member without the variant with >=0.5 phenotype points.

Evidence considered

• The governing APC InSiGHT VCEP specifies BS4 Strong for one affected noncarrier with >=1 phenotype point or two affected noncarriers each with >=0.5 points, and Supporting for one affected noncarrier with >=0.5 points.
• The available case evidence contains no affected noncarrier, relative genotype, or phenotype-point score relevant to BS4.

Still missing

• No affected family member lacking NM_001127510.3:c.7594C>T is documented.
• No genotype results for affected relatives without the variant are available.
• No APC VCEP phenotype-point assessment is available for any affected noncarrier.

Sources

Reasoning

The APC InSiGHT VCEP permits BP2 at supporting strength when the variant is observed in trans with a pathogenic or likely pathogenic APC variant, or at least three times with different pathogenic or likely pathogenic APC variants in unknown phase. The available case evidence contains no documented affected-proband observation, second APC variant, trans/cis phase result, or qualifying recurrence for NM_001127510.3:c.7594C>T (p.His2532Tyr), so BP2 cannot be assessed.

Rule

BP2 supporting requires observation in trans with a (likely) pathogenic APC variant, or at least three observations with different (likely) pathogenic APC variants in unknown phase.

Evidence considered

• The APC InSiGHT VCEP defines BP2 supporting as observation in trans with a pathogenic or likely pathogenic APC variant, or at least three observations with different pathogenic or likely pathogenic APC variants in unknown phase.
• No case-level evidence documents a second APC variant, cis/trans phase, affected-proband observation, or three qualifying unknown-phase occurrences for NM_001127510.3:c.7594C>T (p.His2532Tyr).

Still missing

• A documented affected-proband observation with a second pathogenic or likely pathogenic APC variant in trans is needed, or at least three observations with different pathogenic or likely pathogenic APC variants in unknown phase.

Sources

Reasoning

The APC InSiGHT VCEP limits BP5 to a colorectal polyposis phenotype with an alternate genetic basis, specifically a qualifying (Likely) Pathogenic variant in another adenomatous-polyposis gene. The available evidence does not document such an alternate pathogenic variant or establish that the patient has the required colorectal polyposis phenotype, so BP5 cannot be assessed.

Rule

BP5 Supporting: only applicable for an alternate genetic basis of the colorectal polyposis phenotype; the VCEP specifies qualifying (Likely) Pathogenic variants in another adenomatous polyposis gene under the stated inheritance and age conditions.

Evidence considered

• The governing APC InSiGHT VCEP states that BP5 is applicable only for an alternate genetic basis of the colorectal polyposis phenotype, including qualifying variants in POLD1, POLE, MUTYH, NTHL1, MSH3, or specified mismatch-repair genes by the stated inheritance and age context.
• The available case evidence contains no qualifying alternate-gene Pathogenic or Likely pathogenic result and no documented colorectal polyposis phenotype for this adjudication.

Still missing

• No confirmed (Likely) Pathogenic variant in another qualifying adenomatous-polyposis gene is documented.
• The required colorectal polyposis phenotype is not documented in the available evidence.

Sources