APC c.4072G>A, p.(Ala1358Thr)

Reasoning

The APC VCEP defines BS1 as gnomAD Popmax Filtering Allele Frequency (AF) >= 0.001% (0.00001). The variant has gnomAD v4.1 grpmax FAF 0.0001909 and European non-Finnish AF 0.000212706, both exceeding 0.00001; gnomAD v2.1 grpmax FAF is also 0.00010915. Therefore BS1 is met at strong strength.

Rule

GnomAD Popmax Filtering Allele Frequency (AF) >= 0.001% (0.00001).

Evidence considered

• The APC VCEP specifies BS1 at gnomAD Popmax Filtering Allele Frequency >= 0.001% (0.00001).
• gnomAD v4.1 reports grpmax FAF 0.0001909 and European non-Finnish AF 0.000212706; gnomAD v2.1 reports grpmax FAF 0.00010915, all above 0.00001.

Sources

Reasoning

The APC VCEP applies BP1 at supporting strength to APC missense variants, except for missense variants located in the first 15-amino-acid repeat of the beta-catenin-binding domain, defined as codons 1021-1035. The assessed variant is the missense change p.(Ala1358Thr) at codon 1358, outside that exception. BP1 is therefore met at supporting strength.

Rule

APC VCEP BP1: supporting strength for APC missense variants except variants in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035.

Evidence considered

• The APC VCEP BP1 rule applies to APC missense variants except those in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035.
• The assessed variant is p.(Ala1358Thr), placing it at codon 1358 and outside the stated exception.

Sources

Reasoning

The APC VCEP specifies PS1 for a missense variant producing the same amino-acid change as a previously established pathogenic or likely pathogenic APC variant. It identifies only c.3077A>G p.(Asn1026Ser) and c.3084T>A p.(Ser1028Arg) as the currently established likely pathogenic missense variants, with no pathogenic missense variant established. The assessed variant is NM_001127510.3:c.4072G>A, p.(Ala1358Thr), which is neither of those amino-acid changes, so PS1 is not met.

Rule

APC VCEP PS1: apply when the missense variant results in the same amino-acid change as a previously established pathogenic or likely pathogenic APC variant; other variants at the two specified likely pathogenic positions meet PS1_Moderate.

Evidence considered

• The APC-specific PS1 rule requires the same amino-acid change as a previously established pathogenic or likely pathogenic APC variant.
• The APC VCEP lists c.3077A>G p.(Asn1026Ser) and c.3084T>A p.(Ser1028Arg) as the only currently established likely pathogenic missense variants; the assessed variant is p.(Ala1358Thr).

Sources

Reasoning

The APC VCEP defines PM2 supporting as allele frequency <= 0.000003 when allele count is >1, or allele frequency <0.00001 when allele count is <=1. The variant is observed 22/282130 alleles in gnomAD v2.1 (AF 0.0000779782) and 256/1613982 alleles in gnomAD v4.1 (AF 0.000158614); both allele counts exceed 1 and both frequencies exceed 0.000003. Therefore PM2 is not met.

Rule

Rare in controls: allele frequency <= 0.0003% (0.000003) if allele count is > 1 OR allele frequency < 0.001% (0.00001) if allele count is <= 1.

Evidence considered

• The APC VCEP defines PM2 supporting as AF <= 0.000003 when allele count is >1, or AF <0.00001 when allele count is <=1.
• gnomAD v2.1 reports 22/282130 alleles and AF 0.0000779782; gnomAD v4.1 reports 256/1613982 alleles and AF 0.000158614.

Sources

Reasoning

The APC VCEP PM5 rule requires a different missense change at the same amino-acid residue as a previously established pathogenic or likely pathogenic APC missense variant, with the assessed substitution meeting the specified Grantham-distance comparison. The collected PM5 search identified no useful same-residue comparator for p.(Ala1358Thr). The VCEP's only specified likely pathogenic missense residues are codons 1026 and 1028, not codon 1358; therefore PM5 is not met.

Rule

APC VCEP PM5: a different missense variant at a residue with a previously established pathogenic or likely pathogenic missense variant may qualify, subject to the APC-specific classification and an equal or higher Grantham distance than the reported variant.

Evidence considered

• The APC-specific PM5 rule requires a different missense change at the same residue as an established pathogenic or likely pathogenic APC missense variant and requires the Grantham-distance condition to be satisfied.
• The case-specific PM5 candidate record reports zero same-residue candidates and no useful comparator; the APC VCEP identifies only codons 1026 and 1028 as the relevant established likely pathogenic missense positions.

Sources

Reasoning

The variant is missense, so PP3 is applicable through the APC VCEP's in-silico splicing path. The APC specification requires multiple in-silico splicing predictors to support a deleterious effect for missense variants; SpliceAI predicts no significant splice impact, with a maximum delta score of 0.001, below the supplied generic supporting threshold of 0.2. REVEL 0.358 and BayesDel 0.0425822 do not establish PP3 under the APC specification: APC directs missense computational assessment to in-silico splicing predictors rather than conservation/evolution models, and no governing APC BayesDel cutoff is specified. Therefore PP3 is not met.

Rule

APC VCEP PP3: for missense variants, do not use conservation/evolution computational models; use in-silico splicing predictors to reveal possible splicing effects, with multiple in-silico splicing predictors supporting a deleterious effect.

Evidence considered

• The APC VCEP specification states that missense variants should be assessed with in-silico splicing predictors and that multiple predictors must support a deleterious effect.
• SpliceAI reports DS_AG 0.000, DS_AL 0.000, DS_DG 0.001, and DS_DL 0.000; the maximum delta is 0.001, indicating no significant splice impact.
• The supplied generic SpliceAI calibration defines PP3 supporting at maximum delta >=0.2, from Jaganathan et al. 2019 (PMID:30661751); the observed maximum delta is 0.001.
• REVEL score 0.358 is below the supplied PP3 supporting threshold of 0.644 from Pejaver et al. 2022 (PMID:36413997), and the APC specification does not permit missense conservation/evolution prediction models for PP3.
• BayesDel score 0.0425822 is not used because no generic ACMG-strength calibration is established and the APC specification supplies no BayesDel cutoff.

Sources

Reasoning

The APC VCEP defines BA1 as gnomAD Popmax Filtering Allele Frequency (AF) >= 0.1% (0.001). The highest available population frequency is the gnomAD v4.1 European non-Finnish AF of 0.000212706 (0.02127%), with grpmax FAF 0.0001909; gnomAD v2.1 grpmax FAF is 0.00010915. Both are below 0.001, so BA1 is not met.

Rule

GnomAD Popmax Filtering Allele Frequency (AF) >= 0.1% (0.001).

Evidence considered

• The APC VCEP specifies BA1 at gnomAD Popmax Filtering Allele Frequency >= 0.1% (0.001).
• gnomAD v4.1 reports grpmax FAF 0.0001909 and European non-Finnish AF 0.000212706; gnomAD v2.1 reports grpmax FAF 0.00010915.

Sources

Reasoning

The APC-specific framework makes PS2 applicable and assigns Very Strong for at least 4 de novo scores, Strong for 2–3.5, and Moderate for 1–1.5. The available case evidence contains no proband-level report documenting a de novo APC variant, no maternity or paternity confirmation, and no phenotype-linked parental testing, so a de novo score cannot be calculated.

Rule

APC VCEP PS2: >=4 de novo scores = Very Strong; 2-3.5 = Strong; 1-1.5 = Moderate; de novo scoring uses the APC phenotype and parental-relationship tables.

Evidence considered

• The APC VCEP specification lists PS2 as applicable and defines strength using de novo scores: at least 4 for Very Strong, 2–3.5 for Strong, and 1–1.5 for Moderate.
• No case-specific proband, parental-genotype, maternity, paternity, or family-history observation supporting a de novo event was identified in the available evidence.
• The APC phenotype/de novo table requires phenotype points and distinguishes confirmed from unconfirmed parental relationships; neither case-specific input is available.

Still missing

• Proband clinical phenotype and disease status
• Variant testing results for both biological parents
• Confirmation of maternity and paternity
• Evidence excluding a relevant family history

Sources

Reasoning

The APC InSiGHT VCEP specifies PS3 for damaging RNA findings, including a premature stop codon or exon 13/14 skipping with loss or less than 10% full-length transcript, other qualifying exon-skipping or alternative-transcript findings, or increased beta-catenin transcription activity and/or reduced beta-catenin binding in the APC beta-catenin-binding domain. This missense variant, p.Ala1358Thr, lies within the specified beta-catenin-binding domain (codons 959-2129), so an appropriately validated protein assay could be relevant, but the reviewed evidence contains no variant-specific RNA or protein assay result, quantitative activity measurement, assay control data, or demonstrated damaging effect. ClinVar evidence explicitly states that functional studies have not been performed or reported, and OncoKB reports no variant-specific reviewed functional evidence. PS3 therefore cannot be applied at any strength.

Rule

APC VCEP PS3: RNA assays show a premature stop codon or in-frame skipping of exon 13 or 14 with the specified transcript-loss thresholds, other specified splicing abnormalities, or protein assays show increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by surface plasmon resonance for variants within APC codons 959-2129.

Evidence considered

• The APC InSiGHT VCEP PS3 specification requires defined damaging RNA findings or, for variants in codons 959-2129, increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by surface plasmon resonance.
• The variant is p.Ala1358Thr at codon 1358, within the APC beta-catenin-binding domain specified by the VCEP.
• Reviewed ClinVar evidence states that functional studies have not been performed or reported for this variant.
• OncoKB reports no variant-specific reviewed functional evidence for this variant.

Still missing

• A validated variant-specific functional assay is needed, with appropriate wild-type and disease-relevant controls.
• For RNA testing, transcript structure and full-length transcript proportion are not available.
• For protein testing, beta-catenin-regulated transcription or beta-catenin binding measurements are not available.

Sources

Reasoning

The APC InSiGHT VCEP specification applies PS4 using its phenotype-point system: Very Strong requires ≥16 points, Strong 4–15.5, Moderate 2–3.5, and Supporting 1–1.5 points. The available records indicate that the exact variant has appeared in individuals with colorectal cancer or suspected Lynch syndrome, but they do not provide the individual-level APC phenotype features needed to assign Table 1 points, nor a case-control enrichment estimate with confidence interval. Therefore PS4 cannot be assigned at any strength from the available evidence.

Rule

APC InSiGHT VCEP PS4: ≥16 phenotype points = Very Strong; 4–15.5 = Strong; 2–3.5 = Moderate; 1–1.5 = Supporting; phenotype points are curated using Table 1.

Evidence considered

• The APC InSiGHT VCEP specification states: ≥16 phenotype points for PS4_VeryStrong, 4–15.5 for PS4_Strong, 2–3.5 for PS4_Moderate, and 1–1.5 for PS4_Supporting, with phenotype points curated from Table 1.
• Exact-variant ClinVar submission evidence reports the variant in individuals with colorectal cancer or suspected Lynch syndrome, but does not provide sufficient patient-level phenotype data for VCEP point assignment.
• No case-control odds ratio, relative risk, or confidence interval for this exact variant was identified.

Still missing

• Individual-level phenotype details for each exact-variant carrier are needed to calculate APC VCEP Table 1 phenotype points.
• A case-control enrichment estimate and confidence interval are not available.

Sources

Reasoning

The APC-specific framework makes PM6 applicable and assigns Strong for 2–3.5 de novo scores, Moderate for 1–1.5, and Supporting for 0.5. The available evidence does not document an assumed de novo occurrence, an affected proband, or parental testing without confirmed maternity and paternity; therefore no PM6 score can be assigned.

Rule

APC VCEP PM6: 2-3.5 de novo scores = Strong; 1-1.5 = Moderate; 0.5 = Supporting; de novo scoring uses the APC phenotype and parental-relationship tables.

Evidence considered

• The APC VCEP specification lists PM6 as applicable and defines 2–3.5 de novo scores as Strong, 1–1.5 as Moderate, and 0.5 as Supporting.
• No variant-specific case observation establishes an assumed de novo APC event, and no parental or phenotype data are provided for scoring.
• The APC de novo scoring table requires phenotype points and parental-relationship status, which are absent for this case.

Still missing

• Case report or testing record establishing the variant in an affected proband
• Parental testing results or explicit absence of parental testing
• Maternity and paternity confirmation status
• Phenotype points needed for APC de novo scoring

Sources

Reasoning

The APC-specific framework defines PP1 as Supporting for segregation in 3–4 meioses in at least 1 family, Moderate for 5–6 meioses in at least 1 family, and Strong for at least 7 meioses in at least 2 families. No affected relatives, transmitting relatives, pedigrees, variant-positive relatives, or meiosis count are reported, so segregation cannot be evaluated.

Rule

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

Evidence considered

• The APC VCEP PP1 rule requires segregation in 3–4 meioses for Supporting, 5–6 meioses for Moderate, or at least 7 meioses in at least 2 families for Strong.
• No family pedigree, affected relative, variant-positive relative, or meiosis information is available for this variant.

Still missing

• Pedigree or family structure
• Number of affected relatives tested
• Variant status for each affected relative
• Meiosis count and number of families

Sources

Reasoning

The APC VCEP requires at least 10 healthy-individual points or at least 2 observations in the homozygous state for BS2 strong, with a supporting threshold of at least 3 healthy-individual points. The gnomAD v2.1 and v4.1 records report zero homozygotes, so the homozygote route is not met, but they provide no qualifying individual-level healthy-subject phenotype, age, colonoscopy, or testing-indication data to evaluate the healthy-individual route. BS2 is therefore not assessed.

Rule

Strong: >= 10 points for healthy individuals OR >= 2 times in homozygous state; Supporting: >= 3 points for healthy individuals.

Evidence considered

• The APC VCEP defines BS2 strong as at least 10 healthy-individual points or at least 2 homozygous observations, and BS2 supporting as at least 3 healthy-individual points.
• gnomAD v2.1 and v4.1 each report homozygotes = 0; the available records do not provide qualifying healthy-individual phenotype, age, colonoscopy, or testing-indication data.

Still missing

• Qualifying healthy-individual data needed to calculate the APC VCEP BS2 point count.

Sources

Reasoning

The APC InSiGHT VCEP specifies BS3 for an RNA assay showing no mRNA aberration in a constitutional patient sample, with strong strength requiring demonstrated biallelic expression and/or nonsense-mediated decay inhibition, or supporting strength without those additional controls; it also permits supporting BS3 when a protein assay shows retention of beta-catenin-regulated transcription activity comparable to wild type for variants within APC codons 959-2129. This p.Ala1358Thr variant is within that domain, but the reviewed evidence contains no variant-specific benign RNA or protein assay, no wild-type comparison, and no assay-control or biallelic-expression/NMD evidence. ClinVar evidence states that functional studies have not been performed or reported, and OncoKB reports no variant-specific reviewed functional evidence. BS3 therefore cannot be applied at any strength.

Rule

APC VCEP BS3: strong requires a constitutional-sample RNA assay showing no mRNA aberration plus demonstrated biallelic expression and/or nonsense-mediated-decay inhibition; supporting permits the same RNA result without those controls or a protein assay showing beta-catenin-regulated transcription activity comparable to wild type for variants within APC codons 959-2129.

Evidence considered

• The APC InSiGHT VCEP BS3 specification requires a benign RNA result with defined control requirements or, at supporting strength, retention of beta-catenin-regulated transcription activity comparable to wild type for variants within APC codons 959-2129.
• The variant is p.Ala1358Thr at codon 1358, within the APC beta-catenin-binding domain specified by the VCEP.
• Reviewed ClinVar evidence states that functional studies have not been performed or reported for this variant.
• OncoKB reports no variant-specific reviewed functional evidence for this variant.

Still missing

• A validated variant-specific benign functional assay with appropriate wild-type comparison is needed.
• For RNA testing, constitutional-sample transcript results and biallelic-expression or nonsense-mediated-decay controls are not available.
• For protein testing, comparable beta-catenin-regulated transcription activity relative to wild type is not available.

Sources

Reasoning

The APC-specific framework permits BS4 when an affected member without the variant scores at least 1 phenotype point for Strong, or when at least two affected members without the variant each score at least 0.5 phenotype points for Strong; Supporting requires one affected member without the variant scoring at least 0.5 phenotype points. No affected noncarrier or phenotype-scored relative is reported, so non-segregation cannot be assessed.

Rule

APC VCEP BS4: Strong requires one affected noncarrier with >=1 phenotype point or two affected noncarriers each with >=0.5 points; Supporting requires one affected noncarrier with >=0.5 points.

Evidence considered

• The APC VCEP BS4 rule requires an affected member without the variant scoring at least 1 phenotype point, or at least two such affected members each scoring at least 0.5 points, for Strong.
• The APC VCEP allows Supporting BS4 when one affected member without the variant scores at least 0.5 phenotype points.
• No affected noncarrier, relative-level genotype, pedigree, or phenotype-point score is reported for this case.

Still missing

• Affected relatives lacking the variant
• Variant testing results for those relatives
• Phenotype details and APC phenotype-point scores
• Family pedigree and number of non-segregating affected members

Sources

Reasoning

The APC VCEP permits BP2 at supporting strength when the variant is observed in trans with a (Likely) Pathogenic APC variant or at least three times with different (Likely) Pathogenic APC variants in unknown phase. The available case evidence does not document an affected proband carrying NM_001127510.3:c.4072G>A together with a second pathogenic or likely pathogenic APC variant, does not establish cis/trans phase, and does not report three qualifying unknown-phase observations. Therefore BP2 cannot be applied or excluded from the available evidence.

Rule

BP2 Supporting: observed in trans with a (Likely) Pathogenic APC variant OR at least three times in unknown phase with different (Likely) Pathogenic APC variants.

Evidence considered

• The APC VCEP BP2 rule requires observation in trans with a (Likely) Pathogenic APC variant, or at least three observations in unknown phase with different (Likely) Pathogenic APC variants.
• The case materials provide no documented affected-proband phase data, no qualifying second APC variant in trans, and no three-observation unknown-phase series for NM_001127510.3:c.4072G>A.
• The available literature extraction does not identify this exact APC variant in a report containing phase, affected-proband, or second-allele evidence.

Still missing

• Documented affected-proband observations with a second (Likely) Pathogenic APC variant are unavailable.
• Cis/trans phase information is unavailable.
• A count of at least three observations with different (Likely) Pathogenic APC variants in unknown phase is unavailable.

Sources

Reasoning

The APC InSiGHT VCEP permits BP5 at Supporting strength only for an alternate genetic basis of a colorectal polyposis phenotype, specifically a qualifying (Likely) Pathogenic variant in another adenomatous polyposis gene such as POLD1, POLE, MUTYH, NTHL1, MSH3, or specified mismatch-repair genes. The available case evidence does not document a qualifying alternate-gene variant or establish the required colorectal polyposis phenotype. BP5 therefore cannot be assigned.

Rule

APC InSiGHT VCEP BP5: Supporting only when a (Likely) Pathogenic variant in another specified adenomatous polyposis gene provides an alternate genetic basis and a colorectal polyposis phenotype is present.

Evidence considered

• The APC InSiGHT VCEP BP5 rule is Supporting only for an alternate genetic basis of colorectal polyposis, involving specified (Likely) Pathogenic variants in another adenomatous polyposis gene.
• No qualifying alternate-gene result is present in the available case evidence.

Still missing

• A complete alternate-gene testing result is needed, including variant classification and gene.
• The presence of a colorectal polyposis phenotype must be documented.

Sources