APC c.3479C>A, p.(Thr1160Lys)

Reasoning

The APC VCEP BS1 threshold is gnomAD popmax filtering AF >=0.001% (0.00001). The variant exceeds this threshold in both gnomAD releases: v4.1 highest observed population AF 0.04802% and grpmax FAF 0.031285%, and v2.1 highest observed population AF 0.02329% with grpmax FAF 0.016883%. The result is robust to population and release selection.

Rule

APC VCEP BS1: GnomAD Popmax Filtering Allele Frequency (AF) >=0.001% (0.00001).

Evidence considered

• APC VCEP BS1: gnomAD popmax filtering AF >=0.001% (0.00001).
• gnomAD v4.1: total AF 0.02695% (435/1,613,950 alleles); highest observed population AF 0.04802% (30/62,480); grpmax FAF 0.031285%; zero homozygotes.
• gnomAD v2.1: total AF 0.01134% (32/282,180 alleles); highest observed population AF 0.02329% (30/128,808) in non-Finnish European individuals; grpmax FAF 0.016883%; zero homozygotes.

Sources

Reasoning

The APC VCEP specification (v2.1) states BP1 is applicable to APC (default strength Supporting) with the sole exception of missense variants located in the first 15-amino-acid repeat of the beta-catenin binding domain, codons 1021-1035. This exception reflects that APC disease mechanism is predominantly loss-of-function/truncating (confirmed by the PVS1 and PP2 VCEP comments), so missense variants outside the excepted repeat region are generally consistent with benign supporting evidence per the gene-level BP1 rule. The variant under assessment, p.(Thr1160Lys), falls at codon 1160, which is outside the 1021-1035 excepted repeat, though it does lie within the broader beta-catenin binding domain (codons 959-2129) referenced elsewhere in the specification for PS3/BS3 purposes -- that broader domain reference does not narrow the BP1 exception, which is explicitly scoped only to codons 1021-1035.

Rule

APC VCEP v2.1 BP1: applicable at Supporting strength to APC missense variants except those in codons 1021-1035 (first 15-aa repeat of beta-catenin binding domain).

Evidence considered

• APC VCEP Specifications v2.1, BP1 rule text: 'BP1 is applicable to APC with the exception of missense variants located in the first 15-amino acid repeat of the beta-catenin binding domain (codon 1021-1035).' Default strength Benign Supporting.
• Variant codon position 1160 falls outside the excepted codon range 1021-1035, per protein annotation NP_001120982.1:p.(Thr1160Lys).

Still missing

• The evidence bundle does not include the full underlying generic BP1 justification text (e.g., ClinVar missense benign-variant density data) beyond the codon-1021-1035 exception clause; flagging for human review to confirm the exception boundary and that no additional unmodified generic BP1 trigger conditions apply.

Sources

Reasoning

The APC VCEP specification (v2.1) restricts PS1 to variants resulting in the same amino acid change as a previously established Pathogenic or Likely Pathogenic APC missense variant. The specification explicitly states there are currently only two Likely Pathogenic missense variants in APC: p.(Asn1026Ser) (c.3077A>G) and p.(Ser1028Arg) (c.3084T>A); no missense variant has been classified Pathogenic under the APC-specific modifications. The variant under assessment, NP_001120982.1:p.(Thr1160Lys), does not match either of these established comparator amino acid changes (different residue, position 1160 vs 1026/1028). No other pathogenic missense comparator sharing the same amino acid change at codon 1160 was identified in the evidence bundle.

Rule

APC VCEP v2.1 PS1: same amino acid change as a previously established Pathogenic (Strong) or Likely Pathogenic (Moderate) APC missense variant.

Evidence considered

• APC VCEP Specifications v2.1, PS1 rule text: only two Likely Pathogenic missense variants currently recognized (p.(Asn1026Ser), p.(Ser1028Arg)); no missense variant currently classified Pathogenic; variant under assessment is p.(Thr1160Lys), not matching either established comparator.

Still missing

• No systematic search of a curated same-amino-acid-change comparator database (beyond the two explicitly named APC VCEP Likely Pathogenic missense variants) was available in this bundle.

Sources

Reasoning

The APC VCEP PM2_Supporting rule requires AF <=0.0003% (0.000003) when allele count is >1, or AF <0.001% (0.00001) when allele count is <=1. This allele has AC 435 and total AF 0.02695% in gnomAD v4.1, with highest observed population AF 0.04802%; it therefore exceeds the applicable >1-allele-count threshold by a large margin. gnomAD v2.1 independently reports AC 32 and total AF 0.01134%.

Rule

APC VCEP PM2_Supporting: rare in controls, AF <=0.0003% (0.000003) if AC >1 or AF <0.001% (0.00001) if AC <=1.

Evidence considered

• APC VCEP PM2_Supporting: AF <=0.0003% (0.000003) if allele count >1, or AF <0.001% (0.00001) if allele count <=1.
• gnomAD v4.1: AC 435/1,613,950, total AF 0.02695%; highest observed population AF 0.04802% (30/62,480); grpmax FAF 0.031285%.
• gnomAD v2.1: AC 32/282,180, total AF 0.01134%; highest observed population AF 0.02329% (30/128,808); grpmax FAF 0.016883%.

Sources

Reasoning

The APC VCEP specification restricts PM5 to missense changes at the same amino acid residue as a previously established Pathogenic (Moderate) or Likely Pathogenic (Supporting) APC missense variant, with the caveat that Grantham's distance of the variant under assessment must be equal or higher than the reported comparator variant. The specification names only two established Likely Pathogenic missense residues, codon 1026 (p.Asn1026Ser) and codon 1028 (p.Ser1028Arg); no Pathogenic missense variant is currently recognized. The variant under assessment affects codon 1160, which does not match either established comparator residue. A dedicated same-residue comparator search (pm5_candidates.json) returned zero same-residue candidates (search was also disrupted by an HTTP 429 rate-limit error, so the negative result carries some uncertainty, but no positive same-residue Pathogenic/Likely Pathogenic comparator was found anywhere in the evidence bundle).

Rule

APC VCEP v2.1 PM5: missense change at same residue as established Pathogenic (Moderate) or Likely Pathogenic (Supporting) APC missense variant, with equal/higher Grantham distance.

Evidence considered

• APC VCEP Specifications v2.1, PM5 rule text: only two Likely Pathogenic missense variants recognized (codon 1026, codon 1028); Grantham distance requirement for comparator matching.
• pm5_candidates.json automated same-residue search: 13 total candidates seen, 0 same-residue candidates identified at codon 1160; search partially failed with HTTP 429 error, recommendation flagged as 'no_useful_candidates_found'.

Still missing

• Automated same-residue comparator search for codon 1160 failed to complete fully (HTTP 429 rate limit) and returned zero candidates; a manual ClinVar search restricted to codon 1160 comparators was not independently performed to fully rule out an unflagged same-residue Pathogenic/Likely Pathogenic variant.

Sources

Reasoning

NM_001127510.3:c.3479C>A is a missense variant (NP_001120982.1:p.(Thr1160Lys)). Per the APC VCEP (InSiGHT Hereditary Colorectal Cancer/Polyposis EP) specification v2.1, PP3 for missense variants explicitly excludes conservation/evolutionary computational models (REVEL, BayesDel, aGVGD are not permitted inputs for PP3 in this gene) and instead requires in silico splicing predictors to reveal a possible cryptic splicing effect of the presumed missense change. SpliceAI (queried per VCEP-recommended tool list) predicts no splice impact for this variant: all four delta scores (DS_AG, DS_AL, DS_DG, DS_DL) = 0.00, well below the VCEP's PS1 instructions threshold of 0.2 for even a moderate cryptic-site gain call. Pangolin splice-gain/loss scores are likewise negligible (0.001 / -0.011). No deleterious splicing effect is predicted, so the APC-specific PP3 rule for missense variants is not satisfied.

Rule

APC VCEP (cspec v2.1) PP3, Supporting: Missense variants: do not use conservation/evolutionary computational prediction models; use in silico splicing predictors to reveal possible splicing effects. No qualifying splice-impact prediction was found for this variant.

Evidence considered

• APC VCEP cspec v2.1 PP3 rule: 'Missense variants: Do not use computational prediction models for conservation, evolution, etc. In silico splicing predictors should be used for presumed missense variants to reveal possible splicing effects.'
• SpliceAI Lookup result for NM_001127510.3:c.3479C>A: DS_AG=0.0, DS_AL=0.0, DS_DG=0.0, DS_DL=0.0, max_delta_score=0.0 (evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).')
• Pangolin splice-gain/loss scores negligible: pangolin_SG=0.001, pangolin_SL=-0.011, consistent with SpliceAI's no-impact prediction
• APC VCEP PS1 instructionsToUse (applies to the same recommended splice-predictor set used for PP3): SpliceAI loss of native site considered for scores 0.8-1; cryptic gain considered strong 0.8-1, moderate 0.2-0.8 — this variant's 0.00 score falls well below any impact threshold

Sources

Reasoning

The APC VCEP BA1 threshold is gnomAD popmax filtering AF >=0.1% (0.001). The highest available observed population AF is 0.04802% in gnomAD v4.1 Remaining individuals (30/62,480 alleles), and the gnomAD v4.1 grpmax FAF is 0.031285%; both are below 0.1%.

Rule

APC VCEP BA1: GnomAD Popmax Filtering Allele Frequency (AF) >=0.1% (0.001).

Evidence considered

• APC VCEP BA1: gnomAD popmax filtering AF >=0.1% (0.001).
• gnomAD v4.1: total AF 0.02695% (435/1,613,950 alleles); highest observed population AF 0.04802% (30/62,480) in Remaining individuals; grpmax FAF 0.031285%; zero homozygotes.

Sources

Reasoning

APC VCEP BS2 requires >=10 healthy-individual points, >=3 healthy-individual points for supporting strength, or observation at least twice in the homozygous state. The population datasets report zero homozygotes, and no phenotyped healthy-individual observations meeting the VCEP age, colonoscopy, testing-indication, or phenotype requirements are provided.

Rule

APC VCEP BS2: >=10 healthy-individual points or >=2 homozygous observations for strong; >=3 healthy-individual points for supporting.

Evidence considered

• APC VCEP BS2: strong requires >=10 healthy-individual points or >=2 homozygous observations; supporting requires >=3 healthy-individual points. A 1-point healthy individual requires age >=50 years plus specified colonoscopy/phenotype or testing-indication information; an unspecified control/non-cancer/normal/unaffected individual is worth 0.5 point.
• gnomAD v2.1 reports zero homozygotes (32/282,180 alleles).
• gnomAD v4.1 reports zero homozygotes (435/1,613,950 alleles).

Still missing

• No qualifying healthy-individual observations with APC VCEP-required phenotype and age/testing-indication details are available.
• No homozygous observations are reported in the available gnomAD datasets.

Sources

Reasoning

No variant-specific de novo observation with both parents tested is available in the case-evidence bundle.

Rule

APC VCEP: PS2 applies at Moderate for 1-1.5, Strong for 2-3.5, and Very Strong for >=4 confirmed-de-novo scores; Table 1 assigns 2 points to a proband with >=1 phenotype point and 1 point to a proband with 0.5 phenotype point when parental relationships are confirmed.

Evidence considered

• The APC VCEP specification assigns PS2 according to accumulated de novo scores and requires confirmed parental relationships for the confirmed-de-novo score column; no qualifying case observation is supplied.

Still missing

• Variant testing results for both biological parents.
• Confirmation of maternity and paternity for any putative de novo observation.
• Phenotype information sufficient to assign APC VCEP phenotype points to any proband.

Sources

Reasoning

NM_001127510.3:c.3479C>A (p.Thr1160Lys) is a missense variant. The APC VCEP (cspec v2.1) requires either RNA assay evidence (premature stop codon, exon 13/14 skipping, or other splicing aberration with absent/reduced full-length transcript) or, for missense variants specifically within the beta-catenin binding domain (codons 959-2129), a protein assay showing increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by surface plasmon resonance (PS3_Supporting only; no higher PS3 strength tier applies to missense/protein-assay variants per the VCEP table). Although p.Thr1160Lys falls within codons 959-2129, no protein functional assay data (transcriptional activity or SPR binding) for this specific variant were found anywhere in the case bundle (evidence.json, prefetch.json, vcep_materials.json) or in the retrieved literature set. None of the eight full-text papers retrieved for this case (PMID:18199528, PMID:25645574, PMID:25741868, PMID:26467025, PMID:15604628, PMID:22703879, PMID:25356965, PMID:25452455) report a functional assay of this variant; they are guideline/policy documents or a case-count/rare-variant burden study that does not mention this specific amino acid change. No RNA/splicing assay applies since this is a missense (not synonymous/intronic) change and SpliceAI predicts no splice impact (max delta 0.00), which is not itself a functional-assay result under PS3.

Still missing

• No published or ClinVar-linked in vitro/in vivo functional assay (beta-catenin transcriptional activity assay or SPR binding assay) for p.(Thr1160Lys) was located in the case bundle or retrieved literature.
• If such a functional study exists in the literature but was not captured by this case's PMID retrieval, PS3 should be re-assessed against it.

Reasoning

The APC-specific PS4 specification requires phenotype-point curation, but the available exact-variant report does not provide enough individual-level phenotype detail to assign phenotype points. It reports p.Thr1160Lys in one participant in the 11–99 colorectal-adenoma stratum and one participant with multiple colorectal adenomas of unknown count; it does not establish that either individual meets a qualifying phenotype-point category or provide the required aggregate phenotype-point total.

Rule

APC VCEP PS4: phenotype-point thresholds of 1–1.5 (Supporting), 2–3.5 (Moderate), 4–15.5 (Strong), or at least 16 (Very Strong); phenotype points are assigned using APC VCEP Table 1.

Evidence considered

• APC VCEP PS4 requires phenotype points: Supporting at 1–1.5, Moderate at 2–3.5, Strong at 4–15.5, and Very Strong at 16 or more.
• APC VCEP Table 1 assigns phenotype points only to defined phenotype categories; the report's cohort strata do not supply an individual p.Thr1160Lys carrier's exact adenoma count or other required qualifying features.
• Azzopardi et al. report T1160K once among 161 non-FAP/non-MAP participants with 11–99 colorectal adenomas and once among 201 participants with multiple colorectal adenomas of unknown number. The study assesses a collective burden of rare APC missense variants, not exact-variant case-control enrichment for T1160K.

Still missing

• Individual-level adenoma counts and other APC-VCEP Table 1 phenotype features for each p.Thr1160Lys carrier are required to assign phenotype points.
• Additional independent, phenotype-annotated p.Thr1160Lys observations are required to determine whether any APC-VCEP PS4 threshold is met.

Sources

Reasoning

No variant-specific observation reports the variant as de novo with parental relationships unconfirmed.

Rule

APC VCEP: PM6 applies at Supporting for 0.5, Moderate for 1-1.5, and Strong for 2-3.5 unconfirmed-parentage de novo scores; Table 1 assigns 1 point to a proband with >=1 phenotype point and 0.5 point to a proband with 0.5 phenotype point when parental relationships are unconfirmed.

Evidence considered

• The APC VCEP specification assigns PM6 according to accumulated de novo scores for observations without confirmed parental relationships; no qualifying observation is supplied.

Still missing

• Parental genotypes for any reported proband.
• Documentation of whether parental relationships were confirmed.
• Phenotype information sufficient to assign APC VCEP phenotype points to any proband.

Sources

Reasoning

No pedigree, affected-relative genotype, phenotype, or informative-meiosis data are available to establish co-segregation.

Rule

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

Evidence considered

• The APC VCEP specification requires 3-4 segregating meioses in >=1 family for PP1 Supporting, 5-6 meioses in >=1 family for Moderate, or >=7 meioses in >=2 families for Strong; no segregation dataset is supplied.

Still missing

• Pedigree with affected relatives and their APC c.3479C>A genotypes.
• Phenotype documentation for genotyped affected relatives.
• Count of informative segregations/meioses and number of families.

Sources

Reasoning

The APC VCEP BS3 rule requires either (a) an RNA assay of a synonymous or intronic variant in a constitutional patient sample showing no mRNA aberration (Strong, if biallelic expression/NMD-inhibition demonstrated; Supporting otherwise), or (b) a protein assay showing retention of wild-type-comparable beta-catenin-regulated transcription activity, restricted to missense variants within the beta-catenin binding domain (codons 959-2129). c.3479C>A is missense (p.Thr1160Lys), not synonymous/intronic, so the RNA-assay arm of BS3 does not apply. The variant does fall within codons 959-2129, so the protein-assay arm would be the applicable route, but no protein functional assay (transcriptional activity comparable to wild-type) for this specific variant was found in the case bundle (evidence.json, prefetch.json, vcep_materials.json) or in any of the eight retrieved full-text publications, none of which report functional data on this variant.

Still missing

• No functional protein assay (beta-catenin transcriptional activity, comparable-to-wild-type readout) for p.(Thr1160Lys) was located in the case bundle or retrieved literature.
• RNA-assay arm of BS3 is categorically not applicable since the variant is missense, not synonymous/intronic.

Reasoning

No affected relative tested negative for APC c.3479C>A is documented, and no phenotype-point evidence is available for non-segregation assessment.

Rule

APC VCEP: BS4 Strong requires one affected non-carrier with >=1 phenotype point or two affected non-carriers each with >=0.5 point; Supporting requires one affected non-carrier with >=0.5 point.

Evidence considered

• The APC VCEP specification requires an affected non-carrier with >=1 phenotype point for BS4 Strong, or either one affected non-carrier with >=0.5 point for Supporting or two affected non-carriers each with >=0.5 point for Strong; no qualifying non-segregation observation is supplied.

Still missing

• Genotype result showing an affected relative lacks APC c.3479C>A.
• Phenotype documentation sufficient to assign APC VCEP phenotype points to each affected non-carrier.

Sources

Reasoning

The APC-specific BP2 rule requires either observation in trans with a (Likely) Pathogenic APC variant or at least three observations in unknown phase with different (Likely) Pathogenic APC variants. The consolidated evidence bundle contains no qualifying co-occurring APC variant, phase determination, or count of unknown-phase co-occurrences for this variant.

Rule

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

Evidence considered

• The APC InSiGHT VCEP BP2 Supporting rule is: observed in trans with a (Likely) Pathogenic APC variant, or at least three times in unknown phase with different (Likely) Pathogenic APC variants.
• No qualifying allelic co-occurrence or phase evidence is present in the consolidated case-evidence bundle.

Still missing

• Obtain case-level co-occurrence data identifying any second APC variant, its independently established pathogenicity, and confirmed trans/cis phase; alternatively document at least three distinct unknown-phase co-occurrences with different (Likely) Pathogenic APC variants.

Sources

Reasoning

APC VCEP restricts BP5 to a colorectal-polyposis phenotype with an alternate genetic basis. No individual-level evidence demonstrates an alternate molecular diagnosis in a p.Thr1160Lys carrier.

Rule

APC VCEP BP5: Supporting only for an alternate genetic basis of the colorectal polyposis phenotype.

Evidence considered

• APC VCEP states that BP5 is only applicable for an alternate genetic basis of the colorectal polyposis phenotype.
• Azzopardi et al. describe T1160K in non-FAP/non-MAP colorectal-adenoma cohorts, but do not report a confirmed alternate molecular diagnosis for either T1160K carrier.

Still missing

• A phenotype-defined carrier with a confirmed alternate genetic cause of colorectal polyposis is required to evaluate BP5.

Sources