APC c.3205A>G, p.(Arg1069Gly)

Reasoning

The APC VCEP specifies BS1 at gnomAD Popmax Filtering AF >= 0.00001 (0.001%). gnomAD v2.1 reports Popmax Filtering AF 1.127e-05, which meets the threshold, while gnomAD v4.1 reports 6.88e-06, below it. The criterion is met on the governing threshold using the v2.1 result, but the cross-release discrepancy warrants review.

Rule

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

Evidence considered

• The APC InSiGHT VCEP specifies BS1 for gnomAD Popmax Filtering AF >= 0.00001 (0.001%).
• gnomAD v2.1 reports Popmax Filtering AF 1.127e-05, meeting the threshold.
• gnomAD v4.1 reports Popmax Filtering AF 6.88e-06, below the threshold; this release discrepancy reduces confidence but does not negate the qualifying v2.1 observation.

Still missing

• The gnomAD v2.1 and v4.1 Popmax Filtering AF estimates are discordant around the APC VCEP BS1 threshold.

Sources

Reasoning

The APC VCEP applies BP1 at supporting strength to APC missense variants except those located in the first 15-amino-acid repeat of the beta-catenin-binding domain, codons 1021-1035. This variant is missense p.Arg1069Gly at codon 1069, outside the codon 1021-1035 exception. BP1 supporting is therefore met.

Rule

APC VCEP BP1: supporting for APC missense variants except missense 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 a missense substitution at codon 1069, which is outside the specified exception interval.

Sources

Reasoning

The APC VCEP permits PS1 for a missense variant only when it produces the same amino-acid change as a previously established pathogenic or likely pathogenic variant. The framework identifies only c.3077A>G p.(Asn1026Ser) and c.3084T>A p.(Ser1028Arg) as likely pathogenic missense variants, and neither produces p.Arg1069Gly. The case-specific literature reports p.Arg1069Gly as a VUS in two patients rather than as an established pathogenic comparator. Therefore PS1 is not met.

Rule

APC VCEP PS1: same amino-acid change as a previously established pathogenic variant gives strong evidence, or as a previously established likely pathogenic variant gives moderate evidence; the specified APC missense comparators are p.Asn1026Ser and p.Ser1028Arg.

Evidence considered

• The APC VCEP specifies PS1 for missense variants with the same amino-acid change as a previously established pathogenic or likely pathogenic variant.
• The APC VCEP lists only p.Asn1026Ser and p.Ser1028Arg as currently likely pathogenic missense variants; neither is p.Arg1069Gly.
• A case series reports APC c.3205A>G/p.Arg1069Gly as a VUS in two young patients and states it had not been reported in the FAP literature.

Sources

Reasoning

The APC VCEP specifies PS4 by phenotype points: ">= 16 phenotype points" for Very Strong, "4-15.5 phenotype points" for Strong, "2-3.5 phenotype points" for Moderate, and "1-1.5 phenotype point" for Supporting. The exact variant c.3205A>G (p.Arg1069Gly) was reported in two young patients with colorectal cancer, but the paper states that neither patient had known polyposis and does not document any APC VCEP Table 1 phenotype point. The lowest VCEP band is "1-1.5 phenotype point"; documented qualifying phenotype points = 0, which is not within 1-1.5. For the explicitly written Very Strong comparison, 0 >= 16? no. Therefore PS4 is not met at any strength.

Rule

APC VCEP PS4: >= 16 phenotype points = Very Strong; 4-15.5 = Strong; 2-3.5 = Moderate; 1-1.5 = Supporting.

Evidence considered

• The APC VCEP PS4 rules state: ">= 16 phenotype points" for Very Strong, "4-15.5 phenotype points" for Strong, "2-3.5 phenotype points" for Moderate, and "1-1.5 phenotype point" for Supporting.
• PMID:34545850 explicitly reports APC c.3205A>G/p.Arg1069Gly in two young Cajun patients with colorectal cancer and states that neither patient had known polyposis; no APC VCEP Table 1 phenotype point is documented.
• The explicit VCEP comparison for the Very Strong threshold is 0 >= 16? no; the lowest listed band, 1-1.5 phenotype point, is also not reached.

Sources

Reasoning

The APC VCEP specifies PM2 Supporting as allele frequency <= 0.000003 when allele count is >1, or <0.00001 when allele count is <=1. The all-comers gnomAD v2.1 observation is 6/281850 alleles (AF 2.12879e-05), and gnomAD v4.1 is 23/1614060 alleles (AF 1.42498e-05); both have allele counts >1 and frequencies above 0.000003. PM2 is therefore not met.

Rule

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

Evidence considered

• The APC InSiGHT VCEP defines PM2 Supporting as AF <= 0.000003 when allele count is greater than 1, or AF < 0.00001 when allele count is 1 or less.
• gnomAD v2.1 reports AC 6, AN 281850, and AF 2.12879e-05.
• gnomAD v4.1 reports AC 23, AN 1614060, and AF 1.42498e-05.
• Both observations have allele counts greater than 1 and exceed the applicable PM2 frequency threshold.

Sources

Reasoning

The APC VCEP PM5 rule requires a different missense change at the same amino-acid residue that has been established as pathogenic or likely pathogenic under the APC-specific modifications, with the assessed substitution meeting the required Grantham-distance comparison. The case-specific same-residue search for APC residue 1069 found 13 total candidates but zero same-residue candidates, including zero expert-panel or non-expert-majority pathogenic/likely pathogenic comparators. Therefore PM5 is not met.

Rule

APC VCEP PM5: a different missense change at the same residue may meet moderate or supporting PM5 when the comparator is established as pathogenic or likely pathogenic under APC-specific modifications and the assessed variant's Grantham distance is equal to or greater than the comparator; only p.Asn1026Ser and p.Ser1028Arg are specified APC likely pathogenic missense comparators.

Evidence considered

• The APC VCEP requires a different missense variant at the same residue established as pathogenic or likely pathogenic, plus the specified Grantham-distance comparison.
• The case-specific PM5 search found 13 candidates overall but 0 same-residue candidates, 0 expert-panel pathogenic/likely pathogenic candidates, and 0 non-expert-majority pathogenic/likely pathogenic candidates.

Sources

Reasoning

The APC InSiGHT VCEP permits PP3 at Supporting strength for applicable missense variants. This variant is missense, so the consequence-matched computational path is REVEL only; SpliceAI, BayesDel, and other predictors are not used for PP3. The REVEL score is 0.523, below the generic ClinGen SVI REVEL PP3 Supporting threshold of >=0.644 (Pejaver et al. 2022, PMID:36413997). Therefore PP3 is not met.

Rule

APC InSiGHT VCEP PP3 Supporting for applicable missense variants; generic REVEL PP3 Supporting threshold >=0.644 when no APC-specific REVEL cutoff is supplied.

Evidence considered

• The APC InSiGHT VCEP specifies PP3 at Supporting strength for applicable missense variants.
• The variant consequence is missense (NP_001120982.1:p.Arg1069Gly), so REVEL is the sole permitted PP3 predictor path.
• REVEL = 0.523; the supplied ClinGen SVI calibration threshold for PP3 Supporting is >=0.644 (Pejaver et al. 2022, PMID:36413997), so the threshold is not reached.
• The available SpliceAI and BayesDel results were not used for PP3 because PP3 evidence must come from the single consequence-matched path.

Sources

Reasoning

The APC VCEP specifies BA1 at gnomAD Popmax Filtering AF >= 0.001 (0.1%). The observed Popmax Filtering AF is 1.127e-05 in gnomAD v2.1 and 6.88e-06 in gnomAD v4.1, both 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 for gnomAD Popmax Filtering AF >= 0.001 (0.1%).
• gnomAD v2.1 reports Popmax Filtering AF 1.127e-05; gnomAD v4.1 reports Popmax Filtering AF 6.88e-06.
• Both observed Popmax frequencies are below the governing BA1 threshold.

Sources

Reasoning

The APC VCEP defines BP5 as Supporting only for an alternate genetic basis of a colorectal polyposis phenotype, specifically a qualifying (Likely) Pathogenic variant in another adenomatous polyposis gene. The available exact-variant report describes two colorectal cancer patients without known polyposis and provides no qualifying alternate-gene Pathogenic or Likely pathogenic finding. Therefore the BP5 condition is not met.

Rule

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

Evidence considered

• The APC VCEP BP5 rule states: "Only applicable for an alternate genetic basis of the colorectal polyposis phenotype"; its instructions specify a qualifying (Likely) Pathogenic variant in another adenomatous polyposis gene.
• PMID:34545850 reports the exact APC variant in two young patients with colorectal cancer, states that neither had known polyposis, and does not document a qualifying alternate-gene Pathogenic or Likely pathogenic result.

Sources

Reasoning

The APC VCEP specifies PS2 from de novo scores: 1-1.5 for Moderate, 2-3.5 for Strong, and at least 4 for Very Strong. The available variant-specific report describes c.3205A>G/p.Arg1069Gly in two young patients with colorectal cancer, but provides no parental testing, confirmed maternity or paternity, phenotype-point assignment, or de novo observation. Therefore, no PS2 strength can be assigned.

Rule

APC VCEP PS2: 1-1.5 de novo score = Moderate; 2-3.5 de novo scores = Strong; >=4 de novo scores = Very Strong.

Evidence considered

• The APC VCEP PS2 rule assigns Moderate at 1-1.5 de novo score, Strong at 2-3.5, and Very Strong at >=4.
• The variant-specific study reports the variant in two young Cajun patients with colorectal cancer but does not report parental testing or a confirmed de novo event.
• The same study states that neither patient had known polyposis, so the APC VCEP phenotype-point component cannot be established from this report.

Still missing

• Parental genotypes and confirmation of maternity and paternity are not documented.
• No qualifying APC VCEP de novo score can be calculated without phenotype and parental data.

Sources

Reasoning

The applicable APC InSiGHT VCEP specification permits PS3_Supporting for protein assays showing increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by surface plasmon resonance for variants in the beta-catenin-binding domain (codons 959-2129), and permits stronger PS3 levels for specified RNA findings. APC c.3205A>G (p.Arg1069Gly) lies within codons 959-2129, but the available case-specific literature reports only germline sequencing in two young patients and explicitly provides no functional assay, RNA assay, protein assay, transcriptional measurement, or beta-catenin-binding result for this variant. Therefore, a pathogenic functional effect is not established and PS3 cannot be assigned.

Rule

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

Evidence considered

• The APC InSiGHT VCEP Version 2.1 specification defines PS3_Supporting for increased beta-catenin-regulated transcription activity and/or decreased beta-catenin binding by surface plasmon resonance, restricted to the beta-catenin-binding domain at codons 959-2129; stronger PS3 levels require specified RNA assay findings.
• The variant is APC c.3205A>G, p.Arg1069Gly, at codon 1069 and therefore within the VCEP-defined beta-catenin-binding domain.
• The exact-variant publication describes retrospective germline sequencing of archived colorectal cancer specimens and reports two patients, but provides no RNA or protein functional assay result for p.Arg1069Gly.

Still missing

• A validated APC RNA assay or protein functional assay for p.Arg1069Gly is unavailable.
• No assay controls, replicate data, wild-type comparison, or quantitative functional threshold are reported for this variant.

Sources

Reasoning

The APC VCEP specifies PM6 from assumed de novo scores: 0.5 for Supporting, 1-1.5 for Moderate, and 2-3.5 for Strong. The available variant-specific report documents two affected patients but does not state that either case was de novo, does not provide parental testing, and does not provide the phenotype information needed to calculate a de novo score. PM6 is therefore not assessable.

Rule

APC VCEP PM6: 0.5 de novo score = Supporting; 1-1.5 de novo score = Moderate; 2-3.5 de novo scores = Strong.

Evidence considered

• The APC VCEP PM6 rule assigns Supporting at 0.5 de novo score, Moderate at 1-1.5, and Strong at 2-3.5.
• The variant-specific study reports two patients with the variant but does not characterize either finding as de novo or provide parental genotypes.
• The study provides no APC VCEP phenotype-point assignment for the reported patients.

Still missing

• No report of presumed or confirmed de novo origin is available for either patient.
• Parental testing and phenotype-point data needed for the APC VCEP score are absent.

Sources

Reasoning

The APC VCEP requires segregation in 3-4 meioses in at least one family for PP1 Supporting, 5-6 meioses in at least one family for PP1 Moderate, and at least 7 meioses in at least 2 families for PP1 Strong. The available variant-specific report describes two unrelated young patients but provides no pedigree, affected relatives, tested relatives, or informative meioses. PP1 cannot be assessed.

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 3-4 segregating meioses for Supporting, 5-6 for Moderate, and >=7 meioses in >=2 families for Strong.
• The variant-specific study reports two patients from a retrospective cohort, not familial segregation data, and supplies no informative meiosis count.

Still missing

• No family pedigrees or variant results in affected relatives are available.
• The number of informative segregating meioses and families is unknown.

Sources

Reasoning

The APC VCEP requires either at least 10 healthy-individual points or at least 2 observations in the homozygous state for BS2 Strong. gnomAD v2.1 and v4.1 each report zero homozygotes, but the available evidence does not provide the VCEP-defined healthy-individual phenotype and age data needed to count healthy-individual points. BS2 therefore cannot be assessed.

Rule

APC VCEP BS2 Strong: >=10 healthy-individual points OR >=2 homozygous observations; healthy-individual points require the specified age and clinical criteria.

Evidence considered

• The APC InSiGHT VCEP defines BS2 Strong as at least 10 healthy-individual points or at least 2 homozygous observations, with specific age and phenotype requirements for healthy-individual points.
• gnomAD v2.1 reports homozygotes = 0 and gnomAD v4.1 reports homozygotes = 0.
• No individual-level clinical information is available to establish the VCEP's healthy-individual point threshold.

Still missing

• No qualifying healthy-individual records with the APC VCEP's age, polyp, indication, and phenotype details were provided.

Sources

Reasoning

The applicable APC InSiGHT VCEP specification permits BS3_Supporting when a protein assay shows retention of beta-catenin-regulated transcription activity comparable to wild type for variants within the beta-catenin-binding domain (codons 959-2129), and permits BS3_Strong only for specified RNA assays of synonymous or intronic variants with appropriate biallelic-expression or nonsense-mediated-decay controls. APC c.3205A>G (p.Arg1069Gly) is a missense variant at codon 1069, but no validated protein or RNA assay, wild-type comparison, assay control, or quantitative retention result for this variant is reported. Therefore, benign functional evidence is not established and BS3 cannot be assigned.

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 BS3_Strong; or, for BS3_Supporting, such an RNA assay without those controls or a protein assay shows retention of beta-catenin-regulated transcription activity comparable to wild type for variants within the beta-catenin-binding domain (codons 959-2129 of APC).

Evidence considered

• The APC InSiGHT VCEP Version 2.1 specification defines BS3_Supporting for retention of beta-catenin-regulated transcription activity comparable to wild type in a protein assay for variants within codons 959-2129; BS3_Strong requires a qualifying RNA assay with biallelic-expression demonstration and/or nonsense-mediated-decay inhibition.
• The variant is APC c.3205A>G, p.Arg1069Gly, at codon 1069 and is missense, so the VCEP BS3_Strong synonymous/intronic RNA pathway does not apply.
• The exact-variant publication reports germline sequencing and a clinical VUS observation but no functional assay, wild-type comparison, assay controls, or benign functional result for p.Arg1069Gly.

Still missing

• A validated protein assay comparing p.Arg1069Gly with wild-type APC is unavailable.
• The VCEP BS3_Strong RNA pathway is not applicable to this missense variant, and no variant-specific RNA assay is reported.

Sources

Reasoning

The APC VCEP requires an affected member without the variant to score at least 0.5 phenotype point for BS4 Supporting, or at least 1 point, or two affected non-carriers each scoring at least 0.5 points, for BS4 Strong. The available report contains no family testing, affected non-carrier, pedigree, or phenotype-point data. Absence of reported segregation is not evidence of non-segregation, so BS4 is not assessable.

Rule

APC VCEP BS4: affected member without the variant with >=0.5 phenotype point = Supporting; >=1 point, or two affected non-carriers each with >=0.5 points = Strong.

Evidence considered

• The APC VCEP BS4 rule requires one affected non-carrier with >=0.5 phenotype point for Supporting; Strong requires one with >=1 point or two each with >=0.5 points.
• The variant-specific study reports no affected relatives without the variant and no family-level non-segregation analysis.
• The absence of family information cannot be interpreted as evidence that the variant fails to segregate.

Still missing

• No affected relatives lacking the variant are documented.
• No phenotype-point scores for affected non-carriers are available.

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 report describes c.3205A>G/p.Arg1069Gly in two young patients but provides no phase information and does not identify a second pathogenic or likely pathogenic APC variant in either patient. Thus, the BP2 requirement is not established and remains not assessed.

Rule

Observed in trans with a (Likely) Pathogenic APC variant OR at least 3 times in an unknown phase with different (Likely) Pathogenic APC variants.

Evidence considered

• The APC InSiGHT VCEP specifies BP2 Supporting for observation in trans with a Pathogenic or Likely Pathogenic APC variant, or at least three observations in unknown phase with different Pathogenic or Likely Pathogenic APC variants.
• PMID:34545850 reports APC c.3205A>G/p.Arg1069Gly in two young Cajun patients with colorectal cancer, but does not report phase or a second pathogenic/likely pathogenic APC variant; the paper states the variant had not been reported in individuals with familial adenomatous polyposis.

Still missing

• Documented phase with a Pathogenic or Likely Pathogenic APC variant is unavailable.
• A total of at least three occurrences with different Pathogenic or Likely Pathogenic APC variants in unknown phase is not documented.

Sources