MUTYH c.42C>T, p.(Ile14=)

Reasoning

PS2 (Richards et al. 2015, PMID:25741868) requires a confirmed de novo occurrence with both maternity and paternity confirmed, in a patient with the disease and no family history. No de novo occurrence of MUTYH NM_001128425.2:c.42C>T (NP_001121897.1:p.(Ile14=)) is reported in any source assembled for this case, and no proband, trio, or parental testing exists. The variant-specific clinical literature reports the opposite of a de novo event: Aretz et al. 2006 (PMID:16557584) sequenced the entire MUTYH coding region in 329 unrelated APC-mutation-negative polyposis index patients and found c.42C>T exactly once, in the monoallelic (heterozygous) state, in a single patient (1/658 patient chromosomes, 0.15%), where it is listed among the silent changes; no parental testing was performed for that carrier. Independently, the allele is present in population reference data as a transmitted germline variant (gnomAD v2.1 AF 9.19131e-05, 26/282,876 alleles, 0 homozygotes; gnomAD v4.1 AF 1.71629e-04, 277/1,613,946 alleles, 0 homozygotes), which is not compatible with a recurrent de novo mechanism. MUTYH-associated disease is autosomal recessive (familial adenomatous polyposis 2, MONDO:0012041) per the governing ClinGen InSiGHT specification, so a single heterozygous allele would in any event not satisfy PS2's requirement of a de novo event in a patient with the disease. The governing specification has no criterion-level PS2 rule (framework_complete=false, unstructured ruleset), so generic ACMG/AMP 2015 applies and the criterion is not met.

Rule

PS2 (Richards et al. 2015, PMID:25741868): de novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Pathogenic Strong.

Evidence considered

• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP guidelines for MUTYH v1.0 (doc 1742141534) was retrieved, but it contains no criterion-level rule payload (framework_complete=false, framework_mode=unstructured_ruleset, rule_payload empty); the only machine-readable content is the gene-disease record, which gives MUTYH an autosomal recessive mode of inheritance for familial adenomatous polyposis 2 (MONDO:0012041). Generic ACMG/AMP 2015 criteria therefore govern PS2/PM6/PP1/BS4.
• PS2 rule text (Richards et al. 2015, PMID:25741868): de novo (both maternity and paternity confirmed) in a patient with the disease and no family history; Pathogenic Strong.
• Aretz et al. 2006 (PMID:16557584), Table II under 'Rare variants (identified in monoallelic state only)', Exon 2: 'c.42C>T / p.I14 / 1/658 (0.15)'. Direct quote from the Results, paragraph on monoallelic variants: 'However, only 3 of the patients (0.9%) harboured a mutation of predicted functional relevance (c.817delG, G382D, c.89113A>C); the other substitutions include 4 silent changes (I14, Y90, T136, T469) and 2 missense variants at unconserved sites (R295C, R412C).' The variant is not among the 21 mutations of assumed pathogenic relevance, was never seen biallelically, and no parent/relative genotyping for this variant is reported. The paper's only family segregation analysis (ten siblings/parents of index family no. 26) concerns a different variant, the in-frame deletion p.466delE.
• gnomAD v2.1 (source key gnomad_v2): AF 9.19131e-05, 26/282,876 alleles, homozygotes = 0, highest subpopulation European (non-Finnish) AF 0.000185779 (24/129,186), grpmax FAF 0.0001303 — a low-frequency allele observed in many independent adult individuals, i.e. transmitted rather than recurrently de novo.
• gnomAD v4.1 (source key gnomad_v4): AF 1.71629e-04, 277/1,613,946 alleles, homozygotes = 0, grpmax FAF 0.0001976 (highest subpopulation 'Remaining individuals' AF 0.000224, 14/62,476).
• Sources searched for a de novo report and containing none: the MUTYH LOVD description paper (PMID:20725929) mentions c.42C>T only in a transcript/isoform nomenclature context with no de novo annotation; the ACMG secondary-findings policy statement (PMID:25356965), the EGAPP KRAS/BRAF tumour-testing recommendation (PMID:23429431) and the Spanish SEAP/SEOM CRC biomarker consensus (PMID:22855150) contain no MUTYH variant data at all.

Still missing

• No trio/parental testing is available for any carrier of MUTYH c.42C>T, so a de novo event cannot be formally excluded; however, the population-database and cohort evidence gives no indication of one.

Sources

Reasoning

PS3 requires well-established functional studies demonstrating a damaging effect on MUTYH protein function (Richards et al. 2015, PMID:25741868). NM_001128425.2:c.42C>T is a synonymous substitution in exon 2 of MUTYH (NP_001121897.1:p.(Ile14=)) and no functional assay of any kind has been reported for it. The MUTYH LOVD variant compendium (PMID:20725929) tabulates functional in vivo/in vitro assays performed for MUTYH variants in human transcripts (Table 2; glycosylase activity, DNA binding, complementation, MSH6 interaction, cell survival, splicing and expression) and c.42C>T is not among the entries; the variant appears in that paper only in a transcript/isoform nomenclature discussion. The only patient-level dataset (PMID:16557584) observed the codon-14 change once, in a monoallelic state, in 1 of 329 APC-mutation-negative polyposis index patients, and explicitly grouped it with 4 silent changes rather than with the 3 monoallelic variants 'of predicted functional relevance'; that grouping is a conservation/prediction judgement, not a validated assay result, and the authors provide no assay, expression or mRNA data. No in-silico output substitutes for an assay: SpliceAI returned no score for this variant (missing data, not a negative result) and the Pangolin values available (SG 0.002, SL -0.008) are not calibrated for ACMG/AMP evidence use; REVEL and BayesDel are not available for this variant and BayesDel has no established generic ACMG-strength calibration. The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis CSPEC specification for MUTYH v1.0 (doc 1742141534) was retrieved for this case but contained no structured PS3/BS3 criteria text, so the generic ACMG/AMP 2015 definition was applied. PS3 is therefore not met: the criterion fails for absence of assay evidence establishing a damaging effect, not because a functional assay has shown the variant to be harmless. Biological relevance check: the variant lies in the 5' region of MUTYH where, per PMID:20725929, variants may behave differently in the alpha, beta and gamma transcripts, so any future assay would need isoform-aware design.

Rule

ACMG/AMP 2015 PS3: well-established functional studies showing a deleterious effect are required (PMID:25741868); no gene-specific PS3 specification was available from the MUTYH InSiGHT/CSPEC framework for this case

Evidence considered

• Governing framework check: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MUTYH v1.0 (doc 1742141534) was identified for this case but was retrieved as an unstructured ruleset with an empty criteria payload, so it supplies no gene-specific PS3 specification and the generic ACMG/AMP 2015 PS3 definition was used.
• PS3 definition applied: 'Well-established functional studies show a deleterious effect' (Richards et al. 2015, PMID:25741868).
• PMID:20725929 (MUTYH LOVD) contains a dedicated table of 'Functional In Vivo and In Vitro Assays Performed for MUTYH Variants in Human Transcripts' (Table 2, starting p.1209) covering glycosylase activity, DNA binding, complementation, MSH6 interaction, cell survival, splicing and expression; c.42C>T is not listed in it, and the variant appears in the paper only in a figure-legend discussion of transcript/isoform nomenclature.
• PMID:20725929 direct quote on biological context: 'Notably, variants might have different effects on different MUTYH transcripts, like c.361325G4C/p.(spl?) ... c.39C4T/p.(=) and c.42C4T/p.(=) (near second translation start site) and c.158C4G/p.(Ala53Gly)...'; the same paper states that variants in the 5' region and start of exon 3 should be verified, at least in silico, to aid pathogenicity interpretation.
• PMID:16557584 (Aretz et al.) sequenced the full MUTYH coding region in 329 unrelated APC-mutation-negative German polyposis index patients plus 116 controls; c.42C>T was found once in a monoallelic state (1/658 patient chromosomes) and listed under 'Rare variants (identified in monoallelic state only)'. The authors state: 'However, only 3 of the patients (0.9%) harboured a mutation of predicted functional relevance (c.817delG, G382D, c.89113A>C); the other substitutions include 4 silent changes (I14, Y90, T136, T469) and 2 missense variants at unconserved sites (R295C, R412C).' This is a prediction/conservation-based classification, not an assay, so it cannot supply PS3; it also supplies no biallelic occurrence, segregation or phenotype data for this variant.
• SpliceAI lookup for NM_001128425.2:c.42C>T returned no scores (spliceai_available = false, max_delta_score null, Pangolin SG 0.002 / SL -0.008); SpliceAI missing data must not be read as a delta of 0 and cannot be used either to support a damaging effect or to assert no splice impact.
• In-silico predictors cannot substitute for PS3 here: REVEL was not found and BayesDel was not found for this variant, and BayesDel has no established generic ACMG-strength calibration; accordingly no in-silico score was used to argue a functional effect.
• Screened for functional-evidence leads in the remaining case literature: PMID:26467025 (rules-based scoring system across 338 genes) names neither MUTYH nor this variant and reports only gene-agnostic statistics (e.g. 96% of synonymous variants scored in the benign range); PMID:22855150 (SEAP/SEOM CRC biomarker consensus) lists MYH only in a gene table; PMID:23429431 (EGAPP) and PMID:25356965 (ACMG secondary-findings policy) contain no MUTYH or variant-level data. None provides assay evidence for c.42C>T.

Still missing

• No functional assay result exists for MUTYH c.42C>T (p.Ile14=): the variant is absent from the MUTYH LOVD functional-assay compendium (PMID:20725929, Table 2) and no glycosylase-activity, DNA-binding, complementation, cell-survival, expression or mRNA/splicing assay for it was found in any source retrieved for this case.
• Because the variant sits near the second translation initiation site of the alpha5 transcript, where alpha/beta/gamma isoform consequences may differ, an isoform-aware MUTYH functional assay (e.g. 8-oxoG:A glycosylase activity plus transcript-specific mRNA analysis) would be needed before PS3 could ever be applied.

Sources

Reasoning

PS4 (ACMG/AMP 2015, PMID:25741868) requires that the prevalence of the variant in affected individuals be significantly increased compared with controls. The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH v1.0 (cspec doc 1742141534) was retrieved with an empty criteria array and an empty rule_payload (framework_complete=false), so no gene-specific PS4 rule, phenotype-point scheme or numeric threshold was available and the generic ACMG/AMP criterion was applied. Direction was read from the criterion itself before any verdict: PS4-style enrichment strengthens as the value goes UP, i.e. met requires value >= threshold. The only case-level data that exist for this variant are in PMID:16557584: in 329 unselected, APC-mutation-negative German polyposis index patients, c.42C>T was detected once and only in a monoallelic (heterozygous) state (1/658 chromosomes, 0.15%); it sits in Table II under 'Rare variants (identified in monoallelic state only)', not among the 21 mutations of assumed pathogenic relevance, and is counted among four silent changes. No biallelic carrier was found in those 329 patients or among the 64 unrelated MAP patients, which is the genotype that matters for this recessive disease, and the authors state that monoallelic variants of this kind are not likely to contribute substantially to the MUTYH mutation spectrum or incidence. That study reports no c.42C>T genotype count for its 116 healthy controls (its control statement 'none was detected in 232 chromosomes of normal controls' refers to the splice variant c.89113A>C), so no study-internal odds ratio can be computed for this variant. The only comparator available is gnomAD: v2.1 total AF 9.19131e-05 (26/282876 alleles, NFE 24/129186 = 1.85779e-04, 0 homozygotes) and v4.1 total AF 1.71629e-04 (277/1613946 alleles, grpmax FAF 1.976e-04, 0 homozygotes). Substituting the numbers into the upward comparison: cross-dataset OR = (1/657)/(277/1613669) = 8.87, written out as '8.87 >= 3? yes' on the point estimate (ACMG/AMP 2015 notes that variants with a modest Mendelian effect size have an OR of 3 or greater). However, the criterion itself requires the increase to be statistically significant, and the same dataset gives two-sided Fisher exact p = 0.107, i.e. '0.107 <= 0.05? no'. The enrichment therefore fails at the only comparator available, and that estimate rests on a single case allele (Woolf 95% CI 1.24-63.28, unreliable at these cell counts). Clinically the picture is the opposite of enrichment: the case-cohort frequency (0.15%) is of the same order as the population frequency (0.017% in gnomAD v4.1), all 277 v4.1 carriers are heterozygous, and the variant was never observed in a biallelic MAP genotype. PS4 is not met.

Rule

ACMG/AMP 2015 PS4 (PMID:25741868): prevalence of the variant in affected individuals is significantly increased compared with controls; enrichment strengthens upward (met requires value >= threshold, with an OR of 3 or greater for a modest Mendelian effect size). No gene-specific InSiGHT MUTYH v1.0 PS4 rule was retrievable.

Evidence considered

• PS4 definition and requirement (ACMG/AMP 2015, PMID:25741868): prevalence of the variant in affected individuals is significantly increased compared with controls; the paper adds that 'in general, variants with a modest Mendelian effect size will have an OR of 3 or greater' and that 'showing a statistically significant difference can still be assumed to provide supportive evidence for pathogenicity'.
• Direction check performed before the verdict: PS4 strengthens upward, so met requires value >= threshold. Numbers substituted: cross-dataset OR = (1/657)/(277/1613669) = 8.87 -> '8.87 >= 3? yes' for the point estimate, but two-sided Fisher exact p = 0.107 -> '0.107 <= 0.05? no', so the required statistically significant increase is not present.
• PMID:16557584: c.42C>T was detected once, heterozygously, among 329 unselected APC-mutation-negative German polyposis index patients (1/658 chromosomes, 0.15%), listed in Table II under 'Rare variants (identified in monoallelic state only)' and counted among 4 silent changes; it is not among the 21 mutations of assumed pathogenic relevance, and no biallelic carrier was found in the 329 unselected patients or the 64 unrelated MAP patients.
• PMID:16557584 direct statement on monoallelic variants: 'because of the low incidence of monoallelic MUTYH mutations in our polyposis patients, it is not very likely that these variants contribute substantially to the mutation spectrum and incidence of MUTYH'; the authors also report that only 3 of 9 monoallelic carriers (0.9%) harboured a change of predicted functional relevance, and c.42C>T (I14) was not one of them.
• PMID:16557584 does not report a c.42C>T count for its 116 healthy anonymous blood-donor controls (232 chromosomes); the control-screening sentence in the paper belongs to the c.89113A>C splice variant, so the study supplies no internal case-control comparison for c.42C>T.
• PMID:20725929 (MUTYH LOVD) was checked for case or control counts: c.42C>T appears only in a list of 5' region/exon 2 variants whose consequences may differ between MUTYH transcripts, annotated as a silent change p.(=) near the second translation initiation site; no patient or control counts are given and the variant is absent from the paper's functional in vivo/in vitro assay table.
• gnomAD v2.1 (control arm, GRCh37 1-45800178-G-A): total AF 9.19131e-05 (26/282876 alleles), 0 homozygotes; highest ancestry European (non-Finnish) AF 1.85779e-04 (24/129186 alleles); grpmax FAF 1.303e-04.
• gnomAD v4.1 (control arm, GRCh38 chr1-45334506-G-A): total AF 1.71629e-04 (277/1613946 alleles), 0 homozygotes; highest ancestry Remaining individuals AF 2.24086e-04 (14/62476 alleles); grpmax FAF 1.976e-04. All carriers are heterozygous, so the population data document a recurrent low-frequency allele rather than disease-restricted occurrence.
• The only somatic record for the variant (COSMIC COSV104669912, n = 1) is a somatic occurrence and provides no case-control enrichment for germline disease.
• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications for MUTYH v1.0 (cspec doc 1742141534, https://cspec.genome.network/cspec/ui/svi/doc/1742141534) was identified as the applicable gene-specific framework but contains only inheritance and transcript metadata (autosomal recessive, familial adenomatous polyposis 2, MONDO:0012041; NM_001128425.2), so no VCEP PS4 rule could be applied.

Still missing

• No gene-specific PS4 rule or numeric threshold could be read from the governing InSiGHT MUTYH v1.0 specification (empty criteria/rule_payload), so the generic ACMG/AMP 2015 case-control requirement (with its OR >= 3 guide for a modest Mendelian effect) was applied instead.
• PMID:16557584 reports no control-arm genotype count for c.42C>T, so a study-internal odds ratio cannot be computed; the OR used here necessarily compares a polyposis case series against gnomAD, which is ascertainment-mismatched.
• PMID:23035301 ('MUTYH Polyposis' overview) was triaged as a PS4/PP5 candidate source but has no fetched full text and could not be searched for variant-level case or control counts.

Sources

Reasoning

PM2 (supporting) applies only when the variant is absent or at extremely low frequency in population databases, with the SVI supporting threshold at a filtering allele frequency of 0.0001 or below (PMID:25741868). NM_001128425.2:c.42C>T fails that requirement in every source view available. In the all-comers default sources: gnomAD v4.1 total AF 1.71629e-04 (277/1613946 alleles, 0 homozygotes) with grpmax FAF 1.976e-04 and highest ancestry frequency 2.24086e-04; gnomAD v2.1 total AF 9.19131e-05 (26/282876 alleles) with grpmax FAF 1.303e-04 and European (non-Finnish) frequency 1.85779e-04. The non-cancer subsets, which were checked because a specification calibrated before gnomAD v4 might mandate them, are also above threshold on the ancestry comparison that matters for PM2: gnomAD v2.1 non-cancer exomes report a total AF of 8.86293e-05 (21/236942 alleles, the exomes-only figure) but the European (non-Finnish) frequency is 1.77704e-04 and the exome grpmax FAF is 1.2097e-04; gnomAD v3.1 non-cancer genomes report AF 1.55525e-04 (23/147886) with European (non-Finnish) 3.24064e-04 and grpmax FAF 2.18e-04. gnomAD-Canada v1.0 gives 1.08613e-04 (2/18414 alleles; European non-Finnish 1.70387e-04). Only one figure in the whole case - the exome-cohort total in the gnomAD v2.1 non-cancer subset, 8.86293e-05 - falls under 0.0001, and it does so only because that subset excludes genomes and pools ancestries; the corresponding ancestry-specific and grpmax values (1.77704e-04 and 1.2097e-04) are above threshold, and with 277 carriers in gnomAD v4.1 the variant is plainly not absent from controls. Applying the highest observed ancestry-group frequency, which is the appropriate comparison for PM2 because population stratification can hide elevated risk in a single ancestry, the variant exceeds 0.0001 in every dataset and subset interrogated. PM2 is not met.

Rule

ClinGen SVI / ACMG/AMP 2015 PM2 (supporting): filtering allele frequency <= 0.0001 (PMID:25741868)

Evidence considered

• PM2 threshold applied verbatim from the supplied generic calibration block: PM2 (supporting) when frequency <= 0.0001 (SVI recommendation to downgrade PM2 to supporting; PMID:25741868).
• gnomAD v4.1 all-comers (default source): total AF 1.71629e-04 (277/1613946 alleles, 0 homozygotes); grpmax FAF 1.976e-04; highest ancestry Remaining individuals 2.24086e-04 (14/62476 alleles, 0 homozygotes).
• gnomAD v2.1 all-comers (default source): total AF 9.19131e-05 (26/282876 alleles, 0 homozygotes); grpmax FAF 1.303e-04; highest ancestry European (non-Finnish) 1.85779e-04 (24/129186 alleles, 0 homozygotes).
• gnomAD v2.1 non-cancer exomes-only subset: total AF 8.86293e-05 (21/236942 alleles, 0 homozygotes); European (non-Finnish) 1.77704e-04 (21/118174 alleles); exome grpmax FAF 1.2097e-04 - the total is the only value in the case below 0.0001, while the ancestry-specific and grpmax values are above it.
• gnomAD v3.1 non-cancer genomes-only subset (v3 has no exome cohort): total AF 1.55525e-04 (23/147886 alleles, 0 homozygotes); European (non-Finnish) 3.24064e-04 (21/64802 alleles); grpmax FAF 2.18e-04.
• gnomAD-Canada v1.0 (HostSeq genomes, 10487 genomes): AF 1.08613e-04 (2/18414 alleles, 0 homozygotes); European (non-Finnish) 1.70387e-04 (2/11738 alleles).
• The variant is present as 277 alleles in gnomAD v4.1 and 26 alleles in gnomAD v2.1, so it is not absent from controls; the highest observed ancestry-group frequency in any source is 3.24064e-04, above the 0.0001 supporting threshold.
• The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH v1.0 (cspec doc 1742141534) was consulted for any gene-specific PM2 rule or required population source; its retrieved ruleset contains only inheritance and transcript metadata (autosomal recessive, MONDO:0012041, NM_001128425.2) with no frequency criteria, so the generic ACMG/SVI default was applied.
• ACMG/AMP 2015 frames PM2 for recessive disease against the expected carrier frequency and a race-matched control population (PMID:25741868), which is the same ancestry-specific comparison used here; measured carrier frequency for this variant (roughly 1.7e-04 overall in gnomAD v4.1 with 277 alleles) is not consistent with an absent or vanishingly rare control-population observation.

Still missing

• The governing InSiGHT MUTYH v1.0 specification was retrieved with an empty criteria/rule payload (framework_complete=false), so its gene-specific PM2 frequency threshold and any mandated non-cancer or exome-only population source could not be verified; the generic ACMG/SVI supporting threshold (PM2 at <=0.0001) was applied instead. Human review is warranted because the exome-only total in the gnomAD v2.1 non-cancer subset (8.86293e-05) sits just below 0.0001, so if the specification were to require an exome-only all-comers total rather than an ancestry-specific or grpmax comparison, PM2 could flip to met at supporting strength.

Sources

Reasoning

PM3 requires that a variant be detected in trans with a pathogenic variant in a gene causing a recessive disorder. MUTYH-associated polyposis is autosomal recessive (InSiGHT / ClinGen Hereditary Colorectal Cancer-Polyposis specification, MUTYH version 1.0: MONDO:0012041 'familial adenomatous polyposis 2', 'Autosomal recessive inheritance'), so the criterion is structurally applicable to NM_001128425.2:c.42C>T (NP_001121897.1:p.(Ile14=)). No retrieved source, however, reports this variant in trans with a pathogenic MUTYH allele. The single published clinical observation is from Aretz et al. 2006 (PMID:16557584), a systematic sequencing study of the complete MUTYH coding region (exons 1-16 plus flanking intron boundaries, confirmed by independent second PCR) in 329 unselected APC-mutation-negative polyposis index patients with 116 controls: c.42C>T was detected once, in a heterozygous state (1/658 chromosomes, 0.15%), and Table II lists it explicitly under 'Rare variants (identified in monoallelic state only)', separate from the 21 entries of 'Assumed pathogenic mutations' - which, per the same table's footnote, were all but one identified in a biallelic state. The authors state that only 3 of the 329 patients (0.9%) carried a monoallelic change of predicted functional relevance (c.817delG, G382D, c.89113A>C) and place c.42C>T among the four silent changes (I14, Y90, T136, T469) that were not assigned functional relevance; the variant does not appear among the biallelic patient genotypes in Table I, and no biallelic MAP patient in that cohort carries it. The MUTYH LOVD curation paper (Out et al. 2010, PMID:20725929) mentions c.42C>T only in a list of 5' region/exon 2 variants whose consequences may differ between the alpha, beta and gamma transcripts and isoforms, and reports no patient genotype, no partner allele and no phase information; Table 2 of that paper (functional assays) does not include it. ClinVar variation 138307 carries 11 submissions (no expert-panel submission) reporting only classifications, with no cis/trans phasing or partner-allele information. The in-trans-with-a-pathogenic-variant observation that PM3 requires is therefore absent from the available evidence, and the criterion is not met.

Rule

PM3 (Richards et al. 2015, PMID:25741868): for recessive disorders, detected in trans with a pathogenic variant. Applied generically because the governing MUTYH specification (cspec doc 1742141534) contains no machine-readable PM3 rule; MUTYH inheritance mode confirmed as autosomal recessive from that specification.

Evidence considered

• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH version 1.0 (doc 1742141534) is the applicable gene-specific specification, but it is stored as an unstructured ruleset (framework_mode='unstructured_ruleset', framework_complete=false, criteria=[]) whose payload contains only gene/transcript/mode-of-inheritance metadata and no criterion-level PM3 rule text; the generic ACMG/AMP 2015 PM3 definition was therefore applied. The specification does establish the relevant inheritance mode: MUTYH / MONDO:0012041 'familial adenomatous polyposis 2', preferred mode of inheritance 'Autosomal recessive inheritance', preferred transcript NM_001128425.2.
• Criterion text applied (Richards et al. 2015, PMID:25741868): PM3 - 'For recessive disorders, detected in trans with a pathogenic variant.'
• Aretz et al. 2006 (PMID:16557584): whole-gene MUTYH sequencing in 329 unselected APC-mutation-negative polyposis index patients plus 116 controls. c.42C>T (reported as p.I14) was found in 1/658 chromosomes (0.15%) in a heterozygous state only, listed in Table II under 'Rare variants (identified in monoallelic state only)' rather than under 'Assumed pathogenic mutations'; the paper states that only 3 of 329 patients (0.9%) carried a monoallelic change of predicted functional relevance and names c.42C>T among the silent changes not assigned functional relevance; the biallelic genotypes in Table I never include it and the 21 assumed-pathogenic mutations were 'all but one ... identified in patients with a biallelic mutation state'. No trans partner allele for c.42C>T is reported anywhere in the paper.
• Aretz et al. 2006 discussion frames the monoallelic carriers as heterozygous carriers of low presumed CRC risk (monoallelic frequency of 0.9% 'in accordance with the carrier frequency in the general population (1-2%)'), i.e. not as biallelic MAP patients - so the one observation of this variant does not represent a documented trans configuration with a pathogenic MUTYH allele.
• Out et al. 2010 (PMID:20725929): MUTYH LOVD database/curation paper (291 unique variants). c.42C>T appears only in the transcript/isoform nomenclature discussion as one of the 5' region/exon 2 variants (grouped with c.39C>T) annotated as a silent change near the second translation initiation site and recommended for at least in-silico verification because of differential alpha/beta/gamma transcript effects. No patient genotype, no second/partner allele and no phase information is given, and the variant is absent from the paper's functional assay table.
• ClinVar variation 138307 (exact match to NM_001128425.2(MUTYH):c.42C>T (p.Ile14=), ClinVarID = 138307): 11 submissions from 8 submitters, none expert-panel or VCEP; classifications range from Benign (1 laboratory) and Likely benign (5) to Uncertain significance (2). Submission-level evidence signals mention only in-silico/prediction criteria (PP3-type text), and no submission reports a cis/trans phase determination or a partner pathogenic allele, so the record contributes no allelic evidence for PM3.
• No evidence source in this case reports c.42C>T co-occurring with any MUTYH pathogenic variant in a phase-resolved manner, and none reports the variant as homozygous.

Still missing

• Formal cis/trans phasing of c.42C>T against a pathogenic MUTYH allele is not reported in any retrieved source; the single documented carrier's second allele was not characterised, so a rare in-trans configuration cannot be formally excluded.
• No cohort with phase-resolved (family or allele-specific) MUTYH genotyping names this variant; resolving this would require allele-specific or pedigree-based phase data that do not exist in this case.
• No PM3-directed literature search was performed for this case; the allelic assessment rests on the ClinVar-cited papers (PMID:16557584, PMID:20725929) plus the ClinVar record itself.

Sources

Reasoning

PM6 (Richards et al. 2015, PMID:25741868) requires an assumed de novo occurrence, i.e. a case in which the variant is present in the proband but absent from the tested parents, without confirmation of paternity and maternity. No such case is reported for MUTYH NM_001128425.2:c.42C>T (NP_001121897.1:p.(Ile14=)). No proband or parental genotyping data exist in this case, and the variant-specific literature does not describe it as de novo in any patient: Aretz et al. 2006 (PMID:16557584) detected it in the heterozygous state in only 1 of 329 unrelated APC-mutation-negative polyposis index patients (1/658 chromosomes, 0.15%), alongside three other silent changes and two unconserved missense substitutions that the authors did not assign functional relevance; no family members were tested for this variant. The allele is also present in population reference data (gnomAD v2.1 26/282,876 alleles; gnomAD v4.1 277/1,613,946 alleles; 0 homozygotes in both), indicating an inherited, transmitted allele rather than a de novo event, and MUTYH-associated disease is autosomal recessive, so a single heterozygous allele would not satisfy the disease-consistent requirement of the criterion. Because the affirmative requirement — an assumed de novo observation — is absent from every source, PM6 is not met rather than unassessable. The governing InSiGHT specification provides no criterion-level PM6 rule, so generic ACMG/AMP 2015 applies.

Rule

PM6 (Richards et al. 2015, PMID:25741868): assumed de novo, but without confirmation of paternity and maternity. Pathogenic Moderate.

Evidence considered

• PM6 rule text (Richards et al. 2015, PMID:25741868): assumed de novo, but without confirmation of paternity and maternity; Pathogenic Moderate.
• Aretz et al. 2006 (PMID:16557584): 329 unselected APC-mutation-negative German polyposis index patients plus 116 controls, whole MUTYH coding region sequenced; c.42C>T observed once, monoallelic, 1/658 chromosomes (0.15%), Table II 'Rare variants (identified in monoallelic state only)', Exon 2. No parental or relative testing for this variant is reported anywhere in the paper.
• gnomAD v2.1 and v4.1 (source keys gnomad_v2, gnomad_v4): total AF 9.19131e-05 (26/282,876) and 1.71629e-04 (277/1,613,946) respectively, with 0 homozygotes in each dataset — an inherited allele present in the adult population, not a de novo observation.
• MUTYH LOVD (PMID:20725929): c.42C>T appears only in a list of 5' region/exon 2 variants whose consequences may differ between the alpha, beta and gamma transcripts, annotated p.(=); no de novo or family annotation is provided.
• Governing specification check: the InSiGHT MUTYH v1.0 CSPEC was retrieved but returned an empty criteria array and empty rule_payload (framework_complete=false), so no gene-specific PM6 specification overrides the generic criterion.

Still missing

• No proband-parent genotype data (even unconfirmed-parentage trio data) exist for this variant in any assembled source, so absence of a de novo observation rests on the completeness of the two variant-specific publications and the population databases.

Sources

Reasoning

PP5 applies only when a reputable source reports the variant as pathogenic, and under the required rule for this group that means an exact-variant ClinVar expert-panel classification (Pathogenic or Likely pathogenic); ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions must never trigger it. The exact-variant ClinVar record is VCV000138307 for NM_001128425.2(MUTYH):c.42C>T (p.Ile14=). Its submission audit records 11 submissions from 11 submitters with is_expert_panel=false for every single one and an empty expert_panels map; the overall review status is 'criteria provided, conflicting classifications' (1 star, last updated 2026-05-30). The submissions are ordinary clinical laboratories and curation groups (5 Likely benign, 2 Uncertain significance, 1 Benign, plus two further Likely benign spellings), i.e. precisely the aggregate laboratory assertions that are excluded from PP5. No ClinGen InSiGHT MUTYH VCEP assertion for this variant exists in the record, and the gene-specific InSiGHT MUTYH v1.0 specification returned no criteria text at all. There is therefore no exact-variant expert-panel Pathogenic or Likely pathogenic classification to support PP5, and PP5 is not met.

Rule

PP5 requires an exact-variant ClinVar expert-panel (VCEP) classification of Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions never trigger it. No gene-specific InSiGHT MUTYH v1.0 PP5 rule was retrievable.

Evidence considered

• PP5 rule applied: only an exact-variant ClinVar expert-panel (VCEP) classification of Pathogenic or Likely pathogenic may trigger PP5; ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions are excluded. The ACMG/AMP 2015 criterion (PMID:25741868) is the underlying framework for PP5 as 'reputable source' evidence.
• ClinVar exact-variant record VCV000138307 (NM_001128425.2(MUTYH):c.42C>T, p.Ile14=; variation ID 138307): 11 submissions from 11 submitters, is_expert_panel=false for all, expert_panels empty, review status 'criteria provided, conflicting classifications' (1 star), date last updated 2026-05-30.
• ClinVar submission composition: 5 clinical laboratories report Likely benign, 2 report Uncertain significance, 1 reports Benign and 2 report Likely benign (spelling variants); none of these submitters is an expert panel, and none is a Pathogenic or Likely pathogenic assertion.
• The aggregate ClinVar label (Likely benign as scraped, or 'Conflicting classifications of pathogenicity' via the API) is an aggregate of ordinary lab submissions and was not used as PP5 evidence.
• Governing framework: the InSiGHT MUTYH v1.0 specification (cspec doc 1742141534) was retrieved with an empty criteria array and empty rule_payload, so no gene-specific PP5 rule or strength modification could be applied; the generic expert-panel-only rule for this criterion group was used.

Still missing

• PMID:23035301 ('MUTYH Polyposis' GeneReviews-style overview) was triaged as a PP5/PS4 candidate source but has no fetched full text, so it could not be searched for a variant-level pathogenic assertion; in any case a gene-disease overview does not satisfy the exact-variant expert-panel requirement applied here.
• If the ClinGen InSiGHT MUTYH VCEP publishes a classification for this exact variant after the ClinVar snapshot used here (record last updated 2026-05-30), PP5 would need to be re-run.

Sources

Reasoning

BA1 (stand-alone benign) requires an allele frequency at or above 0.05 (ACMG/AMP 2015, PMID:25741868). NM_001128425.2:c.42C>T (MUTYH, p.(Ile14=)) is present in every population dataset interrogated for this case, but always at a frequency 100-fold or more below that threshold. gnomAD v4.1 all-comers: total AF 1.71629e-04 (277/1613946 alleles, 0 homozygotes), highest ancestry frequency 2.24086e-04 (Remaining individuals, 14/62476), grpmax FAF 1.976e-04. gnomAD v2.1 all-comers: total AF 9.19131e-05 (26/282876 alleles, 0 homozygotes), highest ancestry frequency 1.85779e-04 (European non-Finnish, 24/129186), grpmax FAF 1.303e-04. The non-cancer subsets do not raise the frequency appreciably: gnomAD v2.1 non-cancer exomes (exome figures only) AF 8.86293e-05 (21/236942, 0 homozygotes) with NFE 1.77704e-04 and grpmax FAF 1.2097e-04; gnomAD v3.1 non-cancer genomes (v3 has no exome cohort) AF 1.55525e-04 (23/147886, 0 homozygotes) with NFE 3.24064e-04 and grpmax FAF 2.18e-04. gnomAD-Canada v1.0 (HostSeq genomes) reports the variant at 1.08613e-04 (2/18414 alleles, 0 homozygotes; NFE 1.70387e-04). The highest frequency observed in any ancestry group in any source is 3.24064e-04, roughly 150-fold below the 0.05 stand-alone threshold, and no ancestry reaches even 1e-03. Because the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH v1.0 was retrieved with an empty criteria/rule payload (framework_complete=false, framework_mode=unstructured_ruleset), no gene-specific BA1 threshold or mandated population source could be applied, and the generic ACMG/AMP 2015 threshold was used; every available source (all-comers and non-cancer alike) is equally decisive, so this gap does not affect the call. BA1 is not met.

Rule

ACMG/AMP 2015 BA1: stand-alone benign when allele frequency >= 0.05 (PMID:25741868)

Evidence considered

• gnomAD v2.1 all-comers (GRCh37 1-45800178-G-A): total AF 9.19131e-05 (26/282876 alleles), 0 homozygotes; highest ancestry European (non-Finnish) AF 1.85779e-04 (24/129186 alleles, 0 homozygotes); grpmax FAF 1.303e-04.
• gnomAD v4.1 all-comers (GRCh38 chr1-45334506-G-A): total AF 1.71629e-04 (277/1613946 alleles), 0 homozygotes; highest ancestry Remaining individuals AF 2.24086e-04 (14/62476 alleles, 0 homozygotes); grpmax FAF 1.976e-04.
• gnomAD v2.1 non-cancer subset reported by its exomes-only figures (0 homozygotes): AF 8.86293e-05 (21/236942 alleles); highest ancestry European (non-Finnish) AF 1.77704e-04 (21/118174 alleles); exome grpmax FAF 1.2097e-04.
• gnomAD v3.1 non-cancer subset (genomes only, since v3 has no exome cohort): AF 1.55525e-04 (23/147886 alleles), 0 homozygotes; highest ancestry European (non-Finnish) AF 3.24064e-04 (21/64802 alleles); grpmax FAF 2.18e-04.
• gnomAD-Canada v1.0 (HostSeq genomes; 10487 genomes in dataset): AF 1.08613e-04 (2/18414 alleles), 0 homozygotes; European (non-Finnish) 1.70387e-04 (2/11738 alleles).
• BA1 threshold applied verbatim from the supplied generic calibration block: allele frequency >= 0.05 (ACMG/AMP 2015 stand-alone benign criterion; PMID:25741868).
• Across all six gnomAD v2.1/v4.1/non-cancer/Canada source views the maximum ancestry-group frequency is 3.24064e-04, approximately 150-fold below 0.05, so no dataset or subset approaches the stand-alone benign threshold.
• Governing framework consulted: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MUTYH, Version 1.0 (cspec doc 1742141534, svi_url https://cspec.genome.network/cspec/ui/svi/doc/1742141534); the retrieved ruleset declares autosomal recessive inheritance for familial adenomatous polyposis 2 (MONDO:0012041) but contains no structured BA1 rule, so the generic ACMG/AMP threshold was applied.

Sources

Reasoning

BS1 (strong benign) requires an allele frequency greater than the frequency expected for the disorder, with the generic SVI default set at 0.01 (Whiffin et al. 2017, PMID:28518168). Every population observation for NM_001128425.2:c.42C>T is two to three orders of magnitude below that value. gnomAD v4.1 all-comers total AF 1.71629e-04 (277/1613946 alleles, 0 homozygotes), highest ancestry frequency 2.24086e-04 (Remaining individuals), grpmax FAF 1.976e-04. gnomAD v2.1 all-comers total AF 9.19131e-05 (26/282876), highest ancestry European (non-Finnish) 1.85779e-04 (24/129186), grpmax FAF 1.303e-04. Non-cancer subsets, which were evaluated explicitly in case the specification mandated them, give the same answer: gnomAD v2.1 non-cancer exomes AF 8.86293e-05 (21/236942, 0 homozygotes) with NFE 1.77704e-04 and exome grpmax FAF 1.2097e-04; gnomAD v3.1 non-cancer genomes AF 1.55525e-04 (23/147886, 0 homozygotes) with NFE 3.24064e-04 and grpmax FAF 2.18e-04. gnomAD-Canada v1.0 adds 2/18414 alleles (AF 1.08613e-04). The single highest ancestry-group frequency anywhere is 3.24064e-04, about 30-fold below 0.01. The governing InSiGHT MUTYH v1.0 specification returned an empty criteria payload, so its gene-specific BS1 threshold (and any requirement to use a non-cancer or exome-only source) could not be read; the generic default was applied, and no plausible source selection changes the verdict. BS1 is not met.

Rule

ACMG/AMP 2015 BS1: strong benign when allele frequency > expected for the disorder; generic default threshold >= 0.01 (Whiffin et al. 2017, PMID:28518168)

Evidence considered

• BS1 threshold applied from the supplied generic calibration block: allele frequency >= 0.01, the generic SVI default with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168); the BS1 criterion itself derives from ACMG/AMP 2015 (PMID:25741868).
• gnomAD v2.1 all-comers: total AF 9.19131e-05 (26/282876 alleles, 0 homozygotes); highest ancestry European (non-Finnish) 1.85779e-04 (24/129186 alleles); grpmax FAF 1.303e-04.
• gnomAD v4.1 all-comers: total AF 1.71629e-04 (277/1613946 alleles, 0 homozygotes); highest ancestry Remaining individuals 2.24086e-04 (14/62476 alleles); grpmax FAF 1.976e-04.
• gnomAD v2.1 non-cancer exomes-only subset: AF 8.86293e-05 (21/236942 alleles, 0 homozygotes); NFE 1.77704e-04 (21/118174 alleles); grpmax FAF 1.2097e-04.
• gnomAD v3.1 non-cancer genomes-only subset: AF 1.55525e-04 (23/147886 alleles, 0 homozygotes); NFE 3.24064e-04 (21/64802 alleles); grpmax FAF 2.18e-04.
• gnomAD-Canada v1.0 (HostSeq genomes): AF 1.08613e-04 (2/18414 alleles, 0 homozygotes); NFE 1.70387e-04.
• The maximum ancestry-group frequency across all sources (3.24064e-04, gnomAD v3.1 non-cancer NFE) is about 30-fold below 0.01, so BS1 is not met under either the all-comers default or a non-cancer/exome-only population source.
• MUTYH-associated disease is autosomal recessive (governing specification ruleset, MONDO:0012041 familial adenomatous polyposis 2), so a benign-frequency threshold would in principle be set relative to disease allele frequency rather than a dominant-disorder prevalence; even the generic 0.01 strong-benign default is unreachable here, let alone a value derived for a recessive disorder, which would be higher.
• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH v1.0 (cspec doc 1742141534) retrieved with an empty criteria/rule payload, so no gene-specific BS1 threshold or mandated population source was available.

Sources

Reasoning

BS2 requires the variant to be observed in a healthy adult individual: for a recessive condition, in the homozygous state, and only where full penetrance is expected at an early age. MUTYH is the recessive gene here - the governing specification's ruleset assigns autosomal recessive inheritance to familial adenomatous polyposis 2 (MONDO:0012041) - so the criterion hinges on a homozygous healthy-adult observation, and none exists. Homozygote counts are zero in every dataset interrogated: gnomAD v4.1 0/1613946 alleles (277 carriers, all heterozygous), gnomAD v2.1 0/282876 (26 carriers), gnomAD v2.1 non-cancer exomes 0/236942 (21 carriers), gnomAD v3.1 non-cancer genomes 0/147886 (23 carriers), and gnomAD-Canada v1.0 0/18414 (2 carriers). The literature is consistent with this: in a systematic sequencing study of 329 unrelated APC-mutation-negative polyposis index patients, c.42C>T was identified only in a monoallelic (heterozygous) state, once (1/658 chromosomes), and was classified among silent changes without predicted functional relevance, never as a biallelic MAP genotype (PMID:16557584, Table II). Independently, the second half of BS2's premise is also unmet for this gene: MUTYH-associated polyposis shows incomplete penetrance and adult onset, so the 'full penetrance expected at an early age' condition that BS2 assumes does not hold. With no homozygous observation in any population cohort and no early-onset fully penetrant recessive disease model, BS2 is not met.

Rule

ACMG/AMP 2015 BS2: observed in a healthy adult individual, homozygous for a recessive condition, with full penetrance expected at an early age (PMID:25741868)

Evidence considered

• BS2 definition (ACMG/AMP 2015, PMID:25741868): observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) condition, with full penetrance expected at an early age.
• Inheritance context from the governing specification ruleset (cspec doc 1742141534): MUTYH / familial adenomatous polyposis 2 (MONDO:0012041) is assigned autosomal recessive inheritance with NM_001128425.2 as the preferred transcript, so the recessive (homozygous) branch of BS2 applies.
• Homozygote counts are zero in every population source: gnomAD v4.1 0/1613946 alleles (277 heterozygous carriers); gnomAD v2.1 0/282876 alleles (26 carriers); gnomAD v2.1 non-cancer exomes 0/236942 alleles (21 carriers); gnomAD v3.1 non-cancer genomes 0/147886 alleles (23 carriers); gnomAD-Canada v1.0 (HostSeq) 0/18414 alleles (2 carriers).
• PMID:16557584: c.42C>T was found only once and only in a monoallelic (heterozygous) state among 329 unrelated APC-mutation-negative German polyposis index patients (1/658 chromosomes, 0.15%), listed under 'Rare variants (identified in monoallelic state only)' in Table II and counted among 4 silent changes without predicted functional relevance; no biallelic carrier was reported.
• PMID:20725929 (MUTYH LOVD description paper) mentions c.42C>T only as a silent change p.(=) near the second translation initiation site, in the context of transcript/isoform nomenclature; it reports no homozygous carrier and no healthy-adult homozygous observation.
• MUTYH-associated polyposis has incomplete penetrance and adult onset, so the 'full penetrance expected at an early age' precondition of BS2 is not satisfied even before the homozygous-observation requirement is considered.
• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH v1.0 (cspec doc 1742141534) retrieved with an empty criteria/rule payload, so no gene-specific BS2 modification (for example a recessive-specific homozygote rule) could be applied.

Sources

Reasoning

BS3 requires well-established functional studies demonstrating that a variant has no damaging effect on protein function (Richards et al. 2015, PMID:25741868). NM_001128425.2:c.42C>T is a synonymous substitution (NP_001121897.1:p.(Ile14=)) in exon 2 of MUTYH and no functional assay demonstrating preserved MUTYH function has been performed on it. As with PS3, the MUTYH LOVD functional-assay compendium (PMID:20725929, Table 2) contains no glycosylase-activity, DNA-binding, complementation, cell-survival or expression/splicing result for this variant, so there is no validated assay evidence of normal function to cite. The nearest published statement is that of PMID:16557584, which counted the codon-14 silent change among 4 silent changes not assigned 'predicted functional relevance'; that conclusion was reached from conservation and consequence class rather than from a validated assay, and it therefore cannot establish BS3, which by definition requires a functional study. The in-silico outputs available for this variant cannot substitute for such an assay: SpliceAI produced no score (missing data that must not be treated as a delta of 0, i.e. not evidence of an absent splice effect) and Pangolin SG 0.002/SL -0.008 is not calibrated for ACMG/AMP use. Biological relevance also argues against a confident 'no damaging effect' assertion from generic evidence: per PMID:20725929, c.42C>T lies in the MUTYH 5' region near the second translation initiation site, where variants 'might have different effects on different MUTYH transcripts' (alpha, beta, gamma) and should be verified at least in silico, so a synonymity-based benign functional inference is not secure. The governing MUTYH InSiGHT/CSPEC specification v1.0 held no structured BS3 text, so the generic ACMG/AMP 2015 definition applies. BS3 is therefore not met: the criterion fails for absence of functional-assay evidence of preserved function, not because an assay has shown a damaging effect.

Rule

ACMG/AMP 2015 BS3: well-established functional studies showing no deleterious effect are required (PMID:25741868); no gene-specific BS3 specification was available from the MUTYH InSiGHT/CSPEC framework for this case

Evidence considered

• Governing framework check: the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MUTYH v1.0 (doc 1742141534) was identified for this case but contained no structured BS3 criteria text, so the generic ACMG/AMP 2015 BS3 definition was applied.
• BS3 definition applied: 'Well-established functional studies show no deleterious effect' (Richards et al. 2015, PMID:25741868).
• PMID:20725929 (MUTYH LOVD) Table 2, 'Functional In Vivo and In Vitro Assays Performed for MUTYH Variants in Human Transcripts' (glycosylase activity, DNA binding, complementation, MSH6 interaction, cell survival, splicing, expression), contains no entry for c.42C>T; the variant is discussed only in the context of transcript/isoform nomenclature, with the statement that such 5' region variants should be verified, at least in silico, to aid pathogenicity interpretation. No benign functional result is reported for it anywhere in that paper.
• PMID:16557584 direct quote: 'However, only 3 of the patients (0.9%) harboured a mutation of predicted functional relevance (c.817delG, G382D, c.89113A>C); the other substitutions include 4 silent changes (I14, Y90, T136, T469) and 2 missense variants at unconserved sites (R295C, R412C).' The codon-14 change is thus grouped with silent changes on the basis of predicted consequence, not an assay; the paper reports no expression, mRNA or enzyme-activity measurement for it.
• SpliceAI lookup for NM_001128425.2:c.42C>T returned no scores (max_delta_score null; Pangolin SG 0.002, SL -0.008). This is missing data and was explicitly not used as evidence of an absent splice effect.
• Screened the remaining case literature for assay-based benign functional evidence: PMID:26467025 (338-gene scoring system; names neither MUTYH nor this variant), PMID:22855150 (MYH appears only in a hereditary-CRC gene table), PMID:23429431 (EGAPP somatic CRC pharmacogenomics; MUTYH not mentioned) and PMID:25356965 (ACMG secondary-findings policy; MUTYH not mentioned) provide no functional data bearing on this variant.
• Biological-relevance check for a synonymous change: the substitution does not alter the isoleucine-14 codon or a canonical splice site, but it sits immediately upstream of/at the region involved in the second translation initiation site usage described in PMID:20725929, so a generic 'synonymous change is harmless' inference was not treated as functional evidence for BS3.

Still missing

• No functional assay result exists for MUTYH c.42C>T (p.Ile14=), so absence of a damaging effect cannot be demonstrated: the variant is missing from the MUTYH LOVD functional in vivo/in vitro assay table (PMID:20725929, Table 2) and from all other sources retrieved for this case.
• A MUTYH-isoform-aware functional assay (alpha/beta/gamma transcript effects plus 8-oxoG:A glycosylase activity) is required before BS3 could be applied, given that this 5' region variant may have transcript-specific consequences.
• SpliceAI produced no score for this variant, so the splicing component of any BS3 argument is unresolved rather than negative.

Sources

Reasoning

BP2 is satisfied when a variant is observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern. The dominant-gene clause is inapplicable here: MUTYH-associated disease is autosomal recessive (InSiGHT / ClinGen Hereditary Colorectal Cancer-Polyposis specification, MUTYH version 1.0: MONDO:0012041, 'Autosomal recessive inheritance'), and no dominant MUTYH disorder is specified anywhere in the available sources. For the cis clause, no retrieved source provides any phase information for NM_001128425.2:c.42C>T (NP_001121897.1:p.(Ile14=)) relative to a pathogenic MUTYH allele. Aretz et al. 2006 (PMID:16557584) lists the variant among rare variants observed only in a monoallelic state (1/658 chromosomes, 0.15%) and it never appears in the biallelic genotypes of Table I, meaning it was never seen alongside any of the assumed-pathogenic alleles in a phase-resolved genotype; the authors did not determine, however, whether the single carrier's other allele bore a pathogenic variant. Out et al. 2010 (PMID:20725929) gives no genotype or phase data for the variant at all, and none of the 11 ClinVar submissions for variation 138307 (no expert-panel submission) reports a cis configuration. A specific observation of c.42C>T in cis with a pathogenic MUTYH variant - the only configuration by which BP2 could apply in this recessive gene - has therefore not been made in any source, so BP2 is not met on the available evidence.

Rule

BP2 (Richards et al. 2015, PMID:25741868): observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern. Applied generically because the governing MUTYH specification (cspec doc 1742141534) contains no machine-readable BP2 rule; MUTYH inheritance mode confirmed as autosomal recessive from that specification.

Evidence considered

• Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis specification for MUTYH version 1.0 (doc 1742141534) is the applicable gene-specific specification but carries no machine-readable criterion-level rule text (framework_mode='unstructured_ruleset', framework_complete=false, criteria=[]); it does define the gene's inheritance mode as autosomal recessive (MONDO:0012041 'familial adenomatous polyposis 2'), which removes the dominant-disorder clause of BP2 from consideration. The generic ACMG/AMP 2015 BP2 definition was therefore applied.
• Criterion text applied (Richards et al. 2015, PMID:25741868): BP2 - 'Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.'
• Aretz et al. 2006 (PMID:16557584): MUTYH whole-gene sequencing in 329 APC-mutation-negative polyposis index patients and 116 controls. c.42C>T (p.I14) is listed under 'Rare variants (identified in monoallelic state only)' in Table II at 1/658 chromosomes (0.15%); it is not among the assumed-pathogenic mutations, not among the biallelic genotypes of Table I (the 64 index patients with biallelic mutations all carry other alleles, predominantly Y165C/G382D), and the authors did not phase it against any pathogenic allele. No cis co-occurrence with a pathogenic variant is reported.
• Out et al. 2010 (PMID:20725929): the MUTYH LOVD curation paper mentions c.42C>T only in transcript/isoform nomenclature context (5' region/exon 2 variants, near the second translation start site, with a caution to verify such variants at least in silico) and provides no genotype, no partner allele and no phase information; no functional assay was performed on it.
• ClinVar variation 138307: 11 submissions from 8 submitters, no expert-panel submission; classifications are predominantly benign/likely benign (Benign 1, Likely benign 5) with 2 Uncertain significance. No submission text, criterion list or evidence signal reports c.42C>T in cis (or trans) with a pathogenic MUTYH allele, so the record cannot support BP2.
• Cis/trans configurations are the only allelic configurations relevant to BP2 in this gene: because MUTYH disease is recessive, the 'in trans with a pathogenic variant for a fully penetrant dominant disorder' clause is structurally unavailable, leaving only 'in cis with a pathogenic variant', for which no observation exists.

Still missing

• No cis/trans phasing data exist for c.42C>T with any pathogenic MUTYH allele in the retrieved sources, so the cis configuration BP2 requires is unobserved rather than formally refuted.
• No haplotype-resolved or family-based phase data, and no long-read/allele-specific sequencing, were available for this variant in this case.
• No BP2-directed literature search was performed; the assessment rests on PMID:16557584, PMID:20725929 and the ClinVar record.

Sources

Reasoning

BP5 (ACMG/AMP 2015, PMID:25741868) applies when the variant is found in a case with an alternate molecular basis for the disease. No such case is documented anywhere in the available evidence. This case contributes no case-level data at all: it is a variant-level query with no co-tested genes, no genotype and no phenotype. In the only published series that genotyped c.42C>T (PMID:16557584), the carrier was one of 329 patients selected precisely because APC mutation screening had been negative, so an alternate molecular basis was excluded by design rather than documented, and the same series concludes that monoallelic variants of this type are unlikely to contribute substantially to the MUTYH mutation spectrum or incidence. The ClinVar submission trail for this variant includes a submission (Quest Diagnostics) citing a lethal-prostate-cancer genomics study (PMID:31874108, Mateo et al., J Clin Invest 2020), but that paper does not name this variant in its abstract, was not retrieved in full text, and a somatic driver in a prostate tumour cannot serve as an alternate germline molecular basis for MUTYH-associated polyposis. The only other somatic record for the variant (COSMIC COSV104669912, n = 1) is likewise a somatic occurrence rather than a documented alternate germline basis. With no case having a documented alternate genetic explanation for disease, BP5 is not met; this must not be read as evidence that the variant is pathogenic.

Rule

ACMG/AMP 2015 BP5 (PMID:25741868): supporting benign evidence when the variant is found in a case with an alternate molecular basis for disease. No gene-specific InSiGHT MUTYH v1.0 BP5 rule was retrievable.

Evidence considered

• BP5 definition (ACMG/AMP 2015, PMID:25741868): supporting benign evidence when the variant is found in a case with an alternate molecular basis for disease; the case must have a documented separate genetic explanation.
• No case-level data exist in this case file: the input is a variant-level query, with no co-testing result, genotype, phenotype or alternate-gene result recorded.
• PMID:16557584: the single published carrier was among 329 unselected APC-mutation-negative polyposis index patients (variant monoallelic, 1/658 chromosomes, 0.15%); APC had been excluded in that cohort by design, so no alternate basis was documented for that patient, and the authors state it is not likely that monoallelic variants such as this one contribute substantially to the MUTYH mutation spectrum or incidence.
• ClinVar submission trail for VCV000138307: the Quest Diagnostics submission cites PMID:31874108 (lethal prostate cancer genomics, Mateo et al.), whose abstract does not name c.42C>T; no full text of that paper was retrieved for this case, and somatic prostate-tumour drivers (TP53, PTEN, BRCA2, CDK12, ATM) are not an alternate germline molecular basis for MUTYH-associated polyposis.
• The only somatic record for the variant (COSMIC COSV104669912, n = 1 occurrence) describes a somatic context, not a case with an alternate germline molecular basis, so it does not support BP5.
• Governing framework: the InSiGHT MUTYH v1.0 specification (cspec doc 1742141534) was retrieved with an empty criteria array and empty rule_payload, so any gene-specific BP5 restriction or numeric threshold could not be read; the generic ACMG/AMP definition was applied.

Still missing

• No individual-level or panel-level genotype results exist in this case, so an alternate molecular basis (for example a pathogenic variant in another colorectal polyposis gene) could only be assessed if such data were provided.
• PMID:16557584 does not identify the individual carrier of c.42C>T, nor report any co-existing pathogenic variant in another gene for that patient; PMID:31874108 was not available in full text and does not name the variant in its abstract.
• The InSiGHT MUTYH v1.0 rule payload is empty, so it is unknown whether the gene-specific specification narrows BP5 (for example to specified alternate polyposis genes or to a likelihood-ratio threshold); the generic ACMG/AMP definition was used.

Sources

Reasoning

BP6 applies only when a reputable source reports the variant as benign, and under the required rule for this group that means an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions must never trigger it. The exact-variant record VCV000138307 (NM_001128425.2(MUTYH):c.42C>T, p.Ile14=) contains no expert-panel submission whatsoever: all 11 submissions carry is_expert_panel=false, expert_panels is empty, and the review status is 'criteria provided, conflicting classifications' (1 star, last updated 2026-05-30). Benign-side labels do exist, but only from ordinary laboratories: 5 clinical laboratories report Likely benign, 1 reports Benign and 2 report Likely benign (spelling variants), and the aggregated/majority label is Likely benign. None of those is an expert-panel assertion, so the benign direction of the ClinVar signal cannot be counted. BP6 is not met, and this status must not be read as evidence that the variant is pathogenic.

Rule

BP6 requires an exact-variant ClinVar expert-panel (VCEP) classification of Benign or Likely benign; ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions never trigger it. No gene-specific InSiGHT MUTYH v1.0 BP6 rule was retrievable.

Evidence considered

• BP6 rule applied: only an exact-variant ClinVar expert-panel (VCEP) classification of Benign or Likely benign may trigger BP6; ordinary laboratory submissions, aggregate ClinVar labels and non-expert assertions are excluded. The ACMG/AMP 2015 criterion (PMID:25741868) is the underlying framework for BP6 as 'reputable source' benign evidence.
• ClinVar exact-variant record VCV000138307 (variation ID 138307): 11 submissions from 11 submitters, is_expert_panel=false for all, expert_panels empty, review status 'criteria provided, conflicting classifications' (1 star), date last updated 2026-05-30; submission audit counts 0 expert-panel submissions, 8 usable for classification and 4 usable as criterion leads.
• Benign-side ClinVar submissions are all from ordinary laboratories: 5 Likely benign (Ambry Genetics, Sema4, Labcorp Genetics/Invitae, Color Diagnostics, Labcorp), 1 Benign (GeneDx), and 2 Likely benign spelling variants (All of Us Research Program; Quest Diagnostics), plus 2 Uncertain significance submissions; the aggregate/majority label is Likely benign.
• The aggregate ClinVar label and the individual single-submitter laboratory classifications were explicitly not used to satisfy BP6, because the criterion requires an exact-variant expert-panel assertion.
• Governing framework: the InSiGHT MUTYH v1.0 specification (cspec doc 1742141534) was retrieved with an empty criteria array and empty rule_payload, so no gene-specific BP6 rule or strength could be applied; the generic expert-panel-only rule for this criterion group was used.

Still missing

• If the ClinGen InSiGHT MUTYH VCEP issues an exact-variant Benign or Likely benign classification after the ClinVar snapshot used here (record last updated 2026-05-30), BP6 would need to be re-run.
• The InSiGHT MUTYH v1.0 specification was retrieved without criteria text, so it is unknown whether it permits BP6 at a specified strength or requires a different reputable-source class than the expert-panel rule applied here.

Sources

Reasoning

PP1 (Richards et al. 2015, PMID:25741868) requires co-segregation of the variant with disease in multiple affected family members in a gene definitively known to cause the disease; the generic criterion has no numeric meiosis/LOD threshold, and the governing ClinGen InSiGHT MUTYH specification supplies no PP1 rule (empty criteria array, framework_complete=false). No pedigree, proband, or family-member genotype data were assembled for this case, which is a variant-level query: there is no affected relative genotyped for c.42C>T and therefore no meiosis count, no segregation table, and no LOD score to evaluate. The variant-specific literature cannot substitute: Aretz et al. 2006 (PMID:16557584) reports only allele counts (1/329 index patients, monoallelic) and its single segregation analysis concerns a different variant (ten relatives of index family no. 26 screened for the in-frame deletion p.466delE), while Veldman/Out et al.'s MUTYH LOVD paper (PMID:20725929) lists c.42C>T only in a transcript/isoform nomenclature discussion with no pedigree data. Because the required data type was never generated, PP1 is unassessable rather than failed — absence of a segregation study is not evidence of non-segregation. Note also that MUTYH-associated disease is autosomal recessive, so any future segregation assessment must consider biallelic status rather than simple variant-disease co-segregation.

Rule

PP1 (Richards et al. 2015, PMID:25741868): co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Pathogenic Supporting.

Evidence considered

• PP1 rule text (Richards et al. 2015, PMID:25741868): co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease; Pathogenic Supporting. No meiosis or LOD threshold is specified by the generic criterion, the governing InSiGHT MUTYH specification provides no PP1 rule, and no published segregation threshold for MUTYH was retrieved, so PP1 was evaluated qualitatively for the presence of family data only.
• Aretz et al. 2006 (PMID:16557584): the only family-based analysis in the paper screened ten siblings and parents of index family no. 26 for the in-frame mutation p.466delE ('in all cases, the results were consistent with autosomal recessive inheritance'); nothing comparable was done for c.42C>T, which is reported only as an allele count (Table II, Exon 2, monoallelic, 1/658 chromosomes).
• MUTYH LOVD (PMID:20725929): searched for family/pedigree entries for c.42C>T; the variant appears only in the Figure 1 legend list of 5' region variants with transcript-dependent consequences ('c.39C4T/p.(=) and c.42C4T/p.(=) (near second translation start site)'), with no patient count, family data or segregation information.
• Case-evidence search: the consolidated case evidence contains no occurrence of segregation, pedigree, proband, parental-testing, trio, meioses, or family-history terms for this variant, and no ClinVar submission criterion lead addresses PP1 (criterion leads cite only PMID:16557584, PMID:20725929, PMID:31874108).

Still missing

• No pedigree or genotyped relatives (affected or unaffected) carrying MUTYH c.42C>T, so the number of informative meioses and any co-segregation or LOD evidence are unavailable.
• The case input contains no proband phenotype, family history, or sample provenance, so even a minimal segregation narrative cannot be constructed.

Sources

Reasoning

PP4 (ACMG/AMP 2015, PMID:25741868) requires that the patient's phenotype or family history be highly specific for a disease with a single genetic etiology. This case is a variant-level query: no proband phenotype, family history, age at onset, adenoma count or genotype data are recorded anywhere in the case evidence, so the patient-level prerequisite of PP4 cannot be evaluated at all. The closest available phenotype material is cohort-level or submission-level rather than proband-level: the only published carrier of c.42C>T was one of 329 unselected patients referred with a clinical diagnosis of FAP or attenuated FAP after APC mutation screening was negative (PMID:16557584), and the ClinVar submissions for this exact variant list generic conditions (Carcinoma of colon, Familial adenomatous polyposis 2, Hereditary cancer-predisposing syndrome, 'not provided', 'not specified'). Those submission conditions are not statements about this patient's phenotype. Even if that cohort context were taken as the phenotype evidence, it would not support PP4: adenomatous colorectal polyposis and colorectal cancer are genetically heterogeneous (APC, biallelic MUTYH, POLE/POLD1, NTHL1 and MSH3, plus the mismatch-repair genes), and the one published carrier was heterozygous for a synonymous change (p.Ile14=) that the source itself did not attribute functional relevance to, while MUTYH-associated disease requires biallelic variants. The applicable InSiGHT MUTYH v1.0 specification returned no criteria text, so it is also unknown whether that specification restricts PP4 or handles phenotype specificity through a PS4 phenotype-point scheme. PP4 is therefore not_assessed, and this status must not be read as evidence against the variant.

Rule

ACMG/AMP 2015 PP4 (PMID:25741868): supporting pathogenic evidence when the patient's phenotype or family history is highly specific for a disease with a single genetic etiology; gene-specific InSiGHT MUTYH v1.0 rule text was not retrievable.

Evidence considered

• PP4 definition (ACMG/AMP 2015, PMID:25741868): the patient's phenotype or family history is highly specific for a disease with a single genetic etiology. The same source illustrates that a highly distinctive syndromic presentation supports the criterion strongly whereas a non-specific finding such as developmental delay does not.
• No proband-level phenotype, family history or genotype data are present in this case: the case record is a variant-level query (NM_001128425.2:c.42C>T) with extracted coordinates, population frequencies, in-silico outputs and database records, but no patient ascertainment or clinical description.
• ClinVar submission conditions for VCV000138307 are generic and submission-level (Carcinoma of colon, Familial adenomatous polyposis 2, Hereditary cancer-predisposing syndrome, 'not provided', 'not specified'), not a description of this patient's phenotype, and cannot establish phenotype specificity for a single-gene etiology.
• PMID:16557584: the only published carrier was among 329 unselected APC-mutation-negative index patients referred for a clinical diagnosis of FAP or attenuated FAP; the variant was monoallelic (heterozygous) and was not attributed functional relevance, whereas MUTYH-associated polyposis requires biallelic variants, so the cohort context does not establish that a c.42C>T carrier's phenotype was highly specific for MUTYH-associated disease.
• Adenomatous polyposis and colorectal cancer are genetically heterogeneous (APC, biallelic MUTYH, POLE/POLD1, NTHL1, MSH3, mismatch-repair genes), which further weakens any claim of single-gene phenotype specificity in this cohort.
• Governing framework: the applicable InSiGHT MUTYH v1.0 specification (cspec doc 1742141534) was retrieved with an empty criteria array and empty rule_payload, so no gene-specific PP4 rule or phenotype-point requirement could be read or applied.

Still missing

• A proband-level phenotype description (adenoma number, age at onset, colorectal cancer history) and family history are required to evaluate PP4; this case records only the variant.
• The InSiGHT MUTYH v1.0 criteria text was not retrievable (empty criteria array and rule_payload), so it is unknown whether the gene-specific specification modifies PP4, restricts it to a defined phenotype-point scheme, or marks it not applicable as other InSiGHT colorectal-cancer specifications do for phenotype criteria.
• PMID:16557584 does not state which of the 329 polyposis patients carried c.42C>T, nor give that individual's adenoma count or age, and its phenotype tables cover only biallelic MAP patients.

Sources

Reasoning

BS4 (Richards et al. 2015, PMID:25741868) requires lack of segregation in affected members of a family, i.e. a family in which affected individuals do not carry the variant. No family data of any kind exist for MUTYH NM_001128425.2:c.42C>T: the case contains no pedigree, no affected relatives, and no genotype–phenotype table, and neither variant-specific publication provides family-level information. Aretz et al. 2006 (PMID:16557584) reports the variant only as a heterozygous allele count in 1 of 329 unrelated polyposis index patients and performs no relative testing for it (its only pedigree analysis concerns p.466delE in family no. 26), and the MUTYH LOVD paper (PMID:20725929) lists it only in a transcript/isoform nomenclature context. The population data are not a substitute: the complete absence of homozygotes in gnomAD (0/282,876 alleles in v2.1; 0/1,613,946 alleles in v4.1) reflects a rare heterozygous allele and says nothing about segregation within a family. Because no affected relative was genotyped, non-segregation can neither be demonstrated nor excluded, so BS4 is not assessable rather than met. The governing InSiGHT MUTYH specification contains no criterion-level BS4 rule (framework_complete=false), so generic ACMG/AMP 2015 applies.

Rule

BS4 (Richards et al. 2015, PMID:25741868): lack of segregation in affected members of a family. Benign Strong.

Evidence considered

• BS4 rule text (Richards et al. 2015, PMID:25741868): lack of segregation in affected members of a family; Benign Strong.
• Aretz et al. 2006 (PMID:16557584): no non-segregation data; the variant was identified in the monoallelic state only (Table II, 1/658 chromosomes) and no relatives were genotyped for it, while the paper's family analysis was limited to the unrelated variant p.466delE.
• MUTYH LOVD (PMID:20725929): searched for family/pedigree entries and found only the transcript/isoform nomenclature mention of c.42C>T (p.(=)) near the second translation initiation site.
• gnomAD v4.1 (source key gnomad_v4): 277/1,613,946 alleles with 0 homozygotes — evidence about allele rarity, not about segregation in a family, and therefore not applicable to BS4.
• Case-level search: no pedigree, family-history, or relative-genotype data are present anywhere in the case evidence for this variant.

Still missing

• No family with affected members genotyped for MUTYH c.42C>T, so non-segregation cannot be demonstrated or excluded.
• No proband or relative samples exist in this variant-level case, and the two variant-specific publications report no family studies for this variant.

Sources

Reasoning

BP7 is in scope: NM_001128425.2:c.42C>T is a synonymous substitution (NP_001121897.1:p.(Ile14=)) that does not change the amino-acid sequence or protein length, so BP7 - not PP3/BP4 - is the computational criterion this variant belongs to. Generic ACMG/AMP 2015 BP7 requires two things: (a) splicing prediction algorithms predict no impact on the splice consensus sequence and no creation of a new splice site, and (b) the nucleotide is not highly conserved. Neither can be established from the available evidence. The calibrated splice-impact prediction is simply absent: the SpliceAI lookup returned no score for this variant (max delta unavailable), and that missing result must not be read as a max delta near zero or as evidence that splicing is unaffected. The only splice-adjacent numbers present are Pangolin outputs (splice gain 0.002, splice loss -0.008), which are not calibrated for a benign-direction call in this assessment and therefore cannot satisfy the 'no predicted splice impact' prong. The position also argues against applying BP7 on assumption alone: c.42 is the sixth nucleotide of exon 2 (exon 2 spans c.37-c.157), immediately adjacent to the intron 1 acceptor, a location where a synonymous change can plausibly affect splicing. Finally, no nucleotide-conservation metric for c.42 (phyloP, GERP or equivalent) is available, so the 'not highly conserved' prong is unevaluable as well. BP7 is therefore not assessed rather than applied; the absence of a SpliceAI score is a data gap, not benign evidence. The governing InSiGHT MUTYH specification v1.0 (cspec doc 1742141534) contains no gene-specific BP7 rule, so generic ACMG/AMP 2015 BP7 was applied.

Rule

Generic ACMG/AMP 2015 BP7 (Richards et al., PMID:25741868); no MUTYH-specific BP7 rule exists in the InSiGHT Hereditary Colorectal Cancer/Polyposis specification v1.0 (cspec doc 1742141534)

Evidence considered

• The variant is synonymous (NP_001121897.1:p.(Ile14=)), so BP7 - not PP3/BP4 - is the computational criterion in scope for it.
• SpliceAI returned no score for NM_001128425.2:c.42C>T (no max delta, no acceptor/donor gain or loss values). This is missing data and was not interpreted as a low delta or as evidence of absent splice impact.
• Pangolin values recorded for this variant (splice gain 0.002, splice loss -0.008) are present but are not calibrated for PP3/BP4/BP7 here, so they were not used to satisfy BP7's 'no predicted splice impact' requirement.
• The variant sits six nucleotides into exon 2 (exon 2 spans c.37-c.157 of NM_001128425.2), immediately downstream of the intron 1 acceptor, a position at which a synonymous change could plausibly affect splicing; BP7 was therefore not applied on the basis of the variant type alone.
• No nucleotide-conservation metric for c.42 (phyloP, GERP, phastCons or equivalent) was available in the assembled evidence, so BP7's conservation prong is unevaluable.
• Governing framework consulted first: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis MUTYH specification v1.0 (cspec doc 1742141534) provides no gene-specific BP7 rule; generic ACMG/AMP 2015 BP7 was therefore applied.
• Curated MUTYH literature reviewed for BP7: c.42C>T is listed in the MUTYH LOVD curation among 5'-region/'near second translation start site' variants whose transcript-specific consequences should be verified at least in silico (PMID:20725929), and it appears in a systematic MUTYH sequencing cohort only as a monoallelic silent change (PMID:16557584); neither source provides a splice prediction or conservation metric for this variant.

Still missing

• A calibrated splice-impact prediction for NM_001128425.2:c.42C>T (ideally a valid SpliceAI max delta with its four component deltas) is required to satisfy the 'no impact on splicing or splice-site creation' prong of BP7.
• No nucleotide-conservation metric for position c.42 (phyloP, GERP, phastCons or equivalent) is available for this variant, so the 'nucleotide not highly conserved' prong of BP7 cannot be evaluated.
• The variant lies six nucleotides into exon 2 adjacent to the intron 1 acceptor, so a splice-region-specific assessment may be warranted if a calibrated splice predictor can be obtained.

Sources