CDKN2A c.75A>G, p.(Val25=)

Reasoning

No applicable CDKN2A-specific VCEP specification was found, so the supplied generic PM2 supporting threshold of allele frequency <=0.0001 applies. The variant is present at AF 6.829634155124585e-06 in gnomAD v4.1 all-comers, with the highest observed subpopulation AF 9.32615953837206e-06 in Europeans (non-Finnish), and has zero homozygotes. It is absent from gnomAD v2.1 and from the available non-cancer subsets. These observations are below the PM2 threshold and support PM2 at supporting strength.

Rule

Generic PM2: allele frequency <=0.0001, applied at supporting strength.

Evidence considered

• The case has no applicable CDKN2A-specific VCEP framework; the supplied generic PM2 threshold is AF <=0.0001 at supporting strength.
• gnomAD v4.1 reports total AF 6.829634155124585e-06 from 11/1,610,628 alleles, highest subpopulation AF 9.32615953837206e-06 in Europeans (non-Finnish), and zero homozygotes.
• The variant is absent from gnomAD v2.1 and from the available gnomAD v2.1 and v3.1 non-cancer subsets.

Sources

Reasoning

The variant is synonymous (NM_000077.5:c.75A>G; NP_000068.1:p.(Val25=)), so the applicable computational path is SpliceAI rather than REVEL. SpliceAI is available and the maximum delta score is 0.006, which is below the supplied generic BP4 supporting threshold of <=0.1. Thus the variant has supporting computational evidence for no predicted splice impact under BP4. This prediction is used for BP4 and is not separately counted for PP3 or BP7.

Rule

Synonymous variant: evaluate SpliceAI only; BP4 supporting requires max delta <=0.1.

Evidence considered

• The normalized consequence is synonymous: NM_000077.5:c.75A>G, NP_000068.1:p.(Val25=).
• SpliceAI reports a maximum delta score of 0.006.
• For synonymous variants, SpliceAI is the sole applicable PP3/BP4 path; the supplied generic BP4 supporting threshold is <=0.1, from the SpliceAI calibration of Jaganathan et al. 2019 (PMID:30661751).

Sources

Reasoning

The variant is synonymous (NM_000077.5:c.75A>G; NP_000068.1:p.(Val25=)), so the applicable computational path is SpliceAI rather than REVEL. SpliceAI is available and the maximum delta score is 0.006. This is below the supplied generic SpliceAI PP3 supporting threshold of >=0.2 and the moderate threshold of >=0.5; therefore PP3 is not met. The absent REVEL result is not relevant because REVEL is not the applicable path for a synonymous variant.

Rule

Synonymous variant: evaluate SpliceAI only; PP3 requires max delta >=0.2 supporting or >=0.5 moderate.

Evidence considered

• The normalized consequence is synonymous: NM_000077.5:c.75A>G, NP_000068.1:p.(Val25=).
• SpliceAI reports DS_AG 0.000, DS_AL 0.001, DS_DG 0.001, and DS_DL 0.006; the maximum delta is 0.006.
• For synonymous variants, SpliceAI is the sole applicable PP3/BP4 path; the supplied generic PP3 thresholds are >=0.2 supporting and >=0.5 moderate, from the SpliceAI calibration of Jaganathan et al. 2019 (PMID:30661751).

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact ClinVar record is NM_000077.5(CDKN2A):c.75A>G (p.Val25=), but it has 0 expert-panel submissions; the available classifications are ordinary single-submitter assertions, including Likely benign and Benign. Therefore PP5 is not met.

Rule

PP5 requires an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary submissions, aggregate labels, and non-expert assertions are excluded.

Evidence considered

• ClinVar variation 827146 exactly matches NM_000077.5:c.75A>G (p.Val25=) and reports 0 expert-panel submissions.
• The exact-variant ClinVar submissions are single-submitter records classified as Likely benign or Benign; ordinary laboratory submissions and aggregate labels do not trigger PP5 under this adjudication rule.

Sources

Reasoning

No applicable CDKN2A-specific VCEP specification was found, so the generic ACMG/AMP BA1 threshold of allele frequency >=0.05 applies (Richards et al., PMID:25741868). The variant's gnomAD v4.1 all-comers allele frequency is 6.829634155124585e-06 (11/1,610,628 alleles), and the highest observed population frequency is 9.32615953837206e-06 in Europeans (non-Finnish), both far below 0.05. It is also absent from gnomAD v2.1 and the available non-cancer subsets. Therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1: allele frequency >=0.05.

Evidence considered

• The case has no applicable CDKN2A-specific VCEP framework; generic ACMG/AMP criteria therefore apply.
• gnomAD v4.1 reports 11/1,610,628 alleles, total AF 6.829634155124585e-06, with highest subpopulation AF 9.32615953837206e-06 in Europeans (non-Finnish) and zero homozygotes.
• The generic ACMG/AMP BA1 threshold supplied for this adjudication is AF >=0.05 (Richards et al., PMID:25741868).
• The variant is absent from gnomAD v2.1 and from the available gnomAD v2.1 and v3.1 non-cancer subsets.

Sources

Reasoning

No applicable CDKN2A-specific VCEP specification was found, so the supplied generic BS1 threshold of allele frequency >=0.01 applies. The gnomAD v4.1 all-comers allele frequency is 6.829634155124585e-06, and the highest observed population frequency is 9.32615953837206e-06 in Europeans (non-Finnish), both below 0.01. The variant is absent from gnomAD v2.1 and the available non-cancer subsets. Therefore the population frequency does not meet BS1.

Rule

Generic BS1: allele frequency >=0.01.

Evidence considered

• The case has no applicable CDKN2A-specific VCEP framework; the supplied generic BS1 threshold is AF >=0.01.
• gnomAD v4.1 reports total AF 6.829634155124585e-06 (11/1,610,628 alleles); the highest observed subpopulation AF is 9.32615953837206e-06 in Europeans (non-Finnish).
• The variant is absent from gnomAD v2.1 and from the available gnomAD v2.1 and v3.1 non-cancer subsets.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact ClinVar record is NM_000077.5(CDKN2A):c.75A>G (p.Val25=), but it has 0 expert-panel submissions; its Benign and Likely benign classifications are ordinary single-submitter assertions. Therefore BP6 is not met despite the non-expert benign labels.

Rule

BP6 requires an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary submissions, aggregate labels, and non-expert assertions are excluded.

Evidence considered

• ClinVar variation 827146 exactly matches NM_000077.5:c.75A>G (p.Val25=) and reports 0 expert-panel submissions.
• The exact-variant ClinVar record contains single-submitter Benign and Likely benign assertions; these ordinary laboratory submissions do not trigger BP6 under this adjudication rule.

Sources

Reasoning

No case-specific evidence documents that NM_000077.5:c.75A>G arose de novo in a proband, including confirmed maternity and paternity, parental testing results, or a validated de novo observation. The available material contains no proband-level phenotype and parental-genotype record sufficient to assess PS2.

Rule

Generic ACMG/AMP PS2 requires a confirmed de novo occurrence in an affected individual; strength cannot be assigned without documented parental testing and appropriate maternity/paternity confirmation.

Evidence considered

• No proband, parental-testing, maternity/paternity, or de novo segregation record was identified for NM_000077.5:c.75A>G.
• The variant is synonymous, NM_000077.5:c.75A>G (NP_000068.1:p.(Val25=)), but consequence type does not establish de novo status.

Still missing

• Proband-level clinical record and phenotype consistency are not provided.
• Maternal and paternal relationships are not documented as confirmed.
• Parental testing results for the exact variant are not provided.
• No validated de novo case count or mosaicism assessment is available.

Reasoning

No validated variant-specific functional assay was identified for NM_000077.5:c.75A>G (NP_000068.1:p.(Val25=)). The available evidence contains no experimental result measuring CDKN2A transcript processing, protein function, cell-cycle activity, or another biologically relevant endpoint for this variant, and no assay controls or calibration data are available. The variant is synonymous, and the available SpliceAI prediction is computational evidence rather than PS3 functional evidence.

Evidence considered

• The case evidence identifies NM_000077.5:c.75A>G as a synonymous variant, NP_000068.1:p.(Val25=), with no reported variant-specific laboratory assay.
• SpliceAI max delta score is 0.006, but this is computational splicing prediction and does not constitute validated functional assay evidence for PS3.
• The reviewed literature extraction contains no exact-variant functional experiment, assay result, assay controls, or biological calibration for CDKN2A c.75A>G.

Still missing

• A validated variant-specific functional study with appropriate positive and negative controls is unavailable.
• No experimental measurement of transcript splicing, CDKN2A protein function, or a biologically relevant cellular endpoint is available.

Reasoning

No applicable CDKN2A VCEP or gene-specific framework was available, so generic ACMG/AMP PS4 was considered. The case materials do not provide variant-specific affected-case and control counts, a case-control enrichment analysis, an odds ratio, or another published prevalence statistic for NM_000077.5:c.75A>G (p.Val25=). The available literature extracts either do not mention this exact variant or provide only general CDKN2A disease-risk context, which cannot establish PS4.

Rule

Generic ACMG/AMP PS4 requires statistically significant enrichment of the variant in affected individuals compared with controls; no variant-specific enrichment threshold or statistic is available here.

Evidence considered

• The exact variant is NM_000077.5:c.75A>G (NP_000068.1:p.(V25=)), but no case-control dataset or variant-specific prevalence estimate is reported in the reviewed evidence.
• The reviewed literature extracts for PMID:25394175 and PMID:31672839 provide general cancer-predisposition guidance and CDKN2A carrier-risk context, respectively, not exact-variant case-control enrichment evidence.

Still missing

• Variant-specific case and control counts or a validated enrichment statistic are unavailable.

Sources

Reasoning

No applicable CDKN2A VCEP or gene-specific framework was available, so the generic ACMG/AMP PM3 concept was considered. PM3 requires the variant to be observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive disorder, with strength based on validated affected-proband observations and phase. The available case evidence documents NM_000077.5:c.75A>G as a synonymous CDKN2A variant but provides no affected proband, second pathogenic allele, phase, cis/trans testing, segregation, or inheritance-mode observation. Therefore PM3 cannot be assessed rather than being called absent or met.

Evidence considered

• The case evidence identifies NM_000077.5:c.75A>G in CDKN2A as a synonymous variant, but contains no affected-proband, compound-heterozygous, homozygous, second-allele, phase, or segregation data.
• PM3 cannot be assigned without evidence that the variant is in trans with a pathogenic or likely pathogenic allele in an affected individual under a recessive inheritance model.

Still missing

• Affected-proband observations are not documented.
• No pathogenic or likely pathogenic allele in the same individual is documented.
• Cis/trans phase and the relevant inheritance mode are not documented.

Sources

Reasoning

No case-specific evidence documents a presumed de novo occurrence of NM_000077.5:c.75A>G without confirmed maternity and paternity. There are no affected-proband observations, parental genotype data, or clinical details allowing evaluation of a credible presumed de novo event.

Rule

Generic ACMG/AMP PM6 concerns presumed de novo occurrence when maternity and paternity are not confirmed; variant-specific clinical evidence is required.

Evidence considered

• No presumed de novo case report or family-level observation for NM_000077.5:c.75A>G was identified.
• General disease and variant-classification publications available for this case do not provide variant-specific de novo or parental evidence.

Still missing

• No affected proband with the exact variant is documented.
• No parental genotypes or family relationships are documented.
• No clinical phenotype consistency or de novo case series is available.

Reasoning

No affected relatives, informative meioses, genotype-phenotype co-segregation, or family pedigree data are documented for NM_000077.5:c.75A>G. Therefore, neither supporting segregation evidence nor a calibrated higher strength can be assigned.

Rule

Generic ACMG/AMP PP1 requires co-segregation of the variant with disease in affected family members; strength depends on the number and informativeness of meioses and cannot be assigned here.

Evidence considered

• No family segregation data for NM_000077.5:c.75A>G are available.
• No disease-specific segregation threshold can be applied because the number and informativeness of meioses are not reported.

Still missing

• No pedigree or family structure is provided.
• No affected-relative genotypes are provided.
• No unaffected-relative genotypes or informative meioses are provided.
• No phenotype assessments are available for relatives.

Reasoning

No applicable CDKN2A VCEP or gene-specific framework was available, so generic ACMG/AMP PP4 was considered. The case materials contain no documented patient phenotype, phenotype-match assessment, or disease-specific clinical findings for the individual carrying NM_000077.5:c.75A>G. General statements about CDKN2A-associated melanoma or pancreatic-cancer risk are not sufficiently specific to demonstrate a highly specific phenotype for this exact case.

Rule

Generic ACMG/AMP PP4 requires a phenotype or family history highly specific for a disease associated with the gene; generic gene-level disease risk is insufficient.

Evidence considered

• The reviewed materials identify general CDKN2A disease contexts but do not document the phenotype of the individual carrying NM_000077.5:c.75A>G.
• General CDKN2A risk statements in PMID:31672839 cannot substitute for a highly specific phenotype observed in the case.

Still missing

• A detailed patient phenotype and disease-specific phenotype-match assessment are unavailable.

Sources

Reasoning

No applicable CDKN2A-specific VCEP specification was found. The available population data show zero homozygotes in gnomAD v4.1, but do not establish that identified carriers are healthy adults or unaffected individuals, which is required for BS2. Absence of homozygotes is not evidence that the variant is present in healthy adults and cannot by itself support BS2. No independent healthy-adult carrier observations or phenotype data were provided; BS2 is therefore not assessed.

Rule

Generic BS2 requires the variant to be observed in healthy adults; homozygote absence alone is insufficient.

Evidence considered

• gnomAD v4.1 reports 11 variant alleles and zero homozygotes in the all-comers dataset.
• Population allele counts do not establish unaffected status, age, penetrance, or absence of CDKN2A-associated disease for individual carriers.
• No independent healthy-adult carrier series or phenotype-confirmed unaffected observations are available in the reviewed case evidence.

Still missing

• Verified observations of the variant in unaffected healthy adults with appropriate age and phenotype information are unavailable.

Sources

Reasoning

No validated variant-specific functional assay was identified for NM_000077.5:c.75A>G (NP_000068.1:p.(Val25=)). The available evidence contains no experimental result demonstrating preserved CDKN2A transcript processing, protein function, cell-cycle activity, or another biologically relevant endpoint, and no assay controls or benign-range calibration are available. A lack of functional testing cannot establish BS3, and the available SpliceAI prediction is computational rather than functional evidence.

Evidence considered

• The case evidence identifies NM_000077.5:c.75A>G as a synonymous variant, NP_000068.1:p.(Val25=), with no reported variant-specific laboratory assay.
• SpliceAI max delta score is 0.006, but this is computational splicing prediction and does not constitute validated functional assay evidence for BS3.
• The reviewed literature extraction contains no exact-variant functional experiment, assay result, assay controls, or benign functional calibration for CDKN2A c.75A>G.

Still missing

• A validated variant-specific functional study with appropriate positive and negative controls is unavailable.
• No experimental result establishes preserved transcript processing, CDKN2A protein function, or a benign functional range for this variant.

Reasoning

No family-level testing and phenotype data are available to determine whether NM_000077.5:c.75A>G fails to segregate with disease in affected relatives or is present in unaffected relatives in a way that constitutes meaningful non-segregation. Absence of reported family data is not evidence for BS4.

Rule

Generic ACMG/AMP BS4 requires well-established non-segregation in affected family members or an appropriately informative family context; no such evidence is available.

Evidence considered

• No informative non-segregation observation for NM_000077.5:c.75A>G was identified.
• The absence of family observations cannot be interpreted as evidence that the variant does not segregate with disease.

Still missing

• No affected-relative genotypes and phenotypes are documented.
• No unaffected-relative genotypes and phenotypes are documented.
• No pedigree, penetrance context, or informative non-segregation count is available.

Reasoning

No applicable CDKN2A VCEP or gene-specific framework was available, so the generic ACMG/AMP BP2 concept was considered. BP2 requires observation of the variant in trans with a pathogenic variant for a recessive disorder, or in cis with a pathogenic variant for a fully penetrant dominant disorder, with the relevant phase and disease context established. The available case evidence contains no affected-proband or other individual-level observation, no pathogenic partner allele, no cis/trans phase, and no inheritance-mode documentation for this variant. Therefore BP2 cannot be assessed rather than being called absent or met.

Evidence considered

• The case evidence provides no affected-proband or family-level observation pairing NM_000077.5:c.75A>G with a pathogenic variant.
• BP2 cannot be assigned without documented cis/trans phase and an applicable recessive or fully penetrant dominant disease context.

Still missing

• No individual-level observation with a pathogenic partner allele is documented.
• Cis/trans phase is not documented.
• The applicable inheritance model and penetrance context are not documented.

Sources

Reasoning

No applicable CDKN2A VCEP or gene-specific framework was available, so generic ACMG/AMP BP5 was considered. The case materials do not document that the patient's phenotype is explained by an established pathogenic variant in another gene or by another molecular cause, and no validated BP5-specific comparison or threshold is supplied. The absence of such evidence cannot be converted into BP5.

Rule

Generic ACMG/AMP BP5 requires a pathogenic variant in another gene that explains the patient's phenotype; no such alternative molecular cause is documented.

Evidence considered

• The reviewed case materials contain no documented alternative pathogenic molecular diagnosis that explains the patient's phenotype independently of CDKN2A c.75A>G.
• No BP5-specific numeric threshold is applicable or available; therefore no numeric comparison can be performed.

Still missing

• An established alternative molecular diagnosis or pathogenic variant explaining the phenotype is unavailable.

Reasoning

BP7 is in scope because the variant is synonymous (NM_000077.5:c.75A>G; NP_000068.1:p.(Val25=)). The available SpliceAI result shows a maximum delta of 0.006, but BP7 also requires evidence that the synonymous position is not highly conserved. No conservation metric or governing VCEP-specific BP7 assignment is available in the reviewed evidence. Therefore BP7 cannot be assessed from the current record. The SpliceAI prediction has already been used for BP4 and is not double-counted as BP7.

Rule

BP7 applies only to synonymous variants and requires no predicted splice impact plus evidence that the position is not highly conserved; the prediction cannot be double-counted with BP4.

Evidence considered

• The variant is synonymous: NM_000077.5:c.75A>G, NP_000068.1:p.(Val25=).
• SpliceAI reports a maximum delta score of 0.006, but the reviewed evidence does not provide the conservation component required for BP7.

Still missing

• A conservation metric or governing VCEP-specific BP7 rule for NM_000077.5:c.75A>G is needed.

Sources