PPM1D c.1260+4T>C, p.?

Reasoning

Applying the same generic non-missense in-silico rule (SpliceAI only, since this variant is intronic/non-canonical splice-position and not a missense substitution): SpliceAI max delta score = 0.01, below the BP4 supporting threshold of <0.1. No PPM1D-specific VCEP PP3/BP4 lookup material overrides this generic calibration for this case. BP4 (supporting, benign) is met.

Rule

generic_acmg_pp3_bp4_insilico_splice

Evidence considered

• SpliceAI Lookup (NM_003620.3:c.1260+4T>C, hg37): max delta score = 0.01, below the BP4 supporting threshold of <0.1 defined in the lab's generic in-silico calibration rule for intronic/non-canonical-splice-position variants (generic_acmg_classification_rules.md).
• REVEL and BayesDel were not applicable since this is not a missense variant; in any case BayesDel has no verified published threshold available to this pipeline and would be treated as not_available regardless of variant type.

Sources

Reasoning

NM_003620.3:c.1260+4T>C is an intronic variant located at the +4 position of intron 5 (variant_exonic_positions = '5i'), outside the canonical ±1,±2 splice-donor consensus dinucleotide. No PPM1D-specific VCEP/CSPEC PVS1 framework exists (cspec.found=false; final_classification_framework.found=false), so the generic ClinGen SVI PVS1 decision framework (PMC6185798) was applied per the pvs1_variant_assessment scaffold. That scaffold explicitly determined apply_generic_pvs1_framework=false because the variant does not fall into any of the default null-variant buckets (nonsense, frameshift, or canonical ±1,2 splice-consensus). In silico splice prediction (SpliceAI) further supports no meaningful splicing disruption: DS_AG=0.0, DS_AL=0.004, DS_DG=0.0, DS_DL=0.01, max delta score=0.01, well below any threshold used to infer exon skipping/cryptic splice-site use. Although PPM1D loss-of-function is an established germline disease mechanism (pvs1_gene_context: lof_mechanism_supported=true, gate='eligible'), the gene-level LOF-mechanism eligibility does not substitute for a variant-level predicted-null consequence, which is absent here. No RNA/splicing functional assay data for this specific variant were found in evidence.json, literature_pass.json, or the two full-text ClinVar-cited papers (PMID:17576681, PMID:9536098), which discuss general splice-site prediction/statistics and do not mention this variant. Therefore PVS1 is not met.

Rule

ClinGen SVI PVS1 decision framework (PMC6185798), generic fallback (no PPM1D-specific VCEP)

Evidence considered

• pvs1_variant_assessment scaffold: variant_bucket='other', canonical_splice_consensus=false, apply_generic_pvs1_framework=false, rationale states variant does not fall into default generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus.
• prefetch.json variant_exonic_positions shows the variant sits at intron 5 position +4 ('5i'), i.e. c.1260+4T>C, three nucleotides beyond the canonical +1/+2 splice-donor dinucleotide.
• SpliceAI Lookup result: evidence_sentence 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01)', with DS_AG=0.0, DS_AL=0.004, DS_DG=0.0, DS_DL=0.01 - all far below levels indicative of splice disruption.
• pvs1_gene_context confirms PPM1D germline LOF is an accepted disease mechanism (lof_mechanism_supported=true, pvs1_gene_gate='eligible'), establishing gene-level PVS1 eligibility, but this only gates applicability; it does not itself establish a null variant consequence at this specific position.
• No official CSPEC/VCEP PVS1 framework exists for PPM1D (cspec.found=false in case_summary.json and vcep_materials.json); generic ClinGen SVI PVS1 recommendations (PMC6185798) were used as instructed by pvs1_gene_context.cautions.

Still missing

• No variant-specific RNA/minigene splicing assay confirms or excludes cryptic splicing at this +4 intronic position.
• No PPM1D-specific VCEP PVS1 decision tree (splice subtype table) is available to refine strength if splicing impact were later demonstrated.

Sources

Reasoning

PM2 is not met under the generic ACMG/AMP definition because the variant is present in population databases: 51/1,613,914 alleles in gnomAD v4.1 and 10/250,578 alleles in gnomAD v2.1. Although rare and observed with no homozygotes, it is not absent from controls.

Rule

Generic ACMG/AMP PM2: variant absent from, or not observed in, population databases; a nonzero observed allele count does not meet the generic criterion.

Evidence considered

• gnomAD v4.1 identifies the variant at AF 3.16002e-05 (51/1,613,914 alleles), with zero homozygotes; the highest subpopulation AF is 0.000526998 in South Asians.
• gnomAD v2.1 identifies the variant at AF 3.99077e-05 (10/250,578 alleles), with zero homozygotes; the highest subpopulation AF is 0.000294137 in South Asians.
• The generic ACMG/AMP PM2 definition requires absence from controls; rarity alone does not satisfy the criterion when qualifying population observations are present.

Sources

Reasoning

NM_003620.3:c.1260+4T>C is an intronic variant at a non-canonical splice position (+4, not the invariant +1/+2 donor dinucleotide, and not a missense substitution). No PPM1D-specific CSPEC/VCEP PP3/BP4 lookup material was retrieved for this case (cspec.found=false; vcep_materials empty; final_classification_framework.found=false, generic_acmg fallback in effect), so the lab's generic ACMG in-silico calibration rule for non-missense variants applies: use SpliceAI only. SpliceAI Lookup returned DS_AG=0.0, DS_AL=0.004, DS_DG=0.0, DS_DL=0.01, max delta score = 0.01, well below the PP3 supporting threshold of >0.2. REVEL and BayesDel are not applicable predictors for an intronic (non-missense) variant per the same generic rule, and BayesDel additionally lacks a verified published calibration for this pipeline regardless of variant type. PP3 is therefore not met.

Rule

generic_acmg_pp3_bp4_insilico_splice

Evidence considered

• SpliceAI Lookup (NM_003620.3:c.1260+4T>C, hg37): max delta score = 0.01 (DS_AG=0.0, DS_AL=0.004, DS_DG=0.0, DS_DL=0.01), far below the PP3 supporting threshold of >0.2 applied per the lab's generic in-silico calibration rule for intronic/non-missense variants (generic_acmg_classification_rules.md, SVI-recommended thresholds also used by ATM VCEP per Walker et al. 2023).
• No PPM1D-specific CSPEC or gene-specific PP3/BP4 lookup spreadsheet was found for this case (case_summary.cspec.found=false; vcep_materials.summaries empty; final_classification_framework.found=false), so the generic ACMG/AMP fallback in-silico rule was applied instead of a VCEP-specific rule.

Sources

Reasoning

PP5 is not met. The exact-variant ClinVar record is classified as uncertain significance with criteria provided/single-submitter status, and there are zero expert-panel submissions. Ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify for PP5.

Rule

PP5 applies only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; non-expert and single-submitter assertions are excluded.

Evidence considered

• The exact variant NM_003620.4(PPM1D):c.1260+4T>C is present in ClinVar as uncertain significance, review status criteria provided/single submitter, with one clinical-laboratory submission and zero expert-panel submissions.
• Because no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification is present, the PP5 prerequisite is not satisfied.

Sources

Reasoning

The variant is far below the generic BA1 stand-alone benign threshold of 5%: gnomAD v4.1 reports an overall allele frequency of 0.00316% (51/1,613,914 alleles), and the highest reported population frequency is 0.05270% in South Asians. Therefore BA1 is not met.

Rule

Generic ACMG/AMP BA1 stand-alone benign criterion: allele frequency is sufficiently common, conventionally >5%; observed frequencies are well below this threshold.

Evidence considered

• gnomAD v4.1 reports 51/1,613,914 alleles, AF 3.16002e-05, with zero homozygotes; the highest subpopulation AF is 0.000526998 (0.05270%) in South Asians and the group maximum FAF is 0.000408.
• gnomAD v2.1 reports 10/250,578 alleles, AF 3.99077e-05, with zero homozygotes; the highest subpopulation AF is 0.000294137 (0.02941%) in South Asians.
• Generic ACMG/AMP evaluation was used because no applicable PPM1D VCEP or gene-specific framework was retrieved; BA1 requires a frequency at or above the stand-alone benign threshold, which these observations do not approach.

Sources

Reasoning

BP6 is not met. The exact-variant ClinVar record is uncertain significance from a single laboratory and has no expert-panel benign classification. Ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify for BP6.

Rule

BP6 applies only to an exact-variant ClinVar expert-panel Benign or Likely benign classification; non-expert and single-submitter assertions are excluded.

Evidence considered

• The exact variant NM_003620.4(PPM1D):c.1260+4T>C is present in ClinVar as uncertain significance, review status criteria provided/single submitter, with one clinical-laboratory submission and zero expert-panel submissions.
• Because no exact-variant ClinVar expert-panel Benign or Likely benign classification is present, the BP6 prerequisite is not satisfied.

Sources

Reasoning

No case-specific proband or parental testing data are provided in the evidence bundle. De novo status cannot be established without confirmed variant presence in the proband and confirmed absence in both biological parents, with consideration of parental identity and mosaicism.

Rule

Generic ACMG/AMP PS2 requires confirmation that a variant is de novo in a patient with a disease consistent with the gene/phenotype, with confirmed maternity and paternity; no strength can be assigned without case-level evidence.

Evidence considered

• The consolidated case-evidence bundle contains no proband-level segregation record or parental test result for NM_003620.3:c.1260+4T>C.
• The ClinVar record reports a single-submitter uncertain-significance classification and does not provide usable de novo or parental-testing evidence for this criterion.

Still missing

• Proband genotype confirmation is not documented.
• Maternal and paternal testing results are not documented.
• Biological parentage and adequacy of testing for low-level parental mosaicism are not documented.
• Phenotype consistency and de novo occurrence in the context of a relevant disorder are not documented.

Reasoning

No VCEP/gene-specific framework exists for PPM1D (cspec not found; framework_mode is generic_acmg fallback), so generic ACMG PS3 criteria were used. The evidence bundle contains no functional assay data (no RT-PCR/minigene splicing assay, no biochemical/enzymatic phosphatase activity assay, no cell-based functional study) for NM_003620.3:c.1260+4T>C. The only literature associated with this variant (PMID:17576681, PMID:9536098) are general methodological/statistical surveys of 5' splice site consensus sequences and human exon flanking-region features across many genes -- neither paper mentions PPM1D or this specific variant, and neither reports a validated functional assay result for it. No SpliceAI/computational splicing prediction is cross-usable as PS3 (functional evidence requires wet-lab assay data, not predictors). Therefore PS3 cannot be assessed as met or not_met; it is not_assessed for lack of applicable functional evidence.

Still missing

• No published or submitted functional assay (RNA/minigene splicing assay, RT-PCR on patient RNA, or biochemical PPM1D phosphatase activity assay) exists for c.1260+4T>C in the reviewed sources.
• The two ClinVar-cited PMIDs are general splice-site methodology/statistics papers, not variant-specific functional studies, and do not mention PPM1D or this variant.

Reasoning

No affected-case series, case-control enrichment analysis, allele counts in affected individuals versus controls, or other qualifying disease-enrichment evidence for NM_003620.3:c.1260+4T>C was provided. The available ClinVar record is a single-submitter uncertain-significance assertion and does not establish PS4.

Rule

Generic ACMG/AMP PS4: significant enrichment in affected individuals compared with controls or multiple affected individuals with the same variant, with appropriate statistical support.

Evidence considered

• The case bundle identifies only one exact-variant ClinVar submission, classified as uncertain significance, with review status criteria provided/single submitter; it contains no affected-case or control enrichment data.
• The literature packet contains only splice-site background papers and no exact-variant phenotype or case-control report.

Still missing

• Affected-case and control counts or a validated case-control enrichment analysis for the exact variant are unavailable.

Reasoning

No applicable PPM1D-specific VCEP framework was available, so the generic ACMG/AMP PM3 concept was considered. The case-evidence bundle contains no affected-proband observations, second pathogenic or likely pathogenic allele, phase information, segregation data, or documented inheritance mode establishing a recessive genotype for this variant. PM3 therefore cannot be assessed.

Rule

Generic ACMG/AMP PM3: pathogenic variants observed in trans (phase confirmed or assumed in recessive disease) with a pathogenic variant in an affected individual; not applied without qualifying allelic and phenotype evidence.

Evidence considered

• The consolidated case-evidence bundle identifies PPM1D and NM_003620.3:c.1260+4T>C but provides no affected-proband, biallelic, compound-heterozygous, phase, segregation, or inheritance observations relevant to PM3.
• The bundle reports no gene-specific CSPEC/VCEP framework; generic ACMG/AMP fallback is therefore required, but generic PM3 cannot be applied without evidence of the variant in trans with a pathogenic allele in an affected individual.

Still missing

• Documented disease inheritance mode for the relevant PPM1D condition
• An affected proband or affected individual carrying this variant
• A second pathogenic or likely pathogenic PPM1D variant in the same individual
• Reliable cis/trans phase determination

Reasoning

No case-specific evidence documents a presumed de novo occurrence without parental confirmation. PM6 cannot be applied from the variant's population presence, ClinVar classification, or general splicing literature.

Rule

Generic ACMG/AMP PM6 is used for presumed de novo occurrence when parental testing is unavailable; it requires a documented compatible clinical case and credible evidence supporting de novo status, neither of which is available here.

Evidence considered

• The consolidated case-evidence bundle contains no patient-level report, family study, or parental testing information for this variant.
• The reviewed ClinVar-cited publications concern general splice-site biology or exon statistics and do not report this variant in a de novo clinical case.

Still missing

• A patient with a phenotype consistent with a PPM1D-related disorder is not described.
• The variant is not documented as absent in tested parents or as presumed de novo based on an explicitly described family study.
• Parentage, parental mosaicism, and the completeness of parental testing are not documented.

Reasoning

No affected relatives, informative meioses, cosegregation counts, or family genotypes are documented. Segregation evidence is therefore insufficient to assess PP1 or any upgraded strength.

Rule

Generic ACMG/AMP PP1 requires cosegregation with disease in multiple affected family members; strength depends on the amount and informativeness of segregation evidence. No such evidence is available.

Evidence considered

• The consolidated case-evidence bundle contains no pedigree, family genotype table, affected-relative data, or informative-meiosis count for NM_003620.3:c.1260+4T>C.
• The available literature triage contains no variant-specific familial segregation report relevant to PP1.

Still missing

• No affected relatives with the variant are reported.
• No unaffected relatives tested for the variant are reported in a segregation context.
• No number of informative meioses or segregation statistics are provided.
• No phenotype assessment establishing consistency among relatives is provided.

Reasoning

No patient phenotype, disease-specific clinical features, or highly specific phenotype information was supplied for this variant. Gene-level disease context alone is insufficient to apply PP4.

Rule

Generic ACMG/AMP PP4: patient phenotype or family history is highly specific for a disease with a single-gene etiology.

Evidence considered

• The case bundle provides variant normalization and population/ClinVar data but no patient phenotype or phenotype-to-disease specificity assessment.
• The available literature packet does not report this exact variant in a patient phenotype context.

Still missing

• A documented patient phenotype and a defined, highly specific phenotype for the relevant PPM1D disorder are unavailable.

Reasoning

The variant is rare in gnomAD, but BS1 requires an allele frequency greater than expected for the disorder. The case bundle provides no validated PPM1D disease prevalence, penetrance, inheritance model, or disorder-specific maximum credible allele-frequency threshold. The observed frequency alone is therefore insufficient to determine whether it exceeds the disease-specific expectation.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; application requires a disorder-specific expected-frequency or maximum-credible-frequency threshold.

Evidence considered

• gnomAD v4.1 reports an overall AF of 3.16002e-05 (0.00316%) and a highest subpopulation AF of 0.000526998 (0.05270%) in South Asians; gnomAD v2.1 reports an overall AF of 3.99077e-05 (0.00399%) and a highest subpopulation AF of 0.000294137 (0.02941%) in South Asians.
• No PPM1D VCEP or gene-specific population-frequency threshold was retrieved, and the bundle does not provide the prevalence/penetrance inputs needed to calculate whether these frequencies are greater than expected for the relevant disorder.

Still missing

• A validated PPM1D disease-specific maximum credible allele-frequency threshold is unavailable.
• Disease prevalence, penetrance, inheritance model, and the relevant affected phenotype are not established in the case bundle.

Sources

Reasoning

The population databases show zero observed homozygotes, but they do not establish that the carriers are healthy adults or provide phenotype and follow-up information. The case bundle also does not establish the inheritance model or whether unaffected heterozygotes would be informative for this PPM1D disorder. Therefore BS2 cannot be assessed from the available population data.

Rule

Generic ACMG/AMP BS2: observation in healthy adults, including homozygotes for recessive disorders or heterozygotes for dominant disorders; phenotype and inheritance context must be established.

Evidence considered

• gnomAD v4.1 reports zero homozygotes among 1,613,914 alleles; gnomAD v2.1 reports zero homozygotes among 250,578 alleles.
• The available gnomAD records provide allele counts and ancestry-stratified frequencies but no clinical phenotype, age, health status, ascertainment, or penetrance information for individual carriers.

Still missing

• No phenotype-annotated healthy-adult carrier data or longitudinal follow-up are available.
• The relevant PPM1D inheritance model and penetrance are not established for interpreting unaffected heterozygotes.
• No homozygotes are observed in gnomAD, so the recessive-homozygote component cannot be evaluated as positive evidence.

Sources

Reasoning

No VCEP/gene-specific framework exists for PPM1D (generic_acmg fallback in use). No functional assay evidence of any kind (splicing minigene/RT-PCR, biochemical activity assay) was found in the case evidence bundle that would demonstrate no damaging effect on PPM1D splicing or protein function for this variant. The two associated PMIDs (PMID:17576681, PMID:9536098) are general splice-site consensus/exon-statistics survey papers not specific to PPM1D or this variant, so they cannot serve as functional evidence for or against a damaging effect. BS3 is therefore not_assessed for lack of applicable functional evidence.

Still missing

• No functional/splicing assay data (in vitro or in vivo) is available for c.1260+4T>C to support a benign functional determination.
• No gene-specific (VCEP) calibrated functional assay framework exists for PPM1D.

Reasoning

No tested unaffected relatives or family members with documented absence of the variant are reported in a context where non-segregation could be evaluated. BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4 requires lack of segregation in affected family members or presence of the variant in unaffected family members when the phenotype is expected to be present; informative family genotype and phenotype data are absent.

Evidence considered

• The consolidated case-evidence bundle contains no family testing data showing absence of the variant in unaffected relatives.
• Population frequency data and a single-submitter ClinVar uncertain-significance record do not constitute BS4 non-segregation evidence.

Still missing

• No unaffected relatives with genotype results are documented.
• No pedigree or phenotype ascertainment is provided to establish that tested relatives are informative for BS4.
• No family structure, penetrance information, or number of informative non-segregating relatives is available.

Reasoning

No applicable PPM1D-specific VCEP framework was available, so the generic ACMG/AMP BP2 concept was considered. The case-evidence bundle contains no observations of this variant in cis with a pathogenic variant, no affected or unaffected individual data suitable for BP2, and no phase or inheritance information. BP2 therefore cannot be assessed.

Rule

Generic ACMG/AMP BP2: variant observed in trans/cis with a pathogenic variant in an affected individual or in cis with a pathogenic variant in an unaffected individual, as applicable to the disease model; not applied without documented phase and relevant individual context.

Evidence considered

• The consolidated case-evidence bundle contains no case, family, segregation, phase, cis, or compound-variant observations for NM_003620.3:c.1260+4T>C relevant to BP2.
• Population frequency data and the single-submitter ClinVar record do not establish the allelic configuration required for BP2 and were not used to infer this criterion.

Still missing

• A documented individual carrying this variant together with a pathogenic variant in cis
• Reliable cis/trans phase determination
• Phenotypic and inheritance context for any reported carrier

Reasoning

No evidence shows that the patient has a molecularly confirmed alternate genetic etiology explaining the phenotype, and no qualifying benign alternate-cause observation is available. The single-submitter ClinVar uncertain-significance record cannot establish BP5.

Rule

Generic ACMG/AMP BP5: variant found in an affected individual with an unrelated molecular basis for the disease.

Evidence considered

• The case bundle contains no patient-level alternate diagnosis, segregation-based alternate cause, or molecular workup demonstrating another explanation for disease.
• The exact-variant ClinVar record is uncertain significance and does not provide qualifying BP5 evidence.

Still missing

• A confirmed alternate molecular cause in an affected individual or family is unavailable.
• Relevant patient and family phenotype/genetic workup data are unavailable.