TET2 c.2193A>G, p.(Gln731=)

Reasoning

The variant is extremely rare in population controls: gnomAD v4.1 reports 2/1,614,126 alleles (AF 1.23906e-06; 0 homozygotes), with maximum listed subpopulation AF 1.09786e-05, and gnomAD-Canada reports it absent. gnomAD v2.1 independently reports 2/250,660 alleles (AF 7.97894e-06; 0 homozygotes), with maximum listed subpopulation AF 3.26691e-05. These frequencies are well below the generic PM2 rare-frequency threshold of <0.1%, supporting PM2. No TET2-specific framework was available to modify this assessment.

Rule

Generic population threshold: PM2 supporting when absent or extremely rare in population controls, operationalized here as allele frequency <0.1% with no homozygote signal; ancestry-specific maxima and database coverage must be considered.

Evidence considered

• gnomAD v4.1 reports 2/1,614,126 alleles, AF 1.23906e-06, 0 homozygotes, and maximum listed subpopulation AF 1.09786e-05 in South Asian individuals.
• gnomAD v2.1 reports 2/250,660 alleles, AF 7.97894e-06, 0 homozygotes, and maximum listed subpopulation AF 3.26691e-05 in South Asian individuals.
• gnomAD-Canada v1.0 reports the variant as absent.
• The observed overall and ancestry-specific frequencies are all below the generic operational PM2 threshold of <0.1%; no disease-specific prevalence/penetrance maximum credible frequency was available for a more tailored threshold.

Still missing

• A disease-specific maximum credible allele frequency incorporating TET2 disease prevalence, inheritance, and penetrance was not available; PM2 is therefore limited to supporting strength under the generic operational rule.

Sources

Reasoning

NM_001127208.2:c.2193A>G is a synonymous variant (NP_001120680.1:p.(Gln731=)) not located in a canonical splice consensus region (pvs1_variant_assessment.canonical_splice_consensus=false). SpliceAI predicts no significant effect on splicing (DS_AG=0.001, DS_AL=0.0, DS_DG=0.001, DS_DL=0.0; max_delta_score=0.001), consistent with no creation of a new splice site or disruption of the native splice consensus sequence. This satisfies the splicing-prediction component of BP7 for a synonymous change under the generic ACMG/AMP 2015 framework (no VCEP/CSPEC exists for TET2 in this case to override or supersede this rule).

Rule

generic_acmg_2015

Evidence considered

• Variant is synonymous (p.Gln731=) and does not fall in the canonical splice consensus region per the case's PVS1 variant assessment.
• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.001), supporting no impact on splicing consistent with BP7.

Still missing

• Nucleotide-level conservation (e.g. phyloP/GERP) at this position was not captured in this case's evidence bundle, so the 'nucleotide not highly conserved' component of the classic BP7 definition could not be independently confirmed; flagged for human review.

Sources

Reasoning

No governing VCEP/CSPEC exists for TET2 in this case (framework_mode = generic_acmg; vcep_materials.json shows no cspec url and no gene-specific PP3/BP4 lookup materials), so generic ACMG/AMP applies. NM_001127208.2:c.2193A>G is a synonymous variant (NP_001120680.1:p.(Gln731=)); it produces no amino-acid change, so missense in-silico predictors (REVEL, BayesDel, aGVGD) are not applicable to this substitution and are also not_available in this case's evidence (revel.found=false, bayesdel.found=false). The splice-impact path (SpliceAI) shows no significant predicted splicing effect (DS_AG=0.001, DS_AL=0.0, DS_DG=0.001, DS_DL=0.0; max_delta_score=0.001), far below any threshold used to trigger PP3. There is no computational evidence of a deleterious effect on the gene/gene product, so PP3 is not met.

Rule

generic_acmg_2015

Evidence considered

• SpliceAI predicts no significant splice impact for this variant (max delta score = 0.001; DS_AG=0.001, DS_AL=0.0, DS_DG=0.001, DS_DL=0.0), well below thresholds used to invoke PP3.
• Variant is synonymous (p.Gln731=), so missense-specific predictors (REVEL, BayesDel) are not applicable; REVEL and BayesDel scores are recorded as not found in this case's prefetch data.

Still missing

• No gene-specific (VCEP) PP3/BP4 lookup table available for TET2 to check for a pre-assigned code.
• Missense computational predictors (REVEL, BayesDel) are not applicable/not available for this synonymous change.

Sources

Reasoning

PP5 is not met. ClinVar variation 3967698 is an exact-variant match but has only a single-submitter Likely benign laboratory assertion from Ambry Genetics, with review status 'criteria provided, single submitter' and zero expert-panel submissions. It is not an expert-panel Pathogenic or Likely pathogenic classification and cannot trigger PP5.

Rule

PP5 may be met only by an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; no such classification is present.

Evidence considered

• The exact variant is listed in ClinVar as Likely benign with review status 'criteria provided, single submitter'; the sole submission is from Ambry Genetics and is not an expert-panel assertion.
• The ClinVar submission audit reports expert_panel_submissions = 0 and usable_for_criterion_leads = 0.
• Under the requested rule, ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger PP5.

Sources

Reasoning

No applicable TET2-specific CSPEC/VCEP specification was available, so the generic laboratory population thresholds were used. The variant is far below the BA1 threshold of >1%: gnomAD v4.1 overall AF is 1.23906e-06 (0.000124%) and the maximum reported subpopulation AF is 1.09786e-05 (0.00110%); gnomAD v2.1 overall AF is 7.97894e-06 (0.00080%) and its maximum reported subpopulation AF is 3.26691e-05 (0.00327%). BA1 is therefore not met.

Rule

Generic population threshold: BA1 requires allele frequency >1%; use the highest reliable ancestry-specific frequency when evaluating the threshold.

Evidence considered

• gnomAD v4.1 reports 2/1,614,126 alleles, AF 1.23906e-06, with 0 homozygotes; the highest listed subpopulation AF is South Asian 1.09786e-05 (1/91,086 alleles), also with 0 homozygotes.
• gnomAD v2.1 reports 2/250,660 alleles, AF 7.97894e-06, with 0 homozygotes; the highest listed subpopulation AF is South Asian 3.26691e-05 (1/30,610 alleles), with 0 homozygotes.
• The case has no retrieved TET2-specific VCEP/CSPEC framework; generic ACMG/AMP fallback is documented in the case materials.

Sources

Reasoning

No applicable TET2-specific CSPEC/VCEP specification was available, so the generic laboratory population thresholds were used. The observed frequency is far below the BS1 threshold of >0.3%: gnomAD v4.1 maximum reported subpopulation AF is 1.09786e-05 (0.00110%), and gnomAD v2.1 maximum reported subpopulation AF is 3.26691e-05 (0.00327%). These data do not support a benign frequency inconsistent with disease prevalence.

Rule

Generic population threshold: BS1 requires allele frequency >0.3% when inconsistent with the expected disease prevalence; use the highest reliable ancestry-specific frequency.

Evidence considered

• gnomAD v4.1 reports overall AF 1.23906e-06 and maximum listed subpopulation AF 1.09786e-05 in South Asian individuals; both are substantially below 0.3%.
• gnomAD v2.1 reports overall AF 7.97894e-06 and maximum listed subpopulation AF 3.26691e-05 in South Asian individuals; both are substantially below 0.3%.
• Disease-specific maximum credible allele frequency, penetrance, and prevalence estimates were not retrieved, but the observed allele frequencies are low enough that BS1 is not met under the available generic threshold.

Sources

Reasoning

BS2 requires the variant to be observed in healthy adult individuals, including appropriate homozygous observations where relevant. The variant has 0 homozygotes in both gnomAD v4.1 and gnomAD v2.1, and no healthy-adult clinical observations were provided. Thus, the available population evidence does not satisfy BS2.

Rule

Generic ACMG/AMP BS2: observed in healthy adult individuals, including homozygotes where relevant; population frequency alone without a healthy phenotype observation is insufficient.

Evidence considered

• gnomAD v4.1 reports 0 homozygotes for the variant overall and 0 homozygotes in the highest-frequency South Asian subpopulation.
• gnomAD v2.1 reports 0 homozygotes for the variant overall and 0 homozygotes in the highest-frequency South Asian subpopulation.
• No phenotype-verified healthy-adult observation or disease-specific penetrance analysis was available in the case bundle for BS2.

Still missing

• No independent phenotype-verified healthy-adult carrier or homozygote observations were provided outside population-database summary data.

Sources

Reasoning

BP6 is not met under the requested rule. Although ClinVar contains an exact-variant Likely benign assertion, it is a single-submitter laboratory classification and not an expert-panel classification. Non-expert and ordinary laboratory assertions must not trigger BP6.

Rule

BP6 may be met only by an exact-variant ClinVar expert-panel classification of Benign or Likely benign; the available assertion is non-expert and therefore excluded.

Evidence considered

• ClinVar variation 3967698 is an exact match to NM_001127208.2:c.2193A>G and reports Likely benign with review status 'criteria provided, single submitter'.
• The submission audit identifies one Ambry Genetics clinical-testing submission, is_expert_panel = false, and expert_panel_submissions = 0.
• Under the requested rule, only an exact-variant ClinVar expert-panel Benign or Likely benign classification can support BP6; this record does not qualify.

Sources

Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. There is no record of confirmed variant presence in the proband together with confirmed absence in both biological parents, nor is parental testing methodology or maternity/paternity information provided.

Rule

Generic ACMG/AMP PS2 requires a confirmed de novo variant in the patient with confirmed maternity and paternity; strength depends on the quality and completeness of parental testing and related de novo evidence.

Evidence considered

• The bundle identifies the variant as NM_001127208.2:c.2193A>G in TET2 and contains no proband, parental, trio, or de novo observations.
• The bundle reports no literature PMIDs and no full-text case publications relevant to this criterion.

Still missing

• Proband genotype and phenotype-linked case report are not provided.
• Orthogonal parental testing results for both biological parents are not provided.
• Maternity/paternity confirmation and assessment for parental mosaicism are not provided.

Reasoning

No TET2 VCEP/ClinGen CSpec was found for this variant (cspec.found = false), so generic ACMG applies. The case-evidence bundle contains no functional/enzymatic assay data (no in vitro 5hmC/hydroxymethylation activity assay, no minigene/RNA splicing assay, no cell-based assay) for NM_001127208.2:c.2193A>G. literature_pass.json returned zero PMIDs and vcep_materials.json/fulltext_map.json are empty, so no publication describing a validated functional assay for this variant was located.

Still missing

• No published or curated functional/enzymatic assay data available for this synonymous variant (p.Gln731=)
• No PMIDs were identified by the literature search to evaluate for functional studies

Reasoning

No case-control dataset, affected-case count, statistical enrichment, or validated disease-specific case series for the exact variant NM_001127208.2:c.2193A>G was provided. PS4 therefore cannot be assessed.

Rule

Generic ACMG/AMP PS4 requires a statistically significant excess of the variant in affected individuals compared with controls or a validated disease-specific case series; no such evidence is available.

Evidence considered

• The consolidated bundle contains no phenotype prevalence, case-control, or exact-variant literature evidence; literature_pass.json reports total_pmids = 0.
• The variant is a synonymous TET2 substitution, NM_001127208.2:c.2193A>G (p.Gln731=), but variant consequence alone does not establish PS4 enrichment.

Still missing

• Case-control counts and statistical analysis for the exact variant are unavailable.
• No disease-specific affected-case series with ascertainment and comparator details is available.

Reasoning

PM3 cannot be assessed because the case bundle contains no affected-proband observations, no confirmed pathogenic or likely pathogenic variant in trans, no phase information, and no inheritance or family-genotype data for NM_001127208.2:c.2193A>G (p.Gln731=). The available population, ClinVar, and computational records do not establish recessive disease phase or affected-proband evidence.

Rule

Generic ACMG/AMP PM3: evidence that the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual; phase and disease-relevant inheritance context must be established.

Evidence considered

• The case bundle identifies the variant as NM_001127208.2:c.2193A>G, predicted p.Gln731=, but contains no affected-proband, phase, second-variant, or inheritance observations.
• The bundle reports no applicable TET2 VCEP/CSPEC framework; generic ACMG/AMP fallback is therefore used.
• ClinVar contains one single-submitter Likely benign record without criterion-lead evidence or supporting PMID, which does not establish PM3 evidence.

Still missing

• Affected-proband genotype and phenotype data are not provided.
• A second pathogenic or likely pathogenic variant in the relevant gene is not provided.
• Cis/trans phase information is not provided.
• Parental testing, inheritance mode, and family segregation data are not provided.

Reasoning

No presumed de novo occurrence is documented. The available evidence does not identify a proband, parental testing results, or a case report describing the variant as de novo without complete confirmation of parental genotypes.

Rule

Generic ACMG/AMP PM6 may be considered for a presumed de novo variant when parental origin is not fully confirmed, but only when a documented clinical case and phenotype support the observation; no such case evidence is available here.

Evidence considered

• The consolidated case-evidence bundle contains no family structure, parental testing, meiosis, or de novo narrative for NM_001127208.2:c.2193A>G.
• The only variant-specific clinical database record is a single-submitter ClinVar Likely benign entry without cited case literature; it does not document presumed de novo status.

Still missing

• A clinical observation supporting presumed de novo occurrence is not provided.
• Parental genotype data and the completeness of parental testing are not provided.
• Phenotype consistency and case-level details are not provided.

Reasoning

No affected or unaffected relatives carrying or lacking the variant are reported. Consequently, there are no informative meioses, segregation counts, phenotype concordance data, or family-based likelihood evidence from which to assess PP1.

Rule

Generic ACMG/AMP PP1 requires cosegregation of the variant with disease in affected family members; strength should reflect the number and informativeness of meioses and the consistency of the phenotype.

Evidence considered

• The case-evidence bundle contains no pedigree, familial variant testing, segregation analysis, or affected-relative observations.
• No publication with family-level segregation data for this exact variant was identified in the bundle.

Still missing

• Family pedigree and affected-relative status are not provided.
• Genotypes of informative relatives are not provided.
• Number of informative meioses and phenotype concordance are not provided.

Reasoning

No patient phenotype, clinical diagnosis, or disease-specific phenotype description is available in the case-evidence bundle. Phenotype specificity for NM_001127208.2:c.2193A>G cannot therefore be evaluated.

Rule

Generic ACMG/AMP PP4 requires a phenotype or family history highly specific for a disease with a single-gene etiology; no patient-specific phenotype evidence is available.

Evidence considered

• The case summary and consolidated evidence bundle do not contain patient-level phenotype findings or a disease diagnosis suitable for PP4 assessment.
• General TET2 disease or cancer context would not establish phenotype specificity for this individual variant and was not used to infer PP4.

Still missing

• Patient phenotype and clinical diagnosis are not provided.
• No highly specific phenotype-to-gene/disease concordance assessment is available.

Reasoning

No TET2 VCEP/ClinGen CSpec was found for this variant (cspec.found = false), so generic ACMG applies. The case-evidence bundle contains no functional/enzymatic assay data showing normal (wild-type-like) activity for NM_001127208.2:c.2193A>G. This variant is synonymous (p.Gln731=); SpliceAI lookup evidence is available only as a screenshot/URL reference in source_registry with no extracted score, so it cannot be used to establish a validated splicing-normal functional readout for BS3. literature_pass.json returned zero PMIDs.

Still missing

• No published or curated functional assay data demonstrating normal/wild-type activity for this variant
• SpliceAI screenshot/URL present in source_registry but no extracted splice-impact score available in the bundle to support a functional-normal conclusion

Reasoning

No affected family members, tested relatives, or genotype–phenotype discordance observations are documented. Absence of family data cannot establish non-segregation, so BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4 requires lack of segregation in affected family members when the phenotype is expected to be present; the evidence must be informative and not explained by phenocopy, reduced penetrance, age dependence, or misclassification.

Evidence considered

• The consolidated bundle provides no family pedigree, relative genotypes, or non-segregation observations for this variant.
• No exact-variant publication containing family-based non-segregation evidence was identified in the bundle.

Still missing

• Affected-relative phenotypes and clinical status are not provided.
• Genotypes of affected and unaffected relatives are not provided.
• Informative non-segregation events and pedigree structure are not provided.

Reasoning

BP2 cannot be assessed because the case bundle contains no affected or unaffected individual observations showing NM_001127208.2:c.2193A>G (p.Gln731=) in trans with a pathogenic or likely pathogenic variant, and no phase or inheritance data are available. No cis observation with a pathogenic variant in an affected individual is documented either.

Rule

Generic ACMG/AMP BP2: the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual, or in cis with a pathogenic variant in an affected individual, when that observation supports a benign interpretation of the variant under assessment.

Evidence considered

• The case bundle contains no family, proband, phase, or compound-variant data relevant to BP2.
• The available ClinVar record is a single-submitter Likely benign classification and does not document a BP2 observation.
• The bundle reports no applicable TET2 VCEP/CSPEC framework; generic ACMG/AMP fallback is therefore used.

Still missing

• No individual-level genotype observations are provided.
• No pathogenic or likely pathogenic comparator variant is provided.
• Cis/trans phase is unknown.
• Affected status and inheritance context are unknown.

Reasoning

No affected individual, phenotype, alternative molecular diagnosis, or independent pathogenic variant explaining a disease presentation is documented. BP5 cannot be assessed from the available evidence.

Rule

Generic ACMG/AMP BP5 requires a pathogenic variant in another gene or an alternative molecular explanation that accounts for the patient's phenotype; no such case evidence is available.

Evidence considered

• The consolidated case-evidence bundle provides no patient-level diagnostic context or competing molecular finding.
• The single-submitter ClinVar Likely benign assertion concerns the evaluated variant and is not evidence of an alternative molecular explanation for a patient's phenotype.

Still missing

• No clinical case context is provided in which an alternative molecular explanation could be evaluated.
• No documented alternative pathogenic variant or molecular diagnosis is available.