ETV6 c.1204T>G, p.(Tyr402Asp)

Reasoning

PM2 is met at supporting strength. NM_001987.4:c.1204T>G (ETV6 p.Tyr402Asp) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, supporting extreme rarity in population reference datasets.

Rule

Generic ACMG/AMP PM2: absent from population databases; applied at supporting strength.

Evidence considered

• No ETV6 ClinGen VCEP specification or local gene-specific framework was retrieved for this case; generic ACMG/AMP population-evidence interpretation was used.
• The queried variant was reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 across the queried builds.
• Under the generic ACMG/AMP framework, absence from population controls supports PM2 at supporting strength; no ancestry-specific enrichment, homozygote, or frequency artifact was reported because the variant was absent.

Still missing

• Population absence does not establish pathogenicity and does not supply an ETV6-specific maximum credible allele-frequency calculation.

Sources

Reasoning

No ClinGen VCEP/gene-specific PP3/BP4 lookup or cspec is available for ETV6 (cspec.found=false, vcep_materials empty, framework_mode=generic_acmg), so generic ACMG/AMP missense in-silico evidence applies. NM_001987.4:c.1204T>G / NP_001978.1:p.(Tyr402Asp) is a missense variant (consequence_class=missense; canonical_splice_consensus=false). REVEL (a validated, published multi-tool meta-predictor with a named calibration source, PMID 36413997) gives a score of 0.855 for this variant, which is well above the commonly used pathogenic-supporting REVEL cutoff (~0.7) established by that calibration, supporting a deleterious missense effect. BayesDel was also computed (score 0.187716) but per this pipeline's evidentiary standard no verified published threshold/PMID is available for BayesDel, so it is treated as not_available and excluded from the PP3/BP4 call (not double-counted, not fabricated). SpliceAI predicts no splice impact (max delta score = 0.041, well below any splice-altering threshold), consistent with this variant acting through the missense (not splicing) mechanism; this low splice score does not itself drive PP3/BP4 for a non-splice-region missense variant and is not counted as an independent criterion application. Net effect: one calibrated in-silico missense predictor (REVEL) with a named, cited threshold supports a deleterious effect, so PP3 is met at supporting strength (generic ACMG 2015 framework; no VCEP-specific graduated-strength table exists for ETV6 to justify moderate/strong).

Rule

generic_acmg_pp3_missense_revel

Evidence considered

• REVEL score = 0.855 for NM_001987.4:c.1204T>G (source_registry key 'revel'), exceeding the commonly applied pathogenic-supporting REVEL threshold (~0.7) from the REVEL calibration literature, PMID 36413997.
• SpliceAI max delta score = 0.041 (DS_AG 0.041, DS_AL 0.0, DS_DG 0.007, DS_DL 0.001) indicates no predicted splice impact, consistent with a missense (non-splicing) mechanism for this variant; this does not independently satisfy or negate PP3/BP4 for this missense variant.
• Variant is missense (NP_001978.1:p.(Tyr402Asp)); canonical_splice_consensus=false, so the splice-impact pathway is not the operative mechanism here.

Still missing

• No ETV6-specific VCEP/CSPEC PP3/BP4 lookup table exists to confirm gene-specific predictor choice or graduated strength thresholds.
• aGVGD was not available in the case bundle for this variant.
• BayesDel score exists but is excluded because no verified published calibration/threshold PMID is available to this pipeline.

Sources

Reasoning

PS1 requires a different nucleotide change producing the identical amino acid change (p.Y402D) that has already been established as pathogenic/likely pathogenic. ClinVar was queried for this exact variant (NM_001987.4:c.1204T>G / p.Tyr402Asp) and returned no result (search_status: no_result, found: false); no other nucleotide substitution encoding the same p.Tyr402Asp change was identified anywhere in the assembled evidence bundle, and no PMID in the literature pass discusses this exact amino-acid change. There is no qualifying same-amino-acid comparator to invoke PS1.

Rule

generic_ACMG_2015_PS1

Evidence considered

• ClinVar search for NM_001987.4:c.1204T>G / ETV6 p.Tyr402Asp returned search_status 'no_result' and found=false, i.e. this variant and by extension no reported synonymous-protein-outcome comparator variant is present in ClinVar.

Still missing

• No dedicated same-amino-acid-change (p.Tyr402Asp via alternate codon) ClinVar/literature search beyond the general ClinVar lookup was performed; if a future expanded ClinVar or HGMD search surfaces an alternate-codon p.Tyr402Asp classified P/LP, PS1 should be revisited.

Sources

Reasoning

BA1 is not met. NM_001987.4:c.1204T>G (ETV6 p.Tyr402Asp) was absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore, no allele frequency approaches a stand-alone benign threshold.

Rule

Generic ACMG/AMP BA1: stand-alone benign evidence requires allele frequency above the applicable benign threshold.

Evidence considered

• No ETV6 ClinGen VCEP specification or local gene-specific framework was retrieved for this case; generic ACMG/AMP population-evidence interpretation was used.
• The queried variant was reported absent in gnomAD v2.1 (GRCh37), gnomAD v4.1 (GRCh38), and gnomAD-Canada v1.0.

Sources

Reasoning

BS1 is not met. The variant is absent from the queried population datasets, so there is no allele frequency greater than expected for ETV6-related disease.

Rule

Generic ACMG/AMP BS1: benign strong evidence requires an allele frequency greater than expected for the disorder.

Evidence considered

• No ETV6 ClinGen VCEP specification or local gene-specific framework was retrieved for this case; generic ACMG/AMP population-evidence interpretation was used.
• The queried variant was reported absent in gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; consequently, no overall or ancestry-specific allele frequency is available that could exceed an ETV6 disease-compatible BS1 threshold.

Sources

Reasoning

BS2 is not met. Because the variant is absent from the queried population datasets, there are no observed homozygotes or adult unaffected carriers from these sources to support benignity.

Rule

Generic ACMG/AMP BS2: observe the variant in a healthy adult individual for a fully penetrant early-onset disorder.

Evidence considered

• No ETV6 ClinGen VCEP specification or local gene-specific framework was retrieved for this case; generic ACMG/AMP population-evidence interpretation was used.
• The queried variant was reported absent in gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, precluding observation of homozygotes or unaffected adult carriers in these resources.
• ETV6-related predisposition has variable penetrance and age-dependent hematologic malignancy risk; therefore, an unaffected-carrier assertion would require adequately phenotyped, age-appropriate individuals and cannot be inferred from database absence.

Still missing

• No cohort-level phenotype or age data for carriers are available because no carriers were observed in the queried population datasets.

Sources

Reasoning

BP4 (benign computational prediction) is not met because the calibrated missense predictor available for this variant (REVEL, score 0.855, PMID 36413997 calibration) indicates a deleterious rather than benign effect, and BP4/PP3 are mutually exclusive for the same variant. BayesDel (score 0.187716) is not usable for either PP3 or BP4 because no verified published threshold/PMID for BayesDel is available to this pipeline, so it cannot be cited to support a benign call. SpliceAI predicts no splice impact (max delta score = 0.041), which is consistent with no splice-mediated pathogenicity but is not independently applied as a BP4 call for this missense (non-splice-region) variant, avoiding double counting the same prediction across PP3/BP4/BP7.

Rule

generic_acmg_bp4_missense_revel

Evidence considered

• REVEL score = 0.855 (source_registry key 'revel') is above the pathogenic-supporting threshold from REVEL calibration literature, PMID 36413997, so the calibrated missense predictor does not support a benign call, precluding BP4.

Still missing

• No ETV6-specific VCEP/CSPEC PP3/BP4 lookup table exists to confirm gene-specific predictor choice or thresholds.
• BayesDel score present but excluded from BP4 consideration due to lack of a verified published calibration/threshold PMID for this pipeline.

Sources

Reasoning

No proband-level phenotype, parental genotypes, parentage confirmation, or germline tissue testing is provided. De novo occurrence cannot be established.

Rule

Generic ACMG/AMP fallback: PS2 requires a confirmed de novo occurrence in an affected individual with phenotype consistency.

Evidence considered

• The consolidated case-evidence bundle identifies no ETV6 CSPEC/VCEP or local gene-specific framework; generic ACMG/AMP fallback applies.
• The bundle contains no individual-level family, parental-testing, or phenotype data for NM_001987.4:c.1204T>G.

Still missing

• Obtain validated germline testing for the proband and both biological parents.
• Confirm biological parentage and document whether the proband phenotype is consistent with ETV6-related disease.

Reasoning

No ClinGen VCEP/gene-specific functional assay specification is available for ETV6 (cspec.found=false, vcep_materials empty, framework_mode=generic_acmg). No functional/biochemical assay data (e.g., DNA-binding, transcriptional repression, dimerization, or transformation assays) for NM_001987.4:c.1204T>G / p.(Tyr402Asp) were identified in the case evidence bundle. Literature search returned zero PMIDs overall (literature_pass.json: total_pmids=0), and the fulltext_map is empty, so no full-text papers were available to review for functional characterization of this specific variant. The PVS1 gene-context literature search (focused on germline disease association, not functional assays) likewise did not surface any variant-specific functional study for c.1204T>G.

Still missing

• No validated functional assay (e.g., ETS-domain DNA-binding, transcriptional repression/transactivation, dimerization, or hematopoietic differentiation assay) has been identified for this specific variant.
• No VCEP-approved PS3/BS3 assay framework exists for ETV6 in this case bundle to define assay validation, control, and strength-calibration requirements.
• A targeted literature search specifically for functional characterization of ETV6 p.(Tyr402Asp)/p.Y402D was not performed as part of this case's automated literature pass (0 PMIDs returned).

Reasoning

No case-control or statistically valid case-enrichment data for ETV6 c.1204T>G (p.Tyr402Asp) were retrieved.

Rule

Generic ACMG/AMP PS4 requires a statistically increased prevalence of the variant in affected individuals compared with controls.

Evidence considered

• The literature evidence bundle contains no PMIDs or variant-specific publications, and no case-control data for this variant were retrieved.

Still missing

• Variant-specific affected and control counts, cohort ascertainment, and a valid enrichment analysis are required.

Reasoning

PM1 requires the variant to fall in a mutational hotspot and/or a well-established functional domain without benign variation. The automated cancerhotspots.org lookup for ETV6 Y402 returned no significant hotspot result, and COSMIC returned no somatic recurrence. However, no gene-specific VCEP/CSPEC framework was found for ETV6 (cspec.found=false, gene_vcep_dir=null), and no formal protein-domain boundary annotation (e.g., UniProt ETS domain coordinates) or missense-clustering/benign-variation-density source is present anywhere in this evidence bundle to confirm or refute whether residue 402 lies within a domain meeting PM1's 'well-established functional domain, no benign variation' bar. Applying PM1 based on general knowledge of the ETV6 ETS domain location, without a citable source in this case's evidence pool, would not be adequately grounded.

Rule

generic_ACMG_2015_PM1

Evidence considered

• cancerhotspots.org query for 'ETV6 Y402' returned search_status='no_result', found=false — no statistically significant somatic mutational hotspot at this residue was identified.
• COSMIC search for ETV6 c.1204T>G returned search_status='no_result', found=false — no prior somatic cancer reporting at this position.

Still missing

• No formal protein domain boundary source (e.g., UniProt/InterPro ETS domain coordinates for ETV6/NP_001978.1) present in the evidence bundle to confirm residue 402 domain membership.
• No ClinGen VCEP-defined PM1 hotspot/domain rule available for ETV6 (cspec not found).
• cancerhotspots.org and COSMIC both returned negative/no-result for this residue, arguing against a somatic mutational hotspot, but this does not resolve germline structural/functional domain status.

Reasoning

PM3 cannot be assessed. No affected-proband observation, second ETV6 variant, phase result, or pathogenic/likely pathogenic variant documented in trans with NM_001987.4:c.1204T>G is present in the consolidated case-evidence bundle.

Rule

Generic ACMG/AMP PM3: variant observed in trans with a pathogenic variant for a recessive disorder.

Evidence considered

• No ETV6 CSPEC/VCEP or local gene-specific framework was retrieved; the case designates generic ACMG/AMP fallback.
• Under generic ACMG/AMP, PM3 requires observation of the variant in trans with a pathogenic variant in a recessive disorder. The bundle contains no proband, second-allele, or phase evidence.

Still missing

• Affected-proband data with a qualifying ETV6-associated recessive phenotype, if applicable.
• Identity and classification of any second ETV6 variant and confirmed trans phase.

Sources

Reasoning

PM5 requires a different missense change at the same residue (p.Tyr402X) previously established as pathogenic/likely pathogenic. The dedicated PM5 candidate-harvesting step for this case explicitly did not run: pm5_candidates.json reports eligible_for_classic_pm5_search=false with pm5_mode='unknown' and the stated reason 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting,' yielding zero candidates (total_candidates_seen=0). No alternate amino-acid substitution at codon 402 with an established pathogenic/likely pathogenic ClinVar classification was surfaced anywhere else in this evidence bundle.

Rule

generic_ACMG_2015_PM5

Evidence considered

• pm5_candidates.json: eligible_for_classic_pm5_search=false, pm5_mode='unknown', reason='Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting', candidate_summary.total_candidates_seen=0, recommendation.level='not_applicable' with instruction to not apply PM5 from this artifact alone.

Still missing

• Automated same-residue (codon 402) comparator-variant harvesting was explicitly skipped upstream; a manual ClinVar/literature search for other p.Tyr402* substitutions (e.g., p.Tyr402Cys, p.Tyr402His, p.Tyr402Asn) has not been performed for this case and is required before PM5 can be confidently assessed.

Sources

Reasoning

No reported de novo occurrence is available, and parental testing is not provided. Assumed de novo status cannot be assigned.

Rule

Generic ACMG/AMP fallback: PM6 may be considered only for a de novo occurrence lacking full confirmation; no occurrence is documented here.

Evidence considered

• The consolidated case-evidence bundle identifies no ETV6 CSPEC/VCEP or local gene-specific framework; generic ACMG/AMP fallback applies.
• The bundle contains no report that the variant occurred de novo or that either parent was tested.

Still missing

• Obtain proband and parental germline genotypes, including documentation of any unavailable parent.
• Document the proband phenotype and its consistency with ETV6-related disease.

Reasoning

No pedigree, affected-relative genotypes, unaffected-relative genotypes, or count of informative meioses is provided; segregation cannot be evaluated.

Rule

Generic ACMG/AMP fallback: PP1 requires cosegregation with disease in multiple affected family members; no informative segregations are documented.

Evidence considered

• The consolidated case-evidence bundle identifies no ETV6 CSPEC/VCEP or local gene-specific framework; generic ACMG/AMP fallback applies.
• The bundle contains no family segregation data for NM_001987.4:c.1204T>G.

Still missing

• Obtain a pedigree with relevant ETV6-associated phenotypes and confirmed genotypes for informative relatives.
• Document the number of informative segregations/meioses and account for age-dependent or incomplete penetrance where relevant.

Reasoning

PP2 requires the gene to have a low rate of benign missense variation and missense to be a common mechanism of disease. No ClinGen VCEP/CSPEC framework for ETV6 is available in this case (cspec.found=false) to confirm PP2 applicability, and no gene-level missense constraint metric (e.g., gnomAD missense Z-score / o:e ratio) or benign-missense-rate statistic is present anywhere in the assembled evidence bundle. The gene-context literature review performed for PVS1 purposes (pvs1_gene_context) establishes that ETV6 has a germline loss-of-function disease mechanism supported by disease-focused literature, but that review targeted LOF/truncating mechanism eligibility, not a quantified missense benign-variation rate, so it cannot substitute for the PP2-specific evidence needed here.

Rule

generic_ACMG_2015_PP2

Still missing

• No gene-level missense constraint metric (missense Z-score, o/e ratio) or ClinVar-derived benign-missense-rate statistic retrieved for ETV6 in this evidence bundle.
• No ClinGen VCEP-defined PP2 applicability statement for ETV6 (cspec not found).

Reasoning

No proband phenotype, phenotype-to-gene specificity assessment, or variant-specific clinical report was supplied for this case.

Rule

Generic ACMG/AMP PP4 requires a patient phenotype or family history highly specific for a disease with a single genetic etiology.

Evidence considered

• Although ETV6 is reported in the case bundle as associated with thrombocytopenia and hematologic malignancy predisposition, no phenotype was provided for the individual carrying p.Tyr402Asp; gene-level association alone cannot establish PP4.

Still missing

• Structured proband phenotype and clinical testing context are required to determine whether the presentation is highly specific for an ETV6-associated condition.

Reasoning

ClinVar returned no record for the exact variant; therefore, no exact-variant pathogenic or likely pathogenic expert-panel assertion is available.

Rule

Apply PP5 only to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; laboratory assertions and aggregate labels are insufficient.

Evidence considered

• The retrieved ClinVar search found no exact match for NM_001987.4:c.1204T>G / p.Tyr402Asp and no submissions.

Still missing

• An exact-variant ClinVar submission reviewed by an expert panel and classified as Pathogenic or Likely pathogenic is required.

Sources

Reasoning

No ClinGen VCEP/gene-specific functional assay specification is available for ETV6 (cspec.found=false, vcep_materials empty, framework_mode=generic_acmg). No functional assay data showing normal/wild-type-like activity for NM_001987.4:c.1204T>G / p.(Tyr402Asp) were identified in the case evidence bundle. Literature search returned zero PMIDs overall (literature_pass.json: total_pmids=0), and the fulltext_map is empty, so no full-text papers were available to review for a benign functional readout on this specific variant.

Still missing

• No functional assay data (validated or otherwise) demonstrating wild-type/normal activity for this specific variant were identified.
• No VCEP-approved BS3 assay framework exists for ETV6 in this case bundle to define assay validation, control, and strength-calibration requirements.
• A targeted literature search specifically for functional characterization of ETV6 p.(Tyr402Asp)/p.Y402D was not performed as part of this case's automated literature pass (0 PMIDs returned).

Reasoning

No informative non-segregation evidence is provided. The case contains no genotype-phenotype observations in relatives from which lack of segregation could be established.

Rule

Generic ACMG/AMP fallback: BS4 requires lack of segregation in affected family members; no informative non-segregation data are documented.

Evidence considered

• The consolidated case-evidence bundle identifies no ETV6 CSPEC/VCEP or local gene-specific framework; generic ACMG/AMP fallback applies.
• The bundle contains no relatives with paired genotype and phenotype data for NM_001987.4:c.1204T>G.

Still missing

• Obtain confirmed genotypes and clinically relevant phenotype assessments for informative affected and unaffected relatives.
• Assess penetrance, age, and alternative explanations before interpreting any apparent non-segregation.

Reasoning

BP1 requires the gene's disease mechanism to be predominantly truncating/loss-of-function such that a missense variant is less likely pathogenic. No ClinGen VCEP/CSPEC framework for ETV6 is available to make this determination, and no quantified statement in this evidence bundle establishes that missense variation is depleted among pathogenic ETV6 alleles versus truncating variants. The pvs1_gene_context artifact confirms germline LOF is a supported disease mechanism for ETV6 but does not characterize the relative contribution of missense variants, so it is insufficient on its own to assess BP1 either way.

Rule

generic_ACMG_2015_BP1

Still missing

• No gene-level statement in the evidence bundle on the relative proportion/mechanism of pathogenic missense versus truncating ETV6 variants.
• No ClinGen VCEP-defined BP1 applicability rule for ETV6 (cspec not found).

Reasoning

BP2 cannot be assessed. The consolidated case-evidence bundle provides no observation of NM_001987.4:c.1204T>G in cis with a pathogenic/likely pathogenic ETV6 variant, and no homozygous observation in an unaffected individual.

Rule

Generic ACMG/AMP BP2: observed in cis with a pathogenic variant or observed homozygous in an unaffected individual for a fully penetrant dominant condition.

Evidence considered

• No ETV6 CSPEC/VCEP or local gene-specific framework was retrieved; the case designates generic ACMG/AMP fallback.
• Under generic ACMG/AMP, BP2 requires a cis observation with a pathogenic variant or a homozygous observation in an unaffected individual for a fully penetrant dominant condition. Neither type of observation is available in the bundle.

Still missing

• Phased genotype showing whether this variant is in cis with a pathogenic/likely pathogenic ETV6 variant.
• If relevant to the disease model, a well-documented homozygous unaffected observation with penetrance context.

Sources

Reasoning

No clinical phenotype or independent molecular diagnosis was supplied to assess whether this variant was observed in an individual with an alternative molecular cause for disease.

Rule

Generic ACMG/AMP BP5 requires observation in a case with an alternative molecular basis for disease.

Evidence considered

• The case evidence bundle contains no patient-level phenotype or alternate diagnostic finding.

Still missing

• Proband phenotype, complete diagnostic testing results, and documentation of any alternative molecular diagnosis are required.

Reasoning

ClinVar returned no record for the exact variant; therefore, no exact-variant benign or likely benign expert-panel assertion is available.

Rule

Apply BP6 only to an exact-variant ClinVar expert-panel Benign or Likely benign classification; laboratory assertions and aggregate labels are insufficient.

Evidence considered

• The retrieved ClinVar search found no exact match for NM_001987.4:c.1204T>G / p.Tyr402Asp and no submissions.

Still missing

• An exact-variant ClinVar submission reviewed by an expert panel and classified as Benign or Likely benign is required.

Sources