RET c.1837C>A, p.(Pro613Thr)

Reasoning

NM_020975.5:c.1837C>A (RET p.Pro613Thr) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This supports PM2 at supporting strength under the generic ACMG/AMP framework because the variant is not observed in the available reference population datasets.

Rule

PM2 at supporting strength is applicable when a variant is absent from population databases appropriate for the disease context; this assessment uses the generic ACMG/AMP fallback because no RET-specific specification was available.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent.
• The variant is a missense substitution, NM_020975.5:c.1837C>A, predicted as NP_066124.1:p.(Pro613Thr).
• No applicable RET-specific CSPEC or VCEP framework was retrieved, so generic ACMG/AMP criteria are used.

Still missing

• The bundle does not provide dataset sample sizes, ancestry-specific coverage, or a disease-specific maximum credible allele frequency.

Sources

Reasoning

No governing VCEP/CSPEC was available for RET in this case (cspec.found=false; vcep_materials.json contains no gene-specific PP3/BP4 lookup table), so generic ACMG in-silico assessment applies. SpliceAI predicts no splice impact for this variant (max delta score = 0.013 across all four donor/acceptor gain/loss metrics; DS_AG 0.005, DS_AL 0.013, DS_DG 0.01, DS_DL 0.013), well below the widely used 0.2 high-precision pathogenic-impact threshold from the original SpliceAI calibration publication (Jaganathan et al. 2019, PMID 30661751); Pangolin scores are similarly near zero (SG 0.007, SL -0.01), providing a second concordant splice-prediction tool with no signal. This supports BP4 at the supporting strength level via the splicing-impact route. On the missense-predictor side, REVEL (0.319) falls in the indeterminate zone (does not cross the ClinGen SVI-calibrated benign-supporting threshold of <0.290, PMID 36413997) and BayesDel has no verified published threshold available to this pipeline, so neither contributes a missense-path benign signal; only the splicing evidence supports BP4 here.

Rule

generic_acmg_bp4_splicing

Evidence considered

• SpliceAI (source_registry key 'spliceai') predicts max delta score 0.013, well below the 0.2 high-precision no-impact/impact threshold established in Jaganathan et al. 2019 (PMID 30661751), and Pangolin splice-gain/loss scores (SG 0.007, SL -0.01) concur, supporting BP4 at supporting strength via the splicing route.
• REVEL score 0.319 (source_registry key 'revel') is in the indeterminate zone of the ClinGen SVI-calibrated thresholds (Pejaver et al. 2022, PMID 36413997) and does not itself reach the benign-supporting cutoff (<0.290), so it is not counted as an additional corroborating line for BP4.
• BayesDel score -0.0482401 (source_registry key 'bayesdel') has no verified published calibration threshold/table available to this pipeline and is treated as not_available, so it is not used to support BP4.

Still missing

• REVEL score (0.319) does not itself cross the calibrated benign-supporting threshold (<0.290), so it does not independently corroborate BP4; BP4 here rests on the splicing-prediction line of evidence only.
• BayesDel score is present but has no verified published threshold/citation for this pipeline and cannot be used to corroborate BP4.
• No RET-specific VCEP PP3/BP4 lookup table was found for this variant.

Sources

Reasoning

No governing VCEP/CSPEC was available for RET in this case (cspec.found=false; vcep_materials.json contains no gene-specific PP3/BP4 lookup table), so generic ACMG in-silico assessment applies. Missense path: REVEL score = 0.319, which falls in the indeterminate zone of the ClinGen SVI-calibrated REVEL thresholds (supporting-pathogenic requires >0.644; supporting-benign requires <0.290) and therefore crosses neither threshold. BayesDel score (-0.0482) is available but per this pipeline's calibration status has no verified published threshold/table citation, so it is treated as not_available and cannot be used for PP3. No aGVGD score is present. Splice path: SpliceAI predicts no significant splice impact (max delta score 0.013, well below the established high-precision pathogenic threshold of 0.2 from the original SpliceAI calibration publication), which argues against rather than for a splice-disruption mechanism. No line of computational evidence in this case reaches a pathogenic-supporting threshold, so PP3 is not met.

Rule

generic_acmg_pp3_computational

Evidence considered

• REVEL score 0.319 (source_registry key 'revel') falls between the ClinGen SVI-calibrated REVEL benign-supporting threshold (<0.290) and pathogenic-supporting threshold (>0.644), i.e., indeterminate; thresholds per Pejaver et al. 2022, PMID 36413997.
• BayesDel score -0.0482401 (source_registry key 'bayesdel') is reported but no verified published calibration threshold/table can be named for this pipeline, so it is treated as not_available for PP3 per current calibration policy (BayesDel specifically excluded absent a citable publication/table).
• SpliceAI (source_registry key 'spliceai') predicts max delta score 0.013 (DS_AG 0.005, DS_AL 0.013, DS_DG 0.01, DS_DL 0.013), far below the 0.2 high-precision threshold established in the original SpliceAI publication (Jaganathan et al. 2019, PMID 30661751), indicating no predicted splice impact and therefore no support for PP3 via a splicing mechanism.

Still missing

• REVEL score (0.319) is in the indeterminate zone between calibrated benign and pathogenic thresholds and cannot independently support PP3.
• BayesDel score is present but this pipeline has no verified published threshold/citation for it, so it cannot be used for PP3 per current calibration policy.
• No aGVGD/missense-specific structural predictor score available in this case.
• No RET-specific VCEP PP3/BP4 lookup table was found for this variant.

Sources

Reasoning

The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. No population allele frequency is available that reaches a stand-alone benign threshold; therefore BA1 is not met.

Rule

BA1 requires a population allele frequency high enough for a stand-alone benign classification; no such frequency is observed here.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent.
• Because no allele frequency is reported, the BA1 stand-alone benign frequency threshold cannot be reached.

Still missing

• No independent population dataset with a measurable allele frequency was provided.

Sources

Reasoning

The variant is absent from the available gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 datasets. There is no observed allele frequency above the expected disease-prevalence threshold to support BS1.

Rule

BS1 requires an allele frequency greater than expected for the disorder; no qualifying frequency is available.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent.
• An absent variant cannot satisfy the BS1 requirement for an allele frequency greater than expected for the disorder.

Still missing

• No disease-specific maximum tolerated allele frequency or independent population frequency estimate was provided.

Sources

Reasoning

BP1 applies to missense variants in genes where truncating variants are the primary/well-established disease mechanism and missense variants are rarely pathogenic. RET is not such a gene: OncoKB's gene-level curation and general RET biology (as reflected in the pvs1_gene_context germline literature review) describe RET as a receptor tyrosine kinase in which activating missense variants are a well-established, primary mechanism of disease (e.g. MEN2A/2B), so a gene where missense pathogenicity is common does not satisfy the BP1 rationale.

Rule

Generic ACMG/AMP 2015 (BP1: missense variant in a gene for which primarily truncating variants are known to cause disease) — no RET CSPEC available.

Evidence considered

• OncoKB gene-level summary: 'RET, a receptor tyrosine kinase, is altered by mutation in medullary thyroid cancers and by chromosomal rearrangement in lung cancers, papillary thyroid cancers, and rarely, other solid tumors' — indicating missense/point mutation is a recognized RET oncogenic mechanism, not merely truncation.
• pvs1_gene_context.json germline literature review (PMID:40175156 case report) discusses a germline RET missense variant (p.Met918Trp) causing MEN2B, supporting missense as an established primary germline disease mechanism for RET, which argues against BP1 applicability.

Still missing

• No RET-specific VCEP/CSPEC statement formally excluding BP1 for this gene; conclusion relies on generic-gene-mechanism reasoning from OncoKB gene summary and PVS1 gene-context literature review rather than a dedicated missense-mechanism statistic.

Sources

Reasoning

PS1 requires an independent source establishing the same amino-acid change (p.Pro613Thr) as pathogenic via a different nucleotide change. The only ClinVar record retrieved for this variant is itself Uncertain significance (single submitter), and the retrieval carried a title-mismatch warning (returned record title referenced a different variant, c.2734C>A p.Arg912=), so it cannot serve as an independent pathogenic precedent. No other database or literature source in the bundle reports p.Pro613Thr classified as pathogenic/likely pathogenic by a different codon change.

Rule

Generic ACMG/AMP 2015 (PS1: same amino acid change as an established pathogenic variant, different nucleotide change) — no RET CSPEC available (cspec.found=false in case_summary.json).

Evidence considered

• case_summary.json ClinVar entry for this variant reports classification 'Uncertain significance', review status 'criteria provided, single submitter', with a warning that the retrieved record title (c.2734C>A p.Arg912=) did not match the queried variant, so this ClinVar record cannot be used as a same-amino-acid-change pathogenic precedent for PS1.

Still missing

• No independent ClinVar/literature record confirming p.Pro613Thr (or a synonymous-at-protein-level different-nucleotide variant reaching the same amino acid) as Pathogenic/Likely pathogenic.
• No RET-specific VCEP/CSPEC framework available to define PS1 application rules for this gene.

Sources

Reasoning

No case-specific evidence documents a confirmed de novo occurrence of NM_020975.5:c.1837C>A (NP_066124.1:p.Pro613Thr) in an affected proband with confirmed maternity and paternity and parental testing demonstrating that the variant is absent in both parents.

Rule

Generic ACMG/AMP PS2 requires the variant to occur de novo in an affected individual with confirmed maternity and paternity; without those case data, PS2 is not assessed.

Evidence considered

• The consolidated case-evidence bundle contains no proband, parental-testing, maternity/paternity, or de novo segregation evidence for this variant.

Still missing

• Affected-proband clinical information is not provided.
• Parental genotypes and confirmed maternity/paternity are not provided.
• No validated de novo testing result is provided.

Reasoning

No validated functional assay data (kinase activity, phosphorylation, cell-based transformation, or other RET-relevant functional study) for NM_020975.5:c.1837C>A (p.Pro613Thr) was found anywhere in the case-evidence bundle. No CSPEC/VCEP framework was located for RET in this case (cspec.found=false; final_classification_framework.found=false, generic_acmg fallback), so no gene-specific PS3 calibration is available either. OncoKB reports 'Unknown Oncogenic Effect' with no variant-specific reviewed functional evidence. The single literature hit (PMID:25394175) is a referral-indications practice guideline unrelated to functional assays and does not mention this variant. No basis exists to apply PS3.

Still missing

• No functional/biochemical assay data (e.g., kinase activity, cAMP signaling, transformation assays) identified for this variant in the available sources
• No RET-specific VCEP/CSPEC PS3 assay-validation framework was available in this case to define approved assay types or strength calibration
• OncoKB and literature search did not surface variant-specific functional characterization

Reasoning

No variant-specific case series, case-control enrichment analysis, affected-case count, or control comparison was provided for RET NM_020975.5:c.1837C>A (p.Pro613Thr). The single somatic COSMIC observation is not a germline phenotype or case-control dataset and cannot establish PS4.

Rule

Generic ACMG/AMP PS4 requires a statistically significant excess of affected individuals with the variant compared with controls or other appropriate population data; no applicable RET-specific specification was retrieved.

Evidence considered

• The case bundle reports RET NM_020975.5:c.1837C>A (p.Pro613Thr), but contains no germline case series, phenotype cohort, or case-control comparison for the exact variant.
• COSMIC reports one somatic occurrence (COSV114952636; n=1), which does not provide germline phenotype specificity or case-control enrichment for PS4.

Still missing

• Variant-specific affected-case ascertainment and phenotype data are absent.
• No case-control enrichment statistics or appropriately matched controls are available.
• The only cancer-database observation is one somatic record and is not usable as germline PS4 evidence.

Reasoning

PM1 requires the variant to fall in a well-established mutational hotspot or critical/well-characterized functional domain without benign variation. No RET-specific CSPEC/VCEP domain framework is present in this case (cspec.found=false; vcep_materials note='no cspec url available'), and no registry-tracked source in this bundle provides RET protein-domain boundary or missense-constraint data for codon 613. A hotspot database screen (not a registered evidence source in source_registry.json) returned no statistically significant hotspot at this residue, but this alone is insufficient to positively assign PM1 status without a proper domain/hotspot framework citation.

Rule

Generic ACMG/AMP 2015 (PM1: mutational hotspot or critical/well-established functional domain without benign variation) — no RET CSPEC available.

Evidence considered

• cancerhotspots.org screen for RET P613 returned 'no_result' / 'This variant does not lie in a statistically significant hotspot' (case_summary.json/evidence.json hotspots field), but this source is not present as a key in source_registry.json so it cannot be formally cited as evidence_refs; it is noted here only as context supporting the absence of hotspot evidence.

Still missing

• No RET-specific VCEP/CSPEC domain map (e.g. cadherin-like domain boundaries, cysteine-rich domain boundaries) available as a registered, citable source to determine whether codon 613 sits in a critical functional domain.
• No missense-constraint or hotspot-enrichment statistic (e.g. UniProt/Pfam-annotated domain plus a validated hotspot statistic) available via a source_registry-tracked source for this residue.

Reasoning

No applicable RET-specific VCEP framework was available, so the generic ACMG/AMP framework applies. The case-evidence bundle contains no affected-proband observations, no confirmed pathogenic or likely pathogenic variant in the same individual, and no phasing or inheritance information establishing the target variant in trans with a pathogenic variant for a recessive condition.

Rule

Generic PM3: use only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive condition; strength requires sufficient validated observations and phase evidence.

Evidence considered

• The consolidated case-evidence bundle reports no CSPEC/VCEP specification for RET and no family, proband, phase, or inheritance observations relevant to PM3.
• The bundle identifies the target as NM_020975.5:c.1837C>A (p.Pro613Thr) and provides no evidence of a pathogenic variant in trans or cis in an affected individual.
• Generic ACMG/AMP criteria are used because no applicable gene-specific framework was retrieved.

Still missing

• Affected-proband observations are not available.
• A confirmed pathogenic or likely pathogenic variant for trans comparison is not available.
• Phase and inheritance data are not available.

Sources

Reasoning

No case-specific evidence documents a presumed de novo occurrence of NM_020975.5:c.1837C>A in an affected proband when parental testing is unavailable or incomplete.

Rule

Generic ACMG/AMP PM6 applies to a presumed de novo occurrence in an affected individual when maternity and paternity are confirmed but parental testing is unavailable or incomplete; the required case evidence is absent.

Evidence considered

• The consolidated case-evidence bundle contains no pedigree, family history, parental testing, or presumed de novo observation for this variant.

Still missing

• Affected-proband clinical information is not provided.
• Parental testing status is not provided.
• No clinical report or pedigree establishes a presumed de novo event.

Reasoning

No informative affected relatives, unaffected relatives, phase information, or meioses are reported for NM_020975.5:c.1837C>A, so cosegregation cannot be evaluated.

Rule

Generic ACMG/AMP PP1 requires cosegregation with disease in multiple affected family members; strength cannot be assigned without informative family observations and meioses.

Evidence considered

• The consolidated case-evidence bundle contains no family segregation observations or meiosis counts for this variant.

Still missing

• No pedigree or family structure is provided.
• No genotypes and phenotypes of relatives are provided.
• No number of informative meioses or segregation statistics are provided.

Reasoning

Generic PP2 requires the variant to occur in a gene with a low rate of benign missense variation and where missense variants are a common mechanism of disease. No gnomAD missense constraint metric (e.g. missense Z-score) or benign-missense-rate statistic is present anywhere in this bundle for RET, and no RET CSPEC/VCEP framework is available to state a gene-specific PP2 rule. RET is also known to have a mixed disease mechanism (activating/gain-of-function missense in MEN2A/2B alongside loss-of-function missense/truncating in Hirschsprung disease), which complicates a reliable generic PP2 call without the actual constraint data.

Rule

Generic ACMG/AMP 2015 (PP2: missense variant in a gene with low rate of benign missense variation where missense is a common mechanism of disease) — no RET CSPEC available; required constraint data not present in bundle.

Still missing

• No gnomAD missense Z-score or equivalent benign-missense-rate metric for RET provided in this bundle.
• No RET-specific VCEP/CSPEC statement on whether PP2 is recommended for this gene.

Reasoning

The bundle does not provide the patient's phenotype, a defined RET-associated syndrome diagnosis, or a phenotype-specific differential demonstrating that the clinical presentation is highly specific for a disease caused by RET variation. PP4 therefore cannot be assessed.

Rule

Generic ACMG/AMP PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single genetic etiology; no applicable RET-specific specification was retrieved.

Evidence considered

• The consolidated case-evidence bundle contains variant normalization and database results but no patient phenotype or syndrome-level clinical description sufficient for PP4.

Still missing

• No patient phenotype or clinical summary is available for comparison with RET-associated disease features.
• No phenotype-specific disease definition or differential diagnosis is documented.
• No RET-specific phenotype specificity assessment is available.

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification. ClinVar did not validate an exact match: the returned record is NM_020975.6(RET):c.2734C>A (p.Arg912=), classified Uncertain significance by a single laboratory submission, with no expert-panel submission. Therefore PP5 is not supported.

Rule

Apply PP5 only when the exact variant has a ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary submissions, aggregate labels, non-expert assertions, and mismatched variants do not qualify.

Evidence considered

• ClinVar exact-match validation failed; the returned record is NM_020975.6(RET):c.2734C>A (p.Arg912=), not NM_020975.5:c.1837C>A (p.Pro613Thr).
• The only available submission is from Ambry Genetics, is marked criteria provided/single submitter, is not an expert-panel assertion, and is classified Uncertain significance.

Still missing

• No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is present.
• The available ClinVar record is for a different variant and is a non-expert single-submitter Uncertain significance assertion.

Sources

Reasoning

The available population evidence only states that the variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. It does not document the variant in healthy adults, nor does it provide genotype-level observations or homozygote counts. BS2 therefore cannot be assessed from this bundle.

Rule

BS2 requires observation of the variant in healthy adult individuals in a disease model where that observation is informative; absence from population databases is insufficient.

Evidence considered

• All three available population resources report the variant as absent; absence does not establish the BS2 finding of observation in healthy adults.
• The bundle contains no healthy-adult phenotype or genotype observation for this variant.

Still missing

• No verified healthy-adult carrier observations were provided.
• No genotype counts or homozygote observations were provided.
• No penetrance and inheritance-specific assessment of whether healthy observation would contradict the disease model was provided.

Sources

Reasoning

No functional assay data demonstrating normal/wild-type-equivalent function for NM_020975.5:c.1837C>A (p.Pro613Thr) was found in the case-evidence bundle. No RET-specific CSPEC/VCEP framework was available to define BS3 assay standards. OncoKB and the single retrieved publication (PMID:25394175, a referral-guideline paper not mentioning this variant) provide no functional evidence either supporting or refuting pathogenicity. No basis exists to apply BS3.

Still missing

• No functional assay data (of any validation quality) identified for this variant in the available sources
• No RET-specific VCEP/CSPEC BS3 assay-validation framework was available in this case

Reasoning

No unaffected relatives who are informative for the familial variant are documented, and no non-segregation analysis is available; therefore BS4 cannot be assessed.

Rule

Generic ACMG/AMP BS4 requires lack of segregation in affected family members or presence of the variant in unaffected relatives when the phenotype is expected to be expressed; no such family evidence is available.

Evidence considered

• The consolidated case-evidence bundle contains no unaffected-relative genotypes or non-segregation observations for this variant.

Still missing

• No pedigree or familial disease status is provided.
• No genotypes of unaffected relatives are provided.
• No assessment of age-dependent penetrance or phenotype ascertainment is provided.

Reasoning

No applicable RET-specific VCEP framework was available, so the generic ACMG/AMP framework applies. The case-evidence bundle contains no documented observation of the target variant in cis with a pathogenic variant, no unaffected individual data, and no validated phase or inheritance information supporting BP2.

Rule

Generic BP2: consider when the variant is observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder, with appropriate phenotype and phase context; absent such validated allelic evidence, do not apply.

Evidence considered

• The consolidated case-evidence bundle reports no CSPEC/VCEP specification for RET and no family or individual-level allelic observations relevant to BP2.
• The bundle provides no validated evidence that NM_020975.5:c.1837C>A (p.Pro613Thr) occurs in cis with a pathogenic variant or in unaffected individuals.
• Generic ACMG/AMP criteria are used because no applicable gene-specific framework was retrieved.

Still missing

• Observations in unaffected individuals are not available.
• A pathogenic variant in cis is not documented.
• Phase and inheritance data are not available.

Sources

Reasoning

No clinical case with an established alternate molecular etiology is documented. The one COSMIC somatic observation does not identify an alternate germline cause of a patient's phenotype and cannot establish BP5.

Rule

Generic ACMG/AMP BP5 requires the variant to be found in a patient whose phenotype is explained by an alternative molecular etiology; no applicable RET-specific specification was retrieved.

Evidence considered

• The case bundle reports one somatic COSMIC occurrence for the variant, but provides no affected patient, phenotype, or alternate molecular diagnosis.
• A somatic database occurrence alone cannot satisfy the BP5 requirement for an alternate molecular etiology of the relevant clinical phenotype.

Still missing

• No patient-level phenotype or diagnosis is provided.
• No confirmed alternate molecular etiology is documented for an affected patient.
• The somatic COSMIC observation is not evidence of an alternate germline molecular cause.

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel Benign or Likely benign classification. No exact-variant ClinVar match or expert-panel submission is present; the only returned record is a different RET variant with a non-expert single-submitter Uncertain significance classification. Therefore BP6 is not supported.

Rule

Apply BP6 only when the exact variant has a ClinVar expert-panel classification of Benign or Likely benign; ordinary submissions, aggregate labels, non-expert assertions, and mismatched variants do not qualify.

Evidence considered

• ClinVar did not validate an exact match for NM_020975.5:c.1837C>A; the returned record is NM_020975.6(RET):c.2734C>A (p.Arg912=).
• The available submission is a single-submitter, non-expert Uncertain significance assertion and therefore cannot trigger BP6.

Still missing

• No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present.
• The available ClinVar record is mismatched and non-expert, with an Uncertain significance classification.

Sources