RET c.2073T>C, p.(Gly691=)

Reasoning

PM2 is met at supporting strength. The synonymous RET variant NM_020975.6:c.2073T>C (p.Gly691=) is extremely rare in population databases: AF 1.86e-6 in gnomAD v4.1 and 3.996e-6 in gnomAD v2.1, with no observed homozygotes. It is also absent from gnomAD-Canada v1.0. No RET-specific VCEP or gene framework was available, so the generic ACMG/AMP population-frequency rule is applied.

Rule

Generic ACMG/AMP PM2 at supporting strength: the variant is absent or extremely rare in population databases, with no observed homozygotes when relevant; no RET-specific VCEP rule was available.

Evidence considered

• gnomAD v4.1 reports 3/1,612,054 alleles (AF 1.86098e-6; homozygotes 0), with group maximum FAF 2.8e-7.
• gnomAD v2.1 reports 1/250,230 alleles (AF 3.99632e-6; homozygotes 0).
• The variant is absent from gnomAD-Canada v1.0.
• The available population data support rarity compatible with a rare, highly penetrant Mendelian condition; no population-frequency threshold artifact or ancestry-specific enrichment invalidates PM2.

Sources

Reasoning

RET c.2073T>C is a synonymous variant (NM_020975.6:c.2073T>C, NP_066124.1:p.(G691=)) with no predicted splicing impact: SpliceAI reports a maximum delta score of 0.002 across all four splice-site-change categories (acquired/lost acceptor and donor), far below thresholds used to flag a splice-altering effect. No gene-specific RET VCEP PP3/BP4/BP7 lookup material was found for this case (cspec not found, framework_mode = generic_acmg), so generic ACMG/AMP BP7 criteria are applied: a synonymous variant for which splicing prediction shows no significant effect. BP7 is met at supporting strength.

Evidence considered

• SpliceAI Lookup (source_registry key 'spliceai') for NM_020975.6:c.2073T>C: max_delta_score = 0.002 (DS_AG=0.002, DS_AL=0.001, DS_DG=0.002, DS_DL=0.0); prefetch evidence_sentence states 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).'
• Variant confirmed synonymous via normalization: NP_066124.1:p.(G691=).

Still missing

• Nucleotide-level conservation scores (e.g. phyloP, GERP) for this position were not present anywhere in the case bundle, so the classic 'nucleotide not highly conserved' BP7 sub-criterion could not be independently verified; the determination rests on the SpliceAI no-impact prediction alone

Sources

Reasoning

RET c.2073T>C (NP_066124.1:p.(G691=)) is a synonymous variant, so there is no missense in-silico signal to evaluate (REVEL and BayesDel scores are both absent/not found in prefetch, and BayesDel has no verified published threshold available to this pipeline regardless). The only applicable computational-evidence path for this variant is splicing. SpliceAI predicts no significant splice impact (max delta score = 0.002, well below any pathogenic-impact threshold used in the field, e.g. >=0.2), so there is no computational signal supporting a deleterious effect. PP3 is therefore not met.

Evidence considered

• SpliceAI Lookup (source_registry key 'spliceai') for NM_020975.6:c.2073T>C reports max delta score = 0.002 (DS_AG=0.002, DS_AL=0.001, DS_DG=0.002, DS_DL=0.0), interpreted as predicting no significant splice impact.
• REVEL score not available for this variant (revel.found=false in prefetch.json); BayesDel score not available (bayesdel.found=false in prefetch.json) and in any case BayesDel has no verified published threshold usable by this pipeline for PP3/BP4.

Still missing

• No gene-specific VCEP PP3/BP4 lookup spreadsheet was found for RET in this case (cspec not found; vcep_materials.json reports framework_mode generic_acmg with no cspec url)
• REVEL and BayesDel scores are not available for this variant (both report found=false in prefetch), though this is expected since the variant is synonymous

Sources

Reasoning

BA1 is not met. The variant is far below the generic benign population-frequency threshold of >1%: gnomAD v4.1 reports 3/1,612,054 alleles (AF 1.86e-6; homozygotes 0), and gnomAD v2.1 reports 1/250,230 alleles (AF 3.996e-6; homozygotes 0).

Rule

Generic ACMG/AMP benign frequency threshold: BA1 requires an allele frequency >1% in a population database, absent a more specific disease model or VCEP rule.

Evidence considered

• gnomAD v4.1 contains 3 alternate alleles among 1,612,054 total alleles, for AF 1.86098e-6; no homozygotes were observed.
• gnomAD v2.1 contains 1 alternate allele among 250,230 total alleles, for AF 3.99632e-6; no homozygotes were observed.
• The observed frequencies are orders of magnitude below the generic BA1 threshold of >1%; no ancestry-specific frequency approaches that threshold.

Sources

Reasoning

BS1 is not met. The variant is far below the generic benign-supporting population-frequency threshold of >0.3%: the overall AF is 1.86e-6 in gnomAD v4.1 and 3.996e-6 in gnomAD v2.1, with the highest reported subpopulation AF only 1.60e-5 in gnomAD v4.1 and 1.633e-4 in gnomAD v2.1.

Rule

Generic ACMG/AMP benign-supporting frequency threshold used here: BS1 requires an allele frequency >0.3% in a population database, absent a more specific disease model or VCEP rule.

Evidence considered

• gnomAD v4.1 reports an overall AF of 1.86098e-6 and a highest observed subpopulation AF of 1.60077e-5 in the Remaining individuals group; the maximum group FAF is 2.8e-7.
• gnomAD v2.1 reports an overall AF of 3.99632e-6 and a highest observed subpopulation AF of 1.63292e-4 in the Remaining individuals group.
• All observed frequencies are below the generic BS1 threshold of >0.3%; no disease-prevalence or penetrance model establishes a lower benign threshold that would be exceeded.

Sources

Reasoning

No case-level evidence is provided documenting a de novo occurrence of RET NM_020975.6:c.2073T>C, including confirmed maternity and paternity or parental genotypes. Phenotype consistency for the proband is also not documented.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no evidence of family history; stronger application requires confirmed maternity and paternity and phenotype consistency.

Evidence considered

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

Still missing

• Proband phenotype and disease context
• Maternal and paternal testing results
• Confirmation that the variant is absent from both biological parents
• Assessment of maternity and paternity

Reasoning

No functional/experimental assay data (e.g., splicing minigene, RNA studies, kinase activity assays) for RET NM_020975.6:c.2073T>C (p.(Gly691=)) were found anywhere in the case-evidence bundle. No ClinGen RET VCEP CSPEC was available (framework_mode=generic_acmg, gene_vcep_dir=null), so generic ACMG applies. The three full-text papers with paper_extracts entries (PMID:25356965, PMID:27854360, PMID:11739416) were searched for this variant and confirmed to be gene-level MEN2/secondary-findings policy documents with no variant-specific functional data; none report an assay of this specific variant. SpliceAI predicts no significant splice impact (max delta score 0.00), but this is a computational splice prediction, not a validated functional assay, and is not applicable evidence for PS3.

Still missing

• No RET functional assay (kinase activity, cell transformation, minigene splicing, RNA-seq) has been performed or reported for this specific synonymous variant.
• No ClinGen RET VCEP functional evidence framework was available in this case to specify assay validation thresholds.

Reasoning

No eligible case-control study, cohort enrichment analysis, or sufficiently documented independent affected-case series for RET c.2073T>C (p.(Gly691=)) is present in the supplied evidence.

Rule

Generic ACMG/AMP fallback: PS4 requires statistically increased prevalence in affected individuals compared with controls.

Evidence considered

• No RET c.2073T>C case-control or cohort-enrichment evidence was supplied. The literature packet's PS4 leads are policy/guidance items rather than variant-specific association studies.

Still missing

• Variant-specific affected and control allele counts from an ascertainment-defined study, with an appropriate statistical enrichment analysis.

Sources

Reasoning

No case-level evidence supports an assumed de novo occurrence of RET NM_020975.6:c.2073T>C. Parental genotypes, family history, and proband phenotype are not reported.

Rule

Generic ACMG/AMP PM6: assumed de novo, without confirmed maternity and paternity, in a patient with the disease and no evidence of family history.

Evidence considered

• The consolidated case-evidence bundle provides no report of parental testing, a negative family history, or a phenotype-consistent proband for this variant.

Still missing

• Proband phenotype and disease context
• Parental testing results or a documented basis for assuming de novo status
• Family history

Reasoning

No affected relatives, informative meioses, segregation data, or family pedigree are provided for RET NM_020975.6:c.2073T>C. Therefore cosegregation cannot be evaluated or assigned supporting strength.

Rule

Generic ACMG/AMP PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength depends on the amount and informativeness of segregation evidence.

Evidence considered

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

Still missing

• Family pedigree
• Genotypes and phenotypes of affected relatives
• Number of informative meioses
• Phenotype definition and assessment of affected status

Reasoning

The supplied evidence contains no proband phenotype, family phenotype, or phenotype-specificity analysis for the exact variant; PP4 cannot be evaluated.

Rule

Generic ACMG/AMP fallback: PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single genetic etiology.

Evidence considered

• The ClinVar record lists disease labels but provides no phenotype-bearing case evidence for this exact variant. The extracted RET guidance papers do not mention c.2073T>C or p.(Gly691=).

Still missing

• A documented phenotype for a carrier of RET c.2073T>C and evidence that the phenotype is highly specific for a RET-associated disorder with a low differential diagnosis.

Sources

Reasoning

No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is present. PP5 is therefore not applicable from the available ClinVar submissions.

Rule

Apply PP5 at supporting strength only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion.

Evidence considered

• The exact-variant ClinVar audit identifies three single-submitter laboratory assertions (two Likely benign and one Benign) and zero expert-panel submissions; ordinary submissions and aggregate labels are not used for PP5.

Still missing

• An exact-variant ClinVar expert-panel assertion of Pathogenic or Likely pathogenic.

Sources

Reasoning

BS2 cannot be established from the available population data. No homozygotes are observed in gnomAD v2.1 or v4.1, but the variant has only 1 allele in gnomAD v2.1 and 3 alleles in gnomAD v4.1, and there is no documented observation of unaffected adult homozygotes or an appropriately powered, phenotype-ascertained healthy cohort.

Rule

Generic BS2 requires observation of the variant in a healthy adult individual in a state expected to be affected by a fully penetrant disorder; homozygote absence in a small number of rare-allele observations is insufficient.

Evidence considered

• gnomAD v4.1 reports 0 homozygotes among 1,612,054 alleles, with 3 total alternate alleles.
• gnomAD v2.1 reports 0 homozygotes among 250,230 alleles, with 1 total alternate allele.
• These data document absence of observed homozygotes but do not document healthy adult homozygotes or provide sufficient disease-specific power to use BS2.

Still missing

• No direct evidence of unaffected adult homozygotes is available.
• The absence of homozygotes in the available databases is not sufficient by itself to establish BS2 for this rare allele without an applicable disease model and adequate power.

Sources

Reasoning

No functional/experimental assay data demonstrating normal/wild-type function for RET NM_020975.6:c.2073T>C (p.(Gly691=)) were found anywhere in the case-evidence bundle. No ClinGen RET VCEP CSPEC was available, so generic ACMG applies. The three full-text papers with paper_extracts entries (PMID:25356965, PMID:27854360, PMID:11739416) were confirmed to lack any variant-specific functional or splicing assay results for this variant. SpliceAI predicts no significant splice impact (max delta score 0.00), but a single in silico prediction alone does not constitute the validated, well-established functional assay required to invoke BS3.

Still missing

• No RET functional assay (e.g., minigene splicing assay, kinase activity assay) showing normal function has been performed or reported for this specific synonymous variant.
• SpliceAI in silico null-effect prediction is insufficient alone to meet BS3's requirement for a validated functional study.

Reasoning

No affected family members, tested relatives, segregation results, or non-segregation observations are provided. Absence of family data does not establish that the variant fails to segregate with disease.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; application requires informative family data and consideration of phenocopy, reduced penetrance, and phenotype misclassification.

Evidence considered

• The consolidated case-evidence bundle contains no non-segregation or family-testing evidence for this variant.

Still missing

• Family pedigree and disease status
• Genotypes of affected and unaffected relatives
• Documented non-segregation observations
• Evaluation of phenocopies and reduced penetrance

Reasoning

BP2 (ACMG/AMP 2015, PMID 25741868) requires an observed allele configuration: the variant seen in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern. The case bundle contains no proband genotype data, no family or phase information, and no documented pathogenic RET variant whose phase with c.2073T>C (p.(Gly691=)) could be determined. ClinVar VCV001126022 (3 clinical submissions: Ambry LB, Myriad B, Labcorp LB; no expert panel, no criterion leads) provides no co-occurrence or phase context, and population frequency data (gnomAD v2.1 AF 3.996e-06, 1/250,230 alleles; gnomAD v4.1 AF 1.861e-06, 3/1,612,054 alleles; 0 homozygotes) cannot establish cis/trans configuration. Evidence is insufficient, so BP2 is not assessed.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder; or observed in cis with a pathogenic variant in any inheritance pattern (ACMG/AMP 2015, PMID 25741868).

Evidence considered

• Generic ACMG/AMP 2015 BP2 rule requires an observed phase relationship with a pathogenic variant (in trans for a fully penetrant dominant disorder, or in cis in any inheritance pattern); no such observation exists for this variant.
• ClinVar VCV001126022 contains 3 clinical testing submissions (Ambry Genetics LB 2021-10-30; Myriad Genetics B 2025-02-26; Labcorp/Invitae LB 2020-06-16) with no genotype, phase, or co-occurrence data (submission audit: usable_for_criterion_leads = 0, criterion_leads = [], no validated PMIDs).
• gnomAD v2.1 (1/250,230 alleles, 0 homozygotes) and gnomAD v4.1 (3/1,612,054 alleles, 0 homozygotes) document very low population frequency, but population data cannot establish cis/trans phase with a pathogenic variant.

Still missing

• No proband or family genotype data establishing phase (cis/trans) of c.2073T>C relative to any pathogenic RET variant
• No documented co-occurrence of c.2073T>C with a pathogenic RET variant in any inheritance pattern

Sources

Reasoning

No case-level testing result documents an alternative molecular diagnosis that fully explains an affected individual's phenotype.

Rule

Generic ACMG/AMP fallback: BP5 requires an alternate molecular basis for disease in a case with the variant under assessment.

Evidence considered

• No co-occurring molecular diagnosis or clinical phenotype data were supplied for a carrier of RET c.2073T>C.

Still missing

• Case-level phenotype and molecular testing data showing a separate pathogenic or likely pathogenic variant that fully accounts for the phenotype.

Sources

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present. BP6 is therefore not applicable from the available ClinVar submissions.

Rule

Apply BP6 at supporting strength only for an exact-variant ClinVar expert-panel Benign or Likely benign assertion.

Evidence considered

• The exact-variant ClinVar audit identifies two Likely benign and one Benign single-submitter laboratory assertions, with zero expert-panel submissions; ordinary submissions and aggregate labels are not used for BP6.

Still missing

• An exact-variant ClinVar expert-panel assertion of Benign or Likely benign.

Sources