RET c.2895G>T, p.(Lys965Asn)

Reasoning

The variant is absent (allele frequency 0) from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, well below the <0.1% non-VCEP PM2 threshold, supporting PM2 at supporting strength.

Rule

Generic ACMG/AMP 2015 (PMID:25741868): PM2 requires absence from or extremely low frequency (<0.1%, non-VCEP threshold) in population databases; default strength supporting.

Evidence considered

• Absent from gnomAD v2.1 (exome)
• Absent from gnomAD v4.1 (exome)
• Absent from gnomAD-Canada v1.0 (HostSeq genomes); AC=0, AN=0, AF=0.0, hom=0

Still missing

• Numeric per-population allele counts, homozygote counts, and sequencing depth/coverage at chr10:43123764 were not captured (gnomAD v2.1/v4.1 returned null counts with absence status; gnomAD-Canada API returned AC=0/AN=0); absence was established by direct variant-page lookups with screenshots.

Sources

Reasoning

BP4 (Richards et al. 2015, PMID:25741868) is met when multiple lines of computational evidence suggest no impact on the gene or gene product. Two independent computational lines support no impact for NM_020975.5:c.2895G>T (RET): (1) splicing path — SpliceAI max delta = 0.00 (< 0.1), predicting no splice impact for this deep-exonic (exon 17) missense that is not at a canonical splice consensus position; (2) missense path — BayesDel (noAF) = -0.186199, on the benign/tolerated side of the calibrated BP4 boundary (Feng et al. 2022). REVEL = 0.529 is intermediate and yields no call, so it neither supports nor contradicts BP4. With SpliceAI and BayesDel in agreement on no impact, the 'multiple lines' requirement of BP4 is satisfied; default supporting strength applied (SVI guidance retains PP3/BP4 at supporting). Confidence is moderate rather than high because REVEL is indeterminate and no RET gene-specific PP3/BP4 thresholds exist; a BayesDel calibration-reference caveat is noted in warnings. Framework: generic ACMG/AMP 2015 fallback (no RET CSPEC/VCEP retrieved).

Rule

generic ACMG/AMP 2015 BP4 - multiple lines of computational evidence suggest no impact (SpliceAI + BayesDel)

Evidence considered

• SpliceAI max delta = 0.00 (< 0.1): no predicted splice impact (BP4 splicing sub-path)
• BayesDel noAF score = -0.186199: predicted tolerated/benign (BP4 missense sub-path)
• REVEL v1.3 score = 0.529: intermediate, no call (not conflicting)
• pvs1_variant_assessment: consequence_class = missense, canonical_splice_consensus = false (variant is deep exonic, not at splice consensus)

Sources

Reasoning

Variant is NM_020975.5:c.2895G>T (NP_066124.1:p.Lys965Asn, p.K965N), a missense change in RET exon 17. PS1 requires the same amino-acid change as an established pathogenic variant (e.g., c.2895G>C also producing p.Lys965Asn). No established pathogenic variant at RET residue 965, and no pathogenic p.Lys965Asn allele, was identified: ClinVar VCV002454137 for this allele is Uncertain significance from a single clinical laboratory (Ambry Genetics, SCV003869122, 1-star, no expert panel, no validated PMIDs), and the pm5_candidates artifact harvested 0 same-residue candidates. The only retrieved publication (PMID:25394175) is an ACMG/NSGC referral-indications guideline with no variant-level data. Absence of an established pathogenic comparator means PS1 cannot be met on the collected evidence.

Rule

PS1: Same amino acid change as an established pathogenic variant regardless of nucleotide change (generic ACMG/AMP 2015, PMID:25741868)

Evidence considered

• clinvar
• pm5_candidates

Still missing

• No established pathogenic p.Lys965Asn (or any P/LP variant at RET residue 965) identified in ClinVar or the retrieved literature bundle; a comprehensive literature search for RET K965 pathogenic reports was not performed (only 1 paper in bundle)

Sources

Reasoning

PM1 requires the variant to lie in a mutational hotspot and/or critical well-established functional domain without benign variation. The cancerhotspots screen for RET K965 returned no statistically significant hotspot (evidence.json results.hotspots, query 'RET K965'), and the case evidence contains no curated domain annotation establishing that residue 965 falls in a critical functional sub-region (e.g., UniProt kinase-domain boundaries or a RET-specific hotspot/functional-site specification) with disease-causing missense burden and no benign variation. The variant is absent from gnomAD v2.1 and v4.1, which is consistent with the 'without benign variation' clause at this allele, but gnomAD absence alone is insufficient to satisfy PM1. RET lacks a CSPEC/VCEP specification, so generic ACMG applies and no RET-specific PM1 guidance is available. PM1 not met on available evidence.

Rule

PM1: Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation (generic ACMG/AMP 2015, PMID:25741868)

Evidence considered

• gnomad_v2
• gnomad_v4

Still missing

• No curated functional-domain annotation (e.g., UniProt/InterPro domain boundaries) or RET-specific hotspot evidence for residue 965 was retrieved into the case evidence
• No benign-variation burden data for residue 965 beyond gnomAD absence (no population missense-constraint context for the region)

Sources

Reasoning

PM5 requires a novel missense change at a residue where a different missense change has been determined pathogenic. The pm5_candidates artifact (pm5_candidates.json) reports pm5_mode 'unknown' with 0 same-residue candidates at RET residue 965 (candidate_summary.total_candidates_seen = 0) and recommends not applying PM5 from the artifact alone; no alternate missense change at residue 965 with a pathogenic determination was found in ClinVar (only this allele exists as a 1-submitter VUS). The only retrieved publication (PMID:25394175) reports no same-residue comparators. With no pathogenic alternate missense at residue 965 identified, PM5 is not met on the collected evidence.

Rule

PM5: Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before (generic ACMG/AMP 2015, PMID:25741868)

Evidence considered

• pm5_candidates
• clinvar

Still missing

• Automatic PM5 comparator harvesting was skipped (pm5_mode 'unknown'); no dedicated ClinVar query for alternate missense variants at RET residue 965 (e.g., p.Lys965Glu/Arg/Thr) was completed, so a same-residue pathogenic comparator cannot be fully excluded

Sources

Reasoning

PP3 (Richards et al. 2015, PMID:25741868) requires multiple lines of computational evidence supporting a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). No calibrated in silico line supports a damaging effect for NM_020975.5:c.2895G>T (RET, NP_066124.1:p.(Lys965Asn)): (1) SpliceAI max delta = 0.00 (DS_AG/DS_AL/DS_DG/DS_DL all 0.0), far below any splice-impact decision boundary, predicting no splice impact; (2) BayesDel (noAF) = -0.186199, on the benign/tolerated side of calibrated PP3/BP4 boundaries (Feng et al. 2022); (3) REVEL = 0.529, which lies in the intermediate zone (between the BP4 75%-specificity bound of ~0.073 and the PP3 75%-specificity bound of ~0.773; Pejaver et al. 2022) and therefore yields no call. Zero of the available tools predict a deleterious effect, so PP3 is not met. Framework: generic ACMG/AMP 2015 fallback, because no RET ClinGen CSPEC/VCEP was retrieved (cspec found=false; framework_mode=generic_acmg). The single ClinVar submitter's free-text statement that the alteration is 'predicted to be tolerated by in silico analysis' (Ambry SCV003869122) was not counted as evidence for or against PP3, per instruction not to infer criteria from another source's classification.

Rule

generic ACMG/AMP 2015 PP3 - multiple lines of computational evidence supporting deleterious effect (none satisfied)

Evidence considered

• SpliceAI max delta = 0.00 (DS_AG 0.0, DS_AL 0.0, DS_DG 0.0, DS_DL 0.0): no predicted splice impact
• BayesDel noAF score = -0.186199: benign/tolerated side of calibrated boundaries
• REVEL v1.3 score = 0.529: intermediate zone, no call
• Variant consequence class = missense (NP_066124.1:p.(Lys965Asn)), deep exonic, not canonical splice consensus

Sources

Reasoning

PP5 is applied only when a reputable source reports the variant as pathogenic without available evidence; per the governing group rule, only an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic may trigger PP5, and ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. The ClinVar submission audit for VariationID 2454137 shows 0 expert-panel submissions and a single non-expert clinical laboratory (Ambry Genetics, SCV003869122) classifying the variant as Uncertain significance (1 star). No expert-panel pathogenic assertion exists, so PP5 is not met.

Rule

PP5: Reputable source recently reports variant as pathogenic without available evidence (Richards et al. 2015, PMID:25741868). Group rule restricts PP5 to an exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classification; none exists here, so not_met.

Evidence considered

• ClinVar submission audit: expert_panel_submissions=0, usable_for_criterion_leads=0, single non-expert clinical laboratory submission classified Uncertain significance
• Aggregate ClinVar label (Uncertain significance, 1 star) is a non-expert assertion and per group rule cannot trigger PP5

Still missing

• No ClinVar expert-panel (e.g., ClinGen/INSiGHT-style) classification exists for this variant to review

Sources

Reasoning

The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (observed allele frequency 0), far below the >1% general-population threshold required for BA1 under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP 2015 (PMID:25741868, source_registry key generic_acmg_combination_rules): BA1 requires allele frequency >1% (non-VCEP threshold) in a large, diverse general population cohort.

Evidence considered

• Absent from gnomAD v2.1 (exome) - search_status absent
• Absent from gnomAD v4.1 (exome) - search_status absent
• Absent from gnomAD-Canada v1.0 (HostSeq genomes); AC=0, AN=0, AF=0.0, hom=0

Still missing

• Numeric per-population allele counts and site coverage at chr10:43123764 were not captured in the evidence record; absence was established by direct gnomAD variant-page lookups (screenshots captured), which is sufficient to exclude BA1.

Sources

Reasoning

BS1 requires an allele frequency greater than expected for the disorder; RET-associated hereditary cancer predisposition (MEN2/FMTC) is autosomal dominant and rare, and the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, so the observed frequency (0) does not exceed the expected pathogenic allele frequency.

Rule

Generic ACMG/AMP 2015 (PMID:25741868): BS1 requires allele frequency >0.3% (non-VCEP threshold), greater than expected for the disorder; observed frequency is 0.

Evidence considered

• Absent from gnomAD v2.1 (exome)
• Absent from gnomAD v4.1 (exome)
• Absent from gnomAD-Canada v1.0 (HostSeq genomes); AC=0, AF=0.0

Still missing

• Numeric per-population allele counts and site coverage were not captured in the evidence record; absence across three population datasets is sufficient to exclude BS1.

Sources

Reasoning

No observations of the variant in healthy/unaffected adult controls were identified: the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada with no homozygous carriers, and the single ClinVar germline submission (Ambry Genetics, uncertain significance) is from an individual referred for hereditary cancer-predisposition testing, not an unaffected-control observation.

Rule

Generic ACMG/AMP 2015 (PMID:25741868): BS2 requires observation of the variant in a healthy adult for a disorder with full penetrance; no such observations exist for this variant.

Evidence considered

• Absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0; no homozygotes observed
• ClinVar variation 2454137: single germline submission (Ambry Genetics, 2023), classified Uncertain significance; no healthy-control observation

Still missing

• No dedicated unaffected-control cohort data beyond population databases was available; the ClinVar submission carries no phenotype details to confirm or exclude affected status.

Sources

Reasoning

BP1 applies only when missense variants in the gene are invariably benign because only truncating variants cause disease. This premise fails for RET: activating missense variants are the established germline disease mechanism for MEN2A, MEN2B, and familial medullary thyroid carcinoma (OncoKB gene-level curation: 'Germline heterozygous, activating mutations in RET lead to the highly penetrant familial cancer syndromes...'), while loss-of-function/truncating variants are additionally a germline mechanism (Hirschsprung disease; pvs1_gene_context supports RET LOF as a germline mechanism). Disease in RET is therefore caused by both missense and truncating variants, so a missense change cannot be assumed benign under BP1. BP1 not met.

Rule

BP1: Missense variant in a gene for which primarily truncating variants are known to cause disease (generic ACMG/AMP 2015, PMID:25741868)

Evidence considered

• oncokb
• pvs1_gene_context

Sources

Reasoning

BP6 is applied only when a reputable source reports the variant as benign without available evidence; per the governing group rule, only an exact-variant ClinVar expert-panel classification of Benign/Likely benign may trigger BP6, and ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. The ClinVar submission audit for VariationID 2454137 shows 0 expert-panel submissions and a single non-expert clinical laboratory (Ambry Genetics, SCV003869122) classifying the variant as Uncertain significance (1 star) - not Benign or Likely benign. No expert-panel benign assertion exists, so BP6 is not met.

Rule

BP6: Reputable source recently reports variant as benign without available evidence (Richards et al. 2015, PMID:25741868). Group rule restricts BP6 to an exact-variant ClinVar expert-panel Benign/Likely benign classification; none exists here, so not_met.

Evidence considered

• ClinVar submission audit: expert_panel_submissions=0, single non-expert clinical laboratory submission classified Uncertain significance
• Aggregate ClinVar label (Uncertain significance, 1 star) is neither a benign assertion nor an expert-panel assertion and cannot trigger BP6

Still missing

• No ClinVar expert-panel Benign/Likely benign classification exists for this variant to review

Sources

Reasoning

No de novo occurrence evidence for NM_020975.5:c.2895G>T (p.Lys965Asn) is present in any case artifact. The single ClinVar submission (Ambry Genetics, SCV003869122, VUS, criteria provided/single submitter) records no parental testing, no de novo observation, and no family history information; its only criterion signal is PP3 (in silico tolerated). The literature packet contains no case reports of this variant (only PMID:25394175, an ACMG/NSGC referral-indications guideline with no variant or segregation content). Generic ACMG/AMP 2015 PS2 requires a de novo variant with confirmed parentage in a proband with the disease and no family history; none of these elements is available, so PS2 cannot be evaluated (insufficient evidence, not refuted).

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID:25741868) PS2: 'De novo (paternity and maternity confirmed) variant in a patient with the disease and no family history' — strong evidence of pathogenicity. Applicable only when both parents are tested and shown not to carry the variant with confirmed parentage.

Still missing

• No proband-level de novo observation (variant absent in both biological parents with confirmed parentage/maternity-paternity) is reported anywhere in the case evidence.
• No clinical phenotype/disease status of the proband is provided in the case artifacts, so the 'proband with disease and no family history' precondition cannot be confirmed.
• No parental testing results (either confirming or excluding the variant) are available from the ClinVar submission or literature.

Sources

Reasoning

No well-established functional studies for RET p.(Lys965Asn) are present in the collected evidence. OncoKB explicitly reports no variant-specific reviewed functional evidence (is_variant_specific=false, not_reviewed=true, biological_effect empty, zero citations), classifying the variant as 'Unknown Oncogenic Effect'. COSMIC shows the variant absent from somatic cancers, which is an observation of absence, not a functional assay. The single retrieved publication (PMID:25394175) is an ACMG/NSGC practice guideline on referral indications for cancer predisposition assessment; it does not mention the variant and contains no functional assay data (full-text grep for 'K965', 'Lys965', '2895', 'functional stud', 'assay' returned no hits). Per the governing generic ACMG/AMP 2015 framework (PMID:25741868), PS3 requires well-established in vitro or in vivo functional studies demonstrating a deleterious effect; absent any such study, PS3 cannot be applied.

Rule

PS3: Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (Richards et al. 2015, PMID:25741868). No RET VCEP/CSPEC exists, so generic ACMG applies. Requires actual functional study data; absent here.

Evidence considered

• oncokb
• cosmic
• clinvar
• PMID:25394175

Still missing

• No functional assay data for p.(Lys965Asn): no RET kinase/autophosphorylation, transforming (e.g., NIH-3T3 focus formation), signaling (MAPK/ERK), or cell-based assays reported
• OncoKB confirms no variant-specific reviewed functional evidence is available for curation
• No literature source in this case reports any experimental assessment of this variant

Sources

Reasoning

PS4 requires the prevalence of the variant in affected individuals to be significantly increased compared with controls, established by case-control studies or a sufficiently large case series. No case-control or case-series data exist for RET c.2895G>T (p.Lys965Asn) in any retrieved source: the ClinVar record (VariationID 2454137) carries a single non-expert Uncertain significance submission with zero validated PMIDs and no case-level data, and the only retrieved publication (PMID:25394175) is an ACMG/NSGC referral-indications guideline that does not mention the variant (full-text search for '2895', '965', 'Lys', 'Asn', 'K965' returned zero hits). Absence from gnomAD v2.1/v4.1 and gnomAD-Canada is population-frequency data, not case enrichment, and is evaluated under PM2 by the population group. Evidence is therefore insufficient to assess PS4; the gap is the complete absence of case-control or case-series enrichment data for this exact variant.

Rule

PS4: The prevalence of the variant in affected individuals is significantly increased compared with controls (Richards et al. 2015, PMID:25741868). Requires case-control or case-series enrichment data for the exact variant; none available, so status is not_assessed rather than met.

Evidence considered

• ClinVar VCV002454137 submission audit: 1 clinical laboratory submission (Ambry Genetics SCV003869122), Uncertain significance, 1 star, 0 expert-panel submissions, 0 validated PMIDs, 0 usable criterion leads
• Variant absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada (population absence is not case enrichment; PM2 handled by the population group)
• PMID:25394175 full text reviewed: referral-indications guideline, variant not mentioned

Still missing

• No case-control study or case series reporting RET c.2895G>T in affected individuals versus controls
• No case reports or phenotype-segregation series for p.Lys965Asn in the retrieved literature
• ClinVar record has no validated PMIDs and no case-level observations attached

Sources

Reasoning

No de novo occurrence is reported for this variant in any form. PM6 (assumed/unconfirmed de novo) requires the variant to be absent in both parents without confirmed parentage (or with parentage not verified); no parental genotypes, proband segregation testing, or de novo assertion exists in the ClinVar submission, prefetch, evidence, or literature artifacts. The only retrieved publication (PMID:25394175) is a cancer-predisposition referral guideline and does not describe this variant or any de novo case. Insufficient evidence; PM6 not assessed.

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID:25741868) PM6: 'Assumed de novo, without confirmation of paternity and maternity' — moderate evidence of pathogenicity. Applicable when both parents are tested and do not carry the variant but parentage is not confirmed.

Still missing

• No proband de novo observation (variant absent in both parents, parentage unconfirmed or assumed) is reported.
• No parental genotype data of any kind are available.
• No clinical source in the case bundle asserts the variant arose de novo.

Sources

Reasoning

No co-segregation evidence exists. The case artifacts contain no affected relatives, no family pedigree, no meiosis/segregation counts, and no statement that the variant segregates with disease in any family. The ClinVar submission records no family/co-segregation data and no validated PMIDs. The single literature source (PMID:25394175) is an ACMG/NSGC referral guideline with no variant-specific or segregation content (full-text search for 'segregat', 'de novo', and variant identifiers returned zero matches). PP1 cannot be scored without at least one informative affected family member; insufficient evidence.

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID:25741868) PP1: 'Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease' — supporting evidence of pathogenicity (strength may increase with additional meioses per ClinGen/PS4-adjacent guidance; generic framework applies here).

Still missing

• No affected family members tested for the variant are reported.
• No segregation count (number of informative meioses, affected carriers vs. non-carriers) is available.
• No family history/pedigree data are present in any case artifact.

Sources

Reasoning

PP2 requires (a) missense variants as a common mechanism of disease in the gene AND (b) a low rate of benign missense variation in the gene. For RET, part (a) is supported by gene-level curation: OncoKB background states germline heterozygous activating missense mutations in RET cause MEN2A/MEN2B/FMTC, and the NCBI gene summary notes oncogenic activation via activating point mutations. However, part (b) could not be evaluated: no gene-level missense-constraint data (e.g., gnomAD missense Z-score / observed-expected ratio) was retrieved into the case evidence, and the HCI prior artifact reports 'gene_not_supported' for RET. Because one of PP2's two required components is unevaluable, PP2 is not assessed pending gene-level benign-missense-rate data.

Rule

PP2: Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease (generic ACMG/AMP 2015, PMID:25741868)

Evidence considered

• oncokb

Still missing

• No gene-level missense constraint / low-benign-missense-rate evidence retrieved for RET (e.g., gnomAD missense Z-score, o/e ratio)
• HCI prior not supported for RET (hci_prior found=false, reason 'gene_not_supported'), so no prior-based PP2 score is available

Sources

Reasoning

PP4 requires the proband's phenotype or family history to be highly specific for a disease with a single genetic etiology. No proband phenotype or family-history information is present anywhere in this case: the ClinVar submission lists no conditions and no clinical details, and no case report of this variant exists. Gene-level context that germline RET variants cause MEN2 (medullary thyroid cancer, pheochromocytoma, parathyroid disease) is available from PMID:25394175 and OncoKB, but PP4 must be anchored to the specific patient's presentation, which is absent. Evidence is insufficient to assess PP4; the gap is the missing proband phenotype and family history.

Rule

PP4: Phenotype or family history highly specific for a disease with a single genetic etiology (Richards et al. 2015, PMID:25741868). Requires proband phenotype/family history; none available in this case, so status is not_assessed.

Evidence considered

• ClinVar record lists no conditions for the single submission (conditions: []); no phenotype data attached
• PMID:25394175 provides gene-level RET/MEN2 phenotype context (MTC, pheochromocytoma, parathyroid disease, genotype-phenotype correlations) but no variant-specific or proband phenotype data
• OncoKB provides gene-level RET/MEN2 disease context only; no variant-specific clinical phenotype

Still missing

• Proband phenotype and clinical presentation not provided in the case bundle
• Family history (e.g., medullary thyroid cancer, pheochromocytoma, MEN2 stigmata) not provided
• No case report of this variant describing a specific phenotype

Sources

Reasoning

No well-established functional studies demonstrating a lack of damaging effect exist for RET p.(Lys965Asn). The variant's absence from gnomAD v2.1/v4.1 and gnomAD-Canada is population frequency data, and its absence from COSMIC is somatic-observation data; neither constitutes a functional study. SpliceAI predicts no splice impact (max delta score = 0.00), but SpliceAI is an in-silico splice predictor and, per the governing generic ACMG/AMP 2015 framework (PMID:25741868) and ClinGen SVI usage guidance, cannot substitute for the well-established functional studies BS3 requires. OncoKB provides no variant-specific functional evidence that could support neutrality. BS3 therefore cannot be applied.

Rule

BS3: Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing (Richards et al. 2015, PMID:25741868). In-silico predictors (e.g., SpliceAI) and population/somatic absence are insufficient; no qualifying functional study is available.

Evidence considered

• spliceai
• gnomad_v2
• gnomad_v4
• gnomad_canada
• oncokb

Still missing

• No functional assay demonstrating normal protein function (e.g., preserved RET kinase activity, signaling, or cell-based readouts) for p.(Lys965Asn)
• SpliceAI-only splice neutrality (delta 0.00) is in-silico evidence, not a functional study; no RNA/cDNA or minigene assay available
• No variant-specific functional data of any kind identified in the evidence bundle

Sources

Reasoning

No non-segregation evidence is available. BS4 requires the variant to be absent in an affected family member (or present in an unaffected member) in a way that contradicts segregation; no affected relatives were tested, no pedigree is provided, and no segregation analyses were performed in any artifact. Note: the variant's absence from gnomAD v2.1/v4.1 and gnomAD-Canada is population-frequency evidence (relevant to BA1/BS1/PM2, assessed by other groups) and does NOT constitute BS4, which is strictly a family-segregation observation. Insufficient evidence; BS4 not assessed.

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID:25741868) BS4: 'Non-segregation with disease in affected family members' — strong evidence of benign impact. Requires at least one affected relative who does not carry the variant (or variant present in unaffected relatives in a dominant disease context).

Still missing

• No affected family member genotyped as wild-type for the variant is reported.
• No segregation analysis or LOD-score calculation exists in the case evidence.
• No pedigree/family testing data are available to detect non-segregation.

Sources

Reasoning

BP2 (ACMG/AMP 2015, generic framework since no RET VCEP/CSPEC exists) requires the observation of this variant in trans with a pathogenic variant for a fully dominant disease/gene, or in cis with a pathogenic variant in any inheritance pattern. RET germline cancer-predisposition syndromes are fully dominant, so BP2 is applicable in principle. However, the case bundle contains no allelic observations whatsoever: no affected proband or family phase data, no documented co-occurring pathogenic RET variant in trans or cis, and the sole ClinVar submission (SCV003869122, VUS, 'criteria provided, single submitter') carries no phase/inheritance or co-occurrence information. gnomAD (v2.1, v4.1, Canada) shows the variant is absent from population databases, and no literature reports the variant with any second variant. Because the specific observation BP2 depends on is entirely absent, the criterion cannot be evaluated and is returned not_assessed pending phase/co-occurrence data.

Rule

ACMG/AMP 2015 (Richards et al., PMID:25741868) BP2: 'Observed in trans with a pathogenic variant for a fully dominant disease/gene; or observed in cis with a pathogenic variant in any inheritance pattern' (supporting evidence of benign impact).

Evidence considered

• ClinVar record VCV002454137 (variation 2454137): single 1-star VUS submission with no phase, inheritance, or co-occurrence data; no expert-panel criteria; no valid PMIDs
• Case bundle: no segregation/phase observations, no second RET variant reported in any source (prefetch.json, evidence.json, literature_pass.json, case_summary.json)

Still missing

• No proband or family phase data establishing in-trans vs in-cis relationship with a pathogenic variant
• No documented co-occurring pathogenic RET variant in any tested individual (required for BP2)

Sources

Reasoning

BP5 applies when the variant is found in a case with an alternate molecular basis for disease, making the variant's contribution redundant. No case-level data for RET c.2895G>T exists in any retrieved source: there are no case reports, no validated PMIDs on the ClinVar record, and no report of this variant alongside a pathogenic variant in another gene or another independent explanation for a phenotype. Evidence is insufficient to assess BP5; the gap is the absence of any reported case of this variant with an alternate molecular basis.

Rule

BP5: Variant found in a case with an alternate molecular basis for disease (Richards et al. 2015, PMID:25741868). Requires a documented case; none exists for this variant, so status is not_assessed.

Evidence considered

• ClinVar record contains no case-level data (0 validated PMIDs, no affected-individual observations)
• No literature source in this case reports the variant in any proband

Still missing

• No reported case of RET c.2895G>T with an alternate, independently sufficient molecular explanation for disease
• No case-level observations of this variant at all in the retrieved evidence

Sources