IDH2 c.413C>A, p.(Thr138Asn)

Reasoning

Generic ACMG/AMP 2015 PM2 (Richards et al., PMID 25741868): absent in controls in ESP, 1000 Genomes, or ExAC/gnomAD. The variant NM_002168.3:c.413C>A (p.Thr138Asn) is absent from gnomAD v2.1 exomes, gnomAD v4.1 exomes, and gnomAD-Canada v1.0 genomes (observed germline AF = 0 across large multi-ethnic control cohorts), satisfying PM2 at supporting strength under the generic framework. No IDH2 VCEP exists to supply an alternative calibration (e.g., moderate-strength PM2), so strength is retained at supporting per the 2015 framework. The single COSMIC somatic occurrence (COSV100344117, n=1) does not contradict PM2, which concerns germline control frequency. Criterion met (supporting).

Rule

PM2: absent in controls in ESP, 1000 Genomes, or ExAC (Richards et al. 2015, PMID 25741868) — supporting

Evidence considered

• gnomAD v2.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD v4.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD-Canada v1.0 genomes: variant absent (search_status=absent; evidence.json)
• PM2 definition: absent in controls in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (Richards et al. 2015, PMID 25741868)

Still missing

• PM2 applied at supporting per generic ACMG/AMP 2015; no IDH2 VCEP available to justify a stronger (moderate) PM2 calibration.
• No disease-specific control cohort beyond gnomAD v2.1/v4.1 and gnomAD-Canada v1.0 was available.

Sources

Reasoning

Variant NM_002168.3:c.413C>A (p.Thr138Asn) in IDH2. PS1 requires the same amino acid change as a previously established pathogenic variant, regardless of nucleotide change. No established pathogenic variant producing p.Thr138Asn is documented in any consulted source: ClinVar has no record for this variant under any of the six search terms (exact_match=false); the literature pass returned 0 PMIDs; OncoKB classifies IDH2/T138N as 'Unknown Oncogenic Effect' with no variant-specific reviewed functional evidence and no PMIDs. The only same-amino-acid report is the identical nucleotide change c.413C>A in COSMIC (COSV100344117, somatic n=1), which is a somatic occurrence, not a germline pathogenicity determination, and does not satisfy the 'different nucleotide change' condition. PS1 not met.

Rule

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

Evidence considered

• ClinVar search across six term sets (IDH2[GENE] AND c.413C>A[VARNAME]; NM_002168.3:c.413C>A[VARNAME]; NM_002168.3:c.413C>A; NC_000015.9:g.90631940G>T[VARNAME]; NC_000015.9:g.90631940G>T; IDH2[GENE] AND NM_002168.3:c.413C>A) returned no record (exact_match=false, variation_ids=[]): no established pathogenic variant with the same amino acid change p.Thr138Asn is documented in ClinVar.
• OncoKB variant page IDH2/T138N: classification 'Unknown Oncogenic Effect', is_variant_specific=false, not_reviewed=true, citations_pmids=[]: no variant-specific reviewed evidence establishes p.Thr138Asn (or any same-amino-acid change) as pathogenic.
• Generic ACMG/AMP 2015 PS1 definition (Richards et al., Genet Med 2015, PMID 25741868): PS1 requires the same amino acid change as a previously established pathogenic variant regardless of nucleotide change; no such established variant exists in the consulted sources.

Still missing

• No comprehensive search of other variant databases (e.g., HGMD, LOVD) for alternate nucleotide changes at codon 138; PS1 conclusion rests on ClinVar/literature absence.

Sources

Reasoning

Variant p.Thr138Asn in IDH2. PM1 requires location in a mutational hotspot and/or a critical well-established functional domain (e.g., enzyme active site) without benign variation. The dedicated CancerHotspots query for 'IDH2 T138' returned no statistically significant hotspot row, so T138 is not a documented mutational hotspot (bundle-internal finding; this source has no source_registry key and therefore cannot be formally cited). The well-established IDH2 cancer hotspots are R140 and R172, which are different residues, and no consulted source establishes T138 itself as a critical functional-domain or active-site residue. PM1 not met.

Rule

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

Evidence considered

• CancerHotspots query 'IDH2 T138' returned no result (search_status=no_result, 'This variant does not lie in a statistically significant hotspot'): T138 is not a documented mutational hotspot. (Bundle-internal finding; the CancerHotspots source has no source_registry key and could not be formally cited.)
• ClinVar has no record for c.413C>A and gnomAD v2.1/v4.1/Canada show the variant absent, consistent with the 'without benign variation' clause being satisfiable, but this is secondary; the primary hotspot/domain requirement of PM1 is unmet.
• Generic ACMG/AMP 2015 PM1 definition (Richards et al., Genet Med 2015, PMID 25741868): PM1 requires a mutational hotspot and/or critical well-established functional domain without benign variation; no consulted source establishes T138 as a hotspot or critical domain residue (known IDH2 hotspots R140 and R172 are different residues).

Still missing

• No curated functional-domain annotation for IDH2 residue 138 (e.g., UniProt domain/active-site annotation) was present in the case bundle to assess a domain-based PM1 argument independent of hotspot status.

Sources

Reasoning

Variant p.Thr138Asn in IDH2. PM5 requires a novel missense change at an amino acid residue where a different missense change has previously been determined pathogenic. The dedicated PM5 candidate artifact (pm5_candidates.json) recorded pm5_mode 'unknown' with same_residue_candidates=0 and candidates=[] (automatic same-residue harvesting was skipped), ClinVar has no record, and the literature pass returned 0 PMIDs. No different-missense pathogenic comparator at residue 138 (e.g., T138I, T138S, T138A, T138P) was identified in any consulted source, so the PM5 requirement is not met on available evidence. Residual uncertainty remains because a comprehensive residue-138 ClinVar enumeration of alternate nucleotide changes (c.412A>G/T/C; c.413C>G/T; c.414C>A/G/T) was not performed; flagged for human review.

Rule

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

Evidence considered

• pm5_candidates.json: pm5_mode='unknown', eligible_for_classic_pm5_search=false, same_residue_candidates=0, candidates=[]: no different-missense pathogenic comparator at residue 138 was collected.
• ClinVar search for c.413C>A returned no record (exact_match=false); literature_pass total_pmids=0: no published pathogenic missense at residue 138 identified in the consulted sources.
• Generic ACMG/AMP 2015 PM5 definition (Richards et al., Genet Med 2015, PMID 25741868): novel missense at a residue where a different missense change determined to be pathogenic has been seen before; no such comparator exists in the consulted sources.

Still missing

• Automatic same-residue PM5 candidate harvesting was skipped by the pipeline (pm5_mode=unknown); adjudication relies on ClinVar absence, 0 literature PMIDs, and 0 collected candidates.
• No dedicated ClinVar/germline enumeration of alternate nucleotide changes at codon 138 was available; a human reviewer with database access should confirm absence of pathogenic comparators at residue 138.

Sources

Reasoning

Missense variant NM_002168.3:c.413C>A (p.Thr138Asn) in IDH2. No ClinGen CSPEC/VCEP or gene-specific PP3/BP4 lookup spreadsheet exists for IDH2, so generic ACMG/AMP 2015 (Richards et al., PMID 25741868) applies with the ClinGen SVI in silico working group calibration (Pejaver et al., PMID 36413997). Missense path: REVEL score 0.736 is below the SVI-recommended PP3 threshold of >= 0.932, so the calibrated missense predictor does not support a deleterious effect. Splice path: SpliceAI max delta score 0.00 (all DS_AG/DS_AL/DS_DG/DS_DL = 0.0) is well below the 0.2 splice-impact threshold (Jaganathan et al., PMID 30661751) and predicts no splice impact, so no splice-path PP3 support. BayesDel score (-0.037745) was retrieved but is excluded: no verified published threshold is available to this pipeline, so it is treated as insufficiently calibrated per operating rules. No line of computational evidence supports PP3; PP3 not met.

Rule

PP3 (ACMG/AMP 2015, PMID 25741868) with ClinGen SVI REVEL calibration PP3 >= 0.932 (PMID 36413997)

Evidence considered

• REVEL v1.3 score 0.736 for c.413C>A (chr15:90088708 G>T); ClinGen SVI-recommended PP3 threshold >= 0.932 and BP4 threshold <= 0.016 (Pejaver et al., Am J Hum Genet 2022, PMID 36413997): 0.736 is below the PP3 threshold, so REVEL does not support PP3.
• SpliceAI max delta score 0.00 (DS_AG=0.0, DS_AL=0.0, DS_DG=0.0, DS_DL=0.0) for NM_002168.3:c.413C>A; splice-impact threshold of delta >= 0.2 (Jaganathan et al., Cell 2019, PMID 30661751): no splice impact predicted, providing no PP3 splice-path support.
• Generic ACMG/AMP 2015 criterion definitions (Richards et al., Genet Med 2015, PMID 25741868): PP3 requires multiple lines of computational evidence supporting a deleterious effect on the gene/gene product; none present.

Still missing

• BayesDel score (-0.037745) present but unusable: no verified published threshold available to this pipeline (treated as insufficiently calibrated).
• No ClinGen CSPEC/VCEP or gene-specific in silico specification for IDH2; generic ACMG/AMP 2015 with SVI calibration used instead.

Sources

Reasoning

No IDH2 VCEP/CSPEC exists (cspec found=false; gene_vcep_dir null; vcep_materials.json empty), so the generic ACMG/AMP 2015 framework (Richards et al., PMID 25741868) governs. BA1 requires allele frequency >5% in ESP, 1000 Genomes, or ExAC/gnomAD. The variant NM_002168.3:c.413C>A (p.Thr138Asn) is absent from gnomAD v2.1 (GRCh37 exomes), gnomAD v4.1 (GRCh38 exomes), and gnomAD-Canada v1.0 (genomes) — observed germline allele frequency is 0, far below any BA1 threshold. The single COSMIC somatic occurrence (COSV100344117, n=1) is somatic cancer data, not germline population frequency, and cannot contribute to BA1. Criterion not met.

Rule

BA1: allele frequency >5% in ESP, 1000 Genomes, or ExAC (Richards et al. 2015, PMID 25741868)

Evidence considered

• gnomAD v2.1 exomes: variant absent (search_status=absent, found=false; evidence.json results.gnomad.GNOMAD_V2_1)
• gnomAD v4.1 exomes: variant absent (search_status=absent, found=false; evidence.json results.gnomad.GNOMAD_V4_1)
• gnomAD-Canada v1.0 genomes: variant absent (search_status=absent, found=false; evidence.json results.gnomad.GNOMAD_CANADA_V1)
• BA1 definition: allele frequency >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (Richards et al. 2015, PMID 25741868)

Still missing

• Population-frequency query covers gnomAD v2.1/v4.1 exomes and gnomAD-Canada genomes only; no independent per-ancestry subpopulation allele frequencies were retrieved, though global absence in three large datasets makes any BA1-range frequency implausible.

Sources

Reasoning

Generic ACMG/AMP 2015 BS1 (Richards et al., PMID 25741868) requires an allele frequency greater than expected for the disorder. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (observed germline AF = 0), so the frequency is not greater than expected under any disease model; there is no population-frequency support for benignity. The COSMIC somatic entry (n=1) is not germline population-frequency evidence and is excluded. Criterion not met.

Rule

BS1: allele frequency greater than expected for disorder (Richards et al. 2015, PMID 25741868)

Evidence considered

• gnomAD v2.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD v4.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD-Canada v1.0 genomes: variant absent (search_status=absent; evidence.json)
• BS1 definition: allele frequency is greater than expected for the disorder (Richards et al. 2015, PMID 25741868)

Still missing

• No disease-prevalence/penetrance model for germline IDH2 disease was available in the case bundle, so a prevalence-based BS1 threshold could not be quantified; this is moot while the observed frequency is zero.

Sources

Reasoning

Generic ACMG/AMP 2015 BS2 (Richards et al., PMID 25741868) requires the variant to be observed in a healthy adult individual (homozygous for a recessive disorder, heterozygous for a dominant disorder, or hemizygous for an X-linked disorder) with full penetrance expected at an early age. The variant is not observed in any queried dataset: absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, and absent from ClinVar. The prerequisite positive observation in healthy individuals is unmet; additionally, no germline IDH2 disease prevalence/penetrance parameters were established in this case bundle to support a quantitative BS2 evaluation. Criterion not met.

Rule

BS2: observed in healthy adult individual(s), full penetrance expected at early age (Richards et al. 2015, PMID 25741868)

Evidence considered

• gnomAD v2.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD v4.1 exomes: variant absent (search_status=absent; evidence.json)
• gnomAD-Canada v1.0 genomes: variant absent (search_status=absent; evidence.json)
• ClinVar: no entry for NM_002168.3:c.413C>A (variation_ids empty; evidence.json results.clinvar)
• BS2 definition: observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder with full penetrance expected at an early age (Richards et al. 2015, PMID 25741868)

Still missing

• No established germline IDH2 disease prevalence/penetrance model in the case bundle (no VCEP), precluding any prevalence-based re-evaluation of BS2.
• No dedicated healthy-carrier cohort beyond gnomAD v2.1/v4.1 and gnomAD-Canada v1.0 was queried.

Sources

Reasoning

Variant p.Thr138Asn in IDH2. BP1 applies to a missense variant in a gene for which primarily truncating variants are known to cause disease. This is not the case for IDH2: missense variants are an established disease mechanism. OncoKB gene-level context states IDH2 is 'recurrently mutated in various cancer types' (well-documented somatic missense gain-of-function hotspots R140 and R172), the pvs1_gene_context artifact identified a germline IDH2 disease context (MDS/MPN overlap syndromes) in which disease-relevant IDH2 alterations are missense, and COSMIC documents a somatic missense occurrence of this very amino acid change (T138N, n=1). A truncating-only mechanism is contradicted by all consulted sources. BP1 not met.

Rule

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

Evidence considered

• OncoKB gene-level context: 'IDH2, a cell metabolism enzyme, is recurrently mutated in various cancer types including acute myeloid leukemia, glioblastoma, and cholangiocarcinoma' - missense variants (hotspots R140/R172) are an established disease mechanism, so IDH2 is not a gene where only truncating variants cause disease.
• pvs1_gene_context: germline IDH2 disease context found (disease_names: 'Genomics of myelodysplastic syndrome/myeloproliferative neoplasm overlap syndromes', supporting source PMID 33275756); the disease-relevant IDH2 alterations in these neoplasms are missense, contradicting a truncating-only mechanism.
• COSMIC records the identical amino acid change p.Thr138Asn (COSV100344117, somatic n=1) in cancer, further evidencing missense as a tolerated/selected mechanism in IDH2. (Bundle-internal finding; COSMIC has no source_registry key and could not be formally cited.)
• Generic ACMG/AMP 2015 BP1 definition (Richards et al., Genet Med 2015, PMID 25741868): BP1 applies only when primarily truncating variants are known to cause disease; not the case for IDH2.

Sources

Reasoning

Missense variant NM_002168.3:c.413C>A (p.Thr138Asn) in IDH2, adjudicated under generic ACMG/AMP 2015 (Richards et al., PMID 25741868) with ClinGen SVI in silico calibration (Pejaver et al., PMID 36413997). Missense path: REVEL score 0.736 is well above the SVI-recommended BP4 threshold of <= 0.016, so the calibrated missense predictor does not support a benign effect. Splice path: SpliceAI max delta 0.00 predicts no splice impact, but this is a single line of evidence concerning splicing only; it does not address the protein-level effect of a missense substitution, and BP4 requires multiple lines of computational evidence suggesting no impact on the gene/gene product. Per SVI guidance, REVEL is the governing calibrated predictor for missense PP3/BP4 and its intermediate score here (0.016 < 0.736 < 0.932) supports neither criterion. BayesDel score (-0.037745) excluded: no verified published threshold available to this pipeline. BP4 not met.

Rule

BP4 (ACMG/AMP 2015, PMID 25741868) with ClinGen SVI REVEL calibration BP4 <= 0.016 (PMID 36413997)

Evidence considered

• REVEL v1.3 score 0.736 for c.413C>A (chr15:90088708 G>T); ClinGen SVI-recommended BP4 threshold <= 0.016 (Pejaver et al., Am J Hum Genet 2022, PMID 36413997): 0.736 exceeds the BP4 threshold, so REVEL does not support BP4.
• SpliceAI max delta score 0.00 for NM_002168.3:c.413C>A; delta >= 0.2 indicates splice impact (Jaganathan et al., Cell 2019, PMID 30661751): absence of predicted splice impact was consulted but is insufficient alone for BP4 on a missense variant because it does not address protein-level effect and does not constitute multiple lines of evidence.
• Generic ACMG/AMP 2015 criterion definitions (Richards et al., Genet Med 2015, PMID 25741868): BP4 requires multiple lines of computational evidence suggesting no impact on the gene/gene product; not satisfied.

Still missing

• BayesDel score (-0.037745) present but unusable: no verified published threshold available to this pipeline (treated as insufficiently calibrated).
• Only one splice-path predictor (SpliceAI) available; no conservation/evolutionary predictor output in the case bundle to form multiple lines of BP4-supporting evidence.

Sources

Reasoning

PS2 (de novo, maternity and paternity confirmed) cannot be assessed: the case bundle contains no proband clinical or genotype data whatsoever — no proband phenotype, no parental testing, no maternity/paternity confirmation, and no trio data. ClinVar contains no entry for NM_002168.3:c.413C>A (p.Thr138Asn), so no externally reported confirmed de novo occurrence exists, and the literature pass returned 0 PMIDs. With no proband or parental evidence, there is nothing to evaluate for this criterion.

Rule

Generic ACMG/AMP 2015: PS2 = de novo (maternity and paternity confirmed). Richards et al. 2015, PMID 25741868 (source_registry key: generic_acmg_combination_rules); no IDH2 CSPEC/VCEP exists.

Evidence considered

• clinvar: variant absent from ClinVar — no reported de novo cases
• generic_acmg_combination_rules: PS2 rule definition (Richards et al. 2015, PMID 25741868)

Still missing

• No proband phenotype or genotype data provided in the case bundle
• No parental testing or maternity/paternity confirmation data available
• No literature or ClinVar report of this variant as de novo (literature_pass: 0 PMIDs; ClinVar absent)

Sources

Reasoning

PS3 requires well-established functional studies demonstrating a deleterious effect for the variant in question (Richards et al. 2015, PMID:25741868). No such evidence exists in this case. No VCEP/CSPEC applies to IDH2 (cspec found: false), so the generic ACMG/AMP 2015 framework governs. OncoKB (source_registry key 'oncokb') explicitly reports that no variant-specific reviewed functional evidence exists for IDH2 T138N, classifying it 'Unknown Oncogenic Effect' with not_reviewed=true and zero citations; this is a gene-level page, not a functional assay. The COSMIC record (COSV100344117, somatic count n=1) is a single somatic occurrence in a cancer database and is not functional assay evidence — it documents that the variant has been seen in a tumor, not that its protein function is altered, so it cannot satisfy PS3. In-silico predictors are not functional studies: SpliceAI max delta 0.00 and REVEL 0.736 are computational scores within the PP3/BP4 domain, and BayesDel has no verified published threshold, so none can substitute for PS3. Because no variant-specific functional assay (e.g., IDH2 enzymatic activity, 2-HG production, protein stability) was retrieved and the literature pass returned 0 PMIDs, PS3 cannot be met and is not_assessed pending human literature review.

Rule

PS3: Well-established functional studies show a deleterious effect (Richards et al. 2015, PMID:25741868; default strength Strong, subject to SVI strength calibration). Applied under generic ACMG/AMP fallback because no IDH2 VCEP/CSPEC specification exists (cspec found: false; framework source generic_acmg_combination_rules, PMID:25741868).

Evidence considered

• oncokb: OncoKB reports no variant-specific reviewed functional evidence for IDH2 T138N; classification 'Unknown Oncogenic Effect', not_reviewed=true, citations_pmids=[] — establishes absence of curated functional assay evidence
• spliceai: max delta score 0.00 — in-silico splice prediction only; not a functional study; excluded from PS3
• revel: score 0.736 — in-silico missense predictor; belongs to PP3/BP4 domain, not functional assay evidence; excluded from PS3
• bayesdel: score -0.037745 — no verified published threshold available; excluded from PS3

Still missing

• No variant-specific functional assay evidence for p.Thr138Asn (e.g., IDH2 isocitrate dehydrogenase enzymatic activity, neomorphic 2-hydroxyglutarate production, protein stability/expression assays) was retrieved in this case bundle
• literature_pass.json returned 0 PMIDs and fulltext_map.json is empty; no primary literature is available to search for functional studies of c.413C>A
• OncoKB lists no variant-specific reviewed functional evidence and no citations for IDH2 T138N (classification 'Unknown Oncogenic Effect', not_reviewed=true)
• COSMIC somatic count of 1 (COSV100344117) is not a functional assay and cannot be used as PS3 evidence

Sources

Reasoning

No case-control or cohort data exist for IDH2 c.413C>A: literature_pass.json reports zero PMIDs across all evidence sources, ClinVar has no submissions for this variant, and no affected-vs-control enrichment study is available in the bundle. The only variant-specific observation anywhere is a single somatic occurrence in COSMIC (COSV100344117, n=1); a somatic cancer database entry without a case-control design and without germline context cannot support PS4 under the generic ACMG/AMP 2015 framework. With no enrichment data to evaluate, the criterion cannot be assessed.

Rule

PS4 (generic ACMG/AMP 2015, PMID 25741868): variant prevalence in affected individuals significantly increased compared with controls in a case-control or equivalent cohort study

Evidence considered

• ClinVar query for NM_002168.3:c.413C>A returned no records (search_status no_result, exact_match false), providing no case-level or case-control submissions
• literature_pass.json: total_pmids 0, criteria_index empty
• evidence.json COSMIC entry notes somatic count 1 for COSV100344117, which does not constitute case-control enrichment

Still missing

• No case-control or cohort study reporting c.413C>A frequency in affected individuals vs controls
• literature_pass.json identified zero PMIDs for this variant, so no published enrichment evidence exists
• The single COSMIC somatic occurrence (COSV100344117, n=1) is not germline case-control evidence and COSMIC is not a key in source_registry.json, so it cannot be formally cited

Sources

Reasoning

PM3 (ACMG/AMP 2015, PMID:25741868) requires, for a recessive disorder, the variant observed in trans with a pathogenic variant. No applicable VCEP/CSPEC exists for IDH2 (cspec found=false; vcep_materials empty; framework_mode=generic_acmg), so generic ACMG/AMP 2015 governs. The variant NM_002168.3:c.413C>A (p.Thr138Asn) is a missense in IDH2, a gene for which germline disease (D-2-hydroxyglutaric aciduria type 2, OMIM 613657) is autosomal recessive, so the criterion is structurally applicable in principle. However, there is no evidence of any second allele in any proband: the variant is absent from ClinVar (no variation IDs, no submissions), absent from gnomAD v2.1/v4.1/Canada, literature_pass found 0 PMIDs, fulltext_map is empty, and no publications directory content exists. No affected-proband observations, no phase determination (trans/cis), and no family segregation data are available in the case bundle. The single COSMIC somatic observation (COSV100344117, n=1) and OncoKB 'Unknown Oncogenic Effect' cancer context are somatic-tumor data and do not constitute germline allelic-phase evidence for PM3. Evidence is therefore insufficient to assess PM3; it is not met on the available record, and the specific gap is absence of any second-variant/phase data.

Rule

PM3: For recessive disorders, detected in trans with a pathogenic variant (Richards et al. 2015, PMID:25741868).

Still missing

• No second (biallelic) variant identified in any proband carrying c.413C>A
• No phase determination (trans vs cis) available for c.413C>A with any co-occurring variant
• No affected-proband observations or family segregation data in the evidence bundle
• No germline literature reports of c.413C>A (literature_pass total_pmids=0) that could document trans configuration

Reasoning

PM6 (assumed de novo without confirmation of maternity and paternity) cannot be assessed: there is no parental testing or family genotype information of any kind in the case bundle, and no proband phenotype is provided to establish phenotype consistency. The variant is absent from ClinVar and from all searched literature (0 PMIDs), so no external report supports an assumed de novo origin. Without any parental or proband evidence, PM6 is unevaluable.

Rule

Generic ACMG/AMP 2015: PM6 = assumed de novo, but without confirmation of paternity and maternity. Richards et al. 2015, PMID 25741868 (source_registry key: generic_acmg_combination_rules); no IDH2 CSPEC/VCEP exists.

Evidence considered

• clinvar: variant absent from ClinVar — no reported de novo cases
• generic_acmg_combination_rules: PM6 rule definition (Richards et al. 2015, PMID 25741868)

Still missing

• No parental genotypes (neither parent tested) to support an assumed de novo occurrence
• No proband phenotype or clinical context provided to evaluate phenotype consistency
• No external reports (ClinVar absent; literature_pass 0 PMIDs) of de novo occurrence

Sources

Reasoning

PP1 (co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease) cannot be assessed: the case bundle contains no family segregation data — no affected relatives genotyped, no meioses observed, no segregation or non-segregation events. The only gene-level germline context available (pvs1_gene_context) is literature-derived for MDS/MPN overlap syndromes and defines no inheritance mode (inheritance: []), so IDH2 is not established in this pipeline as a definitively known Mendelian disease gene for segregation purposes. ClinVar is absent for the variant and the literature pass found 0 PMIDs, providing no external segregation reports.

Rule

Generic ACMG/AMP 2015: PP1 = co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Richards et al. 2015, PMID 25741868 (source_registry key: generic_acmg_combination_rules); no IDH2 CSPEC/VCEP exists.

Evidence considered

• clinvar: variant absent from ClinVar — no segregation reports
• pvs1_gene_context: germline disease context is literature-only (MDS/MPN overlap), inheritance mode not defined
• generic_acmg_combination_rules: PP1 rule definition (Richards et al. 2015, PMID 25741868)

Still missing

• No family segregation data: no affected family members genotyped, no meioses counted
• No defined inheritance mode for IDH2 germline disease in the case gene context (inheritance: [])
• No external segregation reports (ClinVar absent; literature_pass 0 PMIDs)

Sources

Reasoning

PP2 requires a 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. The case bundle contains no gene-level data on IDH2's benign missense rate (no gnomAD gene-level missense constraint/Z-score or observed/expected metric, and no gene-specific framework). Although OncoKB gene-level context and pvs1_gene_context establish that IDH2 is recurrently mutated in cancer (somatic missense gain-of-function at R140/R172) and that a germline IDH2 disease context exists (MDS/MPN overlap syndromes, PMID 33275756), the 'low rate of benign missense variation' component of PP2 cannot be established from any consulted source. Evidence is insufficient: PP2 not assessed, gap identified.

Rule

PP2 (ACMG/AMP 2015, PMID 25741868): 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

Evidence considered

• Generic ACMG/AMP 2015 PP2 definition (Richards et al., Genet Med 2015, PMID 25741868): PP2 requires a low rate of benign missense variation in the gene AND missense as a common mechanism of disease; no gene-level benign-missense-rate data are present in the case bundle.
• OncoKB gene-level context: IDH2 'is recurrently mutated in various cancer types including acute myeloid leukemia, glioblastoma, and cholangiocarcinoma' - documents missense as a somatic cancer mechanism but provides no benign-missense-rate quantification.
• pvs1_gene_context: germline IDH2 disease context found (disease_names: 'Genomics of myelodysplastic syndrome/myeloproliferative neoplasm overlap syndromes', PMID 33275756), but this artifact contains no benign-missense-rate data.

Still missing

• Gene-level missense constraint data for IDH2 (e.g., gnomAD missense Z-score or observed/expected ratio) are not present in the case bundle; required to establish a low rate of benign missense variation.
• Germline missense-as-common-disease-mechanism for IDH2 is only indirectly supported (somatic cancer context; MDS/MPN overlap germline literature); no gene-specific ACMG specification exists to resolve the PP2 question.

Sources

Reasoning

No proband phenotype or family history is provided anywhere in the case bundle, so phenotype specificity cannot be evaluated. Even the gene-level germline context available (pvs1_gene_context.json lists IDH2 germline disease context as 'Genomics of myelodysplastic syndrome/myeloproliferative neoplasm overlap syndromes') describes a broad neoplasm category rather than a highly specific phenotype with a single genetic etiology, and it is a pipeline artifact, not a clinical case finding. PP4 requires case-level phenotype/family-history data that are entirely absent here.

Rule

PP4 (generic ACMG/AMP 2015, PMID 25741868): phenotype or family history highly specific for a disease with a single genetic etiology

Evidence considered

• No phenotype or family-history source is present in source_registry.json; case_summary contains no clinical phenotype fields

Still missing

• No proband phenotype or clinical presentation data in the case bundle
• No family history information provided
• No disease-specific VCEP/CSPEC phenotype specification exists for IDH2 (cspec found false)

Reasoning

BS3 requires well-established functional studies demonstrating no damaging effect (Richards et al. 2015, PMID:25741868). No functional studies of any kind exist for this variant in the case bundle. OncoKB (source_registry key 'oncokb') reports no variant-specific reviewed functional evidence ('Unknown Oncogenic Effect', not_reviewed=true, no citations), so there is no assay showing wild-type-equivalent function. Absence from ClinVar and gnomAD v2.1/v4.1/Canada is population/registry absence, not functional evidence, and cannot support BS3. SpliceAI max delta 0.00 is an in-silico prediction and is evaluated under BP4 within the in_silico_splicing group per the generic rules; it does not constitute a 'well-established functional study' and must not be double-counted as BS3. REVEL 0.736 is likewise in-silico (and falls in the PP3/BP4 gray zone of the generic missense rule), and BayesDel has no verified published threshold. With zero PMIDs from the literature pass and no full-text publications available, BS3 cannot be met and is not_assessed pending human literature review for functional assays showing absence of a damaging effect.

Rule

BS3: Well-established functional studies show no damaging effect (Richards et al. 2015, PMID:25741868; default strength Strong, subject to SVI strength calibration). Applied under generic ACMG/AMP fallback because no IDH2 VCEP/CSPEC specification exists (cspec found: false; framework source generic_acmg_combination_rules, PMID:25741868).

Evidence considered

• oncokb: OncoKB reports no variant-specific reviewed functional evidence for IDH2 T138N and no benign/neutral functional annotation — absence of evidence for BS3
• spliceai: max delta score 0.00 — in-silico splice prediction; belongs to BP4/PP3 domain under generic rules, not a functional study; excluded from BS3
• revel: score 0.736 — in-silico missense predictor in the generic gray zone [0.250, 0.750]; not functional assay evidence; excluded from BS3
• bayesdel: score -0.037745 — no verified published threshold; excluded from BS3

Still missing

• No functional study demonstrating absence of a damaging effect for p.Thr138Asn (e.g., enzymatic activity comparable to wild-type IDH2, no neomorphic 2-HG production) was retrieved
• No ClinVar submissions, literature reports, or PMIDs exist for this variant in the case bundle (literature_pass total_pmids=0; ClinVar absent)
• OncoKB provides no benign/neutral functional annotation for T138N, only 'Unknown Oncogenic Effect' with no citations
• In-silico neutrality signals (SpliceAI 0.00, REVEL 0.736) are predictor scores, not well-established functional studies, and are insufficient alone for BS3

Sources

Reasoning

BS4 (lack of segregation in affected family members) cannot be assessed: no family segregation data exist in the case bundle, so it cannot be determined whether any affected relative lacks the variant. Population-absence data (gnomAD v2.1, v4.1, gnomAD-Canada: all absent) do not address BS4, which under the generic ACMG/AMP 2015 framework requires observed non-segregation in affected family members; the sole COSMIC hit is a somatic cancer occurrence (n=1), which is not germline segregation evidence. With no genotyped family members, BS4 is unevaluable.

Rule

Generic ACMG/AMP 2015: BS4 = lack of segregation in affected family members. Richards et al. 2015, PMID 25741868 (source_registry key: generic_acmg_combination_rules); no IDH2 CSPEC/VCEP exists.

Evidence considered

• clinvar: variant absent from ClinVar — no segregation data
• gnomad_v2, gnomad_v4, gnomad_canada: variant absent from population databases; population absence alone does not satisfy BS4's segregation definition
• generic_acmg_combination_rules: BS4 rule definition (Richards et al. 2015, PMID 25741868)

Still missing

• No affected family members genotyped — cannot establish presence or lack of segregation
• No pedigree or meiosis data in the case bundle
• No external non-segregation reports (ClinVar absent; literature_pass 0 PMIDs)

Sources

Reasoning

BP2 (ACMG/AMP 2015, PMID:25741868) requires observation of the variant in trans with a pathogenic variant for a fully dominant disease/gene (or in cis with a pathogenic variant under any inheritance pattern), which supports benignity. No applicable VCEP/CSPEC exists for IDH2 (cspec found=false; framework_mode=generic_acmg), so generic ACMG/AMP 2015 governs. The case bundle contains no observation of c.413C>A in any individual together with any other variant, and no phase information whatsoever: ClinVar has no record for this variant, gnomAD v2.1/v4.1/Canada show absence, literature_pass found 0 PMIDs, and fulltext_map is empty. IDH2 germline disease is autosomal recessive (D-2-hydroxyglutaric aciduria type 2), and no fully dominant germline IDH2 disorder context supporting a trans-with-pathogenic-dominant-allele observation is documented in the bundle. Evidence is insufficient to assess BP2; it is not met on the available record, with the gap being the complete absence of co-occurrence/phase observations.

Rule

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 (Richards et al. 2015, PMID:25741868).

Still missing

• No observation of c.413C>A in trans with a pathogenic variant in any individual
• No observation of c.413C>A in cis with any pathogenic variant
• No family or phase studies exist for this variant (ClinVar absent, 0 literature PMIDs)
• No established fully dominant germline IDH2 disease context in the bundle against which a trans observation could be interpreted

Reasoning

BP5 requires the variant to be found in a case with an established alternate molecular basis for disease. No proband-level data of any kind are present in the bundle (no case report, no segregation/family studies, no alternate-diagnosis documentation), and literature_pass.json found zero PMIDs. The alternate-molecular-basis question therefore cannot be assessed.

Rule

BP5 (generic ACMG/AMP 2015, PMID 25741868): variant found in a case with an alternate molecular basis for disease

Evidence considered

• ClinVar has no submissions for this variant, so no case documentation or alternate-basis reports exist in the registry sources
• literature_pass.json: total_pmids 0

Still missing

• No case-level data documenting an alternate molecular basis for disease in a proband carrying c.413C>A
• No publications or ClinVar submissions describing this variant in affected individuals

Sources