KMT2A c.2040G>T, p.(Ser680=)

Reasoning

The variant is at extremely low frequency in population controls, below the local non-VCEP PM2 threshold of 0.1%: gnomAD v2.1 total AF 0.00107% (3/281,682 alleles, 0 homozygotes) and gnomAD v4.1 total AF 0.00112% (18/1,613,328 alleles, 0 homozygotes). The highest subpopulation frequency (East Asian 0.022% in v4.1, 0.015% in v2.1) and grpmax FAF (0.012% v4.1 / 0.023% v2.1) are also below 0.1%, with no population-specific threshold artifact. PM2 applied at supporting strength (PM2_Supporting) per current ClinGen SVI practice.

Rule

PM2 (ACMG/AMP 2015, PMID 25741868): absent or at extremely low frequency in controls; local non-VCEP threshold allele frequency <0.1%; applied at supporting strength (PM2_Supporting).

Evidence considered

• Local non-VCEP PM2 threshold: allele frequency <0.1% (absent or extremely low frequency in controls, per ACMG/AMP 2015 PM2 definition, PMID 25741868).
• gnomAD v2.1 (gnomad_v2): total AF 1.06503e-05 (0.00107%, 3/281,682 alleles), 0 homozygotes; East Asian max subpopulation AF 0.01505%; grpmax FAF 0.00022756 (0.023%) — all below 0.1%.
• gnomAD v4.1 (gnomad_v4): total AF 1.11571e-05 (0.00112%, 18/1,613,328 alleles), 0 homozygotes; East Asian max subpopulation AF 0.02228%; grpmax FAF 0.00012016 (0.012%) — all below 0.1%.
• The variant is present (not absent) in gnomAD, so PM2 rests on the extremely-low-frequency branch of the criterion, satisfied at 0.001% total AF.
• Strength: supporting (PM2_Supporting) per current ClinGen SVI convention of applying PM2 at supporting strength.
• No threshold artifact: the highest subpopulation AF (East Asian) and grpmax FAF remain below 0.1% in both releases.

Still missing

• gnomAD-Canada v1.0 unavailable (HTTP 500); one additional population resource not queried, but not needed since two large gnomAD releases independently confirm AF <0.1%.

Sources

Reasoning

NM_005933.3:c.2040G>T is a synonymous variant (NP_005924.2:p.(Ser680=)) located deep within exon 3 of NM_005933.3 (exon spans c.503-3156; c.2040 is ~1.5 kb from the 5' exon boundary and ~1.1 kb from the 3' boundary), well outside canonical splice consensus sequences. SpliceAI predicts no impact on splicing: max delta score 0.006 (DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.006), far below the delta >= 0.2 splice-altering threshold (Jaganathan et al. 2019, PMID 30661751), and no alternate splice site creation is predicted. This satisfies the splice-prediction clause of BP7. The 'nucleotide is not highly conserved' clause could not be directly verified because no conservation score was available in the case bundle; the position is a third-codon-position synonymous site with no evidence of strong constraint, but this is an indirect inference and is flagged as a gap.

Rule

BP7 (ACMG/AMP 2015, PMID 25741868): A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new alternate splice site AND the nucleotide is not highly conserved.

Evidence considered

• Variant normalization confirms NM_005933.3:c.2040G>T is synonymous, NP_005924.2:p.(Ser680=), in exon 3 of the KMT2A transcript.
• SpliceAI (Jaganathan et al. 2019, PMID 30661751; spliceailookup.broadinstitute.org) predicts no splice impact for NM_005933.3:c.2040G>T: max delta 0.006 (DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.006), well below the 0.2 splice-altering threshold; no impact on the splice consensus sequence and no creation of an alternate splice site predicted.
• Variant position c.2040 lies ~1.5 kb from the 5' end and ~1.1 kb from the 3' end of exon 3 (exon span c.503-3156), i.e., not within or near any canonical splice consensus sequence.
• No conservation score was available; the 'nucleotide not highly conserved' clause of BP7 is treated as inferred for this synonymous third-codon-position change and recorded as a gap.

Still missing

• No direct nucleotide conservation score (e.g., phyloP/GERP) for chr11:g.118473199 (c.2040) was available in the case bundle; the BP7 clause requiring that the nucleotide is not highly conserved is inferred indirectly (synonymous third-codon-position change) rather than directly verified. If a high conservation score exists at this position, BP7 should be reconsidered.

Sources

Reasoning

No computational evidence supports a deleterious effect. Splice path: SpliceAI max delta score is 0.006 (DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.006), far below the delta >= 0.2 splice-altering threshold recommended in the SpliceAI publication (Jaganathan et al. 2019, PMID 30661751), so there is no splice-impact support for PP3. Missense path: the variant is synonymous (NP_005924.2:p.(Ser680=)), so missense predictors do not apply; moreover REVEL returned no score (not found in REVEL v1.3 lookup, ClinGen SVI calibration PMID 36413997 not applicable without a score) and BayesDel returned no score and has no verified published threshold for PP3/BP4 calibration. No criterion-supporting prediction exists, so PP3 is not met.

Rule

PP3 (ACMG/AMP 2015, PMID 25741868): Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• SpliceAI lookup (spliceailookup.broadinstitute.org) for NM_005933.3:c.2040G>T reports raw max delta score 0.006 (DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.006; displayed summary states max delta ~0.01), far below the delta >= 0.2 high-sensitivity splice-altering threshold recommended by Jaganathan et al. 2019 (PMID 30661751); provides no support for PP3 via the splice path.
• REVEL returned no score for chr11:g.118473199G>T in the REVEL v1.3 lookup (found=false); the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID 36413997) cannot be applied because no score exists.
• BayesDel returned no score (found=false) and no verified published PP3/BP4 calibration threshold is available to this pipeline, so BayesDel cannot contribute to PP3 under any score.
• The variant is synonymous (NP_005924.2:p.(Ser680=) per variant normalization), so missense in-silico predictors (REVEL/BayesDel/aGVGD) are not applicable to this change.

Still missing

• REVEL and BayesDel scores were not available for this variant (lookup found=false), so the missense in-silico path could not be evaluated; aGVGD data were not available either. A missense-computational PP3 assessment is therefore impossible for this synonymous variant regardless of these gaps.

Sources

Reasoning

PP5 is applied only when an exact-variant ClinVar expert-panel classification is Pathogenic/Likely pathogenic (operational rule: supporting strength on a 3-star expert-panel assertion). ClinVar Variation 1576960 (exact match for KMT2A c.2040G>T, p.Ser680=) has zero expert-panel submissions (expert_panel_submissions = 0; expert_panels = {}); its only submission is SCV002380130 from Labcorp Genetics (clinical testing, germline) with review status 'criteria provided, single submitter' (1 star), classified Likely benign. No expert-panel Pathogenic/Likely pathogenic classification exists for this exact variant, so PP5 is not met. Additionally, the existing single-submitter assertion is Likely benign, which could not support PP5 under any reading.

Rule

PP5 operational rule: exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classification (3-star) required; supporting strength when present (Richards et al. 2015, PMID:25741868)

Evidence considered

• ClinVar submission audit (clinvar_submission_audit.json): 1 submission total, 0 expert-panel submissions, review status 'criteria provided, single submitter' (1 star), submitter Labcorp Genetics (clinical laboratory, not an expert panel).
• PP5 operational rule applied: exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classification required; none exists for this variant.

Still missing

• None for the current determination (complete ClinVar submission audit for the exact variant). PP5 should be revisited only if an expert-panel Pathogenic/Likely pathogenic classification of this exact variant is deposited in ClinVar.

Sources

Reasoning

Observed allele frequency is orders of magnitude below the 1% BA1 threshold in both gnomAD releases: total AF 0.00107% (3/281,682 alleles, gnomAD v2.1) and 0.00112% (18/1,613,328 alleles, gnomAD v4.1), with 0 homozygotes in both. The highest population-specific frequency (East Asian, 0.015% in v2.1 and 0.022% in v4.1) and the grpmax FAF (0.023% in v2.1; 0.012% in v4.1) are also far below 1%. No population or threshold artifact approaches the BA1 cutoff.

Rule

BA1 (ACMG/AMP 2015, PMID 25741868): allele frequency >1% in any gnomAD population; local non-VCEP threshold 1%.

Evidence considered

• No ClinGen CSPEC/VCEP specification exists for KMT2A (cspec found=false, framework_mode=generic_acmg); generic ACMG/AMP 2015 (PMID 25741868) applies via generic_acmg_combination_rules, with the local non-VCEP population thresholds BA1 >1%, BS1 >0.3%, PM2 <0.1%.
• gnomAD v2.1 (gnomad_v2): total AF 1.06503e-05 (0.00107%, 3/281,682 alleles), 0 homozygotes; highest subpopulation East Asian AF 0.01505% (3/19,936 alleles); grpmax FAF 0.00022756 (0.023%).
• gnomAD v4.1 (gnomad_v4): total AF 1.11571e-05 (0.00112%, 18/1,613,328 alleles), 0 homozygotes; highest subpopulation East Asian AF 0.02228% (10/44,888 alleles); grpmax FAF 0.00012016 (0.012%).
• BA1 threshold of 1% is not approached by total AF, highest subpopulation AF, or grpmax FAF in either gnomAD release.

Still missing

• gnomAD-Canada v1.0 endpoint returned HTTP 500 and could not be queried; inconsequential given two large, independently collected gnomAD datasets agree.

Sources

Reasoning

BS1 requires an allele frequency greater than expected for the disorder (local non-VCEP threshold 0.3%). The observed frequency is ~0.001% overall (gnomAD v2.1 and v4.1), with a maximum subpopulation frequency of 0.022% (East Asian, v4.1) and grpmax FAF 0.012-0.023% — all well below 0.3%. KMT2A-associated Wiedemann-Steiner syndrome is a rare autosomal dominant disorder, so the frequency expected for a pathogenic allele is far lower than what is observed here; the observed frequency does not exceed expectation for the disorder.

Rule

BS1 (ACMG/AMP 2015, PMID 25741868): allele frequency greater than expected for the disorder; local non-VCEP threshold 0.3% in any gnomAD population.

Evidence considered

• gnomAD v2.1 (gnomad_v2): total AF 1.06503e-05 (0.00107%), East Asian max subpopulation AF 0.01505%, grpmax FAF 0.023%.
• gnomAD v4.1 (gnomad_v4): total AF 1.11571e-05 (0.00112%), East Asian max subpopulation AF 0.02228%, grpmax FAF 0.012%.
• Local non-VCEP BS1 threshold of 0.3% is not reached by total AF, any subpopulation AF, or grpmax FAF; KMT2A disease context (autosomal dominant Wiedemann-Steiner syndrome, rare, mostly de novo pathogenic variants) does not support a higher expected allele frequency.
• No threshold artifact: even the v4.1 genome-only grpmax FAF (0.038%) remains far below 0.3%.

Still missing

• gnomAD-Canada v1.0 unavailable (HTTP 500); inconsequential for BS1 because both gnomAD releases show AF two orders of magnitude below the 0.3% threshold.

Sources

Reasoning

BS2 requires observation of the variant in healthy adult individuals (heterozygous carriers for a dominant disorder) in an appropriately sized cohort. gnomAD v2.1 (3 alleles) and gnomAD v4.1 (18 alleles) report the variant only in heterozygous state with 0 homozygotes, and gnomAD is a general population cohort not phenotype-screened for Wiedemann-Steiner syndrome, an early-onset autosomal dominant neurodevelopmental disorder. Heterozygous carrier status in gnomAD does not establish unaffected adult status, so the healthy-adult observation required for BS2 is not demonstrated.

Rule

BS2 (ACMG/AMP 2015, PMID 25741868): observed in a healthy adult individual for a dominant disorder with full penetrance expected at an early age; requires an appropriately sized cohort.

Evidence considered

• gnomAD v2.1 (gnomad_v2): 3/281,682 alleles, 0 homozygotes; no unaffected-status information per carrier.
• gnomAD v4.1 (gnomad_v4): 18/1,613,328 alleles, 0 homozygotes; no unaffected-status information per carrier.
• KMT2A pathogenic variants cause Wiedemann-Steiner syndrome, a dominant developmental disorder typically manifesting in childhood; gnomAD is not a healthy-adult cohort for this phenotype, so heterozygous presence does not meet the BS2 'healthy adult' requirement.
• No homozygous observations exist that could support BS2 via a recessive-style argument; for a dominant disorder BS2 would additionally require multiple confirmed unaffected adults.

Still missing

• No phenotype-confirmed healthy adult observation for this variant (e.g., unaffected parents in case series or a screened control cohort); gnomAD carriers cannot be assumed unaffected for an early-onset dominant disorder.

Sources

Reasoning

BP2 requires a documented observation of the variant in trans with a pathogenic variant for a fully dominant disorder, or in cis with a pathogenic variant in any inheritance pattern. No such observation exists in any source: no proband or family data, no phase information, and no second pathogenic variant are reported. gnomAD allele counts are unphased population data and ClinVar provides no phase/phenotype detail, so BP2 is not met.

Rule

BP2: Observed in trans with a pathogenic variant for a fully dominant disease/disorder; or observed in cis with a pathogenic variant in any inheritance pattern (Richards et al. 2015, PMID 25741868)

Evidence considered

• No ClinGen CSPEC or KMT2A-specific VCEP exists for this case (vcep_materials.json: cspec not found, framework_mode=generic_acmg); generic ACMG/AMP 2015 rules (Richards et al. 2015, PMID 25741868, via generic_acmg_combination_rules) govern.
• BP2 is defined as: 'Observed in trans with a pathogenic variant for a fully dominant disease/disorder; or observed in cis with a pathogenic variant in any inheritance pattern' (Richards et al. 2015, PMID 25741868).
• No source documents this variant in trans with a pathogenic variant in a fully dominant disorder, nor in cis with any pathogenic variant: ClinVar (VCV001576960, SCV002380130, Likely benign, condition 'not provided') contains no phase, phenotype, or second-variant detail; gnomAD v2.1/v4.1 (3/281682 and 18/1613328 alleles, 0 homozygotes) provide only unphased population allele counts; COSMIC/OncoKB/hotspots contain no somatic record for this variant.
• fulltext_map.json is empty and literature_pass.json lists only the background framework paper PMID 28492532 with no variant-specific findings, so no publication reports an allelic (cis/trans) observation for c.2040G>T.
• The required observation is absent across all sources; BP2 is therefore not met. Phase-resolved proband/family data would be needed to ever apply this criterion.

Still missing

• No proband-level sequencing or family phase data was retrieved for this case; trans/cis status of c.2040G>T with any pathogenic KMT2A variant could not be established.

Sources

Reasoning

The only no-impact computational prediction available is SpliceAI (max delta 0.006), which is credited to BP7, the designated criterion for synonymous variants, to avoid double-counting the same prediction across BP4 and BP7. No independent BP4 evidence exists: REVEL and BayesDel scores are unavailable (and inapplicable to a synonymous variant), and no conservation-based no-impact evidence was collected. BP4 is therefore not applied independently.

Rule

BP4 (ACMG/AMP 2015, PMID 25741868): Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• SpliceAI max delta 0.006 (DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.006) shows no predicted splice impact, but this single prediction is counted once, under BP7 (the criterion designated for synonymous variants), per the no-double-counting rule for PP3/BP4/BP7.
• REVEL and BayesDel returned no scores (found=false) and are missense tools not applicable to the synonymous change p.(Ser680=); no independent BP4 evidence is available.

Still missing

• REVEL/BayesDel missense in-silico scores were not available (found=false), so the missense BP4 path could not be evaluated; for this synonymous variant that path is not applicable in any case.
• No nucleotide conservation score (e.g., phyloP/GERP) was present in the case bundle; conservation-based no-impact evidence for BP4 could not be assessed.

Sources

Reasoning

BP6 is applied only when an exact-variant ClinVar expert-panel classification is Benign/Likely benign (operational rule: supporting strength on a 3-star expert-panel assertion). ClinVar Variation 1576960 (exact match for KMT2A c.2040G>T, p.Ser680=) has zero expert-panel submissions; its only submission is SCV002380130 from Labcorp Genetics with review status 'criteria provided, single submitter' (1 star) classified Likely benign. This is an ordinary laboratory submission, not an expert-panel assertion, so BP6's prerequisite is not met and the criterion is not applied. The single-submitter Likely benign assertion is accordingly noted as context only and does not trigger BP6.

Rule

BP6 operational rule: exact-variant ClinVar expert-panel Benign/Likely benign classification (3-star) required; supporting strength when present (Richards et al. 2015, PMID:25741868)

Evidence considered

• ClinVar submission audit (clinvar_submission_audit.json): 1 submission total, 0 expert-panel submissions; submission SCV002380130 (Labcorp Genetics) is a clinical-laboratory, single-submitter (1-star) Likely benign assertion, not an expert-panel classification.
• BP6 operational rule applied: exact-variant ClinVar expert-panel Benign/Likely benign classification (3-star) required; none exists for this variant.

Still missing

• None for the current determination (complete ClinVar submission audit for the exact variant). BP6 should be revisited only if an expert-panel Benign/Likely benign classification of this exact variant is deposited in ClinVar.

Sources

Reasoning

No applicable VCEP/CSPEC specification exists for KMT2A (vcep_materials.json: framework_complete=false, generic_acmg_fallback), so the generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868) governs. PS2 requires a confirmed de novo occurrence (maternity and paternity confirmed) in a proband with the disease and no family history. The case bundle contains no proband/parental trio data of any kind: an exhaustive search of the consolidated evidence bundle for de novo, parental, proband, meiosis, segregation, and family terms returned zero matches; the single ClinVar submission (SCV002380130, Labcorp, germline, 1 star) discloses no de novo or family-history evidence and cites only the Sherloc methods paper (PMID:28492532), which does not mention this variant; and literature_pass.json contains no segregation/de novo papers (criteria_index empty, fulltext_map.json empty). With no parental genotyping results available, confirmed de novo status cannot be evaluated, so PS2 is not_assessed rather than met or not_met.

Rule

PS2 (Richards et al. 2015, PMID:25741868): de novo (maternity and paternity confirmed) in a patient with the disease and no family history

Evidence considered

• Searched the consolidated case-evidence bundle for the terms de novo, denovo, parent, proband, meios, famil, and segregat; zero matches found across review_manifest.json, case_summary.json, source_registry.json, prefetch.json, evidence.json, literature_pass.json, vcep_materials.json, and fulltext_map.json
• ClinVar record VCV001576960 (SCV002380130, Labcorp Genetics/Invitae) is a single-submitter germline 'Likely benign' entry (criteria provided, 1 star) with empty condition labels and no de novo, parental, or family-history data; its only cited PMID (28492532, Sherloc) is a criteria-methodology paper that does not mention the variant
• literature_pass.json reports zero high- or medium-priority segregation/de novo papers (criteria_index and criterion_screened empty); fulltext_map.json is empty, so no publication full text was available for de novo assessment
• Generic ACMG/AMP 2015 PS2 rule (Richards et al., PMID:25741868) applied: de novo (maternity and paternity confirmed) in a patient with the disease and no family history

Still missing

• No proband/parental trio genotyping data (maternity and paternity confirmed) available for this variant; a confirmed de novo occurrence cannot be established without it
• No proband phenotype/family-history documentation provided to anchor a de novo assessment

Sources

Reasoning

PS3 requires well-established functional studies demonstrating a deleterious effect (generic ACMG/AMP 2015, PMID 25741868). No functional assay evidence for NM_005933.3:c.2040G>T (p.Ser680=) was identified anywhere in the case bundle: no variant-specific functional literature (fulltext_map.json is empty; the only paper in the literature packet, PMID:28492532, is a classification-methodology paper with no variant data), no RNA/cDNA splicing analysis, and no protein activity assay. The only functional-adjacent datum is an in silico SpliceAI prediction of no splice impact (max delta score 0.006), which is not a functional study and cannot support PS3. Evidence is therefore insufficient; PS3 is not assessed.

Evidence considered

• Searched the consolidated case-evidence bundle for functional assay data on NM_005933.3:c.2040G>T (p.Ser680=): none found; no variant-specific functional studies, no RNA/splicing assays, no protein activity assays.
• SpliceAI (in silico) predicts no significant splice impact (max delta score 0.006; DS_AG 0.001, DS_AL 0.0, DS_DG 0.0, DS_DL 0.006); an in silico prediction is not a well-established functional study and provides no evidence of a deleterious effect for PS3.
• OncoKB lists 'Unknown Oncogenic Effect' for KMT2A p.Ser680= with explicitly non-variant-specific curated context; no variant-specific functional annotation.
• COSMIC and Cancer Hotspots returned no records for this variant; no somatic functional evidence.
• Literature packet contained only PMID:28492532 (Sherloc ACMG refinement methodology); reviewed and contains no functional data for this variant (fulltext_map.json empty, publications directory empty).
• Governing framework: generic ACMG/AMP 2015 (PMID 25741868) because no ClinGen CSPEC/VCEP specification exists for KMT2A; PS3 requires well-established functional studies showing a deleterious effect, which are absent here.

Still missing

• No well-established functional assay (e.g., histone H3K4 methyltransferase activity assay, RNA/cDNA splicing analysis) for c.2040G>T identified in literature or case evidence
• No variant-specific functional literature retrieved (fulltext_map.json empty; only background methodology paper PMID:28492532 available)

Sources

Reasoning

PS4 (Richards et al. 2015, PMID:25741868) requires the prevalence of the variant in affected individuals to be significantly increased relative to controls (case-control enrichment). No case-control or case-cohort study for KMT2A c.2040G>T (p.Ser680=) is present in the case bundle. The only retrieved publication (PMID:28492532, Sherloc methods paper, obtained via the ClinVar submission trail) contains no variant-specific or case-level data. ClinVar Variation 1576960 holds a single-submitter laboratory classification with no case-level enrichment data. gnomAD v2.1/v4.1 show the synonymous variant in population controls at low frequency (v4.1 total AF 0.00112%, grpmax FAF 0.0120%), which provides control-frequency context only and no affected-vs-control comparison. Because the positive evidence required by PS4 is entirely absent, the criterion is not assessed and the data gap is identified in gaps_remaining.

Rule

generic_acmg: PS4 case-control enrichment — prevalence in affected individuals significantly increased vs controls (Richards et al. 2015, PMID:25741868)

Evidence considered

• Literature pass (literature_pass.json) retrieved a single publication, PMID:28492532 (Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria), a background/methods paper with no case-control, cohort, or variant-specific data for KMT2A c.2040G>T.
• ClinVar record for the exact variant (Variation 1576960 / VCV001576960) contains one single-submitter (Labcorp) classification with no case-level enrichment data.
• gnomAD v2.1 (total AF 1.07e-05, 3/281682 alleles; grpmax FAF 2.28e-04) and gnomAD v4.1 (total AF 1.12e-05, 18/1613328 alleles; joint grpmax FAF 1.20e-04) show the variant at low frequency in population controls; no affected-vs-control enrichment comparison exists.
• COSMIC returned no somatic report for this variant; somatic absence does not substitute for germline case-control evidence and was not used for PS4.

Still missing

• No case-control or case-cohort enrichment study exists for KMT2A c.2040G>T in the case bundle; the literature pass retrieved only one PMID (28492532) via the ClinVar submission trail, and no dedicated variant-specific case-report search was performed.
• No proband-level case observations of this exact variant are available to estimate prevalence in affected individuals.

Sources

Reasoning

Generic ACMG/AMP 2015 fallback applies (no KMT2A VCEP/CSPEC). PM6 requires an assumed de novo occurrence without confirmation of paternity and maternity. The case bundle contains no proband or parental genotyping data whatsoever (zero matches for de novo/parent/proband/meiosis/family terms across all bundle sections), and the only literature source (PMID:28492532, Sherloc, background_review theme) is not variant-specific. Assumed de novo status therefore cannot be evaluated, and PM6 is not_assessed.

Rule

PM6 (Richards et al. 2015, PMID:25741868): assumed de novo, but without confirmation of paternity and maternity

Evidence considered

• Searched the consolidated case-evidence bundle for the terms de novo, denovo, parent, proband, meios, famil, and segregat; zero matches found in any bundle section
• ClinVar entry VCV001576960 provides no parental-testing or de novo assertions; the single submission (SCV002380130) reports only a germline Likely benign classification without supporting family evidence
• No segregation/de novo publications were triaged for this case (literature_pass.json criteria_index empty; publications.json triage recommended no paper for full review)
• Generic ACMG/AMP 2015 PM6 rule (Richards et al., PMID:25741868) applied: assumed de novo, but without confirmation of paternity and maternity

Still missing

• No proband/parental genotyping data (even without paternity/maternity confirmation) available to support an assumed de novo occurrence
• No publication reports this variant as de novo in any proband

Sources

Reasoning

Generic ACMG/AMP 2015 fallback applies (no KMT2A VCEP/CSPEC). PP1 requires co-segregation of the variant with disease in multiple affected family members in a gene definitively known to cause the disease. No segregation data exist in this case: the evidence bundle contains no family/pedigree information (zero matches for segregation/family/proband terms across all sections), no publication reports this variant, and fulltext_map.json is empty. Co-segregation therefore cannot be evaluated, and PP1 is not_assessed.

Rule

PP1 (Richards et al. 2015, PMID:25741868): co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease

Evidence considered

• Searched the consolidated case-evidence bundle for the terms de novo, denovo, parent, proband, meios, famil, and segregat; zero matches found in any bundle section
• ClinVar submission SCV002380130 discloses no segregation or family-history data (condition labels empty; no family-based assertions)
• literature_pass.json lists no segregation-theme papers (criteria_index empty); the only PMID in the case (28492532, Sherloc) was triaged as background_review with variant_mentioned=false
• Generic ACMG/AMP 2015 PP1 rule (Richards et al., PMID:25741868) applied: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease

Still missing

• No segregation data across affected family members available (no pedigrees, no affected-relative genotyping results)
• No publication reports this variant in any family to support co-segregation

Sources

Reasoning

PP4 (Richards et al. 2015, PMID:25741868) requires the variant carrier's phenotype or family history to be highly specific for a gene with a single genetic etiology. No proband-level phenotypic data for any carrier of KMT2A c.2040G>T (p.Ser680=) exists in the case bundle: the ClinVar submission lists condition 'not provided' with no phenotype details, and the only retrieved publication (PMID:28492532) is a criteria-methods paper with no phenotype data. With no clinical case reports, phenotype specificity cannot be evaluated, so PP4 is not assessed.

Rule

generic_acmg: PP4 phenotype/family history highly specific for a gene with a single genetic etiology (Richards et al. 2015, PMID:25741868)

Evidence considered

• ClinVar submission SCV002380130 for the exact variant reports condition 'not provided' (API conditions list) and contains no phenotype or family-history data.
• The only retrieved publication (PMID:28492532, Sherloc methods paper) contains no phenotype data for this variant or for KMT2A carriers of c.2040G>T.
• No other case reports, case series, or phenotype-focused literature for this exact variant were retrieved by the literature pass.

Still missing

• No clinical case reports or proband phenotype descriptions for this exact variant are available; phenotype-specificity assessment (PP4) requires carrier phenotype/family-history data.

Sources

Reasoning

BS3 requires well-established functional studies showing no damaging effect on protein function or splicing (generic ACMG/AMP 2015, PMID 25741868). No such functional study exists for c.2040G>T in the case bundle: no RNA/cDNA splicing assay, no protein function assay, and no variant-specific functional literature (fulltext_map.json empty; PMID:28492532 is a methodology paper only). SpliceAI in silico prediction of no splice impact (max delta 0.006) was consulted but does not qualify as a well-established functional study under the generic framework. The ClinVar Likely benign classification (single submitter, 1-star) is a final classification, not functional evidence, and was not used to infer BS3. Evidence is therefore insufficient; BS3 is not assessed.

Evidence considered

• SpliceAI (in silico) predicts no significant splice impact for c.2040G>T (max delta score 0.006; DS_AG 0.001, DS_AL 0.0, DS_DG 0.0, DS_DL 0.006); directly consulted for BS3 but in silico prediction is not a well-established functional study.
• No well-established functional study (RNA splicing assay or protein function assay) demonstrating no damaging effect on protein function or splicing was identified for c.2040G>T anywhere in the case bundle.
• ClinVar entry (Likely benign, single submitter SCV002380130, 1-star review status) was not used to infer BS3; a final classification from another source cannot substitute for functional assay evidence.
• Literature packet contained only PMID:28492532 (Sherloc ACMG refinement methodology); no functional data for this variant (fulltext_map.json empty).
• Governing framework: generic ACMG/AMP 2015 (PMID 25741868) because no ClinGen CSPEC/VCEP specification exists for KMT2A; BS3 requires well-established functional studies showing no damaging effect, which are absent here.

Still missing

• No functional assay (RNA/cDNA splicing analysis or protein function assay) demonstrating no damaging effect for c.2040G>T
• SpliceAI in silico prediction alone (max delta score 0.006) is insufficient to meet BS3's requirement for well-established functional studies under generic ACMG/AMP 2015

Sources

Reasoning

Generic ACMG/AMP 2015 fallback applies (no KMT2A VCEP/CSPEC). BS4 (non-segregation) requires documented lack of segregation in affected members of a family, i.e. affected relatives who do not carry the variant or unaffected carriers. No family/segregation data of any kind exist in this case bundle (zero matches for segregation/family/proband/parental terms across all sections), and the ClinVar record provides no segregation assertions. Lack of segregation cannot be demonstrated from absence of family data, so BS4 is not_assessed; in particular, the single-submitter ClinVar 'Likely benign' label was not used to infer BS4, per the rule against inferring criteria from another source's final classification.

Rule

BS4 (Richards et al. 2015, PMID:25741868): lack of segregation in affected members of a family

Evidence considered

• Searched the consolidated case-evidence bundle for the terms de novo, denovo, parent, proband, meios, famil, and segregat; zero matches found in any bundle section
• ClinVar entry VCV001576960 (SCV002380130, Labcorp, Likely benign, single submitter, 1 star) contains no segregation/non-segregation assertions; its 'Likely benign' classification was deliberately not used to infer BS4 or any other criterion in this group
• No segregation-theme publications were triaged (literature_pass.json criteria_index empty; fulltext_map.json empty)
• Generic ACMG/AMP 2015 BS4 rule (Richards et al., PMID:25741868) applied: lack of segregation in affected members of a family

Still missing

• No family segregation studies available; cannot determine whether affected family members lack the variant (BS4) or co-segregate (PP1)
• No unaffected-carrier or affected-non-carrier observations reported for this variant

Sources

Reasoning

BP5 (Richards et al. 2015, PMID:25741868) applies when a variant is found in a case with an alternate molecular basis of disease. No case reports of KMT2A c.2040G>T exist in the case bundle (literature pass retrieved only PMID:28492532, a methods paper; ClinVar contains no case-level data), so no affected individual carrying this variant is available in whom an alternate molecular basis could be documented. The evidence required to evaluate BP5 is absent, so the criterion is not assessed.

Rule

generic_acmg: BP5 variant found in a case with an alternate molecular basis of disease (Richards et al. 2015, PMID:25741868)

Evidence considered

• No proband/case reports of KMT2A c.2040G>T were retrieved: literature_pass total_pmids = 1 (PMID:28492532, Sherloc methods paper, no case data) and ClinVar holds a single-submitter classification with no case-level content.
• No evidence of an alternate molecular basis of disease in any carrier of this variant is available.

Still missing

• No case-level reports of this exact variant exist; evaluating BP5 requires a documented case carrying the variant with an alternate molecular basis of disease.

Sources