ESR1 c.1163T>A, p.(Met388Lys)

Reasoning

No applicable ESR1 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP framework applies. NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys) is reported as absent from gnomAD v2.1 and gnomAD v4.1, the supplied broad population reference datasets. This supports PM2 under the generic ACMG/AMP definition of absence or extreme rarity in population databases. Confidence is limited because the bundle provides no allele-number, coverage, or ancestry-specific denominators, and the gnomAD-Canada result has allele number 0. Human review is requested to confirm that the absence records represent adequate callable coverage for this locus and are appropriate for the disease model.

Rule

generic ACMG/AMP PM2: absent from or extremely rare in population databases

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent, but allele number is 0, so it cannot serve as a reliable denominator for rarity.
• The evidence supports absence in the supplied population datasets but does not permit ancestry-specific frequency estimation or correction for locus coverage.

Still missing

• No numeric allele number, coverage, or ancestry-specific denominator was available for gnomAD v2.1 or v4.1.
• The gnomAD-Canada result has allele number 0 and is not independently informative for rarity.
• No disease-specific prevalence, penetrance, inheritance model, or maximum credible allele-frequency calculation was available.

Sources

Reasoning

No ClinGen VCEP CSPEC is available for ESR1 (case_summary.json cspec.found=false; vcep_materials.json final_classification_framework.found=false), so the generic ACMG/AMP in-silico framework applies. This variant is a missense substitution (NM_001122740.1:c.1163T>A, p.Met388Lys), so the missense computational-evidence path governs, not the splice-impact path. REVEL score is 0.977, which exceeds the ClinGen SVI-recalibrated strong pathogenic threshold of >=0.932 established in the REVEL recalibration study (PMID:36413997, Pejaver et al. 2022). This supports PP3 at strong strength. BayesDel score (0.524984) is present in source_registry but is excluded from this assessment because no verified published threshold/table can be named for it, per pipeline calibration policy; it is therefore treated as not_available for PP3/BP4 rather than used to adjust strength. SpliceAI predicts no splice impact (max delta score 0.002; c.1163 lies well within the exon, ~66 nt from either flanking exon boundary per the mutalyzer exon map), consistent with a purely missense mechanism and not separately actionable for PP3/BP4 since this is not a splice-region variant.

Rule

REVEL >=0.932 -> PP3_Strong (ClinGen SVI recalibration, PMID:36413997)

Evidence considered

• REVEL score = 0.977 for NM_001122740.1:c.1163T>A (NP_001116212.1:p.(Met388Lys)), exceeding the >=0.932 strong-pathogenic threshold from the ClinGen SVI REVEL recalibration (PMID:36413997, Pejaver et al. 2022, Am J Hum Genet), supporting PP3_Strong.
• No CSPEC/VCEP-specific PP3/BP4 lookup table was found for ESR1 (cspec.found=false), so generic ACMG missense in-silico calibration was applied.
• BayesDel score (0.524984) was retrieved but withheld from PP3 scoring because no citable published threshold/table for BayesDel is verified for this pipeline.

Sources

Reasoning

PP5 is not met. The exact variant NM_001122740.1:c.1163T>A is reported as absent from ClinVar, with no expert-panel Pathogenic or Likely pathogenic assertion. No ordinary laboratory submission, aggregate label, or non-expert assertion was used to trigger PP5.

Rule

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

Evidence considered

• The ClinVar search in the consolidated bundle returned no exact result for NM_001122740.1:c.1163T>A; variation IDs, classification, review status, and submissions were empty.
• Under the requested rule, PP5 is restricted to an exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classification, which is not present.

Sources

Reasoning

No applicable ESR1 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP framework applies. The variant NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys) is absent from gnomAD v2.1 and gnomAD v4.1, with no population allele frequency reported that could meet the BA1 stand-alone benign threshold. BA1 is therefore not met. The absence searches do not establish a numeric maximum population frequency or ancestry-specific frequency, but they provide no positive BA1 evidence.

Rule

generic ACMG/AMP BA1: allele frequency at or above the stand-alone benign threshold

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent, but its reported allele number is 0 and therefore it does not provide a usable population denominator.
• No observed allele frequency or ancestry-specific frequency exceeds the BA1 threshold; no threshold artifact can be evaluated because numeric population counts are unavailable.

Still missing

• No numeric allele count, allele number, or ancestry-specific frequency was available from the population sources.

Sources

Reasoning

No applicable ESR1 VCEP or gene-specific framework was retrieved, so the generic ACMG/AMP framework applies. The variant is absent from gnomAD v2.1 and gnomAD v4.1, and no numeric population frequency is available showing that it is greater than expected for a disorder-causing variant. BS1 is not met. Disease prevalence, penetrance, and an ESR1-specific maximum credible allele-frequency threshold were not provided, so no stronger population-threshold conclusion can be made.

Rule

generic ACMG/AMP BS1: allele frequency greater than expected for the disorder

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• gnomAD-Canada v1.0 reports the variant as absent, but its reported allele number is 0 and therefore it does not provide a usable population denominator.
• There is no observed population frequency above a disease-specific or generic BS1 threshold in the supplied evidence.

Still missing

• No disease-specific prevalence, penetrance, inheritance model, or maximum credible allele-frequency threshold was available.
• No numeric allele count, allele number, or ancestry-specific frequency was available.

Sources

Reasoning

The calibrated missense predictor (REVEL = 0.977) indicates a pathogenic-direction prediction well above the benign threshold, so BP4 cannot be applied. SpliceAI predicts no splice impact (max delta = 0.002), but this variant is a missense substitution located mid-exon (not within a splice consensus region), so the negligible SpliceAI score is not evidence of BP4-relevant splice-benign effect and would double-count the same negative computational signal already captured (or not applicable) rather than provide independent benign missense evidence. No qualifying benign in-silico signal is available for BP4.

Rule

REVEL >=0.932 precludes BP4 application (pathogenic-direction prediction); no qualifying benign computational evidence identified

Evidence considered

• REVEL score 0.977 is far above any benign-direction cutoff, precluding BP4 application for the missense in-silico path.
• SpliceAI max delta score = 0.002 (near zero) confirms no predicted splice disruption, but the variant is not splice-proximal so this does not independently support BP4 for a missense substitution.

Sources

Reasoning

BP6 is not met. The exact variant NM_001122740.1:c.1163T>A is reported as absent from ClinVar, with no expert-panel Benign or Likely benign assertion. No ordinary laboratory submission, aggregate label, or non-expert assertion was used to trigger BP6.

Rule

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

Evidence considered

• The ClinVar search in the consolidated bundle returned no exact result for NM_001122740.1:c.1163T>A; variation IDs, classification, review status, and submissions were empty.
• Under the requested rule, BP6 is restricted to an exact-variant ClinVar expert-panel Benign/Likely benign classification, which is not present.

Sources

Reasoning

PS1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No proband-level de novo evidence or parental testing results are provided for NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys). The case bundle contains no documented parental genotypes, maternity/paternity confirmation, or phenotype assessment that would permit PS2 evaluation.

Rule

Generic ACMG/AMP PS2: de novo occurrence in an affected individual with confirmed parentage and appropriate phenotype assessment; do not apply without documented parental testing and case-level evidence.

Evidence considered

• The consolidated case-evidence bundle identifies the variant as NM_001122740.1:c.1163T>A in ESR1, predicted p.(Met388Lys), but contains no family, parental-testing, or de novo observations.
• Generic ACMG/AMP PS2 requires reliable evidence that the variant arose de novo in an affected individual, with appropriate confirmation of parentage and consideration of phenotype specificity; those data are unavailable here.

Still missing

• Documented proband phenotype and indication
• Genotypes of both biological parents at the variant locus
• Confirmation of maternity and paternity or equivalent pedigree validation
• Assessment of whether the variant is absent from both tested parents and whether parental testing was technically adequate

Reasoning

No ClinGen VCEP/CSPEC is available for ESR1 in this case (cspec.found=false), so no gene-specific PS3 functional assay framework applies and generic ACMG PS3 (well-established functional studies showing damaging effect) is used as fallback. No functional assay data for NM_001122740.1:c.1163T>A (p.Met388Lys) was identified: literature_pass.json returned zero PMIDs, OncoKB explicitly states it did not identify variant-specific reviewed functional evidence (Unknown Oncogenic Effect, is_variant_specific=false), and no other functional/biochemical assay source (transactivation, reporter, binding, hormone-response assay) was located in the evidence bundle. Without an identified assay, its validation status, controls, or reported effect size/replicate count, PS3 cannot be applied.

Evidence considered

• literature_pass.json reports total_pmids=0 and note 'No PMIDs found across evidence sources', so no candidate functional-study publications were retrieved for screening.
• OncoKB evidence_sentence: 'OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up.' with classification 'Unknown Oncogenic Effect' and is_variant_specific=false, confirming absence of curated variant-level functional data.
• case_summary.json cspec.found=false and vcep_materials.json note='no cspec url available', confirming no ESR1 VCEP-specific PS3 assay framework is available for this case.

Still missing

• No published functional assay (e.g., transactivation, ligand-binding, transcriptional reporter) for ESR1 p.Met388Lys was located in literature or curated databases.
• No ClinGen ESR1 VCEP specification with a validated PS3 functional assay framework was available for this case.

Sources

Reasoning

No variant-specific affected-case series, case-control enrichment analysis, or statistically interpretable comparison with controls was available for NM_001122740.1:c.1163T>A (NP_001116212.1:p.(Met388Lys)). PS4 cannot be assessed from gene-level or unrelated cancer context.

Rule

Generic ACMG/AMP PS4 requires a statistically significant increased prevalence of the variant in affected individuals compared with appropriate controls; no applicable ESR1-specific specification was retrieved.

Evidence considered

• The consolidated case-evidence bundle reports no PMIDs across evidence sources and no variant-specific case-control evidence.
• The bundle reports only gene-level ESR1 cancer context from OncoKB, not variant-specific phenotype or prevalence evidence.

Still missing

• Variant-specific affected-case counts and an appropriate control comparison are unavailable.
• No publication or curated case series was identified for this exact variant.

Reasoning

PM1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No affected-proband observations, phase information, or pathogenic/likely pathogenic comparator variants in trans or cis are documented in the consolidated case-evidence bundle. PM3 therefore cannot be assessed for this variant.

Rule

Generic ACMG/AMP PM3: pathogenic or likely pathogenic variant identified in trans with the variant being evaluated in a recessive disorder; phase and affected-proband relevance must be established.

Evidence considered

• The case-evidence bundle contains no case-level affected-proband observations or family segregation/phase data relevant to PM3.
• The bundle reports no literature PMIDs and no variant-specific ClinVar record; these sources do not provide usable PM3 evidence.

Still missing

• Affected-proband case data are not available.
• Parental or family testing establishing phase is not available.
• No pathogenic or likely pathogenic variant documented in trans is available for evaluation.

Reasoning

PM5 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No unconfirmed de novo observations are reported for NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys). The available bundle does not identify an affected proband with an apparently de novo variant, nor does it provide pedigree, parental, or phenotype details sufficient for PM6.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in an affected individual when parentage is unconfirmed or parental testing is incomplete; apply only when the case-level observation and phenotype are documented.

Evidence considered

• The consolidated case-evidence bundle contains no case report, family history, parental genotype, or apparently de novo observation for this exact variant.
• Generic ACMG/AMP PM6 is intended for assumed de novo occurrence without confirmed parentage; no such case-level observation is available to assess.

Still missing

• A documented affected proband carrying the exact variant
• Evidence that the variant is apparently de novo despite incomplete or unavailable parentage confirmation
• Phenotype consistency and specificity for the relevant ESR1-associated disorder
• Details of any family structure, parental testing, and technical limitations

Reasoning

No segregation data are available for NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys). The bundle provides no affected or unaffected relatives, meioses, pedigree structure, co-segregation analysis, or phenotype classification, so PP1 and any possible strength upgrade cannot be evaluated.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members; consider stronger application only with sufficient informative meioses and validated phenotype/genotype data.

Evidence considered

• The consolidated case-evidence bundle contains no familial segregation observations for the exact ESR1 variant.
• Generic ACMG/AMP PP1 requires co-segregation with disease in multiple affected family members; neither informative meioses nor affected-relative genotypes are documented.

Still missing

• Pedigree identifying affected and unaffected relatives
• Genotype results for informative relatives
• Number of informative meioses and segregation pattern
• Phenotype definitions, age-dependent penetrance considerations, and clinical consistency in each tested relative
• Any statistical or gene-specific segregation threshold supporting a strength beyond supporting

Reasoning

PP2 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No patient phenotype, clinical presentation, or disease-specific phenotype profile was provided for this case. The available gene-level ESR1 information is insufficient to establish a highly specific phenotype for the variant.

Rule

Generic ACMG/AMP PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single-gene etiology; phenotype data are absent.

Evidence considered

• The consolidated case-evidence bundle contains no clinical phenotype description for the patient.
• The bundle contains no applicable ESR1 VCEP/CSPEC specification and no relevant variant-specific publication.

Still missing

• Patient phenotype and diagnostic context are unavailable.
• No disease-specific phenotype match or phenotype specificity analysis is available.

Reasoning

BS2 requires observation of the variant in healthy adults, including appropriate homozygous or hemizygous individuals when relevant. The supplied evidence contains only population-database absence results and no unaffected-carrier, homozygote, or hemizygote observations. BS2 cannot be assessed from the available evidence.

Rule

generic ACMG/AMP BS2: observed in healthy adults, including appropriate homozygotes or hemizygotes

Evidence considered

• The population sources report absence of the variant, not the presence of the variant in unaffected adults.
• No healthy-individual genotype or phenotype observations are available for evaluating BS2.

Still missing

• No documented unaffected adult carriers were provided.
• No homozygote or hemizygote observations were provided.
• No phenotype, age, penetrance, or ascertainment information for healthy individuals was provided.

Sources

Reasoning

No ClinGen VCEP/CSPEC is available for ESR1 in this case (cspec.found=false), so generic ACMG BS3 (well-established functional studies showing no damaging effect) is used as fallback. No functional assay data of any kind was identified for NM_001122740.1:c.1163T>A (p.Met388Lys) in literature or curated databases (literature_pass.json total_pmids=0; OncoKB explicitly not variant-specific). Absence of a damaging functional result does not itself constitute evidence of a benign/normal functional result, so BS3 cannot be applied.

Evidence considered

• literature_pass.json reports total_pmids=0 and note 'No PMIDs found across evidence sources', so no candidate functional-study publications were retrieved for screening.
• OncoKB evidence_sentence: 'OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up.' with classification 'Unknown Oncogenic Effect' and is_variant_specific=false, confirming absence of curated variant-level functional data (neither damaging nor benign).
• case_summary.json cspec.found=false and vcep_materials.json note='no cspec url available', confirming no ESR1 VCEP-specific BS3 assay framework is available for this case.

Still missing

• No published functional assay demonstrating normal/wild-type activity for ESR1 p.Met388Lys was located.
• No ClinGen ESR1 VCEP specification with a validated BS3 functional assay framework was available for this case.

Sources

Reasoning

No non-segregation evidence is available for NM_001122740.1:c.1163T>A (ESR1; p.Met388Lys). The bundle does not report unaffected relatives who carry the variant, affected relatives who lack it, pedigree structure, or phenotype and age information needed to interpret discordance.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members or presence in unaffected members, interpreted using an appropriate phenotype, age, penetrance, and pedigree context.

Evidence considered

• The consolidated case-evidence bundle contains no relatives, pedigree, or family genotype/phenotype data for this variant.
• Generic ACMG/AMP BS4 requires lack of segregation in affected family members or presence in unaffected family members when the phenotype is expected to be present; no such observations are documented.

Still missing

• Genotypes of relevant affected and unaffected relatives
• Pedigree structure and number of informative relatives
• Clinical phenotypes, ages, and penetrance information for carriers and non-carriers
• Assessment of possible phenocopies, reduced penetrance, or variable expressivity

Reasoning

BP1 could not be assessed because its agent did not produce valid output.

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

No case-level observation of the variant in trans or cis with a pathogenic or likely pathogenic variant, and no inheritance or phase information, is documented in the consolidated case-evidence bundle. BP2 therefore cannot be assessed.

Rule

Generic ACMG/AMP BP2: observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder; the applicable inheritance model and phase must be established.

Evidence considered

• The case-evidence bundle contains no case-level affected-proband observations, phase data, or documented pathogenic/likely pathogenic allele suitable for BP2 evaluation.
• The bundle reports no literature PMIDs and no variant-specific ClinVar record; these sources do not provide usable BP2 evidence.

Still missing

• Case-level allelic observations are not available.
• Parental or family testing establishing cis/trans phase is not available.
• No pathogenic or likely pathogenic allele for a cis/trans comparison is documented.

Reasoning

No affected individual, phenotype, or independent pathogenic molecular explanation for the relevant disease was provided. Therefore BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5 requires an alternate molecular basis for the patient's phenotype, with sufficient clinical context to show that the assessed variant is not causative; those data are absent.

Evidence considered

• The consolidated case-evidence bundle provides no patient-level phenotype or alternate molecular diagnosis.
• Gene-level ESR1 cancer context and absence from population databases do not establish BP5.

Still missing

• An affected individual's clinical context is unavailable.
• No confirmed alternate molecular etiology explaining the phenotype is available.