TSC2 c.3834G>A, p.(Leu1278=)

Reasoning

No applicable TSC2-specific VCEP specification was available, so the generic PM2 rule applies. The variant is rare in population databases: gnomAD v2.1 all-comers exomes show AF 7.9915e-06 (2/250266 alleles; 0 homozygotes), gnomAD v4.1 shows AF 6.20159e-07 (1/1612490 alleles; 0 homozygotes), and the gnomAD v2.1 non-cancer exome subset shows AF 4.2259e-06 (1/236636 alleles; 0 homozygotes). The highest ancestry-specific AF is 1.77016e-05, still below the generic PM2 supporting threshold of 0.0001. The variant is therefore sufficiently rare for PM2 at supporting strength.

Rule

generic_pm2_af_lte_0.0001

Evidence considered

• gnomAD v2.1 all-comers exomes: AF 7.9915e-06, 2/250266 alleles, and 0 homozygotes; maximum ancestry-specific AF 1.77016e-05.
• gnomAD v2.1 non-cancer exomes: AF 4.2259e-06, 1/236636 alleles, and 0 homozygotes.
• gnomAD v4.1: AF 6.20159e-07, 1/1612490 alleles, and 0 homozygotes.
• Generic PM2 supporting threshold: allele frequency <= 0.0001, based on ClinGen SVI recommendations (Richards et al. 2015, PMID:25741868).

Sources

Reasoning

BP7 applies to a synonymous variant with no predicted impact on splicing. NM_000548.5:c.3834G>A is synonymous (NP_000539.2:p.(Leu1278=)); SpliceAI reports DS_AG 0.067, DS_AL 0.112, DS_DG 0.002, and DS_DL 0.073, with max delta 0.112. This is below the published SpliceAI recommended cutoff of 0.2 for significant splice impact (Jaganathan et al. 2019, PMID:30661751), supporting no significant predicted splice effect and BP7 at supporting strength.

Rule

requires_synonymous_and_no_significant_predicted_splice_impact

Evidence considered

• The variant is synonymous: NM_000548.5:c.3834G>A, NP_000539.2:p.(Leu1278=).
• SpliceAI scores are DS_AG 0.067, DS_AL 0.112, DS_DG 0.002, and DS_DL 0.073; maximum delta score is 0.112.
• SpliceAI recommended cutoff for significant splice impact is 0.2, from Jaganathan et al. 2019 (PMID:30661751); max delta 0.112 is below this cutoff and supports BP7's no-predicted-splicing-impact requirement.

Sources

Reasoning

PP5 was restricted to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. The exact ClinVar record is NM_000548.5:c.3834G>A (p.Leu1278=), but the submission audit reports zero expert-panel submissions; the available submissions are one Uncertain significance and one Likely benign, both single-submitter clinical-laboratory assertions. Consequently the required expert-panel Pathogenic/Likely pathogenic assertion is absent and PP5 is not met.

Rule

Case-specific PP5 rule: met only when an exact-variant ClinVar expert panel classifies the variant as Pathogenic or Likely pathogenic; no such assertion exists.

Evidence considered

• ClinVar exact-match audit reports zero expert-panel submissions and only single-submitter laboratory classifications: Uncertain significance and Likely benign.
• Ordinary laboratory submissions and aggregate ClinVar labels were not used to trigger PP5.

Sources

Reasoning

No applicable TSC2-specific VCEP specification was available, so the generic ACMG/AMP population rule applies. The variant is below the generic BA1 stand-alone threshold of 0.05: gnomAD v2.1 all-comers exomes report AF 7.9915e-06 (2/250266 alleles; 0 homozygotes), and gnomAD v4.1 reports AF 6.20159e-07 (1/1612490 alleles; 0 homozygotes). The highest reported ancestry-specific AF is 1.77016e-05 in gnomAD v2.1 European non-Finnish individuals, also far below 0.05. Therefore BA1 is not met.

Rule

generic_ba1_af_gte_0.05

Evidence considered

• gnomAD v2.1 all-comers exomes: AF 7.9915e-06, 2/250266 alleles, and 0 homozygotes; maximum reported ancestry-specific AF 1.77016e-05 in European (non-Finnish) individuals.
• gnomAD v4.1: AF 6.20159e-07, 1/1612490 alleles, and 0 homozygotes.
• Generic BA1 stand-alone threshold: allele frequency >= 0.05, from Richards et al. 2015 ACMG/AMP recommendations (PMID:25741868).

Sources

Reasoning

No applicable TSC2-specific VCEP specification was available, so the generic population-frequency rule applies. The variant's all-comers allele frequencies are 7.9915e-06 in gnomAD v2.1 exomes and 6.20159e-07 in gnomAD v4.1, with the highest ancestry-specific value 1.77016e-05 in gnomAD v2.1 European non-Finnish individuals. These values are below the generic BS1 threshold of 0.01, and the gnomAD v2.1 non-cancer exome frequency is lower still at 4.2259e-06 (1/236636 alleles). Thus there is no population-frequency evidence for BS1.

Rule

generic_bs1_af_gte_0.01

Evidence considered

• gnomAD v2.1 all-comers exomes: AF 7.9915e-06; highest ancestry-specific AF 1.77016e-05 in European (non-Finnish) individuals.
• gnomAD v4.1: AF 6.20159e-07.
• gnomAD v2.1 non-cancer exomes: AF 4.2259e-06, 1/236636 alleles, and 0 homozygotes; this is also below the BS1 threshold.
• Generic BS1 threshold: allele frequency >= 0.01, from the generic SVI default described by Whiffin et al. 2017 (PMID:28518168).

Sources

Reasoning

The available population data show no homozygotes in gnomAD v2.1 all-comers exomes, gnomAD v2.1 non-cancer exomes, or gnomAD v4.1, and only rare heterozygous observations. This does not establish the BS2 requirement of observation in healthy individuals in a configuration that contradicts the known disease model; an unphenotyped gnomAD heterozygote alone is insufficient. Therefore BS2 is not met.

Rule

generic_bs2_requires_appropriate_healthy_individual_observation

Evidence considered

• gnomAD v2.1 all-comers exomes: 2/250266 alleles and 0 homozygotes.
• gnomAD v2.1 non-cancer exomes: 1/236636 alleles and 0 homozygotes.
• gnomAD v4.1: 1/1612490 alleles and 0 homozygotes; population records are not phenotype-confirmed healthy-individual observations sufficient by themselves for BS2.

Sources

Reasoning

BP6 was restricted to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. The exact ClinVar record has one Likely benign single-submitter clinical-laboratory assertion, but the submission audit reports zero expert-panel submissions. Because ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger BP6 under the specified rule, BP6 is not met.

Rule

Case-specific BP6 rule: met only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; no such assertion exists.

Evidence considered

• ClinVar exact-match audit reports one Likely benign single-submitter laboratory assertion and zero expert-panel submissions.
• The single-submitter Likely benign classification was explicitly excluded from BP6 because it is not an expert-panel assertion.

Sources

Reasoning

No case-level information documents the proband's parental testing, confirmed maternity and paternity, parental genotypes, or absence of the variant in either parent. The available variant and literature records do not establish a de novo event, so PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with confirmed maternity and paternity; strength depends on phenotype and parental testing quality.

Evidence considered

• The case records identify NM_000548.5:c.3834G>A in TSC2 but provide no proband-parent genotype comparison or documented de novo status.
• The reviewed literature extracts contain no variant-specific parental testing, de novo, or proband case evidence for c.3834G>A or p.(Leu1278=).

Still missing

• Parental testing results for NM_000548.5:c.3834G>A are not available.
• Confirmed maternity and paternity are not documented.
• Proband phenotype information linked to this variant is not available.

Reasoning

No applicable TSC2 ClinGen/VCEP specification was available, so generic ACMG/AMP functional-evidence guidance was used. The evaluated case materials contain no variant-specific, validated functional assay for NM_000548.5:c.3834G>A (NP_000539.2:p.(Leu1278=)); the available literature records are clinical/reporting or general gene-context sources and do not report assay results for this variant. Therefore, there is insufficient evidence to apply PS3 at any strength. A variant-specific assay demonstrating a disease-relevant functional abnormality with appropriate positive and negative controls would be required.

Rule

Generic ACMG/AMP 2015 PS3: functional studies supportive of a damaging effect require a well-established, disease-relevant assay with appropriate controls; no applicable TSC2-specific rule was available.

Evidence considered

• The case materials identify TSC2 c.3834G>A as synonymous, p.(Leu1278=), but provide no variant-specific functional assay result.
• The extracted literature sources available for this case do not report experimental functional data for this exact variant.

Still missing

• Variant-specific functional assay results are unavailable.
• Assay controls, biological relevance, and quantitative effect size cannot be evaluated.

Reasoning

No applicable TSC2-specific VCEP/CSPEC framework was available, so the generic ACMG/AMP definition was used. PS4 requires a significantly increased prevalence of the variant in affected individuals compared with controls. The available evidence contains no variant-specific case series, case-control counts, odds ratio, likelihood ratio, or other enrichment statistic; ClinVar contains only single-submitter laboratory assertions and the retrieved papers do not report this exact variant. Therefore PS4 cannot be assessed.

Rule

Generic ACMG/AMP PS4: significantly increased prevalence of the variant in affected individuals compared with controls; no numeric threshold is specified in the applicable framework.

Evidence considered

• ClinVar exactly matches NM_000548.5:c.3834G>A (p.Leu1278=), but reports only one uncertain-significance and one likely-benign clinical-laboratory submission, with no expert-panel submission or case-control enrichment data.
• The extracted findings for the retrieved publications provide no exact-variant case or control data relevant to PS4.

Still missing

• Variant-specific affected-case and control counts or a validated enrichment statistic are unavailable.

Sources

Reasoning

No case-level information documents a presumed de novo occurrence without confirmed parental testing. Neither a proband phenotype consistent with a TSC2-related disorder nor parental genotype results are available to support PM6.

Rule

Generic ACMG/AMP PM6: presumed de novo occurrence in a patient with the disease and no family history when maternity and paternity are not confirmed; phenotype consistency remains necessary.

Evidence considered

• The available case evidence does not report a proband with a phenotype consistent with TSC2-related disease together with an unconfirmed but presumed de novo variant.
• The reviewed literature extracts provide no variant-specific de novo or parental-origin evidence for NM_000548.5:c.3834G>A.

Still missing

• Evidence for presumed de novo occurrence is absent.
• Parental testing results are absent.
• A clinically consistent proband phenotype is not documented.

Reasoning

No affected relatives, family structure, genotype results, or informative meioses are documented. Consequently, there is no segregation dataset from which to evaluate whether the variant tracks with disease in this family.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members; strength should reflect the number and informativeness of meioses and phenotype specificity.

Evidence considered

• The case records contain no family pedigree or variant-positive and variant-negative relative data for NM_000548.5:c.3834G>A.
• The reviewed literature extracts contain no variant-specific familial segregation or meiosis information.

Still missing

• Family pedigree and affected-relative information are not available.
• Genotypes of informative relatives are not available.
• The number of informative meioses and phenotype status of relatives are not available.

Reasoning

No applicable TSC2-specific VCEP/CSPEC framework was available, so the generic ACMG/AMP definition was used. PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single-gene etiology. The supplied evidence identifies the variant as synonymous but provides no patient phenotype, family history, or phenotype-specific diagnostic information. Gene-level descriptions of tuberous sclerosis complex in general do not establish this patient's phenotype. Therefore PP4 cannot be assessed.

Rule

Generic ACMG/AMP PP4: patient's phenotype or family history is highly specific for a disease with a single-gene etiology; no patient-level phenotype is available.

Evidence considered

• The case evidence provides no patient-level phenotype or family-history description.
• PMID:27854360 describes TSC1/TSC2-associated tuberous sclerosis complex at the gene-list level, but does not mention this exact variant or a patient phenotype.

Still missing

• Patient phenotype and family-history details are unavailable.

Sources

Reasoning

No applicable TSC2 ClinGen/VCEP specification was available, so generic ACMG/AMP functional-evidence guidance was used. The evaluated case materials contain no variant-specific, validated functional assay showing a normal result for NM_000548.5:c.3834G>A (NP_000539.2:p.(Leu1278=)); absence of assay data cannot establish preserved protein or cellular function. Therefore, there is insufficient evidence to apply BS3 at any strength. A disease-relevant assay with appropriate controls and a demonstrably normal result for the variant would be required.

Rule

Generic ACMG/AMP 2015 BS3: a well-established, disease-relevant functional study showing no damaging effect can support benign evidence when appropriately controlled; no applicable TSC2-specific rule was available.

Evidence considered

• The case materials identify TSC2 c.3834G>A as synonymous, p.(Leu1278=), but provide no variant-specific functional assay result.
• The extracted literature sources available for this case do not report experimental functional data for this exact variant.

Still missing

• Variant-specific functional assay results are unavailable.
• Assay controls, biological relevance, and quantitative normal-function results cannot be evaluated.

Reasoning

No clinically unaffected relatives are documented as having undergone targeted testing for NM_000548.5:c.3834G>A, and no family segregation dataset is available. Therefore, absence of co-segregation cannot be evaluated and BS4 cannot be applied.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members or presence of the variant in unaffected members when the phenotype is sufficiently penetrant and the relatives are informative.

Evidence considered

• The case records provide no genotype results from clinically unaffected relatives and no evidence that the variant fails to segregate with disease.
• The reviewed literature extracts contain no variant-specific non-segregation or unaffected-relative testing evidence.

Still missing

• Test results for clinically unaffected relatives are not available.
• Relative phenotypes and ages are not documented sufficiently to assess unaffected status.
• No informative non-segregation observations are available.

Reasoning

No applicable TSC2-specific VCEP specification was identified, so generic ACMG/AMP logic applies. BP2 would require observation of NM_000548.5:c.3834G>A (p.(Leu1278=)) in trans with a pathogenic variant in this dominant disorder, or in cis with a pathogenic variant in a recessive disorder. The available case evidence contains no second pathogenic or likely pathogenic variant, parental genotypes, genotype-level phase result, or documented cis/trans relationship for the target variant. The lack of an allelic observation prevents assessment; it does not establish that BP2 is unmet.

Rule

BP2 requires the target variant to be observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder.

Evidence considered

• The ClinVar record identifies NM_000548.5:c.3834G>A (p.Leu1278=) but provides no second pathogenic variant or cis/trans phase information.
• The available case materials do not document parental testing, a second pathogenic or likely pathogenic allele, or molecular phase for the target variant.
• No applicable TSC2-specific VCEP specification was identified; generic ACMG/AMP BP2 logic was therefore used.

Still missing

• A second pathogenic or likely pathogenic variant and its cis/trans relationship to NM_000548.5:c.3834G>A are not documented.
• Parental or family genotypes sufficient to establish phase are not available.

Sources

Reasoning

No applicable TSC2-specific VCEP/CSPEC framework was available, so the generic ACMG/AMP definition was used. BP5 requires an alternate molecular basis for the patient's phenotype. The evidence provides no patient phenotype, no alternate pathogenic molecular diagnosis, and no variant-specific clinical report establishing that another cause explains the presentation. The presence of a synonymous variant alone is not evidence of an alternate molecular basis. Therefore BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5: alternate molecular basis for the patient's phenotype; no phenotype or alternate molecular diagnosis is available.

Evidence considered

• ClinVar contains only single-submitter assertions and does not document an alternate molecular diagnosis for a patient with a defined phenotype.
• No case report or family-level clinical evidence establishing another cause was identified.

Still missing

• Patient phenotype and an independently established alternate molecular diagnosis are unavailable.

Sources