Variant classification summary

NM_000548.5:c.729C>G

TSC2 · NP_000539.2:p.(Leu243=) · NM_000548.5

GRCh37: chr16:2106725 C>G · GRCh38: chr16:2056724 C>G

Gene: TSC2 Transcript: NM_000548.5

Final call

Benign

BS1 strong benign BS2 strong benign BP4 supporting benign BP6 supporting benign BP7 supporting benign

Variant details

Gene

TSC2

Transcript

NM_000548.5

Protein

NP_000539.2:p.(Leu243=)

gnomAD AF

0.0031626059525714546 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000548.5:c.729C>G (p.Leu243=) is a synonymous variant in exon 8 of TSC2 with an overall allele frequency of 0.316-0.355% in gnomAD, exceeding the BS1 threshold of >0.3%.

2

This variant has been observed in 10 homozygous individuals in gnomAD v4.1 among 1,612,278 alleles, constituting strong evidence for benignity in a dominant disorder (BS2).

3

SpliceAI predicts no splice impact (max delta = 0.01), and the variant is synonymous with no predicted effect on protein sequence, supporting multiple benign computational evidence lines (BP4, BP7).

4

ClinVar classifies this variant as Benign/Likely benign across 21 clinical laboratory submissions (15 Benign, 6 Likely benign), with criteria provided and no conflicting pathogenic interpretations (BP6).

5

No pathogenic criteria are met. PVS1, PS1, and PM5 are not applicable to this synonymous variant. PS2, PS3, PS4, PS5, PM1, PM2, PM6, PP3, and PP5 are not met. PP1, PP4, BS4, BP2, and BP5 are not assessed due to absence of data. BA1 is not met (overall AF <1%). BP1 and PP2 are not applicable to synonymous variants.

6

Applying generic ACMG/AMP 2015 final combination rules: two strong benign criteria (BS1, BS2) alone satisfy the classification threshold for Benign. Additionally, three supporting benign criteria (BP4, BP6, BP7) reinforce the benign classification.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Benign classification because either BA1 is met or at least two strong benign criteria are present.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_000548.5:c.729C>G is a synonymous variant (NP_000539.2:p.(Leu243=)) and does not fall into any PVS1 null-variant category (nonsense, frameshift, or canonical ±1,2 splice consensus). Per ClinGen SVI PVS1 framework (PMC6185798), the generic PVS1 decision algorithm is not applied to synonymous variants.	pvs1_generic_framework pvs1_variant_assessment
PS1	N/A	PS1 applies when the same amino acid change has been established as pathogenic via a different nucleotide change. NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=) that does not alter the amino acid sequence, so there is no amino acid change to compare against known pathogenic variants.
PS2	Not met	No de novo occurrence with confirmed maternity and paternity has been reported for NM_000548.5:c.729C>G. PMID:15798777 (Sancak et al. 2005) reported TSC1/TSC2 mutations in 490 TSC patients and noted de novo TSC2 mutations, but the specific variant c.729C>G was not identified in the abstract and full-text confirmation is unavailable.
PS3	Not met	No well-established in vitro or in vivo functional studies have been identified that demonstrate a damaging effect of NM_000548.5:c.729C>G on TSC2 function or splicing. PMID:24033266 and PMID:25741868 are methodological and guideline papers, not functional studies of this variant.
PS4	Not met	No case-control studies demonstrating statistically significant enrichment of NM_000548.5:c.729C>G in affected individuals compared to controls have been identified. PMID:15798777 studied TSC patients but the abstract does not mention this variant. The variant is present at appreciable frequency (0.3-0.4%) in population databases, making it unlikely to be enriched in disease cohorts.	gnomad_v2 gnomad_v4
PS5	Not met	PS5 applies when a reputable source reports the variant as pathogenic but independent evidence is unavailable. ClinVar classifies this variant as Benign (15 clinical laboratories) and Likely benign (6 clinical laboratories). No reputable source has asserted pathogenicity.	clinvar
PM1	Not met	NM_000548.5:c.729C>G is not located in a recognized mutational hotspot or well-established critical functional domain of TSC2 without benign variation. The residue Leu243 is not in a statistically significant hotspot (cancerhotspots.org).
PM2	Not met	NM_000548.5:c.729C>G is present in gnomAD at allele frequencies well above the 0.1% PM2 threshold. gnomAD v2.1: 0.355% (1000/281464 alleles), gnomAD v4.1: 0.316% (5099/1,612,278 alleles). This variant is too common in population databases to qualify as absent/rare under PM2.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a different missense change at the same residue that has been established as pathogenic. NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=) with no amino acid change; there is no altered residue to compare against known pathogenic missense variants at position 243.	pm5_candidates
PM6	Not met	No de novo occurrence of NM_000548.5:c.729C>G has been reported without confirmation of paternity/maternity. PMID:15798777 analyzed TSC1/TSC2 mutations including de novo cases, but the specific variant c.729C>G was not identified in the abstract and full-text is unavailable for confirmation.
PP1	Not assessed	No cosegregation data are available for NM_000548.5:c.729C>G. No family studies with this variant have been identified in the reviewed literature.
PP2	N/A	PP2 is specific to missense variants in genes where missense variants are a common disease mechanism and benign missense variation is low. NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=), not a missense change.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. SpliceAI predicts no significant splice impact (max delta score = 0.01). REVEL and BayesDel scores are unavailable for this variant. The synonymous nature of the variant (p.Leu243=) is itself computationally predicted to be silent.	spliceai
PP4	Not assessed	No specific patient phenotype data are available for independent review. The variant is classified as Benign/Likely benign by multiple clinical laboratories in ClinVar, suggesting it is observed in individuals without TSC-specific phenotypes, but individual-level phenotype data are not accessible.	clinvar
PP5	Not met	PP5 requires a reputable source to report the variant as pathogenic. ClinVar classifies NM_000548.5:c.729C>G as Benign (15 clinical laboratories) and Likely benign (6 clinical laboratories). No reputable source has asserted pathogenicity for this variant.	clinvar
BA1	Not met	The overall allele frequency of NM_000548.5:c.729C>G in gnomAD is below the BA1 threshold of >1%. gnomAD v2.1 overall AF=0.355%, v4.1 overall AF=0.316%. While the Finnish subpopulation frequency exceeds 1% (v2.1: 1.20%, v4.1: 1.21%), BA1 is assessed on overall population frequency per standard ACMG/AMP interpretation.	gnomad_v2 gnomad_v4
BS1	Met	The allele frequency of NM_000548.5:c.729C>G exceeds the BS1 threshold of >0.3% in the general population. gnomAD v2.1: 0.355% (1000/281,464 alleles, 0 homozygotes), gnomAD v4.1: 0.316% (5,099/1,612,278 alleles, 10 homozygotes). This frequency is substantially greater than expected for TSC2-associated tuberous sclerosis complex (incidence ~1:6,000-10,000).	gnomad_v2 gnomad_v4
BS2	Met	NM_000548.5:c.729C>G has been observed in 10 homozygous individuals in gnomAD v4.1 (total AF=0.316%, 5,099 heterozygous alleles). Tuberous sclerosis complex is a dominant disorder with high penetrance. Observation of homozygotes and thousands of heterozygotes in a population database of generally healthy individuals constitutes strong evidence for a benign role.	gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrating no deleterious effect of NM_000548.5:c.729C>G have been identified. PMID:24033266 and PMID:25741868 are methodological/guideline papers and do not contain functional data for this variant.
BS4	Not assessed	No cosegregation data in affected families are available for NM_000548.5:c.729C>G. Lack of segregation with disease cannot be assessed without family studies.
BP1	N/A	BP1 applies to missense variants in genes where truncating variants are the primary mechanism of disease. NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=), not a missense change. Additionally, TSC2 disease is caused by both missense and truncating variants.
BP2	Not assessed	No data are available regarding observation of NM_000548.5:c.729C>G in trans with a known pathogenic TSC2 variant. While the presence of 10 homozygotes in gnomAD v4.1 effectively demonstrates observation in trans (biallelic), formal assessment would require individual-level genotype data.	gnomad_v4
BP4	Met	Multiple lines of computational evidence suggest no impact on gene product. SpliceAI predicts no significant splice alteration (max delta score = 0.01). NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=) at a nucleotide position where in silico splicing predictions support a null effect.	spliceai
BP5	Not assessed	No case has been identified where NM_000548.5:c.729C>G was found in an individual with an alternate molecular basis for disease. This information is typically available only from detailed clinical reports.
BP6	Met	Multiple reputable clinical laboratories consistently classify NM_000548.5:c.729C>G as Benign or Likely benign in ClinVar (Variation ID 49382). Fifteen clinical laboratories classify as Benign and six as Likely benign, with criteria provided. No submitting laboratory has asserted pathogenicity.	clinvar
BP7	Met	NM_000548.5:c.729C>G is a synonymous variant (p.Leu243=) for which splicing prediction algorithms predict no impact on splicing. SpliceAI max delta score is 0.01, well below the 0.10 threshold for predicted splice alteration. The nucleotide is not evolutionarily constrained to a degree suggesting functional importance.	spliceai

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