NM_000548.5:c.97G>C

TSC2 · NP_000539.2:p.(Gly33Arg) · NM_000548.5

GRCh37: chr16:2098713 G>C · GRCh38: chr16:2048712 G>C

Gene: TSC2 Transcript: NM_000548.5

Final call

VUS

PM2 supporting BP4 supporting benign

Variant details

Gene

TSC2

Transcript

NM_000548.5

Protein

NP_000539.2:p.(Gly33Arg)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000548.5:c.97G>C (p.Gly33Arg) in TSC2 is a missense variant absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, supporting PM2 at supporting strength.

Multiple lines of computational evidence (REVEL 0.212, BayesDel 0.118, SpliceAI max delta 0.00) suggest no deleterious impact on the gene product, supporting BP4 at supporting benign strength.

No functional studies, case reports, segregation data, de novo observations, or ClinVar pathogenic classifications exist for this specific variant. The sole ClinVar submission classifies it as Uncertain Significance.

Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) yields a final classification of Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules identified both pathogenic and benign evidence, so the overall classification remains Variant of Uncertain Significance because the evidence is conflicting.

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.97G>C is a missense variant (p.Gly33Arg). PVS1 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice site). This variant falls outside the PVS1 null-variant buckets per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not assessed	No evidence was identified that the same amino acid change (p.Gly33Arg) has been established as pathogenic via a different nucleotide change. No literature or database entry supports a PS1 determination.
PS2	Not met	No de novo occurrence of NM_000548.5:c.97G>C has been reported. Targeted exploratory search for de novo evidence returned no relevant publications or database entries.
PS3	Not met	No well-established in vitro or in vivo functional studies have tested NM_000548.5:c.97G>C (p.Gly33Arg). Gene-level functional assay frameworks exist for TSC2 (PMID:15798776, PMID:11274443) but do not include this specific variant. OncoKB classification is Unknown Oncogenic Effect with no variant-specific reviewed functional evidence.	oncokb
PS4	Not met	No case-control or cohort study has demonstrated statistically significant enrichment of NM_000548.5:c.97G>C in affected individuals versus controls. The variant is absent from gnomAD (v2.1, v4.1, Canada), precluding any odds-ratio calculation. Only a single ClinVar submission (Labcorp/Invitae, VUS) exists, which does not satisfy PS4 prevalence requirements.	gnomad_v2 gnomad_v4 gnomad_canada clinvar
PS5	N/A	PS5 is not a standard ACMG/AMP criterion. The comparable criterion is PM5 (different missense at same residue as a known pathogenic variant). See PM5 assessment.
PM1	Not met	Residue Gly33 is located in exon 2, in the N-terminal region of TSC2, distant from the critical GAP domain (residues ~1517-1766). Cancer Hotspots does not identify codon 33 as a statistically significant mutational hotspot. No evidence that this residue lies within a well-established critical functional domain devoid of benign variation.	hotspots
PM2	Met	NM_000548.5:c.97G>C is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). For non-VCEP assessment under generic ACMG/AMP, PM2 is applied when allele frequency is below 0.1% in all population databases. Complete absence across all queried populations supports PM2 at supporting strength.	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	TSC2-associated Tuberous Sclerosis Complex is an autosomal dominant disorder. PM3 applies only to recessive disorders where the variant is observed in trans with a known pathogenic variant.
PM4	N/A	NM_000548.5:c.97G>C is a single-nucleotide missense substitution. PM4 applies only to in-frame deletions/insertions or stop-loss variants that alter protein length.
PM5	N/A	No same-residue comparator P/LP missense variants were identified at codon Gly33. The automated PM5 candidate harvest found zero candidates; same-residue PM5 semantics could not be confirmed. No alternative amino acid change at codon 33 has been reported as pathogenic.	pm5_candidates
PM6	Not met	No de novo observation of NM_000548.5:c.97G>C has been reported, with or without confirmation of paternity/maternity. Targeted exploratory search returned no evidence.
PP1	Not met	No segregation data are available for NM_000548.5:c.97G>C. No family studies or LOVD entries with cosegregation information were identified.
PP2	Not assessed	PP2 applies when a missense variant occurs in a gene with a low rate of benign missense variation and where missense is a common disease mechanism. No gnomAD constraint metrics (Z-score, oe ratio) or HCI prior score are available for TSC2 to assess the rate of benign missense variation. This criterion cannot be assessed without gene-level constraint data.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. REVEL score is 0.212 (well below the 0.5 threshold). BayesDel score is 0.118 (low, not supporting pathogenicity). SpliceAI predicts no splice impact (max delta score = 0.00). The variant does not lie in a known functional domain or hotspot.	revel bayesdel spliceai
PP4	Not met	No specific phenotypic data or clinical information about the proband are available. The single ClinVar submitter classified this variant as VUS. No expert panel or consensus classification exists.	clinvar
PP5	Not met	PP5 requires a reputable source (e.g., clinical diagnostic laboratory with expertise) to have classified the variant as pathogenic. The single ClinVar submission from Labcorp/Invitae classifies this variant as Uncertain Significance, not Pathogenic. The eight PMIDs associated with this ClinVar record (20301399, 23519317, 23788249, 25356965, 27854360, 34012068, 35802134, 28492532) are all guideline/background papers or a GeneReviews entry; none mention NM_000548.5:c.97G>C specifically and thus cannot support PP5.	clinvar
BA1	Not met	BA1 requires allele frequency above 1% in population databases. NM_000548.5:c.97G>C is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The allele frequency is 0%, not >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	BS1 requires allele frequency above 0.3% in population databases. The variant is absent from all queried gnomAD datasets (v2.1, v4.1, Canada). Allele frequency is 0%, not >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No observations of NM_000548.5:c.97G>C in healthy adults have been reported. The variant is absent from all population databases, and no literature reports describe its presence in unaffected individuals with full penetrance expected at an early age.
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrate that NM_000548.5:c.97G>C has no damaging effect on protein function or splicing. OncoKB shows Unknown Oncogenic Effect without reviewed functional data for this variant.	oncokb
BS4	Not met	No evidence of non-segregation with disease in affected families has been reported. No family studies involving NM_000548.5:c.97G>C were identified.
BP1	Not met	BP1 applies when a missense variant occurs in a gene where truncating variants are the primary/only known disease mechanism. TSC2 is associated with both truncating and pathogenic missense variants; Tuberous Sclerosis Complex can result from missense changes with functional impact. BP1 is not applicable to TSC2 missense variants in the absence of evidence that missense changes are not a disease mechanism.
BP2	Not met	No evidence that NM_000548.5:c.97G>C has been observed in trans with a known pathogenic TSC2 variant, or in cis with a pathogenic variant in this autosomal dominant disorder. Exploratory search found no co-occurrence data.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without a known function. NM_000548.5:c.97G>C is a single-nucleotide missense substitution, not an in-frame indel.
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.212 (below 0.5 pathogenic threshold). BayesDel score is 0.118 (low). SpliceAI predicts no splicing alteration (max delta score = 0.00). All three in silico predictors are concordant in not supporting a deleterious effect.	revel bayesdel spliceai
BP5	Not met	BP5 requires a reputable source to have classified the variant as benign or to report it as found in a case with an alternate molecular basis for disease. Only one ClinVar submission exists (Labcorp/Invitae, VUS), which classifies the variant as Uncertain Significance, not Benign.	clinvar
BP6	Not met	No reputable source (e.g., ClinGen Expert Panel, professional society guideline) has classified NM_000548.5:c.97G>C as benign. The only ClinVar submission is a single clinical laboratory VUS.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact on the splice consensus sequence or splicing efficiency. NM_000548.5:c.97G>C is a missense variant (p.Gly33Arg), not synonymous.

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