NM_000368.5:c.2194C>T

TSC1 · NP_000359.1:p.(His732Tyr) · NM_000368.5

GRCh37: chr9:135779052 G>A · GRCh38: chr9:132903665 G>A

Gene: TSC1 Transcript: NM_000368.5

Final call

Benign

BA1 stand-alone benign BS1 strong benign BS2 strong benign BP4 supporting benign BP6 supporting benign

Variant details

Gene

TSC1

Transcript

NM_000368.5

Protein

NP_000359.1:p.(His732Tyr)

gnomAD AF

0.0036008077319996824 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

BA1 is met: allele frequency of 1.38–1.40% in the European (Finnish) population in gnomAD (v2.1: 347/25116 alleles, 3 homozygotes; v4.1: 896/64030 alleles, 11 homozygotes), exceeding the 1% stand-alone benign threshold.

BS1 is met: global allele frequency of 0.36–0.39% in gnomAD (v2.1: 1093/282512 alleles; v4.1: 5806/1,612,416 alleles), exceeding the 0.3% strong benign threshold for a fully penetrant autosomal dominant disorder.

BS2 is met: this variant has been observed in the homozygous state in 7 individuals in gnomAD v2.1 and 28 individuals in gnomAD v4.1. For a highly penetrant autosomal dominant tumor suppressor syndrome, biallelic inactivation would be expected to cause severe or lethal disease; observation of homozygotes in a general population database constitutes strong evidence for a benign role.

BP4 is met: multiple lines of computational evidence (REVEL=0.338, BayesDel=−0.064, SpliceAI max delta=0.09) predict no damaging effect on the gene product.

BP6 is met: ClinVar reports this variant as Benign by 23 clinical laboratories and Likely benign by 4 clinical laboratories (Variation ID: 5103), representing a strong consensus among diagnostic laboratories for a benign classification.

PVS1 is not applicable: this is a missense variant (p.His732Tyr) and does not meet PVS1 null-variant criteria under the ClinGen SVI PVS1 framework (PMC6185798).

PS3 is not met: the only variant-specific functional study (PMID 27425891) demonstrates that hamartin(H732Y) does not produce the neuronal enlargement phenotype observed with pathogenic TSC1 stop mutants (R692X, R786X) in the same experimental system, suggesting it is not functionally equivalent to established loss-of-function variants.

Under generic ACMG/AMP 2015 combination rules, BA1 alone meets the threshold for a Benign classification. Additionally, two strong benign criteria (BS1, BS2) independently satisfy the ≥2 Strong Benign rule for Benign.

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_000368.5:c.2194C>T is a missense variant (p.His732Tyr). Under the ClinGen SVI PVS1 framework (PMC6185798), PVS1 is applicable only to null variants (nonsense, frameshift, canonical splice ±1,2, initiation codon). This variant does not fall into any PVS1 bucket.	pvs1_generic_framework
PS1	Not assessed	PS1 requires a different nucleotide change at the same codon producing the same amino acid change that has been previously classified as pathogenic. No such comparator was identified for c.2194C>T (p.His732Tyr) in ClinVar or the literature.
PS2	Not met	No confirmed de novo occurrence with both maternity and paternity confirmed was identified for this variant in ClinVar, the published literature, or public databases.
PS3	Not met	No variant-specific functional evidence demonstrating a reproducible damaging effect was identified. PMID 27425891 reports that hamartin(H732Y) is frequent in FCDIIb and shows aberrant subcellular distribution in cell culture, but in the same study only the stop mutants (R692X, R786X) — not H732Y — caused the neuronal enlargement phenotype in utero electroporation assays. This functional evidence does not meet the threshold for PS3 and is more consistent with a variant that does not cause the same pathogenic cellular phenotype as established TSC1 loss-of-function mutations.	PMID:27425891
PS4	Not met	PS4 requires a statistically significant enrichment of the variant in affected individuals compared with controls. This variant is present in gnomAD at an overall allele frequency of 0.37–0.39% (v2.1: 1093/282512 alleles; v4.1: 5806/1,612,416 alleles) with 7–28 homozygotes, which is inconsistent with a rare Mendelian disease-causing variant. The high population frequency precludes case-control enrichment analysis.	gnomad_v2 gnomad_v4
PS5	Not assessed	PS5 requires a different nucleotide change at the same codon resulting in a different missense change that has been established as pathogenic. No such pathogenic comparator at codon 732 was identified.
PM1	Not met	While residue H732 lies within the coiled-coil domain (residues ~730–998) critical for TSC1-TSC2 dimerization, PM1 requires a mutational hot spot or critical functional domain without benign variation. This variant itself represents benign variation at this location, as evidenced by its high population frequency (AF ~0.37–0.39%) and multiple homozygotes in gnomAD, indicating that benign missense variation exists within this domain.	gnomad_v2 gnomad_v4
PM2	Not met	Under non-VCEP generic ACMG rules, PM2 requires absence or extremely low frequency (<0.1%) in population databases. This variant is present in gnomAD v2.1 at 0.39% (1093/282512 alleles) and v4.1 at 0.36% (5806/1,612,416 alleles), exceeding the 0.1% threshold.	gnomad_v2 gnomad_v4
PM5	N/A	No same-residue comparator variants suitable for PM5 assessment were identified. The pm5_candidates.json confirms zero eligible candidates.
PM6	Not met	No de novo occurrence without confirmation of maternity and paternity was reported for this variant. PM6 requires a de novo observation where both parents are not confirmed, which was not found in ClinVar submissions or the published literature.
PP1	Not met	No cosegregation data across multiple affected family members was identified for this variant. Given the high population frequency, cosegregation with disease in a large family would be unexpected.
PP2	Not assessed	PP2 assesses whether missense variants are a common mechanism of disease in a gene with low rate of benign missense variation. TSC1 is a tumor suppressor where truncating variants predominate; insufficient data were available to calculate a benign missense constraint metric specific to TSC1.
PP3	Not met	Multiple in silico tools do not support a deleterious effect: REVEL score 0.338 (below the 0.5 threshold for pathogenicity prediction), BayesDel score −0.064 (in the benign range), and SpliceAI max delta score 0.09 (no predicted splice impact). No computational evidence supports a pathogenic role.	revel bayesdel spliceai
PP4	Not met	PP4 is not met because the variant is present at high frequency in the general population (gnomAD AF ~0.37–0.39% with homozygotes), which is inconsistent with a highly specific disease phenotype. The variant has been observed in the homozygous state in presumably healthy individuals from a population database, arguing against a highly specific disease presentation.	gnomad_v2 gnomad_v4
PP5	Not met	PP5 requires a reputable source (e.g., clinical laboratory with expertise) to have reported the variant as pathogenic. ClinVar consensus for this variant is Benign (23 clinical laboratories) and Likely benign (4 clinical laboratories); no expert panel or reputable source has classified it as pathogenic.	clinvar
BA1	Met	Under non-VCEP generic ACMG rules, BA1 requires an allele frequency >1% in any population. This variant has an allele frequency of 1.38% (347/25116 alleles) in the European (Finnish) population in gnomAD v2.1, with 3 homozygotes. In gnomAD v4.1, the Finnish AF is 1.40% (896/64030 alleles, 11 homozygotes). This exceeds the 1% threshold and qualifies as stand-alone benign evidence.	gnomad_v2 gnomad_v4
BS1	Met	Under non-VCEP generic ACMG rules, BS1 requires an allele frequency >0.3% in population databases. This variant has a global allele frequency of 0.39% in gnomAD v2.1 (1093/282512 alleles) and 0.36% in gnomAD v4.1 (5806/1,612,416 alleles), exceeding the 0.3% threshold. TSC1 is an autosomal dominant disorder with high penetrance; a variant at this frequency in the general population is inconsistent with a highly penetrant disease-causing role.	gnomad_v2 gnomad_v4
BS2	Met	This variant has been observed in the homozygous state in 7 individuals in gnomAD v2.1 and 28 individuals in gnomAD v4.1. TSC1-associated tuberous sclerosis complex is an autosomal dominant disorder with high penetrance expected at an early age. Observation of homozygotes in a general population database (gnomAD excludes severe pediatric disease cases) constitutes strong evidence for a benign role, as biallelic inactivation of a fully penetrant AD tumor suppressor gene would be expected to cause severe or lethal disease.	gnomad_v2 gnomad_v4
BS3	Not assessed	No variant-specific functional study designed to demonstrate a benign or neutral effect was identified. While PMID 27425891 reports that hamartin(H732Y) does not cause neuronal enlargement in the same assay where stop mutants (R692X, R786X) produce a clear phenotype, this study was not designed as a dedicated benign-effect functional assay. BS3 requires well-established functional studies showing no damaging effect, which is not met by the available evidence.
BS4	Not met	No reported lack of segregation in affected families was identified for this variant. BS4 requires observation of the variant in a healthy family member who does not have the disease, in the context of a family where other members are affected, demonstrating non-segregation.
BP1	Not assessed	BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease. TSC1 truncating variants are indeed the predominant pathogenic mechanism, and this is a missense variant. However, BP1 also requires the absence of pathogenic missense variants at the same residue, which cannot be fully evaluated without a comprehensive review of all missense variants at codon 732.
BP2	N/A	BP2 applies to variants observed in trans with a pathogenic variant in a recessive disorder. TSC1-associated tuberous sclerosis complex is an autosomal dominant disorder; BP2 is not applicable.
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.338 (below the 0.5 threshold for pathogenic prediction), BayesDel score is −0.064 (firmly in the benign range), and SpliceAI predicts no splice impact (max delta 0.09). At least two independent in silico tools predict a benign effect.	revel bayesdel spliceai
BP5	Not assessed	BP5 applies when a variant is observed in a case with an alternate molecular basis for disease. No data on co-occurrence with an established pathogenic variant in TSC1 or TSC2 in a TSC patient was identified.
BP6	Met	Multiple clinical laboratories have classified this variant as Benign or Likely benign in ClinVar. Specifically, 23 clinical laboratories report this variant as Benign and 4 as Likely benign (ClinVar Variation ID: 5103). Multiple submitters with criteria provided agree on a benign classification, meeting BP6 criteria for a reputable source reporting the variant as benign.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. NM_000368.5:c.2194C>T is a missense variant (p.His732Tyr), not a synonymous change. BP7 is not applicable.

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