NM_000368.4:c.2209-1G>C

TSC1 · NP_000359.1:p.? · NM_000368.4

GRCh37: chr9:135778175 C>G · GRCh38: chr9:132902788 C>G

Gene: TSC1 Transcript: NM_000368.4

Final call

VUS

PVS1 very strong PM2 supporting

Variant details

Gene

TSC1

Transcript

NM_000368.4

Protein

NP_000359.1:p.?

gnomAD AF

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000368.4:c.2209-1G>C disrupts the canonical splice acceptor site at the intron 16/exon 17 boundary of TSC1, a gene in which loss of function is an established mechanism for autosomal dominant tuberous sclerosis complex.

Under ClinGen SVI PVS1 recommendations (PMC6185798), this canonical ±1 splice variant qualifies for PVS1 at very strong weight. SpliceAI predicts acceptor loss with a delta score of 0.99. The affected exon (17 of 23) is predicted to cause a frameshift and NMD if skipped, with no evidence of alternative splicing or population LOF enrichment.

The variant is absent from all population databases (gnomAD v2.1, v4.1, Canada), meeting PM2 at supporting level under generic ACMG/AMP 2015 (<0.1% cutoff).

No additional pathogenic or benign criteria are met. PS3, PM1, PP5, and all other assessed criteria are not met or not applicable due to absence of variant-specific clinical, functional, or literature evidence.

Under generic ACMG/AMP 2015 final combination rules (PMID:25741868), PVS1 (very strong) + PM2 (supporting) does not meet the threshold for Likely Pathogenic (requires 1 very strong + 1 moderate, or 1 strong + 2 supporting). The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	Met	This canonical splice acceptor variant (c.2209-1G>C, intron 16/exon 17 boundary) disrupts the AG dinucleotide at position -1. TSC1 loss of function is an established germline disease mechanism for tuberous sclerosis complex. Under ClinGen SVI PVS1 recommendations (PMC6185798), canonical ±1,2 splice variants in genes with established LOF mechanisms are assigned PVS1 at very strong weight. SpliceAI predicts acceptor loss (delta score 0.99), confirming the predicted splicing defect. The affected exon (17 of 23) is not a biologically irrelevant distal exon or enriched for population LOF variation, and NMD is expected if exon skipping causes a frameshift.	pvs1_gene_context pvs1_variant_assessment pvs1_generic_framework spliceai
PS1	Not met	No known pathogenic variant at the same nucleotide position with the same predicted effect has been identified. PS1 requires a different nucleotide change at the same position producing the same amino acid change, which is not applicable to this splice variant without another established pathogenic splice variant at c.2209-1.	clinvar
PS2	Not met	No de novo data are available for this variant. No family studies or parentage testing has been identified.
PS3	Not met	No variant-specific functional data are available for NM_000368.4:c.2209-1G>C. No experimental studies directly testing this splice variant or systematically characterizing the splice acceptor region were identified in the evidence.
PS4	Not met	No case-control or cohort data are available for this variant. Absent from ClinVar and not reported in any literature as a clinically observed variant in affected individuals.	clinvar
PS5	N/A	PS5 applies only to novel missense variants at a residue where a different pathogenic missense change has been established. This is a splice site variant, not a missense substitution.
PM1	Not met	While the variant disrupts splicing within the TSC1 coiled-coil domain (residues ~717-997), which is critical for TSC1-TSC2 interaction, no specific domain-level PM1 framework has been established for TSC1 by a VCEP, and cancerhotspots.org does not identify this residue as significant. The functional domain argument is plausible but cannot be formally applied under generic ACMG without curated domain boundaries.
PM2	Met	This variant is completely absent from all population databases, including gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada. Under generic ACMG/AMP 2015, PM2 is applied at supporting level for variants with an allele frequency below 0.1% in population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 applies only to missense variants where a different pathogenic amino acid change has been observed at the same residue. This variant is a canonical splice site substitution affecting the intron 16/exon 17 boundary, not a missense change. Protein consequence cannot be determined (NP_000359.1:p.?).	pm5_candidates
PM6	Not met	No de novo data are available for this variant. PM6 requires confirmation that the variant arose de novo with both maternity and paternity confirmed.
PP1	Not met	No segregation data are available for this variant. PP1 requires cosegregation with disease in multiple affected family members.
PP2	N/A	PP2 applies specifically to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. This variant is a canonical splice site substitution, not a missense variant.
PP3	Not met	In silico splice predictions (SpliceAI delta 0.99, acceptor loss) strongly support a damaging splicing effect, but this evidence is already captured by PVS1 for a canonical splice site variant. Under PMC6185798 guidance, PP3 should not be stacked on top of PVS1 for the same splice-effect prediction. BayesDel score (0.313) does not independently predict a damaging effect.	spliceai bayesdel pvs1_generic_framework
PP4	Not assessed	No patient phenotype or clinical data are available for this case. PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. Tuberous sclerosis complex has a recognizable clinical presentation, but without patient-specific phenotype data, PP4 cannot be assessed.
PP5	Not met	This variant is absent from ClinVar. PP5 requires a reputable source (preferably ClinVar 3-star expert panel) to have classified the variant as pathogenic. No such classification exists.	clinvar
BA1	Not met	The variant is absent from all gnomAD population databases. BA1 requires an allele frequency exceeding 1%, which is not met.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all gnomAD population databases. BS1 requires an allele frequency exceeding 0.3%, which is not met.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data on homozygous or hemizygous occurrence in healthy adults are available. The variant is absent from all population databases.
BS3	Not met	No well-established functional studies demonstrate a benign effect for this variant. No experimental data of any kind were identified.
BS4	Not met	No segregation data are available. BS4 requires lack of segregation with disease in affected family members, which requires family-based genotype and phenotype data.
BP1	N/A	BP1 applies specifically to missense variants in genes where primarily truncating variants cause disease. This is a canonical splice site variant disrupting normal splicing, predicted to result in a truncating effect, not a missense variant.
BP2	Not met	No data on observations in trans with a pathogenic variant for TSC1 (autosomal dominant disorder) or in cis with a known pathogenic variant are available.
BP4	Not met	Multiple lines of computational evidence do NOT suggest a benign impact. SpliceAI predicts a strong splice-disrupting effect (delta 0.99, acceptor loss). BayesDel (0.313) does not independently predict benign impact. The weight of in silico evidence favors a damaging effect.	spliceai bayesdel
BP5	Not met	No data on an alternative molecular basis for disease are available. BP5 requires the variant to be found in a case with an established alternative genetic cause for the phenotype.
BP6	Not met	This variant is absent from ClinVar. BP6 requires a reputable source to have classified the variant as benign. No such classification exists.	clinvar
BP7	N/A	BP7 applies to synonymous variants for which splicing prediction algorithms predict no impact on the splice consensus sequence. This variant is a canonical splice site substitution (c.2209-1G>C) with SpliceAI predicting strong splice disruption (delta 0.99).	spliceai

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