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.1 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.2 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).3 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.4 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).5
TSC1
Final classification
VUS
TSC1 c.2209-1G>C · p.?
TSC1
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.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2
VUS
TSC1 c.2209-1G>C
PVS1 + PM2
→
VUS
1
pvs1_gene_contextpvs1_variant_assessment
5
generic_acmg_combination_rules
Gene diagram
· NM_000368.4 · variants mapped to exon structure
TSC1
NM_000368.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PVS1
very strong
Pathogenic
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.
Canonical splice acceptor site disruption at c.2209-1 (AG → AC)TSC1 germline LOF mechanism established via literature (tuberous sclerosis complex)SpliceAI delta score 0.99 (acceptor loss) confirms predicted splicing defect
✓
PM2
supporting
Pathogenic
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.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0 (genomes)
Assessed · not applied
Pathogenic
PS1
No known pathogenic variant at the same nucleotide position with the same predicted effect has been identified.
PS2
No de novo data are available for this variant.
PS3
No variant-specific functional data are available for NM_000368.4:c.2209-1G>C.
PS4
No case-control or cohort data are available for this variant.
PM1
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.
PM6
No de novo data are available for this variant.
PP1
No segregation data are available for this variant.
PP3
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.
PP4
No patient phenotype or clinical data are available for this case.
PP5
This variant is absent from ClinVar.
Benign
BA1
The variant is absent from all gnomAD population databases.
BS1
The variant is absent from all gnomAD population databases.
BS2
No data on homozygous or hemizygous occurrence in healthy adults are available.
BS3
No well-established functional studies demonstrate a benign effect for this variant.
BS4
No segregation data are available.
BP2
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
Multiple lines of computational evidence do NOT suggest a benign impact.
BP5
No data on an alternative molecular basis for disease are available.
BP6
This variant is absent from ClinVar.
N/A · 4
PM5 · PP2 · BP1 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.312875.
Functional
No data
No calibrated functional assay or RNA evidence was identified for this variant.
COSMIC
Somatic evidence
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV53774227, n = 2 times).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Sources & reference links