NM_000548.5:c.3884-23C>T

TSC2 · NP_000539.2:p.? · NM_000548.5

GRCh37: chr16:2133673 C>T · GRCh38: chr16:2083672 C>T

Gene: TSC2 Transcript: NM_000548.5

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

TSC2

Transcript

NM_000548.5

Protein

NP_000539.2:p.?

gnomAD AF

0.0002924562880017573 (v4.1)

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000548.5:c.3884-23C>T is a deep intronic variant in TSC2 located 23 bases upstream of exon 32. SpliceAI predicts no splice impact (max delta score 0.02), suggesting the variant does not alter normal splicing.

This variant is absent from ClinVar and is present in gnomAD at very low overall frequency (AF 0.058% in v2.1, 0.029% in v4.1), meeting PM2 at supporting strength.

SpliceAI predicts no splice impact (max delta 0.02), meeting BP4 at supporting strength. No other in silico tools (REVEL, BayesDel) are applicable to this intronic variant.

No functional studies, clinical reports, segregation data, or de novo observations are available for this variant. No publications were identified through comprehensive literature screening.

With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced. The variant is classified as a Variant of Uncertain Significance (VUS) under the generic ACMG/AMP 2015 framework.

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	N/A	This is a deep intronic variant (c.3884-23C>T, 23 bases upstream of exon 32) that does not fall into the null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants required for PVS1 application. The PVS1 variant assessment explicitly confirms generic PVS1 framework is not eligible.	pvs1_variant_assessment pvs1_gene_context pvs1_generic_framework
PS1	N/A	This is an intronic variant with no protein-level amino acid consequence. PS1 requires the same amino acid change as an established pathogenic variant, which cannot be determined for an intronic substitution.
PS2	Not met	No de novo occurrence data (with confirmed paternity and maternity) is available for this variant. No publications or clinical reports document a de novo observation of NM_000548.5:c.3884-23C>T.
PS3	Not met	No functional experimental data exists for NM_000548.5:c.3884-23C>T. No publications were identified through literature search. SpliceAI predicts no splice impact (max delta 0.02), but this is in silico prediction, not experimental functional evidence suitable for PS3.	spliceai
PS4	Not met	No case-control or affected individual data is available for this variant. The variant is observed in gnomAD at low frequency but no clinical cohort enrichment data has been reported.	gnomad_v2 gnomad_v4
PS5	Not met	This variant has not been reported in any individual with TSC2-related disease. No clinical publications or database submissions identify NM_000548.5:c.3884-23C>T in an affected proband.	clinvar
PM1	Not met	This deep intronic variant (c.3884-23C>T) does not localize to a known mutational hotspot or critical functional domain. Cancerhotspots.org does not list this variant or position as significant. SpliceAI predicts no splice alteration (max delta 0.02), arguing against a functionally critical intronic regulatory position.	spliceai
PM2	Met	This variant is absent from ClinVar and present in gnomAD at very low frequency in the overall population (AF 0.058% in v2.1, 0.029% in v4.1), below the 0.1% threshold for PM2. Grpmax FAF is 0.0105%. Note: 1 homozygote is observed in gnomAD v2.1 and 3 homozygotes in v4.1, concentrated in the Finnish subpopulation (Finnish AF 0.527%), which is unusual for an autosomal dominant tumor suppressor gene but does not negate the low overall population frequency.	gnomad_v2 gnomad_v4
PM5	N/A	This is an intronic variant with no amino acid change. PM5 requires a different missense change at the same residue as a known pathogenic missense variant. The PM5 candidate assessment was unable to parse residue context from the intronic variant, and the automated pipeline confirmed PM5 is not applicable.	pm5_candidates
PM6	Not met	No de novo observation (without confirmed paternity and maternity) has been reported for this variant. PM6 requires at least one de novo report in a patient with disease and no family history.
PP1	Not met	No cosegregation data is available for this variant. No family studies have been reported.
PP2	N/A	This is an intronic substitution, not a missense variant. PP2 applies specifically to missense variants in genes with a low rate of benign missense variation and where missense variants are a common disease mechanism.
PP3	Not met	Multiple lines of computational evidence do NOT support a deleterious effect. SpliceAI predicts no splice impact (max delta score 0.02, well below the 0.1 threshold for any prediction). REVEL and BayesDel scores are not available for this intronic variant. No in silico tool predicts a damaging consequence.	spliceai
PP4	Not met	No patient phenotype or family history data is available for this variant. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not met	This variant is absent from ClinVar. No reputable source, including expert panels, has classified NM_000548.5:c.3884-23C>T as pathogenic. The PP5 criterion requires a reputable source to have reported the variant as pathogenic.	clinvar
BA1	Not met	The overall gnomAD allele frequency of 0.058% (v2.1) is well below the 1% threshold for BA1. This variant is not common enough in the general population to be considered a benign polymorphism under BA1.	gnomad_v2 gnomad_v4
BS1	Not met	The overall gnomAD allele frequency of 0.058% (v2.1) is below the 0.3% threshold for BS1. While the Finnish subpopulation frequency is 0.527%, the grpmax FAF (0.0105%) and overall frequency are the primary metrics used for BS1 and both fall below the threshold.	gnomad_v2 gnomad_v4
BS2	Not met	Although the variant is observed in gnomAD (121-458 alleles including 1-3 homozygotes), individual-level phenotype confirmation is not available. The presence of homozygotes in a population database for an autosomal dominant tumor suppressor gene (TSC2) is notable, but BS2 requires confirmed observation in a healthy adult with full penetrance expected at an early age, which cannot be established from gnomAD alone.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established functional studies demonstrate no damaging effect for this variant. SpliceAI prediction of no splice impact (max delta 0.02) is in silico evidence only and does not constitute the well-established experimental functional data required for BS3.	spliceai
BS4	Not met	No segregation data is available. BS4 requires lack of cosegregation with disease in affected family members, and no family studies have been reported for this variant.
BP1	N/A	This is an intronic substitution, not a missense variant. BP1 applies specifically to missense variants in genes where only truncating variants are known to cause disease.
BP2	Not met	No data on observations in trans with a known pathogenic variant is available. BP2 requires the variant to be observed in trans with a pathogenic variant in a gene associated with a fully penetrant dominant disorder.
BP4	Met	SpliceAI predicts no splice impact (max delta score 0.02), which is well below the 0.1 threshold for any splice-altering prediction category. While REVEL and BayesDel are not available for this intronic variant, the available computational evidence supports a benign interpretation with no predicted effect on splicing.	spliceai
BP5	Not met	No case with an alternate molecular basis for disease has been reported in an individual carrying this variant. BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
BP6	Not met	This variant is absent from ClinVar. No reputable source, including expert panels, has classified NM_000548.5:c.3884-23C>T as benign. The BP6 criterion requires a reputable source to have reported the variant as benign.	clinvar
BP7	N/A	This is an intronic variant (c.3884-23C>T), not a synonymous (silent) variant. BP7 applies specifically to synonymous variants for which splicing prediction algorithms predict no impact and the nucleotide is not highly conserved.
BP3	N/A	BP3 applies to in-frame insertions/deletions in repetitive regions. This variant is a substitution.
PM3	N/A	PM3 applies to recessive disorders where the variant is detected in trans with a pathogenic variant. TSC2 is an autosomal dominant disorder.
PM4	N/A	PM4 applies to non-repeat in-frame deletions/insertions or stop-loss variants. This is a substitution.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.