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TSC2
Final classification
Benign
TSC2 c.4006-8C>T · p.?
TSC2

NM_000548.5:c.4006-8C>T is an intronic variant at position -8 of exon 34 in TSC2, not predicted to alter splicing (SpliceAI delta = 0.00).

Gene
TSC2
Transcript
NM_000548.5
HGVS · transcript:coding
NM_000548.5:c.4006-8C>T
Consequence
N/A
GRCh38
chr16:2084220 C>T
GRCh37
chr16:2134221 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BS1 strong, BS2 strong, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 2 strong benign + 3 supporting benign, which maps to Benign.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BS1 strong, BS2 strong, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 2 strong benign + 3 supporting benign, which maps to Benign.
Classification rationale
BS1BS2BP4BP6BP7 Benign
TSC2 c.4006-8C>T

NM_000548.5:c.4006-8C>T is an intronic variant at position -8 of exon 34 in TSC2, not predicted to alter splicing (SpliceAI delta = 0.00).1 This variant is present in gnomAD at appreciable population frequencies: v2.1 AF=0.2436% (538/220866 alleles, 5 homozygotes) and v4.1 AF=0.3818% (6017/1575890 alleles, 15 homozygotes), with the highest subpopulation frequency in the European (non-Finnish) group at 0.3946% (v2.1) and 0.4712% (v4.1). These frequencies far exceed the expected prevalence of tuberous sclerosis complex (estimated incidence ~1:6000 to 1:10000 live births), meeting BS1 (strong benign).2 Five homozygotes are observed in gnomAD v2.1 and 15 homozygotes in gnomAD v4.1. TSC is an autosomal dominant disorder with near-complete penetrance and significant morbidity; the presence of homozygotes in a general population database is incompatible with pathogenicity, meeting BS2 (strong benign).3 This variant has been classified as Benign by 14 clinical diagnostic laboratories and as Likely benign by 5 clinical laboratories in ClinVar (Variation ID 49281), meeting BP6 (supporting benign).4 SpliceAI predicts no splicing impact (max delta = 0.00), and the variant is an intronic substitution at a non-canonical splice position, meeting BP4 and BP7 (each supporting benign).5 No variant-specific functional studies, de novo observations, cosegregation data, or case-control studies were identified for this variant. The ClinVar criterion-lead submission (SCV000066333, Tuberous sclerosis database) cited PMID:17304050, but the full text of that publication does not mention NM_000548.5:c.4006-8C>T. Classification: Likely Benign. Benign evidence includes BS1 (strong), BS2 (strong), BP4 (supporting), BP6 (supporting), and BP7 (supporting). No pathogenic or likely pathogenic criteria are met. Under the ACMG/AMP 2015 combining criteria, ≥2 strong benign criteria → Likely Benign.6

BS1 + BS2 + BP4 + BP6 + BP7 Benign
Gene diagram · NM_000548.5 · variants mapped to exon structure
TSC2 NM_000548.5
Fetching transcript structure from UCSC…
Applied criteria · 5 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 0.00381816; MAF= 0.38182%, 6017/1575890 alleles, homozygotes = 15) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00471223; MAF= 0.47122%, 5465/1159748 alleles, homozygotes = 13); grpmax FAF= 0.0046076.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.00243587; MAF= 0.24359%, 538/220866 alleles, homozygotes = 5) and has highest observed frequency in the European (non-Finnish) population (AF= 0.00394595; MAF= 0.39459%, 365/92500 alleles, homozygotes = 4); grpmax FAF= 0.00380144.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.38% · 6017 / 1,575,890
      15 hom · FAF 0.46%
      European (non-Finnish)
      5465 / 1,159,748
      0.47%
      13 hom
      Admixed American
      201 / 55,630
      0.36%
      Remaining individuals
      220 / 60,990
      0.36%
      1 hom
      African/African American
      62 / 73,896
      0.084%
      South Asian
      50 / 86,804
      0.058%
      1 hom
      Middle Eastern
      2 / 6,028
      0.033%
      European (Finnish)
      12 / 60,312
      0.02%
      Ashkenazi Jewish
      4 / 28,974
      0.014%
      East Asian
      1 / 42,596
      0.0023%
      + 1 not observed (Amish)
      gnomAD v2.1
      0.24% · 538 / 220,866
      5 hom · FAF 0.38%
      European (non-Finnish)
      365 / 92,500
      0.39%
      4 hom
      Admixed American
      116 / 30,504
      0.38%
      1 hom
      Remaining individuals
      21 / 6,130
      0.34%
      African/African American
      17 / 19,760
      0.086%
      South Asian
      14 / 25,778
      0.054%
      European (Finnish)
      4 / 20,992
      0.019%
      East Asian
      1 / 15,960
      0.0063%
      + 1 not observed (Ashkenazi Jewish)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (14 clinical laboratories) and as Likely benign (5 clinical laboratories). (ClinVarID = 49281)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV104573703, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 9 PMIDs not cited in assessment
      15798777 ↗ Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype--phenotype correlations and comparison of diagnostic DNA techniques in Tuberous Sclerosis Complex. CLINVAR
      17304050 ↗ Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      20301399 ↗ Tuberous Sclerosis Complex. CLINVAR
      23519317 ↗ Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR