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TSC2
Final classification
Benign
TSC2 c.729C>G · p.Leu243=
TSC2

NM_000548.5:c.729C>G (p.Leu243=) is a synonymous variant in exon 8 of TSC2 with an overall allele frequency of 0.316-0.355% in gnomAD, exceeding the BS1 threshold of >0.3%.

Gene
TSC2
Transcript
NM_000548.5
HGVS · transcript:coding
NM_000548.5:c.729C>G
Consequence
N/A
GRCh38
chr16:2056724 C>G
GRCh37
chr16:2106725 C>G
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 benign, BS2 strong benign, 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 benign, BS2 strong benign, 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.729C>G

NM_000548.5:c.729C>G (p.Leu243=) is a synonymous variant in exon 8 of TSC2 with an overall allele frequency of 0.316-0.355% in gnomAD, exceeding the BS1 threshold of >0.3%.1 This variant has been observed in 10 homozygous individuals in gnomAD v4.1 among 1,612,278 alleles, constituting strong evidence for benignity in a dominant disorder (BS2).2 SpliceAI predicts no splice impact (max delta = 0.01), and the variant is synonymous with no predicted effect on protein sequence, supporting multiple benign computational evidence lines (BP4, BP7).3 ClinVar classifies this variant as Benign/Likely benign across 21 clinical laboratory submissions (15 Benign, 6 Likely benign), with criteria provided and no conflicting pathogenic interpretations (BP6).4 No pathogenic criteria are met. PVS1, PS1, and PM5 are not applicable to this synonymous variant. PS2, PS3, PS4, PS5, PM1, PM2, PM6, PP3, and PP5 are not met. PP1, PP4, BS4, BP2, and BP5 are not assessed due to absence of data. BA1 is not met (overall AF <1%). BP1 and PP2 are not applicable to synonymous variants.5 Applying generic ACMG/AMP 2015 final combination rules: two strong benign criteria (BS1, BS2) alone satisfy the classification threshold for Benign. Additionally, three supporting benign criteria (BP4, BP6, BP7) reinforce the benign classification.6

BS1 + BS2 + BP4 + BP6 + BP7 Benign
5 pvs1_generic_framework ↗generic_acmg_combination_rules
6 generic_acmg_combination_rules
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= 0.00316261; MAF= 0.31626%, 5099/1612278 alleles, homozygotes = 10) and has highest observed frequency in the European (Finnish) population (AF= 0.0121182; MAF= 1.21182%, 753/62138 alleles, homozygotes = 4); grpmax FAF= 0.00304706.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.00355285; MAF= 0.35529%, 1000/281464 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 0.0119589; MAF= 1.19589%, 284/23748 alleles, homozygotes = 0); grpmax FAF= 0.0056912.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.32% · 5099 / 1,612,278
      10 hom · FAF 0.3%
      European (Finnish)
      753 / 62,138
      1.2%
      4 hom
      Ashkenazi Jewish
      119 / 29,606
      0.4%
      European (non-Finnish)
      3696 / 1,180,020
      0.31%
      5 hom
      Remaining individuals
      193 / 62,492
      0.31%
      South Asian
      210 / 91,084
      0.23%
      Admixed American
      94 / 60,024
      0.16%
      1 hom
      Middle Eastern
      3 / 6,062
      0.049%
      African/African American
      31 / 75,050
      0.041%
      + 2 not observed (Amish, East Asian)
      gnomAD v2.1
      0.36% · 1000 / 281,464
      0 hom · FAF 0.57%
      European (Finnish)
      284 / 23,748
      1.2%
      Ashkenazi Jewish
      47 / 10,370
      0.45%
      Remaining individuals
      30 / 7,218
      0.42%
      European (non-Finnish)
      507 / 129,170
      0.39%
      South Asian
      57 / 30,616
      0.19%
      Admixed American
      59 / 35,438
      0.17%
      African/African American
      16 / 24,956
      0.064%
      + 1 not observed (East Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (15 clinical laboratories) and as Likely benign (6 clinical laboratories). (ClinVarID = 49382)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV104587071, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      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
      24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants. 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
      9829910 ↗ Exon scanning of the entire TSC2 gene for germline mutations in 40 unrelated patients with tuberous sclerosis. 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