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TSC1
Final classification
VUS
TSC1 c.1438+6G>A · p.?
TSC1

NM_000368.5:c.1438+6G>A is present in gnomAD at very low allele frequency (0.010% in v2.1, 0.015% in v4.1; 28–243 alleles, no homozygotes), meeting PM2 at supporting strength.

Gene
TSC1
Transcript
NM_000368.5
HGVS · transcript:coding
NM_000368.5:c.1438+6G>A
Consequence
N/A
GRCh38
chr9:132906725 C>T
GRCh37
chr9:135782112 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: PM2 supporting, BP6 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP6 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP6 VUS
TSC1 c.1438+6G>A

NM_000368.5:c.1438+6G>A is present in gnomAD at very low allele frequency (0.010% in v2.1, 0.015% in v4.1; 28–243 alleles, no homozygotes), meeting PM2 at supporting strength.1 The variant is reported in ClinVar (ID 48782) with 10 of 15 clinical laboratory submissions classifying as Benign or Likely Benign, meeting BP6 at supporting benign strength. No submission classifies as Pathogenic.2 SpliceAI predicts no significant splicing impact (max delta score 0.10). No other computational or functional evidence supports or refutes a deleterious effect.3 PS2 (de novo), PS3 (functional), PS4 (case-control), PM6 (assumed de novo), PP1 (cosegregation), PP4 (patient phenotype), BS2 (healthy adults), BS3 (benign functional), BS4 (lack of segregation), BP2 (in trans/cis), and BP5 (alternate molecular basis) could not be assessed due to absence of variant-specific clinical or functional data. PVS1 is not met: the variant is at the +6 intronic position outside canonical ±1,2 splice sites, and SpliceAI does not predict a splice alteration. The variant does not qualify as a predicted null variant under ClinGen SVI PVS1 recommendations.4 Using the generic ACMG/AMP 2015 combination rules (PMID:25741868), the variant has one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP6). The net point score is 0, resulting in a classification of Variant of Uncertain Significance (VUS). This is consistent with the conflicting ClinVar aggregate classification.5

PM2 + BP6 VUS
Gene diagram · NM_000368.5 · variants mapped to exon structure
TSC1 NM_000368.5
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      243 / 1,611,274
      0.015%
      Highest · European (non-Finnish)
      0.02%
      Homozygotes
      0
      grpmax FAF
      0.018%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 3 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 236 / 1,177,978 0.02% 0
      European (Finnish) 1 / 63,936 0.0016% 0
      South Asian 1 / 90,784 0.0011% 0
      Admixed American 0 / 59,922
      Amish 0 / 912
      East Asian 0 / 44,858
      Middle Eastern 0 / 6,082
      Ashkenazi Jewish 0 / 29,556
      African/African American 0 / 74,864
      This variant is present in gnomAD v4.1 (AF= 0.000150812; MAF= 0.01508%, 243/1611274 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000200343; MAF= 0.02003%, 236/1177978 alleles, homozygotes = 0); grpmax FAF= 0.00017932.
      Overall AF
      28 / 280,414
      0.01%
      Highest · European (non-Finnish)
      0.02%
      Homozygotes
      0
      grpmax FAF
      0.015%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 2 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 26 / 127,658 0.02% 0
      European (Finnish) 2 / 25,034 0.008% 0
      African/African American 0 / 24,830
      Admixed American 0 / 35,280
      Ashkenazi Jewish 0 / 10,292
      East Asian 0 / 19,814
      Remaining individuals 0 / 7,188
      South Asian 0 / 30,318
      This variant is present in gnomAD v2.1 (AF= 9.98524e-05; MAF= 0.00999%, 28/280414 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000203669; MAF= 0.02037%, 26/127658 alleles, homozygotes = 0); grpmax FAF= 0.00014731.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (7 clinical laboratories) and as Benign (3 clinical laboratories) and as Likely Benign (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory) and as benign (1 clinical laboratory). (ClinVarID = 48782)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10).
      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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Literature · 11 PMIDs triaged · 8 high-priority
      11papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      26467025 ↗ functional
      A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
      We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
      BS3PP5PS3PS4
      20301399 ↗ case observation
      Untitled reference
      PP5PS4
      23519317 ↗ case observation
      Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions.
      The autism spectrum disorders are a collective of conditions that have in common impaired socialization and communication in association with stereotypic behaviors. The reported incidence of autism spectrum disorders has increased dramatically over the past two decades. In addition, increased attention has been paid to these conditions by both lay and professional groups. These trends have resulte
      PP5PS4
      23788249 ↗ case observation
      ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
      In clinical exome and genome sequencing, there is a potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing but of medical value for patient care. The American College of Medical Genetics and Genomics (ACMG) recently published a policy statement on clinical sequencing that emphasized the importance of alerting the pati
      PP5PS4
      25356965 ↗ case observation
      ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
      These recommendations are designed primarily as an educational resource for medical geneticists and other health-care providers to help them provide quality medical genetics services. Adherence to these recommendations does not necessarily ensure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedure
      PP5PS4
      25394175 ↗ case observation
      A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.
      The practice guidelines of the American College of Medical Genetics and Genomics (ACMG) and the National Society of Genetic Counselors (NSGC) are developed by members of the ACMG and NSGC to assist medical geneticists, genetic counselors, and other health-care providers in making decisions about appropriate management of genetic concerns, including access to and/or delivery of services. Each pract
      PP5PS4
      27854360 ↗ case observation
      Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.
      Disclaimer: These recommendations are designed primarily as an educational resource for medical geneticists and other healthcare providers to help them provide quality medical services. Adherence to these recommendations is completely voluntary and does not necessarily assure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests o
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      6Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC