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TERT
Final classification
VUS
TERT c.3334C>A · p.Leu1112Met
TERT

The NM_198253.2:c.3334C>A (p.Leu1112Met) missense variant in TERT is absent from large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_supporting).

Gene
TERT
Transcript
NM_198253.2
HGVS · transcript:coding
NM_198253.2:c.3334C>A
Consequence
N/A
GRCh38
chr5:1253793 G>T
GRCh37
chr5:1253908 G>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, BP4 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
TERT c.3334C>A

The NM_198253.2:c.3334C>A (p.Leu1112Met) missense variant in TERT is absent from large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_supporting).1 Multiple in silico tools predict a benign or neutral effect: REVEL score 0.155, BayesDel score -0.27587, and SpliceAI max delta 0.00 (BP4_supporting).2 This variant has been reported in ClinVar as a Variant of Uncertain Significance by two clinical laboratories (ClinVar ID 816668). No functional studies have been performed on this variant.3 The variant is a missense change at a residue that is not located in a mutational hotspot or well-established critical functional domain, and no alternate pathogenic missense variant at the same codon is known.4 Overall, the available evidence includes one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), yielding a net classification of Variant of Uncertain Significance under the generic ACMG/AMP 2015 framework.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 pm5_candidates
5 generic_acmg_combination_rules
Gene diagram · NM_198253.2 · variants mapped to exon structure
TERT NM_198253.2
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
      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
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 816668)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.155. BayesDel score = -0.27587.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TERT is an enzyme that functions to maintain telomere length and genomic stability. The TERT promoter is frequently mutated in various cancer types.
      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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      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
      20301408 ↗ Pulmonary Fibrosis Predisposition Overview. CLINVAR
      20301779 ↗ Dyskeratosis Congenita and Related Telomere Biology Disorders. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR