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TERT
Final classification
VUS
TERT c.2781A>G · p.Leu927=
TERT

NM_198253.2:c.2781A>G (p.Leu927=) in TERT is a synonymous variant with extremely low population frequency (gnomAD v4.1 AF = 0.00149%, 24/1,613,722 alleles; absent from gnomAD v2.1), meeting PM2 at supporting strength.

Gene
TERT
Transcript
NM_198253.2
HGVS · transcript:coding
NM_198253.2:c.2781A>G
Consequence
N/A
GRCh38
chr5:1264466 T>C
GRCh37
chr5:1264581 T>C
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, BP7 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, BP7 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP7 VUS
TERT c.2781A>G

NM_198253.2:c.2781A>G (p.Leu927=) in TERT is a synonymous variant with extremely low population frequency (gnomAD v4.1 AF = 0.00149%, 24/1,613,722 alleles; absent from gnomAD v2.1), meeting PM2 at supporting strength.1 SpliceAI predicts no splicing alteration (max delta = 0.00), consistent with a silent variant, meeting BP7 at supporting_benign strength.2 PVS1 is not met as this synonymous variant does not qualify as a null variant per the ClinGen SVI PVS1 decision framework (PMC6185798). Computational evidence is insufficient for PP3 or BP4. No variant-specific functional studies, case-control data, segregation data, or de novo observations are available. ClinVar reports mixed classifications (Uncertain significance, Likely benign, Benign) from single submitters without expert panel consensus.3 With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP7), the net evidence weight is indeterminate. This variant is classified as a Variant of Uncertain Significance.4

PM2 + BP7 VUS
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
      This variant is present in gnomAD v4.1 (AF= 1.48725e-05; MAF= 0.00149%, 24/1613722 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 6.40225e-05; MAF= 0.00640%, 4/62478 alleles, homozygotes = 0); grpmax FAF= 9.53e-06.
      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
      0.0015% · 24 / 1,613,722
      0 hom · FAF 0.00095%
      Remaining individuals
      4 / 62,478
      0.0064%
      South Asian
      2 / 91,094
      0.0022%
      European (non-Finnish)
      18 / 1,180,036
      0.0015%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
      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) and as Likely benign (2 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 350629)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      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 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 · 5 PMIDs not cited in assessment
      20301408 ↗ Pulmonary Fibrosis Predisposition Overview. CLINVAR
      20301779 ↗ Dyskeratosis Congenita and Related Telomere Biology Disorders. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR