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TET2
Final classification
Likely Pathogenic
TET2 c.2152del · p.Leu718PhefsTer33
TET2

NM_001127208.2:c.2152delC is a frameshift deletion predicted to result in premature termination at codon 751 (p.Leu718PhefsTer33) in TET2, a gene for which heterozygous germline loss-of-function variants are an established cause of an autoimmune lymphoproliferative syndrome-like phenotype and hematologic malignancy.

Gene
TET2
Transcript
NM_001127208.2
HGVS · transcript:coding
NM_001127208.2:c.2152del
Consequence
N/A
GRCh38
chr4:105236092 AC>A
GRCh37
chr4:106157249 AC>A
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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
TET2 c.2152del

NM_001127208.2:c.2152delC is a frameshift deletion predicted to result in premature termination at codon 751 (p.Leu718PhefsTer33) in TET2, a gene for which heterozygous germline loss-of-function variants are an established cause of an autoimmune lymphoproliferative syndrome-like phenotype and hematologic malignancy.1 This variant is absent from gnomAD population databases (v2.1 exomes, v4.1 exomes/genomes, and gnomAD-Canada v1.0), indicating it is not a common benign polymorphism and supporting evidence for rarity in the general population.2 Under the generic ACMG/AMP 2015 classification framework, application of PVS1 (Very Strong) for a null variant in a gene where loss of function is a known disease mechanism, together with PM2 (Moderate) for absence from population databases, yields a Likely Pathogenic classification (1 Very Strong + 1 Moderate).3

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
3 generic_acmg_combination_rules
Gene diagram · NM_001127208.2 · variants mapped to exon structure
TET2 NM_001127208.2
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 · supports pathogenic
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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 · 2 PMIDs not cited in assessment
      21057493 ↗ Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. ONCOKB
      24315485 ↗ Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. ONCOKB