Starting
Initialising…
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TET2
Final classification
VUS
TET2 c.3796A>T · p.Asn1266Tyr
TET2

NM_001127208.2:c.3796A>T (p.Asn1266Tyr) is a missense variant in exon 6 of TET2. It is absent from gnomAD population databases (0/1,551,256 alleles) and from ClinVar.

Gene
TET2
Transcript
NM_001127208.2
HGVS · transcript:coding
NM_001127208.2:c.3796A>T
Consequence
N/A
GRCh38
chr4:105243771 A>T
GRCh37
chr4:106164928 A>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; combination = 1 supporting, 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
TET2 c.3796A>T

NM_001127208.2:c.3796A>T (p.Asn1266Tyr) is a missense variant in exon 6 of TET2. It is absent from gnomAD population databases (0/1,551,256 alleles) and from ClinVar.1 The variant meets PM2 at supporting strength due to complete absence from large population cohorts.2 In silico predictions are conflicting: REVEL score of 0.707 is indeterminate; BayesDel score of 0.152 does not support pathogenicity; SpliceAI predicts no splicing impact (max delta=0.01). PP3 and BP4 are not met.3 No variant-specific functional studies, de novo reports, segregation data, case-control comparisons, or ClinVar classifications are available for this variant. PS3, PS2/PM6, PP1, PS4, and PP5 are all not met or not assessed.4 Under ACMG/AMP 2015 generic rules, one supporting pathogenic criterion (PM2) with no benign criteria yields a classification of Uncertain Significance.5

PM2 VUS
Gene diagram · NM_001127208.2 · variants mapped to exon structure
TET2 NM_001127208.2
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 0; MAF= 0.00000%, 0/1551256 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/72994 alleles, homozygotes = 0).
      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 / 1,551,256
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 = 0.01). REVEL score = 0.707. BayesDel score = 0.152069.
      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. TET2, a tumor suppressor and DNA demethylase, is frequently mutated in hematologic malignancies.
      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