Starting
Initialising…
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TET2
Final classification
VUS
TET2 c.1413C>T · p.Ser471=
TET2

NM_001127208.2:c.1413C>T (p.Ser471=) is a synonymous variant in TET2 at extremely low population frequency (gnomAD v2.1 AF=0.00142%, 4/282,248 alleles; v4.1 AF=0.00056%, 9/1,614,034 alleles), meeting PM2 at supporting level.

Gene
TET2
Transcript
NM_001127208.2
HGVS · transcript:coding
NM_001127208.2:c.1413C>T
Consequence
N/A
GRCh38
chr4:105235355 C>T
GRCh37
chr4:106156512 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, 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
TET2 c.1413C>T

NM_001127208.2:c.1413C>T (p.Ser471=) is a synonymous variant in TET2 at extremely low population frequency (gnomAD v2.1 AF=0.00142%, 4/282,248 alleles; v4.1 AF=0.00056%, 9/1,614,034 alleles), meeting PM2 at supporting level.1 SpliceAI predicts no splicing impact (max delta=0.00), meeting BP7 (supporting benign) for a synonymous variant without predicted splice alteration.2 ClinVar contains a single submission classifying this variant as Likely benign (Ambry Genetics, criteria provided), though no expert panel review exists. PS5 and PP5 are not met as the classification is not pathogenic.3 No variant-specific literature, functional studies, de novo observations, or segregation data were identified. Multiple criteria could not be assessed due to absence of evidence. The pathogenic evidence (PM2 supporting) and benign evidence (BP7 supporting_benign) are balanced and of equivalent weight. The variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 combination rules.4

PM2 + BP7 VUS
4 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
      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= 5.57609e-06; MAF= 0.00056%, 9/1614034 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.20072e-05; MAF= 0.00320%, 2/62486 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.41719e-05; MAF= 0.00142%, 4/282248 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.108e-05; MAF= 0.00311%, 4/128700 alleles, homozygotes = 0); grpmax FAF= 7.04e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00056% · 9 / 1,614,034
      0 hom · FAF 0.00025%
      Remaining individuals
      2 / 62,486
      0.0032%
      European (non-Finnish)
      7 / 1,180,018
      0.00059%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0014% · 4 / 282,248
      0 hom · FAF 0.0007%
      European (non-Finnish)
      4 / 128,700
      0.0031%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 3806053)
      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