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TET2
Final classification
VUS
TET2 c.5651C>A · p.Thr1884Asn
TET2

NM_001127208.2:c.5651C>A (p.Thr1884Asn) is a missense variant in TET2, a gene with emerging germline disease association involving autoimmune lymphoproliferative syndrome-like phenotypes and hematologic malignancy.

Gene
TET2
Transcript
NM_001127208.2
HGVS · transcript:coding
NM_001127208.2:c.5651C>A
Consequence
N/A
GRCh38
chr4:105276161 C>A
GRCh37
chr4:106197318 C>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: PM2 moderate, BP4 supporting benign; combination = 1 moderate + 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
TET2 c.5651C>A

NM_001127208.2:c.5651C>A (p.Thr1884Asn) is a missense variant in TET2, a gene with emerging germline disease association involving autoimmune lymphoproliferative syndrome-like phenotypes and hematologic malignancy. The variant is absent from gnomAD v2.1 and v4.1 (0/1,551,598 alleles) and gnomAD-Canada, meeting PM2 at moderate strength.1 Multiple in silico tools predict a neutral or benign effect: BayesDel score is -0.27313 (benign), REVEL score is 0.302 (neutral), and SpliceAI delta is 0.00 (no splice impact), meeting BP4 at supporting benign strength.2 The variant is absent from ClinVar and has not been classified by any expert panel. OncoKB reports an 'Unknown Oncogenic Effect' with no variant-specific functional evidence.3 One somatic observation exists in COSMIC (COSV54403709, n=1), but this does not independently support germline pathogenicity. No functional studies, family segregation data, de novo observations, or case-control data are available. Literature search returned zero variant-specific PMIDs. With one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4), this variant does not meet the threshold for Likely Pathogenic (requires ≥2 moderate or ≥1 moderate + ≥4 supporting) or Likely Benign (requires ≥1 strong benign + ≥1 supporting benign, or ≥2 supporting benign). The variant is classified as a Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 rules.4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
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 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_001127208.2:c.5651C>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (0/1,551,598 alleles; AF=0%), and gnomAD-Canada v1.0, meeting the PM2 threshold of <0.1% under the generic ACMG/AMP framework.
Absent from gnomAD v2.1Absent from gnomAD v4.1 (0 alleles / 1551
BP4 supporting Benign
Multiple lines of computational evidence predict no damaging effect. BayesDel score is -0.27313 (benign prediction), REVEL score is 0.302 (neutral, below pathogenicity threshold), and SpliceAI predicts no splice impact (max delta = 0.00).
BayesDel: -0.27313 (benign prediction)REVEL: 0.302 (neutralbelow 0.5 pathogenicity threshold)
Assessed · not applied
Pathogenic
PS3 No well-established functional studies are available for NM_001127208.2:c.5651C>A.
PS4 No case-control or prevalence data are available to assess whether this variant is statistically enriched in affected individuals.
PM1 This variant does not reside in a statistically significant mutational hotspot as determined by Cancer Hotspots analysis.
PM6 No de novo observation data are available for this variant.
PP1 No family segregation data are available for this variant.
PP2 Insufficient data are available to determine whether TET2 has a low rate of benign missense variation and whether missense variants are a common mechanism of disease.
PP3 Multiple in silico tools do not support a deleterious effect.
PP4 No patient phenotype or family history data are available to determine whether the clinical presentation is highly specific for a TET2-related disorder.
PP5 No reputable source has classified this variant as pathogenic.
Benign
BA1 The variant is absent from gnomAD v4.1 (0/1,551,598 alleles; AF=0%), well below the BA1 threshold of >1%.
BS1 The variant is absent from gnomAD v4.1 (0/1,551,598 alleles; AF=0%), well below the BS1 threshold of >0.3%.
BS2 No data are available regarding observation of this variant in healthy adults where full penetrance would be expected at an early age.
BS3 No well-established functional studies are available to demonstrate a lack of damaging effect for this variant.
BS4 No family segregation data are available to assess lack of segregation with disease.
BP1 Insufficient evidence to determine whether TET2-associated germline disease is primarily caused by truncating variants.
BP2 No phase data (cis or trans) are available for this variant with respect to any other variant in TET2.
BP5 No data are available indicating that this variant is found in a case with an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 8 PVS1 · PS1 · PS2 · PM3 · PM4 · PM5 · BP3 · BP7
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%, 0/1551598 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/73134 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 / 1,551,598
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 = 0.00). REVEL score = 0.302. BayesDel score = -0.27313.
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 previously been reported in somatic cancers (COSMIC; COSV54403709, n = 1 times).
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