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LYFE SCIENCES
Project: HERA
NM_001127208.2:c.4164_4167del
p.Met1388IlefsTer59  ·  TET2
ACMG/AMP
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Classification rationale
1

The TET2 c.4164_4167del (p.Met1388IlefsTer59; p.M1388Ifs*59) variant has not been reported in ClinVar.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, placing it below the 0.1% rarity threshold used for PM2 in non-VCEP review.

gnomad_v2 ↗ gnomad_v4 ↗
3

Published TET2 studies identified through curated review show that leukemia-associated TET2 alterations impair 5-hydroxymethylcytosine generation, and structural work supports the functional importance of the C-terminal catalytic region, which is consistent with loss of function as a disease-relevant mechanism for truncating variants.

oncokb ↗ PMID:21057493 ↗ PMID:24315485 ↗
4

SpliceAI predicts no significant additional splice effect for this deletion, with a maximum delta score of 0.00; REVEL and BayesDel are not available for this variant type.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
ClinVar ↗
Functional evidence
03
Functional
OncoKB: 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 ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueM1388
Hotspots ↗