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FLT3
Final classification
VUS
FLT3 c.1792_1793insCTACGTTGATTTCAGAGAATATGA · p.Glu598delinsAlaThrLeuIleSerGluAsnMetLys
FLT3

The FLT3 c.1792_1793insCTACGTTGATTTCAGAGAATATGA (p.(Glu598delinsAlaThrLeuIleSerGluAsnMetLys)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar; however, OncoKB classifies this specific variant as Likely Oncogenic with a likely gain-of-function effect.

Gene
FLT3
Transcript
NM_004119.2
HGVS · transcript:coding
NM_004119.2:c.1792_1793insCTACGTTGATTTCAGAGAATATGA
Consequence
N/A
GRCh38
chr13:28034126 T>TTCATATTCTCTGAAATCAACGTAG
GRCh37
chr13:28608263 T>TTCATATTCTCTGAAATCAACGTAG
Basis Generic ACMG/AMP 2015 final classification combination rules were used because no usable official VCEP/CSPEC or local custom gene-specific final-classification framework was available.
Generic ACMG/AMP 2015 final classification combination rules were used because no usable official VCEP/CSPEC or local custom gene-specific final-classification framework was available.
Classification rationale
PM1PM2 VUS
FLT3 c.1792_1793insCTACGTTGATTTCAGAGAATATGA

The FLT3 c.1792_1793insCTACGTTGATTTCAGAGAATATGA (p.(Glu598delinsAlaThrLeuIleSerGluAsnMetLys)) variant has not been observed in somatic cancers in COSMIC and has not been reported in ClinVar; however, OncoKB classifies this specific variant as Likely Oncogenic with a likely gain-of-function effect.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, with an observed population frequency of 0, which is below the 0.1% PM2 threshold.2 Published studies show that FLT3 internal tandem duplication and related length mutations in the juxtamembrane region are activating, and codons 589-599 form a recurrent cluster; this supports the pathogenic relevance of the E598 region, although a direct functional assay for this exact variant was not identified.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.08.4

PM1 + PM2 VUS
Gene diagram · NM_004119.2 · variants mapped to exon structure
FLT3 NM_004119.2
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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      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.
      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 = 0.08).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Gain-of-function.
      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.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:11090077
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      PMID PMID:11756186
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      PMID PMID:12384447
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      PMID PMID:9737679
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots