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FBXW7
Final classification
VUS
FBXW7 c.1697G>T · p.Trp566Leu
FBXW7

NM_033632.3:c.1697G>T (p.Trp566Leu) is a missense variant in exon 11 of FBXW7, affecting the WD40 repeat domain critical for substrate recognition. The variant is completely absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).

Gene
FBXW7
Transcript
NM_033632.3
HGVS · transcript:coding
NM_033632.3:c.1697G>T
Consequence
N/A
GRCh38
chr4:152324342 C>A
GRCh37
chr4:153245494 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 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
FBXW7 c.1697G>T

NM_033632.3:c.1697G>T (p.Trp566Leu) is a missense variant in exon 11 of FBXW7, affecting the WD40 repeat domain critical for substrate recognition. The variant is completely absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).1 FBXW7 germline loss-of-function and missense variants are established causes of an autosomal dominant neurodevelopmental syndrome with Wilms tumor predisposition (PMID:35395208). The variant alters a highly conserved tryptophan residue within the WD40 domain where pathogenic missense variants cluster (PMID:42111496), though no formal VCEP domain specification exists. The variant has been reported twice in somatic cancers (COSMIC COSV99662097), consistent with a role in tumorigenesis.2 REVEL predicts a damaging score of 0.863, though BayesDel (0.424) does not reach the damaging threshold, and no variant-specific functional studies were identified. Computational evidence alone is insufficient to meet PP3.3 No ClinVar entries, no published variant-specific functional studies, no segregation or de novo data, and no case-control evidence exist for this variant. The variant remains unclassified in all major clinical databases.4

PM2 VUS
Gene diagram · NM_033632.3 · variants mapped to exon structure
FBXW7 NM_033632.3
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
      Absent from gnomAD v4.1.
      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 / ?
      0 hom
      Not observed in any ancestry group.
      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 = 0.12). REVEL score = 0.863. BayesDel score = 0.424003.
      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. FBXW7, a tumor suppressor involved in protein degradation, is inactivated by mutation in various cancer types, most frequently in endometrial and colo
      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; COSV99662097, n = 2 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