Starting
Initialising…
0%
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, a gene in which germline loss-of-function variants cause a neurodevelopmental syndrome with Wilms tumor predisposition.

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, PP3 supporting; combination = 2 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, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
FBXW7 c.1697G>T

NM_033632.3:c.1697G>T (p.Trp566Leu) is a missense variant in exon 11 of FBXW7, a gene in which germline loss-of-function variants cause a neurodevelopmental syndrome with Wilms tumor predisposition.1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the PM2 criterion at supporting strength.2 In silico prediction with REVEL yields a score of 0.863, supporting a deleterious effect and meeting PP3 at supporting strength.3 SpliceAI predicts no significant splicing impact (max delta score 0.12).4 This variant has been reported in somatic cancers (COSMIC COSV99662097, n=2) but has not been observed in ClinVar or any germline disease cohort.5 With only two supporting pathogenic criteria (PM2_Supporting, PP3_Supporting), this variant does not meet the threshold for Likely Pathogenic classification under generic ACMG/AMP 2015 combination rules.6 This variant is classified as a Variant of Uncertain Significance (VUS).7

PM2 + PP3 VUS
1 pvs1_gene_context
3 revel
6 generic_acmg_combination_rules
7 generic_acmg_combination_rules
Gene diagram · NM_033632.3 · variants mapped to exon structure
FBXW7 NM_033632.3
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.
      🇨🇦 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