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CBL
Final classification
VUS
CBL c.1240C>A · p.Gln414Lys
CBL

NM_005188.3:c.1240C>A (p.Gln414Lys) is a missense variant in CBL, a gene associated with RASopathies and myeloid malignancies through loss-of-function and missense mechanisms.

Gene
CBL
Transcript
NM_005188.3
HGVS · transcript:coding
NM_005188.3:c.1240C>A
Consequence
N/A
GRCh38
chr11:119278522 C>A
GRCh37
chr11:119149232 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, BP4 supporting benign; combination = 1 supporting + 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 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CBL c.1240C>A

NM_005188.3:c.1240C>A (p.Gln414Lys) is a missense variant in CBL, a gene associated with RASopathies and myeloid malignancies through loss-of-function and missense mechanisms.1 This variant is absent from all large population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2 at supporting level.2 Multiple lines of computational evidence (BayesDel 0.052, SpliceAI max delta 0.07) predict no damaging impact on the gene product, meeting BP4 at supporting_benign level.3 No functional studies, case reports, segregation data, or literature evidence specific to this variant were identified. The variant is absent from ClinVar and has not been classified by any external source.4 With one pathogenic supporting criterion (PM2_Supporting) and one benign supporting criterion (BP4_Supporting), the evidence is insufficient to classify this variant as either pathogenic or benign. The variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines.5

PM2 + BP4 VUS
1 pvs1_gene_context
3 bayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_005188.3 · variants mapped to exon structure
CBL NM_005188.3
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 = 0.07). REVEL score = 0.596. BayesDel score = 0.0521768.
      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. CBL, a tumor suppressor and ubiquitin ligase, is inactivated by mutation or deletion in various cancer types including myeloid 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 not previously been reported in somatic cancers (COSMIC).
      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