Starting
Initialising…
0%
CBL
Final classification
VUS
CBL c.1147A>C · p.Ile383Leu
CBL

NM_005188.3:c.1147A>C (p.Ile383Leu) is a missense variant in exon 8 of the CBL gene.

Gene
CBL
Transcript
NM_005188.3
HGVS · transcript:coding
NM_005188.3:c.1147A>C
Consequence
N/A
GRCh38
chr11:119278217 A>C
GRCh37
chr11:119148927 A>C
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: PM1 moderate, PM2 supporting, PP3 supporting; combination = 1 moderate + 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: PM1 moderate, PM2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
CBL c.1147A>C

NM_005188.3:c.1147A>C (p.Ile383Leu) is a missense variant in exon 8 of the CBL gene. This variant is located in the CBL RING finger domain (residues 381-420), a critical functional domain where missense variants are an established disease mechanism for Noonan-like syndrome/CBL syndrome (PM1).1 It is extremely rare in population databases: observed in 1 of 251,292 alleles in gnomAD v2.1 (AF=3.98x10^-6) and 1 of 1,612,068 alleles in gnomAD v4.1 (AF=6.20x10^-7), with no homozygotes in any population dataset, meeting PM2 criteria.2 In silico analysis with REVEL (score 0.786) predicts a deleterious effect, though BayesDel (0.134) is discordant (PP3).3 SpliceAI predicts no splice impact (max delta = 0.00).4 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (Labcorp/Invitae, SCV002596392). No expert panel review is available.5 No functional studies, segregation data, case-control analyses, or de novo observations have been reported for this variant in the literature. OncoKB classifies this variant as having Unknown Oncogenic Effect.6 The variant has not been reported in COSMIC and does not lie in a statistically significant cancer hotspot. Overall, applying generic ACMG/AMP 2015 criteria, the evidence is limited to PM1 (moderate) + PM2 (supporting) + PP3 (supporting). No benign criteria are met. This is insufficient to reach a likely pathogenic classification (requires at least 2 moderate or 1 strong). The variant remains a Variant of Uncertain Significance (VUS).

PM1 + PM2 + PP3 VUS
1 pvs1_gene_context
3 revelbayesdel
Gene diagram · NM_005188.3 · variants mapped to exon structure
CBL NM_005188.3
Fetching transcript structure from UCSC…
Applied criteria · 3 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
      This variant is present in gnomAD v4.1 (AF= 6.20321e-07; MAF= 0.00006%, 1/1612068 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66644e-05; MAF= 0.00167%, 1/60008 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.97943e-06; MAF= 0.00040%, 1/251292 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89118e-05; MAF= 0.00289%, 1/34588 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,612,068
      0 hom
      Admixed American
      1 / 60,008
      0.0017%
      + 9 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      0.0004% · 1 / 251,292
      0 hom
      Admixed American
      1 / 34,588
      0.0029%
      + 7 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1716702)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.786. BayesDel score = 0.134053.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 1 PMID not cited in assessment
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR