Starting
Initialising…
0%
CBL
Final classification
Likely Pathogenic
CBL c.1096-1_1096delinsTT · p.?
CBL

NM_005188.3:c.1096-1_1096delinsTT is a canonical splice acceptor site variant in CBL, a gene in which loss of function is a well-established mechanism for Noonan syndrome-like/RASopathy disorders (PVS1 at very strong weight, per ClinGen SVI PVS1 framework PMC6185798).

Gene
CBL
Transcript
NM_005188.3
HGVS · transcript:coding
NM_005188.3:c.1096-1_1096delinsTT
Consequence
N/A
GRCh38
chr11:119278165 GG>TT
GRCh37
chr11:119148875 GG>TT
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: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
CBL c.1096-1_1096delinsTT

NM_005188.3:c.1096-1_1096delinsTT is a canonical splice acceptor site variant in CBL, a gene in which loss of function is a well-established mechanism for Noonan syndrome-like/RASopathy disorders (PVS1 at very strong weight, per ClinGen SVI PVS1 framework PMC6185798).1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (allele frequency = 0), meeting PM2 at moderate strength (absent from population controls, below 0.1% threshold).2 SpliceAI predicts strong disruption of the canonical splice acceptor site (max delta score 0.99, acceptor loss DS_AL=0.99). This splice prediction evidence is captured by PVS1 and is not separately scored as PP3 per PMC6185798 guidance against double-counting.3 The variant has not been reported in ClinVar, COSMIC, or in any publication identified through literature search. No functional studies, segregation data, or de novo reports are available. Multiple criteria (PS2, PS3, PS4, PM1, PM6, PP1, PP4) remain unassessed due to lack of evidence.4 Under ACMG/AMP 2015 generic combination rules (PMID:25741868), one very strong criterion (PVS1) plus one moderate criterion (PM2) supports classification as Likely Pathogenic.5

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
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 · supports pathogenic
      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 possible splice impact for this variant (max delta score = 0.99).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC