NM_005188.3:c.1096-1G>T is a canonical splice acceptor variant in CBL, disrupting the AG dinucleotide at the intron 7 / exon 8 boundary.1 CBL loss-of-function is an established disease mechanism for a RASopathy phenotype with predisposition to juvenile myelomonocytic leukemia (CBL mutation-associated syndrome).2 The variant has been observed as a de novo occurrence in two unrelated individuals with features consistent with CBL-related RASopathy, with confirmed paternity in both cases.3 A minigene assay demonstrated that c.1096-1G>T results in complete skipping of exon 8, which encodes the linker region and RING finger domain critical for CBL E3 ubiquitin ligase function.4 The variant affects the RING finger domain / linker region (exons 8-9), a well-established mutational hotspot where approximately 50% of germline CBL mutations cluster and no benign variation is observed.5 The variant is extremely rare in population databases: absent from gnomAD v2.1 and gnomAD-Canada, and observed in a single heterozygous carrier in gnomAD v4.1 (1/1,590,474 alleles; AF = 0.00006%).6 This variant is classified as Pathogenic in ClinVar (Variation ID: 180815) by five independent clinical laboratories.7 Applying generic ACMG/AMP 2015 combination rules: PVS1 (very_strong) + PS2 (strong) + PM1 (moderate) + PS3 (supporting) + PM2 (supporting) + PP5 (supporting) is sufficient for a Pathogenic classification.8
CBL
Final classification
Pathogenic
CBL c.1096-1G>T · p.?
CBL
NM_005188.3:c.1096-1G>T is a canonical splice acceptor variant in CBL, disrupting the AG dinucleotide at the intron 7 / exon 8 boundary.
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, PS2 strong, PS3 supporting, PM1 moderate, PM2 supporting, PP5 supporting; combination = 1 very strong + 1 strong + 1 moderate + 3 supporting, which maps to Pathogenic.
Classification rationale
PVS1PS2PS3PM1PM2PP5
Pathogenic
CBL c.1096-1G>T
PVS1 + PS2 + PS3 + PM1 + PM2 + PP5
→
Pathogenic
1
pvs1_variant_assessmentspliceai ↗
2
pvs1_gene_contextPMID:25952305 ↗
8
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 · 6 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
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.28743e-07; MAF= 0.00006%, 1/1590474 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.62555e-07; MAF= 0.00009%, 1/1159346 alleles, homozygotes = 0).
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
6.3e-05%
· 1 / 1,590,474
0 hom
0 hom
European (non-Finnish) 1 / 1,159,346 |
8.6e-05% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Pathogenic (5 clinical laboratories). (ClinVarID = 180815)
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.99). BayesDel score = 0.393226.
Functional
No data
No calibrated functional assay or RNA evidence was identified for this variant.
COSMIC
Somatic evidence
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV50635311, n = 8 times).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
Molecular Diversity and Associated Phenotypic Spectrum of Germline CBL Mutations.
Searched
c.1096-1G>T1096-1G
Found
Reports c.1096-1G>T as a de novo heterozygous splice site variant in a boy (case 827-10) with prenatal pleural effusions/hydrops, severe feeding difficulties, failure to thrive, short stature, hypotonia, psychomotor retardation, splenomegaly, and mild pulmonary valve stenosis. Minigene assay in COS1 cells demonstrated that c.1096-1G>T causes complete skipping of exon 8, which encodes the linker region and RING finger domain. Parental DNA confirmed de novo origin.
Variant
✓ Names this variant — characterised directly
Applied to
→PM1 supports · met
→PS2 supports · met
→PS3 supports · met
→PVS1 supports · met
Why
Key paper providing de novo evidence, functional confirmation of exon 8 skipping, and clinical phenotype. Referenced in PVS1, PS2, PS3, PM1, and PP4 assessments.
The c.1096-1G>T transversion found in case 827-10 had not been previously described... Sequencing of the processed transcript RT-PCR products revealed aberrant splicing of the mutant allele, resulting in loss of the entire exon 8.
Location Results: Mutation analysis (paragraphs 1-3); Molecular characterization of splice site mutations (paragraph 2); Clinical features (paragraph 4); Figure 2B · Context Minigene assay using pSPL3 exon trapping vector, transiently transfected in COS1 cells · full text
Unexpected Findings in a Child with Atypical Hemolytic Uremic Syndrome: An Example of How Genomics Is Changing the Clinical Diagnostic Paradigm.
Searched
c.1096-1G>T1096-1G
Found
Reports a de novo heterozygous CBL c.1096-1G>T splice site variant identified by whole-genome sequencing in a child with atypical hemolytic uremic syndrome. The variant was predicted pathogenic and considered the likely explanation for RASopathy features. The paper highlights the expanding clinical spectrum of CBL-related disorders.
Variant
✓ Names this variant — characterised directly
Applied to
→PS2 supports · met
Why
Provides a second independent de novo observation, supporting PS2 at strong level.
Filtering parameters reduced 51 variants to one heterozygous splicing variant in CBL (c.1096-1G>T) predicted to be pathogenic following application of the American College of Medical Genetics and Genomics guidelines.
Location Case presentation; Figure 1 legend · full text
Sources & reference links
Triaged references · 7 PMIDs not cited in assessment
20694012 ↗
Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia.
CLINVAR
24033266 ↗
A systematic approach to assessing the clinical significance of genetic variants.
CLINVAR
25741868 ↗
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
CLINVAR
25173338 ↗
2014 ESC Guidelines on diagnosis and management of hypertrophic cardiomyopathy: the Task Force for the Diagnosis and Management of Hypertrophic Cardiomyopathy of the European Society of Cardiology (ESC).
CLINVAR