CBL c.1007+9del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
Conditions
1
RASopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7 | GERP 2.1, phastCons 1 |
| Non-coding constraint | Z 3.01 | 1 kb window · o/e 0.77 · regional · uncalibrated |
| Overall | ||
| CADD | 4.985 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,908 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,613,898 alleles · very rare
exomes 1/1,461,732 · genomes 2/152,166 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CBL
- Coding
- c.1007+9del
- MANE Select
- NM_005188
- Type
- Deletion
- Location
- chr11:119276142 (GRCh38)
- Gene constraint
- LOEUF 0.622 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.27 · 34 PDB
Similar variants
- CBL c.1096-4_1096-1del Pathogenic/Likely pathogenic ★★ same condition
- CBL c.2435-1_2435del Uncertain significance ★★ same condition
- CBL p.Ile664fs Uncertain significance ★★ same condition
- CBL c.1096-9del Likely benign ★★ same condition
- CBL c.1228-20_1228-17del Benign/Likely benign ★★ same condition
- CBL c.1432-12del Benign/Likely benign ★★ same condition
- CBL c.2251+14_2251+22del Benign/Likely benign ★★ same condition
- CBL c.870-19del Benign/Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cbl-c-1007-plus-9del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown