ABL1 c.253+16del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00484%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | GERP -3.1 |
| Non-coding constraint | Z 2.74 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 5.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00484%
European (non-Finnish) · 57/1,178,330 alleles
Filtering AF
0.00378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00345%
Overall
0.00354%
57/1,611,084 alleles · very rare
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
- ABL1
- Coding
- c.253+16del
- MANE Select
- NM_005157
- dbSNP
- rs1250417704
- Type
- Deletion
- Location
- chr9:130854251 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
Similar variants
- ABL1 c.1679-3del Uncertain significance ★ same type
- ABL1 p.Asp276fs Uncertain significance ★ same type
- ABL1 p.Asp391fs Uncertain significance ★ same type
- ABL1 p.Gln627fs Uncertain significance ★ same type
- ABL1 p.Glu549fs Uncertain significance ★ same type
- ABL1 p.Gly864fs Uncertain significance ★ same type
- ABL1 p.Ile360fs Uncertain significance ★ same type
- ABL1 p.Ile641del Uncertain significance ★ same type
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/abl1-c-253-plus-16del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown