ASXL1 c.252+11del
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.449%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +11 | near-intronic (+11 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 1.4 |
| Overall | ||
| CADD | 1.109 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.449%
Admixed American · 269/59,972 alleles
Filtering AF
0.404%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.387%
Overall
0.0172%
274/1,589,850 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.449% | 223 |
| Remaining individualsnot grpmax-eligible | 0.0081% | 12,342 |
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
- ASXL1
- Coding
- c.252+11del
- MANE Select
- NM_015338
- dbSNP
- rs758156686
- Type
- Deletion
- Location
- chr20:32369134 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 42.74 · 4 PDB
Similar variants
- ASXL1 p.Arg774_Leu775insTer Pathogenic/Likely pathogenic ★★ same type
- ASXL1 p.Gly645fs Likely pathogenic ★★ same type
- ASXL1 p.Leu1425fs Uncertain significance ★★ same type
- ASXL1 c.57+3758_141-394del Likely pathogenic ★ same type
- ASXL1 p.Ala1257fs Likely pathogenic ★ same type
- ASXL1 p.Ala716fs Pathogenic ★ same type
- ASXL1 p.Asp1049fs Pathogenic ★ same type
- ASXL1 p.Asp457fs Pathogenic ★ 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/asxl1-c-252-plus-11del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown