ASXL3 p.Arg769=
c.2307A>G · rs9946495 · VCV1249526
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.65%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 0.36, phastCons 1 |
| Overall | ||
| CADD | 7.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.65%
African / African-American · 4,987/75,006 alleles
Filtering AF
6.49%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.43%
Overall
0.352%
5,681/1,613,886 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.65% | 15 |
| Remaining individualsnot grpmax-eligible | 0.514% | 195 |
| Admixed American | 0.433% | 231 |
| Middle Eastern | 0.115% | 866 |
| South Asian | 0.0242% | 4,140 |
| European (non-Finnish) | 0.00712% | 14,046 |
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
- ASXL3
- Protein
- p.Arg769=
- Coding
- c.2307A>G
- MANE Select
- NM_030632
- dbSNP
- rs9946495
- Type
- single nucleotide variant
- Location
- chr18:33739711 (GRCh38)
- Gene constraint
- LOEUF 0.229 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.70
- Residue 769
- the 'disordered' region
Similar variants
- ASXL3 c.3039+1G>A Pathogenic ★★ same type
- ASXL3 p.Arg1036Ter Pathogenic/Likely pathogenic ★★ same type
- ASXL3 p.Arg1068Ter Pathogenic/Likely pathogenic ★★ same type
- ASXL3 p.Arg1117Ter Pathogenic/Likely pathogenic ★★ same type
- ASXL3 p.Arg1444Ter Pathogenic/Likely pathogenic ★★ same type
- ASXL3 p.Arg1467Ter Pathogenic ★★ same type
- ASXL3 p.Arg1560Ter Pathogenic ★★ same type
- ASXL3 p.Arg1823Ter Pathogenic/Likely 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/asxl3-p-arg769 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown