ASXL1 p.Val978=
c.2934G>A · rs759483182 · VCV750604
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Conditions
1
Inborn genetic diseases
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 -2.8 | GERP -3.8 |
| Overall | ||
| CADD | 0.052 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,020 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.00112%
18/1,614,124 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,010 |
| European (non-Finnish) | 0.00136% | 73,753 |
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
- Protein
- p.Val978=
- Coding
- c.2934G>A
- MANE Select
- NM_015338
- dbSNP
- rs759483182
- Type
- single nucleotide variant
- Location
- chr20:32435646 (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.Arg1415Ter Pathogenic ★★ same condition
- ASXL1 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
- ASXL1 p.Ala1002Asp Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1002Pro Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1041Val Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1172Val Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala1199Thr Uncertain significance ★★ ⚠ same condition
- ASXL1 p.Ala492Asp Uncertain significance ★★ ⚠ 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/asxl1-p-val978 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown