ABHD5 p.Ala11=
c.33C>T · rs762881363 · VCV1558149
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0038%, nfe)
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 -0.55 | GERP -2.6 |
| Overall | ||
| CADD | 2.505 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0038%
European (non-Finnish) · 44/1,157,006 alleles
Filtering AF
0.00288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00257%
Overall
0.00333%
47/1,410,880 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0038% | 26,296 |
| East Asian | 0.00258% | 38,782 |
| Admixed American | 0.00185% | 54,130 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,146 |
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
- ABHD5
- Protein
- p.Ala11=
- Coding
- c.33C>T
- MANE Select
- NM_016006
- dbSNP
- rs762881363
- Type
- single nucleotide variant
- Location
- chr3:43691025 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.62
Similar variants
- ABHD5 c.133+1G>A Likely pathogenic ★★ same type
- ABHD5 c.507-1G>A Pathogenic ★★ same type
- ABHD5 p.Arg184Ter Pathogenic ★★ same type
- ABHD5 p.Arg234Ter Pathogenic ★★ same type
- ABHD5 p.Arg280Ter Pathogenic/Likely pathogenic ★★ same type
- ABHD5 p.Glu336Ter Pathogenic/Likely pathogenic ★★ same type
- ABHD5 p.Arg56His Uncertain significance ★★ ⚠ same type
- ABHD5 p.Asp12Asn 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/abhd5-p-ala11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown