ABHD5 p.Asp346=
c.1038C>T · rs368305449 · VCV1916698
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00212%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.119 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -0.98, phastCons 0.14 |
| Overall | ||
| CADD | 7.379 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00212%
European (non-Finnish) · 25/1,179,950 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00155%
25/1,613,946 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
- ABHD5
- Protein
- p.Asp346=
- Coding
- c.1038C>T
- MANE Select
- NM_016006
- dbSNP
- rs368305449
- Type
- single nucleotide variant
- Location
- chr3:43718520 (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-asp346 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown