ASAH1 p.Val16=
c.48C>G · rs1315283375 · VCV2160986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, afr)
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 0.78 | GERP -1 |
| Overall | ||
| CADD | 3.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,914 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.000751%
12/1,598,228 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,324 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,750 |
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
- ASAH1
- Protein
- p.Val16=
- Coding
- c.48C>G
- MANE Select
- NM_177924
- dbSNP
- rs1315283375
- Type
- single nucleotide variant
- Location
- chr8:18084011 (GRCh38)
- Gene constraint
- LOEUF 1.435 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.97 · 2 PDB
Similar variants
- ASAH1 p.Arg16Pro Uncertain significance ★ same residue
- ASAH1 p.Val16Leu Uncertain significance ★ ⚠ same residue
- ASAH1 c.1098+1G>T Pathogenic/Likely pathogenic ★★ same type
- ASAH1 c.125+1G>A Pathogenic ★★ same type
- ASAH1 c.457+4A>G Pathogenic/Likely pathogenic ★★ same type
- ASAH1 c.648+1G>C Likely pathogenic ★★ same type
- ASAH1 c.786-2A>G Likely pathogenic ★★ same type
- ASAH1 p.Arg254Gly 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/asah1-p-val16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown