ACMSD p.Leu152=
c.456G>A · rs777997475 · VCV764622
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, 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 3.8 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 8.881 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/74,944 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00989%
Overall
0.00118%
19/1,614,086 alleles · ultra-rare
exomes 10/1,461,856 · genomes 9/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 4,996 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| Admixed American | 0.00167% | 60,014 |
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
- ACMSD
- Protein
- p.Leu152=
- Coding
- c.456G>A
- MANE Select
- NM_138326
- dbSNP
- rs777997475
- Type
- single nucleotide variant
- Location
- chr2:134863601 (GRCh38)
- Gene constraint
- LOEUF 1.063 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.67 · 6 PDB
Similar variants
- ACMSD p.Leu152Val Uncertain significance ★ same residue
- ACMSD p.Pro11= Benign ★★ same type
- ACMSD c.677-14G>T Uncertain significance ★ same type
- ACMSD c.948+1G>A Uncertain significance ★ same type
- ACMSD p.Ala101Thr Uncertain significance ★ ⚠ same type
- ACMSD p.Ala121Val Uncertain significance ★ ⚠ same type
- ACMSD p.Ala154Val Uncertain significance ★ ⚠ same type
- ACMSD p.Ala162Val 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/acmsd-p-leu152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown