ACSM1 p.Ser201=
c.603G>A · rs143859924 · VCV747986
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -3.7 |
| Overall | ||
| CADD | 3.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/75,004 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00254%
41/1,612,828 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,167 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,197 |
| South Asian | 0.0022% | 45,510 |
| European (non-Finnish) | 0.00161% | 62,099 |
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
- ACSM1
- Protein
- p.Ser201=
- Coding
- c.603G>A
- MANE Select
- NM_001318890
- dbSNP
- rs143859924
- Type
- single nucleotide variant
- Location
- chr16:20682264 (GRCh38)
- Gene constraint
- LOEUF 1.248 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.80
Similar variants
- ACSM1 p.Lys258Arg Benign ★★ ⚠ same type
- ACSM1 p.Ala285Val Uncertain significance ★ ⚠ same type
- ACSM1 p.Ala336Val Uncertain significance ★ ⚠ same type
- ACSM1 p.Ala37Val Uncertain significance ★ ⚠ same type
- ACSM1 p.Ala493Gly Uncertain significance ★ ⚠ same type
- ACSM1 p.Ala495Val Uncertain significance ★ ⚠ same type
- ACSM1 p.Ala60Pro Uncertain significance ★ ⚠ same type
- ACSM1 p.Arg153Gln 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/acsm1-p-ser201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown