ACSM5 p.Phe55=
c.165C>T · rs370540779 · VCV2646280
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0994%, mid)
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 -0.15 | GERP -3.4, phastCons 0.8 |
| Overall | ||
| CADD | 10.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0994%
Middle Eastern · 6/6,034 alleles
Filtering AF
0.0433%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.0158%
255/1,614,120 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0994% | 1,006 |
| Finnishnot grpmax-eligible | 0.0656% | 1,525 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| East Asian | 0.0379% | 2,639 |
| South Asian | 0.0187% | 5,357 |
| European (non-Finnish) | 0.0124% | 8,082 |
| African / African-American | 0.00267% | 37,518 |
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
- ACSM5
- Protein
- p.Phe55=
- Coding
- c.165C>T
- MANE Select
- NM_017888
- dbSNP
- rs370540779
- Type
- single nucleotide variant
- Location
- chr16:20411649 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.58
Similar variants
- ACSM5 p.Pro144Leu Uncertain significance ★★ ⚠ same type
- ACSM5 c.1001+10G>A Benign ★★ same type
- ACSM5 p.His360Arg Benign ★★ same type
- ACSM5 p.Ala160Val Uncertain significance ★ ⚠ same type
- ACSM5 p.Ala163Ser Uncertain significance ★ ⚠ same type
- ACSM5 p.Arg100Ser Uncertain significance ★ ⚠ same type
- ACSM5 p.Arg157Trp Uncertain significance ★ same type
- ACSM5 p.Arg197Trp 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/acsm5-p-phe55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown