ARSF p.Thr55=
c.165G>A · rs369770883 · VCV3042994
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0113%, amr)
Conditions
1
ARSF-related disorder
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 -20 | GERP -3.1 |
| Overall | ||
| CADD | 0.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0113%
Admixed American · 5/44,168 alleles
Filtering AF
0.0044%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0029%
Overall
0.00108%
13/1,199,483 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0113% | 8,834 |
| Remaining individualsnot grpmax-eligible | 0.00212% | 47,255 |
| South Asian | 0.00181% | 55,357 |
| European (non-Finnish) | 0.000673% | 148,483 |
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
- ARSF
- Protein
- p.Thr55=
- Coding
- c.165G>A
- MANE Select
- NM_001201539
- dbSNP
- rs369770883
- Type
- single nucleotide variant
- Location
- chrX:3076551 (GRCh38)
- Structure
- AlphaFold pLDDT 90.98
Disease context
ARSF-related disorder
Similar variants
- ARSF c.12-10T>G Uncertain significance same condition
- ARSF p.Gly113Ala Uncertain significance ⚠ same condition
- ARSF p.Ala481= Likely benign same condition
- ARSF p.Arg179Cys Likely benign ⚠ same condition
- ARSF p.Arg335Lys Benign same condition
- ARSF p.Gly230Asp Benign same condition
- ARSF p.Ser239Tyr Likely benign same condition
- ARSF c.1102+5G>A Likely benign ★★ 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/arsf-p-thr55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown