Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 98%, eas) — too common for a highly-penetrant pathogenic allele
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 -0.24 | GERP -3.5 |
| Overall | ||
| CADD | 3.752 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
98%
East Asian · 32,819/33,474 alleles
Filtering AF
97.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96.8%
Overall
66.4%
800,140/1,205,210 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 98% | 1 |
| South Asian | 80.6% | 1 |
| Admixed American | 77.9% | 1 |
| Finnishnot grpmax-eligible | 67.6% | 1 |
| Remaining individualsnot grpmax-eligible | 67.1% | 1 |
| Amishnot grpmax-eligible | 65.8% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 64.2% | 2 |
| European (non-Finnish) | 64.1% | 2 |
| Middle Eastern | 60.6% | 2 |
| African / African-American | 60.3% | 2 |
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
- ARSH
- Protein
- p.Leu317=
- Coding
- c.949T>C
- MANE Select
- NM_001011719
- dbSNP
- rs5939407
- Type
- single nucleotide variant
- Location
- chrX:3024068 (GRCh38)
- Structure
- AlphaFold pLDDT 94.15
Similar variants
- ARSH p.Arg358Cys Benign ★★ ⚠ same type
- ARSH p.Arg37His Benign ★★ ⚠ same type
- ARSH p.Met408Ile Benign ★★ same type
- ARSH p.Pro144Thr Benign ★★ ⚠ same type
- ARSH p.Ala100Thr Uncertain significance ★ ⚠ same type
- ARSH p.Ala14Thr Uncertain significance ★ ⚠ same type
- ARSH p.Ala175Val Uncertain significance ★ ⚠ same type
- ARSH p.Ala187Thr 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/arsh-p-leu317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown