CHST8 p.Arg9=
c.27G>A · rs62103464 · VCV774526
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, 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 4.5 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 8.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
Middle Eastern · 78/6,032 alleles
Filtering AF
1.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.977%
Overall
0.829%
13,313/1,605,692 alleles · low-frequency
exomes 12,385/1,453,418 · genomes 928/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.29% | 77 |
| Ashkenazi Jewishnot grpmax-eligible | 1.28% | 78 |
| Finnishnot grpmax-eligible | 1.11% | 90 |
| European (non-Finnish) | 0.914% | 109 |
| Remaining individualsnot grpmax-eligible | 0.79% | 127 |
| Amishnot grpmax-eligible | 0.658% | 152 |
| South Asian | 0.6% | 167 |
| Admixed American | 0.467% | 214 |
| African / African-American | 0.126% | 795 |
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
- CHST8
- Protein
- p.Arg9=
- Coding
- c.27G>A
- MANE Select
- NM_001127895
- dbSNP
- rs62103464
- Type
- single nucleotide variant
- Location
- chr19:33689288 (GRCh38)
- Gene constraint
- LOEUF 1.001 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.90
Similar variants
- CHST8 p.Val186Ala Uncertain significance ★★ ⚠ same type
- CHST8 c.168+64G>A Benign ★★ same type
- CHST8 c.-86-36C>T Benign ★★ same type
- CHST8 p.Leu288= Benign ★★ same type
- CHST8 p.Ala23Gly Uncertain significance ★ ⚠ same type
- CHST8 p.Ala293Pro Uncertain significance ★ ⚠ same type
- CHST8 p.Ala293Ser Uncertain significance ★ ⚠ same type
- CHST8 p.Ala381Thr 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/chst8-p-arg9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown