CHST7 p.Asp266=
c.798T>C · rs146831351 · VCV773924
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.79%, sas)
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 0.28 | GERP -0.99, phastCons 0.99 |
| Overall | ||
| CADD | 11.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.79%
South Asian · 2,134/56,274 alleles
Filtering AF
3.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.6%
Overall
0.332%
4,012/1,208,383 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.79% | 26 |
| African / African-American | 1.27% | 79 |
| East Asian | 1.18% | 85 |
| Remaining individualsnot grpmax-eligible | 0.595% | 168 |
| Finnishnot grpmax-eligible | 0.499% | 200 |
| Middle Eastern | 0.299% | 335 |
| Admixed American | 0.0502% | 1,992 |
| European (non-Finnish) | 0.0221% | 4,516 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00455% | 21,977 |
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
- CHST7
- Protein
- p.Asp266=
- Coding
- c.798T>C
- MANE Select
- NM_019886
- dbSNP
- rs146831351
- Type
- single nucleotide variant
- Location
- chrX:46574729 (GRCh38)
- Structure
- AlphaFold pLDDT 80.60
Similar variants
- CHST7 p.Ala172Thr Uncertain significance ★ ⚠ same type
- CHST7 p.Ala337Thr Uncertain significance ★ ⚠ same type
- CHST7 p.Ala413Ser Uncertain significance ★ ⚠ same type
- CHST7 p.Ala413Thr Uncertain significance ★ ⚠ same type
- CHST7 p.Ala453Val Uncertain significance ★ ⚠ same type
- CHST7 p.Arg323Cys Uncertain significance ★ same type
- CHST7 p.Arg354Ser Uncertain significance ★ same type
- CHST7 p.Arg367Gln 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/chst7-p-asp266 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown