CHST7 p.His421=
c.1263C>T · rs1019139690 · VCV2660386
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.205%, afr)
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 -0.072 | GERP -3.7, phastCons 0.12 |
| Overall | ||
| CADD | 8.268 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.205%
African / African-American · 107/52,076 alleles
Filtering AF
0.174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.162%
Overall
0.0114%
126/1,102,389 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.205% | 487 |
| Middle Eastern | 0.0629% | 1,591 |
| Remaining individualsnot grpmax-eligible | 0.0185% | 5,419 |
| Admixed American | 0.00663% | 15,082 |
| South Asian | 0.00216% | 46,268 |
| European (non-Finnish) | 0.000705% | 141,764 |
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.His421=
- Coding
- c.1263C>T
- MANE Select
- NM_019886
- dbSNP
- rs1019139690
- Type
- single nucleotide variant
- Location
- chrX:46575194 (GRCh38)
- Structure
- AlphaFold pLDDT 80.60
Similar variants
- CHST7 p.Asp266= Benign ★★ same type
- 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
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-his421 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown