STS p.His283=
c.849C>T · VCV3690457
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.102%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.67 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -13 |
| Overall | ||
| CADD | 0.037 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.102%
South Asian · 57/55,611 alleles
Filtering AF
0.0811%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0735%
Overall
0.00612%
73/1,193,572 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.102% | 976 |
| Middle Eastern | 0.0233% | 4,290 |
| African / African-American | 0.0149% | 6,726 |
| Remaining individualsnot grpmax-eligible | 0.00637% | 15,692 |
| Admixed American | 0.00453% | 22,053 |
| European (non-Finnish) | 0.000225% | 444,257 |
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
- STS
- Protein
- p.His283=
- Coding
- c.849C>T
- MANE Select
- NM_001320752
- Type
- single nucleotide variant
- Location
- chrX:7275993 (GRCh38)
- Structure
- AlphaFold pLDDT 94.31 · 2 PDB
- Residue 283
- a β-strand
Similar variants
- STS p.Gly354Arg Likely pathogenic ★★ same type
- STS p.Arg381Ser Uncertain significance ★★ ⚠ same type
- STS p.Asp397Asn Uncertain significance ★★ ⚠ same type
- STS c.1082-55C>T Likely benign ★★ same type
- STS c.1082-76G>A Benign ★★ same type
- STS c.1241+15G>C Benign ★★ same type
- STS c.138-9T>G Likely benign ★★ same type
- STS c.383-16C>T Benign/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/sts-p-his283 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown