DST c.21531+232A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.66%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +232 | deep intronic (+232 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -4.8 |
| Non-coding constraint | Z -0.65 | 1 kb window · o/e 1.05 · regional · uncalibrated |
| Overall | ||
| CADD | 7.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.66%
African / African-American · 1,105/41,552 alleles
Filtering AF
2.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.48%
Overall
0.781%
1,189/152,278 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.66% | 38 |
| Remaining individualsnot grpmax-eligible | 0.71% | 141 |
| Middle Eastern | 0.68% | 147 |
| Admixed American | 0.353% | 283 |
| European (non-Finnish) | 0.0191% | 5,233 |
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
- DST
- Coding
- c.21531+232A>C
- MANE Select
- NM_001374736
- dbSNP
- rs77322792
- Type
- single nucleotide variant
- Location
- chr6:56481818 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
Similar variants
- DST c.22959+1G>A Likely pathogenic ★★ same type
- DST p.Arg1512Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg1696Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Arg22Ter Likely pathogenic ★★ same type
- DST p.Arg7329Ter Pathogenic ★★ same type
- DST p.Cys1828Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Gln1124Ter Pathogenic/Likely pathogenic ★★ same type
- DST p.Gln1366Ter Pathogenic/Likely pathogenic ★★ 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/dst-c-21531-plus-232a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown