DST p.Pro98=
c.294C>T · rs78633225 · VCV1279553
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 6.64%, afr) — too common for a highly-penetrant pathogenic allele
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 -8.6 | GERP -2.9 |
| Overall | ||
| CADD | 0.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.64%
African / African-American · 4,504/67,798 alleles
Filtering AF
6.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.42%
Overall
0.377%
5,156/1,367,594 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.64% | 15 |
| Admixed American | 0.573% | 175 |
| Remaining individualsnot grpmax-eligible | 0.455% | 220 |
| Middle Eastern | 0.44% | 227 |
| South Asian | 0.0295% | 3,386 |
| East Asian | 0.0091% | 10,995 |
| European (non-Finnish) | 0.00891% | 11,229 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00491% | 20,366 |
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
- Protein
- p.Pro98=
- Coding
- c.294C>T
- MANE Select
- NM_001374736
- dbSNP
- rs78633225
- Type
- single nucleotide variant
- Location
- chr6:56900544 (GRCh38)
- Gene constraint
- LOEUF 0.297 · pLI 1.00 (gnomAD)
- Residue 98
- the calponin-homology (ch) 1 domain; the 'actin-binding' region
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-p-pro98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown