DSTYK c.654+7A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00828%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -4.3 |
| Non-coding constraint | Z 3.33 | 1 kb window · o/e 0.77 · regional · uncalibrated |
| Overall | ||
| CADD | 4.311 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00828%
European (non-Finnish) · 97/1,171,432 alleles
Filtering AF
0.00694%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00638%
Overall
0.00637%
102/1,600,144 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00828% | 12,077 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 30,919 |
| East Asian | 0.00224% | 44,672 |
| African / African-American | 0.00134% | 74,672 |
| South Asian | 0.00112% | 89,420 |
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
- DSTYK
- Coding
- c.654+7A>G
- MANE Select
- NM_015375
- dbSNP
- rs544826736
- Type
- single nucleotide variant
- Location
- chr1:205187411 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.02
Similar variants
- DSTYK p.Ala206Val Uncertain significance ★★ ⚠ same type
- DSTYK p.Ala477Ser Uncertain significance ★★ ⚠ same type
- DSTYK p.Ala601Val Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg411Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg462Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg471Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg626Gln Uncertain significance ★★ ⚠ same type
- DSTYK p.Arg635His 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/dstyk-c-654-plus-7a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown