DST c.954+65A>G
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 22.5%, nfe) — 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 | ||
| Splice region | donor +65 | deep intronic (+65 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -0.71 |
| Overall | ||
| CADD | 5.743 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.5%
European (non-Finnish) · 146,985/653,896 alleles
Filtering AF
22.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.3%
Overall
18.1%
181,259/999,648 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 22.5% | 4 |
| Amishnot grpmax-eligible | 20.8% | 5 |
| Middle Eastern | 18.4% | 5 |
| Finnishnot grpmax-eligible | 17.7% | 6 |
| Remaining individualsnot grpmax-eligible | 17.5% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 14.4% | 7 |
| Admixed American | 10.5% | 10 |
| South Asian | 7.05% | 14 |
| African / African-American | 3.77% | 27 |
| East Asian | 0.0475% | 2,106 |
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.954+65A>G
- MANE Select
- NM_001374736
- dbSNP
- rs13206849
- Type
- single nucleotide variant
- Location
- chr6:56701823 (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-954-plus-65a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown