DSPP p.Ser1109=
c.3327T>C · rs765088892 · VCV1221801
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.39%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -1.8 |
| Overall | ||
| CADD | 1.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.39%
East Asian · 622/14,166 alleles
Filtering AF
4.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.99%
Overall
0.931%
4,445/477,388 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.39% | 23 |
| African / African-American | 1.77% | 57 |
| Finnishnot grpmax-eligible | 1.55% | 65 |
| Admixed American | 1.16% | 87 |
| Remaining individualsnot grpmax-eligible | 1.05% | 95 |
| European (non-Finnish) | 0.756% | 132 |
| Ashkenazi Jewishnot grpmax-eligible | 0.696% | 144 |
| Middle Eastern | 0.579% | 173 |
| South Asian | 0.427% | 234 |
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
- DSPP
- Protein
- p.Ser1109=
- Coding
- c.3327T>C
- dbSNP
- rs765088892
- Type
- single nucleotide variant
- Location
- chr4:87615989 (GRCh38)
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/dspp-p-ser1109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown