DSPP p.Ser1094=
c.3282T>C · rs200276196 · VCV2654906
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.452%, sas)
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 -15 | GERP 1 |
| Overall | ||
| CADD | 0.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.452%
South Asian · 179/39,612 alleles
Filtering AF
0.398%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.377%
Overall
0.0521%
216/414,646 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.452% | 221 |
| African / African-American | 0.149% | 673 |
| Middle Eastern | 0.0976% | 1,025 |
| Admixed American | 0.0465% | 2,151 |
| Remaining individualsnot grpmax-eligible | 0.029% | 3,446 |
| Finnishnot grpmax-eligible | 0.00515% | 19,412 |
| European (non-Finnish) | 0.00305% | 32,786 |
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.Ser1094=
- Coding
- c.3282T>C
- dbSNP
- rs200276196
- Type
- single nucleotide variant
- Location
- chr4:87615944 (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-ser1094 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown