DSPP p.Ser1070=
c.3210T>C · rs878944356 · VCV3025314
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0271%, 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 -20 | GERP -2 |
| Overall | ||
| CADD | 0.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0271%
South Asian · 22/81,238 alleles
Filtering AF
0.0183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0155%
Overall
0.00712%
108/1,516,118 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0271% | 3,693 |
| East Asian | 0.0206% | 4,866 |
| Finnishnot grpmax-eligible | 0.0175% | 5,701 |
| Admixed American | 0.0167% | 6,006 |
| African / African-American | 0.014% | 7,122 |
| Remaining individualsnot grpmax-eligible | 0.00509% | 19,652 |
| European (non-Finnish) | 0.00415% | 24,113 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00357% | 27,982 |
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.Ser1070=
- Coding
- c.3210T>C
- dbSNP
- rs878944356
- Type
- single nucleotide variant
- Location
- chr4:87615872 (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-ser1070 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown