DSPP p.Asp1086=
c.3258T>C · VCV3910406
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.173%, 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 -20 | GERP -1.6 |
| Overall | ||
| CADD | 0.578 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
East Asian · 42/24,306 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.117%
Overall
0.0635%
421/662,680 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.173% | 579 |
| Admixed American | 0.146% | 686 |
| Remaining individualsnot grpmax-eligible | 0.0929% | 1,077 |
| Finnishnot grpmax-eligible | 0.0634% | 1,577 |
| South Asian | 0.0569% | 1,758 |
| European (non-Finnish) | 0.0563% | 1,777 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0463% | 2,160 |
| Middle Eastern | 0.0331% | 3,018 |
| African / African-American | 0.0254% | 3,930 |
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.Asp1086=
- Coding
- c.3258T>C
- Type
- single nucleotide variant
- Location
- chr4:87615920 (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-asp1086 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown