DSPP p.Asp1107=
c.3321T>C · rs374679002 · VCV1273251
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.55%, eas) — 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 | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -2 |
| Overall | ||
| CADD | 1.635 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.55%
East Asian · 1,376/14,402 alleles
Filtering AF
9.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.97%
Overall
4.75%
21,545/453,940 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 9.55% | 10 |
| Finnishnot grpmax-eligible | 8.55% | 12 |
| Admixed American | 6.39% | 16 |
| Remaining individualsnot grpmax-eligible | 5.57% | 18 |
| European (non-Finnish) | 4.57% | 22 |
| South Asian | 3.2% | 31 |
| Ashkenazi Jewishnot grpmax-eligible | 2.98% | 34 |
| African / African-American | 2.6% | 38 |
| Middle Eastern | 2.3% | 43 |
| Amishnot grpmax-eligible | 1.79% | 56 |
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.Asp1107=
- Coding
- c.3321T>C
- dbSNP
- rs374679002
- Type
- single nucleotide variant
- Location
- chr4:87615983 (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-asp1107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown