DPP3 c.271-5C>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.705%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -5 | acceptor splice region (-5, within the last 20 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.18 | GERP -1.2 |
| Non-coding constraint | Z 1.41 | 1 kb window · o/e 0.90 · regional · uncalibrated |
| Overall | ||
| CADD | 3.222 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.705%
African / African-American · 529/75,050 alleles
Filtering AF
0.655%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.636%
Overall
0.044%
710/1,614,098 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.705% | 142 |
| Middle Eastern | 0.183% | 548 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Admixed American | 0.0567% | 1,765 |
| South Asian | 0.00769% | 13,010 |
| European (non-Finnish) | 0.00525% | 19,032 |
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
- DPP3
- Coding
- c.271-5C>A
- MANE Select
- NM_130443
- dbSNP
- rs187082477
- Type
- single nucleotide variant
- Location
- chr11:66485168 (GRCh38)
- Gene constraint
- LOEUF 0.827 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.56 · 10 PDB
Similar variants
- DPP3 p.Arg76His Benign ★★ ⚠ same type
- DPP3 p.Leu163Met Benign ★★ ⚠ same type
- DPP3 p.Lys423= Benign ★★ same type
- DPP3 p.Phe331= Benign ★★ same type
- DPP3 p.Phe443= Benign ★★ same type
- DPP3 p.Thr401= Benign ★★ same type
- DPP3 c.573+1G>A Uncertain significance ★ same type
- DPP3 p.Ala22Gly Uncertain significance ★ ⚠ same type
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/dpp3-c-271-minus-5c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown