Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.31%, 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 | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.24 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.62 | GERP -5.5 |
| Non-coding constraint | Z 2.44 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 6.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.31%
East Asian · 2,384/44,856 alleles
Filtering AF
5.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.06%
Overall
0.267%
4,307/1,612,816 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 5.31% | 19 |
| Admixed American | 1.53% | 66 |
| South Asian | 0.244% | 410 |
| Remaining individualsnot grpmax-eligible | 0.219% | 456 |
| Middle Eastern | 0.0992% | 1,008 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0913% | 1,095 |
| African / African-American | 0.0521% | 1,921 |
| European (non-Finnish) | 0.0479% | 2,087 |
| Finnishnot grpmax-eligible | 0.0203% | 4,923 |
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
- DPP4
- Coding
- c.1987+4T>C
- MANE Select
- NM_001935
- dbSNP
- rs2268891
- Type
- single nucleotide variant
- Location
- chr2:162008558 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.45 · 121 PDB
Similar variants
- DPP4 p.Ala16= Benign ★★ same type
- DPP4 p.Gly645= Benign ★★ same type
- DPP4 p.Leu27= Benign ★★ same type
- DPP4 p.Lys539= Likely benign ★★ same type
- DPP4 p.Ser437Thr Benign ★★ ⚠ same type
- DPP4 p.Val266Ile Likely benign ★★ ⚠ same type
- DPP4 p.Ala654Thr Uncertain significance ★ ⚠ same type
- DPP4 p.Ala81Thr 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/dpp4-c-1987-plus-4t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown