DPP6 c.51+164609G>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 17.9%, afr) — 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 +164609 | deep intronic (+164609 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.86 | GERP 1.5, phastCons 0.026 |
| Non-coding constraint | Z 4.78 | 1 kb window · o/e 0.72 · regional · uncalibrated |
| Overall | ||
| CADD | 7.054 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
17.9%
African / African-American · 7,429/41,510 alleles
Filtering AF
17.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.4%
Overall
5.19%
7,983/153,764 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 17.9% | 6 |
| Remaining individualsnot grpmax-eligible | 3.63% | 28 |
| Admixed American | 2.17% | 46 |
| Ashkenazi Jewishnot grpmax-eligible | 1.23% | 81 |
| Middle Eastern | 1.01% | 99 |
| South Asian | 0.241% | 414 |
| European (non-Finnish) | 0.12% | 834 |
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
- DPP6
- Coding
- c.51+164609G>C
- MANE Select
- NM_130797 · reported on NM_001039350
- dbSNP
- rs7798068
- Type
- single nucleotide variant
- Location
- chr7:154052343 (GRCh38)
- Gene constraint
- LOEUF 0.751 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.41 · 8 PDB
Similar variants
- DPP6 p.Gly65Cys Uncertain significance ★★ ⚠ same type
- DPP6 p.Gly65Val Uncertain significance ★★ ⚠ same type
- DPP6 p.Lys223Arg Uncertain significance ★★ ⚠ same type
- DPP6 p.Pro229Thr Uncertain significance ★★ ⚠ same type
- DPP6 c.1261-188G>A Benign ★★ same type
- DPP6 c.1261-48G>A Benign ★★ same type
- DPP6 c.1299+147A>G Benign ★★ same type
- DPP6 c.1299+200A>G Benign ★★ 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/dpp6-c-51-plus-164609g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown