DPF2 p.Asn7=
c.21T>C · rs146359123 · VCV1632492
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.183%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.88 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.183%
East Asian · 82/44,856 alleles
Filtering AF
0.151%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.139%
Overall
0.0108%
174/1,613,858 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.183% | 547 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,314 |
| South Asian | 0.0351% | 2,846 |
| Middle Eastern | 0.033% | 3,031 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,918 |
| European (non-Finnish) | 0.0022% | 45,382 |
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
- DPF2
- Protein
- p.Asn7=
- Coding
- c.21T>C
- MANE Select
- NM_006268
- dbSNP
- rs146359123
- Type
- single nucleotide variant
- Location
- chr11:65333907 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.62 · 9 PDB
Similar variants
- DPF2 p.Asn7Asp Uncertain significance ★ ⚠ same residue
- DPF2 c.904+1G>A Pathogenic ★★ same type
- DPF2 p.Arg350His Pathogenic/Likely pathogenic ★★ same type
- DPF2 p.Asp346Asn Likely pathogenic ★★ same type
- DPF2 p.Asp349Asn Pathogenic/Likely pathogenic ★★ same type
- DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same type
- DPF2 p.Arg38His Uncertain significance ★★ ⚠ same type
- DPF2 p.Arg77Gln 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/dpf2-p-asn7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown