DPF2 c.465+18T>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000425%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +18 | near-intronic (+18 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.74 | GERP -0.91 |
| Non-coding constraint | Z 0.70 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 2.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000425%
European (non-Finnish) · 5/1,176,766 alleles
Filtering AF
0.000125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.1e-05%
Overall
0.000343%
5/1,458,052 alleles · very rare
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
- Coding
- c.465+18T>A
- MANE Select
- NM_006268
- Type
- single nucleotide variant
- Location
- chr11:65341580 (GRCh38)
- Gene constraint
- LOEUF 0.287 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.62 · 9 PDB
Similar variants
- 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
- DPF2 p.Arg83Trp 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-c-465-plus-18t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown