DNER p.Arg698=
c.2094G>A · rs111685443 · VCV716764
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.04%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 9.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.04%
African / African-American · 1,532/75,056 alleles
Filtering AF
1.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.92%
Overall
0.105%
1,702/1,614,128 alleles · low-frequency
exomes 838/1,461,810 · genomes 864/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.04% | 49 |
| Remaining individualsnot grpmax-eligible | 0.138% | 727 |
| Admixed American | 0.102% | 984 |
| Middle Eastern | 0.0498% | 2,009 |
| South Asian | 0.0121% | 8,279 |
| European (non-Finnish) | 0.000763% | 131,114 |
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
- DNER
- Protein
- p.Arg698=
- Coding
- c.2094G>A
- MANE Select
- NM_139072
- dbSNP
- rs111685443
- Type
- single nucleotide variant
- Location
- chr2:229366881 (GRCh38)
- Gene constraint
- LOEUF 0.561 · pLI 0.21 (gnomAD)
- Structure
- AlphaFold pLDDT 70.51
Similar variants
- DNER p.Arg698Gln Uncertain significance ★ same residue
- DNER c.586-10C>T Benign ★★ same type
- DNER p.Pro180= Benign ★★ same type
- DNER p.Thr142Ile Benign ★★ same type
- DNER p.Ala11Val Uncertain significance ★ ⚠ same type
- DNER p.Ala171Thr Uncertain significance ★ ⚠ same type
- DNER p.Ala205Thr Uncertain significance ★ ⚠ same type
- DNER p.Ala234Thr 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/dner-p-arg698 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown