DNAI3 p.Val19=
c.57A>G · rs373932758 · VCV735408
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0831%, nfe)
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 -1.4 | GERP -2.5 |
| Overall | ||
| CADD | 0.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0831%
European (non-Finnish) · 980/1,179,346 alleles
Filtering AF
0.0787%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.077%
Overall
0.0634%
1,021/1,610,924 alleles · ultra-rare
exomes 966/1,458,714 · genomes 55/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0831% | 1,203 |
| Remaining individualsnot grpmax-eligible | 0.0417% | 2,399 |
| Admixed American | 0.0118% | 8,447 |
| African / African-American | 0.00936% | 10,679 |
| Finnishnot grpmax-eligible | 0.00156% | 64,010 |
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
- DNAI3
- Protein
- p.Val19=
- Coding
- c.57A>G
- MANE Select
- NM_145172
- dbSNP
- rs373932758
- Type
- single nucleotide variant
- Location
- chr1:85071998 (GRCh38)
- Gene constraint
- LOEUF 0.879 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.17 · 1 PDB
- Residue 19
- the 'disordered' region
Similar variants
- DNAI3 c.1350+6C>A Benign ★★ same type
- DNAI3 p.Ala308Thr Benign ★★ same type
- DNAI3 p.Arg79= Benign ★★ same type
- DNAI3 p.Asp577= Benign ★★ same type
- DNAI3 p.Glu458= Likely benign ★★ same type
- DNAI3 p.Glu751= Benign ★★ same type
- DNAI3 p.His788= Benign ★★ same type
- DNAI3 p.His817= 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/dnai3-p-val19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown