Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.84%, sas)
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 5.9 | GERP -0.43, phastCons 1 |
| Overall | ||
| CADD | 11.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.84%
South Asian · 2,585/91,070 alleles
Filtering AF
2.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.71%
Overall
0.326%
5,256/1,613,854 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.84% | 35 |
| African / African-American | 2.6% | 38 |
| Ashkenazi Jewishnot grpmax-eligible | 0.743% | 135 |
| Remaining individualsnot grpmax-eligible | 0.414% | 241 |
| Middle Eastern | 0.33% | 303 |
| Admixed American | 0.194% | 516 |
| East Asian | 0.0178% | 5,611 |
| European (non-Finnish) | 0.00831% | 12,040 |
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
- DNAJB1
- Protein
- p.Val288=
- Coding
- c.864T>C
- MANE Select
- NM_006145
- dbSNP
- rs2230251
- Type
- single nucleotide variant
- Location
- chr19:14516099 (GRCh38)
- Gene constraint
- LOEUF 0.953 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.71 · 15 PDB
- Residue 288
- an α-helix
Similar variants
- DNAJB1 p.Asn272= Benign ★★ same type
- DNAJB1 p.Ala265Val Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg119Gln Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg13Cys Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg26Leu Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg290Ser Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg294Trp Uncertain significance ★ ⚠ same type
- DNAJB1 p.Arg30Cys 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/dnajb1-p-val288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown