DNAH9 p.His588=
c.1764C>T · rs8065057 · VCV1535134
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.59%, 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 -2 | GERP -5.1 |
| Overall | ||
| CADD | 3.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.59%
African / African-American · 3,441/74,998 alleles
Filtering AF
4.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.41%
Overall
0.266%
4,301/1,614,006 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.59% | 22 |
| Ashkenazi Jewishnot grpmax-eligible | 0.79% | 127 |
| Middle Eastern | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.426% | 235 |
| Admixed American | 0.345% | 290 |
| South Asian | 0.022% | 4,553 |
| European (non-Finnish) | 0.00864% | 11,568 |
| East Asian | 0.00668% | 14,960 |
| 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
- DNAH9
- Protein
- p.His588=
- Coding
- c.1764C>T
- MANE Select
- NM_001372
- dbSNP
- rs8065057
- Type
- single nucleotide variant
- Location
- chr17:11636762 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI <0.01 (gnomAD)
- Residue 588
- the 'stem' region
Similar variants
- DNAH9 p.His588Gln Uncertain significance ★ ⚠ same residue
- DNAH9 c.11406+1G>T Likely pathogenic ★★ same type
- DNAH9 c.1901+1G>A Likely pathogenic ★★ same type
- DNAH9 c.2928+1G>A Likely pathogenic ★★ same type
- DNAH9 c.5709+1G>T Likely pathogenic ★★ same type
- DNAH9 c.615-2A>G Likely pathogenic ★★ same type
- DNAH9 c.6847+1G>A Likely pathogenic ★★ same type
- DNAH9 p.Arg1344Ter Pathogenic/Likely pathogenic ★★ 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/dnah9-p-his588 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown