Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 72.5%, afr) — too common for a highly-penetrant pathogenic allele
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 | 1.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
72.5%
African / African-American · 54,304/74,910 alleles
Filtering AF
72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 71.8%
Overall
31.6%
509,028/1,613,356 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 72.5% | 1 |
| Finnishnot grpmax-eligible | 36% | 3 |
| Remaining individualsnot grpmax-eligible | 32.4% | 3 |
| South Asian | 31.3% | 3 |
| European (non-Finnish) | 29.9% | 3 |
| Middle Eastern | 29.3% | 3 |
| Amishnot grpmax-eligible | 28.5% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 25.7% | 4 |
| Admixed American | 24.5% | 4 |
| East Asian | 13.9% | 7 |
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.Glu484=
- Coding
- c.1452A>G
- MANE Select
- NM_001372
- dbSNP
- rs9895535
- Type
- single nucleotide variant
- Location
- chr17:11629518 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI <0.01 (gnomAD)
- Residue 484
- the 'stem' region
Similar variants
- DNAH9 p.Glu484Lys 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-glu484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown