DHX9 p.Ile903=
c.2709C>T · rs201506072 · VCV773289
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, mid)
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 -0.33 | GERP -3.5, phastCons 0.1 |
| Overall | ||
| CADD | 4.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
Middle Eastern · 72/6,062 alleles
Filtering AF
0.967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.886%
Overall
0.367%
5,920/1,614,172 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.19% | 84 |
| South Asian | 0.627% | 160 |
| Remaining individualsnot grpmax-eligible | 0.446% | 224 |
| European (non-Finnish) | 0.383% | 261 |
| Ashkenazi Jewishnot grpmax-eligible | 0.382% | 262 |
| Admixed American | 0.275% | 364 |
| Finnishnot grpmax-eligible | 0.22% | 454 |
| African / African-American | 0.0693% | 1,443 |
| East Asian | 0.00669% | 14,957 |
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
- DHX9
- Protein
- p.Ile903=
- Coding
- c.2709C>T
- MANE Select
- NM_001357
- dbSNP
- rs201506072
- Type
- single nucleotide variant
- Location
- chr1:182881348 (GRCh38)
- Gene constraint
- LOEUF 0.263 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.84 · 7 PDB
- Residue 903
- the 'necessary for interaction with h2ax' region; the 'ha2' region; an α-helix; a UniProt-annotated variant site (in mrd75; likely pathogenic)
Similar variants
- DHX9 p.Ala355Thr Uncertain significance ★★ ⚠ same type
- DHX9 p.Asn1133His Uncertain significance ★★ ⚠ same type
- DHX9 p.Pro586Ala Uncertain significance ★★ ⚠ same type
- DHX9 c.364+6G>T Benign ★★ same type
- DHX9 p.Leu244= Benign ★★ same type
- DHX9 p.Tyr875= Benign ★★ same type
- DHX9 c.1141-1G>A Likely pathogenic ★ same type
- DHX9 c.1557+1G>A 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/dhx9-p-ile903 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown