DNHD1 p.His1150=
c.3450T>C · rs563776321 · VCV3038951
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.41%, sas)
Conditions
1
DNHD1-related disorder
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 -3.8 | GERP -3.5 |
| Overall | ||
| CADD | 0.221 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.41%
South Asian · 345/84,066 alleles
Filtering AF
0.375%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.361%
Overall
0.0243%
377/1,551,738 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.41% | 244 |
| Middle Eastern | 0.0501% | 1,997 |
| Remaining individualsnot grpmax-eligible | 0.0283% | 3,536 |
| Admixed American | 0.0118% | 8,502 |
| East Asian | 0.00244% | 40,916 |
| African / African-American | 0.00137% | 73,188 |
| European (non-Finnish) | 0.000349% | 286,747 |
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
- DNHD1
- Protein
- p.His1150=
- Coding
- c.3450T>C
- MANE Select
- NM_144666
- dbSNP
- rs563776321
- Type
- single nucleotide variant
- Location
- chr11:6539905 (GRCh38)
- Gene constraint
- LOEUF 0.897 · pLI <0.01 (gnomAD)
Disease context
DNHD1-related disorder
Similar variants
- DNHD1 p.Glu4486Lys Uncertain significance ★★ ⚠ same condition
- DNHD1 p.His4162Leu Uncertain significance ★★ ⚠ same condition
- DNHD1 p.Arg2840Gln Uncertain significance ★ ⚠ same condition
- DNHD1 p.Gln895Ter Conflicting classifications of pathogenicity ★ same condition
- DNHD1 p.His3335Arg Uncertain significance ★ ⚠ same condition
- DNHD1 p.Ala657Ser Uncertain significance ⚠ same condition
- DNHD1 p.Glu971Lys Uncertain significance ⚠ same condition
- DNHD1 p.Met1535Val Uncertain significance ⚠ same condition
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/dnhd1-p-his1150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown