DNAH2 p.Glu779=
c.2337G>A · rs760576469 · VCV2647372
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0986%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -0.92, phastCons 1 |
| Overall | ||
| CADD | 6.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0986%
Middle Eastern · 6/6,084 alleles
Filtering AF
0.0429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.00372%
60/1,614,036 alleles · ultra-rare
exomes 52/1,461,894 · genomes 8/152,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0986% | 1,014 |
| Admixed American | 0.015% | 6,666 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,415 |
| African / African-American | 0.00667% | 14,982 |
| European (non-Finnish) | 0.0028% | 35,759 |
| East Asian | 0.00223% | 44,896 |
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
- DNAH2
- Protein
- p.Glu779=
- Coding
- c.2337G>A
- MANE Select
- NM_020877
- dbSNP
- rs760576469
- Type
- single nucleotide variant
- Location
- chr17:7759013 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI <0.01 (gnomAD)
- Residue 779
- the 'stem' region
Similar variants
- DNAH2 p.Ala1036Val Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg1533Cys Uncertain significance ★★ ⚠ same type
- DNAH2 p.Arg2538Gln Uncertain significance ★★ same type
- DNAH2 p.Arg3759His Uncertain significance ★★ ⚠ same type
- DNAH2 p.Gln2069Glu Uncertain significance ★★ same type
- DNAH2 p.Ile4043Ser Uncertain significance ★★ ⚠ same type
- DNAH2 p.Pro3819Leu Uncertain significance ★★ ⚠ same type
- DNAH2 c.10169+3G>A Benign ★★ 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/dnah2-p-glu779 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown