Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 82.3%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
primary ciliary dyskinesia
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 -11 | GERP -4.9 |
| Overall | ||
| CADD | 0.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
82.3%
East Asian · 36,905/44,820 alleles
Filtering AF
81.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 81.3%
Overall
44.7%
720,022/1,611,602 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 82.3% | 1 |
| Admixed American | 60.3% | 2 |
| South Asian | 53.2% | 2 |
| Remaining individualsnot grpmax-eligible | 45.5% | 2 |
| Amishnot grpmax-eligible | 44.2% | 2 |
| European (non-Finnish) | 42.9% | 2 |
| Finnishnot grpmax-eligible | 37.4% | 3 |
| African / African-American | 36.8% | 3 |
| Middle Eastern | 36.8% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 36.3% | 3 |
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
- DNAH8
- Protein
- p.Val2560=
- Coding
- c.7680C>T
- MANE Select
- NM_001206927
- dbSNP
- rs6458080
- Type
- single nucleotide variant
- Location
- chr6:38875650 (GRCh38)
- Gene constraint
- LOEUF 0.692 · pLI <0.01 (gnomAD)
- Residue 2560
- a UniProt-annotated variant site (found in a patient with primary ciliary dyskinesia; uncertain significance); the 'aaa 3' region
Disease context
primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Primary ciliary dyskinesia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Neonatal
- Prevalence
- 1-5 / 10 000 (Pakistan)
Similar variants
- DNAH8 p.Val2560Ile Uncertain significance ★ ⚠ same residue
- DNAH8 c.10963-1G>A Likely pathogenic ★★ same condition
- DNAH8 c.11563+1G>T Likely pathogenic ★★ same condition
- DNAH8 c.2664+2T>C Likely pathogenic ★★ same condition
- DNAH8 c.5734-1G>T Likely pathogenic ★★ same condition
- DNAH8 p.Arg1090Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAH8 p.Arg207Ter Pathogenic/Likely pathogenic ★★ same condition
- DNAH8 p.Arg2878Ter Pathogenic ★★ 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/dnah8-p-val2560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown