Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 13 submitters
gnomAD v4.1
Common
common (popmax 74.3%, amr) — too common for a highly-penetrant pathogenic allele
Conditions
2
Jeune syndrome
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 0.23 | GERP -2, phastCons 0.98 |
| Overall | ||
| CADD | 4.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
74.3%
Admixed American · 44,535/59,906 alleles
Filtering AF
73.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 73.5%
Overall
61.9%
998,096/1,612,840 alleles · common
exomes 901,343/1,460,980 · genomes 96,753/151,860 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 74.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 67.3% | 1 |
| African / African-American | 66.8% | 1 |
| Middle Eastern | 65.1% | 2 |
| Finnishnot grpmax-eligible | 63.4% | 2 |
| Remaining individualsnot grpmax-eligible | 62.1% | 2 |
| European (non-Finnish) | 61.6% | 2 |
| South Asian | 55.7% | 2 |
| East Asian | 50.9% | 2 |
| Amishnot grpmax-eligible | 45.9% | 2 |
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
- DYNC2H1
- Protein
- p.His2317=
- Coding
- c.6951C>T
- MANE Select
- NM_001377
- dbSNP
- rs586592
- Type
- single nucleotide variant
- Location
- chr11:103187397 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2317
- the 'aaa 3' region
Similar variants
- DYNC2H1 c.10042+2T>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10462-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.10606-14A>G Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.10695+1G>A Likely pathogenic ★★ same condition
- DYNC2H1 c.10813-2A>G Likely pathogenic ★★ same condition
- DYNC2H1 c.11493+2T>A Likely pathogenic ★★ same condition
- DYNC2H1 c.11650-1G>A Pathogenic/Likely pathogenic ★★ same condition
- DYNC2H1 c.12156+1G>A Pathogenic/Likely 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/dync2h1-p-his2317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown