Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 12 submitters
gnomAD v4.1
Common
common (popmax 70.8%, amr) — too common for a highly-penetrant pathogenic allele
Conditions
2
asphyxiating thoracic dystrophy 3
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 -0.17 | GERP -3.5, phastCons 0.7 |
| Overall | ||
| CADD | 3.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
70.8%
Admixed American · 40,408/57,078 alleles
Filtering AF
70.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 70%
Overall
63.1%
1,003,618/1,589,806 alleles · common
exomes 920,191/1,437,810 · genomes 83,427/151,996 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 70.8% | 1 |
| European (non-Finnish) | 66.2% | 2 |
| Finnishnot grpmax-eligible | 65.9% | 2 |
| Amishnot grpmax-eligible | 64.6% | 2 |
| Remaining individualsnot grpmax-eligible | 60.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 60.4% | 2 |
| Middle Eastern | 56.6% | 2 |
| South Asian | 53.1% | 2 |
| East Asian | 53% | 2 |
| African / African-American | 29% | 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
- DYNC2H1
- Protein
- p.Asp4032=
- Coding
- c.12096T>C
- MANE Select
- NM_001377
- dbSNP
- rs2566913
- Type
- single nucleotide variant
- Location
- chr11:103358299 (GRCh38)
- Gene constraint
- LOEUF 0.859 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 4032
- an α-helix
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-asp4032 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown