DYNC2I2 c.703+30C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.5%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| Splice region | donor +30 | near-intronic (+30 nt from the splice site) |
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -1.4 |
| Overall | ||
| CADD | 2.346 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.5%
African / African-American · 1,836/73,414 alleles
Filtering AF
2.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.37%
Overall
0.138%
2,150/1,553,852 alleles · low-frequency
exomes 1,050/1,401,474 · genomes 1,100/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.5% | 40 |
| Admixed American | 0.191% | 522 |
| Remaining individualsnot grpmax-eligible | 0.173% | 579 |
| Middle Eastern | 0.101% | 994 |
| European (non-Finnish) | 0.00879% | 11,371 |
| South Asian | 0.00594% | 16,843 |
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
- DYNC2I2
- Coding
- c.703+30C>A
- MANE Select
- NM_052844
- dbSNP
- rs73669958
- Type
- single nucleotide variant
- Location
- chr9:128636251 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.66 · 4 PDB
Similar variants
- DYNC2I2 c.1372+1G>A Pathogenic/Likely pathogenic ★★ same type
- DYNC2I2 p.Arg121Ter Pathogenic ★★ same type
- DYNC2I2 p.Arg182Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- DYNC2I2 p.Arg447Trp Pathogenic/Likely pathogenic ★★ same type
- DYNC2I2 p.Ala131Val Uncertain significance ★★ ⚠ same type
- DYNC2I2 p.Ala13Gly Uncertain significance ★★ ⚠ same type
- DYNC2I2 p.Ala219Thr Uncertain significance ★★ ⚠ same type
- DYNC2I2 p.Ala369Val Uncertain significance ★★ ⚠ 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/dync2i2-c-703-plus-30c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown