DYNC2I2 c.435+7del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00322%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.71 | GERP -2.4, phastCons 0.016 |
| Overall | ||
| CADD | 0.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00322%
European (non-Finnish) · 38/1,179,064 alleles
Filtering AF
0.0024%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.00248%
40/1,612,530 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00322% | 31,028 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,412 |
| African / African-American | 0.00134% | 74,870 |
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.435+7del
- MANE Select
- NM_052844
- dbSNP
- rs755728843
- Type
- Deletion
- Location
- chr9:128640684 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.66 · 4 PDB
Similar variants
- DYNC2I2 p.Leu438fs Pathogenic/Likely pathogenic ★★ same type
- DYNC2I2 p.Phe439fs Pathogenic ★★ same type
- DYNC2I2 p.Pro210fs Pathogenic/Likely pathogenic ★★ same type
- DYNC2I2 p.Pro32fs Pathogenic/Likely pathogenic ★★ same type
- DYNC2I2 c.1372+5del Uncertain significance ★★ same type
- DYNC2I2 c.546-1_547del Likely pathogenic ★ same type
- DYNC2I2 p.Gln504_Gly505insTer Pathogenic ★ same type
- DYNC2I2 p.Gln86fs Pathogenic ★ 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-435-plus-7del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown