DCDC2 c.425+33A>G
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +33 | near-intronic (+33 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.38 | GERP -2 |
| Overall | ||
| CADD | 9.767 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.05%
European (non-Finnish) · 24,194/1,179,064 alleles
Filtering AF
2.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.02%
Overall
1.66%
26,745/1,611,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.05% | 49 |
| African / African-American | 1.47% | 68 |
| Remaining individualsnot grpmax-eligible | 1.37% | 73 |
| Admixed American | 0.518% | 193 |
| Finnishnot grpmax-eligible | 0.359% | 278 |
| Ashkenazi Jewishnot grpmax-eligible | 0.169% | 590 |
| Middle Eastern | 0.0992% | 1,008 |
| South Asian | 0.0044% | 22,713 |
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
- DCDC2
- Coding
- c.425+33A>G
- MANE Select
- NM_016356
- dbSNP
- rs35029429
- Type
- single nucleotide variant
- Location
- chr6:24301935 (GRCh38)
- Gene constraint
- LOEUF 1.062 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93 · 1 PDB
Similar variants
- DCDC2 c.294-2A>G Pathogenic ★★ same type
- DCDC2 c.349-2A>G Pathogenic ★★ same type
- DCDC2 c.705-2A>G Pathogenic ★★ same type
- DCDC2 p.Leu297Ter Pathogenic ★★ same type
- DCDC2 p.Met1Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- DCDC2 p.Ser128Ter Pathogenic/Likely pathogenic ★★ same type
- DCDC2 p.Ala153Gly Uncertain significance ★★ ⚠ same type
- DCDC2 p.Ala356Pro 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/dcdc2-c-425-plus-33a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown