DCDC2 c.*124A>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 43.5%, afr) — too common for a highly-penetrant pathogenic allele
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 0.93 | GERP -3.2, phastCons 0.036 |
| Non-coding constraint | Z 1.07 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 2.296 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
43.5%
African / African-American · 23,227/53,436 alleles
Filtering AF
43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 42.8%
Overall
6.4%
37,458/585,542 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 43.5% | 2 |
| Admixed American | 6.61% | 15 |
| Remaining individualsnot grpmax-eligible | 5.87% | 17 |
| Middle Eastern | 3.61% | 28 |
| European (non-Finnish) | 2.83% | 35 |
| Ashkenazi Jewishnot grpmax-eligible | 2.65% | 38 |
| Finnishnot grpmax-eligible | 0.382% | 262 |
| South Asian | 0.168% | 596 |
| East Asian | 0.00277% | 36,108 |
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.*124A>T
- MANE Select
- NM_016356
- dbSNP
- rs7764902
- Type
- single nucleotide variant
- Location
- chr6:24174606 (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-star-124a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown