CDC123 c.489+3A>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.69 | donor loss · deltas |
| Pangolin | Δ0.63 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7 | GERP 2, phastCons 1 |
| Non-coding constraint | Z 0.69 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 15.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.01%
Admixed American · 590/58,628 alleles
Filtering AF
0.939%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.912%
Overall
0.234%
3,755/1,601,592 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.01% | 99 |
| Ashkenazi Jewishnot grpmax-eligible | 0.384% | 261 |
| Remaining individualsnot grpmax-eligible | 0.272% | 367 |
| European (non-Finnish) | 0.229% | 436 |
| East Asian | 0.221% | 452 |
| African / African-American | 0.0549% | 1,822 |
| Middle Eastern | 0.0501% | 1,995 |
| Finnishnot grpmax-eligible | 0.036% | 2,776 |
| South Asian | 0.0348% | 2,875 |
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
- CDC123
- Coding
- c.489+3A>C
- MANE Select
- NM_006023
- dbSNP
- rs149366829
- Type
- single nucleotide variant
- Location
- chr10:12230999 (GRCh38)
- Gene constraint
- LOEUF 1.013 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.82 · 2 PDB
Similar variants
- CDC123 c.847-4A>G Benign ★★ same type
- CDC123 p.Ala113Val Uncertain significance ★ ⚠ same type
- CDC123 p.Ala279Thr Uncertain significance ★ ⚠ same type
- CDC123 p.Ala319Thr Uncertain significance ★ ⚠ same type
- CDC123 p.Arg142Gly Uncertain significance ★ ⚠ same type
- CDC123 p.Arg142His Uncertain significance ★ ⚠ same type
- CDC123 p.Arg167Gln Uncertain significance ★ ⚠ same type
- CDC123 p.Arg210Leu 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/cdc123-c-489-plus-3a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown