Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.4%, afr)
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 2.3 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.4%
African / African-American · 3,296/74,922 alleles
Filtering AF
4.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.22%
Overall
0.233%
3,762/1,611,516 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.4% | 23 |
| Middle Eastern | 0.413% | 242 |
| Remaining individualsnot grpmax-eligible | 0.318% | 315 |
| Admixed American | 0.178% | 563 |
| South Asian | 0.011% | 9,072 |
| European (non-Finnish) | 0.0105% | 9,505 |
| Finnishnot grpmax-eligible | 0.00469% | 21,331 |
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
- CDC23
- Protein
- p.Asp541=
- Coding
- c.1623T>C
- MANE Select
- NM_004661
- dbSNP
- rs2231480
- Type
- single nucleotide variant
- Location
- chr5:138189633 (GRCh38)
- Gene constraint
- LOEUF 0.452 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.74 · 20 PDB
- Residue 541
- a turn
Similar variants
- CDC23 c.1166+2T>G Uncertain significance ★ same type
- CDC23 p.Ala68Asp Uncertain significance ★ ⚠ same type
- CDC23 p.Arg424Gln Uncertain significance ★ ⚠ same type
- CDC23 p.Arg424Trp Uncertain significance ★ ⚠ same type
- CDC23 p.Arg585His Uncertain significance ★ ⚠ same type
- CDC23 p.Asn110His Uncertain significance ★ ⚠ same type
- CDC23 p.Asn23Tyr Uncertain significance ★ ⚠ same type
- CDC23 p.Asn287Ser 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/cdc23-p-asp541 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown