Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.829%, 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 0.27 | GERP -0.02, phastCons 0.98 |
| Overall | ||
| CADD | 11.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.829%
African / African-American · 622/75,050 alleles
Filtering AF
0.775%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.753%
Overall
0.0464%
749/1,614,116 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.829% | 121 |
| Admixed American | 0.127% | 790 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00329% | 30,361 |
| East Asian | 0.00223% | 44,872 |
| European (non-Finnish) | 0.000424% | 236,004 |
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
- CDK5R1
- Protein
- p.Pro70=
- Coding
- c.210C>T
- MANE Select
- NM_003885
- dbSNP
- rs1042845
- Type
- single nucleotide variant
- Location
- chr17:32487830 (GRCh38)
- Gene constraint
- LOEUF 0.234 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.99 · 11 PDB
Similar variants
- CDK5R1 p.Val250Ala Uncertain significance ★★ ⚠ same type
- CDK5R1 p.Asn266= Benign ★★ same type
- CDK5R1 p.Ile143= Benign ★★ same type
- CDK5R1 p.Ala14Val Uncertain significance ★ ⚠ same type
- CDK5R1 p.Arg179Cys Uncertain significance ★ ⚠ same type
- CDK5R1 p.Arg300Trp Uncertain significance ★ ⚠ same type
- CDK5R1 p.Asn64Asp Uncertain significance ★ ⚠ same type
- CDK5R1 p.Asn77Thr 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/cdk5r1-p-pro70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown