Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.71%, 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 0.31 | GERP -3.7, phastCons 0.54 |
| Overall | ||
| CADD | 7.548 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.71%
African / African-American · 3,533/75,052 alleles
Filtering AF
4.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.53%
Overall
0.252%
4,074/1,614,074 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.71% | 21 |
| Middle Eastern | 0.412% | 242 |
| Remaining individualsnot grpmax-eligible | 0.286% | 349 |
| Admixed American | 0.253% | 395 |
| European (non-Finnish) | 0.0148% | 6,742 |
| South Asian | 0.00988% | 10,121 |
| Finnishnot grpmax-eligible | 0.00156% | 64,034 |
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
- CBLB
- Protein
- p.Pro387=
- Coding
- c.1161T>C
- MANE Select
- NM_170662
- dbSNP
- rs9657925
- Type
- single nucleotide variant
- Location
- chr3:105734051 (GRCh38)
- Gene constraint
- LOEUF 0.406 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.88 · 36 PDB
Similar variants
- CBLB p.Arg670Gln Benign/Likely benign ★★ same type
- CBLB p.Pro689= Benign/Likely benign ★★ same type
- CBLB p.Ser622Thr Benign/Likely benign ★★ same type
- CBLB c.2569+1609A>C Uncertain significance ★ same type
- CBLB p.Ala176Pro Uncertain significance ★ ⚠ same type
- CBLB p.Ala2Glu Uncertain significance ★ ⚠ same type
- CBLB p.Ala592Ser Uncertain significance ★ ⚠ same type
- CBLB p.Ala928Val 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/cblb-p-pro387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown