Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.296%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.41 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.19 | GERP -3.5, phastCons 0.21 |
| Overall | ||
| CADD | 8.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.296%
African / African-American · 222/74,948 alleles
Filtering AF
0.264%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.252%
Overall
0.0176%
283/1,610,770 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.296% | 338 |
| Admixed American | 0.0167% | 6,002 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,798 |
| South Asian | 0.0044% | 22,752 |
| European (non-Finnish) | 0.00331% | 30,181 |
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
- CALB1
- Protein
- p.Asp201=
- Coding
- c.603C>T
- MANE Select
- NM_004929
- dbSNP
- rs2229779
- Type
- single nucleotide variant
- Location
- chr8:90060698 (GRCh38)
- Gene constraint
- LOEUF 0.612 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 82.70 · 1 PDB
- Residue 201
- a binding site; the ef-hand 5 domain
Similar variants
- CALB1 p.Ala13Pro Uncertain significance ★ ⚠ same type
- CALB1 p.Ala46Glu Uncertain significance ★ ⚠ same type
- CALB1 p.Asn125Lys Uncertain significance ★ ⚠ same type
- CALB1 p.Asn38Ser Uncertain significance ★ ⚠ same type
- CALB1 p.Asp24Asn Uncertain significance ★ ⚠ same type
- CALB1 p.Asp24His Uncertain significance ★ ⚠ same type
- CALB1 p.Cys257Arg Uncertain significance ★ ⚠ same type
- CALB1 p.Glu86Asp 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/calb1-p-asp201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown