CALB2 p.Asp210=
c.630T>C · rs2042560909 · VCV2613589
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.375 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.75 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.7 |
| Overall | ||
| CADD | 2.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,864 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000547%
8/1,461,808 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,864 |
| European (non-Finnish) | 0.000593% | 168,568 |
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
- CALB2
- Protein
- p.Asp210=
- Coding
- c.630T>C
- MANE Select
- NM_001740
- dbSNP
- rs2042560909
- Type
- single nucleotide variant
- Location
- chr16:71385579 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.29
- Residue 210
- a binding site; the ef-hand 5 domain
Similar variants
- CALB2 p.Ala115Val Uncertain significance ★ ⚠ same type
- CALB2 p.Ala129Val Uncertain significance ★ ⚠ same type
- CALB2 p.Arg145Gln Uncertain significance ★ ⚠ same type
- CALB2 p.Arg145Leu Uncertain significance ★ ⚠ same type
- CALB2 p.Arg161Gln Uncertain significance ★ ⚠ same type
- CALB2 p.Arg258Cys Uncertain significance ★ ⚠ same type
- CALB2 p.Asn231Ser Uncertain significance ★ ⚠ same type
- CALB2 p.Asn236Ser 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/calb2-p-asp210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown