CRYBA2 p.Val36=
c.108C>T · VCV4083960
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.31%, 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 1.9 | GERP -3.2, phastCons 0.87 |
| Overall | ||
| CADD | 10.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.31%
African / African-American · 985/74,958 alleles
Filtering AF
1.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
0.0687%
1,107/1,610,790 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.31% | 76 |
| Admixed American | 0.0851% | 1,175 |
| Remaining individualsnot grpmax-eligible | 0.0786% | 1,272 |
| East Asian | 0.0358% | 2,797 |
| Middle Eastern | 0.0165% | 6,052 |
| European (non-Finnish) | 0.000424% | 235,688 |
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
- CRYBA2
- Protein
- p.Val36=
- Coding
- c.108C>T
- MANE Select
- NM_057093
- Type
- single nucleotide variant
- Location
- chr2:218993069 (GRCh38)
- Gene constraint
- LOEUF 1.372 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.12
- Residue 36
- the beta/gamma crystallin 'greek key' 1 domain
Similar variants
- CRYBA2 p.Ala80Thr Uncertain significance ★★ ⚠ same type
- CRYBA2 c.303+127A>G Benign ★★ same type
- CRYBA2 c.304-16T>C Benign ★★ same type
- CRYBA2 c.303+5G>A Uncertain significance ★ same type
- CRYBA2 c.446+1G>A Uncertain significance ★ same type
- CRYBA2 p.Ala10Pro Uncertain significance ★ ⚠ same type
- CRYBA2 p.Ala34Glu Uncertain significance ★ ⚠ same type
- CRYBA2 p.Ala6Ser 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/cryba2-p-val36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown