CRYBG3 p.Asp1749=
c.5247C>T · rs146175676 · VCV2653995
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.144%, 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 -0.73 | GERP -3.1 |
| Overall | ||
| CADD | 3.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.144%
African / African-American · 93/64,460 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.061%
752/1,231,966 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.144% | 693 |
| South Asian | 0.0782% | 1,279 |
| European (non-Finnish) | 0.0611% | 1,636 |
| Remaining individualsnot grpmax-eligible | 0.0459% | 2,180 |
| Middle Eastern | 0.0312% | 3,208 |
| Admixed American | 0.0253% | 3,951 |
| Finnishnot grpmax-eligible | 0.0187% | 5,350 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0056% | 17,860 |
| East Asian | 0.00315% | 31,698 |
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
- CRYBG3
- Protein
- p.Asp1749=
- Coding
- c.5247C>T
- MANE Select
- NM_153605
- dbSNP
- rs146175676
- Type
- single nucleotide variant
- Location
- chr3:97876441 (GRCh38)
- Gene constraint
- LOEUF 0.623 · pLI <0.01 (gnomAD)
Similar variants
- CRYBG3 p.Gly1408Glu Benign ★★ same type
- CRYBG3 p.Lys2380Arg Likely benign ★★ same type
- CRYBG3 p.Pro1662Thr Benign ★★ same type
- CRYBG3 p.Ser1432Leu Benign ★★ same type
- CRYBG3 p.Val1781Met Benign ★★ same type
- CRYBG3 p.Arg2831His Uncertain significance ★ same type
- CRYBG3 p.Leu2071Ile Uncertain significance ★ same type
- CRYBG3 p.Glu2281Lys Likely benign ★ 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/crybg3-p-asp1749 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown