CAPRIN2 p.Thr763=
c.2289G>A · rs78303008 · VCV779266
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor loss, 7 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.064 | GERP -1, phastCons 0.66 |
| Overall | ||
| CADD | 12.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.05%
European (non-Finnish) · 12,433/1,179,808 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.03%
Overall
0.842%
13,595/1,613,880 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.05% | 95 |
| Remaining individualsnot grpmax-eligible | 0.643% | 155 |
| Middle Eastern | 0.379% | 264 |
| Ashkenazi Jewishnot grpmax-eligible | 0.341% | 293 |
| Admixed American | 0.335% | 299 |
| Finnishnot grpmax-eligible | 0.326% | 306 |
| African / African-American | 0.167% | 600 |
| South Asian | 0.111% | 902 |
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
- CAPRIN2
- Protein
- p.Thr763=
- Coding
- c.2289G>A
- MANE Select
- NM_001385503
- dbSNP
- rs78303008
- Type
- single nucleotide variant
- Location
- chr12:30715074 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.42 · 5 PDB
Similar variants
- CAPRIN2 p.Thr763Met Uncertain significance ★ same residue
- CAPRIN2 c.1800+5C>T Benign ★★ same type
- CAPRIN2 p.Met253Thr Benign ★★ same type
- CAPRIN2 p.Ser668= Benign ★★ same type
- CAPRIN2 p.Tyr806= Benign ★★ same type
- CAPRIN2 c.-12A>G Uncertain significance ★ same type
- CAPRIN2 c.-2A>C Uncertain significance ★ same type
- CAPRIN2 c.-30G>A 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/caprin2-p-thr763 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown