CAPRIN1 c.2001+8A>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP -3.4, phastCons 1 |
| Non-coding constraint | Z 1.07 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 6.763 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
African / African-American · 949/74,392 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0714%
1,129/1,581,786 alleles · low-frequency
exomes 571/1,429,492 · genomes 558/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.154% | 647 |
| Middle Eastern | 0.116% | 859 |
| Admixed American | 0.1% | 999 |
| South Asian | 0.00996% | 10,042 |
| European (non-Finnish) | 0.000782% | 127,839 |
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
- CAPRIN1
- Coding
- c.2001+8A>T
- MANE Select
- NM_005898
- Type
- single nucleotide variant
- Location
- chr11:34097304 (GRCh38)
- Gene constraint
- LOEUF 0.372 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.64 · 6 PDB
Similar variants
- CAPRIN1 p.Arg458Ter Pathogenic ★★ same type
- CAPRIN1 p.Arg132Cys Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Gln206Arg Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Pro424Leu Uncertain significance ★★ ⚠ same type
- CAPRIN1 p.Pro528Thr Uncertain significance ★★ ⚠ same type
- CAPRIN1 c.1122+19G>A Benign ★★ same type
- CAPRIN1 c.217-5C>G Likely pathogenic ★ same type
- CAPRIN1 c.688+5G>A Likely pathogenic ★ 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/caprin1-c-2001-plus-8a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown