CYFIP2 p.Ala880=
c.2640C>T · rs7705781 · VCV1169499
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.05%, 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 1.8 | GERP -0.46, phastCons 1 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.05%
African / African-American · 1,538/75,042 alleles
Filtering AF
1.96%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.93%
Overall
0.114%
1,847/1,613,990 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.05% | 49 |
| Remaining individualsnot grpmax-eligible | 0.253% | 395 |
| Middle Eastern | 0.132% | 758 |
| Admixed American | 0.118% | 845 |
| South Asian | 0.0143% | 7,006 |
| European (non-Finnish) | 0.005% | 19,998 |
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
- CYFIP2
- Protein
- p.Ala880=
- Coding
- c.2640C>T
- MANE Select
- NM_001037333
- dbSNP
- rs7705781
- Type
- single nucleotide variant
- Location
- chr5:157341124 (GRCh38)
- Gene constraint
- LOEUF 0.274 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.28
Similar variants
- CYFIP2 p.Ala880Thr Uncertain significance ★ ⚠ same residue
- CYFIP2 p.Ala880Val Uncertain significance ★ ⚠ same residue
- CYFIP2 p.Arg87Cys Pathogenic/Likely pathogenic ★★ same type
- CYFIP2 p.Arg87Pro Pathogenic/Likely pathogenic ★★ same type
- CYFIP2 p.Glu640Lys Pathogenic ★★ same type
- CYFIP2 p.Tyr108His Likely pathogenic ★★ ⚠ same type
- CYFIP2 p.Ala1074Thr Uncertain significance ★★ ⚠ same type
- CYFIP2 p.Ala773Thr 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/cyfip2-p-ala880 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown