CYFIP1 p.Ala51=
c.153A>G · rs1468608716 · VCV723046
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -6.3 | GERP -4.4 |
| Overall | ||
| CADD | 1.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,878 alleles
Overall
0.000205%
3/1,461,854 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,878 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 8.47e-05% | 1,180,004 |
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
- CYFIP1
- Protein
- p.Ala51=
- Coding
- c.153A>G
- MANE Select
- NM_014608
- dbSNP
- rs1468608716
- Type
- single nucleotide variant
- Location
- chr15:22947057 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.24 · 5 PDB
Similar variants
- CYFIP1 p.Phe600Leu Uncertain significance ★★ ⚠ same type
- CYFIP1 c.3043-4C>G Benign/Likely benign ★★ same type
- CYFIP1 p.Ala1003Val Benign ★★ ⚠ same type
- CYFIP1 p.Ala385Thr Benign ★★ ⚠ same type
- CYFIP1 p.Glu347= Benign ★★ same type
- CYFIP1 p.Gly903Ser Benign/Likely benign ★★ same type
- CYFIP1 p.Ile795Val Benign ★★ same type
- CYFIP1 p.Leu1201= 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/cyfip1-p-ala51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown