CYFIP1 p.Glu347=
c.1041G>A · rs139045862 · VCV769869
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.53%, 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 0.56 | GERP 0.86, phastCons 1 |
| Overall | ||
| CADD | 10.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.53%
African / African-American · 1,148/74,980 alleles
Filtering AF
1.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.43%
Overall
0.08%
1,291/1,612,968 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.53% | 65 |
| Remaining individualsnot grpmax-eligible | 0.11% | 905 |
| Admixed American | 0.0852% | 1,174 |
| Middle Eastern | 0.0165% | 6,060 |
| South Asian | 0.0033% | 30,279 |
| European (non-Finnish) | 0.00161% | 62,081 |
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.Glu347=
- Coding
- c.1041G>A
- MANE Select
- NM_014608
- dbSNP
- rs139045862
- Type
- single nucleotide variant
- Location
- chr15:22932292 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.24 · 5 PDB
- Residue 347
- an α-helix
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.Gly903Ser Benign/Likely benign ★★ same type
- CYFIP1 p.Ile795Val Benign ★★ same type
- CYFIP1 p.Leu1201= Benign ★★ same type
- CYFIP1 p.Pro1033= 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-glu347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown