Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.49%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.37 | acceptor loss, 2 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.25 | GERP -0.082, phastCons 0.55 |
| Overall | ||
| CADD | 10.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.49%
African / African-American · 4,123/75,040 alleles
Filtering AF
5.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.3%
Overall
0.422%
6,815/1,614,178 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.49% | 18 |
| East Asian | 2.64% | 38 |
| Admixed American | 1.11% | 90 |
| Middle Eastern | 0.747% | 134 |
| Remaining individualsnot grpmax-eligible | 0.653% | 153 |
| Ashkenazi Jewishnot grpmax-eligible | 0.236% | 423 |
| South Asian | 0.111% | 902 |
| European (non-Finnish) | 0.0183% | 5,463 |
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
- EEF1A1
- Protein
- p.Pro350=
- Coding
- c.1050A>G
- MANE Select
- NM_001402
- dbSNP
- rs2351124
- Type
- single nucleotide variant
- Location
- chr6:73518244 (GRCh38)
- Gene constraint
- LOEUF 0.126 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.06 · 14 PDB
- Residue 350
- an α-helix
Similar variants
- MTO1 p.Gln595= Benign/Likely benign ★★ same type
- EEF1A1 p.Ala448Ser Uncertain significance ★ ⚠ same type
- EEF1A1 p.Arg321His Uncertain significance ★ ⚠ same type
- EEF1A1 p.Arg96Thr Uncertain significance ★ ⚠ same type
- EEF1A1 p.Asn331His Uncertain significance ★ ⚠ same type
- EEF1A1 p.Asp389Asn Uncertain significance ★ ⚠ same type
- EEF1A1 p.Cys31Trp Uncertain significance ★ ⚠ same type
- EEF1A1 p.Gly151Ser 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/eef1a1-p-pro350 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown