Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, mid)
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 0.69 | GERP -3.4, phastCons 0.24 |
| Overall | ||
| CADD | 0.994 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
Middle Eastern · 70/6,062 alleles
Filtering AF
0.937%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.882%
Overall
0.789%
12,735/1,614,182 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.15% | 87 |
| European (non-Finnish) | 0.902% | 111 |
| Finnishnot grpmax-eligible | 0.831% | 120 |
| South Asian | 0.68% | 147 |
| Remaining individualsnot grpmax-eligible | 0.659% | 152 |
| Admixed American | 0.49% | 204 |
| African / African-American | 0.157% | 636 |
| Ashkenazi Jewishnot grpmax-eligible | 0.152% | 658 |
| East Asian | 0.00668% | 14,961 |
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
- EFS
- Protein
- p.Pro141=
- Coding
- c.423C>T
- MANE Select
- NM_005864
- dbSNP
- rs2231802
- Type
- single nucleotide variant
- Location
- chr14:23360156 (GRCh38)
- Gene constraint
- LOEUF 1.165 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.71
Similar variants
- EFS p.Ala167Thr Uncertain significance ★ ⚠ same type
- EFS p.Ala186Val Uncertain significance ★ ⚠ same type
- EFS p.Ala219Asp Uncertain significance ★ ⚠ same type
- EFS p.Ala262Ser Uncertain significance ★ ⚠ same type
- EFS p.Ala285Ser Uncertain significance ★ ⚠ same type
- EFS p.Ala40Val Uncertain significance ★ ⚠ same type
- EFS p.Ala495Pro Uncertain significance ★ ⚠ same type
- EFS p.Ala498Val 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/efs-p-pro141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown