EDRF1 p.Ser1176=
c.3528A>G · rs150588104 · VCV2640955
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, 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 -0.76 | GERP -2.8 |
| Overall | ||
| CADD | 2.864 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
Middle Eastern · 76/5,194 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1%
Overall
0.199%
3,210/1,613,014 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.46% | 68 |
| Ashkenazi Jewishnot grpmax-eligible | 0.824% | 121 |
| South Asian | 0.622% | 161 |
| Remaining individualsnot grpmax-eligible | 0.264% | 378 |
| European (non-Finnish) | 0.172% | 580 |
| Admixed American | 0.16% | 625 |
| African / African-American | 0.0307% | 3,261 |
| East Asian | 0.00891% | 11,220 |
| Finnishnot grpmax-eligible | 0.00469% | 21,343 |
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
- EDRF1
- Protein
- p.Ser1176=
- Coding
- c.3528A>G
- MANE Select
- NM_001202438
- dbSNP
- rs150588104
- Type
- single nucleotide variant
- Location
- chr10:125753828 (GRCh38)
- Gene constraint
- LOEUF 0.53 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 76.41
Similar variants
- EDRF1 p.Leu159= Benign ★★ same type
- EDRF1 p.Thr480= Benign ★★ same type
- EDRF1 p.Thr731= Benign ★★ same type
- EDRF1 p.Ala1137Ser Uncertain significance ★ ⚠ same type
- EDRF1 p.Ala1210Thr Uncertain significance ★ ⚠ same type
- EDRF1 p.Ala1228Thr Uncertain significance ★ ⚠ same type
- EDRF1 p.Ala203Thr Uncertain significance ★ ⚠ same type
- EDRF1 p.Ala226Ser 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/edrf1-p-ser1176 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown