EDRF1 p.Thr480=
c.1440T>C · rs77665875 · VCV786177
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.2%, 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 -4.9 | GERP -4.1 |
| Overall | ||
| CADD | 2.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.2%
African / African-American · 903/75,008 alleles
Filtering AF
1.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.11%
Overall
0.0726%
1,171/1,613,324 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.2% | 83 |
| Admixed American | 0.0983% | 1,017 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Middle Eastern | 0.0165% | 6,048 |
| European (non-Finnish) | 0.0125% | 7,969 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,787 |
| South Asian | 0.00329% | 30,354 |
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.Thr480=
- Coding
- c.1440T>C
- MANE Select
- NM_001202438
- dbSNP
- rs77665875
- Type
- single nucleotide variant
- Location
- chr10:125734126 (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.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
- EDRF1 p.Ala35Val 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-thr480 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown