EPO p.Lys79=
c.237G>A · rs57694744 · VCV716909
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.873%, 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 2.8 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 6.732 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.873%
African / African-American · 639/73,186 alleles
Filtering AF
0.817%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.795%
Overall
0.0435%
691/1,589,610 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.873% | 115 |
| Admixed American | 0.0471% | 2,125 |
| Remaining individualsnot grpmax-eligible | 0.0358% | 2,793 |
| South Asian | 0.00116% | 86,318 |
| European (non-Finnish) | 0.000341% | 292,877 |
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
- EPO
- Protein
- p.Lys79=
- Coding
- c.237G>A
- MANE Select
- NM_003254 · reported on NM_000799
- dbSNP
- rs57694744
- Type
- single nucleotide variant
- Location
- chr7:100722039 (GRCh38)
- Structure
- AlphaFold pLDDT 90.09 · 13 PDB
- Residue 79
- a disulfide bond; the ntr domain; a turn
Similar variants
- EPO c.14-1G>C Uncertain significance ★★ same type
- EPO c.13+10C>T Benign/Likely benign ★★ same type
- EPO c.247-66G>A Benign ★★ same type
- EPO p.Ala151= Benign ★★ same type
- EPO p.Ala57= Likely benign ★★ same type
- EPO p.Ala87= Likely benign ★★ same type
- EPO p.Asp70Asn Likely benign ★★ same type
- EPO p.Pro114Leu Benign/Likely 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/epo-p-lys79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown