ELN p.Gly522=
c.1566T>A · rs61734584 · VCV213164
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.9%, mid)
Conditions
1
supravalvular aortic stenosis
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 -7 | GERP -13 |
| Overall | ||
| CADD | 0.715 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.9%
Middle Eastern · 176/6,062 alleles
Filtering AF
2.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.42%
Overall
0.276%
4,462/1,614,022 alleles · low-frequency
exomes 4,015/1,461,884 · genomes 447/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.9% | 34 |
| Ashkenazi Jewishnot grpmax-eligible | 2.48% | 40 |
| Remaining individualsnot grpmax-eligible | 0.544% | 184 |
| Admixed American | 0.515% | 194 |
| European (non-Finnish) | 0.223% | 449 |
| South Asian | 0.214% | 467 |
| African / African-American | 0.0987% | 1,014 |
| Finnishnot grpmax-eligible | 0.00625% | 16,005 |
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
- ELN
- Protein
- p.Gly522=
- Coding
- c.1566T>A
- MANE Select
- NM_000501
- dbSNP
- rs61734584
- Type
- single nucleotide variant
- Location
- chr7:74060037 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
- Residue 522
- a modified residue (hydroxyproline; partial)
Similar variants
- ELN c.377-2A>G Pathogenic/Likely pathogenic ★★ same condition
- ELN c.643+1G>C Likely pathogenic ★★ same condition
- ELN c.686-2A>G Likely pathogenic ★★ same condition
- ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ELN c.800-2A>G Pathogenic ★★ same condition
- ELN c.800-3C>G Pathogenic ★★ same condition
- ELN c.82+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ELN c.889+1G>A Pathogenic/Likely pathogenic ★★ same condition
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/eln-p-gly522 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown