ELN p.Ala239=
c.717G>A · rs782502253 · VCV696549
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0767%, amr)
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 -6.6 | GERP 1.9 |
| Overall | ||
| CADD | 0.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0767%
Admixed American · 46/59,972 alleles
Filtering AF
0.0591%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0528%
Overall
0.00589%
95/1,613,822 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0767% | 1,304 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| European (non-Finnish) | 0.00347% | 28,779 |
| South Asian | 0.00329% | 30,361 |
| African / African-American | 0.00134% | 74,844 |
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.Ala239=
- Coding
- c.717G>A
- MANE Select
- NM_000501
- dbSNP
- rs782502253
- Type
- single nucleotide variant
- Location
- chr7:74048173 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
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-ala239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown