ELN c.*238C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.162%, afr)
Conditions
2
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 -0.091 | GERP -0.95 |
| Non-coding constraint | Z 0.91 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 1.593 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.162%
African / African-American · 87/53,712 alleles
Filtering AF
0.134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.124%
Overall
0.0172%
99/577,152 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.162% | 617 |
| Middle Eastern | 0.108% | 925 |
| Admixed American | 0.0147% | 6,808 |
| South Asian | 0.00395% | 25,325 |
| Remaining individualsnot grpmax-eligible | 0.00374% | 26,732 |
| Finnishnot grpmax-eligible | 0.00272% | 36,796 |
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
- Coding
- c.*238C>T
- MANE Select
- NM_000501
- dbSNP
- rs546341976
- Type
- single nucleotide variant
- Location
- chr7:74068938 (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-c-star-238c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown