EOGT c.*293del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 15.2%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.89 | GERP -0.41, phastCons 0.001 |
| Non-coding constraint | Z -1.01 | 1 kb window · o/e 1.08 · regional · uncalibrated |
| Overall | ||
| CADD | 0.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.2%
South Asian · 1,882/12,354 alleles
Filtering AF
14.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.4%
Overall
7.55%
13,658/180,986 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 15.2% | 7 |
| Remaining individualsnot grpmax-eligible | 15.1% | 7 |
| Middle Eastern | 10.3% | 10 |
| European (non-Finnish) | 9.54% | 10 |
| Finnishnot grpmax-eligible | 9.11% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 7.4% | 14 |
| East Asian | 4.17% | 24 |
| Admixed American | 1.63% | 61 |
| African / African-American | 0.997% | 100 |
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
- EOGT
- Coding
- c.*293del
- MANE Select
- NM_001278689
- dbSNP
- rs59164738
- Type
- Deletion
- Location
- chr3:68977325 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71
Similar variants
- EOGT p.Gly359fs Pathogenic/Likely pathogenic ★★ same type
- EOGT p.His27fs Pathogenic/Likely pathogenic ★★ same type
- EOGT c.621-14del Likely benign ★★ same type
- EOGT c.924+1del Likely pathogenic ★ same type
- EOGT p.Arg321fs Likely pathogenic ★ same type
- EOGT p.Leu66fs Pathogenic ★ same type
- EOGT c.1152+10del Benign ★ same type
- EOGT c.1152+70_1152+71del 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/eogt-c-star-293del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown