ELANE c.366+192G>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.6%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +192 | deep intronic (+192 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.42 | GERP -2.7 |
| Overall | ||
| CADD | 1.648 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.6%
European (non-Finnish) · 1,086/68,014 alleles
Filtering AF
1.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.49%
Overall
1.03%
1,572/152,296 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.6% | 63 |
| Middle Eastern | 1.36% | 74 |
| Admixed American | 1.22% | 82 |
| Finnishnot grpmax-eligible | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.993% | 101 |
| Ashkenazi Jewishnot grpmax-eligible | 0.662% | 151 |
| African / African-American | 0.318% | 315 |
| South Asian | 0.228% | 439 |
| East Asian | 0.0386% | 2,588 |
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
- ELANE
- Coding
- c.366+192G>T
- MANE Select
- NM_001972
- dbSNP
- rs17223024
- Type
- single nucleotide variant
- Location
- chr19:853595 (GRCh38)
- Gene constraint
- LOEUF 1.245 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.42 · 38 PDB
Similar variants
- ELANE c.597+1G>A Pathogenic ★★ same type
- ELANE c.597+1G>C Pathogenic ★★ same type
- ELANE c.597+1G>T Pathogenic ★★ same type
- ELANE c.597+5G>A Pathogenic/Likely pathogenic ★★ same type
- ELANE p.Ala57Thr Pathogenic/Likely pathogenic ★★ same type
- ELANE p.Ala57Val Pathogenic/Likely pathogenic ★★ same type
- ELANE p.Ala61Val Pathogenic/Likely pathogenic ★★ ⚠ same type
- ELANE p.Arg103Leu Likely pathogenic ★★ ⚠ 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/elane-c-366-plus-192g-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown