ELANE c.67+1del
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 0.73, phastCons 1 |
| Non-coding constraint | Z 3.68 | 1 kb window · o/e 0.78 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 0.00486% | 20,589 |
| European (non-Finnish)grpmax | 8.48e-05% | 1,179,782 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.67+1del
- MANE Select
- NM_001972
- dbSNP
- rs886039350
- Type
- Deletion
- Location
- chr19:852391 (GRCh38)
- Gene constraint
- LOEUF 1.245 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.42 · 38 PDB
Similar variants
- ELANE p.Pro111_Val112insTer Uncertain significance ★★ same type
- ELANE c.597+5del Pathogenic ★ same type
- ELANE p.Ala195fs Likely pathogenic ★ same type
- ELANE p.Ala236fs Likely pathogenic ★ same type
- ELANE p.Arg182fs Pathogenic ★ same type
- ELANE p.Asn113_Ile120del Pathogenic ★ same type
- ELANE p.Asp201fs Likely pathogenic ★ same type
- ELANE p.Asp230fs 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-67-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown