DLL1 c.412+18del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +18 | near-intronic (+18 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.34 | GERP -3 |
| Overall | ||
| CADD | 0.582 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,179,992 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000682%
11/1,614,024 alleles · very rare
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
- DLL1
- Coding
- c.412+18del
- MANE Select
- NM_005618
- dbSNP
- rs1342031608
- Type
- Deletion
- Location
- chr6:170288711 (GRCh38)
- Gene constraint
- LOEUF 0.236 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.24 · 1 PDB
Similar variants
- DLL1 p.Glu673fs Pathogenic/Likely pathogenic ★★ same type
- DLL1 p.Gly282fs Pathogenic/Likely pathogenic ★★ same type
- DLL1 c.2167-3del Benign/Likely benign ★★ same type
- DLL1 c.351+14del Likely benign ★★ same type
- DLL1 p.Asp601_Ile602delinsVal Benign ★★ same type
- DLL1 c.1033-22_1033-8del Pathogenic ★ same type
- DLL1 c.1249+1del Pathogenic ★ same type
- DLL1 c.1250-8_1250-1del 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/dll1-c-412-plus-18del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown