DLL3 c.652+15C>T
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +15 | near-intronic (+15 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.98 | GERP 0.73, phastCons 0.003 |
| Non-coding constraint | Z 0.87 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 10.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 4.28% | 23 |
| Middle Easterngrpmax | 0.185% | 541 |
| European (non-Finnish) | 0.0817% | 1,224 |
| Remaining individualsnot grpmax-eligible | 0.0642% | 1,559 |
| South Asian | 0.0426% | 2,346 |
| Finnishnot grpmax-eligible | 0.0363% | 2,753 |
| Admixed American | 0.022% | 4,538 |
| African / African-American | 0.00556% | 17,973 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00355% | 28,160 |
| East Asian | 0.00253% | 39,538 |
Amish 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
- DLL3
- Coding
- c.652+15C>T
- MANE Select
- NM_203486
- dbSNP
- rs528327447
- Type
- single nucleotide variant
- Location
- chr19:39503072 (GRCh38)
- Gene constraint
- LOEUF 1.512 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.42
Similar variants
- DLL3 c.652+1G>T Likely pathogenic ★★ same condition
- DLL3 p.Arg238Ter Pathogenic ★★ same condition
- DLL3 p.Cys178Ter Likely pathogenic ★★ same condition
- DLL3 p.Cys207Ter Pathogenic/Likely pathogenic ★★ same condition
- DLL3 p.Cys379Tyr Pathogenic/Likely pathogenic ★★ same condition
- DLL3 p.Gln346Ter Pathogenic/Likely pathogenic ★★ same condition
- DLL3 p.Gly504Asp Pathogenic/Likely pathogenic ★★ same condition
- DLL3 c.1758+20C>G Uncertain significance ★★ ⚠ 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/dll3-c-652-plus-15c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown