DLL3 c.652+7C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00278%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.29 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP -0.63 | GERP -1.2 |
| Non-coding constraint | Z 0.87 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 7.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00278%
African / African-American · 2/71,832 alleles
Filtering AF
0.000462%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000173%
Overall
0.000197%
3/1,522,680 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00278% | 35,916 |
| European (non-Finnish) | 8.76e-05% | 1,141,992 |
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+7C>A
- MANE Select
- NM_203486
- Type
- single nucleotide variant
- Location
- chr19:39503064 (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 type
- DLL3 p.Arg221Ter Pathogenic ★★ same type
- DLL3 p.Arg238Ter Pathogenic ★★ same type
- DLL3 p.Cys178Ter Likely pathogenic ★★ same type
- DLL3 p.Cys207Ter Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Cys379Tyr Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Gln346Ter Pathogenic/Likely pathogenic ★★ same type
- DLL3 p.Gly504Asp Pathogenic/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/dll3-c-652-plus-7c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown