SRCAP c.5658+15del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
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 · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.15 | GERP -5.5 |
| Non-coding constraint | Z -0.91 | 1 kb window · o/e 1.06 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SRCAP
- Coding
- c.5658+15del
- MANE Select
- NM_006662
- dbSNP
- rs2151294724
- Type
- Deletion
- Location
- chr16:30725096 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Similar variants
- SRCAP p.Pro2459fs Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Pro2461fs Pathogenic ★★ same type
- SRCAP p.Ser2463fs Pathogenic ★★ same type
- SRCAP p.Thr572del Uncertain significance ★★ same type
- SRCAP p.Val1012del Uncertain significance ★★ same type
- SRCAP p.Phe1867del Benign/Likely benign ★★ same type
- SRCAP c.1187_1228+67del Likely pathogenic ★ same type
- SRCAP c.1319del 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/srcap-c-5658-plus-15del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown