SRCAP c.2987+17del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.58 | GERP -5.1, phastCons 0.003 |
| Overall | ||
| CADD | 10.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,448 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00278%
Overall
0.000312%
5/1,600,986 alleles · ultra-rare
exomes 4/1,448,758 · genomes 1/152,228 · joint denominator
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
- SRCAP
- Coding
- c.2987+17del
- MANE Select
- NM_006662
- Type
- Deletion
- Location
- chr16:30720347 (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-2987-plus-17del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown