SCRIB c.4770+8del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0676%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -1.2, phastCons 0.082 |
| Overall | ||
| CADD | 8.586 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0676%
European (non-Finnish) · 792/1,170,900 alleles
Filtering AF
0.0637%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0622%
Overall
0.0505%
809/1,602,062 alleles · ultra-rare
exomes 768/1,449,894 · genomes 41/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0676% | 1,478 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,887 |
| African / African-American | 0.00938% | 10,665 |
| Finnishnot grpmax-eligible | 0.00159% | 62,876 |
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
- SCRIB
- Coding
- c.4770+8del
- MANE Select
- NM_182706
- dbSNP
- rs782103174
- Type
- Deletion
- Location
- chr8:143791658 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
Similar variants
- SCRIB p.Ala796fs Uncertain significance ★ 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/scrib-c-4770-plus-8del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown