SCRIB p.Ala1488=
c.4464C>T · rs371082782 · VCV2658908
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.444%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -2.9 |
| Overall | ||
| CADD | 0.787 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.444%
Middle Eastern · 26/5,852 alleles
Filtering AF
0.311%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.267%
Overall
0.0593%
932/1,571,322 alleles · rare
exomes 836/1,419,002 · genomes 96/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.444% | 225 |
| Ashkenazi Jewishnot grpmax-eligible | 0.149% | 671 |
| Remaining individualsnot grpmax-eligible | 0.111% | 898 |
| Admixed American | 0.0856% | 1,168 |
| African / African-American | 0.074% | 1,351 |
| European (non-Finnish) | 0.0569% | 1,759 |
| South Asian | 0.0273% | 3,657 |
| East Asian | 0.00693% | 14,431 |
| Finnishnot grpmax-eligible | 0.00423% | 23,613 |
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
- Protein
- p.Ala1488=
- Coding
- c.4464C>T
- MANE Select
- NM_182706
- dbSNP
- rs371082782
- Type
- single nucleotide variant
- Location
- chr8:143792270 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 1488
- the 'disordered' region
Similar variants
- SCRIB c.3120+10C>G Benign/Likely benign ★★ same type
- SCRIB c.504-9C>T Benign ★★ same type
- SCRIB p.Arg492= Benign ★★ same type
- SCRIB p.Asn647= Benign/Likely benign ★★ same type
- SCRIB p.Leu254= Benign ★★ same type
- SCRIB p.Phe571= Benign ★★ same type
- SCRIB p.Pro1343= Benign ★★ same type
- SCRIB p.Pro1592Leu Likely benign ★★ 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-p-ala1488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown