SCRIB p.Asn647=
c.1941T>C · rs111919660 · VCV718154
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.982%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.6 | GERP -2.7 |
| Overall | ||
| CADD | 0.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.982%
European (non-Finnish) · 11,577/1,178,520 alleles
Filtering AF
0.967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.961%
Overall
0.771%
12,428/1,610,992 alleles · rare
exomes 11,657/1,458,992 · genomes 771/152,000 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.982% | 102 |
| Remaining individualsnot grpmax-eligible | 0.512% | 195 |
| Admixed American | 0.359% | 278 |
| Ashkenazi Jewishnot grpmax-eligible | 0.225% | 445 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| Finnishnot grpmax-eligible | 0.196% | 511 |
| Middle Eastern | 0.165% | 606 |
| African / African-American | 0.151% | 663 |
| South Asian | 0.0022% | 45,416 |
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.Asn647=
- Coding
- c.1941T>C
- MANE Select
- NM_182706
- dbSNP
- rs111919660
- Type
- single nucleotide variant
- Location
- chr8:143808783 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.33 · 42 PDB
- Residue 647
- the 'sufficient for targeting to adherens junction and to inhibit cell proliferation' region; the 'disordered' region
Similar variants
- SCRIB p.Asn647His Uncertain significance ★ ⚠ same residue
- SCRIB c.3120+10C>G Benign/Likely benign ★★ same type
- SCRIB c.504-9C>T Benign ★★ same type
- SCRIB p.Ala1488= Likely benign ★★ same type
- SCRIB p.Arg492= Benign ★★ same type
- SCRIB p.Leu254= Benign ★★ same type
- SCRIB p.Phe571= Benign ★★ same type
- SCRIB p.Pro1343= 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-asn647 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown