SNCAIP p.Ser853=
c.2559G>A · VCV4971748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.147%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -4.5 |
| Overall | ||
| CADD | 0.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
African / African-American · 110/75,014 alleles
Filtering AF
0.124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.116%
Overall
0.0103%
167/1,614,056 alleles · rare
exomes 100/1,461,866 · genomes 67/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.147% | 682 |
| Admixed American | 0.0167% | 6,001 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| European (non-Finnish) | 0.00314% | 31,892 |
| South Asian | 0.0011% | 91,078 |
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
- SNCAIP
- Protein
- p.Ser853=
- Coding
- c.2559G>A
- MANE Select
- NM_005460
- Type
- single nucleotide variant
- Location
- chr5:122451406 (GRCh38)
- Gene constraint
- LOEUF 0.636 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98 · 1 PDB
- Residue 853
- the 'disordered' region
Similar variants
- SNCAIP p.Ala358Val Uncertain significance ★★ ⚠ same type
- SNCAIP p.Ala363Thr Uncertain significance ★★ ⚠ same type
- SNCAIP p.Glu237Lys Uncertain significance ★★ ⚠ same type
- SNCAIP p.Leu148= Uncertain significance ★★ same type
- SNCAIP p.Ser912Arg Uncertain significance ★★ ⚠ same type
- SNCAIP p.Val461Ile Uncertain significance ★★ ⚠ same type
- SNCAIP c.*103C>T Likely benign ★★ same type
- SNCAIP c.*46T>G 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/sncaip-p-ser853 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown