SNCAIP p.Ser80=
c.240G>A · rs147854746 · VCV753378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.37%, eas)
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 -1.4 | GERP -3.7 |
| Overall | ||
| CADD | 7.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.37%
East Asian · 166/44,876 alleles
Filtering AF
0.324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.306%
Overall
0.0226%
364/1,614,128 alleles · rare
exomes 326/1,461,874 · genomes 38/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.37% | 270 |
| African / African-American | 0.0347% | 2,886 |
| European (non-Finnish) | 0.0133% | 7,516 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| South Asian | 0.00659% | 15,179 |
| Finnishnot grpmax-eligible | 0.00156% | 64,028 |
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.Ser80=
- Coding
- c.240G>A
- MANE Select
- NM_005460
- dbSNP
- rs147854746
- Type
- single nucleotide variant
- Location
- chr5:122422977 (GRCh38)
- Gene constraint
- LOEUF 0.636 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 51.98 · 1 PDB
- Residue 80
- 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-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown