SNIP1 p.Arg33=
c.99T>A · rs767321566 · VCV2913120
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
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 0.28 | GERP -4, phastCons 0.95 |
| Overall | ||
| CADD | 10.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,834 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00093%
15/1,612,722 alleles · very rare
exomes 12/1,460,726 · genomes 3/151,996 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,209 |
| South Asian | 0.00659% | 15,166 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,234 |
| European (non-Finnish) | 0.000254% | 393,205 |
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
- SNIP1
- Protein
- p.Arg33=
- Coding
- c.99T>A
- MANE Select
- NM_024700
- dbSNP
- rs767321566
- Type
- single nucleotide variant
- Location
- chr1:37554131 (GRCh38)
- Gene constraint
- LOEUF 0.865 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.66 · 10 PDB
- Residue 33
- the 'disordered' region
Similar variants
- SNIP1 p.Arg144Trp Uncertain significance ★★ ⚠ same type
- SNIP1 p.Arg322Gln Uncertain significance ★★ ⚠ same type
- SNIP1 p.Asp20Gly Uncertain significance ★★ ⚠ same type
- SNIP1 p.Asp383Gly Uncertain significance ★★ ⚠ same type
- SNIP1 p.Asp386Asn Uncertain significance ★★ ⚠ same type
- SNIP1 p.Asp386Glu Uncertain significance ★★ ⚠ same type
- SNIP1 p.Glu32Ala Uncertain significance ★★ ⚠ same type
- SNIP1 p.Glu385Lys 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/snip1-p-arg33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown