SPINT2 p.Ala202=
c.606G>A · rs76692070 · VCV1165106
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.373%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.65 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -5.2 |
| Overall | ||
| CADD | 18.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.373%
African / African-American · 280/74,984 alleles
Filtering AF
0.337%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.323%
Overall
0.0207%
334/1,612,636 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.373% | 268 |
| Middle Eastern | 0.0797% | 1,255 |
| Remaining individualsnot grpmax-eligible | 0.0353% | 2,835 |
| Admixed American | 0.01% | 9,998 |
| South Asian | 0.0033% | 30,327 |
| European (non-Finnish) | 0.00161% | 62,099 |
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
- SPINT2
- Protein
- p.Ala202=
- Coding
- c.606G>A
- MANE Select
- NM_021102
- dbSNP
- rs76692070
- Type
- single nucleotide variant
- Location
- chr19:38291853 (GRCh38)
- Gene constraint
- LOEUF 0.935 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.66 · 1 PDB
- Residue 202
- a UniProt-annotated variant site (in diar3; likely pathogenic)
Similar variants
- SPINT2 p.Ala202Thr Uncertain significance ★ ⚠ same residue
- SPINT2 p.Ala202Val Uncertain significance ★ ⚠ same residue
- SPINT2 p.Tyr163Cys Pathogenic ★★ same type
- SPINT2 p.Ala2Val Uncertain significance ★★ ⚠ same type
- SPINT2 p.Ala89Val Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg182Cys Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg182His Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg185Cys 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/spint2-p-ala202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown