TSPAN12 p.Ser32=
c.96T>A · rs761925454 · VCV1115284
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0517%, amr)
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 1.5 | GERP 0.17, phastCons 1 |
| Overall | ||
| CADD | 8.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0517%
Admixed American · 31/60,000 alleles
Filtering AF
0.0374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0325%
Overall
0.00192%
31/1,613,834 alleles · ultra-rare
exomes 27/1,461,622 · genomes 4/152,212 · joint denominator
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
- TSPAN12
- Protein
- p.Ser32=
- Coding
- c.96T>A
- MANE Select
- NM_012338
- dbSNP
- rs761925454
- Type
- single nucleotide variant
- Location
- chr7:120840080 (GRCh38)
- Gene constraint
- LOEUF 0.655 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 1 PDB
Similar variants
- TSPAN12 p.Ser32fs Pathogenic same residue
- TSPAN12 c.67-2A>G Likely pathogenic ★★ same type
- TSPAN12 p.Cys181Phe Pathogenic ★★ same type
- TSPAN12 p.Cys189Tyr Pathogenic/Likely pathogenic ★★ same type
- TSPAN12 p.Leu101His Likely pathogenic ★★ same type
- TSPAN12 p.Tyr138Cys Pathogenic/Likely pathogenic ★★ same type
- TSPAN12 c.469-3C>T Uncertain significance ★★ same type
- TSPAN12 c.-102G>A 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/tspan12-p-ser32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown