VMA12 p.Val12=
c.36G>A · rs781939580 · VCV751242
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.44 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.21 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -2.8 | |
| Overall | ||
| CADD | 8.936 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Admixed American · 14/60,008 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.00279%
45/1,612,998 alleles · ultra-rare
exomes 38/1,460,774 · genomes 7/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0233% | 4,286 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| European (non-Finnish) | 0.00237% | 42,141 |
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
- VMA12
- Protein
- p.Val12=
- Coding
- c.36G>A
- MANE Select
- NM_152464
- dbSNP
- rs781939580
- Type
- single nucleotide variant
- Location
- chr17:28357706 (GRCh38)
- Structure
- AlphaFold pLDDT 80.82
Similar variants
- VMA12 p.Arg31Pro Pathogenic/Likely pathogenic ★★ ⚠ same type
- VMA12 p.Ala7Thr Uncertain significance ★★ ⚠ same type
- VMA12 p.Arg120His Uncertain significance ★★ ⚠ same type
- VMA12 p.Arg178Trp Uncertain significance ★★ ⚠ same type
- VMA12 p.Arg199Gly Uncertain significance ★★ same type
- VMA12 p.Asn152Ser Uncertain significance ★★ ⚠ same type
- VMA12 p.Asp126His Uncertain significance ★★ ⚠ same type
- TMEM199 c.286-120C>T 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/vma12-p-val12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown