STAT6 p.Val316=
c.948G>A · rs1592567210 · VCV762678
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.177 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.62 | donor gain · deltas |
| Pangolin | Δ0.49 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.7 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 19.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,952 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,038 alleles · very rare
exomes 2/1,461,710 · genomes 0/152,328 · 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
- STAT6
- Protein
- p.Val316=
- Coding
- c.948G>A
- MANE Select
- NM_003153
- dbSNP
- rs1592567210
- Type
- single nucleotide variant
- Location
- chr12:57105204 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.56 (gnomAD)
- Structure
- AlphaFold pLDDT 77.44 · 7 PDB
- Residue 316
- a β-strand
Similar variants
- STAT6 c.1001+10G>A Benign ★★ same type
- STAT6 c.1213-6C>T Benign ★★ same type
- STAT6 c.1744+9A>C Likely benign ★★ same type
- STAT6 p.Ser564= Benign/Likely benign ★★ same type
- STAT6 p.Val269Ile Benign ★★ same type
- STAT6 p.Asp419His Likely pathogenic ★ same type
- STAT6 p.Ala109Val Uncertain significance ★ ⚠ same type
- STAT6 p.Ala245Val 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/stat6-p-val316 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown