ETV6 p.Ser352=
c.1056C>T · rs1947156706 · VCV2869514
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 carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.24 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 13.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,002 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,150 alleles · very rare
exomes 2/1,461,856 · genomes 0/152,294 · 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
- ETV6
- Protein
- p.Ser352=
- Coding
- c.1056C>T
- MANE Select
- NM_001987
- dbSNP
- rs1947156706
- Type
- single nucleotide variant
- Location
- chr12:11884491 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.61 · 43 PDB
- Residue 352
- a DNA-binding region; an α-helix
Similar variants
- ETV6 p.Arg105Ter Pathogenic/Likely pathogenic ★★ same type
- ETV6 p.Arg339Ter Pathogenic ★★ same type
- ETV6 p.Arg359Ter Pathogenic ★★ same type
- ETV6 p.Arg369Gln Pathogenic/Likely pathogenic ★★ same type
- ETV6 p.Arg369Trp Pathogenic/Likely pathogenic ★★ same type
- ETV6 p.Arg378Ter Pathogenic/Likely pathogenic ★★ same type
- ETV6 p.Arg399Cys Pathogenic/Likely pathogenic ★★ same type
- ETV6 p.Arg399His Pathogenic/Likely pathogenic ★★ 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/etv6-p-ser352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown