ETV6 p.Ser428=
c.1284T>C · rs768745810 · VCV2055154
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.107%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -0.75, phastCons 0.44 |
| Overall | ||
| CADD | 4.717 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.107%
Admixed American · 64/59,992 alleles
Filtering AF
0.0857%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0781%
Overall
0.00397%
64/1,613,712 alleles · rare
exomes 60/1,461,604 · genomes 4/152,108 · 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.Ser428=
- Coding
- c.1284T>C
- MANE Select
- NM_001987
- dbSNP
- rs768745810
- Type
- single nucleotide variant
- Location
- chr12:11890971 (GRCh38)
- Gene constraint
- LOEUF 0.44 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.61 · 43 PDB
Similar variants
- ETV6 p.Ser428Asn Uncertain significance ★ ⚠ same residue
- ETV6 p.Arg359Ter Pathogenic ★★ same condition
- ETV6 p.Arg369Gln Pathogenic/Likely pathogenic ★★ same condition
- ETV6 c.1010-3T>C Uncertain significance ★★ same condition
- ETV6 p.Ala247Gly Uncertain significance ★★ ⚠ same condition
- ETV6 p.Ala67Asp Uncertain significance ★★ ⚠ same condition
- ETV6 p.Ala73Ser Uncertain significance ★★ ⚠ same condition
- ETV6 p.Arg127Trp Uncertain significance ★★ ⚠ same condition
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-ser428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown