ETAA1 p.Thr16=
c.48G>T · rs150473742 · VCV708358
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.897%, afr)
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 1.7 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 8.393 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.897%
African / African-American · 671/74,820 alleles
Filtering AF
0.841%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.818%
Overall
0.0504%
808/1,603,148 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.897% | 112 |
| Admixed American | 0.109% | 918 |
| Remaining individualsnot grpmax-eligible | 0.0854% | 1,171 |
| Middle Eastern | 0.0497% | 2,011 |
| Finnishnot grpmax-eligible | 0.0016% | 62,568 |
| European (non-Finnish) | 0.00128% | 78,324 |
| South Asian | 0.00112% | 89,388 |
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
- ETAA1
- Protein
- p.Thr16=
- Coding
- c.48G>T
- MANE Select
- NM_019002
- dbSNP
- rs150473742
- Type
- single nucleotide variant
- Location
- chr2:67397496 (GRCh38)
- Gene constraint
- LOEUF 0.849 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.74 · 5 PDB
- Residue 16
- the 'disordered' region
Similar variants
- ETAA1 p.Thr16Met Uncertain significance ★ ⚠ same residue
- ETAA1 p.Glu588= Benign ★★ same type
- ETAA1 p.Pro861= Benign ★★ same type
- ETAA1 p.Ala40Val Uncertain significance ★ ⚠ same type
- ETAA1 p.Ala48Pro Uncertain significance ★ ⚠ same type
- ETAA1 p.Ala48Val Uncertain significance ★ ⚠ same type
- ETAA1 p.Ala544Val Uncertain significance ★ ⚠ same type
- ETAA1 p.Ala586Thr 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/etaa1-p-thr16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown