ESR1 p.Asn92=
c.276C>T · rs1427814349 · VCV744790
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00182%, amr)
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 -2.2 | GERP -2.5 |
| Overall | ||
| CADD | 7.612 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00182%
Admixed American · 1/55,096 alleles
Overall
7.01e-05%
1/1,426,082 alleles · very rare
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
- ESR1
- Protein
- p.Asn92=
- Coding
- c.276C>T
- MANE Select
- NM_000125
- dbSNP
- rs1427814349
- Type
- single nucleotide variant
- Location
- chr6:151808188 (GRCh38)
- Gene constraint
- LOEUF 0.456 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.14 · 492 PDB
- Residue 92
- the 'modulating (transactivation af-1); mediates interaction with macrod1' region; the 'interaction with ddx5; self-association' region
Similar variants
- SYNE1 p.Arg8746Ter Pathogenic/Likely pathogenic ★★ same type
- ESR1 p.Lys299Arg Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8735Leu Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8738His Uncertain significance ★★ ⚠ same type
- SYNE1 p.Arg8746Gln Uncertain significance ★★ same type
- SYNE1 p.Arg8782Gln Uncertain significance ★★ same type
- SYNE1 p.Arg8782Gly Uncertain significance ★★ same type
- SYNE1 p.Asp8725Asn 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/esr1-p-asn92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown