AMER1 p.His96=
c.288C>T · rs112308756 · VCV2188641
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0633%, 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 -6.8 | GERP -0.67 |
| Overall | ||
| CADD | 0.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0633%
Admixed American · 29/45,789 alleles
Filtering AF
0.0452%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0392%
Overall
0.00347%
42/1,210,029 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0633% | 1,579 |
| Middle Eastern | 0.0457% | 2,187 |
| Remaining individualsnot grpmax-eligible | 0.0105% | 9,521 |
| South Asian | 0.00176% | 56,829 |
| African / African-American | 0.00175% | 57,141 |
| European (non-Finnish) | 0.000447% | 223,816 |
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
- AMER1
- Protein
- p.His96=
- Coding
- c.288C>T
- MANE Select
- NM_152424
- dbSNP
- rs112308756
- Type
- single nucleotide variant
- Location
- chrX:64192999 (GRCh38)
- Structure
- AlphaFold pLDDT 48.88 · 3 PDB
- Residue 96
- the 'disordered' region
Similar variants
- AMER1 p.Arg353Ter Pathogenic ★★ same type
- AMER1 p.Arg358Ter Pathogenic ★★ same type
- AMER1 p.Arg497Ter Pathogenic/Likely pathogenic ★★ same type
- AMER1 p.Gln189Ter Pathogenic ★★ same type
- AMER1 p.Gln335Ter Pathogenic ★★ same type
- AMER1 p.Glu191Ter Pathogenic/Likely pathogenic ★★ same type
- AMER1 p.Ala202Gly Uncertain significance ★★ ⚠ same type
- AMER1 p.Ala229Pro 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/amer1-p-his96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown