AMN c.*133T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.74%, afr) — too common for a highly-penetrant pathogenic allele
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 -1.9 | GERP -1.7 |
| Overall | ||
| CADD | 0.661 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.74%
African / African-American · 5,559/63,608 alleles
Filtering AF
8.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.47%
Overall
0.598%
6,338/1,060,370 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.74% | 11 |
| Remaining individualsnot grpmax-eligible | 0.662% | 151 |
| Middle Eastern | 0.611% | 164 |
| Admixed American | 0.536% | 187 |
| South Asian | 0.026% | 3,844 |
| European (non-Finnish) | 0.0248% | 4,028 |
| East Asian | 0.00259% | 38,584 |
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
- AMN
- Coding
- c.*133T>C
- MANE Select
- NM_030943
- dbSNP
- rs7153925
- Type
- single nucleotide variant
- Location
- chr14:102930813 (GRCh38)
- Gene constraint
- LOEUF 1.446 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.78 · 1 PDB
Similar variants
- AMN c.208-1G>C Pathogenic/Likely pathogenic ★★ same type
- AMN c.296-1G>A Likely pathogenic ★★ same type
- AMN c.44-1G>A Likely pathogenic ★★ same type
- AMN c.760+1G>A Likely pathogenic ★★ same type
- AMN c.844-1G>C Likely pathogenic ★★ same type
- AMN p.Thr41Ile Likely pathogenic ★★ ⚠ same type
- AMN p.Trp391Ter Pathogenic/Likely pathogenic ★★ same type
- AMN c.296-3C>T 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/amn-c-star-133t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown