AMN c.-23G>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 56.6%, 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 -5.5 | GERP -1.7 |
| Non-coding constraint | Z 1.29 | 1 kb window · o/e 0.89 · regional · uncalibrated |
| Overall | ||
| CADD | 1.384 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
56.6%
African / African-American · 42,304/74,698 alleles
Filtering AF
56.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 56%
Overall
38.8%
617,833/1,592,304 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 56.6% | 2 |
| Amishnot grpmax-eligible | 44% | 2 |
| European (non-Finnish) | 39.9% | 3 |
| Middle Eastern | 38.7% | 3 |
| Remaining individualsnot grpmax-eligible | 38.4% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 37.4% | 3 |
| Finnishnot grpmax-eligible | 35.5% | 3 |
| Admixed American | 33.6% | 3 |
| South Asian | 29.5% | 3 |
| East Asian | 11.1% | 9 |
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.-23G>C
- MANE Select
- NM_030943
- dbSNP
- rs2295829
- Type
- single nucleotide variant
- Location
- chr14:102922666 (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-minus-23g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown