AMH p.Phe100=
c.300C>T · rs147472740 · VCV782047
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.1%, eas)
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 -20 | GERP -2.4 |
| Overall | ||
| CADD | 0.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.1%
East Asian · 889/42,332 alleles
Filtering AF
1.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.94%
Overall
0.0981%
1,501/1,529,300 alleles · low-frequency
exomes 1,333/1,377,000 · genomes 168/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.1% | 48 |
| Ashkenazi Jewishnot grpmax-eligible | 0.702% | 143 |
| Remaining individualsnot grpmax-eligible | 0.144% | 693 |
| Admixed American | 0.124% | 806 |
| South Asian | 0.0879% | 1,137 |
| Finnishnot grpmax-eligible | 0.0811% | 1,232 |
| Middle Eastern | 0.0173% | 5,780 |
| European (non-Finnish) | 0.014% | 7,127 |
| African / African-American | 0.00964% | 10,377 |
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
- AMH
- Protein
- p.Phe100=
- Coding
- c.300C>T
- MANE Select
- NM_000479
- dbSNP
- rs147472740
- Type
- single nucleotide variant
- Location
- chr19:2249632 (GRCh38)
- Gene constraint
- LOEUF 1.954 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 69.40 · 3 PDB
Similar variants
- AMH p.Arg40Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Gln217Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Glu389Ter Pathogenic/Likely pathogenic ★★ same type
- AMH p.Gly101Arg Likely pathogenic ★★ same type
- AMH p.Pro151Ser Pathogenic ★★ ⚠ same type
- AMH p.Trp371Ter Pathogenic ★★ same type
- AMH p.Tyr167Cys Pathogenic ★★ ⚠ same type
- AMH p.Ala78Thr 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/amh-p-phe100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown