AMHR2 p.Arg71=
c.211C>A · rs200109472 · VCV731907
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00721%, nfe)
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 |
|---|---|---|
| Pangolin | Δ0.23 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 0.89, phastCons 0.99 |
| Overall | ||
| CADD | 9.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00721%
European (non-Finnish) · 85/1,179,728 alleles
Filtering AF
0.00596%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00549%
Overall
0.00558%
90/1,613,198 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00721% | 13,879 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,617 |
| African / African-American | 0.00134% | 74,894 |
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
- AMHR2
- Protein
- p.Arg71=
- Coding
- c.211C>A
- MANE Select
- NM_020547
- dbSNP
- rs200109472
- Type
- single nucleotide variant
- Location
- chr12:53424449 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.34 · 1 PDB
- Residue 71
- a disulfide bond
Similar variants
- AMHR2 p.Arg71Gln Likely benign ★ same residue
- AMHR2 p.Ala168Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- AMHR2 p.Arg172Ter Pathogenic/Likely pathogenic ★★ same type
- AMHR2 p.Arg22Ter Pathogenic/Likely pathogenic ★★ same type
- AMHR2 p.Arg463Cys Pathogenic/Likely pathogenic ★★ same type
- AMHR2 p.Arg471His Pathogenic/Likely pathogenic ★★ ⚠ same type
- AMHR2 p.Ala118Thr Uncertain significance ★★ ⚠ same type
- AMHR2 p.Ala139Val 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/amhr2-p-arg71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown