AMHR2 p.Cys472=
c.1416C>T · VCV4046762
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.257 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.23 | loss · gain 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1.5, phastCons 0.65 |
| Overall | ||
| CADD | 6.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,040 alleles
Overall
6.84e-05%
1/1,461,888 alleles · very rare
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.Cys472=
- Coding
- c.1416C>T
- MANE Select
- NM_020547
- Type
- single nucleotide variant
- Location
- chr12:53430273 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.34 · 1 PDB
- Residue 472
- the protein kinase domain
Similar variants
- AMHR2 p.Ala139Val Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Arg22Gln Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Arg545Thr Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Cys551Tyr Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Ser432Asn Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Trp367Cys Uncertain significance ★★ ⚠ same condition
- AMHR2 p.Arg59His Likely benign ★★ same condition
- AMHR2 p.Leu542= Benign/Likely benign ★★ same condition
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-cys472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown