CYP19A1 p.Pro22=
c.66T>A · rs780440634 · VCV1094296
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, 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 -1.1 | GERP 0.29 |
| Overall | ||
| CADD | 3.643 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,780 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00918%
Overall
0.000692%
10/1,445,332 alleles · ultra-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
- CYP19A1
- Protein
- p.Pro22=
- Coding
- c.66T>A
- MANE Select
- NM_000103
- dbSNP
- rs780440634
- Type
- single nucleotide variant
- Location
- chr15:51242847 (GRCh38)
- Gene constraint
- LOEUF 0.793 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 91.51 · 11 PDB
Similar variants
- CYP19A1 p.Pro22Ser Uncertain significance ★ same residue
- CYP19A1 c.1263+1G>A Pathogenic/Likely pathogenic ★★ same type
- CYP19A1 c.1263+1G>T Pathogenic/Likely pathogenic ★★ same type
- CYP19A1 c.297-1G>C Likely pathogenic ★★ same type
- CYP19A1 p.Arg115Gln Likely pathogenic ★★ same type
- CYP19A1 p.Arg365Gln Likely pathogenic ★★ same type
- CYP19A1 p.Arg375Cys Likely pathogenic ★★ same type
- CYP19A1 p.Arg457Ter Likely pathogenic ★★ 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/cyp19a1-p-pro22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown