Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.31%, amr)
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 1.4 | GERP 0.43, phastCons 1 |
| Overall | ||
| CADD | 7.583 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.31%
Admixed American · 2,586/60,002 alleles
Filtering AF
4.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.12%
Overall
0.407%
6,537/1,607,146 alleles · low-frequency
exomes 5,368/1,454,884 · genomes 1,169/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 4.31% | 23 |
| Finnishnot grpmax-eligible | 3.47% | 29 |
| Ashkenazi Jewishnot grpmax-eligible | 2.06% | 49 |
| East Asian | 0.591% | 169 |
| Remaining individualsnot grpmax-eligible | 0.453% | 221 |
| Middle Eastern | 0.0496% | 2,015 |
| African / African-American | 0.0467% | 2,140 |
| European (non-Finnish) | 0.0431% | 2,320 |
| South Asian | 0.033% | 3,032 |
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
- PGR
- Protein
- p.Arg623=
- Coding
- c.1869C>A
- MANE Select
- NM_000926
- dbSNP
- rs2020876
- Type
- single nucleotide variant
- Location
- chr11:101091797 (GRCh38)
- Gene constraint
- LOEUF 0.554 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 57.66 · 21 PDB
- Residue 623
- a DNA-binding region; an α-helix
Similar variants
- PGR p.Arg187= Benign ★★ same type
- PGR p.Cys347Ser Benign ★★ same type
- PGR p.Gln536Pro Benign ★★ same type
- PGR p.Gln75Lys Likely benign ★★ same type
- PGR p.Gln868= Benign ★★ same type
- PGR p.Gly263= Benign ★★ same type
- PGR p.Gly435= Likely benign ★★ same type
- PGR p.Gly661= Benign ★★ 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/pgr-p-arg623 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown