PHF20 p.Pro827=
c.2481G>A · rs149353721 · VCV710869
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.08%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -3.4 |
| Overall | ||
| CADD | 4.521 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.08%
African / African-American · 1,559/75,036 alleles
Filtering AF
1.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.96%
Overall
0.125%
2,017/1,614,138 alleles · low-frequency
exomes 1,077/1,461,842 · genomes 940/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.08% | 48 |
| Remaining individualsnot grpmax-eligible | 0.19% | 525 |
| Middle Eastern | 0.165% | 606 |
| Admixed American | 0.153% | 652 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0574% | 1,742 |
| European (non-Finnish) | 0.0178% | 5,619 |
| South Asian | 0.00988% | 10,121 |
| East Asian | 0.00223% | 44,878 |
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
- PHF20
- Protein
- p.Pro827=
- Coding
- c.2481G>A
- MANE Select
- NM_016436
- dbSNP
- rs149353721
- Type
- single nucleotide variant
- Location
- chr20:35938877 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.32 · 7 PDB
Similar variants
- PHF20 c.1826-4G>A Benign ★★ same type
- PHF20 c.2897-6C>T Benign/Likely benign ★★ same type
- PHF20 p.Arg845= Benign ★★ same type
- PHF20 p.Phe621= Benign ★★ same type
- PHF20 p.Ala235Asp Uncertain significance ★ ⚠ same type
- PHF20 p.Ala395Val Uncertain significance ★ ⚠ same type
- PHF20 p.Ala443Thr Uncertain significance ★ ⚠ same type
- PHF20 p.Ala867Val 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/phf20-p-pro827 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown