PHF20 p.Arg845=
c.2535C>T · rs17347322 · VCV708475
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.994%, 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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.5 | GERP -3.5 |
| Overall | ||
| CADD | 10.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.994%
European (non-Finnish) · 11,728/1,180,022 alleles
Filtering AF
0.979%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.973%
Overall
0.834%
13,465/1,614,206 alleles · rare
exomes 12,475/1,461,866 · genomes 990/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.994% | 101 |
| Ashkenazi Jewishnot grpmax-eligible | 0.915% | 109 |
| Remaining individualsnot grpmax-eligible | 0.73% | 137 |
| Admixed American | 0.385% | 260 |
| African / African-American | 0.36% | 278 |
| South Asian | 0.354% | 283 |
| Middle Eastern | 0.247% | 404 |
| Finnishnot grpmax-eligible | 0.231% | 433 |
| East Asian | 0.0535% | 1,870 |
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.Arg845=
- Coding
- c.2535C>T
- MANE Select
- NM_016436
- dbSNP
- rs17347322
- Type
- single nucleotide variant
- Location
- chr20:35938931 (GRCh38)
- Gene constraint
- LOEUF 0.249 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 55.32 · 7 PDB
Similar variants
- PHF20 p.Arg845Cys Uncertain significance ★ ⚠ same residue
- PHF20 c.1826-4G>A Benign ★★ same type
- PHF20 c.2897-6C>T Benign/Likely benign ★★ same type
- PHF20 p.Phe621= Benign ★★ same type
- PHF20 p.Pro827= Benign ★★ same type
- PHF20 p.Ala235Asp Uncertain significance ★ ⚠ same type
- PHF20 p.Ala395Val Uncertain significance ★ ⚠ same type
- PHF20 p.Ala443Thr 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-arg845 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown