PHF2 p.Ser738=
c.2214G>A · rs79708182 · VCV776435
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.47%, 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 -5.3 | GERP -2.8 |
| Overall | ||
| CADD | 0.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.47%
African / African-American · 2,603/75,006 alleles
Filtering AF
3.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.31%
Overall
0.188%
3,030/1,613,050 alleles · low-frequency
exomes 1,590/1,460,766 · genomes 1,440/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.47% | 29 |
| Middle Eastern | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.272% | 368 |
| Admixed American | 0.167% | 600 |
| European (non-Finnish) | 0.0112% | 8,939 |
| South Asian | 0.00549% | 18,212 |
| East Asian | 0.00446% | 22,429 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
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
- PHF2
- Protein
- p.Ser738=
- Coding
- c.2214G>A
- MANE Select
- NM_005392
- dbSNP
- rs79708182
- Type
- single nucleotide variant
- Location
- chr9:93667106 (GRCh38)
- Gene constraint
- LOEUF 0.329 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.14 · 9 PDB
- Residue 738
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- PHF2 c.299+7T>A Benign ★★ same type
- PHF2 c.789+10G>A Benign/Likely benign ★★ same type
- PHF2 p.Asp103= Benign ★★ same type
- PHF2 p.Leu645= Benign/Likely benign ★★ same type
- PHF2 p.Pro786= Benign ★★ same type
- PHF2 p.Pro988= Benign ★★ same type
- PHF2 p.Ser725= Benign ★★ same type
- PHF2 p.Thr124= 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/phf2-p-ser738 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown