PHRF1 p.Phe31=
c.93T>C · rs369756671 · VCV2641075
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -2 |
| Overall | ||
| CADD | 6.865 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,888 alleles
Filtering AF
0.000689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00105%
17/1,612,038 alleles · very rare
exomes 15/1,459,850 · genomes 2/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,444 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,398 |
| European (non-Finnish) | 0.00119% | 84,237 |
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
- PHRF1
- Protein
- p.Phe31=
- Coding
- c.93T>C
- MANE Select
- NM_001286581
- dbSNP
- rs369756671
- Type
- single nucleotide variant
- Location
- chr11:581605 (GRCh38)
- Gene constraint
- LOEUF 0.573 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 46.11
- Residue 31
- the 'disordered' region
Similar variants
- PHRF1 p.Ala1355= Benign ★★ same type
- PHRF1 p.Gly1209Arg Benign ★★ same type
- PHRF1 p.Ser1168Leu Benign ★★ same type
- PHRF1 p.Ser1457Gly Likely benign ★★ same type
- PHRF1 p.Thr959= Likely benign ★★ same type
- PHRF1 p.Ala114Ser Uncertain significance ★ ⚠ same type
- PHRF1 p.Ala114Val Uncertain significance ★ ⚠ same type
- PHRF1 p.Ala1197Ser 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/phrf1-p-phe31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown