CHPF2 p.Phe303=
c.909C>T · rs150602051 · VCV2658186
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.865%, nfe)
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 · C>A here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.7 |
| Overall | ||
| CADD | 12.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.865%
European (non-Finnish) · 10,179/1,177,100 alleles
Filtering AF
0.851%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.845%
Overall
0.689%
11,097/1,610,482 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.865% | 116 |
| Remaining individualsnot grpmax-eligible | 0.502% | 199 |
| Finnishnot grpmax-eligible | 0.369% | 271 |
| Admixed American | 0.155% | 644 |
| African / African-American | 0.145% | 688 |
| South Asian | 0.133% | 752 |
| Ashkenazi Jewishnot grpmax-eligible | 0.132% | 758 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| Middle Eastern | 0.0827% | 1,209 |
| East Asian | 0.00224% | 44,718 |
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
- CHPF2
- Protein
- p.Phe303=
- Coding
- c.909C>T
- MANE Select
- NM_019015
- dbSNP
- rs150602051
- Type
- single nucleotide variant
- Location
- chr7:151236488 (GRCh38)
- Gene constraint
- LOEUF 1.136 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.86
Similar variants
- CHPF2 p.Arg254His Benign ★★ same type
- CHPF2 p.Arg460Gln Benign/Likely benign ★★ same type
- CHPF2 p.Ala189Ser Uncertain significance ★ ⚠ same type
- CHPF2 p.Ala216Thr Uncertain significance ★ ⚠ same type
- CHPF2 p.Ala220Thr Uncertain significance ★ ⚠ same type
- CHPF2 p.Ala352Gly Uncertain significance ★ ⚠ same type
- CHPF2 p.Ala406Val Uncertain significance ★ ⚠ same type
- CHPF2 p.Ala547Pro 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/chpf2-p-phe303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown