CHPF p.Glu699=
c.2097G>A · rs114128742 · VCV786494
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.58%, afr)
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 1.4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 7.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.58%
African / African-American · 2,688/75,068 alleles
Filtering AF
3.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.42%
Overall
0.2%
3,220/1,613,946 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.58% | 28 |
| Middle Eastern | 0.544% | 184 |
| Admixed American | 0.365% | 274 |
| Remaining individualsnot grpmax-eligible | 0.254% | 393 |
| South Asian | 0.00988% | 10,121 |
| European (non-Finnish) | 0.00924% | 10,825 |
| East Asian | 0.00669% | 14,959 |
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
- CHPF
- Protein
- p.Glu699=
- Coding
- c.2097G>A
- MANE Select
- NM_024536
- dbSNP
- rs114128742
- Type
- single nucleotide variant
- Location
- chr2:219539614 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.57 · 2 PDB
Similar variants
- CHPF p.Glu699Gln Uncertain significance ★ ⚠ same residue
- CHPF p.Ser48Pro Benign/Likely benign ★★ same type
- CHPF p.Ala206Ser Uncertain significance ★ ⚠ same type
- CHPF p.Ala286Val Uncertain significance ★ ⚠ same type
- CHPF p.Ala341Thr Uncertain significance ★ ⚠ same type
- CHPF p.Ala343Gly Uncertain significance ★ ⚠ same type
- CHPF p.Ala516Val Uncertain significance ★ ⚠ same type
- CHPF p.Ala530Gly 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/chpf-p-glu699 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown