CENPF p.Glu2328=
c.6984G>A · rs41277192 · VCV770861
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.59%, sas)
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 1.1 | GERP -1.4, phastCons 0.002 |
| Overall | ||
| CADD | 2.203 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.59%
South Asian · 1,448/91,082 alleles
Filtering AF
1.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.49%
Overall
0.762%
12,304/1,614,068 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.59% | 63 |
| Middle Eastern | 1.07% | 93 |
| European (non-Finnish) | 0.839% | 119 |
| Remaining individualsnot grpmax-eligible | 0.714% | 140 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| Admixed American | 0.3% | 333 |
| Ashkenazi Jewishnot grpmax-eligible | 0.267% | 375 |
| Finnishnot grpmax-eligible | 0.136% | 736 |
| African / African-American | 0.123% | 816 |
| East Asian | 0.00446% | 22,428 |
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
- CENPF
- Protein
- p.Glu2328=
- Coding
- c.6984G>A
- MANE Select
- NM_016343
- dbSNP
- rs41277192
- Type
- single nucleotide variant
- Location
- chr1:214646554 (GRCh38)
- Gene constraint
- LOEUF 0.734 · pLI <0.01 (gnomAD)
- Residue 2328
- the 'interaction with nde1 and ndel1' region; the '2 x 177 aa tandem repeats' region
Similar variants
- CENPF p.Glu2328Lys Uncertain significance ★ ⚠ same residue
- CENPF c.1195-2A>G Likely pathogenic ★★ same type
- CENPF c.1323+1G>A Pathogenic ★★ same type
- CENPF p.Arg1667Ter Pathogenic/Likely pathogenic ★★ same type
- CENPF p.Arg2407Ter Pathogenic/Likely pathogenic ★★ same type
- CENPF p.Arg2898Ter Pathogenic ★★ same type
- CENPF p.Arg3094Ter Likely pathogenic ★★ same type
- CENPF p.Glu1257Ter Pathogenic ★★ 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/cenpf-p-glu2328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown