CEP89 p.Asn614=
c.1842C>T · rs10418340 · VCV1631443
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 97.8%, afr) — too common for a highly-penetrant pathogenic allele
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 -4.2 | GERP -3.4 |
| Overall | ||
| CADD | 0.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
97.8%
African / African-American · 73,354/75,028 alleles
Filtering AF
97.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 96.9%
Overall
87.3%
1,408,390/1,613,474 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 97.8% | 1 |
| South Asian | 94.8% | 1 |
| Admixed American | 92.8% | 1 |
| East Asian | 91% | 1 |
| Finnishnot grpmax-eligible | 88.5% | 1 |
| Remaining individualsnot grpmax-eligible | 87.5% | 1 |
| European (non-Finnish) | 85.7% | 1 |
| Middle Eastern | 85% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 82.8% | 1 |
| Amishnot grpmax-eligible | 80.6% | 1 |
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
- CEP89
- Protein
- p.Asn614=
- Coding
- c.1842C>T
- MANE Select
- NM_032816
- dbSNP
- rs10418340
- Type
- single nucleotide variant
- Location
- chr19:32899890 (GRCh38)
- Gene constraint
- LOEUF 1.173 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.08
Similar variants
- CEP89 p.Asn614Thr Uncertain significance ★ same residue
- CEP89 p.Ala291Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala291Val Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala54Val Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala680Thr Uncertain significance ★★ ⚠ same type
- CEP89 p.Ala780Asp Uncertain significance ★★ ⚠ same type
- CEP89 p.Arg102Trp 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/cep89-p-asn614 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown