CEP19 p.Leu73=
c.219A>G · rs142077651 · VCV761410
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.1%, 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 0.26 | GERP -3.1, phastCons 0.99 |
| Overall | ||
| CADD | 8.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.1%
South Asian · 1,001/91,084 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.02%
Overall
0.0812%
1,311/1,614,180 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.1% | 91 |
| East Asian | 0.43% | 233 |
| Remaining individualsnot grpmax-eligible | 0.114% | 880 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.00666% | 15,006 |
| African / African-American | 0.004% | 25,021 |
| European (non-Finnish) | 0.00305% | 32,779 |
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
- CEP19
- Protein
- p.Leu73=
- Coding
- c.219A>G
- MANE Select
- NM_032898
- dbSNP
- rs142077651
- Type
- single nucleotide variant
- Location
- chr3:196707824 (GRCh38)
- Gene constraint
- LOEUF 1.208 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.85
Similar variants
- CEP19 p.Arg32His Uncertain significance ★★ same type
- CEP19 p.Arg37Ter Uncertain significance ★★ same type
- CEP19 p.Arg95Trp Uncertain significance ★★ same type
- CEP19 p.Asn54Ser Uncertain significance ★★ same type
- CEP19 p.Gly27Arg Uncertain significance ★★ same type
- CEP19 p.Ile33Val Uncertain significance ★★ same type
- CEP19 p.Lys111Arg Uncertain significance ★★ same type
- CEP19 p.Met1Thr 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/cep19-p-leu73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown