CEACAM16 p.Pro79=
c.237G>A · rs535370616 · VCV1588755
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, 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 -10 | GERP -4.5 |
| Overall | ||
| CADD | 0.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/74,944 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00335%
54/1,612,904 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,684 |
| East Asian | 0.0112% | 8,966 |
| South Asian | 0.0033% | 30,341 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,224 |
| European (non-Finnish) | 0.00237% | 42,132 |
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
- CEACAM16
- Protein
- p.Pro79=
- Coding
- c.237G>A
- MANE Select
- NM_001039213
- dbSNP
- rs535370616
- Type
- single nucleotide variant
- Location
- chr19:44703548 (GRCh38)
- Gene constraint
- LOEUF 1.139 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.50
Similar variants
- CEACAM16 p.Pro79Leu Uncertain significance ★★ ⚠ same residue
- CEACAM16 c.1267+1G>A Uncertain significance ★★ same type
- CEACAM16 p.Ala198Thr Uncertain significance ★★ ⚠ same type
- CEACAM16 p.Ala355Thr Uncertain significance ★★ ⚠ same type
- CEACAM16 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- CEACAM16 p.Ala375Val Uncertain significance ★★ ⚠ same type
- CEACAM16 p.Ala50Thr Uncertain significance ★★ ⚠ same type
- CEACAM16 p.Arg145Cys 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/ceacam16-p-pro79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown