CEACAM16 p.Thr76=
c.228T>G · rs1974385839 · VCV2847079
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
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 -1.8 | GERP -4.5 |
| Overall | ||
| CADD | 2.351 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,179,822 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000753%
11/1,461,166 alleles · very rare
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.Thr76=
- Coding
- c.228T>G
- MANE Select
- NM_001039213
- dbSNP
- rs1974385839
- Type
- single nucleotide variant
- Location
- chr19:44703539 (GRCh38)
- Gene constraint
- LOEUF 1.139 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.50
Similar variants
- 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
- CEACAM16 p.Arg150His 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-thr76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown