CEACAM3 p.Thr135=
c.405T>C · rs61736640 · VCV769009
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.76%, 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 -6.9 | GERP -3.3 |
| Overall | ||
| CADD | 1.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.76%
African / African-American · 6,501/74,218 alleles
Filtering AF
8.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.51%
Overall
0.469%
7,535/1,607,474 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.76% | 11 |
| Remaining individualsnot grpmax-eligible | 0.646% | 155 |
| Admixed American | 0.59% | 170 |
| Middle Eastern | 0.348% | 287 |
| South Asian | 0.0288% | 3,470 |
| European (non-Finnish) | 0.0194% | 5,161 |
| Finnishnot grpmax-eligible | 0.00472% | 21,209 |
| East Asian | 0.00446% | 22,439 |
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
- CEACAM3
- Protein
- p.Thr135=
- Coding
- c.405T>C
- MANE Select
- NM_001815
- dbSNP
- rs61736640
- Type
- single nucleotide variant
- Location
- chr19:41797929 (GRCh38)
- Gene constraint
- LOEUF 1.359 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.52 · 4 PDB
- Residue 135
- a β-strand; the ig-like v-type domain
Similar variants
- CEACAM3 p.Ala93Pro Benign ★★ same type
- CEACAM3 p.Asn111= Likely benign ★★ same type
- CEACAM3 p.Glu133Gly Benign ★★ ⚠ same type
- CEACAM3 p.Leu78Gln Benign ★★ same type
- CEACAM3 p.Ser77Arg Benign ★★ same type
- CEACAM3 p.Thr103= Benign ★★ same type
- CEACAM3 p.Tyr95Asn Benign ★★ same type
- CEACAM3 p.Val83Ala Benign ★★ 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/ceacam3-p-thr135 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown