CBX2 p.Ile49=
c.147C>T · rs35124694 · VCV1614331
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.03%, mid) — 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 0.78 | GERP -0.22, phastCons 1 |
| Overall | ||
| CADD | 12.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.03%
Middle Eastern · 304/6,040 alleles
Filtering AF
4.57%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.39%
Overall
2.39%
38,594/1,613,810 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 5.03% | 20 |
| European (non-Finnish) | 2.68% | 37 |
| Remaining individualsnot grpmax-eligible | 2.64% | 38 |
| Ashkenazi Jewishnot grpmax-eligible | 2.39% | 42 |
| Admixed American | 2.2% | 46 |
| Finnishnot grpmax-eligible | 1.93% | 52 |
| South Asian | 1.54% | 65 |
| Amishnot grpmax-eligible | 0.877% | 114 |
| African / African-American | 0.396% | 253 |
| East Asian | 0.0156% | 6,411 |
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
- CBX2
- Protein
- p.Ile49=
- Coding
- c.147C>T
- MANE Select
- NM_005189
- dbSNP
- rs35124694
- Type
- single nucleotide variant
- Location
- chr17:79779392 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.29 · 3 PDB
- Residue 49
- the chromo domain; the 'involved in the interaction with h3c15 and h3c1' region
Similar variants
- CBX2 c.288+52G>T Uncertain significance ★★ same type
- CBX2 p.Arg137His Uncertain significance ★★ ⚠ same type
- CBX2 p.Gln349His Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly133Ser Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly287Arg Uncertain significance ★★ ⚠ same type
- CBX2 p.Gly332Asp Uncertain significance ★★ ⚠ same type
- CBX2 p.Met260Val Uncertain significance ★★ ⚠ same type
- CBX2 p.Met404Leu 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/cbx2-p-ile49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown