CBLN2 p.Ser73=
c.219G>A · rs17853471 · VCV1233144
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 46.8%, eas) — 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 -3 | GERP -1.3 |
| Overall | ||
| CADD | 11.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
46.8%
East Asian · 20,927/44,702 alleles
Filtering AF
46.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 46.1%
Overall
2.26%
36,367/1,607,626 alleles · common
exomes 31,882/1,455,376 · genomes 4,485/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 46.8% | 2 |
| Finnishnot grpmax-eligible | 5.88% | 17 |
| Remaining individualsnot grpmax-eligible | 3.41% | 29 |
| Admixed American | 3.41% | 29 |
| South Asian | 3.2% | 31 |
| Middle Eastern | 0.582% | 172 |
| European (non-Finnish) | 0.382% | 262 |
| African / African-American | 0.348% | 287 |
| Ashkenazi Jewishnot grpmax-eligible | 0.305% | 328 |
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
- CBLN2
- Protein
- p.Ser73=
- Coding
- c.219G>A
- MANE Select
- NM_182511
- dbSNP
- rs17853471
- Type
- single nucleotide variant
- Location
- chr18:72541942 (GRCh38)
- Gene constraint
- LOEUF 1.118 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 77.19
Similar variants
- CBLN2 c.-115C>G Benign ★★ same type
- CBLN2 c.-166-135C>A Likely benign ★★ same type
- CBLN2 c.-166-77G>A Benign ★★ same type
- CBLN2 c.-85A>G Benign ★★ same type
- CBLN2 c.*10C>T Benign ★★ same type
- CBLN2 p.Pro25= Benign ★★ same type
- CBLN2 p.Ala174Ser Uncertain significance ★ ⚠ same type
- CBLN2 p.Ala21Thr 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/cbln2-p-ser73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown