CLMN p.Tyr928=
c.2784T>C · rs1128468 · VCV3055637
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 38%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
CLMN-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.30 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 6.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
38%
East Asian · 17,011/44,824 alleles
Filtering AF
37.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 37.3%
Overall
9.87%
159,245/1,613,348 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 38% | 3 |
| South Asian | 18.2% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 15.2% | 7 |
| Middle Eastern | 12.6% | 8 |
| Finnishnot grpmax-eligible | 12.3% | 8 |
| Remaining individualsnot grpmax-eligible | 11.2% | 9 |
| African / African-American | 10.3% | 10 |
| European (non-Finnish) | 8% | 12 |
| Amishnot grpmax-eligible | 6.25% | 16 |
| Admixed American | 5.52% | 18 |
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
- CLMN
- Protein
- p.Tyr928=
- Coding
- c.2784T>C
- MANE Select
- NM_024734
- dbSNP
- rs1128468
- Type
- single nucleotide variant
- Location
- chr14:95193905 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
Disease context
CLMN-related disorder
Similar variants
- CLMN p.Tyr928Cys Likely benign same residue
- CLMN c.608+7C>T Likely benign same condition
- CLMN p.Ala207= Likely benign same condition
- CLMN p.Arg313= Likely benign same condition
- CLMN p.Arg517His Benign same condition
- CLMN p.Glu245= Likely benign same condition
- CLMN p.Glu5= Benign same condition
- CLMN p.Pro261= Likely benign same condition
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/clmn-p-tyr928 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown