CLMN p.Ser784=
c.2352G>A · rs12147696 · VCV770999
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, 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 -8.3 | GERP -4.5 |
| Overall | ||
| CADD | 0.181 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
European (non-Finnish) · 15,118/1,179,958 alleles
Filtering AF
1.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
1.05%
16,961/1,614,020 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.877% | 114 |
| Admixed American | 0.708% | 141 |
| Ashkenazi Jewishnot grpmax-eligible | 0.666% | 150 |
| Finnishnot grpmax-eligible | 0.347% | 288 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| South Asian | 0.304% | 329 |
| African / African-American | 0.221% | 452 |
| Middle Eastern | 0.066% | 1,515 |
| East Asian | 0.00223% | 44,866 |
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.Ser784=
- Coding
- c.2352G>A
- MANE Select
- NM_024734
- dbSNP
- rs12147696
- Type
- single nucleotide variant
- Location
- chr14:95202997 (GRCh38)
- Gene constraint
- LOEUF 0.755 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.84
- Residue 784
- the 'disordered' region
Similar variants
- CLMN c.2511+10C>T Benign ★★ same type
- CLMN c.886-4G>T Likely benign ★★ same type
- CLMN p.Asp592= Benign ★★ same type
- CLMN p.Glu276Lys Likely benign ★★ same type
- CLMN p.Glu357Lys Benign ★★ same type
- CLMN p.Glu771Ala Likely benign ★★ ⚠ same type
- CLMN p.His518= Benign ★★ same type
- CLMN p.Ile900Phe 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/clmn-p-ser784 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown