CNNM1 p.Val428=
c.1284T>G · rs2862600 · VCV1297924
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 94.4%, 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 1.9 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 5.326 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
94.4%
African / African-American · 70,817/75,026 alleles
Filtering AF
93.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 93.6%
Overall
84.1%
1,357,419/1,613,880 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 94.4% | 1 |
| South Asian | 89.4% | 1 |
| East Asian | 87.1% | 1 |
| Remaining individualsnot grpmax-eligible | 84.3% | 1 |
| European (non-Finnish) | 83.6% | 1 |
| Amishnot grpmax-eligible | 83.4% | 1 |
| Finnishnot grpmax-eligible | 83.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 82.3% | 1 |
| Middle Eastern | 77.9% | 1 |
| Admixed American | 72.7% | 1 |
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
- CNNM1
- Protein
- p.Val428=
- Coding
- c.1284T>G
- MANE Select
- NM_020348
- dbSNP
- rs2862600
- Type
- single nucleotide variant
- Location
- chr10:99330671 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 67.07
Similar variants
- CNNM1 c.1717+145G>A Benign ★★ same type
- CNNM1 c.1858+55C>T Benign ★★ same type
- CNNM1 c.2340+88G>A Benign ★★ same type
- CNNM1 c.2776+92A>G Benign ★★ same type
- CNNM1 p.Ala222= Benign ★★ same type
- CNNM1 p.Arg819Gln Benign ★★ same type
- CNNM1 p.Asp828= Benign ★★ same type
- CNNM1 p.Ala103Asp 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/cnnm1-p-val428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown