CNMD p.Val45=
c.135G>T · rs77837850 · VCV718599
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.48%, afr)
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 1.7 | GERP 0.26, phastCons 1 |
| Overall | ||
| CADD | 12.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.48%
African / African-American · 1,744/70,236 alleles
Filtering AF
2.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.35%
Overall
0.123%
1,926/1,571,620 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.48% | 40 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| Middle Eastern | 0.137% | 731 |
| Admixed American | 0.123% | 815 |
| South Asian | 0.00685% | 14,608 |
| European (non-Finnish) | 0.00146% | 68,455 |
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
- CNMD
- Protein
- p.Val45=
- Coding
- c.135G>T
- MANE Select
- NM_007015
- dbSNP
- rs77837850
- Type
- single nucleotide variant
- Location
- chr13:52739109 (GRCh38)
- Gene constraint
- LOEUF 1.225 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.72
Similar variants
- CNMD p.Ala112Thr Uncertain significance ★ ⚠ same type
- CNMD p.Ala139Val Uncertain significance ★ ⚠ same type
- CNMD p.Ala44Thr Uncertain significance ★ ⚠ same type
- CNMD p.Ala94Thr Uncertain significance ★ ⚠ same type
- CNMD p.Arg124His Uncertain significance ★ ⚠ same type
- CNMD p.Arg140Cys Uncertain significance ★ ⚠ same type
- CNMD p.Arg211Lys Uncertain significance ★ ⚠ same type
- CNMD p.Arg218Lys 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/cnmd-p-val45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown