COMMD9 p.Ala79=
c.237C>T · rs150086428 · VCV708568
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.371%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.3 | GERP -4.3 |
| Overall | ||
| CADD | 11.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.371%
European (non-Finnish) · 4,372/1,179,930 alleles
Filtering AF
0.361%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.358%
Overall
0.299%
4,825/1,614,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.371% | 270 |
| Remaining individualsnot grpmax-eligible | 0.267% | 374 |
| Middle Eastern | 0.198% | 505 |
| South Asian | 0.102% | 979 |
| Finnishnot grpmax-eligible | 0.0999% | 1,001 |
| Admixed American | 0.0816% | 1,225 |
| African / African-American | 0.056% | 1,787 |
| East Asian | 0.0557% | 1,795 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
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
- COMMD9
- Protein
- p.Ala79=
- Coding
- c.237C>T
- MANE Select
- NM_014186
- dbSNP
- rs150086428
- Type
- single nucleotide variant
- Location
- chr11:36278557 (GRCh38)
- Gene constraint
- LOEUF 1.513 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.27 · 7 PDB
- Residue 79
- an α-helix
Similar variants
- COMMD9 p.Ala57Ser Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg110Lys Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg122Cys Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg141His Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg187Cys Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg66Cys Uncertain significance ★ ⚠ same type
- COMMD9 p.Arg74Cys Uncertain significance ★ ⚠ same type
- COMMD9 p.Asp125Asn 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/commd9-p-ala79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown