CGN p.Arg973Gln
c.2918G>A · rs79234959 · VCV775599
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.327 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 2.5, phastCons 1 |
| Regional constraint | o/e 0.73 | unconstrained · MANE · 3,161 bp · p 9.1e-06 · regional, not allelic |
| Overall | ||
| CADD | 24.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2%
African / African-American · 1,503/75,030 alleles
Filtering AF
1.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.88%
Overall
0.106%
1,712/1,613,730 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2% | 50 |
| Admixed American | 0.107% | 937 |
| Remaining individualsnot grpmax-eligible | 0.0992% | 1,008 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.00659% | 15,173 |
| European (non-Finnish) | 0.00636% | 15,730 |
| East Asian | 0.00223% | 44,878 |
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
- CGN
- Protein
- p.Arg973Gln
- Coding
- c.2918G>A
- MANE Select
- NM_020770
- dbSNP
- rs79234959
- Type
- single nucleotide variant
- Location
- chr1:151535055 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.44
Similar variants
- CGN p.Arg973Trp Uncertain significance ★ same residue
- CGN p.Ala357= Benign/Likely benign ★★ same type
- CGN p.Arg11Trp Likely benign ★★ same type
- CGN p.Arg227Trp Likely benign ★★ same type
- CGN p.Arg547Lys Benign ★★ same type
- CGN p.Glu771Lys Benign/Likely benign ★★ same type
- CGN p.Ile60= Benign ★★ same type
- CGN p.Ala1035Thr 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/cgn-p-arg973gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown