CHRNG p.Pro103=
c.309G>A · rs148012978 · VCV2712512
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, mid)
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 -9.1 | GERP -3 |
| Overall | ||
| CADD | 5.269 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Middle Eastern · 1/5,926 alleles
Filtering AF
0.00751%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00593%
Overall
0.00341%
55/1,613,100 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0169% | 5,926 |
| South Asian | 0.0132% | 7,589 |
| East Asian | 0.00891% | 11,220 |
| European (non-Finnish) | 0.00305% | 32,777 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
| African / African-American | 0.00133% | 75,038 |
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
- CHRNG
- Protein
- p.Pro103=
- Coding
- c.309G>A
- MANE Select
- NM_005199
- dbSNP
- rs148012978
- Type
- single nucleotide variant
- Location
- chr2:232540670 (GRCh38)
- Gene constraint
- LOEUF 1.286 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.91
Similar variants
- CHRNG c.1380+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHRNG c.350+2T>C Pathogenic/Likely pathogenic ★★ same type
- CHRNG c.351-2A>G Likely pathogenic ★★ same type
- CHRNG c.56-1G>A Pathogenic ★★ same type
- CHRNG c.805+1G>A Likely pathogenic ★★ same type
- CHRNG p.Arg239Cys Pathogenic ★★ same type
- CHRNG p.Arg341Ter Pathogenic/Likely pathogenic ★★ same type
- CHRNG p.Arg46Ter Pathogenic ★★ 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/chrng-p-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown