CHM p.Gly54=
c.162A>G · rs138972750 · VCV702451
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0477%, nfe)
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 -0.094 | GERP -3.8, phastCons 0.81 |
| Overall | ||
| CADD | 9.271 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0477%
European (non-Finnish) · 422/884,163 alleles
Filtering AF
0.0439%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0425%
Overall
0.037%
441/1,190,829 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0477% | 2,095 |
| Remaining individualsnot grpmax-eligible | 0.0213% | 4,693 |
| African / African-American | 0.0126% | 7,919 |
| Admixed American | 0.00226% | 44,197 |
| Finnishnot grpmax-eligible | 0.00221% | 45,322 |
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
- CHM
- Protein
- p.Gly54=
- Coding
- c.162A>G
- MANE Select
- NM_000390
- dbSNP
- rs138972750
- Type
- single nucleotide variant
- Location
- chrX:85981764 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM c.116+1G>A Pathogenic/Likely pathogenic ★★ same type
- CHM c.116+1G>T Pathogenic/Likely pathogenic ★★ same type
- CHM c.1166+1G>A Pathogenic ★★ same type
- CHM c.1166+1G>C Pathogenic ★★ same type
- CHM c.1167-2A>G Pathogenic ★★ same type
- CHM c.1244+1G>A Pathogenic ★★ same type
- CHM c.1244+2T>A Pathogenic/Likely pathogenic ★★ same type
- CHM c.1349+1G>T Pathogenic/Likely 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/chm-p-gly54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown