CHM p.Ser557=
c.1671G>A · rs764777444 · VCV1153914
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00347%, 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 1.6 | GERP -4, phastCons 1 |
| Overall | ||
| CADD | 2.657 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00347%
African / African-American · 2/57,654 alleles
Filtering AF
0.00136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0011%
Overall
0.00192%
21/1,092,177 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00347% | 28,827 |
| European (non-Finnish) | 0.00213% | 46,896 |
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.Ser557=
- Coding
- c.1671G>A
- MANE Select
- NM_000390
- dbSNP
- rs764777444
- Type
- single nucleotide variant
- Location
- chrX:85873151 (GRCh38)
- Structure
- AlphaFold pLDDT 81.05
Similar variants
- CHM p.Ser557Ter Pathogenic ★ same residue
- CHM p.Ser557Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown