CHRDL1 p.Ser15=
c.45G>A · rs139302424 · VCV721170
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.194%, eas)
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 1.3 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 7.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.194%
East Asian · 65/33,476 alleles
Filtering AF
0.156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.143%
Overall
0.013%
156/1,201,648 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.194% | 515 |
| South Asian | 0.0304% | 3,290 |
| Remaining individualsnot grpmax-eligible | 0.019% | 5,255 |
| European (non-Finnish) | 0.00675% | 14,817 |
| African / African-American | 0.00526% | 19,012 |
| Admixed American | 0.00441% | 22,684 |
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
- CHRDL1
- Protein
- p.Ser15=
- Coding
- c.45G>A
- MANE Select
- NM_001143981
- dbSNP
- rs139302424
- Type
- single nucleotide variant
- Location
- chrX:110792137 (GRCh38)
- Structure
- AlphaFold pLDDT 69.79
Similar variants
- CHRDL1 p.Glu117Ter Pathogenic/Likely pathogenic ★★ same type
- CHRDL1 p.Glu423Asp Uncertain significance ★★ ⚠ same type
- CHRDL1 p.Arg209His Benign ★★ same type
- CHRDL1 p.Gln197= Benign/Likely benign ★★ same type
- CHRDL1 p.Lys318= Benign ★★ same type
- CHRDL1 p.Met7Val Benign ★★ same type
- CHRDL1 p.Pro105= Benign/Likely benign ★★ same type
- CHRDL1 p.Thr245= Likely benign ★★ 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/chrdl1-p-ser15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown