CD1C p.Gln23=
c.69G>A · rs115929342 · VCV785845
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.76%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not looked up on this page · why |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.37 | GERP -1.3 |
| Overall | ||
| CADD | 6.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.76%
African / African-American · 2,057/74,490 alleles
Filtering AF
2.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.62%
Overall
0.142%
2,289/1,611,650 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.76% | 36 |
| Remaining individualsnot grpmax-eligible | 0.173% | 578 |
| Middle Eastern | 0.149% | 673 |
| Admixed American | 0.132% | 757 |
| South Asian | 0.0121% | 8,274 |
| European (non-Finnish) | 0.00204% | 49,120 |
| Finnishnot grpmax-eligible | 0.00157% | 63,676 |
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
- CD1C
- Protein
- p.Gln23=
- Coding
- c.69G>A
- MANE Select
- NM_001764 · reported on NM_001765
- dbSNP
- rs115929342
- Type
- single nucleotide variant
- Location
- chr1:158291141 (GRCh38)
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/cd1c-p-gln23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown