CCDC50 c.976+41A>C
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.95%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +41 | near-intronic (+41 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -4.3, phastCons 0.001 |
| Non-coding constraint | Z 2.51 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 0.328 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.95%
African / African-American · 2,936/74,298 alleles
Filtering AF
3.83%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.78%
Overall
0.209%
3,330/1,593,516 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.95% | 25 |
| Remaining individualsnot grpmax-eligible | 0.311% | 321 |
| Admixed American | 0.22% | 455 |
| Middle Eastern | 0.161% | 622 |
| South Asian | 0.0124% | 8,076 |
| European (non-Finnish) | 0.00471% | 21,238 |
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
- CCDC50
- Coding
- c.976+41A>C
- MANE Select
- NM_178335
- dbSNP
- rs77846288
- Type
- single nucleotide variant
- Location
- chr3:191375630 (GRCh38)
- Gene constraint
- LOEUF 0.933 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.90 · 1 PDB
Similar variants
- CCDC50 p.Ala453Val Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg138Pro Uncertain significance ★★ ⚠ same type
- CCDC50 p.Arg227Gln Uncertain significance ★★ same type
- CCDC50 p.Arg227Trp Uncertain significance ★★ same type
- CCDC50 p.Arg270Ter Uncertain significance ★★ same type
- CCDC50 p.Arg274Ter Uncertain significance ★★ same type
- CCDC50 p.Arg305Thr Uncertain significance ★★ same type
- CCDC50 p.Arg309Gly Uncertain significance ★★ 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/ccdc50-c-976-plus-41a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown