Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.56%, 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 1.1 | GERP -0.52, phastCons 1 |
| Overall | ||
| CADD | 1.754 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.56%
African / African-American · 1,921/75,010 alleles
Filtering AF
2.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.43%
Overall
0.129%
2,077/1,612,612 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.56% | 39 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.112% | 893 |
| Admixed American | 0.11% | 909 |
| South Asian | 0.0022% | 45,544 |
| European (non-Finnish) | 0.000932% | 107,273 |
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
- CCDC116
- Protein
- p.Asn302=
- Coding
- c.906C>T
- MANE Select
- NM_152612
- dbSNP
- rs2105575
- Type
- single nucleotide variant
- Location
- chr22:21634969 (GRCh38)
- Gene constraint
- LOEUF 1.158 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.59
Similar variants
- CCDC116 c.73-8C>T Benign ★★ same type
- CCDC116 p.Arg174= Benign ★★ same type
- CCDC116 p.Lys412Arg Benign ★★ same type
- CCDC116 p.Pro293Leu Benign ★★ same type
- CCDC116 p.Thr569= Benign ★★ same type
- CCDC116 p.Val252Met Benign ★★ ⚠ same type
- CCDC116 p.Ala12Asp Uncertain significance ★ ⚠ same type
- CCDC116 p.Ala255Thr 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/ccdc116-p-asn302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown