CCDC24 p.Ile97=
c.291C>T · rs74657675 · VCV2638764
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.664%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.28 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.22 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 1.4, phastCons 0.29 |
| Overall | ||
| CADD | 10.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.664%
European (non-Finnish) · 7,834/1,180,004 alleles
Filtering AF
0.652%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.647%
Overall
0.559%
9,027/1,614,182 alleles · rare
exomes 8,433/1,461,836 · genomes 594/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.664% | 151 |
| Middle Eastern | 0.561% | 178 |
| Ashkenazi Jewishnot grpmax-eligible | 0.503% | 199 |
| Remaining individualsnot grpmax-eligible | 0.491% | 204 |
| South Asian | 0.33% | 303 |
| Finnishnot grpmax-eligible | 0.328% | 305 |
| Admixed American | 0.163% | 613 |
| African / African-American | 0.125% | 798 |
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
- CCDC24
- Protein
- p.Ile97=
- Coding
- c.291C>T
- MANE Select
- NM_152499
- dbSNP
- rs74657675
- Type
- single nucleotide variant
- Location
- chr1:43992376 (GRCh38)
- Gene constraint
- LOEUF 1.553 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.31
Similar variants
- CCDC24 p.Ile97Thr Uncertain significance ★ ⚠ same residue
- CCDC24 p.Ala294Ser Uncertain significance ★ ⚠ same type
- CCDC24 p.Ala305Thr Uncertain significance ★ ⚠ same type
- CCDC24 p.Ala44Ser Uncertain significance ★ ⚠ same type
- CCDC24 p.Arg178Lys Uncertain significance ★ ⚠ same type
- CCDC24 p.Arg178Ser Uncertain significance ★ ⚠ same type
- CCDC24 p.Arg22Cys Uncertain significance ★ ⚠ same type
- CCDC24 p.Arg280Cys 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/ccdc24-p-ile97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown