CDC14A c.309+9del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00155%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.3 | GERP 0.47, phastCons 1 |
| Non-coding constraint | Z 0.22 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 5.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00155%
European (non-Finnish) · 18/1,158,864 alleles
Filtering AF
0.000971%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000801%
Overall
0.00113%
18/1,589,674 alleles · very rare
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
- CDC14A
- Coding
- c.309+9del
- MANE Select
- NM_003672
- dbSNP
- rs1277427053
- Type
- Deletion
- Location
- chr1:100390832 (GRCh38)
- Gene constraint
- LOEUF 1.141 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77
Similar variants
- CDC14A p.Ala451fs Pathogenic ★ same type
- CDC14A p.Tyr126fs Pathogenic ★ same type
- CDC14A c.1299-2del Uncertain significance ★ same type
- CDC14A c.1755+108del Uncertain significance ★ same type
- CDC14A p.Ala458fs Uncertain significance ★ same type
- CDC14A p.Ile183_Val184del Uncertain significance ★ same type
- CDC14A p.Pro205del Uncertain significance ★ same type
- CDC14A p.Ser575fs 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/cdc14a-c-309-plus-9del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown