CDCA7 c.1322+19del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.064 | GERP -1.6, phastCons 0.002 |
| Non-coding constraint | Z 1.65 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 0.028 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,998 alleles
Filtering AF
0.00439%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00279%
Overall
0.00362%
58/1,602,358 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,998 |
| East Asian | 0.0113% | 8,870 |
| South Asian | 0.00774% | 12,919 |
| African / African-American | 0.00539% | 18,542 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,649 |
| European (non-Finnish) | 0.00316% | 31,686 |
| Admixed American | 0.00168% | 59,390 |
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
- CDCA7
- Coding
- c.1322+19del
- MANE Select
- NM_031942
- dbSNP
- rs754138992
- Type
- Deletion
- Location
- chr2:173367297 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
Similar variants
- CDCA7 p.Asn362fs Uncertain significance ★ same type
- CDCA7 p.Gly245fs Uncertain significance ★ same type
- CDCA7 p.Lys18fs Uncertain significance ★ same type
- CDCA7 p.Tyr438_Lys440delinsTer Uncertain significance ★ same type
- CDCA7 c.1185+20del Likely benign ★ same type
- CDCA7 c.1322+17_1322+19del Likely benign ★ same type
- CDCA7 c.1323-12del Benign ★ same type
- CDCA7 c.147+9del Likely benign ★ 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/cdca7-c-1322-plus-19del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown