CDCA7 c.21+3G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0119%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.20 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP 2.7, phastCons 1 |
| Non-coding constraint | Z 0.76 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 18.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0119%
African / African-American · 8/67,072 alleles
Filtering AF
0.00591%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00429%
Overall
0.000701%
10/1,427,412 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0119% | 8,384 |
| Admixed American | 0.00293% | 34,078 |
| Finnishnot grpmax-eligible | 0.00235% | 42,612 |
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.21+3G>A
- MANE Select
- NM_031942
- dbSNP
- rs541138621
- Type
- single nucleotide variant
- Location
- chr2:173354987 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
Similar variants
- CDCA7 c.384+2T>C Uncertain significance ★★ same type
- CDCA7 p.Ala157Val Uncertain significance ★★ ⚠ same type
- CDCA7 p.Ala391Gly Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg134Leu Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg134Trp Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg171Cys Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg171Leu Uncertain significance ★★ ⚠ same type
- CDCA7 p.Arg239Gln 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/cdca7-c-21-plus-3g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown