CDCA7 p.Asn101=
c.303C>T · VCV3604248
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 1.2 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 10.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,084 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.00062%
10/1,614,012 alleles · very rare
exomes 8/1,461,864 · genomes 2/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,361 |
| Admixed American | 0.00167% | 59,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000424% | 236,009 |
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
- Protein
- p.Asn101=
- Coding
- c.303C>T
- MANE Select
- NM_031942
- Type
- single nucleotide variant
- Location
- chr2:173359410 (GRCh38)
- Gene constraint
- LOEUF 0.676 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.93 · 2 PDB
- Residue 101
- the 'disordered' region
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-p-asn101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown