# NM_031942.5(CDCA7):c.147+9del

https://sugi.bio/variant/cdca7-c-147-plus-9del

## Summary

**CDCA7 c.147+9del** is classified **Likely benign** in CDCA7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-10). No gnomAD frequency available for this variant.

**At a glance:** Likely benign · review: Single submitter · rsID rs2468414779 · 1 submitter · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the CDCA7 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CDCA7](https://sugi.bio/atlas/gene/CDCA7/) |
| Coding change (HGVS c.) | c.147+9del |
| MANE Select transcript | [NM_031942](https://www.ncbi.nlm.nih.gov/nuccore/NM_031942) |
| dbSNP | [rs2468414779](https://www.ncbi.nlm.nih.gov/snp/rs2468414779/) |
| Variant type | Deletion |
| Location | chr2:173358846-173358846 (GRCh38) |
| ClinVar | [VCV2002538](https://www.ncbi.nlm.nih.gov/clinvar/variation/2002538/) |

**All HGVS expressions:** `NC_000002.11:g.174223574del`, `NC_000002.12:g.173358846del`, `NG_047202.1:g.9830del`, `NM_031942.5:c.147+9del`, `NM_145810.3:c.147+9del`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 4.072, GERP 2.64, phastCons 1 — highly conserved position (PP3-type support)
- Splice region: **near-intronic (+9 nt from the splice site)**.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CDCA7** population constraint: LOEUF 0.676, pLI 0.002565, missense-Z 1.8093. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **immunodeficiency-centromeric instability-facial anomalies syndrome 3** — Moderate (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 68.93, 33% of residues very-high.

**2 experimental structure(s)** (PDB): [8TLK](https://www.rcsb.org/structure/8TLK), [8YV8](https://www.rcsb.org/structure/8YV8).

## What this gene does {#gene-function}

*Describes the biological roles of CDCA7 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** CDCA7's established molecular role includes hemi-methylated DNA-binding.


### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** hemi-methylated DNA-binding.

**Biological process:** regulation of cell population proliferation.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-06-10.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-06-10 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related CDCA7 variant pages (same residue, condition, or type): [CDCA7 p.Asn362fs](/variant/cdca7-p-asn362fs), [CDCA7 p.Gly245fs](/variant/cdca7-p-gly245fs), [CDCA7 p.Lys18fs](/variant/cdca7-p-lys18fs), [CDCA7 p.Tyr438_Lys440delinsTer](/variant/cdca7-p-tyr438-lys440delinster), [CDCA7 c.1185+20del](/variant/cdca7-c-1185-plus-20del), [CDCA7 c.1322+17_1322+19del](/variant/cdca7-c-1322-plus-17-1322-plus-19del), [CDCA7 c.1322+19del](/variant/cdca7-c-1322-plus-19del), [CDCA7 c.1323-12del](/variant/cdca7-c-1323-minus-12del).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2002538). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*