Is CDCA5 c.243+10C>T pathogenic?

CDCA5 c.243+10C>T is classified Likely benign in CDCA5 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-11). Rare (popmax 0.135%, nfe).

How common is CDCA5 c.243+10C>T in the general population?

CDCA5 c.243+10C>T is rare (popmax 0.135%, nfe) (gnomAD).

CDCA5 c.243+10C>T

rs199992320 · VCV714410

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.135%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +10	near-intronic (+10 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.18	GERP -3.9
Non-coding constraint	Z 0.64	1 kb window · o/e 0.95 · regional · uncalibrated
Overall
CADD	9.989	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.135% European (non-Finnish) · 1,595/1,179,962 alleles

Filtering AF 0.13% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.127%

Overall 0.109% 1,763/1,614,122 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	5.26%	19
European (non-Finnish)grpmax	0.135%	740
Remaining individualsnot grpmax-eligible	0.122%	822
Admixed American	0.04%	2,501
Middle Eastern	0.033%	3,031
African / African-American	0.0213%	4,691
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
Finnishnot grpmax-eligible	0.00156%	64,030

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CDCA5
Coding: c.243+10C>T
MANE Select: NM_080668
dbSNP: rs199992320
Type: single nucleotide variant
Location: chr11:65083354 (GRCh38)
Gene constraint: LOEUF 0.88 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.04

Full CDCA5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDCA5 p.Glu123Lys Benign ★★ same type
CDCA5 p.Gly173= Benign ★★ same type
CDCA5 p.Gly179Arg Benign ★★ same type
CDCA5 p.Pro120= Benign ★★ same type
CDCA5 p.Thr105= Benign ★★ same type
CDCA5 p.Ala51Thr Uncertain significance ★ ⚠ same type
CDCA5 p.Arg148Trp Uncertain significance ★ ⚠ same type
CDCA5 p.Arg4Gly 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/cdca5-c-243-plus-10c-t (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown