148: CHEK2 splice-site variants: minigene dissection

Sanoguera-Miralles L et al., Clinical Chemistry - This episode examines a minigene-based functional study of 52 CHEK2 splice-site variants from the BRIDGES project, reporting widespread splice disruption, characterization of 89 transcripts, and an ACMG/AMP-informed tentative clinical classification. Key terms: CHEK2, splicing, minigene assay, variant classification, breast cancer.

Study Highlights:
The authors selected 52 candidate splice-site variants from 128 intron–exon boundary changes and tested them in three validated CHEK2 minigenes in MCF-7 cells. Forty-six variants (88.5%) impaired splicing and 34 produced negligible full-length transcript, generating a total of 89 different transcripts of which 59 are predicted to introduce premature termination codons. They identified complex outcomes including multi-exon skipping, cryptic site usage and a rare noncanonical TG acceptor activated by c.684-2A>G, and incorporated minigene read-outs into an ACMG/AMP-based point system to tentatively classify variants. The workflow allowed classification of 27 pathogenic/likely pathogenic and 5 likely benign variants, while 20 remained variants of uncertain significance.

Conclusion:
Minigene assays revealed high spliceogenicity among selected CHEK2 variants and, when combined with a modified ACMG/AMP framework, provided tentative clinical classifications but left a substantial fraction (38%) as VUSs, highlighting the need for complementary case-control, family, or patient RNA data.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants

First author:
Sanoguera-Miralles L

Journal:
Clinical Chemistry

DOI:
10.1093/clinchem/hvad125

Reference:
Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clinical Chemistry. 2024;70(1):319–338. doi:10.1093/clinchem/hvad125

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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Episode link: https://basebybase.com/episodes/systematic-minigene-based-splicing-analysis-and-tentative-clinical-classification-of-52-chek2-splice-site-variants

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-09-25.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the spoken content for accuracy of core methods, results, and clinical implications of the CHEK2 minigene splicing analysis, including variant selection, three-minigene design, splicing outcomes, TG acceptor discovery, ACMG/AMP classification, and clinical impact; noted minor terminology variations.
- transcript topics: CHEK2 splicing and cancer risk; Minigene methodology and experimental design; Bioinformatic filtering and variant prioritization; Splicing outcomes and transcript diversity (89 transcripts, 59 with PTCs); ACMG/AMP-based tentative classification (32 variants; 27 P/LP, 5 LB; 20 VUS); Notable c.684-2A>G TG acceptor activation and exon 6 enhancers

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 6
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- 52 CHEK2 splice-site variants were analyzed in minigenes (from BRIDGES dataset).
- Three CHEK2 minigenes spanning all 15 exons were used for assays.
- 46 of 52 variants (88.5%) disrupted splicing; 34 produced negligible full-length transcript.
- 89 distinct transcripts were observed across variants; 59 predicted to introduce premature termination codons.
- 32 variants were tentatively classified by ACMG/AMP framework: 27 pathogenic/likely pathogenic, 5 likely benign; 20 remained VUS.
- Variant c.684-2A>G activated a noncanonical TG acceptor site, with exon 6 enhancers influencing recognition.

QC result: Pass.