Thank you to all the co-authors who contributed to this work, especially Prasanth Sivakumar, Dasha Deen, and Dalia Kasperaviciute (who aren't on BlueSky), and a big thank you to the participants and families whose data made this study possible!

This work highlights the importance of evaluating each gene prior to inclusion in genomic screening and how understanding the proportion of samples with prioritised variants is crucial for service design

Our approach prioritised variants in ~80% of participants from the 100,000 Genomes Project and NHS Genomic Medicine Service with diagnostic variants in genes included in the Generation Study.

We estimate that 3–5% of samples will have prioritised variants requiring manual review by clinical scientists, and that <1% will be taken forward for orthogonal testing and genetic confirmation.

Assessing validity of automated variant prioritisation on a gene level led to changes in rules used in variant prioritisation and conditions included.

Genomic sequencing offers the opportunity to screen for hundreds of rare conditions with a single test. We describe the automated variant prioritisation approach for the Generation Study, which is evaluating genomic newborn screening in 100,000 babies across England.