Appendix 1—table 1. List of data sources.

Annotation type	Source
Exon coordinates	http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz
Exon annotations	Variant Effect Predictor (VEP) v87 using Gencode v19Ranks:https://m.ensembl.org/info/genome/variation/prediction/predicted_data.html
WGS covered regions and exome target regions (gnomAD v2.1.1)	https://gnomad.broadinstitute.org/downloads
Exome target regions(UK Biobank)	https://biobank.ndph.ox.ac.uk/ukb/ukb/auxdata/xgen_plus_spikein.GRCh38.bed (liftovered to hg19)
CpG methylation Testis	GEO Accession GSM1127119 (https://www.ncbi.nlm.nih.gov/geo/)
CpG methylation Ovary	GEO Accession GSM1010980 (https://www.ncbi.nlm.nih.gov/geo/)
CADD	CADD v1.4 (https://cadd.gs.washington.edu/download)
B-statistic	https://doi.org/10.1371/journal.pgen.1000471 (lifted over to hg19)
Functional site annotations	https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/ and https://www.prot2hg.com
De novo mutations	Decode: https://doi.org/10.1126/science.aau1043 (Data S5)DDD: https://doi.org/10.1038/s41586-020-2832-5 (Supp. Table 1)
Polymorphism data	gnomAD: https://gnomad.broadinstitute.org/downloadsUK Biobank: https://biobank.ctsu.ox.ac.uk/showcase/field.cgi?id=23155DiscovEHR: http://www.discovehrshare.com/downloads1,000 Genomes: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
ClinVar	https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz