Exomiser 10 - 13.2.1 use the following default frequency sources:
frequencySources: [
THOUSAND_GENOMES,
TOPMED,
UK10K,
ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL,
EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN,
EXAC_SOUTH_ASIAN, EXAC_EAST_ASIAN,
EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN,
EXAC_OTHER,
GNOMAD_E_AFR,
GNOMAD_E_AMR,
# GNOMAD_E_ASJ,
GNOMAD_E_EAS,
GNOMAD_E_FIN,
GNOMAD_E_NFE,
GNOMAD_E_OTH,
GNOMAD_E_SAS,
GNOMAD_G_AFR,
GNOMAD_G_AMR,
# GNOMAD_G_ASJ,
GNOMAD_G_EAS,
GNOMAD_G_FIN,
GNOMAD_G_NFE,
GNOMAD_G_OTH,
GNOMAD_G_SAS
]
The inclusion of the Finnish (FIN) and Other (OTH) populations should probably not be used as defaults as these are either founder populations (FIN) or too small a population (OTH) to give a reliable filtering frequency.
This is based on the ClinGen SVI BA1 recommendations and the gnomAD filtering allele frequency implementation.
From Updated recommendation for the benign stand-alone ACMG/AMP criterion
We have specified the data sets that we used for this analysis as the six defined subsets of the ExAC database (African, East Asian, European [non-Finnish], Latino, and South Asian)
and later
We have made clear that one should use this criterion to assign a variant as benign if its allele frequency is >0.05 in any one of the six specified data sets when there are at least 2,000 observed alleles at the site in question.
gnomAD filtering allele frequency
This calculation only includes non-bottlenecked populations. For gnomAD v2, popmax filtering allele frequency excludes Ashkenazi Jewish (asj), European Finnish (fin), and "Other" (oth) populations. For gnomAD v3, popmax filtering allele frequency excludes Amish (ami), Ashkenazi Jewish (asj), European Finnish (fin), Middle Eastern (mid), and "Other" (oth) populations.
Exomiser 10 - 13.2.1 use the following default frequency sources:
The inclusion of the Finnish (FIN) and Other (OTH) populations should probably not be used as defaults as these are either founder populations (FIN) or too small a population (OTH) to give a reliable filtering frequency.
This is based on the ClinGen SVI BA1 recommendations and the gnomAD filtering allele frequency implementation.
From Updated recommendation for the benign stand-alone ACMG/AMP criterion
and later
gnomAD filtering allele frequency