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Population frequency

A population frequency filter is applied to prevent common variants being prioritised. For a variant to pass this filter, the population frequency cannot exceed any of the thresholds applied for the mode of inheritance being considered. Variants for which there is no allele population provided in the particular data set and population combination are considered zero.

The datasets used for allele frequency filtering are:

The current GRCh38 allele frequency thresholds for the following populations are as follows:

Dataset tag Population Dataset size (individuals) Dominant inherited disease Recessive inherited disease Mitochondrial genome inherited disease
UK10K ALSPAC 3,854 0.001 0.01 n/a
UK10K TWINSUK 3,571 0.001 0.01 n/a
GNOMAD_GENOMES AFR 4,359 0.001 0.01 n/a
GNOMAD_GENOMES AMR 424 0.003 0.02 n/a
GNOMAD_GENOMES EAS 780 0.003 0.02 n/a
GNOMAD_GENOMES FIN 1,738 0.002 0.01 n/a
GNOMAD_GENOMES NFE 7,718 0.001 0.01 n/a
GNOMAD_GENOMES OTHER 544 0.003 0.02 n/a
GNOMAD_EXOMES AFR 8,128 0.001 0.01 n/a
GNOMAD_EXOMES AMR 17,296 0.001 0.01 n/a
GNOMAD_EXOMES ASJ 5,040 0.001 0.01 n/a
GNOMAD_EXOMES EAS 9,197 0.001 0.01 n/a
GNOMAD_EXOMES FIN 10,824 0.001 0.01 n/a
GNOMAD_EXOMES NFE 56,885 0.001 0.01 n/a
GNOMAD_EXOMES OTH 3,070 0.001 0.01 n/a
DiscovEHR DiscovEHR 50,726 0.001 0.01 n/a
1kG_phase3 AFR 661 0.002 0.01 n/a
1kG_phase3 AMR 347 0.002 0.01 n/a
1kG_phase3 EAS 504 0.002 0.01 n/a
1kG_phase3 EUR 503 0.002 0.01 n/a
1kG_phase3 SAS 489 0.002 0.01 n/a
GEL_aggCOVID_DRAGENv4.0-20230921
(internal ref: 20230921-aggDRAGENv4.0_COVID_v1.1-AFgt0)		 Genomics England custom frequencies 5,415 0.001 0.01 0.001

Note

gnomAD frequencies are extracted from gnomAD v2.0.1.