Table 3 Comparison of allele frequencies for specific variants with GnomAD.

From: The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities

Variant

GnomAD AF

All of Us AF

p value (Two-tailed z test)

Population

BRCA2 c.5946delT (p.Ser1982Argfs*22)

0.0364% (26/71,468)

0.0342% (34/99,336)

0.815

Eur

BRCA2 c.2808_2811delAAAG (p.Lys938Ilefs*7)

0.0014% (2/145,080)

0.0020% (2/99336)

0.703

Eur

BRCA2 c.8537_8538delAG (p.Ser2846Glufs*2)

0.0021% (3/145,182)

0.0010% (1/99,336)

0.525

Eur

LDLR c.682 G > T (p.Glu228X)

0.0024% (2/82,108)

0.0050% (5/99,336)

0.375

Eur

APOL1 G1 p.S342G - rs73885319 (GRCh38:chr22:36265860:A > G)

22.27% (9208/41,338)

22.36% (10,239/45,794)

0.753

Afr

APOL1 G1 p.I384M - rs60910145 GRCh38:chr22:36265988:T > C/G

22.43% (9047/40,338)

21.94% (10,045/45,794)

0.081

Afr

HBB rs334

4.34% (1799/41,432)

4.50% (2,59/45,794)

0.269

Afr

HFE rs1800562

6.05% (4964/82,106)

6.41% (6371/99,336)

0.001

Eur

  1. To evaluate whether self-selection by participants with known genetic diseases impacts our study, we examined the allele frequencies of eight disease-associated variants (four rare, four common) in comparison with GnomAD. Except for a 6% difference in the common HFE rs1800562 alleles, the frequencies in our study closely match those in GnomAD. GnomAD and All of Us allele frequencies are based on biologically independent samples.
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