Table 3.
Comparison of minor allele frequencies of the rs42993393 SNP in phase and out of phase with the mutated UMOD (mUMOD)
| Testing | Population | n | Observed MAF (minor, major) | Comparison database | MAF in comparison group | P value |
|---|---|---|---|---|---|---|
| rs4293993 in phase with mUMOD | 1 per haplotype present in cohort | 129a | 0.1163 (G, A) | TOPMED | 0.18639 | 0.0147 |
| gnomAD | 0.1924 | 0.0082 | ||||
| 1000 genomes | 0.20 | 0.0037 | ||||
| rs4293993 out of phase with mUMOD | UMOD genotyped, rs4293393 genotyped | 554 | 0.1645 (G, A) | TOPMED | 0.18639 | 0.2693 |
| gnomAD | 0.1924 | 0.1629 | ||||
| 1000 Genomes | 0.20 | 0.07958 |
MAF, minor allele frequency.
Conservative testing was used, in which it was assumed that all individuals with the same rs4293393-mUMOD haplotype were related. The MAF of the test population was compared with the MAF found in TOPMED, gnomAD, and 1000 genomes registries.18 All comparisons showed that the MAF deviates from expected population frequencies. The MAF was then determined in available samples for the UMOD allele that was inherited from the unaffected parents. This allele was found to have similar allele frequencies as the control populations.
a
There were 129 unique rs4293393/mUMOD haplotypes.