Table 4.
Additional CPIC-Actionable Variants Detected by Aldy that Were Not Assessed by Panel-Based Genotyping Reference Standard
| Gene | Variant information: rs ID (associated alleles) |
Functional effect† | Variant allele count in development and validation cohorts (total chromosomes) |
Minor allele frequency‡ |
||
|---|---|---|---|---|---|---|
| African | American admixed | European | ||||
| CYP2B6 | rs12721655 (∗8, ∗13) | No function | 2 (328) | <0.001 | — | 0.004 |
| CYP2C19 | rs118203757 (∗24) | No function | 1 (328) | <0.001 | — | <0.001 |
| CYP2D6 | rs774671100 (∗15) | No function | 2 (282) | <0.001 | 0.002 | <0.001 |
| rs79292917 (∗59) | Decreased | 3 (282) | 0.002 | — | 0.005 | |
| rs730882251 (∗62) | No function | 1 (282) | <0.001 | — | <0.001 | |
| DPYD | rs56038477 (HapB3)§ | Decreased | 2 (226) | 0.003 | — | 0.020 |
| G6PD | rs76723693 (A-) | Deficient | 1 (245) | 0.001 | — | <0.001 |
| NUDT15 | rs746071566 (∗2, ∗9) | No function | 2 (164) | <0.001 | — | 0.001 |
—, Data not available; CPIC, Clinical Pharmacogenetics Implementation Consortium; ID, identifier.
Functional effects for each variant are defined by the Pharmacogene Variation Consortium (http://pharmvar.org, last accessed January 13, 2022) or the CPIC (http://cpicpgx.org, last accessed January 13, 2022).
Minor allele frequencies are based on variant frequency data from the Allele Frequency Aggregator project, sponsored by the National Center for Biotechnology Information for all variants except rs12769205. For rs12769205, we report the frequency of ∗35 allele rather than the rs12769205 variant because rs12769205 is also contained in the more common CYP2C19∗2 allele.
The coding variant rs56038477 was used to tag rs75017182 and the HapB3 haplotype.