rs28695233 — CYP2D6

CYP2D6 rs28695233 — An Intronic Sub-Allele Marker

The CYP2D6 gene metabolizes roughly 25% of all prescribed medications, including opioid pain relievers, antidepressants, antipsychotics, and cardiovascular drugs. Its highly polymorphic sequence — over 150 star alleles catalogued — means that careful variant-level characterization is essential for accurate pharmacogenomic interpretation. rs28695233 is an intronic variant at position chr22:42,130,558 (GRCh38), located 53 base pairs downstream of exon 2 in the deep intronic region of CYP2D6 (HGVS: NM_000106.6:c.180+53T>G). The alternate G allele appears at approximately 8% globally in the gnomAD v4 exome dataset.

The Variant in Context

CYP2D6 star alleles are defined by combinations of variants — core variants that alter protein function (by affecting splicing, amino acid sequence, or expression), and sub-allele variants that serve as haplotype markers for specific lineages of the gene without independently changing enzyme activity. The Pharmacogene Variation Consortium (PharmVar)¹¹ Pharmacogene Variation Consortium (PharmVar)
PharmVar maintains the authoritative CYP2D6 star allele nomenclature database at definitive, moderate, and limited evidence levels has catalogued rs28695233 as a sub-allele tag at the [definitive evidence level | definitive: the variant has been confirmed by multiple validated methods and appears in one or more named sub-alleles within the PharmVar database].

Intronic variants 50+ base pairs from splice sites are generally too distal to disrupt canonical splicing, and no published study has demonstrated that rs28695233 alone alters CYP2D6 mRNA processing, protein expression, or metabolic activity. Importantly, it is absent from ClinVar and carries no pharmacogenomic annotation in PharmGKB independent of the haplotype context that defines its sub-allele.

Why It Gets Catalogued

The practical reason sub-allele variants like rs28695233 receive detailed cataloguing is genotyping assay interference. Clinical CYP2D6 allele-calling relies on targeted probes or amplicons designed against specific loci. An unexpected variant at or near a probe target can cause probe dropout, allele imbalance, or ambiguous calls — which a laboratory might misinterpret as a different star allele. By cataloguing sub-allele variants, PharmVar enables laboratories to recognize when an unusual signal is a known background variant rather than a new functional mutation. Pratt et al. 2021²² Pratt et al. 2021
Pratt VM et al. Recommendations for Clinical CYP2D6 Genotyping Allele Selection. J Mol Diagn, 2021 note that sub-allele variants lacking functional consequences are nonetheless important for ensuring accurate assay performance in clinical labs.

The Evidence

No published study has demonstrated an independent pharmacogenomic effect of rs28695233. The CYP2D6 activity score system³³ CYP2D6 activity score system
Gaedigk A et al. The CYP2D6 activity score: translating genotype information into a qualitative measure of CYP2D6 function. Clin Pharmacol Ther, 2008 assigns activity scores based on the core star allele definition, not individual sub-allele variants — meaning rs28695233's presence or absence does not change the CPIC-assigned metabolizer phenotype of the haplotype it rides on.

The most functionally characterized intronic CYP2D6 variants that affect splicing and expression are: rs3892097 (CYP2D6*4, intron 3 splice site, abolishes function), rs28371725 (CYP2D6*41, intron 6, 2988G>A, reduces splicing efficiency ~50%), and rs1058164 (exon 3 synonymous, promotes exon 3 skipping). These have direct, measured functional consequences. rs28695233, by contrast, sits in intron 2 at a deep position (c.180+53) where there is no published evidence of analogous splicing disruption.

Practical Significance

For individuals who receive a clinical CYP2D6 report that mentions rs28695233, the key point is that this variant's haplotype context — not the variant itself — determines the clinical interpretation. The sub-allele carrying this G allele will have a defined star allele designation (e.g., a specific *1 or *2 sub-allele) whose functional classification is determined by that allele's core variants, not by this intronic tag. Carriers of the G allele at rs28695233 are not pharmacogenomically different from non-carriers, unless the haplotype they carry has independent functional variants.

Interactions

Because rs28695233 is a haplotype marker, its clinical significance is entirely determined by the other variants on the same chromosome. Knowing this variant in isolation provides no pharmacogenomic guidance. Complete CYP2D6 star allele diplotyping — incorporating core functional variants like rs3892097 (*4), rs1065852 (*10), rs28371725 (*41), rs16947 (R296C), rs5030655 (*6), and copy number analysis — is required to assign an activity score and metabolizer phenotype. rs28695233 can refine which sub-allele is present within that framework, but it does not change the functional tier.