PharmCAT

Logo

The Pharmacogenomic Clinical Annotation Tool

View the Project on GitHub PharmGKB/PharmCAT

Calling and Reporting on CFTR in PharmCAT

If caller returns reference/reference

Display 'No CPIC variants found' in the diplotype or genotype field and N/A for allele functionality and phenotype.

In the recommendation section:
'No CPIC variants are found. CPIC does not provide recommendations for this genotype. CPIC guidelines reflect the alleles/genotypes known and considered by the guideline authors for inclusion by the time of publication. CPIC guidelines are periodically updated. Read the full guideline.'

If caller returns variant/variant with variant being any name we have in definition file

Display caller output in diplotype or genotype field and N/A for allele functionality and phenotype.

In recommendation section:
For combinations including F508del(CTT), F508del(TCT), G551D, G1244E, G1349D, G178R, G551S, S1251N, S1255P, S549N, S549R(A>C), S549R(T>G), R117H use recommendation as in guideline tool with 'other' being Reference.

If caller returns variant/reference with variant being any name we have in definition file

Display name from caller output (heterozygous), e.g. R553X (heterozygous), in diplotype or genotype field and N/A for allele functionality and phenotype.

Diplotype or genotype = *variant* (heterozygous)
Allele Functionality = N/A
Phenotype = N/A

In recommendation section:

For a heterozygous variant of any of F508del(CTT), F508del(TCT), G551D, G1244E, G1349D, G178R, G551S, S1251N, S1255P, S549N, S549R(A>C), S549R(T>G), R117H use recommendation as in guideline tool in combination with 'other'.