PharmCAT

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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 either Reference or any incidental allele.

For combinations between incidental allele display:
'CPIC does not provide recommendations for this genotype. Variant is included in CPIC supplemental table of variants recommended by the American College of Medical Genetics (ACMG) Cystic Fibrosis Carrier Screening Working Group that should be tested to determine carrier status as a part of population screening programs.'

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'.

For a heterozygous variant of any of incidental allele display:

'CPIC does not provide recommendations for this genotype. Variant is included in CPIC supplemental table of variants recommended by the American College of Medical Genetics (ACMG) Cystic Fibrosis Carrier Screening Working Group that should be tested to determine carrier status as a part of population screening programs.'