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Example clinical scenario

A pregnant woman with an uncomplicated pregnancy presents at 20 weeks’ gestation for the fetal anomaly scan. The sonographer is unable to see a full and typical outline of the baby’s lips and is therefore suspicious of a cleft lip. The rest of the baby’s anatomy appears normal. The patient is referred to a fetal medicine unit for further review.

When to consider genomic testing

Genomic testing should be discussed where a cleft is identified:

  • Around 15% of individuals with facial clefts have an underlying genetic diagnosis. The chance of this is dependant on the type of clefting and any associated anomalies.
    • An isolated unilateral cleft is rarely associated with an underlying diagnosis.
    • The chance is increased with bilateral or midline clefts.
    • Where a facial cleft is seen in combination with other anomalies, the chance of an underlying genetic cause increases.

What do you need to do?

  • Consult the National Genomic Test Directory. From this directory you can access the rare and inherited disease eligibility criteria for information about individual tests and their associated eligibility criteria. You can also access a spreadsheet of all available tests.
  • To find out which genes are included on different gene panels, see the NHS Genomic Medicine Service (GMS) Signed Off Panels Resource.
  • Refer to local guidance regarding fetal medicine referral as further review in a fetal medicine unit is usually warranted.
  • The fetal medicine review will determine whether genomic testing is appropriate, and referral to clinical genetics will be considered. Referral to clinical genetics is not routinely indicated for an isolated facial cleft.
  • The fetal medicine team will decide which testing is most suitable for the patient and/or discuss the case with a multidisciplinary team, depending on the specific clinical scenario and the patient’s wishes.
  • Depending on the clinical scenario, a range of different genomic tests may be considered:
    • Where there is an isolated abnormality:
    • For certain significant or complex anomalies and/or where above testing is non-diagnostic, fetal exome sequencing may be considered:
    • Where a specific genetic condition is considered likely or there is a relevant family history, further guided genomic testing my be recommended.
    • For many of the tests (particularly whole genome and exome sequencing), parental samples are also needed or are helpful.
  • For tests that are undertaken using whole genome sequencing (WGS), you will need to:
  • For tests that do not include WGS, you will need to:
    • complete a test order form and consent (record of discussion) form, available from your local Genomic Laboratory Hub (GLH).
    • include details of the phenotype in the test order form (refer to HPO terms or the clinical summary) as well as the appropriate panel name(s) with associated R number.
    • parental samples may be needed for interpretation of the proband’s result. Parental samples can be taken alongside that of the proband, and their DNA stored, or can be requested at a later date if needed.
  • All of the above tests are DNA based and require an amniocentesis or chorionic villus sample or fetal blood sample in an EDTA tube (purple-topped tube).
  • Information about patient eligibility and test indications was correct at the time of writing. When requesting a test, please refer to the National Genomic Test Directory to confirm the right test for your patient.


For clinicians

For patients

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  • Last reviewed: 03/03/2024
  • Next review due: 03/03/2025
  • Authors: Jenni Petrie
  • Reviewers: Dr Jessica Woods