What it tests for

• If a person and their reproductive partner (co-parent or donor) are carriers for the same autosomal recessive condition

• If the egg contributor to a pregnancy (parent or donor) is a carrier of an X-linked condition

When to consider this test or referring for this test

If a person is planning a pregnancy or in early pregnancy

Medicare Rebate (check MBS item for criteria before ordering)

Yes – for the three-gene screen (CF, SMA, FXS)

73451
73452

No – for expanded carrier screening

Further information

RGCS providers
RGCS point of care resource
RGCS FastTrack CPD
CGE RGCS fact sheet
RACGP fact sheet

When to refer to clinical genetics and/or other non-GP specialist

Autosomal recessive condition

• If the person and their reproductive partner are both carriers for the same autosomal recessive condition

• Do not refer your patient before arranging carrier screening in their reproductive partner

• Do not refer your patient if their partner has been screened for the same condition and is not a carrier

X-linked condition

• If the egg contributor is a carrier for an X-linked condition

• If the egg contributor is a carrier of a Fragile X premutation allele

Refer urgently if there is a current pregnancy

Refer non-urgently if a reproductive couple is planning a pregnancy

What it tests for

• Placental DNA in a pregnant person’s blood is tested for chromosomal conditions

• Most pathology providers will test for chromosomes 21, 18, 13, X and Y

• Some providers will look at additional chromosomes

When to consider this test or referring for this test

From 10 weeks of pregnancy

Medicare Rebate

No

Further information

NIPT providers
NIPT point of care resource
NIPT FastTrack CPD
CGE NIPT/S fact sheet

When to refer to clinical genetics and/or other non-GP specialist

• This is a screening test

• Confirmatory prenatal diagnostic testing via an amniocentesis is recommended for increased chance results

• Referral should be made to a maternal fetal medicine (MFM) service or specialised women's ultrasound provider to arrange prenatal diagnostic testing

• If prenatal diagnostic testing confirms an uncommon chromosome condition your patient can be referred to clinical genetics

• In this context, an uncommon chromosome condition refers to a finding in a chromosome other than chromosomes 21, 18, 13, X and Y

What it tests for

• Tests chromosomes in detail

• Will identify whole extra or missing chromosomes (eg: Down syndrome, Turner syndrome), small extra or missing pieces and microdeletion/ microduplication syndromes (eg: 22q11.2 deletion)

When to consider this test or referring for this test

This is a first line genetic test for a child/adult with developmental delay, intellectual disability, autism, or at least two congenital abnormalities

Medicare Rebate

Yes - 73292

Further information

Requesting this test prior to a paediatrician appointment may speed up diagnosis for a child
RACGP genomic handbook CMA section
eLearning module (coming soon)
CGE CMA fact sheet
CGE CMA testing guide

When to refer to clinical genetics and/or other non-GP specialist

• Refer to clinical genetics when there is an abnormal result – a pathogenic or likely pathogenic copy number variant

• Consider referring to clinical genetics if a variant of uncertain significance is found. Some of these will be innocuous inherited variants and will not be seen by genetics - if in doubt, please contact the local clinical genetics service for a discussion

What it tests for

• Tests whole chromosomes

• Will identify whole extra or missing chromosomes (eg. Down syndrome, Turner syndrome), large extra or missing pieces (duplications or deletions), or large rearrangements (translocations, insertions)

When to consider this test or referring for this test

• If a person has a history of infertility, recurrent miscarriage or recurrent stillbirth

• If a family has a known chromosomal translocation

Medicare Rebate

Yes
73289

Further information

• CMA has superseded karyotyping in most cases, due to its higher accuracy and detail

• Ordering a karyotype alongside a CMA will result in the loss of the Medicare rebate for the karyotype and an out-of-pocket cost for the patient

When to refer to clinical genetics and/or other non-GP specialist

Refer to clinical genetics when there is an abnormal result

What it tests for

Tests the “CGG” repeat number in the FMR1 gene which is associated with FXS

When to consider this test or referring for this test

• Individuals with a family history of FXS

• People with intellectual disability, developmental delay

• People experiencing early menopause or primary ovarian failure (<40 years)

• People experiencing ataxia or neurodegeneration

Medicare Rebate

Yes
73300

Further information

• Requesting this test prior to a non-GP specialist appointment may speed up a diagnosis

• CGE Fragile X fact sheet

• Information for Fragile X premutation carriers

When to refer to clinical genetics and/or other non-GP specialist

• Refer to clinical genetics for a premutation allele carrier or an expanded allele result

• Clinical genetics services may not accept a referral for an intermediate allele result

• For NSW residents, consider referral to the Genetics of Learning Disability (GOLD) service in some instances

What it tests for

Tests for a familial pathogenic variant within the CFTR gene which is associated with CF

When to consider this test or referring for this test

• Carrier testing for an individual with a family history of CF for the laboratory confirmed, specific, pathogenic gene variant identified in the affected individual

• Advise the testing laboratory what the familial CFTR gene variant is to ensure that the variant is included on the carrier testing panel

Medicare Rebate

Yes
73348

Further information

CGE Cystic Fibrosis fact sheet

When to refer to clinical genetics and/or other non-GP specialist

• Refer urgently to clinical genetics if there is a current pregnancy if the person and their reproductive partner are both carriers for CF

• Refer non-urgently to clinical genetics if the person and their reproductive partner are both carriers for CF and they are planning a pregnancy

• Do not refer your patient before arranging carrier screening in their reproductive partner via reproductive genetic carrier screening

• Do not refer your patient if their partner has been screened for CF and is not a carrier for CF

What it tests for

Tests for specific variants in the HFE gene: p.Cys282Tyr and p.His63Asp

When to consider this test or referring for this test

• If a person has an elevated transferrin saturation or elevated serum ferritin on testing of repeated specimens

• The patient has a first degree relative with homozygosity for the p.Cys282Tyr variant or compound heterozygosity for p.Cys282Tyr and p.His63Asp

Medicare Rebate

Yes
73317

Further information

Haemochromatosis Australia

When to refer to clinical genetics and/or other non-GP specialist

• Do not refer to clinical genetics for an affected person OR if reproductive partners (co-parents or donors) are both carriers as it is an adult-onset condition with no pregnancy planning implications

• Refer to haematology/gastroenterology for clinical management as necessary

What it tests for

Factor V Leiden (FVL) tests for specific variant in the F5 gene: c.1601G>A

When to consider this test or referring for this test

• Thrombosis was unprovoked

• Thrombosis occurred <50 years

• Thrombosis occurred in an unusual location

• There is a family history in a first-degree relative

Medicare Rebate

Yes
73308

Further information

Factor V Leiden

When to refer to clinical genetics and/or other non-GP specialist

• Do not refer to clinical genetics for an affected person OR if family planning as it is an adult-onset condition with no pregnancy planning implications

• Refer to haematology for clinical management as necessary

What it tests for

Prothrombin (PT) tests for specific variant in the F2 gene: c.*97G>A

When to consider this test or referring for this test

• Thrombosis was unprovoked

• Thrombosis occurred <50 years

• Thrombosis occurred in an unusual location

• There is a family history in a first-degree relative

Medicare Rebate

Yes
73308

Further information

Prothrombin thrombophilia

When to refer to clinical genetics and/or other non-GP specialist

• Do not refer to clinical genetics for an affected person OR if family planning as it is an adult-onset condition with no pregnancy planning implications

• Refer to haematology for clinical management as necessary

What it tests for

Tests for deletions in the HBA1 and HBA2 genes associated with alpha thalassaemia

When to consider this test or referring for this test

• When a person is suspected of being a carrier for alpha thalassaemia

• When a person cannot be excluded as an alpha thalassaemia carrier and their reproductive partner (co-parent or donor) is a confirmed alpha thalassaemia carrier

Medicare Rebate

Yes
73410

Further information

• RACGP genomics handbook haemoglobinopathies

• CGE Thalassaemia fact sheet

• Appendix A in this document

When to refer to clinical genetics and/or other non-GP specialist

• Refer urgently to clinical genetics if there is a current pregnancy and if both reproductive partners are carriers for alpha thalassaemia

• Refer non-urgently to clinical genetics if both reproductive partners are carriers for alpha thalassaemia and they are planning a pregnancy

• Haematology referral may also be relevant to discuss thalassaemia management during and after a pregnancy for any affected offspring as part of decision making around pregnancy

What it tests for

Tests for changes within the HBB gene associated with beta thalassaemia, sickle cell disease, HbE and other HBB gene variants

When to consider this test or referring for this test

When a person is suspected of being a carrier for a HBB gene variant (beta thalassaemia, sickle cell disease, HbE or other) AND if their reproductive partner (co-parent or donor) is suspected of also being a carrier of a HBB gene variant

Medicare Rebate

No

Further information

• Please note: there can be non-deletional and deletional changes in the HBB gene - a GP can order HBB gene sequencing or deletion testing but the patient will need to pay an out-of-pocket cost which will vary depending upon laboratory

• RACGP genomics handbook haemoglobinopathies

• CGE Thalassaemia fact sheet

• Appendix A in this document

When to refer to clinical genetics and/or other non-GP specialist

• Refer urgently to clinical genetics if there is a current pregnancy and if both reproductive partners are suspected of being a carrier for an HBB gene variant

• Refer non-urgently to clinical genetics if both reproductive partners are suspected of being a carrier for an HBB gene variant and they are planning a pregnancy

• Haematology referral may also be relevant to discuss management after birth of any affected offspring as part of decision making around pregnancy

What it tests for

Tests for a pathogenic familial variant in the FH gene associated with FH

When to consider this test or referring for this test

• Tests an individual with a family history of FH for the laboratory confirmed, specific, pathogenic gene variant identified in the affected individual who is a first or second degree relative

• Advise the testing laboratory what the familial FH gene variant is

Medicare Rebate

Yes
73353

Further information

• CGE Familial Hypercholesterolaemia fact sheet

When to refer to clinical genetics and/or other non-GP specialist

• Refer the index case in the family to a FH clinic or lipid specialist for genetic testing to identify the familial variant

• Family members can have targeted testing for the pathogenic family variant under MBS 73353 via their GP

What it tests for

• Tests for variants in a panel of genes associated with inherited arrhythmias, channelopathies or cardiomyopathies

• Not available in general practice

When to consider this test or referring for this test

When a person has a personal or family history of and inherited cardiac condition 

Medicare Rebate

N/A for GPs

Further information

Genetics in cardiac conditions
Genetic testing in cardiovascular disease

When to refer to clinical genetics and/or other non-GP specialist

• Refer to cardiology for accurate phenotyping

• Some cardiologists will arrange genetic testing for their patients

• Refer to a cardiac genetics clinic, or clinical genetics for genetic testing if required

What it tests for

• In addition to genes associated with breast, ovarian, prostate, colon and uterine cancer, Medicare funded testing is also available for some important but uncommon cancer types and hereditary cancer syndromes

• Not routinely available in general practice, although this is a rapidly changing space

When to consider this test or referring for this test

When a person has cancer and/or a significant family history of cancer both/either of which likely have a genetic basis

Medicare Rebate

N/A for GPs

Further information

EviQ GP referral guidelines for cancer predisposition

When to refer to clinical genetics and/or other non-GP specialist

• A person with cancer needs to be referred to oncology for clinical management – some oncologists or other oncology specialists will arrange genetic testing for their patients

• A person with cancer and/or a family history of cancer can be referred to their local familial cancer service for genetic testing

• Some private clinical genetics pathways (clinical geneticists and genetic counsellors) and pathology companies offer cancer predisposition genetic testing with an out-of-pocket cost but with quicker timeframes

What it tests for

• Tests for the “CAG” repeat in the HTT gene associated with HD

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of HD and/or there is a suspicion of HD based upon clinical presentation

Medicare Rebate

N/A for GPs

Further information

CGE Huntington disease fact sheet

When to refer to clinical genetics and/or other non-GP specialist

• Refer to neurology or specialist HD clinic (for assessment of indicators of HD in a potentially symptomatic patient)

• Refer to clinical genetics for predictive genetic testing if there is a family history of HD and the index case has a genetic diagnosis of HD

What it tests for

• Tests for variants in the FBN1 gene associated with Marfan syndrome

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of Marfan syndrome and/or aortic dissection, or there is a suspicion of Marfan syndrome based on clinical presentation

Medicare Rebate

No

Further information

https://marfan.org/expectations/diagnosis/

When to refer to clinical genetics and/or other non-GP specialist

• Refer to cardiology and ophthalmology (for assessment of indicators of Marfan syndrome)

• Refer to a connective tissue disorders clinic if locally available (or clinical genetics) for diagnosis and genetic testing as appropriate

What it tests for

• Tests for variants in the NF1 or NF2 gene associated with NF1 and NF2 respectively

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of NF1/2, or there is a suspicion of NF1/2 based upon clinical presentation

Medicare Rebate

No

Further information

https://www.ctf.org.au/diagnostic-criteria

When to refer to clinical genetics and/or other non-GP specialist

• Refer to ophthalmology (for assessment of indicators of NF1)

• Refer to a neurogenetics clinic if locally available (or clinical genetics) for diagnosis of NF1/2 and genetic testing as appropriate

What it tests for

• Tests for variants in the DMD gene associated with DMD and BMD

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of DMD/BMD and/or there is a suspicion of DMD/BMD based upon clinical presentation which includes a documented raised CK level in the symptomatic individual

Medicare Rebate

No

Further information

https://medlineplus.gov/genetics/condition/duchenne-and-becker-muscular-dystrophy/

When to refer to clinical genetics and/or other non-GP specialist

• Refer to a neurogenetics clinic if locally available (or clinical genetics) for assessment of indicators of DMD/BMD and diagnosis and genetic testing as appropriate

• A documented raised CK level will need to be sent with the referral

What it tests for

• Tests for variants in the F8 or F9 gene associated with haemophilia A or haemophilia B respectively

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of haemophilia and/or there is a suspicion of haemophilia based upon clinical presentation

Medicare Rebate

No

Further information

https://medlineplus.gov/genetics/condition/hemophilia/#inheritance

When to refer to clinical genetics and/or other non-GP specialist

Refer to haematology (for assessment of indicators of haemophilia and diagnosis) and clinical genetics for genetic testing as appropriate

What it tests for

• Tests for variants in the SMN1 gene which is associated with SMA

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of SMA, or there is a suspicion of SMA based upon clinical presentation

Medicare Rebate

N/A for GPs

Further information

• If a person is identified as a carrier of SMA, their reproductive partner (co-parent or donor) can have SMA carrier screening via a reproductive genetic carrier screening pathway

• SMA is now included on newborn screening to allow early diagnosis and the initiation of treatment

• CGE SMA fact sheet

When to refer to clinical genetics and/or other non-GP specialist

• Refer urgently to clinical genetics if there is a current pregnancy and if both reproductive partners are carriers of SMA

• Refer non-urgently to clinical genetics if both reproductive partners are carriers for SMA and they are planning a pregnancy

• Paediatric neurology referral is important to discuss management during and after birth of any affected offspring as part of decision making around pregnancy

• Do not refer your patient before arranging carrier screening in their reproductive partner

• Do not refer your patient if their partner has been screened for SMA and is not a carrier for SMA

What it tests for

• Tests for variants with the TSC1 and TSC2 genes associated with TSC

• Not available in general practice

When to consider this test or referring for this test

Patient is concerned about a family history of TSC, or there is a suspicion of TSC based upon clinical presentation

Medicare Rebate

No

Further information

Managing TSC across the lifespan – a resource for GPs and other clinicians

When to refer to clinical genetics and/or other non-GP specialist

Most TSC is managed and seen via specialised multidisciplinary TSC clinics around Australia, and details can be found on the TSC Association Website

What it tests for

• Tests for a familial variant within a specific gene associated with the index case’s genetic diagnosis

• Not available in general practice

When to consider this test or referring for this test

Patient has a first-degree relative with a known single-gene genetic condition

Medicare Rebate

N/A for GPs

Further information

Tests can only be ordered by a clinical geneticist or a paediatric specialist in consultation with a clinical geneticist

When to refer to clinical genetics and/or other non-GP specialist

• Refer to the relevant paediatric specialty for accurate phenotyping

• Some paediatric specialists will arrange genetic testing in first degree relatives for their patients

• Refer to clinical genetics for genetic testing of first-degree relatives if required 

What it tests for

• Tests for variants in genes associated with Alport syndrome or cystic kidney disease

• Not available in general practice

When to consider this test or referring for this test

Patient has a relevant family history of Alport syndrome or cystic kidney disease or there is a suspicion of these conditions based upon clinical presentation

Medicare Rebate

N/A for GPs

Further information

Tests can only be ordered by a renal physician or clinical geneticist

When to refer to clinical genetics and/or other non-GP specialist

• Refer to a renal specialist for accurate phenotyping

• Some renal specialists will arrange genetic testing for their patients

• Refer to clinical genetics for genetic testing if required

What it tests for

• Tests for variants in genes associated with retinal dystrophies

• Not available in general practice

When to consider this test or referring for this test

Patient has a relevant family history of a retinal dystrophy and/or there is a suspicion of a retinal dystrophy based upon clinical presentation

Medicare Rebate

No

Further information

• Tests can only be ordered by a specialist physician working in the retinal dystrophy space or clinical geneticist

• Inherited Retinal Disease Pathways

When to refer to clinical genetics and/or other non-GP specialist

• Refer to ophthalmology for assessment of indicators of retinal dystrophies

• Refer to a specialised genetic eye clinics for genetic testing if available

• Refer to clinical genetics for genetic testing if specialised clinics are not available

What it tests for

• Tests for variants in genes associated with childhood onset deafness

• Not available in general practice

When to consider this test or referring for this test

Patient has a relevant family history of hearing loss and/or a diagnosis of hearing loss with onset at <18 years of age

Medicare Rebate

N/A for GPs

Further information

• Tests can only be ordered by a specialist physician working in the deafness space or clinical geneticist

• Newborn hearing tests allow identification of newborns who may have hearing loss so they can undergo a formal diagnostic assessment

When to refer to clinical genetics and/or other non-GP specialist

• Refer to Hearing Australia for a formal diagnostic assessment  

• Refer to local deafness clinic if available (or clinical genetics) for genetic testing

What it tests for

• Tests for many genes involved with childhood onset single gene conditions

• Not available in general practice

When to consider this test or referring for this test

A person is strongly suspected of having a monogenic condition, based on the presence of:

• (i) dysmorphic facial appearance and one or more major structural congenital anomalies; or

• (ii) intellectual disability or global developmental delay of at least moderate severity

Medicare Rebate

N/A for GPs

Further information

Tests can only be ordered by a clinical geneticist (at any age) or a paediatric specialist in consultation with a clinical geneticist (<10 years of age) 

When to refer to clinical genetics and/or other non-GP specialist

• Refer to a developmental paediatrician for formal developmental assessments

• Refer to any additional paediatric non-GP specialists for any additional medical features

• Refer to Clinical Genetics for consideration of trio WES genetic testing if a patient meets the MBS criteria and none of the paediatric non-GP specialists have arranged trio WES independently

What it tests for

There is no substantial evidence to support the use of MTHFR gene testing in routine clinical practice 

When to consider this test or referring for this test

This test shouldn’t be ordered - knowledge of MTHFR gene status is unlikely to change patient management

Medicare Rebate

No

Further information

CGE MTHFR testing fact sheet

When to refer to clinical genetics and/or other non-GP specialist

Do not refer to clinical genetics

What it tests for

There is limited clinical utility to support the use of APOE gene testing in routine clinical practice

When to consider this test or referring for this test

This test shouldn’t be ordered - knowledge of APOE gene status is unlikely to change patient management

Medicare Rebate

No

When to refer to clinical genetics and/or other non-GP specialist

If a person has a clinical diagnosis of early onset dementia and/or a family history genetic testing in other genes may be indicated and a person can be referred to a neurologist or to an adult clinical genetics service

What it tests for

There is currently no available genetic testing for hypermobile Ehlers Danlos Syndrome (hEDS)

When to consider this test or referring for this test

Genetic testing may be possible for rarer forms of EDS, such as classic EDS or vascular EDS, but this needs to be guided by a clinical diagnosis after identification of ‘red flags’ 

Medicare Rebate

No

Futher information

Hypermobility syndromes in children and adolescents - RACGP and https://gptoolkit.ehlers-danlos.org/ are helpful guides for managing hypermobility in primary care

When to refer to clinical genetics and/or other non-GP specialist

• Refer to cardiology (for assessment of indicators of cardiac/vascular involvement)

• Referral pathways can be complex and should only include clinical genetics if clinical findings are suggestive of a rare form of EDS

• Red flags for referral to clinical genetics include: excessive skin fragility, skeletal deformities, vascular involvement, history of internal organ rupture, large hernias, pneumothoraces

What it tests for

This is currently still only available in certain centres and considered research

When to consider this test or referring for this test

While this is considered research it is likely to translate into clinical practice soon

Medicare Rebate

No

Further information

CGE Pharmacogenetics fact sheet

When to refer to clinical genetics and/or other non-GP specialist

Genetics services do not perform pharmacogenomics currently, but this is an evolving space

What it tests for

This is not considered a reliable or clinically relevant test in genetics

When to consider this test or referring for this test

Significant concerns exist around consent, use of data, and reliability of results

Medicare Rebate

No

Further information

• CGE DTC testing resources

• Online or direct to consumer genomic testing HGSA position statement

When to refer to clinical genetics and/or other non-GP specialist

Genetics services will not review direct to consumer results or advise on these