ModifiedUnitedHealthcarePolicy CS017TN.Y

Chromosome Microarray Testing (Non-Oncology Conditions) (for Tennessee Only)

Defines medical necessity and coverage for chromosome microarray testing (aCGH and SNP array) for non-oncology indications for Tennessee Medicaid and CoverKids members.

Policy Summary

PayerUnitedHealthcare

PolicyChromosome Microarray Testing (Non-Oncology Conditions) (for Tennessee Only)

Policy CodePolicy CS017TN.Y

Change TypeICD-10 code updates

Effective DateNov 1, 2025

Next Review Date

Key ActionConfirm applicable ICD-10 diagnosis codes and include listed procedure codes when submitting prior authorization for Tennessee Medicaid/CoverKids.

SourceLink

POLICY UPDATE CHANGES

Updated list of applicable ICD-10 diagnosis codes to reflect annual edits, including added codes Q89.89, Q99.89, QA0.0159, and QA0.8 and removal of Q89.8 and Q99.8.

Archived previous policy version CS017TN.X.

recommendedpre-test counseling stance

ACMG first-linefirst-line indications

Prenatal & pediatricprimary evaluated populations

7 codeslisted procedure codes

19%

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example diagnostic yield (FGR)

Coverage Criteria and Rationale

Medically necessary indications

Chromosome microarray testing using aCGH and/or SNP array is covered when ANY of the following clinical indications apply:

Prenatal/fetal indications: Evaluation of an embryo/fetus in any of the following: intrauterine fetal demise or stillbirth; testing the products of conception following pregnancy loss; individuals undergoing invasive prenatal testing (amniocentesis, chorionic villus sampling, or fetal tissue sampling).

Neurodevelopmental and congenital indications: Evaluation of individuals with one or more of the following: autism spectrum disorder (ASD); isolated severe congenital heart disease; multiple congenital anomalies not specific to a well-delineated genetic syndrome and not identifiable by clinical evaluation alone; developmental delay or intellectual disability when a specific syndrome is not suspected.

Family cascade testing: Evaluation of a biological parent or sibling of a fetus or child with an abnormal or equivocal chromosome microarray result to aid interpretation and recurrence risk assessment.

Not medically necessary

Not medically necessary for other populations:

Not medically necessary: Chromosome microarray testing using aCGH or SNP array is unproven and not medically necessary for populations and clinical situations other than those explicitly listed in the Coverage Rationale due to insufficient evidence of efficacy.

Clinical use contexts and described indications

Clinical contexts described in this section

CMA modalities: Chromosomal microarray analysis (CMA) includes array comparative genomic hybridization (aCGH) and SNP array and may be genome-wide or targeted to known syndromic regions.

Described as aCGH and/or SNP array

Prenatal diagnostic sampling: Diagnostic prenatal CMA requires invasive specimen collection (amniocentesis or chorionic villus sampling) to obtain fetal cells for testing.

Indications and limitations: CMA is applied for congenital anomalies, dysmorphic features, developmental delay/intellectual disability, and other neurodevelopmental disorders; CMA detects CNVs (deletions/duplications) but may identify VUS and cannot detect some abnormalities such as balanced rearrangements.

Limitations include VUS detection and inability to detect balanced rearrangements

FGR and obstetric use:

Covered prenatal/obstetric indications

Covered when ANY of the following prenatal or obstetric conditions apply (per ACOG/ACMG guidance cited):

Fetal structural anomaly undergoing invasive testing: Fetus with one or more major structural abnormalities identified on ultrasound and undergoing invasive prenatal diagnostic testing (CMA may replace fetal karyotype).

ACOG/SMFM recommend CMA as primary prenatal test

Stillbirth/POC evaluation: CMA of fetal tissue or products of conception is recommended in evaluation of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired due to improved detection and success rates compared to karyotype.

ACOG/SMFM support use

Confirmatory testing after abnormal NIPS or reflex to karyotype: CMA on CVS or amniocentesis may be used for confirmatory diagnosis following abnormal noninvasive prenatal screening (NIPS) results or as a reflex following a normal karyotype when small CNVs are suspected.

Per ACMG laboratory practice resource

Medically necessary coverage criteria

Covered when ALL of the following are met (per professional guidance):

Primary clinical indication: The individual/fetus meets an indication supported by professional guidance (e.g., postnatal multiple congenital anomalies, apparently non-syndromic developmental delay/intellectual disability, ASD; or prenatal major fetal structural abnormality or stillbirth when cytogenetic analysis is desired).

ACMG/ACOG/SMFM/AAP/AAN guidance cited

Pretest counseling and informed consent: Comprehensive pretest and posttest genetic counseling and informed consent have been provided and documented, addressing benefits, limitations, possibility of VUS, incidental findings (including non-paternity/consanguinity), and potential adult-onset findings as applicable.

Counseling by genetics-trained personnel recommended

Appropriate testing sequence when syndrome suspected: When a specific, well-delineated genetic syndrome is suspected based on clinical evaluation, targeted testing for that syndrome should be performed first; if negative or not indicated, proceed to CMA (and Fragile X or other targeted tests as appropriate).

Professional societies recommend targeted-first when phenotype suggests single-gene disorder

First-tier indications

Covered when professional guidelines recommend CMA as first-line diagnostic testing for these clinical presentations:

ACMG first-line indications: Initial postnatal evaluation of individuals with multiple congenital anomalies not specific to a well-delineated genetic syndrome; apparently non-syndromic developmental delay/intellectual disability; and autism spectrum disorder — CMA is recommended as first-line.

ACMG technical standard and practice guidance

CCMG first-tier indications: CMA is recommended as a first-tier test for individuals with global developmental delay (GDD), intellectual disability (ID), or ASD; Fragile X testing is advised when suggested by family history or clinical features; WES/panels are second-tier when indicated.

CCMG 2023 position statement

ISCA consensus: ISCA recommends CMA as the first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies, followed by specific gene testing if CMA is negative.

ISCA consensus statement

Second-tier testing

When CMA is negative or when phenotype suggests specific monogenic or syndromic etiology:

Second-tier testing options: Consider targeted single-gene testing, disease-specific panels, or whole exome sequencing (WES) as second-tier testing following a negative CMA when clinical features suggest a specific disorder or when guideline bodies (e.g., CCMG/ACMG) recommend further testing.

WES/panels advised as second-tier per CCMG/ACMG

All uses of chromosome microarray testing that are not explicitly listed under the Coverage Rationale are considered unproven and not medically necessary. The policy specifies that CMA (aCGH and/or SNP array) is proven and medically necessary only for the prenatal and postnatal indications described in the Coverage Rationale; applications outside those stated clinical indications lack sufficient evidence of efficacy and may be denied.

Chromosome microarray platforms (aCGH and SNP array) have technical limitations. CMA cannot reliably detect certain cytogenetic abnormalities such as balanced rearrangements where there is no net gain or loss of chromosomal material; such rearrangements will not be identified by copy-number–based array methods and alternative cytogenetic testing (e.g., karyotype or targeted testing) may be required when balanced rearrangements are suspected.

Professional guidance notes that CMA may not detect balanced cytogenetic abnormalities or uniparental disomy (UPD). When deletion/duplication results, regions of homozygosity, or clinical suspicion raise the possibility of UPD or balanced rearrangement, additional testing (for example, conventional cytogenetics, methylation testing, or targeted assays) may be necessary to clarify mechanism and guide counseling.

Chromosomal microarray analysis would not be considered medically necessary when a diagnosis of a disorder or well‑delineated syndrome is readily apparent from the clinical evaluation alone. In such circumstances, targeted testing directed at the suspected syndrome is preferred and routine use of CMA may be of limited value.

Society guidance does not support routine use of CMA as a first‑line test for evaluation of first‑trimester pregnancy loss. Due to limited data in that context, CMA is not recommended as the first‑line test for first‑trimester pregnancy losses; clinicians should consider the evidence and choose appropriate testing on a case‑by‑case basis.

The Canadian College of Medical Genetics (CCMG) position statement advises that genetic testing is not routinely indicated for individuals with neurodevelopmental disorders when global developmental delay (GDD), intellectual disability (ID), or autism spectrum disorder (ASD) is not present, unless the clinical phenotype suggests a syndromic etiology or an inherited metabolic disorder. In other words, CMA is reserved for cases meeting the CCMG’s criteria rather than indiscriminate use in all neurodevelopmental presentations.

Chromosome microarray testing is considered unproven and not medically necessary for populations and clinical scenarios other than those explicitly listed in the Coverage Rationale. CMA detects genome‑wide copy number variations but has known limitations (for example, VUS and inability to detect some structural changes), and the policy does not support its routine use outside the stated prenatal and postnatal indications.

CMA can identify variants of uncertain significance (VUS) and may produce false positive findings that necessitate further laboratory or familial testing to resolve interpretation. These potential disadvantages should be discussed during pretest counseling and considered when evaluating the clinical utility of CMA in a given case.

In the prenatal setting, when a structurally normal fetus undergoes invasive diagnostic testing, either conventional karyotype or CMA can be performed; CMA is not universally required in every structurally normal fetus. Selection of karyotype versus CMA should be individualized based on the clinical context and counseling, recognizing that CMA generally detects submicroscopic CNVs while karyotype detects balanced rearrangements.

Testing performed without appropriate informed consent or when patients/guardians lack adequate understanding of the potential results and implications may be considered investigational or not medically necessary. The AAN model coverage policy highlights the necessity of documented consent and sufficient pretest knowledge to support the value of microarray testing.

Regulatory status is informational: FDA clearance or approval alone is not a basis for coverage. Genetic tests are regulated under CLIA for laboratory testing, and FDA listings of cleared/approved platforms are provided for information but do not determine medical necessity decisions.

Specific Indications Eligible for Coverage

Prenatal evaluation

Prenatal evaluation — covered indications relevant to intrauterine fetal demise, POC, and invasive prenatal testing:

Intrauterine fetal demise/stillbirth: CMA is indicated for evaluation of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired, using fetal tissue or products of conception as specimen sources.

Products of conception after pregnancy loss: Testing the products of conception following pregnancy loss with CMA is covered to identify chromosomal causes of loss when clinically indicated.

Invasive prenatal diagnostic testing: Individuals undergoing invasive prenatal diagnostic procedures (amniocentesis or CVS) may receive CMA as part of diagnostic evaluation when indications are present.

Individuals with ASD, severe CHD, multiple anomalies, or DD/ID

Procedure and Diagnosis Codes

Covered CPT/HCPCS CodesmixedCovered

0156U	Copy number (e.g., intellectual disability, dysmorphology), sequence analysis.
0209U	Cytogenomic constitutional (genome-wide) analysis, interrogation of genomic regions for copy number, structural changes and areas of homozygosity for chromosomal abnormalities.
81228	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number variants, comparative genomic hybridization [CGH] microarray analysis.
81229	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and single nucleotide polymorphism (SNP) variants, comparative genomic hybridization (CGH) microarray analysis.
81349	Cytogenomic (genome-wide) analysis for constitutional chromosomal abnormalities; interrogation of genomic regions for copy number and loss-of-heterozygosity variants, low-pass sequencing analysis.
81479	Unlisted molecular pathology procedure.
S3870	Comparative genomic hybridization (CGH) microarray testing for developmental delay, autism spectrum disorder and/or intellectual disability.

Sample Applicable ICD-10 CodesICD-10

F70	Mild intellectual disabilities.
F71	Moderate intellectual disabilities.
F72	Severe intellectual disabilities.
F73	Profound intellectual disabilities.
F79	Unspecified intellectual disabilities.
F84.0	Autistic disorder.
F88	Other disorders of psychological development.
F89	Unspecified disorder of psychological development.
R62.0	Delayed milestone in childhood.
R62.51	Failure to thrive (child).

1–10 of 14

1/2

Applicable/Listed Diagnosis CodesICD-10

P02.9
P95	Stillbirth.
Q20.1	Double outlet right ventricle.
Q20.2	Double outlet left ventricle.
Q20.3	Discordant ventriculoarterial connection.
Q20.4	Double inlet ventricle.
Q20.5	Discordant atrioventricular connection.
Q20.6	Isomerism of atrial appendages.
Q20.8	Other congenital malformations of cardiac chambers and connections.
Q20.9	Congenital malformation of cardiac chambers and connections, unspecified.

1–10 of 118

1/12

Referenced Test/Billing Codesmixed

81479	Unlisted molecular pathology procedure — may be used for billing when specific CPT not listed above.
S3870	HCPCS comparative genomic hybridization (CGH) microarray testing — referenced in billing guidance.

Codes Referenced (placeholder)mixed

No codes listed

ICD-10 Edits Effective 11/01/2025ICD-10

Q89.89	Added per 11/01/2025 updates: Other specified congenital malformations.
Q99.89	Added per 11/01/2025 updates: Other specified chromosome abnormalities.
QA0.0159	Added per 11/01/2025 updates: Neurodevelopmental disorder, related to other genes associated with transcription and gene expression.
QA0.8	Added per 11/01/2025 updates: Other neurodevelopmental disorders related to pathogenic variants in other specific genes.
Q89.8	Removed per 11/01/2025 updates.
Q99.8	Removed per 11/01/2025 updates.

Ordering, Documentation, and Follow-up Requirements

Prior Authorization

Codes to verify authorization

Verify applicable procedure and HCPCS/CPT codes with the payer for prior authorization and billing. Codes listed in this policy are reference only; inclusion does not guarantee coverage. Prior authorization requirements may apply.

Common procedure codes to verify for authorization: 0156U, 0209U, 81228, 81229, 81349, 81479, S3870
Confirm state program-specific prior authorization requirements for Tennessee Medicaid and CoverKids before ordering

Documentation Required

Diagnosis codes associated with CMA indications

Use appropriate ICD-10 diagnosis codes to support prior authorization and claims. Ensure diagnoses align with the covered indications in this policy (prenatal structural anomalies, developmental delay/intellectual disability, autism spectrum disorder, multiple congenital anomalies, intrauterine fetal demise/stillbirth, products of conception testing, and related family-member testing).

Examples of applicable diagnosis codes: O35.* series (maternal care for suspected chromosomal abnormality), O36.4XX*, P95, Q20–Q24 (congenital cardiac anomalies), Q87.86, Q89.7, Q89.89, Q90–Q92 series (trisomies/monosomies/other chromosome anomalies), Q93–Q95, Q99.89, QA0.0159, QA0.8, R62.*, Z36.0, Z37.*, Z87.74, Z14.*

Excluded and Not Medically Necessary Uses

Any use of chromosome microarray testing outside the indications listed in the Coverage Rationale is considered unproven and not medically necessary. Requests for CMA when clinical circumstances do not meet the stated prenatal or postnatal indications may not be covered.

The policy text does not enumerate every possible non‑covered test or scenario but explicitly documents technical limitations of CMA (for example, inability to detect balanced rearrangements and potential for VUS and false positives). These technical constraints are relevant when assessing non‑coverage for off‑label or unsupported uses.

Because CMA may not detect balanced cytogenetic abnormalities or uniparental disomy (UPD), CMA alone is insufficient when these specific abnormalities are suspected; additional or alternative testing (e.g., karyotype, methylation studies) should be pursued and CMA should not be relied on as the sole diagnostic assay in those cases.

Routine application of CMA for evaluation of first‑trimester pregnancy loss is not recommended by specialty guidance. When CMA is performed for first‑trimester losses without appropriate indication or consent, the test is considered investigational and not covered under routine use.

CCMG guidance indicates genetic testing, including CMA, is not recommended for individuals with neurodevelopmental concerns in the absence of GDD, ID, or ASD unless the phenotype suggests a syndromic disorder. Use of CMA in such individuals without supporting phenotype may be deemed non‑covered.

Member Eligibility and Testing Scope

When a fetus or child has an abnormal or equivocal CMA result, coverage includes evaluation of the biological parent(s) or sibling(s) to aid interpretation (parental testing to determine de novo versus inherited status is recommended). Parental/family testing is supported to clarify clinical significance and guide counseling.

Documentation in the policy does not provide additional explicit family‑history eligibility detail in this window; however, guidance emphasizes that parental testing and family evaluation are appropriate and should be considered when a proband has an abnormal or uncertain CMA finding.

The policy indicates that targeted testing guided by family history or a specific clinical suspicion should be performed first when appropriate; CMA and parental testing are indicated when targeted testing is negative or when broader CNV assessment is warranted by the clinical scenario.

Coverage for parental or sibling testing is described in association with an affected fetus or child: when an embryo/fetus or child has an abnormal or equivocal CMA result, evaluation of biological parents or siblings is covered to assist with interpretation and recurrence risk assessment.

The policy supports cascade testing in the family context: evaluation of biological parent(s) or sibling(s) is covered when needed to interpret an abnormal or equivocal CMA result in a fetus or child.

No additional explicit family‑testing eligibility criteria are provided in this portion of the policy beyond the statement that parental/sibling testing is appropriate to clarify findings; clinical judgment and documentation of the indication are expected.

Key Definitions

Developmental Delay

DefinitionChildren younger than 5 years who present with delays in attainment of developmental milestones at the expected age

Age contextTerm 'Developmental Delay' is applied to children younger than 5 years

PurposeUsed to identify early delays that may prompt genetic evaluation such as CMA

Intellectual Disability

DefinitionA condition diagnosed before age 18 characterized by below‑average intellectual function and lack of skills necessary for daily living

Diagnostic age cutoffDiagnosis occurs before 18 years of age

Clinical relevance

Evidence Summary and Clinical Background

The policy strongly recommends pre‑test genetic counseling prior to chromosome microarray testing to ensure patients (or guardians) understand the advantages, limitations, and potential outcomes of CMA. Counseling should cover the possibility of identifying variants of uncertain significance, incidental findings, and the limitations of array methods compared with other cytogenetic tests.

Genetic counseling is essential in the prenatal context: comprehensive pretest and posttest counseling by providers with genetics expertise (e.g., genetic counselors, clinical geneticists, or trained obstetric providers) should be documented. Counseling should include discussion of benefits and limitations of CMA versus karyotype, the potential for VUS or incidental findings, and the implications of results for pregnancy management and family planning.

Copy number variations (CNVs) are genomic deletions or duplications that can be benign, pathogenic, or of uncertain significance. CNVs detected by CMA can explain a range of clinical phenotypes including congenital anomalies, developmental delay, and neurodevelopmental disorders; parental testing is frequently required to establish whether a CNV is de novo or inherited and to inform clinical interpretation.

Policy History and Revisions

2025-11-01ICD-10 code updateLatest

Updated list of applicable ICD-10 diagnosis codes: added Q89.89, Q99.89, QA0.0159, and QA0.8; removed Q89.8 and Q99.8.

2025-11-01administrative

Archived previous policy version CS017TN.X as part of the update.

Policy Summary

PayerUnitedHealthcare

PolicyChromosome Microarray Testing (Non-Oncology Conditions) (for Tennessee Only)

Policy CodePolicy CS017TN.Y

Change TypeICD-10 code updates

Effective DateNov 1, 2025

Next Review Date

Key ActionConfirm applicable ICD-10 diagnosis codes and include listed procedure codes when submitting prior authorization for Tennessee Medicaid/CoverKids.

SourceLink

On This Page

In obstetric cohorts, CMA has increased diagnostic yield in fetuses with fetal growth restriction (FGR) accompanied by structural malformations or multiple system malformations; authors recommend considering CMA in FGR contexts pending further study.

Li et al. (2025) single-center cohort cited

Multiple anomalies or certain soft markers: Fetuses with multiple structural anomalies or selected soft markers (e.g., increased nuchal translucency, short femur, mild ventriculomegaly) — particularly when multiple organ systems are involved — where CMA diagnostic yield is higher.

Systematic reviews/meta-analyses support higher yield

Covered postnatal indications in individuals with developmental and congenital presentations:

Autism spectrum disorder: Individuals with autism spectrum disorder (ASD) are covered for CMA when evaluation is for an underlying genetic etiology and a specific syndrome is not already suspected or confirmed.

ACMG/CCMG list CMA as first-tier for ASD

Isolated severe congenital heart disease: Individuals with isolated severe congenital heart disease are covered for CMA when no well-delineated genetic syndrome is identified and testing is intended to evaluate for chromosomal imbalances.

Multiple anomalies not attributable to a specific syndrome: Individuals with multiple congenital anomalies not attributable to a well-delineated genetic syndrome and not identifiable by clinical examination alone are covered for CMA.

Developmental delay/intellectual disability: Individuals with developmental delay or intellectual disability without suspicion of a specific syndrome are covered for CMA as part of diagnostic evaluation.

Evaluation of biological parent or sibling

Covered when needed to interpret familial findings:

Parental or sibling evaluation: Evaluation of a biological parent or sibling is covered when performed to clarify an abnormal or equivocal CMA result in a fetus or child, to determine inheritance (de novo versus inherited) and inform recurrence risk and interpretation.

Diagnosis of chromosomal abnormalities in fetuses, newborns, and children

Diagnosis of chromosomal abnormalities in pediatric and neonatal populations:

Fetuses, newborns, and children with developmental disorders or anomalies: CMA is covered for diagnosis of chromosomal abnormalities in fetuses, newborns, and children presenting with developmental disorders, congenital anomalies, dysmorphic features, DD/ID, or other neurodevelopmental disorders; prenatal diagnostic CMA requires invasive sample collection.

Fetal growth restriction (FGR) indications

FGR contexts where CMA yield is increased:

FGR with structural malformations or multiple system involvement: Fetal growth restriction (FGR), particularly when accompanied by structural malformations or multiple system malformations, is a covered indication for CMA given higher pathogenic CNV detection rates reported in cohort studies.

Li et al. (2025) reported higher pCNV detection in FGR with structural malformations

Prenatal diagnosis for structural anomalies, CHD, increased NT, stillbirth/POC

Prenatal diagnostic scenarios supported by guideline and evidence:

Structural anomalies and non-immune hydrops: Prenatal diagnosis for fetal structural anomalies and non-immune hydrops with anomalies is covered; CMA is recommended as the primary diagnostic test when invasive testing is performed.

ACOG/SMFM recommend CMA as primary test

Congenital heart defects and increased nuchal translucency: CMA is covered for congenital heart defects (especially non-isolated CHD) and for increased nuchal translucency above specified thresholds as part of prenatal diagnostic evaluation.

Systematic reviews show variable yields; consider number of systems involved

Stillbirth/POC evaluation: Evaluation of stillbirth or products of conception with CMA is covered when cytogenetic analysis is desired to improve detection compared to karyotype.

Meta-analyses report diagnostic yields in POC

Postnatal evaluation of multiple anomalies, DD/ID, or ASD

Postnatal first-line indications where CMA is recommended by societies:

Multiple congenital anomalies: Initial postnatal evaluation of individuals with multiple congenital anomalies not specific to a well-delineated syndrome — CMA is recommended as first-line.

ACMG/ISCA/AAP support

Apparently non-syndromic DD/ID/GDD: Individuals with apparently non-syndromic developmental delay, intellectual disability, or global developmental delay — CMA is recommended as the first-line diagnostic test.

ACMG and AAP guidance

Autism spectrum disorder: Initial postnatal evaluation of individuals with autism spectrum disorder — CMA is recommended as a first-tier diagnostic test.

ACMG and CCMG position statements

Prenatal diagnostic testing and stillbirth/POC evaluation

Prenatal diagnostic testing and stillbirth evaluation where CMA can replace karyotype:

Replacement of fetal karyotype: When fetal structural abnormalities are identified and invasive prenatal diagnostic testing is performed, CMA can be used in place of traditional fetal karyotype as recommended by ACOG/SMFM/ACMG.

Stillbirth and POC cytogenetic analysis: CMA is indicated for the evaluation of stillbirth or POC to obtain higher success rates and improved detection of causative abnormalities compared to karyotype.

Unexplained isolated FGR and related prenatal scenarios

SMFM-recommended prenatal FGR scenarios:

Unexplained isolated FGR < 32 weeks or FGR with malformation/polyhydramnios: Offer CMA for unexplained isolated fetal growth restriction diagnosed before 32 weeks of gestation, or for FGR accompanied by malformation or polyhydramnios, per SMFM guidance.

SMFM Consult Series recommendation

Initial postnatal evaluation first-tier recommendations

Initial postnatal evaluation supported by multiple societies:

ACMG/CCMG/ISCA consensus: Initial postnatal evaluation of individuals with multiple congenital anomalies not specific to a well-delineated syndrome, apparently non-syndromic developmental delay/intellectual disability (DD/ID/GDD), or autism spectrum disorder (ASD) — CMA is recommended as the first-tier clinical diagnostic test by ACMG, CCMG, and ISCA.

Check payer-specific code lists and any recent ICD-10 updates before submission

Documentation Required

Indication and documentation required for prenatal CMA

When ordering prenatal CMA, document the prenatal indication and that invasive diagnostic sampling is being performed (e.g., amniocentesis, CVS, fetal tissue). Prenatal CMA is recommended as the primary diagnostic test for fetuses with structural anomalies and may replace karyotype in these circumstances.

Document: ultrasound findings (major structural anomaly or multiple anomalies), indication for invasive testing, and site performing invasive procedure
For intrauterine fetal demise or stillbirth, document intent to pursue cytogenetic evaluation and source of fetal tissue or products of conception

Documentation Required

Pretest counseling and indication confirmation

Confirm that comprehensive pretest genetic counseling and informed consent have been completed and documented prior to ordering CMA, particularly in the prenatal setting. Counseling should cover benefits, limitations, potential for variants of uncertain significance, incidental findings (including adult-onset conditions), non-paternity, and consanguinity.

Document who provided counseling (e.g., OB/GYN with genetics expertise, genetic counselor, trained personnel) and that informed consent was obtained
Ensure discussion of possible outcomes (pathogenic, benign, VUS), follow-up testing (parental studies), and implications for management

Note

Check updated diagnosis codes

Review policy history and payer notices for ICD-10 code updates that may affect authorization and claims processing. Use the most current diagnosis codes when submitting prior authorization requests and claims.

Policy update 11/01/2025: Added Q89.89, Q99.89, QA0.0159, QA0.8; removed Q89.8 and Q99.8
Verify any additional annual ICD-10 updates with the payer prior to submission

Denial Risk

Coverage-limited indications

Tests performed outside the specific, evidence-supported indications listed in this policy are considered unproven and not medically necessary. Order CMA only when the patient's clinical presentation meets the policy's covered indications.

Not medically necessary when a diagnosis is readily apparent from clinical evaluation alone
Unproven for populations/conditions not specified in the policy (e.g., routine screening without indication)

Note

Not applicable content / Program-specific applicability

If content in this provider-action window is not applicable to your care setting or program requirements, follow the specific Tennessee Medicaid or CoverKids ordering rules and document deviations accordingly. Genetic counseling is still strongly recommended even when not explicitly required by the ordering site.

Tennessee Medicaid and CoverKids program rules supersede where specified; verify local requirements
When not applicable, document rationale and alternative steps taken (e.g., referral to genetics)

Prior Authorization

Indication-based requirement

Order CMA as part of prenatal diagnostic evaluation when invasive testing is undertaken for structural fetal abnormalities or certain fetal loss evaluations. CMA is recommended as the first-line cytogenetic test in these scenarios.

Indications: major structural anomalies on ultrasound, intrauterine fetal death/stillbirth when cytogenetic analysis desired, select cases of fetal growth restriction with anomalies
Ensure sample type and handling meet laboratory requirements (amniotic fluid, CVS, fetal tissue, or POC)

Billing Rule

ICD-10 code applicability

ICD-10 diagnosis coding can influence coverage determinations and claims edits. Use specific, accurate ICD-10 codes that reflect the clinical indication for CMA and align with payer policy requirements.

Avoid using nonspecific or inaccurate diagnosis codes that may result in claim denials or requests for additional documentation
When in doubt, include supporting clinical documentation (ultrasound report, clinical notes) with prior authorization

Documentation Required

Genetic counseling recommendation

Genetic counseling by a qualified provider is strongly recommended prior to CMA and should be documented. Counseling facilitates informed decision-making and proper interpretation of results and follow-up planning.

Counseling should be provided by a genetic counselor, clinical geneticist, OB/GYN with genetics expertise, or other trained personnel
Document counseling content, who performed it, and that informed consent was obtained

Documentation Required

Required documentation and counseling

Maintain required documentation for authorization and medical record review: indication, counseling and consent, ultrasound or clinical findings, invasive sampling procedure details, laboratory test ordered, and plan for follow-up (including parental testing if VUS or imbalance identified).

Include the ordering clinician's rationale linking the diagnosis code(s) to clinical findings
Document plans for confirmatory testing and referral to genetics when chromosome imbalances or VUS are identified

Note

Documented limitations of CMA

Be aware of CMA limitations: CMA may not detect balanced rearrangements, low-level mosaicism, some repeat expansions, or point mutations. Additional testing (karyotype, FISH, parental studies, targeted gene testing, or sequencing) may be necessary depending on clinical context and CMA findings.

Limitations to document and counsel: inability to detect balanced translocations, some structural rearrangements without copy number change, and certain types of sequence-level variants
Plan for reflex testing (karyotype, FISH, parental studies) when indicated by CMA results

Documentation Required

Reflex/follow-up testing guidance

Follow reflex and follow-up testing guidance: CMA may be used as confirmatory testing for abnormal NIPS results, as reflex testing after abnormal or normal karyotype when small CNVs are suspected, and as follow-up to POC/karyotype in some cases. Parental testing is recommended to interpret variants of uncertain significance or to determine inheritance.

Use CMA to confirm abnormal NIPS and to evaluate small CNVs reported by NIPS
If CMA identifies CNV of unknown significance, perform parental studies and consider additional cytogenetic testing as appropriate

Documentation Required

Testing sequence for developmental disorders

Follow recommended testing sequence for developmental disorders: if a specific genetic syndrome is suspected, perform targeted testing first. If targeted testing is negative or no specific syndrome is suspected, perform CMA and Fragile X (FMR1) testing as first-tier; consider WES or gene panels as second-tier testing if CMA and targeted tests are unrevealing.

When a recognized syndrome is suspected: order specific targeted genetic tests first (e.g., FMR1 for Fragile X when indicated)
If targeted tests are negative or no syndrome suspected: order CMA (first-tier) ± Fragile X testing; if still negative, consider WES, targeted panels, karyotype, or mitochondrial testing as appropriate

Documentation Required

Testing algorithm

Follow professional testing algorithms: CMA is the first-tier test for unexplained developmental delay/intellectual disability, autism spectrum disorder, and multiple congenital anomalies. Targeted gene testing or WES/panels are recommended as second-tier investigations when CMA is unrevealing or when clinical features suggest a single-gene disorder.

Document why CMA is chosen as first-tier based on clinical presentation
If CMA is non-diagnostic, document consideration of second-tier testing (WES/panels) and rationale for selected follow-up tests

When parental testing is performed to clarify a proband’s CMA result, the laboratory approach and interpretation should follow recognized practice resources; ordering clinicians should document the clinical rationale for family member testing.

Family testing should be considered when results would change clinical management or counseling; the policy supports such testing when it meets that purpose and is connected to an abnormal or equivocal proband result.

An indication for genetic evaluation (e.g., CMA) when a specific syndrome is not suspected

Intrauterine Fetal Demise or Stillbirth

DefinitionFetal death occurring at or after 20 weeks' gestation

Source guidanceACOG/SMFM definitions referenced in policy

Testing implicationCMA of fetal tissue or products of conception is recommended when further cytogenetic analysis is desired

Well-Delineated Genetic Syndrome

DefinitionA recognizable collection of traits or abnormalities that tend to occur together and are associated with a specific disease

Identification methodsDistinguishing characteristics (facial features, physical traits), lab tests, or family history can identify a syndrome

ExamplesExamples include Down syndrome, Klinefelter syndrome, Marfan syndrome, NF1, Prader‑Willi, Rett syndrome, Patau, Edwards, Turner, Williams

CNV

DefinitionAlterations that include deletion and/or duplication of one or more sections of DNA (copy number variations)

Clinical spectrumCNVs may be benign, pathogenic, or of uncertain significance and can underlie congenital anomalies and neurodevelopmental disorders

Detection methodsDetected by CMA modalities such as aCGH or SNP array which identify deletions/duplications across the genome

CMA / aCGH / SNP array

DefinitionChromosome microarray analysis (CMA) encompasses array comparative genomic hybridization (aCGH) and single‑nucleotide polymorphism (SNP) array methods

FunctionLaboratory methods to detect deletions and duplications (CNVs) across the genome; may be targeted or genome‑wide

Prenatal noteDiagnostic prenatal CMA requires invasive fetal cell collection (amniocentesis or CVS)

CMA (chromosomal microarray analysis)

DefinitionCMA (chromosomal microarray analysis) is a genomic test (including array‑CGH and SNP‑array variants) used to detect copy number variations and submicroscopic chromosomal imbalances not detectable by conventional karyotype

Platform variabilityPlatforms include microarray‑based CGH and SNP microarrays; each has specific limitations and information generated

Clinical useUsed for prenatal and postnatal evaluation of congenital anomalies, DD/ID, ASD, and stillbirth/POC assessment

pCNV (pathogenic copy number variation)

DefinitionA copy number variant classified as pathogenic that can contribute to pregnancy loss or fetal anomalies

OccurrencepCNVs have been identified in products of conception and are associated with miscarriage and fetal anomalies

Testing implicationIdentification of pCNVs in POC may inform recurrence risk and further parental evaluation

CMA

DefinitionCMA is chromosomal microarray analysis (including array‑CGH and SNP array) used for detection of CNVs and loss of heterozygosity

First‑line roleACMG recommends CMA as a first‑line test for multiple congenital anomalies, apparently non‑syndromic DD/ID, and ASD

Follow‑upWhen CMA identifies imbalance of unknown significance, parental testing and clinical genetic evaluation are recommended

VUS

DefinitionVariant of uncertain significance (VUS): a CNV whose clinical significance is unclear

Prenatal reporting guidancePolicy references guideline that VUS smaller than 500 Kb deletion or 1 Mb duplication should generally not be reported prenatally

Reporting caveatLarger VUS may be reported if significant evidence suggests pathogenicity; counseling should address VUS implications

CMA (cytogenetic microarray)

Platform descriptionCMA (cytogenetic microarray) refers to microarray‑based CGH and SNP microarray platforms used to detect CNVs

LimitationsDifferent platforms generate different outputs; ordering clinicians should be aware of platform limitations and information provided

Reporting standardsACMG technical guidance addresses interpretation and reporting standards for postnatal settings and follow‑up testing recommendations

CNV (copy number variant)

DefinitionA copy number variant is a deletion or duplication of genomic material that may be classified as pathogenic, benign, or of uncertain significance

Interpretation stepParental testing can help determine whether a CNV is de novo or inherited, aiding clinical interpretation

Clinical significanceCNVs are implicated in congenital anomalies, developmental disorders, and pregnancy loss; resolution should be appropriate for detection of small pathogenic variants in prenatal settings

Chromosome microarray analysis is a genome‑wide method (aCGH and SNP array) used to detect copy number variations (CNVs) — deletions and duplications — and, in SNP arrays, regions of homozygosity. CMA is applied in prenatal and postnatal diagnostic settings to identify submicroscopic chromosomal imbalances that may explain congenital anomalies, developmental delay, intellectual disability, and other neurodevelopmental disorders. For prenatal diagnostic CMA, an invasive sample (amniocentesis or CVS) is required to obtain fetal cells.