ModifiedExcellus Health Plan IncPolicy 2.02.42

Chromosomal Microarray (CMA) Analysis for Prenatal Evaluation and Evaluation of Patients with Developmental Delay/Intellectual Disability or Autism Spectrum Disorder

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Coverage of comparative genomic hybridization/chromosomal microarray analysis for prenatal diagnostic evaluation and for children with developmental delay or intellectual disability, autism spectrum disorder, or multiple nonspecific anomalies, including genetic counseling, qualified laboratory, documentation, and medical-necessity requirements.

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ModifiedExcellus Health Plan IncPolicy 2.02.42

Chromosomal Microarray (CMA) Analysis for Prenatal Evaluation and Evaluation of Patients with Developmental Delay/Intellectual Disability or Autism Spectrum Disorder

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Policy Summary

PayerExcellus Health Plan Inc

PolicyChromosomal Microarray (CMA) Analysis for Prenatal Evaluation and Evaluation of Patients with Developmental Delay/Intellectual Disability or Autism Spectrum Disorder

Policy CodePolicy 2.02.42

Change TypeModified

Effective DateNovember 20, 2025

Next Review DateNovember 1, 2026

Key ActionEnsure indicated metabolic testing has nondiagnostic results and document face-to-face genetic counseling before requesting CMA.

SourceLink

POLICY UPDATE CHANGES

Policy criteria for FMR1 gene analysis were removed because the requirement is no longer needed.

The criterion requiring that genetic testing results have the potential to affect clinical management was removed.

Policy statements were reformatted during the annual review.

3Child clinical indications identified for medically appropriate CMA

CLIA-certifiedLaboratory qualification required

Pre- and post-testGenetic counseling requirement

InvestigationalCMA for other suspected genetic abnormalities in children with delayed development

15-20%Reported diagnostic yield for developmental delay, intellectual disability, and autism

Coverage Criteria

Pediatric developmental, intellectual disability, autism, or multiple-anomaly evaluation

CMA is considered medically appropriate when ALL of the following are met:

ALL of the following

Eligible child indication
- The child is being evaluated for apparent nonsyndromic cognitive developmental delay or intellectual disability.
- The child is being evaluated for autism spectrum disorder.
- The child has multiple anomalies that are not specific to a well-delineated genetic syndrome.
Additional requirements
- Any indicated biochemical tests for metabolic disease have been performed and the results are nondiagnostic.
- Testing is requested after the parent or parents have participated in face-to-face genetic counseling with a healthcare professional who has appropriate genetics training and experience.

Prenatal evaluation

CMA is considered medically appropriate when ALL of the following are met:

Prenatal criteria

The pregnant patient is undergoing invasive prenatal diagnostic testing.
Both policy criteria for prenatal CMA are met.
The source text available for this policy does not state the two underlying criteria.

Chromosomal microarray analysis (CMA) is not medically necessary when it is used to confirm a disorder or syndrome that is routinely diagnosed through clinical evaluation alone.

CPT code 0209U is considered experimental/investigational under this policy.

The codes listed in this policy may not be covered under all circumstances. Coverage remains subject to the member’s applicable benefit, policy criteria, and other plan requirements.

CMA used to confirm a disorder or syndrome that is routinely diagnosed based on clinical evaluation alone is considered not medically necessary.

Coding and Code Status

Policy code-status notationmixed

(E/I)	Experimental/Investigational
(NMN)	Not medically necessary/appropriate

CPT CodesCPTCovered

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.

CPT CodesCPTExperimental

0209U

Cytogenomic constitutional (genome-wide) analysis, interrogation of genomic regions for copy number, structural changes, and areas of homozygosity for chromosomal abnormalities (CNGnome, PerkinElmer Genomics)

HCPCS CodesHCPCSCovered

S3870

Comparative genomic hybridization (CGH) microarray testing for developmental delay, autism spectrum disorder and/or intellectual disability

ICD10 CodesICD-10

E78.71-	Disorders of bile acid and cholesterol metabolism (code range)
F70-F79	Intellectual disabilities (code range)
F84.0	Autistic disorder
G90.1	Familial dysautonomia (Riley-Day)
P29.30-P29.38	Persistent fetal circulation (code range)
Q00.0-Q07.9	Congenital malformations of brain, spinal cord and nervous system (code range)
Q10.0-Q15.9	Congenital malformations of eyelid (code range)
Q16.0-Q17.9	Congenital malformations of ear (code range)
Q18.0-Q18.9	Congenital malformations of face and neck (code range)
Q20.0-Q28.9	Congenital malformations of cardiac chambers, valves, connections and circulatory system (code range)

1–10 of 18

1/2

ICD10 CodesICD-10

Z13.71-Z13.79	Encounter for screening for genetic and chromosomal anomalies (code range)
Z13.810-Z13.818	Encounter for screening for other specified diseases and disorders (code range)
Z13.828	Encounter for screening for other musculoskeletal disorder
Z13.84	Encounter for screening for dental disorders
Z13.89	Encounter for screening for other disorder
Z13.9	Encounter for screening, unspecified
Z36.0-Z36.9	Encounter for antenatal screening (code range)

Provider Requirements and Actions

Documentation Required

Complete Metabolic Evaluation and Parental Counseling

Before requesting CMA for a child, complete any indicated biochemical testing for metabolic disease. CMA is medically appropriate only when those results are nondiagnostic and the parent(s) have completed face-to-face genetic counseling with a healthcare professional who has appropriate genetics training and experience.

Document the metabolic evaluation and its nondiagnostic results.
Document face-to-face genetic counseling with the parent(s), including the counselor’s appropriate genetics training and experience.

Documentation Required

Document Medical Necessity

Support the request with documentation showing a reasonable expectation that an inherited condition exists, based on the family history, pedigree analysis, risk factors, and/or the patient’s signs and symptoms. Autosomal recessive conditions may be present even without a family history.

Include relevant family history and pedigree information.
Document pertinent risk factors, phenotype, symptoms, and clinical findings.

Clinical Background

Chromosomal microarray analysis (CMA) identifies clinically relevant small genomic deletions and duplications, including changes in subtelomeric, pericentromeric, and other chromosome regions, that may not be detected by conventional cytogenetic methods.

Definitions and Terminology

Major malformation

DefinitionA structural defect with a significant effect on function or social acceptability.

Example 1Ventricular septal defect.

Example 2Cleft lip.

Minor malformation

DefinitionA structural abnormality with minimal effect on function or societal acceptance.

Example 1Preauricular ear pit.

Example 2Partial syndactyly (fusion) of the second and third toes.

Covered Clinical Indications

Diagnosing a child with apparent nonsyndromic cognitive developmental delay or intellectual disability

CMA is considered medically appropriate for this indication when the policy’s additional requirements are satisfied.

The child is being evaluated for apparent nonsyndromic cognitive developmental delay or intellectual disability.

Diagnosing a child with autism spectrum disorder

CMA is considered medically appropriate for this indication when the policy’s additional requirements are satisfied.

The child is being evaluated for autism spectrum disorder.

Diagnosing a child with multiple anomalies not specific to a well-delineated genetic syndrome

CMA is considered medically appropriate for this indication when the policy’s additional requirements are satisfied.

Eligibility and Documentation Requirements

Documentation must support a reasonable expectation of an inherited condition based on family history, pedigree analysis, risk factors, and/or symptomatology. When family history or the phenotype suggests a specific syndrome, the record should also address the associated mutation and any need for broader CMA testing.

Before CMA is requested for applicable indications, any indicated biochemical tests for metabolic disease must have been completed with nondiagnostic results. When family history or phenotype suggests a specific syndrome, targeted testing for the associated mutation should be completed before CGH/CMA; if it was not performed, the medical record must explain why proceeding directly to CMA is medically necessary.

Non-Covered and Investigational Uses

CMA is considered investigational for other suspected genetic abnormalities in children with delayed development, including idiopathic growth delay or language delay.

Policy Summary

PayerExcellus Health Plan Inc

PolicyChromosomal Microarray (CMA) Analysis for Prenatal Evaluation and Evaluation of Patients with Developmental Delay/Intellectual Disability or Autism Spectrum Disorder

Policy CodePolicy 2.02.42

Change TypeModified

Effective DateNovember 20, 2025

Next Review DateNovember 1, 2026

Key ActionEnsure indicated metabolic testing has nondiagnostic results and document face-to-face genetic counseling before requesting CMA.

SourceLink

On This Page

Documentation Required

Document Clinical Utility and Management Impact

Document the established clinical utility of CMA and how the results will influence treatment, prevention, or ongoing medical management. Testing should be performed for patient management or treatment, not solely for knowledge.

Explain the expected management or treatment decisions that may change based on the results.
Do not rely on knowledge-only or curiosity-based testing.

Documentation Required

Address Prior Targeted Testing

When the family history or phenotype suggests a specific syndrome, document the results of targeted mutation testing before CGH/CMA. If targeted testing was not performed, document why CGH/CMA is medically necessary instead.

Record prior targeted mutation testing when indicated.
Provide a rationale for proceeding directly to CMA when targeted testing was not performed.

Unsupported block type: documentation

Denial Risk

Other Developmental Delays

CMA is investigational for other suspected genetic abnormalities in children with delayed development, including idiopathic growth delay or language delay, when the child does not meet the medically appropriate indications.

Includes other forms of delayed development not within the covered indication.

Denial Risk

Clinically Diagnosable Syndromes

CMA is not medically necessary solely to confirm a disorder or syndrome that is routinely diagnosed through clinical evaluation alone.

Examples of routinely clinically diagnosed syndromes include Down syndrome, neural tube defects, and achondroplasia, although presentation in very young children or variable syndromes may require additional testing.

Billing Rule

Verify Member Eligibility

Genetic testing coverage is contract dependent. Coverage applies only to eligible members with a valid contract and is not provided for family members who do not have a valid contract.

Verify member eligibility and applicable benefit terms before requesting testing.

Billing Rule

Code Coverage Is Not Automatic

The presence of a listed billing code does not guarantee payment. Codes may not be covered under all circumstances and remain subject to the member’s benefit contract and all applicable medical-necessity criteria.

Confirm coverage under the member’s specific contract.
Ensure documentation satisfies the policy criteria before billing or requesting authorization.

Documentation Required

Provide Face-to-Face Genetic Counseling

Ensure that the parent(s) receive face-to-face genetic counseling from a healthcare professional with appropriate genetics training and experience before CMA is requested.

Document the counseling encounter and the professional’s genetics qualifications.

Prior Authorization

Request CMA After Counseling

Submit the CMA request only after the required face-to-face genetic counseling has occurred. The request should include documentation of the counseling and the applicable clinical, metabolic, and medical-necessity support.

Do not request CMA before the counseling requirement is met.
Include counseling documentation with the request.

Syndrome

DefinitionA recognizable pattern of multiple malformations.

Clinical recognitionSyndrome diagnoses are often relatively straightforward and common enough to be clinically recognized without specialized testing.

When recognition may be difficultConfident identification may be difficult in very young patients or when a syndrome has a variable presentation and additional testing may be needed.

ExamplesDown syndrome, neural tube defects, and achondroplasia.

Global developmental delay

DefinitionFailure to meet expected developmental milestones in several areas of intellectual functioning.

AgeApplies to an individual younger than five (5) years.

Assessment contextUsed when the individual cannot undergo systematic assessment of intellectual functioning, including children too young to participate in standardized testing.

Intellectual disability

DefinitionSignificant limitations in both intellectual functioning and adaptive behavior.

Adaptive skillsLimitations are expressed in conceptual, social, and practical adaptive skills.

AgeApplies to individuals five (5) years or older.

Copy number variation (CNV)

DefinitionA genomic change detected by chromosomal microarray analysis (CMA).

Clinical significance categoriesCNVs may be pathogenic, benign, or of uncertain clinical significance.

Clinical phenotypeCNVs may be associated with variable clinical phenotypes.

Variant of unknown significance (VOUS)

DefinitionA genetic finding whose clinical significance is uncertain.

Prenatal interpretationInterpretation of VOUS findings in prenatal testing may be difficult.

Counseling contextUncertain findings can increase counseling complexity and parental anxiety.

Chromosomal microarray analysis (CMA)

DefinitionA chromosomal microarray-based method of genetic testing.

Testing purposeIdentifies clinically relevant copy number changes, including small deletions and duplications, that may be missed by conventional cytogenetic methods.

Clinical applicationsThe policy addresses CMA in prenatal evaluation and in patients with developmental delay, intellectual disability, or autism spectrum disorder.

E/I

AbbreviationE/I

MeaningExperimental/Investigational.

Policy notationThe abbreviation is used in the policy's code-status notation.

NMN

AbbreviationNMN

MeaningNot medically necessary/appropriate.

Policy notationThe abbreviation is used in the policy's code-status notation.

The child has multiple anomalies that are not specific to a well-delineated genetic syndrome.

Pregnant patients undergoing invasive prenatal diagnostic testing when both policy criteria are met

CMA is considered medically appropriate when ALL of the following are met:

Prenatal invasive diagnostic testing

The pregnant patient is undergoing invasive prenatal diagnostic testing.
Both policy criteria are met.
The source text available for this policy does not state the two underlying criteria.

Guideline-supported first-tier evaluation of developmental delay, intellectual disability, autism spectrum disorder, or multiple congenital anomalies

Professional guidelines identify CMA as a first-tier or first-line evaluation when ANY of the following applies:

Guideline-supported first-tier indications

The patient has apparently nonsyndromic developmental delay or intellectual disability.
The patient has autism spectrum disorder.
The patient has multiple congenital anomalies that are not specific to a well-delineated genetic syndrome.

Prenatal CMA during invasive prenatal diagnosis when major fetal structural abnormalities are identified by ultrasonography

Professional guidelines recommend CMA in this prenatal setting when ALL of the following apply:

ALL of the following

The patient is undergoing invasive prenatal diagnosis.
Ultrasonography identifies one or more major fetal structural abnormalities.

CMA during invasive prenatal diagnosis for a structurally normal fetus and evaluation of fetal demise or stillbirth

Professional guidelines recommend CMA when ALL of the applicable conditions are met:

Prenatal and fetal-demise contexts

ALL of the following
- The fetus is structurally normal.
- The patient is undergoing invasive prenatal diagnostic testing.
ALL of the following
- Intrauterine fetal demise or stillbirth has occurred.
- Further cytogenetic analysis is desired.

Prenatal evaluation — policy-listed covered context

The policy identifies prenatal evaluation as a covered clinical context for CMA, subject to applicable policy criteria and benefit provisions.

The testing is requested for prenatal evaluation.

Evaluation of patients with developmental delay, intellectual disability, or autism spectrum disorder — HCPCS-described indication

The HCPCS-described indication is:

Covered clinical indications

The patient is being evaluated for developmental delay.
The patient is being evaluated for intellectual disability.
The patient is being evaluated for autism spectrum disorder.