ICD-10-CM Code For Other Chromosome Abnormalities, Not Elsewhere Classified: Group Overview

The International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) code group Q99 includes chromosomal abnormalities not classified elsewhere, encompassing rare numeric and structural chromosome disorders beyond specific trisomies or sex chromosome anomalies. These ICD-10-CM diagnosis codes are used to document congenital genetic conditions that may involve developmental delay, multiple organ systems, or atypical chromosomal findings identified by karyotype or molecular testing. Accurate coding within the ICD-10-CM Q99 group supports proper claim adjudication, complete clinical documentation, and appropriate reimbursement.

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ICD-10-CM Q99: Other Chromosome Abnormalities, Not Elsewhere Classified Overview

This group includes chromosomal abnormalities that are not classified elsewhere and typically represent numeric or structural aberrations of chromosomes other than those with dedicated codes. These conditions affect genetic and developmental systems and can present with congenital anomalies, growth or developmental delays, and multisystem involvement. Accurate coding is important for complete clinical documentation and for ensuring appropriate reimbursement and claim processing.

When to Use

Use a code from this group when a documented chromosomal abnormality does not fit the descriptions of other specific ICD-10-CM chromosome disorder categories. These codes apply when laboratory testing or clinical genetics evaluation identifies atypical or rare chromosome abnormalities requiring documentation for care and billing.

ICD-10-CM Codes

10 rows

ICD-10-CM Code	Description
Q99.0	Chimera 46, XX/46, XY
Q99.1	46, XX true hermaphrodite
Q99.2	Fragile X chromosome
Q99.811	Usher syndrome, type 1
Q99.812	Usher syndrome, type 2
Q99.813	Usher syndrome, type 3
Q99.818	Other Usher syndrome
Q99.819	Usher syndrome, unspecified
Q99.89	Other specified chromosome abnormalities
Q99.9	Chromosomal abnormality, unspecified

DRG Codes

11 rows

DRG Code	Description
564	Other Musculoskeletal System and Connective Tissue Diagnoses with MCC
565	Other Musculoskeletal System and Connective Tissue Diagnoses with CC
566	Other Musculoskeletal System and Connective Tissue Diagnoses without CC/MCC
729	Other Male Reproductive System Diagnoses with CC/MCC
730	Other Male Reproductive System Diagnoses without CC/MCC
742	Uterine and Adnexa Procedures for Non-Malignancy with CC/MCC
743	Uterine and Adnexa Procedures for Non-Malignancy without CC/MCC
760	Menstrual and Other Female Reproductive System Disorders with CC/MCC
761	Menstrual and Other Female Reproductive System Disorders without CC/MCC
884	Organic Disturbances and Intellectual Disability
951	Other Factors Influencing Health Status

Typical Clinical Scenarios

An infant is born with multiple congenital anomalies identified on newborn exam and chromosomal microarray demonstrates mosaic trisomy of a sex chromosome not consistent with Turner or Klinefelter syndromes; the neonate is referred for genetics and early developmental intervention for feeding difficulty and hypotonia. A diagnosis from this group is assigned when a chromosomal abnormality other than common named syndromes is confirmed to explain the congenital presentation. Typical codes: Q99.818, Q99.819
A young adult with a long history of non-specific learning disabilities and short stature undergoes karyotyping as part of an evaluation for infertility and is found to have an uncommon structural sex chromosome abnormality (e.g., sex chromosome mosaicism with atypical features). The patient presents for reproductive counseling and baseline health screening, and the atypical chromosomal finding is coded to document the underlying genetic condition impacting care. Typical codes: Q99.811, Q99.812
A hospitalized child with recurrent infections and dysmorphic features is found to have a rare autosomal chromosome abnormality on cytogenetic testing that does not match established named syndromes; the chromosomal result is used to explain the patient’s immunologic issues and guide specialty referrals. A code from this group is used to capture the chromosomal abnormality as a comorbidity affecting management and prognosis. Typical codes: Q99.0, Q99.89

Related Codes

Q90-DOWN-SYNDROME

ICD-10-CM Code For Down Syndrome: Group Overview

Q91-TRISOMY-18-AND-TRISOMY-13

ICD-10-CM Code For Trisomy 18 And Trisomy 13: Group Overview

Q92-OTHER-TRISOMIES-AND-PARTIAL-TRISOMIES

ICD-10-CM Code For Other Trisomies And Partial Trisomies Of The Autosomes Not Elsewhere Classified: Group Overview

Q93-MONOSOMIES-AND-DELETIONS

ICD-10-CM Code For Monosomies And Deletions From The Autosomes Not Elsewhere Classified: Group Overview

Q95-BALANCED-REARRANGEMENTS-AND-STRUCTURAL-MARKERS

ICD-10-CM Code For Balanced Rearrangements And Structural Markers Not Elsewhere Classified: Group Overview

Q96-TURNERS-SYNDROME

ICD-10-CM Code For Turner's Syndrome: Group Overview

Q97-OTHER-SEX-CHROMOSOME-ABNORMALITIES-FEMALE-PHENOTYPE

ICD-10-CM Code For Other Sex Chromosome Abnormalities Female Phenotype Not Elsewhere Classified: Group Overview

Q98-OTHER-SEX-CHROMOSOME-ABNORMALITIES-MALE-PHENOTYPE

ICD-10-CM Code For Other Sex Chromosome Abnormalities Male Phenotype Not Elsewhere Classified: Group Overview

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

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When to Use

ICD-10-CM Codes

10 rows

ICD-10-CM Code	Description
Q99.0	Chimera 46, XX/46, XY
Q99.1	46, XX true hermaphrodite
Q99.2	Fragile X chromosome
Q99.811	Usher syndrome, type 1
Q99.812	Usher syndrome, type 2
Q99.813	Usher syndrome, type 3
Q99.818	Other Usher syndrome
Q99.819	Usher syndrome, unspecified
Q99.89	Other specified chromosome abnormalities
Q99.9	Chromosomal abnormality, unspecified

DRG Codes

11 rows

DRG Code	Description
564	Other Musculoskeletal System and Connective Tissue Diagnoses with MCC
565	Other Musculoskeletal System and Connective Tissue Diagnoses with CC
566	Other Musculoskeletal System and Connective Tissue Diagnoses without CC/MCC
729	Other Male Reproductive System Diagnoses with CC/MCC
730	Other Male Reproductive System Diagnoses without CC/MCC
742	Uterine and Adnexa Procedures for Non-Malignancy with CC/MCC
743	Uterine and Adnexa Procedures for Non-Malignancy without CC/MCC
760	Menstrual and Other Female Reproductive System Disorders with CC/MCC
761	Menstrual and Other Female Reproductive System Disorders without CC/MCC
884	Organic Disturbances and Intellectual Disability
951	Other Factors Influencing Health Status

Typical Clinical Scenarios

An infant is born with multiple congenital anomalies identified on newborn exam and chromosomal microarray demonstrates mosaic trisomy of a sex chromosome not consistent with Turner or Klinefelter syndromes; the neonate is referred for genetics and early developmental intervention for feeding difficulty and hypotonia. A diagnosis from this group is assigned when a chromosomal abnormality other than common named syndromes is confirmed to explain the congenital presentation. Typical codes: Q99.818, Q99.819
A young adult with a long history of non-specific learning disabilities and short stature undergoes karyotyping as part of an evaluation for infertility and is found to have an uncommon structural sex chromosome abnormality (e.g., sex chromosome mosaicism with atypical features). The patient presents for reproductive counseling and baseline health screening, and the atypical chromosomal finding is coded to document the underlying genetic condition impacting care. Typical codes: Q99.811, Q99.812
A hospitalized child with recurrent infections and dysmorphic features is found to have a rare autosomal chromosome abnormality on cytogenetic testing that does not match established named syndromes; the chromosomal result is used to explain the patient’s immunologic issues and guide specialty referrals. A code from this group is used to capture the chromosomal abnormality as a comorbidity affecting management and prognosis. Typical codes: Q99.0, Q99.89

Related Codes

Q90-DOWN-SYNDROME

ICD-10-CM Code For Down Syndrome: Group Overview

Q91-TRISOMY-18-AND-TRISOMY-13

ICD-10-CM Code For Trisomy 18 And Trisomy 13: Group Overview

Q92-OTHER-TRISOMIES-AND-PARTIAL-TRISOMIES

ICD-10-CM Code For Other Trisomies And Partial Trisomies Of The Autosomes Not Elsewhere Classified: Group Overview

Q93-MONOSOMIES-AND-DELETIONS

ICD-10-CM Code For Monosomies And Deletions From The Autosomes Not Elsewhere Classified: Group Overview

Q95-BALANCED-REARRANGEMENTS-AND-STRUCTURAL-MARKERS

ICD-10-CM Code For Balanced Rearrangements And Structural Markers Not Elsewhere Classified: Group Overview

Q96-TURNERS-SYNDROME

ICD-10-CM Code For Turner's Syndrome: Group Overview

Q97-OTHER-SEX-CHROMOSOME-ABNORMALITIES-FEMALE-PHENOTYPE

ICD-10-CM Code For Other Sex Chromosome Abnormalities Female Phenotype Not Elsewhere Classified: Group Overview

Q98-OTHER-SEX-CHROMOSOME-ABNORMALITIES-MALE-PHENOTYPE

ICD-10-CM Code For Other Sex Chromosome Abnormalities Male Phenotype Not Elsewhere Classified: Group Overview

Frequently Asked Questions

References

1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.

Published by

Trek Health powers OpenPayer with a leading commercial payer intelligence platform, seamlessly converting fragmented payer data into actionable insights for provider organizations.

ICD-10-CM Code For Other Chromosome Abnormalities, Not Elsewhere Classified: Group Overview

Sign up for ICD-10-CM Code For Other Chromosome Abnormalities, Not Elsewhere Classified: Group Overview policy alerts

ICD-10-CM Q99: Other Chromosome Abnormalities, Not Elsewhere Classified Overview

ICD-10-CM Code For Other Chromosome Abnormalities, Not Elsewhere Classified: Group Overview

Sign up for ICD-10-CM Code For Other Chromosome Abnormalities, Not Elsewhere Classified: Group Overview policy alerts

ICD-10-CM Q99: Other Chromosome Abnormalities, Not Elsewhere Classified Overview

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

Which conditions are included in the ICD-10-CM Q99 group?

How is coding within the Q99 group used for clinical documentation?

What types of clinical presentations might be associated with Q99 codes?

Which Q99 codes correspond to Usher syndrome subtypes?

How does accurate Q99 coding affect reimbursement and claims?

References

When to Use

ICD-10-CM Codes

DRG Codes

Typical Clinical Scenarios

Related Codes

Which conditions are included in the ICD-10-CM Q99 group?

How is coding within the Q99 group used for clinical documentation?

What types of clinical presentations might be associated with Q99 codes?

Which Q99 codes correspond to Usher syndrome subtypes?

How does accurate Q99 coding affect reimbursement and claims?

References