Af of Khushbuben Hemang Ramani

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Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

Name : AF OF KHUSHBUBEN HEMANG RAMANI Date & Time Collected : 08-Feb-2024 12:00 AM
Sex/Age : Unknown/ Date & Time Received : 09-Feb-2024 02:32 PM
Bill. Loc. : C/o Sagar Dudakiya, Rajkot Date & Time Reported : 26-Feb-2024 04:08 PM
Ref. By : Dr. Shilpen Gondalia MD (Gyn), Rajkot Report Version : 1
Indication : HIGH RISK ON DOUBLE MARKER
Affymetrix CytoScanTM Optima 315k Assay.
Clinical Indication:
High Risk on Double Marker
VUS DETECTED
Karyogram with Copy Number Variant (CNV) of Uncertain Significance detected
Result arr[GRCh37] 16q11.2q12.1(46,503,989_48,824,316)x1

2400107489-AF OF KHUSHBUBEN HEMANG RAMANI--Unknown
Sample Description:
Sample quality is optimum for the test. DNA conc.: 26.6 ng/μl
No Significant maternal contamination was detected.
Key Findings:
CN Chr. Cyto Size No. of ISCN Clinical
State No. band Genes Nomenclature Significance
1 16 q11.2-2320K 21 arr[GRCh37]16q11.2q12.1(46,503,989_4
Variant of
(Loss) q12.1 b 8,824,316)x1 uncertain
significance
(VUS)
*Genetic test results are reported based on the recommendations of American College of Medical Genetics.
Reviewed by Dr. Monica Patel

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Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Chief Consultant Geneticist MD (Path. & Bact.) Ph.D.(Human Genetics)
Consulting Geneticist
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Interpretation:
 Affymetrix CytoScan Optima 315k analysis shows a deletion of 2320 kb on cytoband q11.2-q12.1 on
chromosome 16 {arr arr[GRCh37] 16q11.2q12.1(46,503,989_48,824,316)x1}. Reported copy number
variant covers 14 OMIM genes & it is classified as Variant of Uncertain Significance. The severity of
the condition and the signs and symptoms depend on the size and location of the duplication and
which genes are involved. OMIM phenotype of gene involved in reported aberration is provided in
Gene-Phenotype relationship table.
Recommendations:
 Clinical correlation is suggested & further genetic counselling is recommended.
 Couple Microarray advised
Karyoview:
Fig 1:Genomic View of Duplication/Deletion in the analyzed DNA sample

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Chromosome View :

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Gene Phenotype Inheritance

ABCC11 [Axillary odor, variation in] AD
[Colostrum secretion, variation in] AD
[Earwax, wet/dry] AD
ORC6 Meier-Gorlin syndrome 3 AR
VPS35 {Parkinson disease 17} AD
PHKB Phosphorylase kinase deficiency of liver and muscle, autosomal AR
recessive
GPT2 Neurodevelopmental disorder with microcephaly and spastic AR
paraplegia
SIAH1 Buratti-Harel syndrome AD
ADDITIONAL FINDINGS: LOH DETECTED IN THE ANALYSED SAMPLE.

LOH
1. arr[GRCh37] 1q31.1q32.1(187,950,794_200,502,671)x2 hmz
Test Methodology:
 Chromosomal microarray analysis (CMA) was performed using an Affymetrix CytoScan™ 315K array.
 CytoScan® Optima Array content has been empirically selected from CytoScan® HD Array and consists
of a total of 315,608 features covering control, copy number(CN), and single-nucleotide polymorphism
(SNP) probes.
 There is a total of 18,018 CN and 148,450 SNP markers uniformly spaced over the genome with enhanced
interrogation of 396 regions of prenatal interest. Cumulatively, through the collection of SNPs and non-
polymorphic probes, the application provides the ability to support detection of CNVs, enable the
elucidation of allelic imbalance, identify copy number neutral abnormalities such LOH, and characterize
unbalanced translocation events in the samples of interest.
 Genomic DNA extracted from Peripheral Blood, Saliva, Amniotic fluid, CVS, POC, Cord Blood or any other
standard source issued for further protocol of Affymetrix CytoScanTM Optima 315k assay.
 Data was analyzed using Chromosome Analysis Suite (Hg19).

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Limitations:
 CMA is limited to detection of gain or loss of genomic material. It does not detects low level mosaicism
(<20%), balanced translocations, inversions or point mutations that may be responsible for the clinical
phenotype.
 This assay can detect a minimum resolution of 1 MB for losses, 2 MB for gains, and 5 MB for LOH.
 This assay has increased coverage density (25 markers/100 kb) in 396 empirically selected regions
relevant for prenatal research.
*Variant classification as per ACMG guidelines:

Variant A change in a gene. This could be disease causing (pathogenic) or not disease causing
(benign).
Benign A variant which is very likely to contribute to the development of disease however, the
scientific evidence is currently insufficient to prove this conclusively. Additional
evidence is expected to confirm this assertion of Pathogenicity.
Likely Benign A variant which is known not to be responsible for disease has been detected. Generally
no further action is warranted on such variants when detected.
Pathogenic A disease causing variation in a gene which can explain the patient's symptoms has
been detected. This usually means that a suspected disorder for which testing had been
requested has been confirmed.
Likely A variant which is very likely to contribute to the development of disease however, the
Pathogenic scientific evidence is currently insufficient to prove this conclusively. Additional
evidence is expected to confirm this assertion of pathogenicity.
Variant of A variant has been detected, but it is difficult to classify it as either pathogenic (disease
Uncertain causing) or benign (non-disease causing) based on current available scientific evidence.
Significance Further testing of the patient or family members as recommended by your clinician
may be needed. It is probable that their significance can be assessed only with time,
subject to availability of scientific evidence.

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The undersigned hereby confirms that no sex chromosome information has been passed on to anyone in
whatsoever manner.
References:
1. Levy B., et al. Genomic imbalance in products of conception: single-nucleotide polymorphism chromosomal microarray
analysis.Obstetrics and Gynecology 124(2 Pt 1):202–209 (2014).
2.Wang B. T., et al. Abnormalities in spontaneous abortions detected by G-banding and chromosomal microarray analysis
(CMA) at anational reference laboratory.Molecular Cytogenetics 7:33 (2014).eCollection 2014. doi:10.1186/1755-8166-7-33
------------------ End Of Report ------------------

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Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

Result arr[GRCh37] 16q11.2q12.1(46,503,989_48,824,316)x1

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

 Couple Microarray advised

Fig 1:Genomic View of Duplication/Deletion in the analyzed DNA sample

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

Gene Phenotype Inheritance

ADDITIONAL FINDINGS: LOH DETECTED IN THE ANALYSED SAMPLE.

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

*Variant classification as per ACMG guidelines:

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

Case ID : 2400107489 Sample Type : AMNIOTIC FLUID

Reviewed by Dr. Monica Patel

Dr.Vasundhara Tamhankar Dr.Nirmal A. Vaniawala Dr. Salil Vaniawala

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