Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

ORDER INFO Physician Institution Sample

Name: Jen Ern Tan Name: Hospital Pakar Kanak-kanak,
Email address: Universiti Kebangsaan Malaysia
jenern84@ukm.edu.my Address: Hospital Pakar Kanak-
Phone: +60 12-3977-917 kanak, UKM, Jalan Yaacob Latif,
Bandar Tun Razak, Cheras, Kuala
Lumpur, Malaysia (56000)
Type: buccal swab
Ordered on: 2022-10-28
Collected on: 2022-11-29
Accessioned on: 2022-12-30

CLINICAL INFO Autistic feature, ADHD, Absence seizures, Intellectual disability, EEG with spike-wave complexes (2.5-3.5 Hz), Eyelid
myoclonus

RESULTS
POSITIVE

Intellectual developmental disorder, autosomal dominant 5 (OMIM: 612621)

Gene Variant Classification

SYNGAP1 Genomic Position: 6-33400583-G-A (GRCh37) Pathogenic

cDNA: NM_006772.3:c.509G>A
Protein: NP_006763.2:p.Arg170Gln
Zygosity: Heterozygous
Inheritance: Unknown

A heterozygous pathogenic variant was identified in SYNGAP1. SYNGAP1 is associated with autosomal dominant
'Intellectual developmental disorder, autosomal dominant 5 (OMIM: 612621)'. Although the variant is a known
variant and most likely the variant is de novo, parental testing is recommended.

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 1/
6
 Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

INTERPRETATION SYNGAP1 NM_006772.3:c.509G>A (NP_006763.2:p.Arg170Gln)

Population Data The variant is not observed in the gnomAD v2.1.1 dataset.

Predicted Missense variant

Consequence/Location

Segregation Data None

Computation and In silico tools predict the variant to alter splicing and produce an abnormal transcript
Functional Data (SpliceAI: 0.77).

Previously Reported Same nucleotide change resulting in same amino acid change has been previously
Variant Data reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID:
VCV000375528 / PMID: 26079862). The variant has been previously reported as de
novo in a similarly affected individual (PMID: 25533962).

Disease Association Intellectual developmental disorder, autosomal dominant 5 (OMIM: 612621)

Validation Not performed as the variant was considered high-quality

Variant Classification Pathogenic

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 2/
6
 Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

SECONDARY No clinically significant variant was identified in the 78 medically actionable secondary finding genelist recommended to
FINDINGS be reported by the American College of Medical Genetics and Genomics (ACMG). However, there is a possibility of missing
the disease-causing variant due to the test limitations (see below Recommendations #2, #3, and #5).

RESOURCES Online Mendelian Inheritance in Man®: This report contains information from the Online Mendelian Inheritance in Man®
(OMIM®) database, which has been obtained under a license from Johns Hopkins University. This report does not
represent the entire, unmodified OMIM® database, which is available in its entirety at http://omim.org/downloads.

gnomAD (genome Aggregation Database): https://gnomad.broadinstitute.org

ClinVar (National Center for Biotechnology Information ClinVar Database): https://ncbi.nlm.nih.gov/clinvar

HGVS (Human Genome Variation Society): https://varnomen.hgvs.org

HGMD (The Human Gene Mutation Database) Professional

REFERENCES 1. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm
HL; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence
variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the
Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.
PMID: 25741868; PMCID: PMC4544753.

2. Seo GH, Kim T, Choi IH, Park JY, Lee J, Kim S, Won DG, Oh A, Lee Y, Choi J, Lee H, Kang HG, Cho HY, Cho MH, Kim YJ, Yoon
YH, Eun BL, Desnick RJ, Keum C, Lee BH. Diagnostic yield and clinical utility of whole exome sequencing using an
automated variant prioritization system, EVIDENCE. Clin Genet. 2020 Dec;98(6):562-570. doi: 10.1111/cge.13848. Epub
2020 Sep 17. PMID: 32901917; PMCID: PMC7756481.

3. Miller, D.T., Lee, K., Chung, W.K. et al. ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome
sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2022
Jul;24(7):1407-1414. PMID 35802134

4. Dhong-Gun Won, Dong-Wook Kim, Junwoo Woo, Kyoungyeul Lee. 3Cnet: pathogenicity prediction of human variants
using multitask learning with evolutionary constraints. Bioinformatics. 2021 Jul 16;btab529. doi:
10.1093/bioinformatics/btab529. PMID: 34270679

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 3/
6
 Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

RECOMMEN- 1. Genetic counseling is warranted to review the implications of these results.

DATIONS
2. This test can only reliably detect single nucleotide variants and small (< 20bp) insertions and deletions within the
protein coding exonic regions of the nuclear genome. If other types of variants such as large deletion/duplication,
translocation, inversion, low-level mosaicism, mitochondrial genome variants are suspected, it is recommended to
perform appropriate testing that are designed to detect those types of variants.

3. There are certain exonic regions that are incompletely sequenced due to technical difficulties with amplification,
sequencing and alignment. If variants within these regions are suspected, it is recommended to perform alternate
testing that are designed to sequence those regions/genes adequately.

4. Testing of biological parents and/or other family members by exome sequencing or Sanger sequencing is
recommended to confirm the segregation of the variant(s). For the structural variants including copy number variants
(CNV), only those with exact breakpoints known can be tested by Sanger sequencing.

5. The results in this report are based on currently available scientific and medical information and negative test results
does not rule out a diagnosis of a certain disorder. To ensure newly available information is promptly reflected in the
variant interpretation, 3billion will perform automated daily reanalysis of the data and inform the ordering physician if
a new molecular diagnosis is identified or a variant is reclassified. However, a medical provider may also request a
reanalysis if desired, especially if there is new phenotypic information available from the patient. To be compliant with
Korean Bioethics and Safety Act Article 53 (Provision and Discarding of Materials for Testing), 3billion discards all
specimens after the initial testing and cannot confirm the newly identified variant(s) from reanalysis by Sanger
sequencing unless a new specimen is provided by the patient.

METHODS Genomic DNA was extracted from buccal swab specimen using standard protocol. Exome capture was performed using
xGen Exome Research Panel v2 (Integrated DNA Technologies, Coralville, Iowa, USA) and sequencing was performed
using NovaSeq 6000 (Illumina, San Diego, CA, USA). In total 10,695,112,555 bases of sequence were generated and
uniquely aligned to the Genome Reference Consortium Human Build 37 (GRCh37) and Revised Cambridge Reference
Sequence (rCRS) of the mitochondrial genome, generating 154.10 mean depth-of-coverage within the 34366188 bases
of the captured region, which is approximately 99.3% of the RefSeq protein coding region. Approximately 98.90% of the
targeted bases were covered to a depth of ≥20x. Gene or exon level depth-of-coverage information is available upon
request. In total, 67,951 single nucleotide variants (SNV) and 11,394 small insertions and deletions (indel) were identified.
The entire variant list without annotation or clinical interpretation is available upon request. Despite the insufficient
coverage across 1.10% of the bases (see below for details), these metrics are consistent with high quality exome
sequencing data and deemed adequate for analysis. Variant interpretation was performed using EVIDENCE, a software
developed in-house to prioritize variants based on the guideline recommended by the American College of Medical
Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) (Genet Med. 2015;17:405-424) in the
context of the patient's phenotype, relevant family history and previous test results provided by the ordering physician
(Clin Genet. 2020;98:562-570). Only variants deemed clinically significant and relevant to the patient's primary clinical
indications at the time of variant interpretation will be reported. Only low quality variants will be confirmed by Sanger
sequencing based on the internal studies validating the high accuracy of the variant calling bioinformatics pipeline.

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 4/
6
 Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

This case has been comprehensively reviewed by our clinical team of physicians, geneticists and informaticists.
Report electronically signed by:

Go Hun Seo, M.D, Ph.D.

Chief Medical Officer & Laboratory Director

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 5/
6
 Report date: 2023-02-02

3B-EXOME, Proband Unique identifier: 080930101864

Sex: Female Date of birth: 2008-09-30

CLINICAL USE
Sample ID: EPJ22-WBFL ethinicity: East Asian

DISCLAIMER
This test was developed by 3billion in the purpose of identifying single nucleotide variants and small insertions and deletions within the targeted genomic
regions. This laboratory is certified under the Clinical of American Pathologists as qualified to perform high complexity clinical laboratory testing (CAP#:8750906).
Assay validation and clinical validation were performed following the Korea Institute of Genetic Testing Evaluation and the American College of Medical Genetics
and Genomics (ACMG) Technical Standards and Guidelines Section G (https://www.acmg.net/PDFLibrary/Standards-Guidelines-Clinical-Molecular-Genetics.pdf).
Although this report is being generated for research-use-only (RUO), the test was performed following the standard operation procedure and quality control
measures developed for the clinical testing. This test can only reliably detect single nucleotide variants and small (<20bp) insertions and deletions within the
protein coding exonic regions of the nuclear genome. If other types of variants such as large deletion/duplication, translocation, inversion, low-level mosaicism,
mitochondrial genome variants are suspected, it is recommended to perform appropriate testing that are designed to detect those types of variants. Also, there
are certain exonic regions that are incompletely sequenced due to technical difficulties with amplification, sequencing and alignment. If variants within these
regions are suspected, it is recommended to perform alternate testing that are designed to sequence those regions/genes adequately. This report may not be
copied or reproduced, except in its totality.

© 2021 3billion, Inc. CAP #: 8750906 A. 14F, 416, Teheran-ro, Gangnam-gu, Seoul, Republic of Korea E. support@3billion.io Page 6/
6