1. Basic information

Sample_ID Ordering_Phtsician Sample_Source Sample_Type
Sample Dr. XXX Hospital Blood
Collect_Date Obtained_Date Experiment_Date Report_Date
2025/01/01 2025/01/02 2025/01/08 2025/01/15

2. Sample Experiment QC Summary
number of sequencing reads 875,332,105
number of sequencing reads mapping to genome 872,033,100
Average read coverage 42.53

3. Analysis workflow

4. Attribute abbreviation definition

Inheritance mode

Mode.name Abbreviation
Autosomal Recessive AR
Autosomal Dominant AD
X-linked Recessive XR
X-linked Dominant XD
Mitochondrial Mito

Clinvar

Category.name Abbreviation
Pathogenic P
Likely Pathogenic LP
Uncertain significance VUS
Likely benign LB
Benign B

Zygosity

Category.name Abbreviation
Heterozygous HET
Homozygous HOM

Metabolism status

Category.name Abbreviation
Ultrarapid Metabolizer UM
Normal Metabolizer NM
Intermediate Metabolizer IM
Poor Metabolizer PM
Indeterminate Ind

Other attribute

  • VAF : Variant Allele Fraction
  • DP : Depth of reads coverage
  • EAS : Variant Allele Fraction in east asian (data from gnomAD database)
  • TB : Variant Allele Fraction in Taiwan (data from Taiwan biobank)
  • CADD : CADD is a tool for scoring the deleteriousness of single nucleotide variants, multi-nucleotide substitutions as well as insertion/deletions variants in the human genome. We define that the variant of CADD score >20 as pathogenic variant candidate.
  • OMIM : OMIM is a database which contains the information of human genes and genetic phenotypes.

5. Analysis result

Summary

Inheritance_mode (fit_with_database) Zygosity (fit_with_database) number_of_variants
(a). Pathogenic variants Yes Yes 1
(b). Pathogenic variants NO NO 3
(c). Pathogenic variants - - 2
Uncertain significance - - 8
Other_genetic_variants_Category number_of_variants
Mitochondria Mutations 2
Clonal Hematopoiesis Mutations 1
Pharmacogenomics 6
Carrier Screening 3
HLA Typing 1
High Risk variants associate with disease 11
Uniparental Disomy, UPD 1
Spinal Muscular Atrophy, SMA 0
Runs of homozygosity, ROH 1
Nucleotide Repeat Expansion Disorder 1

(a): Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. And theinheritance mode and zygosity of these variants fit with known database. These variant allele frations are <1% in East Asian and Taiwan population.

(b): Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. But theinheritance mode and zygosity of these variants do not fit with known database. These variant allele frations are <1% in East Asian and Taiwan population.

(c): Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. But the inheritance mode and zygosity of these variants do not record in known database.

(a) Pathogenic variants

Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. And the inheritance mode and zygosity of these variants fit with known database. These variant allele frations are <1% in East Asian and Taiwan population.

Gene Variant Protein VAF Zygosity Clinvar CADD EAS TB Inheritance OMIM_ID Disease_Disorder
RP1 chr8:g.54621087T>C p.Tyr41His 48.7 HET LP 28.2 0.42 0.74 AD,AR 603937 RP1 AXONEMAL MICROTUBULE-ASSOCIATED PROTEIN

(b) Pathogenic variants

Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. But the inheritance mode and zygosity of these variants do not fit with known database. These variant allele frations are <1% in East Asian and Taiwan population.

Gene Variant Protein VAF Zygosity Clinvar CADD EAS TB Inheritance OMIM_ID Disease_Disorder
MFN2 chr1:g.11989192C>G p.Cys8Trp 52.1 HET VUS 22.2 - 0.27 AD 601152 Hereditary motor and sensory neuropathy VIA
LHX4 chr1:g.180230309G>A - 56.3 HET VUS 21.9 0.1 0.47 AD 262700 Pituitary hormone deficiency, combined, 4
UFSP2 chr4:g.185396684G>T - 61.2 HET VUS 20.7 0.08 0.20 AD 617974 Spondyloepimetaphyseal dysplasia, Di Rocco type

(c) Pathogenic variants

Genetic variants are recorded as Pathogenic/Likely Pathogenic in Clinvar database or the CADD score >20. But the inheritance mode and zygosity of these variants do not record in known database.

Gene Variant Protein VAF Zygosity Clinvar CADD EAS TB
MOG chr6:g.29670712G>A p.Glu125Lys 64.5 HET - 29.1 11.30 33.16
NQO1 chr16:g.69711242G>A p.Pro187Ser 54.5 HET - 20.2 44.52 74.82

Uncertain significance

Genetic variants are recorded as uncertain significance variants in Clinvar database. But the inheritance mode and zygosity of these variants do not record in known database.

Gene Variant Protein VAF Zygosity Clinvar CADD EAS TB
HLA-B chr6:g.31357087G>A p.Ala24Cys 32.3 HET VUS 4.9 3.4 4.1
IKZF1 chr7:g.50368084T>C p.Phe80Ser 37.2 HET VUS 10.3 1.1 2.5
SLC45A1 chr1:g.8339601A>G p.Tyr628Cys 47.2 HET VUS 10.3 1.8 1.3
OLAH chr10:g.15115161C>T p.Ala244Val 40.8 HET VUS 8.4 2.3 3.9
PTEN chr10:g.89720659G>T p.Met270IIe 44.3 HET VUS 6.2 4.4 8.9
WNK1 chr12:g.970426T>G p.Val623Gly 59.6 HET VUS 1.5 1.1 12.1
XPO4 chr13:g.21370361G>T p.Thr884Asn 46.9 HET VUS 3.1 1.8 7.6
EXOC3L1 chr16:g.67222999G>A p.Pro44Leu 55.6 HET VUS 2.4 1.7 11.2

Mitochondria Mutations

Variant VAF Clinvar Associated_Disorder
chrM:g.3946G>A 15.2 LP Leigh syndrome
chrM:g.4296G>A 29.3 LP MERRF syndrome

Clonal Hematopoiesis Mutations

Gene Variant VAF
DNMT3A chr2:g.25457155C>T 47.9

Pharmacogenomics

Gene Genotype Metabolism_Status
CYP2B6 *1/*4 Rapid Metabolizer (RM)
CYP3A5 *3/*3 Poor Metabolizer (PM)
UGT1A1 *1/*6 Intermediate Metabolizer (IM)
CYP2C19 *2/*2 Poor Metabolizer (PM)
CYP2C9 *3/*3 Poor Metabolizer (PM)
TPMT *1/*11 Intermediate Metabolizer (IM)

Carrier Screening

Gene Variant Zygosity Associated_Disorder
CEP290 chr12:g.88058868C>T HET Joubert syndrome 5, Leber congenital amaurosis 10
GAA chr14:g.22520970G>A HET Glycogen storage disease type II
CFTR chr7:g.117304834G>C HET Cystic fibrosis

HLA Typing

HLA-A HLA-B HLA-C
A*11:01:01 B*40:01:64 C*12:02:02
A*11:02:01 B*27:05:02 C*07:02:01

High Risk variants associate with disease

Genetic variants listed below are documented as high-risk alleles associated with diseases in published literature.

Your genotypes are marked with *triple-formatted text* (*asterisks*, bold and italics).

Gene Associated_Disease dbSNP_rsID High_risk Medium_risk Low_risk Pubmed_ID
LTA/TNF Type 1 Diabetes rs1799724 TT *CT* CC 19120272
ALDH2 Myocardial Infarction rs671 *AA* AG GG 17459359
MTHFR Hypertension rs1801131 GG *GT* TT 17333388
SLC2A9 Gout rs3733591 *CC* CT TT 20143573
ICAM1 Stroke rs5498 GG *AG* AA 18791855
CXCL8 Osteoarthritis rs2227306 *TT* CT CC 25194757
ADRB3 Hyperuricemia rs4994 GG *AG* AA 23729572
IL12A Hyperthyroidism rs568408 AA *AG* GG 21044109
MYH7B heart failure (dilated cardiomyopathy) rs3746444 *GG* AG AA 20488170
EHMT2 chronic hepatitis B rs652888 GG *AG* AA 23760081
HLA-DQA1 Idiopathic Membranous Nephropathy rs2187668 TT *CT* CC 23813219

Uniparental Disomy, UPD

Chr Location Associated_Disorder
- - -

Spinal Muscular Atrophy, SMA

Is_SMA Is_Carrier SMN1_Copy_Number SMN2_Copy_Number
Negative Negative 2 2

Runs of homozygosity, ROH

Chr Location Covered_Genes
- - -

Nucleotide Repeat Expansion Disorder

Gene Repeat_Motif Number_of_Repeat(Sample/Normal) Associated_Disorder
MARCHF6 TTTTA 25/13 Familial Adult Myoclonic Epilepsy

6. Reference

  1. Screening for autosomal recessive and X-linked conditions during pregnancy and preconception: a practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 2021;PMID: 34285390; PMCID: PMC8488021.
  2. ACMG SF v3.2 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. 2023 Aug;PMID: 37347242; PMCID: PMC10524344.
  3. A 12-gene pharmacogenetic panel to prevent adverse drug reactions: an open-label, multicentre, controlled, cluster-randomised crossover implementation study. Lancet. 2023 Feb 4;PMID: 36739136.
  4. Clonal Hematopoiesis of Indeterminate Potential in Patients with Solid Tumor Malignancies. Cancer Res. 2022 Nov 15;PMID: 36040522.
  5. ClinVar
  6. OMIM
  7. CADD
  8. FOSWIKI
  9. T1K
  10. SMNCopyNumberCaller
  11. Tandem Repeat Finder

7. Disclaimer

The purpose of this genetic analysis service is to assist professionals in providing additional risk assessment information. The results provided after analysis cannot be used as treatment. For the basis for diagnosis, doctors still need to make decisions on diagnosis, treatment and care based on other analysis results and professional judgment. This is not a complete or is a 100% accurate diagnostic tool. Medical knowledge evolves rapidly, and there will be new developments at any time from the research and development process to the publication of results, so this is suitable for scope of use The information in the description may not have been updated to the latest research results. This analysis only discusses specific projects and does not interfere with any treatment. At the same time, it does not authorize any treatment. In addition, taking into account individual differences among patients. The analysis is not intended to interfere with the independent professional judgment of physicians.