Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework

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4. How I curate: applying American Society of Hematology-Clinical Genome Resource Myeloid Malignancy Variant Curation Expert Panel rules for RUNX1 variant curation for germline predisposition to myeloid malignancies
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8. Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level
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13. Diverse Genetic Landscape of Suspected Retinitis Pigmentosa in a Large Korean Cohort
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14. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes
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15. Management of patients with germline predisposition to haematological malignancies considered for allogeneic blood and marrow transplantation: Best practice consensus guidelines from the UK Cancer Genetics Group ( UKCGG ), CanGene‐CanVar , NHS England Genomic Laboratory Hub ( GLH ) Haematological Malignancies Working Group and the British Society of Blood and Marrow Transplantation and cellular therapy ( BSBMTCT )
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16. Specifications of the ACMG/AMP variant curation guidelines for myocilin: Recommendations from the clingen glaucoma expert panel
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17. Classification of missense variants in the N -methyl- d -aspartate receptor GRIN gene family as gain- or loss-of-function
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18. Computational and experimental methods for classifying variants of unknown clinical significance.
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19. Recommendations for the clinical interpretation of genetic variants and presentation of results to patients with inherited bleeding disorders. A UK Haemophilia Centre Doctors’ Organisation Good Practice Paper
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20. A quantitative model to predict pathogenicity of missense variants in the TP53 gene
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21. Two integrated and highly predictive functional analysis-based procedures for the classification of MSH6 variants in Lynch syndrome
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22. Guidelines for releasing a variant effect predictor
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25. Considering complexity in the genetic evaluation of dilated cardiomyopathy
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27. Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care
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28. Splicing predictions, minigene analyses, and ACMG‐AMP clinical classification of 42 germline PALB2 splice‐site variants
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29. The functional impact of 1,570 individual amino acid substitutions in human OTC
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30. Cancer Genomics in Precision Oncology: Applications, Challenges, and Prospects
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31. Minigene‐based splicing analysis and ACMG/AMP‐based tentative classification of 56 ATM variants
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32. Genome-wide prediction of disease variants with a deep protein language model
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33. In-silico Analysis of NF1 Missense Variants in ClinVar: Translating Variant Predictions into Variant Interpretation and Classification
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34. A Bayesian method to estimate variant-induced disease penetrance
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35. Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation
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36. Suggested application of HER2+ breast tumor phenotype for germline TP53 variant classification within ACMG/AMP guidelines
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37. The role of clinical response to treatment in determining pathogenicity of genomic variants
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38. RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants
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39. Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants
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40. An AI-based approach driven by genotypes and phenotypes to uplift the diagnostic yield of genetic diseases
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41. Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions
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42. Optimising clinical care through CDH1-specific germline variant curation: improvement of clinical assertions and updated curation guidelines
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43. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2
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44. Design and Reporting Considerations for Genetic Screening Tests
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45. A practical guide to interpreting germline variants that drive hematopoietic malignancies, bone marrow failure, and chronic cytopenias.
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46. GM1 gangliosidosis type II: Results of a 10-year prospective study
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47. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene
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48. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP
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49. Recommendations by the ClinGen Rett/Angelman-like Expert Panel for Gene-specific Variant Interpretation Methods
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50. Specifications of the ACMG/AMP Variant Classification Guidelines for Germline DICER1 Variant Curation
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51. Clinical implications of VUS reclassification in a single-centre series from application of ACMG/AMP classification rules specified for BRCA1/2
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52. Assessing predictions of the impact of variants on splicing in CAGI5
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53. Genomic screening and genomic diagnostic testing—two very different kettles of fish
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54. Actionable secondary findings in the 73 ACMG-recommended genes in 1559 Thai exomes
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55. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations
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56. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline ATM sequence variants
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57. Functional and in-silico interrogation of rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders
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58. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
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59. Functional analysis and clinical classification of 462 germline BRCA2 missense variants affecting the DNA binding domain
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60. Classification of variants of reduced penetrance in high-penetrance cancer susceptibility genes: Framework for genetics clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group-UK)
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61. Comparison of the frequency of loss‐of‐function LZTR1 variants between schwannomatosis patients and the general population
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62. Targeting de novo loss-of-function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project
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63. Large-scale application of ClinGen-InSiGHT APC-specific ACMG/AMP variant classification criteria leads to substantial reduction in VUS
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64. Accurate germline RUNX1 variant interpretation and its clinical significance
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65. Eye2Gene: prediction of causal inherited retinal disease gene from multimodal imaging using deep-learning
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66. Clinical characteristics and disease progression of retinitis pigmentosa associated with PDE6B mutations in Korean patients
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67. Comparison of the ABC and ACMG systems for variant classification
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68. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing
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69. Comprehensive analysis and ACMG‐based classification of CHEK2 variants in hereditary cancer patients
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70. An updated quantitative model to classify missense variants in the TP53 gene: A novel multifactorial strategy
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71. Revision of RUNX1 variant curation rules
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72. Correspondence on “Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)” by Horak et al
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75. Estimating the Posttest Probability of Long QT Syndrome Diagnosis for Rare KCNH2 Variants
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76. Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies
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77. High rate of detected variants in male PLCZ1 and ACTL7A genes causing failed fertilization after ICSI
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78. Quantifying evidence toward pathogenicity for rare phenotypes: The case of succinate dehydrogenase genes, SDHB and SDHD
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79. Improving genetic diagnosis by disease-specific, ACMG/AMP variant interpretation guidelines for hearing loss
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80. A calibrated cell‐based functional assay to aid classification of MLH1 DNA mismatch repair gene variants
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81. Clinical presentation of congenital hypogonadotropic hypogonadism in males with delayed puberty according to genetic etiology: a systematic review and meta-analysis after reclassification of gene variants
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82. The ACMG SF v3.0 gene list increases returnable variant detection by 22% when compared with v2.0 in the ClinSeq cohort
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83. The future role of facial image analysis in ACMG classification guidelines
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84. vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines
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85. Exome Sequencing and Multigene Panel Testing in 1,411 Patients With Adult-Onset Neurologic Disorders
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86. Frequency of actionable secondary findings in 7472 Korean genomes derived from the National Project of Bio Big Data pilot study
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87. Analyzing the functional effects of DNA variants with gene editing
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88. Multisite Validation of a Functional Assay to Adjudicate SCN5A Brugada Syndrome–Associated Variants
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89. A missense variant effect map for the human tumor-suppressor protein CHK2
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90. Proactive Variant Effect Mapping Aids Diagnosis in Pediatric Cardiac Arrest
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91. Functional significance of channelopathy gene variants in unexplained death
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92. Allelic heterogeneity of Proteus syndrome
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