VARIANT CLASSIFICATION 

Classification of Germline DNA Sequence Variants

Several guidelines and standards have been suggested and improved to interpret DNA sequence variants concurrently with the widespread use of next-generation sequencing (NGS) technologies in clinical practice. American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) joint consensus recommendation for the interpretation of sequence variants are internationally recognised and adopted in common usage (Sue Richards et al., 2015).

The highlights of the ACMG/AMP Guideline regarding its implementation:

• “mutation” and “polymorphism” terms shall be replaced by “variant”.
• Using a standard gene variant nomenclature by the Human Genome Variation Society (HGVS) (den Dunnen et al., 2016)
• Defining 28 criteria, each with an assigned code addresses types of variant evidence (Very Strong, Strong, Moderate, Supporting) (Table 1).

Table 1. Evidence Framework of the criteria by NGS Cloud

• The rules for combining criteria to classify sequence variants (Table 2)

Table 2. Variant Classification

Following the publication of the ACMG/AMP guideline, several different attempts appeared regarding the general recommendations for using above mentioned 28 criteria to improve consistency in usage and transparency in classification rationale (Abou Tayoun et al., 2018) (Ghosh et al., 2018) (Biesecker et al., 2018) (Strande et al., 2018) (Brnich et al., 2020).

NGS Cloud considers both the original ACMG/AMP variant classification guideline and the following other recommendations. It automatically calculates a proposal for ACMG/AMP classification for all the detected variants with the criteria that have been met (Figure 1).

Figure 1. NGS Cloud – Automatic ACMG Classification Recommendation

References:

Abou Tayoun, A. N., Pesaran, T., DiStefano, M. T., Oza, A., Rehm, H. L., Biesecker, L. G., Harrison, S. M., & ClinGen Sequence Variant Interpretation Working Group (ClinGen SVI). (2018). Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion. Human Mutation, 39(11), 1517–1524. https://doi.org/10.1002/humu.23626

Biesecker, L. G., the ClinGen Sequence Variant Interpretation Working Group, & Harrison, S. M. (2018). The ACMG/AMP reputable source criteria for the interpretation of sequence variants. Genetics in Medicine, 20(12), 1687–1688. https://doi.org/10.1038/gim.2018.42

Brnich, S. E., On behalf of the Clinical Genome Resource Sequence Variant Interpretation Working Group, Abou Tayoun, A. N., Couch, F. J., Cutting, G. R., Greenblatt, M. S., Heinen, C. D., Kanavy, D. M., Luo, X., McNulty, S. M., Starita, L. M., Tavtigian, S. V., Wright, M. W., Harrison, S. M., Biesecker, L. G., & Berg, J. S. (2020). Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Medicine, 12(1), 3. https://doi.org/10.1186/s13073-019-0690-2

den Dunnen, J. T., Dalgleish, R., Maglott, D. R., Hart, R. K., Greenblatt, M. S., McGowan-Jordan, J., Roux, A.-F., Smith, T., Antonarakis, S. E., Taschner, P. E. M., & on behalf of the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organisation (HUGO). (2016). HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Human Mutation, 37(6), 564–569. https://doi.org/10.1002/humu.22981

Ghosh, R., Harrison, S. M., Rehm, H. L., Plon, S. E., Biesecker, L. G., & on behalf of ClinGen Sequence Variant Interpretation Working Group. (2018). Updated recommendation for the benign stand‐alone ACMG/AMP criterion. Human Mutation, 39(11), 1525–1530. https://doi.org/10.1002/humu.23642

Strande, N. T., Brnich, S. E., Roman, T. S., & Berg, J. S. (2018). Navigating the nuances of clinical sequence variant interpretation in Mendelian disease. Genetics in Medicine, 20(9), 918–926. https://doi.org/10.1038/s41436-018-0100-y

Sue Richards, Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., Voelkerding, K., & Rehm, H. L. (2015). 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 (; on behalf of the ACMG Laboratory Quality Assurance Committee, Trans.). Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30