Add Interpretation for Germline Analysis
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1.
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From the Cases tab, select an analysis result to open the case. |
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In the Interpretation column, select Case Interpretation. If an interpretation exists for the variant, point to the interpretation and select Edit. |
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In the Selected Associations panel, select New Association, and then select an association level: Variant, Gene, or Gene-Fusion. |
Association level options vary by variant type.
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If you selected Gene or Gene-Fusion, select the applicable gene or gene fusion from the Curation Level drop-down list. |
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Select the Type drop-down arrow, and then select an association type. |
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6.
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From the Transcript drop-down list, select a gene-transcript combination. |
Each gene-transcript combination is listed with the gene name, transcript, HGVSc notation, and predicted consequence. Intergenic regions or regions where no transcripts are available are listed as Intergenis Region.
NOTE
The gene-transcript combination is dependent on the transcript source selected for the case. If you select a different transcript source, the gene-transcript selection is cleared.
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Select the Interpretation drop-down arrow, and then select the interpretation: |
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Pathogenic—Segregates with disease in multiple unrelated cases with control data. The variant is in a highly conserved region. Functional studies or other evidence indicate a deleterious effect on gene expression. |
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Likely Path—Reported in some case studies with or without control data. The variant is in a highly conserved region. Functional studies or other evidence highly suggest a deleterious effect on gene expression. |
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VUS—Nothing about this variant has been reported, or reported information is incomplete or contradictory. |
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Likely Benign—Functionally normal. Reported in a few cases with little or no control data. The variant might be nonconserved and predicted to be tolerated. Based on disease prevalence and penetrance information, the variant frequency is higher than expected in the general population. |
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Benign—Functionally normal. Reported at high frequency in control data and does not segregate with disease. The variant might be nonconserved and predicted to be tolerated. |
Interpretations are subject to the discretion of the laboratory. The criteria provided for the interpretations are examples for assigning an interpretation based on best practices, ACMG guidelines, and actionability.
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Select the Inheritance Mode drop-down arrow, and then select the mode of inheritance: |
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Autosomal Dominant—The gene is on a nonsex chromosome. A single copy of the mutation associated with disease is sufficient to cause the disease. |
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Autosomal Recessive—The gene is on a nonsex chromosome. Two copies of an abnormal gene must be present for disease to develop. |
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X-Linked Dominant—A dominant gene is on the X chromosome. |
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X-Linked Recessive—A mutation in a gene on the X chromosome causes a phenotype to be expressed in males and in females who are homozygous for the gene mutation. |
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Y-Linked—Inheritance of genes on the Y chromosome. |
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Complex/Compound Het—Two heterogenous recessive alleles are present at a locus that can cause disease. |
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De Novo—A gene mutation that is present for the first time in one family member. The mutation occurs in a germ cell of one of the parents or the fertilized egg. |
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[Optional] Select the Phenotype Contribution drop-down arrow, and then select one of the following: |
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Full—The variant contributes to all phenotypes recorded for the subject. |
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None—The variant does not contribute to any phenotypes recorded for the subject. |
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Partial—The variant contributes to the selected phenotypes only. |
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[Optional] Select the Penetrance drop-down arrow and then select the penetrance. |
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[Optional] Select Primary to indicate the variant as the primary association. |
The primary variant is included in the case report.