Variant annotation information
The following table lists the variant annotation information that is displayed on the Sample Variant Data sub-tab.
 | Many of the options that are listed in the variant annotation information columns are also available on the Sample Variant Data sub-tab context menu. |
Column | Description |
|---|---|
ID | System-generated value that identifies the variant. |
Chromosome | The chromosome on which the variant is located. |
Chromosome Position | The chromosome position where the variant is located. |
Chr:ChrPos | The chromsome:chromosome position for the variant location. |
Rs | The dbSNP database identification for the variant. Note: If a value other than N/A is displayed, then it is a hyperlink to the NCBI dbSNP web page for the variant. |
Ref | The reference nucleotide at the variant position. |
Ref AA | The reference amino acid coded for by the codon that includes the variant position. |
Alt | The variant nucleotide at the variant position. |
Alt AA | The variant amino acid coded for by the codon that includes the variant position. |
Type | The type of variant based on the amino acid change that the variant caused. Values are Missense, Synonymous, Frameshift, or Nonsense. |
Coverage | The coverage (number of reads) aligned to the variant location in the sample. |
Pathogenicity | The pathogenicity of the variant, which is the potential for the variant to cause disease. By default, the pathogenicity is always set to an initial value of Unassigned. You must review the information for the variant and then decide what the pathogenicity should be; for example, Deleterious. (If you cannot determine the pathogenicity of the variant, then you can set the status to Unknown.) When you update the pathogenicity and/or status, you can apply the changes to: • the panel group - Applies the changes to the variant for the indicated panel group.The next time that the variant is detected in another sample that has been assigned to this panel group, then this is the pathogenicity that is displayed for the variant. • the sample only - Applies the changes to the variant only for the currently selected sample. You can also update the pathogenicity status and/or add comments for the changes. By default, the status is always set to an initial value of Pending. Note: You can also double-click in the Pathogenicity column to open the Submit Pathogenicity dialog box, or use the context menu option. See Sample Variant Data sub-tab context menu. The following information is relevant to updating the pathogenicity and/or pathogenicity status for a variant: • By default, only five pathogenicities—Deleterious, Likely Deleterious, Unknown, Likely Benign, and Benign—are available. You have the option of adding custom pathogenicities, either by clicking New to open the Add New Pathogenicity dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. • By default, only two statuses—Pending and Confirmed—are available. You have the option of adding custom statuses, either by clicking New to open the Add New Pathogenicity Status dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. • Optionally, you can add supporting information for this pathogenicity change. See To add supporting information for a variant. • You always have the option of updating just the pathogenicity status for a variant. See Pathogenicity Status. • You can also update the pathogenicity on the Patient tab, Variants sub-tab. See Patient tab, Variants sub-tab. |
Pathogenicity Date Time | The date and time that the currently displayed pathogenicity value was assigned to the variant. |
Pathogenicity Status | The status of the selected pathogenicity. You must manually set this value. By default, only two statuses—Pending and Confirmed—are available, and the pathogenicity status is always set to an initial value of Pending. You must review the information for the variant and then decide what the pathogenicity status should be. To open the Submit Pathogenicity dialog box, double-click in this column for a selected variant.You can update the pathogenicity status for the selected variant in this dialog box. When you update the pathogenicity status, you can apply the changes to: • the panel group - Applies the changes to the variant for the indicated panel group.The next time that the variant is detected in another sample that has been assigned to this panel group, then this is the pathogenicity status that is displayed for the variant. • the sample only - Applies the changes to the variant only for the currently selected sample. You can also add a comment for the status change. You have the option of adding custom statuses, either by clicking New to open the Add New Pathogenicity Status dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. The following information is relevant to updating the pathogenicity status for a variant: • You can also double-click in the Status column to open the Update Variant Pathogenicity Status dialog box or use the option that is available on the context menu for the sub-tab. See Sample Variant Data sub-tab context menu. • You can also update the Pathogenicity Status for a variant on the Patient tab, Variants sub-tab. See Patient tab, Variants sub-tab. |
Pathogenicity Status Date Time | The date and time that the currently displayed pathogenicity status was assigned to the variant. |
Zygosity | Indicates whether the variant is heterozygous or homozygous. Note: The selected zygosity is based on the Zygosity settings that you have specified on the Variant Preferences tab of the Settings dialog box. See To specify variant preferences. |
Artifact Type | The artifact type for the selected variant. You must manually set this value. Double-click in this column for the selected variant to open the Update Artifact Type dialog box. You specify the artifact type (for example, Sequencing) for the variant in this dialog box. If the appropriate artifact type is not available, then an option is provided to create a new type. When you specify the artifact type, you can set the artifact type as the following: • Set globally—Selected by default. Set this artifact type for the variant, regardless of the sample in which the variant is detected. • Set for Sample—Set this artifact type for this variant only for the indicated sample. You also have the option of adding comments for the variant artifact type. Note: The default value for Variant Classification is determined by the setting on the Variant Preferences tab on the Settings dialog box. See To specify variant preferences. The following information is relevant to updating the artifact type for a variant: • You can also define artifact types and set the artifact type for a variant on the Variants sub-tab on the Patient tab, on the Variants sub-tab on the Panel Statistics tab from the Runs tab or the Run tab, or on the Sample Variant Data sub-tab on the Sample tab. • You can also double-click in the Artifact Type column to open the Update Variant Artifact Type dialog box, or use the context menu option. See Sample Variant Data sub-tab context menu. • You have the option of adding custom artifact types, either by clicking New to open the Add New Artifact dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. |
Patient Variant Frequency | The frequency at which the variant was detected in the sample. Any value < 1 is allowed, with 1 = 100%, 0.5 = 50%, and so on. |
Gene | The gene on which the variant is located. |
Gene Strand | The strand (+ or -) for the gene in which the variant is located. |
Read Balance | The balance in forward and reverse oriented reads with the variant as reported in the VCF file. |
Exon Number | The exon within the gene in which the variant is located. Includes non-coding exons. “Intron” is displayed for intronic variants. |
Transcript | The accession number for the preferred mRNA transcript that is used for the HGVS nomenclature columns. |
Protein | The accession number for the protein transcript that is associated with the preferred mRNA transcript and is used for the HGVS nomenclature columns. |
Coding Base | The position in the coding regions for the gene where the variant is located. |
Codon Position | The position within the codon where the variant is located (1, 2, or 3). |
AA Position | The amino acid number within the gene for the amino acid coded for by the codon that includes the variant position. |
HGVS Genomic | The HGVS genomic nomenclature for the variant. (www.hgvs.org/mutnomen). |
HGVS Coding | The HGVS coding DNA nomenclature for the variant relative to the reference accession that is shown in the Transcript column. (www.hgvs.org/mutnomen). |
HGVS Protein | The HGVS protein nomenclature for the variant relative to the reference accession that is shown in the Protein column. (www.hgvs.org/mutnomen). |
Variant Comment | The last added comment for the variant. You can also single-click twice in this field, and then add or edit a comment as needed. After you click out of the field, the Add Variant Comment dialog box opens. The comment is displayed in the Variant Comment field in the Variants pane on the Search Results tab, the Variant Comment field on the Sample Variant Data sub-tab on the Sample tab, the Variant Comment field in the Variant pane on the Variant tab, and the Variant Comments pane on the Variant tab. Note: If multiple comments have been added for a variant, then with the exception of the Variant Comments pane on the Variant tab, only the last added comment is displayed here and on the Variants sub-tab on the Patient tab, the Sample Variant Data sub-tab in the Sample tab, the Variant pane on the Variant tab, and the Variant Comments pane on the Variant tab. All the comments that have been added for a variant, including the last added, are displayed in reverse chronological order in the Variant Comments pane on the Variant tab. You can also add comments for a variant with an option on the context menu for this sub-tab. See Add Variant Comment. |
Comment Date Time | The date and time that the currently displayed comment (The last added comment for the variant) was added for the variant. |
Panel | The panel that was used for the run. |
Panel Group | The panel group to which the panel is assigned. |
Trans | Indicates whether the variant is Transition (Ti) or Transversion (Tv). |
Sample | The sample name. |
CDS number | The coding exon number. |
Genotype | The variant genotype. |
Report | Displays a checkbox. For each variant that is to be included in a report, click in the checkbox to select the variant. Tip: You can define variant filtering options to filter for variants only where Report = true or Report = false. |
Interpretation | If an interpretation has been defined for this single variant, then the full interpretation is displayed in this column. If more than one interpretation has been defined for the variant, then the last defined interpretation is displayed. |
Coverage Region Status | Indicates whether the region passed or failed the Quality Control (coverage) settings that were specified for the run’s panel. |