Germline Small Variant Grid

Features

• Review the germline small variants identified by the cancer pipeline and associated annotations
• Apply certain filters (e.g. gene mode of action)
• Search for specific variants within a certain chromosome, region or gene
• View Ensembl or RefSeq transcript identifiers
• Sort the list of variants (e.g. by tier or genomic coordinate)
• Flag a variant for further review
• Add or remove a variant from the GTAB summary
• Add a comment and assign an ACGS classification to a variant
• Report whether the variant has been tested by another method i.e., Standard of Care Testing
• Report whether a variant is likely to be an artefact or a true variant

Variant Grid GuideSearchingSortingFiltersAdvanced FilteringVariant InterpretationAdding Variants to the GTAB summaryPage Errors

An overview of the Variant Grid is shown in the following table

Key

#	Section	Description
1	Information Alerts	Relevant disclaimers and alerts will be shown here in a dropwdown.
2	Search	Search for variants within specific genomic regions, chromosomes or genes. Details on how to search can be found in the "Searching" tab.
3	Filters	Add or remove filters applied to the variant grid. By default, the variant grid will be filtered to display variants in genes belonging to Tier 1 and Tier 3.
4	Actions	Actions including "View Details" - viewing the variant details page, flagging, adding comments, and adding or removing the variant from the GTAB summary.
5	Tier and gene	Tier and HGNC gene symbol(s) which the variant affects. We show the affected genes in the highest tier.
6	GRCh38 coordinates / Ref>Alt allele	Coordinates of the variant and the nucleotide change of the particular variant within a gene. Clicking the IGV icon will show the variant in IGV. The reference and Alternate alleles.
7	Ensembl Transcript & Protein ID or RefSeq Transcript ID	Shows the RefSeq transcript identifier or the Ensembl transcript and protein identifiers for the transcript and protein most severely affected by the variant. If the transcript is a MANE transcript, the MANE Select or MANE Plus Clinical transcript flags will be shown as well.
8	CDS & protein change	Contains the c. and p. HGVS for the canonical transcript. It is recommended that HGVSp. automated predictions should be double-checked during the interpretation and reporting process, especially for small insertion or deletion variants where a minority of variants may have complex nomenclature varying between prediction tools.
9	Most severe consequence	Shows the most severe predicted consequence type (SO terms) that the variant has on any gene transcript and protein sequence.
10	Genotype	Genotype for this variant in this patient. Uses VCF genotype nomenclature where 0 indicates ref allele and 1 indicates alt allele. So 0 / 1 would be heterozygous whereas 1 / 1 would be homozygous for the alt allele
11	Alt & Allele read depth	Reads supporting alt allele and total read count.
12	VCF filter	Shows whether the variant has passed the variant caller filters. For variants that haven’t passed, the reason is shown in red e.g. ‘PloidyConflict’ Genotype call from variant caller not consistent with chromosome ploidy.
13	QC flag	Flags that indicate a variant call may be of a lower quality and at greater risk of being a false positive. Hover over the QC flag for a description. Refer to the variant details documentation for a complete list of QC flags
14	Population frequencies (GEL/gnomAD)	Population germline allele frequency for the variant in GeL and gnomAD exomes dataset.
15	ClinVar	Clinvar ID entry of the variant. Clicking the clinvar icon will show the variant in Clinvar.
16	Classification	The assigned ACGS tiering of a variant. Click the pill to add or edit the classification of a variant.

Tip: Open the transcript overlay

On your variant of interest, click any of the HGNC gene symbols shown under the Tier / Gene column (section 5 of the Variant grid guide) to open the transcript overlay (example shown below).

You can use the search bar to search for variants by:

• Gene symbol e.g., "TP53"
• Coordinates (chromsome, start coordinate and end coordinate) e.g., "17:7660779-7688538"
• Chromosome e.g., "17"

Searching

Searching will filter the variant grid to variants that match the search terms. If no variants are returned, there may be no variants in the chromosome, region or gene specified.

By default, all variants are sorted by Tier ascending and by variant coordinates. Variants can be sorted by Tier or GRCH38 coordinates ascending or descending by using the arrow icon or menu in the column headers. When sorting is applied to a column, the arrow icon will appear next to the column title in the direction of the sort (ascending = up, descending = down).

To change the sorting of the variant grid from Tier to GRCH38 coordinates, follow these steps:

• Click the arrow icon on the column header to sort the grid by GRCH38 coordinates in ascending or descending order
• Click the three dots on the column header and select 'Sort by Coordinates ASC' or 'Sort by Coordinates DESC'
• To reset the variant grid to the default sorting order (by Tier) click the three dots on the column header and select 'Reset to default'

Sorting

Only one sort can be activated at the time. By default, the first 20 variants are shown, sorted by tier and coordinates. To view additional variants, continue to scroll to the bottom of the page. Variants will continue to load as you scroll.

Germline Small Variant Filters

• Tier
• Mode of Action
• Flag status
• VCF filter

By default, the variant grid is filtered by Tier 1 and 3.

Applying filters

1. Click the '+' symbol next to 'Add filter'
2. Chose your filter of interest from the dropdown menu and click the '+' symbol
3. Click on the arrow dropdown and select your filter options e.g., Mode of Action, Oncogene. The variant grid will update accordingly

Removing filters

1. Individual filters can be removed by clicking the 'x' symbol next to the filter
2. Default filtering settings can be restored by clicking the 'Reset' button above the filter toolbar
3. Multi-select filters can be reset by selecting 'Clear'

Counts

The count on the top left shows the number of variants remaining after filters have been applied. The total number is the number of variants the pipeline identified before any quality checks have been applied.

Applying Multiple Filters

For information on applying multiple filters please see the "Advanced Filtering" section

We support applying multiple filters to the variant grid at the same time. The filters we support can be applied at the variant level and the gene level.

Filter	Level
Tier	Variant
Flag status	Variant
VCF filter	Variant
Mode of Action	Gene

• When applying multiple filters at the same level, the filters are exclusive (See example 1)
• When a combination of gene level and variant level filters are applied, first we consider the variant level conditions and then apply the gene level filters which take the entire list of genes annotated to the variant into account (See example 2)

#	Filter 1	Filter 2	Result
1	Tier 1	Flag status: Flagged	Tier 1 variants that are 'Flagged'
2	Tier 3	Mode of Action: Oncogene	Any Tier 3 variant with a gene labelled 'oncogene' (in any tier or untiered)

Using the interpretation drawer, you can add interpretations and comments corresponding to a variant in the variant grid. To open the interpretation drawer, follow these steps:

1. Click the comment icon on any of the variants
2. The interpretation drawer will open on the right of the screen

Tip

Please refer to the following GTAB-related section to know how to add a germline small variant and its interpretation to the GTAB summary.

Variant QualityClassifyingValidationActionabilityComments

Artefact AssessmentArtefact ReasonsArtefact Comment

To indicate whether the variant is likely to be a technical artefact or a true variant, follow these steps:

1. Under "Artefact assessment" click the dropdown arrow and choose the appropriate choice
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The artefact assessment is added to the variant and will appear in the history below
4. All artefact assessment edits will be stored in the history

If a variant has been marked as a likely artefact, the interpretation drawer will display this additional field. To indicate the reason why the variant is likely to be a technical artefact, follow these additional steps:

1. Under "Artefact reasons" click the dropdown arrow and choose the appropriate choice from the options shown above
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The artefact reason is added to the variant and will appear in the history below
4. All artefact reason edits will be stored in the history

If a variant has been marked as a likely artefact, the interpretation drawer will display this additional comment box. To add a supporting comment to your artefact assessment, follow these additional steps:

1. Under "Artefact comment" enter the text you wish to include
2. Click "Comment"
3. The artefact comment is added to the variant and will appear in the history below
4. All artefact comment edits will be stored in the history

Warning

Updating the artefact assessment to "True variant" will remove the artefact reasons and comment data from the interpretation drawer but it will still be available in the variant history.

Classifying

To view or add classifications follow these steps:

1. Click the dropdown arrow and choose the ACGS classification from the menu
2. Click classify
3. The classification is added to the variant and will appear in the history below
4. All classification edits will be stored in the history

ValidationAssay TypeAssay Comment

To indicate whether the variant has been validated, follow these steps:

1. In the "Validation" section of the interpretation drawer, under "Has this variant or entity been tested by another method (either prior to or following receipt of this WGA)?" click the dropdown arrow and choose the appropriate choice
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The validation information is added to the variant and will appear in the history below
4. All validation edits will be stored in the history

If your previous selection indicated the variant has been validated by another method, an "Assay type" dropdown will appear. To select which assay type(s) the variant has also been detected in, follow these additional steps:

1. Under "Assay Type", click the dropdown arrow and choose the appropriate choices
2. The selection will automatically save and the "Saved" icon will appear once saved
3. The assay type is added to the variant and will appear in the history below
4. All assay type edits will be stored in the history

If your previous selection indicated the variant has been validated by another method, an "Assay comment" box will also appear. To add a comment to support the assay types selected, follow these additional steps:

1. Under "Assay Comment", enter the text you wish to include
2. Click "Comment"
3. The assay comment is added to the variant and will appear in the history below
4. All assay comment edits will be stored in the history

Warning

Updating the validation to a "No" option will remove the assay type and comment data from the interpretation drawer but it will still be available in the variant history.

To enter the type of potential actionability associated with a variant, follow these steps:

1. In the "Actionability" section of the interpretation drawer, under "Type of (potential) actionability:" click the dropdown arrow and choose the appropriate choice(s)
2. The selection will automatically save and the "Saved" icon will appear once saved
3. Optional step: An "actionability comment" box will appear where you can add a comment to support the actionability type entry. If required, add your comments to the text field and click comment
4. Optional step: In the "Actionability" section under "How has/will this potentially actionable variant or entity been/be used?" click the dropdown arrow and choose the appropriate choice. Only one can be selected
5. Optional step: A "Utility comment" box will appear where you can add a comment to support the utility type entry. If required, add your comments to the text field and click comment
6. The actionability information is added to the variant and will appear in the history below
7. All validation edits will be stored in the history

Comments

To view or add comments follow these steps:

1. Add your comments to the text field and click comment
2. The comment is added and will appear in the history below
3. To edit the comment, click the three dots next to the date and click edit or delete. Note you can only edit or delete your own comments, for further information see Recording interpretation

You can add any small germline variant and its interpretation to the GTAB summary from the variant grid or interpretation drawer.

To add a small germline variant to the GTAB summary:

1. Click the "Add to GTAB report" icon on any of the variants
2. Go to the GTAB summary:
   • Click the "Go to GTAB report" link from the green message that will appear at the bottom of the variant grid confirming that the variant has been successfully added to the GTAB summary or
   • Click the "GTAB report" icon from the navigation sidebar

Info

At the moment, it is only possible to add variants one by one to the GTAB summary.

Refer to the GTAB summary section for more details.

When we fail to load the gene data needed for search and gene filters to work, you won’t be able to apply any gene list filters or search by gene. All other information on the page will still be available. When we fail to load all variant data, we will show a full page error. In both cases try reloading the page.