Variant Grid

The Variant Grid lists the variants in the selected case, with each row containing data for one variant. The data include biological information and qualitative and quantitative values reported in the analysis result.

The following table lists the contents of each column. Column data vary based on available case and variant data.

Note

All annotations are expressed in the genomic coordinates on the positive strand, including custom annotations.

Variant Column

Lists information about the variant. Possible entries are shown in the following table.

Item	Description
CHR:POS	The chromosome number and position, linked to the associated page of the Ensemble database.
dbSNP/dbVar ID	The rsID entry in dbSNP, linked to the entry in the dbSNP database.
REF	The reference allele.
ALT	The alternate allele.
UCSC	A link to the page for the variant in the University of California Santa Cruz (UCSC) database, if the variant exactly matches the position and allele of the variant listed in UCSC.
COSMIC	A link to the page for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database, if the variant exactly matches the position and allele of a variant listed in COSMIC. If there is no match, a COSMIC ID is not listed in the table.

Select Variant Details to view more variant details or to add curation data to your knowledge base.

Gene Column

Lists details about the affected gene. If a variant affects more than one gene, each gene is listed in a separate row. Possible entries are shown in the following table.

Item	Description
Gene name	The name of the gene, linked to the associated page of the Online Mendelian Inheritance in Man (OMIM) database.
pLI score	The ExAC computed probability that the gene is loss-of-function (LoF) intolerant. High scores (pLI ≥ 0.9) indicate that the gene is extremely LoF intolerant.

Consequence/Allele Column

Lists details about the variant allele and consequence. By default, the column groups variants by SVs, CNVs, and small variants, then by transcript consequence (SVs and small variants) or number of copies (CNVs). Possible entries are shown in the following table.

Item

Description

Consequence

The consequence of the variant, described in Sequence Ontology standardized vocabulary. The color of the text indicates the predicted pathogenicity based on a predetermined rule set.

Green—Likely benign

Gray—VUS

Red—Likely pathogenic

Transcript

The name of the selected transcript, typically a database identifier from RefSeq or Ensembl, linked to the transcript page in the database. BaseSpace Variant Interpreter includes annotations for all transcripts that overlap a variant. Select More Information to view annotations for other transcripts or to select a different transcript.

HGVS cDNA change

The Human Genome Variation Society (HGVS) coding nomenclature.

HGVS AA change

The HGVS protein nomenclature.

Exon

The exon of the variant.

Sift prediction

The predicted effect based on SIFT score, as indicated by the color of the icon.

Green—Tolerated

Green dotted outline—Tolerated–low confidence

Red—Deleterious

Red dotted outline—Deleterious–low confidence

Select In Silico Predictions to view the Sift/PolyPhen information.

PolyPhen prediction

The predicted effect based on PolyPhen score, as indicated by the color of the icon.

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Green—Benign

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Gray—Unknown

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Red outline—Possibly damaging

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Red—Probably damaging

Select In Silico Predictions to view the Sift/PolyPhen information.

Associations Column

Provides details about the association.

Item

Description

Interpretation

The predicted interpretation for a disease. The color of the text indicates the interpreted pathogenicity.
Hover your mouse over the information icon to view an explanation of the prediction.

RUGD Associations

The number displayed indicates the number of entries for the variant. In compact view, a checkmark indicates that entries exist. The color indicates the clinical significance or classification assigned to the allele.
The rows are grouped by pathogenicity. Grid columns are as follows.

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Cases—Your interpretations for the variant in other cases.

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MyKB—The associations curated by your workgroup. These associations are only visible to your workgroup.

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BSKN—The BaseSpace Knowledge Network database, which includes associations curated by Illumina and ClinVar.

Tumor Associations

The summary of associations between the variant and specific tumor types. The rows are grouped by pathogenicity. Grid columns are:

•

Cases—Your interpretations for the variant in other cases.

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MyKB—The associations curated by your workgroup. These associations are only visible to your workgroup.

•

BSKN—The BaseSpace Knowledge Network database, which includes associations curated by Illumina, and ClinVar.

Possible table entries are:

•

—An association is in the database.

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On—A drug response association for the same tumor type exists in BSKN. This entry applies to Predictive associations only.

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Off—A drug response association for a different tumor type exists in BSKN. This entry applies to Predictive associations only.

Population Freq Column

Lists the maximum population frequency and its data source. Select the frequency value to view all population frequency data for the variant.

Zygosity & Metrics Column

Lists the zygosity and variant read metrics. Select More Information to view metrics for germline case family members or other read data not shown in the grid.

Item	Description
Alt Allele Depth	The number of reads called for the Alt Allele.
Filters	The status of the variant call quality as annotated in the VCF file. PASS indicates that all filters were passed. Otherwise, the variant call filter is listed. The filter listed and threshold for passing filter depends on the method of generating the VCF file.
GQX	The conservative measure of genotype quality derived from the minimum of the GQ and QUAL values listed in a germline VCF file. This field is not populated for somatic cases.
Pass Filter	The status of the passing filter. A status of No indicates that not all filters were passed.
Quality Score	The numeric value of variant call quality. Determination of variant quality depends on the variant caller. This field is not populated for somatic cases.
Somatic Q‑score	The numeric value of somatic variant call quality. This field is not populated for germline or Tumor-only cases.
Total Read Depth	The total number of reads passing quality filters at this position.
Variant Read Frequency	The fraction of reads at this position that have the variant allele.
Zygosity	Lists the zygosity derived from genotype including parental inheritance for heterozygous variants. Accurate inheritance reporting for variants found on pseudoautosomal regions is not yet supported. The pedigree diagram displays the genotype of proband and parents associated with the case. Variants are shown only if filters are PASS. Small variants overlapping a CNV loss event undergo an additional genotype and zygosity correction to reflect missing copies. The corrected values are displayed in the grid.

Custom Annotations Column

Lists the custom annotation categories and content sources, and the first two annotations for each. Select More Information to view any additional annotations.

Interpretation Column

Lists interpretation and other information about the variant. Select the interpretation menu to select from the list of actions.

Item	Description
Variant Flag	Flag the variant for review. Selecting the flag in the column heading sorts flagged variants to the top.
Comment	Add comments to the variant. The number of available comments is displayed in the icon.
Add to Report	Include the variant in the report. Only variants that have interpretations can be added to the report.
Send for Curation	Send the variant for curation. The curation progress is displayed in the column.
Case Interpretation	Interpret the case. If the case has an interpretation, the interpretation is displayed.

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