Variant Grid

Assigned variant flags. If more than one flag is assigned, the color indicates the most severe flag.

Select the drop-down arrow to assign or remove a flag.

This column cannot be hidden or moved.

The interpretation status of the variant.

This column cannot be hidden or moved.

IGV visualization link.

This column cannot be hidden or moved.

Indicates whether the variant is a potential compound het, virtual variant,or linked MNV. Select the icon to filter the view to display linked variants only.

This column cannot be hidden or moved.

The sum of all allele counts across all population sources, including custom annotations.

The variant category.

The small variant ref allele and alt allele.

The predicted pathogenicities of the variant, annotated from data in the ClinVar database.

The consequence of the variant. Consequences are specific to the default or selected transcript. Select More to view a summary of consequences observed for the variant across all transcripts.

The cytoband location.

The exon of the variant.

The status of the variant call quality as annotated in the VCF file. PASS indicates that all filters passed. Otherwise, the variant call filter is listed.

The name of the gene. If a variant affects more than one gene, the first gene is listed, followed by the number of additional affected genes. Information about additional genes is listed in the variant details.

The findings for SMA and STR calls.

STR findings are manually curated. If a finding is not assigned, the column entry is blank.

The sum of all male allele counts for allosomal PAR variants across all the population sources, including custom annotations.

The Human Genome Variation Society (HGVS) coding nomenclature.

The sum of all homozygote counts across all the population sources, including custom annotations.

The inheritance pattern of the variant.

The length of the variant. The length calculation for STRs is (difference between repeat number and reference repeat) × number of bp in the repeat.

The mode of inheritance. For information about inheritance criteria, see Mode of Inheritance Logic .

The predicted pathogenicities of the variant, annotated from data in your knowledgebase.

The number of overlapped phenotypes for the variant. Select the information icon to view details about the phenotypes.

The phyloP conservation score.

The gnomAD computed probability that the gene is loss-of-function (LoF) intolerant. High scores (pLI ≥ 0.9) indicate that the gene is extremely LoF intolerant.

The score applies to the selected transcript. If the score is not the highest across all transcripts, the highest score is displayed in parentheses after the transcript score.

Lists the maximum population frequency and its data source, which can be any of the sources listed in Data Sources.

In the variant details view, select the Variant Details tab to view all population frequency data for the variant.

Lists the maximum population frequency provided in a custom annotation file. The column heading in the grid is determined by the column name in the annotation file.

In the variant details view, select the Variant Details tab to view all population frequency data for the variant.

The chromosome number and position.

The predicted pathogenicity score for missense mutations, computed by the PrimateAI engine.

The score applies to the selected transcript. If the score is not the highest across all transcripts, the highest score is displayed in parentheses after the transcript score.

The numeric value of variant call quality. Determination of variant quality depends on the variant caller.

The maximum reported SpliceAI score.

The name of the selected transcript, typically a database identifier from RefSeq or Ensembl.

The variant type.