View Variant Details

View more information about a variant, including gene, transcript, and association details. TruSight Software provides access to curated data from public knowledge bases, and a private knowledge base of associations created by members of your workgroup.

To view variant details, select the row containing the variant.

Variant Details Tab

Lists information about a variant. Data vary depending on variant type.

Item

Description

Variant Type

The variant type.

CHR:POS

The chromosome number and position.

REF

The reference allele.

ALT

The alternate allele.

STR details

Short tandem repeat details.

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Genetic findings—The expansion status: expanded or not expanded.

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Repeat unit—The repeated sequence.

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Reference repeat—The number of repeats in the reference genome.

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Repeat unit—The number of repeats in the sample.

Low Complexity Region (gnomAD)

The variant is found in a low-complexity region (LCR).

Visualizations

Links to visualization browsers.

Resources

Links to public database entries for the variant. ClinVar entries display the number of stars associated with review status.

Zygosity & Metrics

Lists the zygosity and variant read metrics for each subject.

Item	Description
Affected	The affected status of the subject.
Genotype	The genotype of the variant.
Variant Read Frequency (VRF)	The fraction of reads at this position that have the variant allele.
Total Depth	The total number of reads passing quality filters at this position.
Split Reads	The number of split reads.
Paired Reads	The number of paired reads.
Allele Depths	The number of reads called for the ALT Allele.
Filter	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.
Quality Score	The numeric value of variant call quality. Determination of variant quality depends on the variant caller.

CaseLog

Lists the CaseLog data for the subject.

Item	Description
Alternative Allele Frequency	The frequency of the selected alternate allele within your aggregated cases in CaseLog.
Cases	The number of cases, including cases from public and shared data, in which a variant was observed or reported. Selecting More Info displays details about the cases.

Item

Description

Alternative Allele Frequency

The frequency of the selected alternate allele within your aggregated cases in CaseLog.

Cases

The number of cases, including cases from public and shared data, in which a variant was observed or reported.

Selecting More Info displays details about the cases.

MITOMAP (Small Variants)

Lists available MITOMAP data for small variants.

Item

Description

Diseases

The associated phenotypes in the MITOMAP database

Het

The presence of heteroplasmy (mixture of mutant and normal mtDNAs)

Hom

The presence of homoplasmy (pure mutant mtDNAs).

Status

The status of pathogenicity reports. Possible values are:

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Unclear—Pathogenicity is undetermined.

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Reported/Provisional—One or more publications reported as possibly pathogenic.

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Confirmed—Two or more independent labs published reports on the pathogenicity of the variant.

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Point Mutation/Polymorphism—Some publication reports determined the variant mutation to be a non-pathogenic polymorphism.

Significance

The significance of the variant.

GenBank Sequences

The number of GenBank full-length sequences.

PubMed

Links, if available, to PubMed entries for the variant.

SpliceAI

Lists available SpliceAI predictive scores for splice junctions: acceptor gain, donor gain, acceptor loss, or donor loss. For more information, see https://github.com/Illumina/SpliceAI.

Item	Description
Score	The probability that the variant affects the category. The maximum probability across all categories is reported in the variant grid.
Distance	The distance between the splice change relative to the variant position. Positive values are downstream of the variant, negative values are upstream.

Associations

Lists the associations between the variant and disease, and Association Details for each.

Item

Description

Status

Indicates whether the association is selected for inclusion in the report.

Interpretation

The predicted interpretation for a disease. The color of the text indicates the interpreted pathogenicity.

Date

The date the association was added.

Version

The version number of the association.

Association Level

The association level. Possible values are:

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Nucleotide—Specific alterations frequently observed in the disease condition or mentioned in the evidence.

Other association levels are not supported in this release.

Curator Summary

The description of the association provided by the curator.

Knowledge Network

A link to the Knowledge Network entry for the association.

Transcript Tab

Lists details about the variant allele and consequence.

Column	Description
Canonical	The transcript with the longest coding sequence or the longest complementary DNA.
Transcript	The name of the selected transcript, typically a database identifier from RefSeq or Ensembl, linked to the transcript page in the database. TruSight Software includes annotations for all transcripts that overlap a variant.
Gene	The names of genes associated with the transcript.
SIFT	The probability that the effect of an amino acid substitution on the function of a human protein is tolerated.
SIFT prediction	The predicted effect based on SIFT score.
PolyPhen	The probability that the effect of an amino acid substitution on the function of a human protein is damaging.
PolyPhen prediction	The predicted effect based on PolyPhen score.
REVEL	The REVEL predicted pathogenicity of a missense variant.
N-species AA	The N-species amino acid conservation score.
Exon	The exon of the variant.
HGVS cDNA	The HGVS coding nomenclature.
HGVS AA	The HGVS protein nomenclature.
Consequence	The consequence of the variant, described in Sequence Ontology standardized vocabulary.

Gene Details Tab

Lists details about the affected genes.

If more than one gene is affected, the initial view lists a summary of each gene and any overlapping phenotypes. A partial overlap icon indicates that a breakend occurs within the gene.

Select a gene name to view details.

Item	Description
Gene	The gene name and summary description.
Constraint Metrics (gnomAD)	Scores for synZ, misZ, pNull, pLI, pRec, and LOEUF metrics.
Dosage Sensitivity (ClinGen)	The ClinGen evidence classification for haploinsufficiency and triplosensitivity.
Related Diseases	The associated phenotypes in the ClinGen database. Colored icons represent the ClinGen classification of the disease.
PrimateAI	The predicted pathogenicity of missense variants in primate species. Values closer to 1 indicate greater pathogenicity. For more information about the PrimateAI prediction engine, see https://github.com/Illumina/PrimateAI.
Literature search	The results of a literature search for the association, linked to the search results. The label indicates whether overlapping indications exist, followed by the number of results for the gene. For more information, see Literature Search.
Gene database links	Links, if available, to database entries for the gene (eg, OMIM, PubMed, or CaseLog).
Comments	Case-independent comments about the gene. For more information, see Manage Comments. Do not include direct identifiers in comment fields.

Gene Associations

Lists the associations between the gene and disease, and Association Details for each.

Item	Description
Status	Indicates whether the association is selected for inclusion in the report.
Interpretation	The predicted interpretation for a disease. The color of the text indicates the interpreted pathogenicity.
Date	The date the association was added.
Version	The version number of the association.
Knowledge Network	A link to the Knowledge Network entry for the association.

Related articles

View Variant Details