Variant Filters

Variant Category

Filters by variant category.

Type	Description
Small Variant	SNVs, MNVs, insertions, deletions, and indels.
Structural Variant	Insertions, deletions,tandem duplications, and translocation breakends.
Copy Number Variant	Copy number variation, gain, or loss.
Run of Homozygosity	Regions of consecutive variant calls.
Short Tandem Repeats	Regions of repeating short DNA segments.

Small Variant Type

Type	Description
SNV	Single nucleotide variation.
MNV	Multiple nucleotide variation.
Insertion	Insertion of genomic sequence.
Deletion	Deletion of a genomic sequence.
Indel	Deletion and insertion of genomic sequence.

Structural Variant Type

Type	Description
Insertion	Insertion of genomic sequence.
Deletion	Deletion of a genomic sequence.
Tandem Duplication	Duplication of genomic sequence in tandem.
Translocation Breakend	Structural variation that links breakpoints of two different points in the genome.

Copy Number Variant Type

Type	Description
Copy Number Variation	The copy number is increased or decreased relative to the reference sequence.
Copy Number Loss	The copy number is less than the reference sequence.
Copy Number Gain	The copy number is greater than the reference sequence.
Copy Number Neutral	The copy number is the same as the reference sequence.

Small Variant Consequences

Filters data by the specified consequence.

Coding Consequences

Start and Stop Alterations

Filters data by the presence and location of start and stop alterations.

Consequence	Description
Start Loss	The loss of a start codon in the coding sequence.
Stop Gained	The gain of a stop codon in the coding sequence.
Stop Loss	The loss of a stop codon in the coding sequence.
Incomplete Terminal Codon	A change to at least one base of the final codon of an incomplete annotated transcript.
Feature Elongation	The variant causes the extension of a genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.

Splice Site

Filters data by the affected splice site.

Type	Description
Splice Acceptor Variant	The variant affects the canonical splice acceptor site (last two bases of the 3ʹ end of the intron).
Splice Donor Variant	The variant affects the canonical splice donor site (first two bases of the 5ʹ end of the intron).
Splice Region Variant	An indel or substitution in a noncoding splice region of the gene.

Indels

Type	Description
Frameshift Variant	An insertion or deletion in which the number of base pairs is not divisible by 3, causing a frame disruption.
Inframe Deletion	A deletion that does not disrupt the reading frame.
Inframe Insertion	An insertion that does not disrupt the reading frame.

Other

Type	Description
Missense Variant	A single base pair substitution that results in the translation of a different amino acid at that position.
Protein Altering Variant	The variant has a protein-altering coding consequence.
Coding Sequence Variant	The variant changes the coding sequence.

Silent Consequences

Filters data by the variant relationship to a gene.

Type	Description
Intergenic Variant	The variant position is not covered by any gene transcript.
Upstream Gene Variant	The variant position is within 5 kb upstream of the defined transcript start coordinate.
Downstream Gene Variant	The variant position is within 5 kb downstream of the defined transcript end coordinate.
Intron Variant	The variant occurs within an intron.
3-prime UTR Variant	The variant is in the 3ʹ untranslated region of a gene.
5-prime UTR Variant	The variant is in the 5ʹ untranslated region of a gene.
Noncoding Transcript Exon Variant	The variant changes the noncoding exon sequence in a noncoding transcript.
Noncoding Transcript Variant	The variant occurs in a noncoding RNA gene.
Synonymous Variant	The variant does not affect the primary amino acid sequence of the translated protein.
Start Retained Variant	At least one base in the start codon is changed, but the start codon remains.
Stop Retained Variant	At least one base in the terminator codon is changed, but the terminator remains.
Mature MiRNA Variant	The variant occurs within a mature miRNA sequence.
NMD Transcript Variant	The variant is in a transcript and is the target of nonsense‑mediated decay (NMD).
Regulatory Region Ablation	A deletion of a region that contains a regulatory region.
Regulatory Region Amplification	An amplification of a region that contains a regulatory region.
Regulatory Region Variation	The variant occurs in a regulatory region.

Structural Variant Consequences

Transcript Consequences

Filters data by the transcript consequence.

Consequence	Description
Transcript Variant	The variant changes the structure of the transcript.
Transcript Ablation	A deletion of a region that contains a transcript feature.
Transcript Amplification	An amplification of a region that contains a transcript.
Transcript Truncation	A truncation of a region that contains a transcript.
Feature Elongation	The variant causes the extension of a genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.
5-Prime Duplicated Transcript	A partially duplicated transcript in which the 5ʹ end of the transcript is duplicated.
3-Prime Duplicated Transcript	A partially duplicated transcript in which the 3ʹ end of the transcript is duplicated.

Gene Fusion Consequences

Filters data by the gene fusion consequence.

Consequence	Description
Unidirectional Gene Fusion	A fusion of two genes on the same strand.

Copy Number Variant Consequences

Transcript Consequences

Filters data by the transcript consequence.

Consequence	Description
Transcript Variant	The variant changes the structure of the transcript.
Transcript Ablation	A deletion of a region that contains a transcript feature.
Transcript Amplification	An amplification of a region that contains a transcript.
Transcript Truncation	A truncation of a region that contains a transcript.
Feature Elongation	The variant causes the extension of a genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.
5-Prime Duplicated Transcript	A partially duplicated transcript in which the 5ʹ end of the transcript is duplicated.
3-Prime Duplicated Transcript	A partially duplicated transcript in which the 3ʹ end of the transcript is duplicated.

Copy Number Consequences

Filters data by the copy number consequence.

Type	Description
Copy Number Increase	The copy number is increased relative to the reference sequence.
Copy Number Decrease	The copy number is decreased relative to the reference sequence.
Copy Number Change	The copy number is increased or decreased.

Short Tandem Repeat Consequences

Filters data by short tandem repeat consequences: expansion, contraction, and change.

AI Prediction Engine

Filters data by splice mutation probability, as predicted by deep learning engines.

Chromosome

Filters by specified chromosomes. If no chromosome is selected, the chromosome filter is not applied.

Constraint Metrics (gnomAD)

Filters by gnomAD constraint metrics.

Custom Annotation Label

Filters by labels provided in a custom annotation file.

Genes

Filters by specified genes and genes related to specified phenotypes. Gene names are case-sensitive.

Genetic Findings

Filters by the status of the SMN and STR calls for each subject.

Genomic Regions

Filters by specified regions. The input format is chr#:start-end, with multiple regions separated by spaces or new lines.

Haploinsufficiency (ClinGen)

Filters by the ClinGen haploinsufficiency evidence classification.

Mode of Inheritance

Filters data by the mode of inheritance. For information about inheritance criteria, see Mode of Inheritance Logic .

Selecting an inheritance option enables one or more subfilters to select from.

Mode of Inheritance

Description

De Novo (DN)

The variant is not present in the parents.

Dominant (DOM)

At least one parent is affected and the variant is present in all affected subjects.

Present in Proband (PR)

The variant is present in the proband subject.

Recessive (RSG or RCH)

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The variant is present in all affected individuals and is homozygous or hemizygous in the proband (RSG).

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The variant is heterozygous or hemizygous diploid loss in the proband (RCH).

Inheritance Subfilters

Filter	Description
Assume Complete Penetrance	Excludes variants that are homozygous or hemizygous in unaffected individuals. This option is used to find variants for which complete penetrance is expected.
Exclude Ambiguous	Excludes RCH variants that have ambiguous inheritance, if de novo variants are absent or have been filtered out.
Exclude Low Confidence	Excludes de novo variants that are classified as low confidence.
Exclude Observed Homozygotes	Excludes variants observed in a homozygous state within the pedigree.
In Affected	Excludes variants that are not present in all affected individuals.
Not in Unaffected	Excludes variants that are present in unaffected individuals.
Same Genotype in Affected	Returns variants that are homozygous, hemizygous, or hemizygous diploid loss in all affected individuals.
Shared Variant in Affected	Returns RSG variants that are present in all affected individuals or RCH variants where at least one variant from a given variant set for a transcript is present in all affected individuals.
Strict	Returns only recessive variants that are inherited from both parents.

OMIM

Filters data by presence in the OMIM gene database.

Item	Description
Present in OMIM	An OMIM entry exists for the gene.
Has associated OMIM phenotypes (including ?)	A provisional relationship exists between the phenotype and a matching gene at the transcript level.
Has associated OMIM phenotypes (excluding ?)	A relationship exists between the phenotype and a matching gene at the transcript level.

Pathogenicity

Filters data by the pathogenic evidence from ClinVar or your knowledge base.

NOTE

Inclusion and exclusion filters capture all variants that have associations for the selected pathogenicity, regardless of any other pathogenicities associated with the variant. For example, a filter that excludes benign pathogenicities also excludes any variants that have both benign and pathogenic associations.

Item	Description
P (Pathogenic)	Segregates with disease in multiple unrelated cases with control data. The variant is in a highly conserved region. Functional studies or other evidence indicate a deleterious effect on gene expression.
LP (Likely Pathogenic)	Reported in some case studies with or without control data. The variant is in a highly conserved region. Functional studies or other evidence highly suggest a deleterious effect on gene expression.
VUS (Variant of Unknown Significance)	Nothing about this variant has been reported, or reported information is incomplete or contradictory.
LB (Likely Benign)	Functionally normal. Reported in a few cases with little or no control data. The variant might be nonconserved and predicted to be tolerated. Based on disease prevalence and penetrance information, the variant frequency is higher than expected in the general population.
B (Benign)	Functionally normal. Reported at high frequency in control data and does not segregate with disease. The variant might be nonconserved and predicted to be tolerated.

ClinVar Review Status

Filters selected ClinVar pathogenicities by review status.

# of Stars	Description
1	Single submitter or multiple submitters with conflicting evidence.
2	Multiple submitters, no conflicting evidence.
3	Reviewed by expert panel.
4	Practice guideline.

Population Frequency

Filters data based on the allele frequency in population studies. Large variants (eg, CNVs and SVs) are filtered based on aggregate frequency. The aggregate frequency is calculated as the sum of all allele frequencies for annotations where the number of alleles is at least 300 and the reciprocal overlap is above the threshold set in the test definition.

The available population databases vary depending on the selected variant type. For detailed information about the population frequencies, see Population Data.

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To set a variant filter for frequency values, enter a value from 0–1 in the field. Frequency values support precision to 0.00001.

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To filter by the average frequency across all options in a database, enter a value in the All Populations field.

Quality

Filters data by whether variants pass filter.

Sample Metrics

Filters data by read metrics.

Size

Filters data by variant length. Supports decimal values for sizes < 1 Mbp, with precision to 0.001.

Triplosensitivity (ClinGen)

Filters by the ClinGen triplosensitivity classification.

Zygosity

Zygosity	Description
Homozygous	Variants that are present on both alleles.
Heterozygous	Variants that are present on one of two alleles.
Hemizygous	Variants that are present on one allele for non-diploid regions.
Hemizygous Diploid Loss	Variants that are present on one allele, where the other allele is deleted due to a copy number variation.

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Variant Filters