Consequence and Impact Filters

Use the Consequences and Impacts filters to filter data by variants that alter the coding potential of the transcript. Select the checkbox of each filter you want to apply.

Note

Consequences are standardized in accordance with the Sequence Ontology Organization.

Small Variant Consequence Filters

Filter

Description

Stop gain or loss

Filters data by the gain or loss of a stop codon in the coding sequence.

Splice site

Filters data by the affected splice site:

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Splice donor—The variant affects the canonical splice donor site (first two bases of the 5ʹ end of the intron).

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Splice acceptor—The variant affects the canonical splice acceptor site (last two bases of the 3ʹ end of the intron).

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Splice region—An indel or substitution in a noncoding splice region of the gene.

Indels

Filters data by whether an insertion or deletion disrupts the reading frame:

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Frameshift Indels—An insertion or deletion in which the number of base pairs is not divisible by 3, causing a frame disruption.

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Inframe deletion—A deletion that does not disrupt the reading frame.

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Inframe insertion—An insert that does not disrupt the reading frame.

Missense

Filters data by codon variations:

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Initiator codon (ATG) loss—A codon that signals the start of the synthesis of a polypeptide.

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Missense—A single base pair substitution that results in the translation of a different amino acid at that position. Selecting this option enables a list of functional impact filters to select from.

•

Incomplete terminal codon—A change to at least one base of the final codon of an incomplete annotated transcript.

Protein Altering

Filters data by whether the variant has a protein-altering coding consequence.

Silent

Filters data by the variant relationship to a gene:

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Intergenic—The variant position is not covered by any gene transcript.

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Upstream gene—The variant position is within 5 kb upstream of the defined transcript start coordinate.

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Downstream gene—The variant position is within 5 kb downstream of the defined transcript end coordinate.

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Intron—The variant occurs within an intron.

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5-prime UTR—The variant is in the 5ʹ untranslated region of a gene.

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3-prime UTR—The variant is in the 3ʹ untranslated region of a gene.

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Noncoding exon—The variant changes the noncoding exon sequence in a noncoding transcript.

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Noncoding transcript—The variant occurs in a noncoding RNA gene.

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Synonymous—The variant does not affect the primary amino acid sequence of the translated protein.

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Stop retained—At least one base in the terminator codon is changed, but the terminator remains.

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Mature miRNA—The variant occurs within a mature miRNA sequence

•

NMD transcript—The variant is in a transcript and is the target of nonsense-mediated decay (NMD).

Small Variant Functional Impact Filters
Filter	Description
SIFT	Filters data by the SIFT prediction of a deleterious effect of an amino acid substitution on the function of a human protein.
PolyPhen	Filters data by the PolyPhen prediction of a damaging effect of an amino acid substitution on the function of a human protein.

Copy Number Variant Consequence Filters
Filter	Description
Copy Number Variant Consequences	Filters data by copy number consequences: Copy Number Gain, Copy Number Loss, and Loss of Heterozygosity.

Structural Variant Consequence Filters
Filter	Description
Breakend Consequences	Filters data by breakend consequence: Inversion, Deletion, Insertion, Tandem Duplication, or Translocation Breakend.
Fusion Consequences	Filters data by unidirectional gene fusion consequence.

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Consequence and Impact Filters