Variant related fields #
Here is the list of all the available variant-related filters that can be used to query SwissGenVar.
Clinical significance #
Description #
This field corresponds to the clinical significance of the variant.
Content #
The following values can be used to filter:
- Pathogenic
- Likely pathogenic
- Uncertain significance
- Likely benign
- Benign
Data source #
Custom values adjusted from ClinVar.
Causality #
Description #
This field corresponds to the causality of the variant.
Content #
The following values can be used to filter:
- Causative
- Likely causative
- Probably not causative
- Not causative
- VUS
- Variant in a GUS
Data source #
Custom values.
Variant type #
Description #
This field corresponds to the type of the variant.
Content #
The following values from HGVS can be used to filter:
- CNV - amplification
- CNV - deletion
- CNV - insertion/duplication
- Complex
- Complex rearrangement
- Conversion
- Deletion
- Deletion-insertion
- Duplication
- Insertion
- Methylation/epigenetic change
- Repeat variation
- Structural variant
- Substitution
Data source #
Custom values.
Variant effect #
Description #
This field corresponds to the effect of the variant.
Content #
Here is the custom list of terms selected from VEP:
- Missense variant
- Nonsense
- Splicing variant
- Splice acceptor variant
- Splice donor variant
- Regulatory region
- Promoter region
- Inframe variant
- Inframe insertion
- Inframe deletion
- Intron variant
- Synonymous variant
- Stop lost
- Start lost
- Frameshift variant
- Upstream gene variant
- Downstream gene variant
- 5 prime UTR variant
- 3 prime UTR variant
- Exon deletion
- Exon duplication
- Contiguous gene deletion
- Contiguous gene duplication
Data source #
Partly coming from VEP.
Gene locus type #
Description #
This field corresponds to the gene locus type.
Content #
Here is the custom list of terms selected from HGNC:
- Protein coding gene
- Non-coding RNA gene
- long non-coding RNA
- microRNA
- ribosomal RNA
- transfer RNA
- small nuclear RNA
- small nucleolar RNA
- other
- Locus subjected to imprinting
Data source #
Partly coming from HGNC
Gene HUGO symbol #
Description #
This field corresponds to the gene HUGO symbol.
Content #
This filter proposes a list of gene HUGO terms that are already present in the database.
Data source #
HUGO
Location #
Description #
This field corresponds to the location of the variant on a chromosome.
Content #
This filter proposes a list of genomes references (GrCh37 and GrCh38)and allows to enter a chromosome and genomic positions (start and end).
Data source #
None