Ensembl Variation - Variant classification

Sequence variants

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Structural variants

Variant classes

We call the class of a variant according to its component alleles and its mapping to the reference genome, and then display this information on the website. Internally we use Sequence Ontology terms, but we map these to our own 'display' terms where common usage differs from the SO definition (e.g. our term SNP is closer to the SO term SNV). All the classes we call, along with their equivalent SO term, are shown in the table below. We also differentiate somatic mutations from germline variants in the display term, prefixing the term with 'somatic'. If you are working with the API, you can fetch either the SO term or the display term.

*	SO term	SO description	SO accession	Called for (e.g.)
	SNV	SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist.	SO:0001483	Variant
	substitution	A sequence alteration where the length of the change in the variant is the same as that of the reference.	SO:1000002	Variant
	Alu_deletion	A deletion of an Alu mobile element with respect to a reference.	SO:0002070	SV
	Alu_insertion	An insertion of sequence from the Alu family of mobile elements.	SO:0002063	SV
	HERV_deletion	A deletion of the HERV mobile element with respect to a reference.	SO:0002067	SV
	HERV_insertion	An insertion of sequence from the HERV family of mobile elements with respect to a reference.	SO:0002187	SV
	LINE1_deletion	A deletion of a LINE1 mobile element with respect to a reference.	SO:0002069	SV
	LINE1_insertion	An insertion from the Line1 family of mobile elements.	SO:0002064	SV
	SVA_deletion	A deletion of an SVA mobile element.	SO:0002068	SV
	SVA_insertion	An insertion of sequence from the SVA family of mobile elements.	SO:0002065	SV
	complex_chromosomal_rearrangement	A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis.	SO:0002062	SV
	complex_structural_alteration	A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints.	SO:0001784	SV
	complex_substitution	When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change.	SO:1000005	SV
	copy_number_gain	A sequence alteration whereby the copy number of a given regions is greater than the reference sequence.	SO:0001742	SV
	copy_number_loss	A sequence alteration whereby the copy number of a given region is less than the reference sequence.	SO:0001743	SV
	copy_number_variation	A variation that increases or decreases the copy number of a given region.	SO:0001019	SV
	duplication	An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome.	SO:1000035	SV
	interchromosomal_breakpoint	A rearrangement breakpoint between two different chromosomes.	SO:0001873	SV
	interchromosomal_translocation	A translocation where the regions involved are from different chromosomes.	SO:0002060	SV
	intrachromosomal_breakpoint	A rearrangement breakpoint within the same chromosome.	SO:0001874	SV
	intrachromosomal_translocation	A translocation where the regions involved are from the same chromosome.	SO:0002061	SV
	inversion	A continuous nucleotide sequence is inverted in the same position.	SO:1000036	SV
	loss_of_heterozygosity	A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.	SO:0001786	SV
	mobile_element_deletion	A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).	SO:0002066	SV
	mobile_element_insertion	A kind of insertion where the inserted sequence is a mobile element.	SO:0001837	SV
	novel_sequence_insertion	An insertion the sequence of which cannot be mapped to the reference genome.	SO:0001838	SV
	short_tandem_repeat_variation	A variation that expands or contracts a tandem repeat with regard to a reference.	SO:0002096	SV
	tandem_duplication	A duplication consisting of 2 identical adjacent regions.	SO:1000173	SV
	translocation	A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions.	SO:0000199	SV
	deletion	The point at which one or more contiguous nucleotides were excised.	SO:0000159	Variant SV
	indel	A sequence alteration which included an insertion and a deletion, affecting 2 or more bases.	SO:1000032	Variant SV
	insertion	The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence.	SO:0000667	Variant SV
	sequence_alteration	A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence.	SO:0001059	Variant SV
	probe	A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.	SO:0000051	CNV probe

* Corresponding colours for the Ensembl web displays (only for Structural variants). The colours were originally based on the dbVar displays.

Insertion and Deletion coordinates

In Ensembl, an insertion is indicated by start coordinate = end coordinate + 1. For example, an insertion of 'C' between nucleotides 12600 and 12601 on the forward strand is indicated with start and end coordinates as follows:

   12601     12600   

A deletion is indicated by the exact nucleotide coordinates. For example, a three base pair deletion of nucleotides 12600, 12601, and 12602 of the reverse strand will have start and end coordinates of :

   12600     12602