Genetic term	Definition
Allele	One of 2 or more alternate forms of a gene at the same location. For example, a single variant in RAG1 in a patient would be considered heterozygous and present on one “allele.”
Coverage	Percentage of targeted genomic regions sequenced to a minimum predefined read depth.
Germline DNA	DNA derived from germ cells (i.e., sperm and egg cells) and present in all cells. Most of our DNA sequence is germline.
Variant	A change in DNA that is different from published reference genome sequence. Variants can be very common, even present in >90% of the population, or rare, for example present in <1% of the population. This is due to the fact that the reference genome was generated from a small number of individuals.
Single nucleotide variant (SNV)	A genetic change in a single nucleotide, for example the change of a guanine (G) to an alanine (A). This may or may not be associated with altered function of the encoded protein, for example by changing the protein sequence or splicing of the mRNA.
De novo variant	A genetic change resulting for the first time in a germ cell or fertilized egg early during embryogenesis. For example, a child with a germline variant not carried by either parent would have a “de novo” variant.
Somatic variant	A post-zygotic change in DNA of somatic cells (i.e., any cell but a germ cell, for example immune cells or skin cells are somatic cells) that is different from the germline DNA. For example, genetic mutations present in leukemia cells are considered “somatic variants.”
Mosaicism	When cells in the same person have different DNA sequences. Somatic mosaicism refers to different DNA sequences among somatic cells, for example a genetic change in a subset of immune cells. Gonadal mosaicism refers to germ cells having a different sequence than other cells in the same person, for example a mutation in STAT3 found in sperm but not in other cells. This is different from a de novo variant that can occur in a single germ cell. With Gonosomal mosaicism, the genetic variant is present in a portion of both somatic and gonadal cells; in this case, the affected individual may pass the gene on to offspring. This type of mosaicism is due to a mutational event during early embryogenesis.
Reversion mutation	A genetic alteration that reverses the phenotype resulting from the previously mutated gene to wild type functional state. This includes back mutations that restores the wild type sequence or second-site mutations that affect a different site within the protein.
Read depth	Number of sequences computationally aligned to a reference sequence for a given genomic position, for example the number of times a particular fragment of DNA was sequenced. Whole exome sequencing data usually has a “read depth” of at least 100 and whole genome sequencing usually has a “read depth” of at least 30.