Table 4.

Criteria for Classifying Benign Variants

Stand-Alone evidence of benign impact
BA1	Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes, or ExAC
Strong evidence of benign impact
BS1	Allele frequency is greater than expected for disorder (see table 6)
BS2	Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder with full penetrance expected at an early age
BS3	Well-established in vitro or in vivo functional studies shows no damaging effect on protein function or splicing
BS4	Lack of segregation in affected members of a family
	Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation.
Supporting evidence of benign impact
BP1	Missense variant in a gene for which primarily truncating variants are known to cause disease
BP2	Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder; or observed in cis with a pathogenic variant in any inheritance pattern
BP3	In-frame deletions/insertions in a repetitive region without a known function
BP4	Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
	Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant.
BP5	Variant found in a case with an alternate molecular basis for disease
BP6	Reputable source recently reports variant as benign but the evidence is not available to the laboratory to perform an independent evaluation
BP7	A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved