The information provided on the kConFab website is for research purposes only. Published models have been used to arrive at the classification of some gene mutations/variants. This information should be interpreted bearing in mind that the rarity of variants may limit the data informing the models used.

Listed information on classification of gene mutations/variants is subject to change as further information becomes available. It is not intended for clinical use. Individuals or families requiring advice should consult their doctor or contact a local Family Cancer Clinic.

BRCA1 and BRCA2

Variants will be described using dual nomenclature:

1. Nomenclature following HGVS recommendations (http://www.hgvs.org/mutnomen/recs.html), including that for intronic variants.
   
2. Nomenclature following HGVS recommendations, but with the following exceptions:
   1. the nucleotide numbering is from nucleotide 1 of the full gene sequence (Genbank: U14680/ BRCA1; U43746/ BRCA2) not the ATG initiator codon, as coincides with numbering used by BIC(http://research.nhgri.nih.gov/bic/)
   2. the BRCA1 185del AG and the BRCA1 5382insC mutations have not been re-named, following the universal use of the incorrect base numbers in the literature.

Exon boundaries are based upon the following genomic sequences (GenBank) L78833/BRCA1; Z74739, Z73359, X95177/ BRCA2.

Other Genes

Variants will be described using nomenclature following HGVS recommendations (http://www.hgvs.org/mutnomen/recs.html), including that for intronic variants.

P = Pathogenic
LGR = Large Genomic Rearrangement
UV = Unclassified Variant
UVP = regarded as likely to be pathogenic but lacking definitive published evidence
Sp = Splice Site Variant
PM = Polymorphism
LCS = sequence variants considered to be neutral or of low clinical significance; silent variants (This includes the former UV$ and PM& groups, both classified as PM in Deffenbaugh, 2002)

In determining the classifications for variants observed in kConFab families, a literature review is performed and consideration is given to the classification guidelines listed below, with cross-reference to the BIC database (http://research.nhgri.nih.gov/bic/) for BRCA1 and BRCA2, and other relevant mutation databases for other cancer predisposition genes.

Pathogenic P

• All truncating mutations unless there is clear evidence that the mutation is a SNP (eg the 10204 A->T BRCA2 variant in exon 27).
• All large deletions that result in a frameshift.
• Large in-frame deletions that span any one or more exon(s) that encodes established functional domains of the protein e.g. the ring finger domains.
• Genetic variants in highly conserved splice site regions that have been confirmed by in vitro functional studies to cause aberrant splicing leading completely or predominantly to transcripts encoding truncated protein products, and for which there is no evidence that the mutation is a SNP.
• Any variant considered to be of clinical importance according to BIC (http://research.nhgri.nih.gov/bic/)
• Any apparent missense variant that is associated with cancer predisposition in family studies of multi generations, and whose pathogenicity is supported by a combination of some of the following features: it is absent in unaffected controls; it results in a non conservative amino acid substitution; it occurs in a residue conserved across species; it occurs in a functional domain; for BRCA1 variants, the histopathology is indicative of BRCA1 mutation status. In each case, the variant should be referenced to at least one published article that in addition to the above gives convincing functional evidence from several assays that the variant is pathogenic. For example this includes all of the mutations altering the cysteine residues of the ring finger domains.
• Alternatively, the likely pathogenicity of a given BRCA1 or BRCA2 missense variant may be measured using multifactorial likelihood approaches (Goldgar et al 2004, Am J Hum Genet 75:535; Chenevix-Trench et al, Cancer Res 66: 2019), using the recommended cut-off of ≥ 1000:1 in favour of causality.

Large Genomic Rearrangement LGR

• Large genomic rearrangements that cover more than one exon, across no known functional domains, and are not known or confirmed to result in a frameshift.

Unclassified Variant UV

• Missense variants without compelling evidence of pathogenicity.
• Deletion or duplication where the functional significance is unknown, including short to medium size deletions or duplications that conserve the reading frame, and larger in-frame deletions or duplications which span only a single exon that has no established functional domains.
• Variants near but not within consensus splice regions that may disrupt splicing.
• Genetic variants in highly conserved splice site regions that give rise to transcripts that contain in-frame deletions of regions of the gene that do not include essential functional domains.
• Variants in the 3´UTR that may affect RNA stability, and that are not common (>1%) polymorphisms.

If an unclassified variant is regarded as likely to be pathogenic from evidence to date, but is lacking definitive published evidence (as might be required for establishing significance in a clinical setting), it will be denoted as UV(P). This includes BRCA1 or BRCA2 variants with reported odds in favour of causality below 1000:1 required for classification as pathogenic, as measured using multifactorial likelihood approaches (Goldgar et al 2004, Am J Hum Genet 75:535; Chenevix-Trench et al, Cancer Res 66: 2019).

Splice Variant Sp

• Genetic variants in highly conserved splice site regions that have not been characterized in terms of impact on splicing and aberrant transcript production.

Polymorphism PM

• Common polymorphisms found in unaffected controls at a frequency of more than 1%.

Neutral/Low Clinical Significant Variant LCS

• BRCA1 or BRCA2 variants which are described in Deffenbaugh (2002, Genetic Testing 6: 119) or Tavtigian (2005, J Med Genet July 13 [Epub]), or described in trans with a deleterious mutation in the same gene in an individual and occur at a frequency of less than 1% in unaffected controls
• BRCA1 or BRCA2 variants considered neutral variants as measured using multifactorial likelihood approaches (Goldgar et al 2004, Am J Hum Genet 75:535; Chenevix-Trench et al, Cancer Res 66: 2019), using the recommended cut-off of ≥ 100:1 in favour of neutrality.
• Variants confirmed by large well-designed studies to be associated with low-moderate risk of cancer in the general population
• Non-coding, silent variants

Note regarding confirmation of MLPA-detected large deletions detected in a research setting in kConFab participants, in the absence of corroborating results from a clinical testing laboratory:

Deletions of multiple contiguous exons are extremely unlikely to have arisen as false positives by chance in the MLPA assay (Taylor, 2003 Hum Mutat 22: 428). However, apparent deletions of a single exon do need confirmation to see if a point mutation or microdeletion/microinsertion is present that might interfere with MLPA probe hybridisation, either by sequencing the exon in question or by utilising a kit that uses two primer pairs per exon. Such confirmation is required before reportback of research-generated large deletion results to Family Cancer Clinics.