ClinVar Genomic variation as it relates to human health

IARC class based on combined odds from multifactorial likelihood analysis, thresholds for class as per Easton et al. 2007 (PMID: 17924331). Class 1 Not Pathogenic based on posterior probability of pathogenicity = 7.44x10-115. There was no evidence for increased risk of breast cancer (OR 1.03; 95%CI 0.86-1.24) from case-control analysis of 83636 individuals. Nor for a deleterious effect of the variant when co-occurring with a pathogenic variant. Quantitative splicing analysis revealed an exon 3 exclusion rate of 13% in carriers compared to 3% in controls. Exon 3 exclusion from the variant allele is estimated at 20%.

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Multiple conflicting assertions about splice impact; ExAC: 0.5%(36/6594) Finnish chromosomes

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The variant is found in BRCA1-BRCA2,ENDOM-HEREDIC,BR-OV-HEREDIC panel(s).

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

Variant summary: The BRCA2 c.68-7T>A variant involves the alteration of a non-conserved intronic nucleotide. 2/5 splice prediction tools predict a significant impact on normal splicing. Although functional studies evaluating the splicing effect of this variant show a production of a exon 3 deletion transcript wild type control DNA also showed the production of this exon 3 deletion transcript albeit at a lesser quantitative amount (Sanz_2010 and Muller_2010). Furthermore, an additional functional study evaluating the variant of interest's effect on key aspects of BRCA2 function such homologous recombination and sensitivity to DNA damaging agents showed comparable abilities to the wild-type BRCA2. This variant was found in 282/118368 control chromosomes at a frequency of 0.0023824, which is approximately 3.2 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this variant is likely a benign polymorphism. This variant has been reported in many HBOC patients/families. It has been shown not to cosegregate with disease in two families (Santos_2014). In addition, the variant has been reported to co-occur with multiple different deleterious variants in BRCA1/2 (UMD), strongly suggesting for a benign outcome. Most of the clinical diagnostic laboratories in ClinVar have classified this variant as benign/likely benign. Taken together, this variant is classified as benign.

BRCA2: BP4, BS1, BS2

The c.68-7T>A variant has been identified in ~20 families (and 14 affected probands) from our laboratory with breast cancer and 82 times in the UMD-BRCA2 database. In the literature, the variant was identified in 12 of 5594 proband chromosomes from individuals with breast and ovarian cancer, although an inadequate number of control chromosomes were tested to establish the variants' frequency in the general population such that the full spectrum of benign variation may not yet been defined for this gene, and increasing the possibility that this may be a benign variant (Hilton 2002, Muller 2011, Santarosa 1999, Thirthagiri 2008). The variant was identified by the ESP project (0.0015 in EU; 0.0002 in AA), and was identified in the Exome Aggregation Consortium (ExAC) database in all populations listed (European (Non-Finnish), East Asian, African, Latino, South Asian, European (Finnish)) with an overall frequency of 0.002, suggesting this may be a low frequency variant. In addition, this variant was identified by our laboratory in one individual who was homozygous for this variant who developed bilateral breast cancer late in life and the variant was suspected to segregate (in heterozygous form) with breast cancer in two other individuals in the family. However, homozygous deleterious variants of the BRCA2 gene have been demonstrated to cause Fanconi-Anemia, which was not reported in this individual, and increasing the likelihood that this variant is benign, but this information does not rule out the possibility that this variant could have contributed to the cancer in this family. The variant is listed in dbSNP database as coming from a "clinical source" (ID#: rs81002830) and had a frequency of 0.002 in the 1000 Genomes project. This variant was identified in ClinVar (by Invitae as Likely Benign, GeneDx as Benign, Sharing clinical reports project derived from Myriad reports as Uncertain significance (as of 2012 - more recently, in a personal communication Myriad has re-classified this variant as a polymorphism), by the BIC database as Uncertain significance. The c.68-7T>A variant is located in the 3' splice region but does not affect the invariant -1 and -2 positions. However, positions -3 and -5 to -12 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 2 of 4 different programs. However, this information is not predictive enough to rule in or out pathogenicity. Studies have shown the increased rate of exon 3 skipping for this variant (20-30%), but this has also been observed in controls (Muller 2011, Thery 2011, Sanz 2010, Vreeswijk 2009, Houdayer 2012, Santorosa 1999). The c.68-7T>A variant and two other variants located at the same nucleotide position (c.68-7delT, and one c.68-78delAA) were all found to sometimes co-occur with a pathogenic BRCA2 mutation (Muller 2011), increasing the likelihood that this variant does not have clinical significance. In the UMD database, the variant was identified as co-occurring with another pathogenic variant 9x (4x in BRCA2 with: c.1796_1800delCTTAT (p.Ser599X) or c.5130_5133delTGTA (p.Tyr1710X)). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as benign.

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).