ClinVar Miner

Submissions for variant NM_032043.2(BRIP1):c.1474-3T>C (rs552752779)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164980 SCV000215673 uncertain significance Hereditary cancer-predisposing syndrome 2018-01-09 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient or conflicting evidence,In silico models in agreement (benign)
Color RCV000164980 SCV000902752 benign Hereditary cancer-predisposing syndrome 2016-11-17 criteria provided, single submitter clinical testing
Counsyl RCV000662494 SCV000785013 uncertain significance Fanconi anemia, complementation group J; Neoplasm of ovary 2017-03-14 criteria provided, single submitter clinical testing
GeneDx RCV000430204 SCV000512417 benign not specified 2015-09-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Genetic Services Laboratory, University of Chicago RCV000430204 SCV000593766 uncertain significance not specified 2016-12-27 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000348888 SCV000404610 uncertain significance Fanconi anemia 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000387131 SCV000404611 uncertain significance Neoplasm of the breast 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589721 SCV000699667 benign not provided 2017-05-08 criteria provided, single submitter clinical testing Variant summary: The BRIP1 c.1474-3T>C variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing, though ESE finder predicts the variant may introduce an SF2/ASF ESE site at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in the large control database ExAC in 33 of 120864 control chromosomes from all ethnicities, but was predominantly observed in the South Asian subpopulation at a frequency of 0.001879 (31/16496). This frequency is about 30 times the estimated maximal expected allele frequency of a pathogenic BRIP1 variant (0.0000625), strongly suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. Multiple clinical diagnostic laboratories have conflicting classifications for this variant including uncertain significance (4x in ClinVar) and benign (1x in ClinVar). The variant of interest has not, to our knowledge, been reported in affected individuals via publications, nor has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV000199588 SCV000255149 uncertain significance Familial cancer of breast; Fanconi anemia, complementation group J 2017-07-19 criteria provided, single submitter clinical testing

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