ClinVar Miner

Submissions for variant NM_032043.2(BRIP1):c.3099T>C (p.Pro1033=) (rs202228407)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163110 SCV000213620 likely benign Hereditary cancer-predisposing syndrome 2014-06-26 criteria provided, single submitter clinical testing
Invitae RCV001086591 SCV000252877 benign Familial cancer of breast; Fanconi anemia, complementation group J 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000409374 SCV000404578 likely benign Fanconi anemia, complementation group J 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000367622 SCV000404579 uncertain significance Neoplasm of the breast 2016-06-14 criteria provided, single submitter clinical testing
Counsyl RCV000409374 SCV000490041 likely benign Fanconi anemia, complementation group J 2016-10-11 criteria provided, single submitter clinical testing
Counsyl RCV000410011 SCV000490042 likely benign Neoplasm of ovary 2016-10-11 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000506953 SCV000600912 likely benign not specified 2016-10-05 criteria provided, single submitter clinical testing
Color RCV000163110 SCV000684247 benign Hereditary cancer-predisposing syndrome 2016-11-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588516 SCV000699712 benign not provided 2016-05-09 criteria provided, single submitter clinical testing Variant summary: The BRIP1 c.3099T>C (p.Pro1033Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 75/121402 control chromosomes (2 homozygotes), predominantly observed in the Latino subpopulation at a frequency of 0.0064778 (75/11578). This frequency is about 104 times the estimated maximal expected allele frequency of a pathogenic BRIP1 variant (0.0000625), suggesting this is likely a benign polymorphism found primarily in the populations of Latino origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
PreventionGenetics,PreventionGenetics RCV000506953 SCV000807142 benign not specified 2017-03-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000409374 SCV000883523 likely benign Fanconi anemia, complementation group J 2018-09-11 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588516 SCV000887998 benign not provided 2017-11-24 criteria provided, single submitter clinical testing

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