ClinVar Miner

Submissions for variant NM_032043.2(BRIP1):c.1626C>T (p.Ser542=) (rs373709958)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000590445 SCV000885119 likely benign not provided 2017-09-06 criteria provided, single submitter clinical testing The p.Ser542Ser variant (rs373709958) has not been reported in the medical literature, nor has it been previously identified in our laboratory. The variant is listed in the Genome Aggregation Database (gnomAD) browser with an allele frequency of 0.22% in the South Asian population (identified in 67 out of 30,670 chromosomes; 0 homozygotes), and is classified as benign/likely benign in ClinVar (Variant ID: 183873). The nucleotide at position 1,626 is moderately conserved, and computational analyses suggest that this variant does not alter splicing (Alamut software v2.9.0). Based on the available evidence, the p.Ser542Ser variant is classified as likely benign.
Ambry Genetics RCV000162732 SCV000213200 likely benign Hereditary cancer-predisposing syndrome 2014-12-10 criteria provided, single submitter clinical testing
Color RCV000162732 SCV000684143 likely benign Hereditary cancer-predisposing syndrome 2015-08-11 criteria provided, single submitter clinical testing
GeneDx RCV000421920 SCV000512419 benign not specified 2015-04-17 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.
Integrated Genetics/Laboratory Corporation of America RCV000590445 SCV000699670 benign not provided 2017-04-06 criteria provided, single submitter clinical testing Variant summary: The BRIP1 c.1626C>T (p.Ser542Ser) variant involves the alteration of a conserved nucleotide causing a synonymous change, which 3/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts the remove of ESE binding sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 48/121252 (1/2525) control chromosomes, predominantly observed in the South Asian cohort, 38/16490 (1/434), which is about 37 times the estimated maximal expected allele frequency of a pathogenic BRIP1 variant, 1/16000. Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of South Asian origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. Taken together, this variant is classified as benign.
Invitae RCV000200498 SCV000253618 likely benign Familial cancer of breast; Fanconi anemia, complementation group J 2017-12-28 criteria provided, single submitter clinical testing

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