ClinVar Miner

Submissions for variant NM_000527.5(LDLR):c.1987+10G>T (rs375846192)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
LDLR-LOVD, British Heart Foundation RCV000238481 SCV000295795 likely benign Familial hypercholesterolemia 1 2016-03-25 criteria provided, single submitter research
Integrated Genetics/Laboratory Corporation of America RCV000587398 SCV000697218 uncertain significance not provided 2017-05-01 criteria provided, single submitter clinical testing Variant summary: The LDLR c.1987+10G>T variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that the variant creates an SRp40 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 8 of 121282 control chromosomes from all ethnicities, but was exclusively observed in the European (Non-Finnish) subpopulation at a frequency of 0.00012 (8/66658 chromosomes). This frequency is approximately equal to the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508), suggesting this may be a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. In addition, one reputable database has classified this variant as likely benign. To our knowledge, the variant of interest has not been reported in affected individuals via publications, nor has it been evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a VUS-possibly benign until additional information becomes available.

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