ClinVar Miner

Submissions for variant NM_000282.4(PCCA):c.300+3930C>T (rs767934206)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000585986 SCV000696476 uncertain significance not provided 2017-07-11 criteria provided, single submitter clinical testing Variant summary: The PCCA c.300+3930C>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 and ESE finder predicts no effect on ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. The variant is not found in the large control database ExAC, but the exome capture technology used to generate ExAC does not cover deep intronic variants such as the variant of interest. However, the large control database gnomAD, which includes whole genome sequence data, has identified this variant at a frequency of 0.0011313 (35/30938 control chromosomes; 1 homozygote) in all ethnicities, but was predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.002136 (32/14978 chromosomes; 1 homozygote), neither of which exceeds the estimated maximal expected allele frequency of a pathogenic PCCA variant (0.003446). The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS-possibly benign until additional information becomes available.

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