ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.7490-10C>T

gnomAD frequency: 0.00032  dbSNP: rs201304767
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001336 SCV001158526 benign Polycystic kidney disease, adult type 2019-05-29 criteria provided, single submitter clinical testing
GeneDx RCV001577031 SCV001804343 likely benign not provided 2020-07-21 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001577031 SCV002585540 benign not provided 2022-09-01 criteria provided, single submitter clinical testing PKD1: BS1, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292436 SCV001480932 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 c.7490-10C>T variant was not identified in the literature nor was it identified in the ClinVar, GeneInsight-COGR, LOVD 3.0, and PKD1-LOVD, databases. The variant was identified in dbSNP (ID: rs201304767) as “NA”; in ADPKD Mutation Database 1X as Likely Neutral and in the 1000 Genomes Project in 4 of 5000 chromosomes (frequency: 0.0008). Furthermore, the variant was identified in control databases in 138 of 260822 chromosomes at a frequency of 0.0005 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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