ClinVar Miner

Submissions for variant NM_000297.4(PKD2):c.1359A>G (p.Pro453=)

gnomAD frequency: 0.00985  dbSNP: rs17013754
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078579 SCV000110435 benign not specified 2015-12-14 criteria provided, single submitter clinical testing
Invitae RCV000233733 SCV000284557 benign Autosomal dominant polycystic kidney disease 2024-01-29 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000078579 SCV000303526 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001000326 SCV000451554 likely benign Polycystic kidney disease 2 2018-01-12 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.
Athena Diagnostics RCV000712678 SCV000843197 benign not provided 2017-09-21 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001000326 SCV001157035 benign Polycystic kidney disease 2 2019-08-02 criteria provided, single submitter clinical testing
GeneDx RCV000712678 SCV001752283 likely benign not provided 2020-09-21 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001000326 SCV002802521 likely benign Polycystic kidney disease 2 2022-04-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001291923 SCV000592879 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD2 p.Pro453Pro variant was not identified in the literature nor was it identified in the PKD2-LOVD database. The variant was identified in dbSNP (ID: rs17013754) as “With Benign allele.” This variant was identified in the 1000 Genomes Project in 60 of 5000 chromosomes (frequency: 0.012); The HAPMAP-YRI in 6 of 114 chromosomes (frequency: 0.05263158); NHLBI GO Exome Sequencing Project in 2 of 8600 European American (frequency: 0.000232558), and 133 of 4406 African American alleles (frequency: 0.03018611); Exome Aggregation Consortium database (August 8, 2016) in 388 (6 homozygous) of 121396 chromosomes (frequency: 0.003196) in the following populations: African in 346 of 10406 chromosomes (frequency: 0.03325) Latino in 17 of 11572 chromosomes (frequency: 0.001469) South Asian in 13 of 16510 chromosomes (frequency: 0.0007874) European (Non-Finnish) in 9 of 66734 chromosomes (frequency: 0.0001349), and Other in 3 of 908 chromosomes (frequency0.003304) but was not seen in East Asian and European (Finnish) populations, increasing the likelihood this could be a low frequency benign variant; ClinVar and Clinvitae database (Benign by Emory Genetics, Invitae, and Prevention Genetics); GeneInsight COGR database (benign by LMM) and ADPKD Mutation Database (Likely neutral). The p.Pro453Pro variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, and HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.

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