Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| ARUP Laboratories, |
RCV001000827 | SCV001157892 | benign | Polycystic kidney disease, adult type | 2018-10-01 | criteria provided, single submitter | clinical testing | |
| Fulgent Genetics, |
RCV001000827 | SCV002805042 | likely benign | Polycystic kidney disease, adult type | 2021-07-17 | criteria provided, single submitter | clinical testing | |
| Ce |
RCV003392727 | SCV004129899 | benign | not provided | 2022-07-01 | criteria provided, single submitter | clinical testing | PKD1: BS1, BS2 |
| Department of Pathology and Laboratory Medicine, |
RCV001292175 | SCV001480824 | benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKD1 p.Arg3972= variant was identified in 11 of 460 proband chromosomes (frequency: 0.0239) from individuals or families with PKD, and the study classified the variant as a polymorphism (Rossetti 2012). The variant was also identified in dbSNP (ID: rs77634115) as “With Benign allele”, ClinVar (1x as benign by Prevention Genetics), Clinvitae (as benign), ADPKD Mutation Database (as likely neutral). In addition, a different nucleotide change, c.11916C>T, with the same protein consequence, has been classified as benign in several databases, including ClinVar and Clinvitae. The variant was not identified in LOVD 3.0, and PKD1-LOVD databases. The variant was identified in control databases in 200 of 164424 chromosomes at a frequency of 0.0012, in the following populations: African in 181 (1 homozygous) of 15410 chromosomes (freq: 0.012), Latino in 12 of 25050 chromosomes (freq. 0.0005), Other in 1 of 4606 chromosomes (freq. 0.0002), European (Finnish) in 4 of 66128 (freq. 0.0001), European (Non-Finnish) in 4 of 66128 chromosomes (freq. 0.00006), and South Asian in 1 of 23662 chromosomes (freq. 0.00004), increasing the likelihood that this may be a low frequency benign variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017). The p.Arg3972= 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, 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. |