ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.7110-7T>A

gnomAD frequency: 0.00770  dbSNP: rs113034899
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000178589 SCV000230701 benign not specified 2015-01-12 criteria provided, single submitter clinical testing
Invitae RCV000205026 SCV000260197 benign Autosomal recessive polycystic kidney disease 2024-01-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000178589 SCV000315823 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000205026 SCV000464069 likely benign Autosomal recessive polycystic kidney disease 2018-01-13 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000178589 SCV000918004 benign not specified 2017-12-21 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.7110-7T>A variant involves the alteration of a non-conserved intronic nucleotide. 3/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 659/275722 control chromosomes (12 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.025178 (601/23870). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic PKHD1 variant (0.0070711), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. By applying ACMG rules (BS1, BS2), the variant was classified as Benign.
GeneDx RCV001567004 SCV001790610 likely benign not provided 2020-01-06 criteria provided, single submitter clinical testing
Natera, Inc. RCV000205026 SCV002078031 benign Autosomal recessive polycystic kidney disease 2017-08-09 no assertion criteria provided clinical testing

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