ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.2715+7del

gnomAD frequency: 0.00313  dbSNP: rs551015414
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176594 SCV000228271 benign not specified 2017-03-13 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000265356 SCV000464102 uncertain significance Autosomal recessive polycystic kidney disease 2016-06-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000265356 SCV000557646 benign Autosomal recessive polycystic kidney disease 2025-01-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000176594 SCV001360736 benign not specified 2019-09-06 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.2715+7delG alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00099 in 282696 control chromosomes, predominantly at a frequency of 0.0097 within the African or African-American subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 1.4 fold of the estimated maximal expected allele frequency for a pathogenic variant in PKHD1 causing Polycystic Kidney and Hepatic Disease phenotype (0.0071), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no occurrence of c.2715+7delG in individuals affected with Polycystic Kidney and Hepatic Disease and no experimental evidence demonstrating its impact on protein function have been reported. Three submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign (2x)/ uncertain significance (1x). Based on the evidence outlined above, the variant was classified as benign.
Natera, Inc. RCV000265356 SCV002081018 benign Autosomal recessive polycystic kidney disease 2017-08-09 no assertion criteria provided clinical testing

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