ClinVar Miner

Submissions for variant NM_144696.6(AXDND1):c.3032-3141G>A (rs1410592)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000243457 SCV000312206 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000615797 SCV000351498 benign Nephrotic syndrome, idiopathic, steroid-resistant 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Integrated Genetics/Laboratory Corporation of America RCV000587451 SCV000699388 benign not provided 2016-07-05 criteria provided, single submitter clinical testing Variant summary: The NPHS2 c.954C>T (p.Ala318Ala) variant involves the alteration of a non-conserved nucleotide resulting in a synonymous change. One in silico tool (MutationTaster) predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing, howevere these predictions are yet to be confirmed by the functional studies. This variant was found in 75096/121278 control chromosomes (including 23360 homozygotes) at a frequency of 0.6192055, which is approximately 350 times the estimated maximal expected allele frequency of a pathogenic NPHS2 variant (0.0017678), suggesting this variant is a common benign polymorphism. The variant of interest has also been cited as a polymorphism in published reports (Rachmadi_2015). Taken together, this variant is classified as Benign.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000615797 SCV000733958 benign Nephrotic syndrome, idiopathic, steroid-resistant no assertion criteria provided clinical testing

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