ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.2289C>T (p.Val763=) (rs437168)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000246255 SCV000310566 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001094501 SCV000411563 benign Congenital nephrotic syndrome 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Athena Diagnostics Inc RCV000346778 SCV000677367 benign Finnish congenital nephrotic syndrome 2017-04-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586547 SCV000698500 benign not provided 2016-10-31 criteria provided, single submitter clinical testing Variant summary: The NPHS1 c.2289C>T (p.Val763Val) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 10368/121400 control chromosomes (1310 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.4543533 (4728/10406). This frequency is about 135 times the estimated maximal expected allele frequency of a pathogenic NPHS1 variant (0.0033541), suggesting this is a benign common polymorphism found primarily in the populations of African origin. Therefore, this variant is classified as Benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000346778 SCV000743920 benign Finnish congenital nephrotic syndrome 2014-10-10 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000346778 SCV000733875 benign Finnish congenital nephrotic syndrome no assertion criteria provided clinical testing

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