ClinVar Miner

Submissions for variant NM_004646.4(NPHS1):c.65C>T (p.Ala22Val)

gnomAD frequency: 0.00023  dbSNP: rs116617171
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center RCV000490334 SCV000267424 uncertain significance Finnish congenital nephrotic syndrome 2016-03-18 criteria provided, single submitter reference population
Counsyl RCV000490334 SCV000796327 likely benign Finnish congenital nephrotic syndrome 2017-12-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000903298 SCV001047757 benign not provided 2024-10-04 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002271466 SCV002555874 benign not specified 2022-06-14 criteria provided, single submitter clinical testing Variant summary: NPHS1 c.65C>T (p.Ala22Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.001 in 242312 control chromosomes (gnomAD), predominantly at a frequency of 0.013 within the East Asian subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in NPHS1 causing Nephrotic Syndrome, Type 1 (0.0034), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. Four ClinVar submitters have assessed the variant since 2014: one classified the variant as of uncertain significance, one as likely benign, and two as benign. Based on the evidence outlined above, the variant was classified as benign.
Natera, Inc. RCV000490334 SCV001461580 benign Finnish congenital nephrotic syndrome 2020-09-16 no assertion criteria provided clinical testing

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