ClinVar Miner

Submissions for variant NM_133433.4(NIPBL):c.5101T>C (p.Ser1701Pro)

gnomAD frequency: 0.00024  dbSNP: rs139819353
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000591666 SCV000702354 likely benign not specified 2017-01-20 criteria provided, single submitter clinical testing
GeneDx RCV000828951 SCV000970656 likely benign not provided 2018-06-08 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV002532384 SCV002991712 likely benign Cornelia de Lange syndrome 1 2024-02-01 criteria provided, single submitter clinical testing
Revvity Omics, Revvity Omics RCV002532384 SCV003815915 uncertain significance Cornelia de Lange syndrome 1 2021-03-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000591666 SCV004099999 likely benign not specified 2023-09-19 criteria provided, single submitter clinical testing Variant summary: NIPBL c.5101T>C (p.Ser1701Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 396030 control chromosomes (i.e., 49 heterozygotes), predominantly at a frequency of 0.00059 within the Latino subpopulation in the gnomAD database. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance, however are not suggestive of a variant associated with highly-penetrant, early-onset, autosomal dominant disease. To our knowledge, no occurrence of c.5101T>C in individuals affected with Cornelia De Lange Syndrome 1 and no experimental evidence demonstrating its impact on protein function have been reported. Four submitters have reported clinical-significance assessments for this variant to ClinVar after 2014; three submitters classified the variant as likely benign, and one submitter classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.
CeGaT Center for Human Genetics Tuebingen RCV000828951 SCV004160893 likely benign not provided 2022-05-01 criteria provided, single submitter clinical testing NIPBL: BS1

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