ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.*4T>C (rs201044568)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163803 SCV000214386 benign Hereditary cancer-predisposing syndrome 2015-06-28 criteria provided, single submitter clinical testing Other data supporting benign classification;Other strong data supporting benign classification
Invitae RCV000196409 SCV000252674 benign Neurofibromatosis, type 1 2015-08-16 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000374635 SCV000401817 likely benign Café-au-lait macules with pulmonary stenosis 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000196409 SCV000401818 likely benign Neurofibromatosis, type 1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000315760 SCV000401819 likely benign Neurofibromatosis-Noonan syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000372677 SCV000401820 likely benign Neurofibromatosis, familial spinal 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Genetic Services Laboratory, University of Chicago RCV000499461 SCV000595978 likely benign not specified 2016-06-15 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000499461 SCV001158763 benign not specified 2019-04-19 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000499461 SCV001365938 benign not specified 2018-12-28 criteria provided, single submitter clinical testing c.*4T>C in exon 58 of NF1: This variant is not expected to have clinical significance because it has been identified in 2.07% (341/16504) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs201044568).
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV000196409 SCV001479298 benign Neurofibromatosis, type 1 2020-10-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000499461 SCV001572453 benign not specified 2021-04-04 criteria provided, single submitter clinical testing Variant summary: NF1 c.*4T>C is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.0025 in 251374 control chromosomes in the gnomAD database, including 6 homozygotes. The observed variant frequency is approximately 12 fold of the estimated maximal expected allele frequency for a pathogenic variant in NF1 causing Neurofibromatosis Type 1 phenotype (0.00021), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.*4T>C in individuals affected with Neurofibromatosis Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign (n=5)/likely benign (n=2). Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV001553426 SCV001774290 likely benign not provided 2020-08-13 criteria provided, single submitter clinical testing

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