ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.5172G>A (p.Lys1724=) (rs17887014)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000436632 SCV000885833 benign not provided 2017-06-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000163276 SCV000213804 benign Hereditary cancer-predisposing syndrome 2014-06-19 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000436632 SCV000511467 likely benign not provided 2016-06-15 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
GeneDx RCV000436632 SCV000521064 benign not provided 2017-07-18 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.
Integrated Genetics/Laboratory Corporation of America RCV000436632 SCV000696398 benign not provided 2016-08-31 criteria provided, single submitter clinical testing Variant summary: The NF1 c.5172G>A (p.Lys1724Lys) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. This variant was found in 408/119678 control chromosomes (1 homozygote), predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.0047796 (314/65696). This frequency is about 23 times the estimated maximal expected allele frequency of a pathogenic NF1 variant (0.0002084), suggesting this is likely a benign polymorphism found primarily in the populations of European (Non-Finnish) origin. This variant has been reported in nF1 patients with classification of benign. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Invitae RCV000206463 SCV000261809 benign Neurofibromatosis, type 1 2018-01-10 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000218424 SCV000269457 benign not specified 2015-01-13 criteria provided, single submitter clinical testing p.Lys1745Lys in exon 37 of NF1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 0.5% (42/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (; dbSNP rs17887014).
PreventionGenetics RCV000218424 SCV000306275 benign not specified criteria provided, single submitter clinical testing

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