ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.4866G>A (p.Val1622=) (rs17880521)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163317 SCV000213845 benign Hereditary cancer-predisposing syndrome 2014-11-21 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
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000215429 SCV000269456 benign not specified 2014-11-20 criteria provided, single submitter clinical testing p.Val1643Val in exon 37 of NF1: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.2% (21/8600) of Eu ropean American chromosomes and 4.3% (191/4406) of African American chromosomes by the NHLBI Exome sequencing project (http://evs.gs.washington.edu/EVS/; dbSNP rs17880521).
PreventionGenetics,PreventionGenetics RCV000215429 SCV000306273 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000293980 SCV000401761 likely benign Café-au-lait macules with pulmonary stenosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000348881 SCV000401762 likely benign Neurofibromatosis-Noonan syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000396178 SCV000401763 likely benign Neurofibromatosis, type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000309383 SCV000401764 likely benign Neurofibromatosis, familial spinal 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000587787 SCV000521675 benign not provided 2016-06-22 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 RCV000587787 SCV000554968 benign not provided 2019-03-06 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000587787 SCV000604480 benign not provided 2017-11-15 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587787 SCV000696397 benign not provided 2016-08-30 criteria provided, single submitter clinical testing Variant summary: The NF1 c.4866G>A (p.Val1622Val) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 3/5 splice prediction tools predict no significant impact on splicing. ESE finder predicts that this variant may affect ESE site of SC35. This variant was found in 687/121388 control chromosomes (11 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0441346 (459/10400). This frequency is about 212 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 African origin. This variant has been reported in NF1 patients and RT-PCR showed no changes on transcripts; authors classified this variant as a polymorphism (Boulandet, 2000). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.

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