ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.168C>T (p.Ser56=) (rs17881168)

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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 RCV000163256 SCV000213784 benign Hereditary cancer-predisposing syndrome 2014-11-19 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
Invitae RCV000590494 SCV000262455 benign not provided 2019-03-06 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000215995 SCV000269445 benign not specified 2014-11-20 criteria provided, single submitter clinical testing p.Ser56Ser in exon 2 of NF1: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 2% (180/8598) of Euro pean American chromosomes and 0.4% (16/4406) of African American chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP rs1 7881168).
PreventionGenetics,PreventionGenetics RCV000215995 SCV000306240 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000324800 SCV000401673 likely benign Neurofibromatosis-Noonan syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000381546 SCV000401674 likely benign Neurofibromatosis, familial spinal 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000289551 SCV000401675 likely benign Café-au-lait macules with pulmonary stenosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000205406 SCV000401676 likely benign Neurofibromatosis, type 1 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000590494 SCV000518951 benign not provided 2016-09-27 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000590494 SCV000604499 benign not provided 2017-05-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590494 SCV000696387 benign not provided 2016-08-31 criteria provided, single submitter clinical testing Variant summary: The NF1 c.168C>T (p.Ser56Ser) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and ESE finder predicts the loss of ESE binding sites. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 1449/121304 (1/83, 14 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic NF1 variant of 1/4798, suggesting this variant is likely a benign polymorphism. Multiple clinical diagnostic laboratories cite the variant as "benign." Therefore, the variant of interest is classified as Benign.

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