ClinVar Miner

Submissions for variant NM_000267.3(NF1):c.7692C>T (p.Ser2564=) (rs17881980)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000590709 SCV000604486 benign not provided 2018-03-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV000163372 SCV000213911 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
GeneDx RCV000590709 SCV000525365 benign not provided 2016-09-02 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.
Illumina Clinical Services Laboratory,Illumina RCV000381914 SCV000401797 likely benign Café-au-lait macules with pulmonary stenosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000205128 SCV000401798 likely benign Neurofibromatosis, type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000323782 SCV000401799 likely benign Neurofibromatosis, familial spinal 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000376583 SCV000401800 likely benign Neurofibromatosis-Noonan syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590709 SCV000696407 benign not provided 2016-05-12 criteria provided, single submitter clinical testing Variant summary: The NF1 c.7692C>T (p.Ser2564Ser) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools calculating no significant effect on splicing, although these predictions have yet to be functionally assessed. This variant was found in the large, broad control population, ExAC, with an allele frequency of 403/121392 (11 homozygotes, 1/301, freq: 0.00332), predominantly in the African cohort, 371/10404 (1/28, 0.03566, 11 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic NF1 variant of 1/4798 (0.0002084). Therefore, suggesting that the variant of interest is a common polymorphism found in population(s) of African origin. This variant, to our knowledge, has not been reported in affected individuals via publications, although, multiple clinical laboratories cite the variant as "benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Invitae RCV000205128 SCV000262326 benign Neurofibromatosis, type 1 2018-01-25 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000222530 SCV000269464 benign not specified 2014-11-24 criteria provided, single submitter clinical testing Ser2585Ser in exon 53 of NF1: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 3.1% (136/4406) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs17881980).
PreventionGenetics RCV000222530 SCV000306298 benign not specified criteria provided, single submitter clinical testing

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