ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.7461A>G (p.Thr2487=) (rs149924365)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164361 SCV000214995 likely benign Hereditary cancer-predisposing syndrome 2014-06-02 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000220944 SCV000269463 benign not specified 2014-11-24 criteria provided, single submitter clinical testing Thr2487Thr in exon 51 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 0.3% (14/4406) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (; dbSNP rs149924365).
Invitae RCV001084347 SCV000284512 benign Neurofibromatosis, type 1 2020-11-26 criteria provided, single submitter clinical testing
GeneDx RCV000679413 SCV000522536 likely benign not provided 2020-06-15 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000679413 SCV000806316 likely benign not provided 2017-10-10 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000679413 SCV000884241 benign not provided 2017-12-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000220944 SCV000917886 likely benign not specified 2017-12-04 criteria provided, single submitter clinical testing Variant summary: The NF1 c.7398A>G (p.Thr2466Thr) 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. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SF2/ASF. However, these predictions have yet to be confirmed by functional studies. This variant was found in 49/277206 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001873 (45/24030). This frequency is about 9 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. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases, nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as likely benign.

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