ClinVar Miner

Submissions for variant NM_000489.6(ATRX):c.4365GGA[4] (p.Glu1464del)

dbSNP: rs398123423
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000150063 SCV000110826 benign not specified 2013-12-13 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000150063 SCV000150391 benign not specified 2016-03-22 criteria provided, single submitter clinical testing
GeneDx RCV001355369 SCV000570369 benign not provided 2019-03-26 criteria provided, single submitter clinical testing
Invitae RCV000640852 SCV000762453 likely benign Alpha thalassemia-X-linked intellectual disability syndrome 2021-12-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV000715760 SCV000846591 benign History of neurodevelopmental disorder 2017-08-02 criteria provided, single submitter clinical testing Does not segregate with disease in family study (genes with incomplete penetrance);General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;Other data supporting benign classification
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001252425 SCV001428181 uncertain significance Intellectual disability 2019-01-01 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355369 SCV001550241 likely benign not provided no assertion criteria provided clinical testing The ATRX p.Glu1426del variant was not identified in the literature. The variant was identified in dbSNP (ID: rs398123423) and ClinVar (classified as likely benign by GeneDx and Invitae; classified as benign by Genetic Services Laboratory University of Chicago, EGL Genetic Diagnostics and Ambry Genetics). The variant was identified in control databases in 300 of 200007 chromosomes at a frequency of 0.0015 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 50 of 16081 chromosomes (freq: 0.003109), European (non-Finnish) in 217 of 91347 chromosomes (freq: 0.002376), Ashkenazi Jewish in 12 of 7581 chromosomes (freq: 0.001583), Other in 5 of 5218 chromosomes (freq: 0.000958), Latino in 9 of 27673 chromosomes (freq: 0.000325), African in 4 of 18738 chromosomes (freq: 0.000214), East Asian in 2 of 14663 chromosomes (freq: 0.000136), and South Asian in 1 of 18706 chromosomes (freq: 0.000053). This variant is an in-frame deletion resulting in the removal of a glutamic acid (glu) residue at codon 1426; the impact of this alteration on ATRX protein function is not known. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV001355369 SCV001741187 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001355369 SCV001799821 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000150063 SCV001965790 benign not specified no assertion criteria provided clinical testing

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