Submissions for variant NM_139058.3(ARX):c.306GGC[11] (p.Ala115dup)

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Minimum conflict level: Report conflict between different conditions
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Total submissions: 8

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000145054	SCV000192094	benign	not specified	2014-02-11	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV001081429	SCV000291348	likely benign	Developmental and epileptic encephalopathy, 1; Intellectual disability, X-linked, with or without seizures, arx-related	2024-01-30	criteria provided, single submitter	clinical testing
GeneDx	RCV000152797	SCV000564595	likely benign	not provided	2023-02-06	criteria provided, single submitter	clinical testing	See Variant Classification Assertion Criteria.
Ambry Genetics	RCV000624905	SCV000741999	benign	Inborn genetic diseases	2023-08-17	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, 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.
Mendelics	RCV000990556	SCV001141567	benign	Developmental and epileptic encephalopathy, 1	2019-05-28	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000152797	SCV002546154	likely benign	not provided	2024-07-01	criteria provided, single submitter	clinical testing	ARX: BP3
PreventionGenetics, part of Exact Sciences	RCV003422032	SCV004118434	uncertain significance	ARX-related disorder	2023-10-12	criteria provided, single submitter	clinical testing	The ARX c.333_335dupGGC variant is predicted to result in an in-frame duplication (p.Ala115dup). This variant was reported as a maternally-inherited variant in two unrelated male individuals with intellectual disability/developmental delay (reported as c.333_334ins(GCG) in patients #39589 and #41263, Gronskov et al. 2004. PubMed ID: 15199382). However, this variant was not found in a similarly affected family member of the patient #39589 but was identified in an unaffected male control in the same study, suggested by the author that this variant is a rare polymorphism. This variant is reported in 0.078% of alleles in individuals of African descent in gnomAD and has been documented in a hemizygous individual (http://gnomad.broadinstitute.org/variant/X-25031776-T-TGCC). In ClinVar, this variant has conflicting interpretations ranging from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/157755/). This variant falls within a low complexity region, therefore the allele frequency data should be interpreted with caution. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Eurofins Ntd Llc (ga)	RCV000152797	SCV000202187	uncertain significance	not provided	2014-03-18	no assertion criteria provided	clinical testing

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