Submissions for variant NM_007315.4(STAT1):c.1222-5T>C

gnomAD frequency: 0.00135  dbSNP: rs191364028

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	RCV000238853	SCV000297230	benign	not specified	2015-11-20	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000316458	SCV000425815	benign	Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency	2018-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	RCV000768097	SCV000898998	likely benign	Immunodeficiency 31B; Autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome; Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency	2021-12-22	criteria provided, single submitter	clinical testing	STAT1 NM_007315.3 exon 15 c.1222-5T>C: This variant has not been reported in the literature but is present in 0.2% (95/34420) of Latino alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/2-191850391-A-G). This variant is present in ClinVar (Variation ID:252674). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant; splice prediction tools suggest that this variant may not affect splicing. However, further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000768097	SCV001107502	benign	Immunodeficiency 31B; Autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome; Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency	2024-01-29	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV001529790	SCV001748002	likely benign	not provided	2024-06-01	criteria provided, single submitter	clinical testing	STAT1: BS2
Mayo Clinic Laboratories, Mayo Clinic	RCV001529790	SCV004225970	uncertain significance	not provided	2023-02-24	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV001529790	SCV001743870	likely benign	not provided		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV001529790	SCV001799193	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV001529790	SCV001932002	likely benign	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV001529790	SCV001968082	likely benign	not provided		no assertion criteria provided	clinical testing