Submissions for variant NM_001065.4(TNFRSF1A):c.625+10A>G

gnomAD frequency: 0.38055  dbSNP: rs1800693

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000244183	SCV000306335	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000338370	SCV000380679	benign	TNF receptor-associated periodic fever syndrome (TRAPS)	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000244183	SCV000540559	benign	not specified	2016-03-28	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, one paper claims association with MS
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001618221	SCV000605406	benign	not provided	2023-11-29	criteria provided, single submitter	clinical testing
Invitae	RCV000338370	SCV001720366	benign	TNF receptor-associated periodic fever syndrome (TRAPS)	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV001618221	SCV001846747	benign	not provided	2015-03-03	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 24174586, 22801493, 23624563)
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV002262595	SCV002543107	benign	Autoinflammatory syndrome	2022-01-14	criteria provided, single submitter	clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	RCV000244183	SCV004102054	benign	not specified	2023-11-12	criteria provided, single submitter	clinical testing	This variant is classified as Benign based on local population frequency. This variant was detected in 55% of patients studied by a panel of primary immunodeficiencies. Number of patients: 53. Only high quality variants are reported.
OMIM	RCV000030698	SCV000053359	risk factor	Multiple sclerosis, susceptibility to, 5	2012-08-23	no assertion criteria provided	literature only
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas	RCV001354058	SCV001548222	uncertain significance	Susceptibility to severe coronavirus disease (COVID-19)	2021-02-09	no assertion criteria provided	research
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000244183	SCV001740646	benign	not specified		no assertion criteria provided	clinical testing
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas	RCV001836715	SCV001792248	uncertain significance	Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR6	2021-08-07	no assertion criteria provided	research	NA
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000244183	SCV001931384	benign	not specified		no assertion criteria provided	clinical testing
GenomeConnect, ClinGen	RCV001618221	SCV002074811	not provided	not provided		no assertion provided	phenotyping only	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas	RCV003398577	SCV004102847	uncertain significance	Associated with severe COVID-19 disease	2023-07-01	no assertion criteria provided	research