ClinVar Miner

Submissions for variant NM_000448.3(RAG1):c.906C>A (p.Asp302Glu)

gnomAD frequency: 0.02153  dbSNP: rs4151030
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen RCV003398575 SCV004102812 benign Recombinase activating gene 1 deficiency 2023-11-14 reviewed by expert panel curation The c.906C>A (NM_000448.3) variant in RAG1 is a missense variant predicted to cause substitution of Aspartic Acid by Glutamic Acid at amino acid 302 (p.Asp302Glu). The filtering allele frequency (the lower threshold of the 95% CI of 1968/24958) of the c.906C>A variant in RAG1 is 0.07684 for African/African American chromosomes by gnomAD v2.1.1, which is higher than the ClinGen SCID VCEP threshold (>0.00872) for BA1, and therefore meets this criterion (BA1). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, BA1, as specified by the ClinGen SCID VCEP (VCEP specifications version 1).
GeneDx RCV000127710 SCV000171289 benign not specified 2013-12-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000224203 SCV000281102 benign not provided 2015-02-17 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000127710 SCV000304369 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000303729 SCV000371676 benign Histiocytic medullary reticulosis 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.
Illumina Laboratory Services, Illumina RCV000358641 SCV000371677 benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001084268 SCV000646377 benign Combined immunodeficiency with skin granulomas; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2024-01-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000224203 SCV001472881 benign not provided 2023-11-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002490423 SCV002797300 likely benign Combined immunodeficiency due to partial RAG1 deficiency; Combined immunodeficiency with skin granulomas; Histiocytic medullary reticulosis; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive 2022-04-26 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000224203 SCV005316147 benign not provided criteria provided, single submitter not provided
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000030394 SCV000053063 benign Severe combined immunodeficiency disease 2015-06-04 no assertion criteria provided clinical testing

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