ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.339A>C (p.Glu113Asp)

gnomAD frequency: 0.00125  dbSNP: rs11567735
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Total submissions: 4
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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 RCV000640071 SCV004242293 likely benign Immunodeficiency 104 2024-01-10 reviewed by expert panel curation NM_002185.5(IL7R):c.339A>C is a missense variant predicted to cause substitution of Glutamic Acid by Aspartic Acid at amino acid 113 (p.Glu113Asp). The filtering allele frequency (the lower threshold of the 95% CI of 308/75016) of the c.339A>C variant in IL7R is 0.003481 for African/African American chromosomes by gnomAD v4, which is higher than the ClinGen SCID VCEP threshold (>0.00126) for BS1, and therefore meets this criterion (BS1). To our knowledge, this variant has not been reported in the literature in individuals affected with IL7R-related conditions or in functional studies. In summary, this variant meets the criteria to be classified as Likely Benign variant for autosomal recessive severe combined immunodeficiency due to IL7R deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: BS1_met (VCEP specifications version 1).
GeneDx RCV000425029 SCV000513281 likely benign not specified 2015-08-10 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.
Invitae RCV000640071 SCV000761659 likely benign Immunodeficiency 104 2024-01-29 criteria provided, single submitter clinical testing
Baylor Genetics RCV000640071 SCV001529833 uncertain significance Immunodeficiency 104 2018-05-09 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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