ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.1231A>G (p.Thr411Ala)

gnomAD frequency: 0.00398  dbSNP: rs115316501
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Total submissions: 6
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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 RCV000640084 SCV004102831 likely benign Immunodeficiency 104 2023-11-14 reviewed by expert panel curation The c.1231A>G (NM_002185.5) variant in IL7R is a missense variant predicted to cause substitution of Threonine by Alanine at amino acid 411 (p.Thr411Ala). The filtering allele frequency (the lower threshold of the 95% CI of 329/24950) of the c.1231A>G variant in IL7R is 0.01172 in exomes (4 homozygous reported) and 0.01126 in genomes (1 homozygous reported) for African/African American chromosomes by gnomAD v2.1.1. Both values are higher than the ClinGen SCID VCEP threshold (0.00126) for BS1 and therefore meet this criterion (BS1). Five (05) adult homozygous individuals with this variant are present in gnomAD v2.1.1 (African/African American)(BS2_Supporting). The variant has not been identified in the literature. In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: BS1 and BS2_Supporting. (VCEP specifications version 1).
GeneDx RCV000121223 SCV000513282 likely benign not specified 2017-03-03 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 RCV000640084 SCV000761672 benign Immunodeficiency 104 2024-01-31 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000640084 SCV002808513 likely benign Immunodeficiency 104 2022-02-18 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV003457640 SCV004185263 benign not provided 2023-11-01 criteria provided, single submitter clinical testing IL7R: BP4, BS1, BS2
ITMI RCV000121223 SCV000085394 not provided not specified 2013-09-19 no assertion provided reference population

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