ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.412G>A (p.Val138Ile)

gnomAD frequency: 0.72524  dbSNP: rs1494555
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Total submissions: 15
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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 RCV000015965 SCV004242294 benign Immunodeficiency 104 2024-01-23 reviewed by expert panel curation NM_002185.5(IL7R):c.412G>A is a missense variant predicted to cause substitution of Valine by Isoleucine at amino acid 138 (p.Val138Ile). The filtering allele frequency (the lower threshold of the 95% CI of 65661/74940 alleles) of the c.412G>A variant in IL7R is 0.8743 for African/African American chromosomes by gnomAD v.4, which is higher than the ClinGen SCID VCEP threshold (>0.00566) for BA1 and therefore meets this criterion (BA1). Additionally, 367924 homozygous have been described. In summary, this variant meets the criteria to be classified as Benign for autosomal recessive SCID, based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: BA1 (VCEP specifications version 1).
PreventionGenetics, part of Exact Sciences RCV000121214 SCV000308737 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000015965 SCV000457143 benign Immunodeficiency 104 2018-01-13 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 RCV000121214 SCV000539381 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: 1 paper published in 1998 claimed variant was pathogenic for SCID based on identification in 1 proband.
Mendelics RCV000015965 SCV001136819 benign Immunodeficiency 104 2019-05-28 criteria provided, single submitter clinical testing
Pathology and Clinical Laboratory Medicine, King Fahad Medical City RCV000121214 SCV001438932 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000015965 SCV001720365 benign Immunodeficiency 104 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV001711072 SCV001943006 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 20952689, 21326139, 18687755)
Genome-Nilou Lab RCV000015965 SCV001980935 benign Immunodeficiency 104 2021-08-19 criteria provided, single submitter clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan RCV000121214 SCV004233015 benign not specified 2024-01-24 criteria provided, single submitter clinical testing This variant is classified as Benign based on local population frequency. This variant was detected in 83% of patients studied by a panel of primary immunodeficiencies. Number of patients: 79. Only high quality variants are reported.
OMIM RCV000015965 SCV000036232 uncertain significance Immunodeficiency 104 1998-12-01 no assertion criteria provided literature only
ITMI RCV000121214 SCV000085385 not provided not specified 2013-09-19 no assertion provided reference population
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000121214 SCV001742615 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000121214 SCV001932121 benign not specified no assertion criteria provided clinical testing
GenomeConnect, ClinGen RCV001711072 SCV002074671 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.

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