ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.1241C>T (p.Thr414Met)

gnomAD frequency: 0.00456  dbSNP: rs2229232
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Total submissions: 5
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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 RCV000545508 SCV004098872 benign Immunodeficiency 104 2023-10-10 reviewed by expert panel curation The NM_002185.5(IL7R):c.1241C>T (p.Thr414Met) missense variant occurs at a frequency too high for the disease. The filtering allele frequency based on the South Asian population (upper bound of 95% CI of 1076/30502 observed alleles) is 0.03353 in gnomAD v2.1.1, which is above the SCID-VCEP BA1 threshold (>0.00566). Also, 46 adult homozygous individuals with this variant are present in gnomAD v2.1.1 (BS2_Supporting). 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 and BS2_Supporting (SCID VCEP specifications version 1.0).
Illumina Laboratory Services, Illumina RCV000545508 SCV000457158 benign Immunodeficiency 104 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.
GeneDx RCV000121225 SCV000513283 benign not specified 2016-03-22 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 RCV000545508 SCV000638915 benign Immunodeficiency 104 2024-01-31 criteria provided, single submitter clinical testing
ITMI RCV000121225 SCV000085396 not provided not specified 2013-09-19 no assertion provided reference population

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