ClinVar Miner

Submissions for variant NM_002185.5(IL7R):c.1020T>G (p.Leu340=)

gnomAD frequency: 0.00096  dbSNP: rs138731184
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Total submissions: 3
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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 RCV000880895 SCV004102835 likely benign Immunodeficiency 104 2023-11-14 reviewed by expert panel curation The c.1020T>G (p.Leu340=) variant (NM_002185.5) is a synonymous (silent) variant that is not predicted by SpliceAI and varSEAK to impact splicing (BP7). The filtering allele frequency (the lower threshold of the 95% CI of 84/24966) of the c.1020T>G variant in IL7R is 0.002614 for African/African American chromosomes by gnomAD v 2.1.1, which is higher than the ClinGen SCID VCEP threshold (>0.00126) for BS1, and therefore meets this criterion (BS1). No homozygous individuals have been reported (BS2_Supporting). In summary, this variant is classified as Likely Benign for autosomal recessive SCID based on ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP (specification version 1.0): BS1, BS2_Supporting, and BP7.
Invitae RCV000880895 SCV001024020 benign Immunodeficiency 104 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000880895 SCV001315714 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

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