ClinVar Miner

Submissions for variant NM_000206.3(IL2RG):c.963G>A (p.Leu321=)

gnomAD frequency: 0.00002  dbSNP: rs181901993
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Total submissions: 2
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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 RCV000941390 SCV004102795 likely benign X-linked severe combined immunodeficiency 2023-11-14 reviewed by expert panel curation The c.963G>A (p.Leu321=) variant (NM_000206.3) is a synonymous (silent) variant that is not predicted by SpliceAI, varSEAK, and NNSplice. BP7 is met. It occurs at an intermediate allele frequency, with a popmax filtering allele frequency in gnomAD v2.1.1 of 0.0001435 (based on 7/14709 alleles in the East Asian population) which is below the SCID VCEP established threshold of >0.00249. for BS1 and above the PM2 threshold of <0.000124. (BS1 not met, BA1 not met, PM2_Supporting not met). Additionally, three adult hemizygous males with this variant are present in the East Asian population in gnomAD v2.1.1 and one additional in the Other population (BS2). In summary, this variant is classified as a Likely Benign for autosomal recessive SCID based on ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP (specification version 1.0).
Labcorp Genetics (formerly Invitae), Labcorp RCV000941390 SCV001087276 benign X-linked severe combined immunodeficiency 2024-02-01 criteria provided, single submitter clinical testing

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