ClinVar Miner

Submissions for variant NM_000022.4(ADA):c.192G>A (p.Lys64=)

gnomAD frequency: 0.00009  dbSNP: rs144168646
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Total submissions: 7
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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 RCV000892626 SCV004102822 likely benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency 2023-11-14 reviewed by expert panel curation The c.192G>A (p.Lys64=) variant (NM_000022.4) in ADA is a synonymous (silent) variant that is not predicted by SpliceAI and varSEAK to impact splicing (BP7). The highest population minor allele frequency in gnomAD v2.1.1 is 0.002796 (67/19946 alleles) in the East Asian population, which is higher than the ClinGen SCID VCEP threshold (>0.00161) for BS1 and therefore meets this criterion (BS1). 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): BP7 and BS1.
Invitae RCV000892626 SCV001036514 benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000892626 SCV001303125 likely benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genetic Services Laboratory, University of Chicago RCV001818676 SCV002064926 likely benign not specified 2020-07-24 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000892626 SCV002808248 likely benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency 2022-01-28 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003968149 SCV004780917 likely benign ADA-related condition 2020-12-09 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000892626 SCV002095335 likely benign Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency 2020-04-29 no assertion criteria provided clinical testing

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