ClinVar Miner

Submissions for variant NM_000211.5(ITGB2):c.1888G>A (p.Glu630Lys)

gnomAD frequency: 0.00539  dbSNP: rs2230531
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000514987 SCV000610037 likely benign not provided 2017-06-16 criteria provided, single submitter clinical testing
Invitae RCV001083759 SCV000634160 benign Leukocyte adhesion deficiency 1 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001083759 SCV001298393 likely benign Leukocyte adhesion deficiency 1 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.
Fulgent Genetics, Fulgent Genetics RCV001083759 SCV002802949 likely benign Leukocyte adhesion deficiency 1 2022-04-22 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001083759 SCV003920072 likely benign Leukocyte adhesion deficiency 1 2022-07-15 criteria provided, single submitter clinical testing This variant has been reported in the literature in at least 10 individuals with chronic lymphocytic leukemia (CLL) (Goldin 2016 PMID:27629550, Blackburn 2017 PMID:28490671); however at least 1 study did not identify an enrichment of the variant in cases vs. controls. This variant was also identified in 3 individuals with congenital heart defects (Russell 2019 PMID:31453292). This variant is present in the Genome Aggregation Database (Highest reported MAF 2.1% (226/10616) including 8 homozygotes (https://gnomad.broadinstitute.org/variant/21-44888885-C-T?dataset=gnomad_r3). This variant is present in ClinVar, with multiple labs classifying this variant as Benign or Likely Benign (Variation ID:445547). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign.

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