ClinVar Miner

Submissions for variant NM_000211.5(ITGB2):c.741+1G>A

dbSNP: rs1131691763
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000494539 SCV000582778 pathogenic not provided 2015-11-13 criteria provided, single submitter clinical testing The c.741+1 G>A splice site variant in the ITGB2 gene destroys the canonical splice donor site inintron 6. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that issubject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is usedfor protein translation. In addition, the c.741+1 G>A splice variant was not observed inapproximately 6,500 individuals of European and African American ancestry in the NHLBI ExomeSequencing Project, indicating it is not a common benign variant in these populations. Although thisvariant has not been previously reported to our knowledge, we interpret c.741+1 G>A as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV003522981 SCV004317740 likely pathogenic Leukocyte adhesion deficiency 1 2023-08-14 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 of the ITGB2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ITGB2 are known to be pathogenic (PMID: 22134107, 25703682). This variant has not been reported in the literature in individuals affected with ITGB2-related conditions. ClinVar contains an entry for this variant (Variation ID: 430061). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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