ClinVar Miner

Submissions for variant NM_000419.5(ITGA2B):c.1600+16G>T

dbSNP: rs199614885
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen RCV003096022 SCV005061676 benign Glanzmann thrombasthenia 2024-04-16 reviewed by expert panel curation The NM_000419.5(ITGA2B):c.1600+16G>T variant is an intronic variant that is not predicted by SpliceAI to impact splicing (Delta scores 0.00). In addition, it occurs at a nucleotide that is not conserved as shown by phyloP score of 0.2397 (BP7). The highest population minor allele frequency in gnomAD v4.0.0 is 0.002865 (250/75040alleles) in the African/African-American population, which is higher than the ClinGen PD VCEP threshold (>0.0024), and therefore meets this criterion (BA1). In summary this variant is classified as Benign for autosomal recessive Glanzmann thrombasthenia, with ACMG criteria applied as specified by the PD VCEP: BA1, BP7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002266275 SCV002548011 uncertain significance not specified 2022-05-31 criteria provided, single submitter clinical testing Variant summary: ITGA2B c.1600+16G>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00018 in 251450 control chromosomes. To our knowledge, no occurrence of c.1600+16G>T in individuals affected with ITGA2B-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV003096022 SCV002960868 benign Glanzmann thrombasthenia 2024-01-04 criteria provided, single submitter clinical testing

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