ClinVar Miner

Submissions for variant NM_000419.5(ITGA2B):c.2449-11C>T

gnomAD frequency: 0.00026  dbSNP: rs201702898
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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 RCV001122400 SCV004190241 uncertain significance Glanzmann thrombasthenia 2023-11-02 reviewed by expert panel curation The NM_000419.5(ITGA2B):c.2449-11C>T variant is a intronic variant variant that is not predicted by SpliceAI to impact splicing and the nucleotide is only moderately conserved, as shown by phyloP score of 1.044 (BP7). The highest population minor allele frequency in gnomAD v3.1.2 is 0.0007726 (32/41418 alleles) in the African/African American population. This intermediate allele frequency is lower than the ClinGen PD VCEP threshold (>0.00158) for BS1 but higher than the threshold (<0.0001) for PM2_Supporting so no allele frequency criteria were met. In addition, no cases of the variant segregating with Glanzmann thrombasthenia were found in the literature. In summary, this variant meets the criteria to be classified as VUS for autosomal recessive Glanzmann Thrombasthenia with the following ACMG/AMP applied, as specified by the ClinGen PD VCEP: BP7 (VCEP specifications version 2.1)
Illumina Laboratory Services, Illumina RCV001122400 SCV001281114 uncertain significance Glanzmann thrombasthenia 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001122400 SCV003294211 likely benign Glanzmann thrombasthenia 2023-08-17 criteria provided, single submitter clinical testing

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