ClinVar Miner

Submissions for variant NM_000419.5(ITGA2B):c.2621T>G (p.Ile874Ser)

gnomAD frequency: 0.38983  dbSNP: rs5911
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Platelet Disorders Variant Curation Expert Panel, ClinGen RCV000288776 SCV001478547 benign Glanzmann thrombasthenia 2020-11-10 reviewed by expert panel curation The ITGA2B c.2621T>G (p.Ile874Ser) missense variant has been reported many times in the literature as an alloantigenic site. This variant has been observed in cis with several other Glanzmann thrombasthenia variants, including the pathogenic Tyr471Ter and c.1440-13_1440-1del ITGA2B variants and the Pro189Ser ITGB3 variant (PMID: 25728920). It is present in gnomAD at an overall allele frequency of 0.39177 (and 0.43954 in the non-Finnish European population). Computational evidence suggest no impact on the gene/gene product, with a REVEL score of 0.055. In summary, this variant meets criteria to be classified as benign for GT. GT-specific criteria applied: BA1, BP2, BP4.
PreventionGenetics, part of Exact Sciences RCV000246752 SCV000304086 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000288776 SCV000403361 benign Glanzmann thrombasthenia 2018-03-06 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000246752 SCV000515962 benign not specified 2015-09-08 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000288776 SCV001717671 benign Glanzmann thrombasthenia 2024-01-31 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001730470 SCV001980744 benign Glanzmann thrombasthenia 1 2021-08-19 criteria provided, single submitter clinical testing
OMIM RCV000003025 SCV000023183 association BAK PLATELET-SPECIFIC ANTIGEN 2021-04-13 no assertion criteria provided literature only

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