ClinVar Miner

Submissions for variant NM_000518.5(HBB):c.47G>A (p.Trp16Ter) (rs63750783)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000508601 SCV000603905 pathogenic not provided 2017-05-05 criteria provided, single submitter clinical testing The HBB c.47G>A, Trp15Ter variant, also known as Codon 15 (G->A); TGG->TAG, has been reported in individuals with beta thalassemia (Kazazian 1984, HbVar database and references therein). It is listed in the dbSNP variant database (rs63750783), and observed in the general population databases at a frequency of 0.04 percent in the 1000 Genomes Project, and 0.0085 percent in the Genome Aggregation Database (gnomAD). The variant introduces a premature termination codon, but the mRNA is resistant to nonsense-mediated decay (Neu-Yilik 2011); thus it is predicted to result in a truncated protein. Based on the above information, the variant is classified as pathogenic. REFERENCES Link to HbVar database for Codon 15 (G->A); TGG -> TAG: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=791 Kazazian HH Jr et al. Molecular characterization of seven beta-thalassemia mutations in Asian Indians. EMBO J. 1984; 3(3):593-6. Neu-Yilik G et al. Mechanism of escape from nonsense-mediated mRNA decay of human beta-globin transcripts with nonsense mutations in the first exon. RNA. 2011; 17(5):843-54.
Counsyl RCV000576738 SCV000677901 pathogenic beta Thalassemia 2016-02-01 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000576738 SCV000697135 pathogenic beta Thalassemia 2016-05-12 criteria provided, single submitter clinical testing Variant summary: The HBB c.47G>A (p.Trp16X) variant results in a premature termination codon, predicted to cause a truncated or absent HBB protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variant c.48G>A that gives the same codon change has been classified as pathogenic by our laboratory. One in silico tool predicts a damaging outcome for this variant. This variant was found in 14/121364 control chromosomes at a frequency of 0.0001154, which does not exceed the estimated maximal expected allele frequency of a pathogenic HBB variant (0.0111803). This variant has been reported in numerous beta thalassemia patients and is considered as a common disease variant. In addition, multiple reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
OMIM RCV000016657 SCV000036926 pathogenic beta^0^ Thalassemia 1992-04-01 no assertion criteria provided literature only
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000508601 SCV000605842 pathogenic not provided 2017-06-30 criteria provided, single submitter clinical testing

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