chr11-5226930-C-T
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000518.5(HBB):āc.92G>Aā(p.Arg31Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000479 in 1,460,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R31G) has been classified as Pathogenic.
Frequency
Consequence
NM_000518.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251362Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135840
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460506Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726670
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
beta Thalassemia Pathogenic:4
Likely pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Pathogenic, no assertion criteria provided | curation | The ITHANET community portal, The Cyprus Institute of Neurology and Genetics | Nov 25, 2019 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jan 26, 2017 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing;curation | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Feb 02, 2021 | The HBB c.92G>A (p.Arg31Lys) variant (also known as IVS-I (-1) or Codon 30 (G>A)) changes the last nucleotide of exon 1 and is located at the exon 1-intron 1 junction. It is predicted to interfere with proper beta-globin mRNA splicing and may affect normal beta-globin mRNA production. This variant is associated with beta (0)-thalassemia (PMID: 2577233 (1989), and PMID: 19254853 (2009)). - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 11, 2024 | This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 31 of the HBB protein (p.Arg31Lys). This variant also falls at the last nucleotide of exon 1, which is part of the consensus splice site for this exon. This variant is present in population databases (rs33960103, gnomAD 0.006%). This missense change has been observed in individuals with beta thalassemia (PMID: 10815781, 26410419). This variant is also known as p.Arg30Lys, codon 30 (GāĆĆA) , IVS-I (-1). ClinVar contains an entry for this variant (Variation ID: 36337). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the c.92G nucleotide in the HBB gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 2915972, 18056002, 27828729). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. 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. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 01, 2024 | The HBB c.92G>A; p.Arg31Lys variant (also known as IVS-I (-1), codon 30 (G->A), or Arg30Lys when numbered from the mature protein, HbVar ID: 816, rs33960103, ClinVar Variation ID: 36337) is reported in the compound heterozygous state in individuals affected with beta (0) thalassemia (see link to HbVar, Kalaydjieva 1989, Maazoun 2016, Muniz 2000). This variant is only observed on two alleles in the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. This variant is located in the last nucleotide of exon 1 and computational analyses (Alamut v.2.11) predict that this variant may impact splicing by severely weakening the nearby canonical donor splice site. Additionally, another variant at this nucleotide (Hb Monroe variant, c.92G>C; p.Arg31Thr, HbVar ID: 290) has been reported in individuals with beta (0) thalassemia, is shown to affect splicing, and is considered pathogenic (Vidaud 1989). Based on available information, the p.Arg31Lys variant is considered to be likely pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Kalaydjieva L et al. The molecular basis of beta thalassaemia in Bulgaria. J Med Genet. 1989 Oct;26(10):614-8. PMID: 2577233. Maazoun F et al. Symptomatic extramedullary haematopoiesis in beta-thalassemia: A retrospective single centre study. Rev Med Interne. 2016 Jan;37(1):5-12. French. PMID: 26410419. Muniz A et al. Beta-thalassaemia in Cubans: novel allele increases the genetic diversity at the HBB locus in the Caribbean. Am J Hematol. 2000 May;64(1):7-14. PMID: 10815781. Vidaud M et al. A 5' splice-region G----C mutation in exon 1 of the human beta-globin gene inhibits pre-mRNA splicing: a mechanism for beta+-thalassemia. Proc Natl Acad Sci U S A. 1989 Feb;86(3):1041-5. PMID: 2915972. - |
Hb SS disease;C0019025:Hereditary persistence of fetal hemoglobin;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6;CN322236:Beta-thalassemia HBB/LCRB Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at