chr11-5227158-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2PP5_Very_StrongBP4
The ENST00000647020.1(HBB):c.-137C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 554,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
ENST00000647020.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000198 AC: 11AN: 554166Hom.: 0 Cov.: 5 AF XY: 0.0000200 AC XY: 6AN XY: 299838
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:4
Published functional studies demonstrate a damaging effect, as transcient transfection of the gene with c.-137C>G in Hela cells showed reduction of beta-globin mRNA production (PMID: 6086605); Also known as -87C>G using alternate nomenclature; No data available from control populations to assess the frequency of this variant; Located in a regulatory region; This variant is associated with the following publications: (PMID: 2446680, 6188062, 22975760, 6280057, 7655036, 28503568, 2837728, 291719, 21228398, 31395865, 38927598, 37816374, 2375912, 35336809, 9163586, 7507641, 39359944, 38322302, 28385923, 36054783, 6086605, 27821015, 39859286, 20704537, 28399358) -
The HBB c.-137C>G variant (rs33941377, HbVar ID: 758), also known as -87 (C->G), is reported in the literature in multiple individuals affected with beta+ thalassemia (see HbVar database link and references therein, Orkin 1982). This variant is located in a conserved region of the beta globin gene promoter and functional analyses demonstrated a significant reduction in transcription (Treisman 1983). This variant is reported in ClinVar (Variation ID: 15464) and absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Based on available information, this variant is considered to be pathogenic. References: Orkin SH et al. Linkage of beta-thalassaemia mutations and beta-globin gene polymorphisms with DNA polymorphisms in human beta-globin gene cluster. Nature. 1982 Apr 15;296(5858):627-31. PMID: 6280057. Treisman R et al. Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes. Nature. 1983 Apr 14;302(5909):591-6. PMID: 6188062. -
The HBB c.-137C>G pathogenic variant (also known as -87C>G) is located in the 5'-UTR of the HBB gene, and has been reported to deleteriously affected the promoter and transcription level of the beta-globin gene (PMIDs: 28503568 (2017), 2917193 (1989)). This variant is associated with beta(+)-thalassemia (PMIDs: 28503568 (2017), 21228398 (2011), 2917193 (1989), 2446680 (1988), 6280057 (1982)). Based on the available information, this variant is classified as pathogenic. -
This variant occurs in a non-coding region of the HBB gene. It does not change the encoded amino acid sequence of the HBB protein. For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this variant affects HBB function (PMID: 2837728, 6188062). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 15464). This variant is also known as -87C>G. This variant has been observed in individuals with beta-thalassemia (PMID: 2375912, 2446680, 2917193). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). -
beta Thalassemia Pathogenic:2Other:1
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NM_000518.4(HBB):c.-137C>G(aka -87C>G) is classified as likely pathogenic in the context of Hb beta chain-related hemoglobinopathy and is associated with beta thalassemia. Sources cited for classification include the following: PMID 2446680, 2375912, 2917193 and 2837728. Classification of NM_000518.4(HBB):c.-137C>G(aka -87C>G) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
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alpha Thalassemia;C0002895: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
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Beta thalassemia intermedia Pathogenic:1
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Beta-plus-thalassemia Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at