11-5225832-G-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The NM_000518.5(HBB):c.316-106C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,168,954 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
NM_000518.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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HBB | ENST00000335295.4 | c.316-106C>G | intron_variant | Intron 2 of 2 | 1 | NM_000518.5 | ENSP00000333994.3 | |||
HBB | ENST00000647020.1 | c.316-106C>G | intron_variant | Intron 2 of 2 | ENSP00000494175.1 | |||||
HBB | ENST00000475226.1 | n.248-106C>G | intron_variant | Intron 1 of 1 | 2 | |||||
HBB | ENST00000633227.1 | n.*132-106C>G | intron_variant | Intron 2 of 2 | 3 | ENSP00000488004.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000266 AC: 27AN: 1016752Hom.: 0 AF XY: 0.0000305 AC XY: 16AN XY: 524838
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not provided Pathogenic:8
The HBB c.316-106C>G variant (rs34690599, HbVar ID: 891), also known as IVS-II-745 C>G, is reported in the heterozygous state in individuals with beta(+) thalassemia minor and in the homozygous and compound heterozygous state in individuals with transfusion-dependent beta-thalassemia major (Orkin 1982, Ropero 2013, HbVar database). Functional characterization of the variant indicates an accumulation of beta globin transcript containing intron 2 sequences (Orkin 1982). This variant is also reported in ClinVar (Variation ID: 15457). This is an intronic variant in a weakly conserved nucleotide, but computational analyses (Alamut v.2.11) predict that this variant impacts splicing by creating a cryptic donor splice site, consistent with the observed phenotype in functional studies. Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Orkin S et al. Linkage of beta-thalassaemia mutations and beta-globin gene polymorphisms with DNA polymorphisms in human beta-globin gene cluster. Nature. 1982; 296(5858):627-31. PMID: 6280057. Ropero P et al. Association in cis of the mutations +20 (C>T) in the 5' untranslated region and IVS-II-745 (C>G) on the beta-globin gene. Hemoglobin. 2013; 37(2):112-8. PMID: 23425204. -
HBB: PM2, PP4:Moderate, PS4:Moderate, PP3 -
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No data available from control populations to assess the frequency of this variant; This variant is associated with the following publications: (PMID: 2375910, 28399358, 22975760, 19657842, 6280057, 23425204, 2200760, 25408857, 36882369, 32860008, 11559932, 2713503, 25155404, 9163586, 6188062) -
This sequence change falls in intron 2 of the HBB gene. It does not directly change the encoded amino acid sequence of the HBB protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of 55 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with β-thalassemia (PMID: 2713503, 11559932, 23425204, 25155404). This variant is also known as IVS-II-745C>G or IVS2-745C>G. ClinVar contains an entry for this variant (Variation ID: 15457). Studies have shown that this variant alters HBB gene expression (PMID: 6188062). Studies have shown that this variant results in the activation of a cryptic splice site in intron 2 (PMID: 6188062). For these reasons, this variant has been classified as Pathogenic. -
The variant found in at least one symptomatic individual. The variant occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and several have a phenotype known to be consistent with disease. The variant has been shown to be damaging to protein function(s) relevant to disease mechanism. -
beta Thalassemia Pathogenic:5Other:1
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NM_000518.4(HBB):c.316-106C>G(aka IVS2-745C>G) is classified as pathogenic in the context of Hb beta chain-related hemoglobinopathy; it is associated with beta thalassemia and is classified as a beta-plus variant. Sources cited for classification include the following: PMID 11559932 and 6188062. Classification of NM_000518.4(HBB):c.316-106C>G(aka IVS2-745C>G) is based on the following criteria: This is a well-established pathogenic variant in the literature that 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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Beta-thalassemia HBB/LCRB Pathogenic:3
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Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with HBB-related hemoglobinopathies, including beta thalassemia (OMIM). Dominant negative is also a suggested mechanism (PMID: 29700171). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. Variable severity has been reported in sickle cell patients carrying the same variants (PMID: 31788855). In addition, clinical severity of beta-thalassemia patients is also dependent on whether variants in HBB are heterozygous, homozygous or compound heterozygous, and the amount of residual protein that is expressed (PMID: 20301599). (I) 0217 - Non-coding variant with known effect. RNA studies on transfected cells have shown that this variant creates a cryptic splice site within intron 2 leading to retention of 165bps of the intronic sequence (PMID: 6188062). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v3) <0.01 for a recessive condition (5 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by multiple clinical laboratories in ClinVar. It is one of the most common pathogenic Mediterranean variants in this gene and has been reported as homozygous or compound heterozygous in individuals with beta-thalassemia (PMIDs: 20301599, 31903828). This variant has also been reported in individuals with sickle cell disease when in compound heterozygous with the HbS variant (PMID: 31788855). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
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Dominant beta-thalassemia Pathogenic:1
PS3, PM2, PM3, PP4, PP5. -
HBB-related disorder Pathogenic:1
The HBB c.316-106C>G variant is predicted to interfere with splicing. This variant (also described as "IVS-II-745 C>G") has been reported in the heterozygous, compound heterozygous, and homozygous states in multiple individuals with beta thalassemia (Baysal et al. 1992. PubMed ID: 1390250; Sadiq et al. 2001. PubMed ID: 11559932; Ropero et al. 2013. PubMed ID: 23425204; Carrocini et al. 2017. PubMed ID: 28366028; Amin et al. 2020. PubMed ID: 33335418). It has also been observed to co-segregate with disease in a large, multi-generational family from the North Caucasus region currently living in Cyprus (Ergoren et al. 2021. PubMed ID: 33987626). Transcriptional analysis found that this variant leads to the formation of a cryptic splice donor site resulting in the insertion of 55 amino acid residues into the beta-globin mRNA (Treisman et al. 1983. PubMed ID: 6188062). This variant has not been reported in the gnomAD database, indicating this variant is rare. This variant is interpreted as pathogenic. -
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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Hb SS disease 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