rs34500389

Positions:

• chr11-5227103-G-A
• chr11-5227103-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP5 BP4

The ENST00000647020.1(HBB):​c.-82C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 821,440 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 Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000011 (0 hom.)
• Consequence: HBB ENST00000647020.1 5_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3 U:3
• Conservation: PhyloP100: 0.522

Genes affected

HBB (HGNC:4827): (hemoglobin subunit beta) The alpha (HBA) and beta (HBB) loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains. Mutant beta globin causes sickle cell anemia. Absence of beta chain causes beta-zero-thalassemia. Reduced amounts of detectable beta globin causes beta-plus-thalassemia. The order of the genes in the beta-globin cluster is 5'-epsilon -- gamma-G -- gamma-A -- delta -- beta--3'. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-5227103-G-A is Pathogenic according to our data. Variant chr11-5227103-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 439163.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Pathogenic=1}. Variant chr11-5227103-G-A is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBB	NM_000518.5			upstream_gene_variant		ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4			upstream_gene_variant		1	NM_000518.5	ENSP00000333994	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000110 AC: 9 AN: 821440 Hom.: 0 Cov.: 11 AF XY: 0.0000116 AC XY: 5 AN XY: 432430

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000121

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000374

Gnomad4 OTH exome AF: 0.0000508

GnomAD4 genome Cov.: 33

Bravo AF: 0.0000264

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

beta Thalassemia Pathogenic:1 Uncertain:1

Pathogenic, no assertion criteria provided	curation	The ITHANET community portal, The Cyprus Institute of Neurology and Genetics	Nov 25, 2019	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 26, 2017	- -

not provided Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Mar 28, 2023	The HBB c.-82C>T variant (also known as -32 (C>T), rs34500389, HbVar ID: 2536) is reported in the literature in individuals with abnormal hematological findings, but the exact phenotype is unclear (Eng 2007, Hoppe 2013, Wang 2015). This variant is reported in ClinVar (Variation ID: 439163) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant occurs in the 5' untranslated region, one nucleotide upstream of the ATAA box of the beta globin promoter. However, in vitro assays are conflicting on the effects of the variant on TATA-binding protein affinity and gene expression (Kircher 2019, Ponomarenko 2020). Due to conflicting information, the clinical significance of the c.-82C>T variant is uncertain at this time. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Eng B. Three new beta-globin gene promoter mutations identified through newborn screening. Hemoglobin. 2007;31(2):129-34. PMID: 17486493. Hoppe CC. Prenatal and newborn screening for hemoglobinopathies. Int J Lab Hematol. 2013 Jun;35(3):297-305. PMID: 23590658. Kircher M et al. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun. 2019 Aug 8;10(1):3583. PMID: 31395865. Ponomarenko M et al. Unannotated single nucleotide polymorphisms in the TATA box of erythropoiesis genes show in vitro positive involvements in cognitive and mental disorders. BMC Med Genet. 2020 Oct 22;21(Suppl 1):165. PMID: 33092544. Wang S et al. Mutation screening for thalassaemia in the Jino ethnic minority population of Yunnan Province, Southwest China. BMJ Open. 2015 Dec 29;5(12):e010047. PMID: 26715484. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 18, 2023	The HBB c.-82C>T variant is located in the TATA-box in the promoter of the beta-globin gene. This variant is associated with beta(+) thalassemia, and has been observed in a screening study of individuals with hypochromic microcytic anemia and/or positive Hb profiles (PMID: 26715484 (2015)). Co-occurrence of this variant with Hb S results in a Hb S/beta+ thalassemia phenotype (PMID: 17486493 (2007)). A functional study showed this variant had near normal HBB promoter activity, however the result is inconclusive since other known deleterious variants in the promoter also showed similar activities (PMID: 31395865 (2019)). An additional study indicated this variant results in a small 1.5 fold increase in binding affinity to TATA-binding proteins, the physiological effects of which are uncertain (PMID: 33092544 (2020)). Previous names for this variant include -32 (C>T). Based on the available information, this variant is classified as pathogenic. -

HBB-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 29, 2024

The HBB c.-82C>T variant is located in the 5' untranslated region. This variant was reported in an individual with beta thalassemia (Eng et al. 2007. PubMed ID: 17486493). Functional studies of this variant indicated that the expression effect on HBB was not significant, and the promoter activity was 0.96 of wildtype levels (Supplementary Table 10, Kircher et al. 2019. PubMed ID: 31395865). Of note, other variants in the promoter region of HBB have been reported in individuals with beta thalassemia (Eng et al. 2007. PubMed ID: 17486493; Ropero et al. 2017. PubMed ID: 28385923; Supplementary Table 10, Kircher et al. 2019. PubMed ID: 31395865). This variant has not been reported in a large population database, indicating it is rare. In ClinVar, this variant has conflicting interpretations including uncertain significance (3) and pathogenic (2) (https://www.ncbi.nlm.nih.gov/clinvar/variation/439163/). Taken together, we interpret this variant to be likely pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 10, 2024

Variant summary: HBB c.-82C>T (also described as -32C>T in the literature) affects a non-conserved nucleotide that is located in the untranscribed region, one nucleotide upstream to the conserved ATAAA sequence (i.e. the TATA box) therefore, it could affect gene expression. A saturation mutagenesis study reported that this variant had no significant effect on gene expression (Kircher_2019). While another study predicted that this variant changes the HBB TATA box sequence to a more canonical form (i.e. CATAAA to TATAAA) and the authors also demonstrated that the variant resulted in an increased in vitro affinity for TATA-binding protein (TBP) in electrophoretic mobility shift assay (EMSA), concluding that carriers of this variant may be susceptible to mild thalassemia because of the elevated amount of synthesized beta-chains (Ponomarenko_2020). The variant was absent in 31390 control chromosomes (gnomAD). The variant, c.-82C>T has been reported in the literature in an infant who also carried the HbS variant (c.20A>T (p.Glu7Val)) with a hemoglobin pattern suggestive of beta+ thalassemia (Eng_2007), and was also reported in individuals with abnormal hematological findings found during screening, but without specifying the exact phenotype and genotype (Hoppe_2013, Wang_2015). These data do not allow clear conclusions about association of the variant with Beta Thalassemia. The following publications have been ascertained in the context of this evaluation (PMID: 17486493, 23590658, 26715484, 22122796, 31395865, 33092544, 32033288, 33734896). Based on the evidence outlined above, the variant was classified as VUS. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	15
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34500389; hg19: chr11-5248333;