chr11-5226820-C-T

Variant names:

• chr11-5226820-C-T
• rs35004220
• NM_000518.5:c.93-21G>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_000518.5(HBB):​c.93-21G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,608,186 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:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: HBB NM_000518.5 intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:34 O:1
• Conservation: PhyloP100: -0.0740

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 Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-5226820-C-T is Pathogenic according to our data. Variant chr11-5226820-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15454.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226820-C-T is described in Lovd as [Pathogenic]. Variant chr11-5226820-C-T is described in Lovd as [Pathogenic]. Variant chr11-5226820-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.93-21G>A		intron_variant	Intron 1 of 2	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.93-21G>A		intron_variant	Intron 1 of 2	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152100 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000155 AC: 39 AN: 250944 Hom.: 0 AF XY: 0.000184 AC XY: 25 AN XY: 135630

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000869

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000300

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000125 AC: 182 AN: 1456086 Hom.: 0 Cov.: 34 AF XY: 0.000134 AC XY: 97 AN XY: 724710

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000134

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000127

Gnomad4 OTH exome AF: 0.000349

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152100 Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8 AN XY: 74300

Gnomad4 AFR AF: 0.0000242

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000226 Hom.: 0

Bravo AF: 0.000174

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:34 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:11

Nov 21, 2022

Mayo Clinic Laboratories, Mayo Clinic

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 27, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 29, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBB c.93-21G>A variant has been reported in the published literature in multiple individuals affected with beta(+) thalassemia (PMIDs: 6264477 (1981), 6264391 (1981), 1390250 (1992), 30704988 (2019), 35330400 (2022), 37034522 (2023)). Studies have shown that this variant causes aberrant splicing in the majority of the expressed transcripts (PMIDs: 6292841 (1982), 6895866 (1981), 6956887 (1982), 8378346 (1993), 28868125 (2017), 30704988 (2019)). The frequency of this variant in the general population, 0.0037 (10/2668 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -

Aug 26, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 1 of the HBB gene. It does not directly change the encoded amino acid sequence of the HBB protein. This variant is present in population databases (rs35004220, gnomAD 0.03%). This variant has been observed in individual(s) with HBB-related conditions (PMID: 1967205, 2200760, 28366028, 28391758). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS-I-110G>A. ClinVar contains an entry for this variant (Variation ID: 15454). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. For these reasons, this variant has been classified as Pathogenic. -

Dec 10, 2021

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In vitro RNA and functional studies demonstrate a damaging effect with the creation of an alternative splice site causing abnormal gene splicing (Busslinger et al., 1981).; Also known as IVS-I-110G>A; This variant is associated with the following publications: (PMID: 6264391, 21797703, 25087612, 22975760, 28670940, 27979672, 31456457, 31130284, 21228398, 26372288, 1967205, 26016902, 1390250, 6895866, 6264477, 28391758, 28366028, 28667000, 14555304, 9163586, 31589614, 15609277, 9629495, 12702481, 2577233) -

Nov 30, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBB c.93-21G>A variant (rs35004220, ClinVar ID: 15454, HbVar ID: 827), also known as IVS-I-110 G>A, is reported in the literature in multiple individuals affected with beta+ thalassemia (Carrocini 2017, Hussain 2017, Jalilian 2017). This variant is one of the most common beta-thalassemia alleles in Mediterranean and Middle-Eastern countries (Kaplan 1990, HbVar database and references therein). Based on available information, this variant is considered to be pathogenic. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/hbvar.html Carrocini GCS et al. Mutational Profile of Homozygous beta-Thalassemia in Rio de Janeiro, Brazil. Hemoglobin. 2017 Jan;41(1):12-15. PMID: 28366028. Hussain A et al. Rare beta-Globin Gene Mutations in Pakistan. Hemoglobin. 2017 Mar;41(2):100-103. PMID: 28670940. Jalilian M et al. The Frequency of HBB Mutations Among beta-Thalassemia Patients in Hamadan Province, Iran. Hemoglobin. 2017 Jan;41(1):61-64. PMID: 28391758. Kaplan F et al. Beta-thalassemia genes in French-Canadians: haplotype and mutation analysis of Portneuf chromosomes. Am J Hum Genet. 1990 46(1):126-32. PMID: 1967205. -

Jun 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

HBB: PM3:Very Strong, PM2, PP4 -

May 03, 2020

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 27, 2021

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 23, 2021

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 24, 2021

AiLife Diagnostics, AiLife Diagnostics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

beta Thalassemia Pathogenic:9 Other:1

Nov 25, 2019

The ITHANET community portal, The Cyprus Institute of Neurology and Genetics

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

- -

Oct 18, 2019

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NM_000518.4(HBB):c.93-21G>A is classified as pathogenic and is associated with beta thalassemia. Sources cited for classification include the following: PMID 2200760, 1390250, 8330981, 1967205, 1390250, 2200760, 6264477, 6264391. Classification of NM_000518.4(HBB):c.93-21G>A 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. -

May 02, 2023

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The heterozygous c.93-21G>A variant in HBB was identified by our study in four affected members of one family with beta thalassemia. The c.93-21G>A variant in HBB has been identified in over 160 individuals with beta thalassemia (‚Äã‚ÄãPMID: 6264477, PMID: 6264391, PMID: 24106605, PMID: 28391758, PMID: 1390250, PMID: 2200760), but has been identified in 0.03% (37/128830) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs35004220). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID: 15454) and has been interpreted as pathogenic by multiple submitters. Of these 160 individuals, 138 were homozygotes (PMID: 1390250, PMID: 28391758, PMID: 24106605, PMID: 2200760), and 11 were compound heterozygotes who carried pathogenic or likely pathogenic variants in trans (PMID: 2200760, ClinVar Variation ID: 15436, ClinVar Variation ID: 15402, ClinVar Variation ID: 15457, ClinVar Variation ID: 15239; PMID: 6264391, ClinVar Variation ID: 15060; PMID: 24106605, ClinVar Variation ID: 15402, ClinVar Variation ID: 15415), which increases the likelihood that the c.93-21G>A variant is pathogenic. RT-PCR analysis of RNA from affected tissue shows evidence of altered splicing of exon 2, resulting in 19bp insertion, frameshift, and premature truncation (PMID: 16421096); altered splicing was also seen in HeLa cells (PMID: 6895866) and in a humanized mouse model (PMID: 16421096). This variant is located in the 3' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PS3, PM2_Supporting, PM3_VeryStrong (Richards 2015). -

-

Pediatric Molecular Hematology, Schneider Children's Medical Center of Israel

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 16, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 06, 2021

Centogene AG - the Rare Disease Company

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Nov 03, 2022

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.93-21G>A variant in HBB, also known as IVS-I-110 G>A, has been reported in numerous individuals with beta-thalassemia and is one of the most common beta-thalassemia alleles in Mediterranean and Middle-Eastern countries (Kaplan 1990 PMID: 1967205, (Carrocini 2017 PMID: 28366028, Hussain 2017 PMID: 28670940, Jalilian 2017 PMID: 28391758, Baysal 1992 PMID: 1390250) https://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=827). It has also been reported in ClinVar (Variation ID 15454) and has been identified in 14/68028 European chromosomes by gnomAD (https://gnomad.broadinstitute.org). In vitro functional studies support an impact on splicing (Busslinger 1981 PMID: 6895866). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta thalassemia. ACMG/AMP Criteria applied: PM2_Supporting, PS3_Moderate, PM3_very strong. -

Mar 22, 2022

3billion, Medical Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 28391758, 28366028, 2200760). It was observed to be in trans with the other variant (3billion dataset). The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000015454). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0001668). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

May 12, 2021

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Beta-thalassemia HBB/LCRB Pathogenic:6

-

Intergen, Intergen Genetics and Rare Diseases Diagnosis Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 17, 2020

Genetics and Molecular Pathology, SA Pathology

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2024

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

- -

Aug 29, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 09, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. The 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 a suspected effect. Recombinant in vitro functional studies show this variant causes aberrant splicing resulting in a frameshift and premature termination codon, which ultimately results in severely reduced expression of beta-globin (PMID: 29700171). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (42 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is one of the most common Mediterranean variants associated with beta-thalassemia and has been reported as heterozygous, homozygous, or compound heterozygous in individuals with beta-thalassemia. This variant has also been reported in individuals with sickle cell disease when in compound heterozygous with the HbS variant (PMIDs: 28667000, 28366028, 31899996, 31788855, 33851260). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Jul 22, 2024

Institute of Human Genetics, Heidelberg University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn genetic diseases Pathogenic:1

Aug 31, 2015

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.93-21G>A pathogenic mutation (also known as IVS1-110G>A), located in coding intron 1 of the HBB gene, results from a G>A substitution 21 nucleotides before coding exon 2. This mutation was first described in an individual of Turkish Cypriot origin with severe thalassemia intermedia who was compound heterozygous for another pathogenic HBB mutation (Westaway D, Williamson R. Nucleic Acids Res. 1981;9:1777-1788). In a population of Turkish patients affected with beta thalassemia major, 33 individuals were homozygous for this pathogenic mutation and the allele frequency in some Turkish subpopulations is as high as 75% of disease alleles (Fettah A et al. Mediterr J Hematol Infect Dis. 2013;5(1):e2013055 and Baysal et al. Br J Haematol. 1992;81(4):607-9. ). RT-PCR studies from mRNA in both human samples and mouse models demonstrated the presence of aberrant splicing, with 90% of transcripts with abnormal splicing in homozygous mice (Vadolas J. J Biol Chem. 2006 Mar 17;281(11):7399-405). Based on the supporting evidence, c.93-21G>A is interpreted as a disease-causing mutation. -

Fetal hemoglobin quantitative trait locus 1 Pathogenic:1

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was identified as compound heterozygous. -

alpha Thalassemia;C0002895:Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1840779:METHEMOGLOBINEMIA, BETA TYPE;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to;C4693822:Erythrocytosis, familial, 6 Pathogenic:1

Oct 31, 2018

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Beta-thalassemia major Pathogenic:1

Aug 18, 2011

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing;curation

- -

Malaria, susceptibility to Pathogenic:1

Mar 26, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

May 03, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hb SS disease Pathogenic:1

-

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Beta-plus-thalassemia Pathogenic:1

Jan 01, 1990

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.44		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.44		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs35004220; hg19: chr11-5248050;