rs77121243

chr11-5227002-T-Achr11-5227002-T-Cchr11-5227002-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 12P and 9B. PM1 PM5 PP5_Very_Strong BP4 BA1

The NM_000518.5(HBB):c.20A>T(p.Glu7Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,610,650 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E7Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.013 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (31 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:56 B:1 O:4
• Conservation: PhyloP100: 0.690

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 3 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 8 benign, 12 uncertain in NM_000518.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5227003-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 15126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP5: Variant 11-5227002-T-A is Pathogenic according to our data. Variant chr11-5227002-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 15333.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5227002-T-A is described in Lovd as [Pathogenic]. Variant chr11-5227002-T-A is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.007841617). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.20A>T	p.Glu7Val	missense_variant	1/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.20A>T	p.Glu7Val	missense_variant	1/3	1	NM_000518.5	P1

Frequencies

GnomAD3 genomes AF: 0.0127 AC: 1926 AN: 152176 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00718

GnomAD3 exomes AF: 0.00348 AC: 874 AN: 251180 Hom.: 3 AF XY: 0.00266 AC XY: 361 AN XY: 135742

Gnomad AFR exome AF: 0.0470

Gnomad AMR exome AF: 0.00217

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000621

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000528

Gnomad OTH exome AF: 0.00163

GnomAD4 exome AF: 0.00160 AC: 2335 AN: 1458356 Hom.: 31 Cov.: 33 AF XY: 0.00145 AC XY: 1054 AN XY: 725764

Gnomad4 AFR exome AF: 0.0569

Gnomad4 AMR exome AF: 0.00244

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000812

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000316

Gnomad4 OTH exome AF: 0.00333

GnomAD4 genome AF: 0.0127 AC: 1937 AN: 152294 Hom.: 9 Cov.: 32 AF XY: 0.0122 AC XY: 912 AN XY: 74478

Gnomad4 AFR AF: 0.0436

Gnomad4 AMR AF: 0.00588

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00710

Alfa AF: 0.000785 Hom.: 0

ESP6500AA AF: 0.0402 AC: 177

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.00439 AC: 533

Asia WGS AF: 0.0130 AC: 47 AN: 3476

EpiCase AF: 0.000218

EpiControl AF: 0.000178

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:56 Benign:1 Other:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hb SS disease Pathogenic:21 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Apr 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Apr 29, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	Jun 29, 2018	The c.20A>T (p.Glu7Val) variant in HBB (also known as p.Glu6Val) is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). This variant is an established disease-associated mutation and has been reported as pathogenic by multiple clinical diagnostic laboratories in ClinVar (variant ID: 15333). Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	May 06, 2023	The HBB c.20A>T (p.Glu7Val) missense variant, also referred to as p.Glu6Val, has been reported in a homozygous state in more than 1000 individuals with sickle cell anemia (PMID: 25023084; 25023085; 26275168). The highest frequency of this allele in the Genome Aggregation Database is 0.04490 in the African/African-American population (version 2.1.1). This frequency is high, however, carriers are hypothesized to confer protection against Plasmodium falciparum malaria infection (PMID: 21045822). In mice expressing the sickle trait variant, erythrocytes were shown to sickle with deoxygenation, similar to that seen in humans with sickle cell anemia (PMID: 2296310), and in mice with 100% expression of the sickle cell variant, chronic hemolytic anemia with circulating sickled erythrocytes, as well as chronic tissue damage, was observed (PMID: 12124399). Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic for sickle cell disease. -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	Sep 22, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Apr 22, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital	May 09, 2018	[ACMG/AMP: PS3, PM3, PM5, PS4_Moderate, PP5] This alteration is supported by well-established in vitro or in vivo functional studies to have a damaging effect on protein function or splicing [PS3], is detected in trans with a known pathogenic variant [PM3], is a novel missense change at an amino residue where a different missense change has been deemed to be pathogenic [PM5], has previously been observed in multiple unrelated patients with the same phenotype [PS4_Moderate], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5]. -
Pathogenic, no assertion criteria provided	research	Genomics And Bioinformatics Analysis Resource, Columbia University	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomics Facility, Ludwig-Maximilians-Universität München	Dec 28, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000015333, PMID:3267215, PS1_S). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 25023084, 25203083, 25023085, PS4_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 1802884, 2296310, 28356267, 12124399, PS3_S). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 23591685, 29542687, PM3_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000015126,VCV000036301, PMID:19460936,6129204,8294201, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.83, PP3_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	Jan 07, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Feb 06, 2020	PS4, PS3, PP1, PP5, PP4. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 02, 2011	- -
Pathogenic, criteria provided, single submitter	research	H3Africa Consortium	Oct 12, 2022	While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.53, its frequency in African populations is >5%, as there is a high prevalence of sickle cell disease in African ancestry individuals. -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Aug 10, 2022	PS3, PS4, PM3, PP1 -
Pathogenic, criteria provided, single submitter	clinical testing	New York Genome Center	Feb 10, 2021	The c.20A>T (p.Glu7Val) variant in HBB (also known as p.Glu6Val) is the most prevalent genotype associated with sickle cell disease [PMID: 25203083]. This variant is an established disease-associated mutation and has been reported as pathogenic by multiple clinical diagnostic laboratories in ClinVar (variant ID: 15333). This variant is identified in gnomAD in 1826 heterozygous individuals, 9 homozygous individuals, with an allele frequency of 1.27e-2. Based on the available evidence, the c.20A>T (p.Glu7Val) variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense c.20A>T (p.Glu7Val) variant in HBB has been reported in homozygous individuals affected with sickle cell anemia and heterozygous state in sickle cell anemia trait. This is a common, well-known variant that has been observed in individuals affected with sickle cell disease (Kutlar, Ferdane et al.,2010 and Bender, MA.,2003). Experimental studies have shown that this missense change affects hemoglobin polymerization and can result in abnormally-shaped red blood cells (He, Zhenning et al.,2002, Eshbach, Megan L et al.,2017). This variant is reported with the allele frequency 0.4% in the gnomAD and 2.7% in 1000 genome database. It has been submitted to ClinVar as Pathogenic. The amino acid Glu at position 7 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by SIFT and the residue is conserved across species. The amino acid change p.Glu7Val in HBB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital	Mar 10, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 11, 2024	The p.Glu7Val variant (also known as p.Glu6Val or hemoglobin S variant) in HBB is a well-established variant which, in the homozygous state, causes sickle cell anemia and which accounts for 60-70% of sickle cell disease in the US (Bender 2003 PMID: 20301551, Serjeant 1968 PMID: 4232783). Co-inheritance with a second HBB variant associated with abnormal hemoglobin (such as Hb C, Hb D, Hb O, Hb E and β-thalassemia pathogenic variants) also results in sickle cell disease. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 15333) and has been identified in 1799/41432 (4.3%) of African/African American chromosomes, including 9 homozygotes, by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). In vitro functional studies support an impact on protein function as this variant is shown to affect hemoglobin polymerization, resulting in abnormally shaped red blood cells (He 2017 PMID: 12124399, Adachi 1991 PMID: 1802884). Transgenic mouse models have also shown that this variant causes sickle cell disease, as mouse red blood cells with the variant had a sickle shape upon deoxygenation (Greaves 1990 PMID: 2296310). In summary, this variant meets criteria to be classified as pathogenic autosomal recessive sickle cell disease. ACMG/AMP Criteria applied: PM3_Very Strong, PS3. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jan 11, 2022	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	A Heterozygous Missense variant c.20A>T in Exon 1 of the HBB gene that results in the amino acid substitution p.Glu7Val was identified. The observed variant has a minor allele frequency of 0.00348% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic, Likely Benign, and Conflicting Interpretations (Variant ID: 15333). This variant has previously been reported for sickle cell anemia by Jaripour ME, et, al., 2018. Experimental studies have shown that this missense change affects HBB function by Eshbach ML, et, al, 2017. Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -

not provided Pathogenic:15

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 24, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 7 of the HBB protein (p.Glu7Val). This variant is present in population databases (rs334, gnomAD 5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with sickle cell disease (PMID: 19758965, 20301551, 20861612, 26372199). This variant is also known as p.Glu6Val and HbS. ClinVar contains an entry for this variant (Variation ID: 15333). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on HBB protein function. Experimental studies have shown that this missense change affects HBB function (PMID: 1802884, 12124399, 28356267). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 25, 2021	Functional studies using transgenic mouse models showed mouse erythrocytes with this variant sickled upon deoxygenation (Greaves et al., 1990) and kinetic studies indicate this variant drastically decreases the molecular stability of the protein (Adachi et al., 1987); Commonly referred to as p.(E6V) due to the use of alternate nomenclature; This variant is associated with the following publications: (PMID: 20825310, 1802884, 30315176, 3267215, 24123366, 20954261, 22975760, 23065522, 22625666, 19465909, 20305663, 20981092, 22010933, 22028795, 22957039, 23144702, 2296310, 27884173, 27254408, 17393956, 28356267, 26372199, 19758965, 12124399, 22244832, 20861612, 30655275, 30290004, 21329186, 15543018, 30033078, 31553106, 31130284, 31980526, 27650483, 32817264, 32371413, 25023084, 2888754, 31589614, 25087612) -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Sep 15, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 19, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 29, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	HBB: PM3:Very Strong, PS3:Moderate, PM2:Supporting, PP4, BP4 -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Nov 22, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Mar 02, 2016	- -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, no assertion criteria provided	research	Gharavi Laboratory, Columbia University	Sep 16, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 29, 2023	The Hb S variant (HBB: c.20A>T; p.Glu7Val, also known as Glu6Val when numbered from the mature protein, HbVar ID: 226, rs334) is a common pathogenic beta globin variant. Heterozygosity for Hb S is consistent with sickle cell trait. Homozygosity for Hb S results in sickle cell anemia. Hb S in combination with a different pathogenic HBB variant on the opposite chromosome results in various forms of sickle cell disease (see HbVar link and references therein). References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html -

beta Thalassemia Pathogenic:5 Other:1

Pathogenic, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	NM_000518.4:c.20A>T is also known as p.Glu6Lys or HbS in the literature. NM_000518.4:c.20A>T in the HBB gene has an allele frequency of 0.045 in African subpopulation in the gnomAD database. The c.20A>T (p.Glu7Val) variant in HBB is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). Kondani et al reported that among 247 children, 19 (7.7%) were homozygous sickle cell anemia patients (Hb SS) (PMID: 25023084). Experimental studies have shown that this missense change affects hemoglobin polymerization and can result in abnormally-shaped red blood cells (PMID: 12124399; 28356267; 1802884). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS4; PS3; PM3; PP4. -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
not provided, no classification provided	phenotyping only	GenomeConnect - Brain Gene Registry	-	Variant classified as Pathogenic and reported on 02-03-2017 by Baylor Medical Genetics Laboratories. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Aug 28, 2019	A heterozygous missense variant, NM_000518.5(HBB):c.20A>T, has been identified in exon 1 of 3 of the HBB gene. The variant is predicted to result in a major amino acid change from glutamic acid to valine at position 7 of the protein (NP_000509.1(HBB):p.(Glu7Val)). The glutamic acid at this position has low conservation (100 vertebrates, UCSC), and is located within the Hb-beta like functional domain. In silico predictions of pathogenicity for this variant are conflicting (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD database at a frequency of 0.4% (1228 heterozygous, 4 homozygous). An alternative residue change has been reported in the gnomAD database at a frequency of 0.1%. The variant is the cause of hemoglobin S which results in sickle cell anemia and has been previously described as pathogenic and segregated with disease in multiple families (ClinVar; Kwiatkowski, D.P. 2005). Even though often fatal when homozygous or compound heterozygous, it is seen in high frequency (~10%) in populations in Sub-Saharan African and Middle East where it has been positively selected because it confers protection against malaria in heterozygous individuals, which are asymptomatic (Kwiatkowski, D.P. 2005). Additionally, functional studies showed that erythrocytes from transgenic mice expressing human HBB sickle readily on deoxygenation (Greaves, D.R. et al., 1990). A different variant in the same codon resulting in a change to lysine has been reported to cause a mild hemolytic anemia (ClinVar; Kwiatkowski, D.P. 2005). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC. -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 18, 2019	NM_000518.4(HBB):c.20A>T(E7V, aka Hb S) is classified as pathogenic and is associated with hemoglobin S (sickle cell disease). Sources cited for classification include the following: PMID 19061217, 2582106, 22028795, 22625666, 22010933, 2888754, 20954261, 6583683, 1376298. Classification of NM_000518.4(HBB):c.20A>T(E7V, aka Hb S) 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.‚Äã -

HBB-related disorder Pathogenic:3 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jan 14, 2024	The HBB c.20A>T variant is predicted to result in the amino acid substitution p.Glu7Val. This variant, also referred to as p.Glu6Val using legacy nomenclature, has previously been reported to be causative for sickle cell anemia when present in the homozygous state (Engelke et al. 1988. PubMed ID: 3267215; Bender et al. 2017. PubMed ID: 20301551). Individuals heterozygous for this variant have sickle cell trait and are usually asymptomatic but can be at risk for complications (Key and Derebail. 2010. PubMed ID: 21239829). This variant is reported in 4.5% of alleles in individuals of African descent in gnomAD. We interpret this variant as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	The c.20A>T (p.Glu7Val) variant in HBB, also known as p.Glu6Val, is referred to as the hemoglobin S allele (HbS) and causes autosomal recessive sickle cell disease (MIM: #603903) when it is homozygous or compound heterozygous with a different pathogenic variant. Individuals who are heterozygous for the HbS allele have sickle cell trait (SCT). The c.20A>T (p.Glu7Val) variant is the most prevalent genotype associated with sickle cell disease (PMID: 25203083). This variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. It is present at a frequency of 0.4% (1236/282580 heterozygotes and 4/282580 homozygotes) in the gnomAD population database. The c.20A>T (p.Glu7Val) variant is an established disease-causing mutation. Based on the available evidence, c.20A>T(p.Glu7Val) is classified as Pathogenic. -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant identified in multiple registry participants. Variant interpreted as consistent with alpha thalassemia trait and reported on 02-28-2020 by Lab or GTR ID 500068. Variant interpreted as Pathogenic and reported on 07-21-2020 by Lab or GTR ID 1197. Variant interpreted as Pathogenic and reported on 05-26-2021 by Lab or GTR ID 20290. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Mar 05, 2022	Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 13464827; 11880644; 11830454; 12124399; 28356267; 1802884) - PS3.The c.20A>T;p.(Glu7Val) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 15333; PMID: 20301551; PMID: 30002798; PMID: 15658184;PMID: 7384810; PMID: 6268660; PMID: 26372199; PMID: 26275168; PMID: 28356267; PMID: 22625666; PMID: 32527859) - PS4. The p.(Glu7Val) was detected in trans with a pathogenic variant (PMID: 15658184; PMID: 20861612; PMID: 21131035) - PM3_very strong. Pathogenic missense variant in this residue have been reported (ClinVar ID: 15126 PMID: 20301551; 27117572; 26372199) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 21302591; 34334128; 14084634; 26041415) - PP1_strong.and allele frequency is greater than expected for disorder - BS1. In summary, the currently available evidence indicates that the variant is pathogenic. -

Beta-thalassemia HBB/LCRB Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Sep 06, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The missense c.20A>T (p.Glu7Val) variant in HBB gene has been reported previously in homozygous and compound heterozygous state in multiple individuals affected with HBB-related sickle cell anemia (Akinbami et al. 2016; Meher et al. 2016). Experimental studies have shown that this mutation (Glu7Val) in hemoglobin (Hb) causes red blood cells to assume a rigid curved shape that blocks their passage through the vasculature resulting in ischemia, severe pain, and necrosis (Eshbach et al. 2017). The p.Glu7Val variant has 0.4% allele frequency in gnomAD exomes database. This variant has been reported to the ClinVar database as Pathogenic (multiple submissions). The amino acid change p.Glu7Val in HBB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Glutamic acid at position 7 is changed to a Valine changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 22, 2022	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 13, 2023

The c.20A>T (p.E7V) alteration is located in exon 1 of the HBB gene. This alteration results from a A to T substitution at nucleotide position 20, causing the glutamic acid (E) at amino acid position 7 to be replaced by a valine (V). Based on data from gnomAD, the T allele has an overall frequency of 0.44% (1236/282580) total alleles studied. The highest observed frequency was 4.49% (1121/24964) of African/African American alleles. This alteration results in the hemoglobin S (HbS) variant and is associated with sickle cell disease (Ingram, 1956). This amino acid position is not well conserved in available vertebrate species. The p.E7V alteration is known to significantly decrease the solubility of the hemoglobin protein, allowing for the polymerization that ultimately results in red cell sickling (Adachi, 1987). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Anemia Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

New York Genome Center

Jan 16, 2020

- -

Sickle cell-hemoglobin C disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Johns Hopkins Genomics, Johns Hopkins University

Feb 17, 2023

This HBB variant (rs334) reaches polymorphic frequency (>1%) within the African/African American subpopulation in a large population dataset (gnomAD: 1121/24964 total alleles; 4.49%; 4 homozygotes) and has been reported in ClinVar. It is the most common pathogenic HBB variant in individuals of African ancestry. Also known as p.Glu6Val and HbS, it has been reported in a homozygous or compound heterozygous state in individuals with beta-hemoglobinopathies. One bioinformatic tool queried predicts that this substitution would damaging, while another predicts it would be tolerated. Experimental studies have shown that this variant affects the physical and kinetic properties of the hemoglobin protein. Bioinformatic analysis predicts that this missense variant would not affect normal exon 1 splicing, although this has not been confirmed experimentally to our knowledge. We consider c.20A>T (p.Glu7Val) to be pathogenic. -

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

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jun 30, 2021

- -

Malaria, susceptibility to Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center

Mar 25, 2024

- -

Hb SS disease;C0005283:beta Thalassemia;C0700299:Heinz body anemia;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia;C1970028:Malaria, susceptibility to Pathogenic:1

Pathogenic, no assertion criteria provided

research

Division of Human Genetics, Children's Hospital of Philadelphia

Feb 23, 2016

- -

Fetal hemoglobin quantitative trait locus 1 Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City

Jul 19, 2018

- -

See cases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Jan 06, 2022

ACMG classification criteria: PS3, PS4, PM3, BS1 -

Sickle cell disease and related diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Oct 14, 2019

Variant summary: HBB c.20A>T (p.Glu7Val) results in a non-conservative amino acid change located in the Globin domain (IPR000971) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0035 in 251180 control chromosomes in the gnomAD database, including 3 homozygotes. c.20A>T has been reported in the literature in multiple individuals affected with Sickle Cell Disease, an inherited monogenic disease characterized by intravascular sickling, haemolysis, anemia and leukocytosis as well as the association between sickled red blood cells and other blood components (example, Domingos_2014). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in decreased solubility of deoxygenated Hb S, and polymerization which leads to the formation of an extensive network of fibers in red blood cells (example, Adachi_1991). Eleven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Malaria, resistance to Benign:1

protective, no assertion criteria provided

literature only

OMIM

Dec 02, 2011

- -

HEMOGLOBIN S Other:1

not provided, no classification provided

literature only

OMIM

Sep 15, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Uncertain	0.0
CADD	Benign	14
DANN	Benign	0.96
DEOGEN2	Benign	0.11	T;T;.;T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.85
FATHMM_MKL	Benign	0.40	N
MetaRNN	Benign	0.0078	T;T;T;T
MetaSVM	Benign	-0.60	T
MutationAssessor	Pathogenic	3.6	H;H;.;.
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.38	T
PROVEAN	Pathogenic	-4.8	D;.;.;D
REVEL	Uncertain	0.54
Sift	Uncertain	0.025	D;.;.;D
Sift4G	Benign	0.063	T;.;.;.
Polyphen		0.0010	B;B;.;.
Vest4		0.54
MVP		0.95
MPC		0.037
ClinPred		0.049	T
GERP RS		0.15
Varity_R		0.51
gMVP		0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs334; hg19: chr11-5248232;