11-5227003-C-T

Position:

• chr11-5227003-C-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PM1 PM5 PP5_Very_Strong BP4

The ENST00000335295.4(HBB):​c.19G>A​(p.Glu7Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000736 in 1,611,030 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 0.0037 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00042 (6 hom.)
• Consequence: HBB ENST00000335295.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:30 B:1 O:1
• Conservation: PhyloP100: 2.63

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 11 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 ENST00000335295.4
• PM5: Other missense variant is known to change same aminoacid residue: 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.
• PP5: Variant 11-5227003-C-T is Pathogenic according to our data. Variant chr11-5227003-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 15126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5227003-C-T is described in Lovd as [Pathogenic]. Variant chr11-5227003-C-T is described in Lovd as [Likely_pathogenic]. Variant chr11-5227003-C-T is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.01455009). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBB	NM_000518.5	c.19G>A	p.Glu7Lys	missense_variant	1/3	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.19G>A	p.Glu7Lys	missense_variant	1/3	1	NM_000518.5	ENSP00000333994	P1

Frequencies

GnomAD3 genomes AF: 0.00374 AC: 570 AN: 152216 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000785

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: 0.00

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.000916 AC: 230 AN: 251156 Hom.: 1 AF XY: 0.000567 AC XY: 77 AN XY: 135730

Gnomad AFR exome AF: 0.0134

Gnomad AMR exome AF: 0.000260

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000422 AC: 615 AN: 1458696 Hom.: 6 Cov.: 33 AF XY: 0.000376 AC XY: 273 AN XY: 725878

Gnomad4 AFR exome AF: 0.0159

Gnomad4 AMR exome AF: 0.000246

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000117

Gnomad4 OTH exome AF: 0.000896

GnomAD4 genome AF: 0.00375 AC: 571 AN: 152334 Hom.: 1 Cov.: 32 AF XY: 0.00356 AC XY: 265 AN XY: 74508

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.000784

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00115 Hom.: 1

Bravo AF: 0.00536

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.0161 AC: 71

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.00123 AC: 149

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:30 Benign:1 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:12

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 27, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Apr 04, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2024	HBB: PM3:Very Strong, PS3:Moderate, PM2:Supporting, BP4 -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 07, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Aug 16, 2021	PS3, PM5, PM1, PM3 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 29, 2021	One of the most prevalent abnormal hemoglobin variants globally, alongside hemoglobin S (Cook et al., 2013; Piel et al., 2013); When inherited along with a second HBB pathogenic variant, compound heterozygosity could also result in other clinically significant hemoglobinopathies such as sickle-hemoglobin C disease and hemoglobin C-beta thalassemia (Piel et al., 2013); HbC allele frequencies above 15% have been described in West African populations, and the estimated carrier frequency for HbC in the African American population is 1/31 (Piel et al., 2013; Tabor et al., 2014); Published functional studies demonstrate the E7K variant reduces the overall hydrophobicity as compared to wild type hemoglobin (Adachi et al., 1987); Also referred to as E6K, due to alternate nomenclature; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8294201, 23297836, 2888754, 19429541, 20305663, 21228398, 13208767, 13293203, 2412615, 6061750, 25087612, 22975760, 23591685, 22028795, 27117572, 26372199, 28121068, 30604644, 31589614) -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 7 of the HBB protein (p.Glu7Lys). This variant is present in population databases (rs33930165, gnomAD 1.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individuals with beta-hemoglobinopathies (PMID: 20301551, 23297836, 26372199, 27117572). This variant is also known as p.Glu6Lys and HbC. ClinVar contains an entry for this variant (Variation ID: 15126). 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: 2888754). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 27, 2023	The Hb C variant (HBB: c.19G>A; p.Glu7Lys, also known as Glu6Lys when numbered from the mature protein, rs33930165, HbVar ID: 227) is a common pathogenic beta globin variant. Heterozygosity is consistent with Hb C trait. Homozygosity is consistent with a clinical presentation of mild to moderate hemolytic anemia with mild microcytosis and frequent target cells. Hb C in combination with a beta thalassemia variant on the opposite chromosome is often associated with mild microcytic anemia (Cook 2013, HbVar database). REFERENCES Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Cook C et al. The clinical and laboratory spectrum of Hb C (beta6(A3)Glu>Lys, GAG>AAG) disease. Hemoglobin. 2013; 37(1):16-25. PMID: 23297836. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Jun 01, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 09, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Sep 15, 2014	- -

beta Thalassemia Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	NM_000518.4:c.19G>A is also known as p.Glu6Lys or HbC in the literature. NM_000518.4:c.19G>A in the HBB gene has an allele frequency of 0.013 in African subpopulation in the gnomAD database. Boucher et al. reported Mild Microcytic Anemia in an Infant with a compound heterozygosity for Hb C (HBB: c.19G > A) and Hb Osu Christiansborg (HBB:c.157G > A) (PMID: 27117572). In addition, this variant was reported as the most common emoglobin (Hb) abnormality identified in the United States (PMID: 23297836). Experimental studies have shown that this variant affects the kinetic properties of the hemoglobin protein (PMID: 2888754). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS4; PS3; PM3; PP4. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 15, 2019	NM_000518.4(HBB):c.19G>A(E7K, aka Hb C) is classified as pathogenic in the context of Hb beta chain-related hemoglobinopathy and is associated with the hemoglobin C form of disease. Sources cited for classification include the following: PMID 23297836, 23297836, 19061217 and 2888754. Classification of NM_000518.4(HBB):c.19G>A(E7K, aka Hb C) 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. -

Hb SS disease Pathogenic:3 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	May 02, 2019	This variant has been previously reported as a homozygous or compound heterozygous change in patients with Sickle Cell Disease, Hemoglobin C Variant (PMID: 23297836, 23591685). Functional studies have shown that this variant reduces the overall hydrophobicity as compared to wild type hemoglobin (PMID: 2888754). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.12% (349/282566) in the general population and 1.34% (335/24,966) in African populations. In silico tools used to predict the effect of this variant on protein function yield discordant results. Based on the available evidence, the c.19G>A (p.Glu7Lys) variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	New York Genome Center	Feb 10, 2021	The c.19G>A, p.Glu7Lys variant in the HBB gene has been previously reported as a homozygous or compound heterozygous change in patients with Sickle Cell Disease, Hemoglobin C Variant [PMID: 23297836; PMID: 23591685]. Functional studies have shown that this variant reduces the overall hydrophobicity as compared to wild type hemoglobin [PMID:2888754]. It is present in the heterozygous state in the gnomAD population database at a frequency of 0.12% (349/282566) in the general population and 1.34% (335/24,966) in African populations. This variant is an established disease-associated mutation and has been reported as pathogenic by multiple clinical diagnostic laboratories in ClinVar (variant ID: 15126). Based on the available evidence, the c.19G>A (p.Glu7Lys) variant is classified as Pathogenic. -

Beta-thalassemia HBB/LCRB Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 22, 2022	- -
Pathogenic, no assertion criteria provided	research	Genomics And Bioinformatics Analysis Resource, Columbia University	-	- -

HBB-related disorder Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	The c.19G>A (p.Glu7Lys, also known as p.Glu6Lys) variant in HBB is referred to as the hemoglobin C allele (HbC), and causes autosomal recessive hemoglobin C disease when it is homozygous or sickle-hemoglobin C disease when it is compound heterozygous with a hemoglobin S allele (PMID: 20301551, 26372199, 23297836, 27117572). Experimental studies showed that this variant affected the kinetic properties of the hemoglobin protein (PMID: 2888754). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.1% (349/282566). Based on the available evidence, the c.19G>A (p.Glu7Lys) variant is classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	PreventionGenetics, part of Exact Sciences	Jan 03, 2024	The HBB c.19G>A variant is predicted to result in the amino acid substitution p.Glu7Lys. This variant (reported as Glu6Lys) has been identified in the homozygous and compound heterozygous states in individuals with hemoglobin C disease, and is considered one of the most common hemoglobin abnormalities in the United States (Cook et al. 2013. PubMed ID: 23297836). In silico analysis showed that this variant possibly disrupts contact with other molecules as well as interfere with interaction with other regions of the protein (Alanazi et al. 2011. PubMed ID: 22028795). This variant has been observed in >1% of individuals of African ancestry, including 1 homozygote, in a large population database. Based on these observations, we interpret this variant as pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 13, 2023

The c.19G>A (p.E7K) alteration is located in exon 1 (coding exon 1) of the HBB gene. This alteration results from a G to A substitution at nucleotide position 19, causing the glutamic acid (E) at amino acid position 7 to be replaced by a lysine (K). Based on data from gnomAD, the A allele has an overall frequency of 0.1235% (349/282566) total alleles studied. The highest observed frequency was 1.34% (335/24966) of African/African American alleles, including 1 homozygote. This alteration results in the hemoglobin C (HbC) variant. The homozygous state of HbC only results in mild hemolytic anemia, while co-occurrence with another deleterious allele results in a clinically significant disorder (Nagel, 2003; Akinbami, 2016). This amino acid position is not well conserved in available vertebrate species. HbC is less soluble than wild-type hemoglobin (HbA) and tends to crystallize in red blood cells (RBCs), resulting in a decreased ability of RBCs to deform in capillaries and inducing hemolysis (Nagel, 2003). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Sickle cell-hemoglobin C disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Johns Hopkins Genomics, Johns Hopkins University

Sep 14, 2022

This HBB variant (rs33930165) reaches polymorphic frequency (>1%) within the African/African American subpopulation in a large population dataset (gnomAD: 335/24966 total alleles, 1.342%, 1 homozygote) and has been reported in ClinVar. Also known as p.Glu6Lys and HbC, it has been reported in a homozygous or compound heterozygous state in individuals with beta-hemoglobinopathies. Heterozygosity for p.Glu7Lys in the absence of another pathogenic HBB variant results in Hemoglobin C trait (HbAC), which is clinically silent. Two bioinformatic tools queried predict that this substitution would tolerated, but 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.19G>A (p.Glu7Lys) to be pathogenic. -

Inherited hemoglobinopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 10, 2023

The p.Glu7Lys variant in HBB (also known as HbC or p.Glu6Lys in the literature) is a well-described pathogenic variant that along with p.Glu7Val (HbS), is thought to be one of the most prevalent hemoglobin abnormalities (Cook 2013 PMID: 23297836, Piel 2013). In the heterozygous state, the p.Glu7Lys variant is associated with hemoglobin C trait and in the homozygous state this variant results in hemoglobin C disease (Charache 1967 PMID: 6061750, Piel 2013 PMID: 23591685, Cook 2013 PMID: 23297836). In the compound heterozygous state with a second HBB variant associated with abnormal hemoglobin, this variant results in other beta-hemoglobinopathies such as sickle-hemoglobin C disease (co-inheritance with HbS) and hemoglobin C-beta thalassemia (with β-thalassemia pathogenic variants; Piel 2013 PMID: 23591685, Cook 2013 PMID: 23297836, Boucher 2016 PMID: 27117572). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 15126) and has been identified in 1.3% (555/41446) of African American chromosomes, including 1 homozygote, by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). However, this frequency is low enough to be consistent with a recessive carrier frequency, which has been estimated to be at 3.2% (1/31) in the African American population (Piel 2013 PMID: 23591685). In vitro functional studies provide some evidence that this variant affects the kinetic properties of the hemoglobin protein, reducing its overall hydrophobicity (Adachi 1987 PMID: 2888754). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive beta-hemoglobinopathies. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3_supporting, PM5. -

HEMOGLOBIN C Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Dec 02, 2011

- -

Heinz body anemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

DASA

Jan 05, 2022

The c.19G>A;p.(Glu7Lys) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (Clinvar ID: 15126; PMID: 2030155; 27117572; 26372199; 23297836; 19061217; 30604644; 33091040) - PS4. Well-established in vitro or in vivo functional studies support a damaging effect on the gene or gene product (PMID: 15973412) - PS3_supporting. The variant is present at low allele frequencies population databases (rs33930165– gnomAD 0.03745%; ABraOM 0.002989 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Glu7Lys) was detected in trans with a pathogenic variant (PMID: 27117572; 26372199; 23297836; 19061217; 30604644; 33091040) - PM3_very strong The variant co-segregated with disease in multiple affected family members (PMID: 4746100; 13908956) - PP1_supporting. In summary, the currently available evidence indicates that the variant is 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

- -

Hereditary persistence of fetal hemoglobin Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Oct 29, 2022

ACMG classification criteria: PS3 strong, PS4 strong, PM2 moderated, PM3 very strong -

Malaria, resistance to Benign:1

protective, no assertion criteria provided

literature only

OMIM

Dec 02, 2011

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Uncertain	-0.010
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.079	T;T;.;T
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.42
FATHMM_MKL	Benign	0.50	D
LIST_S2	Uncertain	0.94	.;D;D;D
MetaRNN	Benign	0.015	T;T;T;T
MetaSVM	Benign	-0.38	T
MutationAssessor	Uncertain	2.3	M;M;.;.
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.43	T
PROVEAN	Uncertain	-2.6	D;.;.;D
REVEL	Uncertain	0.45
Sift	Uncertain	0.015	D;.;.;D
Sift4G	Benign	0.41	T;.;.;.
Polyphen		0.0050	B;B;.;.
Vest4		0.83
MVP		0.95
MPC		0.037
ClinPred		0.046	T
GERP RS		5.2
Varity_R		0.68
gMVP		0.52

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: rs33930165; hg19: chr11-5248233;