11-5226684-C-T

Variant names:

• chr11-5226684-C-T
• rs33947415
• NM_000518.5:c.208G>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 3P and 2B. PM1 PP5 BP4 BS2_Supporting

The NM_000518.5(HBB):​c.208G>A​(p.Gly70Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 1,614,010 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G70A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00058 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00049 (4 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:9 U:9 O:2
• Conservation: PhyloP100: -1.57
• Publications: 21 publications found

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]

HBB Gene-Disease associations (from GenCC):

• dominant beta-thalassemia

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), ClinGen
• hemoglobin M disease

  Inheritance: AD Classification: DEFINITIVE, MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, ClinGen
• beta thalassemia

  Inheritance: AR Classification: DEFINITIVE Submitted by: Myriad Women’s Health
• beta-thalassemia HBB/LCRB

  Inheritance: AR, SD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• sickle cell disease and related diseases

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• erythrocytosis, familial, 6

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Heinz body anemia

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• sickle cell disease

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• hereditary persistence of fetal hemoglobin-beta-thalassemia syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• beta-thalassemia intermedia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• beta-thalassemia major

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• delta-beta-thalassemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin C disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin C-beta-thalassemia syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin E disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hemoglobin E-beta-thalassemia syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary persistence of fetal hemoglobin-sickle cell disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-beta-thalassemia disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin c disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin d disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• sickle cell-hemoglobin E disease syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000298932 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM1: In a hotspot region, there are 12 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 37 uncertain in NM_000518.5
• PP5: Variant 11-5226684-C-T is Pathogenic according to our data. Variant chr11-5226684-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 15138.
• BP4: Computational evidence support a benign effect (MetaRNN=0.014180064). . Strength limited to SUPPORTING due to the PP5.
• BS2: High Homozygotes in GnomAdExome4 at 4 AR,AD,SD geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.208G>A	p.Gly70Ser	missense_variant	Exon 2 of 3	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.208G>A	p.Gly70Ser	missense_variant	Exon 2 of 3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes AF: 0.000579 AC: 88 AN: 152028 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000221

Gnomad OTH AF: 0.000479

GnomAD2 exomes AF: 0.000943 AC: 237 AN: 251422 AF XY: 0.000883

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000347

Gnomad ASJ exome AF: 0.0178

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000264

Gnomad OTH exome AF: 0.00147

GnomAD4 exome AF: 0.000486 AC: 710 AN: 1461864 Hom.: 4 Cov.: 36 AF XY: 0.000473 AC XY: 344 AN XY: 727240

African (AFR) AF: 0.000388 AC: 13 AN: 33480

American (AMR) AF: 0.000335 AC: 15 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0184 AC: 481 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.0000696 AC: 6 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5766

European-Non Finnish (NFE) AF: 0.0000989 AC: 110 AN: 1111990

Other (OTH) AF: 0.00137 AC: 83 AN: 60396

GnomAD4 genome AF: 0.000578 AC: 88 AN: 152146 Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48 AN XY: 74374

African (AFR) AF: 0.000313 AC: 13 AN: 41516

American (AMR) AF: 0.000196 AC: 3 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000221 AC: 15 AN: 67992

Other (OTH) AF: 0.000474 AC: 1 AN: 2110

Alfa AF: 0.000935 Hom.: 1

Bravo AF: 0.000555

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00105 AC: 9

ExAC AF: 0.000840 AC: 102

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.000164

EpiControl AF: 0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:9 Uncertain:9 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:4 Uncertain:2

Dec 08, 2023

Revvity Omics, Revvity

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 18, 2024

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The HBB c.208G>A (p.Gly70Ser) variant (also known as Hb City of Hope) has been reported as having normal stability, with normal clinical presentation in heterozygotes (HbVar (http://globin.cse.psu.edu/cgi-bin/hbvar/counter) and PMID: 6434492 (1984)). However, compound heterozygous individuals carrying this variant and a severe beta-thalassemia variant on the other allele may present with a beta-thalassemia intermedia phenotype (PMID: 25113778 (2015), 2467892 (1989)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant. -

Aug 08, 2015

Eurofins Ntd Llc (ga)

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 70 of the HBB protein (p.Gly70Ser). This variant is present in population databases (rs33947415, gnomAD 1.8%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosomal recessive mild to moderate beta thalassemia phenotypes and/or severe anemia and immunodeficiency (PMID: 2200760, 2467892, 25113778). 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 p.Gly69Ser, G69S, Hb City of Hope, and Hb CH. ClinVar contains an entry for this variant (Variation ID: 15138). Invitae Evidence 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 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. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Jun 09, 2025

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Heterozygous carriers have not been observed to have any hematologic manifestations (PMID: 21302591, 1353069); Also known as Hb City of Hope (HbCH) and G69S using alternate nomenclature; In silico analysis suggests that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31553106, 34297361, 28802248, 27823958, 31268351, 25113778, 21302591, 1353069, 6434492, 2467892, 34426522, 37028505, 37265972, Karaer2023[CaseReport], 39696913, 38708170) -

Jan 23, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb City of Hope variant (HBB: c.208G>A; p.Gly70Ser, also known as Gly69Ser when numbered from the mature protein; rs33947415, HbVar ID: 377) is reported in the literature in the heterozygous state in asymptomatic individuals (HbVar and references therein), and in trans to a pathogenic variant in an individual presenting with classical beta-thalassemia trait; however, this individual also carried an alpha-thalassemia deletion (--SEA), which could reduce the globin chain imbalance and minimize the clinical impact (Zhou 2019). Hb City of Hope has also been observed in trans to pathogenic HBB variants in several individuals with thalassemia intermedia or moderate to severe anemia (Paridisi 2010, Vinciguerra 2015). This variant is reported in ClinVar (Variation ID: 15138). It is found in the Ashkenazi Jewish population with an overall allele frequency of 1.8% (184/10366 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.584). Due to conflicting information, the clinical significance of the Hb City of Hope variant is uncertain at this time. References: Link to HbVar database: https://globin.bx.psu.edu/hbvar/menu.html Paradisi I et al. Hemoglobin S/hemoglobin City of Hope compound heterozygote with a SubSaharan genetic background and severe bone marrow hypoplasia. Invest Clin. 2010 Sep;51(3):403-14. PMID: 21302591. Vinciguerra M et al. Co-inheritance of the rare B hemoglobin variants Hb Yaounde, Hb Gorwihl and Hb City of Hope with other alterations in globin genes: impact in genetic counseling. Eur J Haematol. 2015 Apr;94(4):322-9. PMID: 25113778. Zhou JY et al. Coinheritance of Hb City of Hope (HBB: c.208G>A) and B-Thalassemia: Compromising the Molecular Diagnosis of the Codons 71/72 (+A) (HBB: c.216_217insA) Mutation by Reverse Dot-Blot Hybridization. Hemoglobin. 2019 Mar;43(2):145-147. PMID: 31268351. -

Hb SS disease Pathogenic:1 Uncertain:2

-

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 18, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

beta Thalassemia Uncertain:2

Feb 24, 2016

Bodamer Research Lab, Boston Children's Hospital

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

alpha Thalassemia;C0002895:Hb SS disease;C0700299:Heinz body anemia;C1858990:Dominant beta-thalassemia;CN322236:Beta-thalassemia HBB/LCRB Pathogenic:1

Jul 24, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Hemoglobinopathy Pathogenic:1

May 15, 2025

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: HBB c.208G>A (p.Gly70Ser) results in a non-conservative amino acid change in 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 0.00049 in 1614010 control chromosomes in the gnomAD v4.0.0 database, including 4 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in HBB causing Hemoglobinopathy (0.00049 vs 0.011), allowing no conclusion about variant significance. This variant (also known as Hb City of Hope or Hb CH; also referred to as Gly69Ser) has been reported in several heterozygous carriers, who were found to be clinically and hematologically unaffected (e.g., Rahbar_1984, Wilson_1986). However, compound heterozygosity with a beta0-thallassemia allele has been reported in two independent patients, who had beta thalassemia intermedia phenotypes (e.g., Kutlar_1989, Oner_1990, Vinciguerra_2015). In addition, compound heterozygosity with HbS (HBB c.20A>T) was reported in an anemic 2-year-old boy (Paradisi_2010). In a recent study, the variant was reported in compound heterozygosity with a beta0-thalassemia allele in a clinically asymptomatic individual, who had classical beta-thalassemia trait based on hematological parameters, but no evidence of anemia, however this patient also carried an alpha-thalassemia deletion (--SEA), which could reduce the globin chain imbalance, thus modifying the clinical phenotype (Zhou_2019). These data, combined with the homozygous occurrences in the gnomAD database, suggest that the variant may primarily cause disease when in trans with a severe allele, and thus, the pathogenicity of the variant may be genotype-dependent. At least one publication reports experimental evidence evaluating an impact on protein expression in patient samples, showing significant reduction in hemoglobin protein when this variant was in trans with a null Q40X allele as compared to related individuals carrying only Q40X (example, Vinciguerra_2015). The following publications have been ascertained in the context of this evaluation (PMID: 1353069, 17932132, 2467892, 26436569, 2200760, 21302591, 6434492, 34092029, 31553106, 25113778, 3957690, 31268351). ClinVar contains an entry for this variant (Variation ID: 15138). While this variant has been reported in the literature, the clinical significance of the variant for autosomal dominant HBB-related conditions could not be established. Based on the evidence outlined above, the variant was classified as likely pathogenic for autosomal recessive beta-thalassemia intermedia. -

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

Jun 30, 2021

Fulgent Genetics, Fulgent Genetics

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

Apr 30, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1

May 04, 2022

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fetal hemoglobin quantitative trait locus 1 Uncertain:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Hemoglobin E Uncertain:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

HEMOGLOBIN CITY OF HOPE Other:1

Dec 12, 2017

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Hb SS disease;C0005283:beta Thalassemia;C1841621:Fetal hemoglobin quantitative trait locus 1;C1858990:Dominant beta-thalassemia Other:1

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.049	T
BayesDel_noAF	Uncertain	0.010
CADD	Benign	0.48
DANN	Benign	0.64
DEOGEN2	Benign	0.022	T;T;.;T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.025	N
LIST_S2	Benign	0.72	.;T;T;T
M_CAP	Benign	0.082	D
MetaRNN	Benign	0.014	T;T;T;T
MetaSVM	Benign	-0.59	T
MutationAssessor	Benign	-0.035	N;N;.;.
PhyloP100		-1.6
PrimateAI	Benign	0.31	T
PROVEAN	Benign	1.3	N;.;.;N
REVEL	Uncertain	0.58
Sift	Benign	0.69	T;.;.;T
Sift4G	Benign	0.75	T;.;.;.
Polyphen		0.0010	B;B;.;.
Vest4		0.80
MVP		0.58
MPC		0.034
ClinPred		0.015	T
GERP RS		-10
PromoterAI		0.00050	Neutral
Varity_R		0.13
gMVP		0.65
Mutation Taster		=10/90	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs33947415; hg19: chr11-5247914;