11-5226684-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1 PM5 PP5 BP4

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. 14/21 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. G70R) 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:5 U:11 O:2
• Conservation: PhyloP100: -1.57

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 4 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 14 uncertain in NM_000518.5
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5226683-C-T is described in Lovd as [Pathogenic].
• 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 id is 15138.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=10, Likely_pathogenic=4, not_provided=1, Pathogenic=1}. Variant chr11-5226684-C-T is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.014180064).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HBB	NM_000518.5	c.208G>A	p.Gly70Ser	missense_variant	2/3	ENST00000335295.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBB	ENST00000335295.4	c.208G>A	p.Gly70Ser	missense_variant	2/3	1	NM_000518.5	P1

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

GnomAD3 exomes AF: 0.000943 AC: 237 AN: 251422 Hom.: 0 AF XY: 0.000883 AC XY: 120 AN XY: 135878

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 SAS exome AF: 0.000131

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

Gnomad4 AFR exome AF: 0.000388

Gnomad4 AMR exome AF: 0.000335

Gnomad4 ASJ exome AF: 0.0184

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000696

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000989

Gnomad4 OTH exome AF: 0.00137

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

Gnomad4 AFR AF: 0.000313

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.0162

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000221

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.000993 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:5 Uncertain:11 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:3 Uncertain:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 08, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 07, 2023	Also known as Hb City of Hope (HbCH) and G69S using alternate nomenclature; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31553106, 34297361, 28802248, 27823958, 31268351, 21302591, 25113778, 1353069, 6434492, 2467892, 34426522) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 08, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 23, 2023	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	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). 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. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 01, 2023	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 (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 (PMIDs: 25113778 (2015), 2467892 (1989)). The frequency of this variant in the general population, 0.018 (184/10366 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. 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. -

Hb SS disease Pathogenic:1 Uncertain:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 24, 2024	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 cause disease when in trans with a null allele, and thus, the pathogenicity of the variant may be genotype-dependent. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 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). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -

beta Thalassemia Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	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. -
Uncertain significance, no assertion criteria provided	clinical testing	Bodamer Research Lab, Boston Children's Hospital	Feb 24, 2016	- -

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

Likely pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jun 30, 2021

- -

Fetal hemoglobin quantitative trait locus 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

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

other, no assertion criteria provided

literature only

OMIM

Dec 12, 2017

- -

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

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

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
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;.;.
MutationTaster	Benign	1.0	N
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
Varity_R		0.13
gMVP		0.65

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: rs33947415; hg19: chr11-5247914;