11-5226954-T-C

Variant names:

• chr11-5226954-T-C
• rs33936254
• NM_000518.5:c.68A>G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2 PM5 BP6

The NM_000518.5(HBB):​c.68A>G​(p.Glu23Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E23K) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1 O:1
• Conservation: PhyloP100: 1.78

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.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5226954-T-G is described in Lovd as [Pathogenic].
• BP6: Variant 11-5226954-T-C is Benign according to our data. Variant chr11-5226954-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 15178.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HBB	NM_000518.5	c.68A>G	p.Glu23Gly	missense_variant	Exon 1 of 3	ENST00000335295.4	NP_000509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBB	ENST00000335295.4	c.68A>G	p.Glu23Gly	missense_variant	Exon 1 of 3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461524 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727106

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1 Benign:1

Dec 07, 2022

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant is associated with normal clinical presentation when in heterozygosity (PMIDs: 3623978 (1987) and 23806067 (2013)). It has also been identified as a common variant in China, seen in a subject with reduced mean corpuscular volume levels from a routine blood analysis, and among subjects with hemoglobin disorders (PMIDs: 29626415 (2018), 26950205 (2016), and 25849334 (2015)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

Jul 22, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Hb G-Taipei variant (HBB: c.68A>G; p.Glu23Gly, also known as Glu22Gly when numbered from the mature protein, rs33936254, HbVar ID: 265) is reported in the heterozygous state in asymptomatic individuals with normal hematological parameters (Lin 2013, Zhang 2015, Zhang 2017, HbVar and references therein). This variant has not been reported with a pathogenic variant on the opposite chromosome, although, other variants at this codon (Glu22Ala, Glu22Gln) exhibit no clinical symptoms when found with a beta0 pathogenic variant in trans (Agrawal 2007, Koseler 2013, Rohe 1973). The Hb G-Taipei variant is listed in ClinVar (Variation ID: 15178). It is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.59). Based on available information, the Hb G-Taipei variant is considered to be likely benign. References: HbVar database link: https://globin.bx.psu.edu/hbvar/menu.html Agrawal M et al. Compound heterozygosity of Hb D(Iran) (beta(22) Glu-->Gln) and beta(0)-thalassemia (619 bp-deletion) in India. Eur J Haematol. 2007 Sep;79(3):248-50. PMID: 17655708. Koseler A et al. Molecular studies on the origin of the Hb G-Coushatta mutation in Denizli province of Turkey. Biochem Genet. 2013; 51(1-2):71-5. PMID: 23001606. Lin M et al. Molecular epidemiological survey of hemoglobinopathies in the Wuxi region of Jiangsu Province, eastern China. Hemoglobin. 2013;37(5):454-66. PMID: 23806067. Rohe R et al. Hemoglobin D Iran alpha A2 beta 22 2-Glu leads to Gln in association with thalassemia. Blood. 1973 Sep;42(3):455-62. PMID: 4725603. Zhang J et al. Genetic heterogeneity of the B-globin gene in various geographic populations of Yunnan in southwestern China. PLoS One. 2015 Apr 7;10(4):e0122956. PMID: 25849334. Zhang XM et al. Effects of hemoglobin variants HbJ Bangkok, HbE, HbG Taipei, and HbH on analysis of glycated hemoglobin via ion-exchange high-performance liquid chromatography. J Clin Lab Anal. 2017 Apr 13. PMID: 28407371. -

HEMOGLOBIN G (TAIPEI) Other:1

Dec 12, 2017

OMIM

Significance: other

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
CADD	Benign	18
DANN	Uncertain	1.0
DEOGEN2	Benign	0.041	T;T;.;T
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.58
FATHMM_MKL	Benign	0.53	D
LIST_S2	Benign	0.25	.;T;T;T
M_CAP	Pathogenic	0.33	D
MetaRNN	Uncertain	0.60	D;D;D;D
MetaSVM	Uncertain	0.14	D
MutationAssessor	Pathogenic	3.3	M;M;.;.
PrimateAI	Benign	0.47	T
PROVEAN	Uncertain	-3.6	D;.;.;D
REVEL	Uncertain	0.59
Sift	Uncertain	0.0060	D;.;.;D
Sift4G	Uncertain	0.037	D;.;.;.
Polyphen		0.0010	B;B;.;.
Vest4		0.86
MutPred		0.63		Gain of catalytic residue at V24 (P = 0.0732);Gain of catalytic residue at V24 (P = 0.0732);Gain of catalytic residue at V24 (P = 0.0732);Gain of catalytic residue at V24 (P = 0.0732);
MVP		0.91
MPC		0.056
ClinPred		0.73	D
GERP RS		2.8
Varity_R		0.40
gMVP		0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs33936254; hg19: chr11-5248184;