chr11-5226963-T-C

Position:

• chr11-5226963-T-C

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PM5 PP5_Very_Strong

The NM_000518.5(HBB):​c.59A>G​(p.Asn20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N20D) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: HBB NM_000518.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:2
• Conservation: PhyloP100: 1.85

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 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-5226962-G-T is described in Lovd as [Pathogenic].
• PP5: Variant 11-5226963-T-C is Pathogenic according to our data. Variant chr11-5226963-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 15258.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-5226963-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HBB	NM_000518.5	c.59A>G	p.Asn20Ser	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.59A>G	p.Asn20Ser	missense_variant	1/3	1	NM_000518.5	ENSP00000333994.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

beta Thalassemia Pathogenic:2 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 20, 2017	Variant summary: The HBB c.59A>G (p.Asn20Ser) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). 5/5 splice prediction tools predict that this variant strengthens a cryptic 5' splicing donor site and affects normal splicing. This prediction has been confirmed by at least one functional study (Gonzalez-Redondo_1989). This variant has been found in multiple patients with beta thalassemia (Yang_1989 and Rujito_2015) and is absent in 121362 control chromosomes. In addition, multiple reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Mar 17, 2017	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 25, 2021	The HBB c.59A>G (p.Asn20Ser) pathogenic variant, also known as Hb Malay, is associated with beta (+)-thalassemia. Individuals heterozygous for Hb Malay have mild microcytosis and hypochromia while homozygous individuals are affected with thalassemia intermedia (PMID: 10861818 (2000), 22335963 (2012), 29695942 (2018)). In addition, this variant has been shown to result in abnormal HBB mRNA splicing (PMID: 2775294 (1989)). -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 21, 2021	This sequence change replaces asparagine with serine at codon 20 of the HBB protein (p.Asn20Ser). The asparagine residue is moderately conserved and there is a small physicochemical difference between asparagine and serine. RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This missense change has been observed in individuals with autosomal recessive beta-thalassemia (PMID: 2736244, 10861818, 25412720). It has also been observed to segregate with disease in related individuals. This variant is also known as CD19AG or Hb Malay. ClinVar contains an entry for this variant (Variation ID: 15258). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Studies have shown that this missense change results in the use of an alternative splice site and introduces a premature termination codon (PMID: 2775294). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

May 02, 2019

The Hb Malay variant (HBB: c.59A>G; p.Asn20Ser, also known as Asn19Ser when numbered from the mature protein; rs33972047) is reported in the literature in numerous individuals affected with beta-thalassemia intermedia, either in the homozygous state or in trans to another pathogenic variant (Amran 2017, Ma 2000, Yang 1989, HbVar and references therein). This variant has been reported to segregate with disease in a family and has also been reported in heterozygous individuals with microcytosis and hypochromia (Amran 2017, Yan 1989). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The asparagine at codon 20 is highly conserved, but computational analyses (SIFT: damaging, PolyPhen-2: benign) predict conflicting effects of this variant on protein structure/function. However, computational analyses (Alamut v.2.11) predict that this variant impacts splicing by creating a novel cryptic donor splice site. Based on available information, the Hb Malay variant is considered to be pathogenic. References: HbVar link to Hb Malay: http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=256 Amran HS et al. Case Series of Homozygous and Compound Heterozygosity of Hb Malay, the Diagnostic Features and Transfusion Requirements. J Biomed Clin Sci. 2017 Dec;2(2)23-25. Ma SK et al. Beta-thalassemia intermedia caused by compound heterozygosity for Hb Malay (beta codon 19 AAC-->AGC; asn-->Ser) and codons 41/42 (-CTTT) beta(0)-thalassemia mutation. Am J Hematol. 2000 Jul;64(3):206-9. Yang KG et al. Molecular characterization of beta-globin gene mutations in Malay patients with Hb E-beta-thalassaemia and thalassaemia major. Br J Haematol. 1989 May;72(1):73-80. -

Beta-Malay-thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 01, 1989

- -

Beta-plus-thalassemia Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 01, 1989

- -

HEMOGLOBIN MALAY Other:1

other, no assertion criteria provided

literature only

OMIM

Dec 12, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Uncertain	0.056	T
BayesDel_noAF	Benign	-0.16
CADD	Pathogenic	27
DANN	Uncertain	0.98
DEOGEN2	Benign	0.043	T;T;.;T
Eigen	Benign	-0.29
Eigen_PC	Benign	-0.28
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Uncertain	0.89	.;D;D;D
M_CAP	Uncertain	0.16	D
MetaRNN	Uncertain	0.49	T;T;T;T
MetaSVM	Uncertain	-0.17	T
MutationAssessor	Benign	1.7	L;L;.;.
PrimateAI	Uncertain	0.48	T
PROVEAN	Uncertain	-2.6	D;.;.;D
REVEL	Uncertain	0.46
Sift	Uncertain	0.0050	D;.;.;D
Sift4G	Benign	0.32	T;.;.;.
Polyphen		0.012	B;B;.;.
Vest4		0.78
MutPred		0.68		Gain of disorder (P = 0.0999);Gain of disorder (P = 0.0999);Gain of disorder (P = 0.0999);Gain of disorder (P = 0.0999);
MVP		0.91
MPC		0.030
ClinPred		0.18	T
GERP RS		4.0
Varity_R		0.39
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.82		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.82		Position offset: 5
DS_DL_spliceai		0.28		Position offset: -33

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

Publications

LitVar

Other links and lift over

dbSNP: rs33972047; hg19: chr11-5248193;